Index

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All Classes and Interfaces|All Packages|Constant Field Values|Serialized Form

A

A - Variable in class net.sf.basedb.plugins.LowessNormalization.SpotData
 
abort - Variable in class net.sf.basedb.clients.web.fileupload.FileUploadProgress
 
ABORT - Static variable in class net.sf.basedb.core.signal.Signal
The ABORT signal, that requests that the receiver should clean up and die.
ABORTING - Enum constant in enum class net.sf.basedb.core.Job.Status
The Signal.ABORT signal has been sent to the job, but it has not yet responded.
about - Variable in class net.sf.basedb.util.extensions.ExtensionBean
 
about - Variable in class net.sf.basedb.util.extensions.manager.ExtensionsFile
 
about - Variable in class net.sf.basedb.util.extensions.Registry.RegisteredExtension
 
about - Variable in class net.sf.basedb.util.extensions.xml.PluginInfo
 
About - Interface in net.sf.basedb.core.plugin
Get information, such as the name, version and authors, about a plugin.
AboutBean - Class in net.sf.basedb.util.extensions
An implementation of the About interface, which complements all getter methods with setter methods.
AboutBean() - Constructor for class net.sf.basedb.util.extensions.AboutBean
Create a new empty about instance.
AboutImpl - Class in net.sf.basedb.core.plugin
A simple implementation of the About interface.
AboutImpl(String, String, String, String, String, String, String) - Constructor for class net.sf.basedb.core.plugin.AboutImpl
Create a new about object without any min or max BASE version requirement.
AboutImpl(String, String, String, String, String, String, String, String, String) - Constructor for class net.sf.basedb.core.plugin.AboutImpl
Create a new About object.
abs(String) - Method in class net.sf.basedb.core.dbengine.AbstractDbEngine
Return ABS(<value>).
abs(String) - Method in interface net.sf.basedb.core.dbengine.DbEngine
Get the function call that takes the absolute of a value.
abs(Expression) - Static method in class net.sf.basedb.core.query.Expressions
Calculate the absolute value of an expression: new expression = abs(e).
AbsConverter - Class in net.sf.basedb.util.jep.convert
Convert Abs function to a Query API Expression.
AbsConverter() - Constructor for class net.sf.basedb.util.jep.convert.AbsConverter
 
AbsExpression - Class in net.sf.basedb.core.query
Calculate the absolute value of an expression: abs(e).
AbsExpression(Expression) - Constructor for class net.sf.basedb.core.query.AbsExpression
 
ABSOLUTE - Enum constant in enum class net.sf.basedb.util.extensions.xml.PathType
Paths should be absolute paths from the root of the web server.
AbsoluteProgressReporter - Interface in net.sf.basedb.core
This is interface is an extension to the ProgressReporter interface.
ABSORBED_DOSE - Static variable in class net.sf.basedb.core.Quantity
The id for the Quantity object representing absorbed dose.
AbstractAnalysisPlugin - Class in net.sf.basedb.core.plugin
This is a base class that is useful for all analysis type plugins.
AbstractAnalysisPlugin() - Constructor for class net.sf.basedb.core.plugin.AbstractAnalysisPlugin
Create a new AbstractAnalysisPlugin.
AbstractBatcher - Class in net.sf.basedb.core
This is an abstract class for batchers that are connected to a single DbControl object.
AbstractBatcher() - Constructor for class net.sf.basedb.core.AbstractBatcher
Constructor for a batcher.
AbstractBioAssaySetExporter - Class in net.sf.basedb.util.export.spotdata
An abstract superclass for all exporters that exports spot data from a bioassay set.
AbstractBioAssaySetExporter() - Constructor for class net.sf.basedb.util.export.spotdata.AbstractBioAssaySetExporter
 
AbstractCustomRequestHandler - Class in net.sf.basedb.clients.jobagent.handlers
Abstract base class for custom request handler implementations.
AbstractCustomRequestHandler() - Constructor for class net.sf.basedb.clients.jobagent.handlers.AbstractCustomRequestHandler
 
AbstractDataWriterFactory<T> - Class in net.sf.basedb.util.bfs
Abstract implementation of a data writer factory.
AbstractDataWriterFactory(FilenameGenerator<T>) - Constructor for class net.sf.basedb.util.bfs.AbstractDataWriterFactory
Create a new factory that uses the given file name generator.
AbstractDbEngine - Class in net.sf.basedb.core.dbengine
An abstract superclass with default implementations for most DbEngine methods.
AbstractDbEngine() - Constructor for class net.sf.basedb.core.dbengine.AbstractDbEngine
Create AbstractDbEngine.
AbstractEntityQuery - Class in net.sf.basedb.core
An abstract implementation of the EntityQuery interface.
AbstractEntityQuery(Item, String, boolean) - Constructor for class net.sf.basedb.core.AbstractEntityQuery
Create a new query returning items of the specified item type using the default optional runtime filter.
AbstractEntityQuery(Item, String, boolean, QueryRuntimeFilter) - Constructor for class net.sf.basedb.core.AbstractEntityQuery
Create a new query returning items of the specified type with a non-default optional runtime filter.
AbstractEntityQuery(Item, Item, String, String, boolean, QueryRuntimeFilter) - Constructor for class net.sf.basedb.core.AbstractEntityQuery
Create a new query that may have different return type and root item type.
AbstractExporterPlugin - Class in net.sf.basedb.core.plugin
An abstract base class for all exporter plugins that wish to implement the ImmediateDownloadExporter interface.
AbstractExporterPlugin() - Constructor for class net.sf.basedb.core.plugin.AbstractExporterPlugin
Create a new AbstractExporterPlugin.
AbstractFieldConverter - Class in net.sf.basedb.util.export.spotdata
Abstract helper class for implementing ExportableFieldConverter.
AbstractFieldConverter(DbControl, BioAssaySet) - Constructor for class net.sf.basedb.util.export.spotdata.AbstractFieldConverter
Creates a new field converter to be used with a specific bioassay set source.
AbstractFilenameGenerator<T> - Class in net.sf.basedb.util.bfs
Abstract superclass for file names generator implementions that will help with ensuring that a generator creates unique file names.
AbstractFilenameGenerator() - Constructor for class net.sf.basedb.util.bfs.AbstractFilenameGenerator
 
AbstractFileUnpacker - Class in net.sf.basedb.util.zip
This is a base class for all plugins that wants to implement the FileUnpacker interface.
AbstractFileUnpacker() - Constructor for class net.sf.basedb.util.zip.AbstractFileUnpacker
 
AbstractFlatFileImporter - Class in net.sf.basedb.plugins
An abstract base class for all importers that imports data from one or more flat files.
AbstractFlatFileImporter() - Constructor for class net.sf.basedb.plugins.AbstractFlatFileImporter
 
AbstractHqlQuery - Class in net.sf.basedb.core
An abstract implementation of the HqlQuery interface.
AbstractHqlQuery(String, String, boolean) - Constructor for class net.sf.basedb.core.AbstractHqlQuery
Create a new HQL query.
AbstractIOSupport - Class in net.sf.basedb.plugins.executor
Abstract base class that is useful for plug-ins that need to implement the IOSupport interface and don't want to be visible as standalone plug-ins.
AbstractIOSupport() - Constructor for class net.sf.basedb.plugins.executor.AbstractIOSupport
 
AbstractItemImporter<I extends BasicItem> - Class in net.sf.basedb.plugins.batchimport
An abstract base class for plug-ins that import items in batch.
AbstractItemImporter() - Constructor for class net.sf.basedb.plugins.batchimport.AbstractItemImporter
 
AbstractJepConversionFunction<T> - Class in net.sf.basedb.util.jep.convert
Abstract superclass implementing the JepConversionFunction interface.
AbstractJepConversionFunction() - Constructor for class net.sf.basedb.util.jep.convert.AbstractJepConversionFunction
 
AbstractJspActionFactory<A extends Action> - Class in net.sf.basedb.clients.web.extensions
An abstract base class for action factories that may need to support adding scripts and stylesheets to the rendered JSP page.
AbstractJspActionFactory() - Constructor for class net.sf.basedb.clients.web.extensions.AbstractJspActionFactory
Create a new factory instance.
AbstractJspFactory - Class in net.sf.basedb.clients.web.extensions
An abstract BASE class for action and renderer factories.
AbstractJspFactory() - Constructor for class net.sf.basedb.clients.web.extensions.AbstractJspFactory
Create a new factory instance.
AbstractJspRendererFactory<A extends Action> - Class in net.sf.basedb.clients.web.extensions
An abstract base class for action factories that may need to support adding scripts and stylesheets to the rendered JSP page.
AbstractJspRendererFactory() - Constructor for class net.sf.basedb.clients.web.extensions.AbstractJspRendererFactory
Create a new factory instance.
AbstractListColumnBean<I,V> - Class in net.sf.basedb.clients.web.extensions.list
A simple bean-like implementation of the ListColumn interface.
AbstractListColumnBean() - Constructor for class net.sf.basedb.clients.web.extensions.list.AbstractListColumnBean
 
AbstractNodeLoader<I> - Class in net.sf.basedb.util.overview.loader
Abstract node loader implementation that does nothing/throws an exception.
AbstractNodeLoader() - Constructor for class net.sf.basedb.util.overview.loader.AbstractNodeLoader
 
AbstractOnSaveAction - Class in net.sf.basedb.clients.web.extensions.edit
Abstract base implementation of the OnSaveAction interface.
AbstractOnSaveAction() - Constructor for class net.sf.basedb.clients.web.extensions.edit.AbstractOnSaveAction
Create a on-save action without a context
AbstractOnSaveAction(JspContext) - Constructor for class net.sf.basedb.clients.web.extensions.edit.AbstractOnSaveAction
Create a on-save action with a jsp context.
AbstractPlugin - Class in net.sf.basedb.core.plugin
This is an abstract base class useful for developing plugins.
AbstractPlugin() - Constructor for class net.sf.basedb.core.plugin.AbstractPlugin
Create a new AbstractPlugin.
AbstractQuery - Class in net.sf.basedb.core
An abstract implementation of the Query interface.
AbstractQuery(String) - Constructor for class net.sf.basedb.core.AbstractQuery
Create a new query.
AbstractQueryCache - Class in net.sf.basedb.core.hibernate
Abstract base class used to cache queries for a session.
AbstractQueryCache() - Constructor for class net.sf.basedb.core.hibernate.AbstractQueryCache
 
AbstractRenderer<A extends Action> - Class in net.sf.basedb.util.extensions
Abstract class that provides a default implementation of the deprecated AbstractRenderer.render(Action) method.
AbstractRenderer() - Constructor for class net.sf.basedb.util.extensions.AbstractRenderer
 
AbstractResultList<I> - Class in net.sf.basedb.core
This is a list of the result from a query.
AbstractResultList(long) - Constructor for class net.sf.basedb.core.AbstractResultList
 
AbstractResultWriter - Class in net.sf.basedb.core.migrate
Abstract base implementation of a result writer that simply store the result set, writer, etc. that are needed later.
AbstractResultWriter(ResultSet, int, Writer, char[]) - Constructor for class net.sf.basedb.core.migrate.AbstractResultWriter
Creates a new writer.
AbstractSignalHandler - Class in net.sf.basedb.core.signal
An abstract base class for signal handler implementations.
AbstractSignalHandler() - Constructor for class net.sf.basedb.core.signal.AbstractSignalHandler
Create a new signal handler, that initially doesn't support any signals at all.
AbstractSignalHandler(Collection<Signal>) - Constructor for class net.sf.basedb.core.signal.AbstractSignalHandler
Create a new signal handler that supports the given signals.
AbstractSignalReceiver - Class in net.sf.basedb.core.signal
Abstract base class that is useful when implementing signal receivers.
AbstractSignalReceiver() - Constructor for class net.sf.basedb.core.signal.AbstractSignalReceiver
Create a new signal receiver.
AbstractSignalTransporter - Class in net.sf.basedb.core.signal
Abstract base class that is useful when implementing signal transporters.
AbstractSignalTransporter() - Constructor for class net.sf.basedb.core.signal.AbstractSignalTransporter
 
AbstractSourceItemTransformer - Class in net.sf.basedb.util.listable
Abstract base class for source item transformers that can be useful for implementing some common functionality.
AbstractSourceItemTransformer(Item, Item) - Constructor for class net.sf.basedb.util.listable.AbstractSourceItemTransformer
Create a new instance that transforms between the given source and target item types.
AbstractSourceItemTransformerFactory - Class in net.sf.basedb.util.listable
Abstract base class for source item transformer factories that can be useful for implementing some common functionality.
AbstractSourceItemTransformerFactory(Item, Item[], Item[]) - Constructor for class net.sf.basedb.util.listable.AbstractSourceItemTransformerFactory
Create a new instance supports transformation between the given source items and target item.
AbstractSqlQuery - Class in net.sf.basedb.core
An abstract implementation of the SqlQuery interface.
AbstractSqlQuery(String) - Constructor for class net.sf.basedb.core.AbstractSqlQuery
 
AbstractSqlQuery.CountWork - Class in net.sf.basedb.core
 
ACCELERATION - Static variable in class net.sf.basedb.core.Quantity
The id for the Quantity object representing acceleration.
accept(File) - Method in class net.sf.basedb.util.OlderThanFileFilter
Accept files that are older than the specified last modified time.
accept(File) - Method in class net.sf.basedb.util.RegexpFileFilter
Accept files with a name matching the regular expression
accept(String) - Method in class net.sf.basedb.core.hibernate.SchemaGenerator.CollectSqlTarget
 
Accept - Enum Class in net.sf.basedb.util.fileset
Accept() - Constructor for enum class net.sf.basedb.util.fileset.Accept
 
acceptDenied - Variable in class net.sf.basedb.util.overview.validator.NullNodeValidator
 
acceptedFile - Variable in class net.sf.basedb.util.fileset.SingleFileValidationAction
 
acceptFile(FileSetMember) - Method in class net.sf.basedb.util.fileset.SingleFileValidationAction
If the file has a file type matching the id given in the constructor it is accepted for immediate validation.
acceptFile(FileSetMember) - Method in interface net.sf.basedb.util.fileset.ValidationAction
Check if the given file is handled by this validator implementation or not?
acceptInsertIfNullReporterOnFeature - Variable in class net.sf.basedb.core.RawDataBatcher
If we should always accept inserts when the feature has a NULL reporter.
acceptInsertIfNullReporterOnFeature(boolean) - Method in class net.sf.basedb.core.RawDataBatcher
Specify if inserts always should be accepted if there is a matching feature that has a NULL reporter.
acceptMissing - Variable in class net.sf.basedb.util.overview.validator.NullNodeValidator
 
AccessControlled - Interface in net.sf.basedb.core
This interface should be implemented by a class representing items which requires the logged in user to have permission to access them.
AccountExpiredException - Exception in net.sf.basedb.core
This exception is thrown if you try to log in with an account that has expired.
AccountExpiredException(String, Date) - Constructor for exception net.sf.basedb.core.AccountExpiredException
Creates a new AccountExpiredException.
aColumn - Static variable in class net.sf.basedb.util.importer.spotdata.MAParser
 
ACT_AS_ANOTHER_USER - Enum constant in enum class net.sf.basedb.core.Permission
This permission allows a user act as another user using the SessionControl.impersonateLogin(int, String) method.
action - Variable in class net.sf.basedb.clients.web.extensions.list.RelatedItemExtensionColumn
 
action - Variable in class net.sf.basedb.clients.web.taglib.table.Table
 
Action - Interface in net.sf.basedb.util.extensions
An action is an object that is added to an ExtensionPoint by an Extension.
Action() - Constructor for enum class net.sf.basedb.core.Transactional.Action
 
actionClass - Variable in class net.sf.basedb.util.extensions.ExtensionPointBean
 
actionClass - Variable in class net.sf.basedb.util.extensions.Registry.RegisteredExtensionPoint
 
ActionClassEventFilter - Class in net.sf.basedb.util.extensions.events
Event filter that only passes on events to extension points with a given action class.
ActionClassEventFilter(Class<? extends Action>) - Constructor for class net.sf.basedb.util.extensions.events.ActionClassEventFilter
Create a new action class filter.
actionFactory - Variable in class net.sf.basedb.util.extensions.ExtensionBean
 
actionFactory - Variable in class net.sf.basedb.util.extensions.Registry.RegisteredExtension
 
ActionFactory<A extends Action> - Interface in net.sf.basedb.util.extensions
An action factory is an object which knows how to create Action:s.
actionId - Variable in class net.sf.basedb.clients.web.extensions.list.RelatedItemColumn.Specification
 
ActionIterator<A extends Action> - Class in net.sf.basedb.util.extensions
Iterator for iterating over all actions that will be created by extensions after a call to Registry.useExtensions(ClientContext, ExtensionsFilter, String...).
ActionIterator(Iterator<ExtensionContext<A>>) - Constructor for class net.sf.basedb.util.extensions.ActionIterator
 
actions - Variable in class net.sf.basedb.clients.web.extensions.menu.FixedMenuItemFactory
 
actions - Variable in class net.sf.basedb.clients.web.extensions.startpage.FixedStartPageFactory
 
actions - Variable in class net.sf.basedb.clients.web.extensions.tabcontrol.FixedTabFactory
 
actions - Variable in class net.sf.basedb.clients.web.extensions.toolbar.FixedButtonFactory
 
actions - Variable in class net.sf.basedb.util.extensions.ActionIterator
 
actions - Variable in class net.sf.basedb.util.extensions.debug.BeanActionFactory
 
actions - Variable in class net.sf.basedb.util.extensions.debug.ProxyActionFactory
 
active - Variable in class net.sf.basedb.clients.web.taglib.tab.TabControl
The ID attribute of the active tab.
activeJobs - Variable in class net.sf.basedb.clients.jobagent.Agent
 
activeProject - Variable in class net.sf.basedb.plugins.batchimport.AbstractItemImporter
 
activeProject - Variable in class net.sf.basedb.plugins.batchimport.AnyToAnyImporter
 
activeProjectId - Variable in class net.sf.basedb.core.AnnotationBatcher
 
activeProjectId - Variable in class net.sf.basedb.core.data.JobData
 
activeProjectId - Variable in class net.sf.basedb.core.SessionControl.LoginInfo
The id of the ProjectData object of the active project.
activeProjectName - Variable in class net.sf.basedb.core.SessionControl.LoginInfo
The name of the the active project.
actualCatalog - Variable in class net.sf.basedb.core.ServiceSessionControl.SessionFactoryConfiguration
 
actualParameters - Variable in class net.sf.basedb.util.jep.SimpleJepFunction
 
actualSchema - Variable in class net.sf.basedb.core.ServiceSessionControl.SessionFactoryConfiguration
 
AdaptiveNumberFormatter - Class in net.sf.basedb.util.formatter
Formats a number for output on a web page adapting thwe number of decimals depending on the order of magnitude of the value.
AdaptiveNumberFormatter(int, boolean) - Constructor for class net.sf.basedb.util.formatter.AdaptiveNumberFormatter
Create a new number formatter.
add(int, I) - Method in class net.sf.basedb.core.AbstractResultList
Not supported.
add(int, T) - Method in class net.sf.basedb.core.UnmodifiableResultList
Not supported.
add(E) - Method in class net.sf.basedb.util.Tree
Not supported.
add(I) - Method in class net.sf.basedb.core.AbstractResultList
Not supported.
add(Long, Long) - Method in class net.sf.basedb.core.DiskUsageStatistics.Summary
 
add(Collection<? extends Integer>) - Method in class net.sf.basedb.core.ItemList
Add all items in the collection to this list.
add(Iterator<? extends Listable>) - Method in class net.sf.basedb.core.ItemList
Add multiple items to this list in one go.
add(K, V) - Method in class net.sf.basedb.util.Enumeration
 
add(DerivedBioAssayData) - Method in class net.sf.basedb.core.DerivedBioAssay.FixDerivedBioAssayParentsRecursivelyAction
Register the given derived bioassay as one that has had it's parent items changed.
add(SystemData) - Static method in class net.sf.basedb.core.SystemItems
Register a system item.
add(ItemQuery<? extends Listable>) - Method in class net.sf.basedb.core.ItemList
Add all items that are returned by the query to this list.
add(Listable) - Method in class net.sf.basedb.core.ItemList
Add an item to this list.
add(Listable) - Method in class net.sf.basedb.core.ItemList.DelayedAdditionManager
 
add(Expression, Expression) - Static method in class net.sf.basedb.core.query.Expressions
Add two expressions: new expression = e1 + e2.
add(InheritSpecification) - Method in class net.sf.basedb.util.annotations.InheritAnnotationsManager.AnnotationTypeFilter
 
add(LogEntry) - Method in class net.sf.basedb.util.extensions.logging.ExtensionsLog
Add a log entry.
add(T) - Method in class net.sf.basedb.core.ItemResultList.ResultListListIterator
This operation is not supported.
add(T) - Method in class net.sf.basedb.core.UnmodifiableResultList
Not supported.
ADD - Enum constant in enum class net.sf.basedb.core.log.ChangeType
 
ADD_MEMBERS - Static variable in class net.sf.basedb.clients.web.ModeInfo
Mode for adding members to an item list.
ADD_ONLY - Enum constant in enum class net.sf.basedb.core.ItemList.SynchronizeOption
Synchronize the members by adding new items matching the filter.
addAll(int, Collection<? extends I>) - Method in class net.sf.basedb.core.AbstractResultList
Not supported.
addAll(int, Collection<? extends T>) - Method in class net.sf.basedb.core.UnmodifiableResultList
Not supported.
addAll(Collection<? extends E>) - Method in class net.sf.basedb.util.Tree
Not supported.
addAll(Collection<? extends I>) - Method in class net.sf.basedb.core.AbstractResultList
Not supported.
addAll(Collection<? extends T>) - Method in class net.sf.basedb.core.UnmodifiableResultList
Not supported.
addAll(ItemList) - Method in class net.sf.basedb.core.ItemList
Add all items from another item list to this list.
addAll(ItemList.DelayedAdditionManager) - Method in class net.sf.basedb.core.ItemList.DelayedAdditionManager
 
addAll(ReporterList) - Method in class net.sf.basedb.core.ReporterList
Add all reporters from another reporter list to this list.
addAllItems(Collection<? extends Annotatable>) - Method in class net.sf.basedb.util.annotations.RunnableInheritAnnotationsManager
Add all items for processing.
AddAllTransformer<I> - Class in net.sf.basedb.util.collections
Collection transformer implementation that adds all elements in the source collection to the destination collection.
AddAllTransformer() - Constructor for class net.sf.basedb.util.collections.AddAllTransformer
 
addAnnotatableParents(DbControl, Set<Annotatable>, AnnotatableData...) - Method in class net.sf.basedb.core.BasicItem
Try to load the the item-class representation of all the data-class items ignoring permission problems.
addAnnotationTypes(Collection<AnnotationType>) - Method in class net.sf.basedb.core.AnnotationBatcher
Add annotation types to work with.
addArrayDesignBlock(BlockInfo) - Method in class net.sf.basedb.core.ArrayDesign
Adds an ArrayDesignBlock to the array design.
addAssayField(AssayField) - Method in class net.sf.basedb.util.export.spotdata.AbstractBioAssaySetExporter
Add information about an assay field that should be exported.
addAssayField(AssayField) - Method in class net.sf.basedb.util.export.spotdata.BaseFileExporter
Adds an assay field to the exported file.
addAssayField(AssayField) - Method in class net.sf.basedb.util.export.spotdata.BfsExporter
 
addAssayFields(Collection<? extends AssayField>) - Method in class net.sf.basedb.util.export.spotdata.BaseFileExporter
Add multiple assay fields in one go.
addAssayFields(Collection<? extends AssayField>) - Method in class net.sf.basedb.util.export.spotdata.BfsExporter
Add multiple assay fields in one go.
addAttributes(StringBuilder, Iterator<DynamicActionAttribute>) - Static method in class net.sf.basedb.clients.web.extensions.DynamicActionAttributeSupport
Append all dynamic action attributes to the string builder.
addAutoJoiner(AutoJoiner<?, ?>) - Method in class net.sf.basedb.core.AbstractQuery
 
addAutoJoiner(AutoJoiner<?, ?>) - Method in interface net.sf.basedb.core.query.Query
 
addBatcher(Batcher) - Method in class net.sf.basedb.core.DbControl
Add a Batcher to the batcher queue.
addButton(String) - Method in class net.sf.basedb.clients.web.taglib.ButtonGroup
 
addBytes(long) - Method in class net.sf.basedb.core.DataCube
 
addBytes(long) - Method in class net.sf.basedb.core.DataCubeExtraValue
 
addBytes(long) - Method in class net.sf.basedb.core.DataCubeFilter
 
addBytes(long) - Method in class net.sf.basedb.core.DataCubeLayer
 
addBytes(long) - Method in class net.sf.basedb.core.Experiment
 
addBytes(long) - Method in class net.sf.basedb.core.ReporterCloneTemplate
 
addCategory(AnnotationTypeCategory) - Method in class net.sf.basedb.core.AnnotationType
Add a category to this annotation type.
addChange(ChangeType, Object, Object[], Object[], String[], Type[], boolean) - Method in class net.sf.basedb.core.log.LoggingInterceptor
If the log manager factory creates an entity logger, add information about the change to the internal list.
addCheckedSource(BioMaterial) - Method in class net.sf.basedb.core.BioMaterialEvent
 
addChild(E) - Method in class net.sf.basedb.util.Tree.Entry
Add a child to the node.
addChild(Node) - Method in class net.sf.basedb.util.overview.Node
Add a child node to this one.
addChildAssay(BaseFileInfo.ChildBioAssay) - Method in class net.sf.basedb.util.importer.spotdata.BaseFileInfo
Add information about a child assay.
addChildBioAssaySets(BioAssaySetData, Set<BioAssaySetData>) - Method in class net.sf.basedb.core.BioAssaySet
Find all bioassaysets that are children to the specified parent (ie.
addChildElements(Map<QueryElement, Object>, QueryElement) - Method in class net.sf.basedb.core.AbstractQuery
 
addChildEntry(Tree.Entry<E>) - Method in class net.sf.basedb.util.Tree.Entry
 
addChildErrors(int) - Method in class net.sf.basedb.util.overview.Node
Add child errors to this node.
addChildReporter(Integer, Integer) - Method in class net.sf.basedb.util.importer.spotdata.BaseFileInfo
Add a child position/reporter mapping from the parsed BASEfile.
addChildWarnings(int) - Method in class net.sf.basedb.util.overview.Node
Add child warnings to this node.
addClonableProperty(ClonableProperty) - Method in class net.sf.basedb.core.ReporterCloneTemplate
Add a clonable property to this template.
addColumn(MetadataImplementor, Table, VirtualColumn) - Static method in class net.sf.basedb.core.HibernateUtil
Add a column to a table.
addColumnDef(ColumnDef, ListColumnAction) - Method in class net.sf.basedb.clients.web.taglib.table.Table
 
AddConverter - Class in net.sf.basedb.util.jep.convert
Convert Add function to a Query API Expression.
AddConverter() - Constructor for class net.sf.basedb.util.jep.convert.AddConverter
 
addData(SqlResultIterator, String...) - Method in class net.sf.basedb.util.plot.ScatterPlot
Add data to the plot.
addData(SqlResultIterator, String, float, HistogramPlot.YAggregate, HistogramPlot.YAggregate) - Method in class net.sf.basedb.util.plot.HistogramPlot
Add data to the plot.
addData(SqlResultIterator, Collection<PlotAnnotation>) - Method in class net.sf.basedb.util.plot.ScatterPlot
Add data to the plot.
addData(SqlResultIterator, Collection<PlotAnnotation>, float, HistogramPlot.YAggregate, HistogramPlot.YAggregate) - Method in class net.sf.basedb.util.plot.HistogramPlot
Add data to the plot.
addDataParser(DataParser) - Method in class net.sf.basedb.util.importer.spotdata.SynchronizedSpotDataParser
Adds a data parser.
addDefaultItem(BasicItem) - Method in class net.sf.basedb.core.Project
Add an item as a default project item.
addDefultRolesAndGroups(Session, UserData) - Static method in class net.sf.basedb.core.User
Add all groups and roles that has been marked as default to the user.
addDirectory(File) - Method in class net.sf.basedb.util.extensions.manager.ExtensionsManager
Add a directory to this manager.
addDynamicAttributes(StringBuilder) - Method in class net.sf.basedb.clients.web.taglib.StylableTag
 
ADDED - Enum constant in enum class net.sf.basedb.core.AnnotationBatcher.Change
A new annotation was created.
addedBytes - Variable in class net.sf.basedb.core.DataCube
 
addedBytes - Variable in class net.sf.basedb.core.Experiment
 
addEntity(Class) - Method in class net.sf.basedb.core.hibernate.NativeQueryWrapper
 
addEntity(String) - Method in class net.sf.basedb.core.hibernate.NativeQueryWrapper
 
addEntity(String, Class) - Method in class net.sf.basedb.core.hibernate.NativeQueryWrapper
 
addEntity(String, Class, LockMode) - Method in class net.sf.basedb.core.hibernate.NativeQueryWrapper
 
addEntity(String, String) - Method in class net.sf.basedb.core.hibernate.NativeQueryWrapper
 
addEntity(String, String, LockMode) - Method in class net.sf.basedb.core.hibernate.NativeQueryWrapper
 
addEntry(String, String...) - Method in class net.sf.basedb.util.bfs.MetadataModel.Section
Add a new entry to this section.
addEntry(MetadataModel.SectionEntry) - Method in class net.sf.basedb.util.bfs.MetadataModel.Section
Add a new entry to this section.
addEntry(Tree.Entry<E>) - Method in class net.sf.basedb.util.Tree
 
addError(String) - Method in class net.sf.basedb.util.jep.FunctionSafeJep
Adds an error message to the "real" JEP parser.
addErrorHandler(Class<? extends Throwable>, ErrorHandler) - Method in class net.sf.basedb.plugins.AbstractFlatFileImporter
Add an error handler for the specified class of error.
addErrorHandler(Class<? extends Throwable>, ErrorHandler) - Method in class net.sf.basedb.util.error.ClassMapErrorHandler
Add an error handler for throwable:s of a specific class.
addErrorMessage(ExtensionsFile, String) - Method in class net.sf.basedb.util.extensions.manager.ProcessResults
Adds a detailed message inidcating a failed operation to a file.
addErrors(int) - Method in class net.sf.basedb.util.overview.Node
Add more errors to this node.
addEventHandler(EventHandler) - Method in class net.sf.basedb.util.bfs.MultiEventHandler
Adds an event handler.
addEventListeners(SessionEventListener...) - Method in class net.sf.basedb.core.hibernate.SessionWrapper
 
addExperimentalFactor(AnnotationType) - Method in class net.sf.basedb.core.Experiment
Add an annotation type as an experimental factor to this experiment.
addExperimentalFactorsAsAssayFields() - Method in class net.sf.basedb.util.export.spotdata.AbstractBioAssaySetExporter
Adds all experimental factors from the experiment that the source bioassay set belongs to as assay fields.
addExperimentParameters(DbControl, Experiment, List<PluginParameter<?>>) - Method in class net.sf.basedb.plugins.RawDataFlatFileImporter
 
AddExpression - Class in net.sf.basedb.core.query
Add two expressions: e1 + e2.
AddExpression(Expression, Expression) - Constructor for class net.sf.basedb.core.query.AddExpression
 
addExtendedProperties(Element, String) - Static method in class net.sf.basedb.core.HibernateUtil
Append <property> tags to the given class tag.
addExtension(Registry.RegisteredExtension<A>) - Method in class net.sf.basedb.util.extensions.Registry.RegisteredExtensionPoint
Add an extension to this extension point.
addExtensionsFile(ExtensionsFile) - Method in class net.sf.basedb.util.extensions.manager.ExtensionsManager
 
addExtraColumns(List<TableColumn>, DbControl, BioAssaySet, String, String, String) - Static method in class net.sf.basedb.clients.web.DynamicUtil
 
addExtraFile(String, String) - Method in class net.sf.basedb.util.export.spotdata.BfsExporter
Add information about an extra data file that is included as part of the BFS.
addExtraFloat(DbControl, String) - Method in class net.sf.basedb.util.importer.spotdata.BaseFileInfo
Add information about an extra float value that appears in the BASEfile.
addExtraFloatParser(ExtraFloatParser) - Method in class net.sf.basedb.util.importer.spotdata.BaseFileInfo.SpotSectionInfo
Add an extra value parser to this section.
addFetch(String, String, String) - Method in class net.sf.basedb.core.hibernate.NativeQueryWrapper
 
addFile(File) - Method in class net.sf.basedb.util.extensions.manager.ExtensionsManager
Add a file to the manager that is supposed to contain extensions.
addFile(String, String) - Method in class net.sf.basedb.util.bfs.MetadataModel
Add an entry to the 'files' section.
addFile(String, UploadedFile) - Method in class net.sf.basedb.clients.web.fileupload.FileUpload
Store information about an uploaded file.
addFilename(String) - Method in class net.sf.basedb.util.bfs.AbstractFilenameGenerator
Add the file name to the list of already generated file names.
addFilter - Variable in class net.sf.basedb.clients.web.SubContext
 
AddFilter() - Constructor for enum class net.sf.basedb.core.ItemContext.AddFilter
 
addFilterConditions(Element, String, HibernateUtil.FilterConfigurator) - Static method in class net.sf.basedb.core.HibernateUtil
Add <filter> conditions to the given class tag.
addFilteredColumn(String, String, boolean) - Method in class net.sf.basedb.clients.web.taglib.table.Table
 
addFilterRows(int) - Method in class net.sf.basedb.core.ItemContext
Add filter rows to the table.
addFix(Fix) - Method in class net.sf.basedb.util.overview.Failure
Add a suggested fix to this failure.
addFormulaColumns(List<TableColumn>, DbControl, RawDataType, Formula.Type, IntensityTransform, String, String, boolean) - Static method in class net.sf.basedb.clients.web.DynamicUtil
 
addFunctions(JEP, JepFunction...) - Static method in class net.sf.basedb.util.jep.Jep
 
addGroup(Group) - Method in class net.sf.basedb.core.Group
Add a group as a member to this group.
addHeaderColumns(int) - Method in class net.sf.basedb.clients.web.taglib.table.HeaderRow
 
addHidden(String, String) - Method in class net.sf.basedb.clients.web.taglib.table.Table
 
addIdAndStyles(StringBuilder, String...) - Method in class net.sf.basedb.clients.web.taglib.StylableTag
Add id, class and style attributes the the stringbuilder.
addIfPresentIn(int, int, Collection<ItemList>) - Method in class net.sf.basedb.core.ItemList
Add items that are present in the specified number of lists to this list.
addIfPresentIn(int, int, Collection<ReporterList>) - Method in class net.sf.basedb.core.ReporterList
Add reporters that are present in the specified number of lists to this list.
addIgnore(File) - Method in class net.sf.basedb.util.extensions.manager.ExtensionsManager
Add a file to the ignore list.
addIntersection(Collection<ItemList>) - Method in class net.sf.basedb.core.ItemList
Add items that are present in ALL OF the given lists to this list.
addIntersection(Collection<ReporterList>) - Method in class net.sf.basedb.core.ReporterList
Add reporters that are present in ALL OF the given lists to this list.
addItem(Annotatable) - Method in class net.sf.basedb.util.annotations.RunnableInheritAnnotationsManager
Add an item that should inherit annotations.
addJoin(String, String) - Method in class net.sf.basedb.core.hibernate.NativeQueryWrapper
 
addJoin(String, String, String) - Method in class net.sf.basedb.core.hibernate.NativeQueryWrapper
 
addJoin(String, String, LockMode) - Method in class net.sf.basedb.core.hibernate.NativeQueryWrapper
 
addManualSingleChange(ChangeType, Object) - Method in class net.sf.basedb.core.log.LoggingInterceptor
Adds a manual non-Hibernate change to the log system.
addManualSingleChange(ChangeType, Object, Object, Object, String, Type) - Method in class net.sf.basedb.core.log.LoggingInterceptor
Adds a manual non-Hibernate change to the log system.
addMeasurement(float) - Method in class net.sf.basedb.util.plot.HistogramPlot.HistogramBin
Add a measurement to this bin.
addMember(File, DataFileType) - Method in class net.sf.basedb.core.FileSet
Add a file as a member to the file set.
addMembers(Set<Integer>, ItemList.DelayedAdditionManager) - Method in class net.sf.basedb.core.ItemList
Add members to this list.
addMembersMode - Variable in class net.sf.basedb.plugins.batchimport.AbstractItemImporter
 
addMenuitem(String) - Method in class net.sf.basedb.clients.web.taglib.menu.Menu
 
addMessage(ExtensionsFile, String) - Method in class net.sf.basedb.util.extensions.manager.ProcessResults
Adds a detailed message indicating a successful operation to a file.
addMessage(ExtensionsFile, String, boolean) - Method in class net.sf.basedb.util.extensions.manager.ProcessResults
 
addMoreColumnMappingParameters(List<PluginParameter<?>>) - Method in class net.sf.basedb.plugins.batchimport.AbstractItemImporter
Add column mapping parameters for item-specific properties.
addMoreColumnMappingParameters(List<PluginParameter<?>>) - Method in class net.sf.basedb.plugins.batchimport.AnnotationTypeImporter
Adds column mappings for name and description.
addMoreColumnMappingParameters(List<PluginParameter<?>>) - Method in class net.sf.basedb.plugins.batchimport.ArrayBatchImporter
Adds column mappings for name, description, protocol, robot, and array design
addMoreColumnMappingParameters(List<PluginParameter<?>>) - Method in class net.sf.basedb.plugins.batchimport.ArrayDesignImporter
Adds column mappings for name, externalId, description, protocol, creation date, original quantity, pooled, parent and used quantity from parent.
addMoreColumnMappingParameters(List<PluginParameter<?>>) - Method in class net.sf.basedb.plugins.batchimport.ArraySlideImporter
Adds column mappings for name, description, array batch, batch index, barcode and destroyed
addMoreColumnMappingParameters(List<PluginParameter<?>>) - Method in class net.sf.basedb.plugins.batchimport.BioPlateImporter
Adds column mappings for name, description, plate type, plate geometry, barcode and freezer.
addMoreColumnMappingParameters(List<PluginParameter<?>>) - Method in class net.sf.basedb.plugins.batchimport.BioSourceImporter
Adds column mappings for name, externalId and description.
addMoreColumnMappingParameters(List<PluginParameter<?>>) - Method in class net.sf.basedb.plugins.batchimport.DerivedBioAssayImporter
Adds column mappings for name, internalId, subtype, description, protocol, hardware, software, parent, data files and permissions.
addMoreColumnMappingParameters(List<PluginParameter<?>>) - Method in class net.sf.basedb.plugins.batchimport.ExtractImporter
Adds column mappings for name, externalId, description, protocol, creation date, original quantity, pooled, parent and used quantity from parent.
addMoreColumnMappingParameters(List<PluginParameter<?>>) - Method in class net.sf.basedb.plugins.batchimport.FileImporter
Adds column mappings for name, externalId and description.
addMoreColumnMappingParameters(List<PluginParameter<?>>) - Method in class net.sf.basedb.plugins.batchimport.KitImporter
Adds column mappings for name and description.
addMoreColumnMappingParameters(List<PluginParameter<?>>) - Method in class net.sf.basedb.plugins.batchimport.PhysicalBioAssayImporter
Adds column mappings for name, externalId, description, protocol, creation date, original quantity, pooled, parent and used quantity from parent.
addMoreColumnMappingParameters(List<PluginParameter<?>>) - Method in class net.sf.basedb.plugins.batchimport.RawBioAssayImporter
Adds column mappings for name, externalId, description, protocol, creation date, original quantity, pooled, parent and used quantity from parent.
addMoreColumnMappingParameters(List<PluginParameter<?>>) - Method in class net.sf.basedb.plugins.batchimport.SampleImporter
Adds column mappings for name, externalId, description, protocol, creation date, original quantity, pooled, parent and used quantity from parent.
addMoreColumnMappingParameters(List<PluginParameter<?>>) - Method in class net.sf.basedb.plugins.batchimport.TagImporter
Adds column mappings for name and description.
addMoreErrorParameters(List<PluginParameter<?>>) - Method in class net.sf.basedb.plugins.batchimport.AbstractItemImporter
Add extra parameters to the "Error handling" section that the subclass needs.
addMoreErrorParameters(List<PluginParameter<?>>) - Method in class net.sf.basedb.plugins.batchimport.PhysicalBioAssayImporter
 
addMoreJobParameters(List<PluginParameter<?>>) - Method in class net.sf.basedb.plugins.batchimport.AbstractItemImporter
Add extra job parameters that the subclass needs.
addMoreJobParameters(List<PluginParameter<?>>) - Method in class net.sf.basedb.plugins.batchimport.ArrayDesignImporter
Add parameter for "Data directory" directory where data files may be located.
addMoreJobParameters(List<PluginParameter<?>>) - Method in class net.sf.basedb.plugins.batchimport.DerivedBioAssayImporter
Add parameter for "Data directory" directory where data files may be located.
addMoreJobParameters(List<PluginParameter<?>>) - Method in class net.sf.basedb.plugins.batchimport.FileImporter
 
addMoreJobParameters(List<PluginParameter<?>>) - Method in class net.sf.basedb.plugins.batchimport.RawBioAssayImporter
Add parameter for "Data directory" directory where data files may be located.
addMoreParsingParameters(List<PluginParameter<?>>) - Method in class net.sf.basedb.plugins.batchimport.AbstractItemImporter
Add extra parameters to the "Parser settings" section that the subclass needs.
addMoreParsingParameters(List<PluginParameter<?>>) - Method in class net.sf.basedb.plugins.batchimport.AnnotationTypeImporter
 
addParameter(String, String) - Method in class net.sf.basedb.clients.web.fileupload.FileUpload
Store the value of a regular form field.
addParameter(AnnotationType) - Method in class net.sf.basedb.core.Protocol
Add an annotation type as a parameter to this protocol.
addParametersWithNamespace(List<PluginParameter<?>>, List<PluginParameter<?>>, String) - Method in class net.sf.basedb.plugins.executor.ExternalProgramExecutor
Add more parameters to a list of parameters with a different namespace.
addParent(DerivedBioAssay) - Method in class net.sf.basedb.core.DerivedBioAssay
Add a derived bioassay as a parent to this derived bioassay.
addParticipant(BioPlate, String, int) - Method in class net.sf.basedb.core.BioPlateEvent
Add a bioplate as a participant in this event.
addPermissions(Group, Set<Permission>) - Method in class net.sf.basedb.core.GroupPermissions
Grant permissions to a group, keeping those that have already been set.
addPermissions(Group, Set<Permission>) - Method in class net.sf.basedb.core.MultiPermissions
Grant permissions to a group, keeping those that have already been set.
addPermissions(Project, Set<Permission>) - Method in class net.sf.basedb.core.MultiPermissions
Grant permissions to a project, keeping those that have already been set.
addPermissions(Project, Set<Permission>) - Method in class net.sf.basedb.core.ProjectPermissions
Grant permissions to a project, keeping those that have already been set.
addPermissions(User, Set<Permission>) - Method in class net.sf.basedb.core.MultiPermissions
Grant permissions to a user, keeping those that have already been set.
addPermissions(User, Set<Permission>) - Method in class net.sf.basedb.core.UserPermissions
Grant permissions to a user, keeping those that have already been set.
addPhysicalBioAssay(PhysicalBioAssay) - Method in class net.sf.basedb.core.DerivedBioAssay
Add a physical bioassay as a parent to this derived bioassay.
addPlate(Plate) - Method in class net.sf.basedb.core.ArrayDesign
Adds a single plate to the plate list.
addQueryHint(String) - Method in class net.sf.basedb.core.hibernate.NativeQueryWrapper
 
addQueryHint(String) - Method in class net.sf.basedb.core.hibernate.QueryWrapper
 
addRawBioAssay(RawBioAssay) - Method in class net.sf.basedb.core.Experiment
Add a raw bioassay to this experiment.
addRawBioAssayParameters(DbControl, RawBioAssay, List<PluginParameter<?>>) - Method in class net.sf.basedb.plugins.RawDataFlatFileImporter
 
addRawDataColumns(List<TableColumn>, DbControl, RawDataType, String, String, String) - Static method in class net.sf.basedb.clients.web.DynamicUtil
 
addRawDataMappings(MetadataSources) - Static method in class net.sf.basedb.core.HibernateUtil
Generate additional mappings for the raw data types.
addReplaceSection - Static variable in class net.sf.basedb.plugins.AnnotationFlatFileImporter
 
addReporter(ReporterData, Float) - Method in class net.sf.basedb.core.ReporterList
Add or update the score for a reporter.
addReporterColumns(List<TableColumn>, DbControl, String, String, String) - Static method in class net.sf.basedb.clients.web.DynamicUtil
 
addReporterColumns(List<TableColumn>, DbControl, ReporterCloneTemplate, String, String, String) - Static method in class net.sf.basedb.clients.web.DynamicUtil
 
addReporterField(DynamicField) - Method in class net.sf.basedb.util.export.spotdata.AbstractBioAssaySetExporter
Add information about a reporter field that should be exported.
addReporterField(DynamicField) - Method in class net.sf.basedb.util.export.spotdata.BaseFileExporter
 
addReporterField(DynamicField) - Method in class net.sf.basedb.util.export.spotdata.BfsExporter
 
addReporterFields(Collection<? extends DynamicField>) - Method in class net.sf.basedb.util.export.spotdata.BaseFileExporter
Add multiple reporter fields in one go.
addReporterFields(Collection<? extends DynamicField>) - Method in class net.sf.basedb.util.export.spotdata.BfsExporter
Add multiple reporter fields in one go.
addReporters(Set<Integer>) - Method in class net.sf.basedb.core.ReporterList
 
addReportUriIfNeeded(String, FilterConfig) - Method in class net.sf.basedb.clients.web.servlet.ContentSecurityPolicyFilter
 
addResources(Vector<URL>, Enumeration<URL>) - Method in class net.sf.basedb.util.JarClassLoader
 
address - Variable in class net.sf.basedb.core.authentication.ExtraUserInformation
 
address - Variable in class net.sf.basedb.core.data.UserData
 
addRestriction(Restriction) - Method in class net.sf.basedb.core.ItemContext.RowRestrictions
 
addRoleKey(RoleKeyData) - Static method in class net.sf.basedb.core.SystemItems
Register a role key.
addRolePermissions(RoleData, Map<Item, Integer>) - Static method in class net.sf.basedb.core.Install
Add permissions for a role for specific item types.
addRoot(String, Class) - Method in class net.sf.basedb.core.hibernate.NativeQueryWrapper
 
addRoot(String, String) - Method in class net.sf.basedb.core.hibernate.NativeQueryWrapper
 
addRow(String...) - Method in class net.sf.basedb.util.bfs.AnnotationModel
Add a row of data to the model.
addRow(String...) - Method in class net.sf.basedb.util.bfs.MatrixModel
Add a row of data to the model.
addScalar(String) - Method in class net.sf.basedb.core.hibernate.NativeQueryWrapper
 
addScalar(String, Type) - Method in class net.sf.basedb.core.hibernate.NativeQueryWrapper
 
addScript(String) - Method in class net.sf.basedb.clients.web.extensions.JspContext
Add an absolute reference to a script that should be included on the generated page with a <script> tag.
addScripts(Collection<String>) - Method in class net.sf.basedb.clients.web.extensions.JspContext
Add several scripts in one go.
addSection(String) - Method in class net.sf.basedb.util.bfs.MetadataModel
Adds a new section to the model.
addSeries(HistogramPlot.HistogramSeries) - Method in class net.sf.basedb.util.plot.HistogramPlot.HistogramDataset
 
addSignal(Signal) - Method in class net.sf.basedb.core.signal.AbstractSignalHandler
Add a signal to the list of supported signals.
addSource(BioMaterial) - Method in class net.sf.basedb.core.BioMaterialEvent
Add a biomaterial as a source to this event.
addSpecification(InheritSpecification) - Method in class net.sf.basedb.util.annotations.RunnableInheritAnnotationsManager
Add a specification with rules for inheriting annotations.
addSpotColumns(List<TableColumn>, DbControl, int, IntensityTransform) - Static method in class net.sf.basedb.clients.web.DynamicUtil
 
addSpotField(DynamicField) - Method in class net.sf.basedb.util.export.spotdata.AbstractBioAssaySetExporter
Add information about a spot field that should be exported.
addSpotField(DynamicField) - Method in class net.sf.basedb.util.export.spotdata.BaseFileExporter
 
addSpotField(DynamicField) - Method in class net.sf.basedb.util.export.spotdata.BfsExporter
Add information about a spot field that should be exported.
addSpotFields(Collection<? extends DynamicField>) - Method in class net.sf.basedb.util.export.spotdata.BaseFileExporter
Add multiple spot fields in one go.
addSpotFields(Collection<? extends DynamicField>) - Method in class net.sf.basedb.util.export.spotdata.BfsExporter
Add multiple spot fields in one go.
addSpotIntensityParser(SpotIntensityParser) - Method in class net.sf.basedb.util.importer.spotdata.FirstPassSectionSpotsParser
Adds a spot intensity parser to the list of used parsers.
addSpotSectionInfo(int, BaseFileInfo.SpotSectionInfo) - Method in class net.sf.basedb.util.importer.spotdata.BaseFileInfo
Adds information about a 'spot' section.
addSqlFunctions(SessionFactoryBuilder, DbEngine) - Static method in class net.sf.basedb.core.HibernateUtil
Add more SQL functions to HQL that are not present in a standard Hibernate installation.
addStaticMappings(MetadataSources, HibernateUtil.FilterConfigurator) - Static method in class net.sf.basedb.core.HibernateUtil
Read all mapping files, which must be named Class.hbm.xml where class is the name of each class.
addStatistics(String, float) - Method in class net.sf.basedb.clients.web.ExperimentExplorer.AnnotationGroup
Add another statisitcal measurement to this group.
addStylesheet(String) - Method in class net.sf.basedb.clients.web.extensions.JspContext
Add an absolute reference to a CSS stylesheet that should be included on the generated page with a <link> tag.
addStylesheets(Collection<String>) - Method in class net.sf.basedb.clients.web.extensions.JspContext
Add several stylesheets in one go.
addSymbol(String) - Method in class net.sf.basedb.core.Unit
Add a symbol to this unit.
addSynchronizedEntityClass(Class) - Method in class net.sf.basedb.core.hibernate.NativeQueryWrapper
 
addSynchronizedEntityName(String) - Method in class net.sf.basedb.core.hibernate.NativeQueryWrapper
 
addSynchronizedQuerySpace(String) - Method in class net.sf.basedb.core.hibernate.NativeQueryWrapper
 
addTab(TabAction) - Method in class net.sf.basedb.clients.web.taglib.tab.TabControl
 
addToBatch(D, PreparedStatement, List<BatchedPropertyInfo>) - Method in class net.sf.basedb.core.BasicBatcher
Add the data object to the batch represented by the prepared statement
addToBatch(Object...) - Method in class net.sf.basedb.core.AnnotationBatcher.UpdateBatcher
Add a new entry to the batch.
addToDefaultRolesAndGroups() - Method in class net.sf.basedb.core.User
Add this user to the groups and roles that has been marked as default for new users.
addToUnlimited - Variable in class net.sf.basedb.plugins.AnnotationFlatFileImporter
 
addToUnlimitedParameter - Static variable in class net.sf.basedb.plugins.AnnotationFlatFileImporter
 
addTransactionalAction(TransactionalAction) - Method in class net.sf.basedb.core.DbControl
Add a transactional action to this DbControl.
addTransferredBytes(long) - Method in class net.sf.basedb.clients.web.fileupload.FileUploadProgress
Adds a value to the number of transfered bytes.
addUnion(Collection<ItemList>) - Method in class net.sf.basedb.core.ItemList
Add items that are present in at least ONE OF the given lists to this list.
addUnion(Collection<ReporterList>) - Method in class net.sf.basedb.core.ReporterList
Add reporters that are present in at least ONE OF the given lists to this list.
addURI(URI) - Method in class net.sf.basedb.util.extensions.manager.ExtensionsManager
Add an URI that points to an XML file containing definitions.
addUsableUnit(Unit) - Method in class net.sf.basedb.core.AnnotationType
Add a unit to be used with this annotation type.
addUsedQuantity(float) - Method in class net.sf.basedb.core.MeasuredBioMaterial.RemainingQuantityAction
Add some used quantity to what has currently been recorded.
addUser(User) - Method in class net.sf.basedb.core.Group
Add a user as a member to this group.
addUser(User) - Method in class net.sf.basedb.core.Role
Assign this Role to a user.
addUsingItems(Set<ItemProxy>, Item, Query<Integer>) - Method in class net.sf.basedb.core.BasicItem
Add items to the set of items using this one.
addUsingItems(Set<ItemProxy>, Query<? extends BasicData>) - Method in class net.sf.basedb.core.BasicItem
Add items to the set of items using this one.
addValue(int, float) - Method in class net.sf.basedb.clients.web.ExperimentExplorer.AnnotationGroup
Add an intensity value to this group.
addValue(AnnotationType, Object, Unit, boolean) - Method in class net.sf.basedb.plugins.AnnotationFlatFileImporter.NewAnnotations
Add an annotation value.
addValueConverter(ValueConverter) - Method in class net.sf.basedb.util.extensions.xml.XmlLoader
Add a value converter to this loader
addWarnings(int) - Method in class net.sf.basedb.util.overview.Node
Add more warnings to this node.
adjustExistingItems(ProgressReporter, int, String, String) - Static method in class net.sf.basedb.core.Update
Adjust the existing items in the database to be compatible with the latest mappings.
adjustRanges() - Method in class net.sf.basedb.util.plot.HistogramPlot
Auto-size of the x and y range doesn't seem to work, so we have to do it manually.
ADMINISTRATOR - Static variable in class net.sf.basedb.core.Role
The id for the Role item representing adminstrators.
AdvancedFieldConverter - Class in net.sf.basedb.util.export.spotdata
Field converter implementation that gives more detailed control how fields are converted and used in the export.
AdvancedFieldConverter(DbControl, BioAssaySet) - Constructor for class net.sf.basedb.util.export.spotdata.AdvancedFieldConverter
Create a new advanced field converter.
affiliations - Variable in class net.sf.basedb.core.data.ExperimentData
 
AFFYMETRIX - Static variable in class net.sf.basedb.core.Platform
The external id for the Affymetrix platform.
AFFYMETRIX_CDF - Static variable in class net.sf.basedb.core.DataFileType
The external ID for the file type representing Affymetrix CDF files.
AFFYMETRIX_CEL - Static variable in class net.sf.basedb.core.DataFileType
The external ID for the file type representing Affymetrix CEL files.
AffymetrixUtil - Class in net.sf.basedb.util.affymetrix
Utility class with Affymetrix-related functionality.
AffymetrixUtil() - Constructor for class net.sf.basedb.util.affymetrix.AffymetrixUtil
 
aFloat(float) - Static method in class net.sf.basedb.core.query.Expressions
Create a constant expression from a float.
AFTER_ENABLE - Static variable in class net.sf.basedb.clients.web.extensions.ExtensionsControl
AFTER_REGISTRATION - Static variable in class net.sf.basedb.util.extensions.events.EventType
This event is sent after an extension or extension point has been registered with a registry.
AFTER_UPDATE - Static variable in class net.sf.basedb.util.extensions.events.EventType
This event is sent during an update of an existing extension point or extension.
afterCommit() - Method in class net.sf.basedb.core.log.db.DbLogManager
 
afterCommit() - Method in interface net.sf.basedb.core.log.LogManager
Called after a successful commit of changes to the database.
afterRollback() - Method in class net.sf.basedb.core.log.db.DbLogManager
 
afterRollback() - Method in interface net.sf.basedb.core.log.LogManager
Called after rollback.
afterTransactionCompletion(Transaction) - Method in class net.sf.basedb.core.log.LoggingInterceptor
Signals successful commit or rollback to the log manager.
agent - Variable in class net.sf.basedb.clients.jobagent.AgentSignalReceiver
 
agent - Variable in class net.sf.basedb.clients.jobagent.handlers.AbstractCustomRequestHandler
 
agent - Variable in class net.sf.basedb.clients.jobagent.handlers.DefaultRequestHandler
 
agent - Variable in class net.sf.basedb.clients.jobagent.handlers.InfoRequestHandler
 
agent - Variable in class net.sf.basedb.clients.jobagent.handlers.MultiProtocolRequestHandler
 
agent - Variable in class net.sf.basedb.clients.jobagent.handlers.PauseRequestHandler
 
agent - Variable in class net.sf.basedb.clients.jobagent.handlers.SignalRequestHandler
 
agent - Variable in class net.sf.basedb.clients.jobagent.handlers.StartRequestHandler
 
agent - Variable in class net.sf.basedb.clients.jobagent.handlers.StopRequestHandler
 
agent - Variable in class net.sf.basedb.clients.jobagent.JobQueueChecker
 
agent - Variable in class net.sf.basedb.clients.jobagent.JobRunner
 
agent - Variable in class net.sf.basedb.clients.jobagent.slotmanager.InternalSlotManager
 
agent - Variable in class net.sf.basedb.clients.jobagent.slotmanager.RemoteSlotManager
 
agent - Variable in class net.sf.basedb.core.Job.ProgressReporterImpl
 
Agent - Class in net.sf.basedb.clients.jobagent
This is the actual job agent application.
Agent(Properties) - Constructor for class net.sf.basedb.clients.jobagent.Agent
Create a new job agent.
AgentController - Class in net.sf.basedb.clients.jobagent
This is the command line controller class for the job agent application.
AgentController(Properties) - Constructor for class net.sf.basedb.clients.jobagent.AgentController
Create a new controller for controlling the job agent specified by the given properties.
agentInfo - Static variable in class net.sf.basedb.core.JobAgent
 
AgentSignalReceiver - Class in net.sf.basedb.clients.jobagent
Signal receiver implementation for job agents that is compatible with the SocketSignalReceiver.
AgentSignalReceiver(Agent) - Constructor for class net.sf.basedb.clients.jobagent.AgentSignalReceiver
 
agentVersionForJobQuery - Variable in class net.sf.basedb.clients.jobagent.JobQueueChecker
The job agent's version when the query was cached.
Aggregations - Class in net.sf.basedb.core.query
A factory class to create aggregate expressions.
Aggregations() - Constructor for class net.sf.basedb.core.query.Aggregations
 
aIndex - Variable in class net.sf.basedb.util.importer.spotdata.MAParser
 
alias - Variable in class net.sf.basedb.core.AnnotationRestriction
 
alias - Variable in enum class net.sf.basedb.core.Item
 
alias - Variable in class net.sf.basedb.core.query.AnnotationExpression
 
alias - Variable in class net.sf.basedb.core.query.AnnotationJoin
 
alias - Variable in class net.sf.basedb.core.query.AnyToAnyRestriction
 
alias - Variable in class net.sf.basedb.core.query.ExpressionSelect
 
alias - Variable in class net.sf.basedb.core.query.HqlElementsExpression
 
alias - Variable in class net.sf.basedb.core.query.HqlIndexExpression
 
alias - Variable in class net.sf.basedb.core.query.HqlInnerJoin
 
alias - Variable in class net.sf.basedb.core.query.HqlLeftJoin
 
alias - Variable in class net.sf.basedb.core.query.HqlPropertyExpression
 
alias - Variable in class net.sf.basedb.core.query.HqlRightJoin
 
alias - Variable in class net.sf.basedb.core.query.HqlSizeExpression
 
alias - Variable in class net.sf.basedb.core.query.SqlColumnExpression
 
alias - Variable in class net.sf.basedb.core.RealTable
The alias to use in queries for this table.
alias - Variable in enum class net.sf.basedb.core.VirtualTable
The alias to use in queries for this table.
alias - Variable in class net.sf.basedb.util.ssl.StaticKeyManager
 
alias(String) - Static method in class net.sf.basedb.core.query.Hql
Same as property(alias, null).
ALIAS_REGEXP - Static variable in class net.sf.basedb.core.query.Hql
An alias can only contain the characters a-z, A-Z or 0-9.
ALIAS_REGEXP - Static variable in class net.sf.basedb.core.query.Selects
An alias can only contain the characters a-z, A-Z or 0-9.
aliasMapping - Static variable in enum class net.sf.basedb.core.Item
 
ALIGNED_SEQUENCE - Static variable in class net.sf.basedb.core.File
The id for the FileType item representing a file containing aligned sequence data.
ALIGNMENT - Static variable in class net.sf.basedb.core.Protocol
The ID for the alignment protocol type, for example a protocol used when creating a DerivedBioAssay representing data that has been aligned against a reference genome.
ALIGNMENT - Static variable in class net.sf.basedb.core.Software
The id for the SoftwareType item representing software used for aligning sequenced data against a known reference database.
all - Static variable in class net.sf.basedb.core.RawDataTypes
 
all - Variable in class net.sf.basedb.util.plot.HistogramPlot.HistogramDataset
 
all(Query) - Static method in class net.sf.basedb.core.query.Expressions
Create a subquery expression: ANY (subquery).
ALL - Enum constant in enum class net.sf.basedb.util.overview.node.ChildNodeDirection
 
ALL - Static variable in enum class net.sf.basedb.core.Include
A non-modifable collection containing all options.
ALL - Static variable in class net.sf.basedb.core.Keyring
 
ALL_ITEM - Static variable in class net.sf.basedb.core.Keyring
 
allCharsets - Static variable in class net.sf.basedb.core.Config
 
allChildExtractsInChain - Variable in class net.sf.basedb.util.AnnotationUtil.AnnotatableWrapper
 
allColumnMappings - Variable in class net.sf.basedb.plugins.gtf.GtfReporterMapImporter
 
allColumnMappings - Variable in class net.sf.basedb.plugins.PlateFlatFileImporter
 
allColumnMappings - Variable in class net.sf.basedb.plugins.RawDataFlatFileImporter
 
allColumnMappings - Variable in class net.sf.basedb.plugins.ReporterFlatFileImporter
 
allColumnMappings - Variable in class net.sf.basedb.plugins.ReporterMapFlatFileImporter
 
allData - Variable in class net.sf.basedb.util.extensions.manager.processor.RegisterExtensionsProcessor
 
AllEventsFilter - Class in net.sf.basedb.util.extensions.events
Event filter that passes all events.
AllEventsFilter() - Constructor for class net.sf.basedb.util.extensions.events.AllEventsFilter
Create a event type filter that passes all events.
allInsertBatchers - Variable in class net.sf.basedb.core.AnnotationBatcher
 
allInsertBatchers - Variable in class net.sf.basedb.core.MigrateRbaToDba
 
allModified - Variable in class net.sf.basedb.core.DerivedBioAssay.FixDerivedBioAssayParentsRecursivelyAction
 
allMustPass - Variable in class net.sf.basedb.util.extensions.events.CombiningEventFilter
 
allNodes - Variable in class net.sf.basedb.util.overview.GenericOverview
 
allObjects - Variable in class net.sf.basedb.util.extensions.manager.ExtensionsFile
 
AllOfFilter<T> - Class in net.sf.basedb.util.filter
A filter implementation that accpets an object if all parent filters accepts it.
AllOfFilter(Collection<? extends Filter<? super T>>) - Constructor for class net.sf.basedb.util.filter.AllOfFilter
Create a new filter.
allow - Variable in class net.sf.basedb.core.signal.SocketSignalReceiver
 
ALLOW_ROOT_NODE - Static variable in class net.sf.basedb.util.overview.loader.BasicItemNodeLoader
 
allowAll - Variable in class net.sf.basedb.core.signal.SocketSignalReceiver
 
AllowAnyHostNameVerifyer - Class in net.sf.basedb.util.ssl
A simple implementation of a host name verifyer that allows all hosts.
AllowAnyHostNameVerifyer() - Constructor for class net.sf.basedb.util.ssl.AllowAnyHostNameVerifyer
 
allowAsRootNode - Variable in class net.sf.basedb.util.overview.loader.BasicItemNodeLoader
 
allowColumnDrag() - Method in class net.sf.basedb.clients.web.taglib.table.Table
Can header columns be dragged for re-ordering?
allowDoublingBack - Variable in class net.sf.basedb.clients.web.extensions.list.RelatedItemColumn.Specification
 
allowedClients - Variable in class net.sf.basedb.core.SessionControl
 
allowForward - Variable in class net.sf.basedb.core.signal.SocketSignalReceiver
 
allowImmediateDownload - Variable in class net.sf.basedb.core.PluginResponse
 
allowImmediateExecution - Variable in class net.sf.basedb.core.data.PluginDefinitionData
 
allowImmediateExecution - Variable in class net.sf.basedb.core.PluginConfigurationRequest
 
allowImmediateExecution - Variable in class net.sf.basedb.core.PluginRequest.RequestImpl
 
allowImmediateExecution - Variable in class net.sf.basedb.core.PluginResponse
 
allowMultiple - Variable in class net.sf.basedb.util.timer.ThreadTimerTask
 
allowRemotePause - Variable in class net.sf.basedb.clients.jobagent.Agent
 
allowRemoteStart - Variable in class net.sf.basedb.clients.jobagent.Agent
 
allowRemoteStop - Variable in class net.sf.basedb.clients.jobagent.Agent
 
allowRendererOverride - Variable in class net.sf.basedb.util.extensions.ExtensionPointBean
 
allowRendererOverride - Variable in class net.sf.basedb.util.extensions.Registry.RegisteredExtensionPoint
 
allowRendererOverride() - Method in interface net.sf.basedb.util.extensions.ExtensionPoint
If an extension is allowed to override the renderer factory with an implementation of its own.
allowRendererOverride() - Method in class net.sf.basedb.util.extensions.ExtensionPointBean
 
allowRendererOverride() - Method in class net.sf.basedb.util.extensions.Registry.RegisteredExtensionPoint
 
allowSaveParameters - Variable in enum class net.sf.basedb.core.plugin.Response.Status
 
allowSaveParameters() - Method in enum class net.sf.basedb.core.plugin.Response.Status
 
allowSubclass - Variable in class net.sf.basedb.util.filter.InstanceOfFilter
 
allowUnmodified - Variable in class net.sf.basedb.util.extensions.manager.filter.ValidAndNewOrModifiedFilter
 
allowUse - Variable in class net.sf.basedb.util.jep.RawFunction
 
allProjects - Variable in class net.sf.basedb.core.snapshot.SnapshotManager
 
allProperties - Static variable in class net.sf.basedb.core.ExtendedProperties
A map from class name --> a list of extended properties of for that class.
allSame(Collection<Set<Permission>>) - Static method in class net.sf.basedb.core.MultiPermissions
Check if a collection of Set:s all contain the same permissions.
allSeries - Variable in class net.sf.basedb.util.plot.ScatterPlot
 
allSql - Variable in class net.sf.basedb.core.hibernate.SchemaGenerator.CollectSqlTarget
 
allSubContexts - Variable in class net.sf.basedb.clients.web.taglib.table.PresetSelector
If true, presets for all subcontexts are included in the preset, otherwise only presets for the current subcontext (default).
allUpdateBatchers - Variable in class net.sf.basedb.core.AnnotationBatcher
 
allUpdateBatchers - Variable in class net.sf.basedb.core.MigrateRbaToDba
 
allVisible - Variable in class net.sf.basedb.clients.web.taglib.table.Table
"all" was specified for the columns attribute.
alphaToNumeric(String) - Static method in class net.sf.basedb.util.Coordinate
Convert an alphanumeric coordinate to a numeric coordinate, case is unimportent.
AlreadyLoggedInException - Exception in net.sf.basedb.core
This exception is thrown if you try to log in but are already logged in.
AlreadyLoggedInException(String) - Constructor for exception net.sf.basedb.core.AlreadyLoggedInException
Creates a new AlreadyLoggedInException.
ALTERNATE_PATH_MATCH - Static variable in class net.sf.basedb.clients.web.servlet.ExtensionsServlet
Alternatively the servlet is: /extensions/servlet and pathInfo is: /[jar-file-name]/[servlet-name]/optional/path/info
alwaysGranted - Variable in class net.sf.basedb.core.plugin.Permissions
 
AMP - Static variable in class net.sf.basedb.clients.web.util.HTML
 
AMPERSAND - Static variable in class net.sf.basedb.clients.web.util.HTML
 
AnalysisFilterPlugin - Interface in net.sf.basedb.core.plugin
This is a tagging interface that should be used by all analysis plug-ins that are filtering data only.
ANALYZE - Enum constant in enum class net.sf.basedb.core.plugin.Plugin.MainType
 
analyzeAfterBatchOperation() - Method in interface net.sf.basedb.core.dbengine.DbEngine
If TRUE, a batcher that inserts, updates or delets a lot of rows in a table should execute the SQL returned by DbEngine.getAnalyzeTableSql(String, String, String) for that table.
analyzeAfterBatchOperation() - Method in class net.sf.basedb.core.dbengine.DefaultDbEngine
Return false.
analyzeAfterBatchOperation() - Method in class net.sf.basedb.core.dbengine.MySQLEngine
Return true.
analyzeAfterBatchOperation() - Method in class net.sf.basedb.core.dbengine.PostgresDbEngine
Return true.
analyzeAfterImport - Variable in class net.sf.basedb.core.Migration
 
analyzeTable(String, String, String) - Method in class net.sf.basedb.core.AbstractBatcher
Update index statistics for a table.
analyzeUserAgent(String) - Static method in class net.sf.basedb.util.HttpUtil
Parse the User-Agent string from a HTTP request and return information about what it actually means.
and(Restriction...) - Static method in class net.sf.basedb.core.query.Restrictions
Combine one or more restrictions with AND: new restriction = r[0] AND r[1] AND ...
AND - Enum constant in enum class net.sf.basedb.core.Operator
 
AndConverter - Class in net.sf.basedb.util.jep.convert
Convert the '&&' operator to a Query API Restriction.
AndConverter() - Constructor for class net.sf.basedb.util.jep.convert.AndConverter
 
AndRestriction - Class in net.sf.basedb.core.query
Combine one or more restrictions with AND: r[0] AND r[1] AND ...
AndRestriction(Restriction...) - Constructor for class net.sf.basedb.core.query.AndRestriction
 
ANGLE - Static variable in class net.sf.basedb.core.Quantity
The id for the Quantity object representing angle.
Annotatable - Interface in net.sf.basedb.core
This interface is implemented by all items which can be annotated.
ANNOTATABLE_FILTER - Static variable in class net.sf.basedb.core.QueryRuntimeFilterFactory
 
AnnotatableData - Interface in net.sf.basedb.core.data
An annotatable item is an item that can be annotated with name/value pairs.
AnnotatableFilter() - Constructor for class net.sf.basedb.core.QueryRuntimeFilterFactory.AnnotatableFilter
 
annotatableItems - Static variable in class net.sf.basedb.core.Metadata
 
AnnotatableProxy - Interface in net.sf.basedb.core
This interface is implemented by items that can be used to hold annotations that are intended for other items.
AnnotatableWrapper(Annotatable, AnnotationUtil.AnnotatableWrapper) - Constructor for class net.sf.basedb.util.AnnotationUtil.AnnotatableWrapper
 
AnnotatableWrapper(Annotatable, AnnotationUtil.Cache) - Constructor for class net.sf.basedb.util.AnnotationUtil.AnnotatableWrapper
 
ANNOTATED - Enum constant in enum class net.sf.basedb.core.Include
Include items that have at least one annotation.
AnnotatedData - Class in net.sf.basedb.core.data
This class extends the CommonData class and implements the AnnotatableData interface.
AnnotatedData() - Constructor for class net.sf.basedb.core.data.AnnotatedData
 
AnnotatedItem - Class in net.sf.basedb.core
This is a helper class for items that need to implement the Annotatable interface.
AnnotatedItem(AnnotatedData) - Constructor for class net.sf.basedb.core.AnnotatedItem
 
annotation - Variable in class net.sf.basedb.util.overview.Fix
 
annotation(AnnotationType, String, Formatter<?>) - Static method in class net.sf.basedb.util.export.spotdata.ExportableFieldFactory
Create an annotation assay field, overriding the title of the annotation type.
annotation(AnnotationType, Formatter<?>) - Static method in class net.sf.basedb.util.export.spotdata.ExportableFieldFactory
Create an annotation assay field.
Annotation - Class in net.sf.basedb.core
This class represents an annotation.
Annotation(AnnotationData) - Constructor for class net.sf.basedb.core.Annotation
 
Annotation(AnnotationData, AnnotationSet) - Constructor for class net.sf.basedb.core.Annotation
 
ANNOTATION - Enum constant in enum class net.sf.basedb.core.Item
The item is an Annotation.
ANNOTATION - Enum constant in enum class net.sf.basedb.plugins.Base1PluginExecuter.Base1JobParameterType
 
ANNOTATION_CLONE_OUTOFSYNC - Static variable in class net.sf.basedb.util.overview.Validator
Validator rule that checks if a cloned annotation value is in sync with the source annotation.
ANNOTATION_CLONED_FROM_UNKNOWNPARENT - Static variable in class net.sf.basedb.util.overview.Validator
Validator rule that checks if a cloned annotation value has lost the reference to the parent item.
ANNOTATION_INHERIT_FROM_DENIEDPARENT - Static variable in class net.sf.basedb.util.overview.Validator
Validator rule that checks if the logged in user has access to the parent item of an inherited annotation value.
ANNOTATION_INHERIT_FROM_NONPARENT - Static variable in class net.sf.basedb.util.overview.Validator
Validator rule that checks if an inherited annotation value is inherited from a parent item.
ANNOTATION_INHERIT_MULTIPLE - Static variable in class net.sf.basedb.util.overview.Validator
Validator rule that checks if two or more inherited annotations have the same annotation type.
ANNOTATION_INVALID_ITEM - Static variable in class net.sf.basedb.util.overview.Validator
Validator rule that checks if an annotation is not valid for the current item type.
ANNOTATION_INVALID_VALUE - Static variable in class net.sf.basedb.util.overview.Validator
Validator rule that checks if an annotation value is invalid according to annotation type specification.
ANNOTATION_IS_PARAMETER - Static variable in class net.sf.basedb.util.overview.Validator
Validator rule that checks if an annotation is a protocol parameter.
ANNOTATION_TOO_MANY_VALUES - Static variable in class net.sf.basedb.util.overview.Validator
Validator rule that checks if an annotation have more values than what the 'multiplicity' setting for the annotation type allow.
Annotation.QueryRuntimeFilterImpl - Class in net.sf.basedb.core
 
Annotation.Source - Enum Class in net.sf.basedb.core
The annotation source.
AnnotationAssayField - Class in net.sf.basedb.util.export.spotdata
Assay field implementation that exports the annotations of a bioassay.
AnnotationAssayField() - Constructor for class net.sf.basedb.util.export.spotdata.AnnotationAssayField
Create a new annotation field.
AnnotationBatcher - Class in net.sf.basedb.core
Batcher implementation for adding, updating and removing multiple annotations to a large number of items in a single transaction while keeping the memory usage as low as possible.
AnnotationBatcher(DbControl, Item) - Constructor for class net.sf.basedb.core.AnnotationBatcher
Create a new batcher instance.
AnnotationBatcher(DbControl, Item, Integer) - Constructor for class net.sf.basedb.core.AnnotationBatcher
Create a new batcher instance.
AnnotationBatcher(DbControl, Item, Project) - Constructor for class net.sf.basedb.core.AnnotationBatcher
Create a new batcher instance.
AnnotationBatcher.Change - Enum Class in net.sf.basedb.core
A flag indicating what type of change that was made to an annotation as a result of calling AnnotationBatcher.setValues(AnnotationType, List, Unit, boolean)
AnnotationBatcher.CurrentAnnotationInfo - Class in net.sf.basedb.core
Holds information about an annotation for the current item.
AnnotationBatcher.InsertBatcher - Class in net.sf.basedb.core
Batcher implementation for inserting into tables.
AnnotationBatcher.UpdateBatcher - Class in net.sf.basedb.core
Batcher implementation for updating and deleting from tables.
AnnotationBetweenRestriction - Class in net.sf.basedb.core
Restricts a query using annotation values between a low and high value.
AnnotationBetweenRestriction(String, int, Type, Object, Object, boolean, boolean) - Constructor for class net.sf.basedb.core.AnnotationBetweenRestriction
AnnotationBetweenRestriction(String, AnnotationType, Object, Object, boolean, boolean) - Constructor for class net.sf.basedb.core.AnnotationBetweenRestriction
AnnotationBetweenRestriction(String, AnnotationType, Object, Object, AnnotationRestriction.Options) - Constructor for class net.sf.basedb.core.AnnotationBetweenRestriction
Create a new annotation restriction.
AnnotationData - Class in net.sf.basedb.core.data
This class holds information about an annotation
AnnotationData() - Constructor for class net.sf.basedb.core.data.AnnotationData
 
AnnotationExpression - Class in net.sf.basedb.core.query
An expression representing the value of an annotation.
AnnotationExpression(String, AnnotationType) - Constructor for class net.sf.basedb.core.query.AnnotationExpression
 
AnnotationFilter - Class in net.sf.basedb.core.snapshot
Filter implementation that finds the annotation snapshot for a given annotation.
AnnotationFilter() - Constructor for class net.sf.basedb.core.snapshot.AnnotationFilter
Create a filter that matches all annotations.
AnnotationFilter(Annotation) - Constructor for class net.sf.basedb.core.snapshot.AnnotationFilter
Create a filter that matches a specfic annotation.
AnnotationFlatFileImporter - Class in net.sf.basedb.plugins
Plug-in for importing annotations from simple text files.
AnnotationFlatFileImporter() - Constructor for class net.sf.basedb.plugins.AnnotationFlatFileImporter
 
AnnotationFlatFileImporter.AnnotationValue - Class in net.sf.basedb.plugins
 
AnnotationFlatFileImporter.NewAnnotations - Class in net.sf.basedb.plugins
Internal cache for storing annotation values from the file for a single item.
AnnotationGroup(int, Set<T>, int, Formatter<T>) - Constructor for class net.sf.basedb.clients.web.ExperimentExplorer.AnnotationGroup
 
annotationId - Variable in class net.sf.basedb.clients.web.extensions.list.RelatedItemColumn.Specification
 
annotationId - Variable in class net.sf.basedb.core.AnnotationBatcher.CurrentAnnotationInfo
 
annotationId - Variable in class net.sf.basedb.core.FastAnnotationLoader.FastAnnotation
The ID of the annotation.
annotationId - Variable in class net.sf.basedb.core.snapshot.AnnotationFilter
 
annotationId - Variable in class net.sf.basedb.core.snapshot.AnnotationSnapshot
 
AnnotationIdMethod - Class in net.sf.basedb.plugins.batchimport
Identification method implementation that can use an annotation for identifying items.
AnnotationIdMethod(AnnotationType) - Constructor for class net.sf.basedb.plugins.batchimport.AnnotationIdMethod
Create a new id method.
AnnotationInfo(int, int, int, int) - Constructor for class net.sf.basedb.core.ProjectSpecificAnnotationsManager.AnnotationInfo
 
AnnotationInfo(int, int, int, int, int, int) - Constructor for class net.sf.basedb.core.ProjectSpecificAnnotationsManager.AnnotationInfo
 
AnnotationInRestriction - Class in net.sf.basedb.core
Restricts a query using annotation values that exists in a set of given values.
AnnotationInRestriction(String, AnnotationType, boolean, boolean, Object...) - Constructor for class net.sf.basedb.core.AnnotationInRestriction
AnnotationInRestriction(String, AnnotationType, AnnotationRestriction.Options, Object...) - Constructor for class net.sf.basedb.core.AnnotationInRestriction
Create a new annotation restriction.
AnnotationJoin - Class in net.sf.basedb.core.query
Join annotations values to the query.
AnnotationJoin(JoinType, String, AnnotationType, String) - Constructor for class net.sf.basedb.core.query.AnnotationJoin
 
AnnotationJoiner(JoinType) - Constructor for class net.sf.basedb.core.HqlQueryJoiners.AnnotationJoiner
 
AnnotationLink - Class in net.sf.basedb.core.data.annotations
Class for mapping the "Annotations" table with shortcuts to all 'FooValues' tables.
AnnotationLink() - Constructor for class net.sf.basedb.core.data.annotations.AnnotationLink
 
AnnotationLoader - Class in net.sf.basedb.util.overview.loader
Node loader implementation for annotations.
AnnotationLoader() - Constructor for class net.sf.basedb.util.overview.loader.AnnotationLoader
 
AnnotationLoaderUtil - Class in net.sf.basedb.core.snapshot
Utility implementation for simple loading of primary annotations via SnapshotManager.
AnnotationLoaderUtil(DbControl, SnapshotManager, AnnotationType) - Constructor for class net.sf.basedb.core.snapshot.AnnotationLoaderUtil
Create a loder that uses the given snapshot manager to load annotations for a single annotation type.
AnnotationLoaderUtil(DbControl, SnapshotManager, AnnotationType, boolean, boolean) - Constructor for class net.sf.basedb.core.snapshot.AnnotationLoaderUtil
Create a loder that uses the given snapshot manager to load annotations for a single annotation type.
AnnotationLogger - Class in net.sf.basedb.core.log.db
Logger for annotations that logs changes as updates to the parent item the annotations belong to.
AnnotationLogger(DbLogManagerFactory) - Constructor for class net.sf.basedb.core.log.db.AnnotationLogger
 
AnnotationModel - Class in net.sf.basedb.util.bfs
A model container for BFS annotation files.
AnnotationModel() - Constructor for class net.sf.basedb.util.bfs.AnnotationModel
Create a new annotation model.
AnnotationNameGenerator - Class in net.sf.basedb.util.overview.node
Since an Annotation isn't Nameable we construct the name from the name of the annotation type, or from the value type if we are not allowed to access the annotation type.
AnnotationNameGenerator() - Constructor for class net.sf.basedb.util.overview.node.AnnotationNameGenerator
 
AnnotationParser - Class in net.sf.basedb.util.bfs
Parser implementation that parses a BFS annotation files.
AnnotationParser() - Constructor for class net.sf.basedb.util.bfs.AnnotationParser
Create a new annotation parser.
AnnotationRestriction - Class in net.sf.basedb.core
Base class for creating restrictions based on annotations.
AnnotationRestriction(String, int, Type, AnnotationRestriction.Options) - Constructor for class net.sf.basedb.core.AnnotationRestriction
Deprecated.
In 3.11
AnnotationRestriction(String, AnnotationType, AnnotationRestriction.Options) - Constructor for class net.sf.basedb.core.AnnotationRestriction
Create a new annotation restriction for an annotation type.
AnnotationRestriction.Options - Class in net.sf.basedb.core
Options that specify which annotations to consider when searching.
annotations - Variable in class net.sf.basedb.clients.web.servlet.ExperimentExplorerPlotServlet.ColumnKey
 
annotations - Variable in class net.sf.basedb.core.data.AnnotationSetData
 
annotations - Variable in class net.sf.basedb.core.data.AnnotationTypeData
 
annotations - Variable in class net.sf.basedb.core.snapshot.AnnotationSetSnapshot
 
Annotations - Class in net.sf.basedb.core.query
A factory class to create restrictions based on annotation values.
Annotations() - Constructor for class net.sf.basedb.core.query.Annotations
 
annotationSection - Static variable in class net.sf.basedb.core.plugin.AbstractPlugin
Section definition for grouping annotation options.
annotationSet - Variable in class net.sf.basedb.core.Annotation
 
annotationSet - Variable in class net.sf.basedb.core.data.AnnotatedData
 
annotationSet - Variable in class net.sf.basedb.core.data.AnnotationData
 
annotationSet - Variable in class net.sf.basedb.core.data.BioAssayData
 
annotationSet - Variable in class net.sf.basedb.core.data.BioAssaySetData
 
annotationSet - Variable in class net.sf.basedb.core.data.PluginDefinitionData
 
annotationSet - Variable in class net.sf.basedb.core.data.ProjectData
 
annotationSet - Variable in class net.sf.basedb.core.data.RootRawBioAssayData
 
annotationSet - Variable in class net.sf.basedb.core.data.WellData
 
annotationSet - Variable in class net.sf.basedb.core.ProjectSpecificAnnotationsManager.AnnotationInfo
 
annotationSet - Variable in class net.sf.basedb.util.overview.validator.ProtocolParameterValidator
 
AnnotationSet - Class in net.sf.basedb.core
An annotation set is the container for all annotations on an item.
AnnotationSet(AnnotationSetData) - Constructor for class net.sf.basedb.core.AnnotationSet
Regular constructor if the item is not known beforehand.
AnnotationSet(AnnotationSetData, Annotatable) - Constructor for class net.sf.basedb.core.AnnotationSet
Special constructor to avoid AnnotationSet.getItem() to hit the database when the item is known beforehand.
ANNOTATIONSET - Enum constant in enum class net.sf.basedb.core.Item
The item is an AnnotationSet.
AnnotationSet.ProjectSpecificAnnotationsRestriction - Class in net.sf.basedb.core
Restriction for matching project-specific annotations against the currently active project.
AnnotationSet.QueryRuntimeFilterImpl - Class in net.sf.basedb.core
 
AnnotationSetData - Class in net.sf.basedb.core.data
This class holds information about a set of annotations.
AnnotationSetData() - Constructor for class net.sf.basedb.core.data.AnnotationSetData
 
annotationSetId - Variable in class net.sf.basedb.core.AnnotationSet.ProjectSpecificAnnotationsRestriction
 
annotationSetId - Variable in class net.sf.basedb.core.data.annotations.AnnotationLink
 
annotationSetId - Variable in class net.sf.basedb.core.MigrateRbaToDba.Rba
 
annotationSetId - Variable in class net.sf.basedb.core.snapshot.AnnotationSetSnapshot
 
annotationSetId - Variable in class net.sf.basedb.core.snapshot.AnnotationSnapshot
 
AnnotationSetLogger - Class in net.sf.basedb.core.log.db
Logger for annotations sets that detects and logs changes to inherited anntations as updates to the parent item that are inheriting the annotations.
AnnotationSetLogger(DbLogManagerFactory) - Constructor for class net.sf.basedb.core.log.db.AnnotationSetLogger
 
AnnotationSetSnapshot - Class in net.sf.basedb.core.snapshot
A snapshot of an annotation set that is used to store information as a file.
AnnotationSetSnapshot() - Constructor for class net.sf.basedb.core.snapshot.AnnotationSetSnapshot
Creates a new, empty snapshot.
AnnotationSetSnapshot.SortByProjectComparator - Class in net.sf.basedb.core.snapshot
Comparator for sorting annotation snapshots so that project-specific annotations appear before default annotations.
AnnotationSetterPlugin - Interface in net.sf.basedb.core.plugin
This is a interface that should be implemented by plug-ins that are setting annotations on items thy create or work with.
AnnotationSimpleRestriction - Class in net.sf.basedb.core
Restricts a query using annotation values with a simple expression: annotation operator value.
AnnotationSimpleRestriction(String, int, Type, Operator, Object, boolean, boolean) - Constructor for class net.sf.basedb.core.AnnotationSimpleRestriction
AnnotationSimpleRestriction(String, int, Type, Operator, List<Object>, boolean, boolean) - Constructor for class net.sf.basedb.core.AnnotationSimpleRestriction
AnnotationSimpleRestriction(String, AnnotationType, Operator, Object, boolean, boolean) - Constructor for class net.sf.basedb.core.AnnotationSimpleRestriction
AnnotationSimpleRestriction(String, AnnotationType, Operator, Object, AnnotationRestriction.Options) - Constructor for class net.sf.basedb.core.AnnotationSimpleRestriction
Create a new annotation restriction using a simple expression: annotation operator value.
AnnotationSimpleRestriction(String, AnnotationType, Operator, List<Object>, AnnotationRestriction.Options) - Constructor for class net.sf.basedb.core.AnnotationSimpleRestriction
Creates a new annotation restriction for a specific valueType.
AnnotationSnapshot - Class in net.sf.basedb.core.snapshot
Stores information about a single primary or inherited annotation or an inherited annotation set.
AnnotationSnapshot() - Constructor for class net.sf.basedb.core.snapshot.AnnotationSnapshot
Create a new, empty annotation snapshot.
AnnotationSnapshot.AnnotationTypeComparator - Class in net.sf.basedb.core.snapshot
Comparator implementation for sorting snapshots by name of annotation type.
AnnotationSnapshot.ProjectComparator - Class in net.sf.basedb.core.snapshot
Comparator implementation for sorting snapshots by name of project.
AnnotationSummary(ExperimentExplorer, DbControl, AnnotationType) - Constructor for class net.sf.basedb.clients.web.ExperimentExplorer.AnnotationSummary
 
annotationType - Variable in class net.sf.basedb.clients.web.ExperimentExplorer.AnnotationSummary
 
annotationType - Variable in class net.sf.basedb.clients.web.plugins.ExportedProperty
 
annotationType - Variable in class net.sf.basedb.core.AnnotationBatcher.CurrentAnnotationInfo
 
annotationType - Variable in class net.sf.basedb.core.AnnotationRestriction
 
annotationType - Variable in class net.sf.basedb.core.data.AnnotationData
 
annotationType - Variable in class net.sf.basedb.core.ProjectSpecificAnnotationsManager.AnnotationInfo
 
annotationType - Variable in class net.sf.basedb.core.query.AnnotationExpression
 
annotationType - Variable in class net.sf.basedb.core.query.AnnotationJoin
 
annotationType - Variable in class net.sf.basedb.plugins.batchimport.AnnotationIdMethod
 
annotationType - Variable in class net.sf.basedb.util.annotations.InheritSpecification
 
annotationType - Variable in class net.sf.basedb.util.overview.Fix
 
AnnotationType - Class in net.sf.basedb.core
Objects of this class defines an annotation type.
AnnotationType(AnnotationTypeData) - Constructor for class net.sf.basedb.core.AnnotationType
 
ANNOTATIONTYPE - Enum constant in enum class net.sf.basedb.core.Item
The item is an AnnotationType.
AnnotationType.RemoveInheritedAnnotationsAction - Class in net.sf.basedb.core
 
AnnotationTypeCategory - Class in net.sf.basedb.core
Objects of this class defines an annotation type category.
AnnotationTypeCategory(AnnotationTypeCategoryData) - Constructor for class net.sf.basedb.core.AnnotationTypeCategory
 
ANNOTATIONTYPECATEGORY - Enum constant in enum class net.sf.basedb.core.Item
The item is an AnnotationTypeCategory.
AnnotationTypeCategoryData - Class in net.sf.basedb.core.data
This data layer class holds information about annotation type categories.
AnnotationTypeCategoryData() - Constructor for class net.sf.basedb.core.data.AnnotationTypeCategoryData
 
annotationTypeCategoryQuery - Variable in class net.sf.basedb.plugins.batchimport.AbstractItemImporter
 
AnnotationTypeComparator(DbControl) - Constructor for class net.sf.basedb.core.snapshot.AnnotationSnapshot.AnnotationTypeComparator
 
AnnotationTypeData - Class in net.sf.basedb.core.data
This class holds information about an annotation type.
AnnotationTypeData() - Constructor for class net.sf.basedb.core.data.AnnotationTypeData
 
AnnotationTypeEnumerationLoader - Class in net.sf.basedb.clients.web.plugins
Data loader implementation for loading the enumeration values collection of an annotation type.
AnnotationTypeEnumerationLoader() - Constructor for class net.sf.basedb.clients.web.plugins.AnnotationTypeEnumerationLoader
 
AnnotationTypeFilter - Class in net.sf.basedb.core.snapshot
Filter implementation that finds all annotation snapshots for a given annotation type.
AnnotationTypeFilter() - Constructor for class net.sf.basedb.core.snapshot.AnnotationTypeFilter
Create a filter that matches all annotation types.
AnnotationTypeFilter(Annotation.Source) - Constructor for class net.sf.basedb.util.annotations.InheritAnnotationsManager.AnnotationTypeFilter
 
AnnotationTypeFilter(AnnotationType) - Constructor for class net.sf.basedb.core.snapshot.AnnotationTypeFilter
Create a filter that matches a specfic annotation type.
annotationTypeId - Variable in class net.sf.basedb.core.AnnotationRestriction
 
annotationTypeId - Variable in class net.sf.basedb.core.data.annotations.AnnotationLink
 
annotationTypeId - Variable in class net.sf.basedb.core.snapshot.AnnotationSnapshot
 
annotationTypeId - Variable in class net.sf.basedb.core.snapshot.AnnotationTypeFilter
 
annotationTypeId - Variable in class net.sf.basedb.util.annotations.InheritSpecification
 
annotationTypeIds - Variable in class net.sf.basedb.clients.web.ExperimentExplorer
The currently selected annotation types on the view page.
annotationTypeIds - Variable in class net.sf.basedb.core.Annotation.QueryRuntimeFilterImpl
 
AnnotationTypeImporter - Class in net.sf.basedb.plugins.batchimport
Plug-in for importing annotation type items in a batch.
AnnotationTypeImporter() - Constructor for class net.sf.basedb.plugins.batchimport.AnnotationTypeImporter
 
AnnotationTypeItemTypesLoader - Class in net.sf.basedb.clients.web.plugins
Data loader implementation for loading the item types collection of an annotation type.
AnnotationTypeItemTypesLoader() - Constructor for class net.sf.basedb.clients.web.plugins.AnnotationTypeItemTypesLoader
 
annotationTypes - Variable in class net.sf.basedb.core.data.AnnotationTypeCategoryData
 
annotationTypes - Variable in class net.sf.basedb.util.annotations.InheritAnnotationsManager.AnnotationTypeFilter
 
annotationTypeSection - Static variable in class net.sf.basedb.plugins.AnnotationFlatFileImporter
Section definition for grouping all mappings of columns to annotation types.
AnnotationUtil - Class in net.sf.basedb.clients.web
Some utility functions for annotations.
AnnotationUtil - Class in net.sf.basedb.util
Utility class for working with annotations.
AnnotationUtil() - Constructor for class net.sf.basedb.clients.web.AnnotationUtil
 
AnnotationUtil() - Constructor for class net.sf.basedb.util.AnnotationUtil
 
AnnotationUtil.AnnotatableWrapper - Class in net.sf.basedb.util
This wrapper class is needed because we need to keep track of extracts linked with raw bioassays and derived bioassays until we have loaded the Extracts of a Physical Bioassay.
AnnotationUtil.Cache - Class in net.sf.basedb.util
 
AnnotationValidator - Class in net.sf.basedb.util.overview.validator
Validator implementation for annotations.
AnnotationValidator() - Constructor for class net.sf.basedb.util.overview.validator.AnnotationValidator
 
AnnotationValue(Object, Unit) - Constructor for class net.sf.basedb.plugins.AnnotationFlatFileImporter.AnnotationValue
 
annotationValues - Variable in class net.sf.basedb.clients.web.ExperimentExplorer.AnnotationGroup
 
AnnotationWriter - Class in net.sf.basedb.util.bfs
 
AnnotationWriter(Writer) - Constructor for class net.sf.basedb.util.bfs.AnnotationWriter
 
any - Variable in class net.sf.basedb.clients.web.extensions.fileviewer.FileViewerContext
 
any(Query) - Static method in class net.sf.basedb.core.query.Expressions
Create a subquery expression: ANY (subquery).
ANY_TO_ANY - Enum constant in enum class net.sf.basedb.clients.web.extensions.fileviewer.FileViewerContext.Type
The context is a list with any-to-any links from a parent item.
AnyLinkColumn - Class in net.sf.basedb.clients.web.extensions.list
A column action implementation that finds an item linked with a any-to-any link.
AnyLinkColumn(int, String, String, Item, Metadata.PropertyPath<BasicItem, ?>, FileViewerUtil) - Constructor for class net.sf.basedb.clients.web.extensions.list.AnyLinkColumn
 
AnyLinkColumnActionFactory - Class in net.sf.basedb.clients.web.extensions.list
Action factory for adding columns to a table that display items that are linked with an any-to-any link.
AnyLinkColumnActionFactory() - Constructor for class net.sf.basedb.clients.web.extensions.list.AnyLinkColumnActionFactory
 
anyToAny(BasicItem) - Static method in class net.sf.basedb.clients.web.extensions.fileviewer.FileViewerContext
Creates an any-to-any listing context where files belong to a parent item.
AnyToAny - Class in net.sf.basedb.core
An any-to-any link is a named, directed link from one item to another item.
AnyToAny(AnyToAnyData) - Constructor for class net.sf.basedb.core.AnyToAny
Creates a new link item from the given data.
AnyToAny(AnyToAnyData, BasicItem) - Constructor for class net.sf.basedb.core.AnyToAny
Special constructor when the from item is known.
ANYTOANY - Enum constant in enum class net.sf.basedb.core.Item
The item is an AnyToAny link.
AnyToAny.FastLinkLoader<S extends BasicItem,T extends BasicItem> - Class in net.sf.basedb.core
Helper class for faster loading of any-to-any links between items.
AnyToAnyData - Class in net.sf.basedb.core.data
Represents a link from one item to any other item.
AnyToAnyData() - Constructor for class net.sf.basedb.core.data.AnyToAnyData
 
AnyToAnyDataLoader - Class in net.sf.basedb.clients.web.plugins
Data loader implementation that load any-to-any links.
AnyToAnyDataLoader(String, Item, Metadata.PropertyPath<BasicItem, ?>) - Constructor for class net.sf.basedb.clients.web.plugins.AnyToAnyDataLoader
Load links with the specified name and target type.
AnyToAnyImporter - Class in net.sf.basedb.plugins.batchimport
Plug-in for importing any-to-any links from simple text files.
AnyToAnyImporter() - Constructor for class net.sf.basedb.plugins.batchimport.AnyToAnyImporter
 
AnyToAnyLinkStatistics - Class in net.sf.basedb.util
Class for holding statisics about any-to-any links between items.
AnyToAnyLinkStatistics() - Constructor for class net.sf.basedb.util.AnyToAnyLinkStatistics
 
AnyToAnyLinkStatistics.Options - Class in net.sf.basedb.util
Options to specify how the statistics should be generated.
AnyToAnyLoader - Class in net.sf.basedb.util.overview.loader
Node loader implementation for any-to-any links.
AnyToAnyLoader() - Constructor for class net.sf.basedb.util.overview.loader.AnyToAnyLoader
 
AnyToAnyLogger - Class in net.sf.basedb.core.log.db
Logger for any-to-any links that logs changes as updates to the 'from' item.
AnyToAnyLogger(DbLogManagerFactory) - Constructor for class net.sf.basedb.core.log.db.AnyToAnyLogger
 
AnyToAnyNameGenerator - Class in net.sf.basedb.util.overview.node
Name generator for any-to-any links.
AnyToAnyNameGenerator() - Constructor for class net.sf.basedb.util.overview.node.AnyToAnyNameGenerator
 
AnyToAnyRestriction - Class in net.sf.basedb.core.query
Expression that can be used to filter on the existence or non-existence of a named any-to-any link.
AnyToAnyRestriction(String, String, Item, boolean, EntityQuery) - Constructor for class net.sf.basedb.core.query.AnyToAnyRestriction
 
AnyToAnyValidator - Class in net.sf.basedb.util.overview.validator
Validator implementation for any-to-any links.
AnyToAnyValidator() - Constructor for class net.sf.basedb.util.overview.validator.AnyToAnyValidator
 
append(String) - Method in class net.sf.basedb.core.Job.ProgressReporterImpl
 
append(String) - Method in class net.sf.basedb.core.Migration.ProgressInputStream
 
append(String) - Method in interface net.sf.basedb.core.ProgressReporter
Append a message to the previous one.
append(String) - Method in class net.sf.basedb.core.signal.ProgressReporterSignalHandler
 
append(String) - Method in class net.sf.basedb.core.SimpleProgressReporter
 
append(String) - Method in class net.sf.basedb.util.ChainedProgressReporter
 
append(String) - Method in class net.sf.basedb.util.ConsoleProgressReporter
 
append(String) - Method in class net.sf.basedb.util.GeoLocation.ResponseFilter
 
append(String) - Method in class net.sf.basedb.util.TransferRateProgressReporter
Forward the call to the parent if one exists.
append(StringBuilder, String) - Method in class net.sf.basedb.util.GeoLocation
 
appendFakeSources(Set<Integer>) - Method in class net.sf.basedb.util.listable.SourceItemTransformerChain
 
appendGroups(StringBuilder, DbControl, List<Expression>, int) - Method in class net.sf.basedb.core.AbstractQuery
 
appendHavings(StringBuilder, DbControl, List<Restriction>, int) - Method in class net.sf.basedb.core.AbstractQuery
 
appendJoins(StringBuilder, DbControl, List<Join>, boolean, int) - Method in class net.sf.basedb.core.AbstractQuery
 
appendLine(StringBuffer, String[], GtfInputStream.Attribute[]) - Method in class net.sf.basedb.util.gtf.GtfInputStream
Append columns to the buffer and separate each with a tab.
appendList(StringBuilder, Collection<String>) - Method in class net.sf.basedb.core.dbengine.MySQLEngine
 
appendList(StringBuilder, Collection<String>) - Method in class net.sf.basedb.core.dbengine.PostgresDbEngine
 
appendListOfValues(StringBuilder, String, String) - Method in class net.sf.basedb.util.formatter.PropertyFilterFormatter
 
appendOrders(StringBuilder, DbControl, List<Order>, int) - Method in class net.sf.basedb.core.AbstractQuery
 
appendPermissionOption(StringBuilder, Permission, Permission, String) - Method in class net.sf.basedb.clients.web.taglib.table.ColumnDef
 
appendProgress(Session, String) - Method in class net.sf.basedb.core.Job.ProgressReporterImpl
 
appendRestrictions(StringBuilder, DbControl, List<Restriction>, int) - Method in class net.sf.basedb.core.AbstractQuery
 
appendScripts(StringBuilder, JspContext) - Method in class net.sf.basedb.clients.web.taglib.Head
 
appendSelects(StringBuilder, DbControl, List<Select>, int) - Method in class net.sf.basedb.core.AbstractQuery
 
appendStyles(StringBuilder, String, boolean, JspContext) - Method in class net.sf.basedb.clients.web.taglib.Head
 
appId - Variable in class net.sf.basedb.core.data.SchemaVersionData
 
appId - Variable in class net.sf.basedb.core.ServiceSessionControl.SessionFactoryConfiguration
 
Application - Class in net.sf.basedb.core
This class represents the BASE application and is the starting point for all client applications.
Application() - Constructor for class net.sf.basedb.core.Application
 
Application.DbCleaner - Class in net.sf.basedb.core
 
Application.Pinger - Class in net.sf.basedb.core
A Pinger is an object that is used to protect another object from timing out by automatically pinging it.
Application.SessionControlCacheCleaner - Class in net.sf.basedb.core
 
Application.StartupOptions - Class in net.sf.basedb.core
Startup optins when starting the BASE application.
apply(List<Plate>, PlateType) - Method in class net.sf.basedb.core.PlateMapping
Apply this mapping to the given list of source plates and generate new plates of the specified type.
applyGraph(RootGraph, GraphSemantic) - Method in class net.sf.basedb.core.hibernate.QueryWrapper
 
applySubCategoryFilter(ItemContext.AddFilter) - Method in class net.sf.basedb.core.ItemContext
 
applyToContext(ItemContext) - Method in class net.sf.basedb.clients.web.SubContext
Apply the new subcontext to the given item context.
approximateNumberOfRows - Variable in class net.sf.basedb.core.dbengine.TableInfo
 
aquireLock(String, boolean, int) - Method in class net.sf.basedb.util.StaticCache
Aquire a read or write lock on a given cache entry.
AREA - Static variable in class net.sf.basedb.core.Quantity
The id for the Quantity object representing area.
ARITHMETIC_MEAN - Enum constant in enum class net.sf.basedb.core.Formula.AverageMethod
 
arrangeData(int, short, Object[][], Object[]) - Method in class net.sf.basedb.util.export.spotdata.BfsExporter
Arrange the data that was returned by the query into the data writers array.
arrangeData(int, short, Object[][], Object[]) - Method in class net.sf.basedb.util.export.spotdata.MatrixBfsExporter
The column number is used to find the assay index.
arrangeData(int, short, Object[][], Object[]) - Method in class net.sf.basedb.util.export.spotdata.SerialBfsExporter
The column number is used to find the assay index.
ARRANGEMENT - Static variable in class net.sf.basedb.core.DerivedBioAssay
The id for the DerivedBioAssayType item representing sequenced data that has been aligned to a reference database.
array - Variable in class net.sf.basedb.util.ArrayIterator
The array to iterate.
arrayBatch - Variable in class net.sf.basedb.core.data.ArraySlideData
 
ArrayBatch - Class in net.sf.basedb.core
This class represents the making of a new batch of microarray slides of a particular design.
ArrayBatch(ArrayBatchData) - Constructor for class net.sf.basedb.core.ArrayBatch
 
ARRAYBATCH - Enum constant in enum class net.sf.basedb.core.Item
The item is an ArrayBatch.
arrayBatchColumnMapping - Static variable in class net.sf.basedb.plugins.batchimport.ArraySlideImporter
 
ArrayBatchData - Class in net.sf.basedb.core.data
This class represents the making of a new batch of microarray slides of a particular design.
ArrayBatchData() - Constructor for class net.sf.basedb.core.data.ArrayBatchData
 
arrayBatches - Variable in class net.sf.basedb.core.data.ArrayDesignData
 
ArrayBatchImporter - Class in net.sf.basedb.plugins.batchimport
Plug-in for importing array batch items in a batch.
ArrayBatchImporter() - Constructor for class net.sf.basedb.plugins.batchimport.ArrayBatchImporter
 
ArrayBatchLoader - Class in net.sf.basedb.util.overview.loader
Node loader implementation for array batches.
ArrayBatchLoader() - Constructor for class net.sf.basedb.util.overview.loader.ArrayBatchLoader
 
arrayBatchMapper - Variable in class net.sf.basedb.plugins.batchimport.ArraySlideImporter
 
ArrayBatchValidator - Class in net.sf.basedb.util.overview.validator
Validator implementation for array batch.
ArrayBatchValidator() - Constructor for class net.sf.basedb.util.overview.validator.ArrayBatchValidator
 
arrayDesign - Variable in class net.sf.basedb.core.data.ArrayBatchData
 
arrayDesign - Variable in class net.sf.basedb.core.data.ArrayDesignBlockData
 
arrayDesign - Variable in class net.sf.basedb.core.data.ArrayDesignPlateData
 
arrayDesign - Variable in class net.sf.basedb.core.data.RawBioAssayData
 
arrayDesign - Variable in class net.sf.basedb.core.FeatureBatcher
The array design this batcher adds features to.
arrayDesign - Variable in class net.sf.basedb.core.RawDataBatcher
The array design the raw bioassay is connected to, if any.
arrayDesign - Variable in class net.sf.basedb.plugins.PrintMapFlatFileImporter
 
arrayDesign - Variable in class net.sf.basedb.plugins.ReporterMapFlatFileImporter
 
ArrayDesign - Class in net.sf.basedb.core
An array design is a description of the design of a microarray slide.
ArrayDesign(ArrayDesignData) - Constructor for class net.sf.basedb.core.ArrayDesign
 
ARRAYDESIGN - Enum constant in enum class net.sf.basedb.core.Item
The item is an ArrayDesign.
arrayDesignBlock - Variable in class net.sf.basedb.core.data.FeatureData
 
ArrayDesignBlock - Class in net.sf.basedb.core
 
ArrayDesignBlock(ArrayDesignBlockData) - Constructor for class net.sf.basedb.core.ArrayDesignBlock
 
ARRAYDESIGNBLOCK - Enum constant in enum class net.sf.basedb.core.Item
The item is an ArrayDesignBlock.
ArrayDesignBlockData - Class in net.sf.basedb.core.data
This holds information about a block in an arraydesign.
ArrayDesignBlockData() - Constructor for class net.sf.basedb.core.data.ArrayDesignBlockData
 
arrayDesignBlocks - Variable in class net.sf.basedb.core.data.ArrayDesignData
 
arrayDesignColumnMapping - Static variable in class net.sf.basedb.plugins.batchimport.ArrayBatchImporter
 
arrayDesignColumnMapping - Static variable in class net.sf.basedb.plugins.batchimport.RawBioAssayImporter
 
arrayDesignData - Variable in class net.sf.basedb.core.FeatureBatcher
Just a copy of the data object for the array design.
ArrayDesignData - Class in net.sf.basedb.core.data
This class holds information about an arrayDesign
ArrayDesignData() - Constructor for class net.sf.basedb.core.data.ArrayDesignData
 
arrayDesignHasBeenSet - Variable in class net.sf.basedb.core.RawBioAssay
 
arrayDesignId - Variable in class net.sf.basedb.core.MigrateRbaToDba.Rba
 
ArrayDesignImporter - Class in net.sf.basedb.plugins.batchimport
Plug-in for importing array design items in a batch.
ArrayDesignImporter() - Constructor for class net.sf.basedb.plugins.batchimport.ArrayDesignImporter
 
arrayDesignLinkId - Variable in class net.sf.basedb.core.MigrateRbaToDba.Rba
 
ArrayDesignLoader - Class in net.sf.basedb.util.overview.loader
Node loader implementation for array designs.
ArrayDesignLoader() - Constructor for class net.sf.basedb.util.overview.loader.ArrayDesignLoader
 
arrayDesignMapper - Variable in class net.sf.basedb.plugins.batchimport.ArrayBatchImporter
 
arrayDesignMapper - Variable in class net.sf.basedb.plugins.batchimport.RawBioAssayImporter
 
arrayDesignParameter - Variable in class net.sf.basedb.plugins.PrintMapFlatFileImporter
 
arrayDesignParameter - Variable in class net.sf.basedb.plugins.ReporterMapFlatFileImporter
 
ArrayDesignPlate - Class in net.sf.basedb.core
 
ArrayDesignPlate(ArrayDesignPlateData) - Constructor for class net.sf.basedb.core.ArrayDesignPlate
 
ARRAYDESIGNPLATE - Enum constant in enum class net.sf.basedb.core.Item
The item is a ArrayDesignPlate connecter.
ArrayDesignPlateData - Class in net.sf.basedb.core.data
This class connects the ArrayDesign with its plates and adding an index to that connection.
ArrayDesignPlateData() - Constructor for class net.sf.basedb.core.data.ArrayDesignPlateData
 
arrayDesigns - Variable in class net.sf.basedb.core.data.JobData
 
arrayDesigns - Variable in class net.sf.basedb.core.data.PlateData
 
arrayDesignType - Variable in class net.sf.basedb.plugins.PrintMapFlatFileImporter
 
arrayDesignType - Variable in class net.sf.basedb.plugins.ReporterMapFlatFileImporter
 
ArrayDesignValidator - Class in net.sf.basedb.util.overview.validator
Validator implementation for array designs.
ArrayDesignValidator() - Constructor for class net.sf.basedb.util.overview.validator.ArrayDesignValidator
 
ArrayIterator<E> - Class in net.sf.basedb.util
This class implements the Iterator interface for an array of objects.
ArrayIterator(E[]) - Constructor for class net.sf.basedb.util.ArrayIterator
Create a new ArrayIterator object.
arraySlide - Variable in class net.sf.basedb.core.data.PhysicalBioAssayData
 
ArraySlide - Class in net.sf.basedb.core
This class represents a physical microarray slide.
ArraySlide(ArraySlideData) - Constructor for class net.sf.basedb.core.ArraySlide
 
ARRAYSLIDE - Enum constant in enum class net.sf.basedb.core.Item
The item is an ArraySlide.
arraySlideColumnMapping - Static variable in class net.sf.basedb.plugins.batchimport.PhysicalBioAssayImporter
 
ArraySlideData - Class in net.sf.basedb.core.data
This class represents a phycsical microarray slide.
ArraySlideData() - Constructor for class net.sf.basedb.core.data.ArraySlideData
 
ArraySlideImporter - Class in net.sf.basedb.plugins.batchimport
Plug-in for importing array slide items in a batch.
ArraySlideImporter() - Constructor for class net.sf.basedb.plugins.batchimport.ArraySlideImporter
 
ArraySlideLoader - Class in net.sf.basedb.util.overview.loader
Node loader implementation for array slides.
ArraySlideLoader() - Constructor for class net.sf.basedb.util.overview.loader.ArraySlideLoader
 
arraySlideMapper - Variable in class net.sf.basedb.plugins.batchimport.PhysicalBioAssayImporter
 
arraySlideQuery - Variable in class net.sf.basedb.plugins.batchimport.AbstractItemImporter
 
arraySlides - Variable in class net.sf.basedb.core.data.ArrayBatchData
 
ArraySlideValidator - Class in net.sf.basedb.util.overview.validator
Validator implementation for array slides.
ArraySlideValidator() - Constructor for class net.sf.basedb.util.overview.validator.ArraySlideValidator
 
asBoolean(Boolean) - Static method in class net.sf.basedb.util.excel.ExcelValue
Create a numeric cell value with boolean format.
asc(Expression) - Static method in class net.sf.basedb.core.query.Orders
Sort the result of a query in ascending order by the expression.
ASC - Enum constant in enum class net.sf.basedb.core.ItemContext.SortDirection
Items are sorted in ascending order.
AscOrder - Class in net.sf.basedb.core.query
Sort the result of a query in ascending order by the expression.
AscOrder(Expression) - Constructor for class net.sf.basedb.core.query.AscOrder
 
asDate - Variable in class net.sf.basedb.util.parser.ConstantMapper
 
asDate(Date, String) - Static method in class net.sf.basedb.util.excel.ExcelValue
Create a date cell value.
asDouble - Variable in class net.sf.basedb.util.parser.ConstantMapper
 
asEnumeration(Collection<String>) - Static method in class net.sf.basedb.util.charset.CharsetUtil
Convert charset names to an enumeration with display-friendly key/title pairs.
asInt(Number) - Static method in class net.sf.basedb.util.excel.ExcelValue
Create a numeric cell value without any decimals.
asJsonObject() - Method in class net.sf.basedb.clients.web.taglib.table.ColumnDef
Get a JSON representation of this column definition.
asLong - Variable in class net.sf.basedb.util.parser.ConstantMapper
 
asNumber(Number, int) - Static method in class net.sf.basedb.util.excel.ExcelValue
Create a numeric cell value and display a given number of decimals.
asNumber(Number, String) - Static method in class net.sf.basedb.util.excel.ExcelValue
Create a numeric cell value with a custom numeric format.
assayAnnotationQuery - Variable in class net.sf.basedb.util.export.spotdata.AbstractFieldConverter
 
assayField(String, String, Type) - Method in class net.sf.basedb.plugins.BfsExporterPlugin
 
AssayField - Interface in net.sf.basedb.util.export.spotdata
Represents a bioassay field that is going to be exported.
assayFields - Variable in class net.sf.basedb.util.export.spotdata.AbstractBioAssaySetExporter
 
assayFields - Variable in class net.sf.basedb.util.importer.spotdata.BaseFileInfo.SpotSectionInfo
 
assayGroups - Variable in class net.sf.basedb.clients.web.ExperimentExplorer.AnnotationSummary
 
assayIndexMap - Variable in class net.sf.basedb.util.export.spotdata.AbstractBioAssaySetExporter
 
assayProperty(String, String, Type, Formatter<?>) - Static method in class net.sf.basedb.util.export.spotdata.ExportableFieldFactory
Create a property assay field.
AssayPropertyField - Class in net.sf.basedb.util.export.spotdata
Assay field implementation that exports a named property from a bioassay.
AssayPropertyField() - Constructor for class net.sf.basedb.util.export.spotdata.AssayPropertyField
Create a new annotation field.
assays - Variable in class net.sf.basedb.util.importer.spotdata.BaseFileInfo.SpotSectionInfo
 
assays - Variable in class net.sf.basedb.util.importer.spotdata.MatrixSpotIntensityEventHandler
 
assays - Variable in class net.sf.basedb.util.importer.spotdata.SerialSpotIntensityEventHandler
 
assaysHaveParentAssaysMapping - Variable in class net.sf.basedb.util.importer.spotdata.BaseFileInfo
 
assayWriter - Variable in class net.sf.basedb.util.export.spotdata.BfsExporter
 
associateFiles(DbControl, Transformation, Directory) - Method in class net.sf.basedb.plugins.Base1PluginExecuter
 
associationsSection - Static variable in class net.sf.basedb.plugins.IlluminaRawDataImporter
Section definition for grouping associations to other items: scan, software, protocol and experiment
asString(String) - Static method in class net.sf.basedb.util.excel.ExcelValue
Create a string cell value.
ASTConstantConverter - Class in net.sf.basedb.util.jep.convert
Converts a constant node to an expression.
ASTConstantConverter() - Constructor for class net.sf.basedb.util.jep.convert.ASTConstantConverter
 
ASTFunNodeConverter - Class in net.sf.basedb.util.jep.convert
Converts a function node to an expression or restriction.
ASTFunNodeConverter() - Constructor for class net.sf.basedb.util.jep.convert.ASTFunNodeConverter
 
asTimestamp(Date, String) - Static method in class net.sf.basedb.util.excel.ExcelValue
Create a timestamp cell value.
ASTVarNodeConverter - Class in net.sf.basedb.util.jep.convert
Converts a variable node to a parameter expression or null.
ASTVarNodeConverter() - Constructor for class net.sf.basedb.util.jep.convert.ASTVarNodeConverter
 
asXml() - Method in class net.sf.basedb.core.Presets
Convert the presets to an XML string.
at - Variable in class net.sf.basedb.clients.web.extensions.list.RelatedItemAnnotationColumn
 
at - Variable in class net.sf.basedb.core.AnnotationType.RemoveInheritedAnnotationsAction
 
at - Variable in class net.sf.basedb.core.snapshot.AnnotationLoaderUtil
 
at - Variable in class net.sf.basedb.util.export.spotdata.AnnotationAssayField
 
AT_OR_DOT - Static variable in class net.sf.basedb.clients.web.util.HTML
 
atBoundary - Variable in class net.sf.basedb.clients.web.fileupload.FileUpload.UploadStatus
TRUE if the FileUpload.checkBoundary(byte[], int, byte[], int) method finds that the line matches the boundary, FALSE otherwise.
atCommit - Variable in class net.sf.basedb.core.DropDynamicTableAction
 
atComp - Variable in class net.sf.basedb.core.snapshot.AnnotationSnapshot.ProjectComparator
 
atFilter - Variable in class net.sf.basedb.clients.web.extensions.list.RelatedItemAnnotationColumn
 
atId - Variable in class net.sf.basedb.core.snapshot.AnnotationLoaderUtil
 
atLastBoundary - Variable in class net.sf.basedb.clients.web.fileupload.FileUpload.UploadStatus
TRUE if the FileUpload.checkBoundary(byte[], int, byte[], int) method finds that the line matches the boundary + two extra dashes (--), FALSE otherwise.
atRollback - Variable in class net.sf.basedb.core.DropDynamicTableAction
 
attribute - Variable in class net.sf.basedb.util.overview.filter.HasAttributeFilter
 
Attribute(String, String) - Constructor for class net.sf.basedb.util.gtf.GtfInputStream.Attribute
 
ATTRIBUTE_KEY - Static variable in class net.sf.basedb.clients.web.extensions.JspContext
The key that is used when storing a JspContext object in a request/page/session/etc. attribute.
ATTRIBUTE_PATTERN - Variable in class net.sf.basedb.util.gtf.GtfInputStream
 
AttributeKey(String, String) - Constructor for class net.sf.basedb.util.extensions.Registry.AttributeKey
 
attributes - Variable in class net.sf.basedb.core.authentication.LoginRequest
 
attributes - Variable in class net.sf.basedb.util.extensions.AboutBean
 
attributes - Variable in class net.sf.basedb.util.extensions.ClientContext
 
attributes - Variable in class net.sf.basedb.util.extensions.Registry
 
attributes - Variable in class net.sf.basedb.util.extensions.Registry.RegisteredAbout
 
attributes - Variable in class net.sf.basedb.util.gtf.GtfInputStream
 
attributes - Variable in class net.sf.basedb.util.overview.Node
 
authenticate() - Method in interface net.sf.basedb.core.authentication.AuthenticationManager
Try to authenticate a user given the login information passed to the factory in the AuthenticationContext.
authenticatedUser - Variable in class net.sf.basedb.core.SessionControl.UnverifiedDeviceInfo
 
AuthenticatedUser - Class in net.sf.basedb.core.authentication
Objects of this class are returned by the AuthenticationManager.authenticate() method and contains information about the authenticated user.
AuthenticatedUser(AuthenticationMethod, String, String) - Constructor for class net.sf.basedb.core.authentication.AuthenticatedUser
Creates a new AuthenticatedUser object without any link to an existing user in BASE.
AuthenticatedUser(AuthenticationMethod, UserData) - Constructor for class net.sf.basedb.core.authentication.AuthenticatedUser
Creates a new AuthenticatedUser object with a link to an existing user in BASE.
AuthenticationContext - Class in net.sf.basedb.core
Gives authentication implementations limited access to the database.
AuthenticationContext(SessionControl, Session, LoginRequest) - Constructor for class net.sf.basedb.core.AuthenticationContext
 
AuthenticationException - Exception in net.sf.basedb.core.authentication
This exception can be thrown when an error occurs during the authentication.
AuthenticationException(String) - Constructor for exception net.sf.basedb.core.authentication.AuthenticationException
Create a new AuthenticationException object
AuthenticationException(String, Throwable) - Constructor for exception net.sf.basedb.core.authentication.AuthenticationException
Create a new AuthenticationException object
AuthenticationException(Throwable) - Constructor for exception net.sf.basedb.core.authentication.AuthenticationException
Create a new AuthenticationException object
AuthenticationManager - Interface in net.sf.basedb.core.authentication
Action interface for external authentication.
authenticationMethod - Variable in class net.sf.basedb.core.data.SessionData
 
authenticationMethod - Variable in class net.sf.basedb.core.SessionControl.LoginInfo
The authentication method used to allow the user to login.
AuthenticationMethod - Class in net.sf.basedb.core.authentication
Holds information about the method that was used to verify a user when logging in.
AuthenticationMethod(String) - Constructor for class net.sf.basedb.core.authentication.AuthenticationMethod
 
authors - Variable in class net.sf.basedb.core.data.ExperimentData
 
AUTO - Enum constant in enum class net.sf.basedb.core.ItemContext.AddFilter
Add a filter only if no filter already exists.
AUTO - Enum constant in enum class net.sf.basedb.core.ReporterCloneBatcher.CloneSource
Select VIRTUAL if the experiment has position data in the virtual database, otherwise the RAW options used.
AutoChildNodeLoader<I> - Class in net.sf.basedb.util.overview.loader
Node loader implementation that automatically loads child nodes.
AutoChildNodeLoader(NodeLoader<I>) - Constructor for class net.sf.basedb.util.overview.loader.AutoChildNodeLoader
 
autoCloseParsers - Variable in class net.sf.basedb.util.importer.spotdata.BfsImporter
 
autoCloseWriters - Variable in class net.sf.basedb.util.export.spotdata.BaseFileExporter
 
autoCloseWriters - Variable in class net.sf.basedb.util.export.spotdata.BfsExporter
 
autoCompress - Variable in class net.sf.basedb.core.data.DirectoryData
 
autoCompress - Variable in class net.sf.basedb.core.data.MimeTypeData
 
autoCompressionEnabled() - Static method in class net.sf.basedb.core.Application
Check if auto-compression has been enabled or not.
autoDetect(ExtensionsInvoker<ConnectionManagerFactory>, URI) - Static method in class net.sf.basedb.util.uri.ConnectionManagerUtil
Use auto-detection and return the first factory that can handle the given uri.
AutoDetectFileFormat - Class in net.sf.basedb.util
This class has methods for autodetecting file formats.
AutoDetectFileFormat() - Constructor for class net.sf.basedb.util.AutoDetectFileFormat
 
AutoDetectFileFormat.IsImportableFilter - Class in net.sf.basedb.util
Filter implementation that filters a collection of ContextUtil.ContextResult:s by checking each plug-ins ability to import a given file.
AutoDetectingImporter - Interface in net.sf.basedb.core.plugin
This interface should be implemented by an import plugin that supports auto-detection of the file format.
autoFormatter - Variable in class net.sf.basedb.util.excel.XlsxTableWriter
 
AutoFormatter - Class in net.sf.basedb.util.excel
Excel formatter implementation that automatically selects a format depending on the type/class of the value.
AutoFormatter() - Constructor for class net.sf.basedb.util.excel.AutoFormatter
 
autoInherit(DbControl, Collection<AnnotationType>, SnapshotManager, boolean) - Method in class net.sf.basedb.core.AnnotationSet
Automatically inherit all annotations of one or more specified annotation types from parent items that are currntly missing from this annotation set
AutoItemExportFormatter - Class in net.sf.basedb.clients.web.formatter
Formatter implementation designed for exporting that generates output with best supported method depending on their type.
AutoItemExportFormatter() - Constructor for class net.sf.basedb.clients.web.formatter.AutoItemExportFormatter
 
autoJoin() - Method in class net.sf.basedb.core.AbstractQuery
 
AutoJoiner<Q extends Query,E extends QueryElement> - Interface in net.sf.basedb.core.query
An AutoJoiner is an object that automatically joins other tables in query depending on other query elements.
autoJoiners - Variable in class net.sf.basedb.core.AbstractQuery
 
autoJoinType - Variable in class net.sf.basedb.core.query.ReporterListExpression
 
AutoLinkFormatter - Class in net.sf.basedb.clients.web.formatter
Formatter implementation that generates a HTML output trying to link items with best supported method depending on their type.
AutoLinkFormatter() - Constructor for class net.sf.basedb.clients.web.formatter.AutoLinkFormatter
 
AutoLinkFormatter(boolean, boolean) - Constructor for class net.sf.basedb.clients.web.formatter.AutoLinkFormatter
 
AutoLinkFormatter(FileViewerUtil) - Constructor for class net.sf.basedb.clients.web.formatter.AutoLinkFormatter
 
autoLoadChildren - Variable in class net.sf.basedb.util.overview.loader.BasicItemNodeLoaderFactory
 
autoLogout() - Static method in class net.sf.basedb.core.Session
Cleanup method that sets a logout-time on all sessions that doesn't have a logout time.
autoLogoutSessions - Variable in class net.sf.basedb.core.Application.StartupOptions
 
autoLogoutSessions(boolean) - Method in class net.sf.basedb.core.Application.StartupOptions
Set to TRUE to automatically set a logout time for all sessions that doesn't have one.
autoPermission - Variable in class net.sf.basedb.core.data.ProjectData
 
autoReload - Variable in class net.sf.basedb.util.units.UnitCache
 
autoShare - Variable in class net.sf.basedb.core.data.DirectoryData
 
autoShow - Variable in class net.sf.basedb.clients.web.taglib.table.Cell
 
autoUnloadPlugins - Static variable in class net.sf.basedb.core.Application
Allow automatic unload of plug-in JAR files or not.
autoUnloadPlugins() - Static method in class net.sf.basedb.core.Application
If external plug-in JAR files should automatically be unloaded if the are modified.
available() - Method in class net.sf.basedb.clients.web.fileupload.FileUpload.UploadStream
 
available() - Method in class net.sf.basedb.util.excel.XlsxToCsvUtil.WorkbookStream
 
available() - Method in class net.sf.basedb.util.gtf.GtfInputStream
 
available() - Method in class net.sf.basedb.util.InputStreamCombiner
 
available() - Method in class net.sf.basedb.util.InputStreamSplitter
 
available() - Method in class net.sf.basedb.util.InputStreamTracker
 
averageMethod - Variable in class net.sf.basedb.clients.web.taglib.table.TableColumn
 
averageMethod - Variable in class net.sf.basedb.core.data.ExtraValueTypeData
 
averageMethod - Variable in class net.sf.basedb.core.data.FormulaData
 
averageMethod - Variable in class net.sf.basedb.core.data.ReporterClonePropertyData
 
averageMethod - Variable in class net.sf.basedb.core.ExtendedProperty
 
averageMethod - Variable in enum class net.sf.basedb.core.IntensityTransform
 
averageMethod - Variable in class net.sf.basedb.util.export.spotdata.JepDynamicField
 
averageMethod - Variable in class net.sf.basedb.util.export.spotdata.SimpleDynamicField
 
AverageMethod(int, String) - Constructor for enum class net.sf.basedb.core.Formula.AverageMethod
 
averageOnReporter - Variable in class net.sf.basedb.util.export.spotdata.AbstractBioAssaySetExporter
 
avg - Variable in class net.sf.basedb.core.query.GeometricMeanExpression
 
avoid(Item, Set<Integer>) - Method in class net.sf.basedb.util.listable.TransformContext
Avoid collected items by removing them from the source set.
avoiding - Variable in class net.sf.basedb.util.listable.TransformContext
 

B

BACKSLASH - Static variable in class net.sf.basedb.clients.web.util.HTML
 
BAM - Static variable in class net.sf.basedb.core.DataFileType
The external ID for the file type representing a BAM (Binary Sequence Alignment/Map) file.
barcode - Variable in class net.sf.basedb.core.data.ArraySlideData
 
barcode - Variable in class net.sf.basedb.core.data.BioPlateData
 
barcode - Variable in class net.sf.basedb.core.data.PlateData
 
BARCODE - Static variable in class net.sf.basedb.core.Tag
The ID for the BARCODE tag type.
BARCODE - Static variable in class net.sf.basedb.plugins.batchimport.PropertyIdMethod
Use the barcode for finding items.
barcodeColumnMapping - Static variable in class net.sf.basedb.plugins.batchimport.ArraySlideImporter
 
barcodeColumnMapping - Static variable in class net.sf.basedb.plugins.batchimport.BioPlateImporter
 
barcodeColumnMapping - Static variable in class net.sf.basedb.plugins.PlateFlatFileImporter
 
barcodeExists(DbControl, String) - Static method in class net.sf.basedb.core.ArraySlide
Checks if a slide with the given barcode already exists in the database.
barcodeMapper - Variable in class net.sf.basedb.plugins.batchimport.ArraySlideImporter
 
barcodeMapper - Variable in class net.sf.basedb.plugins.batchimport.BioPlateImporter
 
barcodeMapper - Variable in class net.sf.basedb.plugins.PlateFlatFileImporter
 
bas - Variable in class net.sf.basedb.plugins.BaseFileExporterPlugin
 
bas - Variable in class net.sf.basedb.plugins.BfsExporterPlugin
 
bas - Variable in class net.sf.basedb.util.jep.ExtraValueFunction
 
base - Variable in class net.sf.basedb.core.query.LogExpression
 
base - Variable in class net.sf.basedb.core.query.PowerExpression
 
Base - Class in net.sf.basedb.clients.web
This class is used to collect some useful methods for the web client into a single place.
Base() - Constructor for class net.sf.basedb.clients.web.Base
 
BASE_APP_ID - Static variable in class net.sf.basedb.core.data.SchemaVersionData
 
BASE_VERSION - Static variable in class net.sf.basedb.clients.web.taglib.Page
The version of BASE.
Base1FieldConverter - Class in net.sf.basedb.util.export.spotdata
Exportable field converter that support BASE 1 naming conventions.
Base1FieldConverter(DbControl, BioAssaySet) - Constructor for class net.sf.basedb.util.export.spotdata.Base1FieldConverter
Create a new converter for the given bioassay set.
Base1JobParameterType(char) - Constructor for enum class net.sf.basedb.plugins.Base1PluginExecuter.Base1JobParameterType
 
Base1PluginExecuter - Class in net.sf.basedb.plugins
This plug-in executes a plug-in from the Base1 system.
Base1PluginExecuter() - Constructor for class net.sf.basedb.plugins.Base1PluginExecuter
 
Base1PluginExecuter.Base1JobParameterType - Enum Class in net.sf.basedb.plugins
 
Base1PluginExecuter.JobParameter - Class in net.sf.basedb.plugins
 
base64_code - Static variable in class net.sf.basedb.util.bcrypt.BCrypt
 
baseBeginDataPart() - Method in class net.sf.basedb.util.basefile.BaseFileWriter
End the header part of the current section (by writing a single % on a line by itself) and start the data part.
baseBeginSection(String) - Method in class net.sf.basedb.util.basefile.BaseFileWriter
Start a new section in the BASEfile.
baseCompleted - Variable in class net.sf.basedb.core.SimpleAbsoluteProgressReporter
 
baseEndSection() - Method in class net.sf.basedb.util.basefile.BaseFileWriter
Ends the current section by writing an empty line.
baseEscape(String) - Method in class net.sf.basedb.util.basefile.BaseFileWriter
Escape new line and carrige return characters in the input to the literal string '\n' and '\r' in the output.
BaseException - Exception in net.sf.basedb.core
This is the base class for exceptions in BASE.
BaseException() - Constructor for exception net.sf.basedb.core.BaseException
Create a new BaseException object.
BaseException(String) - Constructor for exception net.sf.basedb.core.BaseException
Create a new BaseException object with the specified message
BaseException(String, Throwable) - Constructor for exception net.sf.basedb.core.BaseException
Create a new BaseException object with the specified message
BaseException(Throwable) - Constructor for exception net.sf.basedb.core.BaseException
Create a new BaseException object acting as a wrapper for another exception that caused the error.
BaseException(SQLException) - Constructor for exception net.sf.basedb.core.BaseException
Create a new BaseException object where the cause is an SQLException.
BASEFILE_MATRIX - Static variable in class net.sf.basedb.core.DataFileType
The external ID for the file type representing a matrix BASEFile.
BASEFILE_SERIAL - Static variable in class net.sf.basedb.core.DataFileType
The external ID for the file type representing a serial BASEFile.
BaseFileExporter - Class in net.sf.basedb.util.export.spotdata
A superclass for exporters that exports spot data to BASEfile format.
BaseFileExporter() - Constructor for class net.sf.basedb.util.export.spotdata.BaseFileExporter
 
BaseFileExporterPlugin - Class in net.sf.basedb.plugins
Exports bioassay set data as serial or matrix BASEfile:s.
BaseFileExporterPlugin() - Constructor for class net.sf.basedb.plugins.BaseFileExporterPlugin
 
BaseFileExporterPlugin.ExtendedDynamicField - Class in net.sf.basedb.plugins
 
BaseFileExporterSupport - Class in net.sf.basedb.plugins.executor
Exporter implementation for the external program executor that exports data to BASEfile format.
BaseFileExporterSupport() - Constructor for class net.sf.basedb.plugins.executor.BaseFileExporterSupport
 
BaseFileImporter - Class in net.sf.basedb.util.importer.spotdata
Imports spot data from a serial or matrix BASEfile.
BaseFileImporter() - Constructor for class net.sf.basedb.util.importer.spotdata.BaseFileImporter
Create a new importer object.
BaseFileImporter.RawDataProxy - Class in net.sf.basedb.util.importer.spotdata
 
BaseFileImporter.ReporterProxy - Class in net.sf.basedb.util.importer.spotdata
 
BaseFileImporterSupport - Class in net.sf.basedb.plugins.executor
Importer implementation for the external program executor that imports data from BASEfile format.
BaseFileImporterSupport() - Constructor for class net.sf.basedb.plugins.executor.BaseFileImporterSupport
 
BaseFileInfo - Class in net.sf.basedb.util.importer.spotdata
Collects information about a BASEfile as it gets parsed by a BaseFileImporter.
BaseFileInfo(FileWrapper) - Constructor for class net.sf.basedb.util.importer.spotdata.BaseFileInfo
The source file which should be a BASEfile.
BaseFileInfo.ChildBioAssay - Class in net.sf.basedb.util.importer.spotdata
Keeps information about a new child bioassay from the 'assays' section or 'spot' sections.
BaseFileInfo.SpotSectionInfo - Class in net.sf.basedb.util.importer.spotdata
Keeps information about headers and more in a 'spot' section.
BaseFileParser - Class in net.sf.basedb.util.basefile
Parser for serial and matrix BASEfile:s.
BaseFileParser() - Constructor for class net.sf.basedb.util.basefile.BaseFileParser
Creates a new parser object.
BaseFileSectionParser - Interface in net.sf.basedb.util.basefile
A section parser is responsible for parsing and collecting data that is found in a section in a serial or matrix BASEfile.
BaseFileWrapper - Class in net.sf.basedb.util.importer
File wrapper implementation for files that are located on the BASE file system.
BaseFileWrapper(File) - Constructor for class net.sf.basedb.util.importer.BaseFileWrapper
 
BaseFileWriter - Class in net.sf.basedb.util.basefile
Wraps a writer stream and provides methods for easier creation of BASEfiles.
BaseFileWriter(Writer) - Constructor for class net.sf.basedb.util.basefile.BaseFileWriter
Create a new BASEfile writer that is writing it's output to the given writer.
BaseInputStreamLocator - Class in net.sf.basedb.util.bfs
Input stream locator implementation that works with files within a given directory in the BASE file system.
BaseInputStreamLocator(DbControl, Directory) - Constructor for class net.sf.basedb.util.bfs.BaseInputStreamLocator
Create a new input stream locator.
basePrintData(Object...) - Method in class net.sf.basedb.util.basefile.BaseFileWriter
Print a data line to the BASEfile.
basePrintHeader(String, Object) - Method in class net.sf.basedb.util.basefile.BaseFileWriter
Prints a header in the BASEfile.
baseStyle - Variable in class net.sf.basedb.util.excel.CellStyleCreator
 
baseWriteBom() - Method in class net.sf.basedb.util.basefile.BaseFileWriter
Write the beginning-of-file marker (BASEfile) to the output.
basic - Static variable in class net.sf.basedb.core.Item.DefinedPermissions
 
BASIC_FILTER - Static variable in class net.sf.basedb.core.QueryRuntimeFilterFactory
 
BasicBatcher<D extends BatchableData> - Class in net.sf.basedb.core
This is an abstract class for batching functionallity.
BasicBatcher(Session, Class<D>, String) - Constructor for class net.sf.basedb.core.BasicBatcher
Constructor that initiate everything.
BasicChildItem - Class in net.sf.basedb.core
An abstract base class for all items which are child items to a BasicItem parent item.
BasicChildItem(BasicData) - Constructor for class net.sf.basedb.core.BasicChildItem
 
BasicData - Class in net.sf.basedb.core.data
This is the root superclass of all data classes.
BasicData() - Constructor for class net.sf.basedb.core.data.BasicData
 
BasicData2ItemPropertyPath(Item, Type) - Constructor for class net.sf.basedb.core.Metadata.BasicData2ItemPropertyPath
 
BasicFilter() - Constructor for class net.sf.basedb.core.QueryRuntimeFilterFactory.BasicFilter
 
BasicItem - Class in net.sf.basedb.core
This is the root superclass of all item classes.
BasicItem(BasicData) - Constructor for class net.sf.basedb.core.BasicItem
Create a new instance.
BasicItem2DataPropertyPath(Class<C>, Type) - Constructor for class net.sf.basedb.core.Metadata.BasicItem2DataPropertyPath
 
BasicItemFilter - Class in net.sf.basedb.util.overview.filter
A filter implementation that matches against the item that is attached to nodes.
BasicItemFilter(BasicItem) - Constructor for class net.sf.basedb.util.overview.filter.BasicItemFilter
Create a filter that finds nodes that has the given item attached to it.
BasicItemNodeLoader<I extends BasicItem> - Class in net.sf.basedb.util.overview.loader
Abstract class that is useful for all node loaders that works with BasicItem:s.
BasicItemNodeLoader(Object, boolean, NodeNameGenerator<I>) - Constructor for class net.sf.basedb.util.overview.loader.BasicItemNodeLoader
Create a new node loader.
BasicItemNodeLoaderFactory - Class in net.sf.basedb.util.overview.loader
Node loader factory implementation for BasicItem node loaders.
BasicItemNodeLoaderFactory() - Constructor for class net.sf.basedb.util.overview.loader.BasicItemNodeLoaderFactory
Creates a new factory.
BasicItemNodeValidatorFactory - Class in net.sf.basedb.util.overview.validator
Node validator factory implementation for BasicItem node validators.
BasicItemNodeValidatorFactory() - Constructor for class net.sf.basedb.util.overview.validator.BasicItemNodeValidatorFactory
Creates a new factory.
BasicItemToIdTransformer - Class in net.sf.basedb.util.collections
Collection transformer implementation that extracts the ID from BasicItem:s.
BasicItemToIdTransformer() - Constructor for class net.sf.basedb.util.collections.BasicItemToIdTransformer
 
BasicNodeValidator<I> - Class in net.sf.basedb.util.overview.validator
A simple node validation implementation that takes care of missing and denied access to items.
BasicNodeValidator(Validator, Validator) - Constructor for class net.sf.basedb.util.overview.validator.BasicNodeValidator
Creates a new validator.
BatchableData - Interface in net.sf.basedb.core.data
This is a tagging interface only.
BatchAndMapHolder(RawDataBatcher, RawDataType, FlatFileParser) - Constructor for class net.sf.basedb.plugins.IlluminaRawDataImporter.BatchAndMapHolder
 
batchCount - Variable in class net.sf.basedb.core.LogControl
 
batchDate - Variable in class net.sf.basedb.core.AnnotationBatcher
 
batchedExternalIds - Variable in class net.sf.basedb.core.ReporterBatcher
A set containing all batched but not yet flushed external reporter id:s.
BatchedPropertyInfo - Class in net.sf.basedb.core
Holds information about a batchable property.
BatchedPropertyInfo(String, int) - Constructor for class net.sf.basedb.core.BatchedPropertyInfo
Create a new extended property.
batcher - Variable in class net.sf.basedb.plugins.AnnotationFlatFileImporter
 
batcher - Variable in class net.sf.basedb.plugins.IlluminaRawDataImporter.BatchAndMapHolder
 
batcher - Variable in class net.sf.basedb.plugins.PrintMapFlatFileImporter
 
batcher - Variable in class net.sf.basedb.plugins.RawDataFlatFileImporter
 
batcher - Variable in class net.sf.basedb.plugins.ReporterFlatFileImporter
 
batcher - Variable in class net.sf.basedb.plugins.ReporterMapFlatFileImporter
 
Batcher - Interface in net.sf.basedb.core
The basic interface which all batchers must implement.
batchers - Variable in class net.sf.basedb.core.DbControl
A list of batchers that will be closed when DbControl is closed and will be flushed when commit is called.
batchIndex - Variable in class net.sf.basedb.core.data.ArraySlideData
 
batchQuery - Variable in class net.sf.basedb.plugins.batchimport.AbstractItemImporter
 
batchSize - Variable in class net.sf.basedb.core.AbstractBatcher
SQL command batch size.
batchSize - Variable in class net.sf.basedb.core.LogControl
 
BatchUtil - Class in net.sf.basedb.core
Utility class for batching information.
BatchUtil() - Constructor for class net.sf.basedb.core.BatchUtil
 
BCrypt - Class in net.sf.basedb.util.bcrypt
BCrypt implements OpenBSD-style Blowfish password hashing using the scheme described in "A Future-Adaptable Password Scheme" by Niels Provos and David Mazieres.
BCrypt() - Constructor for class net.sf.basedb.util.bcrypt.BCrypt
 
BCRYPT_SALT_LEN - Static variable in class net.sf.basedb.util.bcrypt.BCrypt
 
bean - Variable in class net.sf.basedb.util.extensions.debug.BeanActionFactory
 
BeanActionFactory - Class in net.sf.basedb.util.extensions.debug
Generic action factory class that can generate instances of actions if there exists a bean-like implementation of the action class.
BeanActionFactory() - Constructor for class net.sf.basedb.util.extensions.debug.BeanActionFactory
Creates a new proxy factory.
beanClassName - Variable in class net.sf.basedb.util.extensions.debug.BeanActionFactory
 
before - Variable in class net.sf.basedb.core.DbControl.SaveIf
 
BEFORE_DISABLE - Static variable in class net.sf.basedb.clients.web.extensions.ExtensionsControl
BEFORE_UNREGISTRATION - Static variable in class net.sf.basedb.util.extensions.events.EventType
This event is sent before an extension point or extension is unregistered.
BEFORE_UPDATE - Static variable in class net.sf.basedb.util.extensions.events.EventType
This event is sent during an update of an existing extension point or extension.
beforeTransactionCompletion(Transaction) - Method in class net.sf.basedb.core.log.LoggingInterceptor
Flush remaining changes in the log control.
begin(DbControl) - Method in class net.sf.basedb.clients.web.plugins.SimpleExport
 
begin(DbControl) - Method in class net.sf.basedb.core.plugin.AbstractExporterPlugin
Called just before the export starts.
begin(DbControl) - Method in class net.sf.basedb.plugins.BaseFileExporterPlugin
 
begin(DbControl) - Method in class net.sf.basedb.plugins.BfsExporterPlugin
 
begin(DbControl) - Method in class net.sf.basedb.plugins.GalExporter
 
begin(DbControl) - Method in class net.sf.basedb.plugins.HelpExporter
 
begin(DbControl) - Method in class net.sf.basedb.plugins.PackedFileExporter
 
begin(DbControl) - Method in class net.sf.basedb.plugins.PlateMappingExporter
 
begin(DbControl) - Method in class net.sf.basedb.plugins.PluginConfigurationExporter
 
begin(ExtensionsManager, int) - Method in class net.sf.basedb.clients.web.extensions.LoadServletsProcessor
 
begin(ExtensionsManager, int) - Method in class net.sf.basedb.clients.web.extensions.UninstalledFileProcessor
 
begin(ExtensionsManager, int) - Method in interface net.sf.basedb.util.extensions.manager.ExtensionsFileProcessor
Called by the extensions manager before the processing starts.
begin(ExtensionsManager, int) - Method in class net.sf.basedb.util.extensions.manager.processor.DeleteResourcesProcessor
 
begin(ExtensionsManager, int) - Method in class net.sf.basedb.util.extensions.manager.processor.DisablePluginsProcessor
 
begin(ExtensionsManager, int) - Method in class net.sf.basedb.util.extensions.manager.processor.ExtractResourcesProcessor
 
begin(ExtensionsManager, int) - Method in class net.sf.basedb.util.extensions.manager.processor.IgnoreFileProcessor
 
begin(ExtensionsManager, int) - Method in class net.sf.basedb.util.extensions.manager.processor.MarkAsProcessedProcessor
 
begin(ExtensionsManager, int) - Method in class net.sf.basedb.util.extensions.manager.processor.PluginInstallationProcessor
 
begin(ExtensionsManager, int) - Method in class net.sf.basedb.util.extensions.manager.processor.RegisterExtensionsProcessor
 
begin(ExtensionsManager, int) - Method in class net.sf.basedb.util.extensions.manager.processor.ResetProcessor
 
begin(ExtensionsManager, int) - Method in class net.sf.basedb.util.extensions.manager.processor.UnregisterExtensionsProcessor
 
begin(FlatFileParser) - Method in class net.sf.basedb.plugins.AbstractFlatFileImporter
Called just before parsing of the file begins.
begin(FlatFileParser) - Method in class net.sf.basedb.plugins.AnnotationFlatFileImporter
Setup error handling and pre-load some of the configuration options.
begin(FlatFileParser) - Method in class net.sf.basedb.plugins.batchimport.AbstractItemImporter
Setup error handling and pre-load some of the configuration options.
begin(FlatFileParser) - Method in class net.sf.basedb.plugins.batchimport.AnyToAnyImporter
Setup error handling and pre-load some of the configuration options.
begin(FlatFileParser) - Method in class net.sf.basedb.plugins.IlluminaRawDataImporter
 
begin(FlatFileParser) - Method in class net.sf.basedb.plugins.PlateFlatFileImporter
Create a DbControl and a RawDataBatcher.
begin(FlatFileParser) - Method in class net.sf.basedb.plugins.PlateMappingImporter
Save reference to parser.
begin(FlatFileParser) - Method in class net.sf.basedb.plugins.PrintMapFlatFileImporter
Create a DbControl and a FeatureBatcher.
begin(FlatFileParser) - Method in class net.sf.basedb.plugins.RawDataFlatFileImporter
Prepare for importing the next file.
begin(FlatFileParser) - Method in class net.sf.basedb.plugins.ReporterFlatFileImporter
Create a DbControl and a ReporterBatcher.
begin(FlatFileParser) - Method in class net.sf.basedb.plugins.ReporterMapFlatFileImporter
Create a DbControl and a FeatureBatcher.
beginData() - Method in class net.sf.basedb.plugins.AbstractFlatFileImporter
Called by the parser after the headers have been parsed but before the first data line is parsed.
beginData() - Method in class net.sf.basedb.plugins.AnnotationFlatFileImporter
Setup column mapping.
beginData() - Method in class net.sf.basedb.plugins.batchimport.AbstractItemImporter
Setup column mapping.
beginData() - Method in class net.sf.basedb.plugins.batchimport.AnyToAnyImporter
Setup column mapping.
beginData() - Method in class net.sf.basedb.plugins.IlluminaRawDataImporter
Check column headers and map them to raw bioassays.
beginData() - Method in class net.sf.basedb.plugins.PlateFlatFileImporter
Initialise column Mapper:s.
beginData() - Method in class net.sf.basedb.plugins.PlateMappingImporter
Create a DbControl and a new PlateMapping.
beginData() - Method in class net.sf.basedb.plugins.RawDataFlatFileImporter
Initialise column Mapper:s.
beginData() - Method in class net.sf.basedb.plugins.ReporterFlatFileImporter
Initialise column Mapper:s.
beginData() - Method in class net.sf.basedb.plugins.ReporterMapFlatFileImporter
Initialise column Mapper:s.
beginDocument() - Method in interface net.sf.basedb.clients.web.plugins.ExportTemplate
Start writing the document.
beginDocument() - Method in class net.sf.basedb.clients.web.plugins.PlainTextTemplate
Do nothing.
beginDocument() - Method in class net.sf.basedb.clients.web.plugins.XlsxTemplate
Reset row and column to 0.
beginDocument() - Method in class net.sf.basedb.clients.web.plugins.XMLTemplate
Write XML start (<?
beginExport() - Method in class net.sf.basedb.util.export.spotdata.AbstractBioAssaySetExporter
Make preparations for the export.
beginExport() - Method in class net.sf.basedb.util.export.spotdata.BaseFileExporter
Prepare the export by adding all experimental factors as assay fields if no fields have been specified.
beginExport() - Method in class net.sf.basedb.util.export.spotdata.BfsExporter
Validates that all required properties has been set and initialises other things that are needed.
beginExport() - Method in class net.sf.basedb.util.export.spotdata.MatrixBaseFileExporter
Prepare the export by pre-loading some information and configure the queries that we are going to use.
beginExport() - Method in class net.sf.basedb.util.export.spotdata.SerialBaseFileExporter
Prepare the export by pre-loading some information and configure the queries that we are going to use.
beginItem(int) - Method in interface net.sf.basedb.clients.web.plugins.ExportTemplate
Start writing a new item.
beginItem(int) - Method in class net.sf.basedb.clients.web.plugins.PlainTextTemplate
Reset column number.
beginItem(int) - Method in class net.sf.basedb.clients.web.plugins.XlsxTemplate
Reset column number and create a new row.
beginItem(int) - Method in class net.sf.basedb.clients.web.plugins.XMLTemplate
Begin a new item element.
beginSection(BaseFileParser, FlatFileParser, List<String>) - Method in class net.sf.basedb.util.importer.spotdata.GenericIntensityParser
 
beginSection(BaseFileParser, FlatFileParser, List<String>) - Method in class net.sf.basedb.util.importer.spotdata.MAParser
 
beginSection(BaseFileParser, FlatFileParser, List<String>) - Method in interface net.sf.basedb.util.importer.spotdata.SpotIntensityParser
Prepare for parsing the data section.
beginTransaction() - Method in class net.sf.basedb.core.hibernate.SessionWrapper
 
beginTransaction() - Method in class net.sf.basedb.core.hibernate.StatelessSessionWrapper
 
belongsTo(AnnotationSet) - Method in class net.sf.basedb.core.Annotation
Check if this annotation belongs to the primaray annotations for a specified annotation set.
between(Expression, Expression, Expression) - Static method in class net.sf.basedb.core.query.Restrictions
Compare if one expression falls between two other expressions: new expression = low <= e AND e < high.
BETWEEN - Enum constant in enum class net.sf.basedb.core.Operator
 
betweenInclusive(Expression, Expression, Expression) - Static method in class net.sf.basedb.core.query.Restrictions
Compare if one expression falls between two other expressions (inclusive): new expression = low <= e AND e <= high.
BetweenRestriction - Class in net.sf.basedb.core.query
Compare if one expression falls between to other expressions: e BETWEEN low AND high.
BetweenRestriction(Expression, Expression, Expression, boolean) - Constructor for class net.sf.basedb.core.query.BetweenRestriction
 
bf_crypt_ciphertext - Static variable in class net.sf.basedb.util.bcrypt.BCrypt
 
BFS_METADATA - Static variable in class net.sf.basedb.core.DataFileType
The external ID for the file type representing a BFS metadata file.
BfsExporter - Class in net.sf.basedb.util.export.spotdata
Base class for exporting spotdata to BFS format.
BfsExporter() - Constructor for class net.sf.basedb.util.export.spotdata.BfsExporter
 
BfsExporterPlugin - Class in net.sf.basedb.plugins
Exports bioassay set data to BFS format.
BfsExporterPlugin() - Constructor for class net.sf.basedb.plugins.BfsExporterPlugin
 
BfsExporterPlugin.ExtendedExportableField - Class in net.sf.basedb.plugins
 
BfsExporterSupport - Class in net.sf.basedb.plugins.executor
Exporter implementation for the external program executor that exports data to BFS format.
BfsExporterSupport() - Constructor for class net.sf.basedb.plugins.executor.BfsExporterSupport
 
BfsImporter - Class in net.sf.basedb.util.importer.spotdata
Imports spot data from a serial or matrix BFS.
BfsImporter() - Constructor for class net.sf.basedb.util.importer.spotdata.BfsImporter
Create a new importer object.
BfsImporter.ProgressEventHandler - Class in net.sf.basedb.util.importer.spotdata
 
BfsImporterSupport - Class in net.sf.basedb.plugins.executor
Importer implementation for the external program executor that imports data from BFS format.
BfsImporterSupport() - Constructor for class net.sf.basedb.plugins.executor.BfsImporterSupport
 
BfsParser - Interface in net.sf.basedb.util.bfs
Interface that it is recommended that all BFS parsers should implement.
bfsPrintComment(String) - Method in class net.sf.basedb.util.bfs.MetadataWriter
Prints one or more comment lines to the metadata file.
bfsPrintData(int, Object...) - Method in class net.sf.basedb.util.bfs.AnnotationWriter
Print a data line.
bfsPrintData(Object...) - Method in class net.sf.basedb.util.bfs.DataWriter
Print a data line.
bfsPrintEmptyLine(int) - Method in class net.sf.basedb.util.bfs.MetadataWriter
Print one or more empty lines to the metadata file.
bfsPrintHeaders(String...) - Method in class net.sf.basedb.util.bfs.AnnotationWriter
Print the header line.
bfsPrintSection(String, boolean, boolean) - Method in class net.sf.basedb.util.bfs.MetadataWriter
Start a new section.
bfsPrintValue(String, String...) - Method in class net.sf.basedb.util.bfs.MetadataWriter
Prints a section entry.
bfsPrintValue(String, Formatter<T>, T...) - Method in class net.sf.basedb.util.bfs.MetadataWriter
Prints a section entry.
bfsPrintValue(String, T...) - Method in class net.sf.basedb.util.bfs.MetadataWriter
Prints a section entry.
BINARY_ESCAPE - Variable in class net.sf.basedb.core.migrate.postgres.PostgresResultWriterFactory
 
bins - Variable in class net.sf.basedb.util.plot.HistogramPlot.HistogramSeries
 
bioassay - Variable in class net.sf.basedb.core.data.ArraySlideData
 
bioassay - Variable in class net.sf.basedb.core.data.BioMaterialEventData
 
bioAssay - Variable in class net.sf.basedb.core.data.RawBioAssayData
 
BioAssay - Class in net.sf.basedb.core
Represents the current intensities of raw data after some transformation has been applied to it.
BioAssay(BioAssayData) - Constructor for class net.sf.basedb.core.BioAssay
Creates a new bioassay item from the given data.
BIOASSAY - Enum constant in enum class net.sf.basedb.core.BioMaterialEvent.Type
An event of this type created a physical bioassay.
BIOASSAY - Enum constant in enum class net.sf.basedb.core.Item
The item is a BioAssay
bioAssayColumnMapping - Static variable in class net.sf.basedb.plugins.batchimport.RawBioAssayImporter
 
BioAssayData - Class in net.sf.basedb.core.data
This class holds information about a bioassay.
BioAssayData() - Constructor for class net.sf.basedb.core.data.BioAssayData
 
BioAssayExperimentalFactorLoader - Class in net.sf.basedb.clients.web.plugins
Data loader that gets annotation values for a bioassay including those that are present on the parent raw bioassay(s) without being directly inherited by the bioassay.
BioAssayExperimentalFactorLoader() - Constructor for class net.sf.basedb.clients.web.plugins.BioAssayExperimentalFactorLoader
 
BioAssayExperimentalFactorLoader(SnapshotManager) - Constructor for class net.sf.basedb.clients.web.plugins.BioAssayExperimentalFactorLoader
Creates an experimental factor loader that uses a specific snapshot manager for loading the annotation values.
bioAssayId - Variable in class net.sf.basedb.core.MigrateRbaToDba.Rba
 
bioAssayMapper - Variable in class net.sf.basedb.plugins.batchimport.RawBioAssayImporter
 
bioAssays - Variable in class net.sf.basedb.clients.web.ExperimentExplorer
Maps a bioassays cube column number to it's id for fast loading by the ExperimentExplorer.getBioAssay(DbControl, short) method.
bioAssays - Variable in class net.sf.basedb.core.data.BioAssaySetData
 
bioAssays - Variable in class net.sf.basedb.core.data.RawBioAssayData
 
bioAssays - Variable in class net.sf.basedb.plugins.IlluminaRawDataImporter
 
bioAssays - Variable in class net.sf.basedb.util.export.spotdata.AbstractBioAssaySetExporter
 
bioAssays - Variable in class net.sf.basedb.util.export.spotdata.MatrixBaseFileExporter
 
bioAssays - Variable in class net.sf.basedb.util.export.spotdata.SerialBaseFileExporter
 
bioAssaySet - Variable in class net.sf.basedb.clients.web.ExperimentExplorer
The bioassay set we are exploring.
bioAssaySet - Variable in class net.sf.basedb.core.data.BioAssayData
 
bioAssaySet - Variable in class net.sf.basedb.core.data.ExtraValueData
 
bioAssaySet - Variable in class net.sf.basedb.core.DynamicPositionQuery
 
bioAssaySet - Variable in class net.sf.basedb.core.DynamicSpotQuery
 
bioAssaySet - Variable in class net.sf.basedb.core.FilterBatcher
The bioassayset this batcher inserts data for.
bioAssaySet - Variable in class net.sf.basedb.core.SpotBatcher
The bioassayset this batcher inserts data for.
BioAssaySet - Class in net.sf.basedb.core
A bioassayset represents the current intensities of the raw data after some Transformation has been applied to it.
BioAssaySet(BioAssaySetData) - Constructor for class net.sf.basedb.core.BioAssaySet
Creates a new experiment item from the given data.
BIOASSAYSET - Enum constant in enum class net.sf.basedb.core.Item
The item is a BioAssaySet
BioAssaySetData - Class in net.sf.basedb.core.data
This class holds information about a bioassayset.
BioAssaySetData() - Constructor for class net.sf.basedb.core.data.BioAssaySetData
 
BioAssaySetFilterUtil - Class in net.sf.basedb.util
This is a utility class for plugins that filters bioassay set data.
BioAssaySetFilterUtil() - Constructor for class net.sf.basedb.util.BioAssaySetFilterUtil
 
bioAssaySets - Variable in class net.sf.basedb.core.data.ExperimentData
 
BioAssaySetUtil - Class in net.sf.basedb.util
This is a utility class for BioAssaySet.
BioAssaySetUtil() - Constructor for class net.sf.basedb.util.BioAssaySetUtil
 
bioAssaySpots - Variable in class net.sf.basedb.core.BioAssaySet
Stores the result of BioAssaySet.getSpotCount(int).
bioMaterial - Variable in class net.sf.basedb.core.data.BioMaterialEventData
 
bioMaterial - Variable in class net.sf.basedb.core.data.BioMaterialEventSourceData
 
bioMaterial - Variable in class net.sf.basedb.core.data.BioWellData
 
bioMaterial - Variable in class net.sf.basedb.core.MeasuredBioMaterial.RemainingQuantityAction
 
BioMaterial - Class in net.sf.basedb.core
This is the base class for for the three types of biomaterials: BioSource, Sample and Extract.
BioMaterial(BioMaterialData) - Constructor for class net.sf.basedb.core.BioMaterial
 
BioMaterialData - Class in net.sf.basedb.core.data
This class is the root class for biomaterials.
BioMaterialData() - Constructor for class net.sf.basedb.core.data.BioMaterialData
 
BioMaterialEvent - Class in net.sf.basedb.core
This class represents an event in the life of a MeasuredBioMaterial.
BioMaterialEvent(BioMaterialEventData) - Constructor for class net.sf.basedb.core.BioMaterialEvent
 
BIOMATERIALEVENT - Enum constant in enum class net.sf.basedb.core.Item
The item is a BioMaterialEvent.
BioMaterialEvent.Type - Enum Class in net.sf.basedb.core
The type of the event.
BioMaterialEventData - Class in net.sf.basedb.core.data
This class is used to register events for measured biomaterials.
BioMaterialEventData() - Constructor for class net.sf.basedb.core.data.BioMaterialEventData
 
BioMaterialEventLogger - Class in net.sf.basedb.core.log.db
Logger for biomaterial events that logs UPDATE:s to CREATION and HYBRIDIZATION events as updates to their parent biomaterial/hybridization.
BioMaterialEventLogger(DbLogManagerFactory) - Constructor for class net.sf.basedb.core.log.db.BioMaterialEventLogger
Creates a new biomaterial event logger.
bioMaterialEvents - Variable in class net.sf.basedb.core.data.BioPlateEventParticipantData
 
BioMaterialEventSource - Class in net.sf.basedb.core
Class for holding information about a parent biomaterial that was used in an event that created a child biomaterial or a physical bioassay.
BioMaterialEventSource(DbControl, BioMaterialEventSourceData) - Constructor for class net.sf.basedb.core.BioMaterialEventSource
 
BioMaterialEventSource.BioMaterialEventSourceTransformer - Class in net.sf.basedb.core
 
BioMaterialEventSourceData - Class in net.sf.basedb.core.data
Data class for holding information about a parent biomaterial that was used in an event that created a child biomaterial or a physical bioassay.
BioMaterialEventSourceData() - Constructor for class net.sf.basedb.core.data.BioMaterialEventSourceData
 
BioMaterialEventSourceFormatter - Class in net.sf.basedb.clients.web.plugins
Formatter to handle BioMaterialEventSource items.
BioMaterialEventSourceFormatter() - Constructor for class net.sf.basedb.clients.web.plugins.BioMaterialEventSourceFormatter
Create a new formatter.
BioMaterialEventSourceFormatter(String) - Constructor for class net.sf.basedb.clients.web.plugins.BioMaterialEventSourceFormatter
Create a new formatter.
BioMaterialEventSourceTransformer() - Constructor for class net.sf.basedb.core.BioMaterialEventSource.BioMaterialEventSourceTransformer
 
bioMaterialType - Variable in class net.sf.basedb.core.data.BioPlateTypeData
 
bioPlate - Variable in class net.sf.basedb.core.data.BioPlateEventParticipantData
 
bioPlate - Variable in class net.sf.basedb.core.data.BioWellData
 
BioPlate - Class in net.sf.basedb.core
This class is represents physical bio-plates.
BioPlate(BioPlateData) - Constructor for class net.sf.basedb.core.BioPlate
 
BIOPLATE - Enum constant in enum class net.sf.basedb.core.Item
The item is a BioPlate
bioPlateColumnMapping - Static variable in class net.sf.basedb.plugins.batchimport.SampleImporter
Column mapping parameter for the bioplate
BioPlateData - Class in net.sf.basedb.core.data
This class holds information about a bioplate
BioPlateData() - Constructor for class net.sf.basedb.core.data.BioPlateData
 
BioPlateEvent - Class in net.sf.basedb.core
A bioplate event represents something that happened simultaneously to the biomaterial on one or more bioplates.
BioPlateEvent(BioPlateEventData) - Constructor for class net.sf.basedb.core.BioPlateEvent
 
BIOPLATEEVENT - Enum constant in enum class net.sf.basedb.core.Item
The item is a BioPlateEvent
BioPlateEventData - Class in net.sf.basedb.core.data
This class holds information about a bioplate event.
BioPlateEventData() - Constructor for class net.sf.basedb.core.data.BioPlateEventData
 
BioPlateEventLoader - Class in net.sf.basedb.util.overview.loader
Node loader implementation for bioplate events.
BioPlateEventLoader() - Constructor for class net.sf.basedb.util.overview.loader.BioPlateEventLoader
 
bioPlateEventParticipant - Variable in class net.sf.basedb.core.data.BioMaterialEventData
 
bioPlateEventParticipant - Variable in class net.sf.basedb.core.MeasuredBioMaterial
 
bioPlateEventParticipant - Variable in class net.sf.basedb.core.PhysicalBioAssay
 
BioPlateEventParticipant - Class in net.sf.basedb.core
Holds information about a bioplate that is participating in a bioplate event.
BioPlateEventParticipant(BioPlateEventParticipantData) - Constructor for class net.sf.basedb.core.BioPlateEventParticipant
 
BIOPLATEEVENTPARTICIPANT - Enum constant in enum class net.sf.basedb.core.Item
BioPlateEventParticipantData - Class in net.sf.basedb.core.data
Registers a plate as a participant in a bioplate event.
BioPlateEventParticipantData() - Constructor for class net.sf.basedb.core.data.BioPlateEventParticipantData
 
BioPlateEventType - Class in net.sf.basedb.core
The type of a bioplate event defines what happened in the event.
BioPlateEventType(BioPlateEventTypeData) - Constructor for class net.sf.basedb.core.BioPlateEventType
 
BIOPLATEEVENTTYPE - Enum constant in enum class net.sf.basedb.core.Item
The item is a BioPlateEventType
BioPlateEventTypeData - Class in net.sf.basedb.core.data
Each bioplate event must have a type that defines what happened.
BioPlateEventTypeData() - Constructor for class net.sf.basedb.core.data.BioPlateEventTypeData
 
BioPlateImporter - Class in net.sf.basedb.plugins.batchimport
Plug-in for importing bioplate items in a batch.
BioPlateImporter() - Constructor for class net.sf.basedb.plugins.batchimport.BioPlateImporter
 
BioPlateLoader - Class in net.sf.basedb.util.overview.loader
Node loader implementation for bioplates.
BioPlateLoader() - Constructor for class net.sf.basedb.util.overview.loader.BioPlateLoader
 
bioPlateMapper - Variable in class net.sf.basedb.plugins.batchimport.ExtractImporter
 
bioPlateMapper - Variable in class net.sf.basedb.plugins.batchimport.SampleImporter
 
BioPlateNameGenerator - Class in net.sf.basedb.util.overview.node
Name generator implementation for BioPlate items.
BioPlateNameGenerator(String, String) - Constructor for class net.sf.basedb.util.overview.node.BioPlateNameGenerator
Create a new name generator.
bioPlateQuery - Variable in class net.sf.basedb.plugins.batchimport.AbstractItemImporter
 
bioPlates - Variable in class net.sf.basedb.core.data.BioPlateTypeData
 
bioPlateType - Variable in class net.sf.basedb.core.data.BioPlateData
 
BioPlateType - Class in net.sf.basedb.core
This class represents the type of a bio-plate.
BioPlateType(BioPlateTypeData) - Constructor for class net.sf.basedb.core.BioPlateType
 
BIOPLATETYPE - Enum constant in enum class net.sf.basedb.core.Item
The item is a BioPlateType.
bioPlateTypeColumnMapping - Static variable in class net.sf.basedb.plugins.batchimport.BioPlateImporter
 
BioPlateTypeData - Class in net.sf.basedb.core.data
This class holds information about a biomaterial plate type.
BioPlateTypeData() - Constructor for class net.sf.basedb.core.data.BioPlateTypeData
 
bioPlateTypeMapper - Variable in class net.sf.basedb.plugins.batchimport.BioPlateImporter
 
bioPlateTypeQuery - Variable in class net.sf.basedb.plugins.batchimport.AbstractItemImporter
 
BioPlateValidator - Class in net.sf.basedb.util.overview.validator
Validator implementation for bioplates.
BioPlateValidator() - Constructor for class net.sf.basedb.util.overview.validator.BioPlateValidator
 
BioSource - Class in net.sf.basedb.core
This class represent biosource items.
BioSource(BioSourceData) - Constructor for class net.sf.basedb.core.BioSource
 
BIOSOURCE - Enum constant in enum class net.sf.basedb.core.Item
The item is a BioSource.
BioSourceData - Class in net.sf.basedb.core.data
This represents a biosoruce which is the starting point of all biomaterials.
BioSourceData() - Constructor for class net.sf.basedb.core.data.BioSourceData
 
BioSourceImporter - Class in net.sf.basedb.plugins.batchimport
Plug-in for importing biosource items in a batch.
BioSourceImporter() - Constructor for class net.sf.basedb.plugins.batchimport.BioSourceImporter
 
BioSourceLoader - Class in net.sf.basedb.util.overview.loader
Node loader implementation for biosources.
BioSourceLoader() - Constructor for class net.sf.basedb.util.overview.loader.BioSourceLoader
 
bioSourceQuery - Variable in class net.sf.basedb.plugins.batchimport.AbstractItemImporter
 
BioSourceToSampleTransformer - Class in net.sf.basedb.util.listable
Source item transformer that transform biosource items to their child samples.
BioSourceToSampleTransformer() - Constructor for class net.sf.basedb.util.listable.BioSourceToSampleTransformer
 
BioSourceValidator - Class in net.sf.basedb.util.overview.validator
Validator implementation for biosources.
BioSourceValidator() - Constructor for class net.sf.basedb.util.overview.validator.BioSourceValidator
 
bioWell - Variable in class net.sf.basedb.core.data.MeasuredBioMaterialData
 
BioWell - Class in net.sf.basedb.core
A biowell is located on a BioPlate and contains a MeasuredBioMaterial.
BioWell(BioWellData) - Constructor for class net.sf.basedb.core.BioWell
 
BIOWELL - Enum constant in enum class net.sf.basedb.core.Item
The item is a BioWell
BioWell.LockMode - Enum Class in net.sf.basedb.core
The lock mode for a well is determined by the plate's bio plate type.
bioWellColColumnMapping - Static variable in class net.sf.basedb.plugins.batchimport.SampleImporter
Column mapping parameter for the biowell's column
bioWellColMapper - Variable in class net.sf.basedb.plugins.batchimport.ExtractImporter
 
bioWellColMapper - Variable in class net.sf.basedb.plugins.batchimport.SampleImporter
 
BioWellData - Class in net.sf.basedb.core.data
This class holds information about a bio well on a bio plate.
BioWellData() - Constructor for class net.sf.basedb.core.data.BioWellData
 
BioWellLoader - Class in net.sf.basedb.util.overview.loader
Node loader implementation that load biomaterial on a bioplate.
BioWellLoader() - Constructor for class net.sf.basedb.util.overview.loader.BioWellLoader
 
BioWellNameGenerator - Class in net.sf.basedb.util.overview.node
Name generator implementation for biomaterial items that are located on a biowell.
BioWellNameGenerator() - Constructor for class net.sf.basedb.util.overview.node.BioWellNameGenerator
Create a new biowell name generator.
bioWellRowColumnMapping - Static variable in class net.sf.basedb.plugins.batchimport.SampleImporter
Column mapping parameter for the biowell's row
bioWellRowMapper - Variable in class net.sf.basedb.plugins.batchimport.ExtractImporter
 
bioWellRowMapper - Variable in class net.sf.basedb.plugins.batchimport.SampleImporter
 
bioWells - Variable in class net.sf.basedb.core.data.BioPlateData
 
BlankValue() - Constructor for class net.sf.basedb.util.excel.ExcelValue.BlankValue
 
block - Variable in class net.sf.basedb.core.BlockInfo
The block number.
block - Variable in class net.sf.basedb.core.data.RawData
 
block - Variable in class net.sf.basedb.core.FeatureCoordinate
 
block - Variable in class net.sf.basedb.plugins.LowessNormalization.SpotData
 
block - Variable in class net.sf.basedb.plugins.MedianRatioNormalization.SpotData
 
block - Variable in class net.sf.basedb.plugins.PrintMapFlatFileImporter.MetaBlock
 
BLOCK - Enum constant in enum class net.sf.basedb.plugins.PrintMapFlatFileImporter.Section
 
blockColumnMapping - Static variable in class net.sf.basedb.plugins.RawDataFlatFileImporter
 
blockColumnMapping - Static variable in class net.sf.basedb.plugins.ReporterMapFlatFileImporter
 
blockGroupParameter - Static variable in class net.sf.basedb.plugins.LowessNormalization
 
blockGroupParameter - Static variable in class net.sf.basedb.plugins.MedianRatioNormalization
Used with 2-channel data only
blockGroupSize - Variable in class net.sf.basedb.plugins.LowessNormalization.CallableWorker
 
BlockInfo - Class in net.sf.basedb.core
A BlockInfo object is used to represent the uniqe identifiers of an ArrayDesignBlock.
BlockInfo(int, int) - Constructor for class net.sf.basedb.core.BlockInfo
Create a new block info using the meta coordinates.
BlockInfo(int, int, int) - Constructor for class net.sf.basedb.core.BlockInfo
Create a new block info using meta coordinates.
blockMapper - Variable in class net.sf.basedb.plugins.RawDataFlatFileImporter
 
blockMapper - Variable in class net.sf.basedb.plugins.ReporterMapFlatFileImporter
 
blockNumber - Variable in class net.sf.basedb.core.data.ArrayDesignBlockData
 
blockNumber - Variable in enum class net.sf.basedb.plugins.PrintMapFlatFileImporter.Section
 
blocks - Variable in class net.sf.basedb.core.ArrayDesign
 
blocks - Variable in class net.sf.basedb.plugins.PrintMapFlatFileImporter
 
blocks - Variable in class net.sf.basedb.plugins.ReporterMapFlatFileImporter
 
blockSizeX - Variable in class net.sf.basedb.core.data.ArrayDesignBlockData
 
blockSizeX - Variable in class net.sf.basedb.plugins.PrintMapFlatFileImporter.MetaBlock
 
blockSizeY - Variable in class net.sf.basedb.core.data.ArrayDesignBlockData
 
blockSizeY - Variable in class net.sf.basedb.plugins.PrintMapFlatFileImporter.MetaBlock
 
BLOWFISH_NUM_ROUNDS - Static variable in class net.sf.basedb.util.bcrypt.BCrypt
 
Body - Class in net.sf.basedb.clients.web.taglib
This tag defines the body section of a page.
Body() - Constructor for class net.sf.basedb.clients.web.taglib.Body
 
BOF_EVENT - Static variable in class net.sf.basedb.util.bfs.MetadataParser
Event type that is issued when the beginning-of-file marker is found.
BOF_MARKER - Static variable in class net.sf.basedb.util.bfs.MetadataWriter
 
bofMarker - Variable in class net.sf.basedb.util.parser.FlatFileParser
The regular expression for matching the beginning-of-file marker
bofType - Variable in class net.sf.basedb.util.parser.FlatFileParser
The value that was captured by the bofMarker pattern.
bool(boolean) - Static method in class net.sf.basedb.core.query.Expressions
Create a constant expression from a boolean.
bool(Restriction) - Static method in class net.sf.basedb.core.query.Expressions
Create a boolean expression view of a restriction.
BOOLEAN - Enum constant in enum class net.sf.basedb.core.Type
Boolean type.
BOOLEAN - Static variable in class net.sf.basedb.core.hibernate.TypeWrapper
 
BOOLEAN_FORMAT - Static variable in class net.sf.basedb.clients.web.plugins.SimpleExport
 
BooleanExpression - Class in net.sf.basedb.core.query
A constant boolean expression.
BooleanExpression(boolean) - Constructor for class net.sf.basedb.core.query.BooleanExpression
 
BooleanExpression(Restriction) - Constructor for class net.sf.basedb.core.query.BooleanExpression
 
BooleanFormatter - Class in net.sf.basedb.util.formatter
Formats a boolean value.
BooleanFormatter(BooleanFormatter.Type) - Constructor for class net.sf.basedb.util.formatter.BooleanFormatter
Create a new boolean formatter.
BooleanFormatter.Type - Enum Class in net.sf.basedb.util.formatter
Enum for holding the various types of boolean output.
BooleanParameterType - Class in net.sf.basedb.core
This class represent a parameter type that is a boolean.
BooleanParameterType() - Constructor for class net.sf.basedb.core.BooleanParameterType
Create a new boolean parameter type, allowing null values.
BooleanParameterType(Boolean, boolean) - Constructor for class net.sf.basedb.core.BooleanParameterType
Create a new boolean parameter type.
BooleanParameterType(Boolean, boolean, int, Enumeration<Boolean, String>) - Constructor for class net.sf.basedb.core.BooleanParameterType
 
BooleanParameterValueData - Class in net.sf.basedb.core.data
Boolean parameter value.
BooleanParameterValueData() - Constructor for class net.sf.basedb.core.data.BooleanParameterValueData
 
BooleanParameterValueData(Boolean...) - Constructor for class net.sf.basedb.core.data.BooleanParameterValueData
 
BooleanValue(boolean) - Constructor for class net.sf.basedb.util.excel.ExcelValue.BooleanValue
 
BooleanWriter - Class in net.sf.basedb.core.migrate
Database-independent writer implementation that writes boolean values from a result set.
BooleanWriter(ResultSet, int, Writer, char[]) - Constructor for class net.sf.basedb.core.migrate.BooleanWriter
 
BOTTOM - Static variable in class net.sf.basedb.clients.web.taglib.tab.TabControl
Tabs are at the bottom of the tab control.
boundary - Variable in class net.sf.basedb.clients.web.fileupload.FileUpload
The multipart/formdata boundary
breakCircularReferences(Set<ItemProxy>) - Method in class net.sf.basedb.core.BasicItem
Break references to items that may lead to circular references.
breakCircularReferences(Set<ItemProxy>) - Method in class net.sf.basedb.core.DerivedBioAssay
Any parent bioassays found among the given items are removed from this item.
breakCircularReferences(Set<ItemProxy>) - Method in class net.sf.basedb.core.MeasuredBioMaterial
Any parent items found among the given items are removed from the creation event of this item.
breakCircularReferences(Set<ItemProxy>) - Method in class net.sf.basedb.core.User
If the home directory is found among the items, set it to null.
breakCircularReferences(SessionControl, Set<Identifiable>) - Static method in class net.sf.basedb.core.Trashcan
 
buffer - Variable in class net.sf.basedb.clients.web.fileupload.FileUpload.UploadStream
 
buffer - Variable in class net.sf.basedb.util.gtf.GtfInputStream
 
BUFFER_SIZE - Static variable in class net.sf.basedb.util.FileUtil
 
build - Variable in class net.sf.basedb.core.data.SchemaVersionData
 
build - Static variable in class net.sf.basedb.core.Version
 
buildDelete(String, Dialect) - Static method in class net.sf.basedb.core.BatchUtil
Build delete SQL string and put it in the SQL map.
buildDocument() - Method in class net.sf.basedb.core.Presets
Convert the presets to a XML document.
buildDom(Element) - Method in class net.sf.basedb.core.Presets.Preset
Add XML elements to the parent element for this preset's key-value pairs.
buildFilterSql() - Method in class net.sf.basedb.core.FilterBatcher
Builds the insert SQL statement.
buildInsert(String, Dialect) - Static method in class net.sf.basedb.core.BatchUtil
Build insert SQL string and put it in the SQL map.
buildInsertSelectSql(String) - Method in class net.sf.basedb.core.FilterBatcher
Build the INSERT INTO ...
buildInsertSelectSql(String) - Method in class net.sf.basedb.core.MappingBatcher
Build the INSERT INTO ...
buildInsertSelectSql(String) - Method in class net.sf.basedb.core.PositionBatcher
Build the INSERT INTO ...
buildInsertSelectSql(String) - Method in class net.sf.basedb.core.PositionExtraValueBatcher
Build the INSERT INTO ...
buildInsertSelectSql(String) - Method in class net.sf.basedb.core.SpotBatcher
Build the INSERT INTO ...
buildInsertSelectSql(String) - Method in class net.sf.basedb.core.SpotExtraValueBatcher
Build the INSERT INTO ...
buildInsertSelectSql(VirtualDb, VirtualTable, VirtualColumn[], String) - Static method in class net.sf.basedb.core.BatchUtil
 
buildInsertSql() - Method in class net.sf.basedb.core.ReporterCloneBatcher
Builds the insert SQL statement.
buildInsertSql(VirtualDb, VirtualTable, VirtualColumn[], Object[]) - Static method in class net.sf.basedb.core.BatchUtil
 
buildLockRequest(LockOptions) - Method in class net.sf.basedb.core.hibernate.SessionWrapper
 
buildPositionSql() - Method in class net.sf.basedb.core.PositionBatcher
Builds the insert SQL statement.
buildPropertyAccess(Class, String) - Method in class net.sf.basedb.core.ExtendedPropertyAccessor
 
buildRawMappingSql() - Method in class net.sf.basedb.core.MappingBatcher
Builds the insert SQL statement.
buildRawSelectQuery() - Method in class net.sf.basedb.core.ReporterCloneBatcher
 
buildSelectQuery() - Method in class net.sf.basedb.core.ReporterCloneBatcher
Builds a query that select all reporter properties that should be cloned from the real reporter table.
buildSessionFactory(ServiceSessionControl.SessionFactoryConfiguration) - Method in class net.sf.basedb.core.ServiceSessionControl
Create a session factory for the given configuration.
buildSpotSql() - Method in class net.sf.basedb.core.PositionExtraValueBatcher
Builds the insert SQL statement.
buildSpotSql() - Method in class net.sf.basedb.core.SpotBatcher
Builds the insert SQL statement.
buildSpotSql() - Method in class net.sf.basedb.core.SpotExtraValueBatcher
Builds the insert SQL statement.
buildUpdate(String, Dialect) - Static method in class net.sf.basedb.core.BatchUtil
Build update SQL string and put it in the SQL map.
bulletlist - Variable in class net.sf.basedb.clients.web.taglib.table.CellValue
 
Bundle - Class in net.sf.basedb.clients.web.resources
Declare the names of resource bundles used by the web client.
Bundle() - Constructor for class net.sf.basedb.clients.web.resources.Bundle
 
Button - Class in net.sf.basedb.clients.web.taglib
This tag is used to display a clickable button.
Button - Class in net.sf.basedb.clients.web.taglib.table
This tag creates a button on a toolbar.
Button() - Constructor for class net.sf.basedb.clients.web.taglib.Button
 
Button() - Constructor for class net.sf.basedb.clients.web.taglib.table.Button
 
Button.ButtonActionWrapper - Class in net.sf.basedb.clients.web.taglib.table
 
ButtonAction - Interface in net.sf.basedb.clients.web.extensions.toolbar
Actions represented as buttons in a toolbar.
ButtonActionWrapper() - Constructor for class net.sf.basedb.clients.web.taglib.table.Button.ButtonActionWrapper
 
ButtonBean - Class in net.sf.basedb.clients.web.extensions.toolbar
A simple bean-like implementation of the ButtonAction interface.
ButtonBean() - Constructor for class net.sf.basedb.clients.web.extensions.toolbar.ButtonBean
 
buttonclass - Variable in class net.sf.basedb.clients.web.taglib.Select
 
buttonGroup - Variable in class net.sf.basedb.clients.web.taglib.Button
 
ButtonGroup - Class in net.sf.basedb.clients.web.taglib
This tag is used to group buttons together (horizontally) and make them all have the same size.
ButtonGroup() - Constructor for class net.sf.basedb.clients.web.taglib.ButtonGroup
 
buttonicon - Variable in class net.sf.basedb.clients.web.taglib.Select
 
buttons - Variable in class net.sf.basedb.clients.web.taglib.ButtonGroup
The buttons in this group.
buttonstyle - Variable in class net.sf.basedb.clients.web.taglib.Select
 
buttonTag - Variable in class net.sf.basedb.clients.web.extensions.toolbar.CompactButtonRenderer
 
buttonTag - Variable in class net.sf.basedb.clients.web.extensions.toolbar.CompactButtonRendererFactory
 
buttontitle - Variable in class net.sf.basedb.clients.web.taglib.Select
 
byId(Class<T>) - Method in class net.sf.basedb.core.hibernate.SessionWrapper
 
byId(String) - Method in class net.sf.basedb.core.hibernate.SessionWrapper
 
byMultipleIds(Class<T>) - Method in class net.sf.basedb.core.hibernate.SessionWrapper
 
byMultipleIds(String) - Method in class net.sf.basedb.core.hibernate.SessionWrapper
 
byNaturalId(Class<T>) - Method in class net.sf.basedb.core.hibernate.SessionWrapper
 
byNaturalId(String) - Method in class net.sf.basedb.core.hibernate.SessionWrapper
 
bySimpleNaturalId(Class<T>) - Method in class net.sf.basedb.core.hibernate.SessionWrapper
 
bySimpleNaturalId(String) - Method in class net.sf.basedb.core.hibernate.SessionWrapper
 
ByteArrayWriter - Class in net.sf.basedb.core.migrate
Generic writer implementation that writes byte-array values from a result set.
ByteArrayWriter(ResultSet, int, Writer, char[], char[][]) - Constructor for class net.sf.basedb.core.migrate.ByteArrayWriter
 
bytes - Variable in class net.sf.basedb.core.data.DataCubeData
 
bytes - Variable in class net.sf.basedb.core.data.DataCubeExtraValueData
 
bytes - Variable in class net.sf.basedb.core.data.DataCubeFilterData
 
bytes - Variable in class net.sf.basedb.core.data.DataCubeLayerData
 
bytes - Variable in class net.sf.basedb.core.data.DiskUsageData
 
bytes - Variable in class net.sf.basedb.core.data.ExperimentData
 
bytes - Variable in class net.sf.basedb.core.data.RawBioAssayData
 
bytes - Variable in class net.sf.basedb.core.data.ReporterCloneTemplateData
 
bytes - Variable in class net.sf.basedb.core.FilterBatcher
The number of bytes this batcher has added to the experiment.
bytes - Variable in class net.sf.basedb.core.MappingBatcher
The number of bytes this batcher has added to the experiment.
bytes - Variable in class net.sf.basedb.core.PositionBatcher
The number of bytes this batcher has added to the data cube and experiment.
bytes - Variable in class net.sf.basedb.core.PositionExtraValueBatcher
The number of bytes this batcher has added to the experiment.
bytes - Variable in class net.sf.basedb.core.RawDataBatcher
The number of bytes the spot data is occupying on disk.
bytes - Variable in class net.sf.basedb.core.SpotBatcher
The number of bytes this batcher has added to the experiment.
bytes - Variable in class net.sf.basedb.core.SpotExtraValueBatcher
The number of bytes this batcher has added to the experiment.
BYTES_REGEXP - Static variable in class net.sf.basedb.util.Values
 
bytesPerRow - Variable in class net.sf.basedb.core.FilterBatcher
The number of bytes used by a single row.
bytesPerRow - Variable in class net.sf.basedb.core.MappingBatcher
The number of bytes used by a single row.
bytesPerRow - Variable in class net.sf.basedb.core.PositionBatcher
The number of bytes used by a single row.
bytesPerRow - Variable in class net.sf.basedb.core.PositionExtraValueBatcher
The number of bytes used by a single row.
bytesPerRow - Variable in class net.sf.basedb.core.ReporterCloneBatcher
The number of bytes used by a single row.
bytesPerRow - Variable in class net.sf.basedb.core.SpotBatcher
The number of bytes used by a single row.
bytesPerRow - Variable in class net.sf.basedb.core.SpotExtraValueBatcher
The number of bytes used by a single row.
bzip - Variable in class net.sf.basedb.util.zip.Bzip2FilePacker
 
Bzip2FilePacker - Class in net.sf.basedb.util.zip
This class wraps the TarFilePacker in a BZIP2 stream, creating a tar.bz2 file.
Bzip2FilePacker() - Constructor for class net.sf.basedb.util.zip.Bzip2FilePacker
Create a new packer that compresses files with the BZIP2 format.
Bzip2FileUnpacker - Class in net.sf.basedb.plugins
A plugin for unpacking a bzip2 compressed file to the BASE file system.
Bzip2FileUnpacker() - Constructor for class net.sf.basedb.plugins.Bzip2FileUnpacker
 

C

c - Variable in enum class net.sf.basedb.plugins.Base1PluginExecuter.Base1JobParameterType
 
CABINET - Static variable in class net.sf.basedb.core.Hardware
The id for the HardwareType object representing a cabinet.
cache - Variable in class net.sf.basedb.clients.web.ExperimentExplorer
The cache of reporter ids matching the current reporter filter.
cache - Static variable in class net.sf.basedb.core.DerivedBioAssay.FixDerivedBioAssayParentsRecursivelyAction
 
cache - Variable in class net.sf.basedb.core.hibernate.AbstractQueryCache
 
cache - Static variable in class net.sf.basedb.core.MeasuredBioMaterial.RemainingQuantityAction
We need a single action per DbControl and BioMaterial
cache - Variable in class net.sf.basedb.util.AnnotationUtil.AnnotatableWrapper
 
cache - Variable in class net.sf.basedb.util.bfs.BaseInputStreamLocator
 
cache - Variable in class net.sf.basedb.util.listable.TransformCache
 
cache - Variable in class net.sf.basedb.util.overview.cache.NodeCache
 
cache - Variable in class net.sf.basedb.util.StaticCache.CleanupTask
 
Cache() - Constructor for class net.sf.basedb.util.AnnotationUtil.Cache
 
cacheBase - Variable in class net.sf.basedb.clients.web.servlet.PlotServlet
 
cacheChildNodes(Node) - Method in class net.sf.basedb.util.overview.GenericOverview
 
cacheControl - Variable in class net.sf.basedb.clients.web.servlet.CacheControlFilter
 
cacheControl - Variable in class net.sf.basedb.clients.web.servlet.ImageRemapFilter
 
CacheControlFilter - Class in net.sf.basedb.clients.web.servlet
This is a filter that sets the "Cache-Control" header in the http response.
CacheControlFilter() - Constructor for class net.sf.basedb.clients.web.servlet.CacheControlFilter
 
cachedPaths - Variable in class net.sf.basedb.core.Metadata
 
cachedRssNews - Variable in class net.sf.basedb.clients.web.servlet.RssNewsFeed
 
CacheEntry(long, Set<Integer>) - Constructor for class net.sf.basedb.util.listable.TransformCache.CacheEntry
 
cacheFile - Variable in class net.sf.basedb.util.StreamCacher
 
cacheKey - Variable in class net.sf.basedb.util.overview.cache.DirectionalCacheKey
 
cacheKey - Variable in class net.sf.basedb.util.overview.cache.IndexedCacheKey
 
CacheKey(int, String) - Constructor for class net.sf.basedb.util.units.UnitCache.CacheKey
 
CacheKey(String, Item, Item, SyncFilter.SourceItemTransform, SortedSet<Integer>) - Constructor for class net.sf.basedb.util.listable.TransformCache.CacheKey
 
cacheNewNode(Object, Node, ChildNodeDirection) - Method in class net.sf.basedb.util.overview.node.NodeFactory
Store a node in the node cache if the current overview context supports caching.
cacheOut - Variable in class net.sf.basedb.util.StreamCacher
 
cacheQuery(String, Query<?>) - Method in class net.sf.basedb.core.hibernate.AbstractQueryCache
Cache a query.
cacheRegion - Variable in class net.sf.basedb.util.listable.SourceItemTransformerWithCache
 
cacheRegion - Variable in class net.sf.basedb.util.listable.SourceItemTransformerWithCache.TransformerWithCache
 
cacheRegion - Variable in class net.sf.basedb.util.listable.TransformCache.CacheKey
 
cacheReporterData() - Method in class net.sf.basedb.util.export.spotdata.AbstractBioAssaySetExporter
Loads and caches reporter data in an internal structure for quick access.
cacheResults - Variable in class net.sf.basedb.core.AbstractHqlQuery
If the results should be cached or not.
calculateBoxAndWhiskerStatistics(List<Float>) - Method in class net.sf.basedb.clients.web.servlet.ExperimentExplorerPlotServlet
Creates a box-and-whisker data holder for the given list of values.
calculateIntensities(RawData) - Method in interface net.sf.basedb.util.IntensityCalculator
Calculate intensities from a raw data spot.
calculateIntensities(RawData) - Method in class net.sf.basedb.util.IntensityCalculatorUtil.JepIntensityCalculatorImpl
 
calculateWeights(List<LowessNormalization.SpotData>, double, List<Double>) - Static method in class net.sf.basedb.plugins.LowessNormalization
 
CalendarButton - Class in net.sf.basedb.clients.web.taglib
A special button tag that is used to display a "Calendar" button that opens a popup for selecting a date and time.
CalendarButton() - Constructor for class net.sf.basedb.clients.web.taglib.CalendarButton
 
call() - Method in class net.sf.basedb.core.QueryExecutor.FutureItem
 
call() - Method in class net.sf.basedb.core.QueryExecutor.FutureResultSet
 
call() - Method in class net.sf.basedb.core.QueryExecutor.FutureScrollIterator
 
call() - Method in class net.sf.basedb.core.QueryExecutor.FutureUpdate
 
call() - Method in class net.sf.basedb.plugins.LowessNormalization.CallableWorker
 
CallableWorker(List<LowessNormalization.SpotData>, MACalculator, float, float, int, int) - Constructor for class net.sf.basedb.plugins.LowessNormalization.CallableWorker
 
calledFrom - Variable in class net.sf.basedb.util.StaticCache.State
 
canAdd(BioWell) - Method in enum class net.sf.basedb.core.BioWell.LockMode
Is it allowed to add (a different) biomaterial to the well?
canAdd(BioWellData) - Method in enum class net.sf.basedb.core.BioWell.LockMode
 
canAddBioMaterial() - Method in class net.sf.basedb.core.BioWell
Check if it is possible to add/change biomaterial in this well.
cancel() - Method in class net.sf.basedb.clients.jobagent.JobQueueChecker
 
cancel() - Method in interface net.sf.basedb.core.QueryExecutor.Cancelable
 
cancel() - Method in class net.sf.basedb.core.QueryExecutor.CancelableSession
 
cancel() - Method in class net.sf.basedb.core.QueryExecutor.CancelableStatelessSession
 
cancel() - Method in class net.sf.basedb.core.QueryExecutor.CancelableStatement
 
cancel() - Method in class net.sf.basedb.util.timer.ThreadTimerTask
 
CancelableSession(Session) - Constructor for class net.sf.basedb.core.QueryExecutor.CancelableSession
 
CancelableStatelessSession(StatelessSession) - Constructor for class net.sf.basedb.core.QueryExecutor.CancelableStatelessSession
 
CancelableStatement(Statement) - Constructor for class net.sf.basedb.core.QueryExecutor.CancelableStatement
 
cancelQuery() - Method in class net.sf.basedb.core.hibernate.SessionWrapper
 
cancelQuery() - Method in class net.sf.basedb.core.hibernate.StatelessSessionWrapper
Cancels the currently executing query in the same manner as Session.cancelQuery().
canClear(BioWell) - Method in enum class net.sf.basedb.core.BioWell.LockMode
Is it allowed to clear a well from biomaterial?
canClear(BioWellData) - Method in enum class net.sf.basedb.core.BioWell.LockMode
 
canClearBioMaterial() - Method in class net.sf.basedb.core.BioWell
Check if it is possible to clear the current biomaterial in this well.
canEnumerate - Variable in enum class net.sf.basedb.core.Type
 
canEnumerate() - Method in enum class net.sf.basedb.core.Type
If it makes sense to use values of this type as an enumeration to choose from.
canLogValues(String) - Method in class net.sf.basedb.core.log.EntityLogOptions
Check if it is allowed to log the old and new values of a modified property.
canUseColoring - Variable in enum class net.sf.basedb.core.Formula.Type
 
canUseColoring() - Method in enum class net.sf.basedb.core.Formula.Type
If a formula of this type can use coloring or not.
CAPACITANCE - Static variable in class net.sf.basedb.core.Quantity
The id for the Quantity object representing capacitance.
CaseExpression - Class in net.sf.basedb.core.query
An SQL case expression:
CaseExpression(Expression, WhenStatement...) - Constructor for class net.sf.basedb.core.query.CaseExpression
 
caseInsensitive - Variable in enum class net.sf.basedb.core.FeatureIdentificationMethod
If the feature identifiers may be affect by case sensitivity at the database level or not.
caseInsensitive - Variable in class net.sf.basedb.core.RawDataBatcher
If case should be ignored when comparing strings (external ID)
caseInsensitive() - Method in enum class net.sf.basedb.core.FeatureIdentificationMethod
Return TRUE if this identification method can be case insensitive.
caseInsensitiveComparison() - Method in interface net.sf.basedb.core.dbengine.DbEngine
If the database does case sensitive or case insensitive string comparison in expressions.
caseInsensitiveComparison() - Method in class net.sf.basedb.core.dbengine.DefaultDbEngine
Returns TRUE.
caseInsensitiveComparison() - Method in class net.sf.basedb.core.dbengine.MySQLEngine
Returns TRUE.
caseInsensitiveComparison() - Method in class net.sf.basedb.core.dbengine.PostgresDbEngine
Returns FALSE.
caseWhen(Expression, WhenStatement...) - Static method in class net.sf.basedb.core.query.Expressions
Create a conditional CASE-WHEN expression:
castToDate(String) - Method in class net.sf.basedb.core.dbengine.AbstractDbEngine
 
castToDate(String) - Method in interface net.sf.basedb.core.dbengine.DbEngine
Get a function that casts a date/timestamp to a date (eg. no time should be included in the result).
catalog - Variable in class net.sf.basedb.core.hibernate.SchemaExistsWork
 
catalog - Variable in class net.sf.basedb.core.hibernate.TableExistsWork
 
categories - Variable in class net.sf.basedb.core.data.AnnotationTypeData
 
category - Variable in class net.sf.basedb.clients.web.SubContext
 
categoryColumnMapping - Static variable in class net.sf.basedb.plugins.batchimport.AnnotationTypeImporter
Column mapping parameter for assigning annotation types to categories.
categoryMapper - Variable in class net.sf.basedb.plugins.batchimport.AnnotationTypeImporter
 
CdfFileReporterImporter - Class in net.sf.basedb.plugins
This plug-in can import probesets from Affymetrix CDF files as reporters.
CdfFileReporterImporter() - Constructor for class net.sf.basedb.plugins.CdfFileReporterImporter
Constructor should be empty.
CdfValidationAction - Class in net.sf.basedb.util.affymetrix
Action for validation of CDF files in a file set.
CdfValidationAction(DbControl, ArrayDesign) - Constructor for class net.sf.basedb.util.affymetrix.CdfValidationAction
Create a new action.
CdfValidationFactory - Class in net.sf.basedb.util.affymetrix
Action factory for creating CDF file validators.
CdfValidationFactory() - Constructor for class net.sf.basedb.util.affymetrix.CdfValidationFactory
 
CdfValidator - Class in net.sf.basedb.util.affymetrix
Helper class for working with Affymetrix CDF files.
CdfValidator() - Constructor for class net.sf.basedb.util.affymetrix.CdfValidator
Create a new instance.
Cell - Class in net.sf.basedb.clients.web.taglib.table
This tag defines a new cell in a row.
Cell() - Constructor for class net.sf.basedb.clients.web.taglib.table.Cell
 
cellClass - Variable in class net.sf.basedb.clients.web.extensions.list.AbstractListColumnBean
 
cellClass - Variable in class net.sf.basedb.clients.web.extensions.list.PropertyPathActionFactory
 
cellStyle - Variable in class net.sf.basedb.clients.web.extensions.list.AbstractListColumnBean
 
cellStyle - Variable in class net.sf.basedb.clients.web.extensions.list.PropertyPathActionFactory
 
CellStyleCreator - Class in net.sf.basedb.util.excel
Helper class for keeping track of formatting styles that has been created for given Excel worksheet.
CellStyleCreator(Workbook) - Constructor for class net.sf.basedb.util.excel.CellStyleCreator
Creates a new style creator for the given Excel workbook.
cellType - Variable in class net.sf.basedb.util.excel.XlsxToCsvUtil.CellTypeWithInfo
 
CellTypeWithInfo() - Constructor for class net.sf.basedb.util.excel.XlsxToCsvUtil.CellTypeWithInfo
 
CellValue - Class in net.sf.basedb.clients.web.taglib.table
This tag adds a value to a cell in a row.
CellValue() - Constructor for class net.sf.basedb.clients.web.taglib.table.CellValue
 
CelValidationAction - Class in net.sf.basedb.util.affymetrix
Action for validation of CEL files in a file set.
CelValidationAction(DbControl, RawBioAssay) - Constructor for class net.sf.basedb.util.affymetrix.CelValidationAction
Create a new action.
CelValidationFactory - Class in net.sf.basedb.util.affymetrix
Action factory for creating CEL file validators.
CelValidationFactory() - Constructor for class net.sf.basedb.util.affymetrix.CelValidationFactory
 
CelValidator - Class in net.sf.basedb.util.affymetrix
Helper class for working with Affymetrix CEL files.
CelValidator() - Constructor for class net.sf.basedb.util.affymetrix.CelValidator
Create a new instance.
cfg - Static variable in class net.sf.basedb.core.HibernateUtil
The Hibernate configuration, including all mappings.
cfg - Variable in class net.sf.basedb.core.MigrateRbaToDba.SubtypeMapping
 
CFResultIterator(SqlResultIterator, SqlResultIterator) - Constructor for class net.sf.basedb.clients.web.servlet.PlotServlet.CFResultIterator
 
CFSqlResult() - Constructor for class net.sf.basedb.clients.web.servlet.PlotServlet.CFSqlResult
 
ch - Variable in class net.sf.basedb.util.importer.spotdata.MatrixSpotIntensityEventHandler
 
ch - Variable in class net.sf.basedb.util.importer.spotdata.SerialSpotIntensityEventHandler
 
ch1 - Variable in class net.sf.basedb.plugins.LowessNormalization.SpotData
 
ch1 - Variable in class net.sf.basedb.plugins.MedianRatioNormalization.SpotData
 
ch2 - Variable in class net.sf.basedb.plugins.LowessNormalization.SpotData
 
ch2 - Variable in class net.sf.basedb.plugins.MedianRatioNormalization.SpotData
 
chain - Variable in class net.sf.basedb.util.AnnotationUtil.AnnotatableWrapper
 
chain - Variable in class net.sf.basedb.util.listable.SourceItemTransformerChain
 
CHAIN_ORDER - Static variable in class net.sf.basedb.core.SyncFilter
 
chained - Variable in class net.sf.basedb.core.Job.ProgressReporterImpl
 
ChainedFilter(List<QueryRuntimeFilter>) - Constructor for class net.sf.basedb.core.QueryRuntimeFilterFactory.ChainedFilter
Create a new ChainedFilter object.
ChainedFilter(QueryRuntimeFilter...) - Constructor for class net.sf.basedb.core.QueryRuntimeFilterFactory.ChainedFilter
Create a new ChainedFilter object.
chainedProgress - Variable in class net.sf.basedb.util.export.spotdata.BfsExporter
 
ChainedProgressReporter - Class in net.sf.basedb.util
An implementation of the ProgressReporter interface that chains to another progress reporter while recalculating the percentage values.
ChainedProgressReporter(ProgressReporter) - Constructor for class net.sf.basedb.util.ChainedProgressReporter
Create a new chained progress reporter.
change - Variable in class net.sf.basedb.clients.web.SubContext
 
Change(ChangeType) - Constructor for enum class net.sf.basedb.core.AnnotationBatcher.Change
 
changeCurrentSubContext(DbControl, Item, ServletRequest) - Static method in class net.sf.basedb.clients.web.Base
Change the current subcontext depending on the parameters in the request.
ChangeHistory - Class in net.sf.basedb.core
 
ChangeHistory(ChangeHistoryDetailData) - Constructor for class net.sf.basedb.core.ChangeHistory
 
CHANGEHISTORY - Enum constant in enum class net.sf.basedb.core.Item
The item is a ChangeHistory entry.
CHANGEHISTORY_VALUES - Enum constant in enum class net.sf.basedb.core.Item
Virtual item representing the new and old values column in ChangeHistory which need special access permissions.
ChangeHistory.TransactionInfo - Class in net.sf.basedb.core
Holds information about a single transaction.
ChangeHistoryData - Class in net.sf.basedb.core.data
Represents the changes made in a single transaction.
ChangeHistoryData() - Constructor for class net.sf.basedb.core.data.ChangeHistoryData
 
ChangeHistoryDetailData - Class in net.sf.basedb.core.data
Represents a change (creation/update/deletion) made to a single entity in a transaction.
ChangeHistoryDetailData() - Constructor for class net.sf.basedb.core.data.ChangeHistoryDetailData
 
ChangeHistoryDetailLoader - Class in net.sf.basedb.clients.web.plugins
Data loader implementation for old and new values in the change history which are protected by special permissions.
ChangeHistoryDetailLoader(boolean) - Constructor for class net.sf.basedb.clients.web.plugins.ChangeHistoryDetailLoader
 
ChangeHistoryItemLoader - Class in net.sf.basedb.clients.web.plugins
Data loader implementation for loading the changed item.
ChangeHistoryItemLoader() - Constructor for class net.sf.basedb.clients.web.plugins.ChangeHistoryItemLoader
 
ChangeHistoryUtil - Class in net.sf.basedb.clients.web
Utility class for working with change history.
ChangeHistoryUtil() - Constructor for class net.sf.basedb.clients.web.ChangeHistoryUtil
 
changeHost(URI) - Method in class net.sf.basedb.util.uri.ConnectionParameters
If the connection parameters include a specific host:port or root path a new URI is created were the host:port is replaced and the root path is added to the URI path.
changeInfo - Variable in class net.sf.basedb.core.data.ChangeHistoryDetailData
 
changeReferenceFactorAndOffset(double, double) - Method in class net.sf.basedb.core.Unit
Changes the factor and offset used for converting values in this unit into the reference unit.
changeReferenceFactorAndOffset(SessionControl, Session, UnitData, double, double) - Static method in class net.sf.basedb.core.Unit
 
changes - Variable in class net.sf.basedb.core.log.LoggingInterceptor
 
changeType - Variable in class net.sf.basedb.core.data.ChangeHistoryDetailData
 
changeType - Variable in class net.sf.basedb.core.log.EntityDetails
 
changeType - Variable in class net.sf.basedb.core.log.ManualLogEntry
 
ChangeType - Enum Class in net.sf.basedb.core.log
Enumeration that represents the type of change that has happened.
ChangeType(int, String) - Constructor for enum class net.sf.basedb.core.log.ChangeType
 
ChangeTypeFormatter - Class in net.sf.basedb.core.log
Formatter implementation that converts an integer into it's ChangeType representation and the uses name() as the formatted value.
ChangeTypeFormatter() - Constructor for class net.sf.basedb.core.log.ChangeTypeFormatter
Create a new formatter.
ChangeTypeFormatter(String) - Constructor for class net.sf.basedb.core.log.ChangeTypeFormatter
Create a new formatter.
channel - Variable in class net.sf.basedb.core.RawDataProperty
 
channel(int) - Method in class net.sf.basedb.util.jep.ChannelFunction
Get the value of the specified channel of the current sql result.
channel(int) - Method in class net.sf.basedb.util.jep.RawChannelFunction
Get the value of the specified channel of the current sql result.
channel(int, String, Formatter<?>) - Static method in class net.sf.basedb.util.export.spotdata.ExportableFieldFactory
Create a simple dynamic field that exports the channel intensity of the given channel.
ChannelFunction - Class in net.sf.basedb.util.jep
A JEP function class that adds a ch(int) function to a JEP expression parser.
ChannelFunction() - Constructor for class net.sf.basedb.util.jep.ChannelFunction
Create a new instance of this function.
ChannelFunction(int[], IntensityTransform) - Constructor for class net.sf.basedb.util.jep.ChannelFunction
Create a new instance of this function which can be used to dynamically evaluate expressions.
channelIntensity(int) - Static method in class net.sf.basedb.core.VirtualColumn
Get a column that returns the intensity values for a channel.
channelParameters - Variable in class net.sf.basedb.plugins.JepIntensityTransformer
 
channelRaw(int) - Static method in class net.sf.basedb.core.VirtualColumn
Get a column that stores the raw spot value for a channel.
channels - Variable in class net.sf.basedb.core.data.FormulaData
 
channels - Variable in class net.sf.basedb.core.data.PlatformData
 
channels - Variable in class net.sf.basedb.core.data.PlatformVariantData
 
channels - Variable in class net.sf.basedb.core.RawDataType
 
channels - Variable in class net.sf.basedb.util.importer.spotdata.GenericIntensityParser
 
channels - Variable in class net.sf.basedb.util.importer.spotdata.SecondPassSectionSpotsParser
 
channelToIndex - Variable in class net.sf.basedb.util.jep.ChannelFunction
 
channelToIndex - Variable in class net.sf.basedb.util.jep.RawChannelFunction
 
CHAR_ESCAPE - Variable in class net.sf.basedb.core.migrate.postgres.PostgresResultWriterFactory
 
char64(char) - Static method in class net.sf.basedb.util.bcrypt.BCrypt
Look up the 3 bits base64-encoded by the specified character, range-checking againt conversion table
characterEncoding - Variable in class net.sf.basedb.clients.web.servlet.CharacterEncodingFilter
 
CharacterEncodingFilter - Class in net.sf.basedb.clients.web.servlet
This is a filter that sets the character encoding for both the request and the response.
CharacterEncodingFilter() - Constructor for class net.sf.basedb.clients.web.servlet.CharacterEncodingFilter
 
characterSetColumnMapping - Static variable in class net.sf.basedb.plugins.batchimport.FileImporter
 
characterSetMapper - Variable in class net.sf.basedb.plugins.batchimport.FileImporter
 
CHARGE - Static variable in class net.sf.basedb.core.Quantity
The id for the Quantity object representing electrical charge.
charset - Variable in class net.sf.basedb.clients.web.fileupload.FileUpload
The charset used for decoding header lines.
charset - Variable in class net.sf.basedb.core.data.FileData
 
charset - Variable in class net.sf.basedb.util.charset.CharsetDetector
 
charset - Variable in class net.sf.basedb.util.excel.XlsxToCsvUtil
 
charset - Variable in class net.sf.basedb.util.FileImportInputStream
 
charset - Variable in class net.sf.basedb.util.gtf.GtfInputStream
 
charset - Variable in class net.sf.basedb.util.uri.UriMetadata
 
CHARSET_PARAMETER - Static variable in class net.sf.basedb.plugins.util.Parameters
The name of the parameter that is created by Parameters.charsetParameter(String, String, String, boolean)
CharsetDetector - Class in net.sf.basedb.util.charset
Utility class for testing if a text stream can be parsed using a given character set.
CharsetDetector(Charset) - Constructor for class net.sf.basedb.util.charset.CharsetDetector
Create a detector for the given character set that only detects technical issues.
CharsetDetector(Charset, StringDetector) - Constructor for class net.sf.basedb.util.charset.CharsetDetector
Create a detector for the given character set that uses technical an content-based detection.
charsetParameter(String, String, String) - Static method in class net.sf.basedb.plugins.util.Parameters
 
charsetParameter(String, String, String, boolean) - Static method in class net.sf.basedb.plugins.util.Parameters
Parameter definition that asks for the character encoding used in the file that is imported.
CharsetTesterThread(Charset) - Constructor for class net.sf.basedb.core.File.CharsetTesterThread
 
charsetType - Static variable in class net.sf.basedb.plugins.util.Parameters
Enumerates all available character sets.
CharsetUtil - Class in net.sf.basedb.util.charset
Helper class for working with charsets and enabling the UTF-8 with fallback charsets: X-UTF-8_with_ISO-8859-1_fallback X-UTF-8_with_windows-1252_fallback
CharsetUtil() - Constructor for class net.sf.basedb.util.charset.CharsetUtil
 
charsetWithFallbacksType - Static variable in class net.sf.basedb.plugins.util.Parameters
Enumerates all available character sets and also inlcude fallback type.
chart - Variable in class net.sf.basedb.util.plot.HistogramPlot
 
chart - Variable in class net.sf.basedb.util.plot.ScatterPlot
 
checkAbortAndDelay() - Method in class net.sf.basedb.clients.web.fileupload.FileUpload
Check if upload has been aborted.
checkAllowedSource(BioMaterial, boolean) - Method in class net.sf.basedb.core.BioMaterialEvent
Check if the biomaterial is allowed as a source.
checkAndCreateTables() - Method in class net.sf.basedb.core.BioAssaySet
 
checkAndLoadClass(ClassLoader, String, boolean, Class<C>, Class<?>...) - Static method in class net.sf.basedb.util.ClassUtil
Check if a specified class exists and, optionally, if it has public no-argument constructor and implements a set of specific interfaces or superclasses.
checkBatchAnnotatableUsage(boolean, boolean) - Method in class net.sf.basedb.core.BasicItem
Annotatable items that are used with the AnnotationBatcher must not call Annotatable.getAnnotationSet() in the same transaction.
checkBioAssay(DbControl, int, int) - Method in class net.sf.basedb.util.importer.spotdata.BaseFileInfo
Checks that the bioassay with the given id exists in the database.
checkBioMaterialInWell(DbControl, OverviewContext, Node, Node) - Static method in class net.sf.basedb.util.overview.validator.BioPlateValidator
Check that the main type and subtype of the biomaterial is matching the requirements of the bioplate type.
checkBoundary(byte[], int, byte[], int) - Method in class net.sf.basedb.clients.web.fileupload.FileUpload
Check if the given line matches the boundary.
checkClass(Class<?>, boolean, Class<?>...) - Static method in class net.sf.basedb.util.ClassUtil
Check if a specified class has public no-argument constructor and implements a set of specific interfaces or superclasses.
checkClosed() - Method in class net.sf.basedb.util.extensions.manager.ExtensionsFile.WriteableExtensionsFile
Check if the file has been closed and throws an IllegalStateException if it has.
checkColumnMapping(String, boolean, String) - Method in class net.sf.basedb.plugins.AbstractFlatFileImporter
Check if a column mapping is a valid mapping expression and optionally if it is complex mapping.
checkColumnMapping(FlatFileParser, String, boolean, String) - Method in class net.sf.basedb.plugins.AbstractFlatFileImporter
Checks the syntax column mapping and verifies that the given file parser has found the columns that are used in the file.
checkContext(DbControl, ItemQuery<PluginDefinition>, ItemQuery<PluginConfiguration>, GuiContext, Object) - Static method in class net.sf.basedb.util.ContextUtil
Call the InteractivePlugin.isInContext(GuiContext, Object) method for all plug-ins returned by the queries.
checkCoordinate(MappingCoordinate, int, PlateGeometryData, boolean) - Method in class net.sf.basedb.core.PlateMapping
Checks that the coordinate is within the bouds given by the mapping and geometry.
checkDerivedBioAssaySubtype(DbControl, OverviewContext, Node, Node) - Static method in class net.sf.basedb.util.overview.validator.DerivedBioAssayValidator
Check the subtype of the derived bioassay that is the parent to a child derived bioassay.
checked - Variable in class net.sf.basedb.clients.web.taglib.Input
TRUE if the input element is checked.
checkEntity(IdentifiableData) - Method in class net.sf.basedb.core.hibernate.EntityQueryWrapper
 
checkEntityArray(Object[]) - Method in class net.sf.basedb.core.hibernate.EntityQueryWrapper
 
checkEntityCollection(Collection<?>) - Method in class net.sf.basedb.core.hibernate.EntityQueryWrapper
 
checkExperimentArrayDesign(DbControl, OverviewContext, Node, ArrayDesign) - Method in class net.sf.basedb.util.overview.validator.ArrayDesignValidator
Check if an experiment has used more than one array design.
checkExtractOnBioAssay(DbControl, OverviewContext, Node, Node) - Method in class net.sf.basedb.util.overview.validator.ExtractValidator
 
checkExtractSubtype(DbControl, OverviewContext, Node, Node) - Static method in class net.sf.basedb.util.overview.validator.DerivedBioAssayValidator
Check the subtype of the extract that is the linked with a derived bioassay.
checkExtractSubtype(DbControl, OverviewContext, Node, Node) - Static method in class net.sf.basedb.util.overview.validator.PhysicalBioAssayValidator
Check the subtype of the extract that is the parent to a physical bioassay.
checkExtractTag(DbControl, OverviewContext, Node, Node) - Static method in class net.sf.basedb.util.overview.validator.ExtractValidator
Check the tag of the child extract in relation to a parent extract.
checkForInvalidNumberOperation() - Method in class net.sf.basedb.core.dbengine.AbstractDbEngine
Returns FALSE.
checkForInvalidNumberOperation() - Method in interface net.sf.basedb.core.dbengine.DbEngine
If we need to check for invalid arguments to numerical functions to avoid exceptions from the database.
checkForInvalidNumberOperation() - Method in class net.sf.basedb.core.dbengine.PostgresDbEngine
Returns TRUE.
checkForJobs() - Method in class net.sf.basedb.clients.jobagent.JobQueueChecker
 
checkForSignals() - Method in class net.sf.basedb.core.signal.EnhancedThreadSignalHandler
If at least one signal has been received a SignalReceivedException is thrown.
checkForSignals() - Method in class net.sf.basedb.core.signal.ProgressReporterSignalHandler
If at least one signal has been received a SignalReceivedException is thrown.
checkIfDifferent(Object, Unit) - Method in class net.sf.basedb.core.Annotation
Check if the given value is different from the values already stored in this annotation.
checkIfDifferent(List<?>, Unit) - Method in class net.sf.basedb.core.Annotation
Check if the given values are different from the values already stored in this annotation.
checkIfReportersExists(FusionCDFData, ReporterBatcher, boolean, ReporterType, ProgressReporter) - Method in class net.sf.basedb.util.affymetrix.CdfValidator
Verify if probesets in a CDF file exists as reporters and optionally create those that doesn't exists.
checkImportable(SessionControl, PluginDefinition, PluginConfiguration, File, String, GuiContext, Object) - Static method in class net.sf.basedb.util.AutoDetectFileFormat
 
checkInstallation(DbControl, Collection<PluginInfo>) - Static method in class net.sf.basedb.core.PluginDefinition
Check the installation status of the given list of plug-ins.
checkInternalJobQueue() - Method in class net.sf.basedb.core.InternalJobQueue
 
checkInterrupted() - Static method in class net.sf.basedb.core.signal.ThreadSignalHandler
Utility method to check if the current thread has been interrupted and (may) throw a SignalException if it has.
checkInterval - Variable in class net.sf.basedb.clients.jobagent.Agent
 
checkItemType(Item) - Method in class net.sf.basedb.core.ItemSubtype
Check if this subtype can be used on items of the given type.
checkJdbcDriver(String, String, String) - Static method in class net.sf.basedb.core.HibernateUtil
Check that a JDBC driver is registered and try to load a driver if not.
checkLine(int, String) - Method in class net.sf.basedb.util.charset.SimpleStringDetector
 
checkLine(int, String) - Method in interface net.sf.basedb.util.charset.StringDetector
Check the given line.
checkLocked(String) - Method in class net.sf.basedb.core.Application.StartupOptions
 
checkLocked(String) - Method in class net.sf.basedb.core.ServiceSessionControl.SessionFactoryConfiguration
Check that the
checkMagicNumber(PushbackInputStream, byte[]) - Static method in class net.sf.basedb.util.FileUtil
Take a peek at an input stream and check if the first few bytes matches the bCheck parameter.
checkManualMembersAllowed() - Method in class net.sf.basedb.core.ItemList
 
checkMax(int, String, int) - Static method in class net.sf.basedb.core.IntegerUtil
Check that an integer is equal or lower than a maximum value.
checkMd5 - Variable in class net.sf.basedb.core.File.UploadStream
If the md5 should be checked or not.
checkMemberType(Collection<ItemList>) - Method in class net.sf.basedb.core.ItemList
Checks that the lists have the same member type as this list.
checkMemberType(Item) - Method in class net.sf.basedb.core.ItemList
Checks if the other type is the same type as the member type of this list.
checkMin(int, String, int) - Static method in class net.sf.basedb.core.IntegerUtil
Check that an integer is equal or greater than a minimum value.
checkMinMax(int, String, int, int) - Static method in class net.sf.basedb.core.IntegerUtil
Check that an integer is equal or between a minimum and a maximum value.
checkModified() - Method in class net.sf.basedb.util.extensions.manager.ExtensionsFile
Check if the underlying file has been modified since it was last processed.
checkNext - Variable in class net.sf.basedb.core.DynamicResultIterator
 
checkNext - Variable in class net.sf.basedb.util.extensions.ActionIterator
 
checkNumberOfParameters(int) - Method in class net.sf.basedb.util.jep.ChannelFunction
 
checkNumberOfParameters(int) - Method in class net.sf.basedb.util.jep.ExtraValueFunction
 
checkNumberOfParameters(int) - Method in class net.sf.basedb.util.jep.FunctionSafeJep.UnknownFunction
 
checkNumberOfParameters(int) - Method in class net.sf.basedb.util.jep.InReporterListFunction
 
checkNumberOfParameters(int) - Method in class net.sf.basedb.util.jep.LeftFunction
 
checkNumberOfParameters(int) - Method in class net.sf.basedb.util.jep.Log2Function
 
checkNumberOfParameters(int) - Method in class net.sf.basedb.util.jep.MeanFunction
 
checkNumberOfParameters(int) - Method in class net.sf.basedb.util.jep.NotInReporterListFunction
 
checkNumberOfParameters(int) - Method in class net.sf.basedb.util.jep.PositionFunction
 
checkNumberOfParameters(int) - Method in class net.sf.basedb.util.jep.RawChannelFunction
 
checkNumberOfParameters(int) - Method in class net.sf.basedb.util.jep.RawFunction
 
checkNumberOfParameters(int) - Method in class net.sf.basedb.util.jep.ReporterFunction
 
checkNumberOfParameters(int) - Method in class net.sf.basedb.util.jep.ScoreFunction
 
checkNumberOfParameters(int) - Method in class net.sf.basedb.util.jep.SimpleJepFunction
 
checkNumberOfParameters(int) - Method in class net.sf.basedb.util.parser.ColFunction
 
checkNumberOfParameters(int) - Method in class net.sf.basedb.util.parser.DataNoFunction
 
checkNumberOfParameters(int) - Method in class net.sf.basedb.util.parser.DefaultItemFunction
 
checkNumberOfParameters(int) - Method in class net.sf.basedb.util.parser.LineNoFunction
 
checkParentBioSourceSubtype(DbControl, OverviewContext, Node, Node) - Static method in class net.sf.basedb.util.overview.validator.SampleValidator
Check the subtype of the biosurce that is the parent to a sample.
checkParentExtractSubtype(DbControl, OverviewContext, Node, Node) - Static method in class net.sf.basedb.util.overview.validator.ExtractValidator
Check the subtype of the extract that is the parent to another extract.
checkParentSampleSubtype(DbControl, OverviewContext, Node, Node) - Static method in class net.sf.basedb.util.overview.validator.ExtractValidator
Check the subtype of the sample that is the parent to an extract.
checkParentSampleSubtype(DbControl, OverviewContext, Node, Node) - Static method in class net.sf.basedb.util.overview.validator.SampleValidator
Check the subtype of the sample that is the parent to another sample.
checkPassword(String, String) - Static method in class net.sf.basedb.core.User
Check the plain-text password against the crypted password.
checkPermission(Permission) - Method in class net.sf.basedb.clients.web.extensions.ExtensionsControl
 
checkPermission(Permission) - Method in interface net.sf.basedb.core.AccessControlled
Check if the logged in user has the desired permission on the item, otherwise throw an exception.
checkPermission(Permission) - Method in class net.sf.basedb.core.BasicBatcher
Checks if the logged in user has the specified permission on this item.
checkPermission(Permission) - Method in class net.sf.basedb.core.BasicItem
Checks if the logged in user has the specified permission on this item.
checkPermission(Permission) - Method in class net.sf.basedb.core.BioMaterialEventSource
 
checkPermission(Permission) - Method in class net.sf.basedb.core.Coloring
 
checkPermission(Permission, String) - Method in class net.sf.basedb.clients.web.extensions.ExtensionsControl
For checking the permission and adding a custom message to the PermissionDeniedException if the required permission is missing.
checkPhysicalBioAssaySubtype(DbControl, OverviewContext, Node, Node) - Static method in class net.sf.basedb.util.overview.validator.DerivedBioAssayValidator
Check the subtype of the physical bioassay that is the parent to a derived bioassay.
checkpw(String, String) - Static method in class net.sf.basedb.util.bcrypt.BCrypt
Check that a plaintext password matches a previously hashed one
checkSameArrayDesign(Collection<RawBioAssay>, boolean) - Static method in class net.sf.basedb.util.IntensityCalculatorUtil
 
checkSuperclass - Variable in class net.sf.basedb.util.formatter.MultiFormatter
 
checkSyncFiltersAllowed() - Method in class net.sf.basedb.core.ItemList
 
checkTimeoutOnRemoteSlots() - Method in class net.sf.basedb.clients.jobagent.slotmanager.MasterSlotManager
Check the remote slots to see if they have timed out.
checkUniqueFields(String, String) - Method in class net.sf.basedb.plugins.executor.BaseFileExporterSupport
 
checkUniqueFields(String, String) - Method in class net.sf.basedb.plugins.executor.BfsExporterSupport
 
checkUnsafeScriptableUsage(Extension<?>) - Method in class net.sf.basedb.clients.web.extensions.ExtensionsControl
Checks if the given extension may violate the 'Content Security Policy' for the server.
checkUnsafeScriptableUsage(ExtensionsFile) - Method in class net.sf.basedb.clients.web.extensions.ExtensionsControl
Checks if the given extensions file contain any extensions that may violate the 'Content Security Policy' for the server.
checkUnsafeScriptableUsageInternal(Extension<?>) - Method in class net.sf.basedb.clients.web.extensions.ExtensionsControl
 
checkValues - Variable in class net.sf.basedb.core.ParameterType
 
child - Variable in class net.sf.basedb.clients.web.servlet.PlotServlet.CFResultIterator
 
child - Variable in class net.sf.basedb.clients.web.servlet.PlotServlet.CFSqlResult
 
child - Variable in class net.sf.basedb.core.QueryRuntimeFilterFactory.ChildFilter
The item type of the child item.
child - Variable in class net.sf.basedb.util.importer.spotdata.BaseFileInfo.ChildBioAssay
 
child - Variable in class net.sf.basedb.util.importer.spotdata.SecondPassSectionSpotsParser
 
CHILD_DESCRIPTION - Static variable in class net.sf.basedb.core.plugin.AbstractAnalysisPlugin
The name of the parameter that asks for the description of the child bioassay set.
CHILD_DESCRIPTION - Static variable in class net.sf.basedb.plugins.util.Parameters
The name of the parameter that asks is created by Parameters.childDescriptionParameter(String, String, String)
CHILD_NAME - Static variable in class net.sf.basedb.core.plugin.AbstractAnalysisPlugin
The name of the parameter that asks for the name of the child bioassay set.
CHILD_NAME - Static variable in class net.sf.basedb.plugins.util.Parameters
The name of the parameter that is created by Parameters.childNameParameter(String, String, String)
CHILD_TO_PARENT - Enum constant in enum class net.sf.basedb.core.SyncFilter.SourceItemTransform
Source items are transformed to parent items.
CHILD_TO_PARENT - Static variable in class net.sf.basedb.util.listable.ToBioSourceSourceItemTransformerFactory
 
CHILD_TO_PARENT - Static variable in class net.sf.basedb.util.listable.ToDerivedBioAssaySourceItemTransformerFactory
 
CHILD_TO_PARENT - Static variable in class net.sf.basedb.util.listable.ToExtractSourceItemTransformerFactory
 
CHILD_TO_PARENT - Static variable in class net.sf.basedb.util.listable.ToPhysicalBioAssaySourceItemTransformerFactory
 
CHILD_TO_PARENT - Static variable in class net.sf.basedb.util.listable.ToRawBioAssaySourceItemTransformerFactory
 
CHILD_TO_PARENT - Static variable in class net.sf.basedb.util.listable.ToSampleSourceItemTransformerFactory
 
childAssays - Variable in class net.sf.basedb.util.importer.spotdata.BaseFileInfo
 
ChildBioAssay() - Constructor for class net.sf.basedb.util.importer.spotdata.BaseFileInfo.ChildBioAssay
Create a new object.
ChildBioAssay(int) - Constructor for class net.sf.basedb.util.importer.spotdata.BaseFileInfo.ChildBioAssay
Create a new object
childCreationEvents - Variable in class net.sf.basedb.core.data.BioMaterialData
 
childDescriptionParameter(String, String, String) - Static method in class net.sf.basedb.plugins.util.Parameters
Create a plugin parameter that asks for the description of the child bioassay set.
childErrors - Variable in class net.sf.basedb.util.overview.Node
 
ChildFilter(Item, Item) - Constructor for class net.sf.basedb.core.QueryRuntimeFilterFactory.ChildFilter
Create a new ChildFilter object.
childHasDifferentReporterPositionMapping - Variable in class net.sf.basedb.util.importer.spotdata.BaseFileInfo
 
childId - Variable in class net.sf.basedb.core.data.keyring.GroupGroups
 
ChildItem - Class in net.sf.basedb.core
An abstract base class for all items which are child items to a Shareable parent item.
ChildItem(BasicData) - Constructor for class net.sf.basedb.core.ChildItem
 
childIterator - Variable in class net.sf.basedb.util.Tree.EntryIterator
An iterator over the children of the root entry.
childNameParameter(String, String, String) - Static method in class net.sf.basedb.plugins.util.Parameters
Create a plugin parameter that asks for the name of the child bioassay set.
ChildNodeDirection - Enum Class in net.sf.basedb.util.overview.node
Represents the direction to use for loading child nodes in a tree.
ChildNodeDirection(boolean, boolean, boolean) - Constructor for enum class net.sf.basedb.util.overview.node.ChildNodeDirection
 
ChildNodeLoaderAction - Interface in net.sf.basedb.util.overview.extensions
Load and create child nodes for a given parent node.
children - Variable in class net.sf.basedb.core.data.BioAssayData
 
children - Variable in class net.sf.basedb.core.data.BioMaterialData
 
children - Variable in class net.sf.basedb.core.data.DerivedBioAssayData
 
children - Variable in class net.sf.basedb.core.data.GroupData
 
children - Variable in class net.sf.basedb.core.data.PlateData
 
children - Variable in class net.sf.basedb.util.listable.CollectExtracts
 
children - Variable in class net.sf.basedb.util.overview.Node
 
children - Variable in class net.sf.basedb.util.Tree.Entry
 
childrenLoaded - Variable in class net.sf.basedb.util.overview.Node
 
childReporterPositions - Variable in class net.sf.basedb.util.importer.spotdata.BaseFileInfo
 
childToParent - Variable in class net.sf.basedb.util.listable.AbstractSourceItemTransformerFactory
 
childToParentChain(List<SourceItemTransformer>, Item, Item, boolean) - Static method in class net.sf.basedb.util.listable.ToExtractSourceItemTransformerFactory
Utility method for creating the transformer chain from child items up to extracts.
childWarnings - Variable in class net.sf.basedb.util.overview.Node
 
chIndex - Variable in class net.sf.basedb.util.importer.spotdata.MatrixSpotIntensityEventHandler
 
chIndex - Variable in class net.sf.basedb.util.importer.spotdata.SerialSpotIntensityEventHandler
 
chooseClientAlias(String[], Principal[], Socket) - Method in class net.sf.basedb.util.ssl.StaticKeyManager
 
chooseServerAlias(String, Principal[], Socket) - Method in class net.sf.basedb.util.ssl.StaticKeyManager
 
CIRCULAR_REFERENCE - Static variable in class net.sf.basedb.util.overview.Validator
Validator rule that checks for circular references among pooled items.
CircularRefInfo(DbControl, Identifiable) - Constructor for class net.sf.basedb.core.Trashcan.CircularRefInfo
 
city - Variable in class net.sf.basedb.util.GeoLocation
 
classes - Static variable in class net.sf.basedb.core.ExtendedProperties
A list with the name attribute of all classes found in the xml file.
classLoader - Variable in class net.sf.basedb.core.ServiceSessionControl.SessionFactoryConfiguration
 
classLoader - Variable in class net.sf.basedb.util.extensions.Registry.RegisteredExtension
 
classLoader - Variable in class net.sf.basedb.util.extensions.Registry.RegisteredExtensionPoint
 
classLoaders - Variable in class net.sf.basedb.util.extensions.xml.XmlLoader
 
classLoaders - Static variable in class net.sf.basedb.util.JarClassLoader
A map of all loaded class loaders.
ClassLocal<E> - Class in net.sf.basedb.util
This class is a similar to the JDK ThreadLocal class, but stores one object per class instead of one object per thread.
ClassLocal() - Constructor for class net.sf.basedb.util.ClassLocal
Create a new ClassLocal object.
ClassMapErrorHandler - Class in net.sf.basedb.util.error
Error handler that allows the registration of one or more error handler for subclasses to Throwable.
ClassMapErrorHandler(ErrorHandler) - Constructor for class net.sf.basedb.util.error.ClassMapErrorHandler
Create a new ClassMapErrorHandler.
classMetadata - Variable in class net.sf.basedb.core.Metadata
 
className - Variable in class net.sf.basedb.core.data.PluginDefinitionData
 
className - Variable in class net.sf.basedb.util.extensions.manager.PluginInfoKey
 
className - Variable in class net.sf.basedb.util.extensions.xml.PluginInfo
 
classNameToPath(String) - Method in class net.sf.basedb.util.JarClassLoader
Convert a class name to a file path.
classPath - Variable in class net.sf.basedb.util.JarClassLoader
Contains mappings from class names to the JAR file in which the class implementation can be found.
ClassUtil - Class in net.sf.basedb.util
Utility class for Class objects.
ClassUtil() - Constructor for class net.sf.basedb.util.ClassUtil
 
clazz - Variable in class net.sf.basedb.clients.web.extensions.list.AbstractListColumnBean
 
clazz - Variable in class net.sf.basedb.clients.web.extensions.list.PropertyPathActionFactory
 
clazz - Variable in class net.sf.basedb.clients.web.extensions.login.FieldInfo
 
clazz - Variable in class net.sf.basedb.clients.web.extensions.menu.FixedMenuItemFactory
 
clazz - Variable in class net.sf.basedb.clients.web.extensions.menu.MenuItemBean
 
clazz - Variable in class net.sf.basedb.clients.web.extensions.tabcontrol.FixedTabFactory
 
clazz - Variable in class net.sf.basedb.clients.web.extensions.tabcontrol.IncludeContentTabFactory
 
clazz - Variable in class net.sf.basedb.clients.web.extensions.tabcontrol.TabBean
 
clazz - Variable in class net.sf.basedb.clients.web.extensions.toolbar.ButtonBean
 
clazz - Variable in class net.sf.basedb.clients.web.extensions.toolbar.FixedButtonFactory
 
clazz - Variable in class net.sf.basedb.clients.web.taglib.ExceptionCatcher
 
clazz - Variable in class net.sf.basedb.clients.web.taglib.StylableTag
 
clazz - Variable in class net.sf.basedb.clients.web.taglib.tab.Tab
Optional class attribute.
clazz - Variable in class net.sf.basedb.clients.web.taglib.table.Cell
Optional class attribute
clazz - Variable in class net.sf.basedb.clients.web.taglib.table.CellValue
 
clazz - Variable in class net.sf.basedb.core.ExtendedPropertyAccessor.GetterSetter
 
clazz - Variable in class net.sf.basedb.core.Metadata.BasicItem2DataPropertyPath
 
clazz - Variable in class net.sf.basedb.core.Metadata
 
clazz - Variable in class net.sf.basedb.core.Metadata.NoopPropertyPath
 
clazz - Variable in class net.sf.basedb.core.ParameterType
The class of allowed parameter values.
clazz - Variable in class net.sf.basedb.core.QueryExecutor.FutureItem
 
clazz - Variable in class net.sf.basedb.util.extensions.events.ActionClassEventFilter
 
clazz - Variable in class net.sf.basedb.util.filter.InstanceOfFilter
 
clean() - Method in class net.sf.basedb.util.listable.TransformCache
 
clean(AnnotationBatcher.UpdateBatcher) - Method in class net.sf.basedb.core.MigrateRbaToDba.Rba
Remove links to from the raw bioassay to annotations, files, etc.
cleanable - Variable in class net.sf.basedb.core.DbControl.State
 
cleanable - Variable in class net.sf.basedb.util.StaticCache.LockSafeInputStream
 
cleanable - Variable in class net.sf.basedb.util.StaticCache.LockSafeOutputStream
 
cleanContextFromProperty(Session, Item, String, String, boolean) - Static method in class net.sf.basedb.core.Update
 
cleaner - Static variable in class net.sf.basedb.core.Application
For keeping track of objects that need to be cleaned up.
cleanSessionControlCache(boolean) - Static method in class net.sf.basedb.core.Application
Clean the cache from unused SessionControl objects.
cleanUp() - Method in class net.sf.basedb.core.DbControl
Clear and close all objects.
cleanUp(FileFilter) - Method in class net.sf.basedb.util.StaticCache
Remove all files that matches the specified filter from the cache.
cleanupProjectSpecificAnnotations() - Static method in class net.sf.basedb.core.ProjectSpecificAnnotationsManager
Delete project-specific annotations that belong to projects that no longer exists.
cleanUpTask(FileFilter) - Method in class net.sf.basedb.util.StaticCache
Creates a task that cleans up this cache when it is executed.
CleanupTask(StaticCache, FileFilter) - Constructor for class net.sf.basedb.util.StaticCache.CleanupTask
 
clear() - Method in class net.sf.basedb.core.AbstractResultList
Not supported.
clear() - Method in class net.sf.basedb.core.hibernate.SessionWrapper
 
clear() - Method in class net.sf.basedb.core.snapshot.SnapshotManager
Clear the manager from all memory-cached information.
clear() - Method in class net.sf.basedb.core.UnmodifiableResultList
Not supported.
clear() - Method in class net.sf.basedb.util.AnnotationUtil.Cache
Clear all information from the cache.
clear() - Method in class net.sf.basedb.util.formatter.LookupFormatter
Remove all registered lookup entries.
clear() - Method in class net.sf.basedb.util.Tree
Clear all elements except the root element.
clear(Session) - Static method in class net.sf.basedb.core.HibernateUtil
Clear the session of cached objects.
clearAllRecent() - Method in class net.sf.basedb.core.ItemContext
Clear all recently used values lists.
clearDbControlCache() - Method in class net.sf.basedb.core.SessionControl
 
clearError() - Method in class net.sf.basedb.util.extensions.ActionIterator
Clear any error that has been registered for the current action.
clearError() - Method in class net.sf.basedb.util.extensions.ExtensionContext
 
clearError() - Method in class net.sf.basedb.util.extensions.ExtensionPointContext
 
clearError() - Method in class net.sf.basedb.util.extensions.InvokationContext
Clear the registered error for the current extension or extension point.
clearError() - Method in class net.sf.basedb.util.extensions.Registry.RegisteredExtension
 
clearError() - Method in class net.sf.basedb.util.extensions.Registry.RegisteredExtensionPoint
 
clearErrorList(JEP) - Static method in class net.sf.basedb.util.jep.Jep
This is a workaround for a bug in the JEP error handling.
clearErrors - Variable in class net.sf.basedb.util.extensions.ExtensionsInvoker
 
clearExecuteCommand() - Method in class net.sf.basedb.core.Job
Reset the currently stored execution command to force a plug-in to restart from the beginning instead of at the stored breakpoint.
clearFailures() - Method in class net.sf.basedb.util.overview.Node
Clear all warnings, errors on this node and on all child nodes.
clearLog() - Method in class net.sf.basedb.util.extensions.logging.ExtensionsLog
Clear the log.
clearRecent(String) - Method in class net.sf.basedb.core.ItemContext
Clear the recently used values list.
clearRecent(Item) - Method in class net.sf.basedb.core.ItemContext
Clear the recently used items list from items of the specified type.
clearRecent(Item, String) - Method in class net.sf.basedb.core.ItemContext
Clear the recently used items sublist from items of the specified type.
clearRecent(Item, ItemSubtype) - Method in class net.sf.basedb.core.ItemContext
Clear the recently used items list from items of the specified type.
clearSources() - Method in class net.sf.basedb.core.BioMaterialEvent
Clear the sources collection and return the used quantities to the source biomaterials.
clearSourcesExcept(BioMaterial) - Method in class net.sf.basedb.core.BioMaterialEvent
Clear the sources collection and return the used quantities to the source biomaterials, except for the given biomaterial.
clearState - Variable in class net.sf.basedb.core.PluginResponse
 
clearUsableUnits() - Method in class net.sf.basedb.core.AnnotationType
Clear all units.
clearValueConverters() - Method in class net.sf.basedb.util.extensions.xml.XmlLoader
Remove all value converters.
client - Variable in class net.sf.basedb.core.data.ChangeHistoryData
 
client - Variable in class net.sf.basedb.core.data.ClientDefaultSettingData
 
client - Variable in class net.sf.basedb.core.data.ContextData
 
client - Variable in class net.sf.basedb.core.data.ContextIndex
 
client - Variable in class net.sf.basedb.core.data.HelpData
 
client - Variable in class net.sf.basedb.core.data.SessionData
 
client - Variable in class net.sf.basedb.core.data.UserClientSettingData
 
client - Variable in class net.sf.basedb.core.data.UserDeviceData
 
client - Variable in class net.sf.basedb.core.SessionControl
Information about the ClientData that created this SessionControl.
client - Variable in class net.sf.basedb.plugins.HelpImporter
 
Client - Class in net.sf.basedb.core
This class represents a registered client application.
Client(ClientData) - Constructor for class net.sf.basedb.core.Client
 
CLIENT - Enum constant in enum class net.sf.basedb.core.Item
The item is an Client.
CLIENT_RUNTIME_FILTER - Static variable in class net.sf.basedb.core.UserClientSetting
This filter will only return items if the logged in user has generic read permission to clients.
clientCertificate - Variable in class net.sf.basedb.core.data.FileServerData
 
clientCertificate - Variable in class net.sf.basedb.util.uri.ConnectionParameters
 
clientCertificatePassword - Variable in class net.sf.basedb.util.uri.ConnectionParameters
 
clientContext - Variable in class net.sf.basedb.util.extensions.ExtensionPointContext
 
clientContext - Variable in class net.sf.basedb.util.extensions.ExtensionsInvoker
 
ClientContext - Class in net.sf.basedb.util.extensions
Keeps information about the current context in the client application that extensions can use to decide what actions to generate.
ClientContext() - Constructor for class net.sf.basedb.util.extensions.ClientContext
Create a new context with no session or current item.
ClientContext(DbControl) - Constructor for class net.sf.basedb.util.extensions.ClientContext
Create a new context with a DbControl.
ClientContext(DbControl, Object) - Constructor for class net.sf.basedb.util.extensions.ClientContext
Create a new context with a DbControl and item.
ClientContext(SessionControl) - Constructor for class net.sf.basedb.util.extensions.ClientContext
Create a new context with a session and no DbControl.
ClientContext(SessionControl, Object) - Constructor for class net.sf.basedb.util.extensions.ClientContext
Create a new context with a session and item but no DbControl.
ClientContext(SessionControl, DbControl, Object) - Constructor for class net.sf.basedb.util.extensions.ClientContext
 
ClientData - Class in net.sf.basedb.core.data
This class holds information about a client.
ClientData() - Constructor for class net.sf.basedb.core.data.ClientData
 
ClientDefaultSetting - Class in net.sf.basedb.core
This class is used to represent a setting for specific client application.
ClientDefaultSetting(ClientDefaultSettingData) - Constructor for class net.sf.basedb.core.ClientDefaultSetting
 
CLIENTDEFAULTSETTING - Enum constant in enum class net.sf.basedb.core.Item
The item is an ClientDefaultSetting.
ClientDefaultSettingData - Class in net.sf.basedb.core.data
 
ClientDefaultSettingData() - Constructor for class net.sf.basedb.core.data.ClientDefaultSettingData
 
clientDefaultSettings - Variable in class net.sf.basedb.core.SessionControl
Stores name and value from ClientDefaultSettingData.
clientId - Variable in class net.sf.basedb.core.data.ChangeHistoryData
 
clientId - Variable in class net.sf.basedb.core.log.TransactionDetails
 
ClientInfo(int, String, String) - Constructor for class net.sf.basedb.core.SessionControl.ClientInfo
 
clientItem - Static variable in class net.sf.basedb.plugins.HelpExporter
 
clientItem - Static variable in class net.sf.basedb.plugins.HelpImporter
 
clientParameter - Variable in class net.sf.basedb.plugins.HelpExporter
 
clientParameter - Variable in class net.sf.basedb.plugins.HelpImporter
 
clientPassword - Variable in class net.sf.basedb.core.data.FileServerData
 
clientSettings - Variable in class net.sf.basedb.core.data.UserData
 
clientType - Variable in class net.sf.basedb.plugins.HelpExporter
 
clonableProperty(ClonableProperty) - Static method in class net.sf.basedb.core.VirtualColumn
Get a virtual column view of a cloned reporter property.
ClonableProperty - Class in net.sf.basedb.core
Represents a reporter property that can be cloned to a per-experiment table in the dynamic database.
ClonableProperty(String, String, String, String, Type, int, boolean, Formula.AverageMethod, boolean) - Constructor for class net.sf.basedb.core.ClonableProperty
Create a cloned property representation of a static property.
ClonableProperty(String, ReporterClonePropertyData) - Constructor for class net.sf.basedb.core.ClonableProperty
Create a cloned property representation of a data-layer object.
ClonableProperty(ExtendedProperty) - Constructor for class net.sf.basedb.core.ClonableProperty
Create a cloned property representation of an extended property
ClonableReporterQuery - Interface in net.sf.basedb.core
An interface that indicates that a query may be used together with cloned reporter information.
CLONAL_AMPLIFICATION - Static variable in class net.sf.basedb.core.PhysicalBioAssay
The id for the PhysicalBioAssayType item representing a flow cell.
clone - Variable in class net.sf.basedb.util.annotations.InheritSpecification
 
cloneCachedNode(Object, Node, ChildNodeDirection) - Method in class net.sf.basedb.util.overview.node.NodeFactory
Clones a cached node if the current context supports caching and another node with the given cache key already exists.
CLONED - Enum constant in enum class net.sf.basedb.core.Annotation.Source
The annotation is an inherited annotation with a local copy of the values at the time the copy was made.
CLONED_REPORTERS - Enum constant in enum class net.sf.basedb.core.VirtualTable
Table that holds cloned reporter information for an experiment.
cloneParameter(PluginParameter<T>, T) - Static method in class net.sf.basedb.plugins.util.Parameters
Clone a plug-in parameter but give it a different default value.
cloneParameterWithDefaultValue(PluginParameter<T>) - Method in class net.sf.basedb.core.plugin.AbstractPlugin
Clone a plug-in parameter and set the default value to the value that is already stored in the job or configuration parameters.
cloneReporters(ReporterCloneBatcher.CloneSource, ReporterCloneTemplate, ProgressReporter) - Method in class net.sf.basedb.core.ReporterCloneBatcher
Create a reporter clone table in the dynamic database for this experiment and populate it with the current reporter annotations for all reporters that are part of the experiment.
CloneReportersPlugin - Class in net.sf.basedb.plugins
A plug-in that clone reporter annotations to an experiment.
CloneReportersPlugin() - Constructor for class net.sf.basedb.plugins.CloneReportersPlugin
 
CloneSource() - Constructor for enum class net.sf.basedb.core.ReporterCloneBatcher.CloneSource
 
close() - Method in class net.sf.basedb.clients.jobagent.executors.DummyJobExecutor
 
close() - Method in class net.sf.basedb.clients.jobagent.executors.ProcessJobExecutor
 
close() - Method in class net.sf.basedb.clients.jobagent.executors.ThreadJobExecutor
 
close() - Method in class net.sf.basedb.clients.jobagent.handlers.AbstractCustomRequestHandler
 
close() - Method in interface net.sf.basedb.clients.jobagent.handlers.CustomRequestHandler
This method is called at when the agent is stopped.
close() - Method in class net.sf.basedb.clients.jobagent.handlers.MultiProtocolRequestHandler
Close this handler.
close() - Method in interface net.sf.basedb.clients.jobagent.JobExecutor
This method is called at when the agent is stopped or paused.
close() - Method in class net.sf.basedb.clients.jobagent.slotmanager.InternalSlotManager
 
close() - Method in class net.sf.basedb.clients.jobagent.slotmanager.MasterSlotManager
 
close() - Method in class net.sf.basedb.clients.jobagent.slotmanager.RemoteSlotManager
 
close() - Method in interface net.sf.basedb.clients.jobagent.slotmanager.SlotManager
This method is called when the job agent is shutting down.
close() - Static method in class net.sf.basedb.clients.web.extensions.ExtensionsControl
Shut down the extensions system.
close() - Method in class net.sf.basedb.clients.web.extensions.list.RelatedItemHelper
 
close() - Static method in class net.sf.basedb.clients.web.extensions.service.Services
Stop all services.
close() - Method in class net.sf.basedb.clients.web.plugins.PlainTextTemplate
Do nothing.
close() - Method in class net.sf.basedb.clients.web.plugins.XlsxTemplate
Dispose and close workbook.
close() - Method in class net.sf.basedb.clients.web.plugins.XMLTemplate
Do nothing.
close() - Method in class net.sf.basedb.clients.web.servlet.PlotServlet.CFResultIterator
 
close() - Method in class net.sf.basedb.core.AbstractBatcher
 
close() - Method in class net.sf.basedb.core.AnnotationBatcher.InsertBatcher
Close the batcher.
close() - Method in class net.sf.basedb.core.AnnotationBatcher.UpdateBatcher
Close the batcher.
close() - Method in interface net.sf.basedb.core.Batcher
Flush the batcher and close it.
close() - Method in class net.sf.basedb.core.DataResultIterator
From the ResultIterator interface ---------------------------------
close() - Method in class net.sf.basedb.core.DbControl
Close the connection to the database.
close() - Method in class net.sf.basedb.core.DynamicResultIterator
From the ResultIterator interface ---------------------------------
close() - Method in class net.sf.basedb.core.File.CharsetTesterThread
The file has been uploaded.
close() - Method in class net.sf.basedb.core.File.UploadStream
Close the stream and register the size and location with the file item.
close() - Method in class net.sf.basedb.core.hibernate.SessionWrapper
 
close() - Method in class net.sf.basedb.core.hibernate.StatelessSessionWrapper
 
close() - Method in class net.sf.basedb.core.InternalJobQueue
Cleanup
close() - Method in class net.sf.basedb.core.ItemResultIterator
From the ResultIterator interface ---------------------------------
close() - Method in class net.sf.basedb.core.plugin.ExportOutputStream
 
close() - Method in interface net.sf.basedb.core.query.ResultIterator
Close the iterator and immediately release all resources associated with it.
close() - Method in class net.sf.basedb.core.ReporterScoreResultIterator
From the ResultIterator interface ---------------------------------
close() - Method in class net.sf.basedb.core.ScrollIterator
Close the results and return resources.
close() - Method in class net.sf.basedb.core.SessionControl
Close this session control so it can't be used again.
close() - Method in class net.sf.basedb.util.bfs.AnnotationParser
 
close() - Method in interface net.sf.basedb.util.bfs.BfsParser
Close the parser and relase underlying system resources that are associated with it.
close() - Method in class net.sf.basedb.util.bfs.DataParser
 
close() - Method in class net.sf.basedb.util.bfs.MetadataParser
 
close() - Method in class net.sf.basedb.util.excel.XlsxTableWriter
Closes the workbook unless it was supplied in the constructor from an external source.
close() - Method in class net.sf.basedb.util.excel.XlsxToCsvUtil
Closes the current workbook.
close() - Method in class net.sf.basedb.util.excel.XlsxToCsvUtil.WorkbookStream
 
close() - Method in class net.sf.basedb.util.extensions.manager.ExtensionsFile.WriteableExtensionsFile
Close the writeable file.
close() - Method in class net.sf.basedb.util.gtf.GtfInputStream
 
close() - Method in class net.sf.basedb.util.importer.spotdata.SynchronizedSpotDataParser
 
close() - Method in class net.sf.basedb.util.InputStreamCombiner
Closes all underlying streams.
close() - Method in class net.sf.basedb.util.InputStreamSplitter
 
close() - Method in class net.sf.basedb.util.InputStreamTracker
 
close() - Method in class net.sf.basedb.util.jobagent.JobAgentConnection
Close the connection to the job agent.
close() - Method in class net.sf.basedb.util.jobagent.JobAgentServerConnection
Stop listening for incoming connections.
close() - Method in class net.sf.basedb.util.StaticCache.LockSafeInputStream
 
close() - Method in class net.sf.basedb.util.StaticCache.LockSafeOutputStream
 
close() - Method in class net.sf.basedb.util.StreamCacher
Close the master stream and remove the cached file data.
close() - Method in class net.sf.basedb.util.uri.CloseResourceInputStream
Make sure the client connection manager is closed when the file has been completely downloaded.
close() - Method in class net.sf.basedb.util.zip.Bzip2FilePacker
Finish the BZIP stream.
close() - Method in interface net.sf.basedb.util.zip.FilePacker
End the packing and close.
close() - Method in class net.sf.basedb.util.zip.GzipFilePacker
Finish the GZIP stream.
close() - Method in class net.sf.basedb.util.zip.TarFilePacker
Finish the TAR file.
close() - Method in class net.sf.basedb.util.zip.ZipFilePacker
Finish the ZIP file.
close(int) - Method in class net.sf.basedb.clients.web.util.SimpleSignalProgressReporter
 
close(int) - Method in class net.sf.basedb.core.signal.AbstractSignalReceiver
Close this signal receiver.
close(int) - Method in class net.sf.basedb.core.signal.LocalSignalReceiver
 
close(int) - Method in interface net.sf.basedb.core.signal.SignalReceiver
Close the receiver.
close(int) - Method in class net.sf.basedb.core.signal.SocketSignalReceiver
Close this receiver and the socket it is listening on.
close(Closeable) - Static method in class net.sf.basedb.util.FileUtil
Close a Closeable without throwing an exception.
close(InputStream) - Static method in class net.sf.basedb.util.FileUtil
Close an input stream without throwing an exception.
close(InputStream) - Static method in class net.sf.basedb.util.SocketUtil
Close an InputStream without throwing any exceptions.
close(OutputStream) - Static method in class net.sf.basedb.util.FileUtil
Close an output stream without throwing an exception.
close(Reader) - Static method in class net.sf.basedb.util.SocketUtil
Close a Reader without throwing any exceptions.
close(Writer) - Static method in class net.sf.basedb.util.SocketUtil
Close a Writer without throwing any exceptions.
close(AutoCloseable) - Static method in class net.sf.basedb.util.FileUtil
Close a AutoCloseable without throwing an exception.
close(ServerSocket) - Static method in class net.sf.basedb.util.SocketUtil
Close a server socket without throwing any exceptions.
close(Socket) - Static method in class net.sf.basedb.util.SocketUtil
Close a socket without throwing any exceptions.
close(ServerSocketChannel) - Static method in class net.sf.basedb.util.SocketUtil
Close a server socket channel without throwing any exceptions.
close(Session) - Static method in class net.sf.basedb.core.HibernateUtil
Close a session.
close(StatelessSession) - Static method in class net.sf.basedb.core.HibernateUtil
Close a statless session.
closed - Variable in class net.sf.basedb.core.File.UploadStream
If this file closed or not.
closed - Variable in class net.sf.basedb.core.SessionControl
If the session control has been closed it can no longer be used.
closed - Variable in class net.sf.basedb.util.StaticCache.LockSafeInputStream
 
closed - Variable in class net.sf.basedb.util.StaticCache.LockSafeOutputStream
 
closeJobExecutor() - Method in class net.sf.basedb.clients.jobagent.Agent
Close the job executor.
closeJobQueueChecker() - Method in class net.sf.basedb.clients.jobagent.Agent
Close the job queue checker.
closeLogFile() - Method in class net.sf.basedb.core.plugin.AbstractPlugin
Close the log file created by AbstractPlugin.createLogFile(String).
CloseMyDbControl(RelatedItemHelper) - Constructor for class net.sf.basedb.clients.web.extensions.list.RelatedItemHelper.CloseMyDbControl
 
CloseResourceInputStream - Class in net.sf.basedb.util.uri
Inputstream filter that closes a given resource whenever the parent input stream is closed.
CloseResourceInputStream(InputStream, Closeable) - Constructor for class net.sf.basedb.util.uri.CloseResourceInputStream
Create a new stream.
closeResultSet(ResultSet, String) - Method in class net.sf.basedb.core.AbstractSqlQuery
Close the result set without throwing an exception.
closeServer() - Method in class net.sf.basedb.clients.jobagent.Agent
Close the service listener.
closeSlotManager() - Method in class net.sf.basedb.clients.jobagent.Agent
Close the slot manager.
closeStatement(Statement, String) - Method in class net.sf.basedb.core.AbstractSqlQuery
Close the statement without throwing an exception.
closeTimeout - Variable in class net.sf.basedb.clients.jobagent.Agent
Timeout to wait for jobs to act on the ABORT signal when stopping.
closeTimeout - Variable in class net.sf.basedb.core.InternalJobQueue
Timeout to wait for jobs to act on the ABORT signal when shutting down BASE.
CLUSTER_GENERATION - Static variable in class net.sf.basedb.core.Kit
The ID for the cluster generation (in a flow cell) kit type, for example a protocol used when creating a PhysicalBioAssay.
CLUSTER_GENERATION - Static variable in class net.sf.basedb.core.Protocol
The ID for the cluster generation (in a flow cell) protocol type, for example a protocol used when creating a PhysicalBioAssay.
CLUSTER_GENERATOR - Static variable in class net.sf.basedb.core.Hardware
The id for the HardwareType object representing a cluster generator station.
cmap - Variable in class net.sf.basedb.util.AnnotationUtil.Cache
 
cmd - Variable in class net.sf.basedb.clients.jobagent.CmdLine
 
CmdLine - Class in net.sf.basedb.clients.jobagent
Utility class for parsing command line arguments.
CmdLine(String[]) - Constructor for class net.sf.basedb.clients.jobagent.CmdLine
Create a new object for parsing the command line.
coalesce(String...) - Static method in class net.sf.basedb.core.StringUtil
Return the first non-null value (or null if all values are null).
colFunction - Variable in class net.sf.basedb.util.parser.JepMapper
 
ColFunction - Class in net.sf.basedb.util.parser
Adds a col() function to Jep.
ColFunction(List<String>, NumberFormat) - Constructor for class net.sf.basedb.util.parser.ColFunction
 
ColFunction(List<String>, NumberFormat, Formatter<Date>) - Constructor for class net.sf.basedb.util.parser.ColFunction
 
ColFunction(Map<String, Integer>, NumberFormat) - Constructor for class net.sf.basedb.util.parser.ColFunction
 
ColFunction(Map<String, Integer>, NumberFormat, Formatter<Date>) - Constructor for class net.sf.basedb.util.parser.ColFunction
 
colIndex - Variable in class net.sf.basedb.clients.web.plugins.DynamicQueryWrapper
 
collect(Item, Set<Integer>) - Method in class net.sf.basedb.util.listable.TransformContext
Store collected items for later use if collecting has been enabled.
CollectChildren(boolean, boolean) - Constructor for class net.sf.basedb.util.listable.CollectExtracts.CollectChildren
 
collectChildrenOfCollected(boolean) - Method in class net.sf.basedb.util.listable.CollectExtracts
The created transformer collect the ID:s of all child extracts to the already collected extracts and store them in the CollectExtracts.getCollectedChildren().
collectChildrenOfSource(boolean) - Method in class net.sf.basedb.util.listable.CollectExtracts
The created transformer collect the ID:s of all child extracts to the source extracts and store them in the CollectExtracts.getCollectedChildren().
collected - Variable in class net.sf.basedb.util.listable.CollectExtracts
 
collectedByItemType - Variable in class net.sf.basedb.util.listable.TransformContext
 
collectedExtracts - Variable in class net.sf.basedb.util.listable.CollectedExtractsToDerivedBioAssayTransformer
 
collectedExtracts - Variable in class net.sf.basedb.util.listable.CollectedExtractsToRawBioAssayTransformer
 
collectedExtracts - Variable in class net.sf.basedb.util.listable.DerivedBioAssayToRawBioAssayTransformer
 
collectedExtracts - Variable in class net.sf.basedb.util.listable.ExtractToParentExtractTransformer
 
collectedExtracts - Variable in class net.sf.basedb.util.listable.PhysicalBioAssayToDerivedBioAssayTransformer
 
CollectedExtractsToDerivedBioAssayTransformer - Class in net.sf.basedb.util.listable
Source item transformer implementation that transform collected extract items to derived bioassays.
CollectedExtractsToDerivedBioAssayTransformer(CollectExtracts) - Constructor for class net.sf.basedb.util.listable.CollectedExtractsToDerivedBioAssayTransformer
Create a new collected extracts to derived bioassay transformer.
CollectedExtractsToDerivedBioAssayTransformer(CollectExtracts, boolean) - Constructor for class net.sf.basedb.util.listable.CollectedExtractsToDerivedBioAssayTransformer
Create a new collected extracts to derived bioassay transformer.
CollectedExtractsToRawBioAssayTransformer - Class in net.sf.basedb.util.listable
Source item transformer implementation that transform collected extract items to raw bioassays.
CollectedExtractsToRawBioAssayTransformer(CollectExtracts) - Constructor for class net.sf.basedb.util.listable.CollectedExtractsToRawBioAssayTransformer
Create a new collected extracts to derived bioassay transformer.
CollectExtracts - Class in net.sf.basedb.util.listable
Collect extracts seen on derived bioassays and raw bioassays that has been loaded by other transformers.
CollectExtracts() - Constructor for class net.sf.basedb.util.listable.CollectExtracts
Create a new derived bioassay to physical bioassay transformer.
CollectExtracts.CollectChildren - Class in net.sf.basedb.util.listable
Transformer implementation that collect the child extracts from the source or collected extracts.
CollectExtracts.CollectFromDerivedBioAssays - Class in net.sf.basedb.util.listable
Transformer implementation that given a set of derived bioassays load their linked extracts and store that in the parent class.
CollectExtracts.CollectFromExtracts - Class in net.sf.basedb.util.listable
Transformer implementation that store the given set of extracts in the parent class.
CollectExtracts.CollectFromRawBioAssays - Class in net.sf.basedb.util.listable
Transformer implementation that given a set of raw bioassays load their linked extracts and store that in the parent class.
CollectExtracts.CollectParents - Class in net.sf.basedb.util.listable
Transformer implementation that collect the parent extracts from the source or collected extracts.
CollectExtracts.ResetCollected - Class in net.sf.basedb.util.listable
Transformer implementation that reset the collected extracts before forwarding the call to the parent transformer.
collectFromDerivedBioAssays(boolean) - Method in class net.sf.basedb.util.listable.CollectExtracts
The created transformer collect the ID:s of all extracts linked from the source derived bioassays and then return the same set of derived bioassays again.
CollectFromDerivedBioAssays(boolean) - Constructor for class net.sf.basedb.util.listable.CollectExtracts.CollectFromDerivedBioAssays
 
collectFromExtracts() - Method in class net.sf.basedb.util.listable.CollectExtracts
The created transformer collect the ID:s of all extracts in the source collection and return same set of extracts again.
CollectFromExtracts() - Constructor for class net.sf.basedb.util.listable.CollectExtracts.CollectFromExtracts
 
collectFromRawBioAssays() - Method in class net.sf.basedb.util.listable.CollectExtracts
The created transformer collect the ID:s of all extracts linked from the source raw bioassays and then return the same set of raw bioassays again.
CollectFromRawBioAssays() - Constructor for class net.sf.basedb.util.listable.CollectExtracts.CollectFromRawBioAssays
 
collecting - Variable in class net.sf.basedb.util.listable.TransformContext
 
COLLECTION_SEPARATOR - Static variable in class net.sf.basedb.clients.web.plugins.SimpleExport
 
collectionFormatter - Variable in class net.sf.basedb.clients.web.extensions.list.AbstractListColumnBean
 
CollectionFormatter<I> - Class in net.sf.basedb.util.formatter
Formatter implementation that formats a collection of values to a string by concatenating the values with a given separator.
CollectionFormatter(String, boolean, Formatter<? super I>) - Constructor for class net.sf.basedb.util.formatter.CollectionFormatter
 
CollectionFormatter(Formatter<? super I>) - Constructor for class net.sf.basedb.util.formatter.CollectionFormatter
Create a collection formatting using ", " as separator and skipping null values.
CollectionPropertyPath(Type) - Constructor for class net.sf.basedb.core.Metadata.CollectionPropertyPath
 
collections - Variable in class net.sf.basedb.util.NestedIterator
The array to iterate.
collectionSeparator - Variable in class net.sf.basedb.clients.web.plugins.PlainTextTemplate
 
collectionSeparator - Variable in class net.sf.basedb.clients.web.plugins.XlsxTemplate
 
CollectionTransformer<S,D> - Interface in net.sf.basedb.util.collections
Allows a collection to be transformed by applying some operation to it.
CollectParents(boolean, boolean) - Constructor for class net.sf.basedb.util.listable.CollectExtracts.CollectParents
 
collectParentsOfCollected(boolean) - Method in class net.sf.basedb.util.listable.CollectExtracts
The created transformer collect the ID:s of all parent extracts to the already collected extracts and store them in the CollectExtracts.getCollectedParents().
collectParentsOfSource(boolean) - Method in class net.sf.basedb.util.listable.CollectExtracts
The created transformer collect the ID:s of all parent extracts to the source extracts and store them in the CollectExtracts.getCollectedParents().
CollectSqlTarget() - Constructor for class net.sf.basedb.core.hibernate.SchemaGenerator.CollectSqlTarget
 
CollectSqlTarget(DbEngine, Dialect, SchemaGenerator.Mode, Connection) - Constructor for class net.sf.basedb.core.hibernate.SchemaGenerator.CollectSqlTarget
 
colNo - Variable in class net.sf.basedb.util.excel.XlsxTableWriter
 
colNum - Variable in class net.sf.basedb.clients.web.plugins.PlainTextTemplate
 
colNum - Variable in class net.sf.basedb.clients.web.plugins.XlsxTemplate
 
colOffset - Variable in class net.sf.basedb.util.parser.FlatFileParser.ExcelData
 
color - Variable in class net.sf.basedb.clients.web.ExperimentExplorer.AnnotationGroup
 
ColorFormatter - Class in net.sf.basedb.clients.web.formatter
Formatter that adds a small colored box next to a value.
ColorFormatter(ColorGenerator, Formatter<Number>) - Constructor for class net.sf.basedb.clients.web.formatter.ColorFormatter
Create a new color formatter.
colorGen - Variable in class net.sf.basedb.clients.web.formatter.ColorFormatter
 
ColorGenerator - Class in net.sf.basedb.util
This class is used to generate colors for numerical values.
ColorGenerator(Color, Color, Color, float, float, float, boolean) - Constructor for class net.sf.basedb.util.ColorGenerator
Create a new color generator.
coloring - Variable in class net.sf.basedb.core.data.ExtraValueTypeData
 
coloring - Variable in class net.sf.basedb.core.data.FormulaData
 
coloring - Variable in class net.sf.basedb.core.ExtraValueType
 
coloring - Variable in class net.sf.basedb.core.Formula
 
Coloring - Class in net.sf.basedb.core
This class keeps coloring information for items which can be colored when values are displayed in a client application.
Coloring() - Constructor for class net.sf.basedb.core.Coloring
Create a new independent coloring object.
Coloring(ColoringData, AccessControlled) - Constructor for class net.sf.basedb.core.Coloring
Create Coloring object which links to an existing item.
ColoringData - Class in net.sf.basedb.core.data
Hold coloring information.
ColoringData() - Constructor for class net.sf.basedb.core.data.ColoringData
 
ColoringData(boolean, boolean, Float, Float, Float) - Constructor for class net.sf.basedb.core.data.ColoringData
 
COLORS - Static variable in class net.sf.basedb.clients.web.ExperimentExplorer
Predefined colors for annotation groups
colspan - Variable in class net.sf.basedb.clients.web.taglib.table.Header
 
column - Variable in class net.sf.basedb.clients.web.extensions.list.ListColumnDataLoader
 
column - Variable in class net.sf.basedb.core.data.BioWellData
 
column - Variable in class net.sf.basedb.core.data.FeatureData
 
column - Variable in class net.sf.basedb.core.data.MappingCoordinate
The column number.
column - Variable in class net.sf.basedb.core.data.PlateCoordinate
The column number.
column - Variable in class net.sf.basedb.core.data.RawData
 
column - Variable in class net.sf.basedb.core.data.ReporterClonePropertyData
 
column - Variable in class net.sf.basedb.core.data.WellData
 
column - Variable in class net.sf.basedb.core.DynamicRestriction
 
column - Variable in class net.sf.basedb.core.ExtendedProperty
 
column - Variable in class net.sf.basedb.core.ExtraValueExpression
 
column - Variable in class net.sf.basedb.core.FeatureCoordinate
The column of this feature.
column - Variable in class net.sf.basedb.core.query.SqlColumnExpression
 
column - Variable in class net.sf.basedb.core.query.VirtualColumnExpression
 
column - Variable in class net.sf.basedb.core.RawBioAssayPropertyExpression
 
column - Variable in class net.sf.basedb.core.ReporterPropertyExpression
 
column - Variable in class net.sf.basedb.core.VirtualColumn
The column name in the database of the column.
column - Variable in class net.sf.basedb.plugins.LowessNormalization.SpotData
 
column(VirtualColumn) - Static method in class net.sf.basedb.core.query.Dynamic
Create an expression representing a column in the root table: expression = rootAlias.columnName.
column(VirtualTable, VirtualColumn) - Static method in class net.sf.basedb.core.query.Dynamic
Create an expression representing a column in a table: expression = tableAlias.columnName.
COLUMN - Enum constant in enum class net.sf.basedb.core.ExtraValue.CoordinateType
The extra values are attached to column coordinates only.
COLUMN - Enum constant in enum class net.sf.basedb.core.VirtualTable
Table that maps columns coordinates in a data cube to raw bioassays.
COLUMN - Static variable in class net.sf.basedb.core.VirtualColumn
This column stores the data cube column coordinate.
COLUMN_EXPRESSION - Enum constant in enum class net.sf.basedb.core.Formula.Type
An arbitrary expression that specify one formula only.
COLUMN_EXTRA_FLOAT - Enum constant in enum class net.sf.basedb.core.VirtualTable
Table that stores float column extra values.
COLUMN_EXTRA_INT - Enum constant in enum class net.sf.basedb.core.VirtualTable
Table that stores integer column extra values.
COLUMN_EXTRA_STRING - Enum constant in enum class net.sf.basedb.core.VirtualTable
Table that stores string column extra values.
COLUMN_PREFIX - Static variable in class net.sf.basedb.clients.web.plugins.SimpleExport
 
COLUMN_RESTRICTION - Enum constant in enum class net.sf.basedb.core.Formula.Type
An arbitraty expression that specify one formula only.
columnColumnMapping - Static variable in class net.sf.basedb.plugins.PlateFlatFileImporter
 
columnColumnMapping - Static variable in class net.sf.basedb.plugins.RawDataFlatFileImporter
 
columnColumnMapping - Static variable in class net.sf.basedb.plugins.ReporterMapFlatFileImporter
 
columnContent - Variable in class net.sf.basedb.clients.web.taglib.table.Table
 
columnCount - Variable in class net.sf.basedb.util.bfs.AnnotationWriter
 
columnCount - Variable in class net.sf.basedb.util.bfs.DataWriter
 
ColumnDef - Class in net.sf.basedb.clients.web.taglib.table
This tag defines a column in the table.
ColumnDef() - Constructor for class net.sf.basedb.clients.web.taglib.table.ColumnDef
 
ColumnDef.NullIterator<A,B> - Class in net.sf.basedb.clients.web.taglib.table
Iterator implementation that returns a single null value and nothing more.
columnFilter - Variable in class net.sf.basedb.clients.web.taglib.table.Table
 
columnFormatter - Variable in class net.sf.basedb.clients.web.taglib.table.Table
 
columnHeaders - Variable in class net.sf.basedb.plugins.AnnotationFlatFileImporter
 
columnHeaders - Variable in class net.sf.basedb.util.parser.ColFunction
 
columnHeaders - Variable in class net.sf.basedb.util.parser.FlatFileParser
List of the column names found by splitting the data header using the data splitter regexp.
ColumnHeaders - Class in net.sf.basedb.clients.web.taglib.table
Generate column headers for the columns that has been defined for this table.
ColumnHeaders() - Constructor for class net.sf.basedb.clients.web.taglib.table.ColumnHeaders
 
columnId - Variable in class net.sf.basedb.clients.web.taglib.table.Cell
The ID of the column to which this cell belongs.
columnIndex - Variable in class net.sf.basedb.util.bfs.AnnotationModel
 
ColumnInfo(String, String, Integer, int, boolean, boolean) - Constructor for class net.sf.basedb.core.dbengine.TableInfo.ColumnInfo
Create a new ColumnInfo object.
ColumnKey(Comparable<?>, String) - Constructor for class net.sf.basedb.clients.web.servlet.ExperimentExplorerPlotServlet.ColumnKey
 
columnMapper - Variable in class net.sf.basedb.plugins.PlateFlatFileImporter
 
columnMapper - Variable in class net.sf.basedb.plugins.RawDataFlatFileImporter
 
columnMapper - Variable in class net.sf.basedb.plugins.ReporterMapFlatFileImporter
 
ColumnMapper - Class in net.sf.basedb.util.parser
Returns the string found in the column given by the index set in the constructor.
ColumnMapper(int, String) - Constructor for class net.sf.basedb.util.parser.ColumnMapper
Create a new column mapper.
ColumnMapper(int, String, NumberFormat, boolean) - Constructor for class net.sf.basedb.util.parser.ColumnMapper
ColumnMapper(int, String, NumberFormat, Formatter<Date>, boolean) - Constructor for class net.sf.basedb.util.parser.ColumnMapper
Create a new column mapper using a specific number or date format.
columnMappingParameterName - Variable in class net.sf.basedb.plugins.batchimport.PropertyIdMethod
 
columnName - Variable in class net.sf.basedb.core.Update.DropColumnChange
 
columnNo - Variable in class net.sf.basedb.core.data.DataCubeColumnData
 
columns - Variable in class net.sf.basedb.clients.web.taglib.table.Table
Which columns that should be visible and their order
columns - Variable in class net.sf.basedb.core.data.DataCubeData
 
columns - Variable in class net.sf.basedb.core.data.PlateGeometryData
 
columns - Variable in class net.sf.basedb.core.dbengine.TableInfo
 
columns - Variable in class net.sf.basedb.core.dbengine.TableInfo.IndexInfo
 
columns - Variable in class net.sf.basedb.core.dbengine.TableInfo.PrimaryKeyInfo
 
columns - Variable in class net.sf.basedb.core.ExtraValueJoin
 
columns - Variable in enum class net.sf.basedb.core.VirtualTable
The columns in the table.
columns() - Method in class net.sf.basedb.util.parser.FlatFileParser.Data
The number of columns as determined by the FlatFileParser.setDataSplitterRegexp(Pattern) regular expression.
columnSeparator - Variable in class net.sf.basedb.util.excel.XlsxToCsvUtil
 
columnSubtitle - Variable in class net.sf.basedb.clients.web.taglib.table.Table
 
ColumnSubtitles - Class in net.sf.basedb.clients.web.taglib.table
Generate column subtitle header for the columns that has been defined for this table.
ColumnSubtitles() - Constructor for class net.sf.basedb.clients.web.taglib.table.ColumnSubtitles
 
CombinedPropertyPath(List<Metadata.PropertyPath>) - Constructor for class net.sf.basedb.core.Metadata.CombinedPropertyPath
 
CombiningEventFilter - Class in net.sf.basedb.util.extensions.events
Event filter that only passes on events based on multiple other event filters.
CombiningEventFilter(Collection<EventFilter>, boolean) - Constructor for class net.sf.basedb.util.extensions.events.CombiningEventFilter
Create a new combining event filter.
command - Variable in class net.sf.basedb.core.PluginRequest
 
command - Variable in class net.sf.basedb.core.RequestInformation
 
command - Variable in class net.sf.basedb.plugins.executor.ExternalProgramExecutor.RequestWrapper
 
COMMAND_CONFIGURE_EXTERNAL_PARAMETERS - Static variable in class net.sf.basedb.plugins.executor.ExternalProgramExecutor
 
COMMAND_CONFIGURE_IO_JOB - Static variable in interface net.sf.basedb.plugins.executor.IOSupport
This command is sent to import and export plug-ins in the job configuration sequence: InteractivePlugin.getRequestInformation(GuiContext, String) and InteractivePlugin.configure(GuiContext, Request, Response)
COMMAND_CONFIGURE_IO_PLUGIN - Static variable in interface net.sf.basedb.plugins.executor.IOSupport
This command is sent to import and export plug-ins in the plug-in configuration sequence: InteractivePlugin.getRequestInformation(GuiContext, String) and InteractivePlugin.configure(GuiContext, Request, Response)
COMMAND_CONFIGURE_JOB - Static variable in interface net.sf.basedb.core.plugin.Request
This should be the first command to use when setting the plugin's job parameters.
COMMAND_CONFIGURE_PARSER - Static variable in class net.sf.basedb.plugins.RawDataFlatFileImporter
 
COMMAND_CONFIGURE_PLUGIN - Static variable in interface net.sf.basedb.core.plugin.Request
This should be the first command to use when setting the plugin's configuration.
COMMAND_EXECUTE - Static variable in interface net.sf.basedb.core.plugin.Request
This command will tell the plugin to start its execution.
COMMAND_EXECUTE_IO_JOB - Static variable in interface net.sf.basedb.plugins.executor.IOSupport
This command is sent to import and export plug-ins in the job execution sequence: Plugin.run(Request, Response, ProgressReporter)
COMMAND_MANUAL_CONFIG - Static variable in class net.sf.basedb.plugins.Base1PluginExecuter
This command is used if the user decides to configure the plugin by hand.
COMMAND_SELECT_CONFIGURATIONS - Static variable in class net.sf.basedb.plugins.PluginConfigurationImporter
 
commandHandlers - Variable in class net.sf.basedb.clients.jobagent.handlers.DefaultRequestHandler
 
comment - Variable in class net.sf.basedb.core.authentication.LoginRequest
 
comment - Variable in class net.sf.basedb.core.data.BioMaterialEventData
 
comment - Variable in class net.sf.basedb.core.data.PlateEventData
 
comment - Variable in class net.sf.basedb.core.MigrateRbaToDba.LineMapping
 
commit() - Method in class net.sf.basedb.core.DbControl
Commit all changes made to items and close the connection to the database.
commit(Transaction) - Static method in class net.sf.basedb.core.HibernateUtil
Commit a transaction.
commitQueue - Variable in class net.sf.basedb.core.DbControl
A list of items that need special handling when commit is called.
COMMON - Static variable in class net.sf.basedb.clients.web.resources.Bundle
Resource bundle with strings that are used in lots and lots of places in the web gui.
commonCharsets - Static variable in class net.sf.basedb.core.Config
 
CommonData - Class in net.sf.basedb.core.data
This is a convenience class that extends the SharedData class and implements the NameableData and RemovableData interfaces.
CommonData() - Constructor for class net.sf.basedb.core.data.CommonData
 
commonDom - Static variable in class net.sf.basedb.core.PredefinedQuery
Holds the XML document containing the common queries.
CommonItem - Class in net.sf.basedb.core
 
CommonItem(CommonData) - Constructor for class net.sf.basedb.core.CommonItem
 
commonName - Variable in class net.sf.basedb.plugins.Base1PluginExecuter.JobParameter
 
commonQueryFile - Static variable in class net.sf.basedb.core.PredefinedQuery
The path to the query file with common queries.
CompactButtonRenderer - Class in net.sf.basedb.clients.web.extensions.toolbar
A compact renderer for toolbar button actions, which only only displays the icon.
CompactButtonRenderer(JspContext) - Constructor for class net.sf.basedb.clients.web.extensions.toolbar.CompactButtonRenderer
 
CompactButtonRendererFactory - Class in net.sf.basedb.clients.web.extensions.toolbar
Factory that create CompactButtonRenderer objects for rendering ButtonAction:s.
CompactButtonRendererFactory() - Constructor for class net.sf.basedb.clients.web.extensions.toolbar.CompactButtonRendererFactory
 
ComparableComparator<T extends Comparable<T>> - Class in net.sf.basedb.util
A comparator implemenation for any Comparable objects.
ComparableComparator() - Constructor for class net.sf.basedb.util.ComparableComparator
 
compare(String, String) - Method in class net.sf.basedb.util.StringLengthComparator
 
compare(URI, URI) - Method in class net.sf.basedb.util.extensions.manager.ExtensionsManager.JarFirstURIComparator
 
compare(RawDataType, RawDataType) - Method in class net.sf.basedb.core.RawDataTypes.NameComparator
 
compare(AnnotationSnapshot, AnnotationSnapshot) - Method in class net.sf.basedb.core.snapshot.AnnotationSetSnapshot.SortByProjectComparator
 
compare(AnnotationSnapshot, AnnotationSnapshot) - Method in class net.sf.basedb.core.snapshot.AnnotationSnapshot.AnnotationTypeComparator
 
compare(AnnotationSnapshot, AnnotationSnapshot) - Method in class net.sf.basedb.core.snapshot.AnnotationSnapshot.ProjectComparator
 
compare(T, T) - Method in class net.sf.basedb.util.ComparableComparator
 
compare(T, T) - Method in class net.sf.basedb.util.NameableComparator
 
compare(T, T) - Method in class net.sf.basedb.util.PriorityComparator
 
compare(T, T) - Method in class net.sf.basedb.util.ToStringComparator
 
compareByChainOrder() - Static method in class net.sf.basedb.core.SyncFilter
Create a comparator that sorts sync filters by: Filter group Source item type: BIOSOURCE, SAMPLE, EXTRACT, PHYSICALBIOASSAY, DERIVEDBIOASSAY, RAWBIOASSAY Type of transformation: PARENT_TO_CHILD, NONE, CHILD_TO_PARENT Name Source item must exists is sorted before source item must not exist Id
compareTo(ExperimentExplorer.AnnotationGroup) - Method in class net.sf.basedb.clients.web.ExperimentExplorer.AnnotationGroup
 
compareTo(ExperimentExplorerPlotServlet.ColumnKey) - Method in class net.sf.basedb.clients.web.servlet.ExperimentExplorerPlotServlet.ColumnKey
The ID of the key determines equality.
compareTo(ClonableProperty) - Method in class net.sf.basedb.core.ClonableProperty
Sort by title, but mandatory properties before non-madatory.
compareTo(KeyPermission) - Method in class net.sf.basedb.core.data.keyring.KeyPermission
Compare the keyId of this object to the keyId of another KeyPermission object.
compareTo(PluginKeys) - Method in class net.sf.basedb.core.data.keyring.PluginKeys
Compare the keyId of this object to the keyId of another PluginKeys object.
compareTo(ProjectPermission) - Method in class net.sf.basedb.core.data.keyring.ProjectPermission
Compare the projectId of this object to the projectId of another ProjectPermission object.
compareTo(TableInfo.ColumnInfo) - Method in class net.sf.basedb.core.dbengine.TableInfo.ColumnInfo
 
compareTo(ItemProxy) - Method in class net.sf.basedb.core.ItemProxy
 
compareTo(RawDataType) - Method in class net.sf.basedb.core.RawDataType
Compare the id:s of the raw data types.
compareTo(LowessNormalization.SpotData) - Method in class net.sf.basedb.plugins.LowessNormalization.SpotData
Sort by A in ascending order.
compareTo(MedianRatioNormalization.SpotData) - Method in class net.sf.basedb.plugins.MedianRatioNormalization.SpotData
Sort by ratio in ascending order.
compareTo(AnyToAnyLinkStatistics) - Method in class net.sf.basedb.util.AnyToAnyLinkStatistics
Sort items by count, linkName and targetType.
compareTo(ExtensionsFile) - Method in class net.sf.basedb.util.extensions.manager.ExtensionsFile
 
compareTo(Node) - Method in class net.sf.basedb.util.overview.Node
 
compareTo(PlotAnnotation) - Method in class net.sf.basedb.util.plot.PlotAnnotation
 
compareTo(UnitCache.CacheKey) - Method in class net.sf.basedb.util.units.UnitCache.CacheKey
 
compareWith(String) - Static method in class net.sf.basedb.core.Version
Compare the given version string, which should be of the form a.b or a.b.c, with the current BASE version.
compile(boolean, boolean) - Method in class net.sf.basedb.clients.web.extensions.XJspCompiler
Called when a JSP page needs recompiling.
compile(String, HttpServletRequest, HttpServletResponse) - Method in class net.sf.basedb.clients.web.servlet.CompileAll
Compile all files found in dir, recursively entering subdirectories.
CompileAll - Class in net.sf.basedb.clients.web.servlet
This servlet will scan for all files ending with .jsp and issue a request for them with the parameter jsp_precompile=true therby compiling all JSP files into servlets.
CompileAll() - Constructor for class net.sf.basedb.clients.web.servlet.CompileAll
 
completed - Variable in class net.sf.basedb.core.SimpleAbsoluteProgressReporter
 
complexMappings - Static variable in class net.sf.basedb.plugins.AbstractFlatFileImporter
Parameter that asks if complex column mappings should be enabled or not.
component - Variable in class net.sf.basedb.core.Metadata.ComponentPropertyPath
 
ComponentData - Interface in net.sf.basedb.core.data
Tagging interface that we need all componenets to implement so that we are able to export them properly using generic code.
ComponentPropertyPath(ComponentType, int, Type) - Constructor for class net.sf.basedb.core.Metadata.ComponentPropertyPath
 
CompoundMapper - Class in net.sf.basedb.util.parser
A compound mapper that gets its value by invoking multiple other mappers which are set in the constructor.
CompoundMapper(List<Mapper>) - Constructor for class net.sf.basedb.util.parser.CompoundMapper
Create a new compound mapper.
CompoundMapper(List<Mapper>, NumberFormat, boolean) - Constructor for class net.sf.basedb.util.parser.CompoundMapper
Create a new compound mapper, using a specific number formatter as it's parser.
CompoundMapper(List<Mapper>, NumberFormat, Formatter<Date>, boolean) - Constructor for class net.sf.basedb.util.parser.CompoundMapper
Create a new compound mapper, using a specific number formatter as it's parser.
compress - Variable in class net.sf.basedb.core.File.UploadStream
If the file should be compressed or not.
compress(ProgressReporter) - Method in class net.sf.basedb.core.File
Compress the file stored on the disk.
compressed - Variable in class net.sf.basedb.core.data.FileData
 
compressedSize - Variable in class net.sf.basedb.core.data.FileData
 
compressOrDecompress(ProgressReporter, boolean) - Method in class net.sf.basedb.core.File
 
condition - Variable in class net.sf.basedb.core.dbengine.TableInfo.IndexInfo
 
condition - Variable in class net.sf.basedb.core.HibernateUtil.DelayedFilterDef
 
condition - Variable in class net.sf.basedb.core.query.WhenStatement
 
conditionalExpression(Filter<? extends Query>, Expression, Expression) - Static method in class net.sf.basedb.core.query.Expressions
Create an expression that falls back to one of two expression depending on if the query passes a filter or not.
ConditionalQueryElement - Class in net.sf.basedb.core.query
 
ConditionalQueryElement(Filter<Query>, QueryElement, QueryElement) - Constructor for class net.sf.basedb.core.query.ConditionalQueryElement
 
conditionalRestriction(Filter<? extends Query>, Restriction, Restriction, boolean) - Static method in class net.sf.basedb.core.query.Restrictions
Create a restriction that falls back to one of two restrictions depending on if the query passes a filter or not.
config - Static variable in class net.sf.basedb.core.Config
Variable for holding the configuration properties.
config - Variable in class net.sf.basedb.core.hibernate.SchemaGenerator.CollectSqlTarget
 
config - Variable in class net.sf.basedb.core.plugin.ParameterValuesWrapper
 
config - Variable in class net.sf.basedb.util.ContextUtil.ContextResult
 
Config - Class in net.sf.basedb.core
Use this class to access the configuration settings for BASE.
Config() - Constructor for class net.sf.basedb.core.Config
 
configDir - Static variable in class net.sf.basedb.core.Config
 
configList - Static variable in class net.sf.basedb.plugins.PluginConfigurationExporter
 
configuration - Variable in class net.sf.basedb.core.ParameterValuesImpl
 
configuration - Variable in class net.sf.basedb.core.plugin.AbstractPlugin
 
configuration - Variable in class net.sf.basedb.plugins.gtf.DefaultConfigurationValues
 
ConfigurationException - Exception in net.sf.basedb.core
This exception is thrown by the Config class if there is a problem with finding or loading the configuration settings.
ConfigurationException(String) - Constructor for exception net.sf.basedb.core.ConfigurationException
Creates a new ConfigurationException.
ConfigurationException(String, Throwable) - Constructor for exception net.sf.basedb.core.ConfigurationException
Creates a new ConfigurationException with a cause.
configurationMap - Variable in class net.sf.basedb.plugins.PluginConfigurationImporter
 
configurationParameters - Variable in class net.sf.basedb.core.PluginRequest
 
configurations - Variable in class net.sf.basedb.core.data.PluginDefinitionData
 
configurationValues - Variable in class net.sf.basedb.core.data.PluginConfigurationData
 
configure() - Method in class net.sf.basedb.core.PluginConfiguration
Start the configuration sequence for a plugin.
configure(GuiContext) - Method in class net.sf.basedb.core.Job
Start the configuration sequence for a job.
configure(GuiContext, Request, Response) - Method in class net.sf.basedb.clients.web.plugins.SimpleExport
 
configure(GuiContext, Request, Response) - Method in interface net.sf.basedb.core.plugin.InteractivePlugin
Configure the plugin.
configure(GuiContext, Request, Response) - Method in class net.sf.basedb.plugins.AnnotationFlatFileImporter
 
configure(GuiContext, Request, Response) - Method in class net.sf.basedb.plugins.Base1PluginExecuter
 
configure(GuiContext, Request, Response) - Method in class net.sf.basedb.plugins.BaseFileExporterPlugin
 
configure(GuiContext, Request, Response) - Method in class net.sf.basedb.plugins.batchimport.AbstractItemImporter
 
configure(GuiContext, Request, Response) - Method in class net.sf.basedb.plugins.batchimport.AnnotationTypeImporter
Override this method so that we can make some extra parameter checks: A mapping for 'Value type' must be specified when 'create' or 'create+update' mode is used
configure(GuiContext, Request, Response) - Method in class net.sf.basedb.plugins.batchimport.AnyToAnyImporter
 
configure(GuiContext, Request, Response) - Method in class net.sf.basedb.plugins.BfsExporterPlugin
 
configure(GuiContext, Request, Response) - Method in class net.sf.basedb.plugins.CdfFileReporterImporter
 
configure(GuiContext, Request, Response) - Method in class net.sf.basedb.plugins.executor.BaseFileExporterSupport
 
configure(GuiContext, Request, Response) - Method in class net.sf.basedb.plugins.executor.BaseFileImporterSupport
 
configure(GuiContext, Request, Response) - Method in class net.sf.basedb.plugins.executor.BfsExporterSupport
 
configure(GuiContext, Request, Response) - Method in class net.sf.basedb.plugins.executor.BfsImporterSupport
 
configure(GuiContext, Request, Response) - Method in class net.sf.basedb.plugins.executor.ExternalProgramExecutor
 
configure(GuiContext, Request, Response) - Method in class net.sf.basedb.plugins.executor.FileOnlyImporterSupport
 
configure(GuiContext, Request, Response) - Method in class net.sf.basedb.plugins.FormulaFilter
 
configure(GuiContext, Request, Response) - Method in class net.sf.basedb.plugins.GalExporter
 
configure(GuiContext, Request, Response) - Method in class net.sf.basedb.plugins.gtf.GtfReporterMapImporter
 
configure(GuiContext, Request, Response) - Method in class net.sf.basedb.plugins.HelpExporter
 
configure(GuiContext, Request, Response) - Method in class net.sf.basedb.plugins.HelpImporter
 
configure(GuiContext, Request, Response) - Method in class net.sf.basedb.plugins.IlluminaRawDataImporter
 
configure(GuiContext, Request, Response) - Method in class net.sf.basedb.plugins.IntensityCalculatorPlugin
configure(GuiContext, Request, Response) - Method in class net.sf.basedb.plugins.JepExtraValueCalculator
 
configure(GuiContext, Request, Response) - Method in class net.sf.basedb.plugins.JepIntensityTransformer
 
configure(GuiContext, Request, Response) - Method in class net.sf.basedb.plugins.LowessNormalization
 
configure(GuiContext, Request, Response) - Method in class net.sf.basedb.plugins.ManualDerivedBioAssayCreator
 
configure(GuiContext, Request, Response) - Method in class net.sf.basedb.plugins.ManualTransformCreator
 
configure(GuiContext, Request, Response) - Method in class net.sf.basedb.plugins.MedianRatioNormalization
 
configure(GuiContext, Request, Response) - Method in class net.sf.basedb.plugins.PackedFileExporter
 
configure(GuiContext, Request, Response) - Method in class net.sf.basedb.plugins.PlateFlatFileImporter
configure(GuiContext, Request, Response) - Method in class net.sf.basedb.plugins.PlateMappingExporter
configure(GuiContext, Request, Response) - Method in class net.sf.basedb.plugins.PlateMappingImporter
configure(GuiContext, Request, Response) - Method in class net.sf.basedb.plugins.PluginConfigurationExporter
Store configuration settings for Request.COMMAND_CONFIGURE_JOB.
configure(GuiContext, Request, Response) - Method in class net.sf.basedb.plugins.PluginConfigurationImporter
 
configure(GuiContext, Request, Response) - Method in class net.sf.basedb.plugins.PrintMapFlatFileImporter
configure(GuiContext, Request, Response) - Method in class net.sf.basedb.plugins.RawDataFlatFileImporter
configure(GuiContext, Request, Response) - Method in class net.sf.basedb.plugins.ReporterFlatFileImporter
configure(GuiContext, Request, Response) - Method in class net.sf.basedb.plugins.ReporterMapFlatFileImporter
configure(GuiContext, Request, Response) - Method in class net.sf.basedb.util.zip.AbstractFileUnpacker
 
CONFIGURE_IMPORT - Static variable in class net.sf.basedb.plugins.AnnotationFlatFileImporter
 
CONFIGURE_MAPPING - Static variable in class net.sf.basedb.plugins.AnnotationFlatFileImporter
 
CONFIGURE_OPTIONS - Static variable in class net.sf.basedb.plugins.batchimport.AbstractItemImporter
 
CONFIGURE_OPTIONS - Static variable in class net.sf.basedb.plugins.batchimport.AnyToAnyImporter
 
ConfigureByExample - Interface in net.sf.basedb.util.parser
This is a tagging interface for all plugins that use the FlatFileParser and wants easier configuration of the regular expressions used to parse the file.
configureExecutor - Variable in class net.sf.basedb.plugins.executor.BaseFileExporterSupport
 
configureExecutor - Variable in class net.sf.basedb.plugins.executor.BaseFileImporterSupport
 
configureExecutor - Variable in class net.sf.basedb.plugins.executor.BfsExporterSupport
 
configureExecutor - Variable in class net.sf.basedb.plugins.executor.BfsImporterSupport
 
configureExportImportPluginParameters - Variable in class net.sf.basedb.plugins.executor.ExternalProgramExecutor
 
configureExternalParameters - Variable in class net.sf.basedb.plugins.executor.ExternalProgramExecutor
 
configureImport - Variable in class net.sf.basedb.plugins.AnnotationFlatFileImporter
 
configureJob - Variable in class net.sf.basedb.clients.web.plugins.SimpleExport
 
configureJob - Variable in class net.sf.basedb.plugins.Base1PluginExecuter
Holds info about a job configuration request.
configureJob - Variable in class net.sf.basedb.plugins.BaseFileExporterPlugin
 
configureJob - Variable in class net.sf.basedb.plugins.BfsExporterPlugin
 
configureJob - Variable in class net.sf.basedb.plugins.CdfFileReporterImporter
 
configureJob - Variable in class net.sf.basedb.plugins.executor.BaseFileImporterSupport
 
configureJob - Variable in class net.sf.basedb.plugins.executor.BfsImporterSupport
 
configureJob - Variable in class net.sf.basedb.plugins.executor.ExternalProgramExecutor
 
configureJob - Variable in class net.sf.basedb.plugins.executor.FileOnlyImporterSupport
 
configureJob - Variable in class net.sf.basedb.plugins.FormulaFilter
 
configureJob - Variable in class net.sf.basedb.plugins.GalExporter
 
configureJob - Variable in class net.sf.basedb.plugins.gtf.GtfReporterMapImporter
 
configureJob - Variable in class net.sf.basedb.plugins.HelpExporter
 
configureJob - Variable in class net.sf.basedb.plugins.HelpImporter
 
configureJob - Variable in class net.sf.basedb.plugins.IlluminaRawDataImporter
 
configureJob - Variable in class net.sf.basedb.plugins.IntensityCalculatorPlugin
 
configureJob - Variable in class net.sf.basedb.plugins.JepExtraValueCalculator
 
configureJob - Variable in class net.sf.basedb.plugins.JepIntensityTransformer
 
configureJob - Variable in class net.sf.basedb.plugins.LowessNormalization
 
configureJob - Variable in class net.sf.basedb.plugins.ManualDerivedBioAssayCreator
 
configureJob - Variable in class net.sf.basedb.plugins.ManualTransformCreator
 
configureJob - Variable in class net.sf.basedb.plugins.MedianRatioNormalization
 
configureJob - Variable in class net.sf.basedb.plugins.PackedFileExporter
 
configureJob - Variable in class net.sf.basedb.plugins.PlateFlatFileImporter
 
configureJob - Variable in class net.sf.basedb.plugins.PlateMappingExporter
 
configureJob - Variable in class net.sf.basedb.plugins.PlateMappingImporter
 
configureJob - Variable in class net.sf.basedb.plugins.PluginConfigurationExporter
 
configureJob - Variable in class net.sf.basedb.plugins.PluginConfigurationImporter
 
configureJob - Variable in class net.sf.basedb.plugins.PrintMapFlatFileImporter
 
configureJob - Variable in class net.sf.basedb.plugins.RawDataFlatFileImporter
 
configureJob - Variable in class net.sf.basedb.plugins.ReporterFlatFileImporter
 
configureJob - Variable in class net.sf.basedb.plugins.ReporterMapFlatFileImporter
 
configureJob - Variable in class net.sf.basedb.util.zip.AbstractFileUnpacker
 
configureManual - Variable in class net.sf.basedb.plugins.Base1PluginExecuter
Holds information about a manual plugin configuration request.
configureMapping - Variable in class net.sf.basedb.plugins.AnnotationFlatFileImporter
 
configureOptions - Variable in class net.sf.basedb.plugins.batchimport.AbstractItemImporter
 
configureOptions - Variable in class net.sf.basedb.plugins.batchimport.AnyToAnyImporter
 
configureParser - Variable in class net.sf.basedb.plugins.AnnotationFlatFileImporter
 
configureParser - Variable in class net.sf.basedb.plugins.batchimport.AbstractItemImporter
 
configureParser - Variable in class net.sf.basedb.plugins.batchimport.AnyToAnyImporter
 
configureParser - Variable in class net.sf.basedb.plugins.RawDataFlatFileImporter
 
configurePlugin - Variable in class net.sf.basedb.plugins.Base1PluginExecuter
Holds information about a plugin configuration request.
configurePlugin - Variable in class net.sf.basedb.plugins.executor.ExternalProgramExecutor
 
configurePlugin - Variable in class net.sf.basedb.plugins.gtf.GtfReporterMapImporter
 
configurePlugin - Variable in class net.sf.basedb.plugins.ManualDerivedBioAssayCreator
 
configurePlugin - Variable in class net.sf.basedb.plugins.ManualTransformCreator
 
configurePlugin - Variable in class net.sf.basedb.plugins.PackedFileExporter
 
configurePlugin - Variable in class net.sf.basedb.plugins.PlateFlatFileImporter
 
configurePlugin - Variable in class net.sf.basedb.plugins.ReporterFlatFileImporter
 
configurePlugin - Variable in class net.sf.basedb.plugins.ReporterMapFlatFileImporter
 
configureQuery(DbControl, EntityQuery, boolean) - Method in class net.sf.basedb.core.ItemContext
 
configureQuery(DbControl, EntityQuery, ClientContext, boolean) - Method in class net.sf.basedb.core.ItemContext
Use the settings in this context to configure a query.
configureQuery(DbControl, SqlQuery, List<String>) - Method in class net.sf.basedb.core.ItemContext
Use the settings in this context to configure a dynamic query.
configureQuery(SqlQuery) - Method in interface net.sf.basedb.util.DynamicFilter
Configure the query before it is used.
configureQuery(SqlQuery) - Method in class net.sf.basedb.util.IncludeExcludeFilter
We need the position which is in column 2 (already selected).
configureRawDataType - Variable in class net.sf.basedb.plugins.RawDataFlatFileImporter
 
configureSelection - Variable in class net.sf.basedb.plugins.PluginConfigurationImporter
 
connect() - Method in class net.sf.basedb.util.jobagent.JobAgentConnection
Create a socket connection to the job agent.
connection() - Method in class net.sf.basedb.core.hibernate.StatelessSessionWrapper
Deprecated.
ConnectionClosedException - Exception in net.sf.basedb.core
This exception is thrown when trying to use a DbControl object that has been closed.
ConnectionClosedException() - Constructor for exception net.sf.basedb.core.ConnectionClosedException
Creates a new ConnectionClosedException.
ConnectionManager - Interface in net.sf.basedb.util.uri
A connection manager is used to access the contents and metadata about the resource pointed to by a given URI.
connectionManagerFactory - Variable in class net.sf.basedb.core.data.FileServerData
 
ConnectionManagerFactory - Interface in net.sf.basedb.util.uri
A connection manager factory is responsible for creating connection managers for some subset of URI:s that is supported.
ConnectionManagerUtil - Class in net.sf.basedb.util.uri
Collects utility methods related to connection managers.
ConnectionManagerUtil() - Constructor for class net.sf.basedb.util.uri.ConnectionManagerUtil
 
ConnectionParameters - Class in net.sf.basedb.util.uri
Connection parameters, such as username/password, that may be needed to connect to a server.
ConnectionParameters() - Constructor for class net.sf.basedb.util.uri.ConnectionParameters
Create a new empty parameters object.
connectTimeout - Variable in class net.sf.basedb.clients.jobagent.slotmanager.RemoteSlotManager
 
ConsoleProgressReporter - Class in net.sf.basedb.util
An implementation of the ProgressReporter interface that writes all messages to the standard console.
ConsoleProgressReporter() - Constructor for class net.sf.basedb.util.ConsoleProgressReporter
 
ConsoleProgressReporter(boolean) - Constructor for class net.sf.basedb.util.ConsoleProgressReporter
 
constant - Variable in class net.sf.basedb.util.parser.ConstantMapper
 
ConstantMapper - Class in net.sf.basedb.util.parser
A constant string mapper.
ConstantMapper(Float) - Constructor for class net.sf.basedb.util.parser.ConstantMapper
 
ConstantMapper(Integer) - Constructor for class net.sf.basedb.util.parser.ConstantMapper
 
ConstantMapper(String) - Constructor for class net.sf.basedb.util.parser.ConstantMapper
Create a constant mapper.
ConstantMapper(String, NumberFormat, boolean) - Constructor for class net.sf.basedb.util.parser.ConstantMapper
Create a constant mapper using a specific number formatter as it's parser.
ConstantMapper(String, NumberFormat, Formatter<Date>, boolean) - Constructor for class net.sf.basedb.util.parser.ConstantMapper
Create a constant mapper using a specific number formatter as it's parser.
ConstantMapper(Date, Formatter<Date>) - Constructor for class net.sf.basedb.util.parser.ConstantMapper
 
constructor - Variable in enum class net.sf.basedb.core.Item
 
contact - Variable in class net.sf.basedb.core.data.PluginDefinitionData
 
contact - Variable in class net.sf.basedb.core.plugin.AboutImpl
 
contact - Variable in class net.sf.basedb.util.extensions.AboutBean
 
contact - Variable in class net.sf.basedb.util.extensions.Registry.RegisteredAbout
 
contains(Object) - Method in class net.sf.basedb.core.hibernate.SessionWrapper
 
contains(Object) - Method in class net.sf.basedb.core.ItemResultList
 
contains(Object) - Method in class net.sf.basedb.util.Tree
 
contains(String, Object) - Method in class net.sf.basedb.core.hibernate.SessionWrapper
 
contains(AnnotationUtil.AnnotatableWrapper) - Method in class net.sf.basedb.util.AnnotationUtil.Cache
 
containsAll(Collection<?>) - Method in class net.sf.basedb.core.AbstractResultList
 
containsAll(Collection<?>) - Method in class net.sf.basedb.core.UnmodifiableResultList
 
containsAll(Collection<?>) - Method in class net.sf.basedb.util.Tree
 
containsKey(Object) - Method in class net.sf.basedb.util.formatter.LookupFormatter
Checks if a given key has been registered.
containsKey(Object) - Method in class net.sf.basedb.util.jep.FunctionSafeJep.SafeFunctionTable
If the key is already registered, return TRUE.
content - Variable in class net.sf.basedb.clients.web.extensions.section.SectionBean
 
content - Variable in class net.sf.basedb.clients.web.extensions.tabcontrol.FixedTabFactory
 
content - Variable in class net.sf.basedb.clients.web.extensions.tabcontrol.TabBean
 
content - Variable in class net.sf.basedb.clients.web.taglib.tab.TabControl
The HTML for the contents of the tabs.
ContentSecurityPolicyFilter - Class in net.sf.basedb.clients.web.servlet
This is a filter that sets the "Content-Security-Policy" header in the http response.
ContentSecurityPolicyFilter() - Constructor for class net.sf.basedb.clients.web.servlet.ContentSecurityPolicyFilter
 
ContentSecurityPolicyReportServlet - Class in net.sf.basedb.clients.web.servlet
This is a servlet for posting reports from "Content-Security-Policy" violations.
ContentSecurityPolicyReportServlet() - Constructor for class net.sf.basedb.clients.web.servlet.ContentSecurityPolicyReportServlet
 
contentStyle - Variable in class net.sf.basedb.clients.web.extensions.section.IncludeContentSectionFactory
 
contentStyle - Variable in class net.sf.basedb.clients.web.extensions.section.SectionBean
 
contentStyle - Variable in class net.sf.basedb.clients.web.taglib.HideableSection
Optional style attribute for the content section
contentStyle - Variable in class net.sf.basedb.clients.web.taglib.tab.TabControl
Optional style attribute for the content section
context - Variable in class net.sf.basedb.clients.web.extensions.LoadServletsProcessor
 
context - Variable in class net.sf.basedb.clients.web.extensions.renderer.PrefixSuffixRenderer
 
context - Variable in class net.sf.basedb.clients.web.extensions.ServletWrapper
 
context - Variable in class net.sf.basedb.clients.web.extensions.tabcontrol.IncludeContentTabFactory.Tab
 
context - Variable in class net.sf.basedb.clients.web.extensions.toolbar.CompactButtonRenderer
 
context - Variable in class net.sf.basedb.clients.web.extensions.toolbar.ToolbarButtonRenderer
 
context - Variable in class net.sf.basedb.clients.web.taglib.extensions.Render
 
context - Variable in class net.sf.basedb.clients.web.taglib.extensions.Scripts
 
context - Variable in class net.sf.basedb.clients.web.taglib.extensions.Stylesheets
 
context - Variable in class net.sf.basedb.clients.web.taglib.HideableSection
 
context - Variable in class net.sf.basedb.core.PluginConfigurationRequest
 
context - Variable in class net.sf.basedb.core.signal.ExtensionSignalTransporter
 
context - Variable in class net.sf.basedb.util.overview.node.NodeFactory
 
CONTEXT_BIOASSAYS - Static variable in class net.sf.basedb.core.plugin.AbstractAnalysisPlugin
GuiContext = [Item.BIOASSAY, GuiContext.Type.LIST]
CONTEXT_BIOASSAYSET - Static variable in class net.sf.basedb.core.plugin.AbstractAnalysisPlugin
GuiContext = [Item.BIOASSAYSET, GuiContext.Type.ITEM]
CONTEXT_DERIVEDBIOASSAY - Static variable in class net.sf.basedb.core.plugin.AbstractAnalysisPlugin
GuiContext = [Item.DERIVEDBIOASSAY, GuiContext.Type.ITEM]
CONTEXT_RELATIVE - Enum constant in enum class net.sf.basedb.util.extensions.xml.PathType
Paths should be relative to the web application context.
ContextData - Class in net.sf.basedb.core.data
This class holds context information to help client applications with storing common settings for tables.
ContextData() - Constructor for class net.sf.basedb.core.data.ContextData
 
contextDestroyed(ServletContextEvent) - Method in class net.sf.basedb.clients.web.servlet.StartStopServlet
 
contextId - Variable in class net.sf.basedb.core.ItemContext
 
ContextIndex - Class in net.sf.basedb.core.data
 
ContextIndex() - Constructor for class net.sf.basedb.core.data.ContextIndex
 
ContextIndex(ClientData, int, String, String) - Constructor for class net.sf.basedb.core.data.ContextIndex
 
contextInitialized(ServletContextEvent) - Method in class net.sf.basedb.clients.web.servlet.StartStopServlet
 
contextItem - Variable in class net.sf.basedb.core.data.JobData
 
ContextKey - Class in net.sf.basedb.core
 
ContextKey(Item, String) - Constructor for class net.sf.basedb.core.ContextKey
Create a new ContextKey object from Item and it's subcontext.
contextMessage - Variable in class net.sf.basedb.util.ContextUtil.ContextResult
 
contextPath - Variable in class net.sf.basedb.clients.web.servlet.ImageRemapFilter
 
contextPath - Variable in class net.sf.basedb.clients.web.servlet.RssNewsFeed
 
ContextResult(PluginDefinition, PluginConfiguration, String) - Constructor for class net.sf.basedb.util.ContextUtil.ContextResult
Create a new warning-level result object.
ContextResult(PluginDefinition, PluginConfiguration, Throwable) - Constructor for class net.sf.basedb.util.ContextUtil.ContextResult
Create a new error-level result object.
ContextResult(SessionControl, PluginDefinition, PluginConfiguration, GuiContext, Object) - Constructor for class net.sf.basedb.util.ContextUtil.ContextResult
 
contexts - Variable in class net.sf.basedb.core.data.ClientData
 
contexts - Variable in class net.sf.basedb.core.data.UserData
 
contexts - Variable in class net.sf.basedb.util.extensions.ExtensionsInvoker
 
contextType - Variable in class net.sf.basedb.core.data.GuiContextData
 
contextType - Variable in class net.sf.basedb.core.data.JobData
 
ContextUtil - Class in net.sf.basedb.util
A class with utility methods for plug-ins.
ContextUtil() - Constructor for class net.sf.basedb.util.ContextUtil
 
ContextUtil.ContextResult - Class in net.sf.basedb.util
Class for holding the result of a call to the InteractivePlugin.isInContext(GuiContext, Object) method.
ContextUtil.IsInContextFilter - Class in net.sf.basedb.util
Filter implementation that works on collections of ContextUtil.ContextResult:s and return only those that return true from ContextUtil.ContextResult.isInContext().
CONTINUE - Enum constant in enum class net.sf.basedb.core.plugin.Response.Status
 
continueAfterError - Variable in class net.sf.basedb.plugins.RawDataFlatFileImporter
 
continueLater(String, boolean, Serializable) - Method in class net.sf.basedb.core.Job
This method is used to indicate that a job had to be aborted due to a system shutdown.
continueWithNextFileAfterError(Throwable) - Method in class net.sf.basedb.plugins.AbstractFlatFileImporter
If the importer should continue with the next file after an error.
continueWithNextFileAfterError(Throwable) - Method in class net.sf.basedb.plugins.RawDataFlatFileImporter
We will continue if: The file is not of the correct format, eg. t = UnsupportedFileFormatException.
Controlled - Interface in net.sf.basedb.core
This is the base tagging interface for items that needs special attention by the DbControl object when DbControl.commit() is called.
convert(Enum<T>) - Method in class net.sf.basedb.util.json.EnumConverter
 
convert(String) - Method in class net.sf.basedb.util.extensions.debug.StringConverter
 
convert(String, Method) - Method in class net.sf.basedb.util.extensions.xml.PathConverter
 
convert(String, Method) - Method in interface net.sf.basedb.util.extensions.xml.ValueConverter
Convert a value.
convert(String, Method) - Method in class net.sf.basedb.util.extensions.xml.VariableConverter
 
convert(T) - Method in class net.sf.basedb.util.json.IdentityConverter
 
convert(T) - Method in interface net.sf.basedb.util.json.JsonConverter
Convert the given object to a JSON-compatible object.
convert(T) - Method in class net.sf.basedb.util.json.NameableConverter
 
converter - Variable in class net.sf.basedb.core.snapshot.AnnotationLoaderUtil
 
converter - Static variable in class net.sf.basedb.util.extensions.debug.StringConverter
 
ConverterFactory - Class in net.sf.basedb.util.jep.convert
Keep JepConversionFunction objects for converting built-in JEP object to Query API Expression or Restriction objects.
ConverterFactory() - Constructor for class net.sf.basedb.util.jep.convert.ConverterFactory
 
converters - Variable in class net.sf.basedb.util.extensions.xml.XmlLoader
 
converters - Static variable in class net.sf.basedb.util.jep.convert.ConverterFactory
 
convertJavaDateFormatToExcelFormat(String) - Static method in class net.sf.basedb.util.excel.CellStyleCreator
Converts a Java date format string to the corresponding Excel date format string.
convertNumber(Number) - Method in enum class net.sf.basedb.core.Type
Convert a number to the appropriate class.
convertPresets(ProgressReporter) - Static method in class net.sf.basedb.core.Update
Convert presets to use subtype/subcategories if they have filters that are matching existing configuration.
convertString(Class, String) - Static method in class net.sf.basedb.util.extensions.debug.StringConverter
 
convertSyncFilters(ProgressReporter) - Static method in class net.sf.basedb.core.Update
Convert sync filters to use subtype if they have filters that are matching existing configuration.
convertToNull(String) - Method in class net.sf.basedb.util.parser.FlatFileParser
 
convertToReferenceUnit(double) - Method in class net.sf.basedb.util.units.IdentityUnitConverter
 
convertToReferenceUnit(double) - Method in class net.sf.basedb.util.units.LinearUnitConverter
value(ref) = value(specific) * factor + offset
convertToReferenceUnit(double) - Method in interface net.sf.basedb.util.units.UnitConverter
Convert a value from the specific unit to the reference unit.
convertToSpecificUnit(double) - Method in class net.sf.basedb.util.units.IdentityUnitConverter
 
convertToSpecificUnit(double) - Method in class net.sf.basedb.util.units.LinearUnitConverter
value(specific) = (value(ref) - offset) / factor
convertToSpecificUnit(double) - Method in interface net.sf.basedb.util.units.UnitConverter
Convert a value from the reference unit to the specific unit.
convertValue(String, Class<?>) - Method in class net.sf.basedb.util.extensions.debug.BeanActionFactory
Convert a string value to another type.
convertValues(AnnotationType, List<?>, Unit) - Method in class net.sf.basedb.core.Annotation
 
convertValueToUnit(Session, String, String, Unit) - Method in class net.sf.basedb.core.PropertyFilter
Converts a string to a numeric value with the correct unit.
Coordinate - Class in net.sf.basedb.util
Util class for coordinate transformations in base.
Coordinate() - Constructor for class net.sf.basedb.util.Coordinate
 
COORDINATES - Enum constant in enum class net.sf.basedb.core.FeatureIdentificationMethod
Use coordinates (block, metaGridX, metaGridY, row, column)
coordinateType - Variable in class net.sf.basedb.core.data.DataCubeExtraValueData
 
CoordinateType(int) - Constructor for enum class net.sf.basedb.core.ExtraValue.CoordinateType
 
copy(byte[], int, int) - Method in class net.sf.basedb.util.InputStreamSplitter
Write data to all output streams.
copy(int) - Method in class net.sf.basedb.util.InputStreamSplitter
Write data to all output streams.
copy(InputStream, OutputStream) - Static method in class net.sf.basedb.util.FileUtil
Copy from the input stream to the output stream until end of file is reached.
copy(InputStream, OutputStream, AbsoluteProgressReporter) - Static method in class net.sf.basedb.util.FileUtil
Copy from the input stream to the output stream until end of file is reached.
copy(Reader, Writer) - Static method in class net.sf.basedb.util.FileUtil
Copy from the reader to the writer until end of file is reached.
copy(Reader, Writer, AbsoluteProgressReporter) - Static method in class net.sf.basedb.util.FileUtil
Copy from the reader to the writer until end of file is reached.
copy(Date) - Static method in class net.sf.basedb.core.DateUtil
Get a copy of the date.
copy(File, File) - Method in class net.sf.basedb.plugins.Base1PluginExecuter
Copies the content from a File to a directory on the file system.
copy(About, boolean) - Method in class net.sf.basedb.util.extensions.AboutBean
Copy information from antoher About object to this one.
COPY_ANNOTATIONS - Static variable in class net.sf.basedb.core.plugin.AbstractPlugin
The name of the parameter that asks if annotations should be copied or not.
copyFrom(Annotatable, boolean) - Method in class net.sf.basedb.core.AnnotationSet
Copy annotations from another annotatable item to this annotation set.
copyFrom(ItemContext, boolean) - Method in class net.sf.basedb.core.ItemContext
Copy settings from another context to this context.
copyFromSyncFilter(ItemListSyncFilterData) - Method in class net.sf.basedb.core.ItemContext
 
copyMetadata(FusionCDFData, ArrayDesign) - Method in class net.sf.basedb.util.affymetrix.CdfValidator
Copy metadata from the CDF file to the array design.
copyMetadata(FusionCELData, RawBioAssay) - Method in class net.sf.basedb.util.affymetrix.CelValidator
Copy metadata from the CEL file to the raw bioassay.
copyNotNulls(Collection<? extends T>, T[]) - Static method in class net.sf.basedb.core.query.Restrictions
 
copyNotNulls(T[], T[]) - Static method in class net.sf.basedb.core.query.Restrictions
 
copyObjectsAndTemporaryFilters(ItemContext) - Method in class net.sf.basedb.core.ItemContext
Copies all objects and temporary filters from this context to another context.
copyParametersFrom(Job) - Method in class net.sf.basedb.core.Job
Copy all parameter values from another job.
copyParametersFrom(PluginConfiguration) - Method in class net.sf.basedb.core.PluginConfiguration
Copy all parameter values from another plugin configuration.
copyPermissions(DbControl, Shareable, Shareable) - Static method in class net.sf.basedb.core.ShareableUtil
Copy permissions from one item to another.
copyProperties(File, File) - Static method in class net.sf.basedb.util.zip.PackUtil
Copy certain properties from the archive file to the unpacked file.
copyRedefinedColumnNames(BaseFileParser) - Method in class net.sf.basedb.util.basefile.BaseFileParser
Copy redefined column names from the given parser into this parser.
copyReporterFields(int, Object[], int) - Method in class net.sf.basedb.util.export.spotdata.AbstractBioAssaySetExporter
Copy cached reporter data into a data array.
copyright - Variable in class net.sf.basedb.core.data.PluginDefinitionData
 
copyright - Variable in class net.sf.basedb.core.plugin.AboutImpl
 
copyright - Variable in class net.sf.basedb.util.extensions.AboutBean
 
copyright - Variable in class net.sf.basedb.util.extensions.Registry.RegisteredAbout
 
copySkipped - Variable in class net.sf.basedb.util.InputStreamSplitter
If the InputStreamSplitter.skip(long) method should copy to the output streams or no.
copySubdirectories(DbControl, Directory, Directory, User) - Static method in class net.sf.basedb.core.Directory
This method copies a directory strucure to the destination directory.
copySyncFiltersAndMembers(DbControl, ItemList) - Method in class net.sf.basedb.core.ItemList
Copy all sync filters and list members from the given list.
copyTo - Variable in class net.sf.basedb.util.InputStreamSplitter
Streams to copy the data to.
copyToContext(ItemContext) - Method in class net.sf.basedb.core.SyncFilter
Copy the filter settings in this synchronization filter to the given item context.
copyToStdout - Variable in class net.sf.basedb.util.extensions.logging.ExtensionsLog
 
copyToSyncFilter(ItemListSyncFilterData) - Method in class net.sf.basedb.core.ItemContext
Create a new item list synchronization filter from this context.
correct(double, double, double) - Method in class net.sf.basedb.util.ma.Log10MACalculator
ch1 = old - factor * log10(2) ch2 = old + factor * log10(2)
correct(double, double, double) - Method in class net.sf.basedb.util.ma.Log2MACalculator
ch1 = old - factor ch2 = old + factor
correct(double, double, double) - Method in class net.sf.basedb.util.ma.MACalculator
Apply a correction factor to the ch1 and ch2 intensity values.
couldParse - Variable in class net.sf.basedb.core.File.CharsetTesterThread
 
couldParse() - Method in class net.sf.basedb.core.File.CharsetTesterThread
Returns TRUE if the file seems like valid (UTF-8).
count - Variable in class net.sf.basedb.clients.web.ExperimentExplorer.AnnotationGroup
 
count - Variable in class net.sf.basedb.core.AnnotationBatcher.UpdateBatcher
 
count - Variable in class net.sf.basedb.util.AnyToAnyLinkStatistics
 
count - Variable in class net.sf.basedb.util.plot.HistogramPlot.HistogramBin
 
count(Collection<ItemList>, int, int, ItemList.DelayedAdditionManager) - Static method in class net.sf.basedb.core.ItemList
Count the number of times each item is present in the given lists and return those items that are found in >=minCount and <=maxCount lists.
count(Collection<ReporterList>, int, int) - Static method in class net.sf.basedb.core.ReporterList
Count the number of times each reporter is present in the given lists and return those reporters that are found in >=minCount and <=maxCount lists.
count(DbControl) - Method in class net.sf.basedb.core.AbstractEntityQuery
 
count(DbControl) - Method in class net.sf.basedb.core.AbstractHqlQuery
 
count(DbControl) - Method in class net.sf.basedb.core.AbstractSqlQuery
 
count(DbControl) - Method in interface net.sf.basedb.core.query.Query
Count the number of items/rows that are returned by the query.
count(Expression, boolean) - Static method in class net.sf.basedb.core.query.Aggregations
Calculates the number of values for an expression: new expression = COUNT(e)
COUNT - Enum constant in enum class net.sf.basedb.util.plot.HistogramPlot.YAggregate
Plot the number of spots falling into each bin.
countBioAssaySpots() - Method in class net.sf.basedb.core.BioAssaySet
 
countChildren(boolean) - Method in class net.sf.basedb.core.BioMaterial
Count the number of already existing children to this biomaterial.
countChildren(boolean) - Method in class net.sf.basedb.core.BioSource
Count the number of child samples.
countChildren(boolean) - Method in class net.sf.basedb.core.Extract
Count the number of child extracts.
countChildren(boolean) - Method in class net.sf.basedb.core.Sample
Count the number of child samples or extracts.
counter - Variable in class net.sf.basedb.clients.web.plugins.DynamicQueryWrapper
 
CountExpression - Class in net.sf.basedb.core.query
Count the number of values: COUNT(e)
CountExpression(Expression, boolean) - Constructor for class net.sf.basedb.core.query.CountExpression
 
countExtracts() - Method in class net.sf.basedb.core.Extract
Counts all extracts that have been created from this extract.
countExtracts() - Method in class net.sf.basedb.core.Sample
Counts all extracts that have been created from this sample.
countNotNulls(Object[]) - Static method in class net.sf.basedb.core.query.Restrictions
 
countNotNulls(Collection<?>) - Static method in class net.sf.basedb.core.query.Restrictions
 
countPlugins(DbControl, GuiContext) - Static method in class net.sf.basedb.core.PluginDefinition
Count the number of plugins that can be used in a given context.
countProjectSpecificAnnotations() - Method in class net.sf.basedb.core.AnnotationType
Count the number of project-specific annotations that exists for this annotation type.
countQuery - Variable in class net.sf.basedb.util.export.spotdata.MatrixBaseFileExporter
 
countQuery - Variable in class net.sf.basedb.util.export.spotdata.SerialBaseFileExporter
 
countRawBioAssays() - Method in class net.sf.basedb.core.DerivedBioAssay
Counts all raw bioassays that have been created from this bioassay.
countRootDerivedBioAssays() - Method in class net.sf.basedb.core.PhysicalBioAssay
Counts all root derived bioassays that have been created from this physical bioassay.
country - Variable in class net.sf.basedb.util.GeoLocation
 
countSamples() - Method in class net.sf.basedb.core.BioSource
Counts all samples that have been created from this biosource.
countSamples() - Method in class net.sf.basedb.core.Sample
Counts all samples that have been created from this sample.
countSpotMappings() - Method in class net.sf.basedb.core.DataCube
Count the number of raw data mappings for the spot with the most mappings.
countSpotsAndReporters() - Method in class net.sf.basedb.core.BioAssaySet
Count the number of unique reporters and spots in all bioassays in this bioassayset.
countUnreadMessages(DbControl, User, boolean) - Static method in class net.sf.basedb.core.Message
Count the number of unread messages for the specified or logged in user.
countUsuablePlugins(Collection<ContextUtil.ContextResult>) - Static method in class net.sf.basedb.util.ContextUtil
Count all plug-in / configuration combinations that can be used.
CountWork(SessionControl, String, List<String>) - Constructor for class net.sf.basedb.core.AbstractSqlQuery.CountWork
 
cpuUsage - Variable in class net.sf.basedb.util.jobagent.JobAgentInfo
 
create(File) - Static method in class net.sf.basedb.util.bfs.AnnotationParser
Utility method for creating an annotation parser for a file in the local file system.
create(File) - Static method in class net.sf.basedb.util.bfs.AnnotationWriter
Utility method for creating an annotation writer to a file in the native file system.
create(File) - Static method in class net.sf.basedb.util.bfs.DataParser
Utility method for creating a data parser for a file in the local file system.
create(File) - Static method in class net.sf.basedb.util.bfs.DataWriter
Utility method for creating a data writer to a file in the native file system.
create(File) - Static method in class net.sf.basedb.util.bfs.MetadataParser
Utility method for creating a metadata parser for a file in the local file system.
create(File) - Static method in class net.sf.basedb.util.bfs.MetadataWriter
Utility method for creating a metadata writer to a file in the native file system.
create(InputStream, String, long) - Static method in class net.sf.basedb.util.bfs.AnnotationParser
Utility method for creating an annotation parser when you have an input stream.
create(InputStream, String, long) - Static method in class net.sf.basedb.util.bfs.DataParser
Utility method for creating a data parser when you have an input stream.
create(InputStream, String, long) - Static method in class net.sf.basedb.util.bfs.MetadataParser
Utility method for creating a metadata parser when you have an input stream.
create(OutputStream, String) - Static method in class net.sf.basedb.util.bfs.AnnotationWriter
Utility method for creating an annotation writer when you have an output stream.
create(OutputStream, String) - Static method in class net.sf.basedb.util.bfs.DataWriter
Utility method for creating a data writer when you have an output stream.
create(OutputStream, String) - Static method in class net.sf.basedb.util.bfs.MetadataWriter
Utility method for creating a metadata writer when you have an output stream.
create(Class<?>) - Static method in class net.sf.basedb.core.log.EntityLogOptions
 
create(String) - Static method in class net.sf.basedb.core.ClonableProperty
Create a cloned property from either an extended or static property.
create(String, PropertyFilterData) - Static method in class net.sf.basedb.core.PropertyFilter
Create a property filter instance from what has been saved in the database.
create(String, Item, String) - Static method in class net.sf.basedb.clients.web.plugins.AnyToAnyDataLoader
Create a new data loader that load a value from an any-to-any link.
create(ResultSet, int, Writer, TableInfo.ColumnInfo) - Method in class net.sf.basedb.core.migrate.postgres.PostgresResultWriterFactory
 
create(ResultSet, int, Writer, TableInfo.ColumnInfo) - Method in interface net.sf.basedb.core.migrate.ResultWriterFactory
Create a new result writer.
create(FileServerData) - Static method in class net.sf.basedb.util.uri.ConnectionParameters
Create a parameters object using information from the FileServer object.
create(DbControl, int, RelatedItemColumn.Specification, RelatedItemHelper) - Static method in class net.sf.basedb.clients.web.extensions.list.RelatedItemColumn
For now, we assume that 'expr' is one of: /DIRECTION/ITEMTYPE/subtype-id/#annotationtype-id /DIRECTION/ITEMTYPE/subtype-id/!
create(DbControl, int, Item, String, FileViewerUtil) - Static method in class net.sf.basedb.clients.web.extensions.list.AnyLinkColumn
For now, we assume that 'expr' is |linkName|ITEMTYPE|property ITEMTYPE and property are optional.
create(File) - Static method in class net.sf.basedb.util.bfs.AnnotationParser
Utility method for creating an annotation parser for a file in the BASE file system.
create(File) - Static method in class net.sf.basedb.util.bfs.AnnotationWriter
Utility method for creating an annotation writer to a file in the BASE file system.
create(File) - Static method in class net.sf.basedb.util.bfs.DataParser
Utility method for creating a data parser for a file in the BASE file system.
create(File) - Static method in class net.sf.basedb.util.bfs.DataWriter
Utility method for creating a data writer to a file in the BASE file system.
create(File) - Static method in class net.sf.basedb.util.bfs.MetadataParser
Utility method for creating a metadata parser for a file in the BASE file system.
create(File) - Static method in class net.sf.basedb.util.bfs.MetadataWriter
Utility method for creating a metadata writer to a file in the BASE file system.
create(Item, SyncFilter.SourceItemTransform) - Method in interface net.sf.basedb.util.listable.SourceItemTransformerFactory
Create a source item transformed that can transform between the given source item and the SourceItemTransformerFactory.getTargetItem().
create(Item, SyncFilter.SourceItemTransform) - Method in class net.sf.basedb.util.listable.SourceItemTransformerWithCache
 
create(Item, SyncFilter.SourceItemTransform) - Method in class net.sf.basedb.util.listable.ToBioSourceSourceItemTransformerFactory
 
create(Item, SyncFilter.SourceItemTransform) - Method in class net.sf.basedb.util.listable.ToDerivedBioAssaySourceItemTransformerFactory
 
create(Item, SyncFilter.SourceItemTransform) - Method in class net.sf.basedb.util.listable.ToExtractSourceItemTransformerFactory
 
create(Item, SyncFilter.SourceItemTransform) - Method in class net.sf.basedb.util.listable.ToPhysicalBioAssaySourceItemTransformerFactory
 
create(Item, SyncFilter.SourceItemTransform) - Method in class net.sf.basedb.util.listable.ToRawBioAssaySourceItemTransformerFactory
 
create(Item, SyncFilter.SourceItemTransform) - Method in class net.sf.basedb.util.listable.ToSampleSourceItemTransformerFactory
 
create(Mapper) - Static method in class net.sf.basedb.plugins.batchimport.UsedQuantityMapper
 
CREATE - Enum constant in enum class net.sf.basedb.core.log.ChangeType
 
CREATE - Enum constant in enum class net.sf.basedb.core.Permission
This permission allows a user create new items.
CREATE - Enum constant in enum class net.sf.basedb.core.Transactional.Action
The item is a new item and is beeing saved to the database for the first time.
CREATE_BIOMATERIAL - Static variable in class net.sf.basedb.core.BioPlateEventType
The system ID for "Create" event type.
createAgent(Properties) - Method in class net.sf.basedb.clients.jobagent.AgentController
 
createAllCopy(String) - Static method in class net.sf.basedb.core.ReporterCloneTemplate
 
createAnnotationType(String, String, Type, int, Object[], Item[], Map<String, String>, boolean, boolean, UserData, ItemKeyData) - Static method in class net.sf.basedb.core.Install
Create an AnnotationType.
createBean(Class<? extends Action>) - Method in class net.sf.basedb.util.extensions.debug.BeanActionFactory
Create the bean instance.
createBioPlateEventType(String, String, String) - Static method in class net.sf.basedb.core.Install
createBioPlateType(String, String, Item, ItemSubtypeData, BioWell.LockMode) - Static method in class net.sf.basedb.core.Install
Create a BioPlateType.
createBlockHeaders(List<String>, ArrayDesign, Integer, List<ArrayDesignBlock>) - Method in class net.sf.basedb.plugins.GalExporter
Create header entries for each block in the array design.
createCache() - Static method in class net.sf.basedb.util.AnnotationUtil
createChildBioAssays(DbControl, BioAssaySet, BaseFileInfo, boolean) - Method in class net.sf.basedb.util.importer.spotdata.BaseFileImporter
Helper method for creating new child bioassays using the information found in the BaseFileInfo object.
createChildBioAssaySet(DbControl, BaseFileInfo, Transformation, boolean) - Method in class net.sf.basedb.util.importer.spotdata.BaseFileImporter
Helper method for creating a child bioassay set using the information in the BaseFileInfo object.
createChildNodes(DbControl, OverviewContext, Node) - Method in interface net.sf.basedb.util.overview.extensions.ChildNodeLoaderAction
Create child nodes for the given parent node.
createChildPositionReporterMapping(BioAssaySet, BaseFileInfo, ProgressReporter) - Method in class net.sf.basedb.util.importer.spotdata.BaseFileImporter
Helper method for creating position/reporter mappings for the child bioassay set (which must be in a new datacube).
createChildRawDataMapping(BioAssaySet, BioAssaySet, BaseFileInfo, ProgressReporter) - Method in class net.sf.basedb.util.importer.spotdata.BaseFileImporter
Helper method for creating a rawdata mapping for the child bioassay set.
createClient(UserData, String, String, String, ItemKeyData) - Static method in class net.sf.basedb.core.Install
Create a Client.
createCloseableHttpClient(URI, ConnectionParameters) - Method in class net.sf.basedb.util.uri.http.HttpConnectionManager
Get a HttpClient object that has been configured to access the given URI.
createColumnMappers(FlatFileParser, boolean) - Method in class net.sf.basedb.plugins.batchimport.AbstractItemImporter
Create mappers that can be used to extract data values from the file that is currently being parsed by the ffp FlatFileParser.
createColumnMappers(FlatFileParser, boolean) - Method in class net.sf.basedb.plugins.batchimport.AnnotationTypeImporter
 
createColumnMappers(FlatFileParser, boolean) - Method in class net.sf.basedb.plugins.batchimport.ArrayBatchImporter
 
createColumnMappers(FlatFileParser, boolean) - Method in class net.sf.basedb.plugins.batchimport.ArrayDesignImporter
 
createColumnMappers(FlatFileParser, boolean) - Method in class net.sf.basedb.plugins.batchimport.ArraySlideImporter
 
createColumnMappers(FlatFileParser, boolean) - Method in class net.sf.basedb.plugins.batchimport.BioPlateImporter
 
createColumnMappers(FlatFileParser, boolean) - Method in class net.sf.basedb.plugins.batchimport.BioSourceImporter
 
createColumnMappers(FlatFileParser, boolean) - Method in class net.sf.basedb.plugins.batchimport.DerivedBioAssayImporter
 
createColumnMappers(FlatFileParser, boolean) - Method in class net.sf.basedb.plugins.batchimport.ExtractImporter
 
createColumnMappers(FlatFileParser, boolean) - Method in class net.sf.basedb.plugins.batchimport.FileImporter
 
createColumnMappers(FlatFileParser, boolean) - Method in class net.sf.basedb.plugins.batchimport.KitImporter
 
createColumnMappers(FlatFileParser, boolean) - Method in class net.sf.basedb.plugins.batchimport.PhysicalBioAssayImporter
 
createColumnMappers(FlatFileParser, boolean) - Method in class net.sf.basedb.plugins.batchimport.RawBioAssayImporter
 
createColumnMappers(FlatFileParser, boolean) - Method in class net.sf.basedb.plugins.batchimport.SampleImporter
 
createColumnMappers(FlatFileParser, boolean) - Method in class net.sf.basedb.plugins.batchimport.TagImporter
 
createConnectionManager(URI, ConnectionParameters) - Method in interface net.sf.basedb.util.uri.ConnectionManagerFactory
Create a new handler for accessing the resource at the given URI.
createConnectionManager(URI, ConnectionParameters) - Static method in class net.sf.basedb.util.uri.ConnectionManagerUtil
Utility method for creating a connection manager.
createConnectionManager(URI, ConnectionParameters) - Method in class net.sf.basedb.util.uri.http.HttpConnectionManagerFactory
 
createConnectionManager(File, ConnectionParameters) - Static method in class net.sf.basedb.util.uri.ConnectionManagerUtil
Utility method for creating a connection manager for a file item.
createContext(DbControl, PageContext) - Static method in class net.sf.basedb.clients.web.extensions.ExtensionsControl
Create a new JspContext object with an active DbControl.
createContext(DbControl, PageContext, GuiContext, Object) - Static method in class net.sf.basedb.clients.web.extensions.ExtensionsControl
createContext(DbControl, ItemContext, PageContext, GuiContext, Object) - Static method in class net.sf.basedb.clients.web.extensions.ExtensionsControl
Create a new JspContext object with an active DbControl and a current GuiContext and item.
createContext(SessionControl, PageContext) - Static method in class net.sf.basedb.clients.web.extensions.ExtensionsControl
Create a new JspContext object without an active DbControl.
createCountWork(DbControl) - Method in class net.sf.basedb.core.AbstractSqlQuery
Creates a work item for counting the number of total hits by the query.
createCriteria(Class) - Method in class net.sf.basedb.core.hibernate.SessionWrapper
Deprecated.
createCriteria(Class) - Method in class net.sf.basedb.core.hibernate.StatelessSessionWrapper
Deprecated.
createCriteria(Class, String) - Method in class net.sf.basedb.core.hibernate.SessionWrapper
Deprecated.
createCriteria(Class, String) - Method in class net.sf.basedb.core.hibernate.StatelessSessionWrapper
Deprecated.
createCriteria(String) - Method in class net.sf.basedb.core.hibernate.SessionWrapper
Deprecated.
createCriteria(String) - Method in class net.sf.basedb.core.hibernate.StatelessSessionWrapper
Deprecated.
createCriteria(String, String) - Method in class net.sf.basedb.core.hibernate.SessionWrapper
Deprecated.
createCriteria(String, String) - Method in class net.sf.basedb.core.hibernate.StatelessSessionWrapper
Deprecated.
created - Variable in class net.sf.basedb.clients.jobagent.slotmanager.MasterSlotManager.RemoteSlot
 
created - Variable in class net.sf.basedb.core.data.JobData
 
created - Variable in class net.sf.basedb.core.snapshot.AnnotationSetSnapshot
 
created - Variable in class net.sf.basedb.util.jobagent.JobAgentInfo
 
createDataFileType(String, String, String, Item, String, ItemSubtypeData, Install.ItemSubtypeFT...) - Static method in class net.sf.basedb.core.Install
Create a DataFileType.
createDataWriter(Object, String) - Method in class net.sf.basedb.util.export.spotdata.BfsExporter
Utility method for calling creating a data writer.
createDataWriter(T, String) - Method in class net.sf.basedb.util.bfs.AbstractDataWriterFactory
 
createDataWriter(T, String) - Method in interface net.sf.basedb.util.bfs.DataWriterFactory
Create a data writer for writing data that belongs to the given owner.
createDataWriters() - Method in class net.sf.basedb.util.export.spotdata.BfsExporter
Create the exact number of data writers that is needed to export the desired data.
createDataWriters() - Method in class net.sf.basedb.util.export.spotdata.MatrixBfsExporter
Create one data writer for each registered spot field.
createDataWriters() - Method in class net.sf.basedb.util.export.spotdata.SerialBfsExporter
Create one data writer for each assay in the bioassay set.
createdColumnMapping - Static variable in class net.sf.basedb.plugins.batchimport.SampleImporter
Column mapping parameter for the sample creation date.
createDefaultContext(String, String) - Static method in class net.sf.basedb.clients.web.Base
Create a default context where the sortProperty is also used as the default sticky column.
createDefaultContext(String, String, String) - Static method in class net.sf.basedb.clients.web.Base
Create a default ItemContext with settings for default visible columns and sort property.
createDelayedAdditionManager() - Method in class net.sf.basedb.core.ItemList
 
createDeniedNode(Node) - Method in class net.sf.basedb.util.overview.node.NodeFactory
Create a node representing an item that the logged in user is denied to access.
createDerivedBioAssay(AnnotationBatcher.InsertBatcher) - Method in class net.sf.basedb.core.MigrateRbaToDba.Rba
Create the new derived bioassay.
createdInherited - Variable in class net.sf.basedb.core.ProjectSpecificAnnotationsManager
 
createDirectory(UserData, DirectoryData, String, String, String, ItemKeyData, boolean) - Static method in class net.sf.basedb.core.Install
Create a Directory.
createdMapper - Variable in class net.sf.basedb.plugins.batchimport.BioPlateImporter
 
createdMapper - Variable in class net.sf.basedb.plugins.batchimport.ExtractImporter
 
createdMapper - Variable in class net.sf.basedb.plugins.batchimport.PhysicalBioAssayImporter
 
createdMapper - Variable in class net.sf.basedb.plugins.batchimport.SampleImporter
 
createDom(String, String) - Static method in class net.sf.basedb.util.XmlUtil2
Create a new Document with root element and System id declaration.
createdPrimary - Variable in class net.sf.basedb.core.ProjectSpecificAnnotationsManager
 
createEngine(Dialect) - Static method in class net.sf.basedb.core.dbengine.EngineFactory
Create a new DbEngine object.
createEntityGraph(Class<T>) - Method in class net.sf.basedb.core.hibernate.SessionWrapper
 
createEntityGraph(String) - Method in class net.sf.basedb.core.hibernate.SessionWrapper
 
createExportedProperty(String, String, Metadata, Formatter, ExcelFormatter) - Static method in class net.sf.basedb.clients.web.plugins.ExportedProperty
 
createFactory(Element, ClassLoader, Class<F>, Presets.Preset) - Method in class net.sf.basedb.util.extensions.xml.XmlLoader
Create a new factory instance.
createFailure(OverviewContext, Set<String>, Validator, Node, String) - Method in class net.sf.basedb.util.overview.validator.NameableNodeValidator
Create a failure on this node unless we have created a failure for the same validator already.
createFailure(Validator, Node, String, Fix...) - Method in class net.sf.basedb.util.overview.GenericOverview
Register a failure of a validation rule.
createFailure(Validator, Node, String, Fix...) - Method in interface net.sf.basedb.util.overview.OverviewContext
Register the failure of a validation rule.
createFile(File, String) - Method in class net.sf.basedb.plugins.BfsExporterPlugin
 
createFile(String) - Method in class net.sf.basedb.plugins.executor.ExternalProgramExecutor
Create a new file in the working directory.
createFile(DbControl, Directory, String) - Method in class net.sf.basedb.plugins.BfsExporterPlugin
 
createFilter(Object, String) - Method in class net.sf.basedb.core.hibernate.SessionWrapper
Deprecated.
createFilteredBioAssaySet(DbControl, BioAssaySet, List<BioAssay>, Job, Restriction, ProgressReporter) - Static method in class net.sf.basedb.util.BioAssaySetFilterUtil
Create a filtered bioassay set from a parent bioassay set using a simple restriction.
createFilteredBioAssaySet(DbControl, BioAssaySet, List<BioAssay>, Job, DynamicFilter, ProgressReporter) - Static method in class net.sf.basedb.util.BioAssaySetFilterUtil
 
createFlatFileParser(InputStream) - Method in class net.sf.basedb.util.bfs.AnnotationParser
Create a new flat file parser that can parse BFS annotation files.
createFlatFileParser(InputStream) - Method in class net.sf.basedb.util.bfs.DataParser
Create a new flat file parser that can parse BFS annotation files.
createFlatFileParser(InputStream) - Method in class net.sf.basedb.util.bfs.MetadataParser
Create a new flat file parser that can parse BFS metadata files.
createFont() - Method in class net.sf.basedb.util.excel.CellStyleCreator
Create a new font style.
createFormula(Formula.Type, Type, Formula.Parser, Formula.AverageMethod, IntensityTransform, IntensityTransform, String, String, String, int, String[], ColoringData, UserData, ItemKeyData) - Static method in class net.sf.basedb.core.Install
Create a Formula.
createForwardNode(ArraySlide, DbControl, OverviewContext, Node) - Method in class net.sf.basedb.util.overview.loader.PhysicalBioAssayLoader
Create a forward-loading bioassay node from an array slide.
createForwardNode(BioPlate, DbControl, OverviewContext, Node) - Method in class net.sf.basedb.util.overview.loader.BioWellLoader
Create all-loading biomaterial nodes for each non-empty well on the bioplate.
createForwardNode(BioSource, DbControl, OverviewContext, Node, boolean) - Method in class net.sf.basedb.util.overview.loader.SampleLoader
Create forward-loading sample nodes for the samples that has a given biosource as their parent.
createForwardNode(DbControl, OverviewContext, Node) - Method in class net.sf.basedb.util.overview.loader.AbstractNodeLoader
 
createForwardNode(DbControl, OverviewContext, Node) - Method in class net.sf.basedb.util.overview.loader.ArrayBatchLoader
Create forward-loading array batch nodes from a given array design node.
createForwardNode(DbControl, OverviewContext, Node) - Method in class net.sf.basedb.util.overview.loader.ArraySlideLoader
Create forward-loading array slide nodes from a given array batch node.
createForwardNode(DbControl, OverviewContext, Node) - Method in class net.sf.basedb.util.overview.loader.AutoChildNodeLoader
Call the same method on the 'parent' node loader.
createForwardNode(DbControl, OverviewContext, Node) - Method in class net.sf.basedb.util.overview.loader.BioPlateEventLoader
Create a forward-loading node from a bioplate.
createForwardNode(DbControl, OverviewContext, Node) - Method in class net.sf.basedb.util.overview.loader.BioSourceLoader
Create forward-loading biosource nodes from a biomaterial list for the member biosources.
createForwardNode(DbControl, OverviewContext, Node) - Method in class net.sf.basedb.util.overview.loader.BioWellLoader
Create forward-loading biomaterial nodes from a given bioplate The biomaterial nodes are created directly as child nodes to the bioplate.
createForwardNode(DbControl, OverviewContext, Node) - Method in class net.sf.basedb.util.overview.loader.DerivedBioAssayLoader
Create forward-loading bioassay nodes from a given physical bioassay node or a parent derived bioassay set node.
createForwardNode(DbControl, OverviewContext, Node) - Method in class net.sf.basedb.util.overview.loader.ExperimentLoader
Create property-loading experiment nodes from a given rawbioassay node.
createForwardNode(DbControl, OverviewContext, Node) - Method in class net.sf.basedb.util.overview.loader.ExtensionChildNodeLoader
Call the same method on the 'parent' node loader.
createForwardNode(DbControl, OverviewContext, Node) - Method in class net.sf.basedb.util.overview.loader.ExtractLoader
Create forward-loading extract nodes from a given parent sample or extract.
createForwardNode(DbControl, OverviewContext, Node) - Method in interface net.sf.basedb.util.overview.loader.NodeLoader
Create a forward-loading (from parent to child) node for the given parent node.
createForwardNode(DbControl, OverviewContext, Node) - Method in class net.sf.basedb.util.overview.loader.NullNodeLoader
 
createForwardNode(DbControl, OverviewContext, Node) - Method in class net.sf.basedb.util.overview.loader.PhysicalBioAssayLoader
Create forward-loading physical bioassay nodes from either an extract or an array slide node.
createForwardNode(DbControl, OverviewContext, Node) - Method in class net.sf.basedb.util.overview.loader.RawBioAssayLoader
Create forward-loading raw bioassay nodes from a given parent derived bioassay or extract node.
createForwardNode(DbControl, OverviewContext, Node) - Method in class net.sf.basedb.util.overview.loader.SampleLoader
Create forward-loading sample nodes from a given parent biosource or sample.
createForwardNode(DerivedBioAssay, DbControl, OverviewContext, Node) - Method in class net.sf.basedb.util.overview.loader.DerivedBioAssayLoader
Create forward-loading derived bioassay set nodes that have the given derived bioassay set as the parent
createForwardNode(DerivedBioAssay, DbControl, OverviewContext, Node) - Method in class net.sf.basedb.util.overview.loader.RawBioAssayLoader
 
createForwardNode(Extract, DbControl, OverviewContext, Node) - Method in class net.sf.basedb.util.overview.loader.DerivedBioAssayLoader
 
createForwardNode(Extract, DbControl, OverviewContext, Node) - Method in class net.sf.basedb.util.overview.loader.RawBioAssayLoader
 
createForwardNode(Extract, DbControl, OverviewContext, Node, boolean) - Method in class net.sf.basedb.util.overview.loader.ExtractLoader
Create forward-loading extract nodes for the (pooled) extract that has a given extract among their parents.
createForwardNode(Extract, DbControl, OverviewContext, Node, boolean) - Method in class net.sf.basedb.util.overview.loader.PhysicalBioAssayLoader
Create forward-loading bioassay nodes for the bioassays that has a given extract as a source.
createForwardNode(PhysicalBioAssay, DbControl, OverviewContext, Node) - Method in class net.sf.basedb.util.overview.loader.DerivedBioAssayLoader
Create forward-loading derived bioassay nodes that have the given physical bioassay as the immediate parent (eg. root bioassays).
createForwardNode(Sample, DbControl, OverviewContext, Node, boolean) - Method in class net.sf.basedb.util.overview.loader.ExtractLoader
Create forward-loading extract nodes for the extracts that has a given sample as their parent.
createForwardNode(Sample, DbControl, OverviewContext, Node, boolean) - Method in class net.sf.basedb.util.overview.loader.SampleLoader
Create forward-loading sample nodes for the (pooled) samples that has a given sample as their parent.
createFromExtended(String) - Static method in class net.sf.basedb.core.ClonableProperty
Create a cloned property representation of an extended property.
createFromRegular(String) - Static method in class net.sf.basedb.core.ClonableProperty
Create a cloned property that represents the "static" property with the given name.
createGenericFilter(String, String, Element) - Method in class net.sf.basedb.core.HibernateUtil.FilterConfigurator
Generic filters can be added as <filter< elements in the mapping file.
createGroup(String, String, boolean, boolean, String) - Static method in class net.sf.basedb.core.Install
Create a Group.
createHardware(String, String, String, ItemSubtypeData, UserData, ItemKeyData) - Static method in class net.sf.basedb.core.Install
Create a HardwareData.
createHeader(String, Object) - Method in class net.sf.basedb.plugins.GalExporter
Create a properly formatted GAL header.
createHistory() - Method in class net.sf.basedb.core.log.db.DbLogManager
 
createHomeDirectory(DbControl, User, boolean) - Static method in class net.sf.basedb.core.Directory
Creates a homedirectory for a specified user.
createHqlQuery(String, Class<R>) - Method in class net.sf.basedb.core.LogControl
Creates a Hibernate HQL query with a known return type.
createIndex(Session, boolean, String, String, String...) - Static method in class net.sf.basedb.core.Update
 
createInsertBatcher(Connection, String, int...) - Method in class net.sf.basedb.core.AnnotationBatcher
 
createInsertBatcher(Connection, String, int...) - Method in class net.sf.basedb.core.MigrateRbaToDba
 
createInstance(DbControl, PluginDefinition, String, boolean) - Method in class net.sf.basedb.plugins.executor.ExternalProgramExecutor
Create and initialize a plug-in instance for the given plug-in definition.
createItem(DbControl, FlatFileParser.Data) - Method in class net.sf.basedb.plugins.batchimport.AbstractItemImporter
Create a new item and populate it with data from the current line.
createItem(DbControl, FlatFileParser.Data) - Method in class net.sf.basedb.plugins.batchimport.AnnotationTypeImporter
 
createItem(DbControl, FlatFileParser.Data) - Method in class net.sf.basedb.plugins.batchimport.ArrayBatchImporter
 
createItem(DbControl, FlatFileParser.Data) - Method in class net.sf.basedb.plugins.batchimport.ArrayDesignImporter
 
createItem(DbControl, FlatFileParser.Data) - Method in class net.sf.basedb.plugins.batchimport.ArraySlideImporter
 
createItem(DbControl, FlatFileParser.Data) - Method in class net.sf.basedb.plugins.batchimport.BioPlateImporter
 
createItem(DbControl, FlatFileParser.Data) - Method in class net.sf.basedb.plugins.batchimport.BioSourceImporter
 
createItem(DbControl, FlatFileParser.Data) - Method in class net.sf.basedb.plugins.batchimport.DerivedBioAssayImporter
 
createItem(DbControl, FlatFileParser.Data) - Method in class net.sf.basedb.plugins.batchimport.ExtractImporter
 
createItem(DbControl, FlatFileParser.Data) - Method in class net.sf.basedb.plugins.batchimport.FileImporter
 
createItem(DbControl, FlatFileParser.Data) - Method in class net.sf.basedb.plugins.batchimport.KitImporter
 
createItem(DbControl, FlatFileParser.Data) - Method in class net.sf.basedb.plugins.batchimport.PhysicalBioAssayImporter
 
createItem(DbControl, FlatFileParser.Data) - Method in class net.sf.basedb.plugins.batchimport.RawBioAssayImporter
 
createItem(DbControl, FlatFileParser.Data) - Method in class net.sf.basedb.plugins.batchimport.SampleImporter
 
createItem(DbControl, FlatFileParser.Data) - Method in class net.sf.basedb.plugins.batchimport.TagImporter
 
createItemKey(String, Map<UserData, Integer>, Map<GroupData, Integer>) - Static method in class net.sf.basedb.core.Install
Create an ItemKey.
createItemNode(NodeFactory<? super S>, S, Object, boolean, Node, ChildNodeDirection) - Method in class net.sf.basedb.util.overview.loader.BasicItemNodeLoader
Create a new item node using the supplied node factory.
createItemQuery() - Method in class net.sf.basedb.plugins.batchimport.AbstractItemImporter
Create a new query that returns items of the importable type.
createItemQuery() - Method in class net.sf.basedb.plugins.batchimport.AnnotationTypeImporter
createItemQuery() - Method in class net.sf.basedb.plugins.batchimport.ArrayBatchImporter
createItemQuery() - Method in class net.sf.basedb.plugins.batchimport.ArrayDesignImporter
createItemQuery() - Method in class net.sf.basedb.plugins.batchimport.ArraySlideImporter
createItemQuery() - Method in class net.sf.basedb.plugins.batchimport.BioPlateImporter
createItemQuery() - Method in class net.sf.basedb.plugins.batchimport.BioSourceImporter
createItemQuery() - Method in class net.sf.basedb.plugins.batchimport.DerivedBioAssayImporter
createItemQuery() - Method in class net.sf.basedb.plugins.batchimport.ExtractImporter
createItemQuery() - Method in class net.sf.basedb.plugins.batchimport.FileImporter
createItemQuery() - Method in class net.sf.basedb.plugins.batchimport.KitImporter
createItemQuery() - Method in class net.sf.basedb.plugins.batchimport.PhysicalBioAssayImporter
createItemQuery() - Method in class net.sf.basedb.plugins.batchimport.RawBioAssayImporter
createItemQuery() - Method in class net.sf.basedb.plugins.batchimport.SampleImporter
createItemQuery() - Method in class net.sf.basedb.plugins.batchimport.TagImporter
createItemQuery(ItemList) - Method in class net.sf.basedb.plugins.batchimport.AbstractItemImporter
Create a new query that returns items that are members of the given list.
createItemSpecificFilter(String, Item, String, Element) - Method in class net.sf.basedb.core.HibernateUtil.FilterConfigurator
Item-specific filters are stored internally and registered later by HibernateUtil.FilterConfigurator.registerDelayedFilters(org.hibernate.boot.Metadata).
createItemSpecificFilterDef(String, Item, Element) - Method in class net.sf.basedb.core.HibernateUtil.FilterConfigurator
Clone the <filter-def> with the given name and insert a new item-specific <filter-def> definition into the document given by the <class> element.
createItemSubtype(Item, String, String, String, ItemSubtypeData...) - Static method in class net.sf.basedb.core.Install
Create an ItemSubtype.
createJepExpression(DbControl, String, DynamicQuery) - Static method in class net.sf.basedb.util.BioAssaySetUtil
Parse a JEP expression and create a restrictions that is suitable to be used in a dynamic query.
createJepExpressions(DbControl, RawDataType, String[]) - Static method in class net.sf.basedb.util.IntensityCalculatorUtil
 
createJepIntensityCalculator(DbControl, RawDataType, String...) - Static method in class net.sf.basedb.util.IntensityCalculatorUtil
Create an intensity calculator from mathematical expressions in strings.
createJepRestriction(DbControl, String, DynamicQuery) - Static method in class net.sf.basedb.util.BioAssaySetUtil
Parse a JEP expression and create a restrictions that is suitable to be used in a dynamic query.
createJobExecutor() - Method in class net.sf.basedb.clients.jobagent.Agent
Create a job executor and initialise it.
createJobQueueChecker() - Method in class net.sf.basedb.clients.jobagent.Agent
Create a job queue checker. and register it with the BASE core scheduler.
createJSON(JSONObject, DbControl, Annotation, Formatter<Object>, boolean) - Static method in class net.sf.basedb.clients.web.AnnotationUtil
 
createJsonForAnnotationTypeAndAnnotation(DbControl, AnnotationType, Annotation, Annotation, boolean, Set<AnnotationTypeCategory>) - Static method in class net.sf.basedb.clients.web.AnnotationUtil
 
createKeyManagers(KeyStore, String, String, String) - Static method in class net.sf.basedb.util.ssl.SSLUtil2
 
createKeyStore(InputStream, String, String, String) - Static method in class net.sf.basedb.util.ssl.SSLUtil2
Create a key-store from the given input stream
createLockedCopy() - Method in class net.sf.basedb.core.ReporterCloneTemplate
Create a deep clone of this template.
createLogFile(String) - Method in class net.sf.basedb.core.plugin.AbstractPlugin
Create a log file in the BASE file system for logging detailed information from a plug-in.
createLoggableString(LogControl, Item, int) - Method in class net.sf.basedb.core.log.db.AnyToAnyLogger
 
createLogger() - Method in class net.sf.basedb.util.extensions.logging.ExtensionsLog
Create a logger that adds messages to this log.
createLogger(String) - Static method in class net.sf.basedb.util.extensions.logging.ExtensionsLog
Create a logger that can add entries to the log for the given extension.
createLoginInfo(Session, UserData, String, boolean, AuthenticationMethod, int) - Method in class net.sf.basedb.core.SessionControl
Create a LoginInfo object and load all information that it needs.
createMappers(RawDataType, FlatFileParser) - Method in class net.sf.basedb.plugins.IlluminaRawDataImporter.BatchAndMapHolder
 
createMetadata(URI, HttpResponse) - Method in class net.sf.basedb.util.uri.http.HttpConnectionManager
Read metadata from the given http response and put the information in a UriMetadata object.
createMimeType(String, String, String, ItemSubtypeData, boolean) - Static method in class net.sf.basedb.core.Install
Create a MimeType.
createMissing - Variable in class net.sf.basedb.plugins.ReporterFlatFileImporter
 
createMissingNode(Node) - Method in class net.sf.basedb.util.overview.node.NodeFactory
Create a node representing a missing item.
createMode - Variable in class net.sf.basedb.plugins.batchimport.AbstractItemImporter
 
createMode - Variable in class net.sf.basedb.plugins.batchimport.AnyToAnyImporter
 
createNamedQuery(String) - Method in class net.sf.basedb.core.hibernate.SessionWrapper
 
createNamedQuery(String) - Method in class net.sf.basedb.core.hibernate.StatelessSessionWrapper
 
createNamedQuery(String, Class<R>) - Method in class net.sf.basedb.core.hibernate.StatelessSessionWrapper
 
createNamedQuery(String, Class<T>) - Method in class net.sf.basedb.core.hibernate.SessionWrapper
 
createNamedStoredProcedureQuery(String) - Method in class net.sf.basedb.core.hibernate.SessionWrapper
 
createNativeQuery(String) - Method in class net.sf.basedb.core.hibernate.SessionWrapper
 
createNativeQuery(String) - Method in class net.sf.basedb.core.hibernate.StatelessSessionWrapper
 
createNativeQuery(String, Class) - Method in class net.sf.basedb.core.hibernate.SessionWrapper
 
createNativeQuery(String, Class<R>) - Method in class net.sf.basedb.core.hibernate.StatelessSessionWrapper
 
createNativeQuery(String, String) - Method in class net.sf.basedb.core.hibernate.SessionWrapper
 
createNativeQuery(String, String) - Method in class net.sf.basedb.core.hibernate.StatelessSessionWrapper
 
createNews(String, String) - Static method in class net.sf.basedb.core.Install
Create a News.
createNode(I, Object, Node, ChildNodeDirection) - Method in class net.sf.basedb.util.overview.node.NodeFactory
Create a node representing an existing item.
createNode(I, String, String, Object, Node, ChildNodeDirection) - Method in class net.sf.basedb.util.overview.node.NodeFactory
 
createNodeLoader(Object) - Method in class net.sf.basedb.util.overview.loader.BasicItemNodeLoaderFactory
Create a new node loader for loading nodes for the specified item type.
createNodeLoader(K) - Method in interface net.sf.basedb.util.overview.loader.NodeLoaderFactory
Create a node loader that knows how to load nodes for items that are specified by the given key.
createNodeValidator(Object) - Method in class net.sf.basedb.util.overview.validator.BasicItemNodeValidatorFactory
Create a new node validator that can validate nodes with items of the specified item type.
createNodeValidator(K) - Method in interface net.sf.basedb.util.overview.validator.NodeValidatorFactory
Create a node validator that knows how to validate nodes for items that are specified by the given key.
createNotFoundItems - Variable in class net.sf.basedb.plugins.batchimport.AbstractItemImporter
 
createParameterMap() - Method in class net.sf.basedb.core.RequestInformation
Create a hash from parameter name to PluginParameter objects so that the RequestInformation.getParameter(String) method doesn't have to look in the list.
createPermissions - Variable in class net.sf.basedb.core.Job.SignalKeyring
 
createPlateGeometry(String, String, int, int) - Static method in class net.sf.basedb.core.Install
Create a PlateGeometry.
createPlateMapping(String, String, PlateGeometryData, int, PlateGeometryData, int, String, UserData, ItemKeyData) - Static method in class net.sf.basedb.core.Install
Create a PlateMapping.
createPlatform(String, String, String, boolean, String, int, Install.PlatformFT...) - Static method in class net.sf.basedb.core.Install
Create a Platform.
createPlatformVariant(PlatformData, String, String, String, boolean, String, int, Install.PlatformFT...) - Static method in class net.sf.basedb.core.Install
Create a PlatformVariant.
createPluginConfigurations(String, boolean) - Static method in class net.sf.basedb.core.Install
Create PluginConfigurations from a XML file.
createPluginDefinition(PluginInfo, ItemKey) - Static method in class net.sf.basedb.core.Install
createPluginDefinitions(String, ItemKey, boolean) - Static method in class net.sf.basedb.core.Install
Read plug-in definitions from the given file.
createPluginType(String, String, String, String) - Static method in class net.sf.basedb.core.Install
Create a PluginType.
createPooledReverseNode(Extract, DbControl, OverviewContext, Node) - Method in class net.sf.basedb.util.overview.loader.ExtractLoader
Create reverse-loading extract nodes of a pooled extract.
createPooledReverseNode(Sample, DbControl, OverviewContext, Node) - Method in class net.sf.basedb.util.overview.loader.SampleLoader
Create reverse-loading samples nodes of a sample with other sample(s) as parent items.
createPropertyElement(ExtendedProperty, Namespace) - Static method in class net.sf.basedb.core.HibernateUtil
Creates a <property> tag from an extended property definition.
createPropertyNode(BioPlateEvent, DbControl, OverviewContext, Node) - Method in class net.sf.basedb.util.overview.loader.BioPlateLoader
Create a property node(s) when the parent item is a bioplate event.
createPropertyNode(DbControl, OverviewContext, Node) - Method in class net.sf.basedb.util.overview.loader.AbstractNodeLoader
 
createPropertyNode(DbControl, OverviewContext, Node) - Method in class net.sf.basedb.util.overview.loader.AnnotationLoader
 
createPropertyNode(DbControl, OverviewContext, Node) - Method in class net.sf.basedb.util.overview.loader.AnyToAnyLoader
 
createPropertyNode(DbControl, OverviewContext, Node) - Method in class net.sf.basedb.util.overview.loader.ArrayDesignLoader
Create an array design property node from a raw bioassay or root raw bioassay node.
createPropertyNode(DbControl, OverviewContext, Node) - Method in class net.sf.basedb.util.overview.loader.AutoChildNodeLoader
Call the same method on the 'parent' node loader.
createPropertyNode(DbControl, OverviewContext, Node) - Method in class net.sf.basedb.util.overview.loader.BioPlateLoader
Create a bioplate property node from a biomaterial that is located on a plate or property nodes for each bioplate that is part of a bioplate event.
createPropertyNode(DbControl, OverviewContext, Node) - Method in class net.sf.basedb.util.overview.loader.DataFileLoader
 
createPropertyNode(DbControl, OverviewContext, Node) - Method in class net.sf.basedb.util.overview.loader.ExperimentalFactorLoader
 
createPropertyNode(DbControl, OverviewContext, Node) - Method in class net.sf.basedb.util.overview.loader.ExtensionChildNodeLoader
Call the same method on the 'parent' node loader.
createPropertyNode(DbControl, OverviewContext, Node) - Method in class net.sf.basedb.util.overview.loader.ExtractLoader
A property node is created when moving in the reverse direction so that we can load child extracts+physical bioassays with the ItemSubtype.getPushAnnotations() flag set.
createPropertyNode(DbControl, OverviewContext, Node) - Method in class net.sf.basedb.util.overview.loader.FileLoader
 
createPropertyNode(DbControl, OverviewContext, Node) - Method in class net.sf.basedb.util.overview.loader.HardwareLoader
 
createPropertyNode(DbControl, OverviewContext, Node) - Method in class net.sf.basedb.util.overview.loader.KitLoader
 
createPropertyNode(DbControl, OverviewContext, Node) - Method in interface net.sf.basedb.util.overview.loader.NodeLoader
Create a property node for the given parent node.
createPropertyNode(DbControl, OverviewContext, Node) - Method in class net.sf.basedb.util.overview.loader.NullNodeLoader
 
createPropertyNode(DbControl, OverviewContext, Node) - Method in class net.sf.basedb.util.overview.loader.PhysicalBioAssayLoader
A property node is created when moving in the reverse direction so that we can load child physical bioassays with the ItemSubtype.getPushAnnotations() flag set.
createPropertyNode(DbControl, OverviewContext, Node) - Method in class net.sf.basedb.util.overview.loader.PlatformLoader
 
createPropertyNode(DbControl, OverviewContext, Node) - Method in class net.sf.basedb.util.overview.loader.ProtocolLoader
 
createPropertyNode(DbControl, OverviewContext, Node) - Method in class net.sf.basedb.util.overview.loader.ProtocolParameterLoader
 
createPropertyNode(DbControl, OverviewContext, Node) - Method in class net.sf.basedb.util.overview.loader.SampleLoader
A property node is created when moving in the reverse direction so that we can load child samples+extracts with the ItemSubtype.getPushAnnotations() flag set.
createPropertyNode(DbControl, OverviewContext, Node) - Method in class net.sf.basedb.util.overview.loader.SoftwareLoader
 
createPropertyNode(DbControl, OverviewContext, Node) - Method in class net.sf.basedb.util.overview.loader.TagLoader
 
createPropertyNode(MeasuredBioMaterial, DbControl, OverviewContext, Node) - Method in class net.sf.basedb.util.overview.loader.BioPlateLoader
Create a property node when the parent item is a biomaterial.
createQuantity(String, String, String, String) - Static method in class net.sf.basedb.core.Install
Create a Quantity.
createQuery(String) - Method in class net.sf.basedb.core.hibernate.SessionWrapper
If the same query has been executed before, return the cached instance, otherwise create a new query from the parent session and cache it.
createQuery(String) - Method in class net.sf.basedb.core.hibernate.StatelessSessionWrapper
If the same query has been executed before, return the cached instance, otherwise create a new query from the parent session and cache it.
createQuery(String, Class<R>) - Method in class net.sf.basedb.core.hibernate.StatelessSessionWrapper
 
createQuery(String, Class<T>) - Method in class net.sf.basedb.core.hibernate.SessionWrapper
 
createQuery(CriteriaDelete) - Method in class net.sf.basedb.core.hibernate.SessionWrapper
 
createQuery(CriteriaDelete) - Method in class net.sf.basedb.core.hibernate.StatelessSessionWrapper
 
createQuery(CriteriaQuery<T>) - Method in class net.sf.basedb.core.hibernate.SessionWrapper
 
createQuery(CriteriaQuery<T>) - Method in class net.sf.basedb.core.hibernate.StatelessSessionWrapper
 
createQuery(CriteriaUpdate) - Method in class net.sf.basedb.core.hibernate.SessionWrapper
 
createQuery(CriteriaUpdate) - Method in class net.sf.basedb.core.hibernate.StatelessSessionWrapper
 
createQuery(Item, ItemList) - Method in class net.sf.basedb.plugins.AnnotationFlatFileImporter
Create a query that return items of the specified type.
createQuery(Item, ItemList) - Method in class net.sf.basedb.plugins.batchimport.AnyToAnyImporter
Create a query that return items of the specified type.
createQuery(Session, String) - Static method in class net.sf.basedb.core.HibernateUtil
Create a Hibernate query.
createQuery(Session, String, Class<R>) - Static method in class net.sf.basedb.core.HibernateUtil
Create a Hibernate query with a known return type.
createQuery(StatelessSession, String, Class<R>) - Static method in class net.sf.basedb.core.HibernateUtil
Create a Hibernate query using a stateless session and a known return type.
createQuota(String, String, String, long) - Static method in class net.sf.basedb.core.Install
Create a Quota.
createQuotaType(String, String, String) - Static method in class net.sf.basedb.core.Install
Create a QuotaType.
createReverseNode(DbControl, OverviewContext, Node) - Method in class net.sf.basedb.util.overview.loader.AbstractNodeLoader
 
createReverseNode(DbControl, OverviewContext, Node) - Method in class net.sf.basedb.util.overview.loader.ArrayBatchLoader
Create a reverse-loading array batch node from an array slide node.
createReverseNode(DbControl, OverviewContext, Node) - Method in class net.sf.basedb.util.overview.loader.ArrayDesignLoader
Create a reverse-loading array design node from an array batch node.
createReverseNode(DbControl, OverviewContext, Node) - Method in class net.sf.basedb.util.overview.loader.ArraySlideLoader
Create a reverse-loading array slide node from the hyrbidization node.
createReverseNode(DbControl, OverviewContext, Node) - Method in class net.sf.basedb.util.overview.loader.AutoChildNodeLoader
Call the same method on the 'parent' node loader.
createReverseNode(DbControl, OverviewContext, Node) - Method in class net.sf.basedb.util.overview.loader.BioSourceLoader
Create a reverse-loading biosource node from a sample node.
createReverseNode(DbControl, OverviewContext, Node) - Method in class net.sf.basedb.util.overview.loader.DerivedBioAssayLoader
Create a reverse-loading bioassay node from a cild bioassay node or a raw bioassay node.
createReverseNode(DbControl, OverviewContext, Node) - Method in class net.sf.basedb.util.overview.loader.ExtensionChildNodeLoader
Call the same method on the 'parent' node loader.
createReverseNode(DbControl, OverviewContext, Node) - Method in class net.sf.basedb.util.overview.loader.ExtractLoader
The parent node can be one of: Physical bioassay: Load the source extract(s) and return a folder-type node Extract: Load the parent extracts and return either a folder-type or item-type node depending on the number of parents Raw bioassay: Load the parent extract and return an item-type node Derived bioassay: Load the parent extract and return an item-type node
createReverseNode(DbControl, OverviewContext, Node) - Method in interface net.sf.basedb.util.overview.loader.NodeLoader
Create a reverse-loading (from child to parent) node for the given child node.
createReverseNode(DbControl, OverviewContext, Node) - Method in class net.sf.basedb.util.overview.loader.NullNodeLoader
 
createReverseNode(DbControl, OverviewContext, Node) - Method in class net.sf.basedb.util.overview.loader.PhysicalBioAssayLoader
Create a reverse-loading bioassay node from the derived bioassay node.
createReverseNode(DbControl, OverviewContext, Node) - Method in class net.sf.basedb.util.overview.loader.RawBioAssayLoader
Create a reverse-loading raw bioassay nodes from a given experiment node.
createReverseNode(DbControl, OverviewContext, Node) - Method in class net.sf.basedb.util.overview.loader.RootRawBioAssayLoader
Create a reverse-loading raw bioassay nodes from a given experiment node.
createReverseNode(DbControl, OverviewContext, Node) - Method in class net.sf.basedb.util.overview.loader.SampleLoader
Create reverse-loading sample nodes from an extract node or from a pooled sample.
createReverseNode(DerivedBioAssay, DbControl, OverviewContext, Node) - Method in class net.sf.basedb.util.overview.loader.DerivedBioAssayLoader
Create a reverse-loading bioassay node for the bioassay that is the parent to the given child bioassay.
createReverseNode(DerivedBioAssay, DbControl, OverviewContext, Node) - Method in class net.sf.basedb.util.overview.loader.ExtractLoader
 
createReverseNode(PhysicalBioAssay, DbControl, OverviewContext, Node) - Method in class net.sf.basedb.util.overview.loader.ExtractLoader
Create reverse-loading extract nodes from a physical bioassay.
createReverseNode(RawBioAssay, DbControl, OverviewContext, Node) - Method in class net.sf.basedb.util.overview.loader.DerivedBioAssayLoader
Create a reverse-loading bioassay node for the bioassay that is the parent to the given raw bioassay.
createReverseNode(RawBioAssay, DbControl, OverviewContext, Node) - Method in class net.sf.basedb.util.overview.loader.ExtractLoader
 
createRole(String, String, boolean, String) - Static method in class net.sf.basedb.core.Install
Create a Role.
createRoleKey(Item, String, String, Map<RoleData, Integer>) - Static method in class net.sf.basedb.core.Install
Create a RoleKey.
createRootBioAssaySet(DbControl, Experiment, Collection<RawBioAssay>, Job, Expression[], ProgressReporter) - Static method in class net.sf.basedb.util.IntensityCalculatorUtil
Create a root bioassayset for a given experiment and set of raw bioassays.
createRootBioAssaySet(DbControl, Experiment, Collection<RawBioAssay>, Job, IntensityCalculator, ProgressReporter) - Static method in class net.sf.basedb.util.IntensityCalculatorUtil
Create a root bioassayset for a given experiment and set of raw bioassays.
createRootNode(DbControl, BasicItem) - Method in class net.sf.basedb.util.overview.GenericOverview
 
createRootNode(DbControl, OverviewContext, I) - Method in class net.sf.basedb.util.overview.loader.AbstractNodeLoader
 
createRootNode(DbControl, OverviewContext, I) - Method in class net.sf.basedb.util.overview.loader.AutoChildNodeLoader
Call the same method on the 'parent' node loader.
createRootNode(DbControl, OverviewContext, I) - Method in class net.sf.basedb.util.overview.loader.BasicItemNodeLoader
 
createRootNode(DbControl, OverviewContext, I) - Method in class net.sf.basedb.util.overview.loader.ExtensionChildNodeLoader
Call the same method on the 'parent' node loader.
createRootNode(DbControl, OverviewContext, I) - Method in interface net.sf.basedb.util.overview.loader.NodeLoader
Create a root node for the given item.
createRootNode(DbControl, OverviewContext, I) - Method in class net.sf.basedb.util.overview.loader.NullNodeLoader
 
createRootNode(DbControl, OverviewContext, DerivedBioAssay) - Method in class net.sf.basedb.util.overview.loader.DerivedBioAssayLoader
 
createRootNode(DbControl, OverviewContext, RawBioAssay) - Method in class net.sf.basedb.util.overview.loader.RawBioAssayLoader
 
createSchemaVersion(int) - Static method in class net.sf.basedb.core.Install
Create the schema version.
createSessionFactoryConfiguration(String, String, int, ClassLoader) - Method in class net.sf.basedb.core.ServiceSessionControl
Create an object that can be used for collecting configuration options and other settings that are needed to create session factories for services.
createSimpleEmail() - Static method in class net.sf.basedb.util.EmailUtil
Create a simple text email.
createSingleParentReverseNode(Extract, DbControl, OverviewContext, Node) - Method in class net.sf.basedb.util.overview.loader.ExtractLoader
Create a reverse-loading extract node from an extract.
createSingleParentReverseNode(MeasuredBioMaterial, DbControl, OverviewContext, Node) - Method in class net.sf.basedb.util.overview.loader.SampleLoader
Create a reverse-loading sample node from an extract or sample.
createSlotManager() - Method in class net.sf.basedb.clients.jobagent.Agent
Create a slot manager and initialize it.
createSnapshot(DbControl, int) - Static method in class net.sf.basedb.core.AnnotationSet
Create a new annotation snapshot for the given annotation set.
createSoftware(String, String, String, ItemSubtypeData, UserData, ItemKeyData) - Static method in class net.sf.basedb.core.Install
Create a Software.
createSqlQuery(String) - Method in class net.sf.basedb.core.LogControl
Deprecated.
createSqlQuery(String, Class<R>) - Method in class net.sf.basedb.core.LogControl
Creates a Hibernate SQL query with a known return type.
createSqlQuery(Session, String) - Static method in class net.sf.basedb.core.HibernateUtil
Create a Hibernate SQL query.
createSqlQuery(Session, String, Class<R>) - Static method in class net.sf.basedb.core.HibernateUtil
Create a Hibernate SQL query with a known return type.
createSqlQuery(StatelessSession, String) - Static method in class net.sf.basedb.core.HibernateUtil
Create a Hibernate SQL query using a stateless session.
createSqlQuery(StatelessSession, String, Class<R>) - Static method in class net.sf.basedb.core.HibernateUtil
Create a Hibernate SQL query with a known return type using a stateless session.
createSQLQuery(String) - Method in class net.sf.basedb.core.hibernate.SessionWrapper
If the same query has been executed before, return the cached instance, otherwise create a new query from the parent session and cache it.
createSQLQuery(String) - Method in class net.sf.basedb.core.hibernate.StatelessSessionWrapper
If the same query has been executed before, return the cached instance, otherwise create a new query from the parent session and cache it.
createStandardHeaders(List<String>, ArrayDesign, List<ArrayDesignBlock>) - Method in class net.sf.basedb.plugins.GalExporter
Create the standard headers that are required by the GAL format or that are useful to have in the GAL file.
createStaticTables(SchemaGenerator.Mode, ProgressReporter) - Static method in class net.sf.basedb.core.HibernateUtil
Create the all tables in the database.
createStoredProcedureCall(String) - Method in class net.sf.basedb.core.hibernate.SessionWrapper
 
createStoredProcedureCall(String) - Method in class net.sf.basedb.core.hibernate.StatelessSessionWrapper
 
createStoredProcedureCall(String, Class...) - Method in class net.sf.basedb.core.hibernate.SessionWrapper
 
createStoredProcedureCall(String, Class...) - Method in class net.sf.basedb.core.hibernate.StatelessSessionWrapper
 
createStoredProcedureCall(String, String...) - Method in class net.sf.basedb.core.hibernate.SessionWrapper
 
createStoredProcedureCall(String, String...) - Method in class net.sf.basedb.core.hibernate.StatelessSessionWrapper
 
createStoredProcedureQuery(String) - Method in class net.sf.basedb.core.hibernate.SessionWrapper
 
createStoredProcedureQuery(String, Class...) - Method in class net.sf.basedb.core.hibernate.SessionWrapper
 
createStoredProcedureQuery(String, String...) - Method in class net.sf.basedb.core.hibernate.SessionWrapper
 
createStyle() - Method in class net.sf.basedb.util.excel.CellStyleCreator
Create a new cell style.
createTables(SchemaGenerator.Mode, ProgressReporter, String, String) - Static method in class net.sf.basedb.core.Install
 
createTables(VirtualTable...) - Method in class net.sf.basedb.core.VirtualDb
Create the real database tables for this virtual database.
createTag(String, String, ItemSubtypeData, UserData, ItemKeyData) - Static method in class net.sf.basedb.core.Install
Create a Tag.
createTargetTypeQuery(DbControl) - Method in class net.sf.basedb.clients.web.extensions.list.RelatedItemColumn.Specification
 
createTargetTypeRestriction(DbControl) - Method in class net.sf.basedb.clients.web.extensions.list.RelatedItemColumn.Specification
 
createTempCollection(CollectionTransformer<?, ?>) - Method in class net.sf.basedb.util.collections.MultiStepCollectionTransformer
Create a temporary collection that is suitable for holding an intermediary result.
createTempDirectory(String, String, File) - Static method in class net.sf.basedb.util.FileUtil
Creates a temporary directory.
createTempIdTable(Set<Integer>) - Method in class net.sf.basedb.core.DbControl
Create a temporary table for holding given list of ID values.
createTemporaryWorkingDirectory() - Method in class net.sf.basedb.plugins.executor.ExternalProgramExecutor
Create a temporary working directory in the local file system.
createTrustManagers(KeyStore, String, String) - Static method in class net.sf.basedb.util.ssl.SSLUtil2
 
createUnit(QuantityData, String, String, double, double, String, String...) - Static method in class net.sf.basedb.core.Install
Create a Unit.
createUpdateBatcher(Connection, String, int...) - Method in class net.sf.basedb.core.AnnotationBatcher
 
createUpdateBatcher(Connection, String, int...) - Method in class net.sf.basedb.core.MigrateRbaToDba
 
createUser(String, String, String, String, String, RoleData, QuotaData, boolean, boolean) - Static method in class net.sf.basedb.core.Install
Create a User.
createVirtualTable(VirtualDb, VirtualTable) - Static method in class net.sf.basedb.core.HibernateUtil
Create a table in the dynamic database.
CREATION - Enum constant in enum class net.sf.basedb.core.BioMaterialEvent.Type
An event of this type created a biomaterial.
creationEvent - Variable in class net.sf.basedb.core.data.MeasuredBioMaterialData
 
creationEvent - Variable in class net.sf.basedb.core.data.PhysicalBioAssayData
 
creationEvent - Variable in class net.sf.basedb.core.MeasuredBioMaterial
 
creationEvent - Variable in class net.sf.basedb.core.PhysicalBioAssay
 
creationTime - Variable in class net.sf.basedb.core.DiskUsageStatistics.Summary
 
CropStringMapper - Class in net.sf.basedb.util.parser
A mapper that crops a string if it is longer than a specified length.
CropStringMapper(Mapper, int) - Constructor for class net.sf.basedb.util.parser.CropStringMapper
Create a new CropStringMapper.
cropStrings - Variable in class net.sf.basedb.plugins.AnnotationFlatFileImporter
 
cropStrings - Variable in class net.sf.basedb.plugins.batchimport.AbstractItemImporter
 
cropTooManyValues - Variable in class net.sf.basedb.plugins.AnnotationFlatFileImporter
 
crypt_raw(byte[], byte[], int, int[]) - Method in class net.sf.basedb.util.bcrypt.BCrypt
Perform the central password hashing step in the bcrypt scheme
cryptedPassword - Variable in class net.sf.basedb.core.data.PasswordData
 
cspHeader - Variable in class net.sf.basedb.clients.web.servlet.ContentSecurityPolicyFilter
 
csvBytes - Variable in class net.sf.basedb.util.excel.XlsxToCsvUtil.SheetInfo
 
cube - Variable in class net.sf.basedb.core.DynamicQuery
 
CUBE - Static variable in class net.sf.basedb.core.VirtualColumn
This column stores the data cube number.
cubeNo - Variable in class net.sf.basedb.core.data.DataCubeData
 
cubes - Variable in class net.sf.basedb.core.data.VirtualDbData
 
current - Variable in class net.sf.basedb.clients.web.taglib.Select
The currently selected item.
current - Variable in class net.sf.basedb.clients.web.taglib.SubtypeSelector
 
current - Variable in class net.sf.basedb.clients.web.taglib.table.ExtensionCells
 
current - Variable in class net.sf.basedb.util.NestedIterator
The current iterator.
current - Variable in class net.sf.basedb.util.query.MultiQueryIterator
 
CURRENT - Static variable in class net.sf.basedb.core.Quantity
The id for the Quantity object representing electric current.
currentAction - Variable in class net.sf.basedb.util.extensions.ActionIterator
 
CurrentAnnotationInfo(AnnotationType, Item) - Constructor for class net.sf.basedb.core.AnnotationBatcher.CurrentAnnotationInfo
 
currentAnnotationSetId - Variable in class net.sf.basedb.core.AnnotationBatcher
 
currentClient - Variable in class net.sf.basedb.core.SessionControl
Information about the current ClientData that checked out this SessionControl.
currentContext - Variable in class net.sf.basedb.util.extensions.ActionIterator
 
currentContexts - Variable in class net.sf.basedb.core.SessionControl
Map for storing current contexts.
currentFile - Variable in class net.sf.basedb.plugins.AbstractFlatFileImporter
 
currentFilename - Variable in class net.sf.basedb.clients.web.fileupload.FileUploadProgress
 
currentImageRemapper - Static variable in class net.sf.basedb.clients.web.extensions.skin.ImageRemapperUtil
 
currentIndex - Variable in class net.sf.basedb.plugins.RawDataFlatFileImporter.FileIterator
 
currentInfo - Variable in class net.sf.basedb.core.AnnotationBatcher
 
currentItem - Variable in class net.sf.basedb.core.AnnotationBatcher
 
currentPage - Variable in class net.sf.basedb.clients.web.taglib.table.Navigator
The current page.
currentParticipant - Variable in class net.sf.basedb.util.overview.node.BioPlateNameGenerator
 
currentPosition - Variable in class net.sf.basedb.core.FeatureBatcher
Keeps track of the position number.
currentPosition - Variable in class net.sf.basedb.core.RawDataBatcher
Keeps track of the position number unless the raw bioassay is connected to an array design with features.
currentPosition - Variable in class net.sf.basedb.util.importer.spotdata.PositionEventHandler
 
currentRow - Variable in class net.sf.basedb.clients.web.plugins.XlsxTemplate
 
currentRow - Variable in class net.sf.basedb.util.excel.XlsxTableWriter
 
currentSection - Variable in class net.sf.basedb.util.basefile.BaseFileWriter
 
currentSection - Variable in class net.sf.basedb.util.bfs.MetadataModel
 
currentSection - Variable in class net.sf.basedb.util.bfs.MetadataWriter
 
currentSheet - Variable in class net.sf.basedb.util.excel.XlsxToCsvUtil.WorkbookStream
 
currentStream - Variable in class net.sf.basedb.util.excel.XlsxToCsvUtil.WorkbookStream
 
currentSubCategory - Variable in class net.sf.basedb.clients.web.taglib.SubtypeSelector
 
currentSubcontexts - Variable in class net.sf.basedb.core.SessionControl
Current active subcontext names.
currentWell - Variable in class net.sf.basedb.util.overview.node.BioPlateNameGenerator
 
currentWell - Variable in class net.sf.basedb.util.overview.node.BioWellNameGenerator
 
currentXt - Variable in class net.sf.basedb.util.extensions.ClientContext
 
currentXtPoint - Variable in class net.sf.basedb.util.extensions.ClientContext
 
CurvedScaleFactor(long) - Constructor for class net.sf.basedb.util.InputStreamTracker.CurvedScaleFactor
 
CustomRequestHandler - Interface in net.sf.basedb.clients.jobagent.handlers
An extension to the regular request-handler interface that allows life-cycle control by the job agent.
customRequestHandlerClasses - Variable in class net.sf.basedb.clients.jobagent.Agent
 

D

data - Variable in class net.sf.basedb.clients.web.taglib.table.Row
The parent <tbl:data> tag.
data - Variable in class net.sf.basedb.core.BasicItem
The data class from the net.sf.basedb.core.data layer that holds the data for this item.
data - Variable in class net.sf.basedb.core.BioMaterialEventSource
 
data - Variable in class net.sf.basedb.core.ChangeHistory.TransactionInfo
 
data - Variable in class net.sf.basedb.core.Coloring
 
data - Variable in class net.sf.basedb.core.DataResultIterator
The internal iterator of BasicData objects.
data - Variable in class net.sf.basedb.core.ItemResultIterator
The internal iterator of BasicData objects.
data - Variable in class net.sf.basedb.core.ItemResultList
The internal list of BasicData objects.
data - Variable in class net.sf.basedb.core.ReporterScore
 
data - Variable in class net.sf.basedb.core.ReporterScoreResultIterator
The internal iterator of data layer objects.
data - Variable in class net.sf.basedb.util.bfs.AnnotationModel
 
data - Variable in class net.sf.basedb.util.bfs.MatrixModel
 
data - Variable in class net.sf.basedb.util.importer.spotdata.SynchronizedSpotDataParser.SynchronizedData
 
data - Variable in class net.sf.basedb.util.parser.ColFunction
 
data - Variable in class net.sf.basedb.util.parser.DataNoFunction
 
data - Variable in class net.sf.basedb.util.parser.LineNoFunction
 
data() - Method in class net.sf.basedb.util.parser.FlatFileParser.Data
The data line as an array of strings.
Data - Class in net.sf.basedb.clients.web.taglib.table
This tag begins the data section of the table.
Data() - Constructor for class net.sf.basedb.clients.web.taglib.table.Data
 
Data(int, int, String, String[], boolean, boolean, boolean) - Constructor for class net.sf.basedb.util.parser.FlatFileParser.Data
Create a new data object.
DATA - Enum constant in enum class net.sf.basedb.util.parser.FlatFileParser.LineType
The parsed line is a data line, which could be split into the specified number of columns by FlatFileParser.setDataSplitterRegexp(Pattern).
DATA_EVENT - Static variable in class net.sf.basedb.util.bfs.AnnotationParser
Event thep that is issued for each data line.
DATA_EVENT - Static variable in class net.sf.basedb.util.bfs.DataParser
Event type that is issued for each data line.
DATA_EVENT - Static variable in class net.sf.basedb.util.importer.spotdata.SynchronizedSpotDataParser
Event type that is issued for each data line.
DATA_FILE - Enum constant in enum class net.sf.basedb.clients.web.extensions.fileviewer.FileViewerContext.Type
The context is a list with data-files that are attached to a parent item.
DATA_FILES - Variable in class net.sf.basedb.core.PropertyFilter
 
DATA_FOOTER - Enum constant in enum class net.sf.basedb.util.parser.FlatFileParser.LineType
The parsed line is the data footer line, matching the regular expression specified by FlatFileParser.setDataFooterRegexp(Pattern).
DATA_HEADER - Enum constant in enum class net.sf.basedb.util.parser.FlatFileParser.LineType
The parsed line is the data header line, matching the regular expression specified by FlatFileParser.setDataHeaderRegexp(Pattern).
DatabaseException - Exception in net.sf.basedb.core
Exceptions of this type are thrown when there is an error from the database.
DatabaseException() - Constructor for exception net.sf.basedb.core.DatabaseException
Create a new DatabaseException object.
DatabaseException(String) - Constructor for exception net.sf.basedb.core.DatabaseException
Create a new DatabaseException object with the specified message.
DatabaseException(String, Throwable) - Constructor for exception net.sf.basedb.core.DatabaseException
Create a new DatabaseException object with the specified message
DatabaseException(Throwable) - Constructor for exception net.sf.basedb.core.DatabaseException
Create a new DatabaseException object acting as a wrapper for another exception that caused the error.
databaseVersionNumber - Static variable in class net.sf.basedb.core.Application
The name and version of the database server
dataClass - Variable in class net.sf.basedb.core.BasicBatcher
The class of data objects accepted by this batcher.
dataClass - Variable in class net.sf.basedb.core.DataQuery
The class of the data objects that are returned.
dataClass - Variable in class net.sf.basedb.core.DataResultIterator
The class of the data objects returned by the query (and this object).
dataClass - Variable in enum class net.sf.basedb.core.Item
 
dataClass - Variable in class net.sf.basedb.core.ItemQuery
The data layer class of the item objects that are returned.
dataClassMapping - Static variable in enum class net.sf.basedb.core.Item
 
dataCube - Variable in class net.sf.basedb.core.data.DataCubeColumnData
 
dataCube - Variable in class net.sf.basedb.core.data.DataCubeExtraValueData
 
dataCube - Variable in class net.sf.basedb.core.data.DataCubeFilterData
 
dataCube - Variable in class net.sf.basedb.core.data.DataCubeLayerData
 
dataCube - Variable in class net.sf.basedb.core.MappingBatcher
The datacube this batcher inserts data for.
dataCube - Variable in class net.sf.basedb.core.PositionBatcher
The datacube this batcher inserts data for.
DataCube - Class in net.sf.basedb.core
A data cube is the main unit for an experiment to store analysed data.
DataCube(DataCubeData) - Constructor for class net.sf.basedb.core.DataCube
Creates a new data cube item from the given data.
DATACUBE - Enum constant in enum class net.sf.basedb.core.Item
The item is a DataCube
DataCube.RawMappingQuery - Class in net.sf.basedb.core
Select data from Dynamic#RawParents table.
dataCubeColumn - Variable in class net.sf.basedb.core.data.BioAssayData
 
DataCubeColumn - Class in net.sf.basedb.core
Represents the column coordinate in a data cube.
DataCubeColumn(DataCubeColumnData) - Constructor for class net.sf.basedb.core.DataCubeColumn
Creates a new data cube item from the given data.
DATACUBECOLUMN - Enum constant in enum class net.sf.basedb.core.Item
The item is a DataCubeColumn
DataCubeColumnData - Class in net.sf.basedb.core.data
This class holds information about a single column in a data cube.
DataCubeColumnData() - Constructor for class net.sf.basedb.core.data.DataCubeColumnData
 
DataCubeData - Class in net.sf.basedb.core.data
This class holds information about a single data cube in a virtual database.
DataCubeData() - Constructor for class net.sf.basedb.core.data.DataCubeData
 
dataCubeExtraValue - Variable in class net.sf.basedb.core.data.ExtraValueData
 
DataCubeExtraValue - Class in net.sf.basedb.core
Represents a set of extra value in a data cube.
DataCubeExtraValue(DataCubeExtraValueData) - Constructor for class net.sf.basedb.core.DataCubeExtraValue
Creates a new data cube item from the given data.
DATACUBEEXTRAVALUE - Enum constant in enum class net.sf.basedb.core.Item
The item is a DataCubeExtraValue
DataCubeExtraValueData - Class in net.sf.basedb.core.data
This class holds information about an extra value in a data cube.
DataCubeExtraValueData() - Constructor for class net.sf.basedb.core.data.DataCubeExtraValueData
 
dataCubeFilter - Variable in class net.sf.basedb.core.data.BioAssaySetData
 
DataCubeFilter - Class in net.sf.basedb.core
This represents a filter in a datacube.
DataCubeFilter(DataCubeFilterData) - Constructor for class net.sf.basedb.core.DataCubeFilter
Creates a new data cube item from the given data.
DATACUBEFILTER - Enum constant in enum class net.sf.basedb.core.Item
The item is a DataCubeFilter
DataCubeFilterData - Class in net.sf.basedb.core.data
This class holds information about a single filter in a data cube.
DataCubeFilterData() - Constructor for class net.sf.basedb.core.data.DataCubeFilterData
 
dataCubeLayer - Variable in class net.sf.basedb.core.data.BioAssaySetData
 
DataCubeLayer - Class in net.sf.basedb.core
This represents the layer coordinate in a data cube.
DataCubeLayer(DataCubeLayerData) - Constructor for class net.sf.basedb.core.DataCubeLayer
Creates a new data cube item from the given data.
DATACUBELAYER - Enum constant in enum class net.sf.basedb.core.Item
The item is a DataCubeLayer
DataCubeLayerData - Class in net.sf.basedb.core.data
This class holds information about a single layer in a data cube.
DataCubeLayerData() - Constructor for class net.sf.basedb.core.data.DataCubeLayerData
 
dataCubes - Variable in class net.sf.basedb.core.data.VirtualDbData
 
dataDirectory - Variable in class net.sf.basedb.plugins.batchimport.ArrayDesignImporter
 
dataDirectory - Variable in class net.sf.basedb.plugins.batchimport.DerivedBioAssayImporter
 
dataDirectory - Variable in class net.sf.basedb.plugins.batchimport.RawBioAssayImporter
 
dataFile(BasicItem) - Static method in class net.sf.basedb.clients.web.extensions.fileviewer.FileViewerContext
Creates a data-file listing context where files belong to a parent item.
DATAFILE_INVALID - Static variable in class net.sf.basedb.util.overview.Validator
Validator rule that checks if a data file is valid.
DATAFILE_INVALID_ITEM - Static variable in class net.sf.basedb.util.overview.Validator
Validator rule that checks if a data file can be used on the current item type.
DATAFILE_NOTPLATFORM - Static variable in class net.sf.basedb.util.overview.Validator
Validator rule that checks if a file is registered with a platform/item subtype or not.
DATAFILE_NOTVALIDATED - Static variable in class net.sf.basedb.util.overview.Validator
Validator rule that checks if a data file has been validated or not.
DATAFILE_TOOMANYFILES - Static variable in class net.sf.basedb.util.overview.Validator
Validator rule that checks if there are more than one file of a file type that doesn't allow multiple files.
DataFileFormatter - Class in net.sf.basedb.clients.web.formatter
Formatter implementation for file sets that lists all member files of a given file type
DataFileFormatter(DbControl, DataFileType, ModeInfo) - Constructor for class net.sf.basedb.clients.web.formatter.DataFileFormatter
Creates a new formatter instance for the given file type and list mode.
DataFileFormatter(DbControl, DataFileType, ModeInfo, FileViewerUtil) - Constructor for class net.sf.basedb.clients.web.formatter.DataFileFormatter
Creates a new formatter instance for the given file type and list mode.
DataFileLoader - Class in net.sf.basedb.util.overview.loader
Node loader implementation for data files.
DataFileLoader() - Constructor for class net.sf.basedb.util.overview.loader.DataFileLoader
 
DataFileType - Class in net.sf.basedb.core
This class is used to represent types of files that are used to hold data instead of importing the data into into the database.
DataFileType(DataFileTypeData) - Constructor for class net.sf.basedb.core.DataFileType
Creates a new filetype item from the given data.
DATAFILETYPE - Enum constant in enum class net.sf.basedb.core.Item
The item is a DataFileType
DataFileTypeData - Class in net.sf.basedb.core.data
This class hols information about individual files attached to items that store data in files instead of in the database.
DataFileTypeData() - Constructor for class net.sf.basedb.core.data.DataFileTypeData
 
DataFileValidator - Class in net.sf.basedb.util.overview.validator
Validator implementation for data files.
DataFileValidator() - Constructor for class net.sf.basedb.util.overview.validator.DataFileValidator
 
dataFooter - Variable in class net.sf.basedb.util.parser.FlatFileParser
The regular expression for matching the data footer line.
dataFooterRegexpParameter - Static variable in class net.sf.basedb.plugins.AbstractFlatFileImporter
Parameter definition that asks for the regular expression that matches the data footer.
dataFormat - Variable in class net.sf.basedb.util.excel.CellStyleCreator
 
dataFormat - Variable in class net.sf.basedb.util.excel.XlsxToCsvUtil.SheetInfo
 
dataHeader - Variable in class net.sf.basedb.util.parser.FlatFileParser
The regular expression for matching the data header line.
dataHeaderRegexpParameter - Static variable in class net.sf.basedb.plugins.AbstractFlatFileImporter
Parameter definition that asks for the regular expression that matches the data header.
dataLineNo - Variable in class net.sf.basedb.util.parser.FlatFileParser.Data
 
dataLineNo() - Method in class net.sf.basedb.util.parser.FlatFileParser.Data
The line number of the data in the current section.
dataloader - Variable in class net.sf.basedb.clients.web.plugins.ExportedProperty
 
DataLoader<T> - Interface in net.sf.basedb.clients.web.plugins
A helper interface for the SimpleExport to get data that in some way are associated with an item.
dataNoFunction - Variable in class net.sf.basedb.util.parser.JepMapper
 
DataNoFunction - Class in net.sf.basedb.util.parser
Adds a dataNo() function to Jep.
DataNoFunction() - Constructor for class net.sf.basedb.util.parser.DataNoFunction
 
DataParser - Class in net.sf.basedb.util.bfs
Parser implementation that parses BFS data files.
DataParser() - Constructor for class net.sf.basedb.util.bfs.DataParser
Create a new data parser.
dataParsers - Variable in class net.sf.basedb.util.importer.spotdata.SynchronizedSpotDataParser
 
dataPart - Variable in class net.sf.basedb.util.basefile.BaseFileWriter
 
DataQuery<I extends BasicData> - Class in net.sf.basedb.core
An implementation of the Query interface that returns data objects.
DataQuery(Class<I>, String) - Constructor for class net.sf.basedb.core.DataQuery
Create a new query for the specified item, using the default optional runtime filter.
DataQuery(Class<I>, Item, String, String) - Constructor for class net.sf.basedb.core.DataQuery
Create a query that may have different return type and root entity.
DataQueryWrapper - Class in net.sf.basedb.clients.web.plugins
A query wrapper for DataQuery:s.
DataQueryWrapper(DataQuery<BasicData>) - Constructor for class net.sf.basedb.clients.web.plugins.DataQueryWrapper
Create a new query wrapper.
DataResultIterator<I extends BasicData> - Class in net.sf.basedb.core
Return the results of a DataQuery as an iterator.
DataResultIterator(ScrollIterator<I>, SessionControl, Session, Class<I>, long) - Constructor for class net.sf.basedb.core.DataResultIterator
 
dataSeparator - Variable in class net.sf.basedb.util.export.TableWriter
 
dataSplitter - Variable in class net.sf.basedb.util.parser.FlatFileParser
The regular expression for splitting a data line.
dataSplitterRegexpParameter - Static variable in class net.sf.basedb.plugins.AbstractFlatFileImporter
Parameter definition that asks for the regular expression that splits a data line into individual columns.
datatype - Variable in class net.sf.basedb.clients.web.taglib.table.TableColumn
 
DataWriter - Class in net.sf.basedb.util.bfs
Writer implementation for writing BFS data files.
DataWriter(Writer) - Constructor for class net.sf.basedb.util.bfs.DataWriter
Create a new BFS data writer.
dataWriterFactory - Variable in class net.sf.basedb.util.export.spotdata.BfsExporter
 
DataWriterFactory<T> - Interface in net.sf.basedb.util.bfs
Factory implementations are responsible for creating BFS data writers that accepts data for a given owner object.
dataWriters - Variable in class net.sf.basedb.util.export.spotdata.BfsExporter
 
DATE - Enum constant in enum class net.sf.basedb.core.Type
The parameter is a date value.
DATE - Static variable in class net.sf.basedb.core.hibernate.TypeWrapper
 
DATE_FORMAT - Static variable in class net.sf.basedb.core.DateUtil
 
DATE_FORMAT - Static variable in class net.sf.basedb.core.log.EntityDetails
 
DATE_FORMAT_ERROR - Static variable in class net.sf.basedb.plugins.util.Parameters
DATE_FORMAT_PARAMETER - Static variable in class net.sf.basedb.plugins.util.Parameters
The name of the parameter that is created by Parameters.dateFormatParameter(String, String, String)
DateCopyPropertyPath(Type) - Constructor for class net.sf.basedb.core.Metadata.DateCopyPropertyPath
 
dateFormat - Variable in class net.sf.basedb.core.migrate.DateWriter
 
dateFormat - Variable in class net.sf.basedb.core.migrate.postgres.PostgresResultWriterFactory
PostgreSQL uses 'yyyy-MM-dd' for dates.
dateFormat - Variable in class net.sf.basedb.core.migrate.TimestampWriter
 
dateFormat - Variable in class net.sf.basedb.util.excel.AutoFormatter
 
dateFormat - Variable in class net.sf.basedb.util.excel.XlsxToCsvUtil
 
dateFormat - Variable in class net.sf.basedb.util.formatter.DateFormatter
 
dateFormat - Variable in class net.sf.basedb.util.parser.ColFunction
 
dateFormat - Variable in class net.sf.basedb.util.parser.FlatFileParser
The default date formatter to use when creating mappers.
dateFormat - Variable in class net.sf.basedb.util.parser.JepMapper
 
dateFormatError(String, String, String, String...) - Static method in class net.sf.basedb.plugins.util.Parameters
Create the parameter for handling invalid dates/timestamps.
dateFormatErrorParameter - Static variable in class net.sf.basedb.plugins.AnnotationFlatFileImporter
 
DateFormatException - Exception in net.sf.basedb.core
This exception is thrown when parsing a string into a date failed.
DateFormatException(String) - Constructor for exception net.sf.basedb.core.DateFormatException
Creates a new DateFormatException.
DateFormatException(String, Throwable) - Constructor for exception net.sf.basedb.core.DateFormatException
Creates a new DateFormatException.
dateFormatParameter(String, String, String) - Static method in class net.sf.basedb.plugins.util.Parameters
Parameter definition that asks for the format used by date values when parsed from strings.
dateFormatter - Variable in class net.sf.basedb.plugins.AnnotationFlatFileImporter
 
dateFormatter - Variable in class net.sf.basedb.plugins.batchimport.AbstractItemImporter
 
dateFormatter - Variable in class net.sf.basedb.util.formatter.PropertyFilterFormatter
 
DateFormatter - Class in net.sf.basedb.util.formatter
Format a date for output in a client application.
DateFormatter(String) - Constructor for class net.sf.basedb.util.formatter.DateFormatter
Create a new date formatter.
DateFormatter(DateFormat) - Constructor for class net.sf.basedb.util.formatter.DateFormatter
Create a new date formatter.
DateParameterType - Class in net.sf.basedb.core
This class represent a parameter type that is a date.
DateParameterType() - Constructor for class net.sf.basedb.core.DateParameterType
Create a new date parameter type, allowing null values.
DateParameterType(Date, boolean) - Constructor for class net.sf.basedb.core.DateParameterType
Create a new date parameter type.
DateParameterType(Date, boolean, int, int, int, List<Date>) - Constructor for class net.sf.basedb.core.DateParameterType
Creates a new DateParameterType
DateParameterValueData - Class in net.sf.basedb.core.data
Date parameter value.
DateParameterValueData() - Constructor for class net.sf.basedb.core.data.DateParameterValueData
 
DateParameterValueData(Date...) - Constructor for class net.sf.basedb.core.data.DateParameterValueData
 
dateParser - Variable in class net.sf.basedb.util.parser.ColumnMapper
 
dateParser - Variable in class net.sf.basedb.util.parser.CompoundMapper
 
dateParser - Variable in class net.sf.basedb.util.parser.ConstantMapper
 
DATETIME_FORMAT - Static variable in class net.sf.basedb.core.log.EntityDetails
 
DateUtil - Class in net.sf.basedb.core
Utility methods that will make it easier to handle date values.
DateUtil() - Constructor for class net.sf.basedb.core.DateUtil
 
DateValue(Date, String) - Constructor for class net.sf.basedb.util.excel.ExcelValue.DateValue
 
DateWriter - Class in net.sf.basedb.core.migrate
Generic writer implementation that writes date values from a result set.
DateWriter(ResultSet, int, Writer, char[], FastDateFormat) - Constructor for class net.sf.basedb.core.migrate.DateWriter
 
dbaId - Variable in class net.sf.basedb.core.MigrateRbaToDba.Rba
 
DbCleaner() - Constructor for class net.sf.basedb.core.Application.DbCleaner
 
DbControl - Class in net.sf.basedb.core
A DbControl object is the main object used for communicating with the database.
DbControl(SessionControl, String) - Constructor for class net.sf.basedb.core.DbControl
Create a new object.
DbControl.SaveIf - Class in net.sf.basedb.core
 
DbControl.State - Class in net.sf.basedb.core
Main purpose is to write a warning to the log file in case some user code that created a DbControl instance never called the close() method before the DbControl became uncreachable.
dbControlCache - Variable in class net.sf.basedb.core.SessionControl
Holds all created DbControl object, so we can close them if the user logs out.
dbEngine - Variable in class net.sf.basedb.core.hibernate.DbIndexWork
 
dbEngine - Variable in class net.sf.basedb.core.hibernate.SchemaGenerator.CollectSqlTarget
 
dbEngine - Variable in class net.sf.basedb.core.hibernate.SchemaGenerator
 
dbEngine - Static variable in class net.sf.basedb.core.HibernateUtil
Our extra database specific sql generation that is not possible by the Hibernate dialect.
DbEngine - Interface in net.sf.basedb.core.dbengine
Information about database-specific options that are not covered by the Hibernate Dialect objects.
dbFeatures - Variable in class net.sf.basedb.core.data.ArrayDesignData
 
dbIndexes(boolean, boolean, boolean, boolean) - Static method in class net.sf.basedb.core.HibernateUtil
Prints a lot of useful stuff about the database to standard output.
DbIndexWork - Class in net.sf.basedb.core.hibernate
A work implementation that can create, update and drop indexes on tables.
DbIndexWork(Metadata, Dialect, DbEngine, boolean, boolean, boolean, boolean) - Constructor for class net.sf.basedb.core.hibernate.DbIndexWork
 
DbLogManager - Class in net.sf.basedb.core.log.db
Log manager implementation that logs changes to the database.
DbLogManager(LogControl) - Constructor for class net.sf.basedb.core.log.db.DbLogManager
 
DbLogManagerFactory - Class in net.sf.basedb.core.log.db
Log manager factory implementationt that logs changes to the database.
DbLogManagerFactory() - Constructor for class net.sf.basedb.core.log.db.DbLogManagerFactory
 
DbLogManagerFactory(boolean, boolean) - Constructor for class net.sf.basedb.core.log.db.DbLogManagerFactory
 
dc - Variable in class net.sf.basedb.clients.web.extensions.ExtensionsControl
 
dc - Variable in class net.sf.basedb.clients.web.extensions.list.RelatedItemHelper
 
dc - Variable in class net.sf.basedb.clients.web.formatter.DataFileFormatter
 
dc - Variable in class net.sf.basedb.clients.web.plugins.SimpleExport
 
dc - Variable in class net.sf.basedb.clients.web.taglib.PropertyValue
A DbControl object.
dc - Variable in class net.sf.basedb.clients.web.taglib.SubtypeSelector
 
dc - Variable in class net.sf.basedb.clients.web.taglib.table.ExtensionCells
 
dc - Variable in class net.sf.basedb.core.AbstractBatcher
A reference to the current DbControl object.
dc - Variable in class net.sf.basedb.core.AnyToAny.FastLinkLoader
 
dc - Variable in class net.sf.basedb.core.BasicItem
A reference to the current DbControl object.
dc - Variable in class net.sf.basedb.core.BioMaterialEventSource
 
dc - Variable in class net.sf.basedb.core.DerivedBioAssay.FixDerivedBioAssayParentsRecursivelyAction
 
dc - Variable in class net.sf.basedb.core.DiskUsageStatistics
 
dc - Variable in class net.sf.basedb.core.FastAnnotationLoader
 
dc - Variable in class net.sf.basedb.core.FastAnnotationLoader.FastIterator
 
dc - Variable in class net.sf.basedb.core.ItemResultIterator
The DbControl tthat was used in the query.
dc - Variable in class net.sf.basedb.core.ItemResultList
The DbControl that was used in the query.
dc - Variable in class net.sf.basedb.core.LogControl
 
dc - Variable in class net.sf.basedb.core.MeasuredBioMaterial.RemainingQuantityAction
 
dc - Variable in class net.sf.basedb.core.MigrateRbaToDba
 
dc - Variable in class net.sf.basedb.core.ReporterScoreResultIterator
The DbControl that was used in the query.
dc - Variable in class net.sf.basedb.core.snapshot.AnnotationLoaderUtil
 
dc - Variable in class net.sf.basedb.core.snapshot.AnnotationSnapshot.AnnotationTypeComparator
 
dc - Variable in class net.sf.basedb.core.snapshot.AnnotationSnapshot.ProjectComparator
 
dc - Variable in class net.sf.basedb.plugins.AnnotationFlatFileImporter
 
dc - Variable in class net.sf.basedb.plugins.BaseFileExporterPlugin
 
dc - Variable in class net.sf.basedb.plugins.batchimport.AbstractItemImporter
 
dc - Variable in class net.sf.basedb.plugins.batchimport.AnyToAnyImporter
 
dc - Variable in class net.sf.basedb.plugins.BfsExporterPlugin
 
dc - Variable in class net.sf.basedb.plugins.GalExporter
 
dc - Variable in class net.sf.basedb.plugins.HelpExporter
 
dc - Variable in class net.sf.basedb.plugins.IlluminaRawDataImporter
 
dc - Variable in class net.sf.basedb.plugins.PackedFileExporter
 
dc - Variable in class net.sf.basedb.plugins.PlateFlatFileImporter
 
dc - Variable in class net.sf.basedb.plugins.PlateMappingExporter
 
dc - Variable in class net.sf.basedb.plugins.PlateMappingImporter
 
dc - Variable in class net.sf.basedb.plugins.PluginConfigurationExporter
 
dc - Variable in class net.sf.basedb.plugins.PrintMapFlatFileImporter
 
dc - Variable in class net.sf.basedb.plugins.RawDataFlatFileImporter
 
dc - Variable in class net.sf.basedb.plugins.ReporterFlatFileImporter
 
dc - Variable in class net.sf.basedb.plugins.ReporterMapFlatFileImporter
 
dc - Variable in class net.sf.basedb.util.affymetrix.CdfValidationAction
 
dc - Variable in class net.sf.basedb.util.affymetrix.CelValidationAction
 
dc - Variable in class net.sf.basedb.util.annotations.InheritAnnotationsManager
 
dc - Variable in class net.sf.basedb.util.bfs.BaseInputStreamLocator
 
dc - Variable in class net.sf.basedb.util.bfs.GenericBaseDataWriterFactory
 
dc - Variable in class net.sf.basedb.util.bfs.GenericExtraFileImporter
 
dc - Variable in class net.sf.basedb.util.export.spotdata.AbstractBioAssaySetExporter
 
dc - Variable in class net.sf.basedb.util.export.spotdata.AbstractFieldConverter
 
dc - Variable in class net.sf.basedb.util.extensions.ClientContext
 
dc - Variable in class net.sf.basedb.util.extensions.manager.processor.DisablePluginsProcessor
 
dc - Variable in class net.sf.basedb.util.extensions.manager.processor.PluginInstallationProcessor
 
dc - Variable in class net.sf.basedb.util.formatter.PropertyFilterFormatter
 
dc - Variable in class net.sf.basedb.util.gtf.GtfValidationAction
 
dc - Variable in class net.sf.basedb.util.importer.spotdata.BaseFileImporter
 
dc - Variable in class net.sf.basedb.util.importer.spotdata.BfsImporter
 
dc - Variable in class net.sf.basedb.util.importer.spotdata.FirstPassSectionSpotsParser
 
dc - Variable in class net.sf.basedb.util.importer.spotdata.SecondPassSectionSpotsParser
 
dc - Variable in class net.sf.basedb.util.importer.spotdata.SectionAssaysParser
 
dc - Variable in class net.sf.basedb.util.importer.spotdata.SectionReporterListParser
 
dc - Variable in class net.sf.basedb.util.jep.ExtraValueFunction
 
dc - Variable in class net.sf.basedb.util.jep.InReporterListFunction
 
dc - Variable in class net.sf.basedb.util.jep.MeanFunction
 
dc - Variable in class net.sf.basedb.util.jep.NotInReporterListFunction
 
dc - Variable in class net.sf.basedb.util.jep.RawFunction
 
dc - Variable in class net.sf.basedb.util.jep.ReporterFunction
 
dc - Variable in class net.sf.basedb.util.jep.ScoreFunction
 
dc - Variable in class net.sf.basedb.util.listable.TransformContext
 
dc - Variable in class net.sf.basedb.util.overview.node.NodeFactory
 
dc - Variable in class net.sf.basedb.util.parser.DefaultItemFunction
 
dc - Variable in class net.sf.basedb.util.query.MultiQueryIterator
 
dc - Variable in class net.sf.basedb.util.units.UnitCache
 
dc - Variable in class net.sf.basedb.util.zip.ZipUnpacker
 
debug - Static variable in class net.sf.basedb.util.overview.GenericOverview
 
debug - Static variable in class net.sf.basedb.util.overview.loader.AbstractNodeLoader
 
debug - Static variable in class net.sf.basedb.util.overview.loader.BasicItemNodeLoader
 
debug - Static variable in class net.sf.basedb.util.overview.loader.BasicItemNodeLoaderFactory
 
debug - Static variable in class net.sf.basedb.util.overview.node.NodeFactory
 
debug(String) - Method in class net.sf.basedb.util.extensions.logging.ExtensionsLogger
Log a DEBUG message.
debug(String, Throwable) - Method in class net.sf.basedb.util.extensions.logging.ExtensionsLogger
Log a DEBUG message with an optional stacktrace.
DEBUG - Enum constant in enum class net.sf.basedb.util.extensions.logging.LogLevel
 
DEBUG - Enum constant in enum class net.sf.basedb.util.extensions.LoggingErrorHandlerFactory.Level
 
debugEnabled - Static variable in class net.sf.basedb.core.AbstractEntityQuery
So we don't always have to call logParam.debug()
debugEnabled - Static variable in class net.sf.basedb.core.AbstractHqlQuery
So we don't always have to call logParam.debug()
debugEnabled - Static variable in class net.sf.basedb.core.AbstractQuery
So we don't always have to call logSql.debug()
debugEnabled - Static variable in class net.sf.basedb.core.BasicBatcher
So we don't always have to call logParam.debug()
debugEnabled - Static variable in class net.sf.basedb.core.BatchUtil
So we don't always have to call logSql.debug()
DebugOnSaveAction(JspContext) - Constructor for class net.sf.basedb.clients.web.extensions.edit.DebugOnSaveActionFactory.DebugOnSaveAction
 
DebugOnSaveActionFactory - Class in net.sf.basedb.clients.web.extensions.edit
On-save action factory that create actions that print a log message to System.out for all events.
DebugOnSaveActionFactory() - Constructor for class net.sf.basedb.clients.web.extensions.edit.DebugOnSaveActionFactory
 
DebugOnSaveActionFactory.DebugOnSaveAction - Class in net.sf.basedb.clients.web.extensions.edit
 
debugParamEnabled - Static variable in class net.sf.basedb.core.AbstractSqlQuery
So we don't always have to call logParam.debug()
debugSqlEnabled - Static variable in class net.sf.basedb.core.AbstractBatcher
So we don't always have to call logSql.debug()
debugSqlEnabled - Static variable in class net.sf.basedb.core.AbstractSqlQuery
So we don't always have to call logSql.debug()
debugSqlEnabled - Static variable in class net.sf.basedb.core.AnnotationRestriction
So we don't always have to call logSql.debug()
debugSqlEnabled - Static variable in class net.sf.basedb.core.RawDataBatcher
So we don't always have to call logSql.debug()
debugSqlEnabled - Static variable in class net.sf.basedb.core.VirtualDb
So we don't always have to call logSql.debug()
decapitalize(String) - Static method in class net.sf.basedb.core.StringUtil
Decapitalize the string by making sure the first character is lower-case.
decideOnFirst - Variable in class net.sf.basedb.util.formatter.MultiFormatter
 
DECIMAL_SEPARATOR_PARAMETER - Static variable in class net.sf.basedb.plugins.util.Parameters
The name of the parameter that is created by Parameters.decimalSeparatorParameter(String, String, String)
decimalSeparatorParameter(String, String, String) - Static method in class net.sf.basedb.plugins.util.Parameters
Parameter definition that asks for the decimal separator used by numeric values when parsed from strings.
decode(String) - Method in interface net.sf.basedb.util.encode.EncoderDecoder
 
decode(String) - Method in class net.sf.basedb.util.encode.IdentityEncoderDecoder
 
decode(String) - Method in class net.sf.basedb.util.encode.TabCrLfEncoderDecoder
 
decode(String) - Method in class net.sf.basedb.util.encode.ToSpaceEncoderDecoder
 
decode_base64(String, int) - Static method in class net.sf.basedb.util.bcrypt.BCrypt
Decode a string encoded using bcrypt's base64 scheme to a byte array.
decodeAll(Collection<String>, EncoderDecoder) - Static method in class net.sf.basedb.util.encode.EncodeUtil
Decode all strings in a collection.
decoder - Variable in class net.sf.basedb.util.bfs.AnnotationParser
 
decoder - Variable in class net.sf.basedb.util.bfs.DataParser
 
decoder - Variable in class net.sf.basedb.util.bfs.MetadataParser
 
decodeValue(String) - Method in class net.sf.basedb.util.bfs.AnnotationParser
Decode an encoded value.
decodeValue(String) - Method in class net.sf.basedb.util.bfs.DataParser
Decode an encoded value.
decodeValue(String) - Method in class net.sf.basedb.util.bfs.MetadataParser
Decode an encoded value.
decompress(ProgressReporter) - Method in class net.sf.basedb.core.File
Decompress the file stored on the disk.
deepCopy(Node) - Method in class net.sf.basedb.util.overview.Node
Create a deep copy of this node and all it's children.
deepCopyInternal(Node) - Method in class net.sf.basedb.util.overview.Node
 
DEFAULT - Static variable in class net.sf.basedb.clients.web.ModeInfo
 
DEFAULT - Static variable in class net.sf.basedb.core.Application.StartupOptions
Default startup options that will start BASE for normal operations using the options specified in "base.config".
DEFAULT - Static variable in class net.sf.basedb.core.Quota
The ID for the system default quota, which is assigned to new users unless another quota is specified.
DEFAULT_CHECK_INTERVAL - Static variable in class net.sf.basedb.clients.jobagent.Agent
The default check interval in seconds.
DEFAULT_DATE_FORMAT - Static variable in class net.sf.basedb.clients.web.formatter.FormatterSettings
The default date format for a date formatter = @value
DEFAULT_DATETIME_FORMAT - Static variable in class net.sf.basedb.clients.web.formatter.FormatterSettings
The default datetime format for a datetime formatter = @value
DEFAULT_ERROR - Static variable in class net.sf.basedb.plugins.util.Parameters
DEFAULT_FILTER - Static variable in class net.sf.basedb.util.extensions.Registry
DEFAULT_JOB_EXECUTOR - Static variable in class net.sf.basedb.clients.jobagent.Agent
The default job executor to use if none has been specified in the configuration file.
DEFAULT_LOGIN - Static variable in class net.sf.basedb.clients.web.extensions.login.FieldInfo
This is the default login field.
DEFAULT_MAX_UNKNOWN_LINES - Static variable in class net.sf.basedb.util.parser.FlatFileParser
The default value for the number of unknown lines in a row that may be encountered by the parseHeaders method before it gives up.
DEFAULT_NAME - Static variable in class net.sf.basedb.core.ItemContext
This is the name of the default context which is automatically saved when a user is logging out.
DEFAULT_NUM_DECIMALS - Static variable in class net.sf.basedb.clients.web.formatter.FormatterSettings
The default number of decimals to display by a number formatter = @value
DEFAULT_PAGE_TITLE - Static variable in class net.sf.basedb.clients.web.taglib.Page
The default page title.
DEFAULT_PASSWORD - Static variable in class net.sf.basedb.clients.web.extensions.login.FieldInfo
This is the default password field.
DEFAULT_PORT - Static variable in class net.sf.basedb.core.JobAgent
The default port (47822) where job agents are listening for connections.
DEFAULT_SLOT_MANAGER - Static variable in class net.sf.basedb.clients.jobagent.Agent
The default slot manager to use if none has been specified in the configuration file.
DEFAULT_TIMEOUT - Static variable in class net.sf.basedb.clients.web.fileupload.FileUpload
The default timeout to use when waiting for the next data packet to arrive.
defaultArrayDesignFunction - Variable in class net.sf.basedb.plugins.batchimport.RawBioAssayImporter
 
DefaultConfigurationValues - Class in net.sf.basedb.plugins.gtf
Provides a default configuration values for GTF file parsing when none has been provided by the user.
DefaultConfigurationValues(ParameterValues) - Constructor for class net.sf.basedb.plugins.gtf.DefaultConfigurationValues
 
DefaultDbEngine - Class in net.sf.basedb.core.dbengine
A default DbEngine that is selected if no other can be found.
DefaultDbEngine() - Constructor for class net.sf.basedb.core.dbengine.DefaultDbEngine
Create DefaultDbEngine.
defaultDeleted(int, boolean) - Method in class net.sf.basedb.core.ProjectSpecificAnnotationsManager
A default annotation is being deleted in this transaction.
DefaultEntityLogger - Class in net.sf.basedb.core.log.db
Default logger for all entities that has been tagged with the LoggableData interface.
DefaultEntityLogger(DbLogManagerFactory) - Constructor for class net.sf.basedb.core.log.db.DefaultEntityLogger
Creates a new entity logger.
defaultError(String, String, String, String...) - Static method in class net.sf.basedb.plugins.util.Parameters
Create the default error handling parameter.
defaultErrorHandler - Variable in class net.sf.basedb.util.error.ClassMapErrorHandler
 
defaultErrorHandlerFactory - Variable in class net.sf.basedb.util.extensions.Registry
 
defaultErrorParameter - Static variable in class net.sf.basedb.plugins.AbstractFlatFileImporter
 
defaultErrorParameter - Static variable in class net.sf.basedb.plugins.AnnotationFlatFileImporter
 
DefaultFilter - Class in net.sf.basedb.util.extensions
A default filter implementation that enables all extensions and extension points and sorts the extensions based on the Extension.getIndex() values.
DefaultFilter() - Constructor for class net.sf.basedb.util.extensions.DefaultFilter
Create a new default filter.
defaultFirst - Variable in class net.sf.basedb.core.snapshot.AnnotationSnapshot.ProjectComparator
 
defaultFormat - Variable in class net.sf.basedb.clients.web.servlet.ExperimentExplorerPlotServlet
 
defaultFormat - Variable in class net.sf.basedb.clients.web.servlet.PlotServlet
 
defaultFormatter - Variable in class net.sf.basedb.util.formatter.MultiFormatter
 
defaultGuiContexts - Static variable in class net.sf.basedb.core.plugin.AbstractAnalysisPlugin
The default gui contexts where it makes sense to use an analysis plugin.
defaultHandler - Variable in class net.sf.basedb.clients.jobagent.handlers.MultiProtocolRequestHandler
 
defaultHardwareFunction - Variable in class net.sf.basedb.plugins.batchimport.ArrayBatchImporter
 
defaultHardwareFunction - Variable in class net.sf.basedb.plugins.batchimport.BioPlateImporter
 
defaultHardwareFunction - Variable in class net.sf.basedb.plugins.batchimport.DerivedBioAssayImporter
 
defaultHardwareFunction - Variable in class net.sf.basedb.plugins.batchimport.PhysicalBioAssayImporter
 
defaultHeight - Variable in class net.sf.basedb.clients.web.servlet.ExperimentExplorerPlotServlet
 
defaultHeight - Variable in class net.sf.basedb.clients.web.servlet.PlotServlet
 
defaultIds - Static variable in class net.sf.basedb.clients.web.taglib.Button
 
defaultImages - Static variable in class net.sf.basedb.clients.web.taglib.Button
 
DefaultItemFunction<T extends Nameable> - Class in net.sf.basedb.util.parser
JEP function that can be used to return the name of a default item in a project.
DefaultItemFunction(DbControl, Project, Item) - Constructor for class net.sf.basedb.util.parser.DefaultItemFunction
Create a new function instance.
defaultItems - Variable in class net.sf.basedb.clients.web.taglib.Select
The project default values.
defaultItems - Variable in class net.sf.basedb.core.data.ProjectData
 
defaultKeyManagers - Static variable in class net.sf.basedb.util.ssl.SSLUtil2
 
defaultLogger - Variable in class net.sf.basedb.core.log.db.DbLogManagerFactory
 
defaultMaxRecent - Static variable in class net.sf.basedb.clients.web.Base
 
defaultMimeType - Variable in class net.sf.basedb.clients.web.servlet.Download
 
defaultPlatformFunction - Variable in class net.sf.basedb.plugins.batchimport.ArrayDesignImporter
 
defaultPreset - Variable in class net.sf.basedb.core.Presets
 
defaultPriority - Variable in enum class net.sf.basedb.core.Job.ExecutionTime
 
defaultProtocolFunction - Variable in class net.sf.basedb.plugins.batchimport.ArrayBatchImporter
 
defaultProtocolFunction - Variable in class net.sf.basedb.plugins.batchimport.DerivedBioAssayImporter
 
defaultProtocolFunction - Variable in class net.sf.basedb.plugins.batchimport.PhysicalBioAssayImporter
 
defaultProtocolFunction - Variable in class net.sf.basedb.plugins.batchimport.RawBioAssayImporter
 
defaultPrototolFunction - Variable in class net.sf.basedb.plugins.batchimport.ExtractImporter
 
defaultPrototolFunction - Variable in class net.sf.basedb.plugins.batchimport.SampleImporter
 
defaultReporterContext - Static variable in class net.sf.basedb.clients.web.ExperimentExplorer
The default context for the reporter search page.
DefaultRequestHandler - Class in net.sf.basedb.clients.jobagent.handlers
This is the default request handler for incoming requests to a job agent.
DefaultRequestHandler(Agent) - Constructor for class net.sf.basedb.clients.jobagent.handlers.DefaultRequestHandler
 
defaultScale - Static variable in class net.sf.basedb.clients.web.Base
 
defaultSelects - Variable in class net.sf.basedb.core.DynamicExtraValueQuery
 
defaultSelects - Variable in class net.sf.basedb.core.DynamicPositionQuery
 
defaultSelects - Variable in class net.sf.basedb.core.DynamicSpotQuery
 
defaultSettings - Variable in class net.sf.basedb.core.data.ClientData
 
defaultSettings - Variable in class net.sf.basedb.core.data.UserData
 
defaultSeverity - Variable in class net.sf.basedb.util.overview.Validator
 
defaultSlots - Variable in enum class net.sf.basedb.core.Job.ExecutionTime
 
defaultSocketFactory - Static variable in class net.sf.basedb.util.ssl.SSLUtil2
 
defaultSoftwareFunction - Variable in class net.sf.basedb.plugins.batchimport.DerivedBioAssayImporter
 
defaultSoftwareFunction - Variable in class net.sf.basedb.plugins.batchimport.RawBioAssayImporter
 
defaultSpotContexts - Static variable in class net.sf.basedb.clients.web.ExperimentExplorer
Stores default context for the spot data list on the view page.
defaultsSection - Static variable in class net.sf.basedb.plugins.batchimport.AbstractItemImporter
 
defaultTrustManagers - Static variable in class net.sf.basedb.util.ssl.SSLUtil2
 
defaultUnit - Variable in class net.sf.basedb.core.AnnotationBatcher.CurrentAnnotationInfo
 
defaultUnit - Variable in class net.sf.basedb.core.data.AnnotationTypeData
 
defaultUnitColumnMapping - Static variable in class net.sf.basedb.plugins.batchimport.AnnotationTypeImporter
Column mapping parameter for "Default unit".
defaultUnitMapper - Variable in class net.sf.basedb.plugins.batchimport.AnnotationTypeImporter
 
defaultValue - Variable in class net.sf.basedb.core.data.AnnotationTypeData
 
defaultValue - Variable in class net.sf.basedb.core.ParameterType
Default value of the parameter.
defaultValue - Variable in class net.sf.basedb.core.PluginParameter
A default value that overrides the default set by the parameter type.
defaultValue - Variable in class net.sf.basedb.core.query.ParameterExpression
 
defaultValue - Variable in class net.sf.basedb.plugins.Base1PluginExecuter.JobParameter
 
defaultValue - Variable in class net.sf.basedb.plugins.executor.ParameterDefinition
 
defaultValue - Variable in class net.sf.basedb.util.extensions.debug.StringConverter
 
defaultValue - Variable in class net.sf.basedb.util.formatter.LookupFormatter
 
defaultValueColumnMapping - Static variable in class net.sf.basedb.plugins.batchimport.AnnotationTypeImporter
Column mapping parameter for "Default value".
defaultValueMapper - Variable in class net.sf.basedb.plugins.batchimport.AnnotationTypeImporter
 
defaultValues - Variable in class net.sf.basedb.plugins.gtf.DefaultConfigurationValues
 
defaultVariantFunction - Variable in class net.sf.basedb.plugins.batchimport.ArrayDesignImporter
 
defaultWidth - Variable in class net.sf.basedb.clients.web.servlet.ExperimentExplorerPlotServlet
 
defaultWidth - Variable in class net.sf.basedb.clients.web.servlet.PlotServlet
 
deferred - Variable in class net.sf.basedb.plugins.ReporterFlatFileImporter
 
definedColumns - Variable in class net.sf.basedb.clients.web.taglib.table.Table
The ID of all defined columns
definedPermissions - Variable in enum class net.sf.basedb.core.Item
 
DefinedPermissions() - Constructor for class net.sf.basedb.core.Item.DefinedPermissions
 
defineFilter(Element, Item, String, String, HibernateUtil.FilterConfigurator) - Static method in class net.sf.basedb.core.HibernateUtil
Define a filter for on the given class.
definePackage(String, Manifest) - Method in class net.sf.basedb.util.JarClassLoader
Define the package with the given name using information from a manifest for vendor, title and version.
defultUnit - Variable in class net.sf.basedb.core.snapshot.AnnotationLoaderUtil
 
delayed - Variable in class net.sf.basedb.core.ItemList
 
delayed - Variable in class net.sf.basedb.core.Job.JobSignalTransporter
 
delayedAdd(Listable) - Method in class net.sf.basedb.core.ItemList
 
DelayedAdditionManager(ItemListData) - Constructor for class net.sf.basedb.core.ItemList.DelayedAdditionManager
 
DelayedFilterDef(String, Item, String) - Constructor for class net.sf.basedb.core.HibernateUtil.DelayedFilterDef
 
delayedFilters - Variable in class net.sf.basedb.core.HibernateUtil.FilterConfigurator
 
delayedRemove(Listable) - Method in class net.sf.basedb.core.ItemList
 
delayRegistration - Variable in class net.sf.basedb.util.extensions.manager.processor.IgnoreFileProcessor
 
delayRegistration - Variable in class net.sf.basedb.util.extensions.manager.processor.RegisterExtensionsProcessor
 
delegateFirst - Variable in class net.sf.basedb.util.JarClassLoader
If we should delegate to the parent class loader first.
DelegatingSignalHandler - Class in net.sf.basedb.core.signal
A signal handler implementation that can delegate to other signal handlers, depending on which signal it receives.
DelegatingSignalHandler() - Constructor for class net.sf.basedb.core.signal.DelegatingSignalHandler
Create a new delegating signal handler.
DelegatingSignalHandler(SignalHandler...) - Constructor for class net.sf.basedb.core.signal.DelegatingSignalHandler
Create a new delegating signal handler and register the given handlers as delegates.
delete - Static variable in class net.sf.basedb.core.Item.DefinedPermissions
 
delete(int) - Method in class net.sf.basedb.core.BasicBatcher
Delete a data object by id.
delete(int) - Method in class net.sf.basedb.core.FeatureBatcher
Always throws a PermissionDeniedException, since a feature cannot be modifed once it has been created.
delete(int) - Method in class net.sf.basedb.core.RawDataBatcher
Always throws a PermissionDeniedException, since raw data cannot be modifed once it has been created, except if all spots are deleted at the same time.
delete(D) - Method in class net.sf.basedb.core.BasicBatcher
Delete a data object.
delete(Object) - Method in class net.sf.basedb.core.hibernate.SessionWrapper
 
delete(Object) - Method in class net.sf.basedb.core.hibernate.StatelessSessionWrapper
 
delete(String, int) - Method in class net.sf.basedb.util.StaticCache
Deletes an object from the cache.
delete(String, Object) - Method in class net.sf.basedb.core.hibernate.SessionWrapper
 
delete(String, Object) - Method in class net.sf.basedb.core.hibernate.StatelessSessionWrapper
 
delete(DbControl, Item, Set<Integer>) - Static method in class net.sf.basedb.util.RemovableUtil
 
delete(SessionControl, Collection<? extends Identifiable>, boolean, ProgressReporter) - Static method in class net.sf.basedb.core.Trashcan
Delete items permanently.
DELETE - Enum constant in enum class net.sf.basedb.core.log.ChangeType
 
DELETE - Enum constant in enum class net.sf.basedb.core.Permission
This permission allows a user delete an item.
DELETE - Enum constant in enum class net.sf.basedb.core.Transactional.Action
The item is an existing item which is beeing deleted.
deleteAll() - Method in class net.sf.basedb.core.FeatureBatcher
Delete all features belonging to this array design.
deleteAll() - Method in class net.sf.basedb.core.RawDataBatcher
Delete all raw data.
deleteAll(SessionControl, ProgressReporter) - Static method in class net.sf.basedb.core.Trashcan
Delete all items in the trashcan of the logged in user.
deleteAllCubeData(short) - Method in class net.sf.basedb.core.VirtualDb
Delete all analysed data for the specified data cube.
deleteAllCubeExtraValueData(short, short, VirtualTable) - Method in class net.sf.basedb.core.VirtualDb
Delete all extra value data for the specified extra value type in the specified data cube.
deleteAllCubeFilterData(short, short) - Method in class net.sf.basedb.core.VirtualDb
Delete all analysed data for the specified filter in the specified data cube.
deleteAllCubeLayerData(short, short) - Method in class net.sf.basedb.core.VirtualDb
Delete all analysed data for the specified layer in the specified data cube.
deleteAnalysedData() - Method in class net.sf.basedb.core.BioAssaySet
Called when a bioassayset is about to be deleted.
deleteAnnotationsForNonExistingProjects() - Method in class net.sf.basedb.core.ProjectSpecificAnnotationsManager
 
deleteContext(int) - Method in class net.sf.basedb.core.SessionControl
Delete a context.
deleteCount - Variable in class net.sf.basedb.core.BasicBatcher
 
deleteCurrentContexts(Item, boolean, boolean) - Method in class net.sf.basedb.core.SessionControl
Delete all default contexts for the logged in user.
deleted - Variable in class net.sf.basedb.plugins.ReporterFlatFileImporter
 
DELETED - Enum constant in enum class net.sf.basedb.core.AnnotationBatcher.Change
An existing annotation was deleted.
deleteData(Session, BasicData) - Static method in class net.sf.basedb.core.HibernateUtil
Delete a data item from the database.
deletedDefault - Variable in class net.sf.basedb.core.ProjectSpecificAnnotationsManager
 
DeletedFilter - Class in net.sf.basedb.util.extensions.manager.filter
Filter implementation for extension files that allow only deleted files to pass.
DeletedFilter() - Constructor for class net.sf.basedb.util.extensions.manager.filter.DeletedFilter
Create a new filter.
deleteDir(File) - Method in class net.sf.basedb.plugins.Base1PluginExecuter
Deletes all files and sub directories under dir.
deletedPrimary - Variable in class net.sf.basedb.core.ProjectSpecificAnnotationsManager
 
deleteEmptyAnnotationSets(ProgressReporter) - Static method in class net.sf.basedb.core.AnnotationSet
Delete all empty annotation sets.
deleteEmptyAnnotationSets(Session, ProgressReporter) - Static method in class net.sf.basedb.core.AnnotationSet
Delete all empty annotation sets.
deleteEmptyDirectories(File, boolean) - Static method in class net.sf.basedb.util.FileUtil
Deletes all empty subdirectories and, optionally, also the root directory.
deleteFromAnnotations - Variable in class net.sf.basedb.core.AnnotationBatcher
 
deleteFromParameterValues - Variable in class net.sf.basedb.core.AnnotationBatcher
 
deleteInheritedAnnotations - Variable in class net.sf.basedb.core.AnnotationBatcher
 
deleteItem(BasicItem) - Method in class net.sf.basedb.core.DbControl
Schedule an existing item to be deleted from the database.
deleteMode - Variable in class net.sf.basedb.plugins.ReporterFlatFileImporter
 
deletePreset(String) - Method in class net.sf.basedb.core.Presets
Delete a named preset.
deleteProducts() - Method in class net.sf.basedb.core.Transformation
Delete all product bioassaysets.
deleteRawData() - Method in class net.sf.basedb.core.RawBioAssay
Delete the raw data that has been added to the database for this raw bioassay.
DeleteResourcesProcessor - Class in net.sf.basedb.util.extensions.manager.processor
A file processor implementation that removes all resources that was previously extracted from a JAR file.
DeleteResourcesProcessor(File, ProcessResults) - Constructor for class net.sf.basedb.util.extensions.manager.processor.DeleteResourcesProcessor
Create a new processor.
deleteSnapshotIfModifed - Variable in class net.sf.basedb.core.AnnotationBatcher
 
deleteSql - Variable in class net.sf.basedb.core.BasicBatcher
 
deleteStatement - Variable in class net.sf.basedb.core.BasicBatcher
 
deleteStrayEntries(ProgressReporter) - Static method in class net.sf.basedb.core.ChangeHistory
Delete all history entries that are linking to non-existing items.
deleteStrayLinks(ProgressReporter) - Static method in class net.sf.basedb.core.AnyToAny
Delete all links that are linking to non-existing items.
deleteTempDirectory(File) - Static method in class net.sf.basedb.util.FileUtil
Recursively delete all files and subdirectories within a given directory and the also the given directory itself.
deleteUnusedItemKeys() - Static method in class net.sf.basedb.core.ItemKey
Delete all keys that are currently not used by any item.
deleteUnusedProjectKeys() - Static method in class net.sf.basedb.core.ProjectKey
Delete all keys that are currently not used by any item.
deleteValues - Variable in class net.sf.basedb.core.AnnotationBatcher
 
DELETION_ORDER - Static variable in enum class net.sf.basedb.core.Item
 
deletionOrder - Variable in enum class net.sf.basedb.core.Item
 
delta - Variable in class net.sf.basedb.plugins.LowessNormalization.CallableWorker
 
deltaMidMax - Variable in class net.sf.basedb.util.ColorGenerator
The difference of the RGB components of the mid and max colors. [0] = red; [1] = green; [2] = blue
deltaMinMid - Variable in class net.sf.basedb.util.ColorGenerator
The difference of the RGB components of the min and mid colors. [0] = red; [1] = green; [2] = blue
deltaParameter - Static variable in class net.sf.basedb.plugins.LowessNormalization
 
denied - Variable in class net.sf.basedb.clients.web.taglib.Select
If the logged in user was denied access to the current item.
denied - Variable in class net.sf.basedb.core.data.keyring.PluginKeys
 
denied - Variable in class net.sf.basedb.core.data.PluginPermission
 
denied - Variable in class net.sf.basedb.core.PluginPermission
 
DENIED - Enum constant in enum class net.sf.basedb.core.Permission
This permission denies a user access to an item.
DENIED_ANNOTATIONTYPE - Static variable in class net.sf.basedb.util.overview.Validator
Validator rule that checks for denied access to an annotation type.
DENIED_ANYTOANY - Static variable in class net.sf.basedb.util.overview.Validator
Validator rule that checks for denied access the referenced item in an any-to-any link.
DENIED_ARRAYBATCH - Static variable in class net.sf.basedb.util.overview.Validator
Validator rule that checks for denied access to an array batch.
DENIED_ARRAYDESIGN - Static variable in class net.sf.basedb.util.overview.Validator
Validator rule that checks for denied access to an array design.
DENIED_ARRAYSLIDE - Static variable in class net.sf.basedb.util.overview.Validator
Validator rule that checks for denied access to array slides.
DENIED_BIOPLATE - Static variable in class net.sf.basedb.util.overview.Validator
Validator rule that checks for denied access to a bioplate.
DENIED_BIOSOURCE - Static variable in class net.sf.basedb.util.overview.Validator
Validator rule that checks for denied access to biosource.
DENIED_DATAFILETYPE - Static variable in class net.sf.basedb.util.overview.Validator
Validator rule that checks for denied access to data file types.
DENIED_DERIVEDBIOASSAY - Static variable in class net.sf.basedb.util.overview.Validator
Validator rule that checks for denied access to derived bioassay.
DENIED_EXTRACT - Static variable in class net.sf.basedb.util.overview.Validator
Validator rule that checks for denied access to extracts.
DENIED_FILE - Static variable in class net.sf.basedb.util.overview.Validator
Validator rule that checks for denied access to (data) files.
DENIED_HARDWARE - Static variable in class net.sf.basedb.util.overview.Validator
Validator rule that checks for denied access to hardware.
DENIED_KIT - Static variable in class net.sf.basedb.util.overview.Validator
Validator rule that checks for denied access to kit.
DENIED_PHYSICALBIOASSAY - Static variable in class net.sf.basedb.util.overview.Validator
Validator rule that checks for denied access to physical bioassay.
DENIED_PLATFORM - Static variable in class net.sf.basedb.util.overview.Validator
Validator rule that checks for denied access to platform.
DENIED_PROTOCOL - Static variable in class net.sf.basedb.util.overview.Validator
Validator rule that checks for denied access to protocols.
DENIED_SAMPLE - Static variable in class net.sf.basedb.util.overview.Validator
Validator rule that checks for denied access to samples.
DENIED_SOFTWARE - Static variable in class net.sf.basedb.util.overview.Validator
Validator rule that checks for denied access to software.
DENIED_TAG - Static variable in class net.sf.basedb.util.overview.Validator
Validator rule that checks for denied access to tags.
DENSITY - Static variable in class net.sf.basedb.core.Quantity
The id for the Quantity object representing density.
deny(Set<Permission>) - Static method in enum class net.sf.basedb.core.Permission
Combine the given permission and convert to the integer deny value.
deny(Permission) - Static method in enum class net.sf.basedb.core.Permission
Convert the given permission to the integer deny value.
deny(Permission...) - Static method in enum class net.sf.basedb.core.Permission
Combine the given permissions and convert to the integer deny value.
DENY_ALL_FILTER - Static variable in class net.sf.basedb.core.QueryRuntimeFilterFactory
 
DENY_ITEM - Static variable in class net.sf.basedb.core.Keyring
 
DENY_ROOT_NODE - Static variable in class net.sf.basedb.util.overview.loader.BasicItemNodeLoader
 
DenyAllFilter() - Constructor for class net.sf.basedb.core.QueryRuntimeFilterFactory.DenyAllFilter
 
denyValue - Variable in enum class net.sf.basedb.core.Permission
 
denyValue() - Method in enum class net.sf.basedb.core.Permission
 
DeprecationLogger - Class in net.sf.basedb.clients.web.taglib
Utility class for logging use of deprecated taglib attributes.
DeprecationLogger() - Constructor for class net.sf.basedb.clients.web.taglib.DeprecationLogger
 
depth - Variable in class net.sf.basedb.util.Tree.Entry
 
DerivedBioAssay - Class in net.sf.basedb.core
 
DerivedBioAssay(DerivedBioAssayData) - Constructor for class net.sf.basedb.core.DerivedBioAssay
 
DERIVEDBIOASSAY - Enum constant in enum class net.sf.basedb.core.Item
The item is a DerivedBioAssay.
DerivedBioAssay.FixDerivedBioAssayParentsRecursivelyAction - Class in net.sf.basedb.core
Whenever we modify the parent items to a derived bioassay, we must make sure that the physical bioassays for all child items are synchronized with the same changes.
DerivedBioAssayData - Class in net.sf.basedb.core.data
 
DerivedBioAssayData() - Constructor for class net.sf.basedb.core.data.DerivedBioAssayData
 
DerivedBioAssayImporter - Class in net.sf.basedb.plugins.batchimport
Plug-in for importing derived bioassay items in a batch.
DerivedBioAssayImporter() - Constructor for class net.sf.basedb.plugins.batchimport.DerivedBioAssayImporter
 
DerivedBioAssayLoader - Class in net.sf.basedb.util.overview.loader
 
DerivedBioAssayLoader() - Constructor for class net.sf.basedb.util.overview.loader.DerivedBioAssayLoader
 
derivedBioAssayQuery - Variable in class net.sf.basedb.plugins.batchimport.AbstractItemImporter
 
derivedBioAssays - Variable in class net.sf.basedb.core.data.ExtractData
 
derivedBioAssays - Variable in class net.sf.basedb.core.data.JobData
 
derivedBioAssays - Variable in class net.sf.basedb.core.data.PhysicalBioAssayData
 
DerivedBioAssayToChildDerivedBioAssayTransformer - Class in net.sf.basedb.util.listable
Source item transformer implementation that transform derived bioassay items to child derived bioassays.
DerivedBioAssayToChildDerivedBioAssayTransformer(boolean) - Constructor for class net.sf.basedb.util.listable.DerivedBioAssayToChildDerivedBioAssayTransformer
Create a new derived bioassay to child derived bioassay transformer.
DerivedBioAssayToParentDerivedBioAssayTransformer - Class in net.sf.basedb.util.listable
Source item transformer implementation that transform derived bioassay items to parent derived bioassays.
DerivedBioAssayToParentDerivedBioAssayTransformer(boolean) - Constructor for class net.sf.basedb.util.listable.DerivedBioAssayToParentDerivedBioAssayTransformer
Create a new derived bioassay to parent derived bioassay transformer.
DerivedBioAssayToPhysicalBioAssayTransformer - Class in net.sf.basedb.util.listable
Source item transformer implementation that transform derived bioassay items to physical bioassays.
DerivedBioAssayToPhysicalBioAssayTransformer() - Constructor for class net.sf.basedb.util.listable.DerivedBioAssayToPhysicalBioAssayTransformer
Create a new derived bioassay to physical bioassay transformer.
DerivedBioAssayToRawBioAssayTransformer - Class in net.sf.basedb.util.listable
Source item transformer implementation that transform derived bioassay items to raw bioassays.
DerivedBioAssayToRawBioAssayTransformer() - Constructor for class net.sf.basedb.util.listable.DerivedBioAssayToRawBioAssayTransformer
Create a new derived bioassay to raw bioassay transformer.
DerivedBioAssayToRawBioAssayTransformer(CollectExtracts) - Constructor for class net.sf.basedb.util.listable.DerivedBioAssayToRawBioAssayTransformer
Create a new derived bioassay to raw bioassay transformer that also consider collected parent extracts.
DerivedBioAssayValidator - Class in net.sf.basedb.util.overview.validator
Validator implementation for derived bioassays.
DerivedBioAssayValidator() - Constructor for class net.sf.basedb.util.overview.validator.DerivedBioAssayValidator
 
desc(Expression) - Static method in class net.sf.basedb.core.query.Orders
Sort the result of a query in descending order by the expression.
DESC - Enum constant in enum class net.sf.basedb.core.ItemContext.SortDirection
Items are sorted in descending order.
descending - Variable in class net.sf.basedb.util.NameableComparator
 
descending - Variable in class net.sf.basedb.util.ToStringComparator
 
DescOrder - Class in net.sf.basedb.core.query
Sort the result of a query in descending order by the expression.
DescOrder(Expression) - Constructor for class net.sf.basedb.core.query.DescOrder
 
description - Variable in class net.sf.basedb.clients.jobagent.Agent
 
description - Variable in class net.sf.basedb.clients.web.extensions.plot.OverviewPlotBean
 
description - Variable in class net.sf.basedb.clients.web.extensions.startpage.FixedStartPageFactory
 
description - Variable in class net.sf.basedb.clients.web.extensions.startpage.StartPageBean
 
description - Variable in class net.sf.basedb.clients.web.taglib.table.TableColumn
 
description - Variable in class net.sf.basedb.core.authentication.ExtraUserInformation
 
description - Variable in class net.sf.basedb.core.data.AnyToAnyData
 
description - Variable in class net.sf.basedb.core.data.BioAssayData
 
description - Variable in class net.sf.basedb.core.data.BioAssaySetData
 
description - Variable in class net.sf.basedb.core.data.BioPlateEventTypeData
 
description - Variable in class net.sf.basedb.core.data.BioPlateTypeData
 
description - Variable in class net.sf.basedb.core.data.CommonData
 
description - Variable in class net.sf.basedb.core.data.DataFileTypeData
 
description - Variable in class net.sf.basedb.core.data.ExtraValueTypeData
 
description - Variable in class net.sf.basedb.core.data.GroupData
 
description - Variable in class net.sf.basedb.core.data.HelpData
 
description - Variable in class net.sf.basedb.core.data.ItemListSyncFilterData
 
description - Variable in class net.sf.basedb.core.data.ItemSubtypeData
 
description - Variable in class net.sf.basedb.core.data.MessageData
 
description - Variable in class net.sf.basedb.core.data.MimeTypeData
 
description - Variable in class net.sf.basedb.core.data.NewsData
 
description - Variable in class net.sf.basedb.core.data.ParameterValueData
 
description - Variable in class net.sf.basedb.core.data.PlateEventTypeData
 
description - Variable in class net.sf.basedb.core.data.PlateGeometryData
 
description - Variable in class net.sf.basedb.core.data.PlatformData
 
description - Variable in class net.sf.basedb.core.data.PlatformVariantData
 
description - Variable in class net.sf.basedb.core.data.PluginDefinitionData
 
description - Variable in class net.sf.basedb.core.data.PluginTypeData
 
description - Variable in class net.sf.basedb.core.data.ProjectData
 
description - Variable in class net.sf.basedb.core.data.QuantityData
 
description - Variable in class net.sf.basedb.core.data.QuotaData
 
description - Variable in class net.sf.basedb.core.data.QuotaTypeData
 
description - Variable in class net.sf.basedb.core.data.ReporterClonePropertyData
 
description - Variable in class net.sf.basedb.core.data.ReporterData
 
description - Variable in class net.sf.basedb.core.data.ReporterTypeData
 
description - Variable in class net.sf.basedb.core.data.RoleData
 
description - Variable in class net.sf.basedb.core.data.RoleKeyData
 
description - Variable in class net.sf.basedb.core.data.RootRawBioAssayData
 
description - Variable in class net.sf.basedb.core.data.TransformationData
 
description - Variable in class net.sf.basedb.core.data.UnitData
 
description - Variable in class net.sf.basedb.core.data.UserData
 
description - Variable in class net.sf.basedb.core.data.UserDeviceData
 
description - Variable in class net.sf.basedb.core.ExtendedProperty
 
description - Variable in class net.sf.basedb.core.IntensityFormula
 
description - Variable in class net.sf.basedb.core.MigrateRbaToDba.Rba
 
description - Variable in class net.sf.basedb.core.ParameterInfo
 
description - Variable in class net.sf.basedb.core.plugin.AboutImpl
 
description - Variable in class net.sf.basedb.core.PluginParameter
A longer help text explaining what the particular parameter is needed for.
description - Variable in class net.sf.basedb.core.RawDataType
 
description - Variable in class net.sf.basedb.core.RequestInformation
 
description - Variable in class net.sf.basedb.core.signal.Signal
 
description - Variable in class net.sf.basedb.plugins.executor.ParameterDefinition
 
description - Variable in class net.sf.basedb.util.extensions.AboutBean
 
description - Variable in class net.sf.basedb.util.extensions.ExtensionPointBean
 
description - Variable in class net.sf.basedb.util.extensions.Registry.RegisteredAbout
 
description - Variable in class net.sf.basedb.util.extensions.Registry.RegisteredExtensionPoint
 
description - Variable in class net.sf.basedb.util.overview.Validator
 
description - Variable in class net.sf.basedb.util.uri.http.HttpConnectionManagerFactory
 
DESCRIPTION - Static variable in class net.sf.basedb.core.ClonableProperty
The property name of the "static" property ReporterData.getDescription()
descriptionColumnMapping - Static variable in class net.sf.basedb.plugins.batchimport.AbstractItemImporter
 
descriptionColumnMapping - Static variable in class net.sf.basedb.plugins.ReporterFlatFileImporter
 
descriptionMapper - Variable in class net.sf.basedb.plugins.batchimport.AnnotationTypeImporter
 
descriptionMapper - Variable in class net.sf.basedb.plugins.batchimport.AnyToAnyImporter
 
descriptionMapper - Variable in class net.sf.basedb.plugins.batchimport.ArrayBatchImporter
 
descriptionMapper - Variable in class net.sf.basedb.plugins.batchimport.ArrayDesignImporter
 
descriptionMapper - Variable in class net.sf.basedb.plugins.batchimport.ArraySlideImporter
 
descriptionMapper - Variable in class net.sf.basedb.plugins.batchimport.BioPlateImporter
 
descriptionMapper - Variable in class net.sf.basedb.plugins.batchimport.BioSourceImporter
 
descriptionMapper - Variable in class net.sf.basedb.plugins.batchimport.DerivedBioAssayImporter
 
descriptionMapper - Variable in class net.sf.basedb.plugins.batchimport.ExtractImporter
 
descriptionMapper - Variable in class net.sf.basedb.plugins.batchimport.FileImporter
 
descriptionMapper - Variable in class net.sf.basedb.plugins.batchimport.KitImporter
 
descriptionMapper - Variable in class net.sf.basedb.plugins.batchimport.PhysicalBioAssayImporter
 
descriptionMapper - Variable in class net.sf.basedb.plugins.batchimport.RawBioAssayImporter
 
descriptionMapper - Variable in class net.sf.basedb.plugins.batchimport.SampleImporter
 
descriptionMapper - Variable in class net.sf.basedb.plugins.batchimport.TagImporter
 
descriptionMapper - Variable in class net.sf.basedb.plugins.ReporterFlatFileImporter
 
descriptionParameter - Static variable in class net.sf.basedb.plugins.PlateMappingImporter
 
descriptionType - Static variable in class net.sf.basedb.core.plugin.AbstractAnalysisPlugin
A parameter type for description parameters.
descriptor - Variable in class net.sf.basedb.util.overview.Failure
 
deserializeObject(ObjectInputStream) - Method in class net.sf.basedb.core.snapshot.AnnotationSnapshot
 
design - Variable in class net.sf.basedb.plugins.IlluminaRawDataImporter
 
design - Variable in class net.sf.basedb.util.affymetrix.CdfValidationAction
 
design - Variable in class net.sf.basedb.util.gtf.GtfValidationAction
 
designQuery - Variable in class net.sf.basedb.plugins.batchimport.AbstractItemImporter
 
destColumnMapper - Variable in class net.sf.basedb.plugins.PlateMappingImporter
 
destinationCount - Variable in class net.sf.basedb.core.data.PlateMappingData
 
destinationGeometry - Variable in class net.sf.basedb.core.data.PlateMappingData
 
destinationIndex - Variable in class net.sf.basedb.core.data.PlateData
 
destPlateMapper - Variable in class net.sf.basedb.plugins.PlateMappingImporter
 
destRowMapper - Variable in class net.sf.basedb.plugins.PlateMappingImporter
 
destroy() - Method in class net.sf.basedb.clients.web.servlet.CacheControlFilter
 
destroy() - Method in class net.sf.basedb.clients.web.servlet.CharacterEncodingFilter
 
destroy() - Method in class net.sf.basedb.clients.web.servlet.ContentSecurityPolicyFilter
 
destroy() - Method in class net.sf.basedb.clients.web.servlet.ImageRemapFilter
 
destroyed - Variable in class net.sf.basedb.core.data.ArraySlideData
 
destroyed - Variable in class net.sf.basedb.core.data.BioPlateData
 
destroyed - Variable in class net.sf.basedb.core.data.PlateData
 
destroyedColumnMapping - Static variable in class net.sf.basedb.plugins.batchimport.ArraySlideImporter
 
destroyedMapper - Variable in class net.sf.basedb.plugins.batchimport.ArraySlideImporter
 
detach(Object) - Method in class net.sf.basedb.core.hibernate.SessionWrapper
 
DetachedItemException - Exception in net.sf.basedb.core
This exception is thrown when trying to use an item that has been detached from the DbControl that manages it.
DetachedItemException(String) - Constructor for exception net.sf.basedb.core.DetachedItemException
Creates a new DetachedItemException.
detachItem(BasicItem) - Method in class net.sf.basedb.core.DbControl
Detach an item from this DbControl.
detail - Variable in exception net.sf.basedb.clients.web.WebException
A more detailed description of the error message.
detailedProperties - Variable in class net.sf.basedb.core.log.db.AnnotationSetLogger
 
detailedProperties - Variable in class net.sf.basedb.core.log.db.BioMaterialEventLogger
 
detailedProperties - Variable in class net.sf.basedb.core.log.db.DbLogManagerFactory
 
detailedProperties - Variable in class net.sf.basedb.core.log.db.DefaultEntityLogger
 
detailedProperties - Variable in class net.sf.basedb.core.log.db.ManualEntryLogger
 
detailedProperties - Variable in class net.sf.basedb.core.log.db.PlateEventLogger
 
details - Variable in class net.sf.basedb.core.data.ChangeHistoryData
 
details - Variable in class net.sf.basedb.core.data.PlateMappingData
 
details - Variable in class net.sf.basedb.core.log.LoggingInterceptor.LogDetails
 
detector - Variable in class net.sf.basedb.core.File.CharsetTesterThread
 
determineProperBooleanType(int, Object, Type) - Method in class net.sf.basedb.core.hibernate.QueryWrapper
Deprecated.
determineProperBooleanType(String, Object, Type) - Method in class net.sf.basedb.core.hibernate.QueryWrapper
Deprecated.
device - Variable in class net.sf.basedb.core.data.SessionData
 
device - Variable in class net.sf.basedb.core.SessionControl.UnverifiedDeviceInfo
 
deviceId - Variable in class net.sf.basedb.core.SessionControl.LoginInfo
The id of the UserDevice in use.
deviceName - Variable in class net.sf.basedb.core.SessionControl.LoginInfo
 
DeviceNotVerifiedException - Exception in net.sf.basedb.core
This exception can be thrown when a user is trying to login from a device that has not been verified.
DeviceNotVerifiedException() - Constructor for exception net.sf.basedb.core.DeviceNotVerifiedException
 
devices - Variable in class net.sf.basedb.core.data.ClientData
 
devices - Variable in class net.sf.basedb.core.data.UserData
 
deviceToken - Variable in class net.sf.basedb.core.authentication.LoginRequest
 
dialect - Variable in class net.sf.basedb.core.AnnotationBatcher
 
dialect - Variable in class net.sf.basedb.core.dbengine.TableInfo
 
dialect - Variable in class net.sf.basedb.core.hibernate.DbIndexWork
 
dialect - Variable in class net.sf.basedb.core.hibernate.SchemaGenerator.CollectSqlTarget
 
dialect - Variable in class net.sf.basedb.core.hibernate.SchemaGenerator
 
dialect - Static variable in class net.sf.basedb.core.HibernateUtil
The Hibernate database dialect in use.
dialect - Variable in class net.sf.basedb.core.MigrateRbaToDba
 
dialectDom - Static variable in class net.sf.basedb.core.PredefinedQuery
Holds the XML document containing the dialect-specific queries.
dialectQueryFile - Static variable in class net.sf.basedb.core.PredefinedQuery
The path to the query file with dialect-specific queries.
Diff3 - Class in net.sf.basedb.util
This class is helpful when a client application needs to implement long-running transactions and still be able to update items with as few clashes as possible.
Diff3(BasicItem, BasicItem) - Constructor for class net.sf.basedb.util.Diff3
Create a new Diff3 object to compare properties of the oldItem and newItem.
DIFFERENT_TAG - Static variable in class net.sf.basedb.util.overview.Validator
Validator rule that checks if the parent to a tagged extract has a different tag.
dir - Variable in class net.sf.basedb.util.bfs.BaseInputStreamLocator
 
dir - Variable in class net.sf.basedb.util.bfs.DiskInputStreamLocator
 
dir - Variable in class net.sf.basedb.util.bfs.GenericBaseDataWriterFactory
 
dir - Variable in class net.sf.basedb.util.bfs.GenericDiskDataWriterFactory
 
dir - Variable in class net.sf.basedb.util.bfs.GenericExtraFileImporter
 
direction - Variable in class net.sf.basedb.clients.web.extensions.list.RelatedItemColumn.Specification
 
direction - Variable in class net.sf.basedb.util.overview.cache.DirectionalCacheKey
 
direction - Variable in class net.sf.basedb.util.overview.Node
 
DirectionalCacheKey - Class in net.sf.basedb.util.overview.cache
Cache key implementation that bundles another cache key with a node direction.
DirectionalCacheKey(Object, ChildNodeDirection) - Constructor for class net.sf.basedb.util.overview.cache.DirectionalCacheKey
 
directionRaw - Variable in class net.sf.basedb.clients.web.extensions.list.RelatedItemColumn.Specification
 
directories - Variable in class net.sf.basedb.core.Path
The directory part of the path.
directories - Variable in class net.sf.basedb.util.extensions.manager.ExtensionsManager
 
directory - Variable in class net.sf.basedb.core.data.ExperimentData
 
directory - Variable in class net.sf.basedb.core.data.FileData
 
directory - Variable in class net.sf.basedb.core.Migration
 
Directory - Class in net.sf.basedb.core
This is used to represent directory items.
Directory(DirectoryData) - Constructor for class net.sf.basedb.core.Directory
Creates a new directory item from the given data.
DIRECTORY - Enum constant in enum class net.sf.basedb.core.Item
The item is a Directory.
DIRECTORY - Enum constant in enum class net.sf.basedb.core.Path.Type
The path is a path to a Directory.
DIRECTORY_CACHE - Static variable in class net.sf.basedb.core.Directory
 
DirectoryData - Class in net.sf.basedb.core.data
This class holds information about directories.
DirectoryData() - Constructor for class net.sf.basedb.core.data.DirectoryData
 
directoryGui - Static variable in class net.sf.basedb.plugins.PackedFileExporter
 
directoryPattern - Variable in class net.sf.basedb.util.RegexpFileFilter
 
dirty - Variable in class net.sf.basedb.core.log.EntityDetails
 
disableAll() - Method in class net.sf.basedb.core.QueryRuntimeFilterManager
Disable all filters.
disableATPermissionCheck - Variable in class net.sf.basedb.core.Annotation
 
disableATPermissionCheck() - Method in class net.sf.basedb.core.Annotation
 
disableChangeLogColumnMapping - Static variable in class net.sf.basedb.plugins.batchimport.AnnotationTypeImporter
Column mapping parameter for "Disabled history log" flag.
disableChangeLogMapper - Variable in class net.sf.basedb.plugins.batchimport.AnnotationTypeImporter
 
disabled - Variable in class net.sf.basedb.clients.web.taglib.Button
If the button should be enabled or not.
disabled - Variable in class net.sf.basedb.clients.web.taglib.Select
If the selection list should be enabled or not.
disabled - Variable in class net.sf.basedb.clients.web.taglib.table.Button
IF the button is disabled or not.
disabled - Variable in class net.sf.basedb.core.data.ItemListSyncFilterData
 
disabled - Variable in class net.sf.basedb.core.data.PluginConfigurationData
 
disabled - Variable in class net.sf.basedb.core.data.PluginDefinitionData
 
disabled - Variable in class net.sf.basedb.core.data.UserData
 
disabled - Variable in class net.sf.basedb.core.snapshot.DisabledInheritanceFilter
 
disabled - Variable in class net.sf.basedb.util.extensions.debug.BeanActionFactory
 
disabled - Variable in class net.sf.basedb.util.extensions.debug.ProxyActionFactory
 
disabled - Variable in class net.sf.basedb.util.extensions.xml.PluginInfo
 
disabled - Variable in class net.sf.basedb.util.overview.validator.BasicItemNodeValidatorFactory
 
disabled - Variable in class net.sf.basedb.util.StaticCache
 
disabledClazz - Variable in class net.sf.basedb.clients.web.extensions.menu.PermissionMenuItemFactory
 
disabledClazz - Variable in class net.sf.basedb.clients.web.extensions.toolbar.PermissionButtonFactory
 
disableDeviceVerification() - Method in class net.sf.basedb.core.User
Disable device verification.
disabledExtensionPoints - Variable in class net.sf.basedb.util.extensions.manager.Settings
 
disabledExtensions - Variable in class net.sf.basedb.util.extensions.manager.Settings
 
disabledIcon - Variable in class net.sf.basedb.clients.web.extensions.menu.PermissionMenuItemFactory
 
disabledIcon - Variable in class net.sf.basedb.clients.web.extensions.toolbar.PermissionButtonFactory
 
disabledInheritanceFilter - Variable in class net.sf.basedb.core.snapshot.SnapshotManager
 
DisabledInheritanceFilter - Class in net.sf.basedb.core.snapshot
Filter implementation that filters away annotations that have an annotation type with inheritance disabled.
DisabledInheritanceFilter(DbControl) - Constructor for class net.sf.basedb.core.snapshot.DisabledInheritanceFilter
Create a new filter.
DisabledInheritanceFilter(DisabledInheritanceFilter) - Constructor for class net.sf.basedb.core.snapshot.DisabledInheritanceFilter
Create a clone of another filter instance.
disabledStyle - Variable in class net.sf.basedb.clients.web.extensions.menu.PermissionMenuItemFactory
 
disabledStyle - Variable in class net.sf.basedb.clients.web.extensions.toolbar.PermissionButtonFactory
 
disabledTitle - Variable in class net.sf.basedb.clients.web.extensions.menu.PermissionMenuItemFactory
 
disabledTitle - Variable in class net.sf.basedb.clients.web.extensions.toolbar.PermissionButtonFactory
 
disabledTooltip - Variable in class net.sf.basedb.clients.web.extensions.menu.PermissionMenuItemFactory
 
disabledTooltip - Variable in class net.sf.basedb.clients.web.extensions.toolbar.PermissionButtonFactory
 
disableExtensions - Variable in class net.sf.basedb.core.Application.StartupOptions
 
disableExtensions(boolean) - Method in class net.sf.basedb.core.Application.StartupOptions
Set to TRUE to disable loading external extensions.
disableFetchProfile(String) - Method in class net.sf.basedb.core.hibernate.SessionWrapper
 
disableFilter(String) - Method in class net.sf.basedb.core.hibernate.SessionWrapper
 
disableFilter(String) - Method in class net.sf.basedb.core.QueryRuntimeFilterManager
Disable a filter.
disableFilter(Session, String) - Static method in class net.sf.basedb.core.HibernateUtil
Disable the filter with the given name.
disableFilters(DbControl) - Method in class net.sf.basedb.core.AbstractEntityQuery
Disable all enabled runtime query filters for the query.
disableForItem(Item) - Method in class net.sf.basedb.core.AnnotationType
Disable this annotation type to be used for items of the specified type.
disableInheritance - Variable in class net.sf.basedb.core.data.AnnotationTypeData
 
disableInheritanceColumnMapping - Static variable in class net.sf.basedb.plugins.batchimport.AnnotationTypeImporter
Column mapping parameter for "Disable inheritance" flag.
disableInheritanceMapper - Variable in class net.sf.basedb.plugins.batchimport.AnnotationTypeImporter
 
disableInProject - Variable in class net.sf.basedb.clients.web.taglib.table.PresetSelector
If the 'in project' option should be included in the preset selector or not.
disableInternalJobQueue - Variable in class net.sf.basedb.core.Application.StartupOptions
 
disableInternalJobQueue(boolean) - Method in class net.sf.basedb.core.Application.StartupOptions
Set to TRUE to disable the internal job queue.
disableLogOfValues - Variable in class net.sf.basedb.core.data.AnnotationTypeData
 
disableManualMembers - Variable in class net.sf.basedb.core.data.ItemListData
 
disableOthers - Variable in class net.sf.basedb.clients.web.taglib.table.PresetSelector
If the 'owned by others' option should be included in the preset selector or not.
disableOverflowCheck - Variable in class net.sf.basedb.clients.web.extensions.list.AbstractListColumnBean
 
disableOverflowCheck - Variable in class net.sf.basedb.clients.web.extensions.list.PropertyPathActionFactory
 
disableOverflowCheck - Variable in class net.sf.basedb.clients.web.taglib.table.Cell
 
disableOwnedBy - Variable in class net.sf.basedb.clients.web.taglib.table.PresetSelector
If the 'owned by me' option should be included in the preset selector or not.
DisablePluginsProcessor - Class in net.sf.basedb.util.extensions.manager.processor
File processor implementation that disables plug-ins.
DisablePluginsProcessor(DbControl, ProcessResults) - Constructor for class net.sf.basedb.util.extensions.manager.processor.DisablePluginsProcessor
Create a new processor.
disableRawJoinOnMergedData - Variable in class net.sf.basedb.core.DynamicSpotQuery
 
disableRemoved - Variable in class net.sf.basedb.clients.web.taglib.table.PresetSelector
If the 'removed' option should be included in the preset selector or not.
disableSharedTo - Variable in class net.sf.basedb.clients.web.taglib.table.PresetSelector
If the 'shared to me' option should be included in the preset selector or not.
disableSyncFilters - Variable in class net.sf.basedb.core.data.ItemListData
 
DisallowedValueException - Exception in net.sf.basedb.core
Exception that is thrown when a value is not found among a set of allowed values, for example, when setting an annotation value.
DisallowedValueException() - Constructor for exception net.sf.basedb.core.DisallowedValueException
Create a new DisallowedValueException object.
DisallowedValueException(String) - Constructor for exception net.sf.basedb.core.DisallowedValueException
Create a new DisallowedValueException exception.
DisallowedValueException(String, Object) - Constructor for exception net.sf.basedb.core.DisallowedValueException
Create a new DisallowedValueException object.
disconnect() - Method in class net.sf.basedb.core.DbControl
Deprecated.
In 3.12. Applications should use separate DbControl instead.
disconnect() - Method in class net.sf.basedb.core.hibernate.SessionWrapper
 
discriminators - Variable in class net.sf.basedb.core.AnnotationBatcher
 
DiskConsumable - Interface in net.sf.basedb.core
This interface is implemented by items that can use a lot of disk space.
DiskConsumableData - Interface in net.sf.basedb.core.data
A diskconsumable item is an item that occupies a lot of diskspace and should be controlled by the quota system.
diskConsumableItems - Static variable in class net.sf.basedb.core.Metadata
 
DiskFileWrapper - Class in net.sf.basedb.util.importer
File wrapper implementation for files that are located on the local disk.
DiskFileWrapper(File) - Constructor for class net.sf.basedb.util.importer.DiskFileWrapper
 
DiskInputStreamLocator - Class in net.sf.basedb.util.bfs
Input stream locator implementation that works with files on the local file system.
DiskInputStreamLocator(File) - Constructor for class net.sf.basedb.util.bfs.DiskInputStreamLocator
Create a new input stream locator.
diskUsage - Variable in class net.sf.basedb.core.data.ExperimentData
 
diskUsage - Variable in class net.sf.basedb.core.data.FileData
 
diskUsage - Variable in class net.sf.basedb.core.data.RawBioAssayData
 
diskUsage - Variable in class net.sf.basedb.core.DiskUsageStatistics.Summary
 
DiskUsage - Class in net.sf.basedb.core
This class is used to represent the disk usage of DiskConsumable items.
DiskUsage(DiskUsageData) - Constructor for class net.sf.basedb.core.DiskUsage
Create a new DiskUsage item.
DISKUSAGE - Enum constant in enum class net.sf.basedb.core.Item
The item is a DiskUsage.
DiskUsageData - Class in net.sf.basedb.core.data
This class holds information about a users and/or groups disk usage.
DiskUsageData() - Constructor for class net.sf.basedb.core.data.DiskUsageData
Creates a new DiskUsageData.
DiskUsageStatistics - Class in net.sf.basedb.core
Get disk usage statistics for the BASE server.
DiskUsageStatistics(DbControl) - Constructor for class net.sf.basedb.core.DiskUsageStatistics
Create a new disk usage statistics object.
DiskUsageStatistics.Summary - Class in net.sf.basedb.core
Holds summary disk usage information for the total disk usage or for a specific user or group.
display(int, String) - Method in class net.sf.basedb.core.Job.ProgressReporterImpl
 
display(int, String) - Method in interface net.sf.basedb.core.ProgressReporter
Display a progress message.
display(int, String) - Method in class net.sf.basedb.core.signal.ProgressReporterSignalHandler
 
display(int, String) - Method in class net.sf.basedb.core.SimpleProgressReporter
 
display(int, String) - Method in class net.sf.basedb.util.ChainedProgressReporter
 
display(int, String) - Method in class net.sf.basedb.util.ConsoleProgressReporter
 
display(int, String) - Method in class net.sf.basedb.util.GeoLocation.ResponseFilter
 
display(int, String) - Method in class net.sf.basedb.util.TransferRateProgressReporter
Forward the call to the parent if one exists.
displayAbsolute(long, String) - Method in interface net.sf.basedb.core.AbsoluteProgressReporter
Display a progress message.
displayAbsolute(long, String) - Method in class net.sf.basedb.core.SimpleAbsoluteProgressReporter
 
displayAbsolute(long, String) - Method in class net.sf.basedb.util.GeoLocation.ResponseFilter
 
displayAbsolute(long, String) - Method in class net.sf.basedb.util.TransferRateProgressReporter
Forward the call to the parent if one exists.
displayName - Variable in class net.sf.basedb.clients.web.extensions.login.LoginFormBean
 
displaySymbol - Variable in class net.sf.basedb.core.data.UnitData
 
displayValue - Variable in enum class net.sf.basedb.core.BioMaterialEvent.Type
 
displayValue - Variable in enum class net.sf.basedb.core.BioWell.LockMode
 
displayValue - Variable in enum class net.sf.basedb.core.FeatureIdentificationMethod
Returned by the toString method.
displayValue - Variable in enum class net.sf.basedb.core.Formula.AverageMethod
 
displayValue - Variable in enum class net.sf.basedb.core.Formula.Parser
 
displayValue - Variable in enum class net.sf.basedb.core.Formula.Type
 
displayValue - Variable in enum class net.sf.basedb.core.IntensityTransform
Returned by the toString method.
displayValue - Variable in enum class net.sf.basedb.core.Item
 
displayValue - Variable in enum class net.sf.basedb.core.ItemContext.SortDirection
The string value of this direction.
displayValue - Variable in enum class net.sf.basedb.core.Job.ExecutionTime
 
displayValue - Variable in enum class net.sf.basedb.core.Job.Status
 
displayValue - Variable in enum class net.sf.basedb.core.Job.Type
 
displayValue - Variable in enum class net.sf.basedb.core.Location
Returned by the toString method.
displayValue - Variable in enum class net.sf.basedb.core.Permission
 
displayValue - Variable in enum class net.sf.basedb.core.plugin.Plugin.MainType
 
displayValue - Variable in enum class net.sf.basedb.core.Type
 
displayValue - Variable in enum class net.sf.basedb.util.overview.Severity
 
distinct - Variable in class net.sf.basedb.core.AbstractQuery
If the query should only return the same item once or not.
distinct - Variable in class net.sf.basedb.core.query.CountExpression
 
divide(Expression, Expression) - Static method in class net.sf.basedb.core.query.Expressions
Divide one expression by another: new expression = e1 / e2.
DivideConverter - Class in net.sf.basedb.util.jep.convert
Convert Divide function to a Query API Expression.
DivideConverter() - Constructor for class net.sf.basedb.util.jep.convert.DivideConverter
 
DivideExpression - Class in net.sf.basedb.core.query
Divide one expression by another: e1 / e2.
DivideExpression(Expression, Expression) - Constructor for class net.sf.basedb.core.query.DivideExpression
 
doAfterBody() - Method in class net.sf.basedb.clients.web.taglib.table.ExtensionCells
 
doCatch(Throwable) - Method in class net.sf.basedb.clients.web.taglib.ExceptionCatcher
 
doCatch(Throwable) - Method in class net.sf.basedb.clients.web.taglib.table.Cell
 
doctype - Variable in class net.sf.basedb.clients.web.taglib.Page
The <!
doEndTag() - Method in class net.sf.basedb.clients.web.taglib.Body
 
doEndTag() - Method in class net.sf.basedb.clients.web.taglib.ButtonGroup
 
doEndTag() - Method in class net.sf.basedb.clients.web.taglib.ExceptionCatcher
 
doEndTag() - Method in class net.sf.basedb.clients.web.taglib.Head
 
doEndTag() - Method in class net.sf.basedb.clients.web.taglib.HideableSection
 
doEndTag() - Method in class net.sf.basedb.clients.web.taglib.Icon
 
doEndTag() - Method in class net.sf.basedb.clients.web.taglib.menu.Menu
 
doEndTag() - Method in class net.sf.basedb.clients.web.taglib.Page
 
doEndTag() - Method in class net.sf.basedb.clients.web.taglib.path.Path
 
doEndTag() - Method in class net.sf.basedb.clients.web.taglib.tab.Tab
 
doEndTag() - Method in class net.sf.basedb.clients.web.taglib.tab.TabControl
 
doEndTag() - Method in class net.sf.basedb.clients.web.taglib.table.Cell
 
doEndTag() - Method in class net.sf.basedb.clients.web.taglib.table.Data
 
doEndTag() - Method in class net.sf.basedb.clients.web.taglib.table.Form
 
doEndTag() - Method in class net.sf.basedb.clients.web.taglib.table.Header
 
doEndTag() - Method in class net.sf.basedb.clients.web.taglib.table.HeaderRow
 
doEndTag() - Method in class net.sf.basedb.clients.web.taglib.table.Headers
 
doEndTag() - Method in class net.sf.basedb.clients.web.taglib.table.Label
 
doEndTag() - Method in class net.sf.basedb.clients.web.taglib.table.Navigator
 
doEndTag() - Method in class net.sf.basedb.clients.web.taglib.table.Panel
 
doEndTag() - Method in class net.sf.basedb.clients.web.taglib.table.PresetSelector
 
doEndTag() - Method in class net.sf.basedb.clients.web.taglib.table.Row
 
doEndTag() - Method in class net.sf.basedb.clients.web.taglib.table.Rows
 
doEndTag() - Method in class net.sf.basedb.clients.web.taglib.table.Table
 
doEndTag() - Method in class net.sf.basedb.clients.web.taglib.table.Toolbar
 
doExport() - Method in class net.sf.basedb.util.export.spotdata.AbstractBioAssaySetExporter
Run the export.
doExport(Connection) - Method in class net.sf.basedb.core.Migration
Perform the export.
doExport(ExportOutputStream, ProgressReporter) - Method in class net.sf.basedb.core.plugin.AbstractExporterPlugin
Implements immediate downloading.
doExport(ExportOutputStream, ProgressReporter) - Method in interface net.sf.basedb.core.plugin.ImmediateDownloadExporter
Perform the export.
doFilter(ServletRequest, ServletResponse, FilterChain) - Method in class net.sf.basedb.clients.web.servlet.CacheControlFilter
 
doFilter(ServletRequest, ServletResponse, FilterChain) - Method in class net.sf.basedb.clients.web.servlet.CharacterEncodingFilter
 
doFilter(ServletRequest, ServletResponse, FilterChain) - Method in class net.sf.basedb.clients.web.servlet.ContentSecurityPolicyFilter
 
doFilter(ServletRequest, ServletResponse, FilterChain) - Method in class net.sf.basedb.clients.web.servlet.ImageRemapFilter
 
doFinally() - Method in class net.sf.basedb.clients.web.taglib.ExceptionCatcher
 
doFinally() - Method in class net.sf.basedb.clients.web.taglib.table.Cell
 
doGet(HttpServletRequest, HttpServletResponse) - Method in class net.sf.basedb.clients.web.servlet.CompileAll
 
doGet(HttpServletRequest, HttpServletResponse) - Method in class net.sf.basedb.clients.web.servlet.Download
 
doGet(HttpServletRequest, HttpServletResponse) - Method in class net.sf.basedb.clients.web.servlet.ExperimentExplorerPlotServlet
 
doGet(HttpServletRequest, HttpServletResponse) - Method in class net.sf.basedb.clients.web.servlet.ExtensionsServlet
 
doGet(HttpServletRequest, HttpServletResponse) - Method in class net.sf.basedb.clients.web.servlet.PlotServlet
 
doGet(HttpServletRequest, HttpServletResponse) - Method in class net.sf.basedb.clients.web.servlet.RssNewsFeed
 
doGet(HttpServletRequest, HttpServletResponse) - Method in class net.sf.basedb.clients.web.servlet.Upload
 
doImport() - Method in class net.sf.basedb.util.importer.spotdata.BaseFileImporter
Start the import.
doImport() - Method in class net.sf.basedb.util.importer.spotdata.BfsImporter
Start the import.
doImport(InputStream, ProgressReporter) - Method in interface net.sf.basedb.core.plugin.AutoDetectingImporter
Import the data from the given InputStream.
doImport(InputStream, ProgressReporter) - Method in class net.sf.basedb.plugins.AbstractFlatFileImporter
 
doImport(InputStream, ProgressReporter) - Method in class net.sf.basedb.plugins.AnnotationFlatFileImporter
 
doImport(InputStream, ProgressReporter) - Method in class net.sf.basedb.plugins.CdfFileReporterImporter
 
doImport(InputStream, ProgressReporter) - Method in class net.sf.basedb.plugins.HelpImporter
 
doImport(InputStream, ProgressReporter) - Method in class net.sf.basedb.plugins.PluginConfigurationImporter
 
doImport(Connection) - Method in class net.sf.basedb.core.Migration
Perform the import.
doInsert(RawData, String, String, boolean) - Method in class net.sf.basedb.core.RawDataBatcher
Do the actual insert.
domainRange - Variable in class net.sf.basedb.util.plot.HistogramPlot
 
done() - Method in class net.sf.basedb.core.plugin.AbstractPlugin
Clears the variables set by the init method.
done() - Method in interface net.sf.basedb.core.plugin.Plugin
This method is called when the core is finished with the plugin object.
done() - Method in class net.sf.basedb.core.PluginRequest
Aborts the execution of the plugin.
done(ExtensionsManager) - Method in class net.sf.basedb.clients.web.extensions.LoadServletsProcessor
 
done(ExtensionsManager) - Method in class net.sf.basedb.clients.web.extensions.UninstalledFileProcessor
 
done(ExtensionsManager) - Method in interface net.sf.basedb.util.extensions.manager.ExtensionsFileProcessor
Called by the extensions manager after a successful completion of the processing.
done(ExtensionsManager) - Method in class net.sf.basedb.util.extensions.manager.processor.DeleteResourcesProcessor
 
done(ExtensionsManager) - Method in class net.sf.basedb.util.extensions.manager.processor.DisablePluginsProcessor
 
done(ExtensionsManager) - Method in class net.sf.basedb.util.extensions.manager.processor.ExtractResourcesProcessor
 
done(ExtensionsManager) - Method in class net.sf.basedb.util.extensions.manager.processor.IgnoreFileProcessor
 
done(ExtensionsManager) - Method in class net.sf.basedb.util.extensions.manager.processor.MarkAsProcessedProcessor
 
done(ExtensionsManager) - Method in class net.sf.basedb.util.extensions.manager.processor.PluginInstallationProcessor
 
done(ExtensionsManager) - Method in class net.sf.basedb.util.extensions.manager.processor.RegisterExtensionsProcessor
 
done(ExtensionsManager) - Method in class net.sf.basedb.util.extensions.manager.processor.ResetProcessor
 
done(ExtensionsManager) - Method in class net.sf.basedb.util.extensions.manager.processor.UnregisterExtensionsProcessor
 
done(ExtensionsManager, Throwable) - Method in class net.sf.basedb.clients.web.extensions.LoadServletsProcessor
 
done(ExtensionsManager, Throwable) - Method in class net.sf.basedb.clients.web.extensions.UninstalledFileProcessor
 
done(ExtensionsManager, Throwable) - Method in interface net.sf.basedb.util.extensions.manager.ExtensionsFileProcessor
Called by the extensions manager if an exception was thrown by the processor.
done(ExtensionsManager, Throwable) - Method in class net.sf.basedb.util.extensions.manager.processor.DeleteResourcesProcessor
 
done(ExtensionsManager, Throwable) - Method in class net.sf.basedb.util.extensions.manager.processor.DisablePluginsProcessor
 
done(ExtensionsManager, Throwable) - Method in class net.sf.basedb.util.extensions.manager.processor.ExtractResourcesProcessor
 
done(ExtensionsManager, Throwable) - Method in class net.sf.basedb.util.extensions.manager.processor.IgnoreFileProcessor
 
done(ExtensionsManager, Throwable) - Method in class net.sf.basedb.util.extensions.manager.processor.MarkAsProcessedProcessor
 
done(ExtensionsManager, Throwable) - Method in class net.sf.basedb.util.extensions.manager.processor.PluginInstallationProcessor
 
done(ExtensionsManager, Throwable) - Method in class net.sf.basedb.util.extensions.manager.processor.RegisterExtensionsProcessor
 
done(ExtensionsManager, Throwable) - Method in class net.sf.basedb.util.extensions.manager.processor.ResetProcessor
 
done(ExtensionsManager, Throwable) - Method in class net.sf.basedb.util.extensions.manager.processor.UnregisterExtensionsProcessor
 
DONE - Enum constant in enum class net.sf.basedb.core.Job.Status
The job has finished successfully.
DONE - Enum constant in enum class net.sf.basedb.core.plugin.Response.Status
 
doneError(String) - Method in class net.sf.basedb.core.Job
Register the job as completed with an error.
doneError(String, Collection<? extends Throwable>) - Method in class net.sf.basedb.core.Job
Register the job as completed with an error.
doneError(String, Collection<? extends Throwable>, Date) - Method in class net.sf.basedb.core.Job
Register the job as completed with an error.
doneOk(String) - Method in class net.sf.basedb.core.Job
Register the job as successfully completed.
doneOk(String, Date) - Method in class net.sf.basedb.core.Job
Register the job as successfully completed.
doneWithItem(DbControl, I, int) - Method in class net.sf.basedb.plugins.batchimport.AbstractItemImporter
Called when the importer is finished with an item.
doneWithItem(DbControl, ArrayDesign, int) - Method in class net.sf.basedb.plugins.batchimport.ArrayDesignImporter
Validate data files if they have been set.
doneWithItem(DbControl, DerivedBioAssay, int) - Method in class net.sf.basedb.plugins.batchimport.DerivedBioAssayImporter
Validate data files if they have been set.
doneWithItem(DbControl, RawBioAssay, int) - Method in class net.sf.basedb.plugins.batchimport.RawBioAssayImporter
Validate data files if they have been set.
doPost(HttpServletRequest, HttpServletResponse) - Method in class net.sf.basedb.clients.web.servlet.CompileAll
 
doPost(HttpServletRequest, HttpServletResponse) - Method in class net.sf.basedb.clients.web.servlet.ContentSecurityPolicyReportServlet
 
doPost(HttpServletRequest, HttpServletResponse) - Method in class net.sf.basedb.clients.web.servlet.Download
 
doPost(HttpServletRequest, HttpServletResponse) - Method in class net.sf.basedb.clients.web.servlet.ExtensionsServlet
 
doPost(HttpServletRequest, HttpServletResponse) - Method in class net.sf.basedb.clients.web.servlet.PlotServlet
doPost(HttpServletRequest, HttpServletResponse) - Method in class net.sf.basedb.clients.web.servlet.Upload
 
doRecursively(DbControl, Directory, Filter<? super Directory>, Filter<? super File>) - Static method in class net.sf.basedb.util.FileUtil
Do something recursively to all files and sub-directories in specified root directory.
doReturningWork(ReturningWork<T>) - Method in class net.sf.basedb.core.hibernate.SessionWrapper
 
doReturningWork(Session, ReturningWork<R>) - Static method in class net.sf.basedb.core.HibernateUtil
Execute some arbitrary JDBC code using the same database connection as the Hibernate session.
doStartTag() - Method in class net.sf.basedb.clients.web.taglib.Body
 
doStartTag() - Method in class net.sf.basedb.clients.web.taglib.Button
 
doStartTag() - Method in class net.sf.basedb.clients.web.taglib.ButtonGroup
 
doStartTag() - Method in class net.sf.basedb.clients.web.taglib.extensions.Render
 
doStartTag() - Method in class net.sf.basedb.clients.web.taglib.extensions.Scripts
 
doStartTag() - Method in class net.sf.basedb.clients.web.taglib.extensions.Stylesheets
 
doStartTag() - Method in class net.sf.basedb.clients.web.taglib.Head
 
doStartTag() - Method in class net.sf.basedb.clients.web.taglib.Help
 
doStartTag() - Method in class net.sf.basedb.clients.web.taglib.HideableSection
 
doStartTag() - Method in class net.sf.basedb.clients.web.taglib.Icon
 
doStartTag() - Method in class net.sf.basedb.clients.web.taglib.Input
 
doStartTag() - Method in class net.sf.basedb.clients.web.taglib.menu.Menu
 
doStartTag() - Method in class net.sf.basedb.clients.web.taglib.menu.Menuitem
 
doStartTag() - Method in class net.sf.basedb.clients.web.taglib.menu.Menuseparator
 
doStartTag() - Method in class net.sf.basedb.clients.web.taglib.menu.Submenu
 
doStartTag() - Method in class net.sf.basedb.clients.web.taglib.Page
 
doStartTag() - Method in class net.sf.basedb.clients.web.taglib.path.Path
 
doStartTag() - Method in class net.sf.basedb.clients.web.taglib.path.PathElement
 
doStartTag() - Method in class net.sf.basedb.clients.web.taglib.PropertyValue
 
doStartTag() - Method in class net.sf.basedb.clients.web.taglib.Select
 
doStartTag() - Method in class net.sf.basedb.clients.web.taglib.SubtypeSelector
 
doStartTag() - Method in class net.sf.basedb.clients.web.taglib.tab.Tab
 
doStartTag() - Method in class net.sf.basedb.clients.web.taglib.tab.TabControl
 
doStartTag() - Method in class net.sf.basedb.clients.web.taglib.table.Button
 
doStartTag() - Method in class net.sf.basedb.clients.web.taglib.table.Cell
 
doStartTag() - Method in class net.sf.basedb.clients.web.taglib.table.CellValue
 
doStartTag() - Method in class net.sf.basedb.clients.web.taglib.table.ColumnDef
 
doStartTag() - Method in class net.sf.basedb.clients.web.taglib.table.ColumnHeaders
 
doStartTag() - Method in class net.sf.basedb.clients.web.taglib.table.ColumnSubtitles
 
doStartTag() - Method in class net.sf.basedb.clients.web.taglib.table.Data
 
doStartTag() - Method in class net.sf.basedb.clients.web.taglib.table.ExtensionCells
 
doStartTag() - Method in class net.sf.basedb.clients.web.taglib.table.Form
 
doStartTag() - Method in class net.sf.basedb.clients.web.taglib.table.Header
 
doStartTag() - Method in class net.sf.basedb.clients.web.taglib.table.HeaderRow
 
doStartTag() - Method in class net.sf.basedb.clients.web.taglib.table.Headers
 
doStartTag() - Method in class net.sf.basedb.clients.web.taglib.table.Hidden
 
doStartTag() - Method in class net.sf.basedb.clients.web.taglib.table.Label
 
doStartTag() - Method in class net.sf.basedb.clients.web.taglib.table.Panel
 
doStartTag() - Method in class net.sf.basedb.clients.web.taglib.table.PresetSelector
 
doStartTag() - Method in class net.sf.basedb.clients.web.taglib.table.PropertyFilter
 
doStartTag() - Method in class net.sf.basedb.clients.web.taglib.table.Row
 
doStartTag() - Method in class net.sf.basedb.clients.web.taglib.table.Rows
 
doStartTag() - Method in class net.sf.basedb.clients.web.taglib.table.Table
 
doStartTag() - Method in class net.sf.basedb.clients.web.taglib.table.Toolbar
 
doStartTag() - Method in class net.sf.basedb.clients.web.taglib.Zoom
 
DOUBLE - Enum constant in enum class net.sf.basedb.core.Type
Double type.
DOUBLE - Static variable in class net.sf.basedb.core.hibernate.TypeWrapper
 
DOUBLE_QUOTE - Static variable in class net.sf.basedb.clients.web.util.HTML
 
DoubleParameterType - Class in net.sf.basedb.core
This class represent a parameter type that is a double.
DoubleParameterType() - Constructor for class net.sf.basedb.core.DoubleParameterType
Create a new double parameter type, without any limits and allowing null values.
DoubleParameterType(Double, Double, Double, boolean) - Constructor for class net.sf.basedb.core.DoubleParameterType
Create a new double parameter type.
DoubleParameterType(Double, Double, Double, boolean, int, int, int, List<Double>) - Constructor for class net.sf.basedb.core.DoubleParameterType
Create a new double parameter type with a list of allowed values.
DoubleParameterValueData - Class in net.sf.basedb.core.data
Double parameter value.
DoubleParameterValueData() - Constructor for class net.sf.basedb.core.data.DoubleParameterValueData
 
DoubleParameterValueData(Double...) - Constructor for class net.sf.basedb.core.data.DoubleParameterValueData
 
doubleValues - Variable in class net.sf.basedb.util.formatter.NumberFormatter
 
DoubleWriter - Class in net.sf.basedb.core.migrate
Database-independent writer implementation that writes double values from a result set.
DoubleWriter(ResultSet, int, Writer, char[]) - Constructor for class net.sf.basedb.core.migrate.DoubleWriter
 
doUpload(OutputStream, UploadedFile) - Method in class net.sf.basedb.clients.web.fileupload.FileUpload
Upload a single file section to the specified output stream
download - Variable in class net.sf.basedb.clients.web.servlet.Download
 
download(OutputStream, long) - Method in class net.sf.basedb.core.File
Download the physical file for this file item.
Download - Class in net.sf.basedb.clients.web.servlet
 
Download() - Constructor for class net.sf.basedb.clients.web.servlet.Download
 
DOWNLOAD - Enum constant in enum class net.sf.basedb.core.log.ChangeType
 
DOWNLOAD_IMMEDIATELY - Enum constant in enum class net.sf.basedb.core.plugin.Response.Status
 
downloadable - Variable in enum class net.sf.basedb.core.Location
If the file can be downloaded from this location.
downloadCache - Variable in class net.sf.basedb.core.File
Files that are EXTERNAL are cached locally per transaction
downloadImmediately(ExportOutputStream, ProgressReporter) - Method in class net.sf.basedb.core.PluginResponse
 
doWork(Work) - Method in class net.sf.basedb.core.hibernate.SessionWrapper
 
doWork(Session, Work) - Static method in class net.sf.basedb.core.HibernateUtil
Execute some arbitrary JDBC code using the same database connection as the Hibernate session.
dragColumns - Variable in class net.sf.basedb.clients.web.taglib.table.Table
 
dropAllTables() - Method in class net.sf.basedb.core.VirtualDb
Drop all real database tables in this virtual database.
dropClonedReporters() - Method in class net.sf.basedb.core.ReporterCloneBatcher
Drop the cloned reporter information from the dynamic database.
dropColumn(Session, String, String, ProgressReporter) - Static method in class net.sf.basedb.core.Update
 
DropColumnChange(String, String) - Constructor for class net.sf.basedb.core.Update.DropColumnChange
 
dropConstraintsBeforeImport - Variable in class net.sf.basedb.core.Migration
 
dropDynamicTable(String) - Static method in class net.sf.basedb.core.HibernateUtil
 
DropDynamicTableAction - Class in net.sf.basedb.core
Transactional action that can drop a table from the dynamic database after a successful commit and/or rollback.
DropDynamicTableAction(String, boolean, boolean) - Constructor for class net.sf.basedb.core.DropDynamicTableAction
Create a new drop table action.
dropForeignKeysUsedInIndex() - Method in class net.sf.basedb.core.dbengine.AbstractDbEngine
 
dropForeignKeysUsedInIndex() - Method in interface net.sf.basedb.core.dbengine.DbEngine
When dropping an index, must foreign keys that uses the same columns also be dropped (before dropping the index)?
dropForeignKeysUsedInIndex() - Method in class net.sf.basedb.core.dbengine.MySQLEngine
 
dropIndex(Session, boolean, String, String...) - Static method in class net.sf.basedb.core.Update
 
dropIndexes - Variable in class net.sf.basedb.core.hibernate.DbIndexWork
 
dropNotNullConstraint(Session, String, String, String) - Static method in class net.sf.basedb.core.Update
 
dropPrimaryKeyBeforeImport - Variable in class net.sf.basedb.core.Migration
 
dropTable(Session, String) - Static method in class net.sf.basedb.core.Update
 
dropVirtualTable(VirtualDb, VirtualTable) - Static method in class net.sf.basedb.core.HibernateUtil
Drop a table in the dynamic database.
DRY_RUN_PARAMETER - Static variable in class net.sf.basedb.plugins.util.Parameters
The name of the parameter that is created by Parameters.logFileParameter(String, String, String)
dryRun - Variable in class net.sf.basedb.core.data.JobData
 
dryRun - Variable in class net.sf.basedb.core.PluginConfigurationRequest
 
dryRun - Variable in class net.sf.basedb.core.PluginResponse
 
dryRun - Variable in class net.sf.basedb.plugins.AnnotationFlatFileImporter
 
dryRun - Variable in class net.sf.basedb.plugins.batchimport.AbstractItemImporter
 
dryRun - Variable in class net.sf.basedb.plugins.batchimport.AnyToAnyImporter
 
dryRunParameter(String, String, Boolean) - Static method in class net.sf.basedb.plugins.util.Parameters
Parameter definition that enable/disable dry-run of a plug-in.
dtdFile - Static variable in class net.sf.basedb.core.ExtendedProperties
The DTD which is used to validate the XML file.
dtdFile - Static variable in class net.sf.basedb.core.PredefinedQuery
The DTD which is used to validate the XML file.
dtdFile - Static variable in class net.sf.basedb.core.Presets
The DTD which is used to validate the XML data.
dtdFile - Static variable in class net.sf.basedb.core.RawDataTypes
The DTD which is used to validate the XML file.
dtdFile - Static variable in class net.sf.basedb.plugins.Base1PluginExecuter
 
dtdFile - Static variable in class net.sf.basedb.plugins.executor.ParameterDefinition
 
dtdFile - Variable in class net.sf.basedb.util.XmlUtil2.Validator
 
dtdFileName - Static variable in class net.sf.basedb.plugins.HelpImporter
 
dtdFileName - Static variable in class net.sf.basedb.plugins.PluginConfigurationImporter
 
DummyJobExecutor - Class in net.sf.basedb.clients.jobagent.executors
This is dummy job executor implementation which just sets the status of each job to Job.Status.DONE without actually executing the job.
DummyJobExecutor() - Constructor for class net.sf.basedb.clients.jobagent.executors.DummyJobExecutor
 
DummyService - Class in net.sf.basedb.clients.web.extensions.service
A dummy service implementation that prints out the current time on System.out every x seconds (default = 10) when the service is running.
DummyService() - Constructor for class net.sf.basedb.clients.web.extensions.service.DummyService
 
duplicateFeatureErrorParameter - Static variable in class net.sf.basedb.plugins.RawDataFlatFileImporter
 
duplicateFeatureErrorParameter - Static variable in class net.sf.basedb.plugins.ReporterMapFlatFileImporter
 
DuplicateWizardException - Exception in net.sf.basedb.clients.web
This exception is thrown when a plug-in configuration wizard is open and the user tries to open a second one.
DuplicateWizardException() - Constructor for exception net.sf.basedb.clients.web.DuplicateWizardException
Create a new exception.
DuplicateWizardException(String) - Constructor for exception net.sf.basedb.clients.web.DuplicateWizardException
Create a new exception with a message.
DuplicateWizardException(String, Throwable) - Constructor for exception net.sf.basedb.clients.web.DuplicateWizardException
Create a new exception with a cause and a message.
DuplicateWizardException(Throwable) - Constructor for exception net.sf.basedb.clients.web.DuplicateWizardException
Create a new exception with a cause.
Dynamic - Class in net.sf.basedb.core.query
A factory class to create expressions, joins, etc. that are only used by queries in the dynamic database.
Dynamic() - Constructor for class net.sf.basedb.core.query.Dynamic
 
DynamicActionAttribute - Class in net.sf.basedb.clients.web.extensions
Class for holding the name and value of a dynamic action attribute.
DynamicActionAttribute(String, String) - Constructor for class net.sf.basedb.clients.web.extensions.DynamicActionAttribute
Create a new dynamic action attribute.
DynamicActionAttributes - Interface in net.sf.basedb.clients.web.extensions
Supplementary interface for actions that need to be able to support dynamic attributes that are not pre-defined by the actual Action.
DynamicActionAttributeSupport - Class in net.sf.basedb.clients.web.extensions
Abstract base class intended to be extended by Action implementations that want to support dynamic action attributes.
DynamicActionAttributeSupport() - Constructor for class net.sf.basedb.clients.web.extensions.DynamicActionAttributeSupport
 
dynamicAttributes - Variable in class net.sf.basedb.clients.web.extensions.AbstractJspFactory
 
dynamicAttributes - Variable in class net.sf.basedb.clients.web.extensions.DynamicActionAttributeSupport
 
dynamicAttributes - Variable in class net.sf.basedb.clients.web.taglib.StylableTag
 
dynamicAttributes - Variable in class net.sf.basedb.clients.web.taglib.tab.Tab
 
dynamicCatalog - Static variable in class net.sf.basedb.core.Application
The name of the dynamic database.
dynamicDbIndexes(boolean, boolean, boolean) - Static method in class net.sf.basedb.core.HibernateUtil
Prints a lot of useful stuff about the dynamic database to standard output.
DynamicExtraValueQuery - Class in net.sf.basedb.core
Represents a query for extra values in the dynamic database.
DynamicExtraValueQuery(DataCube, VirtualTable, VirtualColumn...) - Constructor for class net.sf.basedb.core.DynamicExtraValueQuery
Create a new dynamic query.
DynamicField - Interface in net.sf.basedb.util.export.spotdata
Represents a spot or reporter field that is going to be exported from a bioassay set.
DynamicFilter - Interface in net.sf.basedb.util
This interface is used together with the BioAssaySetFilterUtil class to help a plugin filter the data of a bioassay set.
DynamicJoin - Class in net.sf.basedb.core
Represents a join between two virtual tables in a dynamic query: leftTable JOIN rightTable ON columns.
DynamicJoin(VirtualDb, JoinType, VirtualTable, VirtualColumn...) - Constructor for class net.sf.basedb.core.DynamicJoin
Create a new join using the root entity table as the left table.
DynamicJoin(VirtualDb, JoinType, VirtualTable, VirtualColumn[], VirtualTable, VirtualColumn[]) - Constructor for class net.sf.basedb.core.DynamicJoin
Create a new join between two tables with possible different colum names in the left and right tables.
DynamicJoin(VirtualDb, JoinType, VirtualTable, VirtualTable, VirtualColumn...) - Constructor for class net.sf.basedb.core.DynamicJoin
Create a new join between two tables.
DynamicPositionQuery - Class in net.sf.basedb.core
Represents a query for position information against the dynamic database.
DynamicPositionQuery(BioAssaySet) - Constructor for class net.sf.basedb.core.DynamicPositionQuery
Create a new dynamic query.
DynamicPositionQuery(Experiment) - Constructor for class net.sf.basedb.core.DynamicPositionQuery
 
DynamicPositionQueryJoiners - Class in net.sf.basedb.core
This class collects AutoJoiner:s for DynamicPositionQuery queries.
DynamicPositionQueryJoiners() - Constructor for class net.sf.basedb.core.DynamicPositionQueryJoiners
 
DynamicPositionQueryJoiners.ExtraValueJoiner - Class in net.sf.basedb.core
Joiner for extra values.
DynamicPositionQueryJoiners.ReporterJoiner - Class in net.sf.basedb.core
Joiner for reporters
DynamicPositionQueryJoiners.ReporterListJoiner - Class in net.sf.basedb.core
Auto joiner for reporter lists.
DynamicQuery - Class in net.sf.basedb.core
Represents a query against the dynamic database.
DynamicQuery(DataCube, VirtualTable, IntensityTransform) - Constructor for class net.sf.basedb.core.DynamicQuery
Create a new dynamic query.
DynamicQuery(VirtualDb, VirtualTable) - Constructor for class net.sf.basedb.core.DynamicQuery
Create a new non-restricted dynamic query.
DynamicQueryWrapper - Class in net.sf.basedb.clients.web.plugins
A query wrapper for DynamicQuery:s.
DynamicQueryWrapper(SqlQuery) - Constructor for class net.sf.basedb.clients.web.plugins.DynamicQueryWrapper
Create a new query wrapper.
DynamicRawDataQuery - Class in net.sf.basedb.core
Represents a query for raw data in a "dynamic" way.
DynamicRawDataQuery(RawBioAssay) - Constructor for class net.sf.basedb.core.DynamicRawDataQuery
Create a new dynamic query for raw data.
DynamicRawDataQuery(RawDataType) - Constructor for class net.sf.basedb.core.DynamicRawDataQuery
Create a new dynamic query for raw data.
DynamicRawDataQuery.RawBioAssayJoiner - Class in net.sf.basedb.core
Auto joiner for raw bioassays.
DynamicRawDataQuery.ReporterJoiner - Class in net.sf.basedb.core
Auto joiner for reporters.
DynamicRawDataQuery.ReporterListJoiner - Class in net.sf.basedb.core
Auto joiner for reporter lists.
DynamicReporterQuery - Class in net.sf.basedb.core
Represents a query for reporter data in a "dynamic" way.
DynamicReporterQuery() - Constructor for class net.sf.basedb.core.DynamicReporterQuery
Create a new dynamic query for reporter data.
DynamicReporterQuery(VirtualDb) - Constructor for class net.sf.basedb.core.DynamicReporterQuery
Create a new dynamic query for reporter data using cloned reporter information.
DynamicReporterQuery.MasterReporterJoiner - Class in net.sf.basedb.core
Auto joiner for master reporter table.
DynamicReporterQuery.ReporterListJoiner - Class in net.sf.basedb.core
Auto joiner for reporter lists.
DynamicRestriction - Class in net.sf.basedb.core
Creates a restriction that compares a dynamic column with a constant value: tableAlias.column = value or queryRootAlias.column = value
DynamicRestriction(VirtualColumn, int) - Constructor for class net.sf.basedb.core.DynamicRestriction
Create a new restriction for column in the root entity of the query: queryRootAlias.column = value.
DynamicRestriction(VirtualTable, VirtualColumn, int) - Constructor for class net.sf.basedb.core.DynamicRestriction
Create a new restriction for column in a joined table: tableAlias.column = value.
DynamicResultIterator - Class in net.sf.basedb.core
An iterator view of the result of an AbstractSqlQuery.
DynamicResultIterator(ResultSet, long, int) - Constructor for class net.sf.basedb.core.DynamicResultIterator
Create a new result iterator.
DynamicResultIterator.SqlResultImpl - Class in net.sf.basedb.core
Implements the SqlResult interface.
dynamicSchema - Static variable in class net.sf.basedb.core.Application
The name of the dynamic schema.
DynamicSpotQuery - Class in net.sf.basedb.core
Represents a query for spot information in the dynamic database.
DynamicSpotQuery(BioAssaySet) - Constructor for class net.sf.basedb.core.DynamicSpotQuery
Create a new dynamic query.
DynamicSpotQueryJoiners - Class in net.sf.basedb.core
This class collects AutoJoiner:s for DynamicSpotQuery queries.
DynamicSpotQueryJoiners() - Constructor for class net.sf.basedb.core.DynamicSpotQueryJoiners
 
DynamicSpotQueryJoiners.ExtraValueJoiner - Class in net.sf.basedb.core
Joiner for extra values.
DynamicSpotQueryJoiners.RawDataJoiner - Class in net.sf.basedb.core
Joiner for raw data.
DynamicSpotQueryJoiners.ReporterJoiner - Class in net.sf.basedb.core
Joiner for reporters
DynamicSpotQueryJoiners.ReporterListJoiner - Class in net.sf.basedb.core
Joiner for reporter lists.
DynamicUtil - Class in net.sf.basedb.clients.web
This class is used to collect some useful methods for building and executing dynamic queries.
DynamicUtil() - Constructor for class net.sf.basedb.clients.web.DynamicUtil
 
DynamicUtil.SelectedInfo - Class in net.sf.basedb.clients.web
 

E

e - Variable in class net.sf.basedb.core.query.BetweenRestriction
 
e - Variable in class net.sf.basedb.core.query.CountExpression
 
e - Variable in class net.sf.basedb.core.query.GeometricMeanExpression
 
e - Variable in class net.sf.basedb.core.query.MaxExpression
 
e - Variable in class net.sf.basedb.core.query.MeanExpression
 
e - Variable in class net.sf.basedb.core.query.MinExpression
 
e - Variable in class net.sf.basedb.core.query.QuadraticMeanExpression
 
e - Variable in class net.sf.basedb.core.query.RlikeRestriction
 
e - Variable in class net.sf.basedb.core.query.SumExpression
 
e1 - Variable in class net.sf.basedb.core.query.AbsExpression
 
e1 - Variable in class net.sf.basedb.core.query.AddExpression
 
e1 - Variable in class net.sf.basedb.core.query.DivideExpression
 
e1 - Variable in class net.sf.basedb.core.query.EqRestriction
 
e1 - Variable in class net.sf.basedb.core.query.ExpExpression
 
e1 - Variable in class net.sf.basedb.core.query.ExpressionSelect
 
e1 - Variable in class net.sf.basedb.core.query.GteqRestriction
 
e1 - Variable in class net.sf.basedb.core.query.GtRestriction
 
e1 - Variable in class net.sf.basedb.core.query.InRestriction
 
e1 - Variable in class net.sf.basedb.core.query.LikeRestriction
 
e1 - Variable in class net.sf.basedb.core.query.LogExpression
 
e1 - Variable in class net.sf.basedb.core.query.LteqRestriction
 
e1 - Variable in class net.sf.basedb.core.query.LtRestriction
 
e1 - Variable in class net.sf.basedb.core.query.MultiplyExpression
 
e1 - Variable in class net.sf.basedb.core.query.NegateExpression
 
e1 - Variable in class net.sf.basedb.core.query.NeqRestriction
 
e1 - Variable in class net.sf.basedb.core.query.SqrtExpression
 
e1 - Variable in class net.sf.basedb.core.query.SubtractExpression
 
e1 - Variable in class net.sf.basedb.core.query.ToDateExpression
 
e2 - Variable in class net.sf.basedb.core.query.AddExpression
 
e2 - Variable in class net.sf.basedb.core.query.DivideExpression
 
e2 - Variable in class net.sf.basedb.core.query.EqRestriction
 
e2 - Variable in class net.sf.basedb.core.query.GteqRestriction
 
e2 - Variable in class net.sf.basedb.core.query.GtRestriction
 
e2 - Variable in class net.sf.basedb.core.query.InRestriction
 
e2 - Variable in class net.sf.basedb.core.query.LikeRestriction
 
e2 - Variable in class net.sf.basedb.core.query.LteqRestriction
 
e2 - Variable in class net.sf.basedb.core.query.LtRestriction
 
e2 - Variable in class net.sf.basedb.core.query.MultiplyExpression
 
e2 - Variable in class net.sf.basedb.core.query.NeqRestriction
 
e2 - Variable in class net.sf.basedb.core.query.SubtractExpression
 
EDIT_ITEMS - Static variable in class net.sf.basedb.clients.web.extensions.edit.EditUtil
An array containing all items that we are registering extension points for.
EditUtil - Class in net.sf.basedb.clients.web.extensions.edit
Utility class for handling edit-dialog related extensions.
EditUtil() - Constructor for class net.sf.basedb.clients.web.extensions.edit.EditUtil
 
ekskey(byte[], byte[]) - Method in class net.sf.basedb.util.bcrypt.BCrypt
Perform the "enhanced key schedule" step described by Provos and Mazieres in "A Future-Adaptable Password Scheme" http://www.openbsd.org/papers/bcrypt-paper.ps
ElementIterator(Iterator<Tree.Entry<E>>) - Constructor for class net.sf.basedb.util.Tree.ElementIterator
 
elements(String, String) - Static method in class net.sf.basedb.core.query.Hql
Create an elements expression for a property that is a collection of values.
elseExpression - Variable in class net.sf.basedb.core.query.CaseExpression
 
email - Variable in class net.sf.basedb.core.authentication.ExtraUserInformation
 
email - Variable in class net.sf.basedb.core.data.PluginDefinitionData
 
email - Variable in class net.sf.basedb.core.data.UserData
 
email - Variable in class net.sf.basedb.core.plugin.AboutImpl
 
email - Variable in class net.sf.basedb.util.extensions.AboutBean
 
email - Variable in class net.sf.basedb.util.extensions.Registry.RegisteredAbout
 
EMAIL_REGEXP - Static variable in class net.sf.basedb.clients.web.util.HTML
This pattern can be used to find email addresses.
EMAIL_REGEXP - Static variable in class net.sf.basedb.util.EmailUtil
This pattern can be used to find email addresses.
EmailUtil - Class in net.sf.basedb.util
Utility class for email sending.
EmailUtil() - Constructor for class net.sf.basedb.util.EmailUtil
 
EMPTY_CELL - Static variable in class net.sf.basedb.util.excel.ExcelValue
 
EMPTY_STRING - Static variable in class net.sf.basedb.clients.web.fileupload.FileUpload
 
emptyCell() - Static method in class net.sf.basedb.util.excel.ExcelValue
This creates a blank cell.
emptyIsNull - Variable in class net.sf.basedb.util.parser.FlatFileParser.Data
 
emptyIsNull - Variable in class net.sf.basedb.util.parser.FlatFileParser
If null should be returned for empty columns (instead of an empty string).
emptyMap - Variable in class net.sf.basedb.core.InternalJobQueue.JobQueueKeyring
 
emptyMap - Variable in class net.sf.basedb.core.Job.SignalKeyring
 
emptyMap - Variable in class net.sf.basedb.core.ServiceSessionControl.ServicesKeyring
 
emptySet - Variable in class net.sf.basedb.core.InternalJobQueue.JobQueueKeyring
 
emptySet - Variable in class net.sf.basedb.core.Job.SignalKeyring
 
emptySet - Variable in class net.sf.basedb.core.ServiceSessionControl.ServicesKeyring
 
EMTPY_OBJECT_ARRAY - Static variable in class net.sf.basedb.core.log.LoggingInterceptor
 
EMTPY_STRING_ARRAY - Static variable in class net.sf.basedb.core.log.LoggingInterceptor
 
EMTPY_TYPE_ARRAY - Static variable in class net.sf.basedb.core.log.LoggingInterceptor
 
enableAllInFile(String, boolean) - Method in class net.sf.basedb.clients.web.extensions.ExtensionsControl
Enable or disable all extensions and extension points in a file.
enableAnnotationTypes(Connection, List<Integer>) - Method in class net.sf.basedb.core.MigrateRbaToDba
Make sure that the annotation types that are used by the migrated raw bioassays are enabled for derived bioassays.
enabled - Variable in class net.sf.basedb.clients.web.extensions.menu.FixedMenuItemFactory
 
enabled - Variable in class net.sf.basedb.clients.web.extensions.menu.MenuItemBean
 
enabled - Variable in class net.sf.basedb.clients.web.extensions.toolbar.ButtonBean
 
enabled - Variable in class net.sf.basedb.clients.web.extensions.toolbar.FixedButtonFactory
 
enabled - Static variable in class net.sf.basedb.clients.web.servlet.RssNewsFeed
 
enabled - Variable in class net.sf.basedb.clients.web.taglib.Icon
If the icon should be enabled or not (if an onclick has been set).
enabled - Variable in class net.sf.basedb.clients.web.taglib.menu.Menuitem
If the menu item is enabled.
enabled - Variable in class net.sf.basedb.clients.web.taglib.menu.Submenu
If the menu item is enabled.
enabled - Variable in class net.sf.basedb.clients.web.taglib.path.PathElement
 
enabled - Static variable in class net.sf.basedb.util.EmailUtil
 
enabledClazz - Variable in class net.sf.basedb.clients.web.extensions.menu.PermissionMenuItemFactory
 
enabledClazz - Variable in class net.sf.basedb.clients.web.extensions.toolbar.PermissionButtonFactory
 
enableDeviceVerification(String) - Method in class net.sf.basedb.core.User
Verify the email and enables device verification.
enabledFilters - Variable in class net.sf.basedb.core.QueryRuntimeFilterManager
The names of already enabled filters.
enabledIcon - Variable in class net.sf.basedb.clients.web.extensions.menu.PermissionMenuItemFactory
 
enabledIcon - Variable in class net.sf.basedb.clients.web.extensions.toolbar.PermissionButtonFactory
 
enableDownloadLink - Variable in class net.sf.basedb.clients.web.taglib.PropertyValue
Use for files only, if the view/download link should be enabled or not.
enabledPermission - Variable in class net.sf.basedb.clients.web.extensions.menu.PermissionMenuItemFactory
 
enabledPermission - Variable in class net.sf.basedb.clients.web.extensions.toolbar.PermissionButtonFactory
 
enabledStyle - Variable in class net.sf.basedb.clients.web.extensions.menu.PermissionMenuItemFactory
 
enabledStyle - Variable in class net.sf.basedb.clients.web.extensions.toolbar.PermissionButtonFactory
 
enabledTitle - Variable in class net.sf.basedb.clients.web.extensions.menu.PermissionMenuItemFactory
 
enabledTitle - Variable in class net.sf.basedb.clients.web.extensions.toolbar.PermissionButtonFactory
 
enabledTooltip - Variable in class net.sf.basedb.clients.web.extensions.menu.PermissionMenuItemFactory
 
enabledTooltip - Variable in class net.sf.basedb.clients.web.extensions.toolbar.PermissionButtonFactory
 
enableEditLink - Variable in class net.sf.basedb.clients.web.formatter.AutoLinkFormatter
 
enableEditLink - Variable in class net.sf.basedb.clients.web.formatter.LinkedFileFormatter
 
enableEditLink - Variable in class net.sf.basedb.clients.web.formatter.LinkedItemFormatter
 
enableEditLink - Variable in class net.sf.basedb.clients.web.taglib.PropertyValue
Possible to open an edit popup or not with the linked property
enableExtension(String, boolean) - Method in class net.sf.basedb.clients.web.extensions.ExtensionsControl
Enable/disable an extension.
enableExtension(String, boolean) - Method in class net.sf.basedb.util.extensions.manager.Settings
Enable/disable an extension.
enableExtensionPoint(String, boolean) - Method in class net.sf.basedb.clients.web.extensions.ExtensionsControl
Enable/disable an extension point.
enableExtensionPoint(String, boolean) - Method in class net.sf.basedb.util.extensions.manager.Settings
Enable/disable an extension point.
enableFetchProfile(String) - Method in class net.sf.basedb.core.hibernate.SessionWrapper
 
enableFileTypes(Connection, List<Integer>) - Method in class net.sf.basedb.core.MigrateRbaToDba
Make sure that the data file types that are used by the migrated raw bioassays are enabled for derived bioassays.
enableFilter(String) - Method in class net.sf.basedb.core.hibernate.SessionWrapper
 
enableFilter(String) - Method in class net.sf.basedb.core.QueryRuntimeFilterManager
Enable a filter, unless it has already been enabled
enableFilter(Session, String) - Static method in class net.sf.basedb.core.HibernateUtil
Enable the filter with the given name.
enableFilters(DbControl) - Method in class net.sf.basedb.core.AbstractEntityQuery
Enable runtime query filters for the query.
enableFilters(QueryRuntimeFilterManager, EntityQuery, DbControl) - Method in class net.sf.basedb.core.Annotation.QueryRuntimeFilterImpl
 
enableFilters(QueryRuntimeFilterManager, EntityQuery, DbControl) - Method in class net.sf.basedb.core.AnnotationSet.QueryRuntimeFilterImpl
 
enableFilters(QueryRuntimeFilterManager, EntityQuery, DbControl) - Method in class net.sf.basedb.core.FileSet.QueryRuntimeFilterImpl
 
enableFilters(QueryRuntimeFilterManager, EntityQuery, DbControl) - Method in class net.sf.basedb.core.FileSetMember.QueryRuntimeFilterImpl
 
enableFilters(QueryRuntimeFilterManager, EntityQuery, DbControl) - Method in class net.sf.basedb.core.Group.QueryRuntimeFilterImpl
 
enableFilters(QueryRuntimeFilterManager, EntityQuery, DbControl) - Method in class net.sf.basedb.core.Message.QueryRuntimeFilterImpl
 
enableFilters(QueryRuntimeFilterManager, EntityQuery, DbControl) - Method in class net.sf.basedb.core.News.QueryRuntimeFilterImpl
 
enableFilters(QueryRuntimeFilterManager, EntityQuery, DbControl) - Method in class net.sf.basedb.core.Project.QueryRuntimeFilterImpl
 
enableFilters(QueryRuntimeFilterManager, EntityQuery, DbControl) - Method in interface net.sf.basedb.core.QueryRuntimeFilter
Enable the filters based on the options specified by the query and the logged in users permissions.
enableFilters(QueryRuntimeFilterManager, EntityQuery, DbControl) - Method in class net.sf.basedb.core.QueryRuntimeFilterFactory.AnnotatableFilter
 
enableFilters(QueryRuntimeFilterManager, EntityQuery, DbControl) - Method in class net.sf.basedb.core.QueryRuntimeFilterFactory.BasicFilter
 
enableFilters(QueryRuntimeFilterManager, EntityQuery, DbControl) - Method in class net.sf.basedb.core.QueryRuntimeFilterFactory.ChainedFilter
enableFilters(QueryRuntimeFilterManager, EntityQuery, DbControl) - Method in class net.sf.basedb.core.QueryRuntimeFilterFactory.ChildFilter
 
enableFilters(QueryRuntimeFilterManager, EntityQuery, DbControl) - Method in class net.sf.basedb.core.QueryRuntimeFilterFactory.DenyAllFilter
 
enableFilters(QueryRuntimeFilterManager, EntityQuery, DbControl) - Method in class net.sf.basedb.core.QueryRuntimeFilterFactory.OwnableFilter
 
enableFilters(QueryRuntimeFilterManager, EntityQuery, DbControl) - Method in class net.sf.basedb.core.QueryRuntimeFilterFactory.RemovableFilter
 
enableFilters(QueryRuntimeFilterManager, EntityQuery, DbControl) - Method in class net.sf.basedb.core.QueryRuntimeFilterFactory.ShareableFilter
 
enableFilters(QueryRuntimeFilterManager, EntityQuery, DbControl) - Method in class net.sf.basedb.core.Quota.QueryRuntimeFilterImpl
 
enableFilters(QueryRuntimeFilterManager, EntityQuery, DbControl) - Method in class net.sf.basedb.core.Role.QueryRuntimeFilterImpl
 
enableFilters(QueryRuntimeFilterManager, EntityQuery, DbControl) - Method in class net.sf.basedb.core.Session.QueryRuntimeFilterImpl
 
enableFilters(QueryRuntimeFilterManager, EntityQuery, DbControl) - Method in class net.sf.basedb.core.User.QueryRuntimeFilterImpl
 
enableFilters(QueryRuntimeFilterManager, EntityQuery, DbControl) - Method in class net.sf.basedb.core.UserDevice.QueryRuntimeFilterImpl
 
enableForItem(Item) - Method in class net.sf.basedb.core.AnnotationType
Enable this annotation type to be used for items of the specified type.
enablePropertyLink - Variable in class net.sf.basedb.clients.web.taglib.PropertyValue
A link to the property item or not.
enableViewDownload - Variable in class net.sf.basedb.clients.web.formatter.AutoLinkFormatter
 
enableViewDownload - Variable in class net.sf.basedb.clients.web.formatter.LinkedFileFormatter
 
encipher(int[], int) - Method in class net.sf.basedb.util.bcrypt.BCrypt
Blowfish encipher a single 64-bit block encoded as two 32-bit halves
encode(String) - Method in interface net.sf.basedb.util.encode.EncoderDecoder
 
encode(String) - Method in class net.sf.basedb.util.encode.IdentityEncoderDecoder
 
encode(String) - Method in class net.sf.basedb.util.encode.TabCrLfEncoderDecoder
 
encode(String) - Method in class net.sf.basedb.util.encode.ToSpaceEncoderDecoder
 
encode_base64(byte[], int) - Static method in class net.sf.basedb.util.bcrypt.BCrypt
Encode a byte array using bcrypt's slightly-modified base64 encoding scheme.
encodeAll(Collection<String>, EncoderDecoder) - Static method in class net.sf.basedb.util.encode.EncodeUtil
Encode all strings in a collection.
encodeAndJoin(Collection<String>, EncoderDecoder, String, boolean) - Static method in class net.sf.basedb.util.encode.EncodeUtil
Encode all strings in a collection and join them into a single string.
encoder - Variable in class net.sf.basedb.util.bfs.MetadataWriter
 
encoder - Variable in class net.sf.basedb.util.excel.XlsxToCsvUtil
 
encoder - Variable in class net.sf.basedb.util.export.TableWriter
 
EncoderDecoder - Interface in net.sf.basedb.util.encode
Interface for encoding and decoding strings to make them work in a certain context.
encodeTags(String) - Static method in class net.sf.basedb.clients.web.util.HTML
Scans a string for HTML tags and replaces all & with &amp;, < with &lt;, > with &gt; and all " with "
encodeTags(String, String) - Static method in class net.sf.basedb.clients.web.util.HTML
Scans a string for HTML tags and replaces all < and > for tags not found in the safeTags pattern with &lt; and &gt; respectively.
encodeTags(String, Pattern) - Static method in class net.sf.basedb.clients.web.util.HTML
Scans a string for HTML tags and replaces all < and > for tags not found matching the safeTags pattern with &lt; and &gt; respectively.
EncodeUtil - Class in net.sf.basedb.util.encode
Utility functions for encoding/decoding strings.
EncodeUtil() - Constructor for class net.sf.basedb.util.encode.EncodeUtil
 
encodeValue(String) - Method in class net.sf.basedb.util.bfs.MetadataWriter
Encode a value for use in a BFS file.
encryptPassword(String) - Static method in class net.sf.basedb.core.User
Encrypt the plain-text password.
end - Variable in class net.sf.basedb.clients.web.fileupload.FileUpload.UploadStream
 
end - Variable in class net.sf.basedb.util.ChainedProgressReporter
 
end(boolean) - Method in class net.sf.basedb.clients.web.plugins.SimpleExport
 
end(boolean) - Method in class net.sf.basedb.core.plugin.AbstractExporterPlugin
Called just after everything has been committed to the database, or immediately after an error has ocurred.
end(boolean) - Method in class net.sf.basedb.plugins.AbstractFlatFileImporter
Called just after the last line of the file has been parsed, or immediately after an error has ocurred.
end(boolean) - Method in class net.sf.basedb.plugins.AnnotationFlatFileImporter
Now it's time to update the items in the cache with the new annotation values.
end(boolean) - Method in class net.sf.basedb.plugins.BaseFileExporterPlugin
 
end(boolean) - Method in class net.sf.basedb.plugins.batchimport.AbstractItemImporter
 
end(boolean) - Method in class net.sf.basedb.plugins.batchimport.AnyToAnyImporter
 
end(boolean) - Method in class net.sf.basedb.plugins.BfsExporterPlugin
 
end(boolean) - Method in class net.sf.basedb.plugins.GalExporter
 
end(boolean) - Method in class net.sf.basedb.plugins.HelpExporter
 
end(boolean) - Method in class net.sf.basedb.plugins.IlluminaRawDataImporter
If successful: Close batchers Associate with experiment if there is one Commit If not successful: Delete raw bioassays that has been created Rollback
end(boolean) - Method in class net.sf.basedb.plugins.PackedFileExporter
 
end(boolean) - Method in class net.sf.basedb.plugins.PlateFlatFileImporter
Close and commit/rollback and DbControl.
end(boolean) - Method in class net.sf.basedb.plugins.PlateMappingExporter
 
end(boolean) - Method in class net.sf.basedb.plugins.PlateMappingImporter
Close and commit/rollback the DbControl.
end(boolean) - Method in class net.sf.basedb.plugins.PluginConfigurationExporter
 
end(boolean) - Method in class net.sf.basedb.plugins.PrintMapFlatFileImporter
 
end(boolean) - Method in class net.sf.basedb.plugins.RawDataFlatFileImporter
Close and commit/rollback the RawDataBatcher and DbControl.
end(boolean) - Method in class net.sf.basedb.plugins.ReporterFlatFileImporter
Close and commit/rollback the ReporterBatcher and DbControl.
end(boolean) - Method in class net.sf.basedb.plugins.ReporterMapFlatFileImporter
Close and commit/rollback the FeatureBatcher and DbControl.
END_OF_FILE_EVENT - Static variable in class net.sf.basedb.util.bfs.AnnotationParser
Event type that is issued when the end-of-file had been reached.
END_OF_FILE_EVENT - Static variable in class net.sf.basedb.util.bfs.DataParser
Event type that is issued when the end-of-file had been reached.
END_OF_FILE_EVENT - Static variable in class net.sf.basedb.util.bfs.MetadataParser
Event type that is issued when the end-of-file had been reached.
endColumnDefinitions() - Method in class net.sf.basedb.clients.web.taglib.table.Table
 
endColumnFilters() - Method in class net.sf.basedb.clients.web.taglib.table.Table
 
endDate - Variable in class net.sf.basedb.core.data.NewsData
 
endDocument(ProgressReporter) - Method in interface net.sf.basedb.clients.web.plugins.ExportTemplate
End writing the document.
endDocument(ProgressReporter) - Method in class net.sf.basedb.clients.web.plugins.PlainTextTemplate
Do nothing.
endDocument(ProgressReporter) - Method in class net.sf.basedb.clients.web.plugins.XlsxTemplate
Write the Excel workbook to the output stream and close.
endDocument(ProgressReporter) - Method in class net.sf.basedb.clients.web.plugins.XMLTemplate
Close the document tags.
ended - Variable in class net.sf.basedb.core.data.JobData
 
endExport(RuntimeException) - Method in class net.sf.basedb.util.export.spotdata.AbstractBioAssaySetExporter
End the export and clean up/close all aquired resources.
endExport(RuntimeException) - Method in class net.sf.basedb.util.export.spotdata.BaseFileExporter
 
endExport(RuntimeException) - Method in class net.sf.basedb.util.export.spotdata.BfsExporter
Clean up.
endExport(RuntimeException) - Method in class net.sf.basedb.util.export.spotdata.MatrixBaseFileExporter
 
endExport(RuntimeException) - Method in class net.sf.basedb.util.export.spotdata.SerialBaseFileExporter
 
endIndex - Variable in class net.sf.basedb.core.FastAnnotationLoader.FastIterator
 
endItem() - Method in interface net.sf.basedb.clients.web.plugins.ExportTemplate
End writing an item
endItem() - Method in class net.sf.basedb.clients.web.plugins.PlainTextTemplate
Write a newline.
endItem() - Method in class net.sf.basedb.clients.web.plugins.XlsxTemplate
Do nothing.
endItem() - Method in class net.sf.basedb.clients.web.plugins.XMLTemplate
Write the current item element to the export stream.
endTime - Variable in class net.sf.basedb.util.extensions.manager.ProcessResults
 
endX - Variable in class net.sf.basedb.util.plot.HistogramPlot.HistogramBin
 
ENERGY - Static variable in class net.sf.basedb.core.Quantity
The id for the Quantity object representing energy.
EngineFactory - Class in net.sf.basedb.core.dbengine
Creates DbEngine objects based on the Hibernate dialect.
EngineFactory() - Constructor for class net.sf.basedb.core.dbengine.EngineFactory
 
EnhancedThreadSignalHandler - Class in net.sf.basedb.core.signal
An extension to the thread signal handler that supports any number of signals.
EnhancedThreadSignalHandler(Collection<Signal>) - Constructor for class net.sf.basedb.core.signal.EnhancedThreadSignalHandler
Create a new signal handler that supports the specified signals.
EnhancedThreadSignalHandler(Signal...) - Constructor for class net.sf.basedb.core.signal.EnhancedThreadSignalHandler
Create a signal handler that supports the specified signals.
ensureProductParentCorrectness(BioMaterialEventData) - Static method in class net.sf.basedb.core.BioMaterialEvent
Ensure that the MeasuredBioMaterial.getParent() and MeasuredBioMaterial.getParentType() reflect the current sources collection.
entity - Variable in class net.sf.basedb.core.log.EntityDetails
 
entity(BasicItem) - Static method in class net.sf.basedb.core.query.Hql
Create an expression representing an item which is a subclass of BasicItem.
entity(BasicData) - Static method in class net.sf.basedb.core.query.Hql
Create an expression representing an item which is a subclass of BasicData, for example a reporter.
ENTITY_COLLECTION - Variable in class net.sf.basedb.core.PropertyFilter
 
EntityDetails - Class in net.sf.basedb.core.log
Contains detailed information about the changes made to an entity during a transaction.
EntityDetails(Object, ChangeType, Object[], Object[], String[], Type[]) - Constructor for class net.sf.basedb.core.log.EntityDetails
 
EntityLogger - Interface in net.sf.basedb.core.log
Entity logger implementations are created by a LogManagerFactory when a change to a logged entity has been detected.
EntityLogOptions - Class in net.sf.basedb.core.log
This class collect some static information related to logging for entities.
EntityLogOptions(Class<?>) - Constructor for class net.sf.basedb.core.log.EntityLogOptions
 
entityName - Variable in class net.sf.basedb.core.BasicBatcher
The entity name as known to Hibernate.
entityName - Variable in class net.sf.basedb.core.Metadata
 
entityParameter(String, Item) - Static method in class net.sf.basedb.core.query.Hql
Create an expression for a parameter which must be an entity of a specified type.
EntityPropertyPath(ClassMetadata, String, Type) - Constructor for class net.sf.basedb.core.Metadata.EntityPropertyPath
 
EntityQuery - Interface in net.sf.basedb.core.query
This a HQL query that return enitities, ie. items.
EntityQueryWrapper<R> - Class in net.sf.basedb.core.hibernate
Wraps a hibernate query and adds checks so that unsaved items aren't added to the query as parameters.
EntityQueryWrapper(Query<R>) - Constructor for class net.sf.basedb.core.hibernate.EntityQueryWrapper
 
entries - Variable in class net.sf.basedb.util.bfs.MetadataModel.Section
 
entries - Variable in class net.sf.basedb.util.Enumeration
 
entries - Variable in class net.sf.basedb.util.Tree
 
Entry(K, V) - Constructor for class net.sf.basedb.util.Enumeration.Entry
 
Entry(Tree<E>, E, Tree.Entry<E>) - Constructor for class net.sf.basedb.util.Tree.Entry
 
ENTRY_DATE - Static variable in class net.sf.basedb.core.ClonableProperty
The property name of the "static" property ReporterData.getEntryDate()
ENTRY_EVENT - Static variable in class net.sf.basedb.util.bfs.MetadataParser
Event type that is issued for each entry in a section in the order they are present in the file.
entryDate - Variable in class net.sf.basedb.core.data.AnnotationTypeCategoryData
 
entryDate - Variable in class net.sf.basedb.core.data.AnnotationTypeData
 
entryDate - Variable in class net.sf.basedb.core.data.ArrayBatchData
 
entryDate - Variable in class net.sf.basedb.core.data.ArrayDesignData
 
entryDate - Variable in class net.sf.basedb.core.data.ArraySlideData
 
entryDate - Variable in class net.sf.basedb.core.data.BioMaterialEventData
 
entryDate - Variable in class net.sf.basedb.core.data.BioPlateData
 
entryDate - Variable in class net.sf.basedb.core.data.BioPlateEventData
 
entryDate - Variable in class net.sf.basedb.core.data.BioSourceData
 
entryDate - Variable in class net.sf.basedb.core.data.ClientData
 
entryDate - Variable in class net.sf.basedb.core.data.DerivedBioAssayData
 
entryDate - Variable in class net.sf.basedb.core.data.ExperimentData
 
entryDate - Variable in class net.sf.basedb.core.data.ExtraValueTypeData
 
entryDate - Variable in class net.sf.basedb.core.data.FormulaData
 
entryDate - Variable in class net.sf.basedb.core.data.GroupData
 
entryDate - Variable in class net.sf.basedb.core.data.HardwareData
 
entryDate - Variable in class net.sf.basedb.core.data.ItemSubtypeData
 
entryDate - Variable in class net.sf.basedb.core.data.KitData
 
entryDate - Variable in class net.sf.basedb.core.data.MimeTypeData
 
entryDate - Variable in class net.sf.basedb.core.data.NewsData
 
entryDate - Variable in class net.sf.basedb.core.data.PlateData
 
entryDate - Variable in class net.sf.basedb.core.data.PlateEventData
 
entryDate - Variable in class net.sf.basedb.core.data.PlateGeometryData
 
entryDate - Variable in class net.sf.basedb.core.data.PlateMappingData
 
entryDate - Variable in class net.sf.basedb.core.data.PlateTypeData
 
entryDate - Variable in class net.sf.basedb.core.data.PluginConfigurationData
 
entryDate - Variable in class net.sf.basedb.core.data.PluginDefinitionData
 
entryDate - Variable in class net.sf.basedb.core.data.PluginTypeData
 
entryDate - Variable in class net.sf.basedb.core.data.ProjectData
 
entryDate - Variable in class net.sf.basedb.core.data.ProtocolData
 
entryDate - Variable in class net.sf.basedb.core.data.QuotaTypeData
 
entryDate - Variable in class net.sf.basedb.core.data.RawBioAssayData
 
entryDate - Variable in class net.sf.basedb.core.data.ReporterCloneTemplateData
 
entryDate - Variable in class net.sf.basedb.core.data.ReporterData
 
entryDate - Variable in class net.sf.basedb.core.data.ReporterListData
 
entryDate - Variable in class net.sf.basedb.core.data.ReporterTypeData
 
entryDate - Variable in class net.sf.basedb.core.data.RoleData
 
entryDate - Variable in class net.sf.basedb.core.data.SoftwareData
 
entryDate - Variable in class net.sf.basedb.core.data.TagData
 
entryDate - Variable in class net.sf.basedb.core.data.UserData
 
entryDate - Variable in class net.sf.basedb.core.data.UserDeviceData
 
entryDate - Variable in class net.sf.basedb.core.MigrateRbaToDba.Rba
 
entryDate - Variable in class net.sf.basedb.core.ReporterBatcher
Date to to give new reporters.
entryIterator - Variable in class net.sf.basedb.util.Tree.ElementIterator
The entry iterator.
entryIterator() - Method in class net.sf.basedb.util.Tree
Create an iterator for the tree that returns entry object.
entryIterator(E) - Method in class net.sf.basedb.util.Tree
Create an iterator for the tree starting at a specific node.
EntryIterator(Tree.Entry<E>) - Constructor for class net.sf.basedb.util.Tree.EntryIterator
Create an iterator that starts at the specified entry.
enumClass - Variable in class net.sf.basedb.util.formatter.EnumFormatter
 
EnumConverter<T extends Enum<T>> - Class in net.sf.basedb.util.json
Converted implementation that create JSON objects with the NAME of enumeration.
EnumConverter() - Constructor for class net.sf.basedb.util.json.EnumConverter
 
enumeration - Variable in class net.sf.basedb.clients.web.extensions.list.AbstractListColumnBean
 
enumeration - Variable in class net.sf.basedb.clients.web.taglib.table.ColumnDef
Options for enum.
enumeration - Variable in class net.sf.basedb.core.ParameterType
List of allowed values.
Enumeration<K,V> - Class in net.sf.basedb.util
 
Enumeration() - Constructor for class net.sf.basedb.util.Enumeration
 
ENUMERATION - Enum constant in enum class net.sf.basedb.plugins.Base1PluginExecuter.Base1JobParameterType
 
Enumeration.Entry<K,V> - Class in net.sf.basedb.util
 
enumerationColumnMapping - Static variable in class net.sf.basedb.plugins.batchimport.AnnotationTypeImporter
Column mapping parameter for "Enumeration".
enumerationMapper - Variable in class net.sf.basedb.plugins.batchimport.AnnotationTypeImporter
 
enumerationSplitter - Variable in class net.sf.basedb.plugins.batchimport.AnnotationTypeImporter
 
enumerationSplitterRegexpParameter - Static variable in class net.sf.basedb.plugins.batchimport.AnnotationTypeImporter
Regular expression splitter parameter for enumerations.
enumerationValues - Variable in class net.sf.basedb.core.data.AnnotationTypeData
 
EnumFormatter<T extends Enum<T>> - Class in net.sf.basedb.util.formatter
Formatter implementation that converts an enum constant into it's name() as the formatted value.
EnumFormatter(Class<T>) - Constructor for class net.sf.basedb.util.formatter.EnumFormatter
Create a new formatter.
EnumFormatter(Class<T>, String) - Constructor for class net.sf.basedb.util.formatter.EnumFormatter
Create a new formatter.
enumOptions - Variable in class net.sf.basedb.plugins.Base1PluginExecuter.JobParameter
 
eof - Variable in class net.sf.basedb.clients.web.fileupload.FileUpload.UploadStatus
TRUE if the end of the stream is reached, FALSE otherwise
eof() - Method in class net.sf.basedb.clients.web.fileupload.FileUpload
Check if the end of the upload has been reached or not.
eof(int) - Method in class net.sf.basedb.util.charset.SimpleStringDetector
 
eof(int) - Method in interface net.sf.basedb.util.charset.StringDetector
This is called when the end of file has been reached and the checkLine method has returned false for all lines.
ep - Variable in class net.sf.basedb.clients.web.formatter.ExtendedPropertyFormatter
 
EP_ALL - Static variable in class net.sf.basedb.clients.web.extensions.list.ListColumnUtil
ID for the list column extension point that appear on all list pages.
EP_ALL - Static variable in class net.sf.basedb.clients.web.extensions.toolbar.ToolbarUtil
ID:s for the toolbar extension point that appear on all pages.
EP_ANNOTATABLE - Static variable in class net.sf.basedb.clients.web.extensions.list.ListColumnUtil
ID for the list column extension point that appear on all pages that list Annotatable items.
EP_ANNOTATABLE - Static variable in class net.sf.basedb.clients.web.extensions.toolbar.ToolbarUtil
ID:s for the toolbar extension point that appear on all pages that displays Annotatable items.
EP_OWNABLE - Static variable in class net.sf.basedb.clients.web.extensions.list.ListColumnUtil
ID for the list column extension point that appear on all pages that list Ownable items.
EP_OWNABLE - Static variable in class net.sf.basedb.clients.web.extensions.toolbar.ToolbarUtil
ID:s for the toolbar extension point that appear on all pages that displays Ownable items.
EP_PREFIX - Static variable in class net.sf.basedb.clients.web.extensions.list.ListColumnUtil
ID prefixes for list column extension point.
EP_PREFIX - Static variable in class net.sf.basedb.clients.web.extensions.toolbar.ToolbarUtil
ID prefixes for toolbar extension point.
EP_PREFIX_EDIT - Static variable in class net.sf.basedb.clients.web.extensions.edit.EditUtil
ID prefix for tabcontrol extension points on edit pages.
EP_PREFIX_SAVE - Static variable in class net.sf.basedb.clients.web.extensions.edit.EditUtil
ID prefix for tabcontrol extension points on edit pages.
EP_REMOVABLE - Static variable in class net.sf.basedb.clients.web.extensions.list.ListColumnUtil
ID for the list column extension point that appear on all pages that list Removable items.
EP_REMOVABLE - Static variable in class net.sf.basedb.clients.web.extensions.toolbar.ToolbarUtil
ID:s for the toolbar extension point that appear on all pages that displays Removable items.
EP_SHAREABLE - Static variable in class net.sf.basedb.clients.web.extensions.list.ListColumnUtil
ID for the list column extension point that appear on all pages that list Shareable items.
EP_SHAREABLE - Static variable in class net.sf.basedb.clients.web.extensions.toolbar.ToolbarUtil
ID:s for the toolbar extension point that appear on all pages that displays Shareable items.
eq(Expression, Expression) - Static method in class net.sf.basedb.core.query.Restrictions
Compare if two expressions are equal: new restriction = e1 == e2.
EQ - Enum constant in enum class net.sf.basedb.core.Operator
 
EqRestriction - Class in net.sf.basedb.core.query
Compare if two expressions are equal: e1 == e2, or e1 IS NULL
EqRestriction(Expression, Expression) - Constructor for class net.sf.basedb.core.query.EqRestriction
 
equals(Object) - Method in class net.sf.basedb.clients.web.extensions.ServletWrapperKey
 
equals(Object) - Method in class net.sf.basedb.clients.web.ModeInfo.ModeContext
 
equals(Object) - Method in class net.sf.basedb.clients.web.servlet.ExperimentExplorerPlotServlet.ColumnKey
 
equals(Object) - Method in class net.sf.basedb.core.AnnotationBetweenRestriction
This restriction is equal to another AnnotationBetweenRestriction if they have the same annotation type, upper and lower bound and inheritance setting.
equals(Object) - Method in class net.sf.basedb.core.AnnotationInRestriction
This restriction is equal to another AnnotationInRestriction if they have the same annotation type, list of values and inheritance setting.
equals(Object) - Method in class net.sf.basedb.core.AnnotationSimpleRestriction
This restriction is equal to another AnnotationSimpleRestriction if they have the same annotation type, operator, list of values and inheritance setting.
equals(Object) - Method in class net.sf.basedb.core.BasicItem
Check if this item is equal to another item.
equals(Object) - Method in class net.sf.basedb.core.BlockInfo
Check if this object is equal to another BlockInfo object.
equals(Object) - Method in class net.sf.basedb.core.ClonableProperty
 
equals(Object) - Method in class net.sf.basedb.core.ContextKey
Check if this object is equal to another ContextKey object.
equals(Object) - Method in class net.sf.basedb.core.data.BasicData
Check if this item is equal to another item.
equals(Object) - Method in class net.sf.basedb.core.data.BioMaterialData
It may happen that lazy-loaded proxies are put in the same collection as already loaded "real" objects in which case the BasicData.equals() method doesns't work.
equals(Object) - Method in class net.sf.basedb.core.data.ContextIndex
Check if this object is equal to another ContextIndex object.
equals(Object) - Method in class net.sf.basedb.core.data.FileTypeIndex
Check if this object is equal to another FileTypeIndex object.
equals(Object) - Method in class net.sf.basedb.core.data.GuiContextData
Check if this object is equal to another GuiContext object.
equals(Object) - Method in class net.sf.basedb.core.data.keyring.GroupGroups
Check if this object is equal to another GroupGroups object.
equals(Object) - Method in class net.sf.basedb.core.data.keyring.GroupKeys
Check if this object is equal to another GroupKeys object.
equals(Object) - Method in class net.sf.basedb.core.data.keyring.GroupProjects
Check if this object is equal to another GroupProjects object.
equals(Object) - Method in class net.sf.basedb.core.data.keyring.PluginKeys
Check if this object is equal to another RoleKeys object.
equals(Object) - Method in class net.sf.basedb.core.data.keyring.ProjectKeys
Check if this object is equal to another ProjectKeys object.
equals(Object) - Method in class net.sf.basedb.core.data.keyring.RoleKeys
Check if this object is equal to another RoleKeys object.
equals(Object) - Method in class net.sf.basedb.core.data.keyring.UserGroups
Check if this object is equal to another UserGroups object.
equals(Object) - Method in class net.sf.basedb.core.data.keyring.UserKeys
Check if this object is equal to another UserKeys object.
equals(Object) - Method in class net.sf.basedb.core.data.keyring.UserProjects
Check if this object is equal to another UserProjects object.
equals(Object) - Method in class net.sf.basedb.core.data.keyring.UserRoles
Check if this object is equal to another UserRoles object.
equals(Object) - Method in class net.sf.basedb.core.data.MappingCoordinate
Check if this object is equal to another MappingCoordinate object.
equals(Object) - Method in class net.sf.basedb.core.data.PlateCoordinate
Check if this object is equal to another PlateCoordinateData object.
equals(Object) - Method in class net.sf.basedb.core.data.QuotaIndex
Check if this object is equal to another QuotaIndex object.
equals(Object) - Method in class net.sf.basedb.core.data.ReporterListScoreData
 
equals(Object) - Method in class net.sf.basedb.core.data.VersionedParameter
Check if this object is equal to another VersionedParameter object.
equals(Object) - Method in class net.sf.basedb.core.DynamicJoin
This join is equal to another DynamicJoin if they join between the same tables using the same columns and join types.
equals(Object) - Method in class net.sf.basedb.core.DynamicRestriction
This restriction is equal to another DynamicRestriction if their table, column and values are equal.
equals(Object) - Method in class net.sf.basedb.core.ExtraValueExpression
This expression is equal to another ExtraValueExpression if they represents the same extra value.
equals(Object) - Method in class net.sf.basedb.core.ExtraValueJoin
This join is equal to another ExtraValueJoin if they join to the same extra value with the same join type.
equals(Object) - Method in class net.sf.basedb.core.FeatureCoordinate
Check if this object is equal to another FeatureCoordinate object.
equals(Object) - Method in class net.sf.basedb.core.HasAnnotationRestriction
This restriction is equal to another HasAnnotationRestriction if they have the same annotation type, inheritance setting and annotation check.
equals(Object) - Method in class net.sf.basedb.core.ItemProxy
Check if this item is equal to another item.
equals(Object) - Method in class net.sf.basedb.core.ItemResultList
 
equals(Object) - Method in class net.sf.basedb.core.MeanRawDataPropertyExpression
This expression is equal to another MeanRawDataPropertyExpression if they represent the same raw data property.
equals(Object) - Method in class net.sf.basedb.core.plugin.GuiContext
 
equals(Object) - Method in class net.sf.basedb.core.query.AbsExpression
This expression is equal to another AbsExpression if their child expressions are equal.
equals(Object) - Method in class net.sf.basedb.core.query.AddExpression
This expression is equal to another AddExpression if their child expressions are equal (ignoring the order).
equals(Object) - Method in class net.sf.basedb.core.query.AndRestriction
This restriction is equal to another AndRestriction if both contains the same restrictions (disregarding order).
equals(Object) - Method in class net.sf.basedb.core.query.AnnotationJoin
This join is equal to another AnnotationJoin if they join to the same annotation type with the same alias.
equals(Object) - Method in class net.sf.basedb.core.query.AnyToAnyRestriction
This expression is equal to another AnyToAnyRestriction if their named link, 'hasLink' and subquery restriction are the same.
equals(Object) - Method in class net.sf.basedb.core.query.AscOrder
This expression is equal to another AscOrder if their child expressions are equal.
equals(Object) - Method in class net.sf.basedb.core.query.BetweenRestriction
This restriction is equal to another BetweenRestriction if their child expressions are equal.
equals(Object) - Method in class net.sf.basedb.core.query.BooleanExpression
This expression is equal to another BooleanExpression if their values or restrictions are equal.
equals(Object) - Method in class net.sf.basedb.core.query.CaseExpression
This expression is equal to another CaseExpression if both contains the same when statements (disregarding order) and else expression.
equals(Object) - Method in class net.sf.basedb.core.query.ConditionalQueryElement
This query element is equal to another ConditionalQueryElement if their filter and child elements are equal.
equals(Object) - Method in class net.sf.basedb.core.query.CountExpression
This expression is equal to another CountExpression if their child expressions are equal and have the same DISTINCT setting.
equals(Object) - Method in class net.sf.basedb.core.query.DescOrder
This expression is equal to another DescOrder if their child expressions are equal.
equals(Object) - Method in class net.sf.basedb.core.query.DivideExpression
This expression is equal to another DivideExpression if their child expressions are equal.
equals(Object) - Method in class net.sf.basedb.core.query.EqRestriction
This restriction is equal to another EqRestriction if their child restrictions are equal (ignoring the order).
equals(Object) - Method in class net.sf.basedb.core.query.ExpExpression
This expression is equal to another ExpExpression if their child expressions are equal.
equals(Object) - Method in class net.sf.basedb.core.query.ExpressionSelect
This expression is equal to another ExpressionSelect if their child expressions and aliases are equal.
equals(Object) - Method in class net.sf.basedb.core.query.FloatExpression
This expression is equal to another FloatExpression if their values are equal.
equals(Object) - Method in class net.sf.basedb.core.query.GeometricMeanExpression
This expression is equal to another GeometricMeanExpression if their child expressions are equal.
equals(Object) - Method in class net.sf.basedb.core.query.GteqRestriction
This restriction is equal to another GteqRestriction if their child restrictions are equal.
equals(Object) - Method in class net.sf.basedb.core.query.GtRestriction
This restriction is equal to another GtRestriction if their child restrictions are equal.
equals(Object) - Method in class net.sf.basedb.core.query.HqlElementsExpression
This expression is equal to another HqlElementsExpression if their alias and property expressions are equal.
equals(Object) - Method in class net.sf.basedb.core.query.HqlEntityExpression
This expression is equal to another HqlEntityExpression if they represent the same item.
equals(Object) - Method in class net.sf.basedb.core.query.HqlEntityParameterExpression
This expression is equal to another HqlEntityParameterExpression if their names are equal.
equals(Object) - Method in class net.sf.basedb.core.query.HqlExpression
This expression is equal to another HqlExpression if their child expressions are equal.
equals(Object) - Method in class net.sf.basedb.core.query.HqlIndexExpression
This expression is equal to another HqlIndexExpression if their alias and property expressions are equal.
equals(Object) - Method in class net.sf.basedb.core.query.HqlInnerJoin
This join is equal to another HqlInnerJoin if they join to the same property with the same alias and use the same condition and fetch mode.
equals(Object) - Method in class net.sf.basedb.core.query.HqlLeftJoin
This join is equal to another HqlLeftJoin if they join to the same property with the same alias and use the same condition and fetch mode.
equals(Object) - Method in class net.sf.basedb.core.query.HqlPropertyExpression
This expression is equal to another HqlPropertyExpression if their alias, property and index expressions are equal.
equals(Object) - Method in class net.sf.basedb.core.query.HqlRightJoin
This join is equal to another HqlRightJoin if they join to the same property with the same alias and use the same condition.
equals(Object) - Method in class net.sf.basedb.core.query.HqlSizeExpression
This expression is equal to another HqlSizeExpression if their alias and property expressions are equal.
equals(Object) - Method in class net.sf.basedb.core.query.InRestriction
This expression is equal to another InRestriction if both contains the same main expressions and list of expressions (disregarding order).
equals(Object) - Method in class net.sf.basedb.core.query.IntegerExpression
This expression is equal to another IntegerExpression if their values are equal.
equals(Object) - Method in class net.sf.basedb.core.query.LikeRestriction
This restriction is equal to another LikeRestriction if their child restrictions are equal.
equals(Object) - Method in class net.sf.basedb.core.query.LogExpression
This expression is equal to another LogExpression if their child expressions and bases are equal.
equals(Object) - Method in class net.sf.basedb.core.query.LteqRestriction
This restriction is equal to another LteqRestriction if their child restrictions are equal.
equals(Object) - Method in class net.sf.basedb.core.query.LtRestriction
This restriction is equal to another LtRestriction if their child restrictions are equal.
equals(Object) - Method in class net.sf.basedb.core.query.MaxExpression
This expression is equal to another MaxExpression if their child expressions are equal.
equals(Object) - Method in class net.sf.basedb.core.query.MeanExpression
This expression is equal to another MeanExpression if their child expressions are equal.
equals(Object) - Method in class net.sf.basedb.core.query.MinExpression
This expression is equal to another MinExpression if their child expressions are equal.
equals(Object) - Method in class net.sf.basedb.core.query.MultiplyExpression
This expression is equal to another MultiplyExpression if their child expressions are equal (ignoring the order).
equals(Object) - Method in class net.sf.basedb.core.query.NegateExpression
This expression is equal to another NegateExpression if their child expressions are equal.
equals(Object) - Method in class net.sf.basedb.core.query.NeqRestriction
This restriction is equal to another NeqRestriction if their child restrictions are equal (ignoring the order).
equals(Object) - Method in class net.sf.basedb.core.query.NotRestriction
This restriction is equal to another NotRestriction if their child restrictions are equal.
equals(Object) - Method in class net.sf.basedb.core.query.OrRestriction
This restriction is equal to another OrRestriction if both contains the same restrictions (disregarding order).
equals(Object) - Method in class net.sf.basedb.core.query.ParameterExpression
This expression is equal to another ParameterExpression if their names expressions are equal.
equals(Object) - Method in class net.sf.basedb.core.query.PowerExpression
This expression is equal to another MultiplyExpression if their child expressions are equal.
equals(Object) - Method in class net.sf.basedb.core.query.QuadraticMeanExpression
This expression is equal to another QuadraticMeanExpression if their child expressions are equal.
equals(Object) - Method in class net.sf.basedb.core.query.QueryParameter
 
equals(Object) - Method in class net.sf.basedb.core.query.ReporterListExpression
This expression is equal to another ReporterListExpression if they use the same property from the same reporter list and uses the same auto join type.
equals(Object) - Method in class net.sf.basedb.core.query.RlikeRestriction
This restriction is equal to another RlikeRestriction if their child restrictions are equal.
equals(Object) - Method in class net.sf.basedb.core.query.SelectedExpression
This expression is equal to another SelectedExpression if their child expressions are equal.
equals(Object) - Method in class net.sf.basedb.core.query.SharedToRestriction
This restriction is equal to another SharedToRestriction if their child restrictions and other parameters are equal.
equals(Object) - Method in class net.sf.basedb.core.query.SqlColumnExpression
This expression is equal to another SqlColumnExpression if their aliases and columns are equal.
equals(Object) - Method in class net.sf.basedb.core.query.SqrtExpression
This expression is equal to another SqrtExpression if their child expressions are equal.
equals(Object) - Method in class net.sf.basedb.core.query.SubqueryExpression
This expression is equal to another SubqueryExpression if they use the same operator and reference the same subquery instance.
equals(Object) - Method in class net.sf.basedb.core.query.SubtractExpression
This expression is equal to another AddExpression if their child expressions are equal.
equals(Object) - Method in class net.sf.basedb.core.query.SumExpression
This expression is equal to another SumExpression if their child expressions are equal.
equals(Object) - Method in class net.sf.basedb.core.query.ToDateExpression
This expression is equal to another ToDateExpression if their child expressions are equal.
equals(Object) - Method in class net.sf.basedb.core.query.VirtualColumnExpression
This expression is equal to another VirtualColumnExpression if their tables and columns are equal.
equals(Object) - Method in class net.sf.basedb.core.query.WhenStatement
This statement is equal to another WhenStatement if both have equal conditions and values.
equals(Object) - Method in class net.sf.basedb.core.RawBioAssayPropertyExpression
This expression is equal to another RawBioAssayPropertyExpression if they represent the same reporter property.
equals(Object) - Method in class net.sf.basedb.core.RawDataPropertyExpression
This expression is equal to another RawDataPropertyExpression if they represent the same raw data property.
equals(Object) - Method in class net.sf.basedb.core.RawDataType
 
equals(Object) - Method in class net.sf.basedb.core.RealJoin
This join is equal to another RealJoin if they join between the same tables using the same columns and join types.
equals(Object) - Method in class net.sf.basedb.core.ReporterListJoin
This join is equal to another ReporterListJoin if they join to the same reporter list with the same join type.
equals(Object) - Method in class net.sf.basedb.core.ReporterPropertyExpression
This expression is equal to another ReporterPropertyExpression if they represent the same reporter property.
equals(Object) - Method in class net.sf.basedb.core.SessionControl.MainContext
 
equals(Object) - Method in class net.sf.basedb.core.signal.Signal
Two signals are equal if they have the same ID.
equals(Object) - Method in class net.sf.basedb.core.VirtualColumn
A virtual column is equal to another if both have the same name.
equals(Object) - Method in class net.sf.basedb.plugins.BaseFileExporterPlugin.ExtendedDynamicField
An extended dynamic field is equal to another field if their parent fields equal.
equals(Object) - Method in class net.sf.basedb.util.AnnotationUtil.AnnotatableWrapper
A wrapper is equal to another if they references the same item and chain of extracts.
equals(Object) - Method in class net.sf.basedb.util.AnyToAnyLinkStatistics
 
equals(Object) - Method in class net.sf.basedb.util.export.spotdata.AnnotationAssayField
An assay field is equal to another assay field if it uses the same annotation type and has the same title.
equals(Object) - Method in class net.sf.basedb.util.export.spotdata.AssayPropertyField
An assay field is equal to another assay field if it uses the same property and has the same title.
equals(Object) - Method in class net.sf.basedb.util.export.spotdata.JepDynamicField
A jep dynamic field is equal to another field if it uses the same jep expression and has the same title.
equals(Object) - Method in class net.sf.basedb.util.export.spotdata.SimpleDynamicField
A dynamic field is equal to another field if it uses the same expression and has the same title.
equals(Object) - Method in class net.sf.basedb.util.extensions.manager.ExtensionKey
 
equals(Object) - Method in class net.sf.basedb.util.extensions.manager.ExtensionPointKey
 
equals(Object) - Method in class net.sf.basedb.util.extensions.manager.ExtensionsFile
 
equals(Object) - Method in class net.sf.basedb.util.extensions.manager.FactoryParametersKey
 
equals(Object) - Method in class net.sf.basedb.util.extensions.manager.PluginInfoKey
 
equals(Object) - Method in class net.sf.basedb.util.extensions.Registry.AttributeKey
 
equals(Object) - Method in class net.sf.basedb.util.gtf.GtfInputStream.Attribute
 
equals(Object) - Method in class net.sf.basedb.util.jobagent.JobInfo
 
equals(Object) - Method in class net.sf.basedb.util.listable.TransformCache.CacheKey
 
equals(Object) - Method in class net.sf.basedb.util.overview.cache.DirectionalCacheKey
 
equals(Object) - Method in class net.sf.basedb.util.overview.cache.IndexedCacheKey
 
equals(Object) - Method in class net.sf.basedb.util.overview.Failure
One failure is the same as another if they have the same validator but different nodes referencing the same item with equal descriptors.
equals(Object) - Method in class net.sf.basedb.util.overview.validator.ExtractValidator.TagPosition
 
equals(Object) - Method in class net.sf.basedb.util.Tree
Equality only tests if the object is the same instance of this tree.
equals(Object) - Method in class net.sf.basedb.util.units.UnitCache.CacheKey
 
equals(Object, Object) - Static method in class net.sf.basedb.util.EqualsHelper
Check if two objects are equal according to their equals implementation.
EqualsConverter - Class in net.sf.basedb.util.jep.convert
Convert the '==' operator to a Query API Restriction.
EqualsConverter() - Constructor for class net.sf.basedb.util.jep.convert.EqualsConverter
 
EqualsFilter<T> - Class in net.sf.basedb.util.filter
A filter implementation that only accepts an object if it is equal (using Object.equals()) to a given object.
EqualsFilter(T) - Constructor for class net.sf.basedb.util.filter.EqualsFilter
Create a new filter.
EqualsHelper - Class in net.sf.basedb.util
Helper class for implementing equals and hash code calculations in classes.
EqualsHelper() - Constructor for class net.sf.basedb.util.EqualsHelper
 
EQUIVALENT_DOSE - Static variable in class net.sf.basedb.core.Quantity
The id for the Quantity object representing equivalent dose.
error - Variable in class net.sf.basedb.clients.web.extensions.list.RelatedItemErrorColumn
 
error - Variable in class net.sf.basedb.core.SimpleProgressReporter
 
error - Variable in class net.sf.basedb.util.FileCopyRunnable
 
error(String) - Method in class net.sf.basedb.util.extensions.logging.ExtensionsLogger
Log an ERROR message.
error(String, Throwable) - Method in class net.sf.basedb.util.extensions.logging.ExtensionsLogger
Log an ERROR message with an optional stacktrace.
error(SAXParseException) - Method in class net.sf.basedb.util.XmlUtil2.Validator
Errors thrown with a detailed error message.
ERROR - Enum constant in enum class net.sf.basedb.core.Job.Status
The job has finished with an error.
ERROR - Enum constant in enum class net.sf.basedb.core.plugin.Response.Status
 
ERROR - Enum constant in enum class net.sf.basedb.util.extensions.logging.LogLevel
 
ERROR - Enum constant in enum class net.sf.basedb.util.extensions.LoggingErrorHandlerFactory.Level
 
ERROR - Enum constant in enum class net.sf.basedb.util.overview.Severity
The rule generate errors.
ERROR_SECTION - Static variable in class net.sf.basedb.plugins.util.Parameters
The name of the parameter created by Parameters.errorSection(String, String).
errorClazz - Variable in class net.sf.basedb.clients.web.taglib.table.Cell
Optional class attribute for errors.
errorHandler - Variable in class net.sf.basedb.plugins.AbstractFlatFileImporter
 
errorHandler - Variable in class net.sf.basedb.plugins.AnnotationFlatFileImporter
 
errorHandler - Variable in class net.sf.basedb.plugins.batchimport.AbstractItemImporter
 
errorHandler - Variable in class net.sf.basedb.util.extensions.ExtensionPointContext
 
ErrorHandler - Interface in net.sf.basedb.util.error
An interface to make it easier to implement dynamic error handling.
ErrorHandler<A extends Action> - Interface in net.sf.basedb.util.extensions
Error handlers are created by the factory for each request/use of an extension point.
errorHandlerFactory - Variable in class net.sf.basedb.util.extensions.ExtensionPointBean
 
errorHandlerFactory - Variable in class net.sf.basedb.util.extensions.ExtensionPointContext
 
errorHandlerFactory - Variable in class net.sf.basedb.util.extensions.Registry.RegisteredExtensionPoint
 
ErrorHandlerFactory<A extends Action> - Interface in net.sf.basedb.util.extensions
Error handler factories are responsible for creating error handlers.
errorHandlers - Variable in class net.sf.basedb.util.error.ClassMapErrorHandler
Map of registered error handlers.
errorIfNotFound - Variable in class net.sf.basedb.plugins.PlateFlatFileImporter
 
errorIfNotFound - Variable in class net.sf.basedb.plugins.ReporterMapFlatFileImporter
 
errorList - Variable in class net.sf.basedb.core.PluginResponse
 
errorMessage - Variable in class net.sf.basedb.core.data.FileSetMemberData
 
errors - Variable in class net.sf.basedb.plugins.executor.ExternalProgramExecutor.ResponseWrapper
 
errors - Variable in class net.sf.basedb.util.fileset.ValidationRenderer
 
errorSection - Static variable in class net.sf.basedb.plugins.AbstractFlatFileImporter
Section definition for grouping error handling options.
errorSection - Static variable in class net.sf.basedb.plugins.util.Parameters
Section definition for grouping error handling options.
errorSection(String, String) - Static method in class net.sf.basedb.plugins.util.Parameters
Create a parameter starting an error section.
escape(String) - Method in class net.sf.basedb.clients.web.plugins.PlainTextTemplate
Replace newlines and tabs with a space.
escape(String) - Method in class net.sf.basedb.clients.web.plugins.XMLTemplate
 
ESCAPE - Variable in class net.sf.basedb.core.migrate.ByteArrayWriter
 
ESCAPE - Variable in class net.sf.basedb.core.migrate.TextWriter
 
estimated - Variable in class net.sf.basedb.clients.jobagent.slotmanager.Slot
 
estimatedExecutionTime - Variable in class net.sf.basedb.core.data.JobData
 
estimatedExecutionTime - Variable in class net.sf.basedb.core.PluginResponse
 
evaluate(Annotatable) - Method in class net.sf.basedb.clients.web.extensions.list.RawDataTypeFilter
 
evaluate(Annotatable) - Method in class net.sf.basedb.clients.web.extensions.list.SubtypeFilter
 
evaluate(Annotatable) - Method in class net.sf.basedb.util.annotations.InheritAnnotationsManager.UsableParentFilter
 
evaluate(EntityQuery) - Method in class net.sf.basedb.core.query.ReturnClassFilter
Returns TRUE if the EntityQuery.getItemType() returns an item type whose Item.getItemClass() is compatible with the specified class.
evaluate(AnnotationSnapshot) - Method in class net.sf.basedb.clients.web.util.ProjectSpecificInfoFilter
Evaluate the annotation snapshot and update the flags if the snapshot is a project-specific annotation and overrides a default value.
evaluate(AnnotationSnapshot) - Method in class net.sf.basedb.core.snapshot.AnnotationFilter
 
evaluate(AnnotationSnapshot) - Method in class net.sf.basedb.core.snapshot.AnnotationLoaderUtil
 
evaluate(AnnotationSnapshot) - Method in class net.sf.basedb.core.snapshot.AnnotationTypeFilter
 
evaluate(AnnotationSnapshot) - Method in class net.sf.basedb.core.snapshot.DisabledInheritanceFilter
 
evaluate(AnnotationSnapshot) - Method in class net.sf.basedb.core.snapshot.ProjectFilter
 
evaluate(AnnotationSnapshot) - Method in class net.sf.basedb.util.annotations.InheritAnnotationsManager.AnnotationTypeFilter
 
evaluate(AnnotationSnapshot) - Method in class net.sf.basedb.util.annotations.InheritSpecification
 
evaluate(ContextUtil.ContextResult) - Method in class net.sf.basedb.util.AutoDetectFileFormat.IsImportableFilter
 
evaluate(ContextUtil.ContextResult) - Method in class net.sf.basedb.util.ContextUtil.IsInContextFilter
 
evaluate(ExtensionsFile) - Method in class net.sf.basedb.clients.web.extensions.IgnoreFilter
 
evaluate(ExtensionsFile) - Method in class net.sf.basedb.clients.web.extensions.InstallFilter
 
evaluate(ExtensionsFile) - Method in class net.sf.basedb.clients.web.extensions.UninstallFilter
 
evaluate(ExtensionsFile) - Method in class net.sf.basedb.util.extensions.manager.filter.DeletedFilter
 
evaluate(ExtensionsFile) - Method in class net.sf.basedb.util.extensions.manager.filter.InstalledFilter
 
evaluate(ExtensionsFile) - Method in class net.sf.basedb.util.extensions.manager.filter.InvalidAndModifiedFilter
 
evaluate(ExtensionsFile) - Method in class net.sf.basedb.util.extensions.manager.filter.ValidAndNewOrModifiedFilter
 
evaluate(ExtensionsFile) - Method in class net.sf.basedb.util.extensions.manager.filter.WasProcessedFilter
 
evaluate(Node) - Method in class net.sf.basedb.util.overview.filter.BasicItemFilter
 
evaluate(Node) - Method in class net.sf.basedb.util.overview.filter.HasAttributeFilter
 
evaluate(Node) - Method in class net.sf.basedb.util.overview.filter.ItemTypeFilter
 
evaluate(Node) - Method in class net.sf.basedb.util.overview.filter.NodeTypeFilter
 
evaluate(HttpResponse) - Method in class net.sf.basedb.util.GeoLocation.ResponseFilter
 
evaluate(Element) - Method in class net.sf.basedb.util.extensions.xml.ExtensionPointFilter
 
evaluate(Element) - Method in class net.sf.basedb.util.extensions.xml.PluginDefinitionFilter
 
evaluate(T) - Method in class net.sf.basedb.util.filter.AllOfFilter
 
evaluate(T) - Method in class net.sf.basedb.util.filter.EqualsFilter
 
evaluate(T) - Method in interface net.sf.basedb.util.filter.Filter
Evaluate if the given object should pass the filter or not.
evaluate(T) - Method in class net.sf.basedb.util.filter.IdentityFilter
 
evaluate(T) - Method in class net.sf.basedb.util.filter.InstanceOfFilter
 
evaluate(T) - Method in class net.sf.basedb.util.filter.InverseFilter
 
evaluate(T) - Method in class net.sf.basedb.util.filter.NoneOfFilter
 
evaluate(T) - Method in class net.sf.basedb.util.filter.NotNullFilter
 
evaluate(T) - Method in class net.sf.basedb.util.filter.OneOfFilter
 
evaluate(T) - Method in class net.sf.basedb.util.filter.StaticFilter
 
evaluateFormula(Cell) - Method in class net.sf.basedb.util.excel.XlsxToCsvUtil.SheetInfo
 
evaluateFormulas - Variable in class net.sf.basedb.util.excel.XlsxToCsvUtil
 
evenodd - Variable in class net.sf.basedb.clients.web.taglib.table.Table
Keep track of which class to use for the next row.
event - Variable in class net.sf.basedb.core.data.BioMaterialEventSourceData
 
event - Variable in class net.sf.basedb.core.data.BioPlateEventParticipantData
 
eventDate - Variable in class net.sf.basedb.core.data.BioMaterialEventData
 
eventDate - Variable in class net.sf.basedb.core.data.BioPlateData
 
eventDate - Variable in class net.sf.basedb.core.data.BioPlateEventData
 
eventDate - Variable in class net.sf.basedb.core.data.PlateEventData
 
EventFilter - Interface in net.sf.basedb.util.extensions.events
A filter for events before they are sent to an EventHandler.
EventHandler - Interface in net.sf.basedb.util.bfs
Event handlers are used for reacting to various parsing events when parsing BFS files.
EventHandler - Interface in net.sf.basedb.util.extensions.events
An event handler receives events about things happening to extensions and extension points.
eventHandlers - Variable in class net.sf.basedb.util.extensions.Registry
 
eventParticipants - Variable in class net.sf.basedb.core.data.BioPlateData
 
events - Variable in class net.sf.basedb.core.data.BioPlateEventTypeData
 
events - Variable in class net.sf.basedb.core.data.MeasuredBioMaterialData
 
events - Variable in class net.sf.basedb.core.data.PlateData
 
eventType - Variable in class net.sf.basedb.core.data.BioMaterialEventData
 
eventType - Variable in class net.sf.basedb.core.data.BioPlateEventData
 
eventType - Variable in class net.sf.basedb.util.extensions.events.ExtensionEventFilter
 
EventType<T> - Class in net.sf.basedb.util.bfs
Defines an event type that is sent in event notifications to event handlers.
EventType - Class in net.sf.basedb.util.extensions.events
Represents different types of event.
EventType(String) - Constructor for class net.sf.basedb.util.bfs.EventType
Create a new event type object.
EventType(String) - Constructor for class net.sf.basedb.util.extensions.events.EventType
Create a new event type.
EventTypeFilter - Class in net.sf.basedb.util.extensions.events
Event filter that only passes on events of a specifiec event type.
EventTypeFilter(EventType) - Constructor for class net.sf.basedb.util.extensions.events.EventTypeFilter
Create a new event type filter.
eventTypes - Variable in class net.sf.basedb.core.data.PlateTypeData
 
EVERYONE - Static variable in class net.sf.basedb.core.Group
The id of the Everyone group where all users are (virtual) members.
EVERYONE - Static variable in class net.sf.basedb.core.Keyring
 
evict(Object) - Method in class net.sf.basedb.core.hibernate.SessionWrapper
 
evictData(Session, BasicData) - Static method in class net.sf.basedb.core.HibernateUtil
Remove a data item from the internal cache of Hibernate.
evictFromSecondLevelCacheIfModified - Variable in class net.sf.basedb.core.AnnotationBatcher
 
EvictPropertyPath(Type) - Constructor for class net.sf.basedb.core.Metadata.EvictPropertyPath
 
exampleDataLines - Variable in class net.sf.basedb.plugins.AnnotationFlatFileImporter
 
ExcelData(XlsxToCsvUtil.SheetInfo, int, int, int, String, String[], boolean, boolean, boolean) - Constructor for class net.sf.basedb.util.parser.FlatFileParser.ExcelData
Create a new data object.
excelFormatter - Variable in class net.sf.basedb.clients.web.plugins.ExportedProperty
 
ExcelFormatter<T,E> - Interface in net.sf.basedb.util.excel
Interface that is intended to be implemented by formatters that also want to support generating output for excel.
excelParsedLinesOffset - Variable in class net.sf.basedb.util.parser.FlatFileParser
The value of the parsedLines when the current Excel sheet is parsed.
excelSheet - Variable in class net.sf.basedb.util.parser.FlatFileParser
Excel sheet that is currently being parsed.
excelSheetName - Variable in class net.sf.basedb.util.parser.FlatFileParser
Name of the Excel sheet to parse if the file is an Excel file.
excelSheetParameter - Static variable in class net.sf.basedb.plugins.AbstractFlatFileImporter
Parameter definition for specifying the name of the sheet to use if the selected file is an Excel file.
ExcelValue<T> - Class in net.sf.basedb.util.excel
Represents a value and style format that should be written to a cell in an excel worksheet.
ExcelValue(T, String) - Constructor for class net.sf.basedb.util.excel.ExcelValue
 
ExcelValue.BlankValue<T> - Class in net.sf.basedb.util.excel
Represents a blank cell.
ExcelValue.BooleanValue - Class in net.sf.basedb.util.excel
Represents a cell with a numeric value.
ExcelValue.DateValue - Class in net.sf.basedb.util.excel
Represents a cell with a date value.
ExcelValue.IntValue - Class in net.sf.basedb.util.excel
Represents a cell with a numeric value without decimals.
ExcelValue.NumericValue - Class in net.sf.basedb.util.excel
Represents a cell with a numeric value.
ExcelValue.StringValue - Class in net.sf.basedb.util.excel
Represents a cell with a string value.
excelWorkbook - Variable in class net.sf.basedb.util.parser.FlatFileParser
Excel workbook that has been loaded.
exception - Variable in class net.sf.basedb.clients.web.fileupload.FileUploadProgress
 
exception - Variable in class net.sf.basedb.core.ItemContext
 
ExceptionCatcher - Class in net.sf.basedb.clients.web.taglib
This tag is a wrapper that catches any errors in it's body and outputs the error message.
ExceptionCatcher() - Constructor for class net.sf.basedb.clients.web.taglib.ExceptionCatcher
 
ExceptionInterruptHandler - Class in net.sf.basedb.core.signal
Interrupt handler implementation that always throw a SignalException.
ExceptionInterruptHandler(String) - Constructor for class net.sf.basedb.core.signal.ExceptionInterruptHandler
 
exclude - Variable in class net.sf.basedb.plugins.LowessNormalization.SpotData
 
exclude(Collection<Include>) - Method in class net.sf.basedb.core.AbstractEntityQuery
 
exclude(Collection<Include>) - Method in interface net.sf.basedb.core.query.EntityQuery
 
exclude(Include...) - Method in class net.sf.basedb.core.AbstractEntityQuery
 
exclude(Include...) - Method in interface net.sf.basedb.core.query.EntityQuery
Specify options for which items to exclude from the result.
excludeDefaultValues - Variable in class net.sf.basedb.core.AnnotationRestriction.Options
 
excludeDefaultValues() - Method in class net.sf.basedb.core.AnnotationRestriction.Options
Should default values (for project-specific annotation types) be excluded from the query or not.
excludeLimit - Variable in class net.sf.basedb.util.IncludeExcludeFilter
 
execDirectory - Variable in class net.sf.basedb.plugins.Base1PluginExecuter
This is the directory where the plugin will generate its output.
execNameParameter - Variable in class net.sf.basedb.plugins.Base1PluginExecuter
The name of the executable.
execPathParameter - Static variable in class net.sf.basedb.plugins.Base1PluginExecuter
The path to where the plug-in executer can find the executables.
executable - Variable in enum class net.sf.basedb.core.Job.Status
 
execute(Connection) - Method in class net.sf.basedb.core.hibernate.DbIndexWork
 
execute(Connection) - Method in class net.sf.basedb.core.hibernate.ExecuteUpdateWork
From the Work interface -----------------------
execute(Connection) - Method in class net.sf.basedb.core.hibernate.GetCurrentCatalogWork
From the Work interface -----------------------
execute(Connection) - Method in class net.sf.basedb.core.hibernate.MultiUpdateWork
From the Work interface -----------------------
execute(Connection) - Method in class net.sf.basedb.core.hibernate.ResultSetWork
From the Work interface -----------------------
execute(Connection) - Method in class net.sf.basedb.core.hibernate.SavePointWork
From the Work interface -----------------------
execute(Connection) - Method in class net.sf.basedb.core.hibernate.SchemaExistsWork
From the Work interface -----------------------
execute(Connection) - Method in class net.sf.basedb.core.hibernate.SchemaGenerator
 
execute(Connection) - Method in class net.sf.basedb.core.hibernate.TableExistsWork
From the Work interface -----------------------
execute(Connection) - Method in class net.sf.basedb.core.hibernate.TableInfoWork
From the Work interface -----------------------
execute(Connection) - Method in class net.sf.basedb.core.MigrateRbaToDba
 
execute(Connection) - Method in class net.sf.basedb.core.Migration
 
execute(ProgressReporter, String) - Method in class net.sf.basedb.core.Job
Start the execution sequence for a job.
execute(ProgressReporter, String, String, JobAgentSettings) - Method in class net.sf.basedb.core.Job
Start the execution sequence for a job.
execute(ProgressReporter, String, JobAgentSettings) - Method in class net.sf.basedb.core.Job
 
EXECUTE_IMMEDIATELY - Enum constant in enum class net.sf.basedb.core.plugin.Response.Status
 
executeCommand - Variable in class net.sf.basedb.core.data.JobData
 
executeJob(SessionControl, Agent, Job, JobAgentSettings, Job.ExecutionTime) - Method in class net.sf.basedb.clients.jobagent.executors.DummyJobExecutor
 
executeJob(SessionControl, Agent, Job, JobAgentSettings, Job.ExecutionTime) - Method in class net.sf.basedb.clients.jobagent.executors.ProcessJobExecutor
 
executeJob(SessionControl, Agent, Job, JobAgentSettings, Job.ExecutionTime) - Method in class net.sf.basedb.clients.jobagent.executors.ThreadJobExecutor
 
executeJob(SessionControl, Agent, Job, JobAgentSettings, Job.ExecutionTime) - Method in interface net.sf.basedb.clients.jobagent.JobExecutor
Execute the specified job.
executeQuery(PreparedStatement, SessionControl) - Static method in class net.sf.basedb.core.QueryExecutor
Execute a query by calling PreparedStatement.executeQuery().
executeUpdate() - Method in class net.sf.basedb.core.hibernate.QueryWrapper
 
executeUpdate(PreparedStatement, SessionControl) - Static method in class net.sf.basedb.core.QueryExecutor
Execute a query by calling PreparedStatement.executeUpdate().
executeUpdate(Query<?>) - Static method in class net.sf.basedb.core.HibernateUtil
Exceute an update or delete query.
ExecuteUpdateWork - Class in net.sf.basedb.core.hibernate
A JDBC work implementation that executes an update/insert/delete query and returns the number of rows that was affected by the query.
ExecuteUpdateWork(SessionControl, String) - Constructor for class net.sf.basedb.core.hibernate.ExecuteUpdateWork
Create a new work item.
EXECUTING - Enum constant in enum class net.sf.basedb.core.Job.Status
The job is executing.
ExecutionTime(int, String, int, int) - Constructor for enum class net.sf.basedb.core.Job.ExecutionTime
 
executor - Variable in class net.sf.basedb.plugins.executor.AbstractIOSupport
 
executorClass - Variable in class net.sf.basedb.clients.jobagent.Agent
 
existed - Variable in class net.sf.basedb.util.JarClassLoader.JarInfo
 
exists() - Method in class net.sf.basedb.core.ClonableProperty
Check if this cloned property still exists.
exists() - Method in class net.sf.basedb.util.extensions.manager.ExtensionsFile
Check if the file exists.
exists(String) - Method in class net.sf.basedb.core.Presets
Check if a preset with the given name exists.
exists(String) - Static method in class net.sf.basedb.util.JarClassLoader
Check if a class loader for the given JAR file exists.
exists(String) - Method in class net.sf.basedb.util.StaticCache
Checks if a cache entry exists or not.
exists(String, boolean, boolean) - Method in class net.sf.basedb.core.ReporterBatcher
Check if a reporter with a given external id exists in the database or has been added to the batch queue of insertion.
exists(String, String, Item, EntityQuery) - Static method in class net.sf.basedb.core.query.AnyToAnyRestriction
Create a restriction that restrict a query to return items that has a linked item with the given link name.
exists(DbControl, BasicItem, String) - Static method in class net.sf.basedb.core.AnyToAny
Check if an item has a link with a given name.
exists(DbControl, Directory, String) - Static method in class net.sf.basedb.core.Directory
Checks if a subdirectory with the specified name exists in a directory.
exists(DbControl, Directory, String) - Static method in class net.sf.basedb.core.File
Checks if a file with the specified name exists in the directory.
exists(Session, Class<?>, int) - Static method in class net.sf.basedb.core.HibernateUtil
Checks if an item with the specified ID exists in the database.
existsInDb - Variable in class net.sf.basedb.core.dbengine.TableInfo
 
existsInDb() - Method in class net.sf.basedb.core.dbengine.TableInfo
Check if the table exists in the database or not.
exp(String) - Method in class net.sf.basedb.core.dbengine.AbstractDbEngine
Return EXP(<value>).
exp(String) - Method in interface net.sf.basedb.core.dbengine.DbEngine
Get the function call that calculates the exponential of a value.
exp(Expression) - Static method in class net.sf.basedb.core.query.Expressions
Calculate the exponential of an expression: new expression = exp(e).
expand(Set<Permission>) - Static method in enum class net.sf.basedb.core.Permission
Expand the given set of permissions to make sure it includes all implicitely granted permissions.
expand(DbControl, Node, boolean) - Method in class net.sf.basedb.util.overview.GenericOverview
Load children of a node.
ExpConverter - Class in net.sf.basedb.util.jep.convert
Convert Exp function to a Query API Expression.
ExpConverter() - Constructor for class net.sf.basedb.util.jep.convert.ExpConverter
 
expectedNumBlocks - Variable in class net.sf.basedb.plugins.PrintMapFlatFileImporter
 
experiment - Variable in class net.sf.basedb.clients.web.ExperimentExplorer
 
experiment - Variable in class net.sf.basedb.core.data.BioAssaySetData
 
experiment - Variable in class net.sf.basedb.core.data.JobData
 
experiment - Variable in class net.sf.basedb.core.data.ReporterListData
 
experiment - Variable in class net.sf.basedb.core.data.RootRawBioAssayData
 
experiment - Variable in class net.sf.basedb.core.data.TransformationData
 
experiment - Variable in class net.sf.basedb.core.data.VirtualDbData
 
experiment - Variable in class net.sf.basedb.core.ReporterCloneBatcher
The experiment this batcher inserts data for.
experiment - Variable in class net.sf.basedb.plugins.IlluminaRawDataImporter
 
Experiment - Class in net.sf.basedb.core
An experiment is the starting point of the analysis in BASE.
Experiment(ExperimentData) - Constructor for class net.sf.basedb.core.Experiment
Creates a new experiment item from the given data.
EXPERIMENT - Enum constant in enum class net.sf.basedb.core.Item
The item is an Experiment
EXPERIMENT - Static variable in class net.sf.basedb.core.QuotaType
The ID for experiments.
ExperimentalFactorLoader - Class in net.sf.basedb.util.overview.loader
Node loader implementation for experimental factors.
ExperimentalFactorLoader() - Constructor for class net.sf.basedb.util.overview.loader.ExperimentalFactorLoader
 
experimentalFactors - Variable in class net.sf.basedb.core.data.ExperimentData
 
ExperimentalFactorValidator - Class in net.sf.basedb.util.overview.validator
Validator implementation for experimental factors.
ExperimentalFactorValidator() - Constructor for class net.sf.basedb.util.overview.validator.ExperimentalFactorValidator
 
ExperimentData - Class in net.sf.basedb.core.data
Holds information about an experiment.
ExperimentData() - Constructor for class net.sf.basedb.core.data.ExperimentData
 
experimentDesign - Variable in class net.sf.basedb.core.data.ExperimentData
 
ExperimentExplorer - Class in net.sf.basedb.clients.web
A class for storing settings and doing work related to the experiment explorer tool in the web interface.
ExperimentExplorer(BioAssaySet) - Constructor for class net.sf.basedb.clients.web.ExperimentExplorer
Create a new experiment explorer.
ExperimentExplorer.AnnotationGroup - Class in net.sf.basedb.clients.web
An annotation group contains statistical information about the spot values falling into the group.
ExperimentExplorer.AnnotationSummary - Class in net.sf.basedb.clients.web
An annotation summary object keeps track of intensities and other statistical information based on the annotation group.
ExperimentExplorer.InExpression - Class in net.sf.basedb.clients.web
Creates a list of (numerical) values that can be used as the right-hand operand to the IN operator.
ExperimentExplorer.ReporterPositions - Class in net.sf.basedb.clients.web
Cache entry for a reporter with positions.
ExperimentExplorerPlotServlet - Class in net.sf.basedb.clients.web.servlet
Plot servlet for generating plots from experiment explorer.
ExperimentExplorerPlotServlet() - Constructor for class net.sf.basedb.clients.web.servlet.ExperimentExplorerPlotServlet
 
ExperimentExplorerPlotServlet.ColumnKey - Class in net.sf.basedb.clients.web.servlet
Uses as a column key in the plots.
ExperimentLoader - Class in net.sf.basedb.util.overview.loader
Node loader implementation for experiments.
ExperimentLoader() - Constructor for class net.sf.basedb.util.overview.loader.ExperimentLoader
 
experimentParameter - Variable in class net.sf.basedb.plugins.IntensityCalculatorPlugin
 
experiments - Variable in class net.sf.basedb.core.data.AnnotationTypeData
 
experiments - Variable in class net.sf.basedb.core.data.RawBioAssayData
 
experimentType - Variable in class net.sf.basedb.core.data.ExperimentData
 
experimentType - Variable in class net.sf.basedb.plugins.IntensityCalculatorPlugin
 
ExperimentValidator - Class in net.sf.basedb.util.overview.validator
Validator implementation for experiments.
ExperimentValidator() - Constructor for class net.sf.basedb.util.overview.validator.ExperimentValidator
 
ExpExpression - Class in net.sf.basedb.core.query
Calculate the exponential of an expression: exp(e).
ExpExpression(Expression) - Constructor for class net.sf.basedb.core.query.ExpExpression
 
expirationDate - Variable in class net.sf.basedb.core.data.KitData
 
expirationDate - Variable in class net.sf.basedb.core.data.UserData
 
expirationDateColumnMapping - Static variable in class net.sf.basedb.plugins.batchimport.KitImporter
Column mapping parameter for the kit expiration date.
expirationDateMapper - Variable in class net.sf.basedb.plugins.batchimport.KitImporter
 
explicitClean() - Method in class net.sf.basedb.core.DbControl.State
Explicit cleanup of the DbControl is happening.
explorer - Variable in class net.sf.basedb.clients.web.ExperimentExplorer.AnnotationSummary
 
exponent - Variable in class net.sf.basedb.core.query.PowerExpression
 
export - Variable in class net.sf.basedb.core.Migration
 
EXPORT - Enum constant in enum class net.sf.basedb.core.plugin.Plugin.MainType
 
exportable - Variable in class net.sf.basedb.clients.web.extensions.list.AbstractListColumnBean
 
exportable - Variable in class net.sf.basedb.clients.web.extensions.list.PropertyPathActionFactory
 
exportable - Variable in class net.sf.basedb.clients.web.taglib.table.ColumnDef
If the column is exportable or not
exportable - Variable in class net.sf.basedb.clients.web.taglib.table.TableColumn
 
ExportableField - Interface in net.sf.basedb.util.export.spotdata
Interface that represents an exportable field.
ExportableFieldConverter - Interface in net.sf.basedb.util.export.spotdata
Defines method for converting a string representation to an exportable assay or dynamic field that can be used with AbstractBioAssaySetExporter implementations.
ExportableFieldFactory - Class in net.sf.basedb.util.export.spotdata
Utility class with factory methods that helps with the creation of exportable fields.
ExportableFieldFactory() - Constructor for class net.sf.basedb.util.export.spotdata.ExportableFieldFactory
 
ExportableFieldFormatter - Class in net.sf.basedb.util.export.spotdata
Formatter implementation that formats an exportable field by returning the column title.
ExportableFieldFormatter() - Constructor for class net.sf.basedb.util.export.spotdata.ExportableFieldFormatter
Create a new formatter.
ExportableFieldFormatter(String) - Constructor for class net.sf.basedb.util.export.spotdata.ExportableFieldFormatter
Create a new formatter.
exportableFields - Variable in class net.sf.basedb.plugins.BaseFileExporterPlugin
 
exportableFields - Variable in class net.sf.basedb.plugins.BfsExporterPlugin
 
exportAll(String, ProgressReporter) - Static method in class net.sf.basedb.core.Migration
Export the current BASE database to data files in the directory on the given path.
exportAssayAnnotations() - Method in class net.sf.basedb.util.export.spotdata.BfsExporter
Export the assay annotations.
exportAssaysSectionData() - Method in class net.sf.basedb.util.export.spotdata.BaseFileExporter
Export data for the 'assays' section that contains information about the bioassays in the source bioassay set.
exportAssaysSectionHeaders() - Method in class net.sf.basedb.util.export.spotdata.BaseFileExporter
Exports headers for the 'assays' section which contains metadata information about the assays in the bioassay set.
exportCompressed - Variable in class net.sf.basedb.core.Migration
 
exportContext - Variable in class net.sf.basedb.clients.web.extensions.list.ListColumnExportRenderer
 
exportData(DbControl, Directory, ProgressReporter) - Method in class net.sf.basedb.plugins.Base1PluginExecuter
Export the bioassay set to a file called 'stdin.txt' in the plugin directory.
exportedPositions - Variable in class net.sf.basedb.util.export.spotdata.BfsExporter
 
ExportedProperty - Class in net.sf.basedb.clients.web.plugins
 
ExportedProperty(String, String, Metadata.PropertyPath, AnnotationType, boolean, Unit, Formatter, ExcelFormatter, DataLoader) - Constructor for class net.sf.basedb.clients.web.plugins.ExportedProperty
 
exporter - Variable in class net.sf.basedb.plugins.executor.ExternalProgramExecutor
 
exportFormatter - Variable in class net.sf.basedb.clients.web.extensions.list.AbstractListColumnBean
 
exportFormatterClass - Variable in class net.sf.basedb.clients.web.extensions.list.PropertyPathActionFactory
 
exportGal(DbControl, ArrayDesign, Integer, PrintWriter, ProgressReporter) - Method in class net.sf.basedb.plugins.GalExporter
Exports an array design with features to a GAL file.
exportGlobalFooter() - Method in class net.sf.basedb.util.export.spotdata.AbstractBioAssaySetExporter
Export global footer or other data that only appears once in the end of the exported file.
exportGlobalFooter() - Method in class net.sf.basedb.util.export.spotdata.BfsExporter
Exports reporter annotations.
exportGlobalHeader() - Method in class net.sf.basedb.util.export.spotdata.AbstractBioAssaySetExporter
Export global headers or other data that only appear once in the beginning of the exported file.
exportGlobalHeader() - Method in class net.sf.basedb.util.export.spotdata.BaseFileExporter
Export 'settings' and 'assays' sections.
exportGlobalHeader() - Method in class net.sf.basedb.util.export.spotdata.BfsExporter
Export the metadata and assay annotations.
exportMetadata() - Method in class net.sf.basedb.util.export.spotdata.BfsExporter
Export the metadata file which contains information about the other files (reporter annotations, assay annotations and spot data), plug-in parameters, etc.
ExportOutputStream - Class in net.sf.basedb.core.plugin
An output stream used for immediate download from export plugins.
ExportOutputStream(OutputStream) - Constructor for class net.sf.basedb.core.plugin.ExportOutputStream
Create a new export stream.
exportPath - Variable in class net.sf.basedb.clients.web.extensions.list.PropertyPathActionFactory.PropertyPathAction
 
exportProperties(DbControl, ExportOutputStream, String, String, List<ExportedProperty>, Item, Query, ProgressReporter) - Method in class net.sf.basedb.clients.web.plugins.SimpleExport
Exports properties from a query to an output stream.
exportProperty - Variable in class net.sf.basedb.clients.web.extensions.list.AbstractListColumnBean
 
exportProperty - Variable in class net.sf.basedb.clients.web.extensions.list.PropertyPathActionFactory
 
exportProperty - Variable in class net.sf.basedb.clients.web.taglib.table.ColumnDef
Optional property used for exporting.
exportReporterAnnotations(ProgressReporter, long) - Method in class net.sf.basedb.util.export.spotdata.BfsExporter
Export the reporter annotations.
exportSectionData() - Method in class net.sf.basedb.util.export.spotdata.AbstractBioAssaySetExporter
Export section data.
exportSectionData() - Method in class net.sf.basedb.util.export.spotdata.BfsExporter
Export all spot data.
exportSectionData() - Method in class net.sf.basedb.util.export.spotdata.MatrixBaseFileExporter
Exports data for all bioassays in a single 'spots' section.
exportSectionData() - Method in class net.sf.basedb.util.export.spotdata.SerialBaseFileExporter
Exports data for the current bioassay in a 'spots' section.
exportSectionFooter() - Method in class net.sf.basedb.util.export.spotdata.AbstractBioAssaySetExporter
End the section by exporting a footer.
exportSectionFooter() - Method in class net.sf.basedb.util.export.spotdata.MatrixBaseFileExporter
Ends the 'spots' section.
exportSectionFooter() - Method in class net.sf.basedb.util.export.spotdata.SerialBaseFileExporter
Ends the current 'spots' section.
exportSectionHeader() - Method in class net.sf.basedb.util.export.spotdata.AbstractBioAssaySetExporter
Start a new section in the export by exporting section headers.
exportSectionHeader() - Method in class net.sf.basedb.util.export.spotdata.MatrixBaseFileExporter
Exports headers for a single 'spots' section.
exportSectionHeader() - Method in class net.sf.basedb.util.export.spotdata.SerialBaseFileExporter
Exports headers for a 'spots' section, and make preparations for the current data section (one section per bioassay).
exportSettingsSection() - Method in class net.sf.basedb.util.export.spotdata.BaseFileExporter
Export the settings section which contains all parameter values registered with BaseFileExporter.setParameter(String, String).
exportSpotData(ProgressReporter, long) - Method in class net.sf.basedb.util.export.spotdata.BfsExporter
Export spot data.
exportSpotSectionData(List<BioAssay>, DynamicSpotQuery, ProgressReporter, long) - Method in class net.sf.basedb.util.export.spotdata.BaseFileExporter
Export the spot data of a 'spot' section.
exportSpotSectionHeaders(List<BioAssay>, long) - Method in class net.sf.basedb.util.export.spotdata.BaseFileExporter
Start a new 'spot' section and export the standard headers: 'channels, 'assays', 'columns', 'assayFields' and 'count'.
exportStream - Variable in class net.sf.basedb.clients.web.plugins.PlainTextTemplate
 
exportStream - Variable in class net.sf.basedb.clients.web.plugins.XMLTemplate
 
ExportTemplate - Interface in net.sf.basedb.clients.web.plugins
A helper interface for the SimpleExport class to make it easier to output exported data in different formats.
exportTitle - Variable in class net.sf.basedb.clients.web.extensions.list.AbstractListColumnBean
 
exportTitle - Variable in class net.sf.basedb.clients.web.taglib.table.ColumnDef
Alternate title to use when exporting.
expression - Variable in class net.sf.basedb.clients.web.extensions.list.RelatedItemColumn.Specification
 
expression - Variable in class net.sf.basedb.core.query.AscOrder
 
expression - Variable in class net.sf.basedb.core.query.DescOrder
 
expression - Variable in class net.sf.basedb.core.query.HqlExpression
The restriction or expression as a string.
expression - Variable in class net.sf.basedb.core.query.VirtualColumnExpression.WrappedExpression
 
expression - Variable in class net.sf.basedb.util.export.spotdata.SimpleDynamicField
 
expression - Variable in class net.sf.basedb.util.parser.JepMapper
 
expression(String, String) - Static method in class net.sf.basedb.core.query.Hql
 
expression(String, AnnotationType) - Static method in class net.sf.basedb.core.query.Annotations
Create an expression representing the value of an annotation to a joined item of the query.
expression(AnnotationType) - Static method in class net.sf.basedb.core.query.Annotations
Create an expression representing the value of an annotation to the root item of the query.
expression(Expression, String) - Static method in class net.sf.basedb.core.query.Selects
Same as expression(e1, alias, false).
expression(Expression, String, boolean) - Static method in class net.sf.basedb.core.query.Selects
Create a selection from an expression, optionally giving it an alias.
Expression - Interface in net.sf.basedb.core.query
An expression query element.
expressionOperator - Variable in enum class net.sf.basedb.core.Operator
 
expressionParameter - Static variable in class net.sf.basedb.plugins.JepExtraValueCalculator
 
expressions - Variable in class net.sf.basedb.core.IntensityFormula
 
Expressions - Class in net.sf.basedb.core.query
A factory class to create expressions.
Expressions() - Constructor for class net.sf.basedb.core.query.Expressions
 
ExpressionSelect - Class in net.sf.basedb.core.query
A selection query element that selects an expression, optionally giving it an alias.
ExpressionSelect(Expression, String, boolean) - Constructor for class net.sf.basedb.core.query.ExpressionSelect
 
ExtendableData - Interface in net.sf.basedb.core.data
This class is inherited by data classes that supports per-server additions of columns to the underlying database table.
extended - Variable in class net.sf.basedb.core.authentication.ExtraUserInformation
 
ExtendedAbout - Interface in net.sf.basedb.util.extensions
Adds extra information to the About interface.
ExtendedDynamicField(String, boolean, DynamicField) - Constructor for class net.sf.basedb.plugins.BaseFileExporterPlugin.ExtendedDynamicField
 
ExtendedDynamicField(String, String, boolean, DynamicField) - Constructor for class net.sf.basedb.plugins.BaseFileExporterPlugin.ExtendedDynamicField
 
ExtendedExportableField(String, boolean, ExportableField) - Constructor for class net.sf.basedb.plugins.BfsExporterPlugin.ExtendedExportableField
 
ExtendedExportableField(String, String, boolean, ExportableField) - Constructor for class net.sf.basedb.plugins.BfsExporterPlugin.ExtendedExportableField
 
extendedMappers - Variable in class net.sf.basedb.plugins.RawDataFlatFileImporter
 
extendedMappers - Variable in class net.sf.basedb.plugins.ReporterFlatFileImporter
 
extendedProperties - Variable in class net.sf.basedb.core.data.RawData
 
extendedProperties - Variable in class net.sf.basedb.core.data.ReporterData
 
extendedProperties - Variable in class net.sf.basedb.core.data.UserData
 
extendedProperties - Variable in class net.sf.basedb.core.ReporterBatcher
The extended properties for reporters
ExtendedProperties - Class in net.sf.basedb.core
This class is used for reading XML files with information about extended properties.
ExtendedProperties() - Constructor for class net.sf.basedb.core.ExtendedProperties
 
extendedPropertiesFile - Static variable in class net.sf.basedb.core.Application
The path to the file containing extended properties.
extendedProperty - Variable in class net.sf.basedb.core.data.ReporterClonePropertyData
 
ExtendedProperty - Class in net.sf.basedb.core
Holds information about an extended property for a class.
ExtendedProperty(String, String, String, String, Type, int, boolean, boolean, boolean, boolean, boolean, Formula.AverageMethod, List<ExtendedPropertyLinker>) - Constructor for class net.sf.basedb.core.ExtendedProperty
Create a new extended property.
ExtendedPropertyAccessor - Class in net.sf.basedb.core
This class is used to interface with Hibernate for extended properties.
ExtendedPropertyAccessor() - Constructor for class net.sf.basedb.core.ExtendedPropertyAccessor
Create a new ExtendedPropertyAccessor object.
ExtendedPropertyAccessor.GetterSetter - Class in net.sf.basedb.core
This class implements the Hibernate Getter and Setter interfaces.
ExtendedPropertyFormatter<T> - Class in net.sf.basedb.clients.web.formatter
Formatter for extended property values.
ExtendedPropertyFormatter(ExtendedProperty, Formatter<T>) - Constructor for class net.sf.basedb.clients.web.formatter.ExtendedPropertyFormatter
Create an extended property formatter.
ExtendedPropertyLinker - Class in net.sf.basedb.core
Used to create links from extended property values.
ExtendedPropertyLinker(String, String) - Constructor for class net.sf.basedb.core.ExtendedPropertyLinker
 
extension - Variable in class net.sf.basedb.core.data.DataFileTypeData
 
extension - Variable in class net.sf.basedb.core.data.MimeTypeData
 
extension - Variable in class net.sf.basedb.util.extensions.ExtensionContext
 
Extension<A extends Action> - Interface in net.sf.basedb.util.extensions
Represents a concrete implementation of an extension to an extension point.
EXTENSION_COMPARATOR - Static variable in class net.sf.basedb.util.extensions.Registry
Comparator that sort extensions according to their names.
EXTENSION_ID_COMPARATOR - Static variable in class net.sf.basedb.util.extensions.Registry
Comparator that sort extensions according to their ids.
EXTENSION_KEY - Static variable in class net.sf.basedb.clients.web.extensions.JspContext
The key that is used when storing an Extension object in a request/page/session/etc. attribute.
EXTENSION_POINT_ID - Static variable in class net.sf.basedb.clients.web.extensions.service.Services
 
EXTENSION_POINT_ID - Static variable in class net.sf.basedb.util.uri.ConnectionManagerUtil
The ID of the connection manager extension point.
ExtensionBean<A extends Action> - Class in net.sf.basedb.util.extensions
A bean-like implementation of the Extension interface.
ExtensionBean() - Constructor for class net.sf.basedb.util.extensions.ExtensionBean
Create a new empty extension bean.
ExtensionBean(String, String, float, About, ActionFactory<? extends A>, RendererFactory<? super A>) - Constructor for class net.sf.basedb.util.extensions.ExtensionBean
Create a new fully initialised extension bean.
ExtensionCells - Class in net.sf.basedb.clients.web.taglib.table
Tag for generating content from extension columns.
ExtensionCells() - Constructor for class net.sf.basedb.clients.web.taglib.table.ExtensionCells
 
ExtensionChildNodeLoader<I> - Class in net.sf.basedb.util.overview.loader
Wrapper for node loaders that automatically hooks into the extension system when loading child nodes for a parent node.
ExtensionChildNodeLoader(NodeLoader<I>) - Constructor for class net.sf.basedb.util.overview.loader.ExtensionChildNodeLoader
Wrap the given parent node loader.
extensionColumns - Variable in class net.sf.basedb.clients.web.taglib.table.ExtensionCells
 
extensionColumns - Variable in class net.sf.basedb.clients.web.taglib.table.Table
 
ExtensionContext<A extends Action> - Class in net.sf.basedb.util.extensions
Invokation context for an extension.
ExtensionContext(ExtensionPointContext<A>, Registry.RegisteredExtension<A>) - Constructor for class net.sf.basedb.util.extensions.ExtensionContext
 
ExtensionEventFilter - Class in net.sf.basedb.util.extensions.events
Event filter that only passes events for a specific extension.
ExtensionEventFilter(String, EventType) - Constructor for class net.sf.basedb.util.extensions.events.ExtensionEventFilter
Create a new extension event filter.
ExtensionEventFilter(Extension<?>, EventType) - Constructor for class net.sf.basedb.util.extensions.events.ExtensionEventFilter
Create a new extension event filter.
extensionId - Variable in class net.sf.basedb.clients.web.extensions.list.RelatedItemColumn.Specification
 
extensionId - Variable in class net.sf.basedb.clients.web.extensions.service.DummyService
 
extensionId - Variable in class net.sf.basedb.clients.web.taglib.extensions.Scripts
 
extensionId - Variable in class net.sf.basedb.clients.web.taglib.extensions.Stylesheets
 
extensionId - Variable in class net.sf.basedb.util.extensions.logging.ExtensionsLog
 
extensionIsRegistered(String) - Method in class net.sf.basedb.util.extensions.Registry
Checks if an extension is registered or not.
ExtensionKey - Class in net.sf.basedb.util.extensions.manager
Key implementation used to identify extensions.
ExtensionKey(String) - Constructor for class net.sf.basedb.util.extensions.manager.ExtensionKey
Create a new key for an extension with the given id.
ExtensionKey(Extension<?>) - Constructor for class net.sf.basedb.util.extensions.manager.ExtensionKey
Create a new key for an extension.
ExtensionNodeValidator<I> - Class in net.sf.basedb.util.overview.validator
Wrapper for node validators that hooks into the extension system when validating nodes.
ExtensionNodeValidator(NodeValidator<I>, Object) - Constructor for class net.sf.basedb.util.overview.validator.ExtensionNodeValidator
Wrap the given parent node validator.
extensionPoint - Variable in class net.sf.basedb.util.extensions.ExtensionBean
 
extensionPoint - Variable in class net.sf.basedb.util.extensions.ExtensionPointContext
 
extensionPoint - Variable in class net.sf.basedb.util.extensions.Registry.RegisteredExtension
 
ExtensionPoint<A extends Action> - Interface in net.sf.basedb.util.extensions
An extension point is a place, defined by a client application, that can be extended.
EXTENSIONPOINT_COMPARATOR - Static variable in class net.sf.basedb.util.extensions.Registry
Comparator that sort extension points according to their names.
EXTENSIONPOINT_ID_COMPARATOR - Static variable in class net.sf.basedb.util.extensions.Registry
Comparator that sort extensions according to their ids.
ExtensionPointBean<A extends Action> - Class in net.sf.basedb.util.extensions
A bean-like implementation of the ExtensionPoint interface.
ExtensionPointBean() - Constructor for class net.sf.basedb.util.extensions.ExtensionPointBean
Create a new empty extension point bean.
ExtensionPointBean(String, String, String, Class<A>, RendererFactory<A>, boolean) - Constructor for class net.sf.basedb.util.extensions.ExtensionPointBean
Create a new fully initialised extension point bean.
ExtensionPointContext<A extends Action> - Class in net.sf.basedb.util.extensions
Invokation context for an extension point.
ExtensionPointContext(Registry, ClientContext, Registry.RegisteredExtensionPoint<A>, ErrorHandlerFactory<? super A>) - Constructor for class net.sf.basedb.util.extensions.ExtensionPointContext
 
ExtensionPointEventFilter - Class in net.sf.basedb.util.extensions.events
Event filter that only passes events for a specific extension point.
ExtensionPointEventFilter(String) - Constructor for class net.sf.basedb.util.extensions.events.ExtensionPointEventFilter
Create a new extension point event filter
ExtensionPointEventFilter(ExtensionPoint<?>) - Constructor for class net.sf.basedb.util.extensions.events.ExtensionPointEventFilter
Create a new extension point event filter.
ExtensionPointFilter - Class in net.sf.basedb.util.extensions.xml
Filter implementation that can be used to match extension points and extensions based on the ID of the extension point.
ExtensionPointFilter(String) - Constructor for class net.sf.basedb.util.extensions.xml.ExtensionPointFilter
Create a new filter based on the given pattern.
ExtensionPointFilter(Pattern) - Constructor for class net.sf.basedb.util.extensions.xml.ExtensionPointFilter
Create a new filter based on the given pattern.
extensionPointId - Variable in class net.sf.basedb.core.signal.ExtensionSignalTransporter
 
extensionPointIsRegistered(String) - Method in class net.sf.basedb.util.extensions.Registry
Checks if an extension point is registered or not.
ExtensionPointKey - Class in net.sf.basedb.util.extensions.manager
Key implementation used to identify extension points.
ExtensionPointKey(String) - Constructor for class net.sf.basedb.util.extensions.manager.ExtensionPointKey
Create a new key for an extension point with the given id.
ExtensionPointKey(ExtensionPoint<?>) - Constructor for class net.sf.basedb.util.extensions.manager.ExtensionPointKey
Create a new key for an extension point.
extensionPoints - Variable in class net.sf.basedb.util.extensions.manager.processor.RegisterExtensionsProcessor.FileData
 
extensionPoints - Variable in class net.sf.basedb.util.extensions.Registry
 
extensionPoints - Variable in class net.sf.basedb.util.extensions.xml.XmlLoader
 
extensions - Variable in class net.sf.basedb.clients.web.taglib.extensions.Render
 
extensions - Variable in class net.sf.basedb.clients.web.taglib.tab.TabControl
 
extensions - Variable in class net.sf.basedb.clients.web.taglib.table.ColumnDef
 
extensions - Static variable in class net.sf.basedb.plugins.Bzip2FileUnpacker
 
extensions - Static variable in class net.sf.basedb.plugins.GzipFileUnpacker
 
extensions - Static variable in class net.sf.basedb.plugins.TarFileUnpacker
 
extensions - Static variable in class net.sf.basedb.plugins.ZipFileUnpacker
 
extensions - Variable in class net.sf.basedb.util.extensions.manager.processor.RegisterExtensionsProcessor.FileData
 
extensions - Variable in class net.sf.basedb.util.extensions.Registry
 
extensions - Variable in class net.sf.basedb.util.extensions.Registry.RegisteredExtensionPoint
 
extensions - Variable in class net.sf.basedb.util.extensions.xml.XmlLoader
 
ExtensionsControl - Class in net.sf.basedb.clients.web.extensions
Controller class for the extension system in the web client.
ExtensionsControl(DbControl, Set<Permission>) - Constructor for class net.sf.basedb.clients.web.extensions.ExtensionsControl
 
ExtensionsFile - Class in net.sf.basedb.util.extensions.manager
Represents a file with extensions in it.
ExtensionsFile(ExtensionsManager, File) - Constructor for class net.sf.basedb.util.extensions.manager.ExtensionsFile
Create a new extensions file backed by a real file on the file system.
ExtensionsFile(ExtensionsManager, File, boolean) - Constructor for class net.sf.basedb.util.extensions.manager.ExtensionsFile
Create a new extensions file backed by a real file on the file system.
ExtensionsFile(ExtensionsManager, File, URI, String, boolean) - Constructor for class net.sf.basedb.util.extensions.manager.ExtensionsFile
 
ExtensionsFile(ExtensionsManager, URI) - Constructor for class net.sf.basedb.util.extensions.manager.ExtensionsFile
Create a new extension file backed by an URI.
ExtensionsFile.WriteableExtensionsFile - Class in net.sf.basedb.util.extensions.manager
An extensions file with additional methods that allows adding or modifying information in the underlying extensions file.
ExtensionsFileProcessor - Interface in net.sf.basedb.util.extensions.manager
Interface that is used to request a callback for each extensions file managed by an extensions manager.
ExtensionsFilter - Interface in net.sf.basedb.util.extensions
Allows extensions and extension points to be enabled/disabled and sorted externally.
ExtensionSignalTransporter - Class in net.sf.basedb.core.signal
A signal transporter implementation send all signals to extensions extending the "net.sf.basedb.core.signal" extension point.
ExtensionSignalTransporter() - Constructor for class net.sf.basedb.core.signal.ExtensionSignalTransporter
 
ExtensionSignalTransporter.SendSignalRenderer - Class in net.sf.basedb.core.signal
 
ExtensionsInvoker<A extends Action> - Class in net.sf.basedb.util.extensions
Object of this class handles a single invokation of the extensions for one or several extension points.
ExtensionsInvoker(ClientContext, Collection<ExtensionContext<A>>) - Constructor for class net.sf.basedb.util.extensions.ExtensionsInvoker
Creates a new invoker object.
extensionsJar - Variable in class net.sf.basedb.clients.web.extensions.XJspCompiler
 
ExtensionsLog - Class in net.sf.basedb.util.extensions.logging
Instances hold the log entries for a single extension.
ExtensionsLog(String) - Constructor for class net.sf.basedb.util.extensions.logging.ExtensionsLog
 
ExtensionsLogger - Class in net.sf.basedb.util.extensions.logging
A simple logger that services can use to send log message to the BASE core.
ExtensionsLogger(ExtensionsLog) - Constructor for class net.sf.basedb.util.extensions.logging.ExtensionsLogger
 
ExtensionsLogger(ExtensionsLog, Logger) - Constructor for class net.sf.basedb.util.extensions.logging.ExtensionsLogger
 
ExtensionsManager - Class in net.sf.basedb.util.extensions.manager
An extensions manager is responsible for handling a group of extensions in the form of files stored in the file system.
ExtensionsManager(Registry, File) - Constructor for class net.sf.basedb.util.extensions.manager.ExtensionsManager
Create a new extensions manager and use the given registry to store extensions.
ExtensionsManager.JarFirstURIComparator - Class in net.sf.basedb.util.extensions.manager
Compare URI:s so that 'jar:' scheme always are listed first.
ExtensionsServlet - Class in net.sf.basedb.clients.web.servlet
This servlet is acting as a proxy for requests to extension defined servlets.
ExtensionsServlet() - Constructor for class net.sf.basedb.clients.web.servlet.ExtensionsServlet
 
ExtensionsUtil - Class in net.sf.basedb.util.extensions
Utility class collecting some useful functions related to extensions.
ExtensionsUtil() - Constructor for class net.sf.basedb.util.extensions.ExtensionsUtil
 
EXTERNAL - Enum constant in enum class net.sf.basedb.core.Location
The item is stored externally.
EXTERNAL - Static variable in class net.sf.basedb.core.authentication.AuthenticationMethod
This is a generic external authentication method.
EXTERNAL_ID - Static variable in class net.sf.basedb.core.ClonableProperty
The property name of the "static" property ReporterData.getExternalId().
EXTERNAL_ID - Static variable in class net.sf.basedb.plugins.batchimport.PropertyIdMethod
Use the external ID for finding items.
externalId - Variable in class net.sf.basedb.clients.jobagent.Agent
 
externalId - Variable in class net.sf.basedb.core.authentication.AuthenticatedUser
 
externalId - Variable in class net.sf.basedb.core.data.AnnotationTypeData
 
externalId - Variable in class net.sf.basedb.core.data.BioMaterialData
 
externalId - Variable in class net.sf.basedb.core.data.BioPlateData
 
externalId - Variable in class net.sf.basedb.core.data.ClientData
 
externalId - Variable in class net.sf.basedb.core.data.DataFileTypeData
 
externalId - Variable in class net.sf.basedb.core.data.ExtraValueTypeData
 
externalId - Variable in class net.sf.basedb.core.data.FeatureData
 
externalId - Variable in class net.sf.basedb.core.data.HelpData
 
externalId - Variable in class net.sf.basedb.core.data.ItemListData
 
externalId - Variable in class net.sf.basedb.core.data.JobAgentData
 
externalId - Variable in class net.sf.basedb.core.data.JobData
 
externalId - Variable in class net.sf.basedb.core.data.PlatformData
 
externalId - Variable in class net.sf.basedb.core.data.PlatformVariantData
 
externalId - Variable in class net.sf.basedb.core.data.ProtocolData
 
externalId - Variable in class net.sf.basedb.core.data.ReporterData
 
externalId - Variable in class net.sf.basedb.core.data.ReporterListData
 
externalId - Variable in class net.sf.basedb.core.data.UserData
 
externalId - Variable in class net.sf.basedb.core.RawDataBatcher.ReporterProxy
 
externalId - Variable in class net.sf.basedb.core.SessionControl.ClientInfo
 
externalIdColumnMapping - Static variable in class net.sf.basedb.plugins.AnnotationFlatFileImporter
 
externalIdColumnMapping - Static variable in class net.sf.basedb.plugins.batchimport.AbstractItemImporter
 
externalIdIsUsed(DbControl, String) - Static method in class net.sf.basedb.core.User
Check if an external ID already exists in the database
externalIdMapper - Variable in class net.sf.basedb.plugins.batchimport.AnnotationTypeImporter
 
externalIdMapper - Variable in class net.sf.basedb.plugins.batchimport.BioSourceImporter
 
externalIdMapper - Variable in class net.sf.basedb.plugins.batchimport.ExtractImporter
 
externalIdMapper - Variable in class net.sf.basedb.plugins.batchimport.SampleImporter
 
externalIndex - Variable in class net.sf.basedb.util.importer.spotdata.PositionEventHandler
 
ExternalProgramExecutor - Class in net.sf.basedb.plugins.executor
 
ExternalProgramExecutor() - Constructor for class net.sf.basedb.plugins.executor.ExternalProgramExecutor
 
ExternalProgramExecutor.RequestWrapper - Class in net.sf.basedb.plugins.executor
 
ExternalProgramExecutor.ResponseWrapper - Class in net.sf.basedb.plugins.executor
 
externalReporterId - Variable in class net.sf.basedb.core.RawDataBatcher.FeatureInfo
 
externalWorkbook - Variable in class net.sf.basedb.util.excel.XlsxTableWriter
 
EXTRA - Static variable in class net.sf.basedb.core.VirtualColumn
This column stores the data cube extra value number.
EXTRA_FLOAT - Static variable in class net.sf.basedb.core.VirtualColumn
This column stores extra float values.
EXTRA_INT - Static variable in class net.sf.basedb.core.VirtualColumn
This column stores extra integer values.
EXTRA_STRING - Static variable in class net.sf.basedb.core.VirtualColumn
This column stores extra string values.
EXTRA_VALUE_INNER - Static variable in class net.sf.basedb.core.DynamicPositionQueryJoiners
This instance joins extra values with an inner join.
EXTRA_VALUE_INNER - Static variable in class net.sf.basedb.core.DynamicSpotQueryJoiners
This instance joins extra values with an inner join.
EXTRA_VALUE_LEFT - Static variable in class net.sf.basedb.core.DynamicPositionQueryJoiners
This instance joins extra values with a left join.
EXTRA_VALUE_LEFT - Static variable in class net.sf.basedb.core.DynamicSpotQueryJoiners
This instance joins extra values with a left join.
extract - Variable in class net.sf.basedb.core.data.DerivedBioAssayData
 
extract - Variable in class net.sf.basedb.core.data.RawBioAssayData
 
extract - Variable in class net.sf.basedb.util.AnnotationUtil.AnnotatableWrapper
 
Extract - Class in net.sf.basedb.core
This class is used to represent extract items.
Extract(ExtractData) - Constructor for class net.sf.basedb.core.Extract
 
EXTRACT - Enum constant in enum class net.sf.basedb.core.Item
The item is an Extract.
EXTRACT - Static variable in class net.sf.basedb.util.overview.NodeAttribute
Store a reference to an extract on a node.
EXTRACT_PATH - Static variable in class net.sf.basedb.util.overview.NodeAttribute
Store the ID values of extracts that should be followed on upstream paths as long as the current extract is not among one of the given parent extracts.
extractAndCreateRawBioAssays(DbControl, List<String>, boolean, File) - Method in class net.sf.basedb.plugins.IlluminaRawDataImporter
Extract array names and raw data property names from the column headers.
extractColumnMapping - Static variable in class net.sf.basedb.plugins.batchimport.DerivedBioAssayImporter
 
extractColumnMapping - Static variable in class net.sf.basedb.plugins.batchimport.RawBioAssayImporter
 
ExtractData - Class in net.sf.basedb.core.data
This represents an extract.
ExtractData() - Constructor for class net.sf.basedb.core.data.ExtractData
 
extractHasBeenSet - Variable in class net.sf.basedb.core.DerivedBioAssay
 
extractId - Variable in class net.sf.basedb.core.MigrateRbaToDba.Rba
 
ExtractImporter - Class in net.sf.basedb.plugins.batchimport
Plug-in for importing extract items in a batch.
ExtractImporter() - Constructor for class net.sf.basedb.plugins.batchimport.ExtractImporter
 
EXTRACTION - Static variable in class net.sf.basedb.core.Kit
The ID for the extraction kit type, for example a kit used when creating an Extract from a Sample.
EXTRACTION - Static variable in class net.sf.basedb.core.Protocol
The ID for the extraction protocol type, for example a protocol used when creating an Extract from a Sample.
ExtractLoader - Class in net.sf.basedb.util.overview.loader
Node loader implementation for extracts.
ExtractLoader() - Constructor for class net.sf.basedb.util.overview.loader.ExtractLoader
 
extractMapper - Variable in class net.sf.basedb.plugins.batchimport.DerivedBioAssayImporter
 
extractMapper - Variable in class net.sf.basedb.plugins.batchimport.RawBioAssayImporter
 
ExtractNameGenerator - Class in net.sf.basedb.util.overview.node
Name generator implementation for Extract items.
ExtractNameGenerator(String, String) - Constructor for class net.sf.basedb.util.overview.node.ExtractNameGenerator
Create a new name generator.
extractPositionColumnMapping - Static variable in class net.sf.basedb.plugins.batchimport.PhysicalBioAssayImporter
 
extractPositionMapper - Variable in class net.sf.basedb.plugins.batchimport.PhysicalBioAssayImporter
 
extractQuery - Variable in class net.sf.basedb.plugins.batchimport.AbstractItemImporter
 
ExtractResourcesProcessor - Class in net.sf.basedb.util.extensions.manager.processor
A file processor implementation that extracts resources from JAR files.
ExtractResourcesProcessor(File, Pattern, String, ProcessResults) - Constructor for class net.sf.basedb.util.extensions.manager.processor.ExtractResourcesProcessor
Create a new processor.
ExtractResourcesProcessor(File, ProcessResults) - Constructor for class net.sf.basedb.util.extensions.manager.processor.ExtractResourcesProcessor
Create a new processor.
extractsInChain - Variable in class net.sf.basedb.util.AnnotationUtil.AnnotatableWrapper
 
ExtractToChildExtractTransformer - Class in net.sf.basedb.util.listable
Source item transformer implementation that transform extract items to their child extract items.
ExtractToChildExtractTransformer(boolean) - Constructor for class net.sf.basedb.util.listable.ExtractToChildExtractTransformer
Create a new extract to child extract transformer.
ExtractToChildExtractTransformer(boolean, boolean) - Constructor for class net.sf.basedb.util.listable.ExtractToChildExtractTransformer
Create a new extract to child extract transformer that only load children has a subtype with "push annotations" set.
ExtractToParentExtractTransformer - Class in net.sf.basedb.util.listable
Source item transformer implementation that transform extract items to their parent extract items.
ExtractToParentExtractTransformer(boolean) - Constructor for class net.sf.basedb.util.listable.ExtractToParentExtractTransformer
Create a new extract to parent extract transformer.
ExtractToParentExtractTransformer(boolean, boolean) - Constructor for class net.sf.basedb.util.listable.ExtractToParentExtractTransformer
Create a new extract to parent extract transformer that only load parents to extracts that has a subtype with "push annotations" set.
ExtractToParentExtractTransformer(boolean, CollectExtracts) - Constructor for class net.sf.basedb.util.listable.ExtractToParentExtractTransformer
Create a new extract to parent extract transformer that is considering extracts collected on downstream derived and raw bioassays.
ExtractToPhysicalBioAssayTransformer - Class in net.sf.basedb.util.listable
Source item transformer implementation that transform extract items to physical bioassays.
ExtractToPhysicalBioAssayTransformer() - Constructor for class net.sf.basedb.util.listable.ExtractToPhysicalBioAssayTransformer
Create a new extract to physical bioassay transformer.
ExtractToSampleTransformer - Class in net.sf.basedb.util.listable
Source item transformer that transform extract items to their parent samples.
ExtractToSampleTransformer() - Constructor for class net.sf.basedb.util.listable.ExtractToSampleTransformer
 
ExtractToSampleTransformer(boolean) - Constructor for class net.sf.basedb.util.listable.ExtractToSampleTransformer
Create a new extract to sample transformer that only load parent samples to extracts that has a subtype with "push annotations" set.
ExtractValidator - Class in net.sf.basedb.util.overview.validator
Validator implementation for extracts.
ExtractValidator() - Constructor for class net.sf.basedb.util.overview.validator.ExtractValidator
 
ExtractValidator.TagPosition - Class in net.sf.basedb.util.overview.validator
 
extraField - Variable in class net.sf.basedb.clients.web.extensions.login.LoginFormBean
 
extraFileImporter - Variable in class net.sf.basedb.util.importer.spotdata.BfsImporter
 
ExtraFileImporter - Interface in net.sf.basedb.util.bfs
Implementors are responsible for importing extra files specified in the BFS metadata file into the BASE file system.
extraFiles - Variable in class net.sf.basedb.util.export.spotdata.BfsExporter
 
extraFilter - Variable in class net.sf.basedb.core.snapshot.AnnotationLoaderUtil
 
ExtraFloatParser - Class in net.sf.basedb.util.importer.spotdata
Parser that is responsible for extracting extra float values from the 'spot' section in a BASEfile.
ExtraFloatParser(String, int) - Constructor for class net.sf.basedb.util.importer.spotdata.ExtraFloatParser
Creates a new extra value parser.
extraFloats - Variable in class net.sf.basedb.util.importer.spotdata.BaseFileInfo
 
extraFloats - Variable in class net.sf.basedb.util.importer.spotdata.BaseFileInfo.SpotSectionInfo
 
extraInfo - Variable in class net.sf.basedb.core.authentication.AuthenticatedUser
 
extraNo - Variable in class net.sf.basedb.core.data.DataCubeExtraValueData
 
extraQuery - Variable in class net.sf.basedb.util.export.spotdata.AbstractFieldConverter
 
extraSql - Variable in class net.sf.basedb.core.PositionExtraValueBatcher
The statement that inserts spot data.
extraSql - Variable in class net.sf.basedb.core.SpotExtraValueBatcher
The statement that inserts spot data.
extraSqlStatement - Variable in class net.sf.basedb.core.PositionExtraValueBatcher
The SQL string for the PositionExtraValueBatcher.extraSql statement.
extraSqlStatement - Variable in class net.sf.basedb.core.SpotExtraValueBatcher
The SQL string for the SpotExtraValueBatcher.extraSql statement.
extraToIndex - Variable in class net.sf.basedb.util.jep.ExtraValueFunction
 
ExtraUserInformation - Class in net.sf.basedb.core.authentication
Class for holding extra information about a user.
ExtraUserInformation() - Constructor for class net.sf.basedb.core.authentication.ExtraUserInformation
Creates a new ExtraUserInformation object.
extraValue - Variable in class net.sf.basedb.core.ExtraValueExpression
 
extraValue - Variable in class net.sf.basedb.core.ExtraValueJoin
 
extraValue - Variable in class net.sf.basedb.core.PositionExtraValueBatcher
The extra value object which links the extra value type.
extraValue - Variable in class net.sf.basedb.core.SpotExtraValueBatcher
The extra value object which links the extra value type.
extraValue(ExtraValue) - Static method in class net.sf.basedb.core.query.Dynamic
Create an expression representing the extra value of a spot or position.
extraValue(ExtraValueType, String, Formatter<?>) - Static method in class net.sf.basedb.util.export.spotdata.ExportableFieldFactory
Create a JEP dynamic field that exports an extra value.
extraValue(Type) - Static method in class net.sf.basedb.core.VirtualColumn
Get a column that stores the calculated extra values for a value type.
ExtraValue - Class in net.sf.basedb.core
Represents extra values attached to a BioAssaySet.
ExtraValue(ExtraValueData) - Constructor for class net.sf.basedb.core.ExtraValue
Creates a new extra value item from the given data.
EXTRAVALUE - Enum constant in enum class net.sf.basedb.core.Item
The item is an ExtraValue
EXTRAVALUE_DATA - Static variable in class net.sf.basedb.core.File
The id for the FileType item representing a file containing analysed extra value data.
ExtraValue.CoordinateType - Enum Class in net.sf.basedb.core
Defines which coordinates in the data cube the extra values are attached to.
extraValueColumns - Static variable in class net.sf.basedb.core.VirtualColumn
A cache of virtual column objects for extra value types.
ExtraValueData - Class in net.sf.basedb.core.data
This represents the use of extra values that have been calculated for a bioassayset.
ExtraValueData() - Constructor for class net.sf.basedb.core.data.ExtraValueData
 
ExtraValueExpression - Class in net.sf.basedb.core
Represents the value of an extra value in a dynamic query: alias.value.
ExtraValueExpression(ExtraValue) - Constructor for class net.sf.basedb.core.ExtraValueExpression
Create a new expression for the specified extra value.
ExtraValueFunction - Class in net.sf.basedb.util.jep
A JEP function class that adds a xtra(int) function to a JEP expression parser.
ExtraValueFunction(DbControl, Map<Integer, Integer>) - Constructor for class net.sf.basedb.util.jep.ExtraValueFunction
Create a new instance of this function which can be used to dynamically evaluate expressions.
ExtraValueFunction(DbControl, BioAssaySet) - Constructor for class net.sf.basedb.util.jep.ExtraValueFunction
Create a new instance of this function.
ExtraValueJoin - Class in net.sf.basedb.core
Represents a join to an extra value in a dynamic query: leftTable JOIN extraValueTable ON ...
ExtraValueJoin(ExtraValue, JoinType) - Constructor for class net.sf.basedb.core.ExtraValueJoin
Create a new join using the root entity table as the left table.
ExtraValueJoiner(JoinType) - Constructor for class net.sf.basedb.core.DynamicPositionQueryJoiners.ExtraValueJoiner
 
ExtraValueJoiner(JoinType) - Constructor for class net.sf.basedb.core.DynamicSpotQueryJoiners.ExtraValueJoiner
 
extraValues - Variable in class net.sf.basedb.core.data.BioAssaySetData
 
extraValues - Variable in class net.sf.basedb.core.data.DataCubeData
 
extraValues - Variable in class net.sf.basedb.core.data.ExtraValueTypeData
 
extraValueType - Variable in class net.sf.basedb.core.data.ExtraValueData
 
ExtraValueType - Class in net.sf.basedb.core
Defines extra values that can be calculated by plugins or some other application and inserted as part of a BioAssaySet.
ExtraValueType(ExtraValueTypeData) - Constructor for class net.sf.basedb.core.ExtraValueType
Creates a new extra value type item.
EXTRAVALUETYPE - Enum constant in enum class net.sf.basedb.core.Item
The item is an ExtraValueType
ExtraValueTypeData - Class in net.sf.basedb.core.data
This represents the definitiona of an extra value type that can be calculated by a plugin.
ExtraValueTypeData() - Constructor for class net.sf.basedb.core.data.ExtraValueTypeData
 
extraValueTypeParameter - Variable in class net.sf.basedb.plugins.JepExtraValueCalculator
 

F

factor - Variable in class net.sf.basedb.util.units.LinearUnitConverter
 
factorQuery - Variable in class net.sf.basedb.util.export.spotdata.AbstractFieldConverter
 
factory - Variable in class net.sf.basedb.clients.web.extensions.skin.FixedSkinActionFactory.MySkinAction
 
factory - Variable in class net.sf.basedb.core.log.db.AnnotationLogger
 
factory - Variable in class net.sf.basedb.core.log.db.AnnotationSetLogger
 
factory - Variable in class net.sf.basedb.core.log.db.AnyToAnyLogger
 
factory - Variable in class net.sf.basedb.core.log.db.BioMaterialEventLogger
 
factory - Variable in class net.sf.basedb.core.log.db.DefaultEntityLogger
 
factory - Variable in class net.sf.basedb.core.log.db.FileSetMemberLogger
 
factory - Variable in class net.sf.basedb.core.log.db.ManualEntryLogger
 
factory - Variable in class net.sf.basedb.core.log.db.PlateEventLogger
 
factory - Variable in class net.sf.basedb.core.log.LoggingInterceptor.LogManagerAndFactory
 
factory - Variable in class net.sf.basedb.util.extensions.manager.FactoryParametersKey
 
factory - Variable in class net.sf.basedb.util.listable.SourceItemTransformerWithCache
 
factory - Variable in class net.sf.basedb.util.uri.http.HttpConnectionManagerActionFactory
 
factoryId - Variable in class net.sf.basedb.util.uri.ConnectionParameters
 
factoryKey - Variable in class net.sf.basedb.util.overview.loader.BasicItemNodeLoader
 
factoryParameters - Variable in class net.sf.basedb.util.extensions.xml.XmlLoader
 
FactoryParametersKey - Class in net.sf.basedb.util.extensions.manager
Key implementation used for configuration parameters for factories.
FactoryParametersKey(Object) - Constructor for class net.sf.basedb.util.extensions.manager.FactoryParametersKey
Create a new key for the given factory.
failIfItemExists - Variable in class net.sf.basedb.plugins.batchimport.AbstractItemImporter
 
failIfMultipleFoundItems - Variable in class net.sf.basedb.plugins.AnnotationFlatFileImporter
 
failIfMultipleFoundItems - Variable in class net.sf.basedb.plugins.batchimport.AbstractItemImporter
 
failIfMultipleFoundReferences - Variable in class net.sf.basedb.plugins.batchimport.AbstractItemImporter
 
failIfMultipleFoundTargets - Variable in class net.sf.basedb.plugins.batchimport.AnyToAnyImporter
 
failIfMultiplePositions - Variable in class net.sf.basedb.plugins.batchimport.PhysicalBioAssayImporter
 
failIfMultipleSourceItems - Variable in class net.sf.basedb.plugins.batchimport.AnyToAnyImporter
 
failIfNotFoundItems - Variable in class net.sf.basedb.plugins.batchimport.AbstractItemImporter
 
failIfNotFoundReference - Variable in class net.sf.basedb.plugins.batchimport.AbstractItemImporter
 
failIfNotFoundSource - Variable in class net.sf.basedb.plugins.batchimport.AnyToAnyImporter
 
failIfNotFoundTarget - Variable in class net.sf.basedb.plugins.batchimport.AnyToAnyImporter
 
failIfNoUsePermissionToReference - Variable in class net.sf.basedb.plugins.batchimport.AbstractItemImporter
 
failIfNoUsePermissionToTarget - Variable in class net.sf.basedb.plugins.batchimport.AnyToAnyImporter
 
failIfNoWritePermissionToItem - Variable in class net.sf.basedb.plugins.batchimport.AbstractItemImporter
 
failIfNoWritePermissionToSource - Variable in class net.sf.basedb.plugins.batchimport.AnyToAnyImporter
 
failIfTooManyValues - Variable in class net.sf.basedb.plugins.AnnotationFlatFileImporter
 
failIfUsed - Variable in class net.sf.basedb.plugins.ReporterFlatFileImporter
 
failSafe - Variable in class net.sf.basedb.core.AbstractQuery
If transactions must be able to continue after an SQL failure or not.
Failure - Class in net.sf.basedb.util.overview
Holds information about a failed validation.
Failure(ValidationRuleAction, Node) - Constructor for class net.sf.basedb.util.overview.Failure
Create a new validation failure.
Failure(ValidationRuleAction, Node, String) - Constructor for class net.sf.basedb.util.overview.Failure
Create a new validation failure with a detailed message.
Failure(ValidationRuleAction, Node, String, Fix...) - Constructor for class net.sf.basedb.util.overview.Failure
Create a new validation failure with a detailed message and a list of suggested fixes.
failures - Variable in class net.sf.basedb.util.overview.GenericOverview
 
failureSummary - Variable in class net.sf.basedb.util.overview.Validator
 
FallbackIdMethod - Class in net.sf.basedb.plugins.batchimport
Identification method implementation that first tries a parent id method, and, if no item is found and the identifier is a number, tries to load the item by id.
FallbackIdMethod(String, String, IdMethod) - Constructor for class net.sf.basedb.plugins.batchimport.FallbackIdMethod
Create a new id method.
FALSE - Static variable in class net.sf.basedb.core.migrate.BooleanWriter
 
FALSE - Static variable in class net.sf.basedb.util.excel.ExcelValue
 
falseValue - Variable in enum class net.sf.basedb.util.formatter.BooleanFormatter.Type
 
FastAnnotation(Object[]) - Constructor for class net.sf.basedb.core.FastAnnotationLoader.FastAnnotation
 
FastAnnotationLoader<T> - Class in net.sf.basedb.core
Implements an API for simple and fast loading of annotation values optimized for situations when a single annotation is needed for many (=thousands) of items.
FastAnnotationLoader(DbControl, AnnotationType) - Constructor for class net.sf.basedb.core.FastAnnotationLoader
 
FastAnnotationLoader.FastAnnotation<T> - Class in net.sf.basedb.core
Holds information about a single annotation value.
FastAnnotationLoader.FastIterator<T> - Class in net.sf.basedb.core
Iterator implementation that splits the query into multiple calls depending on the max number of parameters that can be used in a query.
FastIterator(DbControl, AnnotationType, Item, int, boolean, List<Integer>) - Constructor for class net.sf.basedb.core.FastAnnotationLoader.FastIterator
 
FastLinkLoader(DbControl, Item, String, Item) - Constructor for class net.sf.basedb.core.AnyToAny.FastLinkLoader
 
FATAL - Enum constant in enum class net.sf.basedb.util.extensions.LoggingErrorHandlerFactory.Level
 
fatalError(SAXParseException) - Method in class net.sf.basedb.util.XmlUtil2.Validator
Fatal errors thrown with a detailed error message.
favicon - Variable in class net.sf.basedb.clients.web.extensions.skin.FixedSkinActionFactory
 
favicon - Variable in class net.sf.basedb.clients.web.taglib.Page
The 'favicon' to use.
fax - Variable in class net.sf.basedb.core.authentication.ExtraUserInformation
 
fax - Variable in class net.sf.basedb.core.data.UserData
 
feature - Variable in class net.sf.basedb.core.data.RawData
 
Feature - Class in net.sf.basedb.core
This is a utility class for Features.
Feature() - Constructor for class net.sf.basedb.core.Feature
 
FEATURE - Enum constant in enum class net.sf.basedb.core.Item
The item is a Feature.
FEATURE_EXTRACTION - Static variable in class net.sf.basedb.core.Protocol
The ID for the feature extraction protocol type, for example a protocol used for analysing one or more images to create a raw data file.
FEATURE_EXTRACTION - Static variable in class net.sf.basedb.core.Software
The id for the SoftwareType item representing the softwaretype "feature extraction software".
FEATURE_ID - Enum constant in enum class net.sf.basedb.core.FeatureIdentificationMethod
Use the external feature ID.
featureBatcher - Variable in class net.sf.basedb.core.ArrayDesign
 
FeatureBatcher - Class in net.sf.basedb.core
Batcher class for Features or AffyFeatures.
FeatureBatcher(DbControl, ArrayDesign) - Constructor for class net.sf.basedb.core.FeatureBatcher
 
FeatureCoordinate - Class in net.sf.basedb.core
Represents the coordinate of a feature on an array design.
FeatureCoordinate(Integer, Integer, Integer, Integer, Integer) - Constructor for class net.sf.basedb.core.FeatureCoordinate
Create new object with the specified row and column.
FeatureData - Class in net.sf.basedb.core.data
This class holds information about a regular feature.
FeatureData() - Constructor for class net.sf.basedb.core.data.FeatureData
 
FeatureData(ArrayDesignBlockData, ReporterData) - Constructor for class net.sf.basedb.core.data.FeatureData
Create a new feature which is linked to a reporter only.
FeatureData(ArrayDesignBlockData, WellData) - Constructor for class net.sf.basedb.core.data.FeatureData
Create a new feature which is linked to a well.
featureDiameter - Variable in class net.sf.basedb.core.data.ArrayDesignBlockData
 
featureId - Variable in class net.sf.basedb.core.RawDataBatcher.FeatureInfo
 
featureIdColumnMapping - Static variable in class net.sf.basedb.plugins.RawDataFlatFileImporter
 
featureIdColumnMapping - Static variable in class net.sf.basedb.plugins.ReporterMapFlatFileImporter
 
featureIdentificationMethod - Variable in class net.sf.basedb.core.data.ArrayDesignData
 
FeatureIdentificationMethod - Enum Class in net.sf.basedb.core
This enumeration defines constants that are used to specify which method to use for identifying features on an array design.
FeatureIdentificationMethod(int, boolean, String) - Constructor for enum class net.sf.basedb.core.FeatureIdentificationMethod
Creates a new feature identification method.
featureIdentificationParameter - Static variable in class net.sf.basedb.plugins.IlluminaRawDataImporter
 
featureIdentificationParameter - Static variable in class net.sf.basedb.plugins.ReporterMapFlatFileImporter
 
featureIdMapper - Variable in class net.sf.basedb.plugins.RawDataFlatFileImporter
 
featureIdMapper - Variable in class net.sf.basedb.plugins.ReporterMapFlatFileImporter
 
featureIds - Variable in class net.sf.basedb.core.FeatureBatcher
Holds identification of already inserted features.
FeatureInfo(FeatureData) - Constructor for class net.sf.basedb.core.RawDataBatcher.FeatureInfo
 
featureMismatchErrorParameter - Static variable in class net.sf.basedb.plugins.IlluminaRawDataImporter
 
featureMismatchErrorParameter - Static variable in class net.sf.basedb.plugins.RawDataFlatFileImporter
 
featureProxy - Variable in class net.sf.basedb.core.RawDataBatcher
 
FeatureProxy() - Constructor for class net.sf.basedb.core.RawDataBatcher.FeatureProxy
 
features - Variable in class net.sf.basedb.core.data.ArrayDesignBlockData
 
fetch - Variable in class net.sf.basedb.core.query.HqlInnerJoin
 
fetch - Variable in class net.sf.basedb.core.query.HqlLeftJoin
 
fetchSize - Variable in class net.sf.basedb.core.Migration
 
ffp - Variable in class net.sf.basedb.plugins.AnnotationFlatFileImporter
 
ffp - Variable in class net.sf.basedb.plugins.batchimport.AbstractItemImporter
 
ffp - Variable in class net.sf.basedb.plugins.batchimport.AnyToAnyImporter
 
ffp - Variable in class net.sf.basedb.plugins.IlluminaRawDataImporter
 
ffp - Variable in class net.sf.basedb.plugins.PlateFlatFileImporter
 
ffp - Variable in class net.sf.basedb.plugins.PlateMappingImporter
 
ffp - Variable in class net.sf.basedb.plugins.RawDataFlatFileImporter
 
ffp - Variable in class net.sf.basedb.plugins.ReporterFlatFileImporter
 
ffp - Variable in class net.sf.basedb.plugins.ReporterMapFlatFileImporter
 
ffp - Variable in class net.sf.basedb.util.bfs.AnnotationParser
 
ffp - Variable in class net.sf.basedb.util.bfs.DataParser
 
ffp - Variable in class net.sf.basedb.util.bfs.MetadataParser
 
FieldInfo - Class in net.sf.basedb.clients.web.extensions.login
Information about a the login/password fields on the login form.
FieldInfo() - Constructor for class net.sf.basedb.clients.web.extensions.login.FieldInfo
 
FieldInfo(String, boolean) - Constructor for class net.sf.basedb.clients.web.extensions.login.FieldInfo
 
file - Variable in class net.sf.basedb.clients.web.extensions.fileviewer.FileViewerContext
 
file - Variable in class net.sf.basedb.core.data.FileSetMemberData
 
file - Variable in class net.sf.basedb.core.data.ProtocolData
 
file - Variable in class net.sf.basedb.core.File.UploadStream
The file to write to.
file - Variable in class net.sf.basedb.util.AutoDetectFileFormat.IsImportableFilter
 
file - Variable in class net.sf.basedb.util.extensions.manager.ExtensionsFile
 
file - Variable in class net.sf.basedb.util.extensions.manager.Settings
 
file - Variable in class net.sf.basedb.util.FileExportOutputStream
 
file - Variable in class net.sf.basedb.util.FileImportInputStream
 
file - Variable in class net.sf.basedb.util.importer.BaseFileWrapper
 
file - Variable in class net.sf.basedb.util.importer.DiskFileWrapper
 
file - Variable in class net.sf.basedb.util.importer.spotdata.BaseFileInfo
 
file() - Static method in class net.sf.basedb.clients.web.extensions.fileviewer.FileViewerContext
Creates a file-listing or single-file context without any other related items.
File - Class in net.sf.basedb.core
This class is used to represent individual file items and information about them.
File(FileData) - Constructor for class net.sf.basedb.core.File
Creates a new file item from the given data.
FILE - Enum constant in enum class net.sf.basedb.clients.web.extensions.fileviewer.FileViewerContext.Type
The context is a regular file listing context.
FILE - Enum constant in enum class net.sf.basedb.core.Item
The item is a File.
FILE - Enum constant in enum class net.sf.basedb.core.Path.Type
The path is a path to a File.
FILE - Static variable in class net.sf.basedb.core.QuotaType
The ID for the file.
FILE_INFORMATION - Enum constant in enum class net.sf.basedb.plugins.PrintMapFlatFileImporter.Section
 
FILE_VERSION - Static variable in class net.sf.basedb.core.snapshot.AnnotationSetSnapshot
The version number for the file format in use when serializing this data.
File.CharsetTesterThread - Class in net.sf.basedb.core
 
File.UploadStream - Class in net.sf.basedb.core
This class is used for uploading a file.
fileActions - Variable in class net.sf.basedb.clients.web.extensions.fileviewer.FileViewerUtil
 
FileAttachable - Interface in net.sf.basedb.core
A FileAttachable item is an item that can have a File attached to it.
FileAttachableData - Interface in net.sf.basedb.core.data
A fileattachable item is an item which can have a File attached to it.
fileCache - Variable in class net.sf.basedb.plugins.batchimport.AbstractItemImporter
 
fileColumnMapping - Static variable in class net.sf.basedb.plugins.batchimport.ArrayDesignImporter
 
fileColumnMapping - Static variable in class net.sf.basedb.plugins.batchimport.DerivedBioAssayImporter
 
fileColumnMapping - Static variable in class net.sf.basedb.plugins.batchimport.RawBioAssayImporter
 
fileContext - Variable in class net.sf.basedb.clients.web.extensions.fileviewer.FileViewerUtil
 
FileCopyRunnable - Class in net.sf.basedb.util
Runnable implementation that copies data from an input stream to an output stream when executed.
FileCopyRunnable(InputStream, OutputStream) - Constructor for class net.sf.basedb.util.FileCopyRunnable
Create a new file copy object.
FileData - Class in net.sf.basedb.core.data
This class holds information about a file.
FileData() - Constructor for class net.sf.basedb.core.data.FileData
 
FileData() - Constructor for class net.sf.basedb.util.extensions.manager.processor.RegisterExtensionsProcessor.FileData
 
FileExportOutputStream - Class in net.sf.basedb.util
An extension to the ExportOutputStream class which directs the output to a File in BASE.
FileExportOutputStream(File, boolean) - Constructor for class net.sf.basedb.util.FileExportOutputStream
Create a new export stream that writes the exported data to a file in the BASE filesystem
fileFeatures - Variable in class net.sf.basedb.core.data.ArrayDesignData
 
fileFromKey(String) - Method in class net.sf.basedb.util.StaticCache
 
fileGui - Static variable in class net.sf.basedb.plugins.PackedFileExporter
 
fileId - Variable in class net.sf.basedb.util.importer.spotdata.BaseFileInfo.ChildBioAssay
 
FileImporter - Class in net.sf.basedb.plugins.batchimport
Plug-in for importing file items in a batch.
FileImporter() - Constructor for class net.sf.basedb.plugins.batchimport.FileImporter
 
FileImporter.PathIdMethod - Class in net.sf.basedb.plugins.batchimport
 
FileImportInputStream - Class in net.sf.basedb.util
An extension to the ImportInputStream class which reads from a file on the BASE file system.
FileImportInputStream(File, long, String) - Constructor for class net.sf.basedb.util.FileImportInputStream
Create a new import stream that reads data from a file in the BASE filesystem.
fileIterator - Variable in class net.sf.basedb.plugins.RawDataFlatFileImporter
 
FileIterator(List<RawBioAssay>, List<File>) - Constructor for class net.sf.basedb.plugins.RawDataFlatFileImporter.FileIterator
 
FileLoader - Class in net.sf.basedb.util.overview.loader
Node loader implementation for files.
FileLoader() - Constructor for class net.sf.basedb.util.overview.loader.FileLoader
 
fileMapper - Variable in class net.sf.basedb.plugins.batchimport.ArrayDesignImporter
 
fileMapper - Variable in class net.sf.basedb.plugins.batchimport.DerivedBioAssayImporter
 
fileMapper - Variable in class net.sf.basedb.plugins.batchimport.RawBioAssayImporter
 
filename - Variable in class net.sf.basedb.clients.web.fileupload.FileUpload.SectionHeaders
 
filename - Variable in class net.sf.basedb.clients.web.fileupload.UploadedFile
 
filename - Variable in class net.sf.basedb.core.Path
The filename part of the path.
filename - Variable in class net.sf.basedb.plugins.HelpImporter
 
filename - Variable in class net.sf.basedb.util.bfs.AnnotationParser
 
filename - Variable in class net.sf.basedb.util.bfs.AnnotationWriter
 
filename - Variable in class net.sf.basedb.util.bfs.DataParser
 
filename - Variable in class net.sf.basedb.util.bfs.DataWriter
 
filename - Variable in class net.sf.basedb.util.bfs.MetadataParser
 
filename - Variable in class net.sf.basedb.util.bfs.MetadataWriter
 
FILENAME_PATTERN - Static variable in class net.sf.basedb.clients.web.fileupload.FileUpload
 
filenameGenerator - Variable in class net.sf.basedb.util.bfs.AbstractDataWriterFactory
 
FilenameGenerator<T> - Interface in net.sf.basedb.util.bfs
File name generators are used together with DataWriterFactory implementations to generate file names for BFS data files.
fileOnly - Variable in class net.sf.basedb.core.data.PlatformData
 
fileOnly - Variable in class net.sf.basedb.core.data.PlatformVariantData
 
fileOnly - Variable in class net.sf.basedb.core.RawDataType
 
FileOnlyImporterSupport - Class in net.sf.basedb.plugins.executor
Importer implementation for the external program executor that uploads all created files to BASE and attaches them to a child bioassay set.
FileOnlyImporterSupport() - Constructor for class net.sf.basedb.plugins.executor.FileOnlyImporterSupport
 
FilePacker - Interface in net.sf.basedb.util.zip
This interface should be implemented by classes that can pack files and directories from BASE file system.
fileParameter - Static variable in class net.sf.basedb.plugins.AbstractFlatFileImporter
Parameter definition that asks for the file that should be imported.
fileParameter - Static variable in class net.sf.basedb.plugins.Base1PluginExecuter
Parameter definition that asks for the configuration file that should be imported.
fileParameter - Variable in class net.sf.basedb.plugins.HelpImporter
 
FileParameterType - Class in net.sf.basedb.core
This class represent a parameter type that is a file.
FileParameterType() - Constructor for class net.sf.basedb.core.FileParameterType
Create a new file parameter type, allowing null values.
FileParameterType(File, boolean, int) - Constructor for class net.sf.basedb.core.FileParameterType
Create a new file parameter type.
FilePathFormatter - Class in net.sf.basedb.util.formatter
Formatter implementation that format File items to their complete paths.
FilePathFormatter() - Constructor for class net.sf.basedb.util.formatter.FilePathFormatter
Create a new formatter.
FilePathFormatter(String) - Constructor for class net.sf.basedb.util.formatter.FilePathFormatter
Create a new formatter.
filePattern - Variable in class net.sf.basedb.util.RegexpFileFilter
 
fileResults - Variable in class net.sf.basedb.util.extensions.manager.ProcessResults
 
FileResults(ExtensionsFile, ProcessResults.FileResults) - Constructor for class net.sf.basedb.util.extensions.manager.ProcessResults.FileResults
 
files - Variable in class net.sf.basedb.clients.web.fileupload.FileUpload
Contains information about uploaded files name --> UploadedFile
files - Variable in class net.sf.basedb.core.data.DirectoryData
 
files - Variable in class net.sf.basedb.core.data.FileServerData
 
files - Variable in class net.sf.basedb.plugins.RawDataFlatFileImporter.FileIterator
 
files - Variable in class net.sf.basedb.util.bfs.MetadataModel
 
fileServer - Variable in class net.sf.basedb.core.data.FileData
 
FileServer - Class in net.sf.basedb.core
This class represents a file server that is used to store external files.
FileServer(FileServerData) - Constructor for class net.sf.basedb.core.FileServer
 
FILESERVER - Enum constant in enum class net.sf.basedb.core.Item
The item is a FileServer.
fileServerColumnMapping - Static variable in class net.sf.basedb.plugins.batchimport.FileImporter
 
FileServerData - Class in net.sf.basedb.core.data
File entries that are external files can be linked to a file server.
FileServerData() - Constructor for class net.sf.basedb.core.data.FileServerData
 
fileServerMapper - Variable in class net.sf.basedb.plugins.batchimport.FileImporter
 
fileServerQuery - Variable in class net.sf.basedb.plugins.batchimport.AbstractItemImporter
 
fileSet - Variable in class net.sf.basedb.core.data.ArrayDesignData
 
fileSet - Variable in class net.sf.basedb.core.data.BioAssaySetData
 
fileSet - Variable in class net.sf.basedb.core.data.DerivedBioAssayData
 
fileSet - Variable in class net.sf.basedb.core.data.ExtraValueData
 
fileSet - Variable in class net.sf.basedb.core.data.FileSetMemberData
 
fileSet - Variable in class net.sf.basedb.core.data.RawBioAssayData
 
FileSet - Class in net.sf.basedb.core
A file set is the container for files that have been attach to an item to hold data instead of importing it to the database.
FileSet(FileSetData) - Constructor for class net.sf.basedb.core.FileSet
Regular constructor if the item is not known beforehand.
FileSet(FileSetData, FileStoreEnabled) - Constructor for class net.sf.basedb.core.FileSet
Special constructor to avoid FileSet.getItem() to hit the database when the item is known beforehand.
FILESET - Enum constant in enum class net.sf.basedb.core.Item
The item is a FileSet
FileSet.QueryRuntimeFilterImpl - Class in net.sf.basedb.core
 
FileSetData - Class in net.sf.basedb.core.data
This class collects all files used to store data for an item that store data in files instead of in the database.
FileSetData() - Constructor for class net.sf.basedb.core.data.FileSetData
 
fileSetId - Variable in class net.sf.basedb.core.MigrateRbaToDba.Rba
 
FileSetMember - Class in net.sf.basedb.core
This class represents a file that is member of a file set.
FileSetMember(FileSetMemberData) - Constructor for class net.sf.basedb.core.FileSetMember
Creates a new member item from the given data.
FILESETMEMBER - Enum constant in enum class net.sf.basedb.core.Item
The item is a FileSetMember
FileSetMember.QueryRuntimeFilterImpl - Class in net.sf.basedb.core
 
FileSetMemberData - Class in net.sf.basedb.core.data
This class hols information about individual files attached to items that store data in files instead of in the database.
FileSetMemberData() - Constructor for class net.sf.basedb.core.data.FileSetMemberData
 
FileSetMemberLoader - Class in net.sf.basedb.clients.web.plugins
Data loader implementation that load the files in a file set in FileStoreEnabled items.
FileSetMemberLoader() - Constructor for class net.sf.basedb.clients.web.plugins.FileSetMemberLoader
 
FileSetMemberLoader(DataFileType, Metadata.PropertyPath<FileSetMember, ?>) - Constructor for class net.sf.basedb.clients.web.plugins.FileSetMemberLoader
Load only members of the given file type and then use the given property path to load a specific property of the member.
FileSetMemberLogger - Class in net.sf.basedb.core.log.db
Logger for file set members that logs changes as updates to the parent item the file belong to.
FileSetMemberLogger(DbLogManagerFactory) - Constructor for class net.sf.basedb.core.log.db.FileSetMemberLogger
 
FileSetMemberNameGenerator - Class in net.sf.basedb.util.overview.node
Since a FileSetMember isn't Nameable we construct the name by combining the name of the file type and the name of the file.
FileSetMemberNameGenerator() - Constructor for class net.sf.basedb.util.overview.node.FileSetMemberNameGenerator
 
fileSize - Variable in class net.sf.basedb.util.bfs.AnnotationParser
 
fileSize - Variable in class net.sf.basedb.util.bfs.DataParser
 
fileSize - Variable in class net.sf.basedb.util.bfs.MetadataParser
 
fileSpots - Variable in class net.sf.basedb.core.data.RawBioAssayData
 
fileSpotsMapper - Variable in class net.sf.basedb.plugins.batchimport.RawBioAssayImporter
 
fileSpotsMapping - Static variable in class net.sf.basedb.plugins.batchimport.RawBioAssayImporter
 
filesToIgnore - Variable in class net.sf.basedb.util.extensions.manager.processor.IgnoreFileProcessor
 
FileStoreEnabled - Interface in net.sf.basedb.core
This interface is implemented by items that can use files instead of the database for storing data.
FileStoreEnabledData - Interface in net.sf.basedb.core.data
Items implementing this interface can store data in files instead of in the database.
fileStoreEnabledItems - Static variable in class net.sf.basedb.core.Metadata
 
FileStoreUtil - Class in net.sf.basedb.core
Utility class working with FileStoreEnabled items.
FileStoreUtil() - Constructor for class net.sf.basedb.core.FileStoreUtil
 
fileType - Variable in class net.sf.basedb.clients.web.extensions.fileviewer.FileViewerContext
 
fileType - Variable in class net.sf.basedb.clients.web.formatter.DataFileFormatter
 
fileType - Variable in class net.sf.basedb.clients.web.plugins.FileSetMemberLoader
 
fileType - Variable in class net.sf.basedb.core.data.FileSetMemberData
 
fileType - Variable in class net.sf.basedb.core.data.FileTypeIndex
 
fileType - Variable in class net.sf.basedb.core.data.ItemSubtypeFileTypeData
 
fileType - Variable in class net.sf.basedb.core.data.MimeTypeData
 
fileType - Variable in class net.sf.basedb.core.data.PlatformFileTypeData
 
fileType - Variable in class net.sf.basedb.core.Install.PlatformFT
 
fileType - Static variable in class net.sf.basedb.plugins.AbstractFlatFileImporter
 
fileType - Variable in class net.sf.basedb.util.overview.Fix
 
fileTypeColumnMapping - Static variable in class net.sf.basedb.plugins.batchimport.ArrayDesignImporter
 
fileTypeColumnMapping - Static variable in class net.sf.basedb.plugins.batchimport.DerivedBioAssayImporter
 
fileTypeColumnMapping - Static variable in class net.sf.basedb.plugins.batchimport.RawBioAssayImporter
 
fileTypeId - Variable in class net.sf.basedb.util.fileset.SingleFileValidationAction
 
FileTypeIndex - Class in net.sf.basedb.core.data
This is a helper class for the PlatformData item to help with the Hibernate mapping to PlatformFileTypeData object.
FileTypeIndex() - Constructor for class net.sf.basedb.core.data.FileTypeIndex
 
FileTypeIndex(PlatformVariantData, DataFileTypeData) - Constructor for class net.sf.basedb.core.data.FileTypeIndex
 
fileTypeMapper - Variable in class net.sf.basedb.plugins.batchimport.ArrayDesignImporter
 
fileTypeMapper - Variable in class net.sf.basedb.plugins.batchimport.DerivedBioAssayImporter
 
fileTypeMapper - Variable in class net.sf.basedb.plugins.batchimport.RawBioAssayImporter
 
fileTypeQuery - Variable in class net.sf.basedb.plugins.batchimport.AbstractItemImporter
 
fileTypes - Variable in class net.sf.basedb.core.data.ItemSubtypeData
 
fileTypes - Variable in class net.sf.basedb.core.data.PlatformData
 
fileTypes - Variable in class net.sf.basedb.core.data.PlatformVariantData
 
fileTypes - Variable in class net.sf.basedb.core.MigrateRbaToDba.LineMapping
 
fileTypes - Variable in class net.sf.basedb.core.MigrateRbaToDba.Rba
 
FileUnpacker - Interface in net.sf.basedb.util.zip
This interface should be implemented by plugins that can unpack a single compressed file into the BASE file system.
FileUpload - Class in net.sf.basedb.clients.web.fileupload
Objects of this class are used to handle file upload from browsers using the standard mechanism described in RFC1867.
FileUpload(ServletRequest) - Constructor for class net.sf.basedb.clients.web.fileupload.FileUpload
Create a new FileUpload object which will read the posted data from the given ServletRequest object.
FileUpload(ServletRequest, int, long) - Constructor for class net.sf.basedb.clients.web.fileupload.FileUpload
Create a new FileUpload object which will read the posted data from the given ServletRequest object limiting the transfer rate.
FileUpload.SectionHeaders - Class in net.sf.basedb.clients.web.fileupload
This class contains information extracted from the section headers for a form field or file upload field.
FileUpload.UploadStatus - Class in net.sf.basedb.clients.web.fileupload
This class contains information about the read status on the ServletInputStream
FileUpload.UploadStream - Class in net.sf.basedb.clients.web.fileupload
 
FileUploadProgress - Class in net.sf.basedb.clients.web.fileupload
Objects of this class holds information about the progress of an upload.
FileUploadProgress(long) - Constructor for class net.sf.basedb.clients.web.fileupload.FileUploadProgress
Create a new FileUploadProgress object.
FileUtil - Class in net.sf.basedb.util
This class collects some useful methods for file and stream handling.
FileUtil() - Constructor for class net.sf.basedb.util.FileUtil
 
FileValidator - Class in net.sf.basedb.util.overview.validator
Validator implementation for files.
FileValidator() - Constructor for class net.sf.basedb.util.overview.validator.FileValidator
 
fileViewer - Variable in class net.sf.basedb.clients.web.extensions.list.AnyLinkColumn
 
fileViewer - Variable in class net.sf.basedb.clients.web.formatter.AutoLinkFormatter
 
fileViewer - Variable in class net.sf.basedb.clients.web.formatter.DataFileFormatter
 
fileViewer - Variable in class net.sf.basedb.clients.web.formatter.LinkedFileFormatter
 
FileViewerContext - Class in net.sf.basedb.clients.web.extensions.fileviewer
This class is used for holding information about a file that is beeing displayed in the GUI in some context.
FileViewerContext(FileViewerContext.Type, BasicItem) - Constructor for class net.sf.basedb.clients.web.extensions.fileviewer.FileViewerContext
 
FileViewerContext.Type - Enum Class in net.sf.basedb.clients.web.extensions.fileviewer
 
FileViewerUtil - Class in net.sf.basedb.clients.web.extensions.fileviewer
Helper class for handling the "file-viewer" extension point.
FileViewerUtil(JspContext, FileViewerContext) - Constructor for class net.sf.basedb.clients.web.extensions.fileviewer.FileViewerUtil
FileWrapper - Interface in net.sf.basedb.util.importer
Wrapper around files that provide some basic information about the file.
fillText - Variable in class net.sf.basedb.clients.web.taglib.menu.Menu
Optional text to display to the far right of a horizontal menu
filter - Variable in class net.sf.basedb.core.query.ConditionalQueryElement
 
filter - Variable in class net.sf.basedb.util.extensions.manager.processor.ExtractResourcesProcessor
 
filter - Variable in class net.sf.basedb.util.extensions.Registry.RegisteredEventHandler
 
filter - Variable in class net.sf.basedb.util.extensions.xml.XmlLoader
 
filter - Variable in class net.sf.basedb.util.IncludeExcludeFilter
 
filter - Variable in class net.sf.basedb.util.StaticCache.CleanupTask
 
filter(Collection<? extends T>, Filter<? super T>) - Static method in class net.sf.basedb.util.filter.FilterUtil
Filter a collection and return a new collection with the objects that passes the Filter.evaluate(Object) method.
Filter<T> - Interface in net.sf.basedb.util.filter
A filter is something that selectes or rejects an object due to some property of it.
FILTER - Enum constant in enum class net.sf.basedb.core.VirtualTable
Table that holds column/position coordinates that remains after a filtering operation has been applied to a data cube layer.
FILTER - Static variable in class net.sf.basedb.core.VirtualColumn
This column stores the data cube filter number.
filterable - Variable in class net.sf.basedb.clients.web.extensions.list.AbstractListColumnBean
 
filterable - Variable in class net.sf.basedb.clients.web.extensions.list.PropertyPathActionFactory
 
filterable - Variable in class net.sf.basedb.clients.web.taglib.table.ColumnDef
If the column is filterable or not
filterable - Variable in class net.sf.basedb.clients.web.taglib.table.TableColumn
 
filterAnnotationType - Variable in class net.sf.basedb.clients.web.extensions.list.RelatedItemColumn.Specification
 
filterAnnotationTypeName - Variable in class net.sf.basedb.clients.web.extensions.list.RelatedItemColumn.Specification
 
filterAnnotationValue - Variable in class net.sf.basedb.clients.web.extensions.list.RelatedItemColumn.Specification
 
filterBatcher - Variable in class net.sf.basedb.core.BioAssaySet
The one and only filter batcher for this bioassayset.
FilterBatcher - Class in net.sf.basedb.core
Batcher class for filtered bioassaysets.
FilterBatcher(DbControl, BioAssaySet) - Constructor for class net.sf.basedb.core.FilterBatcher
Create a new filter batcher for a bioassayset.
filterChain - Variable in class net.sf.basedb.core.QueryRuntimeFilterFactory.ChainedFilter
The list of chained filters.
filterClass - Variable in class net.sf.basedb.clients.web.extensions.list.AbstractListColumnBean
 
filterClass - Variable in class net.sf.basedb.clients.web.taglib.table.ColumnDef
Extra CSS class to add to the filter table cell.
FilterConfigurator() - Constructor for class net.sf.basedb.core.HibernateUtil.FilterConfigurator
 
filterGroup - Variable in class net.sf.basedb.core.data.ItemListSyncFilterData
 
filterItemList - Variable in class net.sf.basedb.clients.web.extensions.list.RelatedItemColumn.Specification
 
filterItemListName - Variable in class net.sf.basedb.clients.web.extensions.list.RelatedItemColumn.Specification
 
filterManager - Variable in class net.sf.basedb.core.AbstractEntityQuery
The manager of the runtime query filters.
filterNo - Variable in class net.sf.basedb.core.data.DataCubeFilterData
 
filterOnSelectedItems(EntityQuery) - Method in class net.sf.basedb.core.ItemContext
Add a filter to the given query that restricts it to only return items that have been selected.
filterProperty - Variable in class net.sf.basedb.clients.web.extensions.list.AbstractListColumnBean
 
filterProperty - Variable in class net.sf.basedb.clients.web.extensions.list.PropertyPathActionFactory
 
filterProperty - Variable in class net.sf.basedb.clients.web.taglib.table.ColumnDef
Optional property used for filtering.
filters - Variable in class net.sf.basedb.core.data.DataCubeData
 
filters - Variable in class net.sf.basedb.core.SyncFilter
 
filters - Variable in class net.sf.basedb.util.extensions.events.CombiningEventFilter
 
filterSql - Variable in class net.sf.basedb.core.FilterBatcher
The statement that inserts filter data.
filterSqlStatement - Variable in class net.sf.basedb.core.FilterBatcher
The SQL string for the FilterBatcher.filterSql statement.
filterTemplates - Variable in class net.sf.basedb.core.HibernateUtil.FilterConfigurator
 
filterText - Variable in class net.sf.basedb.clients.web.extensions.list.AbstractListColumnBean
 
filterText - Variable in class net.sf.basedb.clients.web.taglib.table.ColumnDef
Text to display in the filter cell when the column is not filterable.
FilterUtil - Class in net.sf.basedb.util.filter
Utility class for working with and using filters.
FilterUtil() - Constructor for class net.sf.basedb.util.filter.FilterUtil
 
fiMethod - Variable in class net.sf.basedb.core.FeatureBatcher
 
fiMethod - Variable in class net.sf.basedb.core.RawDataBatcher
The method to use for identifying features.
fiMethod - Variable in class net.sf.basedb.plugins.IlluminaRawDataImporter
 
finalizeRegistration(ExtensionsManager) - Method in class net.sf.basedb.util.extensions.manager.processor.IgnoreFileProcessor
Finalize the ignore registration.
finalizeRegistration(ExtensionsManager, boolean) - Method in class net.sf.basedb.util.extensions.manager.processor.RegisterExtensionsProcessor
 
find(Class<T>, Object) - Method in class net.sf.basedb.core.hibernate.SessionWrapper
 
find(Class<T>, Object, Map<String, Object>) - Method in class net.sf.basedb.core.hibernate.SessionWrapper
 
find(Class<T>, Object, LockModeType) - Method in class net.sf.basedb.core.hibernate.SessionWrapper
 
find(Class<T>, Object, LockModeType, Map<String, Object>) - Method in class net.sf.basedb.core.hibernate.SessionWrapper
 
find(Set<QuotaIndex>) - Method in class net.sf.basedb.core.data.QuotaIndex
Find the quota entry in the given set that correpsonds to the same quota type and location as this index.
find(DbControl, ItemQuery<I>, String) - Method in class net.sf.basedb.plugins.batchimport.AnnotationIdMethod
Find all items with property = identifier.
find(DbControl, ItemQuery<I>, String) - Method in class net.sf.basedb.plugins.batchimport.FallbackIdMethod
First, find items using the parent id method.
find(DbControl, ItemQuery<I>, String) - Method in class net.sf.basedb.plugins.batchimport.FileImporter.PathIdMethod
 
find(DbControl, ItemQuery<I>, String) - Method in interface net.sf.basedb.plugins.batchimport.IdMethod
Try to find items with this query method.
find(DbControl, ItemQuery<I>, String) - Method in class net.sf.basedb.plugins.batchimport.InternalIdMethod
Find the item with id = identifier
find(DbControl, ItemQuery<I>, String) - Method in class net.sf.basedb.plugins.batchimport.MultiPropertyIdMethod
Find all items with property[0] = identifier, or property[1] = identifier, ....
find(DbControl, ItemQuery<I>, String) - Method in class net.sf.basedb.plugins.batchimport.PropertyIdMethod
Find all items with property = identifier.
find(AnnotationSetSnapshot) - Method in class net.sf.basedb.core.snapshot.AnnotationLoaderUtil
Same as findAll but only return a boolean instead of the number of snapshots found.
find(AnnotationSetSnapshot, Filter<AnnotationSnapshot>) - Method in class net.sf.basedb.core.snapshot.AnnotationLoaderUtil
Same as findAll but only return a boolean instead of the number of snapshots found.
FIND_WHAT - Static variable in exception net.sf.basedb.core.ItemModifiedException
A pattern to extract the Xxxx and id parts from a string containing [net.sf.basedb.core.data.XxxxData#id].
findAll(Set<String>) - Method in class net.sf.basedb.core.dbengine.TableInfo
Find all indexes with the given set of columns.
findAll(AnnotationSetSnapshot) - Method in class net.sf.basedb.core.snapshot.AnnotationLoaderUtil
Find and load annotations from the given annotation set snapshot.
findAll(AnnotationSetSnapshot, Filter<AnnotationSnapshot>) - Method in class net.sf.basedb.core.snapshot.AnnotationLoaderUtil
Find and load annotations from the given annotation set snapshot using an optional extra filter.
findAll(Filter<? super Node>) - Method in class net.sf.basedb.util.overview.Node
Find all nodes in the parent chain that matches the given filter.
findAllDefaultData(Item, ItemSubtypeData, boolean) - Method in class net.sf.basedb.core.Project
Find all default items in this project of the given item type (required) and subtype (optional).
findAnnotations(DbControl, Annotatable, Filter<? super AnnotationSnapshot>, boolean) - Method in class net.sf.basedb.core.snapshot.SnapshotManager
 
findAnnotations(DbControl, Annotatable, Filter<? super AnnotationSnapshot>, boolean, boolean) - Method in class net.sf.basedb.core.snapshot.SnapshotManager
Utility method for calling getSnapshot and findAnnotations in one go.
findAnnotations(DbControl, AnnotationSetSnapshot, Filter<? super AnnotationSnapshot>, boolean) - Method in class net.sf.basedb.core.snapshot.SnapshotManager
Find annotations.
findAnnotations(DbControl, AnnotationSetSnapshot, Filter<? super AnnotationSnapshot>, boolean, boolean) - Method in class net.sf.basedb.core.snapshot.SnapshotManager
Search in a snapshot for all annotations matching a given filter.
findAnnotationTypeCategory(DbControl, IdMethod, String) - Method in class net.sf.basedb.plugins.batchimport.AbstractItemImporter
Find an annotation type category with a given identifier.
findArrayBatch(DbControl, IdMethod, String) - Method in class net.sf.basedb.plugins.batchimport.AbstractItemImporter
Find an array batch with a given identifier.
findArrayDesign(DbControl, IdMethod, String) - Method in class net.sf.basedb.plugins.batchimport.AbstractItemImporter
Find an array design with a given identifier.
findArraySlide(DbControl, IdMethod, String) - Method in class net.sf.basedb.plugins.batchimport.AbstractItemImporter
Find an array slide with a given identifier.
findBioAssay(List<DerivedBioAssay>, String) - Method in class net.sf.basedb.plugins.IlluminaRawDataImporter
 
findBioPlate(DbControl, IdMethod, String) - Method in class net.sf.basedb.plugins.batchimport.AbstractItemImporter
Find a bioplate with a given identifier.
findBioPlateType(DbControl, IdMethod, String) - Method in class net.sf.basedb.plugins.batchimport.AbstractItemImporter
Find a bioplate type with a given identifier.
findBioSource(DbControl, IdMethod, String) - Method in class net.sf.basedb.plugins.batchimport.AbstractItemImporter
findBioSource(DbControl, IdMethod, String, ItemSubtype) - Method in class net.sf.basedb.plugins.batchimport.AbstractItemImporter
Find a biosource with a given identifier.
findBioWell(DbControl, BioPlate, String, String) - Method in class net.sf.basedb.plugins.batchimport.AbstractItemImporter
Find a well on a bioplate.
findChildren - Variable in class net.sf.basedb.core.BioAssaySet
Query to retrieve children for a bioassayset.
findClass(String) - Method in class net.sf.basedb.util.JarClassLoader
 
findClass(String) - Method in class net.sf.basedb.util.JarClassLoader.JarClassLoaderProxy
 
findColumn - Static variable in class net.sf.basedb.util.parser.FlatFileParser
Pattern used to find column mappings in a string, ie. abc \col\ def
findColumn(String) - Method in class net.sf.basedb.core.dbengine.TableInfo
Find information about a column with the given name.
findColumn(String) - Method in class net.sf.basedb.util.parser.ColFunction
Find column index by checking each column header against a regular expression.
findColumnHeaderIndex(String) - Method in class net.sf.basedb.util.parser.FlatFileParser
Find the index of a column header using a regular expression for pattern matching.
findConstructor(Class<I>, Object[]) - Static method in class net.sf.basedb.util.ClassUtil
Find a constructor for the specified class which takes parameters of the specified types taking superclasses and interfaces into account.
findDataFileType(DbControl, IdMethod, String) - Method in class net.sf.basedb.plugins.batchimport.AbstractItemImporter
Find a data file type with a given identifier.
findDefaultData(DbControl, String, boolean) - Method in class net.sf.basedb.core.Project
 
findDefaultData(Item, ItemSubtypeData, boolean) - Method in class net.sf.basedb.core.Project
Find a default item in this project of the given item type (required) and subtype (optional).
findDefaultItem() - Method in class net.sf.basedb.util.parser.DefaultItemFunction
Find a default item.
findDefaultItems(DbControl, Item, boolean) - Method in class net.sf.basedb.core.Project
Find the default items of the given item type.
findDefaultItems(DbControl, ItemSubtype, boolean) - Method in class net.sf.basedb.core.Project
Find the default (subtypable) items that has the given subtype.
findDefaultItemsOfRelatedSubtype(DbControl, ItemSubtype, Item) - Method in class net.sf.basedb.core.Project
Utility method for finding default items of the given relatedType.
findDefaultRelatedData(DbControl, Subtypable, Item, boolean) - Method in class net.sf.basedb.core.Project
 
findDerivedBioAssay(DbControl, IdMethod, String, ItemSubtype) - Method in class net.sf.basedb.plugins.batchimport.AbstractItemImporter
Find a derived bioassay with a given identifier.
findExtract(DbControl, IdMethod, String) - Method in class net.sf.basedb.plugins.batchimport.AbstractItemImporter
findExtract(DbControl, IdMethod, String, ItemSubtype) - Method in class net.sf.basedb.plugins.batchimport.AbstractItemImporter
Find an extract with a given identifier.
findFactory(URI) - Static method in class net.sf.basedb.util.uri.ConnectionManagerUtil
Find a factory for the given URI.
findFiles(File, FileFilter) - Static method in class net.sf.basedb.util.FileUtil
Find files matching a given filter in a directory.
findFileServer(DbControl, IdMethod, String) - Method in class net.sf.basedb.plugins.batchimport.AbstractItemImporter
Find a file server with a given identifier.
findFirstCommon(Collection<T>, Collection<T>, T) - Static method in class net.sf.basedb.util.ListUtil
Find the first entry in the master collection that is also present in the check collection.
findForeignKeyName(String, Set<String>, String) - Method in class net.sf.basedb.core.dbengine.TableInfo
Check if there is a foreign key with the same name or exactly the same set of columns referencing the same table.
findGeometry(DbControl, int, int) - Method in class net.sf.basedb.plugins.PlateMappingImporter
 
findHardware(DbControl, IdMethod, String) - Method in class net.sf.basedb.plugins.batchimport.AbstractItemImporter
findHardware(DbControl, IdMethod, String, ItemSubtype) - Method in class net.sf.basedb.plugins.batchimport.AbstractItemImporter
Find a hardware with a given identifier.
findHybridization(DbControl, IdMethod, String) - Method in class net.sf.basedb.plugins.batchimport.AbstractItemImporter
Find a hybridization with a given identifier.
findId - Static variable in class net.sf.basedb.clients.web.servlet.Download
 
findIndexName(String, Set<String>) - Method in class net.sf.basedb.core.dbengine.TableInfo
Check if there is an index with the same name or exactly the same set of columns.
findItemSubtype(DbControl, Item, FlatFileParser.Data) - Method in class net.sf.basedb.plugins.batchimport.AbstractItemImporter
Try to find subtype from the given file data.
findItemSubtype(DbControl, IdMethod, Item, String) - Method in class net.sf.basedb.plugins.batchimport.AbstractItemImporter
Find an item subtype with a given identifier.
findKit(DbControl, IdMethod, String, ItemSubtype) - Method in class net.sf.basedb.plugins.batchimport.AbstractItemImporter
Find a kit with a given identifier.
findLabeledExtract(DbControl, IdMethod, String) - Method in class net.sf.basedb.plugins.batchimport.AbstractItemImporter
Find a labled extract with a given identifier.
findMany - Static variable in class net.sf.basedb.clients.web.ModeInfo
 
findMaxBytes(Set<QuotaIndex>) - Method in class net.sf.basedb.core.data.QuotaIndex
Find the quota index entry in the given set and return the 'maxBytes' value.
findMethod(Class<?>, String, Class<?>...) - Static method in class net.sf.basedb.util.ClassUtil
Find a method in a clazz with the given name that takes the given list of arguments.
findOne - Static variable in class net.sf.basedb.clients.web.ModeInfo
 
findOtherUnit(Session, String) - Method in class net.sf.basedb.core.Unit
Find the unit with a given symbol that has the same quantity as this unit.
findParticipant(BioPlateData) - Method in class net.sf.basedb.core.BioPlateEvent
Find the participant object for the given bioplate.
findPermissionTemplate(DbControl, IdMethod, String) - Method in class net.sf.basedb.plugins.batchimport.AbstractItemImporter
Find a permission template with a given identifier.
findPhysicalBioAssay(DbControl, IdMethod, String, ItemSubtype) - Method in class net.sf.basedb.plugins.batchimport.AbstractItemImporter
Find a physical bioassay with a given identifier.
findPlateGeometry(DbControl, IdMethod, String) - Method in class net.sf.basedb.plugins.batchimport.AbstractItemImporter
Find a plate geometry with a given identifier.
findPlatform(DbControl, IdMethod, String) - Method in class net.sf.basedb.plugins.batchimport.AbstractItemImporter
Find a platform with a given identifier.
findPlugins(DbControl, GuiContext, File, String, PluginDefinition) - Static method in class net.sf.basedb.util.AutoDetectFileFormat
Find all plugins with configurations which can import the specified file.
findProjectSpecific - Variable in class net.sf.basedb.core.ProjectSpecificAnnotationsManager
 
findProjectSpecificAnnotation(Annotation, int) - Method in class net.sf.basedb.core.ProjectSpecificAnnotationsManager
Find a project-specific annotation for a given default annotation.
findProtocol(DbControl, IdMethod, String) - Method in class net.sf.basedb.plugins.batchimport.AbstractItemImporter
findProtocol(DbControl, IdMethod, String, ItemSubtype) - Method in class net.sf.basedb.plugins.batchimport.AbstractItemImporter
Find a protocol with a given identifier.
findRange - Static variable in class net.sf.basedb.clients.web.servlet.Download
 
findRawDataType(DbControl, Platform, PlatformVariant, String) - Method in class net.sf.basedb.plugins.batchimport.AbstractItemImporter
Find a matching raw data type.
findReferencedItem(DbControl, IdMethod, ItemQuery<T>, String, int, boolean) - Method in class net.sf.basedb.plugins.batchimport.AbstractItemImporter
Find a referenced item.
findReferencedItemWithSubtype(DbControl, IdMethod, ItemQuery<T>, String, ItemSubtype, boolean) - Method in class net.sf.basedb.plugins.batchimport.AbstractItemImporter
Find a referenced item with a subtype.
findReporter - Variable in class net.sf.basedb.core.RawDataBatcher
A query to find reporters by the external id.
findReporter - Variable in class net.sf.basedb.core.ReporterBatcher
A query to find reporters by the external id.
findResource(String) - Method in class net.sf.basedb.util.JarClassLoader
 
findResource(String) - Method in class net.sf.basedb.util.JarClassLoader.JarClassLoaderProxy
 
findResources(String) - Method in class net.sf.basedb.util.JarClassLoader
 
findResources(String) - Method in class net.sf.basedb.util.JarClassLoader.JarClassLoaderProxy
 
findSample(DbControl, IdMethod, String) - Method in class net.sf.basedb.plugins.batchimport.AbstractItemImporter
findSample(DbControl, IdMethod, String, ItemSubtype) - Method in class net.sf.basedb.plugins.batchimport.AbstractItemImporter
Find a sample with a given identifier.
findSetterMethod(String, Class<?>) - Method in class net.sf.basedb.util.extensions.debug.BeanActionFactory
Find a setter method for the specified parameter.
findSoftware(DbControl, IdMethod, String) - Method in class net.sf.basedb.plugins.batchimport.AbstractItemImporter
findSoftware(DbControl, IdMethod, String, ItemSubtype) - Method in class net.sf.basedb.plugins.batchimport.AbstractItemImporter
Find a software with a given identifier.
findTag(DbControl, IdMethod, String) - Method in class net.sf.basedb.plugins.batchimport.AbstractItemImporter
findTag(DbControl, IdMethod, String, ItemSubtype) - Method in class net.sf.basedb.plugins.batchimport.AbstractItemImporter
Find a tag with a given identifier.
findTargetItem(String, String, FlatFileParser.Data) - Method in class net.sf.basedb.plugins.batchimport.AnyToAnyImporter
 
findUnit(int, String) - Method in class net.sf.basedb.util.units.UnitCache
Finds a unit with a given symbol for a given quantity.
findUnit(String, String) - Method in class net.sf.basedb.util.units.UnitCache
Finds a unit with a given symbol for a given quantity.
findUnit(DbControl, IdMethod, String) - Method in class net.sf.basedb.plugins.batchimport.AbstractItemImporter
Find a unit with a given identifier.
findUnit(Quantity, String) - Method in class net.sf.basedb.util.units.UnitCache
Finds a unit with a given symbol for a given quantity.
findUsers(String, QueryParameter...) - Method in class net.sf.basedb.core.AuthenticationContext
Find users in the database using a "free" restriction.
findValue(String, boolean, boolean) - Method in class net.sf.basedb.core.AnnotationType
This method should be used on enumerated string annotation types to find a matching predefined string value, optionally ignoring case and white-space.
findVariant(DbControl, Platform, IdMethod, String) - Method in class net.sf.basedb.plugins.batchimport.AbstractItemImporter
Find a platform variant with a given identifier.
findWell(int, int, int) - Method in class net.sf.basedb.plugins.PrintMapFlatFileImporter
 
findWhat(StaleStateException) - Static method in exception net.sf.basedb.core.ItemModifiedException
 
FINGERPRINT_LENGTH - Static variable in class net.sf.basedb.core.data.FileServerData
 
FINGERPRINT_LENGTH - Static variable in class net.sf.basedb.core.FileServer
The length of the SSH fingerprint that can be stored in the database.
FINGERPRINT_PATTERN - Static variable in class net.sf.basedb.core.FileServer
Deprecated.
FINGERPRINT_TYPE_MD5 - Static variable in class net.sf.basedb.core.FileServer
The fingerprint is a MD5 fingprint.
FINGERPRINT_TYPE_SHA256 - Static variable in class net.sf.basedb.core.FileServer
The fingerprint is a SHA256 fingprint.
fingerprintType - Variable in class net.sf.basedb.core.data.FileServerData
 
finish(Throwable) - Method in class net.sf.basedb.plugins.AbstractFlatFileImporter
Called once when all files has been imported or when exiting due to an error.
finish(Throwable) - Method in class net.sf.basedb.plugins.RawDataFlatFileImporter
Commit/rollback transaction if needed.
finishedFileSize - Variable in class net.sf.basedb.plugins.AbstractFlatFileImporter
 
firstAssayFieldIndex - Variable in class net.sf.basedb.util.importer.spotdata.BaseFileInfo.SpotSectionInfo
 
firstColumn - Variable in class net.sf.basedb.util.excel.XlsxToCsvUtil.SheetInfo
 
FirstPassSectionSpotsParser - Class in net.sf.basedb.util.importer.spotdata
Parses a 'spots' section of a BASEfile with bioassay set spot data.
FirstPassSectionSpotsParser(DbControl, BaseFileInfo, BioAssaySet) - Constructor for class net.sf.basedb.util.importer.spotdata.FirstPassSectionSpotsParser
Creates a new 'section spot' parser for the first pass.
firstResult - Variable in class net.sf.basedb.core.AbstractQuery
The index of the first result that should be returned by the query.
firstRow - Variable in class net.sf.basedb.util.excel.XlsxToCsvUtil.SheetInfo
 
fitFraction - Variable in class net.sf.basedb.plugins.LowessNormalization.CallableWorker
 
fitFractionParameter - Static variable in class net.sf.basedb.plugins.LowessNormalization
 
Fix - Class in net.sf.basedb.util.overview
Holds information about a suggested fix to a failure.
Fix(String, BasicItem) - Constructor for class net.sf.basedb.util.overview.Fix
Create a new suggested fix for an item.
Fix(String, BasicItem, Annotation) - Constructor for class net.sf.basedb.util.overview.Fix
Create a new suggested fix for the annotation of an item.
Fix(String, BasicItem, AnnotationType, boolean) - Constructor for class net.sf.basedb.util.overview.Fix
Create a new suggested fix for the annotation of an item.
Fix(String, BasicItem, DataFileType) - Constructor for class net.sf.basedb.util.overview.Fix
 
Fix(String, BasicItem, FileSetMember) - Constructor for class net.sf.basedb.util.overview.Fix
 
FixDerivedBioAssayParentsRecursivelyAction(DbControl) - Constructor for class net.sf.basedb.core.DerivedBioAssay.FixDerivedBioAssayParentsRecursivelyAction
 
FixedButtonFactory - Class in net.sf.basedb.clients.web.extensions.toolbar
A simple implementation of a toolbar button action factory that creates the same fixed button for all users not using any context information.
FixedButtonFactory() - Constructor for class net.sf.basedb.clients.web.extensions.toolbar.FixedButtonFactory
Create a new factory instance.
FixedMenuItemFactory - Class in net.sf.basedb.clients.web.extensions.menu
A simple implementation of a menu item action factory that creates the same fixed menu item for all users not using any context information.
FixedMenuItemFactory() - Constructor for class net.sf.basedb.clients.web.extensions.menu.FixedMenuItemFactory
Create a new factory instance.
FixedSkinActionFactory - Class in net.sf.basedb.clients.web.extensions.skin
A simple action factory implementation that always include the given skin on all pages.
FixedSkinActionFactory() - Constructor for class net.sf.basedb.clients.web.extensions.skin.FixedSkinActionFactory
Create a new factory instance.
FixedSkinActionFactory.MySkinAction - Class in net.sf.basedb.clients.web.extensions.skin
 
FixedStartPageFactory - Class in net.sf.basedb.clients.web.extensions.startpage
A simple start page action factory.
FixedStartPageFactory() - Constructor for class net.sf.basedb.clients.web.extensions.startpage.FixedStartPageFactory
Create a new factory instance.
FixedTabFactory - Class in net.sf.basedb.clients.web.extensions.tabcontrol
A simple implementation of a tab action factory that creates the same fixed tab for all users not using any context information.
FixedTabFactory() - Constructor for class net.sf.basedb.clients.web.extensions.tabcontrol.FixedTabFactory
Create a new factory instance.
fixes - Variable in class net.sf.basedb.util.overview.Failure
 
fixPaths(Presets.Preset) - Method in class net.sf.basedb.util.extensions.manager.Settings
Fix paths in older config files.
fixSomeMoreThings(Metadata) - Static method in class net.sf.basedb.core.HibernateUtil
Other things that we may have to fix before the final build.
fixString(String) - Method in class net.sf.basedb.util.parser.FlatFileParser.Data
Fix the value string according to options for 'emptyIsNull', 'nullIsNull', etc.
fixUnitSymbolColumnDefinition(Element) - Static method in class net.sf.basedb.core.HibernateUtil
Fixes the definition of the UnitSymbols.symbol column so that it is case-sensitive.
fkColumns - Variable in class net.sf.basedb.core.dbengine.TableInfo.ForeignKeyInfo
 
flags - Variable in class net.sf.basedb.clients.web.formatter.NiceFormatter
 
FlatFileParser - Class in net.sf.basedb.util.parser
This class can be used to parse data from flat text files and from Excel workbooks in xlsx format.
FlatFileParser() - Constructor for class net.sf.basedb.util.parser.FlatFileParser
Create a new FlatFileParser object.
FlatFileParser.Data - Class in net.sf.basedb.util.parser
This class holds data about a line parsed by the FlatFileParser.hasMoreData() method.
FlatFileParser.ExcelData - Class in net.sf.basedb.util.parser
Subclass that is used to return data when the source file is an Excel file.
FlatFileParser.Line - Class in net.sf.basedb.util.parser
This class holds data about a line parsed by the FlatFileParser.parseHeaders() method.
FlatFileParser.LineType - Enum Class in net.sf.basedb.util.parser
Represents the type of a line matched or unmatched by the parser.
FLOAT - Enum constant in enum class net.sf.basedb.core.Type
Float type.
FLOAT - Enum constant in enum class net.sf.basedb.plugins.Base1PluginExecuter.Base1JobParameterType
 
FLOAT - Static variable in class net.sf.basedb.core.hibernate.TypeWrapper
 
FloatConverter - Class in net.sf.basedb.util.jep.convert
Convert a Number constant to a Query API Expression from the float value.
FloatConverter() - Constructor for class net.sf.basedb.util.jep.convert.FloatConverter
 
FloatExpression - Class in net.sf.basedb.core.query
A constant float expression.
FloatExpression(float) - Constructor for class net.sf.basedb.core.query.FloatExpression
 
FloatParameterType - Class in net.sf.basedb.core
This class represent a parameter type that is a float.
FloatParameterType() - Constructor for class net.sf.basedb.core.FloatParameterType
Create a new float parameter type, without any limits and allowing null values.
FloatParameterType(Float, Float, Float, boolean) - Constructor for class net.sf.basedb.core.FloatParameterType
Create a new float parameter type.
FloatParameterType(Float, Float, Float, boolean, int, int, int, List<Float>) - Constructor for class net.sf.basedb.core.FloatParameterType
 
FloatParameterValueData - Class in net.sf.basedb.core.data
Float parameter value.
FloatParameterValueData() - Constructor for class net.sf.basedb.core.data.FloatParameterValueData
 
FloatParameterValueData(Float...) - Constructor for class net.sf.basedb.core.data.FloatParameterValueData
 
FloatWriter - Class in net.sf.basedb.core.migrate
Database-independent writer implementation that writes double values from a result set.
FloatWriter(ResultSet, int, Writer, char[]) - Constructor for class net.sf.basedb.core.migrate.FloatWriter
 
FLOW_RATE - Static variable in class net.sf.basedb.core.Quantity
The id for the Quantity object representing flow rate.
flush() - Method in class net.sf.basedb.core.AnnotationBatcher
Flush the batchers.
flush() - Method in class net.sf.basedb.core.AnnotationBatcher.UpdateBatcher
Flush and execute the statements added to the batch.
flush() - Method in class net.sf.basedb.core.BasicBatcher
 
flush() - Method in interface net.sf.basedb.core.Batcher
Flush the batcher and send all remaining items in memory to the database.
flush() - Method in class net.sf.basedb.core.FilterBatcher
 
flush() - Method in class net.sf.basedb.core.hibernate.SessionWrapper
 
flush() - Method in class net.sf.basedb.core.LogControl
Flushes any batched changes to the database.
flush() - Method in class net.sf.basedb.core.MappingBatcher
 
flush() - Method in class net.sf.basedb.core.MigrateRbaToDba
Flush all batchers
flush() - Method in class net.sf.basedb.core.plugin.ExportOutputStream
 
flush() - Method in class net.sf.basedb.core.PositionBatcher
 
flush() - Method in class net.sf.basedb.core.PositionExtraValueBatcher
 
flush() - Method in class net.sf.basedb.core.ReporterCloneBatcher
 
flush() - Method in class net.sf.basedb.core.SpotBatcher
 
flush() - Method in class net.sf.basedb.core.SpotExtraValueBatcher
 
flush(Session) - Static method in class net.sf.basedb.core.HibernateUtil
Flush all changed objects to the database.
flushDelete() - Method in class net.sf.basedb.core.BasicBatcher
Flush the SQL delete command buffer.
flushInsert() - Method in class net.sf.basedb.core.BasicBatcher
Flush the SQL insert command buffer.
flushInsert() - Method in class net.sf.basedb.core.ReporterBatcher
Flush and clear the internal cache of external reporter id:s.
flushInternal() - Method in class net.sf.basedb.core.ReporterCloneBatcher
 
FlushSessionAction(Session) - Constructor for class net.sf.basedb.core.ServiceSessionControl.FlushSessionAction
 
flushUpdate() - Method in class net.sf.basedb.core.BasicBatcher
Flush the SQL insert command buffer.
FOLDER - Enum constant in enum class net.sf.basedb.util.overview.Node.Type
 
FORCE - Enum constant in enum class net.sf.basedb.core.ItemContext.AddFilter
Always add a filter, overwriting an existing one.
FORCE - Static variable in class net.sf.basedb.core.Quantity
The id for the Quantity object representing force.
forceItemPermission() - Method in class net.sf.basedb.clients.web.ModeInfo
 
forceMimeType - Variable in class net.sf.basedb.clients.web.servlet.Download
 
forceStop - Variable in class net.sf.basedb.core.signal.ThreadSignalHandler
If TRUE, call Thread.stop() instead of Thread.interrupt()
forceUpdate - Variable in class net.sf.basedb.util.extensions.manager.processor.RegisterExtensionsProcessor
 
ForeignKeyInfo(String, String) - Constructor for class net.sf.basedb.core.dbengine.TableInfo.ForeignKeyInfo
Create a new ForeignKeyInfo object.
foreignKeys - Variable in class net.sf.basedb.core.dbengine.TableInfo
 
forgetOldResults(ExtensionsFile) - Method in class net.sf.basedb.util.extensions.manager.ProcessResults
Forget old processing results for the given file.
Form - Class in net.sf.basedb.clients.web.taglib.table
An alternative layout for tables which contains only one row.
Form() - Constructor for class net.sf.basedb.clients.web.taglib.table.Form
 
format - Variable in class net.sf.basedb.util.excel.ExcelValue
 
format - Variable in class net.sf.basedb.util.formatter.DateFormatter
 
format - Variable in class net.sf.basedb.util.formatter.IntegerFormatter
 
format - Variable in class net.sf.basedb.util.formatter.NumberFormatFormatter
 
format(Boolean) - Method in class net.sf.basedb.util.formatter.BooleanFormatter
 
format(Enum<T>) - Method in class net.sf.basedb.util.formatter.EnumFormatter
 
format(Integer) - Method in class net.sf.basedb.core.log.ChangeTypeFormatter
 
format(Integer) - Method in class net.sf.basedb.util.formatter.ItemTypeFormatter
 
format(Integer) - Method in class net.sf.basedb.util.formatter.ValueTypeFormatter
 
format(Integer) - Method in class net.sf.basedb.util.formatter.WellCoordinateFormatter
 
format(Number) - Method in class net.sf.basedb.clients.web.formatter.ColorFormatter
 
format(Number) - Method in class net.sf.basedb.util.formatter.AdaptiveNumberFormatter
 
format(Number) - Method in class net.sf.basedb.util.formatter.IntegerFormatter
 
format(Number) - Method in class net.sf.basedb.util.formatter.NumberFormatFormatter
 
format(Number) - Method in class net.sf.basedb.util.formatter.NumberFormatter
 
format(Object) - Method in class net.sf.basedb.util.formatter.MultiFormatter
 
format(String) - Method in class net.sf.basedb.clients.web.formatter.NiceFormatter
 
format(String) - Method in class net.sf.basedb.clients.web.formatter.StringFormatter
 
format(Collection<I>) - Method in class net.sf.basedb.util.formatter.CollectionFormatter
 
format(Date) - Method in class net.sf.basedb.util.formatter.DateFormatter
 
format(BasicItem) - Method in class net.sf.basedb.clients.web.formatter.AutoItemExportFormatter
 
format(BasicItem) - Method in class net.sf.basedb.clients.web.formatter.AutoLinkFormatter
 
format(BioMaterialEventSource) - Method in class net.sf.basedb.clients.web.plugins.BioMaterialEventSourceFormatter
 
format(File) - Method in class net.sf.basedb.clients.web.formatter.LinkedFileFormatter
 
format(File) - Method in class net.sf.basedb.util.formatter.FilePathFormatter
 
format(FileSet) - Method in class net.sf.basedb.clients.web.formatter.DataFileFormatter
Lists the name of all member files in the file set that are of the configured file type.
format(Identifiable) - Method in class net.sf.basedb.util.formatter.IdentifiableFormatter
 
format(Nameable) - Method in class net.sf.basedb.clients.web.formatter.LinkedItemFormatter
 
format(Nameable) - Method in class net.sf.basedb.util.formatter.NameableFormatter
 
format(PropertyFilter) - Method in class net.sf.basedb.util.formatter.PropertyFilterFormatter
 
format(ExportableField) - Method in class net.sf.basedb.util.export.spotdata.ExportableFieldFormatter
 
format(T) - Method in class net.sf.basedb.clients.web.formatter.ExtendedPropertyFormatter
 
format(T) - Method in interface net.sf.basedb.util.formatter.Formatter
Format a value by converting it to a string.
format(T) - Method in class net.sf.basedb.util.formatter.LookupFormatter
 
format(T) - Method in class net.sf.basedb.util.formatter.PrefixSuffixFormatter
 
format(T) - Method in class net.sf.basedb.util.formatter.ToStringFormatter
 
FORMAT - Static variable in class net.sf.basedb.clients.web.plugins.SimpleExport
 
FORMAT_BASEFILE_MATRIX - Static variable in class net.sf.basedb.plugins.BaseFileExporterPlugin
 
FORMAT_BASEFILE_SERIAL - Static variable in class net.sf.basedb.plugins.BaseFileExporterPlugin
 
formatBytes(Long) - Static method in class net.sf.basedb.util.Values
Formats a value using units of bytes, kilobytes, megabytes or gigabytes.
formatBytes(Long, int) - Static method in class net.sf.basedb.util.Values
Formats a value using units of bytes, kilobytes, megabytes or gigabytes.
formatDate(Date) - Static method in class net.sf.basedb.core.DateUtil
Formats a date in yyyy-MM-dd format.
formatLineBreaks(String) - Static method in class net.sf.basedb.clients.web.util.HTML
Finds all linebreaks in a string and replaces them with a <br> tag, except that leading and trailing linebreaks will be removed.
formatMessage(String, Object...) - Static method in class net.sf.basedb.util.Values
Insert the values of parameters into a template message.
formatNumber(Float, int) - Static method in class net.sf.basedb.util.Values
Formats a decimal number with the specified number of decimals.
formatNumber(Float, int, String) - Static method in class net.sf.basedb.util.Values
Formats a decimal number with the specified number of decimals and optionally adding a unit.
formatter - Variable in class net.sf.basedb.clients.web.extensions.list.AbstractListColumnBean
 
formatter - Variable in class net.sf.basedb.clients.web.plugins.ExportedProperty
 
formatter - Variable in class net.sf.basedb.clients.web.taglib.table.Cell
 
formatter - Variable in class net.sf.basedb.clients.web.taglib.table.ColumnDef
 
formatter - Variable in class net.sf.basedb.clients.web.taglib.table.TableColumn
 
formatter - Variable in class net.sf.basedb.util.export.spotdata.AnnotationAssayField
 
formatter - Variable in class net.sf.basedb.util.export.spotdata.AssayPropertyField
 
formatter - Variable in class net.sf.basedb.util.export.spotdata.JepDynamicField
 
formatter - Variable in class net.sf.basedb.util.export.spotdata.SimpleDynamicField
 
formatter - Variable in class net.sf.basedb.util.formatter.MultiFormatter
 
Formatter<T> - Interface in net.sf.basedb.util.formatter
A Formatter formats an object to a string suitable for output in a client application.
formatterClass - Variable in class net.sf.basedb.clients.web.extensions.list.PropertyPathActionFactory
 
FormatterFactory - Class in net.sf.basedb.clients.web.formatter
Factory class for creating formatters for various data types.
FormatterFactory() - Constructor for class net.sf.basedb.clients.web.formatter.FormatterFactory
 
formatters - Variable in class net.sf.basedb.util.export.TableWriter
 
formatters - Variable in class net.sf.basedb.util.formatter.MultiFormatter
 
FormatterSettings - Class in net.sf.basedb.clients.web.formatter
This is autility class for getting and setting formatter-related settings for the logged in user.
FormatterSettings() - Constructor for class net.sf.basedb.clients.web.formatter.FormatterSettings
 
formatTime(long) - Static method in class net.sf.basedb.util.Values
Formats a number of seconds to a more proper time format.
formatTimestamp(Date) - Static method in class net.sf.basedb.core.DateUtil
Formats a timestamp in yyyy-MM-dd HH:mm:ss format.
formatType - Variable in class net.sf.basedb.plugins.PrintMapFlatFileImporter
 
FormatType() - Constructor for enum class net.sf.basedb.plugins.PrintMapFlatFileImporter.FormatType
 
formName - Variable in class net.sf.basedb.clients.web.fileupload.UploadedFile
 
formula(Formula, String, Formatter<?>) - Static method in class net.sf.basedb.util.export.spotdata.ExportableFieldFactory
Create a JEP dynamic field that exports the result of the JEP expression in a formula.
Formula - Class in net.sf.basedb.core
This class represents a formula.
Formula(FormulaData) - Constructor for class net.sf.basedb.core.Formula
 
FORMULA - Enum constant in enum class net.sf.basedb.core.Item
The item is a Formula
Formula.AverageMethod - Enum Class in net.sf.basedb.core
The average method used for the values of this formula.
Formula.Parser - Enum Class in net.sf.basedb.core
The parser used to parse the formula.
Formula.Type - Enum Class in net.sf.basedb.core
The type of formula indicats in which situations it can be used.
FormulaData - Class in net.sf.basedb.core.data
This class holds information about a formula used in the analysis of raw data and bioassay sets.
FormulaData() - Constructor for class net.sf.basedb.core.data.FormulaData
 
formulaEval - Variable in class net.sf.basedb.util.excel.XlsxToCsvUtil.SheetInfo
 
FormulaFilter - Class in net.sf.basedb.plugins
This plugin provides methods to filter a bioassayset based on formulas entered by the user.
FormulaFilter() - Constructor for class net.sf.basedb.plugins.FormulaFilter
Constructor should be empty.
formulaParameter - Variable in class net.sf.basedb.plugins.IntensityCalculatorPlugin
 
formulaQuery - Variable in class net.sf.basedb.util.export.spotdata.AbstractFieldConverter
 
formulas - Variable in class net.sf.basedb.core.data.FormulaData
 
formulas - Variable in class net.sf.basedb.core.RawDataType
 
formulaToExpression(String, JepFunction...) - Static method in class net.sf.basedb.util.jep.Jep
Convert JEP expression to a Query API Expression.
formulaToRestriction(String, JepFunction...) - Static method in class net.sf.basedb.util.jep.Jep
Convert JEP expression to a Query API Restriction.
formulaType - Variable in class net.sf.basedb.plugins.IntensityCalculatorPlugin
 
FORWARD - Enum constant in enum class net.sf.basedb.util.overview.node.ChildNodeDirection
Child nodes should be loaded in the forward-loading direction.
ForwardingSignalHandler - Class in net.sf.basedb.core.signal
A signal handler implementation that forwards the signal to another signal transporter.
ForwardingSignalHandler(SignalTransporter) - Constructor for class net.sf.basedb.core.signal.ForwardingSignalHandler
Create a new forwarding signal handler.
forwardSignalMessageIfNeeded(String) - Method in class net.sf.basedb.core.signal.SocketSignalReceiver
If the message has forwarding information, forward the message to the other host.
forwardTo - Variable in class net.sf.basedb.core.signal.ForwardingSignalHandler
The signal transporter to forward signals to.
forwardTo - Variable in class net.sf.basedb.core.signal.ProgressReporterSignalHandler
Original progress reporter that progress updates should be forwarded to.
forwardTo(ProgressReporter) - Method in class net.sf.basedb.core.signal.ProgressReporterSignalHandler
Set the progress reporter that progress information should be forwarded to.
FPKM_TRACKING - Static variable in class net.sf.basedb.core.DataFileType
The external ID for the file type representing a FPKM tracking file.
FRACTION - Static variable in class net.sf.basedb.core.Quantity
The id for the Quantity object representing fractions.
freeWells - Variable in class net.sf.basedb.core.data.BioPlateData
 
freezer - Variable in class net.sf.basedb.core.data.BioPlateData
 
FREEZER - Static variable in class net.sf.basedb.core.Hardware
The id for the HardwareType object representing a freezer.
FREQUENCY - Static variable in class net.sf.basedb.core.Quantity
The id for the Quantity object representing frequency.
from - Variable in class net.sf.basedb.core.AnyToAny
 
from - Variable in class net.sf.basedb.core.data.MessageData
 
from(String...) - Static method in class net.sf.basedb.util.Enumeration
Create a new enumeration from a list strings.
FROM - Enum constant in enum class net.sf.basedb.core.query.QuerySection
 
fromClass(Class<?>) - Static method in enum class net.sf.basedb.core.Item
Get the Item object when you know either the item or data class.
fromDataClass(Class<? extends BasicData>) - Static method in enum class net.sf.basedb.core.Item
Get the Item object when you know the data class.
fromDataObject(BasicData) - Static method in enum class net.sf.basedb.core.Item
Get the Item object when you have a data layer object.
fromDeniedInt(int) - Static method in enum class net.sf.basedb.core.Permission
Convert an integer value to a set of denied permissions.
fromHex(String) - Static method in class net.sf.basedb.util.ColorGenerator
Convert a hexadecimal color string such as one used in HTML to a Color object.
fromHibernateType(Type) - Static method in enum class net.sf.basedb.core.Type
Try to find a matching Type instance given a Hibernate Type object.
fromId - Variable in class net.sf.basedb.core.data.AnyToAnyData
 
fromId - Variable in class net.sf.basedb.core.data.MessageData
 
fromInherited - Variable in class net.sf.basedb.util.overview.Fix
 
fromInt(int) - Static method in enum class net.sf.basedb.core.Include
Convert an integer value to a set of includes.
fromInt(int) - Static method in enum class net.sf.basedb.core.Permission
Convert an integer value to a set of granted permissions.
fromItemClass(Class<? extends BasicItem>) - Static method in enum class net.sf.basedb.core.Item
Get the Item object when you know the item class.
fromItems(Collection<? extends Nameable>, String) - Static method in class net.sf.basedb.util.Enumeration
Create a new enumeration from a list of basic items.
fromItems(Collection<? extends Nameable>, String, String) - Static method in class net.sf.basedb.util.Enumeration
Create a new enumeration from a list of basic items.
fromJson(JSONObject) - Static method in class net.sf.basedb.util.GeoLocation
Convert JSON data from freegeoip to a GeoLocation instance.
fromOther(double, Unit) - Method in class net.sf.basedb.core.Unit
Convert a value from another unit to this unit.
fromReferenceUnit(double) - Method in class net.sf.basedb.core.Unit
Convert a value from the reference unit to this unit.
fromString(String) - Static method in enum class net.sf.basedb.plugins.PrintMapFlatFileImporter.Section
 
fromType - Variable in class net.sf.basedb.core.AnyToAny.FastLinkLoader
 
fromType - Variable in class net.sf.basedb.core.data.AnyToAnyData
 
fromType(String) - Static method in class net.sf.basedb.util.formatter.BooleanFormatter
Create a formatter for boolean values.
fromValue(int) - Static method in enum class net.sf.basedb.core.BioMaterialEvent.Type
Get the BioMaterialEvent.Type object when you know the integer code.
fromValue(int) - Static method in enum class net.sf.basedb.core.BioWell.LockMode
Get the Lock mode object when you know the integer code.
fromValue(int) - Static method in enum class net.sf.basedb.core.ExtraValue.CoordinateType
Get the CoordinateType object when you know the integer code.
fromValue(int) - Static method in enum class net.sf.basedb.core.FeatureIdentificationMethod
Get the FeatureIdentificationMethod object when you know the integer code.
fromValue(int) - Static method in enum class net.sf.basedb.core.Formula.AverageMethod
Get the Formula.AverageMethod object when you know the integer code.
fromValue(int) - Static method in enum class net.sf.basedb.core.Formula.Parser
Get the Formula.Parser object when you know the integer code.
fromValue(int) - Static method in enum class net.sf.basedb.core.Formula.Type
Get the Formula.Type object when you know the integer code.
fromValue(int) - Static method in enum class net.sf.basedb.core.IntensityTransform
Get the SpotDataTransform object when you know the integer code.
fromValue(int) - Static method in enum class net.sf.basedb.core.Item
Get the Item object when you know the integer code.
fromValue(int) - Static method in enum class net.sf.basedb.core.ItemContext.SortDirection
Get the SortDirection object when you know the integer code.
fromValue(int) - Static method in enum class net.sf.basedb.core.Job.ExecutionTime
Get the Job.Status object when you know the integer code.
fromValue(int) - Static method in enum class net.sf.basedb.core.Job.Status
Get the Job.Status object when you know the integer code.
fromValue(int) - Static method in enum class net.sf.basedb.core.Job.Type
Get the Job.Status object when you know the integer code.
fromValue(int) - Static method in enum class net.sf.basedb.core.Location
Get the Location object when you know the integer code.
fromValue(int) - Static method in enum class net.sf.basedb.core.log.ChangeType
Get the change type corresponding to the given numerical value.
fromValue(int) - Static method in enum class net.sf.basedb.core.Operator
Get the Operator object when you know the integer code.
fromValue(int) - Static method in enum class net.sf.basedb.core.plugin.GuiContext.Type
Get the GuiContext.Type object when you know the integer code.
fromValue(int) - Static method in enum class net.sf.basedb.core.plugin.Plugin.MainType
 
fromValue(int) - Static method in enum class net.sf.basedb.core.Type
Get the Type object when you know the integer code.
fromValue(String) - Static method in enum class net.sf.basedb.core.Type
Get the Type object when you know the string value.
fu - Variable in class net.sf.basedb.clients.web.fileupload.UploadedFile
 
FULL - Enum constant in enum class net.sf.basedb.core.ItemList.SynchronizeOption
Synchronize the members so that it contains all of the items matching the filter and no items not matching the filter.
fullFieldName - Variable in class net.sf.basedb.util.overview.extensions.ReflectValidationRuleActionFactory
 
function(String) - Method in class net.sf.basedb.util.formatter.PropertyFilterFormatter
 
functions - Static variable in class net.sf.basedb.util.jep.Jep
 
FunctionSafeJep - Class in net.sf.basedb.util.jep
Extension to the JEP parser that provides better error handling for unknown functions.
FunctionSafeJep() - Constructor for class net.sf.basedb.util.jep.FunctionSafeJep
Create a new function-safe JEP parser.
FunctionSafeJep.SafeFunctionTable - Class in net.sf.basedb.util.jep
Function table implementation that pretends that all possible functions exists, but sends an error message if someone tries to use a function that doesn't really exists.
FunctionSafeJep.UnknownFunction - Class in net.sf.basedb.util.jep
Represents an unknown function that appears in an expression.
FutureItem(Class<T>, Query<T>) - Constructor for class net.sf.basedb.core.QueryExecutor.FutureItem
 
FutureResultSet(PreparedStatement) - Constructor for class net.sf.basedb.core.QueryExecutor.FutureResultSet
 
FutureScrollIterator(Query<T>) - Constructor for class net.sf.basedb.core.QueryExecutor.FutureScrollIterator
 
FutureUpdate(PreparedStatement) - Constructor for class net.sf.basedb.core.QueryExecutor.FutureUpdate
 
FuzzyMatch(String, String, double) - Constructor for class net.sf.basedb.util.fuzzy.StringMatcher.FuzzyMatch
 

G

GalExporter - Class in net.sf.basedb.plugins
Exports an array design with features to a GAL file.
GalExporter() - Constructor for class net.sf.basedb.plugins.GalExporter
 
GB - Static variable in class net.sf.basedb.util.Values
 
GENE_ID - Static variable in class net.sf.basedb.util.gtf.GtfInputStream.Attribute
 
geneAveragesParameter - Variable in class net.sf.basedb.plugins.Base1PluginExecuter
If the data should be exported averaged per gene.
geneIdIndex - Variable in class net.sf.basedb.util.gtf.GtfInputStream
 
generateCFPlot(BioAssay, String, String) - Method in class net.sf.basedb.clients.web.servlet.PlotServlet
Generates a correction-factor plot, which is plotting the MA-data for the parent together with the difference in M between the parent and child.
generateDefaultName(FilePacker, Directory, Collection<Nameable>) - Method in class net.sf.basedb.plugins.PackedFileExporter
Generate a default name without a path for the packed file.
generateDefaultPath(FilePacker, Directory, Collection<Nameable>) - Method in class net.sf.basedb.plugins.PackedFileExporter
Generate a default path for the packed file.
generatedFiles - Variable in class net.sf.basedb.util.bfs.AbstractFilenameGenerator
 
generateExportTitle(String) - Method in class net.sf.basedb.clients.web.extensions.list.RelatedItemColumn.Specification
Generates an export title using target item type and subtype as prefix.
generateRandomId(int) - Static method in class net.sf.basedb.core.Application
Generate a random id.
generateSignalMessage(Signal) - Method in class net.sf.basedb.core.signal.AbstractSignalTransporter
Generate a signal message string for the given signal.
generateSubtitle() - Method in class net.sf.basedb.clients.web.extensions.list.RelatedItemColumn.Specification
 
generateTitle(String) - Method in class net.sf.basedb.clients.web.extensions.list.RelatedItemColumn.Specification
Generates a title using target item type and subtype as prefix.
generateTitle(String, String) - Method in class net.sf.basedb.clients.web.ModeInfo
 
generateTooltip(String) - Method in class net.sf.basedb.clients.web.extensions.list.RelatedItemColumn.Specification
Generates a tooltip using target item type and subtype as prefix.
generators - Variable in class net.sf.basedb.clients.web.extensions.plot.OverviewPlotBean
 
GENERIC - Static variable in class net.sf.basedb.core.BioPlateEventType
The system ID for "Generic" event type.
GENERIC - Static variable in class net.sf.basedb.core.Platform
The external id for the Generic platform.
GENERIC_EXTRAVALUE_DATA - Static variable in class net.sf.basedb.core.DataFileType
The external ID for the file type representing generic analysed extra value data.
GENERIC_PRINT_MAP - Static variable in class net.sf.basedb.core.DataFileType
The external ID for the file type representing a generic print map (array design layout) of any type.
GENERIC_RAW_DATA - Static variable in class net.sf.basedb.core.DataFileType
The external ID for the file type representing a generic raw data file of any type.
GENERIC_REPORTER_MAP - Static variable in class net.sf.basedb.core.DataFileType
The external ID for the file type representing a generic reporter map (array design layout) of any type.
GENERIC_SPOT_DATA - Static variable in class net.sf.basedb.core.DataFileType
The external ID for the file type representing generic analysed spot data.
GenericBaseDataWriterFactory<T> - Class in net.sf.basedb.util.bfs
Generic implementation of a data writer factory that create files in the BASE file system.
GenericBaseDataWriterFactory(DbControl, Directory, FilenameGenerator<T>) - Constructor for class net.sf.basedb.util.bfs.GenericBaseDataWriterFactory
Create a new factory that creates files in the given directory.
GenericDiskDataWriterFactory<T> - Class in net.sf.basedb.util.bfs
Generic implementation of a data writer factory that create files on the local file system.
GenericDiskDataWriterFactory(File, FilenameGenerator<T>) - Constructor for class net.sf.basedb.util.bfs.GenericDiskDataWriterFactory
Create a new factory that creates files in the given directory.
GenericExtraFileImporter - Class in net.sf.basedb.util.bfs
Extra file importer implementation that imports file to a specified directory in the BASE file system.
GenericExtraFileImporter(DbControl, Directory, boolean) - Constructor for class net.sf.basedb.util.bfs.GenericExtraFileImporter
Create a new extra file importer.
GenericIntensityParser - Class in net.sf.basedb.util.importer.spotdata
Generic spot intensity parser implementation that looks for 'intensity1', ..., 'intensityN' data columns for any number of channels.
GenericIntensityParser(int) - Constructor for class net.sf.basedb.util.importer.spotdata.GenericIntensityParser
Creates a new parser for the specified number of channels.
GenericOverview - Class in net.sf.basedb.util.overview
Implementation for holding a generic overview of items.
GenericOverview(DbControl, BasicItem, Project) - Constructor for class net.sf.basedb.util.overview.GenericOverview
Create a new generic overview.
genericType - Variable in class net.sf.basedb.core.data.DataFileTypeData
 
gensalt() - Static method in class net.sf.basedb.util.bcrypt.BCrypt
Generate a salt for use with the BCrypt.hashpw() method, selecting a reasonable default for the number of hashing rounds to apply
gensalt(int) - Static method in class net.sf.basedb.util.bcrypt.BCrypt
Generate a salt for use with the BCrypt.hashpw() method
gensalt(int, SecureRandom) - Static method in class net.sf.basedb.util.bcrypt.BCrypt
Generate a salt for use with the BCrypt.hashpw() method
GENSALT_DEFAULT_LOG2_ROUNDS - Static variable in class net.sf.basedb.util.bcrypt.BCrypt
 
GeoLocation - Class in net.sf.basedb.util
Utility class for geographic location.
GeoLocation() - Constructor for class net.sf.basedb.util.GeoLocation
 
GeoLocation.ResponseFilter - Class in net.sf.basedb.util
We only accept "200" status response, "application/json" content type and not more than 1K bytes (should be a lot less under normal operations).
GEOMETRIC_MEAN - Enum constant in enum class net.sf.basedb.core.Formula.AverageMethod
 
geometricMean(Expression) - Static method in class net.sf.basedb.core.query.Aggregations
Calculates the geometric mean of all values for an expression: new expression = EXP(AVG(LN(e))).
GeometricMeanExpression - Class in net.sf.basedb.core.query
Calculates the geometric mean of an expression: EXP(AVG(LN(e)))
GeometricMeanExpression(Expression) - Constructor for class net.sf.basedb.core.query.GeometricMeanExpression
 
geometryQuery - Variable in class net.sf.basedb.plugins.batchimport.AbstractItemImporter
 
get - Variable in class net.sf.basedb.util.uri.http.HttpConnectionManager.TimeoutTimer
 
get(char) - Static method in enum class net.sf.basedb.plugins.Base1PluginExecuter.Base1JobParameterType
 
get(int) - Method in class net.sf.basedb.core.ItemResultList
Get a BasicItem derived object.
get(int) - Method in class net.sf.basedb.util.parser.FlatFileParser.Data
Deprecated.
In 3.15, use FlatFileParser.Data.getString(int) instead or one of the other getXxx() method to return a given data type directly
get(int, int) - Method in interface net.sf.basedb.core.query.SqlResultList
 
get(int, String) - Method in interface net.sf.basedb.core.query.SqlResultList
 
get(Class<E>, BasicData) - Method in class net.sf.basedb.core.ItemResultList
 
get(Class<T>, Serializable) - Method in class net.sf.basedb.core.hibernate.SessionWrapper
 
get(Class<T>, Serializable, LockMode) - Method in class net.sf.basedb.core.hibernate.SessionWrapper
 
get(Class<T>, Serializable, LockOptions) - Method in class net.sf.basedb.core.hibernate.SessionWrapper
 
get(Class, Serializable) - Method in class net.sf.basedb.core.hibernate.StatelessSessionWrapper
 
get(Class, Serializable, LockMode) - Method in class net.sf.basedb.core.hibernate.StatelessSessionWrapper
 
get(Object) - Method in class net.sf.basedb.core.ExtendedPropertyAccessor.GetterSetter
Get the value of the extended property.
get(Object) - Method in class net.sf.basedb.util.ClassLocal
Get the object associated with the class of the specified instance.
get(Object) - Method in class net.sf.basedb.util.formatter.LookupFormatter
Get registered lookup value for a given key
get(String) - Method in class net.sf.basedb.clients.web.extensions.skin.ImageRemapper
Get the remapped image for the given source image.
get(String) - Static method in class net.sf.basedb.clients.web.ModeInfo
 
get(String, Serializable) - Method in class net.sf.basedb.core.hibernate.SessionWrapper
 
get(String, Serializable) - Method in class net.sf.basedb.core.hibernate.StatelessSessionWrapper
 
get(String, Serializable, LockMode) - Method in class net.sf.basedb.core.hibernate.SessionWrapper
 
get(String, Serializable, LockMode) - Method in class net.sf.basedb.core.hibernate.StatelessSessionWrapper
 
get(String, Serializable, LockOptions) - Method in class net.sf.basedb.core.hibernate.SessionWrapper
 
get(JspContext) - Static method in class net.sf.basedb.clients.web.extensions.fileviewer.FileViewerUtil
Get an existing instance that is stored in the given JSP context.
get(DbControl) - Static method in class net.sf.basedb.clients.web.extensions.ExtensionsControl
Get an extension control object for managing the installed extensions.
get(DbControl) - Static method in class net.sf.basedb.core.DerivedBioAssay.FixDerivedBioAssayParentsRecursivelyAction
Get an instance tht handles the fixes for the given DbControl.
get(DbControl, MeasuredBioMaterialData) - Static method in class net.sf.basedb.core.MeasuredBioMaterial.RemainingQuantityAction
 
get(DbControl, ItemQuery<? extends E>...) - Static method in class net.sf.basedb.util.query.MultiQueryIterator
Create a new iterator for the given list of queries.
get(AnnotationUtil.AnnotatableWrapper) - Method in class net.sf.basedb.util.AnnotationUtil.Cache
 
get(TransformCache.CacheKey) - Method in class net.sf.basedb.util.listable.TransformCache
Get a cached entry if.
getAbout() - Method in interface net.sf.basedb.util.extensions.Extension
Get information about the extensions.
getAbout() - Method in class net.sf.basedb.util.extensions.ExtensionBean
 
getAbout() - Method in class net.sf.basedb.util.extensions.manager.ExtensionsFile
Get information about the extensions in this file.
getAbout() - Method in class net.sf.basedb.util.extensions.Registry.RegisteredExtension
 
getAbout() - Method in class net.sf.basedb.util.extensions.xml.PluginInfo
Get information about the authors of the plug-in.
getAbsolutePath(String) - Static method in class net.sf.basedb.core.File
Convert a relative path back to an absolute file path.
getAbstract() - Method in class net.sf.basedb.core.data.ExperimentData
Get the abstract for this experiment.
getAbstract() - Method in class net.sf.basedb.core.Experiment
Get the abstract text for the publication for this experiment.
getAcceptedFile() - Method in class net.sf.basedb.util.fileset.SingleFileValidationAction
Get the file that was last accepted by the SingleFileValidationAction.acceptFile(FileSetMember) method.
getAction() - Method in class net.sf.basedb.clients.web.taglib.table.Table
 
getActionClass() - Method in interface net.sf.basedb.util.extensions.ExtensionPoint
Get the class object that represents the type of action that can be added to this extension point.
getActionClass() - Method in class net.sf.basedb.util.extensions.ExtensionPointBean
 
getActionClass() - Method in class net.sf.basedb.util.extensions.Registry.RegisteredExtensionPoint
 
getActionFactory() - Method in interface net.sf.basedb.util.extensions.Extension
Get the factory class for creating actions.
getActionFactory() - Method in class net.sf.basedb.util.extensions.ExtensionBean
 
getActionFactory() - Method in class net.sf.basedb.util.extensions.Registry.RegisteredExtension
 
getActionId() - Method in class net.sf.basedb.clients.web.extensions.list.RelatedItemColumn.Specification
Get the action id from the expression.
getActions() - Method in class net.sf.basedb.util.extensions.ExtensionContext
getActions() - Method in class net.sf.basedb.util.extensions.ExtensionPointContext
Always null, since this is an extension point context.
getActions() - Method in class net.sf.basedb.util.extensions.InvokationContext
Get the actions, or null if there is no current extension.
getActions(InvokationContext<? super A>) - Method in interface net.sf.basedb.util.extensions.ActionFactory
This method may be called one or several times for each request.
getActions(InvokationContext<? super OnSaveAction>) - Method in class net.sf.basedb.clients.web.extensions.edit.DebugOnSaveActionFactory
 
getActions(InvokationContext<? super ListColumnAction<I, V>>) - Method in class net.sf.basedb.clients.web.extensions.list.PropertyPathActionFactory
 
getActions(InvokationContext<? super ListColumnAction<Annotatable, Object>>) - Method in class net.sf.basedb.clients.web.extensions.list.RelatedItemColumnActionFactory
 
getActions(InvokationContext<? super ListColumnAction<BasicItem, Object>>) - Method in class net.sf.basedb.clients.web.extensions.list.AnyLinkColumnActionFactory
 
getActions(InvokationContext<? super LoginFormAction>) - Method in class net.sf.basedb.clients.web.extensions.login.PasswordLoginFormFactory
 
getActions(InvokationContext<? super MenuItemAction>) - Method in class net.sf.basedb.clients.web.extensions.menu.FixedMenuItemFactory
 
getActions(InvokationContext<? super MenuItemAction>) - Method in class net.sf.basedb.clients.web.extensions.menu.PermissionMenuItemFactory
 
getActions(InvokationContext<? super OverviewPlotAction>) - Method in class net.sf.basedb.clients.web.extensions.plot.MAPlotFactory
 
getActions(InvokationContext<? super SectionAction>) - Method in class net.sf.basedb.clients.web.extensions.section.IncludeContentSectionFactory
 
getActions(InvokationContext<? super ServiceControllerAction>) - Method in class net.sf.basedb.clients.web.extensions.service.DummyService
 
getActions(InvokationContext<? super SkinAction>) - Method in class net.sf.basedb.clients.web.extensions.skin.FixedSkinActionFactory
 
getActions(InvokationContext<? super StartPageAction>) - Method in class net.sf.basedb.clients.web.extensions.startpage.FixedStartPageFactory
 
getActions(InvokationContext<? super TabAction>) - Method in class net.sf.basedb.clients.web.extensions.tabcontrol.FixedTabFactory
 
getActions(InvokationContext<? super TabAction>) - Method in class net.sf.basedb.clients.web.extensions.tabcontrol.IncludeContentTabFactory
 
getActions(InvokationContext<? super ButtonAction>) - Method in class net.sf.basedb.clients.web.extensions.fileviewer.ViewAndDownloadActionFactory
 
getActions(InvokationContext<? super ButtonAction>) - Method in class net.sf.basedb.clients.web.extensions.toolbar.FixedButtonFactory
 
getActions(InvokationContext<? super ButtonAction>) - Method in class net.sf.basedb.clients.web.extensions.toolbar.PermissionButtonFactory
 
getActions(InvokationContext<? super LogManagerFactory>) - Method in class net.sf.basedb.core.log.db.DbLogManagerFactory
 
getActions(InvokationContext<? super CdfValidationAction>) - Method in class net.sf.basedb.util.affymetrix.CdfValidationFactory
 
getActions(InvokationContext<? super CelValidationAction>) - Method in class net.sf.basedb.util.affymetrix.CelValidationFactory
 
getActions(InvokationContext<? super Action>) - Method in class net.sf.basedb.util.extensions.debug.BeanActionFactory
 
getActions(InvokationContext<? super Action>) - Method in class net.sf.basedb.util.extensions.debug.ProxyActionFactory
 
getActions(InvokationContext<? super GtfValidationAction>) - Method in class net.sf.basedb.util.gtf.GtfValidationFactory
 
getActions(InvokationContext<? super ValidationRuleAction>) - Method in class net.sf.basedb.util.overview.extensions.ReflectValidationRuleActionFactory
 
getActions(InvokationContext<? super ConnectionManagerFactory>) - Method in class net.sf.basedb.util.uri.http.HttpConnectionManagerActionFactory
 
getActive() - Method in class net.sf.basedb.clients.web.taglib.tab.TabControl
 
getActive(DbControl) - Static method in class net.sf.basedb.core.Project
Get the currently active project if any.
getActiveProjectId() - Method in class net.sf.basedb.core.data.JobData
The ID of the project that should be made active when running this job.
getActiveProjectId() - Method in class net.sf.basedb.core.Job
The ID of the project that should be made the active project while running this job.
getActiveProjectId() - Method in class net.sf.basedb.core.SessionControl
Get the id of the active project, or 0 if no project is active.
getActiveProjectName() - Method in class net.sf.basedb.core.SessionControl
Get the name of the active project, or null if no project is active.
getActiveProjectPermissions() - Method in class net.sf.basedb.core.SessionControl
Get the permissions that the logged in user has in the currently active project.
getActiveRoles() - Method in class net.sf.basedb.core.SessionControl
Get the id of all active roles where the logged in user is a member.
getActualCatalog() - Method in class net.sf.basedb.core.ServiceSessionControl.SessionFactoryConfiguration
The actual catalog that will be used by BASE.
getActualSchema() - Method in class net.sf.basedb.core.ServiceSessionControl.SessionFactoryConfiguration
The actual schema that will be used by BASE.
getActualUnit(DbControl) - Method in class net.sf.basedb.core.snapshot.AnnotationSnapshot
Get the unit that is most relevant for this annotation.
getActualValues() - Method in class net.sf.basedb.core.snapshot.AnnotationSnapshot
Get the annotation values that are most relevant for this annotation.
getActualValues(UnitConverter, Type) - Method in class net.sf.basedb.core.snapshot.AnnotationSnapshot
Get the annotations values, optionally converted to some specific unit and type of values.
getAddFilter() - Method in class net.sf.basedb.clients.web.SubContext
 
getAddress() - Method in class net.sf.basedb.core.authentication.ExtraUserInformation
The postal address to the user.
getAddress() - Method in class net.sf.basedb.core.data.UserData
Get the address for the user, or null if unknown.
getAddress() - Method in class net.sf.basedb.core.User
Get the address for the user, or null if unknown.
getAdvancedAssayField(String, boolean) - Method in class net.sf.basedb.util.export.spotdata.AdvancedFieldConverter
Convert an expression to an assay field.
getAdvancedReporterField(String, boolean) - Method in class net.sf.basedb.util.export.spotdata.AdvancedFieldConverter
Convert an expression to a reporter field.
getAdvancedSpotField(String, boolean) - Method in class net.sf.basedb.util.export.spotdata.AdvancedFieldConverter
Convert an expression to a spot field.
getAffiliations() - Method in class net.sf.basedb.core.data.ExperimentData
Get the affiliations for this experiment.
getAffiliations() - Method in class net.sf.basedb.core.Experiment
Get the affiliations for this experiment.
getAge() - Method in class net.sf.basedb.core.DiskUsageStatistics.Summary
Get the age of this summary object since it was created in seconds.
getAge() - Method in class net.sf.basedb.util.jobagent.JobAgentInfo
Get the age in milliseconds of this object.
getAgent() - Method in class net.sf.basedb.clients.jobagent.handlers.AbstractCustomRequestHandler
 
getAgent() - Method in class net.sf.basedb.clients.jobagent.slotmanager.InternalSlotManager
Get the job agent this slot manager belongs to.
getAgentInfo(JobAgent) - Static method in class net.sf.basedb.core.JobAgent
Get a JobAgentInfo for a job agent.
getAlias() - Method in enum class net.sf.basedb.core.Item
Get the alias for this item, which is used in queries,
getAlias() - Method in class net.sf.basedb.core.query.AnnotationExpression
 
getAlias() - Method in class net.sf.basedb.core.query.ExpressionSelect
 
getAlias() - Method in interface net.sf.basedb.core.query.Select
Get the alias of the selected expression.
getAlias() - Method in class net.sf.basedb.core.RealTable
Get the alias of this table.
getAlias() - Method in enum class net.sf.basedb.core.VirtualTable
Get the alias of this table.
getAlias(int) - Method in class net.sf.basedb.core.RealTable
Get the alias of this table, using the ID of the item to make it unique.
getAlias(BasicItem) - Method in class net.sf.basedb.core.RealTable
Get the alias of this table, using the ID of the item to make it unique.
getAll() - Static method in class net.sf.basedb.core.ClonableProperty
Get a list containing cloned property representation for all static and extended properties.
getAllAnnotatableParentItems(DbControl, Annotatable, Filter<Annotatable>) - Static method in class net.sf.basedb.util.AnnotationUtil
Get all annotatable parent items for a given item.
getAllAnnotatableParentItems(DbControl, Annotatable, Filter<Annotatable>, AnnotationUtil.Cache) - Static method in class net.sf.basedb.util.AnnotationUtil
Get all annotatable parent items for a given item.
getAllAnnotationTypesWithInheritanceDisabled(DbControl) - Static method in class net.sf.basedb.core.AnnotationType
Load the IDs of all annotation types with the disable inheritance flag set.
getAllCharsets() - Static method in class net.sf.basedb.core.Config
Get a set containing all character sets known to the current java virtual machine.
getAllCharsets(boolean) - Static method in class net.sf.basedb.util.charset.CharsetUtil
Get all charsets that Config.getAllCharsets() returns and optionally include the fallback charsets.
getAllChildren(DbControl, Set<Integer>) - Method in class net.sf.basedb.util.overview.loader.ExtractLoader
 
getAllColumnMappings() - Method in class net.sf.basedb.plugins.gtf.GtfReporterMapImporter
 
getAllColumnMappings() - Method in class net.sf.basedb.plugins.PlateFlatFileImporter
 
getAllColumnMappings() - Method in class net.sf.basedb.plugins.ReporterMapFlatFileImporter
 
getAllColumnMappings(boolean) - Method in class net.sf.basedb.plugins.ReporterFlatFileImporter
 
getAllColumnMappings(RawDataType) - Method in class net.sf.basedb.plugins.RawDataFlatFileImporter
Loads the column mappings if they hasn't been loaded already.
getAllCurrentContexts(boolean, boolean) - Method in class net.sf.basedb.core.SessionControl
Get a list with the current default contexts.
getAllExtended() - Method in class net.sf.basedb.core.data.RawData
 
getAllItems() - Method in class net.sf.basedb.core.ItemList
Get a query that returns all items that can possibly be members of this list.
getAllMandatory() - Static method in class net.sf.basedb.core.ClonableProperty
Get a list with all mandatory properties that must be cloned.
getAllMembers(DbControl, Set<Integer>) - Static method in class net.sf.basedb.core.User
Load the ID:s of all users that are direct members of the specified groups.
getAllMembers(Session, Collection<Integer>) - Static method in class net.sf.basedb.core.User
 
getAllObjects() - Method in class net.sf.basedb.util.extensions.manager.ExtensionsFile
Get a list of all objects defined in this extensions file.
getAllowImmediateExecution() - Method in class net.sf.basedb.core.data.PluginDefinitionData
If the plugin is allowed to be immediately executed or if it must be added to the job queue.
getAllowImmediateExecution() - Method in class net.sf.basedb.core.PluginDefinition
If immediate execution of jobs are allowed or if they always must go through the job queue.
getAllowMultiple() - Method in class net.sf.basedb.core.data.ItemSubtypeFileTypeData
If multiple files of this type are allowed in a file set or not.
getAllowMultiple() - Method in class net.sf.basedb.core.data.PlatformFileTypeData
If multiple files of this type are allowed in a file set or not.
getAllowMultiple() - Method in class net.sf.basedb.core.ItemSubtypeFileType
Check if more than one file of this type is allowed in a file set or not.
getAllowMultiple() - Method in class net.sf.basedb.core.PlatformFileType
Check if more than one file of this type is allowed in a file set or not.
getAllowMultiple() - Method in interface net.sf.basedb.core.UsableDataFileType
A flag indicating if it is allowed to attach multiple files or only a single one of the given type.
getAllParentExtracts(DbControl, OverviewContext, PhysicalBioAssay) - Static method in class net.sf.basedb.util.overview.validator.PhysicalBioAssayValidator
Get all parent extracts that are associated with the given physical bioassay.
getAllPermissions(SharedData) - Method in class net.sf.basedb.core.SessionControl
getAllPermissions(Item, UserData, ItemKeyData, ProjectKeyData) - Method in class net.sf.basedb.core.InternalJobQueue.JobQueueKeyring
Return 0.
getAllPermissions(Item, UserData, ItemKeyData, ProjectKeyData) - Method in class net.sf.basedb.core.Job.SignalKeyring
Return 0.
getAllPermissions(Item, UserData, ItemKeyData, ProjectKeyData) - Method in class net.sf.basedb.core.Keyring
 
getAllPermissions(Item, UserData, ItemKeyData, ProjectKeyData) - Method in class net.sf.basedb.core.ServiceSessionControl.ServicesKeyring
Return 0.
getAllPermissions(Item, UserData, ItemKeyData, ProjectKeyData) - Method in class net.sf.basedb.core.SessionControl
Get the combined permissions for an item of the specified type, owned by the specified user and shared with the specified item and project keys.
getAllResults() - Method in class net.sf.basedb.util.extensions.manager.ProcessResults
 
getAllRoles() - Method in class net.sf.basedb.core.SessionControl
Get the id of all roles where the logged in user is a member.
getAllRules(DbControl, GenericOverview) - Static method in class net.sf.basedb.util.overview.OverviewUtil
Get all static and extension validation rules grouped by relationship.
getAllSamples(TransformContext, Set<Integer>) - Method in class net.sf.basedb.util.listable.PushToParentsTransformer
 
getAllsubcontexts() - Method in class net.sf.basedb.clients.web.taglib.table.PresetSelector
 
getAlwaysGranted() - Method in class net.sf.basedb.core.plugin.Permissions
Get the permissions that the plugin always should be granted, even if the logged in user doesn't have the permissions already.
getAnalyzeTableSql(String, String, String) - Method in interface net.sf.basedb.core.dbengine.DbEngine
Generate SQL to update the index statistics for a table.
getAnalyzeTableSql(String, String, String) - Method in class net.sf.basedb.core.dbengine.DefaultDbEngine
Return null.
getAnalyzeTableSql(String, String, String) - Method in class net.sf.basedb.core.dbengine.MySQLEngine
Generate analyze table <catalog>.<table>.
getAnalyzeTableSql(String, String, String) - Method in class net.sf.basedb.core.dbengine.PostgresDbEngine
Generate ANALYZE <schema>.<table>.
getAndSetCurrentContext(SessionControl, Item, String, PageContext, ItemContext) - Static method in class net.sf.basedb.clients.web.Base
Same as: getAndSetCurrentContext(sc, itemType, subContext, pageContext.getRequest(), defaultContext, false).
getAndSetCurrentContext(SessionControl, Item, String, ServletRequest, ItemContext, boolean) - Static method in class net.sf.basedb.clients.web.Base
Get the current context and update it from request information if available.
getAndSetCurrentContext(SessionControl, Item, PageContext, ItemContext) - Static method in class net.sf.basedb.clients.web.Base
Same as: getAndSetCurrentContext(sc, itemType, null, pageContext.getRequest(), defaultContext, false).
getAndSetCurrentContext(SessionControl, Item, PageContext, ItemContext, boolean) - Static method in class net.sf.basedb.clients.web.Base
Same as: getAndSetCurrentContext(sc, itemType, null, pageContext.getRequest(), defaultContext, resetTemporary).
getAndSetReporterContext(SessionControl, PageContext) - Method in class net.sf.basedb.clients.web.ExperimentExplorer
Get and update the current settings for the reporter context.
getAndSetSpotContext(SessionControl, PageContext) - Method in class net.sf.basedb.clients.web.ExperimentExplorer
Get and update the current settings for the spot context.
getAnnotatable() - Method in class net.sf.basedb.util.AnnotationUtil.AnnotatableWrapper
The annotatable that we are wrapping.
getAnnotatableFromNode(DbControl, Node) - Static method in class net.sf.basedb.util.overview.loader.AnnotationLoader
Get the annotatable item from the node.
getAnnotatableItems() - Static method in class net.sf.basedb.core.Metadata
Get a set containing all Annotatable item types.
getAnnotatableParents() - Method in interface net.sf.basedb.core.Annotatable
Get all parents objects which are annotatable and the logged in user has read permission to.
getAnnotatableParents() - Method in class net.sf.basedb.core.ArrayBatch
Get the array design.
getAnnotatableParents() - Method in class net.sf.basedb.core.ArrayDesign
Get the plates, if any.
getAnnotatableParents() - Method in class net.sf.basedb.core.ArraySlide
Get the array batch.
getAnnotatableParents() - Method in class net.sf.basedb.core.BioAssay
Get the parent bioassay set, all parent bioassays and all parent root raw bioassays.
getAnnotatableParents() - Method in class net.sf.basedb.core.BioAssaySet
Get the parent bioassay set (if any) and the experiment.
getAnnotatableParents() - Method in class net.sf.basedb.core.BioMaterial
Get all child biomaterial items with a subtype that has the ItemSubtype.getPushAnnotations() flag set.
getAnnotatableParents() - Method in class net.sf.basedb.core.BioPlate
Get the freezer.
getAnnotatableParents() - Method in class net.sf.basedb.core.DerivedBioAssay
Get the extract and parent bioassays or physical bioassays.
getAnnotatableParents() - Method in class net.sf.basedb.core.Experiment
Always null.
getAnnotatableParents() - Method in class net.sf.basedb.core.Extract
Get the tag and parent extracts.
getAnnotatableParents() - Method in class net.sf.basedb.core.File
 
getAnnotatableParents() - Method in class net.sf.basedb.core.FileServer
 
getAnnotatableParents() - Method in class net.sf.basedb.core.Hardware
 
getAnnotatableParents() - Method in class net.sf.basedb.core.ItemList
Always returns null
getAnnotatableParents() - Method in class net.sf.basedb.core.Kit
 
getAnnotatableParents() - Method in class net.sf.basedb.core.MeasuredBioMaterial
Get the biosource or pooled samples and the bioplate the biomaterial is located on.
getAnnotatableParents() - Method in class net.sf.basedb.core.PhysicalBioAssay
Get the extracts and array slide.
getAnnotatableParents() - Method in class net.sf.basedb.core.Plate
Get the parent plates, if any.
getAnnotatableParents() - Method in class net.sf.basedb.core.PluginConfiguration
 
getAnnotatableParents() - Method in class net.sf.basedb.core.PluginDefinition
 
getAnnotatableParents() - Method in class net.sf.basedb.core.Project
 
getAnnotatableParents() - Method in class net.sf.basedb.core.Protocol
 
getAnnotatableParents() - Method in class net.sf.basedb.core.RawBioAssay
Get the parent derived bioassay and extract, if any.
getAnnotatableParents() - Method in class net.sf.basedb.core.RootRawBioAssay
Get the raw bioassay.
getAnnotatableParents() - Method in class net.sf.basedb.core.Software
 
getAnnotatableParents() - Method in class net.sf.basedb.core.Tag
 
getAnnotatableParents() - Method in class net.sf.basedb.core.Well
Get the parent well, if any.
getAnnotatableParents(int, Collection<Extract>) - Method in class net.sf.basedb.core.PhysicalBioAssay
Get the extracts, possible on a specific assay position or only a given set of specific extracts, and the array slide.
getAnnotatableParents(int, Extract) - Method in class net.sf.basedb.core.PhysicalBioAssay
Get the extracts, possible on a specific assay position or only a specific extract, and the array slide.
getAnnotatableParents(Collection<? extends MeasuredBioMaterial>) - Method in class net.sf.basedb.core.MeasuredBioMaterial
Get the annotable parents, possible only a given set of specific parents items.
getAnnotatableParents(DbControl, OverviewContext, Annotatable) - Static method in class net.sf.basedb.util.overview.OverviewUtil
Get all annotatable parent items for the given item.
getAnnotatableParentWrappers(DbControl) - Method in class net.sf.basedb.util.AnnotationUtil.AnnotatableWrapper
Get all annotatable parents wrapped inside AnnotatableWrapper:s
getAnnotation() - Method in class net.sf.basedb.util.overview.Fix
Get the annotation that needs to be edited for this fix.
getAnnotation(AnnotationType) - Method in class net.sf.basedb.core.AnnotationSet
Get the Annotation object of the specified annotation type.
getAnnotationFormatter(SessionControl, Annotation, Unit) - Static method in class net.sf.basedb.clients.web.formatter.FormatterFactory
Get a formatter for nice formatting of annotation values, including units.
getAnnotationGroup(short) - Method in class net.sf.basedb.clients.web.ExperimentExplorer.AnnotationSummary
Get the annotation group for the bioassay with the give data cube column.
getAnnotationGroups() - Method in class net.sf.basedb.clients.web.ExperimentExplorer.AnnotationSummary
Get all annotation groups that was found among the bioassays.
getAnnotationId() - Method in class net.sf.basedb.clients.web.extensions.list.RelatedItemColumn.Specification
Get the annotation id from the expression.
getAnnotationIdMethods(DbControl) - Method in class net.sf.basedb.plugins.batchimport.AbstractItemImporter
Get identification methods that are based on annotations.
getAnnotationJoiner(JoinType) - Static method in class net.sf.basedb.core.HqlQueryJoiners
Get an annotation auto joiner.
getAnnotationMessage() - Method in interface net.sf.basedb.core.AnnotatableProxy
A help message that should tell users how the proxied annotations are used.
getAnnotationMessage() - Method in interface net.sf.basedb.core.plugin.AnnotationSetterPlugin
Get a message that explains what the plug-in does with the annotations it has.
getAnnotationMessage() - Method in class net.sf.basedb.core.PluginConfiguration
Get a message explaining what the proxy does with the annotations.
getAnnotationMessage() - Method in class net.sf.basedb.core.PluginDefinition
Get a message explaining what the proxy does with the annotations.
getAnnotationMessage() - Method in class net.sf.basedb.plugins.ManualDerivedBioAssayCreator
 
getAnnotationMessage() - Method in class net.sf.basedb.plugins.ManualTransformCreator
 
getAnnotationMessage() - Method in class net.sf.basedb.plugins.RawDataFlatFileImporter
 
getAnnotations() - Method in interface net.sf.basedb.core.data.AnnotatableData
Short-cut to all annotations belonging to this item.
getAnnotations() - Method in class net.sf.basedb.core.data.AnnotatedData
 
getAnnotations() - Method in class net.sf.basedb.core.data.AnnotationSetData
The annotations in this annotation set.
getAnnotations() - Method in class net.sf.basedb.core.data.AnnotationTypeData
This is the inverse end.
getAnnotations() - Method in class net.sf.basedb.core.data.BioAssayData
 
getAnnotations() - Method in class net.sf.basedb.core.data.BioAssaySetData
 
getAnnotations() - Method in class net.sf.basedb.core.data.PluginDefinitionData
 
getAnnotations() - Method in class net.sf.basedb.core.data.ProjectData
 
getAnnotations() - Method in class net.sf.basedb.core.data.RootRawBioAssayData
 
getAnnotations() - Method in class net.sf.basedb.core.data.WellData
 
getAnnotations() - Method in class net.sf.basedb.core.snapshot.AnnotationSetSnapshot
Get a list with the all annotations in this snapshot.
getAnnotations(Annotation.Source) - Method in class net.sf.basedb.core.AnnotationSet
Get a query returning annotations with the specified source.
getAnnotationSet() - Method in interface net.sf.basedb.core.Annotatable
Get the annotation set containing the annotations for this item.
getAnnotationSet() - Method in class net.sf.basedb.core.AnnotatedItem
 
getAnnotationSet() - Method in class net.sf.basedb.core.Annotation
Get the annotation set this annotation belongs to.
getAnnotationSet() - Method in class net.sf.basedb.core.BioAssay
 
getAnnotationSet() - Method in class net.sf.basedb.core.BioAssaySet
 
getAnnotationSet() - Method in interface net.sf.basedb.core.data.AnnotatableData
Get the annotation set that holds the annotations for an item.
getAnnotationSet() - Method in class net.sf.basedb.core.data.AnnotatedData
 
getAnnotationSet() - Method in class net.sf.basedb.core.data.AnnotationData
Get the annotation set this annotation primarily belongs to.
getAnnotationSet() - Method in class net.sf.basedb.core.data.BioAssayData
 
getAnnotationSet() - Method in class net.sf.basedb.core.data.BioAssaySetData
 
getAnnotationSet() - Method in class net.sf.basedb.core.data.PluginDefinitionData
 
getAnnotationSet() - Method in class net.sf.basedb.core.data.ProjectData
 
getAnnotationSet() - Method in class net.sf.basedb.core.data.RootRawBioAssayData
 
getAnnotationSet() - Method in class net.sf.basedb.core.data.WellData
 
getAnnotationSet() - Method in class net.sf.basedb.core.PluginDefinition
 
getAnnotationSet() - Method in class net.sf.basedb.core.Project
 
getAnnotationSet() - Method in class net.sf.basedb.core.RootRawBioAssay
 
getAnnotationSet() - Method in class net.sf.basedb.core.Well
 
getAnnotationSet(DbControl) - Method in class net.sf.basedb.core.snapshot.AnnotationSetSnapshot
Get the annotation set this is a snapshot of.
getAnnotationSetId() - Method in class net.sf.basedb.core.data.annotations.AnnotationLink
 
getAnnotationSetId() - Method in class net.sf.basedb.core.snapshot.AnnotationSetSnapshot
Get the id of the annotation set this is a snapshot of.
getAnnotationSummary(DbControl, AnnotationType) - Method in class net.sf.basedb.clients.web.ExperimentExplorer
Get an AnnotationSummary object which can be used to calculate means and other values for each annotation group.
getAnnotationType() - Method in class net.sf.basedb.clients.web.ExperimentExplorer.AnnotationSummary
Get the annotation type this summary is based on.
getAnnotationType() - Method in class net.sf.basedb.core.Annotation
Get the annotation type of this annotation.
getAnnotationType() - Method in class net.sf.basedb.core.AnnotationBatcher.CurrentAnnotationInfo
Get the annotation type.
getAnnotationType() - Method in class net.sf.basedb.core.data.AnnotationData
Get the type of this annotation.
getAnnotationType() - Method in class net.sf.basedb.core.query.AnnotationExpression
 
getAnnotationType() - Method in class net.sf.basedb.core.snapshot.AnnotationLoaderUtil
The annotation type that this loader load annotations from.
getAnnotationType() - Method in class net.sf.basedb.util.annotations.InheritSpecification
 
getAnnotationType() - Method in class net.sf.basedb.util.export.spotdata.AnnotationAssayField
Get the configured annotation type.
getAnnotationType() - Method in class net.sf.basedb.util.overview.Fix
Get the annotation type of the annotation that needs to be edited for this fix.
getAnnotationType(DbControl) - Method in class net.sf.basedb.core.snapshot.AnnotationSnapshot
Get the annotation type.
getAnnotationTypeEnum(DbControl, AnnotationType) - Static method in class net.sf.basedb.clients.web.Base
Get an Enumeration that is suitable to use in a column definition for a table for an annotation type.
getAnnotationTypeId() - Method in class net.sf.basedb.core.data.annotations.AnnotationLink
 
getAnnotationTypeId() - Method in class net.sf.basedb.core.snapshot.AnnotationSnapshot
Get the id of the annotation type.
getAnnotationTypeIds() - Method in class net.sf.basedb.clients.web.ExperimentExplorer
Get the selected annotation types.
getAnnotationTypes() - Method in interface net.sf.basedb.core.AnnotatableProxy
Get the annotation types that can be proxied.
getAnnotationTypes() - Method in class net.sf.basedb.core.data.AnnotationTypeCategoryData
This is the inverse end.
getAnnotationTypes() - Method in interface net.sf.basedb.core.plugin.AnnotationSetterPlugin
Create a query that returns the annotation types that can be used by the current plug-in.
getAnnotationTypes() - Method in class net.sf.basedb.core.PluginConfiguration
Get the annotation types that can be used by this configuration.
getAnnotationTypes() - Method in class net.sf.basedb.core.PluginDefinition
Get the annotation types that can be used by this configuration.
getAnnotationTypes() - Method in class net.sf.basedb.plugins.Base1PluginExecuter
Get the experimental factors connected to a experiment.
getAnnotationTypes() - Method in class net.sf.basedb.plugins.ManualDerivedBioAssayCreator
Return a query that finds annotation types for bioassay sets.
getAnnotationTypes() - Method in class net.sf.basedb.plugins.ManualTransformCreator
Return a query that finds annotation types for bioassay sets.
getAnnotationTypes() - Method in class net.sf.basedb.plugins.RawDataFlatFileImporter
Return a query that finds annotation types for raw bioassays.
getAnnotationTypes(DbControl, boolean) - Method in class net.sf.basedb.clients.web.ExperimentExplorer
Get the annotation types that are of interest in this experiment.
getAnnotationTypes(Item) - Method in class net.sf.basedb.core.AnnotationTypeCategory
Gets a query that returns the annotation types that are members of this category
getAnnotationTypesQuery(AnnotatableProxy) - Static method in class net.sf.basedb.clients.web.Base
Get a query that returns all annotation types defined for a AnnotatableProxy item.
getAnnotationTypesQuery(Item) - Static method in class net.sf.basedb.clients.web.Base
Get a query that returns all annotation types defined for a particular item type.
getAnnotationTypesQuery(Item, Boolean) - Static method in class net.sf.basedb.clients.web.Base
Get a query that returns all annotation types defined for a particular item type and, optionally, with a specific protocol parameter setting.
getAnnotationValues() - Method in class net.sf.basedb.clients.web.ExperimentExplorer.AnnotationGroup
Get all annotation values in this annotation group.
getAnnotationValues(DbControl, SnapshotManager, BioAssay, AnnotationType) - Static method in class net.sf.basedb.util.BioAssaySetUtil
Find the annotation values for a given annotation type on a bioassay.
getAnyToAny() - Method in class net.sf.basedb.clients.web.extensions.fileviewer.FileViewerContext
Get the current any-to-any link pointing to the file.
getAppId() - Method in class net.sf.basedb.core.data.SchemaVersionData
The ID of the application the schema version is valid for.
getAppId() - Method in class net.sf.basedb.core.hibernate.SessionFactoryConfiguration
Deprecated.
Get the application id for schema versioning.
getAppId() - Method in class net.sf.basedb.core.ServiceSessionControl.SessionFactoryConfiguration
Get the application id for schema versioning.
getApproximateRowCountSql(String, String, String) - Method in class net.sf.basedb.core.dbengine.AbstractDbEngine
 
getApproximateRowCountSql(String, String, String) - Method in interface net.sf.basedb.core.dbengine.DbEngine
Get an SQL statement that returns an approximate count for the number of rows in the given table.
getApproximateRowCountSql(String, String, String) - Method in class net.sf.basedb.core.dbengine.MySQLEngine
 
getApproximateRowCountSql(String, String, String) - Method in class net.sf.basedb.core.dbengine.PostgresDbEngine
 
getApproximateSize() - Method in class net.sf.basedb.core.hibernate.TypeWrapper
Get the number of bytes a single value for this type occupies in a database (approximately).
getArrayBatch() - Method in class net.sf.basedb.core.ArraySlide
Get the ArrayBatch item to which this slide belongs.
getArrayBatch() - Method in class net.sf.basedb.core.data.ArraySlideData
Get the arrayBatch of this slide.
getArrayBatches() - Method in class net.sf.basedb.core.ArrayDesign
Get a query that returns the batches for this design.
getArrayBatches() - Method in class net.sf.basedb.core.data.ArrayDesignData
This is the inverse end.
getArrayDesign() - Method in class net.sf.basedb.core.ArrayBatch
Get the ArrayDesign item that was used for this batch.
getArrayDesign() - Method in class net.sf.basedb.core.ArrayDesignBlock
Get the ArrayDesign that is linked with this block.
getArrayDesign() - Method in class net.sf.basedb.core.ArrayDesignPlate
Gets this item's ArrayDesign.
getArrayDesign() - Method in class net.sf.basedb.core.data.ArrayBatchData
Get the array design item that was used for this batch.
getArrayDesign() - Method in class net.sf.basedb.core.data.ArrayDesignBlockData
Used by Hibernate to link with ArrayDesign.
getArrayDesign() - Method in class net.sf.basedb.core.data.ArrayDesignPlateData
Get the ArrayDesign
getArrayDesign() - Method in class net.sf.basedb.core.data.RawBioAssayData
Get the array design used for the hybridization this raw bio assay comes from.
getArrayDesign() - Method in class net.sf.basedb.core.DerivedBioAssay
Get the array design connected to this derived bioassay by following the path from the physical bioassay to the array slide to the array batch to the array design.
getArrayDesign() - Method in class net.sf.basedb.core.FeatureBatcher
Get the array design this batcher is used for.
getArrayDesign() - Method in class net.sf.basedb.core.RawBioAssay
Get the ArrayDesign this raw data uses.
getArrayDesignBlock() - Method in class net.sf.basedb.core.data.FeatureData
Get the arraydesignblock of this feature.
getArrayDesignBlock(DbControl, FeatureData) - Static method in class net.sf.basedb.core.Feature
Get the array design block from a feature.
getArrayDesignBlocks() - Method in class net.sf.basedb.core.ArrayDesign
Get a query that returns the block of this array design.
getArrayDesignBlocks() - Method in class net.sf.basedb.core.data.ArrayDesignData
This is the inverse end.
getArrayDesignPlates() - Method in class net.sf.basedb.core.ArrayDesign
Get plate connections for this array design.
getArrayDesigns() - Method in class net.sf.basedb.core.data.JobData
This is the inverse end.
getArrayDesigns() - Method in class net.sf.basedb.core.data.PlateData
Used by Hibernate to link with the arraydesign for this plate.
getArraySlide() - Method in class net.sf.basedb.core.data.PhysicalBioAssayData
Get the array slide.
getArraySlide() - Method in class net.sf.basedb.core.PhysicalBioAssay
Get the ArraySlide this hyridization is using.
getArraySlides() - Method in class net.sf.basedb.core.ArrayBatch
Get a query that returns the slides in this batch.
getArraySlides() - Method in class net.sf.basedb.core.data.ArrayBatchData
This is the inverse end.
getAssayAnnotationField(String, String) - Method in class net.sf.basedb.util.export.spotdata.AbstractFieldConverter
Get an assay annotation field.
getAssayAnnotationsWriter() - Method in class net.sf.basedb.util.export.spotdata.BfsExporter
Get the writer were assay annotations should be printed.
getAssayField(String, boolean) - Method in class net.sf.basedb.util.export.spotdata.AdvancedFieldConverter
 
getAssayField(String, boolean) - Method in interface net.sf.basedb.util.export.spotdata.ExportableFieldConverter
Create an assay field for the given name.
getAssayField(String, boolean) - Method in class net.sf.basedb.util.export.spotdata.StandardFieldConverter
Find an assay field.
getAssayFields() - Method in class net.sf.basedb.util.export.spotdata.AbstractBioAssaySetExporter
Get the list of registered assay fields, in the order they were registered.
getAssayFields() - Method in class net.sf.basedb.util.export.spotdata.BaseFileExporter
 
getAssayFields() - Method in class net.sf.basedb.util.export.spotdata.BfsExporter
 
getAssayFields() - Method in class net.sf.basedb.util.importer.spotdata.BaseFileInfo.SpotSectionInfo
Get a list with all assay data fields, in the order they appear in the file.
getAssayFields(DbControl, BioAssaySet) - Method in class net.sf.basedb.plugins.BfsExporterPlugin
 
getAssayIndex(short) - Method in class net.sf.basedb.util.export.spotdata.AbstractBioAssaySetExporter
Get the cached index value for an assay when you know the assay's column number.
getAssayPropertyField(String, String) - Method in class net.sf.basedb.util.export.spotdata.AbstractFieldConverter
Get a static assay property field, such as name, description or id.
getAssays() - Method in class net.sf.basedb.util.importer.spotdata.BaseFileInfo.SpotSectionInfo
Get a list with the ID:s of all assays in the section, in the order they appear in the data columns.
getAssaysHaveParentAssaysMapping() - Method in class net.sf.basedb.util.importer.spotdata.BaseFileInfo
A flag that indicates if the BASEfile includes a mapping from child to parent assays.
getAssayValue(DbControl, BioAssay) - Method in class net.sf.basedb.util.export.spotdata.AnnotationAssayField
Return all annotation values that are related to the specified bioassay, or null if not configured.
getAssayValue(DbControl, BioAssay) - Method in interface net.sf.basedb.util.export.spotdata.AssayField
Get the values for the given bioassay.
getAssayValue(DbControl, BioAssay) - Method in class net.sf.basedb.util.export.spotdata.AssayPropertyField
Return all values that are given by the specified property.
getAssociatedDataFileType(DataFileType, boolean) - Method in class net.sf.basedb.core.ItemSubtype
Get information about a data file type that has been associated with this item subtype.
getAttribute(String) - Method in class net.sf.basedb.core.authentication.LoginRequest
Get the value of an extra attribute to use for the login request.
getAttribute(String) - Method in class net.sf.basedb.util.extensions.AboutBean
 
getAttribute(String) - Method in class net.sf.basedb.util.extensions.ClientContext
Get an attribute of the context.
getAttribute(String) - Method in interface net.sf.basedb.util.extensions.ExtendedAbout
Get extra information
getAttribute(String) - Method in class net.sf.basedb.util.extensions.ExtensionContext
 
getAttribute(String) - Method in class net.sf.basedb.util.extensions.ExtensionPointContext
Always null, since this is an extension point context.
getAttribute(String) - Method in class net.sf.basedb.util.extensions.InvokationContext
Get the value of an attribute that has been registered for the extension.
getAttribute(String) - Method in class net.sf.basedb.util.extensions.Registry.RegisteredAbout
 
getAttribute(String, String) - Method in class net.sf.basedb.util.extensions.Registry
Get the value of a extra attribute for a registered extension or extension point.
getAttribute(NodeAttribute<T>) - Method in class net.sf.basedb.util.overview.Node
Get the value for a node attribute.
getAttributeNames() - Method in class net.sf.basedb.util.extensions.AboutBean
 
getAttributeNames() - Method in interface net.sf.basedb.util.extensions.ExtendedAbout
Get all extra attribute names.
getAttributeNames() - Method in class net.sf.basedb.util.extensions.Registry.RegisteredAbout
 
getAttributesString(Object) - Static method in class net.sf.basedb.clients.web.extensions.DynamicActionAttributeSupport
If the object implements DynamicActionAttributes interface, get a string with all dynamic attributes, otherwise an empty string.
getAuthenticationMethod() - Method in class net.sf.basedb.core.authentication.AuthenticatedUser
Get the authentication method that was used to verify the login.
getAuthenticationMethod() - Method in class net.sf.basedb.core.data.SessionData
Get the authentication method used for this session.
getAuthenticationMethod() - Method in class net.sf.basedb.core.Session
Get the authentication method that was used to login to this session.
getAuthenticationMethod() - Method in class net.sf.basedb.core.SessionControl
Get the method that was used to authenticate the currently logged in user.
getAuthors() - Method in class net.sf.basedb.core.data.ExperimentData
Get the authors for this experiment.
getAuthors() - Method in class net.sf.basedb.core.Experiment
Get the authors of the publication for this experiment.
getAutoCompress() - Method in class net.sf.basedb.core.data.DirectoryData
If files that are uploaded to this directory be compressed or not.
getAutoCompress() - Method in class net.sf.basedb.core.data.MimeTypeData
If files of this MIME type should use auto-compression or not.
getAutoCompress() - Method in class net.sf.basedb.core.Directory
If files that are uploaded to this directory should be compressed or not.
getAutoCompress() - Method in class net.sf.basedb.core.MimeType
If files of this MIME type should automatically be compressed when they are uploaded to BASE.
getAutoFormatter() - Method in class net.sf.basedb.util.excel.XlsxTableWriter
Get the auto-formatter instance to use for columns that has no specified formatter via TableWriter.setColumnFormatter(int, Formatter).
getAutoJoinType() - Method in class net.sf.basedb.core.query.ReporterListExpression
Get the join type for automatic joins.
getAutoPermission() - Method in class net.sf.basedb.core.data.ProjectData
The permissions to use with automatic sharing to this project.
getAutoPermission() - Method in class net.sf.basedb.core.Project
The permissions to use when automatically sharing new items to the project when it is the active project.
getAutoShare() - Method in class net.sf.basedb.core.data.DirectoryData
If new files and subdirectories should inherit the share permission on this directory or not.
getAutoShare() - Method in class net.sf.basedb.core.Directory
If new files and subdirectories that are created in this directory automatically should be shared wtih the same permissions as this directory.
getAverageExpression(Expression) - Method in enum class net.sf.basedb.core.Formula.AverageMethod
Given an expression, create an expression that takes the correct average of it.
getAverageMethod() - Method in class net.sf.basedb.clients.web.taglib.table.TableColumn
 
getAverageMethod() - Method in class net.sf.basedb.core.data.ExtraValueTypeData
The average method for thid formula: 0 = none, Formula.AverageMethod.NONE; no average is defined for this formula 1 = geometric mean, Formula.AverageMethod.GEOMETRIC_MEAN; this formula uses geometric mean 2 = arithmetic mean, Formula.AverageMethod.ARITHMETIC_MEAN; this formula uses arithmetic mean 3 = min, Formula.AverageMethod.MIN; this formula uses the min value as a "mean" 4 = max, Formula.AverageMethod.MAX; this formula uses the max value as a "mean"
getAverageMethod() - Method in class net.sf.basedb.core.data.FormulaData
The average method for thid formula: 0 = none, Formula.AverageMethod.NONE; no average is defined for this formula 1 = geometric mean, Formula.AverageMethod.GEOMETRIC_MEAN; this formula uses geometric mean 2 = arithmetic mean, Formula.AverageMethod.ARITHMETIC_MEAN; this formula uses arithmetic mean 3 = min, Formula.AverageMethod.MIN; this formula uses the min value as a "mean" 4 = max, Formula.AverageMethod.MAX; this formula uses the max value as a "mean"
getAverageMethod() - Method in class net.sf.basedb.core.data.ReporterClonePropertyData
The code for the averate method to use when calculating averages.
getAverageMethod() - Method in class net.sf.basedb.core.ExtendedProperty
Which method to use when calculating the average of a set of values.
getAverageMethod() - Method in class net.sf.basedb.core.ExtraValueType
Get the average method for this extra value type.
getAverageMethod() - Method in class net.sf.basedb.core.Formula
Get the average method for this formula.
getAverageMethod() - Method in enum class net.sf.basedb.core.IntensityTransform
Get the averaging method to use when averaging values that has been transformed with the specified transformation.
getAverageMethod() - Method in class net.sf.basedb.util.export.spotdata.JepDynamicField
Get the average method to use if the exporter is exporting averaged data.
getAverageMethod() - Method in class net.sf.basedb.util.export.spotdata.SimpleDynamicField
Get the average method to use if the exporter is exporting averaged data.
getAverageOnReporter() - Method in class net.sf.basedb.util.export.spotdata.AbstractBioAssaySetExporter
 
getAverageOnReporter() - Method in class net.sf.basedb.util.export.spotdata.BaseFileExporter
 
getAvg() - Method in class net.sf.basedb.core.query.GeometricMeanExpression
 
getAwtColor() - Method in class net.sf.basedb.clients.web.ExperimentExplorer.AnnotationGroup
Get the AWT color object that corresponds to the HTML color string.
getBarcode() - Method in class net.sf.basedb.core.ArraySlide
Get the barcode of the slide.
getBarcode() - Method in class net.sf.basedb.core.BioPlate
Gets the barcode of this bio plate.
getBarcode() - Method in class net.sf.basedb.core.data.ArraySlideData
Get the barcode of the slide.
getBarcode() - Method in class net.sf.basedb.core.data.BioPlateData
Get the barcode for the bioplate.
getBarcode() - Method in class net.sf.basedb.core.data.PlateData
Get the barcode for the plate.
getBarcode() - Method in class net.sf.basedb.core.Plate
Get the barcode of this plate.
getBaseFileParser() - Method in class net.sf.basedb.util.importer.spotdata.BaseFileImporter
Get the underlying parser for the BASEfile.
getBaseFileWriter() - Method in class net.sf.basedb.util.export.spotdata.BaseFileExporter
Get the writer that writes the data to the file.
getBaseStyle() - Method in class net.sf.basedb.util.excel.CellStyleCreator
Get the current base style for new cells.
getBaseVersion() - Method in class net.sf.basedb.clients.web.taglib.Page
 
getBasicData() - Method in class net.sf.basedb.core.BasicItem
 
getBatchIndex() - Method in class net.sf.basedb.core.ArraySlide
Get the index of this slide in the batch.
getBatchIndex() - Method in class net.sf.basedb.core.data.ArraySlideData
Get the index of this slide in the batch.
getBatchSize() - Method in class net.sf.basedb.core.AbstractBatcher
 
getBatchSize() - Method in interface net.sf.basedb.core.Batcher
Get the current batch size of the batcher.
getBestMatch(String, Collection<? extends String>) - Method in class net.sf.basedb.util.fuzzy.StringMatcher
Find the string that is most similar to a given string in a list of strings.
getBestPairs(Collection<? extends String>, Collection<? extends String>) - Method in class net.sf.basedb.util.fuzzy.StringMatcher
Match strings in two lists.
getBFSSubtype() - Method in class net.sf.basedb.util.export.spotdata.BfsExporter
Get the BFS subtype.
getBFSSubtype() - Method in class net.sf.basedb.util.export.spotdata.MatrixBfsExporter
 
getBFSSubtype() - Method in class net.sf.basedb.util.export.spotdata.SerialBfsExporter
 
getBin(int) - Method in class net.sf.basedb.util.plot.HistogramPlot.HistogramSeries
 
getBioAssay(DbControl, short) - Method in class net.sf.basedb.clients.web.ExperimentExplorer
Get the bioassay with the specified column number in the data cube.
getBioAssays() - Method in class net.sf.basedb.core.BioAssaySet
Get a query returning the bioassays that are part of this bioassayset.
getBioAssays() - Method in class net.sf.basedb.core.data.BioAssaySetData
This is the inverse end.
getBioAssays() - Method in class net.sf.basedb.core.data.RawBioAssayData
This is the inverse end.
getBioAssays() - Method in class net.sf.basedb.util.export.spotdata.AbstractBioAssaySetExporter
Get a list with all bioassays in the source bioassay set.
getBioAssaySet() - Method in class net.sf.basedb.core.BioAssay
Get the bioassayset this bioassay belongs to.
getBioAssaySet() - Method in class net.sf.basedb.core.data.BioAssayData
Get the bioassayset this bioassay belongs to.
getBioAssaySet() - Method in class net.sf.basedb.core.data.ExtraValueData
Get the bioassayset this extra value belongs to.
getBioAssaySet() - Method in class net.sf.basedb.core.ExtraValue
Get the bioassayset this extra value belongs to.
getBioAssaySet(DbControl) - Method in class net.sf.basedb.clients.web.ExperimentExplorer
Get the bioassay set that is currently beeing explored.
getBioAssaySets() - Method in class net.sf.basedb.core.data.ExperimentData
This is the inverse end.
getBioAssaySets() - Method in class net.sf.basedb.core.Experiment
Get a query that return all bioassaysets in this experiment.
getBioMaterial() - Method in class net.sf.basedb.core.BioMaterialEvent
Get the MeasuredBioMaterial that was affected or created by this event.
getBioMaterial() - Method in class net.sf.basedb.core.BioMaterialEventSource
Get the biomaterial that was used as a source in this event.
getBioMaterial() - Method in class net.sf.basedb.core.BioWell
Gets the MeasuredBioMaterial connected to this biowell.
getBioMaterial() - Method in class net.sf.basedb.core.data.BioMaterialEventData
Get the biomaterial produced or affected by this event.
getBioMaterial() - Method in class net.sf.basedb.core.data.BioMaterialEventSourceData
Get the parent biomaterial that was used in the event.
getBioMaterial() - Method in class net.sf.basedb.core.data.BioWellData
The MeasuredBioMaterialData used in this well.
getBioMaterial(PlateCoordinate) - Method in class net.sf.basedb.core.BioPlate
Get the biomaterial in the well at the given location.
getBioMaterialEvents() - Method in class net.sf.basedb.core.BioPlateEvent
Get a query returning all biomaterial events linked to this event.
getBioMaterialEvents() - Method in class net.sf.basedb.core.data.BioPlateEventParticipantData
This is the inverse end.
getBioMaterialType() - Method in class net.sf.basedb.core.BioPlateType
Get the biomaterial type that can be stored on plates of this type.
getBioMaterialType() - Method in class net.sf.basedb.core.BioWell
Get the type of biomaterial that is placed in this well.
getBioMaterialType() - Method in class net.sf.basedb.core.data.BioPlateTypeData
If set, plates using this type can only hold the specific biomaterial type (eg. samples, extracts or labeled extracts).
getBioPlate() - Method in class net.sf.basedb.core.BioPlateEventParticipant
Get the BioPlate.
getBioPlate() - Method in class net.sf.basedb.core.data.BioPlateEventParticipantData
The bioplate that is participating in the event.
getBioPlate() - Method in class net.sf.basedb.core.data.BioWellData
The bioplate this well belongs to.
getBioPlateEventParticipant() - Method in class net.sf.basedb.core.BioMaterialEvent
Get the bioplate event participant that is the master of this event.
getBioPlateEventParticipant() - Method in class net.sf.basedb.core.data.BioMaterialEventData
Get the bioplate event that is the master event for this event.
getBioPlates() - Method in class net.sf.basedb.core.BioPlateType
Creates a query that returns all bioplates that are using this type.
getBioPlates() - Method in class net.sf.basedb.core.data.BioPlateTypeData
The bioplates that use this type.
getBioPlateType() - Method in class net.sf.basedb.core.BioPlate
Get the BioPlateType of this bioplate.
getBioPlateType() - Method in class net.sf.basedb.core.data.BioPlateData
Get the type of the bioplate.
getBioWell() - Method in class net.sf.basedb.core.data.MeasuredBioMaterialData
Get the bio well.
getBioWell() - Method in class net.sf.basedb.core.MeasuredBioMaterial
Get the well this biomaterial is located in.
getBioWell(int, int) - Method in class net.sf.basedb.core.BioPlate
Gets bio well for specific location.
getBioWell(PlateCoordinate) - Method in class net.sf.basedb.core.BioPlate
Gets bio well for specific location.
getBioWells() - Method in class net.sf.basedb.core.BioPlate
Gets a query that returns all BioWells on this plate.
getBioWells() - Method in class net.sf.basedb.core.data.BioPlateData
The wells on this plate.
getBlock() - Method in class net.sf.basedb.core.BlockInfo
Get the block number.
getBlock() - Method in class net.sf.basedb.core.data.RawData
 
getBlock() - Method in class net.sf.basedb.core.FeatureCoordinate
 
getBlock() - Method in class net.sf.basedb.plugins.PrintMapFlatFileImporter.MetaBlock
 
getBlockNumber() - Method in class net.sf.basedb.core.ArrayDesignBlock
Get the block number of this block.
getBlockNumber() - Method in class net.sf.basedb.core.data.ArrayDesignBlockData
Get the block number of this block.
getBlockNumber() - Method in enum class net.sf.basedb.plugins.PrintMapFlatFileImporter.Section
 
getBlockSizeX() - Method in class net.sf.basedb.core.ArrayDesignBlock
Get the number of columns in this block.
getBlockSizeX() - Method in class net.sf.basedb.core.data.ArrayDesignBlockData
Get the maximum number of rows in this block.
getBlockSizeX() - Method in class net.sf.basedb.plugins.PrintMapFlatFileImporter.MetaBlock
 
getBlockSizeY() - Method in class net.sf.basedb.core.ArrayDesignBlock
Get the number of rows in this block.
getBlockSizeY() - Method in class net.sf.basedb.core.data.ArrayDesignBlockData
Get the maximum number of columns in this block.
getBlockSizeY() - Method in class net.sf.basedb.plugins.PrintMapFlatFileImporter.MetaBlock
 
getBofType() - Method in class net.sf.basedb.util.parser.FlatFileParser
Get the value captured by the BOF marker regular expression.
getBoolean(String) - Static method in class net.sf.basedb.core.Config
Get the configuration setting specified by key as a boolean value.
getBoolean(String) - Method in class net.sf.basedb.plugins.Base1PluginExecuter
Creates a boolean from a string.
getBoolean(String) - Static method in class net.sf.basedb.util.Values
Convert a string to a boolean. '0', 'no', 'false', '' and the null string are converted to FALSE, all other values are converted to TRUE.
getBoolean(String, boolean) - Static method in class net.sf.basedb.util.Values
Convert a string to a boolean.
getBooleanAttribute(Element, String, boolean) - Static method in class net.sf.basedb.util.XmlUtil2
Get the value of an attribute as a boolean.
getBooleanFormatParameter() - Method in class net.sf.basedb.clients.web.plugins.SimpleExport
 
getBooleanFormatter(SessionControl) - Static method in class net.sf.basedb.clients.web.formatter.FormatterFactory
Get the logged in user's formatter for boolean values.
getBooleanOption(String, boolean) - Method in class net.sf.basedb.core.AnnotationType
Get an option and convert the value to a boolean.
getBooleanValues() - Method in class net.sf.basedb.core.data.annotations.AnnotationLink
 
getBuild() - Static method in class net.sf.basedb.core.Application
Get the build number.
getBuild() - Method in class net.sf.basedb.core.data.SchemaVersionData
The build number.
getBuild() - Static method in class net.sf.basedb.core.Version
Get the build version.
getButtonclass() - Method in class net.sf.basedb.clients.web.taglib.Select
 
getButtonicon() - Method in class net.sf.basedb.clients.web.taglib.Select
 
getButtonstyle() - Method in class net.sf.basedb.clients.web.taglib.Select
 
getButtonTag() - Method in class net.sf.basedb.clients.web.extensions.toolbar.CompactButtonRenderer
Get the HTML tag to use for the "button".
getButtonTag() - Method in class net.sf.basedb.clients.web.extensions.toolbar.CompactButtonRendererFactory
Get the HTML tag to use for the "button".
getButtontitle() - Method in class net.sf.basedb.clients.web.taglib.Select
 
getByClassName(DbControl, String) - Static method in class net.sf.basedb.core.PluginDefinition
Get a PluginDefinition item when you know the class name.
getByExtension(DbControl, String) - Static method in class net.sf.basedb.core.MimeType
Get a MimeType item when you know the file extension.
getByExternalId(String) - Method in class net.sf.basedb.core.ReporterBatcher
Get a reporter when you know the external id.
getByExternalId(String, boolean) - Method in class net.sf.basedb.core.ReporterBatcher
Get a reporter when you know the external id.
getByExternalId(DbControl, String) - Static method in class net.sf.basedb.core.Client
Get a Client item when you know the external ID.
getByExternalId(DbControl, String) - Static method in class net.sf.basedb.core.DataFileType
Get a DataFileType item when you know the external ID.
getByExternalId(DbControl, String) - Static method in class net.sf.basedb.core.ExtraValueType
Get a ExtraValueType when you know the external id.
getByExternalId(DbControl, String) - Static method in class net.sf.basedb.core.JobAgent
Get a JobAgent item when you know the external ID.
getByExternalId(DbControl, String) - Static method in class net.sf.basedb.core.Platform
Get a Platform item when you know the external ID.
getByExternalId(DbControl, String) - Static method in class net.sf.basedb.core.PlatformVariant
Get a PlatformVariant item when you know the external ID.
getByExternalId(DbControl, String) - Static method in class net.sf.basedb.core.Reporter
Get a ReporterData object when you know the external id.
getByExternalId(DbControl, String, Experiment) - Static method in class net.sf.basedb.core.Reporter
Get a ReporterData object when you know the external id, possibly using the cloned reporter annotations of the given experiment.
getById - Variable in enum class net.sf.basedb.core.Item
 
getById(DbControl, int) - Static method in class net.sf.basedb.core.Annotation
Get an Annotation item when you know the id.
getById(DbControl, int) - Static method in class net.sf.basedb.core.AnnotationSet
Get an AnnotationSet item when you know the id.
getById(DbControl, int) - Static method in class net.sf.basedb.core.AnnotationType
Get an AnnotationType item when you know the id.
getById(DbControl, int) - Static method in class net.sf.basedb.core.AnnotationTypeCategory
Get an AnnotationTypeCategory item when you know the id.
getById(DbControl, int) - Static method in class net.sf.basedb.core.AnyToAny
Get an AnyToAny link when you know the id.
getById(DbControl, int) - Static method in class net.sf.basedb.core.ArrayBatch
Get a ArrayBatch object when you know the ID.
getById(DbControl, int) - Static method in class net.sf.basedb.core.ArrayDesign
Get an ArrayDesign item when you know the ID.
getById(DbControl, int) - Static method in class net.sf.basedb.core.ArrayDesignBlock
Get a ArrayDesignBlock object when you know the ID.
getById(DbControl, int) - Static method in class net.sf.basedb.core.ArrayDesignPlate
Get a ArrayDesignPlate item when you know the id.
getById(DbControl, int) - Static method in class net.sf.basedb.core.ArraySlide
Get a ArraySlide object when you know the ID.
getById(DbControl, int) - Static method in class net.sf.basedb.core.BioAssay
Get a BioAssay item when you know the id.
getById(DbControl, int) - Static method in class net.sf.basedb.core.BioAssaySet
Get a BioAssaySet item when you know the id.
getById(DbControl, int) - Static method in class net.sf.basedb.core.BioMaterial
Get a biomaterial item when you know the id.
getById(DbControl, int) - Static method in class net.sf.basedb.core.BioMaterialEvent
Get a BioMaterialEvent item when you know the id.
getById(DbControl, int) - Static method in class net.sf.basedb.core.BioPlate
Gets a BioPlate when knowing the item's id
getById(DbControl, int) - Static method in class net.sf.basedb.core.BioPlateEvent
Get a BioPlateEvent item when you know the id.
getById(DbControl, int) - Static method in class net.sf.basedb.core.BioPlateEventParticipant
Get a BioPlateEventParticipant item when you know the id.
getById(DbControl, int) - Static method in class net.sf.basedb.core.BioPlateEventType
Gets a BioPlate event type when knowing the item's id
getById(DbControl, int) - Static method in class net.sf.basedb.core.BioPlateType
Gets a BioPlate type when knowing the item's id
getById(DbControl, int) - Static method in class net.sf.basedb.core.BioSource
Get an BioSource item when you know the id.
getById(DbControl, int) - Static method in class net.sf.basedb.core.BioWell
Get a BioWell item when you know the id.
getById(DbControl, int) - Static method in class net.sf.basedb.core.ChangeHistory
Get a ChangeHistory item when you know the ID.
getById(DbControl, int) - Static method in class net.sf.basedb.core.Client
Get a Client item when you know the ID.
getById(DbControl, int) - Static method in class net.sf.basedb.core.ClientDefaultSetting
Get a ClientDefaultSetting item when you know the ID.
getById(DbControl, int) - Static method in class net.sf.basedb.core.DataCube
Get a VirtualDb item when you know the id.
getById(DbControl, int) - Static method in class net.sf.basedb.core.DataCubeColumn
Get a DataCubeColumn item when you know the id.
getById(DbControl, int) - Static method in class net.sf.basedb.core.DataCubeExtraValue
Get a DataCubeExtraValue item when you know the id.
getById(DbControl, int) - Static method in class net.sf.basedb.core.DataCubeFilter
Get a DataCubeFilter item when you know the id.
getById(DbControl, int) - Static method in class net.sf.basedb.core.DataCubeLayer
Get a DataCubeLayer item when you know the id.
getById(DbControl, int) - Static method in class net.sf.basedb.core.DataFileType
Get a DataFileType object when you know the ID.
getById(DbControl, int) - Static method in class net.sf.basedb.core.DerivedBioAssay
Get a DerivedBioAssay item when you know the id.
getById(DbControl, int) - Static method in class net.sf.basedb.core.Directory
Get a Directory item when you know the ID.
getById(DbControl, int) - Static method in class net.sf.basedb.core.Experiment
Get an Experiment item when you know the id.
getById(DbControl, int) - Static method in class net.sf.basedb.core.Extract
Get an Extract item when you know the id.
getById(DbControl, int) - Static method in class net.sf.basedb.core.ExtraValue
Get an ExtraValue item when you know the id.
getById(DbControl, int) - Static method in class net.sf.basedb.core.ExtraValueType
Get an ExtraValueType object when you know the id.
getById(DbControl, int) - Static method in class net.sf.basedb.core.File
Get a File item when you know the id.
getById(DbControl, int) - Static method in class net.sf.basedb.core.FileServer
Get a FileServer item when you know the ID.
getById(DbControl, int) - Static method in class net.sf.basedb.core.FileSet
Get a FileSet item when you know the id.
getById(DbControl, int) - Static method in class net.sf.basedb.core.FileSetMember
Get a FileSetMember object when you know the ID.
getById(DbControl, int) - Static method in class net.sf.basedb.core.Formula
Get a Formula item when you know the ID.
getById(DbControl, int) - Static method in class net.sf.basedb.core.GlobalDefaultSetting
Get a ClientDefaultSetting item when you know the ID.
getById(DbControl, int) - Static method in class net.sf.basedb.core.Group
Get a Group item when you know the ID.
getById(DbControl, int) - Static method in class net.sf.basedb.core.Hardware
Get a Hardware item when you know the ID.
getById(DbControl, int) - Static method in class net.sf.basedb.core.Help
Get a Help item when you know the ID.
getById(DbControl, int) - Method in enum class net.sf.basedb.core.Item
Get the item of the type represented by this enumeration constant with the specified id.
getById(DbControl, int) - Static method in class net.sf.basedb.core.ItemKey
Get an ItemKey item when you know the ID.
getById(DbControl, int) - Static method in class net.sf.basedb.core.ItemList
Get an ItemList item when you know the id.
getById(DbControl, int) - Static method in class net.sf.basedb.core.ItemSubtype
Get an item subtype object when you know the ID.
getById(DbControl, int) - Static method in class net.sf.basedb.core.ItemSubtypeFileType
Get a PlatformFileType object when you know the ID.
getById(DbControl, int) - Static method in class net.sf.basedb.core.Job
Get a Job item when you know the id.
getById(DbControl, int) - Static method in class net.sf.basedb.core.JobAgent
Get a JobAgent object when you know the ID.
getById(DbControl, int) - Static method in class net.sf.basedb.core.JobAgentSettings
Get a JobAgentSettings item when you know the ID.
getById(DbControl, int) - Static method in class net.sf.basedb.core.Kit
Get a Kit item when you know the ID.
getById(DbControl, int) - Static method in class net.sf.basedb.core.Message
Get a Message item when you know the id.
getById(DbControl, int) - Static method in class net.sf.basedb.core.MimeType
Get a MimeType object when you know the ID.
getById(DbControl, int) - Static method in class net.sf.basedb.core.News
Get a News item when you know the ID.
getById(DbControl, int) - Static method in class net.sf.basedb.core.PermissionTemplate
Get a permission template item when you know the id.
getById(DbControl, int) - Static method in class net.sf.basedb.core.PhysicalBioAssay
Get a Hybridization item when you know the id.
getById(DbControl, int) - Static method in class net.sf.basedb.core.Plate
Get a Plate item when you know the id.
getById(DbControl, int) - Static method in class net.sf.basedb.core.PlateEvent
Get a PlateEvent item when you know the id.
getById(DbControl, int) - Static method in class net.sf.basedb.core.PlateEventType
Get a PlateEventType item when you know the id.
getById(DbControl, int) - Static method in class net.sf.basedb.core.PlateGeometry
Get a PlateGeometry item when you know the id.
getById(DbControl, int) - Static method in class net.sf.basedb.core.PlateMapping
Get a PlateMapping item when you know the id.
getById(DbControl, int) - Static method in class net.sf.basedb.core.PlateType
Get a PlateType item when you know the id.
getById(DbControl, int) - Static method in class net.sf.basedb.core.Platform
Get a Platform object when you know the ID.
getById(DbControl, int) - Static method in class net.sf.basedb.core.PlatformFileType
Get a PlatformFileType object when you know the ID.
getById(DbControl, int) - Static method in class net.sf.basedb.core.PlatformVariant
Get a PlatformVariant object when you know the ID.
getById(DbControl, int) - Static method in class net.sf.basedb.core.PluginConfiguration
Get a PluginConfiguration item when you know the ID.
getById(DbControl, int) - Static method in class net.sf.basedb.core.PluginDefinition
Get a PluginDefinition item when you know the ID.
getById(DbControl, int) - Static method in class net.sf.basedb.core.PluginType
Get a PluginType object when you know the ID.
getById(DbControl, int) - Static method in class net.sf.basedb.core.Project
Get a Project item when you know the ID.
getById(DbControl, int) - Static method in class net.sf.basedb.core.ProjectKey
Get a ProjectKey item when you know the ID.
getById(DbControl, int) - Static method in class net.sf.basedb.core.Protocol
Get a Protocol item when you know the ID.
getById(DbControl, int) - Static method in class net.sf.basedb.core.Quantity
Get a Quantity object when you know the ID.
getById(DbControl, int) - Static method in class net.sf.basedb.core.Quota
Get a Quota item when you know the ID.
getById(DbControl, int) - Static method in class net.sf.basedb.core.QuotaType
Get a QuotaType object when you know the id.
getById(DbControl, int) - Static method in class net.sf.basedb.core.RawBioAssay
Get a RawBioAssay object when you know the id.
getById(DbControl, int) - Static method in class net.sf.basedb.core.Reporter
Get a ReporterData object when you know the ID.
getById(DbControl, int) - Static method in class net.sf.basedb.core.ReporterCloneTemplate
Get a reporter clone template item when you know the id.
getById(DbControl, int) - Static method in class net.sf.basedb.core.ReporterList
Get a ReporterList item when you know the ID.
getById(DbControl, int) - Static method in class net.sf.basedb.core.ReporterType
Get a ReporterType object when you know the ID.
getById(DbControl, int) - Static method in class net.sf.basedb.core.Role
Get a Role item when you know the ID.
getById(DbControl, int) - Static method in class net.sf.basedb.core.RoleKey
Get a RoleKey item when you know the ID.
getById(DbControl, int) - Static method in class net.sf.basedb.core.RootRawBioAssay
Get a RootRawBioAssay item when you know the id.
getById(DbControl, int) - Static method in class net.sf.basedb.core.Sample
Get an Sample item when you know the id.
getById(DbControl, int) - Static method in class net.sf.basedb.core.Session
Get a Session item when you know the ID.
getById(DbControl, int) - Static method in class net.sf.basedb.core.Setting
Get a Setting item when you know the ID.
getById(DbControl, int) - Static method in class net.sf.basedb.core.Software
Get a Software item when you know the ID.
getById(DbControl, int) - Static method in class net.sf.basedb.core.SyncFilter
Get a SyncFilter item when you know the id.
getById(DbControl, int) - Static method in class net.sf.basedb.core.Tag
Get a Tag item when you know the id.
getById(DbControl, int) - Static method in class net.sf.basedb.core.Transformation
Get a Transformation item when you know the id.
getById(DbControl, int) - Static method in class net.sf.basedb.core.Unit
Get a Unit object when you know the ID.
getById(DbControl, int) - Static method in class net.sf.basedb.core.User
Get a User item when you know the ID.
getById(DbControl, int) - Static method in class net.sf.basedb.core.UserClientSetting
Get a UserClientSetting item when you know the ID.
getById(DbControl, int) - Static method in class net.sf.basedb.core.UserDefaultSetting
Get a UserDefaultSetting item when you know the ID.
getById(DbControl, int) - Static method in class net.sf.basedb.core.UserDevice
Get a UserDevice item when you know the ID.
getById(DbControl, int) - Static method in class net.sf.basedb.core.VirtualDb
Get a VirtualDb item when you know the id.
getById(DbControl, int) - Static method in class net.sf.basedb.core.Well
Get a Well item when you know the id.
getById(DbControl, int, boolean) - Static method in class net.sf.basedb.core.Annotation
Get an Annotation item when you know the id and ignore the rules for project-specific annotations when modifying the values.
getById(DbControl, int, Experiment) - Static method in class net.sf.basedb.core.Reporter
Get a ReporterData object when you know the ID, possibly using the cloned reporter annotations of the given experiment.
getById(DbControl, String) - Static method in class net.sf.basedb.core.BioPlateEventType
Gets a BioPlate event type when knowing the item's system id
getByInterfaceName(DbControl, String) - Static method in class net.sf.basedb.core.PluginType
Get a PluginType object when you know the interface name it represents.
getByItemType(DbControl, Item) - Static method in class net.sf.basedb.core.RoleKey
Get a RoleKey item when you know the Item type.
getByName(String) - Static method in enum class net.sf.basedb.util.formatter.BooleanFormatter.Type
Get the type by name of the static constant defined in this class.
getByName(DbControl, BasicItem, String) - Static method in class net.sf.basedb.core.AnyToAny
Get an AnyToAny link when you know the item it is linking from and the name of the link.
getByPath(DbControl, Path) - Static method in class net.sf.basedb.core.Directory
Get a Directory item when you know the path.
getByPath(DbControl, Path, boolean) - Static method in class net.sf.basedb.core.Directory
Get an existing Directory or create a new one if the given path doesn't exists.
getByPath(DbControl, Path, boolean) - Static method in class net.sf.basedb.core.File
Get a File item when you know the path.
getBytes() - Method in class net.sf.basedb.core.data.DataCubeData
The number of bytes the analysed data in this cube occupies on disk.
getBytes() - Method in class net.sf.basedb.core.data.DataCubeExtraValueData
The number of bytes the extra values data occupies on disk.
getBytes() - Method in class net.sf.basedb.core.data.DataCubeFilterData
The number of bytes the analysed data in this cube occupies on disk.
getBytes() - Method in class net.sf.basedb.core.data.DataCubeLayerData
The number of bytes the analysed data in this cube occupies on disk.
getBytes() - Method in class net.sf.basedb.core.data.DiskUsageData
Get the number of bytes the DiskConsumable item is using.
getBytes() - Method in class net.sf.basedb.core.data.ExperimentData
The number of bytes the analysed data in this experiment occupies on disk.
getBytes() - Method in class net.sf.basedb.core.data.RawBioAssayData
The number of bytes the raw data occupies on disk.
getBytes() - Method in class net.sf.basedb.core.data.ReporterCloneTemplateData
The number of bytes the cloned reporter information uses in the dynamic database.
getBytes() - Method in class net.sf.basedb.core.DataCube
Gets the number of bytes the analysed data in this cube occupies on disk.
getBytes() - Method in class net.sf.basedb.core.DataCubeExtraValue
Get the number of bytes the data stored in this layer occupies on disk.
getBytes() - Method in class net.sf.basedb.core.DataCubeFilter
Get the number of bytes the data stored in this filter occupies on disk.
getBytes() - Method in class net.sf.basedb.core.DataCubeLayer
Get the number of bytes the data stored in this layer occupies on disk.
getBytes() - Method in interface net.sf.basedb.core.DiskConsumable
Get the absolute number of bytes this item uses.
getBytes() - Method in class net.sf.basedb.core.DiskUsage
Get the number of bytes the DiskConsumable item is using.
getBytes() - Method in class net.sf.basedb.core.Experiment
 
getBytes() - Method in class net.sf.basedb.core.File
 
getBytes() - Method in class net.sf.basedb.core.RawBioAssay
 
getBytes() - Method in class net.sf.basedb.core.ReporterCloneTemplate
Get the number of bytes the cloned reporter information use in the database.
getBytesPerRow(Experiment) - Method in enum class net.sf.basedb.core.VirtualTable
 
getBytesPerRow(VirtualDb) - Method in enum class net.sf.basedb.core.VirtualTable
Get the number of bytes a single row in the database occupies.
getByType(FlatFileParser.Data, Type) - Method in interface net.sf.basedb.util.parser.Mapper
 
getCache() - Method in class net.sf.basedb.util.listable.TransformContext
Get a cache that can be used for storing transformation results for some time.
getCachedDownloadStream() - Method in class net.sf.basedb.core.File
Get a (possible) cached stream for reading from the file.
getCachedObject(Object) - Method in class net.sf.basedb.util.overview.GenericOverview
Retreive an object stored in the overview cache.
getCachedObject(Object) - Method in interface net.sf.basedb.util.overview.OverviewContext
Retreive an object stored in the overview cache.
getCachedQuery(String) - Method in class net.sf.basedb.core.hibernate.AbstractQueryCache
Get a cached query.
getCachedQuery(String, Class<T>) - Method in class net.sf.basedb.core.hibernate.AbstractQueryCache
 
getCacheKey(int) - Static method in class net.sf.basedb.core.snapshot.SnapshotManager
The static cache key under which the snapshot for the annotation set with the given id is cached.
getCacheMode() - Method in class net.sf.basedb.core.hibernate.QueryWrapper
 
getCacheMode() - Method in class net.sf.basedb.core.hibernate.SessionWrapper
 
getCacheRegion() - Method in class net.sf.basedb.core.hibernate.QueryWrapper
 
getCacheSize() - Method in class net.sf.basedb.clients.web.ExperimentExplorer
The number of reporter id'd to cache.
getCaseSensitiveVarchar(int) - Method in class net.sf.basedb.core.dbengine.AbstractDbEngine
Return null.
getCaseSensitiveVarchar(int) - Method in interface net.sf.basedb.core.dbengine.DbEngine
Generate a column declaration that creates a case-sensitive variable-length string column type.
getCaseSensitiveVarchar(int) - Method in class net.sf.basedb.core.dbengine.MySQLEngine
Return varchar(length) CHARACTER SET utf8 COLLATE utf8_bin.
getCatalog() - Method in class net.sf.basedb.core.ServiceSessionControl
 
getCatalogName(String, String) - Method in class net.sf.basedb.core.dbengine.AbstractDbEngine
Return the catalog name.
getCatalogName(String, String) - Method in interface net.sf.basedb.core.dbengine.DbEngine
Get the catalog name to use for referencing the given catalog/schema pair.
getCatalogName(String, String) - Method in class net.sf.basedb.core.dbengine.MySQLEngine
Generates a catalog name by combining the catalog and schema name (catalog_schema).
getCategories() - Method in class net.sf.basedb.core.AnnotationType
Get a query that returns the categories an annotation type belongs to.
getCategories() - Method in class net.sf.basedb.core.data.AnnotationTypeData
Get the set that manages the categories of this annotation type.
getCategories() - Method in class net.sf.basedb.core.ItemSubtype
Get a query returning the annotation type categories that are related to this subtype (sub-categories are not checked).
getCategories(List<?>) - Method in class net.sf.basedb.core.ItemSubtype
Get a query returning the annotation type categories that are related to this subtype and associated with the given subcategories.
getCell(int, int) - Method in class net.sf.basedb.util.excel.XlsxToCsvUtil.SheetInfo
Get the cell at the specified row and column.
getCellClass() - Method in class net.sf.basedb.clients.web.extensions.list.AbstractListColumnBean
 
getCellClass() - Method in interface net.sf.basedb.clients.web.extensions.list.ListColumnAction
Optional extra classes to add to table cell (td) tags for this column.
getCellStyle() - Method in class net.sf.basedb.clients.web.extensions.list.AbstractListColumnBean
 
getCellStyle() - Method in interface net.sf.basedb.clients.web.extensions.list.ListColumnAction
Optional extra style definition to add to table cell (td) tags for this column.
getCellStyle(String) - Method in class net.sf.basedb.util.excel.CellStyleCreator
Get the cell style for the given format string.
getCellStyleCreator() - Method in class net.sf.basedb.util.excel.XlsxTableWriter
Get the style creator that can be used for custom styling of cells.
getCellValueAsDate(Cell, Formatter<Date>, boolean) - Method in class net.sf.basedb.util.excel.XlsxToCsvUtil.SheetInfo
Get the cell value as a date.
getCellValueAsNumber(Cell, NumberFormat, boolean) - Method in class net.sf.basedb.util.excel.XlsxToCsvUtil.SheetInfo
Get the cell value as a number.
getCellValueAsString(Cell) - Method in class net.sf.basedb.util.excel.XlsxToCsvUtil.SheetInfo
Get the the cell value as a string.
getCertificate(InputStream, String, String) - Static method in class net.sf.basedb.util.ssl.SSLUtil2
Get the certificate that is found in the given input stream.
getCertificateChain(String) - Method in class net.sf.basedb.util.ssl.StaticKeyManager
 
getChangeHistory() - Method in class net.sf.basedb.core.data.ChangeHistoryDetailData
Get the main history entry the details belong to.
getChangeInfo() - Method in class net.sf.basedb.core.ChangeHistory
Get some additional free-text information about the change.
getChangeInfo() - Method in class net.sf.basedb.core.data.ChangeHistoryDetailData
Get more information about this change.
getChangesBy(Job) - Static method in class net.sf.basedb.core.ChangeHistory
Get all changes made by the specified job.
getChangesBy(User) - Static method in class net.sf.basedb.core.ChangeHistory
Get all changes made by the specified user.
getChangesIn(Session) - Static method in class net.sf.basedb.core.ChangeHistory
Get all changes made in the specified session.
getChangeType() - Method in class net.sf.basedb.core.ChangeHistory
Get the type of change that was made.
getChangeType() - Method in class net.sf.basedb.core.data.ChangeHistoryDetailData
The type of the change: 1 = create, 2 = update, 3 = delete
getChangeType() - Method in class net.sf.basedb.core.log.EntityDetails
Was it a creation/update/deletion?
getChangeType() - Method in class net.sf.basedb.core.log.ManualLogEntry
Get the change type.
getChannel() - Method in class net.sf.basedb.core.RawDataProperty
Get the channel this property belongs to.
getChannels() - Method in class net.sf.basedb.core.data.FormulaData
The number of required channels in the experiment to use this formula, or 0 if the number of channels doesn't matter.
getChannels() - Method in class net.sf.basedb.core.data.PlatformData
The number of channels this platform uses.
getChannels() - Method in class net.sf.basedb.core.data.PlatformVariantData
The number of channels this platform variant uses.
getChannels() - Method in class net.sf.basedb.core.Formula
Get the number of channels required to be able to use this formula.
getChannels() - Method in class net.sf.basedb.core.RawDataType
The number of channels in this raw data type.
getCharacterSet() - Method in class net.sf.basedb.core.data.FileData
Get the character set used in this file (for text-files only).
getCharacterSet() - Method in class net.sf.basedb.core.File
Get the character set used in this file (for text-files only).
getCharacterSet() - Method in class net.sf.basedb.core.plugin.ImportInputStream
Get the character set used by the source if it is a text-file.
getCharacterSet() - Method in class net.sf.basedb.util.FileImportInputStream
Calls File.getCharacterSet(), unless a character set was specified in the constructor.
getCharacterSet() - Method in class net.sf.basedb.util.importer.BaseFileWrapper
 
getCharacterSet() - Method in class net.sf.basedb.util.importer.DiskFileWrapper
 
getCharacterSet() - Method in interface net.sf.basedb.util.importer.FileWrapper
Get the character set used in the file.
getCharacterSet() - Method in class net.sf.basedb.util.importer.spotdata.BaseFileInfo
Get the character set used by the file, or null if not known.
getCharacterSet() - Method in class net.sf.basedb.util.uri.UriMetadata
Get the character set used by the resource.
getCharset() - Static method in class net.sf.basedb.core.Config
Get the default character set to use when no other has been specified.
getCharset() - Method in class net.sf.basedb.core.File.CharsetTesterThread
 
getCharset() - Method in class net.sf.basedb.plugins.AbstractFlatFileImporter
Get the character set the file uses.
getCharset() - Method in class net.sf.basedb.util.charset.CharsetDetector
Get the character set this detector is configured to use.
getCharset() - Method in class net.sf.basedb.util.excel.XlsxToCsvUtil
Get the current character set.
getCharset(String) - Static method in class net.sf.basedb.util.charset.CharsetUtil
Get a character set by name.
getCharset(Request) - Method in class net.sf.basedb.plugins.AbstractFlatFileImporter
Get the character set the file uses.
getChart() - Method in class net.sf.basedb.util.plot.HistogramPlot
Get the underlying JFreeChar object.
getChart() - Method in class net.sf.basedb.util.plot.ScatterPlot
Get the underlying JFreeChar object.
getChild() - Method in class net.sf.basedb.util.importer.spotdata.BaseFileInfo.ChildBioAssay
Get the real child bioassay object once it has been created and scheduled for saving into the database.
getChild(String) - Method in class net.sf.basedb.util.overview.Node
Get the child node with a specific name.
getChildAssay(int) - Method in class net.sf.basedb.util.importer.spotdata.BaseFileInfo
Get the child bioassay with the given id (from the BASEfile).
getChildAssays() - Method in class net.sf.basedb.util.importer.spotdata.BaseFileInfo
Get information about all child bioassays referenced in the file.
getChildColumns(short) - Method in class net.sf.basedb.util.importer.spotdata.BaseFileInfo
Get all child columns that have been mapped to the specified parent column.
getChildCreationEvents() - Method in class net.sf.basedb.core.BioMaterial
Get a query returning all events where this biomaterial has been used as a source item.
getChildCreationEvents() - Method in class net.sf.basedb.core.data.BioMaterialData
This is the inverse end.
getChildDescriptionParameter(String, String, String) - Method in class net.sf.basedb.core.plugin.AbstractAnalysisPlugin
Create a plugin parameter that asks for the description of the child bioassay set.
getChildErrors() - Method in class net.sf.basedb.util.overview.Node
Get the number of errors to children of this node.
getChildExtracts() - Method in class net.sf.basedb.core.Extract
Creates a query that returns all child (pooled) extracts that has this extracts as one of it's sources.
getChildHasDifferentReporterPositionMapping() - Method in class net.sf.basedb.util.importer.spotdata.BaseFileInfo
A flag that indicates if the child data has a different position/reporter mapping than the parent bioassay set.
getChildId() - Method in class net.sf.basedb.core.data.keyring.GroupGroups
Get the id of the child group.
getChildNameParameter(String, String, String) - Method in class net.sf.basedb.core.plugin.AbstractAnalysisPlugin
Create a plugin parameter that asks for the name of the child bioassay set.
getChildNodeDirection() - Method in class net.sf.basedb.util.overview.Node
Get the direction to use when loading children of this node.
getChildPlates() - Method in class net.sf.basedb.core.Plate
Get a query returning the child plates of this plate.
getChildren() - Method in class net.sf.basedb.clients.web.ExperimentExplorer.InExpression
 
getChildren() - Method in class net.sf.basedb.core.AnnotationRestriction
 
getChildren() - Method in class net.sf.basedb.core.AnnotationSet.ProjectSpecificAnnotationsRestriction
 
getChildren() - Method in class net.sf.basedb.core.data.BioAssayData
This is the inverse end to BioAssayData.getParents().
getChildren() - Method in class net.sf.basedb.core.data.BioMaterialData
This is the inverse end.
getChildren() - Method in class net.sf.basedb.core.data.DerivedBioAssayData
This is the inverse end.
getChildren() - Method in class net.sf.basedb.core.data.GroupData
Get the set that manages which other groups are members of this group.
getChildren() - Method in class net.sf.basedb.core.data.PlateData
The childs plates created by plate mappings.
getChildren() - Method in class net.sf.basedb.core.DerivedBioAssay
Get all child derived bioassays.
getChildren() - Method in class net.sf.basedb.core.DynamicJoin
 
getChildren() - Method in class net.sf.basedb.core.DynamicRestriction
 
getChildren() - Method in class net.sf.basedb.core.ExtraValueExpression
 
getChildren() - Method in class net.sf.basedb.core.ExtraValueJoin
 
getChildren() - Method in class net.sf.basedb.core.MeanRawDataPropertyExpression
 
getChildren() - Method in class net.sf.basedb.core.query.AbsExpression
 
getChildren() - Method in class net.sf.basedb.core.query.AddExpression
 
getChildren() - Method in class net.sf.basedb.core.query.AndRestriction
 
getChildren() - Method in class net.sf.basedb.core.query.AnnotationJoin
 
getChildren() - Method in class net.sf.basedb.core.query.AnyToAnyRestriction
 
getChildren() - Method in class net.sf.basedb.core.query.AscOrder
 
getChildren() - Method in class net.sf.basedb.core.query.BetweenRestriction
 
getChildren() - Method in class net.sf.basedb.core.query.BooleanExpression
 
getChildren() - Method in class net.sf.basedb.core.query.CaseExpression
 
getChildren() - Method in class net.sf.basedb.core.query.ConditionalQueryElement
 
getChildren() - Method in class net.sf.basedb.core.query.CountExpression
 
getChildren() - Method in class net.sf.basedb.core.query.DescOrder
 
getChildren() - Method in class net.sf.basedb.core.query.DivideExpression
 
getChildren() - Method in class net.sf.basedb.core.query.EqRestriction
 
getChildren() - Method in class net.sf.basedb.core.query.ExpExpression
 
getChildren() - Method in class net.sf.basedb.core.query.ExpressionSelect
 
getChildren() - Method in class net.sf.basedb.core.query.FloatExpression
 
getChildren() - Method in class net.sf.basedb.core.query.GeometricMeanExpression
 
getChildren() - Method in class net.sf.basedb.core.query.GteqRestriction
 
getChildren() - Method in class net.sf.basedb.core.query.GtRestriction
 
getChildren() - Method in class net.sf.basedb.core.query.HqlElementsExpression
 
getChildren() - Method in class net.sf.basedb.core.query.HqlEntityExpression
 
getChildren() - Method in class net.sf.basedb.core.query.HqlEntityParameterExpression
 
getChildren() - Method in class net.sf.basedb.core.query.HqlExpression
 
getChildren() - Method in class net.sf.basedb.core.query.HqlIndexExpression
 
getChildren() - Method in class net.sf.basedb.core.query.HqlInnerJoin
 
getChildren() - Method in class net.sf.basedb.core.query.HqlLeftJoin
 
getChildren() - Method in class net.sf.basedb.core.query.HqlPropertyExpression
 
getChildren() - Method in class net.sf.basedb.core.query.HqlRightJoin
 
getChildren() - Method in class net.sf.basedb.core.query.HqlSizeExpression
 
getChildren() - Method in class net.sf.basedb.core.query.IdListRestriction
 
getChildren() - Method in class net.sf.basedb.core.query.InRestriction
 
getChildren() - Method in class net.sf.basedb.core.query.IntegerExpression
 
getChildren() - Method in class net.sf.basedb.core.query.LikeRestriction
 
getChildren() - Method in class net.sf.basedb.core.query.LogExpression
 
getChildren() - Method in class net.sf.basedb.core.query.LteqRestriction
 
getChildren() - Method in class net.sf.basedb.core.query.LtRestriction
 
getChildren() - Method in class net.sf.basedb.core.query.MaxExpression
 
getChildren() - Method in class net.sf.basedb.core.query.MeanExpression
 
getChildren() - Method in class net.sf.basedb.core.query.MinExpression
 
getChildren() - Method in class net.sf.basedb.core.query.MultiplyExpression
 
getChildren() - Method in class net.sf.basedb.core.query.NegateExpression
 
getChildren() - Method in class net.sf.basedb.core.query.NeqRestriction
 
getChildren() - Method in class net.sf.basedb.core.query.NotRestriction
 
getChildren() - Method in class net.sf.basedb.core.query.OrRestriction
 
getChildren() - Method in class net.sf.basedb.core.query.ParameterExpression
 
getChildren() - Method in class net.sf.basedb.core.query.PermissionRestriction
 
getChildren() - Method in class net.sf.basedb.core.query.PowerExpression
 
getChildren() - Method in class net.sf.basedb.core.query.QuadraticMeanExpression
 
getChildren() - Method in interface net.sf.basedb.core.query.QueryElement
Get the children of this query element or null if it has no children.
getChildren() - Method in class net.sf.basedb.core.query.ReporterListExpression
 
getChildren() - Method in class net.sf.basedb.core.query.RlikeRestriction
 
getChildren() - Method in class net.sf.basedb.core.query.SelectedExpression
 
getChildren() - Method in class net.sf.basedb.core.query.SharedToRestriction
 
getChildren() - Method in class net.sf.basedb.core.query.SqlColumnExpression
 
getChildren() - Method in class net.sf.basedb.core.query.SqrtExpression
 
getChildren() - Method in class net.sf.basedb.core.query.SubqueryExpression
 
getChildren() - Method in class net.sf.basedb.core.query.SubtractExpression
 
getChildren() - Method in class net.sf.basedb.core.query.SumExpression
 
getChildren() - Method in class net.sf.basedb.core.query.ToDateExpression
 
getChildren() - Method in class net.sf.basedb.core.query.VirtualColumnExpression
 
getChildren() - Method in class net.sf.basedb.core.query.VirtualColumnExpression.WrappedExpression
 
getChildren() - Method in class net.sf.basedb.core.RawBioAssayPropertyExpression
 
getChildren() - Method in class net.sf.basedb.core.RawDataPropertyExpression
 
getChildren() - Method in class net.sf.basedb.core.RealJoin
 
getChildren() - Method in class net.sf.basedb.core.ReporterListJoin
 
getChildren() - Method in class net.sf.basedb.core.ReporterPropertyExpression
 
getChildren() - Method in class net.sf.basedb.util.overview.Node
Get all child nodes of this node.
getChildren() - Method in class net.sf.basedb.util.Tree.Entry
Get the list of entries for the children to this node.
getChildReporterPositions() - Method in class net.sf.basedb.util.importer.spotdata.BaseFileInfo
Get a map with all added child position/reporter mappings.
getChildSamples() - Method in class net.sf.basedb.core.Sample
Creates a query that returns all child (pooled) samples that has this sample as one of it's sources.
getChildWarnings() - Method in class net.sf.basedb.util.overview.Node
Get the number of warnings to children of this node.
getCircularRef(Node, BasicItem) - Static method in class net.sf.basedb.util.overview.OverviewUtil
Find the first parent node that has a reference to the given item.
getCity() - Method in class net.sf.basedb.util.GeoLocation
 
getClasses() - Static method in class net.sf.basedb.core.ExtendedProperties
Get a list with the name of all classes.
getClassLoader() - Method in class net.sf.basedb.core.hibernate.SessionFactoryConfiguration
Deprecated.
Get the schema.
getClassLoader() - Method in class net.sf.basedb.core.ServiceSessionControl.SessionFactoryConfiguration
Get the class loader used for accessing mapped classes.
getClassLoader() - Method in class net.sf.basedb.util.extensions.ExtensionContext
The class loader is the class loader that loaded the action factory of the extension.
getClassLoader() - Method in class net.sf.basedb.util.extensions.ExtensionPointContext
The class loader is the class loader that loaded the action class of the extension point.
getClassLoader() - Method in class net.sf.basedb.util.extensions.InvokationContext
Get the class loader that is used for the given extension or extension point.
getClassLoader() - Method in class net.sf.basedb.util.extensions.manager.ExtensionsFile
Get the class loader used to load classes for the extension.
getClassLoader() - Method in class net.sf.basedb.util.extensions.Registry.RegisteredExtension
 
getClassLoader() - Method in class net.sf.basedb.util.extensions.Registry.RegisteredExtensionPoint
 
getClassMapping(String) - Static method in class net.sf.basedb.core.HibernateUtil
 
getClassMappings() - Static method in class net.sf.basedb.core.HibernateUtil
 
getClassMetadata(String) - Static method in class net.sf.basedb.core.HibernateUtil
 
getClassName() - Method in class net.sf.basedb.core.data.PluginDefinitionData
Get the class name of the Java class that implements this plugin.
getClassName() - Method in class net.sf.basedb.core.PluginDefinition
Get the class name of the Java class that implements this plugin.
getClassName() - Method in class net.sf.basedb.util.extensions.xml.PluginInfo
Get the class name of the plug-in.
getClazz() - Method in class net.sf.basedb.clients.web.extensions.list.AbstractListColumnBean
 
getClazz() - Method in interface net.sf.basedb.clients.web.extensions.list.ListColumnAction
Optional HTML class attribute that is used to style the column through CSS.
getClazz() - Method in class net.sf.basedb.clients.web.extensions.login.FieldInfo
Get a class attribute that can used to style the input field.
getClazz() - Method in class net.sf.basedb.clients.web.extensions.menu.FixedMenuItemFactory
 
getClazz() - Method in interface net.sf.basedb.clients.web.extensions.menu.MenuItemAction
Class attribute to add to the main menu tag.
getClazz() - Method in class net.sf.basedb.clients.web.extensions.menu.MenuItemBean
 
getClazz() - Method in class net.sf.basedb.clients.web.extensions.tabcontrol.FixedTabFactory
 
getClazz() - Method in class net.sf.basedb.clients.web.extensions.tabcontrol.IncludeContentTabFactory.Tab
 
getClazz() - Method in interface net.sf.basedb.clients.web.extensions.tabcontrol.TabAction
Class attribute of the main tab tag.
getClazz() - Method in class net.sf.basedb.clients.web.extensions.tabcontrol.TabBean
 
getClazz() - Method in interface net.sf.basedb.clients.web.extensions.toolbar.ButtonAction
Class attribute of the main button tag.
getClazz() - Method in class net.sf.basedb.clients.web.extensions.toolbar.ButtonBean
 
getClazz() - Method in class net.sf.basedb.clients.web.extensions.toolbar.FixedButtonFactory
 
getClazz() - Method in class net.sf.basedb.clients.web.taglib.Body
 
getClazz() - Method in class net.sf.basedb.clients.web.taglib.ExceptionCatcher
 
getClazz() - Method in class net.sf.basedb.clients.web.taglib.StylableTag
 
getClazz() - Method in class net.sf.basedb.clients.web.taglib.tab.Tab
 
getClazz() - Method in class net.sf.basedb.clients.web.taglib.table.Button.ButtonActionWrapper
 
getClazz() - Method in class net.sf.basedb.clients.web.taglib.table.Cell
 
getClazz() - Method in class net.sf.basedb.clients.web.taglib.table.CellValue
 
getClearState() - Method in class net.sf.basedb.core.PluginResponse
If set after a job configuration sequence, the saved state should be cleared before starting the job.
getClient() - Method in class net.sf.basedb.core.ClientDefaultSetting
Get the client application this setting is valid for.
getClient() - Method in class net.sf.basedb.core.data.ChangeHistoryData
 
getClient() - Method in class net.sf.basedb.core.data.ClientDefaultSettingData
Get the client application this setting is valid for.
getClient() - Method in class net.sf.basedb.core.data.ContextData
Get the client which uses this context.
getClient() - Method in class net.sf.basedb.core.data.ContextIndex
Get the client which uses this context.
getClient() - Method in class net.sf.basedb.core.data.HelpData
Get the client for this help text.
getClient() - Method in class net.sf.basedb.core.data.SessionData
Get the client application the user was using.
getClient() - Method in class net.sf.basedb.core.data.UserClientSettingData
Get the client application this setting is valid for.
getClient() - Method in class net.sf.basedb.core.data.UserDeviceData
Get the client application this device is associated with.
getClient() - Method in class net.sf.basedb.core.Help
Get the client application this setting is valid for.
getClient() - Method in class net.sf.basedb.core.Session
Get the client application the user was using in this session.
getClient() - Method in class net.sf.basedb.core.UserClientSetting
Get the client application this setting is valid for.
getClient() - Method in class net.sf.basedb.core.UserDevice
Get the client application the user was using with this device.
getClient(DbControl) - Method in class net.sf.basedb.core.ChangeHistory
Load the client application that was used when the change was made.
getClient(DbControl) - Method in class net.sf.basedb.core.ChangeHistory.TransactionInfo
Load the client application that was used in the transaction.
getClient(DbControl, ChangeHistory, boolean, boolean) - Static method in class net.sf.basedb.clients.web.ChangeHistoryUtil
Get the client application that was used to make the change in HTML format.
getClientAliases(String, Principal[]) - Method in class net.sf.basedb.util.ssl.StaticKeyManager
 
getClientCertificate() - Method in class net.sf.basedb.core.data.FileServerData
Get the client certificate that we need to send to the server to make the server accept our connection.
getClientCertificate() - Method in class net.sf.basedb.core.FileServer
Get the client certificate that BASE should use to authenticate with the server when connecting with https.
getClientCertificate() - Method in class net.sf.basedb.util.uri.ConnectionParameters
Get the client certificate that BASE should use to authenticate with the server when connecting using SSL.
getClientCertificatePassword() - Method in class net.sf.basedb.core.data.FileServerData
Get the password that is used to unlock the client certificate.
getClientCertificatePassword() - Method in class net.sf.basedb.core.FileServer
Get the password that is needed to unlock the client certificate.
getClientCertificatePassword() - Method in class net.sf.basedb.util.uri.ConnectionParameters
Get the password that is needed to unlock the client certificate.
getClientContext() - Method in class net.sf.basedb.util.extensions.ExtensionContext
 
getClientContext() - Method in class net.sf.basedb.util.extensions.ExtensionPointContext
 
getClientContext() - Method in class net.sf.basedb.util.extensions.ExtensionsInvoker
Get the client context that is used by this invoker.
getClientContext() - Method in class net.sf.basedb.util.extensions.InvokationContext
Get the client context that was passed to the Registry.useExtensions(ClientContext, ExtensionsFilter, String...) method.
getClientDefaultSetting(String) - Method in class net.sf.basedb.core.SessionControl
Get the value of the ClientDefaultSetting with the specified name.
getClientId() - Method in class net.sf.basedb.core.ChangeHistory
Get the ID of the client application that was used to make the change.
getClientId() - Method in class net.sf.basedb.core.ChangeHistory.TransactionInfo
Get the ID of the client application that was used in the transaction.
getClientId() - Method in class net.sf.basedb.core.data.ChangeHistoryData
The ID of the client application the user used to make the change.
getClientId() - Method in class net.sf.basedb.core.log.TransactionDetails
Get the ID of the client appliction that is used, or 0 if not known.
getClientId() - Method in class net.sf.basedb.core.SessionControl
Get the id of the Client application that created this SessionControl.
getClientName() - Method in class net.sf.basedb.core.SessionControl
Get the name of the Client application that created this SessionControl.
getClientSettings() - Method in class net.sf.basedb.core.data.UserData
This is the inverse end.
getClientSettings(Client) - Method in class net.sf.basedb.core.User
Get a query that returns the settings for the specified client.
getClientWithExternalId(String) - Method in class net.sf.basedb.core.SessionControl
 
getClientX509Certificate() - Method in class net.sf.basedb.core.FileServer
Get the X.509 certificate for the client.
getClonableProperties() - Method in class net.sf.basedb.core.ReporterCloneTemplate
Get a list with all clonable properties in this template.
getClonableProperties(ReporterCloneTemplateData) - Static method in class net.sf.basedb.core.ReporterCloneTemplate
 
getClonableProperty(String) - Method in class net.sf.basedb.core.ReporterCloneTemplate
Get information about a clonable property that is included in this template.
getClone() - Method in class net.sf.basedb.util.annotations.InheritSpecification
 
getClonedSelectSql(VirtualDb) - Static method in class net.sf.basedb.core.Reporter
Generate an SQL statement for selecting ALL reporter properties from a cloned table.
getCmd() - Method in class net.sf.basedb.clients.jobagent.CmdLine
Get the command parameter
getCollected() - Method in class net.sf.basedb.util.listable.CollectExtracts
Get all extracts that has been collected.
getCollectedChildren() - Method in class net.sf.basedb.util.listable.CollectExtracts
getCollectedParents() - Method in class net.sf.basedb.util.listable.CollectExtracts
getCollectionFormatter() - Method in class net.sf.basedb.clients.web.extensions.list.AbstractListColumnBean
 
getCollectionFormatter() - Method in interface net.sf.basedb.clients.web.extensions.list.ListColumnAction
Get a formatter that is intended to format a collection of values that have been retrieved from this action.
getCollectionSeparatorParameter() - Method in class net.sf.basedb.clients.web.plugins.SimpleExport
 
getColor() - Method in class net.sf.basedb.clients.web.ExperimentExplorer.AnnotationGroup
Get a color code for HTML that is as distinct as possible from the color of the other groups.
getColor(float) - Method in class net.sf.basedb.util.ColorGenerator
Get the color for the value.
getColor(String) - Method in class net.sf.basedb.clients.web.servlet.ExperimentExplorerPlotServlet.ColumnKey
 
getColorFormatter(SessionControl, Coloring, Formatter<Number>) - Static method in class net.sf.basedb.clients.web.formatter.FormatterFactory
Get a formatter that adds a color box to the display which is a visual representation of the value.
getColorGenerator(SessionControl, Coloring) - Static method in class net.sf.basedb.clients.web.Base
 
getColoring() - Method in class net.sf.basedb.core.data.ExtraValueTypeData
Get the coloring information for this extra value type.
getColoring() - Method in class net.sf.basedb.core.data.FormulaData
Get the coloring information for this formula.
getColoring() - Method in class net.sf.basedb.core.ExtraValueType
Get coloring information for this extra value.
getColoring() - Method in class net.sf.basedb.core.Formula
Get coloring information for this formula.
getColspan() - Method in class net.sf.basedb.clients.web.taglib.table.Header
 
getColumn() - Method in class net.sf.basedb.clients.web.taglib.table.Cell
 
getColumn() - Method in class net.sf.basedb.core.BioWell
Gets the column index where this well is located.
getColumn() - Method in class net.sf.basedb.core.data.BioWellData
The column coordinate of this well.
getColumn() - Method in class net.sf.basedb.core.data.FeatureData
Get the column coordinate of the feature.
getColumn() - Method in class net.sf.basedb.core.data.MappingCoordinate
Get the column number.
getColumn() - Method in class net.sf.basedb.core.data.PlateCoordinate
Get the column number.
getColumn() - Method in class net.sf.basedb.core.data.RawData
 
getColumn() - Method in class net.sf.basedb.core.data.ReporterClonePropertyData
Get the name of database column.
getColumn() - Method in class net.sf.basedb.core.data.WellData
The column coordinate of this well.
getColumn() - Method in class net.sf.basedb.core.ExtendedProperty
Get the database column of the extended property.
getColumn() - Method in class net.sf.basedb.core.FeatureCoordinate
 
getColumn() - Method in class net.sf.basedb.core.VirtualColumn
Get the database column name of the column.
getColumn() - Method in class net.sf.basedb.core.Well
Get the column coordinate of this well on the plate.
getColumn(String) - Static method in class net.sf.basedb.core.RawBioAssayPropertyExpression
 
getColumn(String) - Static method in class net.sf.basedb.core.ReporterPropertyExpression
 
getColumn(RawDataType, String) - Static method in class net.sf.basedb.core.RawDataPropertyExpression
Get the database column name for the specified property of the specified raw data type.
getColumnContent() - Method in class net.sf.basedb.clients.web.taglib.table.Table
 
getColumnCount() - Method in class net.sf.basedb.util.bfs.AnnotationModel
Get the number of column.
getColumnCount() - Method in class net.sf.basedb.util.bfs.AnnotationWriter
Get the number of data columns.
getColumnCount() - Method in class net.sf.basedb.util.bfs.DataWriter
Get the number of data columns.
getColumnCount() - Method in class net.sf.basedb.util.bfs.MatrixModel
Get the number of columns.
getColumnFormatter(int) - Method in class net.sf.basedb.util.export.TableWriter
 
getColumnHeaderIndex(String) - Method in class net.sf.basedb.util.parser.FlatFileParser
Get the index of a column header with a given name.
getColumnHeaders() - Method in class net.sf.basedb.util.parser.FlatFileParser
Get all column headers that were found by splitting the line matching the FlatFileParser.setDataHeaderRegexp(Pattern) pattern using the FlatFileParser.setDataSplitterRegexp(Pattern) pattern.
getColumnIndex(String) - Method in class net.sf.basedb.util.bfs.AnnotationModel
Get the column index for a given header.
getColumnMappingParameterName() - Method in class net.sf.basedb.plugins.batchimport.AnnotationIdMethod
 
getColumnMappingParameterName() - Method in class net.sf.basedb.plugins.batchimport.FallbackIdMethod
 
getColumnMappingParameterName() - Method in class net.sf.basedb.plugins.batchimport.FileImporter.PathIdMethod
 
getColumnMappingParameterName() - Method in interface net.sf.basedb.plugins.batchimport.IdMethod
 
getColumnMappingParameterName() - Method in class net.sf.basedb.plugins.batchimport.InternalIdMethod
 
getColumnMappingParameterName() - Method in class net.sf.basedb.plugins.batchimport.MultiPropertyIdMethod
 
getColumnMappingParameterName() - Method in class net.sf.basedb.plugins.batchimport.PropertyIdMethod
 
getColumnName(RawDataProperty, RawBioAssay) - Static method in class net.sf.basedb.plugins.IlluminaRawDataImporter
Convert a raw data property to a column name.
getColumnNo() - Method in class net.sf.basedb.core.data.DataCubeColumnData
The column number of this column in the data cube.
getColumnNo() - Method in class net.sf.basedb.core.DataCubeColumn
Get the number of this column.
getColumnPrefixParameter() - Method in class net.sf.basedb.clients.web.plugins.SimpleExport
 
getColumnRestriction(PropertyFilter) - Method in interface net.sf.basedb.core.query.QueryFilterAction
Generate a restriction for the given filter.
getColumns() - Method in class net.sf.basedb.clients.web.taglib.table.Table
 
getColumns() - Method in class net.sf.basedb.core.BioPlate
Get the number of rows on this plate.
getColumns() - Method in class net.sf.basedb.core.data.DataCubeData
This is the inverse end.
getColumns() - Method in class net.sf.basedb.core.data.PlateGeometryData
The number of rows in this geometry.
getColumns() - Method in class net.sf.basedb.core.dbengine.TableInfo
Get information about the columns in the table.
getColumns() - Method in class net.sf.basedb.core.dbengine.TableInfo.IndexInfo
 
getColumns() - Method in class net.sf.basedb.core.dbengine.TableInfo.PrimaryKeyInfo
 
getColumns() - Method in class net.sf.basedb.core.PlateGeometry
Get the number of columns in this geometry.
getColumns(Experiment) - Method in enum class net.sf.basedb.core.VirtualTable
Get all columns in this table.
getColumns(VirtualDb) - Method in enum class net.sf.basedb.core.VirtualTable
Get all columns in this table.
getColumnSeparator() - Method in class net.sf.basedb.util.excel.XlsxToCsvUtil
Get the current column separator.
getColumnsFile(TableInfo) - Method in class net.sf.basedb.core.Migration
Get the columns file for the given table.
getColumnSubtitles() - Method in class net.sf.basedb.clients.web.taglib.table.Table
 
getCommand() - Method in class net.sf.basedb.core.plugin.NamespaceRequestWrapper
 
getCommand() - Method in interface net.sf.basedb.core.plugin.Request
The command the plugin should execute.
getCommand() - Method in class net.sf.basedb.core.PluginRequest
Get the command this request will issue to the plugin when PluginRequest.invoke() is called.
getCommand() - Method in class net.sf.basedb.core.PluginRequest.RequestImpl
 
getCommand() - Method in class net.sf.basedb.core.RequestInformation
Get the command this request information object is valid for.
getCommand() - Method in class net.sf.basedb.plugins.executor.ExternalProgramExecutor.RequestWrapper
 
getComment() - Method in class net.sf.basedb.core.authentication.LoginRequest
Get the comment to use.
getComment() - Method in class net.sf.basedb.core.BioMaterialEvent
Get the comment about this event.
getComment() - Method in class net.sf.basedb.core.data.BioMaterialEventData
Get the comment about this event.
getComment() - Method in class net.sf.basedb.core.data.PlateEventData
Get the comment about this event.
getComment() - Method in class net.sf.basedb.core.hibernate.QueryWrapper
 
getComment() - Method in class net.sf.basedb.core.PlateEvent
Get the comment about this event.
getCommonCharsets() - Static method in class net.sf.basedb.core.Config
Get a set containing the most common character sets used by text files.
getCommonName() - Method in class net.sf.basedb.plugins.Base1PluginExecuter.JobParameter
 
getCommonPrefix(Collection<String>) - Static method in class net.sf.basedb.core.StringUtil
Find the longest common prefix for a collection of strings.
getCompleted() - Method in class net.sf.basedb.core.SimpleAbsoluteProgressReporter
Get completed number of ticks of the task.
getCompressedSize() - Method in class net.sf.basedb.core.data.FileData
Get the size in bytes that this FileData object uses after compression.
getCompressedSize() - Method in class net.sf.basedb.core.File
Get the compressed size of this file.
getCondition() - Method in class net.sf.basedb.core.dbengine.TableInfo.IndexInfo
If a condition is specificed a partial index is created for rows that matches the conditions.
getCondition() - Method in class net.sf.basedb.core.query.WhenStatement
Get the condition of this statement.
getConfigDirectory() - Static method in class net.sf.basedb.core.Config
Get the directory where the BASE configuration files are located.
getConfigurationInstallOption(int) - Method in class net.sf.basedb.plugins.PluginConfigurationImporter
Returns if a configuration in a certain place/order in the XML-file should be imported
getConfigurations() - Method in class net.sf.basedb.core.data.PluginDefinitionData
This is the inverse end.
getConfigurationValues() - Method in class net.sf.basedb.core.data.PluginConfigurationData
Used by Hibernate to link with configuration values.
getConfigurationValues() - Method in class net.sf.basedb.core.hibernate.SchemaGenerator.CollectSqlTarget
 
getConfiguredColors(SessionControl) - Static method in class net.sf.basedb.clients.web.Base
 
getConfiguredJobParameters() - Method in class net.sf.basedb.plugins.HelpImporter
 
getConfiguredJobParameters() - Method in class net.sf.basedb.plugins.PluginConfigurationImporter
 
getConfiguredQuery(DbControl, ItemContext, boolean, ItemQuery<T>, ModeInfo) - Static method in class net.sf.basedb.clients.web.Base
getConfiguredQuery(DbControl, ItemContext, ClientContext, boolean, ItemQuery<T>, ModeInfo) - Static method in class net.sf.basedb.clients.web.Base
Configures a query.
getConfiguredSelectionParameters() - Method in class net.sf.basedb.plugins.PluginConfigurationImporter
Gets request information to set which configuration to import
getConfigureExecutorParameters(String) - Method in class net.sf.basedb.plugins.executor.BaseFileExporterSupport
 
getConfigureExecutorParameters(String) - Method in class net.sf.basedb.plugins.executor.BaseFileImporterSupport
 
getConfigureExecutorParameters(String) - Method in class net.sf.basedb.plugins.executor.BfsExporterSupport
 
getConfigureExecutorParameters(String) - Method in class net.sf.basedb.plugins.executor.BfsImporterSupport
 
getConfigureExecutorParameters(String) - Method in class net.sf.basedb.plugins.executor.FileOnlyImporterSupport
 
getConfigureExportImportPluginParameters() - Method in class net.sf.basedb.plugins.executor.ExternalProgramExecutor
 
getConfigureExternalParameters() - Method in class net.sf.basedb.plugins.executor.ExternalProgramExecutor
 
getConfigureImportParameters(GuiContext) - Method in class net.sf.basedb.plugins.AnnotationFlatFileImporter
Step 3 of 3.
getConfigureJobParameters() - Method in class net.sf.basedb.plugins.Base1PluginExecuter
Creates the information needed for job configuration and initiates the parameters.
getConfigureJobParameters() - Method in class net.sf.basedb.plugins.executor.ExternalProgramExecutor
 
getConfigureJobParameters() - Method in class net.sf.basedb.plugins.IntensityCalculatorPlugin
 
getConfigureJobParameters() - Method in class net.sf.basedb.plugins.JepExtraValueCalculator
 
getConfigureJobParameters() - Method in class net.sf.basedb.plugins.LowessNormalization
 
getConfigureJobParameters() - Method in class net.sf.basedb.plugins.MedianRatioNormalization
 
getConfigureJobParameters(Boolean) - Method in class net.sf.basedb.plugins.GalExporter
 
getConfigureJobParameters(Boolean) - Method in class net.sf.basedb.plugins.HelpExporter
 
getConfigureJobParameters(Boolean) - Method in class net.sf.basedb.plugins.PluginConfigurationExporter
 
getConfigureJobParameters(String) - Method in class net.sf.basedb.plugins.executor.BaseFileImporterSupport
 
getConfigureJobParameters(String) - Method in class net.sf.basedb.plugins.executor.BfsImporterSupport
 
getConfigureJobParameters(String) - Method in class net.sf.basedb.plugins.executor.FileOnlyImporterSupport
 
getConfigureJobParameters(GuiContext) - Method in class net.sf.basedb.clients.web.plugins.SimpleExport
 
getConfigureJobParameters(GuiContext) - Method in class net.sf.basedb.plugins.BfsExporterPlugin
 
getConfigureJobParameters(GuiContext) - Method in class net.sf.basedb.plugins.CdfFileReporterImporter
 
getConfigureJobParameters(GuiContext) - Method in class net.sf.basedb.plugins.FormulaFilter
 
getConfigureJobParameters(GuiContext) - Method in class net.sf.basedb.plugins.IlluminaRawDataImporter
 
getConfigureJobParameters(GuiContext) - Method in class net.sf.basedb.plugins.JepIntensityTransformer
 
getConfigureJobParameters(GuiContext) - Method in class net.sf.basedb.plugins.ManualDerivedBioAssayCreator
 
getConfigureJobParameters(GuiContext) - Method in class net.sf.basedb.plugins.ManualTransformCreator
 
getConfigureJobParameters(GuiContext) - Method in class net.sf.basedb.plugins.PlateFlatFileImporter
 
getConfigureJobParameters(GuiContext) - Method in class net.sf.basedb.plugins.PlateMappingImporter
 
getConfigureJobParameters(GuiContext) - Method in class net.sf.basedb.plugins.PrintMapFlatFileImporter
 
getConfigureJobParameters(GuiContext) - Method in class net.sf.basedb.plugins.RawDataFlatFileImporter
 
getConfigureJobParameters(GuiContext) - Method in class net.sf.basedb.plugins.ReporterFlatFileImporter
 
getConfigureJobParameters(GuiContext) - Method in class net.sf.basedb.plugins.ReporterMapFlatFileImporter
 
getConfigureJobParameters(GuiContext) - Method in class net.sf.basedb.util.zip.AbstractFileUnpacker
 
getConfigureJobParameters(GuiContext, Boolean) - Method in class net.sf.basedb.plugins.BaseFileExporterPlugin
 
getConfigureJobParameters(GuiContext, Boolean) - Method in class net.sf.basedb.plugins.PackedFileExporter
 
getConfigureJobParameters(GuiContext, Boolean) - Method in class net.sf.basedb.plugins.PlateMappingExporter
 
getConfigureMappingParameters(GuiContext) - Method in class net.sf.basedb.plugins.AnnotationFlatFileImporter
Step 2 of 3.
getConfigureOptionsParameters(GuiContext) - Method in class net.sf.basedb.plugins.batchimport.AbstractItemImporter
 
getConfigureOptionsParameters(GuiContext) - Method in class net.sf.basedb.plugins.batchimport.AnyToAnyImporter
 
getConfigureParserParameters(GuiContext, boolean) - Method in class net.sf.basedb.plugins.AnnotationFlatFileImporter
 
getConfigureParserParameters(GuiContext, boolean) - Method in class net.sf.basedb.plugins.batchimport.AbstractItemImporter
 
getConfigureParserParameters(GuiContext, boolean) - Method in class net.sf.basedb.plugins.batchimport.AnyToAnyImporter
 
getConfigureParserParameters(RawDataType) - Method in class net.sf.basedb.plugins.RawDataFlatFileImporter
 
getConfigurePluginParameters() - Method in class net.sf.basedb.plugins.Base1PluginExecuter
Creates the information needed for plugin configuration and initiates the parameters.
getConfigurePluginParameters() - Method in class net.sf.basedb.plugins.executor.ExternalProgramExecutor
 
getConfigurePluginParameters() - Method in class net.sf.basedb.plugins.PackedFileExporter
 
getConfigurePluginParameters(GuiContext) - Method in class net.sf.basedb.plugins.gtf.GtfReporterMapImporter
 
getConfigurePluginParameters(GuiContext) - Method in class net.sf.basedb.plugins.ManualDerivedBioAssayCreator
 
getConfigurePluginParameters(GuiContext) - Method in class net.sf.basedb.plugins.ManualTransformCreator
 
getConfigurePluginParameters(GuiContext) - Method in class net.sf.basedb.plugins.PlateFlatFileImporter
 
getConfigurePluginParameters(GuiContext) - Method in class net.sf.basedb.plugins.ReporterFlatFileImporter
 
getConfigurePluginParameters(GuiContext) - Method in class net.sf.basedb.plugins.ReporterMapFlatFileImporter
 
getConfigureRawDataTypeParameters() - Method in class net.sf.basedb.plugins.RawDataFlatFileImporter
 
getConnection(Integer) - Method in class net.sf.basedb.core.JobAgent
Get a connection object for connecting to the job agent.
getConnection(Session) - Static method in class net.sf.basedb.core.HibernateUtil
Get the underlying JDBC connection from the Hibernate session.
getConnectionManagerFactory() - Method in class net.sf.basedb.core.data.FileServerData
Get the ID of the connection manager factory that should be used to retreieve the file contents and metadata.
getConnectionManagerFactoryId() - Method in class net.sf.basedb.core.FileServer
Get the ID of the connection manager factory that should be used to access file contents and metadata.
getConnectionManagerFactoryId() - Method in class net.sf.basedb.util.uri.ConnectionParameters
Get the connection manager factory that we should use to access the file, or null to use auto-detection.
getConnectionProperties() - Static method in class net.sf.basedb.core.HibernateUtil
Read database configuration properties from the base.config file and map them to Hibernate settings.
getConstructor() - Method in enum class net.sf.basedb.core.Item
Get the default constructor for new objects of this type.
getContact() - Method in class net.sf.basedb.core.data.PluginDefinitionData
Get contact information for the plugin.
getContact() - Method in interface net.sf.basedb.core.plugin.About
Contact information to get more information about the plugin.
getContact() - Method in class net.sf.basedb.core.plugin.AboutImpl
 
getContact() - Method in class net.sf.basedb.core.PluginDefinition
Get contact information for the plugin.
getContact() - Method in class net.sf.basedb.util.extensions.AboutBean
 
getContact() - Method in class net.sf.basedb.util.extensions.Registry.RegisteredAbout
 
getContent() - Method in class net.sf.basedb.clients.web.extensions.section.IncludeContentSectionFactory.Section
 
getContent() - Method in interface net.sf.basedb.clients.web.extensions.section.SectionAction
Get the (HTML) contents of the section.
getContent() - Method in class net.sf.basedb.clients.web.extensions.section.SectionBean
 
getContent() - Method in class net.sf.basedb.clients.web.extensions.tabcontrol.FixedTabFactory
 
getContent() - Method in class net.sf.basedb.clients.web.extensions.tabcontrol.IncludeContentTabFactory.Tab
 
getContent() - Method in interface net.sf.basedb.clients.web.extensions.tabcontrol.TabAction
Get the (HTML) contents of the tab.
getContent() - Method in class net.sf.basedb.clients.web.extensions.tabcontrol.TabBean
 
getContent() - Method in class net.sf.basedb.clients.web.taglib.tab.Tab
 
getContentLength(HttpResponse) - Static method in class net.sf.basedb.util.HttpUtil
Get the content length from the headers in the response.
getContentstyle() - Method in class net.sf.basedb.clients.web.taglib.HideableSection
 
getContentstyle() - Method in class net.sf.basedb.clients.web.taglib.tab.TabControl
 
getContentStyle() - Method in class net.sf.basedb.clients.web.extensions.section.IncludeContentSectionFactory.Section
 
getContentStyle() - Method in interface net.sf.basedb.clients.web.extensions.section.SectionAction
Extra CSS style attributes that will be added to the style attribute of the content section tag.
getContentStyle() - Method in class net.sf.basedb.clients.web.extensions.section.SectionBean
 
getContentType(HttpResponse) - Static method in class net.sf.basedb.util.HttpUtil
Get the content type of the content from the headers in the response.
getContext() - Method in class net.sf.basedb.clients.web.taglib.HideableSection
 
getContext(int) - Method in class net.sf.basedb.core.SessionControl
Load a context without making it the current context.
getContextId() - Method in class net.sf.basedb.core.ItemContext
Get the database ID of this context.
getContextItem() - Method in class net.sf.basedb.core.data.JobData
The item type of the context that was active when configuring this job. null = no context was known
getContextMessage() - Method in class net.sf.basedb.util.ContextUtil.ContextResult
Get the warning level message, or the message from Throwable.getMessage() if this is an error-level object.
getContextMessages(Collection<ContextUtil.ContextResult>, boolean, boolean) - Static method in class net.sf.basedb.util.ContextUtil
Get all messages from plug-in / configurations combinations that can't be used.
getContextNames(Item) - Method in class net.sf.basedb.core.SessionControl
Same as: getContextNames(item, getCurrentSubcontext(item))
getContextNames(Item, String) - Method in class net.sf.basedb.core.SessionControl
Get a list with the names of all named contexts for a given item and subcontext.
getContexts() - Method in class net.sf.basedb.core.data.ClientData
This is the inverse end.
getContexts() - Method in class net.sf.basedb.core.data.UserData
The saved contexts for the user.
getContextType() - Method in class net.sf.basedb.core.data.GuiContextData
 
getContextType() - Method in class net.sf.basedb.core.data.JobData
The context type that was active when configuring this job. 0 = single item, 1 = list
getConvertedValue(String, Method) - Method in class net.sf.basedb.util.extensions.xml.XmlLoader
 
getConverter(Object) - Static method in class net.sf.basedb.util.jep.convert.ConverterFactory
Get a converter for the specified built-in JEP object.
getConverter(PostfixMathCommandI, Operator) - Method in class net.sf.basedb.util.jep.convert.ASTFunNodeConverter
Get a converter by first checking the if one exists for the given function, and then for the given operator symbol.
getConverterByClass(Object) - Static method in class net.sf.basedb.util.jep.convert.ConverterFactory
Get a converter for the specified built-in JEP object by checking if a converter has been registered for it's class.
getConverters() - Static method in class net.sf.basedb.util.jep.convert.ConverterFactory
Get all registered converters.
getCookie(HttpServletRequest, String) - Static method in class net.sf.basedb.clients.web.Base
Get the cookie with the specified name.
getCookieValue(HttpServletRequest, String) - Static method in class net.sf.basedb.clients.web.Base
Get the value of the cookie with the specified name.
getCoordinate() - Method in class net.sf.basedb.core.BioWell
Get a string representation of the coordinate for this well.
getCoordinateType() - Method in class net.sf.basedb.core.data.DataCubeExtraValueData
If the extra value is a spot extra value, a position extra value or a column extra value.
getCoordinateType() - Method in class net.sf.basedb.core.DataCubeExtraValue
Get the coordinate type the extra values are attached to.
getCoordinateType() - Method in class net.sf.basedb.core.ExtraValue
Get information about which coordinates in the data cube the extra values are attached to.
getCopyAnnotationsParmeter(String, String, Boolean) - Method in class net.sf.basedb.core.plugin.AbstractPlugin
Parameter definition that asks if annotations should be copied from the plug-in definition/configuration to other items.
getCopyright() - Method in class net.sf.basedb.core.data.PluginDefinitionData
Get a copyright notice for the plugin.
getCopyright() - Method in interface net.sf.basedb.core.plugin.About
A copyright notice.
getCopyright() - Method in class net.sf.basedb.core.plugin.AboutImpl
 
getCopyright() - Method in class net.sf.basedb.core.PluginDefinition
Get a copyright notice for the plugin.
getCopyright() - Method in class net.sf.basedb.util.extensions.AboutBean
 
getCopyright() - Method in class net.sf.basedb.util.extensions.Registry.RegisteredAbout
 
getCoreTimer() - Static method in class net.sf.basedb.core.Application
 
getCount() - Method in class net.sf.basedb.util.AnyToAnyLinkStatistics
Get the number of links that was found among the sampled items.
getCount() - Method in class net.sf.basedb.util.plot.HistogramPlot.HistogramBin
Get the number of values in this bin.
getCount(int) - Method in class net.sf.basedb.clients.web.ExperimentExplorer.AnnotationGroup
Get the number of intensity values added to the specified channel.
getCountHqlQuery(DbControl) - Method in class net.sf.basedb.core.AbstractHqlQuery
Build the count query and set parameter values for it.
getCountQuery(boolean) - Method in class net.sf.basedb.util.export.spotdata.BaseFileExporter
Get a configured query that counts the number of data lines that is about to be written in a data section.
getCountQuery(DbControl, boolean) - Method in class net.sf.basedb.core.AbstractQuery
Build the query string for returning the total count.
getCountry() - Method in class net.sf.basedb.util.GeoLocation
 
getCpuUsage() - Method in class net.sf.basedb.core.JobAgent
Get the current CPU usage in percent of the server where the job agent is running.
getCpuUsage() - Method in class net.sf.basedb.util.jobagent.JobAgentInfo
Get the CPU usage in percent.
getCreated() - Method in class net.sf.basedb.clients.jobagent.slotmanager.MasterSlotManager.RemoteSlot
 
getCreated() - Method in class net.sf.basedb.core.data.JobData
Get the date and time the job was created.
getCreated() - Method in class net.sf.basedb.core.Job
Get the date and time the job was registered in the database.
getCreateForeignKeySql(String, String, String, String, Set<String>, String, Set<String>) - Method in interface net.sf.basedb.core.dbengine.DbEngine
Generates SQL that creates a foreign key constraint between two tables.
getCreateForeignKeySql(String, String, String, String, Set<String>, String, Set<String>) - Method in class net.sf.basedb.core.dbengine.DefaultDbEngine
 
getCreateForeignKeySql(String, String, String, String, Set<String>, String, Set<String>) - Method in class net.sf.basedb.core.dbengine.MySQLEngine
Generate alter table schema.table add constraint name foreign key (columns) references refTable (refColumns)
getCreateForeignKeySql(String, String, String, String, Set<String>, String, Set<String>) - Method in class net.sf.basedb.core.dbengine.PostgresDbEngine
Generate alter table schema.table add constraint name foreign key (columns) references refTable (refColumns)
getCreateIndexSql(String, String, String, String, Set<String>, boolean) - Method in interface net.sf.basedb.core.dbengine.DbEngine
Generate SQL to create an index.
getCreateIndexSql(String, String, String, String, Set<String>, boolean) - Method in class net.sf.basedb.core.dbengine.DefaultDbEngine
Generates create [unique] index <name> on <catalog>.<schema>.<table> (<columns>) which should work for most databases.
getCreateIndexSql(String, String, String, String, Set<String>, boolean) - Method in class net.sf.basedb.core.dbengine.MySQLEngine
Generate alter table <catalog>.<table> add [unique] index <name> (<columns>).
getCreateIndexSql(String, String, String, String, Set<String>, boolean) - Method in class net.sf.basedb.core.dbengine.PostgresDbEngine
Generate alter table <schema>.<table> add constraint <name> unique (<columns>) for a unique index, create index <name> on <schema>.<table> (<columns>) for other indexes.
getCreatePartialIndexSql(String, String, String, String, Set<String>, String) - Method in class net.sf.basedb.core.dbengine.AbstractDbEngine
Default implementation returns a regular non-unique index.
getCreatePartialIndexSql(String, String, String, String, Set<String>, String) - Method in interface net.sf.basedb.core.dbengine.DbEngine
Generate SQL to create a partial index.
getCreatePartialIndexSql(String, String, String, String, Set<String>, String) - Method in class net.sf.basedb.core.dbengine.PostgresDbEngine
Creates a partial index which is the same as a regular index + 'WHERE [condition]';
getCreatePrimaryKeySql(String, String, String, String, Set<String>) - Method in interface net.sf.basedb.core.dbengine.DbEngine
Generate SQL to create a primary key for a table.
getCreatePrimaryKeySql(String, String, String, String, Set<String>) - Method in class net.sf.basedb.core.dbengine.DefaultDbEngine
 
getCreatePrimaryKeySql(String, String, String, String, Set<String>) - Method in class net.sf.basedb.core.dbengine.MySQLEngine
Generate alter table catalog.table add primary key (columns)
getCreatePrimaryKeySql(String, String, String, String, Set<String>) - Method in class net.sf.basedb.core.dbengine.PostgresDbEngine
Generate alter table schema.table add constraint name primary key (columns).
getCreateSchemaSql(String, String) - Method in interface net.sf.basedb.core.dbengine.DbEngine
Generate an SQL statement to create the given schema.
getCreateSchemaSql(String, String) - Method in class net.sf.basedb.core.dbengine.DefaultDbEngine
Generate create schema <catalog>.<schema>.
getCreateSchemaSql(String, String) - Method in class net.sf.basedb.core.dbengine.MySQLEngine
Generate create schema <catalog>.
getCreateSchemaSql(String, String) - Method in class net.sf.basedb.core.dbengine.PostgresDbEngine
Generate create schema <schema>.
getCreateTemporaryIdTable(String) - Method in interface net.sf.basedb.core.dbengine.DbEngine
Generate SQL for creating a temporary table with a single 'id' column that is the primary key.
getCreateTemporaryIdTable(String) - Method in class net.sf.basedb.core.dbengine.PostgresDbEngine
CREATE TEMPORARY TABLE <table> (id integer PRIMARY KEY) ON COMMIT DROP
getCreationEvent() - Method in class net.sf.basedb.core.data.MeasuredBioMaterialData
Get the event that created this biomaterial.
getCreationEvent() - Method in class net.sf.basedb.core.data.PhysicalBioAssayData
Get the event that created this bioassay.
getCreationEvent() - Method in class net.sf.basedb.core.MeasuredBioMaterial
Get the event that represents the creation of this biomaterial.
getCreationEvent() - Method in class net.sf.basedb.core.PhysicalBioAssay
Get the event that represents the creation of this hybridization.
getCriteriaBuilder() - Method in class net.sf.basedb.core.hibernate.SessionWrapper
 
getCryptedPassword() - Method in class net.sf.basedb.core.data.PasswordData
Get the crypted password.
getCubeNo() - Method in class net.sf.basedb.core.data.DataCubeData
The cube number of this cube in the virtual database.
getCubeNo() - Method in class net.sf.basedb.core.DataCube
Get the number of this data cube.
getCubes() - Method in class net.sf.basedb.core.data.VirtualDbData
The number of data cubes in the virtual database.
getCubes() - Method in class net.sf.basedb.core.VirtualDb
Get the number of DataCube:s in this virtual database.
getCurrent() - Method in class net.sf.basedb.clients.web.taglib.Select
 
getCurrent() - Method in class net.sf.basedb.clients.web.taglib.SubtypeSelector
 
getCurrentBioAssaySet(DbControl) - Method in class net.sf.basedb.core.plugin.AbstractAnalysisPlugin
Get the current source bioassay set.
getCurrentBioAssaySet(DbControl) - Method in class net.sf.basedb.plugins.executor.ExternalProgramExecutor
Get the bioassay set that is used as the source for the job.
GetCurrentCatalogWork - Class in net.sf.basedb.core.hibernate
A work implementation that return the name of the current database catalog.
GetCurrentCatalogWork() - Constructor for class net.sf.basedb.core.hibernate.GetCurrentCatalogWork
Create a new work item.
getCurrentClientId() - Method in class net.sf.basedb.core.SessionControl
Get the id of the Client application that checked out this SessionControl from Application.getSessionControl(String, String, String, boolean).
getCurrentClientName() - Method in class net.sf.basedb.core.SessionControl
Get the name of the Client application that checked out this SessionControl from Application.getSessionControl(String, String, String, boolean).
getCurrentConfiguration(DbControl) - Method in class net.sf.basedb.core.plugin.AbstractPlugin
Get the plug-in configuration that this is currently in use or null.
getCurrentConfigurationParameterValues(String) - Method in class net.sf.basedb.core.PluginRequest
Get the values that are currently stored in the plugin configuration related to this request.
getCurrentContext() - Method in class net.sf.basedb.clients.web.extensions.JspContext
Get the current item context.
getCurrentContext(Item) - Method in class net.sf.basedb.core.SessionControl
Same as: getCurrentContext(item, null, null).
getCurrentContext(Item, String) - Method in class net.sf.basedb.core.SessionControl
Same as: getCurrentContext(item, subContext, null).
getCurrentContext(Item, String, ItemContext) - Method in class net.sf.basedb.core.SessionControl
Get the current context.
getCurrentContext(Item, ItemContext) - Method in class net.sf.basedb.core.SessionControl
Same as: getCurrentContext(item, null, defaultContext).
getCurrentDerivedBioAssay(DbControl) - Method in class net.sf.basedb.core.plugin.AbstractAnalysisPlugin
Get the current source derived bioassay.
getCurrentDirectory(DbControl) - Method in class net.sf.basedb.util.zip.AbstractFileUnpacker
Get the current directory or null there is no current or it can't be loaded.
getCurrentExcelWorkbook() - Method in class net.sf.basedb.util.parser.FlatFileParser
If the input stream that is being parsed is an Excel document, this method returns information about it.
getCurrentExperiment(DbControl) - Method in class net.sf.basedb.core.plugin.AbstractAnalysisPlugin
Get the current experiment from information in the current context: SessionControl.getCurrentContext(Item.EXPERIMENT).
getCurrentExtension() - Method in class net.sf.basedb.util.extensions.ClientContext
Get the currently active extension point.
getCurrentExtensionPoint() - Method in class net.sf.basedb.util.extensions.ClientContext
Get the currently active extension point.
getCurrentExternalClientId() - Method in class net.sf.basedb.core.SessionControl
Get the external id of the Client application that checked out this SessionControl from Application.getSessionControl(String, String, String, boolean).
getCurrentFile() - Method in class net.sf.basedb.plugins.RawDataFlatFileImporter.FileIterator
 
getCurrentFile(DbControl) - Method in class net.sf.basedb.util.zip.AbstractFileUnpacker
Get the current file or null there is no current or it can't be loaded.
getCurrentFilename() - Method in class net.sf.basedb.clients.web.fileupload.FileUploadProgress
Get the name of the file that is currently beeing transferred.
getCurrentItem() - Method in class net.sf.basedb.util.extensions.ClientContext
Get the currently active item.
getCurrentJob(DbControl) - Method in class net.sf.basedb.core.plugin.AbstractPlugin
Get the job that is executing this plugin or null.
getCurrentJobParameterValues(String) - Method in class net.sf.basedb.core.PluginRequest
Get the values that are currently stored in the job related to this request.
getCurrentLine() - Method in class net.sf.basedb.util.bfs.AnnotationParser
 
getCurrentLine() - Method in interface net.sf.basedb.util.bfs.BfsParser
Get the current line number.
getCurrentLine() - Method in class net.sf.basedb.util.bfs.DataParser
 
getCurrentLine() - Method in class net.sf.basedb.util.bfs.MetadataParser
 
getCurrentLine() - Method in class net.sf.basedb.util.importer.spotdata.SynchronizedSpotDataParser
 
getCurrentLockMode(Object) - Method in class net.sf.basedb.core.hibernate.SessionWrapper
 
getCurrentMapper() - Static method in class net.sf.basedb.clients.web.extensions.skin.ImageRemapperUtil
Get the current image remapper.
getCurrentMatchingSource(DbControl) - Method in class net.sf.basedb.core.SyncFilter
Get the number of items that is currently matching this filter.
getCurrentNodeName() - Method in class net.sf.basedb.util.overview.node.BioWellNameGenerator
 
getCurrentOverview(SessionControl) - Static method in class net.sf.basedb.util.overview.OverviewUtil
Get the currently cached overview.
getCurrentParameterValue(String) - Method in class net.sf.basedb.core.PluginRequest
 
getCurrentParameterValues(String) - Method in class net.sf.basedb.core.PluginRequest
Get the values that are currently stored in the job or plugin configuration related to this request.
getCurrentPosition() - Method in class net.sf.basedb.util.importer.spotdata.PositionEventHandler
Get the current position.
getCurrentRawBioAssay() - Method in class net.sf.basedb.plugins.RawDataFlatFileImporter.FileIterator
 
getCurrentRow() - Method in class net.sf.basedb.util.excel.XlsxTableWriter
Get row that was the last one to be printed.
getCurrentSection() - Method in class net.sf.basedb.util.basefile.BaseFileWriter
 
getCurrentSection() - Method in class net.sf.basedb.util.bfs.MetadataWriter
Get the name of the current section.
getCurrentSessionId() - Method in class net.sf.basedb.core.SessionControl
Get the id of the current user session, or 0 if no user is logged in.
getCurrentSheet() - Method in class net.sf.basedb.util.parser.FlatFileParser
If the input stream that is being parsed is an Excel document, this method returns information about the current worksheet.
getCurrentSubcontext(SessionControl.MainContext) - Method in class net.sf.basedb.core.SessionControl
Get the currently active subcontext for the item.
getCurrentTitlePrefix() - Method in class net.sf.basedb.util.overview.node.BioWellNameGenerator
 
getCurrentValue(Cell) - Method in class net.sf.basedb.clients.web.taglib.table.ExtensionCells
Get the value for the current column and item and update other settings for the cell.
getCustomRequestHandlerClasses() - Method in class net.sf.basedb.clients.jobagent.Agent
 
getData() - Method in class net.sf.basedb.core.AnnotatedItem
 
getData() - Method in class net.sf.basedb.core.Annotation
 
getData() - Method in class net.sf.basedb.core.AnnotationSet
 
getData() - Method in class net.sf.basedb.core.AnnotationType
 
getData() - Method in class net.sf.basedb.core.AnnotationTypeCategory
 
getData() - Method in class net.sf.basedb.core.AnyToAny
 
getData() - Method in class net.sf.basedb.core.ArrayBatch
 
getData() - Method in class net.sf.basedb.core.ArrayDesign
 
getData() - Method in class net.sf.basedb.core.ArrayDesignBlock
 
getData() - Method in class net.sf.basedb.core.ArrayDesignPlate
 
getData() - Method in class net.sf.basedb.core.ArraySlide
 
getData() - Method in class net.sf.basedb.core.BasicItem
Get the BasicData object that holds all data for this item.
getData() - Method in class net.sf.basedb.core.BioAssay
 
getData() - Method in class net.sf.basedb.core.BioAssaySet
 
getData() - Method in class net.sf.basedb.core.BioMaterial
 
getData() - Method in class net.sf.basedb.core.BioMaterialEvent
 
getData() - Method in class net.sf.basedb.core.BioPlate
 
getData() - Method in class net.sf.basedb.core.BioPlateEvent
 
getData() - Method in class net.sf.basedb.core.BioPlateEventParticipant
 
getData() - Method in class net.sf.basedb.core.BioPlateEventType
 
getData() - Method in class net.sf.basedb.core.BioPlateType
 
getData() - Method in class net.sf.basedb.core.BioSource
 
getData() - Method in class net.sf.basedb.core.BioWell
 
getData() - Method in class net.sf.basedb.core.ChangeHistory
 
getData() - Method in class net.sf.basedb.core.Client
 
getData() - Method in class net.sf.basedb.core.ClientDefaultSetting
 
getData() - Method in class net.sf.basedb.core.CommonItem
 
getData() - Method in class net.sf.basedb.core.DataCube
 
getData() - Method in class net.sf.basedb.core.DataCubeColumn
 
getData() - Method in class net.sf.basedb.core.DataCubeExtraValue
 
getData() - Method in class net.sf.basedb.core.DataCubeFilter
 
getData() - Method in class net.sf.basedb.core.DataCubeLayer
 
getData() - Method in class net.sf.basedb.core.DataFileType
 
getData() - Method in class net.sf.basedb.core.DerivedBioAssay
 
getData() - Method in class net.sf.basedb.core.Directory
 
getData() - Method in class net.sf.basedb.core.DiskUsage
 
getData() - Method in class net.sf.basedb.core.Experiment
 
getData() - Method in class net.sf.basedb.core.Extract
 
getData() - Method in class net.sf.basedb.core.ExtraValue
 
getData() - Method in class net.sf.basedb.core.ExtraValueType
 
getData() - Method in class net.sf.basedb.core.File
 
getData() - Method in class net.sf.basedb.core.FileServer
 
getData() - Method in class net.sf.basedb.core.FileSet
 
getData() - Method in class net.sf.basedb.core.FileSetMember
 
getData() - Method in class net.sf.basedb.core.Formula
 
getData() - Method in class net.sf.basedb.core.GlobalDefaultSetting
 
getData() - Method in class net.sf.basedb.core.Group
 
getData() - Method in class net.sf.basedb.core.Hardware
 
getData() - Method in class net.sf.basedb.core.Help
 
getData() - Method in class net.sf.basedb.core.ItemKey
 
getData() - Method in class net.sf.basedb.core.ItemList
 
getData() - Method in class net.sf.basedb.core.ItemSubtype
 
getData() - Method in class net.sf.basedb.core.ItemSubtypeFileType
 
getData() - Method in class net.sf.basedb.core.Job
 
getData() - Method in class net.sf.basedb.core.JobAgent
 
getData() - Method in class net.sf.basedb.core.JobAgentSettings
 
getData() - Method in class net.sf.basedb.core.Kit
 
getData() - Method in class net.sf.basedb.core.MeasuredBioMaterial
 
getData() - Method in class net.sf.basedb.core.Message
 
getData() - Method in class net.sf.basedb.core.MimeType
 
getData() - Method in class net.sf.basedb.core.News
 
getData() - Method in class net.sf.basedb.core.OwnedItem
 
getData() - Method in class net.sf.basedb.core.PermissionTemplate
 
getData() - Method in class net.sf.basedb.core.PhysicalBioAssay
 
getData() - Method in class net.sf.basedb.core.Plate
 
getData() - Method in class net.sf.basedb.core.PlateEvent
 
getData() - Method in class net.sf.basedb.core.PlateEventType
 
getData() - Method in class net.sf.basedb.core.PlateGeometry
 
getData() - Method in class net.sf.basedb.core.PlateMapping
 
getData() - Method in class net.sf.basedb.core.PlateType
 
getData() - Method in class net.sf.basedb.core.Platform
 
getData() - Method in class net.sf.basedb.core.PlatformFileType
 
getData() - Method in class net.sf.basedb.core.PlatformVariant
 
getData() - Method in class net.sf.basedb.core.PluginConfiguration
 
getData() - Method in class net.sf.basedb.core.PluginDefinition
 
getData() - Method in class net.sf.basedb.core.PluginType
 
getData() - Method in class net.sf.basedb.core.Project
 
getData() - Method in class net.sf.basedb.core.ProjectKey
 
getData() - Method in class net.sf.basedb.core.PropertyFilter
Create a new database filter object from this filter.
getData() - Method in class net.sf.basedb.core.Protocol
 
getData() - Method in class net.sf.basedb.core.Quantity
 
getData() - Method in class net.sf.basedb.core.Quota
 
getData() - Method in class net.sf.basedb.core.QuotaType
 
getData() - Method in class net.sf.basedb.core.RawBioAssay
 
getData() - Method in class net.sf.basedb.core.ReporterCloneTemplate
 
getData() - Method in class net.sf.basedb.core.ReporterList
 
getData() - Method in class net.sf.basedb.core.ReporterScore
 
getData() - Method in class net.sf.basedb.core.ReporterType
 
getData() - Method in class net.sf.basedb.core.Role
 
getData() - Method in class net.sf.basedb.core.RoleKey
 
getData() - Method in class net.sf.basedb.core.RootRawBioAssay
 
getData() - Method in class net.sf.basedb.core.Sample
 
getData() - Method in class net.sf.basedb.core.Session
 
getData() - Method in class net.sf.basedb.core.Setting
 
getData() - Method in class net.sf.basedb.core.SharedItem
 
getData() - Method in class net.sf.basedb.core.Software
 
getData() - Method in class net.sf.basedb.core.SyncFilter
 
getData() - Method in class net.sf.basedb.core.Tag
 
getData() - Method in class net.sf.basedb.core.Transformation
 
getData() - Method in class net.sf.basedb.core.Unit
 
getData() - Method in class net.sf.basedb.core.User
 
getData() - Method in class net.sf.basedb.core.UserClientSetting
 
getData() - Method in class net.sf.basedb.core.UserDefaultSetting
 
getData() - Method in class net.sf.basedb.core.UserDevice
 
getData() - Method in class net.sf.basedb.core.VirtualDb
 
getData() - Method in class net.sf.basedb.core.Well
 
getData() - Method in class net.sf.basedb.util.importer.spotdata.SynchronizedSpotDataParser.SynchronizedData
Get the current data line, split into columns.
getData(int, int) - Method in class net.sf.basedb.util.bfs.AnnotationModel
Get the data element at a given row and column index.
getData(int, int) - Method in class net.sf.basedb.util.bfs.MatrixModel
Get the data element at a given row and column index.
getData(int, String) - Method in class net.sf.basedb.util.bfs.AnnotationModel
Get the data element at a given row and column.
getData(String, UserData, ClientData, boolean) - Method in class net.sf.basedb.core.ItemContext
Create a new database context object from this context.
getData(DbControl, ExportedProperty, I) - Method in class net.sf.basedb.clients.web.extensions.list.ListColumnDataLoader
 
getData(DbControl, ExportedProperty, AnnotationType) - Method in class net.sf.basedb.clients.web.plugins.AnnotationTypeEnumerationLoader
 
getData(DbControl, ExportedProperty, AnnotationType) - Method in class net.sf.basedb.clients.web.plugins.AnnotationTypeItemTypesLoader
 
getData(DbControl, ExportedProperty, BasicItem) - Method in class net.sf.basedb.clients.web.plugins.AnyToAnyDataLoader
 
getData(DbControl, ExportedProperty, BasicItem) - Method in class net.sf.basedb.clients.web.plugins.ItemQueryWrapper
Uses a Metadata object to get the value of the specified property.
getData(DbControl, ExportedProperty, BasicItem) - Method in class net.sf.basedb.clients.web.plugins.MapValueLoader
 
getData(DbControl, ExportedProperty, BioAssay) - Method in class net.sf.basedb.clients.web.plugins.BioAssayExperimentalFactorLoader
 
getData(DbControl, ExportedProperty, ChangeHistory) - Method in class net.sf.basedb.clients.web.plugins.ChangeHistoryDetailLoader
 
getData(DbControl, ExportedProperty, ChangeHistory) - Method in class net.sf.basedb.clients.web.plugins.ChangeHistoryItemLoader
 
getData(DbControl, ExportedProperty, BasicData) - Method in class net.sf.basedb.clients.web.plugins.DataQueryWrapper
Uses a Metadata object to get the value of the specified property.
getData(DbControl, ExportedProperty, FileStoreEnabled) - Method in class net.sf.basedb.clients.web.plugins.FileSetMemberLoader
 
getData(DbControl, ExportedProperty, MeasuredBioMaterial) - Method in class net.sf.basedb.clients.web.plugins.ParentBioMaterialEventSourceLoader
 
getData(DbControl, ExportedProperty, MeasuredBioMaterial) - Method in class net.sf.basedb.clients.web.plugins.ParentBioMaterialLoader
 
getData(DbControl, ExportedProperty, Nameable) - Method in class net.sf.basedb.clients.web.plugins.PathLoader
 
getData(DbControl, ExportedProperty, PhysicalBioAssay) - Method in class net.sf.basedb.clients.web.plugins.ParentBioMaterialEventSourceLoaderFromBioAssay
 
getData(DbControl, ExportedProperty, SqlResult) - Method in class net.sf.basedb.clients.web.plugins.DynamicQueryWrapper
Calls SqlResult.getObject(int) and increases the column index for each call.
getData(DbControl, ExportedProperty, ReporterScore) - Method in class net.sf.basedb.clients.web.plugins.ReporterScoreQueryWrapper
Uses a Metadata object to get the value of the specified property.
getData(DbControl, ExportedProperty, T) - Method in interface net.sf.basedb.clients.web.plugins.DataLoader
Get the value for the specified property.
getData(DbControl, ExportedProperty, T) - Method in class net.sf.basedb.clients.web.plugins.ItemQueryLoader
 
getDatabaseVersionString() - Static method in class net.sf.basedb.core.Application
Gets the version of the database server
getDataByName(Session, int, Item, String) - Static method in class net.sf.basedb.core.AnyToAny
Get an any-to-any link.
getDataClass() - Method in enum class net.sf.basedb.core.Item
Get the data object that is used to store information in the database for items of this type.
getDataClassName(Object) - Static method in class net.sf.basedb.core.log.EntityDetails
 
getDataCube() - Method in class net.sf.basedb.core.BioAssaySet
Get the data cube this biossayset stores it's data in.
getDataCube() - Method in class net.sf.basedb.core.data.DataCubeColumnData
Get the data cube this column belongs to.
getDataCube() - Method in class net.sf.basedb.core.data.DataCubeExtraValueData
Get the data cube this filter belongs to.
getDataCube() - Method in class net.sf.basedb.core.data.DataCubeFilterData
Get the data cube this filter belongs to.
getDataCube() - Method in class net.sf.basedb.core.data.DataCubeLayerData
Get the data cube this layer belongs to.
getDataCube() - Method in class net.sf.basedb.core.DataCubeColumn
Get the data cube this layer belongs to.
getDataCube() - Method in class net.sf.basedb.core.DataCubeExtraValue
Get the data cube this extra value belongs to.
getDataCube() - Method in class net.sf.basedb.core.DataCubeFilter
Get the data cube this filter belongs to.
getDataCube() - Method in class net.sf.basedb.core.DataCubeLayer
Get the data cube this layer belongs to.
getDataCube() - Method in class net.sf.basedb.core.DynamicQuery
 
getDataCube() - Method in class net.sf.basedb.core.ExtraValue
 
getDataCubeColumn() - Method in class net.sf.basedb.core.BioAssay
Get the DataCubeColumn object where this bioassay store it's data.
getDataCubeColumn() - Method in class net.sf.basedb.core.data.BioAssayData
Get the column this bioassay stores it's data in.
getDataCubeColumnNo() - Method in class net.sf.basedb.core.BioAssay
Get the column coordinate in the data cube that this bioassay stores it's data in.
getDataCubeExtraValue() - Method in class net.sf.basedb.core.data.ExtraValueData
Get the data cube extra value where the extra values are stored.
getDataCubeExtraValue() - Method in class net.sf.basedb.core.ExtraValue
 
getDataCubeFilter() - Method in class net.sf.basedb.core.BioAssaySet
Get the data cube filter this biossayset uses to filter spot data.
getDataCubeFilter() - Method in class net.sf.basedb.core.data.BioAssaySetData
Get the filter used by this bioassayset.
getDataCubeFilterNo() - Method in class net.sf.basedb.core.BioAssaySet
Get the number of the filter that this bioassayset is using, or 0 if no filter is used.
getDataCubeLayer() - Method in class net.sf.basedb.core.BioAssaySet
Get the data cube layer this biossayset stores it's data in.
getDataCubeLayer() - Method in class net.sf.basedb.core.data.BioAssaySetData
Get the layer this bioassayset stores it's data in.
getDataCubeLayerNo() - Method in class net.sf.basedb.core.BioAssay
Get the layer coordinate in the data cube that this bioassay stores it's data in.
getDataCubeLayerNo() - Method in class net.sf.basedb.core.BioAssaySet
Get the layer coordinate in the data cube that this bioassayset stores it's data in.
getDataCubeNo() - Method in class net.sf.basedb.core.BioAssay
Get the number of the data cube this bioassay stores it's data in.
getDataCubeNo() - Method in class net.sf.basedb.core.BioAssaySet
Get the number of the data cube this bioassayset stores it's data in.
getDataCubeNo() - Method in class net.sf.basedb.core.DataCubeColumn
Get the number of the data cube this layer belongs to.
getDataCubeNo() - Method in class net.sf.basedb.core.DataCubeExtraValue
Get the number of the data cube this extra value belongs to.
getDataCubeNo() - Method in class net.sf.basedb.core.DataCubeFilter
Get the number of the data cube this filter belongs to.
getDataCubeNo() - Method in class net.sf.basedb.core.DataCubeLayer
Get the number of the data cube this layer belongs to.
getDataCubeNo() - Method in class net.sf.basedb.core.ExtraValue
Get the number of the data cube the extra values are stored in.
getDataCubes() - Method in class net.sf.basedb.core.data.VirtualDbData
This is the inverse end.
getDataFile(DbControl, FileStoreEnabled, String, boolean) - Static method in class net.sf.basedb.core.FileStoreUtil
Get the file of the given data file type in the FileStoreEnabled item's file set assuming that at most one file exists.
getDataFile(TableInfo) - Method in class net.sf.basedb.core.Migration
Get the data file for the given table.
getDataFile(TableInfo, boolean) - Method in class net.sf.basedb.core.Migration
Get the data file for the given table.
getDataFileColumns(Item, String) - Static method in class net.sf.basedb.clients.web.Base
Get a query returning all data file types that are needed to display file set members for the given columns.
getDataFiles(DbControl, FileStoreEnabled, String, boolean) - Static method in class net.sf.basedb.core.FileStoreUtil
Get the file of the given data file type in the FileStoreEnabled item's file set.
getDataFileType() - Method in class net.sf.basedb.core.data.FileSetMemberData
Get the type of this file.
getDataFileType() - Method in class net.sf.basedb.core.data.FileTypeIndex
 
getDataFileType() - Method in class net.sf.basedb.core.data.ItemSubtypeFileTypeData
Get the file type.
getDataFileType() - Method in class net.sf.basedb.core.data.PlatformFileTypeData
Get the file type.
getDataFileType() - Method in class net.sf.basedb.core.FileSetMember
Get the type of the file.
getDataFileType() - Method in class net.sf.basedb.core.ItemSubtypeFileType
Get the type of the file.
getDataFileType() - Method in class net.sf.basedb.core.PlatformFileType
Get the type of the file.
getDataFileType() - Method in interface net.sf.basedb.core.UsableDataFileType
Get the data file type the information applies to.
getDataFileType() - Method in class net.sf.basedb.util.overview.Fix
 
getDataFileTypes() - Method in class net.sf.basedb.core.ItemSubtype
Get a query returning the data file types that have been associated with this subtype.
getDataFileTypes(Item, FileStoreEnabled, Platform, PlatformVariant, ItemSubtype) - Static method in class net.sf.basedb.clients.web.Base
Get a query that returns all data file types for a specific platform/variant/subtype that can be used on a given item type.
getDataSeparator() - Method in class net.sf.basedb.util.export.TableWriter
The data separator string is written between each data column in the output.
getDatatype() - Method in class net.sf.basedb.clients.web.taglib.table.ColumnDef
 
getDatatype() - Method in class net.sf.basedb.clients.web.taglib.table.TableColumn
 
getDataValue(Object) - Static method in class net.sf.basedb.core.Values
Convert an item values to a data value.
getDataValues(List<?>) - Static method in class net.sf.basedb.core.Values
Convert a list of item values to data values.
getDataWriterFactory() - Method in class net.sf.basedb.util.export.spotdata.BfsExporter
Get the factory that creates data writers.
getDate() - Method in class net.sf.basedb.util.extensions.logging.LogEntry
The timestamp of the log entry as a date.
getDate(int, Formatter<Date>, boolean) - Method in class net.sf.basedb.util.parser.FlatFileParser.Data
Get the value as a date.
getDate(int, Formatter<Date>, boolean) - Method in class net.sf.basedb.util.parser.FlatFileParser.ExcelData
 
getDate(String[], Formatter<Date>) - Static method in class net.sf.basedb.util.Values
 
getDate(FlatFileParser.Data) - Method in class net.sf.basedb.util.parser.ColumnMapper
 
getDate(FlatFileParser.Data) - Method in class net.sf.basedb.util.parser.CompoundMapper
 
getDate(FlatFileParser.Data) - Method in class net.sf.basedb.util.parser.ConstantMapper
 
getDate(FlatFileParser.Data) - Method in class net.sf.basedb.util.parser.CropStringMapper
 
getDate(FlatFileParser.Data) - Method in class net.sf.basedb.util.parser.JepMapper
 
getDate(FlatFileParser.Data) - Method in interface net.sf.basedb.util.parser.Mapper
Get the value for the line of data as a date.
getDate(FlatFileParser.Data) - Method in class net.sf.basedb.util.parser.NullIfExceptionMapper
 
getDate(HttpResponse, String, Date) - Static method in class net.sf.basedb.util.HttpUtil
 
getDateCellStyle(String) - Method in class net.sf.basedb.util.excel.CellStyleCreator
Get the cell style for the given date format string.
getDateFormat() - Method in class net.sf.basedb.util.excel.AutoFormatter
 
getDateFormat() - Method in class net.sf.basedb.util.excel.XlsxToCsvUtil
Get the date formatter that is used for formatting cells with date-like values.
getDateFormat() - Method in class net.sf.basedb.util.formatter.DateFormatter
Get access to the underlying DateFormat object used for formatting and parsing dates.
getDateFormat(SessionControl) - Static method in class net.sf.basedb.clients.web.formatter.FormatterSettings
Get format string for a date formatter.
getDateFormatter(String) - Method in class net.sf.basedb.plugins.AbstractFlatFileImporter
 
getDateFormatter(SessionControl) - Static method in class net.sf.basedb.clients.web.formatter.FormatterFactory
Get the logged in user's date formatter.
getDateMapper(String) - Method in class net.sf.basedb.util.parser.FlatFileParser
Get a mapper using the default date format.
getDateTimeFormat(SessionControl) - Static method in class net.sf.basedb.clients.web.formatter.FormatterSettings
Get format string for a datetime formatter.
getDateTimeFormatter(SessionControl) - Static method in class net.sf.basedb.clients.web.formatter.FormatterFactory
Get the logged in user's datetime formatter.
getDateValues() - Method in class net.sf.basedb.core.data.annotations.AnnotationLink
 
getDbcontrol() - Method in class net.sf.basedb.clients.web.taglib.PropertyValue
 
getDbControl() - Method in class net.sf.basedb.core.AbstractBatcher
Get the DbControl object that currently manages this batcher.
getDbControl() - Method in class net.sf.basedb.core.BasicItem
Get the DbControl object that currently manages this item.
getDbControl() - Method in class net.sf.basedb.util.export.spotdata.AbstractBioAssaySetExporter
Get the current DbControl.
getDbControl() - Method in class net.sf.basedb.util.export.spotdata.AbstractFieldConverter
Get the DbControl to use for database access.
getDbControl() - Method in class net.sf.basedb.util.extensions.ClientContext
Get the current DbControl.
getDbControl() - Method in class net.sf.basedb.util.importer.spotdata.BaseFileImporter
Get the current DbControl.
getDbControl() - Method in class net.sf.basedb.util.importer.spotdata.BfsImporter
Get the current DbControl.
getDbControl() - Method in class net.sf.basedb.util.listable.TransformContext
Get the DbControl to use in this transformation context.
getDbControl() - Method in class net.sf.basedb.util.units.UnitCache
Get the DbControl that is currently used for database access.
getDbEngine() - Static method in class net.sf.basedb.core.HibernateUtil
Get the database engine.
getDc() - Method in class net.sf.basedb.clients.web.taglib.SubtypeSelector
 
getDecimalSeparator() - Method in class net.sf.basedb.plugins.AbstractFlatFileImporter
Get the decimal separator used by numbers in the file.
getDecimalSeparator() - Method in class net.sf.basedb.plugins.IlluminaRawDataImporter
 
getDefault() - Method in class net.sf.basedb.core.Presets
Get the default preset.
getDefaultAnnotation() - Method in class net.sf.basedb.core.Annotation
Get the default annotation that this project-specific annotation is overriding.
getDefaultClazz(int) - Method in class net.sf.basedb.clients.web.taglib.Body
 
getDefaultDateFormat() - Method in class net.sf.basedb.util.parser.FlatFileParser
Get the default date format.
getDefaultErrorHandlerFactory() - Method in class net.sf.basedb.clients.web.extensions.ExtensionsControl
Get the default error handling factory.
getDefaultErrorHandlerFactory() - Method in class net.sf.basedb.util.extensions.Registry
Get the default error handler factory.
getDefaultFileExtension() - Method in interface net.sf.basedb.clients.web.plugins.ExportTemplate
Get the default file extension to give to files generated by this template.
getDefaultFileExtension() - Method in class net.sf.basedb.clients.web.plugins.PlainTextTemplate
 
getDefaultFileExtension() - Method in class net.sf.basedb.clients.web.plugins.XlsxTemplate
 
getDefaultFileExtension() - Method in class net.sf.basedb.clients.web.plugins.XMLTemplate
 
getDefaultId(String) - Method in class net.sf.basedb.clients.web.taglib.Button
 
getDefaultImage(String) - Method in class net.sf.basedb.clients.web.taglib.Button
 
getDefaultItemFunction(Item) - Method in class net.sf.basedb.plugins.batchimport.AbstractItemImporter
Create a DefaultItemFunction for the given item type.
getDefaultItems() - Method in class net.sf.basedb.core.data.ProjectData
The default items to use in this project
getDefaultItems(DbControl) - Method in class net.sf.basedb.core.Project
Get a list with all default items added to this project.
getDefaultItems(DbControl, Item) - Method in class net.sf.basedb.core.Project
Get a list with all default items of a given item type added to this project.
getDefaultKeyManagers() - Static method in class net.sf.basedb.util.ssl.SSLUtil2
Get the default keys manages as configured in the base.config file by ssl.keystore.* settings.
getDefaultNumberFormat() - Method in class net.sf.basedb.util.parser.FlatFileParser
Get the default number format.
getDefaultPriority() - Method in enum class net.sf.basedb.core.Job.ExecutionTime
The default thread priority to use when executing jobs in with this execution time.
getDefaultRawDataType() - Method in class net.sf.basedb.core.Project
Gets the default raw data type for this project.
getDefaultRememberDevice() - Method in class net.sf.basedb.core.SessionControl.UnverifiedDeviceInfo
The preferred setting for the "rememberDevice" parameter when verifying the device.
getDefaultReporterContext() - Method in class net.sf.basedb.clients.web.ExperimentExplorer
Get the default reporter context that is used to initialise the actual context.
getDefaultSelects() - Method in class net.sf.basedb.core.AbstractSqlQuery
 
getDefaultSelects() - Method in class net.sf.basedb.core.DataCube.RawMappingQuery
 
getDefaultSelects() - Method in class net.sf.basedb.core.DynamicExtraValueQuery
Default selection: column, position, extraValue
getDefaultSelects() - Method in class net.sf.basedb.core.DynamicPositionQuery
Default selection: position
getDefaultSelects() - Method in class net.sf.basedb.core.DynamicRawDataQuery
No default selection.
getDefaultSelects() - Method in class net.sf.basedb.core.DynamicReporterQuery
No default selection.
getDefaultSelects() - Method in class net.sf.basedb.core.DynamicSpotQuery
Default selection: column, postion, ch1, ch2, ...
getDefaultSetting(String) - Method in class net.sf.basedb.core.Client
Get the default setting with the specified name.
getDefaultSettings() - Method in class net.sf.basedb.core.Client
Get a query that will return all default settings for this client.
getDefaultSettings() - Method in class net.sf.basedb.core.data.ClientData
This is the inverse end.
getDefaultSettings() - Method in class net.sf.basedb.core.data.UserData
This is the inverse end.
getDefaultSettings() - Method in class net.sf.basedb.core.User
Get a query that returns all default settings for this user.
getDefaultSeverity() - Method in interface net.sf.basedb.util.overview.extensions.ValidationRuleAction
Get the default severity level.
getDefaultSeverity() - Method in class net.sf.basedb.util.overview.Validator
Get the default severity level.
getDefaultSlots() - Method in enum class net.sf.basedb.core.Job.ExecutionTime
The default number of execution slots available for jobs with this execution time in the internal job queue.
getDefaultSpotContext() - Method in class net.sf.basedb.clients.web.ExperimentExplorer
Get the default spot context that is used to initialise the actual context.
getDefaultSystemId(Item) - Static method in class net.sf.basedb.core.Hardware
Get the system id for the hardware subtype that should be used on an item that doesn't have a subtype.
getDefaultSystemId(Item) - Static method in class net.sf.basedb.core.Kit
Get the system id for the kit subtype that should be used on an item that doesn't have a subtype.
getDefaultSystemId(Item) - Static method in class net.sf.basedb.core.Protocol
Get the system id for the protocol subtype that should be used on an item that doesn't have a subtype.
getDefaultSystemId(Item) - Static method in class net.sf.basedb.core.Software
Get the system id for the software subtype that should be used on an item that doesn't have a subtype.
getDefaultTimestampFormat() - Method in class net.sf.basedb.util.parser.FlatFileParser
Get the default timestamp format.
getDefaultTransactionName(String) - Method in class net.sf.basedb.core.SessionControl
Generate a default transaction name with an optional suffix.
getDefaultTrustManagers() - Static method in class net.sf.basedb.util.ssl.SSLUtil2
Get the default trust manages as configured in the base.config file by ssl.truststore.* settings.
getDefaultUnit() - Method in class net.sf.basedb.core.AnnotationBatcher.CurrentAnnotationInfo
Get the default unit for the annotation type.
getDefaultUnit() - Method in class net.sf.basedb.core.AnnotationType
Get the default unit for this annotation type.
getDefaultUnit() - Method in class net.sf.basedb.core.data.AnnotationTypeData
Get the unit used to store annotation values for this type.
getDefaultValue() - Method in class net.sf.basedb.core.AnnotationType
Get the recommended default value for new annotations of this annotation type.
getDefaultValue() - Method in class net.sf.basedb.core.data.AnnotationTypeData
The default value of new annotations.
getDefaultValue() - Method in class net.sf.basedb.core.ParameterType
Get the default value.
getDefaultValue() - Method in class net.sf.basedb.core.PluginParameter
Get the default value for this parameter or null if no default has been specified
getDefaultValue() - Method in class net.sf.basedb.core.query.ParameterExpression
Get the default value of the parameter.
getDefaultValue() - Method in class net.sf.basedb.plugins.Base1PluginExecuter.JobParameter
 
getDefaultValue() - Method in class net.sf.basedb.plugins.executor.ParameterDefinition
Get the default value for this parameter.
getDefaultValue() - Method in class net.sf.basedb.util.formatter.LookupFormatter
Get the default value.
getDefinedPermissions() - Method in enum class net.sf.basedb.core.Item
Get the permissions which are meaningful to assign to an item if this type.
getDelegate() - Method in class net.sf.basedb.core.hibernate.SessionWrapper
 
getDelegateFirst() - Method in class net.sf.basedb.util.JarClassLoader
If this class loader delegates to the parent class loader before or after trying to find the class by itself.
getDeletePropertyOrder(Class<? extends BatchableData>) - Static method in class net.sf.basedb.core.BatchUtil
Get the order of properties in the delete SQL.
getDeletePropertyOrder(String) - Static method in class net.sf.basedb.core.BatchUtil
Get the order of properties in the delete SQL.
getDeleteSql(Class<? extends BatchableData>) - Static method in class net.sf.basedb.core.BatchUtil
Get the SQL that deletes a new row of the specified class.
getDeleteSql(String) - Static method in class net.sf.basedb.core.BatchUtil
Get the SQL that deletes a new row of the specified class.
getDeletionOrder() - Method in enum class net.sf.basedb.core.Item
Get a value indicating the deletion order.
getDenied() - Method in class net.sf.basedb.core.data.keyring.PluginKeys
Get the denied permissions.
getDenied() - Method in class net.sf.basedb.core.data.PluginPermission
The plugin's permission can be set to always be used or only if the user has it already.
getDenied(RoleKey) - Method in class net.sf.basedb.core.PluginDefinition
Get the permissions that have been denied to this plugin.
getDeniedItemFix(DbControl, Node, Node) - Method in class net.sf.basedb.util.overview.validator.BasicNodeValidator
Subclasses should override this method if they have a suggessted fix for an access denied problem.
getDeniedNodeName(Node) - Method in class net.sf.basedb.util.overview.node.AnnotationNameGenerator
 
getDeniedNodeName(Node) - Method in class net.sf.basedb.util.overview.node.AnyToAnyNameGenerator
 
getDeniedNodeName(Node) - Method in class net.sf.basedb.util.overview.node.BioWellNameGenerator
 
getDeniedNodeName(Node) - Method in class net.sf.basedb.util.overview.node.FileSetMemberNameGenerator
 
getDeniedNodeName(Node) - Method in class net.sf.basedb.util.overview.node.ItemListMemberNameGenerator
 
getDeniedNodeName(Node) - Method in class net.sf.basedb.util.overview.node.NameableNameGenerator
 
getDeniedNodeName(Node) - Method in interface net.sf.basedb.util.overview.node.NodeNameGenerator
Generate a name for a node when the item exists, but the current user doesn't have permission to access read the item.
getDeniedNodeTitle(Node) - Method in class net.sf.basedb.util.overview.node.AnnotationNameGenerator
 
getDeniedNodeTitle(Node) - Method in class net.sf.basedb.util.overview.node.AnyToAnyNameGenerator
 
getDeniedNodeTitle(Node) - Method in class net.sf.basedb.util.overview.node.BioWellNameGenerator
 
getDeniedNodeTitle(Node) - Method in class net.sf.basedb.util.overview.node.FileSetMemberNameGenerator
 
getDeniedNodeTitle(Node) - Method in class net.sf.basedb.util.overview.node.ItemListMemberNameGenerator
 
getDeniedNodeTitle(Node) - Method in class net.sf.basedb.util.overview.node.NameableNameGenerator
 
getDeniedNodeTitle(Node) - Method in interface net.sf.basedb.util.overview.node.NodeNameGenerator
Generate a title for a node when the item exists, but the current user doesn't have permission to access read the item.
getDependingLists() - Method in class net.sf.basedb.core.ItemList
Get a query that return all item lists that are used by synchronization filters in this list.
getDepth() - Method in class net.sf.basedb.util.Tree.Entry
Get the depth of this entry within the tree.
getDerivedBioAssays() - Method in class net.sf.basedb.core.data.ExtractData
This is the inverse end.
getDerivedBioAssays() - Method in class net.sf.basedb.core.data.JobData
This is the inverse end.
getDerivedBioAssays() - Method in class net.sf.basedb.core.data.PhysicalBioAssayData
This is the inverse end.
getDerivedBioAssays() - Method in class net.sf.basedb.core.Extract
Get a query that returns all derived bioassays created from this extract.
getDerivedBioAssays() - Method in class net.sf.basedb.core.PhysicalBioAssay
Get a query that returns all derived bioassay created from this physical bioassay.
getDescription() - Method in class net.sf.basedb.clients.jobagent.Agent
Get the agent.description configuration value.
getDescription() - Method in interface net.sf.basedb.clients.web.extensions.plot.OverviewPlotAction
A description of the overview plots.
getDescription() - Method in class net.sf.basedb.clients.web.extensions.plot.OverviewPlotBean
 
getDescription() - Method in class net.sf.basedb.clients.web.extensions.startpage.FixedStartPageFactory
 
getDescription() - Method in interface net.sf.basedb.clients.web.extensions.startpage.StartPageAction
Get an optional description of the start page.
getDescription() - Method in class net.sf.basedb.clients.web.extensions.startpage.StartPageBean
 
getDescription() - Method in class net.sf.basedb.clients.web.taglib.table.TableColumn
 
getDescription() - Method in class net.sf.basedb.core.AnyToAny
 
getDescription() - Method in class net.sf.basedb.core.authentication.ExtraUserInformation
A description of the user.
getDescription() - Method in class net.sf.basedb.core.BioAssay
 
getDescription() - Method in class net.sf.basedb.core.BioAssaySet
 
getDescription() - Method in class net.sf.basedb.core.BioPlateEventType
 
getDescription() - Method in class net.sf.basedb.core.BioPlateType
 
getDescription() - Method in class net.sf.basedb.core.CommonItem
 
getDescription() - Method in class net.sf.basedb.core.data.AnyToAnyData
 
getDescription() - Method in class net.sf.basedb.core.data.BioAssayData
 
getDescription() - Method in class net.sf.basedb.core.data.BioAssaySetData
 
getDescription() - Method in class net.sf.basedb.core.data.BioPlateEventTypeData
 
getDescription() - Method in class net.sf.basedb.core.data.BioPlateTypeData
 
getDescription() - Method in class net.sf.basedb.core.data.CommonData
 
getDescription() - Method in class net.sf.basedb.core.data.DataFileTypeData
 
getDescription() - Method in class net.sf.basedb.core.data.ExtraValueTypeData
 
getDescription() - Method in class net.sf.basedb.core.data.GroupData
 
getDescription() - Method in class net.sf.basedb.core.data.HelpData
 
getDescription() - Method in class net.sf.basedb.core.data.ItemListSyncFilterData
 
getDescription() - Method in class net.sf.basedb.core.data.ItemSubtypeData
 
getDescription() - Method in class net.sf.basedb.core.data.MessageData
 
getDescription() - Method in class net.sf.basedb.core.data.MimeTypeData
 
getDescription() - Method in interface net.sf.basedb.core.data.NameableData
Get the description for the item.
getDescription() - Method in class net.sf.basedb.core.data.NewsData
 
getDescription() - Method in class net.sf.basedb.core.data.ParameterValueData
Get the description of the parameter.
getDescription() - Method in class net.sf.basedb.core.data.PlateEventTypeData
 
getDescription() - Method in class net.sf.basedb.core.data.PlateGeometryData
 
getDescription() - Method in class net.sf.basedb.core.data.PlatformData
 
getDescription() - Method in class net.sf.basedb.core.data.PlatformVariantData
 
getDescription() - Method in class net.sf.basedb.core.data.PluginDefinitionData
Get a description of the plugin.
getDescription() - Method in class net.sf.basedb.core.data.PluginTypeData
 
getDescription() - Method in class net.sf.basedb.core.data.ProjectData
 
getDescription() - Method in class net.sf.basedb.core.data.QuantityData
 
getDescription() - Method in class net.sf.basedb.core.data.QuotaData
 
getDescription() - Method in class net.sf.basedb.core.data.QuotaTypeData
 
getDescription() - Method in class net.sf.basedb.core.data.ReporterClonePropertyData
Get a description of the property.
getDescription() - Method in class net.sf.basedb.core.data.ReporterData
 
getDescription() - Method in class net.sf.basedb.core.data.ReporterTypeData
 
getDescription() - Method in class net.sf.basedb.core.data.RoleData
 
getDescription() - Method in class net.sf.basedb.core.data.RoleKeyData
Get the description for the item.
getDescription() - Method in class net.sf.basedb.core.data.RootRawBioAssayData
 
getDescription() - Method in class net.sf.basedb.core.data.TransformationData
 
getDescription() - Method in class net.sf.basedb.core.data.UnitData
 
getDescription() - Method in class net.sf.basedb.core.data.UserData
 
getDescription() - Method in class net.sf.basedb.core.data.UserDeviceData
 
getDescription() - Method in class net.sf.basedb.core.DataFileType
 
getDescription() - Method in class net.sf.basedb.core.Directory
 
getDescription() - Method in class net.sf.basedb.core.ExtendedProperty
Get a description of the extended property.
getDescription() - Method in class net.sf.basedb.core.ExtraValueType
 
getDescription() - Method in class net.sf.basedb.core.Group
 
getDescription() - Method in class net.sf.basedb.core.Help
 
getDescription() - Method in class net.sf.basedb.core.IntensityFormula
Get a description of the intensity formula.
getDescription() - Method in class net.sf.basedb.core.ItemSubtype
 
getDescription() - Method in class net.sf.basedb.core.Message
 
getDescription() - Method in class net.sf.basedb.core.MimeType
 
getDescription() - Method in interface net.sf.basedb.core.Nameable
Get the description for the item.
getDescription() - Method in class net.sf.basedb.core.News
 
getDescription() - Method in class net.sf.basedb.core.ParameterInfo
 
getDescription() - Method in class net.sf.basedb.core.PlateEventType
 
getDescription() - Method in class net.sf.basedb.core.PlateGeometry
 
getDescription() - Method in class net.sf.basedb.core.Platform
 
getDescription() - Method in class net.sf.basedb.core.PlatformVariant
 
getDescription() - Method in interface net.sf.basedb.core.plugin.About
A description of the plugin and what it does.
getDescription() - Method in class net.sf.basedb.core.plugin.AboutImpl
 
getDescription() - Method in class net.sf.basedb.core.PluginParameter
Get a description of the parameter.
getDescription() - Method in class net.sf.basedb.core.PluginType
 
getDescription() - Method in class net.sf.basedb.core.Project
 
getDescription() - Method in class net.sf.basedb.core.Quantity
 
getDescription() - Method in class net.sf.basedb.core.Quota
 
getDescription() - Method in class net.sf.basedb.core.QuotaType
 
getDescription() - Method in class net.sf.basedb.core.RawDataType
Get a description of this raw data type.
getDescription() - Method in class net.sf.basedb.core.ReporterType
 
getDescription() - Method in class net.sf.basedb.core.RequestInformation
Get a description of the request.
getDescription() - Method in class net.sf.basedb.core.Role
 
getDescription() - Method in class net.sf.basedb.core.RoleKey
 
getDescription() - Method in class net.sf.basedb.core.RootRawBioAssay
 
getDescription() - Method in class net.sf.basedb.core.signal.Signal
Get the description of the what the signal means and how receivers should behave when the signal is sent to them
getDescription() - Method in class net.sf.basedb.core.SyncFilter
 
getDescription() - Method in class net.sf.basedb.core.Transformation
 
getDescription() - Method in class net.sf.basedb.core.Unit
 
getDescription() - Method in class net.sf.basedb.core.User
 
getDescription() - Method in class net.sf.basedb.core.UserDevice
 
getDescription() - Method in class net.sf.basedb.plugins.executor.ParameterDefinition
Get a description/help text about this parameter.
getDescription() - Method in class net.sf.basedb.util.extensions.AboutBean
 
getDescription() - Method in interface net.sf.basedb.util.extensions.ExtensionPoint
Get a description of the extension point.
getDescription() - Method in class net.sf.basedb.util.extensions.ExtensionPointBean
 
getDescription() - Method in class net.sf.basedb.util.extensions.Registry.RegisteredAbout
 
getDescription() - Method in class net.sf.basedb.util.extensions.Registry.RegisteredExtensionPoint
 
getDescription() - Method in class net.sf.basedb.util.jep.convert.AbsConverter
 
getDescription() - Method in class net.sf.basedb.util.jep.convert.AbstractJepConversionFunction
 
getDescription() - Method in class net.sf.basedb.util.jep.convert.AddConverter
 
getDescription() - Method in class net.sf.basedb.util.jep.convert.AndConverter
 
getDescription() - Method in class net.sf.basedb.util.jep.convert.DivideConverter
 
getDescription() - Method in class net.sf.basedb.util.jep.convert.EqualsConverter
 
getDescription() - Method in class net.sf.basedb.util.jep.convert.ExpConverter
 
getDescription() - Method in class net.sf.basedb.util.jep.convert.GreaterConverter
 
getDescription() - Method in class net.sf.basedb.util.jep.convert.GreaterEqualsConverter
 
getDescription() - Method in class net.sf.basedb.util.jep.convert.IfConverter
 
getDescription() - Method in interface net.sf.basedb.util.jep.convert.JepConversionFunction
Get a short description of the function or operator
getDescription() - Method in class net.sf.basedb.util.jep.convert.LessConverter
 
getDescription() - Method in class net.sf.basedb.util.jep.convert.LessEqualsConverter
 
getDescription() - Method in class net.sf.basedb.util.jep.convert.LogarithmConverter
 
getDescription() - Method in class net.sf.basedb.util.jep.convert.MultiplyConverter
 
getDescription() - Method in class net.sf.basedb.util.jep.convert.NaturalLogarithmConverter
 
getDescription() - Method in class net.sf.basedb.util.jep.convert.NotConverter
 
getDescription() - Method in class net.sf.basedb.util.jep.convert.NotEqualsConverter
 
getDescription() - Method in class net.sf.basedb.util.jep.convert.OrConverter
 
getDescription() - Method in class net.sf.basedb.util.jep.convert.SquareRootConverter
 
getDescription() - Method in class net.sf.basedb.util.jep.convert.SubtractConverter
 
getDescription() - Method in class net.sf.basedb.util.jep.convert.UMinusConverter
 
getDescription() - Method in interface net.sf.basedb.util.overview.extensions.ValidationRuleAction
Get a lengthier description of the validation that takes place
getDescription() - Method in class net.sf.basedb.util.overview.Validator
Get a lengthier description of the validation that takes place
getDescription() - Method in interface net.sf.basedb.util.uri.ConnectionManagerFactory
Get a longer description that can be used by client applications to show more information about the capabilities of the factory to the users.
getDescription() - Method in class net.sf.basedb.util.uri.http.HttpConnectionManagerFactory
 
getDescription() - Method in class net.sf.basedb.util.zip.Bzip2FilePacker
 
getDescription() - Method in interface net.sf.basedb.util.zip.FilePacker
Get a short description of this file format that is suitable for display in selection list boxes.
getDescription() - Method in class net.sf.basedb.util.zip.GzipFilePacker
 
getDescription() - Method in class net.sf.basedb.util.zip.TarFilePacker
 
getDescription() - Method in class net.sf.basedb.util.zip.ZipFilePacker
 
getDescriptor() - Method in class net.sf.basedb.util.overview.Failure
 
getDestinationCount() - Method in class net.sf.basedb.core.data.PlateMappingData
The produced number of destination plates.
getDestinationCount() - Method in class net.sf.basedb.core.PlateMapping
Get the number of produced destination plates.
getDestinationGeometry() - Method in class net.sf.basedb.core.data.PlateMappingData
The required geometry of destination plates in this mapping.
getDestinationGeometry() - Method in class net.sf.basedb.core.PlateMapping
Get the PlateGeometry of the created plates.
getDestinationIndex() - Method in class net.sf.basedb.core.data.PlateData
If the plate was created by a plate mapping, this is the index of this plate in the list of created plates.
getDestinationIndex() - Method in class net.sf.basedb.core.Plate
If the plate was created by a plate mapping, this is the index of this plate in the list of created plates.
getDetail() - Method in exception net.sf.basedb.clients.web.WebException
Get the detailed description of the error message.
getDetails() - Method in class net.sf.basedb.core.data.ChangeHistoryData
This is the inverse end.
getDetails() - Method in class net.sf.basedb.core.data.PlateMappingData
For each destination coordinate we can get the source coordinate.
getDevice() - Method in class net.sf.basedb.core.data.SessionData
Get the device the user was using.
getDevice() - Method in class net.sf.basedb.core.Session
Get the device the user was using in this session.
getDeviceId() - Method in class net.sf.basedb.core.SessionControl
Get the id of the UserDevice in use.
getDeviceName() - Method in class net.sf.basedb.core.SessionControl
Get the name of the UserDevice in use.
getDevices() - Method in class net.sf.basedb.core.data.ClientData
This is the inverse end.
getDevices() - Method in class net.sf.basedb.core.data.UserData
This is the inverse end.
getDeviceToken() - Method in class net.sf.basedb.core.authentication.LoginRequest
Get the deviceToken to use.
getDeviceToken() - Method in class net.sf.basedb.core.SessionControl.UnverifiedDeviceInfo
Get the token for this device.
getDialect() - Static method in class net.sf.basedb.core.HibernateUtil
Get the database dialect.
getDifference() - Method in interface net.sf.basedb.core.DiskConsumable
Get the number of bytes this items now is using compared to when it was loaded from the database.
getDifference() - Method in class net.sf.basedb.core.Experiment
 
getDifference() - Method in class net.sf.basedb.core.File
Always 0.
getDifference() - Method in class net.sf.basedb.core.RawBioAssay
Always 0.
getDirection() - Method in class net.sf.basedb.clients.web.extensions.list.RelatedItemColumn.Specification
Get the parsed value of the DIRECTION.
getDirection() - Method in class net.sf.basedb.clients.web.taglib.table.Table
 
getDirectionImage(ItemContext.SortDirection) - Method in class net.sf.basedb.clients.web.taglib.table.Table
Get sort direction <img> element for the given direction.
getDirectionRaw() - Method in class net.sf.basedb.clients.web.extensions.list.RelatedItemColumn.Specification
Get the raw value of the DIRECTION.
getDirectory() - Method in class net.sf.basedb.core.data.ExperimentData
Get the associated DirectoryData item directory where it is recommended for plugins to save files related to the experiment.
getDirectory() - Method in class net.sf.basedb.core.data.FileData
Get the associated DirectoryData item.
getDirectory() - Method in class net.sf.basedb.core.Experiment
Get the associated directory where it is recommended that plugins store files that are related to this experiment.
getDirectory() - Method in class net.sf.basedb.core.File
Get the associated Directory item.
getDirectory(int) - Method in class net.sf.basedb.core.Path
Get the name of the i:th directory on the path, starting with 0.
getDirectory(DbControl, Path) - Method in class net.sf.basedb.plugins.batchimport.FileImporter
 
getDirectory(DbControl, Path) - Method in class net.sf.basedb.plugins.TarFileUnpacker
Get the directory for the specified path.
getDirectory(Path) - Method in class net.sf.basedb.util.zip.ZipUnpacker
Get the directory for the specified path.
getDirectoryCount() - Method in class net.sf.basedb.core.Path
Get the number of directories on the path.
getDirectoryParameter(String, String) - Method in class net.sf.basedb.util.zip.AbstractFileUnpacker
Get a plugin parameter that asks for the directory where the unpacked files are stored.
getDirectoryTree(DbControl, Directory) - Static method in class net.sf.basedb.util.FileUtil
Get the complete tree of sub-directories from a given directory.
getDirty(int) - Method in class net.sf.basedb.core.log.EntityDetails
 
getDisableInheritance() - Method in class net.sf.basedb.core.AnnotationType
If this flag is set, annotations of this type can't be inherited to child items.
getDisableInheritance() - Method in class net.sf.basedb.core.data.AnnotationTypeData
If this flag is set, annotation of this type can't be inherited.
getDisableinproject() - Method in class net.sf.basedb.clients.web.taglib.table.PresetSelector
 
getDisableLogOfValues() - Method in class net.sf.basedb.core.AnnotationType
If this flag is set, the change history logging will not include actual annotation values.
getDisableLogOfValues() - Method in class net.sf.basedb.core.data.AnnotationTypeData
If this flag is set, logging of actual annotation values should not be done in the change history.
getDisableManualMembers() - Method in class net.sf.basedb.core.data.ItemListData
If set, manually adding/removing members is disabled
getDisableManualMembers() - Method in class net.sf.basedb.core.ItemList
If this flag is set manual modification of members is disabled.
getDisableothers() - Method in class net.sf.basedb.clients.web.taglib.table.PresetSelector
 
getDisableOverflowCheck() - Method in class net.sf.basedb.clients.web.extensions.list.AbstractListColumnBean
 
getDisableOverflowCheck() - Method in interface net.sf.basedb.clients.web.extensions.list.ListColumnAction
If set, text overflow check is disabled for this column.
getDisableownedby() - Method in class net.sf.basedb.clients.web.taglib.table.PresetSelector
 
getDisableRawJoinOnMergedData() - Method in class net.sf.basedb.core.DynamicSpotQuery
 
getDisableremoved() - Method in class net.sf.basedb.clients.web.taglib.table.PresetSelector
 
getDisablesharedto() - Method in class net.sf.basedb.clients.web.taglib.table.PresetSelector
 
getDisableSyncFilters() - Method in class net.sf.basedb.core.data.ItemListData
If set, syncing members with sync filter is disabled
getDisableSyncFilters() - Method in class net.sf.basedb.core.ItemList
If this flag is set synchronization of members with sync filters is disabled.
getDiskConsumableItems() - Static method in class net.sf.basedb.core.Metadata
Get a set containing all DiskConsumable item types.
getDiskUsage() - Method in interface net.sf.basedb.core.data.DiskConsumableData
Get the DiskUsageData that this item use.
getDiskUsage() - Method in class net.sf.basedb.core.data.ExperimentData
 
getDiskUsage() - Method in class net.sf.basedb.core.data.FileData
 
getDiskUsage() - Method in class net.sf.basedb.core.data.RawBioAssayData
 
getDiskUsage(GroupData, QuotaTypeData, Location) - Method in class net.sf.basedb.core.DbControl
Get the disk usage for the specified group at the specified location and quota type.
getDiskUsage(UserData, QuotaTypeData, Location) - Method in class net.sf.basedb.core.DbControl
Get the disk usage for the specified user at the specified location and quota type.
getDiskUsage(QuotaType, Location) - Method in class net.sf.basedb.core.Group
Get the used number of bytes for the specified quota type and location.
getDiskUsage(QuotaType, Location) - Method in class net.sf.basedb.core.User
Get the used number of bytes for the specified quota type and location.
getDisplayAsList() - Method in class net.sf.basedb.core.AnnotationType
Check if the enumeration values should be displayed as a selection list or as radio buttons/checkboxes by the client application.
getDisplayName() - Method in interface net.sf.basedb.clients.web.extensions.login.LoginFormAction
Get a name that can be displayed for users in a selection list or similar to switch between different login methods.
getDisplayName() - Method in class net.sf.basedb.clients.web.extensions.login.LoginFormBean
 
getDisplayName() - Method in class net.sf.basedb.clients.web.extensions.login.PasswordLoginFormFactory
 
getDisplayName() - Method in interface net.sf.basedb.util.uri.ConnectionManagerFactory
Get a short string that is suitable for use in selection lists, etc.
getDisplayName() - Method in class net.sf.basedb.util.uri.http.HttpConnectionManagerFactory
 
getDisplaySymbol() - Method in class net.sf.basedb.core.data.UnitData
The symbol to display together with values of this unit.
getDisplaySymbol() - Method in class net.sf.basedb.core.Unit
Get the display symbol to use when displaying values with this unit.
getDoctype() - Method in class net.sf.basedb.clients.web.taglib.Page
 
getDomainOrder() - Method in class net.sf.basedb.util.plot.HistogramPlot.HistogramDataset
 
getDouble(int, NumberFormat, boolean) - Method in class net.sf.basedb.util.parser.FlatFileParser.Data
Get the value as a double.
getDouble(int, NumberFormat, boolean) - Method in class net.sf.basedb.util.parser.FlatFileParser.ExcelData
 
getDouble(String) - Static method in class net.sf.basedb.util.Values
Convert a string to a double.
getDouble(String[]) - Static method in class net.sf.basedb.util.Values
Convert an array of strings to an array of Double:s.
getDouble(String, double) - Static method in class net.sf.basedb.util.Values
Convert a string to a double.
getDouble(String, Double) - Static method in class net.sf.basedb.util.Values
 
getDouble(FlatFileParser.Data) - Method in class net.sf.basedb.util.parser.ColumnMapper
 
getDouble(FlatFileParser.Data) - Method in class net.sf.basedb.util.parser.CompoundMapper
 
getDouble(FlatFileParser.Data) - Method in class net.sf.basedb.util.parser.ConstantMapper
 
getDouble(FlatFileParser.Data) - Method in class net.sf.basedb.util.parser.CropStringMapper
 
getDouble(FlatFileParser.Data) - Method in class net.sf.basedb.util.parser.JepMapper
 
getDouble(FlatFileParser.Data) - Method in interface net.sf.basedb.util.parser.Mapper
Get the value for the line of data as a double.
getDouble(FlatFileParser.Data) - Method in class net.sf.basedb.util.parser.NullIfExceptionMapper
 
getDoubleFormatter(SessionControl) - Static method in class net.sf.basedb.clients.web.formatter.FormatterFactory
Get the logged in user's number formatter for double values.
getDoubleOption(String, Double) - Method in class net.sf.basedb.core.AnnotationType
Get an option and convert the value to a double.
getDoubleValues() - Method in class net.sf.basedb.core.data.annotations.AnnotationLink
 
getDownloadStream(long) - Method in class net.sf.basedb.core.File
Get an InputStream that can be used to download the physical file for this file item.
getDragcolumns() - Method in class net.sf.basedb.clients.web.taglib.table.Table
 
getDropForeignKeySql(String, String, String, String) - Method in interface net.sf.basedb.core.dbengine.DbEngine
Generate SQL to drop a foreign key constraint.
getDropForeignKeySql(String, String, String, String) - Method in class net.sf.basedb.core.dbengine.DefaultDbEngine
Generate alter table <catalog>.<schema>.<table> drop constraint <name>
getDropForeignKeySql(String, String, String, String) - Method in class net.sf.basedb.core.dbengine.MySQLEngine
Generate alter table <catalog>.<table> drop foreign key <name>
getDropForeignKeySql(String, String, String, String) - Method in class net.sf.basedb.core.dbengine.PostgresDbEngine
Generate alter table <schema>.<table> DROP CONSTRAINT <name>
getDropIndexSql(String, String, String, String, boolean) - Method in interface net.sf.basedb.core.dbengine.DbEngine
Generate SQL to drop an index.
getDropIndexSql(String, String, String, String, boolean) - Method in class net.sf.basedb.core.dbengine.DefaultDbEngine
Generate drop index <catalog>.<schema>.<table>.<name>.
getDropIndexSql(String, String, String, String, boolean) - Method in class net.sf.basedb.core.dbengine.MySQLEngine
Generate drop index <name> on <catalog>.<table>.
getDropIndexSql(String, String, String, String, boolean) - Method in class net.sf.basedb.core.dbengine.PostgresDbEngine
Generate alter table <schema>.<table> drop constraint <name> for unique indexes, drop index <schema>.<name> for other indexes.
getDropPrimaryKey(String, String, String, String) - Method in interface net.sf.basedb.core.dbengine.DbEngine
Generate SQL that drops the primary key from a table.
getDropPrimaryKey(String, String, String, String) - Method in class net.sf.basedb.core.dbengine.DefaultDbEngine
 
getDropPrimaryKey(String, String, String, String) - Method in class net.sf.basedb.core.dbengine.MySQLEngine
Generate alter table catalog.table drop primary key
getDropPrimaryKey(String, String, String, String) - Method in class net.sf.basedb.core.dbengine.PostgresDbEngine
Generate alter table schema.table drop constraint name
getDynamicActionAttributes() - Method in class net.sf.basedb.clients.web.extensions.AbstractJspFactory
 
getDynamicActionAttributes() - Method in interface net.sf.basedb.clients.web.extensions.DynamicActionAttributes
Get an iterator that return all dynamic attributes.
getDynamicActionAttributes() - Method in class net.sf.basedb.clients.web.extensions.DynamicActionAttributeSupport
 
getDynamicActionAttributes() - Method in interface net.sf.basedb.clients.web.extensions.list.ListColumnAction
Get extra attributes that will be outputted in the HTML for the list column.
getDynamicActionAttributes() - Method in class net.sf.basedb.clients.web.extensions.skin.FixedSkinActionFactory.MySkinAction
 
getDynamicActionAttributes() - Method in class net.sf.basedb.clients.web.taglib.StylableTag
 
getDynamicActionAttributes() - Method in class net.sf.basedb.clients.web.taglib.tab.Tab
 
getDynamicActionAttributes() - Method in class net.sf.basedb.clients.web.taglib.table.Button.ButtonActionWrapper
 
getDynamicAttribute(String) - Method in class net.sf.basedb.clients.web.taglib.StylableTag
Get the dynamic attribute for the given name
getDynamicCatalog() - Static method in class net.sf.basedb.core.Application
Get the name of the dynamic catalog.
getDynamicExpression(DbControl, SqlQuery, String) - Static method in class net.sf.basedb.core.ItemContext
Create an Expression from a string.
getDynamicQuery() - Static method in class net.sf.basedb.core.Reporter
Get a dynamic query object configured to retrieve reporter information.
getDynamicQuery(Experiment) - Static method in class net.sf.basedb.core.Reporter
Get a dynamic query object configured to retrieve reporter information from either the master reporter table or a cloned reporter table in the given experiment.
getDynamicRawData() - Method in class net.sf.basedb.core.RawBioAssay
Get a dynamic query that returns the raw data of this raw bioassay.
getDynamicRestriction(DbControl, SqlQuery) - Method in class net.sf.basedb.core.PropertyFilter
 
getDynamicSchema() - Static method in class net.sf.basedb.core.Application
Get the name of the dynamic schema.
getDynamicSelect(DbControl, SqlQuery, String) - Static method in class net.sf.basedb.core.ItemContext
Same as ItemContext.getDynamicExpression(DbControl, SqlQuery, String) but generates a select object instead.
getEffectiveFilter() - Method in class net.sf.basedb.core.ItemContext.PropertyFilterPair
 
getEffectiveMaxMemory() - Method in class net.sf.basedb.core.JobAgentSettings
Get the effective maximum amount of memory the plugin is allowed to use.
getEffectivePriority(Job) - Method in class net.sf.basedb.core.JobAgentSettings
Get the effective priority for the specified job, when the priority boost is taken into account.
getElementClass() - Method in class net.sf.basedb.core.DynamicPositionQueryJoiners.ExtraValueJoiner
 
getElementClass() - Method in class net.sf.basedb.core.DynamicPositionQueryJoiners.ReporterJoiner
 
getElementClass() - Method in class net.sf.basedb.core.DynamicPositionQueryJoiners.ReporterListJoiner
 
getElementClass() - Method in class net.sf.basedb.core.DynamicRawDataQuery.RawBioAssayJoiner
 
getElementClass() - Method in class net.sf.basedb.core.DynamicRawDataQuery.ReporterJoiner
 
getElementClass() - Method in class net.sf.basedb.core.DynamicRawDataQuery.ReporterListJoiner
 
getElementClass() - Method in class net.sf.basedb.core.DynamicReporterQuery.MasterReporterJoiner
 
getElementClass() - Method in class net.sf.basedb.core.DynamicReporterQuery.ReporterListJoiner
 
getElementClass() - Method in class net.sf.basedb.core.DynamicSpotQueryJoiners.ExtraValueJoiner
 
getElementClass() - Method in class net.sf.basedb.core.DynamicSpotQueryJoiners.RawDataJoiner
 
getElementClass() - Method in class net.sf.basedb.core.DynamicSpotQueryJoiners.ReporterJoiner
 
getElementClass() - Method in class net.sf.basedb.core.DynamicSpotQueryJoiners.ReporterListJoiner
 
getElementClass() - Method in class net.sf.basedb.core.HqlQueryJoiners.AnnotationJoiner
 
getElementClass() - Method in class net.sf.basedb.core.HqlQueryJoiners.ReporterListJoiner
 
getElementClass() - Method in interface net.sf.basedb.core.query.AutoJoiner
The type of the query element the implementation works for.
getEmail() - Method in class net.sf.basedb.core.authentication.ExtraUserInformation
 
getEmail() - Method in class net.sf.basedb.core.data.PluginDefinitionData
Get an email address that can be used to get more information about the plugin.
getEmail() - Method in class net.sf.basedb.core.data.UserData
Get the email address to the user, or null if unknown.
getEmail() - Method in interface net.sf.basedb.core.plugin.About
An email adress to get more information about the plugin.
getEmail() - Method in class net.sf.basedb.core.plugin.AboutImpl
 
getEmail() - Method in class net.sf.basedb.core.PluginDefinition
Get an email address that can be used to get more information about the plugin.
getEmail() - Method in class net.sf.basedb.core.User
Get the email address to the user.
getEmail() - Method in class net.sf.basedb.util.extensions.AboutBean
 
getEmail() - Method in class net.sf.basedb.util.extensions.Registry.RegisteredAbout
 
getEnabledFilter(String) - Method in class net.sf.basedb.core.hibernate.SessionWrapper
 
getEnabledItems() - Method in class net.sf.basedb.core.AnnotationType
Get the Item types this annotation type is enabled for.
getEnableDownloadLink() - Method in class net.sf.basedb.clients.web.taglib.PropertyValue
 
getEnableEditLink() - Method in class net.sf.basedb.clients.web.taglib.PropertyValue
 
getEnablePropertyLink() - Method in class net.sf.basedb.clients.web.taglib.PropertyValue
 
getEncodedName(Nameable, boolean) - Static method in class net.sf.basedb.clients.web.Base
Encode the name of the nameable item using the HTML.encodeTags(String) method.
getEncoder() - Method in class net.sf.basedb.util.excel.XlsxToCsvUtil
Get the current encoder.
getEncoder() - Method in class net.sf.basedb.util.export.TableWriter
Get the current default encoder for this writer.
getEndDate() - Method in class net.sf.basedb.core.data.NewsData
Get the last day this news item should be shown.
getEndDate() - Method in class net.sf.basedb.core.News
Get the end date and time for this news item to be published.
getEnded() - Method in class net.sf.basedb.core.data.JobData
Get the date and time the job was ended or null if the job hasn't ended.
getEnded() - Method in class net.sf.basedb.core.Job
Get the date and time the job ended.
getEndTime() - Method in class net.sf.basedb.util.extensions.manager.ProcessResults
Get the end time of the scan as a millisecond value.
getEndX() - Method in class net.sf.basedb.util.plot.HistogramPlot.HistogramBin
 
getEndX(int, int) - Method in class net.sf.basedb.util.plot.HistogramPlot.HistogramDataset
 
getEndXValue(int, int) - Method in class net.sf.basedb.util.plot.HistogramPlot.HistogramDataset
 
getEndY(int, int) - Method in class net.sf.basedb.util.plot.HistogramPlot.HistogramDataset
 
getEndYValue(int, int) - Method in class net.sf.basedb.util.plot.HistogramPlot.HistogramDataset
 
getEntity() - Method in class net.sf.basedb.core.log.EntityDetails
Get the entity that was changed.
getEntityGraph(String) - Method in class net.sf.basedb.core.hibernate.SessionWrapper
 
getEntityGraphs(Class<T>) - Method in class net.sf.basedb.core.hibernate.SessionWrapper
 
getEntityLogger(LogManager, Object) - Method in class net.sf.basedb.core.log.db.DbLogManagerFactory
If a special logger has been registered for the class of the given entity, use that logger, otherwise use the default logger.
getEntityLogger(LogManager, Object) - Method in interface net.sf.basedb.core.log.LogManagerFactory
Get/create an entity logger for logging changes to the given entity.
getEntityLogOptions(Object) - Static method in class net.sf.basedb.core.log.EntityLogOptions
Get the logging options for the given entity.
getEntityLogOptionsForClass(Class<?>) - Static method in class net.sf.basedb.core.log.EntityLogOptions
Get the logging options for the given class of entities.
getEntityManagerFactory() - Method in class net.sf.basedb.core.hibernate.SessionWrapper
 
getEntityName() - Method in class net.sf.basedb.core.RawDataType
 
getEntityName(Object) - Method in class net.sf.basedb.core.hibernate.SessionWrapper
 
getEntriesByKey(K) - Method in class net.sf.basedb.util.Enumeration
Get a list with all entries that equals the given key.
getEntriesByValue(V) - Method in class net.sf.basedb.util.Enumeration
Get a list with all entries that equals the given value.
getEntry(int) - Method in class net.sf.basedb.util.bfs.MetadataModel.Section
Get the entry in this section with the given index.
getEntry(int) - Method in class net.sf.basedb.util.Enumeration
 
getEntry(E) - Method in class net.sf.basedb.util.Tree
Get the entry for an arbitrary node.
getEntry(String) - Method in class net.sf.basedb.util.bfs.MetadataModel.Section
Get the first entry in this section with a given key.
getEntryCount() - Method in class net.sf.basedb.util.bfs.MetadataModel.Section
Get the number of entries in this section.
getEntryDate() - Method in class net.sf.basedb.core.AnnotationType
 
getEntryDate() - Method in class net.sf.basedb.core.AnnotationTypeCategory
 
getEntryDate() - Method in class net.sf.basedb.core.ArrayBatch
 
getEntryDate() - Method in class net.sf.basedb.core.ArrayDesign
 
getEntryDate() - Method in class net.sf.basedb.core.ArraySlide
 
getEntryDate() - Method in class net.sf.basedb.core.BioMaterialEvent
Get the date this event was added to the database.
getEntryDate() - Method in class net.sf.basedb.core.BioPlate
 
getEntryDate() - Method in class net.sf.basedb.core.BioPlateEvent
 
getEntryDate() - Method in class net.sf.basedb.core.BioSource
 
getEntryDate() - Method in class net.sf.basedb.core.Client
 
getEntryDate() - Method in class net.sf.basedb.core.data.AnnotationTypeCategoryData
 
getEntryDate() - Method in class net.sf.basedb.core.data.AnnotationTypeData
 
getEntryDate() - Method in class net.sf.basedb.core.data.ArrayBatchData
 
getEntryDate() - Method in class net.sf.basedb.core.data.ArrayDesignData
 
getEntryDate() - Method in class net.sf.basedb.core.data.ArraySlideData
 
getEntryDate() - Method in class net.sf.basedb.core.data.BioMaterialEventData
 
getEntryDate() - Method in class net.sf.basedb.core.data.BioPlateData
 
getEntryDate() - Method in class net.sf.basedb.core.data.BioPlateEventData
 
getEntryDate() - Method in class net.sf.basedb.core.data.BioSourceData
 
getEntryDate() - Method in class net.sf.basedb.core.data.ClientData
 
getEntryDate() - Method in class net.sf.basedb.core.data.DerivedBioAssayData
 
getEntryDate() - Method in class net.sf.basedb.core.data.ExperimentData
 
getEntryDate() - Method in class net.sf.basedb.core.data.ExtraValueTypeData
 
getEntryDate() - Method in class net.sf.basedb.core.data.FormulaData
 
getEntryDate() - Method in class net.sf.basedb.core.data.GroupData
 
getEntryDate() - Method in class net.sf.basedb.core.data.HardwareData
 
getEntryDate() - Method in class net.sf.basedb.core.data.ItemSubtypeData
 
getEntryDate() - Method in class net.sf.basedb.core.data.KitData
 
getEntryDate() - Method in class net.sf.basedb.core.data.MimeTypeData
 
getEntryDate() - Method in class net.sf.basedb.core.data.NewsData
 
getEntryDate() - Method in class net.sf.basedb.core.data.PlateData
 
getEntryDate() - Method in class net.sf.basedb.core.data.PlateEventData
Get the date this event was added to the database.
getEntryDate() - Method in class net.sf.basedb.core.data.PlateGeometryData
 
getEntryDate() - Method in class net.sf.basedb.core.data.PlateMappingData
 
getEntryDate() - Method in class net.sf.basedb.core.data.PlateTypeData
 
getEntryDate() - Method in class net.sf.basedb.core.data.PluginConfigurationData
 
getEntryDate() - Method in class net.sf.basedb.core.data.PluginDefinitionData
 
getEntryDate() - Method in class net.sf.basedb.core.data.PluginTypeData
 
getEntryDate() - Method in class net.sf.basedb.core.data.ProjectData
 
getEntryDate() - Method in class net.sf.basedb.core.data.ProtocolData
 
getEntryDate() - Method in class net.sf.basedb.core.data.QuotaTypeData
 
getEntryDate() - Method in class net.sf.basedb.core.data.RawBioAssayData
 
getEntryDate() - Method in interface net.sf.basedb.core.data.RegisteredData
Get the date this item was added to the database.
getEntryDate() - Method in class net.sf.basedb.core.data.ReporterCloneTemplateData
 
getEntryDate() - Method in class net.sf.basedb.core.data.ReporterData
 
getEntryDate() - Method in class net.sf.basedb.core.data.ReporterListData
 
getEntryDate() - Method in class net.sf.basedb.core.data.ReporterTypeData
 
getEntryDate() - Method in class net.sf.basedb.core.data.RoleData
 
getEntryDate() - Method in class net.sf.basedb.core.data.SoftwareData
 
getEntryDate() - Method in class net.sf.basedb.core.data.TagData
 
getEntryDate() - Method in class net.sf.basedb.core.data.UserData
 
getEntryDate() - Method in class net.sf.basedb.core.data.UserDeviceData
 
getEntryDate() - Method in class net.sf.basedb.core.DerivedBioAssay
 
getEntryDate() - Method in class net.sf.basedb.core.Experiment
 
getEntryDate() - Method in class net.sf.basedb.core.ExtraValueType
 
getEntryDate() - Method in class net.sf.basedb.core.Formula
 
getEntryDate() - Method in class net.sf.basedb.core.Group
 
getEntryDate() - Method in class net.sf.basedb.core.Hardware
 
getEntryDate() - Method in class net.sf.basedb.core.ItemSubtype
 
getEntryDate() - Method in class net.sf.basedb.core.Kit
 
getEntryDate() - Method in class net.sf.basedb.core.MeasuredBioMaterial
 
getEntryDate() - Method in class net.sf.basedb.core.MimeType
 
getEntryDate() - Method in class net.sf.basedb.core.News
 
getEntryDate() - Method in class net.sf.basedb.core.PhysicalBioAssay
 
getEntryDate() - Method in class net.sf.basedb.core.Plate
 
getEntryDate() - Method in class net.sf.basedb.core.PlateEvent
Get the date this event was added to the database.
getEntryDate() - Method in class net.sf.basedb.core.PlateGeometry
 
getEntryDate() - Method in class net.sf.basedb.core.PlateMapping
 
getEntryDate() - Method in class net.sf.basedb.core.PlateType
 
getEntryDate() - Method in class net.sf.basedb.core.PluginConfiguration
 
getEntryDate() - Method in class net.sf.basedb.core.PluginDefinition
 
getEntryDate() - Method in class net.sf.basedb.core.PluginType
 
getEntryDate() - Method in class net.sf.basedb.core.Project
 
getEntryDate() - Method in class net.sf.basedb.core.Protocol
 
getEntryDate() - Method in class net.sf.basedb.core.QuotaType
 
getEntryDate() - Method in class net.sf.basedb.core.RawBioAssay
 
getEntryDate() - Method in interface net.sf.basedb.core.Registered
Get the date that the item was registered in the database.
getEntryDate() - Method in class net.sf.basedb.core.ReporterCloneTemplate
 
getEntryDate() - Method in class net.sf.basedb.core.ReporterList
 
getEntryDate() - Method in class net.sf.basedb.core.ReporterType
 
getEntryDate() - Method in class net.sf.basedb.core.Role
 
getEntryDate() - Method in class net.sf.basedb.core.Software
 
getEntryDate() - Method in class net.sf.basedb.core.Tag
 
getEntryDate() - Method in class net.sf.basedb.core.User
 
getEntryDate() - Method in class net.sf.basedb.core.UserDevice
 
getEnumeration() - Method in class net.sf.basedb.clients.web.extensions.list.AbstractListColumnBean
 
getEnumeration() - Method in interface net.sf.basedb.clients.web.extensions.list.ListColumnAction
Get an enumeration of possible values that can be found in the column.
getEnumeration() - Method in class net.sf.basedb.clients.web.taglib.table.ColumnDef
 
getEnumeration() - Method in class net.sf.basedb.core.ParameterType
Get the list of values to choose from as an enumeration.
getEnumerationValues() - Method in class net.sf.basedb.core.data.AnnotationTypeData
The allowed values if this is an enumeration.
getEnumOptions() - Method in class net.sf.basedb.plugins.Base1PluginExecuter.JobParameter
 
getError() - Method in class net.sf.basedb.core.SimpleProgressReporter
Get error that happened while processing some action that was reported via this progress reporter.
getError() - Method in class net.sf.basedb.util.ContextUtil.ContextResult
Get the exception that caused the error, or null if this is a warning-level object.
getError() - Method in class net.sf.basedb.util.FileCopyRunnable
Get the exception that was thrown when executing the file copy operation.
getErrorclazz() - Method in class net.sf.basedb.clients.web.taglib.table.Cell
 
getErrorHandler() - Method in class net.sf.basedb.util.extensions.ExtensionContext
 
getErrorHandler() - Method in class net.sf.basedb.util.extensions.ExtensionPointContext
 
getErrorHandler() - Method in class net.sf.basedb.util.extensions.InvokationContext
Get the error handler used in this context.
getErrorHandler(String, ErrorHandler) - Method in class net.sf.basedb.plugins.AbstractFlatFileImporter
 
getErrorHandler(InvokationContext<? extends A>) - Method in interface net.sf.basedb.util.extensions.ErrorHandlerFactory
Get an error handler for the current context.
getErrorHandler(InvokationContext<? extends Action>) - Method in class net.sf.basedb.util.extensions.LoggingErrorHandlerFactory
 
getErrorHandler(InvokationContext<? extends Action>) - Method in class net.sf.basedb.util.extensions.RethrowErrorHandlerFactory
 
getErrorHandlerFactory() - Method in interface net.sf.basedb.util.extensions.ExtensionPoint
Get the error handler factory that should be used with this extension point.
getErrorHandlerFactory() - Method in class net.sf.basedb.util.extensions.ExtensionPointBean
 
getErrorHandlerFactory() - Method in class net.sf.basedb.util.extensions.Registry.RegisteredExtensionPoint
 
getErrorList() - Method in class net.sf.basedb.core.PluginResponse
Get a list containing detailed error messages if the status is Response.Status.ERROR.
getErrorMessage() - Method in class net.sf.basedb.core.data.FileSetMemberData
The error message if the file validation failed.
getErrorMessage() - Method in class net.sf.basedb.core.FileSetMember
Get the error message if the validation failed.
getErrorOption(String) - Method in class net.sf.basedb.plugins.AbstractFlatFileImporter
Get the value for an error handling parameter.
getErrors() - Method in class net.sf.basedb.plugins.executor.ExternalProgramExecutor.ResponseWrapper
 
getEstimatedExecutionTime() - Method in class net.sf.basedb.clients.jobagent.slotmanager.Slot
Get the estimated execution time for this slot.
getEstimatedExecutionTime() - Method in class net.sf.basedb.core.data.JobData
Get the estimated execution time of the job. 0 = <1 minute, 1 = 1 - 10 minutes, 2 = <1 hour, 3 = >1 hour
getEstimatedExecutionTime() - Method in class net.sf.basedb.core.Job
Get the estimated execution time of the job.
getEstimatedExecutionTime() - Method in class net.sf.basedb.core.PluginResponse
Get the estimated execution time of the job.
getEvaluateFormulas() - Method in class net.sf.basedb.util.excel.XlsxToCsvUtil
If TRUE, formulas are evaluated and the result is written to the CSV file.
getEvent() - Method in class net.sf.basedb.core.BioMaterialEventSource
Get the event that this information belongs to.
getEvent() - Method in class net.sf.basedb.core.BioPlateEventParticipant
Get the BioPlateEvent.
getEvent() - Method in class net.sf.basedb.core.data.BioMaterialEventSourceData
Get the event that created something from the parent biomaterial.
getEvent() - Method in class net.sf.basedb.core.data.BioPlateEventParticipantData
The bioplate event.
getEvent(PlateEventType) - Method in class net.sf.basedb.core.Plate
Get the event for the specified event type.
getEventDate() - Method in class net.sf.basedb.core.BioMaterialEvent
Get the date this event was done in the lab.
getEventDate() - Method in class net.sf.basedb.core.BioPlate
Get the date this plate was created.
getEventDate() - Method in class net.sf.basedb.core.BioPlateEvent
Get the date this event was done in the lab.
getEventDate() - Method in class net.sf.basedb.core.data.BioMaterialEventData
Get the date this event happened in the lab.
getEventDate() - Method in class net.sf.basedb.core.data.BioPlateData
Get the date this plate was created in the lab.
getEventDate() - Method in class net.sf.basedb.core.data.BioPlateEventData
Get the date this event happened in the lab.
getEventDate() - Method in class net.sf.basedb.core.data.PlateEventData
Get the date this event happened in the lab.
getEventDate() - Method in class net.sf.basedb.core.PlateEvent
Get the date this event was done in the lab.
getEventParticipants() - Method in class net.sf.basedb.core.data.BioPlateData
This is the inverse end.
getEvents() - Method in class net.sf.basedb.core.BioPlate
Get a query returning events that this plate has been a part of.
getEvents() - Method in class net.sf.basedb.core.data.BioPlateEventTypeData
This is the inverse end.
getEvents() - Method in class net.sf.basedb.core.data.MeasuredBioMaterialData
This is the inverse end.
getEvents() - Method in class net.sf.basedb.core.data.PlateData
The event for this plate.
getEvents() - Method in class net.sf.basedb.core.MeasuredBioMaterial
Get a query that returns all events for this biomaterial.
getEvents() - Method in class net.sf.basedb.core.Plate
Get a query that returns all event types for this plate type.
getEventSource(BioMaterial) - Method in class net.sf.basedb.core.BioMaterialEvent
Get information about a biomaterial used as a source to this event.
getEventSources() - Method in class net.sf.basedb.core.BioMaterialEvent
Create a special query that return BioMaterialEventSource objects.
getEventSources(DbControl, int) - Method in class net.sf.basedb.core.BioMaterialEvent
Utility method for finding all sources on a given bioassay position.
getEventType() - Method in class net.sf.basedb.core.BioMaterialEvent
Get the type of event.
getEventType() - Method in class net.sf.basedb.core.BioPlateEvent
Get the event type of this event.
getEventType() - Method in class net.sf.basedb.core.data.BioMaterialEventData
Get the type of event, 1=creation event, 2=hybridization event, 3=other event
getEventType() - Method in class net.sf.basedb.core.data.BioPlateEventData
The type of the event.
getEventTypes() - Method in class net.sf.basedb.core.data.PlateTypeData
The event types defined for this plate type.
getEventTypes() - Method in class net.sf.basedb.core.PlateType
Get a query that returns all event types for this plate type.
getExcelSheet() - Method in class net.sf.basedb.util.parser.FlatFileParser
Get the name of the Excel sheet that should be or is parsed.
getExcelValue(Boolean) - Method in enum class net.sf.basedb.util.formatter.BooleanFormatter.Type
 
getException() - Method in class net.sf.basedb.clients.web.fileupload.FileUploadProgress
Get the exception that caused the upload to fail.
getException() - Method in class net.sf.basedb.core.ItemContext
Get the exception that is the cause for the error in ItemContext.configureQuery(DbControl, EntityQuery, boolean).
getExceptionHandler() - Method in class net.sf.basedb.core.hibernate.SchemaGenerator.CollectSqlTarget
 
getExcludeReportersParameters(DbControl) - Method in class net.sf.basedb.plugins.LowessNormalization
 
getExecDirectory() - Method in class net.sf.basedb.plugins.Base1PluginExecuter
Get the exec directory as a java.io.File.
getExecLine() - Method in class net.sf.basedb.plugins.Base1PluginExecuter
 
getExecuteCommand() - Method in class net.sf.basedb.core.data.JobData
The command to send to the plug-in when starting to execute it.
getExecuteCommand() - Method in class net.sf.basedb.core.Job
The command to send to the plug-in when starting to execute it.
getExecutionRequest(ProgressReporter) - Method in class net.sf.basedb.core.PluginResponse
 
getExecutor() - Method in class net.sf.basedb.plugins.executor.AbstractIOSupport
Get the external program executor that invoked the plug-in.
getExernalPluginParameters(DbControl, BioAssaySet) - Method in class net.sf.basedb.plugins.executor.ExternalProgramExecutor
 
getExistingLinkStatistics(DbControl, ItemQuery<?>, AnyToAnyLinkStatistics.Options) - Static method in class net.sf.basedb.core.AnyToAny
Get information about existing links from the items that are returned by the given query.
getExistingSessionControl(PageContext, boolean) - Static method in class net.sf.basedb.clients.web.Base
Get an existing SessionControl object given a PageContext and optionally check that a user is logged in.
getExistingSessionControl(PageContext, Permission, Item) - Static method in class net.sf.basedb.clients.web.Base
Get an existing SessionControl object given a PageContext and check for generic (role-based) permission to an item type.
getExistingSessionControl(ServletRequest, boolean) - Static method in class net.sf.basedb.clients.web.Base
Get a session control for the BASE web client "net.sf.basedb.clients.web".
getExistingSessionControl(ServletRequest, String, boolean) - Static method in class net.sf.basedb.clients.web.Base
Get an existing SessionControl object given a ServletRequest object and optionally check that a user is logged in.
getExistingSessionControl(ServletRequest, Permission, Item) - Static method in class net.sf.basedb.clients.web.Base
Get an existing SessionControl object given a ServletRequest and check for generic (role-based) permission to an item type.
getExpectedFileSubtype(DbControl, BasicItem) - Method in class net.sf.basedb.util.overview.validator.FileValidator
Get the subtype of the associated file that we expect for the given parent item.
getExpectedHardwareSubtype(DbControl, BasicItem) - Method in class net.sf.basedb.util.overview.validator.HardwareValidator
Get the subtype of the associated hardware that we expect for the given parent item.
getExpectedKitSubtype(DbControl, BasicItem, boolean) - Method in class net.sf.basedb.util.overview.validator.KitValidator
Get the subtype of the associated kit that we expect for the given parent item.
getExpectedProtocolSubtype(DbControl, BasicItem) - Method in class net.sf.basedb.util.overview.validator.ProtocolValidator
Get the subtype of the associated protocol that we expect for the given parent item.
getExpectedSoftwareSubtype(DbControl, BasicItem) - Method in class net.sf.basedb.util.overview.validator.SoftwareValidator
Get the subtype of the associated software that we expect for the given parent item.
getExpectedTagSubtype(DbControl, BasicItem) - Method in class net.sf.basedb.util.overview.validator.TagValidator
Get the subtype of the associated tag that we expect for the given parent item.
getExperiment() - Method in class net.sf.basedb.core.BioAssay
Get the experiment this bioassay belongs to.
getExperiment() - Method in class net.sf.basedb.core.BioAssaySet
Get the experiment this bioassayset belongs to.
getExperiment() - Method in class net.sf.basedb.core.data.BioAssaySetData
Get the experiment this bioassayset belongs to.
getExperiment() - Method in class net.sf.basedb.core.data.JobData
The experiment this job is a part of.
getExperiment() - Method in class net.sf.basedb.core.data.ReporterListData
Get the experiment this reporter list belongs to.
getExperiment() - Method in class net.sf.basedb.core.data.RootRawBioAssayData
Get the experiment this root raw bioassay belongs to.
getExperiment() - Method in class net.sf.basedb.core.data.TransformationData
Get the experiment this bioassayset belongs to.
getExperiment() - Method in class net.sf.basedb.core.data.VirtualDbData
Get the experiment that stores it's data in this virtual database.
getExperiment() - Method in class net.sf.basedb.core.DataCube
Get the experiment this data cube belongs to.
getExperiment() - Method in class net.sf.basedb.core.ExtraValue
Get the experiment this extra value belongs to.
getExperiment() - Method in class net.sf.basedb.core.Job
Get the experiment this job is a part of.
getExperiment() - Method in class net.sf.basedb.core.ReporterCloneBatcher
Get the current experiment this batcher is used with.
getExperiment() - Method in class net.sf.basedb.core.ReporterList
Get the experiment this reporter list belongs to.
getExperiment() - Method in class net.sf.basedb.core.RootRawBioAssay
Get the experiment this root raw bioassay belongs to.
getExperiment() - Method in class net.sf.basedb.core.Transformation
Get the experiment this transformation belongs to.
getExperiment() - Method in class net.sf.basedb.core.VirtualDb
Get the experiment this set of tables stores data for.
getExperiment(DbControl) - Method in class net.sf.basedb.clients.web.ExperimentExplorer
Get the experiment that is currently beeing explored.
getExperimentalFactorField(String, String) - Method in class net.sf.basedb.util.export.spotdata.AbstractFieldConverter
Get an experimental factor assay field.
getExperimentalFactors() - Method in class net.sf.basedb.core.data.ExperimentData
The annotation types which describes the experimental factors for this experiment.
getExperimentalFactors() - Method in class net.sf.basedb.core.Experiment
Get a query that returns all annotation types used as experimental factors for this experiment.
getExperimentDesign() - Method in class net.sf.basedb.core.data.ExperimentData
Get the experimental design for this experiment.
getExperimentDesign() - Method in class net.sf.basedb.core.Experiment
Get the a text describing the experimental design.
getExperiments() - Method in class net.sf.basedb.core.data.AnnotationTypeData
This is the inverse end.
getExperiments() - Method in class net.sf.basedb.core.data.RawBioAssayData
This is the inverse end.
getExperiments() - Method in class net.sf.basedb.core.RawBioAssay
Get a query that returns all experiments where this raw bioassay is used.
getExperimentType() - Method in class net.sf.basedb.core.data.ExperimentData
Get the experimental type for this experiment.
getExperimentType() - Method in class net.sf.basedb.core.Experiment
Get the a text describing the experiment type.
getExpirationDate() - Method in class net.sf.basedb.core.data.KitData
Get expiration date for the kit.
getExpirationDate() - Method in class net.sf.basedb.core.data.UserData
Get the expiration date for this user account, or null if no expiration date is set.
getExpirationDate() - Method in class net.sf.basedb.core.Kit
Get the expiration date of the kit.
getExpirationDate() - Method in class net.sf.basedb.core.User
Get the expire date of the account.
getExplorer(BioAssaySet) - Static method in class net.sf.basedb.clients.web.ExperimentExplorer
Get the existing experiment explorer for a bioassayset or create a new one if none exist yet.
getExportable() - Method in class net.sf.basedb.clients.web.taglib.table.TableColumn
 
getExportableFields(DbControl, BioAssaySet) - Method in class net.sf.basedb.plugins.BaseFileExporterPlugin
 
getExportableFields(DbControl, BioAssaySet) - Method in class net.sf.basedb.plugins.BfsExporterPlugin
 
getExporter(DbControl, boolean, boolean) - Method in class net.sf.basedb.plugins.executor.ExternalProgramExecutor
Get an instance of the exporter plug-in.
getExportFormatter() - Method in class net.sf.basedb.clients.web.extensions.list.AbstractListColumnBean
 
getExportFormatter() - Method in interface net.sf.basedb.clients.web.extensions.list.ListColumnAction
Get a formatter that converts the exported value to a string that is written to the file.
getExportproperty() - Method in class net.sf.basedb.clients.web.taglib.table.ColumnDef
 
getExportProperty() - Method in class net.sf.basedb.clients.web.extensions.list.AbstractListColumnBean
 
getExportProperty() - Method in interface net.sf.basedb.clients.web.extensions.list.ListColumnAction
Override the default property when this column is used for exporting.
getExporttitle() - Method in class net.sf.basedb.clients.web.taglib.table.ColumnDef
 
getExportTitle() - Method in class net.sf.basedb.clients.web.extensions.list.AbstractListColumnBean
 
getExportTitle() - Method in interface net.sf.basedb.clients.web.extensions.list.ListColumnAction
Alternative column title that should be used when exporting data from a table.
getExportValue(RelatedItemHelper, Annotatable, SourceItemTransformer) - Method in class net.sf.basedb.clients.web.extensions.list.RelatedItemColumn
Alternate implementation for loading data.
getExportValue(RelatedItemHelper, Annotatable, SourceItemTransformer) - Method in class net.sf.basedb.clients.web.extensions.list.RelatedItemExtensionColumn
 
getExportValue(RelatedItemHelper, Annotatable, SourceItemTransformer) - Method in class net.sf.basedb.clients.web.extensions.list.RelatedItemMultiHopColumn
 
getExportValue(DbControl, I) - Method in class net.sf.basedb.clients.web.extensions.list.AbstractListColumnBean
This implementation simply forward to ListColumnAction.getValue(DbControl, Object).
getExportValue(DbControl, I) - Method in interface net.sf.basedb.clients.web.extensions.list.ListColumnAction
Get the value that should be used when exporting to a file.
getExportValue(DbControl, I) - Method in class net.sf.basedb.clients.web.extensions.list.PropertyPathActionFactory.PropertyPathAction
 
getExportValue(DbControl, Annotatable) - Method in class net.sf.basedb.clients.web.extensions.list.RelatedItemColumn
We finalize this implementation to make sure that the helper implementation always get a chance to re-cycle transactions.
getExpression() - Method in class net.sf.basedb.clients.web.extensions.list.RelatedItemColumn.Specification
Get the full expression that defines the targeted item and property.
getExpression() - Method in class net.sf.basedb.core.query.ExpressionSelect
 
getExpression() - Method in interface net.sf.basedb.core.query.Select
Get the expression object representing the selected expression.
getExpression() - Method in class net.sf.basedb.util.export.spotdata.SimpleDynamicField
Get the configured express.
getExpression(DbControl, DynamicQuery, BioAssaySet, boolean) - Method in class net.sf.basedb.plugins.BaseFileExporterPlugin.ExtendedDynamicField
 
getExpression(DbControl, DynamicQuery, BioAssaySet, boolean) - Method in interface net.sf.basedb.util.export.spotdata.DynamicField
Get an expression that selects the data that should be exported.
getExpression(DbControl, DynamicQuery, BioAssaySet, boolean) - Method in class net.sf.basedb.util.export.spotdata.JepDynamicField
Converts the configured JEP expression using the BioAssaySetUtil.createJepExpression(DbControl, String, DynamicQuery) method.
getExpression(DbControl, DynamicQuery, BioAssaySet, boolean) - Method in class net.sf.basedb.util.export.spotdata.SimpleDynamicField
Returns the configured expression.
getExpressions() - Method in class net.sf.basedb.core.IntensityFormula
Get the expressions used to calculate the intensities.
getExtended(String) - Method in class net.sf.basedb.core.authentication.ExtraUserInformation
Get an extended property value.
getExtended(String) - Method in interface net.sf.basedb.core.data.ExtendableData
Get the value of an extended property.
getExtended(String) - Method in class net.sf.basedb.core.data.RawData
 
getExtended(String) - Method in class net.sf.basedb.core.data.ReporterData
 
getExtended(String) - Method in class net.sf.basedb.core.data.UserData
 
getExtended(String) - Method in class net.sf.basedb.core.User
Gets an extended property with a certain name
getExtendedPropertyFiles() - Static method in class net.sf.basedb.core.Application
Get the path to the XML file containing extended properties.
getExtendedPropertyFormatter(SessionControl, ExtendedProperty) - Static method in class net.sf.basedb.clients.web.formatter.FormatterFactory
Get a formatter for an extended property.
getExtends() - Method in interface net.sf.basedb.util.extensions.Extension
Get the ID of the extension point this extension is extending.
getExtends() - Method in class net.sf.basedb.util.extensions.ExtensionBean
 
getExtends() - Method in class net.sf.basedb.util.extensions.Registry.RegisteredExtension
 
getExtension() - Method in class net.sf.basedb.clients.web.fileupload.UploadedFile
Get the extension of the original filename.
getExtension() - Method in class net.sf.basedb.core.data.DataFileTypeData
Get the extension that files of this type usually have.
getExtension() - Method in class net.sf.basedb.core.data.MimeTypeData
Get the extension for this MimeType item.
getExtension() - Method in class net.sf.basedb.core.DataFileType
Get the common file extension for data files of this type.
getExtension() - Method in class net.sf.basedb.core.MimeType
Get the extension for this MimeType item.
getExtension() - Method in class net.sf.basedb.util.extensions.ActionIterator
Get the extension that created the current action.
getExtension() - Method in class net.sf.basedb.util.extensions.ExtensionContext
 
getExtension() - Method in class net.sf.basedb.util.extensions.ExtensionPointContext
Always null, since this is an extension point context.
getExtension() - Method in class net.sf.basedb.util.extensions.InvokationContext
Get information about the extension.
getExtension(String) - Method in class net.sf.basedb.clients.web.extensions.ExtensionsControl
Get the extension with a given ID.
getExtension(String) - Method in class net.sf.basedb.util.extensions.Registry
Get the extension with a given ID.
getExtensionClassLoader() - Method in class net.sf.basedb.clients.web.extensions.XJspCompiler
Get a class loader that can load classes from the current web application as well as the extensions JAR file.
getExtensionColumns() - Method in class net.sf.basedb.clients.web.taglib.table.Table
 
getExtensionId() - Method in class net.sf.basedb.clients.web.extensions.list.RelatedItemColumn.Specification
Get the extension id from the expression.
getExtensionId() - Method in class net.sf.basedb.util.extensions.logging.ExtensionsLog
Get the extension id of the log.
getExtensionPoint() - Method in class net.sf.basedb.util.extensions.ActionIterator
Get the extension point that the current action belongs to.
getExtensionPoint() - Method in class net.sf.basedb.util.extensions.ExtensionContext
 
getExtensionPoint() - Method in class net.sf.basedb.util.extensions.ExtensionPointContext
 
getExtensionPoint() - Method in class net.sf.basedb.util.extensions.InvokationContext
Get information about the extension point.
getExtensionPoint() - Method in class net.sf.basedb.util.extensions.Registry.RegisteredExtension
Get the extension point this extension is registered with.
getExtensionPoint(String) - Method in class net.sf.basedb.clients.web.extensions.ExtensionsControl
Get the extension point with a given ID.
getExtensionPoint(String) - Method in class net.sf.basedb.util.extensions.Registry
Get the extension point with a given ID.
getExtensionPoints() - Method in class net.sf.basedb.clients.web.extensions.ExtensionsControl
Get an list returning all registered extension points.
getExtensionPoints() - Method in class net.sf.basedb.util.extensions.Registry
Get a list with all registered extension points.
getExtensionPoints() - Method in class net.sf.basedb.util.extensions.xml.XmlLoader
Get a list with all loaded extension points.
getExtensions() - Method in class net.sf.basedb.clients.web.extensions.ExtensionsControl
Get a list returning all registered extensions.
getExtensions() - Method in class net.sf.basedb.plugins.Bzip2FileUnpacker
Return a set containing the strings [ bz2 ].
getExtensions() - Method in class net.sf.basedb.plugins.GzipFileUnpacker
Return a set containing the strings [ gz ].
getExtensions() - Method in class net.sf.basedb.plugins.TarFileUnpacker
Return a set containing the strings [ tar, tar.gz, tgz, tar.bz2 ].
getExtensions() - Method in class net.sf.basedb.plugins.ZipFileUnpacker
Return a set containing the strings [ zip, jar ].
getExtensions() - Method in class net.sf.basedb.util.extensions.Registry
Get a list with all registered extensions.
getExtensions() - Method in class net.sf.basedb.util.extensions.Registry.RegisteredExtensionPoint
Get all extensions registered with this extension point.
getExtensions() - Method in class net.sf.basedb.util.extensions.xml.XmlLoader
Get a list with all loaded extensions.
getExtensions() - Method in interface net.sf.basedb.util.zip.FileUnpacker
Get the file extensions that this unpacker supports.
getExtensions(String) - Method in class net.sf.basedb.clients.web.extensions.ExtensionsControl
Get a list returning all registered extensions for a specific extension point.
getExtensions(String) - Method in class net.sf.basedb.util.extensions.Registry
Get a list with all registered extensions for a given extension point.
getExtensionsFile() - Method in class net.sf.basedb.util.extensions.manager.ExtensionsFile.WriteableExtensionsFile
Get the underlying extensions file (for readin information)
getExtensionsFile() - Method in class net.sf.basedb.util.extensions.manager.ProcessResults.FileResults
 
getExtensionsManager() - Static method in class net.sf.basedb.core.Application
 
getExternalClientId() - Method in class net.sf.basedb.core.SessionControl
Get the external id of the Client application that created this SessionControl.
getExternalId() - Method in class net.sf.basedb.core.AnnotationType
Get the external id of the annotation type.
getExternalId() - Method in class net.sf.basedb.core.authentication.AuthenticatedUser
Get the external id for the user.
getExternalId() - Method in class net.sf.basedb.core.BioMaterial
Get the external id of the biomaterial.
getExternalId() - Method in class net.sf.basedb.core.BioPlate
Gets the external id of this bio plate
getExternalId() - Method in class net.sf.basedb.core.Client
Get the external id for this Client item.
getExternalId() - Method in class net.sf.basedb.core.data.AnnotationTypeData
Get the external id for the biomaterial
getExternalId() - Method in class net.sf.basedb.core.data.BioMaterialData
Get the external id for the biomaterial
getExternalId() - Method in class net.sf.basedb.core.data.BioPlateData
Get the external id for the biomaterial
getExternalId() - Method in class net.sf.basedb.core.data.ClientData
Get the external id for this Client item.
getExternalId() - Method in class net.sf.basedb.core.data.DataFileTypeData
Get the external id for the item.
getExternalId() - Method in class net.sf.basedb.core.data.ExtraValueTypeData
Get the external id for this ExtraValueType item.
getExternalId() - Method in class net.sf.basedb.core.data.FeatureData
Get the external id for this FeatureData item.
getExternalId() - Method in class net.sf.basedb.core.data.HelpData
Get the external id for this Help item.
getExternalId() - Method in class net.sf.basedb.core.data.ItemListData
Get the external id for this ItemList item.
getExternalId() - Method in class net.sf.basedb.core.data.JobAgentData
Get the external ID for the job agent.
getExternalId() - Method in class net.sf.basedb.core.data.JobData
External ID of a job running on an external system.
getExternalId() - Method in class net.sf.basedb.core.data.PlatformData
Get the external id for the item.
getExternalId() - Method in class net.sf.basedb.core.data.PlatformVariantData
Get the external id for the item.
getExternalId() - Method in class net.sf.basedb.core.data.ProtocolData
Get the external id for the protocol.
getExternalId() - Method in class net.sf.basedb.core.data.ReporterData
Get the external id for this ReporterData item.
getExternalId() - Method in class net.sf.basedb.core.data.ReporterListData
Get the external id for this ReporterList item.
getExternalId() - Method in class net.sf.basedb.core.data.UserData
Get the external ID for the user account.
getExternalId() - Method in class net.sf.basedb.core.DataFileType
Get the external id for the data file type.
getExternalId() - Method in class net.sf.basedb.core.ExtraValueType
Get the external id for this ExtraValueType item.
getExternalId() - Method in class net.sf.basedb.core.Help
Get the external id for this Help item.
getExternalId() - Method in class net.sf.basedb.core.ItemList
Get the external id for this list.
getExternalId() - Method in class net.sf.basedb.core.Job
Get the external ID of a job running on an external server.
getExternalId() - Method in class net.sf.basedb.core.JobAgent
Get the external id for the job agent.
getExternalId() - Method in class net.sf.basedb.core.Platform
Get the external id for the platform.
getExternalId() - Method in class net.sf.basedb.core.PlatformVariant
Get the external id for the platform variant.
getExternalId() - Method in class net.sf.basedb.core.Protocol
Get the external id of the protocol.
getExternalId() - Method in class net.sf.basedb.core.RawDataBatcher.ReporterProxy
 
getExternalId() - Method in class net.sf.basedb.core.ReporterList
Get the external id for this ReporterList item.
getExternalId() - Method in class net.sf.basedb.core.User
Get the external id for the user account.
getExtract() - Method in class net.sf.basedb.core.data.DerivedBioAssayData
Get the extract that this bioassay is related to.
getExtract() - Method in class net.sf.basedb.core.DerivedBioAssay
Get the extract that is the parent of the data in this derived bioassay.
getExtract(Annotatable) - Static method in class net.sf.basedb.util.AnnotationUtil.AnnotatableWrapper
Get the extract to use.
getExtract(DerivedBioAssay) - Method in class net.sf.basedb.util.overview.loader.DerivedBioAssayLoader
Get the extract that is associated with the current derived bioassay
getExtract(RawBioAssay) - Method in class net.sf.basedb.util.overview.loader.RawBioAssayLoader
Get the extract that is associated with the current raw bioassay
getExtractChain(DbControl, Node) - Method in class net.sf.basedb.util.overview.loader.DerivedBioAssayLoader
 
getExtractChain(DbControl, Node) - Method in class net.sf.basedb.util.overview.loader.RawBioAssayLoader
 
getExtractChain(Node) - Method in class net.sf.basedb.util.overview.loader.ExtractLoader
 
getExtracts() - Method in class net.sf.basedb.core.Sample
Get a query that returns all extracts created from this sample.
getExtracts(int) - Method in class net.sf.basedb.core.PhysicalBioAssay
Get a query that returns extracts connected to this bioassay.
getExtraField() - Method in interface net.sf.basedb.clients.web.extensions.login.LoginFormAction
An optional extra field on the login form.
getExtraField() - Method in class net.sf.basedb.clients.web.extensions.login.LoginFormBean
 
getExtraFilesDirectory(DbControl, String) - Method in class net.sf.basedb.plugins.executor.BaseFileImporterSupport
 
getExtraFilesDirectory(DbControl, String) - Method in class net.sf.basedb.plugins.executor.BfsImporterSupport
 
getExtraFilesDirectory(DbControl, String) - Method in class net.sf.basedb.plugins.executor.FileOnlyImporterSupport
 
getExtraFloat(String) - Method in class net.sf.basedb.util.importer.spotdata.BaseFileInfo
Get the extra value type that has the given external id.
getExtraFloatParsers() - Method in class net.sf.basedb.util.importer.spotdata.BaseFileInfo.SpotSectionInfo
Get the list of extra value parsers that exists for this section.
getExtraInformation() - Method in class net.sf.basedb.core.authentication.AuthenticatedUser
Get extra information about the user.
getExtraNo() - Method in class net.sf.basedb.core.data.DataCubeExtraValueData
The number of this extra value in the data cube.
getExtraNo() - Method in class net.sf.basedb.core.DataCubeExtraValue
Get the extra value number.
getExtraNo() - Method in class net.sf.basedb.core.ExtraValue
Get the number in the data cube of the extra values.
getExtraValue() - Method in class net.sf.basedb.core.ExtraValueExpression
 
getExtraValue() - Method in class net.sf.basedb.core.SpotExtraValueBatcher
Get the extra value item representing all extra values.
getExtraValue(ExtraValueType) - Method in class net.sf.basedb.core.BioAssaySet
Get the extra value of the specified type in this bioassayset.
getExtraValueField(String, ExtraValue.CoordinateType, String) - Method in class net.sf.basedb.util.export.spotdata.AbstractFieldConverter
Get an extra value dynamic field.
getExtraValueFields(DbControl, BioAssaySet) - Method in class net.sf.basedb.plugins.BaseFileExporterPlugin
 
getExtraValueFields(DbControl, BioAssaySet) - Method in class net.sf.basedb.plugins.BfsExporterPlugin
 
getExtraValueJoiner(JoinType) - Static method in class net.sf.basedb.core.DynamicPositionQueryJoiners
Get a joiner instance for extra values for the specified join type.
getExtraValueJoiner(JoinType) - Static method in class net.sf.basedb.core.DynamicSpotQueryJoiners
Get a joiner instance for extra values for the specified join type.
getExtraValues() - Method in class net.sf.basedb.core.BioAssaySet
Get a query returning the extra values that are part of this bioassayset.
getExtraValues() - Method in class net.sf.basedb.core.data.BioAssaySetData
The extra values calculated for this bioassayset.
getExtraValues() - Method in class net.sf.basedb.core.data.DataCubeData
This is the inverse end.
getExtraValues() - Method in class net.sf.basedb.core.data.ExtraValueTypeData
This is the inverse end.
getExtraValueType() - Method in class net.sf.basedb.core.data.ExtraValueData
Get the type of this extra value.
getExtraValueType() - Method in class net.sf.basedb.core.ExtraValue
Get the type of the extra values.
getExtraValueTypes() - Method in class net.sf.basedb.core.BioAssaySet
Get a query returning all extra values types that are used in this bioassay set.
getFactories() - Static method in class net.sf.basedb.util.uri.ConnectionManagerUtil
Get a list with all connection manager factories.
getFactory(String) - Static method in class net.sf.basedb.util.uri.ConnectionManagerUtil
Get the connection manager factory with the given extension id.
getFactoryParameters(Object) - Method in class net.sf.basedb.util.extensions.xml.XmlLoader
Get a XML-like string representation of the parameters that was used to initialise a factory.
getFailures() - Method in class net.sf.basedb.util.overview.GenericOverview
Get a list containing all validation failures.
getFailureSummary() - Method in interface net.sf.basedb.util.overview.extensions.ValidationRuleAction
Get a short summary that is displayed when the validation fails
getFailureSummary() - Method in class net.sf.basedb.util.overview.Validator
Get a short summary that is displayed when the validation fails
getFallbackLocale(String, Locale) - Method in class net.sf.basedb.util.resources.Utf8PropertiesResourceBundleControl
We don't need a fallback locale.
getFastLoader(DbControl) - Method in class net.sf.basedb.core.AnnotationType
Create a loader that can be used for fast loading of annotation values for multiple items.
getFastLoader(DbControl, Item, String, Item) - Static method in class net.sf.basedb.core.AnyToAny
Create an optimized implementation for loading the target item of a given named link from multiple source items.
getFavicon() - Method in class net.sf.basedb.clients.web.extensions.skin.FixedSkinActionFactory
 
getFavicon() - Method in class net.sf.basedb.clients.web.extensions.skin.FixedSkinActionFactory.MySkinAction
 
getFavicon() - Method in interface net.sf.basedb.clients.web.extensions.skin.SkinAction
Get the full path to a favicon for the BASE site.
getFavicon() - Method in class net.sf.basedb.clients.web.taglib.Page
 
getFax() - Method in class net.sf.basedb.core.authentication.ExtraUserInformation
The fax number to the user.
getFax() - Method in class net.sf.basedb.core.data.UserData
Get the fax number to the user, or null if unknown.
getFax() - Method in class net.sf.basedb.core.User
Get the fax number to the user, or null if unknown.
getFeature() - Method in class net.sf.basedb.core.data.RawData
The feature this raw data is connected with.
getFeature(RawDataBatcher.FeatureProxy) - Method in class net.sf.basedb.core.RawDataBatcher.FeatureInfo
 
getFeatureBatcher(FeatureIdentificationMethod, Job) - Method in class net.sf.basedb.core.ArrayDesign
Get a feature batcher which can be used to add regular features to the array design.
getFeatureById(int) - Method in class net.sf.basedb.core.ArrayDesign
Get a feature when you know the id.
getFeatureById(int, boolean) - Method in class net.sf.basedb.core.ArrayDesign
Get a feature when you know the id.
getFeatureCoordinate(FeatureData) - Static method in class net.sf.basedb.core.Feature
Get the coordinate of the feature.
getFeatureDiameter() - Method in class net.sf.basedb.core.ArrayDesignBlock
Get the expected diameter of spots on the slide.
getFeatureDiameter() - Method in class net.sf.basedb.core.data.ArrayDesignBlockData
The expected diameter of spots.
getFeatureIdentificationMethod() - Method in class net.sf.basedb.core.ArrayDesign
Get the method used to identify features on this array design.
getFeatureIdentificationMethod() - Method in class net.sf.basedb.core.data.ArrayDesignData
The method to use for identiying features. 1 = COORDINATES, 2 = POSITION, 3 = FEATURE_ID
getFeatures() - Method in class net.sf.basedb.core.ArrayDesign
Get a query that returns the regular features of this array design.
getFeatures() - Method in class net.sf.basedb.core.data.ArrayDesignBlockData
Used by Hibernate to link with features.
getFetchSize() - Method in class net.sf.basedb.core.hibernate.QueryWrapper
 
getField() - Method in class net.sf.basedb.plugins.BfsExporterPlugin.ExtendedExportableField
 
getFile() - Method in class net.sf.basedb.clients.web.extensions.fileviewer.FileViewerContext
Get the current file.
getFile() - Method in interface net.sf.basedb.core.data.FileAttachableData
Get the file that is attached to the item.
getFile() - Method in class net.sf.basedb.core.data.FileSetMemberData
Get the file.
getFile() - Method in class net.sf.basedb.core.data.ProtocolData
 
getFile() - Method in interface net.sf.basedb.core.FileAttachable
Get the file that is attached to the item.
getFile() - Method in class net.sf.basedb.core.FileSetMember
Get the file this item is representing in the file set.
getFile() - Method in class net.sf.basedb.core.plugin.ExportOutputStream
If the export stream is going to a BASE File object, use this method to access it.
getFile() - Method in class net.sf.basedb.core.Protocol
 
getFile() - Method in class net.sf.basedb.util.extensions.manager.ExtensionsFile
Get the underlying file on the file system.
getFile() - Method in class net.sf.basedb.util.FileExportOutputStream
 
getFile(int) - Method in class net.sf.basedb.util.bfs.MetadataModel
Get the file entry with a given index.
getFile(String) - Method in class net.sf.basedb.clients.web.extensions.ExtensionsControl
Get information about an installed extensions file.
getFile(String) - Method in class net.sf.basedb.clients.web.fileupload.FileUpload
Get the file information for an uplodaded file.
getFile(String) - Method in class net.sf.basedb.util.bfs.BaseInputStreamLocator
 
getFile(String) - Method in class net.sf.basedb.util.bfs.MetadataModel
Get the file entry for a given key.
getFile(DbControl, Directory, String, boolean) - Static method in class net.sf.basedb.core.File
Get a File item when you know the directory and filename.
getFileByObjectKey(ObjectKey<?>) - Method in class net.sf.basedb.clients.web.extensions.ExtensionsControl
Find out which file the given object is defined in.
getFileByObjectKey(ObjectKey<?>) - Method in class net.sf.basedb.util.extensions.manager.ExtensionsManager
Find out which file the object with the given key was defined.
getFileByURI(String) - Method in class net.sf.basedb.util.extensions.manager.ExtensionsManager
Get the extension file that is located at the given URI.
getFileContext() - Method in class net.sf.basedb.clients.web.extensions.fileviewer.FileViewerUtil
Get the file context.
getFileCount() - Method in class net.sf.basedb.util.bfs.MetadataModel
Get the number of entries in the 'files' section.
getFileExtension() - Method in class net.sf.basedb.util.zip.Bzip2FilePacker
 
getFileExtension() - Method in interface net.sf.basedb.util.zip.FilePacker
Gets the extension that files, packed with this tool, should have, for example, zip or tar.gz Don't include the first dot!
getFileExtension() - Method in class net.sf.basedb.util.zip.GzipFilePacker
 
getFileExtension() - Method in class net.sf.basedb.util.zip.TarFilePacker
 
getFileExtension() - Method in class net.sf.basedb.util.zip.ZipFilePacker
 
getFileFormatParameter() - Static method in class net.sf.basedb.plugins.BaseFileExporterPlugin
Create a plug-in parameter that asks for the BASEFile subtype to use in the export.
getFileFormatParameter() - Static method in class net.sf.basedb.plugins.BfsExporterPlugin
Create a plug-in parameter that asks for the BFS subtype to use in the export.
getFileId() - Method in class net.sf.basedb.util.importer.spotdata.BaseFileInfo.ChildBioAssay
Get the id of the child bioassay as it appears in the BASEfile.
getFileIterator() - Method in class net.sf.basedb.plugins.AbstractFlatFileImporter
Get an iterator that returns the files to be imported.
getFileIterator() - Method in class net.sf.basedb.plugins.RawDataFlatFileImporter
 
getFileLinks(String, File, String) - Static method in class net.sf.basedb.clients.web.Base
Get view/download links for a file.
getFilename() - Method in class net.sf.basedb.clients.web.fileupload.UploadedFile
Get the original filename of the uploaded file.
getFilename() - Method in class net.sf.basedb.core.Path
Get the filename part of the path.
getFilename() - Method in class net.sf.basedb.core.plugin.ImportInputStream
Get the name of the source.
getFilename() - Method in class net.sf.basedb.util.bfs.AnnotationParser
Get the file name that this parser is reading from.
getFilename() - Method in class net.sf.basedb.util.bfs.AnnotationWriter
Get the file name that this writer is printing to.
getFilename() - Method in interface net.sf.basedb.util.bfs.BfsParser
Get the filename of the file that is being parsed.
getFilename() - Method in class net.sf.basedb.util.bfs.DataParser
Get the file name that this parser is reading from.
getFilename() - Method in class net.sf.basedb.util.bfs.DataWriter
Get the file name that this writer is printing to.
getFilename() - Method in class net.sf.basedb.util.bfs.MetadataParser
Get the file name that this writer is printing to.
getFilename() - Method in class net.sf.basedb.util.bfs.MetadataWriter
Get the file name that this writer is printing to.
getFilename() - Method in class net.sf.basedb.util.FileImportInputStream
getFilename() - Method in class net.sf.basedb.util.importer.spotdata.SynchronizedSpotDataParser
 
getFileNameGeneratorParameter() - Static method in class net.sf.basedb.plugins.BfsExporterPlugin
Create a plug-in parameter that asks for the file name generation strategy.
getFileOnlyRawDataTypes() - Static method in class net.sf.basedb.core.RawDataTypes
Get the raw data types that are representations of file-only Platform:s.
getFiles() - Method in class net.sf.basedb.clients.web.extensions.ExtensionsControl
Get an list returning all XML/JAR files which contains installed extensions.
getFiles() - Method in class net.sf.basedb.core.data.DirectoryData
This is the inverse end.
getFiles() - Method in class net.sf.basedb.core.data.FileServerData
This is the inverse end.
getFiles() - Method in class net.sf.basedb.core.Directory
Get a query that return all files in this directory.
getFiles() - Method in class net.sf.basedb.core.FileServer
Get a query returning all files that has been registered with this server.
getFiles() - Method in class net.sf.basedb.util.extensions.manager.ExtensionsManager
Get a list of all extension files managed by this manager.
getFileServer() - Method in class net.sf.basedb.core.data.FileData
Get the associated FileServerData item.
getFileServer() - Method in class net.sf.basedb.core.File
Get the file server on which the external file is located.
getFileSet() - Method in class net.sf.basedb.core.ArrayDesign
 
getFileSet() - Method in class net.sf.basedb.core.BioAssaySet
 
getFileSet() - Method in class net.sf.basedb.core.data.ArrayDesignData
 
getFileSet() - Method in class net.sf.basedb.core.data.BioAssaySetData
 
getFileSet() - Method in class net.sf.basedb.core.data.DerivedBioAssayData
 
getFileSet() - Method in class net.sf.basedb.core.data.ExtraValueData
 
getFileSet() - Method in class net.sf.basedb.core.data.FileSetMemberData
Get the file set this file belongs to.
getFileSet() - Method in interface net.sf.basedb.core.data.FileStoreEnabledData
Get the file set attached to this item.
getFileSet() - Method in class net.sf.basedb.core.data.RawBioAssayData
 
getFileSet() - Method in class net.sf.basedb.core.DerivedBioAssay
 
getFileSet() - Method in class net.sf.basedb.core.ExtraValue
 
getFileSet() - Method in class net.sf.basedb.core.FileSetMember
Get the file set the file is a member of.
getFileSet() - Method in interface net.sf.basedb.core.FileStoreEnabled
Get the file set that collects all files that holds data for this item.
getFileSet() - Method in class net.sf.basedb.core.RawBioAssay
 
getFileSetMember() - Method in class net.sf.basedb.util.overview.Fix
 
getFileSetMembers() - Method in class net.sf.basedb.core.data.DataFileTypeData
This is the inverse end.
getFileSize() - Method in class net.sf.basedb.util.bfs.AnnotationParser
Get the size in bytes of the file that this parser is reading from.
getFileSize() - Method in interface net.sf.basedb.util.bfs.BfsParser
Get the size of the file that is being parsed.
getFileSize() - Method in class net.sf.basedb.util.bfs.DataParser
Get the size in bytes of the file that this parser is reading from.
getFileSize() - Method in class net.sf.basedb.util.bfs.MetadataParser
Get the size in bytes of the file that this parser is reading from.
getFileSize() - Method in class net.sf.basedb.util.importer.spotdata.SynchronizedSpotDataParser
 
getFileStoreEnabledItems() - Static method in class net.sf.basedb.core.Metadata
Get a set containing all FileStoreEnabled item types.
getFileType() - Method in class net.sf.basedb.clients.web.extensions.fileviewer.FileViewerContext
Get the current data file type.
getFileType() - Method in class net.sf.basedb.core.data.MimeTypeData
Get the associated ItemSubtypeData item.
getFileType() - Method in class net.sf.basedb.core.MimeType
Get the associated file subtype item.
getFileType(DataFileType, PlatformVariant, boolean) - Method in class net.sf.basedb.core.Platform
Get information about a file type that has been registered with this platform/variant.
getFileTypes() - Method in class net.sf.basedb.core.data.ItemSubtypeData
The file types that can be used on items of this subtype.
getFileTypes() - Method in class net.sf.basedb.core.data.PlatformData
The file types that can be used on this platform.
getFileTypes() - Method in class net.sf.basedb.core.data.PlatformVariantData
The additional file types that can be used on this platform variant.
getFileTypes(boolean) - Method in class net.sf.basedb.core.PlatformVariant
Get a query returning file types registered with this platform variant.
getFileTypes(PlatformVariant, boolean) - Method in class net.sf.basedb.core.Platform
Get the file types registered with this platform.
getFileValues(String) - Method in class net.sf.basedb.clients.web.fileupload.FileUpload
Get the file information for uplodaded files.
getFilltext() - Method in class net.sf.basedb.clients.web.taglib.menu.Menu
 
getFilterable() - Method in class net.sf.basedb.clients.web.taglib.table.TableColumn
 
getFilterAnnotationType(DbControl) - Method in class net.sf.basedb.clients.web.extensions.list.RelatedItemColumn.Specification
 
getFilterBatcher() - Method in class net.sf.basedb.core.BioAssaySet
Get a batcher used to insert the position/column coordinates that remain after some filter has been applied to the spot data of a bioassayset.
getFilterclass() - Method in class net.sf.basedb.clients.web.taglib.table.ColumnDef
 
getFilterClass() - Method in class net.sf.basedb.clients.web.extensions.list.AbstractListColumnBean
 
getFilterClass() - Method in interface net.sf.basedb.clients.web.extensions.list.ListColumnAction
Extra CSS class to add to the filter table cell.
getFilterGroup() - Method in class net.sf.basedb.core.data.ItemListSyncFilterData
Get the group for this filter.
getFilterGroup() - Method in class net.sf.basedb.core.SyncFilter
Get the group this synchronization filter belongs to.
getFilterItemList(DbControl) - Method in class net.sf.basedb.clients.web.extensions.list.RelatedItemColumn.Specification
 
getFilterNo() - Method in class net.sf.basedb.core.data.DataCubeFilterData
The number of this filter in the data cube.
getFilterNo() - Method in class net.sf.basedb.core.DataCubeFilter
Get the number of this filter.
getFilterproperty() - Method in class net.sf.basedb.clients.web.taglib.table.ColumnDef
 
getFilterProperty() - Method in class net.sf.basedb.clients.web.extensions.list.AbstractListColumnBean
 
getFilterProperty() - Method in interface net.sf.basedb.clients.web.extensions.list.ListColumnAction
Override the default property when this column is used for filtering.
getFilterRestriction(String, int, DbControl, EntityQuery) - Method in class net.sf.basedb.core.ItemContext
Create a restriction from a property filter on the given filter row.
getFilterRestriction(String, DbControl, EntityQuery) - Method in class net.sf.basedb.core.ItemContext
Create a restriction from a property filter on filter row 0.
getFilterrows() - Method in class net.sf.basedb.clients.web.taglib.table.Table
 
getFilterRows() - Method in class net.sf.basedb.core.ItemContext
Get the number of filter rows to display on the list page.
getFilterRows() - Method in class net.sf.basedb.core.SyncFilter
Get the number of filter rows in this filter.
getFilters() - Method in class net.sf.basedb.core.data.DataCubeData
This is the inverse end.
getFiltertext() - Method in class net.sf.basedb.clients.web.taglib.table.ColumnDef
 
getFilterText() - Method in class net.sf.basedb.clients.web.extensions.list.AbstractListColumnBean
 
getFilterText() - Method in interface net.sf.basedb.clients.web.extensions.list.ListColumnAction
A text to display in the filter cell when the column is not filterable.
getFingerprintType() - Method in class net.sf.basedb.core.data.FileServerData
Get the type of SSH fingerprint.
getFingerprintType() - Method in class net.sf.basedb.core.FileServer
Get the type of the SSH fingerprint.
getFirst(ExtensionsInvoker<ConnectionManagerFactory>) - Static method in class net.sf.basedb.util.uri.ConnectionManagerUtil
Get the first factory returned by the invoker.
getFirstAssayFieldIndex() - Method in class net.sf.basedb.util.importer.spotdata.BaseFileInfo.SpotSectionInfo
The index of the first data column that contains assay data.
getFirstColumn() - Method in class net.sf.basedb.util.excel.XlsxToCsvUtil.SheetInfo
Get the column number for the first column that contains data.
getFirstMatching(DbControl, ItemQuery<T>, String, PropertyFilter) - Static method in class net.sf.basedb.clients.web.Base
 
getFirstNode(Filter<? super Node>) - Method in class net.sf.basedb.util.overview.Node
Find the first node (including this) that matches a filter.
getFirstNull(Object[]) - Static method in class net.sf.basedb.core.query.Expressions
Test if there is null in the array.
getFirstNull(Object[]) - Static method in class net.sf.basedb.core.query.Restrictions
Test if there is null in the array.
getFirstParent(Filter<? super Node>) - Method in class net.sf.basedb.util.overview.Node
Find the first parent node that matches a filter.
getFirstResult() - Method in class net.sf.basedb.core.AbstractQuery
 
getFirstResult() - Method in class net.sf.basedb.core.hibernate.QueryWrapper
 
getFirstResult() - Method in interface net.sf.basedb.core.query.Query
The number of the row the query should start returning.
getFirstRow() - Method in class net.sf.basedb.util.excel.XlsxToCsvUtil.SheetInfo
Get the row number for the first row that contains data.
getFixes() - Method in class net.sf.basedb.util.overview.Failure
Get a list of suggested fixes.
getFkColumns() - Method in class net.sf.basedb.core.dbengine.TableInfo.ForeignKeyInfo
 
getFloat(int) - Method in class net.sf.basedb.clients.web.servlet.PlotServlet.CFSqlResult
 
getFloat(int) - Method in class net.sf.basedb.core.DynamicResultIterator.SqlResultImpl
 
getFloat(int) - Method in interface net.sf.basedb.core.query.SqlResult
Get the value of the specified column as a float.
getFloat(int) - Method in class net.sf.basedb.util.parser.FlatFileParser.Data
Shortcut for getFloat(index, null, true)
getFloat(int, NumberFormat, boolean) - Method in class net.sf.basedb.util.parser.FlatFileParser.Data
Get the value as a float.
getFloat(int, NumberFormat, boolean) - Method in class net.sf.basedb.util.parser.FlatFileParser.ExcelData
 
getFloat(String) - Static method in class net.sf.basedb.util.Values
Convert a string to an float.
getFloat(String[]) - Static method in class net.sf.basedb.util.Values
Convert an array of strings to an array of Float:s.
getFloat(String, float) - Static method in class net.sf.basedb.util.Values
Convert a string to an integer.
getFloat(String, Float) - Static method in class net.sf.basedb.util.Values
 
getFloat(FlatFileParser.Data) - Method in class net.sf.basedb.util.parser.ColumnMapper
 
getFloat(FlatFileParser.Data) - Method in class net.sf.basedb.util.parser.CompoundMapper
 
getFloat(FlatFileParser.Data) - Method in class net.sf.basedb.util.parser.ConstantMapper
 
getFloat(FlatFileParser.Data) - Method in class net.sf.basedb.util.parser.CropStringMapper
 
getFloat(FlatFileParser.Data) - Method in class net.sf.basedb.util.parser.JepMapper
 
getFloat(FlatFileParser.Data) - Method in interface net.sf.basedb.util.parser.Mapper
Get the value for the line of data as a float.
getFloat(FlatFileParser.Data) - Method in class net.sf.basedb.util.parser.NullIfExceptionMapper
 
getFloatOption(String, Float) - Method in class net.sf.basedb.core.AnnotationType
Get an option and convert the value to a float.
getFloatValues() - Method in class net.sf.basedb.core.data.annotations.AnnotationLink
 
getFlushMode() - Method in class net.sf.basedb.core.hibernate.QueryWrapper
Deprecated.
getFlushMode() - Method in class net.sf.basedb.core.hibernate.SessionWrapper
 
getForeignKeys() - Method in class net.sf.basedb.core.dbengine.TableInfo
Get information about the foreign keys in the table.
getForInsert(Object, Map, SharedSessionContractImplementor) - Method in class net.sf.basedb.core.ExtendedPropertyAccessor.GetterSetter
Get the value of the extended property.
getFormat() - Method in class net.sf.basedb.util.excel.ExcelValue
Get the format string.
getFormatName() - Method in class net.sf.basedb.plugins.Bzip2FileUnpacker
 
getFormatName() - Method in class net.sf.basedb.plugins.GzipFileUnpacker
 
getFormatName() - Method in class net.sf.basedb.plugins.TarFileUnpacker
 
getFormatName() - Method in class net.sf.basedb.plugins.ZipFileUnpacker
 
getFormatName() - Method in interface net.sf.basedb.util.zip.FileUnpacker
Get the name of the compressed file format this unpacker supports.
getFormatParameter() - Method in class net.sf.basedb.clients.web.plugins.SimpleExport
 
getFormats(String) - Method in class net.sf.basedb.util.resources.Utf8PropertiesResourceBundleControl
This control only handle property files.
getFormattedAndSortedFilters(Collection<PropertyFilter>, Formatter<PropertyFilter>) - Static method in class net.sf.basedb.core.SyncFilter
Utility method for formatting and sorting a list of property filters.
getFormatter() - Method in class net.sf.basedb.clients.web.extensions.list.AbstractListColumnBean
 
getFormatter() - Method in interface net.sf.basedb.clients.web.extensions.list.ListColumnAction
Get a formatter that converts the current value to a string that is displayed in the column.
getFormatter() - Method in class net.sf.basedb.clients.web.taglib.table.Cell
 
getFormatter() - Method in class net.sf.basedb.clients.web.taglib.table.ColumnDef
 
getFormatter() - Method in class net.sf.basedb.clients.web.taglib.table.TableColumn
 
getFormatter() - Method in class net.sf.basedb.plugins.BaseFileExporterPlugin.ExtendedDynamicField
 
getFormatter() - Method in class net.sf.basedb.util.export.spotdata.AnnotationAssayField
 
getFormatter() - Method in class net.sf.basedb.util.export.spotdata.AssayPropertyField
 
getFormatter() - Method in interface net.sf.basedb.util.export.spotdata.ExportableField
Get a formatter that converts the values in this field to strings.
getFormatter() - Method in class net.sf.basedb.util.export.spotdata.JepDynamicField
 
getFormatter() - Method in class net.sf.basedb.util.export.spotdata.SimpleDynamicField
 
getFormatter(Object) - Method in class net.sf.basedb.util.formatter.MultiFormatter
 
getFormatter(String) - Method in class net.sf.basedb.clients.web.taglib.table.Table
 
getFormatter(InvokationContext, String) - Method in class net.sf.basedb.clients.web.extensions.list.PropertyPathActionFactory
Create a formatter instance that should be used for the online table.
getFormatter(Formatter<T>) - Method in class net.sf.basedb.core.Unit
Create a formatter for formatting values with this unit.
getFormName() - Method in class net.sf.basedb.clients.web.fileupload.UploadedFile
Get the name of the form field that this file was selected in.
getFormula(int) - Method in class net.sf.basedb.core.Formula
Get an expression.
getFormulaField(String, String) - Method in class net.sf.basedb.util.export.spotdata.AbstractFieldConverter
Get a formula dynamic field.
getFormulaFields(DbControl, BioAssaySet) - Method in class net.sf.basedb.plugins.BaseFileExporterPlugin
 
getFormulaFields(DbControl, BioAssaySet) - Method in class net.sf.basedb.plugins.BfsExporterPlugin
 
getFormulaFormatter(SessionControl, Formula) - Static method in class net.sf.basedb.clients.web.formatter.FormatterFactory
Get a formatter that knows how to format results from formulas.
getFormulas() - Method in class net.sf.basedb.core.data.FormulaData
Get the list of formulas.
getFormulas() - Method in class net.sf.basedb.core.Formula
Get all expressions as an unmodifiable list.
getFormulaType() - Method in class net.sf.basedb.core.Formula
Get the type of formula.
getFreeWells() - Method in class net.sf.basedb.core.BioPlate
Get the number of free wells on this plate.
getFreeWells() - Method in class net.sf.basedb.core.data.BioPlateData
Get the number of wells that are free on the bioplate.
getFreezer() - Method in class net.sf.basedb.core.BioPlate
Gets the storage location of this bio plate
getFreezer() - Method in class net.sf.basedb.core.data.BioPlateData
Get the hardware, ie. freezer where the plate is kept.
getFriends() - Method in class net.sf.basedb.core.SessionControl
Get the id of all friends to logged in user.
getFrom() - Method in class net.sf.basedb.core.AnyToAny
Get the item this link is linking from.
getFrom() - Method in class net.sf.basedb.core.data.MessageData
The name of the user this message is from.
getFrom() - Method in class net.sf.basedb.core.Message
Get the name of the sender of this message.
getFromId() - Method in class net.sf.basedb.core.AnyToAny
Get the ID of the item this link is linking from.
getFromId() - Method in class net.sf.basedb.core.data.AnyToAnyData
The ID of the item we are linking from.
getFromId() - Method in class net.sf.basedb.core.data.MessageData
The id of the user if this message was from a real user.
getFromType() - Method in class net.sf.basedb.core.AnyToAny.FastLinkLoader
The source item type.
getFromType() - Method in class net.sf.basedb.core.AnyToAny
Get the type of the item this link is linking from.
getFromType() - Method in class net.sf.basedb.core.data.AnyToAnyData
The type code of the item we are linking from.
getFullClass(String...) - Method in class net.sf.basedb.clients.web.taglib.CalendarButton
Make sure that "auto-init" is added to the class attribute.
getFullClass(String...) - Method in class net.sf.basedb.clients.web.taglib.StylableTag
Get the full class (eg. main and subclass) as a single string.
getFullPermissionNames(Set<Permission>, String) - Static method in class net.sf.basedb.clients.web.PermissionUtil
Create a comma-separated string with "readable" permission names.
getFullPermissionNames(Identifiable) - Static method in class net.sf.basedb.clients.web.PermissionUtil
 
getFullQuotedTableName(DbEngine) - Method in class net.sf.basedb.core.dbengine.TableInfo
Get the fully quialified and quoted table name using the quoting rules from the given DBEngine
getFunctionName() - Method in class net.sf.basedb.util.jep.ChannelFunction
 
getFunctionName() - Method in class net.sf.basedb.util.jep.ExtraValueFunction
 
getFunctionName() - Method in class net.sf.basedb.util.jep.InReporterListFunction
 
getFunctionName() - Method in interface net.sf.basedb.util.jep.JepFunction
Get the name of this function.
getFunctionName() - Method in class net.sf.basedb.util.jep.LeftFunction
 
getFunctionName() - Method in class net.sf.basedb.util.jep.Log2Function
 
getFunctionName() - Method in class net.sf.basedb.util.jep.MeanFunction
 
getFunctionName() - Method in class net.sf.basedb.util.jep.NotInReporterListFunction
 
getFunctionName() - Method in class net.sf.basedb.util.jep.PositionFunction
 
getFunctionName() - Method in class net.sf.basedb.util.jep.RawChannelFunction
 
getFunctionName() - Method in class net.sf.basedb.util.jep.RawFunction
 
getFunctionName() - Method in class net.sf.basedb.util.jep.ReporterFunction
 
getFunctionName() - Method in class net.sf.basedb.util.jep.ScoreFunction
 
getFunctionName() - Method in class net.sf.basedb.util.jep.SimpleJepFunction
 
getFunctionName() - Method in class net.sf.basedb.util.parser.ColFunction
 
getFunctionName() - Method in class net.sf.basedb.util.parser.DataNoFunction
 
getFunctionName() - Method in class net.sf.basedb.util.parser.DefaultItemFunction
 
getFunctionName() - Method in class net.sf.basedb.util.parser.LineNoFunction
 
getFunctions() - Static method in class net.sf.basedb.util.jep.Jep
Get a list of built-in functions supported by the Jep.jepToExpression(JEP) converter.
getFutureResult(Callable<T>, QueryExecutor.Cancelable, SessionControl) - Static method in class net.sf.basedb.core.QueryExecutor
Run the callable and wait for the result.
getGenericDataFiles(DbControl, FileStoreEnabled, String) - Static method in class net.sf.basedb.core.FileStoreUtil
Get all files with a specific generic ItemSubtype in a given item's file set.
getGenericMembers(DbControl, FileStoreEnabled, String) - Static method in class net.sf.basedb.core.FileStoreUtil
Get all file members with a specific generic ItemSubtype in a given item's file set.
getGenericPlatformFileTypes(DbControl, FileStoreEnabled, String) - Static method in class net.sf.basedb.core.FileStoreUtil
Get a list of all platform file types that has the specified generic ItemSubtype.
getGenericType() - Method in class net.sf.basedb.core.data.DataFileTypeData
Get the generic file type of files with this member type.
getGenericType() - Method in class net.sf.basedb.core.DataFileType
Get the generic file type for this data file type.
getGetter() - Method in class net.sf.basedb.core.ExtendedPropertyAccessor.GetterSetter
 
getGlobalSignalId() - Method in class net.sf.basedb.core.signal.AbstractSignalTransporter
Get the raw ID string that was passed to the AbstractSignalTransporter.init(String) method.
getGlobalSignalId(SignalHandler) - Method in class net.sf.basedb.core.signal.AbstractSignalReceiver
Generate a signal ID string.
getGlobalSignalId(SignalHandler) - Method in class net.sf.basedb.core.signal.SocketSignalReceiver
Override ID generation so we can add proxy information if needed.
getGranted() - Method in class net.sf.basedb.core.data.keyring.PluginKeys
Get the granted permissions.
getGranted() - Method in class net.sf.basedb.core.data.PluginPermission
The permissions for the plugin
getGranted(RoleKey) - Method in class net.sf.basedb.core.PluginDefinition
Get the permissions that have been granted to this plugin.
getGroup() - Method in class net.sf.basedb.core.data.DiskUsageData
Get the GroupData that owns the DiskConsumable item.
getGroup() - Method in class net.sf.basedb.core.DiskUsage
Get the group that owns the DiskConsumable item or null if ther is none.
getGroupId() - Method in class net.sf.basedb.core.data.keyring.GroupKeys
Get the id of the group.
getGroupId() - Method in class net.sf.basedb.core.data.keyring.GroupProjects
Get the id of the group.
getGroupId() - Method in class net.sf.basedb.core.data.keyring.UserGroups
Get the id of the group.
getGroupIds(Permission) - Method in class net.sf.basedb.core.ItemKey
Get the ID:s of all groups that have the specified permission in this item key.
getGroupPermissions() - Method in class net.sf.basedb.core.GroupPermissions
Get the internal representation of the permissions.
getGroups() - Method in class net.sf.basedb.core.data.ItemKeyData
Get the map that manages which groups that have permissions for this key.
getGroups() - Method in class net.sf.basedb.core.data.ProjectData
Get the map that manages which users are members of this project and their permissions.
getGroups() - Method in class net.sf.basedb.core.data.UserData
This is the inverse end.
getGroups() - Method in class net.sf.basedb.core.Group
Get a query that returns the groups that are members of this group.
getGroups() - Method in class net.sf.basedb.core.InternalJobQueue.JobQueueKeyring
Return empty set.
getGroups() - Method in class net.sf.basedb.core.Job.SignalKeyring
Return empty set.
getGroups() - Method in class net.sf.basedb.core.MultiPermissions
Get a query that returns all groups appearing in at least one of the item keys.
getGroups() - Method in class net.sf.basedb.core.Project
Get a query that returns the groups that are members of this project.
getGroups() - Method in class net.sf.basedb.core.ServiceSessionControl.ServicesKeyring
Return empty set.
getGroups() - Method in class net.sf.basedb.core.SessionControl
Get the id of all groups where the logged in user is a member, directly or indirectly.
getGroups() - Method in class net.sf.basedb.core.User
Get a query that returns the groups where this user is a member.
getGroups(boolean) - Method in class net.sf.basedb.core.Keyring
 
getGroupsRecursive(DbControl, Set<Integer>) - Static method in class net.sf.basedb.core.Group
Load all groups withing groups.
getGroupsRecursive(Session, Collection<Integer>) - Static method in class net.sf.basedb.core.Group
 
getGuiContext() - Method in class net.sf.basedb.clients.web.extensions.JspContext
Get the current GuiContext.
getGuiContext() - Method in class net.sf.basedb.core.PluginConfigurationRequest
Get the context of the client application when this configuration request was created.
getGuiContexts() - Method in class net.sf.basedb.clients.web.plugins.SimpleExport
 
getGuiContexts() - Method in class net.sf.basedb.core.data.PluginDefinitionData
The item code for all items where it makes sense to use the plugin in a client application.
getGuiContexts() - Method in class net.sf.basedb.core.plugin.AbstractAnalysisPlugin
 
getGuiContexts() - Method in interface net.sf.basedb.core.plugin.InteractivePlugin
Get a set containing all items that the plugin handles.
getGuiContexts() - Method in class net.sf.basedb.core.PluginDefinition
Get the Item types where it makes sense to use this plugin for a client application.
getGuiContexts() - Method in class net.sf.basedb.plugins.AnnotationFlatFileImporter
This plug-in works in list context of all Annotatable items, except bioassay sets, bioassays and wells because they are not standalone items.
getGuiContexts() - Method in class net.sf.basedb.plugins.BaseFileExporterPlugin
 
getGuiContexts() - Method in class net.sf.basedb.plugins.batchimport.AnnotationTypeImporter
 
getGuiContexts() - Method in class net.sf.basedb.plugins.batchimport.AnyToAnyImporter
This plug-in works in list context of all Nameable items, except bioassay sets, bioassays and wells because they are not standalone items.
getGuiContexts() - Method in class net.sf.basedb.plugins.batchimport.ArrayBatchImporter
 
getGuiContexts() - Method in class net.sf.basedb.plugins.batchimport.ArrayDesignImporter
 
getGuiContexts() - Method in class net.sf.basedb.plugins.batchimport.ArraySlideImporter
 
getGuiContexts() - Method in class net.sf.basedb.plugins.batchimport.BioPlateImporter
 
getGuiContexts() - Method in class net.sf.basedb.plugins.batchimport.BioSourceImporter
 
getGuiContexts() - Method in class net.sf.basedb.plugins.batchimport.DerivedBioAssayImporter
 
getGuiContexts() - Method in class net.sf.basedb.plugins.batchimport.ExtractImporter
 
getGuiContexts() - Method in class net.sf.basedb.plugins.batchimport.FileImporter
 
getGuiContexts() - Method in class net.sf.basedb.plugins.batchimport.KitImporter
 
getGuiContexts() - Method in class net.sf.basedb.plugins.batchimport.PhysicalBioAssayImporter
 
getGuiContexts() - Method in class net.sf.basedb.plugins.batchimport.RawBioAssayImporter
 
getGuiContexts() - Method in class net.sf.basedb.plugins.batchimport.SampleImporter
 
getGuiContexts() - Method in class net.sf.basedb.plugins.batchimport.TagImporter
 
getGuiContexts() - Method in class net.sf.basedb.plugins.BfsExporterPlugin
 
getGuiContexts() - Method in class net.sf.basedb.plugins.CdfFileReporterImporter
 
getGuiContexts() - Method in class net.sf.basedb.plugins.executor.AbstractIOSupport
 
getGuiContexts() - Method in class net.sf.basedb.plugins.FormulaFilter
 
getGuiContexts() - Method in class net.sf.basedb.plugins.GalExporter
 
getGuiContexts() - Method in class net.sf.basedb.plugins.HelpExporter
 
getGuiContexts() - Method in class net.sf.basedb.plugins.HelpImporter
 
getGuiContexts() - Method in class net.sf.basedb.plugins.IlluminaRawDataImporter
 
getGuiContexts() - Method in class net.sf.basedb.plugins.IntensityCalculatorPlugin
 
getGuiContexts() - Method in class net.sf.basedb.plugins.JepExtraValueCalculator
 
getGuiContexts() - Method in class net.sf.basedb.plugins.JepIntensityTransformer
 
getGuiContexts() - Method in class net.sf.basedb.plugins.ManualDerivedBioAssayCreator
 
getGuiContexts() - Method in class net.sf.basedb.plugins.PackedFileExporter
 
getGuiContexts() - Method in class net.sf.basedb.plugins.PlateFlatFileImporter
 
getGuiContexts() - Method in class net.sf.basedb.plugins.PlateMappingExporter
Return a set containing the context:s [PLATEMAPPING, ITEM].
getGuiContexts() - Method in class net.sf.basedb.plugins.PlateMappingImporter
Return a set containing the context:s [PLATEMAPPING, LIST].
getGuiContexts() - Method in class net.sf.basedb.plugins.PluginConfigurationExporter
 
getGuiContexts() - Method in class net.sf.basedb.plugins.PluginConfigurationImporter
 
getGuiContexts() - Method in class net.sf.basedb.plugins.PrintMapFlatFileImporter
 
getGuiContexts() - Method in class net.sf.basedb.plugins.RawDataFlatFileImporter
 
getGuiContexts() - Method in class net.sf.basedb.plugins.ReporterFlatFileImporter
Return a set containing the context:s [REPORTER, LIST], [REPORTERLIST, ITEM], [REPORTERSCORE, LIST].
getGuiContexts() - Method in class net.sf.basedb.plugins.ReporterMapFlatFileImporter
Return a set containing the element [ARRAYDESIGN, ITEM].
getGuiContexts() - Method in class net.sf.basedb.util.zip.AbstractFileUnpacker
 
getGuiTitle() - Method in class net.sf.basedb.plugins.BaseFileExporterPlugin.ExtendedDynamicField
 
getGuiTitle() - Method in class net.sf.basedb.plugins.BfsExporterPlugin.ExtendedExportableField
 
getHandlerId() - Method in class net.sf.basedb.core.signal.AbstractSignalTransporter
Get the local handler ID part of the signal URI.
getHardware() - Method in class net.sf.basedb.core.BioMaterialEvent
Get the Hardware that was used in this event.
getHardware() - Method in class net.sf.basedb.core.BioPlateEvent
Get the Hardware that was used in this event.
getHardware() - Method in class net.sf.basedb.core.data.BioMaterialEventData
Get the hardware used in this event
getHardware() - Method in class net.sf.basedb.core.data.BioPlateEventData
Get the hardware used in this event
getHardware() - Method in class net.sf.basedb.core.data.DerivedBioAssayData
Get the hardware used to create this bioassay set.
getHardware() - Method in class net.sf.basedb.core.data.PlateEventData
Get the hardware used in this event.
getHardware() - Method in class net.sf.basedb.core.DerivedBioAssay
Get the Hardware that was used when creating this bioassay set.
getHardware() - Method in class net.sf.basedb.core.PlateEvent
Get the Hardware that was used in this event.
getHasData() - Method in class net.sf.basedb.core.data.RawBioAssayData
If the raw bioassay has data or not.
getHasFeatures() - Method in class net.sf.basedb.core.data.ArrayDesignData
If the array design has features or not.
getHashString(String) - Static method in class net.sf.basedb.util.MD5
Calculates the MD5 hash of an UTF-8 encoded string.
getHashString(MessageDigest) - Static method in class net.sf.basedb.util.MD5
 
getHeader(int) - Method in class net.sf.basedb.util.bfs.AnnotationModel
Get the column header for a given column index.
getHeader(String) - Method in class net.sf.basedb.core.RawBioAssay
Get the value for the raw data header with the specified name.
getHeader(String) - Method in class net.sf.basedb.util.parser.FlatFileParser
Get the value of the header with the specified name.
getHeaderAttribute(String, Pattern) - Method in class net.sf.basedb.clients.web.fileupload.FileUpload
 
getHeaderNames() - Method in class net.sf.basedb.core.RawBioAssay
Get the names of all raw data headers.
getHeaderNames() - Method in class net.sf.basedb.util.parser.FlatFileParser
Get the names of all headers found by the FlatFileParser.parseHeaders() method.
getHeaders() - Method in class net.sf.basedb.core.data.RawBioAssayData
File headers from the raw data file.
getHeaders() - Method in class net.sf.basedb.util.bfs.AnnotationModel
Get all column headers.
getHeight() - Method in interface net.sf.basedb.clients.web.extensions.plot.PlotGenerator
Get the height of the generated image.
getHeight() - Method in class net.sf.basedb.clients.web.extensions.plot.PlotGeneratorBean
 
getHeight() - Method in class net.sf.basedb.core.AnnotationType
Get the recommended height in characters a client application should use to render an input field for annotations of this annotation type.
getHeight() - Method in class net.sf.basedb.core.data.AnnotationTypeData
The recommended height (lines) to display input fields for this annotation in client applications.
getHeight() - Method in class net.sf.basedb.core.ParameterType
Get the height of the input field for the parameter in the GUI.
getHelp() - Method in interface net.sf.basedb.clients.web.extensions.login.LoginFormAction
Optional help text that is displayed on the login form to aid the user when logging in.
getHelp() - Method in class net.sf.basedb.clients.web.extensions.login.LoginFormBean
 
getHelp() - Method in class net.sf.basedb.clients.web.extensions.login.PasswordLoginFormFactory
 
getHelp() - Method in class net.sf.basedb.core.Client
Get a query that will return all help texts for this client.
getHelpByExternalId(DbControl, String, boolean) - Method in class net.sf.basedb.core.Client
Get a Help item when you know the external ID.
getHelpid() - Method in class net.sf.basedb.clients.web.taglib.Help
 
getHelpid() - Method in class net.sf.basedb.clients.web.taglib.tab.Tab
 
getHelpId() - Method in class net.sf.basedb.clients.web.extensions.tabcontrol.FixedTabFactory
 
getHelpId() - Method in class net.sf.basedb.clients.web.extensions.tabcontrol.IncludeContentTabFactory.Tab
 
getHelpId() - Method in interface net.sf.basedb.clients.web.extensions.tabcontrol.TabAction
The external id of a help text that the user can display to get more information about how to use the information in this tab.
getHelpId() - Method in class net.sf.basedb.clients.web.extensions.tabcontrol.TabBean
 
getHelpId() - Method in class net.sf.basedb.clients.web.taglib.tab.Tab
 
getHelpTexts() - Method in class net.sf.basedb.core.data.ClientData
This is the inverse end.
getHibernateConfig() - Method in class net.sf.basedb.core.hibernate.SessionFactoryConfiguration
Deprecated.
Get the underlying Hibernate configuration instance.
getHibernateFlushMode() - Method in class net.sf.basedb.core.hibernate.QueryWrapper
 
getHibernateFlushMode() - Method in class net.sf.basedb.core.hibernate.SessionWrapper
 
getHibernateSession() - Method in class net.sf.basedb.core.DbControl
Get the underlying Hibernate session.
getHibernateType() - Method in class net.sf.basedb.core.hibernate.TypeWrapper
Get the underlying Hibernate type.
getHibernateType() - Method in class net.sf.basedb.core.Metadata.BasicData2ItemPropertyPath
 
getHibernateType() - Method in class net.sf.basedb.core.Metadata.BasicItem2DataPropertyPath
 
getHibernateType() - Method in class net.sf.basedb.core.Metadata.CollectionPropertyPath
 
getHibernateType() - Method in class net.sf.basedb.core.Metadata.CombinedPropertyPath
 
getHibernateType() - Method in class net.sf.basedb.core.Metadata.ComponentPropertyPath
 
getHibernateType() - Method in class net.sf.basedb.core.Metadata.DateCopyPropertyPath
 
getHibernateType() - Method in class net.sf.basedb.core.Metadata.EntityPropertyPath
 
getHibernateType() - Method in class net.sf.basedb.core.Metadata.EvictPropertyPath
 
getHibernateType() - Method in class net.sf.basedb.core.Metadata.IdentifierPropertyPath
 
getHibernateType() - Method in class net.sf.basedb.core.Metadata.MapPropertyPath
 
getHibernateType() - Method in class net.sf.basedb.core.Metadata.NoopPropertyPath
 
getHibernateType() - Method in interface net.sf.basedb.core.Metadata.PropertyPath
Get type information about the value that is returned by this path.
getHibernateType() - Method in class net.sf.basedb.core.Metadata.ReporterScore2DataPropertyPath
 
getHiddenFilteredColumns() - Method in class net.sf.basedb.clients.web.taglib.table.Table
 
getHiddenMembers() - Method in class net.sf.basedb.core.data.GroupData
A flag indicating if members of the group should be hidden to each other or not.
getHideclazz() - Method in class net.sf.basedb.clients.web.taglib.HideableSection
 
getHideClazz() - Method in class net.sf.basedb.clients.web.extensions.section.IncludeContentSectionFactory.Section
 
getHideClazz() - Method in interface net.sf.basedb.clients.web.extensions.section.SectionAction
Additional class attribute of the main section tag that is used when the section is hidden.
getHideClazz() - Method in class net.sf.basedb.clients.web.extensions.section.SectionBean
 
getHighestScoreIdx(double[][]) - Method in class net.sf.basedb.util.fuzzy.StringMatcher
 
getHighlight() - Method in class net.sf.basedb.clients.web.taglib.table.Row
 
getHints() - Method in class net.sf.basedb.core.hibernate.QueryWrapper
 
getHistoryOf(BasicItem) - Static method in class net.sf.basedb.core.ChangeHistory
Get the history for a given item.
getHome() - Method in class net.sf.basedb.util.extensions.xml.PathConverter
Get the value of the home path.
getHome(Extension<?>) - Method in class net.sf.basedb.clients.web.extensions.JspContext
Get the URL to the home directory for a given extension.
getHomeDirectory() - Method in class net.sf.basedb.core.data.UserData
Get the home directory for this user.
getHomeDirectory() - Method in class net.sf.basedb.core.User
Get the home Directory for this user.
getHomeUrl(String) - Static method in class net.sf.basedb.clients.web.extensions.ExtensionsControl
Get the URL to the home directory of extension with the given ID.
getHost() - Method in class net.sf.basedb.core.data.FileServerData
Get the name:port of the actual host to use for all files using this server (overrides the host specified in the file url)
getHost() - Method in class net.sf.basedb.core.FileServer
Get the name:port of the host that should override the host:port in the file url for files using this file server.
getHost() - Method in class net.sf.basedb.util.uri.ConnectionParameters
Get the host:port that should override the host:port specified by the file URI.
getHostName() - Static method in class net.sf.basedb.core.Application
Get the host name of the server running BASE.
getHref() - Method in class net.sf.basedb.clients.web.taglib.Icon
 
getHref() - Method in class net.sf.basedb.clients.web.taglib.path.PathElement
 
getHTML(ButtonAction, boolean, boolean) - Method in class net.sf.basedb.clients.web.extensions.toolbar.ToolbarButtonRenderer
Generate the HTML that is needed to create a toolbar button.
getIcon() - Method in class net.sf.basedb.clients.web.extensions.menu.FixedMenuItemFactory
 
getIcon() - Method in interface net.sf.basedb.clients.web.extensions.menu.MenuItemAction
Get an absolute reference to an image that will be displayed in the menu.
getIcon() - Method in class net.sf.basedb.clients.web.extensions.menu.MenuItemBean
 
getIcon() - Method in interface net.sf.basedb.clients.web.extensions.toolbar.ButtonAction
Get a reference to an image that will be displayed in the menu.
getIcon() - Method in class net.sf.basedb.clients.web.extensions.toolbar.ButtonBean
 
getIcon() - Method in class net.sf.basedb.clients.web.extensions.toolbar.FixedButtonFactory
 
getIcon() - Method in class net.sf.basedb.clients.web.taglib.menu.Menuitem
 
getIcon() - Method in class net.sf.basedb.clients.web.taglib.menu.Submenu
 
getIcon() - Method in class net.sf.basedb.clients.web.taglib.table.Button.ButtonActionWrapper
 
getIcon() - Method in enum class net.sf.basedb.util.extensions.logging.LogLevel
Get the icon that represents this log level.
getId() - Method in class net.sf.basedb.clients.jobagent.Agent
Get the agent.id configuration value.
getId() - Method in class net.sf.basedb.clients.jobagent.slotmanager.Slot
Get the id of the slot.
getId() - Method in class net.sf.basedb.clients.web.ExperimentExplorer.AnnotationGroup
The ID of the group.
getId() - Method in class net.sf.basedb.clients.web.extensions.list.AbstractListColumnBean
 
getId() - Method in interface net.sf.basedb.clients.web.extensions.list.ListColumnAction
ID attribute of the column.
getId() - Method in interface net.sf.basedb.clients.web.extensions.login.LoginFormAction
Get the ID of this login form.
getId() - Method in class net.sf.basedb.clients.web.extensions.login.LoginFormBean
 
getId() - Method in class net.sf.basedb.clients.web.extensions.login.PasswordLoginFormFactory
 
getId() - Method in class net.sf.basedb.clients.web.extensions.menu.FixedMenuItemFactory
 
getId() - Method in interface net.sf.basedb.clients.web.extensions.menu.MenuItemAction
ID attribute of the main menu tag.
getId() - Method in class net.sf.basedb.clients.web.extensions.menu.MenuItemBean
 
getId() - Method in interface net.sf.basedb.clients.web.extensions.plot.OverviewPlotAction
The ID of the overview plots.
getId() - Method in class net.sf.basedb.clients.web.extensions.plot.OverviewPlotBean
 
getId() - Method in interface net.sf.basedb.clients.web.extensions.plot.PlotGenerator
Get the ID of the image.
getId() - Method in class net.sf.basedb.clients.web.extensions.plot.PlotGeneratorBean
 
getId() - Method in class net.sf.basedb.clients.web.extensions.section.IncludeContentSectionFactory.Section
 
getId() - Method in interface net.sf.basedb.clients.web.extensions.section.SectionAction
ID attribute of the main section tag.
getId() - Method in class net.sf.basedb.clients.web.extensions.section.SectionBean
 
getId() - Method in class net.sf.basedb.clients.web.extensions.skin.FixedSkinActionFactory
 
getId() - Method in class net.sf.basedb.clients.web.extensions.skin.FixedSkinActionFactory.MySkinAction
 
getId() - Method in interface net.sf.basedb.clients.web.extensions.skin.SkinAction
Get the ID of the extension.
getId() - Method in class net.sf.basedb.clients.web.extensions.startpage.FixedStartPageFactory
 
getId() - Method in interface net.sf.basedb.clients.web.extensions.startpage.StartPageAction
Get the ID of the the action.
getId() - Method in class net.sf.basedb.clients.web.extensions.startpage.StartPageBean
 
getId() - Method in class net.sf.basedb.clients.web.extensions.tabcontrol.FixedTabFactory
 
getId() - Method in class net.sf.basedb.clients.web.extensions.tabcontrol.IncludeContentTabFactory.Tab
 
getId() - Method in interface net.sf.basedb.clients.web.extensions.tabcontrol.TabAction
ID attribute of the main tab tag.
getId() - Method in class net.sf.basedb.clients.web.extensions.tabcontrol.TabBean
 
getId() - Method in interface net.sf.basedb.clients.web.extensions.toolbar.ButtonAction
ID attribute of the main button tag.
getId() - Method in class net.sf.basedb.clients.web.extensions.toolbar.ButtonBean
 
getId() - Method in class net.sf.basedb.clients.web.extensions.toolbar.FixedButtonFactory
 
getId() - Method in class net.sf.basedb.clients.web.taglib.Button
 
getId() - Method in class net.sf.basedb.clients.web.taglib.table.Button.ButtonActionWrapper
 
getId() - Method in class net.sf.basedb.clients.web.taglib.table.TableColumn
 
getId() - Method in class net.sf.basedb.core.BasicItem
 
getId() - Method in class net.sf.basedb.core.data.annotations.AnnotationLink
 
getId() - Method in class net.sf.basedb.core.data.BasicData
Get the id of the item.
getId() - Method in interface net.sf.basedb.core.data.IdentifiableData
Get the id for the item.
getId() - Method in class net.sf.basedb.core.data.UserData
We must override this method because the id must be the same as the id for the password.
getId() - Method in interface net.sf.basedb.core.Identifiable
Get the id for the item.
getId() - Method in class net.sf.basedb.core.ItemContext
Get the ID of the current item in this context.
getId() - Method in class net.sf.basedb.core.ItemProxy
 
getId() - Method in class net.sf.basedb.core.ParameterValuesImpl
 
getId() - Method in class net.sf.basedb.core.plugin.NamespaceParameterValuesWrapper
 
getId() - Method in interface net.sf.basedb.core.plugin.ParameterValues
Get the ID of the job or configuration the parameters comes from.
getId() - Method in class net.sf.basedb.core.plugin.ParameterValuesWrapper
Get the ID of either the job or the configuration, depending in the preferJob parameter that was set when creating this object.
getId() - Method in class net.sf.basedb.core.RawDataBatcher.FeatureProxy
 
getId() - Method in class net.sf.basedb.core.RawDataBatcher.ReporterProxy
 
getId() - Method in class net.sf.basedb.core.RawDataType
Get the id of this raw data type.
getId() - Method in class net.sf.basedb.core.SessionControl
Get the id of this SessionControl.
getId() - Method in class net.sf.basedb.core.signal.Signal
Get the signal ID.
getId() - Method in class net.sf.basedb.core.snapshot.AnnotationLoaderUtil
The ID of the annotation type that this loader load annotations from.
getId() - Method in class net.sf.basedb.plugins.BaseFileExporterPlugin.ExtendedDynamicField
 
getId() - Method in class net.sf.basedb.plugins.BfsExporterPlugin.ExtendedExportableField
 
getId() - Method in class net.sf.basedb.plugins.gtf.DefaultConfigurationValues
 
getId() - Method in interface net.sf.basedb.util.extensions.Extension
Get the ID of the extension.
getId() - Method in class net.sf.basedb.util.extensions.ExtensionBean
 
getId() - Method in interface net.sf.basedb.util.extensions.ExtensionPoint
Get the ID of the extension point.
getId() - Method in class net.sf.basedb.util.extensions.ExtensionPointBean
 
getId() - Method in class net.sf.basedb.util.extensions.Registry.RegisteredExtension
 
getId() - Method in class net.sf.basedb.util.extensions.Registry.RegisteredExtensionPoint
 
getId() - Method in class net.sf.basedb.util.importer.spotdata.BaseFileImporter.RawDataProxy
 
getId() - Method in class net.sf.basedb.util.importer.spotdata.BaseFileImporter.ReporterProxy
 
getId() - Method in class net.sf.basedb.util.importer.spotdata.ExtraFloatParser
Get the external id of the extra value type.
getId() - Method in interface net.sf.basedb.util.overview.extensions.ValidationRuleAction
Get the unique ID of this validation rule.
getId() - Method in class net.sf.basedb.util.overview.Node
Get a unique ID for this node.
getId() - Method in class net.sf.basedb.util.overview.Validator
Get the unique ID of this validator.
getId() - Method in interface net.sf.basedb.util.uri.ConnectionManagerFactory
Get the ID of this connection manager factory.
getId() - Method in class net.sf.basedb.util.uri.http.HttpConnectionManagerFactory
 
getId(String) - Static method in class net.sf.basedb.core.SystemItems
Get the numeric id for an item when you know the system id.
getId(BasicItem) - Method in class net.sf.basedb.clients.web.plugins.ItemQueryWrapper
getId(BasicData) - Method in class net.sf.basedb.clients.web.plugins.DataQueryWrapper
getId(SqlResult) - Method in class net.sf.basedb.clients.web.plugins.DynamicQueryWrapper
Keeps a counter which is incremented at each call to this method.
getId(ReporterScore) - Method in class net.sf.basedb.clients.web.plugins.ReporterScoreQueryWrapper
getId(T) - Method in interface net.sf.basedb.clients.web.plugins.QueryWrapper
Get the ID of the specified item.
getIdentifier(Object) - Method in class net.sf.basedb.core.hibernate.SessionWrapper
 
getIdentifier(FeatureData) - Method in enum class net.sf.basedb.core.FeatureIdentificationMethod
Get the feature identifier for this method.
getIdentifier(RawData, String) - Method in enum class net.sf.basedb.core.FeatureIdentificationMethod
Get a feature identifier using this method
getIdFromPath(DbControl, Path) - Static method in class net.sf.basedb.core.Directory
Get the id of a directory when you know the path.
getIdHqlQuery(DbControl) - Method in class net.sf.basedb.core.AbstractHqlQuery
Build the ID query and set parameter values for it.
getIdMethod(DbControl, String) - Method in class net.sf.basedb.plugins.batchimport.AbstractItemImporter
Get the id method to use for finding items.
getIdMethod(DbControl, String) - Method in class net.sf.basedb.plugins.batchimport.FileImporter
We need to initialize the PathIdMethod when this is called.
getIdMethod(DbControl, Item, String) - Method in class net.sf.basedb.plugins.AnnotationFlatFileImporter
 
getIdMethod(DbControl, Item, String) - Method in class net.sf.basedb.plugins.batchimport.AnyToAnyImporter
 
getIdMethods() - Method in class net.sf.basedb.plugins.batchimport.AbstractItemImporter
Get an array with all identification methods that can be used to find items.
getIdMethods() - Method in class net.sf.basedb.plugins.batchimport.AnnotationTypeImporter
getIdMethods() - Method in class net.sf.basedb.plugins.batchimport.ArrayBatchImporter
getIdMethods() - Method in class net.sf.basedb.plugins.batchimport.ArrayDesignImporter
getIdMethods() - Method in class net.sf.basedb.plugins.batchimport.ArraySlideImporter
getIdMethods() - Method in class net.sf.basedb.plugins.batchimport.BioPlateImporter
getIdMethods() - Method in class net.sf.basedb.plugins.batchimport.BioSourceImporter
getIdMethods() - Method in class net.sf.basedb.plugins.batchimport.DerivedBioAssayImporter
getIdMethods() - Method in class net.sf.basedb.plugins.batchimport.ExtractImporter
getIdMethods() - Method in class net.sf.basedb.plugins.batchimport.FileImporter
getIdMethods() - Method in class net.sf.basedb.plugins.batchimport.KitImporter
getIdMethods() - Method in class net.sf.basedb.plugins.batchimport.PhysicalBioAssayImporter
getIdMethods() - Method in class net.sf.basedb.plugins.batchimport.RawBioAssayImporter
getIdMethods() - Method in class net.sf.basedb.plugins.batchimport.SampleImporter
getIdMethods() - Method in class net.sf.basedb.plugins.batchimport.TagImporter
getIdMethods(DbControl, Item) - Method in class net.sf.basedb.plugins.AnnotationFlatFileImporter
 
getIdMethods(DbControl, Item) - Static method in class net.sf.basedb.plugins.batchimport.AnnotationIdMethod
Get identification methods that are based on annotations.
getIdMethods(DbControl, Item) - Method in class net.sf.basedb.plugins.batchimport.AnyToAnyImporter
 
getIdPrefix() - Method in class net.sf.basedb.clients.web.taglib.StylableTag
Optional prefix to include in the 'id' attribute.
getIdPrefix() - Method in class net.sf.basedb.clients.web.taglib.table.ColumnDef
 
getIdQuery(DbControl, boolean) - Method in class net.sf.basedb.core.AbstractQuery
Build a query string that is identical to the main query but only return the ID values.
getIgnoredFiles() - Method in class net.sf.basedb.clients.web.extensions.ExtensionsControl
Get files that are currently ignored.
getIgnoredFiles() - Method in class net.sf.basedb.util.extensions.manager.Settings
Get a list with all files that are ignored.
getIgnoredFiles(boolean) - Method in class net.sf.basedb.util.extensions.manager.ExtensionsManager
Get all ignored files.
getIgnoredLines() - Method in class net.sf.basedb.util.parser.FlatFileParser
Get the number of lines that the last call to FlatFileParser.nextData() or FlatFileParser.hasMoreData() ignored because they matched the ignore regular expression.
getIgnoredSql() - Method in class net.sf.basedb.core.hibernate.SchemaGenerator
Get a list with the SQL statements that was ignored in the last run.
getIgnoreSubtypeFilter() - Method in class net.sf.basedb.core.ItemContext
 
getImage() - Method in class net.sf.basedb.clients.web.taglib.Button
 
getImage() - Method in class net.sf.basedb.clients.web.taglib.Help
 
getImage() - Method in class net.sf.basedb.clients.web.taglib.Icon
 
getImage() - Method in class net.sf.basedb.clients.web.taglib.table.Button
 
getImage() - Method in class net.sf.basedb.clients.web.taglib.table.Label
 
getImage() - Method in class net.sf.basedb.clients.web.taglib.Zoom
 
getImage() - Method in class net.sf.basedb.core.data.PlateMappingData
An optional name of a small image with a graphical representation of the mapping.
getImage() - Method in class net.sf.basedb.core.PlateMapping
Get the name of a small image that is a graphical representation of the mapping.
getImageRemapDir() - Method in class net.sf.basedb.clients.web.extensions.skin.FixedSkinActionFactory
 
getImpersonated() - Method in class net.sf.basedb.core.data.SessionData
Check if another user is acting as the user of this session.
getImpersonated() - Method in class net.sf.basedb.core.Session
Check if another user was acting as the user of this session.
getImpersonatedSessionControl(Job) - Method in class net.sf.basedb.clients.jobagent.Agent
Get a session control where the owner of the job has been impersonated and the active project has been set if needed.
getImplementingItems(Class<?>) - Static method in class net.sf.basedb.core.Metadata
Get all Item:s implementing/extinding the specified interface/class.
getImporter(DbControl, boolean, boolean) - Method in class net.sf.basedb.plugins.executor.ExternalProgramExecutor
Get an instance of the importer plug-in.
getImportFileType() - Method in class net.sf.basedb.plugins.ManualTransformCreator
 
getInactiveRoles() - Method in class net.sf.basedb.core.Keyring
 
getInactiveRoles() - Method in class net.sf.basedb.core.SessionControl
Get the id of all inactive roles where the logged in user is a member.
getInclude() - Method in class net.sf.basedb.core.data.ContextData
Flags for specifying include options to an entity query.
getInclude() - Method in class net.sf.basedb.core.data.ItemListSyncFilterData
Flags for specifying include options to an entity query.
getInclude() - Method in class net.sf.basedb.core.ItemContext
Get a Set object to specify Include options for a query.
getInclude() - Method in class net.sf.basedb.util.listable.TransformContext
Include options when executing queries to find parent/child items.
getIndex() - Method in class net.sf.basedb.core.BioPlateEventParticipant
Get the index of the plate in this event.
getIndex() - Method in class net.sf.basedb.core.data.BioPlateEventParticipantData
Get the index of this plate in the event.
getIndex() - Method in interface net.sf.basedb.util.extensions.Extension
The extensions in an extension point are by default ordered by their index value.
getIndex() - Method in class net.sf.basedb.util.extensions.ExtensionBean
 
getIndex() - Method in class net.sf.basedb.util.extensions.Registry.RegisteredExtension
 
getIndex(String) - Method in class net.sf.basedb.clients.web.servlet.PlotServlet.CFResultIterator
 
getIndex(String) - Method in class net.sf.basedb.core.DynamicResultIterator
 
getIndex(String) - Method in class net.sf.basedb.core.log.EntityDetails
Get the array index of the given property.
getIndex(String) - Method in interface net.sf.basedb.core.query.SqlResultIterator
Get the index number of a selected column.
getIndex(String) - Method in class net.sf.basedb.util.bfs.MetadataModel.Section
Get the index of the first entry with the given key.
getIndex(String, String[], Comparator<String>) - Method in class net.sf.basedb.core.Metadata
 
getIndexes() - Method in class net.sf.basedb.core.dbengine.TableInfo
Get information about the indexes in the table.
getInfo() - Method in class net.sf.basedb.clients.jobagent.AgentController
Get info about running job agent by sending an info request to the agents remote control service.
getInfo() - Method in class net.sf.basedb.core.JobAgent
Get info about the running job agent.
getInfo(boolean) - Method in class net.sf.basedb.util.jobagent.JobAgentConnection
Send an info or status request to the job agent.
getInheritedAnnotation(DbControl) - Method in class net.sf.basedb.core.snapshot.AnnotationSnapshot
Get the parent annotation this annotation is inherited from.
getInheritedAnnotationColumns(String) - Static method in class net.sf.basedb.clients.web.Base
Get a query returning all annotation types that are needed to display inherited annotations for the given columns.
getInheritedAnnotationId() - Method in class net.sf.basedb.core.snapshot.AnnotationSnapshot
Get the ID of the annotation this annotation is inherited from.
getInheritedAnnotationSet(DbControl) - Method in class net.sf.basedb.core.snapshot.AnnotationSnapshot
Get the annotation set this annotation is inherited from.
getInheritedAnnotationSetId() - Method in class net.sf.basedb.core.snapshot.AnnotationSnapshot
Get the ID of the annotation set this annotation is inherited from.
getInheritedFrom() - Method in class net.sf.basedb.core.Annotation
Get the parent annotation if this is an inherited or cloned annotation.
getInheritedFrom() - Method in class net.sf.basedb.core.data.AnnotationData
The parent annotation if this is an inherited or cloned annotation.
getInheritedFrom() - Method in class net.sf.basedb.core.snapshot.AnnotationSnapshot
Get a snapshot for the annotation this is inherited from.
getInheritingAnnotations() - Method in class net.sf.basedb.core.data.AnnotationData
Other annotations which inherit this annotation.
getInitial() - Method in class net.sf.basedb.clients.web.taglib.HideableSection
 
getInitializedFlatFileParser() - Method in class net.sf.basedb.plugins.AbstractFlatFileImporter
Get an initialized parser that is configured by job or configuration values.
getInitializedFlatFileParser() - Method in class net.sf.basedb.plugins.IlluminaRawDataImporter
Create a FlatFileParser that can parse Illumina data files: Data splitter: (,|\t) Header regexp: (.+)=(.*?)
getInitializedFlatFileParser() - Method in class net.sf.basedb.plugins.PlateMappingImporter
 
getInitializedFlatFileParser() - Method in class net.sf.basedb.plugins.PrintMapFlatFileImporter
 
getInitializedFlatFileParser(InputStream, String) - Method in class net.sf.basedb.plugins.Base1PluginExecuter
Creates a FlatFileParser for a plugin configuration file.
getInitializedFlatFileParser(InputStream, String) - Method in class net.sf.basedb.util.basefile.BaseFileParser
Creates a FlatFileParser for parsing a BASEfile.
getInitializedFlatFileParser(ParameterValues) - Method in class net.sf.basedb.plugins.AbstractFlatFileImporter
Create and initialise a flat file parser by setting all regular expressions and other options.
getInitParameter(String) - Method in class net.sf.basedb.clients.web.extensions.ServletWrapper
 
getInitParameterNames() - Method in class net.sf.basedb.clients.web.extensions.ServletWrapper
 
getInputStream() - Method in class net.sf.basedb.clients.web.fileupload.UploadedFile
Get an input stream for uploading the file.
getInputStream() - Method in class net.sf.basedb.util.importer.BaseFileWrapper
 
getInputStream() - Method in class net.sf.basedb.util.importer.DiskFileWrapper
 
getInputStream() - Method in interface net.sf.basedb.util.importer.FileWrapper
Get an input stream that reads data from the file.
getInputStream() - Method in interface net.sf.basedb.util.uri.ConnectionManager
Get an InputStream for reading the contents of the resource.
getInputStream() - Method in class net.sf.basedb.util.uri.http.HttpConnectionManager
 
getInputStream(long) - Method in class net.sf.basedb.util.uri.http.HttpConnectionManager
 
getInputStream(long) - Method in interface net.sf.basedb.util.uri.ResumableConnectionManager
Get an InputStream for reading the contents of the resource.
getInputStream(File) - Method in class net.sf.basedb.core.Migration
Get a stream for reading from the given file.
getInputStream(File) - Static method in class net.sf.basedb.util.FileUtil
Get a buffered InputStream object reading from the specified file.
getInputStream(String) - Method in class net.sf.basedb.util.bfs.BaseInputStreamLocator
Finds and opens an input stream to the file with the given filename.
getInputStream(String) - Method in class net.sf.basedb.util.bfs.DiskInputStreamLocator
Finds and opens an input stream to the file with the given filename.
getInputStream(String) - Method in interface net.sf.basedb.util.bfs.InputStreamLocator
Create an input stream that reads data from the given named resource.
getInputStream(String, int) - Method in class net.sf.basedb.util.StaticCache
Get a lock-safe input stream.
getInputStream(UploadedFile) - Method in class net.sf.basedb.clients.web.fileupload.FileUpload
Get an input stream for reading from the current file section.
getInsertAutoIncrementSql(PersistentClass) - Method in interface net.sf.basedb.core.dbengine.DbEngine
Return a SQL fragment that can be used in an INSERT INTO statement to generate an ID for new rows.
getInsertAutoIncrementSql(PersistentClass) - Method in class net.sf.basedb.core.dbengine.DefaultDbEngine
 
getInsertAutoIncrementSql(PersistentClass) - Method in class net.sf.basedb.core.dbengine.MySQLEngine
 
getInsertAutoIncrementSql(PersistentClass) - Method in class net.sf.basedb.core.dbengine.PostgresDbEngine
 
getInsertPropertyOrder(Class<? extends BatchableData>) - Static method in class net.sf.basedb.core.BatchUtil
Get the order of properties in the insert SQL.
getInsertPropertyOrder(String) - Static method in class net.sf.basedb.core.BatchUtil
Get the order of properties in the insert SQL.
getInsertSql(Class<? extends BatchableData>) - Static method in class net.sf.basedb.core.BatchUtil
Get the SQL that inserts a new row of the specified class.
getInsertSql(String) - Static method in class net.sf.basedb.core.BatchUtil
Get the SQL that inserts a new row of the specified class.
getInstalledFiles() - Method in class net.sf.basedb.util.extensions.manager.Settings
Get a list with all files that are installed.
getInstalledSchemaVersion() - Method in class net.sf.basedb.core.hibernate.SessionFactoryConfiguration
Deprecated.
Get the schema version that was installed prior to updating it.
getInstalledSchemaVersion() - Method in class net.sf.basedb.core.ServiceSessionControl.SessionFactoryConfiguration
Get the currently installed version of the schema or 0 if not installed.
getInstallMode() - Method in class net.sf.basedb.core.ServiceSessionControl.SessionFactoryConfiguration
Get the installation mode that BASE will use when creating the session factory.
getInstance() - Static method in class net.sf.basedb.util.jep.Log2Function
Get the singleton instance of this function.
getInstance(Class<I>) - Static method in class net.sf.basedb.core.Metadata
Get the metadata instance for the specified type of item.
getInstance(Class<I>, String) - Static method in class net.sf.basedb.core.Metadata
Get the metadata instance for the item with the specified entity name.
getInstance(String) - Static method in class net.sf.basedb.core.authentication.AuthenticationMethod
Get an instance of this class for the given authentication method.
getInstance(String) - Static method in class net.sf.basedb.util.JarClassLoader
Get a class loader for the specified JAR file.
getInstance(String, boolean) - Static method in class net.sf.basedb.util.JarClassLoader
Get a class loader for the specified JAR file, optionally unloading an the old one if the JAR file has been modified.
getInstanceIfEnabled(SessionControl) - Static method in class net.sf.basedb.core.log.db.DbLogManagerFactory
Get the current database log manager factory if database logging is enabled.
getInt(int) - Method in class net.sf.basedb.clients.web.servlet.PlotServlet.CFSqlResult
 
getInt(int) - Method in class net.sf.basedb.core.DynamicResultIterator.SqlResultImpl
 
getInt(int) - Method in interface net.sf.basedb.core.query.SqlResult
Get the value of the specified column as an integer.
getInt(int) - Method in class net.sf.basedb.util.parser.FlatFileParser.Data
Shortcut for getInt(index, null, true)
getInt(int, NumberFormat, boolean) - Method in class net.sf.basedb.util.parser.FlatFileParser.Data
Get the value as an integer.
getInt(int, NumberFormat, boolean) - Method in class net.sf.basedb.util.parser.FlatFileParser.ExcelData
 
getInt(Integer) - Static method in class net.sf.basedb.core.IntegerUtil
Get the value of an Integer.
getInt(Integer, int) - Static method in class net.sf.basedb.core.IntegerUtil
Get the value of an Integer.
getInt(String) - Static method in class net.sf.basedb.core.Config
Get the configuration setting specified by key as an integer value.
getInt(String) - Static method in class net.sf.basedb.core.IntegerUtil
Get the int value of an String.
getInt(String) - Static method in class net.sf.basedb.util.Values
Convert a string to an integer.
getInt(String[]) - Static method in class net.sf.basedb.util.Values
Convert an array of strings to an array of Integer:s.
getInt(String, int) - Static method in class net.sf.basedb.core.Config
Get the configuration setting specified by key as an integer value.
getInt(String, int) - Static method in class net.sf.basedb.core.IntegerUtil
Get the int value of an String.
getInt(String, int) - Static method in class net.sf.basedb.util.Values
Convert a string to an integer.
getInt(FlatFileParser.Data) - Method in class net.sf.basedb.util.parser.ColumnMapper
 
getInt(FlatFileParser.Data) - Method in class net.sf.basedb.util.parser.CompoundMapper
 
getInt(FlatFileParser.Data) - Method in class net.sf.basedb.util.parser.ConstantMapper
 
getInt(FlatFileParser.Data) - Method in class net.sf.basedb.util.parser.CropStringMapper
 
getInt(FlatFileParser.Data) - Method in class net.sf.basedb.util.parser.JepMapper
 
getInt(FlatFileParser.Data) - Method in interface net.sf.basedb.util.parser.Mapper
Get the value for the line of data as an integer.
getInt(FlatFileParser.Data) - Method in class net.sf.basedb.util.parser.NullIfExceptionMapper
 
getIntAttribute(Element, String, int) - Static method in class net.sf.basedb.util.XmlUtil2
Get the value of an attribute as an integer.
getIntCellStyle() - Method in class net.sf.basedb.util.excel.CellStyleCreator
Get the cell style for formatting numbers without decimals.
getInteger(String, Integer) - Static method in class net.sf.basedb.util.Values
 
getIntegerValues() - Method in class net.sf.basedb.core.data.annotations.AnnotationLink
 
getIntensityField(String, String) - Method in class net.sf.basedb.util.export.spotdata.AbstractFieldConverter
Create a dynamic field for spot intensity if the field name has the pattern 'Ch X' where 'X' is a channel number between 1 and the number of channels in the raw data type used by the source bioassay set.
getIntensityField(String, String) - Method in class net.sf.basedb.util.export.spotdata.Base1FieldConverter
Create a dynamic field for spot intensity if the field name has the pattern 'intensityX' where 'X' is a channel number between 1 and the number of channels in the raw data type used by the source bioassay set.
getIntensityFormula(String) - Method in class net.sf.basedb.core.RawDataType
 
getIntensityFormulas() - Method in class net.sf.basedb.core.RawDataType
 
getIntensityTransform() - Method in class net.sf.basedb.core.BioAssaySet
Get information about in what way the spot intensities has been transformed before they were stored in the database.
getIntensityTransform() - Method in class net.sf.basedb.core.data.BioAssaySetData
A flag indicating how the spot intensities has been transformed before it was stored in the database: 0 = no transformation; 1 = 2-log; 2 = 10-log
getIntensityTransform() - Method in class net.sf.basedb.core.DynamicQuery
Get the intensity transform that was used to store spot intensities for the root bioassay set in this query.
getIntensityTransform() - Method in class net.sf.basedb.util.importer.spotdata.BaseFileImporter
Get the intensity transform
getInterfaceName() - Method in class net.sf.basedb.core.data.PluginTypeData
Get the interface name a plugin must implement to be of this type.
getInterfaceName() - Method in class net.sf.basedb.core.PluginType
Get the class name of the Java class that implements this plugin.
getInterfaces(Class<?>) - Static method in class net.sf.basedb.util.ClassUtil
Get all interfaces a class implements, including those implemented by superclasses.
getInternalId() - Method in class net.sf.basedb.core.authentication.AuthenticatedUser
Get the internal id for the user (0 if not known)
getInternalId() - Method in class net.sf.basedb.util.extensions.xml.PluginInfo
Get the internal if of this plug-in.
getInternalName() - Method in class net.sf.basedb.core.data.FileData
Get the internal name accosiated with this file.
getInternalName() - Method in class net.sf.basedb.core.File
Get the internal name of this file.
getIntFormatter(SessionControl) - Static method in class net.sf.basedb.clients.web.formatter.FormatterFactory
Get the logged in user's formatter for integral numbers.
getIntOption(String, Integer) - Method in class net.sf.basedb.core.AnnotationType
Get an option and convert the value to an integer.
getInvoker() - Method in class net.sf.basedb.clients.web.extensions.fileviewer.FileViewerUtil
Get the invoker that is handling the extensions.
getInvoker(DbControl) - Method in class net.sf.basedb.core.FileSet
 
getInvoker(ClientContext, ExtensionsFilter) - Static method in class net.sf.basedb.util.uri.ConnectionManagerUtil
Get an invoker for using the connection manager factory extensions.
getInvoker(Extension<ServiceControllerAction>) - Static method in class net.sf.basedb.clients.web.extensions.service.Services
 
getItem() - Method in class net.sf.basedb.clients.web.taglib.PropertyValue
 
getItem() - Method in class net.sf.basedb.clients.web.taglib.SubtypeSelector
 
getItem() - Method in class net.sf.basedb.clients.web.taglib.table.Table
 
getItem() - Method in class net.sf.basedb.core.AnnotationSet
Get the item this annotation set belongs to.
getItem() - Method in class net.sf.basedb.core.ContextKey
 
getItem() - Method in class net.sf.basedb.core.DiskUsage
Get the item this disk usage holds information for
getItem() - Method in class net.sf.basedb.core.FileSet
Get the item this file set belongs to.
getItem() - Method in class net.sf.basedb.core.log.ManualLogEntry
Get the item this log entry is related to.
getItem() - Method in class net.sf.basedb.core.plugin.GuiContext
 
getItem() - Method in class net.sf.basedb.util.overview.Fix
Get the item that needs to be edited for this fix.
getItem() - Method in class net.sf.basedb.util.overview.Node
Get the item that is related to this node.
getItem(Class<I>, BasicData, Object...) - Method in class net.sf.basedb.core.DbControl
Get an item object for a known data object, using the cache if possible.
getItem(DbControl) - Method in class net.sf.basedb.core.AnnotationSet
Get the item this annotation set belongs to using a specific DbControl for database access.
getItem(DbControl) - Method in class net.sf.basedb.core.ChangeHistory
Load the item that was changed.
getItem(DbControl) - Method in class net.sf.basedb.core.ItemProxy
 
getItem(DbControl) - Method in class net.sf.basedb.core.snapshot.AnnotationSetSnapshot
Get item the annotations belong to.
getItem(DbControl) - Method in class net.sf.basedb.util.overview.Node
Get the item that is related to this node and make sure that it is loaded with the current DbControl.
getItem(DbControl, ChangeHistory, boolean, boolean) - Static method in class net.sf.basedb.clients.web.ChangeHistoryUtil
Get the item that was changed in HTML format.
getItemClass() - Method in enum class net.sf.basedb.core.Item
Get the class object that is used to handle items of this type.
getItemCount() - Method in class net.sf.basedb.util.plot.HistogramPlot.HistogramSeries
 
getItemCount(int) - Method in class net.sf.basedb.util.plot.HistogramPlot.HistogramDataset
 
getItemForAnnotationTypes() - Method in class net.sf.basedb.plugins.batchimport.AbstractItemImporter
Does the importer want to use annotation types as identifiers importing?
getItemForAnnotationTypes() - Method in class net.sf.basedb.plugins.batchimport.ArrayBatchImporter
Enable annotations as item identifier.
getItemForAnnotationTypes() - Method in class net.sf.basedb.plugins.batchimport.ArrayDesignImporter
Enable annotations as item identifier.
getItemForAnnotationTypes() - Method in class net.sf.basedb.plugins.batchimport.ArraySlideImporter
Enable annotations as item identifier.
getItemForAnnotationTypes() - Method in class net.sf.basedb.plugins.batchimport.BioPlateImporter
Enable annotations as item identifier.
getItemForAnnotationTypes() - Method in class net.sf.basedb.plugins.batchimport.BioSourceImporter
Enable annotations as item identifier.
getItemForAnnotationTypes() - Method in class net.sf.basedb.plugins.batchimport.DerivedBioAssayImporter
Enable annotations as item identifier.
getItemForAnnotationTypes() - Method in class net.sf.basedb.plugins.batchimport.ExtractImporter
Enable annotations as item identifier.
getItemForAnnotationTypes() - Method in class net.sf.basedb.plugins.batchimport.KitImporter
Enable annotations as item identifier.
getItemForAnnotationTypes() - Method in class net.sf.basedb.plugins.batchimport.PhysicalBioAssayImporter
Enable annotations as item identifier.
getItemForAnnotationTypes() - Method in class net.sf.basedb.plugins.batchimport.RawBioAssayImporter
Enable annotations as item identifier.
getItemForAnnotationTypes() - Method in class net.sf.basedb.plugins.batchimport.SampleImporter
Enable annotations as item identifier.
getItemForAnnotationTypes() - Method in class net.sf.basedb.plugins.batchimport.TagImporter
Enable annotations as item identifier.
getItemForSubtypes() - Method in class net.sf.basedb.plugins.batchimport.AbstractItemImporter
Does the importer want to use item subtypes when importing?
getItemForSubtypes() - Method in class net.sf.basedb.plugins.batchimport.BioSourceImporter
 
getItemForSubtypes() - Method in class net.sf.basedb.plugins.batchimport.DerivedBioAssayImporter
 
getItemForSubtypes() - Method in class net.sf.basedb.plugins.batchimport.ExtractImporter
 
getItemForSubtypes() - Method in class net.sf.basedb.plugins.batchimport.FileImporter
 
getItemForSubtypes() - Method in class net.sf.basedb.plugins.batchimport.KitImporter
 
getItemForSubtypes() - Method in class net.sf.basedb.plugins.batchimport.PhysicalBioAssayImporter
 
getItemForSubtypes() - Method in class net.sf.basedb.plugins.batchimport.SampleImporter
 
getItemForSubtypes() - Method in class net.sf.basedb.plugins.batchimport.TagImporter
 
getItemId() - Method in class net.sf.basedb.core.AnnotationBatcher.CurrentAnnotationInfo
Get the id of the current item.
getItemId() - Method in class net.sf.basedb.core.AnnotationSet
Get the ID of the item this annotation set belongs to.
getItemId() - Method in class net.sf.basedb.core.ChangeHistory
Get the ID of the item that was changed.
getItemId() - Method in class net.sf.basedb.core.data.AnnotationSetData
The ID if the item this annotation set is associated with.
getItemId() - Method in class net.sf.basedb.core.data.ChangeHistoryDetailData
The ID of the item that was changed
getItemId() - Method in class net.sf.basedb.core.data.ContextData
Get the current item ID or 0 if no item is current.
getItemId() - Method in class net.sf.basedb.core.snapshot.AnnotationSetSnapshot
Get the ID of the item the annotations in this snapshot belong to.
getItemKey() - Method in interface net.sf.basedb.core.data.ShareableData
Get the ItemKeyData for the item.
getItemKey() - Method in class net.sf.basedb.core.data.SharedData
 
getItemKey() - Method in interface net.sf.basedb.core.Shareable
Get the ItemKey that is used to share this item to users and groups.
getItemKey() - Method in class net.sf.basedb.core.SharedItem
 
getItemKeyId() - Method in class net.sf.basedb.core.SessionControl
Get the id of the ItemKey that new items should be shared to according to the settings in the currently active project.
getItemKeys() - Method in class net.sf.basedb.core.data.GroupData
This is the inverse end.
getItemKeys() - Method in class net.sf.basedb.core.data.UserData
This is the inverse end.
getItemKeys() - Method in class net.sf.basedb.core.InternalJobQueue.JobQueueKeyring
Return empty set.
getItemKeys() - Method in class net.sf.basedb.core.Job.SignalKeyring
Return empty set.
getItemKeys() - Method in class net.sf.basedb.core.ServiceSessionControl.ServicesKeyring
Return empty set.
getItemKeys() - Method in class net.sf.basedb.core.SessionControl
Get the id of all item keys where the logged in user has read permission.
getItemKeys(Permission) - Method in class net.sf.basedb.core.Keyring
 
getItemKeys(Permission) - Method in class net.sf.basedb.core.SessionControl
Get the id of all item keys where the logged in user has the requested permission.
getItemList() - Method in class net.sf.basedb.core.data.ItemListSyncFilterData
Get the item list this sync filter belongs to.
getItemList() - Method in class net.sf.basedb.core.SyncFilter
Get the item list this filter belongs to.
getItemListFromContext(DbControl, GuiContext) - Method in class net.sf.basedb.plugins.AnnotationFlatFileImporter
If the current context is the "Members" tab for an item list we load the item list and will later require that all items to be annotated are members of that list.
getItemListFromContext(DbControl, GuiContext) - Method in class net.sf.basedb.plugins.batchimport.AbstractItemImporter
If the current context is the "Members" tab for an item list we load the item list and will later require that all items to be annotated are members of that list.
getItemListFromContext(DbControl, GuiContext) - Method in class net.sf.basedb.plugins.batchimport.AnyToAnyImporter
If the current context is the "Members" tab for an item list we load the item list and will later require that all items to be linked are members of that list.
getItemListsEnum(DbControl, ItemContext, Filter<? super ItemList>) - Static method in class net.sf.basedb.clients.web.Base
Get available item lists as an Enumeration that is suitable to use in a column definition for a table.
getItemListsEnum(DbControl, Item, Collection<Include>) - Static method in class net.sf.basedb.clients.web.Base
Get available item lists as an Enumeration that is suitable to use in a column definition for a table.
getItemListsEnum(DbControl, Item, Collection<Include>, Filter<? super ItemList>) - Static method in class net.sf.basedb.clients.web.Base
Get available item lists as an Enumeration that is suitable to use in a column definition for a table.
getItemPermission() - Method in class net.sf.basedb.core.AbstractEntityQuery
 
getItemPermission() - Method in class net.sf.basedb.core.ItemContext
The permission the logged in user must have for items returned by a query.
getItemPermission() - Method in interface net.sf.basedb.core.query.EntityQuery
The logged in user's permission on the items returned by this query.
getItems() - Method in class net.sf.basedb.core.MultiPermissions
Returns the items that are handled within this class.
getItems() - Method in class net.sf.basedb.core.ParameterType
Get the list of values to choose from.
getItems(Collection<Item>) - Method in class net.sf.basedb.core.MultiPermissions
Get all items of specific item types.
getItems(Set<Item>, int, int, Permission, Set<Include>, Restriction) - Method in class net.sf.basedb.core.Project
Load the items in a project.
getItems(Set<Item>, int, int, Permission, Restriction) - Method in class net.sf.basedb.core.User
Load the items owned by this user.
getItems(DbControl, Set<Item>, int, int) - Static method in class net.sf.basedb.core.Trashcan
 
getItems(DbControl, Set<Item>, int, int, Restriction) - Static method in class net.sf.basedb.core.Trashcan
Load all items flagged for deletion that are owned by or removed by the logged in user.
getItems(DbControl, Item, int, int) - Static method in class net.sf.basedb.core.Trashcan
 
getItems(DbControl, ItemQuery<T>, Restriction...) - Method in class net.sf.basedb.plugins.IlluminaRawDataImporter
Sort the items by name and add USE permission filter to the query.
getItems(Item) - Method in class net.sf.basedb.core.MultiPermissions
Get all items of a specific item type.
getItems(Item, int, int, Permission) - Method in class net.sf.basedb.core.User
 
getItems(Item, int, int, Permission, Set<Include>) - Method in class net.sf.basedb.core.Project
 
getItemSubtype() - Method in class net.sf.basedb.clients.web.SubContext
The new item subtype.
getItemSubtype() - Method in class net.sf.basedb.core.AnnotationTypeCategory
Get the item subtype that is linked to this category of annotations.
getItemSubtype() - Method in class net.sf.basedb.core.BioMaterial
 
getItemSubtype() - Method in class net.sf.basedb.core.BioPlateType
Get the subtype that biomaterial items should have when placed on a plate with this bioplate type.
getItemSubtype() - Method in class net.sf.basedb.core.data.AnnotationTypeCategoryData
The subtype that is linked to this category of annotations.
getItemSubtype() - Method in class net.sf.basedb.core.data.BioMaterialData
 
getItemSubtype() - Method in class net.sf.basedb.core.data.BioPlateTypeData
Get the subtype of biomaterials that can be placed on plates of this type.
getItemSubtype() - Method in class net.sf.basedb.core.data.ContextData
Get the subtype of items that is associated with this context.
getItemSubtype() - Method in class net.sf.basedb.core.data.DerivedBioAssayData
 
getItemSubtype() - Method in class net.sf.basedb.core.data.FileData
 
getItemSubtype() - Method in class net.sf.basedb.core.data.HardwareData
 
getItemSubtype() - Method in class net.sf.basedb.core.data.ItemListData
Get the subtype of items that can be members in this list.
getItemSubtype() - Method in class net.sf.basedb.core.data.ItemListSyncFilterData
Subtype context filter.
getItemSubtype() - Method in class net.sf.basedb.core.data.ItemSubtypeFileTypeData
Get the item subtype.
getItemSubtype() - Method in class net.sf.basedb.core.data.JobData
 
getItemSubtype() - Method in class net.sf.basedb.core.data.KitData
 
getItemSubtype() - Method in class net.sf.basedb.core.data.PhysicalBioAssayData
 
getItemSubtype() - Method in class net.sf.basedb.core.data.ProtocolData
 
getItemSubtype() - Method in class net.sf.basedb.core.data.SoftwareData
 
getItemSubtype() - Method in interface net.sf.basedb.core.data.SubtypableData
Get the subtype of the item.
getItemSubtype() - Method in class net.sf.basedb.core.data.TagData
 
getItemSubtype() - Method in class net.sf.basedb.core.DerivedBioAssay
 
getItemSubtype() - Method in class net.sf.basedb.core.Extract
 
getItemSubtype() - Method in class net.sf.basedb.core.File
 
getItemSubtype() - Method in class net.sf.basedb.core.Hardware
 
getItemSubtype() - Method in class net.sf.basedb.core.ItemList
Get the subtype of items that can be members in this list.
getItemSubtype() - Method in class net.sf.basedb.core.ItemSubtype
 
getItemSubtype() - Method in class net.sf.basedb.core.ItemSubtypeFileType
Get the item subtype.
getItemSubtype() - Method in class net.sf.basedb.core.Job
 
getItemSubtype() - Method in class net.sf.basedb.core.Kit
 
getItemSubtype() - Method in class net.sf.basedb.core.MeasuredBioMaterial
 
getItemSubtype() - Method in class net.sf.basedb.core.PhysicalBioAssay
 
getItemSubtype() - Method in class net.sf.basedb.core.Protocol
 
getItemSubtype() - Method in class net.sf.basedb.core.Sample
 
getItemSubtype() - Method in class net.sf.basedb.core.Software
 
getItemSubtype() - Method in interface net.sf.basedb.core.Subtypable
Get the subtype of the item.
getItemSubtype() - Method in class net.sf.basedb.core.SyncFilter
Get the subtype that items must match.
getItemSubtype() - Method in class net.sf.basedb.core.Tag
 
getItemSubtype() - Method in class net.sf.basedb.util.annotations.InheritSpecification
 
getItemSubtype(DbControl) - Method in class net.sf.basedb.clients.web.extensions.list.RelatedItemColumn.Specification
 
getItemSubtype(DbControl) - Method in class net.sf.basedb.core.ItemContext
Get the subtype that is related to this context.
getItemSubtypes() - Method in class net.sf.basedb.core.data.DataFileTypeData
The subtypes that this file type can be used with.
getItemSubtypes() - Method in class net.sf.basedb.core.DataFileType
Get a query returning the item subtypes that files of this type can be used on.
getItemtype() - Method in class net.sf.basedb.clients.web.taglib.SubtypeSelector
 
getItemType() - Method in class net.sf.basedb.core.AbstractEntityQuery
 
getItemType() - Method in class net.sf.basedb.core.AnnotationBatcher.CurrentAnnotationInfo
Get the item type of the item.
getItemType() - Method in class net.sf.basedb.core.AnnotationSet
Get the Item type of the item this annotation set belongs to.
getItemType() - Method in class net.sf.basedb.core.ChangeHistory
Get the type of the item that was changed.
getItemType() - Method in class net.sf.basedb.core.data.AnnotationSetData
Get the item type this annotation set is associated with.
getItemType() - Method in class net.sf.basedb.core.data.ChangeHistoryDetailData
The type code of the item that was changed.
getItemType() - Method in class net.sf.basedb.core.data.ContextData
Get the item type this context is valid for.
getItemType() - Method in class net.sf.basedb.core.data.ContextIndex
 
getItemType() - Method in class net.sf.basedb.core.data.DataFileTypeData
The item type this file type can be associated with.
getItemType() - Method in class net.sf.basedb.core.data.DiskUsageData
Get the item type this annotation set is associated with.
getItemType() - Method in class net.sf.basedb.core.data.FileSetData
Get the item type this file set is associated with.
getItemType() - Method in class net.sf.basedb.core.data.GuiContextData
 
getItemType() - Method in class net.sf.basedb.core.data.ItemSubtypeData
Get the item type this subtype can be applied to.
getItemType() - Method in class net.sf.basedb.core.data.RoleKeyData
Get the code for the type of items this role key applies to.
getItemType() - Method in class net.sf.basedb.core.DataFileType
Get the type of item files of this type can be used on.
getItemType() - Method in class net.sf.basedb.core.DataResultIterator
Get the type of items contained in this list.
getItemType() - Method in class net.sf.basedb.core.DiskUsage
Get the Item type of the item this annotation set belongs to.
getItemType() - Method in class net.sf.basedb.core.FileSet
Get the Item type of the item this file set belongs to.
getItemType() - Method in class net.sf.basedb.core.ItemContext
Get the type of item this object is storing context for.
getItemType() - Method in class net.sf.basedb.core.ItemResultIterator
Get the type of items contained in this list.
getItemType() - Method in class net.sf.basedb.core.ItemResultList
Get the type of items contained in this list.
getItemType() - Method in class net.sf.basedb.core.plugin.Permissions
Get the item type the permissions are valid for.
getItemType() - Method in interface net.sf.basedb.core.query.EntityQuery
The type of items the query returns.
getItemType() - Method in class net.sf.basedb.core.query.HqlEntityParameterExpression
Get the type of entites that are accepted by the parameter.
getItemType() - Method in class net.sf.basedb.core.query.QueryParameter
The parameter should be an entity of the given item type.
getItemType() - Method in class net.sf.basedb.core.ReporterScoreResultIterator
Get the type of items contained in this list.
getItemType() - Method in class net.sf.basedb.core.RoleKey
Get the Item type for the type of items this role key applies to.
getItemType() - Method in class net.sf.basedb.core.snapshot.AnnotationSetSnapshot
Get the item type of the item the annotations in this snapshot belong to.
getItemType() - Method in class net.sf.basedb.util.overview.Node
Get the item type of the item that this node related to this node.
getItemTypes() - Method in class net.sf.basedb.core.data.AnnotationTypeData
The item code for all items this annotation type can be applied to.
getItemValue(DbControl, Object) - Static method in class net.sf.basedb.core.Values
Convert a a data value to a item value.
getItemValues(DbControl, List<?>) - Static method in class net.sf.basedb.core.Values
Convert a list of data values to item values.
getJarFile() - Method in class net.sf.basedb.core.data.PluginDefinitionData
Get the file name of the JAR file where the plugin class is located.
getJarFile() - Method in class net.sf.basedb.core.data.PluginTypeData
Get the file name of the JAR file where the plugin class is located.
getJarFile() - Method in class net.sf.basedb.core.PluginDefinition
Get the name of the JAR file that contains this plug-in.
getJarFile() - Method in class net.sf.basedb.core.PluginType
Get the name of the JAR file that contains this plug-in.
getJarPath() - Method in class net.sf.basedb.core.PluginDefinition
Get the path to the JAR file that contains the plugin class file.
getJarPath() - Method in class net.sf.basedb.core.PluginType
Get the path to the JAR file that contains the plugin class file.
getJdbcBatchSize() - Method in class net.sf.basedb.core.hibernate.SessionWrapper
 
getJdbcBatchSize() - Method in class net.sf.basedb.core.hibernate.StatelessSessionWrapper
 
getJdbcFetchSize() - Static method in class net.sf.basedb.core.HibernateUtil
The number of rows to load at a time when reading from the database.
getJep() - Method in class net.sf.basedb.util.export.spotdata.JepDynamicField
Get the configured JEP expression.
getJepExpression() - Method in class net.sf.basedb.clients.web.taglib.table.TableColumn
 
getJepFunctions(DbControl, boolean) - Method in class net.sf.basedb.core.AbstractSqlQuery
Create custom JEP function that can be used with the current query.
getJepFunctions(DbControl, boolean) - Method in class net.sf.basedb.core.DataCube.RawMappingQuery
No JEP functions can be used with this type of query.
getJepFunctions(DbControl, boolean) - Method in class net.sf.basedb.core.DynamicExtraValueQuery
The following JEP functions can be used: pos(): PositionFunction
getJepFunctions(DbControl, boolean) - Method in class net.sf.basedb.core.DynamicPositionQuery
The following JEP function can be used: pos(): PositionFunction rep(property): ReporterFunction score(reporter-list-id): ScoreFunction xtra(extra-value-id): ExtraValueFunction (if a bioassay set has been specified) inList(reporter-list-id): InReporterListFunction (only if restrictions=true) notInList(reporter-list-id): NotInReporterListFunction (only if restrictions=true)
getJepFunctions(DbControl, boolean) - Method in class net.sf.basedb.core.DynamicRawDataQuery
 
getJepFunctions(DbControl, boolean) - Method in class net.sf.basedb.core.DynamicReporterQuery
The following JEP functions can be used: rep(property): ReporterFunction mrep(property): ReporterFunction (only for cloned reporters) inList(reporter-list-id): InReporterListFunction (only if restrictions=true) notInList(reporter-list-id): NotInReporterListFunction (only if restrictions=true)
getJepFunctions(DbControl, boolean) - Method in class net.sf.basedb.core.DynamicSpotQuery
The following JEP functions can be used: ch(n): ChannelFunction rawCh(n): RawChannelFunction pos(): PositionFunction rep(property): ReporterFunction score(reporter-list-id): ScoreFunction xtra(extra-value-id): ExtraValueFunction (if a bioassay set has been specified) raw(property): RawFunction inList(reporter-list-id): InReporterListFunction (only if restrictions=true) notInList(reporter-list-id): NotInReporterListFunction (only if restrictions=true)
getJob() - Method in class net.sf.basedb.core.ArrayDesign
Get the job that imported features to this array design.
getJob() - Method in class net.sf.basedb.core.data.ArrayDesignData
Get the job that was used to import features to this array desing
getJob() - Method in class net.sf.basedb.core.data.ChangeHistoryData
 
getJob() - Method in class net.sf.basedb.core.data.DerivedBioAssayData
Get the job used to create this bioassay set.
getJob() - Method in class net.sf.basedb.core.data.ExtraValueData
Get the job that was used to execute this calculate this extra value.
getJob() - Method in class net.sf.basedb.core.data.MessageData
If this message is a message about a job completion (or failure) this property contains a reference to that job.
getJob() - Method in class net.sf.basedb.core.data.RawBioAssayData
Get the job that was used to import raw data to this raw bioassay
getJob() - Method in class net.sf.basedb.core.data.TransformationData
Get the job that was used to execute this transformation
getJob() - Method in class net.sf.basedb.core.DerivedBioAssay
Get the job that created this bioassay.
getJob() - Method in class net.sf.basedb.core.ExtraValue
Get the job that created the extra values.
getJob() - Method in class net.sf.basedb.core.InternalJobQueue.JobRunner
Get the job.
getJob() - Method in class net.sf.basedb.core.Message
Get the Job this message is about.
getJob() - Method in class net.sf.basedb.core.ParameterValuesImpl
 
getJob() - Method in class net.sf.basedb.core.plugin.NamespaceParameterValuesWrapper
 
getJob() - Method in interface net.sf.basedb.core.plugin.ParameterValues
Get the job that we are executing/configuring.
getJob() - Method in class net.sf.basedb.core.plugin.ParameterValuesWrapper
 
getJob() - Method in class net.sf.basedb.core.PluginRequest
Get the job for the request or null if we are not configuring/executing a job.
getJob() - Method in class net.sf.basedb.core.RawBioAssay
Get the job that created or imported data to this raw bioassay.
getJob() - Method in class net.sf.basedb.core.Transformation
Get the job that executed this transformation.
getJob() - Method in class net.sf.basedb.plugins.gtf.DefaultConfigurationValues
 
getJob(DbControl) - Method in class net.sf.basedb.core.ChangeHistory
Load the job that was executing when the change was made.
getJob(DbControl) - Method in class net.sf.basedb.core.ChangeHistory.TransactionInfo
Load the job that was executing the transaction.
getJob(DbControl, ChangeHistory, boolean, boolean) - Static method in class net.sf.basedb.clients.web.ChangeHistoryUtil
Get the job that made the change in HTML format.
getJobAgent() - Method in class net.sf.basedb.core.data.JobAgentSettingsData
The job agent these settings belong to.
getJobAgent() - Method in class net.sf.basedb.core.Job
Get the job agent this job should run on, is running on or was running on.
getJobAgent() - Method in class net.sf.basedb.core.JobAgentSettings
Get the job agent that owns these settings.
getJobAgent(DbControl) - Method in class net.sf.basedb.clients.jobagent.Agent
Get the JobAgent item corresponding to this agent.
getJobAgentId() - Method in class net.sf.basedb.core.data.JobData
The ID of the job agent this job should run/is running/was running on.
getJobAgentSettings() - Method in class net.sf.basedb.core.data.PluginDefinitionData
This is the inverse end.
getJobExecutorClass(String) - Method in class net.sf.basedb.clients.jobagent.Agent
Get the class object for the configured job executor.
getJobId() - Method in class net.sf.basedb.core.ChangeHistory
Get the ID of the job that was executing when the change was made
getJobId() - Method in class net.sf.basedb.core.ChangeHistory.TransactionInfo
Get the ID of the job that was executing the transaction.
getJobId() - Method in class net.sf.basedb.core.data.ChangeHistoryData
The ID of the job that was making the changes.
getJobId() - Method in class net.sf.basedb.core.log.TransactionDetails
Get the ID of the currently running job or 0 if no job is running.
getJobId() - Method in class net.sf.basedb.core.SessionControl
Get the id of the job that is currently running with this session control.
getJobId() - Method in class net.sf.basedb.util.jobagent.JobInfo
Get the ID of the job.
getJobInfo() - Method in class net.sf.basedb.util.jobagent.JobAgentInfo
Get detailed information about the running jobs.
getJobName() - Method in class net.sf.basedb.core.log.TransactionDetails
Utility method for loading the name of the currently executing job.
getJobName() - Method in class net.sf.basedb.core.SessionControl
Get the name of the job that is currently running with this session control.
getJobOrConfigurationValue(String) - Method in class net.sf.basedb.core.plugin.AbstractPlugin
Get the value for a job or configuration parameter.
getJobParameterObjectsFromXML(String, boolean) - Method in class net.sf.basedb.plugins.Base1PluginExecuter
 
getJobParameters() - Method in class net.sf.basedb.plugins.Base1PluginExecuter
Reads the configuration file an creates the parameters found there.
getJobParametersFromXML(String, boolean) - Method in class net.sf.basedb.plugins.Base1PluginExecuter
 
getJobs() - Method in class net.sf.basedb.core.data.ExperimentData
This is the inverse end.
getJobs() - Method in class net.sf.basedb.core.PluginConfiguration
Get a query that returns the jobs using this plugin configuration.
getJobSessionControl(Job) - Method in class net.sf.basedb.core.SessionControl
Create a new session control for executing a job.
getJobType() - Method in class net.sf.basedb.core.Job
Get the type of job, ie. if it is a job executed by a plugin or not.
getJoinAlias() - Method in class net.sf.basedb.core.ExtraValue
The alias used when joining this extra value into a query.
getJoinAlias() - Method in class net.sf.basedb.core.query.AnnotationExpression
 
getJoinAlias() - Method in class net.sf.basedb.core.query.ReporterListExpression
 
getJoinExpression() - Method in enum class net.sf.basedb.core.query.JoinType
 
getJoinProperty() - Method in class net.sf.basedb.core.query.ReporterListExpression
 
getJspContext() - Method in class net.sf.basedb.clients.web.extensions.edit.AbstractOnSaveAction
Set the JSP context of the current invokation.
getJspContext() - Method in class net.sf.basedb.clients.web.extensions.fileviewer.FileViewerUtil
Get the JSP context.
getJspPage() - Method in class net.sf.basedb.core.RequestInformation
The name of the jsp page to use for displaying the input form for requesting parameters.
getKey() - Method in class net.sf.basedb.util.bfs.MetadataModel.SectionEntry
Get the key of the entry.
getKey() - Method in class net.sf.basedb.util.Enumeration.Entry
 
getKey() - Method in class net.sf.basedb.util.fuzzy.StringMatcher.FuzzyMatch
Get the key string.
getKey() - Method in class net.sf.basedb.util.StaticCache.LockEntry
 
getKey(int) - Method in class net.sf.basedb.util.bfs.MetadataModel.Section
Get the key of the entry at the given index.
getKey(int) - Method in class net.sf.basedb.util.Enumeration
 
getKey(String, Item, Item, SyncFilter.SourceItemTransform, Set<Integer>) - Static method in class net.sf.basedb.util.listable.TransformCache
 
getKey(Item, Item, SyncFilter.SourceItemTransform, Set<Integer>) - Static method in class net.sf.basedb.util.listable.TransformCache
Get a key that is able to identify a given transformation.
getKeyId() - Method in class net.sf.basedb.core.data.keyring.KeyPermission
Get the id of the key.
getKeyId() - Method in class net.sf.basedb.core.data.keyring.PluginKeys
Gets the id of the RoleKey
getKeys() - Method in class net.sf.basedb.core.data.RoleData
This is the inverse end.
getKeys() - Method in class net.sf.basedb.core.Presets.Preset
Get all keys in this preset.
getKeys() - Method in class net.sf.basedb.util.QueryParameters
Get all keys that are present in the query string.
getKit() - Method in class net.sf.basedb.core.BioMaterialEvent
Get the Kit that was used in this event.
getKit() - Method in class net.sf.basedb.core.BioPlateEvent
Get the Kit that was used in this event.
getKit() - Method in class net.sf.basedb.core.data.BioMaterialEventData
Get the kit used in this event.
getKit() - Method in class net.sf.basedb.core.data.BioPlateEventData
Get the kit used in this event.
getKit() - Method in class net.sf.basedb.core.data.DerivedBioAssayData
Get the kit used to create this bioassay set.
getKit() - Method in class net.sf.basedb.core.DerivedBioAssay
Get the Kit that was used when creating this bioassay.
getLabel() - Method in class net.sf.basedb.core.data.ParameterValueData
Get the label of the parameter.
getLabel() - Method in class net.sf.basedb.core.ParameterInfo
 
getLabel() - Method in class net.sf.basedb.core.PluginParameter
Get the label of the parameter.
getLastAccess() - Method in class net.sf.basedb.core.SessionControl
Get the time this object last was accessed.
getLastColumn() - Method in class net.sf.basedb.util.excel.XlsxToCsvUtil.SheetInfo
Get the column number for the last column that contains data.
getLastError() - Method in class net.sf.basedb.util.extensions.Registry.RegisteredExtension
 
getLastError() - Method in class net.sf.basedb.util.extensions.Registry.RegisteredExtensionPoint
 
getLastExtensionError(String) - Method in class net.sf.basedb.clients.web.extensions.ExtensionsControl
Get information about the last error that happened when rendering an extension.
getLastExtensionError(String) - Method in class net.sf.basedb.util.extensions.Registry
Get information about the last error that happened when rendering an extension.
getLastExtensionPointError(String) - Method in class net.sf.basedb.clients.web.extensions.ExtensionsControl
Get information about the last error that happened when rendering an extension point.
getLastExtensionPointError(String) - Method in class net.sf.basedb.util.extensions.Registry
Get information about the last error that happened when rendering an extension point.
getLastGuiContext() - Method in class net.sf.basedb.core.Job
Get the gui-context that was active when this job was created.
getLastModified() - Method in class net.sf.basedb.util.uri.UriMetadata
Get the date and time the resource was last modified.
getLastModified(HttpResponse) - Static method in class net.sf.basedb.util.HttpUtil
Get the date the content was last modified from the headers in the response.
getLastProcessResults() - Method in class net.sf.basedb.util.extensions.manager.ExtensionsManager
Get the results of the last processing.
getLastRemoteId() - Method in class net.sf.basedb.core.data.UserDeviceData
Get the remote id (=ip address) of the last login from this device.
getLastRemoteId() - Method in class net.sf.basedb.core.UserDevice
Get the remote ID of the host the user used for this device the last time.
getLastRow() - Method in class net.sf.basedb.util.excel.XlsxToCsvUtil.SheetInfo
Get the row number for the last row that contains data.
getLastScanResults() - Method in class net.sf.basedb.clients.web.extensions.ExtensionsControl
Get the results of the last scan (manual or automatic).
getLastSource() - Method in class net.sf.basedb.core.data.ReporterData
Get the source that was used when this reporter was last updated.
getLastSyncMatchingSource() - Method in class net.sf.basedb.core.SyncFilter
Get the number of source items that matched this particular filter during the last synchronization.
getLastSyncMatchingTransformed() - Method in class net.sf.basedb.core.SyncFilter
Get the number of transformed items that matched this particular filter during the last synchronization.
getLastSyncProperties() - Method in class net.sf.basedb.core.data.ItemListSyncFilterData
A string representation of properties that was affecting that last filter during the last sync.
getLastUpdate() - Method in class net.sf.basedb.core.Annotation
Get the date and time the values in this annotation was last updated.
getLastUpdate() - Method in class net.sf.basedb.core.data.AnnotationData
Get the date and time the values in this annotation was last updated.
getLastUpdate() - Method in class net.sf.basedb.core.data.FileData
Get the date and time the actual file data was last updated.
getLastUpdate() - Method in class net.sf.basedb.core.data.ReporterData
Get the date and time the information about this reporter last was updated.
getLastUpdate() - Method in class net.sf.basedb.core.File
Get the date and time the actual file data was last updated.
getLastUpdated() - Method in class net.sf.basedb.clients.jobagent.slotmanager.MasterSlotManager.RemoteSlot
 
getLastUsed() - Method in class net.sf.basedb.core.data.UserDeviceData
Get the date and time the user last logged in from this device.
getLastUsed() - Method in class net.sf.basedb.core.UserDevice
Get the date and time the user last used this device.
getLatitude() - Method in class net.sf.basedb.util.GeoLocation
 
getLayerNo() - Method in class net.sf.basedb.core.data.DataCubeLayerData
The layer number of this layer in the data cube.
getLayerNo() - Method in class net.sf.basedb.core.DataCubeLayer
Get the number of this layer.
getLayers() - Method in class net.sf.basedb.core.data.DataCubeData
This is the inverse end.
getLeftTableAlias(Query) - Method in class net.sf.basedb.core.RealJoin
 
getLeftTableColumn() - Method in class net.sf.basedb.core.RealJoin
 
getLength() - Method in class net.sf.basedb.core.data.ReporterClonePropertyData
The maximum length of string value types.
getLength() - Method in class net.sf.basedb.core.ExtendedProperty
Get the maximum allowed length of the property value.
getLength() - Method in class net.sf.basedb.core.plugin.ImportInputStream
Get the length of the stream in number of bytes.
getLength() - Method in class net.sf.basedb.util.FileImportInputStream
Calls File.getSize() to get the file size.
getLength() - Method in class net.sf.basedb.util.uri.UriMetadata
Get the length in bytes of the resource.
getLevel() - Method in class net.sf.basedb.util.extensions.logging.LogEntry
The level of the log entry.
getLimit() - Method in class net.sf.basedb.core.signal.ProgressReporterSignalHandler
Get the percentage limit where signal checking becomes disabled.
getLimitHandler() - Method in class net.sf.basedb.core.AbstractSqlQuery
Get a handler for adding LIMIT and OFFSET parameters to an SQL statement.
getLine(int) - Method in class net.sf.basedb.util.parser.FlatFileParser
Get the line with the specified number.
getLineCount() - Method in class net.sf.basedb.util.bfs.MetadataWriter
Get the number of lines that has been written to this file so far, including all comment lines, empty lines, sections headers, etc.
getLineCount() - Method in class net.sf.basedb.util.parser.FlatFileParser
Get the number of lines that the FlatFileParser.parseHeaders() method parsed.
getLines() - Method in class net.sf.basedb.util.parser.FlatFileParser
Get the lines read by FlatFileParser.parseHeaders().
getLink(String, String, Item, int, boolean) - Static method in class net.sf.basedb.clients.web.Base
 
getLink(String, String, Item, int, boolean, String) - Static method in class net.sf.basedb.clients.web.Base
 
getLink(String, Nameable, Integer, boolean, boolean, boolean, boolean) - Static method in class net.sf.basedb.clients.web.ChangeHistoryUtil
 
getLink(S) - Method in class net.sf.basedb.core.AnyToAny.FastLinkLoader
Get the any-to-any link.
getLinkedFile(String, File, boolean, boolean, boolean, String) - Static method in class net.sf.basedb.clients.web.Base
 
getLinkedItem(DbControl, BasicItem) - Method in class net.sf.basedb.clients.web.plugins.AnyToAnyDataLoader
Get the item that is linked to by this any-to-any link definition.
getLinkedName(String, Nameable, boolean, boolean) - Static method in class net.sf.basedb.clients.web.Base
 
getLinkName() - Method in class net.sf.basedb.core.AnyToAny.FastLinkLoader
The link name.
getLinkName() - Method in class net.sf.basedb.util.AnyToAnyLinkStatistics
Get the name of the link.
getLinksFrom(BasicItem) - Static method in class net.sf.basedb.core.AnyToAny
Get a query that returns all links linking from the specified item.
getLinksTo(BasicItem) - Static method in class net.sf.basedb.core.AnyToAny
Get a query that returns all links linking to the specified item.
getList() - Method in class net.sf.basedb.clients.web.taglib.table.CellValue
 
getListableItems() - Static method in class net.sf.basedb.core.Metadata
Get a set containing all Listable item types.
getListableItems(Item, SyncFilter.SourceItemTransform) - Static method in class net.sf.basedb.util.listable.ListableUtil
Get all item types that can have the specified relation to the with the given item type.
getListMemberType() - Method in class net.sf.basedb.core.SyncFilter
 
getLobHelper() - Method in class net.sf.basedb.core.hibernate.SessionWrapper
 
getLocale() - Static method in class net.sf.basedb.core.Config
Get the default locale configured for the server.
getLocale() - Method in class net.sf.basedb.core.SessionControl
Get the locale that is curently assigned to this session control.
getLocale() - Method in class net.sf.basedb.util.resources.ResourceBundleWrapper
Get the actual locale used by the bundle, which may be a different locale from the one that was used to load it.
getLocalHost() - Static method in class net.sf.basedb.util.SocketUtil
Get the local address of the local host.
getLocalSignalHandlerId(SignalHandler) - Method in class net.sf.basedb.core.signal.AbstractSignalReceiver
Get the local signal handler id of the given signal handler.
getLocation() - Method in class net.sf.basedb.core.data.DiskUsageData
Get the location of the DiskConsumable item.
getLocation() - Method in class net.sf.basedb.core.data.FileData
Get the Location of this FileData
getLocation() - Method in class net.sf.basedb.core.data.QuotaIndex
 
getLocation() - Method in class net.sf.basedb.core.data.SessionData
Get the location of the user (if known).
getLocation() - Method in class net.sf.basedb.core.data.UserDeviceData
Get the location of the user (if known).
getLocation() - Method in interface net.sf.basedb.core.DiskConsumable
Get the Location the items is stored at.
getLocation() - Method in class net.sf.basedb.core.DiskUsage
Get the location of the DiskConsumable item.
getLocation() - Method in class net.sf.basedb.core.Experiment
getLocation() - Method in class net.sf.basedb.core.File
 
getLocation() - Method in class net.sf.basedb.core.RawBioAssay
getLocation() - Method in class net.sf.basedb.core.Session
Get the location of the host the user used for this session.
getLocation() - Method in class net.sf.basedb.core.UserDevice
Get the last known location of the device.
getLocation(AuthenticationMethod) - Method in class net.sf.basedb.core.SessionControl
 
getLocationFromIp(String) - Static method in class net.sf.basedb.util.GeoLocation
Try to convert the given ip address to a location.
getLocationLatitude() - Method in class net.sf.basedb.core.data.SessionData
Get the location latitude of the user (if known).
getLocationLatitude() - Method in class net.sf.basedb.core.data.UserDeviceData
Get the location latitude of the user (if known).
getLocationLatitude() - Method in class net.sf.basedb.core.Session
Get the location latitude of the host the user used for this session.
getLocationLatitude() - Method in class net.sf.basedb.core.UserDevice
Get the last known location latitude of the device.
getLocationLongitude() - Method in class net.sf.basedb.core.data.SessionData
Get the location longitude of the user (if known).
getLocationLongitude() - Method in class net.sf.basedb.core.data.UserDeviceData
Get the location longitude of the user (if known).
getLocationLongitude() - Method in class net.sf.basedb.core.Session
Get the location longitude of the host the user used for this session.
getLocationLongitude() - Method in class net.sf.basedb.core.UserDevice
Get the last known location longitude of the device.
getLockMode() - Method in class net.sf.basedb.core.BioPlateType
Get the lock mode for wells located on plates of this plate type.
getLockMode() - Method in class net.sf.basedb.core.BioWell
Get the lock mode of this well.
getLockMode() - Method in class net.sf.basedb.core.data.BioPlateTypeData
A flag indicating if plates with this type have locked wells or not. 0 = not locked; 1 = locked-after-move; 2 = locked-after-add; 3=locked-after-create
getLockMode() - Method in class net.sf.basedb.core.hibernate.QueryWrapper
 
getLockMode(Object) - Method in class net.sf.basedb.core.hibernate.SessionWrapper
 
getLockOptions() - Method in class net.sf.basedb.core.hibernate.QueryWrapper
 
getLog(String, boolean) - Static method in class net.sf.basedb.util.extensions.logging.ExtensionsLog
Get the service log for the given extension.
getLogChangeType() - Method in enum class net.sf.basedb.core.AnnotationBatcher.Change
 
getLogControl() - Method in class net.sf.basedb.core.DbControl
Get the log controller for this db control.
getLogControl() - Method in class net.sf.basedb.core.log.db.DbLogManager
 
getLogControl() - Method in interface net.sf.basedb.core.log.LogManager
Get the log controller that is used in this transaction.
getLogEntries() - Method in class net.sf.basedb.util.extensions.logging.ExtensionsLog
Get an iterator that is returning all entries in the log.
getLoggedInUserId() - Method in class net.sf.basedb.core.SessionControl
Get the id of the logged in user, or 0 if no user is logged in.
getLoggedInUserLogin() - Method in class net.sf.basedb.core.SessionControl
Get the login name of the currently logged in user.
getLoggedInUserName() - Method in class net.sf.basedb.core.SessionControl
Get the name of the currently logged in user.
getLogger() - Static method in class net.sf.basedb.core.Application
Get the BASE core logger.
getLogger(String, boolean) - Static method in class net.sf.basedb.util.extensions.logging.ExtensionsLog
Get a logger that can add entries to the log for the given extension.
getLoggingInterceptor() - Method in class net.sf.basedb.core.DbControl
Get the logging interceptor for this db control.
getLogin() - Method in class net.sf.basedb.clients.jobagent.Agent
Get the agent.user configuration value.
getLogin() - Method in class net.sf.basedb.core.authentication.AuthenticatedUser
Get the login string for the user.
getLogin() - Method in class net.sf.basedb.core.authentication.LoginRequest
Get the login name to use.
getLogin() - Method in class net.sf.basedb.core.data.UserData
Get the login for the user account.
getLogin() - Method in class net.sf.basedb.core.User
Get the login for the user account.
getLoginComment() - Method in class net.sf.basedb.core.data.SessionData
Get the login comment.
getLoginComment() - Method in class net.sf.basedb.core.Session
Get the login comment.
getLoginField() - Method in interface net.sf.basedb.clients.web.extensions.login.LoginFormAction
Get attributes for the login field on the form.
getLoginField() - Method in class net.sf.basedb.clients.web.extensions.login.LoginFormBean
 
getLoginField() - Method in class net.sf.basedb.clients.web.extensions.login.PasswordLoginFormFactory
 
getLogInfo() - Method in class net.sf.basedb.core.log.ManualLogEntry
Get information about the log entry.
getLoginRequest() - Method in class net.sf.basedb.core.AuthenticationContext
Get the login request information.
getLoginTime() - Method in class net.sf.basedb.core.data.SessionData
Get the date and time the user logged in.
getLoginTime() - Method in class net.sf.basedb.core.Session
Get the date and time the user logged in.
getLogManager(LogControl) - Method in class net.sf.basedb.core.log.db.DbLogManagerFactory
Creates a new DbLogManager.
getLogManager(LogControl) - Method in interface net.sf.basedb.core.log.LogManagerFactory
Get/create a log manager to log events in a given transaction.
getLogoutTime() - Method in class net.sf.basedb.core.data.SessionData
Get the date and time the user logged out.
getLogoutTime() - Method in class net.sf.basedb.core.Session
Get the date and time the user logged out.
getLong(int, NumberFormat, boolean) - Method in class net.sf.basedb.util.parser.FlatFileParser.Data
Get the value as a long.
getLong(int, NumberFormat, boolean) - Method in class net.sf.basedb.util.parser.FlatFileParser.ExcelData
 
getLong(String) - Static method in class net.sf.basedb.util.Values
Convert a string to a long.
getLong(String[]) - Static method in class net.sf.basedb.util.Values
Convert an array of strings to an array of Long:s.
getLong(String, long) - Static method in class net.sf.basedb.core.Config
Get the configuration setting specified by key as a long value.
getLong(String, long) - Static method in class net.sf.basedb.util.Values
Convert a string to an long.
getLong(String, Long) - Static method in class net.sf.basedb.util.Values
Convert a string to an long.
getLong(FlatFileParser.Data) - Method in class net.sf.basedb.util.parser.ColumnMapper
 
getLong(FlatFileParser.Data) - Method in class net.sf.basedb.util.parser.CompoundMapper
 
getLong(FlatFileParser.Data) - Method in class net.sf.basedb.util.parser.ConstantMapper
 
getLong(FlatFileParser.Data) - Method in class net.sf.basedb.util.parser.CropStringMapper
 
getLong(FlatFileParser.Data) - Method in class net.sf.basedb.util.parser.JepMapper
 
getLong(FlatFileParser.Data) - Method in interface net.sf.basedb.util.parser.Mapper
Get the value for the line of data as a long.
getLong(FlatFileParser.Data) - Method in class net.sf.basedb.util.parser.NullIfExceptionMapper
 
getLong(HttpResponse, String, Long) - Static method in class net.sf.basedb.util.HttpUtil
 
getLongFormatter(SessionControl) - Static method in class net.sf.basedb.clients.web.formatter.FormatterFactory
Get the logged in user's formatter for long numbers.
getLongitude() - Method in class net.sf.basedb.util.GeoLocation
 
getLongOption(String, Long) - Method in class net.sf.basedb.core.AnnotationType
Get an option and convert the value to a long.
getLongValues() - Method in class net.sf.basedb.core.data.annotations.AnnotationLink
 
getLowerLimit() - Method in class net.sf.basedb.core.DoubleParameterType
Get the lowst valid value of the parameter.
getLowerLimit() - Method in class net.sf.basedb.core.FloatParameterType
Get the lowst valid value of the parameter.
getLowerLimit() - Method in class net.sf.basedb.core.IntegerParameterType
Get the lowest valid value of the parameter.
getLowerLimit() - Method in class net.sf.basedb.core.LongParameterType
Get the lowest valid value of the parameter.
getMACalculator() - Method in enum class net.sf.basedb.core.IntensityTransform
Get a MA calculator implementation that is suitable for calculating MA-values for the given source data type.
getMainContext(Item) - Method in class net.sf.basedb.clients.web.ModeInfo
Get a main context for this mode.
getMainHqlQuery(DbControl, Class<R>) - Method in class net.sf.basedb.core.AbstractHqlQuery
Build the main query and set parameter values for it.
getMainItemType() - Method in class net.sf.basedb.core.ItemSubtype
Get the main item type that the subtype belongs to.
getMainQuery(DbControl, boolean) - Method in class net.sf.basedb.core.AbstractQuery
Build the main query string.
getMaintenance() - Static method in class net.sf.basedb.core.Version
Get the maintentance version.
getMaintenanceVersion() - Static method in class net.sf.basedb.core.Application
Get the maintenance version.
getMainType() - Method in class net.sf.basedb.clients.web.plugins.SimpleExport
 
getMainType() - Method in class net.sf.basedb.core.data.PluginDefinitionData
Get the main type of plugin.
getMainType() - Method in class net.sf.basedb.core.plugin.AbstractAnalysisPlugin
 
getMainType() - Method in class net.sf.basedb.core.plugin.AbstractExporterPlugin
 
getMainType() - Method in interface net.sf.basedb.core.plugin.Plugin
Get the type of the plugin.
getMainType() - Method in class net.sf.basedb.core.PluginDefinition
Get the type of plugin.
getMainType() - Method in class net.sf.basedb.plugins.AbstractFlatFileImporter
getMainType() - Method in class net.sf.basedb.plugins.BfsExporterPlugin
 
getMainType() - Method in class net.sf.basedb.plugins.CdfFileReporterImporter
 
getMainType() - Method in class net.sf.basedb.plugins.CloneReportersPlugin
 
getMainType() - Method in class net.sf.basedb.plugins.executor.BaseFileExporterSupport
 
getMainType() - Method in class net.sf.basedb.plugins.executor.BaseFileImporterSupport
 
getMainType() - Method in class net.sf.basedb.plugins.executor.BfsExporterSupport
 
getMainType() - Method in class net.sf.basedb.plugins.executor.BfsImporterSupport
 
getMainType() - Method in class net.sf.basedb.plugins.executor.FileOnlyImporterSupport
 
getMainType() - Method in class net.sf.basedb.plugins.HelpImporter
 
getMainType() - Method in class net.sf.basedb.plugins.IntensityCalculatorPlugin
Returns the main plugin type this plugin belongs to.
getMainType() - Method in class net.sf.basedb.plugins.PluginConfigurationImporter
 
getMainType() - Method in class net.sf.basedb.util.zip.AbstractFileUnpacker
 
getMajor() - Static method in class net.sf.basedb.core.Version
Get the major version.
getMajorVersion() - Static method in class net.sf.basedb.core.Application
Get the major version.
getManualConfigureParameters() - Method in class net.sf.basedb.plugins.Base1PluginExecuter
Creates the information needed for manual configuration and initiates the parameters.
getMapper(String) - Method in class net.sf.basedb.util.parser.FlatFileParser
Get a mapper using the default number format.
getMapper(String, boolean) - Method in class net.sf.basedb.util.parser.FlatFileParser
Get a mapper using the default number format.
getMapper(String, NumberFormat) - Method in class net.sf.basedb.util.parser.FlatFileParser
Get a mapper using a specific number format.
getMapper(String, NumberFormat, boolean) - Method in class net.sf.basedb.util.parser.FlatFileParser
 
getMapper(String, NumberFormat, boolean, JepFunction...) - Method in class net.sf.basedb.util.parser.FlatFileParser
 
getMapper(String, NumberFormat, Formatter<Date>, boolean, JepFunction...) - Method in class net.sf.basedb.util.parser.FlatFileParser
Create a mapper object that maps an expression string to a value.
getMapper(String, Formatter<Date>, boolean) - Method in class net.sf.basedb.util.parser.FlatFileParser
Get a mapper using the specified date format.
getMapper(String, JepFunction...) - Method in class net.sf.basedb.util.parser.FlatFileParser
 
getMapper(FlatFileParser, String, Integer, Mapper) - Method in class net.sf.basedb.plugins.AbstractFlatFileImporter
 
getMapper(FlatFileParser, String, Integer, Mapper, JepFunction...) - Method in class net.sf.basedb.plugins.AbstractFlatFileImporter
Get a mapper for the specified flat file parser.
getMapping() - Static method in class net.sf.basedb.core.HibernateUtil
 
getMappingBatcher() - Method in class net.sf.basedb.core.BioAssaySet
Get a batcher used to insert mappings to raw data.
getMappingBatcher() - Method in class net.sf.basedb.core.DataCube
 
getMappings() - Method in class net.sf.basedb.core.data.VirtualDbData
The number of cube mappings in the virtual database.
getMappings() - Method in class net.sf.basedb.core.VirtualDb
Get the number of DataCubeMapping:s in this virtual database.
getMasterReporterJoiner(JoinType) - Static method in class net.sf.basedb.core.DynamicReporterQuery
Get a joiner instance for joining the master reporter table when the root query is against the cloned reporters table.
getMatching(DbControl) - Method in class net.sf.basedb.core.SyncFilter
 
getMatchingReporters(DbControl) - Method in class net.sf.basedb.clients.web.ExperimentExplorer
Get the number of reporters matching the current reporter filter.
getMatchingSource() - Method in class net.sf.basedb.core.data.ItemListSyncFilterData
The number of matching source items during that last sync.
getMatchingTransformed() - Method in class net.sf.basedb.core.data.ItemListSyncFilterData
The number of matching items after the transform during that last sync.
getMax() - Method in class net.sf.basedb.util.plot.HistogramPlot.HistogramBin
Get the maximum of all values in this bin.
getMaxAge() - Method in class net.sf.basedb.core.DiskUsageStatistics
Get the max age in seconds for a disk usage summary object before it is reloaded from the database again.
getMaxBaseVersion() - Method in interface net.sf.basedb.core.plugin.About
Get the maximum BASE version were to plug-in no longer is expected to work.
getMaxBaseVersion() - Method in class net.sf.basedb.core.plugin.AboutImpl
 
getMaxBaseVersion() - Method in class net.sf.basedb.util.extensions.AboutBean
 
getMaxBaseVersion() - Method in class net.sf.basedb.util.extensions.Registry.RegisteredAbout
 
getMaxBytes() - Method in class net.sf.basedb.core.data.QuotaIndex
 
getMaxEntries() - Method in class net.sf.basedb.util.extensions.logging.ExtensionsLog
Get the max number of entries to keep in the log.
getMaxLength() - Method in class net.sf.basedb.core.AnnotationType
Get the maximum allowed string length for a Type.STRING annotation.
getMaxLength() - Method in class net.sf.basedb.core.StringParameterType
Get the max length of the parameter.
getMaxMemory() - Method in class net.sf.basedb.core.data.JobAgentSettingsData
The max amount of memory the plugin can use.
getMaxMemory() - Method in class net.sf.basedb.core.data.PluginDefinitionData
The max amount of memory the plugin can use.
getMaxMemory() - Method in class net.sf.basedb.core.JobAgentSettings
Get the maximum amount of memory the plugin is allowed to use.
getMaxMemory() - Method in class net.sf.basedb.core.PluginDefinition
Get the maximum amount of memory the plugins is allowed to use.
getMaxParametersInQuery() - Method in class net.sf.basedb.core.dbengine.AbstractDbEngine
Returns 10000.
getMaxParametersInQuery() - Method in interface net.sf.basedb.core.dbengine.DbEngine
Get the maximum number of parameters that can be used in a prepared statement for a query.
getMaxProjectPermission() - Method in class net.sf.basedb.core.Keyring
Get the max project permission within the currently active project.
getMaxRandomSamples() - Method in class net.sf.basedb.util.AnyToAnyLinkStatistics.Options
 
getMaxRawMappingsForSpot() - Method in class net.sf.basedb.core.BioAssaySet
Get the number of mappings to raw data spots for the spot with the most number of mappings.
getMaxRawMappingsForSpot() - Method in class net.sf.basedb.core.data.DataCubeData
The maximum number of raw data spots a single spot in this data cube is mapped to.
getMaxRawMappingsForSpot() - Method in class net.sf.basedb.core.DataCube
Get the number of mappings to raw data spots for the spot with the most number of mappings.
getMaxRecent(SessionControl) - Static method in class net.sf.basedb.clients.web.Base
Get the setting for the maximum number of recently used items to save.
getMaxResults() - Method in class net.sf.basedb.core.AbstractQuery
 
getMaxResults() - Method in class net.sf.basedb.core.hibernate.QueryWrapper
 
getMaxResults() - Method in interface net.sf.basedb.core.query.Query
The maximum number of rows returned by the query.
getMaxUrlLength() - Method in class net.sf.basedb.clients.web.taglib.Page
 
getMaxValue() - Method in class net.sf.basedb.core.Coloring
Get the value that represents the maximum value.
getMaxValue() - Method in class net.sf.basedb.core.data.ColoringData
The value for the ax endpoint color.
getMaxValueDouble() - Method in class net.sf.basedb.core.AnnotationType
Get the maximum allowed value for a Type.FLOAT or Type.DOUBLE annotation.
getMaxValueLong() - Method in class net.sf.basedb.core.AnnotationType
Get the maximum allowed value for an Type.INT or Type.LONG annotation.
getMaxY(int) - Method in class net.sf.basedb.util.plot.HistogramPlot.HistogramSeries
 
getMaxY(HistogramPlot.HistogramBin) - Method in enum class net.sf.basedb.util.plot.HistogramPlot.YAggregate
 
getMaybeGranted() - Method in class net.sf.basedb.core.plugin.Permissions
Get the permissions that the plugin should be granted only if the logged in user already have the permissions.
getMd5() - Method in class net.sf.basedb.core.data.FileData
Get the MD5 hash of the file contents.
getMd5() - Method in class net.sf.basedb.core.data.ItemListSyncFilterData
Get the MD5 hash of the concatenated ID values.
getMd5() - Method in class net.sf.basedb.core.File
Get the MD5 hash of the file contents, or null if not known.
getMd5() - Method in class net.sf.basedb.util.uri.UriMetadata
Get the MD5 checksum of the resource.
getMd5AtLastSync() - Method in class net.sf.basedb.core.data.ItemListData
Get the MD5 hash of the concatenated ID values from the last sync.
getMean() - Method in class net.sf.basedb.util.plot.HistogramPlot.HistogramBin
Get the mean of all values in this bin.
getMean(int) - Method in class net.sf.basedb.clients.web.ExperimentExplorer.AnnotationGroup
Get the mean of the intensity values for the given channel.
getMember() - Method in class net.sf.basedb.clients.web.extensions.fileviewer.FileViewerContext
Get the current file set member information for the file.
getMember() - Method in class net.sf.basedb.core.ExtendedPropertyAccessor.GetterSetter
Always return null.
getMember() - Method in class net.sf.basedb.util.fileset.ValidatingFileSetMember
Get the file set member that this proxy represents.
getMember(DataFileType) - Method in class net.sf.basedb.core.FileSet
Get the member of the given type assuming that there is only a single member of that type.
getMemberRestriction() - Method in class net.sf.basedb.core.ItemList
Get a restriction that mathces members in this list.
getMembers() - Method in class net.sf.basedb.core.data.FileSetData
The members of this file set.
getMembers() - Method in class net.sf.basedb.core.data.ItemListData
Get the set that manages which items that are part of this list.
getMembers() - Method in class net.sf.basedb.core.FileSet
Get the members of this file set.
getMembers() - Method in class net.sf.basedb.core.ItemList
Get a query that returns all items that are members of this list.
getMembers(String) - Method in class net.sf.basedb.core.FileSet
Get a query that returns all members in a file set with a specific generic ItemSubtype.
getMembers(DataFileType) - Method in class net.sf.basedb.core.FileSet
Get a query that returns all members in a file set with a specific DataFileType.
getMemberType() - Method in class net.sf.basedb.core.data.ItemListData
Get the type of items this list can hold.
getMemberType() - Method in class net.sf.basedb.core.ItemList
Get the item type of members on this list.
getMemberTypes() - Method in class net.sf.basedb.core.FileSet
Get a query that return the DataFileType for all members of this file set.
getMenu() - Method in class net.sf.basedb.clients.web.taglib.Page
 
getMenuId() - Method in class net.sf.basedb.clients.web.extensions.menu.FixedMenuItemFactory
 
getMenuId() - Method in interface net.sf.basedb.clients.web.extensions.menu.MenuItemAction
The ID of the menu where this menu item belongs, or null if it belongs to the top-level menu.
getMenuId() - Method in class net.sf.basedb.clients.web.extensions.menu.MenuItemBean
 
getMessage() - Method in class net.sf.basedb.core.ItemContext
Get a message that should be displayed by a client application as soon as it is appropriate to do so.
getMessage() - Method in class net.sf.basedb.core.PluginResponse
Get the return message from the plugin.
getMessage() - Method in class net.sf.basedb.core.SimpleProgressReporter
Get the last progress message this progress reporter should display.
getMessage() - Method in class net.sf.basedb.plugins.executor.ExternalProgramExecutor.ResponseWrapper
 
getMessage() - Method in class net.sf.basedb.util.extensions.logging.LogEntry
Get the log message.
getMessage() - Method in class net.sf.basedb.util.fileset.ValidatingFileSetMember
Get the error message if the file failed validation.
getMessage() - Method in class net.sf.basedb.util.overview.Failure
Get a message explaining the failure.
getMessage() - Method in class net.sf.basedb.util.overview.Fix
Get a message explaining what needs to be fixed.
getMessage(String) - Method in class net.sf.basedb.plugins.executor.ExternalProgramExecutor.ResponseWrapper
 
getMessages() - Method in class net.sf.basedb.core.data.JobData
This is the inverse end.
getMessages() - Method in class net.sf.basedb.core.data.UserData
This is the inverse end.
getMessages() - Method in class net.sf.basedb.core.User
Get a query that returns all messages for the user.
getMessages() - Method in class net.sf.basedb.util.extensions.manager.ProcessResults.FileResults
A list of detailed messages, indicating the results of individual operation on this file.
getMetaColumn() - Method in class net.sf.basedb.core.FeatureCoordinate
 
getMetadata() - Method in interface net.sf.basedb.util.uri.ConnectionManager
Get metadata about the resource.
getMetadata() - Method in class net.sf.basedb.util.uri.http.HttpConnectionManager
 
getMetadata(ObjectKey<M>) - Method in class net.sf.basedb.util.extensions.manager.ExtensionsFile
Get metadata registered for a given given key.
getMetadataKeysOfClass(Class<T>) - Method in class net.sf.basedb.util.extensions.manager.ExtensionsFile
Get a list of all metadata defined in this extensions file that are keyed with the specified class or interface.
getMetadataParser() - Method in class net.sf.basedb.util.importer.spotdata.BfsImporter
 
getMetadataPrefix() - Method in class net.sf.basedb.util.basefile.BaseFileWriter
The metadata prefix is written to the beginning of each line that is not a data line.
getMetadataSources() - Method in class net.sf.basedb.core.ServiceSessionControl.SessionFactoryConfiguration
Get an object for registering mapped entity classes.
getMetadataWriter() - Method in class net.sf.basedb.util.export.spotdata.BfsExporter
Get the writer were metadata should be printed.
getMetaGridX() - Method in class net.sf.basedb.core.ArrayDesignBlock
Get the column coordinate of this block.
getMetaGridX() - Method in class net.sf.basedb.core.BlockInfo
Get the row or x meta coordinate.
getMetaGridX() - Method in class net.sf.basedb.core.data.ArrayDesignBlockData
Get the row coordinate of this block.
getMetaGridX() - Method in class net.sf.basedb.core.data.RawData
 
getMetaGridX() - Method in class net.sf.basedb.plugins.PrintMapFlatFileImporter.MetaBlock
 
getMetaGridY() - Method in class net.sf.basedb.core.ArrayDesignBlock
Get the row coordinate of this block.
getMetaGridY() - Method in class net.sf.basedb.core.BlockInfo
Get the column or y meta coordinate.
getMetaGridY() - Method in class net.sf.basedb.core.data.ArrayDesignBlockData
Get the column coordinate of this block.
getMetaGridY() - Method in class net.sf.basedb.core.data.RawData
 
getMetaGridY() - Method in class net.sf.basedb.plugins.PrintMapFlatFileImporter.MetaBlock
 
getMetamodel() - Method in class net.sf.basedb.core.hibernate.SessionWrapper
 
getMetaRow() - Method in class net.sf.basedb.core.FeatureCoordinate
 
getMethod() - Method in class net.sf.basedb.core.authentication.AuthenticationMethod
Get the name of the authentication method.
getMethod() - Method in class net.sf.basedb.core.ExtendedPropertyAccessor.GetterSetter
Always return null.
getMethod() - Method in class net.sf.basedb.plugins.batchimport.AnnotationIdMethod
 
getMethod() - Method in class net.sf.basedb.plugins.batchimport.FallbackIdMethod
 
getMethod() - Method in class net.sf.basedb.plugins.batchimport.FileImporter.PathIdMethod
 
getMethod() - Method in interface net.sf.basedb.plugins.batchimport.IdMethod
The name of this method, which should be unique among the methods that can be used at a given time.
getMethod() - Method in class net.sf.basedb.plugins.batchimport.InternalIdMethod
 
getMethod() - Method in class net.sf.basedb.plugins.batchimport.MultiPropertyIdMethod
 
getMethod() - Method in class net.sf.basedb.plugins.batchimport.PropertyIdMethod
 
getMethod(Class<?>, String, Class<?>) - Method in class net.sf.basedb.util.extensions.debug.BeanActionFactory
Get a method with a specific name with optionally, takes a single parameter of given type.
getMethodName() - Method in class net.sf.basedb.core.ExtendedPropertyAccessor.GetterSetter
Always return null.
getMethodName(String, String) - Method in class net.sf.basedb.util.extensions.debug.BeanActionFactory
Convert the parameter name to a method name.
getMiameAnnotationTypes(DbControl, OverviewContext, Item) - Static method in class net.sf.basedb.util.overview.OverviewUtil
Get all annotation types that has been marked as "Required for MIAME".
getMidValue() - Method in class net.sf.basedb.core.Coloring
Get the value that represents the midpoint value.
getMidValue() - Method in class net.sf.basedb.core.data.ColoringData
The value for the midpoint color.
getMillisecondsSinceStart() - Method in class net.sf.basedb.clients.web.fileupload.FileUploadProgress
Get the number of milliseconds since the start of the upload.
getMimeType() - Method in class net.sf.basedb.clients.web.fileupload.UploadedFile
Get the MIME type of the uploaded file.
getMimeType() - Method in interface net.sf.basedb.clients.web.plugins.ExportTemplate
Get the MIME type to assign to files generated by this template.
getMimeType() - Method in class net.sf.basedb.clients.web.plugins.PlainTextTemplate
 
getMimeType() - Method in class net.sf.basedb.clients.web.plugins.XlsxTemplate
 
getMimeType() - Method in class net.sf.basedb.clients.web.plugins.XMLTemplate
 
getMimeType() - Method in class net.sf.basedb.core.data.FileData
Get the mime type of this FileData item.
getMimeType() - Method in class net.sf.basedb.core.File
The mimetype of this File.
getMimeType() - Method in class net.sf.basedb.core.plugin.ImportInputStream
Get the MIME type of the source.
getMimeType() - Method in class net.sf.basedb.util.FileImportInputStream
getMimeType() - Method in class net.sf.basedb.util.uri.UriMetadata
Get the MIME type of the resource.
getMimeType() - Method in class net.sf.basedb.util.zip.Bzip2FilePacker
 
getMimeType() - Method in interface net.sf.basedb.util.zip.FilePacker
Gets the MIME type to give compressed files from this packer
getMimeType() - Method in class net.sf.basedb.util.zip.GzipFilePacker
 
getMimeType() - Method in class net.sf.basedb.util.zip.TarFilePacker
 
getMimeType() - Method in class net.sf.basedb.util.zip.ZipFilePacker
 
getMimeType(DbControl, String, String) - Static method in class net.sf.basedb.core.MimeType
Get the MIME type of a given file name or extension.
getMimeTypes() - Method in class net.sf.basedb.plugins.Bzip2FileUnpacker
Return a set containing the strings [ application/x-bzip2 ].
getMimeTypes() - Method in class net.sf.basedb.plugins.GzipFileUnpacker
Return a set containing the strings [ application/x-gzip ].
getMimeTypes() - Method in class net.sf.basedb.plugins.TarFileUnpacker
Return a set containing the strings [ application/x-tar, application/x-gzip, application/x-bzip2 ].
getMimeTypes() - Method in class net.sf.basedb.plugins.ZipFileUnpacker
Return a set containing the strings [ application/zip, application/java-archive ].
getMimeTypes() - Method in interface net.sf.basedb.util.zip.FileUnpacker
Get the MIME type for the file formats this unpacker supports.
getMin() - Method in class net.sf.basedb.util.plot.HistogramPlot.HistogramBin
Get the minumum of all values in this bin.
getMinBaseVersion() - Method in interface net.sf.basedb.core.plugin.About
Get the minimum BASE version that the plug-in requires.
getMinBaseVersion() - Method in class net.sf.basedb.core.plugin.AboutImpl
 
getMinBaseVersion() - Method in class net.sf.basedb.util.extensions.AboutBean
 
getMinBaseVersion() - Method in class net.sf.basedb.util.extensions.Registry.RegisteredAbout
 
getMinCount() - Method in class net.sf.basedb.util.AnyToAnyLinkStatistics.Options
 
getMinFraction() - Method in class net.sf.basedb.util.AnyToAnyLinkStatistics.Options
 
getMinor() - Static method in class net.sf.basedb.core.Version
Get the minor version.
getMinorVersion() - Static method in class net.sf.basedb.core.Application
Get the minor version.
getMinValue() - Method in class net.sf.basedb.core.Coloring
Get the value that represents the minimum value.
getMinValue() - Method in class net.sf.basedb.core.data.ColoringData
The value for the minimum endpoint color.
getMinValueDouble() - Method in class net.sf.basedb.core.AnnotationType
Get the minumum allowed value for a Type.FLOAT or Type.DOUBLE annotation.
getMinValueLong() - Method in class net.sf.basedb.core.AnnotationType
Get the minumum allowed value for an Type.INT or Type.LONG annotation.
getMinY(int) - Method in class net.sf.basedb.util.plot.HistogramPlot.HistogramSeries
 
getMinY(HistogramPlot.HistogramBin) - Method in enum class net.sf.basedb.util.plot.HistogramPlot.YAggregate
 
getMissingDataFileTypes() - Method in class net.sf.basedb.core.FileSet
Get a query that is returning all file types that have been marked as required by the associated platform but has no member in this file set.
getMissingItemFix(DbControl, Node) - Method in class net.sf.basedb.util.overview.validator.AnnotationValidator
 
getMissingItemFix(DbControl, Node) - Method in class net.sf.basedb.util.overview.validator.AnyToAnyValidator
 
getMissingItemFix(DbControl, Node) - Method in class net.sf.basedb.util.overview.validator.ArrayBatchValidator
The suggested fix is to add an array batch to the slide.
getMissingItemFix(DbControl, Node) - Method in class net.sf.basedb.util.overview.validator.ArrayDesignValidator
The suggested fix is to add an array design to the raw bioassay.
getMissingItemFix(DbControl, Node) - Method in class net.sf.basedb.util.overview.validator.ArraySlideValidator
The suggested fix is to add an array slide to the bioassay.
getMissingItemFix(DbControl, Node) - Method in class net.sf.basedb.util.overview.validator.BasicNodeValidator
Subclasses should override this method if they have a suggessted fix for a missing item problem.
getMissingItemFix(DbControl, Node) - Method in class net.sf.basedb.util.overview.validator.BioPlateValidator
 
getMissingItemFix(DbControl, Node) - Method in class net.sf.basedb.util.overview.validator.BioSourceValidator
 
getMissingItemFix(DbControl, Node) - Method in class net.sf.basedb.util.overview.validator.DataFileValidator
 
getMissingItemFix(DbControl, Node) - Method in class net.sf.basedb.util.overview.validator.DerivedBioAssayValidator
 
getMissingItemFix(DbControl, Node) - Method in class net.sf.basedb.util.overview.validator.ExperimentalFactorValidator
 
getMissingItemFix(DbControl, Node) - Method in class net.sf.basedb.util.overview.validator.ExperimentValidator
 
getMissingItemFix(DbControl, Node) - Method in class net.sf.basedb.util.overview.validator.ExtractValidator
The suggested fix is to add parent extracts to the physical bioassay or one or more extracts to the pooled extract.
getMissingItemFix(DbControl, Node) - Method in class net.sf.basedb.util.overview.validator.FileValidator
 
getMissingItemFix(DbControl, Node) - Method in class net.sf.basedb.util.overview.validator.HardwareValidator
 
getMissingItemFix(DbControl, Node) - Method in class net.sf.basedb.util.overview.validator.KitValidator
 
getMissingItemFix(DbControl, Node) - Method in class net.sf.basedb.util.overview.validator.PhysicalBioAssayValidator
 
getMissingItemFix(DbControl, Node) - Method in class net.sf.basedb.util.overview.validator.PlatformValidator
 
getMissingItemFix(DbControl, Node) - Method in class net.sf.basedb.util.overview.validator.ProtocolParameterValidator
 
getMissingItemFix(DbControl, Node) - Method in class net.sf.basedb.util.overview.validator.ProtocolValidator
 
getMissingItemFix(DbControl, Node) - Method in class net.sf.basedb.util.overview.validator.RawBioAssayValidator
 
getMissingItemFix(DbControl, Node) - Method in class net.sf.basedb.util.overview.validator.SampleValidator
The suggested fix is to add a parent sample to the extract or one or more samples to the pooled sample.
getMissingItemFix(DbControl, Node) - Method in class net.sf.basedb.util.overview.validator.SoftwareValidator
 
getMissingItemFix(DbControl, Node) - Method in class net.sf.basedb.util.overview.validator.TagValidator
 
getMissingNodeName(Node) - Method in class net.sf.basedb.util.overview.node.AnnotationNameGenerator
 
getMissingNodeName(Node) - Method in class net.sf.basedb.util.overview.node.AnyToAnyNameGenerator
 
getMissingNodeName(Node) - Method in class net.sf.basedb.util.overview.node.BioWellNameGenerator
 
getMissingNodeName(Node) - Method in class net.sf.basedb.util.overview.node.FileSetMemberNameGenerator
 
getMissingNodeName(Node) - Method in class net.sf.basedb.util.overview.node.ItemListMemberNameGenerator
 
getMissingNodeName(Node) - Method in class net.sf.basedb.util.overview.node.NameableNameGenerator
 
getMissingNodeName(Node) - Method in interface net.sf.basedb.util.overview.node.NodeNameGenerator
Generate a name for a node when the item is missing.
getMissingNodeTitle(Node) - Method in class net.sf.basedb.util.overview.node.AnnotationNameGenerator
 
getMissingNodeTitle(Node) - Method in class net.sf.basedb.util.overview.node.AnyToAnyNameGenerator
 
getMissingNodeTitle(Node) - Method in class net.sf.basedb.util.overview.node.BioWellNameGenerator
 
getMissingNodeTitle(Node) - Method in class net.sf.basedb.util.overview.node.FileSetMemberNameGenerator
 
getMissingNodeTitle(Node) - Method in class net.sf.basedb.util.overview.node.ItemListMemberNameGenerator
 
getMissingNodeTitle(Node) - Method in class net.sf.basedb.util.overview.node.NameableNameGenerator
 
getMissingNodeTitle(Node) - Method in interface net.sf.basedb.util.overview.node.NodeNameGenerator
Generate a title for a node when the item is missing.
getModifiedProperties(String, String, String) - Method in class net.sf.basedb.core.log.EntityDetails
Get all modified properties as a string, separating each property name with the given separator.
getMultiPermissions(DbControl, Item, Set<Integer>) - Static method in class net.sf.basedb.util.ShareableUtil
 
getMultiplicity() - Method in class net.sf.basedb.core.AnnotationType
Get the multiplicity.
getMultiplicity() - Method in class net.sf.basedb.core.data.AnnotationTypeData
How many values are allowed for this annotations of this type. 0 = no limit
getMultiplicity() - Method in class net.sf.basedb.core.ParameterType
Get how many values that can be tied to this parameter. 0 is unlimited values and 1 is default.
getName() - Method in class net.sf.basedb.clients.jobagent.Agent
Get the agent.name configuration value.
getName() - Method in class net.sf.basedb.clients.web.extensions.DynamicActionAttribute
Get the name of the dynamic attribute.
getName() - Method in class net.sf.basedb.clients.web.extensions.startpage.FixedStartPageFactory
 
getName() - Method in interface net.sf.basedb.clients.web.extensions.startpage.StartPageAction
Get the name of the start page.
getName() - Method in class net.sf.basedb.clients.web.extensions.startpage.StartPageBean
 
getName() - Method in class net.sf.basedb.clients.web.ModeInfo
 
getName() - Method in class net.sf.basedb.clients.web.SubContext
Get the name of the subcontext.
getName() - Method in class net.sf.basedb.clients.web.taglib.Input
 
getName() - Method in class net.sf.basedb.clients.web.taglib.table.Hidden
 
getName() - Method in class net.sf.basedb.core.AnyToAny
 
getName() - Method in class net.sf.basedb.core.authentication.ExtraUserInformation
The full name of the user.
getName() - Method in class net.sf.basedb.core.BatchedPropertyInfo
Get the name of the property.
getName() - Method in class net.sf.basedb.core.BioAssay
 
getName() - Method in class net.sf.basedb.core.BioAssaySet
 
getName() - Method in class net.sf.basedb.core.BioPlateEventType
 
getName() - Method in class net.sf.basedb.core.BioPlateType
 
getName() - Method in class net.sf.basedb.core.ChangeHistory
Get the name of the transaction that initiated the change.
getName() - Method in class net.sf.basedb.core.ChangeHistory.TransactionInfo
Get the name of the transaction.
getName() - Method in class net.sf.basedb.core.CommonItem
 
getName() - Method in class net.sf.basedb.core.data.AnyToAnyData
 
getName() - Method in class net.sf.basedb.core.data.BioAssayData
 
getName() - Method in class net.sf.basedb.core.data.BioAssaySetData
 
getName() - Method in class net.sf.basedb.core.data.BioPlateEventTypeData
 
getName() - Method in class net.sf.basedb.core.data.BioPlateTypeData
 
getName() - Method in class net.sf.basedb.core.data.ChangeHistoryData
Get the name of the transaction.
getName() - Method in class net.sf.basedb.core.data.ClientDefaultSettingData
Used by Hibernate to link with setting name.
getName() - Method in class net.sf.basedb.core.data.CommonData
 
getName() - Method in class net.sf.basedb.core.data.ContextData
Get the name of this Context item.
getName() - Method in class net.sf.basedb.core.data.ContextIndex
Get the name of this Context item.
getName() - Method in class net.sf.basedb.core.data.DataFileTypeData
 
getName() - Method in class net.sf.basedb.core.data.DirectoryData
Get the name of the item.
getName() - Method in class net.sf.basedb.core.data.ExtraValueTypeData
 
getName() - Method in class net.sf.basedb.core.data.FileData
Get the name of the item.
getName() - Method in class net.sf.basedb.core.data.GlobalDefaultSettingData
Used by Hibernate to link with setting name.
getName() - Method in class net.sf.basedb.core.data.GroupData
 
getName() - Method in class net.sf.basedb.core.data.HelpData
 
getName() - Method in class net.sf.basedb.core.data.ItemListSyncFilterData
 
getName() - Method in class net.sf.basedb.core.data.ItemSubtypeData
Get the name of the subtype which must be unique for subtypes related to a given item type.
getName() - Method in class net.sf.basedb.core.data.MessageData
 
getName() - Method in class net.sf.basedb.core.data.MimeTypeData
 
getName() - Method in interface net.sf.basedb.core.data.NameableData
Get the name of the item.
getName() - Method in class net.sf.basedb.core.data.NewsData
 
getName() - Method in class net.sf.basedb.core.data.PlateEventTypeData
 
getName() - Method in class net.sf.basedb.core.data.PlateGeometryData
 
getName() - Method in class net.sf.basedb.core.data.PlatformData
 
getName() - Method in class net.sf.basedb.core.data.PlatformVariantData
 
getName() - Method in class net.sf.basedb.core.data.PluginDefinitionData
Get the name of the plugin.
getName() - Method in class net.sf.basedb.core.data.PluginTypeData
 
getName() - Method in class net.sf.basedb.core.data.ProjectData
 
getName() - Method in class net.sf.basedb.core.data.QuantityData
 
getName() - Method in class net.sf.basedb.core.data.QuotaData
 
getName() - Method in class net.sf.basedb.core.data.QuotaTypeData
 
getName() - Method in class net.sf.basedb.core.data.ReporterData
 
getName() - Method in class net.sf.basedb.core.data.ReporterTypeData
 
getName() - Method in class net.sf.basedb.core.data.RoleData
 
getName() - Method in class net.sf.basedb.core.data.RoleKeyData
Get the name of the role key.
getName() - Method in class net.sf.basedb.core.data.RootRawBioAssayData
 
getName() - Method in class net.sf.basedb.core.data.SettingData
Used by Hibernate to link with setting name.
getName() - Method in class net.sf.basedb.core.data.TransformationData
 
getName() - Method in class net.sf.basedb.core.data.UnitData
 
getName() - Method in class net.sf.basedb.core.data.UserClientSettingData
Used by Hibernate to link with setting name.
getName() - Method in class net.sf.basedb.core.data.UserData
 
getName() - Method in class net.sf.basedb.core.data.UserDefaultSettingData
Used by Hibernate to link with setting name.
getName() - Method in class net.sf.basedb.core.data.UserDeviceData
 
getName() - Method in class net.sf.basedb.core.data.VersionedParameter
Get the parameter name.
getName() - Method in class net.sf.basedb.core.DataFileType
 
getName() - Method in class net.sf.basedb.core.DbControl
Get the name of this transaction.
getName() - Method in class net.sf.basedb.core.dbengine.TableInfo.ColumnInfo
 
getName() - Method in class net.sf.basedb.core.dbengine.TableInfo.ForeignKeyInfo
 
getName() - Method in class net.sf.basedb.core.dbengine.TableInfo.IndexInfo
 
getName() - Method in class net.sf.basedb.core.dbengine.TableInfo.PrimaryKeyInfo
 
getName() - Method in class net.sf.basedb.core.Directory
 
getName() - Method in class net.sf.basedb.core.ExtendedProperty
Get the name of the extended property.
getName() - Method in class net.sf.basedb.core.ExtraValueType
 
getName() - Method in class net.sf.basedb.core.Group
 
getName() - Method in class net.sf.basedb.core.Help
 
getName() - Method in class net.sf.basedb.core.IntensityFormula
Get the name of the intensity formula.
getName() - Method in class net.sf.basedb.core.ItemContext
Get the name of this context.
getName() - Method in class net.sf.basedb.core.ItemSubtype
 
getName() - Method in class net.sf.basedb.core.log.TransactionDetails
Get the name of this transaction.
getName() - Method in class net.sf.basedb.core.LogControl
Get the name of this transaction.
getName() - Method in class net.sf.basedb.core.Message
 
getName() - Method in class net.sf.basedb.core.MimeType
 
getName() - Method in interface net.sf.basedb.core.Nameable
Get the name of the item.
getName() - Method in class net.sf.basedb.core.News
 
getName() - Method in class net.sf.basedb.core.PlateEventType
 
getName() - Method in class net.sf.basedb.core.PlateGeometry
 
getName() - Method in class net.sf.basedb.core.Platform
 
getName() - Method in class net.sf.basedb.core.PlatformVariant
 
getName() - Method in interface net.sf.basedb.core.plugin.About
The name of the plugin.
getName() - Method in class net.sf.basedb.core.plugin.AboutImpl
 
getName() - Method in class net.sf.basedb.core.PluginParameter
Get the parameter name.
getName() - Method in class net.sf.basedb.core.PluginType
 
getName() - Method in class net.sf.basedb.core.Presets.Preset
Get the name of this preset.
getName() - Method in class net.sf.basedb.core.Project
 
getName() - Method in class net.sf.basedb.core.Quantity
 
getName() - Method in class net.sf.basedb.core.query.HqlEntityParameterExpression
Get the name of the parameter.
getName() - Method in class net.sf.basedb.core.query.ParameterExpression
Get the name of the parameter.
getName() - Method in class net.sf.basedb.core.query.QueryParameter
Get the name of the parameter.
getName() - Method in class net.sf.basedb.core.Quota
 
getName() - Method in class net.sf.basedb.core.QuotaType
 
getName() - Method in class net.sf.basedb.core.RawDataType
Get the name of this raw data type.
getName() - Method in class net.sf.basedb.core.ReporterType
 
getName() - Method in class net.sf.basedb.core.Role
 
getName() - Method in class net.sf.basedb.core.RoleKey
 
getName() - Method in class net.sf.basedb.core.RootRawBioAssay
 
getName() - Method in class net.sf.basedb.core.Setting
Get the name of this setting.
getName() - Method in class net.sf.basedb.core.signal.Signal
Get the short name of the signal.
getName() - Method in class net.sf.basedb.core.SyncFilter
 
getName() - Method in class net.sf.basedb.core.Transformation
 
getName() - Method in class net.sf.basedb.core.Unit
 
getName() - Method in class net.sf.basedb.core.User
 
getName() - Method in class net.sf.basedb.core.UserDevice
 
getName() - Method in class net.sf.basedb.core.VirtualColumn
Get the name of the column.
getName() - Method in class net.sf.basedb.plugins.Base1PluginExecuter.JobParameter
 
getName() - Method in class net.sf.basedb.plugins.executor.ParameterDefinition
Get the name of the parameter.
getName() - Method in enum class net.sf.basedb.plugins.PrintMapFlatFileImporter.Section
 
getName() - Method in class net.sf.basedb.util.bfs.MetadataModel.Section
Get the name of the section.
getName() - Method in class net.sf.basedb.util.ContextUtil.ContextResult
Get the name of the plug-in configuration or, if the configuration is null, of the plug-in definition
getName() - Method in class net.sf.basedb.util.excel.XlsxToCsvUtil.SheetInfo
Get the name of the sheet.
getName() - Method in class net.sf.basedb.util.extensions.AboutBean
 
getName() - Method in interface net.sf.basedb.util.extensions.ExtensionPoint
Get the name of the extension point.
getName() - Method in class net.sf.basedb.util.extensions.ExtensionPointBean
 
getName() - Method in class net.sf.basedb.util.extensions.manager.ExtensionsFile
Get the name of the file.
getName() - Method in class net.sf.basedb.util.extensions.Registry.RegisteredAbout
 
getName() - Method in class net.sf.basedb.util.extensions.Registry.RegisteredExtensionPoint
 
getName() - Method in class net.sf.basedb.util.importer.BaseFileWrapper
 
getName() - Method in class net.sf.basedb.util.importer.DiskFileWrapper
 
getName() - Method in interface net.sf.basedb.util.importer.FileWrapper
Get the name of the file.
getName() - Method in class net.sf.basedb.util.importer.spotdata.BaseFileInfo.ChildBioAssay
Get the name of the child bioassay.
getName() - Method in class net.sf.basedb.util.importer.spotdata.BaseFileInfo
Get the name of the file.
getName() - Method in class net.sf.basedb.util.jep.convert.AbsConverter
 
getName() - Method in class net.sf.basedb.util.jep.convert.AbstractJepConversionFunction
 
getName() - Method in class net.sf.basedb.util.jep.convert.AddConverter
 
getName() - Method in class net.sf.basedb.util.jep.convert.AndConverter
 
getName() - Method in class net.sf.basedb.util.jep.convert.DivideConverter
 
getName() - Method in class net.sf.basedb.util.jep.convert.EqualsConverter
 
getName() - Method in class net.sf.basedb.util.jep.convert.ExpConverter
 
getName() - Method in class net.sf.basedb.util.jep.convert.GreaterConverter
 
getName() - Method in class net.sf.basedb.util.jep.convert.GreaterEqualsConverter
 
getName() - Method in class net.sf.basedb.util.jep.convert.IfConverter
 
getName() - Method in interface net.sf.basedb.util.jep.convert.JepConversionFunction
Get the name of the function or the symbol of the operator
getName() - Method in class net.sf.basedb.util.jep.convert.LessConverter
 
getName() - Method in class net.sf.basedb.util.jep.convert.LessEqualsConverter
 
getName() - Method in class net.sf.basedb.util.jep.convert.LogarithmConverter
 
getName() - Method in class net.sf.basedb.util.jep.convert.MultiplyConverter
 
getName() - Method in class net.sf.basedb.util.jep.convert.NaturalLogarithmConverter
 
getName() - Method in class net.sf.basedb.util.jep.convert.NotConverter
 
getName() - Method in class net.sf.basedb.util.jep.convert.NotEqualsConverter
 
getName() - Method in class net.sf.basedb.util.jep.convert.OrConverter
 
getName() - Method in class net.sf.basedb.util.jep.convert.SquareRootConverter
 
getName() - Method in class net.sf.basedb.util.jep.convert.SubtractConverter
 
getName() - Method in class net.sf.basedb.util.jep.convert.UMinusConverter
 
getName() - Method in class net.sf.basedb.util.overview.Node
Get the name of this node.
getName() - Method in class net.sf.basedb.util.plot.HistogramPlot.HistogramSeries
 
getName() - Method in class net.sf.basedb.util.plot.PlotAnnotation
The name of the annotation, which will be used as a label in the image.
getName() - Method in class net.sf.basedb.util.resources.ResourceBundleWrapper
Get the base name of the resource bundle.
getName(BasicItem) - Method in class net.sf.basedb.clients.web.taglib.Select
 
getName(Extension<?>) - Static method in class net.sf.basedb.util.extensions.ExtensionsUtil
Get the name of the extension.
getNameableItems() - Static method in class net.sf.basedb.core.Metadata
Get a set containing all Nameable item types.
getNamedContexts(Item) - Method in class net.sf.basedb.core.SessionControl
Get all named contexts that are owner by the logged in user.
getNamedNativeQuery(String) - Method in class net.sf.basedb.core.hibernate.SessionWrapper
 
getNamedNativeQuery(String) - Method in class net.sf.basedb.core.hibernate.StatelessSessionWrapper
 
getNamedParameters() - Method in class net.sf.basedb.core.hibernate.QueryWrapper
Deprecated.
getNamedProcedureCall(String) - Method in class net.sf.basedb.core.hibernate.SessionWrapper
 
getNamedProcedureCall(String) - Method in class net.sf.basedb.core.hibernate.StatelessSessionWrapper
 
getNamedQuery(String) - Method in class net.sf.basedb.core.hibernate.SessionWrapper
If the same query has been executed before, return the cached instance, otherwise create a new query from the parent session and cache it.
getNamedQuery(String) - Method in class net.sf.basedb.core.hibernate.StatelessSessionWrapper
If the same query has been executed before, return the cached instance, otherwise create a new query from the parent session and cache it.
getNew(String) - Static method in class net.sf.basedb.core.Reporter
Get a new instance of a reporter, and setting the external ID.
getNew(DbControl) - Static method in class net.sf.basedb.core.AnnotationTypeCategory
Creates a new AnnotationTypeCategory item.
getNew(DbControl) - Static method in class net.sf.basedb.core.BioPlateType
Creates a new bioplate type.
getNew(DbControl) - Static method in class net.sf.basedb.core.BioSource
Create a new BioSource item.
getNew(DbControl) - Static method in class net.sf.basedb.core.Extract
Create a new Extract item.
getNew(DbControl) - Static method in class net.sf.basedb.core.FileServer
Create a new FileServer item.
getNew(DbControl) - Static method in class net.sf.basedb.core.Formula
Create a new Formula item.
getNew(DbControl) - Static method in class net.sf.basedb.core.Group
Create a new Group item.
getNew(DbControl) - Static method in class net.sf.basedb.core.Hardware
Create a new Hardware item.
getNew(DbControl) - Static method in class net.sf.basedb.core.Kit
Create a new Kit item.
getNew(DbControl) - Static method in class net.sf.basedb.core.MimeType
Create a new MimeType item.
getNew(DbControl) - Static method in class net.sf.basedb.core.PermissionTemplate
Create a new permission template item.
getNew(DbControl) - Static method in class net.sf.basedb.core.PhysicalBioAssay
Create a new PhysicalBioAssay item.
getNew(DbControl) - Static method in class net.sf.basedb.core.Project
Create a new Project item.
getNew(DbControl) - Static method in class net.sf.basedb.core.Protocol
Create a new Protocol item.
getNew(DbControl) - Static method in class net.sf.basedb.core.ReporterBatcher
Create a new batcher for reporters.
getNew(DbControl) - Static method in class net.sf.basedb.core.ReporterCloneTemplate
Create a new reporter clone template item.
getNew(DbControl) - Static method in class net.sf.basedb.core.ReporterList
Create a new ReporterList item.
getNew(DbControl) - Static method in class net.sf.basedb.core.ReporterType
Create a new ReporterType item.
getNew(DbControl) - Static method in class net.sf.basedb.core.Role
Create a new Role item.
getNew(DbControl) - Static method in class net.sf.basedb.core.Sample
Create a new Sample item.
getNew(DbControl) - Static method in class net.sf.basedb.core.Software
Create a new Software item.
getNew(DbControl) - Static method in class net.sf.basedb.core.Tag
Create a new Tag item.
getNew(DbControl) - Static method in class net.sf.basedb.core.VirtualDb
Create a new DynamicTables item.
getNew(DbControl, boolean, Job) - Static method in class net.sf.basedb.core.DerivedBioAssay
Create a new parent-less derived bioassay.
getNew(DbControl, int, int) - Static method in class net.sf.basedb.core.PlateGeometry
Create a new PlateGeometry item.
getNew(DbControl, long) - Static method in class net.sf.basedb.core.Quota
Create a new Quota item.
getNew(DbControl, String) - Static method in class net.sf.basedb.core.BioPlateEventType
Creates a new bioplate event type.
getNew(DbControl, String) - Static method in class net.sf.basedb.core.Client
Create a new Client item.
getNew(DbControl, String) - Static method in class net.sf.basedb.core.JobAgent
Create a new JobAgent item.
getNew(DbControl, String) - Static method in class net.sf.basedb.core.Quantity
Create a new Quantity item.
getNew(DbControl, String, int) - Static method in class net.sf.basedb.core.Platform
Create a new file-only platform.
getNew(DbControl, String, String) - Static method in class net.sf.basedb.core.GlobalDefaultSetting
Create a new GlobalDefaultSetting item.
getNew(DbControl, String, String) - Static method in class net.sf.basedb.core.PluginType
Create a new PluginType item.
getNew(DbControl, String, String) - Static method in class net.sf.basedb.core.User
Create a new User item.
getNew(DbControl, String, String, boolean) - Static method in class net.sf.basedb.core.PluginDefinition
Create a new PluginDefinition item.
getNew(DbControl, String, Item) - Static method in class net.sf.basedb.core.DataFileType
Create a new data file type.
getNew(DbControl, String, RawDataType) - Static method in class net.sf.basedb.core.Platform
Create a new platform which may optionally import data into the database.
getNew(DbControl, String, Type) - Static method in class net.sf.basedb.core.ExtraValueType
Create a new ExtraValue item.
getNew(DbControl, Date, Date) - Static method in class net.sf.basedb.core.News
Create a new News item.
getNew(DbControl, Annotatable) - Static method in class net.sf.basedb.core.AnnotationSet
Create a new annotation set for the specified item.
getNew(DbControl, ArrayBatch) - Static method in class net.sf.basedb.core.ArraySlide
Create a new ArraySlide item.
getNew(DbControl, ArrayDesign) - Static method in class net.sf.basedb.core.ArrayBatch
Create a new ArrayBatch item.
getNew(DbControl, ArrayDesign) - Static method in class net.sf.basedb.core.FeatureBatcher
Create a new batcher for regular features.
getNew(DbControl, ArrayDesign, BlockInfo) - Static method in class net.sf.basedb.core.ArrayDesignBlock
 
getNew(DbControl, BasicItem, BasicItem, String, boolean) - Static method in class net.sf.basedb.core.AnyToAny
Create a new AnyToAny link
getNew(DbControl, BioAssaySet, DataCubeColumn) - Static method in class net.sf.basedb.core.BioAssay
Create a new BioAssay item.
getNew(DbControl, BioAssaySet, ExtraValueType, DataCubeExtraValue, Job) - Static method in class net.sf.basedb.core.ExtraValue
Create a new ExtraValue item.
getNew(DbControl, BioPlateEventParticipant) - Static method in class net.sf.basedb.core.Extract
Create a new Extract item as part of a master bioplate event.
getNew(DbControl, BioPlateEventParticipant) - Static method in class net.sf.basedb.core.PhysicalBioAssay
Create a new PhysicalBioAssay item as part of a master bioplate event.
getNew(DbControl, BioPlateEventParticipant) - Static method in class net.sf.basedb.core.Sample
Create a new Sample item as part of a master bioplate event.
getNew(DbControl, BioPlateEvent, BioPlate) - Static method in class net.sf.basedb.core.BioPlateEventParticipant
Creates a new participant for the given event and bioplate.
getNew(DbControl, BioPlateEventType) - Static method in class net.sf.basedb.core.BioPlateEvent
Create a new BioPlateEvent item.
getNew(DbControl, Client, String) - Static method in class net.sf.basedb.core.Help
Create a new Help item.
getNew(DbControl, Client, String, String) - Static method in class net.sf.basedb.core.ClientDefaultSetting
Create a new ClientDefaultSetting item.
getNew(DbControl, DataCube) - Static method in class net.sf.basedb.core.DataCubeColumn
Create a new DataCubeColumn item.
getNew(DbControl, DataCube) - Static method in class net.sf.basedb.core.DataCubeFilter
Create a new DataCubeFilter item.
getNew(DbControl, DataCube) - Static method in class net.sf.basedb.core.DataCubeLayer
Create a new DataCubeLayer item.
getNew(DbControl, DataCube, Type, ExtraValue.CoordinateType) - Static method in class net.sf.basedb.core.DataCubeExtraValue
Create a new DataCubeExtraValue item.
getNew(DbControl, DerivedBioAssay, Job) - Static method in class net.sf.basedb.core.DerivedBioAssay
Create a new child derived bioassay from a parent derived bioassay.
getNew(DbControl, Directory) - Static method in class net.sf.basedb.core.Directory
Create a new Directory item.
getNew(DbControl, Directory) - Static method in class net.sf.basedb.core.File
Create a new File item.
getNew(DbControl, Experiment, Job) - Static method in class net.sf.basedb.core.Transformation
Create a new Transformation item.
getNew(DbControl, FileSet, File, DataFileType) - Static method in class net.sf.basedb.core.FileSetMember
Create a new member in a file set.
getNew(DbControl, FileStoreEnabled) - Static method in class net.sf.basedb.core.FileSet
Create a new file set for the specified item.
getNew(DbControl, Item) - Static method in class net.sf.basedb.core.ItemList
Create a new ItemList item.
getNew(DbControl, Item) - Static method in class net.sf.basedb.core.ItemSubtype
Create a new item subtype item.
getNew(DbControl, ItemSubtype, DataFileType) - Static method in class net.sf.basedb.core.ItemSubtypeFileType
Create a new item linking a file type to an item subtype.
getNew(DbControl, JobAgent, PluginDefinition) - Static method in class net.sf.basedb.core.JobAgentSettings
Create a new JobAgentSettings item.
getNew(DbControl, MeasuredBioMaterial) - Static method in class net.sf.basedb.core.BioMaterialEvent
Create a new BioMaterialEvent of the BioMaterialEvent.Type.OTHER type.
getNew(DbControl, MeasuredBioMaterial, BioPlateEventParticipant) - Static method in class net.sf.basedb.core.BioMaterialEvent
Create a new BioMaterialEvent of the BioMaterialEvent.Type.OTHER type that is linked with a master BioPlateEventParticipant.
getNew(DbControl, Path) - Static method in class net.sf.basedb.core.Directory
Create a new or existing Directory from a path.
getNew(DbControl, PhysicalBioAssay, Job) - Static method in class net.sf.basedb.core.DerivedBioAssay
Create a new (root) derived bioassay from a physical bioassay.
getNew(DbControl, PlateGeometry) - Static method in class net.sf.basedb.core.PlateType
Create a new PlateType item.
getNew(DbControl, PlateGeometry, int, PlateGeometry, int) - Static method in class net.sf.basedb.core.PlateMapping
Create a new PlateMapping item.
getNew(DbControl, PlateGeometry, BioPlateType) - Static method in class net.sf.basedb.core.BioPlate
Creates a new bioplate with a specific plate geometry and type.
getNew(DbControl, Plate, PlateEventType) - Static method in class net.sf.basedb.core.PlateEvent
Create a new PlateEvent item.
getNew(DbControl, PlateType) - Static method in class net.sf.basedb.core.Plate
Create a new Plate item.
getNew(DbControl, PlateType) - Static method in class net.sf.basedb.core.PlateEventType
Create a new PlateEventType item.
getNew(DbControl, Platform) - Static method in class net.sf.basedb.core.ArrayDesign
Create a new ArrayDesign item for a given platform.
getNew(DbControl, Platform, String) - Static method in class net.sf.basedb.core.PlatformVariant
Create a new variant of a platform.
getNew(DbControl, Platform, String, int) - Static method in class net.sf.basedb.core.PlatformVariant
Create a new file-only variant of a platform.
getNew(DbControl, Platform, String, RawDataType) - Static method in class net.sf.basedb.core.PlatformVariant
Create a new platform variant which may optionally import data into the database.
getNew(DbControl, Platform, PlatformVariant, DataFileType) - Static method in class net.sf.basedb.core.PlatformFileType
Create a new item linking a file type to a platform/variant.
getNew(DbControl, Platform, RawDataType) - Static method in class net.sf.basedb.core.RawBioAssay
Create a new raw bioassay for a specific platform and/or raw data type.
getNew(DbControl, PlatformVariant) - Static method in class net.sf.basedb.core.ArrayDesign
Create a new ArrayDesign item for a given platform variant.
getNew(DbControl, PlatformVariant, RawDataType) - Static method in class net.sf.basedb.core.RawBioAssay
Create a new raw bioassay for a specific platform variant.
getNew(DbControl, PluginDefinition) - Static method in class net.sf.basedb.core.PluginConfiguration
Create a new PluginConfiguration item.
getNew(DbControl, PluginDefinition, PluginConfiguration, Experiment) - Static method in class net.sf.basedb.core.Job
Create a new Job item.
getNew(DbControl, Quantity, String) - Static method in class net.sf.basedb.core.Unit
Create a new Unit item.
getNew(DbControl, RawBioAssay, FeatureIdentificationMethod) - Static method in class net.sf.basedb.core.RawDataBatcher
Create a new batcher for raw data.
getNew(DbControl, RawDataType) - Static method in class net.sf.basedb.core.Experiment
Create a new Experiment item.
getNew(DbControl, Transformation, DataCubeLayer) - Static method in class net.sf.basedb.core.BioAssaySet
Create a new BioAssaySet item.
getNew(DbControl, Type) - Static method in class net.sf.basedb.core.AnnotationType
Create a new AnnotationType item.
getNew(DbControl, User, String, String) - Static method in class net.sf.basedb.core.UserDefaultSetting
Create a new UserDefaultSetting item.
getNew(DbControl, User, String, User, Job) - Static method in class net.sf.basedb.core.Message
Create a new Message item.
getNew(DbControl, User, Client, String, String) - Static method in class net.sf.basedb.core.UserClientSetting
Create a new UserClientSetting item.
getNew(DbControl, VirtualDb) - Static method in class net.sf.basedb.core.DataCube
Create a new DataCube item.
getNewBioAssayEvent(DbControl, PhysicalBioAssay, BioPlateEventParticipant) - Static method in class net.sf.basedb.core.BioMaterialEvent
Create a new BioMaterialEvent of the BioMaterialEvent.Type.BIOASSAY type.
getNewChildren() - Method in class net.sf.basedb.util.overview.Node
Get all new children to this node.
getNewCreationEvent(DbControl, MeasuredBioMaterial, BioPlateEventParticipant) - Static method in class net.sf.basedb.core.BioMaterialEvent
Create a new BioMaterialEvent of the BioMaterialEvent.Type.CREATION type (creation event).
getNewFile(boolean) - Method in class net.sf.basedb.core.File
Get a new random file path.
getNewImageRemapperIfNeeded(ServletContext) - Static method in class net.sf.basedb.clients.web.extensions.skin.ImageRemapperUtil
Get a new image remapper if it is needed, otherwise null.
getNewInherited(DbControl, AnnotationSet, AnnotationData, boolean) - Static method in class net.sf.basedb.core.Annotation
Create a new inherited or cloned annotation.
getNewOrCurrentOverview(DbControl, BasicItem, Project) - Static method in class net.sf.basedb.util.overview.OverviewUtil
Get the current overview or create a new overview.
getNewOrExisting(DbControl, BasicItem, String, BasicItem, boolean) - Static method in class net.sf.basedb.core.AnyToAny
Get a new or existing AnyToAny link.
getNewOrExisting(DbControl, ProjectPermissions) - Static method in class net.sf.basedb.core.ProjectKey
Create a new or load an existing ProjectKey when you have a combination of project/permission values.
getNewOrExisting(DbControl, UserPermissions, GroupPermissions) - Static method in class net.sf.basedb.core.ItemKey
Create a new or load an existing ItemKey when you have a combination of user/group/permission values.
getNewOrExistingId(Session, Map<ProjectData, Integer>) - Static method in class net.sf.basedb.core.ProjectKey
Find the ID of an existing key with exactly the same project/permission combination.
getNewOrExistingKey(Session, Map<UserData, Integer>, Map<GroupData, Integer>) - Static method in class net.sf.basedb.core.ItemKey
Find the ID of an existing key with exactly the same user/group/permission combination.
getNewOverview(DbControl, BasicItem, Project) - Static method in class net.sf.basedb.util.overview.OverviewUtil
Create a new overview for the given item and project.
getNewParameterVersion() - Method in class net.sf.basedb.core.PluginConfiguration
Increase the version number once per transaction.
getNewPrimary(DbControl, AnnotationSet, AnnotationTypeData) - Static method in class net.sf.basedb.core.Annotation
Create a new primary annotation.
getNewsDate() - Method in class net.sf.basedb.core.data.NewsData
Get the news date of this news item.
getNewsDate() - Method in class net.sf.basedb.core.News
Get the date that is shown in listings.
getNewsFeed(String, boolean) - Method in class net.sf.basedb.clients.web.servlet.RssNewsFeed
Generate the XML string for the news feed.
getNewStream() - Method in class net.sf.basedb.util.StreamCacher
Get a new stream that appears to be reading from the start of the master stream.
getNewSystemMessage(DbControl, UserData, String, UserData, JobData) - Static method in class net.sf.basedb.core.Message
Create a new Message from the system.
getNewValue() - Method in class net.sf.basedb.core.ChangeHistory
Get the new value of the property had immediately after this change.
getNewValue() - Method in class net.sf.basedb.core.data.ChangeHistoryDetailData
Get the new value after the change.
getNewValue() - Method in class net.sf.basedb.core.log.ManualLogEntry
New value after the change.
getNewValues() - Method in class net.sf.basedb.core.AnnotationBatcher.CurrentAnnotationInfo
Get the new annotation values.
getNextColumnId() - Method in class net.sf.basedb.clients.web.taglib.table.ExtensionCells
This is called by the Cell taglib when the next extension column is about to be processed.
getNextColumnNo() - Method in class net.sf.basedb.core.DataCube
Generate the next available column number.
getNextCommand() - Method in class net.sf.basedb.core.PluginResponse
Get the next command sent via Response.Status.CONTINUE.
getNextCubeNo() - Method in class net.sf.basedb.core.VirtualDb
Generate the next available cube number.
getNextEntry(TarInputStream) - Static method in class net.sf.basedb.util.zip.TarUtil
Get the next entry from a TAR input stream.
getNextExtraValueNo() - Method in class net.sf.basedb.core.DataCube
Generate the next available extra value number.
getNextFilename(Object, String) - Method in class net.sf.basedb.util.bfs.SequenceFilenameGenerator
 
getNextFilename(Object, String) - Method in class net.sf.basedb.util.bfs.SuggestedFilenameGenerator
 
getNextFilename(T, String) - Method in interface net.sf.basedb.util.bfs.FilenameGenerator
Get the next file name.
getNextFileNumber() - Method in class net.sf.basedb.util.bfs.SequenceFilenameGenerator
Get the next file number.
getNextFilterNo() - Method in class net.sf.basedb.core.DataCube
Generate the next available filter number.
getNextLayerNo() - Method in class net.sf.basedb.core.DataCube
Generate the next available layer number.
getNextLine() - Method in class net.sf.basedb.util.gtf.GtfInputStream
Read the next line from the GTF file and split on tab character.
getNextRequest() - Method in class net.sf.basedb.core.PluginResponse
Get a PluginRequest object that handles the next request, if status is Response.Status.CONTINUE.
getNextRowClass() - Method in class net.sf.basedb.clients.web.taglib.table.Table
 
getNode() - Method in class net.sf.basedb.core.data.JobData
The name of the node where the job is executing.
getNode() - Method in class net.sf.basedb.core.Job
Get the name of the node where the job is executing.
getNode() - Method in class net.sf.basedb.util.overview.Failure
Get the node that failed validation.
getNode() - Method in class net.sf.basedb.util.Tree.Entry
Get the node element object.
getNode(String) - Method in class net.sf.basedb.util.overview.GenericOverview
Get the node with the given ID.
getNode(K) - Method in class net.sf.basedb.util.overview.cache.NodeCache
 
getNodeCache() - Method in class net.sf.basedb.util.overview.GenericOverview
This overview implementation doesn't currently support node caching.
getNodeCache() - Method in interface net.sf.basedb.util.overview.OverviewContext
Get the current node cache.
getNodeFactory(DbControl, OverviewContext) - Method in class net.sf.basedb.util.overview.loader.BasicItemNodeLoader
Get a node factory that can be used to create item nodes.
getNodeFactory(DbControl, OverviewContext, NodeValidator<? super I>, NodeNameGenerator<? super I>) - Method in class net.sf.basedb.util.overview.loader.BasicItemNodeLoader
Get a node factory that can be used to create item nodes using a non-default name generator and validator.
getNodeLoader(OverviewContext, Object) - Method in class net.sf.basedb.util.overview.loader.BasicItemNodeLoader
Get a node loader for a specific item type using the current context's node loader factory.
getNodeLoaderFactory() - Method in class net.sf.basedb.util.overview.GenericOverview
Get the current node loader factory.
getNodeLoaderFactory() - Method in interface net.sf.basedb.util.overview.OverviewContext
Get the node loader factory that is used to create node loaders.
getNodeLoaderFactory(OverviewContext) - Method in class net.sf.basedb.util.overview.loader.BasicItemNodeLoader
Get the node loader factory used by the current context.
getNodeName(I, Node) - Method in class net.sf.basedb.util.overview.node.NameableNameGenerator
 
getNodeName(I, Node) - Method in interface net.sf.basedb.util.overview.node.NodeNameGenerator
Generate a name for the new node that is about to be created.
getNodeName(Annotation, Node) - Method in class net.sf.basedb.util.overview.node.AnnotationNameGenerator
 
getNodeName(AnyToAny, Node) - Method in class net.sf.basedb.util.overview.node.AnyToAnyNameGenerator
 
getNodeName(FileSetMember, Node) - Method in class net.sf.basedb.util.overview.node.FileSetMemberNameGenerator
 
getNodeName(Listable, Node) - Method in class net.sf.basedb.util.overview.node.ItemListMemberNameGenerator
 
getNodeName(MeasuredBioMaterial, Node) - Method in class net.sf.basedb.util.overview.node.BioWellNameGenerator
 
getNodeNameGenerator() - Method in class net.sf.basedb.util.overview.loader.BasicItemNodeLoader
Get the name generator that is used by this loader.
getNodeTitle(I, Node) - Method in class net.sf.basedb.util.overview.node.NameableNameGenerator
 
getNodeTitle(I, Node) - Method in interface net.sf.basedb.util.overview.node.NodeNameGenerator
Generate a title for the new node that is about to be created.
getNodeTitle(Annotation, Node) - Method in class net.sf.basedb.util.overview.node.AnnotationNameGenerator
 
getNodeTitle(AnyToAny, Node) - Method in class net.sf.basedb.util.overview.node.AnyToAnyNameGenerator
 
getNodeTitle(BioPlate, Node) - Method in class net.sf.basedb.util.overview.node.BioPlateNameGenerator
The base of the title is generated by the superclass.
getNodeTitle(Extract, Node) - Method in class net.sf.basedb.util.overview.node.ExtractNameGenerator
The base of the title is generated by the superclass.
getNodeTitle(FileSetMember, Node) - Method in class net.sf.basedb.util.overview.node.FileSetMemberNameGenerator
 
getNodeTitle(Listable, Node) - Method in class net.sf.basedb.util.overview.node.ItemListMemberNameGenerator
 
getNodeTitle(MeasuredBioMaterial, Node) - Method in class net.sf.basedb.util.overview.node.BioWellNameGenerator
 
getNodeType() - Method in class net.sf.basedb.util.overview.Node
Get the node type of this node.
getNodeValidator() - Method in class net.sf.basedb.util.overview.node.NodeFactory
Get the node validator that is used by this factory.
getNodeValidator(OverviewContext) - Method in class net.sf.basedb.util.overview.loader.BasicItemNodeLoader
Get the default node validator for nodes of this type.
getNodeValidatorFactory() - Method in class net.sf.basedb.util.overview.GenericOverview
Get the current node validator factory.
getNodeValidatorFactory() - Method in interface net.sf.basedb.util.overview.OverviewContext
Get the node validator factory that is used to create node validators.
getNodeValidatorFactory(OverviewContext) - Method in class net.sf.basedb.util.overview.loader.BasicItemNodeLoader
Get the node validator factory used by the current context.
getNoDuplicates() - Method in class net.sf.basedb.util.annotations.InheritSpecification
 
getNoSkin() - Method in class net.sf.basedb.clients.web.taglib.Page
 
getNotNull() - Method in class net.sf.basedb.core.ParameterType
Check if the parameter can be null.
getNulltext() - Method in class net.sf.basedb.clients.web.taglib.PropertyValue
 
getNullValue() - Method in class net.sf.basedb.util.export.TableWriter
The null value string is written to the output instead of null data values.
getNumAcceptedWithNullReporterOnFeature() - Method in class net.sf.basedb.core.RawDataBatcher
Get the number of accepted inserts because of features with a NULL reporter.
getNumAnnotations() - Method in class net.sf.basedb.plugins.AnnotationFlatFileImporter.NewAnnotations
The total numer of annotation values that has been added to this cache.
getNumArrays() - Method in class net.sf.basedb.core.ArrayDesign
Get the number of arrays on a single slide.
getNumArrays() - Method in class net.sf.basedb.core.data.ArrayDesignData
The number of arrays on a single slide.
getNumberFormat() - Method in class net.sf.basedb.plugins.AbstractFlatFileImporter
Get a number formatter that is able to parse numbers with the specified decimal separator.
getNumberFormat() - Method in class net.sf.basedb.util.excel.XlsxToCsvUtil
Get the formatter that is used for formatting cells with numeric values.
getNumberFormat(char, char) - Static method in class net.sf.basedb.util.NumberFormatUtil
 
getNumberFormatter(SessionControl) - Static method in class net.sf.basedb.clients.web.formatter.FormatterFactory
Get the logged in user's number formatter for float values.
getNumberOfParameters() - Method in class net.sf.basedb.util.jep.ChannelFunction
 
getNumberOfParameters() - Method in class net.sf.basedb.util.jep.ExtraValueFunction
 
getNumberOfParameters() - Method in class net.sf.basedb.util.jep.FunctionSafeJep.UnknownFunction
 
getNumberOfParameters() - Method in class net.sf.basedb.util.jep.InReporterListFunction
 
getNumberOfParameters() - Method in class net.sf.basedb.util.jep.LeftFunction
 
getNumberOfParameters() - Method in class net.sf.basedb.util.jep.Log2Function
 
getNumberOfParameters() - Method in class net.sf.basedb.util.jep.MeanFunction
 
getNumberOfParameters() - Method in class net.sf.basedb.util.jep.NotInReporterListFunction
 
getNumberOfParameters() - Method in class net.sf.basedb.util.jep.PositionFunction
 
getNumberOfParameters() - Method in class net.sf.basedb.util.jep.RawChannelFunction
 
getNumberOfParameters() - Method in class net.sf.basedb.util.jep.RawFunction
 
getNumberOfParameters() - Method in class net.sf.basedb.util.jep.ReporterFunction
 
getNumberOfParameters() - Method in class net.sf.basedb.util.jep.ScoreFunction
 
getNumberOfParameters() - Method in class net.sf.basedb.util.jep.SimpleJepFunction
 
getNumberOfParameters() - Method in class net.sf.basedb.util.parser.ColFunction
 
getNumberOfParameters() - Method in class net.sf.basedb.util.parser.DataNoFunction
 
getNumberOfParameters() - Method in class net.sf.basedb.util.parser.DefaultItemFunction
 
getNumberOfParameters() - Method in class net.sf.basedb.util.parser.LineNoFunction
 
getNumBioAssays() - Method in class net.sf.basedb.clients.web.ExperimentExplorer
Get the number of bioassays in the bioassayset.
getNumBytes(FlatFileParser) - Method in class net.sf.basedb.plugins.AbstractFlatFileImporter
Get the number of bytes read from the file.
getNumBytes(FlatFileParser) - Method in class net.sf.basedb.plugins.gtf.GtfReporterImporter
Get the number of bytes read from the original file.
getNumBytes(FlatFileParser) - Method in class net.sf.basedb.plugins.gtf.GtfReporterMapImporter
Get the number of bytes read from the original file.
getNumChildren() - Method in class net.sf.basedb.util.Tree.Entry
Get the number of children added to this node.
getNumColumns() - Method in class net.sf.basedb.core.data.DataCubeData
The number of columns in this data cube.
getNumColumns() - Method in class net.sf.basedb.core.DataCube
Get the number of columns created in this data cube.
getNumDbFeatures() - Method in class net.sf.basedb.core.ArrayDesign
Get the number of features on this array design that are stored in the database.
getNumDbFeatures() - Method in class net.sf.basedb.core.data.ArrayDesignData
The number of features on this array design that are stored in the database.
getNumDbSpots() - Method in class net.sf.basedb.core.RawBioAssay
Get the number of spots on this raw bioassay that are stored in the database.
getNumDecimals(Number) - Method in class net.sf.basedb.util.formatter.AdaptiveNumberFormatter
 
getNumDecimals(SessionControl) - Static method in class net.sf.basedb.clients.web.formatter.FormatterSettings
Get the number of decimals a number formatter should display.
getNumDeleted() - Method in class net.sf.basedb.util.extensions.manager.ExtensionsManager
Get the number of deleted files that was found in the last call to ExtensionsManager.scanForChanges().
getNumDeleted() - Method in class net.sf.basedb.util.extensions.manager.processor.DeleteResourcesProcessor
Get the total number of resources that was deleted.
getNumEntries() - Method in class net.sf.basedb.util.extensions.logging.ExtensionsLog
Get the current number of entries in the log.
getNumError() - Method in class net.sf.basedb.clients.web.extensions.LoadServletsProcessor
Get the number of files that was had an error.
getNumError() - Method in class net.sf.basedb.plugins.AnnotationFlatFileImporter.NewAnnotations
Number of annotations that was couldn't be set by the call to the AnnotationFlatFileImporter.NewAnnotations.setNewAnnotations(AnnotationFlatFileImporter, AnnotationBatcher, boolean, boolean, boolean, boolean) method because of an error (too many values).
getNumError() - Method in class net.sf.basedb.util.extensions.manager.processor.DeleteResourcesProcessor
Get the number of files that was had an error.
getNumError() - Method in class net.sf.basedb.util.extensions.manager.processor.DisablePluginsProcessor
Get the number of files that was had an error.
getNumError() - Method in class net.sf.basedb.util.extensions.manager.processor.ExtractResourcesProcessor
Get the number of files that was had an error.
getNumError() - Method in class net.sf.basedb.util.extensions.manager.processor.PluginInstallationProcessor
Get the number of files that was had an error.
getNumError() - Method in class net.sf.basedb.util.extensions.manager.processor.RegisterExtensionsProcessor
Get the number of files that was had an error.
getNumError() - Method in class net.sf.basedb.util.extensions.manager.processor.UnregisterExtensionsProcessor
Get the number of files that was had an error.
getNumErrorFiles() - Method in class net.sf.basedb.util.extensions.manager.ProcessResults
The number of extension files that could not be completely loaded because of an error.
getNumErrors() - Method in class net.sf.basedb.util.extensions.logging.ExtensionsLog
Get the current number of error entries in the log.
getNumErrors() - Method in class net.sf.basedb.util.overview.Node
Get the number of errors on this node.
getNumExtensions() - Method in class net.sf.basedb.util.extensions.ExtensionsInvoker
Get the number of enabled extensions in this invokation.
getNumExtracted() - Method in class net.sf.basedb.util.extensions.manager.processor.ExtractResourcesProcessor
Get the total number of resources that was extracts.
getNumExtraValues() - Method in class net.sf.basedb.core.data.DataCubeData
The number of extra values in this data cube.
getNumExtraValues() - Method in class net.sf.basedb.core.DataCube
Get the number of extra values created for this data cube.
getNumFileFeatures() - Method in class net.sf.basedb.core.ArrayDesign
Get the number of features on this array design that are stored inside files.
getNumFileFeatures() - Method in class net.sf.basedb.core.data.ArrayDesignData
The number of features on this array design that are stored inside files.
getNumFileReporters() - Method in class net.sf.basedb.core.BioAssaySet
Get the number of unique reporters for data that is stored in files.
getNumFileReporters() - Method in class net.sf.basedb.core.data.BioAssaySetData
The number of unique reporters as stored in files in this bioassayset.
getNumFiles() - Method in class net.sf.basedb.clients.web.extensions.LoadServletsProcessor
Get the number of files that was successfully processed.
getNumFiles() - Method in class net.sf.basedb.clients.web.extensions.UninstalledFileProcessor
Get the number of files that was processed.
getNumFiles() - Method in class net.sf.basedb.util.extensions.manager.processor.DeleteResourcesProcessor
Get the number of files that was successfully processed.
getNumFiles() - Method in class net.sf.basedb.util.extensions.manager.processor.DisablePluginsProcessor
Get the number of files that was successfully processed.
getNumFiles() - Method in class net.sf.basedb.util.extensions.manager.processor.ExtractResourcesProcessor
Get the number of files that was successfully processed.
getNumFiles() - Method in class net.sf.basedb.util.extensions.manager.processor.IgnoreFileProcessor
Get the number of files that was processed.
getNumFiles() - Method in class net.sf.basedb.util.extensions.manager.processor.MarkAsProcessedProcessor
Get the number of files that was processed.
getNumFiles() - Method in class net.sf.basedb.util.extensions.manager.processor.PluginInstallationProcessor
Get the number of files that was successfully processed.
getNumFiles() - Method in class net.sf.basedb.util.extensions.manager.processor.RegisterExtensionsProcessor
Get the number of files that was successfully processed.
getNumFiles() - Method in class net.sf.basedb.util.extensions.manager.processor.ResetProcessor
Get the number of files that was processed.
getNumFiles() - Method in class net.sf.basedb.util.extensions.manager.processor.UnregisterExtensionsProcessor
Get the number of files that was successfully processed.
getNumFileSpots() - Method in class net.sf.basedb.core.BioAssay
Get the number of spots that are stored in files.
getNumFileSpots() - Method in class net.sf.basedb.core.BioAssaySet
Get the number of spots that are stored in files.
getNumFileSpots() - Method in class net.sf.basedb.core.data.BioAssayData
The number of unique spots in this bioassayset.
getNumFileSpots() - Method in class net.sf.basedb.core.data.BioAssaySetData
The number of unique spots in this bioassayset.
getNumFileSpots() - Method in class net.sf.basedb.core.data.RawBioAssayData
The number of spots on this raw bioassay that are stored inside files.
getNumFileSpots() - Method in class net.sf.basedb.core.RawBioAssay
Get the number of spots on this raw bioassay that are stored inside files.
getNumFileValues() - Method in class net.sf.basedb.core.data.ExtraValueData
The number of extra values that are stored in files.
getNumFileValues() - Method in class net.sf.basedb.core.ExtraValue
Get the number of values that are stored in files.
getNumFilteredColumns() - Method in class net.sf.basedb.clients.web.taglib.table.Table
 
getNumFilters() - Method in class net.sf.basedb.core.data.DataCubeData
The number of filters in this data cube.
getNumFilters() - Method in class net.sf.basedb.core.DataCube
Get the number of filters created for this data cube.
getNumFormulas() - Method in class net.sf.basedb.core.Formula
Get the number of expression defined by this formula.
getNumIgnored() - Method in class net.sf.basedb.util.extensions.manager.ExtensionsManager
Get the number of ignored files that was found in the last call to ExtensionsManager.scanForChanges().
getNumLayers() - Method in class net.sf.basedb.core.data.DataCubeData
The number of layers in this data cube.
getNumLayers() - Method in class net.sf.basedb.core.DataCube
Get the number of layers created in this data cube.
getNumLines() - Method in class net.sf.basedb.util.gtf.GtfInputStream
Get the number of lines parsed so far.
getNumMembers(DataFileType) - Method in class net.sf.basedb.core.FileSet
Get the number of members in the file set of the specified type.
getNumModified() - Method in class net.sf.basedb.util.extensions.manager.ExtensionsManager
Get the number of modified files that was found in the last call to ExtensionsManager.scanForChanges().
getNumNew() - Method in class net.sf.basedb.util.extensions.manager.ExtensionsManager
Get the number of new files that was found in the last call to ExtensionsManager.scanForChanges().
getNumPlates() - Method in class net.sf.basedb.core.ArrayDesign
The number of plates connected to this array design.
getNumPlugins() - Method in class net.sf.basedb.util.extensions.manager.processor.DisablePluginsProcessor
Get the total number of plug-in installed or updated by the processor.
getNumPlugins() - Method in class net.sf.basedb.util.extensions.manager.processor.PluginInstallationProcessor
Get the total number of plug-in installed or updated by the processor.
getNumPositions() - Method in class net.sf.basedb.core.data.DataCubeData
The number of positions in this data cube.
getNumPositions() - Method in class net.sf.basedb.core.DataCube
Get the number of positions created in this data cube.
getNumPositions(DbControl, int) - Method in class net.sf.basedb.clients.web.ExperimentExplorer
Get the number of unique positions the reporter of the specifed index is present in among all the bioassays in the bioassay set.
getNumPropertyFilters() - Method in class net.sf.basedb.core.ItemContext
Get the total number of property filters stored in this context.
getNumPropertyFilters(int) - Method in class net.sf.basedb.core.ItemContext
Get the number of property filters stored in this context for the given filter row.
getNumRead() - Method in class net.sf.basedb.util.InputStreamSplitter
Get the number of bytes that has been read or skipped from the input stream.
getNumRead() - Method in class net.sf.basedb.util.InputStreamTracker
Get the number of bytes read or skipped from the input stream.
getNumRecent(String) - Method in class net.sf.basedb.core.ItemContext
Get the number of recently used value in the list.
getNumRecent(Item) - Method in class net.sf.basedb.core.ItemContext
Get the number of recently used items in the list.
getNumRecent(Item, String) - Method in class net.sf.basedb.core.ItemContext
Get the number of recently used items in a list with a sublist.
getNumRecent(Item, ItemSubtype) - Method in class net.sf.basedb.core.ItemContext
Get the number of recently used items in the list.
getNumRegistered() - Method in class net.sf.basedb.util.extensions.manager.processor.RegisterExtensionsProcessor
Get the number of extensions + extension points that was registered.
getNumRemoved() - Method in class net.sf.basedb.plugins.AnnotationFlatFileImporter.NewAnnotations
getNumReplaced() - Method in class net.sf.basedb.plugins.AnnotationFlatFileImporter.NewAnnotations
getNumReporters() - Method in class net.sf.basedb.clients.web.ExperimentExplorer
Get the total number of unique reporters found in the bioassayset.
getNumReporters() - Method in class net.sf.basedb.core.BioAssaySet
Get the number of unique reporters among all bioassays in this bioassayset.
getNumReporters() - Method in class net.sf.basedb.core.data.BioAssaySetData
The number of unique reporters in this bioassayset.
getNumReportersNotFound() - Method in class net.sf.basedb.core.RawDataBatcher
Get the number of reporters that was not found.
getNumServlets() - Method in class net.sf.basedb.clients.web.extensions.LoadServletsProcessor
Get the total number of servlets found during the last processing.
getNumSet() - Method in class net.sf.basedb.plugins.AnnotationFlatFileImporter.NewAnnotations
getNumSheets() - Method in class net.sf.basedb.util.excel.XlsxToCsvUtil
Get the number of sheets in the workbook.
getNumSkippedLines() - Method in class net.sf.basedb.util.parser.FlatFileParser
Get the number of lines that the last call to FlatFileParser.nextData() or FlatFileParser.hasMoreData() ignored because they matched the ignore regular expression or couldn't be interpreted as data lines.
getNumSkippedMissingFeature() - Method in class net.sf.basedb.core.RawDataBatcher
Get the number of skipped inserts because of a missing feature.
getNumSpots() - Method in class net.sf.basedb.clients.web.ExperimentExplorer
Get the total number of spots in the bioassayset.
getNumSpots() - Method in class net.sf.basedb.core.BioAssay
Get the number of spots in this bioassay.
getNumSpots() - Method in class net.sf.basedb.core.BioAssaySet
Get the number of spots in all bioassays in this bioassayset.
getNumSpots() - Method in class net.sf.basedb.core.data.BioAssayData
The number of unique spots in this bioassay.
getNumSpots() - Method in class net.sf.basedb.core.data.BioAssaySetData
The number of unique spots in this bioassayset.
getNumStatements() - Method in class net.sf.basedb.core.hibernate.SchemaGenerator.CollectSqlTarget
 
getNumUniqueTranscriptIds() - Method in class net.sf.basedb.util.gtf.GtfInputStream
Get the number of unique transcript ids found so far.
getNumUnmodified() - Method in class net.sf.basedb.util.extensions.manager.ExtensionsManager
Get the number of unmodified files that was found in the last call to ExtensionsManager.scanForChanges().
getNumUnregistered() - Method in class net.sf.basedb.util.extensions.manager.processor.RegisterExtensionsProcessor
Get the number of extensions + extension points that was unregistered.
getNumUnregistered() - Method in class net.sf.basedb.util.extensions.manager.processor.UnregisterExtensionsProcessor
Get the number of extensions + extension points that was unregistered.
getNumValues() - Method in class net.sf.basedb.core.data.ExtraValueData
The number of extra values that have been inserted.
getNumValues() - Method in class net.sf.basedb.core.ExtraValue
Get the number of extra values inserted.
getNumValues(String) - Method in class net.sf.basedb.util.QueryParameters
Get the number of values for a key.
getNumWarnings() - Method in class net.sf.basedb.util.extensions.logging.ExtensionsLog
Get the current number of warning entries in the log.
getNumWarnings() - Method in class net.sf.basedb.util.overview.Node
Get the number of warnings on this node.
getObject(int) - Method in class net.sf.basedb.clients.web.servlet.PlotServlet.CFSqlResult
 
getObject(int) - Method in class net.sf.basedb.core.DynamicResultIterator.SqlResultImpl
 
getObject(int) - Method in interface net.sf.basedb.core.query.SqlResult
Get the value of the specified column as an object.
getObject(String) - Method in class net.sf.basedb.core.ItemContext
Get an object.
getObjectForKey(ObjectKey<O>) - Method in class net.sf.basedb.clients.web.extensions.ExtensionsControl
Get the object that was registered for the given key.
getObjectForKey(ObjectKey<O>) - Method in class net.sf.basedb.util.extensions.manager.ExtensionsFile
Get the object that was registered for the given key.
getObjectsOfClass(Class<T>) - Method in class net.sf.basedb.util.extensions.manager.ExtensionsFile
Get a list of all objects defined in this extensions file that are of the specified class or interface.
getOldItem(SessionControl, T, int) - Static method in class net.sf.basedb.clients.web.Base
Get the old item that is stored in the SessionControl:s session setting itemType.item.
getOldValue() - Method in class net.sf.basedb.core.ChangeHistory
Get the old value of the property had before this change.
getOldValue() - Method in class net.sf.basedb.core.data.ChangeHistoryDetailData
Get the previous value before the change.
getOldValue() - Method in class net.sf.basedb.core.log.ManualLogEntry
Old value before the change.
getOldValues() - Method in class net.sf.basedb.core.AnnotationBatcher.CurrentAnnotationInfo
Get the old annotation values.
getOldValues() - Method in class net.sf.basedb.core.data.ParameterValueData
Get the old values that has been replaced by new values in this session.
getOpen() - Method in class net.sf.basedb.clients.web.taglib.menu.Menu
 
getOperator() - Method in class net.sf.basedb.core.data.PropertyFilterData
Get the operator used for this filter.
getOperator() - Method in class net.sf.basedb.core.PropertyFilter
Get the operator to use in the filter.
getOperators() - Static method in class net.sf.basedb.util.jep.Jep
Get a list of built-in operators supported by the Jep.jepToExpression(JEP) and Jep.jepToRestriction(JEP) converter.
getOptimizeTableSql(String, String, String) - Method in interface net.sf.basedb.core.dbengine.DbEngine
Generate SQL to optimize a table.
getOptimizeTableSql(String, String, String) - Method in class net.sf.basedb.core.dbengine.DefaultDbEngine
Return null.
getOptimizeTableSql(String, String, String) - Method in class net.sf.basedb.core.dbengine.MySQLEngine
Generate optimize table <catalog>.<table>.
getOptimizeTableSql(String, String, String) - Method in class net.sf.basedb.core.dbengine.PostgresDbEngine
Generate VACUUM FULL <schema>.<table>.
getOption(String) - Method in class net.sf.basedb.clients.jobagent.CmdLine
Get the value for the specified option
getOption(String) - Method in class net.sf.basedb.core.AnnotationType
Get an option.
getOption(String) - Method in class net.sf.basedb.plugins.executor.ParameterDefinition
Get the value for an option.
getOption(String, String) - Method in class net.sf.basedb.clients.jobagent.CmdLine
Get the value for an option.
getOption(ValidationRuleAction, String, String) - Method in class net.sf.basedb.util.overview.ValidationOptions
Get the configured option for a validator rule.
getOptionalFilter(Item) - Static method in class net.sf.basedb.core.QueryRuntimeFilterFactory
Get the default optional runtime filter for the speicified item type.
getOptions() - Method in class net.sf.basedb.core.data.AnnotationTypeData
Additional options depending on the value type.
getOptions() - Method in class net.sf.basedb.plugins.Base1PluginExecuter.JobParameter
 
getOptions() - Method in class net.sf.basedb.plugins.executor.ParameterDefinition
Get the names of other options that are defined for this parmeter.
getOrCreate(JspContext, FileViewerContext) - Static method in class net.sf.basedb.clients.web.extensions.fileviewer.FileViewerUtil
Get an existing instance or create a new instance.
getOrdinal() - Method in class net.sf.basedb.core.data.PlateEventTypeData
The ordinal of this event type among all event types defined for the plate type.
getOrdinal() - Method in class net.sf.basedb.core.PlateEventType
Get the order of this event among the list of events.
getOrganisation() - Method in class net.sf.basedb.core.authentication.ExtraUserInformation
The organisation of the user.
getOrganisation() - Method in class net.sf.basedb.core.data.UserData
Get the organisation this user works for, or null if unknown.
getOrganisation() - Method in class net.sf.basedb.core.User
Get the organisation this user works for, or null if unknown.
getOriginalBioMaterial() - Method in class net.sf.basedb.core.BioWell
Get the original biomaterial that was placed in this biowell.
getOriginalBioMaterial() - Method in class net.sf.basedb.core.data.BioWellData
The MeasuredBioMaterialData used in this well.
getOriginalPermissions() - Method in class net.sf.basedb.core.GroupPermissions
Get the internal representation of the original permissions.
getOriginalPermissions() - Method in class net.sf.basedb.core.ProjectPermissions
Get the internal representation of the original permissions.
getOriginalPermissions() - Method in class net.sf.basedb.core.UserPermissions
Get the internal representation of the original permissions.
getOriginalPermissions(Group) - Method in class net.sf.basedb.core.GroupPermissions
Get the original permissions for a group if this object was created with the GroupPermissions(ItemKey) constructor.
getOriginalPermissions(Project) - Method in class net.sf.basedb.core.ProjectPermissions
Get the original permissions for a project if this object was created with the ProjectPermissions(ProjectKey) constructor.
getOriginalPermissions(User) - Method in class net.sf.basedb.core.UserPermissions
Get the original permissions for a user if this object was created with the UserPermissions(ItemKey) constructor.
getOriginalQuantity() - Method in class net.sf.basedb.core.data.MeasuredBioMaterialData
Get the original quantity of the biomaterial.
getOriginalQuantity() - Method in class net.sf.basedb.core.MeasuredBioMaterial
Get the original quantity of the biomaterial.
getOriginX() - Method in class net.sf.basedb.core.ArrayDesignBlock
Get the distance from the left edge of the slide to the top left spot in the block.
getOriginX() - Method in class net.sf.basedb.core.data.ArrayDesignBlockData
Get the distance from the left edge of the slide to the top left spot in the block.
getOriginX() - Method in class net.sf.basedb.plugins.PrintMapFlatFileImporter.MetaBlock
 
getOriginY() - Method in class net.sf.basedb.core.ArrayDesignBlock
Get the distance from the top edge of the slide to the top left spot in the block.
getOriginY() - Method in class net.sf.basedb.core.data.ArrayDesignBlockData
Get the distance from the top edge of the slide to the top left spot in the block.
getOriginY() - Method in class net.sf.basedb.plugins.PrintMapFlatFileImporter.MetaBlock
 
getOut() - Method in class net.sf.basedb.clients.web.extensions.JspContext
Get a writer object that can be used to return generated text to the response that is sent back to the browser.
getOutputStream(File) - Method in class net.sf.basedb.core.Migration
Get a stream for writing to the given file.
getOutputStream(File) - Static method in class net.sf.basedb.util.FileUtil
Get a buffered OutputStream object writing to the specified file.
getOutputStream(String) - Method in class net.sf.basedb.util.bfs.AbstractDataWriterFactory
Create an output stream for writing to a file with the given filename.
getOutputStream(String) - Method in class net.sf.basedb.util.bfs.GenericBaseDataWriterFactory
Create a new file in the data directory with the given file name.
getOutputStream(String) - Method in class net.sf.basedb.util.bfs.GenericDiskDataWriterFactory
Create a new file in the data directory with the given file name.
getOutputStream(String, int) - Method in class net.sf.basedb.util.StaticCache
Get a lock-safe output stream.
getOverrideId() - Method in class net.sf.basedb.core.data.AnnotationData
The ID of the default annotation that this project-specific annotation is overriding. 0 for default annotations.
getOverrideId() - Method in class net.sf.basedb.core.data.annotations.AnnotationLink
 
getOverrideId() - Method in class net.sf.basedb.core.snapshot.AnnotationSnapshot
Get the id of the default annotation that this project-specific annotation is overriding.
getOverwrite() - Method in class net.sf.basedb.core.plugin.AbstractExporterPlugin
Get the configured value for the overwrite parameter.
getOverwrite() - Method in class net.sf.basedb.util.zip.AbstractFileUnpacker
If existing file should be overwritten or not.
getOverwriteAnnotationsParameters(String, String, Boolean) - Method in class net.sf.basedb.core.plugin.AbstractPlugin
Parameter definition that asks if copied annotations should overwrite existing annotations or not.
getOverwriteParameter(String, String) - Method in class net.sf.basedb.core.plugin.AbstractExporterPlugin
Get a plugin parameter that asks if existing files can be overwritten or not.
getOverwriteParameter(String, String) - Method in class net.sf.basedb.util.zip.AbstractFileUnpacker
Get a plugin parameter that asks if existing files should be overwritten or not.
getOwnableItems() - Static method in class net.sf.basedb.core.Metadata
Get a set containing all Ownable item types.
getOwner() - Method in interface net.sf.basedb.core.data.OwnableData
Get the UserData that is the owner of the item.
getOwner() - Method in class net.sf.basedb.core.data.OwnedData
 
getOwner() - Method in interface net.sf.basedb.core.Ownable
Get the User that is the owner of the item.
getOwner() - Method in class net.sf.basedb.core.OwnedItem
 
getPacker() - Method in class net.sf.basedb.plugins.PackedFileExporter
Get the FilePacker that has been configured in the current configuration.
getPacker(String) - Method in class net.sf.basedb.plugins.PackedFileExporter
Create a FilePacker from the given class.
getPage() - Method in class net.sf.basedb.clients.web.taglib.table.Navigator
 
getPage() - Method in class net.sf.basedb.clients.web.taglib.table.Table
 
getPage() - Method in class net.sf.basedb.core.data.ContextData
Get the current page number, starting at 0.
getPage() - Method in class net.sf.basedb.core.ItemContext
Get the current table page.
getPageContext() - Method in class net.sf.basedb.clients.web.extensions.JspContext
Get the JSP Page context object for the current request.
getPageType() - Method in class net.sf.basedb.clients.web.ModeInfo
 
getPageType() - Method in exception net.sf.basedb.clients.web.WebException
Get the page type to display the error message in.
getParameter(int) - Method in class net.sf.basedb.core.hibernate.QueryWrapper
 
getParameter(int, Class<T>) - Method in class net.sf.basedb.core.hibernate.QueryWrapper
 
getParameter(String) - Method in class net.sf.basedb.clients.web.extensions.AbstractJspFactory
Get a generic parameter value.
getParameter(String) - Method in class net.sf.basedb.clients.web.fileupload.FileUpload
Get the value for a form field.
getParameter(String) - Method in class net.sf.basedb.core.hibernate.QueryWrapper
 
getParameter(String) - Method in class net.sf.basedb.core.RequestInformation
Get the plugin parameter with the specified name.
getParameter(String) - Method in class net.sf.basedb.util.export.spotdata.BaseFileExporter
Get the current value of a 'settings' parameter.
getParameter(String) - Method in class net.sf.basedb.util.export.spotdata.BfsExporter
Get the current value of a parameter.
getParameter(String, Class<T>) - Method in class net.sf.basedb.core.hibernate.QueryWrapper
 
getParameterClass() - Method in class net.sf.basedb.core.ParameterType
Get the class a value must have to match this parameter type.
getParameterDefinition() - Method in class net.sf.basedb.plugins.executor.ProgramParameter
Get the definition of this parameter.
getParameterDefinitions(boolean) - Method in class net.sf.basedb.plugins.executor.ExternalProgramExecutor
Get the current program parameter definitions.
getParameterInfo(String) - Method in class net.sf.basedb.core.Job
Get extra information about a parameter.
getParameterInfo(String) - Method in class net.sf.basedb.core.PluginConfiguration
Get extra information about a parameter in the latest version.
getParameterInfo(String, int) - Method in class net.sf.basedb.core.PluginConfiguration
Get extra information about a parameter in a specific version.
getParameterMetadata() - Method in class net.sf.basedb.core.hibernate.QueryWrapper
 
getParameterName(String) - Method in class net.sf.basedb.util.extensions.debug.ProxyActionFactory
Convert a method name to a parameter name.
getParameterNames() - Method in class net.sf.basedb.clients.web.fileupload.FileUpload
Get the names for all fields used in the form, excluding file input fields.
getParameterNames() - Method in class net.sf.basedb.core.AbstractQuery
 
getParameterNames() - Method in class net.sf.basedb.core.Job
Get the names of all parameters for the job.
getParameterNames() - Method in class net.sf.basedb.core.PluginConfiguration
Get the names of all configuration values in the latest version.
getParameterNames() - Method in interface net.sf.basedb.core.query.Query
Get a set with the names for all parameters in this query.
getParameterNames(int) - Method in class net.sf.basedb.core.PluginConfiguration
Get the names of all configuration values in a specific version.
getParameters() - Method in class net.sf.basedb.core.AbstractQuery
Get all query parameters.
getParameters() - Method in class net.sf.basedb.core.data.JobData
The parameters for this job.
getParameters() - Method in class net.sf.basedb.core.data.ProtocolData
This set manages the parameters for this protcol.
getParameters() - Method in class net.sf.basedb.core.hibernate.QueryWrapper
 
getParameters() - Method in class net.sf.basedb.core.Protocol
Get a query that returns all annotation types used as parameters for this protocol.
getParameters() - Method in class net.sf.basedb.core.RequestInformation
Get a list containing the information about the parameters needed for the current request.
getParametersFromBaseFile(File) - Method in class net.sf.basedb.plugins.Base1PluginExecuter
Get the data from the configuration file.
getParameterType() - Method in class net.sf.basedb.core.PluginParameter
Get the parameter type, which tells the client application the data type and allowed values for the parameter.
getParameterType(Class<T>, List<?>) - Method in class net.sf.basedb.core.PluginConfiguration
Gets the ParameterType to use with a class.
getParameterType(String) - Method in class net.sf.basedb.core.AbstractQuery
Get the type of the parameter, or null if not known.
getParameterValue(int) - Method in class net.sf.basedb.core.hibernate.QueryWrapper
 
getParameterValue(String) - Method in class net.sf.basedb.core.AbstractQuery
Get the value of the named parameter.
getParameterValue(String) - Method in class net.sf.basedb.core.hibernate.QueryWrapper
 
getParameterValue(String) - Method in class net.sf.basedb.core.Job
Get the value of a named parameter.
getParameterValue(String) - Method in class net.sf.basedb.core.plugin.NamespaceRequestWrapper
 
getParameterValue(String) - Method in interface net.sf.basedb.core.plugin.Request
Get the value for the parameter with the specified name.
getParameterValue(String) - Method in class net.sf.basedb.core.PluginRequest.RequestImpl
 
getParameterValue(String) - Method in class net.sf.basedb.plugins.executor.ExternalProgramExecutor.RequestWrapper
 
getParameterValue(String, Class<?>) - Method in class net.sf.basedb.util.extensions.debug.ProxyActionFactory
Get the value of a parameter.
getParameterValue(Parameter<T>) - Method in class net.sf.basedb.core.hibernate.QueryWrapper
 
getParameterValues() - Method in class net.sf.basedb.core.Job
Get the configuration parameters as a ParameterValues object.
getParameterValues(int) - Method in class net.sf.basedb.core.PluginConfiguration
Get the configuration parameters as a ParameterValues object.
getParameterValues(String) - Method in class net.sf.basedb.clients.web.fileupload.FileUpload
Get an array of values for a form field.
getParameterValues(String) - Method in class net.sf.basedb.core.Job
Get the values of a named parameter.
getParameterValues(String) - Method in class net.sf.basedb.core.plugin.NamespaceRequestWrapper
 
getParameterValues(String) - Method in interface net.sf.basedb.core.plugin.Request
Get the values for the parameter with the specified name.
getParameterValues(String) - Method in class net.sf.basedb.core.PluginConfiguration
Get the values of a configuration parameter in the latest version.
getParameterValues(String) - Method in class net.sf.basedb.core.PluginRequest.RequestImpl
 
getParameterValues(String) - Method in class net.sf.basedb.plugins.executor.ExternalProgramExecutor.RequestWrapper
 
getParameterValues(String, int) - Method in class net.sf.basedb.core.PluginConfiguration
Get the values of a configuration parameter in a specific version.
getParameterValuesImpl() - Method in class net.sf.basedb.core.Job
Get a write-protected ParameterValuesImpl object.
getParameterValuesImpl(int) - Method in class net.sf.basedb.core.PluginConfiguration
Get a write-protected ParameterValuesImpl object so a job can read the paremeters.
getParameterVersion() - Method in class net.sf.basedb.core.data.JobData
Get the parameter version of the configuration used for this job.
getParameterVersion() - Method in class net.sf.basedb.core.data.PluginConfigurationData
Get the current/latest parameter version.
getParameterVersion() - Method in class net.sf.basedb.core.Job
Get the version number of the configuration parameters used for this job.
getParameterVersion() - Method in class net.sf.basedb.core.PluginConfiguration
Get the latest version number of the parameters.
getParent() - Method in class net.sf.basedb.clients.web.extensions.renderer.PrefixSuffixRenderer
 
getParent() - Method in class net.sf.basedb.core.data.DirectoryData
Get the parent directory of this directory.
getParent() - Method in class net.sf.basedb.core.data.MeasuredBioMaterialData
Get the parent biomaterial.
getParent() - Method in class net.sf.basedb.core.data.WellData
If the plate was created from a PlateMappingData this property points to the well on the source plate used in the mapping.
getParent() - Method in class net.sf.basedb.core.Directory
Get the parent directory of this directory.
getParent() - Method in class net.sf.basedb.core.MeasuredBioMaterial
Get the parent biomaterial if there is a single parent item only.
getParent() - Method in class net.sf.basedb.core.Path
Get the parent path.
getParent() - Method in class net.sf.basedb.core.Well
Get the parent well.
getParent() - Method in interface net.sf.basedb.util.extensions.WrappingRenderer
Get the current parent renderer.
getParent() - Method in class net.sf.basedb.util.overview.Node
Get the parent of this node.
getParent() - Method in class net.sf.basedb.util.Tree.Entry
Get the entry for the parent node.
getParentBioAssay() - Method in class net.sf.basedb.core.data.RawBioAssayData
Get the derived bioassay that this raw bioassay has been created from.
getParentBioAssay() - Method in class net.sf.basedb.core.RawBioAssay
Get the DerivedBioAssay this raw bioassay is created from.
getParentExtract() - Method in class net.sf.basedb.core.data.RawBioAssayData
Get the derived bioassay that this raw bioassay has been created from.
getParentExtract() - Method in class net.sf.basedb.core.RawBioAssay
Get the Extract this raw bioassay is created from.
getParentFileSets() - Method in class net.sf.basedb.core.ArrayDesign
There are no parent file sets.
getParentFileSets() - Method in class net.sf.basedb.core.BioAssaySet
Get the file set from the parent bioassay set if it exists.
getParentFileSets() - Method in class net.sf.basedb.core.DerivedBioAssay
 
getParentFileSets() - Method in class net.sf.basedb.core.ExtraValue
Get the file set from the parent bioassay set if it exists.
getParentFileSets() - Method in interface net.sf.basedb.core.FileStoreEnabled
Get the file sets of parent item(s) that are related to the current item.
getParentFileSets() - Method in class net.sf.basedb.core.RawBioAssay
Get the file set from the array design, if it exists.
getParentHasNullReporter() - Method in class net.sf.basedb.util.importer.spotdata.BaseFileInfo
A flag that indicates if at least one position in the parent bioassay set has a null reporter or not.
getParentHasZeroReporter() - Method in class net.sf.basedb.util.importer.spotdata.BaseFileInfo
A flag that indicates if at least one position in the parent bioassay set has a reporter with ID=0.
getParentId() - Method in class net.sf.basedb.core.data.keyring.GroupGroups
Get the id of the parent group.
getParentInformation(DbControl, Node) - Method in class net.sf.basedb.util.overview.validator.ProtocolParameterValidator
Load parent item information from the current protocol node.
getParentItem() - Method in class net.sf.basedb.clients.web.extensions.fileviewer.FileViewerContext
If the context has a parent item this method returns it.
getParentPlates() - Method in class net.sf.basedb.core.Plate
Get a query returning the parent plates of this plate.
getParentProperties(DbControl, BioAssay, Metadata.PropertyPath<RawBioAssay, ?>) - Static method in class net.sf.basedb.util.BioAssaySetUtil
Find the values of parent properties for a given bioassay.
getParentQuery() - Method in class net.sf.basedb.core.hibernate.NativeQueryWrapper
Get the underlying parent query from Hibernate.
getParents() - Method in class net.sf.basedb.core.BioAssay
Get a query for loading the parents bioassays to this bioassay.
getParents() - Method in class net.sf.basedb.core.data.BioAssayData
Get a set that manages the parent bioassays the data in this bioassay is based on.
getParents() - Method in class net.sf.basedb.core.data.DerivedBioAssayData
A set that manages the parent bioassays that this derived bioassay related to.
getParents() - Method in class net.sf.basedb.core.data.GroupData
This is the inverse end.
getParents() - Method in class net.sf.basedb.core.data.ItemSubtypeData
This is the inverse end.
getParents() - Method in class net.sf.basedb.core.data.PlateData
If the plate was created by a PlateMappingData the source plates are kept here.
getParents() - Method in class net.sf.basedb.core.DerivedBioAssay
Get all parent derived bioassays.
getParents() - Method in class net.sf.basedb.util.importer.spotdata.BaseFileInfo.ChildBioAssay
Get the parent assays of this child.
getParentSession() - Method in class net.sf.basedb.core.hibernate.SessionWrapper
Get the underlying parent session from Hibernate.
getParentSession() - Method in class net.sf.basedb.core.hibernate.StatelessSessionWrapper
Get the underlying parent session from Hibernate.
getParentSet() - Method in class net.sf.basedb.core.data.PlateData
Duplicate of PlateData.getParents() but with a set instead of a map.
getParentSubtypes() - Method in class net.sf.basedb.core.ItemSubtype
Get a query returning all subtypes that have a relation to this subtype.
getParentSubtypes(DbControl, Subtypable, Item) - Static method in class net.sf.basedb.core.ItemSubtype
Utility method for locating all subtypes that have a relationship to the subtype of the given item.
getParentType() - Method in class net.sf.basedb.core.BasicChildItem
Get the type of item that is the parent of this item.
getParentType() - Method in class net.sf.basedb.core.data.MeasuredBioMaterialData
Get the type of the parent item.
getParentType() - Method in class net.sf.basedb.core.ItemSubtypeFileType
 
getParentType() - Method in class net.sf.basedb.core.MeasuredBioMaterial
Get the item type of the parent biomaterial.
getParentType() - Method in class net.sf.basedb.core.PlatformFileType
 
getParentType() - Method in class net.sf.basedb.core.PlatformVariant
 
getParseAllExcelSheets() - Method in class net.sf.basedb.util.parser.FlatFileParser
 
getParsedBytes() - Method in class net.sf.basedb.util.bfs.AnnotationParser
 
getParsedBytes() - Method in interface net.sf.basedb.util.bfs.BfsParser
Get the number of parsed bytes so far.
getParsedBytes() - Method in class net.sf.basedb.util.bfs.DataParser
 
getParsedBytes() - Method in class net.sf.basedb.util.bfs.MetadataParser
 
getParsedBytes() - Method in class net.sf.basedb.util.charset.CharsetDetector
Get the number of bytes that the last test operation parsed.
getParsedBytes() - Method in class net.sf.basedb.util.importer.spotdata.SynchronizedSpotDataParser
 
getParsedBytes() - Method in class net.sf.basedb.util.parser.FlatFileParser
Get the number of parsed bytes so far.
getParsedCharacters() - Method in class net.sf.basedb.util.parser.FlatFileParser
Get the number of parsed characters so far.
getParsedDataLines() - Method in class net.sf.basedb.util.parser.FlatFileParser
Get the number of parsed data lines so far in the current section.
getParsedLines() - Method in class net.sf.basedb.util.charset.CharsetDetector
 
getParsedLines() - Method in class net.sf.basedb.util.parser.FlatFileParser
Get the number of parsed lines so far.
getParsedSections() - Method in class net.sf.basedb.util.parser.FlatFileParser
Get the number of found sections so far.
getParser() - Method in class net.sf.basedb.core.data.FormulaData
Which parser to use to convert the formula to an expression or restriction. 1 = JEP
getParser() - Method in class net.sf.basedb.core.Formula
Get the parser that converts the formula to an expresion or restriction.
getParser() - Method in class net.sf.basedb.util.importer.spotdata.SynchronizedSpotDataParser.SynchronizedData
The underlying parser.
getParsingFailure() - Method in class net.sf.basedb.util.charset.CharsetDetector
If the last test failed, get the exception that was thrown by the parser.
getParticipant(BioPlate) - Method in class net.sf.basedb.core.BioPlateEvent
Get the participant object representing the given bioplate in this event.
getParticipants() - Method in class net.sf.basedb.core.BioPlateEvent
Get a query returning all participants in the event.
getParticipants() - Method in class net.sf.basedb.core.data.BioPlateEventData
This is the inverse end.
getPassword() - Method in class net.sf.basedb.clients.jobagent.Agent
Get the agent.password configuration value.
getPassword() - Method in class net.sf.basedb.core.authentication.LoginRequest
Get the password to use.
getPassword() - Method in class net.sf.basedb.core.data.FileServerData
Get the password that is used to login to the server.
getPassword() - Method in class net.sf.basedb.core.data.UserData
Get the PasswordData object which allows you to change the password for the user.
getPassword() - Method in class net.sf.basedb.core.FileServer
Get the password that is used when authenticating with the file server.
getPassword() - Method in class net.sf.basedb.util.uri.ConnectionParameters
Get the password that should be used to authenticate the user.
getPasswordField() - Method in interface net.sf.basedb.clients.web.extensions.login.LoginFormAction
Get attributes for the password field on the form.
getPasswordField() - Method in class net.sf.basedb.clients.web.extensions.login.LoginFormBean
 
getPasswordField() - Method in class net.sf.basedb.clients.web.extensions.login.PasswordLoginFormFactory
 
getPasswordParameter() - Method in interface net.sf.basedb.util.zip.FilePacker
The default implementation return a parameter asking for a password.
getPasswordParameter() - Method in class net.sf.basedb.util.zip.ZipFilePacker
Get the encyption password parameter.
getPath() - Method in class net.sf.basedb.core.Directory
Get the complete path to this directory.
getPath() - Method in class net.sf.basedb.core.File
Get the complete path of this file.
getPath() - Method in class net.sf.basedb.core.Metadata.BasicData2ItemPropertyPath
 
getPath() - Method in class net.sf.basedb.core.Metadata.BasicItem2DataPropertyPath
 
getPath() - Method in class net.sf.basedb.core.Metadata.CollectionPropertyPath
 
getPath() - Method in class net.sf.basedb.core.Metadata.CombinedPropertyPath
 
getPath() - Method in class net.sf.basedb.core.Metadata.ComponentPropertyPath
 
getPath() - Method in class net.sf.basedb.core.Metadata.DateCopyPropertyPath
 
getPath() - Method in class net.sf.basedb.core.Metadata.EntityPropertyPath
 
getPath() - Method in class net.sf.basedb.core.Metadata.EvictPropertyPath
 
getPath() - Method in class net.sf.basedb.core.Metadata.IdentifierPropertyPath
 
getPath() - Method in class net.sf.basedb.core.Metadata.MapPropertyPath
 
getPath() - Method in class net.sf.basedb.core.Metadata.NoopPropertyPath
 
getPath() - Method in interface net.sf.basedb.core.Metadata.PropertyPath
Get the path that this object represents.
getPath() - Method in class net.sf.basedb.core.Metadata.ReporterScore2DataPropertyPath
 
getPathInfo() - Method in class net.sf.basedb.clients.web.extensions.RequestWrapper
From the HttpServletRequestInterface ------------------------------------
getPathType() - Method in class net.sf.basedb.core.PathParameterType
Get the type of the path to ask for.
getPattern(String) - Method in class net.sf.basedb.plugins.AbstractFlatFileImporter
 
getPattern(String, int, int) - Method in class net.sf.basedb.util.export.spotdata.AdvancedFieldConverter
 
getPattern(ParameterValues, String) - Method in class net.sf.basedb.plugins.AbstractFlatFileImporter
 
getPercent() - Method in class net.sf.basedb.core.SimpleProgressReporter
Get the last percentage completed of the task.
getPercentComplete() - Method in class net.sf.basedb.core.data.JobData
If the job is running, how many percent has been completed.
getPercentComplete() - Method in class net.sf.basedb.core.Job
An estimate of the percentage of the work currently completed by an executing job.
getPercentile(List<? extends Number>, int) - Method in class net.sf.basedb.clients.web.servlet.ExperimentExplorerPlotServlet
Calculates the percentile values from a sorted list of values.
getPermanentSelects() - Method in class net.sf.basedb.core.AbstractQuery
Get all permanent selects.
getPermission() - Method in class net.sf.basedb.core.data.keyring.KeyPermission
Get the permission.
getPermission() - Method in class net.sf.basedb.core.data.keyring.ProjectPermission
Get the permission.
getPermissionCode(Set<Permission>) - Static method in class net.sf.basedb.clients.web.PermissionUtil
Translate the given set of permissions to an integer code that can be used to later recreate the set again.
getPermissionForUse() - Method in class net.sf.basedb.core.ChildItem
Get the permission that is required on the parent item that gives use permission on the child item.
getPermissionForWriteDeleteAndCreate() - Method in class net.sf.basedb.core.BasicChildItem
Get the permission that is required on the parent item that gives write, delete and create permission on the child item.
getPermissionForWriteDeleteAndCreate() - Method in class net.sf.basedb.core.BioAssay
USE permission is enough to be able to manage bioassays.
getPermissionForWriteDeleteAndCreate() - Method in class net.sf.basedb.core.BioAssaySet
USE permission is enough to be able to manage bioassay sets.
getPermissionForWriteDeleteAndCreate() - Method in class net.sf.basedb.core.ChildItem
Get the permission that is required on the parent item that gives write, delete and create permission on the child item.
getPermissionForWriteDeleteAndCreate() - Method in class net.sf.basedb.core.DataCube
USE permission is enough to be able to manage data cubes.
getPermissionForWriteDeleteAndCreate() - Method in class net.sf.basedb.core.DataCubeColumn
USE permission is enough to be able to manage data cubes.
getPermissionForWriteDeleteAndCreate() - Method in class net.sf.basedb.core.DataCubeExtraValue
USE permission is enough to be able to manage data cubes.
getPermissionForWriteDeleteAndCreate() - Method in class net.sf.basedb.core.DataCubeFilter
USE permission is enough to be able to manage data cubes.
getPermissionForWriteDeleteAndCreate() - Method in class net.sf.basedb.core.DataCubeLayer
USE permission is enough to be able to manage data cubes.
getPermissionForWriteDeleteAndCreate() - Method in class net.sf.basedb.core.ExtraValue
USE permission is enough to be able to manage extra values.
getPermissionForWriteDeleteAndCreate() - Method in class net.sf.basedb.core.RootRawBioAssay
WRITE permission is required to be able to manage root raw bioassays.
getPermissionForWriteDeleteAndCreate() - Method in class net.sf.basedb.core.Transformation
USE permission is enough to be able to manage transformations.
getPermissionForWriteDeleteAndCreate() - Method in class net.sf.basedb.core.VirtualDb
USE permission is enough to be able to manage virtual db.
getPermissionGroups() - Static method in class net.sf.basedb.clients.web.PermissionUtil
 
getPermissions() - Method in class net.sf.basedb.clients.web.extensions.ExtensionsControl
 
getPermissions() - Method in interface net.sf.basedb.core.AccessControlled
Get the logged in user's permissions on the item.
getPermissions() - Method in class net.sf.basedb.core.BasicBatcher
 
getPermissions() - Method in class net.sf.basedb.core.BasicItem
 
getPermissions() - Method in class net.sf.basedb.core.BioMaterialEventSource
 
getPermissions() - Method in class net.sf.basedb.core.Coloring
 
getPermissions() - Method in class net.sf.basedb.core.data.PluginDefinitionData
Get a map containing the rolekey and the permissions for this plugin.
getPermissions() - Method in class net.sf.basedb.core.plugin.AbstractPlugin
Return null, which gives the plugin the same permissions as the logged in user.
getPermissions() - Method in interface net.sf.basedb.core.plugin.Plugin
Get the permissions this plugin requires to function as expected.
getPermissions() - Method in class net.sf.basedb.plugins.AnnotationFlatFileImporter
Request read access to File:s, read access to annotation types and write access to all annotatable items.
getPermissions() - Method in class net.sf.basedb.plugins.Base1PluginExecuter
 
getPermissions() - Method in class net.sf.basedb.plugins.BaseFileExporterPlugin
Request create and write access to File:s and Directory:s and read access to Experiment:s and User:s.
getPermissions() - Method in class net.sf.basedb.plugins.CdfFileReporterImporter
Request create and write access to Reporter:s and read access to File:s ArrayDesign:s, ReporterType:s, Platform:s and DataFileType:s
getPermissions() - Method in class net.sf.basedb.plugins.CloneReportersPlugin
Request write permission to Experiment:s and Reporter clone templates and read permission to reporters.
getPermissions() - Method in class net.sf.basedb.plugins.FormulaFilter
Request use access to Experiment:s and read access to Job:s and ReporterLists.
getPermissions() - Method in class net.sf.basedb.plugins.GalExporter
Request create and write access to File:s, Directory:s and ArrayDesign:s read access to User:s and forced read access to DataFileType:s.
getPermissions() - Method in class net.sf.basedb.plugins.HelpExporter
Request create and write access to File:s and Directory:s and read access to Client:s and User:s.
getPermissions() - Method in class net.sf.basedb.plugins.HelpImporter
Request write access to Client:s and read access to File:s.
getPermissions() - Method in class net.sf.basedb.plugins.IntensityCalculatorPlugin
Request use access to Experiment:s and read access to RawBioAssay:s, ArrayDesign:s, Formulas:s, Job:s and and Reporter:s.
getPermissions() - Method in class net.sf.basedb.plugins.JepExtraValueCalculator
Request use access to Experiment:s and ExtraValueType:s and read access to Job:s.
getPermissions() - Method in class net.sf.basedb.plugins.JepIntensityTransformer
Request use access to Experiment:s and read access to Job:s.
getPermissions() - Method in class net.sf.basedb.plugins.LowessNormalization
Request use access to Experiment:s and read access to Job:s.
getPermissions() - Method in class net.sf.basedb.plugins.MedianRatioNormalization
Request use access to Experiment:s and read access to Job:s.
getPermissions() - Method in class net.sf.basedb.plugins.PackedFileExporter
Request create and delete access to File:s and Directory:s.
getPermissions() - Method in class net.sf.basedb.plugins.PlateFlatFileImporter
Request create access to Plate:s, use access to PlateType:s and read access to Reporter:s, PlateGeometry:s and File:s.
getPermissions() - Method in class net.sf.basedb.plugins.PlateMappingExporter
Request create and write access to File:s and Directory:s and read access to PlateMapping:s and PlateGeometries.
getPermissions() - Method in class net.sf.basedb.plugins.PlateMappingImporter
Request create and write access to PlateMapping:s, create and use access to PlateGeometries and read access to File:s.
getPermissions() - Method in class net.sf.basedb.plugins.PluginConfigurationExporter
Request create and write access to File:s and Directory:s and read access to PluginConfigurations:s, PluginDefinition:s and User:s.
getPermissions() - Method in class net.sf.basedb.plugins.PrintMapFlatFileImporter
Request write access to ArrayDesign:s, read access to Plate:s, Reporter:s, DataFileType:s, Platform:s and File:s.
getPermissions() - Method in class net.sf.basedb.plugins.RawDataFlatFileImporter
Request write access to RawBioAssay:s and read access to ArrayDesign:s, File:s, Reporter:s, Platform:s and DataFileType:s
getPermissions() - Method in class net.sf.basedb.plugins.ReporterFlatFileImporter
Request create, write and delete access to Reporter:s, write access to ReporterList:s and read access to File:s and ReporterType:s.
getPermissions() - Method in class net.sf.basedb.plugins.ReporterMapFlatFileImporter
Request write access to ArrayDesign:s, read access to Reporter:s, DataFileType:s, Platform:s and File:s.
getPermissions() - Method in class net.sf.basedb.util.zip.AbstractFileUnpacker
Request create and write access to File:s and Directory:s.
getPermissions(int) - Static method in class net.sf.basedb.clients.web.PermissionUtil
Translate a given integer to a set of permissions.
getPermissions(Group) - Method in class net.sf.basedb.core.GroupPermissions
Get the permissions for a group.
getPermissions(Group) - Method in class net.sf.basedb.core.ItemKey
Get the permissions for a group.
getPermissions(Group) - Method in class net.sf.basedb.core.MultiPermissions
Get the permissions for a group.
getPermissions(Group) - Method in class net.sf.basedb.core.Project
Get the permissions for a group in this project.
getPermissions(Project) - Method in class net.sf.basedb.core.MultiPermissions
Get the permissions for a project.
getPermissions(Project) - Method in class net.sf.basedb.core.ProjectKey
Get the permissions for a project.
getPermissions(Project) - Method in class net.sf.basedb.core.ProjectPermissions
Get the permissions for a project.
getPermissions(Role) - Method in class net.sf.basedb.core.RoleKey
Get the permissions for a role.
getPermissions(User) - Method in class net.sf.basedb.core.ItemKey
Get the permissions for a user.
getPermissions(User) - Method in class net.sf.basedb.core.MultiPermissions
Get the permissions for a user.
getPermissions(User) - Method in class net.sf.basedb.core.Project
Get the permissions for a user in this project.
getPermissions(User) - Method in class net.sf.basedb.core.UserPermissions
Get the permissions for a user.
getPermissionTemplate() - Method in class net.sf.basedb.core.data.ProjectData
A permission template can be used to set default permissions when this project is active.
getPermissionTemplate() - Method in class net.sf.basedb.core.Project
Get the permission template that is used to share new items when this project is active.
getPhone() - Method in class net.sf.basedb.core.authentication.ExtraUserInformation
The phone number to the user.
getPhone() - Method in class net.sf.basedb.core.data.UserData
Get the phone number to the user, or null if unknown.
getPhone() - Method in class net.sf.basedb.core.User
Get the phone number to the user, or null if unknown.
getPhysicalBioAssay() - Method in class net.sf.basedb.core.ArraySlide
Get the PhysicalBioAssay item which was used on this slide.
getPhysicalBioAssay() - Method in class net.sf.basedb.core.BioMaterialEvent
Get the PhysicalBioAssay that was created by this event.
getPhysicalBioAssay() - Method in class net.sf.basedb.core.data.ArraySlideData
Get the bioassay.
getPhysicalBioAssay() - Method in class net.sf.basedb.core.data.BioMaterialEventData
Get the physical bioassay that was created by this event.
getPhysicalBioAssays() - Method in class net.sf.basedb.core.data.DerivedBioAssayData
A set that manages the parent physical bioassays that this derived bioassay is related to.
getPhysicalBioAssays() - Method in class net.sf.basedb.core.DerivedBioAssay
Get a query that returns the physical bioassays used to create this derived bioassay.
getPhysicalBioAssays() - Method in class net.sf.basedb.core.Extract
Get a query that returns all bioassays created from this extract.
getPhysicalBioAssays(DbControl, OverviewContext, DerivedBioAssay) - Static method in class net.sf.basedb.util.overview.validator.PhysicalBioAssayValidator
Get all physical bioassays that are parents to the given derived bioassay.
getPlaceHolder() - Method in class net.sf.basedb.clients.web.extensions.login.FieldInfo
Get a placeholder text that is displayed in the field when it is empty.
getPlainConnection() - Static method in class net.sf.basedb.core.HibernateUtil
 
getPlate() - Method in class net.sf.basedb.core.ArrayDesignPlate
Gets the Plate that belongs to this item.
getPlate() - Method in class net.sf.basedb.core.BioWell
Get the BioPlate this biowell belongs to.
getPlate() - Method in class net.sf.basedb.core.data.ArrayDesignPlateData
Get the Plate.
getPlate() - Method in class net.sf.basedb.core.data.MappingCoordinate
Get the plate number.
getPlate() - Method in class net.sf.basedb.core.data.PlateEventData
The plate this event belongs to.
getPlate() - Method in class net.sf.basedb.core.data.WellData
The plate this well belongs to.
getPlate() - Method in class net.sf.basedb.core.PlateEvent
Get the Plate this event belongs to.
getPlate() - Method in class net.sf.basedb.core.Well
Get the Plate this event belongs to.
getPlate(int) - Method in class net.sf.basedb.core.ArrayDesign
Get a Plate from a given position.
getPlateCoordinate() - Method in class net.sf.basedb.core.BioWell
Get the plate coordinate representation of the coordinate for this well.
getPlateEvents() - Method in class net.sf.basedb.core.data.PlateEventTypeData
This is the inverse end.
getPlateEventType() - Method in class net.sf.basedb.core.data.PlateEventData
The event type of this event.
getPlateEventType() - Method in class net.sf.basedb.core.PlateEvent
Get the PlateEventType of this event.
getPlateGeometry() - Method in class net.sf.basedb.core.BioPlate
Get the PlateGeometry of this bioplate.
getPlateGeometry() - Method in class net.sf.basedb.core.data.BioPlateData
The geometry of this plate type.
getPlateGeometry() - Method in class net.sf.basedb.core.data.PlateTypeData
The geometry of this plate type.
getPlateGeometry() - Method in class net.sf.basedb.core.PlateType
Get the PlateGeometry of this plate type.
getPlateMapping() - Method in class net.sf.basedb.core.data.PlateData
If this plate was created by a plate mapping, it is linked here.
getPlateMapping() - Method in class net.sf.basedb.core.Plate
Get the PlateMapping used to create this plate.
getPlatePosition(Plate) - Method in class net.sf.basedb.core.ArrayDesign
Get the position of a Plate in this array design.
getPlates() - Method in class net.sf.basedb.core.ArrayDesign
Get a query that returns the plates that are used by this arraydesign.
getPlates() - Method in class net.sf.basedb.core.data.ArrayDesignData
The plates this design is made from.
getPlates() - Method in class net.sf.basedb.core.data.PlateTypeData
The plates of this type.
getPlates() - Method in class net.sf.basedb.core.PlateType
Get a query that returns all plates of this plate type.
getPlateType() - Method in class net.sf.basedb.core.data.PlateData
The plate type of this plate.
getPlateType() - Method in class net.sf.basedb.core.data.PlateEventTypeData
The plate type this event type belongs to.
getPlateType() - Method in class net.sf.basedb.core.Plate
Get the PlateType of this plate.
getPlateType() - Method in class net.sf.basedb.core.PlateEventType
Get the PlateType this event type belongs to.
getPlateTypes() - Method in class net.sf.basedb.core.data.PlateGeometryData
This is the invers end.
getPlateTypes() - Method in class net.sf.basedb.core.PlateGeometry
Get a query returning all plate types using this geometry.
getPlatform() - Method in class net.sf.basedb.core.ArrayDesign
 
getPlatform() - Method in class net.sf.basedb.core.BioAssaySet
 
getPlatform() - Method in class net.sf.basedb.core.data.ArrayDesignData
Get the platform this raw bioassay uses
getPlatform() - Method in class net.sf.basedb.core.data.PlatformFileTypeData
Get the platform.
getPlatform() - Method in class net.sf.basedb.core.data.PlatformVariantData
The parent platform of this variant.
getPlatform() - Method in class net.sf.basedb.core.data.RawBioAssayData
Get the platform this raw bioassay uses.
getPlatform() - Method in class net.sf.basedb.core.DerivedBioAssay
 
getPlatform() - Method in class net.sf.basedb.core.ExtraValue
 
getPlatform() - Method in interface net.sf.basedb.core.FileStoreEnabled
Get the platform the item is related to.
getPlatform() - Method in class net.sf.basedb.core.PlatformFileType
Get the platform.
getPlatform() - Method in class net.sf.basedb.core.PlatformVariant
Get that platform this is a variant of.
getPlatform() - Method in class net.sf.basedb.core.RawBioAssay
 
getPlatform(DbControl) - Method in class net.sf.basedb.core.RawDataType
Get the platform that this raw data type is associated with.
getPlatformRawDataType(Session, String) - Static method in class net.sf.basedb.core.RawDataTypes
 
getPlatforms() - Method in class net.sf.basedb.core.data.DataFileTypeData
This is the inverse end.
getPlatforms() - Method in class net.sf.basedb.core.DataFileType
Get a query that returns all platforms/variants that are using this file type.
getPlotGenerators() - Method in interface net.sf.basedb.clients.web.extensions.plot.OverviewPlotAction
The plot generates that contains information for each image that is generated.
getPlotGenerators() - Method in class net.sf.basedb.clients.web.extensions.plot.OverviewPlotBean
 
getPlugin() - Method in class net.sf.basedb.core.data.ChangeHistoryData
 
getPlugin() - Method in class net.sf.basedb.core.PluginRequest
Get the plugin object.
getPlugin(DbControl) - Method in class net.sf.basedb.core.ChangeHistory
Load the plug-in that made the change.
getPlugin(DbControl) - Method in class net.sf.basedb.core.ChangeHistory.TransactionInfo
Load the plug-in that was executing the transaction.
getPlugin(DbControl, ChangeHistory, boolean, boolean) - Static method in class net.sf.basedb.clients.web.ChangeHistoryUtil
Get the plug-in that made the change in HTML format.
getPluginConfiguration() - Method in class net.sf.basedb.core.data.JobData
The plugin configuration for the plugin.
getPluginConfiguration() - Method in class net.sf.basedb.core.Job
Get the PluginConfiguration defining the plugin this job should execute.
getPluginConfiguration() - Method in class net.sf.basedb.core.ParameterValuesImpl
 
getPluginConfiguration() - Method in class net.sf.basedb.core.plugin.NamespaceParameterValuesWrapper
 
getPluginConfiguration() - Method in interface net.sf.basedb.core.plugin.ParameterValues
Get the configuration that we are using/configuring.
getPluginConfiguration() - Method in class net.sf.basedb.core.plugin.ParameterValuesWrapper
 
getPluginConfiguration() - Method in class net.sf.basedb.plugins.gtf.DefaultConfigurationValues
 
getPluginConfiguration() - Method in class net.sf.basedb.util.ContextUtil.ContextResult
Get the plugin configuration that was checked, or null.
getPluginConfigurations() - Method in class net.sf.basedb.core.PluginDefinition
Get a query that returns the configurations for this plugin definition.
getPluginDefinition() - Method in class net.sf.basedb.core.data.JobAgentSettingsData
The plugin these settings are used for.
getPluginDefinition() - Method in class net.sf.basedb.core.data.JobData
The plugin that executes the job.
getPluginDefinition() - Method in class net.sf.basedb.core.data.PluginConfigurationData
Get the plugin definition for this configuration.
getPluginDefinition() - Method in class net.sf.basedb.core.Job
Get the PluginConfiguration defining the plugin this job should execute.
getPluginDefinition() - Method in class net.sf.basedb.core.JobAgentSettings
Get the plugin that these settings are used for.
getPluginDefinition() - Method in class net.sf.basedb.core.ParameterValuesImpl
 
getPluginDefinition() - Method in class net.sf.basedb.core.plugin.NamespaceParameterValuesWrapper
 
getPluginDefinition() - Method in interface net.sf.basedb.core.plugin.ParameterValues
Get the plugin that we are executing/configuring.
getPluginDefinition() - Method in class net.sf.basedb.core.plugin.ParameterValuesWrapper
Get the PluginDefinition of either the job or the configuration, depending in the preferJob parameter that was set when creating this object.
getPluginDefinition() - Method in class net.sf.basedb.core.PluginConfiguration
Get the plugin definition for this configuration.
getPluginDefinition() - Method in class net.sf.basedb.plugins.gtf.DefaultConfigurationValues
 
getPluginDefinition() - Method in class net.sf.basedb.util.ContextUtil.ContextResult
Get the plugin definition that was checked.
getPluginDefinitionId() - Method in class net.sf.basedb.core.data.keyring.PluginKeys
Gets the id of the plugin
getPluginDefinitions() - Method in class net.sf.basedb.util.extensions.xml.XmlLoader
Get a list with all loaded plug-in definitions.
getPluginDirectory(DbControl, String) - Method in class net.sf.basedb.plugins.Base1PluginExecuter
Get a directory
getPluginId() - Method in class net.sf.basedb.core.ChangeHistory
Get the ID of the plug-in that was making the change.
getPluginId() - Method in class net.sf.basedb.core.ChangeHistory.TransactionInfo
Get the ID of the plug-in that was executing the transaction.
getPluginId() - Method in class net.sf.basedb.core.data.ChangeHistoryData
The ID of the plug-in that was making the changes.
getPluginId() - Method in class net.sf.basedb.core.log.TransactionDetails
Get the ID of the currently running plug-in or 0 if no plug-in is running.
getPluginId() - Method in class net.sf.basedb.core.SessionControl
Get the id of the plug-in that is currently running with this session control.
getPluginName() - Method in class net.sf.basedb.core.log.TransactionDetails
Utility method for loading the name of the currently executing plugin.
getPluginName() - Method in class net.sf.basedb.core.SessionControl
Get the name of the plug-in that is currently running with this session control.
getPluginParameter() - Method in class net.sf.basedb.plugins.Base1PluginExecuter.JobParameter
 
getPluginPermissions() - Method in class net.sf.basedb.core.Annotation
 
getPluginPermissions() - Method in class net.sf.basedb.core.AnnotationSet
 
getPluginPermissions() - Method in class net.sf.basedb.core.AnyToAny
 
getPluginPermissions() - Method in class net.sf.basedb.core.BasicBatcher
 
getPluginPermissions() - Method in class net.sf.basedb.core.BasicChildItem
 
getPluginPermissions() - Method in class net.sf.basedb.core.BasicItem
 
getPluginPermissions() - Method in class net.sf.basedb.core.ChildItem
 
getPluginPermissions() - Method in class net.sf.basedb.core.FeatureBatcher
 
getPluginPermissions() - Method in class net.sf.basedb.core.FileSet
 
getPluginPermissions() - Method in class net.sf.basedb.core.FileSetMember
 
getPluginPermissions() - Method in class net.sf.basedb.core.ItemKey
 
getPluginPermissions() - Method in class net.sf.basedb.core.Project
Make sure plug-ins always has at least read access to the active project.
getPluginPermissions() - Method in class net.sf.basedb.core.ProjectKey
 
getPluginPermissions() - Method in class net.sf.basedb.core.RawDataBatcher
 
getPluginPermissions() - Method in class net.sf.basedb.core.ReporterCloneTemplate
 
getPluginPermissions() - Method in class net.sf.basedb.core.RoleKey
 
getPluginPermissions() - Method in class net.sf.basedb.core.User
Make sure plug-ins always has at least read access to the logged in user.
getPluginPermissions(Item) - Method in class net.sf.basedb.core.Keyring
Get the active plugin's permissions to an unspecified item of a certain Item type.
getPluginPermissions(Item) - Method in class net.sf.basedb.core.SessionControl
Get all plugin-specific permissions for the specified item type.
getPlugins() - Method in class net.sf.basedb.core.data.JobAgentData
The plugins that can be executed by this job agent.
getPlugins() - Method in class net.sf.basedb.core.data.PluginTypeData
The plugin implementing this interface.
getPlugins() - Method in class net.sf.basedb.core.PluginType
Get a query that returns the plugin definitions which implements this type.
getPluginsDir() - Method in class net.sf.basedb.clients.web.extensions.XJspCompiler
Get the path to the plug-in directory from BASE.
getPluginsDirectory() - Static method in class net.sf.basedb.core.Application
Get the directory where plug-ins and extensions must be installed.
getPluginSessionControl(PluginDefinition, Job) - Method in class net.sf.basedb.core.PluginSessionControl
Create a new session control for executing a plugin using the same parent as this session control has.
getPluginSessionControl(PluginDefinition, Job) - Method in class net.sf.basedb.core.SessionControl
Create a new session control for executing a plugin.
getPluginTypes() - Method in class net.sf.basedb.core.data.PluginDefinitionData
The plugin types of this plugin, ie. all interfaces that it implements.
getPluginTypes() - Method in class net.sf.basedb.core.PluginDefinition
Get a query that returns the plugin types for this plugin definition.
getPluginVersion() - Method in class net.sf.basedb.core.data.JobData
Get the version of the plugin used to execute this job at the time the job was executed or registered.
getPluginVersion() - Method in class net.sf.basedb.core.Job
Get the version of the plugin used to execute this job at the time the job was executed or registered.
getPort() - Method in class net.sf.basedb.clients.jobagent.Agent
Get the agent.port configuration value.
getPort() - Method in class net.sf.basedb.core.data.JobAgentData
The port the job agent is listening on. null if it doesn't listen.
getPort() - Method in class net.sf.basedb.core.JobAgent
Get the port the job agent is listening on.
getPosition() - Method in class net.sf.basedb.core.ArrayDesignPlate
Gets the position of this item.
getPosition() - Method in class net.sf.basedb.core.BioMaterialEventSource
Get the position that the source biomaterial was used on in the event.
getPosition() - Method in class net.sf.basedb.core.BioPlate
Get the position within the "storage location" for this bioplate.
getPosition() - Method in class net.sf.basedb.core.data.ArrayDesignPlateData
Get the index.
getPosition() - Method in class net.sf.basedb.core.data.BioMaterialEventSourceData
Get the position of the parent biomaterial as it was used in the event.
getPosition() - Method in class net.sf.basedb.core.data.BioPlateData
Get the position in the storage location were the bioplate is stored.
getPosition() - Method in class net.sf.basedb.core.data.FeatureData
Get the position number of the feature.
getPosition() - Method in class net.sf.basedb.core.data.RawData
 
getPosition() - Method in class net.sf.basedb.core.RawDataBatcher.FeatureInfo
 
getPosition() - Method in class net.sf.basedb.plugins.Base1PluginExecuter.JobParameter
 
getPosition(DbControl, int, int) - Method in class net.sf.basedb.clients.web.ExperimentExplorer
Get the position number of the position specified by the given reporter and position index.
getPositionBatcher() - Method in class net.sf.basedb.core.BioAssaySet
Get a batcher that links position coordinates to reporters for the data cube this bioassayset uses.
getPositionBatcher() - Method in class net.sf.basedb.core.DataCube
 
getPositionData() - Method in class net.sf.basedb.core.BioAssaySet
Get a query that returns position data for the data cube where this bioassayset is located.
getPositionExtraValueBatcher(Class<I>, ExtraValueType, Job) - Method in class net.sf.basedb.core.BioAssaySet
Get a batcher that is used to insert extra values per position of the specified type.
getPositionIndex() - Method in class net.sf.basedb.clients.web.ExperimentExplorer
Get the index of the current position.
getPositionIndex() - Method in class net.sf.basedb.util.importer.spotdata.BaseFileInfo.SpotSectionInfo
The index of the 'position' data column.
getPredefinedQuery(Session, String) - Static method in class net.sf.basedb.core.HibernateUtil
Get a predefined HQL query.
getPredefinedQuery(Session, String, Class<R>, String...) - Static method in class net.sf.basedb.core.HibernateUtil
Get a predefined HQL query with a known return type.
getPredefinedQuery(Session, String, String...) - Static method in class net.sf.basedb.core.HibernateUtil
Get a predefined HQL query.
getPredefinedQuery(StatelessSession, String, Class<R>) - Static method in class net.sf.basedb.core.HibernateUtil
Get a predefined HQL query with a known return type using the stateless session.
getPredefinedSQLQuery(Session, String, Class<R>, String...) - Static method in class net.sf.basedb.core.HibernateUtil
Get a predefined SQL query with a known return type.
getPredefinedSQLQuery(Session, String, String...) - Static method in class net.sf.basedb.core.HibernateUtil
Get a predefined SQL query.
getPredefinedSQLQuery(StatelessSession, String) - Static method in class net.sf.basedb.core.HibernateUtil
Get a predefined SQL query using the stateless session.
getPredefinedSQLQuery(StatelessSession, String, Class<R>) - Static method in class net.sf.basedb.core.HibernateUtil
Get a predefined SQL query with a known return type using the stateless session.
getPrefix() - Method in class net.sf.basedb.clients.web.taglib.table.CellValue
 
getPrefix() - Method in class net.sf.basedb.util.bfs.SequenceFilenameGenerator
Get the prefix that is used for file name generation.
getPrefixedStream(XlsxToCsvUtil.SheetInfo) - Method in class net.sf.basedb.util.excel.XlsxToCsvUtil.WorkbookStream
Create a combined stream by adding a "prefix": [sheet-name] and then the regular CSV stream for the given worksheet.
getPreset(String) - Method in class net.sf.basedb.core.Presets
Get a named preset.
getPreviousState() - Method in class net.sf.basedb.core.log.EntityDetails
Get an array with the previous state of the entity.
getPrimaryKey() - Method in class net.sf.basedb.core.dbengine.TableInfo
Get information about the primary key of the table
getPrintRobot() - Method in class net.sf.basedb.core.ArrayBatch
Get the print robot used for printing the arrays.
getPrintRobot() - Method in class net.sf.basedb.core.data.ArrayBatchData
Get the hardware used for creating this batch.
getPriority() - Method in class net.sf.basedb.core.data.JobData
The jobs priority.
getPriority() - Method in class net.sf.basedb.core.Job
Get the priority of the job.
getPriorityBoost() - Method in class net.sf.basedb.core.data.JobAgentSettingsData
The priority boost for this plugin.
getPriorityBoost() - Method in class net.sf.basedb.core.JobAgentSettings
Get the priority boost given to jobs executed by this plugin.
getPrivateKey(String) - Method in class net.sf.basedb.util.ssl.StaticKeyManager
 
getProcessResults() - Method in class net.sf.basedb.util.extensions.manager.processor.DisablePluginsProcessor
 
getProcessResults() - Method in class net.sf.basedb.util.extensions.manager.processor.PluginInstallationProcessor
 
getProcessResults() - Method in class net.sf.basedb.util.extensions.manager.processor.RegisterExtensionsProcessor
 
getProducer() - Method in class net.sf.basedb.core.hibernate.QueryWrapper
 
getProducts() - Method in class net.sf.basedb.core.data.TransformationData
This is the inverse end.
getProducts() - Method in class net.sf.basedb.core.Transformation
Get a query that return all bioassaysets created by this transformation.
getProgramParameters() - Method in class net.sf.basedb.plugins.executor.ExternalProgramExecutor
Get all program parameters and their values.
getProgress() - Method in class net.sf.basedb.clients.web.fileupload.FileUpload
Get progress information about the upload.
getProgress(FlatFileParser) - Method in class net.sf.basedb.plugins.AbstractFlatFileImporter
Get the progress of import as a percentage value.
getProgress(FlatFileParser) - Method in class net.sf.basedb.plugins.AnnotationFlatFileImporter
Overriding default implementation since we want file parsing to only use 'progressParser'% and the remaining 'progressDatabase'% for storing to the database.
getProgressReporter() - Method in class net.sf.basedb.util.export.spotdata.AbstractBioAssaySetExporter
Get the progress reporter
getProgressReporter() - Method in class net.sf.basedb.util.importer.spotdata.BaseFileImporter
Get the progress reporter.
getProgressReporter() - Method in class net.sf.basedb.util.importer.spotdata.BfsImporter
Get the progress reporter.
getProgressReporter(ProgressReporter) - Method in class net.sf.basedb.core.Job
Get a progress reporter that reports progress by updating the information in the database.
getProject() - Method in class net.sf.basedb.core.Annotation
Get the project that this project-specific annotation belongs to.
getProject() - Method in class net.sf.basedb.core.data.ChangeHistoryData
 
getProject() - Method in class net.sf.basedb.util.overview.GenericOverview
Get the project of this overview is using for validating against project defaults (may be null).
getProject() - Method in interface net.sf.basedb.util.overview.OverviewContext
Get the project the overview is using as the "current" project.
getProject(DbControl) - Method in class net.sf.basedb.core.ChangeHistory
Load the project that was active when the change was made.
getProject(DbControl) - Method in class net.sf.basedb.core.ChangeHistory.TransactionInfo
Load the project that was active during the transaction.
getProject(DbControl) - Method in class net.sf.basedb.core.snapshot.AnnotationSnapshot
Get the project that a project-specific annotation belongs to.
getProject(DbControl, ChangeHistory, boolean, boolean) - Static method in class net.sf.basedb.clients.web.ChangeHistoryUtil
Get the project that was active when the change was made in HTML format.
getProjectAnnotation(AnnotationType, Project) - Method in class net.sf.basedb.core.AnnotationSet
Get a value for a project-specific annotation using the specified project instead of the currently active project.
getProjectAnnotations() - Method in class net.sf.basedb.core.AnnotationType
If this flag is set, annotation values can be set per project.
getProjectAnnotations() - Method in class net.sf.basedb.core.data.AnnotationTypeData
If this flag is set, annotation values can be set per project.
getProjectAnnotations(Annotation.Source, Project) - Method in class net.sf.basedb.core.AnnotationSet
Get a query returning annotations with the specified source and belonging to the specified project (or default values if projectId=0).
getProjectDefaultPlatform(DbControl) - Method in class net.sf.basedb.plugins.batchimport.AbstractItemImporter
Get the default platform of the currently active project.
getProjectDefaultRawDataType(DbControl) - Method in class net.sf.basedb.plugins.batchimport.AbstractItemImporter
Get the default raw data type of the currently active project.
getProjectDefaults() - Method in class net.sf.basedb.core.data.ProjectData
Gets the default values
getProjectDefaultVariant(DbControl) - Method in class net.sf.basedb.plugins.batchimport.AbstractItemImporter
Get the default platform variant of the currently active project.
getProjectId() - Method in class net.sf.basedb.core.Annotation
Get the ID of the project that this project-specicif annotation belongs to.
getProjectId() - Method in class net.sf.basedb.core.AnnotationBatcher.CurrentAnnotationInfo
Get the id of the project this annotation belong to.
getProjectId() - Method in class net.sf.basedb.core.ChangeHistory
Get the ID of the project that was active when the change was made.
getProjectId() - Method in class net.sf.basedb.core.ChangeHistory.TransactionInfo
Get the ID of the project that was active during the transaction.
getProjectId() - Method in class net.sf.basedb.core.data.AnnotationData
The ID of the project that this annotation belongs to. 0 is used for default annotations.
getProjectId() - Method in class net.sf.basedb.core.data.annotations.AnnotationLink
 
getProjectId() - Method in class net.sf.basedb.core.data.ChangeHistoryData
The ID of the project that was active when the changes were made.
getProjectId() - Method in class net.sf.basedb.core.data.keyring.ProjectKeys
Get the id of the project.
getProjectId() - Method in class net.sf.basedb.core.data.keyring.ProjectPermission
Get the id of the project.
getProjectId() - Method in class net.sf.basedb.core.log.TransactionDetails
Get the ID of the currently active project, or 0 if no project is active.
getProjectId() - Method in class net.sf.basedb.core.snapshot.AnnotationSnapshot
Get the id of the project that this project-specific annotation belongs to.
getProjectIds(Permission) - Method in class net.sf.basedb.core.ProjectKey
Get the ID:s of all projects that are shared with this project key having the specified permission.
getProjectKey() - Method in interface net.sf.basedb.core.data.ShareableData
Get the ProjectKeyData for the item.
getProjectKey() - Method in class net.sf.basedb.core.data.SharedData
 
getProjectKey() - Method in interface net.sf.basedb.core.Shareable
Get the ProjectKey that is used to share this item to projects.
getProjectKey() - Method in class net.sf.basedb.core.SharedItem
 
getProjectKeyId() - Method in class net.sf.basedb.core.SessionControl
Get the id of the ProjectKey that can be used to share an item to the active project with full permission, or 0 if no project is active or the logged in user only has read permission to the active project.
getProjectKeys() - Method in class net.sf.basedb.core.data.ProjectData
This is the inverse end.
getProjectKeys() - Method in class net.sf.basedb.core.InternalJobQueue.JobQueueKeyring
Return empty set.
getProjectKeys() - Method in class net.sf.basedb.core.Job.SignalKeyring
Return empty set.
getProjectKeys() - Method in class net.sf.basedb.core.ServiceSessionControl.ServicesKeyring
Return empty set.
getProjectKeys() - Method in class net.sf.basedb.core.SessionControl
Get the id of all project keys where the logged in user has read permission.
getProjectKeys(Permission) - Method in class net.sf.basedb.core.Keyring
 
getProjectKeys(Permission) - Method in class net.sf.basedb.core.SessionControl
Get the id of all project keys where the logged in user has the requested permission.
getProjectName() - Method in class net.sf.basedb.core.log.TransactionDetails
Utility method for loading the name of the currently active project.
getProjectName(int) - Method in class net.sf.basedb.core.log.TransactionDetails
Get the name of the project with the given id.
getProjectName(DbControl) - Method in class net.sf.basedb.core.snapshot.AnnotationSnapshot
Get the name of project if the annotation is a project-specific value.
getProjectPermission(Project) - Method in class net.sf.basedb.core.SessionControl
 
getProjectPermissions() - Method in class net.sf.basedb.core.ProjectPermissions
Get the internal representation of the permissions.
getProjects() - Method in class net.sf.basedb.core.data.GroupData
This is the inverse end.
getProjects() - Method in class net.sf.basedb.core.data.PermissionTemplateData
This is the inverse end.
getProjects() - Method in class net.sf.basedb.core.data.ProjectKeyData
Get the map that manages which projects that have permissions for this key.
getProjects() - Method in class net.sf.basedb.core.data.UserData
This is the inverse end.
getProjects() - Method in class net.sf.basedb.core.Group
Get a query that returns the projects that this group is a member of.
getProjects() - Method in class net.sf.basedb.core.InternalJobQueue.JobQueueKeyring
Return empty map.
getProjects() - Method in class net.sf.basedb.core.Job.SignalKeyring
Return empty map.
getProjects() - Method in class net.sf.basedb.core.Keyring
 
getProjects() - Method in class net.sf.basedb.core.MultiPermissions
Get a query that returns all projects appearing in at least one of the project keys.
getProjects() - Method in class net.sf.basedb.core.PermissionTemplate
Get a query that returns all projects that use this permission template.
getProjects() - Method in class net.sf.basedb.core.ServiceSessionControl.ServicesKeyring
Return empty map.
getProjects() - Method in class net.sf.basedb.core.SessionControl
Get the id of all projects where the logged in user is a member, directly or indirectly.
getProjects() - Method in class net.sf.basedb.core.User
Get a query that returns the projects where this user is a member.
getProjectSpecificAnnotationsManager() - Method in class net.sf.basedb.core.DbControl
Get the manager used for handling project specific annotations in this transaction.
getPrompt() - Method in class net.sf.basedb.clients.web.extensions.login.FieldInfo
Get the prompt that is associated with the field.
getProperties() - Method in class net.sf.basedb.core.data.ReporterCloneTemplateData
Get the map that manages cloned properties.
getProperties() - Method in class net.sf.basedb.core.hibernate.SessionWrapper
 
getProperties() - Method in class net.sf.basedb.core.log.EntityDetails
Get an array with the names of all properties.
getProperties() - Method in class net.sf.basedb.core.RawDataType
Get a list of RawDataProperty:s with definitions for the extra properties that has been defined for this raw data type.
getProperties(String) - Static method in class net.sf.basedb.core.ExtendedProperties
Get a list of extended properties for the specified class.
getProperties(String, boolean) - Static method in class net.sf.basedb.core.ExtendedProperties
Get a list of extended properties for the specified class.
getProperty() - Method in class net.sf.basedb.clients.web.extensions.list.AbstractListColumnBean
 
getProperty() - Method in interface net.sf.basedb.clients.web.extensions.list.ListColumnAction
The property name for referencing data in the column.
getProperty() - Method in class net.sf.basedb.clients.web.extensions.list.RelatedItemColumn.Specification
Get the property from the expression.
getProperty() - Method in class net.sf.basedb.clients.web.taglib.PropertyValue
 
getProperty() - Method in class net.sf.basedb.clients.web.taglib.table.ColumnDef
 
getProperty() - Method in class net.sf.basedb.clients.web.taglib.table.TableColumn
 
getProperty() - Method in class net.sf.basedb.core.PropertyFilter
Get the name of the property this filter is used on.
getProperty() - Method in class net.sf.basedb.plugins.batchimport.PropertyIdMethod
 
getProperty() - Method in class net.sf.basedb.util.export.spotdata.AssayPropertyField
Get the configured property.
getProperty(String) - Method in class net.sf.basedb.clients.jobagent.Agent
Get a configuration property.
getProperty(String) - Method in class net.sf.basedb.core.RawDataType
 
getProperty(String) - Method in class net.sf.basedb.util.extensions.xml.PluginInfo
 
getProperty(String, String) - Static method in class net.sf.basedb.core.ExtendedProperties
Find an extended property in a given class.
getPropertyAccessStrategy() - Method in class net.sf.basedb.core.ExtendedPropertyAccessor.GetterSetter
 
getPropertyFilter(String) - Method in class net.sf.basedb.core.ItemContext
Get a filter for a property on filter row 0.
getPropertyFilter(String, int) - Method in class net.sf.basedb.core.ItemContext
Get a filter for a property.
getPropertyFilter(String, int) - Method in class net.sf.basedb.core.SyncFilter
Get a filter for a property on a given filter row.
getPropertyFilters() - Method in class net.sf.basedb.core.data.ContextData
Get the map that manages property filters in this context.
getPropertyFilters() - Method in class net.sf.basedb.core.data.ItemListSyncFilterData
Get the map that manages property filters in this sync filter.
getPropertyFilters() - Method in class net.sf.basedb.core.ItemContext
Get a collection of all property filters stored in this context.
getPropertyFilters(int) - Method in class net.sf.basedb.core.ItemContext
Get a collection of all property filters stored in this context for a given filter row.
getPropertyFilters(int) - Method in class net.sf.basedb.core.SyncFilter
Get the filters in the given filter row.
getPropertyFilterString(PropertyFilter, Formatter<Date>) - Static method in class net.sf.basedb.clients.web.Base
Convert a property filter to a displayable string with operator + value.
getPropertyName(String) - Method in class net.sf.basedb.core.log.EntityLogOptions
Convert a method name into a property name.
getPropertyObject(String) - Method in class net.sf.basedb.core.ItemContext
 
getPropertyPath(Object, String) - Method in class net.sf.basedb.clients.web.taglib.PropertyValue
 
getPropertyPath(String, boolean) - Method in class net.sf.basedb.core.Metadata
Get a property path that can be used to retrieve a value from an item instead of using the regular get methods.
getPropertyValue(D, String) - Method in class net.sf.basedb.core.BasicBatcher
Get the value of a protected property value on a data object using Hibernate built-in reflection methods.
getPropertyValue(String) - Method in class net.sf.basedb.core.ItemContext
Get the value of a property filter on row 0.
getPropertyValue(String, int) - Method in class net.sf.basedb.core.ItemContext
Get the value of a property filter on the given filter row.
getProtocol() - Method in interface net.sf.basedb.core.Annotatable
A protcol used in the creation of an item that is used to attach annotations for the protocol parameters.
getProtocol() - Method in class net.sf.basedb.core.AnnotatedItem
Default implementation returns null.
getProtocol() - Method in class net.sf.basedb.core.ArrayBatch
Get the Protocol used for printing the arrays.
getProtocol() - Method in class net.sf.basedb.core.BioAssay
Default implementation returns null.
getProtocol() - Method in class net.sf.basedb.core.BioAssaySet
Default implementation returns null.
getProtocol() - Method in class net.sf.basedb.core.BioMaterialEvent
Get the Protocol describing the procedure used in this event.
getProtocol() - Method in class net.sf.basedb.core.BioPlateEvent
Get the Protocol describing the procedure used in this event.
getProtocol() - Method in class net.sf.basedb.core.data.ArrayBatchData
Get the protocol used for printing the arrays.
getProtocol() - Method in class net.sf.basedb.core.data.BioMaterialEventData
Get the protocol used in this event.
getProtocol() - Method in class net.sf.basedb.core.data.BioPlateEventData
Get the protocol used in this event.
getProtocol() - Method in class net.sf.basedb.core.data.DerivedBioAssayData
Get the protocol used to create this bioassay set.
getProtocol() - Method in class net.sf.basedb.core.data.PlateEventData
The protocol used for the event.
getProtocol() - Method in class net.sf.basedb.core.data.RawBioAssayData
Get the protocol used for the image analysis.
getProtocol() - Method in class net.sf.basedb.core.DerivedBioAssay
 
getProtocol() - Method in class net.sf.basedb.core.MeasuredBioMaterial
Get the protocol from the creation event.
getProtocol() - Method in class net.sf.basedb.core.PhysicalBioAssay
Get the protocol from the creation event.
getProtocol() - Method in class net.sf.basedb.core.PlateEvent
Get the Protocol that was followed in this event.
getProtocol() - Method in class net.sf.basedb.core.PluginDefinition
 
getProtocol() - Method in class net.sf.basedb.core.Project
Default implementation returns null.
getProtocol() - Method in class net.sf.basedb.core.RawBioAssay
Get the Protocol used while analysing the scanned images.
getProtocol() - Method in class net.sf.basedb.core.RootRawBioAssay
 
getProtocol() - Method in class net.sf.basedb.core.Well
 
getProtocolParametersQuery(Protocol) - Static method in class net.sf.basedb.clients.web.Base
Get a query that returns all annotation types assigned as parameters to a specific protocol.
getProtocols() - Method in class net.sf.basedb.core.data.AnnotationTypeData
This is the inverse end.
getProtocolType() - Method in class net.sf.basedb.core.data.PlateEventTypeData
The protocol type that events of this event type should pick their protocols from.
getProtocolType() - Method in class net.sf.basedb.core.PlateEventType
Get the associated protocol type item.
getProxy(int) - Static method in class net.sf.basedb.core.Reporter
Get a proxy reporter object.
getProxyTag(Annotatable) - Method in class net.sf.basedb.clients.web.extensions.list.RelatedItemColumn
Generate a proxy tag that is returned instead of actual data.
getPublication() - Method in class net.sf.basedb.core.data.ExperimentData
Get the publication for this experiment.
getPublication() - Method in class net.sf.basedb.core.Experiment
Get the publication text.
getPublicationDate() - Method in class net.sf.basedb.core.data.ExperimentData
Get the publication date for this experiment.
getPublicationDate() - Method in class net.sf.basedb.core.Experiment
Get the date this experiment was published.
getPublicLocalHost() - Static method in class net.sf.basedb.util.SocketUtil
Get the external address of the local host.
getPubMedId() - Method in class net.sf.basedb.core.data.ExperimentData
Get the publication for this experiment.
getPubMedId() - Method in class net.sf.basedb.core.Experiment
Get the PubMed ID of the publication.
getPushAnnotations() - Method in class net.sf.basedb.core.data.ItemSubtypeData
If this flag is set, the annotations on items of this subtype should be enabled for pushing to the parent item.
getPushAnnotations() - Method in class net.sf.basedb.core.ItemSubtype
If this flag is set, the annotations on items of this subtype can be pushed to the parent item.
getQualifiedTableName() - Method in class net.sf.basedb.core.RealTable
Get the quoted table name of this table in the database.
getQualifiedTableName(VirtualDb) - Method in enum class net.sf.basedb.core.VirtualTable
Get the real table name of this table in the database, quoted and with catalog/schema information prepended to it.
getQuantity() - Method in class net.sf.basedb.core.AnnotationType
Get the quantity for this annotation type.
getQuantity() - Method in class net.sf.basedb.core.data.AnnotationTypeData
Get the quantity this annotation type uses.
getQuantity() - Method in class net.sf.basedb.core.data.UnitData
Get the quantity this unit belongs to.
getQuantity() - Method in class net.sf.basedb.core.data.UnitSymbolData
Get the quantity this symbol belongs to.
getQuantity() - Method in class net.sf.basedb.core.Unit
Get the quantity this unit belongs to.
getQuery - Variable in enum class net.sf.basedb.core.Item
 
getQuery() - Static method in class net.sf.basedb.core.Annotation
Get a query configured to retrieve annotations.
getQuery() - Static method in class net.sf.basedb.core.AnnotationSet
Get a ItemQuery object configured to retrieve AnnotationSet items.
getQuery() - Static method in class net.sf.basedb.core.AnnotationTypeCategory
Get a ItemQuery object configured to retrieve AnnotationTypeCategory items.
getQuery() - Static method in class net.sf.basedb.core.ArrayBatch
Get a ItemQuery that returns array batches.
getQuery() - Static method in class net.sf.basedb.core.ArrayDesign
Get a ItemQuery object configured to retrieve array designs.
getQuery() - Static method in class net.sf.basedb.core.ArraySlide
Get a ItemQuery object configured to retrieve array slides.
getQuery() - Static method in class net.sf.basedb.core.BioPlate
Gets query that selects all available bioplates
getQuery() - Static method in class net.sf.basedb.core.BioPlateEvent
Get a query that returns bioplate event items.
getQuery() - Static method in class net.sf.basedb.core.BioPlateEventType
Gets query that returns bioplate event types.
getQuery() - Static method in class net.sf.basedb.core.BioPlateType
Gets query that selects all available bioplates
getQuery() - Static method in class net.sf.basedb.core.BioSource
Get a query that returns biosource items.
getQuery() - Static method in class net.sf.basedb.core.Client
Get a new query object for this class.
getQuery() - Static method in class net.sf.basedb.core.DataFileType
Get a query configured to retrieve DataFileType items.
getQuery() - Static method in class net.sf.basedb.core.DerivedBioAssay
Get a query that returns derived bioassay.
getQuery() - Static method in class net.sf.basedb.core.Directory
Get a query configured to retrieve directories.
getQuery() - Static method in class net.sf.basedb.core.Experiment
Get a query configured to retrieve experiments
getQuery() - Static method in class net.sf.basedb.core.Extract
Get a query that returns extracts.
getQuery() - Static method in class net.sf.basedb.core.ExtraValueType
Get a query configured to retrieve extra value types.
getQuery() - Static method in class net.sf.basedb.core.File
Get a query configured to retrieve File items.
getQuery() - Static method in class net.sf.basedb.core.FileServer
Get a new query object for this class.
getQuery() - Static method in class net.sf.basedb.core.FileSet
Get a ItemQuery object configured to retrieve FileSet items.
getQuery() - Static method in class net.sf.basedb.core.Formula
Get a new query object for this class.
getQuery() - Static method in class net.sf.basedb.core.GlobalDefaultSetting
Get a query configured to retrieve global default settings.
getQuery() - Static method in class net.sf.basedb.core.Group
Get a query configured to retrieve groups.
getQuery() - Static method in class net.sf.basedb.core.Hardware
Get a query configured to retrieve hardware.
getQuery() - Method in enum class net.sf.basedb.core.Item
Get a query returning items of this type.
getQuery() - Method in class net.sf.basedb.core.ItemContext
 
getQuery() - Static method in class net.sf.basedb.core.ItemList
Get a query that returns item lists.
getQuery() - Static method in class net.sf.basedb.core.Job
Get a query configured to retrieve jobs.
getQuery() - Static method in class net.sf.basedb.core.JobAgent
Get an ItemQuery that returns job agents.
getQuery() - Static method in class net.sf.basedb.core.Kit
Get a query configured to retrieve kits.
getQuery() - Static method in class net.sf.basedb.core.MimeType
Get a query configured to retrieve MIME types.
getQuery() - Static method in class net.sf.basedb.core.News
Get a query configured to retrieve news.
getQuery() - Static method in class net.sf.basedb.core.PermissionTemplate
Get a query that returns permission templates.
getQuery() - Static method in class net.sf.basedb.core.PhysicalBioAssay
Get a query that returns physical bioassays.
getQuery() - Static method in class net.sf.basedb.core.Plate
Get a query that returns plates.
getQuery() - Static method in class net.sf.basedb.core.PlateGeometry
Get a query configured to retrieve plate geometries.
getQuery() - Static method in class net.sf.basedb.core.PlateMapping
Get a query that returns plate mappings.
getQuery() - Static method in class net.sf.basedb.core.PlateType
Get a query that returns plate types.
getQuery() - Static method in class net.sf.basedb.core.Platform
Get a query configured to retrieve Platform items.
getQuery() - Static method in class net.sf.basedb.core.PlatformVariant
Get a query configured to retrieve PlatformVariant items.
getQuery() - Static method in class net.sf.basedb.core.PluginConfiguration
Get a query configured to retrieve plugin configurations.
getQuery() - Static method in class net.sf.basedb.core.PluginDefinition
Get a query that returns plugin definitions.
getQuery() - Static method in class net.sf.basedb.core.PluginType
Get a query configured to retrieve plugin types.
getQuery() - Static method in class net.sf.basedb.core.Project
Get a query configured to retrieve projects.
getQuery() - Static method in class net.sf.basedb.core.Protocol
Get a query configured to retrieve protocols.
getQuery() - Static method in class net.sf.basedb.core.Quantity
Get a query configured to retrieve quantities.
getQuery() - Static method in class net.sf.basedb.core.Quota
Get a query configured to retrieve quota.
getQuery() - Static method in class net.sf.basedb.core.QuotaType
Get a query configured to retrieve QuotaType.
getQuery() - Static method in class net.sf.basedb.core.RawBioAssay
Get a query configured to retrieve raw bioassays.
getQuery() - Static method in class net.sf.basedb.core.Reporter
Get a query object configured to retrieve reporters.
getQuery() - Static method in class net.sf.basedb.core.ReporterCloneTemplate
Get a query that returns reporter clone templates.
getQuery() - Static method in class net.sf.basedb.core.ReporterList
Get a new query object for this class.
getQuery() - Static method in class net.sf.basedb.core.ReporterType
Get a query configured to retrieve reporter types.
getQuery() - Static method in class net.sf.basedb.core.Role
Get a ItemQuery object configured to retrieve Role items.
getQuery() - Static method in class net.sf.basedb.core.RoleKey
Get a query object configured to retrieve role keys.
getQuery() - Static method in class net.sf.basedb.core.RootRawBioAssay
Get a query configured to retrieve raw bioassays.
getQuery() - Static method in class net.sf.basedb.core.Sample
Get a query that returns samples.
getQuery() - Static method in class net.sf.basedb.core.Software
Get a query configured to retrieve software.
getQuery() - Static method in class net.sf.basedb.core.Tag
Get a query that returns tags.
getQuery() - Static method in class net.sf.basedb.core.Unit
Get a query configured to retrieve units.
getQuery() - Static method in class net.sf.basedb.core.User
Get a query configured to retrieve users.
getQuery(Collection<RawBioAssay>) - Static method in class net.sf.basedb.core.DynamicRawDataQuery
Create a new dynamic query for raw data.
getQuery(ArrayDesign) - Static method in class net.sf.basedb.core.ArrayDesignBlock
Get a query configured to retrieve array design blocks for the specified array design.
getQuery(ArrayDesign) - Static method in class net.sf.basedb.core.ArrayDesignPlate
Get a query that returns ArrayDesignPlates connections for the specified array design.
getQuery(BioAssaySet) - Static method in class net.sf.basedb.core.BioAssay
Get a query configured to retrieve bioassays in a given bioassayset.
getQuery(BioAssaySet) - Static method in class net.sf.basedb.core.ExtraValue
Get a query configured to retrieve extra values in a given bioassayset.
getQuery(BioAssaySet) - Static method in class net.sf.basedb.core.Transformation
Get a query configured to retrieve transformations using the given bioassayset as source.
getQuery(BioMaterial) - Static method in class net.sf.basedb.core.BioMaterialEventSource
Get a query returning event information where a given biomaterial has been used as a source.
getQuery(BioMaterialEvent) - Static method in class net.sf.basedb.core.BioMaterialEventSource
Get a query returning source information for a given (creation) event.
getQuery(BioPlate) - Static method in class net.sf.basedb.core.BioPlateEventParticipant
Get a query configured to return all event participants for a bioplate.
getQuery(BioPlate) - Static method in class net.sf.basedb.core.BioWell
Get a query configured to retrieve wells for a plate.
getQuery(BioPlateEvent) - Static method in class net.sf.basedb.core.BioPlateEventParticipant
Get a query configured to return all participants for a bioplate event.
getQuery(Client) - Static method in class net.sf.basedb.core.ClientDefaultSetting
Get a query object configured to retrieve default settings for the specified client application.
getQuery(Client) - Static method in class net.sf.basedb.core.Help
Get a query configured to retrieve help texts for the specified client application.
getQuery(DataFileType) - Static method in class net.sf.basedb.core.ItemSubtypeFileType
Get the item subtype types that have been registered for a specific data file type.
getQuery(Experiment) - Static method in class net.sf.basedb.core.BioAssaySet
Get a query configured to retrieve bioassaysets for a given experiment.
getQuery(Experiment) - Static method in class net.sf.basedb.core.Transformation
Get a query configured to retrieve transformations for a given experiment.
getQuery(FileSet) - Static method in class net.sf.basedb.core.FileSetMember
Get a query configured to retrieve FileSetMember items.
getQuery(FileStoreEnabled) - Static method in class net.sf.basedb.core.DataFileType
Get a query configured to retrieve DataFileType:s that can be used on a given item.
getQuery(Formula.Type, RawDataType, IntensityTransform) - Static method in class net.sf.basedb.core.Formula
Get a query that return formulas that can be used with the specified raw data type.
getQuery(Item) - Static method in class net.sf.basedb.core.AnnotationType
Get a ItemQuery that returns annotation types.
getQuery(Item) - Static method in class net.sf.basedb.core.ItemSubtype
Get a query configured to retrieve item types.
getQuery(ItemList) - Static method in class net.sf.basedb.core.SyncFilter
Get a query configured to retrieve sync filters for the specified item list.
getQuery(ItemSubtype) - Static method in class net.sf.basedb.core.ItemSubtypeFileType
Get the file types that have been registered for a specific item subtype.
getQuery(JobAgent) - Static method in class net.sf.basedb.core.JobAgentSettings
Get a query configured to retrieve settings for the specified agent.
getQuery(MeasuredBioMaterial) - Static method in class net.sf.basedb.core.BioMaterialEvent
Get a query that returns events for a biomaterial.
getQuery(Plate) - Static method in class net.sf.basedb.core.PlateEvent
Get a query configured to retrieve plate events for the specified plate.
getQuery(Plate) - Static method in class net.sf.basedb.core.Well
Get a query configured to retrieve wells for a plate.
getQuery(PlateType) - Static method in class net.sf.basedb.core.PlateEventType
Get a query configured to retrieve event types for the specified plate type
getQuery(Platform, PlatformVariant, boolean) - Static method in class net.sf.basedb.core.PlatformFileType
Get the file types that have been registered for a specific platform and variant.
getQuery(Platform, PlatformVariant, Item, ItemSubtype) - Static method in class net.sf.basedb.core.DataFileType
Get a query to retrieve DataFileType:s that can be used on specific platform/variant for a given item and/or generic file type.
getQuery(GuiContext, String) - Static method in class net.sf.basedb.core.PluginConfiguration
Get a query that returns all plugins configurations related to a specified GUI context and implementing a certain interface.
getQuery(GuiContext, String) - Static method in class net.sf.basedb.core.PluginDefinition
Get a query that returns all plugins related to a specified GUI context and implementing a certain interface.
getQuery(PluginDefinition) - Static method in class net.sf.basedb.core.JobAgentSettings
Get a query configured to retrieve settings for the specified plugin.
getQuery(RawBioAssay) - Static method in class net.sf.basedb.core.DynamicRawDataQuery
Create a new dynamic query for raw data.
getQuery(ReporterList) - Static method in class net.sf.basedb.core.ReporterScore
Get a query object configured to retrieve reporters.
getQuery(Transformation) - Static method in class net.sf.basedb.core.BioAssaySet
Get a query configured to retrieve bioassaysets created by a given transformation.
getQuery(User) - Static method in class net.sf.basedb.core.Message
Get a query configured to retrieve messages for the specified user.
getQuery(User) - Static method in class net.sf.basedb.core.Session
Get a query configured to retrieve sessions for the specified user.
getQuery(User) - Static method in class net.sf.basedb.core.UserDefaultSetting
Get a query configured to retrieve default settings for a user.
getQuery(User) - Static method in class net.sf.basedb.core.UserDevice
Get a query configured to retrieve devices for the specified user.
getQuery(User, Client) - Static method in class net.sf.basedb.core.UserClientSetting
Get a query configured to retrieve client specific settings for a user.
getQuery(User, Group) - Static method in class net.sf.basedb.core.DiskUsage
Get a query configured to retrieve disk usage for the specified user.
getQueryClass() - Method in class net.sf.basedb.core.DynamicPositionQueryJoiners.ExtraValueJoiner
 
getQueryClass() - Method in class net.sf.basedb.core.DynamicPositionQueryJoiners.ReporterJoiner
 
getQueryClass() - Method in class net.sf.basedb.core.DynamicPositionQueryJoiners.ReporterListJoiner
 
getQueryClass() - Method in class net.sf.basedb.core.DynamicRawDataQuery.RawBioAssayJoiner
 
getQueryClass() - Method in class net.sf.basedb.core.DynamicRawDataQuery.ReporterJoiner
 
getQueryClass() - Method in class net.sf.basedb.core.DynamicRawDataQuery.ReporterListJoiner
 
getQueryClass() - Method in class net.sf.basedb.core.DynamicReporterQuery.MasterReporterJoiner
 
getQueryClass() - Method in class net.sf.basedb.core.DynamicReporterQuery.ReporterListJoiner
 
getQueryClass() - Method in class net.sf.basedb.core.DynamicSpotQueryJoiners.ExtraValueJoiner
 
getQueryClass() - Method in class net.sf.basedb.core.DynamicSpotQueryJoiners.RawDataJoiner
 
getQueryClass() - Method in class net.sf.basedb.core.DynamicSpotQueryJoiners.ReporterJoiner
 
getQueryClass() - Method in class net.sf.basedb.core.DynamicSpotQueryJoiners.ReporterListJoiner
 
getQueryClass() - Method in class net.sf.basedb.core.HqlQueryJoiners.AnnotationJoiner
 
getQueryClass() - Method in class net.sf.basedb.core.HqlQueryJoiners.ReporterListJoiner
 
getQueryClass() - Method in interface net.sf.basedb.core.query.AutoJoiner
The type of the query the implementation works for.
getQueryFile() - Static method in class net.sf.basedb.core.Application
Get the path to the XML file containing predefined queries for SQL and HQL.
getQueryOptions() - Method in class net.sf.basedb.core.hibernate.QueryWrapper
Deprecated.
getQueryParameter(String) - Method in class net.sf.basedb.core.AbstractQuery
 
getQueryParameter(String) - Method in interface net.sf.basedb.core.query.Query
Get parameter information for the parameter with given name.
getQueryPropertyInspector() - Method in class net.sf.basedb.core.VirtualDb
Return a filter that can be used to check that a query is only using cloned reporter properties for sorting, filtering, etc.
getQueryRestriction() - Method in interface net.sf.basedb.core.query.QueryFilterAction
Generate a restriction for the entire query after all column and row filters has been processed.
getQueryReturns() - Method in class net.sf.basedb.core.hibernate.NativeQueryWrapper
Deprecated.
getQuerySection() - Method in class net.sf.basedb.core.AbstractQuery
 
getQuerySection() - Method in interface net.sf.basedb.core.query.Query
Get the current section of the query that is beeing built.
getQueryString() - Method in class net.sf.basedb.core.hibernate.QueryWrapper
 
getQueryString(String, String...) - Static method in class net.sf.basedb.core.PredefinedQuery
Get the query string for the predefined query with the specified name.
getQueryType() - Method in class net.sf.basedb.core.AbstractEntityQuery
 
getQueryType() - Method in class net.sf.basedb.core.AbstractHqlQuery
 
getQueryType() - Method in class net.sf.basedb.core.AbstractSqlQuery
 
getQueryType() - Method in interface net.sf.basedb.core.query.Query
Get the type of query.
getQuota() - Method in class net.sf.basedb.core.data.GroupData
Get the quota object which holds quota information for this group.
getQuota() - Method in class net.sf.basedb.core.data.UserData
Get the quota object which holds quota information for this user.
getQuota() - Method in class net.sf.basedb.core.Group
Get the Quota that applies to the group.
getQuota() - Method in class net.sf.basedb.core.User
Get the Quota that applies to the user.
getQuotaGroup() - Method in class net.sf.basedb.core.data.UserData
Get the group this user is sharing quota with, or null if this user only has it's own quota.
getQuotaGroup() - Method in class net.sf.basedb.core.User
Get the Group whose Quota also applies to the user.
getQuotaType() - Method in class net.sf.basedb.core.data.DiskUsageData
Get the QuotaTypeData for this DiskUsageData.
getQuotaType() - Method in class net.sf.basedb.core.data.QuotaIndex
 
getQuotaType() - Method in class net.sf.basedb.core.DiskUsage
Get the QuotaType the DiskConsumable item is using.
getQuotaTypes() - Method in class net.sf.basedb.core.DiskUsageStatistics
Get the list of quota types that are registered for DiskConsumable items.
getQuotaTypeSystemId() - Method in interface net.sf.basedb.core.DiskConsumable
Get the QuotaType system id of this item.
getQuotaTypeSystemId() - Method in class net.sf.basedb.core.Experiment
getQuotaTypeSystemId() - Method in class net.sf.basedb.core.File
getQuotaTypeSystemId() - Method in class net.sf.basedb.core.RawBioAssay
getQuotaValue(QuotaType, Location) - Method in class net.sf.basedb.core.Quota
Get the quota for the specified type and location.
getQuotaValues() - Method in class net.sf.basedb.core.data.QuotaData
 
getQuotedName(String) - Method in class net.sf.basedb.core.dbengine.AbstractDbEngine
Put quotes (") around the name.
getQuotedName(String) - Method in interface net.sf.basedb.core.dbengine.DbEngine
Quote the name with the database specific quote character.
getQuotedName(String) - Method in class net.sf.basedb.core.dbengine.MySQLEngine
Put quotes (`) around the name.
getRawBioAssay() - Method in class net.sf.basedb.core.data.RawData
The raw bioassay this raw data spot belongs to.
getRawBioAssay() - Method in class net.sf.basedb.core.data.RootRawBioAssayData
Get the raw bioassay root raw bioassay is derived from.
getRawBioAssay() - Method in class net.sf.basedb.core.DynamicRawDataQuery
 
getRawBioAssay() - Method in class net.sf.basedb.core.RawDataBatcher
Get the raw bioassay this batcher is used for.
getRawBioAssay() - Method in class net.sf.basedb.core.RootRawBioAssay
Get the raw bioassay this root raw bioassay is representing.
getRawBioAssay(DbControl, RawData) - Static method in class net.sf.basedb.core.RawDataUtil
Get the raw bioassay the raw data belongs to.
getRawBioAssayData - Static variable in class net.sf.basedb.core.RawDataUtil
Method for calling RawData.getRawBioAssay()
getRawBioAssayQuery(Experiment) - Method in class net.sf.basedb.plugins.RawDataFlatFileImporter
Get a query that returns all raw bioassays which it may be possible to import raw data to for the given experiment.
getRawBioAssays() - Method in class net.sf.basedb.core.BioAssay
 
getRawBioAssays() - Method in class net.sf.basedb.core.data.DerivedBioAssayData
This is the inverse end.
getRawBioAssays() - Method in class net.sf.basedb.core.data.ExperimentData
Duplicates the mapping ExperimentData.getRootRawBioAssays().
getRawBioAssays() - Method in class net.sf.basedb.core.data.ExtractData
This is the inverse end.
getRawBioAssays() - Method in class net.sf.basedb.core.data.JobData
This is the inverse end.
getRawBioAssays() - Method in class net.sf.basedb.core.DerivedBioAssay
 
getRawBioAssays() - Method in class net.sf.basedb.core.Experiment
Get a query that returns the raw bioassays used in this experiment.
getRawBioAssays() - Method in class net.sf.basedb.core.Extract
Get a query that returns all raw bioassays created from this extract.
getRawData() - Method in class net.sf.basedb.core.RawBioAssay
Get a query that returns the raw data of this raw bioassay.
getRawData() - Method in class net.sf.basedb.util.jep.MeanFunction
Get the current raw data object used when evaluating the JEP expression.
getRawData() - Method in class net.sf.basedb.util.jep.RawFunction
Get the current raw data object used when evaluating the JEP expression.
getRawDataBatcher(FeatureIdentificationMethod, Job) - Method in class net.sf.basedb.core.RawBioAssay
Get a raw data batcher object which can be used to add raw data to the raw bioassay.
getRawDataById(int) - Method in class net.sf.basedb.core.RawBioAssay
Get a raw data spot when you know the id.
getRawDataById(int, boolean) - Method in class net.sf.basedb.core.RawBioAssay
Get a raw data spot when you know the id.
getRawDataById(DbControl, int) - Method in class net.sf.basedb.core.RawDataType
 
getRawdataFields(BioAssaySet) - Method in class net.sf.basedb.plugins.BaseFileExporterPlugin
 
getRawdataFields(BioAssaySet) - Method in class net.sf.basedb.plugins.BfsExporterPlugin
 
getRawDataJoiner(JoinType) - Static method in class net.sf.basedb.core.DynamicSpotQueryJoiners
Get a joiner instance for raw data for the specified join type.
getRawDataProperty(String, String) - Method in class net.sf.basedb.util.export.spotdata.AbstractFieldConverter
Find an extended raw data property with the given name and create a dynamic field from it using exportTitle as the title.
getRawDataType() - Method in class net.sf.basedb.clients.web.extensions.list.RelatedItemColumn.Specification
 
getRawDataType() - Method in class net.sf.basedb.core.BioAssay
Get the raw data type the experiment uses for the raw data.
getRawDataType() - Method in class net.sf.basedb.core.BioAssaySet
Get the raw data type this experiment uses for the raw data.
getRawDataType() - Method in class net.sf.basedb.core.data.ExperimentData
Get the name of the raw data type used in this experiment.
getRawDataType() - Method in class net.sf.basedb.core.data.FormulaData
The name of raw data type this formula can be used on, or null if it can be used on any raw data type.
getRawDataType() - Method in class net.sf.basedb.core.data.ItemListData
Get the raw data type of raw bioassays that can be members in this list.
getRawDataType() - Method in class net.sf.basedb.core.data.PlatformData
The raw data type this platform is locked to, or null.
getRawDataType() - Method in class net.sf.basedb.core.data.PlatformVariantData
The raw data type this platform variant is locked to, or null.
getRawDataType() - Method in class net.sf.basedb.core.data.RawBioAssayData
Get the name of the raw data type used by this raw bio assay.
getRawDataType() - Method in class net.sf.basedb.core.DataCube
Get the raw data type this experiment uses for the raw data.
getRawDataType() - Method in class net.sf.basedb.core.DynamicRawDataQuery
 
getRawDataType() - Method in class net.sf.basedb.core.Experiment
Get the raw data type this experiment uses for the raw data.
getRawDataType() - Method in class net.sf.basedb.core.ExtraValue
Get the raw data type the experiment uses for the raw data.
getRawDataType() - Method in class net.sf.basedb.core.Formula
Get the raw data type this formula can be used on.
getRawDataType() - Method in class net.sf.basedb.core.ItemList
Get the raw data type of raw bioassays that can be members in this list.
getRawDataType() - Method in class net.sf.basedb.core.Platform
Get the raw data type this platform is locked to.
getRawDataType() - Method in class net.sf.basedb.core.PlatformVariant
Get the raw data type this platform variant is locked to.
getRawDataType() - Method in class net.sf.basedb.core.RawBioAssay
Get the raw data type this raw bioassay uses for the raw data.
getRawDataType() - Method in class net.sf.basedb.core.VirtualDb
Get the raw data type the experiment uses for the raw data.
getRawDataType() - Method in class net.sf.basedb.util.jep.RawFunction
Get the raw data type this function uses.
getRawDataType(String) - Static method in class net.sf.basedb.core.RawDataTypes
Get a information about a raw data type.
getRawDataTypeFiles() - Static method in class net.sf.basedb.core.Application
Get the path to the XML file containing raw data type definitions.
getRawDataTypes() - Static method in class net.sf.basedb.core.RawDataTypes
Get a collection with all raw data types that has been defined.
getRawParents() - Method in class net.sf.basedb.core.data.BioAssayData
Get a set that manages the raw parent bioassays the data in this bioassay is based on.
getRawSources() - Method in class net.sf.basedb.core.data.TransformationData
Get the source raw bioassays for the transformation.
getRawSources() - Method in class net.sf.basedb.core.Transformation
Get a query that returns the raw bioassay sources used by this transformation.
getRealTable() - Method in class net.sf.basedb.core.RawDataType
 
getReceivedSignals() - Method in class net.sf.basedb.core.signal.DelegatingSignalHandler
Get the list of received signals.
getReceivedSignals() - Method in class net.sf.basedb.core.signal.EnhancedThreadSignalHandler
Get the list of received signals.
getReceivedSignals() - Method in class net.sf.basedb.core.signal.ProgressReporterSignalHandler
Get the list of received signals.
getReceiverId() - Method in class net.sf.basedb.core.signal.AbstractSignalReceiver
Get the receiver ID that was passed to the AbstractSignalReceiver.init(String) method.
getReceiverId() - Method in class net.sf.basedb.core.signal.AbstractSignalTransporter
Get the receiverId part of the signal URI.
getRecent() - Method in class net.sf.basedb.clients.web.taglib.Select
 
getRecent(String) - Method in class net.sf.basedb.core.ItemContext
Get all recently used values for the specified key.
getRecent(String, int) - Method in class net.sf.basedb.core.ItemContext
 
getRecent(DbControl, Item) - Method in class net.sf.basedb.core.ItemContext
Get all recently used items of the specified type.
getRecent(DbControl, Item, int) - Method in class net.sf.basedb.core.ItemContext
 
getRecent(DbControl, Item, String) - Method in class net.sf.basedb.core.ItemContext
Get all recently used items of the specified type in a given sublist.
getRecent(DbControl, Item, String, int) - Method in class net.sf.basedb.core.ItemContext
 
getRecent(DbControl, Item, ItemSubtype) - Method in class net.sf.basedb.core.ItemContext
Get all recently used items of the specified type.
getRecentSettingName(String) - Method in class net.sf.basedb.core.ItemContext
 
getRedefinedColumnName(String, String) - Method in class net.sf.basedb.util.basefile.BaseFileParser
Get the redefined column name for a section.
getRefColumns() - Method in class net.sf.basedb.core.dbengine.TableInfo.ForeignKeyInfo
 
getReference(Class<T>, Object) - Method in class net.sf.basedb.core.hibernate.SessionWrapper
 
getReferenceFactor() - Method in class net.sf.basedb.core.data.UnitData
Factor that controls how this unit relates to the reference unit of the quantity.
getReferenceFactor() - Method in class net.sf.basedb.core.Unit
Get the factor that is used for converting values in this unit into the reference unit of the quantity.
getReferenceOffset() - Method in class net.sf.basedb.core.data.UnitData
An offset that controls how this unit relates to the reference unit of the quantity.
getReferenceOffset() - Method in class net.sf.basedb.core.Unit
Get the offset that is used for converting values in this unit into the reference unit of the quantity.
getReferenceUnit() - Method in class net.sf.basedb.core.data.QuantityData
The reference unit that all units of must relate to.
getReferenceUnit() - Method in class net.sf.basedb.core.Quantity
The reference unit describes the unit that all other units must relate to.
getRefName() - Method in class net.sf.basedb.core.dbengine.TableInfo.ForeignKeyInfo
 
getRegion() - Method in class net.sf.basedb.util.GeoLocation
 
getRegistry() - Method in class net.sf.basedb.util.extensions.ExtensionContext
 
getRegistry() - Method in class net.sf.basedb.util.extensions.ExtensionPointContext
 
getRegistry() - Method in class net.sf.basedb.util.extensions.InvokationContext
Get the registry where this invokation originated from.
getRegistry() - Method in class net.sf.basedb.util.extensions.manager.ExtensionsManager
Get the registry in which all extensions that are managed by this manager are stored.
getRegistryBuilder() - Method in class net.sf.basedb.core.ServiceSessionControl.SessionFactoryConfiguration
Get the registry for collecting configuration options.
getRelatedItems(Annotatable, SourceItemTransformer) - Method in class net.sf.basedb.clients.web.extensions.list.RelatedItemColumn
Get all parent or child items to the requested item that matches the specified filter.
getRelatedItems(Item) - Static method in class net.sf.basedb.core.ItemSubtype
Get a list with (subtypable) items that are related to the given item (which should also be subtypable).
getRelatedSubtype(DbControl, Subtypable, Item...) - Static method in class net.sf.basedb.core.ItemSubtype
Utility method for locating a subtype that is related to the subtype of a given item.
getRelatedSubtype(DbControl, Subtypable, Item, int) - Static method in class net.sf.basedb.core.ItemSubtype
Same as ItemSubtype.getRelatedSubtype(DbControl, Subtypable, Item, int, int) with the same id for the last two parameters.
getRelatedSubtype(DbControl, Subtypable, Item, int, int) - Static method in class net.sf.basedb.core.ItemSubtype
Utility method for loading a subtype that is related to the subtype of the given item.
getRelatedSubtype(Item) - Method in class net.sf.basedb.core.ItemSubtype
Get a related subtype of another item type.
getRelatedSubtypes() - Method in class net.sf.basedb.core.data.ItemSubtypeData
 
getRelatedSubtypes() - Method in class net.sf.basedb.core.ItemSubtype
Get a query returning all subtypes that are related to this subtype.
getRelativePath(File) - Static method in class net.sf.basedb.core.File
Get the relative path of the specified file from the base upload directory and convert directory separator to forward slash.
getReload() - Method in class net.sf.basedb.core.InternalJobQueue.JobQueueKeyring
Never reload since everything is static.
getReload() - Method in class net.sf.basedb.core.Job.SignalKeyring
Never reload since everything is static.
getReload() - Method in class net.sf.basedb.core.Keyring
 
getReload() - Method in class net.sf.basedb.core.ServiceSessionControl.ServicesKeyring
Never reload since everything is static.
getRemainingQuantity() - Method in class net.sf.basedb.core.data.MeasuredBioMaterialData
Get the remaining quantity of the biomaterial.
getRemainingQuantity() - Method in class net.sf.basedb.core.MeasuredBioMaterial
Get the remaining quantity of the biomaterial.
getRemoteAddresses(String) - Method in class net.sf.basedb.clients.jobagent.Agent
Split the string at commas and try to create an InetAddress for each part.
getRemoteId() - Method in class net.sf.basedb.core.data.SessionData
Get the login comment.
getRemoteId() - Method in class net.sf.basedb.core.Session
Get the remote ID of the host the user used for this session.
getRemoteId() - Method in class net.sf.basedb.core.SessionControl
Get the remote id that was passed to the Application.newSessionControl(String,String,String) method when creating this object.
getRemoteSlot(String) - Method in class net.sf.basedb.clients.jobagent.slotmanager.MasterSlotManager
Get the remote slot with the given id.
getRemoteSlot(Job.ExecutionTime) - Method in class net.sf.basedb.clients.jobagent.slotmanager.MasterSlotManager
Create a slot for a job on a remote job agent with the specified estimated execution time.
getRemovableItems() - Static method in class net.sf.basedb.core.Metadata
Get a set containing all Removable item types.
getRemove() - Method in class net.sf.basedb.util.annotations.InheritSpecification
 
getRemovedBy() - Method in class net.sf.basedb.core.BioAssaySet
 
getRemovedBy() - Method in class net.sf.basedb.core.BioPlateEventType
 
getRemovedBy() - Method in class net.sf.basedb.core.BioPlateType
 
getRemovedBy() - Method in class net.sf.basedb.core.CommonItem
 
getRemovedBy() - Method in class net.sf.basedb.core.data.BioAssaySetData
 
getRemovedBy() - Method in class net.sf.basedb.core.data.BioPlateEventTypeData
 
getRemovedBy() - Method in class net.sf.basedb.core.data.BioPlateTypeData
 
getRemovedBy() - Method in class net.sf.basedb.core.data.CommonData
 
getRemovedBy() - Method in class net.sf.basedb.core.data.DataFileTypeData
 
getRemovedBy() - Method in class net.sf.basedb.core.data.ExtraValueTypeData
 
getRemovedBy() - Method in class net.sf.basedb.core.data.GroupData
 
getRemovedBy() - Method in class net.sf.basedb.core.data.ItemSubtypeData
 
getRemovedBy() - Method in class net.sf.basedb.core.data.MessageData
 
getRemovedBy() - Method in class net.sf.basedb.core.data.MimeTypeData
 
getRemovedBy() - Method in class net.sf.basedb.core.data.NewsData
 
getRemovedBy() - Method in class net.sf.basedb.core.data.PlateEventTypeData
 
getRemovedBy() - Method in class net.sf.basedb.core.data.PlateGeometryData
 
getRemovedBy() - Method in class net.sf.basedb.core.data.PlatformData
 
getRemovedBy() - Method in class net.sf.basedb.core.data.PlatformVariantData
 
getRemovedBy() - Method in class net.sf.basedb.core.data.PluginDefinitionData
 
getRemovedBy() - Method in class net.sf.basedb.core.data.PluginTypeData
 
getRemovedBy() - Method in class net.sf.basedb.core.data.ProjectData
 
getRemovedBy() - Method in class net.sf.basedb.core.data.QuantityData
 
getRemovedBy() - Method in class net.sf.basedb.core.data.QuotaData
 
getRemovedBy() - Method in interface net.sf.basedb.core.data.RemovableData
Get the ID of the user that removed this item.
getRemovedBy() - Method in class net.sf.basedb.core.data.ReporterTypeData
 
getRemovedBy() - Method in class net.sf.basedb.core.data.RoleData
 
getRemovedBy() - Method in class net.sf.basedb.core.data.TransformationData
 
getRemovedBy() - Method in class net.sf.basedb.core.data.UnitData
 
getRemovedBy() - Method in class net.sf.basedb.core.data.UserData
 
getRemovedBy() - Method in class net.sf.basedb.core.DataFileType
 
getRemovedBy() - Method in class net.sf.basedb.core.Directory
 
getRemovedBy() - Method in class net.sf.basedb.core.ExtraValueType
 
getRemovedBy() - Method in class net.sf.basedb.core.Group
 
getRemovedBy() - Method in class net.sf.basedb.core.ItemSubtype
 
getRemovedBy() - Method in class net.sf.basedb.core.Message
 
getRemovedBy() - Method in class net.sf.basedb.core.MimeType
 
getRemovedBy() - Method in class net.sf.basedb.core.News
 
getRemovedBy() - Method in class net.sf.basedb.core.PlateEventType
 
getRemovedBy() - Method in class net.sf.basedb.core.PlateGeometry
 
getRemovedBy() - Method in class net.sf.basedb.core.Platform
 
getRemovedBy() - Method in class net.sf.basedb.core.PlatformVariant
 
getRemovedBy() - Method in class net.sf.basedb.core.PluginType
 
getRemovedBy() - Method in class net.sf.basedb.core.Project
 
getRemovedBy() - Method in class net.sf.basedb.core.Quantity
 
getRemovedBy() - Method in class net.sf.basedb.core.Quota
 
getRemovedBy() - Method in interface net.sf.basedb.core.Removable
Get the user that flagged this item for removal.
getRemovedBy() - Method in class net.sf.basedb.core.ReporterType
 
getRemovedBy() - Method in class net.sf.basedb.core.Role
 
getRemovedBy() - Method in class net.sf.basedb.core.Transformation
 
getRemovedBy() - Method in class net.sf.basedb.core.Unit
 
getRemovedBy() - Method in class net.sf.basedb.core.User
 
getRemoveJobWhenFinished() - Method in class net.sf.basedb.core.data.JobData
If the core should delete the job when it's finished successfully.
getRemoveJobWhenFinished() - Method in class net.sf.basedb.core.Job
If the job should flagged for deletion after it's done successfully.
getRenderer() - Method in class net.sf.basedb.util.extensions.ActionIterator
Gets the renderer for the current action.
getRenderer() - Method in class net.sf.basedb.util.extensions.ExtensionContext
If the extension point allows it and this extension specifies a renderer factory, create a new renderer from it.
getRenderer() - Method in class net.sf.basedb.util.extensions.ExtensionPointContext
If the extension point defines a renderer factory, creates a new renderer unless one already exists.
getRenderer() - Method in class net.sf.basedb.util.extensions.InvokationContext
Get the renderer, if any.
getRenderer(InvokationContext<? extends A>) - Method in interface net.sf.basedb.util.extensions.RendererFactory
Get a renderer for a given context.
getRenderer(InvokationContext<? extends ButtonAction>) - Method in class net.sf.basedb.clients.web.extensions.toolbar.CompactButtonRendererFactory
 
getRenderer(InvokationContext<? extends ButtonAction>) - Method in class net.sf.basedb.clients.web.extensions.toolbar.ToolbarButtonRendererFactory
 
getRendererFactory() - Method in interface net.sf.basedb.util.extensions.Extension
Get an optional factory class for creating renderers for the actions.
getRendererFactory() - Method in class net.sf.basedb.util.extensions.ExtensionBean
 
getRendererFactory() - Method in interface net.sf.basedb.util.extensions.ExtensionPoint
This is an optional factory for creating Renderer instances.
getRendererFactory() - Method in class net.sf.basedb.util.extensions.ExtensionPointBean
 
getRendererFactory() - Method in class net.sf.basedb.util.extensions.Registry.RegisteredExtension
 
getRendererFactory() - Method in class net.sf.basedb.util.extensions.Registry.RegisteredExtensionPoint
 
getReplaceExisting() - Method in class net.sf.basedb.util.annotations.InheritSpecification
 
getReporter() - Method in class net.sf.basedb.core.data.FeatureData
Get the reporter of the feature.
getReporter() - Method in class net.sf.basedb.core.data.RawData
The reporter this raw data is connected with.
getReporter() - Method in class net.sf.basedb.core.data.ReporterListScoreData
Get the reporter.
getReporter() - Method in class net.sf.basedb.core.data.WellData
The reporter used in this well.
getReporter() - Method in class net.sf.basedb.core.ReporterScore
Get the reporter.
getReporter() - Method in class net.sf.basedb.core.Well
Get the reporter in this well.
getReporter() - Method in class net.sf.basedb.util.jep.ReporterFunction
Get the current reporter object used when evaluating the JEP expression.
getReporter(boolean) - Method in class net.sf.basedb.core.Well
Get the reporter in this well.
getReporter(DbControl, int) - Method in class net.sf.basedb.clients.web.ExperimentExplorer
Get the reporter for the specified index.
getReporter(RawDataBatcher.ReporterProxy) - Method in class net.sf.basedb.core.RawDataBatcher.FeatureInfo
 
getReporterAnnotationsWriter() - Method in class net.sf.basedb.util.export.spotdata.BfsExporter
Get the writer were reporter annotations should be printed.
getReporterCloneBatcher(DbControl) - Method in class net.sf.basedb.core.Experiment
Get a batcher for managing cloned reporter information for this experiment.
getReporterCloneTemplate() - Method in class net.sf.basedb.core.data.VirtualDbData
Get the template used for creating the cloned reporter table in this virtual database, or null if there is no cloned reporter information.
getReporterCloneTemplate() - Method in class net.sf.basedb.core.VirtualDb
Get the reporter clone template that is active in the current virtual database.
getReporterField(String, boolean) - Method in class net.sf.basedb.util.export.spotdata.AdvancedFieldConverter
 
getReporterField(String, boolean) - Method in class net.sf.basedb.util.export.spotdata.Base1FieldConverter
Convert a reporter field.
getReporterField(String, boolean) - Method in interface net.sf.basedb.util.export.spotdata.ExportableFieldConverter
Create a reporter dynamic field for the given name.
getReporterField(String, boolean) - Method in class net.sf.basedb.util.export.spotdata.StandardFieldConverter
Find a reporter dynamic field.
getReporterFields() - Method in class net.sf.basedb.plugins.BaseFileExporterPlugin
 
getReporterFields() - Static method in class net.sf.basedb.plugins.BfsExporterPlugin
 
getReporterFields() - Method in class net.sf.basedb.util.export.spotdata.AbstractBioAssaySetExporter
Get the list of registered reporter fields, in the order they were registered.
getReporterFields() - Method in class net.sf.basedb.util.export.spotdata.BaseFileExporter
 
getReporterFields() - Method in class net.sf.basedb.util.export.spotdata.BfsExporter
 
getReporterId() - Method in class net.sf.basedb.core.data.ReporterListScoreData
The id of the reporter.
getReporterId(int) - Method in class net.sf.basedb.clients.web.ExperimentExplorer
Get the reporter id for the specified index.
getReporterIndex() - Method in class net.sf.basedb.clients.web.ExperimentExplorer
Get the index of the current reporter.
getReporterJoiner(JoinType) - Static method in class net.sf.basedb.core.DynamicPositionQueryJoiners
Get a joiner instance for reporters for the specified join type.
getReporterJoiner(JoinType) - Static method in class net.sf.basedb.core.DynamicSpotQueryJoiners
Get a joiner instance for reporters for the specified join type.
getReporterList() - Method in class net.sf.basedb.core.data.ReporterListScoreData
The reporter list this reporter and score belongs to.
getReporterList() - Method in class net.sf.basedb.core.query.ReporterListExpression
Get the reporter list.
getReporterListJoiner(JoinType) - Static method in class net.sf.basedb.core.DynamicPositionQueryJoiners
Get a joiner instance for reporter lists for the specified join type.
getReporterListJoiner(JoinType) - Static method in class net.sf.basedb.core.DynamicReporterQuery
Get a joiner instance for reporter lists for the specified join type.
getReporterListJoiner(JoinType) - Static method in class net.sf.basedb.core.DynamicSpotQueryJoiners
Get a joiner instance for raw data for the specified join type.
getReporterListJoiner(JoinType) - Static method in class net.sf.basedb.core.HqlQueryJoiners
Get a joiner instance for raw data for the specified join type.
getReporterLists() - Method in class net.sf.basedb.core.data.ExperimentData
This is the inverse end.
getReporterListScores() - Method in class net.sf.basedb.core.data.ReporterData
The lists this reporter is used in.
getReporterListScores() - Method in class net.sf.basedb.core.data.ReporterListData
The list of reporters and their scores.
getReporterListsEnum(DbControl) - Static method in class net.sf.basedb.clients.web.Base
 
getReporterProperty(String, String) - Method in class net.sf.basedb.util.export.spotdata.AbstractFieldConverter
Get a static or extended reporter property field, such as name, description or id.
getReporterQuery() - Method in class net.sf.basedb.util.export.spotdata.AbstractBioAssaySetExporter
Get a configured query for position data that returns all fields that has been registered with AbstractBioAssaySetExporter.addReporterField(DynamicField).
getReporterQuery(DbControl, List<String>) - Method in class net.sf.basedb.clients.web.ExperimentExplorer
Get a query returning the reporter data used by the reporter search page.
getReporters() - Method in class net.sf.basedb.core.ArrayDesign
Get a query that returns the reporters on this array design.
getReporters() - Method in class net.sf.basedb.core.data.ReporterTypeData
This is the inverse end.
getReporters() - Method in class net.sf.basedb.core.Plate
Get a query that returns the reporters on this plate.
getReporters() - Method in class net.sf.basedb.core.RawBioAssay
Get a query that returns the reporters on this raw bioassay.
getReporterScores() - Method in class net.sf.basedb.core.ReporterList
Get a query returning ReporterScore objects.
getReporterType() - Method in class net.sf.basedb.core.data.ReporterData
Get the ReporterTypeData of this the reporter.
getReporterType(String) - Method in class net.sf.basedb.plugins.ReporterFlatFileImporter
 
getReporterType(DbControl, ReporterData) - Static method in class net.sf.basedb.core.Reporter
Get the reporter type item from a reporter data object.
getRequestInformation() - Method in class net.sf.basedb.core.PluginConfigurationRequest
Get the request information object containing information about the parameters needed for the plugin.
getRequestInformation(GuiContext, String) - Method in class net.sf.basedb.clients.web.plugins.SimpleExport
 
getRequestInformation(GuiContext, String) - Method in interface net.sf.basedb.core.plugin.InteractivePlugin
This method will return the RequestInformation for a given command, i.e.
getRequestInformation(GuiContext, String) - Method in class net.sf.basedb.plugins.AnnotationFlatFileImporter
 
getRequestInformation(GuiContext, String) - Method in class net.sf.basedb.plugins.Base1PluginExecuter
 
getRequestInformation(GuiContext, String) - Method in class net.sf.basedb.plugins.BaseFileExporterPlugin
 
getRequestInformation(GuiContext, String) - Method in class net.sf.basedb.plugins.batchimport.AbstractItemImporter
 
getRequestInformation(GuiContext, String) - Method in class net.sf.basedb.plugins.batchimport.AnyToAnyImporter
 
getRequestInformation(GuiContext, String) - Method in class net.sf.basedb.plugins.BfsExporterPlugin
 
getRequestInformation(GuiContext, String) - Method in class net.sf.basedb.plugins.CdfFileReporterImporter
 
getRequestInformation(GuiContext, String) - Method in class net.sf.basedb.plugins.executor.BaseFileExporterSupport
 
getRequestInformation(GuiContext, String) - Method in class net.sf.basedb.plugins.executor.BaseFileImporterSupport
 
getRequestInformation(GuiContext, String) - Method in class net.sf.basedb.plugins.executor.BfsExporterSupport
 
getRequestInformation(GuiContext, String) - Method in class net.sf.basedb.plugins.executor.BfsImporterSupport
 
getRequestInformation(GuiContext, String) - Method in class net.sf.basedb.plugins.executor.ExternalProgramExecutor
 
getRequestInformation(GuiContext, String) - Method in class net.sf.basedb.plugins.executor.FileOnlyImporterSupport
 
getRequestInformation(GuiContext, String) - Method in class net.sf.basedb.plugins.FormulaFilter
 
getRequestInformation(GuiContext, String) - Method in class net.sf.basedb.plugins.GalExporter
 
getRequestInformation(GuiContext, String) - Method in class net.sf.basedb.plugins.gtf.GtfReporterMapImporter
 
getRequestInformation(GuiContext, String) - Method in class net.sf.basedb.plugins.HelpExporter
 
getRequestInformation(GuiContext, String) - Method in class net.sf.basedb.plugins.HelpImporter
 
getRequestInformation(GuiContext, String) - Method in class net.sf.basedb.plugins.IlluminaRawDataImporter
 
getRequestInformation(GuiContext, String) - Method in class net.sf.basedb.plugins.IntensityCalculatorPlugin
The Request.COMMAND_CONFIGURE_PLUGIN command will not ask for any parameters.
getRequestInformation(GuiContext, String) - Method in class net.sf.basedb.plugins.JepExtraValueCalculator
 
getRequestInformation(GuiContext, String) - Method in class net.sf.basedb.plugins.JepIntensityTransformer
 
getRequestInformation(GuiContext, String) - Method in class net.sf.basedb.plugins.LowessNormalization
 
getRequestInformation(GuiContext, String) - Method in class net.sf.basedb.plugins.ManualDerivedBioAssayCreator
 
getRequestInformation(GuiContext, String) - Method in class net.sf.basedb.plugins.ManualTransformCreator
 
getRequestInformation(GuiContext, String) - Method in class net.sf.basedb.plugins.MedianRatioNormalization
 
getRequestInformation(GuiContext, String) - Method in class net.sf.basedb.plugins.PackedFileExporter
 
getRequestInformation(GuiContext, String) - Method in class net.sf.basedb.plugins.PlateFlatFileImporter
The Request.COMMAND_CONFIGURE_PLUGIN command will ask for parser regular expressions and column mappings.
getRequestInformation(GuiContext, String) - Method in class net.sf.basedb.plugins.PlateMappingExporter
 
getRequestInformation(GuiContext, String) - Method in class net.sf.basedb.plugins.PlateMappingImporter
 
getRequestInformation(GuiContext, String) - Method in class net.sf.basedb.plugins.PluginConfigurationExporter
 
getRequestInformation(GuiContext, String) - Method in class net.sf.basedb.plugins.PluginConfigurationImporter
 
getRequestInformation(GuiContext, String) - Method in class net.sf.basedb.plugins.PrintMapFlatFileImporter
The Request.COMMAND_CONFIGURE_PLUGIN command will ask for parser regular expressions and column mappings.
getRequestInformation(GuiContext, String) - Method in class net.sf.basedb.plugins.RawDataFlatFileImporter
The Request.COMMAND_CONFIGURE_PLUGIN command will ask for what type of rawdata to import.
getRequestInformation(GuiContext, String) - Method in class net.sf.basedb.plugins.ReporterFlatFileImporter
The Request.COMMAND_CONFIGURE_PLUGIN command will ask for parser regular expressions, column mappings and the reporter type.
getRequestInformation(GuiContext, String) - Method in class net.sf.basedb.plugins.ReporterMapFlatFileImporter
The Request.COMMAND_CONFIGURE_PLUGIN command will ask for parser regular expressions and column mappings.
getRequestInformation(GuiContext, String) - Method in class net.sf.basedb.util.zip.AbstractFileUnpacker
 
getRequiredFilter(Item) - Static method in class net.sf.basedb.core.QueryRuntimeFilterFactory
Get the required runtime filter for the speicified item type.
getRequiredHeader(FlatFileParser, String, String, String) - Method in class net.sf.basedb.util.basefile.BaseFileParser
Get the value of a required header.
getRequiredHeader(FlatFileParser, String, String, String, String) - Method in class net.sf.basedb.util.basefile.BaseFileParser
Get the value of a header as a list of sub-values.
getRequiredIndex(List<String>, String, String, String, int, String) - Method in class net.sf.basedb.util.basefile.BaseFileParser
Get the index of value in a list of values or throw an exception if the value is not found.
getRequiredString(String, String) - Static method in class net.sf.basedb.core.Config
Get a required configuration setting.
getRequiresConfiguration() - Method in class net.sf.basedb.core.data.PluginDefinitionData
If the plugin requires a configurations or not.
getResetClassLoader() - Method in class net.sf.basedb.util.extensions.manager.processor.ResetProcessor
 
getResetrrorFlag() - Method in class net.sf.basedb.util.extensions.manager.processor.ResetProcessor
 
getResource(String) - Method in class net.sf.basedb.util.JarClassLoader
 
getResourceBundle() - Method in class net.sf.basedb.util.resources.ResourceBundleWrapper
Get access to the underlying resource bundle.
getResourceBundle(String, Locale) - Static method in class net.sf.basedb.util.resources.ResourceBundleFactory
Same as getResouceBundle(name, locale, null).
getResourceBundle(String, Locale, ClassLoader) - Static method in class net.sf.basedb.util.resources.ResourceBundleFactory
Get a resource bundle for the given locale.
getResourceBundle(String, SessionControl) - Static method in class net.sf.basedb.util.resources.ResourceBundleFactory
Same as getResouceBundle(name, sc, null).
getResourceBundle(String, SessionControl, ClassLoader) - Static method in class net.sf.basedb.util.resources.ResourceBundleFactory
Get a resource bundle for the given session control.
getResources(String) - Method in class net.sf.basedb.util.JarClassLoader
 
getResponseImpl() - Method in class net.sf.basedb.core.PluginResponse
Get a new reponse object.
getRestriction() - Method in class net.sf.basedb.core.ItemContext.QueryRestrictions
 
getRestriction(DbControl, EntityQuery) - Method in class net.sf.basedb.core.PropertyFilter
Create a restriction from the filter.
getRestriction(DbControl, EntityQuery, ClientContext) - Method in class net.sf.basedb.core.PropertyFilter
Create a restriction from the filter.
getRestriction(Expression, Expression) - Method in enum class net.sf.basedb.core.Operator
 
getRestriction(Expression, Expression[]) - Method in enum class net.sf.basedb.core.Operator
 
getRestrictionSql(Query, DbControl) - Method in class net.sf.basedb.core.AnnotationBetweenRestriction
 
getRestrictionSql(Query, DbControl) - Method in class net.sf.basedb.core.AnnotationInRestriction
 
getRestrictionSql(Query, DbControl) - Method in class net.sf.basedb.core.AnnotationRestriction
Get an SQL fragment that includes the actual restriction.
getRestrictionSql(Query, DbControl) - Method in class net.sf.basedb.core.AnnotationSimpleRestriction
 
getRestrictionSql(Query, DbControl) - Method in class net.sf.basedb.core.HasAnnotationRestriction
 
getResult(ResultSet) - Method in class net.sf.basedb.core.AbstractSqlQuery.CountWork
 
getResult(ResultSet) - Method in class net.sf.basedb.core.hibernate.ResultSetWork
This method needs to be overridden by subclasses to extract the result from the ResultSet.
getResultIntensityTransform() - Method in class net.sf.basedb.core.data.FormulaData
A flag indicating what kind of result spot data this formula generates, or null if it generates the same kind of data that is used as source. 0 = no transformation; 1 = 2-log; 2 = 10-log
getResultIntensityTransform() - Method in class net.sf.basedb.core.Formula
Get the spot intensity transformation that this formula generates.
getResults(ExtensionsFile) - Method in class net.sf.basedb.util.extensions.manager.ProcessResults
Get the results for a specific extensions file.
getResync() - Method in class net.sf.basedb.util.annotations.InheritSpecification
 
getReturnAliases() - Method in class net.sf.basedb.core.hibernate.QueryWrapper
Deprecated.
getReturnType() - Method in class net.sf.basedb.core.ExtendedPropertyAccessor.GetterSetter
Always return null.
getReturnTypes() - Method in class net.sf.basedb.core.hibernate.QueryWrapper
Deprecated.
getReverseDirection() - Method in enum class net.sf.basedb.core.ItemContext.SortDirection
Get the reverse sort direction.
getRole() - Method in class net.sf.basedb.core.BioPlateEventParticipant
Get the role that the plate has in this event.
getRole() - Method in class net.sf.basedb.core.data.BioPlateEventParticipantData
Get the role of the plate in the event.
getRoleId() - Method in class net.sf.basedb.core.data.keyring.RoleKeys
Get the id of the role.
getRoleId() - Method in class net.sf.basedb.core.data.keyring.UserRoles
Get the id of the role.
getRoleKeyId(Item) - Static method in class net.sf.basedb.core.SystemItems
Get the numeric id for a RoleKey when you know the Item type of the RoleKey.
getRolePermissions(Item) - Method in class net.sf.basedb.core.InternalJobQueue.JobQueueKeyring
Return Permission.ACT_AS_ANOTHER_USER if itemType = Item.SYSTEM, 0 otherwise.
getRolePermissions(Item) - Method in class net.sf.basedb.core.Job.SignalKeyring
Return Permission.WRITE if itemType = Item.JOB, Permission.READ if Item.USER and Permission.CREATE if Item.MESSAGE or 0 otherwise.
getRolePermissions(Item) - Method in class net.sf.basedb.core.Keyring
Get the logged in user's permission to an unspecified item of a certain Item type.
getRolePermissions(Item) - Method in class net.sf.basedb.core.ServiceSessionControl.ServicesKeyring
Return Permission.ACT_AS_ANOTHER_USER if itemType = Item.SYSTEM, 0 otherwise.
getRolePermissions(Item) - Method in class net.sf.basedb.core.SessionControl
Get all role-based permissions for the specified type of items.
getRoles() - Method in class net.sf.basedb.core.data.RoleKeyData
Get the map that manages which roles that have permissions for this key.
getRoles() - Method in class net.sf.basedb.core.data.UserData
This is the inverse end.
getRoles() - Method in class net.sf.basedb.core.InternalJobQueue.JobQueueKeyring
Return empty set.
getRoles() - Method in class net.sf.basedb.core.Job.SignalKeyring
Return empty set.
getRoles() - Method in class net.sf.basedb.core.Keyring
 
getRoles() - Method in class net.sf.basedb.core.ServiceSessionControl.ServicesKeyring
Return empty set.
getRoles() - Method in class net.sf.basedb.core.SessionControl
getRoles() - Method in class net.sf.basedb.core.User
Get a query that returns the roles where this user is a member.
getRoot() - Method in class net.sf.basedb.clients.web.extensions.JspContext
Get the URL to the web application root as a string.
getRoot() - Method in class net.sf.basedb.clients.web.taglib.menu.Menu
 
getRoot() - Method in class net.sf.basedb.clients.web.taglib.Page
 
getRoot() - Method in class net.sf.basedb.clients.web.taglib.path.Path
 
getRoot() - Method in class net.sf.basedb.clients.web.taglib.PropertyValue
 
getRoot() - Method in class net.sf.basedb.util.extensions.xml.PathConverter
Get the value of the root path.
getRootAlias() - Method in class net.sf.basedb.core.AbstractHqlQuery
The alias of the item that is the root of this query.
getRootAlias() - Method in class net.sf.basedb.core.DynamicQuery
The alias of the item that is returned by this query.
getRootAlias() - Method in class net.sf.basedb.core.DynamicRawDataQuery
The alias of the item that is returned by this query.
getRootAlias() - Method in class net.sf.basedb.core.DynamicReporterQuery
The alias of the item that is returned by this query.
getRootAlias() - Method in interface net.sf.basedb.core.query.Query
The alias of the root-entity in the FROM part.
getRootDerivedBioAssays() - Method in class net.sf.basedb.core.data.PhysicalBioAssayData
This is the inverse end with an extra restriction
getRootDerivedBioAssays() - Method in class net.sf.basedb.core.PhysicalBioAssay
Get a query that returns all root derived bioassay created from this physical bioassay.
getRootEntry() - Method in class net.sf.basedb.util.Tree
Get the entry for the root node.
getRootItem() - Method in class net.sf.basedb.util.overview.GenericOverview
Get the root item of this overview.
getRootNode() - Method in class net.sf.basedb.util.overview.GenericOverview
Get the root node.
getRootPath() - Method in class net.sf.basedb.core.data.FileServerData
Get the root path that must be added to all URI:s using this file server.
getRootPath() - Method in class net.sf.basedb.core.FileServer
 
getRootPath() - Method in class net.sf.basedb.util.uri.ConnectionParameters
Get the root path that must be added to all URI:s used with these connection parameters.
getRootPath(DbControl) - Method in class net.sf.basedb.plugins.batchimport.FileImporter
 
getRootRawBioAssay(RawBioAssay) - Method in class net.sf.basedb.core.Experiment
Get the root raw bioassay that represents the given raw bioassay in this experiment.
getRootRawBioAssays() - Method in class net.sf.basedb.core.BioAssay
 
getRootRawBioAssays() - Method in class net.sf.basedb.core.data.ExperimentData
Manages which raw bioassays are available in the experiment.
getRootRawBioAssays() - Method in class net.sf.basedb.core.Experiment
Get a query that returns the root raw bioassays used in this experiment.
getRootTable() - Method in class net.sf.basedb.core.DynamicQuery
 
getRootTable() - Method in class net.sf.basedb.core.DynamicRawDataQuery
 
getRootTransformations() - Method in class net.sf.basedb.core.Experiment
Get a query that return all root transformations in this experiment.
getRootType() - Method in class net.sf.basedb.core.AbstractEntityQuery
 
getRootType() - Method in interface net.sf.basedb.core.query.EntityQuery
The type of items that is the root of the query.
getRow() - Method in class net.sf.basedb.clients.web.taglib.table.PropertyFilter
 
getRow() - Method in class net.sf.basedb.core.BioWell
Gets the row index where this well is located.
getRow() - Method in class net.sf.basedb.core.data.BioWellData
The row coordinate of this well.
getRow() - Method in class net.sf.basedb.core.data.FeatureData
Get the row coordinate of the feature.
getRow() - Method in class net.sf.basedb.core.data.MappingCoordinate
Get the row number.
getRow() - Method in class net.sf.basedb.core.data.PlateCoordinate
Get the row number.
getRow() - Method in class net.sf.basedb.core.data.RawData
 
getRow() - Method in class net.sf.basedb.core.data.WellData
The row coordinate of this well.
getRow() - Method in class net.sf.basedb.core.FeatureCoordinate
 
getRow() - Method in class net.sf.basedb.core.Well
Get the row coordinate of this well on the plate.
getRow(int) - Method in class net.sf.basedb.core.ItemContext.QueryRestrictions
 
getRowById(int) - Method in class net.sf.basedb.util.bfs.AnnotationModel
 
getRowByIndex(int) - Method in class net.sf.basedb.util.bfs.AnnotationModel
 
getRowByIndex(int) - Method in class net.sf.basedb.util.bfs.MatrixModel
 
getRowCount() - Method in class net.sf.basedb.util.bfs.AnnotationModel
Get the number of rows.
getRowCount() - Method in class net.sf.basedb.util.bfs.MatrixModel
Get the number of rows.
getRowCount(DbEngine, Connection, boolean) - Method in class net.sf.basedb.core.dbengine.TableInfo
Count the number of rows in the table.
getRowId(int) - Method in class net.sf.basedb.util.bfs.AnnotationModel
Get the row id for a given row.
getRowIndex() - Method in class net.sf.basedb.core.PropertyFilter
Get the filter row index this filter is part of.
getRowIndex(int) - Method in class net.sf.basedb.util.bfs.AnnotationModel
Get the row index for a given row id.
getRowRestriction() - Method in class net.sf.basedb.core.ItemContext.RowRestrictions
 
getRowRestriction(int) - Method in interface net.sf.basedb.core.query.QueryFilterAction
Generate a restriction for the given filter row.
getRows() - Method in class net.sf.basedb.core.BioPlate
Get the number of rows on this plate.
getRows() - Method in class net.sf.basedb.core.data.PlateGeometryData
The number of rows in this geometry.
getRows() - Method in class net.sf.basedb.core.PlateGeometry
Get the number of rows in this geometry.
getRowSelectionForLimitHandler() - Method in class net.sf.basedb.core.AbstractSqlQuery
Get a RowSelection object to be used with a LimitHandler so that it can modify and add parameters to the SQL.
getRowSeparator() - Method in class net.sf.basedb.util.excel.XlsxToCsvUtil
Get the current row separator.
getRowsperpage() - Method in class net.sf.basedb.clients.web.taglib.table.Navigator
 
getRowsPerPage() - Method in class net.sf.basedb.core.data.ContextData
Get the number of rows that are displayed on each table page.
getRowsPerPage() - Method in class net.sf.basedb.core.ItemContext
Get the number of rows the current table page is displaying.
getRunningJobs() - Method in class net.sf.basedb.clients.jobagent.Agent
Get a set containing the ID:s of the jobs that are currently beeing executed by this job agent.
getSafeRawDataType(String) - Static method in class net.sf.basedb.core.RawDataTypes
Get a information about a raw data type or throw an exception if the raw data type is not found.
getSameUnitsParameter() - Method in class net.sf.basedb.clients.web.plugins.SimpleExport
 
getSamples() - Method in class net.sf.basedb.core.BioSource
Get a query that returns all samples created from this biosource.
getSampleSize() - Method in class net.sf.basedb.util.AnyToAnyLinkStatistics
Get the number of items that was sampled to generated the statistics.
getSaveAsParameter(String, String, String, boolean) - Method in class net.sf.basedb.core.plugin.AbstractExporterPlugin
Get a plugin parameter that asks for the path to a file where the exported data should be saved.
getSaveAsPath(DbControl) - Method in class net.sf.basedb.core.plugin.AbstractExporterPlugin
Get the configured path where the exported data should be saved.
getSaveTo() - Method in class net.sf.basedb.core.plugin.AbstractExporterPlugin
Get the file object that the current export is writing to.
getSc() - Method in class net.sf.basedb.clients.web.taglib.table.Table
 
getScale(SessionControl) - Static method in class net.sf.basedb.clients.web.Base
Get the display scale setting.
getScheduled() - Method in class net.sf.basedb.core.data.JobData
Get the date and time the job was scheduled to the job queue, or null if it hasn't been scheduled yet.
getScheduled() - Method in class net.sf.basedb.core.Job
Get the date and time the job was scheduled to the job queue.
getScheduler() - Static method in class net.sf.basedb.core.Application
Get a scheduler that can be used for registering TimerTask for executions.
getSchema() - Method in class net.sf.basedb.core.hibernate.SessionFactoryConfiguration
Deprecated.
Get the schema.
getSchema() - Method in class net.sf.basedb.core.ServiceSessionControl.SessionFactoryConfiguration
Get the schema.
getSchemaName(String, String) - Method in class net.sf.basedb.core.dbengine.AbstractDbEngine
Return the schema name.
getSchemaName(String, String) - Method in interface net.sf.basedb.core.dbengine.DbEngine
Get the schema name to use for referencing the given catalog/schema pair.
getSchemaName(String, String) - Method in class net.sf.basedb.core.dbengine.MySQLEngine
Return null.
getSchemaValidatedXML(InputStream, String, String...) - Static method in class net.sf.basedb.util.XmlUtil2
Validate an XML input stream using XML schemas.
getSchemaValidatedXML(URL, String...) - Static method in class net.sf.basedb.util.XmlUtil2
Validate an XML file using XML schemas.
getSchemaVersion() - Static method in class net.sf.basedb.core.Application
Get the current database schema version number.
getSchemaVersion() - Method in class net.sf.basedb.core.data.SchemaVersionData
The current schema version.
getSchemaVersion() - Method in class net.sf.basedb.core.hibernate.SessionFactoryConfiguration
Deprecated.
Get the schema version of the current configuration.
getSchemaVersion() - Method in class net.sf.basedb.core.ServiceSessionControl.SessionFactoryConfiguration
Get the schema version of the current configuration.
getSchemaVersion(Session, String) - Static method in class net.sf.basedb.core.Update
 
getSchemaVersionInTransaction(Session, String) - Static method in class net.sf.basedb.core.Update
Get the current schema version number as it is stored in the database.
getScore() - Method in class net.sf.basedb.core.data.ReporterListScoreData
Get the score for the reporter, or null if no score has been set.
getScore() - Method in class net.sf.basedb.core.ReporterScore
Get the score for this reporter or null if no score has been set.
getScore() - Method in class net.sf.basedb.util.fuzzy.StringMatcher.FuzzyMatch
Get the similarity score of the key/value strings.
getScore(String, String) - Method in class net.sf.basedb.util.fuzzy.StringMatcher
Get the similarity score of two strings.
getScore(ReporterData) - Method in class net.sf.basedb.core.ReporterList
Get the score for the specified reporter.
getScripts() - Method in class net.sf.basedb.clients.web.extensions.AbstractJspFactory
Get a set with all script references.
getScripts() - Method in class net.sf.basedb.clients.web.extensions.JspContext
Get all scripts that has been added to this context.
getScripts() - Method in class net.sf.basedb.clients.web.taglib.Head
 
getScripts(String) - Method in class net.sf.basedb.clients.web.extensions.JspContext
Get all scripts that has been added to this context by the given extension
getScriptSourceInput() - Method in class net.sf.basedb.core.hibernate.SchemaGenerator.CollectSqlTarget
 
getScriptTargetOutput() - Method in class net.sf.basedb.core.hibernate.SchemaGenerator.CollectSqlTarget
 
getSection() - Method in class net.sf.basedb.core.BioPlate
Get the section within the "storage location" for this bioplate.
getSection() - Method in class net.sf.basedb.core.data.BioPlateData
Get the section in the storage location were the bioplate is stored.
getSection(int) - Method in class net.sf.basedb.util.bfs.MetadataModel
Get the section at a given index.
getSection(String) - Method in class net.sf.basedb.util.bfs.MetadataModel
Get the first section with a given name.
getSectionCount() - Method in class net.sf.basedb.util.bfs.MetadataModel
Get the number of sections.
getSectionCount() - Method in class net.sf.basedb.util.bfs.MetadataWriter
Get the number of sections that has been written to this file so far.
getSectionCount(String) - Method in class net.sf.basedb.util.basefile.BaseFileParser
The number of times we have seen a certain section in the file.
getSectionParser(String) - Method in class net.sf.basedb.util.basefile.BaseFileParser
Get the parser that is currently registered for a section.
getSelectdefault() - Method in class net.sf.basedb.clients.web.taglib.Select
 
getSelected() - Method in class net.sf.basedb.core.ItemContext
Get a Set object to specify the ID:s of all items that are currently selected.
getSelectedColumns(ItemContext, List<TableColumn>, boolean) - Static method in class net.sf.basedb.clients.web.DynamicUtil
 
getSelectrecent() - Method in class net.sf.basedb.clients.web.taglib.Select
 
getSelects() - Method in class net.sf.basedb.core.AbstractQuery
Get all non-permanent selects.
getSender() - Method in class net.sf.basedb.core.Message
Get the user that sent this message.
getSendMessage() - Method in class net.sf.basedb.core.data.JobData
If the core should send a message to the owner when the job is finished or not.
getSendMessage() - Method in class net.sf.basedb.core.Job
If a message should be sent to the owner once the job has finished or not.
getSendMessagesAsEmail() - Method in class net.sf.basedb.core.data.UserData
If this flag is set, all messages to this user are sent as an email also, but only if: the server admin has configured an outgoing smtp server and the user has supplied a valid email address.
getSendMessagesAsEmail() - Method in class net.sf.basedb.core.User
If this flag has been set, messges to the user is also sent as an email.
getSeparator() - Method in class net.sf.basedb.clients.web.taglib.path.Path
 
getSeparator() - Method in class net.sf.basedb.clients.web.taglib.table.CellValue
 
getSeriesCount() - Method in class net.sf.basedb.util.plot.HistogramPlot.HistogramDataset
 
getSeriesKey(int) - Method in class net.sf.basedb.util.plot.HistogramPlot.HistogramDataset
 
getServer() - Method in class net.sf.basedb.core.data.JobAgentData
Get the server name or ip that this jobagent is running on.
getServer() - Method in class net.sf.basedb.core.data.JobData
The name of the server where the job is executing.
getServer() - Method in class net.sf.basedb.core.Job
Get the name of the server where the job is executing.
getServer() - Method in class net.sf.basedb.core.JobAgent
Get the name or IP-adress of the server were the job agent is running.
getServerAliases(String, Principal[]) - Method in class net.sf.basedb.util.ssl.StaticKeyManager
 
getServerAndNode() - Method in class net.sf.basedb.core.Job
Utility method for getting both the server and node as a single string (for display purposes).
getServerCertificate() - Method in class net.sf.basedb.core.data.FileServerData
Get the public server certificate indicating that we should trust https connections to the server.
getServerCertificate() - Method in class net.sf.basedb.core.FileServer
Get the public server certificate that indicates that we should only trust the server if it can present a certificate that matches this.
getServerCertificate() - Method in class net.sf.basedb.util.uri.ConnectionParameters
Get the public server certificate that indicates that we should only trust the server if it can present a certificate that matches this.
getServerInfo() - Method in class net.sf.basedb.core.File
 
getServerName() - Method in class net.sf.basedb.clients.jobagent.Agent
Get the host name of the server where the job agent is running.
getServerName() - Method in class net.sf.basedb.clients.web.taglib.Page
 
getServerX509Certificate() - Method in class net.sf.basedb.core.FileServer
Get the X.509 certificate for the server.
getServletContext() - Method in class net.sf.basedb.clients.web.extensions.ServletWrapper
 
getServletName() - Method in class net.sf.basedb.clients.web.extensions.ServletWrapper
 
getServletPath() - Method in class net.sf.basedb.clients.web.extensions.RequestWrapper
 
getServlets() - Method in class net.sf.basedb.clients.web.extensions.ServletLoader
Get a list with all loaded servlet definitions.
getServletUrl(String, String) - Static method in class net.sf.basedb.clients.web.extensions.ExtensionsControl
Get the base URL for servlets in the extension with the given ID.
getSession() - Method in class net.sf.basedb.core.data.ChangeHistoryData
 
getSession() - Method in class net.sf.basedb.core.hibernate.SessionWrapper
Deprecated.
getSession() - Method in class net.sf.basedb.core.LogControl
 
getSession(DbControl) - Method in class net.sf.basedb.core.ChangeHistory
Load the session in which the change was made.
getSession(DbControl) - Method in class net.sf.basedb.core.ChangeHistory.TransactionInfo
Load the session in which the change was made.
getSession(DbControl, ChangeHistory, boolean, boolean) - Static method in class net.sf.basedb.clients.web.ChangeHistoryUtil
Get the session in which the changes was made in HTML format.
getSessionControl() - Method in class net.sf.basedb.clients.jobagent.Agent
Get a session control with the configured user logged in.
getSessionControl() - Method in class net.sf.basedb.clients.web.taglib.Page
 
getSessionControl() - Method in class net.sf.basedb.core.AbstractBatcher
Get the SessionControl object that manages this item.
getSessionControl() - Method in class net.sf.basedb.core.BasicItem
Get the SessionControl object that manages this item.
getSessionControl() - Method in class net.sf.basedb.core.DbControl
Get the SessionControl object that owns this DbControl object.
getSessionControl() - Method in class net.sf.basedb.core.PluginRequest
 
getSessionControl() - Method in class net.sf.basedb.util.extensions.ClientContext
Get the current session control.
getSessionControl(String, String, String, boolean) - Static method in class net.sf.basedb.core.Application
Get an existing SessionControl object if you know the id.
getSessionControl(PageContext, boolean) - Static method in class net.sf.basedb.clients.web.Base
Get a new or existing SessionControl object given a PageContext.
getSessionControl(ServletRequest, boolean) - Static method in class net.sf.basedb.clients.web.Base
Get a session control for the BASE web client "net.sf.basedb.clients.web".
getSessionControl(ServletRequest, String, boolean) - Static method in class net.sf.basedb.clients.web.Base
Get a new or existing SessionControl object given a ServletRequest instance.
getSessionFactory() - Method in class net.sf.basedb.core.hibernate.SessionWrapper
 
getSessionFactory() - Static method in class net.sf.basedb.core.HibernateUtil
Get the configured session factory.
getSessionId() - Method in class net.sf.basedb.core.ChangeHistory
Get the ID of the session in which the change was made.
getSessionId() - Method in class net.sf.basedb.core.ChangeHistory.TransactionInfo
Get the ID of the session the transaction.
getSessionId() - Method in class net.sf.basedb.core.data.ChangeHistoryData
The ID of the session in which the changes happened.
getSessionId() - Method in class net.sf.basedb.core.log.TransactionDetails
Get the ID of the session or 0 if no user is logged in.
getSessions() - Method in class net.sf.basedb.core.data.ClientData
This is the invers end.
getSessions() - Method in class net.sf.basedb.core.data.UserData
This is the inverse end.
getSessions() - Method in class net.sf.basedb.core.data.UserDeviceData
This is the inverse end but we do not map with inverse="true" cascade="delete" since we want Hibernate to set SessionData.device_id = null instead of deleting sessions.
getSessions() - Method in class net.sf.basedb.core.UserDevice
Get a query for loading login session from this device.
getSessionSetting(String) - Method in class net.sf.basedb.core.SessionControl
Get the value of a session setting with the specified name.
getSet(Map<String, Set<String>>, String) - Method in class net.sf.basedb.clients.web.extensions.JspContext
Get the Set that is stored under the given key.
getSetParameterMethod(Class<?>) - Method in class net.sf.basedb.util.extensions.xml.XmlLoader
Check if the bean class has a setParameter(String, String) method and return it's reference if it has.
getSetter() - Method in class net.sf.basedb.core.ExtendedPropertyAccessor.GetterSetter
 
getSetterMethod(Class<?>, String) - Method in class net.sf.basedb.util.extensions.xml.XmlLoader
Get the setter method for a given tag name.
getSetterMethodNameFromTag(String) - Method in class net.sf.basedb.util.extensions.xml.XmlLoader
Convert the tag name to a setter method name.
getSetting(String) - Method in class net.sf.basedb.core.ItemContext
Get a value.
getSetting(String) - Method in class net.sf.basedb.core.Presets.Preset
Get the value for the setting with the specified name.
getSetting(String, String) - Method in class net.sf.basedb.clients.web.extensions.ExtensionsControl
Get a configuration setting for an extension.
getSetting(String, String) - Method in class net.sf.basedb.core.ItemContext
Get a value from the settings or the default value if no current value exists.
getSetting(String, String) - Method in class net.sf.basedb.util.extensions.manager.Settings
Get a configuration setting for an extension.
getSettings() - Method in class net.sf.basedb.core.data.ContextData
Get a map for other settings.
getSettings() - Method in class net.sf.basedb.core.JobAgent
Get a query that returns all plugin-specific settings for this job agent.
getSettings() - Method in class net.sf.basedb.util.extensions.manager.ExtensionsManager
Get the settings for the extension manager.
getSettings(Job) - Method in class net.sf.basedb.core.JobAgent
Get the settings for the plugin that is used for the specified job.
getSettings(PluginDefinition, boolean) - Method in class net.sf.basedb.core.JobAgent
Get the settings for the specified plugin.
getSettingsForExtension(String) - Method in class net.sf.basedb.util.extensions.manager.Settings
Get a preset containing settings for the given extesion.
getSeverity(ValidationRuleAction) - Method in class net.sf.basedb.util.overview.ValidationOptions
Get the severity level for the specified validator rule.
getShareableItems() - Static method in class net.sf.basedb.core.Metadata
Get a set containing all Shareable item types.
getSharedParent() - Method in class net.sf.basedb.core.ArrayDesignBlock
 
getSharedParent() - Method in class net.sf.basedb.core.ArrayDesignPlate
 
getSharedParent() - Method in class net.sf.basedb.core.BioAssay
Get the experiment.
getSharedParent() - Method in class net.sf.basedb.core.BioAssaySet
Get the experiment.
getSharedParent() - Method in class net.sf.basedb.core.BioMaterialEvent
 
getSharedParent() - Method in class net.sf.basedb.core.BioPlateEventParticipant
 
getSharedParent() - Method in class net.sf.basedb.core.BioWell
 
getSharedParent() - Method in class net.sf.basedb.core.ChildItem
Get the shareable parent item of this child item.
getSharedParent() - Method in class net.sf.basedb.core.DataCube
Get the experiment.
getSharedParent() - Method in class net.sf.basedb.core.DataCubeColumn
Get the experiment.
getSharedParent() - Method in class net.sf.basedb.core.DataCubeExtraValue
Get the experiment.
getSharedParent() - Method in class net.sf.basedb.core.DataCubeFilter
Get the experiment.
getSharedParent() - Method in class net.sf.basedb.core.DataCubeLayer
Get the experiment.
getSharedParent() - Method in class net.sf.basedb.core.ExtraValue
Get the experiment.
getSharedParent() - Method in class net.sf.basedb.core.Help
 
getSharedParent() - Method in class net.sf.basedb.core.JobAgentSettings
 
getSharedParent() - Method in class net.sf.basedb.core.PlateEvent
 
getSharedParent() - Method in class net.sf.basedb.core.PlateEventType
 
getSharedParent() - Method in class net.sf.basedb.core.RootRawBioAssay
Get the experiment.
getSharedParent() - Method in class net.sf.basedb.core.SyncFilter
 
getSharedParent() - Method in class net.sf.basedb.core.Transformation
Get the experiment.
getSharedParent() - Method in class net.sf.basedb.core.VirtualDb
Get the experiment.
getSharedParent() - Method in class net.sf.basedb.core.Well
 
getSharedPermissions(ShareableData) - Method in class net.sf.basedb.core.InternalJobQueue.JobQueueKeyring
Return 0.
getSharedPermissions(ShareableData) - Method in class net.sf.basedb.core.Job.SignalKeyring
Return 0.
getSharedPermissions(ShareableData) - Method in class net.sf.basedb.core.Keyring
 
getSharedPermissions(ShareableData) - Method in class net.sf.basedb.core.ServiceSessionControl.ServicesKeyring
Return 0.
getSharedPermissions(ShareableData) - Method in class net.sf.basedb.core.SessionControl
Get the shared permissions for a ShareableData object.
getSharedTo(DbControl, SharedItem) - Static method in class net.sf.basedb.util.ShareableUtil
Gets a list with the projects, groups and users(in that order) that an item is shared to.
getShareToEveryOneKey(DbControl, Permission) - Static method in class net.sf.basedb.core.ItemKey
Get a key that can be used to share items to the EVERYONE group with the given permissions.
getSheet() - Method in class net.sf.basedb.util.excel.XlsxTableWriter
Get the current sheet in the workbook.
getSheetAsCsv(int) - Method in class net.sf.basedb.util.excel.XlsxToCsvUtil
Convert the given sheet to an CSV InputStream.
getSheetAsCsv(String) - Method in class net.sf.basedb.util.excel.XlsxToCsvUtil
Convert the given named sheet to a CSV InputStream.
getSheetNames() - Method in class net.sf.basedb.util.excel.XlsxToCsvUtil
Get the names of the sheets in the workbook.
getShort(int) - Method in class net.sf.basedb.clients.web.servlet.PlotServlet.CFSqlResult
 
getShort(int) - Method in class net.sf.basedb.core.DynamicResultIterator.SqlResultImpl
 
getShort(int) - Method in interface net.sf.basedb.core.query.SqlResult
Get the value of the specified column as a short.
getShortEntityName(String) - Static method in class net.sf.basedb.core.HibernateUtil
Removes the package name part of a class name and any ending 'Data'.
getShortName() - Method in class net.sf.basedb.core.AnnotationTypeCategory
A short name can be used in some places instead of the normal name.
getShortName() - Method in class net.sf.basedb.core.data.AnnotationTypeCategoryData
A short name can be used in some places instead of the normal name.
getShortName() - Method in class net.sf.basedb.plugins.executor.AbstractIOSupport
A default implementation to maintain backwards compatibility.
getShortName() - Method in class net.sf.basedb.plugins.executor.BaseFileExporterSupport
 
getShortName() - Method in class net.sf.basedb.plugins.executor.BaseFileImporterSupport
 
getShortName() - Method in class net.sf.basedb.plugins.executor.BfsExporterSupport
 
getShortName() - Method in class net.sf.basedb.plugins.executor.BfsImporterSupport
 
getShortName() - Method in class net.sf.basedb.plugins.executor.FileOnlyImporterSupport
 
getShortName() - Method in interface net.sf.basedb.plugins.executor.IOSupport
Get a short name of the plug-in.
getShortPermissions(Identifiable) - Static method in class net.sf.basedb.clients.web.PermissionUtil
 
getShow() - Method in class net.sf.basedb.clients.web.taglib.table.ColumnDef
 
getShow() - Method in class net.sf.basedb.clients.web.taglib.table.TableColumn
 
getShowclazz() - Method in class net.sf.basedb.clients.web.taglib.HideableSection
 
getShowClazz() - Method in class net.sf.basedb.clients.web.extensions.section.IncludeContentSectionFactory.Section
 
getShowClazz() - Method in interface net.sf.basedb.clients.web.extensions.section.SectionAction
Additional class attribute of the main section tag that is used when the section is visible.
getShowClazz() - Method in class net.sf.basedb.clients.web.extensions.section.SectionBean
 
getSignal() - Method in exception net.sf.basedb.core.signal.UnsupportedSignalException
Get the signal that is not supported.
getSignal(String) - Static method in class net.sf.basedb.core.signal.Signal
Get the signal with a given ID.
getSignalHandler() - Method in class net.sf.basedb.clients.web.plugins.SimpleExport
 
getSignalHandler() - Method in interface net.sf.basedb.core.signal.SignalTarget
Get the signal handler that is handling signals on behalf of this object.
getSignalHandler() - Method in class net.sf.basedb.plugins.AbstractFlatFileImporter
Create a new ThreadSignalHandler that supports the Signal.ABORT signal.
getSignalHandler() - Method in class net.sf.basedb.plugins.Base1PluginExecuter
 
getSignalHandler() - Method in class net.sf.basedb.plugins.BaseFileExporterPlugin
 
getSignalHandler() - Method in class net.sf.basedb.plugins.BfsExporterPlugin
 
getSignalHandler() - Method in class net.sf.basedb.plugins.CdfFileReporterImporter
 
getSignalHandler() - Method in class net.sf.basedb.plugins.CloneReportersPlugin
 
getSignalHandler() - Method in class net.sf.basedb.plugins.executor.ExternalProgramExecutor
 
getSignalHandler() - Method in class net.sf.basedb.plugins.FormulaFilter
 
getSignalHandler() - Method in class net.sf.basedb.plugins.GalExporter
 
getSignalHandler() - Method in class net.sf.basedb.plugins.HelpExporter
 
getSignalHandler() - Method in class net.sf.basedb.plugins.HelpImporter
 
getSignalHandler() - Method in class net.sf.basedb.plugins.IntensityCalculatorPlugin
 
getSignalHandler() - Method in class net.sf.basedb.plugins.JepExtraValueCalculator
 
getSignalHandler() - Method in class net.sf.basedb.plugins.JepIntensityTransformer
 
getSignalHandler() - Method in class net.sf.basedb.plugins.LowessNormalization
 
getSignalHandler() - Method in class net.sf.basedb.plugins.MedianRatioNormalization
 
getSignalHandler() - Method in class net.sf.basedb.plugins.PackedFileExporter
 
getSignalHandler() - Method in class net.sf.basedb.plugins.PlateMappingExporter
 
getSignalHandler() - Method in class net.sf.basedb.plugins.PluginConfigurationExporter
 
getSignalHandler() - Method in class net.sf.basedb.plugins.PluginConfigurationImporter
 
getSignalHandler() - Method in class net.sf.basedb.util.zip.AbstractFileUnpacker
 
getSignalHandler(String) - Method in class net.sf.basedb.core.signal.AbstractSignalReceiver
Get the signal handler with a given ID.
getSignalReceiver() - Method in class net.sf.basedb.clients.jobagent.Agent
Get the signal receiver that is processing signal messages on behalf of this job agent.
getSignalReceiver() - Static method in class net.sf.basedb.core.InternalJobQueue
Get the signal receiver used by the internal job queue.
getSignalReceiver(String) - Static method in class net.sf.basedb.core.signal.LocalSignalReceiver
Get a signal receiver with a given ID.
getSignals() - Static method in class net.sf.basedb.core.signal.Signal
Get all registered signals.
getSignals() - Method in exception net.sf.basedb.core.signal.SignalReceivedException
Get the signals that has been received.
getSignalTransporter() - Method in class net.sf.basedb.core.data.JobData
Identifies the signal transporter to use.
getSignalTransporter() - Method in class net.sf.basedb.core.Job
Create and initialise a signal transporter object that can be used to send signal to the plug-in running this job.
getSignalTransporterClass() - Method in class net.sf.basedb.clients.web.util.SimpleSignalProgressReporter
This class does not need any signal transporter.
getSignalTransporterClass() - Method in class net.sf.basedb.core.signal.LocalSignalReceiver
 
getSignalTransporterClass() - Method in interface net.sf.basedb.core.signal.SignalReceiver
Get the signal transporter class that should be used to send signals to this receiver.
getSignalTransporterClass() - Method in class net.sf.basedb.core.signal.SocketSignalReceiver
 
getSignalURI() - Method in class net.sf.basedb.core.signal.AbstractSignalTransporter
Get the URI representation of the global signal ID.
getSize() - Method in class net.sf.basedb.core.data.FileData
Get the size in bytes for this FileData object.
getSize() - Method in class net.sf.basedb.core.data.ItemListData
The number of biomaterials in the list.
getSize() - Method in class net.sf.basedb.core.data.PhysicalBioAssayData
The number size of the bioassay.
getSize() - Method in class net.sf.basedb.core.data.ReporterListData
The number of reporter in the list.
getSize() - Method in class net.sf.basedb.core.dbengine.TableInfo.ColumnInfo
 
getSize() - Method in class net.sf.basedb.core.File
Get the (uncompressed) size of this file.
getSize() - Method in class net.sf.basedb.core.ItemList
Get the number of members in this list.
getSize() - Method in class net.sf.basedb.core.PhysicalBioAssay
Get the size of the bioassay.
getSize() - Method in class net.sf.basedb.core.ReporterList
Get the number of reporter in this reporter list.
getSize() - Method in class net.sf.basedb.core.snapshot.AnnotationSetSnapshot
Get the number of annotations.
getSize() - Method in class net.sf.basedb.core.VirtualColumn
Get the maximum size of data in the column if it is a string.
getSize() - Method in class net.sf.basedb.util.excel.XlsxToCsvUtil.SheetInfo
Get the size of the CSV in bytes.
getSize() - Method in class net.sf.basedb.util.importer.BaseFileWrapper
 
getSize() - Method in class net.sf.basedb.util.importer.DiskFileWrapper
 
getSize() - Method in interface net.sf.basedb.util.importer.FileWrapper
Get the size of the file.
getSize() - Method in class net.sf.basedb.util.importer.spotdata.BaseFileInfo
Get the file size.
getSize(String) - Method in class net.sf.basedb.util.bfs.BaseInputStreamLocator
 
getSize(String) - Method in class net.sf.basedb.util.bfs.DiskInputStreamLocator
 
getSize(String) - Method in interface net.sf.basedb.util.bfs.InputStreamLocator
Get the size in bytes of the given named resource.
getSizeAtLastSync() - Method in class net.sf.basedb.core.data.ItemListData
The size of the item list after the last sync, -1 if it has never been synced.
getSizeAtLastSync() - Method in class net.sf.basedb.core.ItemList
Get the size of the list at the last sync.
getSkinActions() - Method in class net.sf.basedb.clients.web.taglib.Page
Get all skin extension actions.
getSkinContext() - Method in class net.sf.basedb.clients.web.taglib.Page
Get the JSP context used for invoking skin extensions.
getSkippedLines() - Method in class net.sf.basedb.util.parser.FlatFileParser
Get lines that was skipped during the last call to FlatFileParser.nextData() or FlatFileParser.hasMoreData().
getSlot() - Method in class net.sf.basedb.clients.jobagent.slotmanager.MasterSlotManager.RemoteSlot
 
getSlot() - Method in class net.sf.basedb.util.jobagent.JobInfo
Get the slot the job is using on the job agent.
getSlot(Job) - Method in class net.sf.basedb.clients.jobagent.Agent
Find a free slot for executing a job.
getSlot(Job) - Method in class net.sf.basedb.clients.jobagent.slotmanager.InternalSlotManager
 
getSlot(Job) - Method in class net.sf.basedb.clients.jobagent.slotmanager.RemoteSlotManager
 
getSlot(Job) - Method in interface net.sf.basedb.clients.jobagent.slotmanager.SlotManager
Get a slot for the specified job.
getSlot(Job.ExecutionTime) - Method in class net.sf.basedb.clients.jobagent.slotmanager.InternalSlotManager
Get a slot for a job with the given estimated execution time.
getSlotManagerClass(String) - Method in class net.sf.basedb.clients.jobagent.Agent
Get the class object for the configured slot manager.
getSnapshot() - Method in class net.sf.basedb.core.snapshot.AnnotationLoaderUtil
Get the snapshot for the last annotation found when calling AnnotationLoaderUtil.findAll(AnnotationSetSnapshot).
getSnapshot(DbControl, int) - Method in class net.sf.basedb.core.snapshot.SnapshotManager
Get the annotation snapshot for the annotation set with the given id.
getSnapshotDate() - Method in class net.sf.basedb.core.snapshot.AnnotationSetSnapshot
Get the date and time this snapshot was created.
getSnapshotManager() - Method in class net.sf.basedb.clients.web.ExperimentExplorer
Get the snapshot manager that is used to load annotation values.
getSnapshotManager() - Method in class net.sf.basedb.util.export.spotdata.AbstractBioAssaySetExporter
Get the current snapshot manager.
getSnapshotManager() - Method in class net.sf.basedb.util.export.spotdata.AbstractFieldConverter
Get the snapshot manager to use with annotation-based fields.
getSnapshotManager() - Method in class net.sf.basedb.util.overview.GenericOverview
Get the current snapshot manager.
getSnapshotManager() - Method in interface net.sf.basedb.util.overview.OverviewContext
Get the snapshot manager that is used to load annotation values.
getSnapshots() - Method in class net.sf.basedb.core.snapshot.AnnotationLoaderUtil
Get all snapshots found by the last AnnotationLoaderUtil.findAll(AnnotationSetSnapshot) call.
getSoftware() - Method in class net.sf.basedb.core.data.DerivedBioAssayData
Get the software used to create this bioassay set.
getSoftware() - Method in class net.sf.basedb.core.data.RawBioAssayData
Get the software used to analyse the scanned image and produce the raw data.
getSoftware() - Method in class net.sf.basedb.core.DerivedBioAssay
Get the Software that was used when creating this bioassay set.
getSoftware() - Method in class net.sf.basedb.core.RawBioAssay
Get the Software used while analysing the scanned images.
getSortable() - Method in class net.sf.basedb.clients.web.taglib.table.TableColumn
 
getSortby() - Method in class net.sf.basedb.clients.web.taglib.table.Table
 
getSortDirection() - Method in class net.sf.basedb.core.data.ContextData
Get the sort direction, 0 = ascending, 1 = descending
getSortDirection() - Method in class net.sf.basedb.core.ItemContext
If the items are sorted in ascending or descending order.
getSortDirection(String) - Method in class net.sf.basedb.clients.web.taglib.table.Table
Get the sort direction on the given column.
getSortedRawDataTypes(Comparator<RawDataType>) - Static method in class net.sf.basedb.core.RawDataTypes
Get all raw data types sorted according to the given comparator.
getSortOrder() - Method in class net.sf.basedb.core.ItemContext
Get the current sort property as an Order instance.
getSortproperty() - Method in class net.sf.basedb.clients.web.taglib.table.ColumnDef
 
getSortProperty() - Method in class net.sf.basedb.clients.web.extensions.list.AbstractListColumnBean
 
getSortProperty() - Method in interface net.sf.basedb.clients.web.extensions.list.ListColumnAction
Override the default property when this column is used for sorting.
getSortProperty() - Method in class net.sf.basedb.core.data.ContextData
Get property name to sort on.
getSortProperty() - Method in class net.sf.basedb.core.ItemContext
Get the name of the property the current listing is sorted by.
getSource() - Method in class net.sf.basedb.core.Annotation
Get the annotation source.
getSource() - Method in class net.sf.basedb.core.data.AnnotationData
The annotation source. 0 = primary, 1 = inherited, 2 = cloned For primary annotations, only one annotation per annotation type is supported.
getSource() - Method in class net.sf.basedb.core.data.annotations.AnnotationLink
 
getSource() - Method in class net.sf.basedb.core.data.TransformationData
Get the source bioassayset for the transformation.
getSource() - Method in class net.sf.basedb.core.snapshot.AnnotationSnapshot
Get the source of the annotation.
getSource() - Method in class net.sf.basedb.core.Transformation
Get the source bioassayset used by this transformation.
getSource() - Method in class net.sf.basedb.util.export.spotdata.AbstractBioAssaySetExporter
Get the source bioassay set.
getSource() - Method in class net.sf.basedb.util.export.spotdata.AbstractFieldConverter
Get the source bioassay set.
getSourceBioAssays(DbControl) - Method in class net.sf.basedb.core.plugin.AbstractAnalysisPlugin
Gets a list of bioassays that were selected from the current bioassay set, to use for the analysis.
getSourceBioAssaySet(DbControl) - Method in class net.sf.basedb.core.plugin.AbstractAnalysisPlugin
Get the bioassay set that is used as the source for the plugin.
getSourceBioAssaySetParameter(String, String) - Method in class net.sf.basedb.core.plugin.AbstractAnalysisPlugin
Get a plugin parameter that asks for a bioassay set to use as data source for the plugin.
getSourceBioAssaysParameter(String, String) - Method in class net.sf.basedb.core.plugin.AbstractAnalysisPlugin
Gets a plugin parameter that asks for a subset of bioassays to use as data source for the plugin.
getSourceCoordinate(MappingCoordinate) - Method in class net.sf.basedb.core.PlateMapping
Get the source coordinate for a given destination coordinate.
getSourceCount() - Method in class net.sf.basedb.core.data.PlateMappingData
The required number of source plates.
getSourceCount() - Method in class net.sf.basedb.core.PlateMapping
Get the number of required source plates.
getSourceDerivedBioAssay(DbControl) - Method in class net.sf.basedb.core.plugin.AbstractAnalysisPlugin
Get the derived bioassay that is used as the source for the plugin.
getSourceDerivedBioAssayParameter(String, String) - Method in class net.sf.basedb.core.plugin.AbstractAnalysisPlugin
Get a plugin parameter that asks for a derived bioassay to use as data source for the plugin.
getSourceFileWrapper() - Method in class net.sf.basedb.util.importer.spotdata.BaseFileImporter
Get the source file.
getSourceGeometry() - Method in class net.sf.basedb.core.data.PlateMappingData
The required geometry of source plates in this mapping.
getSourceGeometry() - Method in class net.sf.basedb.core.PlateMapping
Get the PlateGeometry that is required for source plates.
getSourceIndex(Plate) - Method in class net.sf.basedb.core.Plate
If this plate was created by a PlateMapping and the specified plate is a parent, get the index of the parent plate in the list of source plates used by the plate mapping.
getSourceIntensityTransform() - Method in class net.sf.basedb.core.data.FormulaData
A flag indicating what kind of spot source data that the formula can be used with, or null if the formula can be used with any kind of source data. 0 = no transformation; 1 = 2-log; 2 = 10-log
getSourceIntensityTransform() - Method in class net.sf.basedb.core.Formula
Get the intensity transformation that is required on spot data if this formula should generate the correct result.
getSourceItemMustExist() - Method in class net.sf.basedb.core.SyncFilter
If set, a source item that matches the filter must exist, otherwise it must not exist.
getSourceItemTransform() - Method in class net.sf.basedb.core.data.ItemListSyncFilterData
The transform to use for converting filter matches to list members. 0 = none; 1 = parent to child, 2 = child to parent
getSourceItemTransformation() - Method in class net.sf.basedb.core.SyncFilter
Get the transformation to use for converting the items matching this filter to list members.
getSourceItemType() - Method in class net.sf.basedb.core.data.ItemListSyncFilterData
Get the type of items that this filter is applies to.
getSourceItemType() - Method in class net.sf.basedb.core.SyncFilter
Get the source item type that this synchronization filter applies to.
getSourceItemType() - Method in class net.sf.basedb.util.listable.AbstractSourceItemTransformer
 
getSourceItemType() - Method in class net.sf.basedb.util.listable.PushToParentsTransformer
 
getSourceItemType() - Method in interface net.sf.basedb.util.listable.SourceItemTransformer
Get the item type of the source items.
getSourceItemType() - Method in class net.sf.basedb.util.listable.SourceItemTransformerChain
Get the source item type of the first step in the chain.
getSourceItemType() - Method in class net.sf.basedb.util.listable.SourceItemTransformerWithCache.TransformerWithCache
 
getSourceMustExist() - Method in class net.sf.basedb.core.data.ItemListSyncFilterData
If set, the source item must exist, otherwise it must not exist.
getSources() - Method in class net.sf.basedb.core.BioMaterialEvent
Get a query that return all biomaterials used as sources for this event.
getSources() - Method in class net.sf.basedb.core.data.BioMaterialEventData
Get a map containing information about the source biomaterials used in the event.
getSourceType() - Method in class net.sf.basedb.clients.web.extensions.list.RelatedItemColumn.Specification
Get the source item type.
getSourceType() - Method in class net.sf.basedb.core.hibernate.SchemaGenerator.CollectSqlTarget
 
getSpacingX() - Method in class net.sf.basedb.core.ArrayDesignBlock
Get the x spacing between the spots in the slide.
getSpacingX() - Method in class net.sf.basedb.core.data.ArrayDesignBlockData
Get the x spacing.
getSpacingX() - Method in class net.sf.basedb.plugins.PrintMapFlatFileImporter.MetaBlock
 
getSpacingY() - Method in class net.sf.basedb.core.ArrayDesignBlock
Get the y spacing between the spots in the slide.
getSpacingY() - Method in class net.sf.basedb.core.data.ArrayDesignBlockData
Get the y spacing.
getSpacingY() - Method in class net.sf.basedb.plugins.PrintMapFlatFileImporter.MetaBlock
 
getSpecification() - Method in class net.sf.basedb.clients.web.extensions.list.RelatedItemColumn
Get the specification for this column.
getSpotBatcher() - Method in class net.sf.basedb.core.BioAssaySet
Get a batcher used to insert spot data for this bioassayset.
getSpotCount(int) - Method in class net.sf.basedb.core.BioAssaySet
Get the number of spots in a single bioassay.
getSpotData() - Method in class net.sf.basedb.core.BioAssay
Get a query that returns spot data for this bioassay.
getSpotData() - Method in class net.sf.basedb.core.BioAssaySet
Get a query that returns spot data for this bioassayset.
getSpotExtraValueBatcher(Class<I>, ExtraValueType, Job) - Method in class net.sf.basedb.core.BioAssaySet
Get a batcher that is used to insert extra values per spot of the specified type.
getSpotField(String, boolean) - Method in class net.sf.basedb.util.export.spotdata.AdvancedFieldConverter
 
getSpotField(String, boolean) - Method in class net.sf.basedb.util.export.spotdata.Base1FieldConverter
Convert a spot field.
getSpotField(String, boolean) - Method in interface net.sf.basedb.util.export.spotdata.ExportableFieldConverter
Create a spot dynamic field for the given name.
getSpotField(String, boolean) - Method in class net.sf.basedb.util.export.spotdata.StandardFieldConverter
Find a spot dynamic field.
getSpotFields() - Method in class net.sf.basedb.util.export.spotdata.AbstractBioAssaySetExporter
Get the list of registered spot fields, in the order they were registered.
getSpotFields() - Method in class net.sf.basedb.util.export.spotdata.BaseFileExporter
 
getSpotFields() - Method in class net.sf.basedb.util.export.spotdata.BfsExporter
 
getSpotFields(BioAssaySet) - Method in class net.sf.basedb.plugins.BaseFileExporterPlugin
 
getSpotFields(BioAssaySet) - Method in class net.sf.basedb.plugins.BfsExporterPlugin
 
getSpotIntensityParser() - Method in class net.sf.basedb.util.importer.spotdata.BaseFileInfo.SpotSectionInfo
Get the spot intensity parser that should be used for parsing spot intensities in this section.
getSpotQuery(boolean) - Method in class net.sf.basedb.util.export.spotdata.AbstractBioAssaySetExporter
Get a configured query for spot data that returns all fields that has been registered with AbstractBioAssaySetExporter.addSpotField(DynamicField).
getSpotQuery(DbControl, int, int, List<TableColumn>) - Method in class net.sf.basedb.clients.web.ExperimentExplorer
Get a query returning spot data for a given reporter and position.
getSpots() - Method in class net.sf.basedb.core.data.RawBioAssayData
The number of data spots in this raw bio assay, that are stored in the database.
getSpots() - Method in class net.sf.basedb.core.RawBioAssay
Utility method that either returns the number of db spots or the number of file spots.
getSpotSectionInfo(int) - Method in class net.sf.basedb.util.importer.spotdata.BaseFileInfo
Get information about a spot section.
getSql() - Method in class net.sf.basedb.core.AnnotationBatcher.InsertBatcher
The SQL statement this batcher is executing.
getSql() - Method in class net.sf.basedb.core.AnnotationBatcher.UpdateBatcher
The SQL statement this batcher is executing.
getSql() - Method in class net.sf.basedb.core.hibernate.ResultSetWork
The sql that is executed by this work.
getSql() - Method in class net.sf.basedb.core.hibernate.SchemaGenerator.CollectSqlTarget
 
getSqlSymbol() - Method in enum class net.sf.basedb.core.Operator
Get the SQL symbol for this operator.
getSqlType() - Method in class net.sf.basedb.core.dbengine.TableInfo.ColumnInfo
 
getSQLType() - Method in class net.sf.basedb.core.hibernate.TypeWrapper
Get the SQL code for database columns that can store this type.
getSQLType() - Method in enum class net.sf.basedb.core.Type
Get the type of this parameter as specified by the java.sql.Types class.
getSqlTypeCode() - Method in class net.sf.basedb.core.BatchedPropertyInfo
Get the sql type code as defined by Types.
getSqrt() - Method in class net.sf.basedb.core.query.QuadraticMeanExpression
 
getSshFingerprint() - Method in class net.sf.basedb.core.data.FileServerData
Get the fingerprint of the SSH public key for the server that must be verified when (if) it is accessed via the SSH protocol.
getSshFingerprint() - Method in class net.sf.basedb.core.FileServer
 
getSshFingerprint() - Method in class net.sf.basedb.util.uri.ConnectionParameters
Get the SSH fingerprint of the server.
getSshPrivateKey() - Method in class net.sf.basedb.core.data.FileServerData
Get the SSH private key that we need to send to the server to make the server accept our connection.
getSshPrivateKey() - Method in class net.sf.basedb.core.FileServer
Get the private key that BASE should use to authenticate with the server when connecting with SSH.
getSshPrivateKey() - Method in class net.sf.basedb.util.uri.ConnectionParameters
Get the private key that should be used to authenticate with the server when connecting using SSH.
getSshPrivateKeyFormat() - Method in class net.sf.basedb.core.data.FileServerData
Get the private key format.
getSshPrivateKeyFormat() - Method in class net.sf.basedb.core.FileServer
Get the format of the SSH private key.
getSshPrivateKeyFormat() - Method in class net.sf.basedb.util.uri.ConnectionParameters
Get the format of the SSH private key (if known).
getSshPrivateKeyPassword() - Method in class net.sf.basedb.core.data.FileServerData
Get the password that is used to unlock the SSH private key.
getSshPrivateKeyPassword() - Method in class net.sf.basedb.core.FileServer
Get the password that is needed to unlock the SSH private key.
getSshPrivateKeyPassword() - Method in class net.sf.basedb.util.uri.ConnectionParameters
Get the password that is needed to unlock the SSH private key.
getSSLContext(byte[], byte[], String) - Static method in class net.sf.basedb.util.ssl.SSLUtil2
Create a SSL context that optionally uses the given trusted server certificate and client certificate.
getSSLSocketFactory() - Static method in class net.sf.basedb.util.ssl.SSLUtil2
Get a SSL Socket Factory object that is used to create SSL sockets.
getSSLSocketFactory(byte[], byte[], String) - Static method in class net.sf.basedb.util.ssl.SSLUtil2
Create a SSL socket factory that optionally uses the given trusted server certificate and client certificate.
getSSLSocketFactory2() - Method in class net.sf.basedb.core.FileServer
Get a socket factory that can be used to create SSL connections to the given server.
getStacktrace() - Method in class net.sf.basedb.util.extensions.logging.LogEntry
Get the stacktrace of the log entry.
getStackTrace() - Method in class net.sf.basedb.core.data.JobData
Get the stack trace in case of an error
getStackTrace() - Method in class net.sf.basedb.core.Job
Get the stack trace in case the job ended with an error
getStartDate() - Method in class net.sf.basedb.core.data.NewsData
Get the first day this news item should be shown.
getStartDate() - Method in class net.sf.basedb.core.News
Get the start date and time for this news item to be published.
getStarted() - Method in class net.sf.basedb.core.data.JobData
Get the date and time the job was started or null if the job hasn't been started.
getStarted() - Method in class net.sf.basedb.core.Job
Get the date and time the job was started.
getStartTime() - Method in class net.sf.basedb.util.extensions.manager.ProcessResults
Get the start time of the scan as a millisecond value.
getStartX() - Method in class net.sf.basedb.util.plot.HistogramPlot.HistogramBin
 
getStartX(int, int) - Method in class net.sf.basedb.util.plot.HistogramPlot.HistogramDataset
 
getStartXValue(int, int) - Method in class net.sf.basedb.util.plot.HistogramPlot.HistogramDataset
 
getStartY(int, int) - Method in class net.sf.basedb.util.plot.HistogramPlot.HistogramDataset
 
getStartYValue(int, int) - Method in class net.sf.basedb.util.plot.HistogramPlot.HistogramDataset
 
getState() - Method in class net.sf.basedb.core.log.EntityDetails
Get an array with the current state of the entity.
getState() - Method in class net.sf.basedb.core.plugin.NamespaceRequestWrapper
 
getState() - Method in interface net.sf.basedb.core.plugin.Request
getState() - Method in class net.sf.basedb.core.PluginRequest.RequestImpl
 
getState() - Method in class net.sf.basedb.core.PluginResponse
Get the state information that the plug-in wants to save until it is restarted again.
getState() - Method in class net.sf.basedb.plugins.executor.ExternalProgramExecutor.RequestWrapper
 
getStatelessSession() - Method in class net.sf.basedb.core.DbControl
Get a stateless Hibernate session using the same database connection as the regular session.
getStaticCache() - Static method in class net.sf.basedb.core.Application
Get the static cache mananger.
getStaticRules() - Static method in class net.sf.basedb.util.overview.OverviewUtil
Get all static (built-in) validation rules grouped by relationship.
getStatistics() - Method in class net.sf.basedb.core.hibernate.SessionWrapper
 
getStatistics(String) - Method in class net.sf.basedb.clients.web.ExperimentExplorer.AnnotationGroup
Get the sum of all values added with the ExperimentExplorer.AnnotationGroup.addStatistics(String, float) method with the given key.
getStatistics(DbControl) - Static method in class net.sf.basedb.core.DiskUsage
 
getStatus() - Method in class net.sf.basedb.clients.jobagent.AgentController
Get status info about running job agent by sending an info request to the agents r emote control service.
getStatus() - Method in class net.sf.basedb.core.data.JobData
Get the status of the job. 1 = waiting, 2 = running, 3 = completed ok, 4 = error
getStatus() - Method in class net.sf.basedb.core.Job
Get the status of the job.
getStatus() - Method in class net.sf.basedb.core.PluginResponse
Get the status of the response.
getStatus() - Method in class net.sf.basedb.util.extensions.manager.ProcessResults.FileResults
A short status message indicating the completed results on this file.
getStatusMessage() - Method in class net.sf.basedb.core.data.JobData
Get a status message.
getStatusMessage() - Method in class net.sf.basedb.core.Job
Get a message about the current status of the job.
getStdev() - Method in class net.sf.basedb.util.plot.HistogramPlot.HistogramBin
Get the standard deviation of all values in this bin.
getStickyCol() - Method in class net.sf.basedb.clients.web.taglib.table.Table
 
getStorageType() - Method in class net.sf.basedb.core.BioPlateType
Get the subtype of storage location where plates of this type are usually stored.
getStorageType() - Method in class net.sf.basedb.core.data.BioPlateTypeData
Get the subtype of storage location where plates of this type are usually stored.
getStream(String) - Method in class net.sf.basedb.util.extensions.manager.ExtensionsFile
Get an input stream for reading the resource specified by the given path
getString(boolean) - Method in enum class net.sf.basedb.util.formatter.BooleanFormatter.Type
 
getString(int) - Method in class net.sf.basedb.clients.web.servlet.PlotServlet.CFSqlResult
 
getString(int) - Method in class net.sf.basedb.core.DynamicResultIterator.SqlResultImpl
 
getString(int) - Method in interface net.sf.basedb.core.query.SqlResult
Get the value of the specified column as a string.
getString(int) - Method in class net.sf.basedb.util.parser.FlatFileParser.Data
Get the value in the specified column.
getString(int) - Method in class net.sf.basedb.util.parser.FlatFileParser.ExcelData
 
getString(String) - Static method in class net.sf.basedb.core.Config
Get the configuration setting specified by key as a String value.
getString(String) - Static method in class net.sf.basedb.util.Values
Convert a string to a string, and map NULL to the empty string.
getString(String, boolean, String...) - Method in class net.sf.basedb.util.resources.ResourceBundleWrapper
Utility method for returning the value for the key given by key.0 (variant=false) or key.1 (variant=true) depending on the value of the variant parameter.
getString(String, int, String...) - Method in class net.sf.basedb.util.resources.ResourceBundleWrapper
Utility method for returning the value for the key given by: key.index.
getString(String, String) - Static method in class net.sf.basedb.core.Config
Get the configuration setting specified by key as a String value.
getString(String, String) - Static method in class net.sf.basedb.util.Values
Convert a string to a string.
getString(String, String...) - Method in class net.sf.basedb.util.resources.ResourceBundleWrapper
Get a string value from the bundle.
getString(Collection<?>, String, boolean) - Static method in class net.sf.basedb.util.Values
 
getString(Collection<T>, String, boolean, Formatter<? super T>) - Static method in class net.sf.basedb.util.Values
 
getString(FlatFileParser.Data) - Method in class net.sf.basedb.util.parser.ColumnMapper
 
getString(FlatFileParser.Data) - Method in class net.sf.basedb.util.parser.CompoundMapper
Get a value by invoking each mapper in the order they appear in the list and concatenating the result.
getString(FlatFileParser.Data) - Method in class net.sf.basedb.util.parser.ConstantMapper
 
getString(FlatFileParser.Data) - Method in class net.sf.basedb.util.parser.CropStringMapper
Use the parent mapper to get the string value.
getString(FlatFileParser.Data) - Method in class net.sf.basedb.util.parser.JepMapper
 
getString(FlatFileParser.Data) - Method in interface net.sf.basedb.util.parser.Mapper
Get the value for the line of data as a string.
getString(FlatFileParser.Data) - Method in class net.sf.basedb.util.parser.NullIfExceptionMapper
 
getString(HttpResponse, String, String) - Static method in class net.sf.basedb.util.HttpUtil
 
getStringFormatter(SessionControl) - Static method in class net.sf.basedb.clients.web.formatter.FormatterFactory
Get a formattater that is encoding strings for HTML output.
getStringFormatter(SessionControl, boolean) - Static method in class net.sf.basedb.clients.web.formatter.FormatterFactory
Get the logged in user's formatter for strings.
getStringOrNull(String) - Static method in class net.sf.basedb.util.Values
Convert the empty string ("") to null after removing leading and trailing whitespace.
getStringValue() - Method in enum class net.sf.basedb.core.Type
Get the string value representation of this type.
getStringValues() - Method in class net.sf.basedb.core.data.annotations.AnnotationLink
 
getStyle() - Method in class net.sf.basedb.clients.web.extensions.list.AbstractListColumnBean
 
getStyle() - Method in interface net.sf.basedb.clients.web.extensions.list.ListColumnAction
Optional HTML style attribute that is used to style the column through CSS.
getStyle() - Method in class net.sf.basedb.clients.web.extensions.login.FieldInfo
Get a style attribute that can used to style the input field.
getStyle() - Method in class net.sf.basedb.clients.web.extensions.menu.FixedMenuItemFactory
 
getStyle() - Method in interface net.sf.basedb.clients.web.extensions.menu.MenuItemAction
Extra CSS style attributes that will be added to the style attribute of the menu item div.
getStyle() - Method in class net.sf.basedb.clients.web.extensions.menu.MenuItemBean
 
getStyle() - Method in class net.sf.basedb.clients.web.extensions.section.IncludeContentSectionFactory.Section
 
getStyle() - Method in interface net.sf.basedb.clients.web.extensions.section.SectionAction
Extra CSS style attributes that will be added to the style attribute of the main section tag.
getStyle() - Method in class net.sf.basedb.clients.web.extensions.section.SectionBean
 
getStyle() - Method in class net.sf.basedb.clients.web.extensions.tabcontrol.FixedTabFactory
 
getStyle() - Method in class net.sf.basedb.clients.web.extensions.tabcontrol.IncludeContentTabFactory.Tab
 
getStyle() - Method in interface net.sf.basedb.clients.web.extensions.tabcontrol.TabAction
Extra CSS style attributes that will be added to the style attribute of the main tab tag.
getStyle() - Method in class net.sf.basedb.clients.web.extensions.tabcontrol.TabBean
 
getStyle() - Method in interface net.sf.basedb.clients.web.extensions.toolbar.ButtonAction
Extra CSS style attributes that will be added to the style attribute of the main button tag.
getStyle() - Method in class net.sf.basedb.clients.web.extensions.toolbar.ButtonBean
 
getStyle() - Method in class net.sf.basedb.clients.web.extensions.toolbar.FixedButtonFactory
 
getStyle() - Method in class net.sf.basedb.clients.web.taglib.StylableTag
 
getStyle() - Method in class net.sf.basedb.clients.web.taglib.tab.Tab
 
getStyle() - Method in class net.sf.basedb.clients.web.taglib.table.Button.ButtonActionWrapper
 
getStyle() - Method in class net.sf.basedb.clients.web.taglib.table.Cell
 
getStyle() - Method in class net.sf.basedb.clients.web.taglib.table.CellValue
 
getStyles() - Method in class net.sf.basedb.clients.web.taglib.Head
 
getStylesheets() - Method in class net.sf.basedb.clients.web.extensions.AbstractJspFactory
Get a set with all stylesheet references.
getStylesheets() - Method in class net.sf.basedb.clients.web.extensions.JspContext
Get all stylesheets that has been added to this context.
getStylesheets(String) - Method in class net.sf.basedb.clients.web.extensions.JspContext
Get all stylesheets that has been added to this context by the given extension.
getSubCategories() - Method in class net.sf.basedb.core.data.ItemSubtypeData
This is the inverse end.
getSubCategoriesAnnotationType() - Method in class net.sf.basedb.core.AnnotationTypeCategory
Short-cut for calling getItemSubtype().getSubCategoriesAnnotationType().
getSubCategoriesAnnotationType() - Method in class net.sf.basedb.core.data.ItemSubtypeData
Get the annotation type that should be used to divide this subtype into sub-categories when mapped to annotation type categories.
getSubCategoriesAnnotationType() - Method in class net.sf.basedb.core.ItemSubtype
Get the annotation type that should be used to divide this subtype into sub-categories when mapped to annotation type categories.
getSubCategoriesEnumeration() - Method in class net.sf.basedb.core.AnnotationTypeCategory
Short-cut for calling getSubCategoriesAnnotationType().getValues()
getSubCategoriesValueType() - Method in class net.sf.basedb.core.AnnotationTypeCategory
Short-cut for calling getSubCategoriesAnnotationType().getValueType()
getSubcategory() - Method in class net.sf.basedb.clients.web.taglib.SubtypeSelector
 
getSubCategory() - Method in class net.sf.basedb.clients.web.SubContext
The new sub-category.
getSubCategory() - Method in class net.sf.basedb.core.data.ContextData
Get the annotation type category that is associated with this context.
getSubCategory(DbControl) - Method in class net.sf.basedb.core.ItemContext
Get the sub-category that is related to this context.
getSubCategoryFilter() - Method in class net.sf.basedb.core.ItemContext
Get the filter on the sub-category annotation column.
getSubCategoryFilterName() - Method in class net.sf.basedb.core.ItemContext
Check if this context has a filter on the sub-category annotation.
getSubCategoryValues() - Method in class net.sf.basedb.core.AnnotationTypeCategory
Get the list of values that are used to match this category.
getSubCategoryValues() - Method in class net.sf.basedb.core.data.AnnotationTypeCategoryData
The values to match for subcategories.
getSubclass() - Method in class net.sf.basedb.clients.web.taglib.StylableTag
 
getSubclass() - Method in class net.sf.basedb.clients.web.taglib.table.Cell
 
getSubcontext() - Method in class net.sf.basedb.clients.web.taglib.table.Table
 
getSubContext() - Method in class net.sf.basedb.clients.web.ExperimentExplorer
Get the subcontext name used for the ItemContext objects related to this explorer.
getSubContext() - Method in class net.sf.basedb.core.ContextKey
 
getSubContext() - Method in class net.sf.basedb.core.data.ContextData
Get the subcontext this context belongs to.
getSubContext() - Method in class net.sf.basedb.core.data.ContextIndex
Get the subcontext this Context belongs to.
getSubContext() - Method in class net.sf.basedb.core.data.JobData
The name of the subcontext that was active whjen configuring this job.
getSubContext() - Method in class net.sf.basedb.core.ItemContext
Get the sub-context name of this context.
getSubContext() - Method in class net.sf.basedb.core.plugin.GuiContext
 
getSubdirectories() - Method in class net.sf.basedb.core.data.DirectoryData
This is the inverse end.
getSubDirectories() - Method in class net.sf.basedb.core.Directory
Get a query that return subdirectories of this directory.
getSubid() - Method in class net.sf.basedb.clients.web.taglib.menu.Submenu
 
getSubmenuId() - Method in class net.sf.basedb.clients.web.extensions.menu.FixedMenuItemFactory
 
getSubmenuId() - Method in interface net.sf.basedb.clients.web.extensions.menu.MenuItemAction
The ID of a new submenu.
getSubmenuId() - Method in class net.sf.basedb.clients.web.extensions.menu.MenuItemBean
 
getSubtitle() - Method in class net.sf.basedb.clients.web.extensions.list.AbstractListColumnBean
 
getSubtitle() - Method in interface net.sf.basedb.clients.web.extensions.list.ListColumnAction
An optional subtitle.
getSubtitle() - Method in class net.sf.basedb.clients.web.taglib.table.ColumnDef
 
getSubtypableItems() - Static method in class net.sf.basedb.core.Metadata
Get a set containing all Subtypable item types.
getSubtype() - Method in class net.sf.basedb.clients.web.extensions.list.RelatedItemColumn.Specification
Get the target subtype from the expression.
getSubtype() - Method in class net.sf.basedb.util.bfs.MetadataModel
Get the BFS subtype.
getSubtype() - Method in class net.sf.basedb.util.bfs.MetadataWriter
Get the BFS subtype.
getSubtypeName() - Method in class net.sf.basedb.clients.web.extensions.list.RelatedItemColumn.Specification
Get the name of the targeted subtype.
getSubtypes() - Method in class net.sf.basedb.clients.web.taglib.SubtypeSelector
 
getSubtypesQuery(Item) - Static method in class net.sf.basedb.clients.web.Base
Get a query that returns all subtypes for the given main item type.
getSuccessMessage() - Method in class net.sf.basedb.clients.web.plugins.SimpleExport
 
getSuccessMessage() - Method in class net.sf.basedb.core.plugin.AbstractExporterPlugin
Called if the export was successful to let the subclass generate a simple message that is sent back to the core and user interface.
getSuccessMessage() - Method in class net.sf.basedb.plugins.BaseFileExporterPlugin
 
getSuccessMessage() - Method in class net.sf.basedb.plugins.BfsExporterPlugin
 
getSuccessMessage() - Method in class net.sf.basedb.plugins.GalExporter
 
getSuccessMessage() - Method in class net.sf.basedb.plugins.HelpExporter
 
getSuccessMessage() - Method in class net.sf.basedb.plugins.HelpImporter
 
getSuccessMessage() - Method in class net.sf.basedb.plugins.PackedFileExporter
 
getSuccessMessage() - Method in class net.sf.basedb.plugins.PlateMappingExporter
 
getSuccessMessage() - Method in class net.sf.basedb.plugins.PluginConfigurationExporter
 
getSuccessMessage(int) - Method in class net.sf.basedb.plugins.AbstractFlatFileImporter
Called if the parsing was successful to let the subclass generate a simple message that is sent back to the core and user interface.
getSuccessMessage(int) - Method in class net.sf.basedb.plugins.AnnotationFlatFileImporter
 
getSuccessMessage(int) - Method in class net.sf.basedb.plugins.batchimport.AbstractItemImporter
 
getSuccessMessage(int) - Method in class net.sf.basedb.plugins.batchimport.AnyToAnyImporter
 
getSuccessMessage(int) - Method in class net.sf.basedb.plugins.IlluminaRawDataImporter
 
getSuccessMessage(int) - Method in class net.sf.basedb.plugins.PlateFlatFileImporter
Return x plates inserted.
getSuccessMessage(int) - Method in class net.sf.basedb.plugins.PlateMappingImporter
Return Platemapping 'name' created..
getSuccessMessage(int) - Method in class net.sf.basedb.plugins.PrintMapFlatFileImporter
 
getSuccessMessage(int) - Method in class net.sf.basedb.plugins.RawDataFlatFileImporter
Return x spots inserted.
getSuccessMessage(int) - Method in class net.sf.basedb.plugins.ReporterFlatFileImporter
Return x new reporters; y updated reporters; z reporters added to list.
getSuccessMessage(int) - Method in class net.sf.basedb.plugins.ReporterMapFlatFileImporter
Return x features inserted; y blocks inserted.
getSuffix() - Method in class net.sf.basedb.clients.web.taglib.table.CellValue
 
getSuffix() - Static method in class net.sf.basedb.core.Version
Get the version suffix string (eg "-dev" for development versions)
getSuffix() - Method in class net.sf.basedb.util.bfs.SequenceFilenameGenerator
Get the suffix that is used for file name generation.
getSuggestedJobName() - Method in class net.sf.basedb.core.PluginResponse
Get the job name that was suggested by the job.
getSum() - Method in class net.sf.basedb.util.plot.HistogramPlot.HistogramBin
Get the sum of all values in this bin.
getSum(int) - Method in class net.sf.basedb.clients.web.ExperimentExplorer.AnnotationGroup
Get the sum of intensities for the specified channel.
getSummary() - Method in class net.sf.basedb.util.extensions.manager.ProcessResults
Get a summary of the scan results as a textual description.
getSummary(Group) - Method in class net.sf.basedb.core.DiskUsageStatistics
Get a summary of the disk usage for the specified group.
getSummary(User) - Method in class net.sf.basedb.core.DiskUsageStatistics
Get a summary of the disk usage for the specified user.
getSummaryOfUserAgent(String) - Static method in class net.sf.basedb.util.HttpUtil
Get a summary of the user agent: Browser with major version Operating system with version Typy of device (eg. desktop, phone, etc.)
getSupportedSignals() - Method in class net.sf.basedb.core.Job.JobSignalTransporter
 
getSupportedSignals() - Method in class net.sf.basedb.core.signal.AbstractSignalHandler
 
getSupportedSignals() - Method in class net.sf.basedb.core.signal.AbstractSignalTransporter
 
getSupportedSignals() - Method in class net.sf.basedb.core.signal.DelegatingSignalHandler
 
getSupportedSignals() - Method in interface net.sf.basedb.core.signal.SignalHandler
Get all signals that are supported by this handler.
getSupportedSignals() - Method in interface net.sf.basedb.core.signal.SignalTransporter
Get a collection containing the signals supported, by the signal handler.
getSupportedSourceItems(SyncFilter.SourceItemTransform) - Method in class net.sf.basedb.util.listable.AbstractSourceItemTransformerFactory
 
getSupportedSourceItems(SyncFilter.SourceItemTransform) - Method in interface net.sf.basedb.util.listable.SourceItemTransformerFactory
Get the supported source item types when transforming in the specified direction.
getSupportedSourceItems(SyncFilter.SourceItemTransform) - Method in class net.sf.basedb.util.listable.SourceItemTransformerWithCache
 
getSupportsConfigurations() - Method in class net.sf.basedb.core.data.PluginDefinitionData
If the plugin supports configurations or not.
getSupportsDeviceVerification() - Method in class net.sf.basedb.core.Client
This flag indicates if the registered client application supports device verification or not.
getSupportsDeviceVerification() - Method in class net.sf.basedb.core.data.ClientData
A flag indicating if this client application supports device verification.
getSymbol() - Method in class net.sf.basedb.core.data.ReporterData
Get the gene symbol of the reporter.
getSymbol() - Method in class net.sf.basedb.core.data.UnitSymbolData
The symbol, which must be unique for a given quantity.
getSymbol() - Method in enum class net.sf.basedb.core.Operator
Get the symbol for this operator, useful for display in client applications.
getSymbols() - Method in class net.sf.basedb.core.data.QuantityData
This is the inverse end.
getSymbols() - Method in class net.sf.basedb.core.data.UnitData
This is the inverse end.
getSymbols() - Method in class net.sf.basedb.core.Unit
Get all symbols that are registered for this unit.
getSyncDate() - Method in class net.sf.basedb.core.data.ItemListData
Get the date and time the list members was last synchronized by the filter context.
getSyncDate() - Method in class net.sf.basedb.core.ItemList
Get the last sync date+time.
getSyncFilters() - Method in class net.sf.basedb.core.data.ItemListData
This is the inverse end.
getSyncFilters() - Method in class net.sf.basedb.core.ItemList
Get a query returning all synchronization filters for this list
getSynchronizedQuerySpaces() - Method in class net.sf.basedb.core.hibernate.NativeQueryWrapper
 
getSyncProperties(ItemListSyncFilterData) - Static method in class net.sf.basedb.core.SyncFilter
Get a string representing the current syncfilter properties that may affect the end result even if the query return the same items.
getSystemId() - Method in class net.sf.basedb.core.BioPlateEventType
 
getSystemId() - Method in class net.sf.basedb.core.data.BioPlateEventTypeData
 
getSystemId() - Method in class net.sf.basedb.core.data.DirectoryData
 
getSystemId() - Method in class net.sf.basedb.core.data.GroupData
 
getSystemId() - Method in class net.sf.basedb.core.data.ItemSubtypeData
Override the property definition since we may have to update the system id during installation.
getSystemId() - Method in class net.sf.basedb.core.data.QuantityData
 
getSystemId() - Method in class net.sf.basedb.core.data.QuotaData
 
getSystemId() - Method in class net.sf.basedb.core.data.QuotaTypeData
 
getSystemId() - Method in class net.sf.basedb.core.data.RoleData
 
getSystemId() - Method in interface net.sf.basedb.core.data.SystemData
Get the system id for the item.
getSystemId() - Method in class net.sf.basedb.core.data.UserData
 
getSystemId() - Method in class net.sf.basedb.core.Directory
 
getSystemId() - Method in class net.sf.basedb.core.Group
 
getSystemId() - Method in class net.sf.basedb.core.ItemSubtype
 
getSystemId() - Method in class net.sf.basedb.core.Quantity
 
getSystemId() - Method in class net.sf.basedb.core.Quota
 
getSystemId() - Method in class net.sf.basedb.core.QuotaType
 
getSystemId() - Method in class net.sf.basedb.core.Role
 
getSystemId() - Method in interface net.sf.basedb.core.SystemItem
Get the system id for the item.
getSystemId() - Method in class net.sf.basedb.core.User
 
getTabcontrol() - Method in class net.sf.basedb.clients.web.taglib.Help
 
getTabindex() - Method in class net.sf.basedb.clients.web.taglib.Button
 
getTabindex() - Method in class net.sf.basedb.clients.web.taglib.Help
 
getTabindex() - Method in class net.sf.basedb.clients.web.taglib.Icon
 
getTabindex() - Method in class net.sf.basedb.clients.web.taglib.Input
 
getTabindex() - Method in class net.sf.basedb.clients.web.taglib.Select
 
getTabindex() - Method in class net.sf.basedb.clients.web.taglib.tab.Tab
 
getTabindex() - Method in class net.sf.basedb.clients.web.taglib.table.Button
 
getTabindex() - Method in class net.sf.basedb.clients.web.taglib.Zoom
 
getTabIndex() - Method in class net.sf.basedb.clients.web.extensions.tabcontrol.FixedTabFactory
 
getTabIndex() - Method in class net.sf.basedb.clients.web.extensions.tabcontrol.IncludeContentTabFactory.Tab
 
getTabIndex() - Method in interface net.sf.basedb.clients.web.extensions.tabcontrol.TabAction
Get the tab index used to control focus order when tabbing.
getTabIndex() - Method in class net.sf.basedb.clients.web.extensions.tabcontrol.TabBean
 
getTabIndex() - Method in interface net.sf.basedb.clients.web.extensions.toolbar.ButtonAction
Get the tab index used to control focus order when tabbing.
getTabIndex() - Method in class net.sf.basedb.clients.web.extensions.toolbar.ButtonBean
 
getTabIndex() - Method in class net.sf.basedb.clients.web.extensions.toolbar.FixedButtonFactory
 
getTabIndex() - Method in class net.sf.basedb.clients.web.taglib.tab.Tab
 
getTabIndex() - Method in class net.sf.basedb.clients.web.taglib.table.Button.ButtonActionWrapper
 
getTable() - Method in class net.sf.basedb.clients.web.taglib.SubtypeSelector
 
getTable() - Method in class net.sf.basedb.clients.web.taglib.table.ColumnHeaders
 
getTable() - Method in class net.sf.basedb.clients.web.taglib.table.ColumnSubtitles
 
getTable() - Method in class net.sf.basedb.clients.web.taglib.table.Data
 
getTable() - Method in class net.sf.basedb.clients.web.taglib.table.Headers
 
getTable() - Method in class net.sf.basedb.clients.web.taglib.table.PropertyFilter
 
getTable() - Method in class net.sf.basedb.clients.web.taglib.table.Row
 
getTable() - Method in class net.sf.basedb.clients.web.taglib.table.Rows
 
getTable() - Method in class net.sf.basedb.core.dbengine.TableInfo
Get the table this information is representing.
getTableInfo(Session, String) - Static method in class net.sf.basedb.core.Update
 
getTableName() - Method in class net.sf.basedb.core.RawDataType
Get the name of the database table that is used to store the extra properties of this raw data type.
getTableName() - Method in class net.sf.basedb.core.RealTable
Get the unquoted table name of this table in the database.
getTableName() - Method in enum class net.sf.basedb.core.Type
Get the name of the database table, parameter and annotation values of this value type are stored in.
getTableName(VirtualDb) - Method in enum class net.sf.basedb.core.VirtualTable
Get the real table name of this table in the database.
getTag() - Method in class net.sf.basedb.core.data.ExtractData
The tag used for tagging the extract so that it can be tracked on physical bioassays.
getTag() - Method in class net.sf.basedb.core.Extract
Get the tag that has been applied to this extract in order to be able to distinguish it from other extracts on a physical bioassay.
getTargetIds() - Method in class net.sf.basedb.util.listable.TransformCache.CacheEntry
 
getTargetItem() - Method in class net.sf.basedb.util.listable.AbstractSourceItemTransformerFactory
 
getTargetItem() - Method in interface net.sf.basedb.util.listable.SourceItemTransformerFactory
Get the target item type of this transformer factory.
getTargetItem() - Method in class net.sf.basedb.util.listable.SourceItemTransformerWithCache
 
getTargetItemType() - Method in class net.sf.basedb.util.listable.AbstractSourceItemTransformer
 
getTargetItemType() - Method in class net.sf.basedb.util.listable.PushToParentsTransformer
 
getTargetItemType() - Method in interface net.sf.basedb.util.listable.SourceItemTransformer
Get the item type of the target items.
getTargetItemType() - Method in class net.sf.basedb.util.listable.SourceItemTransformerChain
Get the target item type of the last step in the chain.
getTargetItemType() - Method in class net.sf.basedb.util.listable.SourceItemTransformerWithCache.TransformerWithCache
 
getTargetType() - Method in class net.sf.basedb.clients.web.extensions.list.RelatedItemColumn.Specification
Get the target ITEMTYPE from the expression.
getTargetType() - Method in class net.sf.basedb.util.AnyToAnyLinkStatistics
Get the item type of the target item for the link.
getTargetTypes() - Method in class net.sf.basedb.core.hibernate.SchemaGenerator.CollectSqlTarget
 
getTenantIdentifier() - Method in class net.sf.basedb.core.hibernate.SessionWrapper
 
getTenantIdentifier() - Method in class net.sf.basedb.core.hibernate.StatelessSessionWrapper
 
GetterSetter(PropertyAccessStrategy, Class<?>, String) - Constructor for class net.sf.basedb.core.ExtendedPropertyAccessor.GetterSetter
Create a new getter or setter.
getTextarea() - Method in class net.sf.basedb.clients.web.taglib.Zoom
 
getTextValues() - Method in class net.sf.basedb.core.data.annotations.AnnotationLink
 
getThetaJoin(Query, DbControl) - Method in class net.sf.basedb.core.DynamicJoin
 
getThetaJoin(Query, DbControl) - Method in class net.sf.basedb.core.ExtraValueJoin
 
getThetaJoin(Query, DbControl) - Method in class net.sf.basedb.core.query.AnnotationJoin
 
getThetaJoin(Query, DbControl) - Method in class net.sf.basedb.core.query.HqlInnerJoin
 
getThetaJoin(Query, DbControl) - Method in class net.sf.basedb.core.query.HqlLeftJoin
 
getThetaJoin(Query, DbControl) - Method in class net.sf.basedb.core.query.HqlRightJoin
 
getThetaJoin(Query, DbControl) - Method in interface net.sf.basedb.core.query.Join
 
getThetaJoin(Query, DbControl) - Method in class net.sf.basedb.core.RealJoin
 
getThetaJoin(Query, DbControl) - Method in class net.sf.basedb.core.ReporterListJoin
 
getThetaJoinCondition(Query, DbControl) - Method in class net.sf.basedb.core.DynamicJoin
 
getThetaJoinCondition(Query, DbControl) - Method in class net.sf.basedb.core.ExtraValueJoin
 
getThetaJoinCondition(Query, DbControl) - Method in class net.sf.basedb.core.query.AnnotationJoin
 
getThetaJoinCondition(Query, DbControl) - Method in class net.sf.basedb.core.query.HqlInnerJoin
 
getThetaJoinCondition(Query, DbControl) - Method in class net.sf.basedb.core.query.HqlLeftJoin
 
getThetaJoinCondition(Query, DbControl) - Method in class net.sf.basedb.core.query.HqlRightJoin
 
getThetaJoinCondition(Query, DbControl) - Method in interface net.sf.basedb.core.query.Join
 
getThetaJoinCondition(Query, DbControl) - Method in class net.sf.basedb.core.RealJoin
 
getThetaJoinCondition(Query, DbControl) - Method in class net.sf.basedb.core.ReporterListJoin
 
getThisAnnotation(DbControl) - Method in class net.sf.basedb.core.snapshot.AnnotationSnapshot
Get the annotation this is a snapshot of.
getThisAnnotationId() - Method in class net.sf.basedb.core.snapshot.AnnotationSnapshot
Get the id of the annotation this is a snapshot of.
getThisAnnotationSet(DbControl) - Method in class net.sf.basedb.core.snapshot.AnnotationSnapshot
Get the annotation set this annotation belongs to.
getThisAnnotationSetId() - Method in class net.sf.basedb.core.snapshot.AnnotationSnapshot
Get the id of the annotation set this is a snapshot of.
getThisItem(DbControl) - Method in class net.sf.basedb.core.snapshot.AnnotationSnapshot
Get the item that this annotation belongs to.
getThisItemId() - Method in class net.sf.basedb.core.snapshot.AnnotationSnapshot
Get the id of the item this annotation belongs to.
getThisItemType() - Method in class net.sf.basedb.core.snapshot.AnnotationSnapshot
Get the item type of the item this annotation belongs to.
getThisLastUpdate() - Method in class net.sf.basedb.core.snapshot.AnnotationSnapshot
Get the date+time this annotation was last updated.
getThisUnit(DbControl) - Method in class net.sf.basedb.core.snapshot.AnnotationSnapshot
Get the unit the annotatation values should use for display.
getThisUnitId() - Method in class net.sf.basedb.core.snapshot.AnnotationSnapshot
Get the id of the unit that the annotation values should use when displayed.
getThisValues() - Method in class net.sf.basedb.core.snapshot.AnnotationSnapshot
Get the annotation values for this annotation.
getThousandsSeparator(SessionControl) - Static method in class net.sf.basedb.clients.web.formatter.FormatterSettings
Get the separator character to use as a "thousands" separator in large numbers.
getThreadPriority(Job.ExecutionTime) - Method in class net.sf.basedb.clients.jobagent.Agent
Get the thread priority to use for the specified execution time slot.
getTime() - Method in class net.sf.basedb.core.ChangeHistory
Get the date and time the change was made.
getTime() - Method in class net.sf.basedb.core.ChangeHistory.TransactionInfo
Get the date and time of the transaction.
getTime() - Method in class net.sf.basedb.core.data.ChangeHistoryData
Get the time of the change.
getTime() - Method in class net.sf.basedb.util.extensions.manager.ProcessResults.FileResults
Get the time of the results as a millisecond value.
getTime(int) - Method in class net.sf.basedb.util.timer.PerformanceTimer
Get the current time of a timer.
getTimeout() - Method in class net.sf.basedb.core.hibernate.QueryWrapper
Deprecated.
getTimeout() - Method in class net.sf.basedb.util.listable.TransformCache.CacheEntry
 
getTimerTask(TimerTask, boolean) - Method in class net.sf.basedb.util.timer.Scheduler
 
getTimeSent() - Method in class net.sf.basedb.core.data.MessageData
Get the date and time this message was sent.
getTimeSent() - Method in class net.sf.basedb.core.Message
Get the date and time the message was sent.
getTimestamp() - Method in class net.sf.basedb.util.extensions.logging.LogEntry
The timestamp of the log entry.
getTimestampFormat() - Method in class net.sf.basedb.util.excel.XlsxToCsvUtil
Get the date formatter that is used for formatting cells with timestamp-like values.
getTimestampFormatter(String) - Method in class net.sf.basedb.plugins.AbstractFlatFileImporter
 
getTimestampMapper(String) - Method in class net.sf.basedb.util.parser.FlatFileParser
Get a mapper using the default timestamp format.
getTimestampValues() - Method in class net.sf.basedb.core.data.annotations.AnnotationLink
 
getTimstampFormat() - Method in class net.sf.basedb.util.excel.AutoFormatter
 
getTitle() - Method in class net.sf.basedb.clients.web.ExperimentExplorer.AnnotationGroup
Get the title of this annotation group.
getTitle() - Method in class net.sf.basedb.clients.web.extensions.list.AbstractListColumnBean
 
getTitle() - Method in interface net.sf.basedb.clients.web.extensions.list.ListColumnAction
The column title.
getTitle() - Method in class net.sf.basedb.clients.web.extensions.menu.FixedMenuItemFactory
 
getTitle() - Method in interface net.sf.basedb.clients.web.extensions.menu.MenuItemAction
Get the title of the menu.
getTitle() - Method in class net.sf.basedb.clients.web.extensions.menu.MenuItemBean
 
getTitle() - Method in interface net.sf.basedb.clients.web.extensions.plot.OverviewPlotAction
The title of the overview plots.
getTitle() - Method in class net.sf.basedb.clients.web.extensions.plot.OverviewPlotBean
 
getTitle() - Method in interface net.sf.basedb.clients.web.extensions.plot.PlotGenerator
Get the title of the generated image.
getTitle() - Method in class net.sf.basedb.clients.web.extensions.plot.PlotGeneratorBean
 
getTitle() - Method in class net.sf.basedb.clients.web.extensions.section.IncludeContentSectionFactory.Section
 
getTitle() - Method in interface net.sf.basedb.clients.web.extensions.section.SectionAction
Get the title of the section.
getTitle() - Method in class net.sf.basedb.clients.web.extensions.section.SectionBean
 
getTitle() - Method in class net.sf.basedb.clients.web.extensions.tabcontrol.FixedTabFactory
 
getTitle() - Method in class net.sf.basedb.clients.web.extensions.tabcontrol.IncludeContentTabFactory.Tab
 
getTitle() - Method in interface net.sf.basedb.clients.web.extensions.tabcontrol.TabAction
Get the title of the tab.
getTitle() - Method in class net.sf.basedb.clients.web.extensions.tabcontrol.TabBean
 
getTitle() - Method in interface net.sf.basedb.clients.web.extensions.toolbar.ButtonAction
Get the title of the button.
getTitle() - Method in class net.sf.basedb.clients.web.extensions.toolbar.ButtonBean
 
getTitle() - Method in class net.sf.basedb.clients.web.extensions.toolbar.FixedButtonFactory
 
getTitle() - Method in class net.sf.basedb.clients.web.taglib.Button
 
getTitle() - Method in class net.sf.basedb.clients.web.taglib.HideableSection
 
getTitle() - Method in class net.sf.basedb.clients.web.taglib.Input
 
getTitle() - Method in class net.sf.basedb.clients.web.taglib.menu.Menuitem
 
getTitle() - Method in class net.sf.basedb.clients.web.taglib.menu.Submenu
 
getTitle() - Method in class net.sf.basedb.clients.web.taglib.Page
 
getTitle() - Method in class net.sf.basedb.clients.web.taglib.path.PathElement
 
getTitle() - Method in class net.sf.basedb.clients.web.taglib.tab.Tab
 
getTitle() - Method in class net.sf.basedb.clients.web.taglib.table.Button.ButtonActionWrapper
 
getTitle() - Method in class net.sf.basedb.clients.web.taglib.table.Button
 
getTitle() - Method in class net.sf.basedb.clients.web.taglib.table.ColumnDef
 
getTitle() - Method in class net.sf.basedb.clients.web.taglib.table.Label
 
getTitle() - Method in class net.sf.basedb.clients.web.taglib.table.Table
 
getTitle() - Method in class net.sf.basedb.clients.web.taglib.table.TableColumn
 
getTitle() - Method in class net.sf.basedb.clients.web.taglib.Zoom
 
getTitle() - Method in exception net.sf.basedb.clients.web.WebException
Get the title of the error message.
getTitle() - Static method in class net.sf.basedb.core.Application
Get the "display title" of this server.
getTitle() - Method in class net.sf.basedb.core.data.ExperimentData
Get the title for this experiment.
getTitle() - Method in class net.sf.basedb.core.data.ReporterClonePropertyData
Get the title of the property.
getTitle() - Method in class net.sf.basedb.core.Experiment
Get the title for the publication for this experiment.
getTitle() - Method in class net.sf.basedb.core.ExtendedProperty
Get the title of the extended property.
getTitle() - Method in class net.sf.basedb.core.IntensityFormula
Get the title of the intensity formula.
getTitle() - Method in class net.sf.basedb.core.RequestInformation
Get the title of the request.
getTitle() - Method in class net.sf.basedb.plugins.BaseFileExporterPlugin.ExtendedDynamicField
 
getTitle() - Method in class net.sf.basedb.plugins.batchimport.AnnotationIdMethod
 
getTitle() - Method in class net.sf.basedb.plugins.batchimport.FallbackIdMethod
 
getTitle() - Method in class net.sf.basedb.plugins.batchimport.FileImporter.PathIdMethod
 
getTitle() - Method in interface net.sf.basedb.plugins.batchimport.IdMethod
The display title of the method.
getTitle() - Method in class net.sf.basedb.plugins.batchimport.InternalIdMethod
 
getTitle() - Method in class net.sf.basedb.plugins.batchimport.MultiPropertyIdMethod
 
getTitle() - Method in class net.sf.basedb.plugins.batchimport.PropertyIdMethod
 
getTitle() - Method in class net.sf.basedb.util.export.spotdata.AnnotationAssayField
Returns the name of the configured annotation type, or the empty string if not configured.
getTitle() - Method in class net.sf.basedb.util.export.spotdata.AssayPropertyField
 
getTitle() - Method in interface net.sf.basedb.util.export.spotdata.ExportableField
Get the column header.
getTitle() - Method in class net.sf.basedb.util.export.spotdata.JepDynamicField
 
getTitle() - Method in class net.sf.basedb.util.export.spotdata.SimpleDynamicField
 
getTitle() - Method in interface net.sf.basedb.util.overview.extensions.ValidationRuleAction
Get the title of this validator rule.
getTitle() - Method in class net.sf.basedb.util.overview.Node
Get the display title of this node.
getTitle() - Method in class net.sf.basedb.util.overview.Validator
Get the title of this validator.
getTo() - Method in class net.sf.basedb.core.AnyToAny
Get the item this link is linking to.
getTo() - Method in class net.sf.basedb.core.data.MessageData
The user this message is to.
getTo() - Method in class net.sf.basedb.core.Message
Get the User this message was sent to.
getTo(S) - Method in class net.sf.basedb.core.AnyToAny.FastLinkLoader
Get the target item that is linked from the source item by the named link.
getToId() - Method in class net.sf.basedb.core.AnyToAny
Get the ID of the item this link is linking to.
getToId() - Method in class net.sf.basedb.core.data.AnyToAnyData
The ID of the item we are linking to.
getToken() - Method in class net.sf.basedb.core.data.UserDeviceData
Get the device token.
getToolParameters(List<String>) - Method in class net.sf.basedb.plugins.ManualDerivedBioAssayCreator
 
getToolParameters(List<String>) - Method in class net.sf.basedb.plugins.ManualTransformCreator
 
getTooltip() - Method in class net.sf.basedb.clients.web.extensions.list.AbstractListColumnBean
 
getTooltip() - Method in interface net.sf.basedb.clients.web.extensions.list.ListColumnAction
An optional tooltip that is displayed when the mouse is over the column header.
getTooltip() - Method in class net.sf.basedb.clients.web.extensions.login.FieldInfo
Get a tooltip text that is displayed when the user holds the mouse over the input field.
getTooltip() - Method in class net.sf.basedb.clients.web.extensions.menu.FixedMenuItemFactory
 
getTooltip() - Method in interface net.sf.basedb.clients.web.extensions.menu.MenuItemAction
A tooltip that is shown as a yellow popup when the user points the mouse at the menu item.
getTooltip() - Method in class net.sf.basedb.clients.web.extensions.menu.MenuItemBean
 
getTooltip() - Method in class net.sf.basedb.clients.web.extensions.tabcontrol.FixedTabFactory
 
getTooltip() - Method in class net.sf.basedb.clients.web.extensions.tabcontrol.IncludeContentTabFactory.Tab
 
getTooltip() - Method in interface net.sf.basedb.clients.web.extensions.tabcontrol.TabAction
A tooltip that is shown as a yellow popup when the user points the mouse at the tab.
getTooltip() - Method in class net.sf.basedb.clients.web.extensions.tabcontrol.TabBean
 
getTooltip() - Method in interface net.sf.basedb.clients.web.extensions.toolbar.ButtonAction
A tooltip that is shown as a yellow popup when the user points the mouse at the button.
getTooltip() - Method in class net.sf.basedb.clients.web.extensions.toolbar.ButtonBean
 
getTooltip() - Method in class net.sf.basedb.clients.web.extensions.toolbar.FixedButtonFactory
 
getTooltip() - Method in class net.sf.basedb.clients.web.taglib.Button
 
getTooltip() - Method in class net.sf.basedb.clients.web.taglib.Help
 
getTooltip() - Method in class net.sf.basedb.clients.web.taglib.Icon
 
getTooltip() - Method in class net.sf.basedb.clients.web.taglib.menu.Menuitem
 
getTooltip() - Method in class net.sf.basedb.clients.web.taglib.menu.Submenu
 
getTooltip() - Method in class net.sf.basedb.clients.web.taglib.path.PathElement
 
getTooltip() - Method in class net.sf.basedb.clients.web.taglib.PropertyValue
 
getTooltip() - Method in class net.sf.basedb.clients.web.taglib.tab.Tab
 
getTooltip() - Method in class net.sf.basedb.clients.web.taglib.table.Button.ButtonActionWrapper
 
getTooltip() - Method in class net.sf.basedb.clients.web.taglib.table.Button
 
getTooltip() - Method in class net.sf.basedb.clients.web.taglib.table.ColumnDef
 
getTooltip() - Method in class net.sf.basedb.clients.web.taglib.table.Label
 
getTooltip() - Method in class net.sf.basedb.clients.web.taglib.Zoom
 
getTotal() - Method in class net.sf.basedb.core.DiskUsageStatistics.Summary
Get the total disk usage in bytes
getTotal() - Method in class net.sf.basedb.core.SimpleAbsoluteProgressReporter
Get the end point of the task.
getTotal(Location) - Method in class net.sf.basedb.core.DiskUsageStatistics.Summary
Get the total disk usage of the specified location in bytes.
getTotal(QuotaType) - Method in class net.sf.basedb.core.DiskUsageStatistics.Summary
Get the total disk usage for the specified quota type in bytes.
getTotal(QuotaType, Location) - Method in class net.sf.basedb.core.DiskUsageStatistics.Summary
Get the total disk usage of the specified location and quota type in bytes.
getTotalBytes() - Method in class net.sf.basedb.clients.web.fileupload.FileUploadProgress
Get the total number of bytes expected to upload.
getTotalCount() - Method in class net.sf.basedb.clients.web.servlet.PlotServlet.CFResultIterator
 
getTotalCount() - Method in class net.sf.basedb.core.AbstractResultList
 
getTotalCount() - Method in class net.sf.basedb.core.DataResultIterator
From the QueryResult interface ---------------------------------
getTotalCount() - Method in class net.sf.basedb.core.DynamicResultIterator
From the QueryResult interface ---------------------------------
getTotalCount() - Method in class net.sf.basedb.core.ItemResultIterator
From the QueryResult interface ---------------------------------
getTotalCount() - Method in interface net.sf.basedb.core.query.QueryResult
Get the total number of items returned by the query, ignoring any limits set by Query.setFirstResult(int) and Query.setMaxResults(int).
getTotalCount() - Method in class net.sf.basedb.core.ReporterScoreResultIterator
From the QueryResult interface ---------------------------------
getTotalCount() - Method in class net.sf.basedb.core.UnmodifiableResultList
 
getTotalFileSize() - Method in class net.sf.basedb.plugins.AbstractFlatFileImporter
Get the total file size of all files that are going to be imported.
getTotalFileSize() - Method in class net.sf.basedb.plugins.RawDataFlatFileImporter
 
getTotalInsertCount() - Method in class net.sf.basedb.core.BasicBatcher
Gets the total number of inserts done by the batcher
getTotalInsertCount() - Method in class net.sf.basedb.core.MappingBatcher
Get the total number of mappings to raw data create by this mapper.
getTotalMemory() - Method in class net.sf.basedb.core.JobAgent
Get the total memory in bytes of the server where the job agent is running.
getTotalMemory() - Method in class net.sf.basedb.util.jobagent.JobAgentInfo
Get the total memory on the job agent's server in bytes.
getTotalrows() - Method in class net.sf.basedb.clients.web.taglib.table.Navigator
 
getTotalSummary() - Method in class net.sf.basedb.core.DiskUsageStatistics
Get a summary of the total disk usage.
getTotalWells() - Method in class net.sf.basedb.core.BioPlate
Get the total number of wells on this plate.
getToType() - Method in class net.sf.basedb.core.AnyToAny.FastLinkLoader
The target item type.
getToType() - Method in class net.sf.basedb.core.AnyToAny
Get the type of the item this link is linking to.
getToType() - Method in class net.sf.basedb.core.data.AnyToAnyData
The type code of the item we are linking to.
getTransaction() - Method in class net.sf.basedb.core.hibernate.SessionWrapper
 
getTransaction() - Method in class net.sf.basedb.core.hibernate.StatelessSessionWrapper
 
getTransactionDetails() - Method in class net.sf.basedb.core.LogControl
Get information about the current transaction.
getTransactionId() - Method in class net.sf.basedb.core.ChangeHistory
Get the ID of the transaction that initiated the change.
getTransactionId() - Method in class net.sf.basedb.core.ChangeHistory.TransactionInfo
Get the ID of the transaction.
getTransactionInfo(DbControl, int) - Static method in class net.sf.basedb.core.ChangeHistory
Load information about a single transaction.
getTransferredBytes() - Method in class net.sf.basedb.clients.web.fileupload.FileUploadProgress
Get the number of bytes that have been uploaded so far.
getTransformation() - Method in class net.sf.basedb.core.BioAssaySet
Get the transformation that created this bioassayset.
getTransformation() - Method in class net.sf.basedb.core.data.BioAssaySetData
Get the transformation that created this bioassayset.
getTransformation() - Method in class net.sf.basedb.util.importer.spotdata.BaseFileImporter
Get the destination transformation.
getTransformation() - Method in class net.sf.basedb.util.importer.spotdata.BfsImporter
Get the destination transformation.
getTransformationName(DbControl) - Method in class net.sf.basedb.core.plugin.AbstractAnalysisPlugin
Generate a name for the transformation based on the plugin and it's configuration.
getTransformationNameParameter(String, String, String) - Method in class net.sf.basedb.core.plugin.AbstractAnalysisPlugin
Create a plugin parameter that asks for the name of the transformation.
getTransformations() - Method in class net.sf.basedb.core.BioAssaySet
Get a query that return all transformations using this bioassayset as a source.
getTransformations() - Method in class net.sf.basedb.core.data.BioAssaySetData
This is the inverse end.
getTransformations() - Method in class net.sf.basedb.core.data.ExperimentData
This is the inverse end.
getTransformations() - Method in class net.sf.basedb.core.data.JobData
This is the inverse end.
getTransformations() - Method in class net.sf.basedb.core.data.RawBioAssayData
This is the inverse end.
getTransformations() - Method in class net.sf.basedb.core.Experiment
Get a query that return all transformations including root transformations in this experiment.
getTransformer() - Method in class net.sf.basedb.clients.web.extensions.list.RelatedItemColumn
Get the transformer implementation that is used to turn source item into target items.
getTransformerFactory(Item) - Static method in class net.sf.basedb.util.listable.ListableUtil
Create a source item transformer factory that can transform items to the given target item type.
getTransformerFactory(Item, boolean) - Static method in class net.sf.basedb.util.listable.ListableUtil
Create a source item transformer factory that can transform items to the given target item type.
getTray() - Method in class net.sf.basedb.core.BioPlate
Get the tray within the "storage location" for this bioplate.
getTray() - Method in class net.sf.basedb.core.data.BioPlateData
Get the tray in the storage location were the bioplate is stored.
getType() - Method in class net.sf.basedb.clients.web.extensions.fileviewer.FileViewerContext
Get the context type that the file is being displayed in.
getType() - Method in class net.sf.basedb.clients.web.extensions.menu.FixedMenuItemFactory
 
getType() - Method in interface net.sf.basedb.clients.web.extensions.menu.MenuItemAction
The type of menu item.
getType() - Method in class net.sf.basedb.clients.web.extensions.menu.MenuItemBean
 
getType() - Method in class net.sf.basedb.clients.web.taglib.Input
 
getType() - Method in class net.sf.basedb.clients.web.taglib.menu.Menu
 
getType() - Method in class net.sf.basedb.core.Annotation
 
getType() - Method in class net.sf.basedb.core.AnnotationSet
 
getType() - Method in class net.sf.basedb.core.AnnotationType
 
getType() - Method in class net.sf.basedb.core.AnnotationTypeCategory
 
getType() - Method in class net.sf.basedb.core.AnyToAny
 
getType() - Method in class net.sf.basedb.core.ArrayBatch
 
getType() - Method in class net.sf.basedb.core.ArrayDesign
 
getType() - Method in class net.sf.basedb.core.ArrayDesignBlock
 
getType() - Method in class net.sf.basedb.core.ArrayDesignPlate
 
getType() - Method in class net.sf.basedb.core.ArraySlide
 
getType() - Method in class net.sf.basedb.core.BasicBatcher
Get the type of item supported by the batcher.
getType() - Method in class net.sf.basedb.core.BioAssay
 
getType() - Method in class net.sf.basedb.core.BioAssaySet
 
getType() - Method in class net.sf.basedb.core.BioMaterialEvent
 
getType() - Method in class net.sf.basedb.core.BioPlate
 
getType() - Method in class net.sf.basedb.core.BioPlateEvent
 
getType() - Method in class net.sf.basedb.core.BioPlateEventParticipant
 
getType() - Method in class net.sf.basedb.core.BioPlateEventType
 
getType() - Method in class net.sf.basedb.core.BioPlateType
 
getType() - Method in class net.sf.basedb.core.BioSource
 
getType() - Method in class net.sf.basedb.core.BioWell
 
getType() - Method in class net.sf.basedb.core.ChangeHistory
 
getType() - Method in class net.sf.basedb.core.Client
 
getType() - Method in class net.sf.basedb.core.ClientDefaultSetting
 
getType() - Method in class net.sf.basedb.core.data.FormulaData
The type of formula: 1 = intensity expression; raw data type required, 1 formula for each channel 2 = intensity transformation; raw data type or channels required, 1 formula for each channel 3 = column expression; raw data type or channels required, 1 formula only 4 = column restriction; raw data type or channels required, 1 formula only
getType() - Method in class net.sf.basedb.core.data.JobData
The type of job: 1 = run plugin, 2 = other
getType() - Method in class net.sf.basedb.core.DataCube
 
getType() - Method in class net.sf.basedb.core.DataCubeColumn
 
getType() - Method in class net.sf.basedb.core.DataCubeExtraValue
 
getType() - Method in class net.sf.basedb.core.DataCubeFilter
 
getType() - Method in class net.sf.basedb.core.DataCubeLayer
 
getType() - Method in class net.sf.basedb.core.DataFileType
 
getType() - Method in class net.sf.basedb.core.dbengine.TableInfo.ColumnInfo
 
getType() - Method in class net.sf.basedb.core.DerivedBioAssay
 
getType() - Method in class net.sf.basedb.core.Directory
 
getType() - Method in class net.sf.basedb.core.DiskUsage
 
getType() - Method in class net.sf.basedb.core.Experiment
 
getType() - Method in class net.sf.basedb.core.ExtendedProperty
Get the type of the extended property.
getType() - Method in class net.sf.basedb.core.Extract
 
getType() - Method in class net.sf.basedb.core.ExtraValue
 
getType() - Method in class net.sf.basedb.core.ExtraValueType
 
getType() - Method in class net.sf.basedb.core.FeatureBatcher
 
getType() - Method in class net.sf.basedb.core.File
 
getType() - Method in class net.sf.basedb.core.FileServer
 
getType() - Method in class net.sf.basedb.core.FileSet
 
getType() - Method in class net.sf.basedb.core.FileSetMember
 
getType() - Method in class net.sf.basedb.core.Formula
 
getType() - Method in class net.sf.basedb.core.GlobalDefaultSetting
 
getType() - Method in class net.sf.basedb.core.Group
 
getType() - Method in class net.sf.basedb.core.Hardware
 
getType() - Method in class net.sf.basedb.core.Help
 
getType() - Method in interface net.sf.basedb.core.Identifiable
Get the type of item represented by the object.
getType() - Method in class net.sf.basedb.core.ItemKey
 
getType() - Method in class net.sf.basedb.core.ItemList
 
getType() - Method in class net.sf.basedb.core.ItemProxy
 
getType() - Method in class net.sf.basedb.core.ItemSubtype
 
getType() - Method in class net.sf.basedb.core.ItemSubtypeFileType
 
getType() - Method in class net.sf.basedb.core.Job
 
getType() - Method in class net.sf.basedb.core.JobAgent
 
getType() - Method in class net.sf.basedb.core.JobAgentSettings
 
getType() - Method in class net.sf.basedb.core.Kit
 
getType() - Method in class net.sf.basedb.core.Message
 
getType() - Method in class net.sf.basedb.core.MimeType
 
getType() - Method in class net.sf.basedb.core.News
 
getType() - Method in class net.sf.basedb.core.Path
Get the type of the path.
getType() - Method in class net.sf.basedb.core.PermissionTemplate
 
getType() - Method in class net.sf.basedb.core.PhysicalBioAssay
 
getType() - Method in class net.sf.basedb.core.Plate
 
getType() - Method in class net.sf.basedb.core.PlateEvent
 
getType() - Method in class net.sf.basedb.core.PlateEventType
 
getType() - Method in class net.sf.basedb.core.PlateGeometry
 
getType() - Method in class net.sf.basedb.core.PlateMapping
 
getType() - Method in class net.sf.basedb.core.PlateType
 
getType() - Method in class net.sf.basedb.core.Platform
 
getType() - Method in class net.sf.basedb.core.PlatformFileType
 
getType() - Method in class net.sf.basedb.core.PlatformVariant
 
getType() - Method in class net.sf.basedb.core.plugin.GuiContext
 
getType() - Method in class net.sf.basedb.core.PluginConfiguration
 
getType() - Method in class net.sf.basedb.core.PluginDefinition
 
getType() - Method in class net.sf.basedb.core.PluginType
 
getType() - Method in class net.sf.basedb.core.Project
 
getType() - Method in class net.sf.basedb.core.ProjectKey
 
getType() - Method in class net.sf.basedb.core.Protocol
 
getType() - Method in class net.sf.basedb.core.Quantity
 
getType() - Method in class net.sf.basedb.core.query.QueryParameter
Get the type of the parameter.
getType() - Method in class net.sf.basedb.core.Quota
 
getType() - Method in class net.sf.basedb.core.QuotaType
 
getType() - Method in class net.sf.basedb.core.RawBioAssay
 
getType() - Method in class net.sf.basedb.core.RawDataBatcher
 
getType() - Method in class net.sf.basedb.core.ReporterBatcher
 
getType() - Method in class net.sf.basedb.core.ReporterCloneTemplate
 
getType() - Method in class net.sf.basedb.core.ReporterList
 
getType() - Method in class net.sf.basedb.core.ReporterType
Get the type of item represented by the object.
getType() - Method in class net.sf.basedb.core.Role
 
getType() - Method in class net.sf.basedb.core.RoleKey
 
getType() - Method in class net.sf.basedb.core.RootRawBioAssay
 
getType() - Method in class net.sf.basedb.core.Sample
 
getType() - Method in class net.sf.basedb.core.Session
 
getType() - Method in class net.sf.basedb.core.Software
 
getType() - Method in class net.sf.basedb.core.SyncFilter
 
getType() - Method in class net.sf.basedb.core.Tag
 
getType() - Method in class net.sf.basedb.core.Transformation
 
getType() - Method in class net.sf.basedb.core.Unit
 
getType() - Method in class net.sf.basedb.core.User
 
getType() - Method in class net.sf.basedb.core.UserClientSetting
 
getType() - Method in class net.sf.basedb.core.UserDefaultSetting
 
getType() - Method in class net.sf.basedb.core.UserDevice
 
getType() - Method in class net.sf.basedb.core.VirtualDb
 
getType() - Method in class net.sf.basedb.core.Well
 
getType() - Method in class net.sf.basedb.plugins.Base1PluginExecuter.JobParameter
 
getType() - Method in class net.sf.basedb.plugins.BaseFileExporterPlugin.ExtendedDynamicField
 
getType() - Method in class net.sf.basedb.plugins.executor.ParameterDefinition
Get the type of the parameter.
getType() - Method in class net.sf.basedb.util.export.spotdata.AnnotationAssayField
Return the value type of the annotation type, or null if not configured.
getType() - Method in class net.sf.basedb.util.export.spotdata.AssayPropertyField
 
getType() - Method in interface net.sf.basedb.util.export.spotdata.ExportableField
Get the data type of the field.
getType() - Method in class net.sf.basedb.util.export.spotdata.JepDynamicField
 
getType() - Method in class net.sf.basedb.util.export.spotdata.SimpleDynamicField
 
getType() - Method in class net.sf.basedb.util.extensions.xml.PluginInfo
Get the main type of the plug-in.
getTypeCode() - Method in class net.sf.basedb.clients.web.taglib.Page
 
getTypeFormatter(SessionControl, Type) - Static method in class net.sf.basedb.clients.web.formatter.FormatterFactory
Get a formattater that is encoding strings for HTML output.
getTypeFormatter(SessionControl, Type, boolean) - Static method in class net.sf.basedb.clients.web.formatter.FormatterFactory
Get a formatter suitable for displaying values of the given type.
getTypeHelper() - Method in class net.sf.basedb.core.hibernate.SessionWrapper
 
getTypes() - Method in class net.sf.basedb.core.log.EntityDetails
Get an array representing the data type for each property.
getTypeWrapper() - Method in enum class net.sf.basedb.core.Type
Get a wrapper for accessing underlying type information from Hibernate.
getTypeWrapper() - Method in class net.sf.basedb.core.VirtualColumn
Get a wrapper for accessing underlying type information from Hibernate.
getUniqueKeys() - Method in class net.sf.basedb.util.bfs.MetadataWriter
Checks if the current section requires entry names to be unique or not.
getUnit() - Method in class net.sf.basedb.clients.web.taglib.table.ColumnDef
 
getUnit() - Method in class net.sf.basedb.core.Annotation
Get the unit used for the values in this annotation.
getUnit() - Method in class net.sf.basedb.core.data.AnnotationData
Get the unit used for the annotation values.
getUnit() - Method in class net.sf.basedb.core.data.PropertyFilterData
 
getUnit() - Method in class net.sf.basedb.core.data.UnitSymbolData
Get the unit this symbol belongs to.
getUnit() - Method in class net.sf.basedb.core.snapshot.AnnotationLoaderUtil
Get the unit of the last annotation values that was found by AnnotationLoaderUtil.find(AnnotationSetSnapshot).
getUnit(String) - Method in class net.sf.basedb.core.Quantity
Get a a unit by symbol, also checking among the aliases.
getUnit(DbControl, String, String) - Static method in class net.sf.basedb.util.units.UnitUtil
Find the unit with a given symbol for a given quantity.
getUnit(Session, String) - Method in class net.sf.basedb.core.Quantity
Get the unit with a given symbol, or null if no unit is found.
getUnitConverter(Unit) - Method in class net.sf.basedb.core.Annotation
Get a converter for converting the values in this annotation to a specific unit.
getUnitConverter(Unit) - Method in class net.sf.basedb.core.Unit
Create a unit converter for converting from the reference unit (other) to this unit.
getUnitConverter(Unit, Unit) - Method in class net.sf.basedb.core.AnnotationBatcher
Get/create a unit converter for converting between two units.
getUnitFormatter(Formatter<T>, Unit) - Method in class net.sf.basedb.core.Annotation
Wrap a parent formatter with a formatter for units.
getUnitId() - Method in class net.sf.basedb.core.AnnotationBatcher.CurrentAnnotationInfo
Get the ID of the unit this annotation is using.
getUnits() - Method in class net.sf.basedb.core.data.QuantityData
This is the inverse end.
getUnits() - Method in class net.sf.basedb.core.Quantity
Get a query that returns all units of this quantity.
getUnitSymbol() - Method in class net.sf.basedb.core.snapshot.AnnotationLoaderUtil
Get the unit symbol of the last annotation values that was found by AnnotationLoaderUtil.find(AnnotationSetSnapshot).
getUnitSymbol(Unit) - Method in class net.sf.basedb.core.Annotation
Shortcut for Unit.getDisplaySymbol(), but also checks the default unit of the annotation type.
getUnknownLines() - Method in class net.sf.basedb.util.parser.FlatFileParser
Get the number of lines that the last call to FlatFileParser.nextData() or FlatFileParser.hasMoreData() ignored because they couldn't be interpreted as data lines.
getUnpackDirectory(DbControl) - Method in class net.sf.basedb.util.zip.AbstractFileUnpacker
Get the directory where the unpacked files are placed by the plugin.
getUnselectedtext() - Method in class net.sf.basedb.clients.web.taglib.Select
 
getUnverifiedDeviceInfo() - Method in class net.sf.basedb.core.SessionControl
Get information about a device that is currently waiting to be verified.
getUpdatePropertyOrder(Class<? extends BatchableData>) - Static method in class net.sf.basedb.core.BatchUtil
Get the order of properties in the update SQL.
getUpdatePropertyOrder(String) - Static method in class net.sf.basedb.core.BatchUtil
Get the order of properties in the update SQL.
getUpdateSql(Class<? extends BatchableData>) - Static method in class net.sf.basedb.core.BatchUtil
Get the SQL that updates a new row of the specified class.
getUpdateSql(String) - Static method in class net.sf.basedb.core.BatchUtil
Get the SQL that updates a new row of the specified class.
getUploadStream(boolean) - Method in class net.sf.basedb.core.File
Get an OutputStream that can be used to upload a physical file for this file item.
getUploadStream(boolean, Boolean) - Method in class net.sf.basedb.core.File
Get an OutputStream that can be used to upload a physical file for this file item.
getUpperLimit() - Method in class net.sf.basedb.core.DoubleParameterType
Get the highest valid value of the parameter.
getUpperLimit() - Method in class net.sf.basedb.core.FloatParameterType
Get the highest valid value of the parameter.
getUpperLimit() - Method in class net.sf.basedb.core.IntegerParameterType
Get the highest valid value of the parameter.
getUpperLimit() - Method in class net.sf.basedb.core.LongParameterType
Get the highest valid value of the parameter.
getURI() - Method in class net.sf.basedb.core.File
Get the URL of an external file as an URI.
getURI() - Method in class net.sf.basedb.util.extensions.manager.ExtensionsFile
Get an URI that points to the extensions file.
getURI() - Method in interface net.sf.basedb.util.uri.ConnectionManager
Get the URI of the resource we are interested in.
getURI() - Method in class net.sf.basedb.util.uri.http.HttpConnectionManager
 
getUrl() - Method in interface net.sf.basedb.clients.web.extensions.plot.PlotGenerator
Get the URL to a servlet that is used to generate the image.
getUrl() - Method in class net.sf.basedb.clients.web.extensions.plot.PlotGeneratorBean
 
getUrl() - Method in class net.sf.basedb.clients.web.extensions.startpage.FixedStartPageFactory
 
getUrl() - Method in interface net.sf.basedb.clients.web.extensions.startpage.StartPageAction
Get the URL to the start page.
getUrl() - Method in class net.sf.basedb.clients.web.extensions.startpage.StartPageBean
 
getUrl() - Method in class net.sf.basedb.core.authentication.ExtraUserInformation
An URL to the user homepage (or similar).
getUrl() - Method in class net.sf.basedb.core.data.FileData
Get the URL to the file.
getUrl() - Method in class net.sf.basedb.core.data.PluginDefinitionData
Get a URL with more information about the plugin.
getUrl() - Method in class net.sf.basedb.core.data.UserData
Get the URL to the user's homepage, or null if unknown.
getUrl() - Method in class net.sf.basedb.core.File
Get the URL to the (external) file.
getUrl() - Method in interface net.sf.basedb.core.plugin.About
An URL to get more information about the plugin.
getUrl() - Method in class net.sf.basedb.core.plugin.AboutImpl
 
getUrl() - Method in class net.sf.basedb.core.PluginDefinition
Get a URL with more information about the plugin.
getUrl() - Method in class net.sf.basedb.core.User
Get the URL to the user's homepage.
getUrl() - Method in class net.sf.basedb.util.extensions.AboutBean
 
getUrl() - Method in class net.sf.basedb.util.extensions.Registry.RegisteredAbout
 
getUrl(Object) - Method in class net.sf.basedb.core.ExtendedProperty
Create a link for this extended property.
getUrl(Object) - Method in class net.sf.basedb.core.ExtendedPropertyLinker
Create a link.
getURLToMap(Float, Float) - Static method in class net.sf.basedb.util.GeoLocation
Get an URL that opens a map marking the given position.
getUsableUnits() - Method in class net.sf.basedb.core.AnnotationType
Get a query for returning the units that are considered "usable" for this annotation type.
getUsableUnits() - Method in class net.sf.basedb.core.data.AnnotationTypeData
The units that it makes sense to use with this annotation type.
getUseDeviceVerification() - Method in class net.sf.basedb.core.data.UserData
A flag indicating if this user want to use device verification.
getUseDeviceVerification() - Method in class net.sf.basedb.core.User
A flag indicating if device verification has been enabled for this account.
getUsedMemory() - Method in class net.sf.basedb.core.JobAgent
Get the current memory usage in bytes of the server where the job agent is running.
getUsedMemory() - Method in class net.sf.basedb.util.jobagent.JobAgentInfo
Get the used memory on the job agent's server in bytes.
getUsedQuantity() - Method in class net.sf.basedb.core.BioMaterialEvent
Get the quantity that was used from the biomaterial by this event.
getUsedQuantity() - Method in class net.sf.basedb.core.BioMaterialEventSource
Get the quantity that was used from the source biomaterial by the event.
getUsedQuantity() - Method in class net.sf.basedb.core.data.BioMaterialEventData
Get the used quantity of the biomaterial affected by this event.
getUsedQuantity() - Method in class net.sf.basedb.core.data.BioMaterialEventSourceData
Get the used quantity from the parent biomaterial.
getUsedQuantity(MeasuredBioMaterial) - Method in class net.sf.basedb.core.BioMaterialEvent
Get the quantity that was used by this event for the specified biomaterial.
getUsedQuantity(FlatFileParser.Data, BioMaterialEventSource) - Method in class net.sf.basedb.plugins.batchimport.UsedQuantityMapper
Get the used quantity from the parent item.
getUsedSlot() - Method in class net.sf.basedb.core.InternalJobQueue.JobRunner
The slot the job is executing in.
getUsedUnits() - Method in class net.sf.basedb.core.data.UnitData
This is the inverse end.
getUsedWells() - Method in class net.sf.basedb.core.BioPlate
Get the number of used wells on this plate.
getUseInternalJobQueue() - Method in class net.sf.basedb.core.data.PluginDefinitionData
If the plug-in can be executed with the internal job queue or not.
getUseInternalJobQueue() - Method in class net.sf.basedb.core.PluginDefinition
If this plug-in can be executed by the internal job queue or not.
getUseNullIfException() - Method in class net.sf.basedb.util.parser.FlatFileParser
 
getUsePermissions() - Method in class net.sf.basedb.core.data.PluginDefinitionData
If the permissions for this plugin should be used or not.
getUsePermissions() - Method in class net.sf.basedb.core.PluginDefinition
Check if this plugin should execute with or without permissions.
getUser() - Method in class net.sf.basedb.core.BioMaterialEvent
Get the User that is responsible for this event.
getUser() - Method in class net.sf.basedb.core.data.BioMaterialEventData
Get the user that is responsible for this event, typically this is the user that entered the information in the database.
getUser() - Method in class net.sf.basedb.core.data.ChangeHistoryData
 
getUser() - Method in class net.sf.basedb.core.data.ContextData
Get the user that owns this context.
getUser() - Method in class net.sf.basedb.core.data.DiskUsageData
Get the user that owns the DiskConsumable item.
getUser() - Method in class net.sf.basedb.core.data.PasswordData
Get the user this password is referring to.
getUser() - Method in class net.sf.basedb.core.data.PlateEventData
Get the user that is responsible for this event, typically this is the user that entered the information in the database.
getUser() - Method in class net.sf.basedb.core.data.SessionData
Get the user that logged in with this session.
getUser() - Method in class net.sf.basedb.core.data.UserClientSettingData
Get the user this setting is valid for.
getUser() - Method in class net.sf.basedb.core.data.UserDefaultSettingData
Get the user this setting is valid for.
getUser() - Method in class net.sf.basedb.core.data.UserDeviceData
The user that this device is associated with.
getUser() - Method in class net.sf.basedb.core.DiskUsage
Get the user that owns the DiskConsumable item.
getUser() - Method in class net.sf.basedb.core.PlateEvent
Get the User that is responsible for this event.
getUser() - Method in class net.sf.basedb.core.Session
Get the user that logged in with this session.
getUser() - Method in class net.sf.basedb.core.UserClientSetting
Get the user this setting is valid for.
getUser() - Method in class net.sf.basedb.core.UserDefaultSetting
Get the user this setting is valid for.
getUser() - Method in class net.sf.basedb.core.UserDevice
Get the user that owns this device.
getUser(DbControl) - Method in class net.sf.basedb.core.ChangeHistory
Load the user that made the change.
getUser(DbControl) - Method in class net.sf.basedb.core.ChangeHistory.TransactionInfo
Load the user that made the change.
getUser(DbControl, ChangeHistory, boolean, boolean) - Static method in class net.sf.basedb.clients.web.ChangeHistoryUtil
Get the user that made the change in HTML format.
getUserAgent() - Method in class net.sf.basedb.core.data.UserDeviceData
Get a string with more information about the device (eg.
getUserAgent() - Method in class net.sf.basedb.core.UserDevice
Get the user agent string of this device.
getUserByExternalId(String) - Method in class net.sf.basedb.core.AuthenticationContext
Load a user item from the BASE database given an external id.
getUserById(int) - Method in class net.sf.basedb.core.AuthenticationContext
Load a user item from the BASE database given an internal id.
getUserByLogin(String) - Method in class net.sf.basedb.core.AuthenticationContext
Load a user item from the BASE database given a login name.
getUserClientSetting(String) - Method in class net.sf.basedb.core.SessionControl
Get the value of the UserClientSetting with the specified name.
getUserDefaultSetting(String) - Method in class net.sf.basedb.core.SessionControl
Get the value of the UserDefaultSetting with the specified name.
getUserEmail() - Method in class net.sf.basedb.core.SessionControl.UnverifiedDeviceInfo
Get the email to the user.
getUserFilesDirectory() - Static method in class net.sf.basedb.core.Application
Get the path to the directory where uploaded files are stored.
getUserId() - Method in class net.sf.basedb.core.authentication.LoginRequest
Get the user id to use.
getUserId() - Method in class net.sf.basedb.core.ChangeHistory
Get the ID of the user that made the change.
getUserId() - Method in class net.sf.basedb.core.ChangeHistory.TransactionInfo
Get the ID of the user that executed the transaction.
getUserId() - Method in class net.sf.basedb.core.data.ChangeHistoryData
The ID of the user that made the change.
getUserId() - Method in class net.sf.basedb.core.data.keyring.UserGroups
Get the id of the user.
getUserId() - Method in class net.sf.basedb.core.data.keyring.UserKeys
Get the id of the user.
getUserId() - Method in class net.sf.basedb.core.data.keyring.UserProjects
Get the id of the user.
getUserId() - Method in class net.sf.basedb.core.data.keyring.UserRoles
Get the id of the user.
getUserId() - Method in class net.sf.basedb.core.log.TransactionDetails
Get the ID of the currently logged in user, or 0 if no user is logged in.
getUserIds(Permission) - Method in class net.sf.basedb.core.ItemKey
Get the ID:s of all users that have the specified permission in this item key.
getUserLogin() - Method in class net.sf.basedb.core.Path
Get the userlogin part of the path.
getUsername() - Method in class net.sf.basedb.core.data.FileServerData
Get the username that is used to login to the server.
getUsername() - Method in class net.sf.basedb.core.FileServer
Get the username that is required to authenticate with the file server.
getUsername() - Method in class net.sf.basedb.util.uri.ConnectionParameters
Get the username that should be used to authenticate the user.
getUserName() - Method in class net.sf.basedb.core.log.TransactionDetails
Utility method for loading the name of the currently logged in user.
getUserName() - Method in class net.sf.basedb.core.SessionControl.UnverifiedDeviceInfo
Get the name of the user.
getUserPermissions() - Method in class net.sf.basedb.core.UserPermissions
Get the internal representation of the permissions.
getUsers() - Method in class net.sf.basedb.core.data.GroupData
Get the set that manages which users are members of this group.
getUsers() - Method in class net.sf.basedb.core.data.ItemKeyData
Get the map that manages which users that have permissions for this key.
getUsers() - Method in class net.sf.basedb.core.data.ProjectData
Get the map that manages which users are members of this project and their permissions.
getUsers() - Method in class net.sf.basedb.core.data.RoleData
Get the set that manages which users are members of this role.
getUsers() - Method in class net.sf.basedb.core.Group
Get a query that returns the users that are members of this group.
getUsers() - Method in class net.sf.basedb.core.InternalJobQueue.JobQueueKeyring
Return empty set.
getUsers() - Method in class net.sf.basedb.core.Job.SignalKeyring
Return empty set.
getUsers() - Method in class net.sf.basedb.core.Keyring
Get all users that share group membership with the logged in user.
getUsers() - Method in class net.sf.basedb.core.MultiPermissions
Get a query that returns all users appearing in at least one of the item keys.
getUsers() - Method in class net.sf.basedb.core.Project
Get a query that returns the users that are members of this project.
getUsers() - Method in class net.sf.basedb.core.Role
Get a query that returns the users that are members of this role.
getUsers() - Method in class net.sf.basedb.core.ServiceSessionControl.ServicesKeyring
Return empty set.
getUserSettings() - Method in class net.sf.basedb.core.data.ClientData
This is the inverse end.
getUsingItems() - Method in class net.sf.basedb.core.AnnotationSet
Get the item this annotation set belongs to.
getUsingItems() - Method in class net.sf.basedb.core.AnnotationType
Get all: Annotations of this type Experiments that are using this annotation type as an experimental factor Protocols that are using this annotation type as a protocol parameter
getUsingItems() - Method in class net.sf.basedb.core.ArrayBatch
Get all: ArraySlide:s in this batch
getUsingItems() - Method in class net.sf.basedb.core.ArrayDesign
Get all: ArrayBatch:s of this design RawBioAssay:s of this design
getUsingItems() - Method in class net.sf.basedb.core.ArrayDesignBlock
Get the array design this block is a part of.
getUsingItems() - Method in class net.sf.basedb.core.ArrayDesignPlate
Get the array design this plate is used on.
getUsingItems() - Method in class net.sf.basedb.core.ArraySlide
Get the bioassay that was used on this plate.
getUsingItems() - Method in class net.sf.basedb.core.BasicItem
Get all items that are using this item.
getUsingItems() - Method in class net.sf.basedb.core.BioPlate
Gets all MeasuredBioMaterial located on this plate and all child plates created from this plate.
getUsingItems() - Method in class net.sf.basedb.core.BioPlateEventType
Gets all BioPlates and BioPlateEventDefinitions using this type
getUsingItems() - Method in class net.sf.basedb.core.BioPlateType
Gets all BioPlates and BioPlateEventDefinitions using this type
getUsingItems() - Method in class net.sf.basedb.core.BioSource
Get all: Sample:s created from this biosource
getUsingItems() - Method in class net.sf.basedb.core.BioWell
Adds the MeasuredBioMaterial,used in this well, to the Set.
getUsingItems() - Method in class net.sf.basedb.core.DataFileType
Get all: FileSetMember:s using this file type Platform:s using this file type ItemSubtype:s using this file type
getUsingItems() - Method in class net.sf.basedb.core.DerivedBioAssay
Get all: Child derived bioassays Child raw bioassays
getUsingItems() - Method in class net.sf.basedb.core.Directory
Get all: File:s in this directory Sub-Directory:s in this directory User:s having this directory as their home-directory Experiment:s having this directory as the plugin directory
getUsingItems() - Method in class net.sf.basedb.core.DiskUsage
Get the item this disk usage information belongs to.
getUsingItems() - Method in class net.sf.basedb.core.Extract
Get all: Child extracts created from the extract PhysicalBioAssay:s created from this extract DerivedBioAssay:s referencing the extract RawBioAssay:s referencing the extract
getUsingItems() - Method in class net.sf.basedb.core.ExtraValueType
Get all: ExtraValue:s of this type
getUsingItems() - Method in class net.sf.basedb.core.File
Get all: FileAttachable items with this file attached
getUsingItems() - Method in class net.sf.basedb.core.FileServer
Get all files registered with this server.
getUsingItems() - Method in class net.sf.basedb.core.FileSet
Get the item this file set belongs to.
getUsingItems() - Method in class net.sf.basedb.core.Group
Get all: User:s assigned to this group as a quota group
getUsingItems() - Method in class net.sf.basedb.core.Hardware
Get all: DerivedBioAssay:s with this hardware ArrayBatch:s with this hardware BioMaterial:s and PhysicalBioAssay:s with this hardware Plate:s with this hardware
getUsingItems() - Method in class net.sf.basedb.core.ItemKey
Get all: Shareable items shared to this key
getUsingItems() - Method in class net.sf.basedb.core.ItemSubtype
Get all: Subtypable items of this subtype.
getUsingItems() - Method in class net.sf.basedb.core.Job
Get the transformation and raw bioassays using this job.
getUsingItems() - Method in class net.sf.basedb.core.Kit
Get all: BioMaterial:s and PhysicalBioAssay:s using this kit BioPlateEvent:s with this kit DerivedBioAssay: with this kit
getUsingItems() - Method in class net.sf.basedb.core.MeasuredBioMaterial
Get all: BioMaterial:s where this item has been used as a source
getUsingItems() - Method in class net.sf.basedb.core.PermissionTemplate
Get all: Project:s using this permission template
getUsingItems() - Method in class net.sf.basedb.core.PhysicalBioAssay
Get all: (root) DerivedBioAssay:s created from this physical bioassay
getUsingItems() - Method in class net.sf.basedb.core.Plate
Get all: Child plates ArrayDesign:s using this plate
getUsingItems() - Method in class net.sf.basedb.core.PlateEventType
Get all: PlateEvent:s of this type
getUsingItems() - Method in class net.sf.basedb.core.PlateGeometry
Get all: PlateType:s of this geometry PlateMapping:s using this geometry BioPlate:s using this geometry
getUsingItems() - Method in class net.sf.basedb.core.PlateMapping
Get all: Plate:s created with this mapping
getUsingItems() - Method in class net.sf.basedb.core.PlateType
Get all: Plate:s created from this plate type
getUsingItems() - Method in class net.sf.basedb.core.Platform
Get all: ArrayDesign:s and RawBioAssay:s using this platform
getUsingItems() - Method in class net.sf.basedb.core.PlatformVariant
Get all: ArrayDesign:s and RawBioAssay:s using this platform variant
getUsingItems() - Method in class net.sf.basedb.core.PluginConfiguration
Get all: Job:s using this configuration
getUsingItems() - Method in class net.sf.basedb.core.PluginDefinition
Get all: PluginConfiguration:s created from this plugin Job:s using this plugin
getUsingItems() - Method in class net.sf.basedb.core.ProjectKey
Get all: Shareable items shared to this key
getUsingItems() - Method in class net.sf.basedb.core.Protocol
Get all: a BioMaterial:s and PhysicalBioAssay:s using this protocol a Plate:s using this protocol an ArrayBatch:s using this protocol a DerivedBioAssay:s using this protocol a RawBioAssay:s using this protocol
getUsingItems() - Method in class net.sf.basedb.core.Quantity
Get all: Unit:s for this quantity AnnotationType:s using this quantity
getUsingItems() - Method in class net.sf.basedb.core.Quota
Get all: User:s assigned to this quota Group:s assigned to this quota
getUsingItems() - Method in class net.sf.basedb.core.RawBioAssay
Get all: Experiment:s using this raw bioassay Transformation:s using this raw bioassay
getUsingItems() - Method in class net.sf.basedb.core.ReporterCloneTemplate
Get all: Experiment that is using this template
getUsingItems() - Method in class net.sf.basedb.core.ReporterType
Get all: Reporter:s of this type
getUsingItems() - Method in class net.sf.basedb.core.Sample
Get all: Extract:s created from this sample Pooled samples
getUsingItems() - Method in class net.sf.basedb.core.Software
Get all: RawBioAssay:s created with this software DerivedBioAssay: created with this software
getUsingItems() - Method in class net.sf.basedb.core.Tag
Get all: Extract:s marked with this tag
getUsingItems() - Method in class net.sf.basedb.core.Unit
Get all: AnnotationType:s using this unit as default unit Annotation:s using this unit
getUsingItems() - Method in class net.sf.basedb.core.User
Get all: Ownable items owned by this user
getUsingItems() - Method in class net.sf.basedb.core.Well
Get all: Child wells Features derived from this well
getValidatedXml(String, URL) - Static method in class net.sf.basedb.util.XmlUtil2
 
getValidatedXml(URL, URL) - Static method in class net.sf.basedb.util.XmlUtil2
Load and validate an XML file against a DTD, and return it as a Document object.
getValidatedXML(InputStream, URL, String) - Static method in class net.sf.basedb.util.XmlUtil2
Validate an InputStream against a DTD file and return it as a Document
getValidationError() - Method in class net.sf.basedb.util.extensions.manager.ExtensionsFile
Get more information about the error that caused the validation to fail.
getValidationOptions() - Method in class net.sf.basedb.util.overview.GenericOverview
Get the validation options currently in use.
getValidationOptions() - Method in interface net.sf.basedb.util.overview.OverviewContext
Get the validation options that are currently in effect.
getValidationPresets(SessionControl) - Static method in class net.sf.basedb.util.overview.OverviewUtil
Get the validation options presets for the currently logged in user.
getValidationRule(InvokationContext<? super ValidationRuleAction>) - Method in class net.sf.basedb.util.overview.extensions.ReflectValidationRuleActionFactory
 
getValidator() - Method in class net.sf.basedb.util.overview.Failure
Get the validation rule that failed.
getValidators(DbControl) - Method in class net.sf.basedb.util.overview.validator.ExtensionNodeValidator
 
getValue() - Method in class net.sf.basedb.clients.web.extensions.DynamicActionAttribute
Get the value of the dynamic attribute.
getValue() - Method in class net.sf.basedb.clients.web.taglib.Input
 
getValue() - Method in class net.sf.basedb.clients.web.taglib.table.Cell
 
getValue() - Method in class net.sf.basedb.clients.web.taglib.table.CellValue
 
getValue() - Method in class net.sf.basedb.clients.web.taglib.table.Hidden
 
getValue() - Method in enum class net.sf.basedb.core.BioMaterialEvent.Type
Get the integer value that is used when storing a BioMaterialEvent.Type to the database.
getValue() - Method in enum class net.sf.basedb.core.BioWell.LockMode
Get the integer value that is used when storing a lock mode to the database.
getValue() - Method in class net.sf.basedb.core.data.PropertyFilterData
Get the value used in this filter.
getValue() - Method in class net.sf.basedb.core.data.SettingData
Get the value of this setting.
getValue() - Method in enum class net.sf.basedb.core.ExtraValue.CoordinateType
Get the integer value that is used when storing a CoordinateType in the database.
getValue() - Method in enum class net.sf.basedb.core.FeatureIdentificationMethod
Get the integer value that is used when storing the feature identification method to the database.
getValue() - Method in enum class net.sf.basedb.core.Formula.AverageMethod
Get the integer value that is used when storing a Formula.AverageMethod in the database.
getValue() - Method in enum class net.sf.basedb.core.Formula.Parser
Get the integer value that is used when storing a Formula.Parser in the database.
getValue() - Method in enum class net.sf.basedb.core.Formula.Type
Get the integer value that is used when storing a Formula.Type in the database.
getValue() - Method in enum class net.sf.basedb.core.Include
 
getValue() - Method in enum class net.sf.basedb.core.IntensityTransform
Get the integer value that is used when storing a transform in the database.
getValue() - Method in enum class net.sf.basedb.core.Item
Get the integer value that is used when storing an item to the database.
getValue() - Method in enum class net.sf.basedb.core.ItemContext.SortDirection
Get the integer value that is used when storing an location to the database.
getValue() - Method in enum class net.sf.basedb.core.Job.ExecutionTime
Get the integer value that is used when storing a Job.ExecutionTime in the database.
getValue() - Method in enum class net.sf.basedb.core.Job.Status
Get the integer value that is used when storing a Job.Status to the database.
getValue() - Method in enum class net.sf.basedb.core.Job.Type
Get the integer value that is used when storing a Job.Status to the database.
getValue() - Method in enum class net.sf.basedb.core.Location
Get the integer value that is used when storing an location to the database.
getValue() - Method in enum class net.sf.basedb.core.log.ChangeType
Get the numerical value for this change type.
getValue() - Method in enum class net.sf.basedb.core.Operator
Get the integer value that is used when storing an operator in the database.
getValue() - Method in enum class net.sf.basedb.core.plugin.GuiContext.Type
Get the integer value that is used when storing a GuiContext.Type to the database.
getValue() - Method in enum class net.sf.basedb.core.plugin.Plugin.MainType
 
getValue() - Method in class net.sf.basedb.core.PropertyFilter
Get the value to use in the filter.
getValue() - Method in class net.sf.basedb.core.query.QueryParameter
Get the value of the parameter.
getValue() - Method in class net.sf.basedb.core.query.WhenStatement
Get the value returned by this statement
getValue() - Method in class net.sf.basedb.core.Setting
Get the value of this setting.
getValue() - Method in enum class net.sf.basedb.core.Type
Get the integer value that is used when storing a type in the database.
getValue() - Method in class net.sf.basedb.util.bfs.MetadataModel.SectionEntry
Get the value of the entry.
getValue() - Method in class net.sf.basedb.util.Enumeration.Entry
 
getValue() - Method in class net.sf.basedb.util.excel.ExcelValue
Get the stored value.
getValue() - Method in class net.sf.basedb.util.fuzzy.StringMatcher.FuzzyMatch
Get the value string.
getValue(int) - Method in class net.sf.basedb.util.bfs.MetadataModel.Section
Get the value of the entry at the given index.
getValue(int) - Method in class net.sf.basedb.util.Enumeration
 
getValue(String) - Method in class net.sf.basedb.core.ParameterValuesImpl
 
getValue(String) - Method in class net.sf.basedb.core.plugin.NamespaceParameterValuesWrapper
 
getValue(String) - Method in interface net.sf.basedb.core.plugin.ParameterValues
Get a single value for a specific parameter.
getValue(String) - Method in class net.sf.basedb.core.plugin.ParameterValuesWrapper
Get the value of the parameter with the specified name.
getValue(String) - Method in class net.sf.basedb.plugins.gtf.DefaultConfigurationValues
 
getValue(String) - Method in class net.sf.basedb.util.bfs.MetadataModel.Section
Get the value of the first entry with a given key.
getValue(String) - Method in class net.sf.basedb.util.QueryParameters
Get the (single) value for a key.
getValue(String, String) - Method in class net.sf.basedb.util.bfs.MetadataModel
Utility method for getting the value of the first entry in the first section that matches the given section and key name.
getValue(Map<String, List<String>>, String) - Method in class net.sf.basedb.util.jobagent.JobAgentInfo
 
getValue(Map<String, List<String>>, String) - Method in class net.sf.basedb.util.jobagent.JobInfo
 
getValue(RelatedItemHelper, Annotatable, SourceItemTransformer) - Method in class net.sf.basedb.clients.web.extensions.list.RelatedItemAnnotationColumn
 
getValue(RelatedItemHelper, Annotatable, SourceItemTransformer) - Method in class net.sf.basedb.clients.web.extensions.list.RelatedItemColumn
Alternate implementation for loading data.
getValue(RelatedItemHelper, Annotatable, SourceItemTransformer) - Method in class net.sf.basedb.clients.web.extensions.list.RelatedItemErrorColumn
 
getValue(RelatedItemHelper, Annotatable, SourceItemTransformer) - Method in class net.sf.basedb.clients.web.extensions.list.RelatedItemExtensionColumn
 
getValue(RelatedItemHelper, Annotatable, SourceItemTransformer) - Method in class net.sf.basedb.clients.web.extensions.list.RelatedItemListColumn
 
getValue(RelatedItemHelper, Annotatable, SourceItemTransformer) - Method in class net.sf.basedb.clients.web.extensions.list.RelatedItemMultiHopColumn
 
getValue(RelatedItemHelper, Annotatable, SourceItemTransformer) - Method in class net.sf.basedb.clients.web.extensions.list.RelatedItemPropertyColumn
 
getValue(DbControl, C) - Method in class net.sf.basedb.core.Metadata.BasicData2ItemPropertyPath
 
getValue(DbControl, C) - Method in class net.sf.basedb.core.Metadata.BasicItem2DataPropertyPath
 
getValue(DbControl, C) - Method in class net.sf.basedb.core.Metadata.CombinedPropertyPath
 
getValue(DbControl, C) - Method in class net.sf.basedb.core.Metadata.ComponentPropertyPath
 
getValue(DbControl, C) - Method in class net.sf.basedb.core.Metadata.EntityPropertyPath
 
getValue(DbControl, C) - Method in class net.sf.basedb.core.Metadata.EvictPropertyPath
 
getValue(DbControl, C) - Method in class net.sf.basedb.core.Metadata.NoopPropertyPath
 
getValue(DbControl, C) - Method in interface net.sf.basedb.core.Metadata.PropertyPath
Get the value as defined by the implementation for the given item.
getValue(DbControl, I) - Method in interface net.sf.basedb.clients.web.extensions.list.ListColumnAction
Get the value that should be displayed in the column.
getValue(DbControl, I) - Method in class net.sf.basedb.clients.web.extensions.list.PropertyPathActionFactory.PropertyPathAction
 
getValue(DbControl, Collection<C>) - Method in class net.sf.basedb.core.Metadata.CollectionPropertyPath
 
getValue(DbControl, Date) - Method in class net.sf.basedb.core.Metadata.DateCopyPropertyPath
 
getValue(DbControl, Map) - Method in class net.sf.basedb.core.Metadata.MapPropertyPath
 
getValue(DbControl, Annotatable) - Method in class net.sf.basedb.clients.web.extensions.list.RelatedItemColumn
We finalize this implementation to make sure that the helper implementation always get a chance to re-cycle transactions.
getValue(DbControl, BasicItem) - Method in class net.sf.basedb.clients.web.extensions.list.AnyLinkColumn
 
getValue(DbControl, IdentifiableData) - Method in class net.sf.basedb.core.Metadata.IdentifierPropertyPath
 
getValue(DbControl, ReporterScore) - Method in class net.sf.basedb.core.Metadata.ReporterScore2DataPropertyPath
 
getValue(FlatFileParser.Data) - Method in class net.sf.basedb.util.parser.ColumnMapper
Deprecated.
getValue(FlatFileParser.Data) - Method in class net.sf.basedb.util.parser.CompoundMapper
Deprecated.
getValue(FlatFileParser.Data) - Method in class net.sf.basedb.util.parser.ConstantMapper
Deprecated.
getValue(FlatFileParser.Data) - Method in class net.sf.basedb.util.parser.CropStringMapper
Deprecated.
getValue(FlatFileParser.Data) - Method in class net.sf.basedb.util.parser.JepMapper
Deprecated.
getValue(FlatFileParser.Data) - Method in interface net.sf.basedb.util.parser.Mapper
Deprecated.
In 3.15, use Mapper.getString(FlatFileParser.Data) instead or one of the other getXxxx() methods to get a given data type directly
getValue(FlatFileParser.Data) - Method in class net.sf.basedb.util.parser.NullIfExceptionMapper
Deprecated.
getValue(FlatFileParser.Data, int) - Method in class net.sf.basedb.util.importer.spotdata.ExtraFloatParser
Get the extra value from the data.
getValue(T, T, T) - Method in class net.sf.basedb.util.Diff3
Get the correct value to set on the newItem object.
getValueAsObject() - Method in class net.sf.basedb.core.PropertyFilter
Get the value as an object of the correct type.
getValueAsObject() - Method in class net.sf.basedb.util.jep.FunctionSafeJep
Override the superclass method so that exceptions are passed on instead of swallowed.
getValueAsObject(String, Unit, boolean) - Method in class net.sf.basedb.core.PropertyFilter
 
getValueAsObject(Unit, boolean) - Method in class net.sf.basedb.core.PropertyFilter
Get the value as an object of the proper type converted to the specified unit.
getValueClass() - Method in enum class net.sf.basedb.core.Type
Get the class of objects that can be used as values for this type.
getValueCount() - Method in class net.sf.basedb.util.bfs.MetadataModel.SectionEntry
Get the number of values in the entry.
getValueCount() - Method in class net.sf.basedb.util.bfs.MetadataWriter
Get the number of values that has been written to the current section so far.
getValueId() - Method in class net.sf.basedb.core.data.annotations.AnnotationLink
 
getValueList2(Element, Class<T>) - Method in class net.sf.basedb.core.PluginConfiguration
Gets the list of values for a parameter from the XML-file.
getValues() - Method in class net.sf.basedb.core.Annotation
Get the values this annotation contains.
getValues() - Method in class net.sf.basedb.core.AnnotationType
Get the list of allowed values if this annotation type is an enumeration.
getValues() - Method in class net.sf.basedb.core.data.AnnotationData
The values of this annotation.
getValues() - Method in class net.sf.basedb.core.data.BooleanParameterValueData
 
getValues() - Method in class net.sf.basedb.core.data.DateParameterValueData
 
getValues() - Method in class net.sf.basedb.core.data.DoubleParameterValueData
 
getValues() - Method in class net.sf.basedb.core.data.FloatParameterValueData
 
getValues() - Method in class net.sf.basedb.core.data.IntegerParameterValueData
 
getValues() - Method in class net.sf.basedb.core.data.ItemParameterValueData
 
getValues() - Method in class net.sf.basedb.core.data.LongParameterValueData
 
getValues() - Method in class net.sf.basedb.core.data.ParameterValueData
Get values of this parameter.
getValues() - Method in class net.sf.basedb.core.data.StringParameterValueData
 
getValues() - Method in class net.sf.basedb.core.data.TextParameterValueData
 
getValues() - Method in class net.sf.basedb.core.data.TimestampParameterValueData
 
getValues() - Method in class net.sf.basedb.core.ExtraValue
Get a query returning the extra values.
getValues() - Method in class net.sf.basedb.core.ParameterInfo
 
getValues() - Method in class net.sf.basedb.core.snapshot.AnnotationLoaderUtil
Get the values from the last annotation found when calling AnnotationLoaderUtil.find(AnnotationSetSnapshot)
getValues() - Method in class net.sf.basedb.plugins.executor.ProgramParameter
Get the values for this parameter.
getValues() - Method in class net.sf.basedb.util.bfs.MetadataModel.SectionEntry
Get all values.
getValues() - Method in class net.sf.basedb.util.plot.PlotAnnotation
The values that falls into this annotation.
getValues(int) - Method in class net.sf.basedb.util.bfs.MetadataModel.Section
Get the values of the entry at the given index.
getValues(String) - Method in class net.sf.basedb.core.ParameterValuesImpl
 
getValues(String) - Method in class net.sf.basedb.core.plugin.NamespaceParameterValuesWrapper
 
getValues(String) - Method in interface net.sf.basedb.core.plugin.ParameterValues
Get a List of values for a specific parameter.
getValues(String) - Method in class net.sf.basedb.core.plugin.ParameterValuesWrapper
Get the values of the parameter with the specified name.
getValues(String) - Method in class net.sf.basedb.plugins.gtf.DefaultConfigurationValues
 
getValues(String) - Method in class net.sf.basedb.util.bfs.MetadataModel.Section
Get the values of the first entry with a given key.
getValues(String) - Method in class net.sf.basedb.util.QueryParameters
Get all values for a key.
getValues(String, String) - Method in class net.sf.basedb.util.bfs.MetadataModel
Utility method for getting the values of the first entry in the first section that matches the given section and key name.
getValues(Map<String, List<String>>, String) - Method in class net.sf.basedb.util.jobagent.JobAgentInfo
 
getValues(Unit) - Method in class net.sf.basedb.core.Annotation
Get the values for this annotation in a specific unit.
getValuesAsObjects() - Method in class net.sf.basedb.core.PropertyFilter
Splits the value string at each "|" and creates a list with objects from the substrings that were found.
getValuesAsObjects(String, Unit, boolean) - Method in class net.sf.basedb.core.PropertyFilter
 
getValuesAsObjects(Unit, boolean) - Method in class net.sf.basedb.core.PropertyFilter
Same as PropertyFilter.getValueAsObject(Unit, boolean) but the filter string is first split at each "|".
getValueSeparator() - Method in class net.sf.basedb.core.PropertyFilter
 
getValuesOrMask() - Method in class net.sf.basedb.core.ParameterInfo
Utility method for getting the values or a mask (*****) if the ParameterInfo.isMasked() flag is set.
getValuesOrMask(String) - Method in class net.sf.basedb.core.ParameterInfo
Utility method for getting the values or a mask if the ParameterInfo.isMasked() flag is set.
getValuesVersion() - Method in class net.sf.basedb.core.Annotation
Get the version number of the item keeping the values.
getValueType() - Method in class net.sf.basedb.clients.web.extensions.list.AbstractListColumnBean
 
getValueType() - Method in interface net.sf.basedb.clients.web.extensions.list.ListColumnAction
The data type of the values that are referenced by the property.
getValueType() - Method in class net.sf.basedb.clients.web.taglib.table.ColumnDef
 
getValueType() - Method in class net.sf.basedb.core.Annotation
Get the value type for this annotation type.
getValueType() - Method in class net.sf.basedb.core.AnnotationBatcher.CurrentAnnotationInfo
getValueType() - Method in class net.sf.basedb.core.AnnotationType
Get the value type for this annotation type.
getValueType() - Method in class net.sf.basedb.core.data.AnnotationTypeData
The code for the value type.
getValueType() - Method in class net.sf.basedb.core.data.BooleanParameterValueData
 
getValueType() - Method in class net.sf.basedb.core.data.DataCubeExtraValueData
The type of value, ie. int, float or string.
getValueType() - Method in class net.sf.basedb.core.data.DateParameterValueData
 
getValueType() - Method in class net.sf.basedb.core.data.DoubleParameterValueData
 
getValueType() - Method in class net.sf.basedb.core.data.ExtraValueTypeData
The code for the value type.
getValueType() - Method in class net.sf.basedb.core.data.FloatParameterValueData
 
getValueType() - Method in class net.sf.basedb.core.data.FormulaData
The code for the value type. null = not known or doesn't care.
getValueType() - Method in class net.sf.basedb.core.data.IntegerParameterValueData
 
getValueType() - Method in class net.sf.basedb.core.data.ItemParameterValueData
 
getValueType() - Method in class net.sf.basedb.core.data.LongParameterValueData
 
getValueType() - Method in class net.sf.basedb.core.data.ParameterValueData
Get the type of parameter values that are store in this parameter.
getValueType() - Method in class net.sf.basedb.core.data.PropertyFilterData
Get the type of value user for this filter.
getValueType() - Method in class net.sf.basedb.core.data.ReporterClonePropertyData
The code for the value type.
getValueType() - Method in class net.sf.basedb.core.data.StringParameterValueData
 
getValueType() - Method in class net.sf.basedb.core.data.TextParameterValueData
 
getValueType() - Method in class net.sf.basedb.core.data.TimestampParameterValueData
 
getValueType() - Method in class net.sf.basedb.core.DataCubeExtraValue
Get the value type of the extra values.
getValueType() - Method in class net.sf.basedb.core.ExtraValue
Get the type of values.
getValueType() - Method in class net.sf.basedb.core.ExtraValueType
Get the value type for this extra value type.
getValueType() - Method in class net.sf.basedb.core.Formula
Get the type of values that this formula produces.
getValueType() - Method in enum class net.sf.basedb.core.Formula.Type
Get the type of values that formulas of this type must produce or null if it can be any type of values.
getValueType() - Method in class net.sf.basedb.core.ParameterInfo
Get the matching Type for the values stored in this parameter.
getValueType() - Method in class net.sf.basedb.core.ParameterType
Get the date type of values that can be stored in this parameter.
getValueType() - Method in class net.sf.basedb.core.PropertyFilter
Get the type of the property.
getValueType() - Method in class net.sf.basedb.core.query.ParameterExpression
Get the type of value.
getValueType() - Method in class net.sf.basedb.plugins.batchimport.MultiPropertyIdMethod
 
getValueType() - Method in class net.sf.basedb.plugins.batchimport.PropertyIdMethod
 
getVariable(String) - Method in class net.sf.basedb.util.extensions.xml.VariableConverter
Get the value of a variable.
getVariant() - Method in class net.sf.basedb.core.ArrayDesign
 
getVariant() - Method in class net.sf.basedb.core.BioAssaySet
 
getVariant() - Method in class net.sf.basedb.core.data.ArrayDesignData
Get the platform variant this raw bioassay uses, or null.
getVariant() - Method in class net.sf.basedb.core.data.FileTypeIndex
 
getVariant() - Method in class net.sf.basedb.core.data.PlatformFileTypeData
Get the platform variant or null.
getVariant() - Method in class net.sf.basedb.core.data.RawBioAssayData
Get the platform variant this raw bioassay uses, or null.
getVariant() - Method in class net.sf.basedb.core.DerivedBioAssay
 
getVariant() - Method in class net.sf.basedb.core.ExtraValue
 
getVariant() - Method in interface net.sf.basedb.core.FileStoreEnabled
Get the platform variant the item is related to.
getVariant() - Method in class net.sf.basedb.core.PlatformFileType
Get the platform variant.
getVariant() - Method in class net.sf.basedb.core.RawBioAssay
 
getVariant(DbControl) - Method in class net.sf.basedb.core.RawDataType
Get the platform variant that this raw data type is associated with.
getVariantRawDataType(Session, String) - Static method in class net.sf.basedb.core.RawDataTypes
 
getVariants() - Method in class net.sf.basedb.core.data.PlatformData
The variants of this platform.
getVariants() - Method in class net.sf.basedb.core.Platform
Get a query that returns variants of this platform.
getVersion() - Method in class net.sf.basedb.core.BasicItem
 
getVersion() - Method in class net.sf.basedb.core.data.BasicData
Get the version of the item.
getVersion() - Method in interface net.sf.basedb.core.data.IdentifiableData
Get the version of this item.
getVersion() - Method in class net.sf.basedb.core.data.VersionedParameter
Get the parameter version.
getVersion() - Method in interface net.sf.basedb.core.Identifiable
Get the version number of the item.
getVersion() - Method in interface net.sf.basedb.core.plugin.About
The version of the plugin software.
getVersion() - Method in class net.sf.basedb.core.plugin.AboutImpl
 
getVersion() - Static method in class net.sf.basedb.core.Version
 
getVersion() - Method in class net.sf.basedb.util.extensions.AboutBean
 
getVersion() - Method in class net.sf.basedb.util.extensions.Registry.RegisteredAbout
 
getVersionParameter(String) - Static method in class net.sf.basedb.clients.web.taglib.Head
Get query parameter to the given absolute path (including root directory).
getVersionString() - Static method in class net.sf.basedb.core.Application
Get the BASE version string.
getVersionString() - Method in class net.sf.basedb.core.data.HardwareData
 
getVersionString() - Method in class net.sf.basedb.core.data.PluginDefinitionData
Get the version of the plugin.
getVersionString() - Method in class net.sf.basedb.core.data.SoftwareData
 
getVersionString() - Method in class net.sf.basedb.core.Hardware
Get the versionstring of this Hardware item.
getVersionString() - Method in class net.sf.basedb.core.PluginDefinition
Get the version of the plugin.
getVersionString() - Method in class net.sf.basedb.core.Software
Get the versionstring of this Software item.
getVersionSuffix() - Method in class net.sf.basedb.core.Application
Get the version suffix (eg.
getVirtualColumn() - Method in class net.sf.basedb.core.ExtraValue
Get the virtual column object that represents the column where the extra values are stored.
getVirtualDb() - Method in class net.sf.basedb.core.BioAssaySet
Get the virtual database this bioassayset stores it's data in.
getVirtualDb() - Method in interface net.sf.basedb.core.ClonableReporterQuery
Get the virtual database that the query is using.
getVirtualDb() - Method in class net.sf.basedb.core.data.DataCubeData
Get the virtual database this cube belongs to.
getVirtualDb() - Method in class net.sf.basedb.core.data.ExperimentData
Get the virtual database this experiment stores the analyzed data in.
getVirtualDb() - Method in class net.sf.basedb.core.DataCube
Get the virtual database this cube is a part of.
getVirtualDb() - Method in class net.sf.basedb.core.DataCubeColumn
Get the virtual database this column belongs to.
getVirtualDb() - Method in class net.sf.basedb.core.DataCubeExtraValue
Get the virtual database this extra value belongs to.
getVirtualDb() - Method in class net.sf.basedb.core.DataCubeFilter
Get the virtual database this filter belongs to.
getVirtualDb() - Method in class net.sf.basedb.core.DataCubeLayer
Get the virtual database this layer belongs to.
getVirtualDb() - Method in class net.sf.basedb.core.DynamicQuery
Get the virtual database that this query is using.
getVirtualDb() - Method in class net.sf.basedb.core.DynamicReporterQuery
Get the virtual database that this query is using.
getVirtualDb() - Method in class net.sf.basedb.core.Experiment
Get the virtual database ite that is used to manage experiment-specific tables in the dynamic database for this experiment.
getVirtualDb() - Method in class net.sf.basedb.core.ExtraValue
 
getVirtualTable() - Method in class net.sf.basedb.core.DataCubeExtraValue
Get the virtual table this extra value stores it's data in.
getVirtualTable() - Method in class net.sf.basedb.core.ExtraValue
 
getVirtualTable(Type) - Method in enum class net.sf.basedb.core.ExtraValue.CoordinateType
Get the VirtualTable used to store extra values of this coordinate type given the value type.
getVisibleColumns() - Method in class net.sf.basedb.clients.web.taglib.table.Table
 
getWaitingJobs() - Method in class net.sf.basedb.core.JobAgent
Get a query that returns all jobs that are waiting to be executed sorted by their priority taking the priority boost into account.
getWebAppClassLoader() - Method in class net.sf.basedb.clients.web.extensions.XJspCompiler
Get the class loader for the web application this JSP is located in.
getWell() - Method in class net.sf.basedb.core.data.FeatureData
Get the well of the feature.
getWell(int, int) - Method in class net.sf.basedb.core.Plate
Get the well on the specified plate coordinate.
getWell(DbControl, FeatureData) - Static method in class net.sf.basedb.core.Feature
Get the well from a feature.
getWells() - Method in class net.sf.basedb.core.data.PlateData
The wells on this plate.
getWells() - Method in class net.sf.basedb.core.Plate
Get a query returning all wells for this plate.
getWhichItemsParameter() - Method in class net.sf.basedb.clients.web.plugins.SimpleExport
 
getWhichPropertiesParameter() - Method in class net.sf.basedb.clients.web.plugins.SimpleExport
 
getWidth() - Method in interface net.sf.basedb.clients.web.extensions.plot.PlotGenerator
Get the width of the generated image.
getWidth() - Method in class net.sf.basedb.clients.web.extensions.plot.PlotGeneratorBean
 
getWidth() - Method in class net.sf.basedb.core.AnnotationType
Get the recommended width in characters a client application should use to render an input field for annotations of this annotation type.
getWidth() - Method in class net.sf.basedb.core.data.AnnotationTypeData
The recommended width (characters) to display input fields for this annotation in client applications.
getWidth() - Method in class net.sf.basedb.core.ParameterType
Get the width of the input field in the GUI.
getWorkbook() - Method in class net.sf.basedb.util.excel.XlsxTableWriter
Get the workbook.
getWorkbook() - Method in class net.sf.basedb.util.excel.XlsxToCsvUtil
Get the current workbook.
getWorkbookAsCsv() - Method in class net.sf.basedb.util.excel.XlsxToCsvUtil
Convert all sheets in the workbook to a single CSV-like stream.
getWorkingDirectory() - Method in class net.sf.basedb.plugins.executor.ExternalProgramExecutor
Get the current working directory were data files for the external program are stored.
getWriteableFile() - Method in class net.sf.basedb.util.extensions.manager.ExtensionsFile
Get a writeable view for the current file.
getWriteTrailingColumns() - Method in class net.sf.basedb.util.excel.XlsxToCsvUtil
If TRUE, trailing empty columns are written to the CSV file so that all lines have the same number of columns.
getX() - Method in class net.sf.basedb.core.data.RawData
 
getX() - Method in class net.sf.basedb.util.plot.HistogramPlot.TempSeries
 
getX(int, int) - Method in class net.sf.basedb.util.plot.HistogramPlot.HistogramDataset
 
getXml(String, URL, boolean) - Static method in class net.sf.basedb.util.XmlUtil2
Parse a string containing XML, optionally validating it against a DTD, and return it as a Document object.
getXmlLoader() - Method in class net.sf.basedb.util.extensions.manager.processor.PluginInstallationProcessor
Get the loader the processor is using for parsing xml files with plug-in definitions.
getXmlLoader() - Method in class net.sf.basedb.util.extensions.manager.processor.RegisterExtensionsProcessor
Get the loader the processor is using for parsing xml files with extension definitions.
getXmlStream() - Method in class net.sf.basedb.util.extensions.manager.ExtensionsFile
Get an input stream for reading the XML file containing the extension definitions.
getXValue(int, int) - Method in class net.sf.basedb.util.plot.HistogramPlot.HistogramDataset
 
getY() - Method in class net.sf.basedb.core.data.RawData
 
getY() - Method in class net.sf.basedb.util.plot.HistogramPlot.TempSeries
 
getY(int, int) - Method in class net.sf.basedb.util.plot.HistogramPlot.HistogramDataset
 
getYValue(int, int) - Method in class net.sf.basedb.util.plot.HistogramPlot.HistogramDataset
 
getZipFile(DbControl) - Method in class net.sf.basedb.util.zip.AbstractFileUnpacker
Get the file that is going to be unpacked by the plugin.
getZipFileParameter(String, String) - Method in class net.sf.basedb.util.zip.AbstractFileUnpacker
Get a plugin parameter that asks for the file that is going to be unpacked.
GlobalDefaultSetting - Class in net.sf.basedb.core
This class is used to represent a global default setting.
GlobalDefaultSetting(GlobalDefaultSettingData) - Constructor for class net.sf.basedb.core.GlobalDefaultSetting
 
GLOBALDEFAULTSETTING - Enum constant in enum class net.sf.basedb.core.Item
The item is an GlobalDefaultSetting.
GlobalDefaultSettingData - Class in net.sf.basedb.core.data
 
GlobalDefaultSettingData() - Constructor for class net.sf.basedb.core.data.GlobalDefaultSettingData
 
globalSignalId - Variable in class net.sf.basedb.core.signal.AbstractSignalTransporter
 
globalVersion - Static variable in class net.sf.basedb.clients.web.taglib.Head
 
grant(Set<Permission>) - Static method in enum class net.sf.basedb.core.Permission
Combine the given permission and convert to the integer grant value.
grant(Permission) - Static method in enum class net.sf.basedb.core.Permission
Convert the given permission to the integer grant value.
grant(Permission...) - Static method in enum class net.sf.basedb.core.Permission
Combine the given permissions and convert to the integer grant value.
granted - Variable in class net.sf.basedb.core.data.keyring.PluginKeys
 
granted - Variable in class net.sf.basedb.core.data.PluginPermission
 
granted - Variable in class net.sf.basedb.core.PluginPermission
 
grantValue - Variable in enum class net.sf.basedb.core.Permission
 
grantValue() - Method in enum class net.sf.basedb.core.Permission
 
GreaterConverter - Class in net.sf.basedb.util.jep.convert
Convert the '>' operator to a Query API Restriction.
GreaterConverter() - Constructor for class net.sf.basedb.util.jep.convert.GreaterConverter
 
GreaterEqualsConverter - Class in net.sf.basedb.util.jep.convert
Convert the '>=' operator to a Query API Restriction.
GreaterEqualsConverter() - Constructor for class net.sf.basedb.util.jep.convert.GreaterEqualsConverter
 
group - Variable in class net.sf.basedb.core.data.DiskUsageData
 
group(Expression) - Method in class net.sf.basedb.core.AbstractEntityQuery
Not supported.
group(Expression) - Method in class net.sf.basedb.core.AbstractQuery
 
group(Expression) - Method in interface net.sf.basedb.core.query.Query
Add an expression query element to the group list.
Group - Class in net.sf.basedb.core
This class is used to represent groups.
Group(GroupData) - Constructor for class net.sf.basedb.core.Group
 
GROUP - Enum constant in enum class net.sf.basedb.core.Item
The item is a Group.
Group.QueryRuntimeFilterImpl - Class in net.sf.basedb.core
A runtime filter implementation that limits a query to only return groups where the logged in user is a member unless the logged in user has generic read permission.
GROUPBY - Enum constant in enum class net.sf.basedb.core.query.QuerySection
 
GroupData - Class in net.sf.basedb.core.data
This class holds information about a group.
GroupData() - Constructor for class net.sf.basedb.core.data.GroupData
 
GroupGroups - Class in net.sf.basedb.core.data.keyring
Class for mapping the GroupGroups table.
GroupGroups() - Constructor for class net.sf.basedb.core.data.keyring.GroupGroups
Create a new GroupGroups object.
groupId - Variable in class net.sf.basedb.core.data.keyring.GroupKeys
 
groupId - Variable in class net.sf.basedb.core.data.keyring.GroupProjects
 
groupId - Variable in class net.sf.basedb.core.data.keyring.UserGroups
 
GroupKeys - Class in net.sf.basedb.core.data.keyring
Class for mapping the GroupKeys table.
GroupKeys() - Constructor for class net.sf.basedb.core.data.keyring.GroupKeys
Create a new GroupKeys object.
groupPermanent(Expression) - Method in class net.sf.basedb.core.AbstractEntityQuery
Not supported.
groupPermanent(Expression) - Method in class net.sf.basedb.core.AbstractQuery
 
groupPermanent(Expression) - Method in interface net.sf.basedb.core.query.Query
Permanently add an expression query element to the group list.
groupPermissions - Variable in class net.sf.basedb.core.GroupPermissions
 
groupPermissions - Variable in class net.sf.basedb.core.MultiPermissions
 
GroupPermissions - Class in net.sf.basedb.core
This class is used to specify permissions to share an item to groups.
GroupPermissions() - Constructor for class net.sf.basedb.core.GroupPermissions
Create a new empty object.
GroupPermissions(ItemKey) - Constructor for class net.sf.basedb.core.GroupPermissions
Create a new object, and initialise it with the permissions from a ItemKey.
GroupProjects - Class in net.sf.basedb.core.data.keyring
Class for mapping the GroupProjects table.
GroupProjects() - Constructor for class net.sf.basedb.core.data.keyring.GroupProjects
Create a new GroupProjects object.
groups - Variable in class net.sf.basedb.clients.web.ExperimentExplorer.AnnotationSummary
 
groups - Variable in class net.sf.basedb.core.AbstractQuery
List of group expressions added to the query.
groups - Variable in class net.sf.basedb.core.data.ItemKeyData
 
groups - Variable in class net.sf.basedb.core.data.ProjectData
 
groups - Variable in class net.sf.basedb.core.data.UserData
 
groups - Variable in class net.sf.basedb.core.Keyring
Holds the ID of all groups that the user is a member of, directly or indirectly.
groups - Variable in class net.sf.basedb.core.query.SharedToRestriction
 
groupsWithNonHiddenMembers - Variable in class net.sf.basedb.core.Keyring
A subset of the 'groups' set that holds the id of the groups that has hiddenMembers = false
gt(Expression, Expression) - Static method in class net.sf.basedb.core.query.Restrictions
Compare if one expression is greater than another: new restriction = e1 > e2.
GT - Enum constant in enum class net.sf.basedb.core.Operator
 
GT - Static variable in class net.sf.basedb.clients.web.util.HTML
 
gteq(Expression, Expression) - Static method in class net.sf.basedb.core.query.Restrictions
Compare if one expression is greater than or equal to another: new restriction = e1 >= e2.
GTEQ - Enum constant in enum class net.sf.basedb.core.Operator
 
GteqRestriction - Class in net.sf.basedb.core.query
Compare if one expression is greater than or equal to another: e1 > e2.
GteqRestriction(Expression, Expression) - Constructor for class net.sf.basedb.core.query.GteqRestriction
 
GtfInputStream - Class in net.sf.basedb.util.gtf
Input stream implementation that reads from a GTF file and converts it to a simple tab-separated file with a single line of column headers.
GtfInputStream(InputStream, String, boolean) - Constructor for class net.sf.basedb.util.gtf.GtfInputStream
Create a new input stream reading from the master.
GtfInputStream.Attribute - Class in net.sf.basedb.util.gtf
 
GtfReporterImporter - Class in net.sf.basedb.plugins.gtf
Reporter importer implementation that create reporters from information in GTF files.
GtfReporterImporter() - Constructor for class net.sf.basedb.plugins.gtf.GtfReporterImporter
 
GtfReporterMapImporter - Class in net.sf.basedb.plugins.gtf
Import features to an array design from a GTF file.
GtfReporterMapImporter() - Constructor for class net.sf.basedb.plugins.gtf.GtfReporterMapImporter
 
GtfValidationAction - Class in net.sf.basedb.util.gtf
Action for validation of GTF files in a file set.
GtfValidationAction(DbControl, ArrayDesign, int) - Constructor for class net.sf.basedb.util.gtf.GtfValidationAction
Create a new action.
GtfValidationFactory - Class in net.sf.basedb.util.gtf
Action factory for creating GTF file validators.
GtfValidationFactory() - Constructor for class net.sf.basedb.util.gtf.GtfValidationFactory
 
GtRestriction - Class in net.sf.basedb.core.query
Compare if one expression is greater than another: e1 > e2.
GtRestriction(Expression, Expression) - Constructor for class net.sf.basedb.core.query.GtRestriction
 
GUEST - Static variable in class net.sf.basedb.core.Role
The id for the Role item representing guests.
guiContext - Variable in class net.sf.basedb.clients.web.extensions.JspContext
 
GuiContext - Class in net.sf.basedb.core.plugin
 
GuiContext(Item, GuiContext.Type) - Constructor for class net.sf.basedb.core.plugin.GuiContext
 
GuiContext(Item, GuiContext.Type, String) - Constructor for class net.sf.basedb.core.plugin.GuiContext
 
GuiContext.Type - Enum Class in net.sf.basedb.core.plugin
 
GuiContextData - Class in net.sf.basedb.core.data
This is a helper component for the PluginDefinitionData item to store the contexts where a plugin can be used in a client application.
GuiContextData() - Constructor for class net.sf.basedb.core.data.GuiContextData
 
GuiContextData(int, int) - Constructor for class net.sf.basedb.core.data.GuiContextData
 
guiContexts - Static variable in class net.sf.basedb.clients.web.plugins.SimpleExport
 
guiContexts - Variable in class net.sf.basedb.core.data.PluginDefinitionData
 
guiContexts - Static variable in class net.sf.basedb.plugins.AnnotationFlatFileImporter
 
guiContexts - Static variable in class net.sf.basedb.plugins.BaseFileExporterPlugin
 
guiContexts - Static variable in class net.sf.basedb.plugins.batchimport.AnnotationTypeImporter
 
guiContexts - Static variable in class net.sf.basedb.plugins.batchimport.AnyToAnyImporter
 
guiContexts - Static variable in class net.sf.basedb.plugins.batchimport.ArrayBatchImporter
 
guiContexts - Static variable in class net.sf.basedb.plugins.batchimport.ArrayDesignImporter
 
guiContexts - Static variable in class net.sf.basedb.plugins.batchimport.ArraySlideImporter
 
guiContexts - Static variable in class net.sf.basedb.plugins.batchimport.BioPlateImporter
 
guiContexts - Static variable in class net.sf.basedb.plugins.batchimport.BioSourceImporter
 
guiContexts - Static variable in class net.sf.basedb.plugins.batchimport.DerivedBioAssayImporter
 
guiContexts - Static variable in class net.sf.basedb.plugins.batchimport.ExtractImporter
 
guiContexts - Static variable in class net.sf.basedb.plugins.batchimport.FileImporter
 
guiContexts - Static variable in class net.sf.basedb.plugins.batchimport.KitImporter
 
guiContexts - Static variable in class net.sf.basedb.plugins.batchimport.PhysicalBioAssayImporter
 
guiContexts - Static variable in class net.sf.basedb.plugins.batchimport.RawBioAssayImporter
 
guiContexts - Static variable in class net.sf.basedb.plugins.batchimport.SampleImporter
 
guiContexts - Static variable in class net.sf.basedb.plugins.batchimport.TagImporter
 
guiContexts - Static variable in class net.sf.basedb.plugins.BfsExporterPlugin
 
guiContexts - Static variable in class net.sf.basedb.plugins.CdfFileReporterImporter
 
guiContexts - Static variable in class net.sf.basedb.plugins.FormulaFilter
 
guiContexts - Static variable in class net.sf.basedb.plugins.GalExporter
 
guiContexts - Static variable in class net.sf.basedb.plugins.HelpExporter
 
guiContexts - Static variable in class net.sf.basedb.plugins.HelpImporter
 
guiContexts - Static variable in class net.sf.basedb.plugins.IlluminaRawDataImporter
 
guiContexts - Static variable in class net.sf.basedb.plugins.IntensityCalculatorPlugin
 
guiContexts - Static variable in class net.sf.basedb.plugins.JepExtraValueCalculator
 
guiContexts - Static variable in class net.sf.basedb.plugins.JepIntensityTransformer
 
guiContexts - Static variable in class net.sf.basedb.plugins.PackedFileExporter
 
guiContexts - Static variable in class net.sf.basedb.plugins.PlateFlatFileImporter
 
guiContexts - Static variable in class net.sf.basedb.plugins.PlateMappingExporter
 
guiContexts - Static variable in class net.sf.basedb.plugins.PlateMappingImporter
 
guiContexts - Static variable in class net.sf.basedb.plugins.PluginConfigurationExporter
 
guiContexts - Static variable in class net.sf.basedb.plugins.PluginConfigurationImporter
 
guiContexts - Static variable in class net.sf.basedb.plugins.PrintMapFlatFileImporter
 
guiContexts - Static variable in class net.sf.basedb.plugins.RawDataFlatFileImporter
 
guiContexts - Static variable in class net.sf.basedb.plugins.ReporterFlatFileImporter
 
guiContexts - Static variable in class net.sf.basedb.plugins.ReporterMapFlatFileImporter
 
guiContexts - Static variable in class net.sf.basedb.util.zip.AbstractFileUnpacker
The context is always [ FILE, ITEM].
guiTitle - Variable in class net.sf.basedb.plugins.BaseFileExporterPlugin.ExtendedDynamicField
 
guiTitle - Variable in class net.sf.basedb.plugins.BfsExporterPlugin.ExtendedExportableField
 
gzip - Variable in class net.sf.basedb.util.zip.GzipFilePacker
 
GzipFilePacker - Class in net.sf.basedb.util.zip
This class wraps the TarFilePacker in a GZIP stream, creating a tar.gz file.
GzipFilePacker() - Constructor for class net.sf.basedb.util.zip.GzipFilePacker
Create a new packer that compresses files with the gzip format.
GzipFileUnpacker - Class in net.sf.basedb.plugins
A plugin for unpacking a gzipped file to the BASE file system.
GzipFileUnpacker() - Constructor for class net.sf.basedb.plugins.GzipFileUnpacker
 

H

H_BOOLEAN - Static variable in class net.sf.basedb.core.hibernate.TypeWrapper
 
H_DATE - Static variable in class net.sf.basedb.core.hibernate.TypeWrapper
 
H_DOUBLE - Static variable in class net.sf.basedb.core.hibernate.TypeWrapper
 
H_FLOAT - Static variable in class net.sf.basedb.core.hibernate.TypeWrapper
 
H_INTEGER - Static variable in class net.sf.basedb.core.hibernate.TypeWrapper
 
H_LONG - Static variable in class net.sf.basedb.core.hibernate.TypeWrapper
 
H_SHORT - Static variable in class net.sf.basedb.core.hibernate.TypeWrapper
 
H_STRING - Static variable in class net.sf.basedb.core.hibernate.TypeWrapper
 
H_TEXT - Static variable in class net.sf.basedb.core.hibernate.TypeWrapper
 
H_TIMESTAMP - Static variable in class net.sf.basedb.core.hibernate.TypeWrapper
 
handleBof(EventHandler, String) - Method in class net.sf.basedb.util.bfs.MetadataParser
Handle the beginning-of-file marker event.
handleCmd(Socket, String) - Method in class net.sf.basedb.clients.jobagent.handlers.DefaultRequestHandler
 
handleCmd(Socket, String) - Method in class net.sf.basedb.clients.jobagent.handlers.InfoRequestHandler
 
handleCmd(Socket, String) - Method in class net.sf.basedb.clients.jobagent.handlers.MultiProtocolRequestHandler
 
handleCmd(Socket, String) - Method in class net.sf.basedb.clients.jobagent.handlers.PauseRequestHandler
 
handleCmd(Socket, String) - Method in class net.sf.basedb.clients.jobagent.handlers.PingRequestHandler
 
handleCmd(Socket, String) - Method in class net.sf.basedb.clients.jobagent.handlers.SignalRequestHandler
 
handleCmd(Socket, String) - Method in class net.sf.basedb.clients.jobagent.handlers.StartRequestHandler
 
handleCmd(Socket, String) - Method in class net.sf.basedb.clients.jobagent.handlers.StopRequestHandler
 
handleCmd(Socket, String) - Method in class net.sf.basedb.clients.jobagent.slotmanager.MasterSlotManager.RemoteSlotRequestHandler
 
handleCmd(Socket, String) - Method in interface net.sf.basedb.util.jobagent.RequestHandler
Handle a command that was sent by an incoming request.
handleData(EventHandler, String[]) - Method in class net.sf.basedb.util.bfs.AnnotationParser
Handle the data event.
handleData(EventHandler, String[]) - Method in class net.sf.basedb.util.bfs.DataParser
Handle the data event.
handleData(FlatFileParser.Data) - Method in class net.sf.basedb.plugins.AbstractFlatFileImporter
Called by the parser for every line in the file that is a data line.
handleData(FlatFileParser.Data) - Method in class net.sf.basedb.plugins.AnnotationFlatFileImporter
Read annotations from a single data line.
handleData(FlatFileParser.Data) - Method in class net.sf.basedb.plugins.batchimport.AbstractItemImporter
 
handleData(FlatFileParser.Data) - Method in class net.sf.basedb.plugins.batchimport.AnyToAnyImporter
 
handleData(FlatFileParser.Data) - Method in class net.sf.basedb.plugins.IlluminaRawDataImporter
 
handleData(FlatFileParser.Data) - Method in class net.sf.basedb.plugins.PlateFlatFileImporter
 
handleData(FlatFileParser.Data) - Method in class net.sf.basedb.plugins.PlateMappingImporter
Add a mapping detail.
handleData(FlatFileParser.Data) - Method in class net.sf.basedb.plugins.PrintMapFlatFileImporter
 
handleData(FlatFileParser.Data) - Method in class net.sf.basedb.plugins.RawDataFlatFileImporter
 
handleData(FlatFileParser.Data) - Method in class net.sf.basedb.plugins.ReporterFlatFileImporter
 
handleData(FlatFileParser.Data) - Method in class net.sf.basedb.plugins.ReporterMapFlatFileImporter
 
handleEndOfFile(EventHandler) - Method in class net.sf.basedb.util.bfs.AnnotationParser
Handle the end-of-file event.
handleEndOfFile(EventHandler) - Method in class net.sf.basedb.util.bfs.DataParser
Handle the end-of-file event.
handleEndOfFile(EventHandler) - Method in class net.sf.basedb.util.bfs.MetadataParser
Handle the end-of-file event.
handleEntry(EventHandler, MetadataModel.SectionEntry) - Method in class net.sf.basedb.util.bfs.MetadataParser
Handle the section entry event.
handleError(A, String, Throwable) - Method in class net.sf.basedb.util.extensions.ExtensionContext
 
handleError(String, Throwable) - Method in class net.sf.basedb.util.extensions.ExtensionContext
 
handleError(String, Throwable) - Method in class net.sf.basedb.util.extensions.ExtensionPointContext
 
handleError(Throwable) - Method in class net.sf.basedb.util.error.ClassMapErrorHandler
 
handleError(Throwable) - Method in interface net.sf.basedb.util.error.ErrorHandler
Handle an error.
handleError(Throwable) - Method in class net.sf.basedb.util.error.SimpleErrorHandler
Return TRUE if all errors should be ignored, otherwise re-throw the throwable.
handleError(InvokationContext<? extends A>, A, String, Throwable) - Method in interface net.sf.basedb.util.extensions.ErrorHandler
Handle an exception that has happened.
handleError(InvokationContext<? extends Action>, Action, String, Throwable) - Method in class net.sf.basedb.util.extensions.LoggingErrorHandlerFactory
 
handleError(InvokationContext<? extends Action>, Action, String, Throwable) - Method in class net.sf.basedb.util.extensions.RethrowErrorHandlerFactory
 
handleEvent(EventType<T>, T, BfsParser) - Method in class net.sf.basedb.util.bfs.AnnotationModel
 
handleEvent(EventType<T>, T, BfsParser) - Method in interface net.sf.basedb.util.bfs.EventHandler
The method is called by the parser when it has found something interesting in a BFS file.
handleEvent(EventType<T>, T, BfsParser) - Method in class net.sf.basedb.util.bfs.MatrixModel
 
handleEvent(EventType<T>, T, BfsParser) - Method in class net.sf.basedb.util.bfs.MultiEventHandler
Resends the incoming event to all registered event handlers.
handleEvent(EventType, Object, BfsParser) - Method in class net.sf.basedb.util.bfs.MetadataModel
 
handleEvent(EventType, Object, BfsParser) - Method in class net.sf.basedb.util.importer.spotdata.BfsImporter.ProgressEventHandler
 
handleEvent(EventType, Object, BfsParser) - Method in class net.sf.basedb.util.importer.spotdata.MatrixSpotIntensityEventHandler
Extract the spot intensity values from the data files and batch insert them using the spot batcher.
handleEvent(EventType, Object, BfsParser) - Method in class net.sf.basedb.util.importer.spotdata.PositionEventHandler
Get the position number from the given parser/column.
handleEvent(EventType, Object, BfsParser) - Method in class net.sf.basedb.util.importer.spotdata.SerialSpotIntensityEventHandler
Extract the spot intensity values from the data files and batch insert them using the spot batcher.
handleEvent(EventType) - Method in class net.sf.basedb.util.extensions.ActionIterator
Send the event to event handlers registered in the registry.
handleEvent(EventType, ExtensionPoint<?>, Extension<?>) - Method in class net.sf.basedb.clients.web.extensions.service.ServicesEventHandler
 
handleEvent(EventType, ExtensionPoint<?>, Extension<?>) - Method in interface net.sf.basedb.util.extensions.events.EventHandler
Handle an event.
handleEvent(EventType, ExtensionPoint<?>, Extension<?>) - Method in class net.sf.basedb.util.extensions.Registry
Send an event to all event handlers.
handleHeader(EventHandler, String[]) - Method in class net.sf.basedb.util.bfs.AnnotationParser
Handle the header-found event.
handleHeader(FlatFileParser.Line) - Method in class net.sf.basedb.plugins.AbstractFlatFileImporter
Called by the parser for every line in the file that is a header line.
handleHeader(FlatFileParser.Line) - Method in class net.sf.basedb.plugins.IlluminaRawDataImporter
Copy headers so that we can set them on the raw bioassays in beginData()
handleHeader(FlatFileParser.Line) - Method in class net.sf.basedb.plugins.PrintMapFlatFileImporter
 
handleHeader(FlatFileParser.Line) - Method in class net.sf.basedb.plugins.RawDataFlatFileImporter
 
handleInterrupt() - Method in class net.sf.basedb.core.signal.EnhancedThreadSignalHandler
Throws a SignalReceivedException if one ore more signals has been received.
handleInterrupt() - Method in class net.sf.basedb.core.signal.ExceptionInterruptHandler
 
handleInterrupt() - Method in interface net.sf.basedb.core.signal.InterruptHandler
This method is called when the worker thread has been interrupted by some other thread.
handler - Variable in class net.sf.basedb.clients.web.util.SimpleSignalProgressReporter
 
handler - Variable in class net.sf.basedb.util.extensions.Registry.RegisteredEventHandler
 
handlerIds - Variable in class net.sf.basedb.core.signal.AbstractSignalReceiver
 
handlers - Variable in class net.sf.basedb.clients.jobagent.handlers.MultiProtocolRequestHandler
 
handlers - Variable in class net.sf.basedb.core.signal.AbstractSignalReceiver
Maps local signal handler ID to -> signal handler itself.
handlers - Variable in class net.sf.basedb.core.signal.DelegatingSignalHandler
Holds the registered signal handlers.
handlers - Variable in class net.sf.basedb.util.bfs.MultiEventHandler
 
handleSection(EventHandler, String) - Method in class net.sf.basedb.util.bfs.MetadataParser
Handle the new section event.
handleSection(FlatFileParser.Line) - Method in class net.sf.basedb.plugins.AbstractFlatFileImporter
Called by the parser for every line in the file that is a section line.
handleSection(FlatFileParser.Line) - Method in class net.sf.basedb.plugins.PrintMapFlatFileImporter
 
handleSectionEnd(EventHandler, String) - Method in class net.sf.basedb.util.bfs.MetadataParser
Handle the end-of-section event.
handleSignal(Signal) - Method in class net.sf.basedb.core.signal.DelegatingSignalHandler
Handler the given signal by invoking SignalHandler.handleSignal(Signal) on each registered signal handler.
handleSignal(Signal) - Method in class net.sf.basedb.core.signal.EnhancedThreadSignalHandler
When a supported signal is received Thread.interrupt() is called on the worker thread that was registered when this object was created.
handleSignal(Signal) - Method in class net.sf.basedb.core.signal.ForwardingSignalHandler
Forwards the signal to the signal transporter given in the constructor.
handleSignal(Signal) - Method in class net.sf.basedb.core.signal.ProgressReporterSignalHandler
When signals are receieved, they are stored in a temporary list in the order they come in.
handleSignal(Signal) - Method in interface net.sf.basedb.core.signal.SignalHandler
Handle the given signal.
handleSignal(Signal) - Method in class net.sf.basedb.core.signal.ThreadSignalHandler
Only handles the Signal.ABORT signal.
hardware - Variable in class net.sf.basedb.core.data.BioMaterialEventData
 
hardware - Variable in class net.sf.basedb.core.data.BioPlateEventData
 
hardware - Variable in class net.sf.basedb.core.data.DerivedBioAssayData
 
hardware - Variable in class net.sf.basedb.core.data.PlateEventData
 
Hardware - Class in net.sf.basedb.core
This class is used to represent individual hardware items and information about them.
Hardware(HardwareData) - Constructor for class net.sf.basedb.core.Hardware
Creates a new hardware item.
HARDWARE - Enum constant in enum class net.sf.basedb.core.Item
The item is a Hardware.
hardwareColumnMapping - Static variable in class net.sf.basedb.plugins.batchimport.ArrayBatchImporter
 
hardwareColumnMapping - Static variable in class net.sf.basedb.plugins.batchimport.BioPlateImporter
 
hardwareColumnMapping - Static variable in class net.sf.basedb.plugins.batchimport.DerivedBioAssayImporter
 
hardwareColumnMapping - Static variable in class net.sf.basedb.plugins.batchimport.PhysicalBioAssayImporter
 
HardwareData - Class in net.sf.basedb.core.data
This class holds information about a Hardware.
HardwareData() - Constructor for class net.sf.basedb.core.data.HardwareData
 
hardwareHasBeenSet - Variable in class net.sf.basedb.core.BioMaterialEvent
 
hardwareHasBeenSet - Variable in class net.sf.basedb.core.DerivedBioAssay
 
HardwareLoader - Class in net.sf.basedb.util.overview.loader
Node loader implementation for hardware.
HardwareLoader() - Constructor for class net.sf.basedb.util.overview.loader.HardwareLoader
 
hardwareMapper - Variable in class net.sf.basedb.plugins.batchimport.ArrayBatchImporter
 
hardwareMapper - Variable in class net.sf.basedb.plugins.batchimport.BioPlateImporter
 
hardwareMapper - Variable in class net.sf.basedb.plugins.batchimport.DerivedBioAssayImporter
 
hardwareMapper - Variable in class net.sf.basedb.plugins.batchimport.PhysicalBioAssayImporter
 
hardwareQuery - Variable in class net.sf.basedb.plugins.batchimport.AbstractItemImporter
 
HardwareValidator - Class in net.sf.basedb.util.overview.validator
Validator implementation for hardware.
HardwareValidator() - Constructor for class net.sf.basedb.util.overview.validator.HardwareValidator
 
HAS_CANCELBUTTON - Static variable in class net.sf.basedb.clients.web.ModeInfo
 
HAS_CHECK - Static variable in class net.sf.basedb.clients.web.ModeInfo
 
HAS_CLOSEBUTTON - Static variable in class net.sf.basedb.clients.web.ModeInfo
 
HAS_EDITLINK - Static variable in class net.sf.basedb.clients.web.ModeInfo
 
HAS_FILTER - Static variable in class net.sf.basedb.clients.web.ModeInfo
 
HAS_ICONS - Static variable in class net.sf.basedb.clients.web.ModeInfo
 
HAS_NAVIGATOR - Static variable in class net.sf.basedb.clients.web.ModeInfo
 
HAS_OKBUTTON - Static variable in class net.sf.basedb.clients.web.ModeInfo
 
HAS_PROPERTYLINK - Static variable in class net.sf.basedb.clients.web.ModeInfo
 
HAS_RADIO - Static variable in class net.sf.basedb.clients.web.ModeInfo
 
HAS_TOOLBAR - Static variable in class net.sf.basedb.clients.web.ModeInfo
 
hasAborted - Variable in class net.sf.basedb.core.signal.ThreadSignalHandler
If TRUE, at least one ABORT signal has been recieved.
hasAborted() - Method in class net.sf.basedb.clients.web.fileupload.FileUploadProgress
Check if the upload has been requested to be aborted.
hasActiveValidator(DbControl) - Method in class net.sf.basedb.core.DataFileType
Check if there is at least one extension that claims to support validation of files of this type.
hasAllRequiredFiles() - Method in class net.sf.basedb.core.FileSet
Checks if this file set contains a file for each DataFileType that is required according to what has been specified by the Platform and PlatformVariant.
hasAnnotatableItem - Variable in class net.sf.basedb.core.MultiPermissions
 
hasAnnotatableItem() - Method in class net.sf.basedb.core.MultiPermissions
Is any of the items to share an annotatable item?
hasAnnotation(AnnotationType, Annotation.Source) - Method in class net.sf.basedb.core.AnnotationSet
Check if the annotation set contains an annotation of the specified type.
HasAnnotationRestriction - Class in net.sf.basedb.core
Restricts a query by the presence of absence of an annotation.
HasAnnotationRestriction(String, int, boolean, boolean, boolean) - Constructor for class net.sf.basedb.core.HasAnnotationRestriction
HasAnnotationRestriction(String, AnnotationType, boolean, boolean, boolean) - Constructor for class net.sf.basedb.core.HasAnnotationRestriction
HasAnnotationRestriction(String, AnnotationType, boolean, AnnotationRestriction.Options) - Constructor for class net.sf.basedb.core.HasAnnotationRestriction
Create a new restriction that checks if an item has been annotatated or not.
hasArrayDesign() - Method in class net.sf.basedb.core.RawBioAssay
Check if this raw bioassay is connected to an array design or not.
hasAttribute(NodeAttribute<?>) - Method in class net.sf.basedb.util.overview.Node
Check if the node has a value for the given attribute.
HasAttributeFilter - Class in net.sf.basedb.util.overview.filter
A filter implementation that checks if a value for a given attribute exists on a node.
HasAttributeFilter(NodeAttribute<?>) - Constructor for class net.sf.basedb.util.overview.filter.HasAttributeFilter
Create a filter that finds nodes that has value for the given attribute.
HasAttributeFilter(NodeAttribute<?>, Object) - Constructor for class net.sf.basedb.util.overview.filter.HasAttributeFilter
Create a filter that finds nodes that has a specific value for the given attribute.
hasAutoJoined - Variable in class net.sf.basedb.core.AbstractQuery
 
hasBeenAccepted - Variable in class net.sf.basedb.util.fileset.ValidatingFileSetMember
 
hasBeenAccepted() - Method in class net.sf.basedb.util.fileset.ValidatingFileSetMember
Has this member been accepted for validation by at least one validator?
hasBeenAnnotatated - Variable in class net.sf.basedb.core.HasAnnotationRestriction
 
hasBeenCalledFromAnnotationBatcher - Variable in class net.sf.basedb.core.BasicItem
 
hasBeenCalledFromGetAnnotationSet - Variable in class net.sf.basedb.core.BasicItem
 
hasBeenUsed - Variable in class net.sf.basedb.core.AnnotationBatcher.CurrentAnnotationInfo
 
hasBeenUsed() - Method in class net.sf.basedb.core.BioWell
If the original biomaterial in this well has been moved to another plate (eg. for final storage in a freezer).
hasBom - Variable in class net.sf.basedb.util.basefile.BaseFileWriter
 
hasCancelButton - Variable in class net.sf.basedb.clients.web.ModeInfo
 
hasCancelButton() - Method in class net.sf.basedb.clients.web.ModeInfo
 
hasCategoryOrSubtype(AnnotationTypeCategory, ItemSubtype) - Method in class net.sf.basedb.core.ItemContext
Checks if this context has a matching category or subtype.
hasChanged - Variable in class net.sf.basedb.util.extensions.manager.Settings
 
hasChanged() - Method in class net.sf.basedb.util.JarClassLoader.JarClassLoaderProxy
 
hasChanged(boolean) - Method in class net.sf.basedb.util.JarClassLoader
Check if the JAR file this class loader loads is classes from has changed since this class loader was created.
hasChanged(Group) - Method in class net.sf.basedb.core.GroupPermissions
Check if the current permissions for the group has been changed from the original permissions.
hasChanged(Project) - Method in class net.sf.basedb.core.ProjectPermissions
Check if the current permissions for the project has been changed from the original permissions.
hasChanged(User) - Method in class net.sf.basedb.core.UserPermissions
Check if the current permissions for the user has been changed from the original permissions.
hasCheck - Variable in class net.sf.basedb.clients.web.ModeInfo
 
hasCheck() - Method in class net.sf.basedb.clients.web.ModeInfo
 
hasClonableProperty(String) - Method in class net.sf.basedb.core.ReporterCloneTemplate
Check if this template contains a clonable property with the given name.
hasClonedReporterProperty(String) - Method in class net.sf.basedb.core.VirtualDb
Checks if this virtual db has cloned the given reporter property or not.
hasClonedReporters - Variable in class net.sf.basedb.core.DynamicQuery
 
hasClonedReporters - Variable in class net.sf.basedb.core.DynamicReporterQuery
 
hasClonedReporters() - Method in interface net.sf.basedb.core.ClonableReporterQuery
Check if the virtual database that this query is using has cloned reporter annotations or not.
hasClonedReporters() - Method in class net.sf.basedb.core.DynamicQuery
Check if the virtual database that this query is using has cloned reporter annotations or not.
hasClonedReporters() - Method in class net.sf.basedb.core.DynamicReporterQuery
Check if the virtual database that this query is using has cloned reporter annotations or not.
hasClonedReporters() - Method in class net.sf.basedb.core.VirtualDb
Check if this virtual db is storing cloned reporter information or not.
hasCloseButton - Variable in class net.sf.basedb.clients.web.ModeInfo
 
hasCloseButton() - Method in class net.sf.basedb.clients.web.ModeInfo
 
hasColumn(VirtualColumn) - Method in enum class net.sf.basedb.core.VirtualTable
Check if the specified column is part of the virtual table or not.
hasCompleted - Variable in class net.sf.basedb.util.uri.http.HttpConnectionManager.TimeoutTimer
 
hasContext() - Method in class net.sf.basedb.core.Job
Checks if this job has saved information about the context that was active when this job was created.
hasCreatedRenderer - Variable in class net.sf.basedb.util.extensions.ExtensionContext
 
hasCreatedRenderer - Variable in class net.sf.basedb.util.extensions.ExtensionPointContext
 
hasData - Variable in class net.sf.basedb.core.data.RawBioAssayData
 
hasData() - Method in class net.sf.basedb.core.RawBioAssay
If raw data has been added to this raw bioassay or not.
hasDataFile(DbControl, FileStoreEnabled, String, boolean) - Static method in class net.sf.basedb.core.FileStoreUtil
Check if a file of the given data file type is present in a FileStoreEnabled item's file set.
hasDataNo - Variable in class net.sf.basedb.util.parser.JepMapper
 
hasDatePart(String) - Method in class net.sf.basedb.util.excel.XlsxToCsvUtil
 
hasDefaultForItem(BasicItem) - Method in class net.sf.basedb.core.Project
Check if the project has a default item that has the same class and subtype as the given item.
hasDefaultOfType(Item, ItemSubtype) - Method in class net.sf.basedb.core.Project
Check if the project has a default item of the given item type and (optional) subtype.
hasDisabledRawJoin() - Method in class net.sf.basedb.core.DynamicSpotQuery
Check if joining to raw data has been disabled.
hasEditLink - Variable in class net.sf.basedb.clients.web.ModeInfo
 
hasEditLink() - Method in class net.sf.basedb.clients.web.ModeInfo
 
hasError - Variable in class net.sf.basedb.plugins.executor.ExternalProgramExecutor.ResponseWrapper
 
hasError - Variable in class net.sf.basedb.util.extensions.manager.ExtensionsFile
 
hasError - Variable in class net.sf.basedb.util.extensions.manager.ProcessResults.FileResults
 
hasError - Variable in class net.sf.basedb.util.extensions.manager.ProcessResults
 
hasError() - Method in class net.sf.basedb.plugins.executor.ExternalProgramExecutor.ResponseWrapper
 
hasError() - Method in class net.sf.basedb.util.extensions.manager.ExtensionsFile
If there was an error when registering the extensions in this file.
hasError() - Method in class net.sf.basedb.util.extensions.manager.ProcessResults.FileResults
If there was an error in this file or not.
hasError() - Method in class net.sf.basedb.util.extensions.manager.ProcessResults
Check if the scan was successful or not.
hasError() - Method in class net.sf.basedb.util.FileCopyRunnable
A boolean flag indicating if the copying was sucessful or not.
hasEvent(PlateEventType) - Method in class net.sf.basedb.core.Plate
Check if an event for the specified event type has been created for this plate.
hasExceededQuota(QuotaType, Location) - Method in class net.sf.basedb.core.User
Check if the user has used more quota than what has been assigned.
hasExtensionFilter(String) - Method in class net.sf.basedb.core.ItemContext
Checks if there is an extension filter with a property starting with !
hasExternalId(Item) - Method in class net.sf.basedb.plugins.AnnotationFlatFileImporter
Check if the current item has an 'externalId' property.
hasExternalId(Item) - Method in class net.sf.basedb.plugins.batchimport.AnyToAnyImporter
Check if the current item has an 'externalId' property.
hasExtraInformation() - Method in class net.sf.basedb.core.authentication.AuthenticatedUser
Check if extra information about the user has been provided.
hasFeatures - Variable in class net.sf.basedb.core.data.ArrayDesignData
 
hasFeatures() - Method in class net.sf.basedb.core.ArrayDesign
Check if this array design has information about features, either in the database or in files.
hasFeatures() - Method in class net.sf.basedb.core.ArrayDesignBlock
Checks if this ArrayDesignBlock has any features.
hasFileSet() - Method in class net.sf.basedb.core.ArrayDesign
 
hasFileSet() - Method in class net.sf.basedb.core.BioAssaySet
 
hasFileSet() - Method in class net.sf.basedb.core.DerivedBioAssay
 
hasFileSet() - Method in class net.sf.basedb.core.ExtraValue
 
hasFileSet() - Method in interface net.sf.basedb.core.FileStoreEnabled
Check if this item has a file set.
hasFileSet() - Method in class net.sf.basedb.core.RawBioAssay
 
hasFilter - Variable in class net.sf.basedb.clients.web.ModeInfo
 
hasFilter() - Method in class net.sf.basedb.clients.web.ModeInfo
 
HASH - Static variable in class net.sf.basedb.clients.web.util.HTML
 
hashCode - Variable in class net.sf.basedb.core.data.BasicData
Stores the hash code of the item.
hashCode - Variable in class net.sf.basedb.core.DynamicJoin
 
hashCode - Variable in class net.sf.basedb.core.query.AndRestriction
 
hashCode - Variable in class net.sf.basedb.core.query.CaseExpression
 
hashCode - Variable in class net.sf.basedb.core.query.InRestriction
 
hashCode - Variable in class net.sf.basedb.core.query.OrRestriction
 
hashCode() - Method in class net.sf.basedb.clients.web.extensions.ServletWrapperKey
 
hashCode() - Method in class net.sf.basedb.clients.web.ModeInfo.ModeContext
 
hashCode() - Method in class net.sf.basedb.clients.web.servlet.ExperimentExplorerPlotServlet.ColumnKey
 
hashCode() - Method in class net.sf.basedb.core.AnnotationBetweenRestriction
 
hashCode() - Method in class net.sf.basedb.core.AnnotationInRestriction
 
hashCode() - Method in class net.sf.basedb.core.AnnotationRestriction
 
hashCode() - Method in class net.sf.basedb.core.AnnotationSimpleRestriction
 
hashCode() - Method in class net.sf.basedb.core.BasicItem
The hash code is calculated at object construction and remains the same during the objects lifetime.
hashCode() - Method in class net.sf.basedb.core.BlockInfo
Calculate the hash code for the object.
hashCode() - Method in class net.sf.basedb.core.ClonableProperty
 
hashCode() - Method in class net.sf.basedb.core.ContextKey
Calculate the hash code for the object.
hashCode() - Method in class net.sf.basedb.core.data.BasicData
For new items (getId() returns 0) the hash code is the same as returned by the System.identityHashCode() method.
hashCode() - Method in class net.sf.basedb.core.data.ContextIndex
Calculate the hash code for the object.
hashCode() - Method in class net.sf.basedb.core.data.FileTypeIndex
Calculate the hash code for the object.
hashCode() - Method in class net.sf.basedb.core.data.GuiContextData
Calculate the hash code for the object.
hashCode() - Method in class net.sf.basedb.core.data.keyring.GroupGroups
Calculate the hash code for the object.
hashCode() - Method in class net.sf.basedb.core.data.keyring.GroupKeys
Calculate the hash code for the object.
hashCode() - Method in class net.sf.basedb.core.data.keyring.GroupProjects
Calculate the hash code for the object.
hashCode() - Method in class net.sf.basedb.core.data.keyring.PluginKeys
Calculate the hash code for the object.
hashCode() - Method in class net.sf.basedb.core.data.keyring.ProjectKeys
Calculate the hash code for the object.
hashCode() - Method in class net.sf.basedb.core.data.keyring.RoleKeys
Calculate the hash code for the object.
hashCode() - Method in class net.sf.basedb.core.data.keyring.UserGroups
Calculate the hash code for the object.
hashCode() - Method in class net.sf.basedb.core.data.keyring.UserKeys
Calculate the hash code for the object.
hashCode() - Method in class net.sf.basedb.core.data.keyring.UserProjects
Calculate the hash code for the object.
hashCode() - Method in class net.sf.basedb.core.data.keyring.UserRoles
Calculate the hash code for the object.
hashCode() - Method in class net.sf.basedb.core.data.MappingCoordinate
Calculate the hash code for the object.
hashCode() - Method in class net.sf.basedb.core.data.PlateCoordinate
Calculate the hash code for the object.
hashCode() - Method in class net.sf.basedb.core.data.QuotaIndex
Calculate the hash code for the object.
hashCode() - Method in class net.sf.basedb.core.data.ReporterListScoreData
 
hashCode() - Method in class net.sf.basedb.core.data.VersionedParameter
Calculate the hash code for the object.
hashCode() - Method in class net.sf.basedb.core.DynamicJoin
 
hashCode() - Method in class net.sf.basedb.core.DynamicRestriction
 
hashCode() - Method in class net.sf.basedb.core.ExtraValueExpression
 
hashCode() - Method in class net.sf.basedb.core.ExtraValueJoin
 
hashCode() - Method in class net.sf.basedb.core.FeatureCoordinate
Calculate the hash code for the object.
hashCode() - Method in class net.sf.basedb.core.HasAnnotationRestriction
 
hashCode() - Method in class net.sf.basedb.core.ItemProxy
The hash code is calculated from the Item.getValue() and the id.
hashCode() - Method in class net.sf.basedb.core.ItemResultList
 
hashCode() - Method in class net.sf.basedb.core.MeanRawDataPropertyExpression
 
hashCode() - Method in class net.sf.basedb.core.plugin.GuiContext
 
hashCode() - Method in class net.sf.basedb.core.query.AbsExpression
 
hashCode() - Method in class net.sf.basedb.core.query.AddExpression
 
hashCode() - Method in class net.sf.basedb.core.query.AndRestriction
 
hashCode() - Method in class net.sf.basedb.core.query.AnnotationJoin
 
hashCode() - Method in class net.sf.basedb.core.query.AnyToAnyRestriction
 
hashCode() - Method in class net.sf.basedb.core.query.AscOrder
 
hashCode() - Method in class net.sf.basedb.core.query.BetweenRestriction
 
hashCode() - Method in class net.sf.basedb.core.query.BooleanExpression
 
hashCode() - Method in class net.sf.basedb.core.query.CaseExpression
 
hashCode() - Method in class net.sf.basedb.core.query.ConditionalQueryElement
 
hashCode() - Method in class net.sf.basedb.core.query.CountExpression
 
hashCode() - Method in class net.sf.basedb.core.query.DescOrder
 
hashCode() - Method in class net.sf.basedb.core.query.DivideExpression
 
hashCode() - Method in class net.sf.basedb.core.query.EqRestriction
 
hashCode() - Method in class net.sf.basedb.core.query.ExpExpression
 
hashCode() - Method in class net.sf.basedb.core.query.ExpressionSelect
 
hashCode() - Method in class net.sf.basedb.core.query.FloatExpression
 
hashCode() - Method in class net.sf.basedb.core.query.GeometricMeanExpression
 
hashCode() - Method in class net.sf.basedb.core.query.GteqRestriction
 
hashCode() - Method in class net.sf.basedb.core.query.GtRestriction
 
hashCode() - Method in class net.sf.basedb.core.query.HqlElementsExpression
 
hashCode() - Method in class net.sf.basedb.core.query.HqlEntityExpression
 
hashCode() - Method in class net.sf.basedb.core.query.HqlEntityParameterExpression
 
hashCode() - Method in class net.sf.basedb.core.query.HqlExpression
 
hashCode() - Method in class net.sf.basedb.core.query.HqlIndexExpression
 
hashCode() - Method in class net.sf.basedb.core.query.HqlInnerJoin
 
hashCode() - Method in class net.sf.basedb.core.query.HqlLeftJoin
 
hashCode() - Method in class net.sf.basedb.core.query.HqlPropertyExpression
 
hashCode() - Method in class net.sf.basedb.core.query.HqlRightJoin
 
hashCode() - Method in class net.sf.basedb.core.query.HqlSizeExpression
 
hashCode() - Method in class net.sf.basedb.core.query.InRestriction
 
hashCode() - Method in class net.sf.basedb.core.query.IntegerExpression
 
hashCode() - Method in class net.sf.basedb.core.query.LikeRestriction
 
hashCode() - Method in class net.sf.basedb.core.query.LogExpression
 
hashCode() - Method in class net.sf.basedb.core.query.LteqRestriction
 
hashCode() - Method in class net.sf.basedb.core.query.LtRestriction
 
hashCode() - Method in class net.sf.basedb.core.query.MaxExpression
 
hashCode() - Method in class net.sf.basedb.core.query.MeanExpression
 
hashCode() - Method in class net.sf.basedb.core.query.MinExpression
 
hashCode() - Method in class net.sf.basedb.core.query.MultiplyExpression
 
hashCode() - Method in class net.sf.basedb.core.query.NegateExpression
 
hashCode() - Method in class net.sf.basedb.core.query.NeqRestriction
 
hashCode() - Method in class net.sf.basedb.core.query.NotRestriction
 
hashCode() - Method in class net.sf.basedb.core.query.OrRestriction
 
hashCode() - Method in class net.sf.basedb.core.query.ParameterExpression
 
hashCode() - Method in class net.sf.basedb.core.query.PowerExpression
 
hashCode() - Method in class net.sf.basedb.core.query.QuadraticMeanExpression
 
hashCode() - Method in class net.sf.basedb.core.query.QueryParameter
 
hashCode() - Method in class net.sf.basedb.core.query.ReporterListExpression
 
hashCode() - Method in class net.sf.basedb.core.query.RlikeRestriction
 
hashCode() - Method in class net.sf.basedb.core.query.SelectedExpression
 
hashCode() - Method in class net.sf.basedb.core.query.SharedToRestriction
 
hashCode() - Method in class net.sf.basedb.core.query.SqlColumnExpression
 
hashCode() - Method in class net.sf.basedb.core.query.SqrtExpression
 
hashCode() - Method in class net.sf.basedb.core.query.SubqueryExpression
 
hashCode() - Method in class net.sf.basedb.core.query.SubtractExpression
 
hashCode() - Method in class net.sf.basedb.core.query.SumExpression
 
hashCode() - Method in class net.sf.basedb.core.query.ToDateExpression
 
hashCode() - Method in class net.sf.basedb.core.query.VirtualColumnExpression
 
hashCode() - Method in class net.sf.basedb.core.query.WhenStatement
 
hashCode() - Method in class net.sf.basedb.core.RawBioAssayPropertyExpression
 
hashCode() - Method in class net.sf.basedb.core.RawDataPropertyExpression
 
hashCode() - Method in class net.sf.basedb.core.RawDataType
 
hashCode() - Method in class net.sf.basedb.core.RealJoin
 
hashCode() - Method in class net.sf.basedb.core.ReporterListJoin
 
hashCode() - Method in class net.sf.basedb.core.ReporterPropertyExpression
 
hashCode() - Method in class net.sf.basedb.core.SessionControl.MainContext
 
hashCode() - Method in class net.sf.basedb.core.signal.Signal
The hashcode for a signal is the same as the hashcode for the ID.
hashCode() - Method in class net.sf.basedb.core.VirtualColumn
 
hashCode() - Method in class net.sf.basedb.plugins.BaseFileExporterPlugin.ExtendedDynamicField
 
hashCode() - Method in class net.sf.basedb.util.AnnotationUtil.AnnotatableWrapper
 
hashCode() - Method in class net.sf.basedb.util.AnyToAnyLinkStatistics
 
hashCode() - Method in class net.sf.basedb.util.export.spotdata.AnnotationAssayField
 
hashCode() - Method in class net.sf.basedb.util.export.spotdata.AssayPropertyField
 
hashCode() - Method in class net.sf.basedb.util.export.spotdata.JepDynamicField
 
hashCode() - Method in class net.sf.basedb.util.export.spotdata.SimpleDynamicField
 
hashCode() - Method in class net.sf.basedb.util.extensions.manager.ExtensionKey
 
hashCode() - Method in class net.sf.basedb.util.extensions.manager.ExtensionPointKey
 
hashCode() - Method in class net.sf.basedb.util.extensions.manager.ExtensionsFile
 
hashCode() - Method in class net.sf.basedb.util.extensions.manager.FactoryParametersKey
 
hashCode() - Method in class net.sf.basedb.util.extensions.manager.PluginInfoKey
 
hashCode() - Method in class net.sf.basedb.util.extensions.Registry.AttributeKey
 
hashCode() - Method in class net.sf.basedb.util.gtf.GtfInputStream.Attribute
 
hashCode() - Method in class net.sf.basedb.util.jobagent.JobInfo
 
hashCode() - Method in class net.sf.basedb.util.listable.TransformCache.CacheKey
 
hashCode() - Method in class net.sf.basedb.util.overview.cache.DirectionalCacheKey
 
hashCode() - Method in class net.sf.basedb.util.overview.cache.IndexedCacheKey
 
hashCode() - Method in class net.sf.basedb.util.overview.Failure
 
hashCode() - Method in class net.sf.basedb.util.overview.validator.ExtractValidator.TagPosition
 
hashCode() - Method in class net.sf.basedb.util.Tree
 
hashCode() - Method in class net.sf.basedb.util.units.UnitCache.CacheKey
From the Object class ---------------------
hashCode(Object) - Static method in class net.sf.basedb.util.EqualsHelper
Get the hashcode for an object.
hashCode(T...) - Static method in class net.sf.basedb.util.EqualsHelper
Hashcode calculation for an array of objects that doesn't depend on the position in the array.
hasHiddenCharacters() - Method in class net.sf.basedb.clients.web.extensions.login.FieldInfo
If set, the input fields has hidden characters, otherwise they are visible.
hasHiddenMembers() - Method in class net.sf.basedb.core.Group
Does this group have hidden members?
hashpw(String, String) - Static method in class net.sf.basedb.util.bcrypt.BCrypt
Hash a password using the OpenBSD bcrypt scheme
hasIcons - Variable in class net.sf.basedb.clients.web.ModeInfo
 
hasIcons() - Method in class net.sf.basedb.clients.web.ModeInfo
 
hasImages - Variable in class net.sf.basedb.clients.web.taglib.table.Toolbar
If buttons should display images.
hasImages() - Method in class net.sf.basedb.clients.web.taglib.table.Toolbar
 
hasItemSubtype() - Method in class net.sf.basedb.core.ItemContext
Is this context limited to return items of a given subtype or not?
hasJoined - Variable in class net.sf.basedb.core.HqlQueryJoiners.AnnotationJoiner
 
hasLineNo - Variable in class net.sf.basedb.util.parser.JepMapper
 
hasLink - Variable in class net.sf.basedb.core.query.AnyToAnyRestriction
 
hasMember(DataFileType) - Method in class net.sf.basedb.core.FileSet
Check if the file set contains at least one file of the specified type.
hasMoreData() - Method in class net.sf.basedb.util.parser.FlatFileParser
Check if the input stream contains more data.
hasMoreSections() - Method in class net.sf.basedb.util.parser.FlatFileParser
Check if the input stream contains more sections.
hasNavigator - Variable in class net.sf.basedb.clients.web.ModeInfo
 
hasNavigator() - Method in class net.sf.basedb.clients.web.ModeInfo
 
hasNext - Variable in class net.sf.basedb.clients.web.taglib.table.ColumnDef.NullIterator
 
hasNext - Variable in class net.sf.basedb.core.DynamicResultIterator
 
hasNext - Variable in class net.sf.basedb.util.extensions.ActionIterator
 
hasNext() - Method in class net.sf.basedb.clients.web.servlet.PlotServlet.CFResultIterator
 
hasNext() - Method in class net.sf.basedb.clients.web.taglib.table.ColumnDef.NullIterator
 
hasNext() - Method in class net.sf.basedb.core.DataResultIterator
 
hasNext() - Method in class net.sf.basedb.core.DynamicResultIterator
 
hasNext() - Method in class net.sf.basedb.core.FastAnnotationLoader.FastIterator
 
hasNext() - Method in class net.sf.basedb.core.ItemResultIterator
 
hasNext() - Method in class net.sf.basedb.core.ItemResultList.ResultListIterator
 
hasNext() - Method in class net.sf.basedb.core.ItemResultList.ResultListListIterator
 
hasNext() - Method in class net.sf.basedb.core.ReporterScoreResultIterator
 
hasNext() - Method in class net.sf.basedb.core.ScrollIterator
 
hasNext() - Method in class net.sf.basedb.plugins.RawDataFlatFileImporter.FileIterator
 
hasNext() - Method in class net.sf.basedb.util.ArrayIterator
 
hasNext() - Method in class net.sf.basedb.util.extensions.ActionIterator
 
hasNext() - Method in class net.sf.basedb.util.NestedIterator
 
hasNext() - Method in class net.sf.basedb.util.query.MultiQueryIterator
 
hasNext() - Method in class net.sf.basedb.util.Tree.ElementIterator
 
hasNext() - Method in class net.sf.basedb.util.Tree.EntryIterator
 
hasOkButton - Variable in class net.sf.basedb.clients.web.ModeInfo
 
hasOkButton() - Method in class net.sf.basedb.clients.web.ModeInfo
 
hasOption(String) - Method in class net.sf.basedb.clients.jobagent.CmdLine
Check if an option was specified or not.
hasParameterValue(String) - Method in class net.sf.basedb.core.AbstractQuery
 
hasParameterValue(String) - Method in interface net.sf.basedb.core.query.Query
Check if a value for the specified parameter has been set or not.
hasPassword() - Method in class net.sf.basedb.core.FileServer
Is a password set or not?
hasPermission(int, Permission) - Static method in enum class net.sf.basedb.core.Permission
Checks if the given Permission is granted by the permissions code.
hasPermission(DbControl, Permission) - Method in class net.sf.basedb.core.snapshot.AnnotationSnapshot
Check if the logged in user has the request permission on this annotation or annotation set.
hasPermission(Permission) - Method in class net.sf.basedb.clients.web.extensions.ExtensionsControl
 
hasPermission(Permission) - Method in interface net.sf.basedb.core.AccessControlled
Check if the logged in user has the desired permission on the item.
hasPermission(Permission) - Method in class net.sf.basedb.core.BasicBatcher
Checks if the logged in user has the specified permission on this item.
hasPermission(Permission) - Method in class net.sf.basedb.core.BasicItem
Checks if the logged in user has the specified permission on this item.
hasPermission(Permission) - Method in class net.sf.basedb.core.BioMaterialEventSource
 
hasPermission(Permission) - Method in class net.sf.basedb.core.Coloring
 
hasPermission(Permission, Item) - Method in class net.sf.basedb.core.SessionControl
Check if the logged in user has the specfied permission for all item of the specified type.
hasPermission(SessionControl, Permission) - Method in class net.sf.basedb.clients.web.extensions.menu.PermissionMenuItemFactory
 
hasPermission(ClientContext, Item, Permission) - Method in class net.sf.basedb.clients.web.extensions.toolbar.PermissionButtonFactory
 
hasPrevious() - Method in class net.sf.basedb.core.ItemResultList.ResultListListIterator
 
hasPrintedHeaders - Variable in class net.sf.basedb.util.bfs.AnnotationWriter
 
hasPrintedHeaders() - Method in class net.sf.basedb.util.bfs.AnnotationWriter
Checks if headers has already been printed or not.
hasProjectAnnotation(AnnotationType, Annotation.Source, Project) - Method in class net.sf.basedb.core.AnnotationSet
Check if the annotation set contains an annotation of the specified type.
hasProjectSpecificAnnotation() - Method in class net.sf.basedb.clients.web.util.ProjectSpecificInfoFilter
Check if the project-specific flag is set.
hasPropertyFilter(String) - Method in class net.sf.basedb.core.ItemContext
Checks if there is a filter for the given property regardless of filter row.
hasPropertyLink - Variable in class net.sf.basedb.clients.web.ModeInfo
 
hasPropertyLink() - Method in class net.sf.basedb.clients.web.ModeInfo
 
hasRadio - Variable in class net.sf.basedb.clients.web.ModeInfo
 
hasRadio() - Method in class net.sf.basedb.clients.web.ModeInfo
 
hasReceived(Signal) - Method in class net.sf.basedb.core.signal.DelegatingSignalHandler
Check if the given signal has been received by this signal handler.
hasReceived(Signal) - Method in class net.sf.basedb.core.signal.EnhancedThreadSignalHandler
Check if the given signal has been received by this signal handler.
hasReceived(Signal) - Method in class net.sf.basedb.core.signal.ThreadSignalHandler
Check if the given signal has been received by this signal handler.
hasReceivedSignals() - Method in class net.sf.basedb.core.signal.DelegatingSignalHandler
Check if any signals has been received by this handler.
hasReceivedSignals() - Method in class net.sf.basedb.core.signal.EnhancedThreadSignalHandler
Check if any signals has been received by this handler.
hasReceivedSignals() - Method in class net.sf.basedb.core.signal.ProgressReporterSignalHandler
Check if any signals has been received by this handler.
hasRequiredAssayFields(BaseFileParser, FlatFileParser, List<String>) - Method in class net.sf.basedb.util.importer.spotdata.GenericIntensityParser
 
hasRequiredAssayFields(BaseFileParser, FlatFileParser, List<String>) - Method in class net.sf.basedb.util.importer.spotdata.MAParser
 
hasRequiredAssayFields(BaseFileParser, FlatFileParser, List<String>) - Method in interface net.sf.basedb.util.importer.spotdata.SpotIntensityParser
Check the list of assay fields to see if all columns that are required are present or not.
hasSignalTransporter() - Method in class net.sf.basedb.core.Job
Checks if a signal transporter has been registered for this job or not.
hasSingleParent() - Method in class net.sf.basedb.core.MeasuredBioMaterial
Checks if this biomaterial has a single parent item or not.
hasSshPrivateKey() - Method in class net.sf.basedb.core.FileServer
Check if a SSH private key has been set on this file server.
hasStickyHeaders() - Method in class net.sf.basedb.clients.web.taglib.table.Table
 
hasSubCategory() - Method in class net.sf.basedb.core.ItemContext
Is this context related to a given annotation type category or not?
hasSyncFilters() - Method in class net.sf.basedb.core.ItemList
Does this item list define any sync filters?
hasSystemPermission(Permission) - Method in class net.sf.basedb.core.SessionControl
Check if the logged in user has the specified system permission.
hasTable(VirtualTable) - Method in class net.sf.basedb.core.VirtualDb
Check if a real database table for this virtual database exists.
hasText - Variable in class net.sf.basedb.clients.web.taglib.table.Toolbar
If buttons should display text.
hasText() - Method in class net.sf.basedb.clients.web.taglib.table.Toolbar
 
hasTimedOut - Variable in class net.sf.basedb.util.uri.http.HttpConnectionManager.TimeoutTimer
 
hasTimedOut() - Method in class net.sf.basedb.util.uri.http.HttpConnectionManager.TimeoutTimer
 
hasTimePart(String) - Method in class net.sf.basedb.util.excel.XlsxToCsvUtil
 
hasToolbar - Variable in class net.sf.basedb.clients.web.ModeInfo
 
hasToolbar() - Method in class net.sf.basedb.clients.web.ModeInfo
 
hasUnit() - Method in class net.sf.basedb.core.Annotation
Checks if the values in this annotation has a unit.
hasValidFile() - Method in class net.sf.basedb.clients.web.extensions.ServletLoader
Checks if an XML file has passed validation in the ServletLoader.validateXmlFile(InputStream, String) method.
hasValidFile() - Method in class net.sf.basedb.util.extensions.xml.XmlLoader
Checks if an XML file has passed validation in the XmlLoader.validateXmlFile(InputStream, String) method.
having(Restriction) - Method in class net.sf.basedb.core.AbstractEntityQuery
Not supported.
having(Restriction) - Method in class net.sf.basedb.core.AbstractQuery
 
having(Restriction) - Method in interface net.sf.basedb.core.query.Query
Add a restriction query element to the having list.
HAVING - Enum constant in enum class net.sf.basedb.core.query.QuerySection
 
havingPermanent(Restriction) - Method in class net.sf.basedb.core.AbstractEntityQuery
Not supported.
havingPermanent(Restriction) - Method in class net.sf.basedb.core.AbstractQuery
 
havingPermanent(Restriction) - Method in interface net.sf.basedb.core.query.Query
Permanently add a restriction query element to the having list.
havings - Variable in class net.sf.basedb.core.AbstractQuery
List of having restrictions added to the query.
Head - Class in net.sf.basedb.clients.web.taglib
This tag defines the header section of a page.
Head() - Constructor for class net.sf.basedb.clients.web.taglib.Head
 
header - Variable in class net.sf.basedb.util.parser.FlatFileParser
The regular expression for matching a header line.
Header - Class in net.sf.basedb.clients.web.taglib.table
This tag defines a header column among the colummns or on a row.
Header() - Constructor for class net.sf.basedb.clients.web.taglib.table.Header
 
HEADER - Enum constant in enum class net.sf.basedb.util.parser.FlatFileParser.LineType
The parsed line is a header line, matching the regular expression specified by FlatFileParser.setHeaderRegexp(Pattern).
HEADER_EVENT - Static variable in class net.sf.basedb.util.bfs.AnnotationParser
Event type that is issued when the header line is found.
HEADER_REGEXP - Static variable in class net.sf.basedb.util.jobagent.JobAgentConnection
Regexp used to parse a typical answer.
headerLines - Variable in class net.sf.basedb.plugins.IlluminaRawDataImporter
 
headerPart - Variable in class net.sf.basedb.util.basefile.BaseFileWriter
 
headerRegexpParameter - Static variable in class net.sf.basedb.plugins.AbstractFlatFileImporter
Parameter definition that asks for the regular expression that splits a header line in key/value pair.
HeaderRow - Class in net.sf.basedb.clients.web.taglib.table
Container tag for a single header row in a table.
HeaderRow() - Constructor for class net.sf.basedb.clients.web.taglib.table.HeaderRow
 
headers - Variable in class net.sf.basedb.clients.web.taglib.table.Form
 
headers - Variable in class net.sf.basedb.core.data.RawBioAssayData
 
headers - Variable in class net.sf.basedb.util.bfs.AnnotationModel
 
headers - Variable in class net.sf.basedb.util.parser.FlatFileParser
Map of header lines parsed by the FlatFileParser.parseHeaders() method.
Headers - Class in net.sf.basedb.clients.web.taglib.table
Container tag for header rows in a table.
Headers() - Constructor for class net.sf.basedb.clients.web.taglib.table.Headers
 
height - Variable in class net.sf.basedb.clients.web.extensions.plot.MAPlotFactory
 
height - Variable in class net.sf.basedb.clients.web.extensions.plot.PlotGeneratorBean
 
height - Variable in class net.sf.basedb.core.data.AnnotationTypeData
 
height - Variable in class net.sf.basedb.core.ParameterType
Height of the input field for the parameter in the GUI.
help - Variable in class net.sf.basedb.clients.web.extensions.login.LoginFormBean
 
Help - Class in net.sf.basedb.clients.web.taglib
This tag is used to make it easier to add help features on a BASE web page.
Help - Class in net.sf.basedb.core
This class is used to represent a help text for a client application.
Help() - Constructor for class net.sf.basedb.clients.web.taglib.Help
 
Help(HelpData) - Constructor for class net.sf.basedb.core.Help
Creates a new help item
HELP - Enum constant in enum class net.sf.basedb.core.Item
The item is a Help.
HelpData - Class in net.sf.basedb.core.data
This class holds information about an help item.
HelpData() - Constructor for class net.sf.basedb.core.data.HelpData
 
helper - Variable in class net.sf.basedb.clients.web.extensions.list.RelatedItemColumn
 
helper - Variable in class net.sf.basedb.clients.web.extensions.list.RelatedItemHelper.CloseMyDbControl
 
HelpExporter - Class in net.sf.basedb.plugins
This plugin exports helptexts stored in the database to a XML-file.
HelpExporter() - Constructor for class net.sf.basedb.plugins.HelpExporter
 
helpid - Variable in class net.sf.basedb.clients.web.taglib.Help
The keyword of the helptopic
helpid - Variable in class net.sf.basedb.clients.web.taglib.tab.Tab
The help ID for this tab.
helpId - Variable in class net.sf.basedb.clients.web.extensions.tabcontrol.FixedTabFactory
 
helpId - Variable in class net.sf.basedb.clients.web.extensions.tabcontrol.IncludeContentTabFactory
 
helpId - Variable in class net.sf.basedb.clients.web.extensions.tabcontrol.TabBean
 
HelpImporter - Class in net.sf.basedb.plugins
This plugin imports helptexts into database from a XML-file.
HelpImporter() - Constructor for class net.sf.basedb.plugins.HelpImporter
 
helpList - Static variable in class net.sf.basedb.plugins.HelpExporter
 
helpList - Static variable in class net.sf.basedb.plugins.HelpImporter
 
helpTexts - Variable in class net.sf.basedb.core.data.ClientData
 
hibernateType - Variable in class net.sf.basedb.core.hibernate.TypeWrapper
 
hibernateType - Variable in class net.sf.basedb.core.Metadata.BasicData2ItemPropertyPath
 
hibernateType - Variable in class net.sf.basedb.core.Metadata.BasicItem2DataPropertyPath
 
hibernateType - Variable in class net.sf.basedb.core.Metadata.CollectionPropertyPath
 
hibernateType - Variable in class net.sf.basedb.core.Metadata.ComponentPropertyPath
 
hibernateType - Variable in class net.sf.basedb.core.Metadata.DateCopyPropertyPath
 
hibernateType - Variable in class net.sf.basedb.core.Metadata.EntityPropertyPath
 
hibernateType - Variable in class net.sf.basedb.core.Metadata.EvictPropertyPath
 
hibernateType - Variable in class net.sf.basedb.core.Metadata.IdentifierPropertyPath
 
hibernateType - Variable in class net.sf.basedb.core.Metadata.MapPropertyPath
 
hibernateType - Variable in class net.sf.basedb.core.Metadata.NoopPropertyPath
 
hibernateType - Variable in class net.sf.basedb.core.Metadata.ReporterScore2DataPropertyPath
 
HibernateUtil - Class in net.sf.basedb.core
This class collects most of the functionality we need for using Hibernate.
HibernateUtil() - Constructor for class net.sf.basedb.core.HibernateUtil
 
HibernateUtil.DelayedFilterDef - Class in net.sf.basedb.core
 
HibernateUtil.FilterConfigurator - Class in net.sf.basedb.core
Helper class for defining filters at runtime.
hidden - Variable in class net.sf.basedb.core.ExtendedProperty
 
hidden - Variable in class net.sf.basedb.core.PluginParameter
If the parameter should be hidden from user input or not.
Hidden - Class in net.sf.basedb.clients.web.taglib.table
This tag defines a hidden input element that should be included in the form.
Hidden() - Constructor for class net.sf.basedb.clients.web.taglib.table.Hidden
 
HIDDEN_STRING - Enum constant in enum class net.sf.basedb.plugins.Base1PluginExecuter.Base1JobParameterType
 
hiddenCharacters - Variable in class net.sf.basedb.clients.web.extensions.login.FieldInfo
 
hiddenFilteredColumns - Variable in class net.sf.basedb.clients.web.taglib.table.Table
 
hiddenForm - Variable in class net.sf.basedb.clients.web.taglib.table.Table
 
hiddenMembers - Variable in class net.sf.basedb.core.data.GroupData
 
HideableSection - Class in net.sf.basedb.clients.web.taglib
This tag is used to display a section on a web page that can be shown/hidden by the user by clicking on an icon on it's title.
HideableSection() - Constructor for class net.sf.basedb.clients.web.taglib.HideableSection
 
hideClass - Variable in class net.sf.basedb.clients.web.taglib.HideableSection
 
hideClazz - Variable in class net.sf.basedb.clients.web.extensions.section.IncludeContentSectionFactory
 
hideClazz - Variable in class net.sf.basedb.clients.web.extensions.section.SectionBean
 
high - Variable in class net.sf.basedb.core.query.BetweenRestriction
 
highExcludeParameter - Static variable in class net.sf.basedb.plugins.MedianRatioNormalization
 
highlight - Variable in class net.sf.basedb.clients.web.taglib.table.Row
Optional class attribute that is applied when the mouse is over the current row.
highValue - Variable in class net.sf.basedb.core.AnnotationBetweenRestriction
 
hilo - Variable in class net.sf.basedb.util.plot.HistogramPlot
 
HILOMAXMIN - Enum constant in enum class net.sf.basedb.util.plot.HistogramPlot.YAggregate
Plot a high/low bar for each bin with the maximum and minimum values.
HILOSTDEV - Enum constant in enum class net.sf.basedb.util.plot.HistogramPlot.YAggregate
Plot a high/low bar for each bin with the mean +/- 1 standard deviation.
histogram - Variable in class net.sf.basedb.util.plot.HistogramPlot
 
HistogramBin(float, float) - Constructor for class net.sf.basedb.util.plot.HistogramPlot.HistogramBin
Create a new HistogramBin.
HistogramDataset() - Constructor for class net.sf.basedb.util.plot.HistogramPlot.HistogramDataset
 
HistogramPlot - Class in net.sf.basedb.util.plot
A simple plot utility for generating histogram plots without the need to delve deep into the JFreePlot package.
HistogramPlot(String, String, XYItemRenderer) - Constructor for class net.sf.basedb.util.plot.HistogramPlot
Create a new HistogramPlot.
HistogramPlot.HistogramBin - Class in net.sf.basedb.util.plot
Represents a single bin in a histogram.
HistogramPlot.HistogramDataset - Class in net.sf.basedb.util.plot
An dataset implementation for histogram data that allows us to send data to JFreeChart the way we want.
HistogramPlot.HistogramSeries - Class in net.sf.basedb.util.plot
Collects information about one histogram series.
HistogramPlot.TempSeries - Class in net.sf.basedb.util.plot
Helper class for storing histogram data that needs to split into different annotations.
HistogramPlot.YAggregate - Enum Class in net.sf.basedb.util.plot
Defines what to to plot on the y axis in a histogram plot.
HistogramSeries(String, float[], float[], float, HistogramPlot.YAggregate, float, float) - Constructor for class net.sf.basedb.util.plot.HistogramPlot.HistogramSeries
Create a new HistogramSeries.
HistogramSeries(String, HistogramPlot.HistogramSeries, HistogramPlot.YAggregate) - Constructor for class net.sf.basedb.util.plot.HistogramPlot.HistogramSeries
Create a new HistogramSeries that is using data from another series.
history - Variable in class net.sf.basedb.core.data.ChangeHistoryDetailData
 
history - Variable in class net.sf.basedb.core.log.db.DbLogManager
 
HOLDER - Static variable in class net.sf.basedb.core.AbstractQuery
 
holders - Variable in class net.sf.basedb.plugins.IlluminaRawDataImporter
 
home - Variable in class net.sf.basedb.util.extensions.xml.PathConverter
 
HOME - Static variable in class net.sf.basedb.core.Directory
The id for the Directory item representing the home directory.
homeDirectory - Variable in class net.sf.basedb.core.data.UserData
 
host - Variable in class net.sf.basedb.clients.web.servlet.RssNewsFeed
 
host - Variable in class net.sf.basedb.core.data.FileServerData
 
host - Variable in class net.sf.basedb.util.uri.ConnectionParameters
 
hostName - Static variable in class net.sf.basedb.core.Application
The host name of the server running BASE.
hostName - Static variable in class net.sf.basedb.util.EmailUtil
 
hostPort - Static variable in class net.sf.basedb.util.EmailUtil
 
Hql - Class in net.sf.basedb.core.query
A factory class to create expressions, joins, etc. that are only used by HQL queries.
Hql() - Constructor for class net.sf.basedb.core.query.Hql
 
HQL - Enum constant in enum class net.sf.basedb.core.query.QueryType
The query is using Hibernate Query Language.
HqlElementsExpression - Class in net.sf.basedb.core.query
An expression representing the elements collection of a collection of a Hibernate entity: elements(alias.property).
HqlElementsExpression(String, String) - Constructor for class net.sf.basedb.core.query.HqlElementsExpression
 
HqlEntityExpression - Class in net.sf.basedb.core.query
An expression representing a Hibernate entity.
HqlEntityExpression(BasicItem) - Constructor for class net.sf.basedb.core.query.HqlEntityExpression
 
HqlEntityExpression(BasicData) - Constructor for class net.sf.basedb.core.query.HqlEntityExpression
 
HqlEntityParameterExpression - Class in net.sf.basedb.core.query
Entity parameter expression.
HqlEntityParameterExpression(String, Item) - Constructor for class net.sf.basedb.core.query.HqlEntityParameterExpression
 
HqlExpression - Class in net.sf.basedb.core.query
A class holding an expression or a restriction where a prefix can be used to represent a root alias in a HQL.
HqlExpression(String, String) - Constructor for class net.sf.basedb.core.query.HqlExpression
 
HqlIndexExpression - Class in net.sf.basedb.core.query
An expression representing the index collection of a map or list of a Hibernate entity: index(alias.property)
HqlIndexExpression(String, String) - Constructor for class net.sf.basedb.core.query.HqlIndexExpression
 
HqlInnerJoin - Class in net.sf.basedb.core.query
Inner joins an association to another item: JOIN <alias.property> <joinedAlias> to the query.
HqlInnerJoin(String, String, String, Restriction, boolean) - Constructor for class net.sf.basedb.core.query.HqlInnerJoin
 
HqlLeftJoin - Class in net.sf.basedb.core.query
Left joins an association to another item: LEFT JOIN <alias.property> <joinedAlias> to the query.
HqlLeftJoin(String, String, String, Restriction, boolean) - Constructor for class net.sf.basedb.core.query.HqlLeftJoin
 
hqlMode - Variable in class net.sf.basedb.core.query.ReporterListExpression
 
HqlPropertyExpression - Class in net.sf.basedb.core.query
An expression representing the property of a Hibernate entity: alias.property or alias.property[index]
HqlPropertyExpression(String, String, Expression) - Constructor for class net.sf.basedb.core.query.HqlPropertyExpression
 
HqlQuery - Interface in net.sf.basedb.core.query
This is a query that is using HQL (Hibernate Query Language) as the query language.
HqlQueryJoiners - Class in net.sf.basedb.core
This class collects AutoJoiner:s for HqlQuery queries.
HqlQueryJoiners() - Constructor for class net.sf.basedb.core.HqlQueryJoiners
 
HqlQueryJoiners.AnnotationJoiner - Class in net.sf.basedb.core
Joiner for annotations.
HqlQueryJoiners.ReporterListJoiner - Class in net.sf.basedb.core
Joiner for reporter lists.
HqlRightJoin - Class in net.sf.basedb.core.query
Right joins an association to another item: RIGHT JOIN <alias.property> <joinedAlias> to the query.
HqlRightJoin(String, String, String, Restriction) - Constructor for class net.sf.basedb.core.query.HqlRightJoin
 
HqlSizeExpression - Class in net.sf.basedb.core.query
An expression representing the size of the of a collection of a Hibernate entity: size(alias.property).
HqlSizeExpression(String, String) - Constructor for class net.sf.basedb.core.query.HqlSizeExpression
 
href - Variable in class net.sf.basedb.clients.web.taglib.Icon
If present, the icon is enclosed with an <a> tag that opens the given url in a new window.
href - Variable in class net.sf.basedb.clients.web.taglib.path.PathElement
URL to the linked page.
hSession - Variable in class net.sf.basedb.core.DbControl.State
 
hStatelessSession - Variable in class net.sf.basedb.core.DbControl.State
 
HTML - Class in net.sf.basedb.clients.web.util
This class contains a set of static methods that may be useful in a web application for handling text/HTML strings.
HTML() - Constructor for class net.sf.basedb.clients.web.util.HTML
 
hTransaction - Variable in class net.sf.basedb.core.DbControl.State
 
HTTP_DATE_FORMAT - Static variable in class net.sf.basedb.util.HttpUtil
 
HttpConnectionManager - Class in net.sf.basedb.util.uri.http
Connection manager implementation that support HTTP and HTTPS URI:s.
HttpConnectionManager(URI, ConnectionParameters) - Constructor for class net.sf.basedb.util.uri.http.HttpConnectionManager
 
HttpConnectionManager.TimeoutTimer - Class in net.sf.basedb.util.uri.http
 
HttpConnectionManagerActionFactory - Class in net.sf.basedb.util.uri.http
Action factory for http connection manager factory.
HttpConnectionManagerActionFactory() - Constructor for class net.sf.basedb.util.uri.http.HttpConnectionManagerActionFactory
 
HttpConnectionManagerFactory - Class in net.sf.basedb.util.uri.http
Connection manager factory for HTTP and HTTPS URI:s.
HttpConnectionManagerFactory() - Constructor for class net.sf.basedb.util.uri.http.HttpConnectionManagerFactory
Create a new http connection manager factory.
HttpUtil - Class in net.sf.basedb.util
Useful methods related to HTTP stuff in general and Apache HTTP components in particular.
HttpUtil() - Constructor for class net.sf.basedb.util.HttpUtil
 
hybQuery - Variable in class net.sf.basedb.plugins.batchimport.AbstractItemImporter
 
HYBRIDIZATION - Static variable in class net.sf.basedb.core.Kit
The ID for the hybridization kit type, for example a kit used when creating a PhysicalBioAssay from a set of (labeled) Extract:s.
HYBRIDIZATION - Static variable in class net.sf.basedb.core.PhysicalBioAssay
The id for the PhysicalBioAssayType item representing a hybridization.
HYBRIDIZATION - Static variable in class net.sf.basedb.core.Protocol
The ID for the hybridization protocol type, for example a protocol used when creating a PhysicalBioAssay from a set of (labeled) Extract:s.
HYBRIDIZATION_STATION - Static variable in class net.sf.basedb.core.Hardware
The id for the HardwareType object representing a hybridization station.

I

icon - Variable in class net.sf.basedb.clients.web.extensions.menu.FixedMenuItemFactory
 
icon - Variable in class net.sf.basedb.clients.web.extensions.menu.MenuItemBean
 
icon - Variable in class net.sf.basedb.clients.web.extensions.toolbar.ButtonBean
 
icon - Variable in class net.sf.basedb.clients.web.extensions.toolbar.FixedButtonFactory
 
icon - Variable in class net.sf.basedb.clients.web.taglib.menu.Menuitem
An icon to display.
icon - Variable in class net.sf.basedb.clients.web.taglib.menu.Submenu
An icon to display.
icon - Variable in enum class net.sf.basedb.util.extensions.logging.LogLevel
 
Icon - Class in net.sf.basedb.clients.web.taglib
This tag is used to make it easier to display icons on a BASE web page.
Icon() - Constructor for class net.sf.basedb.clients.web.taglib.Icon
 
id - Variable in class net.sf.basedb.clients.jobagent.slotmanager.Slot
 
id - Variable in class net.sf.basedb.clients.web.ExperimentExplorer.AnnotationGroup
 
id - Variable in class net.sf.basedb.clients.web.ExperimentExplorer.ReporterPositions
 
id - Variable in class net.sf.basedb.clients.web.extensions.list.AbstractListColumnBean
 
id - Variable in class net.sf.basedb.clients.web.extensions.list.PropertyPathActionFactory
 
id - Variable in class net.sf.basedb.clients.web.extensions.login.LoginFormBean
 
id - Variable in class net.sf.basedb.clients.web.extensions.menu.FixedMenuItemFactory
 
id - Variable in class net.sf.basedb.clients.web.extensions.menu.MenuItemBean
 
id - Variable in class net.sf.basedb.clients.web.extensions.menu.PermissionMenuItemFactory
 
id - Variable in class net.sf.basedb.clients.web.extensions.plot.OverviewPlotBean
 
id - Variable in class net.sf.basedb.clients.web.extensions.plot.PlotGeneratorBean
 
id - Variable in class net.sf.basedb.clients.web.extensions.section.IncludeContentSectionFactory
 
id - Variable in class net.sf.basedb.clients.web.extensions.section.SectionBean
 
id - Variable in class net.sf.basedb.clients.web.extensions.skin.FixedSkinActionFactory
 
id - Variable in class net.sf.basedb.clients.web.extensions.startpage.FixedStartPageFactory
 
id - Variable in class net.sf.basedb.clients.web.extensions.startpage.StartPageBean
 
id - Variable in class net.sf.basedb.clients.web.extensions.tabcontrol.FixedTabFactory
 
id - Variable in class net.sf.basedb.clients.web.extensions.tabcontrol.IncludeContentTabFactory
 
id - Variable in class net.sf.basedb.clients.web.extensions.tabcontrol.TabBean
 
id - Variable in class net.sf.basedb.clients.web.extensions.toolbar.ButtonBean
 
id - Variable in class net.sf.basedb.clients.web.extensions.toolbar.FixedButtonFactory
 
id - Variable in class net.sf.basedb.clients.web.extensions.toolbar.PermissionButtonFactory
 
id - Variable in class net.sf.basedb.clients.web.servlet.ExperimentExplorerPlotServlet.ColumnKey
 
id - Variable in class net.sf.basedb.clients.web.taglib.table.TableColumn
 
id - Variable in class net.sf.basedb.core.data.annotations.AnnotationLink
 
id - Variable in class net.sf.basedb.core.data.BasicData
 
id - Variable in class net.sf.basedb.core.ItemProxy
 
id - Variable in class net.sf.basedb.core.ParameterValuesImpl
The id of the job or configuration.
id - Variable in class net.sf.basedb.core.ProjectSpecificAnnotationsManager.AnnotationInfo
 
id - Variable in class net.sf.basedb.core.query.HqlEntityExpression
 
id - Variable in class net.sf.basedb.core.RawDataBatcher.FeatureProxy
 
id - Variable in class net.sf.basedb.core.RawDataBatcher.ReporterProxy
 
id - Variable in class net.sf.basedb.core.RawDataType
 
id - Variable in class net.sf.basedb.core.SessionControl.ClientInfo
 
id - Variable in class net.sf.basedb.core.SessionControl
The id of the object.
id - Variable in class net.sf.basedb.core.signal.Signal
 
id - Variable in class net.sf.basedb.plugins.BaseFileExporterPlugin.ExtendedDynamicField
 
id - Variable in class net.sf.basedb.plugins.BfsExporterPlugin.ExtendedExportableField
 
id - Variable in class net.sf.basedb.util.bfs.EventType
 
id - Variable in class net.sf.basedb.util.extensions.events.ExtensionEventFilter
 
id - Variable in class net.sf.basedb.util.extensions.events.ExtensionPointEventFilter
 
id - Variable in class net.sf.basedb.util.extensions.ExtensionBean
 
id - Variable in class net.sf.basedb.util.extensions.ExtensionPointBean
 
id - Variable in class net.sf.basedb.util.extensions.manager.ExtensionKey
 
id - Variable in class net.sf.basedb.util.extensions.manager.ExtensionPointKey
 
id - Variable in class net.sf.basedb.util.extensions.Registry.AttributeKey
 
id - Variable in class net.sf.basedb.util.extensions.Registry.RegisteredExtension
 
id - Variable in class net.sf.basedb.util.extensions.Registry.RegisteredExtensionPoint
 
id - Variable in class net.sf.basedb.util.extensions.SingleExtensionFilter
 
id - Variable in class net.sf.basedb.util.extensions.xml.PluginInfo
 
id - Variable in class net.sf.basedb.util.importer.spotdata.BaseFileImporter.RawDataProxy
 
id - Variable in class net.sf.basedb.util.importer.spotdata.BaseFileImporter.ReporterProxy
 
id - Variable in class net.sf.basedb.util.importer.spotdata.ExtraFloatParser
 
id - Variable in class net.sf.basedb.util.overview.Validator
 
id - Variable in class net.sf.basedb.util.uri.http.HttpConnectionManagerFactory
 
ID - Static variable in class net.sf.basedb.core.ClonableProperty
The property name of the "static" property BasicData.getId().
idAnnotationColumnMapping - Static variable in class net.sf.basedb.plugins.AnnotationFlatFileImporter
Column mapping parameter for the annotation column used for item identification.
idAnnotationColumnMapping - Static variable in class net.sf.basedb.plugins.batchimport.AbstractItemImporter
Column mapping parameter for the annotation column used for item identification.
idColumnMapping - Static variable in class net.sf.basedb.plugins.batchimport.AnyToAnyImporter
 
Identifiable - Interface in net.sf.basedb.core
An Identifiable item is an item which has an id a type and a version.
IdentifiableData - Interface in net.sf.basedb.core.data
An identifiable item is an item which has an id and a version.
IdentifiableFormatter - Class in net.sf.basedb.util.formatter
Formatter to handle Identifiable items.
IdentifiableFormatter() - Constructor for class net.sf.basedb.util.formatter.IdentifiableFormatter
Create a new formatter.
IdentifiableFormatter(String) - Constructor for class net.sf.basedb.util.formatter.IdentifiableFormatter
Create a new formatter.
identificationSection - Static variable in class net.sf.basedb.plugins.AnnotationFlatFileImporter
 
identificationSection - Static variable in class net.sf.basedb.plugins.batchimport.AbstractItemImporter
 
identificationSection - Static variable in class net.sf.basedb.plugins.batchimport.AnyToAnyImporter
 
IdentifierPropertyPath(Type) - Constructor for class net.sf.basedb.core.Metadata.IdentifierPropertyPath
 
IdentityConverter<T> - Class in net.sf.basedb.util.json
Simple "converter" implementation that simply return the same object.
IdentityConverter() - Constructor for class net.sf.basedb.util.json.IdentityConverter
 
IdentityEncoderDecoder - Class in net.sf.basedb.util.encode
Encoder decoder implementation that doesn't encode or decode anything.
IdentityEncoderDecoder() - Constructor for class net.sf.basedb.util.encode.IdentityEncoderDecoder
 
IdentityFilter<T> - Class in net.sf.basedb.util.filter
A filter implementation that only accepts an object if it is identical (==) to a given object.
IdentityFilter(T) - Constructor for class net.sf.basedb.util.filter.IdentityFilter
Create a new filter.
IdentityScaleFactor() - Constructor for class net.sf.basedb.util.InputStreamTracker.IdentityScaleFactor
 
IdentityUnitConverter - Class in net.sf.basedb.util.units
A unit "converter" that doesn't modify the values.
IdentityUnitConverter() - Constructor for class net.sf.basedb.util.units.IdentityUnitConverter
Create a new unit converter.
idExpression - Variable in class net.sf.basedb.core.query.IdListRestriction
 
idList - Variable in class net.sf.basedb.core.query.IdListRestriction
 
idList(DbControl) - Method in class net.sf.basedb.core.AbstractEntityQuery
 
idList(DbControl) - Method in interface net.sf.basedb.core.query.EntityQuery
Execute the query and return the ID values of all items matching the query.
IdListRestriction - Class in net.sf.basedb.core.query
Restriction that filters on a list of ID values: id IN (a, b, c, ....)
IdListRestriction() - Constructor for class net.sf.basedb.core.query.IdListRestriction
 
IdListRestriction(boolean) - Constructor for class net.sf.basedb.core.query.IdListRestriction
 
IdListRestriction(boolean, Set<Integer>) - Constructor for class net.sf.basedb.core.query.IdListRestriction
 
IdListRestriction(String, boolean, Collection<Integer>) - Constructor for class net.sf.basedb.core.query.IdListRestriction
 
IdListRestriction(String, Collection<Integer>) - Constructor for class net.sf.basedb.core.query.IdListRestriction
 
IdListRestriction(Set<Integer>) - Constructor for class net.sf.basedb.core.query.IdListRestriction
 
idMapper - Variable in class net.sf.basedb.plugins.batchimport.AbstractItemImporter
 
idMapper - Variable in class net.sf.basedb.plugins.batchimport.AnyToAnyImporter
 
idMapper - Variable in class net.sf.basedb.plugins.ReporterFlatFileImporter
 
idMapping - Variable in class net.sf.basedb.plugins.AnnotationFlatFileImporter
 
idMapping - Variable in class net.sf.basedb.plugins.batchimport.AbstractItemImporter
 
idMethod - Variable in class net.sf.basedb.plugins.AnnotationFlatFileImporter
 
idMethod - Variable in class net.sf.basedb.plugins.batchimport.AbstractItemImporter
 
idMethod - Variable in class net.sf.basedb.plugins.batchimport.AnyToAnyImporter
 
IdMethod - Interface in net.sf.basedb.plugins.batchimport
Represents an 'identification method', eg. a way to find an item among the items that already exists in the database.
idPropertyName - Variable in class net.sf.basedb.core.BasicBatcher
The name of the ID property.
IfConverter - Class in net.sf.basedb.util.jep.convert
Convert If function to a Query API Expression.
IfConverter() - Constructor for class net.sf.basedb.util.jep.convert.IfConverter
 
ifFalse - Variable in class net.sf.basedb.core.query.ConditionalQueryElement
 
ifFound - Variable in class net.sf.basedb.util.charset.SimpleStringDetector
 
ifTrue - Variable in class net.sf.basedb.core.query.ConditionalQueryElement
 
ignore - Variable in class net.sf.basedb.util.extensions.manager.ExtensionsManager
 
ignore - Variable in class net.sf.basedb.util.parser.FlatFileParser
The regular expression for matching a comment line.
IGNORE - Enum constant in enum class net.sf.basedb.util.overview.Severity
The rule is ignored.
ignoreActiveProject - Variable in class net.sf.basedb.core.Annotation
 
ignoreAllErrors - Variable in class net.sf.basedb.util.error.SimpleErrorHandler
 
ignored - Static variable in class net.sf.basedb.clients.web.PermissionUtil
All items which permissions depend on some other item only.
IGNORED - Enum constant in enum class net.sf.basedb.util.parser.FlatFileParser.LineType
The parsed line was ignored since it matched the regular expression specified by FlatFileParser.setIgnoreRegexp(Pattern).
ignoredFiles - Variable in class net.sf.basedb.util.extensions.manager.Settings
 
ignoredLines - Variable in class net.sf.basedb.util.parser.FlatFileParser
Number of ignored lines in the FlatFileParser.nextData() method.
ignoredSql - Variable in class net.sf.basedb.core.hibernate.SchemaGenerator
 
ignoreErrorFlag - Variable in class net.sf.basedb.clients.web.extensions.InstallFilter
 
ignoreFilename - Variable in class net.sf.basedb.util.FileExportOutputStream
 
IgnoreFileProcessor - Class in net.sf.basedb.util.extensions.manager.processor
Processor implementation for ignoring files.
IgnoreFileProcessor(ProcessResults) - Constructor for class net.sf.basedb.util.extensions.manager.processor.IgnoreFileProcessor
 
IgnoreFilter - Class in net.sf.basedb.clients.web.extensions
Filter implementation that selects only those extensions that was selected for ignoring by the user in the gui.
IgnoreFilter(HttpServletRequest) - Constructor for class net.sf.basedb.clients.web.extensions.IgnoreFilter
 
ignoreNonExistingColumns - Variable in class net.sf.basedb.util.parser.ColFunction
 
ignoreNonExistingColumns - Variable in class net.sf.basedb.util.parser.FlatFileParser
If non-existing columns should be ignored (true) or result in an exception (false)
ignoreNotFoundItems - Variable in class net.sf.basedb.plugins.AnnotationFlatFileImporter
 
ignoreRegexpParameter - Static variable in class net.sf.basedb.plugins.AbstractFlatFileImporter
Parameter definition that asks for the regular expression that matches a line that should be ignored.
ignoreSubtypeFilter - Variable in class net.sf.basedb.core.ItemContext
 
ignoreUseInternalJobQueueFlag - Variable in class net.sf.basedb.core.InternalJobQueue
If the PluginDefinitionData.getUseInternalJobQueue() setting should be ignored or not.
illumina - Variable in class net.sf.basedb.plugins.IlluminaRawDataImporter
 
IlluminaRawDataImporter - Class in net.sf.basedb.plugins
An importer plug-in for Illumina raw data.
IlluminaRawDataImporter() - Constructor for class net.sf.basedb.plugins.IlluminaRawDataImporter
 
IlluminaRawDataImporter.BatchAndMapHolder - Class in net.sf.basedb.plugins
Holds a RawBioAssay and the RawDataBatcher to use for import and the Mapper for all it's data columns.
image - Variable in class net.sf.basedb.clients.web.taglib.Button
The image to display.
image - Variable in class net.sf.basedb.clients.web.taglib.Help
The path to the help icon
image - Variable in class net.sf.basedb.clients.web.taglib.Icon
The filename of the image.
image - Variable in class net.sf.basedb.clients.web.taglib.table.Button
An optional image to show in the button.
image - Variable in class net.sf.basedb.clients.web.taglib.table.Label
An optional image to show in the button.
image - Variable in class net.sf.basedb.clients.web.taglib.Zoom
The path to the help icon
image - Variable in class net.sf.basedb.core.data.PlateMappingData
 
IMAGE - Static variable in class net.sf.basedb.core.File
The id for the FileType item representing an image file.
IMAGE_EXTENSION - Static variable in class net.sf.basedb.clients.web.util.HTML
 
ImageRemapFilter - Class in net.sf.basedb.clients.web.servlet
This is a filter that remaps request to images to some other image.
ImageRemapFilter() - Constructor for class net.sf.basedb.clients.web.servlet.ImageRemapFilter
 
ImageRemapper - Class in net.sf.basedb.clients.web.extensions.skin
Remaps image URLs.
ImageRemapper() - Constructor for class net.sf.basedb.clients.web.extensions.skin.ImageRemapper
Creates a new image remapper.
ImageRemapperUtil - Class in net.sf.basedb.clients.web.extensions.skin
Utility class for working with image remapping.
ImageRemapperUtil() - Constructor for class net.sf.basedb.clients.web.extensions.skin.ImageRemapperUtil
 
ImmediateDownloadExporter - Interface in net.sf.basedb.core.plugin
This interface should be implemented by export plugins that supports immediate download to the client application.
impersonated - Variable in class net.sf.basedb.core.data.SessionData
 
impersonated - Variable in class net.sf.basedb.core.SessionControl.LoginInfo
If the logged in user was logged in with the SessionControl.impersonateLogin(int, String)
impersonateLogin(int, String) - Method in class net.sf.basedb.core.PluginSessionControl
 
impersonateLogin(int, String) - Method in class net.sf.basedb.core.SessionControl
Log in as another user or create a clone of the currently logged in user's session.
impersonateLogin(Ownable, String) - Method in class net.sf.basedb.core.SessionControl
Log in as the owner of the specified item.
IMPORT - Enum constant in enum class net.sf.basedb.core.plugin.Plugin.MainType
 
importableFileTypes - Variable in class net.sf.basedb.plugins.ManualTransformCreator
 
importAll - Variable in class net.sf.basedb.plugins.PluginConfigurationImporter
 
importAll(String, ProgressReporter) - Static method in class net.sf.basedb.core.Migration
Import data to a BASE database.
importAllParameter - Static variable in class net.sf.basedb.plugins.PluginConfigurationImporter
 
importData(DbControl, File, Transformation, IntensityTransform, ProgressReporter) - Method in class net.sf.basedb.plugins.Base1PluginExecuter
Imports the data from the file stdout.txt in the execution directory.
importer - Variable in class net.sf.basedb.plugins.executor.ExternalProgramExecutor
 
importExtraFile(String, InputStreamLocator) - Method in interface net.sf.basedb.util.bfs.ExtraFileImporter
Import the file data into a file in the BASE file system.
importExtraFile(String, InputStreamLocator) - Method in class net.sf.basedb.util.bfs.GenericExtraFileImporter
 
importFromCdf(DbControl, FusionCDFData, ProgressReporter) - Method in class net.sf.basedb.plugins.CdfFileReporterImporter
 
importFromFile(TableInfo, File, File, DbEngine, Statement, ProgressReporter) - Method in class net.sf.basedb.core.Migration
Import data to the given table.
ImportInputStream - Class in net.sf.basedb.core.plugin
An input stream used for input to import plug-ins.
ImportInputStream(InputStream) - Constructor for class net.sf.basedb.core.plugin.ImportInputStream
Create a new import stream.
importPluginConfigurationsFromJar(String, String, HashMap<Integer, Boolean>, boolean, boolean) - Method in class net.sf.basedb.plugins.PluginConfigurationImporter
Imports plugin configurations direct from an xml file, located in a jar.
importTempFiles(DbControl, File[], Directory) - Method in class net.sf.basedb.plugins.Base1PluginExecuter
 
in - Variable in class net.sf.basedb.clients.jobagent.executors.ProcessJobExecutor.StreamRedirector
 
in - Variable in class net.sf.basedb.clients.web.ExperimentExplorer.InExpression
 
in - Variable in class net.sf.basedb.clients.web.fileupload.FileUpload
The stream coming from the browser.
in - Variable in class net.sf.basedb.plugins.LowessNormalization.CallableWorker
 
in - Variable in class net.sf.basedb.util.bfs.AnnotationParser
 
in - Variable in class net.sf.basedb.util.bfs.DataParser
 
in - Variable in class net.sf.basedb.util.bfs.MetadataParser
 
in - Variable in class net.sf.basedb.util.FileCopyRunnable
 
in - Variable in class net.sf.basedb.util.InputStreamCombiner
 
in - Variable in class net.sf.basedb.util.InputStreamSplitter
The source input stream to read from.
in - Variable in class net.sf.basedb.util.InputStreamTracker
The source input stream to read from.
in(Expression, Expression...) - Static method in class net.sf.basedb.core.query.Restrictions
Check if an expression is contained in a set of other expressions: e1 IN (e2[0], e2[1], ...)
in(Expression, Query) - Static method in class net.sf.basedb.core.query.Restrictions
Create a subquery restriction: e1 IN (subquery).
IN - Enum constant in enum class net.sf.basedb.core.Operator
 
IN_PROJECT - Enum constant in enum class net.sf.basedb.core.Include
Include items in the active project.
inactive - Variable in class net.sf.basedb.core.data.KitData
 
inactiveColumnMapping - Static variable in class net.sf.basedb.plugins.batchimport.KitImporter
Column mapping parameter for the kit inactive flag.
inactiveMapper - Variable in class net.sf.basedb.plugins.batchimport.KitImporter
 
inactiveRoles - Variable in class net.sf.basedb.core.Keyring
Holds the ID of the roles that are inactive.
include - Variable in class net.sf.basedb.clients.web.extensions.section.IncludeContentSectionFactory
 
include - Variable in class net.sf.basedb.clients.web.extensions.tabcontrol.IncludeContentTabFactory
 
include - Variable in class net.sf.basedb.core.data.ContextData
 
include - Variable in class net.sf.basedb.core.data.ItemListSyncFilterData
 
include - Variable in class net.sf.basedb.core.ItemContext
 
include - Variable in class net.sf.basedb.util.listable.TransformContext
 
include(Collection<Include>) - Method in class net.sf.basedb.core.AbstractEntityQuery
 
include(Collection<Include>) - Method in interface net.sf.basedb.core.query.EntityQuery
 
include(Include...) - Method in class net.sf.basedb.core.AbstractEntityQuery
 
include(Include...) - Method in interface net.sf.basedb.core.query.EntityQuery
Specify options for which items to include in the result.
Include - Enum Class in net.sf.basedb.core
This enumeration defines constants that are used to specify which items to include in a query.
Include(int) - Constructor for enum class net.sf.basedb.core.Include
Constructor for Permission enums.
includeChildBioAssays - Variable in class net.sf.basedb.util.listable.CollectedExtractsToDerivedBioAssayTransformer
 
includeChildrenThatPushToParent - Variable in class net.sf.basedb.util.listable.ToExtractSourceItemTransformerFactory
 
includeChildrenThatPushToParent - Variable in class net.sf.basedb.util.listable.ToSampleSourceItemTransformerFactory
 
IncludeContentSectionFactory - Class in net.sf.basedb.clients.web.extensions.section
A section action factory implementation that includes another resource as the content of a section.
IncludeContentSectionFactory() - Constructor for class net.sf.basedb.clients.web.extensions.section.IncludeContentSectionFactory
Create a new factory instance.
IncludeContentSectionFactory.Section - Class in net.sf.basedb.clients.web.extensions.section
 
IncludeContentTabFactory - Class in net.sf.basedb.clients.web.extensions.tabcontrol
A tab action factory implementation that includes another resource as the content of tab.
IncludeContentTabFactory() - Constructor for class net.sf.basedb.clients.web.extensions.tabcontrol.IncludeContentTabFactory
Create a new factory instance.
IncludeContentTabFactory.Tab - Class in net.sf.basedb.clients.web.extensions.tabcontrol
 
includeDefault - Variable in class net.sf.basedb.core.FastAnnotationLoader
 
IncludeExcludeFilter - Class in net.sf.basedb.util
 
IncludeExcludeFilter(DbControl, BioAssaySet, List<BioAssay>, Restriction, Integer, Integer) - Constructor for class net.sf.basedb.util.IncludeExcludeFilter
 
includeInherited - Variable in class net.sf.basedb.core.AnnotationRestriction.Options
 
includeInherited() - Method in class net.sf.basedb.core.AnnotationRestriction.Options
Should inherited annotations be included in the search or not.
includeLimit - Variable in class net.sf.basedb.util.IncludeExcludeFilter
 
includePrimary - Variable in class net.sf.basedb.core.AnnotationRestriction.Options
 
includePrimary() - Method in class net.sf.basedb.core.AnnotationRestriction.Options
Should primary annotations be included in the search or not.
includes - Variable in class net.sf.basedb.core.AbstractEntityQuery
Flags specifying which items to include.
includes - Variable in class net.sf.basedb.plugins.batchimport.AnyToAnyImporter
 
includeSource - Variable in class net.sf.basedb.util.listable.CollectExtracts.CollectChildren
 
includeSource - Variable in class net.sf.basedb.util.listable.CollectExtracts.CollectParents
 
includeSourcesInTarget - Variable in class net.sf.basedb.util.listable.DerivedBioAssayToChildDerivedBioAssayTransformer
 
includeSourcesInTarget - Variable in class net.sf.basedb.util.listable.DerivedBioAssayToParentDerivedBioAssayTransformer
 
includeSourcesInTarget - Variable in class net.sf.basedb.util.listable.ExtractToChildExtractTransformer
 
includeSourcesInTarget - Variable in class net.sf.basedb.util.listable.ExtractToParentExtractTransformer
 
includeSourcesInTarget - Variable in class net.sf.basedb.util.listable.SampleToChildSampleTransformer
 
includeSourcesInTarget - Variable in class net.sf.basedb.util.listable.SampleToParentSampleTransformer
 
includeSpot(SqlResult) - Method in interface net.sf.basedb.util.DynamicFilter
Check if a spot should be included in the filtered output or not.
includeSpot(SqlResult) - Method in class net.sf.basedb.util.IncludeExcludeFilter
Check if a spot should be included in the filtered output or not.
inclusive - Variable in class net.sf.basedb.core.query.BetweenRestriction
 
incoming - Variable in class net.sf.basedb.util.jobagent.JobAgentServerConnection.RequestHandlerThread
 
INCORRECT_BIOASSAY_POSITION - Static variable in class net.sf.basedb.util.overview.Validator
Validator rule that checks if the position of an extract on a physical bioassay is between 1 and the size of the bioassay.
INCORRECT_BIOMATERIAL_TYPE - Static variable in class net.sf.basedb.util.overview.Validator
Validator that checks if the biomaterial on a bioplate is of the correct item type.
INCORRECT_BIOSOURCE_TYPE - Static variable in class net.sf.basedb.util.overview.Validator
Validator that checks if the parent biosource of a sample has the expected subtype.
INCORRECT_DERIVEDBIOASSAY_TYPE - Static variable in class net.sf.basedb.util.overview.Validator
Validator that checks if a derived bioassay has the expected subtype.
INCORRECT_EXTRACT_TYPE - Static variable in class net.sf.basedb.util.overview.Validator
Validator that checks if the parent extract of a extract/bioassay has the expected subtype.
INCORRECT_FILETYPE - Static variable in class net.sf.basedb.util.overview.Validator
Validator rule that checks if the file attached to an item has a correct file type.
INCORRECT_HARDWARETYPE - Static variable in class net.sf.basedb.util.overview.Validator
Validator rule that checks if the hardware attached to an item has a correct hardware type.
INCORRECT_KITTYPE - Static variable in class net.sf.basedb.util.overview.Validator
Validator rule that checks if the kit attached to an item has a correct kit type.
INCORRECT_PHYSICALBIOASSAY_TYPE - Static variable in class net.sf.basedb.util.overview.Validator
Validator that checks if a physical bioassay has the expected subtype.
INCORRECT_PROTOCOLTYPE - Static variable in class net.sf.basedb.util.overview.Validator
Validator rule that checks if the protocol attached to an item has a correct protocol type.
INCORRECT_SAMPLE_TYPE - Static variable in class net.sf.basedb.util.overview.Validator
Validator that checks if the parent sample of a sample/extract has the expected subtype.
INCORRECT_SOFTWARETYPE - Static variable in class net.sf.basedb.util.overview.Validator
Validator rule that checks if the software attached to an item has a correct software type.
INCORRECT_TAGTYPE - Static variable in class net.sf.basedb.util.overview.Validator
Validator rule that checks if the tag attached to an extract has a correct subtype.
increaseCount() - Method in class net.sf.basedb.util.plot.HistogramPlot.HistogramBin
Increase the count value in this bin.
increaseSectionCount(String, int) - Method in class net.sf.basedb.util.basefile.BaseFileParser
Counts the number of times a section has been seen in the file.
index - Variable in class net.sf.basedb.clients.web.extensions.list.AnyLinkColumn
 
index - Variable in class net.sf.basedb.clients.web.extensions.list.RelatedItemColumn
 
index - Variable in class net.sf.basedb.core.data.BioPlateEventParticipantData
 
index - Variable in class net.sf.basedb.core.Metadata.ComponentPropertyPath
 
index - Variable in class net.sf.basedb.core.migrate.AbstractResultWriter
 
index - Variable in class net.sf.basedb.core.query.HqlPropertyExpression
 
index - Variable in class net.sf.basedb.util.ArrayIterator
The index of the next element to return.
index - Variable in class net.sf.basedb.util.extensions.ExtensionBean
 
index - Variable in class net.sf.basedb.util.extensions.Registry.RegisteredExtension
 
index - Variable in class net.sf.basedb.util.gtf.GtfInputStream
 
index - Variable in class net.sf.basedb.util.importer.spotdata.GenericIntensityParser
 
index - Variable in class net.sf.basedb.util.InputStreamCombiner
 
index - Variable in class net.sf.basedb.util.NestedIterator
The index of the next collection to return.
index - Variable in class net.sf.basedb.util.overview.cache.IndexedCacheKey
 
index - Variable in class net.sf.basedb.util.parser.ColumnMapper
 
index(String, String) - Static method in class net.sf.basedb.core.query.Hql
Create an index expression for a property that is a map or a list.
index_64 - Static variable in class net.sf.basedb.util.bcrypt.BCrypt
 
INDEX_COMPARATOR_CTX - Static variable in class net.sf.basedb.util.extensions.DefaultFilter
Comparator used to order a list of invokation contexts by the index value of the extension.
INDEX_COMPARATOR_EXT - Static variable in class net.sf.basedb.util.extensions.DefaultFilter
Comparator used to order a list of extensions by the index value of the extension.
indexColumnMapping - Static variable in class net.sf.basedb.plugins.batchimport.ArraySlideImporter
 
indexed - Variable in class net.sf.basedb.core.VirtualColumn
If the column should be indexed or not.
INDEXED - Static variable in class net.sf.basedb.core.VirtualColumn
Used in constructor to tell that the column should be indexed.
IndexedCacheKey - Class in net.sf.basedb.util.overview.cache
Cache key implementation that bundles another cache key with an index.
IndexedCacheKey(Object, int) - Constructor for class net.sf.basedb.util.overview.cache.IndexedCacheKey
 
IndexedCacheKey(Object, BasicItem) - Constructor for class net.sf.basedb.util.overview.cache.IndexedCacheKey
Create a cache key using the id of the BasicItem as the index.
indexes - Variable in class net.sf.basedb.core.dbengine.TableInfo
 
IndexInfo(String, boolean) - Constructor for class net.sf.basedb.core.dbengine.TableInfo.IndexInfo
Create a new IndexInfo object.
indexMapper - Variable in class net.sf.basedb.plugins.batchimport.ArraySlideImporter
 
indexOf(Object) - Method in class net.sf.basedb.core.ItemResultList
 
InExpression(int...) - Constructor for class net.sf.basedb.clients.web.ExperimentExplorer.InExpression
 
InExpression(Collection<? extends Number>) - Constructor for class net.sf.basedb.clients.web.ExperimentExplorer.InExpression
 
info - Variable in class net.sf.basedb.core.PluginDefinition
 
info - Variable in class net.sf.basedb.util.excel.XlsxToCsvUtil.CellTypeWithInfo
 
info - Variable in class net.sf.basedb.util.importer.spotdata.FirstPassSectionSpotsParser
 
info - Variable in class net.sf.basedb.util.importer.spotdata.SecondPassSectionSpotsParser
 
info - Variable in class net.sf.basedb.util.importer.spotdata.SectionAssaysParser
 
info - Variable in class net.sf.basedb.util.importer.spotdata.SectionReporterListParser
 
info(String) - Method in class net.sf.basedb.util.extensions.logging.ExtensionsLogger
Log an INFO message.
info(String, Throwable) - Method in class net.sf.basedb.util.extensions.logging.ExtensionsLogger
Log an INFO message with an optional stacktrace.
INFO - Enum constant in enum class net.sf.basedb.util.extensions.logging.LogLevel
 
INFO - Enum constant in enum class net.sf.basedb.util.extensions.LoggingErrorHandlerFactory.Level
 
InfoRequestHandler - Class in net.sf.basedb.clients.jobagent.handlers
This is a request handler for the info and status commands.
InfoRequestHandler(Agent) - Constructor for class net.sf.basedb.clients.jobagent.handlers.InfoRequestHandler
 
inheritAll(AnnotationSet, boolean) - Method in class net.sf.basedb.core.AnnotationSet
Utility method for inheriting or cloning all annotations from the given annotation set.
inheritAnnotation(Annotation, boolean) - Method in class net.sf.basedb.core.AnnotationSet
Inherit or clone an annotation.
InheritAnnotationsManager - Class in net.sf.basedb.util.annotations
Manager class for batch inheriting of annotations.
InheritAnnotationsManager(DbControl, SnapshotManager, List<InheritSpecification>) - Constructor for class net.sf.basedb.util.annotations.InheritAnnotationsManager
 
InheritAnnotationsManager.AnnotationTypeFilter - Class in net.sf.basedb.util.annotations
Filter for finding annotation types to process.
InheritAnnotationsManager.UsableParentFilter - Class in net.sf.basedb.util.annotations
Filter used to find parent items that are annotated and for which the current user has permission to USE the annotations.
INHERITED - Enum constant in enum class net.sf.basedb.core.Annotation.Source
The annotation is an inherited annotation without a local copy of the values.
inheritedCreated(int, int, int, int, int, int) - Method in class net.sf.basedb.core.ProjectSpecificAnnotationsManager
An INHERITED/CLONED annotation has been created in this transaction.
inheritedFrom - Variable in class net.sf.basedb.core.data.AnnotationData
 
inheritedFrom - Variable in class net.sf.basedb.core.snapshot.AnnotationSnapshot
 
inheritedFromId - Variable in class net.sf.basedb.core.snapshot.AnnotationSnapshot
 
inheritedFromSetId - Variable in class net.sf.basedb.core.snapshot.AnnotationSnapshot
 
inheritingAnnotations - Variable in class net.sf.basedb.core.data.AnnotationData
 
InheritSpecification - Class in net.sf.basedb.util.annotations
Class for holding rules for how annotations should be inherited from parent items.
InheritSpecification(AnnotationType) - Constructor for class net.sf.basedb.util.annotations.InheritSpecification
Creates a new specification for the given annotation type.
init() - Static method in class net.sf.basedb.clients.web.extensions.service.Services
Initialise and start the installed services.
init() - Method in class net.sf.basedb.clients.web.servlet.Download
 
init() - Method in class net.sf.basedb.clients.web.servlet.ExperimentExplorerPlotServlet
 
init() - Method in class net.sf.basedb.clients.web.servlet.PlotServlet
 
init() - Method in class net.sf.basedb.clients.web.servlet.RssNewsFeed
 
init() - Static method in class net.sf.basedb.core.BatchUtil
Generate SQL for all BatchableData classes for insert, update and delete operations.
init() - Static method in class net.sf.basedb.core.Config
Loads the settings from the configuration file.
init() - Static method in class net.sf.basedb.core.ExtendedProperties
Initialize the class.
init() - Static method in class net.sf.basedb.core.Keyring
 
init() - Static method in class net.sf.basedb.core.Metadata
 
init() - Static method in class net.sf.basedb.core.PredefinedQuery
Load and parse the file with predefined queries.
init() - Static method in class net.sf.basedb.core.QueryExecutor
This will create a new thread for each query.
init() - Static method in class net.sf.basedb.core.QueryRuntimeFilterFactory
 
init() - Static method in class net.sf.basedb.core.RawDataTypes
Initialize the class.
init() - Static method in class net.sf.basedb.core.RawDataUtil
Initialise the class.
init() - Method in class net.sf.basedb.core.ServiceSessionControl.SessionFactoryConfiguration
 
init() - Static method in class net.sf.basedb.core.SystemItems
Initialize the class and load all mappings for item.systemId --> item.id and for RoleKeyData.itemType --> RoleKeyData.id
init() - Static method in class net.sf.basedb.core.Version
Loads the settings from the configuration file.
init() - Static method in class net.sf.basedb.util.EmailUtil
 
init() - Method in class net.sf.basedb.util.JarClassLoader.JarClassLoaderProxy
Initialize the proxy.
init(String) - Method in class net.sf.basedb.clients.jobagent.AgentSignalReceiver
Initialise the receiver.
init(String) - Method in class net.sf.basedb.clients.web.util.SimpleSignalProgressReporter
Nothing need to be initilized.
init(String) - Method in class net.sf.basedb.core.Job.JobSignalTransporter
 
init(String) - Method in class net.sf.basedb.core.signal.AbstractSignalReceiver
Initialise the signal receiver.
init(String) - Method in class net.sf.basedb.core.signal.AbstractSignalTransporter
Initialise the transporter.
init(String) - Method in class net.sf.basedb.core.signal.LocalSignalReceiver
Initialise the signal receiver.
init(String) - Method in interface net.sf.basedb.core.signal.SignalReceiver
Initialise the signal receiver.
init(String) - Method in interface net.sf.basedb.core.signal.SignalTransporter
Initialise the signal transporter.
init(String) - Method in class net.sf.basedb.core.signal.SocketSignalReceiver
Initialise the receiver.
init(String, String, String) - Method in class net.sf.basedb.util.uri.http.HttpConnectionManagerFactory
Initialize this factory with some information.
init(FilterConfig) - Method in class net.sf.basedb.clients.web.servlet.CacheControlFilter
 
init(FilterConfig) - Method in class net.sf.basedb.clients.web.servlet.CharacterEncodingFilter
 
init(FilterConfig) - Method in class net.sf.basedb.clients.web.servlet.ContentSecurityPolicyFilter
 
init(FilterConfig) - Method in class net.sf.basedb.clients.web.servlet.ImageRemapFilter
 
init(ServletContext) - Static method in class net.sf.basedb.clients.web.extensions.ExtensionsControl
Initialise the extension system.
init(ServletContext) - Static method in class net.sf.basedb.clients.web.extensions.skin.ImageRemapperUtil
Initialized at server startup.
init(Agent) - Method in class net.sf.basedb.clients.jobagent.executors.DummyJobExecutor
 
init(Agent) - Method in class net.sf.basedb.clients.jobagent.executors.ProcessJobExecutor
 
init(Agent) - Method in class net.sf.basedb.clients.jobagent.executors.ThreadJobExecutor
 
init(Agent) - Method in class net.sf.basedb.clients.jobagent.handlers.AbstractCustomRequestHandler
 
init(Agent) - Method in interface net.sf.basedb.clients.jobagent.handlers.CustomRequestHandler
Initialize the request handler.
init(Agent) - Method in interface net.sf.basedb.clients.jobagent.JobExecutor
Initialize the job executor.
init(Agent) - Method in class net.sf.basedb.clients.jobagent.slotmanager.InternalSlotManager
 
init(Agent) - Method in class net.sf.basedb.clients.jobagent.slotmanager.MasterSlotManager
 
init(Agent) - Method in class net.sf.basedb.clients.jobagent.slotmanager.RemoteSlotManager
 
init(Agent) - Method in interface net.sf.basedb.clients.jobagent.slotmanager.SlotManager
Initialize the slot manager.
init(AnnotationData) - Method in class net.sf.basedb.core.snapshot.AnnotationSnapshot
Initialize the snapshot with information from the given annotation.
init(AnnotationSetData) - Method in class net.sf.basedb.core.snapshot.AnnotationSetSnapshot
Initialise the snapshot with data from the given annotation set, including values for all primary annotations and information about inherited annotations.
init(SessionControl, ParameterValues, ParameterValues) - Method in class net.sf.basedb.core.plugin.AbstractPlugin
Store copies of the session control, plugin and job configuration.
init(SessionControl, ParameterValues, ParameterValues) - Method in interface net.sf.basedb.core.plugin.Plugin
This method is called right after the plugin object has been constructed to pass the configuration and job parameters to the plugin.
init(SessionControl, ParameterValues, ParameterValues) - Method in class net.sf.basedb.plugins.gtf.GtfReporterImporter
 
init(SessionControl, ParameterValues, ParameterValues) - Method in class net.sf.basedb.plugins.gtf.GtfReporterMapImporter
 
init(SessionControl, ParameterValues, ParameterValues, ExternalProgramExecutor) - Method in class net.sf.basedb.plugins.executor.AbstractIOSupport
 
init(SessionControl, ParameterValues, ParameterValues, ExternalProgramExecutor) - Method in interface net.sf.basedb.plugins.executor.IOSupport
Replaces the regular plug-in initialisation method.
init(JspCompilationContext, JspServletWrapper) - Method in class net.sf.basedb.clients.web.extensions.XJspCompiler
Initialises the compiler.
init_key() - Method in class net.sf.basedb.util.bcrypt.BCrypt
Initialise the Blowfish key schedule
init1() - Static method in class net.sf.basedb.core.HibernateUtil
First step of initialising this class.
init2() - Static method in class net.sf.basedb.core.HibernateUtil
Second step of initialising this class.
initBean(Class<? extends Action>) - Method in class net.sf.basedb.util.extensions.debug.BeanActionFactory
Create the bean object.
initBeanWithReflection(Object, Element, Presets.Preset) - Method in class net.sf.basedb.util.extensions.xml.XmlLoader
Initialise a bean using reflection.
initCollection(BasicItem, String) - Method in class net.sf.basedb.core.DbControl
Initialise a collection on an item.
initCollection(Session, BasicData, String) - Static method in class net.sf.basedb.core.HibernateUtil
Initialise a collection on a data object.
initDatabase(SchemaGenerator.Mode, ProgressReporter, String, String) - Static method in class net.sf.basedb.core.Install
Initialise the BASE database by creating all items that are required for BASE to work properly.
initDefaultAttributes() - Method in class net.sf.basedb.clients.web.taglib.CalendarButton
 
initDefaultAttributes() - Method in class net.sf.basedb.clients.web.taglib.StylableTag
Initialize default attributes.
initFactory(InvokationContext<? super ConnectionManagerFactory>) - Method in class net.sf.basedb.util.uri.http.HttpConnectionManagerActionFactory
 
initFilters() - Method in class net.sf.basedb.core.SyncFilter
 
initFunTab() - Method in class net.sf.basedb.util.jep.FunctionSafeJep
Overrides the regular function lookup table by replacing it with a function table that pretends that all functions has been registered, but then generates an error message if it doesn't exists.
initGuiContexts() - Method in class net.sf.basedb.clients.web.plugins.SimpleExport
 
initialised - Static variable in class net.sf.basedb.clients.web.extensions.ExtensionsControl
 
initialised - Static variable in class net.sf.basedb.clients.web.extensions.service.Services
 
initialised - Variable in class net.sf.basedb.util.extensions.debug.BeanActionFactory
 
initialised - Variable in class net.sf.basedb.util.extensions.debug.ProxyActionFactory
 
initialized - Static variable in class net.sf.basedb.clients.web.taglib.Page
 
initialized - Static variable in class net.sf.basedb.util.EmailUtil
 
initializeDirtynessForSomeProperties() - Method in class net.sf.basedb.core.log.EntityDetails
We must initialize "dirtyness" for collections and some other properties from the constructor.
initialTab - Variable in class net.sf.basedb.clients.web.taglib.tab.TabControl
The ID of the tab that is initially active.
initialValue(Object) - Method in class net.sf.basedb.util.ClassLocal
Subclasses may override this to initialize the object stored for that class.
initPermissions(int, int) - Method in class net.sf.basedb.core.Annotation
READ permission is granted if the logged in user has READ permission on the associated item and annotation type.
initPermissions(int, int) - Method in class net.sf.basedb.core.AnnotationSet
READ permission is granted to all users.
initPermissions(int, int) - Method in class net.sf.basedb.core.AnyToAny
Permissions are granted based on the permission on the from item.
initPermissions(int, int) - Method in class net.sf.basedb.core.ArrayDesignBlock
WRITE and DELETE permissions are always denied.
initPermissions(int, int) - Method in class net.sf.basedb.core.BasicBatcher
Initialise the logged in user's permissions for this batcher.
initPermissions(int, int) - Method in class net.sf.basedb.core.BasicChildItem
If the logged in user has read permission for the parent, read permission is granted.
initPermissions(int, int) - Method in class net.sf.basedb.core.BasicItem
Initialise the logged in user's permissions for this item.
initPermissions(int, int) - Method in class net.sf.basedb.core.BioAssay
Deny DELETE permission.
initPermissions(int, int) - Method in class net.sf.basedb.core.BioMaterialEvent
READ permission is granted and DELETE permissions is denied to evereyone for creation events.
initPermissions(int, int) - Method in class net.sf.basedb.core.BioPlateEventParticipant
 
initPermissions(int, int) - Method in class net.sf.basedb.core.ChangeHistory
WRITE permission and higher is always denied.
initPermissions(int, int) - Method in class net.sf.basedb.core.ChildItem
If the logged in user has read permission for the parent, read permission is granted.
initPermissions(int, int) - Method in class net.sf.basedb.core.ClientDefaultSetting
READ permission is granted if the logged in user has READ permission to the client application.
initPermissions(int, int) - Method in class net.sf.basedb.core.DataCubeColumn
Deny DELETE permission.
initPermissions(int, int) - Method in class net.sf.basedb.core.Directory
 
initPermissions(int, int) - Method in class net.sf.basedb.core.DiskUsage
READ permission is granted if the logged in user is the owner of this disk usage.
initPermissions(int, int) - Method in class net.sf.basedb.core.FeatureBatcher
Grant read permission if the logged in user has read permission to the array design.
initPermissions(int, int) - Method in class net.sf.basedb.core.File
Check the write protected flag and deny DELETE if it is set.
initPermissions(int, int) - Method in class net.sf.basedb.core.FileSet
READ permission is granted to all users.
initPermissions(int, int) - Method in class net.sf.basedb.core.FileSetMember
READ permission is granted to all users.
initPermissions(int, int) - Method in class net.sf.basedb.core.GlobalDefaultSetting
READ permission is always granted.
initPermissions(int, int) - Method in class net.sf.basedb.core.Group
If the logged in user is a member of this group, read permission is granted.
initPermissions(int, int) - Method in class net.sf.basedb.core.ItemKey
WRITE permission is always denied.
initPermissions(int, int) - Method in class net.sf.basedb.core.ItemSubtype
If this is a system protocol type, delete and create permissions are revoked.
initPermissions(int, int) - Method in class net.sf.basedb.core.Job
Grant read permission if the logged in user has read permission to the experiment the job belongs to.
initPermissions(int, int) - Method in class net.sf.basedb.core.Message
Read, write an delete permission is granted if the logged in user is the same as the user the message is to.
initPermissions(int, int) - Method in class net.sf.basedb.core.News
Read permission is granted if today is between the start and end date.
initPermissions(int, int) - Method in class net.sf.basedb.core.OwnedItem
If the logged in user is the owner of this item, DELETE, SET_OWNER and SET_PERMISSION permission is granted.
initPermissions(int, int) - Method in class net.sf.basedb.core.Platform
Deny deletion of the GENERIC and Affymetrix platform.
initPermissions(int, int) - Method in class net.sf.basedb.core.PluginType
All users get READ access.
initPermissions(int, int) - Method in class net.sf.basedb.core.Project
If the logged in user is a member of this project, read or use permission is granted.
initPermissions(int, int) - Method in class net.sf.basedb.core.ProjectKey
WRITE permission is always denied.
initPermissions(int, int) - Method in class net.sf.basedb.core.Quantity
If this is a system quantity, delete and create permissions are revoked.
initPermissions(int, int) - Method in class net.sf.basedb.core.Quota
The logged in user has read permission to the quota assigned to him/her, directly or through group quota.
initPermissions(int, int) - Method in class net.sf.basedb.core.QuotaType
The logged in user has read permission to the quota assigned to him/her.
initPermissions(int, int) - Method in class net.sf.basedb.core.RawDataBatcher
Grant read permission if the logged in user has read permission to the raw bioassay.
initPermissions(int, int) - Method in class net.sf.basedb.core.ReporterCloneTemplate
Locked templates are READ-able by all, and everything else is denied.
initPermissions(int, int) - Method in class net.sf.basedb.core.Role
If the logged in user is a member of this role, read permission is granted.
initPermissions(int, int) - Method in class net.sf.basedb.core.RoleKey
CREATE and DELETE permissions are always denied.
initPermissions(int, int) - Method in class net.sf.basedb.core.RootRawBioAssay
Deny DELETE permission.
initPermissions(int, int) - Method in class net.sf.basedb.core.Session
READ permission is granted if the logged in user is the owner of this session.
initPermissions(int, int) - Method in class net.sf.basedb.core.Setting
Add permissions granted to Item.SETTING.
initPermissions(int, int) - Method in class net.sf.basedb.core.SharedItem
Grant permissions according to the item and project keys.
initPermissions(int, int) - Method in class net.sf.basedb.core.User
If the logged in user is the same as this user RESTRICTED_WRITE permissions is granted, unless it is a multiuser account.
initPermissions(int, int) - Method in class net.sf.basedb.core.UserClientSetting
READ permission is granted if the logged in user is the owner of this setting.
initPermissions(int, int) - Method in class net.sf.basedb.core.UserDefaultSetting
READ permission is granted if the logged in user is the owner of this setting.
initPermissions(int, int) - Method in class net.sf.basedb.core.UserDevice
DELETE permission is granted if the logged in user is the owner of this device.
initPlatforms(Session) - Static method in class net.sf.basedb.core.RawDataTypes
Load file-only platforms and create raw data types for them.
initPropertyFilters(Map<String, PropertyFilterData>) - Method in class net.sf.basedb.core.ItemContext
Initialize the property filters by loading them from the given map.
initProxy(Class<? extends Action>) - Method in class net.sf.basedb.util.extensions.debug.ProxyActionFactory
Initialise the proxy class.
initQuery(ItemQuery<I>, String) - Method in class net.sf.basedb.util.overview.GenericOverview
Same as GenericOverview.initQuery(ItemQuery, Order...) but easier to use when sorting the items in ascending order by a single column.
initQuery(ItemQuery<I>, String) - Method in interface net.sf.basedb.util.overview.OverviewContext
Same as OverviewContext.initQuery(ItemQuery, Order...) but easier to use when sorting the items in ascending order by a single column.
initQuery(ItemQuery<I>, Order...) - Method in class net.sf.basedb.util.overview.GenericOverview
Initialise a query with "global options" and optionally a sort order.
initQuery(ItemQuery<I>, Order...) - Method in interface net.sf.basedb.util.overview.OverviewContext
Initialise a query with "global options" and optionally a sort order.
initReferenceQuery(DbControl, IdMethod, ItemQuery<T>, boolean) - Method in class net.sf.basedb.plugins.batchimport.AbstractItemImporter
Initialise a query that is used to find referenced items.
initReporterCache(DbControl) - Method in class net.sf.basedb.clients.web.ExperimentExplorer
 
initStaticFields(PageContext) - Static method in class net.sf.basedb.clients.web.taglib.Page
Initialize static fields.
INNER - Enum constant in enum class net.sf.basedb.core.query.JoinType
Use an inner join, ie. only select rows present in both tables.
innerJoin(String, String) - Static method in class net.sf.basedb.core.query.Hql
Same as innerJoin(null, propert, joinedAlias)
innerJoin(String, String, String) - Static method in class net.sf.basedb.core.query.Hql
Create an inner join query element.
innerJoin(String, String, String, boolean) - Static method in class net.sf.basedb.core.query.Hql
Same as innerJoin(null, propert, joinedAlias, null, false)
innerJoin(String, String, String, Restriction, boolean) - Static method in class net.sf.basedb.core.query.Hql
Create an inner join query element and optionally prefetch the joined items in the same query.
innerJoin(String, AnnotationType, String) - Static method in class net.sf.basedb.core.query.Annotations
Create an inner join between an already joined element of a query and the annotation values for the given annotation type.
innerJoin(AnnotationType, String) - Static method in class net.sf.basedb.core.query.Annotations
Create an inner join between the root element of a query and the annotation values for the given annotation type.
Input - Class in net.sf.basedb.clients.web.taglib
This tag is used to make it easier to add <input> elements on a BASE web page.
Input() - Constructor for class net.sf.basedb.clients.web.taglib.Input
 
InputStreamCombiner - Class in net.sf.basedb.util
An input stream implementation that reads one or more input streams sequentially.
InputStreamCombiner(InputStream...) - Constructor for class net.sf.basedb.util.InputStreamCombiner
Create a new stream combiner using the given streams to read from
InputStreamLocator - Interface in net.sf.basedb.util.bfs
Defines a generic interface for opening an input stream from a named resource.
InputStreamSplitter - Class in net.sf.basedb.util
This class can be used to split an input stream into one or more additional output streams.
InputStreamSplitter(InputStream, boolean, boolean, OutputStream...) - Constructor for class net.sf.basedb.util.InputStreamSplitter
Create a new input stream splitter.
InputStreamSplitter(InputStream, OutputStream...) - Constructor for class net.sf.basedb.util.InputStreamSplitter
Create a new input stream splitter.
InputStreamTracker - Class in net.sf.basedb.util
This class is used to keep track of the number of bytes read from the underlying input stream.
InputStreamTracker(InputStream) - Constructor for class net.sf.basedb.util.InputStreamTracker
Create a new input stream tracker.
InputStreamTracker(InputStream, InputStreamTracker.ScaleFactor) - Constructor for class net.sf.basedb.util.InputStreamTracker
Create a new input stream tracker.
InputStreamTracker.CurvedScaleFactor - Class in net.sf.basedb.util
Apply a curved scale factor that has a max upper limit.
InputStreamTracker.IdentityScaleFactor - Class in net.sf.basedb.util
Do not scale number of bytes.
InputStreamTracker.LinearScaleFactor - Class in net.sf.basedb.util
Apply a linear scale factor so that when we have read N actual bytes the getNumRead() method return N*scale bytes.
InputStreamTracker.ScaleFactor - Interface in net.sf.basedb.util
A scale factor can be used to match number of read bytes to something that better resembles actual progress.
InReporterListFunction - Class in net.sf.basedb.util.jep
A JEP function class that adds a inList(reporterListId) function to a JEP expression parser.
InReporterListFunction(DbControl) - Constructor for class net.sf.basedb.util.jep.InReporterListFunction
Create a new instance of this function.
InRestriction - Class in net.sf.basedb.core.query
Compare if one expression is contained in a set of other expressions: e1 IN (e2[0], e2[1], ...)
InRestriction(Expression, Expression...) - Constructor for class net.sf.basedb.core.query.InRestriction
 
insert(int, I) - Method in class net.sf.basedb.core.PositionExtraValueBatcher
Insert an extra value for a given position coordinate.
insert(int, ReporterData) - Method in class net.sf.basedb.core.PositionBatcher
Link a position to a reporter.
insert(short, int) - Method in class net.sf.basedb.core.FilterBatcher
Insert a column/position coordinate that passed the filter.
insert(short, int, float...) - Method in class net.sf.basedb.core.SpotBatcher
Insert intensities for a given column/position coordinate.
insert(short, int, I) - Method in class net.sf.basedb.core.SpotExtraValueBatcher
Insert an extra value for a given column/position coordinate.
insert(short, int, RawData) - Method in class net.sf.basedb.core.MappingBatcher
Link a spot to a raw data.
insert(D) - Method in class net.sf.basedb.core.BasicBatcher
Insert a data object.
insert(Object) - Method in class net.sf.basedb.core.hibernate.StatelessSessionWrapper
 
insert(Object...) - Method in class net.sf.basedb.core.AnnotationBatcher.InsertBatcher
Execute an insert SQL statement with the given parameter values.
insert(String, Object) - Method in class net.sf.basedb.core.hibernate.StatelessSessionWrapper
 
insert(AbstractSqlQuery) - Method in class net.sf.basedb.core.FilterBatcher
Insert column/position coordinates using a query.
insert(AbstractSqlQuery) - Method in class net.sf.basedb.core.MappingBatcher
Insert mapping to raw spots using a query.
insert(AbstractSqlQuery) - Method in class net.sf.basedb.core.PositionBatcher
Insert position/reporter links using a query.
insert(AbstractSqlQuery) - Method in class net.sf.basedb.core.PositionExtraValueBatcher
Insert position extra values using a query.
insert(AbstractSqlQuery) - Method in class net.sf.basedb.core.SpotBatcher
Insert spot intensities using a query.
insert(AbstractSqlQuery) - Method in class net.sf.basedb.core.SpotExtraValueBatcher
Insert extra values using a query.
insert(FeatureData) - Method in class net.sf.basedb.core.FeatureBatcher
Set the position number and add the feature to the insert queue.
insert(RawData) - Method in class net.sf.basedb.core.RawDataBatcher
 
insert(RawData, String, String) - Method in class net.sf.basedb.core.RawDataBatcher
Insert a raw data spot and verify the external id of the reporter.
insert(ReporterData) - Method in class net.sf.basedb.core.ReporterBatcher
Insert and add the external reporter id to the internal cache.
insertable - Variable in class net.sf.basedb.core.ExtendedProperty
 
InsertBatcher(Connection, String, int...) - Constructor for class net.sf.basedb.core.AnnotationBatcher.InsertBatcher
Prepare a new batcher for the given SQL statement.
insertCount - Variable in class net.sf.basedb.core.BasicBatcher
 
insertCountTotal - Variable in class net.sf.basedb.core.BasicBatcher
Counts the number of inserts done by the batcher.
insertIntoAnnotations - Variable in class net.sf.basedb.core.AnnotationBatcher
 
insertIntoAnnotationSets - Variable in class net.sf.basedb.core.AnnotationBatcher
 
insertIntoDetails - Variable in class net.sf.basedb.core.LogControl
 
insertIntoParameterValues - Variable in class net.sf.basedb.core.AnnotationBatcher
 
insertPropertyOrder - Variable in class net.sf.basedb.core.BasicBatcher
 
insertSql - Variable in class net.sf.basedb.core.BasicBatcher
 
insertSql - Variable in class net.sf.basedb.core.ReporterCloneBatcher
The statement that inserts cloned reporter data.
insertSqlStatement - Variable in class net.sf.basedb.core.ReporterCloneBatcher
The SQL string for the ReporterCloneBatcher.insertSql statement.
insertStatement - Variable in class net.sf.basedb.core.BasicBatcher
 
insertValues - Variable in class net.sf.basedb.core.AnnotationBatcher
 
inspectSchemaGenerationSQL(String, Dialect, SchemaGenerator.Mode) - Method in class net.sf.basedb.core.dbengine.AbstractDbEngine
Skip all "create index ..." statements.
inspectSchemaGenerationSQL(String, Dialect, SchemaGenerator.Mode) - Method in interface net.sf.basedb.core.dbengine.DbEngine
Let the DbEninge inspect a schema generation sql statment and possible modify it before it is sent to the database.
inspectWorkingDirectory() - Method in class net.sf.basedb.plugins.executor.ExternalProgramExecutor
Check the working directory for new files.
Install - Class in net.sf.basedb.core
This class contains static methods used to install items into an empty database.
Install() - Constructor for class net.sf.basedb.core.Install
 
INSTALL - Enum constant in enum class net.sf.basedb.core.hibernate.SchemaGenerator.Mode
Creating a fresh installation.
Install.ItemSubtypeFT - Class in net.sf.basedb.core
 
Install.PlatformFT - Class in net.sf.basedb.core
 
installation - Variable in class net.sf.basedb.core.Application.StartupOptions
 
installation(boolean) - Method in class net.sf.basedb.core.Application.StartupOptions
Set to TRUE when starting a new installation.
InstalledFileProcessor - Class in net.sf.basedb.clients.web.extensions
File processor implementation that sets a final result status for each processed file (eg.
InstalledFileProcessor(ProcessResults) - Constructor for class net.sf.basedb.clients.web.extensions.InstalledFileProcessor
 
installedFiles - Variable in class net.sf.basedb.util.extensions.manager.Settings
 
InstalledFilter - Class in net.sf.basedb.util.extensions.manager.filter
Filter implementation for extension files that allow installed files to pass.
InstalledFilter(Settings) - Constructor for class net.sf.basedb.util.extensions.manager.filter.InstalledFilter
Create a new filter.
InstalledFilter(Settings, Filter<ExtensionsFile>) - Constructor for class net.sf.basedb.util.extensions.manager.filter.InstalledFilter
Create a new filter with an optional chained parent filted.
installedObjects - Variable in class net.sf.basedb.util.extensions.manager.ExtensionsManager
 
installedSchemaVersion - Variable in class net.sf.basedb.core.ServiceSessionControl.SessionFactoryConfiguration
 
InstallFilter - Class in net.sf.basedb.clients.web.extensions
Filter implementation that selects only those extensions that was selected by the user in the gui.
InstallFilter(HttpServletRequest) - Constructor for class net.sf.basedb.clients.web.extensions.InstallFilter
 
InstallFilter(HttpServletRequest, boolean) - Constructor for class net.sf.basedb.clients.web.extensions.InstallFilter
Create a filter that allow us to ignore the error flag.
installHelpTexts(Client, boolean, InputStream, String) - Method in class net.sf.basedb.plugins.HelpImporter
This method installs the helptexts from an inputstream.
installMode - Variable in class net.sf.basedb.core.ServiceSessionControl.SessionFactoryConfiguration
 
installOrUpdate(DbControl, PluginInfo, String, ItemKey) - Static method in class net.sf.basedb.core.PluginDefinition
Install or update the plug-in definition with information from the info object.
installUnits(String, boolean) - Static method in class net.sf.basedb.core.Install
 
INSTANCE - Static variable in class net.sf.basedb.clients.web.extensions.login.PasswordLoginFormFactory
The default password login form.
INSTANCE - Static variable in class net.sf.basedb.util.resources.Utf8PropertiesResourceBundleControl
The one and only instance.
InstanceOfFilter<T> - Class in net.sf.basedb.util.filter
A filter implementation that accepts all objects that are (sub)classes of a specified class.
InstanceOfFilter(Class<?>, boolean) - Constructor for class net.sf.basedb.util.filter.InstanceOfFilter
Create a new filter.
instances - Static variable in class net.sf.basedb.core.Metadata
Cache of Metadata instances.
INT - Enum constant in enum class net.sf.basedb.core.Type
Integer type.
integer(int) - Static method in class net.sf.basedb.core.query.Expressions
Create a constant expression from an integer.
INTEGER - Enum constant in enum class net.sf.basedb.plugins.Base1PluginExecuter.Base1JobParameterType
 
INTEGER - Static variable in class net.sf.basedb.core.hibernate.TypeWrapper
 
IntegerConverter - Class in net.sf.basedb.util.jep.convert
Convert an Integer constant to a Query API Expression.
IntegerConverter() - Constructor for class net.sf.basedb.util.jep.convert.IntegerConverter
 
IntegerExpression - Class in net.sf.basedb.core.query
A constant integer expression.
IntegerExpression(int) - Constructor for class net.sf.basedb.core.query.IntegerExpression
 
IntegerFormatter - Class in net.sf.basedb.util.formatter
Formats a number as an integer.
IntegerFormatter(boolean) - Constructor for class net.sf.basedb.util.formatter.IntegerFormatter
Create a new integer formatter.
IntegerFormatter(boolean, Character) - Constructor for class net.sf.basedb.util.formatter.IntegerFormatter
Create a new integer formatter with a thousands separator.
IntegerParameterType - Class in net.sf.basedb.core
This class represent a parameter type that is an integer.
IntegerParameterType() - Constructor for class net.sf.basedb.core.IntegerParameterType
Create a new integer parameter type, without any limits and allowing null values.
IntegerParameterType(Integer, Integer, Integer, boolean) - Constructor for class net.sf.basedb.core.IntegerParameterType
Create a new integer parameter type.
IntegerParameterType(Integer, Integer, Integer, boolean, int, int, int, List<Integer>) - Constructor for class net.sf.basedb.core.IntegerParameterType
 
IntegerParameterValueData - Class in net.sf.basedb.core.data
Integer parameter value.
IntegerParameterValueData() - Constructor for class net.sf.basedb.core.data.IntegerParameterValueData
 
IntegerParameterValueData(Integer...) - Constructor for class net.sf.basedb.core.data.IntegerParameterValueData
 
IntegerUtil - Class in net.sf.basedb.core
Utility methods that will make it easier to implement data validation for integer attributes.
IntegerUtil() - Constructor for class net.sf.basedb.core.IntegerUtil
 
IntegerWriter - Class in net.sf.basedb.core.migrate
Database-independent writer implementation that writes integer values from a result set.
IntegerWriter(ResultSet, int, Writer, char[]) - Constructor for class net.sf.basedb.core.migrate.IntegerWriter
 
INTENSITY - Enum constant in enum class net.sf.basedb.core.plugin.Plugin.MainType
 
INTENSITY_EXPRESSION - Enum constant in enum class net.sf.basedb.core.Formula.Type
The formula represents an intensity measurement expression.
INTENSITY_TRANSFORMATION - Enum constant in enum class net.sf.basedb.core.Formula.Type
The formula represents a intensity transformation expression.
IntensityCalculator - Interface in net.sf.basedb.util
This interface is used together with the IntensityCalculatorUtil class to help a plugin calculate intensities from raw data spots.
IntensityCalculatorPlugin - Class in net.sf.basedb.plugins
This plugin provides methods to calculate the intensity for a root bioassayset using different formulas.
IntensityCalculatorPlugin() - Constructor for class net.sf.basedb.plugins.IntensityCalculatorPlugin
Constructor should be empty.
IntensityCalculatorUtil - Class in net.sf.basedb.util
This is a utility class for plugins that calculate intensities from raw spot data.
IntensityCalculatorUtil() - Constructor for class net.sf.basedb.util.IntensityCalculatorUtil
 
IntensityCalculatorUtil.JepIntensityCalculatorImpl - Class in net.sf.basedb.util
An implementation of the IntensityCalculator interface using JEP expressions.
IntensityFormula - Class in net.sf.basedb.core
Holds information about the formulas used to calculate intensities from a raw data spot.
IntensityFormula(String, String, String, String[]) - Constructor for class net.sf.basedb.core.IntensityFormula
Create a new intensity formula.
intensityTransform - Variable in class net.sf.basedb.core.data.BioAssaySetData
 
IntensityTransform - Enum Class in net.sf.basedb.core
Gives information in what way spot intensities has been transformed before they were stored in the database.
IntensityTransform(int, String, boolean, Formula.AverageMethod) - Constructor for enum class net.sf.basedb.core.IntensityTransform
Creates a new intensity transform.
interactive - Variable in class net.sf.basedb.core.data.PluginDefinitionData
 
InteractivePlugin - Interface in net.sf.basedb.core.plugin
An interactive plugin is a Plugin that supports interactive configuration in a user session.
interfaceName - Variable in class net.sf.basedb.core.data.PluginTypeData
 
INTERNAL - Static variable in class net.sf.basedb.core.authentication.AuthenticationMethod
This is special-case internal login used by job queue, etc.
INTERNAL_ID - Static variable in class net.sf.basedb.plugins.batchimport.InternalIdMethod
Use the internal ID for finding items.
internalFile - Variable in class net.sf.basedb.core.File
The path to the internal file.
internalId - Variable in class net.sf.basedb.core.authentication.AuthenticatedUser
 
internalId - Variable in class net.sf.basedb.util.extensions.xml.PluginInfo
 
internalIdColumnMapping - Static variable in class net.sf.basedb.plugins.AnnotationFlatFileImporter
 
internalIdColumnMapping - Static variable in class net.sf.basedb.plugins.batchimport.AbstractItemImporter
 
InternalIdMethod - Class in net.sf.basedb.plugins.batchimport
Identification method implementation that finds an item by using the getById() method.
InternalIdMethod(String, String) - Constructor for class net.sf.basedb.plugins.batchimport.InternalIdMethod
Create a new id method.
internalJobQueue - Static variable in class net.sf.basedb.core.Application
The internal job queue reference if it is enabled.
InternalJobQueue - Class in net.sf.basedb.core
A simple implementation of a job queue that executes jobs in order of priority and longest waiting time.
InternalJobQueue() - Constructor for class net.sf.basedb.core.InternalJobQueue
Create the job queue.
InternalJobQueue.JobQueueKeyring - Class in net.sf.basedb.core
Our own keyring containing the permissions we need to execute the jobs.
InternalJobQueue.JobRunner - Class in net.sf.basedb.core
Encapsulates the running of a job in a separate thread.
internalName - Variable in class net.sf.basedb.core.data.FileData
 
internalPrintBofMarker() - Method in class net.sf.basedb.util.bfs.MetadataWriter
Prints the beginning-of-file marker.
internalPrintComment(String) - Method in class net.sf.basedb.util.bfs.MetadataWriter
Print a single-line comment.
internalPrintSection(String) - Method in class net.sf.basedb.util.bfs.MetadataWriter
Prints a section header assuming that the name has already been encoded.
internalPrintValue(String, String) - Method in class net.sf.basedb.util.bfs.MetadataWriter
Prints a section entry assuming that the key and value has already been encoded.
InternalSlotManager - Class in net.sf.basedb.clients.jobagent.slotmanager
The internal slot manager assigns slot to jobs based on their estimated execution time.
InternalSlotManager() - Constructor for class net.sf.basedb.clients.jobagent.slotmanager.InternalSlotManager
 
interruptHandler - Static variable in class net.sf.basedb.core.signal.ThreadSignalHandler
Keep per-thread interupt handlers.
InterruptHandler - Interface in net.sf.basedb.core.signal
An interface for handling thread interrupts.
intersect(IdListRestriction) - Method in class net.sf.basedb.core.query.IdListRestriction
Merge this id list with another list.
intersection(Collection<ItemList>, ItemList.DelayedAdditionManager) - Static method in class net.sf.basedb.core.ItemList
Create a set with the intersection of the items in the given lists.
intersection(Collection<ReporterList>) - Static method in class net.sf.basedb.core.ReporterList
Create a set with the intersection of the reporter ID:s in the given lists.
interval - Variable in class net.sf.basedb.clients.web.extensions.service.DummyService
 
interval - Variable in class net.sf.basedb.util.ProgressInputStream
 
IntValue(Number) - Constructor for class net.sf.basedb.util.excel.ExcelValue.IntValue
 
INV_LN10x2 - Static variable in class net.sf.basedb.util.ma.MACalculator
 
INV_LN2 - Static variable in class net.sf.basedb.plugins.LowessNormalization.SpotData
 
INV_LN2 - Static variable in class net.sf.basedb.util.ma.MACalculator
 
INV_LOG10_2 - Static variable in class net.sf.basedb.util.ma.Log10MACalculator
 
INV_LOG2_10x2 - Static variable in class net.sf.basedb.util.ma.Log2MACalculator
 
invalid - Static variable in class net.sf.basedb.core.Path
A regexp checking for invalid characters.
INVALID_CHARACTERS - Static variable in class net.sf.basedb.core.Path
These characters are not valid within a file or directory name: "~\\/:;*?<>|\""
INVALID_USE_OF_NULL_ERROR - Static variable in class net.sf.basedb.plugins.util.Parameters
InvalidAndModifiedFilter - Class in net.sf.basedb.util.extensions.manager.filter
Filter implementation for extension files that allow modified but invalid files to pass.
InvalidAndModifiedFilter() - Constructor for class net.sf.basedb.util.extensions.manager.filter.InvalidAndModifiedFilter
Create a new filter.
InvalidAnnotationException - Exception in net.sf.basedb.core
 
InvalidAnnotationException() - Constructor for exception net.sf.basedb.core.InvalidAnnotationException
Create a new InvalidAnnotationException object.
InvalidAnnotationException(String) - Constructor for exception net.sf.basedb.core.InvalidAnnotationException
Create a new InvalidAnnotationException object with the specified message.
InvalidAnnotationException(AnnotationType, Item) - Constructor for exception net.sf.basedb.core.InvalidAnnotationException
Create a new InvalidAnnotationException object when the annotation type cannot be used for the specified item type.
invalidColumnsErrorParameter - Static variable in class net.sf.basedb.plugins.IlluminaRawDataImporter
 
InvalidDataException - Exception in net.sf.basedb.core
Exceptions of this type are thrown when invalid data is encountered.
InvalidDataException() - Constructor for exception net.sf.basedb.core.InvalidDataException
Create a new InvalidDataException object.
InvalidDataException(String) - Constructor for exception net.sf.basedb.core.InvalidDataException
Create a new InvalidDataException object with the specified message.
InvalidDataException(String, Throwable) - Constructor for exception net.sf.basedb.core.InvalidDataException
Create a new InvalidDataException object with the specified message.
InvalidDataException(Throwable) - Constructor for exception net.sf.basedb.core.InvalidDataException
Create a new InvalidDataException object.
invalidEnumErrorParameter - Static variable in class net.sf.basedb.plugins.AnnotationFlatFileImporter
 
InvalidPasswordException - Exception in net.sf.basedb.core.authentication
This exception can be thrown when the password is invalid.
InvalidPasswordException - Exception in net.sf.basedb.core
Exceptions of this type are thrown when user tries to log in, but the password is incorrect.
InvalidPasswordException(String) - Constructor for exception net.sf.basedb.core.authentication.InvalidPasswordException
Create a new InvalidPasswordException object
InvalidPasswordException(String) - Constructor for exception net.sf.basedb.core.InvalidPasswordException
Create a new InvalidPasswordException object with the specified message
InvalidPasswordException(String, String) - Constructor for exception net.sf.basedb.core.authentication.InvalidPasswordException
Create a new InvalidPasswordException object
InvalidPasswordException(String, Throwable) - Constructor for exception net.sf.basedb.core.InvalidPasswordException
Create a new InvalidPasswordException object with the specified message
InvalidPathException - Exception in net.sf.basedb.core
This exception is thrown when BASE is trying to parse a path which is invalid.
InvalidPathException(String) - Constructor for exception net.sf.basedb.core.InvalidPathException
Create a new InvalidPathException object.
InvalidRelationException - Exception in net.sf.basedb.core
Exceptions of this type are thrown when a ValidationAction has detected that a file related to the main file is invalid.
InvalidRelationException() - Constructor for exception net.sf.basedb.core.InvalidRelationException
Create a new InvalidRelationException object.
InvalidRelationException(String) - Constructor for exception net.sf.basedb.core.InvalidRelationException
Create a new InvalidRelationException object with the specified message.
InvalidRelationException(String, Throwable) - Constructor for exception net.sf.basedb.core.InvalidRelationException
Create a new InvalidRelationException object with the specified message.
InvalidRelationException(Throwable) - Constructor for exception net.sf.basedb.core.InvalidRelationException
Create a new InvalidRelationException object.
invalidUseOfNullError(String, String, String, String...) - Static method in class net.sf.basedb.plugins.util.Parameters
Create the parameter for handling required but missing values.
invalidUseOfNullErrorParameter - Static variable in class net.sf.basedb.plugins.AbstractFlatFileImporter
 
InvalidUseOfNullException - Exception in net.sf.basedb.core
This exception is thrown when an object field or a parameter that mustn't be null is set to null.
InvalidUseOfNullException() - Constructor for exception net.sf.basedb.core.InvalidUseOfNullException
Create a new InvalidUseOfNullException object.
InvalidUseOfNullException(String) - Constructor for exception net.sf.basedb.core.InvalidUseOfNullException
Create a new InvalidUseOfNullException object.
invariantEquals(List<?>, List<?>) - Static method in class net.sf.basedb.util.EqualsHelper
Checks if two lists contains equal elements disregarding their positions in the array.
invariantEquals(T[], T[]) - Static method in class net.sf.basedb.util.EqualsHelper
Checks if two arrays contains equal elements disregarding their positions in the array.
InverseFilter<T> - Class in net.sf.basedb.util.filter
A filter implementation that negates the result of a parent filter.
InverseFilter(Filter<? super T>) - Constructor for class net.sf.basedb.util.filter.InverseFilter
 
INVLN2 - Static variable in class net.sf.basedb.util.ColorGenerator
Constant holding the value of 1 / ln(2).
InvokationContext<A extends Action> - Class in net.sf.basedb.util.extensions
Keeps contextual information about a single invokation of extensions.
InvokationContext() - Constructor for class net.sf.basedb.util.extensions.InvokationContext
 
invoke() - Method in class net.sf.basedb.core.PluginConfigurationRequest
 
invoke() - Method in class net.sf.basedb.core.PluginExecutionRequest
 
invoke() - Method in class net.sf.basedb.core.PluginRequest
Invoke the plugin and let it do it's work.
invoke(Object, Method, Object[]) - Method in class net.sf.basedb.util.extensions.debug.ProxyActionFactory
 
IOSupport - Interface in net.sf.basedb.plugins.executor
This interface is a tagging interface that should be implemented by export and import plug-ins that knows how to cooperate with the external program executor.
ip - Variable in class net.sf.basedb.core.signal.SocketSignalReceiver
 
IS_COMPACT - Static variable in class net.sf.basedb.clients.web.ModeInfo
 
isAcceptableParent(Annotatable) - Method in class net.sf.basedb.util.annotations.InheritSpecification
Checks if the parent item has a subtype matching the subtype (if any) in this specification.
isAcceptedByValidator(ValidationAction) - Method in class net.sf.basedb.util.fileset.ValidatingFileSetMember
Check if the member is accepted by the given validator.
isAffymetrix(FileStoreEnabled) - Static method in class net.sf.basedb.util.affymetrix.AffymetrixUtil
Check if the item is using the affymetrix platform.
isAllowedControl(InetAddress, String) - Method in class net.sf.basedb.clients.jobagent.Agent
Check if the computer specified by the given address is allowed to control this job agent.
isAllowedHost(InetAddress) - Method in class net.sf.basedb.core.signal.SocketSignalReceiver
Checks if the specified remote host is allowed to send signals to this receiver.
isAllowedImmediateExecution() - Method in class net.sf.basedb.core.plugin.NamespaceRequestWrapper
 
isAllowedImmediateExecution() - Method in interface net.sf.basedb.core.plugin.Request
If this plugin has been allowed immediate execution or not.
isAllowedImmediateExecution() - Method in class net.sf.basedb.core.PluginRequest.RequestImpl
 
isAllowedImmediateExecution() - Method in class net.sf.basedb.plugins.executor.ExternalProgramExecutor.RequestWrapper
 
isAllowedToUseClient(String) - Method in class net.sf.basedb.core.SessionControl
Checks if this session control can be used by the given client application.
isAnExcelFile(InputStream) - Static method in class net.sf.basedb.util.excel.XlsxToCsvUtil
Check if the given stream is an Excel file by looking at the first few bytes.
isAnnotatable() - Method in enum class net.sf.basedb.core.Item
Is this an item that supports annotations?
isAnnotated() - Method in interface net.sf.basedb.core.Annotatable
Check if this item has an annotation set.
isAnnotated() - Method in class net.sf.basedb.core.AnnotatedItem
 
isAnnotated() - Method in class net.sf.basedb.core.BioAssay
 
isAnnotated() - Method in class net.sf.basedb.core.BioAssaySet
 
isAnnotated() - Method in class net.sf.basedb.core.PluginDefinition
 
isAnnotated() - Method in class net.sf.basedb.core.Project
 
isAnnotated() - Method in class net.sf.basedb.core.RootRawBioAssay
 
isAnnotated() - Method in class net.sf.basedb.core.Well
 
isAnnotation - Variable in class net.sf.basedb.clients.web.taglib.table.ColumnDef
If the property is an annotation or not.
isAnnotation() - Method in class net.sf.basedb.clients.web.taglib.table.ColumnDef
 
isAnnotation() - Method in class net.sf.basedb.util.export.spotdata.AnnotationAssayField
 
isAnnotation() - Method in interface net.sf.basedb.util.export.spotdata.AssayField
A boolean flag indicating if the field is an annotation or not.
isAnnotation() - Method in class net.sf.basedb.util.export.spotdata.AssayPropertyField
 
isAnnotationFix() - Method in class net.sf.basedb.util.overview.Fix
If this fix involves editing an annotation or not.
isAssignable(Class<?>[], Object[]) - Static method in class net.sf.basedb.util.ClassUtil
Check if one array of class objects is assignment compatible with values in another array.
isAssociatedDataFileType(DataFileType) - Method in class net.sf.basedb.core.ItemSubtype
Checks if the given data file type is associated with this subtype or not.
isAttached(BasicItem) - Method in class net.sf.basedb.core.DbControl
Check if an item is attached to this DbControl.
isAutoLoadingChildren() - Method in class net.sf.basedb.util.overview.loader.BasicItemNodeLoaderFactory
Get the auto load children setting.
isAutoReload() - Method in class net.sf.basedb.util.units.UnitCache
If units that are no longer connected to a DbControl should automatcally by reloaded with the current DbControl or not.
isAveragable() - Method in class net.sf.basedb.clients.web.taglib.table.TableColumn
 
isAveragable() - Method in class net.sf.basedb.core.ExtendedProperty
If it makes sense to take the average of multiple values for this property or not.
isAvoiding() - Method in class net.sf.basedb.util.listable.TransformContext
 
isBasicItem() - Method in enum class net.sf.basedb.core.Item
Is this item representing a BasicItem object or not?
isBound(Parameter<?>) - Method in class net.sf.basedb.core.hibernate.QueryWrapper
 
isCacheable() - Method in class net.sf.basedb.core.hibernate.QueryWrapper
Deprecated.
isCachingResult() - Method in class net.sf.basedb.core.AbstractHqlQuery
 
isCachingResult() - Method in interface net.sf.basedb.core.query.HqlQuery
If the query results are cached or not.
isCallable() - Method in class net.sf.basedb.core.hibernate.NativeQueryWrapper
 
isChange() - Method in class net.sf.basedb.clients.web.SubContext
Is the context changed or not?
isChecked() - Method in class net.sf.basedb.clients.web.taglib.Input
 
isChildrenLoaded() - Method in class net.sf.basedb.util.overview.Node
 
isClosed - Variable in class net.sf.basedb.clients.jobagent.handlers.MultiProtocolRequestHandler
 
isClosed - Variable in class net.sf.basedb.core.DbControl
Is the connection closed or not?
isClosed - Variable in class net.sf.basedb.core.DynamicResultIterator
 
isClosed - Variable in class net.sf.basedb.core.ScrollIterator
 
isClosed - Variable in class net.sf.basedb.util.extensions.manager.ExtensionsFile.WriteableExtensionsFile
 
isClosed() - Method in class net.sf.basedb.clients.jobagent.handlers.MultiProtocolRequestHandler
If the request handler is closed, it will igore all method calls.
isClosed() - Method in class net.sf.basedb.clients.web.servlet.PlotServlet.CFResultIterator
 
isClosed() - Method in class net.sf.basedb.core.AbstractBatcher
Check if this batcher is closed or not.
isClosed() - Method in interface net.sf.basedb.core.Batcher
Check if the batcher has been closed or not.
isClosed() - Method in class net.sf.basedb.core.DataResultIterator
 
isClosed() - Method in class net.sf.basedb.core.DbControl
Check if the connection to the database has been closed.
isClosed() - Method in class net.sf.basedb.core.DynamicResultIterator
 
isClosed() - Method in class net.sf.basedb.core.ItemResultIterator
 
isClosed() - Method in interface net.sf.basedb.core.query.ResultIterator
Check if the iterator has been closed.
isClosed() - Method in class net.sf.basedb.core.ReporterScoreResultIterator
 
isClosed() - Method in class net.sf.basedb.core.ScrollIterator
Check if the results has been closed.
isClosed() - Method in class net.sf.basedb.core.SessionControl
If this session control has been closed or not.
isCollecting() - Method in class net.sf.basedb.util.listable.TransformContext
 
isColumnSticky(String) - Method in class net.sf.basedb.clients.web.taglib.table.Table
 
isColumnVisible(String) - Method in class net.sf.basedb.clients.web.taglib.table.Table
 
isCompact - Variable in class net.sf.basedb.clients.web.ModeInfo
 
isCompact() - Method in class net.sf.basedb.clients.web.ModeInfo
 
isCompressed() - Method in class net.sf.basedb.core.data.FileData
If the file is stored in a compressed format or not.
isCompressed() - Method in class net.sf.basedb.core.File
If this file is stored in a compressed format or not.
isConnected() - Method in class net.sf.basedb.core.DbControl
Deprecated.
In 3.11. Applications should use separate DbControl instead.
isConnected() - Method in class net.sf.basedb.core.hibernate.SessionWrapper
 
isConnected() - Method in class net.sf.basedb.core.hibernate.StatelessSessionWrapper
 
isCopyingToStdout() - Method in class net.sf.basedb.util.extensions.logging.ExtensionsLog
Are log entries copied to standard output?
isCorrectBasicData(Object) - Method in class net.sf.basedb.core.plugin.GuiContext
Checks if the specified object is an instance of the BasicData subclass used by the Item in this context.
isCorrectBasicItem(Object) - Method in class net.sf.basedb.core.plugin.GuiContext
Checks if the specified object is an instance of the BasicItem subclass used by the Item in this context.
isCorrectType(Object) - Method in enum class net.sf.basedb.core.Type
Check if the value is an object of the correct type.
isCounting - Variable in class net.sf.basedb.core.AbstractQuery
If the Query.count(DbControl) method is executing or not.
isCounting() - Method in class net.sf.basedb.core.AbstractQuery
 
isCounting() - Method in interface net.sf.basedb.core.query.Query
Check if the query is executing the Query.count(DbControl) method or not
isDataFileFix() - Method in class net.sf.basedb.util.overview.Fix
 
isDebug - Static variable in class net.sf.basedb.core.Trashcan
 
isDebugEnabled - Variable in class net.sf.basedb.core.AnnotationBatcher
 
isDebugEnabled - Static variable in class net.sf.basedb.core.ProjectSpecificAnnotationsManager
 
isDebugEnabled - Variable in class net.sf.basedb.util.extensions.logging.ExtensionsLog
 
isDebugEnabled() - Method in class net.sf.basedb.util.extensions.logging.ExtensionsLog
Is the debug-level enabled?
isDebugEnabled() - Method in class net.sf.basedb.util.extensions.logging.ExtensionsLogger
Check if DEBUG logging has been enabled or not.
isDefault - Variable in class net.sf.basedb.core.data.GroupData
 
isDefault - Variable in class net.sf.basedb.core.data.RoleData
 
isDefault() - Method in class net.sf.basedb.core.data.GroupData
If this group should be assigned to new users by default or not.
isDefault() - Method in class net.sf.basedb.core.data.RoleData
If this role should be assigned to new users by default or not.
isDefault() - Method in class net.sf.basedb.core.Group
If this group should be assigned to new users by default or not.
isDefault() - Method in class net.sf.basedb.core.Role
If this role should be assigned to new users by default or not.
isDefaultItem(BasicItem) - Method in class net.sf.basedb.core.Project
Check if the given item is a default item in this project.
isDefaultReadOnly() - Method in class net.sf.basedb.core.hibernate.SessionWrapper
 
isDenied() - Method in class net.sf.basedb.clients.web.taglib.Select
 
isDenied(int) - Method in class net.sf.basedb.core.Keyring
Checks if the DENIED bit is set in the permission.
isDenied(Permission, Item) - Method in class net.sf.basedb.core.SessionControl
Check if the logged in user has been denied the specified permission for items of the specified type.
isDeniedPermission(int, Permission) - Static method in enum class net.sf.basedb.core.Permission
Checks if the given Permission is denied by the permissions code.
isDestroyed() - Method in class net.sf.basedb.core.ArraySlide
Check if the slide is flagged as destroyed or not.
isDestroyed() - Method in class net.sf.basedb.core.BioPlate
Check if the plate has been destroyed.
isDestroyed() - Method in class net.sf.basedb.core.data.ArraySlideData
Check if the slide is flagged as destroyed or not.
isDestroyed() - Method in class net.sf.basedb.core.data.BioPlateData
If the plate has been destroyed.
isDestroyed() - Method in class net.sf.basedb.core.data.PlateData
If the plate has been destroyed.
isDestroyed() - Method in class net.sf.basedb.core.Plate
Check if the plate has been destroyed.
isDetached() - Method in class net.sf.basedb.core.BasicItem
Check if this item is attached to a DbControl object or not.
isDirty() - Method in class net.sf.basedb.core.hibernate.SessionWrapper
 
isDisabled() - Method in class net.sf.basedb.clients.web.taglib.Button
 
isDisabled() - Method in class net.sf.basedb.clients.web.taglib.Select
 
isDisabled() - Method in class net.sf.basedb.clients.web.taglib.table.Button
 
isDisabled() - Method in class net.sf.basedb.core.data.ItemListSyncFilterData
If set, the filter is disabled and should not be used when syncing.
isDisabled() - Method in class net.sf.basedb.core.data.PluginConfigurationData
If the plugin is enabled or disabled. // Mapped in hibernate-properties-PluginConfigurationData.xml since annotation doesn't support a default value
isDisabled() - Method in class net.sf.basedb.core.data.PluginDefinitionData
If the plugin is enabled or disabled. // Mapped in hibernate-properties-PluginDefinitionData.xml since annotation doesn't support a default value
isDisabled() - Method in class net.sf.basedb.core.data.UserData
Check if this account is disabled or enabled.
isDisabled() - Method in class net.sf.basedb.core.PluginConfiguration
Checks if this plugin configuration is disabled or not.
isDisabled() - Method in class net.sf.basedb.core.PluginDefinition
Checks if this plugin is disabled or not.
isDisabled() - Method in class net.sf.basedb.core.SyncFilter
If set, this filter is disabled and is not used when syncing.
isDisabled() - Method in class net.sf.basedb.core.User
Check if this account has been disabled.
isDisabled() - Method in class net.sf.basedb.util.extensions.xml.PluginInfo
Is this plug-in enabled or not?
isDisabled() - Method in class net.sf.basedb.util.overview.validator.BasicItemNodeValidatorFactory
 
isDisabled() - Method in interface net.sf.basedb.util.overview.validator.NodeValidatorFactory
Check if node validation has been disabled.
isDisabled() - Method in class net.sf.basedb.util.StaticCache
Check if the cache has been disabled.
isDistinct() - Method in class net.sf.basedb.core.AbstractQuery
 
isDistinct() - Method in interface net.sf.basedb.core.query.Query
If this query returns distinct results of not.
isDoublingBackAllowed() - Method in class net.sf.basedb.clients.web.extensions.list.RelatedItemColumn.Specification
Enabled on a multi-hop path if the path down to the related child from the parent item is allowed to traverse the same items as the path up from the source child item to the parent.
isDownloadable() - Method in enum class net.sf.basedb.core.Location
A flag indicating if a file that is stored at this location can be downloaded by a call to File.getDownloadStream(long) or File.download(java.io.OutputStream, long).
isDryRun() - Method in class net.sf.basedb.core.data.JobData
If the job should be/was executed as a dry-run job.
isDryRun() - Method in class net.sf.basedb.core.Job
Check if the job should be/was executed as a dry-run job.
isDryRun() - Method in class net.sf.basedb.core.PluginResponse
Check if the job should be executed or was executed in dry-run mode.
isEffectivelyTrusted() - Method in class net.sf.basedb.core.JobAgentSettings
If the plugin is a trusted plugin or not.
isEmpty() - Method in class net.sf.basedb.core.BioWell
Is this well empty?
isEmpty() - Method in class net.sf.basedb.core.ItemResultList
 
isEmpty() - Method in class net.sf.basedb.util.formatter.LookupFormatter
Checks if the lookup map is empty or not.
isEmpty() - Method in class net.sf.basedb.util.Tree
 
isEmptyDatabase() - Static method in class net.sf.basedb.core.HibernateUtil
Check if the main database has any tables.
isEnabled() - Method in class net.sf.basedb.clients.web.extensions.menu.FixedMenuItemFactory
 
isEnabled() - Method in interface net.sf.basedb.clients.web.extensions.menu.MenuItemAction
If the menu item should be enabled or disabled.
isEnabled() - Method in class net.sf.basedb.clients.web.extensions.menu.MenuItemBean
 
isEnabled() - Method in interface net.sf.basedb.clients.web.extensions.toolbar.ButtonAction
If the button should be enabled or disabled.
isEnabled() - Method in class net.sf.basedb.clients.web.extensions.toolbar.ButtonBean
 
isEnabled() - Method in class net.sf.basedb.clients.web.extensions.toolbar.FixedButtonFactory
 
isEnabled() - Static method in class net.sf.basedb.clients.web.servlet.RssNewsFeed
Check if the rss servlet has been enabled or not.
isEnabled() - Method in class net.sf.basedb.clients.web.taglib.Icon
 
isEnabled() - Method in class net.sf.basedb.clients.web.taglib.menu.Menuitem
 
isEnabled() - Method in class net.sf.basedb.clients.web.taglib.menu.Submenu
 
isEnabled() - Method in class net.sf.basedb.clients.web.taglib.path.PathElement
 
isEnabled() - Method in class net.sf.basedb.clients.web.taglib.table.Button.ButtonActionWrapper
 
isEnabled() - Static method in class net.sf.basedb.util.EmailUtil
Check if email sending has been enabled for the server or not.
isEnabled(User) - Static method in class net.sf.basedb.util.EmailUtil
Check if email sending is enabled for the given user.
isEnabled(Extension<?>) - Method in class net.sf.basedb.clients.web.extensions.ExtensionsControl
Check if an extension is enabled of disabled.
isEnabled(Extension<?>) - Method in class net.sf.basedb.util.extensions.DefaultFilter
 
isEnabled(Extension<?>) - Method in interface net.sf.basedb.util.extensions.ExtensionsFilter
Check if an extension is enabled or disabled.
isEnabled(Extension<?>) - Method in class net.sf.basedb.util.extensions.manager.Settings
 
isEnabled(Extension<?>) - Method in class net.sf.basedb.util.extensions.SingleExtensionFilter
 
isEnabled(ExtensionPoint<?>) - Method in class net.sf.basedb.clients.web.extensions.ExtensionsControl
Check if an extension point is enabled of disabled.
isEnabled(ExtensionPoint<?>) - Method in class net.sf.basedb.util.extensions.DefaultFilter
 
isEnabled(ExtensionPoint<?>) - Method in interface net.sf.basedb.util.extensions.ExtensionsFilter
Check if an extension point is enabled or disabled.
isEnabled(ExtensionPoint<?>) - Method in class net.sf.basedb.util.extensions.manager.Settings
 
isEnabled(ExtensionPoint<?>) - Method in class net.sf.basedb.util.extensions.SingleExtensionFilter
 
isEnabledForItem(Item) - Method in class net.sf.basedb.core.AnnotationType
Check if this annotation type can be used to annotate item of the specified type.
isEnumeration - Variable in class net.sf.basedb.core.data.AnnotationTypeData
 
isEnumeration() - Method in class net.sf.basedb.core.AnnotationType
Check if this annotation type provides a list of predefined allowed values.
isEnumeration() - Method in class net.sf.basedb.core.data.AnnotationTypeData
If this annotation type defines a list of allowed values or not.
isEnumeration() - Method in class net.sf.basedb.core.ParameterType
Check if the parameter type enumerates the allowed values or not.
isEqualOrNull(Object, Object) - Static method in class net.sf.basedb.util.Diff3
Check if two objects are both null or equal as defined by the Object.equals(Object) method.
isEqualOrNull(String, String) - Static method in class net.sf.basedb.core.StringUtil
Check if two strings are equal or both are null.
isEqualOrNull(String, String, boolean) - Static method in class net.sf.basedb.core.StringUtil
Check if two strings are equal or both are null.
isError() - Method in class net.sf.basedb.util.ContextUtil.ContextResult
If this is an error-level object.
isExecutable() - Method in enum class net.sf.basedb.core.Job.Status
If the Job.execute(ProgressReporter, String) method can be called when the job is in this status or not.
isExecuting - Variable in class net.sf.basedb.util.timer.ThreadTimerTask
 
isExportable() - Method in class net.sf.basedb.clients.web.extensions.list.AbstractListColumnBean
 
isExportable() - Method in interface net.sf.basedb.clients.web.extensions.list.ListColumnAction
A flag to indicate if it is possible to export this column with the generic table exporter or not.
isExportable() - Method in class net.sf.basedb.clients.web.taglib.table.ColumnDef
 
isExpressionOperator() - Method in enum class net.sf.basedb.core.Operator
 
isExtendable(String) - Static method in class net.sf.basedb.core.ExtendedProperties
Check if extended properties has been defined for the specified class.
isExtendedProperty - Variable in class net.sf.basedb.core.ClonableProperty
 
isExtendedProperty() - Method in class net.sf.basedb.core.ClonableProperty
Is this cloned property an extended property or a "static" property?
isExtendedProperty() - Method in class net.sf.basedb.core.data.ReporterClonePropertyData
If the column is an extended or "static" property.
isExtensionFilter(String) - Method in class net.sf.basedb.core.PropertyFilter
Checks if this filter is an extension filter.
isFailSafe() - Method in class net.sf.basedb.core.AbstractQuery
 
isFailSafe() - Method in interface net.sf.basedb.core.query.Query
Check if a failure of this query should still allow the current transaction to continue.
isFetchProfileEnabled(String) - Method in class net.sf.basedb.core.hibernate.SessionWrapper
 
isFileOnly() - Method in class net.sf.basedb.core.data.PlatformData
If this platform can only be used with files.
isFileOnly() - Method in class net.sf.basedb.core.data.PlatformVariantData
If this platform variant can only be used with files.
isFileOnly() - Method in class net.sf.basedb.core.Platform
Check if the platform is a file-only platform or if it allows data to be imported into the database.
isFileOnly() - Method in class net.sf.basedb.core.PlatformVariant
Check if the platform variant is a file-only variant or if it allows data to be imported into the database.
isFileOnlyPlatform() - Method in class net.sf.basedb.core.ArrayDesign
Check if this array design uses a file-only platform or variant.
isFileOnlyPlatform() - Method in class net.sf.basedb.core.RawBioAssay
Check if this raw bioassay uses a file-only platform or variant.
isFilterable() - Method in class net.sf.basedb.clients.web.extensions.list.AbstractListColumnBean
 
isFilterable() - Method in interface net.sf.basedb.clients.web.extensions.list.ListColumnAction
A flag to indicate if filtering on this column is enabled or not.
isFilterable() - Method in class net.sf.basedb.clients.web.taglib.table.ColumnDef
 
isFirstChild(E) - Method in class net.sf.basedb.util.Tree.Entry
Check if the specified object is the first child to this node.
isFriendOf(User) - Method in class net.sf.basedb.core.SessionControl
Check if the logged in user is a friend of of the specified user.
isFromInherited() - Method in class net.sf.basedb.util.overview.Fix
If this fix involves editing an inherited annotation or a primary annotation.
isFunction() - Method in class net.sf.basedb.util.jep.convert.AbsConverter
 
isFunction() - Method in class net.sf.basedb.util.jep.convert.AbstractJepConversionFunction
 
isFunction() - Method in class net.sf.basedb.util.jep.convert.ExpConverter
 
isFunction() - Method in class net.sf.basedb.util.jep.convert.IfConverter
 
isFunction() - Method in interface net.sf.basedb.util.jep.convert.JepConversionFunction
If this converter is a built-in function.
isFunction() - Method in class net.sf.basedb.util.jep.convert.LogarithmConverter
 
isFunction() - Method in class net.sf.basedb.util.jep.convert.NaturalLogarithmConverter
 
isFunction() - Method in class net.sf.basedb.util.jep.convert.SquareRootConverter
 
isHidden - Variable in class net.sf.basedb.clients.web.taglib.table.Cell
 
isHidden() - Method in class net.sf.basedb.core.ExtendedProperty
Check if the value of this property is hidden or not.
isHidden() - Method in class net.sf.basedb.core.PluginParameter
Check if the parameter is a hidden parameter or not.
isHomeDirectory() - Method in class net.sf.basedb.core.Directory
Returns TRUE if this directory is a subdirectory to Directory.HOME.
isIdentifier - Variable in class net.sf.basedb.core.data.AnnotationTypeData
 
isIdentifier() - Method in class net.sf.basedb.core.AnnotationType
If this flag is set, annotation values are considered to be alternate identifiers for the items they belong to.
isIdentifier() - Method in class net.sf.basedb.core.data.AnnotationTypeData
If this flag is set, annotation values can be used as identifiers to items.
isIdentifierColumnMapping - Static variable in class net.sf.basedb.plugins.batchimport.AnnotationTypeImporter
Column mapping parameter for "Is identifier" flag.
isIdentifierMapper - Variable in class net.sf.basedb.plugins.batchimport.AnnotationTypeImporter
 
isIgnored() - Method in class net.sf.basedb.util.extensions.manager.ExtensionsFile
Is this an extension file that should be ignored?
isIgnoredFile(File) - Method in class net.sf.basedb.util.extensions.manager.Settings
Check if the given file is marked as ignored.
isIgnoringActiveProject() - Method in class net.sf.basedb.core.Annotation
Checks if this annotation is ignoring the currently active project.
isImpersonated() - Method in class net.sf.basedb.core.SessionControl
Check if the logged in user was impersonated by another user.
isImportable(InputStream) - Method in interface net.sf.basedb.core.plugin.AutoDetectingImporter
Check if the given InputStream can be imported by this plugin.
isImportable(InputStream) - Method in class net.sf.basedb.plugins.AbstractFlatFileImporter
 
isImportable(InputStream) - Method in class net.sf.basedb.plugins.CdfFileReporterImporter
 
isImportable(InputStream) - Method in class net.sf.basedb.plugins.HelpImporter
 
isImportable(InputStream) - Method in class net.sf.basedb.plugins.PluginConfigurationImporter
 
isImportable(FlatFileParser) - Method in class net.sf.basedb.plugins.AbstractFlatFileImporter
This method is called by the AbstractFlatFileImporter.isImportable(InputStream) method after FlatFileParser.nextSection() and FlatFileParser.parseHeaders() has been called and if data has been found.
isImportable(FlatFileParser) - Method in class net.sf.basedb.plugins.IlluminaRawDataImporter
Check that the first line contains the text "Illumina"
isImportable(FlatFileParser) - Method in class net.sf.basedb.plugins.PrintMapFlatFileImporter
Check that the file is a TAM or MwBr file.
IsImportableFilter(File, Filter<? super ContextUtil.ContextResult>) - Constructor for class net.sf.basedb.util.AutoDetectFileFormat.IsImportableFilter
 
isInactive() - Method in class net.sf.basedb.core.data.KitData
A flag indicating if this kit is no longer active.
isInactive() - Method in class net.sf.basedb.core.Kit
Check if the kit is inactive.
isInCategory(AnnotationType) - Method in class net.sf.basedb.core.AnnotationTypeCategory
Checks if the given annotation type is a member in this category.
isInCategoryOrSubtype(AnnotationTypeCategory, ItemSubtype) - Method in class net.sf.basedb.core.snapshot.AnnotationLoaderUtil
Checks if this annotation type is related to the given category or subtype.
isIncluded(Collection<Include>) - Method in class net.sf.basedb.core.AbstractEntityQuery
 
isIncluded(Collection<Include>) - Method in interface net.sf.basedb.core.query.EntityQuery
 
isIncluded(Include...) - Method in class net.sf.basedb.core.AbstractEntityQuery
 
isIncluded(Include...) - Method in interface net.sf.basedb.core.query.EntityQuery
Check which options are set for the items to include in the result
isInContext() - Method in class net.sf.basedb.util.ContextUtil.ContextResult
If the context check was successful and generate no warnings or error.
isInContext(GuiContext) - Method in class net.sf.basedb.core.PluginDefinition
Check if it makes sense to use this plugin in the context of the specified item.
isInContext(GuiContext, Object) - Method in class net.sf.basedb.clients.web.plugins.SimpleExport
 
isInContext(GuiContext, Object) - Method in class net.sf.basedb.core.plugin.AbstractAnalysisPlugin
Check that the item is a bioassayset/derived bioassay and that the logged in user has permission to use the current item.
isInContext(GuiContext, Object) - Method in interface net.sf.basedb.core.plugin.InteractivePlugin
Check if the plugin can be used on the specified object.
isInContext(GuiContext, Object) - Method in class net.sf.basedb.plugins.AnnotationFlatFileImporter
 
isInContext(GuiContext, Object) - Method in class net.sf.basedb.plugins.Base1PluginExecuter
Checks if the BioAssaySet has the number of channels specified by the configuration and that it has the extra values.
isInContext(GuiContext, Object) - Method in class net.sf.basedb.plugins.BaseFileExporterPlugin
 
isInContext(GuiContext, Object) - Method in class net.sf.basedb.plugins.batchimport.AbstractItemImporter
 
isInContext(GuiContext, Object) - Method in class net.sf.basedb.plugins.batchimport.AnyToAnyImporter
 
isInContext(GuiContext, Object) - Method in class net.sf.basedb.plugins.BfsExporterPlugin
 
isInContext(GuiContext, Object) - Method in class net.sf.basedb.plugins.CdfFileReporterImporter
If used from an array design context, verify that the array design is an affymetrix chip.
isInContext(GuiContext, Object) - Method in class net.sf.basedb.plugins.executor.AbstractIOSupport
 
isInContext(GuiContext, Object) - Method in class net.sf.basedb.plugins.executor.ExternalProgramExecutor
 
isInContext(GuiContext, Object) - Method in class net.sf.basedb.plugins.FormulaFilter
 
isInContext(GuiContext, Object) - Method in class net.sf.basedb.plugins.GalExporter
 
isInContext(GuiContext, Object) - Method in class net.sf.basedb.plugins.gtf.GtfReporterMapImporter
 
isInContext(GuiContext, Object) - Method in class net.sf.basedb.plugins.HelpExporter
 
isInContext(GuiContext, Object) - Method in class net.sf.basedb.plugins.HelpImporter
 
isInContext(GuiContext, Object) - Method in class net.sf.basedb.plugins.IlluminaRawDataImporter
If used from an experiment context, verify that the experiment is an 'illumina' experiment and that the logged in user has permission to write.
isInContext(GuiContext, Object) - Method in class net.sf.basedb.plugins.IntensityCalculatorPlugin
Check that the current experiment stores it's raw data in the database.
isInContext(GuiContext, Object) - Method in class net.sf.basedb.plugins.JepExtraValueCalculator
 
isInContext(GuiContext, Object) - Method in class net.sf.basedb.plugins.JepIntensityTransformer
 
isInContext(GuiContext, Object) - Method in class net.sf.basedb.plugins.LowessNormalization
 
isInContext(GuiContext, Object) - Method in class net.sf.basedb.plugins.ManualDerivedBioAssayCreator
Adds check of the item subtype.
isInContext(GuiContext, Object) - Method in class net.sf.basedb.plugins.MedianRatioNormalization
 
isInContext(GuiContext, Object) - Method in class net.sf.basedb.plugins.PackedFileExporter
Check that at least one file or directory has been selected.
isInContext(GuiContext, Object) - Method in class net.sf.basedb.plugins.PlateFlatFileImporter
Always null, since plugin doesn't operate on individual items.
isInContext(GuiContext, Object) - Method in class net.sf.basedb.plugins.PlateMappingExporter
Always null.
isInContext(GuiContext, Object) - Method in class net.sf.basedb.plugins.PlateMappingImporter
Always null.
isInContext(GuiContext, Object) - Method in class net.sf.basedb.plugins.PluginConfigurationExporter
 
isInContext(GuiContext, Object) - Method in class net.sf.basedb.plugins.PluginConfigurationImporter
 
isInContext(GuiContext, Object) - Method in class net.sf.basedb.plugins.PrintMapFlatFileImporter
Returns null if the item is a ArrayDesign that doesn't already have any features and isn't an affy design.
isInContext(GuiContext, Object) - Method in class net.sf.basedb.plugins.RawDataFlatFileImporter
Returns null if the item is a RawBioAssay of the correct RawDataType and doesn't already have spots.
isInContext(GuiContext, Object) - Method in class net.sf.basedb.plugins.ReporterFlatFileImporter
Null if the context is Item.REPORTERLIST and the item is a ReporterList.
isInContext(GuiContext, Object) - Method in class net.sf.basedb.plugins.ReporterMapFlatFileImporter
Returns null if the item is a ArrayDesign that doesn't already have any features and is using a supported platform/variant.
isInContext(GuiContext, Object) - Method in class net.sf.basedb.util.zip.AbstractFileUnpacker
 
IsInContextFilter() - Constructor for class net.sf.basedb.util.ContextUtil.IsInContextFilter
 
isInDatabase() - Method in class net.sf.basedb.core.BasicItem
Checks if the item has been saved to the database or not.
isIndexed() - Method in class net.sf.basedb.core.VirtualColumn
If the column is indexed or not.
isInherited(Annotation) - Method in class net.sf.basedb.core.AnnotationSet
Check if an annotation is inherited or not by this annotation set.
isInInsertQueue(String) - Method in class net.sf.basedb.core.ReporterBatcher
 
isInitialised - Static variable in class net.sf.basedb.core.BatchUtil
 
isInitialised - Static variable in class net.sf.basedb.core.Config
 
isInitialised - Static variable in class net.sf.basedb.core.ExtendedProperties
 
isInitialised - Static variable in class net.sf.basedb.core.HibernateUtil
 
isInitialised - Static variable in class net.sf.basedb.core.Keyring
 
isInitialised - Static variable in class net.sf.basedb.core.Metadata
 
isInitialised - Static variable in class net.sf.basedb.core.PredefinedQuery
 
isInitialised - Static variable in class net.sf.basedb.core.QueryRuntimeFilterFactory
 
isInitialised - Static variable in class net.sf.basedb.core.RawDataTypes
 
isInitialised - Static variable in class net.sf.basedb.core.RawDataUtil
 
isInitialised - Static variable in class net.sf.basedb.core.SystemItems
 
isInitialized - Variable in class net.sf.basedb.util.JarClassLoader.JarClassLoaderProxy
 
isInitialized() - Static method in class net.sf.basedb.clients.web.extensions.ExtensionsControl
Is the extension system initialized?
isInRelatedCategory(AnnotationType) - Method in class net.sf.basedb.core.ItemSubtype
Checks if the given annotation type is a member in any category that is related to this subtype.
isInsertable() - Method in class net.sf.basedb.core.ExtendedProperty
Check if the value of this property should be inserted into the datbase when creating new items.
isInstalled() - Method in class net.sf.basedb.util.extensions.manager.ExtensionsFile
Is this file installed into the system or not?
isInstalled() - Method in class net.sf.basedb.util.extensions.xml.PluginInfo
Is this plug-in installed or not?
isInstalledFile(File) - Method in class net.sf.basedb.util.extensions.manager.Settings
Check if the given file is marked as installed.
isInSync(DbControl) - Method in class net.sf.basedb.core.ItemList
Checks if all enabled sync filters appears to be in sync or not.
isInSync(DbControl) - Method in class net.sf.basedb.core.SyncFilter
Checks if the items that are currently matching this filter are the same as the items that matched it during the last sync.
isInteractive() - Method in class net.sf.basedb.core.data.PluginDefinitionData
If the plugin is interactive or not.
isInteractive() - Method in class net.sf.basedb.core.PluginDefinition
Check if the plugin is interactive or not.
isInWell() - Method in class net.sf.basedb.core.MeasuredBioMaterial
Check if this biomaterial is located in a well on a bioplate or not.
isJar - Variable in class net.sf.basedb.util.extensions.manager.ExtensionsFile
 
isJar() - Method in class net.sf.basedb.util.extensions.manager.ExtensionsFile
If the file name ends with '.jar' the file is considered a JAR file.
isJoinedToTransaction() - Method in class net.sf.basedb.core.hibernate.SessionWrapper
 
isLastChild(E) - Method in class net.sf.basedb.util.Tree.Entry
Check if the specified object is the last child to this node.
isLazy() - Method in class net.sf.basedb.clients.web.extensions.list.RelatedItemColumn
Is this column lazy-loaded?
isListening() - Method in class net.sf.basedb.util.jobagent.JobAgentServerConnection
Is a listener active or not for this server.
isListOperator - Variable in enum class net.sf.basedb.core.Operator
 
isListOperator() - Method in enum class net.sf.basedb.core.Operator
Gets if the operator should be used with a list or not.
isLocalHost(InetAddress) - Static method in class net.sf.basedb.util.SocketUtil
Check if the specfied address is the local host or not.
isLocked() - Method in class net.sf.basedb.clients.web.taglib.table.Navigator
 
isLocked() - Method in class net.sf.basedb.core.data.ReporterCloneTemplateData
The template is locked when it is used by a VirtualDbData.
isLocked() - Method in class net.sf.basedb.core.ReporterCloneTemplate
If the template is locked it means that it is used by an experiment and can't be modified or deleted.
isLocked() - Method in class net.sf.basedb.util.Enumeration
 
isLockedColumns() - Method in class net.sf.basedb.util.bfs.DataWriter
Checks if the number of columns has been locked or not.
isLockedInWell() - Method in class net.sf.basedb.core.MeasuredBioMaterial
Check if this biomaterial is placed in a well that it can't be removed from.
isLogarithmic() - Method in class net.sf.basedb.core.Coloring
If we should take the logarithm of values before the color is generated or not.
isLogarithmic() - Method in class net.sf.basedb.core.data.ColoringData
If values should be logarithmised or not.
isLoggable(Object) - Method in class net.sf.basedb.core.log.db.DbLogManagerFactory
 
isLoggable(Object) - Method in interface net.sf.basedb.core.log.LogManagerFactory
Checks if changes to the given entity should be logged or not.
isLoggedIn() - Method in class net.sf.basedb.core.SessionControl
Checks if a user is logged in or not.
isLogging() - Method in class net.sf.basedb.core.plugin.AbstractPlugin
Checks if logging is enabled.
isLoggingDetailedProperties() - Method in class net.sf.basedb.core.log.db.DbLogManagerFactory
Should individual log entries for each changed property be created or not?
isLoggingOldPropertyValues() - Method in class net.sf.basedb.core.log.db.DbLogManagerFactory
Should log entries with old property values be created or not?
isMandatory - Variable in class net.sf.basedb.core.ClonableProperty
 
isMandatory() - Method in class net.sf.basedb.core.ClonableProperty
Check if this property is mandatory in all clone templates.
isMandatory() - Method in class net.sf.basedb.core.data.ReporterClonePropertyData
If the column is a mandatory that must be in all clone templates.
isMasked() - Method in class net.sf.basedb.core.data.ParameterValueData
A flag indicating if the value should be masked when displayed in client applications (eg. since it may be a password) NOTE!
isMasked() - Method in class net.sf.basedb.core.ParameterInfo
Should this parameter be masked in the GUI?
isMasked() - Method in class net.sf.basedb.core.ParameterType
Should this parameter be masked in the GUI?
isMasked() - Method in class net.sf.basedb.core.PasswordParameterType
 
isMember(AnnotationTypeCategory) - Method in class net.sf.basedb.core.AnnotationType
Checks if the annotation type is a member of a category.
isMember(Group) - Method in class net.sf.basedb.core.Group
Checks if a group is a member of this group.
isMember(Listable) - Method in class net.sf.basedb.core.ItemList
Check if the given item is a member of this list.
isMember(User) - Method in class net.sf.basedb.core.Group
Checks if a user is a member of this group.
isMember(User) - Method in class net.sf.basedb.core.Role
Check if the given user is member of this role or not.
isMemberOf(Group) - Method in class net.sf.basedb.core.SessionControl
Check if the logged in user is a member, directly or indirectly, of the specified group.
isMemberOf(Project) - Method in class net.sf.basedb.core.SessionControl
Check if the logged in user is a member, directly or indirectly, of the specified project.
isMemberOf(Role) - Method in class net.sf.basedb.core.SessionControl
Check if the logged in user is a member of the specified role.
isModified() - Method in class net.sf.basedb.core.hibernate.SchemaGenerator.SqlStatement
 
isMultiHop() - Method in class net.sf.basedb.clients.web.extensions.list.RelatedItemColumn.Specification
If the property starts with a '/' it is a multi-hop specification.
isMultiple() - Method in class net.sf.basedb.plugins.executor.ParameterDefinition
Can this parameter have multiple values or only one?
isMultiuserAccount() - Method in class net.sf.basedb.core.data.UserData
Check if this account has enabled the multiuser feature.
isMultiuserAccount() - Method in class net.sf.basedb.core.User
Check if the user account is a multiuser account or not.
isNegationOperator - Variable in enum class net.sf.basedb.core.Operator
 
isNegationOperator() - Method in enum class net.sf.basedb.core.Operator
Negation operators typically need to handle 'null' checks a bit differently.
isNew - Variable in class net.sf.basedb.util.extensions.manager.ExtensionsFile
 
isNew() - Method in class net.sf.basedb.util.extensions.manager.ExtensionsFile
If the file is a new file not previously processed by the extension system.
isNewitem() - Method in class net.sf.basedb.clients.web.taglib.Select
 
isNotFound() - Method in class net.sf.basedb.util.extensions.xml.PluginInfo
Does this plug-in exists on the server or not?
isNotLoggable(String) - Method in class net.sf.basedb.core.log.EntityLogOptions
Check if the method corresponding to the given property name has been annotated with the NotLoggable annotation or not.
isNotPartOf(String, String, ReporterList) - Static method in class net.sf.basedb.core.query.Hql
 
isNotPartOf(ReporterList) - Static method in class net.sf.basedb.core.query.Dynamic
 
isNullable - Variable in class net.sf.basedb.core.dbengine.TableInfo.ColumnInfo
 
isNullable() - Method in class net.sf.basedb.core.data.ReporterClonePropertyData
If the column is nullable or not.
isNullable() - Method in class net.sf.basedb.core.dbengine.TableInfo.ColumnInfo
 
isNullable() - Method in class net.sf.basedb.core.ExtendedProperty
Check if the property allows null values or not.
isNullable() - Method in class net.sf.basedb.core.VirtualColumn
If null values are allowed in the column or not.
isNumerical - Variable in enum class net.sf.basedb.core.Type
 
isNumerical() - Method in enum class net.sf.basedb.core.Type
If the values of this type are numerical values.
isOld() - Method in class net.sf.basedb.core.DiskUsageStatistics.Summary
Check if this summary object is old by comparing it's age to the DiskUsageStatistics.getMaxAge().
isOnlyDirty(String) - Method in class net.sf.basedb.core.log.EntityDetails
Checks if the given property is the only modified property.
isOpen() - Method in class net.sf.basedb.core.hibernate.SessionWrapper
 
isOpen() - Method in class net.sf.basedb.core.hibernate.StatelessSessionWrapper
 
isOperator() - Method in class net.sf.basedb.util.jep.convert.AbstractJepConversionFunction
 
isOperator() - Method in class net.sf.basedb.util.jep.convert.AddConverter
 
isOperator() - Method in class net.sf.basedb.util.jep.convert.AndConverter
 
isOperator() - Method in class net.sf.basedb.util.jep.convert.DivideConverter
 
isOperator() - Method in class net.sf.basedb.util.jep.convert.EqualsConverter
 
isOperator() - Method in class net.sf.basedb.util.jep.convert.GreaterConverter
 
isOperator() - Method in class net.sf.basedb.util.jep.convert.GreaterEqualsConverter
 
isOperator() - Method in interface net.sf.basedb.util.jep.convert.JepConversionFunction
If this converter is a built-in operator.
isOperator() - Method in class net.sf.basedb.util.jep.convert.LessConverter
 
isOperator() - Method in class net.sf.basedb.util.jep.convert.LessEqualsConverter
 
isOperator() - Method in class net.sf.basedb.util.jep.convert.MultiplyConverter
 
isOperator() - Method in class net.sf.basedb.util.jep.convert.NotConverter
 
isOperator() - Method in class net.sf.basedb.util.jep.convert.NotEqualsConverter
 
isOperator() - Method in class net.sf.basedb.util.jep.convert.OrConverter
 
isOperator() - Method in class net.sf.basedb.util.jep.convert.SubtractConverter
 
isOperator() - Method in class net.sf.basedb.util.jep.convert.UMinusConverter
Convert to expression by calling Expressions.negate(Expression).
isOutDated(boolean) - Method in class net.sf.basedb.clients.web.extensions.XJspCompiler
Checks if the extensions JAR file has been modified.
isOverridingDefault() - Method in class net.sf.basedb.core.Annotation
Is this (project-specific) annotation overriding a default value?
isOwner() - Method in interface net.sf.basedb.core.Ownable
Check if the logged in user is the owner of this item or not.
isOwner() - Method in class net.sf.basedb.core.OwnedItem
 
isPackageDefined(String) - Method in class net.sf.basedb.util.JarClassLoader
 
isParameter(Annotation) - Method in class net.sf.basedb.core.Protocol
Check if the annotation is parameter to this protocol.
isParameter(AnnotationType) - Method in class net.sf.basedb.core.Protocol
Check if the annotation type is a parameter to this protocol.
isParticipant(BioPlate) - Method in class net.sf.basedb.core.BioPlateEvent
Check if the given bioplate is a participant of this event.
isPartOf(String, String, ReporterList) - Static method in class net.sf.basedb.core.query.Hql
 
isPartOf(ReporterList) - Static method in class net.sf.basedb.core.query.Dynamic
 
isPaused() - Method in class net.sf.basedb.util.jobagent.JobAgentInfo
If the job agent is paused or running.
isPermanent() - Method in class net.sf.basedb.core.query.QueryParameter
Check if the parameter is a permanent parameter.
isPlateEvent() - Method in class net.sf.basedb.core.BioMaterialEvent
Check if this event is related with a bioplate event.
isPlatform(String) - Method in class net.sf.basedb.core.ArrayDesign
Check if the platform/variant of this array design has the given external ID.
isPlatform(String) - Method in class net.sf.basedb.core.RawBioAssay
Check if the platform/variant of this raw bioassay has the given external ID.
isPlatformFile() - Method in class net.sf.basedb.core.FileSetMember
Checks if this file is part of the platform/variant the parent item belongs to.
isPrimaryKey() - Method in class net.sf.basedb.core.VirtualColumn
If the column is part of the primary key or not.
isProjectSpecific() - Method in class net.sf.basedb.core.Annotation
Is this annotation a project-specific annotation?
isPropertyPathProtected(String) - Method in class net.sf.basedb.core.log.EntityLogOptions
Check if the method corresponding to the given property name has been annotated with the PropertyPathProtected annotation or not.
isProtocolParameter - Variable in class net.sf.basedb.core.data.AnnotationTypeData
 
isProtocolParameter() - Method in class net.sf.basedb.core.AnnotationType
If this annotation type is intended to be used as a protocol parameter or as a regular annotations.
isProtocolParameter() - Method in class net.sf.basedb.core.data.AnnotationTypeData
If this annotation type is intended to be used as a protocol parameter or as a regular annotation.
isProtocolParameter(Protocol) - Method in class net.sf.basedb.core.AnnotationType
Check if this annotation type is a parameter to the specified protocol.
isPublic - Variable in class net.sf.basedb.core.data.ContextData
 
isPublic() - Method in class net.sf.basedb.core.data.ContextData
If the settings are public (ie. can be used by anyone) or not.
isQuotaLimited() - Method in enum class net.sf.basedb.core.Location
A flag indicating if a file that is stored at this location should be included in quota limit.
isRead - Variable in class net.sf.basedb.core.data.MessageData
 
isRead() - Method in class net.sf.basedb.core.data.MessageData
Check if the message has been read or not.
isRead() - Method in class net.sf.basedb.core.Message
Check if the message has been read or not.
isReadonly() - Method in class net.sf.basedb.core.AbstractHqlQuery
 
isReadonly() - Method in class net.sf.basedb.core.AbstractQuery
 
isReadonly() - Method in class net.sf.basedb.core.DynamicRawDataQuery
 
isReadonly() - Method in class net.sf.basedb.core.DynamicReporterQuery
 
isReadonly() - Method in interface net.sf.basedb.core.query.Query
If this query is readonly and cannot be structurally modified.
isReadOnly() - Method in class net.sf.basedb.core.hibernate.QueryWrapper
Deprecated.
isReadOnly(Object) - Method in class net.sf.basedb.core.hibernate.SessionWrapper
 
isRegistrationDelayed() - Method in class net.sf.basedb.util.extensions.manager.processor.IgnoreFileProcessor
Is the actual registration delayed or not?
isRegistrationDelayed() - Method in class net.sf.basedb.util.extensions.manager.processor.RegisterExtensionsProcessor
Is the actual registration delayed or not?
isRelated(DbControl, OverviewContext, Extract, Extract) - Static method in class net.sf.basedb.util.overview.validator.ExtractValidator
Check if two given extracts have a parent-child relationship.
isRemoved() - Method in class net.sf.basedb.core.BioAssaySet
 
isRemoved() - Method in class net.sf.basedb.core.BioPlateEventType
 
isRemoved() - Method in class net.sf.basedb.core.BioPlateType
 
isRemoved() - Method in class net.sf.basedb.core.CommonItem
 
isRemoved() - Method in class net.sf.basedb.core.DataFileType
 
isRemoved() - Method in class net.sf.basedb.core.Directory
 
isRemoved() - Method in class net.sf.basedb.core.ExtraValueType
 
isRemoved() - Method in class net.sf.basedb.core.Group
 
isRemoved() - Method in class net.sf.basedb.core.ItemSubtype
 
isRemoved() - Method in class net.sf.basedb.core.Message
 
isRemoved() - Method in class net.sf.basedb.core.MimeType
 
isRemoved() - Method in class net.sf.basedb.core.News
 
isRemoved() - Method in class net.sf.basedb.core.PlateEventType
 
isRemoved() - Method in class net.sf.basedb.core.PlateGeometry
 
isRemoved() - Method in class net.sf.basedb.core.Platform
 
isRemoved() - Method in class net.sf.basedb.core.PlatformVariant
 
isRemoved() - Method in class net.sf.basedb.core.PluginDefinition
 
isRemoved() - Method in class net.sf.basedb.core.PluginType
 
isRemoved() - Method in class net.sf.basedb.core.Project
 
isRemoved() - Method in class net.sf.basedb.core.Quantity
 
isRemoved() - Method in class net.sf.basedb.core.Quota
 
isRemoved() - Method in interface net.sf.basedb.core.Removable
Check if the removed flag is set for this item.
isRemoved() - Method in class net.sf.basedb.core.ReporterType
 
isRemoved() - Method in class net.sf.basedb.core.Role
 
isRemoved() - Method in class net.sf.basedb.core.Transformation
 
isRemoved() - Method in class net.sf.basedb.core.Unit
 
isRemoved() - Method in class net.sf.basedb.core.User
 
isRemoved() - Method in class net.sf.basedb.plugins.Base1PluginExecuter.JobParameter
 
isReporterField() - Method in class net.sf.basedb.plugins.BaseFileExporterPlugin.ExtendedDynamicField
 
isReporterField() - Method in class net.sf.basedb.plugins.BfsExporterPlugin.ExtendedExportableField
 
isRequired() - Method in class net.sf.basedb.clients.web.taglib.Select
 
isRequired() - Method in class net.sf.basedb.core.data.ItemSubtypeFileTypeData
If a file of this type is required or not.
isRequired() - Method in class net.sf.basedb.core.data.PlatformFileTypeData
If a file of this type is required or not.
isRequired() - Method in class net.sf.basedb.core.ItemSubtypeFileType
Check if a file of this type is required or not.
isRequired() - Method in class net.sf.basedb.core.PlatformFileType
Check if a file of this type is required or not.
isRequired() - Method in interface net.sf.basedb.core.UsableDataFileType
A flag indicating if a file should be required or not.
isRequired() - Method in class net.sf.basedb.plugins.executor.ParameterDefinition
Is this parameter a required parameter or not?
isRequiredForMiame() - Method in class net.sf.basedb.core.AnnotationType
Check an annotation of this annotation type required for an item to be compliant with the MIAME recommendation.
isRequiredForMiame() - Method in class net.sf.basedb.core.data.AnnotationTypeData
If an annotation of this type must be present for an annotatable item to be compliant with MIAME.
isRestrictedEdit() - Method in class net.sf.basedb.core.ExtendedProperty
Check if the value of this property is restricted for editing or not.
isReturningTotalCount() - Method in class net.sf.basedb.core.AbstractQuery
 
isReturningTotalCount() - Method in interface net.sf.basedb.core.query.Query
If this query returns the total count or not.
isRoleInactive(int) - Method in class net.sf.basedb.core.SessionControl
Is the given role inactive or not?
isRolledBack - Variable in class net.sf.basedb.core.DbControl
If the current transaction has been rolled back or not.
isRolledBack() - Method in class net.sf.basedb.core.DbControl
If the transaction was rolled back, either as a call to DbControl.close() or because of an error during DbControl.commit().
isRoot - Variable in class net.sf.basedb.core.data.DerivedBioAssayData
 
isRoot() - Method in class net.sf.basedb.core.data.DerivedBioAssayData
A flag indicating if this is a root derived bioassay or not.
isRoot() - Method in class net.sf.basedb.core.DerivedBioAssay
Check if this bioassay set is derived from one or more physical bioassays or from derived bioassays.
isRootDirectory() - Method in class net.sf.basedb.core.Directory
Returns TRUE if this directories parent equals null and therfore is a root directory.
isRunning - Variable in class net.sf.basedb.clients.jobagent.Agent
 
isRunning - Static variable in class net.sf.basedb.core.Application
If BASE is running or not.
isRunning - Variable in class net.sf.basedb.core.File.CharsetTesterThread
 
isRunning - Variable in class net.sf.basedb.util.timer.PerformanceTimer
 
isRunning() - Method in class net.sf.basedb.clients.jobagent.Agent
Check if the job agent is running or not.
isRunning() - Method in class net.sf.basedb.clients.web.extensions.service.DummyService
 
isRunning() - Method in interface net.sf.basedb.clients.web.extensions.service.ServiceControllerAction
Is the service running or not?
isRunning() - Static method in class net.sf.basedb.core.Application
Check if BASE is running.
isRunning(int) - Method in class net.sf.basedb.util.timer.PerformanceTimer
Check if a timer is running or not.
isSameArrayDesign(ArrayDesign) - Method in class net.sf.basedb.core.RawBioAssay
Checks if the given array design is the same as already set on this raw bioassay.
isSearchingInheritedAnnotations() - Method in class net.sf.basedb.core.snapshot.AnnotationLoaderUtil
Is this loader searching for inherited annotations?
isSearchingPrimaryAnnotations() - Method in class net.sf.basedb.core.snapshot.AnnotationLoaderUtil
Is this loader searching for primary annotations?
isSelectionMode() - Method in class net.sf.basedb.clients.web.ModeInfo
 
isShared() - Method in interface net.sf.basedb.core.Shareable
Check if this item has been shared or not.
isShared() - Method in class net.sf.basedb.core.SharedItem
 
isSkip() - Method in class net.sf.basedb.clients.web.taglib.table.Hidden
 
isSnapshotInvalid() - Method in class net.sf.basedb.core.AnnotationSet
Get the status of the 'invalid snapshot' flag.
isSortable() - Method in class net.sf.basedb.clients.web.extensions.list.AbstractListColumnBean
 
isSortable() - Method in interface net.sf.basedb.clients.web.extensions.list.ListColumnAction
A flag to indicate if sorting by this column is enabled for not.
isSortable() - Method in class net.sf.basedb.clients.web.taglib.table.ColumnDef
 
isSource(BioMaterial) - Method in class net.sf.basedb.core.BioMaterialEvent
Check if the given biomaterial has been used as a source in this event.
isStateless() - Method in class net.sf.basedb.core.AbstractHqlQuery
If queries are using the stateless Hibernate session or the regular session.
isSticky() - Method in class net.sf.basedb.core.data.NewsData
Sticky news should be sorted before non-sticky news regardless of the date.
isSticky() - Method in class net.sf.basedb.core.News
Sticky news items should be sorted before non-sticky ones, but that is up to the client application to implement.
isStoredInDb() - Method in class net.sf.basedb.core.RawDataType
If the raw data of this raw data type can be stored in the database or not.
isStringType() - Method in class net.sf.basedb.core.dbengine.TableInfo.ColumnInfo
 
isSymmetrical() - Method in interface net.sf.basedb.util.encode.EncoderDecoder
 
isSymmetrical() - Method in class net.sf.basedb.util.encode.IdentityEncoderDecoder
 
isSymmetrical() - Method in class net.sf.basedb.util.encode.TabCrLfEncoderDecoder
 
isSymmetrical() - Method in class net.sf.basedb.util.encode.ToSpaceEncoderDecoder
 
isSystemItem() - Method in class net.sf.basedb.core.BioPlateEventType
 
isSystemItem() - Method in class net.sf.basedb.core.Directory
 
isSystemItem() - Method in class net.sf.basedb.core.Group
 
isSystemItem() - Method in class net.sf.basedb.core.ItemSubtype
 
isSystemItem() - Method in class net.sf.basedb.core.Quantity
 
isSystemItem() - Method in class net.sf.basedb.core.Quota
 
isSystemItem() - Method in class net.sf.basedb.core.QuotaType
 
isSystemItem() - Method in class net.sf.basedb.core.Role
 
isSystemItem() - Method in interface net.sf.basedb.core.SystemItem
Check if the item is a system item or not.
isSystemItem() - Method in class net.sf.basedb.core.User
 
isTemporal - Variable in enum class net.sf.basedb.core.Type
 
isTemporal() - Method in enum class net.sf.basedb.core.Type
If the values of this type are date/time related.
isTemporary() - Method in class net.sf.basedb.core.PropertyFilter
Is this filter a temporary filter or not.
isText - Variable in enum class net.sf.basedb.core.Type
 
isText() - Method in enum class net.sf.basedb.core.Type
If the values of this type are text values.
isTraceEnabled() - Method in class net.sf.basedb.util.extensions.logging.ExtensionsLogger
Check if TRACE logging has been enabled or not.
isTransformed - Variable in enum class net.sf.basedb.core.IntensityTransform
If the intensities are transformed or not.
isTransformed() - Method in enum class net.sf.basedb.core.IntensityTransform
Does this intensity transformation represents a transformation that has modified the spot intensity values or not?
isTrulyUnique() - Method in class net.sf.basedb.plugins.batchimport.AnnotationIdMethod
 
isTrulyUnique() - Method in class net.sf.basedb.plugins.batchimport.FallbackIdMethod
 
isTrulyUnique() - Method in class net.sf.basedb.plugins.batchimport.FileImporter.PathIdMethod
 
isTrulyUnique() - Method in interface net.sf.basedb.plugins.batchimport.IdMethod
If the identification method is truly unique or not.
isTrulyUnique() - Method in class net.sf.basedb.plugins.batchimport.InternalIdMethod
 
isTrulyUnique() - Method in class net.sf.basedb.plugins.batchimport.MultiPropertyIdMethod
 
isTrulyUnique() - Method in class net.sf.basedb.plugins.batchimport.PropertyIdMethod
 
isTrusted() - Method in class net.sf.basedb.core.data.JobAgentSettingsData
If the plugin should be trusted or not.
isTrusted() - Method in class net.sf.basedb.core.data.PluginDefinitionData
If the plugin should be trusted or not.
isTrusted() - Method in class net.sf.basedb.core.JobAgentSettings
If the plugin is a trusted plugin or not.
isTrusted() - Method in class net.sf.basedb.core.PluginDefinition
If this plugin is trusted or not.
isUnique - Variable in class net.sf.basedb.core.dbengine.TableInfo.ColumnInfo
 
isUnique - Variable in class net.sf.basedb.core.dbengine.TableInfo.IndexInfo
 
isUnique() - Method in class net.sf.basedb.core.dbengine.TableInfo.ColumnInfo
 
isUnique() - Method in class net.sf.basedb.core.dbengine.TableInfo.IndexInfo
 
isUnique() - Method in class net.sf.basedb.core.VirtualColumn
If the column must contain unique values or not.
isUnique(String) - Method in class net.sf.basedb.util.bfs.AbstractDataWriterFactory
Checks if the suggested file name has already been used by this data writer factory or not.
isUnique(String) - Method in class net.sf.basedb.util.bfs.AbstractFilenameGenerator
Checks if the suggested file name has already been generated by this file name generator or not.
isUnsafeInlineScriptsAllowed() - Static method in class net.sf.basedb.clients.web.servlet.ContentSecurityPolicyFilter
Checks if the current policy allows 'unsafe-inline' for the 'script-src' attribute.
isUpdateable() - Method in class net.sf.basedb.core.ExtendedProperty
Check if the value of this property should be updated in the database when an item is updated.
isUpToDate() - Method in class net.sf.basedb.core.snapshot.AnnotationSnapshot
A primary or inherited annotation is always up-to-date.
isUsableUnit(Unit) - Method in class net.sf.basedb.core.AnnotationType
Checks if the given unit is a unit that has been specified as a "usable" unit for this annotation type.
isUsed() - Method in class net.sf.basedb.core.AnnotationSet
Always return TRUE.
isUsed() - Method in class net.sf.basedb.core.AnnotationType
Checks if: Annotations of this type exists Experiments are using this annotation type as an experimental factor Protocols are using this annotation type as a protocol parameter
isUsed() - Method in class net.sf.basedb.core.AnyToAny
Always FALSE.
isUsed() - Method in class net.sf.basedb.core.ArrayBatch
 
isUsed() - Method in class net.sf.basedb.core.ArrayDesign
 
isUsed() - Method in class net.sf.basedb.core.ArrayDesignBlock
Array design blocks are always used by an array design.
isUsed() - Method in class net.sf.basedb.core.ArrayDesignPlate
Always TRUE.
isUsed() - Method in class net.sf.basedb.core.ArraySlide
 
isUsed() - Method in class net.sf.basedb.core.BasicItem
Check if this item is used by some other item.
isUsed() - Method in class net.sf.basedb.core.BioPlate
Check if there are any MeasuredBioMaterial on this plate.
isUsed() - Method in class net.sf.basedb.core.BioPlateEventType
Check if there are any BioPlateEvents using this type.
isUsed() - Method in class net.sf.basedb.core.BioPlateType
Check if there are any BioPlates or BioPlateEventDefinitions using this type.
isUsed() - Method in class net.sf.basedb.core.BioSource
Check that: no Sample has been created from this biosource
isUsed() - Method in class net.sf.basedb.core.BioWell
Check if a MeasuredBioMaterial is linked to this bio-well
isUsed() - Method in class net.sf.basedb.core.DataFileType
Check if: A file has been tagged with this type in a file set A platform is using this file type
isUsed() - Method in class net.sf.basedb.core.DerivedBioAssay
 
isUsed() - Method in class net.sf.basedb.core.Directory
Check that: no files are in the directory no subdirectories are in the directory no user has this directory as the home directory
isUsed() - Method in class net.sf.basedb.core.DiskUsage
 
isUsed() - Method in class net.sf.basedb.core.Extract
Check that: no PhysicalBioAssay:s has been created from this item no Extract:s has been created from this item no DerivedBioAssay is referencing this item no RawBioAssay is referencing this item
isUsed() - Method in class net.sf.basedb.core.ExtraValueType
Check if: Any ExtraValue:s of this type exists
isUsed() - Method in class net.sf.basedb.core.File
Checks if: A FileAttachable item is using this key.
isUsed() - Method in class net.sf.basedb.core.FileServer
Checks if there are files registered with this server.
isUsed() - Method in class net.sf.basedb.core.FileSet
Always return TRUE.
isUsed() - Method in class net.sf.basedb.core.Group
Checks if: A user has been assigned this group as a quota group There are also other items that can reference a group: DiscUsage Other groups ItemKeys Projects Users (as group members) The links to all these items are automatically deleted if the group is deleted and aren't included in this check.
isUsed() - Method in class net.sf.basedb.core.Hardware
Check if: a DerivedBioAssay is linked to this hardware an ArrayBatch is linked to this hardware a BioMaterialEvent is linked to this hardware a PlateEvent is linked to this hardware
isUsed() - Method in class net.sf.basedb.core.ItemKey
Checks if: A Shareable item is using this key.
isUsed() - Method in class net.sf.basedb.core.ItemSubtype
Checks if: any Subtypable item is using this subtype.
isUsed() - Method in class net.sf.basedb.core.Job
Return TRUE if the status is EXECUTING or: a transformation is linked to this job a raw bioassay is linked to this job an array design is linked to this job FALSE otherwise.
isUsed() - Method in class net.sf.basedb.core.Kit
Check if: a BioMaterialEvent is linked to this kit a BioPlateEvent is linked to this kit
isUsed() - Method in class net.sf.basedb.core.MeasuredBioMaterial
Check that: no pooled biomaterial has been created from this item
isUsed() - Method in class net.sf.basedb.core.PermissionTemplate
Check if: A Project uses this template
isUsed() - Method in class net.sf.basedb.core.PhysicalBioAssay
Check that: No DerivedBioAssay:s use the physical bioassay
isUsed() - Method in class net.sf.basedb.core.Plate
Check if: another Plate has been created from this one (via a PlateMapping) any ArrayDesign:s are using this plate Wells are deleted automatically.
isUsed() - Method in class net.sf.basedb.core.PlateEventType
Check if: A PlateEvent of this type exists
isUsed() - Method in class net.sf.basedb.core.PlateGeometry
Check if: A PlateType with this geometry exists A PlateMapping to/from this geometry exists A BioPlate that uses this geometry exists
isUsed() - Method in class net.sf.basedb.core.PlateMapping
Check if: A Plate has been created from this mapping
isUsed() - Method in class net.sf.basedb.core.PlateType
Check if: Any Plate:s of this type exists
isUsed() - Method in class net.sf.basedb.core.Platform
Check if: any raw bioassays or array design are using this platform
isUsed() - Method in class net.sf.basedb.core.PlatformVariant
Check if: any raw bioassays or array design are using this platform variant
isUsed() - Method in class net.sf.basedb.core.PluginConfiguration
Check if: A Job is using this plugin configuration
isUsed() - Method in class net.sf.basedb.core.PluginDefinition
Check if a PluginConfiguration is using this definition.
isUsed() - Method in class net.sf.basedb.core.ProjectKey
Checks if: A Shareable item is using this key.
isUsed() - Method in class net.sf.basedb.core.Protocol
Check if this protocol is used by: a BioMaterialEvent a PlateEvent an ArrayBatch a DerivedBioAssay a RawBioAssay
isUsed() - Method in class net.sf.basedb.core.Quantity
Check if: Units for this quantity exists.
isUsed() - Method in class net.sf.basedb.core.Quota
Checks if: a Group has been assigned this quota a User has been assigned this quota
isUsed() - Method in class net.sf.basedb.core.QuotaType
 
isUsed() - Method in class net.sf.basedb.core.RawBioAssay
Check if: An Experiment is using this raw bioassay A Transformation is using this raw bio raw data type will also be updated.
isUsed() - Method in class net.sf.basedb.core.ReporterCloneTemplate
Check if: An experiment/virtualdb is using this template
isUsed() - Method in class net.sf.basedb.core.ReporterType
Check if any reporters of this type exists.
isUsed() - Method in class net.sf.basedb.core.RoleKey
Always return TRUE.
isUsed() - Method in class net.sf.basedb.core.Sample
Check that: no Extract:s has been created from this item no Sample:s has been created from this item
isUsed() - Method in class net.sf.basedb.core.Software
Check if: a RawBioAssay was created with this software a DerivedBioassay was created with this software
isUsed() - Method in class net.sf.basedb.core.Tag
Check if: Some Extract:s are marked with this tag
isUsed() - Method in class net.sf.basedb.core.Unit
Check if: Annotation types are using this unit as default unit Annotations are using this unit
isUsed() - Method in class net.sf.basedb.core.User
Checks if: any Ownable item is owned by this user A user can also be referenced from groups, roles, projects, item keys, sessions and settings, but those references are automatically deleted if the user is deleted and aren't inclued in this check.
isUsed() - Method in class net.sf.basedb.core.Well
Check if: a Feature is linked to this well another Well has this well as it's parent well
isUsedByOther(PhysicalBioAssay) - Method in class net.sf.basedb.core.ArraySlide
Checks if this array slide is used by a different bioassay than the given one.
isUsedKey(String) - Method in class net.sf.basedb.util.bfs.MetadataWriter
Checks if the current section already has an entry for the given key or not.
isUsing(RawBioAssay) - Method in class net.sf.basedb.core.Experiment
Check if a raw bioassay is used in this experiment.
isUsingColors() - Method in class net.sf.basedb.core.Coloring
If this item should be colored or not.
isUsingColors() - Method in class net.sf.basedb.core.data.ColoringData
If colors should be used or not.
isUsingNonRemovableItem(Set<ItemProxy>) - Method in class net.sf.basedb.core.Trashcan.CircularRefInfo
Check if all using items of the main items is found among the 'itemsToRemove'.
isUsingTo() - Method in class net.sf.basedb.core.AnyToAny
If this link counts as using the destination item.
isUsingTo() - Method in class net.sf.basedb.core.data.AnyToAnyData
If the link counts as using the item we are linking to.
isValid - Variable in class net.sf.basedb.util.extensions.manager.ExtensionsFile
 
isValid - Variable in class net.sf.basedb.util.fileset.ValidationRenderer
 
isValid() - Method in class net.sf.basedb.core.data.FileSetMemberData
If the file has been validated or not.
isValid() - Method in class net.sf.basedb.core.FileSetMember
Check if the file has been validated and if it passed or not.
isValid() - Method in class net.sf.basedb.util.extensions.manager.ExtensionsFile
Is the file a valid extensions file according to the last performed validation.
isValidColumnName(String) - Method in class net.sf.basedb.core.dbengine.AbstractDbEngine
Checks that the name only contains the following characters: a-zA-Z0-9_ It must also start with a letter or underscore.
isValidColumnName(String) - Method in interface net.sf.basedb.core.dbengine.DbEngine
Check if a given string is valid to be used as a column name in the current database.
isValidEmail(String) - Static method in class net.sf.basedb.clients.web.util.HTML
Checks if the given string looks like an email address.
isValidEmail(String) - Static method in class net.sf.basedb.util.EmailUtil
Checks if the given string looks like an email address.
isValidKey(String) - Static method in class net.sf.basedb.util.StaticCache
Checks if the given key is a vilid cache entry key.
isValidName(String) - Method in class net.sf.basedb.core.dbengine.AbstractDbEngine
Check that the name only contains a-zA-Z0-9_ and starts with a letter or underscore.
isValidName(String) - Static method in class net.sf.basedb.core.ExtendedProperty
Check that the name only contains a-zA-Z0-9_ and starts with a letter or underscore.
isValidName(String) - Static method in class net.sf.basedb.core.Path
Check if a name is valid as a partial path name, ie. it must not contain any of the characters in Path.INVALID_CHARACTERS.
isValidSoFar - Variable in class net.sf.basedb.util.fileset.ValidatingFileSetMember
 
isValidSoFar() - Method in class net.sf.basedb.util.fileset.ValidatingFileSetMember
Is the member considered valid so far in the validation process?
isValidTableName(String) - Method in class net.sf.basedb.core.dbengine.AbstractDbEngine
Checks that the name only contains the following characters: a-zA-Z0-9_ It must also start with a letter or underscore.
isValidTableName(String) - Method in interface net.sf.basedb.core.dbengine.DbEngine
Check if a given string is valid to be used as a table name in the current database.
isValidUrl(String) - Static method in class net.sf.basedb.clients.web.util.HTML
Checks if the given string looks like an URL.
isVerbose - Variable in class net.sf.basedb.core.hibernate.DbIndexWork
 
isVerified - Variable in class net.sf.basedb.core.data.UserDeviceData
 
isVerified() - Method in class net.sf.basedb.core.data.UserDeviceData
This flag is TRUE if the device has been verified (by sending a code via email).
isVerified() - Method in class net.sf.basedb.core.UserDevice
Has this device been verified or not?
isVerifyOnly() - Method in class net.sf.basedb.core.authentication.LoginRequest
If this flag is set, the login parameters are only verified and the actual login is aborted.
isVertical() - Method in class net.sf.basedb.clients.web.taglib.menu.Menu
 
isVisible() - Method in class net.sf.basedb.clients.web.extensions.menu.FixedMenuItemFactory
 
isVisible() - Method in interface net.sf.basedb.clients.web.extensions.menu.MenuItemAction
If the menu item should be visible or not.
isVisible() - Method in class net.sf.basedb.clients.web.extensions.menu.MenuItemBean
 
isVisible() - Method in class net.sf.basedb.clients.web.extensions.tabcontrol.FixedTabFactory
 
isVisible() - Method in class net.sf.basedb.clients.web.extensions.tabcontrol.IncludeContentTabFactory.Tab
 
isVisible() - Method in interface net.sf.basedb.clients.web.extensions.tabcontrol.TabAction
If the tab should be visible or not.
isVisible() - Method in class net.sf.basedb.clients.web.extensions.tabcontrol.TabBean
 
isVisible() - Method in interface net.sf.basedb.clients.web.extensions.toolbar.ButtonAction
If the button should be visible or not.
isVisible() - Method in class net.sf.basedb.clients.web.extensions.toolbar.ButtonBean
 
isVisible() - Method in class net.sf.basedb.clients.web.extensions.toolbar.FixedButtonFactory
 
isVisible() - Method in class net.sf.basedb.clients.web.taglib.Button
 
isVisible() - Method in class net.sf.basedb.clients.web.taglib.Help
 
isVisible() - Method in class net.sf.basedb.clients.web.taglib.HideableSection
 
isVisible() - Method in class net.sf.basedb.clients.web.taglib.Icon
 
isVisible() - Method in class net.sf.basedb.clients.web.taglib.Input
 
isVisible() - Method in class net.sf.basedb.clients.web.taglib.menu.Menuitem
 
isVisible() - Method in class net.sf.basedb.clients.web.taglib.menu.Menuseparator
 
isVisible() - Method in class net.sf.basedb.clients.web.taglib.menu.Submenu
 
isVisible() - Method in class net.sf.basedb.clients.web.taglib.path.PathElement
 
isVisible() - Method in class net.sf.basedb.clients.web.taglib.Select
 
isVisible() - Method in class net.sf.basedb.clients.web.taglib.tab.Tab
 
isVisible() - Method in class net.sf.basedb.clients.web.taglib.table.Button.ButtonActionWrapper
 
isVisible() - Method in class net.sf.basedb.clients.web.taglib.table.Button
 
isVisible() - Method in class net.sf.basedb.clients.web.taglib.table.Cell
 
isVisible() - Method in class net.sf.basedb.clients.web.taglib.table.Header
 
isVisible() - Method in class net.sf.basedb.clients.web.taglib.table.Label
 
isVisible() - Method in class net.sf.basedb.clients.web.taglib.table.Navigator
 
isVisible() - Method in class net.sf.basedb.clients.web.taglib.table.Panel
 
isVisible() - Method in class net.sf.basedb.clients.web.taglib.table.PresetSelector
 
isVisible() - Method in class net.sf.basedb.clients.web.taglib.table.Row
 
isVisible() - Method in class net.sf.basedb.clients.web.taglib.table.Toolbar
 
isVisible() - Method in class net.sf.basedb.clients.web.taglib.Zoom
 
isWriteProtected() - Method in class net.sf.basedb.core.data.FileData
If the actual file contents should be write protected or not.
isWriteProtected() - Method in class net.sf.basedb.core.File
Check if the file data is write protected.
isWriteProtected() - Method in class net.sf.basedb.core.ParameterValuesImpl
 
isWritingData() - Method in class net.sf.basedb.util.basefile.BaseFileWriter
 
isWritingHeaders() - Method in class net.sf.basedb.util.basefile.BaseFileWriter
 
isXJsp - Variable in class net.sf.basedb.clients.web.extensions.XJspCompiler
 
it - Variable in class net.sf.basedb.core.FastAnnotationLoader.FastIterator
 
item - Variable in class net.sf.basedb.clients.web.taglib.extensions.Render
 
item - Variable in class net.sf.basedb.clients.web.taglib.PropertyValue
The item.
item - Variable in class net.sf.basedb.clients.web.taglib.SubtypeSelector
 
item - Variable in class net.sf.basedb.clients.web.taglib.table.ExtensionCells
 
item - Variable in class net.sf.basedb.core.AnnotationSet
The item this annotation set belongs to.
item - Variable in class net.sf.basedb.core.Coloring
 
item - Variable in class net.sf.basedb.core.ContextKey
 
item - Variable in class net.sf.basedb.core.DbControl.SaveIf
 
item - Variable in class net.sf.basedb.core.DiskUsage
The item this diks usage information belongs to.
item - Variable in class net.sf.basedb.core.FileSet
The item this file set belongs to.
item - Variable in class net.sf.basedb.core.log.ManualLogEntry
 
item - Variable in class net.sf.basedb.core.plugin.GuiContext
 
item - Variable in class net.sf.basedb.core.query.HqlEntityExpression
 
item - Variable in class net.sf.basedb.core.SessionControl.MainContext
 
item - Variable in class net.sf.basedb.core.Trashcan.CircularRefInfo
 
item - Variable in class net.sf.basedb.plugins.AnnotationFlatFileImporter.NewAnnotations
 
item - Variable in class net.sf.basedb.util.AnnotationUtil.AnnotatableWrapper
 
item - Variable in class net.sf.basedb.util.extensions.ClientContext
 
item - Variable in class net.sf.basedb.util.overview.filter.BasicItemFilter
 
item - Variable in class net.sf.basedb.util.overview.Fix
 
item - Variable in class net.sf.basedb.util.overview.Node
 
item() - Method in class net.sf.basedb.core.SessionControl.MainContext
Get the item of this main context.
item(DbControl, Item, int) - Method in class net.sf.basedb.util.formatter.PropertyFilterFormatter
 
item(Item) - Static method in class net.sf.basedb.core.plugin.GuiContext
Shortcut to create a single-item context.
item(Item, String) - Static method in class net.sf.basedb.core.plugin.GuiContext
Shortcut to create a single-item context with a subcontext.
Item - Enum Class in net.sf.basedb.core
This class defines constants for various items in BASE.
Item(int, String, String, Class<? extends BasicItem>, Class<? extends BasicData>, Set<Permission>, float) - Constructor for enum class net.sf.basedb.core.Item
 
ITEM - Enum constant in enum class net.sf.basedb.core.plugin.GuiContext.Type
 
ITEM - Enum constant in enum class net.sf.basedb.util.overview.Node.Type
 
ITEM - Static variable in class net.sf.basedb.clients.web.extensions.toolbar.ToolbarUtil
 
Item.DefinedPermissions - Class in net.sf.basedb.core
Helper class to make it easier to set up the defined permissions.
ItemAlreadyExistsException - Exception in net.sf.basedb.core
This exception is thrown when trying to save an object and another object with the same ID already exists.
ItemAlreadyExistsException(String) - Constructor for exception net.sf.basedb.core.ItemAlreadyExistsException
Creates a new ItemAlreadyExistsException.
itemCache - Variable in class net.sf.basedb.core.DbControl
A cache of already loaded items.
itemCache - Variable in class net.sf.basedb.plugins.AnnotationFlatFileImporter
 
itemCache - Variable in class net.sf.basedb.plugins.batchimport.AbstractItemImporter
Cache that holds loaded/created items.
itemCache - Variable in class net.sf.basedb.util.parser.DefaultItemFunction
 
itemClass - Variable in enum class net.sf.basedb.core.Item
 
itemClass - Variable in class net.sf.basedb.core.ItemQuery
The class of the item objects that are returned.
itemClass - Variable in class net.sf.basedb.core.ItemResultIterator
The class of the items returned by the query (and this object).
itemClass - Variable in class net.sf.basedb.core.ItemResultList
The class of the items returned by the query (and this object).
itemClass - Variable in class net.sf.basedb.core.ItemResultList.ResultListIterator
 
itemClass - Variable in class net.sf.basedb.core.ItemResultList.ResultListListIterator
 
itemClassMapping - Static variable in enum class net.sf.basedb.core.Item
 
itemContext - Variable in class net.sf.basedb.clients.web.extensions.JspContext
 
ItemContext - Class in net.sf.basedb.core
This item is a helper class for client applications when they need to store information about the current context for plugins that needs to find out the current context of the running client application.
ItemContext(String, ItemContext.SortDirection, int, int) - Constructor for class net.sf.basedb.core.ItemContext
Create a new context.
ItemContext(ContextData) - Constructor for class net.sf.basedb.core.ItemContext
Create a new context from a loaded database object.
ItemContext(Item, String, String) - Constructor for class net.sf.basedb.core.ItemContext
Create a new empty context.
ItemContext(Item, ItemListSyncFilterData) - Constructor for class net.sf.basedb.core.ItemContext
Initialize the context from an item list synchronization filter.
ItemContext(Item, PropertyFilter...) - Constructor for class net.sf.basedb.core.ItemContext
Initialize the context with the special purpose of configuring a query with the given filters.
ItemContext.AddFilter - Enum Class in net.sf.basedb.core
ItemContext.PropertyFilterPair - Class in net.sf.basedb.core
Holds a pair of filter.
ItemContext.QueryRestrictions - Class in net.sf.basedb.core
 
ItemContext.RowRestrictions - Class in net.sf.basedb.core
 
ItemContext.SortDirection - Enum Class in net.sf.basedb.core
Enumeration used to specify the sort direction.
itemElement - Variable in class net.sf.basedb.clients.web.plugins.XMLTemplate
 
itemExistsErrorParameter - Static variable in class net.sf.basedb.plugins.batchimport.AbstractItemImporter
 
itemId - Variable in class net.sf.basedb.core.AnnotationBatcher.CurrentAnnotationInfo
 
itemId - Variable in class net.sf.basedb.core.data.AnnotationSetData
 
itemId - Variable in class net.sf.basedb.core.data.ChangeHistoryDetailData
 
itemId - Variable in class net.sf.basedb.core.data.ContextData
 
itemId - Variable in class net.sf.basedb.core.FastAnnotationLoader.FastAnnotation
The ID of the item the annotation belongs to.
itemId - Variable in class net.sf.basedb.core.ItemContext
 
itemId - Variable in class net.sf.basedb.core.snapshot.AnnotationSetSnapshot
 
itemId - Variable in class net.sf.basedb.core.snapshot.AnnotationSnapshot
 
itemIdPrefix - Variable in class net.sf.basedb.clients.web.plugins.XMLTemplate
 
itemIds - Variable in class net.sf.basedb.core.FastAnnotationLoader.FastIterator
 
ItemInUseException - Exception in net.sf.basedb.core
This exception is thrown when trying delete an item that is used (reference to) by some other item or items.
ItemInUseException(String) - Constructor for exception net.sf.basedb.core.ItemInUseException
Creates a new ItemInUseException.
ItemInUseException(String, Throwable) - Constructor for exception net.sf.basedb.core.ItemInUseException
Creates a new ItemInUseException with a cause.
itemIsMissing(DbControl, Item, Integer) - Method in class net.sf.basedb.core.MigrateRbaToDba.LineMapping
 
itemKey - Variable in class net.sf.basedb.core.data.SharedData
 
ItemKey - Class in net.sf.basedb.core
This class is used to get information about which users and groups a Shareable item has been shared to.
ItemKey(ItemKeyData) - Constructor for class net.sf.basedb.core.ItemKey
 
ITEMKEY - Enum constant in enum class net.sf.basedb.core.Item
The item is an ItemKey.
ItemKeyData - Class in net.sf.basedb.core.data
This class holds information access privileges for users and groups.
ItemKeyData() - Constructor for class net.sf.basedb.core.data.ItemKeyData
 
itemKeyId - Variable in class net.sf.basedb.core.MigrateRbaToDba.Rba
 
itemKeyId - Variable in class net.sf.basedb.core.SessionControl.LoginInfo
The id of the ItemKeyData object that new items should be shared to.
itemKeys - Variable in class net.sf.basedb.core.data.GroupData
 
itemKeys - Variable in class net.sf.basedb.core.data.UserData
 
itemKeys - Variable in class net.sf.basedb.core.Keyring
A set holding all item keys, which is needed for efficient listing of shared items.
itemKeySet - Variable in class net.sf.basedb.core.SharedItem
 
itemList - Variable in class net.sf.basedb.core.data.ItemListSyncFilterData
 
itemList - Variable in class net.sf.basedb.plugins.AnnotationFlatFileImporter
 
itemList - Variable in class net.sf.basedb.plugins.batchimport.AbstractItemImporter
 
itemList - Variable in class net.sf.basedb.plugins.batchimport.AnyToAnyImporter
 
Itemlist(Object[]) - Constructor for class net.sf.basedb.core.MigrateRbaToDba.Itemlist
 
ItemList - Class in net.sf.basedb.core
This class represents a list of items.
ItemList(ItemListData) - Constructor for class net.sf.basedb.core.ItemList
 
ITEMLIST - Enum constant in enum class net.sf.basedb.core.Item
The item is an ItemList
ItemList.DelayedAdditionManager - Class in net.sf.basedb.core
Handles items that should be added as members to the list, but since they were created in the same transaction doesn't have any ID until later in the commit phase.
ItemList.SynchronizeOption - Enum Class in net.sf.basedb.core
Options for synchronizing an existing item list with a current settings in an ItemContext.
ItemListData - Class in net.sf.basedb.core.data
This represents an arbitrary collection of items.
ItemListData() - Constructor for class net.sf.basedb.core.data.ItemListData
 
ItemListLoader - Class in net.sf.basedb.util.overview.loader
Node loader implementation for item lists.
ItemListLoader() - Constructor for class net.sf.basedb.util.overview.loader.ItemListLoader
 
ItemListMemberNameGenerator - Class in net.sf.basedb.util.overview.node
Name generator used for item list members.
ItemListMemberNameGenerator() - Constructor for class net.sf.basedb.util.overview.node.ItemListMemberNameGenerator
 
ItemListSyncFilterData - Class in net.sf.basedb.core.data
Synchronization options for item lists.
ItemListSyncFilterData() - Constructor for class net.sf.basedb.core.data.ItemListSyncFilterData
 
itemMapper - Variable in class net.sf.basedb.plugins.AnnotationFlatFileImporter
 
ItemModifiedException - Exception in net.sf.basedb.core
This exception is thrown when trying to save an item to the database that has been updated (or deleted) by another process in the meantime.
ItemModifiedException(String) - Constructor for exception net.sf.basedb.core.ItemModifiedException
Creates a new ItemModifiedException.
ItemModifiedException(StaleStateException) - Constructor for exception net.sf.basedb.core.ItemModifiedException
Create a new ItemModifiedException trying to find the item information from the Hibernate exception.
itemNotFoundErrorParameter - Static variable in class net.sf.basedb.plugins.AnnotationFlatFileImporter
 
itemNotFoundErrorParameter - Static variable in class net.sf.basedb.plugins.batchimport.AbstractItemImporter
 
itemNotFoundErrorParameter - Static variable in class net.sf.basedb.plugins.batchimport.AnyToAnyImporter
 
ItemNotFoundException - Exception in net.sf.basedb.core
This exception is thrown when trying to load an item from the database that does not exist.
ItemNotFoundException(String) - Constructor for exception net.sf.basedb.core.ItemNotFoundException
Creates a new ItemNotFoundException.
ItemNotFoundException(String, Throwable) - Constructor for exception net.sf.basedb.core.ItemNotFoundException
Creates a new ItemNotFoundException.
ItemParameterType<T extends BasicItem> - Class in net.sf.basedb.core
This class represent a parameter type that is an object derived from BasicData.
ItemParameterType(Class<T>, List<T>) - Constructor for class net.sf.basedb.core.ItemParameterType
Create a new item parameter type, allowing null values.
ItemParameterType(Class<T>, T, boolean, int, List<T>) - Constructor for class net.sf.basedb.core.ItemParameterType
 
ItemParameterValueData - Class in net.sf.basedb.core.data
Item parameter value.
ItemParameterValueData() - Constructor for class net.sf.basedb.core.data.ItemParameterValueData
 
ItemParameterValueData(BasicData...) - Constructor for class net.sf.basedb.core.data.ItemParameterValueData
 
itemPermissions - Variable in class net.sf.basedb.core.Keyring
Two-dimensional array for holding the permissions for ItemKey:s.
ItemProxy - Class in net.sf.basedb.core
 
ItemProxy(int, Item) - Constructor for class net.sf.basedb.core.ItemProxy
 
itemQuery - Variable in class net.sf.basedb.plugins.AnnotationFlatFileImporter
 
itemQuery - Variable in class net.sf.basedb.plugins.batchimport.AbstractItemImporter
 
itemQuery - Variable in class net.sf.basedb.plugins.batchimport.AnyToAnyImporter
 
ItemQuery<I extends BasicItem> - Class in net.sf.basedb.core
An implementation of the Query interface that returns item objects.
ItemQuery(Class<I>) - Constructor for class net.sf.basedb.core.ItemQuery
Create a new query for the specified item, using the default optional runtime filter.
ItemQuery(Class<I>, QueryRuntimeFilter) - Constructor for class net.sf.basedb.core.ItemQuery
Create a new query for the specified item, using a non-default optional runtime filter.
ItemQueryLoader<T extends BasicItem> - Class in net.sf.basedb.clients.web.plugins
A class that uses a given query to load data.
ItemQueryLoader(ItemQuery<?>, String) - Constructor for class net.sf.basedb.clients.web.plugins.ItemQueryLoader
 
ItemQueryWrapper - Class in net.sf.basedb.clients.web.plugins
A query wrapper for ItemQuery:s.
ItemQueryWrapper(ItemQuery<BasicItem>) - Constructor for class net.sf.basedb.clients.web.plugins.ItemQueryWrapper
Create a new query wrapper.
ItemResultIterator<I extends BasicItem> - Class in net.sf.basedb.core
Return the results of an ItemQuery as an iterator.
ItemResultIterator(ScrollIterator<? extends BasicData>, DbControl, Class<I>, long) - Constructor for class net.sf.basedb.core.ItemResultIterator
 
ItemResultList<I extends BasicItem> - Class in net.sf.basedb.core
Return the results of an ItemQuery as a list.
ItemResultList(List<? extends BasicData>, DbControl, Class<I>, long) - Constructor for class net.sf.basedb.core.ItemResultList
 
ItemResultList.ResultListIterator<T extends BasicItem> - Class in net.sf.basedb.core
Inner class to implement the iterator returned by the ItemResultList.iterator() method.
ItemResultList.ResultListListIterator<T extends BasicItem> - Class in net.sf.basedb.core
Inner class to implement the iterator returned by the ItemResultList.listIterator() method.
items - Variable in class net.sf.basedb.clients.web.extensions.list.RelatedItemHelper
 
items - Variable in class net.sf.basedb.core.MultiPermissions
 
items - Variable in class net.sf.basedb.core.ParameterType
List of allowed values.
items - Variable in class net.sf.basedb.util.annotations.RunnableInheritAnnotationsManager
 
ItemSubtype - Class in net.sf.basedb.core
Item subtypes can be used to classify items into sub-categories.
ItemSubtype(ItemSubtypeData) - Constructor for class net.sf.basedb.core.ItemSubtype
 
ITEMSUBTYPE - Enum constant in enum class net.sf.basedb.core.Item
The item is a ItemSubtype.
ItemSubtypeData - Class in net.sf.basedb.core.data
Item subtypes can be used to classify items into sub-categories.
ItemSubtypeData() - Constructor for class net.sf.basedb.core.data.ItemSubtypeData
 
ItemSubtypeFileType - Class in net.sf.basedb.core
This class represents a specific DataFileType that is associated with an item subtype.
ItemSubtypeFileType(ItemSubtypeFileTypeData) - Constructor for class net.sf.basedb.core.ItemSubtypeFileType
Creates a new member item from the given data.
ITEMSUBTYPEFILETYPE - Enum constant in enum class net.sf.basedb.core.Item
The item is a ItemSubtypeFileType
ItemSubtypeFileTypeData - Class in net.sf.basedb.core.data
This class hols information about which file types can be used together with item subtypes.
ItemSubtypeFileTypeData() - Constructor for class net.sf.basedb.core.data.ItemSubtypeFileTypeData
 
ItemSubtypeFT(ItemSubtypeData, boolean, boolean) - Constructor for class net.sf.basedb.core.Install.ItemSubtypeFT
 
itemSubtypes - Variable in class net.sf.basedb.core.data.DataFileTypeData
 
itemToCheck - Variable in class net.sf.basedb.clients.web.extensions.menu.PermissionMenuItemFactory
 
itemToCheck - Variable in class net.sf.basedb.clients.web.extensions.toolbar.PermissionButtonFactory
 
itemType - Variable in class net.sf.basedb.clients.web.extensions.list.SubtypeFilter
 
itemType - Variable in class net.sf.basedb.clients.web.plugins.XMLTemplate
 
itemType - Variable in class net.sf.basedb.clients.web.taglib.SubtypeSelector
 
itemType - Variable in class net.sf.basedb.clients.web.taglib.table.Table
 
itemType - Variable in class net.sf.basedb.core.AnnotationBatcher.CurrentAnnotationInfo
 
itemType - Variable in class net.sf.basedb.core.AnnotationBatcher
 
itemType - Variable in class net.sf.basedb.core.data.AnnotationSetData
 
itemType - Variable in class net.sf.basedb.core.data.ChangeHistoryDetailData
 
itemType - Variable in class net.sf.basedb.core.data.ContextData
 
itemType - Variable in class net.sf.basedb.core.data.ContextIndex
 
itemType - Variable in class net.sf.basedb.core.data.DataFileTypeData
 
itemType - Variable in class net.sf.basedb.core.data.DiskUsageData
 
itemType - Variable in class net.sf.basedb.core.data.FileSetData
 
itemType - Variable in class net.sf.basedb.core.data.GuiContextData
 
itemType - Variable in class net.sf.basedb.core.data.ItemSubtypeData
 
itemType - Variable in class net.sf.basedb.core.data.RoleKeyData
 
itemType - Variable in class net.sf.basedb.core.DataResultIterator
The type of items returned by the query.
itemType - Variable in class net.sf.basedb.core.HibernateUtil.DelayedFilterDef
 
itemType - Variable in class net.sf.basedb.core.ItemContext
 
itemType - Variable in class net.sf.basedb.core.ItemResultIterator
The type of items returned by the query.
itemType - Variable in class net.sf.basedb.core.ItemResultList
The type of items returned by the query.
itemType - Variable in class net.sf.basedb.core.Metadata.BasicData2ItemPropertyPath
 
itemType - Variable in class net.sf.basedb.core.plugin.Permissions
 
itemType - Variable in class net.sf.basedb.core.query.HqlEntityParameterExpression
 
itemType - Variable in class net.sf.basedb.core.query.PermissionRestriction
 
itemType - Variable in class net.sf.basedb.core.query.QueryParameter
 
itemType - Variable in class net.sf.basedb.core.QueryRuntimeFilterManager
 
itemType - Variable in class net.sf.basedb.core.ReporterScoreResultIterator
The type of items returned by the query.
itemType - Variable in class net.sf.basedb.core.snapshot.AnnotationSetSnapshot
 
itemType - Variable in class net.sf.basedb.core.snapshot.AnnotationSnapshot
 
itemType - Variable in class net.sf.basedb.plugins.AnnotationFlatFileImporter
 
itemType - Variable in class net.sf.basedb.plugins.batchimport.AnyToAnyImporter
 
itemType - Variable in class net.sf.basedb.util.listable.PushToParentsTransformer
 
itemType - Variable in class net.sf.basedb.util.overview.filter.BasicItemFilter
 
itemType - Variable in class net.sf.basedb.util.overview.filter.ItemTypeFilter
 
itemType - Variable in class net.sf.basedb.util.parser.DefaultItemFunction
 
ItemTypeFilter - Class in net.sf.basedb.util.overview.filter
A filter implementation that mathces item types on nodes.
ItemTypeFilter(Item) - Constructor for class net.sf.basedb.util.overview.filter.ItemTypeFilter
Create a filter that finds nodes that has an attached item of the given item type.
ItemTypeFormatter - Class in net.sf.basedb.util.formatter
Formatter implementation that converts an integer into it's Item representation and the uses name() as the formatted value.
ItemTypeFormatter() - Constructor for class net.sf.basedb.util.formatter.ItemTypeFormatter
Create a new formatter.
ItemTypeFormatter(String) - Constructor for class net.sf.basedb.util.formatter.ItemTypeFormatter
Create a new formatter.
itemTypes - Variable in class net.sf.basedb.core.data.AnnotationTypeData
 
itemTypesColumnMapping - Static variable in class net.sf.basedb.plugins.batchimport.AnnotationTypeImporter
Column mapping parameter for "Item types".
itemTypesMapper - Variable in class net.sf.basedb.plugins.batchimport.AnnotationTypeImporter
 
iterate() - Method in class net.sf.basedb.core.hibernate.QueryWrapper
Deprecated.
iterate() - Method in class net.sf.basedb.util.extensions.ExtensionsInvoker
Create an iterator that iterates over all Action:s created by the extensions.
iterate(DbControl) - Method in class net.sf.basedb.clients.web.plugins.DataQueryWrapper
iterate(DbControl) - Method in class net.sf.basedb.clients.web.plugins.DynamicQueryWrapper
iterate(DbControl) - Method in class net.sf.basedb.clients.web.plugins.ItemQueryWrapper
iterate(DbControl) - Method in interface net.sf.basedb.clients.web.plugins.QueryWrapper
Get the ResultIterator for the query.
iterate(DbControl) - Method in class net.sf.basedb.clients.web.plugins.ReporterScoreQueryWrapper
iterate(DbControl) - Method in class net.sf.basedb.core.AbstractSqlQuery
Execute the query.
iterate(DbControl) - Method in class net.sf.basedb.core.DataQuery
Execute the query and return the results as an iterator.
iterate(DbControl) - Method in class net.sf.basedb.core.ItemQuery
Execute the query and return the results as an iterator.
iterate(DbControl) - Method in interface net.sf.basedb.core.query.SqlQuery
 
iterate(DbControl) - Method in class net.sf.basedb.core.ReporterScoreQuery
Execute the query and return the results as an iterator.
iterations - Variable in class net.sf.basedb.plugins.LowessNormalization.CallableWorker
 
iterator - Variable in class net.sf.basedb.core.ItemResultList.ResultListIterator
 
iterator - Variable in class net.sf.basedb.core.ItemResultList.ResultListListIterator
 
iterator - Variable in class net.sf.basedb.util.extensions.ActionIterator
 
iterator() - Method in class net.sf.basedb.core.ItemResultList
 
iterator() - Method in class net.sf.basedb.core.Presets
Iterate over all named presets.
iterator() - Method in class net.sf.basedb.core.Presets.Preset
Iterate over all settings.
iterator() - Method in class net.sf.basedb.util.extensions.ExtensionsInvoker
 
iterator() - Method in class net.sf.basedb.util.Tree
 
iterParameter - Static variable in class net.sf.basedb.plugins.LowessNormalization
 

J

JarClassLoader - Class in net.sf.basedb.util
A class loader implementation that loads classes from JAR files.
JarClassLoader(String) - Constructor for class net.sf.basedb.util.JarClassLoader
Create a new JAR file class loader.
JarClassLoader.JarClassLoaderProxy - Class in net.sf.basedb.util
A proxy class loader is typically needed when one extension depends on another extension.
JarClassLoader.JarInfo - Class in net.sf.basedb.util
 
JarClassLoaderProxy(String) - Constructor for class net.sf.basedb.util.JarClassLoader.JarClassLoaderProxy
Creates a proxy class loader for the given JAR file.
jarFile - Variable in class net.sf.basedb.clients.web.extensions.ServletWrapperKey
 
jarFile - Variable in class net.sf.basedb.core.data.PluginDefinitionData
 
jarFile - Variable in class net.sf.basedb.core.data.PluginTypeData
 
jarFile - Variable in class net.sf.basedb.util.JarClassLoader.JarInfo
 
jarFiles - Variable in class net.sf.basedb.util.JarClassLoader
For keeping track of jar files listed by Class-Path entry in the manifest file.
JarFirstURIComparator() - Constructor for class net.sf.basedb.util.extensions.manager.ExtensionsManager.JarFirstURIComparator
 
JarInfo(File) - Constructor for class net.sf.basedb.util.JarClassLoader.JarInfo
 
jarLoader - Variable in class net.sf.basedb.util.extensions.manager.ExtensionsFile
 
jarPath - Variable in class net.sf.basedb.util.JarClassLoader.JarClassLoaderProxy
 
jarSize - Variable in class net.sf.basedb.util.JarClassLoader
The size of the JAR file.
jarTimeStamp - Variable in class net.sf.basedb.util.JarClassLoader
The timestamp of the JAR file.
javaBin - Variable in class net.sf.basedb.clients.jobagent.executors.ProcessJobExecutor
 
javaScriptEncode(String) - Static method in class net.sf.basedb.clients.web.util.HTML
Escape a string to make it safe for use in a JavaScript statement.
jdbcFetchSize - Static variable in class net.sf.basedb.core.HibernateUtil
Number of rows to load at a time when iterating over a result set.
jep - Variable in class net.sf.basedb.util.export.spotdata.JepDynamicField
 
jep - Variable in class net.sf.basedb.util.jep.FunctionSafeJep.SafeFunctionTable
 
jep(String, String, Type, Formula.AverageMethod, Formatter<?>) - Static method in class net.sf.basedb.util.export.spotdata.ExportableFieldFactory
Create a JEP dynamic field.
Jep - Class in net.sf.basedb.util.jep
Utility class for parsing mathematical expressions.
Jep() - Constructor for class net.sf.basedb.util.jep.Jep
 
JEP - Enum constant in enum class net.sf.basedb.core.Formula.Parser
Use the JEP parser.
JepConversionFunction<T> - Interface in net.sf.basedb.util.jep.convert
Convert a built-in JEP function or operation to a Query API Expression or Restriction.
JepDynamicField - Class in net.sf.basedb.util.export.spotdata
A dynamic field implementation that uses a JEP expression to generate the expression that is needed to select the data.
JepDynamicField() - Constructor for class net.sf.basedb.util.export.spotdata.JepDynamicField
Create a new object.
jepErrorList - Static variable in class net.sf.basedb.util.jep.Jep
 
jepExpression - Variable in class net.sf.basedb.clients.web.taglib.table.TableColumn
 
JepExpressionFunction - Interface in net.sf.basedb.util.jep
This interface should be implemented by JEP functions that can also be converted into an Expression that can be used in queries.
JepExtraValueCalculator - Class in net.sf.basedb.plugins
This plugin caluclates extra values from a bioassayset using mathematical formulas entered by the user.
JepExtraValueCalculator() - Constructor for class net.sf.basedb.plugins.JepExtraValueCalculator
 
JepFunction - Interface in net.sf.basedb.util.jep
This interface should be implemented by objects that can perform some kind of calculation for a JEP expression.
JepIntensityCalculatorImpl(JEP[], RawFunction, MeanFunction) - Constructor for class net.sf.basedb.util.IntensityCalculatorUtil.JepIntensityCalculatorImpl
 
JepIntensityTransformer - Class in net.sf.basedb.plugins
This plugin transform channel intensities using mathematical formulas entered by the user.
JepIntensityTransformer() - Constructor for class net.sf.basedb.plugins.JepIntensityTransformer
Constructor should be empty.
JepMapper - Class in net.sf.basedb.util.parser
A mapper that uses Jep to calculate the final value.
JepMapper(String, List<String>) - Constructor for class net.sf.basedb.util.parser.JepMapper
Create a new JepMapper.
JepMapper(String, List<String>, NumberFormat) - Constructor for class net.sf.basedb.util.parser.JepMapper
JepMapper(String, List<String>, NumberFormat, boolean) - Constructor for class net.sf.basedb.util.parser.JepMapper
JepMapper(String, List<String>, NumberFormat, boolean, JepFunction...) - Constructor for class net.sf.basedb.util.parser.JepMapper
JepMapper(String, List<String>, NumberFormat, Formatter<Date>, boolean, JepFunction...) - Constructor for class net.sf.basedb.util.parser.JepMapper
 
JepRestrictionFunction - Interface in net.sf.basedb.util.jep
This interface should be implemented by JEP functions that can also be converted into a Restriction that can be used in queries.
jeps - Variable in class net.sf.basedb.util.IntensityCalculatorUtil.JepIntensityCalculatorImpl
 
jepToExpression(JEP) - Static method in class net.sf.basedb.util.jep.Jep
Convert a JEP expression to a Query API Expression.
jepToRestriction(JEP) - Static method in class net.sf.basedb.util.jep.Jep
Convert a JEP expression to a Query API Restriction.
job - Variable in class net.sf.basedb.clients.jobagent.JobRunner
 
job - Variable in class net.sf.basedb.core.data.ArrayDesignData
 
job - Variable in class net.sf.basedb.core.data.ChangeHistoryData
 
job - Variable in class net.sf.basedb.core.data.DerivedBioAssayData
 
job - Variable in class net.sf.basedb.core.data.ExtraValueData
 
job - Variable in class net.sf.basedb.core.data.MessageData
 
job - Variable in class net.sf.basedb.core.data.RawBioAssayData
 
job - Variable in class net.sf.basedb.core.data.TransformationData
 
job - Variable in class net.sf.basedb.core.Job.ProgressReporterImpl
 
job - Variable in class net.sf.basedb.core.ParameterValuesImpl
 
job - Variable in class net.sf.basedb.core.plugin.AbstractPlugin
 
job - Variable in class net.sf.basedb.core.plugin.ParameterValuesWrapper
 
job - Variable in class net.sf.basedb.core.PluginRequest
 
job - Variable in class net.sf.basedb.core.Transformation
 
Job - Class in net.sf.basedb.core
This class represents the execution of a job.
Job(JobData) - Constructor for class net.sf.basedb.core.Job
 
JOB - Enum constant in enum class net.sf.basedb.core.Item
The item is a Job
Job.ExecutionTime - Enum Class in net.sf.basedb.core
A rough estimate of the execution time of a job.
Job.JobSignalTransporter - Class in net.sf.basedb.core
Wrapper for the signal transporter that intercepts the ABORT signal and changes the job's status to ABORTING.
Job.ProgressReporterImpl - Class in net.sf.basedb.core
Implements the ProgressReporter interface and stores the percentage completed for the current job.
Job.SignalKeyring - Class in net.sf.basedb.core
Our own keyring containing the permissions signal handlers may need to update job status, eq.
Job.Status - Enum Class in net.sf.basedb.core
The status of a job.
Job.Type - Enum Class in net.sf.basedb.core
The type of job.
jobAgent - Variable in class net.sf.basedb.core.data.JobAgentSettingsData
 
JobAgent - Class in net.sf.basedb.core
This class represents a job agent, which is a program running in another virtual machine on the same or a different server.
JobAgent(JobAgentData) - Constructor for class net.sf.basedb.core.JobAgent
 
JOBAGENT - Enum constant in enum class net.sf.basedb.core.Item
The item is a JobAgent
JOBAGENT - Static variable in class net.sf.basedb.core.Role
The id for the Role item representing job agents.
JobAgentConnection - Class in net.sf.basedb.util.jobagent
This class is used by client applications to communicate with job agents.
JobAgentConnection(int, int) - Constructor for class net.sf.basedb.util.jobagent.JobAgentConnection
Create a connection to the local job agent running on the specified port.
JobAgentConnection(String, int, int) - Constructor for class net.sf.basedb.util.jobagent.JobAgentConnection
Create a connection to the job agent running on the specified server and listening on the specified port.
JobAgentData - Class in net.sf.basedb.core.data
This class holds information about a job agent.
JobAgentData() - Constructor for class net.sf.basedb.core.data.JobAgentData
 
jobAgentId - Variable in class net.sf.basedb.core.data.JobData
 
JobAgentInfo - Class in net.sf.basedb.util.jobagent
This class can hold information about the status of a job agent.
JobAgentInfo() - Constructor for class net.sf.basedb.util.jobagent.JobAgentInfo
Create a new info object and set all values to null.
JobAgentInfo(Boolean, Integer, Long, Long, Set<JobInfo>) - Constructor for class net.sf.basedb.util.jobagent.JobAgentInfo
Create a new info object.
JobAgentInfo(String) - Constructor for class net.sf.basedb.util.jobagent.JobAgentInfo
Create a new info object and parse the answer from a JobAgentConnection to get the values.
JobAgentServerConnection - Class in net.sf.basedb.util.jobagent
This class is used by job agents to listen for incoming requests from client applications.
JobAgentServerConnection(int, RequestHandler, Logger) - Constructor for class net.sf.basedb.util.jobagent.JobAgentServerConnection
Create a new server connection.
JobAgentServerConnection.ListenerThread - Class in net.sf.basedb.util.jobagent
This class is used for listening to the specified socket for incoming connections.
JobAgentServerConnection.RequestHandlerThread - Class in net.sf.basedb.util.jobagent
This class is used for forwarding requests to a RequestHandler.
jobAgentSettings - Variable in class net.sf.basedb.core.data.PluginDefinitionData
 
JobAgentSettings - Class in net.sf.basedb.core
This class contains a job agent's settings for a specific plugin.
JobAgentSettings(JobAgentSettingsData) - Constructor for class net.sf.basedb.core.JobAgentSettings
 
JOBAGENTSETTINGS - Enum constant in enum class net.sf.basedb.core.Item
The item is a JobAgentSettings
JobAgentSettingsData - Class in net.sf.basedb.core.data
This class holds information about plugin settings for a particular job agent.
JobAgentSettingsData() - Constructor for class net.sf.basedb.core.data.JobAgentSettingsData
 
jobData - Variable in class net.sf.basedb.core.InternalJobQueue.JobRunner
 
JobData - Class in net.sf.basedb.core.data
This class holds information about a job.
JobData() - Constructor for class net.sf.basedb.core.data.JobData
 
jobDone(InternalJobQueue.JobRunner) - Method in class net.sf.basedb.core.InternalJobQueue
Called from a InternalJobQueue.JobRunner when it has finished executing the job.
jobDone(Job, Slot) - Method in class net.sf.basedb.clients.jobagent.Agent
Used by JobRunner to tell that a job has finished executing and that the used slot should be released.
jobExecutor - Variable in class net.sf.basedb.clients.jobagent.Agent
 
jobExecutor - Variable in class net.sf.basedb.clients.jobagent.JobRunner
 
JobExecutor - Interface in net.sf.basedb.clients.jobagent
This interface must be implemented by all classes that want's to act as a job executor.
jobId - Variable in class net.sf.basedb.core.data.ChangeHistoryData
 
jobId - Variable in class net.sf.basedb.core.InternalJobQueue.JobRunner
 
jobId - Variable in class net.sf.basedb.core.Job.ProgressReporterImpl
 
jobId - Variable in class net.sf.basedb.core.log.TransactionDetails
 
jobId - Variable in class net.sf.basedb.core.MigrateRbaToDba.Rba
 
jobId - Variable in class net.sf.basedb.core.SessionControl
 
jobId - Variable in class net.sf.basedb.util.jobagent.JobInfo
 
JobInfo - Class in net.sf.basedb.util.jobagent
Hold information about a job that is running on a job agent.
JobInfo(int, Map<String, List<String>>) - Constructor for class net.sf.basedb.util.jobagent.JobInfo
Create a new JobInfo object using information from the answer to a JobAgentConnection request.
JobInfo(Job, Job.ExecutionTime) - Constructor for class net.sf.basedb.util.jobagent.JobInfo
Create a new JobInfo object.
jobName - Variable in class net.sf.basedb.core.log.TransactionDetails
 
jobName - Variable in class net.sf.basedb.core.SessionControl
 
JobParameter(String...) - Constructor for class net.sf.basedb.plugins.Base1PluginExecuter.JobParameter
 
JobParameter(Element) - Constructor for class net.sf.basedb.plugins.Base1PluginExecuter.JobParameter
 
jobParameters - Variable in class net.sf.basedb.core.PluginRequest
 
jobParameters - Variable in class net.sf.basedb.plugins.Base1PluginExecuter
This list holds the job parameters derived from the configuration file.
jobParametersParameter - Variable in class net.sf.basedb.plugins.Base1PluginExecuter
This parameter describes the job parameters that the base1 plugin needs.
jobPermissions - Variable in class net.sf.basedb.core.InternalJobQueue.JobQueueKeyring
 
jobQuery - Variable in class net.sf.basedb.clients.jobagent.JobQueueChecker
Cached query for waiting jobs.
jobQueueChecker - Variable in class net.sf.basedb.clients.jobagent.Agent
 
JobQueueChecker - Class in net.sf.basedb.clients.jobagent
This class is given the responsibility to check the job queue for jobs that are awaiting execution.
JobQueueChecker(Agent) - Constructor for class net.sf.basedb.clients.jobagent.JobQueueChecker
 
JobQueueKeyring() - Constructor for class net.sf.basedb.core.InternalJobQueue.JobQueueKeyring
 
JobRunner - Class in net.sf.basedb.clients.jobagent
A runnable class that makes it possible to execute each job in it's own thread.
JobRunner(Agent, Job, JobAgentSettings, JobExecutor) - Constructor for class net.sf.basedb.clients.jobagent.JobRunner
Create a new job execution thread.
JobRunner(JobData, Job.ExecutionTime) - Constructor for class net.sf.basedb.core.InternalJobQueue.JobRunner
 
jobs - Variable in class net.sf.basedb.core.data.ExperimentData
 
jobs - Variable in class net.sf.basedb.util.jobagent.JobAgentInfo
 
JobSignalTransporter(SignalTransporter) - Constructor for class net.sf.basedb.core.Job.JobSignalTransporter
 
join(Collection<?>, String, boolean) - Static method in class net.sf.basedb.core.StringUtil
Join a collection of values to a string, using the specified delimiator.
join(Join) - Method in class net.sf.basedb.core.AbstractQuery
 
join(Join) - Method in interface net.sf.basedb.core.query.Query
Add a join query element to the join list.
Join - Interface in net.sf.basedb.core.query
A join query element.
JOIN - Enum constant in enum class net.sf.basedb.core.query.QuerySection
 
joinAlias - Variable in class net.sf.basedb.core.query.ReporterListExpression
 
joinedAlias - Variable in class net.sf.basedb.core.query.AnnotationJoin
 
joinedAlias - Variable in class net.sf.basedb.core.query.HqlInnerJoin
 
joinedAlias - Variable in class net.sf.basedb.core.query.HqlLeftJoin
 
joinedAlias - Variable in class net.sf.basedb.core.query.HqlRightJoin
 
joinedItems - Variable in class net.sf.basedb.core.DynamicPositionQuery
 
joinedItems - Variable in class net.sf.basedb.core.DynamicRawDataQuery
 
joinedItems - Variable in class net.sf.basedb.core.DynamicReporterQuery
 
joinedItems - Variable in class net.sf.basedb.core.DynamicSpotQuery
 
joinExpression - Variable in enum class net.sf.basedb.core.query.JoinType
 
joinExtraValue(ExtraValue, JoinType) - Method in class net.sf.basedb.core.DynamicPositionQuery
Join extra values in the query.
joinExtraValue(ExtraValue, JoinType) - Method in class net.sf.basedb.core.DynamicSpotQuery
Join extra values in the query.
joinIfNeeded(DynamicPositionQuery, ExtraValueExpression) - Method in class net.sf.basedb.core.DynamicPositionQueryJoiners.ExtraValueJoiner
 
joinIfNeeded(DynamicPositionQuery, ReporterListExpression) - Method in class net.sf.basedb.core.DynamicPositionQueryJoiners.ReporterListJoiner
 
joinIfNeeded(DynamicPositionQuery, ReporterPropertyExpression) - Method in class net.sf.basedb.core.DynamicPositionQueryJoiners.ReporterJoiner
 
joinIfNeeded(DynamicRawDataQuery, ReporterListExpression) - Method in class net.sf.basedb.core.DynamicRawDataQuery.ReporterListJoiner
 
joinIfNeeded(DynamicRawDataQuery, RawBioAssayPropertyExpression) - Method in class net.sf.basedb.core.DynamicRawDataQuery.RawBioAssayJoiner
 
joinIfNeeded(DynamicRawDataQuery, ReporterPropertyExpression) - Method in class net.sf.basedb.core.DynamicRawDataQuery.ReporterJoiner
 
joinIfNeeded(DynamicReporterQuery, ReporterListExpression) - Method in class net.sf.basedb.core.DynamicReporterQuery.ReporterListJoiner
 
joinIfNeeded(DynamicReporterQuery, ReporterPropertyExpression) - Method in class net.sf.basedb.core.DynamicReporterQuery.MasterReporterJoiner
 
joinIfNeeded(DynamicSpotQuery, ExtraValueExpression) - Method in class net.sf.basedb.core.DynamicSpotQueryJoiners.ExtraValueJoiner
 
joinIfNeeded(DynamicSpotQuery, ReporterListExpression) - Method in class net.sf.basedb.core.DynamicSpotQueryJoiners.ReporterListJoiner
 
joinIfNeeded(DynamicSpotQuery, RawDataPropertyExpression) - Method in class net.sf.basedb.core.DynamicSpotQueryJoiners.RawDataJoiner
 
joinIfNeeded(DynamicSpotQuery, ReporterPropertyExpression) - Method in class net.sf.basedb.core.DynamicSpotQueryJoiners.ReporterJoiner
 
joinIfNeeded(HqlQuery, AnnotationExpression) - Method in class net.sf.basedb.core.HqlQueryJoiners.AnnotationJoiner
 
joinIfNeeded(HqlQuery, ReporterListExpression) - Method in class net.sf.basedb.core.HqlQueryJoiners.ReporterListJoiner
 
joinIfNeeded(Q, E) - Method in interface net.sf.basedb.core.query.AutoJoiner
Automatically join the tables that is is needed by the query element unless they are already joined.
joinMasterReporters(JoinType) - Method in class net.sf.basedb.core.DynamicReporterQuery
Join the master reporter table into this query.
joinPermanent(Join) - Method in class net.sf.basedb.core.AbstractQuery
 
joinPermanent(Join) - Method in interface net.sf.basedb.core.query.Query
Permanently add a join query element to the join list.
joinProperty - Variable in class net.sf.basedb.core.query.ReporterListExpression
 
joinRawBioAssay(JoinType) - Method in class net.sf.basedb.core.DynamicRawDataQuery
Join information about raw bioassays in the query.
joinRawData(JoinType) - Method in class net.sf.basedb.core.DynamicSpotQuery
Join information about raw data in the query.
joinReporterList(ReporterList, JoinType) - Method in class net.sf.basedb.core.DynamicPositionQuery
Makes a join with a ReporterList
joinReporterList(ReporterList, JoinType) - Method in class net.sf.basedb.core.DynamicRawDataQuery
Makes a join with a ReporterList
joinReporterList(ReporterList, JoinType) - Method in class net.sf.basedb.core.DynamicReporterQuery
Makes a join with a ReporterList
joinReporterList(ReporterList, JoinType) - Method in class net.sf.basedb.core.DynamicSpotQuery
Makes a join with a ReporterList
joinReporters(JoinType) - Method in class net.sf.basedb.core.DynamicPositionQuery
Join information about reporters in the query.
joinReporters(JoinType) - Method in class net.sf.basedb.core.DynamicRawDataQuery
Join information about reporters in the query.
joinReporters(JoinType) - Method in class net.sf.basedb.core.DynamicSpotQuery
Join information about reporters in the query.
joinReporters(JoinType, boolean) - Method in class net.sf.basedb.core.DynamicPositionQuery
Join information about reporters in the query.
joinReporters(JoinType, boolean) - Method in class net.sf.basedb.core.DynamicSpotQuery
Join information about reporters in the query.
joins - Variable in class net.sf.basedb.core.AbstractQuery
List of joins added to the query.
joinTransaction() - Method in class net.sf.basedb.core.hibernate.SessionWrapper
 
joinType - Variable in class net.sf.basedb.core.DynamicJoin
 
joinType - Variable in class net.sf.basedb.core.DynamicPositionQueryJoiners.ExtraValueJoiner
 
joinType - Variable in class net.sf.basedb.core.DynamicPositionQueryJoiners.ReporterJoiner
 
joinType - Variable in class net.sf.basedb.core.DynamicPositionQueryJoiners.ReporterListJoiner
 
joinType - Variable in class net.sf.basedb.core.DynamicRawDataQuery.RawBioAssayJoiner
 
joinType - Variable in class net.sf.basedb.core.DynamicRawDataQuery.ReporterJoiner
 
joinType - Variable in class net.sf.basedb.core.DynamicRawDataQuery.ReporterListJoiner
 
joinType - Variable in class net.sf.basedb.core.DynamicReporterQuery.MasterReporterJoiner
 
joinType - Variable in class net.sf.basedb.core.DynamicReporterQuery.ReporterListJoiner
 
joinType - Variable in class net.sf.basedb.core.DynamicSpotQueryJoiners.ExtraValueJoiner
 
joinType - Variable in class net.sf.basedb.core.DynamicSpotQueryJoiners.RawDataJoiner
 
joinType - Variable in class net.sf.basedb.core.DynamicSpotQueryJoiners.ReporterJoiner
 
joinType - Variable in class net.sf.basedb.core.DynamicSpotQueryJoiners.ReporterListJoiner
 
joinType - Variable in class net.sf.basedb.core.ExtraValueJoin
 
joinType - Variable in class net.sf.basedb.core.HqlQueryJoiners.AnnotationJoiner
 
joinType - Variable in class net.sf.basedb.core.HqlQueryJoiners.ReporterListJoiner
 
joinType - Variable in class net.sf.basedb.core.query.AnnotationJoin
 
joinType - Variable in class net.sf.basedb.core.RealJoin
 
joinType - Variable in class net.sf.basedb.core.ReporterListJoin
 
JoinType - Enum Class in net.sf.basedb.core.query
An enumeration used to specify the type of join.
JoinType(String) - Constructor for enum class net.sf.basedb.core.query.JoinType
 
jsonColumnDefs - Variable in class net.sf.basedb.clients.web.taglib.table.Table
 
JsonConverter<T> - Interface in net.sf.basedb.util.json
Implementations should convert a given object to an object that can be serialized into a JSON string.
JsonUtil - Class in net.sf.basedb.util.json
Utility functions for working with JSON data.
JsonUtil() - Constructor for class net.sf.basedb.util.json.JsonUtil
 
jspContext - Variable in class net.sf.basedb.clients.web.extensions.edit.AbstractOnSaveAction
 
jspContext - Variable in class net.sf.basedb.clients.web.extensions.fileviewer.FileViewerUtil
 
jspContext - Variable in class net.sf.basedb.clients.web.extensions.list.RelatedItemHelper
 
jspContext - Variable in class net.sf.basedb.clients.web.extensions.section.IncludeContentSectionFactory.Section
 
jspContext - Variable in class net.sf.basedb.clients.web.taglib.table.ColumnDef
 
JspContext - Class in net.sf.basedb.clients.web.extensions
Context object for the web application.
JspContext(SessionControl, DbControl, ItemContext, PageContext, GuiContext, Object) - Constructor for class net.sf.basedb.clients.web.extensions.JspContext
 
jspPage - Variable in class net.sf.basedb.core.RequestInformation
 

K

kB - Static variable in class net.sf.basedb.util.Values
 
keepFirstWord - Static variable in class net.sf.basedb.clients.web.taglib.Button
 
keepSkippedLines - Variable in class net.sf.basedb.util.parser.FlatFileParser
If unknown or ignored lines should be kept.
key - Variable in class net.sf.basedb.util.bfs.MetadataModel.SectionEntry
 
key - Variable in class net.sf.basedb.util.Enumeration.Entry
 
key - Variable in class net.sf.basedb.util.fuzzy.StringMatcher.FuzzyMatch
 
key - Variable in class net.sf.basedb.util.gtf.GtfInputStream.Attribute
 
key - Variable in class net.sf.basedb.util.overview.validator.ExtensionNodeValidator
 
key - Variable in class net.sf.basedb.util.StaticCache.LockSafeInputStream
 
key - Variable in class net.sf.basedb.util.StaticCache.LockSafeOutputStream
 
key(byte[]) - Method in class net.sf.basedb.util.bcrypt.BCrypt
Key the Blowfish cipher
Key - Class in net.sf.basedb.core
This is the base class for keys.
Key(KeyData) - Constructor for class net.sf.basedb.core.Key
 
KeyData - Class in net.sf.basedb.core.data
This abstract class is the base class for the key classes which holds access privileges for users, groups, projects and roles.
KeyData() - Constructor for class net.sf.basedb.core.data.KeyData
 
keyId - Variable in class net.sf.basedb.core.data.keyring.KeyPermission
 
keyId - Variable in class net.sf.basedb.core.data.keyring.PluginKeys
 
KeyPermission - Class in net.sf.basedb.core.data.keyring
Class for holding a keyId and a permission value.
KeyPermission() - Constructor for class net.sf.basedb.core.data.keyring.KeyPermission
Create a new KeyPermission object.
keyRef - Variable in class net.sf.basedb.util.StaticCache.LockEntry
 
keyring - Variable in class net.sf.basedb.core.SessionControl.LoginInfo
The Keyring of the logged in user.
Keyring - Class in net.sf.basedb.core
Objects of this class holds information about a user's access permissions, group and role membership.
Keyring(int) - Constructor for class net.sf.basedb.core.Keyring
Create a new Keyring object.
Keyring(Keyring, int, boolean) - Constructor for class net.sf.basedb.core.Keyring
 
Keyring.ReloadTask - Class in net.sf.basedb.core
 
keys - Variable in class net.sf.basedb.core.data.RoleData
 
keyStore - Variable in class net.sf.basedb.util.ssl.StaticKeyManager
 
kit - Variable in class net.sf.basedb.core.data.BioMaterialEventData
 
kit - Variable in class net.sf.basedb.core.data.BioPlateEventData
 
kit - Variable in class net.sf.basedb.core.data.DerivedBioAssayData
 
Kit - Class in net.sf.basedb.core
This class is used to represent a kit of reagents and other stuff used in the lab process.
Kit(KitData) - Constructor for class net.sf.basedb.core.Kit
Creates a new kit item.
KIT - Enum constant in enum class net.sf.basedb.core.Item
The item is a Kit.
KIT_USED_AFTER_EXPIRATIONDATE - Static variable in class net.sf.basedb.util.overview.Validator
Validator rule that checks if a kit has been used after it's exiration date.
kitColumnMapping - Static variable in class net.sf.basedb.plugins.batchimport.AbstractItemImporter
 
KitData - Class in net.sf.basedb.core.data
This class holds information about a kit.
KitData() - Constructor for class net.sf.basedb.core.data.KitData
 
KitImporter - Class in net.sf.basedb.plugins.batchimport
Plug-in for importing kit items in a batch.
KitImporter() - Constructor for class net.sf.basedb.plugins.batchimport.KitImporter
 
KitLoader - Class in net.sf.basedb.util.overview.loader
Node loader implementation for kits.
KitLoader() - Constructor for class net.sf.basedb.util.overview.loader.KitLoader
 
kitMapper - Variable in class net.sf.basedb.plugins.batchimport.DerivedBioAssayImporter
 
kitMapper - Variable in class net.sf.basedb.plugins.batchimport.ExtractImporter
 
kitMapper - Variable in class net.sf.basedb.plugins.batchimport.PhysicalBioAssayImporter
 
kitMapper - Variable in class net.sf.basedb.plugins.batchimport.SampleImporter
 
kitQuery - Variable in class net.sf.basedb.plugins.batchimport.AbstractItemImporter
 
KitValidator - Class in net.sf.basedb.util.overview.validator
Validator implementation for kits.
KitValidator() - Constructor for class net.sf.basedb.util.overview.validator.KitValidator
 
knownFiles - Variable in class net.sf.basedb.plugins.executor.ExternalProgramExecutor
Files that are known to exists in the working directory.

L

label - Variable in class net.sf.basedb.core.data.ParameterValueData
 
label - Variable in class net.sf.basedb.core.ParameterInfo
 
label - Variable in class net.sf.basedb.core.PluginParameter
A short label used by the client application as in the GUI.
Label - Class in net.sf.basedb.clients.web.taglib.table
This tag creates a label on a toolbar.
Label() - Constructor for class net.sf.basedb.clients.web.taglib.table.Label
 
LABEL - Static variable in class net.sf.basedb.core.Tag
The ID for the LABEL tag type.
LABELED - Static variable in class net.sf.basedb.core.Extract
The id for the ExtractType item representing a labeled extract.
labeledExtractQuery - Variable in class net.sf.basedb.plugins.batchimport.AbstractItemImporter
 
LABELING - Static variable in class net.sf.basedb.core.Kit
The ID for the labeling kit type, for example a kit used when creating a labeled extract from an Extract.
LABELING - Static variable in class net.sf.basedb.core.Protocol
The ID for the labeling protocol type, for example a protocol used when creating a labeled extract from an Extract.
LAST_SOURCE - Static variable in class net.sf.basedb.core.ClonableProperty
The property name of the "static" property ReporterData.getLastSource()
LAST_UPDATE - Static variable in class net.sf.basedb.core.ClonableProperty
The property name of the "static" property ReporterData.getLastUpdate()
lastAccess - Variable in class net.sf.basedb.core.SessionControl
The time of the last access to this object.
lastColumn - Variable in class net.sf.basedb.util.excel.XlsxToCsvUtil.SheetInfo
 
lastCountDc - Variable in class net.sf.basedb.core.AbstractHqlQuery
The most recent DbControl used to build/execute the count query.
lastCountQuery - Variable in class net.sf.basedb.core.AbstractHqlQuery
The most recent count query.
lastError - Variable in class net.sf.basedb.util.extensions.Registry.RegisteredExtension
 
lastError - Variable in class net.sf.basedb.util.extensions.Registry.RegisteredExtensionPoint
 
lastErrorAction - Variable in class net.sf.basedb.util.extensions.Registry.RegisteredExtension
 
lastErrorAction - Variable in class net.sf.basedb.util.extensions.Registry.RegisteredExtensionPoint
 
lastIdDc - Variable in class net.sf.basedb.core.AbstractHqlQuery
The most recent DbControl used to build/execute the ID query.
lastIdentifier - Variable in class net.sf.basedb.plugins.batchimport.AbstractItemImporter
 
lastIdQuery - Variable in class net.sf.basedb.core.AbstractHqlQuery
The most recent id query.
lastIndexOf(Object) - Method in class net.sf.basedb.core.ItemResultList
 
lastItem - Variable in class net.sf.basedb.plugins.batchimport.AbstractItemImporter
 
lastLength - Variable in class net.sf.basedb.util.extensions.manager.ExtensionsFile
 
lastMainDc - Variable in class net.sf.basedb.core.AbstractHqlQuery
The most recent DbControl used to build/execute the main query.
lastMainQuery - Variable in class net.sf.basedb.core.AbstractHqlQuery
The most recent main query.
lastModified - Variable in class net.sf.basedb.clients.web.extensions.XJspCompiler
 
lastModified - Variable in class net.sf.basedb.util.extensions.manager.ExtensionsFile
 
lastModified - Variable in class net.sf.basedb.util.JarClassLoader.JarInfo
 
lastModified - Variable in class net.sf.basedb.util.uri.UriMetadata
 
lastMsg - Variable in class net.sf.basedb.core.Migration.ProgressInputStream
 
lastName - Variable in class net.sf.basedb.util.extensions.xml.XmlLoader
 
lastProtocolNode - Variable in class net.sf.basedb.util.overview.validator.ProtocolParameterValidator
 
lastReset - Static variable in class net.sf.basedb.clients.web.servlet.RssNewsFeed
 
lastResults - Variable in class net.sf.basedb.util.extensions.manager.ExtensionsManager
 
lastRow - Variable in class net.sf.basedb.util.excel.XlsxToCsvUtil.SheetInfo
 
lastSource - Variable in class net.sf.basedb.core.data.ReporterData
The source of the last update
lastSyncProperties - Variable in class net.sf.basedb.core.data.ItemListSyncFilterData
 
lastUpdate - Static variable in class net.sf.basedb.clients.web.servlet.RssNewsFeed
 
lastUpdate - Variable in class net.sf.basedb.core.data.AnnotationData
 
lastUpdate - Variable in class net.sf.basedb.core.data.FileData
 
lastUpdate - Variable in class net.sf.basedb.core.data.ReporterData
The last update date.
lastUpdate - Variable in class net.sf.basedb.core.Job.ProgressReporterImpl
 
lastUpdate - Variable in class net.sf.basedb.core.snapshot.AnnotationSnapshot
 
lastUpdated - Variable in class net.sf.basedb.clients.jobagent.slotmanager.MasterSlotManager.RemoteSlot
 
lastUpdated - Variable in class net.sf.basedb.core.AnnotationBatcher.CurrentAnnotationInfo
 
lastUsed - Variable in class net.sf.basedb.core.data.UserDeviceData
 
lastValue - Variable in class net.sf.basedb.core.Job.ProgressReporterImpl
 
latitude - Variable in class net.sf.basedb.util.GeoLocation
 
LAYER - Static variable in class net.sf.basedb.core.VirtualColumn
This column stores the data cube layer coordinate.
layerNo - Variable in class net.sf.basedb.core.data.DataCubeLayerData
 
layers - Variable in class net.sf.basedb.core.data.DataCubeData
 
lazy - Variable in class net.sf.basedb.clients.web.extensions.list.RelatedItemHelper
 
LEADING_TRAILING_LINEBREAKS - Static variable in class net.sf.basedb.clients.web.util.HTML
 
leaveStdinParameter - Variable in class net.sf.basedb.plugins.Base1PluginExecuter
If the plug-in should leave the stdin.txt after execution.
leaveStdoutParameter - Variable in class net.sf.basedb.plugins.Base1PluginExecuter
If the plug-in should leave the stdout.txt after execution.
left - Variable in class net.sf.basedb.core.DynamicJoin
 
left - Variable in class net.sf.basedb.core.ExtraValueJoin
 
LEFT - Enum constant in enum class net.sf.basedb.core.query.JoinType
Use a left join, ie. select all rows from the left table and use null if no row is present in the right table.
leftAlias - Variable in class net.sf.basedb.core.ReporterListJoin
 
leftColumn - Variable in class net.sf.basedb.core.ReporterListJoin
 
leftColumns - Variable in class net.sf.basedb.core.DynamicJoin
 
LeftFunction - Class in net.sf.basedb.util.jep
Adds a left(string, index|string) function to Jep.
LeftFunction() - Constructor for class net.sf.basedb.util.jep.LeftFunction
 
leftJoin(String, String) - Static method in class net.sf.basedb.core.query.Hql
Same as leftJoin(null, propert, joinedAlias, null, false)
leftJoin(String, String, String, Restriction, boolean) - Static method in class net.sf.basedb.core.query.Hql
Create a left join query element.
leftJoin(String, AnnotationType, String) - Static method in class net.sf.basedb.core.query.Annotations
Create a left join between an already joined element of a query and the annotation values for the given annotation type.
leftJoin(AnnotationType, String) - Static method in class net.sf.basedb.core.query.Annotations
Create a left join between the root element of a query and the annotation values for the given annotation type.
leftPad(String, char, int) - Static method in class net.sf.basedb.util.MD5
If the string is shorter than the specified length, it is left padded with the specified character.
length - Variable in class net.sf.basedb.core.data.ReporterClonePropertyData
 
length - Variable in class net.sf.basedb.core.ExtendedProperty
 
length - Variable in class net.sf.basedb.util.uri.UriMetadata
 
LENGTH - Static variable in class net.sf.basedb.core.Quantity
The id for the Quantity object representing length.
lengthOfContextPath - Variable in class net.sf.basedb.clients.web.servlet.ImageRemapFilter
 
LessConverter - Class in net.sf.basedb.util.jep.convert
Convert the '<' operator to a Query API Restriction.
LessConverter() - Constructor for class net.sf.basedb.util.jep.convert.LessConverter
 
LessEqualsConverter - Class in net.sf.basedb.util.jep.convert
Convert the '<=' operator to a Query API Restriction.
LessEqualsConverter() - Constructor for class net.sf.basedb.util.jep.convert.LessEqualsConverter
 
level - Variable in class net.sf.basedb.util.extensions.logging.LogEntry
 
level - Variable in class net.sf.basedb.util.extensions.LoggingErrorHandlerFactory
 
Level() - Constructor for enum class net.sf.basedb.util.extensions.LoggingErrorHandlerFactory.Level
 
LIBRARY - Static variable in class net.sf.basedb.core.Extract
The id for the ExtractType item representing a library.
LIBRARY_PREPARATION - Static variable in class net.sf.basedb.core.Kit
The ID for the library preparation kit type, for example a kit used when creating a library extract from an Extract.
LIBRARY_PREPARATION - Static variable in class net.sf.basedb.core.Protocol
The ID for the library preparation protocol type, for example a protocol used when creating a library extract from an Extract.
like(Expression, Expression) - Static method in class net.sf.basedb.core.query.Restrictions
Check if one expression matches another: e1 LIKE e2
LIKE - Enum constant in enum class net.sf.basedb.core.Operator
 
like_in(Expression, Expression...) - Static method in class net.sf.basedb.core.query.Restrictions
Check if one expression matches any expressions in an array: (e1 LIKE e2.1) OR (e1 LIKE e2.2) OR ....
LIKE_IN - Enum constant in enum class net.sf.basedb.core.Operator
 
LikeRestriction - Class in net.sf.basedb.core.query
Check if one expression matches another: e1 LIKE e2
LikeRestriction(Expression, Expression) - Constructor for class net.sf.basedb.core.query.LikeRestriction
 
limit - Variable in class net.sf.basedb.core.DynamicResultIterator
 
limit - Variable in class net.sf.basedb.core.signal.ProgressReporterSignalHandler
When the progress has reached this limit signal checking becomes disabled.
line - Variable in class net.sf.basedb.core.MigrateRbaToDba.LineMapping
 
line - Variable in class net.sf.basedb.util.parser.FlatFileParser.Data
 
line - Variable in class net.sf.basedb.util.parser.FlatFileParser.Line
 
line() - Method in class net.sf.basedb.util.parser.FlatFileParser.Data
The entire line as it was read from the input stream.
line() - Method in class net.sf.basedb.util.parser.FlatFileParser.Line
The entire line as it was read from the input stream.
Line(int, String, String, String) - Constructor for class net.sf.basedb.util.parser.FlatFileParser.Line
Create a new header line object.
Line(int, String, String, FlatFileParser.LineType) - Constructor for class net.sf.basedb.util.parser.FlatFileParser.Line
Create a new section line object.
Line(int, String, FlatFileParser.LineType) - Constructor for class net.sf.basedb.util.parser.FlatFileParser.Line
Create a new line object.
LinearScaleFactor(float) - Constructor for class net.sf.basedb.util.InputStreamTracker.LinearScaleFactor
 
LinearUnitConverter - Class in net.sf.basedb.util.units
A linear unit converter is a converter implementation were all units can be converted to another unit using a multiplication factor and/or an offset.
LinearUnitConverter(double, double) - Constructor for class net.sf.basedb.util.units.LinearUnitConverter
Create a new unit converter.
LinearUnitConverter(double, double, double, double) - Constructor for class net.sf.basedb.util.units.LinearUnitConverter
Create a unit converter that converts between two units that are both related to a third "common" unit by given factors and offsets.
LinearUnitConverter(Unit) - Constructor for class net.sf.basedb.util.units.LinearUnitConverter
Create a new unit converter that converts to/from a given unit.
LinearUnitConverter(Unit, Unit) - Constructor for class net.sf.basedb.util.units.LinearUnitConverter
Create a new unit converter that converts to/from given specific and reference unit.
LINEBREAKS_REGEXP - Static variable in class net.sf.basedb.clients.web.util.HTML
This pattern can be used to find line breaks.
lineCount - Variable in class net.sf.basedb.util.bfs.MetadataWriter
 
LineMapping(int, String) - Constructor for class net.sf.basedb.core.MigrateRbaToDba.LineMapping
 
lineNo - Variable in class net.sf.basedb.core.MigrateRbaToDba.LineMapping
 
lineNo - Variable in class net.sf.basedb.util.parser.FlatFileParser.Data
 
lineNo - Variable in class net.sf.basedb.util.parser.FlatFileParser.Line
 
lineNo() - Method in class net.sf.basedb.util.parser.FlatFileParser.Data
The line number of the data in the input stream.
lineNo() - Method in class net.sf.basedb.util.parser.FlatFileParser.Line
The line number of this line in the input stream.
lineNoFunction - Variable in class net.sf.basedb.util.parser.JepMapper
 
LineNoFunction - Class in net.sf.basedb.util.parser
Adds a lineNo() function to Jep.
LineNoFunction() - Constructor for class net.sf.basedb.util.parser.LineNoFunction
 
lineNum - Variable in class net.sf.basedb.util.gtf.GtfInputStream
 
lines - Variable in class net.sf.basedb.core.MigrateRbaToDba.SubtypeMapping
 
lines - Variable in class net.sf.basedb.util.parser.FlatFileParser
List of lines parsed by the FlatFileParser.parseHeaders() method.
linesToParse - Variable in class net.sf.basedb.util.gtf.GtfValidationAction
 
linesToParse - Variable in class net.sf.basedb.util.importer.spotdata.SecondPassSectionSpotsParser
 
lineTester - Variable in class net.sf.basedb.util.charset.CharsetDetector
 
LineType(String) - Constructor for enum class net.sf.basedb.util.parser.FlatFileParser.LineType
 
LINK_EMAIL - Static variable in class net.sf.basedb.clients.web.util.HTML
This flag is used in HTML.scanForLinks(String,int) when you want to create links for email addresses.
LINK_URL - Static variable in class net.sf.basedb.clients.web.util.HTML
This flag is used in HTML.scanForLinks(String,int) when you want to create links for URL:s.
linkAnnotations(AnnotationBatcher.UpdateBatcher) - Method in class net.sf.basedb.core.MigrateRbaToDba.Rba
Link the annotation set to the new derived bioassay.
linkAnyToAny(AnnotationBatcher.UpdateBatcher, AnnotationBatcher.UpdateBatcher) - Method in class net.sf.basedb.core.MigrateRbaToDba.Rba
Link any-to-any links with the new derived bioassay.
linkArrayDesign(AnnotationBatcher.InsertBatcher) - Method in class net.sf.basedb.core.MigrateRbaToDba.Rba
 
linkAttributes(ClientContext) - Method in class net.sf.basedb.util.extensions.ClientContext
Link this context to the other context with respect to attributes.
linkChangeHistory(AnnotationBatcher.UpdateBatcher) - Method in class net.sf.basedb.core.MigrateRbaToDba.Rba
Link change history entries with the new derived bioassay.
linkDescriptionColumnMapping - Static variable in class net.sf.basedb.plugins.batchimport.AnyToAnyImporter
 
LinkedFileFormatter - Class in net.sf.basedb.clients.web.formatter
Formatter implementation that generates a HTML output linking a file item.
LinkedFileFormatter() - Constructor for class net.sf.basedb.clients.web.formatter.LinkedFileFormatter
 
LinkedFileFormatter(boolean, boolean) - Constructor for class net.sf.basedb.clients.web.formatter.LinkedFileFormatter
 
LinkedFileFormatter(FileViewerUtil) - Constructor for class net.sf.basedb.clients.web.formatter.LinkedFileFormatter
 
LinkedItemFormatter - Class in net.sf.basedb.clients.web.formatter
Formatter implementation that generates a HTML output linking a nameable item.
LinkedItemFormatter() - Constructor for class net.sf.basedb.clients.web.formatter.LinkedItemFormatter
 
LinkedItemFormatter(boolean) - Constructor for class net.sf.basedb.clients.web.formatter.LinkedItemFormatter
 
linkedQuery - Variable in class net.sf.basedb.core.query.AnyToAnyRestriction
 
linkedRestriction - Variable in class net.sf.basedb.core.query.AnyToAnyRestriction
 
linkedTo - Variable in class net.sf.basedb.core.query.AnyToAnyRestriction
 
linkers - Variable in class net.sf.basedb.core.ExtendedProperty
 
linkFiles(AnnotationBatcher.UpdateBatcher, AnnotationBatcher.UpdateBatcher) - Method in class net.sf.basedb.core.MigrateRbaToDba.Rba
Link the file set to the new derived bioassay and update file types on members.
linkItemValues(Connection, Map<Integer, Integer>) - Method in class net.sf.basedb.core.MigrateRbaToDba
Change raw bioassays that have been used as job parameters to the new derived bioassay.
linkName - Variable in class net.sf.basedb.clients.web.extensions.list.AnyLinkColumn
 
linkName - Variable in class net.sf.basedb.clients.web.plugins.AnyToAnyDataLoader
 
linkName - Variable in class net.sf.basedb.core.AnyToAny.FastLinkLoader
 
linkName - Variable in class net.sf.basedb.core.query.AnyToAnyRestriction
 
linkName - Variable in class net.sf.basedb.util.AnyToAnyLinkStatistics
 
linkNameColumnMapping - Static variable in class net.sf.basedb.plugins.batchimport.AnyToAnyImporter
 
linkNameMapper - Variable in class net.sf.basedb.plugins.batchimport.AnyToAnyImporter
 
linkParentBioAssays(AnnotationBatcher.UpdateBatcher, AnnotationBatcher.UpdateBatcher) - Method in class net.sf.basedb.core.MigrateRbaToDba.Rba
 
links - Variable in class net.sf.basedb.core.AnyToAny.FastLinkLoader
 
links - Variable in class net.sf.basedb.core.data.AnnotatedData
 
links - Variable in class net.sf.basedb.core.data.BioAssayData
 
links - Variable in class net.sf.basedb.core.data.BioAssaySetData
 
links - Variable in class net.sf.basedb.core.data.PluginDefinitionData
 
links - Variable in class net.sf.basedb.core.data.ProjectData
 
links - Variable in class net.sf.basedb.core.data.RootRawBioAssayData
 
links - Variable in class net.sf.basedb.core.data.WellData
 
linkType - Variable in class net.sf.basedb.clients.web.plugins.AnyToAnyDataLoader
 
list - Variable in class net.sf.basedb.clients.web.taglib.table.CellValue
 
list - Variable in class net.sf.basedb.core.ItemList.DelayedAdditionManager
 
list() - Method in class net.sf.basedb.core.hibernate.QueryWrapper
 
list(DbControl) - Method in class net.sf.basedb.core.ItemQuery
Execute the query and return the results as a list.
list(DbControl) - Method in class net.sf.basedb.core.SpecialQuery
Get the result of the query as a list.
list(Item) - Static method in class net.sf.basedb.core.plugin.GuiContext
Shortcut to create a list context.
list(Item, String) - Static method in class net.sf.basedb.core.plugin.GuiContext
Shortcut to create a list context with a subcontext.
LIST - Enum constant in enum class net.sf.basedb.core.plugin.GuiContext.Type
 
LIST - Static variable in class net.sf.basedb.clients.web.extensions.toolbar.ToolbarUtil
 
LIST_ITEMS - Static variable in class net.sf.basedb.clients.web.extensions.list.ListColumnUtil
An array containing all items that we are registering an extension point for.
Listable - Interface in net.sf.basedb.core
Tagging interface for items that can be put in an ItemList.
listableItems - Static variable in class net.sf.basedb.core.Metadata
 
ListableUtil - Class in net.sf.basedb.util.listable
Utility class for working with Listable items.
ListableUtil() - Constructor for class net.sf.basedb.util.listable.ListableUtil
 
ListColumnAction<I,V> - Interface in net.sf.basedb.clients.web.extensions.list
Action that inserts a new column into a table listing.
ListColumnDataLoader<I> - Class in net.sf.basedb.clients.web.extensions.list
Data loader implementation that acts as a proxy to a ListColumnAction object.
ListColumnDataLoader(ListColumnAction<I, ?>) - Constructor for class net.sf.basedb.clients.web.extensions.list.ListColumnDataLoader
 
ListColumnExportRenderer<I> - Class in net.sf.basedb.clients.web.extensions.list
Renderer implementation that add formatter and data loader implementation for a list column that can be exported.
ListColumnExportRenderer(ItemContext) - Constructor for class net.sf.basedb.clients.web.extensions.list.ListColumnExportRenderer
 
ListColumnUtil - Class in net.sf.basedb.clients.web.extensions.list
Utility class for list column extension points.
ListColumnUtil() - Constructor for class net.sf.basedb.clients.web.extensions.list.ListColumnUtil
 
listener - Variable in class net.sf.basedb.core.signal.SocketSignalReceiver
 
listener - Variable in class net.sf.basedb.util.jobagent.JobAgentServerConnection
 
ListenerThread(ServerSocketChannel) - Constructor for class net.sf.basedb.core.signal.SocketSignalReceiver.ListenerThread
 
ListenerThread(ServerSocketChannel, RequestHandler, Logger) - Constructor for class net.sf.basedb.util.jobagent.JobAgentServerConnection.ListenerThread
 
listenOnSocket() - Method in class net.sf.basedb.clients.jobagent.AgentSignalReceiver
Do not open any socket.
listenOnSocket() - Method in class net.sf.basedb.core.signal.SocketSignalReceiver
Start listening for incoming signals.
listId - Variable in class net.sf.basedb.core.MigrateRbaToDba.Itemlist
 
listIterator() - Method in class net.sf.basedb.core.ItemResultList
 
listIterator(int) - Method in class net.sf.basedb.core.ItemResultList
 
listMemberType - Variable in class net.sf.basedb.core.SyncFilter
 
listQuery - Variable in class net.sf.basedb.clients.web.extensions.list.RelatedItemListColumn
 
listTables(DatabaseMetaData, String, String) - Static method in class net.sf.basedb.core.dbengine.TableInfo
List all tables that are present in the given catalog and/or schema.
listToMap(List<? extends SettingData>) - Method in class net.sf.basedb.core.SessionControl
Copy settings from a List to a Map.
ListUtil - Class in net.sf.basedb.util
 
ListUtil() - Constructor for class net.sf.basedb.util.ListUtil
 
ln(String) - Method in class net.sf.basedb.core.dbengine.AbstractDbEngine
Return LN(<value>).
ln(String) - Method in interface net.sf.basedb.core.dbengine.DbEngine
Get the function call that takes the natural logarithm of a value.
ln(String) - Method in class net.sf.basedb.core.dbengine.MySQLEngine
Return LOG(<value>).
ln(Expression) - Static method in class net.sf.basedb.core.query.Expressions
Calculate the natural logarithm of an expression: new expression = ln(e).
LN2 - Static variable in enum class net.sf.basedb.core.IntensityTransform
 
load(Class<T>, Serializable) - Method in class net.sf.basedb.core.hibernate.SessionWrapper
 
load(Class<T>, Serializable, LockMode) - Method in class net.sf.basedb.core.hibernate.SessionWrapper
 
load(Class<T>, Serializable, LockOptions) - Method in class net.sf.basedb.core.hibernate.SessionWrapper
 
load(Object, Serializable) - Method in class net.sf.basedb.core.hibernate.SessionWrapper
 
load(String, int) - Method in class net.sf.basedb.util.StaticCache
Read a serializable object from the cache.
load(String, Serializable) - Method in class net.sf.basedb.core.hibernate.SessionWrapper
 
load(String, Serializable, LockMode) - Method in class net.sf.basedb.core.hibernate.SessionWrapper
 
load(String, Serializable, LockOptions) - Method in class net.sf.basedb.core.hibernate.SessionWrapper
 
load(String, ClassLoader, int) - Method in class net.sf.basedb.util.StaticCache
 
load(Collection<? extends Annotatable>) - Method in class net.sf.basedb.core.FastAnnotationLoader
Load the annotation values for all items in the given collection.
load(Iterator<? extends Annotatable>) - Method in class net.sf.basedb.core.FastAnnotationLoader
Load the annotation values for all items returned by the given iterator.
load(ItemQuery<? extends Annotatable>) - Method in class net.sf.basedb.core.FastAnnotationLoader
Load the annotation values for all items returned by the query.
loadAbout(Element) - Method in class net.sf.basedb.util.extensions.xml.XmlLoader
Load information in an <about> tag.
loadAnnotationInfo - Variable in class net.sf.basedb.core.AnnotationBatcher
 
loadAnnotationValues - Variable in class net.sf.basedb.core.AnnotationBatcher
 
loadAttributes(ItemContext, String) - Method in class net.sf.basedb.util.extensions.ClientContext
Load attributes to this context from the given ItemContext instance.
loadCdfFile(File) - Method in class net.sf.basedb.util.affymetrix.CdfValidator
Load a CDF file using the Affymetric Fusion SDK.
loadCelFile(File) - Method in class net.sf.basedb.util.affymetrix.CelValidator
Load a CEL file using the Affymetric Fusion SDK.
loadChildNodes(DbControl, OverviewContext, Node) - Method in class net.sf.basedb.util.overview.loader.AbstractNodeLoader
Load childs nodes.
loadChildNodes(DbControl, OverviewContext, Node) - Method in class net.sf.basedb.util.overview.loader.AutoChildNodeLoader
Call the same method on the 'parent' node loader.
loadChildNodes(DbControl, OverviewContext, Node) - Method in class net.sf.basedb.util.overview.loader.BioWellLoader
Delegate loading of child nodes to the actual item loader that this node is representing.
loadChildNodes(DbControl, OverviewContext, Node) - Method in class net.sf.basedb.util.overview.loader.ExtensionChildNodeLoader
Call the same method on the 'parent' node loader.
loadChildNodes(DbControl, OverviewContext, Node) - Method in interface net.sf.basedb.util.overview.loader.NodeLoader
Load child nodes of the current node unless they have been loaded already.
loadChildNodes(DbControl, OverviewContext, Node) - Method in class net.sf.basedb.util.overview.loader.NullNodeLoader
 
loadChildNodesOfFolderNode(DbControl, OverviewContext, Node) - Method in class net.sf.basedb.util.overview.loader.AbstractNodeLoader
Iterates the children of a folder-type node and loads the children for each one of them.
loadChildNodesOfItemNode(DbControl, OverviewContext, Node) - Method in class net.sf.basedb.util.overview.loader.AbstractNodeLoader
Loads child nodes of an item-type node.
loadClass(String, boolean) - Method in class net.sf.basedb.util.JarClassLoader
 
loadClassData(File, String) - Method in class net.sf.basedb.util.JarClassLoader
Load the byte[] of the given class.
loadClasses(Set<String>, Document, String) - Static method in class net.sf.basedb.core.ExtendedProperties
Load the classes and put their names in the ExtendedProperties.classes variable.
loadClassInternal(ClassLoader, String) - Method in class net.sf.basedb.util.JarClassLoader
 
loadClientDefaultSettings(Session, int) - Method in class net.sf.basedb.core.SessionControl
Load client applications default settings.
loadContext(int) - Method in class net.sf.basedb.core.SessionControl
Load a context and make it the current context.
loadContext(int, boolean) - Method in class net.sf.basedb.core.SessionControl
Load a context and make it the current context, optionally copying temporary filters and objects from the current context to the loaded context.
loadContext(SessionControl, int, ItemContext) - Static method in class net.sf.basedb.clients.web.Base
 
loadContextInternal(int) - Method in class net.sf.basedb.core.SessionControl
Load a context with the specified ID.
loadContextInternal(Item, String, String) - Method in class net.sf.basedb.core.SessionControl
Load a named context.
loadData(Class<T>, Query<T>, StatelessSession, SessionControl) - Static method in class net.sf.basedb.core.QueryExecutor
Executes a Hibernate query on a stateless session.
loadData(Query<T>) - Static method in class net.sf.basedb.core.HibernateUtil
Load a data item from the database using a query.
loadData(Session, Class<T>, int) - Static method in class net.sf.basedb.core.HibernateUtil
Load a data item from the database when you know the id.
loadData(Session, Class<T>, String, int) - Static method in class net.sf.basedb.core.HibernateUtil
Load a data item from the database when you know the id.
loadData(StatelessSession, Class<T>, int) - Static method in class net.sf.basedb.core.HibernateUtil
Load a data item from the database using a statless session when you know the id.
loadData(StatelessSession, Class<T>, String, int) - Static method in class net.sf.basedb.core.HibernateUtil
Load a data item from the database using a statless session when you know the id.
loadDevice(Session, LoginRequest, AuthenticatedUser) - Method in class net.sf.basedb.core.SessionControl
Verify the device the user is using.
loadDiskUsage(Query<Object[]>) - Method in class net.sf.basedb.core.DiskUsageStatistics.Summary
 
loadDocument(InputStream, String) - Method in class net.sf.basedb.clients.web.extensions.ServletLoader
Load and validate the XML file.
loadDocument(InputStream, String) - Method in class net.sf.basedb.util.extensions.xml.XmlLoader
Load and validate the XML file.
loader - Variable in class net.sf.basedb.util.extensions.manager.processor.PluginInstallationProcessor
 
loader - Variable in class net.sf.basedb.util.extensions.manager.processor.RegisterExtensionsProcessor
 
loader - Variable in class net.sf.basedb.util.extensions.Registry.RegisteredEventHandler
 
loader - Variable in class net.sf.basedb.util.JarClassLoader.JarClassLoaderProxy
 
loaders - Variable in class net.sf.basedb.util.overview.loader.BasicItemNodeLoaderFactory
 
loadExtendedPropertiesFile() - Static method in class net.sf.basedb.core.ExtendedProperties
Load and parse the file with predefined queries.
loadExtensionPoints(Document, ClassLoader, About) - Method in class net.sf.basedb.util.extensions.xml.XmlLoader
Create extension points from an XML document.
loadExtensions(Document, ClassLoader, About) - Method in class net.sf.basedb.util.extensions.xml.XmlLoader
Create extensions from an XML document.
loadExtracts() - Method in class net.sf.basedb.util.AnnotationUtil.AnnotatableWrapper
Load extracts in parent chain.
loadFiles(DbControl, Collection<Nameable>, Directory) - Method in class net.sf.basedb.plugins.PackedFileExporter
Load files and subdirectories in the given directory.
loadFilesAndDirectories(DbControl, Collection<Nameable>, Collection<Integer>, Collection<Integer>, boolean) - Method in class net.sf.basedb.plugins.PackedFileExporter
Load specified files and directories and put them in loadedFiles.
loadFilterTemplates(String) - Method in class net.sf.basedb.core.HibernateUtil.FilterConfigurator
 
loadForward - Variable in enum class net.sf.basedb.util.overview.node.ChildNodeDirection
 
loadForward() - Method in enum class net.sf.basedb.util.overview.node.ChildNodeDirection
 
loadForwardChildNodes(DbControl, OverviewContext, Node) - Method in class net.sf.basedb.util.overview.loader.AbstractNodeLoader
Load forward-loading child nodes.
loadForwardChildNodes(DbControl, OverviewContext, Node) - Method in class net.sf.basedb.util.overview.loader.ArrayBatchLoader
Loads the array slide nodes that is related to the given batch node.
loadForwardChildNodes(DbControl, OverviewContext, Node) - Method in class net.sf.basedb.util.overview.loader.ArrayDesignLoader
Loads the array batch nodes that has been created with the given design node.
loadForwardChildNodes(DbControl, OverviewContext, Node) - Method in class net.sf.basedb.util.overview.loader.ArraySlideLoader
Loads the physical bioassay node that is related to the given array slide node.
loadForwardChildNodes(DbControl, OverviewContext, Node) - Method in class net.sf.basedb.util.overview.loader.BioPlateEventLoader
Loads the bioplates that are part of the event.
loadForwardChildNodes(DbControl, OverviewContext, Node) - Method in class net.sf.basedb.util.overview.loader.BioPlateLoader
Loads the non-empty biowells on the bioplate.
loadForwardChildNodes(DbControl, OverviewContext, Node) - Method in class net.sf.basedb.util.overview.loader.BioSourceLoader
Loads the sample nodes that has been created from the given biosource node.
loadForwardChildNodes(DbControl, OverviewContext, Node) - Method in class net.sf.basedb.util.overview.loader.DerivedBioAssayLoader
Loads all child derived bioassay and raw bioassay nodes.
loadForwardChildNodes(DbControl, OverviewContext, Node) - Method in class net.sf.basedb.util.overview.loader.ExtractLoader
Loads the child extracts and physical bioassays that has been created from this extract.
loadForwardChildNodes(DbControl, OverviewContext, Node) - Method in class net.sf.basedb.util.overview.loader.ItemListLoader
Loads the list members.
loadForwardChildNodes(DbControl, OverviewContext, Node) - Method in class net.sf.basedb.util.overview.loader.PhysicalBioAssayLoader
Load forward-loading child nodes: Derived bioassay sets (root): DerivedBioAssayLoader.createForwardNode(DbControl, OverviewContext, Node) Array slide in reverse direction (if the parent node is an extract): ArraySlideLoader.createReverseNode(DbControl, OverviewContext, Node) Extracts in reverse direction (if the parent node is the array slide): ExtractLoader.createReverseNode(DbControl, OverviewContext, Node)
loadForwardChildNodes(DbControl, OverviewContext, Node) - Method in class net.sf.basedb.util.overview.loader.RawBioAssayLoader
Loads all experiment nodes where the given raw bioassay is used.
loadForwardChildNodes(DbControl, OverviewContext, Node) - Method in class net.sf.basedb.util.overview.loader.SampleLoader
Loads the pooled samples and extracts that has been created from this sample.
loadFrom(InputStream, String) - Method in class net.sf.basedb.core.Presets
Load presets from a stream.
loadFrom(String) - Method in class net.sf.basedb.core.Presets
Load presets from an XML string.
loadFromPreset(Presets.Preset, boolean) - Method in class net.sf.basedb.util.overview.ValidationOptions
Load validation options from a Presets.Preset.
loadGlobalAbout(Document) - Method in class net.sf.basedb.util.extensions.xml.XmlLoader
Load the global about tag from the document.
loadGroups(Session) - Method in class net.sf.basedb.core.Keyring
Loads group membership for the user and put that information in the Keyring.groups and Keyring.groupsWithNonHiddenMembers variables.
loadIdToNameMap(Session, String) - Static method in class net.sf.basedb.core.Update
 
loadInherited - Variable in class net.sf.basedb.clients.web.plugins.ExportedProperty
 
loadIntensityFormulas(Element, int, String) - Static method in class net.sf.basedb.core.RawDataTypes
Load the intensity formulas for the specified raw data type node and return a list of IntensityFormula objects.
loadInterfaceInformation(String, String) - Method in class net.sf.basedb.core.PluginType
 
loadItem(I) - Method in class net.sf.basedb.core.DbControl
Load an item from the database.
loadItem(Class<I>, int) - Method in class net.sf.basedb.core.DbControl
Load an item from the database when you now the id.
loadItemByDataClass(Class<I>, Class<D>, int) - Method in class net.sf.basedb.core.DbControl
Load an item from the database when you know the id.
loadItemId(Session, Item, int) - Static method in class net.sf.basedb.core.AnnotationSet
Load the id of the item that this annotation set belongs to.
loadItemKeys(Session) - Method in class net.sf.basedb.core.Keyring
Load all ItemKey:s for the logged in user and put the result in Keyring.itemPermissions
loadIterator(Query<T>, boolean, SessionControl) - Static method in class net.sf.basedb.core.HibernateUtil
Scroll through the result of a query using an iterator.
loadIterator(Query<T>, StatelessSession, SessionControl) - Static method in class net.sf.basedb.core.QueryExecutor
Executes a Hibernate query that returns an iterator on a stateless session.
loadJarFile(File, boolean) - Method in class net.sf.basedb.util.JarClassLoader
Open the specified JAR file, list all entries and put them in the JarClassLoader.classPath mapping.
loadJsonForBatchInherit(DbControl, AnnotationType) - Static method in class net.sf.basedb.clients.web.AnnotationUtil
Load information about categories and subtypes of an annotation type that are useful for deciding about inheriting annotations from parent items, The result is returned as a JSON object intended to be used by the "Batch inherit annotations" feature in the web interface.
loadLastValidatedFile(ClassLoader, boolean) - Method in class net.sf.basedb.clients.web.extensions.ServletLoader
Continue loading servlet definitions from the last validated XML file.
loadLastValidatedFile(ClassLoader, boolean) - Method in class net.sf.basedb.util.extensions.xml.XmlLoader
Continue loading extensions from the last validated XML file.
loadList(Query<T>, SessionControl) - Static method in class net.sf.basedb.core.HibernateUtil
Load a List of items from the database using a query.
loadMaxProjectPermission(Session, ProjectData) - Method in class net.sf.basedb.core.Keyring
Find out the logged in user's maximum permission to the active project and put the result in Keyring.maxProjectPermission.
loadMemberNodes(BasicItemNodeLoader<T>, DbControl, OverviewContext, Node) - Static method in class net.sf.basedb.util.overview.loader.ItemListLoader
Utiltity method to be used by other loaders to load members of an item list.
loadMinimalDirectoryTree(DbControl, Collection<Include>, Directory...) - Static method in class net.sf.basedb.util.FileUtil
Load a minimal directory tree that includes at least all the specified directories and their parent directories all the way up to the root or as far as the logged in user has read permission.
loadMinimalDirectoryTree(DbControl, Directory...) - Static method in class net.sf.basedb.util.FileUtil
Load a minimal directory tree that includes at least all the specified directories and their parent directories all the way up to the root or as far as the logged in user has read permission.
loadParentReporterPositions(DbControl, BioAssaySet) - Method in class net.sf.basedb.util.importer.spotdata.BaseFileInfo
Load position/reporter mapping from the parent bioassay set.
loadParents - Variable in class net.sf.basedb.util.listable.CollectExtracts.CollectFromDerivedBioAssays
 
loadPluginDefinitions(Document, ClassLoader, About) - Method in class net.sf.basedb.util.extensions.xml.XmlLoader
Load plug-in information from an XML document.
loadPluginInformation(String, String, boolean) - Method in class net.sf.basedb.core.PluginDefinition
Load a plugin and copy information to the internal data structure.
loadPluginPermissionKeys(Session) - Method in class net.sf.basedb.core.Keyring
Load all PluginKeys:s for the active plugin.
loadPresets(Document) - Method in class net.sf.basedb.core.Presets
Parse an XML Document and load all presets.
loadProjectKeys(Session) - Method in class net.sf.basedb.core.Keyring
Load all ProjectKey:s for the logged in user.
loadProjects(Session) - Method in class net.sf.basedb.core.Keyring
Loads project membership for the user and put that information in the Keyring.projects variable.
loadProperties(Set<String>, Element, String) - Static method in class net.sf.basedb.core.ExtendedProperties
Load the properties for the specified class node and put the list in the ExtendedProperties.allProperties variable.
loadProperties(Element, int, String) - Static method in class net.sf.basedb.core.RawDataTypes
Load the properties for the specified raw data type node and return a list of RawDataProperty objects.
loadProperty - Variable in enum class net.sf.basedb.util.overview.node.ChildNodeDirection
 
loadProperty() - Method in enum class net.sf.basedb.util.overview.node.ChildNodeDirection
 
loadPropertyChildNodes(DbControl, OverviewContext, Node) - Method in class net.sf.basedb.util.overview.loader.AbstractNodeLoader
Load property-type child nodes.
loadPropertyChildNodes(DbControl, OverviewContext, Node) - Method in class net.sf.basedb.util.overview.loader.AnyToAnyLoader
Loads property nodes of an any-to-any node.
loadPropertyChildNodes(DbControl, OverviewContext, Node) - Method in class net.sf.basedb.util.overview.loader.ArrayBatchLoader
Loads property nodes of an array batch.
loadPropertyChildNodes(DbControl, OverviewContext, Node) - Method in class net.sf.basedb.util.overview.loader.ArrayDesignLoader
Loads property nodes of an array design.
loadPropertyChildNodes(DbControl, OverviewContext, Node) - Method in class net.sf.basedb.util.overview.loader.ArraySlideLoader
Loads property nodes of an array slide.
loadPropertyChildNodes(DbControl, OverviewContext, Node) - Method in class net.sf.basedb.util.overview.loader.BioPlateEventLoader
Loads property nodes of an event.
loadPropertyChildNodes(DbControl, OverviewContext, Node) - Method in class net.sf.basedb.util.overview.loader.BioPlateLoader
Load the freezer node.
loadPropertyChildNodes(DbControl, OverviewContext, Node) - Method in class net.sf.basedb.util.overview.loader.BioSourceLoader
Loads property nodes of an array design.
loadPropertyChildNodes(DbControl, OverviewContext, Node) - Method in class net.sf.basedb.util.overview.loader.DataFileLoader
Loads property nodes of files.
loadPropertyChildNodes(DbControl, OverviewContext, Node) - Method in class net.sf.basedb.util.overview.loader.DerivedBioAssayLoader
Loads property nodes of a derived bioassay set.
loadPropertyChildNodes(DbControl, OverviewContext, Node) - Method in class net.sf.basedb.util.overview.loader.ExperimentLoader
loadPropertyChildNodes(DbControl, OverviewContext, Node) - Method in class net.sf.basedb.util.overview.loader.ExtractLoader
Loads property nodes of an extract.
loadPropertyChildNodes(DbControl, OverviewContext, Node) - Method in class net.sf.basedb.util.overview.loader.FileLoader
Loads annotations for the given file node.
loadPropertyChildNodes(DbControl, OverviewContext, Node) - Method in class net.sf.basedb.util.overview.loader.HardwareLoader
Loads annotations and hardware parameters for the given hardware node.
loadPropertyChildNodes(DbControl, OverviewContext, Node) - Method in class net.sf.basedb.util.overview.loader.ItemListLoader
Loads property nodes of a item list.
loadPropertyChildNodes(DbControl, OverviewContext, Node) - Method in class net.sf.basedb.util.overview.loader.KitLoader
Loads annotations for the given kit node.
loadPropertyChildNodes(DbControl, OverviewContext, Node) - Method in class net.sf.basedb.util.overview.loader.PhysicalBioAssayLoader
Loads property nodes of a physical bioassay.
loadPropertyChildNodes(DbControl, OverviewContext, Node) - Method in class net.sf.basedb.util.overview.loader.ProtocolLoader
Loads annotations and protocol parameters for the given protocol node.
loadPropertyChildNodes(DbControl, OverviewContext, Node) - Method in class net.sf.basedb.util.overview.loader.RawBioAssayLoader
loadPropertyChildNodes(DbControl, OverviewContext, Node) - Method in class net.sf.basedb.util.overview.loader.RootRawBioAssayLoader
loadPropertyChildNodes(DbControl, OverviewContext, Node) - Method in class net.sf.basedb.util.overview.loader.SampleLoader
Loads property nodes of a sample.
loadPropertyChildNodes(DbControl, OverviewContext, Node) - Method in class net.sf.basedb.util.overview.loader.SoftwareLoader
Loads annotations and software parameters for the given software node.
loadPropertyChildNodes(DbControl, OverviewContext, Node) - Method in class net.sf.basedb.util.overview.loader.TagLoader
Loads annotations and tag parameters for the given tag node.
loadRawDataTypes(Set<String>, Document, String) - Static method in class net.sf.basedb.core.RawDataTypes
Load the raw data types and put the information in the RawDataTypes.rawDataTypes map.
loadRawDataTypesFile() - Static method in class net.sf.basedb.core.RawDataTypes
Load and parse the file with raw data types.
loadRecent(DbControl, Item, String) - Method in class net.sf.basedb.core.ItemContext
 
loadRecent(DbControl, Item, String, int) - Method in class net.sf.basedb.core.ItemContext
 
loadReverse - Variable in enum class net.sf.basedb.util.overview.node.ChildNodeDirection
 
loadReverse() - Method in enum class net.sf.basedb.util.overview.node.ChildNodeDirection
 
loadReverseChildNodes(DbControl, OverviewContext, Node) - Method in class net.sf.basedb.util.overview.loader.AbstractNodeLoader
Load reverse-loading child nodes.
loadReverseChildNodes(DbControl, OverviewContext, Node) - Method in class net.sf.basedb.util.overview.loader.ArrayBatchLoader
Loads the array design node that is the parent of this array batch.
loadReverseChildNodes(DbControl, OverviewContext, Node) - Method in class net.sf.basedb.util.overview.loader.ArraySlideLoader
Loads the array batch node that is the parent of this array slide.
loadReverseChildNodes(DbControl, OverviewContext, Node) - Method in class net.sf.basedb.util.overview.loader.BioSourceLoader
A biosource usually don't have any reverse child nodes.
loadReverseChildNodes(DbControl, OverviewContext, Node) - Method in class net.sf.basedb.util.overview.loader.DerivedBioAssayLoader
Loads the parent bioassay or the parent physical bioassay.
loadReverseChildNodes(DbControl, OverviewContext, Node) - Method in class net.sf.basedb.util.overview.loader.ExperimentLoader
Loads the root raw bioassay nodes that are part of this experiment
loadReverseChildNodes(DbControl, OverviewContext, Node) - Method in class net.sf.basedb.util.overview.loader.ExtractLoader
Load either the parent sample or extract(s) and child extracts+physical bioassays with a subtype that has ItemSubtype.getPushAnnotations() flag set.
loadReverseChildNodes(DbControl, OverviewContext, Node) - Method in class net.sf.basedb.util.overview.loader.PhysicalBioAssayLoader
loadReverseChildNodes(DbControl, OverviewContext, Node) - Method in class net.sf.basedb.util.overview.loader.RawBioAssayLoader
Loads the derived bioassay node that this raw bioassay is created from.
loadReverseChildNodes(DbControl, OverviewContext, Node) - Method in class net.sf.basedb.util.overview.loader.RootRawBioAssayLoader
Loads the derived bioassay node that this raw bioassay is created from.
loadReverseChildNodes(DbControl, OverviewContext, Node) - Method in class net.sf.basedb.util.overview.loader.SampleLoader
If the sample is a pooled sample, loads the parent samples that it was pooled from.
loadRoleKeys(Session) - Method in class net.sf.basedb.core.Keyring
Load all RoleKey:s for the logged in user and put the result in Keyring.rolePermissions
loadRoles(Session) - Method in class net.sf.basedb.core.Keyring
Loads role membership for the user and put that information in the Keyring.roles variable.
loadServletClass(String, ClassLoader) - Method in class net.sf.basedb.clients.web.extensions.ServletLoader
Load the servlet class.
loadServlets(Document, ClassLoader) - Method in class net.sf.basedb.clients.web.extensions.ServletLoader
Load the servlet definitions from an XML document.
LoadServletsProcessor - Class in net.sf.basedb.clients.web.extensions
Processor implementation that define servlets based on what it can find in the META-INF/servlets.xml file.
LoadServletsProcessor(ServletContext, ProcessResults) - Constructor for class net.sf.basedb.clients.web.extensions.LoadServletsProcessor
 
loadState(ClassLoader) - Method in class net.sf.basedb.core.Job
Load the saved state from the cache.
loadUserClientSettings(Session, int, int) - Method in class net.sf.basedb.core.SessionControl
Load users client-specific settings.
loadUserDefaultSettings(Session, int) - Method in class net.sf.basedb.core.SessionControl
Load users default settings.
loadUsers(Session) - Method in class net.sf.basedb.core.Keyring
Load all users which are member of at least one group where the logged in user is also a member and put that information in the Keyring.users variable.
loadXmlFile(InputStream, String, ClassLoader, boolean) - Method in class net.sf.basedb.clients.web.extensions.ServletLoader
Load a servlet definition XML file.
loadXmlFile(InputStream, String, ClassLoader, boolean) - Method in class net.sf.basedb.util.extensions.xml.XmlLoader
Load an extensions definition XML file.
loadXmlFile2(InputStream, String) - Static method in class net.sf.basedb.core.PluginConfiguration
Load a configurations xml file from the given stream.
LOCAL_HOST - Static variable in class net.sf.basedb.util.SocketUtil
 
locale - Static variable in class net.sf.basedb.core.Config
 
LocalSignalReceiver - Class in net.sf.basedb.core.signal
A signal receiver implementation that can receive signals from the local virtual machine only.
LocalSignalReceiver() - Constructor for class net.sf.basedb.core.signal.LocalSignalReceiver
Create a new local signal receiver.
LocalSignalTransporter - Class in net.sf.basedb.core.signal
A signal transporter implementation that can transport signals within the local virtual machine only.
LocalSignalTransporter() - Constructor for class net.sf.basedb.core.signal.LocalSignalTransporter
Create a new signal transporter instance.
localVersion - Variable in class net.sf.basedb.clients.web.taglib.Head
 
location - Variable in class net.sf.basedb.core.data.DiskUsageData
 
location - Variable in class net.sf.basedb.core.data.FileData
 
location - Variable in class net.sf.basedb.core.data.QuotaIndex
 
location - Variable in class net.sf.basedb.core.data.SessionData
 
location - Variable in class net.sf.basedb.core.data.UserDeviceData
 
location - Variable in class net.sf.basedb.core.SessionControl
Location of the remote IP.
Location - Enum Class in net.sf.basedb.core
This enumeration defines constants that are used to specify different file storage locations.
Location(int, String, boolean, boolean) - Constructor for enum class net.sf.basedb.core.Location
Creates a new location.
locationLat - Variable in class net.sf.basedb.core.data.SessionData
 
locationLat - Variable in class net.sf.basedb.core.data.UserDeviceData
 
locationLoaded - Variable in class net.sf.basedb.core.SessionControl
 
locationLong - Variable in class net.sf.basedb.core.data.SessionData
 
locationLong - Variable in class net.sf.basedb.core.data.UserDeviceData
 
locator - Variable in class net.sf.basedb.util.importer.spotdata.BfsImporter
 
lock - Variable in class net.sf.basedb.util.extensions.logging.ExtensionsLog
 
lock - Variable in class net.sf.basedb.util.StaticCache.State
 
lock() - Method in class net.sf.basedb.core.Application.StartupOptions
Lock the options for additional modifications.
lock() - Method in class net.sf.basedb.util.Enumeration
 
lock(Object, LockModeType) - Method in class net.sf.basedb.core.hibernate.SessionWrapper
 
lock(Object, LockModeType, Map<String, Object>) - Method in class net.sf.basedb.core.hibernate.SessionWrapper
 
lock(Object, LockMode) - Method in class net.sf.basedb.core.hibernate.SessionWrapper
 
lock(String, Object, LockMode) - Method in class net.sf.basedb.core.hibernate.SessionWrapper
 
lockData(Session, BasicData, LockOptions) - Static method in class net.sf.basedb.core.HibernateUtil
Reconnect a disconnected data object to the session, discarding changes that have been made while the object was disconnected.
locked - Variable in class net.sf.basedb.clients.web.taglib.table.Navigator
 
locked - Variable in class net.sf.basedb.core.Application.StartupOptions
 
locked - Variable in class net.sf.basedb.core.data.ReporterCloneTemplateData
 
locked - Variable in class net.sf.basedb.util.Enumeration
 
LOCKED_AFTER_ADD - Enum constant in enum class net.sf.basedb.core.BioWell.LockMode
It is allowed to add biomaterial once to the well.
LOCKED_AFTER_CREATE - Enum constant in enum class net.sf.basedb.core.BioWell.LockMode
It is allowed to add biomaterial once to the well, but it most be done at the same time the plate is creted.
LOCKED_AFTER_MOVE - Enum constant in enum class net.sf.basedb.core.BioWell.LockMode
It is allowed to add biomaterial once to the well.
lockedColumns - Variable in class net.sf.basedb.util.bfs.DataWriter
 
LockEntry(ReadWriteLock, String) - Constructor for class net.sf.basedb.util.StaticCache.LockEntry
 
lockMode - Variable in class net.sf.basedb.core.data.BioPlateTypeData
 
LockMode(int, String) - Constructor for enum class net.sf.basedb.core.BioWell.LockMode
 
locks - Variable in class net.sf.basedb.util.StaticCache
 
LockSafeInputStream(InputStream, StaticCache.LockEntry) - Constructor for class net.sf.basedb.util.StaticCache.LockSafeInputStream
 
LockSafeOutputStream(OutputStream, StaticCache.LockEntry) - Constructor for class net.sf.basedb.util.StaticCache.LockSafeOutputStream
 
log - Static variable in class net.sf.basedb.clients.jobagent.Agent
Log job agent events.
log - Static variable in class net.sf.basedb.clients.jobagent.AgentController
Log job agent events.
log - Static variable in class net.sf.basedb.clients.jobagent.executors.DummyJobExecutor
Log job agent events.
log - Static variable in class net.sf.basedb.clients.jobagent.executors.ProcessJobExecutor
Log job agent events.
log - Static variable in class net.sf.basedb.clients.jobagent.executors.ThreadJobExecutor
Log job agent events.
log - Static variable in class net.sf.basedb.clients.jobagent.handlers.DefaultRequestHandler
Log job agent events.
log - Static variable in class net.sf.basedb.clients.jobagent.handlers.InfoRequestHandler
 
log - Static variable in class net.sf.basedb.clients.jobagent.handlers.MultiProtocolRequestHandler
Logger.
log - Static variable in class net.sf.basedb.clients.jobagent.JobQueueChecker
Log job agent events.
log - Static variable in class net.sf.basedb.clients.jobagent.JobRunner
Log job agent events.
log - Static variable in class net.sf.basedb.clients.jobagent.slotmanager.InternalSlotManager
 
log - Static variable in class net.sf.basedb.clients.jobagent.slotmanager.MasterSlotManager
 
log - Static variable in class net.sf.basedb.clients.jobagent.slotmanager.RemoteSlotManager
 
log - Static variable in class net.sf.basedb.clients.web.extensions.ExtensionsControl
 
log - Static variable in class net.sf.basedb.clients.web.extensions.LoadServletsProcessor
 
log - Static variable in class net.sf.basedb.clients.web.extensions.service.Services
 
log - Static variable in class net.sf.basedb.clients.web.extensions.service.ServicesEventHandler
 
log - Static variable in class net.sf.basedb.clients.web.extensions.service.StartServiceRenderer
 
log - Static variable in class net.sf.basedb.clients.web.extensions.service.StopServiceRenderer
 
log - Variable in class net.sf.basedb.clients.web.extensions.XJspCompiler
 
log - Static variable in class net.sf.basedb.clients.web.fileupload.FileUpload
Debug file upload.
log - Static variable in class net.sf.basedb.clients.web.servlet.ContentSecurityPolicyReportServlet
 
log - Static variable in class net.sf.basedb.clients.web.taglib.DeprecationLogger
 
log - Static variable in class net.sf.basedb.core.AnnotationBatcher
 
log - Static variable in class net.sf.basedb.core.Application
Log core events.
log - Static variable in class net.sf.basedb.core.DbControl
Log core events.
log - Static variable in class net.sf.basedb.core.DynamicResultIterator
Logger.
log - Static variable in class net.sf.basedb.core.ExtendedProperties
Log core events.
log - Static variable in class net.sf.basedb.core.hibernate.DbIndexWork
 
log - Static variable in class net.sf.basedb.core.hibernate.SchemaGenerator
 
log - Static variable in class net.sf.basedb.core.HibernateUtil
Log core events.
log - Static variable in class net.sf.basedb.core.Install
Log core events.
log - Static variable in class net.sf.basedb.core.InternalJobQueue
Log job queue events.
log - Static variable in class net.sf.basedb.core.JobAgent
Log events.
log - Static variable in class net.sf.basedb.core.Keyring
Log core events.
log - Static variable in class net.sf.basedb.core.PredefinedQuery
Log core events.
log - Static variable in class net.sf.basedb.core.ProjectSpecificAnnotationsManager
 
log - Static variable in class net.sf.basedb.core.query.Hql
Log core events.
log - Static variable in class net.sf.basedb.core.RawDataTypes
Log core events.
log - Static variable in class net.sf.basedb.core.ServiceSessionControl
 
log - Static variable in class net.sf.basedb.core.SessionControl
Log core events.
log - Static variable in class net.sf.basedb.core.Trashcan
Log trashcan events.
log - Static variable in class net.sf.basedb.core.Update
Log core events.
log - Variable in class net.sf.basedb.util.ColorGenerator
 
log - Variable in class net.sf.basedb.util.extensions.logging.ExtensionsLogger
 
log - Static variable in class net.sf.basedb.util.extensions.LoggingErrorHandlerFactory
 
log - Static variable in class net.sf.basedb.util.extensions.manager.ExtensionsFile
 
log - Static variable in class net.sf.basedb.util.extensions.manager.ExtensionsManager
 
log - Static variable in class net.sf.basedb.util.extensions.manager.filter.DeletedFilter
 
log - Static variable in class net.sf.basedb.util.extensions.manager.filter.InstalledFilter
 
log - Static variable in class net.sf.basedb.util.extensions.manager.filter.InvalidAndModifiedFilter
 
log - Static variable in class net.sf.basedb.util.extensions.manager.filter.ValidAndNewOrModifiedFilter
 
log - Static variable in class net.sf.basedb.util.extensions.manager.processor.DeleteResourcesProcessor
 
log - Static variable in class net.sf.basedb.util.extensions.manager.processor.DisablePluginsProcessor
 
log - Static variable in class net.sf.basedb.util.extensions.manager.processor.ExtractResourcesProcessor
 
log - Static variable in class net.sf.basedb.util.extensions.manager.processor.PluginInstallationProcessor
 
log - Static variable in class net.sf.basedb.util.extensions.manager.processor.RegisterExtensionsProcessor
 
log - Static variable in class net.sf.basedb.util.extensions.manager.processor.ResetProcessor
 
log - Static variable in class net.sf.basedb.util.extensions.manager.processor.UnregisterExtensionsProcessor
 
log - Static variable in class net.sf.basedb.util.extensions.Registry
 
log - Static variable in class net.sf.basedb.util.extensions.RethrowErrorHandlerFactory
 
log - Static variable in class net.sf.basedb.util.extensions.xml.ExtensionPointFilter
 
log - Static variable in class net.sf.basedb.util.extensions.xml.XmlLoader
 
log - Static variable in class net.sf.basedb.util.JarClassLoader
 
log - Static variable in class net.sf.basedb.util.overview.GenericOverview
 
log - Static variable in class net.sf.basedb.util.overview.loader.AbstractNodeLoader
 
log - Static variable in class net.sf.basedb.util.overview.loader.BasicItemNodeLoader
 
log - Static variable in class net.sf.basedb.util.overview.loader.BasicItemNodeLoaderFactory
 
log - Static variable in class net.sf.basedb.util.overview.node.NodeFactory
 
log - Static variable in class net.sf.basedb.util.resources.ResourceBundleWrapper
 
log - Static variable in class net.sf.basedb.util.StaticCache
Log static cache events.
log - Static variable in class net.sf.basedb.util.timer.ThreadTimerTask
 
log - Static variable in class net.sf.basedb.util.XmlUtil2
Log core events.
log(double, Expression) - Static method in class net.sf.basedb.core.query.Expressions
Calculate the n-based logarithm of an expression: new expression = log(n, e).
log(String) - Method in class net.sf.basedb.core.plugin.AbstractPlugin
Log a message to the log file created by AbstractPlugin.createLogFile(String).
log(String, Throwable) - Method in class net.sf.basedb.core.plugin.AbstractPlugin
Log a message and stack trace to the log file created by AbstractPlugin.createLogFile(String).
log(String, FlatFileParser.Data) - Method in class net.sf.basedb.plugins.AbstractFlatFileImporter
Log a message about a data line to the log file created by AbstractPlugin.createLogFile(String).
log(String, FlatFileParser.Data, Throwable) - Method in class net.sf.basedb.plugins.AbstractFlatFileImporter
Log an error message about a data line to the log file created by AbstractPlugin.createLogFile(String).
log(String, FlatFileParser.Line) - Method in class net.sf.basedb.plugins.AbstractFlatFileImporter
Log a message about a header line to the log file created by AbstractPlugin.createLogFile(String).
log(String, FlatFileParser.Line, Throwable) - Method in class net.sf.basedb.plugins.AbstractFlatFileImporter
Log an error message about a header line to the log file created by AbstractPlugin.createLogFile(String).
log(ChangeHistoryData) - Method in class net.sf.basedb.core.LogControl
Add a main entry the change history table.
log(ChangeHistoryDetailData) - Method in class net.sf.basedb.core.LogControl
Adds information about a modified entity to the change history table.
log(LogLevel, String) - Method in class net.sf.basedb.util.extensions.logging.ExtensionsLogger
Log a message at the specified level.
log(LogLevel, String, Throwable) - Method in class net.sf.basedb.util.extensions.logging.ExtensionsLogger
Log a message at the specified level with an optional stacktrace.
log(Logger, String, Throwable) - Method in enum class net.sf.basedb.util.extensions.LoggingErrorHandlerFactory.Level
 
log10(Expression) - Static method in class net.sf.basedb.core.query.Expressions
Calculate the 10-based logarithm of an expression: new expression = log10(e).
LOG10 - Enum constant in enum class net.sf.basedb.core.IntensityTransform
Spot intensities are stored as base-10 logged values
LOG10_2 - Static variable in class net.sf.basedb.util.ma.Log10MACalculator
 
Log10MACalculator - Class in net.sf.basedb.util.ma
MA calculator for log2-transformed spot intensity values.
Log10MACalculator() - Constructor for class net.sf.basedb.util.ma.Log10MACalculator
 
log2(Number) - Method in class net.sf.basedb.util.jep.Log2Function
Calculate the 2-based logarithm of the argument.
log2(Expression) - Static method in class net.sf.basedb.core.query.Expressions
Calculate the 2-based logarithm of an expression: new expression = log2(e).
LOG2 - Enum constant in enum class net.sf.basedb.core.IntensityTransform
Spot intensities are stored as base-2 logged values
LOG2 - Static variable in class net.sf.basedb.util.jep.Log2Function
The natural logarithm of 2.
Log2Function - Class in net.sf.basedb.util.jep
A JEP function class that adds a log2(expression) function to a JEP expression parser.
Log2Function() - Constructor for class net.sf.basedb.util.jep.Log2Function
Create a new instance of this function.
Log2MACalculator - Class in net.sf.basedb.util.ma
MA calculator for log2-transformed spot intensity values.
Log2MACalculator() - Constructor for class net.sf.basedb.util.ma.Log2MACalculator
 
LogarithmConverter - Class in net.sf.basedb.util.jep.convert
Convert Logarithm function to a Query API Expression.
LogarithmConverter() - Constructor for class net.sf.basedb.util.jep.convert.LogarithmConverter
 
logarithmic - Variable in class net.sf.basedb.core.data.ColoringData
 
logChangeDetails(Collection<ChangeHistoryDetailData>, EntityDetails) - Method in class net.sf.basedb.core.log.db.DbLogManager
Log the given details to the database.
logChangeDetails(ChangeHistoryDetailData, EntityDetails) - Method in class net.sf.basedb.core.log.db.DbLogManager
Log the given details to the database.
logChanges(LogManager, EntityDetails) - Method in class net.sf.basedb.core.log.db.AnnotationLogger
 
logChanges(LogManager, EntityDetails) - Method in class net.sf.basedb.core.log.db.AnnotationSetLogger
 
logChanges(LogManager, EntityDetails) - Method in class net.sf.basedb.core.log.db.AnyToAnyLogger
 
logChanges(LogManager, EntityDetails) - Method in class net.sf.basedb.core.log.db.BioMaterialEventLogger
 
logChanges(LogManager, EntityDetails) - Method in class net.sf.basedb.core.log.db.DefaultEntityLogger
logChanges(LogManager, EntityDetails) - Method in class net.sf.basedb.core.log.db.FileSetMemberLogger
 
logChanges(LogManager, EntityDetails) - Method in class net.sf.basedb.core.log.db.ManualEntryLogger
 
logChanges(LogManager, EntityDetails) - Method in class net.sf.basedb.core.log.db.PlateEventLogger
 
logChanges(LogManager, EntityDetails) - Method in interface net.sf.basedb.core.log.EntityLogger
Called when changes has been detected to an entity.
logChanges(LogManager, EntityDetails) - Method in class net.sf.basedb.core.MigrateRbaToDba.MigratedLogger
 
logChangeType - Variable in enum class net.sf.basedb.core.AnnotationBatcher.Change
 
logControl - Variable in class net.sf.basedb.core.DbControl
Handles logging of changes to items.
logControl - Variable in class net.sf.basedb.core.log.db.DbLogManager
 
logControl - Variable in class net.sf.basedb.core.log.LoggingInterceptor
 
logControl - Variable in class net.sf.basedb.core.log.TransactionDetails
 
LogControl - Class in net.sf.basedb.core
Gives information about the current transaction and gives log implementations limited access to the database.
LogControl(DbControl) - Constructor for class net.sf.basedb.core.LogControl
 
logDc - Variable in class net.sf.basedb.core.plugin.AbstractPlugin
 
LogDetails(LogManager, EntityLogger, EntityDetails) - Constructor for class net.sf.basedb.core.log.LoggingInterceptor.LogDetails
 
logEntries - Variable in class net.sf.basedb.util.extensions.logging.ExtensionsLog
 
logEntry(ManualLogEntry) - Method in class net.sf.basedb.core.DbControl
Add a manual log entry to the history log.
LogEntry - Class in net.sf.basedb.util.extensions.logging
An entry in the log.
LogEntry(LogLevel, String, Throwable) - Constructor for class net.sf.basedb.util.extensions.logging.LogEntry
 
LogExpression - Class in net.sf.basedb.core.query
Take the n-based logarithm of an expression: log(n, e).
LogExpression(double, Expression) - Constructor for class net.sf.basedb.core.query.LogExpression
 
logfile - Variable in class net.sf.basedb.core.plugin.AbstractPlugin
 
LOGFILE_PARAMETER - Static variable in class net.sf.basedb.plugins.util.Parameters
The name of the parameter that is created by Parameters.logFileParameter(String, String, String)
logFileParameter(String, String, String) - Static method in class net.sf.basedb.plugins.util.Parameters
Parameter definition that asks for the path to a log file that a plug-in can use for logging detailed information about it's progress.
LoggableData - Interface in net.sf.basedb.core.data
Tagging interface that should be implemented by all data classes that we want to log in the change history tables.
loggableWithoutValues - Variable in class net.sf.basedb.core.log.EntityLogOptions
 
LoggableWithoutValues - Annotation Interface in net.sf.basedb.core.data
Getter methods that are annotated with this annotation should not have their old/new values logged in the change history log.
logger - Static variable in class net.sf.basedb.clients.web.util.SimpleSignalProgressReporter
Log signals processing.
logger - Variable in class net.sf.basedb.core.log.LoggingInterceptor.LogDetails
 
logger - Variable in class net.sf.basedb.core.plugin.AbstractPlugin
 
logger - Static variable in class net.sf.basedb.core.signal.AbstractSignalReceiver
Log signals processing.
logger - Static variable in class net.sf.basedb.core.signal.AbstractSignalTransporter
Log signals processing.
logger - Static variable in class net.sf.basedb.core.signal.DelegatingSignalHandler
Log signals processing.
logger - Static variable in class net.sf.basedb.core.signal.EnhancedThreadSignalHandler
Log signals processing.
logger - Static variable in class net.sf.basedb.core.signal.ExtensionSignalTransporter
 
logger - Static variable in class net.sf.basedb.core.signal.ForwardingSignalHandler
Log signals processing.
logger - Static variable in class net.sf.basedb.core.signal.LocalSignalReceiver
Log signals processing.
logger - Static variable in class net.sf.basedb.core.signal.LocalSignalTransporter
Log signals processing.
logger - Static variable in class net.sf.basedb.core.signal.ProgressReporterSignalHandler
Log signals processing.
logger - Static variable in class net.sf.basedb.core.signal.SocketSignalReceiver
Log signals processing.
logger - Static variable in class net.sf.basedb.core.signal.SocketSignalTransporter
Log signals processing.
logger - Static variable in class net.sf.basedb.core.signal.ThreadSignalHandler
Log signals processing.
logger - Variable in class net.sf.basedb.util.jobagent.JobAgentServerConnection.ListenerThread
 
logger - Variable in class net.sf.basedb.util.jobagent.JobAgentServerConnection
 
logger - Variable in class net.sf.basedb.util.jobagent.JobAgentServerConnection.RequestHandlerThread
 
LoggingErrorHandlerFactory - Class in net.sf.basedb.util.extensions
Exception handler factory implementation that logs error messages using the default logging mechanism.
LoggingErrorHandlerFactory() - Constructor for class net.sf.basedb.util.extensions.LoggingErrorHandlerFactory
Create a new error-level loggin error handler factory.
LoggingErrorHandlerFactory(String) - Constructor for class net.sf.basedb.util.extensions.LoggingErrorHandlerFactory
Create a new custom-level logging error handler factory.
LoggingErrorHandlerFactory.Level - Enum Class in net.sf.basedb.util.extensions
Log level implementations for slf4j.
loggingInterceptor - Variable in class net.sf.basedb.core.AnnotationBatcher
 
LoggingInterceptor - Class in net.sf.basedb.core.log
Interceptor that attaches to Hibernate sessions to provide logging of items that are updated/created/deleted.
LoggingInterceptor(LogControl, ExtensionsInvoker<LogManagerFactory>) - Constructor for class net.sf.basedb.core.log.LoggingInterceptor
Creates a new interceptor.
LoggingInterceptor.LogDetails - Class in net.sf.basedb.core.log
 
LoggingInterceptor.LogManagerAndFactory - Class in net.sf.basedb.core.log
 
logHandlers - Variable in class net.sf.basedb.core.log.LoggingInterceptor
 
login - Variable in class net.sf.basedb.clients.jobagent.Agent
 
login - Variable in class net.sf.basedb.core.authentication.AuthenticatedUser
 
login - Variable in class net.sf.basedb.core.authentication.LoginRequest
 
login - Variable in class net.sf.basedb.core.data.UserData
 
login(LoginRequest) - Method in class net.sf.basedb.core.PluginSessionControl
 
login(LoginRequest) - Method in class net.sf.basedb.core.SessionControl
Log in to BASE.
login(Keyring) - Method in class net.sf.basedb.core.PluginSessionControl
 
login(Keyring) - Method in class net.sf.basedb.core.SessionControl
 
loginComment - Variable in class net.sf.basedb.core.data.SessionData
 
LoginException - Exception in net.sf.basedb.core.authentication
This exception can be thrown when an error occurs during the authentication, but it is not known if the username or password is causing the problem.
LoginException - Exception in net.sf.basedb.core
Exceptions of this type are thrown when the BASE server uses an external authentication plug-in and it is not clear if the login or password is causing the failure.
LoginException(String) - Constructor for exception net.sf.basedb.core.authentication.LoginException
Create a new LoginException object
LoginException(String) - Constructor for exception net.sf.basedb.core.LoginException
Create a new LoginException object with the specified message
LoginException(String, Throwable) - Constructor for exception net.sf.basedb.core.authentication.LoginException
Create a new LoginException object
LoginException(String, Throwable) - Constructor for exception net.sf.basedb.core.LoginException
Create a new LoginException object with the specified message
loginField - Variable in class net.sf.basedb.clients.web.extensions.login.LoginFormBean
 
logInfo - Variable in class net.sf.basedb.core.log.ManualLogEntry
 
LoginFormAction - Interface in net.sf.basedb.clients.web.extensions.login
An action for customizing the login form.
LoginFormBean - Class in net.sf.basedb.clients.web.extensions.login
A simple implementation of the LoginFormAction interface.
LoginFormBean() - Constructor for class net.sf.basedb.clients.web.extensions.login.LoginFormBean
 
loginInfo - Variable in class net.sf.basedb.core.SessionControl
Login information for the logged in user.
LoginInfo() - Constructor for class net.sf.basedb.core.SessionControl.LoginInfo
 
LoginInfo(SessionControl.LoginInfo) - Constructor for class net.sf.basedb.core.SessionControl.LoginInfo
 
loginIsUsed(DbControl, String) - Static method in class net.sf.basedb.core.User
Check if a login name already exists in the database
loginRequest - Variable in class net.sf.basedb.core.AuthenticationContext
 
loginRequest - Variable in class net.sf.basedb.core.SessionControl.UnverifiedDeviceInfo
 
LoginRequest - Class in net.sf.basedb.core.authentication
Hold information about a login request such as login, password, etc.
LoginRequest() - Constructor for class net.sf.basedb.core.authentication.LoginRequest
 
LoginRequest(int, String) - Constructor for class net.sf.basedb.core.authentication.LoginRequest
Create a login request with user id + password
LoginRequest(int, String, String) - Constructor for class net.sf.basedb.core.authentication.LoginRequest
Create a login request with user id + password + deviceToken
LoginRequest(String, String) - Constructor for class net.sf.basedb.core.authentication.LoginRequest
Create a login request with login + password
LoginRequest(String, String, String) - Constructor for class net.sf.basedb.core.authentication.LoginRequest
Create a login request with login + password + deviceToken
logInterceptor - Variable in class net.sf.basedb.core.DbControl
 
logInterceptor - Variable in class net.sf.basedb.core.MigrateRbaToDba
 
loginTime - Variable in class net.sf.basedb.core.data.SessionData
 
logInvoker - Variable in class net.sf.basedb.core.log.LoggingInterceptor
 
LogLevel - Enum Class in net.sf.basedb.util.extensions.logging
The level of the log message.
LogLevel(String) - Constructor for enum class net.sf.basedb.util.extensions.logging.LogLevel
 
LogManager - Interface in net.sf.basedb.core.log
Manages the logging of changes made in a single transaction.
LogManagerAndFactory(LogManagerFactory, LogManager) - Constructor for class net.sf.basedb.core.log.LoggingInterceptor.LogManagerAndFactory
 
LogManagerFactory - Interface in net.sf.basedb.core.log
A log manager factory handles the creation of log managers and entity loggers.
logOptions - Variable in class net.sf.basedb.core.log.EntityDetails
 
logout() - Method in class net.sf.basedb.core.PluginSessionControl
Do nothing, a plugin is not allowed to log out.
logout() - Method in class net.sf.basedb.core.SessionControl
Log out of BASE.
logoutTime - Variable in class net.sf.basedb.core.data.SessionData
 
logParam - Static variable in class net.sf.basedb.core.AbstractEntityQuery
Log all parameter bindings to prepared statement.
logParam - Static variable in class net.sf.basedb.core.AbstractHqlQuery
Log all parameter bindings to prepared statement.
logParam - Static variable in class net.sf.basedb.core.AbstractSqlQuery
Log all parameter bindings to prepared statement.
logParam - Static variable in class net.sf.basedb.core.BasicBatcher
Log all parameter bindings to prepared statement.
logs - Static variable in class net.sf.basedb.util.extensions.logging.ExtensionsLog
 
logServer - Static variable in class net.sf.basedb.clients.jobagent.Agent
Log job agent server events.
logSql - Static variable in class net.sf.basedb.core.AbstractBatcher
Log all SQL statements.
logSql - Static variable in class net.sf.basedb.core.AbstractQuery
Log all SQL statements.
logSql - Static variable in class net.sf.basedb.core.AbstractSqlQuery
Log all SQL statements.
logSql - Static variable in class net.sf.basedb.core.AnnotationRestriction
Log all SQL statements.
logSql - Static variable in class net.sf.basedb.core.BatchUtil
Log all SQL statements.
logSql - Static variable in class net.sf.basedb.core.HibernateUtil
Log all batcher SQL statements.
logSql - Static variable in class net.sf.basedb.core.RawDataBatcher
Log all SQL statements.
logSql - Static variable in class net.sf.basedb.core.VirtualDb
Log all SQL statements.
logSQLExceptionChain(Logger, SQLException) - Static method in class net.sf.basedb.core.LogUtil
Log the chained exceptions of an SQLException.
logTo(Logger, String, Throwable) - Method in enum class net.sf.basedb.util.extensions.logging.LogLevel
 
LogUtil - Class in net.sf.basedb.core
Utility class for LOG4J logging.
LogUtil() - Constructor for class net.sf.basedb.core.LogUtil
 
LONG - Enum constant in enum class net.sf.basedb.core.Job.ExecutionTime
The job takes more than 1 hour to execute.
LONG - Enum constant in enum class net.sf.basedb.core.Type
Long integer type.
LONG - Static variable in class net.sf.basedb.core.hibernate.TypeWrapper
 
LONG_LINK_FLAG - Static variable in class net.sf.basedb.util.zip.TarUtil
The TAR header flag that must be set for @LongLink entries.
LONG_LINK_NAME - Static variable in class net.sf.basedb.util.zip.TarUtil
TAR has a limit of 100 characters in file names.
longitude - Variable in class net.sf.basedb.util.GeoLocation
 
LongParameterType - Class in net.sf.basedb.core
This class represent a parameter type that is a long.
LongParameterType() - Constructor for class net.sf.basedb.core.LongParameterType
Create a new long parameter type, without any limits and allowing null values.
LongParameterType(Long, Long, Long, boolean) - Constructor for class net.sf.basedb.core.LongParameterType
Create a new long parameter type.
LongParameterType(Long, Long, Long, boolean, int, int, int, List<Long>) - Constructor for class net.sf.basedb.core.LongParameterType
 
LongParameterValueData - Class in net.sf.basedb.core.data
Long parameter value.
LongParameterValueData() - Constructor for class net.sf.basedb.core.data.LongParameterValueData
 
LongParameterValueData(Long...) - Constructor for class net.sf.basedb.core.data.LongParameterValueData
 
longValues - Variable in class net.sf.basedb.util.formatter.IntegerFormatter
 
LongWriter - Class in net.sf.basedb.core.migrate
Database-independent writer implementation that writes long values from a result set.
LongWriter(ResultSet, int, Writer, char[]) - Constructor for class net.sf.basedb.core.migrate.LongWriter
 
LookupFormatter<T> - Class in net.sf.basedb.util.formatter
A formatter implementation that uses a map to lookup values from a set of keys.
LookupFormatter() - Constructor for class net.sf.basedb.util.formatter.LookupFormatter
Create a new lookup formatter
LookupFormatter(Map<? extends T, ? extends String>) - Constructor for class net.sf.basedb.util.formatter.LookupFormatter
Create a new lookup formatter and initialise it with the key-value pairs in the given map.
LookupFormatter(Enumeration<? extends T, ? extends String>) - Constructor for class net.sf.basedb.util.formatter.LookupFormatter
Create a new lookup formatter and initialise it with the key-value pairs in the given enumeration.
lookupUnitInDb(UnitCache.CacheKey, boolean) - Method in class net.sf.basedb.util.units.UnitCache
Lookup a unit in the database and optionally add it to the cache.
low - Variable in class net.sf.basedb.core.query.BetweenRestriction
 
lowerLimit - Variable in class net.sf.basedb.core.DoubleParameterType
The lower limit of the parameter.
lowerLimit - Variable in class net.sf.basedb.core.FloatParameterType
The lower limit of the parameter.
lowerLimit - Variable in class net.sf.basedb.core.IntegerParameterType
The lower limit of the parameter.
lowerLimit - Variable in class net.sf.basedb.core.LongParameterType
The lower limit of the parameter.
lowess(List<LowessNormalization.SpotData>, double, int, double) - Static method in class net.sf.basedb.plugins.LowessNormalization
 
LowessNormalization - Class in net.sf.basedb.plugins
 
LowessNormalization() - Constructor for class net.sf.basedb.plugins.LowessNormalization
 
LowessNormalization.CallableWorker - Class in net.sf.basedb.plugins
 
LowessNormalization.SpotData - Class in net.sf.basedb.plugins
 
lowessSection - Static variable in class net.sf.basedb.plugins.LowessNormalization
Section for lowess options
lowExcludeParameter - Static variable in class net.sf.basedb.plugins.MedianRatioNormalization
 
lowValue - Variable in class net.sf.basedb.core.AnnotationBetweenRestriction
 
lt(Expression, Expression) - Static method in class net.sf.basedb.core.query.Restrictions
Compare if one expression is less than another: new restriction = e1 < e2.
LT - Enum constant in enum class net.sf.basedb.core.Operator
 
LT - Static variable in class net.sf.basedb.clients.web.util.HTML
 
lteq(Expression, Expression) - Static method in class net.sf.basedb.core.query.Restrictions
Compare if one expression is less than or equal to another: new restriction = e1 <= e2.
LTEQ - Enum constant in enum class net.sf.basedb.core.Operator
 
LteqRestriction - Class in net.sf.basedb.core.query
Compare if one expression is less than or equal to another: e1 <= e2.
LteqRestriction(Expression, Expression) - Constructor for class net.sf.basedb.core.query.LteqRestriction
 
LtRestriction - Class in net.sf.basedb.core.query
Compare if one expression is less than another: e1 < e2.
LtRestriction(Expression, Expression) - Constructor for class net.sf.basedb.core.query.LtRestriction
 

M

M - Variable in class net.sf.basedb.plugins.LowessNormalization.SpotData
 
M - Variable in class net.sf.basedb.plugins.MedianRatioNormalization.SpotData
 
MA(double, double) - Method in class net.sf.basedb.util.ma.Log10MACalculator
M = (ch1 - ch2) / log10(2) A = (ch1 + ch2) / 2
MA(double, double) - Method in class net.sf.basedb.util.ma.Log2MACalculator
M = ch1 - ch2 A = (ch1 + ch2) / (2 * log2(10))
MA(double, double) - Method in class net.sf.basedb.util.ma.MACalculator
Calculate the M and A values from the ch1 and ch2 intensity values.
mac - Variable in class net.sf.basedb.plugins.LowessNormalization.CallableWorker
 
MACalculator - Class in net.sf.basedb.util.ma
Calculates M and A values for 2-channel data.
MACalculator() - Constructor for class net.sf.basedb.util.ma.MACalculator
 
MAGNETIC_FIELD - Static variable in class net.sf.basedb.core.Quantity
The id for the Quantity object representing magnetic field.
MAGNETIC_FLUX - Static variable in class net.sf.basedb.core.Quantity
The id for the Quantity object representing magnetic flux.
main(String[]) - Static method in class net.sf.basedb.clients.jobagent.AgentController
 
main(String[]) - Static method in class net.sf.basedb.clients.jobagent.executors.ThreadJobExecutor
 
mainContext - Variable in class net.sf.basedb.util.extensions.ExtensionContext
 
MainContext(Item) - Constructor for class net.sf.basedb.core.SessionControl.MainContext
 
mainDir - Variable in class net.sf.basedb.util.extensions.manager.processor.DeleteResourcesProcessor
 
mainDir - Variable in class net.sf.basedb.util.extensions.manager.processor.ExtractResourcesProcessor
 
mainJarFile - Variable in class net.sf.basedb.util.JarClassLoader
The main JAR file to load classes from.
maintenance - Static variable in class net.sf.basedb.core.Version
 
mainType - Variable in class net.sf.basedb.core.data.PluginDefinitionData
 
MainType(int, String) - Constructor for enum class net.sf.basedb.core.plugin.Plugin.MainType
 
major - Static variable in class net.sf.basedb.core.Version
 
makeSafe(String) - Method in class net.sf.basedb.core.dbengine.TableInfo
Sometime the database put quotes around names.
makeSafeCreateTable(String, String, String, String) - Method in class net.sf.basedb.core.dbengine.AbstractDbEngine
Return the SQL unmodified.
makeSafeCreateTable(String, String, String, String) - Method in interface net.sf.basedb.core.dbengine.DbEngine
Create a "safe" CREATE TABLE query string that will not fail if the table already exists.
makeSafeCreateTable(String, String, String, String) - Method in class net.sf.basedb.core.dbengine.MySQLEngine
Replace "create table" with "create table if not exists"...
makeSafeFilename(String, String) - Static method in class net.sf.basedb.core.Path
Convert a string to a name that is safe to use as a filename.
makeSafeHeaderValue(String) - Method in class net.sf.basedb.plugins.GalExporter
Removes "unsafe" characters in the value.
makeUnique(String) - Method in class net.sf.basedb.util.bfs.AbstractFilenameGenerator
Make sure that a file name is unique.
makeValidKey(String, String) - Static method in class net.sf.basedb.util.StaticCache
Convert a possible invalid cache key to a valid one by replacing invalid characters with the replacement string.
manager - Static variable in class net.sf.basedb.clients.web.extensions.ExtensionsControl
 
manager - Variable in class net.sf.basedb.clients.web.extensions.list.RelatedItemHelper
 
manager - Variable in class net.sf.basedb.core.log.LoggingInterceptor.LogDetails
 
manager - Variable in class net.sf.basedb.core.log.LoggingInterceptor.LogManagerAndFactory
 
manager - Variable in class net.sf.basedb.core.snapshot.AnnotationLoaderUtil
 
manager - Variable in class net.sf.basedb.util.extensions.manager.ExtensionsFile
 
manager - Variable in class net.sf.basedb.util.extensions.manager.Settings
 
mandatory - Variable in class net.sf.basedb.core.data.ReporterClonePropertyData
 
MANDATORY - Static variable in class net.sf.basedb.core.ClonableProperty
 
manifest - Variable in class net.sf.basedb.util.JarClassLoader.JarInfo
 
manipulateDocument(Document, HibernateUtil.FilterConfigurator) - Static method in class net.sf.basedb.core.HibernateUtil
Some XML files require manipulation by us before they are registered.
ManualDerivedBioAssayCreator - Class in net.sf.basedb.plugins
Plug-in that allows a user to manually register an external analysis procedure for derived bioassays and to upload files that was generated by it.
ManualDerivedBioAssayCreator() - Constructor for class net.sf.basedb.plugins.ManualDerivedBioAssayCreator
 
ManualEntryLogger - Class in net.sf.basedb.core.log.db
Logger for manual entries.
ManualEntryLogger(DbLogManagerFactory) - Constructor for class net.sf.basedb.core.log.db.ManualEntryLogger
Creates a new plate event logger.
ManualLogEntry - Class in net.sf.basedb.core.log
Represents a manual entry into the change history log.
ManualLogEntry(BasicItem, ChangeType, String) - Constructor for class net.sf.basedb.core.log.ManualLogEntry
Create a new log entry.
ManualLogEntry(BasicItem, ChangeType, String, String, String) - Constructor for class net.sf.basedb.core.log.ManualLogEntry
Create a new log entry with optional old and new values.
ManualTransformCreator - Class in net.sf.basedb.plugins
Plug-in that allows a user to manually register an external analysis procedure and to upload files that was generated by it.
ManualTransformCreator() - Constructor for class net.sf.basedb.plugins.ManualTransformCreator
 
map - Variable in class net.sf.basedb.clients.web.extensions.skin.ImageRemapper
 
map - Variable in class net.sf.basedb.util.formatter.LookupFormatter
 
map(String, String) - Method in class net.sf.basedb.clients.web.extensions.skin.ImageRemapper
Remap a source image to a destination image.
MAParser - Class in net.sf.basedb.util.importer.spotdata
Spot intensity parser implementation for 2-channel data that looks for M/A values in the spot data and converts them to ch1/ch2 intensity values.
MAParser() - Constructor for class net.sf.basedb.util.importer.spotdata.MAParser
Creates a new MA-parser.
mapKey - Variable in class net.sf.basedb.clients.web.plugins.MapValueLoader
 
MAPlotFactory - Class in net.sf.basedb.clients.web.extensions.plot
Factory for generating MA and correction factor plots for 2-channel data.
MAPlotFactory() - Constructor for class net.sf.basedb.clients.web.extensions.plot.MAPlotFactory
 
mapParentChildColumns(short, short) - Method in class net.sf.basedb.util.importer.spotdata.BaseFileInfo
Maps a parent data cube column to a child cube column.
mapper - Variable in class net.sf.basedb.plugins.batchimport.UsedQuantityMapper
 
Mapper - Interface in net.sf.basedb.util.parser
Represents a mapping expression that gets a single value from a line of data.
mappers - Variable in class net.sf.basedb.plugins.AnnotationFlatFileImporter
 
mappers - Variable in class net.sf.basedb.plugins.IlluminaRawDataImporter.BatchAndMapHolder
 
mappers - Variable in class net.sf.basedb.util.parser.CompoundMapper
 
mapping - Variable in class net.sf.basedb.core.MigrateRbaToDba
 
mapping - Variable in class net.sf.basedb.plugins.PlateMappingExporter
 
MAPPING - Enum constant in enum class net.sf.basedb.plugins.PrintMapFlatFileImporter.Section
 
mappingBatcher - Variable in class net.sf.basedb.core.DataCube
 
MappingBatcher - Class in net.sf.basedb.core
Batcher class for inserting parent mapping information in the dynamic database.
MappingBatcher(DbControl, DataCube) - Constructor for class net.sf.basedb.core.MappingBatcher
Create a new position batcher for a data cube.
MappingCoordinate - Class in net.sf.basedb.core.data
This class defines a mapping coordinate, which is a triplet of plate number, row and column.
MappingCoordinate() - Constructor for class net.sf.basedb.core.data.MappingCoordinate
Create new object.
MappingCoordinate(int, int, int) - Constructor for class net.sf.basedb.core.data.MappingCoordinate
Create new MappingCoordinate with the specified plate, row and column.
mappings - Variable in class net.sf.basedb.core.data.VirtualDbData
 
mappingSection - Static variable in class net.sf.basedb.plugins.AbstractFlatFileImporter
Section definition for grouping all column mapping expressions
MapPropertyPath(Type) - Constructor for class net.sf.basedb.core.Metadata.MapPropertyPath
 
mapToSubtype(MigrateRbaToDba.Itemlist) - Method in class net.sf.basedb.core.MigrateRbaToDba.SubtypeMapping
Map a subtype to the given item list.
mapToSubtype(MigrateRbaToDba.Rba) - Method in class net.sf.basedb.core.MigrateRbaToDba.SubtypeMapping
Map a subtype to the given raw bioassay.
MapValueLoader - Class in net.sf.basedb.clients.web.plugins
Data loader implementation that load values from a map collection.
MapValueLoader(Metadata.PropertyPath<BasicItem, Map<?, ?>>, Object) - Constructor for class net.sf.basedb.clients.web.plugins.MapValueLoader
Load values from a map.
mapZeroToNull - Variable in class net.sf.basedb.util.importer.spotdata.FirstPassSectionSpotsParser
 
mark(int) - Method in class net.sf.basedb.clients.web.fileupload.FileUpload.UploadStream
Not supported.
mark(int) - Method in class net.sf.basedb.util.InputStreamSplitter
 
mark(int) - Method in class net.sf.basedb.util.InputStreamTracker
 
markAsProcessed() - Method in class net.sf.basedb.util.extensions.manager.ExtensionsFile.WriteableExtensionsFile
Mark the file as fully processed by the extensions manager.
MarkAsProcessedProcessor - Class in net.sf.basedb.util.extensions.manager.processor
File processor implementation that marks all extension files as processed.
MarkAsProcessedProcessor() - Constructor for class net.sf.basedb.util.extensions.manager.processor.MarkAsProcessedProcessor
 
markSupported() - Method in class net.sf.basedb.clients.web.fileupload.FileUpload.UploadStream
Not supported.
markSupported() - Method in class net.sf.basedb.util.gtf.GtfInputStream
 
markSupported() - Method in class net.sf.basedb.util.InputStreamSplitter
 
markSupported() - Method in class net.sf.basedb.util.InputStreamTracker
 
MARKUP - Static variable in class net.sf.basedb.clients.web.util.HTML
Pattern that matches everything inside a HTML tag.
masked - Variable in class net.sf.basedb.core.data.ParameterValueData
 
masked - Variable in class net.sf.basedb.core.ParameterInfo
 
MASS - Static variable in class net.sf.basedb.core.Quantity
The id for the Quantity object representing mass.
master - Variable in class net.sf.basedb.clients.jobagent.slotmanager.MasterSlotManager.RemoteSlotRequestHandler
 
master - Variable in class net.sf.basedb.clients.jobagent.slotmanager.MasterSlotManager.RemoteSlotTimeoutChecker
 
master - Variable in class net.sf.basedb.clients.jobagent.slotmanager.RemoteSlotManager.RemoteSlotPinger
 
master - Variable in class net.sf.basedb.util.ChainedProgressReporter
 
master - Variable in class net.sf.basedb.util.gtf.GtfInputStream
 
master - Variable in class net.sf.basedb.util.jep.ReporterFunction
 
master - Variable in class net.sf.basedb.util.StreamCacher
 
masterParser - Variable in class net.sf.basedb.util.importer.spotdata.SynchronizedSpotDataParser
 
MasterReporterJoiner(JoinType) - Constructor for class net.sf.basedb.core.DynamicReporterQuery.MasterReporterJoiner
 
MasterSlotManager - Class in net.sf.basedb.clients.jobagent.slotmanager
An extension to the internal slot manager which also accepts slot assignment from remote job agents.
MasterSlotManager() - Constructor for class net.sf.basedb.clients.jobagent.slotmanager.MasterSlotManager
 
MasterSlotManager.RemoteSlot - Class in net.sf.basedb.clients.jobagent.slotmanager
A remote slot is a slot with some information about when it was created and last updated.
MasterSlotManager.RemoteSlotRequestHandler - Class in net.sf.basedb.clients.jobagent.slotmanager
Request handler implementation that accepts requests for slots from remote hosts.
MasterSlotManager.RemoteSlotTimeoutChecker - Class in net.sf.basedb.clients.jobagent.slotmanager
Task that is scheduled at regular intervals to check for timed out slots.
matcher - Variable in class net.sf.basedb.util.fuzzy.StringMatcher
 
matches(MigrateRbaToDba.Itemlist) - Method in class net.sf.basedb.core.MigrateRbaToDba.LineMapping
 
matches(MigrateRbaToDba.Rba) - Method in class net.sf.basedb.core.MigrateRbaToDba.LineMapping
 
matching - Variable in class net.sf.basedb.core.SyncFilter
 
matchingMd5 - Variable in class net.sf.basedb.core.SyncFilter
 
matchingReporters - Variable in class net.sf.basedb.clients.web.ExperimentExplorer
Number of reporter that match the reporter search.
matchingSource - Variable in class net.sf.basedb.core.data.ItemListSyncFilterData
 
matchingTransformed - Variable in class net.sf.basedb.core.data.ItemListSyncFilterData
 
MatrixBaseFileExporter - Class in net.sf.basedb.util.export.spotdata
Exporter implementation that exports bioassay set data as a matrix BASEfile.
MatrixBaseFileExporter() - Constructor for class net.sf.basedb.util.export.spotdata.MatrixBaseFileExporter
Create a new matrix BASEfile exporter.
MatrixBfsExporter - Class in net.sf.basedb.util.export.spotdata
BFS exporter implementation that exports spot data in matrix format.
MatrixBfsExporter() - Constructor for class net.sf.basedb.util.export.spotdata.MatrixBfsExporter
Create a new matrix BFS exporter.
MatrixModel - Class in net.sf.basedb.util.bfs
A model container for BFS data files.
MatrixModel() - Constructor for class net.sf.basedb.util.bfs.MatrixModel
Create a new annotation model.
MatrixSpotIntensityEventHandler - Class in net.sf.basedb.util.importer.spotdata
Event handler that extracts spot intensity information from matrix BFS data files and inserts the values to a spot batcher.
MatrixSpotIntensityEventHandler(SpotBatcher, PositionEventHandler, BioAssay[], int[]) - Constructor for class net.sf.basedb.util.importer.spotdata.MatrixSpotIntensityEventHandler
Create a new spot instensity event handler.
max - Variable in class net.sf.basedb.util.InputStreamTracker.CurvedScaleFactor
 
max - Variable in class net.sf.basedb.util.plot.HistogramPlot.HistogramBin
 
max(Expression) - Static method in class net.sf.basedb.core.query.Aggregations
Calculates the maximum value of an expression: new expression = MAX(e)
MAX - Enum constant in enum class net.sf.basedb.core.Formula.AverageMethod
 
MAX - Enum constant in enum class net.sf.basedb.util.plot.HistogramPlot.YAggregate
Plot the maximum of all y-values for spots falling into each bin.
MAX_ABSTRACT_LENGTH - Static variable in class net.sf.basedb.core.data.ExperimentData
 
MAX_ABSTRACT_LENGTH - Static variable in class net.sf.basedb.core.Experiment
The maximum length of the abstract property that can be stored in the database.
MAX_ADDRESS_LENGTH - Static variable in class net.sf.basedb.core.data.UserData
The maximum length of the address that can be stored in the database.
MAX_ADDRESS_LENGTH - Static variable in class net.sf.basedb.core.User
The maximum length of the address that can be stored in the database.
MAX_AFFILIATIONS_LENGTH - Static variable in class net.sf.basedb.core.data.ExperimentData
 
MAX_AFFILIATIONS_LENGTH - Static variable in class net.sf.basedb.core.Experiment
The maximum length of the affiliations property that can be stored in the database.
MAX_AUTHENTICATION_METHOD - Static variable in class net.sf.basedb.core.data.SessionData
The maximum length of the authentication method that can be stored in the database.
MAX_AUTHORS_LENGTH - Static variable in class net.sf.basedb.core.data.ExperimentData
 
MAX_AUTHORS_LENGTH - Static variable in class net.sf.basedb.core.Experiment
The maximum length of the authors property that can be stored in the database.
MAX_BARCODE_LENGTH - Static variable in class net.sf.basedb.core.ArraySlide
The maximum length of the barcode that can be stored in the database.
MAX_BARCODE_LENGTH - Static variable in class net.sf.basedb.core.BioPlate
The maximum length of the barcode that can be stored in the database.
MAX_BARCODE_LENGTH - Static variable in class net.sf.basedb.core.data.ArraySlideData
 
MAX_BARCODE_LENGTH - Static variable in class net.sf.basedb.core.data.BioPlateData
The maximum length of the barcode that can be stored in the database.
MAX_BARCODE_LENGTH - Static variable in class net.sf.basedb.core.data.PlateData
The maximum length of the barcode that can be stored in the database.
MAX_BARCODE_LENGTH - Static variable in class net.sf.basedb.core.Plate
The maximum length of the barcode that can be stored in the database.
MAX_CERTIFICATE_LENGTH - Static variable in class net.sf.basedb.core.data.FileServerData
 
MAX_CERTIFICATE_LENGTH - Static variable in class net.sf.basedb.core.FileServer
The maximum length of the server certificate that can be stored in the database.
MAX_CHANGE_INFO_LENGTH - Static variable in class net.sf.basedb.core.data.ChangeHistoryDetailData
 
MAX_CHARSET_LENGTH - Static variable in class net.sf.basedb.core.data.FileData
 
MAX_CHARSET_LENGTH - Static variable in class net.sf.basedb.core.File
The maximum length of the character set that can be stored in the database.
MAX_CLASSNAME_LENGTH - Static variable in class net.sf.basedb.core.data.PluginDefinitionData
The maximum length of the class name that can be stored in the database.
MAX_CLASSNAME_LENGTH - Static variable in class net.sf.basedb.core.PluginDefinition
The maximum length of the class name that can be stored in the database.
MAX_COLUMN_LENGTH - Static variable in class net.sf.basedb.core.data.ReporterClonePropertyData
The maximum length of the column that can be stored in the database.
MAX_COMMAND_LENGTH - Static variable in class net.sf.basedb.core.data.JobData
The maximum allowed length of the execute command.
MAX_COMMENT_LENGTH - Static variable in class net.sf.basedb.core.BioMaterialEvent
The maximum length of the comment about this event.
MAX_COMMENT_LENGTH - Static variable in class net.sf.basedb.core.data.BioMaterialEventData
The maximum length of the comment about this event.
MAX_COMMENT_LENGTH - Static variable in class net.sf.basedb.core.data.PlateEventData
The maximum length of the comment about this event.
MAX_COMMENT_LENGTH - Static variable in class net.sf.basedb.core.PlateEvent
The maximum length of the comment about this event.
MAX_CONNECTION_MANAGER_FACTORY_LENGTH - Static variable in class net.sf.basedb.core.data.FileServerData
 
MAX_CONNECTION_MANAGER_FACTORY_LENGTH - Static variable in class net.sf.basedb.core.FileServer
The maximum length of the connection manager factory id that can be stored in the database.
MAX_CONTACT_LENGTH - Static variable in class net.sf.basedb.core.data.PluginDefinitionData
The maximum length of the contact information that can be stored in the database.
MAX_CONTACT_LENGTH - Static variable in class net.sf.basedb.core.PluginDefinition
The maximum length of the contact information that can be stored in the database.
MAX_COPYRIGHT_LENGTH - Static variable in class net.sf.basedb.core.data.PluginDefinitionData
The maximum length of the copyright notice that can be stored in the database.
MAX_COPYRIGHT_LENGTH - Static variable in class net.sf.basedb.core.PluginDefinition
The maximum length of the copyright notice that can be stored in the database.
MAX_DEFAULT_VALUE_LENGTH - Static variable in class net.sf.basedb.core.AnnotationType
The maximum length of the default value.
MAX_DEFAULT_VALUE_LENGTH - Static variable in class net.sf.basedb.core.data.AnnotationTypeData
 
MAX_DESCRIPTION_LENGTH - Static variable in interface net.sf.basedb.core.data.NameableData
The maximum length of the description of the item that can be stored in the database.
MAX_DESCRIPTION_LENGTH - Static variable in class net.sf.basedb.core.data.ParameterValueData
The maximum length of the description of the parameter that can be stored in the database.
MAX_DESCRIPTION_LENGTH - Static variable in class net.sf.basedb.core.data.PluginDefinitionData
The maximum length of the url that can be stored in the database.
MAX_DESCRIPTION_LENGTH - Static variable in interface net.sf.basedb.core.Nameable
The maximum length of the description.
MAX_EMAIL_LENGTH - Static variable in class net.sf.basedb.core.data.PluginDefinitionData
The maximum length of the email address that can be stored in the database.
MAX_EMAIL_LENGTH - Static variable in class net.sf.basedb.core.data.UserData
The maximum length of the email address that can be stored in the database.
MAX_EMAIL_LENGTH - Static variable in class net.sf.basedb.core.PluginDefinition
The maximum length of the email address that can be stored in the database.
MAX_EMAIL_LENGTH - Static variable in class net.sf.basedb.core.User
The maximum length of the email address that can be stored in the database.
MAX_EXPERIMENT_DESIGN_LENGTH - Static variable in class net.sf.basedb.core.data.ExperimentData
 
MAX_EXPERIMENT_DESIGN_LENGTH - Static variable in class net.sf.basedb.core.Experiment
The maximum length of the experimentDesign property that can be stored in the database.
MAX_EXPERIMENT_TYPE_LENGTH - Static variable in class net.sf.basedb.core.data.ExperimentData
 
MAX_EXPERIMENT_TYPE_LENGTH - Static variable in class net.sf.basedb.core.Experiment
The maximum length of the experimentType property that can be stored in the database.
MAX_EXTENSION_LENGTH - Static variable in class net.sf.basedb.core.data.DataFileTypeData
The maximum length of the file extension that can be stored in the database.
MAX_EXTENSION_LENGTH - Static variable in class net.sf.basedb.core.data.MimeTypeData
 
MAX_EXTENSION_LENGTH - Static variable in class net.sf.basedb.core.DataFileType
The maximum length of the file extension that can be stored in the database.
MAX_EXTENSION_LENGTH - Static variable in class net.sf.basedb.core.MimeType
The maximum length of the extension variable that can be stored in the database.
MAX_EXTERNAL_ID_LENGTH - Static variable in class net.sf.basedb.core.AnnotationType
The maximum length of the external id that can be stored in the database.
MAX_EXTERNAL_ID_LENGTH - Static variable in class net.sf.basedb.core.BioMaterial
The maximum length of the external id that can be stored in the database.
MAX_EXTERNAL_ID_LENGTH - Static variable in class net.sf.basedb.core.Client
The maximum length of the external id variable that can be stored in the database.
MAX_EXTERNAL_ID_LENGTH - Static variable in class net.sf.basedb.core.data.AnnotationTypeData
The maximum length of the external id that can be stored in the database.
MAX_EXTERNAL_ID_LENGTH - Static variable in class net.sf.basedb.core.data.BioMaterialData
The maximum length of the external id that can be stored in the database.
MAX_EXTERNAL_ID_LENGTH - Static variable in class net.sf.basedb.core.data.BioPlateData
The maximum length of the external id that can be stored in the database.
MAX_EXTERNAL_ID_LENGTH - Static variable in class net.sf.basedb.core.data.ClientData
The maximum length of the external ID that can be stored in the database.
MAX_EXTERNAL_ID_LENGTH - Static variable in class net.sf.basedb.core.data.DataFileTypeData
The maximum length of the external ID that can be stored in the database.
MAX_EXTERNAL_ID_LENGTH - Static variable in class net.sf.basedb.core.data.ExtraValueTypeData
The maximum length of the external id that can be stored in the database.
MAX_EXTERNAL_ID_LENGTH - Static variable in class net.sf.basedb.core.data.FeatureData
The maximum length of the external ID that can be stored in the database.
MAX_EXTERNAL_ID_LENGTH - Static variable in class net.sf.basedb.core.data.HelpData
The maximum length of the external ID that can be stored in the database.
MAX_EXTERNAL_ID_LENGTH - Static variable in class net.sf.basedb.core.data.ItemListData
The maximum length of the external ID that can be stored in the database.
MAX_EXTERNAL_ID_LENGTH - Static variable in class net.sf.basedb.core.data.JobAgentData
The maximum length of the external ID that can be stored in the database.
MAX_EXTERNAL_ID_LENGTH - Static variable in class net.sf.basedb.core.data.JobData
The maximum allowed length of the external ID.
MAX_EXTERNAL_ID_LENGTH - Static variable in class net.sf.basedb.core.data.PlatformData
The maximum length of the external ID that can be stored in the database.
MAX_EXTERNAL_ID_LENGTH - Static variable in class net.sf.basedb.core.data.PlatformVariantData
The maximum length of the external ID that can be stored in the database.
MAX_EXTERNAL_ID_LENGTH - Static variable in class net.sf.basedb.core.data.ProtocolData
The maximum length of the external id that can be stored in the database.
MAX_EXTERNAL_ID_LENGTH - Static variable in class net.sf.basedb.core.data.ReporterData
The maximum length of the external ID that can be stored in the database.
MAX_EXTERNAL_ID_LENGTH - Static variable in class net.sf.basedb.core.data.ReporterListData
The maximum length of the external ID that can be stored in the database.
MAX_EXTERNAL_ID_LENGTH - Static variable in class net.sf.basedb.core.data.UserData
The maximum length of the external ID that can be stored in the database.
MAX_EXTERNAL_ID_LENGTH - Static variable in class net.sf.basedb.core.DataFileType
The maximum length of the external ID that can be stored in the database.
MAX_EXTERNAL_ID_LENGTH - Static variable in class net.sf.basedb.core.ExtraValueType
The maximum length of the external id variable that can be stored in the database.
MAX_EXTERNAL_ID_LENGTH - Static variable in class net.sf.basedb.core.Help
The maximum length of the external id variable that can be stored in the database.
MAX_EXTERNAL_ID_LENGTH - Static variable in class net.sf.basedb.core.ItemList
The maximum length of the external id variable that can be stored in the database.
MAX_EXTERNAL_ID_LENGTH - Static variable in class net.sf.basedb.core.Job
The maximum allowed length of the external ID.
MAX_EXTERNAL_ID_LENGTH - Static variable in class net.sf.basedb.core.JobAgent
The maximum length of the external ID that can be stored in the database.
MAX_EXTERNAL_ID_LENGTH - Static variable in class net.sf.basedb.core.Platform
The maximum length of the external ID that can be stored in the database.
MAX_EXTERNAL_ID_LENGTH - Static variable in class net.sf.basedb.core.PlatformVariant
The maximum length of the external ID that can be stored in the database.
MAX_EXTERNAL_ID_LENGTH - Static variable in class net.sf.basedb.core.Protocol
The maximum length of the external id that can be stored in the database.
MAX_EXTERNAL_ID_LENGTH - Static variable in class net.sf.basedb.core.ReporterList
The maximum length of the external id variable that can be stored in the database.
MAX_EXTERNAL_ID_LENGTH - Static variable in class net.sf.basedb.core.User
The maximum length of the external ID that can be stored in the database.
MAX_FAX_LENGTH - Static variable in class net.sf.basedb.core.data.UserData
The maximum length of the fax that can be stored in the database.
MAX_FAX_LENGTH - Static variable in class net.sf.basedb.core.User
The maximum length of the fax that can be stored in the database.
MAX_FORMAT_LENGTH - Static variable in class net.sf.basedb.core.data.FileServerData
 
MAX_FORMAT_LENGTH - Static variable in class net.sf.basedb.core.FileServer
The maximum length of the SSH private key format path that can be stored in the database.
MAX_FORMULA_LENGTH - Static variable in class net.sf.basedb.core.data.FormulaData
The maximum allowed length of a formula.
MAX_FORMULA_LENGTH - Static variable in class net.sf.basedb.core.Formula
The maximum length of the formula that can be stored in the database.
MAX_FROM_LENGTH - Static variable in class net.sf.basedb.core.data.MessageData
The maximum length of the from property.
MAX_FROM_LENGTH - Static variable in class net.sf.basedb.core.Message
The maximum length of the sender name.
MAX_HEADER_NAME_LENGTH - Static variable in class net.sf.basedb.core.data.RawBioAssayData
 
MAX_HEADER_NAME_LENGTH - Static variable in class net.sf.basedb.core.RawBioAssay
The maximum length of the name of a header that can be stored in the database.
MAX_HEADER_VALUE_LENGTH - Static variable in class net.sf.basedb.core.data.RawBioAssayData
 
MAX_HEADER_VALUE_LENGTH - Static variable in class net.sf.basedb.core.RawBioAssay
The maximum length of the value of a header that can be stored in the database.
MAX_HOST_LENGTH - Static variable in class net.sf.basedb.core.data.FileServerData
 
MAX_HOST_LENGTH - Static variable in class net.sf.basedb.core.FileServer
The maximum length of the host name:port that can be stored in the database.
MAX_IMAGE_LENGTH - Static variable in class net.sf.basedb.core.data.PlateMappingData
The maximum length of the image name that can be stored in the database.
MAX_IMAGE_LENGTH - Static variable in class net.sf.basedb.core.PlateMapping
The maximum length of the image name that can be stored in the database.
MAX_INFORMATION_LENGTH - Static variable in interface net.sf.basedb.core.plugin.About
The maximum length of the strings returned by the methods in this interface that can be stored in the database.
MAX_INTERFACENAME_LENGTH - Static variable in class net.sf.basedb.core.data.PluginTypeData
The maximum length of the interface name that can be stored in the database.
MAX_INTERFACENAME_LENGTH - Static variable in class net.sf.basedb.core.PluginType
The maximum length of the interface name that can be stored in the database.
MAX_ITEMS_IN_TRANSACTION - Static variable in class net.sf.basedb.clients.web.extensions.list.RelatedItemHelper
 
MAX_JARFILE_LENGTH - Static variable in class net.sf.basedb.core.data.PluginDefinitionData
 
MAX_JARFILE_LENGTH - Static variable in class net.sf.basedb.core.data.PluginTypeData
 
MAX_JARFILE_LENGTH - Static variable in class net.sf.basedb.core.PluginDefinition
The maximum length of the jar path name that can be stored in the database.
MAX_JARFILE_LENGTH - Static variable in class net.sf.basedb.core.PluginType
The maximum length of the jar path name that can be stored in the database.
MAX_LABEL_LENGTH - Static variable in class net.sf.basedb.core.data.ParameterValueData
The maximum length of the label of the parameter that can be stored in the database.
MAX_LAST_SOURCE_LENGTH - Static variable in class net.sf.basedb.core.data.ReporterData
The maximum length of the last source that can be stored in the database.
MAX_LOCATION_LENGTH - Static variable in class net.sf.basedb.core.data.SessionData
The maximum length of the location that can be stored in the database.
MAX_LOCATION_LENGTH - Static variable in class net.sf.basedb.core.data.UserDeviceData
The maximum length of the location that can be stored in the database.
MAX_LOGIN_COMMENT_LENGTH - Static variable in class net.sf.basedb.core.data.SessionData
The maximum length of the login comment that can be stored in the database.
MAX_LOGIN_LENGTH - Static variable in class net.sf.basedb.core.data.UserData
The maximum length of the login that can be stored in the database.
MAX_LOGIN_LENGTH - Static variable in class net.sf.basedb.core.User
The maximum length of the login that can be stored in the database.
MAX_MIMETYPE_LENGTH - Static variable in class net.sf.basedb.core.data.FileData
 
MAX_MIMETYPE_LENGTH - Static variable in class net.sf.basedb.core.File
The maximum length of the MIME type that can be stored in the database.
MAX_NAME_LENGTH - Static variable in class net.sf.basedb.core.data.ContextData
The maximum length of the name that can be stored in the database.
MAX_NAME_LENGTH - Static variable in interface net.sf.basedb.core.data.NameableData
The maximum length of the name of the item that can be stored in the database.
MAX_NAME_LENGTH - Static variable in class net.sf.basedb.core.data.PluginDefinitionData
The maximum length of the name that can be stored in the database.
MAX_NAME_LENGTH - Static variable in class net.sf.basedb.core.data.SettingData
The maximum length of the name of the setting that can be stored in the database.
MAX_NAME_LENGTH - Static variable in interface net.sf.basedb.core.Nameable
The maximum length of the name of the item that can be stored in the database.
MAX_NAME_LENGTH - Static variable in class net.sf.basedb.core.PluginDefinition
The maximum length of the name that can be stored in the database.
MAX_NAME_LENGTH - Static variable in class net.sf.basedb.core.Setting
The maximum length of the name that can be stored in the database.
MAX_NAME_LENGTH - Static variable in class net.sf.basedb.util.zip.TarUtil
Maximum file name length.
MAX_NEW_VALUE_LENGTH - Static variable in class net.sf.basedb.core.data.ChangeHistoryDetailData
 
MAX_OLD_VALUE_LENGTH - Static variable in class net.sf.basedb.core.data.ChangeHistoryDetailData
 
MAX_OPTION_LENGTH - Static variable in class net.sf.basedb.core.AnnotationType
The maximum length of an option.
MAX_OPTION_LENGTH - Static variable in class net.sf.basedb.core.data.AnnotationTypeData
 
MAX_ORGANISATION_LENGTH - Static variable in class net.sf.basedb.core.data.UserData
The maximum length of the organisation that can be stored in the database.
MAX_ORGANISATION_LENGTH - Static variable in class net.sf.basedb.core.User
The maximum length of the organisation that can be stored in the database.
MAX_PARENTS - Static variable in class net.sf.basedb.util.JarClassLoader
 
MAX_PASSWORD_LENGTH - Static variable in class net.sf.basedb.core.data.FileServerData
 
MAX_PASSWORD_LENGTH - Static variable in class net.sf.basedb.core.FileServer
The maximum length of the password that can be stored in the database.
MAX_PHONE_LENGTH - Static variable in class net.sf.basedb.core.data.UserData
The maximum length of the phone that can be stored in the database.
MAX_PHONE_LENGTH - Static variable in class net.sf.basedb.core.User
The maximum length of the phone that can be stored in the database.
MAX_PLUGIN_VERSION_LENGTH - Static variable in class net.sf.basedb.core.data.JobData
The maximum allowed length of the plugin version.
MAX_POSITION_LENGTH - Static variable in class net.sf.basedb.core.BioPlate
The maximum length of the position coordinate that can be stored in the database.
MAX_POSITION_LENGTH - Static variable in class net.sf.basedb.core.data.BioPlateData
The maximum length of the position coordinate that can be stored in the database.
MAX_PRIVATE_KEY_LENGTH - Static variable in class net.sf.basedb.core.data.FileServerData
 
MAX_PRIVATE_KEY_LENGTH - Static variable in class net.sf.basedb.core.FileServer
The maximum length of the SSH private key that can be stored in the database.
MAX_PUBLICATION_LENGTH - Static variable in class net.sf.basedb.core.data.ExperimentData
 
MAX_PUBLICATION_LENGTH - Static variable in class net.sf.basedb.core.Experiment
The maximum length of the publication property that can be stored in the database.
MAX_PUBMEDID_LENGTH - Static variable in class net.sf.basedb.core.data.ExperimentData
 
MAX_PUBMEDID_LENGTH - Static variable in class net.sf.basedb.core.Experiment
The maximum length of the pubMedId property that can be stored in the database.
MAX_RAWDATATYPE_LENGTH - Static variable in class net.sf.basedb.core.data.FormulaData
The maximum allowed length of the raw data type name.
MAX_REFERENCE_UNIT_LENGTH - Static variable in class net.sf.basedb.core.data.QuantityData
 
MAX_REFERENCE_UNIT_LENGTH - Static variable in class net.sf.basedb.core.Quantity
The maximum length of the reference unit that can be stored in the database.
MAX_REMOTE_ID_LENGTH - Static variable in class net.sf.basedb.core.data.SessionData
The maximum length of the remote ID that can be stored in the database.
MAX_REMOTE_ID_LENGTH - Static variable in class net.sf.basedb.core.data.UserDeviceData
The maximum length of the remote ID that can be stored in the database.
MAX_REPORT_LENGTH - Static variable in class net.sf.basedb.clients.web.servlet.ContentSecurityPolicyReportServlet
 
MAX_ROLE_LENGTH - Static variable in class net.sf.basedb.core.BioPlateEventParticipant
The maximum length of the role string that can be stored in the database.
MAX_ROLE_LENGTH - Static variable in class net.sf.basedb.core.data.BioPlateEventParticipantData
 
MAX_ROOT_PATH_LENGTH - Static variable in class net.sf.basedb.core.data.FileServerData
 
MAX_ROOT_PATH_LENGTH - Static variable in class net.sf.basedb.core.FileServer
The maximum length of the root path that can be stored in the database.
MAX_SECTION_LENGTH - Static variable in class net.sf.basedb.core.BioPlate
The maximum length of the section coordinate that can be stored in the database.
MAX_SECTION_LENGTH - Static variable in class net.sf.basedb.core.data.BioPlateData
The maximum length of the section coordinate that can be stored in the database.
MAX_SERVER_LENGTH - Static variable in class net.sf.basedb.core.data.JobAgentData
The maximum length of the server that can be stored in the database.
MAX_SERVER_LENGTH - Static variable in class net.sf.basedb.core.data.JobData
The maximum allowed length of the server name.
MAX_SERVER_LENGTH - Static variable in class net.sf.basedb.core.Job
The maximum allowed length of the server name.
MAX_SERVER_LENGTH - Static variable in class net.sf.basedb.core.JobAgent
The maximum length of the server name that can be stored in the database.
MAX_SIGNAL_TRANSPORTER_LENGTH - Static variable in class net.sf.basedb.core.data.JobData
The maximum allowed length of the signal transporter string.
MAX_SORTPROPERTY_LENGTH - Static variable in class net.sf.basedb.core.data.ContextData
The maximum length of the sort order that can be stored in the database.
MAX_STACK_TRACE_LENGTH - Static variable in class net.sf.basedb.core.data.JobData
The maximum allowed length of the stack trace message.
MAX_STACK_TRACE_LENGTH - Static variable in class net.sf.basedb.core.Job
The maximum allowed length of the stack trace message.
MAX_STATUS_MESSAGE_LENGTH - Static variable in class net.sf.basedb.core.data.JobData
The maximum allowed length of the status message.
MAX_STATUS_MESSAGE_LENGTH - Static variable in class net.sf.basedb.core.Job
The maximum allowed length of the status message.
MAX_SUBCONTEXT_LENGTH - Static variable in class net.sf.basedb.core.data.ContextData
The maximum length of the name that can be stored in the database.
MAX_SUBCONTEXT_LENGTH - Static variable in class net.sf.basedb.core.data.JobData
The maximum allowed length of the subcontext name.
MAX_SYMBOL_LENGTH - Static variable in class net.sf.basedb.core.data.ReporterData
The maximum length of the gene symbol that can be stored in the database.
MAX_SYMBOL_LENGTH - Static variable in class net.sf.basedb.core.data.UnitData
 
MAX_SYMBOL_LENGTH - Static variable in class net.sf.basedb.core.Unit
The maximum length of the display symbol that can be stored in the database.
MAX_SYSTEM_ID_LENGTH - Static variable in interface net.sf.basedb.core.data.SystemData
The maximum length of the system ID of the item that can be stored in the database.
MAX_SYSTEM_ID_LENGTH - Static variable in interface net.sf.basedb.core.SystemItem
The maximum length of the system ID that can be stored in the database.
MAX_TITLE_LENGTH - Static variable in class net.sf.basedb.core.data.ExperimentData
 
MAX_TITLE_LENGTH - Static variable in class net.sf.basedb.core.Experiment
The maximum length of the title property that can be stored in the database.
MAX_TOKEN_LENGTH - Static variable in class net.sf.basedb.core.data.UserDeviceData
The maximum length of the device token that can be stored in the database.
MAX_TRAY_LENGTH - Static variable in class net.sf.basedb.core.BioPlate
The maximum length of the tray coordinate that can be stored in the database.
MAX_TRAY_LENGTH - Static variable in class net.sf.basedb.core.data.BioPlateData
The maximum length of the tray coordinate that can be stored in the database.
MAX_URL_LENGTH - Static variable in class net.sf.basedb.clients.web.taglib.Page
 
MAX_URL_LENGTH - Static variable in class net.sf.basedb.core.data.FileData
 
MAX_URL_LENGTH - Static variable in class net.sf.basedb.core.data.PluginDefinitionData
The maximum length of the url that can be stored in the database.
MAX_URL_LENGTH - Static variable in class net.sf.basedb.core.data.UserData
The maximum length of the url that can be stored in the database.
MAX_URL_LENGTH - Static variable in class net.sf.basedb.core.File
The maximum length of the URL type that can be stored in the database.
MAX_URL_LENGTH - Static variable in class net.sf.basedb.core.PluginDefinition
The maximum length of the url that can be stored in the database.
MAX_URL_LENGTH - Static variable in class net.sf.basedb.core.User
The maximum length of the url that can be stored in the database.
MAX_USER_AGENT_LENGTH - Static variable in class net.sf.basedb.core.data.UserDeviceData
The maximum length of the user agent that can be stored in the database.
MAX_USERNAME_LENGTH - Static variable in class net.sf.basedb.core.data.FileServerData
 
MAX_USERNAME_LENGTH - Static variable in class net.sf.basedb.core.FileServer
The maximum length of the username that can be stored in the database.
MAX_VALUE - Static variable in enum class net.sf.basedb.core.Item
 
MAX_VALUE_LENGTH - Static variable in class net.sf.basedb.core.data.PropertyFilterData
The maximum length of the value that can be stored in the database.
MAX_VALUE_LENGTH - Static variable in class net.sf.basedb.core.data.SettingData
The maximum length of the value of the setting that can be stored in the database.
MAX_VALUE_LENGTH - Static variable in class net.sf.basedb.core.PropertyFilter
The maximum allowed length of a filter value.
MAX_VALUE_LENGTH - Static variable in class net.sf.basedb.core.Setting
The maximum length of the value that can be stored in the database.
MAX_VERSION_LENGTH - Static variable in class net.sf.basedb.core.data.PluginDefinitionData
The maximum length of the version that can be stored in the database.
MAX_VERSION_LENGTH - Static variable in class net.sf.basedb.core.PluginDefinition
The maximum length of the version that can be stored in the database.
MAX_VERSIONSTRING_LENGTH - Static variable in class net.sf.basedb.core.data.HardwareData
 
MAX_VERSIONSTRING_LENGTH - Static variable in class net.sf.basedb.core.data.SoftwareData
 
MAX_VERSIONSTRING_LENGTH - Static variable in class net.sf.basedb.core.Hardware
The maximum length of the version variable that can be stored in the database.
MAX_VERSIONSTRING_LENGTH - Static variable in class net.sf.basedb.core.Software
The maximum length of the version variable that can be stored in the database.
maxAge - Variable in class net.sf.basedb.core.DiskUsageStatistics
 
maxAge - Variable in class net.sf.basedb.util.OlderThanFileFilter
 
maxBaseVersion - Variable in class net.sf.basedb.core.plugin.AboutImpl
 
maxBaseVersion - Variable in class net.sf.basedb.util.extensions.AboutBean
 
maxBaseVersion - Variable in class net.sf.basedb.util.extensions.Registry.RegisteredAbout
 
maxBytes - Variable in class net.sf.basedb.core.data.QuotaIndex
 
maxChannelsParameter - Variable in class net.sf.basedb.plugins.Base1PluginExecuter
The maximum number of channels, 0 means unlimited.
maxCharacters - Variable in class net.sf.basedb.clients.web.taglib.table.Cell
 
maxColor - Variable in class net.sf.basedb.util.ColorGenerator
 
maxDataColumns - Variable in class net.sf.basedb.util.parser.FlatFileParser
The maximun number of allowed data columns for a line to be considered a data line.
maxDataColumnsParameter - Static variable in class net.sf.basedb.plugins.AbstractFlatFileImporter
Parameter definition that asks for the maximum number of columns produced by the data splitter regexp for a line to be a data line.
maxDelay - Variable in class net.sf.basedb.util.TransferRateProgressReporter
 
maxEntries - Variable in class net.sf.basedb.util.extensions.logging.ExtensionsLog
 
MaxExpression - Class in net.sf.basedb.core.query
Calculates the maximum of an expression: MIN(e)
MaxExpression(Expression) - Constructor for class net.sf.basedb.core.query.MaxExpression
 
maxHeight - Variable in class net.sf.basedb.clients.web.servlet.ExperimentExplorerPlotServlet
 
maxHeight - Variable in class net.sf.basedb.clients.web.servlet.PlotServlet
 
maxHeight - Variable in class net.sf.basedb.clients.web.taglib.table.Cell
 
maxLength - Variable in class net.sf.basedb.core.StringParameterType
 
maxLength - Variable in class net.sf.basedb.util.parser.CropStringMapper
 
maxMemory - Variable in class net.sf.basedb.core.data.JobAgentSettingsData
 
maxMemory - Variable in class net.sf.basedb.core.data.PluginDefinitionData
 
maxParameters - Variable in class net.sf.basedb.core.FastAnnotationLoader.FastIterator
 
maxPosition - Variable in class net.sf.basedb.core.PositionBatcher
The maximum position number inserted by the batcher.
maxProjectPermission - Variable in class net.sf.basedb.core.Keyring
Holds the logged in user's maximum Permission within the active project.
maxRandomSamples - Variable in class net.sf.basedb.util.AnyToAnyLinkStatistics.Options
 
maxRawMappings - Variable in class net.sf.basedb.core.data.DataCubeData
 
maxResults - Variable in class net.sf.basedb.core.AbstractQuery
The maximum number of items that should be returned by the query.
maxSlots - Variable in class net.sf.basedb.clients.jobagent.slotmanager.InternalSlotManager
 
maxSlots - Variable in class net.sf.basedb.core.InternalJobQueue
The maximum number of threads that are allowed in each slot.
maxTicksPerSecond - Variable in class net.sf.basedb.util.TransferRateProgressReporter
 
maxUnknownLines - Variable in class net.sf.basedb.util.parser.FlatFileParser
The maximum number of unkown lines to parse before giving up.
maxValue - Variable in class net.sf.basedb.core.data.ColoringData
 
maxValue - Variable in class net.sf.basedb.util.ColorGenerator
 
maxValueColumnMapping - Static variable in class net.sf.basedb.plugins.batchimport.AnnotationTypeImporter
Column mapping parameter for "Max value".
maxValueMapper - Variable in class net.sf.basedb.plugins.batchimport.AnnotationTypeImporter
 
maxWidth - Variable in class net.sf.basedb.clients.web.servlet.ExperimentExplorerPlotServlet
 
maxWidth - Variable in class net.sf.basedb.clients.web.servlet.PlotServlet
 
maxWidth - Variable in class net.sf.basedb.clients.web.taglib.table.Cell
 
maybeEquals(Object) - Method in class net.sf.basedb.core.AnnotationRestriction
Check as many things as possible to try to determine if the other object is equal to this object.
maybeGranted - Variable in class net.sf.basedb.core.plugin.Permissions
 
maybeStopRunningJobs() - Method in class net.sf.basedb.clients.jobagent.Agent
Try to stop running jobs by interrupting the threads they are executing in.
MB - Static variable in class net.sf.basedb.util.Values
 
mColumn - Static variable in class net.sf.basedb.util.importer.spotdata.MAParser
 
md5 - Variable in class net.sf.basedb.core.data.FileData
 
md5 - Variable in class net.sf.basedb.core.data.ItemListSyncFilterData
 
md5 - Variable in class net.sf.basedb.core.File.UploadStream
The md5 sum calculater.
md5 - Variable in class net.sf.basedb.util.uri.UriMetadata
 
MD5 - Class in net.sf.basedb.util
This class calculates the MD5 hash of a string and returns it represented as a hexadecimal string.
MD5() - Constructor for class net.sf.basedb.util.MD5
 
MD5_FINGERPRINT_PATTERN - Static variable in class net.sf.basedb.core.FileServer
Pattern that matches a SSH MD5 fingerprint: 16 pairs of hexadecimal numbers separated with colon.
md5AtLastSync - Variable in class net.sf.basedb.core.data.ItemListData
 
mean - Variable in class net.sf.basedb.util.IntensityCalculatorUtil.JepIntensityCalculatorImpl
 
mean(String) - Method in class net.sf.basedb.util.jep.MeanFunction
Get the value of the specified property of the current raw data object.
mean(Expression) - Static method in class net.sf.basedb.core.query.Aggregations
Calculates the arithmetic mean of all values for an expression: new expression = AVG(e)
MEAN - Enum constant in enum class net.sf.basedb.util.plot.HistogramPlot.YAggregate
Plot the mean of all y-values for spots falling into each bin.
MeanExpression - Class in net.sf.basedb.core.query
Calculates the arithmetic mean of an expression: AVG(e)
MeanExpression(Expression) - Constructor for class net.sf.basedb.core.query.MeanExpression
 
MeanFunction - Class in net.sf.basedb.util.jep
A JEP function class that adds a mean(string) function to a JEP expression parser.
MeanFunction(DbControl) - Constructor for class net.sf.basedb.util.jep.MeanFunction
Create a new instance of this function working with raw data of the specified raw bio assay.
meanRawData(String) - Static method in class net.sf.basedb.core.query.Dynamic
Create an expression representing the mean value of a property of a raw data spot. expression = mean(rawdata.property).
MeanRawDataPropertyExpression - Class in net.sf.basedb.core
An expression representing the mean value of property of a raw data spot.
MeanRawDataPropertyExpression(String) - Constructor for class net.sf.basedb.core.MeanRawDataPropertyExpression
 
means - Variable in class net.sf.basedb.util.jep.MeanFunction
Holds a cache of the values.
MeasuredBioMaterial - Class in net.sf.basedb.core
This class is the base class for measured biomaterial items.
MeasuredBioMaterial(MeasuredBioMaterialData) - Constructor for class net.sf.basedb.core.MeasuredBioMaterial
 
MeasuredBioMaterial.RemainingQuantityAction - Class in net.sf.basedb.core
Transaction handler for updating the remaining quantity of a biomaterial based on the sum of the used quantity in this transaction.
MeasuredBioMaterialData - Class in net.sf.basedb.core.data
This class is the root class for measured biomaterials, ie biomaterials for where the quantity is tracked.
MeasuredBioMaterialData() - Constructor for class net.sf.basedb.core.data.MeasuredBioMaterialData
 
median(float[], int, int) - Method in class net.sf.basedb.plugins.MedianRatioNormalization
 
median(List<MedianRatioNormalization.SpotData>) - Method in class net.sf.basedb.plugins.MedianRatioNormalization
 
medianCorrection(List<LowessNormalization.SpotData>, Double[]) - Static method in class net.sf.basedb.plugins.LowessNormalization
 
MedianRatioNormalization - Class in net.sf.basedb.plugins
 
MedianRatioNormalization() - Constructor for class net.sf.basedb.plugins.MedianRatioNormalization
 
MedianRatioNormalization.SpotData - Class in net.sf.basedb.plugins
 
medianRatioSection - Static variable in class net.sf.basedb.plugins.MedianRatioNormalization
Section for normalization options
MEDIUM - Enum constant in enum class net.sf.basedb.core.Job.ExecutionTime
The job shouldn't take less than 1 hour to execute.
member - Variable in class net.sf.basedb.clients.web.extensions.fileviewer.FileViewerContext
 
member - Variable in class net.sf.basedb.util.fileset.ValidatingFileSetMember
 
member - Variable in class net.sf.basedb.util.overview.Fix
 
memberQuery - Variable in class net.sf.basedb.clients.web.formatter.DataFileFormatter
 
memberQuery - Variable in class net.sf.basedb.clients.web.plugins.FileSetMemberLoader
 
members - Variable in class net.sf.basedb.core.data.DataFileTypeData
 
members - Variable in class net.sf.basedb.core.data.FileSetData
 
members - Variable in class net.sf.basedb.core.data.ItemListData
 
members - Variable in class net.sf.basedb.util.fileset.ResetMetadataRenderer
 
members - Variable in class net.sf.basedb.util.fileset.ValidationRenderer
 
memberType - Variable in class net.sf.basedb.core.data.ItemListData
 
menu - Variable in class net.sf.basedb.clients.web.taglib.menu.Menuitem
The parent Menu.
menu - Variable in class net.sf.basedb.clients.web.taglib.menu.Menuseparator
 
menu - Variable in class net.sf.basedb.clients.web.taglib.menu.Submenu
The parent Menu.
menu - Variable in class net.sf.basedb.clients.web.taglib.Page
The name of the menu that should be displayed on the current page.
Menu - Class in net.sf.basedb.clients.web.taglib.menu
This tag defines a drop-down menu that is is opened when the user moves the mouse over or clicks at the title of the menu.
Menu() - Constructor for class net.sf.basedb.clients.web.taglib.menu.Menu
 
MENU - Static variable in class net.sf.basedb.clients.web.resources.Bundle
Resource bundle with string that are used in the menu.
menuId - Variable in class net.sf.basedb.clients.web.extensions.menu.FixedMenuItemFactory
 
menuId - Variable in class net.sf.basedb.clients.web.extensions.menu.MenuItemBean
 
menuId - Variable in class net.sf.basedb.clients.web.extensions.menu.PermissionMenuItemFactory
 
Menuitem - Class in net.sf.basedb.clients.web.taglib.menu
This tag defines a menu item inside a drop-down menu.
Menuitem() - Constructor for class net.sf.basedb.clients.web.taglib.menu.Menuitem
 
MENUITEM - Enum constant in enum class net.sf.basedb.clients.web.extensions.menu.MenuItemAction.MenuType
This is a real menu item.
MenuItemAction - Interface in net.sf.basedb.clients.web.extensions.menu
An action for extensions to the menu system.
MenuItemAction.MenuType - Enum Class in net.sf.basedb.clients.web.extensions.menu
 
MenuItemBean - Class in net.sf.basedb.clients.web.extensions.menu
A simple bean-like implementation of the MenuItemAction interface.
MenuItemBean() - Constructor for class net.sf.basedb.clients.web.extensions.menu.MenuItemBean
Create a new empty menu item action.
Menuseparator - Class in net.sf.basedb.clients.web.taglib.menu
This tag defines a horizontal separator line inside a drop-down menu.
Menuseparator() - Constructor for class net.sf.basedb.clients.web.taglib.menu.Menuseparator
 
MenuType() - Constructor for enum class net.sf.basedb.clients.web.extensions.menu.MenuItemAction.MenuType
 
merge(Integer...) - Static method in enum class net.sf.basedb.core.Permission
Merges a list of integer permission values.
merge(Object) - Method in class net.sf.basedb.core.hibernate.SessionWrapper
 
merge(String, Object) - Method in class net.sf.basedb.core.hibernate.SessionWrapper
 
merge(DbControl, ItemKey...) - Static method in class net.sf.basedb.core.ShareableUtil
Merge one or more item keys into a new item key that combines all the permissions.
merge(DbControl, ProjectKey...) - Static method in class net.sf.basedb.core.ShareableUtil
Merge one or more project keys into a new project key that combines all the permissions.
merge(ItemKey) - Method in class net.sf.basedb.core.GroupPermissions
Merge the permissions for all groups from the given item key with the permissions in this object.
merge(ItemKey) - Method in class net.sf.basedb.core.MultiPermissions
Merge the permissions from the given item key keeping those that has already been set.
merge(ItemKey) - Method in class net.sf.basedb.core.UserPermissions
Merge the permissions for all users from the given item key with the permissions in this object.
merge(EntityLogOptions) - Method in class net.sf.basedb.core.log.EntityLogOptions
Merge log options from the other object into this object.
merge(ProjectKey) - Method in class net.sf.basedb.core.MultiPermissions
Merge the permissions from the given project key keeping those that has already been set.
merge(ProjectKey) - Method in class net.sf.basedb.core.ProjectPermissions
Merge the permissions for all projects from the given project key with the permissions in this object.
mergeAnd(IdListRestriction) - Method in class net.sf.basedb.core.query.IdListRestriction
Merge this list with another list with AND logic respecting the notIn setting.
message - Variable in class net.sf.basedb.core.ItemContext
 
message - Variable in class net.sf.basedb.core.PluginResponse
 
message - Variable in class net.sf.basedb.core.signal.ExceptionInterruptHandler
 
message - Variable in class net.sf.basedb.core.SimpleAbsoluteProgressReporter
 
message - Variable in class net.sf.basedb.core.SimpleProgressReporter
 
message - Variable in class net.sf.basedb.plugins.executor.ExternalProgramExecutor.ResponseWrapper
 
message - Variable in class net.sf.basedb.util.extensions.logging.LogEntry
 
message - Variable in class net.sf.basedb.util.fileset.ValidatingFileSetMember
 
message - Variable in class net.sf.basedb.util.fileset.ValidationRenderer
 
message - Variable in class net.sf.basedb.util.overview.Failure
 
message - Variable in class net.sf.basedb.util.overview.Fix
 
Message - Class in net.sf.basedb.core
This class represents a message.
Message(MessageData) - Constructor for class net.sf.basedb.core.Message
 
MESSAGE - Enum constant in enum class net.sf.basedb.core.Item
The item is a Message.
Message.QueryRuntimeFilterImpl - Class in net.sf.basedb.core
A runtime filter implementation that limits a query to only return messages for the currently logged in user unless the logged in user has generic read permission.
MessageData - Class in net.sf.basedb.core.data
This class holds information about messages.
MessageData() - Constructor for class net.sf.basedb.core.data.MessageData
 
messagePrefix - Variable in class net.sf.basedb.util.ChainedProgressReporter
 
messages - Variable in class net.sf.basedb.core.data.JobData
 
messages - Variable in class net.sf.basedb.core.data.UserData
 
messages - Variable in class net.sf.basedb.util.extensions.manager.ProcessResults.FileResults
 
MetaBlock(int) - Constructor for class net.sf.basedb.plugins.PrintMapFlatFileImporter.MetaBlock
 
metaBlocks - Variable in class net.sf.basedb.plugins.PrintMapFlatFileImporter
 
metaColumn - Variable in class net.sf.basedb.core.FeatureCoordinate
 
metadata - Variable in class net.sf.basedb.core.hibernate.DbIndexWork
 
metadata - Variable in class net.sf.basedb.core.hibernate.SchemaGenerator
 
metadata - Static variable in class net.sf.basedb.core.HibernateUtil
The mappings related to a configuration.
metadata - Variable in class net.sf.basedb.core.Metadata.EntityPropertyPath
 
metadata - Variable in class net.sf.basedb.util.export.spotdata.AssayPropertyField
 
metadata - Variable in class net.sf.basedb.util.uri.http.HttpConnectionManager
 
metaData - Variable in class net.sf.basedb.core.BasicBatcher
Hibernate metadata for the batchable object.
metaData - Static variable in class net.sf.basedb.core.Feature
 
metaData - Static variable in class net.sf.basedb.core.Reporter
 
metaData - Variable in class net.sf.basedb.util.jep.RawFunction
 
metaData - Variable in class net.sf.basedb.util.jep.ReporterFunction
 
Metadata<C> - Class in net.sf.basedb.core
Utility methods for retreiving metadata about items.
Metadata(Class<C>, String) - Constructor for class net.sf.basedb.core.Metadata
 
Metadata.BasicData2ItemPropertyPath<C extends BasicData,V extends BasicItem> - Class in net.sf.basedb.core
Property path implementation that converts a BasicData object to a BasicItem.
Metadata.BasicItem2DataPropertyPath<C extends BasicItem,V extends BasicData> - Class in net.sf.basedb.core
Property path implementation that converts a BasicItem to a BasicData object.
Metadata.CollectionPropertyPath<C> - Class in net.sf.basedb.core
Property path implementation which wraps a collection inside an unmodifiable collection.
Metadata.CombinedPropertyPath<C,V> - Class in net.sf.basedb.core
Property path implementation that combines a list of property paths to create a long chain.
Metadata.ComponentPropertyPath<C,V> - Class in net.sf.basedb.core
Property path implementation which gets a value from a component.
Metadata.DateCopyPropertyPath - Class in net.sf.basedb.core
Property path implementation clones a Date.
Metadata.EntityPropertyPath<C,V> - Class in net.sf.basedb.core
Property path implementation which gets a value from an entity.
Metadata.EvictPropertyPath<C> - Class in net.sf.basedb.core
Property path implementation that evicts the selected item from the Hibernate first-level cache.
Metadata.IdentifierPropertyPath - Class in net.sf.basedb.core
Property path implementation which gets the id from an entity.
Metadata.MapPropertyPath - Class in net.sf.basedb.core
Property path implementation which wraps a map inside an unmodifiable map.
Metadata.NoopPropertyPath<C> - Class in net.sf.basedb.core
Property path implementation that does nothing.
Metadata.PropertyPath<C,V> - Interface in net.sf.basedb.core
Contract for getting the value of a specific property for an item.
Metadata.ReporterScore2DataPropertyPath - Class in net.sf.basedb.core
Property path implementation that converts a ReporterScore to a ReporterListScoreData object.
MetadataModel - Class in net.sf.basedb.util.bfs
A model container of the contents of a BFS metadata file.
MetadataModel() - Constructor for class net.sf.basedb.util.bfs.MetadataModel
Create a new metadata model.
MetadataModel.Section - Class in net.sf.basedb.util.bfs
Holds information about a section.
MetadataModel.SectionEntry - Class in net.sf.basedb.util.bfs
Holds information about a section entry.
metadataParser - Variable in class net.sf.basedb.util.importer.spotdata.BfsImporter
 
MetadataParser - Class in net.sf.basedb.util.bfs
Parser implementation that parses a BFS metadata file.
MetadataParser() - Constructor for class net.sf.basedb.util.bfs.MetadataParser
Create a new metadata parser.
metadataPrefix - Variable in class net.sf.basedb.util.basefile.BaseFileWriter
 
metadataSources - Variable in class net.sf.basedb.core.ServiceSessionControl.SessionFactoryConfiguration
 
metadataWriter - Variable in class net.sf.basedb.util.export.spotdata.BfsExporter
 
MetadataWriter - Class in net.sf.basedb.util.bfs
Writer implementation for writing BFS metadata files.
MetadataWriter(Writer) - Constructor for class net.sf.basedb.util.bfs.MetadataWriter
Create a new BFS metadata writer.
metaGridX - Variable in class net.sf.basedb.core.BlockInfo
The X coordinate of the block.
metaGridX - Variable in class net.sf.basedb.core.data.ArrayDesignBlockData
 
metaGridX - Variable in class net.sf.basedb.core.data.RawData
 
metaGridX - Variable in class net.sf.basedb.plugins.PrintMapFlatFileImporter.MetaBlock
 
metaGridXColumnMapping - Static variable in class net.sf.basedb.plugins.RawDataFlatFileImporter
 
metaGridXColumnMapping - Static variable in class net.sf.basedb.plugins.ReporterMapFlatFileImporter
 
metaGridXMapper - Variable in class net.sf.basedb.plugins.RawDataFlatFileImporter
 
metaGridXMapper - Variable in class net.sf.basedb.plugins.ReporterMapFlatFileImporter
 
metaGridY - Variable in class net.sf.basedb.core.BlockInfo
The Y coordinate of the block.
metaGridY - Variable in class net.sf.basedb.core.data.ArrayDesignBlockData
 
metaGridY - Variable in class net.sf.basedb.core.data.RawData
 
metaGridY - Variable in class net.sf.basedb.plugins.PrintMapFlatFileImporter.MetaBlock
 
metaGridYColumnMapping - Static variable in class net.sf.basedb.plugins.RawDataFlatFileImporter
 
metaGridYColumnMapping - Static variable in class net.sf.basedb.plugins.ReporterMapFlatFileImporter
 
metaGridYMapper - Variable in class net.sf.basedb.plugins.RawDataFlatFileImporter
 
metaGridYMapper - Variable in class net.sf.basedb.plugins.ReporterMapFlatFileImporter
 
metaRow - Variable in class net.sf.basedb.core.FeatureCoordinate
 
method - Variable in class net.sf.basedb.core.authentication.AuthenticatedUser
 
method - Variable in class net.sf.basedb.core.authentication.AuthenticationMethod
 
method - Variable in class net.sf.basedb.plugins.batchimport.FallbackIdMethod
 
method - Variable in class net.sf.basedb.plugins.batchimport.InternalIdMethod
 
method - Variable in class net.sf.basedb.plugins.batchimport.MultiPropertyIdMethod
 
method - Variable in class net.sf.basedb.plugins.batchimport.PropertyIdMethod
 
methods - Static variable in class net.sf.basedb.core.authentication.AuthenticationMethod
 
MEV_TDMS - Static variable in class net.sf.basedb.core.DataFileType
The external ID for the file type representing a MeV TDMS (Tab-Delimited Multiple Sample) file.
miameColumnMapping - Static variable in class net.sf.basedb.plugins.batchimport.AnnotationTypeImporter
Column mapping parameter for "Required for MIAME" flag.
miameMapper - Variable in class net.sf.basedb.plugins.batchimport.AnnotationTypeImporter
 
MICROARRAY_IMAGE - Static variable in class net.sf.basedb.core.DataFileType
The external ID for the file type representing scanned microarray image.
midColor - Variable in class net.sf.basedb.util.ColorGenerator
 
midValue - Variable in class net.sf.basedb.core.data.ColoringData
 
midValue - Variable in class net.sf.basedb.util.ColorGenerator
 
migrateAll(SessionControl, File, boolean, ProgressReporter) - Static method in class net.sf.basedb.core.MigrateRbaToDba
 
MigratedLogger() - Constructor for class net.sf.basedb.core.MigrateRbaToDba.MigratedLogger
 
MigrateRbaToDba - Class in net.sf.basedb.core
 
MigrateRbaToDba(DbControl, MigrateRbaToDba.SubtypeMapping, ProgressReporter) - Constructor for class net.sf.basedb.core.MigrateRbaToDba
 
MigrateRbaToDba.Itemlist - Class in net.sf.basedb.core
 
MigrateRbaToDba.LineMapping - Class in net.sf.basedb.core
 
MigrateRbaToDba.MigratedLogger - Class in net.sf.basedb.core
Used for adding log entries to the database if that is enabled.
MigrateRbaToDba.Rba - Class in net.sf.basedb.core
Hold information a raw bioassay.
MigrateRbaToDba.SubtypeMapping - Class in net.sf.basedb.core
Hold the mappings defined in the mapping file.
Migration - Class in net.sf.basedb.core
Class for migrating a database to PostgreSQL.
Migration(boolean, File, Session, ProgressReporter) - Constructor for class net.sf.basedb.core.Migration
 
Migration.ProgressInputStream - Class in net.sf.basedb.core
 
mimeType - Variable in class net.sf.basedb.clients.web.fileupload.FileUpload.SectionHeaders
 
mimeType - Variable in class net.sf.basedb.clients.web.fileupload.UploadedFile
 
mimeType - Variable in class net.sf.basedb.core.data.FileData
 
mimeType - Variable in class net.sf.basedb.util.uri.UriMetadata
 
MimeType - Class in net.sf.basedb.core
This class is used to represent mime types.
MimeType(MimeTypeData) - Constructor for class net.sf.basedb.core.MimeType
Creates a new mimetype item from the given data.
MIMETYPE - Enum constant in enum class net.sf.basedb.core.Item
The item is a MimeType.
mimeTypeColumnMapping - Static variable in class net.sf.basedb.plugins.batchimport.FileImporter
 
MimeTypeData - Class in net.sf.basedb.core.data
This class holds information about mimetypes
MimeTypeData() - Constructor for class net.sf.basedb.core.data.MimeTypeData
 
mimeTypeMapper - Variable in class net.sf.basedb.plugins.batchimport.FileImporter
 
mimeTypes - Static variable in class net.sf.basedb.plugins.Bzip2FileUnpacker
 
mimeTypes - Static variable in class net.sf.basedb.plugins.GzipFileUnpacker
 
mimeTypes - Static variable in class net.sf.basedb.plugins.TarFileUnpacker
 
mimeTypes - Static variable in class net.sf.basedb.plugins.ZipFileUnpacker
 
min - Variable in class net.sf.basedb.util.plot.HistogramPlot.HistogramBin
 
min(Expression) - Static method in class net.sf.basedb.core.query.Aggregations
Calculates the minimum value of an expression: new expression = MIN(e)
MIN - Enum constant in enum class net.sf.basedb.core.Formula.AverageMethod
 
MIN - Enum constant in enum class net.sf.basedb.util.plot.HistogramPlot.YAggregate
Plot the minimum of all y-values for spots falling into each bin.
minBaseVersion - Variable in class net.sf.basedb.core.plugin.AboutImpl
 
minBaseVersion - Variable in class net.sf.basedb.util.extensions.AboutBean
 
minBaseVersion - Variable in class net.sf.basedb.util.extensions.Registry.RegisteredAbout
 
minChannelsParameter - Variable in class net.sf.basedb.plugins.Base1PluginExecuter
The minimum number of channels.
minColor - Variable in class net.sf.basedb.util.ColorGenerator
 
minCount - Variable in class net.sf.basedb.util.AnyToAnyLinkStatistics.Options
 
minDataColumns - Variable in class net.sf.basedb.util.parser.FlatFileParser
The minimun number of allowed data columns for a line to be considered a data line.
minDataColumnsParameter - Static variable in class net.sf.basedb.plugins.AbstractFlatFileImporter
Parameter definition that asks for the minimum number of columns produced by the data splitter regexp for a line to be a data line.
mIndex - Variable in class net.sf.basedb.util.importer.spotdata.MAParser
 
MINE - Enum constant in enum class net.sf.basedb.core.Include
Include item owned by the logged in user.
MinExpression - Class in net.sf.basedb.core.query
Calculates the minumum of an expression: MIN(e)
MinExpression(Expression) - Constructor for class net.sf.basedb.core.query.MinExpression
 
minFraction - Variable in class net.sf.basedb.util.AnyToAnyLinkStatistics.Options
 
minIntensityParameter - Variable in class net.sf.basedb.plugins.MedianRatioNormalization
 
minor - Static variable in class net.sf.basedb.core.Version
 
minValue - Variable in class net.sf.basedb.core.data.ColoringData
 
minValue - Variable in class net.sf.basedb.util.ColorGenerator
 
minValueColumnMapping - Static variable in class net.sf.basedb.plugins.batchimport.AnnotationTypeImporter
Column mapping parameter for "Min value".
minValueMapper - Variable in class net.sf.basedb.plugins.batchimport.AnnotationTypeImporter
 
missing(String, String) - Method in class net.sf.basedb.util.formatter.PropertyFilterFormatter
 
missing(String, String, Item, EntityQuery) - Static method in class net.sf.basedb.core.query.AnyToAnyRestriction
Create a restriction that restrict a query to return items that is missing a linked item with the given link name.
MISSING_ANYTOANY - Static variable in class net.sf.basedb.util.overview.Validator
Validator rule that checks for a missing reference in an any-to-any link.
MISSING_ARRAYBATCH - Static variable in class net.sf.basedb.util.overview.Validator
Validator rule that checks for missing array batch.
MISSING_ARRAYDESIGN - Static variable in class net.sf.basedb.util.overview.Validator
Validator rule that checks for missing array design.
MISSING_ARRAYSLIDE - Static variable in class net.sf.basedb.util.overview.Validator
Validator rule that checks for missing array slide.
MISSING_BIOPLATE - Static variable in class net.sf.basedb.util.overview.Validator
Validator rule that checks for missing bioplate location.
MISSING_BIOSOURCE - Static variable in class net.sf.basedb.util.overview.Validator
Validator rule that checks for missing biosource.
MISSING_DATAFILE - Static variable in class net.sf.basedb.util.overview.Validator
Validator rule that checks if all files required by the platform are present or not.
MISSING_DERIVEDBIOASSAY - Static variable in class net.sf.basedb.util.overview.Validator
Validator rule that checks for missing parent derived bioassay.
MISSING_EXTRACT - Static variable in class net.sf.basedb.util.overview.Validator
Validator rule that checks for missing extract.
MISSING_FACTORVALUE - Static variable in class net.sf.basedb.util.overview.Validator
Validator rule that checks for missing experimental factor value.
MISSING_FILE - Static variable in class net.sf.basedb.util.overview.Validator
Validator rule that checks for denied access to (data) files.
MISSING_HARDWARE - Static variable in class net.sf.basedb.util.overview.Validator
Validator rule that checks for missing hardware.
MISSING_KIT - Static variable in class net.sf.basedb.util.overview.Validator
Validator rule that checks for missing kits.
MISSING_MIAME_ANNOTATION - Static variable in class net.sf.basedb.util.overview.Validator
Validator rule that checks for missing "Required for MIAME" annotation.
MISSING_PARAMETER - Static variable in class net.sf.basedb.util.overview.Validator
Validator rule that checks for missing protocol parameter values.
MISSING_PHYSICALBIOASSAY - Static variable in class net.sf.basedb.util.overview.Validator
Validator rule that checks for missing physical bioassay.
MISSING_PROTOCOL - Static variable in class net.sf.basedb.util.overview.Validator
Validator rule that checks for missing protocols.
MISSING_SAMPLE - Static variable in class net.sf.basedb.util.overview.Validator
Validator rule that checks for missing sample.
MISSING_SOFTWARE - Static variable in class net.sf.basedb.util.overview.Validator
Validator rule that checks for missing software.
MISSING_TAG - Static variable in class net.sf.basedb.util.overview.Validator
Validator rule that checks for missing tag.
missingReporterErrorParameter - Static variable in class net.sf.basedb.plugins.IlluminaRawDataImporter
 
missingReporterErrorParameter - Static variable in class net.sf.basedb.plugins.PlateFlatFileImporter
 
missingReporterErrorParameter - Static variable in class net.sf.basedb.plugins.RawDataFlatFileImporter
 
missingReporterErrorParameter - Static variable in class net.sf.basedb.plugins.ReporterMapFlatFileImporter
 
missingWellErrorParameter - Static variable in class net.sf.basedb.plugins.PrintMapFlatFileImporter
 
mode - Variable in class net.sf.basedb.clients.web.formatter.DataFileFormatter
 
mode - Variable in class net.sf.basedb.clients.web.ModeInfo.ModeContext
 
mode - Variable in class net.sf.basedb.core.hibernate.SchemaGenerator.CollectSqlTarget
 
mode - Variable in class net.sf.basedb.core.hibernate.SchemaGenerator
 
mode() - Method in class net.sf.basedb.clients.web.ModeInfo.ModeContext
 
Mode(boolean, boolean) - Constructor for enum class net.sf.basedb.core.hibernate.SchemaGenerator.Mode
 
ModeContext(Item, ModeInfo) - Constructor for class net.sf.basedb.clients.web.ModeInfo.ModeContext
 
ModeInfo - Class in net.sf.basedb.clients.web
 
ModeInfo(String, String, String, boolean, boolean, boolean, boolean, boolean, boolean, boolean, boolean, boolean, boolean, boolean, boolean, Permission, boolean) - Constructor for class net.sf.basedb.clients.web.ModeInfo
 
ModeInfo.ModeContext - Class in net.sf.basedb.clients.web
This implementation create main contextes from a mode and item type which means that we can have different default subcontexts for the default list pages and for selection list pages.
modes - Static variable in class net.sf.basedb.clients.web.ModeInfo
 
modified - Variable in class net.sf.basedb.core.hibernate.SchemaGenerator.SqlStatement
 
modified - Variable in class net.sf.basedb.core.SessionControl.SettingInfo
If the setting has been modified while the user was logged in or not
MOLAR_CONCENTRATION - Static variable in class net.sf.basedb.core.Quantity
The id for the Quantity object representing substance concentration.
MOMENTUM - Static variable in class net.sf.basedb.core.Quantity
The id for the Quantity object representing momentum.
moreAttributes - Variable in class net.sf.basedb.clients.web.extensions.DynamicActionAttributeSupport
 
MOVE - Static variable in class net.sf.basedb.core.BioPlateEventType
The system ID for "Move" event type.
MultiEventHandler - Class in net.sf.basedb.util.bfs
Event handler implementation that forwards a single event to multiple event handlers.
MultiEventHandler() - Constructor for class net.sf.basedb.util.bfs.MultiEventHandler
Create a new event handler.
MultiFormatter - Class in net.sf.basedb.util.formatter
A generic formatter that can be used to format objects of mixed classes.
MultiFormatter(Formatter<Object>, boolean) - Constructor for class net.sf.basedb.util.formatter.MultiFormatter
Create a new multi formatter.
MultiFormatter(Formatter<Object>, boolean, boolean) - Constructor for class net.sf.basedb.util.formatter.MultiFormatter
Create a new multi formatter.
multiHop - Variable in class net.sf.basedb.clients.web.extensions.list.RelatedItemColumn.Specification
 
MultiPermissions - Class in net.sf.basedb.core
This is a helper class that is very useful when you have a collection of Shareable items and want to modify some permissions on all of them without affecting the rest of the permissions.
MultiPermissions(Collection<? extends SharedItem>) - Constructor for class net.sf.basedb.core.MultiPermissions
Create a new MultiPermissions object and feed it the collection of Shareable items that you want to modify.
multiple - Variable in class net.sf.basedb.clients.web.taglib.table.ColumnDef
 
multiple - Variable in class net.sf.basedb.core.data.ItemSubtypeFileTypeData
 
multiple - Variable in class net.sf.basedb.core.data.PlatformFileTypeData
 
multiple - Variable in class net.sf.basedb.core.Install.ItemSubtypeFT
 
multiple - Variable in class net.sf.basedb.core.Install.PlatformFT
 
multiple - Variable in class net.sf.basedb.plugins.executor.ParameterDefinition
 
MULTIPLE_ARRAYDESIGNS - Static variable in class net.sf.basedb.util.overview.Validator
Validator rule that checks if all raw bioassays in an experiment uses the same array design.
multipleItemsFoundErrorParameter - Static variable in class net.sf.basedb.plugins.AnnotationFlatFileImporter
 
multipleItemsFoundErrorParameter - Static variable in class net.sf.basedb.plugins.batchimport.AbstractItemImporter
 
multipleItemsFoundErrorParameter - Static variable in class net.sf.basedb.plugins.batchimport.AnyToAnyImporter
 
multiplePositionsError - Static variable in class net.sf.basedb.plugins.batchimport.PhysicalBioAssayImporter
 
multipleReferencesFoundErrorParameter - Static variable in class net.sf.basedb.plugins.batchimport.AbstractItemImporter
 
multipleTargetsFoundErrorParameter - Static variable in class net.sf.basedb.plugins.batchimport.AnyToAnyImporter
 
multiplicity - Variable in class net.sf.basedb.core.data.AnnotationTypeData
 
multiplicity - Variable in class net.sf.basedb.core.ParameterType
How many values that can be tied to this parameter. 0 is unlimited values and 1 is default.
multiplicityColumnMapping - Static variable in class net.sf.basedb.plugins.batchimport.AnnotationTypeImporter
Column mapping parameter for annotation multiplicty.
multiplicityMapper - Variable in class net.sf.basedb.plugins.batchimport.AnnotationTypeImporter
 
multiply(Expression, Expression) - Static method in class net.sf.basedb.core.query.Expressions
Multiply two expressions: new expression = e1 * e2.
MultiplyConverter - Class in net.sf.basedb.util.jep.convert
Convert Multiply function to a Query API Expression.
MultiplyConverter() - Constructor for class net.sf.basedb.util.jep.convert.MultiplyConverter
 
MultiplyExpression - Class in net.sf.basedb.core.query
Multiply two expressions: e1 * e2.
MultiplyExpression(Expression, Expression) - Constructor for class net.sf.basedb.core.query.MultiplyExpression
 
MultiPropertyIdMethod - Class in net.sf.basedb.plugins.batchimport
Identification method implementation that can use a multiple properties (eg, name, id, externalId, etc.) for identifying items.
MultiPropertyIdMethod(String, String, String[], boolean, Type) - Constructor for class net.sf.basedb.plugins.batchimport.MultiPropertyIdMethod
Create a new id method.
MultiProtocolRequestHandler - Class in net.sf.basedb.clients.jobagent.handlers
Request handler implementation that forwards all requests to a registered protocol-specific handler.
MultiProtocolRequestHandler(Agent, RequestHandler) - Constructor for class net.sf.basedb.clients.jobagent.handlers.MultiProtocolRequestHandler
Create a new multi-protocol request handler.
MultiQueryIterator<E extends BasicItem> - Class in net.sf.basedb.util.query
Helper class for executing multiple queries and return the result as a single iterator.
MultiQueryIterator(DbControl, ItemQuery<? extends E>[]) - Constructor for class net.sf.basedb.util.query.MultiQueryIterator
 
MultiStepCollectionTransformer<S,D> - Class in net.sf.basedb.util.collections
Collection transformer implementation that transforms a source collection into the destination collection using multiple steps.
MultiStepCollectionTransformer(List<CollectionTransformer<?, ?>>) - Constructor for class net.sf.basedb.util.collections.MultiStepCollectionTransformer
 
MultiUpdateWork - Class in net.sf.basedb.core.hibernate
A JDBC Work implementation that executes multiple queries that doesn't return any result.
MultiUpdateWork(Collection<String>) - Constructor for class net.sf.basedb.core.hibernate.MultiUpdateWork
Create a new work item.
multiuserAccount - Variable in class net.sf.basedb.core.data.UserData
 
MWBR - Enum constant in enum class net.sf.basedb.plugins.PrintMapFlatFileImporter.FormatType
 
MySkinAction(FixedSkinActionFactory, String) - Constructor for class net.sf.basedb.clients.web.extensions.skin.FixedSkinActionFactory.MySkinAction
 
MySQLEngine - Class in net.sf.basedb.core.dbengine
Database engine for My SQL.
MySQLEngine() - Constructor for class net.sf.basedb.core.dbengine.MySQLEngine
Create MySQLEngine.

N

n - Variable in class net.sf.basedb.util.basefile.BaseFileWriter
 
name - Variable in class net.sf.basedb.clients.jobagent.Agent
 
name - Variable in class net.sf.basedb.clients.web.extensions.DynamicActionAttribute
 
name - Variable in class net.sf.basedb.clients.web.extensions.ServletWrapper
 
name - Variable in class net.sf.basedb.clients.web.extensions.startpage.FixedStartPageFactory
 
name - Variable in class net.sf.basedb.clients.web.extensions.startpage.StartPageBean
 
name - Variable in class net.sf.basedb.clients.web.fileupload.FileUpload.SectionHeaders
 
name - Variable in class net.sf.basedb.clients.web.ModeInfo
 
name - Variable in class net.sf.basedb.clients.web.plugins.ExportedProperty
 
name - Variable in class net.sf.basedb.clients.web.SubContext
 
name - Variable in class net.sf.basedb.clients.web.taglib.Input
The name of the input element.
name - Variable in class net.sf.basedb.clients.web.taglib.table.Hidden
The name of the element.
name - Variable in class net.sf.basedb.core.authentication.ExtraUserInformation
 
name - Variable in class net.sf.basedb.core.BatchedPropertyInfo
 
name - Variable in class net.sf.basedb.core.data.AnyToAnyData
 
name - Variable in class net.sf.basedb.core.data.BioAssayData
 
name - Variable in class net.sf.basedb.core.data.BioAssaySetData
 
name - Variable in class net.sf.basedb.core.data.BioPlateEventTypeData
 
name - Variable in class net.sf.basedb.core.data.BioPlateTypeData
 
name - Variable in class net.sf.basedb.core.data.ChangeHistoryData
 
name - Variable in class net.sf.basedb.core.data.CommonData
 
name - Variable in class net.sf.basedb.core.data.ContextData
 
name - Variable in class net.sf.basedb.core.data.ContextIndex
 
name - Variable in class net.sf.basedb.core.data.DataFileTypeData
 
name - Variable in class net.sf.basedb.core.data.ExtraValueTypeData
 
name - Variable in class net.sf.basedb.core.data.GroupData
 
name - Variable in class net.sf.basedb.core.data.HelpData
 
name - Variable in class net.sf.basedb.core.data.ItemListSyncFilterData
 
name - Variable in class net.sf.basedb.core.data.ItemSubtypeData
 
name - Variable in class net.sf.basedb.core.data.MessageData
 
name - Variable in class net.sf.basedb.core.data.MimeTypeData
 
name - Variable in class net.sf.basedb.core.data.NewsData
 
name - Variable in class net.sf.basedb.core.data.PlateEventTypeData
 
name - Variable in class net.sf.basedb.core.data.PlateGeometryData
 
name - Variable in class net.sf.basedb.core.data.PlatformData
 
name - Variable in class net.sf.basedb.core.data.PlatformVariantData
 
name - Variable in class net.sf.basedb.core.data.PluginDefinitionData
 
name - Variable in class net.sf.basedb.core.data.PluginTypeData
 
name - Variable in class net.sf.basedb.core.data.ProjectData
 
name - Variable in class net.sf.basedb.core.data.QuantityData
 
name - Variable in class net.sf.basedb.core.data.QuotaData
 
name - Variable in class net.sf.basedb.core.data.QuotaTypeData
 
name - Variable in class net.sf.basedb.core.data.ReporterData
 
name - Variable in class net.sf.basedb.core.data.ReporterTypeData
 
name - Variable in class net.sf.basedb.core.data.RoleData
 
name - Variable in class net.sf.basedb.core.data.RoleKeyData
 
name - Variable in class net.sf.basedb.core.data.RootRawBioAssayData
 
name - Variable in class net.sf.basedb.core.data.SettingData
 
name - Variable in class net.sf.basedb.core.data.TransformationData
 
name - Variable in class net.sf.basedb.core.data.UnitData
 
name - Variable in class net.sf.basedb.core.data.UserData
 
name - Variable in class net.sf.basedb.core.data.UserDeviceData
 
name - Variable in class net.sf.basedb.core.data.VersionedParameter
The name of the parameter.
name - Variable in class net.sf.basedb.core.DbControl
The name of this transaction.
name - Variable in class net.sf.basedb.core.dbengine.TableInfo.ColumnInfo
 
name - Variable in class net.sf.basedb.core.dbengine.TableInfo.ForeignKeyInfo
 
name - Variable in class net.sf.basedb.core.dbengine.TableInfo.IndexInfo
 
name - Variable in class net.sf.basedb.core.dbengine.TableInfo.PrimaryKeyInfo
 
name - Variable in class net.sf.basedb.core.ExtendedProperty
 
name - Variable in class net.sf.basedb.core.HibernateUtil.DelayedFilterDef
 
name - Variable in class net.sf.basedb.core.IntensityFormula
 
name - Variable in class net.sf.basedb.core.ItemContext
 
name - Variable in class net.sf.basedb.core.LogControl
 
name - Variable in class net.sf.basedb.core.MigrateRbaToDba.Itemlist
 
name - Variable in class net.sf.basedb.core.MigrateRbaToDba.Rba
 
name - Variable in class net.sf.basedb.core.plugin.AboutImpl
 
name - Variable in class net.sf.basedb.core.PluginParameter
The name of the parameter that the plugin use to identify the value with.
name - Variable in class net.sf.basedb.core.Presets.Preset
The name of this preset.
name - Variable in class net.sf.basedb.core.query.HqlEntityParameterExpression
 
name - Variable in class net.sf.basedb.core.query.ParameterExpression
 
name - Variable in class net.sf.basedb.core.query.QueryParameter
 
name - Variable in class net.sf.basedb.core.RawDataType
 
name - Variable in class net.sf.basedb.core.SessionControl.ClientInfo
 
name - Variable in class net.sf.basedb.core.signal.Signal
 
name - Variable in class net.sf.basedb.core.VirtualColumn
The name of the column.
name - Variable in class net.sf.basedb.plugins.Base1PluginExecuter.JobParameter
 
name - Variable in class net.sf.basedb.plugins.executor.ParameterDefinition
 
name - Variable in enum class net.sf.basedb.plugins.PrintMapFlatFileImporter.Section
 
name - Variable in class net.sf.basedb.util.bfs.MetadataModel.Section
 
name - Variable in class net.sf.basedb.util.excel.XlsxTableWriter
 
name - Variable in class net.sf.basedb.util.extensions.AboutBean
 
name - Variable in class net.sf.basedb.util.extensions.events.EventType
 
name - Variable in class net.sf.basedb.util.extensions.ExtensionPointBean
 
name - Variable in class net.sf.basedb.util.extensions.manager.ExtensionsFile
 
name - Variable in class net.sf.basedb.util.extensions.Registry.AttributeKey
 
name - Variable in class net.sf.basedb.util.extensions.Registry.RegisteredAbout
 
name - Variable in class net.sf.basedb.util.extensions.Registry.RegisteredExtensionPoint
 
name - Variable in class net.sf.basedb.util.importer.spotdata.BaseFileInfo.ChildBioAssay
 
name - Variable in class net.sf.basedb.util.jep.FunctionSafeJep.UnknownFunction
 
name - Variable in class net.sf.basedb.util.jep.SimpleJepFunction
 
name - Variable in class net.sf.basedb.util.overview.Node
 
name - Variable in class net.sf.basedb.util.parser.ColumnMapper
 
name - Variable in class net.sf.basedb.util.parser.FlatFileParser.Line
 
name - Variable in class net.sf.basedb.util.plot.HistogramPlot.HistogramSeries
 
name - Variable in class net.sf.basedb.util.plot.HistogramPlot.TempSeries
 
name - Variable in class net.sf.basedb.util.plot.PlotAnnotation
 
name - Variable in class net.sf.basedb.util.resources.ResourceBundleWrapper
 
name - Variable in class net.sf.basedb.util.uri.http.HttpConnectionManagerFactory
 
name() - Method in class net.sf.basedb.util.parser.FlatFileParser.Line
The name of the header if the line is a header line.
name(String) - Method in class net.sf.basedb.util.formatter.PropertyFilterFormatter
 
NAME - Static variable in class net.sf.basedb.core.ClonableProperty
The property name of the "static" property ReporterData.getName()
NAME - Static variable in class net.sf.basedb.plugins.batchimport.PropertyIdMethod
Use the name for finding items.
NAME_COMPARATOR - Static variable in class net.sf.basedb.util.extensions.xml.PluginInfo
Comparator that sort plug-ins according to their names.
NAME_OR_BARCODE - Static variable in class net.sf.basedb.plugins.batchimport.MultiPropertyIdMethod
Use the name or barcode for finding items.
NAME_OR_BARCODE_OR_ID - Static variable in class net.sf.basedb.plugins.batchimport.FallbackIdMethod
 
NAME_OR_EXTERNALID - Static variable in class net.sf.basedb.plugins.batchimport.MultiPropertyIdMethod
Use the name or external ID for finding items.
NAME_OR_EXTERNALID_OR_ID - Static variable in class net.sf.basedb.plugins.batchimport.FallbackIdMethod
 
NAME_OR_ID - Static variable in class net.sf.basedb.plugins.batchimport.FallbackIdMethod
Use the name for finding items.
NAME_OR_SYSTEMID - Static variable in class net.sf.basedb.plugins.batchimport.MultiPropertyIdMethod
Use the name or system Id for finding items.
NAME_OR_SYSTEMID_OR_ID - Static variable in class net.sf.basedb.plugins.batchimport.FallbackIdMethod
Use the name or system ID for finding items.
NAME_OR_UNITSYMBOL - Static variable in class net.sf.basedb.plugins.batchimport.MultiPropertyIdMethod
Use the name or unit symbol for finding items.
NAME_OR_UNITSYMBOL_OR_ID - Static variable in class net.sf.basedb.plugins.batchimport.FallbackIdMethod
ID method that can be used for units.
NAME_PATTERN - Static variable in class net.sf.basedb.clients.web.fileupload.FileUpload
 
Nameable - Interface in net.sf.basedb.core
A Nameable item is an item that has a name and description.
NameableComparator<T extends Nameable> - Class in net.sf.basedb.util
An implementation of the Comparator interface which uses the name of Nameable items to compare the objects.
NameableComparator(boolean) - Constructor for class net.sf.basedb.util.NameableComparator
Create a new comparator.
NameableConverter<T extends Nameable> - Class in net.sf.basedb.util.json
Simple "converter" implementation that create JSON objects with the name and id of Nameable items.
NameableConverter() - Constructor for class net.sf.basedb.util.json.NameableConverter
 
NameableData - Interface in net.sf.basedb.core.data
A nameable item is an item that has a name and, optionally, a description.
NameableFormatter - Class in net.sf.basedb.util.formatter
Formatter to handle Nameable items.
NameableFormatter() - Constructor for class net.sf.basedb.util.formatter.NameableFormatter
Create a new formatter.
NameableFormatter(String) - Constructor for class net.sf.basedb.util.formatter.NameableFormatter
Create a new formatter.
nameableItems - Static variable in class net.sf.basedb.core.Metadata
 
NameableNameGenerator<I extends Nameable> - Class in net.sf.basedb.util.overview.node
Name generator implementation for Nameable items.
NameableNameGenerator(String, String) - Constructor for class net.sf.basedb.util.overview.node.NameableNameGenerator
Create a new name generator.
NameableNodeValidator<I extends Nameable> - Class in net.sf.basedb.util.overview.validator
 
NameableNodeValidator(Validator, Validator) - Constructor for class net.sf.basedb.util.overview.validator.NameableNodeValidator
Creates a new validator.
NameableUtil - Class in net.sf.basedb.core
Utility methods that will make it easier to implement the Nameable interface, including data validation.
NameableUtil() - Constructor for class net.sf.basedb.core.NameableUtil
 
nameColumnMapping - Static variable in class net.sf.basedb.plugins.AnnotationFlatFileImporter
 
nameColumnMapping - Static variable in class net.sf.basedb.plugins.batchimport.AbstractItemImporter
 
nameColumnMapping - Static variable in class net.sf.basedb.plugins.PlateFlatFileImporter
 
nameColumnMapping - Static variable in class net.sf.basedb.plugins.ReporterFlatFileImporter
 
NameComparator() - Constructor for class net.sf.basedb.core.RawDataTypes.NameComparator
 
namedCubes - Variable in class net.sf.basedb.core.Transformation
Internal cache of named cubes used by the newProduct method.
namedFormulas - Variable in class net.sf.basedb.core.RawDataType
 
namedLayers - Variable in class net.sf.basedb.core.Transformation
Internal cache of named layers used by the newProduct method.
namedParameter - Static variable in class net.sf.basedb.core.AbstractSqlQuery
Pattern that finds a named parameter in an SQL string.
namedProperties - Variable in class net.sf.basedb.core.RawDataType
 
nameGenerator - Variable in class net.sf.basedb.util.overview.loader.BasicItemNodeLoader
 
nameGenerator - Variable in class net.sf.basedb.util.overview.node.NodeFactory
 
nameMapper - Variable in class net.sf.basedb.plugins.batchimport.AnnotationTypeImporter
 
nameMapper - Variable in class net.sf.basedb.plugins.batchimport.ArrayBatchImporter
 
nameMapper - Variable in class net.sf.basedb.plugins.batchimport.ArrayDesignImporter
 
nameMapper - Variable in class net.sf.basedb.plugins.batchimport.ArraySlideImporter
 
nameMapper - Variable in class net.sf.basedb.plugins.batchimport.BioPlateImporter
 
nameMapper - Variable in class net.sf.basedb.plugins.batchimport.BioSourceImporter
 
nameMapper - Variable in class net.sf.basedb.plugins.batchimport.DerivedBioAssayImporter
 
nameMapper - Variable in class net.sf.basedb.plugins.batchimport.ExtractImporter
 
nameMapper - Variable in class net.sf.basedb.plugins.batchimport.KitImporter
 
nameMapper - Variable in class net.sf.basedb.plugins.batchimport.PhysicalBioAssayImporter
 
nameMapper - Variable in class net.sf.basedb.plugins.batchimport.RawBioAssayImporter
 
nameMapper - Variable in class net.sf.basedb.plugins.batchimport.SampleImporter
 
nameMapper - Variable in class net.sf.basedb.plugins.batchimport.TagImporter
 
nameMapper - Variable in class net.sf.basedb.plugins.PlateFlatFileImporter
 
nameMapper - Variable in class net.sf.basedb.plugins.ReporterFlatFileImporter
 
nameOfItem(DbControl, Item, int, boolean) - Method in class net.sf.basedb.util.formatter.PropertyFilterFormatter
 
namePaddingParameter - Variable in class net.sf.basedb.plugins.PlateFlatFileImporter
 
nameParameter - Static variable in class net.sf.basedb.plugins.IntensityCalculatorPlugin
 
nameParameter - Static variable in class net.sf.basedb.plugins.PlateMappingImporter
 
namePrefix - Variable in class net.sf.basedb.util.overview.node.NameableNameGenerator
 
names - Variable in class net.sf.basedb.util.timer.PerformanceTimer
 
namespace - Static variable in class net.sf.basedb.clients.web.extensions.ServletLoader
The name of the servlets namespace.
namespace - Variable in class net.sf.basedb.core.plugin.NamespaceParameterValuesWrapper
 
namespace - Variable in class net.sf.basedb.core.plugin.NamespaceRequestWrapper
 
NAMESPACE - Static variable in class net.sf.basedb.util.extensions.xml.XmlLoader
The name of the extensions namespace.
NAMESPACE_EXPORTER - Static variable in class net.sf.basedb.plugins.executor.ExternalProgramExecutor
The namespace for the exporter plug-in parameters.
NAMESPACE_EXTERNAL - Static variable in class net.sf.basedb.plugins.executor.ExternalProgramExecutor
The namespace for the external program parameters.
NAMESPACE_IMPORTER - Static variable in class net.sf.basedb.plugins.executor.ExternalProgramExecutor
The namespace for the importer plug-in parameters.
NamespaceParameterValuesWrapper - Class in net.sf.basedb.core.plugin
A helper class that wraps a parameter values object with a namespace.
NamespaceParameterValuesWrapper(ParameterValues, String) - Constructor for class net.sf.basedb.core.plugin.NamespaceParameterValuesWrapper
Create a new namespace wrapper for the parent parameter values.
NamespacePluginParameter<T> - Class in net.sf.basedb.core.plugin
A helper class that wraps a plug-in parameter object with a namespace.
NamespacePluginParameter(PluginParameter<T>, String) - Constructor for class net.sf.basedb.core.plugin.NamespacePluginParameter
Create a new parameter wrapper for the plug-in parameter.
NamespaceRequestWrapper - Class in net.sf.basedb.core.plugin
A helper class that wraps a request object with a namespace.
NamespaceRequestWrapper(Request, String) - Constructor for class net.sf.basedb.core.plugin.NamespaceRequestWrapper
Create a new namespace wrapper for the parent request.
nameTemplate - Variable in enum class net.sf.basedb.core.VirtualTable
The name template, # is replaced by the ID of the VirtualDb item.
nameType - Static variable in class net.sf.basedb.core.plugin.AbstractAnalysisPlugin
A parameter type for name parameters which are required and must have a value.
nameType - Static variable in class net.sf.basedb.plugins.IntensityCalculatorPlugin
 
NativeQueryWrapper<R> - Class in net.sf.basedb.core.hibernate
A simple wrapper around hibernate native (SQL) queries which simply forwards all calls to a parent query.
NativeQueryWrapper(NativeQuery<R>) - Constructor for class net.sf.basedb.core.hibernate.NativeQueryWrapper
 
NativeSQLFunction - Class in net.sf.basedb.core.hibernate
Helper class for mixing native SQL with HQL queries.
NativeSQLFunction() - Constructor for class net.sf.basedb.core.hibernate.NativeSQLFunction
 
NaturalLogarithmConverter - Class in net.sf.basedb.util.jep.convert
Convert NaturalLogarithm function to a Query API Expression.
NaturalLogarithmConverter() - Constructor for class net.sf.basedb.util.jep.convert.NaturalLogarithmConverter
 
Navigator - Class in net.sf.basedb.clients.web.taglib.table
This tag is used to display a navigator for a pageable table of items.
Navigator() - Constructor for class net.sf.basedb.clients.web.taglib.table.Navigator
 
NBSP - Static variable in class net.sf.basedb.util.formatter.PrefixSuffixFormatter
The character representing a non-breaking space.
needNewLine - Variable in class net.sf.basedb.util.ConsoleProgressReporter
 
needResourcesPerExtension - Variable in class net.sf.basedb.clients.web.extensions.JspContext
 
needSynchronize - Variable in class net.sf.basedb.core.BioPlateEvent
 
needToParseDate - Variable in class net.sf.basedb.util.parser.ConstantMapper
 
needToParseNumeric - Variable in class net.sf.basedb.util.parser.ConstantMapper
 
needWrapper - Variable in class net.sf.basedb.util.listable.CollectExtracts
 
negate(Expression) - Static method in class net.sf.basedb.core.query.Expressions
Negate an expression: new expression = -e1.
NegateExpression - Class in net.sf.basedb.core.query
Negate an expression: -e1.
NegateExpression(Expression) - Constructor for class net.sf.basedb.core.query.NegateExpression
 
neq(Expression, Expression) - Static method in class net.sf.basedb.core.query.Restrictions
Compare if two expressions are inequal: new restriction = e1 <> e2.
NEQ - Enum constant in enum class net.sf.basedb.core.Operator
 
NeqRestriction - Class in net.sf.basedb.core.query
Compare if two expressions are inequal: e1 <> e2, or NOT e1 IS NULL
NeqRestriction(Expression, Expression) - Constructor for class net.sf.basedb.core.query.NeqRestriction
 
NestedIterator<E> - Class in net.sf.basedb.util
This class implements the Iterator interface for iterating multiple collections as if it was one big collection.
NestedIterator(Collection<? extends E>...) - Constructor for class net.sf.basedb.util.NestedIterator
Create a new ArrayIterator object.
net.sf.basedb.clients.jobagent - package net.sf.basedb.clients.jobagent
 
net.sf.basedb.clients.jobagent.executors - package net.sf.basedb.clients.jobagent.executors
 
net.sf.basedb.clients.jobagent.handlers - package net.sf.basedb.clients.jobagent.handlers
 
net.sf.basedb.clients.jobagent.slotmanager - package net.sf.basedb.clients.jobagent.slotmanager
 
net.sf.basedb.clients.web - package net.sf.basedb.clients.web
 
net.sf.basedb.clients.web.extensions - package net.sf.basedb.clients.web.extensions
 
net.sf.basedb.clients.web.extensions.edit - package net.sf.basedb.clients.web.extensions.edit
 
net.sf.basedb.clients.web.extensions.fileviewer - package net.sf.basedb.clients.web.extensions.fileviewer
 
net.sf.basedb.clients.web.extensions.list - package net.sf.basedb.clients.web.extensions.list
 
net.sf.basedb.clients.web.extensions.login - package net.sf.basedb.clients.web.extensions.login
 
net.sf.basedb.clients.web.extensions.menu - package net.sf.basedb.clients.web.extensions.menu
 
net.sf.basedb.clients.web.extensions.plot - package net.sf.basedb.clients.web.extensions.plot
 
net.sf.basedb.clients.web.extensions.renderer - package net.sf.basedb.clients.web.extensions.renderer
 
net.sf.basedb.clients.web.extensions.section - package net.sf.basedb.clients.web.extensions.section
 
net.sf.basedb.clients.web.extensions.service - package net.sf.basedb.clients.web.extensions.service
 
net.sf.basedb.clients.web.extensions.skin - package net.sf.basedb.clients.web.extensions.skin
 
net.sf.basedb.clients.web.extensions.startpage - package net.sf.basedb.clients.web.extensions.startpage
 
net.sf.basedb.clients.web.extensions.tabcontrol - package net.sf.basedb.clients.web.extensions.tabcontrol
 
net.sf.basedb.clients.web.extensions.toolbar - package net.sf.basedb.clients.web.extensions.toolbar
 
net.sf.basedb.clients.web.fileupload - package net.sf.basedb.clients.web.fileupload
This package contains classes for handling file uploads from a browser using the standard described in RFC1867.
net.sf.basedb.clients.web.formatter - package net.sf.basedb.clients.web.formatter
 
net.sf.basedb.clients.web.plugins - package net.sf.basedb.clients.web.plugins
 
net.sf.basedb.clients.web.resources - package net.sf.basedb.clients.web.resources
 
net.sf.basedb.clients.web.servlet - package net.sf.basedb.clients.web.servlet
 
net.sf.basedb.clients.web.taglib - package net.sf.basedb.clients.web.taglib
 
net.sf.basedb.clients.web.taglib.extensions - package net.sf.basedb.clients.web.taglib.extensions
 
net.sf.basedb.clients.web.taglib.menu - package net.sf.basedb.clients.web.taglib.menu
This package is a taglib that can be used on JSP pages to build a simple drop-down menu system with unlimited levels.
net.sf.basedb.clients.web.taglib.path - package net.sf.basedb.clients.web.taglib.path
 
net.sf.basedb.clients.web.taglib.tab - package net.sf.basedb.clients.web.taglib.tab
 
net.sf.basedb.clients.web.taglib.table - package net.sf.basedb.clients.web.taglib.table
 
net.sf.basedb.clients.web.util - package net.sf.basedb.clients.web.util
 
net.sf.basedb.core - package net.sf.basedb.core
This package contains the core business logic of BASE.
net.sf.basedb.core.authentication - package net.sf.basedb.core.authentication
 
net.sf.basedb.core.data - package net.sf.basedb.core.data
This package contains pure data-holder classes which are mapped to the database using Hibernate.
net.sf.basedb.core.data.annotations - package net.sf.basedb.core.data.annotations
 
net.sf.basedb.core.data.keyring - package net.sf.basedb.core.data.keyring
This package contains helper classes for the Keyring class.
net.sf.basedb.core.dbengine - package net.sf.basedb.core.dbengine
 
net.sf.basedb.core.hibernate - package net.sf.basedb.core.hibernate
 
net.sf.basedb.core.log - package net.sf.basedb.core.log
 
net.sf.basedb.core.log.db - package net.sf.basedb.core.log.db
 
net.sf.basedb.core.migrate - package net.sf.basedb.core.migrate
 
net.sf.basedb.core.migrate.postgres - package net.sf.basedb.core.migrate.postgres
 
net.sf.basedb.core.plugin - package net.sf.basedb.core.plugin
 
net.sf.basedb.core.query - package net.sf.basedb.core.query
This package contains the core of the Query API.
net.sf.basedb.core.signal - package net.sf.basedb.core.signal
 
net.sf.basedb.core.snapshot - package net.sf.basedb.core.snapshot
 
net.sf.basedb.plugins - package net.sf.basedb.plugins
 
net.sf.basedb.plugins.batchimport - package net.sf.basedb.plugins.batchimport
 
net.sf.basedb.plugins.executor - package net.sf.basedb.plugins.executor
 
net.sf.basedb.plugins.gtf - package net.sf.basedb.plugins.gtf
 
net.sf.basedb.plugins.util - package net.sf.basedb.plugins.util
 
net.sf.basedb.util - package net.sf.basedb.util
This package contains some useful utility classes and methods.
net.sf.basedb.util.affymetrix - package net.sf.basedb.util.affymetrix
 
net.sf.basedb.util.annotations - package net.sf.basedb.util.annotations
 
net.sf.basedb.util.basefile - package net.sf.basedb.util.basefile
 
net.sf.basedb.util.bcrypt - package net.sf.basedb.util.bcrypt
 
net.sf.basedb.util.bfs - package net.sf.basedb.util.bfs
 
net.sf.basedb.util.charset - package net.sf.basedb.util.charset
 
net.sf.basedb.util.collections - package net.sf.basedb.util.collections
 
net.sf.basedb.util.encode - package net.sf.basedb.util.encode
 
net.sf.basedb.util.error - package net.sf.basedb.util.error
 
net.sf.basedb.util.excel - package net.sf.basedb.util.excel
 
net.sf.basedb.util.export - package net.sf.basedb.util.export
 
net.sf.basedb.util.export.spotdata - package net.sf.basedb.util.export.spotdata
 
net.sf.basedb.util.extensions - package net.sf.basedb.util.extensions
 
net.sf.basedb.util.extensions.debug - package net.sf.basedb.util.extensions.debug
 
net.sf.basedb.util.extensions.events - package net.sf.basedb.util.extensions.events
 
net.sf.basedb.util.extensions.logging - package net.sf.basedb.util.extensions.logging
 
net.sf.basedb.util.extensions.manager - package net.sf.basedb.util.extensions.manager
 
net.sf.basedb.util.extensions.manager.filter - package net.sf.basedb.util.extensions.manager.filter
 
net.sf.basedb.util.extensions.manager.processor - package net.sf.basedb.util.extensions.manager.processor
 
net.sf.basedb.util.extensions.xml - package net.sf.basedb.util.extensions.xml
 
net.sf.basedb.util.fileset - package net.sf.basedb.util.fileset
 
net.sf.basedb.util.filter - package net.sf.basedb.util.filter
 
net.sf.basedb.util.formatter - package net.sf.basedb.util.formatter
 
net.sf.basedb.util.fuzzy - package net.sf.basedb.util.fuzzy
 
net.sf.basedb.util.gtf - package net.sf.basedb.util.gtf
 
net.sf.basedb.util.importer - package net.sf.basedb.util.importer
 
net.sf.basedb.util.importer.spotdata - package net.sf.basedb.util.importer.spotdata
 
net.sf.basedb.util.jep - package net.sf.basedb.util.jep
 
net.sf.basedb.util.jep.convert - package net.sf.basedb.util.jep.convert
 
net.sf.basedb.util.jobagent - package net.sf.basedb.util.jobagent
 
net.sf.basedb.util.json - package net.sf.basedb.util.json
 
net.sf.basedb.util.listable - package net.sf.basedb.util.listable
 
net.sf.basedb.util.ma - package net.sf.basedb.util.ma
 
net.sf.basedb.util.overview - package net.sf.basedb.util.overview
 
net.sf.basedb.util.overview.cache - package net.sf.basedb.util.overview.cache
 
net.sf.basedb.util.overview.extensions - package net.sf.basedb.util.overview.extensions
 
net.sf.basedb.util.overview.filter - package net.sf.basedb.util.overview.filter
 
net.sf.basedb.util.overview.loader - package net.sf.basedb.util.overview.loader
 
net.sf.basedb.util.overview.node - package net.sf.basedb.util.overview.node
 
net.sf.basedb.util.overview.validator - package net.sf.basedb.util.overview.validator
 
net.sf.basedb.util.parser - package net.sf.basedb.util.parser
 
net.sf.basedb.util.plot - package net.sf.basedb.util.plot
 
net.sf.basedb.util.query - package net.sf.basedb.util.query
 
net.sf.basedb.util.resources - package net.sf.basedb.util.resources
 
net.sf.basedb.util.ssl - package net.sf.basedb.util.ssl
 
net.sf.basedb.util.timer - package net.sf.basedb.util.timer
 
net.sf.basedb.util.transform - package net.sf.basedb.util.transform
 
net.sf.basedb.util.units - package net.sf.basedb.util.units
 
net.sf.basedb.util.uri - package net.sf.basedb.util.uri
 
net.sf.basedb.util.uri.http - package net.sf.basedb.util.uri.http
 
net.sf.basedb.util.zip - package net.sf.basedb.util.zip
 
NEW_SCHEMA_VERSION - Static variable in class net.sf.basedb.core.Install
The schema version to give to new installations.
NewAnnotations(Annotatable) - Constructor for class net.sf.basedb.plugins.AnnotationFlatFileImporter.NewAnnotations
Create a new cache for the specified item.
newArrayBatch() - Method in class net.sf.basedb.core.ArrayDesign
Create a new ArrayBatch with this design.
newArraySlide() - Method in class net.sf.basedb.core.ArrayBatch
Create a new ArraySlide item for this batch.
newBioAssay(Collection<BioAssay>) - Method in class net.sf.basedb.core.BioAssaySet
Create a new BioAssay with links to multiple parent bioassays.
newBioAssay(BioAssay) - Method in class net.sf.basedb.core.BioAssaySet
Create a new BioAssay in this bioassayset using a single parent.
newBioAssay(DataCubeColumn, Collection<BioAssay>) - Method in class net.sf.basedb.core.BioAssaySet
Create a new bioassay and link to the parents.
newBundle(String, Locale, String, ClassLoader, boolean) - Method in class net.sf.basedb.util.resources.Utf8PropertiesResourceBundleControl
Load property files using UTF-8.
newCh1 - Variable in class net.sf.basedb.plugins.LowessNormalization.SpotData
 
newCh2 - Variable in class net.sf.basedb.plugins.LowessNormalization.SpotData
 
newChildren - Variable in class net.sf.basedb.util.overview.Node
 
newClientSetting(Client, String, String) - Method in class net.sf.basedb.core.User
Create a new client application setting for this user.
newColumn() - Method in class net.sf.basedb.core.DataCube
Create a new column in this database.
newDataCube() - Method in class net.sf.basedb.core.VirtualDb
Create a new data cube in this virtual database.
newDbControl() - Method in class net.sf.basedb.core.SessionControl
Create a new DbControl object for this session.
newDbControl(String) - Method in class net.sf.basedb.core.SessionControl
Create a new name DbControl object for this session.
newDefaultSetting(String, String) - Method in class net.sf.basedb.core.Client
Create a new default setting for this client.
newDefaultSetting(String, String) - Method in class net.sf.basedb.core.User
Create a new default setting for this user.
newDynamicMapping(VirtualDb, VirtualTable, boolean) - Static method in class net.sf.basedb.core.HibernateUtil
Create a new org.hibernate.mapping.Table object for the specified table.
newEvent() - Method in class net.sf.basedb.core.MeasuredBioMaterial
Create a new event for this biomaterial.
newEvent(BioPlateEventParticipant) - Method in class net.sf.basedb.core.MeasuredBioMaterial
Create a new event for this biomaterial that is part of a master bioplate event.
newEventType() - Method in class net.sf.basedb.core.PlateType
Create a new event type for this plate type.
newExtract(Float) - Method in class net.sf.basedb.core.Sample
Create a new Extract from this sample.
newExtract(Float, BioPlateEventParticipant) - Method in class net.sf.basedb.core.Sample
Create a new Extract from this sample as part of a master bioplate event.
newExtraValue(Type, ExtraValue.CoordinateType) - Method in class net.sf.basedb.core.DataCube
Create a new extra vlaue in this data cube.
newFeature(ArrayDesignBlock, ReporterData) - Method in class net.sf.basedb.core.FeatureBatcher
Create a new feature.
newFeature(ArrayDesignBlock, Well) - Method in class net.sf.basedb.core.FeatureBatcher
Create a new feature.
newFilter() - Method in class net.sf.basedb.core.DataCube
Create a new filter in this datacube.
newHelp(String) - Method in class net.sf.basedb.core.Client
Create a new help text for this client.
newInstance() - Method in class net.sf.basedb.core.PluginDefinition
Get an unitialized instance of the plugin.
newInstance() - Static method in class net.sf.basedb.util.MD5
 
newInstance(Class<I>) - Static method in class net.sf.basedb.util.ClassUtil
Utility method for creating a new instance from a class with a default no-argument constructor.
newInstance(Class<P>) - Method in class net.sf.basedb.core.PluginDefinition
Get an unitialized instance of the plugin implementation.
newInstance(Class<P>, SessionControl, PluginConfiguration, Job) - Method in class net.sf.basedb.core.PluginDefinition
Get an initialized instance of the plugin implementation.
newInstance(ClassLoader, String, Class<I>, Class<?>...) - Static method in class net.sf.basedb.util.ClassUtil
Utility method for creating a new instance from a class (given by name) with a default no-argument constructor.
newInstance(String) - Static method in class net.sf.basedb.util.JarClassLoader
Get a new class loader for the specified jar file.
newInstance(String, String, ClassLoader, boolean) - Method in class net.sf.basedb.core.PluginDefinition
Create a new object instance of the given class.
newInternalFile - Variable in class net.sf.basedb.core.File
The path to a newly uploaded file.
newItem - Variable in class net.sf.basedb.clients.web.taglib.Select
If the link is from a new item or an old item.
newItem(Class<I>, Object...) - Method in class net.sf.basedb.core.DbControl
Create a new item.
newJep(String, JepFunction...) - Static method in class net.sf.basedb.util.jep.Jep
Create a new JEP expression.
newJob(Experiment) - Method in class net.sf.basedb.core.PluginConfiguration
Create a new Job for this plugin configuration.
newLayer() - Method in class net.sf.basedb.core.DataCube
Create a new layer in this datacube.
NEWLINE - Static variable in class net.sf.basedb.clients.web.plugins.XMLTemplate
 
NEWLINE - Static variable in class net.sf.basedb.clients.web.util.HTML
 
newMapperIsNeeded - Static variable in class net.sf.basedb.clients.web.extensions.skin.ImageRemapperUtil
 
newParameterValueData() - Method in class net.sf.basedb.core.BooleanParameterType
Create a new BooleanParameterValueData object.
newParameterValueData() - Method in class net.sf.basedb.core.DateParameterType
Create a new DateParameterValueData object.
newParameterValueData() - Method in class net.sf.basedb.core.DoubleParameterType
Create a new DoubleParameterValueData object.
newParameterValueData() - Method in class net.sf.basedb.core.FileParameterType
Create a new ItemParameterValueData object.
newParameterValueData() - Method in class net.sf.basedb.core.FloatParameterType
Create a new FloatParameterValueData object.
newParameterValueData() - Method in class net.sf.basedb.core.IntegerParameterType
Create a new IntegerParameterValueData object.
newParameterValueData() - Method in class net.sf.basedb.core.ItemParameterType
Create a new ItemParameterValueData object.
newParameterValueData() - Method in class net.sf.basedb.core.LongParameterType
Create a new LongParameterValueData object.
newParameterValueData() - Method in class net.sf.basedb.core.ParameterType
Create a new ParameterValueData subclass which is used to store values of this value type in the database.
newParameterValueData() - Method in class net.sf.basedb.core.PasswordParameterType
Create a new StringParameterValueData object.
newParameterValueData() - Method in class net.sf.basedb.core.PathParameterType
Create a new TextParameterValueData object.
newParameterValueData() - Method in class net.sf.basedb.core.StringParameterType
Create a new TextParameterValueData object.
newParameterValueData() - Method in class net.sf.basedb.core.TimestampParameterType
Create a new TimestampParameterValueData object.
newParameterValueData() - Method in enum class net.sf.basedb.core.Type
Create a new ParameterValueData subclass which is used to store values of this value type in the database.
newParameterVersion - Variable in class net.sf.basedb.core.PluginConfiguration
 
newPinger(SessionControl) - Static method in class net.sf.basedb.core.Application
Create a new Pinger object that is used to keep a session control alive.
newPlate() - Method in class net.sf.basedb.core.PlateType
Create a new plate of this plate type.
newPlateType() - Method in class net.sf.basedb.core.PlateGeometry
Create a new PlateType of this geometry.
newPluginConfiguration() - Method in class net.sf.basedb.core.PluginDefinition
Create a new PluginConfiguration for this plugin.
newPluginSessionControl(SessionControl, PluginDefinition, Job) - Static method in class net.sf.basedb.core.Application
Create a new session control for executing plugins.
newProduct(String, String, boolean) - Method in class net.sf.basedb.core.Transformation
Create a new product bioassayset from this transformation.
newRawData() - Method in class net.sf.basedb.core.RawDataBatcher
Create a new raw data object.
newReporter(String) - Method in class net.sf.basedb.core.ReporterType
Create a new ReporterData object of this type.
newReporterCloneTable - Variable in class net.sf.basedb.core.Experiment
 
newRootBioAssay(Collection<RawBioAssay>) - Method in class net.sf.basedb.core.BioAssaySet
Create a new BioAssay with links to raw bioassays.
News - Class in net.sf.basedb.core
This class represents news items.
News(NewsData) - Constructor for class net.sf.basedb.core.News
 
NEWS - Enum constant in enum class net.sf.basedb.core.Item
The item is a News.
News.QueryRuntimeFilterImpl - Class in net.sf.basedb.core
 
newSample() - Method in class net.sf.basedb.core.BioSource
Create a new Sample from this biosource.
NewsData - Class in net.sf.basedb.core.data
This class holds information about news items.
NewsData() - Constructor for class net.sf.basedb.core.data.NewsData
 
newsDate - Variable in class net.sf.basedb.core.data.NewsData
 
newSession() - Static method in class net.sf.basedb.core.HibernateUtil
Create a new Hibernate session.
newSession(Connection) - Static method in class net.sf.basedb.core.HibernateUtil
 
newSession(Interceptor, Connection) - Static method in class net.sf.basedb.core.HibernateUtil
Create a new Hibernate session, optionally with an interceptor.
newSession(SessionBuilder<?>, DbControl) - Method in class net.sf.basedb.core.ServiceSessionControl
Create a new Hibernate session for the given session factory that is piggy-backed on the given DbControl transaction.
newSessionControl(String, String, String) - Static method in class net.sf.basedb.core.Application
Create a new SessionControl object.
newStatelessSession(Session) - Static method in class net.sf.basedb.core.HibernateUtil
 
newSubDirectory() - Method in class net.sf.basedb.core.Directory
Create a new subdirectory to this directory.
newSyncFilter(DbControl) - Method in class net.sf.basedb.core.ItemList
Creates a new sync filter for this list.
newThreads - Variable in class net.sf.basedb.util.timer.Scheduler
 
newTransaction(Session) - Static method in class net.sf.basedb.core.HibernateUtil
Create a new transaction for a session.
newTransformation(Job) - Method in class net.sf.basedb.core.BioAssaySet
Create a new transformation using this bioassayset as it's source bioassayset.
newTransformation(Job, Collection<RawBioAssay>) - Method in class net.sf.basedb.core.Experiment
Create a new root transformation for this experiment.
newValue - Variable in class net.sf.basedb.core.data.ChangeHistoryDetailData
 
newValue - Variable in class net.sf.basedb.core.log.ManualLogEntry
 
newValues - Variable in class net.sf.basedb.core.AnnotationBatcher.CurrentAnnotationInfo
 
newVariant(String) - Method in class net.sf.basedb.core.Platform
Create a new PlatformVariant of this platform.
next - Variable in class net.sf.basedb.clients.web.servlet.PlotServlet.CFResultIterator
 
next - Variable in class net.sf.basedb.core.FastAnnotationLoader.FastIterator
 
next - Variable in class net.sf.basedb.util.Tree.EntryIterator
The next element to return.
next() - Method in class net.sf.basedb.clients.web.fileupload.FileUpload
Read from the input stream until a file section is found or the end is encountered.
next() - Method in class net.sf.basedb.clients.web.servlet.PlotServlet.CFResultIterator
 
next() - Method in class net.sf.basedb.clients.web.taglib.table.ColumnDef.NullIterator
 
next() - Method in class net.sf.basedb.core.DataResultIterator
 
next() - Method in class net.sf.basedb.core.DynamicResultIterator
Get the results in the next row.
next() - Method in class net.sf.basedb.core.FastAnnotationLoader.FastIterator
 
next() - Method in class net.sf.basedb.core.ItemResultIterator
 
next() - Method in class net.sf.basedb.core.ItemResultList.ResultListIterator
 
next() - Method in class net.sf.basedb.core.ItemResultList.ResultListListIterator
 
next() - Method in class net.sf.basedb.core.ReporterScoreResultIterator
 
next() - Method in class net.sf.basedb.core.ScrollIterator
 
next() - Method in class net.sf.basedb.plugins.RawDataFlatFileImporter.FileIterator
 
next() - Method in class net.sf.basedb.util.ArrayIterator
 
next() - Method in class net.sf.basedb.util.extensions.ActionIterator
 
next() - Method in class net.sf.basedb.util.NestedIterator
 
next() - Method in class net.sf.basedb.util.query.MultiQueryIterator
 
next() - Method in class net.sf.basedb.util.Tree.ElementIterator
 
next() - Method in class net.sf.basedb.util.Tree.EntryIterator
 
nextBioAssay - Variable in class net.sf.basedb.util.export.spotdata.SerialBaseFileExporter
 
nextBuffer - Variable in class net.sf.basedb.clients.web.fileupload.FileUpload.UploadStream
 
nextCleanup - Variable in class net.sf.basedb.util.listable.TransformCache
 
nextCommand - Variable in class net.sf.basedb.core.PluginResponse
 
nextData - Variable in class net.sf.basedb.util.parser.FlatFileParser
The next available data line as parsed by the FlatFileParser.hasMoreData() method.
nextData() - Method in class net.sf.basedb.util.bfs.AnnotationParser
Get the next data line in the annotations file.
nextData() - Method in class net.sf.basedb.util.bfs.DataParser
Get the next data line in the file.
nextData() - Method in class net.sf.basedb.util.parser.FlatFileParser
Get the next available data.
nextElement - Variable in class net.sf.basedb.core.ScrollIterator
 
nextEnd - Variable in class net.sf.basedb.clients.web.fileupload.FileUpload.UploadStream
 
nextEntry() - Method in class net.sf.basedb.util.bfs.MetadataParser
Get the next entry in the current section.
nextFileNum - Variable in class net.sf.basedb.util.bfs.SequenceFilenameGenerator
 
nextHop - Variable in class net.sf.basedb.clients.web.extensions.list.RelatedItemMultiHopColumn
 
nextIndex - Variable in class net.sf.basedb.util.excel.XlsxToCsvUtil.WorkbookStream
 
nextIndex() - Method in class net.sf.basedb.core.ItemResultList.ResultListListIterator
 
nextIterator() - Method in class net.sf.basedb.core.FastAnnotationLoader.FastIterator
Create a new query that load annotations for items between startIndex and endIndex.
nextProgress - Variable in class net.sf.basedb.util.ProgressInputStream
 
nextProgressReport - Variable in class net.sf.basedb.util.importer.spotdata.FirstPassSectionSpotsParser
 
nextProgressReport - Variable in class net.sf.basedb.util.importer.spotdata.SecondPassSectionSpotsParser
 
nextProgressReport - Variable in class net.sf.basedb.util.importer.spotdata.SectionReporterListParser
 
nextQuery - Variable in class net.sf.basedb.util.query.MultiQueryIterator
 
nextReport - Variable in class net.sf.basedb.util.importer.spotdata.BfsImporter.ProgressEventHandler
 
nextSection - Variable in class net.sf.basedb.util.parser.FlatFileParser
The line that last matched the FlatFileParser.section.
nextSection() - Method in class net.sf.basedb.util.bfs.MetadataParser
Parse to the next section in the metadata file.
nextSection() - Method in class net.sf.basedb.util.parser.FlatFileParser
Get the next line that matches the section regular expression.
nextSheet() - Method in class net.sf.basedb.util.excel.XlsxToCsvUtil.WorkbookStream
Switch to the next worksheet.
nextSpec - Variable in class net.sf.basedb.clients.web.extensions.list.RelatedItemMultiHopColumn
 
nextStatusUpdateRequest - Variable in class net.sf.basedb.core.InternalJobQueue
Time when the next status update request for external jobs is scheduled.
nextStream() - Method in class net.sf.basedb.util.InputStreamCombiner
 
nextTick - Variable in class net.sf.basedb.core.Migration.ProgressInputStream
 
nextToken(String) - Method in class net.sf.basedb.util.jep.FunctionSafeJep.SafeFunctionTable
Get the next token in the parser.
nextValueType - Variable in class net.sf.basedb.util.parser.ColFunction
 
niceFormat(String) - Static method in class net.sf.basedb.clients.web.util.HTML
A convenience method for doing encodeTags(in, SAFE_TAGS), scanForLinks(in, "_blank") and formatLineBreaks(in) in a single operation.
niceFormat(String, int) - Static method in class net.sf.basedb.clients.web.util.HTML
A convenience method for doing encodeTags(in, SAFE_TAGS), scanForLinks(in, flags, "_blank") and formatLineBreaks(in) in a single operation.
niceFormat(String, int, String) - Static method in class net.sf.basedb.clients.web.util.HTML
A convenience method for doing encodeTags(in, SAFE_TAGS), scanForLinks(in, flags, link_target) and formatLineBreaks(in) in a single operation.
niceFormat(String, String) - Static method in class net.sf.basedb.clients.web.util.HTML
A convenience method for doing encodeTags(in, SAFE_TAGS), scanForLinks(in, target) and formatLineBreaks(in) in a single operation.
NiceFormatter - Class in net.sf.basedb.clients.web.formatter
Nicely format a string for output on a web page.
NiceFormatter() - Constructor for class net.sf.basedb.clients.web.formatter.NiceFormatter
Create a new formatter with default options: HTML.LINK_EMAIL + HTML.LINK_URL + HTML.SMART_IMAGES
NiceFormatter(int) - Constructor for class net.sf.basedb.clients.web.formatter.NiceFormatter
Create a new formatter with options.
NO - Enum constant in enum class net.sf.basedb.core.ItemContext.AddFilter
Do not any filter.
NO_AUTO_JOIN_PREFIXES - Static variable in class net.sf.basedb.core.ItemContext
 
NO_CANCELBUTTON - Static variable in class net.sf.basedb.clients.web.ModeInfo
 
NO_CHANGE - Enum constant in enum class net.sf.basedb.core.AnnotationBatcher.Change
The annotation was not changed.
NO_CHECK - Static variable in class net.sf.basedb.clients.web.ModeInfo
 
NO_CLOSEBUTTON - Static variable in class net.sf.basedb.clients.web.ModeInfo
 
NO_EDITLINK - Static variable in class net.sf.basedb.clients.web.ModeInfo
 
NO_FILTER - Static variable in class net.sf.basedb.clients.web.ModeInfo
 
NO_ICONS - Static variable in class net.sf.basedb.clients.web.ModeInfo
 
NO_NAVIGATOR - Static variable in class net.sf.basedb.clients.web.ModeInfo
 
NO_OKBUTTON - Static variable in class net.sf.basedb.clients.web.ModeInfo
 
NO_PERMISSION - Static variable in class net.sf.basedb.clients.web.ModeInfo
 
NO_PLUGIN - Static variable in class net.sf.basedb.core.PluginPermission
 
NO_PROPERTYLINK - Static variable in class net.sf.basedb.clients.web.ModeInfo
 
NO_RADIO - Static variable in class net.sf.basedb.clients.web.ModeInfo
 
NO_TOOLBAR - Static variable in class net.sf.basedb.clients.web.ModeInfo
 
noAutoCompression - Static variable in class net.sf.basedb.core.Application
If auto-compression has been enabled or not.
NoAutoUnlinkAnyToAny - Interface in net.sf.basedb.core.data
Tagging interface for items that are unlikely to be linked via an AnyToAny link.
node - Variable in class net.sf.basedb.core.data.JobData
 
node - Variable in class net.sf.basedb.core.Job.ProgressReporterImpl
 
node - Variable in class net.sf.basedb.util.overview.Failure
 
node - Variable in class net.sf.basedb.util.Tree.Entry
 
Node - Class in net.sf.basedb.util.overview
A node in an overview.
Node(String, String, BasicItem) - Constructor for class net.sf.basedb.util.overview.Node
Create an item-type root node.
Node(String, String, Node) - Constructor for class net.sf.basedb.util.overview.Node
Create a folder-type child node.
Node(String, String, Node, BasicItem) - Constructor for class net.sf.basedb.util.overview.Node
Create an item-type child node
Node(String, String, Node, BasicItem, ChildNodeDirection) - Constructor for class net.sf.basedb.util.overview.Node
Create an item-type child node
Node(String, String, Node, BasicItem, Node.Type, ChildNodeDirection) - Constructor for class net.sf.basedb.util.overview.Node
 
Node(String, String, Node, ChildNodeDirection) - Constructor for class net.sf.basedb.util.overview.Node
Create a folder-type child node.
Node(Node, Node) - Constructor for class net.sf.basedb.util.overview.Node
Make a copy of a node
Node.Type - Enum Class in net.sf.basedb.util.overview
The type of node.
NodeAttribute<T> - Class in net.sf.basedb.util.overview
Defines per-node attributes that can be used to store extra information together with a node that doesn't fit the regular properties.
NodeAttribute() - Constructor for class net.sf.basedb.util.overview.NodeAttribute
 
nodeCache - Variable in class net.sf.basedb.util.overview.GenericOverview
 
NodeCache<K> - Class in net.sf.basedb.util.overview.cache
A cache implementation for nodes.
NodeCache() - Constructor for class net.sf.basedb.util.overview.cache.NodeCache
 
NodeFactory<I extends BasicItem> - Class in net.sf.basedb.util.overview.node
A node factory is responsible for creating item-type nodes.
NodeFactory(DbControl, OverviewContext, NodeValidator<? super I>, NodeNameGenerator<? super I>) - Constructor for class net.sf.basedb.util.overview.node.NodeFactory
Create a node factory.
nodeId - Variable in class net.sf.basedb.util.overview.Node
 
NodeLoader<I> - Interface in net.sf.basedb.util.overview.loader
A node loader is an object that knows how to create a node for some specific item and how to load forward and reverse nodes for related items.
nodeLoaderFactory - Variable in class net.sf.basedb.util.overview.GenericOverview
 
NodeLoaderFactory<L,K> - Interface in net.sf.basedb.util.overview.loader
A node loader factory is a class that know how to create NodeLoader:s for a given key domain.
NodeNameGenerator<I> - Interface in net.sf.basedb.util.overview.node
A name generator is an object that can create the name and title for a node when given the item that should be attached to the node.
nodeToExpression(Node) - Static method in class net.sf.basedb.util.jep.Jep
Convert a node with it's children to an expression.
nodeToInt(Node) - Static method in class net.sf.basedb.util.jep.Jep
Convert a node to an integer value.
nodeToRestriction(Node) - Static method in class net.sf.basedb.util.jep.Jep
Convert a node with it's children to a restriction.
nodeToString(Node) - Static method in class net.sf.basedb.util.jep.Jep
Convert a node to a string value.
nodeType - Variable in class net.sf.basedb.util.overview.filter.NodeTypeFilter
 
NodeTypeFilter - Class in net.sf.basedb.util.overview.filter
A filter implementation that matches the node type.
NodeTypeFilter(Node.Type) - Constructor for class net.sf.basedb.util.overview.filter.NodeTypeFilter
Create a filter that finds nodes of the given node type.
NodeValidator<I> - Interface in net.sf.basedb.util.overview.validator
A node validator is responsible for checking the "validity" of a node.
NodeValidatorAction<I> - Interface in net.sf.basedb.util.overview.extensions
The same as a NodeValidator.
nodeValidatorFactory - Variable in class net.sf.basedb.util.overview.GenericOverview
 
NodeValidatorFactory<L,K> - Interface in net.sf.basedb.util.overview.validator
A node validator factory is a class that know how to create NodeValidator:s for a given key domain.
noDuplicates - Variable in class net.sf.basedb.util.annotations.InheritSpecification
 
NONDEFAULT_ARRAYDESIGN - Static variable in class net.sf.basedb.util.overview.Validator
Validator rule that checks if an item uses a different array design than specified by the project default.
NONDEFAULT_HARDWARE - Static variable in class net.sf.basedb.util.overview.Validator
Validator rule that checks if an item uses a different hardware than specified by the project default.
NONDEFAULT_PLATFORM - Static variable in class net.sf.basedb.util.overview.Validator
Validator rule that checks if an item uses a different platform / variant than specified by the project default.
NONDEFAULT_PROTOCOL - Static variable in class net.sf.basedb.util.overview.Validator
Validator rule that checks if an item uses a different protocol than specified by the project default.
NONDEFAULT_RAWDATATYPE - Static variable in class net.sf.basedb.util.overview.Validator
Validator rule that checks if an item uses a different raw data type than specified by the project default.
NONDEFAULT_SOFTWARE - Static variable in class net.sf.basedb.util.overview.Validator
Validator rule that checks if an item uses a different software than specified by the project default.
NONE - Enum constant in enum class net.sf.basedb.core.FeatureIdentificationMethod
None, because the array design is a file-only platform.
NONE - Enum constant in enum class net.sf.basedb.core.Formula.AverageMethod
 
NONE - Enum constant in enum class net.sf.basedb.core.IntensityTransform
No transformation has been applied to the spot intensities.
NONE - Enum constant in enum class net.sf.basedb.core.SyncFilter.SourceItemTransform
No transformation of source items is done.
NONE - Enum constant in enum class net.sf.basedb.util.overview.node.ChildNodeDirection
Represents an end-point node.
NoneOfFilter<T> - Class in net.sf.basedb.util.filter
A filter implementation that accpets an object only if at none of the parent filters accepts it.
NoneOfFilter(Collection<? extends Filter<? super T>>) - Constructor for class net.sf.basedb.util.filter.NoneOfFilter
Create a new filter.
NONMATCHING_SPOTCOUNT - Static variable in class net.sf.basedb.util.overview.Validator
Validator rule that checks if the number of raw data spots are the same as the number of features (given a certain threshold).
NONMATHCING_ARRAYDESIGN - Static variable in class net.sf.basedb.util.overview.Validator
Validator rule that checks if the array design for a raw bioassay matches the array design of the associated physical bioassay.
NonRestartable - Interface in net.sf.basedb.core.plugin
This is a tagging interface that should be implemented by the plug-ins that don't support restart and reconfiguration of a job after an interrupted execution.
NONUNIQUE_NAME_FOR_TYPE - Static variable in class net.sf.basedb.util.overview.Validator
Validator rule that checks if two items of the same type has the same name.
NONUNIQUE_NAME_GLOBAL - Static variable in class net.sf.basedb.util.overview.Validator
Validator rule that checks if two items of different type has the same name.
NONUNIQUE_TAG - Static variable in class net.sf.basedb.util.overview.Validator
Validator rule that checks if a physical bioassay has more than one tagged extract with the same tag and position.
NoopPropertyPath(Class<C>, Type) - Constructor for class net.sf.basedb.core.Metadata.NoopPropertyPath
 
noPaging - Variable in class net.sf.basedb.core.ItemContext
 
noRawMapping - Variable in class net.sf.basedb.core.MappingBatcher
If the data cube has already received it's data and no raw data can be linked.
normalize(List<LowessNormalization.SpotData>, MACalculator) - Method in class net.sf.basedb.plugins.LowessNormalization.CallableWorker
Normalize the spot data.
normalize(DbControl, BioAssaySet, Job, float, float, float, int, ProgressReporter) - Method in class net.sf.basedb.plugins.MedianRatioNormalization
Normalise the source bioassay set using MEDIAN-RATIO normalization.
normalize(DbControl, BioAssaySet, Job, float, float, int, int, ProgressReporter) - Method in class net.sf.basedb.plugins.LowessNormalization
Normalise the source bioassay set using LOWESS normalization.
normalize(DbControl, BioAssaySet, Job, float, float, int, int, ReporterList, ProgressReporter) - Method in class net.sf.basedb.plugins.LowessNormalization
Normalise the source bioassay set using LOWESS normalization.
normalize1ch(DbControl, BioAssaySet, Job, float, float, float, ProgressReporter) - Method in class net.sf.basedb.plugins.MedianRatioNormalization
Normalise the source bioassay set using MEDIAN-RATIO normalization.
noSkin - Variable in class net.sf.basedb.clients.web.taglib.Page
Set to TRUE to not use skin on the page.
not(Restriction) - Static method in class net.sf.basedb.core.query.Restrictions
Negate a restriction: new restriction = NOT r
NOT - Enum constant in enum class net.sf.basedb.core.Operator
 
NOT_ANNOTATED - Enum constant in enum class net.sf.basedb.core.Include
Include items that have no annotations.
NOT_COMPACT - Static variable in class net.sf.basedb.clients.web.ModeInfo
 
NOT_REMOVED - Enum constant in enum class net.sf.basedb.core.Include
Include items flagged as not removed.
NOT_SELECTION_MODE - Static variable in class net.sf.basedb.clients.web.ModeInfo
 
noTabs - Variable in class net.sf.basedb.clients.web.taglib.tab.TabControl
If the tabs should be displayed or not.
notAmongSelected() - Method in class net.sf.basedb.core.AnnotationRestriction
If the main restriction should match items that had annotations among the selected annotation sets, or not.
notAmongSelected() - Method in class net.sf.basedb.core.HasAnnotationRestriction
 
NotConverter - Class in net.sf.basedb.util.jep.convert
Convert Not function to a Query API Restriction.
NotConverter() - Constructor for class net.sf.basedb.util.jep.convert.NotConverter
 
NotEqualsConverter - Class in net.sf.basedb.util.jep.convert
Convert the '!
NotEqualsConverter() - Constructor for class net.sf.basedb.util.jep.convert.NotEqualsConverter
 
notFound - Variable in class net.sf.basedb.util.extensions.xml.PluginInfo
 
notifyThread - Variable in class net.sf.basedb.clients.web.util.SimpleSignalProgressReporter
 
notifyThread - Variable in class net.sf.basedb.core.signal.AbstractSignalReceiver
 
notIn - Variable in class net.sf.basedb.core.query.IdListRestriction
 
NOTIN - Enum constant in enum class net.sf.basedb.core.Operator
 
NotInReporterListFunction - Class in net.sf.basedb.util.jep
A JEP function class that adds a notInList(reporterListId) function to a JEP expression parser.
NotInReporterListFunction(DbControl) - Constructor for class net.sf.basedb.util.jep.NotInReporterListFunction
Create a new instance of this function.
NOTLIKE - Enum constant in enum class net.sf.basedb.core.Operator
 
notLike_in(Expression, Expression...) - Static method in class net.sf.basedb.core.query.Restrictions
Check if one expression doesn't matches any of the expressions in an array.
NOTLIKE_IN - Enum constant in enum class net.sf.basedb.core.Operator
 
NotLoggable - Annotation Interface in net.sf.basedb.core.data
Getter methods that are annotated with this annotation should not trigger a log entry even if their values have changed.
notLoggableProperties - Variable in class net.sf.basedb.core.log.EntityLogOptions
 
NotLoggedInException - Exception in net.sf.basedb.core
This exception is thrown if you try to perform a function that requires a user to be logged in without beeing logged in.
NotLoggedInException() - Constructor for exception net.sf.basedb.core.NotLoggedInException
Creates a new NotLoggedInException.
notNull - Variable in class net.sf.basedb.core.ParameterType
If the parameter can be null or not.
NotNullFilter<T> - Class in net.sf.basedb.util.filter
A filter implementation that rejects all null objects.
NotNullFilter(boolean) - Constructor for class net.sf.basedb.util.filter.NotNullFilter
Create a new filter.
NotRestriction - Class in net.sf.basedb.core.query
Negate a restriction: NOT r
NotRestriction(Restriction) - Constructor for class net.sf.basedb.core.query.NotRestriction
 
noUsePermissionToReferenceErrorParameter - Static variable in class net.sf.basedb.plugins.batchimport.AbstractItemImporter
 
noUsePermissionToTargetErrorParameter - Static variable in class net.sf.basedb.plugins.batchimport.AnyToAnyImporter
 
noWritePermissionToItemErrorParameter - Static variable in class net.sf.basedb.plugins.batchimport.AbstractItemImporter
 
noWritePermissionToItemErrorParameter - Static variable in class net.sf.basedb.plugins.batchimport.AnyToAnyImporter
 
NULL_ESCAPE - Variable in class net.sf.basedb.core.migrate.AbstractResultWriter
 
NULL_ESCAPE - Variable in class net.sf.basedb.core.migrate.postgres.PostgresResultWriterFactory
PostgreSQL uses "\N" for null values.
nullable - Variable in class net.sf.basedb.core.data.ReporterClonePropertyData
 
nullable - Variable in class net.sf.basedb.core.ExtendedProperty
 
nullable - Variable in class net.sf.basedb.core.VirtualColumn
If the column should be nullable or not.
NULLABLE - Static variable in class net.sf.basedb.core.ClonableProperty
 
NULLABLE - Static variable in class net.sf.basedb.core.VirtualColumn
Used in constructor to tell that the column should be nullable.
nullIfException - Variable in class net.sf.basedb.plugins.IlluminaRawDataImporter
 
nullIfException - Variable in class net.sf.basedb.plugins.RawDataFlatFileImporter
 
nullIfException - Variable in class net.sf.basedb.plugins.ReporterFlatFileImporter
 
nullIfException - Variable in class net.sf.basedb.util.parser.ColumnMapper
 
nullIfException - Variable in class net.sf.basedb.util.parser.CompoundMapper
 
nullIfException - Variable in class net.sf.basedb.util.parser.ConstantMapper
 
NullIfExceptionMapper - Class in net.sf.basedb.util.parser
A mapper that returns null if there is an exception when parsing the input data.
NullIfExceptionMapper(Mapper) - Constructor for class net.sf.basedb.util.parser.NullIfExceptionMapper
Create a new CropStringMapper.
nullIfMissingReporter - Variable in class net.sf.basedb.plugins.IlluminaRawDataImporter
 
nullifyClonedReferences - Variable in class net.sf.basedb.core.AnnotationBatcher
 
nullIsEmptyString - Variable in class net.sf.basedb.util.encode.TabCrLfEncoderDecoder
 
nullIsNull - Variable in class net.sf.basedb.util.parser.FlatFileParser.Data
 
nullIsNull - Variable in class net.sf.basedb.util.parser.FlatFileParser
If null should be returned for the string NULL (ignoring case) or not.
NullIterator() - Constructor for class net.sf.basedb.clients.web.taglib.table.ColumnDef.NullIterator
 
NullNodeLoader<I> - Class in net.sf.basedb.util.overview.loader
A node loader implementation that doesn't load any nodes.
NullNodeLoader() - Constructor for class net.sf.basedb.util.overview.loader.NullNodeLoader
 
NullNodeValidator<I> - Class in net.sf.basedb.util.overview.validator
A node validator implementation that accepts all nodes, except missing items and denied access items (depending on configuration).
NullNodeValidator() - Constructor for class net.sf.basedb.util.overview.validator.NullNodeValidator
Create a new validator with default settings.
NullNodeValidator(boolean, boolean) - Constructor for class net.sf.basedb.util.overview.validator.NullNodeValidator
Created a new validator that accepts denied and/or missing nodes.
nullSafeAnd(Collection<? extends Restriction>) - Static method in class net.sf.basedb.core.query.Restrictions
Combine one or more restrictions with AND: new restriction = r[0] AND r[1] AND ...
nullSafeAnd(Restriction...) - Static method in class net.sf.basedb.core.query.Restrictions
Combine one or more restrictions with AND ignoring null elements.
nullSafeOr(Collection<? extends Restriction>) - Static method in class net.sf.basedb.core.query.Restrictions
Combine one or more restrictions with OR ignoring null elements.
nullSafeOr(Restriction...) - Static method in class net.sf.basedb.core.query.Restrictions
Combine one or more restrictions with OR ignoring null elements.
nullText - Variable in class net.sf.basedb.clients.web.taglib.PropertyValue
What to show if the value is null.
nullValue - Variable in class net.sf.basedb.clients.web.plugins.BioMaterialEventSourceFormatter
 
nullValue - Variable in class net.sf.basedb.core.log.ChangeTypeFormatter
 
nullValue - Variable in class net.sf.basedb.util.export.spotdata.ExportableFieldFormatter
 
nullValue - Variable in class net.sf.basedb.util.export.TableWriter
 
nullValue - Variable in class net.sf.basedb.util.formatter.EnumFormatter
 
nullValue - Variable in class net.sf.basedb.util.formatter.FilePathFormatter
 
nullValue - Variable in class net.sf.basedb.util.formatter.IdentifiableFormatter
 
nullValue - Variable in class net.sf.basedb.util.formatter.ItemTypeFormatter
 
nullValue - Variable in class net.sf.basedb.util.formatter.NameableFormatter
 
nullValue - Variable in class net.sf.basedb.util.formatter.ValueTypeFormatter
 
numAcceptedWithNullReporterOnFeature - Variable in class net.sf.basedb.core.RawDataBatcher
The number of accepted inserts were the feature had a NULL reporter
numAddedToList - Variable in class net.sf.basedb.plugins.ReporterFlatFileImporter
 
numAnnotations - Variable in class net.sf.basedb.plugins.AnnotationFlatFileImporter.NewAnnotations
 
numAnnotations - Variable in class net.sf.basedb.plugins.AnnotationFlatFileImporter
 
numArrays - Variable in class net.sf.basedb.core.data.ArrayDesignData
 
numArraysColumnMapping - Static variable in class net.sf.basedb.plugins.batchimport.ArrayDesignImporter
 
numArraysMapper - Variable in class net.sf.basedb.plugins.batchimport.ArrayDesignImporter
 
NUMBER_FORMAT_ERROR - Static variable in class net.sf.basedb.plugins.util.Parameters
NUMBER_OUT_OF_RANGE_ERROR - Static variable in class net.sf.basedb.plugins.util.Parameters
numberFormat - Variable in class net.sf.basedb.plugins.AnnotationFlatFileImporter
 
numberFormat - Variable in class net.sf.basedb.plugins.batchimport.AnnotationTypeImporter
 
numberFormat - Variable in class net.sf.basedb.util.excel.XlsxToCsvUtil
 
numberFormat - Variable in class net.sf.basedb.util.parser.ColFunction
 
numberFormat - Variable in class net.sf.basedb.util.parser.FlatFileParser
The default number formatter to use for creating mappers.
numberFormat - Variable in class net.sf.basedb.util.parser.JepMapper
 
numberFormat(int) - Static method in class net.sf.basedb.util.excel.ExcelValue
Creates a format string for formatting numbers with the given number of decimals (between 0 and 15).
numberFormatError(String, String, String, String...) - Static method in class net.sf.basedb.plugins.util.Parameters
Create the parameter for handling invalid numbers.
numberFormatErrorParameter - Static variable in class net.sf.basedb.plugins.AbstractFlatFileImporter
 
numberFormatErrorParameter - Static variable in class net.sf.basedb.plugins.AnnotationFlatFileImporter
 
NumberFormatFormatter - Class in net.sf.basedb.util.formatter
Formatter implementation for numeric values that simply wrap a NumberFormat instance.
NumberFormatFormatter(NumberFormat) - Constructor for class net.sf.basedb.util.formatter.NumberFormatFormatter
Create a new number formatter.
numberFormatter - Variable in class net.sf.basedb.clients.web.formatter.ColorFormatter
 
NumberFormatter - Class in net.sf.basedb.util.formatter
Formats a number for output on a web page.
NumberFormatter(int, boolean) - Constructor for class net.sf.basedb.util.formatter.NumberFormatter
Create a new number formatter.
NumberFormatUtil - Class in net.sf.basedb.util
Utility class for working with NumberFormat object.
NumberFormatUtil() - Constructor for class net.sf.basedb.util.NumberFormatUtil
 
numberOfRows - Variable in class net.sf.basedb.core.dbengine.TableInfo
 
numberOutOfRangeError(String, String, String, String...) - Static method in class net.sf.basedb.plugins.util.Parameters
Create the parameter for handling numeric values that are outside the allowed range.
numberOutOfRangeErrorParameter - Static variable in class net.sf.basedb.plugins.AbstractFlatFileImporter
 
numberOutOfRangeErrorParameter - Static variable in class net.sf.basedb.plugins.AnnotationFlatFileImporter
 
NumberOutOfRangeException - Exception in net.sf.basedb.core
This exception is thrown when an item's field or a parameter that only accepts numeric values within a certain range are passed a value outside that range.
NumberOutOfRangeException() - Constructor for exception net.sf.basedb.core.NumberOutOfRangeException
Create a new NumberOutOfRangeException object.
NumberOutOfRangeException(String) - Constructor for exception net.sf.basedb.core.NumberOutOfRangeException
 
NumberOutOfRangeException(String, double, double, boolean) - Constructor for exception net.sf.basedb.core.NumberOutOfRangeException
Create a new NumberOutOfRangeException object when the parameter is less than a minimum or greater than a maximum value.
NumberOutOfRangeException(String, double, double, double) - Constructor for exception net.sf.basedb.core.NumberOutOfRangeException
Create a new NumberOutOfRangeException object when the parameter is outside both a minimum and a maximum allowed value.
NumberOutOfRangeException(String, long, long, boolean) - Constructor for exception net.sf.basedb.core.NumberOutOfRangeException
Create a new NumberOutOfRangeException object when the parameter is less than a minimum or greater than a maximum value.
NumberOutOfRangeException(String, long, long, long) - Constructor for exception net.sf.basedb.core.NumberOutOfRangeException
Create a new NumberOutOfRangeException object when the parameter is outside both a minimum and a maximum allowed value.
numBlocks - Variable in class net.sf.basedb.plugins.PrintMapFlatFileImporter
 
numBlocks - Variable in class net.sf.basedb.plugins.ReporterMapFlatFileImporter
 
numChannels - Variable in class net.sf.basedb.core.SpotBatcher
The number of channels used in the raw data type of the experiment where the bioassayset belongs.
numChildren() - Method in class net.sf.basedb.util.overview.Node
Get the number of child nodes in this node.
numColumns - Variable in class net.sf.basedb.clients.web.taglib.table.HeaderRow
 
numColumns - Variable in class net.sf.basedb.core.data.DataCubeData
 
numColumns - Variable in class net.sf.basedb.util.bfs.AnnotationParser
 
numColumns - Variable in class net.sf.basedb.util.bfs.DataParser
 
numColumns - Variable in class net.sf.basedb.util.bfs.MatrixModel
 
numCreated - Variable in class net.sf.basedb.plugins.batchimport.AbstractItemImporter
 
numCreated - Variable in class net.sf.basedb.plugins.batchimport.AnyToAnyImporter
 
numDataColumnsType - Static variable in class net.sf.basedb.plugins.AbstractFlatFileImporter
 
numDecimals - Variable in class net.sf.basedb.util.formatter.NumberFormatter
 
numDeleted - Variable in class net.sf.basedb.plugins.ReporterFlatFileImporter
 
numDeleted - Variable in class net.sf.basedb.util.extensions.manager.ExtensionsManager
 
numDeleted - Variable in class net.sf.basedb.util.extensions.manager.processor.DeleteResourcesProcessor
 
numElements - Variable in class net.sf.basedb.clients.web.taglib.path.Path
Keeps track of the number of path elements so separators can be added.
numEntries - Variable in class net.sf.basedb.util.extensions.logging.ExtensionsLog
 
numericToAlpha(int) - Static method in class net.sf.basedb.util.Coordinate
Convert a numeric coordinate to an alphanumeric coordinate.
NumericValue(Number, String) - Constructor for class net.sf.basedb.util.excel.ExcelValue.NumericValue
 
numError - Variable in class net.sf.basedb.clients.web.extensions.LoadServletsProcessor
 
numError - Variable in class net.sf.basedb.plugins.AnnotationFlatFileImporter.NewAnnotations
 
numError - Variable in class net.sf.basedb.plugins.AnnotationFlatFileImporter
 
numError - Variable in class net.sf.basedb.plugins.batchimport.AbstractItemImporter
 
numError - Variable in class net.sf.basedb.util.extensions.manager.processor.DeleteResourcesProcessor
 
numError - Variable in class net.sf.basedb.util.extensions.manager.processor.DisablePluginsProcessor
 
numError - Variable in class net.sf.basedb.util.extensions.manager.processor.ExtractResourcesProcessor
 
numError - Variable in class net.sf.basedb.util.extensions.manager.processor.PluginInstallationProcessor
 
numError - Variable in class net.sf.basedb.util.extensions.manager.processor.RegisterExtensionsProcessor
 
numError - Variable in class net.sf.basedb.util.extensions.manager.processor.UnregisterExtensionsProcessor
 
numErrorFiles - Variable in class net.sf.basedb.util.extensions.manager.ProcessResults
 
numErrors - Variable in class net.sf.basedb.util.extensions.logging.ExtensionsLog
 
numErrors - Variable in class net.sf.basedb.util.overview.Node
 
numExisted - Variable in class net.sf.basedb.plugins.batchimport.AbstractItemImporter
 
numExists - Variable in class net.sf.basedb.plugins.ReporterFlatFileImporter
 
numExported - Variable in class net.sf.basedb.plugins.GalExporter
 
numExported - Variable in class net.sf.basedb.plugins.HelpExporter
 
numExported - Variable in class net.sf.basedb.plugins.PluginConfigurationExporter
 
numExtraValues - Variable in class net.sf.basedb.core.data.DataCubeData
 
numFeatures - Variable in class net.sf.basedb.plugins.PrintMapFlatFileImporter
 
numFeatures - Variable in class net.sf.basedb.plugins.ReporterMapFlatFileImporter
 
numFileReporters - Variable in class net.sf.basedb.core.data.BioAssaySetData
 
numFiles - Variable in class net.sf.basedb.clients.web.extensions.LoadServletsProcessor
 
numFiles - Variable in class net.sf.basedb.clients.web.extensions.UninstalledFileProcessor
 
numFiles - Variable in class net.sf.basedb.plugins.PackedFileExporter
 
numFiles - Variable in class net.sf.basedb.util.extensions.manager.processor.DeleteResourcesProcessor
 
numFiles - Variable in class net.sf.basedb.util.extensions.manager.processor.DisablePluginsProcessor
 
numFiles - Variable in class net.sf.basedb.util.extensions.manager.processor.ExtractResourcesProcessor
 
numFiles - Variable in class net.sf.basedb.util.extensions.manager.processor.IgnoreFileProcessor
 
numFiles - Variable in class net.sf.basedb.util.extensions.manager.processor.MarkAsProcessedProcessor
 
numFiles - Variable in class net.sf.basedb.util.extensions.manager.processor.PluginInstallationProcessor
 
numFiles - Variable in class net.sf.basedb.util.extensions.manager.processor.RegisterExtensionsProcessor
 
numFiles - Variable in class net.sf.basedb.util.extensions.manager.processor.ResetProcessor
 
numFiles - Variable in class net.sf.basedb.util.extensions.manager.processor.UnregisterExtensionsProcessor
 
numFileSpots - Variable in class net.sf.basedb.core.data.BioAssayData
 
numFileSpots - Variable in class net.sf.basedb.core.data.BioAssaySetData
 
numFileValues - Variable in class net.sf.basedb.core.data.ExtraValueData
 
numFilteredColumns - Variable in class net.sf.basedb.clients.web.taglib.table.Table
 
numFilterRows - Variable in class net.sf.basedb.clients.web.taglib.table.Table
Number of filter rows in the table.
numFilterRows - Variable in class net.sf.basedb.core.ItemContext
 
numFilterRows - Variable in class net.sf.basedb.core.SyncFilter
 
numFilters - Variable in class net.sf.basedb.core.data.DataCubeData
 
numHeaderColumns - Variable in class net.sf.basedb.clients.web.taglib.table.Table
 
numHeaderColumns() - Method in class net.sf.basedb.clients.web.taglib.table.Table
 
numIgnored - Variable in class net.sf.basedb.util.extensions.manager.ExtensionsManager
 
numImported - Variable in class net.sf.basedb.plugins.HelpImporter
 
numInserted - Variable in class net.sf.basedb.plugins.IlluminaRawDataImporter
 
numInserted - Variable in class net.sf.basedb.plugins.ReporterFlatFileImporter
 
numItemNotFound - Variable in class net.sf.basedb.plugins.AnnotationFlatFileImporter
 
numItems - Variable in class net.sf.basedb.core.AnnotationBatcher
 
numItems - Variable in class net.sf.basedb.plugins.AnnotationFlatFileImporter
 
numLayers - Variable in class net.sf.basedb.core.data.DataCubeData
 
numLines - Variable in class net.sf.basedb.core.Migration.ProgressInputStream
 
numModified - Variable in class net.sf.basedb.util.extensions.manager.ExtensionsManager
 
numMultiLines - Variable in class net.sf.basedb.plugins.batchimport.AbstractItemImporter
 
numNew - Variable in class net.sf.basedb.util.extensions.manager.ExtensionsManager
 
numNewChildren() - Method in class net.sf.basedb.util.overview.Node
Get the number of new children added to this node since the last call to Node.getNewChildren().
numNotFound - Variable in class net.sf.basedb.plugins.batchimport.AbstractItemImporter
 
numNotFound - Variable in class net.sf.basedb.plugins.ReporterFlatFileImporter
 
numParameters - Variable in class net.sf.basedb.util.jep.ChannelFunction
 
numParameters - Variable in class net.sf.basedb.util.jep.ExtraValueFunction
 
numParameters - Variable in class net.sf.basedb.util.jep.InReporterListFunction
 
numParameters - Variable in class net.sf.basedb.util.jep.MeanFunction
 
numParameters - Variable in class net.sf.basedb.util.jep.NotInReporterListFunction
 
numParameters - Variable in class net.sf.basedb.util.jep.RawChannelFunction
 
numParameters - Variable in class net.sf.basedb.util.jep.RawFunction
 
numParameters - Variable in class net.sf.basedb.util.jep.ReporterFunction
 
numParameters - Variable in class net.sf.basedb.util.jep.ScoreFunction
 
numParameters - Variable in class net.sf.basedb.util.jep.SimpleJepFunction
 
numParameters - Variable in class net.sf.basedb.util.parser.DefaultItemFunction
 
numPlates - Variable in class net.sf.basedb.plugins.PlateFlatFileImporter
 
numPositions - Variable in class net.sf.basedb.core.data.DataCubeData
 
numRawBioAssays - Variable in class net.sf.basedb.plugins.IlluminaRawDataImporter
 
numRead - Variable in class net.sf.basedb.util.InputStreamSplitter
 
numRead - Variable in class net.sf.basedb.util.InputStreamTracker
The number of bytes that has been read from the underlying input stream so far.
numReadAtMark - Variable in class net.sf.basedb.util.InputStreamTracker
The number of bytes that had been read when InputStreamTracker.mark(int) was called.
numRegistered - Variable in class net.sf.basedb.util.extensions.manager.processor.RegisterExtensionsProcessor
 
numRemoved - Variable in class net.sf.basedb.plugins.AnnotationFlatFileImporter.NewAnnotations
 
numRemoved - Variable in class net.sf.basedb.plugins.AnnotationFlatFileImporter
 
numRemoved - Variable in class net.sf.basedb.plugins.batchimport.AnyToAnyImporter
 
numReplaced - Variable in class net.sf.basedb.plugins.AnnotationFlatFileImporter.NewAnnotations
 
numReplaced - Variable in class net.sf.basedb.plugins.AnnotationFlatFileImporter
 
numReporters - Variable in class net.sf.basedb.core.data.BioAssaySetData
 
numReportersNotFound - Variable in class net.sf.basedb.core.RawDataBatcher
The number of reporters that was not found.
numReturned - Variable in class net.sf.basedb.util.query.MultiQueryIterator
 
numRows(long) - Method in class net.sf.basedb.core.Migration
 
numRowsFormat - Variable in class net.sf.basedb.core.Migration
 
numSelected - Variable in class net.sf.basedb.plugins.PluginConfigurationExporter
 
numServlets - Variable in class net.sf.basedb.clients.web.extensions.LoadServletsProcessor
 
numSet - Variable in class net.sf.basedb.plugins.AnnotationFlatFileImporter.NewAnnotations
 
numSkipped - Variable in class net.sf.basedb.plugins.batchimport.AnyToAnyImporter
 
numSkippedMissingFeature - Variable in class net.sf.basedb.core.RawDataBatcher
The number of skipped inserts due to missing feature
numSpots - Variable in class net.sf.basedb.core.data.BioAssayData
 
numSpots - Variable in class net.sf.basedb.core.data.BioAssaySetData
 
numStatements - Variable in class net.sf.basedb.core.hibernate.SchemaGenerator.CollectSqlTarget
 
numTabs - Variable in class net.sf.basedb.clients.web.taglib.tab.TabControl
The number of tabs.
numTotal - Variable in class net.sf.basedb.plugins.HelpImporter
 
numTotalExtracted - Variable in class net.sf.basedb.util.extensions.manager.processor.ExtractResourcesProcessor
 
numTotalPlugins - Variable in class net.sf.basedb.util.extensions.manager.processor.DisablePluginsProcessor
 
numTotalPlugins - Variable in class net.sf.basedb.util.extensions.manager.processor.PluginInstallationProcessor
 
numUnmodified - Variable in class net.sf.basedb.util.extensions.manager.ExtensionsManager
 
numUnregistered - Variable in class net.sf.basedb.util.extensions.manager.processor.RegisterExtensionsProcessor
 
numUnregistered - Variable in class net.sf.basedb.util.extensions.manager.processor.UnregisterExtensionsProcessor
 
numUpdated - Variable in class net.sf.basedb.plugins.batchimport.AbstractItemImporter
 
numUpdated - Variable in class net.sf.basedb.plugins.batchimport.AnyToAnyImporter
 
numUpdated - Variable in class net.sf.basedb.plugins.HelpImporter
 
numUpdated - Variable in class net.sf.basedb.plugins.ReporterFlatFileImporter
 
numUsed - Variable in class net.sf.basedb.plugins.ReporterFlatFileImporter
 
numValues - Variable in class net.sf.basedb.core.data.ExtraValueData
 
numVisibleColumns() - Method in class net.sf.basedb.clients.web.taglib.table.Table
 
numWarnings - Variable in class net.sf.basedb.util.extensions.logging.ExtensionsLog
 
numWarnings - Variable in class net.sf.basedb.util.overview.Node
 
numWells - Variable in class net.sf.basedb.plugins.PlateFlatFileImporter
 

O

object - Variable in class net.sf.basedb.util.filter.EqualsFilter
 
object - Variable in class net.sf.basedb.util.filter.IdentityFilter
 
objectCache - Variable in class net.sf.basedb.util.overview.GenericOverview
 
ObjectKey<O> - Interface in net.sf.basedb.util.extensions.manager
Instances of object keys should be something that uniquely identifies an object that has been defined by an extension.
objectMetadata - Variable in class net.sf.basedb.util.extensions.manager.ExtensionsFile
 
objects - Variable in class net.sf.basedb.core.ItemContext
 
objects - Variable in class net.sf.basedb.util.ClassLocal
 
OFF - Enum constant in enum class net.sf.basedb.util.extensions.LoggingErrorHandlerFactory.Level
 
OFFLINE - Enum constant in enum class net.sf.basedb.core.Location
The item is offline and doesn't use any quota.
offset - Variable in class net.sf.basedb.core.Job.ProgressReporterImpl
 
offset - Variable in class net.sf.basedb.util.extensions.ActionIterator
 
offset - Variable in class net.sf.basedb.util.units.LinearUnitConverter
 
offsetMid - Variable in class net.sf.basedb.util.ColorGenerator
The RGB components of the midpoint color. [0] = red; [1] = green; [2] = blue
offsetMin - Variable in class net.sf.basedb.util.ColorGenerator
The RGB components of the min color. [0] = red; [1] = green; [2] = blue
olderThan(long) - Method in class net.sf.basedb.util.StaticCache
Creates a file filter that matches all files that are older than the specified age.
OlderThanFileFilter - Class in net.sf.basedb.util
An implementation of the FileFilter interface that filter files based on their age.
OlderThanFileFilter(long, boolean) - Constructor for class net.sf.basedb.util.OlderThanFileFilter
Create a new file filter that matches files that are older than the specified age.
oldFileResults - Variable in class net.sf.basedb.util.extensions.manager.ProcessResults
 
oldPropertyValues - Variable in class net.sf.basedb.core.log.db.AnnotationSetLogger
 
oldPropertyValues - Variable in class net.sf.basedb.core.log.db.BioMaterialEventLogger
 
oldPropertyValues - Variable in class net.sf.basedb.core.log.db.DbLogManagerFactory
 
oldPropertyValues - Variable in class net.sf.basedb.core.log.db.DefaultEntityLogger
 
oldPropertyValues - Variable in class net.sf.basedb.core.log.db.ManualEntryLogger
 
oldReporterCloneTable - Variable in class net.sf.basedb.core.Experiment
 
oldValue - Variable in class net.sf.basedb.clients.web.plugins.ChangeHistoryDetailLoader
 
oldValue - Variable in class net.sf.basedb.core.data.ChangeHistoryDetailData
 
oldValue - Variable in class net.sf.basedb.core.log.ManualLogEntry
 
oldValues - Variable in class net.sf.basedb.core.data.ParameterValueData
 
on - Variable in class net.sf.basedb.core.query.HqlInnerJoin
 
on - Variable in class net.sf.basedb.core.query.HqlLeftJoin
 
on - Variable in class net.sf.basedb.core.query.HqlRightJoin
 
ON_COMMIT - Static variable in class net.sf.basedb.clients.web.extensions.edit.OnSaveRenderer
Renderer that calls the OnSaveAction.onCommit() method.
ON_SAVE - Static variable in class net.sf.basedb.clients.web.extensions.edit.OnSaveRenderer
Renderer that calls the OnSaveAction.onSave() method.
onAdd(BioWellData, MeasuredBioMaterialData) - Method in enum class net.sf.basedb.core.BioWell.LockMode
Called when biomaterial is added to a well.
onAfterCommit() - Method in class net.sf.basedb.clients.web.extensions.list.RelatedItemHelper.CloseMyDbControl
 
onAfterCommit() - Method in class net.sf.basedb.core.AnnotationType.RemoveInheritedAnnotationsAction
 
onAfterCommit() - Method in class net.sf.basedb.core.DerivedBioAssay.FixDerivedBioAssayParentsRecursivelyAction
 
onAfterCommit() - Method in class net.sf.basedb.core.DropDynamicTableAction
 
onAfterCommit() - Method in class net.sf.basedb.core.ItemList.DelayedAdditionManager
 
onAfterCommit() - Method in class net.sf.basedb.core.Job.JobSignalTransporter
 
onAfterCommit() - Method in class net.sf.basedb.core.MeasuredBioMaterial.RemainingQuantityAction
 
onAfterCommit() - Method in class net.sf.basedb.core.ProjectSpecificAnnotationsManager
 
onAfterCommit() - Method in class net.sf.basedb.core.ServiceSessionControl.FlushSessionAction
 
onAfterCommit() - Method in interface net.sf.basedb.core.TransactionalAction
Called after a successful commit.
onAfterCommit(Transactional.Action) - Method in class net.sf.basedb.core.BasicItem
This method is called on each Transactional object after a successful commit to the database.
onAfterCommit(Transactional.Action) - Method in class net.sf.basedb.core.Experiment
Remove old reporter clone table after a successful commit.
onAfterCommit(Transactional.Action) - Method in class net.sf.basedb.core.File
 
onAfterCommit(Transactional.Action) - Method in class net.sf.basedb.core.Job
If the Signal.ABORT signal is waiting to be sent send it.
onAfterCommit(Transactional.Action) - Method in class net.sf.basedb.core.Message
Send the message as an email if requested by the user.
onAfterCommit(Transactional.Action) - Method in class net.sf.basedb.core.Platform
Register file-only platforms as raw data type after insert and unregister after delete.
onAfterCommit(Transactional.Action) - Method in class net.sf.basedb.core.PlatformVariant
Register file-only platforms as raw data type after insert and unregister after delete.
onAfterCommit(Transactional.Action) - Method in class net.sf.basedb.core.PluginConfiguration
Reset parameter version so that adding new parameters will increase the version the next time.
onAfterCommit(Transactional.Action) - Method in class net.sf.basedb.core.VirtualDb
Remove all dynamic tables if action == Action.DELETE
onAfterInsert() - Method in class net.sf.basedb.core.Annotation
 
onAfterInsert() - Method in class net.sf.basedb.core.BasicItem
This method is called on all items directly after Hibernate has inserted it into the database.
onAfterInsert() - Method in class net.sf.basedb.core.BioPlateEventType
 
onAfterInsert() - Method in class net.sf.basedb.core.PluginDefinition
 
onBeforeClose() - Method in class net.sf.basedb.core.AbstractBatcher
Let a subclass cleanup itself before the connection to the database is closed.
onBeforeClose() - Method in class net.sf.basedb.core.AnnotationBatcher
 
onBeforeClose() - Method in class net.sf.basedb.core.BasicBatcher
Close all open SQL statements.
onBeforeClose() - Method in class net.sf.basedb.core.FeatureBatcher
Set the hasFeature flag on the array design if features has been added.
onBeforeClose() - Method in class net.sf.basedb.core.FilterBatcher
Close open SQL statements.
onBeforeClose() - Method in class net.sf.basedb.core.MappingBatcher
Update bytes on data cube and close open SQL statements.
onBeforeClose() - Method in class net.sf.basedb.core.PositionBatcher
Update bytes and max position on the datacube and close open SQL statements.
onBeforeClose() - Method in class net.sf.basedb.core.PositionExtraValueBatcher
Update disk usage and close open SQL statements
onBeforeClose() - Method in class net.sf.basedb.core.RawDataBatcher
Update the spot count and disk usage on the raw bioassay.
onBeforeClose() - Method in class net.sf.basedb.core.ReporterCloneBatcher
Update disk usage and close open SQL statements.
onBeforeClose() - Method in class net.sf.basedb.core.SpotBatcher
Update disk usage and close open SQL statements
onBeforeClose() - Method in class net.sf.basedb.core.SpotExtraValueBatcher
Update disk usage and close open SQL statements
onBeforeCommit() - Method in class net.sf.basedb.clients.web.extensions.list.RelatedItemHelper.CloseMyDbControl
 
onBeforeCommit() - Method in class net.sf.basedb.core.AnnotationType.RemoveInheritedAnnotationsAction
 
onBeforeCommit() - Method in class net.sf.basedb.core.DerivedBioAssay.FixDerivedBioAssayParentsRecursivelyAction
 
onBeforeCommit() - Method in class net.sf.basedb.core.DropDynamicTableAction
 
onBeforeCommit() - Method in class net.sf.basedb.core.ItemList.DelayedAdditionManager
 
onBeforeCommit() - Method in class net.sf.basedb.core.MeasuredBioMaterial.RemainingQuantityAction
 
onBeforeCommit() - Method in class net.sf.basedb.core.ProjectSpecificAnnotationsManager
 
onBeforeCommit() - Method in class net.sf.basedb.core.ServiceSessionControl.FlushSessionAction
 
onBeforeCommit() - Method in interface net.sf.basedb.core.TransactionalAction
This method is called before the commit is about to happen.
onBeforeCommit(D, Transactional.Action) - Method in class net.sf.basedb.core.BasicBatcher
Called after the object has been validated just before the SQL is added to the batch queue.
onBeforeCommit(ReporterData, Transactional.Action) - Method in class net.sf.basedb.core.ReporterBatcher
Set the last update date to today's date and change the last source of update.
onBeforeCommit(Transactional.Action) - Method in class net.sf.basedb.core.Annotation
Nullify links to this annotation from cloned annotations when this annotation is deleted (since the cloned annotation should not be deleted).
onBeforeCommit(Transactional.Action) - Method in class net.sf.basedb.core.AnnotationSet
Remove the cached snapshot if needed.
onBeforeCommit(Transactional.Action) - Method in class net.sf.basedb.core.AnyToAny
We may have to set the AnyToAny.getFromId() and/or AnyToAny.getToId() values if those items are also created in the same transaction.
onBeforeCommit(Transactional.Action) - Method in class net.sf.basedb.core.BasicItem
This method is called on each Transactional item and on all items if the action is Transactional.Action.CREATE or Transactional.Action.DELETE before a commit is issued to the database.
onBeforeCommit(Transactional.Action) - Method in class net.sf.basedb.core.BioAssay
 
onBeforeCommit(Transactional.Action) - Method in class net.sf.basedb.core.BioAssaySet
On creation, count the number of spots and reporters in the bioassays attached to this bioassayset.
onBeforeCommit(Transactional.Action) - Method in class net.sf.basedb.core.BioMaterialEvent
Return used guantity to biomaterials on delete action.
onBeforeCommit(Transactional.Action) - Method in class net.sf.basedb.core.BioPlate
 
onBeforeCommit(Transactional.Action) - Method in class net.sf.basedb.core.BioPlateEvent
 
onBeforeCommit(Transactional.Action) - Method in class net.sf.basedb.core.BioPlateEventParticipant
 
onBeforeCommit(Transactional.Action) - Method in class net.sf.basedb.core.DataCube
Delete data and update disk usage information on the experiment if action == Action.DELETE
onBeforeCommit(Transactional.Action) - Method in class net.sf.basedb.core.DataCubeExtraValue
Delete data and update disk usage information on the experiment if action == Action.DELETE
onBeforeCommit(Transactional.Action) - Method in class net.sf.basedb.core.DataCubeFilter
Delete data and update disk usage information on the experiment if action == Action.DELETE
onBeforeCommit(Transactional.Action) - Method in class net.sf.basedb.core.DataCubeLayer
Delete data and update disk usage information on the experiment if action == Action.DELETE
onBeforeCommit(Transactional.Action) - Method in class net.sf.basedb.core.DerivedBioAssay
Automatically try to assign an extract from parent items at creation time.
onBeforeCommit(Transactional.Action) - Method in class net.sf.basedb.core.Experiment
 
onBeforeCommit(Transactional.Action) - Method in class net.sf.basedb.core.File
 
onBeforeCommit(Transactional.Action) - Method in class net.sf.basedb.core.Group
Set group to null in disk usage where this group is referenced.
onBeforeCommit(Transactional.Action) - Method in class net.sf.basedb.core.Job
Set's the project id to the currently active project.
onBeforeCommit(Transactional.Action) - Method in class net.sf.basedb.core.MeasuredBioMaterial
Make sure the creation event is created at the same time this item is created and that source biomaterials get their used quantities back if this item is deleted.
onBeforeCommit(Transactional.Action) - Method in class net.sf.basedb.core.OwnedItem
onBeforeCommit(Transactional.Action) - Method in class net.sf.basedb.core.PhysicalBioAssay
Make sure the creation event is created at the same time this item is created and that source biomaterials get their used quantities back if this item is deleted.
onBeforeCommit(Transactional.Action) - Method in class net.sf.basedb.core.Project
 
onBeforeCommit(Transactional.Action) - Method in class net.sf.basedb.core.RawBioAssay
Delete raw data if it exists.
onBeforeCommit(Transactional.Action) - Method in class net.sf.basedb.core.SharedItem
If a project is active, automatically share the new item according to the settings of that project, unless a project or item key has been explicitely set (including null).
onBeforeCommit(Transactional.Action) - Method in class net.sf.basedb.core.Transformation
Delete the product bioassaysets when deleting this transction.
onBeforeCommit(Transactional.Action) - Method in class net.sf.basedb.core.Unit
Set property filters that use this unit to null when the unit is deleted.
onClear(BioWellData, MeasuredBioMaterialData) - Method in enum class net.sf.basedb.core.BioWell.LockMode
Called when a well is cleared from an existing biomaterial.
onClick - Variable in class net.sf.basedb.clients.web.extensions.toolbar.PermissionButtonFactory
 
onCommit() - Method in class net.sf.basedb.clients.web.extensions.edit.AbstractOnSaveAction
 
onCommit() - Method in class net.sf.basedb.clients.web.extensions.edit.DebugOnSaveActionFactory.DebugOnSaveAction
 
onCommit() - Method in interface net.sf.basedb.clients.web.extensions.edit.OnSaveAction
This event is fired after a successful commit.
onDelete(Object, Serializable, Object[], String[], Type[]) - Method in class net.sf.basedb.core.log.LoggingInterceptor
Adds a DELETE event to the log.
ONE_ZERO - Enum constant in enum class net.sf.basedb.util.formatter.BooleanFormatter.Type
Display 1/0.
OneOfFilter<T> - Class in net.sf.basedb.util.filter
A filter implementation that accpets an object if at least one parent filters accepts it.
OneOfFilter(Collection<? extends Filter<? super T>>) - Constructor for class net.sf.basedb.util.filter.OneOfFilter
Create a new filter.
onFlushDirty(Object, Serializable, Object[], Object[], String[], Type[]) - Method in class net.sf.basedb.core.log.LoggingInterceptor
Adds an UPDATE event to the log.
onRollback() - Method in class net.sf.basedb.clients.web.extensions.list.RelatedItemHelper.CloseMyDbControl
 
onRollback() - Method in class net.sf.basedb.core.AnnotationType.RemoveInheritedAnnotationsAction
 
onRollback() - Method in class net.sf.basedb.core.DerivedBioAssay.FixDerivedBioAssayParentsRecursivelyAction
 
onRollback() - Method in class net.sf.basedb.core.DropDynamicTableAction
 
onRollback() - Method in class net.sf.basedb.core.ItemList.DelayedAdditionManager
 
onRollback() - Method in class net.sf.basedb.core.MeasuredBioMaterial.RemainingQuantityAction
 
onRollback() - Method in class net.sf.basedb.core.ProjectSpecificAnnotationsManager
 
onRollback() - Method in class net.sf.basedb.core.ServiceSessionControl.FlushSessionAction
 
onRollback() - Method in interface net.sf.basedb.core.TransactionalAction
Called after an unsuccessful commit.
onRollback(Exception) - Method in class net.sf.basedb.clients.web.extensions.edit.AbstractOnSaveAction
 
onRollback(Exception) - Method in class net.sf.basedb.clients.web.extensions.edit.DebugOnSaveActionFactory.DebugOnSaveAction
 
onRollback(Exception) - Method in interface net.sf.basedb.clients.web.extensions.edit.OnSaveAction
This event is fired after an error that caused the save action to rollback.
onRollback(Exception) - Static method in class net.sf.basedb.clients.web.extensions.edit.OnSaveRenderer
Renderer that calls the OnSaveAction.onRollback(Exception) method.
onRollback(Transactional.Action) - Method in class net.sf.basedb.core.BasicItem
This method is called on each Transactional object after an unsuccessful commit to the database.
onRollback(Transactional.Action) - Method in class net.sf.basedb.core.Experiment
Remove new reporter clone table after a rollback.
onRollback(Transactional.Action) - Method in class net.sf.basedb.core.File
 
onSave() - Method in class net.sf.basedb.clients.web.extensions.edit.AbstractOnSaveAction
 
onSave() - Method in class net.sf.basedb.clients.web.extensions.edit.DebugOnSaveActionFactory.DebugOnSaveAction
 
onSave() - Method in interface net.sf.basedb.clients.web.extensions.edit.OnSaveAction
This event is fired first to let the action do something with the current item.
onSave(Object, Serializable, Object[], String[], Type[]) - Method in class net.sf.basedb.core.log.LoggingInterceptor
Adds a CREATE event to the log.
OnSaveAction - Interface in net.sf.basedb.clients.web.extensions.edit
Action that is called when an item is saved in gui.
OnSaveRenderer - Class in net.sf.basedb.clients.web.extensions.edit
Renderer implementations for OnSaveAction:s.
OnSaveRenderer() - Constructor for class net.sf.basedb.clients.web.extensions.edit.OnSaveRenderer
 
open - Variable in class net.sf.basedb.clients.web.taglib.menu.Menu
If submenus opens as soon as the mouse enters or a click is required.
open() - Method in class net.sf.basedb.util.extensions.manager.ExtensionsFile.WriteableExtensionsFile
 
open() - Method in class net.sf.basedb.util.jobagent.JobAgentServerConnection
Start listening for incoming connections.
operator - Variable in class net.sf.basedb.core.AnnotationSimpleRestriction
 
operator - Variable in class net.sf.basedb.core.data.PropertyFilterData
 
operator - Variable in class net.sf.basedb.core.PropertyFilter
 
operator - Variable in class net.sf.basedb.core.query.SubqueryExpression
 
operator(String) - Method in class net.sf.basedb.util.formatter.PropertyFilterFormatter
 
Operator - Enum Class in net.sf.basedb.core
 
Operator(int, String, String, boolean, boolean, boolean) - Constructor for enum class net.sf.basedb.core.Operator
 
operators - Static variable in class net.sf.basedb.util.jep.Jep
 
optionalBooleanType - Static variable in class net.sf.basedb.plugins.AnnotationFlatFileImporter
 
optionalBooleanType - Static variable in class net.sf.basedb.plugins.batchimport.AnyToAnyImporter
 
optionalColumnMapping - Static variable in class net.sf.basedb.plugins.AnnotationFlatFileImporter
 
optionalColumnMapping - Static variable in class net.sf.basedb.plugins.batchimport.AbstractItemImporter
 
optionalColumnMapping - Static variable in class net.sf.basedb.plugins.batchimport.AnyToAnyImporter
 
optionalColumnMapping - Static variable in class net.sf.basedb.plugins.RawDataFlatFileImporter
 
optionalColumnMapping - Static variable in class net.sf.basedb.plugins.ReporterFlatFileImporter
 
optionalColumnMapping - Static variable in class net.sf.basedb.plugins.ReporterMapFlatFileImporter
 
optionalFilter - Variable in class net.sf.basedb.core.AbstractEntityQuery
Optional runtime filter.
optionalFilters - Static variable in class net.sf.basedb.core.QueryRuntimeFilterFactory
 
optionalNameType - Static variable in class net.sf.basedb.core.plugin.AbstractAnalysisPlugin
A parameter type for name parameters which are optional.
optionalRegexpType - Static variable in class net.sf.basedb.plugins.AbstractFlatFileImporter
 
optionalSaveAsType - Static variable in class net.sf.basedb.core.plugin.AbstractExporterPlugin
 
options - Variable in class net.sf.basedb.clients.jobagent.CmdLine
 
options - Variable in class net.sf.basedb.clients.jobagent.executors.ProcessJobExecutor
 
options - Variable in class net.sf.basedb.core.AnnotationRestriction
 
options - Variable in class net.sf.basedb.core.data.AnnotationTypeData
 
options - Static variable in class net.sf.basedb.core.log.EntityLogOptions
 
options - Variable in class net.sf.basedb.plugins.Base1PluginExecuter.JobParameter
 
options - Variable in class net.sf.basedb.plugins.executor.ParameterDefinition
 
options - Variable in class net.sf.basedb.util.overview.ValidationOptions
Other options.
Options() - Constructor for class net.sf.basedb.core.AnnotationRestriction.Options
Creates the default options.
Options() - Constructor for class net.sf.basedb.util.AnyToAnyLinkStatistics.Options
 
or(Restriction...) - Static method in class net.sf.basedb.core.query.Restrictions
Combine one or more restrictions with OR: new restriction = r[0] OR r[1] ...
OR - Enum constant in enum class net.sf.basedb.core.Operator
 
OrConverter - Class in net.sf.basedb.util.jep.convert
Convert the '||' operator to a Query API Restriction.
OrConverter() - Constructor for class net.sf.basedb.util.jep.convert.OrConverter
 
order(Order) - Method in class net.sf.basedb.core.AbstractQuery
 
order(Order) - Method in interface net.sf.basedb.core.query.Query
Add an ordering query element to the orderby list.
Order - Interface in net.sf.basedb.core.query
An ordering query element.
ORDERBY - Enum constant in enum class net.sf.basedb.core.query.QuerySection
 
orderPermanent(Order) - Method in class net.sf.basedb.core.AbstractQuery
 
orderPermanent(Order) - Method in interface net.sf.basedb.core.query.Query
Permanently add an ordering query element to the orderby list.
orders - Variable in class net.sf.basedb.core.AbstractQuery
List of orders added to the query.
Orders - Class in net.sf.basedb.core.query
A factory class to create order by expressions.
Orders() - Constructor for class net.sf.basedb.core.query.Orders
 
ordinal - Variable in class net.sf.basedb.core.data.PlateEventTypeData
 
organisation - Variable in class net.sf.basedb.core.authentication.ExtraUserInformation
 
organisation - Variable in class net.sf.basedb.core.data.UserData
 
original - Variable in class net.sf.basedb.core.hibernate.SchemaGenerator.SqlStatement
 
originalBioMaterial - Variable in class net.sf.basedb.core.data.BioWellData
 
originalPermissions - Variable in class net.sf.basedb.core.GroupPermissions
 
originalPermissions - Variable in class net.sf.basedb.core.ProjectPermissions
 
originalPermissions - Variable in class net.sf.basedb.core.UserPermissions
 
originalQuantity - Variable in class net.sf.basedb.core.data.MeasuredBioMaterialData
 
originalQuantityColumnMapping - Static variable in class net.sf.basedb.plugins.batchimport.SampleImporter
Column mapping parameter for the original quantity.
originalQuantityMapper - Variable in class net.sf.basedb.plugins.batchimport.ExtractImporter
 
originalQuantityMapper - Variable in class net.sf.basedb.plugins.batchimport.SampleImporter
 
originalServletPath - Variable in class net.sf.basedb.clients.web.extensions.RequestWrapper
 
originX - Variable in class net.sf.basedb.core.data.ArrayDesignBlockData
 
originX - Variable in class net.sf.basedb.plugins.PrintMapFlatFileImporter.MetaBlock
 
originY - Variable in class net.sf.basedb.core.data.ArrayDesignBlockData
 
originY - Variable in class net.sf.basedb.plugins.PrintMapFlatFileImporter.MetaBlock
 
OrRestriction - Class in net.sf.basedb.core.query
Combine one or more restrictions with OR: r[0] OR r[1] OR ...
OrRestriction(Restriction...) - Constructor for class net.sf.basedb.core.query.OrRestriction
 
OTHER - Enum constant in enum class net.sf.basedb.core.BioMaterialEvent.Type
An event of this type affected a single biomaterial in some way.
OTHER - Enum constant in enum class net.sf.basedb.core.Job.Type
The job is executed by some other program.
OTHER - Enum constant in enum class net.sf.basedb.core.plugin.Plugin.MainType
 
OTHER - Static variable in class net.sf.basedb.core.Hardware
The id for the HardwareType object representing something else.
otherLogger - Variable in class net.sf.basedb.util.extensions.logging.ExtensionsLogger
 
OTHERS - Enum constant in enum class net.sf.basedb.core.Include
Include items owned by other users.
out - Variable in class net.sf.basedb.clients.jobagent.executors.ProcessJobExecutor.StreamRedirector
 
out - Variable in class net.sf.basedb.clients.web.plugins.XlsxTemplate
 
out - Variable in class net.sf.basedb.core.plugin.ExportOutputStream
 
out - Variable in class net.sf.basedb.util.export.spotdata.BaseFileExporter
 
out - Variable in class net.sf.basedb.util.export.spotdata.MatrixBaseFileExporter
 
out - Variable in class net.sf.basedb.util.export.spotdata.SerialBaseFileExporter
 
out - Variable in class net.sf.basedb.util.FileCopyRunnable
 
overridden - Static variable in class net.sf.basedb.core.Config
Properties that has been programmatically overridden.
override - Variable in class net.sf.basedb.clients.web.util.ProjectSpecificInfoFilter
 
overrideId - Variable in class net.sf.basedb.core.AnnotationBatcher.CurrentAnnotationInfo
 
overrideId - Variable in class net.sf.basedb.core.data.AnnotationData
 
overrideId - Variable in class net.sf.basedb.core.data.annotations.AnnotationLink
 
overrideId - Variable in class net.sf.basedb.core.FastAnnotationLoader.FastAnnotation
The ID of the default annotation this value is overriding.
overrideId - Variable in class net.sf.basedb.core.snapshot.AnnotationSnapshot
 
overridesDefaultAnnotation() - Method in class net.sf.basedb.clients.web.util.ProjectSpecificInfoFilter
Check if the override flag is set.
OverviewContext - Interface in net.sf.basedb.util.overview
Interface that should be implemented by overview generating classes.
OverviewPlotAction - Interface in net.sf.basedb.clients.web.extensions.plot
Action for generating overview plots for a bioassay set.
OverviewPlotBean - Class in net.sf.basedb.clients.web.extensions.plot
A simple bean-like implementation of the OverviewPlotAction interface.
OverviewPlotBean() - Constructor for class net.sf.basedb.clients.web.extensions.plot.OverviewPlotBean
 
OverviewUtil - Class in net.sf.basedb.util.overview
Utility class for the overview generation functionality.
OverviewUtil() - Constructor for class net.sf.basedb.util.overview.OverviewUtil
 
overwrite - Variable in class net.sf.basedb.plugins.HelpImporter
 
overwrite - Variable in class net.sf.basedb.util.bfs.GenericExtraFileImporter
 
OVERWRITE - Static variable in class net.sf.basedb.core.plugin.AbstractExporterPlugin
OVERWRITE - Static variable in class net.sf.basedb.util.zip.AbstractFileUnpacker
The name of the parameter that asks if existing files should be overwritten or not.
OVERWRITE_ANNOTATIONS - Static variable in class net.sf.basedb.core.plugin.AbstractPlugin
The name of the parameter that asks if annotations should be overwritten or not.
overWriteParameter - Variable in class net.sf.basedb.plugins.HelpImporter
 
overwriteType - Static variable in class net.sf.basedb.core.plugin.AbstractExporterPlugin
 
ownable - Static variable in class net.sf.basedb.core.Item.DefinedPermissions
 
Ownable - Interface in net.sf.basedb.core
An Ownable item is an item which has a User as its owner.
ownable_annotatable - Static variable in class net.sf.basedb.core.Item.DefinedPermissions
 
OWNABLE_FILTER - Static variable in class net.sf.basedb.core.QueryRuntimeFilterFactory
 
OwnableData - Interface in net.sf.basedb.core.data
An ownable item is an item which has an owner.
OwnableFilter() - Constructor for class net.sf.basedb.core.QueryRuntimeFilterFactory.OwnableFilter
 
ownableItems - Static variable in class net.sf.basedb.core.Metadata
 
OwnableUtil - Class in net.sf.basedb.core
Utility methods that will make it easier to implement the Ownable interface, including data validation.
OwnableUtil - Class in net.sf.basedb.util
 
OwnableUtil() - Constructor for class net.sf.basedb.core.OwnableUtil
 
OwnableUtil() - Constructor for class net.sf.basedb.util.OwnableUtil
 
OwnedData - Class in net.sf.basedb.core.data
This class extends the BasicData class and implements the OwnableData interface.
OwnedData() - Constructor for class net.sf.basedb.core.data.OwnedData
 
OwnedItem - Class in net.sf.basedb.core
This class inherits from the BasicItem class and implements the Ownable interface.
OwnedItem(OwnedData) - Constructor for class net.sf.basedb.core.OwnedItem
 
owner - Variable in class net.sf.basedb.core.data.OwnedData
 
ownerId - Variable in class net.sf.basedb.core.InternalJobQueue.JobRunner
 
ownerId - Variable in class net.sf.basedb.core.MigrateRbaToDba.Rba
 

P

P - Variable in class net.sf.basedb.util.bcrypt.BCrypt
 
P_orig - Static variable in class net.sf.basedb.util.bcrypt.BCrypt
 
pack(String, InputStream, long, long) - Method in interface net.sf.basedb.util.zip.FilePacker
Compress the uncompressed input stream to an entry with the given name into the outputstream.
pack(String, InputStream, long, long) - Method in class net.sf.basedb.util.zip.TarFilePacker
Create a new TarEntry and write the compressed data to it.
pack(String, InputStream, long, long) - Method in class net.sf.basedb.util.zip.ZipFilePacker
Create a new entry and write the compressed data to it.
PackedFileExporter - Class in net.sf.basedb.plugins
Plug-in that packs one or more selected files and directories into a single file.
PackedFileExporter() - Constructor for class net.sf.basedb.plugins.PackedFileExporter
Create new instance.
packerParameter - Variable in class net.sf.basedb.plugins.PackedFileExporter
 
PackUtil - Class in net.sf.basedb.util.zip
 
PackUtil() - Constructor for class net.sf.basedb.util.zip.PackUtil
 
page - Variable in class net.sf.basedb.clients.web.taglib.Body
The parent <base:page> tag.
page - Variable in class net.sf.basedb.clients.web.taglib.Head
The parent <base:page> tag.
page - Variable in class net.sf.basedb.clients.web.taglib.Help
The parent <base:page> tag.
page - Variable in class net.sf.basedb.clients.web.taglib.HideableSection
The parent <base:page> tag.
page - Variable in class net.sf.basedb.clients.web.taglib.Icon
The parent <base:page> tag.
page - Variable in class net.sf.basedb.clients.web.taglib.table.Table
The parent <base:page> tag.
page - Variable in class net.sf.basedb.clients.web.taglib.Zoom
The parent <base:page> tag.
page - Variable in class net.sf.basedb.core.data.ContextData
 
page - Variable in class net.sf.basedb.core.ItemContext
 
Page - Class in net.sf.basedb.clients.web.taglib
This tag should be used together with the <base:head> and <base:body> tags on every JSP page in BASE.
Page() - Constructor for class net.sf.basedb.clients.web.taglib.Page
 
PAGE_TYPE_DEFAULT - Static variable in class net.sf.basedb.clients.web.taglib.Page
This is the default page type.
PAGE_TYPE_IFRAME - Static variable in class net.sf.basedb.clients.web.taglib.Page
The page is in a separate iframe .
PAGE_TYPE_INCLUDE - Static variable in class net.sf.basedb.clients.web.taglib.Page
This page is an included page.
PAGE_TYPE_POPUP - Static variable in class net.sf.basedb.clients.web.taglib.Page
The page is a popup dialouge.
pageContext - Variable in class net.sf.basedb.clients.web.extensions.JspContext
 
pageType - Variable in class net.sf.basedb.clients.web.ModeInfo
 
pageType - Variable in exception net.sf.basedb.clients.web.WebException
The type of page to display the error message in.
Panel - Class in net.sf.basedb.clients.web.taglib.table
This tag creates a panel in the table.
Panel() - Constructor for class net.sf.basedb.clients.web.taglib.table.Panel
 
parameter(String) - Static method in class net.sf.basedb.core.query.Expressions
Create an expression for a parameter without a default value or type.
parameter(String, Object) - Static method in class net.sf.basedb.core.query.Expressions
Create an expression for a parameter with a default value but no type.
parameter(String, Object, Type) - Static method in class net.sf.basedb.core.query.Expressions
Create an expression for a parameter with a default value and type.
parameter(String, Type) - Static method in class net.sf.basedb.core.query.Expressions
Create an expression for a typed parameter without a default value.
PARAMETER_DEBUG_MODE - Static variable in class net.sf.basedb.plugins.executor.ExternalProgramExecutor
Parameter name for debug mode flag.
PARAMETER_EXPORTER_CLASS - Static variable in class net.sf.basedb.plugins.executor.ExternalProgramExecutor
Parameter name for the class that has been selected as the exporter.
PARAMETER_EXTERNAL_CMDLINE - Static variable in class net.sf.basedb.plugins.executor.ExternalProgramExecutor
Parameter name for the command line options to the external program.
PARAMETER_EXTERNAL_PARAMETERS - Static variable in class net.sf.basedb.plugins.executor.ExternalProgramExecutor
Parameter name for the xml holding the parameter definitions to the external program.
PARAMETER_EXTERNAL_PATH - Static variable in class net.sf.basedb.plugins.executor.ExternalProgramExecutor
Parameter name for the path to the external program.
PARAMETER_FILEFORMAT - Static variable in class net.sf.basedb.plugins.BaseFileExporterPlugin
 
PARAMETER_FILEFORMAT - Static variable in class net.sf.basedb.plugins.BfsExporterPlugin
 
PARAMETER_FILENAMEGENERATOR - Static variable in class net.sf.basedb.plugins.BfsExporterPlugin
 
PARAMETER_IMPORTER_CLASS - Static variable in class net.sf.basedb.plugins.executor.ExternalProgramExecutor
Parameter name for the class that has been selected as the importer.
PARAMETER_NUM_CHANNELS - Static variable in class net.sf.basedb.plugins.executor.ExternalProgramExecutor
Parameter name for the required number of channels.
PARAMETER_RAW_DATA_TYPE - Static variable in class net.sf.basedb.plugins.executor.ExternalProgramExecutor
Parameter name for the required raw data type.
PARAMETER_REGEXP - Static variable in class net.sf.basedb.core.query.Expressions
A parameter name can only contain the characters a-z, A-Z or 0-9.
PARAMETER_SOURCE_BIOASSSAYSET - Static variable in class net.sf.basedb.plugins.executor.ExternalProgramExecutor
Parameter name for the source bioassay set.
PARAMETER_SOURCE_TRANSFORM - Static variable in class net.sf.basedb.plugins.executor.ExternalProgramExecutor
Parameter name for the required intensity transform of the source bioassay set.
parameterDefinition - Variable in class net.sf.basedb.plugins.executor.ProgramParameter
 
ParameterDefinition - Class in net.sf.basedb.plugins.executor
Represents a parameter definition for the external program.
ParameterDefinition() - Constructor for class net.sf.basedb.plugins.executor.ParameterDefinition
Create a new empty parameter definition.
ParameterException - Exception in net.sf.basedb.core
This exception is thrown by classes that uses the parameter system, ParameterType and ParameterValueData.
ParameterException(String) - Constructor for exception net.sf.basedb.core.ParameterException
Creates a new ParameterException.
ParameterExpression - Class in net.sf.basedb.core.query
Parameter expression.
ParameterExpression(String, Object, Type) - Constructor for class net.sf.basedb.core.query.ParameterExpression
 
parameterInfo - Variable in class net.sf.basedb.core.PluginRequest
 
ParameterInfo - Class in net.sf.basedb.core
Get information about a plugin configuration or parameter.
ParameterInfo(DbControl, ParameterValueData<?>) - Constructor for class net.sf.basedb.core.ParameterInfo
 
parameterMap - Variable in class net.sf.basedb.core.RequestInformation
 
parameterName - Variable in class net.sf.basedb.clients.web.plugins.ItemQueryLoader
 
parameterName - Variable in class net.sf.basedb.core.query.AnyToAnyRestriction
 
parameterOrder - Variable in class net.sf.basedb.core.AbstractSqlQuery.CountWork
 
parameters - Variable in class net.sf.basedb.clients.web.extensions.ServletWrapper
 
parameters - Variable in class net.sf.basedb.clients.web.fileupload.FileUpload
Contains information about regular input field parameters name --> value
parameters - Variable in class net.sf.basedb.core.AbstractQuery
Parameters values added to the query.
parameters - Variable in class net.sf.basedb.core.AnnotationSimpleRestriction
 
parameters - Variable in class net.sf.basedb.core.data.JobData
 
parameters - Variable in class net.sf.basedb.core.data.ProtocolData
 
parameters - Variable in class net.sf.basedb.core.ParameterValuesImpl
Preloaded parameter values, if the write protected flag is set.
parameters - Variable in class net.sf.basedb.core.RequestInformation
 
parameters - Variable in class net.sf.basedb.plugins.executor.ExternalProgramExecutor.RequestWrapper
 
parameters - Variable in class net.sf.basedb.util.export.spotdata.BaseFileExporter
 
parameters - Variable in class net.sf.basedb.util.export.spotdata.BfsExporter
 
parameters - Variable in class net.sf.basedb.util.extensions.debug.BeanActionFactory
 
parameters - Variable in class net.sf.basedb.util.extensions.debug.ProxyActionFactory
 
parameters - Variable in class net.sf.basedb.util.QueryParameters
 
parameters - Variable in class net.sf.basedb.util.uri.http.HttpConnectionManager
 
Parameters - Class in net.sf.basedb.plugins.util
Utility class for creating some useful plug-in parameters.
Parameters() - Constructor for class net.sf.basedb.plugins.util.Parameters
 
ParameterType<T> - Class in net.sf.basedb.core
This is the base class for all parameter types.
ParameterType(Type, Class<T>) - Constructor for class net.sf.basedb.core.ParameterType
Creates a parameter type with no default value and allowing null values.
ParameterType(Type, Class<T>, T, boolean) - Constructor for class net.sf.basedb.core.ParameterType
Creates a new parameter type.
ParameterType(Type, Class<T>, T, boolean, int, int, int) - Constructor for class net.sf.basedb.core.ParameterType
 
ParameterType(Type, Class<T>, T, boolean, int, int, int, List<T>) - Constructor for class net.sf.basedb.core.ParameterType
 
ParameterType(Type, Class<T>, T, boolean, int, int, int, Enumeration<T, String>, boolean) - Constructor for class net.sf.basedb.core.ParameterType
 
parameterTypes - Variable in class net.sf.basedb.core.AnnotationBatcher.InsertBatcher
 
parameterTypes - Variable in class net.sf.basedb.core.AnnotationBatcher.UpdateBatcher
 
parameterTypes - Variable in class net.sf.basedb.core.ParameterValuesImpl
 
parameterTypes - Variable in class net.sf.basedb.core.ReporterCloneBatcher
 
ParameterValueData<T> - Class in net.sf.basedb.core.data
The base class for the different types of parameter values.
ParameterValueData() - Constructor for class net.sf.basedb.core.data.ParameterValueData
 
ParameterValueData(T...) - Constructor for class net.sf.basedb.core.data.ParameterValueData
 
ParameterValues - Interface in net.sf.basedb.core.plugin
This interface is used by the plugin to access the different parameters attached to its job and configuration.
ParameterValuesImpl - Class in net.sf.basedb.core
An implementation of the ParameterValues interface that lets a plugin write the job's configuration.
ParameterValuesImpl(Job, boolean) - Constructor for class net.sf.basedb.core.ParameterValuesImpl
 
ParameterValuesImpl(PluginConfiguration, int, boolean) - Constructor for class net.sf.basedb.core.ParameterValuesImpl
 
ParameterValuesImpl(PluginDefinition) - Constructor for class net.sf.basedb.core.ParameterValuesImpl
Empty parameter values
ParameterValuesWrapper - Class in net.sf.basedb.core.plugin
A helper class that will wrap the parameter values from one job, one configuration and one request object.
ParameterValuesWrapper(Request, ParameterValues, ParameterValues, boolean) - Constructor for class net.sf.basedb.core.plugin.ParameterValuesWrapper
 
parameterVersion - Variable in class net.sf.basedb.core.data.JobData
 
parameterVersion - Variable in class net.sf.basedb.core.data.PluginConfigurationData
 
parent - Variable in class net.sf.basedb.clients.web.extensions.renderer.PrefixSuffixRenderer
 
parent - Variable in class net.sf.basedb.clients.web.servlet.PlotServlet.CFResultIterator
 
parent - Variable in class net.sf.basedb.clients.web.servlet.PlotServlet.CFSqlResult
 
parent - Variable in class net.sf.basedb.core.data.DirectoryData
 
parent - Variable in class net.sf.basedb.core.data.MeasuredBioMaterialData
 
parent - Variable in class net.sf.basedb.core.data.WellData
 
parent - Variable in class net.sf.basedb.core.plugin.NamespaceParameterValuesWrapper
 
parent - Variable in class net.sf.basedb.core.plugin.NamespaceRequestWrapper
 
parent - Variable in class net.sf.basedb.core.PluginSessionControl
 
parent - Variable in class net.sf.basedb.core.ProjectSpecificAnnotationsManager.AnnotationInfo
 
parent - Variable in class net.sf.basedb.core.QueryRuntimeFilterFactory.ChildFilter
The item type of the parent item.
parent - Variable in class net.sf.basedb.core.snapshot.DisabledInheritanceFilter
 
parent - Variable in class net.sf.basedb.plugins.BaseFileExporterPlugin.ExtendedDynamicField
 
parent - Variable in class net.sf.basedb.plugins.batchimport.FallbackIdMethod
 
parent - Variable in class net.sf.basedb.plugins.BfsExporterPlugin.ExtendedExportableField
 
parent - Variable in class net.sf.basedb.plugins.executor.ExternalProgramExecutor.RequestWrapper
 
parent - Variable in class net.sf.basedb.util.AutoDetectFileFormat.IsImportableFilter
 
parent - Variable in class net.sf.basedb.util.excel.WrappedFormatter
 
parent - Variable in class net.sf.basedb.util.extensions.manager.filter.InstalledFilter
 
parent - Variable in class net.sf.basedb.util.extensions.manager.filter.ValidAndNewOrModifiedFilter
 
parent - Variable in class net.sf.basedb.util.filter.InverseFilter
 
parent - Variable in class net.sf.basedb.util.formatter.CollectionFormatter
 
parent - Variable in class net.sf.basedb.util.formatter.PrefixSuffixFormatter
 
parent - Variable in class net.sf.basedb.util.importer.spotdata.FirstPassSectionSpotsParser
 
parent - Variable in class net.sf.basedb.util.listable.CollectExtracts.ResetCollected
 
parent - Variable in class net.sf.basedb.util.overview.loader.AutoChildNodeLoader
 
parent - Variable in class net.sf.basedb.util.overview.loader.ExtensionChildNodeLoader
 
parent - Variable in class net.sf.basedb.util.overview.Node
 
parent - Variable in class net.sf.basedb.util.overview.validator.ExtensionNodeValidator
 
parent - Variable in class net.sf.basedb.util.parser.CropStringMapper
 
parent - Variable in class net.sf.basedb.util.parser.NullIfExceptionMapper
 
parent - Variable in class net.sf.basedb.util.PriorityComparator
 
parent - Variable in class net.sf.basedb.util.resources.ResourceBundleWrapper
 
parent - Variable in class net.sf.basedb.util.TransferRateProgressReporter
 
parent - Variable in class net.sf.basedb.util.Tree.Entry
 
PARENT_EXTRACT_MISMATCH - Static variable in class net.sf.basedb.util.overview.Validator
Validator rule that checks if a child a raw- or derived- bioassay has a different extract than the parent bioassay.
PARENT_TO_CHILD - Enum constant in enum class net.sf.basedb.core.SyncFilter.SourceItemTransform
Source items are transformed to child items.
PARENT_TO_CHILD - Static variable in class net.sf.basedb.util.listable.ToBioSourceSourceItemTransformerFactory
 
PARENT_TO_CHILD - Static variable in class net.sf.basedb.util.listable.ToDerivedBioAssaySourceItemTransformerFactory
 
PARENT_TO_CHILD - Static variable in class net.sf.basedb.util.listable.ToExtractSourceItemTransformerFactory
 
PARENT_TO_CHILD - Static variable in class net.sf.basedb.util.listable.ToPhysicalBioAssaySourceItemTransformerFactory
 
PARENT_TO_CHILD - Static variable in class net.sf.basedb.util.listable.ToRawBioAssaySourceItemTransformerFactory
 
PARENT_TO_CHILD - Static variable in class net.sf.basedb.util.listable.ToSampleSourceItemTransformerFactory
 
ParentBioMaterialEventSourceLoader - Class in net.sf.basedb.clients.web.plugins
This is a loader implementation that load information about all source biomaterial for a given child biomaterial.
ParentBioMaterialEventSourceLoader() - Constructor for class net.sf.basedb.clients.web.plugins.ParentBioMaterialEventSourceLoader
 
ParentBioMaterialEventSourceLoaderFromBioAssay - Class in net.sf.basedb.clients.web.plugins
This is a loader implementation that load information about all source biomaterial for a given physical bioassay.
ParentBioMaterialEventSourceLoaderFromBioAssay() - Constructor for class net.sf.basedb.clients.web.plugins.ParentBioMaterialEventSourceLoaderFromBioAssay
 
ParentBioMaterialLoader - Class in net.sf.basedb.clients.web.plugins
This class get data from the parents to a MeasuredBioMaterial
ParentBioMaterialLoader(ItemQuery<? extends BioMaterial>, String) - Constructor for class net.sf.basedb.clients.web.plugins.ParentBioMaterialLoader
 
parentChildColumnMapping - Variable in class net.sf.basedb.util.importer.spotdata.BaseFileInfo
 
parentColumnMapping - Static variable in class net.sf.basedb.plugins.batchimport.DerivedBioAssayImporter
Column mapping parameter for the parent (physical bioassay OR derived bioassay)
parentColumnMapping - Static variable in class net.sf.basedb.plugins.batchimport.SampleImporter
Column mapping parameter for the parent (biosource OR sample)
parentHasNullReporter - Variable in class net.sf.basedb.util.importer.spotdata.BaseFileInfo
 
parentHasZeroReporter - Variable in class net.sf.basedb.util.importer.spotdata.BaseFileInfo
 
parentId - Variable in class net.sf.basedb.core.data.keyring.GroupGroups
 
parentItem - Variable in class net.sf.basedb.clients.web.extensions.fileviewer.FileViewerContext
 
parentItem - Variable in class net.sf.basedb.util.overview.validator.ProtocolParameterValidator
 
parentItemNode - Variable in class net.sf.basedb.util.overview.validator.ProtocolParameterValidator
 
parentMapper - Variable in class net.sf.basedb.plugins.batchimport.DerivedBioAssayImporter
 
parentMapper - Variable in class net.sf.basedb.plugins.batchimport.ExtractImporter
 
parentMapper - Variable in class net.sf.basedb.plugins.batchimport.PhysicalBioAssayImporter
 
parentMapper - Variable in class net.sf.basedb.plugins.batchimport.SampleImporter
 
parentOverride - Variable in class net.sf.basedb.core.ProjectSpecificAnnotationsManager.AnnotationInfo
 
parentReporterPositions - Variable in class net.sf.basedb.util.importer.spotdata.BaseFileInfo
 
parents - Variable in class net.sf.basedb.core.data.BioAssayData
 
parents - Variable in class net.sf.basedb.core.data.DerivedBioAssayData
 
parents - Variable in class net.sf.basedb.core.data.GroupData
 
parents - Variable in class net.sf.basedb.core.data.ItemSubtypeData
 
parents - Variable in class net.sf.basedb.core.data.PlateData
 
parents - Variable in class net.sf.basedb.util.filter.AllOfFilter
 
parents - Variable in class net.sf.basedb.util.filter.NoneOfFilter
 
parents - Variable in class net.sf.basedb.util.filter.OneOfFilter
 
parents - Variable in class net.sf.basedb.util.importer.spotdata.BaseFileInfo.ChildBioAssay
 
parents - Variable in class net.sf.basedb.util.listable.CollectExtracts
 
parentSet - Variable in class net.sf.basedb.core.data.PlateData
 
parentSet - Variable in class net.sf.basedb.core.ProjectSpecificAnnotationsManager.AnnotationInfo
 
parentToChild - Variable in class net.sf.basedb.util.listable.AbstractSourceItemTransformerFactory
 
parentType - Variable in class net.sf.basedb.core.data.MeasuredBioMaterialData
 
parentTypeColumnMapping - Static variable in class net.sf.basedb.plugins.batchimport.DerivedBioAssayImporter
Column mapping parameter for the parent type.
parentTypeColumnMapping - Static variable in class net.sf.basedb.plugins.batchimport.SampleImporter
Column mapping parameter for the parent type.
parentTypeMapper - Variable in class net.sf.basedb.plugins.batchimport.DerivedBioAssayImporter
 
parentTypeMapper - Variable in class net.sf.basedb.plugins.batchimport.ExtractImporter
 
parentTypeMapper - Variable in class net.sf.basedb.plugins.batchimport.SampleImporter
 
parse(InputStream, String) - Method in class net.sf.basedb.util.basefile.BaseFileParser
Parse the given input stream.
parse(DbControl, Metadata, String, String, boolean, Formatter, ExcelFormatter, Formatter<Boolean>, boolean, DataLoader) - Static method in class net.sf.basedb.clients.web.plugins.ExportedProperty
 
parse(Item, String) - Static method in class net.sf.basedb.clients.web.extensions.list.RelatedItemColumn.Specification
 
parse(EventHandler) - Method in class net.sf.basedb.util.bfs.AnnotationParser
Parse the input stream and notify the specified event handler with events.
parse(EventHandler) - Method in class net.sf.basedb.util.bfs.DataParser
Parse the input stream and notify the specified event handler with events.
parse(EventHandler) - Method in class net.sf.basedb.util.bfs.MetadataParser
Parse the input stream and notify the specified event handler with events.
parse(EventHandler) - Method in class net.sf.basedb.util.importer.spotdata.SynchronizedSpotDataParser
Begin parsing and issue events to the given event handler.
parseAllExcelSheets - Variable in class net.sf.basedb.util.parser.FlatFileParser
Flag to indicate if only a single (=false) or all (=true) Excel sheets should be parsed in one go.
parseAnswer(String) - Static method in class net.sf.basedb.util.jobagent.JobAgentConnection
Utility method for parsing a 'typical' answer from a job agent.
parseAttributes(String) - Method in class net.sf.basedb.util.gtf.GtfInputStream
Parse attributes from the given template string.
parseBuildNumber(String) - Static method in class net.sf.basedb.core.Version
Find the first digits in a string and return those as the build number.
parseBytes(String, Long) - Static method in class net.sf.basedb.util.Values
Parses a string containing the number of bytes formatted as the Values.formatBytes(Long) method.
parseDate() - Method in class net.sf.basedb.util.parser.ConstantMapper
 
parseDate(String) - Method in class net.sf.basedb.plugins.batchimport.AbstractItemImporter
parsedBytes - Variable in class net.sf.basedb.util.charset.CharsetDetector
 
parsedCharacters - Variable in class net.sf.basedb.util.parser.FlatFileParser
The total number of parsed characters so far.
parsedDataLines - Variable in class net.sf.basedb.util.parser.FlatFileParser
The number of data lines parsed in the current section so far.
parsedFile - Variable in class net.sf.basedb.util.XmlUtil2.Validator
 
parsedLines - Variable in class net.sf.basedb.util.charset.CharsetDetector
 
parsedLines - Variable in class net.sf.basedb.util.parser.FlatFileParser
The total number of lines parsed so far.
parsedSections - Variable in class net.sf.basedb.util.parser.FlatFileParser
The number of sections parsed so far.
parseException - Variable in class net.sf.basedb.util.parser.ConstantMapper
 
parseHeaders() - Method in class net.sf.basedb.util.parser.FlatFileParser
Start parsing the input stream.
parseInitParameters(String) - Method in class net.sf.basedb.core.signal.SocketSignalReceiver
Parse the initialisation parameters.
parseNumeric() - Method in class net.sf.basedb.util.parser.ConstantMapper
 
parseParameters(String, List<String>) - Method in class net.sf.basedb.core.AbstractSqlQuery
Parse the given SQL and find named parameters.
parseQueryString(String) - Static method in class net.sf.basedb.util.QueryParameters
Parses a string in HTTP query format (key1=value1&key2=value2...) and returns it as a QueryParameters object.
parser - Variable in class net.sf.basedb.core.data.FormulaData
 
parser - Variable in class net.sf.basedb.util.importer.spotdata.BaseFileImporter
 
parser - Variable in class net.sf.basedb.util.importer.spotdata.SynchronizedSpotDataParser.SynchronizedData
 
parser - Variable in class net.sf.basedb.util.parser.ColumnMapper
 
parser - Variable in class net.sf.basedb.util.parser.CompoundMapper
 
parser - Variable in class net.sf.basedb.util.parser.ConstantMapper
 
parser - Variable in class net.sf.basedb.util.parser.JepMapper
 
Parser(int, String) - Constructor for enum class net.sf.basedb.core.Formula.Parser
 
parserIndex - Variable in class net.sf.basedb.util.importer.spotdata.PositionEventHandler
 
parsers - Variable in class net.sf.basedb.util.basefile.BaseFileParser
 
parserSection - Static variable in class net.sf.basedb.plugins.AbstractFlatFileImporter
Section definition for grouping all file parser settings (ie. regular expressions)
parseSection(BaseFileParser, FlatFileParser) - Method in interface net.sf.basedb.util.basefile.BaseFileSectionParser
Parse the current section.
parseSection(BaseFileParser, FlatFileParser) - Method in class net.sf.basedb.util.importer.spotdata.FirstPassSectionSpotsParser
 
parseSection(BaseFileParser, FlatFileParser) - Method in class net.sf.basedb.util.importer.spotdata.SecondPassSectionSpotsParser
 
parseSection(BaseFileParser, FlatFileParser) - Method in class net.sf.basedb.util.importer.spotdata.SectionAssaysParser
 
parseSection(BaseFileParser, FlatFileParser) - Method in class net.sf.basedb.util.importer.spotdata.SectionReporterListParser
 
parseSimpleAnswer(String) - Static method in class net.sf.basedb.util.jobagent.JobAgentConnection
Utility method for parsing a 'typical' answer from a job agent.
parseString(String) - Method in class net.sf.basedb.clients.web.formatter.AutoItemExportFormatter
 
parseString(String) - Method in class net.sf.basedb.clients.web.formatter.AutoLinkFormatter
 
parseString(String) - Method in class net.sf.basedb.clients.web.formatter.ColorFormatter
 
parseString(String) - Method in class net.sf.basedb.clients.web.formatter.DataFileFormatter
Not supported
parseString(String) - Method in class net.sf.basedb.clients.web.formatter.ExtendedPropertyFormatter
 
parseString(String) - Method in class net.sf.basedb.clients.web.formatter.LinkedFileFormatter
 
parseString(String) - Method in class net.sf.basedb.clients.web.formatter.LinkedItemFormatter
 
parseString(String) - Method in class net.sf.basedb.clients.web.formatter.NiceFormatter
 
parseString(String) - Method in class net.sf.basedb.clients.web.formatter.StringFormatter
 
parseString(String) - Method in class net.sf.basedb.clients.web.plugins.BioMaterialEventSourceFormatter
 
parseString(String) - Static method in class net.sf.basedb.core.DateUtil
Parses a string to create a Date without time.
parseString(String) - Method in class net.sf.basedb.core.ExtendedProperty
Parse a string and return an object of the correct type for this property.
parseString(String) - Method in class net.sf.basedb.core.log.ChangeTypeFormatter
 
parseString(String) - Method in enum class net.sf.basedb.core.Type
Parse a string and return a value of the correct type.
parseString(String) - Method in class net.sf.basedb.util.export.spotdata.ExportableFieldFormatter
 
parseString(String) - Method in class net.sf.basedb.util.formatter.BooleanFormatter
 
parseString(String) - Method in class net.sf.basedb.util.formatter.CollectionFormatter
 
parseString(String) - Method in class net.sf.basedb.util.formatter.DateFormatter
 
parseString(String) - Method in class net.sf.basedb.util.formatter.EnumFormatter
 
parseString(String) - Method in class net.sf.basedb.util.formatter.FilePathFormatter
 
parseString(String) - Method in interface net.sf.basedb.util.formatter.Formatter
Parse a string and return a value of the correct type.
parseString(String) - Method in class net.sf.basedb.util.formatter.IdentifiableFormatter
 
parseString(String) - Method in class net.sf.basedb.util.formatter.IntegerFormatter
 
parseString(String) - Method in class net.sf.basedb.util.formatter.ItemTypeFormatter
 
parseString(String) - Method in class net.sf.basedb.util.formatter.LookupFormatter
 
parseString(String) - Method in class net.sf.basedb.util.formatter.MultiFormatter
 
parseString(String) - Method in class net.sf.basedb.util.formatter.NameableFormatter
 
parseString(String) - Method in class net.sf.basedb.util.formatter.NumberFormatFormatter
 
parseString(String) - Method in class net.sf.basedb.util.formatter.NumberFormatter
 
parseString(String) - Method in class net.sf.basedb.util.formatter.PrefixSuffixFormatter
 
parseString(String) - Method in class net.sf.basedb.util.formatter.PropertyFilterFormatter
 
parseString(String) - Method in class net.sf.basedb.util.formatter.ToStringFormatter
 
parseString(String) - Method in class net.sf.basedb.util.formatter.ValueTypeFormatter
 
parseString(String) - Method in class net.sf.basedb.util.formatter.WellCoordinateFormatter
 
parseString(String, NumberFormat, boolean) - Method in class net.sf.basedb.core.ExtendedProperty
Parse a string and return an object of the correct type for this property.
parseString(String, NumberFormat, boolean) - Method in enum class net.sf.basedb.core.Type
Parse a string and return a value of the correct type using a specific number format for numerical values, optionally ignoring unparsable numbers.
parseString(String, Formatter<Date>, boolean) - Method in enum class net.sf.basedb.core.Type
Parse a string and return a value of the correct type using a specific date format for date values, optionally ignoring unparsable dates.
parseStrings(String[]) - Method in enum class net.sf.basedb.core.Type
Parse an array of strings and try to convert them to values of the correct object type.
parseTimestamp(String) - Static method in class net.sf.basedb.core.DateUtil
Parses a string to create a Date including time.
parseToBof() - Method in class net.sf.basedb.util.bfs.AnnotationParser
Parse the header line of the annotations file.
parseToBof() - Method in class net.sf.basedb.util.bfs.DataParser
Initialize parsing of the data file.
parseToBof() - Method in class net.sf.basedb.util.bfs.MetadataParser
Parse the start of the file until the beginning-of-file marker (BFSfile) is found.
parseToBof() - Method in class net.sf.basedb.util.parser.FlatFileParser
Parse the file until the beginning-of-file marker is found.
parseToBytes() - Method in class net.sf.basedb.util.excel.XlsxToCsvUtil.SheetInfo
 
parseToCsv() - Method in class net.sf.basedb.util.excel.XlsxToCsvUtil.SheetInfo
Convert the sheet to a CSV and get an InputStream for reading the data.
parseXml(String, boolean) - Static method in class net.sf.basedb.plugins.executor.ParameterDefinition
Parse an XML document containing parameter definitions.
parsingFailure - Variable in class net.sf.basedb.util.charset.CharsetDetector
 
participants - Variable in class net.sf.basedb.core.data.BioPlateEventData
 
pass - Variable in class net.sf.basedb.util.filter.StaticFilter
 
password - Variable in class net.sf.basedb.clients.jobagent.Agent
 
password - Variable in class net.sf.basedb.core.authentication.LoginRequest
 
password - Variable in class net.sf.basedb.core.data.FileServerData
 
password - Variable in class net.sf.basedb.core.data.UserData
 
password - Variable in class net.sf.basedb.util.ssl.StaticKeyManager
 
password - Variable in class net.sf.basedb.util.uri.ConnectionParameters
 
password - Variable in class net.sf.basedb.util.zip.ZipFilePacker
 
PASSWORD - Static variable in class net.sf.basedb.core.authentication.AuthenticationMethod
This is the regular internal username/password verification authentication method.
PasswordData - Class in net.sf.basedb.core.data
This class holds the password for a user.
PasswordData() - Constructor for class net.sf.basedb.core.data.PasswordData
 
passwordField - Variable in class net.sf.basedb.clients.web.extensions.login.LoginFormBean
 
PasswordLoginFormFactory - Class in net.sf.basedb.clients.web.extensions.login
A version of the default login form that can be installed as an extension.
PasswordLoginFormFactory() - Constructor for class net.sf.basedb.clients.web.extensions.login.PasswordLoginFormFactory
 
PasswordParameterType - Class in net.sf.basedb.core
This class represent a parameter type that is a password (or any other type of masked string).
PasswordParameterType() - Constructor for class net.sf.basedb.core.PasswordParameterType
Create a new password parameter type, setting the max length to 255 and nulls are allowed.
PasswordParameterType(Integer, boolean) - Constructor for class net.sf.basedb.core.PasswordParameterType
Create a new password parameter type.
path - Variable in class net.sf.basedb.clients.web.extensions.list.PropertyPathActionFactory.PropertyPathAction
 
path - Variable in class net.sf.basedb.clients.web.taglib.path.PathElement
The parent Path.
path - Variable in class net.sf.basedb.core.Metadata.CombinedPropertyPath
 
Path - Class in net.sf.basedb.clients.web.taglib.path
This tag defines a navigation path.
Path - Class in net.sf.basedb.core
This class is used represent the path to a Directory or File item.
Path() - Constructor for class net.sf.basedb.clients.web.taglib.path.Path
 
Path(String, String[], String) - Constructor for class net.sf.basedb.core.Path
Create a new Path object.
Path(String, Path.Type) - Constructor for class net.sf.basedb.core.Path
Create a new Path object by parsing the given string.
Path(Path, String) - Constructor for class net.sf.basedb.core.Path
Create a new Path object.
PATH_MATCH - Static variable in class net.sf.basedb.clients.web.extensions.XJspCompiler
Path to JSP must match: /extensions/[jar-file-name]/[jsp-path].xjsp group(1) = JAR name, group(2) = JSP path
PATH_MATCH - Static variable in class net.sf.basedb.clients.web.servlet.ContentSecurityPolicyFilter
 
PATH_MATCH - Static variable in class net.sf.basedb.clients.web.servlet.ExtensionsServlet
Path to servlet must match: /extensions/[jar-file-name]/[servlet-name]/optional/path/info.servlet group(1) = Servlet path; group(2) = JAR name, group(3) = Servlet name group(4) = Path info (not including .servlet)
PATH_MATCH - Static variable in class net.sf.basedb.clients.web.taglib.Head
 
PATH_OR_ID - Static variable in class net.sf.basedb.plugins.batchimport.FileImporter.PathIdMethod
 
Path.Type - Enum Class in net.sf.basedb.core
An enum that describes what type the path is
pathCanBeUsed(String, boolean) - Method in class net.sf.basedb.core.plugin.AbstractExporterPlugin
See if file path already exists and if it's allowed to overwrite it.
pathColumnMapping - Static variable in class net.sf.basedb.plugins.AnnotationFlatFileImporter
 
pathColumnMapping - Static variable in class net.sf.basedb.plugins.batchimport.FileImporter
 
pathComparator - Static variable in class net.sf.basedb.clients.web.servlet.CompileAll
 
pathConverter - Variable in class net.sf.basedb.clients.web.extensions.WebClientRegisterExtensionsProcessor
 
PathConverter - Class in net.sf.basedb.util.extensions.xml
A value converter that can be used on all setter methods that has been annotated with the PathSetter and PathType annotations.
PathConverter() - Constructor for class net.sf.basedb.util.extensions.xml.PathConverter
Create a new empty path converter.
PathConverter(String, String) - Constructor for class net.sf.basedb.util.extensions.xml.PathConverter
Create a new initialised path converter.
PathElement - Class in net.sf.basedb.clients.web.taglib.path
This tag defines an element of a path.
PathElement() - Constructor for class net.sf.basedb.clients.web.taglib.path.PathElement
 
pathIdMethod - Variable in class net.sf.basedb.plugins.batchimport.FileImporter
 
PathIdMethod(String) - Constructor for class net.sf.basedb.plugins.batchimport.FileImporter.PathIdMethod
 
pathInfo - Variable in class net.sf.basedb.clients.web.extensions.RequestWrapper
 
PathLoader - Class in net.sf.basedb.clients.web.plugins
This is a loader implementation that load the path of a file or directory.
PathLoader() - Constructor for class net.sf.basedb.clients.web.plugins.PathLoader
 
pathMapper - Variable in class net.sf.basedb.plugins.batchimport.FileImporter
 
PathParameterType - Class in net.sf.basedb.core
This class represent a parameter type that is a path to either a directory or a file.
PathParameterType(Path.Type) - Constructor for class net.sf.basedb.core.PathParameterType
Create a new optional path parameter type.
PathParameterType(Path.Type, String, boolean) - Constructor for class net.sf.basedb.core.PathParameterType
Create a new path parameter type.
PathParameterType(Path.Type, String, boolean, int, int, int, List<String>) - Constructor for class net.sf.basedb.core.PathParameterType
 
paths - Variable in class net.sf.basedb.plugins.TarFileUnpacker
 
paths - Variable in class net.sf.basedb.util.zip.ZipUnpacker
Cache of directories.
PathSetter - Annotation Interface in net.sf.basedb.util.extensions.xml
Indicates that a factory setter method which takes a string as it's input will have the value scanned by a PathConverter before the setter method is invoked.
pathTitles - Static variable in class net.sf.basedb.clients.web.extensions.list.RelatedItemPropertyColumn
 
pathToDirectory - Variable in class net.sf.basedb.plugins.batchimport.FileImporter
 
pathToTitle(String) - Static method in class net.sf.basedb.clients.web.extensions.list.RelatedItemPropertyColumn
Convert some paths to a more user-friendly title instead.
pathType - Variable in class net.sf.basedb.core.PathParameterType
 
pathType() - Element in annotation interface net.sf.basedb.util.extensions.xml.PathSetter
The type of path that should be generated.
PathType - Enum Class in net.sf.basedb.util.extensions.xml
Specify the type of paths.
PathType() - Constructor for enum class net.sf.basedb.util.extensions.xml.PathType
 
pattern - Variable in class net.sf.basedb.util.extensions.xml.ExtensionPointFilter
 
patterns - Variable in class net.sf.basedb.util.export.spotdata.AdvancedFieldConverter
 
pause() - Method in class net.sf.basedb.clients.jobagent.Agent
Pause the job agent.
pause(String, String, Serializable) - Method in class net.sf.basedb.core.Job
This method is used to indicate that a job has been paused, either by manual interaction or by some other trigger.
PAUSE - Enum constant in enum class net.sf.basedb.core.plugin.Response.Status
 
PAUSE - Static variable in class net.sf.basedb.core.signal.Signal
The PAUSE signal, that requests that the receiver should update the pause whatever it is doing and return control to the system.
pauseAgent() - Method in class net.sf.basedb.clients.jobagent.AgentController
Pause a running job agent by sending a stop request to the agents remote control service.
paused - Variable in class net.sf.basedb.util.jobagent.JobAgentInfo
 
PAUSED - Enum constant in enum class net.sf.basedb.core.Job.Status
The job has been paused.
PauseRequestHandler - Class in net.sf.basedb.clients.jobagent.handlers
This is a request handler for the pause command.
PauseRequestHandler(Agent) - Constructor for class net.sf.basedb.clients.jobagent.handlers.PauseRequestHandler
 
percent - Variable in class net.sf.basedb.core.signal.ProgressReporterSignalHandler
The current percentage status.
percent - Variable in class net.sf.basedb.core.SimpleProgressReporter
 
PERCENT - Static variable in class net.sf.basedb.clients.web.util.HTML
 
percentComplete - Variable in class net.sf.basedb.core.data.JobData
 
performActions(HttpServletRequest) - Method in class net.sf.basedb.clients.web.extensions.ExtensionsControl
Perform the requested actions (install/uninstall) as given in the request form.
PerformanceTimer - Class in net.sf.basedb.util.timer
A simple timer for measuring code performance.
PerformanceTimer(String...) - Constructor for class net.sf.basedb.util.timer.PerformanceTimer
Create a new timer object for measuring one or more times.
performChange(Session) - Method in class net.sf.basedb.core.Update.DropColumnChange
 
performChange(Session) - Method in class net.sf.basedb.core.Update.SchemaChange
 
performExport(ExportOutputStream, ProgressReporter) - Method in class net.sf.basedb.clients.web.plugins.SimpleExport
 
performExport(ExportOutputStream, ProgressReporter) - Method in class net.sf.basedb.core.plugin.AbstractExporterPlugin
Perform the export.
performExport(ExportOutputStream, ProgressReporter) - Method in class net.sf.basedb.plugins.BaseFileExporterPlugin
 
performExport(ExportOutputStream, ProgressReporter) - Method in class net.sf.basedb.plugins.GalExporter
 
performExport(ExportOutputStream, ProgressReporter) - Method in class net.sf.basedb.plugins.HelpExporter
 
performExport(ExportOutputStream, ProgressReporter) - Method in class net.sf.basedb.plugins.PackedFileExporter
 
performExport(ExportOutputStream, ProgressReporter) - Method in class net.sf.basedb.plugins.PlateMappingExporter
 
performExport(ExportOutputStream, ProgressReporter) - Method in class net.sf.basedb.plugins.PluginConfigurationExporter
 
performExport(ProgressReporter) - Method in class net.sf.basedb.plugins.BfsExporterPlugin
 
performIO(DbControl, ProgressReporter) - Method in class net.sf.basedb.plugins.executor.AbstractIOSupport
Perform the IO operation.
performIO(DbControl, ProgressReporter) - Method in class net.sf.basedb.plugins.executor.BaseFileExporterSupport
 
performIO(DbControl, ProgressReporter) - Method in class net.sf.basedb.plugins.executor.BaseFileImporterSupport
 
performIO(DbControl, ProgressReporter) - Method in class net.sf.basedb.plugins.executor.BfsExporterSupport
 
performIO(DbControl, ProgressReporter) - Method in class net.sf.basedb.plugins.executor.BfsImporterSupport
 
performIO(DbControl, ProgressReporter) - Method in class net.sf.basedb.plugins.executor.FileOnlyImporterSupport
 
permanent - Variable in class net.sf.basedb.core.query.QueryParameter
 
permanentGroups - Variable in class net.sf.basedb.core.AbstractQuery
List of permanent group expressions added to the query.
permanentHavings - Variable in class net.sf.basedb.core.AbstractQuery
List of permanent having restrictions added to the query.
permanentJoins - Variable in class net.sf.basedb.core.AbstractQuery
List of permanent joins added to the query.
permanentOrders - Variable in class net.sf.basedb.core.AbstractQuery
List of permanent orders added to the query.
permanentRestrictions - Variable in class net.sf.basedb.core.AbstractQuery
List of permanent restrictions added to the query.
permanentSelects - Variable in class net.sf.basedb.core.AbstractQuery
List of permanent selections added to the query.
permission - Variable in class net.sf.basedb.clients.web.ModeInfo
 
permission - Variable in class net.sf.basedb.core.AbstractEntityQuery
The logged in user's permission on the items.
permission - Variable in class net.sf.basedb.core.data.keyring.KeyPermission
 
permission - Variable in class net.sf.basedb.core.data.keyring.ProjectPermission
 
permission - Variable in class net.sf.basedb.core.ItemContext
 
permission - Variable in class net.sf.basedb.core.query.PermissionRestriction
 
Permission - Enum Class in net.sf.basedb.core
This enumeration defined constants for permissions.
Permission(int, int, String) - Constructor for enum class net.sf.basedb.core.Permission
Constructor for Permission enums.
PermissionButtonFactory - Class in net.sf.basedb.clients.web.extensions.toolbar
A button factory that can hide or disable button items based on the logged in user's permissions.
PermissionButtonFactory() - Constructor for class net.sf.basedb.clients.web.extensions.toolbar.PermissionButtonFactory
Create a new factory instance.
PermissionDeniedException - Exception in net.sf.basedb.core
This exception is thrown when trying to load or manipulate an item in the database and you don't have the required permission.
PermissionDeniedException(String) - Constructor for exception net.sf.basedb.core.PermissionDeniedException
Creates a new PermissionDeniedException.
PermissionDeniedException(String, Throwable) - Constructor for exception net.sf.basedb.core.PermissionDeniedException
Creates a new PermissionDeniedException.
PermissionDeniedException(Permission) - Constructor for exception net.sf.basedb.core.PermissionDeniedException
Creates a new PermissionDeniedException.
PermissionDeniedException(Permission, String) - Constructor for exception net.sf.basedb.core.PermissionDeniedException
Creates a new PermissionDeniedException.
permissionForKey(int, int[][]) - Method in class net.sf.basedb.core.Keyring
Returns the permission value for the specified key or PERMISSION.DENIED if not found in the array of keys.
permissionGroups - Static variable in class net.sf.basedb.clients.web.PermissionUtil
 
PermissionMenuItemFactory - Class in net.sf.basedb.clients.web.extensions.menu
A menu item factory that can hide or disable menu items based on the logged in user's permissions.
PermissionMenuItemFactory() - Constructor for class net.sf.basedb.clients.web.extensions.menu.PermissionMenuItemFactory
Create a new factory instance.
PermissionRestriction - Class in net.sf.basedb.core.query
Restriction that inserts an "impossible" filter requirement (1=0) if the logged in user is lacking a given permission.
PermissionRestriction(Permission, Item) - Constructor for class net.sf.basedb.core.query.PermissionRestriction
 
permissions - Variable in class net.sf.basedb.clients.web.extensions.ExtensionsControl
 
permissions - Variable in class net.sf.basedb.core.BasicBatcher
The logged in user's permission to this item.
permissions - Variable in class net.sf.basedb.core.BasicItem
The logged in user's permission to this item.
permissions - Variable in class net.sf.basedb.core.data.PluginDefinitionData
 
permissions - Static variable in class net.sf.basedb.plugins.AnnotationFlatFileImporter
 
permissions - Static variable in class net.sf.basedb.plugins.Base1PluginExecuter
The plug-in permissions.
permissions - Static variable in class net.sf.basedb.plugins.BaseFileExporterPlugin
 
permissions - Static variable in class net.sf.basedb.plugins.CdfFileReporterImporter
 
permissions - Static variable in class net.sf.basedb.plugins.FormulaFilter
 
permissions - Static variable in class net.sf.basedb.plugins.GalExporter
 
permissions - Static variable in class net.sf.basedb.plugins.HelpExporter
 
permissions - Static variable in class net.sf.basedb.plugins.HelpImporter
 
permissions - Static variable in class net.sf.basedb.plugins.IntensityCalculatorPlugin
 
permissions - Static variable in class net.sf.basedb.plugins.JepExtraValueCalculator
 
permissions - Static variable in class net.sf.basedb.plugins.JepIntensityTransformer
 
permissions - Static variable in class net.sf.basedb.plugins.LowessNormalization
 
permissions - Static variable in class net.sf.basedb.plugins.MedianRatioNormalization
 
permissions - Static variable in class net.sf.basedb.plugins.PackedFileExporter
 
permissions - Static variable in class net.sf.basedb.plugins.PlateFlatFileImporter
 
permissions - Static variable in class net.sf.basedb.plugins.PlateMappingExporter
 
permissions - Static variable in class net.sf.basedb.plugins.PlateMappingImporter
 
permissions - Static variable in class net.sf.basedb.plugins.PluginConfigurationExporter
 
permissions - Static variable in class net.sf.basedb.plugins.PrintMapFlatFileImporter
 
permissions - Static variable in class net.sf.basedb.plugins.RawDataFlatFileImporter
 
permissions - Static variable in class net.sf.basedb.plugins.ReporterFlatFileImporter
 
permissions - Static variable in class net.sf.basedb.plugins.ReporterMapFlatFileImporter
 
permissions - Static variable in class net.sf.basedb.util.zip.AbstractFileUnpacker
 
Permissions - Class in net.sf.basedb.core.plugin
This class holds permissions requested by a plugin.
Permissions(Item, Set<Permission>, Set<Permission>) - Constructor for class net.sf.basedb.core.plugin.Permissions
 
permissionTemplate - Variable in class net.sf.basedb.core.data.ProjectData
 
PermissionTemplate - Class in net.sf.basedb.core
A permission template with permissions to users, groups and projects.
PermissionTemplate(PermissionTemplateData) - Constructor for class net.sf.basedb.core.PermissionTemplate
 
PERMISSIONTEMPLATE - Enum constant in enum class net.sf.basedb.core.Item
The item is a PermissionTemplate.
permissionTemplateColumnMapping - Static variable in class net.sf.basedb.plugins.batchimport.AbstractItemImporter
 
PermissionTemplateData - Class in net.sf.basedb.core.data
A permission template with permissions to users, groups and projects.
PermissionTemplateData() - Constructor for class net.sf.basedb.core.data.PermissionTemplateData
 
permissionTemplateMapper - Variable in class net.sf.basedb.plugins.batchimport.AbstractItemImporter
 
permissionTemplateQuery - Variable in class net.sf.basedb.plugins.batchimport.AbstractItemImporter
 
permissionTimeout - Static variable in class net.sf.basedb.core.Application
Number of minutes permission information can be kept in memory before it must be reloaded.
permissionTimeout() - Static method in class net.sf.basedb.core.Application
Get the maximum number of minutes permission information for a logged in user is kept in memory before beeing reloaded.
PermissionUtil - Class in net.sf.basedb.clients.web
This class is used to collect some useful methods for assigning permissions to roles and shared items.
PermissionUtil() - Constructor for class net.sf.basedb.clients.web.PermissionUtil
 
persist(Object) - Method in class net.sf.basedb.core.hibernate.SessionWrapper
 
persist(String, Object) - Method in class net.sf.basedb.core.hibernate.SessionWrapper
 
phone - Variable in class net.sf.basedb.core.authentication.ExtraUserInformation
 
phone - Variable in class net.sf.basedb.core.data.UserData
 
PHYSICAL_BIOASSAY - Static variable in class net.sf.basedb.core.BioPlateEventType
The system ID for "Hybridization" event type.
PhysicalBioAssay - Class in net.sf.basedb.core
A physical bioassay is a representation of the process of performing an experiment one or more Extract:s.
PhysicalBioAssay(PhysicalBioAssayData) - Constructor for class net.sf.basedb.core.PhysicalBioAssay
 
PHYSICALBIOASSAY - Enum constant in enum class net.sf.basedb.core.Item
The item is a PhysicalBioAssay.
PhysicalBioAssayData - Class in net.sf.basedb.core.data
This class holds information about a physical bioassay (eg. a hybridization or similar).
PhysicalBioAssayData() - Constructor for class net.sf.basedb.core.data.PhysicalBioAssayData
 
PhysicalBioAssayImporter - Class in net.sf.basedb.plugins.batchimport
Plug-in for importing physical bioassays items in a batch.
PhysicalBioAssayImporter() - Constructor for class net.sf.basedb.plugins.batchimport.PhysicalBioAssayImporter
 
PhysicalBioAssayLoader - Class in net.sf.basedb.util.overview.loader
Node loader implementation for physical bioassays.
PhysicalBioAssayLoader() - Constructor for class net.sf.basedb.util.overview.loader.PhysicalBioAssayLoader
 
physicalBioAssayQuery - Variable in class net.sf.basedb.plugins.batchimport.AbstractItemImporter
 
physicalBioAssays - Variable in class net.sf.basedb.core.data.DerivedBioAssayData
 
PhysicalBioAssayToDerivedBioAssayTransformer - Class in net.sf.basedb.util.listable
Source item transformer implementation that transform physical bioassay items to derived bioassays.
PhysicalBioAssayToDerivedBioAssayTransformer() - Constructor for class net.sf.basedb.util.listable.PhysicalBioAssayToDerivedBioAssayTransformer
Create a new physical bioassay to derived bioassay transformer.
PhysicalBioAssayToDerivedBioAssayTransformer(CollectExtracts) - Constructor for class net.sf.basedb.util.listable.PhysicalBioAssayToDerivedBioAssayTransformer
Create a new physical bioassay to derived bioassay transformer using the collected extracts to limit the returned items.
PhysicalBioAssayToExtractTransformer - Class in net.sf.basedb.util.listable
Source item transformer implementation that transform physical bioassay items to extracts.
PhysicalBioAssayToExtractTransformer() - Constructor for class net.sf.basedb.util.listable.PhysicalBioAssayToExtractTransformer
Create a new physical bioassay to extract transformer.
PhysicalBioAssayValidator - Class in net.sf.basedb.util.overview.validator
Validator implementation for physical bioassays.
PhysicalBioAssayValidator() - Constructor for class net.sf.basedb.util.overview.validator.PhysicalBioAssayValidator
 
ping() - Method in class net.sf.basedb.core.Application.Pinger
Ping the SessionControl by updating the last access time: SessionControl.updateLastAccess()
Pinger(SessionControl) - Constructor for class net.sf.basedb.core.Application.Pinger
 
pingers - Static variable in class net.sf.basedb.core.Application
 
pingerTask - Variable in class net.sf.basedb.clients.jobagent.slotmanager.RemoteSlotManager
 
pingRemoteSlots() - Method in class net.sf.basedb.clients.jobagent.slotmanager.RemoteSlotManager
Ping the the remote host with all active slots.
PingRequestHandler - Class in net.sf.basedb.clients.jobagent.handlers
This is a request handler for the ping command.
PingRequestHandler(Agent) - Constructor for class net.sf.basedb.clients.jobagent.handlers.PingRequestHandler
Create a new handler for the ping command.
pip - Variable in class net.sf.basedb.core.File.CharsetTesterThread
 
pkInfo - Variable in class net.sf.basedb.core.dbengine.TableInfo
 
PLACE_ON_PLATE - Static variable in class net.sf.basedb.core.BioPlateEventType
The system ID for "Place-on-plate" event type.
placeHolder - Variable in class net.sf.basedb.clients.web.extensions.login.FieldInfo
 
PlainTextTemplate - Class in net.sf.basedb.clients.web.plugins
A plain text template that exports data in tab-delimited format.
PlainTextTemplate(Writer, List<ExportedProperty>, Item) - Constructor for class net.sf.basedb.clients.web.plugins.PlainTextTemplate
Create a new template.
PlainTextTemplate(Writer, List<ExportedProperty>, Item, String) - Constructor for class net.sf.basedb.clients.web.plugins.PlainTextTemplate
Create a new template.
plate - Variable in class net.sf.basedb.core.data.ArrayDesignPlateData
 
plate - Variable in class net.sf.basedb.core.data.MappingCoordinate
The plate number.
plate - Variable in class net.sf.basedb.core.data.PlateEventData
 
plate - Variable in class net.sf.basedb.core.data.WellData
 
Plate - Class in net.sf.basedb.core
This class is represents physical plates.
Plate(PlateData) - Constructor for class net.sf.basedb.core.Plate
 
PLATE - Enum constant in enum class net.sf.basedb.core.Item
The item is a Plate.
PLATE - Static variable in class net.sf.basedb.core.File
The id for the FileType item representing a plate file.
PLATE_MAPPING - Static variable in class net.sf.basedb.core.File
The id for the FileType item representing a plate mapping file.
PlateCoordinate - Class in net.sf.basedb.core.data
This class defines a plate coordinate, which is row and column on a plate.
PlateCoordinate() - Constructor for class net.sf.basedb.core.data.PlateCoordinate
Create new object.
PlateCoordinate(int, int) - Constructor for class net.sf.basedb.core.data.PlateCoordinate
Create new PlateCoordinate with the specified row and column.
PlateData - Class in net.sf.basedb.core.data
This class holds information about a plate.
PlateData() - Constructor for class net.sf.basedb.core.data.PlateData
 
PlateEvent - Class in net.sf.basedb.core
This class represents an event in the life of a Plate.
PlateEvent(PlateEventData) - Constructor for class net.sf.basedb.core.PlateEvent
 
PLATEEVENT - Enum constant in enum class net.sf.basedb.core.Item
The item is a PlateEvent.
PlateEventData - Class in net.sf.basedb.core.data
This class holds information about a plate event.
PlateEventData() - Constructor for class net.sf.basedb.core.data.PlateEventData
 
PlateEventLogger - Class in net.sf.basedb.core.log.db
Logger for plate events that logs changes as updates to the plate the event belongs to.
PlateEventLogger(DbLogManagerFactory) - Constructor for class net.sf.basedb.core.log.db.PlateEventLogger
Creates a new plate event logger.
plateEvents - Variable in class net.sf.basedb.core.data.PlateEventTypeData
 
plateEventType - Variable in class net.sf.basedb.core.data.PlateEventData
 
PlateEventType - Class in net.sf.basedb.core
This class is used together with the PlateType class to define event types for plates.
PlateEventType(PlateEventTypeData) - Constructor for class net.sf.basedb.core.PlateEventType
 
PLATEEVENTTYPE - Enum constant in enum class net.sf.basedb.core.Item
The item is a PlateEventType.
PlateEventTypeData - Class in net.sf.basedb.core.data
This class holds information about a plate event type.
PlateEventTypeData() - Constructor for class net.sf.basedb.core.data.PlateEventTypeData
 
PlateFlatFileImporter - Class in net.sf.basedb.plugins
 
PlateFlatFileImporter() - Constructor for class net.sf.basedb.plugins.PlateFlatFileImporter
 
plateGeometry - Variable in class net.sf.basedb.core.data.BioPlateData
 
plateGeometry - Variable in class net.sf.basedb.core.data.PlateTypeData
 
PlateGeometry - Class in net.sf.basedb.core
This class defines a plate geometry, which is the number of rows and columns of wells on a Plate.
PlateGeometry(PlateGeometryData) - Constructor for class net.sf.basedb.core.PlateGeometry
 
PLATEGEOMETRY - Enum constant in enum class net.sf.basedb.core.Item
The item is a PlateGeometry.
plateGeometryColumnMapping - Static variable in class net.sf.basedb.plugins.batchimport.BioPlateImporter
 
PlateGeometryData - Class in net.sf.basedb.core.data
This class holds information about a plate geometry.
PlateGeometryData() - Constructor for class net.sf.basedb.core.data.PlateGeometryData
 
plateGeometryMapper - Variable in class net.sf.basedb.plugins.batchimport.BioPlateImporter
 
plateMapping - Variable in class net.sf.basedb.core.data.PlateData
 
PlateMapping - Class in net.sf.basedb.core
This class represents a mapping from one plate geometry to another.
PlateMapping(PlateMappingData) - Constructor for class net.sf.basedb.core.PlateMapping
 
PLATEMAPPING - Enum constant in enum class net.sf.basedb.core.Item
The item is a PlateMapping.
PlateMappingData - Class in net.sf.basedb.core.data
This class holds information about a plate mapping.
PlateMappingData() - Constructor for class net.sf.basedb.core.data.PlateMappingData
 
PlateMappingExporter - Class in net.sf.basedb.plugins
Exporter for plate mappings.
PlateMappingExporter() - Constructor for class net.sf.basedb.plugins.PlateMappingExporter
Create a new importer.
PlateMappingImporter - Class in net.sf.basedb.plugins
Importer for plate mappings.
PlateMappingImporter() - Constructor for class net.sf.basedb.plugins.PlateMappingImporter
Create a new importer.
plateMappingParameter - Variable in class net.sf.basedb.plugins.PlateMappingExporter
 
plateNamePadding - Variable in class net.sf.basedb.plugins.PlateFlatFileImporter
 
plateNamePrefix - Variable in class net.sf.basedb.plugins.PlateFlatFileImporter
 
plateNamePrefixParameter - Variable in class net.sf.basedb.plugins.PlateFlatFileImporter
 
plates - Variable in class net.sf.basedb.core.data.ArrayDesignData
 
plates - Variable in class net.sf.basedb.core.data.PlateTypeData
 
plates - Variable in class net.sf.basedb.plugins.PlateFlatFileImporter
 
plateType - Variable in class net.sf.basedb.core.data.PlateData
 
plateType - Variable in class net.sf.basedb.core.data.PlateEventTypeData
 
plateType - Variable in class net.sf.basedb.plugins.PlateFlatFileImporter
 
PlateType - Class in net.sf.basedb.core
This class represents plate types, which is a name, description, geometry and a list of event types.
PlateType(PlateTypeData) - Constructor for class net.sf.basedb.core.PlateType
 
PLATETYPE - Enum constant in enum class net.sf.basedb.core.Item
The item is a PlateType.
PlateTypeData - Class in net.sf.basedb.core.data
This class holds information about a plate type.
PlateTypeData() - Constructor for class net.sf.basedb.core.data.PlateTypeData
 
plateTypeParameter - Variable in class net.sf.basedb.plugins.PlateFlatFileImporter
 
plateTypes - Variable in class net.sf.basedb.core.data.PlateGeometryData
 
plateTypeType - Variable in class net.sf.basedb.plugins.PlateFlatFileImporter
 
platform - Variable in class net.sf.basedb.core.data.ArrayDesignData
 
platform - Variable in class net.sf.basedb.core.data.PlatformFileTypeData
 
platform - Variable in class net.sf.basedb.core.data.PlatformVariantData
 
platform - Variable in class net.sf.basedb.core.data.RawBioAssayData
 
platform - Variable in class net.sf.basedb.core.RawDataType
 
Platform - Class in net.sf.basedb.core
This class is used to represent an experimental platform in BASE.
Platform(PlatformData) - Constructor for class net.sf.basedb.core.Platform
Creates a new filetype item from the given data.
PLATFORM - Enum constant in enum class net.sf.basedb.core.Item
The item is a Platform
platformColumnMapping - Static variable in class net.sf.basedb.plugins.batchimport.ArrayDesignImporter
 
platformColumnMapping - Static variable in class net.sf.basedb.plugins.batchimport.RawBioAssayImporter
 
PlatformData - Class in net.sf.basedb.core.data
This class hols information about experimental platforms.
PlatformData() - Constructor for class net.sf.basedb.core.data.PlatformData
 
PlatformFileType - Class in net.sf.basedb.core
This class represents a specific DataFileType that is part of a platform.
PlatformFileType(PlatformFileTypeData) - Constructor for class net.sf.basedb.core.PlatformFileType
Creates a new member item from the given data.
PLATFORMFILETYPE - Enum constant in enum class net.sf.basedb.core.Item
The item is a PlatformFileType
PlatformFileTypeData - Class in net.sf.basedb.core.data
This class hols information about which file types are used on which experimental platforms and variants.
PlatformFileTypeData() - Constructor for class net.sf.basedb.core.data.PlatformFileTypeData
 
PlatformFT(DataFileTypeData, boolean, boolean) - Constructor for class net.sf.basedb.core.Install.PlatformFT
 
platformId - Variable in class net.sf.basedb.core.MigrateRbaToDba.LineMapping
 
platformId - Variable in class net.sf.basedb.core.MigrateRbaToDba.Rba
 
PlatformLoader - Class in net.sf.basedb.util.overview.loader
Node loader implementation for platform and platform variant.
PlatformLoader() - Constructor for class net.sf.basedb.util.overview.loader.PlatformLoader
 
platformMapper - Variable in class net.sf.basedb.plugins.batchimport.ArrayDesignImporter
 
platformMapper - Variable in class net.sf.basedb.plugins.batchimport.RawBioAssayImporter
 
platformQuery - Variable in class net.sf.basedb.plugins.batchimport.AbstractItemImporter
 
platforms - Variable in class net.sf.basedb.core.data.DataFileTypeData
 
platformTypes - Static variable in class net.sf.basedb.core.RawDataTypes
 
PlatformValidator - Class in net.sf.basedb.util.overview.validator
Validator implementation for platforms/variants.
PlatformValidator() - Constructor for class net.sf.basedb.util.overview.validator.PlatformValidator
 
PlatformVariant - Class in net.sf.basedb.core
Represents variants of a Platform.
PlatformVariant(PlatformVariantData) - Constructor for class net.sf.basedb.core.PlatformVariant
Creates a new filetype item from the given data.
PLATFORMVARIANT - Enum constant in enum class net.sf.basedb.core.Item
The item is a PlatformVariant
PlatformVariantData - Class in net.sf.basedb.core.data
This class hols information about variants of experimental platforms.
PlatformVariantData() - Constructor for class net.sf.basedb.core.data.PlatformVariantData
 
plot - Variable in class net.sf.basedb.util.plot.HistogramPlot
 
plot - Variable in class net.sf.basedb.util.plot.ScatterPlot
 
PlotAnnotation - Class in net.sf.basedb.util.plot
Used to map spot data into different annotations.
PlotAnnotation(String, int) - Constructor for class net.sf.basedb.util.plot.PlotAnnotation
Create a new PlotAnnotation.
PlotAnnotation(String, Collection<Integer>) - Constructor for class net.sf.basedb.util.plot.PlotAnnotation
Create a new PlotAnnotation.
PlotGenerator - Interface in net.sf.basedb.clients.web.extensions.plot
Contains information about a single image in an overview plot.
PlotGeneratorBean - Class in net.sf.basedb.clients.web.extensions.plot
A simple bean-like implementation of the PlotGenerator interface.
PlotGeneratorBean() - Constructor for class net.sf.basedb.clients.web.extensions.plot.PlotGeneratorBean
 
PlotServlet - Class in net.sf.basedb.clients.web.servlet
This servlet can plot spot data for a bioassay or bioassay set.
PlotServlet() - Constructor for class net.sf.basedb.clients.web.servlet.PlotServlet
 
PlotServlet.CFResultIterator - Class in net.sf.basedb.clients.web.servlet
Special implementation of a SqlResultIterator that combines the result from the parent and child into one virtual iterator.
PlotServlet.CFSqlResult - Class in net.sf.basedb.clients.web.servlet
A single result row that is combined from the parent and child results. 1 --> parent A, 2 --> parent M, 3 --> parent M - child M
plugin - Variable in class net.sf.basedb.core.data.ChangeHistoryData
 
plugin - Variable in class net.sf.basedb.core.ParameterValuesImpl
 
plugin - Variable in class net.sf.basedb.core.PluginRequest
 
plugin - Variable in class net.sf.basedb.util.ContextUtil.ContextResult
 
Plugin - Interface in net.sf.basedb.core.plugin
This interface must be implemented by all plugins to BASE.
Plugin.MainType - Enum Class in net.sf.basedb.core.plugin
 
pluginConfiguration - Variable in class net.sf.basedb.core.data.JobData
 
pluginConfiguration - Variable in class net.sf.basedb.core.PluginRequest
 
PluginConfiguration - Class in net.sf.basedb.core
This class is used to configure a plugin.
PluginConfiguration(PluginConfigurationData) - Constructor for class net.sf.basedb.core.PluginConfiguration
 
PLUGINCONFIGURATION - Enum constant in enum class net.sf.basedb.core.Item
The item is a PluginConfiguration
PluginConfigurationData - Class in net.sf.basedb.core.data
This data class is used to configure a plugin.
PluginConfigurationData() - Constructor for class net.sf.basedb.core.data.PluginConfigurationData
 
PluginConfigurationExporter - Class in net.sf.basedb.plugins
This plugin exports parameters of a pluginconfiguration into an XML-file.
PluginConfigurationExporter() - Constructor for class net.sf.basedb.plugins.PluginConfigurationExporter
 
PluginConfigurationImporter - Class in net.sf.basedb.plugins
This plugin imports pluginconfiguration from an XML-file.
PluginConfigurationImporter() - Constructor for class net.sf.basedb.plugins.PluginConfigurationImporter
 
pluginConfigurationList - Static variable in class net.sf.basedb.plugins.PluginConfigurationImporter
 
PluginConfigurationRequest - Class in net.sf.basedb.core
Configures a plugin or job.
PluginConfigurationRequest(SessionControl, InteractivePlugin, String, PluginConfiguration, ParameterValuesImpl, Job, ParameterValuesImpl, GuiContext, PluginDefinition, boolean) - Constructor for class net.sf.basedb.core.PluginConfigurationRequest
 
pluginDefinition - Variable in class net.sf.basedb.core.data.JobAgentSettingsData
 
pluginDefinition - Variable in class net.sf.basedb.core.data.JobData
 
pluginDefinition - Variable in class net.sf.basedb.core.data.PluginConfigurationData
 
pluginDefinition - Variable in class net.sf.basedb.core.PluginRequest
 
PluginDefinition - Class in net.sf.basedb.core
A plugin definition represents the executable plugin.
PluginDefinition(PluginDefinitionData) - Constructor for class net.sf.basedb.core.PluginDefinition
 
PLUGINDEFINITION - Enum constant in enum class net.sf.basedb.core.Item
The item is a PluginDefinition
PluginDefinitionData - Class in net.sf.basedb.core.data
This class represent an installed plugin.
PluginDefinitionData() - Constructor for class net.sf.basedb.core.data.PluginDefinitionData
 
PluginDefinitionFilter - Class in net.sf.basedb.util.extensions.xml
Filter implementation that only matches tags for plug-in definitions.
PluginDefinitionFilter() - Constructor for class net.sf.basedb.util.extensions.xml.PluginDefinitionFilter
Create a new filter.
pluginDefinitionId - Variable in class net.sf.basedb.core.data.keyring.PluginKeys
 
pluginDefinitions - Variable in class net.sf.basedb.util.extensions.xml.XmlLoader
 
pluginDirectoryParameter - Variable in class net.sf.basedb.plugins.Base1PluginExecuter
The directory where the plug-in will store it's output.
PluginExecutionRequest - Class in net.sf.basedb.core
Executes a job.
PluginExecutionRequest(PluginRequest<? extends Plugin>, String) - Constructor for class net.sf.basedb.core.PluginExecutionRequest
 
PluginExecutionRequest(SessionControl, Plugin, String, PluginConfiguration, ParameterValuesImpl, Job, ParameterValuesImpl, PluginDefinition) - Constructor for class net.sf.basedb.core.PluginExecutionRequest
 
pluginId - Variable in class net.sf.basedb.core.data.ChangeHistoryData
 
pluginId - Variable in class net.sf.basedb.core.Keyring
The running plugin's ID.
pluginId - Variable in class net.sf.basedb.core.log.TransactionDetails
 
pluginId - Variable in class net.sf.basedb.core.SessionControl
 
PluginInfo - Class in net.sf.basedb.util.extensions.xml
Object for holding information about a plug-in definition as it is loaded from the extensions definition file.
PluginInfo(String) - Constructor for class net.sf.basedb.util.extensions.xml.PluginInfo
Create a new information object.
PluginInfoKey - Class in net.sf.basedb.util.extensions.manager
Key implementation used to identify plug-in definitions.
PluginInfoKey(String) - Constructor for class net.sf.basedb.util.extensions.manager.PluginInfoKey
Create a new key for a plug-in with the given class name.
PluginInfoKey(PluginInfo) - Constructor for class net.sf.basedb.util.extensions.manager.PluginInfoKey
Create a new key for an plug-in definition.
PluginInstallationProcessor - Class in net.sf.basedb.util.extensions.manager.processor
File processor implementation that load and install plug-ins.
PluginInstallationProcessor(DbControl, ProcessResults) - Constructor for class net.sf.basedb.util.extensions.manager.processor.PluginInstallationProcessor
Create a new processor.
PluginKeys - Class in net.sf.basedb.core.data.keyring
Class for mapping the PluginKeys table.
PluginKeys() - Constructor for class net.sf.basedb.core.data.keyring.PluginKeys
Create new PluginKeys object
pluginName - Variable in class net.sf.basedb.core.log.TransactionDetails
 
pluginName - Variable in class net.sf.basedb.core.SessionControl
 
PluginParameter<T> - Class in net.sf.basedb.core
Contains information about a single parameter that the plugin needs for a request.
PluginParameter(String, String, String, ParameterType<T>) - Constructor for class net.sf.basedb.core.PluginParameter
Constructor that sets all members except the default value.
PluginParameter(String, String, String, T, ParameterType<T>) - Constructor for class net.sf.basedb.core.PluginParameter
Constructor that sets all members.
PluginPermission - Class in net.sf.basedb.core.data
 
PluginPermission - Class in net.sf.basedb.core
 
PluginPermission() - Constructor for class net.sf.basedb.core.data.PluginPermission
 
PluginPermission(int, int) - Constructor for class net.sf.basedb.core.data.PluginPermission
 
PluginPermission(int, int) - Constructor for class net.sf.basedb.core.PluginPermission
 
pluginPermissions - Variable in class net.sf.basedb.core.Keyring
Two-dimensional array for holding the permission for PluginDefinition:s.
PluginRequest<P extends Plugin> - Class in net.sf.basedb.core
Configures or executes a plugin.
PluginRequest(PluginRequest<? extends P>, String) - Constructor for class net.sf.basedb.core.PluginRequest
 
PluginRequest(SessionControl, P, String, PluginConfiguration, ParameterValuesImpl, Job, ParameterValuesImpl, PluginDefinition) - Constructor for class net.sf.basedb.core.PluginRequest
 
PluginRequest.RequestImpl - Class in net.sf.basedb.core
An implementation of the Request interface that is passed to the plugin.
PluginResponse - Class in net.sf.basedb.core
Get the response from a configuration step or execution of a plugin.
PluginResponse(PluginConfigurationRequest, boolean, boolean, boolean) - Constructor for class net.sf.basedb.core.PluginResponse
 
PluginResponse.ResponseImpl - Class in net.sf.basedb.core
An implementation of the Response interface used by the plugin to return information to the client.
plugins - Variable in class net.sf.basedb.core.data.JobAgentData
 
plugins - Variable in class net.sf.basedb.core.data.PluginTypeData
 
pluginsDir - Variable in class net.sf.basedb.clients.web.extensions.XJspCompiler
 
pluginsDir - Variable in class net.sf.basedb.util.extensions.manager.Settings
 
pluginsDirectory - Static variable in class net.sf.basedb.core.Application
The one and only place where plug-ins can be installed.
PluginSessionControl - Class in net.sf.basedb.core
This is a special session control implementation that is used for executing plugins that prevents them from logging in or out.
PluginSessionControl(String, SessionControl, PluginDefinition, Job) - Constructor for class net.sf.basedb.core.PluginSessionControl
Create a new plugin session control
PluginType - Class in net.sf.basedb.core
 
PluginType(PluginTypeData) - Constructor for class net.sf.basedb.core.PluginType
Creates a plugin type item.
PLUGINTYPE - Enum constant in enum class net.sf.basedb.core.Item
The item is a PluginType
PluginTypeData - Class in net.sf.basedb.core.data
This class represent an interface that a plugin can implement.
PluginTypeData() - Constructor for class net.sf.basedb.core.data.PluginTypeData
 
pluginTypes - Variable in class net.sf.basedb.core.data.PluginDefinitionData
 
pluginVersion - Variable in class net.sf.basedb.core.data.JobData
 
PLUS - Static variable in class net.sf.basedb.clients.web.util.HTML
 
pm - Variable in class net.sf.basedb.plugins.PlateMappingImporter
 
policy - Variable in class net.sf.basedb.clients.web.servlet.ContentSecurityPolicyFilter
 
POOLING - Static variable in class net.sf.basedb.core.Protocol
The ID for the pooling protocol type, for example a protocol used when creating a biomaterial item (Sample or Extract) from a set of other biomaterial items.
pop - Variable in class net.sf.basedb.core.File.CharsetTesterThread
 
port - Variable in class net.sf.basedb.clients.jobagent.Agent
 
port - Variable in class net.sf.basedb.clients.jobagent.AgentController
 
port - Variable in class net.sf.basedb.core.data.JobAgentData
 
port - Variable in class net.sf.basedb.core.signal.SocketSignalReceiver
 
port - Variable in class net.sf.basedb.util.jobagent.JobAgentConnection
 
port - Variable in class net.sf.basedb.util.jobagent.JobAgentServerConnection
 
pos - Variable in class net.sf.basedb.clients.web.ExperimentExplorer.ReporterPositions
 
pos - Variable in class net.sf.basedb.util.parser.ColFunction
 
posBatcher - Variable in class net.sf.basedb.util.importer.spotdata.PositionEventHandler
 
posCache - Variable in class net.sf.basedb.clients.web.ExperimentExplorer
 
posIndex - Variable in class net.sf.basedb.util.importer.spotdata.PositionEventHandler
 
position - Variable in class net.sf.basedb.clients.web.taglib.tab.TabControl
The position of the tabs.
position - Variable in class net.sf.basedb.core.data.ArrayDesignPlateData
 
position - Variable in class net.sf.basedb.core.data.BioMaterialEventSourceData
 
position - Variable in class net.sf.basedb.core.data.BioPlateData
 
position - Variable in class net.sf.basedb.core.data.FeatureData
 
position - Variable in class net.sf.basedb.core.data.RawData
 
position - Variable in class net.sf.basedb.core.RawDataBatcher.FeatureInfo
 
position - Variable in class net.sf.basedb.plugins.Base1PluginExecuter.JobParameter
 
position - Variable in class net.sf.basedb.plugins.LowessNormalization.SpotData
 
position - Variable in class net.sf.basedb.plugins.MedianRatioNormalization.SpotData
 
position - Variable in class net.sf.basedb.util.overview.validator.ExtractValidator.TagPosition
 
POSITION - Enum constant in enum class net.sf.basedb.core.ExtraValue.CoordinateType
The extra values are attached to position coordinates only.
POSITION - Enum constant in enum class net.sf.basedb.core.FeatureIdentificationMethod
Use position number.
POSITION - Enum constant in enum class net.sf.basedb.core.VirtualTable
Table that maps position coordinates in a data cube to reporters.
POSITION - Static variable in class net.sf.basedb.core.VirtualColumn
This column stores the data cube position coordinate.
POSITION_EXTRA_FLOAT - Enum constant in enum class net.sf.basedb.core.VirtualTable
Table that stores float position extra values.
POSITION_EXTRA_INT - Enum constant in enum class net.sf.basedb.core.VirtualTable
Table that stores integer position extra values.
POSITION_EXTRA_STRING - Enum constant in enum class net.sf.basedb.core.VirtualTable
Table that stores string position extra values.
positionBatcher - Variable in class net.sf.basedb.core.DataCube
 
PositionBatcher - Class in net.sf.basedb.core
Batcher class for per-position data in the dynamic database.
PositionBatcher(DbControl, DataCube) - Constructor for class net.sf.basedb.core.PositionBatcher
Create a new position batcher for a data cube.
positionColumnMapping - Static variable in class net.sf.basedb.plugins.batchimport.BioPlateImporter
 
positionColumnMapping - Static variable in class net.sf.basedb.plugins.RawDataFlatFileImporter
 
positionColumnMapping - Static variable in class net.sf.basedb.plugins.ReporterMapFlatFileImporter
 
positionCount - Variable in class net.sf.basedb.util.IncludeExcludeFilter
 
PositionEventHandler - Class in net.sf.basedb.util.importer.spotdata
Event handler implementation intended to be used with a SynchronizedSpotDataParser to extract the position number from the parsed data.
PositionEventHandler(int, int, PositionBatcher, int, int) - Constructor for class net.sf.basedb.util.importer.spotdata.PositionEventHandler
Create a new event handler.
PositionExtraValueBatcher<I> - Class in net.sf.basedb.core
Batcher class for per-position extra values.
PositionExtraValueBatcher(DbControl, ExtraValue) - Constructor for class net.sf.basedb.core.PositionExtraValueBatcher
Create a new spot batcher for a bioassayset.
positionExtraValueBatchers - Variable in class net.sf.basedb.core.BioAssaySet
Cache of already created position extra value batchers.
PositionFunction - Class in net.sf.basedb.util.jep
A JEP function class that adds a pos function to a JEP expression parser.
PositionFunction() - Constructor for class net.sf.basedb.util.jep.PositionFunction
 
positionHandler - Variable in class net.sf.basedb.util.importer.spotdata.MatrixSpotIntensityEventHandler
 
positionHandler - Variable in class net.sf.basedb.util.importer.spotdata.SerialSpotIntensityEventHandler
 
positionIndex - Variable in class net.sf.basedb.clients.web.ExperimentExplorer
The index of the curren position on the view page.
positionIndex - Variable in class net.sf.basedb.util.importer.spotdata.BaseFileInfo.SpotSectionInfo
 
positionMapper - Variable in class net.sf.basedb.plugins.batchimport.BioPlateImporter
 
positionMapper - Variable in class net.sf.basedb.plugins.RawDataFlatFileImporter
 
positionMapper - Variable in class net.sf.basedb.plugins.ReporterMapFlatFileImporter
 
positionSql - Variable in class net.sf.basedb.core.PositionBatcher
The statement that inserts the position/reporter link.
positionSqlStatement - Variable in class net.sf.basedb.core.PositionBatcher
The SQL string for the PositionBatcher.positionSql statement.
postDeniedItem(DbControl, OverviewContext, Node, Node) - Method in class net.sf.basedb.util.overview.validator.BasicNodeValidator
Submits the BasicNodeValidator.ruleDenied validator to the context as a failure unless it is null.
postDeniedItem(DbControl, OverviewContext, Node, Node) - Method in class net.sf.basedb.util.overview.validator.ExtensionNodeValidator
Call the same method on the parent validator and then on all extension validator actions.
postDeniedItem(DbControl, OverviewContext, Node, Node) - Method in interface net.sf.basedb.util.overview.validator.NodeValidator
Validate an item that the current user doen't have access to after a node has been created for it.
postDeniedItem(DbControl, OverviewContext, Node, Node) - Method in class net.sf.basedb.util.overview.validator.NullNodeValidator
Do nothing.
postFlush(Iterator) - Method in class net.sf.basedb.core.log.LoggingInterceptor
Collects all log events and sends them to the each EntityLogger.
PostgresDbEngine - Class in net.sf.basedb.core.dbengine
Database engine for Postgres.
PostgresDbEngine() - Constructor for class net.sf.basedb.core.dbengine.PostgresDbEngine
Create PostgresDbEngine.
PostgresResultWriterFactory - Class in net.sf.basedb.core.migrate.postgres
Result writer factory implementation for formatting result values suitable for importing by a PostgreSQL database.
PostgresResultWriterFactory() - Constructor for class net.sf.basedb.core.migrate.postgres.PostgresResultWriterFactory
 
postMissingItem(DbControl, OverviewContext, Node, Node) - Method in class net.sf.basedb.util.overview.validator.BasicNodeValidator
Do nothing.
postMissingItem(DbControl, OverviewContext, Node, Node) - Method in class net.sf.basedb.util.overview.validator.ExtensionNodeValidator
Call the same method on the parent validator and then on all extension validator actions.
postMissingItem(DbControl, OverviewContext, Node, Node) - Method in interface net.sf.basedb.util.overview.validator.NodeValidator
Validate a missing item after a node has been created for it.
postMissingItem(DbControl, OverviewContext, Node, Node) - Method in class net.sf.basedb.util.overview.validator.NullNodeValidator
Do nothing.
postProcessQuery(String) - Method in class net.sf.basedb.core.AbstractHqlQuery
Processes the query so that joined paths that are found in other parts of the query are replaced with the join alias.
postProcessQuery(String) - Method in class net.sf.basedb.core.AbstractQuery
Allows a subclass to modify the query.
postValidate(DbControl, OverviewContext, Node, Node) - Method in class net.sf.basedb.util.overview.validator.AnnotationValidator
 
postValidate(DbControl, OverviewContext, Node, Node) - Method in class net.sf.basedb.util.overview.validator.AnyToAnyValidator
 
postValidate(DbControl, OverviewContext, Node, Node) - Method in class net.sf.basedb.util.overview.validator.ArrayDesignValidator
 
postValidate(DbControl, OverviewContext, Node, Node) - Method in class net.sf.basedb.util.overview.validator.BasicNodeValidator
Do nothing.
postValidate(DbControl, OverviewContext, Node, Node) - Method in class net.sf.basedb.util.overview.validator.BioPlateValidator
 
postValidate(DbControl, OverviewContext, Node, Node) - Method in class net.sf.basedb.util.overview.validator.BioSourceValidator
 
postValidate(DbControl, OverviewContext, Node, Node) - Method in class net.sf.basedb.util.overview.validator.DataFileValidator
 
postValidate(DbControl, OverviewContext, Node, Node) - Method in class net.sf.basedb.util.overview.validator.DerivedBioAssayValidator
 
postValidate(DbControl, OverviewContext, Node, Node) - Method in class net.sf.basedb.util.overview.validator.ExperimentValidator
 
postValidate(DbControl, OverviewContext, Node, Node) - Method in class net.sf.basedb.util.overview.validator.ExtensionNodeValidator
Call the same method on the parent validator and then on all extension validator actions.
postValidate(DbControl, OverviewContext, Node, Node) - Method in class net.sf.basedb.util.overview.validator.ExtractValidator
 
postValidate(DbControl, OverviewContext, Node, Node) - Method in class net.sf.basedb.util.overview.validator.FileValidator
Checks if the file is of the correct file type.
postValidate(DbControl, OverviewContext, Node, Node) - Method in class net.sf.basedb.util.overview.validator.HardwareValidator
Checks if the hardware is of the correct hardware type and, if a project is active, the hardware is included as a default hardware for the project.
postValidate(DbControl, OverviewContext, Node, Node) - Method in class net.sf.basedb.util.overview.validator.KitValidator
Checks if the hardware is of the correct hardware type and, if a project is active, the hardware is included as a default hardware for the project.
postValidate(DbControl, OverviewContext, Node, Node) - Method in class net.sf.basedb.util.overview.validator.NameableNodeValidator
 
postValidate(DbControl, OverviewContext, Node, Node) - Method in interface net.sf.basedb.util.overview.validator.NodeValidator
Validate an existing item after a node has been created for it.
postValidate(DbControl, OverviewContext, Node, Node) - Method in class net.sf.basedb.util.overview.validator.NullNodeValidator
Do nothing.
postValidate(DbControl, OverviewContext, Node, Node) - Method in class net.sf.basedb.util.overview.validator.PhysicalBioAssayValidator
 
postValidate(DbControl, OverviewContext, Node, Node) - Method in class net.sf.basedb.util.overview.validator.PlatformValidator
Checks if the platform is the same as the default for the project.
postValidate(DbControl, OverviewContext, Node, Node) - Method in class net.sf.basedb.util.overview.validator.ProtocolParameterValidator
 
postValidate(DbControl, OverviewContext, Node, Node) - Method in class net.sf.basedb.util.overview.validator.ProtocolValidator
Checks if the protocol is of the correct protocol type and, if a project is active, the protocol is the same as the default for the project.
postValidate(DbControl, OverviewContext, Node, Node) - Method in class net.sf.basedb.util.overview.validator.RawBioAssayValidator
 
postValidate(DbControl, OverviewContext, Node, Node) - Method in class net.sf.basedb.util.overview.validator.SampleValidator
 
postValidate(DbControl, OverviewContext, Node, Node) - Method in class net.sf.basedb.util.overview.validator.SoftwareValidator
Checks if the software is of the correct software type and, if a project is active, the software is the same as the default for the project.
postValidate(DbControl, OverviewContext, Node, Node) - Method in class net.sf.basedb.util.overview.validator.TagValidator
Checks if the tag is of the correct subtype.
postValidateFolder(DbControl, OverviewContext, Node, Node) - Method in class net.sf.basedb.util.overview.validator.AnnotationValidator
 
postValidateFolder(DbControl, OverviewContext, Node, Node) - Method in class net.sf.basedb.util.overview.validator.BasicNodeValidator
Do nothing.
postValidateFolder(DbControl, OverviewContext, Node, Node) - Method in class net.sf.basedb.util.overview.validator.DataFileValidator
 
postValidateFolder(DbControl, OverviewContext, Node, Node) - Method in class net.sf.basedb.util.overview.validator.ExtensionNodeValidator
Call the same method on the parent validator and then on all extension validator actions.
postValidateFolder(DbControl, OverviewContext, Node, Node) - Method in class net.sf.basedb.util.overview.validator.ExtractValidator
If the parent is a physical bioassay, check that extracts on the same position has different tags.
postValidateFolder(DbControl, OverviewContext, Node, Node) - Method in interface net.sf.basedb.util.overview.validator.NodeValidator
Validate a folder node after all child (item-type) nodes has been added to the folder.
postValidateFolder(DbControl, OverviewContext, Node, Node) - Method in class net.sf.basedb.util.overview.validator.NullNodeValidator
Do nothing.
postValidateFolder(NodeFactory<I>, Node, Node, boolean) - Method in class net.sf.basedb.util.overview.loader.BasicItemNodeLoader
 
postValidateFolder(Node, Node) - Method in class net.sf.basedb.util.overview.node.NodeFactory
 
POTENTIAL - Static variable in class net.sf.basedb.core.Quantity
The id for the Quantity object representing electrical potential.
power(String, String) - Method in class net.sf.basedb.core.dbengine.AbstractDbEngine
Return POWER(<base>, <exponent>).
power(String, String) - Method in interface net.sf.basedb.core.dbengine.DbEngine
Get the function call that calculates base raised to the power of exponent For example: POW(base, value)
power(Expression, Expression) - Static method in class net.sf.basedb.core.query.Expressions
Calculate the first expression raised to the power of the second expression: new expression = e1 ^ e2
POWER - Static variable in class net.sf.basedb.core.Quantity
The id for the Quantity object representing power.
POWER_USER - Static variable in class net.sf.basedb.core.Role
The id for the Role item representing power users.
PowerExpression - Class in net.sf.basedb.core.query
Calculate the power: base ^ exponent
PowerExpression(Expression, Expression) - Constructor for class net.sf.basedb.core.query.PowerExpression
 
precision - Variable in class net.sf.basedb.util.formatter.AdaptiveNumberFormatter
 
PredefinedQuery - Class in net.sf.basedb.core
This class is used for reading XML files with information about predefined queries.
PredefinedQuery() - Constructor for class net.sf.basedb.core.PredefinedQuery
 
preDeniedItem(DbControl, OverviewContext, Node) - Method in class net.sf.basedb.util.overview.validator.BasicNodeValidator
 
preDeniedItem(DbControl, OverviewContext, Node) - Method in class net.sf.basedb.util.overview.validator.ExtensionNodeValidator
Call the same method on the parent validator and then on all extension validator actions.
preDeniedItem(DbControl, OverviewContext, Node) - Method in interface net.sf.basedb.util.overview.validator.NodeValidator
Validate an item that the current user doen't have access to before creating a node for it.
preDeniedItem(DbControl, OverviewContext, Node) - Method in class net.sf.basedb.util.overview.validator.NullNodeValidator
 
preferJob - Variable in class net.sf.basedb.core.plugin.ParameterValuesWrapper
 
prefix - Variable in class net.sf.basedb.clients.web.extensions.fileviewer.FileViewerUtil
 
prefix - Variable in class net.sf.basedb.clients.web.extensions.renderer.PrefixSuffixRenderer
 
prefix - Variable in class net.sf.basedb.clients.web.taglib.table.CellValue
 
prefix - Variable in class net.sf.basedb.core.query.HqlExpression
Prefix used to indentify where to put the root alias.
prefix - Variable in class net.sf.basedb.util.bfs.SequenceFilenameGenerator
 
prefix - Variable in class net.sf.basedb.util.formatter.PrefixSuffixFormatter
 
PrefixSuffixFormatter<T> - Class in net.sf.basedb.util.formatter
Formats a value with optional prefix and suffix.
PrefixSuffixFormatter(String, boolean, Formatter<T>, String, boolean) - Constructor for class net.sf.basedb.util.formatter.PrefixSuffixFormatter
Create a new formatter.
PrefixSuffixFormatter(String, Formatter<T>, String) - Constructor for class net.sf.basedb.util.formatter.PrefixSuffixFormatter
Create a new formatter.
PrefixSuffixRenderer<A extends Action> - Class in net.sf.basedb.clients.web.extensions.renderer
A wrapping renderer for HTML output that can wrap the HTML generated by a parent renderer with a prefix and/or suffix.
PrefixSuffixRenderer(JspContext, String, String) - Constructor for class net.sf.basedb.clients.web.extensions.renderer.PrefixSuffixRenderer
Create a prefix/suffix renderer that has no initial parent.
PrefixSuffixRenderer(JspContext, Renderer<? super A>, String, String) - Constructor for class net.sf.basedb.clients.web.extensions.renderer.PrefixSuffixRenderer
Create a prefix/suffix renderer with an initial parent.
preload(Restriction, Restriction) - Method in class net.sf.basedb.core.AnyToAny.FastLinkLoader
Pre-load links between source and target item type with the given link name and optionally extra restrictions for the any-to-any link and/or the target item type.
preloadAll() - Method in class net.sf.basedb.core.AnyToAny.FastLinkLoader
Pre-load all links between source and target item type with the given link name.
preloaded - Variable in class net.sf.basedb.core.RawDataBatcher
Holds info about the features of an array design.
preloadFeatures() - Method in class net.sf.basedb.core.RawDataBatcher
 
preMissingItem(DbControl, OverviewContext, Node) - Method in class net.sf.basedb.util.overview.validator.ArrayDesignValidator
 
preMissingItem(DbControl, OverviewContext, Node) - Method in class net.sf.basedb.util.overview.validator.BasicNodeValidator
Submits the BasicNodeValidator.ruleMissing validator to the context as a failure unless it is null.
preMissingItem(DbControl, OverviewContext, Node) - Method in class net.sf.basedb.util.overview.validator.DerivedBioAssayValidator
If the parent raw bioassay has a link to an extract, we ignore the missing derived bioassay.
preMissingItem(DbControl, OverviewContext, Node) - Method in class net.sf.basedb.util.overview.validator.ExtensionNodeValidator
Call the same method on the parent validator and then on all extension validator actions.
preMissingItem(DbControl, OverviewContext, Node) - Method in class net.sf.basedb.util.overview.validator.ExtractValidator
Do not report missing items if the parent node is a derived or (root) raw bioassay.
preMissingItem(DbControl, OverviewContext, Node) - Method in class net.sf.basedb.util.overview.validator.FileValidator
If the parent item has a subtype that is related to a FILE subtype, report the missing item as a Validator.MISSING_FILE failure.
preMissingItem(DbControl, OverviewContext, Node) - Method in class net.sf.basedb.util.overview.validator.HardwareValidator
If the parent item has a subtype that is related to a HARDWARE subtype, report the missing item as a Validator.MISSING_HARDWARE failure.
preMissingItem(DbControl, OverviewContext, Node) - Method in class net.sf.basedb.util.overview.validator.KitValidator
If the parent item has a subtype that is related to a KIT subtype, report the missing item as a Validator.MISSING_KIT failure.
preMissingItem(DbControl, OverviewContext, Node) - Method in interface net.sf.basedb.util.overview.validator.NodeValidator
Validate a missing item before creating a node for it.
preMissingItem(DbControl, OverviewContext, Node) - Method in class net.sf.basedb.util.overview.validator.NullNodeValidator
 
preMissingItem(DbControl, OverviewContext, Node) - Method in class net.sf.basedb.util.overview.validator.ProtocolValidator
If the parent item has a subtype that is related to a PROTOCOL subtype, report the missing item as a Validator.MISSING_PROTOCOL failure.
preMissingItem(DbControl, OverviewContext, Node) - Method in class net.sf.basedb.util.overview.validator.SoftwareValidator
If the parent item has a subtype that is related to a SOFTWARE subtype, report the missing item as a Validator.MISSING_SOFTWARE failure.
preMissingItem(DbControl, OverviewContext, Node) - Method in class net.sf.basedb.util.overview.validator.TagValidator
If the parent item has a subtype that is related to a TAG subtype, report the missing item as a Validator.MISSING_TAG failure.
prepare() - Method in class net.sf.basedb.core.hibernate.SchemaGenerator.CollectSqlTarget
 
prepareActionFactory() - Method in class net.sf.basedb.util.extensions.ExtensionContext
 
prepareAssayIndexMap(List<BioAssay>, int, int) - Method in class net.sf.basedb.util.export.spotdata.AbstractBioAssaySetExporter
Prepare a cache that maps the bioassay column (BioAssay.getDataCubeColumnNo()) value to an index in the 'data' array this is generated.
prepareContext(JspContext) - Method in class net.sf.basedb.clients.web.extensions.AbstractJspFactory
Prepare the JSP context by adding all registered script and stylesheet references to it.
prepareContext(InvokationContext<? extends A>) - Method in class net.sf.basedb.clients.web.extensions.AbstractJspRendererFactory
If scripts and stylesheets has been added to the factory, propagates those to the JspContext.
prepareContext(InvokationContext<? extends A>) - Method in interface net.sf.basedb.util.extensions.RendererFactory
This method is called once for each request/use of an extension and should be used by a factory to initialise the context with resources that the actions may need.
prepareContext(InvokationContext<? super A>) - Method in class net.sf.basedb.clients.web.extensions.AbstractJspActionFactory
If scripts and stylesheets has been added to the factory, propagates those to the JspContext.
prepareContext(InvokationContext<? super A>) - Method in interface net.sf.basedb.util.extensions.ActionFactory
This method is called once for each request/use of an extension and have two purposes: The factory should decide if the extension should be enabled or not.
prepareContext(InvokationContext<? super ListColumnAction<Annotatable, Object>>) - Method in class net.sf.basedb.clients.web.extensions.list.RelatedItemColumnActionFactory
We get the "columns" setting from the current ItemContext and check if there seems to be an entry for a related item.
prepareContext(InvokationContext<? super ListColumnAction<BasicItem, Object>>) - Method in class net.sf.basedb.clients.web.extensions.list.AnyLinkColumnActionFactory
We get the "columns" setting from the current ItemContext and check if there seems to be an entry for a related item.
prepareContext(InvokationContext<? super MenuItemAction>) - Method in class net.sf.basedb.clients.web.extensions.menu.PermissionMenuItemFactory
 
prepareContext(InvokationContext<? super OverviewPlotAction>) - Method in class net.sf.basedb.clients.web.extensions.plot.MAPlotFactory
Checks if the bioassay set has 2-channel data in the database.
prepareContext(InvokationContext<? super ServiceControllerAction>) - Method in class net.sf.basedb.clients.web.extensions.service.DummyService
 
prepareContext(InvokationContext<? super LogManagerFactory>) - Method in class net.sf.basedb.core.log.db.DbLogManagerFactory
 
prepareContext(InvokationContext<? super CdfValidationAction>) - Method in class net.sf.basedb.util.affymetrix.CdfValidationFactory
 
prepareContext(InvokationContext<? super CelValidationAction>) - Method in class net.sf.basedb.util.affymetrix.CelValidationFactory
 
prepareContext(InvokationContext<? super Action>) - Method in class net.sf.basedb.util.extensions.debug.BeanActionFactory
 
prepareContext(InvokationContext<? super Action>) - Method in class net.sf.basedb.util.extensions.debug.ProxyActionFactory
 
prepareContext(InvokationContext<? super GtfValidationAction>) - Method in class net.sf.basedb.util.gtf.GtfValidationFactory
 
prepareContext(InvokationContext<? super ValidationRuleAction>) - Method in class net.sf.basedb.util.overview.extensions.ReflectValidationRuleActionFactory
 
prepareContext(InvokationContext<? super ConnectionManagerFactory>) - Method in class net.sf.basedb.util.uri.http.HttpConnectionManagerActionFactory
 
PREPARED - Enum constant in enum class net.sf.basedb.core.Job.Status
The job is beeing prepared for execution.
prepareForCheck(InputStream) - Static method in class net.sf.basedb.util.excel.XlsxToCsvUtil
Prepare the input stream for checking with XlsxToCsvUtil.isAnExcelFile(InputStream).
prepareQuery(DbControl, ItemQuery<I>) - Method in class net.sf.basedb.plugins.batchimport.AnnotationIdMethod
Adds a restriction to the query: property = :identifier
prepareQuery(DbControl, ItemQuery<I>) - Method in class net.sf.basedb.plugins.batchimport.FallbackIdMethod
Adds a restriction to the query: property = :identifier
prepareQuery(DbControl, ItemQuery<I>) - Method in class net.sf.basedb.plugins.batchimport.FileImporter.PathIdMethod
 
prepareQuery(DbControl, ItemQuery<I>) - Method in interface net.sf.basedb.plugins.batchimport.IdMethod
Initialise a query to be used by this identification method.
prepareQuery(DbControl, ItemQuery<I>) - Method in class net.sf.basedb.plugins.batchimport.InternalIdMethod
Adds a restriction to the query: id = :identifier
prepareQuery(DbControl, ItemQuery<I>) - Method in class net.sf.basedb.plugins.batchimport.MultiPropertyIdMethod
Adds a restriction to the query: property[0] = :identifier OR property[1] = :identifier ....
prepareQuery(DbControl, ItemQuery<I>) - Method in class net.sf.basedb.plugins.batchimport.PropertyIdMethod
Adds a restriction to the query: property = :identifier
prepareRendererFactory() - Method in class net.sf.basedb.util.extensions.ExtensionContext
 
prepareRendererFactory() - Method in class net.sf.basedb.util.extensions.ExtensionPointContext
 
prepareRendererFactory() - Method in class net.sf.basedb.util.extensions.InvokationContext
Prepare the renderer factory if the extension or extension point has one.
Preset() - Constructor for class net.sf.basedb.core.Presets.Preset
 
Preset(String) - Constructor for class net.sf.basedb.core.Presets.Preset
 
Preset(Element) - Constructor for class net.sf.basedb.core.Presets.Preset
Load preset name and key-value pairs from XML Document.
presets - Variable in class net.sf.basedb.core.Presets
 
presets - Variable in class net.sf.basedb.util.extensions.manager.Settings
 
Presets - Class in net.sf.basedb.core
This is a generic class for handling named presets consisting of multiple key/value pairs.
Presets() - Constructor for class net.sf.basedb.core.Presets
Create a new empty presets object.
Presets.Preset - Class in net.sf.basedb.core
Represents a single preset.
PresetSelector - Class in net.sf.basedb.clients.web.taglib.table
Special tag for generating a list of saved contexts and other settings.
PresetSelector() - Constructor for class net.sf.basedb.clients.web.taglib.table.PresetSelector
 
presetsSetting - Static variable in class net.sf.basedb.util.overview.OverviewUtil
Name of setting to store saved presets.
PRESSURE - Static variable in class net.sf.basedb.core.Quantity
The id for the Quantity object representing pressure.
preValidate(DbControl, OverviewContext, I, Node) - Method in class net.sf.basedb.util.overview.validator.BasicNodeValidator
Subclasses should override this method if the need more validation for an existing and accessible item.
preValidate(DbControl, OverviewContext, I, Node) - Method in class net.sf.basedb.util.overview.validator.ExtensionNodeValidator
Call the same method on the parent validator and then on all extension validator actions.
preValidate(DbControl, OverviewContext, I, Node) - Method in interface net.sf.basedb.util.overview.validator.NodeValidator
Validate an existing item before creating a node for it.
preValidate(DbControl, OverviewContext, I, Node) - Method in class net.sf.basedb.util.overview.validator.NullNodeValidator
 
previous() - Method in class net.sf.basedb.core.ItemResultList.ResultListListIterator
 
previousIndex() - Method in class net.sf.basedb.core.ItemResultList.ResultListListIterator
 
previousState - Variable in class net.sf.basedb.core.log.EntityDetails
 
primary - Variable in class net.sf.basedb.core.ItemContext.PropertyFilterPair
 
PRIMARY - Enum constant in enum class net.sf.basedb.core.Annotation.Source
The annotation is a primary annotation.
PRIMARY - Enum constant in enum class net.sf.basedb.core.Location
The item is stored in primary storage.
PRIMARY_KEY - Static variable in class net.sf.basedb.core.VirtualColumn
Used in constructor to tell that the column is part of the primary key.
primaryCreated(int, int, int, int) - Method in class net.sf.basedb.core.ProjectSpecificAnnotationsManager
A PRIMARY annotation has been created in this transaction.
primaryKey - Variable in class net.sf.basedb.core.VirtualColumn
If the column should be part of the primary key or not.
PrimaryKeyInfo(String, Set<String>) - Constructor for class net.sf.basedb.core.dbengine.TableInfo.PrimaryKeyInfo
Create a new PrimaryKeyInfo object.
print(boolean) - Method in class net.sf.basedb.util.excel.XlsxTableWriter
 
print(char) - Method in class net.sf.basedb.util.excel.XlsxTableWriter
 
print(char[]) - Method in class net.sf.basedb.util.excel.XlsxTableWriter
 
print(double) - Method in class net.sf.basedb.util.excel.XlsxTableWriter
 
print(float) - Method in class net.sf.basedb.util.excel.XlsxTableWriter
 
print(int) - Method in class net.sf.basedb.util.excel.XlsxTableWriter
 
print(long) - Method in class net.sf.basedb.util.excel.XlsxTableWriter
 
print(Writer) - Method in class net.sf.basedb.util.bfs.MetadataModel
Utility method for printing the contents of this model object to a stream.
print(Object) - Method in class net.sf.basedb.util.excel.XlsxTableWriter
 
print(String) - Method in class net.sf.basedb.util.excel.XlsxTableWriter
 
PRINT_MAP - Static variable in class net.sf.basedb.core.File
The id for the FileType item representing a print map file.
PRINT_ROBOT - Static variable in class net.sf.basedb.core.Hardware
The id for the HardwareType object representing a print robot.
printHelp() - Static method in class net.sf.basedb.clients.jobagent.AgentController
 
PRINTING - Static variable in class net.sf.basedb.core.Protocol
The ID for the printing protocol type, for example a protocol used when printing a batch of array slides using a print robot.
println() - Method in class net.sf.basedb.util.excel.XlsxTableWriter
 
println(boolean) - Method in class net.sf.basedb.util.excel.XlsxTableWriter
 
println(char) - Method in class net.sf.basedb.util.excel.XlsxTableWriter
 
println(char[]) - Method in class net.sf.basedb.util.excel.XlsxTableWriter
 
println(double) - Method in class net.sf.basedb.util.excel.XlsxTableWriter
 
println(float) - Method in class net.sf.basedb.util.excel.XlsxTableWriter
 
println(int) - Method in class net.sf.basedb.util.excel.XlsxTableWriter
 
println(long) - Method in class net.sf.basedb.util.excel.XlsxTableWriter
 
println(Object) - Method in class net.sf.basedb.util.excel.XlsxTableWriter
 
println(String) - Method in class net.sf.basedb.util.excel.XlsxTableWriter
 
PrintMapFlatFileImporter - Class in net.sf.basedb.plugins
A plugin that imports an ArrayDesign from a printmap.
PrintMapFlatFileImporter() - Constructor for class net.sf.basedb.plugins.PrintMapFlatFileImporter
 
PrintMapFlatFileImporter.FormatType - Enum Class in net.sf.basedb.plugins
 
PrintMapFlatFileImporter.MetaBlock - Class in net.sf.basedb.plugins
 
PrintMapFlatFileImporter.Section - Enum Class in net.sf.basedb.plugins
 
printMapMember - Variable in class net.sf.basedb.plugins.PrintMapFlatFileImporter
 
printRobot - Variable in class net.sf.basedb.core.data.ArrayBatchData
 
printUsage() - Static method in class net.sf.basedb.clients.jobagent.AgentController
 
priorities - Variable in class net.sf.basedb.clients.jobagent.Agent
The thread priority to use when executing jobs in each slot.
priorities - Variable in class net.sf.basedb.core.InternalJobQueue
The thread priority to use when executing jobs in each slot.
priority - Variable in class net.sf.basedb.core.data.JobData
 
priority - Variable in class net.sf.basedb.util.PriorityComparator
 
priorityBoost - Variable in class net.sf.basedb.core.data.JobAgentSettingsData
 
PriorityComparator<T> - Class in net.sf.basedb.util
A comparator implemenation that sorts a given set of objects before all other object.
PriorityComparator(Collection<T>, Comparator<? super T>) - Constructor for class net.sf.basedb.util.PriorityComparator
Create a new comparator.
PriorityComparator(SortedSet<T>) - Constructor for class net.sf.basedb.util.PriorityComparator
Create a new comparator using the same sort order as the given sorted set.
process(Annotatable) - Method in class net.sf.basedb.util.annotations.InheritAnnotationsManager
Process the given item, inheriting and/or removing annotations as specified by the rules.
processFile(ExtensionsManager, ExtensionsFile.WriteableExtensionsFile) - Method in class net.sf.basedb.clients.web.extensions.InstalledFileProcessor
 
processFile(ExtensionsManager, ExtensionsFile.WriteableExtensionsFile) - Method in class net.sf.basedb.clients.web.extensions.LoadServletsProcessor
 
processFile(ExtensionsManager, ExtensionsFile.WriteableExtensionsFile) - Method in class net.sf.basedb.clients.web.extensions.UninstalledFileProcessor
 
processFile(ExtensionsManager, ExtensionsFile.WriteableExtensionsFile) - Method in class net.sf.basedb.clients.web.extensions.WebClientRegisterExtensionsProcessor
 
processFile(ExtensionsManager, ExtensionsFile.WriteableExtensionsFile) - Method in interface net.sf.basedb.util.extensions.manager.ExtensionsFileProcessor
Called by the extensions manager for each extensions file that it manages.
processFile(ExtensionsManager, ExtensionsFile.WriteableExtensionsFile) - Method in class net.sf.basedb.util.extensions.manager.processor.DeleteResourcesProcessor
 
processFile(ExtensionsManager, ExtensionsFile.WriteableExtensionsFile) - Method in class net.sf.basedb.util.extensions.manager.processor.DisablePluginsProcessor
 
processFile(ExtensionsManager, ExtensionsFile.WriteableExtensionsFile) - Method in class net.sf.basedb.util.extensions.manager.processor.ExtractResourcesProcessor
 
processFile(ExtensionsManager, ExtensionsFile.WriteableExtensionsFile) - Method in class net.sf.basedb.util.extensions.manager.processor.IgnoreFileProcessor
 
processFile(ExtensionsManager, ExtensionsFile.WriteableExtensionsFile) - Method in class net.sf.basedb.util.extensions.manager.processor.MarkAsProcessedProcessor
 
processFile(ExtensionsManager, ExtensionsFile.WriteableExtensionsFile) - Method in class net.sf.basedb.util.extensions.manager.processor.PluginInstallationProcessor
 
processFile(ExtensionsManager, ExtensionsFile.WriteableExtensionsFile) - Method in class net.sf.basedb.util.extensions.manager.processor.RegisterExtensionsProcessor
 
processFile(ExtensionsManager, ExtensionsFile.WriteableExtensionsFile) - Method in class net.sf.basedb.util.extensions.manager.processor.ResetProcessor
 
processFile(ExtensionsManager, ExtensionsFile.WriteableExtensionsFile) - Method in class net.sf.basedb.util.extensions.manager.processor.UnregisterExtensionsProcessor
 
processFiles(ExtensionsFileProcessor) - Method in class net.sf.basedb.util.extensions.manager.ExtensionsManager
Process all know file with the given processer.
processFiles(ExtensionsFileProcessor, Filter<ExtensionsFile>) - Method in class net.sf.basedb.util.extensions.manager.ExtensionsManager
Process all known extension files with the given processor.
ProcessJobExecutor - Class in net.sf.basedb.clients.jobagent.executors
This is a job executor which starts a new process for each job to be executed.
ProcessJobExecutor() - Constructor for class net.sf.basedb.clients.jobagent.executors.ProcessJobExecutor
 
ProcessJobExecutor.StreamRedirector - Class in net.sf.basedb.clients.jobagent.executors
Used for redirecting standard output to a string.
ProcessResults - Class in net.sf.basedb.util.extensions.manager
Class for collecting results from a scan for new/deleted/updated extensions.
ProcessResults() - Constructor for class net.sf.basedb.util.extensions.manager.ProcessResults
Create a new process results object.
ProcessResults(ProcessResults) - Constructor for class net.sf.basedb.util.extensions.manager.ProcessResults
Create a new process results object, keeping information about previous results.
ProcessResults.FileResults - Class in net.sf.basedb.util.extensions.manager
Scan results for a single XML or JAR file.
processSignalMessage(String) - Method in class net.sf.basedb.clients.jobagent.AgentSignalReceiver
Make this method public so SignalRequestHandler can call it.
processSignalMessage(String) - Method in class net.sf.basedb.core.signal.AbstractSignalReceiver
Process a signal message.
processSignalMessage(String) - Method in class net.sf.basedb.core.signal.SocketSignalReceiver
Process the incoming message.
products - Variable in class net.sf.basedb.core.data.TransformationData
 
ProgramParameter - Class in net.sf.basedb.plugins.executor
A program parameter definition and it's values for a specific job.
ProgramParameter() - Constructor for class net.sf.basedb.plugins.executor.ProgramParameter
Create a new parameter object.
progress - Variable in class net.sf.basedb.clients.web.fileupload.FileUpload
Progress information for the upload
progress - Variable in class net.sf.basedb.core.hibernate.SchemaGenerator
 
progress - Variable in class net.sf.basedb.core.MigrateRbaToDba
 
progress - Variable in class net.sf.basedb.core.Migration
 
progress - Variable in class net.sf.basedb.core.Migration.ProgressInputStream
 
progress - Variable in class net.sf.basedb.core.PluginConfigurationRequest
 
progress - Variable in class net.sf.basedb.core.PluginExecutionRequest
 
progress - Variable in class net.sf.basedb.core.SimpleProgressReporter
 
progress - Variable in class net.sf.basedb.plugins.AnnotationFlatFileImporter
 
progress - Variable in class net.sf.basedb.util.annotations.RunnableInheritAnnotationsManager
 
progress - Variable in class net.sf.basedb.util.basefile.BaseFileParser
 
progress - Variable in class net.sf.basedb.util.export.spotdata.AbstractBioAssaySetExporter
 
progress - Variable in class net.sf.basedb.util.export.spotdata.MatrixBaseFileExporter
 
progress - Variable in class net.sf.basedb.util.importer.spotdata.BaseFileImporter
 
progress - Variable in class net.sf.basedb.util.importer.spotdata.BfsImporter
 
progress - Variable in class net.sf.basedb.util.importer.spotdata.BfsImporter.ProgressEventHandler
 
progress - Variable in class net.sf.basedb.util.ProgressInputStream
 
progressDatabase - Variable in class net.sf.basedb.plugins.AnnotationFlatFileImporter
 
ProgressEventHandler(ProgressReporter, long) - Constructor for class net.sf.basedb.util.importer.spotdata.BfsImporter.ProgressEventHandler
 
ProgressInputStream - Class in net.sf.basedb.util
Input stream wrapper that calls a progress reporter at regular intervals.
ProgressInputStream(InputStream, AbsoluteProgressReporter) - Constructor for class net.sf.basedb.util.ProgressInputStream
Create a new input stream using the default 1MB interval.
ProgressInputStream(InputStream, AbsoluteProgressReporter, long) - Constructor for class net.sf.basedb.util.ProgressInputStream
Create a new input stream using the specified interval.
ProgressInputStream(InputStream, ProgressReporter) - Constructor for class net.sf.basedb.core.Migration.ProgressInputStream
 
progressParser - Variable in class net.sf.basedb.plugins.AnnotationFlatFileImporter
 
progressReport(String) - Method in class net.sf.basedb.util.ProgressInputStream
Send a progress report with the given message.
ProgressReporter - Interface in net.sf.basedb.core
Certain methods in BASE can report their progress back to the calling client application if they are giving an object that implements this interface.
ProgressReporterImpl(Job, String, String, JobAgent, ProgressReporter) - Constructor for class net.sf.basedb.core.Job.ProgressReporterImpl
 
ProgressReporterSignalHandler - Class in net.sf.basedb.core.signal
An implementation of a signal handler that uses a ProgressReporter to communicate signals back to the target.
ProgressReporterSignalHandler(Collection<Signal>) - Constructor for class net.sf.basedb.core.signal.ProgressReporterSignalHandler
Create a new progress reporter signal handler that supports the specified signals.
progressReportInterval - Variable in class net.sf.basedb.util.importer.spotdata.FirstPassSectionSpotsParser
 
progressReportInterval - Variable in class net.sf.basedb.util.importer.spotdata.SecondPassSectionSpotsParser
 
progressReportInterval - Variable in class net.sf.basedb.util.importer.spotdata.SectionReporterListParser
 
project - Variable in class net.sf.basedb.core.data.ChangeHistoryData
 
project - Variable in class net.sf.basedb.core.ProjectSpecificAnnotationsManager.AnnotationInfo
 
project - Variable in class net.sf.basedb.util.overview.GenericOverview
 
project - Variable in class net.sf.basedb.util.parser.DefaultItemFunction
 
Project - Class in net.sf.basedb.core
This class is used to represent projects.
Project(ProjectData) - Constructor for class net.sf.basedb.core.Project
 
PROJECT - Enum constant in enum class net.sf.basedb.core.Item
The item is a Project.
Project.QueryRuntimeFilterImpl - Class in net.sf.basedb.core
A runtime filter implementation that limits a query to only return projects where the logged in user is a member or owner unless the logged in user has generic read permission.
projectAnnotations - Variable in class net.sf.basedb.core.data.AnnotationTypeData
 
ProjectComparator(DbControl, boolean) - Constructor for class net.sf.basedb.core.snapshot.AnnotationSnapshot.ProjectComparator
 
ProjectData - Class in net.sf.basedb.core.data
This class holds information about a project.
ProjectData() - Constructor for class net.sf.basedb.core.data.ProjectData
 
projectDefaults - Variable in class net.sf.basedb.core.data.ProjectData
 
ProjectFilter - Class in net.sf.basedb.core.snapshot
Filter implementation that finds all annotation snapshots for a given set of projects.
ProjectFilter(Collection<Integer>) - Constructor for class net.sf.basedb.core.snapshot.ProjectFilter
Create a filter that matches the given projects ID values.
ProjectFilter(Collection<Project>, boolean) - Constructor for class net.sf.basedb.core.snapshot.ProjectFilter
Create a filter that matches the given projects and optionally default values.
ProjectFilter(DbControl) - Constructor for class net.sf.basedb.core.snapshot.ProjectFilter
Create a filter that matches all projects that the current user has access to including the default values.
projectId - Variable in class net.sf.basedb.core.AnnotationBatcher.CurrentAnnotationInfo
 
projectId - Variable in class net.sf.basedb.core.AnnotationBatcher
 
projectId - Variable in class net.sf.basedb.core.data.AnnotationData
 
projectId - Variable in class net.sf.basedb.core.data.annotations.AnnotationLink
 
projectId - Variable in class net.sf.basedb.core.data.ChangeHistoryData
 
projectId - Variable in class net.sf.basedb.core.data.keyring.ProjectKeys
 
projectId - Variable in class net.sf.basedb.core.data.keyring.ProjectPermission
 
projectId - Variable in class net.sf.basedb.core.FastAnnotationLoader.FastAnnotation
The ID of the project if the value is a project-specific annotation, or 0 if this is a default annotation.
projectId - Variable in class net.sf.basedb.core.FastAnnotationLoader
 
projectId - Variable in class net.sf.basedb.core.Keyring
The active project's ID.
projectId - Variable in class net.sf.basedb.core.log.TransactionDetails
 
projectId - Variable in class net.sf.basedb.core.snapshot.AnnotationSnapshot
 
projectId - Variable in class net.sf.basedb.core.snapshot.SnapshotManager
 
projectKey - Variable in class net.sf.basedb.core.data.SharedData
 
ProjectKey - Class in net.sf.basedb.core
This class is used to get information about which projects a Shareable item has been shared to.
ProjectKey(ProjectKeyData) - Constructor for class net.sf.basedb.core.ProjectKey
 
PROJECTKEY - Enum constant in enum class net.sf.basedb.core.Item
The item is a ProjectKey.
ProjectKeyData - Class in net.sf.basedb.core.data
This class holds information access privileges for projects.
ProjectKeyData() - Constructor for class net.sf.basedb.core.data.ProjectKeyData
 
projectKeyId - Variable in class net.sf.basedb.core.MigrateRbaToDba.Rba
 
projectKeyId - Variable in class net.sf.basedb.core.SessionControl.LoginInfo
The id of the ProjectKeyData object that new items should be shared to.
projectKeys - Variable in class net.sf.basedb.core.data.ProjectData
 
projectKeys - Variable in class net.sf.basedb.core.Keyring
A set holding all project keys, which is needed for efficient listing of shared items.
ProjectKeys - Class in net.sf.basedb.core.data.keyring
Class for mapping the ProjectKeys table.
ProjectKeys() - Constructor for class net.sf.basedb.core.data.keyring.ProjectKeys
Create a new ProjectKeys object.
projectKeySet - Variable in class net.sf.basedb.core.SharedItem
 
projectName - Variable in class net.sf.basedb.core.log.TransactionDetails
 
projectNames - Variable in class net.sf.basedb.core.log.TransactionDetails
 
ProjectPermission - Class in net.sf.basedb.core.data.keyring
Class for holding a project id and a permission value.
ProjectPermission() - Constructor for class net.sf.basedb.core.data.keyring.ProjectPermission
Create a new ProjectPermission object.
projectPermissions - Variable in class net.sf.basedb.core.Keyring
Two-dimensional array for holding the permissions for ProjectKey:s.
projectPermissions - Variable in class net.sf.basedb.core.MultiPermissions
 
projectPermissions - Variable in class net.sf.basedb.core.ProjectPermissions
 
ProjectPermissions - Class in net.sf.basedb.core
This class is used to specify permissions to share an item to projects.
ProjectPermissions() - Constructor for class net.sf.basedb.core.ProjectPermissions
Create a new empty object.
ProjectPermissions(ProjectKey) - Constructor for class net.sf.basedb.core.ProjectPermissions
Create a new object, and initialise it with the permissions from a ProjectKey.
projects - Variable in class net.sf.basedb.core.data.GroupData
 
projects - Variable in class net.sf.basedb.core.data.PermissionTemplateData
 
projects - Variable in class net.sf.basedb.core.data.ProjectKeyData
 
projects - Variable in class net.sf.basedb.core.data.UserData
 
projects - Variable in class net.sf.basedb.core.Keyring
Holds the ID and permission of all projects that the user is a member of, directly or via a group.
projects - Variable in class net.sf.basedb.core.query.SharedToRestriction
 
projects - Variable in class net.sf.basedb.core.snapshot.ProjectFilter
 
projectSpecific - Variable in class net.sf.basedb.clients.web.util.ProjectSpecificInfoFilter
 
ProjectSpecificAnnotationsManager - Class in net.sf.basedb.core
Internal class for keeping the "override_id" column in the "Annotations" table synchronized when annotations are creted and deleted.
ProjectSpecificAnnotationsManager(Session) - Constructor for class net.sf.basedb.core.ProjectSpecificAnnotationsManager
 
ProjectSpecificAnnotationsManager.AnnotationInfo - Class in net.sf.basedb.core
Holds some information about the annotation that has been created.
ProjectSpecificAnnotationsRestriction(int) - Constructor for class net.sf.basedb.core.AnnotationSet.ProjectSpecificAnnotationsRestriction
 
ProjectSpecificInfoFilter - Class in net.sf.basedb.clients.web.util
Helper class for finding out information about about annotation snapshots returned by AnnotationLoaderUtil.findAll(net.sf.basedb.core.snapshot.AnnotationSetSnapshot, Filter) method.
ProjectSpecificInfoFilter() - Constructor for class net.sf.basedb.clients.web.util.ProjectSpecificInfoFilter
 
prompt - Variable in class net.sf.basedb.clients.web.extensions.login.FieldInfo
 
properties - Variable in class net.sf.basedb.clients.jobagent.Agent
 
properties - Variable in class net.sf.basedb.clients.jobagent.AgentController
 
properties - Variable in class net.sf.basedb.clients.web.plugins.PlainTextTemplate
 
properties - Variable in class net.sf.basedb.clients.web.plugins.XlsxTemplate
 
properties - Variable in class net.sf.basedb.clients.web.plugins.XMLTemplate
 
properties - Variable in class net.sf.basedb.core.data.ReporterCloneTemplateData
 
properties - Variable in class net.sf.basedb.core.log.EntityDetails
 
properties - Variable in class net.sf.basedb.core.RawDataType
 
properties - Variable in class net.sf.basedb.plugins.batchimport.MultiPropertyIdMethod
 
properties - Variable in class net.sf.basedb.util.extensions.xml.PluginInfo
 
property - Variable in class net.sf.basedb.clients.web.extensions.list.AbstractListColumnBean
 
property - Variable in class net.sf.basedb.clients.web.extensions.list.AnyLinkColumn
 
property - Variable in class net.sf.basedb.clients.web.extensions.list.PropertyPathActionFactory
 
property - Variable in class net.sf.basedb.clients.web.extensions.list.RelatedItemColumn.Specification
 
property - Variable in class net.sf.basedb.clients.web.extensions.list.RelatedItemPropertyColumn
 
property - Variable in class net.sf.basedb.clients.web.taglib.PropertyValue
The name of the property.
property - Variable in class net.sf.basedb.clients.web.taglib.table.ColumnDef
The name of the property on the item class.
property - Variable in class net.sf.basedb.clients.web.taglib.table.TableColumn
 
property - Variable in class net.sf.basedb.core.ExtendedPropertyAccessor.GetterSetter
 
property - Variable in class net.sf.basedb.core.MeanRawDataPropertyExpression
 
property - Variable in class net.sf.basedb.core.Metadata.EntityPropertyPath
 
property - Variable in class net.sf.basedb.core.PropertyFilter
 
property - Variable in class net.sf.basedb.core.query.HqlElementsExpression
 
property - Variable in class net.sf.basedb.core.query.HqlIndexExpression
 
property - Variable in class net.sf.basedb.core.query.HqlInnerJoin
 
property - Variable in class net.sf.basedb.core.query.HqlLeftJoin
 
property - Variable in class net.sf.basedb.core.query.HqlPropertyExpression
 
property - Variable in class net.sf.basedb.core.query.HqlRightJoin
 
property - Variable in class net.sf.basedb.core.query.HqlSizeExpression
 
property - Variable in class net.sf.basedb.core.query.ReporterListExpression
 
property - Variable in class net.sf.basedb.core.RawBioAssayPropertyExpression
 
property - Variable in class net.sf.basedb.core.RawDataPropertyExpression
 
property - Variable in class net.sf.basedb.core.ReporterPropertyExpression
 
property - Variable in class net.sf.basedb.plugins.batchimport.PropertyIdMethod
 
property - Variable in class net.sf.basedb.util.export.spotdata.AssayPropertyField
 
property(String) - Static method in class net.sf.basedb.core.query.Hql
Same as property(null, property).
property(String, String) - Static method in class net.sf.basedb.core.query.Hql
Create an expression representing a property of an object or joined alias.
property(String, String, Expression) - Static method in class net.sf.basedb.core.query.Hql
Create an expression representing the value of an indexed property.
PROPERTY - Enum constant in enum class net.sf.basedb.util.overview.node.ChildNodeDirection
Only property child nodes should be loaded.
PROPERTY_REGEXP - Static variable in class net.sf.basedb.core.query.Hql
A property can only contain the characters a-zA-Z0-9, period(.), underscore(_) or hash (#) It cannot begin or end with a period/hash and cannot have two periods/hashes in a sequence.
propertyDeleteOrders - Static variable in class net.sf.basedb.core.BatchUtil
Mapping classes/entity names to property update orders.
PropertyFilter - Class in net.sf.basedb.clients.web.taglib.table
Special tag for outputting the filter HTML that a ColumnDef has registered with the Table object.
PropertyFilter - Class in net.sf.basedb.core
Used to store filter settings in the current context.
PropertyFilter() - Constructor for class net.sf.basedb.clients.web.taglib.table.PropertyFilter
 
PropertyFilter(String) - Constructor for class net.sf.basedb.core.PropertyFilter
Create a new filter for a property on filter row 0.
PropertyFilter(String, int) - Constructor for class net.sf.basedb.core.PropertyFilter
Create a new filter for a property.
PropertyFilter(String, int, PropertyFilterData) - Constructor for class net.sf.basedb.core.PropertyFilter
Create a new filter from a loaded database object.
PropertyFilter(String, Operator, String, Type) - Constructor for class net.sf.basedb.core.PropertyFilter
Create a new filter for a property.
PropertyFilter(String, Operator, String, Type, boolean) - Constructor for class net.sf.basedb.core.PropertyFilter
Create a new filter for a property.
PropertyFilterData - Class in net.sf.basedb.core.data
This class holds context information to help client applications with storing common settings for tables.
PropertyFilterData() - Constructor for class net.sf.basedb.core.data.PropertyFilterData
 
PropertyFilterFormatter - Class in net.sf.basedb.util.formatter
Formatter for PropertyFilter items.
PropertyFilterFormatter(DbControl, Formatter<Date>) - Constructor for class net.sf.basedb.util.formatter.PropertyFilterFormatter
Create a new formatter.
PropertyFilterFormatter(DbControl, Formatter<Date>, boolean) - Constructor for class net.sf.basedb.util.formatter.PropertyFilterFormatter
Create a new formatter with option to create HTML-like tags around elements.
PropertyFilterPair() - Constructor for class net.sf.basedb.core.ItemContext.PropertyFilterPair
 
propertyFilters - Variable in class net.sf.basedb.core.data.ContextData
 
propertyFilters - Variable in class net.sf.basedb.core.data.ItemListSyncFilterData
 
propertyFilters - Variable in class net.sf.basedb.core.ItemContext
 
PropertyIdMethod - Class in net.sf.basedb.plugins.batchimport
Identification method implementation that can use a single property (eg, name, id, externalId, etc.) for identifying items.
PropertyIdMethod(String, String, String, String, boolean, Type) - Constructor for class net.sf.basedb.plugins.batchimport.PropertyIdMethod
Create a new id method.
propertyInsertOrders - Static variable in class net.sf.basedb.core.BatchUtil
Mapping classes/entity names to property insert orders.
propertyInspector - Variable in class net.sf.basedb.core.ItemContext
 
propertyPath - Variable in class net.sf.basedb.clients.web.plugins.AnyToAnyDataLoader
 
propertyPath - Variable in class net.sf.basedb.clients.web.plugins.ExportedProperty
 
propertyPath - Variable in class net.sf.basedb.clients.web.plugins.FileSetMemberLoader
 
propertyPath - Variable in class net.sf.basedb.clients.web.plugins.MapValueLoader
 
propertyPath - Variable in class net.sf.basedb.util.export.spotdata.AssayPropertyField
 
PropertyPathAction(Metadata.PropertyPath<I, V>, Metadata.PropertyPath<I, ?>) - Constructor for class net.sf.basedb.clients.web.extensions.list.PropertyPathActionFactory.PropertyPathAction
 
PropertyPathActionFactory<I,V> - Class in net.sf.basedb.clients.web.extensions.list
A factory implementation that generates list columns based on a property path as used by the Metadata class.
PropertyPathActionFactory() - Constructor for class net.sf.basedb.clients.web.extensions.list.PropertyPathActionFactory
 
PropertyPathActionFactory.PropertyPathAction<I,V> - Class in net.sf.basedb.clients.web.extensions.list
A concrete implementation of the ListColumnAction interface.
PropertyPathProtected - Annotation Interface in net.sf.basedb.core.data
Getter methods that are annotated with this annotation should can not use Metadata.getPropertyPath to retreive their values.
propertyPathProtectedProperties - Variable in class net.sf.basedb.core.log.EntityLogOptions
 
propertyToColumn - Static variable in class net.sf.basedb.core.RawBioAssayPropertyExpression
 
propertyToColumn - Static variable in class net.sf.basedb.core.ReporterPropertyExpression
 
propertyToColumnCache - Static variable in class net.sf.basedb.core.RawDataPropertyExpression
 
propertyUpdateOrders - Static variable in class net.sf.basedb.core.BatchUtil
Mapping classes/entity names to property delete orders.
PropertyValue - Class in net.sf.basedb.clients.web.taglib
This tag is used to display the property of a BasicItem.
PropertyValue() - Constructor for class net.sf.basedb.clients.web.taglib.PropertyValue
 
protocol - Variable in class net.sf.basedb.core.data.ArrayBatchData
 
protocol - Variable in class net.sf.basedb.core.data.BioMaterialEventData
 
protocol - Variable in class net.sf.basedb.core.data.BioPlateEventData
 
protocol - Variable in class net.sf.basedb.core.data.DerivedBioAssayData
 
protocol - Variable in class net.sf.basedb.core.data.PlateEventData
 
protocol - Variable in class net.sf.basedb.core.data.RawBioAssayData
 
protocol - Variable in class net.sf.basedb.plugins.IlluminaRawDataImporter
 
Protocol - Class in net.sf.basedb.core
This class is used to represent individual protocol items and information about them.
Protocol(ProtocolData) - Constructor for class net.sf.basedb.core.Protocol
Creates a new protocol item.
PROTOCOL - Enum constant in enum class net.sf.basedb.core.Item
The item is a Protocol.
PROTOCOL - Static variable in class net.sf.basedb.core.File
The id for the FileType item representing a protocol.
protocolColumnMapping - Static variable in class net.sf.basedb.plugins.batchimport.AbstractItemImporter
 
ProtocolData - Class in net.sf.basedb.core.data
 
ProtocolData() - Constructor for class net.sf.basedb.core.data.ProtocolData
 
protocolHasBeenSet - Variable in class net.sf.basedb.core.ArrayBatch
 
protocolHasBeenSet - Variable in class net.sf.basedb.core.BioMaterialEvent
 
protocolHasBeenSet - Variable in class net.sf.basedb.core.DerivedBioAssay
 
protocolHasBeenSet - Variable in class net.sf.basedb.core.RawBioAssay
 
protocolId - Variable in class net.sf.basedb.core.MigrateRbaToDba.Rba
 
ProtocolLoader - Class in net.sf.basedb.util.overview.loader
Node loader implementation for protocols.
ProtocolLoader() - Constructor for class net.sf.basedb.util.overview.loader.ProtocolLoader
 
protocolMapper - Variable in class net.sf.basedb.plugins.batchimport.ArrayBatchImporter
 
protocolMapper - Variable in class net.sf.basedb.plugins.batchimport.DerivedBioAssayImporter
 
protocolMapper - Variable in class net.sf.basedb.plugins.batchimport.ExtractImporter
 
protocolMapper - Variable in class net.sf.basedb.plugins.batchimport.PhysicalBioAssayImporter
 
protocolMapper - Variable in class net.sf.basedb.plugins.batchimport.RawBioAssayImporter
 
protocolMapper - Variable in class net.sf.basedb.plugins.batchimport.SampleImporter
 
protocolParameterColumnMapping - Static variable in class net.sf.basedb.plugins.batchimport.AnnotationTypeImporter
Column mapping parameter for "Protocol parameter" flag.
ProtocolParameterLoader - Class in net.sf.basedb.util.overview.loader
Node loader implementation for protocol parameters.
ProtocolParameterLoader() - Constructor for class net.sf.basedb.util.overview.loader.ProtocolParameterLoader
 
protocolParameterMapper - Variable in class net.sf.basedb.plugins.batchimport.AnnotationTypeImporter
 
ProtocolParameterValidator - Class in net.sf.basedb.util.overview.validator
Validator implementation for protocol parameters.
ProtocolParameterValidator() - Constructor for class net.sf.basedb.util.overview.validator.ProtocolParameterValidator
 
protocolQuery - Variable in class net.sf.basedb.plugins.batchimport.AbstractItemImporter
 
protocols - Variable in class net.sf.basedb.core.data.AnnotationTypeData
 
protocolType - Variable in class net.sf.basedb.core.data.PlateEventTypeData
 
ProtocolValidator - Class in net.sf.basedb.util.overview.validator
Validator implementation for protocols.
ProtocolValidator() - Constructor for class net.sf.basedb.util.overview.validator.ProtocolValidator
 
proxy - Variable in class net.sf.basedb.core.signal.SocketSignalReceiver
 
proxy - Variable in class net.sf.basedb.core.Trashcan.CircularRefInfo
 
proxy - Variable in class net.sf.basedb.util.extensions.debug.ProxyActionFactory
 
ProxyActionFactory - Class in net.sf.basedb.util.extensions.debug
Generic action factory class that can generate instances of actions if the action class is an interface.
ProxyActionFactory() - Constructor for class net.sf.basedb.util.extensions.debug.ProxyActionFactory
Creates a new proxy factory.
proxyLoaders - Variable in class net.sf.basedb.util.JarClassLoader
Class loaders for extensions.
ps - Variable in class net.sf.basedb.core.QueryExecutor.FutureResultSet
 
ps - Variable in class net.sf.basedb.core.QueryExecutor.FutureUpdate
 
pspManager - Variable in class net.sf.basedb.core.DbControl
 
publication - Variable in class net.sf.basedb.core.data.ExperimentData
 
publicationDate - Variable in class net.sf.basedb.core.data.ExperimentData
 
pubMedId - Variable in class net.sf.basedb.core.data.ExperimentData
 
pushAnnotations - Variable in class net.sf.basedb.core.data.ItemSubtypeData
 
pushOnly - Variable in class net.sf.basedb.util.listable.ExtractToChildExtractTransformer
 
pushOnly - Variable in class net.sf.basedb.util.listable.ExtractToParentExtractTransformer
 
pushOnly - Variable in class net.sf.basedb.util.listable.ExtractToSampleTransformer
 
pushOnly - Variable in class net.sf.basedb.util.listable.SampleToBioSourceTransformer
 
pushOnly - Variable in class net.sf.basedb.util.listable.SampleToChildSampleTransformer
 
pushOnly - Variable in class net.sf.basedb.util.listable.SampleToParentSampleTransformer
 
PushToParentsTransformer - Class in net.sf.basedb.util.listable
Transformer implementation that can be used to to find parent items to children that have a subtype with the "push annotations to parent" flag set.
PushToParentsTransformer(Item) - Constructor for class net.sf.basedb.util.listable.PushToParentsTransformer
 
put(AnnotationUtil.AnnotatableWrapper, Set<AnnotationUtil.AnnotatableWrapper>) - Method in class net.sf.basedb.util.AnnotationUtil.Cache
 
put(T, String) - Method in class net.sf.basedb.util.formatter.LookupFormatter
Add a lookup key/value pair.
putAll(Map<? extends T, ? extends String>) - Method in class net.sf.basedb.util.formatter.LookupFormatter
Copy multiple lookup key/value pairs from a map
putAll(Enumeration<? extends T, ? extends String>) - Method in class net.sf.basedb.util.formatter.LookupFormatter
Copy multiple lookup key/value pairs from an enumeration.
putNextEntry(TarEntry, TarOutputStream) - Static method in class net.sf.basedb.util.zip.TarUtil
Put the next entry to a TAR stream.
putNode(K, Node) - Method in class net.sf.basedb.util.overview.cache.NodeCache
 

Q

QUADRATIC_MEAN - Enum constant in enum class net.sf.basedb.core.Formula.AverageMethod
 
quadraticMean(Expression) - Static method in class net.sf.basedb.core.query.Aggregations
Calculates the quadratic mean, also called Root Mean Square, for an expression: new expression = sqrt(AVG(e*e))
QuadraticMeanExpression - Class in net.sf.basedb.core.query
Calculates the quadratic mean of an expression
QuadraticMeanExpression(Expression) - Constructor for class net.sf.basedb.core.query.QuadraticMeanExpression
 
quantity - Variable in class net.sf.basedb.core.data.AnnotationTypeData
 
quantity - Variable in class net.sf.basedb.core.data.UnitData
 
quantity - Variable in class net.sf.basedb.core.data.UnitSymbolData
 
Quantity - Class in net.sf.basedb.core
This class is used to represent a quantity for specifying units to annotations.
Quantity(QuantityData) - Constructor for class net.sf.basedb.core.Quantity
Creates a quantity item.
QUANTITY - Enum constant in enum class net.sf.basedb.core.Item
The item is a Quantity.
QuantityData - Class in net.sf.basedb.core.data
This class holds information quantities.
QuantityData() - Constructor for class net.sf.basedb.core.data.QuantityData
 
quantityId - Variable in class net.sf.basedb.util.units.UnitCache.CacheKey
 
queries - Variable in class net.sf.basedb.util.query.MultiQueryIterator
 
query - Variable in class net.sf.basedb.clients.web.plugins.DataQueryWrapper
 
query - Variable in class net.sf.basedb.clients.web.plugins.DynamicQueryWrapper
 
query - Variable in class net.sf.basedb.clients.web.plugins.ItemQueryLoader
 
query - Variable in class net.sf.basedb.clients.web.plugins.ItemQueryWrapper
 
query - Variable in class net.sf.basedb.clients.web.plugins.ParentBioMaterialEventSourceLoader
 
query - Variable in class net.sf.basedb.clients.web.plugins.ParentBioMaterialEventSourceLoaderFromBioAssay
 
query - Variable in class net.sf.basedb.clients.web.plugins.PathLoader
 
query - Variable in class net.sf.basedb.clients.web.plugins.ReporterScoreQueryWrapper
 
query - Variable in class net.sf.basedb.core.hibernate.NativeQueryWrapper
 
query - Variable in class net.sf.basedb.core.hibernate.QueryWrapper
 
query - Variable in class net.sf.basedb.core.ItemContext
 
query - Variable in class net.sf.basedb.core.QueryExecutor.FutureItem
 
query - Variable in class net.sf.basedb.core.QueryExecutor.FutureScrollIterator
 
query - Variable in class net.sf.basedb.util.listable.RestrictionTransformer
 
query - Variable in class net.sf.basedb.util.units.UnitCache
 
Query - Interface in net.sf.basedb.core.query
This defines the simplest form of a relational query.
QueryElement - Interface in net.sf.basedb.core.query
A query element is used in various places in a Query to build the structure of the query.
QueryExecutor - Class in net.sf.basedb.core
Utility class for executing SQL and Hibernate queries.
QueryExecutor() - Constructor for class net.sf.basedb.core.QueryExecutor
 
QueryExecutor.Cancelable - Interface in net.sf.basedb.core
Interface to be implemented by classes that knows how to cancel a query.
QueryExecutor.CancelableSession - Class in net.sf.basedb.core
Cancels the query running in a Hibernate session.
QueryExecutor.CancelableStatelessSession - Class in net.sf.basedb.core
Cancels a query running in a stateless Hibernate session.
QueryExecutor.CancelableStatement - Class in net.sf.basedb.core
Cancels a statement by calling Statement.cancel().
QueryExecutor.FutureItem<T> - Class in net.sf.basedb.core
 
QueryExecutor.FutureResultSet - Class in net.sf.basedb.core
A callable implementation the calls PreparedStatement.executeQuery()
QueryExecutor.FutureScrollIterator<T> - Class in net.sf.basedb.core
Calls Query.scroll(ScrollMode) and returns the result as a ScrollIterator.
QueryExecutor.FutureUpdate - Class in net.sf.basedb.core
A callable implementation the calls PreparedStatement.executeUpdate()
queryFile - Static variable in class net.sf.basedb.core.Application
The path to the file containing predefined queries.
QueryFilterAction - Interface in net.sf.basedb.core.query
Actions for creating restrictions on queries.
QueryParameter - Class in net.sf.basedb.core.query
Holds information (name, type and value) about a single parameter to a query.
QueryParameter(String) - Constructor for class net.sf.basedb.core.query.QueryParameter
Create a new empty non-permanent query parameter.
QueryParameter(String, boolean, Type, Object) - Constructor for class net.sf.basedb.core.query.QueryParameter
Create a new query parameter.
QueryParameters - Class in net.sf.basedb.util
Utiltity class for parsing string values in the form of HTTP request query parameters:
QueryParameters(String) - Constructor for class net.sf.basedb.util.QueryParameters
 
QueryRestrictions() - Constructor for class net.sf.basedb.core.ItemContext.QueryRestrictions
 
QueryResult - Interface in net.sf.basedb.core.query
This is the root interface for query results.
QueryRuntimeFilter - Interface in net.sf.basedb.core
Represents a filter that is applied to a query just before it is executed in order to limit the result.
QueryRuntimeFilterFactory - Class in net.sf.basedb.core
This is a factory class for QueryRuntimeFilter implementations.
QueryRuntimeFilterFactory() - Constructor for class net.sf.basedb.core.QueryRuntimeFilterFactory
 
QueryRuntimeFilterFactory.AnnotatableFilter - Class in net.sf.basedb.core
A required filter for Annotatable items.
QueryRuntimeFilterFactory.BasicFilter - Class in net.sf.basedb.core
An optional default filter for BasicItem:s that are not Ownable or Shareable.
QueryRuntimeFilterFactory.ChainedFilter - Class in net.sf.basedb.core
Chains one or more filters into a single filter.
QueryRuntimeFilterFactory.ChildFilter - Class in net.sf.basedb.core
An optional filter that can be used by BasicItem:s to replace the QueryRuntimeFilterFactory.BasicFilter.
QueryRuntimeFilterFactory.DenyAllFilter - Class in net.sf.basedb.core
A required filter for all items, which checks if the logged in user has been "granted" the Permission.DENIED permission for a specific item type.
QueryRuntimeFilterFactory.OwnableFilter - Class in net.sf.basedb.core
An optional default filter for Ownable items that are not Shareable.
QueryRuntimeFilterFactory.RemovableFilter - Class in net.sf.basedb.core
A required filter for Removable items.
QueryRuntimeFilterFactory.ShareableFilter - Class in net.sf.basedb.core
An optional default filter for Shareable items.
QueryRuntimeFilterImpl() - Constructor for class net.sf.basedb.core.Annotation.QueryRuntimeFilterImpl
 
QueryRuntimeFilterImpl() - Constructor for class net.sf.basedb.core.AnnotationSet.QueryRuntimeFilterImpl
 
QueryRuntimeFilterImpl() - Constructor for class net.sf.basedb.core.FileSet.QueryRuntimeFilterImpl
 
QueryRuntimeFilterImpl() - Constructor for class net.sf.basedb.core.FileSetMember.QueryRuntimeFilterImpl
 
QueryRuntimeFilterImpl() - Constructor for class net.sf.basedb.core.Group.QueryRuntimeFilterImpl
 
QueryRuntimeFilterImpl() - Constructor for class net.sf.basedb.core.Message.QueryRuntimeFilterImpl
 
QueryRuntimeFilterImpl() - Constructor for class net.sf.basedb.core.News.QueryRuntimeFilterImpl
 
QueryRuntimeFilterImpl() - Constructor for class net.sf.basedb.core.Project.QueryRuntimeFilterImpl
 
QueryRuntimeFilterImpl() - Constructor for class net.sf.basedb.core.Quota.QueryRuntimeFilterImpl
 
QueryRuntimeFilterImpl() - Constructor for class net.sf.basedb.core.Role.QueryRuntimeFilterImpl
 
QueryRuntimeFilterImpl() - Constructor for class net.sf.basedb.core.Session.QueryRuntimeFilterImpl
 
QueryRuntimeFilterImpl() - Constructor for class net.sf.basedb.core.User.QueryRuntimeFilterImpl
 
QueryRuntimeFilterImpl() - Constructor for class net.sf.basedb.core.UserDevice.QueryRuntimeFilterImpl
 
QueryRuntimeFilterManager - Class in net.sf.basedb.core
This class manages the enabling/disabling of QueryRuntimeFilter:s.
QueryRuntimeFilterManager(DbControl, Item) - Constructor for class net.sf.basedb.core.QueryRuntimeFilterManager
Create a new manager for the DbControl.
querySection - Variable in class net.sf.basedb.core.AbstractQuery
The section of the query that is currently beeing built.
QuerySection - Enum Class in net.sf.basedb.core.query
Indicates which part of a query that is currently beeing built.
QuerySection() - Constructor for enum class net.sf.basedb.core.query.QuerySection
 
QueryType - Enum Class in net.sf.basedb.core.query
A type representing the language of the query.
QueryType() - Constructor for enum class net.sf.basedb.core.query.QueryType
 
QueryWrapper<R> - Class in net.sf.basedb.core.hibernate
A simple wrapper around hibernate queries which simply forwards all calls to a parent query.
QueryWrapper<T> - Interface in net.sf.basedb.clients.web.plugins
A helper interface for the SimpleExport class to make it easier to interact with different types of queries.
QueryWrapper(Query<R>) - Constructor for class net.sf.basedb.core.hibernate.QueryWrapper
 
queue - Variable in class net.sf.basedb.core.ItemList.DelayedAdditionManager
 
queue() - Method in class net.sf.basedb.core.ItemList.DelayedAdditionManager
 
queuedInsertCount - Variable in class net.sf.basedb.core.FilterBatcher
The number of queued inserts.
queuedInsertCount - Variable in class net.sf.basedb.core.MappingBatcher
The number of queued inserts.
queuedInsertCount - Variable in class net.sf.basedb.core.PositionBatcher
The number of queued inserts.
queuedInsertCount - Variable in class net.sf.basedb.core.PositionExtraValueBatcher
The number of queued inserts.
queuedInsertCount - Variable in class net.sf.basedb.core.SpotBatcher
The number of queued inserts.
queuedInsertCount - Variable in class net.sf.basedb.core.SpotExtraValueBatcher
The number of queued inserts.
quota - Variable in class net.sf.basedb.core.data.GroupData
 
quota - Variable in class net.sf.basedb.core.data.UserData
 
Quota - Class in net.sf.basedb.core
This class is used to represent disk quota settings for users and groups.
Quota(QuotaData) - Constructor for class net.sf.basedb.core.Quota
Create a new Quota item.
QUOTA - Enum constant in enum class net.sf.basedb.core.Item
The item is a Quota.
Quota.QueryRuntimeFilterImpl - Class in net.sf.basedb.core
A runtime filter implementation that limits a query to only return the quota assigned to the logged in user unless the logged in user has generic read permission.
QuotaData - Class in net.sf.basedb.core.data
This file holds information about a qouta.
QuotaData() - Constructor for class net.sf.basedb.core.data.QuotaData
 
QuotaException - Exception in net.sf.basedb.core
This exception is thrown to signal that the user's quota has been exceeded and that an DiskConsumable item cannot be saved.
QuotaException() - Constructor for exception net.sf.basedb.core.QuotaException
Create a new QuotaException object.
QuotaException(Location, QuotaTypeData, long, long) - Constructor for exception net.sf.basedb.core.QuotaException
Create a new QuotaException object.
quotaGroup - Variable in class net.sf.basedb.core.data.UserData
 
QuotaIndex - Class in net.sf.basedb.core.data
This is a helper class for the QuotaData item to help with the Hibernate mapping between quota and quota type/location/max bytes.
QuotaIndex() - Constructor for class net.sf.basedb.core.data.QuotaIndex
 
QuotaIndex(QuotaTypeData, int) - Constructor for class net.sf.basedb.core.data.QuotaIndex
 
quotaLimited - Variable in enum class net.sf.basedb.core.Location
If this location is limited by quota.
quotaType - Variable in class net.sf.basedb.core.data.DiskUsageData
 
quotaType - Variable in class net.sf.basedb.core.data.QuotaIndex
 
QuotaType - Class in net.sf.basedb.core
This class represents the different types a quota can have.
QuotaType(QuotaTypeData) - Constructor for class net.sf.basedb.core.QuotaType
Creates a new QuotaType item.
QUOTATYPE - Enum constant in enum class net.sf.basedb.core.Item
The item is a QuotaType.
QuotaTypeData - Class in net.sf.basedb.core.data
This class holds information about different QuotaTypes.
QuotaTypeData() - Constructor for class net.sf.basedb.core.data.QuotaTypeData
 
quotaTypes - Variable in class net.sf.basedb.core.DiskUsageStatistics
 
quotaValues - Variable in class net.sf.basedb.core.data.QuotaData
 
quote(String) - Static method in class net.sf.basedb.core.HibernateUtil
Quote a string with the default quote type for the current database engine.
QUOTE - Static variable in class net.sf.basedb.clients.web.util.HTML
 

R

r - Variable in class net.sf.basedb.core.query.BooleanExpression
 
r - Variable in class net.sf.basedb.core.query.NotRestriction
 
r - Variable in class net.sf.basedb.util.basefile.BaseFileWriter
 
RADIOACTIVITY - Static variable in class net.sf.basedb.core.Quantity
The id for the Quantity object representing radioactivity.
rangeMidMax - Variable in class net.sf.basedb.util.ColorGenerator
The inverted difference between the max and mid values: 1 / (maxValue - midValue)
rangeMinMid - Variable in class net.sf.basedb.util.ColorGenerator
The inverted difference between the mid and min values: 1 / (midValue - minValue)
rangeRange - Variable in class net.sf.basedb.util.plot.HistogramPlot
 
raw - Variable in class net.sf.basedb.util.IntensityCalculatorUtil.JepIntensityCalculatorImpl
 
raw(String) - Method in class net.sf.basedb.util.jep.RawFunction
Get the value of the specified property of the current raw data object.
raw(String) - Method in class net.sf.basedb.util.jep.ReporterFunction
Get the value of the specified property of the current raw data object.
RAW - Enum constant in enum class net.sf.basedb.core.ReporterCloneBatcher.CloneSource
Use the raw data for all raw bioassays in the experiment as the source for reporters.
RAW_DATA - Static variable in class net.sf.basedb.core.File
The id for the FileType item representing a raw data file.
RAW_DATA - Static variable in class net.sf.basedb.core.QuotaType
The ID for the raw data.
rawBioAssay - Variable in class net.sf.basedb.core.data.RawData
 
rawBioAssay - Variable in class net.sf.basedb.core.data.RootRawBioAssayData
 
rawBioAssay - Variable in class net.sf.basedb.core.DynamicRawDataQuery
 
rawBioAssay - Variable in class net.sf.basedb.core.RawDataBatcher
The raw bioassay this batcher adds raw data to.
rawBioAssay - Variable in class net.sf.basedb.plugins.RawDataFlatFileImporter
 
rawBioAssay - Variable in class net.sf.basedb.util.jep.MeanFunction
 
rawBioAssay(String) - Static method in class net.sf.basedb.core.query.Dynamic
Create an expression representing a property of a raw bioassay.
RawBioAssay - Class in net.sf.basedb.core
A rawbioassay represents the raw data generated from a single DerivedBioAssay.
RawBioAssay(RawBioAssayData) - Constructor for class net.sf.basedb.core.RawBioAssay
 
RAWBIOASSAY - Enum constant in enum class net.sf.basedb.core.Item
The item is a RawBioAssay.
RAWBIOASSAY_ID - Static variable in class net.sf.basedb.core.VirtualColumn
This column stores the id of a raw bioassay.
rawBioAssayData - Variable in class net.sf.basedb.core.RawDataBatcher
Just a copy of the data object for the raw bioassay.
RawBioAssayData - Class in net.sf.basedb.core.data
This class holds information about a raw bioassay, which is the raw data extracted from a scan.
RawBioAssayData() - Constructor for class net.sf.basedb.core.data.RawBioAssayData
 
RawBioAssayImporter - Class in net.sf.basedb.plugins.batchimport
Plug-in for importing raw bioassay items in a batch.
RawBioAssayImporter() - Constructor for class net.sf.basedb.plugins.batchimport.RawBioAssayImporter
 
RawBioAssayJoiner(JoinType) - Constructor for class net.sf.basedb.core.DynamicRawDataQuery.RawBioAssayJoiner
 
RawBioAssayLoader - Class in net.sf.basedb.util.overview.loader
Node loader implementation for raw bioassays.
RawBioAssayLoader() - Constructor for class net.sf.basedb.util.overview.loader.RawBioAssayLoader
 
RawBioAssayPropertyExpression - Class in net.sf.basedb.core
An expression representing the property of a raw bioassay.
RawBioAssayPropertyExpression(String) - Constructor for class net.sf.basedb.core.RawBioAssayPropertyExpression
Create a new raw bioassay property expression.
rawBioAssays - Variable in class net.sf.basedb.core.data.DerivedBioAssayData
 
rawBioAssays - Variable in class net.sf.basedb.core.data.ExperimentData
 
rawBioAssays - Variable in class net.sf.basedb.core.data.ExtractData
 
rawBioAssays - Variable in class net.sf.basedb.core.data.JobData
 
rawBioAssays - Variable in class net.sf.basedb.plugins.IlluminaRawDataImporter
 
rawBioAssays - Variable in class net.sf.basedb.plugins.RawDataFlatFileImporter.FileIterator
 
RAWBIOASSAYS - Static variable in class net.sf.basedb.core.RealTable
 
rawBioAssaysParameter - Variable in class net.sf.basedb.plugins.IntensityCalculatorPlugin
 
rawBioAssaysType - Variable in class net.sf.basedb.plugins.IntensityCalculatorPlugin
 
RawBioAssayToDerivedBioAssayTransformer - Class in net.sf.basedb.util.listable
Source item transformer implementation that transform raw bioassay items to derived bioassays.
RawBioAssayToDerivedBioAssayTransformer() - Constructor for class net.sf.basedb.util.listable.RawBioAssayToDerivedBioAssayTransformer
Create a new raw bioassay to derived bioassay transformer.
RawBioAssayValidator - Class in net.sf.basedb.util.overview.validator
Validator implementation for raw bioassays and root raw bioassays.
RawBioAssayValidator() - Constructor for class net.sf.basedb.util.overview.validator.RawBioAssayValidator
 
RawChannelFunction - Class in net.sf.basedb.util.jep
A JEP function class that adds a rawCh(int) function to a JEP expression parser.
RawChannelFunction() - Constructor for class net.sf.basedb.util.jep.RawChannelFunction
Create a new instance of this function.
RawChannelFunction(int[]) - Constructor for class net.sf.basedb.util.jep.RawChannelFunction
Create a new instance of this function which can be used to dynamically evaluate expressions.
rawData - Variable in class net.sf.basedb.util.jep.MeanFunction
 
rawData - Variable in class net.sf.basedb.util.jep.RawFunction
 
rawData(String) - Static method in class net.sf.basedb.core.query.Dynamic
Create an expression representing a property of a raw data spot.
rawData(String, String, Type, Formula.AverageMethod, Formatter<?>) - Static method in class net.sf.basedb.util.export.spotdata.ExportableFieldFactory
Create a simple dynamic field that exports a raw data value.
rawData(RawDataProperty, String, Formatter<?>) - Static method in class net.sf.basedb.util.export.spotdata.ExportableFieldFactory
Create a simple dynamic field that exports a raw data value.
RawData - Class in net.sf.basedb.core.data
Represents the measurements for single raw data spot.
RawData() - Constructor for class net.sf.basedb.core.data.RawData
 
RawData(RawBioAssayData) - Constructor for class net.sf.basedb.core.data.RawData
 
RAWDATA - Enum constant in enum class net.sf.basedb.core.Item
The item is a RawData spot.
RAWDATA_ID - Static variable in class net.sf.basedb.core.VirtualColumn
This column stores the id of a raw date object.
RAWDATA_INNER - Static variable in class net.sf.basedb.core.DynamicSpotQueryJoiners
This instance joins raw data with an inner join.
RAWDATA_LEFT - Static variable in class net.sf.basedb.core.DynamicSpotQueryJoiners
This instance joins raw data with a left join.
rawDataBatcher - Variable in class net.sf.basedb.core.RawBioAssay
 
RawDataBatcher - Class in net.sf.basedb.core
Batcher class for raw data.
RawDataBatcher(DbControl, RawBioAssay, FeatureIdentificationMethod) - Constructor for class net.sf.basedb.core.RawDataBatcher
 
RawDataBatcher.FeatureInfo - Class in net.sf.basedb.core
 
RawDataBatcher.FeatureProxy - Class in net.sf.basedb.core
 
RawDataBatcher.ReporterProxy - Class in net.sf.basedb.core
 
RawDataFlatFileImporter - Class in net.sf.basedb.plugins
A plugin that imports rawdata from a flatfile.
RawDataFlatFileImporter() - Constructor for class net.sf.basedb.plugins.RawDataFlatFileImporter
 
RawDataFlatFileImporter.FileIterator - Class in net.sf.basedb.plugins
 
RawDataJoiner(JoinType) - Constructor for class net.sf.basedb.core.DynamicSpotQueryJoiners.RawDataJoiner
 
rawDataMember - Variable in class net.sf.basedb.plugins.RawDataFlatFileImporter
 
RawDataProperty - Class in net.sf.basedb.core
Holds information about an extended property for raw data.
RawDataProperty(String, String, String, String, Type, int, boolean, Formula.AverageMethod, int) - Constructor for class net.sf.basedb.core.RawDataProperty
Create a new rawdata property.
RawDataPropertyExpression - Class in net.sf.basedb.core
An expression representing the property of a raw data spot.
RawDataPropertyExpression(String) - Constructor for class net.sf.basedb.core.RawDataPropertyExpression
 
RawDataProxy() - Constructor for class net.sf.basedb.util.importer.spotdata.BaseFileImporter.RawDataProxy
 
rawDataType - Variable in class net.sf.basedb.core.data.ExperimentData
 
rawDataType - Variable in class net.sf.basedb.core.data.FormulaData
 
rawDataType - Variable in class net.sf.basedb.core.data.ItemListData
 
rawDataType - Variable in class net.sf.basedb.core.data.PlatformData
 
rawDataType - Variable in class net.sf.basedb.core.data.PlatformVariantData
 
rawDataType - Variable in class net.sf.basedb.core.data.RawBioAssayData
 
rawDataType - Variable in class net.sf.basedb.core.DynamicRawDataQuery
 
rawDataType - Variable in class net.sf.basedb.core.MigrateRbaToDba.Itemlist
 
rawDataType - Variable in class net.sf.basedb.core.MigrateRbaToDba.LineMapping
 
rawDataType - Variable in class net.sf.basedb.core.MigrateRbaToDba.Rba
 
rawDataType - Variable in class net.sf.basedb.core.RawDataBatcher
The type of raw data to batch.
rawDataType - Variable in class net.sf.basedb.util.jep.RawFunction
 
RawDataType - Class in net.sf.basedb.core
This class holds information about a raw data type.
RawDataType(String, String, String, int, boolean, PlatformData, PlatformVariantData, String, List<RawDataProperty>, List<IntensityFormula>) - Constructor for class net.sf.basedb.core.RawDataType
 
RawDataType(String, String, String, int, String, List<RawDataProperty>, List<IntensityFormula>) - Constructor for class net.sf.basedb.core.RawDataType
Create a new RawDataType.
RawDataType(PlatformData) - Constructor for class net.sf.basedb.core.RawDataType
Create a new raw data type representing a file-only platform.
RawDataType(PlatformVariantData) - Constructor for class net.sf.basedb.core.RawDataType
Create a new raw data type representing a file-only platform variant.
rawDataTypeColumnMapping - Static variable in class net.sf.basedb.plugins.batchimport.RawBioAssayImporter
 
RawDataTypeFilter - Class in net.sf.basedb.clients.web.extensions.list
Filter implementation that accept raw bioassay items of a given raw data type.
RawDataTypeFilter(RawDataType) - Constructor for class net.sf.basedb.clients.web.extensions.list.RawDataTypeFilter
 
rawDataTypeMapper - Variable in class net.sf.basedb.plugins.batchimport.RawBioAssayImporter
 
rawDataTypeParameter - Variable in class net.sf.basedb.plugins.RawDataFlatFileImporter
 
rawDataTypes - Static variable in class net.sf.basedb.core.RawDataTypes
A map from raw data type name --> RawDataType.
RawDataTypes - Class in net.sf.basedb.core
This class is used for reading the XML configuration file with information about raw data types.
RawDataTypes() - Constructor for class net.sf.basedb.core.RawDataTypes
 
RawDataTypes.NameComparator - Class in net.sf.basedb.core
Comparator implementation that sorts raw data types according to their name.
rawDataTypesFile - Static variable in class net.sf.basedb.core.Application
The path to the file containing raw data types.
rawDataTypeType - Variable in class net.sf.basedb.plugins.RawDataFlatFileImporter
 
RawDataUtil - Class in net.sf.basedb.core
Utiltity class for getting and setting non-public properties of raw data objects.
RawDataUtil() - Constructor for class net.sf.basedb.core.RawDataUtil
 
rawField(String, String, Type, Formula.AverageMethod) - Method in class net.sf.basedb.plugins.BaseFileExporterPlugin
 
rawField(String, String, Type, Formula.AverageMethod) - Method in class net.sf.basedb.plugins.BfsExporterPlugin
 
RawFunction - Class in net.sf.basedb.util.jep
A JEP function class that adds a raw(string) function to a JEP expression parser.
RawFunction(boolean) - Constructor for class net.sf.basedb.util.jep.RawFunction
Create a new instance of this function.
RawFunction(DbControl, RawDataType, boolean) - Constructor for class net.sf.basedb.util.jep.RawFunction
Create a new instance of this function working with raw data of the specified raw data type.
RawMappingQuery(DataCube) - Constructor for class net.sf.basedb.core.DataCube.RawMappingQuery
 
rawMappingSql - Variable in class net.sf.basedb.core.MappingBatcher
The statement that inserts the spot/raw data link.
rawMappingSqlStatement - Variable in class net.sf.basedb.core.MappingBatcher
The SQL string for the MappingBatcher.rawMappingSql statement.
rawParents - Variable in class net.sf.basedb.core.data.BioAssayData
 
RAWPARENTS - Enum constant in enum class net.sf.basedb.core.VirtualTable
Table that maps column/position coordinates in a data cube to the id's of the raw spots their intensities where calculated from.
rawSources - Variable in class net.sf.basedb.core.data.TransformationData
 
rba - Variable in class net.sf.basedb.plugins.IlluminaRawDataImporter.BatchAndMapHolder
 
rba - Variable in class net.sf.basedb.util.affymetrix.CelValidationAction
 
Rba(Object[]) - Constructor for class net.sf.basedb.core.MigrateRbaToDba.Rba
 
rbaId - Variable in class net.sf.basedb.core.MigrateRbaToDba.Rba
 
rdt - Variable in class net.sf.basedb.clients.web.extensions.list.RawDataTypeFilter
 
read - Static variable in class net.sf.basedb.core.Item.DefinedPermissions
 
read() - Method in class net.sf.basedb.clients.web.fileupload.FileUpload.UploadStream
 
read() - Method in class net.sf.basedb.util.excel.XlsxToCsvUtil.WorkbookStream
 
read() - Method in class net.sf.basedb.util.gtf.GtfInputStream
 
read() - Method in class net.sf.basedb.util.InputStreamCombiner
 
read() - Method in class net.sf.basedb.util.InputStreamSplitter
 
read() - Method in class net.sf.basedb.util.InputStreamTracker
 
read(byte[]) - Method in class net.sf.basedb.clients.web.fileupload.FileUpload.UploadStream
 
read(byte[]) - Method in class net.sf.basedb.core.Migration.ProgressInputStream
 
read(byte[]) - Method in class net.sf.basedb.util.gtf.GtfInputStream
 
read(byte[]) - Method in class net.sf.basedb.util.InputStreamCombiner
 
read(byte[]) - Method in class net.sf.basedb.util.InputStreamSplitter
 
read(byte[]) - Method in class net.sf.basedb.util.InputStreamTracker
 
read(byte[], int, int) - Method in class net.sf.basedb.clients.web.fileupload.FileUpload.UploadStream
 
read(byte[], int, int) - Method in class net.sf.basedb.core.Migration.ProgressInputStream
 
read(byte[], int, int) - Method in class net.sf.basedb.util.excel.XlsxToCsvUtil.WorkbookStream
 
read(byte[], int, int) - Method in class net.sf.basedb.util.gtf.GtfInputStream
 
read(byte[], int, int) - Method in class net.sf.basedb.util.InputStreamCombiner
 
read(byte[], int, int) - Method in class net.sf.basedb.util.InputStreamSplitter
 
read(byte[], int, int) - Method in class net.sf.basedb.util.InputStreamTracker
 
read(byte[], int, int) - Method in class net.sf.basedb.util.ProgressInputStream
 
read(InputStream) - Static method in class net.sf.basedb.util.FileUtil
Read from the input stream until the end is reached.
read(String, int) - Method in class net.sf.basedb.util.StaticCache
Get an input stream for reading binary information from the cache.
read(String, OutputStream, int) - Method in class net.sf.basedb.util.StaticCache
Read binary information from the cache.
read(Socket, boolean) - Static method in class net.sf.basedb.util.SocketUtil
Read input from a socket.
READ - Enum constant in enum class net.sf.basedb.core.Permission
This permission allows a user read information about an item.
readData(DbControl, DynamicSpotQuery, BioAssay, MACalculator) - Method in class net.sf.basedb.plugins.LowessNormalization
 
reader - Variable in class net.sf.basedb.util.gtf.GtfInputStream
 
reader - Variable in class net.sf.basedb.util.parser.FlatFileParser
Reads from the given input stream
readFormData(byte[]) - Method in class net.sf.basedb.clients.web.fileupload.FileUpload
Read from ServletInputStream until the boundary is found.
readLine(byte[], int, int) - Method in class net.sf.basedb.clients.web.fileupload.FileUpload
Read next line of data into a buffer.
readLineAsString() - Method in class net.sf.basedb.clients.web.fileupload.FileUpload
Reads the next line of input and returns it as a string.
readLock - Variable in class net.sf.basedb.util.StaticCache.State
 
readLock() - Method in class net.sf.basedb.util.extensions.manager.ExtensionsFile
Try to aquire a read-lock.
readLock() - Method in class net.sf.basedb.util.StaticCache.LockEntry
 
readMore() - Method in class net.sf.basedb.util.gtf.GtfInputStream
Read more data from the GTF file.
readMoreData() - Method in class net.sf.basedb.clients.web.fileupload.FileUpload.UploadStream
Read the next line from the ServletInputStream until the boundary is found on a line by itself.
readObject(ObjectInputStream) - Method in class net.sf.basedb.clients.web.taglib.extensions.Render
 
readObject(ObjectInputStream) - Method in class net.sf.basedb.clients.web.taglib.extensions.Scripts
 
readObject(ObjectInputStream) - Method in class net.sf.basedb.clients.web.taglib.extensions.Stylesheets
 
readObject(ObjectInputStream) - Method in class net.sf.basedb.clients.web.taglib.table.ExtensionCells
 
readObject(ObjectInputStream) - Method in class net.sf.basedb.core.data.ContextIndex
 
readObject(ObjectInputStream) - Method in class net.sf.basedb.core.data.FileTypeIndex
 
readObject(ObjectInputStream) - Method in class net.sf.basedb.core.data.QuotaIndex
 
readObject(ObjectInputStream) - Method in class net.sf.basedb.core.data.ReporterListScoreData
 
readObject(ObjectInputStream) - Method in class net.sf.basedb.core.log.LoggingInterceptor
 
readObject(ObjectInputStream) - Method in class net.sf.basedb.core.snapshot.AnnotationSetSnapshot
 
readObject(ObjectInputStream) - Method in class net.sf.basedb.core.snapshot.AnnotationSnapshot
 
readObject(ObjectInputStream) - Method in class net.sf.basedb.util.jep.FunctionSafeJep.SafeFunctionTable
 
readPermissions - Variable in class net.sf.basedb.core.Job.SignalKeyring
 
readSectionHeaders() - Method in class net.sf.basedb.clients.web.fileupload.FileUpload
Read from ServletInputStream until an empty line is found.
readToBoundary(byte[]) - Method in class net.sf.basedb.clients.web.fileupload.FileUpload
Read from ServletInputStream until the boundary is found on a line by itself.
readToEnd - Variable in class net.sf.basedb.util.InputStreamSplitter
If the remainder of the input stream should be copied if it is closed before the end.
readValue(ObjectInputStream) - Method in enum class net.sf.basedb.core.Type
Read a value of this type to the input stream.
readWorkbook(InputStream) - Method in class net.sf.basedb.util.excel.XlsxToCsvUtil
Read an Excel workbook from the stream.
RealJoin - Class in net.sf.basedb.core
Represents a join from one virtual table in the dynamic database to a table in the regular database or between two tables in the regular database.
RealJoin(JoinType, RealTable, RealTable, String) - Constructor for class net.sf.basedb.core.RealJoin
Create a new join between two regular tables.
RealJoin(JoinType, VirtualTable, RealTable, VirtualColumn) - Constructor for class net.sf.basedb.core.RealJoin
Create a new join between a virtual and a regular table.
realTable - Variable in class net.sf.basedb.core.RawDataType
 
RealTable - Class in net.sf.basedb.core
This class defines constants that are used to specify a table in the regular (non-dynamic) database while doing analysis with dynamic queries.
RealTable(String, String) - Constructor for class net.sf.basedb.core.RealTable
Creates a new table.
reattachItem(T, boolean) - Method in class net.sf.basedb.core.DbControl
Reattach a detached item from this DbControl.
recalculateFreeWells(ProgressReporter) - Static method in class net.sf.basedb.core.Update
Vefify and update the free wells of all bioplates.
recalculateRemainingQuantity(ProgressReporter) - Static method in class net.sf.basedb.core.Update
Vefify and update the remaining quantity of all biomaterials.
received - Variable in class net.sf.basedb.core.signal.DelegatingSignalHandler
List holding received signals.
received - Variable in class net.sf.basedb.core.signal.EnhancedThreadSignalHandler
 
received - Variable in class net.sf.basedb.core.signal.ProgressReporterSignalHandler
 
receiverId - Variable in class net.sf.basedb.core.signal.AbstractSignalReceiver
 
receiverId - Variable in class net.sf.basedb.core.signal.LocalSignalReceiver
 
receivers - Static variable in class net.sf.basedb.core.signal.LocalSignalReceiver
Holds all registered signal receivers.
recent - Variable in class net.sf.basedb.clients.web.taglib.Select
List of recently used items.
reconnect() - Method in class net.sf.basedb.core.DbControl
Deprecated.
In 3.12. Applications should use separate DbControl instead.
reconnect(Connection) - Method in class net.sf.basedb.core.hibernate.SessionWrapper
 
recursive - Variable in class net.sf.basedb.util.OlderThanFileFilter
 
recycle(DbControl, Annotatable) - Method in class net.sf.basedb.clients.web.extensions.list.RelatedItemHelper
Re-cycle transactions if needed and re-load the given item in the new transaction.
redefinedColumnNames - Variable in class net.sf.basedb.util.basefile.BaseFileParser
 
REF_SEQ_GTF - Static variable in class net.sf.basedb.core.DataFileType
The external ID for the file type representing a GTF reference file that define the features on an array design that we are interested in.
refColumns - Variable in class net.sf.basedb.core.dbengine.TableInfo.ForeignKeyInfo
 
referenceFactor - Variable in class net.sf.basedb.core.data.UnitData
 
referenceNotFoundErrorParameter - Static variable in class net.sf.basedb.plugins.batchimport.AbstractItemImporter
 
referenceOffset - Variable in class net.sf.basedb.core.data.UnitData
 
referenceUnit - Variable in class net.sf.basedb.core.data.QuantityData
 
ReflectValidationRuleActionFactory - Class in net.sf.basedb.util.overview.extensions
Factory implementation for validation rule actions that uses reflection to access the value of a public static field and return that as the validation rule.
ReflectValidationRuleActionFactory() - Constructor for class net.sf.basedb.util.overview.extensions.ReflectValidationRuleActionFactory
 
refName - Variable in class net.sf.basedb.core.dbengine.TableInfo.ForeignKeyInfo
 
refresh(Object) - Method in class net.sf.basedb.core.hibernate.SessionWrapper
 
refresh(Object) - Method in class net.sf.basedb.core.hibernate.StatelessSessionWrapper
 
refresh(Object, Map<String, Object>) - Method in class net.sf.basedb.core.hibernate.SessionWrapper
 
refresh(Object, LockModeType) - Method in class net.sf.basedb.core.hibernate.SessionWrapper
 
refresh(Object, LockModeType, Map<String, Object>) - Method in class net.sf.basedb.core.hibernate.SessionWrapper
 
refresh(Object, LockMode) - Method in class net.sf.basedb.core.hibernate.SessionWrapper
 
refresh(Object, LockMode) - Method in class net.sf.basedb.core.hibernate.StatelessSessionWrapper
 
refresh(Object, LockOptions) - Method in class net.sf.basedb.core.hibernate.SessionWrapper
 
refresh(String, Object) - Method in class net.sf.basedb.core.hibernate.SessionWrapper
 
refresh(String, Object) - Method in class net.sf.basedb.core.hibernate.StatelessSessionWrapper
 
refresh(String, Object, LockMode) - Method in class net.sf.basedb.core.hibernate.StatelessSessionWrapper
 
refresh(String, Object, LockOptions) - Method in class net.sf.basedb.core.hibernate.SessionWrapper
 
refresh(Session, BasicData) - Static method in class net.sf.basedb.core.HibernateUtil
Reload the data from the database for a given entity.
refreshItem(BasicItem) - Method in class net.sf.basedb.core.DbControl
Reload the item from the database.
regexp - Variable in class net.sf.basedb.core.ExtendedPropertyLinker
 
regexp - Variable in class net.sf.basedb.core.query.RlikeRestriction
 
RegexpFileFilter - Class in net.sf.basedb.util
An implementation of the FileFilter interface that filter files and directories based on regular expressions.
RegexpFileFilter(String, String) - Constructor for class net.sf.basedb.util.RegexpFileFilter
Create a new file filter from a string regular expressions.
RegexpFileFilter(Pattern, Pattern) - Constructor for class net.sf.basedb.util.RegexpFileFilter
Create a new file filter from patterns.
region - Variable in class net.sf.basedb.util.GeoLocation
 
register(Registry, String, String) - Static method in class net.sf.basedb.clients.web.extensions.list.ListColumnUtil
 
register(Registry, String, String) - Static method in class net.sf.basedb.clients.web.extensions.toolbar.ToolbarUtil
 
registerAgent() - Method in class net.sf.basedb.clients.jobagent.AgentController
 
registerCheckedNodeLoader(Object, Class<? extends NodeLoader<? extends BasicItem>>) - Method in class net.sf.basedb.util.overview.loader.BasicItemNodeLoaderFactory
Register a node loader implementation that you are sure fulfills the requirements.
registerCheckedNodeValidator(Object, Class<?>) - Method in class net.sf.basedb.util.overview.validator.BasicItemNodeValidatorFactory
Register a node loader implementation that you are sure fulfills the requirements.
registerCleanup(Object, Runnable) - Static method in class net.sf.basedb.core.Application
Register an action that needs to be performed when the monitored object becomes unreachable.
registerConverter(Object, JepConversionFunction<?>) - Static method in class net.sf.basedb.util.jep.convert.ConverterFactory
Add a converter for a specific object.
registerCustomRequestHandlers(MultiProtocolRequestHandler) - Method in class net.sf.basedb.clients.jobagent.Agent
 
registerDefaultNodeLoaders() - Method in class net.sf.basedb.util.overview.loader.BasicItemNodeLoaderFactory
Registers default item node loaders from BioSource to Experiment, etc.
registerDefaultNodeValidators() - Method in class net.sf.basedb.util.overview.validator.BasicItemNodeValidatorFactory
Registers default item node validators from BioSource to Experiment, etc.
registerDelayedFilters(Metadata) - Method in class net.sf.basedb.core.HibernateUtil.FilterConfigurator
Registered - Interface in net.sf.basedb.core
Items that implements this interface has their registration date stored in the database.
RegisteredAbout(About) - Constructor for class net.sf.basedb.util.extensions.Registry.RegisteredAbout
Create a new registered about by copying the information from the parameter.
registeredColumnMapping - Static variable in class net.sf.basedb.plugins.batchimport.AbstractItemImporter
Column mapping parameter for the item registration date.
RegisteredData - Interface in net.sf.basedb.core.data
Adds the date an item was registered in the database.
RegisteredEventHandler(EventHandler, EventFilter, ClassLoader) - Constructor for class net.sf.basedb.util.extensions.Registry.RegisteredEventHandler
 
RegisteredExtension(Extension<A>, Registry.RegisteredExtensionPoint<? super A>, ClassLoader) - Constructor for class net.sf.basedb.util.extensions.Registry.RegisteredExtension
Create a new registered extension by copying the information from the parameter.
RegisteredExtensionPoint(ExtensionPoint<A>, ClassLoader) - Constructor for class net.sf.basedb.util.extensions.Registry.RegisteredExtensionPoint
Create a new registered extension point by copying the information from the parameter.
registerEditTab(Registry, String, String) - Static method in class net.sf.basedb.clients.web.extensions.edit.EditUtil
 
registeredMapper - Variable in class net.sf.basedb.plugins.batchimport.AnnotationTypeImporter
 
registeredMapper - Variable in class net.sf.basedb.plugins.batchimport.ArrayBatchImporter
 
registeredMapper - Variable in class net.sf.basedb.plugins.batchimport.ArrayDesignImporter
 
registeredMapper - Variable in class net.sf.basedb.plugins.batchimport.ArraySlideImporter
 
registeredMapper - Variable in class net.sf.basedb.plugins.batchimport.BioPlateImporter
 
registeredMapper - Variable in class net.sf.basedb.plugins.batchimport.BioSourceImporter
 
registeredMapper - Variable in class net.sf.basedb.plugins.batchimport.DerivedBioAssayImporter
 
registeredMapper - Variable in class net.sf.basedb.plugins.batchimport.ExtractImporter
 
registeredMapper - Variable in class net.sf.basedb.plugins.batchimport.KitImporter
 
registeredMapper - Variable in class net.sf.basedb.plugins.batchimport.PhysicalBioAssayImporter
 
registeredMapper - Variable in class net.sf.basedb.plugins.batchimport.RawBioAssayImporter
 
registeredMapper - Variable in class net.sf.basedb.plugins.batchimport.SampleImporter
 
registeredMapper - Variable in class net.sf.basedb.plugins.batchimport.TagImporter
 
registerEventHandler(EventHandler, EventFilter, ClassLoader) - Method in class net.sf.basedb.util.extensions.Registry
Register an event handler for responding to events happening to extension points and extensions in the registry.
registerExtension(Extension<A>, ClassLoader) - Method in class net.sf.basedb.util.extensions.Registry
Register an extension.
registerExtensionPoint(ExtensionPoint<A>, ClassLoader) - Method in class net.sf.basedb.util.extensions.Registry
Register an extension point.
registerExtensionPoints(RegisterExtensionsProcessor.FileData, Registry, boolean) - Method in class net.sf.basedb.util.extensions.manager.processor.RegisterExtensionsProcessor
 
registerExtensionPoints(Registry) - Static method in class net.sf.basedb.clients.web.extensions.edit.EditUtil
Registers tabcontrol and on-save extension points with the given registry.
registerExtensionPoints(Registry) - Static method in class net.sf.basedb.clients.web.extensions.list.ListColumnUtil
 
registerExtensionPoints(Registry) - Static method in class net.sf.basedb.clients.web.extensions.toolbar.ToolbarUtil
 
registerExtensionPoints(Registry, boolean) - Method in class net.sf.basedb.util.extensions.xml.XmlLoader
Register all loaded extension points with a registry.
registerExtensions(RegisterExtensionsProcessor.FileData, ExtensionsManager, boolean) - Method in class net.sf.basedb.util.extensions.manager.processor.RegisterExtensionsProcessor
 
registerExtensions(Registry, boolean) - Method in class net.sf.basedb.util.extensions.xml.XmlLoader
Register all loaded extensions with a registry.
RegisterExtensionsProcessor - Class in net.sf.basedb.util.extensions.manager.processor
Extension file processor implementation that will load the extension definitions from each file and register them with the registry that is managed by the manager.
RegisterExtensionsProcessor(XmlLoader, ProcessResults) - Constructor for class net.sf.basedb.util.extensions.manager.processor.RegisterExtensionsProcessor
Create a new processor.
RegisterExtensionsProcessor.FileData - Class in net.sf.basedb.util.extensions.manager.processor
Keep track of the extension points and extensions found in a file.
registerFactory(RegisterExtensionsProcessor.FileData, Object) - Method in class net.sf.basedb.util.extensions.manager.processor.RegisterExtensionsProcessor
Register factory parameters for the given factory instance.
registerFileOnlyRawDataType(RawDataType) - Static method in class net.sf.basedb.core.RawDataTypes
 
registerFormatter(Class<? extends T>, Formatter<T>) - Method in class net.sf.basedb.util.formatter.MultiFormatter
Register a formatter for the specified class.
registerHandler(RequestHandler, String...) - Method in class net.sf.basedb.clients.jobagent.handlers.DefaultRequestHandler
 
registerMetadata(ObjectKey<M>, M) - Method in class net.sf.basedb.util.extensions.manager.ExtensionsFile.WriteableExtensionsFile
Register metadata about an object.
registerNodeLoader(Object, Class<? extends NodeLoader<? extends BasicItem>>) - Method in class net.sf.basedb.util.overview.loader.BasicItemNodeLoaderFactory
Register a node loader implementation.
registerNodeValidator(Item, Class<? extends NodeValidator<? extends BasicItem>>) - Method in class net.sf.basedb.util.overview.validator.BasicItemNodeValidatorFactory
Register a node validator implementation.
registerObject(ObjectKey<?>, ExtensionsFile) - Method in class net.sf.basedb.util.extensions.manager.ExtensionsManager
Register an object as defined by the given extensions file.
registerObject(ObjectKey<O>, O) - Method in class net.sf.basedb.util.extensions.manager.ExtensionsFile.WriteableExtensionsFile
Register an object as "defined" by this extensions file.
registerOnSave(Registry, String, String, RethrowErrorHandlerFactory) - Static method in class net.sf.basedb.clients.web.extensions.edit.EditUtil
 
registerParameters(List<PluginParameter<?>>) - Method in class net.sf.basedb.core.PluginRequest
Keep track of all parameters so that we can save label and description in the ParameterValuesImpl.saveParameters(Job, Map) method.
registerProtocols(RequestHandler, String...) - Method in class net.sf.basedb.clients.jobagent.handlers.MultiProtocolRequestHandler
Register a handler for one or more protocols.
registerRequestHandler(RequestHandler, String...) - Method in class net.sf.basedb.clients.jobagent.Agent
Register a request handler for one or more protocols.
registerSignal(String, String, String) - Static method in class net.sf.basedb.core.signal.Signal
Register a signal.
registerSignalHandler(SignalHandler) - Method in class net.sf.basedb.clients.web.util.SimpleSignalProgressReporter
This return null when there is no need for a global id.
registerSignalHandler(SignalHandler) - Method in class net.sf.basedb.core.signal.AbstractSignalReceiver
Register a signal handler with this receiver.
registerSignalHandler(SignalHandler) - Method in class net.sf.basedb.core.signal.DelegatingSignalHandler
Register a signal handler to delegate to.
registerSignalHandler(SignalHandler) - Method in interface net.sf.basedb.core.signal.SignalReceiver
Register a signal handler with this receiver.
registerSignalReceiver(SignalReceiver) - Method in class net.sf.basedb.core.PluginExecutionRequest
Register a signal receiver that will receive signals for this job.
registry - Static variable in class net.sf.basedb.clients.web.extensions.ExtensionsControl
 
registry - Variable in class net.sf.basedb.util.extensions.ExtensionPointContext
 
registry - Variable in class net.sf.basedb.util.extensions.manager.ExtensionsManager
 
Registry - Class in net.sf.basedb.util.extensions
A registry for keeping track of extensions points and installed extensions.
Registry() - Constructor for class net.sf.basedb.util.extensions.Registry
Create a new empty registry.
Registry.AttributeKey - Class in net.sf.basedb.util.extensions
Identifies attribute.
Registry.RegisteredAbout - Class in net.sf.basedb.util.extensions
 
Registry.RegisteredEventHandler - Class in net.sf.basedb.util.extensions
 
Registry.RegisteredExtension<A extends Action> - Class in net.sf.basedb.util.extensions
Internal representation of an extension.
Registry.RegisteredExtensionPoint<A extends Action> - Class in net.sf.basedb.util.extensions
Internal representation of an extension point.
registryBuilder - Variable in class net.sf.basedb.core.ServiceSessionControl.SessionFactoryConfiguration
 
relatedAnnotationTypes - Variable in class net.sf.basedb.core.ItemSubtype
 
RelatedItemAnnotationColumn - Class in net.sf.basedb.clients.web.extensions.list
Related item column that load annotation values from the parent or child items.
RelatedItemAnnotationColumn(DbControl, int, RelatedItemColumn.Specification, RelatedItemHelper, AnnotationType) - Constructor for class net.sf.basedb.clients.web.extensions.list.RelatedItemAnnotationColumn
 
RelatedItemColumn - Class in net.sf.basedb.clients.web.extensions.list
A column action implementation that finds a parent or child item of a given subtype and then get an annotation or other property value from it.
RelatedItemColumn(DbControl, int, RelatedItemColumn.Specification, RelatedItemHelper) - Constructor for class net.sf.basedb.clients.web.extensions.list.RelatedItemColumn
 
RelatedItemColumn.Specification - Class in net.sf.basedb.clients.web.extensions.list
Represents a specification for loading a related parent or child item.
RelatedItemColumnActionFactory - Class in net.sf.basedb.clients.web.extensions.list
Action factory for adding columns to a table that pull data from a parent or child item from an arbitrary location up or down the chain of linked items.
RelatedItemColumnActionFactory() - Constructor for class net.sf.basedb.clients.web.extensions.list.RelatedItemColumnActionFactory
 
RelatedItemErrorColumn - Class in net.sf.basedb.clients.web.extensions.list
Related item column that displays an error message.
RelatedItemErrorColumn(int, RelatedItemColumn.Specification, RelatedItemHelper, String) - Constructor for class net.sf.basedb.clients.web.extensions.list.RelatedItemErrorColumn
 
RelatedItemExtensionColumn - Class in net.sf.basedb.clients.web.extensions.list
Related item column that get values from an extension.
RelatedItemExtensionColumn(DbControl, int, RelatedItemColumn.Specification, RelatedItemHelper, ListColumnAction<Annotatable, ?>) - Constructor for class net.sf.basedb.clients.web.extensions.list.RelatedItemExtensionColumn
 
RelatedItemHelper - Class in net.sf.basedb.clients.web.extensions.list
Helper class for storing request-scoped objects that may be useful to re-use between multiple columns.
RelatedItemHelper(SessionControl, JspContext, boolean) - Constructor for class net.sf.basedb.clients.web.extensions.list.RelatedItemHelper
 
RelatedItemHelper.CloseMyDbControl - Class in net.sf.basedb.clients.web.extensions.list
 
RelatedItemListColumn - Class in net.sf.basedb.clients.web.extensions.list
Related item column that get the item lists that the parent or child item is a member of.
RelatedItemListColumn(DbControl, int, RelatedItemColumn.Specification, Filter<? super ItemList>, RelatedItemHelper) - Constructor for class net.sf.basedb.clients.web.extensions.list.RelatedItemListColumn
 
RelatedItemMultiHopColumn - Class in net.sf.basedb.clients.web.extensions.list
Related item column that get values from multiple hops betweeen child->parent->child.
RelatedItemMultiHopColumn(DbControl, int, RelatedItemColumn.Specification, RelatedItemHelper, RelatedItemColumn) - Constructor for class net.sf.basedb.clients.web.extensions.list.RelatedItemMultiHopColumn
 
RelatedItemPropertyColumn - Class in net.sf.basedb.clients.web.extensions.list
Related item column that get values from parent or child items by specifying a "property path".
RelatedItemPropertyColumn(DbControl, int, RelatedItemColumn.Specification, RelatedItemHelper, Metadata.PropertyPath<? super Annotatable, ?>) - Constructor for class net.sf.basedb.clients.web.extensions.list.RelatedItemPropertyColumn
 
relatedItems - Static variable in class net.sf.basedb.core.ItemSubtype
 
relatedSubtypes - Variable in class net.sf.basedb.core.data.ItemSubtypeData
 
release() - Method in class net.sf.basedb.core.hibernate.SchemaGenerator.CollectSqlTarget
 
releaseRemoteSlot(String) - Method in class net.sf.basedb.clients.jobagent.slotmanager.MasterSlotManager
Release the remote slot with the given id.
releaseSavepoint(Connection, Savepoint, String) - Method in class net.sf.basedb.core.AbstractSqlQuery
Release the given savepoint.
releaseSlot(Slot) - Method in class net.sf.basedb.clients.jobagent.slotmanager.InternalSlotManager
 
releaseSlot(Slot) - Method in class net.sf.basedb.clients.jobagent.slotmanager.RemoteSlotManager
 
releaseSlot(Slot) - Method in interface net.sf.basedb.clients.jobagent.slotmanager.SlotManager
Called by the job agent when the job has finished exeuting.
reload - Variable in class net.sf.basedb.core.Keyring
TRUE if the Timer has signaled that it is time to reload the information.
reload() - Method in class net.sf.basedb.core.Keyring
Reload all permission information
reloadPermissions() - Method in class net.sf.basedb.core.SessionControl
Tell the core to reload the logged in users permission the next time the client application needs to check the permissions.
reloadSettings(boolean, boolean) - Method in class net.sf.basedb.core.SessionControl
Reloads user- and client-specific settings.
ReloadTask() - Constructor for class net.sf.basedb.core.Keyring.ReloadTask
 
remainingQuantity - Variable in class net.sf.basedb.core.data.MeasuredBioMaterialData
 
RemainingQuantityAction(DbControl, MeasuredBioMaterialData) - Constructor for class net.sf.basedb.core.MeasuredBioMaterial.RemainingQuantityAction
 
remapAllTo(ImageRemapper, String) - Static method in class net.sf.basedb.clients.web.extensions.skin.ImageRemapperUtil
Scan the given url for images (png and gif) and remap them.
remapDir - Variable in class net.sf.basedb.clients.web.extensions.skin.FixedSkinActionFactory
 
remapImages(ImageRemapper) - Method in class net.sf.basedb.clients.web.extensions.skin.FixedSkinActionFactory.MySkinAction
 
remapImages(ImageRemapper) - Method in interface net.sf.basedb.clients.web.extensions.skin.SkinAction
Remap images to another location.
remember - Variable in class net.sf.basedb.clients.web.taglib.tab.TabControl
If it should try to remember the last active tab on the page
rememberLast - Variable in class net.sf.basedb.util.extensions.LoggingErrorHandlerFactory
 
rememberLastLogin - Variable in class net.sf.basedb.clients.web.extensions.login.LoginFormBean
 
rememberLastLogin() - Method in interface net.sf.basedb.clients.web.extensions.login.LoginFormAction
If TRUE, the browser is asked to remember the last login used.
rememberLastLogin() - Method in class net.sf.basedb.clients.web.extensions.login.LoginFormBean
 
rememberLastLogin() - Method in class net.sf.basedb.clients.web.extensions.login.PasswordLoginFormFactory
 
remote - Variable in class net.sf.basedb.clients.jobagent.Agent
 
remoteHost - Variable in class net.sf.basedb.clients.jobagent.slotmanager.RemoteSlotManager
 
remoteId - Variable in class net.sf.basedb.core.data.SessionData
 
remoteId - Variable in class net.sf.basedb.core.data.UserDeviceData
 
remoteId - Variable in class net.sf.basedb.core.SessionControl
The remote IP.
remotePort - Variable in class net.sf.basedb.clients.jobagent.slotmanager.RemoteSlotManager
 
remoteRequestHandler - Variable in class net.sf.basedb.clients.jobagent.slotmanager.MasterSlotManager
 
RemoteSlot(Slot) - Constructor for class net.sf.basedb.clients.jobagent.slotmanager.MasterSlotManager.RemoteSlot
 
RemoteSlotManager - Class in net.sf.basedb.clients.jobagent.slotmanager
Slot manager implementation that requests slots from another job agent.
RemoteSlotManager() - Constructor for class net.sf.basedb.clients.jobagent.slotmanager.RemoteSlotManager
 
RemoteSlotManager.RemoteSlotPinger - Class in net.sf.basedb.clients.jobagent.slotmanager
Task that is scheduled at regular intervals to send ping commands to the remote host.
RemoteSlotPinger(RemoteSlotManager) - Constructor for class net.sf.basedb.clients.jobagent.slotmanager.RemoteSlotManager.RemoteSlotPinger
 
RemoteSlotRequestHandler(MasterSlotManager) - Constructor for class net.sf.basedb.clients.jobagent.slotmanager.MasterSlotManager.RemoteSlotRequestHandler
 
remoteSlots - Variable in class net.sf.basedb.clients.jobagent.slotmanager.MasterSlotManager
 
remoteSlots - Variable in class net.sf.basedb.clients.jobagent.slotmanager.RemoteSlotManager
 
RemoteSlotTimeoutChecker(MasterSlotManager) - Constructor for class net.sf.basedb.clients.jobagent.slotmanager.MasterSlotManager.RemoteSlotTimeoutChecker
 
Removable - Interface in net.sf.basedb.core
A Removable item is an item that can be flagged as removed.
REMOVABLE_FILTER - Static variable in class net.sf.basedb.core.QueryRuntimeFilterFactory
 
RemovableData - Interface in net.sf.basedb.core.data
A removable item is an item that can be flagged as removed.
RemovableFilter() - Constructor for class net.sf.basedb.core.QueryRuntimeFilterFactory.RemovableFilter
 
removableItems - Static variable in class net.sf.basedb.core.Metadata
 
RemovableUtil - Class in net.sf.basedb.util
 
RemovableUtil() - Constructor for class net.sf.basedb.util.RemovableUtil
 
remove - Variable in class net.sf.basedb.util.annotations.InheritSpecification
 
remove() - Method in class net.sf.basedb.clients.web.servlet.PlotServlet.CFResultIterator
Not supported.
remove() - Method in class net.sf.basedb.core.DataResultIterator
Not supported.
remove() - Method in class net.sf.basedb.core.DynamicResultIterator
Not supported.
remove() - Method in class net.sf.basedb.core.ItemResultIterator
Not supported.
remove() - Method in class net.sf.basedb.core.ItemResultList.ResultListIterator
This operation is not supported.
remove() - Method in class net.sf.basedb.core.ItemResultList.ResultListListIterator
This operation is not supported.
remove() - Method in class net.sf.basedb.core.ReporterScoreResultIterator
Not supported.
remove() - Method in class net.sf.basedb.core.ScrollIterator
Not supported.
remove() - Method in class net.sf.basedb.plugins.RawDataFlatFileImporter.FileIterator
 
remove() - Method in class net.sf.basedb.util.ArrayIterator
This operation is not supported.
remove() - Method in class net.sf.basedb.util.extensions.ActionIterator
Not supported.
remove() - Method in class net.sf.basedb.util.NestedIterator
This operation is not supported.
remove() - Method in class net.sf.basedb.util.query.MultiQueryIterator
 
remove() - Method in class net.sf.basedb.util.Tree.ElementIterator
Not supported.
remove() - Method in class net.sf.basedb.util.Tree.EntryIterator
Not supported.
remove(int) - Method in class net.sf.basedb.core.AbstractResultList
Not supported.
remove(int) - Method in class net.sf.basedb.core.UnmodifiableResultList
Not supported.
remove(int) - Method in class net.sf.basedb.util.Enumeration
 
remove(Object) - Method in class net.sf.basedb.core.AbstractResultList
Not supported.
remove(Object) - Method in class net.sf.basedb.core.hibernate.SessionWrapper
 
remove(Object) - Method in class net.sf.basedb.core.UnmodifiableResultList
Not supported.
remove(Object) - Method in class net.sf.basedb.util.formatter.LookupFormatter
Remove an entry from the lookup map.
remove(Object) - Method in class net.sf.basedb.util.Tree
Not supported.
remove(Listable) - Method in class net.sf.basedb.core.ItemList.DelayedAdditionManager
 
remove(Listable) - Method in class net.sf.basedb.core.ItemList
Deprecated.
remove(IdListRestriction) - Method in class net.sf.basedb.core.query.IdListRestriction
Merge this id list with another list by removing ids that are found in the other list.
REMOVE - Enum constant in enum class net.sf.basedb.core.log.ChangeType
 
REMOVE_ONLY - Enum constant in enum class net.sf.basedb.core.ItemList.SynchronizeOption
Synchronize the members by removing items that doesn't match the filter.
removeAll(Collection<?>) - Method in class net.sf.basedb.core.AbstractResultList
Not supported.
removeAll(Collection<?>) - Method in class net.sf.basedb.core.UnmodifiableResultList
Not supported.
removeAll(Collection<?>) - Method in class net.sf.basedb.util.Tree
Not supported.
removeAll(ItemList) - Method in class net.sf.basedb.core.ItemList
Remove all items from this list that are present in the other list.
removeAll(ItemList.DelayedAdditionManager) - Method in class net.sf.basedb.core.ItemList.DelayedAdditionManager
 
removeAll(ReporterList) - Method in class net.sf.basedb.core.ReporterList
Remove all reporters from this list that are present in the other list.
removeAllInherited(AnnotationSet) - Method in class net.sf.basedb.core.AnnotationSet
Utility method to stop inheriting all annotations in the given annotation set.
removeAllMembers() - Method in class net.sf.basedb.core.FileSet
Remove all members in a file set.
removeAllOfType(DataFileType) - Method in class net.sf.basedb.core.FileSet
Remove all member files of the given type.
removeAllOfTypeExcept(DataFileType, File) - Method in class net.sf.basedb.core.FileSet
Remove all member files of the given type.
removeAllPropertyFilters() - Method in class net.sf.basedb.core.ItemContext
Deprecated.
removeAllPropertyFilters(String) - Method in class net.sf.basedb.core.ItemContext
Remove all property filters for the given property.
removeAllPropertyFilters(ItemContext.AddFilter) - Method in class net.sf.basedb.core.ItemContext
Remove all property filters from this context and optionally re-apply sub-category filter.
removeAllTemporaryFilters() - Method in class net.sf.basedb.core.ItemContext
Remove all temporary filters.
RemoveAllTransformer<I> - Class in net.sf.basedb.util.collections
Collection transformer implementation that removes all elements in the source collection from the destination collection.
RemoveAllTransformer() - Constructor for class net.sf.basedb.util.collections.RemoveAllTransformer
 
removeAnnotation(AnnotationType) - Method in class net.sf.basedb.core.AnnotationSet
Delete the primary annotation of the specified annotation type.
removeAnnotations() - Method in interface net.sf.basedb.core.Annotatable
Remove all annotations from this item, by deleting the annotation set.
removeAnnotations() - Method in class net.sf.basedb.core.AnnotatedItem
 
removeAnnotations() - Method in class net.sf.basedb.core.BioAssay
 
removeAnnotations() - Method in class net.sf.basedb.core.BioAssaySet
 
removeAnnotations() - Method in class net.sf.basedb.core.PluginDefinition
 
removeAnnotations() - Method in class net.sf.basedb.core.Project
 
removeAnnotations() - Method in class net.sf.basedb.core.RootRawBioAssay
 
removeAnnotations() - Method in class net.sf.basedb.core.Well
 
removeAnyToAnyLinkedTo(DbControl, ItemQuery<AnyToAny>, boolean) - Static method in class net.sf.basedb.util.RemovableUtil
 
removeAssociatedDataFileType(DataFileType) - Method in class net.sf.basedb.core.ItemSubtype
Remove the association between this subtype and the given data file type.
removeBatcher(Batcher) - Method in class net.sf.basedb.core.DbControl
Remove a Batcher from the batcher queue.
removeCategory(AnnotationTypeCategory) - Method in class net.sf.basedb.core.AnnotationType
Remove a category from this annotation type.
removeClonableProperty(String) - Method in class net.sf.basedb.core.ReporterCloneTemplate
Remove the property with the given name from this template
removeContext(Session, int) - Static method in class net.sf.basedb.core.Update
Remove context-related information for the given item type.
removed - Variable in class net.sf.basedb.plugins.Base1PluginExecuter.JobParameter
 
REMOVED - Enum constant in enum class net.sf.basedb.core.Include
Include items flagged as removed.
removedBy - Variable in class net.sf.basedb.core.data.BioAssaySetData
 
removedBy - Variable in class net.sf.basedb.core.data.BioPlateEventTypeData
 
removedBy - Variable in class net.sf.basedb.core.data.BioPlateTypeData
 
removedBy - Variable in class net.sf.basedb.core.data.CommonData
 
removedBy - Variable in class net.sf.basedb.core.data.DataFileTypeData
 
removedBy - Variable in class net.sf.basedb.core.data.ExtraValueTypeData
 
removedBy - Variable in class net.sf.basedb.core.data.GroupData
 
removedBy - Variable in class net.sf.basedb.core.data.ItemSubtypeData
 
removedBy - Variable in class net.sf.basedb.core.data.MessageData
 
removedBy - Variable in class net.sf.basedb.core.data.MimeTypeData
 
removedBy - Variable in class net.sf.basedb.core.data.NewsData
 
removedBy - Variable in class net.sf.basedb.core.data.PlateEventTypeData
 
removedBy - Variable in class net.sf.basedb.core.data.PlateGeometryData
 
removedBy - Variable in class net.sf.basedb.core.data.PlatformData
 
removedBy - Variable in class net.sf.basedb.core.data.PlatformVariantData
 
removedBy - Variable in class net.sf.basedb.core.data.PluginDefinitionData
 
removedBy - Variable in class net.sf.basedb.core.data.PluginTypeData
 
removedBy - Variable in class net.sf.basedb.core.data.ProjectData
 
removedBy - Variable in class net.sf.basedb.core.data.QuantityData
 
removedBy - Variable in class net.sf.basedb.core.data.QuotaData
 
removedBy - Variable in class net.sf.basedb.core.data.ReporterTypeData
 
removedBy - Variable in class net.sf.basedb.core.data.RoleData
 
removedBy - Variable in class net.sf.basedb.core.data.TransformationData
 
removedBy - Variable in class net.sf.basedb.core.data.UnitData
 
removedBy - Variable in class net.sf.basedb.core.data.UserData
 
removedBy - Variable in class net.sf.basedb.core.MigrateRbaToDba.Rba
 
removeDefaultItem(BasicItem) - Method in class net.sf.basedb.core.Project
Remove an item from the list of default items for this project.
removeDependingItems(DbControl, Removable, boolean) - Static method in class net.sf.basedb.util.RemovableUtil
Sets the removed-flag for all subitems to a parent
removeEventHandler(EventHandler) - Method in class net.sf.basedb.util.bfs.MultiEventHandler
Removes an event handler.
removeExisting - Variable in class net.sf.basedb.plugins.AnnotationFlatFileImporter
 
removeExistingParameter - Static variable in class net.sf.basedb.plugins.AnnotationFlatFileImporter
 
removeExperimentalFactor(AnnotationType) - Method in class net.sf.basedb.core.Experiment
Remove an annotation type from the experimental factors for this experiment.
removeExtension(String) - Method in class net.sf.basedb.util.extensions.Registry.RegisteredExtensionPoint
Remove the extension with a given ID.
removeFile(File) - Method in class net.sf.basedb.util.extensions.manager.ExtensionsManager
Remove a file from the extensions manager.
removeFileSetMembers(DbControl, FileStoreEnabled, boolean) - Static method in class net.sf.basedb.util.RemovableUtil
 
removeFilesParameter - Variable in class net.sf.basedb.plugins.PackedFileExporter
 
removeFileType(DataFileType, PlatformVariant) - Method in class net.sf.basedb.core.Platform
Remove a file type from this platform/variant.
removeFilter - Variable in class net.sf.basedb.util.annotations.InheritAnnotationsManager
 
removeFilterRow(int) - Method in class net.sf.basedb.core.ItemContext
Remove all filters from the specified filter row.
removeFromCache() - Method in class net.sf.basedb.core.MeasuredBioMaterial.RemainingQuantityAction
 
removeGroup(Group) - Method in class net.sf.basedb.core.Group
Remove a group that is a member of this group.
removeHeader(String) - Method in class net.sf.basedb.core.RawBioAssay
Remove a specific header from the raw bioassay.
removeHeaders() - Method in class net.sf.basedb.core.RawBioAssay
Remove all headers from the raw bioassay.
removeIfPresentIn(int, int, Collection<ItemList>) - Method in class net.sf.basedb.core.ItemList
Remove items that are present in the specified number of lists from this list.
removeIfPresentIn(int, int, Collection<ReporterList>) - Method in class net.sf.basedb.core.ReporterList
Remove reporters that are present in the specified number of lists from this list.
removeIgnore(File) - Method in class net.sf.basedb.util.extensions.manager.ExtensionsManager
Remove a file from the ignore list.
removeInheritedAnnotation(Annotation) - Method in class net.sf.basedb.core.AnnotationSet
Remove an inherited an annotation.
RemoveInheritedAnnotationsAction(AnnotationType) - Constructor for class net.sf.basedb.core.AnnotationType.RemoveInheritedAnnotationsAction
 
removeIntersection(Collection<ItemList>) - Method in class net.sf.basedb.core.ItemList
Remove items that are present in ALL OF the given lists from this list.
removeIntersection(Collection<ReporterList>) - Method in class net.sf.basedb.core.ReporterList
Remove reporters that are present in ALL OF the given lists from this list.
removeItem(Listable) - Method in class net.sf.basedb.core.ItemList
Remove an item from the list.
removeItems(Collection<? extends Integer>) - Method in class net.sf.basedb.core.ItemList
Remove all items in the collection from this list.
removeItems(Iterator<? extends Listable>) - Method in class net.sf.basedb.core.ItemList
Remove multiple items from this list in one go.
removeItems(ItemQuery<? extends Listable>) - Method in class net.sf.basedb.core.ItemList
Remove all items that are returned by the query from this list.
removeJobWhenFinished - Variable in class net.sf.basedb.core.data.JobData
 
removeMember(File, DataFileType) - Method in class net.sf.basedb.core.FileSet
Remove a file as a member from the file set.
removeMember(FileSetMember) - Method in class net.sf.basedb.core.FileSet
Remove the given member from this file set.
removeMembers(Set<Integer>, ItemList.DelayedAdditionManager) - Method in class net.sf.basedb.core.ItemList
Remove members from this list
removeMembersMode - Variable in class net.sf.basedb.plugins.batchimport.AbstractItemImporter
 
removeMode - Variable in class net.sf.basedb.plugins.batchimport.AnyToAnyImporter
 
removeObject(String) - Method in class net.sf.basedb.core.ItemContext
Remove a value.
removeParameter(AnnotationType) - Method in class net.sf.basedb.core.Protocol
Remove an annotation type from the parameters for this protocol.
removeParent(DerivedBioAssay) - Method in class net.sf.basedb.core.DerivedBioAssay
Remove a derived bioassay as a parent item for this derived bioassay.
removeParticipant(BioPlate) - Method in class net.sf.basedb.core.BioPlateEvent
Remove the given bioplate from this event.
removePhysicalBioAssay(PhysicalBioAssay) - Method in class net.sf.basedb.core.DerivedBioAssay
Remove a physical bioassay as a parent item for this derived bioassay.
removeProjectAnnotation(AnnotationType, Project) - Method in class net.sf.basedb.core.AnnotationSet
Delete the primary annotation of the specified annotation type.
removePropertyFilter(String) - Method in class net.sf.basedb.core.ItemContext
Remove a property filter on filter row 0.
removePropertyFilter(String, int) - Method in class net.sf.basedb.core.ItemContext
Remove a property filter on the given filter row.
removeRawBioAssay(RawBioAssay) - Method in class net.sf.basedb.core.Experiment
Remove a raw bioassay from this experiment.
removeRecursively(DbControl, Item, Set<Integer>, boolean) - Static method in class net.sf.basedb.util.RemovableUtil
Set the removed flag for selected items, including the subitems.
removeRelatedSubtype(Item) - Method in class net.sf.basedb.core.ItemSubtype
Remove the related subtype for the given item type.
removeReporter(ReporterData) - Method in class net.sf.basedb.core.ReporterList
Remove a reporter from the reporter list.
removeReporters(Set<Integer>) - Method in class net.sf.basedb.core.ReporterList
 
removeSetting(String) - Method in class net.sf.basedb.core.ItemContext
Remove a value.
removeSignal(Signal) - Method in class net.sf.basedb.core.signal.AbstractSignalHandler
Remove a signal from the list of supported signals.
removeSnapshot(int) - Static method in class net.sf.basedb.core.snapshot.SnapshotManager
Removes a snapshot from the static cache.
removeSnapshots(Collection<Integer>) - Static method in class net.sf.basedb.core.snapshot.SnapshotManager
Removes a list of snapshots from the static cache.
removeSnapshots(List<Integer>) - Static method in class net.sf.basedb.core.snapshot.SnapshotManager
 
removeSource(BioMaterial) - Method in class net.sf.basedb.core.BioMaterialEvent
Remove a biomaterial used as a source.
removeState() - Method in class net.sf.basedb.core.Job
Remove the saved state from the cache.
removeSymbol(String) - Method in class net.sf.basedb.core.Unit
Remove a symbol from this unit.
removeTemporaryFilter(String) - Method in class net.sf.basedb.core.ItemContext
Remote a temporary filter for the given property on filter row 0.
removeTemporaryFilter(String, int) - Method in class net.sf.basedb.core.ItemContext
Remote a temporary filter for the given property.
removeUnion(Collection<ItemList>) - Method in class net.sf.basedb.core.ItemList
Remove items that are present in at least ONE OF the given lists from this list.
removeUnion(Collection<ReporterList>) - Method in class net.sf.basedb.core.ReporterList
Remove reporters that are present in at least ONE OF the given lists from this list.
removeUsableUnit(Unit) - Method in class net.sf.basedb.core.AnnotationType
Remove a unit from this annotation type.
removeUser(User) - Method in class net.sf.basedb.core.Group
Remove a user that is a member of this group.
removeUser(User) - Method in class net.sf.basedb.core.Role
Revoke this Role from a user.
removeValueConverter(ValueConverter) - Method in class net.sf.basedb.util.extensions.xml.XmlLoader
Remove a converter.
render() - Method in class net.sf.basedb.clients.web.extensions.fileviewer.FileViewerUtil
Render the extensions with the current file context information and write it to the JSP output.
render(A) - Method in class net.sf.basedb.clients.web.extensions.renderer.PrefixSuffixRenderer
Deprecated.
render(A) - Method in class net.sf.basedb.util.extensions.AbstractRenderer
Deprecated.
render(A) - Method in interface net.sf.basedb.util.extensions.Renderer
Deprecated.
In 3.19.8, implement the Renderer.render(Action, Extension) method instead. This method will never be called from the BASE core except for the default implementation of Renderer.render(Action, Extension).
render(A, Extension<? extends A>) - Method in class net.sf.basedb.clients.web.extensions.renderer.PrefixSuffixRenderer
 
render(A, Extension<? extends A>) - Method in interface net.sf.basedb.util.extensions.Renderer
Render the action in the client application.
render(ListColumnAction<I, ?>, Extension<? extends ListColumnAction<I, ?>>) - Method in class net.sf.basedb.clients.web.extensions.list.ListColumnExportRenderer
 
render(ServiceControllerAction, Extension<? extends ServiceControllerAction>) - Method in class net.sf.basedb.clients.web.extensions.service.StartServiceRenderer
Calls ServiceControllerAction.start() on the service.
render(ServiceControllerAction, Extension<? extends ServiceControllerAction>) - Method in class net.sf.basedb.clients.web.extensions.service.StopServiceRenderer
Calls ServiceControllerAction.stop() on the service.
render(TabAction) - Method in class net.sf.basedb.clients.web.taglib.tab.TabControl
Deprecated.
render(TabAction, Extension<? extends TabAction>) - Method in class net.sf.basedb.clients.web.taglib.tab.TabControl
 
render(ButtonAction, Extension<? extends ButtonAction>) - Method in class net.sf.basedb.clients.web.extensions.toolbar.CompactButtonRenderer
Generates a linked icon:
render(ButtonAction, Extension<? extends ButtonAction>) - Method in class net.sf.basedb.clients.web.extensions.toolbar.ToolbarButtonRenderer
Generates a toolbar button.
render(SignalHandler, Extension<? extends SignalHandler>) - Method in class net.sf.basedb.core.signal.ExtensionSignalTransporter.SendSignalRenderer
 
render(Renderer<A>) - Method in class net.sf.basedb.util.extensions.ExtensionsInvoker
Render all actions using a specific renderer.
render(ValidationAction, Extension<? extends ValidationAction>) - Method in class net.sf.basedb.util.fileset.ResetMetadataRenderer
 
render(ValidationAction, Extension<? extends ValidationAction>) - Method in class net.sf.basedb.util.fileset.ValidationRenderer
 
render(Type, List, SessionFactoryImplementor) - Method in class net.sf.basedb.core.hibernate.NativeSQLFunction
 
Render - Class in net.sf.basedb.clients.web.taglib.extensions
Tag for rendering extensions.
Render() - Constructor for class net.sf.basedb.clients.web.taglib.extensions.Render
 
renderAsString() - Method in class net.sf.basedb.clients.web.extensions.fileviewer.FileViewerUtil
Render the extensions with the current file context information and return it as a string.
renderDefault() - Method in class net.sf.basedb.util.extensions.ExtensionsInvoker
Render all actions using the renderers created by the default renderer factories as specified by the registered extension points and/or extensions.
renderDefault(WrappingRenderer<A>) - Method in class net.sf.basedb.util.extensions.ExtensionsInvoker
Render all actions by wrapping the default renderers by the given wrapping renderer.
renderer - Variable in class net.sf.basedb.clients.web.taglib.extensions.Render
 
renderer - Variable in class net.sf.basedb.util.extensions.ExtensionContext
 
renderer - Variable in class net.sf.basedb.util.extensions.ExtensionPointContext
 
Renderer<A extends Action> - Interface in net.sf.basedb.util.extensions
A renderer is an object that knows how to render an action in the client interface.
rendererFactory - Variable in class net.sf.basedb.util.extensions.ExtensionBean
 
rendererFactory - Variable in class net.sf.basedb.util.extensions.ExtensionPointBean
 
rendererFactory - Variable in class net.sf.basedb.util.extensions.Registry.RegisteredExtension
 
rendererFactory - Variable in class net.sf.basedb.util.extensions.Registry.RegisteredExtensionPoint
 
RendererFactory<A extends Action> - Interface in net.sf.basedb.util.extensions
A renderer factory is a factory that can create Renderer objects.
renderWithEvent(Renderer<A>, EventType) - Method in class net.sf.basedb.util.extensions.ExtensionsInvoker
Render all actions using a specific renderer and send the specified event to event handlers.
rep - Variable in class net.sf.basedb.util.extensions.Registry.RegisteredExtension
 
REPLACE_VALUE - Static variable in class net.sf.basedb.core.ExtendedPropertyLinker
 
replaceDefaultItem(BasicItem) - Method in class net.sf.basedb.core.Project
Replace an existing default that has the same class and subtype as the given item with the given item.
replaceExisting - Variable in class net.sf.basedb.plugins.AnnotationFlatFileImporter
 
replaceExisting - Variable in class net.sf.basedb.util.annotations.InheritSpecification
 
replaceExistingParameter - Static variable in class net.sf.basedb.plugins.AnnotationFlatFileImporter
 
replaceInCommaSeparatedList(String, String, String) - Static method in class net.sf.basedb.core.Update
 
replacement - Variable in class net.sf.basedb.util.extensions.manager.processor.ExtractResourcesProcessor
 
replaceValuesIfDifferent(List<?>, boolean) - Method in class net.sf.basedb.core.data.DateParameterValueData
Overrides the parent method since we need date-specific equals and we want to get rid of the time part of the date.
replaceValuesIfDifferent(List<?>, boolean) - Method in class net.sf.basedb.core.data.ParameterValueData
Replace the values in the database with the new values in the specified list.
replaceValuesIfDifferent(List<?>, boolean) - Method in class net.sf.basedb.core.data.TimestampParameterValueData
Overrides the parent method since we need date-specific equals implementation.
replaceWithJoinAliases(String) - Method in class net.sf.basedb.core.AbstractHqlQuery
Replaces parts of the query with joined aliases.
replicate(Object, ReplicationMode) - Method in class net.sf.basedb.core.hibernate.SessionWrapper
 
replicate(String, Object, ReplicationMode) - Method in class net.sf.basedb.core.hibernate.SessionWrapper
 
reporter - Variable in class net.sf.basedb.core.data.FeatureData
 
reporter - Variable in class net.sf.basedb.core.data.RawData
 
reporter - Variable in class net.sf.basedb.core.data.ReporterListScoreData
 
reporter - Variable in class net.sf.basedb.core.data.ReporterTypeData
The reporters that have this type.
reporter - Variable in class net.sf.basedb.core.data.WellData
 
reporter - Variable in class net.sf.basedb.util.jep.ReporterFunction
 
reporter(String) - Static method in class net.sf.basedb.core.query.Dynamic
Create an expression representing a property of a reporter.
reporter(String, Boolean) - Static method in class net.sf.basedb.core.query.Dynamic
Create an expression representing a property of a reporter.
reporter(String, String, Type, Formula.AverageMethod, Formatter<?>) - Static method in class net.sf.basedb.util.export.spotdata.ExportableFieldFactory
Create a simple dynamic field that exports reporter annotation values.
reporter(ExtendedProperty, String, Formatter<?>) - Static method in class net.sf.basedb.util.export.spotdata.ExportableFieldFactory
Create a simple dynamic field that exports reporter annotation values.
Reporter - Class in net.sf.basedb.core
This is an utilitiy class for reporters.
Reporter() - Constructor for class net.sf.basedb.core.Reporter
 
REPORTER - Enum constant in enum class net.sf.basedb.core.Item
The item is a Reporter.
REPORTER - Static variable in class net.sf.basedb.core.File
The id for the FileType item representing a reporter file.
REPORTER_EXTERNAL_ID - Static variable in class net.sf.basedb.core.VirtualColumn
Column for storing the external reporter id.
REPORTER_ID - Static variable in class net.sf.basedb.core.VirtualColumn
This column stores the id of a reporter.
REPORTER_ID_PK - Static variable in class net.sf.basedb.core.VirtualColumn
Column for storing the id of a reporter when it is part of the primary key.
REPORTER_LIST_INNER - Static variable in class net.sf.basedb.core.DynamicPositionQueryJoiners
This instance joins reporter lists with an inner join, unless the ReporterListExpression.getAutoJoinType() method overrides the default.
REPORTER_LIST_INNER - Static variable in class net.sf.basedb.core.DynamicSpotQueryJoiners
This instance joins reporter lists with an inner join, unless the ReporterListExpression.getAutoJoinType() method overrides the default.
REPORTER_LIST_INNER - Static variable in class net.sf.basedb.core.HqlQueryJoiners
This instance joins reporter lists with an inner join, unless the ReporterListExpression.getAutoJoinType() method overrides the default.
REPORTER_LIST_LEFT - Static variable in class net.sf.basedb.core.DynamicPositionQueryJoiners
This instance joins reporter lists with a left join, unless the ReporterListExpression.getAutoJoinType() method overrides the default.
REPORTER_LIST_LEFT - Static variable in class net.sf.basedb.core.DynamicSpotQueryJoiners
This instance joins reporter lists with a left join, unless the ReporterListExpression.getAutoJoinType() method overrides the default.
REPORTER_LIST_LEFT - Static variable in class net.sf.basedb.core.HqlQueryJoiners
This instance joins reporter lists with a left join, unless the ReporterListExpression.getAutoJoinType() method overrides the default.
REPORTER_LIST_SCORES - Static variable in class net.sf.basedb.core.RealTable
 
REPORTER_MAP - Static variable in class net.sf.basedb.core.File
The id for the FileType item representing a reporter map file.
REPORTER_VERSION - Static variable in class net.sf.basedb.core.VirtualColumn
Column for storing the original version of a reporter that is cloned to a virtual table.
reporterBatcher - Variable in class net.sf.basedb.plugins.PlateFlatFileImporter
 
reporterBatcher - Variable in class net.sf.basedb.plugins.ReporterMapFlatFileImporter
 
reporterBatcher - Variable in class net.sf.basedb.util.importer.spotdata.PositionEventHandler
 
ReporterBatcher - Class in net.sf.basedb.core
Batcher class for reporters.
ReporterBatcher(DbControl) - Constructor for class net.sf.basedb.core.ReporterBatcher
 
reporterCache - Variable in class net.sf.basedb.util.export.spotdata.AbstractBioAssaySetExporter
 
reporterCloneBatcher - Variable in class net.sf.basedb.core.Experiment
 
ReporterCloneBatcher - Class in net.sf.basedb.core
Batcher implementation that is used to handle cloned reporter information in the dynamic database.
ReporterCloneBatcher(DbControl, Experiment) - Constructor for class net.sf.basedb.core.ReporterCloneBatcher
 
ReporterCloneBatcher.CloneSource - Enum Class in net.sf.basedb.core
Specifies which source table to use for finding out which reporters that are part of the current experiment.
ReporterClonePropertyData - Class in net.sf.basedb.core.data
This class holds information about cloned reporter properties.
ReporterClonePropertyData() - Constructor for class net.sf.basedb.core.data.ReporterClonePropertyData
 
reporterCloneTemplate - Variable in class net.sf.basedb.core.data.VirtualDbData
 
ReporterCloneTemplate - Class in net.sf.basedb.core
A reporter clone template is a definition of which reporter properties/annotations that should be cloned to a per-experiment table in the dynamic database.
ReporterCloneTemplate(ReporterCloneTemplateData) - Constructor for class net.sf.basedb.core.ReporterCloneTemplate
 
REPORTERCLONETEMPLATE - Enum constant in enum class net.sf.basedb.core.Item
The item is a ReporterCloneTemplate.
ReporterCloneTemplateData - Class in net.sf.basedb.core.data
A template for holding information about reporter properties that are/should be cloned in the dynamic database.
ReporterCloneTemplateData() - Constructor for class net.sf.basedb.core.data.ReporterCloneTemplateData
 
reporterColumnMapping - Static variable in class net.sf.basedb.plugins.PlateFlatFileImporter
 
ReporterData - Class in net.sf.basedb.core.data
This class represents the idea of clone, oligo or some other reporter for a gene.
ReporterData() - Constructor for class net.sf.basedb.core.data.ReporterData
 
ReporterData(int) - Constructor for class net.sf.basedb.core.data.ReporterData
Create a reporter object with a given ID.
reporterField - Variable in class net.sf.basedb.plugins.BaseFileExporterPlugin.ExtendedDynamicField
 
reporterField - Variable in class net.sf.basedb.plugins.BfsExporterPlugin.ExtendedExportableField
 
reporterField(String, String, Type, Formula.AverageMethod) - Method in class net.sf.basedb.plugins.BaseFileExporterPlugin
 
reporterField(String, String, Type, Formula.AverageMethod) - Static method in class net.sf.basedb.plugins.BfsExporterPlugin
 
reporterFields - Variable in class net.sf.basedb.util.export.spotdata.AbstractBioAssaySetExporter
 
ReporterFlatFileImporter - Class in net.sf.basedb.plugins
A plugin that imports reporter from a flat file.
ReporterFlatFileImporter() - Constructor for class net.sf.basedb.plugins.ReporterFlatFileImporter
Create a new importer.
ReporterFunction - Class in net.sf.basedb.util.jep
A JEP function class that adds a rep(string) or mrep(string) function to a JEP expression parser.
ReporterFunction() - Constructor for class net.sf.basedb.util.jep.ReporterFunction
Create a new instance of this function.
ReporterFunction(boolean) - Constructor for class net.sf.basedb.util.jep.ReporterFunction
Create a new instance of this function.
ReporterFunction(DbControl, RawDataType) - Constructor for class net.sf.basedb.util.jep.ReporterFunction
Create a new instance of this function working with reporters.
reporterId - Variable in class net.sf.basedb.core.data.ReporterListScoreData
 
reporterId - Variable in class net.sf.basedb.core.RawDataBatcher.FeatureInfo
 
reporterIdColumnMapping - Static variable in class net.sf.basedb.plugins.RawDataFlatFileImporter
 
reporterIdColumnMapping - Static variable in class net.sf.basedb.plugins.ReporterFlatFileImporter
 
reporterIdColumnMapping - Static variable in class net.sf.basedb.plugins.ReporterMapFlatFileImporter
 
reporterIndex - Variable in class net.sf.basedb.clients.web.ExperimentExplorer
The index of the current reporter on the view page.
reporterIndex - Variable in class net.sf.basedb.util.importer.spotdata.PositionEventHandler
 
reporterIsUsedErrorParameter - Static variable in class net.sf.basedb.plugins.ReporterFlatFileImporter
 
ReporterJoiner(JoinType) - Constructor for class net.sf.basedb.core.DynamicPositionQueryJoiners.ReporterJoiner
 
ReporterJoiner(JoinType) - Constructor for class net.sf.basedb.core.DynamicRawDataQuery.ReporterJoiner
 
ReporterJoiner(JoinType) - Constructor for class net.sf.basedb.core.DynamicSpotQueryJoiners.ReporterJoiner
 
reporterList - Variable in class net.sf.basedb.core.data.ReporterListScoreData
 
reporterList - Variable in class net.sf.basedb.core.query.ReporterListExpression
 
reporterList - Variable in class net.sf.basedb.core.ReporterListJoin
 
reporterList - Variable in class net.sf.basedb.plugins.ReporterFlatFileImporter
 
ReporterList - Class in net.sf.basedb.core
 
ReporterList(ReporterListData) - Constructor for class net.sf.basedb.core.ReporterList
 
REPORTERLIST - Enum constant in enum class net.sf.basedb.core.Item
The item is a ReporterType.
ReporterListData - Class in net.sf.basedb.core.data
This class holds information about a reporter list.
ReporterListData() - Constructor for class net.sf.basedb.core.data.ReporterListData
 
ReporterListExpression - Class in net.sf.basedb.core.query
Represents a property of a reporter list in a dynamic query: alias.property.
ReporterListExpression(ReporterList, String, String, String, JoinType) - Constructor for class net.sf.basedb.core.query.ReporterListExpression
 
ReporterListExpression(ReporterList, String, JoinType) - Constructor for class net.sf.basedb.core.query.ReporterListExpression
Create a new expression for the specified reporter list.
ReporterListJoin - Class in net.sf.basedb.core
Represents a join to a reporter list in a dynamic query: leftTable JOIN ReporterListScores ON ...
ReporterListJoin(ReporterList, JoinType, RealTable, String) - Constructor for class net.sf.basedb.core.ReporterListJoin
Create a new join to a reporter list using the given RealTable as the left table.
ReporterListJoin(ReporterList, JoinType, VirtualTable, VirtualColumn) - Constructor for class net.sf.basedb.core.ReporterListJoin
Create a new join to a reporter list using the given VirtualTable as the left table.
ReporterListJoiner(JoinType) - Constructor for class net.sf.basedb.core.DynamicPositionQueryJoiners.ReporterListJoiner
 
ReporterListJoiner(JoinType) - Constructor for class net.sf.basedb.core.DynamicRawDataQuery.ReporterListJoiner
 
ReporterListJoiner(JoinType) - Constructor for class net.sf.basedb.core.DynamicReporterQuery.ReporterListJoiner
 
ReporterListJoiner(JoinType) - Constructor for class net.sf.basedb.core.DynamicSpotQueryJoiners.ReporterListJoiner
 
ReporterListJoiner(JoinType) - Constructor for class net.sf.basedb.core.HqlQueryJoiners.ReporterListJoiner
 
reporterListParameter - Variable in class net.sf.basedb.plugins.ReporterFlatFileImporter
 
reporterLists - Variable in class net.sf.basedb.core.data.ExperimentData
 
ReporterListScoreData - Class in net.sf.basedb.core.data
This class holds information about the score of a reporter in a reporter list.
ReporterListScoreData() - Constructor for class net.sf.basedb.core.data.ReporterListScoreData
 
reporterListScores - Variable in class net.sf.basedb.core.data.ReporterData
 
ReporterMapFlatFileImporter - Class in net.sf.basedb.plugins
A plugin that imports features to an ArrayDesign from a flat file.
ReporterMapFlatFileImporter() - Constructor for class net.sf.basedb.plugins.ReporterMapFlatFileImporter
Create a new importer.
reporterMapMember - Variable in class net.sf.basedb.plugins.ReporterMapFlatFileImporter
 
reporterMapper - Variable in class net.sf.basedb.plugins.IlluminaRawDataImporter
 
reporterMapper - Variable in class net.sf.basedb.plugins.PlateFlatFileImporter
 
reporterMapper - Variable in class net.sf.basedb.plugins.RawDataFlatFileImporter
 
reporterMapper - Variable in class net.sf.basedb.plugins.ReporterMapFlatFileImporter
 
ReporterPositions(int, int[]) - Constructor for class net.sf.basedb.clients.web.ExperimentExplorer.ReporterPositions
 
reporterPrefix - Variable in class net.sf.basedb.plugins.PlateFlatFileImporter
 
reporterPrefixParameter - Variable in class net.sf.basedb.plugins.PlateFlatFileImporter
 
ReporterPropertyExpression - Class in net.sf.basedb.core
An expression representing the property of a reporter.
ReporterPropertyExpression(String) - Constructor for class net.sf.basedb.core.ReporterPropertyExpression
Create a new reporter property expression.
ReporterPropertyExpression(String, Boolean) - Constructor for class net.sf.basedb.core.ReporterPropertyExpression
Create a new reporter property expression.
reporterProxy - Variable in class net.sf.basedb.core.RawDataBatcher
 
ReporterProxy() - Constructor for class net.sf.basedb.core.RawDataBatcher.ReporterProxy
 
ReporterProxy() - Constructor for class net.sf.basedb.util.importer.spotdata.BaseFileImporter.ReporterProxy
 
reporters - Variable in class net.sf.basedb.core.data.ReporterListData
 
REPORTERS - Static variable in class net.sf.basedb.core.RealTable
 
REPORTERS_INNER - Static variable in class net.sf.basedb.core.DynamicPositionQueryJoiners
This instance joins reporters with an inner join.
REPORTERS_INNER - Static variable in class net.sf.basedb.core.DynamicSpotQueryJoiners
This instance joins reporters with an inner join.
REPORTERS_LEFT - Static variable in class net.sf.basedb.core.DynamicPositionQueryJoiners
This instance joins reporters with a left join.
REPORTERS_LEFT - Static variable in class net.sf.basedb.core.DynamicSpotQueryJoiners
This instance joins reporters with a left join.
ReporterScore - Class in net.sf.basedb.core
Get information about the reporters and their score in a reporter list.
ReporterScore(ReporterListScoreData) - Constructor for class net.sf.basedb.core.ReporterScore
 
REPORTERSCORE - Enum constant in enum class net.sf.basedb.core.Item
The item is a ReporterScore.
ReporterScore2DataPropertyPath(Type) - Constructor for class net.sf.basedb.core.Metadata.ReporterScore2DataPropertyPath
 
ReporterScoreQuery - Class in net.sf.basedb.core
This is a temporary solution to query against the reporter list's score.
ReporterScoreQuery() - Constructor for class net.sf.basedb.core.ReporterScoreQuery
Create a new query for the specified item, using the default optional runtime filter.
ReporterScoreQueryWrapper - Class in net.sf.basedb.clients.web.plugins
A query wrapper for ReporterScoreQuery:s.
ReporterScoreQueryWrapper(ReporterScoreQuery) - Constructor for class net.sf.basedb.clients.web.plugins.ReporterScoreQueryWrapper
Create a new query wrapper.
ReporterScoreResultIterator - Class in net.sf.basedb.core
This is a temporary solution for returning reporter list scores as an iterator.
ReporterScoreResultIterator(ScrollIterator<ReporterListScoreData>, DbControl, long) - Constructor for class net.sf.basedb.core.ReporterScoreResultIterator
 
reporterType - Variable in class net.sf.basedb.core.data.ReporterData
 
reporterType - Variable in class net.sf.basedb.plugins.ReporterFlatFileImporter
 
ReporterType - Class in net.sf.basedb.core
This class holds reporter type information.
ReporterType(ReporterTypeData) - Constructor for class net.sf.basedb.core.ReporterType
Constructor that sets reporter type data.
REPORTERTYPE - Enum constant in enum class net.sf.basedb.core.Item
The item is a ReporterType.
reporterTypeColumnMapping - Static variable in class net.sf.basedb.plugins.ReporterFlatFileImporter
 
ReporterTypeData - Class in net.sf.basedb.core.data
This class holds reporter type information.
ReporterTypeData() - Constructor for class net.sf.basedb.core.data.ReporterTypeData
Default constructor.
reporterTypeMapper - Variable in class net.sf.basedb.plugins.ReporterFlatFileImporter
 
reporterTypeParameter - Variable in class net.sf.basedb.plugins.ReporterFlatFileImporter
 
reporterTypes - Variable in class net.sf.basedb.plugins.ReporterFlatFileImporter
 
reporterWriter - Variable in class net.sf.basedb.util.export.spotdata.BfsExporter
 
reportInterval - Variable in class net.sf.basedb.util.importer.spotdata.BfsImporter.ProgressEventHandler
 
reportOnly - Variable in class net.sf.basedb.clients.web.servlet.ContentSecurityPolicyFilter
 
request - Variable in class net.sf.basedb.clients.web.extensions.IgnoreFilter
 
request - Variable in class net.sf.basedb.clients.web.extensions.InstallFilter
 
request - Variable in class net.sf.basedb.clients.web.extensions.UninstallFilter
 
request - Variable in class net.sf.basedb.core.plugin.ParameterValuesWrapper
 
request - Variable in class net.sf.basedb.core.PluginResponse
 
Request - Interface in net.sf.basedb.core.plugin
Pass request information to a plugin.
requestExternalStatusUpdate() - Method in class net.sf.basedb.core.InternalJobQueue
 
requestHandler - Variable in class net.sf.basedb.clients.jobagent.Agent
 
requestHandler - Variable in class net.sf.basedb.util.jobagent.JobAgentServerConnection.ListenerThread
 
requestHandler - Variable in class net.sf.basedb.util.jobagent.JobAgentServerConnection
 
requestHandler - Variable in class net.sf.basedb.util.jobagent.JobAgentServerConnection.RequestHandlerThread
 
RequestHandler - Interface in net.sf.basedb.util.jobagent
A request handler object takes care of an incoming request from a JobAgentServerConnection, processes it and returns an answer.
RequestHandlerThread(Socket, RequestHandler, Logger) - Constructor for class net.sf.basedb.util.jobagent.JobAgentServerConnection.RequestHandlerThread
 
RequestImpl(boolean) - Constructor for class net.sf.basedb.core.PluginRequest.RequestImpl
 
RequestInformation - Class in net.sf.basedb.core
Get information about the parameters the plugin needs for a particular request.
RequestInformation(String, String, String, List<PluginParameter<?>>) - Constructor for class net.sf.basedb.core.RequestInformation
 
RequestInformation(String, String, String, List<PluginParameter<?>>, String) - Constructor for class net.sf.basedb.core.RequestInformation
 
requestParameters - Variable in class net.sf.basedb.core.PluginRequest
 
requestStatusUpdate() - Method in class net.sf.basedb.core.Job
Request that the underlying job updates the status information about itself.
RequestWrapper - Class in net.sf.basedb.clients.web.extensions
Wrapper for HttpServletRequest that allows us to set proper servlet path and path info attributes for an extension servlet.
RequestWrapper(String, Request) - Constructor for class net.sf.basedb.plugins.executor.ExternalProgramExecutor.RequestWrapper
 
RequestWrapper(HttpServletRequest, String, String) - Constructor for class net.sf.basedb.clients.web.extensions.RequestWrapper
 
required - Variable in class net.sf.basedb.clients.web.taglib.Select
If a value is required or not.
required - Variable in class net.sf.basedb.core.data.ItemSubtypeFileTypeData
 
required - Variable in class net.sf.basedb.core.data.PlatformFileTypeData
 
required - Variable in class net.sf.basedb.core.Install.ItemSubtypeFT
 
required - Variable in class net.sf.basedb.core.Install.PlatformFT
 
required - Variable in class net.sf.basedb.plugins.executor.ParameterDefinition
 
requiredColumnMapping - Static variable in class net.sf.basedb.plugins.batchimport.AbstractItemImporter
 
requiredColumnMapping - Static variable in class net.sf.basedb.plugins.batchimport.AnyToAnyImporter
 
requiredColumnMapping - Static variable in class net.sf.basedb.plugins.RawDataFlatFileImporter
 
requiredColumnMapping - Static variable in class net.sf.basedb.plugins.ReporterFlatFileImporter
 
requiredColumnMapping - Static variable in class net.sf.basedb.plugins.ReporterMapFlatFileImporter
 
requiredFeatureIdColumnMapping - Static variable in class net.sf.basedb.plugins.gtf.GtfReporterMapImporter
 
requiredFilter - Variable in class net.sf.basedb.core.AbstractEntityQuery
The required runtime filter.
requiredFilters - Static variable in class net.sf.basedb.core.QueryRuntimeFilterFactory
 
requiredForMiame - Variable in class net.sf.basedb.core.data.AnnotationTypeData
 
requiredRegexpType - Static variable in class net.sf.basedb.plugins.AbstractFlatFileImporter
 
requiredSaveAsType - Static variable in class net.sf.basedb.core.plugin.AbstractExporterPlugin
 
requiredStringParameter - Static variable in class net.sf.basedb.plugins.PlateMappingImporter
 
requireEmptyDatabase - Variable in enum class net.sf.basedb.core.hibernate.SchemaGenerator.Mode
 
requireEmptyDatabase() - Method in enum class net.sf.basedb.core.hibernate.SchemaGenerator.Mode
Does this installation mode require an empty database or not?
requiresConfiguration - Variable in class net.sf.basedb.core.data.PluginDefinitionData
 
requiresConfiguration() - Method in class net.sf.basedb.clients.web.plugins.SimpleExport
 
requiresConfiguration() - Method in class net.sf.basedb.core.plugin.AbstractPlugin
Returns FALSE, since that is how the plugins used to work before this method was introduced.
requiresConfiguration() - Method in interface net.sf.basedb.core.plugin.Plugin
Return TRUE if the plugin requires a configuration when executing a job.
requiresConfiguration() - Method in class net.sf.basedb.core.PluginDefinition
Check if the plugin requires a configuration to execute a job.
requiresConfiguration() - Method in class net.sf.basedb.plugins.AbstractFlatFileImporter
Return TRUE, since the implementation requires it for finding the regular expressions used by the FlatFileParser.
requiresConfiguration() - Method in class net.sf.basedb.plugins.AnnotationFlatFileImporter
 
requiresConfiguration() - Method in class net.sf.basedb.plugins.Base1PluginExecuter
 
requiresConfiguration() - Method in class net.sf.basedb.plugins.BaseFileExporterPlugin
 
requiresConfiguration() - Method in class net.sf.basedb.plugins.batchimport.AbstractItemImporter
 
requiresConfiguration() - Method in class net.sf.basedb.plugins.batchimport.AnyToAnyImporter
 
requiresConfiguration() - Method in class net.sf.basedb.plugins.BfsExporterPlugin
 
requiresConfiguration() - Method in class net.sf.basedb.plugins.CdfFileReporterImporter
 
requiresConfiguration() - Method in class net.sf.basedb.plugins.CloneReportersPlugin
 
requiresConfiguration() - Method in class net.sf.basedb.plugins.executor.AbstractIOSupport
 
requiresConfiguration() - Method in class net.sf.basedb.plugins.executor.ExternalProgramExecutor
 
requiresConfiguration() - Method in class net.sf.basedb.plugins.FormulaFilter
 
requiresConfiguration() - Method in class net.sf.basedb.plugins.GalExporter
 
requiresConfiguration() - Method in class net.sf.basedb.plugins.HelpExporter
 
requiresConfiguration() - Method in class net.sf.basedb.plugins.HelpImporter
 
requiresConfiguration() - Method in class net.sf.basedb.plugins.IlluminaRawDataImporter
 
requiresConfiguration() - Method in class net.sf.basedb.plugins.IntensityCalculatorPlugin
 
requiresConfiguration() - Method in class net.sf.basedb.plugins.JepExtraValueCalculator
 
requiresConfiguration() - Method in class net.sf.basedb.plugins.JepIntensityTransformer
 
requiresConfiguration() - Method in class net.sf.basedb.plugins.LowessNormalization
 
requiresConfiguration() - Method in class net.sf.basedb.plugins.ManualDerivedBioAssayCreator
 
requiresConfiguration() - Method in class net.sf.basedb.plugins.ManualTransformCreator
 
requiresConfiguration() - Method in class net.sf.basedb.plugins.MedianRatioNormalization
 
requiresConfiguration() - Method in class net.sf.basedb.plugins.PackedFileExporter
 
requiresConfiguration() - Method in class net.sf.basedb.plugins.PlateFlatFileImporter
 
requiresConfiguration() - Method in class net.sf.basedb.plugins.PlateMappingExporter
 
requiresConfiguration() - Method in class net.sf.basedb.plugins.PlateMappingImporter
 
requiresConfiguration() - Method in class net.sf.basedb.plugins.PluginConfigurationExporter
Always false
requiresConfiguration() - Method in class net.sf.basedb.plugins.PluginConfigurationImporter
 
requiresConfiguration() - Method in class net.sf.basedb.plugins.PrintMapFlatFileImporter
 
requiresConfiguration() - Method in class net.sf.basedb.plugins.RawDataFlatFileImporter
 
requiresConfiguration() - Method in class net.sf.basedb.plugins.ReporterFlatFileImporter
 
requiresConfiguration() - Method in class net.sf.basedb.plugins.ReporterMapFlatFileImporter
 
requiresConfiguration() - Method in class net.sf.basedb.util.zip.AbstractFileUnpacker
Returns FALSE.
reset() - Method in class net.sf.basedb.clients.web.ExperimentExplorer.AnnotationGroup
Resets all collected statistics in this group.
reset() - Method in class net.sf.basedb.clients.web.ExperimentExplorer.AnnotationSummary
Reset the collected statistics in all annotation groups.
reset() - Method in class net.sf.basedb.clients.web.fileupload.FileUpload.UploadStream
Not supported.
reset() - Static method in class net.sf.basedb.clients.web.servlet.RssNewsFeed
Reset the feed and force it to regenerate it's content.
reset() - Method in class net.sf.basedb.clients.web.util.ProjectSpecificInfoFilter
Reset the flags to false.
reset() - Method in class net.sf.basedb.core.AbstractHqlQuery
Reset all non-permanent query elements of the query and clear cached queries.
reset() - Method in class net.sf.basedb.core.AbstractQuery
Resets the query, allowing you to add more restrictions, joins, order objects and parameters.
reset() - Method in class net.sf.basedb.core.DiskUsageStatistics
Reset the internal cache of already loaded statistics.
reset() - Method in class net.sf.basedb.core.DynamicPositionQuery
Reset join information.
reset() - Method in class net.sf.basedb.core.DynamicSpotQuery
Reset join information.
reset() - Method in interface net.sf.basedb.core.query.Query
Reset the query, removing all non-permanent query elements and parameter values.
reset() - Method in class net.sf.basedb.util.gtf.GtfInputStream
 
reset() - Method in class net.sf.basedb.util.InputStreamSplitter
 
reset() - Method in class net.sf.basedb.util.InputStreamTracker
 
reset(int) - Method in class net.sf.basedb.util.timer.PerformanceTimer
Reset a timer.
reset(DbControl) - Method in class net.sf.basedb.util.overview.GenericOverview
Reset the overview and re-create the root node.
reset(DynamicPositionQuery) - Method in class net.sf.basedb.core.DynamicPositionQueryJoiners.ExtraValueJoiner
 
reset(DynamicPositionQuery) - Method in class net.sf.basedb.core.DynamicPositionQueryJoiners.ReporterJoiner
 
reset(DynamicPositionQuery) - Method in class net.sf.basedb.core.DynamicPositionQueryJoiners.ReporterListJoiner
 
reset(DynamicRawDataQuery) - Method in class net.sf.basedb.core.DynamicRawDataQuery.RawBioAssayJoiner
 
reset(DynamicRawDataQuery) - Method in class net.sf.basedb.core.DynamicRawDataQuery.ReporterJoiner
 
reset(DynamicRawDataQuery) - Method in class net.sf.basedb.core.DynamicRawDataQuery.ReporterListJoiner
 
reset(DynamicReporterQuery) - Method in class net.sf.basedb.core.DynamicReporterQuery.MasterReporterJoiner
 
reset(DynamicReporterQuery) - Method in class net.sf.basedb.core.DynamicReporterQuery.ReporterListJoiner
 
reset(DynamicSpotQuery) - Method in class net.sf.basedb.core.DynamicSpotQueryJoiners.ExtraValueJoiner
 
reset(DynamicSpotQuery) - Method in class net.sf.basedb.core.DynamicSpotQueryJoiners.RawDataJoiner
 
reset(DynamicSpotQuery) - Method in class net.sf.basedb.core.DynamicSpotQueryJoiners.ReporterJoiner
 
reset(DynamicSpotQuery) - Method in class net.sf.basedb.core.DynamicSpotQueryJoiners.ReporterListJoiner
 
reset(Response.Status) - Method in class net.sf.basedb.core.PluginResponse
 
reset(HqlQuery) - Method in class net.sf.basedb.core.HqlQueryJoiners.AnnotationJoiner
 
reset(HqlQuery) - Method in class net.sf.basedb.core.HqlQueryJoiners.ReporterListJoiner
 
reset(Q) - Method in interface net.sf.basedb.core.query.AutoJoiner
Called to indicate that Query.reset() has been called on the given query.
resetAll() - Method in class net.sf.basedb.util.timer.PerformanceTimer
Reset all timers.
resetCache() - Method in class net.sf.basedb.util.units.UnitCache
Clear the cache of all units.
resetClassLoader - Variable in class net.sf.basedb.util.extensions.manager.processor.ResetProcessor
 
resetClassLoader() - Method in class net.sf.basedb.util.extensions.manager.ExtensionsFile.WriteableExtensionsFile
Reset the classloader for this file, forcing a new instance in case the JAR file has been changed.
resetCollected() - Method in class net.sf.basedb.util.listable.CollectExtracts
Clear all collected extracts in order to prepare for a new collection.
resetCollected() - Method in class net.sf.basedb.util.listable.TransformContext
Clear all collected items and disable both 'collecting' and 'avoiding'.
ResetCollected(SourceItemTransformer) - Constructor for class net.sf.basedb.util.listable.CollectExtracts.ResetCollected
 
resetDynamicAttributes() - Method in class net.sf.basedb.clients.web.taglib.StylableTag
Clear all dynamic attributes.
resetErrorFlag - Variable in class net.sf.basedb.util.extensions.manager.processor.ResetProcessor
 
resetMetadata() - Method in class net.sf.basedb.util.affymetrix.CdfValidationAction
 
resetMetadata() - Method in class net.sf.basedb.util.affymetrix.CelValidationAction
 
resetMetadata() - Method in interface net.sf.basedb.util.fileset.ValidationAction
Reset all metadata that this class normally can set.
resetMetadata() - Method in class net.sf.basedb.util.gtf.GtfValidationAction
 
resetMetadata(ArrayDesign) - Method in class net.sf.basedb.util.affymetrix.CdfValidator
Reset metadata on the given array design.
resetMetadata(RawBioAssay) - Method in class net.sf.basedb.util.affymetrix.CelValidator
Reset metadata on the given raw bioassay.
ResetMetadataRenderer - Class in net.sf.basedb.util.fileset
Renderer implementation for resetting metadata for the members of a file set.
ResetMetadataRenderer(List<ValidatingFileSetMember>) - Constructor for class net.sf.basedb.util.fileset.ResetMetadataRenderer
Create a new renderer instance.
ResetProcessor - Class in net.sf.basedb.util.extensions.manager.processor
File processor implementation that reset the error flag, class loader, etc.
ResetProcessor(ProcessResults) - Constructor for class net.sf.basedb.util.extensions.manager.processor.ResetProcessor
Create a new processor instance using default settings.
resetTemporary() - Method in class net.sf.basedb.core.AbstractQuery
 
RESISTANCE - Static variable in class net.sf.basedb.core.Quantity
The id for the Quantity object representing electrical resistance.
resolveEntity(String, String) - Method in class net.sf.basedb.util.XmlUtil2.Validator
This method is called when the parser wants a reference to the DTD file.
resolvePath(String, String) - Static method in class net.sf.basedb.plugins.batchimport.FileImporter
 
resource - Variable in class net.sf.basedb.util.uri.CloseResourceInputStream
 
ResourceBundleFactory - Class in net.sf.basedb.util.resources
Factory for loading resource bundles.
ResourceBundleFactory() - Constructor for class net.sf.basedb.util.resources.ResourceBundleFactory
 
ResourceBundleWrapper - Class in net.sf.basedb.util.resources
A wrapper around ResourceBundle objects.
ResourceBundleWrapper(String, ResourceBundle) - Constructor for class net.sf.basedb.util.resources.ResourceBundleWrapper
The wrapper is created by ResourceBundleFactory.
RESOURCES_URL - Static variable in class net.sf.basedb.clients.web.extensions.ExtensionsControl
The location where the extensions resources are extracted.
RESOURCES_URL - Static variable in class net.sf.basedb.clients.web.extensions.XJspCompiler
The location where the extensions resources are extracted.
resourcesPath - Variable in class net.sf.basedb.clients.web.extensions.WebClientRegisterExtensionsProcessor
 
response - Variable in class net.sf.basedb.clients.web.util.ServletExportOutputStream
 
response - Variable in class net.sf.basedb.core.PluginResponse
 
Response - Interface in net.sf.basedb.core.plugin
The response interface used by the core.
Response.Status - Enum Class in net.sf.basedb.core.plugin
 
responseFilter - Variable in class net.sf.basedb.util.uri.http.HttpConnectionManager
 
ResponseFilter() - Constructor for class net.sf.basedb.util.GeoLocation.ResponseFilter
 
ResponseImpl() - Constructor for class net.sf.basedb.core.PluginResponse.ResponseImpl
 
ResponseWrapper() - Constructor for class net.sf.basedb.plugins.executor.ExternalProgramExecutor.ResponseWrapper
 
restart(Extension<ServiceControllerAction>) - Static method in class net.sf.basedb.clients.web.extensions.service.Services
Restart services as a result of an administrator has uninstalled an extension or is updating/disabling an existing on.
restorePath(Directory) - Static method in class net.sf.basedb.util.RemovableUtil
Restores the path to a directory
restrict(Restriction) - Method in class net.sf.basedb.core.AbstractQuery
 
restrict(Restriction) - Method in interface net.sf.basedb.core.query.Query
Add a restriction query element to the restriction list.
RESTRICTED_WRITE - Enum constant in enum class net.sf.basedb.core.Permission
This permission allows a user to update some information about an item.
restrictedEdit - Variable in class net.sf.basedb.core.ExtendedProperty
 
restriction(String, String) - Static method in class net.sf.basedb.core.query.Hql
 
Restriction - Interface in net.sf.basedb.core.query
A restriction query element.
restrictions - Variable in class net.sf.basedb.core.AbstractQuery
List of restrictions added to the query.
restrictions - Variable in class net.sf.basedb.core.ItemContext.RowRestrictions
 
restrictions - Variable in class net.sf.basedb.core.query.AndRestriction
 
restrictions - Variable in class net.sf.basedb.core.query.OrRestriction
 
Restrictions - Class in net.sf.basedb.core.query
A factory class to create restrictions.
Restrictions() - Constructor for class net.sf.basedb.core.query.Restrictions
 
RestrictionTransformer - Class in net.sf.basedb.util.listable
Transformer implementation that is intended to provide a final filtering of target items.
RestrictionTransformer(SourceItemTransformer, ItemQuery<?>) - Constructor for class net.sf.basedb.util.listable.RestrictionTransformer
Create a new transformer and use the given query to find the target items.
RestrictionTransformer(SourceItemTransformer, Restriction) - Constructor for class net.sf.basedb.util.listable.RestrictionTransformer
Create a new transformer and apply the given restriction to items before they are returned.
restrictPermanent(Restriction) - Method in class net.sf.basedb.core.AbstractQuery
 
restrictPermanent(Restriction) - Method in interface net.sf.basedb.core.query.Query
Permanently add a restriction query element to the restriction list.
restrictSource(DynamicSpotQuery, List<BioAssay>) - Method in class net.sf.basedb.core.plugin.AbstractAnalysisPlugin
Restricts a query to only include values from listed bioassays
restrictToPushAnnotationSubtypes(ItemQuery<? extends Subtypable>) - Static method in class net.sf.basedb.util.overview.OverviewUtil
Add a restriction to the query that limit the returned result to those items that has a subtype with the ItemSubtype.getPushAnnotations() flag set.
result - Variable in class net.sf.basedb.util.jep.ChannelFunction
 
result - Variable in class net.sf.basedb.util.jep.ExtraValueFunction
 
result - Variable in class net.sf.basedb.util.jep.RawChannelFunction
 
result - Variable in class net.sf.basedb.util.jep.ScoreFunction
 
result - Variable in class net.sf.basedb.util.parser.FlatFileParser.Data
 
resultIntensityTransform - Variable in class net.sf.basedb.core.data.FormulaData
 
ResultIterator<I> - Interface in net.sf.basedb.core.query
Return the result of a query as an iterator.
ResultList<I> - Interface in net.sf.basedb.core.query
Return the result of a query as a list.
ResultListIterator(Iterator<? extends BasicData>, Class<T>) - Constructor for class net.sf.basedb.core.ItemResultList.ResultListIterator
 
ResultListListIterator(ListIterator<? extends BasicData>, Class<T>) - Constructor for class net.sf.basedb.core.ItemResultList.ResultListListIterator
 
results - Variable in class net.sf.basedb.clients.web.extensions.InstalledFileProcessor
 
results - Variable in class net.sf.basedb.clients.web.extensions.LoadServletsProcessor
 
results - Variable in class net.sf.basedb.clients.web.extensions.UninstalledFileProcessor
 
results - Variable in class net.sf.basedb.core.DynamicResultIterator
The results of the query.
results - Variable in class net.sf.basedb.core.ScrollIterator
 
results - Variable in class net.sf.basedb.util.extensions.manager.filter.WasProcessedFilter
 
results - Variable in class net.sf.basedb.util.extensions.manager.processor.DeleteResourcesProcessor
 
results - Variable in class net.sf.basedb.util.extensions.manager.processor.DisablePluginsProcessor
 
results - Variable in class net.sf.basedb.util.extensions.manager.processor.ExtractResourcesProcessor
 
results - Variable in class net.sf.basedb.util.extensions.manager.processor.IgnoreFileProcessor
 
results - Variable in class net.sf.basedb.util.extensions.manager.processor.PluginInstallationProcessor
 
results - Variable in class net.sf.basedb.util.extensions.manager.processor.RegisterExtensionsProcessor
 
results - Variable in class net.sf.basedb.util.extensions.manager.processor.ResetProcessor
 
results - Variable in class net.sf.basedb.util.extensions.manager.processor.UnregisterExtensionsProcessor
 
ResultSetWork<R> - Class in net.sf.basedb.core.hibernate
A work implementation that executes an SQL query on the connection, and returns a value that is picked by a subclass from the resulting ResultSet.
ResultSetWork(SessionControl, String) - Constructor for class net.sf.basedb.core.hibernate.ResultSetWork
Create a new work item.
ResultWriter - Interface in net.sf.basedb.core.migrate
Interface for quick writing of data from a JDBC result set to a writer.
ResultWriterFactory - Interface in net.sf.basedb.core.migrate
Interface for factories that knows how to create result writers.
ResumableConnectionManager - Interface in net.sf.basedb.util.uri
An extension to the ConnectionManager interface that add support for specifying a start offset when downloading the external file.
resync - Variable in class net.sf.basedb.util.annotations.InheritSpecification
 
resyncCloned() - Method in class net.sf.basedb.core.Annotation
If this is a cloned annotation, resync the cloned values.
resyncFilter - Variable in class net.sf.basedb.util.annotations.InheritAnnotationsManager
 
resyncFilter(DbControl, ItemList.SynchronizeOption, boolean, ProgressReporter) - Method in class net.sf.basedb.core.ItemList
Re-sync with the current synchronization filter.
retainAll(Collection<?>) - Method in class net.sf.basedb.core.AbstractResultList
Not supported.
retainAll(Collection<?>) - Method in class net.sf.basedb.core.UnmodifiableResultList
Not supported.
retainAll(Collection<?>) - Method in class net.sf.basedb.util.Tree
Not supported.
retainAll(ItemList) - Method in class net.sf.basedb.core.ItemList
Remove all items from this list that are NOT present in the other list.
retainAll(ItemList.DelayedAdditionManager) - Method in class net.sf.basedb.core.ItemList.DelayedAdditionManager
 
retainAll(ReporterList) - Method in class net.sf.basedb.core.ReporterList
Remove all reporters from this list that are NOT present in the other list.
retainIfPresentIn(int, int, Collection<ItemList>) - Method in class net.sf.basedb.core.ItemList
Retain items that are present in the specified number of lists in this list.
retainIfPresentIn(int, int, Collection<ReporterList>) - Method in class net.sf.basedb.core.ReporterList
Retain reporters that are present in the specified number of lists in this list.
retainIntersection(Collection<ItemList>) - Method in class net.sf.basedb.core.ItemList
Retain items that are present in ALL OF the given lists in this list.
retainIntersection(Collection<ReporterList>) - Method in class net.sf.basedb.core.ReporterList
Retain reporters that are present in ALL OF the given lists in this list.
retainMembers(Set<Integer>, ItemList.DelayedAdditionManager) - Method in class net.sf.basedb.core.ItemList
Keep only specified members in this list
retainReporters(Set<Integer>) - Method in class net.sf.basedb.core.ReporterList
 
retainUnion(Collection<ItemList>) - Method in class net.sf.basedb.core.ItemList
Retain items that are present in at least ONE OF the given lists in this list.
retainUnion(Collection<ReporterList>) - Method in class net.sf.basedb.core.ReporterList
Retain reporters that are present in at least ONE OF the given lists in this list.
RethrowErrorHandlerFactory - Class in net.sf.basedb.util.extensions
Extension to the logging error handler factory that create error handlers that re-throw the original exception.
RethrowErrorHandlerFactory() - Constructor for class net.sf.basedb.util.extensions.RethrowErrorHandlerFactory
 
retry(boolean, boolean) - Method in class net.sf.basedb.core.Job
Retry a job which finished with an error or a successful dry-run job.
returnArray - Variable in class net.sf.basedb.core.ScrollIterator
 
returnClass - Variable in class net.sf.basedb.core.query.ReturnClassFilter
 
ReturnClassFilter - Class in net.sf.basedb.core.query
Filter implementation that checks if the items returned by a EntityQuery are compatible with the specified class.
ReturnClassFilter(Class<?>) - Constructor for class net.sf.basedb.core.query.ReturnClassFilter
Creates a filter that matches the specified item class.
returnedRows - Variable in class net.sf.basedb.core.DynamicResultIterator
 
returnKeys - Variable in class net.sf.basedb.util.resources.ResourceBundleWrapper
 
returnTotalCount - Variable in class net.sf.basedb.core.AbstractQuery
If the query should calculate the total number of matching items in the case that limits have been set with AbstractQuery.firstResult or AbstractQuery.maxResults.
returnType - Variable in class net.sf.basedb.core.AbstractEntityQuery
The item type returned by the query, eg.
REVERSE - Enum constant in enum class net.sf.basedb.util.overview.node.ChildNodeDirection
Child nodes should be loaded in the reverse-loading direction.
right - Variable in class net.sf.basedb.core.DynamicJoin
 
right - Variable in class net.sf.basedb.core.ExtraValueJoin
 
right - Variable in class net.sf.basedb.core.RealJoin
 
right - Variable in class net.sf.basedb.core.ReporterListJoin
 
rightColumns - Variable in class net.sf.basedb.core.DynamicJoin
 
rightJoin(String, String) - Static method in class net.sf.basedb.core.query.Hql
Same as rightJoin(null, propert, joinedAlias, null)
rightJoin(String, String, String, Restriction) - Static method in class net.sf.basedb.core.query.Hql
Create a right join query element.
rLeft - Variable in class net.sf.basedb.core.RealJoin
 
rLeftColumn - Variable in class net.sf.basedb.core.RealJoin
 
rlike(String, String) - Method in class net.sf.basedb.core.dbengine.AbstractDbEngine
Return <value> = <regexp>
rlike(String, String) - Method in interface net.sf.basedb.core.dbengine.DbEngine
Get a function/expression that matches the left value against the right value which should be a regular expression.
rlike(String, String) - Method in class net.sf.basedb.core.dbengine.MySQLEngine
Return <value> RLIKE <regexp>.
rlike(String, String) - Method in class net.sf.basedb.core.dbengine.PostgresDbEngine
Return <value> ~ <regexp>.
rlike(Expression, Expression) - Static method in class net.sf.basedb.core.query.Restrictions
Check if an expression matches a regular expression.
RLIKE - Enum constant in enum class net.sf.basedb.core.Operator
 
RlikeRestriction - Class in net.sf.basedb.core.query
Checks if an expression matches a regular expression: e RLIKE regexp (MySQL) or e ~ regexp (Postgres).
RlikeRestriction(Expression, Expression) - Constructor for class net.sf.basedb.core.query.RlikeRestriction
 
robotHasBeenSet - Variable in class net.sf.basedb.core.ArrayBatch
 
role - Variable in class net.sf.basedb.core.data.BioPlateEventParticipantData
 
Role - Class in net.sf.basedb.core
This class is used to represent roles.
Role(RoleData) - Constructor for class net.sf.basedb.core.Role
 
ROLE - Enum constant in enum class net.sf.basedb.core.Item
The item is a Role.
Role.QueryRuntimeFilterImpl - Class in net.sf.basedb.core
A runtime filter implementation that limits a query to only return roles where the logged in user is a member unless the logged in user has generic read permission.
RoleData - Class in net.sf.basedb.core.data
This class holds information about a role.
RoleData() - Constructor for class net.sf.basedb.core.data.RoleData
 
roleId - Variable in class net.sf.basedb.core.data.keyring.RoleKeys
 
roleId - Variable in class net.sf.basedb.core.data.keyring.UserRoles
 
RoleKey - Class in net.sf.basedb.core
This class is used to represent a role key.
RoleKey(RoleKeyData) - Constructor for class net.sf.basedb.core.RoleKey
 
ROLEKEY - Enum constant in enum class net.sf.basedb.core.Item
The item is a RoleKey.
RoleKeyData - Class in net.sf.basedb.core.data
This class holds information access privileges for roles.
RoleKeyData() - Constructor for class net.sf.basedb.core.data.RoleKeyData
 
roleKeys - Static variable in class net.sf.basedb.core.SystemItems
An array to hold mappings for RoleKeyData: RoleKeyData.itemType --> RoleKeyData.id
RoleKeys - Class in net.sf.basedb.core.data.keyring
Class for mapping the RoleKeys table.
RoleKeys() - Constructor for class net.sf.basedb.core.data.keyring.RoleKeys
Create a new RoleKeys object.
rolePermissions - Variable in class net.sf.basedb.core.Keyring
Two-dimensional array for holding the permissions for RoleKey:s.
roles - Variable in class net.sf.basedb.core.data.RoleKeyData
 
roles - Variable in class net.sf.basedb.core.data.UserData
 
roles - Variable in class net.sf.basedb.core.Keyring
Holds the ID of all roles that the user is a member of.
rollback() - Method in class net.sf.basedb.core.DbControl
Rollback the transaction.
rollback(Transaction) - Static method in class net.sf.basedb.core.HibernateUtil
Rollback a transaction.
rollbackToSavepoint(Connection, Savepoint, String) - Method in class net.sf.basedb.core.AbstractSqlQuery
Rollback the current transaction to the given savepoint.
root - Variable in class net.sf.basedb.util.extensions.xml.PathConverter
 
root - Variable in class net.sf.basedb.util.StaticCache
 
root - Variable in class net.sf.basedb.util.Tree
 
ROOT - Static variable in class net.sf.basedb.clients.web.taglib.menu.Menu
The path to the root directory of this webserver.
ROOT - Static variable in class net.sf.basedb.clients.web.taglib.Page
The path to the root directory of this webserver.
ROOT - Static variable in class net.sf.basedb.clients.web.taglib.path.Path
The path to the root directory of this webserver.
ROOT - Variable in class net.sf.basedb.clients.web.taglib.PropertyValue
 
ROOT - Static variable in class net.sf.basedb.core.Directory
The id for the Directory item representing the root.
ROOT - Static variable in class net.sf.basedb.core.Keyring
 
ROOT - Static variable in class net.sf.basedb.core.User
The system id for the User representing the root account.
ROOT - Static variable in class net.sf.basedb.plugins.batchimport.FileImporter.PathIdMethod
 
ROOT() - Static method in class net.sf.basedb.clients.web.taglib.Page
Static version of Page.getRoot().
rootAlias - Variable in class net.sf.basedb.core.AbstractHqlQuery
The alias for the root table.
rootAlias - Variable in class net.sf.basedb.core.DynamicReporterQuery
 
rootDerivedBioAssays - Variable in class net.sf.basedb.core.data.PhysicalBioAssayData
 
rootEntity - Variable in class net.sf.basedb.core.AbstractQuery
The root enitity.
rootItem - Variable in class net.sf.basedb.util.overview.GenericOverview
 
rootNode - Variable in class net.sf.basedb.util.overview.GenericOverview
 
rootPath - Variable in class net.sf.basedb.core.data.FileServerData
 
rootPath - Variable in class net.sf.basedb.plugins.batchimport.FileImporter.PathIdMethod
 
rootPath - Variable in class net.sf.basedb.plugins.batchimport.FileImporter
 
rootPath - Variable in class net.sf.basedb.util.StaticCache
 
rootPath - Variable in class net.sf.basedb.util.uri.ConnectionParameters
 
RootRawBioAssay - Class in net.sf.basedb.core
Represents the use of a raw bioassay in an experiment.
RootRawBioAssay(RootRawBioAssayData) - Constructor for class net.sf.basedb.core.RootRawBioAssay
Creates a new root raw bioassay item from the given data.
ROOTRAWBIOASSAY - Enum constant in enum class net.sf.basedb.core.Item
The item is a RootRawBioAssay.
RootRawBioAssayData - Class in net.sf.basedb.core.data
This class holds the link between experiments and raw bioassays including an annotation set that is representing the experimental factor values.
RootRawBioAssayData() - Constructor for class net.sf.basedb.core.data.RootRawBioAssayData
 
RootRawBioAssayLoader - Class in net.sf.basedb.util.overview.loader
Node loader implementation for root raw bioassays.
RootRawBioAssayLoader() - Constructor for class net.sf.basedb.util.overview.loader.RootRawBioAssayLoader
 
rootRawBioAssays - Variable in class net.sf.basedb.core.data.ExperimentData
 
rootTable - Variable in class net.sf.basedb.core.DynamicQuery
 
rootTable - Variable in class net.sf.basedb.core.DynamicRawDataQuery
 
rootType - Variable in class net.sf.basedb.core.AbstractEntityQuery
The root item type we start with in the query. eq.
row - Variable in class net.sf.basedb.clients.web.taglib.table.PropertyFilter
 
row - Variable in class net.sf.basedb.core.data.BioWellData
 
row - Variable in class net.sf.basedb.core.data.FeatureData
 
row - Variable in class net.sf.basedb.core.data.MappingCoordinate
The row number.
row - Variable in class net.sf.basedb.core.data.PlateCoordinate
The row number.
row - Variable in class net.sf.basedb.core.data.RawData
 
row - Variable in class net.sf.basedb.core.data.WellData
 
row - Variable in class net.sf.basedb.core.FeatureCoordinate
The row of this feature.
Row - Class in net.sf.basedb.clients.web.taglib.table
This tag defines a new row in the table.
Row() - Constructor for class net.sf.basedb.clients.web.taglib.table.Row
 
rowclass - Static variable in class net.sf.basedb.clients.web.taglib.table.Table
The class names for even and odd row respectively.
rowColumnMapping - Static variable in class net.sf.basedb.plugins.PlateFlatFileImporter
 
rowColumnMapping - Static variable in class net.sf.basedb.plugins.RawDataFlatFileImporter
 
rowColumnMapping - Static variable in class net.sf.basedb.plugins.ReporterMapFlatFileImporter
 
rowIdList - Variable in class net.sf.basedb.core.ItemContext.RowRestrictions
 
rowIndex - Variable in class net.sf.basedb.core.ItemContext.RowRestrictions
 
rowIndex - Variable in class net.sf.basedb.core.PropertyFilter
 
rowIndex - Variable in class net.sf.basedb.util.bfs.AnnotationModel
 
rowMapper - Variable in class net.sf.basedb.plugins.PlateFlatFileImporter
 
rowMapper - Variable in class net.sf.basedb.plugins.RawDataFlatFileImporter
 
rowMapper - Variable in class net.sf.basedb.plugins.ReporterMapFlatFileImporter
 
rowNo - Variable in class net.sf.basedb.util.excel.XlsxTableWriter
 
rowNum - Variable in class net.sf.basedb.clients.web.plugins.XlsxTemplate
 
rowOffset - Variable in class net.sf.basedb.util.parser.FlatFileParser.ExcelData
 
rowRestrictions - Variable in class net.sf.basedb.core.ItemContext.QueryRestrictions
 
RowRestrictions(int) - Constructor for class net.sf.basedb.core.ItemContext.RowRestrictions
 
rows - Variable in class net.sf.basedb.core.data.PlateGeometryData
 
Rows - Class in net.sf.basedb.clients.web.taglib.table
This tag is a place-holder for <tbl:row> tags.
Rows() - Constructor for class net.sf.basedb.clients.web.taglib.table.Rows
 
rowSeparator - Variable in class net.sf.basedb.util.excel.XlsxToCsvUtil
 
rowsPerPage - Variable in class net.sf.basedb.clients.web.taglib.table.Navigator
The number of rows to display on a single page.
rowsPerPage - Variable in class net.sf.basedb.core.data.ContextData
 
rowsPerPage - Variable in class net.sf.basedb.core.ItemContext
 
rs - Variable in class net.sf.basedb.core.migrate.AbstractResultWriter
 
RssNewsFeed - Class in net.sf.basedb.clients.web.servlet
A servlet that generates a RSS feed from the public news on the BASE server.
RssNewsFeed() - Constructor for class net.sf.basedb.clients.web.servlet.RssNewsFeed
 
rule - Variable in class net.sf.basedb.util.overview.extensions.ReflectValidationRuleActionFactory
 
rule - Variable in class net.sf.basedb.util.overview.Failure
 
ruleDenied - Variable in class net.sf.basedb.util.overview.validator.BasicNodeValidator
 
ruleMissing - Variable in class net.sf.basedb.util.overview.validator.BasicNodeValidator
 
run() - Method in class net.sf.basedb.clients.jobagent.executors.ProcessJobExecutor.StreamRedirector
 
run() - Method in class net.sf.basedb.clients.jobagent.executors.ThreadJobExecutor.ShutdownHook
 
run() - Method in class net.sf.basedb.clients.jobagent.JobQueueChecker
 
run() - Method in class net.sf.basedb.clients.jobagent.JobRunner
Find a free slot to use and then pass control to the JobExecutor.executeJob(SessionControl, Agent, Job, JobAgentSettings, Job.ExecutionTime) method.
run() - Method in class net.sf.basedb.clients.jobagent.slotmanager.MasterSlotManager.RemoteSlotTimeoutChecker
 
run() - Method in class net.sf.basedb.clients.jobagent.slotmanager.RemoteSlotManager.RemoteSlotPinger
 
run() - Method in class net.sf.basedb.core.Application.DbCleaner
 
run() - Method in class net.sf.basedb.core.Application.SessionControlCacheCleaner
 
run() - Method in class net.sf.basedb.core.DbControl.State
 
run() - Method in class net.sf.basedb.core.File.CharsetTesterThread
Runs in a separate thread.
run() - Method in class net.sf.basedb.core.InternalJobQueue.JobRunner
Execute the job.
run() - Method in class net.sf.basedb.core.InternalJobQueue
Check the database for jobs that are waiting to be executed.
run() - Method in class net.sf.basedb.core.Keyring.ReloadTask
 
run() - Method in class net.sf.basedb.core.PluginExecutionRequest
 
run() - Method in class net.sf.basedb.core.signal.SocketSignalReceiver.ListenerThread
 
run() - Method in class net.sf.basedb.util.annotations.RunnableInheritAnnotationsManager
 
run() - Method in class net.sf.basedb.util.FileCopyRunnable
 
run() - Method in class net.sf.basedb.util.jobagent.JobAgentServerConnection.ListenerThread
 
run() - Method in class net.sf.basedb.util.jobagent.JobAgentServerConnection.RequestHandlerThread
 
run() - Method in class net.sf.basedb.util.StaticCache.CleanupTask
 
run() - Method in class net.sf.basedb.util.StaticCache.State
 
run() - Method in class net.sf.basedb.util.timer.ThreadTimerTask
 
run() - Method in class net.sf.basedb.util.uri.http.HttpConnectionManager.TimeoutTimer
 
run(Stack) - Method in class net.sf.basedb.util.jep.ChannelFunction
 
run(Stack) - Method in class net.sf.basedb.util.jep.ExtraValueFunction
 
run(Stack) - Method in class net.sf.basedb.util.jep.FunctionSafeJep.UnknownFunction
 
run(Stack) - Method in class net.sf.basedb.util.jep.InReporterListFunction
 
run(Stack) - Method in class net.sf.basedb.util.jep.LeftFunction
 
run(Stack) - Method in class net.sf.basedb.util.jep.Log2Function
 
run(Stack) - Method in class net.sf.basedb.util.jep.MeanFunction
 
run(Stack) - Method in class net.sf.basedb.util.jep.NotInReporterListFunction
 
run(Stack) - Method in class net.sf.basedb.util.jep.PositionFunction
 
run(Stack) - Method in class net.sf.basedb.util.jep.RawChannelFunction
 
run(Stack) - Method in class net.sf.basedb.util.jep.RawFunction
 
run(Stack) - Method in class net.sf.basedb.util.jep.ReporterFunction
 
run(Stack) - Method in class net.sf.basedb.util.jep.ScoreFunction
 
run(Stack) - Method in class net.sf.basedb.util.jep.SimpleJepFunction
 
run(Stack) - Method in class net.sf.basedb.util.parser.ColFunction
 
run(Stack) - Method in class net.sf.basedb.util.parser.DataNoFunction
 
run(Stack) - Method in class net.sf.basedb.util.parser.DefaultItemFunction
 
run(Stack) - Method in class net.sf.basedb.util.parser.LineNoFunction
 
run(Request, Response, ProgressReporter) - Method in class net.sf.basedb.core.plugin.AbstractExporterPlugin
Checks the AbstractExporterPlugin.SAVE_AS parameter for the path to save the exported data.
run(Request, Response, ProgressReporter) - Method in interface net.sf.basedb.core.plugin.Plugin
Run the plugin.
run(Request, Response, ProgressReporter) - Method in class net.sf.basedb.plugins.AbstractFlatFileImporter
Implements the Request.COMMAND_EXECUTE command.
run(Request, Response, ProgressReporter) - Method in class net.sf.basedb.plugins.Base1PluginExecuter
 
run(Request, Response, ProgressReporter) - Method in class net.sf.basedb.plugins.BfsExporterPlugin
 
run(Request, Response, ProgressReporter) - Method in class net.sf.basedb.plugins.CdfFileReporterImporter
 
run(Request, Response, ProgressReporter) - Method in class net.sf.basedb.plugins.CloneReportersPlugin
 
run(Request, Response, ProgressReporter) - Method in class net.sf.basedb.plugins.executor.AbstractIOSupport
run(Request, Response, ProgressReporter) - Method in class net.sf.basedb.plugins.executor.ExternalProgramExecutor
 
run(Request, Response, ProgressReporter) - Method in class net.sf.basedb.plugins.FormulaFilter
 
run(Request, Response, ProgressReporter) - Method in class net.sf.basedb.plugins.HelpImporter
 
run(Request, Response, ProgressReporter) - Method in class net.sf.basedb.plugins.IntensityCalculatorPlugin
 
run(Request, Response, ProgressReporter) - Method in class net.sf.basedb.plugins.JepExtraValueCalculator
 
run(Request, Response, ProgressReporter) - Method in class net.sf.basedb.plugins.JepIntensityTransformer
 
run(Request, Response, ProgressReporter) - Method in class net.sf.basedb.plugins.LowessNormalization
 
run(Request, Response, ProgressReporter) - Method in class net.sf.basedb.plugins.ManualDerivedBioAssayCreator
 
run(Request, Response, ProgressReporter) - Method in class net.sf.basedb.plugins.ManualTransformCreator
 
run(Request, Response, ProgressReporter) - Method in class net.sf.basedb.plugins.MedianRatioNormalization
 
run(Request, Response, ProgressReporter) - Method in class net.sf.basedb.plugins.PluginConfigurationImporter
 
run(Request, Response, ProgressReporter) - Method in class net.sf.basedb.util.zip.AbstractFileUnpacker
 
RUN_PLUGIN - Enum constant in enum class net.sf.basedb.core.Job.Type
The job is executed by a plugin.
runExporter(Request, Response, ProgressReporter) - Method in class net.sf.basedb.plugins.executor.ExternalProgramExecutor
Execute the exporter plug-in using the supplied parameters.
runExternalProgram(String, String, File, String, String, ProgressReporter) - Method in class net.sf.basedb.plugins.executor.ExternalProgramExecutor
Run the external program.
runImporter(Request, Response, ProgressReporter) - Method in class net.sf.basedb.plugins.executor.ExternalProgramExecutor
Execute the importer plug-in using the supplied parameters.
RunnableInheritAnnotationsManager - Class in net.sf.basedb.util.annotations
Utility class for processing multiple items with a InheritAnnotationsManager in a separated thread with progress reporting.
RunnableInheritAnnotationsManager(SessionControl) - Constructor for class net.sf.basedb.util.annotations.RunnableInheritAnnotationsManager
Create a new instance that should use the given session control.
runners - Variable in class net.sf.basedb.core.InternalJobQueue
Holds all currently executing jobs.
runnersGroup - Variable in class net.sf.basedb.clients.jobagent.Agent
The group were all job runners are placed.
runnersGroup - Variable in class net.sf.basedb.core.InternalJobQueue
The group were all job runners are placed.
running - Variable in class net.sf.basedb.clients.web.extensions.service.DummyService
 
RUNTIME_FILTER - Static variable in class net.sf.basedb.core.AnnotationSet
This filter gives everybody read permission to annotations.
RUNTIME_FILTER - Static variable in class net.sf.basedb.core.ArrayDesignPlate
This filter will only return items if the logged in user has generic read permission to array designs.
RUNTIME_FILTER - Static variable in class net.sf.basedb.core.ClientDefaultSetting
This filter will only return items if the logged in user has generic read permission to clients.
RUNTIME_FILTER - Static variable in class net.sf.basedb.core.FileSet
This filter gives everybody read permission to file sets.
RUNTIME_FILTER - Static variable in class net.sf.basedb.core.FileSetMember
This filter gives everybody read permission to file set members.
RUNTIME_FILTER - Static variable in class net.sf.basedb.core.Group
This filter will limit a query to only return groups where the logged in user is a member unless the logged in user has generic read permission.
RUNTIME_FILTER - Static variable in class net.sf.basedb.core.Help
This filter will only return items if the logged in user has generic read permission to clients.
RUNTIME_FILTER - Static variable in class net.sf.basedb.core.ItemSubtypeFileType
This filter will only return items if the logged in user has generic read permission to item subtypes.
RUNTIME_FILTER - Static variable in class net.sf.basedb.core.JobAgentSettings
This filter will only return items if the logged in user has generic read permission to job agents.
RUNTIME_FILTER - Static variable in class net.sf.basedb.core.Message
This filter will limit a query to only return messages for the logged in user unless the logged in user has generic read permission.
RUNTIME_FILTER - Static variable in class net.sf.basedb.core.News
This filter limits the returned news items to those where todays date falls between the start and end dates unless the logged in user has generic read permission.
RUNTIME_FILTER - Static variable in class net.sf.basedb.core.PlateEvent
This filter will only return items if the logged in user has generic read permission to plates.
RUNTIME_FILTER - Static variable in class net.sf.basedb.core.PlateEventType
This filter will only return items if the logged in user has generic read permission to plate types.
RUNTIME_FILTER - Static variable in class net.sf.basedb.core.PlatformFileType
This filter will only return items if the logged in user has generic read permission to platforms.
RUNTIME_FILTER - Static variable in class net.sf.basedb.core.PlatformVariant
This filter will only return items if the logged in user has generic read permission to platforms.
RUNTIME_FILTER - Static variable in class net.sf.basedb.core.Project
This filter will limit a query to only return projects where the logged in user is a member or owner unless the logged in user has generic read permission.
RUNTIME_FILTER - Static variable in class net.sf.basedb.core.Quota
This filter will only return the logged in user's quota unless the logged in user has generic read permission.
RUNTIME_FILTER - Static variable in class net.sf.basedb.core.Role
This filter will limit a query to only return roles where the logged in user is a member unless the logged in user has generic read permission.
RUNTIME_FILTER - Static variable in class net.sf.basedb.core.RoleKey
This filter will only return items if the logged in user has generic read permission to roles.
RUNTIME_FILTER - Static variable in class net.sf.basedb.core.Session
This filter will limit a query to only return sessions for the logged in user unless the logged in user has generic read permission.
RUNTIME_FILTER - Static variable in class net.sf.basedb.core.User
This filter will limit a query to only return users which are members of at least one of the groups where the logged in user is a member unless the logged in user has generic read permission.
RUNTIME_FILTER - Static variable in class net.sf.basedb.core.UserDefaultSetting
This filter will only return items if the logged in user has generic read permission to users.
RUNTIME_FILTER - Static variable in class net.sf.basedb.core.UserDevice
This filter will limit a query to only return devices for the logged in user unless the logged in user has generic read permission.
rwLock - Variable in class net.sf.basedb.util.extensions.manager.ExtensionsFile
 
rwLock - Variable in class net.sf.basedb.util.StaticCache.LockEntry
 

S

s - Variable in class net.sf.basedb.core.QueryExecutor.CancelableStatement
 
S - Variable in class net.sf.basedb.util.bcrypt.BCrypt
 
S_orig - Static variable in class net.sf.basedb.util.bcrypt.BCrypt
 
SAFE_TAGS - Static variable in class net.sf.basedb.clients.web.util.HTML
This pattern is a list of HTML tags considered "safe".
safeEquals(Date, Date, boolean) - Static method in class net.sf.basedb.core.DateUtil
Compare two date instances for equality while protecting from strange implementations in the java.util.Date and java.sql.Timestamp classes.
SafeFunctionTable(FunctionSafeJep) - Constructor for class net.sf.basedb.util.jep.FunctionSafeJep.SafeFunctionTable
 
safeIdList(DbControl, ItemQuery<?>, String, Set<Integer>) - Method in class net.sf.basedb.util.listable.AbstractSourceItemTransformer
Safely execute the query even if the number of values in the 'values' set is higher than DbEngine.getMaxParametersInQuery().
safeInvariantEquals(List<Date>, List<Date>, boolean) - Static method in class net.sf.basedb.core.DateUtil
Checks if two lists contains equal elements disregarding their positions in the array.
safeToDrop(TableInfo.IndexInfo) - Method in class net.sf.basedb.core.dbengine.TableInfo
It is safe to drop an index if it is not the primary key.
SAM - Static variable in class net.sf.basedb.core.DataFileType
The external ID for the file type representing a SAM (Sequence Alignment/Map) file.
SAME_UNITS - Static variable in class net.sf.basedb.clients.web.plugins.SimpleExport
 
sameVersion - Variable in class net.sf.basedb.util.Diff3
 
Sample - Class in net.sf.basedb.core
This class is used to represent sample items.
Sample(SampleData) - Constructor for class net.sf.basedb.core.Sample
 
SAMPLE - Enum constant in enum class net.sf.basedb.core.Item
The item is a Sample.
SampleData - Class in net.sf.basedb.core.data
This represents a sample.
SampleData() - Constructor for class net.sf.basedb.core.data.SampleData
 
SampleImporter - Class in net.sf.basedb.plugins.batchimport
Plug-in for importing sample items in a batch.
SampleImporter() - Constructor for class net.sf.basedb.plugins.batchimport.SampleImporter
 
SampleLoader - Class in net.sf.basedb.util.overview.loader
Node loader implementation for samples.
SampleLoader() - Constructor for class net.sf.basedb.util.overview.loader.SampleLoader
 
sampleQuery - Variable in class net.sf.basedb.plugins.batchimport.AbstractItemImporter
 
sampleSize - Variable in class net.sf.basedb.util.AnyToAnyLinkStatistics
 
SampleToBioSourceTransformer - Class in net.sf.basedb.util.listable
Source item transformer that transform sample items to their parent biosources.
SampleToBioSourceTransformer() - Constructor for class net.sf.basedb.util.listable.SampleToBioSourceTransformer
 
SampleToBioSourceTransformer(boolean) - Constructor for class net.sf.basedb.util.listable.SampleToBioSourceTransformer
Create a new sample to biosource transformer that only load parent biosources to sample that has a subtype with "push annotations" set.
SampleToChildSampleTransformer - Class in net.sf.basedb.util.listable
Source item transformer implementation that transform sample items to their child sample items.
SampleToChildSampleTransformer(boolean) - Constructor for class net.sf.basedb.util.listable.SampleToChildSampleTransformer
Create a new sample to child sample transformer.
SampleToChildSampleTransformer(boolean, boolean) - Constructor for class net.sf.basedb.util.listable.SampleToChildSampleTransformer
Create a new sample to child sample transformer that only load children that has a subtype with "push annotations" set.
SampleToExtractTransformer - Class in net.sf.basedb.util.listable
Source item transformer that transform sample items to their child extract.
SampleToExtractTransformer() - Constructor for class net.sf.basedb.util.listable.SampleToExtractTransformer
 
SampleToParentSampleTransformer - Class in net.sf.basedb.util.listable
Source item transformer implementation that transform sample items to their parent sample items.
SampleToParentSampleTransformer(boolean) - Constructor for class net.sf.basedb.util.listable.SampleToParentSampleTransformer
Create a new sample to parent sample transformer.
SampleToParentSampleTransformer(boolean, boolean) - Constructor for class net.sf.basedb.util.listable.SampleToParentSampleTransformer
Create a new sample to parent sample transformer that only load parents to samples that has a subtype with "push annotations" set.
SampleValidator - Class in net.sf.basedb.util.overview.validator
Validator implementation for sample.
SampleValidator() - Constructor for class net.sf.basedb.util.overview.validator.SampleValidator
 
SAMPLING - Static variable in class net.sf.basedb.core.Kit
The ID for the sampling kit type, for example a kit used when creating a Sample from a BioSource.
SAMPLING - Static variable in class net.sf.basedb.core.Protocol
The ID for the sampling protocol type, for example a protocol used when creating a Sample from a BioSource.
save() - Method in class net.sf.basedb.util.extensions.manager.Settings
Save the settings to disk.
save(Object) - Method in class net.sf.basedb.core.hibernate.SessionWrapper
 
save(String, Object) - Method in class net.sf.basedb.core.hibernate.SessionWrapper
 
SAVE_AS - Static variable in class net.sf.basedb.core.plugin.AbstractExporterPlugin
saveAllCurrentContexts(Session, UserData, ClientData) - Method in class net.sf.basedb.core.SessionControl
 
saveAllUserSettings(Session) - Method in class net.sf.basedb.core.SessionControl
Saves all user settings.
saveCurrentContextAs(Item, String, boolean, boolean) - Method in class net.sf.basedb.core.SessionControl
Same as: saveCurrentContextAs(item, null, name, overwrite, isPublic).
saveCurrentContextAs(Item, String, String, boolean, boolean) - Method in class net.sf.basedb.core.SessionControl
Save the current context as a named context.
saveData(Session, BasicData) - Static method in class net.sf.basedb.core.HibernateUtil
Save a new data object to the database.
saveData(StatelessSession, BasicData) - Static method in class net.sf.basedb.core.HibernateUtil
Save a new data object to the database.
SaveIf(BasicItem, boolean) - Constructor for class net.sf.basedb.core.DbControl.SaveIf
 
saveIfQueue - Variable in class net.sf.basedb.core.DbControl
Lists items that are saved only if the parent item is also saved.
saveImageToFile(DbControl, BufferedImage, String, String, boolean) - Method in class net.sf.basedb.clients.web.servlet.ExperimentExplorerPlotServlet
 
saveItem(BasicItem) - Method in class net.sf.basedb.core.DbControl
Schedule a new item to be saved in the database.
saveItemIf(BasicItem, BasicItem, boolean) - Method in class net.sf.basedb.core.DbControl
Schedule a new item to be saved in the database if another item is also saved.
saveOrUpdate(Object) - Method in class net.sf.basedb.core.hibernate.SessionWrapper
 
saveOrUpdate(String, Object) - Method in class net.sf.basedb.core.hibernate.SessionWrapper
 
saveParameters(DbControl) - Method in class net.sf.basedb.core.PluginResponse
Save all parameters that has been configured during the configuration sequence to the database.
saveParameters(DbControl, GuiContext) - Method in class net.sf.basedb.core.PluginRequest
Save all parameters that have got values in this request/response session.
saveParameters(Job, Map<String, PluginParameter<?>>) - Method in class net.sf.basedb.core.ParameterValuesImpl
 
saveParameters(PluginConfiguration, Map<String, PluginParameter<?>>) - Method in class net.sf.basedb.core.ParameterValuesImpl
 
SavePointWork<R> - Class in net.sf.basedb.core.hibernate
A wrapper work that protects a parent work with a savepoint.
SavePointWork(ReturningWork<R>) - Constructor for class net.sf.basedb.core.hibernate.SavePointWork
Create a new work item.
saveSettings() - Method in class net.sf.basedb.clients.web.extensions.ExtensionsControl
Save the settings.
saveSettings(Session, Query<I>, Map<String, SessionControl.SettingInfo>, Class<I>, UserData, ClientData) - Method in class net.sf.basedb.core.SessionControl
Save settings when a user logs out.
saveState(Serializable) - Method in class net.sf.basedb.core.Job
Save the job state to the static cache.
saveTo - Variable in class net.sf.basedb.core.plugin.AbstractExporterPlugin
 
saveTo(OutputStream) - Method in class net.sf.basedb.util.excel.XlsxTableWriter
Save the workbook to the given stream.
saveToPreset(Presets.Preset) - Method in class net.sf.basedb.util.overview.ValidationOptions
Save the current settings to a preset.
saveValidationPresets(SessionControl) - Static method in class net.sf.basedb.util.overview.OverviewUtil
Save the validation option presets for the logged in user.
sc - Variable in class net.sf.basedb.clients.jobagent.Agent
 
sc - Variable in class net.sf.basedb.clients.web.extensions.list.RelatedItemHelper
 
sc - Variable in class net.sf.basedb.clients.web.servlet.RssNewsFeed
 
sc - Variable in class net.sf.basedb.clients.web.taglib.Page
The SessionControl object in use for this request.
sc - Variable in class net.sf.basedb.clients.web.taglib.table.Table
 
sc - Variable in class net.sf.basedb.core.AbstractBatcher
 
sc - Variable in class net.sf.basedb.core.Application.Pinger
 
sc - Variable in class net.sf.basedb.core.DataResultIterator
The SessionControl
sc - Variable in class net.sf.basedb.core.DbControl
 
sc - Variable in class net.sf.basedb.core.hibernate.ExecuteUpdateWork
 
sc - Variable in class net.sf.basedb.core.hibernate.ResultSetWork
 
sc - Variable in class net.sf.basedb.core.InternalJobQueue
The job queues session controller.
sc - Variable in class net.sf.basedb.core.Job.ProgressReporterImpl
 
sc - Variable in class net.sf.basedb.core.plugin.AbstractPlugin
 
sc - Variable in class net.sf.basedb.core.PluginRequest
 
sc - Variable in class net.sf.basedb.util.annotations.RunnableInheritAnnotationsManager
 
sc - Variable in class net.sf.basedb.util.extensions.ClientContext
 
scale - Variable in class net.sf.basedb.util.ChainedProgressReporter
 
scale - Variable in class net.sf.basedb.util.InputStreamTracker.LinearScaleFactor
 
scale(long) - Method in class net.sf.basedb.util.InputStreamTracker.CurvedScaleFactor
 
scale(long) - Method in class net.sf.basedb.util.InputStreamTracker.IdentityScaleFactor
 
scale(long) - Method in class net.sf.basedb.util.InputStreamTracker.LinearScaleFactor
 
scale(long) - Method in interface net.sf.basedb.util.InputStreamTracker.ScaleFactor
 
scaleFactor - Variable in class net.sf.basedb.util.InputStreamTracker
A scale factor to apply when counting bytes.
scan(DbControl, HttpServletRequest) - Static method in class net.sf.basedb.clients.web.extensions.ExtensionsControl
 
SCAN - Static variable in class net.sf.basedb.core.DerivedBioAssay
The id for the DerivedBioAssayType item representing a scanned hybridization.
scanForChanges() - Method in class net.sf.basedb.clients.web.extensions.ExtensionsControl
Scan the managed directories for new/updated/deleted extensions.
scanForChanges() - Method in class net.sf.basedb.util.extensions.manager.ExtensionsManager
Scan the managed directories for new, updated and deleted files.
scanForInstalledFiles(File, Settings) - Method in class net.sf.basedb.util.extensions.manager.ExtensionsManager
Scan the given directory and add files that are installed according to the settings.
scanForLinks(String) - Static method in class net.sf.basedb.clients.web.util.HTML
Scans a string for email addresses and URL:s and replaces them with <a href="---"> tags.
scanForLinks(String, int) - Static method in class net.sf.basedb.clients.web.util.HTML
Scans a string for email addresses and URL:s and replaces them with <a href="---"> tags.
scanForLinks(String, int, String) - Static method in class net.sf.basedb.clients.web.util.HTML
Scans a string for email addresses and URL:s and replaces them with <a href="---"> tags.
scanForLinks(String, String) - Static method in class net.sf.basedb.clients.web.util.HTML
Scans a string for email addresses and URL:s and replaces them with <a href="---"> tags.
scanForNewFiles(File) - Method in class net.sf.basedb.util.extensions.manager.ExtensionsManager
Scan the given directory and add files that are new.
SCANNER - Static variable in class net.sf.basedb.core.Hardware
The id for the HardwareType object representing a scanner.
SCANNING - Static variable in class net.sf.basedb.core.Protocol
The ID for the scanning protocol type, for example a protocol used for scanning the microarray slide after an experiment.
ScatterPlot - Class in net.sf.basedb.util.plot
A simple plot utility for generating scatter plots without the need to delve deep into the JFreePlot package.
ScatterPlot(String, String) - Constructor for class net.sf.basedb.util.plot.ScatterPlot
Create a new ScatterPlot.
scHasBeenSet - Variable in class net.sf.basedb.clients.web.taglib.Page
 
schedule(TimerTask, long, boolean) - Method in class net.sf.basedb.util.timer.Scheduler
 
schedule(TimerTask, long, long, boolean) - Method in class net.sf.basedb.util.timer.Scheduler
 
schedule(TimerTask, Date, boolean) - Method in class net.sf.basedb.util.timer.Scheduler
 
schedule(TimerTask, Date, long, boolean) - Method in class net.sf.basedb.util.timer.Scheduler
 
scheduleAtFixedRate(TimerTask, long, long, boolean) - Method in class net.sf.basedb.util.timer.Scheduler
 
scheduleAtFixedRate(TimerTask, Date, long, boolean) - Method in class net.sf.basedb.util.timer.Scheduler
 
scheduled - Variable in class net.sf.basedb.core.data.JobData
 
scheduler - Static variable in class net.sf.basedb.core.Application
An interface for adding timed task to the core timer.
Scheduler - Class in net.sf.basedb.util.timer
This class is a cousin to the standard Timer class but only allows scheduling of tasks.
Scheduler(Timer, boolean) - Constructor for class net.sf.basedb.util.timer.Scheduler
Create a new scheduler object.
schema - Variable in class net.sf.basedb.core.hibernate.SchemaExistsWork
 
schema - Variable in class net.sf.basedb.core.hibernate.TableExistsWork
 
schema - Variable in class net.sf.basedb.core.ServiceSessionControl.SessionFactoryConfiguration
 
SCHEMA_FILE_URL - Static variable in class net.sf.basedb.util.extensions.xml.XmlLoader
The URL pointing to the extensions.xsd schema.
SchemaChange() - Constructor for class net.sf.basedb.core.Update.SchemaChange
 
schemaExists(String, String) - Method in class net.sf.basedb.core.ServiceSessionControl
 
SchemaExistsWork - Class in net.sf.basedb.core.hibernate
A work implementation that checks if a given catalog+schema exists in the database or not.
SchemaExistsWork(String, String) - Constructor for class net.sf.basedb.core.hibernate.SchemaExistsWork
Create a new work item.
schemaFileURL - Static variable in class net.sf.basedb.clients.web.extensions.ServletLoader
The URL pointing to the servlets.xsd schema.
SchemaGenerator - Class in net.sf.basedb.core.hibernate
Replaces the Hibernate SchemaExport and SchemaUpdate tools.
SchemaGenerator(Metadata, Dialect, DbEngine, SchemaGenerator.Mode, ProgressReporter) - Constructor for class net.sf.basedb.core.hibernate.SchemaGenerator
Create a new schema generator.
SchemaGenerator.CollectSqlTarget - Class in net.sf.basedb.core.hibernate
Helper class used for collecting SQL statements generated by Hibernate schema creation/update tools.
SchemaGenerator.Mode - Enum Class in net.sf.basedb.core.hibernate
The installation mode.
SchemaGenerator.SqlStatement - Class in net.sf.basedb.core.hibernate
 
schemaVersion - Static variable in class net.sf.basedb.core.Application
 
schemaVersion - Variable in class net.sf.basedb.core.data.SchemaVersionData
 
schemaVersion - Static variable in class net.sf.basedb.core.Install
 
schemaVersion - Variable in class net.sf.basedb.core.ServiceSessionControl.SessionFactoryConfiguration
 
SchemaVersionData - Class in net.sf.basedb.core.data
This class holds information about the current schema version of the database.
SchemaVersionData() - Constructor for class net.sf.basedb.core.data.SchemaVersionData
 
score - Variable in class net.sf.basedb.core.data.ReporterListScoreData
 
score - Variable in class net.sf.basedb.util.fuzzy.StringMatcher.FuzzyMatch
 
score() - Method in class net.sf.basedb.util.jep.ScoreFunction
Get the score value from the current sql result.
score(ReporterList) - Static method in class net.sf.basedb.core.query.Dynamic
 
scoreColumnMapping - Static variable in class net.sf.basedb.plugins.ReporterFlatFileImporter
 
ScoreFunction - Class in net.sf.basedb.util.jep
A JEP function class that adds a score(reporterListId) function to a JEP expression parser.
ScoreFunction(DbControl) - Constructor for class net.sf.basedb.util.jep.ScoreFunction
Create a new instance of this function.
ScoreFunction(DbControl, int) - Constructor for class net.sf.basedb.util.jep.ScoreFunction
Create a new instance of this function which can be used to dynamically evaluate expressions.
scoreIndex - Variable in class net.sf.basedb.util.jep.ScoreFunction
 
scoreMapper - Variable in class net.sf.basedb.plugins.ReporterFlatFileImporter
 
scripts - Variable in class net.sf.basedb.clients.web.extensions.AbstractJspFactory
 
scripts - Variable in class net.sf.basedb.clients.web.extensions.JspContext
 
scripts - Variable in class net.sf.basedb.clients.web.taglib.Head
A comma-separated list of JavaScript filenames.
Scripts - Class in net.sf.basedb.clients.web.taglib.extensions
Tag for creating <script> tags from a JspContext.
Scripts() - Constructor for class net.sf.basedb.clients.web.taglib.extensions.Scripts
 
scroll() - Method in class net.sf.basedb.core.hibernate.QueryWrapper
 
scroll(ScrollMode) - Method in class net.sf.basedb.core.hibernate.QueryWrapper
 
ScrollIterator<E> - Class in net.sf.basedb.core
This is an iterator view of the result from a query using the Hibernate ScrollableResults object.
ScrollIterator(ScrollableResults, boolean) - Constructor for class net.sf.basedb.core.ScrollIterator
 
searchInherited - Variable in class net.sf.basedb.core.snapshot.AnnotationLoaderUtil
 
searchPrimary - Variable in class net.sf.basedb.core.snapshot.AnnotationLoaderUtil
 
secondLevelCache - Variable in class net.sf.basedb.core.AnnotationBatcher
 
SecondPassSectionSpotsParser - Class in net.sf.basedb.util.importer.spotdata
The second pass of the 'spots' section extracts spot and extra value data.
SecondPassSectionSpotsParser(DbControl, BaseFileInfo, BioAssaySet, int) - Constructor for class net.sf.basedb.util.importer.spotdata.SecondPassSectionSpotsParser
Creates a new 'section spot' parser for the first pass.
section - Variable in class net.sf.basedb.core.data.BioPlateData
 
section - Variable in class net.sf.basedb.plugins.PrintMapFlatFileImporter
 
section - Variable in class net.sf.basedb.util.parser.FlatFileParser
The regular expression for matching the fist line of a section.
Section(String) - Constructor for enum class net.sf.basedb.plugins.PrintMapFlatFileImporter.Section
 
Section(String) - Constructor for class net.sf.basedb.util.bfs.MetadataModel.Section
Create a new section.
Section(JspContext) - Constructor for class net.sf.basedb.clients.web.extensions.section.IncludeContentSectionFactory.Section
 
SECTION - Enum constant in enum class net.sf.basedb.util.parser.FlatFileParser.LineType
The parsed line is the line starting a section, matching the regular expression specified by FlatFileParser.setSectionRegexp(Pattern).
SECTION - Static variable in class net.sf.basedb.util.importer.spotdata.FirstPassSectionSpotsParser
The section of the BASEfile this parser can parse, eg.
SECTION_END_EVENT - Static variable in class net.sf.basedb.util.bfs.MetadataParser
Event type that is issued at the end of each section in the file.
SECTION_EVENT - Static variable in class net.sf.basedb.util.bfs.MetadataParser
Event type that is issued for each new section that is found in the file.
SectionAction - Interface in net.sf.basedb.clients.web.extensions.section
Action that inserts a new section in a jsp page.
SectionAssaysParser - Class in net.sf.basedb.util.importer.spotdata
Parses the 'assays' section of a BASEfile with bioassay set spot data.
SectionAssaysParser(DbControl, BaseFileInfo) - Constructor for class net.sf.basedb.util.importer.spotdata.SectionAssaysParser
Creates a new 'section assays' parser.
SectionBean - Class in net.sf.basedb.clients.web.extensions.section
A simple bean-like implementation of the SectionAction interface.
SectionBean() - Constructor for class net.sf.basedb.clients.web.extensions.section.SectionBean
 
sectionColumnMapping - Static variable in class net.sf.basedb.plugins.batchimport.BioPlateImporter
 
sectionCount - Variable in class net.sf.basedb.util.basefile.BaseFileParser
 
sectionCount - Variable in class net.sf.basedb.util.bfs.MetadataWriter
 
sectionCount - Variable in class net.sf.basedb.util.importer.spotdata.FirstPassSectionSpotsParser
 
sectionCount - Variable in class net.sf.basedb.util.importer.spotdata.SecondPassSectionSpotsParser
 
sectionCount - Variable in class net.sf.basedb.util.importer.spotdata.SectionReporterListParser
 
sectionEntries - Variable in class net.sf.basedb.util.bfs.MetadataParser
 
SectionEntry(String, String) - Constructor for class net.sf.basedb.util.bfs.MetadataModel.SectionEntry
Create a new single-valued section entry.
SectionEntry(String, String...) - Constructor for class net.sf.basedb.util.bfs.MetadataModel.SectionEntry
Create a new section entry with an array of values.
SectionHeaders(String, String, String) - Constructor for class net.sf.basedb.clients.web.fileupload.FileUpload.SectionHeaders
 
sectionMapper - Variable in class net.sf.basedb.plugins.batchimport.BioPlateImporter
 
sectionRegexpParameter - Static variable in class net.sf.basedb.plugins.AbstractFlatFileImporter
Parameter definition that asks for the regular expression that matches a section line and extracts the section name.
SectionReporterListParser - Class in net.sf.basedb.util.importer.spotdata
Parses the 'reporterlist' section of a BASEfile.
SectionReporterListParser(DbControl, BaseFileInfo, Transformation) - Constructor for class net.sf.basedb.util.importer.spotdata.SectionReporterListParser
 
sections - Variable in class net.sf.basedb.util.bfs.MetadataModel
 
seemsLikeAnExcelFile(File) - Static method in class net.sf.basedb.util.excel.XlsxToCsvUtil
Check the MIME type and file extension to see if the file could be an Excel file.
select - Variable in class net.sf.basedb.core.query.SelectedExpression
 
select(ExtraValue, String) - Static method in class net.sf.basedb.core.query.Dynamic
Select an extra value.
select(Select) - Method in class net.sf.basedb.core.AbstractEntityQuery
Not supported.
select(Select) - Method in class net.sf.basedb.core.AbstractQuery
 
select(Select) - Method in interface net.sf.basedb.core.query.Query
Add a selection query element to the selection list.
select(VirtualColumn) - Static method in class net.sf.basedb.core.query.Dynamic
Select a column in the root table.
select(VirtualTable, VirtualColumn) - Static method in class net.sf.basedb.core.query.Dynamic
Select a column in a joined or the root table.
Select - Class in net.sf.basedb.clients.web.taglib
This tag is used to display a selection list of items.
Select - Interface in net.sf.basedb.core.query
A selection query element.
Select() - Constructor for class net.sf.basedb.clients.web.taglib.Select
 
SELECT - Enum constant in enum class net.sf.basedb.core.query.QuerySection
 
SELECT_FILTER - Static variable in class net.sf.basedb.clients.web.ModeInfo
 
SELECT_JOBAGENT - Enum constant in enum class net.sf.basedb.core.Permission
This permission allows a user to specify which job agent a job should be executed on using Job.setJobAgent(JobAgent).
selectdefault - Variable in class net.sf.basedb.clients.web.taglib.Select
If the default item should be selected for new items with no current or recently used items.
selected - Variable in class net.sf.basedb.core.ItemContext
 
selected(Select) - Static method in class net.sf.basedb.core.query.Expressions
Create an expression for an already selected query element.
selectedColumns - Variable in class net.sf.basedb.clients.web.DynamicUtil.SelectedInfo
 
selectedDirs - Variable in class net.sf.basedb.plugins.PackedFileExporter
 
SelectedExpression - Class in net.sf.basedb.core.query
An expression representing an already selected expression.
SelectedExpression(Select) - Constructor for class net.sf.basedb.core.query.SelectedExpression
 
selectedFiles - Variable in class net.sf.basedb.plugins.PackedFileExporter
 
selectedFilesAndDirs - Variable in class net.sf.basedb.plugins.PackedFileExporter
 
selectedIds - Variable in class net.sf.basedb.clients.web.DynamicUtil.SelectedInfo
 
SelectedInfo(List<String>, List<String>, List<TableColumn>) - Constructor for class net.sf.basedb.clients.web.DynamicUtil.SelectedInfo
 
selectedProperties - Variable in class net.sf.basedb.clients.web.DynamicUtil.SelectedInfo
 
selectedSubtype - Variable in class net.sf.basedb.plugins.batchimport.AbstractItemImporter
 
SELECTION_MODE - Static variable in class net.sf.basedb.clients.web.ModeInfo
 
selectionMode - Variable in class net.sf.basedb.clients.web.ModeInfo
 
SELECTMULTIPLE - Static variable in class net.sf.basedb.clients.web.ModeInfo
 
SELECTMULTIPLE_NOBUTTONS - Static variable in class net.sf.basedb.clients.web.ModeInfo
 
SELECTONE - Static variable in class net.sf.basedb.clients.web.ModeInfo
 
selectOrderByColumnsIfDistinct() - Method in class net.sf.basedb.core.dbengine.AbstractDbEngine
Returns FALSE.
selectOrderByColumnsIfDistinct() - Method in interface net.sf.basedb.core.dbengine.DbEngine
If the database requires that columns appearing in the ORDER BY part of the query must also be part of the SELECT list when using the DISTINCT keyword.
selectOrderByColumnsIfDistinct() - Method in class net.sf.basedb.core.dbengine.PostgresDbEngine
Returns TRUE.
selectPermanent(Select) - Method in class net.sf.basedb.core.AbstractEntityQuery
Not supported.
selectPermanent(Select) - Method in class net.sf.basedb.core.AbstractQuery
 
selectPermanent(Select) - Method in interface net.sf.basedb.core.query.Query
Permanently add a selection query element to the selection list.
selectRawBioAssay(String) - Static method in class net.sf.basedb.core.query.Dynamic
Select a column in the rawbioassay table.
selectRawData(String) - Static method in class net.sf.basedb.core.query.Dynamic
Select a column in the raw data table.
selectRecent - Variable in class net.sf.basedb.clients.web.taglib.Select
If we can select the most recently used item for new items with nu current item.
selectReporter(String) - Static method in class net.sf.basedb.core.query.Dynamic
Select a column in the reporters table.
selectReporter(String, Boolean) - Static method in class net.sf.basedb.core.query.Dynamic
Select a column in the reporters table.
selects - Variable in class net.sf.basedb.core.AbstractQuery
List of selections added to the query.
Selects - Class in net.sf.basedb.core.query
A factory class to create select expressions.
Selects() - Constructor for class net.sf.basedb.core.query.Selects
 
send(String) - Method in class net.sf.basedb.util.jobagent.JobAgentConnection
Send a remote control command to the job agent.
send(String, Signal) - Method in class net.sf.basedb.core.signal.LocalSignalReceiver
Send the signal to a registered handler.
send(Socket, String, boolean) - Static method in class net.sf.basedb.util.SocketUtil
Send output to a socket.
send(Signal) - Method in class net.sf.basedb.core.Job.JobSignalTransporter
 
send(Signal) - Method in class net.sf.basedb.core.signal.ExtensionSignalTransporter
 
send(Signal) - Method in class net.sf.basedb.core.signal.LocalSignalTransporter
Send the signal to a local signal receiver.
send(Signal) - Method in interface net.sf.basedb.core.signal.SignalTransporter
Send a signal.
send(Signal) - Method in class net.sf.basedb.core.signal.SocketSignalTransporter
Connect to the remote host and send the signal.
sendAsEmail - Variable in class net.sf.basedb.core.Message
 
sendAsEmail() - Method in class net.sf.basedb.core.Message
Send this message as an email.
sendCmd(Socket, String) - Method in class net.sf.basedb.util.jobagent.JobAgentConnection
Send a command to the job agent and return the answer.
sendEmailVerificationCode(String) - Method in class net.sf.basedb.core.User
Send a verification code to the currently registered email address.
senderEmail - Static variable in class net.sf.basedb.util.EmailUtil
 
senderName - Static variable in class net.sf.basedb.util.EmailUtil
 
sendErrorMessage(SessionControl, int, Throwable) - Method in class net.sf.basedb.core.InternalJobQueue
 
sendMessage - Variable in class net.sf.basedb.core.data.JobData
 
sendMessage() - Method in class net.sf.basedb.core.Job
Send a message to the owner of the job when the job has finished
sendMessagesAsEmail - Variable in class net.sf.basedb.core.data.UserData
 
sendPause() - Method in class net.sf.basedb.util.jobagent.JobAgentConnection
 
sendPing() - Method in class net.sf.basedb.util.jobagent.JobAgentConnection
Send the ping command to the job agent.
SendSignalRenderer(Signal) - Constructor for class net.sf.basedb.core.signal.ExtensionSignalTransporter.SendSignalRenderer
 
sendStart() - Method in class net.sf.basedb.util.jobagent.JobAgentConnection
Send a start request to the job agent.
sendStop() - Method in class net.sf.basedb.util.jobagent.JobAgentConnection
 
sendTo(SignalHandler) - Method in class net.sf.basedb.core.signal.ShutdownSignalSender
 
sendTo(SignalHandler) - Method in interface net.sf.basedb.core.signal.SignalSender
Send a signal to the specific signal handler.
sendTo(SignalHandler) - Method in class net.sf.basedb.core.signal.SimpleSignalSender
 
sendToAll(SignalSender) - Method in class net.sf.basedb.clients.web.util.SimpleSignalProgressReporter
 
sendToAll(SignalSender) - Method in class net.sf.basedb.core.signal.AbstractSignalReceiver
 
sendToAll(SignalSender) - Method in interface net.sf.basedb.core.signal.SignalReceiver
Let the signal sender send one or more signals to all registered signal handlers on this reciever.
separator - Variable in class net.sf.basedb.clients.web.taglib.path.Path
 
separator - Variable in class net.sf.basedb.clients.web.taglib.table.CellValue
 
separator - Static variable in class net.sf.basedb.core.File
 
separator - Variable in class net.sf.basedb.util.formatter.CollectionFormatter
 
SEPARATOR - Enum constant in enum class net.sf.basedb.clients.web.extensions.menu.MenuItemAction.MenuType
This is a separator line.
SequenceFilenameGenerator - Class in net.sf.basedb.util.bfs
File name generator implementation that generates file names using a simple numerical counter.
SequenceFilenameGenerator() - Constructor for class net.sf.basedb.util.bfs.SequenceFilenameGenerator
Create a new sequence file name generator.
SequenceFilenameGenerator(String, String, int) - Constructor for class net.sf.basedb.util.bfs.SequenceFilenameGenerator
Create a new sequence file name generator.
SEQUENCER - Static variable in class net.sf.basedb.core.Hardware
The id for the HardwareType object representing a sequencer.
SEQUENCES - Static variable in class net.sf.basedb.core.DerivedBioAssay
The id for the DerivedBioAssayType item representing original sequenced data.
SEQUENCING - Static variable in class net.sf.basedb.core.Kit
The ID for the sequencing kit type, for example a kit used when creating a DerivedBioAssay from a PhysicalBioAssay.
SEQUENCING - Static variable in class net.sf.basedb.core.Platform
The external id for the generic Sequencing platform.
SEQUENCING - Static variable in class net.sf.basedb.core.Protocol
The ID for the sequencing protocol type, for example a protocol used when creating a DerivedBioAssay from a PhysicalBioAssay
SEQUENCING_EXPRESSION - Static variable in class net.sf.basedb.core.PlatformVariant
The external id for the expression-like sequencing data.
SerialBaseFileExporter - Class in net.sf.basedb.util.export.spotdata
Exporter implementation that exports bioassay set data as a serial BASEfile.
SerialBaseFileExporter() - Constructor for class net.sf.basedb.util.export.spotdata.SerialBaseFileExporter
Create a new serial BASEfile exporter.
SerialBfsExporter - Class in net.sf.basedb.util.export.spotdata
BFS exporter implementation that exports spot data in serial format.
SerialBfsExporter() - Constructor for class net.sf.basedb.util.export.spotdata.SerialBfsExporter
Create a new serial BFS exporter.
serialFormatParameter - Variable in class net.sf.basedb.plugins.Base1PluginExecuter
This parameter describes if the data should be exported in serial format or in matrix.
serializeObject(ObjectOutputStream) - Method in class net.sf.basedb.core.snapshot.AnnotationSnapshot
 
SerialSpotIntensityEventHandler - Class in net.sf.basedb.util.importer.spotdata
Event handler that extracts spot intensity information from serial BFS data files and inserts the values to a spot batcher.
SerialSpotIntensityEventHandler(SpotBatcher, PositionEventHandler, BioAssay[], int[]) - Constructor for class net.sf.basedb.util.importer.spotdata.SerialSpotIntensityEventHandler
Create a new spot instensity event handler.
serialVersionUID - Static variable in exception net.sf.basedb.clients.web.DuplicateWizardException
 
serialVersionUID - Static variable in exception net.sf.basedb.clients.web.fileupload.UploadAbortedException
 
serialVersionUID - Static variable in class net.sf.basedb.clients.web.servlet.CompileAll
 
serialVersionUID - Static variable in class net.sf.basedb.clients.web.servlet.ContentSecurityPolicyReportServlet
 
serialVersionUID - Static variable in class net.sf.basedb.clients.web.servlet.Download
 
serialVersionUID - Static variable in class net.sf.basedb.clients.web.servlet.ExperimentExplorerPlotServlet
 
serialVersionUID - Static variable in class net.sf.basedb.clients.web.servlet.ExtensionsServlet
 
serialVersionUID - Static variable in class net.sf.basedb.clients.web.servlet.PlotServlet
 
serialVersionUID - Static variable in class net.sf.basedb.clients.web.servlet.RssNewsFeed
 
serialVersionUID - Static variable in class net.sf.basedb.clients.web.servlet.StartStopServlet
 
serialVersionUID - Static variable in class net.sf.basedb.clients.web.servlet.Upload
 
serialVersionUID - Static variable in class net.sf.basedb.clients.web.taglib.Body
 
serialVersionUID - Static variable in class net.sf.basedb.clients.web.taglib.Button
 
serialVersionUID - Static variable in class net.sf.basedb.clients.web.taglib.ButtonGroup
 
serialVersionUID - Static variable in class net.sf.basedb.clients.web.taglib.CalendarButton
 
serialVersionUID - Static variable in class net.sf.basedb.clients.web.taglib.ExceptionCatcher
 
serialVersionUID - Static variable in class net.sf.basedb.clients.web.taglib.extensions.Render
 
serialVersionUID - Static variable in class net.sf.basedb.clients.web.taglib.extensions.Scripts
 
serialVersionUID - Static variable in class net.sf.basedb.clients.web.taglib.extensions.Stylesheets
 
serialVersionUID - Static variable in class net.sf.basedb.clients.web.taglib.Head
 
serialVersionUID - Static variable in class net.sf.basedb.clients.web.taglib.Help
 
serialVersionUID - Static variable in class net.sf.basedb.clients.web.taglib.HideableSection
 
serialVersionUID - Static variable in class net.sf.basedb.clients.web.taglib.Icon
 
serialVersionUID - Static variable in class net.sf.basedb.clients.web.taglib.Input
 
serialVersionUID - Static variable in class net.sf.basedb.clients.web.taglib.menu.Menuitem
 
serialVersionUID - Static variable in class net.sf.basedb.clients.web.taglib.menu.Menuseparator
 
serialVersionUID - Static variable in class net.sf.basedb.clients.web.taglib.menu.Submenu
 
serialVersionUID - Static variable in class net.sf.basedb.clients.web.taglib.Page
 
serialVersionUID - Static variable in class net.sf.basedb.clients.web.taglib.path.Path
 
serialVersionUID - Static variable in class net.sf.basedb.clients.web.taglib.path.PathElement
 
serialVersionUID - Static variable in class net.sf.basedb.clients.web.taglib.PropertyValue
 
serialVersionUID - Static variable in class net.sf.basedb.clients.web.taglib.Select
 
serialVersionUID - Static variable in class net.sf.basedb.clients.web.taglib.StylableTag
 
serialVersionUID - Static variable in class net.sf.basedb.clients.web.taglib.SubtypeSelector
 
serialVersionUID - Static variable in class net.sf.basedb.clients.web.taglib.tab.Tab
 
serialVersionUID - Static variable in class net.sf.basedb.clients.web.taglib.tab.TabControl
 
serialVersionUID - Static variable in class net.sf.basedb.clients.web.taglib.table.Button
 
serialVersionUID - Static variable in class net.sf.basedb.clients.web.taglib.table.Cell
 
serialVersionUID - Static variable in class net.sf.basedb.clients.web.taglib.table.CellValue
 
serialVersionUID - Static variable in class net.sf.basedb.clients.web.taglib.table.ColumnDef
 
serialVersionUID - Static variable in class net.sf.basedb.clients.web.taglib.table.ColumnHeaders
 
serialVersionUID - Static variable in class net.sf.basedb.clients.web.taglib.table.ColumnSubtitles
 
serialVersionUID - Static variable in class net.sf.basedb.clients.web.taglib.table.Data
 
serialVersionUID - Static variable in class net.sf.basedb.clients.web.taglib.table.ExtensionCells
 
serialVersionUID - Static variable in class net.sf.basedb.clients.web.taglib.table.Form
 
serialVersionUID - Static variable in class net.sf.basedb.clients.web.taglib.table.Header
 
serialVersionUID - Static variable in class net.sf.basedb.clients.web.taglib.table.HeaderRow
 
serialVersionUID - Static variable in class net.sf.basedb.clients.web.taglib.table.Headers
 
serialVersionUID - Static variable in class net.sf.basedb.clients.web.taglib.table.Hidden
 
serialVersionUID - Static variable in class net.sf.basedb.clients.web.taglib.table.Label
 
serialVersionUID - Static variable in class net.sf.basedb.clients.web.taglib.table.Navigator
 
serialVersionUID - Static variable in class net.sf.basedb.clients.web.taglib.table.Panel
 
serialVersionUID - Static variable in class net.sf.basedb.clients.web.taglib.table.PresetSelector
 
serialVersionUID - Static variable in class net.sf.basedb.clients.web.taglib.table.PropertyFilter
 
serialVersionUID - Static variable in class net.sf.basedb.clients.web.taglib.table.Row
 
serialVersionUID - Static variable in class net.sf.basedb.clients.web.taglib.table.Rows
 
serialVersionUID - Static variable in class net.sf.basedb.clients.web.taglib.table.Table
 
serialVersionUID - Static variable in class net.sf.basedb.clients.web.taglib.table.Toolbar
 
serialVersionUID - Static variable in class net.sf.basedb.clients.web.taglib.Zoom
 
serialVersionUID - Static variable in exception net.sf.basedb.clients.web.WebException
 
serialVersionUID - Static variable in exception net.sf.basedb.core.AccountExpiredException
 
serialVersionUID - Static variable in exception net.sf.basedb.core.AlreadyLoggedInException
 
serialVersionUID - Static variable in exception net.sf.basedb.core.authentication.AuthenticationException
 
serialVersionUID - Static variable in exception net.sf.basedb.core.authentication.InvalidPasswordException
 
serialVersionUID - Static variable in exception net.sf.basedb.core.authentication.LoginException
 
serialVersionUID - Static variable in exception net.sf.basedb.core.authentication.UnknownLoginException
 
serialVersionUID - Static variable in exception net.sf.basedb.core.BaseException
 
serialVersionUID - Static variable in exception net.sf.basedb.core.ConfigurationException
 
serialVersionUID - Static variable in exception net.sf.basedb.core.ConnectionClosedException
 
serialVersionUID - Static variable in class net.sf.basedb.core.data.AnnotationSetData
 
serialVersionUID - Static variable in class net.sf.basedb.core.data.ContextIndex
 
serialVersionUID - Static variable in class net.sf.basedb.core.data.FileTypeIndex
 
serialVersionUID - Static variable in class net.sf.basedb.core.data.GuiContextData
 
serialVersionUID - Static variable in class net.sf.basedb.core.data.keyring.GroupGroups
 
serialVersionUID - Static variable in class net.sf.basedb.core.data.keyring.GroupKeys
 
serialVersionUID - Static variable in class net.sf.basedb.core.data.keyring.GroupProjects
 
serialVersionUID - Static variable in class net.sf.basedb.core.data.keyring.PluginKeys
 
serialVersionUID - Static variable in class net.sf.basedb.core.data.keyring.ProjectKeys
 
serialVersionUID - Static variable in class net.sf.basedb.core.data.keyring.RoleKeys
 
serialVersionUID - Static variable in class net.sf.basedb.core.data.keyring.UserGroups
 
serialVersionUID - Static variable in class net.sf.basedb.core.data.keyring.UserKeys
 
serialVersionUID - Static variable in class net.sf.basedb.core.data.keyring.UserProjects
 
serialVersionUID - Static variable in class net.sf.basedb.core.data.keyring.UserRoles
 
serialVersionUID - Static variable in class net.sf.basedb.core.data.MappingCoordinate
 
serialVersionUID - Static variable in class net.sf.basedb.core.data.PlateCoordinate
 
serialVersionUID - Static variable in class net.sf.basedb.core.data.QuotaIndex
 
serialVersionUID - Static variable in class net.sf.basedb.core.data.ReporterListScoreData
 
serialVersionUID - Static variable in class net.sf.basedb.core.data.VersionedParameter
 
serialVersionUID - Static variable in exception net.sf.basedb.core.DatabaseException
 
serialVersionUID - Static variable in exception net.sf.basedb.core.DateFormatException
 
serialVersionUID - Static variable in exception net.sf.basedb.core.DetachedItemException
 
serialVersionUID - Static variable in exception net.sf.basedb.core.DeviceNotVerifiedException
 
serialVersionUID - Static variable in exception net.sf.basedb.core.DisallowedValueException
 
serialVersionUID - Static variable in class net.sf.basedb.core.ExtendedPropertyAccessor.GetterSetter
 
serialVersionUID - Static variable in class net.sf.basedb.core.hibernate.SessionWrapper
 
serialVersionUID - Static variable in class net.sf.basedb.core.hibernate.StatelessSessionWrapper
 
serialVersionUID - Static variable in exception net.sf.basedb.core.InvalidAnnotationException
 
serialVersionUID - Static variable in exception net.sf.basedb.core.InvalidDataException
 
serialVersionUID - Static variable in exception net.sf.basedb.core.InvalidPasswordException
 
serialVersionUID - Static variable in exception net.sf.basedb.core.InvalidPathException
 
serialVersionUID - Static variable in exception net.sf.basedb.core.InvalidRelationException
 
serialVersionUID - Static variable in exception net.sf.basedb.core.InvalidUseOfNullException
 
serialVersionUID - Static variable in exception net.sf.basedb.core.ItemAlreadyExistsException
 
serialVersionUID - Static variable in exception net.sf.basedb.core.ItemInUseException
 
serialVersionUID - Static variable in exception net.sf.basedb.core.ItemModifiedException
 
serialVersionUID - Static variable in exception net.sf.basedb.core.ItemNotFoundException
 
serialVersionUID - Static variable in class net.sf.basedb.core.log.LoggingInterceptor
 
serialVersionUID - Static variable in exception net.sf.basedb.core.LoginException
 
serialVersionUID - Static variable in exception net.sf.basedb.core.NotLoggedInException
 
serialVersionUID - Static variable in exception net.sf.basedb.core.NumberOutOfRangeException
 
serialVersionUID - Static variable in exception net.sf.basedb.core.ParameterException
 
serialVersionUID - Static variable in exception net.sf.basedb.core.PermissionDeniedException
 
serialVersionUID - Static variable in exception net.sf.basedb.core.QuotaException
 
serialVersionUID - Static variable in exception net.sf.basedb.core.signal.SignalException
 
serialVersionUID - Static variable in exception net.sf.basedb.core.signal.SignalReceivedException
 
serialVersionUID - Static variable in exception net.sf.basedb.core.signal.UnsupportedSignalException
 
serialVersionUID - Static variable in class net.sf.basedb.core.snapshot.AnnotationSetSnapshot
 
serialVersionUID - Static variable in class net.sf.basedb.core.snapshot.AnnotationSnapshot
 
serialVersionUID - Static variable in exception net.sf.basedb.core.StringTooLongException
 
serialVersionUID - Static variable in class net.sf.basedb.core.UnmodifiableResultList
 
serialVersionUID - Static variable in exception net.sf.basedb.core.UnsavedItemException
 
serialVersionUID - Static variable in exception net.sf.basedb.core.UnsupportedFileFormatException
 
serialVersionUID - Static variable in class net.sf.basedb.util.Enumeration
 
serialVersionUID - Static variable in class net.sf.basedb.util.jep.FunctionSafeJep.SafeFunctionTable
 
serialVersionUID - Static variable in class net.sf.basedb.util.jep.FunctionSafeJep.UnknownFunction
 
serialVersionUID - Static variable in class net.sf.basedb.util.NameableComparator
 
serialVersionUID - Static variable in class net.sf.basedb.util.plot.HistogramPlot.HistogramBin
 
serialVersionUID - Static variable in class net.sf.basedb.util.plot.HistogramPlot.HistogramDataset
 
serialVersionUID - Static variable in class net.sf.basedb.util.plot.HistogramPlot.HistogramSeries
 
serialVersionUID - Static variable in class net.sf.basedb.util.ToStringComparator
 
server - Variable in class net.sf.basedb.clients.jobagent.Agent
 
server - Variable in class net.sf.basedb.core.data.JobAgentData
 
server - Variable in class net.sf.basedb.core.data.JobData
 
server - Variable in class net.sf.basedb.core.Job.ProgressReporterImpl
 
server - Variable in class net.sf.basedb.util.jobagent.JobAgentConnection
 
SERVER_NAME - Static variable in class net.sf.basedb.clients.web.taglib.Page
The name of this webserver.
serverAddress - Variable in class net.sf.basedb.clients.jobagent.Agent
 
serverCertificate - Variable in class net.sf.basedb.core.data.FileServerData
 
serverCertificate - Variable in class net.sf.basedb.util.uri.ConnectionParameters
 
service - Static variable in class net.sf.basedb.core.QueryExecutor
 
service(HttpServletRequest, HttpServletResponse) - Method in class net.sf.basedb.clients.web.extensions.ServletWrapper
Service a request to the wrapped servlet.
service(RequestHandler) - Method in class net.sf.basedb.clients.jobagent.Agent
Start the listener service that listens for control commands such as start, stop, pause and info.
SERVICE_STARTED - Static variable in class net.sf.basedb.clients.web.extensions.service.Services
Events of this type are sent to the extensions registry whenever a service extension is started.
SERVICE_STOPPED - Static variable in class net.sf.basedb.clients.web.extensions.service.Services
Events of this type are sent to the extensions registry whenever a service extension is stopped.
ServiceControllerAction - Interface in net.sf.basedb.clients.web.extensions.service
Action for controlling services installed under the extensions system.
Services - Class in net.sf.basedb.clients.web.extensions.service
Utility class for starting and stopping services.
Services() - Constructor for class net.sf.basedb.clients.web.extensions.service.Services
 
ServiceSessionControl - Class in net.sf.basedb.core
A special session control implementation used for services.
ServiceSessionControl() - Constructor for class net.sf.basedb.core.ServiceSessionControl
 
ServiceSessionControl.FlushSessionAction - Class in net.sf.basedb.core
Flushes the given session before the transaction is committed.
ServiceSessionControl.ServicesKeyring - Class in net.sf.basedb.core
Our own keyring containing the only permission: Permission.ACT_AS_ANOTHER_USER.
ServiceSessionControl.SessionFactoryConfiguration - Class in net.sf.basedb.core
Used for creating a configuration that is the basis for building a session factory.
ServicesEventHandler - Class in net.sf.basedb.clients.web.extensions.service
Event handler for managing services when new extension are added or existing extension are updated or deleted.
ServicesEventHandler() - Constructor for class net.sf.basedb.clients.web.extensions.service.ServicesEventHandler
 
ServicesKeyring() - Constructor for class net.sf.basedb.core.ServiceSessionControl.ServicesKeyring
 
ServicesUtil - Class in net.sf.basedb.core
Utility class for the "services" extension point.
ServicesUtil() - Constructor for class net.sf.basedb.core.ServicesUtil
 
SERVLET_URL - Static variable in class net.sf.basedb.clients.web.extensions.ExtensionsControl
The location where extension servlets are registered.
servletClass - Variable in class net.sf.basedb.clients.web.extensions.ServletWrapper
 
servletContext - Static variable in class net.sf.basedb.clients.web.extensions.ExtensionsControl
 
servletContext - Static variable in class net.sf.basedb.clients.web.extensions.skin.ImageRemapperUtil
 
ServletExportOutputStream - Class in net.sf.basedb.clients.web.util
An extension to the ExportOutputStream class which directs the output to the response stream of a HttpServletResponse object.
ServletExportOutputStream(HttpServletResponse) - Constructor for class net.sf.basedb.clients.web.util.ServletExportOutputStream
Create a new servlet export stream.
ServletLoader - Class in net.sf.basedb.clients.web.extensions
Loads servlet definitions from an XML file.
ServletLoader() - Constructor for class net.sf.basedb.clients.web.extensions.ServletLoader
Create a new XML loader instance.
servletName - Variable in class net.sf.basedb.clients.web.extensions.ServletWrapperKey
 
servletPath - Variable in class net.sf.basedb.clients.web.extensions.plot.MAPlotFactory
 
servletPath - Variable in class net.sf.basedb.clients.web.extensions.RequestWrapper
 
servlets - Variable in class net.sf.basedb.clients.web.extensions.ServletLoader
 
servletsPath - Variable in class net.sf.basedb.clients.web.extensions.WebClientRegisterExtensionsProcessor
 
ServletWrapper - Class in net.sf.basedb.clients.web.extensions
A wrapper class for servlets defined by extensions.
ServletWrapper(Class<? extends Servlet>, String) - Constructor for class net.sf.basedb.clients.web.extensions.ServletWrapper
 
ServletWrapperKey - Class in net.sf.basedb.clients.web.extensions
Key implementation used to identify servlets.
ServletWrapperKey(String, String) - Constructor for class net.sf.basedb.clients.web.extensions.ServletWrapperKey
Create a new key for a servlet defined in a file with the given name.
session - Variable in class net.sf.basedb.core.AuthenticationContext
 
session - Variable in class net.sf.basedb.core.data.ChangeHistoryData
 
session - Variable in class net.sf.basedb.core.DataResultIterator
The Hibernate Session that was used in the query, null if a stateless session is used.
session - Variable in class net.sf.basedb.core.hibernate.SessionWrapper
 
session - Variable in class net.sf.basedb.core.hibernate.StatelessSessionWrapper
 
session - Static variable in class net.sf.basedb.core.Install
 
session - Variable in class net.sf.basedb.core.LogControl
 
session - Variable in class net.sf.basedb.core.MigrateRbaToDba
 
session - Variable in class net.sf.basedb.core.Migration
 
session - Variable in class net.sf.basedb.core.ProjectSpecificAnnotationsManager
 
session - Variable in class net.sf.basedb.core.QueryExecutor.CancelableSession
 
session - Variable in class net.sf.basedb.core.QueryExecutor.CancelableStatelessSession
 
session - Variable in class net.sf.basedb.core.QueryRuntimeFilterManager
The Hibernate session where the filters should be enabled.
session - Variable in class net.sf.basedb.core.ServiceSessionControl.FlushSessionAction
 
Session - Class in net.sf.basedb.core
A session represents the time between login and logout for a single user.
Session(SessionData) - Constructor for class net.sf.basedb.core.Session
 
SESSION - Enum constant in enum class net.sf.basedb.core.Item
The item is an Session.
Session.QueryRuntimeFilterImpl - Class in net.sf.basedb.core
A runtime filter implementation that limits a query to only return sessions for the currently logged in user unless the logged in user has generic read permission.
sessionCache - Static variable in class net.sf.basedb.core.Application
A cache of SessionControl objects.
sessionCacheTimeout - Static variable in class net.sf.basedb.core.Application
Number of minutes a SessionControl object can be unused before it is removed from the cache.
sessionCacheTimeout() - Static method in class net.sf.basedb.core.Application
Gets the maximum number of minutes before an active session is logged out.
sessionControl - Static variable in class net.sf.basedb.core.Install
 
SessionControl - Class in net.sf.basedb.core
This class handles user sessions.
SessionControl(String, String, boolean, String) - Constructor for class net.sf.basedb.core.SessionControl
Creates a new SessionControl object.
SessionControl(String, SessionControl, PluginDefinition, Job) - Constructor for class net.sf.basedb.core.SessionControl
Create a new session control object using another one as the template.
SessionControl.ClientInfo - Class in net.sf.basedb.core
 
SessionControl.LoginInfo - Class in net.sf.basedb.core
Internal class to hold information about the logged in user.
SessionControl.MainContext - Class in net.sf.basedb.core
Represents a main context for which a "current" subcontext can be assigned.
SessionControl.SettingInfo - Class in net.sf.basedb.core
Internal class to hold information about a setting
SessionControl.UnverifiedDeviceInfo - Class in net.sf.basedb.core
Class for storing temporary device information for a user that has been authenticated but before a device has been verified.
SessionControlCacheCleaner() - Constructor for class net.sf.basedb.core.Application.SessionControlCacheCleaner
 
SessionData - Class in net.sf.basedb.core.data
This class holds information about a session.
SessionData() - Constructor for class net.sf.basedb.core.data.SessionData
 
SessionFactoryConfiguration - Class in net.sf.basedb.core.hibernate
SessionFactoryConfiguration(String, ClassLoader) - Constructor for class net.sf.basedb.core.hibernate.SessionFactoryConfiguration
Deprecated.
Create a configuration instance.
SessionFactoryConfiguration(String, String, int, ClassLoader) - Constructor for class net.sf.basedb.core.ServiceSessionControl.SessionFactoryConfiguration
 
sessionId - Variable in class net.sf.basedb.core.data.ChangeHistoryData
 
sessionId - Variable in class net.sf.basedb.core.log.TransactionDetails
 
sessionId - Variable in class net.sf.basedb.core.SessionControl.LoginInfo
The id of the SessionData.
sessions - Variable in class net.sf.basedb.core.data.ClientData
 
sessions - Variable in class net.sf.basedb.core.data.UserData
 
sessions - Variable in class net.sf.basedb.core.data.UserDeviceData
 
sessionSettings - Variable in class net.sf.basedb.core.SessionControl
Stores name and value of session settings.
sessionWithOptions() - Method in class net.sf.basedb.core.hibernate.SessionWrapper
 
SessionWrapper - Class in net.sf.basedb.core.hibernate
Wrapper around Hibernate sessions that includes a query cache.
SessionWrapper(Session) - Constructor for class net.sf.basedb.core.hibernate.SessionWrapper
Creates a new session wrapper
set(int, I) - Method in class net.sf.basedb.core.AbstractResultList
Not supported.
set(int, T) - Method in class net.sf.basedb.core.UnmodifiableResultList
Not supported.
set(Object, E) - Method in class net.sf.basedb.util.ClassLocal
Store an object and associate it with the class of the specified instance.
set(Object, Object, SessionFactoryImplementor) - Method in class net.sf.basedb.core.ExtendedPropertyAccessor.GetterSetter
Set the value of the extended property.
set(T) - Method in class net.sf.basedb.core.ItemResultList.ResultListListIterator
This operation is not supported.
SET_OWNER - Enum constant in enum class net.sf.basedb.core.Permission
This permission allows a user change the owner of an item.
SET_PERMISSION - Enum constant in enum class net.sf.basedb.core.Permission
This permission allows a user change the access permission to an item.
setAbort() - Method in class net.sf.basedb.clients.web.fileupload.FileUploadProgress
Request that the upload should be aborted.
setAbout(About) - Method in class net.sf.basedb.util.extensions.ExtensionBean
 
setAbout(About) - Method in class net.sf.basedb.util.extensions.xml.PluginInfo
 
setAbout(About, boolean) - Method in class net.sf.basedb.core.PluginDefinition
Update the plug-in information with the information in the about object.
setAbsolute(long, String) - Method in class net.sf.basedb.core.SimpleAbsoluteProgressReporter
Set a basic progress level.
setAbstract(String) - Method in class net.sf.basedb.core.data.ExperimentData
 
setAbstract(String) - Method in class net.sf.basedb.core.Experiment
Set the abstract text for the publication of this experiment.
setAction(String) - Method in class net.sf.basedb.clients.web.taglib.table.Table
 
setActionClass(Class<A>) - Method in class net.sf.basedb.util.extensions.ExtensionPointBean
 
setActionFactory(ActionFactory<? extends A>) - Method in class net.sf.basedb.util.extensions.ExtensionBean
 
setActive(String) - Method in class net.sf.basedb.clients.web.taglib.tab.TabControl
 
setActiveProject(ProjectData) - Method in class net.sf.basedb.core.Keyring
Set the active project.
setActiveProject(Project) - Method in class net.sf.basedb.core.SessionControl
Set the active project.
setActiveProjectId(int) - Method in class net.sf.basedb.core.data.JobData
 
setAddress(String) - Method in class net.sf.basedb.core.authentication.ExtraUserInformation
 
setAddress(String) - Method in class net.sf.basedb.core.data.UserData
 
setAddress(String) - Method in class net.sf.basedb.core.User
Set the address for the user, or null if unknown.
setAffiliations(String) - Method in class net.sf.basedb.core.data.ExperimentData
 
setAffiliations(String) - Method in class net.sf.basedb.core.Experiment
Set the affiliations for this experiment.
setAllowImmediateExecution(boolean) - Method in class net.sf.basedb.core.data.PluginDefinitionData
 
setAllowImmediateExecution(boolean) - Method in class net.sf.basedb.core.PluginDefinition
 
setAllowMultiple(boolean) - Method in class net.sf.basedb.core.data.ItemSubtypeFileTypeData
 
setAllowMultiple(boolean) - Method in class net.sf.basedb.core.data.PlatformFileTypeData
 
setAllowMultiple(boolean) - Method in class net.sf.basedb.core.ItemSubtypeFileType
Allow or disallow multiple files of this file type in a file set.
setAllowMultiple(boolean) - Method in class net.sf.basedb.core.PlatformFileType
Allow or disallow multiple files of this file type in a file set.
setAllowRendererOverrider(boolean) - Method in class net.sf.basedb.util.extensions.ExtensionPointBean
 
setAllProjects() - Method in class net.sf.basedb.core.snapshot.SnapshotManager
Search for project-specific annotations for all projects including the default values.
setAllsubcontexts(boolean) - Method in class net.sf.basedb.clients.web.taglib.table.PresetSelector
 
setAnalyzeAfterImport(boolean) - Method in class net.sf.basedb.core.Migration
Should we execute an analyis command after the import has been completed.
setAnnotation(boolean) - Method in class net.sf.basedb.clients.web.taglib.table.ColumnDef
 
setAnnotation(Annotation) - Method in class net.sf.basedb.core.snapshot.AnnotationFilter
Set the annotation this filter should match.
setAnnotationId(int) - Method in class net.sf.basedb.core.snapshot.AnnotationFilter
Set the annotation this filter should match.
setAnnotations(Set<AnnotationData>) - Method in class net.sf.basedb.core.data.AnnotationSetData
 
setAnnotations(Set<AnnotationData>) - Method in class net.sf.basedb.core.data.AnnotationTypeData
 
setAnnotations(Set<AnnotationLink>) - Method in class net.sf.basedb.core.data.AnnotatedData
 
setAnnotations(Set<AnnotationLink>) - Method in class net.sf.basedb.core.data.BioAssayData
 
setAnnotations(Set<AnnotationLink>) - Method in class net.sf.basedb.core.data.BioAssaySetData
 
setAnnotations(Set<AnnotationLink>) - Method in class net.sf.basedb.core.data.PluginDefinitionData
 
setAnnotations(Set<AnnotationLink>) - Method in class net.sf.basedb.core.data.ProjectData
 
setAnnotations(Set<AnnotationLink>) - Method in class net.sf.basedb.core.data.RootRawBioAssayData
 
setAnnotations(Set<AnnotationLink>) - Method in class net.sf.basedb.core.data.WellData
 
setAnnotationSet(AnnotationSetData) - Method in interface net.sf.basedb.core.data.AnnotatableData
Change the annotation set.
setAnnotationSet(AnnotationSetData) - Method in class net.sf.basedb.core.data.AnnotatedData
 
setAnnotationSet(AnnotationSetData) - Method in class net.sf.basedb.core.data.AnnotationData
 
setAnnotationSet(AnnotationSetData) - Method in class net.sf.basedb.core.data.BioAssayData
 
setAnnotationSet(AnnotationSetData) - Method in class net.sf.basedb.core.data.BioAssaySetData
 
setAnnotationSet(AnnotationSetData) - Method in class net.sf.basedb.core.data.PluginDefinitionData
 
setAnnotationSet(AnnotationSetData) - Method in class net.sf.basedb.core.data.ProjectData
 
setAnnotationSet(AnnotationSetData) - Method in class net.sf.basedb.core.data.RootRawBioAssayData
 
setAnnotationSet(AnnotationSetData) - Method in class net.sf.basedb.core.data.WellData
 
setAnnotationSetId(int) - Method in class net.sf.basedb.core.data.annotations.AnnotationLink
 
setAnnotationType(AnnotationType) - Method in class net.sf.basedb.core.snapshot.AnnotationTypeFilter
Set the annotation type this filter should match.
setAnnotationType(AnnotationType) - Method in class net.sf.basedb.util.export.spotdata.AnnotationAssayField
Set the annotation type of the annotations that should be exported in this field.
setAnnotationType(AnnotationTypeData) - Method in class net.sf.basedb.core.data.AnnotationData
 
setAnnotationTypeId(int) - Method in class net.sf.basedb.core.data.annotations.AnnotationLink
 
setAnnotationTypeIds(Collection<Integer>) - Method in class net.sf.basedb.clients.web.ExperimentExplorer
Update the selected annotation types.
setAnnotationTypes(Set<AnnotationTypeData>) - Method in class net.sf.basedb.core.data.AnnotationTypeCategoryData
 
setAppId(String) - Method in class net.sf.basedb.core.data.SchemaVersionData
 
setArrayBatch(ArrayBatch) - Method in class net.sf.basedb.core.ArraySlide
Set the ArrayBatch this arrayslide belongs to.
setArrayBatch(ArrayBatchData) - Method in class net.sf.basedb.core.data.ArraySlideData
 
setArrayBatches(Set<ArrayBatchData>) - Method in class net.sf.basedb.core.data.ArrayDesignData
 
setArrayDesign(ArrayDesign) - Method in class net.sf.basedb.core.ArrayBatch
Set the ArrayDesign used in this ArrayBatch.
setArrayDesign(ArrayDesign) - Method in class net.sf.basedb.core.ArrayDesignBlock
Set the ArrayDesign for this block.
setArrayDesign(ArrayDesign) - Method in class net.sf.basedb.core.RawBioAssay
Set the ArrayDesign this raw data uses.
setArrayDesign(ArrayDesignData) - Method in class net.sf.basedb.core.data.ArrayBatchData
 
setArrayDesign(ArrayDesignData) - Method in class net.sf.basedb.core.data.ArrayDesignBlockData
 
setArrayDesign(ArrayDesignData) - Method in class net.sf.basedb.core.data.ArrayDesignPlateData
 
setArrayDesign(ArrayDesignData) - Method in class net.sf.basedb.core.data.RawBioAssayData
 
setArrayDesignBlock(ArrayDesignBlockData) - Method in class net.sf.basedb.core.data.FeatureData
 
setArrayDesignBlocks(Set<ArrayDesignBlockData>) - Method in class net.sf.basedb.core.data.ArrayDesignData
 
setArrayDesigns(Set<ArrayDesignData>) - Method in class net.sf.basedb.core.data.JobData
 
setArrayDesigns(Set<ArrayDesignPlateData>) - Method in class net.sf.basedb.core.data.PlateData
 
setArraySlide(ArraySlide) - Method in class net.sf.basedb.core.PhysicalBioAssay
Set the ArraySlide this hybridization is using.
setArraySlide(ArraySlideData) - Method in class net.sf.basedb.core.data.PhysicalBioAssayData
 
setArraySlides(Set<ArraySlideData>) - Method in class net.sf.basedb.core.data.ArrayBatchData
 
setAssayAnnotationsWriter(AnnotationWriter) - Method in class net.sf.basedb.util.export.spotdata.BfsExporter
Set the stream were assay annotations should be written.
setAssayFields(List<String>) - Method in class net.sf.basedb.util.importer.spotdata.BaseFileInfo.SpotSectionInfo
Set the list of all assay data fields, in the order the appear in the file.
setAssays(List<Integer>) - Method in class net.sf.basedb.util.importer.spotdata.BaseFileInfo.SpotSectionInfo
Set a list with the ID:s of all assays, in the order the appearu in the data columns.
setAssaysHaveParentAssaysMapping(boolean) - Method in class net.sf.basedb.util.importer.spotdata.BaseFileInfo
Set a flag that indicates if the BASEfile includes a mapping from child to parent assays.
setAttribute(String, Object) - Method in class net.sf.basedb.util.extensions.ClientContext
Set an attribute of the context.
setAttribute(String, String) - Method in class net.sf.basedb.core.authentication.LoginRequest
Set an extra attribute to use for the login request.
setAttribute(String, String) - Method in class net.sf.basedb.util.extensions.AboutBean
Set an attribute for the given name.
setAttribute(String, String, Object) - Method in class net.sf.basedb.util.extensions.Registry
Set an extra attribute on a registered extension or extension point.
setAttribute(NodeAttribute<T>, T) - Method in class net.sf.basedb.util.overview.Node
Set a node attribute.
setAuthenticationMethod(String) - Method in class net.sf.basedb.core.data.SessionData
 
setAuthors(String) - Method in class net.sf.basedb.core.data.ExperimentData
 
setAuthors(String) - Method in class net.sf.basedb.core.Experiment
Set the authors of the publication for this experiment.
setAutoCloseParsers(boolean) - Method in class net.sf.basedb.util.importer.spotdata.BfsImporter
If this option is set then all parsers are automatically closed when all data has been read to them.
setAutoCloseWriters(boolean) - Method in class net.sf.basedb.util.export.spotdata.BaseFileExporter
If this option is set then all writers are automatically closed when all data has been writted to them.
setAutoCloseWriters(boolean) - Method in class net.sf.basedb.util.export.spotdata.BfsExporter
If this option is set then all writers are automatically closed when all data has been writted to them.
setAutoCompress(boolean) - Method in class net.sf.basedb.core.data.DirectoryData
 
setAutoCompress(boolean) - Method in class net.sf.basedb.core.data.MimeTypeData
 
setAutoCompress(boolean) - Method in class net.sf.basedb.core.Directory
Set if files of should automatically be compressed when they are uploaded to this directory.
setAutoCompress(boolean) - Method in class net.sf.basedb.core.MimeType
Set if files of this MIME type should automatically be compressed when they are uploaded to BASE.
setAutoJoinType(JoinType) - Method in class net.sf.basedb.core.AbstractEntityQuery
Specify the join type of automatic joins.
setAutoJoinType(JoinType) - Method in class net.sf.basedb.core.DynamicPositionQuery
Specify the join type of automatic joins.
setAutoJoinType(JoinType) - Method in class net.sf.basedb.core.DynamicRawDataQuery
Specify the join type of automatic joins.
setAutoJoinType(JoinType) - Method in class net.sf.basedb.core.DynamicReporterQuery
Specify the join type of automatic joins.
setAutoJoinType(JoinType) - Method in class net.sf.basedb.core.DynamicSpotQuery
Specify the join type of automatic joins.
setAutoLoadChildren(boolean) - Method in class net.sf.basedb.util.overview.loader.BasicItemNodeLoaderFactory
Set a flag that determines if the factory should create node loaders that automatically loads child nodes or not.
setAutoPermission(int) - Method in class net.sf.basedb.core.data.ProjectData
 
setAutoPermission(Set<Permission>) - Method in class net.sf.basedb.core.Project
Set the default permissions to use when automatically sharing new item the project when it is the active project.
setAutoReload(boolean) - Method in class net.sf.basedb.util.units.UnitCache
Specifies if a cached unit that may have been loaded by a closed DbControl should be reloaded with the current DbControl or not.
setAutoShare(boolean) - Method in class net.sf.basedb.core.data.DirectoryData
 
setAutoShare(boolean) - Method in class net.sf.basedb.core.Directory
Set if new files and subdirectories of should automatically be shared with the same permissions as this directory.
setAutoshow(boolean) - Method in class net.sf.basedb.clients.web.taglib.table.Cell
 
setAverageMethod(int) - Method in class net.sf.basedb.core.data.ExtraValueTypeData
 
setAverageMethod(int) - Method in class net.sf.basedb.core.data.FormulaData
 
setAverageMethod(int) - Method in class net.sf.basedb.core.data.ReporterClonePropertyData
 
setAverageMethod(Formula.AverageMethod) - Method in class net.sf.basedb.core.ExtraValueType
Set the average method of the extra value type..
setAverageMethod(Formula.AverageMethod) - Method in class net.sf.basedb.core.Formula
Set the average method of the formula.
setAverageMethod(Formula.AverageMethod) - Method in class net.sf.basedb.util.export.spotdata.JepDynamicField
Set the average method to use when exporting averaged data.
setAverageMethod(Formula.AverageMethod) - Method in class net.sf.basedb.util.export.spotdata.SimpleDynamicField
Set the average method to use when exporting averaged data.
setAverageOnReporter(boolean) - Method in class net.sf.basedb.util.export.spotdata.AbstractBioAssaySetExporter
Specify if the exported data should be averaged on reporter or not.
setAverageOnReporter(boolean) - Method in class net.sf.basedb.util.export.spotdata.BaseFileExporter
 
setAvoiding() - Method in class net.sf.basedb.util.listable.TransformContext
Shortcut for enabling 'avoiding' and disabling 'collecting'.
setAvoiding(boolean) - Method in class net.sf.basedb.util.listable.TransformContext
Enable/disable avoiding of returning any source items that has been previously collected.
setBarcode(String) - Method in class net.sf.basedb.core.ArraySlide
Set the barcode for the slide.
setBarcode(String) - Method in class net.sf.basedb.core.BioPlate
Sets the bio plates barcode
setBarcode(String) - Method in class net.sf.basedb.core.data.ArraySlideData
 
setBarcode(String) - Method in class net.sf.basedb.core.data.BioPlateData
 
setBarcode(String) - Method in class net.sf.basedb.core.data.PlateData
 
setBarcode(String) - Method in class net.sf.basedb.core.Plate
Set the barcode for the plate.
setBaseStyle(CellStyle) - Method in class net.sf.basedb.util.excel.CellStyleCreator
Set a base style to use for new cells.
setBatchIndex(int) - Method in class net.sf.basedb.core.ArraySlide
Set the index of this slide in the batch.
setBatchIndex(int) - Method in class net.sf.basedb.core.data.ArraySlideData
 
setBatchSize(int) - Method in class net.sf.basedb.core.AbstractBatcher
 
setBatchSize(int) - Method in interface net.sf.basedb.core.Batcher
Sets the batch size.
setBeanClass(String) - Method in class net.sf.basedb.util.extensions.debug.BeanActionFactory
Set the name of the class to use as a bean.
setBigDecimal(int, BigDecimal) - Method in class net.sf.basedb.core.hibernate.QueryWrapper
Deprecated.
setBigDecimal(String, BigDecimal) - Method in class net.sf.basedb.core.hibernate.QueryWrapper
Deprecated.
setBigInteger(int, BigInteger) - Method in class net.sf.basedb.core.hibernate.QueryWrapper
Deprecated.
setBigInteger(String, BigInteger) - Method in class net.sf.basedb.core.hibernate.QueryWrapper
Deprecated.
setBinary(int, byte[]) - Method in class net.sf.basedb.core.hibernate.QueryWrapper
Deprecated.
setBinary(String, byte[]) - Method in class net.sf.basedb.core.hibernate.QueryWrapper
Deprecated.
setBioAssays(Set<BioAssayData>) - Method in class net.sf.basedb.core.data.BioAssaySetData
 
setBioAssays(Set<BioAssayData>) - Method in class net.sf.basedb.core.data.RawBioAssayData
 
setBioAssaySet(BioAssaySet) - Method in class net.sf.basedb.core.BioAssay
Set the experiment.
setBioAssaySet(BioAssaySet) - Method in class net.sf.basedb.core.ExtraValue
Set the bioassayset.
setBioAssaySet(BioAssaySetData) - Method in class net.sf.basedb.core.data.BioAssayData
 
setBioAssaySet(BioAssaySetData) - Method in class net.sf.basedb.core.data.ExtraValueData
 
setBioAssaySets(Set<BioAssaySetData>) - Method in class net.sf.basedb.core.data.ExperimentData
 
setBioMaterial(BioMaterialData) - Method in class net.sf.basedb.core.data.BioMaterialEventSourceData
 
setBioMaterial(MeasuredBioMaterialData) - Method in class net.sf.basedb.core.data.BioMaterialEventData
 
setBioMaterial(MeasuredBioMaterialData) - Method in class net.sf.basedb.core.data.BioWellData
 
setBioMaterial(MeasuredBioMaterial) - Method in class net.sf.basedb.core.BioMaterialEvent
Set the biomaterial that was affected or created by this event.
setBioMaterialEvents(Set<BioMaterialEventData>) - Method in class net.sf.basedb.core.data.BioPlateEventParticipantData
 
setBioMaterialType(Integer) - Method in class net.sf.basedb.core.data.BioPlateTypeData
 
setBioMaterialType(Item) - Method in class net.sf.basedb.core.BioPlateType
Set the type of biomaterial that can be stored on plates with this type.
setBioPlate(BioPlateData) - Method in class net.sf.basedb.core.data.BioPlateEventParticipantData
 
setBioPlate(BioPlateData) - Method in class net.sf.basedb.core.data.BioWellData
 
setBioPlateEventParticipant(BioPlateEventParticipant) - Method in class net.sf.basedb.core.MeasuredBioMaterial
 
setBioPlateEventParticipant(BioPlateEventParticipant) - Method in class net.sf.basedb.core.PhysicalBioAssay
 
setBioPlateEventParticipant(BioPlateEventParticipantData) - Method in class net.sf.basedb.core.data.BioMaterialEventData
 
setBioPlates(Set<BioPlateData>) - Method in class net.sf.basedb.core.data.BioPlateTypeData
 
setBioPlateType(BioPlateType) - Method in class net.sf.basedb.core.BioPlate
 
setBioPlateType(BioPlateTypeData) - Method in class net.sf.basedb.core.data.BioPlateData
 
setBioWell(BioWell) - Method in class net.sf.basedb.core.MeasuredBioMaterial
Sets the BioWell where this biomaterial is located.
setBioWell(BioWellData) - Method in class net.sf.basedb.core.data.MeasuredBioMaterialData
 
setBioWells(Map<PlateCoordinate, BioWellData>) - Method in class net.sf.basedb.core.data.BioPlateData
 
setBlock(Integer) - Method in class net.sf.basedb.core.data.RawData
 
setBlockNumber(int) - Method in class net.sf.basedb.core.ArrayDesignBlock
Set the block number of this block.
setBlockNumber(int) - Method in class net.sf.basedb.core.data.ArrayDesignBlockData
 
setBlockNumber(int) - Method in enum class net.sf.basedb.plugins.PrintMapFlatFileImporter.Section
 
setBlockSizeX(int) - Method in class net.sf.basedb.core.ArrayDesignBlock
Set the number of columns in this block.
setBlockSizeX(int) - Method in class net.sf.basedb.core.data.ArrayDesignBlockData
 
setBlockSizeX(Integer) - Method in class net.sf.basedb.plugins.PrintMapFlatFileImporter.MetaBlock
 
setBlockSizeY(int) - Method in class net.sf.basedb.core.ArrayDesignBlock
Set the number of rows in this block.
setBlockSizeY(int) - Method in class net.sf.basedb.core.data.ArrayDesignBlockData
 
setBlockSizeY(Integer) - Method in class net.sf.basedb.plugins.PrintMapFlatFileImporter.MetaBlock
 
setBlockValue(PrintMapFlatFileImporter.MetaBlock, FlatFileParser.Line) - Method in class net.sf.basedb.plugins.PrintMapFlatFileImporter
 
setBofMarkerRegexp(Pattern) - Method in class net.sf.basedb.util.parser.FlatFileParser
Set a regular expression that maches a beginning-of-file marker.
setBoolean(int, boolean) - Method in class net.sf.basedb.core.hibernate.QueryWrapper
Deprecated.
setBoolean(String, boolean) - Method in class net.sf.basedb.core.hibernate.QueryWrapper
Deprecated.
setBooleanValues(List<Boolean>) - Method in class net.sf.basedb.core.data.annotations.AnnotationLink
 
setBuild(int) - Method in class net.sf.basedb.core.data.SchemaVersionData
 
setBulletlist(boolean) - Method in class net.sf.basedb.clients.web.taglib.table.CellValue
 
setButtonclass(String) - Method in class net.sf.basedb.clients.web.taglib.Select
 
setButtonicon(String) - Method in class net.sf.basedb.clients.web.taglib.Select
 
setButtonstyle(String) - Method in class net.sf.basedb.clients.web.taglib.Select
 
setButtonTag(String) - Method in class net.sf.basedb.clients.web.extensions.toolbar.CompactButtonRenderer
Set the HTML tag to use for the "button".
setButtonTag(String) - Method in class net.sf.basedb.clients.web.extensions.toolbar.CompactButtonRendererFactory
Set the HTML tag to use for the "button".
setButtontitle(String) - Method in class net.sf.basedb.clients.web.taglib.Select
 
setByte(int, byte) - Method in class net.sf.basedb.core.hibernate.QueryWrapper
Deprecated.
setByte(String, byte) - Method in class net.sf.basedb.core.hibernate.QueryWrapper
Deprecated.
setBytes(long) - Method in class net.sf.basedb.core.data.DataCubeData
 
setBytes(long) - Method in class net.sf.basedb.core.data.DataCubeExtraValueData
 
setBytes(long) - Method in class net.sf.basedb.core.data.DataCubeFilterData
 
setBytes(long) - Method in class net.sf.basedb.core.data.DataCubeLayerData
 
setBytes(long) - Method in class net.sf.basedb.core.data.DiskUsageData
 
setBytes(long) - Method in class net.sf.basedb.core.data.ExperimentData
 
setBytes(long) - Method in class net.sf.basedb.core.data.RawBioAssayData
 
setBytes(long) - Method in class net.sf.basedb.core.data.ReporterCloneTemplateData
 
setCacheable(boolean) - Method in class net.sf.basedb.core.hibernate.NativeQueryWrapper
 
setCacheable(boolean) - Method in class net.sf.basedb.core.hibernate.QueryWrapper
 
setCachedObject(Object, Object) - Method in class net.sf.basedb.util.overview.GenericOverview
Store an auxilliary object in the overview cache.
setCachedObject(Object, Object) - Method in interface net.sf.basedb.util.overview.OverviewContext
Store an auxilliary object in the overview cache.
setCacheMode(CacheMode) - Method in class net.sf.basedb.core.hibernate.NativeQueryWrapper
 
setCacheMode(CacheMode) - Method in class net.sf.basedb.core.hibernate.QueryWrapper
 
setCacheMode(CacheMode) - Method in class net.sf.basedb.core.hibernate.SessionWrapper
 
setCacheRegion(String) - Method in class net.sf.basedb.core.hibernate.NativeQueryWrapper
 
setCacheRegion(String) - Method in class net.sf.basedb.core.hibernate.QueryWrapper
 
setCacheResult(boolean) - Method in class net.sf.basedb.core.AbstractHqlQuery
 
setCacheResult(boolean) - Method in interface net.sf.basedb.core.query.HqlQuery
Specify if the query results should be cached or not.
setCalendar(int, Calendar) - Method in class net.sf.basedb.core.hibernate.QueryWrapper
Deprecated.
setCalendar(String, Calendar) - Method in class net.sf.basedb.core.hibernate.QueryWrapper
Deprecated.
setCalendarDate(int, Calendar) - Method in class net.sf.basedb.core.hibernate.QueryWrapper
Deprecated.
setCalendarDate(String, Calendar) - Method in class net.sf.basedb.core.hibernate.QueryWrapper
Deprecated.
setCategories(Set<AnnotationTypeCategoryData>) - Method in class net.sf.basedb.core.data.AnnotationTypeData
 
setCellClass(String) - Method in class net.sf.basedb.clients.web.extensions.list.AbstractListColumnBean
 
setCellClass(String) - Method in class net.sf.basedb.clients.web.extensions.list.PropertyPathActionFactory
 
setCellStyle(String) - Method in class net.sf.basedb.clients.web.extensions.list.AbstractListColumnBean
 
setCellStyle(String) - Method in class net.sf.basedb.clients.web.extensions.list.PropertyPathActionFactory
 
setChangeHistory(ChangeHistoryData) - Method in class net.sf.basedb.core.data.ChangeHistoryDetailData
 
setChangeInfo(String) - Method in class net.sf.basedb.core.data.ChangeHistoryDetailData
 
setChangeType(int) - Method in class net.sf.basedb.core.data.ChangeHistoryDetailData
 
setChannels(int) - Method in class net.sf.basedb.core.data.FormulaData
 
setChannels(int) - Method in class net.sf.basedb.core.data.PlatformData
 
setChannels(int) - Method in class net.sf.basedb.core.data.PlatformVariantData
 
setChannels(int) - Method in class net.sf.basedb.core.Formula
Set the number of channels that are required to use this formula.
setChannels(int) - Method in class net.sf.basedb.core.Platform
Set the number of channels for a file-only platform.
setChannels(int) - Method in class net.sf.basedb.core.PlatformVariant
Set the number of channels for a file-only platform variant.
setCharacter(int, char) - Method in class net.sf.basedb.core.hibernate.QueryWrapper
Deprecated.
setCharacter(String, char) - Method in class net.sf.basedb.core.hibernate.QueryWrapper
Deprecated.
setCharacterSet(String) - Method in class net.sf.basedb.clients.web.util.ServletExportOutputStream
setCharacterSet(String) - Method in class net.sf.basedb.core.data.FileData
 
setCharacterSet(String) - Method in class net.sf.basedb.core.File
Set the character set used in this file (for text-files only).
setCharacterSet(String) - Method in class net.sf.basedb.core.plugin.ExportOutputStream
Do nothing should be overridden by subclasses.
setCharacterSet(String) - Method in class net.sf.basedb.util.FileExportOutputStream
setCharacterSet(String) - Method in class net.sf.basedb.util.uri.UriMetadata
 
setCharset(Charset) - Method in class net.sf.basedb.util.excel.XlsxToCsvUtil
Set the character set to use for the text.
setChecked(boolean) - Method in class net.sf.basedb.clients.web.taglib.Input
 
setChild(BioAssay) - Method in class net.sf.basedb.util.importer.spotdata.BaseFileInfo.ChildBioAssay
Set the real child bioassay object.
setChildCreationEvents(Set<BioMaterialEventSourceData>) - Method in class net.sf.basedb.core.data.BioMaterialData
 
setChildHasDifferentReporterPositionMapping(boolean) - Method in class net.sf.basedb.util.importer.spotdata.BaseFileInfo
Set a flag that indicates if the child data has a different position/reporter mapping than the parent bioassay set.
setChildId(int) - Method in class net.sf.basedb.core.data.keyring.GroupGroups
Set the id of the child group.
setChildren(Set<BioAssayData>) - Method in class net.sf.basedb.core.data.BioAssayData
 
setChildren(Set<DerivedBioAssayData>) - Method in class net.sf.basedb.core.data.DerivedBioAssayData
 
setChildren(Set<GroupData>) - Method in class net.sf.basedb.core.data.GroupData
 
setChildren(Set<MeasuredBioMaterialData>) - Method in class net.sf.basedb.core.data.BioMaterialData
 
setChildren(Set<PlateData>) - Method in class net.sf.basedb.core.data.PlateData
 
setChildrenLoaded() - Method in class net.sf.basedb.util.overview.Node
Sets a flag to indicate that all children has been loaded.
setCity(String) - Method in class net.sf.basedb.util.GeoLocation
 
setClassName(String) - Method in class net.sf.basedb.core.data.PluginDefinitionData
 
setClassName(String) - Method in class net.sf.basedb.core.PluginDefinition
The class name cannot be changed.
setClassName(String) - Method in class net.sf.basedb.util.extensions.xml.PluginInfo
 
setClazz(String) - Method in class net.sf.basedb.clients.web.extensions.list.AbstractListColumnBean
 
setClazz(String) - Method in class net.sf.basedb.clients.web.extensions.list.PropertyPathActionFactory
 
setClazz(String) - Method in class net.sf.basedb.clients.web.extensions.login.FieldInfo
 
setClazz(String) - Method in class net.sf.basedb.clients.web.extensions.menu.FixedMenuItemFactory
 
setClazz(String) - Method in class net.sf.basedb.clients.web.extensions.menu.MenuItemBean
 
setClazz(String) - Method in class net.sf.basedb.clients.web.extensions.tabcontrol.FixedTabFactory
 
setClazz(String) - Method in class net.sf.basedb.clients.web.extensions.tabcontrol.IncludeContentTabFactory
 
setClazz(String) - Method in class net.sf.basedb.clients.web.extensions.tabcontrol.TabBean
 
setClazz(String) - Method in class net.sf.basedb.clients.web.extensions.toolbar.ButtonBean
 
setClazz(String) - Method in class net.sf.basedb.clients.web.extensions.toolbar.FixedButtonFactory
 
setClazz(String) - Method in class net.sf.basedb.clients.web.extensions.toolbar.PermissionButtonFactory
Set the class to use in all cases.
setClazz(String) - Method in class net.sf.basedb.clients.web.taglib.ExceptionCatcher
 
setClazz(String) - Method in class net.sf.basedb.clients.web.taglib.StylableTag
 
setClazz(String) - Method in class net.sf.basedb.clients.web.taglib.tab.Tab
 
setClazz(String) - Method in class net.sf.basedb.clients.web.taglib.table.Cell
 
setClazz(String) - Method in class net.sf.basedb.clients.web.taglib.table.CellValue
 
setClearErrors(boolean) - Method in class net.sf.basedb.util.extensions.ExtensionsInvoker
Set a flag to indicate if existing errors should be cleared before an action is rendered.
setClearState() - Method in interface net.sf.basedb.core.plugin.Response
This can be used in the configuration phase of a plug-in to clear the stored state and nextCommand information.
setClearState() - Method in class net.sf.basedb.core.PluginResponse.ResponseImpl
 
setClearState() - Method in class net.sf.basedb.plugins.executor.ExternalProgramExecutor.ResponseWrapper
 
setClient(Client) - Method in class net.sf.basedb.core.ClientDefaultSetting
Set the client application this setting is valid for.
setClient(Client) - Method in class net.sf.basedb.core.Help
Set the client application this setting is valid for.
setClient(Client) - Method in class net.sf.basedb.core.UserClientSetting
Set the client application this setting is valid for.
setClient(ClientData) - Method in class net.sf.basedb.core.data.ChangeHistoryData
 
setClient(ClientData) - Method in class net.sf.basedb.core.data.ClientDefaultSettingData
 
setClient(ClientData) - Method in class net.sf.basedb.core.data.ContextData
 
setClient(ClientData) - Method in class net.sf.basedb.core.data.ContextIndex
 
setClient(ClientData) - Method in class net.sf.basedb.core.data.HelpData
 
setClient(ClientData) - Method in class net.sf.basedb.core.data.SessionData
 
setClient(ClientData) - Method in class net.sf.basedb.core.data.UserClientSettingData
 
setClient(ClientData) - Method in class net.sf.basedb.core.data.UserDeviceData
 
setClientCertificate(byte[]) - Method in class net.sf.basedb.core.data.FileServerData
 
setClientCertificate(byte[]) - Method in class net.sf.basedb.core.FileServer
Set the client certificate that BASE should use to authenticate with the server when connecting with https.
setClientCertificate(byte[]) - Method in class net.sf.basedb.util.uri.ConnectionParameters
 
setClientCertificatePassword(String) - Method in class net.sf.basedb.core.data.FileServerData
 
setClientCertificatePassword(String) - Method in class net.sf.basedb.core.FileServer
Set the password that is needed to unlock the client certificate.
setClientCertificatePassword(String) - Method in class net.sf.basedb.util.uri.ConnectionParameters
 
setClientId(Integer) - Method in class net.sf.basedb.core.data.ChangeHistoryData
 
setClientSettings(Set<UserClientSettingData>) - Method in class net.sf.basedb.core.data.UserData
 
setClone(boolean) - Method in class net.sf.basedb.util.annotations.InheritSpecification
Set a flag to inherit annotations by cloning the original values.
setCollecting() - Method in class net.sf.basedb.util.listable.TransformContext
Shortcut for enabling 'collecting' and disabling 'avoiding'.
setCollecting(boolean) - Method in class net.sf.basedb.util.listable.TransformContext
Enable/disable collecting of all source items that the transformers in this context are using.
setCollectionFormatter(Formatter<Collection<? super V>>) - Method in class net.sf.basedb.clients.web.extensions.list.AbstractListColumnBean
 
setColor(String) - Method in class net.sf.basedb.clients.web.ExperimentExplorer.AnnotationGroup
Sets the color for this annotation group.
setColor(String, Color) - Method in class net.sf.basedb.clients.web.servlet.ExperimentExplorerPlotServlet.ColumnKey
 
setColoring(ColoringData) - Method in class net.sf.basedb.core.data.ExtraValueTypeData
 
setColoring(ColoringData) - Method in class net.sf.basedb.core.data.FormulaData
 
setColorsAuto() - Method in class net.sf.basedb.clients.web.ExperimentExplorer.AnnotationSummary
Arranges the colors of the groups in the order they are returned by the ExperimentExplorer.AnnotationSummary.getAnnotationGroups() set.
setColspan(int) - Method in class net.sf.basedb.clients.web.taglib.table.Header
 
setColumn(int) - Method in class net.sf.basedb.core.data.BioWellData
 
setColumn(int) - Method in class net.sf.basedb.core.data.FeatureData
 
setColumn(int) - Method in class net.sf.basedb.core.data.MappingCoordinate
Set the location.
setColumn(int) - Method in class net.sf.basedb.core.data.PlateCoordinate
Set the location.
setColumn(int) - Method in class net.sf.basedb.core.data.WellData
 
setColumn(Integer) - Method in class net.sf.basedb.core.data.RawData
 
setColumn(String) - Method in class net.sf.basedb.clients.web.taglib.table.Cell
 
setColumn(String) - Method in class net.sf.basedb.core.data.ReporterClonePropertyData
 
setColumnContent(String, String) - Method in class net.sf.basedb.clients.web.taglib.table.Table
 
setColumnCount(int) - Method in class net.sf.basedb.util.bfs.DataWriter
Set the number of data columns.
setColumnFilter(String, int, String) - Method in class net.sf.basedb.clients.web.taglib.table.Table
 
setColumnFormatter(int, Formatter<?>) - Method in class net.sf.basedb.util.export.TableWriter
Set a data formatter for a given column.
setColumnNo(short) - Method in class net.sf.basedb.core.data.DataCubeColumnData
 
setColumnNo(short) - Method in class net.sf.basedb.core.DataCubeColumn
 
setColumns(int) - Method in class net.sf.basedb.core.data.PlateGeometryData
 
setColumns(int) - Method in class net.sf.basedb.core.PlateGeometry
The number of columns cannot be changed, used at object creation only.
setColumns(String) - Method in class net.sf.basedb.clients.web.taglib.table.Table
 
setColumns(Set<DataCubeColumnData>) - Method in class net.sf.basedb.core.data.DataCubeData
 
setColumnSeparator(String) - Method in class net.sf.basedb.util.excel.XlsxToCsvUtil
Set the column separator.
setComment(String) - Method in class net.sf.basedb.core.authentication.LoginRequest
Set the comment to use.
setComment(String) - Method in class net.sf.basedb.core.BioMaterialEvent
Set the comment about this event.
setComment(String) - Method in class net.sf.basedb.core.data.BioMaterialEventData
 
setComment(String) - Method in class net.sf.basedb.core.data.PlateEventData
 
setComment(String) - Method in class net.sf.basedb.core.hibernate.NativeQueryWrapper
 
setComment(String) - Method in class net.sf.basedb.core.hibernate.QueryWrapper
 
setComment(String) - Method in class net.sf.basedb.core.PlateEvent
Set the comment about this event.
setCompleted() - Method in class net.sf.basedb.util.uri.http.HttpConnectionManager.TimeoutTimer
 
setCompressed(boolean) - Method in class net.sf.basedb.core.data.FileData
 
setCompressedSize(long) - Method in class net.sf.basedb.core.data.FileData
 
setCondition(String) - Method in class net.sf.basedb.core.dbengine.TableInfo.IndexInfo
 
setConfigurations(Set<PluginConfigurationData>) - Method in class net.sf.basedb.core.data.PluginDefinitionData
 
setConfigurationValues(Map<VersionedParameter, ParameterValueData<?>>) - Method in class net.sf.basedb.core.data.PluginConfigurationData
 
setConfigured(PluginResponse) - Method in class net.sf.basedb.core.Job.ProgressReporterImpl
 
setConnectionManagerFactory(String) - Method in class net.sf.basedb.core.data.FileServerData
 
setConnectionManagerFactoryId(String) - Method in class net.sf.basedb.core.FileServer
Set the ID of the connection manager factory.
setConnectionManagerFactoryId(String) - Method in class net.sf.basedb.util.uri.ConnectionParameters
 
setContact(String) - Method in class net.sf.basedb.core.data.PluginDefinitionData
 
setContact(String) - Method in class net.sf.basedb.core.PluginDefinition
Set contact information for this plug-in.
setContact(String) - Method in class net.sf.basedb.util.extensions.AboutBean
 
setContent(String) - Method in class net.sf.basedb.clients.web.extensions.section.SectionBean
 
setContent(String) - Method in class net.sf.basedb.clients.web.extensions.tabcontrol.FixedTabFactory
 
setContent(String) - Method in class net.sf.basedb.clients.web.extensions.tabcontrol.TabBean
 
setContentLength(long) - Method in class net.sf.basedb.clients.web.util.ServletExportOutputStream
setContentLength(long) - Method in class net.sf.basedb.core.plugin.ExportOutputStream
Do nothing.
setContentLength(long) - Method in class net.sf.basedb.util.FileExportOutputStream
Ignored.
setContentstyle(String) - Method in class net.sf.basedb.clients.web.taglib.HideableSection
 
setContentstyle(String) - Method in class net.sf.basedb.clients.web.taglib.tab.TabControl
 
setContentStyle(String) - Method in class net.sf.basedb.clients.web.extensions.section.IncludeContentSectionFactory
 
setContentStyle(String) - Method in class net.sf.basedb.clients.web.extensions.section.SectionBean
 
setContext(JspContext) - Method in class net.sf.basedb.clients.web.taglib.extensions.Render
 
setContext(JspContext) - Method in class net.sf.basedb.clients.web.taglib.extensions.Scripts
 
setContext(JspContext) - Method in class net.sf.basedb.clients.web.taglib.extensions.Stylesheets
 
setContext(ItemContext) - Method in class net.sf.basedb.clients.web.taglib.HideableSection
 
setContext(ClientContext) - Method in class net.sf.basedb.core.signal.ExtensionSignalTransporter
 
setContextClassLoader() - Method in class net.sf.basedb.clients.web.extensions.XJspCompiler
Sets the context class loader if this JSP page is an extension JSP page and if the extensions JAR file has been modified since the last time the class loader was set.
setContextItem(Integer) - Method in class net.sf.basedb.core.data.JobData
 
setContexts(Map<ContextIndex, ContextData>) - Method in class net.sf.basedb.core.data.UserData
 
setContexts(Set<ContextData>) - Method in class net.sf.basedb.core.data.ClientData
 
setContextType(int) - Method in class net.sf.basedb.core.data.GuiContextData
 
setContextType(Integer) - Method in class net.sf.basedb.core.data.JobData
 
setContinue(String) - Method in interface net.sf.basedb.core.plugin.Response
This method will continue the configuration or execution of the job with a new command to the plugin.
setContinue(String) - Method in class net.sf.basedb.core.PluginResponse.ResponseImpl
 
setContinue(String) - Method in class net.sf.basedb.plugins.executor.ExternalProgramExecutor.ResponseWrapper
 
setContinue(String, Serializable) - Method in interface net.sf.basedb.core.plugin.Response
Can be used by an executing job to also store state information that will be restored when the job is starting up again.
setContinue(String, Serializable) - Method in class net.sf.basedb.core.PluginResponse.ResponseImpl
 
setContinue(String, Serializable) - Method in class net.sf.basedb.plugins.executor.ExternalProgramExecutor.ResponseWrapper
 
setCoordinateType(int) - Method in class net.sf.basedb.core.data.DataCubeExtraValueData
 
setCoordinateType(ExtraValue.CoordinateType) - Method in class net.sf.basedb.core.DataCubeExtraValue
Set the coordinate type.
setCopyright(String) - Method in class net.sf.basedb.core.data.PluginDefinitionData
 
setCopyright(String) - Method in class net.sf.basedb.core.PluginDefinition
Update copyright information about this plug-in.
setCopyright(String) - Method in class net.sf.basedb.util.extensions.AboutBean
 
setCopyToStdout(boolean) - Method in class net.sf.basedb.util.extensions.logging.ExtensionsLog
Enable or disable copies of log entries to standard output.
setCount(int) - Method in class net.sf.basedb.util.AnyToAnyLinkStatistics
 
setCounting(boolean) - Method in class net.sf.basedb.core.AbstractQuery
Set the counting status of the query.
setCountry(String) - Method in class net.sf.basedb.util.GeoLocation
 
setCreated(Date) - Method in class net.sf.basedb.core.data.JobData
 
setCreationEvent(BioMaterialEventData) - Method in class net.sf.basedb.core.data.MeasuredBioMaterialData
 
setCreationEvent(BioMaterialEventData) - Method in class net.sf.basedb.core.data.PhysicalBioAssayData
 
setCryptedPassword(String) - Method in class net.sf.basedb.core.data.PasswordData
Set the encrypted password.
setCubeNo(short) - Method in class net.sf.basedb.core.data.DataCubeData
 
setCubeNo(short) - Method in class net.sf.basedb.core.DataCube
 
setCubes(short) - Method in class net.sf.basedb.core.data.VirtualDbData
 
setCurNumberOfParameters(int) - Method in class net.sf.basedb.util.jep.ChannelFunction
 
setCurNumberOfParameters(int) - Method in class net.sf.basedb.util.jep.ExtraValueFunction
 
setCurNumberOfParameters(int) - Method in class net.sf.basedb.util.jep.FunctionSafeJep.UnknownFunction
 
setCurNumberOfParameters(int) - Method in class net.sf.basedb.util.jep.InReporterListFunction
 
setCurNumberOfParameters(int) - Method in class net.sf.basedb.util.jep.LeftFunction
 
setCurNumberOfParameters(int) - Method in class net.sf.basedb.util.jep.Log2Function
 
setCurNumberOfParameters(int) - Method in class net.sf.basedb.util.jep.MeanFunction
 
setCurNumberOfParameters(int) - Method in class net.sf.basedb.util.jep.NotInReporterListFunction
 
setCurNumberOfParameters(int) - Method in class net.sf.basedb.util.jep.PositionFunction
Can't be changed.
setCurNumberOfParameters(int) - Method in class net.sf.basedb.util.jep.RawChannelFunction
 
setCurNumberOfParameters(int) - Method in class net.sf.basedb.util.jep.RawFunction
 
setCurNumberOfParameters(int) - Method in class net.sf.basedb.util.jep.ReporterFunction
 
setCurNumberOfParameters(int) - Method in class net.sf.basedb.util.jep.ScoreFunction
 
setCurNumberOfParameters(int) - Method in class net.sf.basedb.util.jep.SimpleJepFunction
 
setCurNumberOfParameters(int) - Method in class net.sf.basedb.util.parser.ColFunction
 
setCurNumberOfParameters(int) - Method in class net.sf.basedb.util.parser.DataNoFunction
 
setCurNumberOfParameters(int) - Method in class net.sf.basedb.util.parser.DefaultItemFunction
 
setCurNumberOfParameters(int) - Method in class net.sf.basedb.util.parser.LineNoFunction
 
setCurrent(BasicItem) - Method in class net.sf.basedb.clients.web.taglib.Select
 
setCurrent(ItemSubtype) - Method in class net.sf.basedb.clients.web.taglib.SubtypeSelector
 
setCurrentAnyToAny(BasicItem, File, AnyToAny) - Method in class net.sf.basedb.clients.web.extensions.fileviewer.FileViewerContext
Sets the current any-to-any linked file and change the parent item.
setCurrentAnyToAny(File, AnyToAny) - Method in class net.sf.basedb.clients.web.extensions.fileviewer.FileViewerContext
Sets the current any-to-any linked file.
setCurrentBioWell(BioWell) - Method in class net.sf.basedb.util.overview.node.BioPlateNameGenerator
Set the current biowell object that should be used when generating names for bioplates that are reached by navigating via a biomaterial.
setCurrentClient(String) - Method in class net.sf.basedb.core.SessionControl
 
setCurrentDataFile(BasicItem, File, DataFileType, FileSetMember) - Method in class net.sf.basedb.clients.web.extensions.fileviewer.FileViewerContext
Sets the current data file and change the parent item.
setCurrentDataFile(File, DataFileType, FileSetMember) - Method in class net.sf.basedb.clients.web.extensions.fileviewer.FileViewerContext
Sets the current data file.
setCurrentEventParticipant(BioPlateEventParticipant) - Method in class net.sf.basedb.util.overview.node.BioPlateNameGenerator
Set the current bioplate event participant object that should be used when generating names for bioplates that are part of a bioplate event.
setCurrentExtension(Extension<?>) - Method in class net.sf.basedb.util.extensions.ClientContext
 
setCurrentExtensionPoint(ExtensionPoint<?>) - Method in class net.sf.basedb.util.extensions.ClientContext
 
setCurrentFile(File) - Method in class net.sf.basedb.clients.web.extensions.fileviewer.FileViewerContext
Set the current file.
setCurrentFilename(String) - Method in class net.sf.basedb.clients.web.fileupload.FileUploadProgress
Sets the name of the file that is currently uploading
setCurrentItem(Object) - Method in class net.sf.basedb.util.extensions.ClientContext
Set the currently active item.
setCurrentItem(Annotatable) - Method in class net.sf.basedb.core.AnnotationBatcher
Set the current item to work with from now on.
setCurrentMapper(ImageRemapper) - Static method in class net.sf.basedb.clients.web.extensions.skin.ImageRemapperUtil
Changes the current image remapper.
setCurrentSubcontext(SessionControl.MainContext, String) - Method in class net.sf.basedb.core.SessionControl
Change the currently active subcontext for the item.
setCurrentSubtype(ItemSubtype) - Method in class net.sf.basedb.util.parser.DefaultItemFunction
Set the current subtype to use when looking for default items.
setCurrentWell(BioWell) - Method in class net.sf.basedb.util.overview.node.BioWellNameGenerator
Set the well we are currently working with.
setData(String[]) - Method in class net.sf.basedb.util.importer.spotdata.SynchronizedSpotDataParser.SynchronizedData
 
setData(FlatFileParser.Data) - Method in class net.sf.basedb.util.parser.DataNoFunction
 
setData(FlatFileParser.Data) - Method in class net.sf.basedb.util.parser.LineNoFunction
 
setData(FlatFileParser.Data, Type) - Method in class net.sf.basedb.util.parser.ColFunction
 
setData(FlatFileParser.Data, Type) - Method in class net.sf.basedb.util.parser.JepMapper
 
setDataCube(DataCubeData) - Method in class net.sf.basedb.core.data.DataCubeColumnData
 
setDataCube(DataCubeData) - Method in class net.sf.basedb.core.data.DataCubeExtraValueData
 
setDataCube(DataCubeData) - Method in class net.sf.basedb.core.data.DataCubeFilterData
 
setDataCube(DataCubeData) - Method in class net.sf.basedb.core.data.DataCubeLayerData
 
setDataCube(DataCube) - Method in class net.sf.basedb.core.DataCubeColumn
Set the experiment.
setDataCube(DataCube) - Method in class net.sf.basedb.core.DataCubeExtraValue
Set the data cube.
setDataCube(DataCube) - Method in class net.sf.basedb.core.DataCubeFilter
Set the data cube.
setDataCube(DataCube) - Method in class net.sf.basedb.core.DataCubeLayer
Set the data cube.
setDataCubeColumn(DataCubeColumnData) - Method in class net.sf.basedb.core.data.BioAssayData
 
setDataCubeColumn(DataCubeColumn) - Method in class net.sf.basedb.core.BioAssay
 
setDataCubeExtraValue(DataCubeExtraValueData) - Method in class net.sf.basedb.core.data.ExtraValueData
 
setDataCubeExtraValue(DataCubeExtraValue) - Method in class net.sf.basedb.core.ExtraValue
 
setDataCubeFilter(DataCubeFilterData) - Method in class net.sf.basedb.core.data.BioAssaySetData
 
setDataCubeFilter(DataCubeFilter) - Method in class net.sf.basedb.core.BioAssaySet
 
setDataCubeLayer(DataCubeLayerData) - Method in class net.sf.basedb.core.data.BioAssaySetData
 
setDataCubeLayer(DataCubeLayer) - Method in class net.sf.basedb.core.BioAssaySet
 
setDataCubes(Set<DataCubeData>) - Method in class net.sf.basedb.core.data.VirtualDbData
 
setDataFile(DbControl, FileStoreEnabled, String, File) - Static method in class net.sf.basedb.core.FileStoreUtil
Set or remove a file to FileStoreEnabled item based on the file's DataFileType.
setDataFileType(DataFileTypeData) - Method in class net.sf.basedb.core.data.FileSetMemberData
 
setDataFileType(DataFileTypeData) - Method in class net.sf.basedb.core.data.FileTypeIndex
 
setDataFileType(DataFileTypeData) - Method in class net.sf.basedb.core.data.ItemSubtypeFileTypeData
 
setDataFileType(DataFileTypeData) - Method in class net.sf.basedb.core.data.PlatformFileTypeData
 
setDataFooterRegexp(Pattern) - Method in class net.sf.basedb.util.parser.FlatFileParser
Set a regular expression that can be matched against a data footer.
setDataHeaderRegexp(Pattern) - Method in class net.sf.basedb.util.parser.FlatFileParser
Set a regular expression that can be matched against the data header.
setDataSeparator(String) - Method in class net.sf.basedb.util.export.TableWriter
Change the data separator string.
setDataSplitterRegexp(Pattern) - Method in class net.sf.basedb.util.parser.FlatFileParser
Set a regular expression that is used to split a data line into columns.
setDatatype(String) - Method in class net.sf.basedb.clients.web.taglib.table.ColumnDef
 
setDataWriterFactory(DataWriterFactory<?>) - Method in class net.sf.basedb.util.export.spotdata.BfsExporter
Set the data writer factory to use for generating spot data files.
setDate(int, Date) - Method in class net.sf.basedb.core.hibernate.QueryWrapper
Deprecated.
setDate(String, Date) - Method in class net.sf.basedb.core.hibernate.QueryWrapper
Deprecated.
setDateFormat(String) - Method in class net.sf.basedb.util.excel.AutoFormatter
Set the data format template to use for date values (=dates with all time components at 0).
setDateFormat(SessionControl, String) - Static method in class net.sf.basedb.clients.web.formatter.FormatterSettings
Set the format string for a date formatter.
setDateFormat(Formatter<Date>) - Method in class net.sf.basedb.util.excel.XlsxToCsvUtil
Set a date formatter to use for formatting cells with date-like values.
setDateOrToday(Date) - Static method in class net.sf.basedb.core.DateUtil
Make a copy of the date.
setDateTimeFormat(SessionControl, String) - Static method in class net.sf.basedb.clients.web.formatter.FormatterSettings
Set the format string for a datetime formatter.
setDateValues(List<Date>) - Method in class net.sf.basedb.core.data.annotations.AnnotationLink
 
setDbcontrol(DbControl) - Method in class net.sf.basedb.clients.web.taglib.PropertyValue
 
setDbControl(DbControl) - Method in class net.sf.basedb.core.AbstractBatcher
Set the DbControl that is controlling this batcher.
setDbControl(DbControl) - Method in class net.sf.basedb.core.BasicItem
Set the DbControl object that should manage this item.
setDbControl(DbControl) - Method in class net.sf.basedb.core.DiskUsageStatistics
Set the DbControl which will be used to get statisics if it is not cached.
setDbControl(DbControl) - Method in class net.sf.basedb.util.export.spotdata.AbstractBioAssaySetExporter
Set's the DbControl that should be used to get data from the database.
setDbControl(DbControl) - Method in class net.sf.basedb.util.importer.spotdata.BaseFileImporter
Set's the DbControl that should be used to get data from the database.
setDbControl(DbControl) - Method in class net.sf.basedb.util.importer.spotdata.BfsImporter
Set's the DbControl that should be used to get data from the database.
setDbControl(DbControl) - Method in class net.sf.basedb.util.units.UnitCache
Set the DbControl to use for database access
setDc(DbControl) - Method in class net.sf.basedb.clients.web.taglib.SubtypeSelector
 
setDc(DbControl) - Method in class net.sf.basedb.clients.web.taglib.table.ExtensionCells
 
setDebugEnabled(boolean) - Method in class net.sf.basedb.util.extensions.logging.ExtensionsLog
Enable or disable debug-level logging.
setDefault(boolean) - Method in class net.sf.basedb.core.data.GroupData
 
setDefault(boolean) - Method in class net.sf.basedb.core.data.RoleData
 
setDefault(boolean) - Method in class net.sf.basedb.core.Group
If this group should be assigned to new users by default or not.
setDefault(boolean) - Method in class net.sf.basedb.core.Role
If this role should be assigned to new users by default or not.
setDefaultDateFormat(Formatter<Date>) - Method in class net.sf.basedb.util.parser.FlatFileParser
Set the default date format to use when creating mappers.
setDefaultErrorHandlerFactory(ErrorHandlerFactory<Action>) - Method in class net.sf.basedb.util.extensions.Registry
Set the default error handler factory.
setDefaultitem(BasicItem) - Method in class net.sf.basedb.clients.web.taglib.Select
 
setDefaultitems(List<? extends BasicItem>) - Method in class net.sf.basedb.clients.web.taglib.Select
 
setDefaultItems(ItemParameterValueData) - Method in class net.sf.basedb.core.data.ProjectData
 
setDefaultNumberFormat(NumberFormat) - Method in class net.sf.basedb.util.parser.FlatFileParser
Set the default number format to use when creating mappers.
setDefaultRawDataType(RawDataType) - Method in class net.sf.basedb.core.Project
Sets a raw data type to be used as default for a project.
setDefaultReadOnly(boolean) - Method in class net.sf.basedb.core.hibernate.SessionWrapper
 
setDefaultSettings(Set<ClientDefaultSettingData>) - Method in class net.sf.basedb.core.data.ClientData
 
setDefaultSettings(Set<UserDefaultSettingData>) - Method in class net.sf.basedb.core.data.UserData
 
setDefaultTimestampFormat(Formatter<Date>) - Method in class net.sf.basedb.util.parser.FlatFileParser
Set the default timestamp format to use when creating mappers.
setDefaultUnit(UnitData) - Method in class net.sf.basedb.core.data.AnnotationTypeData
 
setDefaultUnit(Unit) - Method in class net.sf.basedb.core.AnnotationType
Set the default unit to use for this annotation type.
setDefaultValue(String) - Method in class net.sf.basedb.core.AnnotationType
Set the recommended default value for new annotation of this annotation type.
setDefaultValue(String) - Method in class net.sf.basedb.core.data.AnnotationTypeData
 
setDefaultValue(String) - Method in class net.sf.basedb.plugins.executor.ParameterDefinition
Set the default value for this parameter.
setDefaultValue(String) - Method in class net.sf.basedb.util.formatter.LookupFormatter
Set a default value that is returned by the LookupFormatter.format(Object) method in case no lookup has been specified for a key.
setDelayRegistration(boolean) - Method in class net.sf.basedb.util.extensions.manager.processor.IgnoreFileProcessor
Set a flag to indicate if the actual registration of the found extensions and extension points should be delayed or not.
setDelayRegistration(boolean) - Method in class net.sf.basedb.util.extensions.manager.processor.RegisterExtensionsProcessor
Set a flag to indicate if the actual registration of the found extensions and extension points should be delayed or not.
setDelegateFirst(boolean) - Method in class net.sf.basedb.util.JarClassLoader
If the class loader should delegate to the parent class loader before trying to find the class by it's own.
setDenied(boolean) - Method in class net.sf.basedb.clients.web.taglib.Select
 
setDenied(int) - Method in class net.sf.basedb.core.data.keyring.PluginKeys
Set the denied permissions.
setDenied(int) - Method in class net.sf.basedb.core.data.PluginPermission
 
setDerivedBioAssays(Set<DerivedBioAssayData>) - Method in class net.sf.basedb.core.data.ExtractData
 
setDerivedBioAssays(Set<DerivedBioAssayData>) - Method in class net.sf.basedb.core.data.JobData
 
setDerivedBioAssays(Set<DerivedBioAssayData>) - Method in class net.sf.basedb.core.data.PhysicalBioAssayData
 
setDescription(String) - Method in class net.sf.basedb.clients.web.extensions.plot.OverviewPlotBean
 
setDescription(String) - Method in class net.sf.basedb.clients.web.extensions.startpage.FixedStartPageFactory
 
setDescription(String) - Method in class net.sf.basedb.clients.web.extensions.startpage.StartPageBean
 
setDescription(String) - Method in class net.sf.basedb.core.AnyToAny
 
setDescription(String) - Method in class net.sf.basedb.core.authentication.ExtraUserInformation
 
setDescription(String) - Method in class net.sf.basedb.core.BioAssay
 
setDescription(String) - Method in class net.sf.basedb.core.BioAssaySet
 
setDescription(String) - Method in class net.sf.basedb.core.BioPlateEvent
Set the description.
setDescription(String) - Method in class net.sf.basedb.core.BioPlateEventType
 
setDescription(String) - Method in class net.sf.basedb.core.BioPlateType
 
setDescription(String) - Method in class net.sf.basedb.core.CommonItem
 
setDescription(String) - Method in class net.sf.basedb.core.data.AnyToAnyData
 
setDescription(String) - Method in class net.sf.basedb.core.data.BioAssayData
 
setDescription(String) - Method in class net.sf.basedb.core.data.BioAssaySetData
 
setDescription(String) - Method in class net.sf.basedb.core.data.BioPlateEventTypeData
 
setDescription(String) - Method in class net.sf.basedb.core.data.BioPlateTypeData
 
setDescription(String) - Method in class net.sf.basedb.core.data.CommonData
 
setDescription(String) - Method in class net.sf.basedb.core.data.DataFileTypeData
 
setDescription(String) - Method in class net.sf.basedb.core.data.ExtraValueTypeData
 
setDescription(String) - Method in class net.sf.basedb.core.data.GroupData
 
setDescription(String) - Method in class net.sf.basedb.core.data.HelpData
 
setDescription(String) - Method in class net.sf.basedb.core.data.ItemListSyncFilterData
 
setDescription(String) - Method in class net.sf.basedb.core.data.ItemSubtypeData
 
setDescription(String) - Method in class net.sf.basedb.core.data.MessageData
 
setDescription(String) - Method in class net.sf.basedb.core.data.MimeTypeData
 
setDescription(String) - Method in interface net.sf.basedb.core.data.NameableData
Set the description for the item.
setDescription(String) - Method in class net.sf.basedb.core.data.NewsData
 
setDescription(String) - Method in class net.sf.basedb.core.data.ParameterValueData
 
setDescription(String) - Method in class net.sf.basedb.core.data.PlateEventTypeData
 
setDescription(String) - Method in class net.sf.basedb.core.data.PlateGeometryData
 
setDescription(String) - Method in class net.sf.basedb.core.data.PlatformData
 
setDescription(String) - Method in class net.sf.basedb.core.data.PlatformVariantData
 
setDescription(String) - Method in class net.sf.basedb.core.data.PluginDefinitionData
 
setDescription(String) - Method in class net.sf.basedb.core.data.PluginTypeData
 
setDescription(String) - Method in class net.sf.basedb.core.data.ProjectData
 
setDescription(String) - Method in class net.sf.basedb.core.data.QuantityData
 
setDescription(String) - Method in class net.sf.basedb.core.data.QuotaData
 
setDescription(String) - Method in class net.sf.basedb.core.data.QuotaTypeData
 
setDescription(String) - Method in class net.sf.basedb.core.data.ReporterClonePropertyData
 
setDescription(String) - Method in class net.sf.basedb.core.data.ReporterData
 
setDescription(String) - Method in class net.sf.basedb.core.data.ReporterTypeData
 
setDescription(String) - Method in class net.sf.basedb.core.data.RoleData
 
setDescription(String) - Method in class net.sf.basedb.core.data.RoleKeyData
 
setDescription(String) - Method in class net.sf.basedb.core.data.RootRawBioAssayData
 
setDescription(String) - Method in class net.sf.basedb.core.data.TransformationData
 
setDescription(String) - Method in class net.sf.basedb.core.data.UnitData
 
setDescription(String) - Method in class net.sf.basedb.core.data.UserData
 
setDescription(String) - Method in class net.sf.basedb.core.data.UserDeviceData
 
setDescription(String) - Method in class net.sf.basedb.core.DataFileType
 
setDescription(String) - Method in class net.sf.basedb.core.Directory
 
setDescription(String) - Method in class net.sf.basedb.core.ExtraValueType
 
setDescription(String) - Method in class net.sf.basedb.core.Group
 
setDescription(String) - Method in class net.sf.basedb.core.Help
 
setDescription(String) - Method in class net.sf.basedb.core.ItemSubtype
 
setDescription(String) - Method in class net.sf.basedb.core.Message
 
setDescription(String) - Method in class net.sf.basedb.core.MimeType
 
setDescription(String) - Method in interface net.sf.basedb.core.Nameable
Set the description for the item.
setDescription(String) - Method in class net.sf.basedb.core.News
 
setDescription(String) - Method in class net.sf.basedb.core.PlateEventType
 
setDescription(String) - Method in class net.sf.basedb.core.PlateGeometry
 
setDescription(String) - Method in class net.sf.basedb.core.Platform
 
setDescription(String) - Method in class net.sf.basedb.core.PlatformVariant
 
setDescription(String) - Method in class net.sf.basedb.core.PluginType
 
setDescription(String) - Method in class net.sf.basedb.core.Project
 
setDescription(String) - Method in class net.sf.basedb.core.Quantity
 
setDescription(String) - Method in class net.sf.basedb.core.Quota
 
setDescription(String) - Method in class net.sf.basedb.core.QuotaType
 
setDescription(String) - Method in class net.sf.basedb.core.ReporterCloneTemplate
Allow the description to be changed with RESTRICTED_WRITE permission.
setDescription(String) - Method in class net.sf.basedb.core.ReporterType
 
setDescription(String) - Method in class net.sf.basedb.core.Role
 
setDescription(String) - Method in class net.sf.basedb.core.RoleKey
 
setDescription(String) - Method in class net.sf.basedb.core.RootRawBioAssay
 
setDescription(String) - Method in class net.sf.basedb.core.SyncFilter
 
setDescription(String) - Method in class net.sf.basedb.core.Transformation
 
setDescription(String) - Method in class net.sf.basedb.core.Unit
 
setDescription(String) - Method in class net.sf.basedb.core.User
 
setDescription(String) - Method in class net.sf.basedb.core.UserDevice
 
setDescription(String) - Method in class net.sf.basedb.plugins.executor.ParameterDefinition
Set a description/help text for this parmeter.
setDescription(String) - Method in class net.sf.basedb.util.extensions.AboutBean
 
setDescription(String) - Method in class net.sf.basedb.util.extensions.ExtensionPointBean
 
setDescription(NameableData, String) - Static method in class net.sf.basedb.core.NameableUtil
Set the description of a NameableData object.
setDescriptor(Object) - Method in class net.sf.basedb.util.overview.Failure
Set a descriptor on this failure.
setDestinationCount(int) - Method in class net.sf.basedb.core.data.PlateMappingData
 
setDestinationCount(int) - Method in class net.sf.basedb.core.PlateMapping
Set the number of produced destination plates.
setDestinationGeometry(PlateGeometryData) - Method in class net.sf.basedb.core.data.PlateMappingData
 
setDestinationGeometry(PlateGeometry) - Method in class net.sf.basedb.core.PlateMapping
Set the destination geometry.
setDestinationIndex(int) - Method in class net.sf.basedb.core.data.PlateData
 
setDestroyed(boolean) - Method in class net.sf.basedb.core.ArraySlide
Set if the slide should be flagged as destroyed.
setDestroyed(boolean) - Method in class net.sf.basedb.core.BioPlate
Set the destroyed flag.
setDestroyed(boolean) - Method in class net.sf.basedb.core.data.ArraySlideData
 
setDestroyed(boolean) - Method in class net.sf.basedb.core.data.BioPlateData
 
setDestroyed(boolean) - Method in class net.sf.basedb.core.data.PlateData
 
setDestroyed(boolean) - Method in class net.sf.basedb.core.Plate
Set the destroyed flag.
setDetails(Map<MappingCoordinate, MappingCoordinate>) - Method in class net.sf.basedb.core.data.PlateMappingData
 
setDetails(Set<ChangeHistoryDetailData>) - Method in class net.sf.basedb.core.data.ChangeHistoryData
 
setDevice(UserDeviceData) - Method in class net.sf.basedb.core.data.SessionData
 
setDevices(Set<UserDeviceData>) - Method in class net.sf.basedb.core.data.ClientData
 
setDevices(Set<UserDeviceData>) - Method in class net.sf.basedb.core.data.UserData
 
setDeviceToken(String) - Method in class net.sf.basedb.core.authentication.LoginRequest
Set the deviceToken to use.
setDirection(String) - Method in class net.sf.basedb.clients.web.taglib.table.Table
 
setDirection(ItemContext.SortDirection) - Method in class net.sf.basedb.clients.web.taglib.table.Table
 
setDirectory(DirectoryData) - Method in class net.sf.basedb.core.data.ExperimentData
 
setDirectory(DirectoryData) - Method in class net.sf.basedb.core.data.FileData
 
setDirectory(Directory) - Method in class net.sf.basedb.core.Experiment
Set the directory where it is recommended that plugins store files that are related to this experiment.
setDirectory(Directory) - Method in class net.sf.basedb.core.File
Set the directory of this File item.
setDirty(int, int) - Method in class net.sf.basedb.core.log.EntityDetails
Set the dirtyness for the property with the given index.
setDisabled(boolean) - Method in class net.sf.basedb.clients.web.taglib.Button
 
setDisabled(boolean) - Method in class net.sf.basedb.clients.web.taglib.Select
 
setDisabled(boolean) - Method in class net.sf.basedb.clients.web.taglib.table.Button
 
setDisabled(boolean) - Method in class net.sf.basedb.core.data.ItemListSyncFilterData
 
setDisabled(boolean) - Method in class net.sf.basedb.core.data.PluginConfigurationData
 
setDisabled(boolean) - Method in class net.sf.basedb.core.data.PluginDefinitionData
 
setDisabled(boolean) - Method in class net.sf.basedb.core.data.UserData
 
setDisabled(boolean) - Method in class net.sf.basedb.core.PluginConfiguration
Disabled or enable this plugin configuration.
setDisabled(boolean) - Method in class net.sf.basedb.core.PluginDefinition
Disabled or enable this plugin.
setDisabled(boolean) - Method in class net.sf.basedb.core.SyncFilter
Disabled/enable this filter.
setDisabled(boolean) - Method in class net.sf.basedb.core.User
Disables or enables the account.
setDisabled(boolean) - Method in class net.sf.basedb.util.extensions.xml.PluginInfo
 
setDisabled(boolean) - Method in class net.sf.basedb.util.overview.validator.BasicItemNodeValidatorFactory
 
setDisabled(boolean) - Method in interface net.sf.basedb.util.overview.validator.NodeValidatorFactory
Disable/enabled node validation programmatically.
setDisabled(boolean) - Method in class net.sf.basedb.util.StaticCache
Disable or enable the cache.
setDisabled(String) - Method in class net.sf.basedb.util.extensions.debug.BeanActionFactory
Sets the disabled/enabled status of this factory.
setDisabled(String) - Method in class net.sf.basedb.util.extensions.debug.ProxyActionFactory
Sets the disabled/enabled status of this factory.
setDisabledClazz(String) - Method in class net.sf.basedb.clients.web.extensions.menu.PermissionMenuItemFactory
Set the class to use when the menu is disabled.
setDisabledClazz(String) - Method in class net.sf.basedb.clients.web.extensions.toolbar.PermissionButtonFactory
Set the class to use when the button is disabled.
setDisabledIcon(String) - Method in class net.sf.basedb.clients.web.extensions.menu.PermissionMenuItemFactory
Set the icon to use when the menu is disabled.
setDisabledIcon(String) - Method in class net.sf.basedb.clients.web.extensions.toolbar.PermissionButtonFactory
Set the icon to use when the button is disabled.
setDisabledStyle(String) - Method in class net.sf.basedb.clients.web.extensions.menu.PermissionMenuItemFactory
Set the style to use when the menu is disabled.
setDisabledStyle(String) - Method in class net.sf.basedb.clients.web.extensions.toolbar.PermissionButtonFactory
Set the style to use when the button is disabled.
setDisabledTitle(String) - Method in class net.sf.basedb.clients.web.extensions.menu.PermissionMenuItemFactory
Set the title of the menu item when it is disabled.
setDisabledTitle(String) - Method in class net.sf.basedb.clients.web.extensions.toolbar.PermissionButtonFactory
Set the title of the button when it is disabled.
setDisabledTooltip(String) - Method in class net.sf.basedb.clients.web.extensions.menu.PermissionMenuItemFactory
Set the tooltip of the menu item when it is disabled.
setDisabledTooltip(String) - Method in class net.sf.basedb.clients.web.extensions.toolbar.PermissionButtonFactory
Set the tooltip of the button when it is disabled.
setDisableInheritance(boolean) - Method in class net.sf.basedb.core.AnnotationType
If this flag is set, annotations of this type can't be inherited to child items.
setDisableInheritance(boolean) - Method in class net.sf.basedb.core.data.AnnotationTypeData
 
setDisableinproject(boolean) - Method in class net.sf.basedb.clients.web.taglib.table.PresetSelector
 
setDisableLogOfValues(boolean) - Method in class net.sf.basedb.core.AnnotationType
If this flag is set, the change history logging will not include actual annotation values.
setDisableLogOfValues(boolean) - Method in class net.sf.basedb.core.data.AnnotationTypeData
 
setDisableManualMembers(boolean) - Method in class net.sf.basedb.core.data.ItemListData
 
setDisableManualMembers(boolean) - Method in class net.sf.basedb.core.ItemList
Disable or enable manual modification of members.
setDisableothers(boolean) - Method in class net.sf.basedb.clients.web.taglib.table.PresetSelector
 
setDisableOverflowCheck(boolean) - Method in class net.sf.basedb.clients.web.extensions.list.AbstractListColumnBean
 
setDisableOverflowCheck(boolean) - Method in class net.sf.basedb.clients.web.extensions.list.PropertyPathActionFactory
 
setDisableOverflowCheck(boolean) - Method in class net.sf.basedb.clients.web.taglib.table.Cell
 
setDisableownedby(boolean) - Method in class net.sf.basedb.clients.web.taglib.table.PresetSelector
 
setDisableRawJoinOnMergedData(boolean) - Method in class net.sf.basedb.core.DynamicSpotQuery
Disable automatic and manual joining of raw data if the bioassay set contains merged data.
setDisableremoved(boolean) - Method in class net.sf.basedb.clients.web.taglib.table.PresetSelector
 
setDisablesharedto(boolean) - Method in class net.sf.basedb.clients.web.taglib.table.PresetSelector
 
setDisableSyncFilters(boolean) - Method in class net.sf.basedb.core.data.ItemListData
 
setDisableSyncFilters(boolean) - Method in class net.sf.basedb.core.ItemList
Disable or enable synchronization of members with sync filters.
setDiskUsage(DiskUsageData) - Method in class net.sf.basedb.core.data.ExperimentData
 
setDiskUsage(DiskUsageData) - Method in class net.sf.basedb.core.data.FileData
 
setDiskUsage(DiskUsageData) - Method in class net.sf.basedb.core.data.RawBioAssayData
 
setDisplayAsList(boolean) - Method in class net.sf.basedb.core.AnnotationType
Set if the enumeration values should be displayed as a selection list or as radio buttons/checkboxes by the client application.
setDisplayName(String) - Method in class net.sf.basedb.clients.web.extensions.login.LoginFormBean
 
setDisplaySymbol(String) - Method in class net.sf.basedb.core.data.UnitData
 
setDisplaySymbol(String) - Method in class net.sf.basedb.core.Unit
Set the display symbol for this unit.
setDistinct(boolean) - Method in class net.sf.basedb.core.AbstractQuery
 
setDistinct(boolean) - Method in interface net.sf.basedb.core.query.Query
Specify if the query should only return distinct rows.
setDoctype(String) - Method in class net.sf.basedb.clients.web.taglib.Page
 
setDone(String) - Method in interface net.sf.basedb.core.plugin.Response
This will end the job execution and report it as a success.
setDone(String) - Method in class net.sf.basedb.core.PluginResponse.ResponseImpl
 
setDone(String) - Method in class net.sf.basedb.plugins.executor.ExternalProgramExecutor.ResponseWrapper
 
setDone(String, Job.ExecutionTime) - Method in interface net.sf.basedb.core.plugin.Response
This will end the configuration of a job and set the estimated execution time for it.
setDone(String, Job.ExecutionTime) - Method in class net.sf.basedb.core.PluginResponse.ResponseImpl
 
setDone(String, Job.ExecutionTime) - Method in class net.sf.basedb.plugins.executor.ExternalProgramExecutor.ResponseWrapper
 
setDouble(int, double) - Method in class net.sf.basedb.core.hibernate.QueryWrapper
Deprecated.
setDouble(String, double) - Method in class net.sf.basedb.core.hibernate.QueryWrapper
Deprecated.
setDoubleValues(List<Double>) - Method in class net.sf.basedb.core.data.annotations.AnnotationLink
 
setDownloadImmediately(String, Job.ExecutionTime, boolean) - Method in interface net.sf.basedb.core.plugin.Response
This will end the configuration of a export job, and start to execute it for immediate download.
setDownloadImmediately(String, Job.ExecutionTime, boolean) - Method in class net.sf.basedb.core.PluginResponse.ResponseImpl
 
setDownloadImmediately(String, Job.ExecutionTime, boolean) - Method in class net.sf.basedb.plugins.executor.ExternalProgramExecutor.ResponseWrapper
 
setDragcolumns(Boolean) - Method in class net.sf.basedb.clients.web.taglib.table.Table
 
setDropConstraintsBeforeImport(boolean) - Method in class net.sf.basedb.core.Migration
Should we drop the unique constraints and indexes before importing data?
setDropPrimaryKeyBeforeImport(boolean) - Method in class net.sf.basedb.core.Migration
Should we drop the primary key before importing data?
setDryRun(boolean) - Method in class net.sf.basedb.core.data.JobData
 
setDryRun(boolean) - Method in interface net.sf.basedb.core.plugin.Response
A plug-in may call this method in it's configuration phase or after it has been executed to indicate that the job should be or was executed as a dry-run job.
setDryRun(boolean) - Method in class net.sf.basedb.core.PluginResponse.ResponseImpl
 
setDryRun(boolean) - Method in class net.sf.basedb.plugins.executor.ExternalProgramExecutor.ResponseWrapper
 
setDynamic(Iterator<DynamicActionAttribute>) - Method in class net.sf.basedb.clients.web.taglib.menu.Menuitem
 
setDynamic(Iterator<DynamicActionAttribute>) - Method in class net.sf.basedb.clients.web.taglib.menu.Menuseparator
 
setDynamic(Iterator<DynamicActionAttribute>) - Method in class net.sf.basedb.clients.web.taglib.menu.Submenu
 
setDynamicActionAttributesSource(DynamicActionAttributes) - Method in class net.sf.basedb.clients.web.extensions.DynamicActionAttributeSupport
Set the source of dynamic action attributes.
setDynamicAttribute(String, Object) - Method in class net.sf.basedb.clients.web.extensions.DynamicActionAttributeSupport
Adds a dynamic attribute to the action.
setDynamicAttribute(String, String, Object) - Method in class net.sf.basedb.clients.web.taglib.StylableTag
 
setDynamicAttribute(String, String, Object) - Method in class net.sf.basedb.clients.web.taglib.tab.Tab
 
setEmail(String) - Method in class net.sf.basedb.core.authentication.ExtraUserInformation
The email address to the user.
setEmail(String) - Method in class net.sf.basedb.core.data.PluginDefinitionData
 
setEmail(String) - Method in class net.sf.basedb.core.data.UserData
 
setEmail(String) - Method in class net.sf.basedb.core.PluginDefinition
Set the email address that can be used to contact the developer of the plug-in.
setEmail(String) - Method in class net.sf.basedb.core.User
Set the email address to the user, or null if unknown.
setEmail(String) - Method in class net.sf.basedb.util.extensions.AboutBean
 
setEnabled(boolean) - Method in class net.sf.basedb.clients.web.extensions.menu.FixedMenuItemFactory
 
setEnabled(boolean) - Method in class net.sf.basedb.clients.web.extensions.menu.MenuItemBean
 
setEnabled(boolean) - Method in class net.sf.basedb.clients.web.extensions.toolbar.ButtonBean
 
setEnabled(boolean) - Method in class net.sf.basedb.clients.web.extensions.toolbar.FixedButtonFactory
 
setEnabled(boolean) - Method in class net.sf.basedb.clients.web.taglib.Icon
 
setEnabled(boolean) - Method in class net.sf.basedb.clients.web.taglib.menu.Menuitem
 
setEnabled(boolean) - Method in class net.sf.basedb.clients.web.taglib.menu.Submenu
 
setEnabled(boolean) - Method in class net.sf.basedb.clients.web.taglib.path.PathElement
 
setEnabled(String) - Method in class net.sf.basedb.clients.web.extensions.menu.FixedMenuItemFactory
 
setEnabled(String) - Method in class net.sf.basedb.clients.web.extensions.toolbar.FixedButtonFactory
 
setEnabledClazz(String) - Method in class net.sf.basedb.clients.web.extensions.menu.PermissionMenuItemFactory
Set the class to use when the menu is enabled.
setEnabledClazz(String) - Method in class net.sf.basedb.clients.web.extensions.toolbar.PermissionButtonFactory
Set the class to use when the button is enabled.
setEnabledIcon(String) - Method in class net.sf.basedb.clients.web.extensions.menu.PermissionMenuItemFactory
Set the icon to use when the menu is enabled.
setEnabledIcon(String) - Method in class net.sf.basedb.clients.web.extensions.toolbar.PermissionButtonFactory
Set the icon to use when the button is enabled.
setEnableDownloadLink(boolean) - Method in class net.sf.basedb.clients.web.taglib.PropertyValue
 
setEnabledPermission(String) - Method in class net.sf.basedb.clients.web.extensions.menu.PermissionMenuItemFactory
Set the minimum permission that is required to make the menu item enabled.
setEnabledPermission(String) - Method in class net.sf.basedb.clients.web.extensions.toolbar.PermissionButtonFactory
Set the minimum permission that is required to make the button enabled.
setEnabledStyle(String) - Method in class net.sf.basedb.clients.web.extensions.menu.PermissionMenuItemFactory
Set the style to use when the menu is enabled.
setEnabledStyle(String) - Method in class net.sf.basedb.clients.web.extensions.toolbar.PermissionButtonFactory
Set the style to use when the button is enabled.
setEnabledTitle(String) - Method in class net.sf.basedb.clients.web.extensions.menu.PermissionMenuItemFactory
Set the title of the menu item when it is enabled.
setEnabledTitle(String) - Method in class net.sf.basedb.clients.web.extensions.toolbar.PermissionButtonFactory
Set the title of the button when it is enabled.
setEnabledTooltip(String) - Method in class net.sf.basedb.clients.web.extensions.menu.PermissionMenuItemFactory
Set the tooltip of the menu item when it is enabled.
setEnabledTooltip(String) - Method in class net.sf.basedb.clients.web.extensions.toolbar.PermissionButtonFactory
Set the tooltip of the button when it is enabled.
setEnableEditLink(boolean) - Method in class net.sf.basedb.clients.web.taglib.PropertyValue
 
setEnablePropertyLink(boolean) - Method in class net.sf.basedb.clients.web.taglib.PropertyValue
 
setEncoder(EncoderDecoder) - Method in class net.sf.basedb.util.excel.XlsxToCsvUtil
Set the encoder to use for converting text values so that they do not conflict with column or row separators.
setEncoder(EncoderDecoder) - Method in class net.sf.basedb.util.export.TableWriter
Change the encoder.
setEndDate(Date) - Method in class net.sf.basedb.core.data.NewsData
 
setEndDate(Date) - Method in class net.sf.basedb.core.News
Set the end date and time for this item to be published.
setEnded() - Method in class net.sf.basedb.util.extensions.manager.ProcessResults
Set the end time of the scan.
setEnded(Date) - Method in class net.sf.basedb.core.data.JobData
 
setEnded(PluginResponse, boolean) - Method in class net.sf.basedb.core.Job.ProgressReporterImpl
 
setEntity(int, Object) - Method in class net.sf.basedb.core.hibernate.EntityQueryWrapper
Deprecated.
setEntity(int, Object) - Method in class net.sf.basedb.core.hibernate.QueryWrapper
Deprecated.
setEntity(String, Object) - Method in class net.sf.basedb.core.hibernate.EntityQueryWrapper
Deprecated.
setEntity(String, Object) - Method in class net.sf.basedb.core.hibernate.QueryWrapper
Deprecated.
setEntityParameter(String, BasicItem) - Method in class net.sf.basedb.core.AbstractHqlQuery
 
setEntityParameter(String, BasicItem) - Method in interface net.sf.basedb.core.query.HqlQuery
Set the value of an entity parameter.
setEntryDate(Date) - Method in class net.sf.basedb.core.AnnotationType
 
setEntryDate(Date) - Method in class net.sf.basedb.core.AnnotationTypeCategory
 
setEntryDate(Date) - Method in class net.sf.basedb.core.ArrayBatch
 
setEntryDate(Date) - Method in class net.sf.basedb.core.ArrayDesign
 
setEntryDate(Date) - Method in class net.sf.basedb.core.ArraySlide
 
setEntryDate(Date) - Method in class net.sf.basedb.core.BioMaterialEvent
 
setEntryDate(Date) - Method in class net.sf.basedb.core.BioPlate
 
setEntryDate(Date) - Method in class net.sf.basedb.core.BioPlateEvent
 
setEntryDate(Date) - Method in class net.sf.basedb.core.BioSource
 
setEntryDate(Date) - Method in class net.sf.basedb.core.Client
 
setEntryDate(Date) - Method in class net.sf.basedb.core.data.AnnotationTypeCategoryData
 
setEntryDate(Date) - Method in class net.sf.basedb.core.data.AnnotationTypeData
 
setEntryDate(Date) - Method in class net.sf.basedb.core.data.ArrayBatchData
 
setEntryDate(Date) - Method in class net.sf.basedb.core.data.ArrayDesignData
 
setEntryDate(Date) - Method in class net.sf.basedb.core.data.ArraySlideData
 
setEntryDate(Date) - Method in class net.sf.basedb.core.data.BioMaterialEventData
 
setEntryDate(Date) - Method in class net.sf.basedb.core.data.BioPlateData
 
setEntryDate(Date) - Method in class net.sf.basedb.core.data.BioPlateEventData
 
setEntryDate(Date) - Method in class net.sf.basedb.core.data.BioSourceData
 
setEntryDate(Date) - Method in class net.sf.basedb.core.data.ClientData
 
setEntryDate(Date) - Method in class net.sf.basedb.core.data.DerivedBioAssayData
 
setEntryDate(Date) - Method in class net.sf.basedb.core.data.ExperimentData
 
setEntryDate(Date) - Method in class net.sf.basedb.core.data.ExtraValueTypeData
 
setEntryDate(Date) - Method in class net.sf.basedb.core.data.FormulaData
 
setEntryDate(Date) - Method in class net.sf.basedb.core.data.GroupData
 
setEntryDate(Date) - Method in class net.sf.basedb.core.data.HardwareData
 
setEntryDate(Date) - Method in class net.sf.basedb.core.data.ItemSubtypeData
 
setEntryDate(Date) - Method in class net.sf.basedb.core.data.KitData
 
setEntryDate(Date) - Method in class net.sf.basedb.core.data.MimeTypeData
 
setEntryDate(Date) - Method in class net.sf.basedb.core.data.NewsData
 
setEntryDate(Date) - Method in class net.sf.basedb.core.data.PlateData
 
setEntryDate(Date) - Method in class net.sf.basedb.core.data.PlateEventData
 
setEntryDate(Date) - Method in class net.sf.basedb.core.data.PlateGeometryData
 
setEntryDate(Date) - Method in class net.sf.basedb.core.data.PlateMappingData
 
setEntryDate(Date) - Method in class net.sf.basedb.core.data.PlateTypeData
 
setEntryDate(Date) - Method in class net.sf.basedb.core.data.PluginConfigurationData
 
setEntryDate(Date) - Method in class net.sf.basedb.core.data.PluginDefinitionData
 
setEntryDate(Date) - Method in class net.sf.basedb.core.data.PluginTypeData
 
setEntryDate(Date) - Method in class net.sf.basedb.core.data.ProjectData
 
setEntryDate(Date) - Method in class net.sf.basedb.core.data.ProtocolData
 
setEntryDate(Date) - Method in class net.sf.basedb.core.data.QuotaTypeData
 
setEntryDate(Date) - Method in class net.sf.basedb.core.data.RawBioAssayData
 
setEntryDate(Date) - Method in class net.sf.basedb.core.data.ReporterCloneTemplateData
 
setEntryDate(Date) - Method in class net.sf.basedb.core.data.ReporterData
 
setEntryDate(Date) - Method in class net.sf.basedb.core.data.ReporterListData
 
setEntryDate(Date) - Method in class net.sf.basedb.core.data.ReporterTypeData
 
setEntryDate(Date) - Method in class net.sf.basedb.core.data.RoleData
 
setEntryDate(Date) - Method in class net.sf.basedb.core.data.SoftwareData
 
setEntryDate(Date) - Method in class net.sf.basedb.core.data.TagData
 
setEntryDate(Date) - Method in class net.sf.basedb.core.data.UserData
 
setEntryDate(Date) - Method in class net.sf.basedb.core.data.UserDeviceData
 
setEntryDate(Date) - Method in class net.sf.basedb.core.DerivedBioAssay
 
setEntryDate(Date) - Method in class net.sf.basedb.core.Experiment
 
setEntryDate(Date) - Method in class net.sf.basedb.core.ExtraValueType
 
setEntryDate(Date) - Method in class net.sf.basedb.core.Formula
 
setEntryDate(Date) - Method in class net.sf.basedb.core.Group
 
setEntryDate(Date) - Method in class net.sf.basedb.core.Hardware
 
setEntryDate(Date) - Method in class net.sf.basedb.core.ItemSubtype
 
setEntryDate(Date) - Method in class net.sf.basedb.core.Kit
 
setEntryDate(Date) - Method in class net.sf.basedb.core.MeasuredBioMaterial
 
setEntryDate(Date) - Method in class net.sf.basedb.core.MimeType
 
setEntryDate(Date) - Method in class net.sf.basedb.core.News
 
setEntryDate(Date) - Method in class net.sf.basedb.core.PhysicalBioAssay
 
setEntryDate(Date) - Method in class net.sf.basedb.core.Plate
 
setEntryDate(Date) - Method in class net.sf.basedb.core.PlateEvent
 
setEntryDate(Date) - Method in class net.sf.basedb.core.PlateGeometry
 
setEntryDate(Date) - Method in class net.sf.basedb.core.PlateMapping
 
setEntryDate(Date) - Method in class net.sf.basedb.core.PlateType
 
setEntryDate(Date) - Method in class net.sf.basedb.core.PluginConfiguration
 
setEntryDate(Date) - Method in class net.sf.basedb.core.PluginDefinition
 
setEntryDate(Date) - Method in class net.sf.basedb.core.PluginType
 
setEntryDate(Date) - Method in class net.sf.basedb.core.Project
 
setEntryDate(Date) - Method in class net.sf.basedb.core.Protocol
 
setEntryDate(Date) - Method in class net.sf.basedb.core.QuotaType
 
setEntryDate(Date) - Method in class net.sf.basedb.core.RawBioAssay
 
setEntryDate(Date) - Method in interface net.sf.basedb.core.Registered
Set the date the entry was registered in the database.
setEntryDate(Date) - Method in class net.sf.basedb.core.ReporterCloneTemplate
 
setEntryDate(Date) - Method in class net.sf.basedb.core.ReporterList
 
setEntryDate(Date) - Method in class net.sf.basedb.core.ReporterType
 
setEntryDate(Date) - Method in class net.sf.basedb.core.Role
 
setEntryDate(Date) - Method in class net.sf.basedb.core.Software
 
setEntryDate(Date) - Method in class net.sf.basedb.core.Tag
 
setEntryDate(Date) - Method in class net.sf.basedb.core.User
 
setEntryDate(Date) - Method in class net.sf.basedb.core.UserDevice
 
setEnumeration(boolean) - Method in class net.sf.basedb.core.AnnotationType
Set if this annotation type should provide a list of predefined allowed values.
setEnumeration(boolean) - Method in class net.sf.basedb.core.data.AnnotationTypeData
 
setEnumeration(Enumeration<String, String>) - Method in class net.sf.basedb.clients.web.extensions.list.AbstractListColumnBean
 
setEnumeration(Enumeration<String, String>) - Method in class net.sf.basedb.clients.web.taglib.table.ColumnDef
 
setEnumerationValues(ParameterValueData<?>) - Method in class net.sf.basedb.core.data.AnnotationTypeData
 
setError(boolean) - Method in class net.sf.basedb.util.extensions.manager.ExtensionsFile.WriteableExtensionsFile
Sets the error status.
setError(A, Throwable) - Method in class net.sf.basedb.util.extensions.ExtensionContext
 
setError(A, Throwable) - Method in class net.sf.basedb.util.extensions.ExtensionPointContext
 
setError(A, Throwable) - Method in class net.sf.basedb.util.extensions.InvokationContext
Register an error for the current extension or extension point.
setError(A, Throwable) - Method in class net.sf.basedb.util.extensions.Registry.RegisteredExtension
 
setError(A, Throwable) - Method in class net.sf.basedb.util.extensions.Registry.RegisteredExtensionPoint
 
setError(String, Throwable) - Method in class net.sf.basedb.core.PluginResponse
Set a singe error message.
setError(String, Throwable) - Method in class net.sf.basedb.util.extensions.ActionIterator
Register an error with a message for the current action.
setError(String, List<? extends Throwable>) - Method in interface net.sf.basedb.core.plugin.Response
This will end the job execution or configuration and report it as a failure.
setError(String, List<? extends Throwable>) - Method in class net.sf.basedb.core.PluginResponse.ResponseImpl
 
setError(String, List<? extends Throwable>) - Method in class net.sf.basedb.plugins.executor.ExternalProgramExecutor.ResponseWrapper
 
setError(Throwable) - Method in class net.sf.basedb.core.SimpleProgressReporter
Set an error that happened while processing some action that was reported via this progress reporter.
setError(Throwable) - Method in class net.sf.basedb.util.extensions.ActionIterator
Register an error for the current action.
setErrorclazz(String) - Method in class net.sf.basedb.clients.web.taglib.table.Cell
 
setErrorHandlerFactory(ErrorHandlerFactory<? super A>) - Method in class net.sf.basedb.util.extensions.ExtensionPointBean
 
setErrorMessage(String) - Method in class net.sf.basedb.core.data.FileSetMemberData
 
setErrors(int) - Method in class net.sf.basedb.util.overview.Node
Set the number of errors that was found while validating this node.
setEstimatedExecutionTime(int) - Method in class net.sf.basedb.core.data.JobData
 
setEvaluateFormulas(boolean) - Method in class net.sf.basedb.util.excel.XlsxToCsvUtil
 
setEvent(BioMaterialEventData) - Method in class net.sf.basedb.core.data.BioMaterialEventSourceData
 
setEvent(BioPlateEventData) - Method in class net.sf.basedb.core.data.BioPlateEventParticipantData
 
setEventDate(Date) - Method in class net.sf.basedb.core.BioMaterialEvent
Set the date this event was done in the lab.
setEventDate(Date) - Method in class net.sf.basedb.core.BioPlate
Set the date this plate was created.
setEventDate(Date) - Method in class net.sf.basedb.core.BioPlateEvent
Set the date this event was done in the lab.
setEventDate(Date) - Method in class net.sf.basedb.core.data.BioMaterialEventData
 
setEventDate(Date) - Method in class net.sf.basedb.core.data.BioPlateData
 
setEventDate(Date) - Method in class net.sf.basedb.core.data.BioPlateEventData
 
setEventDate(Date) - Method in class net.sf.basedb.core.data.PlateEventData
 
setEventDate(Date) - Method in class net.sf.basedb.core.PlateEvent
Set the date this event was done in the lab.
setEventParticipants(Set<BioPlateEventParticipantData>) - Method in class net.sf.basedb.core.data.BioPlateData
 
setEvents(Map<PlateEventTypeData, PlateEventData>) - Method in class net.sf.basedb.core.data.PlateData
 
setEvents(Set<BioMaterialEventData>) - Method in class net.sf.basedb.core.data.MeasuredBioMaterialData
 
setEvents(Set<BioPlateEventData>) - Method in class net.sf.basedb.core.data.BioPlateEventTypeData
 
setEventType(int) - Method in class net.sf.basedb.core.data.BioMaterialEventData
 
setEventType(BioPlateEventType) - Method in class net.sf.basedb.core.BioPlateEvent
 
setEventType(BioPlateEventTypeData) - Method in class net.sf.basedb.core.data.BioPlateEventData
 
setEventTypes(Set<PlateEventTypeData>) - Method in class net.sf.basedb.core.data.PlateTypeData
 
setExcelSheet(String) - Method in class net.sf.basedb.util.parser.FlatFileParser
Set the name of Excel worksheet to parse if the given file is an Excel file, otherwise this is ignored.
setException(Throwable) - Method in class net.sf.basedb.clients.web.fileupload.FileUpload
Set exception information on the associated FileUploadProgress object.
setException(Throwable) - Method in class net.sf.basedb.clients.web.fileupload.FileUploadProgress
Set the exception that caused the upload to fail.
setException(Throwable) - Method in class net.sf.basedb.core.ItemContext
Set the exception that is the cause for the error in ItemContext.configureQuery(DbControl, EntityQuery, boolean).
setExcludeDefaultValues(boolean) - Method in class net.sf.basedb.core.AnnotationRestriction.Options
 
setExecuteCommand(String) - Method in class net.sf.basedb.core.data.JobData
 
setExecuteImmediately(String, Job.ExecutionTime, boolean) - Method in interface net.sf.basedb.core.plugin.Response
This will end the configuration of a job, and start to execute it immediately if the plugin is permitted to do so.
setExecuteImmediately(String, Job.ExecutionTime, boolean) - Method in class net.sf.basedb.core.PluginResponse.ResponseImpl
 
setExecuteImmediately(String, Job.ExecutionTime, boolean) - Method in class net.sf.basedb.plugins.executor.ExternalProgramExecutor.ResponseWrapper
 
setExperiment(ExperimentData) - Method in class net.sf.basedb.core.data.BioAssaySetData
 
setExperiment(ExperimentData) - Method in class net.sf.basedb.core.data.JobData
 
setExperiment(ExperimentData) - Method in class net.sf.basedb.core.data.ReporterListData
 
setExperiment(ExperimentData) - Method in class net.sf.basedb.core.data.RootRawBioAssayData
 
setExperiment(ExperimentData) - Method in class net.sf.basedb.core.data.TransformationData
 
setExperiment(ExperimentData) - Method in class net.sf.basedb.core.data.VirtualDbData
 
setExperiment(Experiment) - Method in class net.sf.basedb.core.BioAssaySet
Set the experiment.
setExperiment(Experiment) - Method in class net.sf.basedb.core.Job
Set the experiment this job is part of.
setExperiment(Experiment) - Method in class net.sf.basedb.core.ReporterList
Set the experiment.
setExperiment(Experiment) - Method in class net.sf.basedb.core.Transformation
Set the experiment.
setExperimentalFactors(Set<AnnotationTypeData>) - Method in class net.sf.basedb.core.data.ExperimentData
 
setExperimentDesign(String) - Method in class net.sf.basedb.core.data.ExperimentData
 
setExperimentDesign(String) - Method in class net.sf.basedb.core.Experiment
Set a text describing the experimental design.
setExperiments(Set<ExperimentData>) - Method in class net.sf.basedb.core.data.AnnotationTypeData
 
setExperiments(Set<ExperimentData>) - Method in class net.sf.basedb.core.data.RawBioAssayData
 
setExperimentType(String) - Method in class net.sf.basedb.core.data.ExperimentData
 
setExperimentType(String) - Method in class net.sf.basedb.core.Experiment
Set a text describing the experiment type.
setExpirationDate(Date) - Method in class net.sf.basedb.core.data.KitData
 
setExpirationDate(Date) - Method in class net.sf.basedb.core.data.UserData
 
setExpirationDate(Date) - Method in class net.sf.basedb.core.Kit
Set the expiration date.
setExpirationDate(Date) - Method in class net.sf.basedb.core.User
Sets the expiration date of the account.
setExportable(boolean) - Method in class net.sf.basedb.clients.web.extensions.list.AbstractListColumnBean
 
setExportable(boolean) - Method in class net.sf.basedb.clients.web.taglib.table.ColumnDef
 
setExportable(String) - Method in class net.sf.basedb.clients.web.extensions.list.PropertyPathActionFactory
 
setExportCompressed(boolean) - Method in class net.sf.basedb.core.Migration
Should the exporter compress the data files or leave them as is?
setExportFormatter(Formatter<?>) - Method in class net.sf.basedb.clients.web.extensions.list.AbstractListColumnBean
 
setExportFormatterClass(String) - Method in class net.sf.basedb.clients.web.extensions.list.PropertyPathActionFactory
 
setExportproperty(String) - Method in class net.sf.basedb.clients.web.taglib.table.ColumnDef
 
setExportProperty(String) - Method in class net.sf.basedb.clients.web.extensions.list.AbstractListColumnBean
 
setExportProperty(String) - Method in class net.sf.basedb.clients.web.extensions.list.PropertyPathActionFactory
 
setExporttitle(String) - Method in class net.sf.basedb.clients.web.taglib.table.ColumnDef
 
setExportTitle(String) - Method in class net.sf.basedb.clients.web.extensions.list.AbstractListColumnBean
 
setExpression(Expression) - Method in class net.sf.basedb.util.export.spotdata.SimpleDynamicField
Set the expression used to select data in the query.
setExtended(String, Object) - Method in class net.sf.basedb.core.authentication.ExtraUserInformation
Set the value of an extended property.
setExtended(String, Object) - Method in interface net.sf.basedb.core.data.ExtendableData
Set the value of an extended property.
setExtended(String, Object) - Method in class net.sf.basedb.core.data.RawData
 
setExtended(String, Object) - Method in class net.sf.basedb.core.data.ReporterData
 
setExtended(String, Object) - Method in class net.sf.basedb.core.data.UserData
 
setExtended(String, Object) - Method in class net.sf.basedb.core.User
Sets an extended property
setExtendedProperty(boolean) - Method in class net.sf.basedb.core.data.ReporterClonePropertyData
 
setExtends(String) - Method in class net.sf.basedb.util.extensions.ExtensionBean
 
setExtension(String) - Method in class net.sf.basedb.clients.web.taglib.extensions.Scripts
 
setExtension(String) - Method in class net.sf.basedb.clients.web.taglib.extensions.Stylesheets
 
setExtension(String) - Method in class net.sf.basedb.core.data.DataFileTypeData
 
setExtension(String) - Method in class net.sf.basedb.core.data.MimeTypeData
 
setExtension(String) - Method in class net.sf.basedb.core.DataFileType
Set the most common gile extension for data file of this type.
setExtension(String) - Method in class net.sf.basedb.core.MimeType
Set the extension variable for this MimeType item.
setExtensionPointId(String) - Method in class net.sf.basedb.core.signal.ExtensionSignalTransporter
 
setExtensions(ExtensionsInvoker<?>) - Method in class net.sf.basedb.clients.web.taglib.extensions.Render
 
setExtensions(ExtensionsInvoker<ListColumnAction<I, ?>>) - Method in class net.sf.basedb.clients.web.taglib.table.ColumnDef
 
setExtensions(ExtensionsInvoker<TabAction>) - Method in class net.sf.basedb.clients.web.taglib.tab.TabControl
 
setExtensionVersion(String, String) - Static method in class net.sf.basedb.clients.web.taglib.Head
Register the version for an exteniosn JAR file.
setExternalId(String) - Method in class net.sf.basedb.core.AnnotationType
Set the external id of the annotation type.
setExternalId(String) - Method in class net.sf.basedb.core.BioMaterial
Set the external id of the biomaterial.
setExternalId(String) - Method in class net.sf.basedb.core.BioPlate
Sets the external id of this bio plate
setExternalId(String) - Method in class net.sf.basedb.core.Client
Set the external id for this Client item.
setExternalId(String) - Method in class net.sf.basedb.core.data.AnnotationTypeData
 
setExternalId(String) - Method in class net.sf.basedb.core.data.BioMaterialData
 
setExternalId(String) - Method in class net.sf.basedb.core.data.BioPlateData
 
setExternalId(String) - Method in class net.sf.basedb.core.data.ClientData
 
setExternalId(String) - Method in class net.sf.basedb.core.data.DataFileTypeData
 
setExternalId(String) - Method in class net.sf.basedb.core.data.ExtraValueTypeData
 
setExternalId(String) - Method in class net.sf.basedb.core.data.FeatureData
 
setExternalId(String) - Method in class net.sf.basedb.core.data.HelpData
 
setExternalId(String) - Method in class net.sf.basedb.core.data.ItemListData
 
setExternalId(String) - Method in class net.sf.basedb.core.data.JobAgentData
 
setExternalId(String) - Method in class net.sf.basedb.core.data.JobData
 
setExternalId(String) - Method in class net.sf.basedb.core.data.PlatformData
 
setExternalId(String) - Method in class net.sf.basedb.core.data.PlatformVariantData
 
setExternalId(String) - Method in class net.sf.basedb.core.data.ProtocolData
 
setExternalId(String) - Method in class net.sf.basedb.core.data.ReporterData
 
setExternalId(String) - Method in class net.sf.basedb.core.data.ReporterListData
 
setExternalId(String) - Method in class net.sf.basedb.core.data.UserData
 
setExternalId(String) - Method in class net.sf.basedb.core.DataFileType
 
setExternalId(String) - Method in class net.sf.basedb.core.ExtraValueType
Set the external id for this Client item.
setExternalId(String) - Method in class net.sf.basedb.core.Help
Set the external id for this Help item.
setExternalId(String) - Method in class net.sf.basedb.core.ItemList
Set the external id for this list.
setExternalId(String) - Method in class net.sf.basedb.core.Job
Set the external ID.
setExternalId(String) - Method in class net.sf.basedb.core.JobAgent
Set the external id for the job agent.
setExternalId(String) - Method in class net.sf.basedb.core.Platform
 
setExternalId(String) - Method in class net.sf.basedb.core.PlatformVariant
 
setExternalId(String) - Method in class net.sf.basedb.core.Protocol
Set the external id of the protocol.
setExternalId(String) - Method in class net.sf.basedb.core.ReporterList
Set the external id for this ReporterList item.
setExternalId(String) - Method in class net.sf.basedb.core.User
Set the external id for the user account.
setExtract(ExtractData) - Method in class net.sf.basedb.core.data.DerivedBioAssayData
 
setExtract(Extract) - Method in class net.sf.basedb.core.DerivedBioAssay
Set the extract that is the parent of data in this bioassay.
setExtraField(FieldInfo) - Method in class net.sf.basedb.clients.web.extensions.login.LoginFormBean
 
setExtraFileImporter(ExtraFileImporter) - Method in class net.sf.basedb.util.importer.spotdata.BfsImporter
 
setExtraInformation(ExtraUserInformation) - Method in class net.sf.basedb.core.authentication.AuthenticatedUser
Set extra information about the user.
setExtraNo(short) - Method in class net.sf.basedb.core.data.DataCubeExtraValueData
 
setExtraNo(short) - Method in class net.sf.basedb.core.DataCubeExtraValue
 
setExtraValues(Map<ExtraValueTypeData, ExtraValueData>) - Method in class net.sf.basedb.core.data.BioAssaySetData
 
setExtraValues(Set<DataCubeExtraValueData>) - Method in class net.sf.basedb.core.data.DataCubeData
 
setExtraValues(Set<ExtraValueData>) - Method in class net.sf.basedb.core.data.ExtraValueTypeData
 
setExtraValueType(ExtraValueTypeData) - Method in class net.sf.basedb.core.data.ExtraValueData
 
setExtraValueType(ExtraValueType) - Method in class net.sf.basedb.core.ExtraValue
Set the extra value type.
setFailSafe(boolean) - Method in class net.sf.basedb.core.AbstractQuery
 
setFailSafe(boolean) - Method in interface net.sf.basedb.core.query.Query
Set this flag to ensure that the transaction used to execute the query is allowed to continue even after a failure at the SQL level of this query.
setFavicon(String) - Method in class net.sf.basedb.clients.web.extensions.skin.FixedSkinActionFactory
 
setFavicon(String) - Method in class net.sf.basedb.clients.web.taglib.Page
 
setFax(String) - Method in class net.sf.basedb.core.authentication.ExtraUserInformation
 
setFax(String) - Method in class net.sf.basedb.core.data.UserData
 
setFax(String) - Method in class net.sf.basedb.core.User
Set the fax number to the user, or null if unknown.
setFeature(FeatureData) - Method in class net.sf.basedb.core.data.RawData
 
setFeatureDiameter(int) - Method in class net.sf.basedb.core.ArrayDesignBlock
Set the expected diameter of spots on the slide.
setFeatureDiameter(int) - Method in class net.sf.basedb.core.data.ArrayDesignBlockData
 
setFeatureIdentificationMethod(int) - Method in class net.sf.basedb.core.data.ArrayDesignData
 
setFeatures(Set<FeatureData>) - Method in class net.sf.basedb.core.data.ArrayDesignBlockData
 
setFetchSize(int) - Method in class net.sf.basedb.core.hibernate.NativeQueryWrapper
 
setFetchSize(int) - Method in class net.sf.basedb.core.hibernate.QueryWrapper
 
setFetchSize(int) - Method in class net.sf.basedb.core.Migration
Set the JDBC fetch size to use when fetching rows from the database.
setField(String) - Method in class net.sf.basedb.util.overview.extensions.ReflectValidationRuleActionFactory
 
setFile(FileData) - Method in interface net.sf.basedb.core.data.FileAttachableData
Attach a file to the item.
setFile(FileData) - Method in class net.sf.basedb.core.data.FileSetMemberData
 
setFile(FileData) - Method in class net.sf.basedb.core.data.ProtocolData
 
setFile(File) - Method in interface net.sf.basedb.core.FileAttachable
Attach a file to the item.
setFile(File) - Method in class net.sf.basedb.core.Protocol
 
setFileId(int) - Method in class net.sf.basedb.util.importer.spotdata.BaseFileInfo.ChildBioAssay
Set the id of the child bioassay as it appears in the BASEfile.
setFilename(String) - Method in class net.sf.basedb.clients.web.util.ServletExportOutputStream
Calls HttpServletResponse.setHeader(java.lang.String, java.lang.String) with the following values: response.setHeader("Content-Disposition", "attachment;filename=<filename>"); If the filename contains unsafe characters it is URL encoded.
setFilename(String) - Method in class net.sf.basedb.core.plugin.ExportOutputStream
Do nothing.
setFilename(String) - Method in class net.sf.basedb.util.bfs.AnnotationParser
Set the file name that this parser is reading from.
setFilename(String) - Method in class net.sf.basedb.util.bfs.AnnotationWriter
Set the file name that this writer is printing to.
setFilename(String) - Method in class net.sf.basedb.util.bfs.DataParser
Set the file name that this parser is reading from.
setFilename(String) - Method in class net.sf.basedb.util.bfs.DataWriter
Set the file name that this writer is printing to.
setFilename(String) - Method in class net.sf.basedb.util.bfs.MetadataParser
Set the file name that this writer is printing to.
setFilename(String) - Method in class net.sf.basedb.util.bfs.MetadataWriter
Set the file name that this writer is printing to.
setFilename(String) - Method in class net.sf.basedb.util.FileExportOutputStream
Calls File.setName(String) unless file names should be ignored.
setFileOnly(boolean) - Method in class net.sf.basedb.core.data.PlatformData
 
setFileOnly(boolean) - Method in class net.sf.basedb.core.data.PlatformVariantData
 
setFileProperties(File) - Method in class net.sf.basedb.util.bfs.GenericBaseDataWriterFactory
Set file properties on the newly created file object.
setFiles(Set<FileData>) - Method in class net.sf.basedb.core.data.DirectoryData
 
setFiles(Set<FileData>) - Method in class net.sf.basedb.core.data.FileServerData
 
setFileServer(FileServerData) - Method in class net.sf.basedb.core.data.FileData
 
setFileServer(FileServer) - Method in class net.sf.basedb.core.File
Set the file server on which this external file is located.
setFileSet(FileSetData) - Method in class net.sf.basedb.core.data.ArrayDesignData
 
setFileSet(FileSetData) - Method in class net.sf.basedb.core.data.BioAssaySetData
 
setFileSet(FileSetData) - Method in class net.sf.basedb.core.data.DerivedBioAssayData
 
setFileSet(FileSetData) - Method in class net.sf.basedb.core.data.ExtraValueData
 
setFileSet(FileSetData) - Method in class net.sf.basedb.core.data.FileSetMemberData
 
setFileSet(FileSetData) - Method in interface net.sf.basedb.core.data.FileStoreEnabledData
Attach a file set to the item.
setFileSet(FileSetData) - Method in class net.sf.basedb.core.data.RawBioAssayData
 
setFileSetMembers(Set<FileSetMemberData>) - Method in class net.sf.basedb.core.data.DataFileTypeData
 
setFileSize(long) - Method in class net.sf.basedb.util.bfs.AnnotationParser
Set the size of the file or -1 if not known.
setFileSize(long) - Method in class net.sf.basedb.util.bfs.DataParser
Set the size of the file or -1 if not known.
setFileSize(long) - Method in class net.sf.basedb.util.bfs.MetadataParser
Set the size of the file or -1 if not known.
setFileType(ItemSubtypeData) - Method in class net.sf.basedb.core.data.MimeTypeData
 
setFileType(ItemSubtype) - Method in class net.sf.basedb.core.MimeType
Set the filetype of this item.
setFileTypes(Map<DataFileTypeData, ItemSubtypeFileTypeData>) - Method in class net.sf.basedb.core.data.ItemSubtypeData
 
setFileTypes(Map<FileTypeIndex, PlatformFileTypeData>) - Method in class net.sf.basedb.core.data.PlatformData
 
setFileTypes(Set<PlatformFileTypeData>) - Method in class net.sf.basedb.core.data.PlatformVariantData
 
setFilltext(String) - Method in class net.sf.basedb.clients.web.taglib.menu.Menu
 
setFilter(Filter<Element>) - Method in class net.sf.basedb.util.extensions.xml.XmlLoader
Set a filter that all <extension-point>, <extension>, <ref> and <plugin-definition> tags must pass to be loaded and registered.
setFilterable(boolean) - Method in class net.sf.basedb.clients.web.extensions.list.AbstractListColumnBean
 
setFilterable(boolean) - Method in class net.sf.basedb.clients.web.taglib.table.ColumnDef
 
setFilterable(String) - Method in class net.sf.basedb.clients.web.extensions.list.PropertyPathActionFactory
 
setFilterclass(String) - Method in class net.sf.basedb.clients.web.taglib.table.ColumnDef
 
setFilterClass(String) - Method in class net.sf.basedb.clients.web.extensions.list.AbstractListColumnBean
 
setFilterGroup(String) - Method in class net.sf.basedb.core.data.ItemListSyncFilterData
 
setFilterGroup(String) - Method in class net.sf.basedb.core.SyncFilter
Set the group that this synchronization filter belongs to.
setFilterNo(short) - Method in class net.sf.basedb.core.data.DataCubeFilterData
 
setFilterNo(short) - Method in class net.sf.basedb.core.DataCubeFilter
 
setFilterproperty(String) - Method in class net.sf.basedb.clients.web.taglib.table.ColumnDef
 
setFilterProperty(String) - Method in class net.sf.basedb.clients.web.extensions.list.AbstractListColumnBean
 
setFilterProperty(String) - Method in class net.sf.basedb.clients.web.extensions.list.PropertyPathActionFactory
 
setFilterrows(int) - Method in class net.sf.basedb.clients.web.taglib.table.Table
 
setFilters(Set<DataCubeFilterData>) - Method in class net.sf.basedb.core.data.DataCubeData
 
setFiltertext(String) - Method in class net.sf.basedb.clients.web.taglib.table.ColumnDef
 
setFilterText(String) - Method in class net.sf.basedb.clients.web.extensions.list.AbstractListColumnBean
 
setFingerprintType(String) - Method in class net.sf.basedb.core.data.FileServerData
 
setFirstAssayFieldIndex(int) - Method in class net.sf.basedb.util.importer.spotdata.BaseFileInfo.SpotSectionInfo
Set the index of the first data column that contains assay data.
setFirstResult(int) - Method in class net.sf.basedb.core.AbstractQuery
 
setFirstResult(int) - Method in class net.sf.basedb.core.hibernate.NativeQueryWrapper
 
setFirstResult(int) - Method in class net.sf.basedb.core.hibernate.QueryWrapper
 
setFirstResult(int) - Method in interface net.sf.basedb.core.query.Query
Specify that the query should start returning rows from the specified row number. 0 = start returning from the first row.
setFloat(int, float) - Method in class net.sf.basedb.core.hibernate.QueryWrapper
Deprecated.
setFloat(String, float) - Method in class net.sf.basedb.core.hibernate.QueryWrapper
Deprecated.
setFloatValues(List<Float>) - Method in class net.sf.basedb.core.data.annotations.AnnotationLink
 
setFlushMode(FlushModeType) - Method in class net.sf.basedb.core.hibernate.NativeQueryWrapper
 
setFlushMode(FlushModeType) - Method in class net.sf.basedb.core.hibernate.QueryWrapper
 
setFlushMode(FlushModeType) - Method in class net.sf.basedb.core.hibernate.SessionWrapper
 
setFlushMode(FlushMode) - Method in class net.sf.basedb.core.hibernate.NativeQueryWrapper
 
setFlushMode(FlushMode) - Method in class net.sf.basedb.core.hibernate.QueryWrapper
Deprecated.
setFlushMode(FlushMode) - Method in class net.sf.basedb.core.hibernate.SessionWrapper
Deprecated.
setForceStop(boolean) - Method in class net.sf.basedb.core.signal.ThreadSignalHandler
Deprecated.
In 3.14. Calling this is ignored and the signal handler will always use the interrupt method.
setForceUpdate(boolean) - Method in class net.sf.basedb.util.extensions.manager.processor.RegisterExtensionsProcessor
Set a flag to indicate if already registered extensions should be re-registered or not.
setFormatter(Formatter<?>) - Method in class net.sf.basedb.clients.web.taglib.table.ColumnDef
 
setFormatter(Formatter<?>) - Method in class net.sf.basedb.clients.web.taglib.table.TableColumn
 
setFormatter(Formatter<?>) - Method in class net.sf.basedb.util.export.spotdata.AnnotationAssayField
Set a formatter to use for formatting the exported values.
setFormatter(Formatter<?>) - Method in class net.sf.basedb.util.export.spotdata.AssayPropertyField
Set a formatter to use for formatting the exported values.
setFormatter(Formatter<?>) - Method in class net.sf.basedb.util.export.spotdata.JepDynamicField
Set a formatter to use for formatting the exported values.
setFormatter(Formatter<?>) - Method in class net.sf.basedb.util.export.spotdata.SimpleDynamicField
Set a formatter to use for formatting the exported values.
setFormatter(Formatter<? super V>) - Method in class net.sf.basedb.clients.web.extensions.list.AbstractListColumnBean
 
setFormatterClass(String) - Method in class net.sf.basedb.clients.web.extensions.list.PropertyPathActionFactory
 
setFormulas(List<String>) - Method in class net.sf.basedb.core.data.FormulaData
 
setFormulas(List<String>) - Method in class net.sf.basedb.core.Formula
Set the expressions used by this formula.
setFormulaType(Formula.Type) - Method in class net.sf.basedb.core.Formula
Set the type of the formula.
setFreeWells(int) - Method in class net.sf.basedb.core.data.BioPlateData
 
setFreezer(HardwareData) - Method in class net.sf.basedb.core.data.BioPlateData
 
setFreezer(Hardware) - Method in class net.sf.basedb.core.BioPlate
Sets the freezer where this bio plate is stored
setFrom(String) - Method in class net.sf.basedb.core.data.MessageData
 
setFrom(String) - Method in class net.sf.basedb.core.Message
Set the name of the sender of the message.
setFrom(BasicItem) - Method in class net.sf.basedb.core.AnyToAny
 
setFromId(int) - Method in class net.sf.basedb.core.data.AnyToAnyData
 
setFromId(int) - Method in class net.sf.basedb.core.data.MessageData
 
setFromType(int) - Method in class net.sf.basedb.core.data.AnyToAnyData
 
setGenericDataFile(DbControl, FileStoreEnabled, String, String, File) - Static method in class net.sf.basedb.core.FileStoreUtil
Set or remove a file to FileStoreEnabled item based on the file's generic ItemSubtype.
setGenericType(ItemSubtypeData) - Method in class net.sf.basedb.core.data.DataFileTypeData
 
setGenericType(ItemSubtype) - Method in class net.sf.basedb.core.DataFileType
Set the generic file type of this item.
setGranted(int) - Method in class net.sf.basedb.core.data.keyring.PluginKeys
Set the granted permissions.
setGranted(int) - Method in class net.sf.basedb.core.data.PluginPermission
 
setGroup(GroupData) - Method in class net.sf.basedb.core.data.DiskUsageData
 
setGroupId(int) - Method in class net.sf.basedb.core.data.keyring.GroupKeys
Set the id of the group.
setGroupId(int) - Method in class net.sf.basedb.core.data.keyring.GroupProjects
Set the id of the group.
setGroupId(int) - Method in class net.sf.basedb.core.data.keyring.UserGroups
Set the id of the group.
setGroups(Map<GroupData, Integer>) - Method in class net.sf.basedb.core.data.ItemKeyData
 
setGroups(Map<GroupData, Integer>) - Method in class net.sf.basedb.core.data.ProjectData
 
setGroups(Set<GroupData>) - Method in class net.sf.basedb.core.data.UserData
 
setGuiContexts(Set<GuiContextData>) - Method in class net.sf.basedb.core.data.PluginDefinitionData
 
setGuiContexts(Set<GuiContext>) - Method in class net.sf.basedb.core.PluginDefinition
Set the contexts where this plugin can be used.
setHardware(HardwareData) - Method in class net.sf.basedb.core.data.BioMaterialEventData
 
setHardware(HardwareData) - Method in class net.sf.basedb.core.data.BioPlateEventData
 
setHardware(HardwareData) - Method in class net.sf.basedb.core.data.DerivedBioAssayData
 
setHardware(HardwareData) - Method in class net.sf.basedb.core.data.PlateEventData
 
setHardware(Hardware) - Method in class net.sf.basedb.core.BioMaterialEvent
Get the Hardware that was used in this event.
setHardware(Hardware) - Method in class net.sf.basedb.core.BioPlateEvent
Set the Hardware that was used in this event.
setHardware(Hardware) - Method in class net.sf.basedb.core.DerivedBioAssay
Set the Hardware that was used when creating this bioassay set.
setHardware(Hardware) - Method in class net.sf.basedb.core.PlateEvent
Set the Hardware that was used in this event.
setHasData(boolean) - Method in class net.sf.basedb.core.data.RawBioAssayData
 
setHasFeatures(boolean) - Method in class net.sf.basedb.core.data.ArrayDesignData
 
setHasHiddenCharacters(boolean) - Method in class net.sf.basedb.clients.web.extensions.login.FieldInfo
 
setHeader(String, String) - Method in class net.sf.basedb.core.RawBioAssay
Set the value for a raw data header.
setHeader(RawBioAssay, String, String) - Method in class net.sf.basedb.util.affymetrix.CelValidator
 
setHeaderRegexp(Pattern) - Method in class net.sf.basedb.util.parser.FlatFileParser
Set a regular expression that can be matched against a header.
setHeaders(String...) - Method in class net.sf.basedb.util.bfs.AnnotationModel
Set the column headers.
setHeaders(Map<String, String>) - Method in class net.sf.basedb.core.data.RawBioAssayData
 
setHeight(int) - Method in class net.sf.basedb.clients.web.extensions.plot.PlotGeneratorBean
 
setHeight(int) - Method in class net.sf.basedb.core.AnnotationType
Set the recommended height in characters a client application should use to render an input field for annotations of this annotation type.
setHeight(int) - Method in class net.sf.basedb.core.data.AnnotationTypeData
 
setHeight(String) - Method in class net.sf.basedb.clients.web.extensions.plot.MAPlotFactory
 
setHelp(String) - Method in class net.sf.basedb.clients.web.extensions.login.LoginFormBean
 
setHelpid(String) - Method in class net.sf.basedb.clients.web.taglib.Help
 
setHelpid(String) - Method in class net.sf.basedb.clients.web.taglib.tab.Tab
 
setHelpId(String) - Method in class net.sf.basedb.clients.web.extensions.tabcontrol.FixedTabFactory
 
setHelpId(String) - Method in class net.sf.basedb.clients.web.extensions.tabcontrol.IncludeContentTabFactory
 
setHelpId(String) - Method in class net.sf.basedb.clients.web.extensions.tabcontrol.TabBean
 
setHelpTexts(Set<HelpData>) - Method in class net.sf.basedb.core.data.ClientData
 
setHibernateFlushMode(FlushMode) - Method in class net.sf.basedb.core.hibernate.NativeQueryWrapper
 
setHibernateFlushMode(FlushMode) - Method in class net.sf.basedb.core.hibernate.QueryWrapper
 
setHibernateFlushMode(FlushMode) - Method in class net.sf.basedb.core.hibernate.SessionWrapper
 
setHiddenMembers(boolean) - Method in class net.sf.basedb.core.data.GroupData
 
setHiddenMembers(boolean) - Method in class net.sf.basedb.core.Group
Set the hidden members flag for this group.
setHideclazz(String) - Method in class net.sf.basedb.clients.web.taglib.HideableSection
 
setHideClazz(String) - Method in class net.sf.basedb.clients.web.extensions.section.IncludeContentSectionFactory
 
setHideClazz(String) - Method in class net.sf.basedb.clients.web.extensions.section.SectionBean
 
setHighlight(String) - Method in class net.sf.basedb.clients.web.taglib.table.Row
 
setHightligh(String) - Method in class net.sf.basedb.clients.web.taglib.table.Row
Deprecated.
In 3.18 due to type in the method name
setHint(String, Object) - Method in class net.sf.basedb.core.hibernate.NativeQueryWrapper
 
setHint(String, Object) - Method in class net.sf.basedb.core.hibernate.QueryWrapper
 
setHome(String) - Method in class net.sf.basedb.util.extensions.xml.PathConverter
Set the value of the home path.
setHomeDirectory(DirectoryData) - Method in class net.sf.basedb.core.data.UserData
 
setHomeDirectory(Directory) - Method in class net.sf.basedb.core.User
Set the home directory for the user.
setHost(String) - Method in class net.sf.basedb.core.data.FileServerData
 
setHost(String) - Method in class net.sf.basedb.core.FileServer
Set the host:port that should overrride the host:port specified in file urls.
setHost(String) - Method in class net.sf.basedb.util.uri.ConnectionParameters
 
setHref(String) - Method in class net.sf.basedb.clients.web.taglib.Icon
 
setHref(String) - Method in class net.sf.basedb.clients.web.taglib.path.PathElement
 
setIcon(String) - Method in class net.sf.basedb.clients.web.extensions.menu.FixedMenuItemFactory
 
setIcon(String) - Method in class net.sf.basedb.clients.web.extensions.menu.MenuItemBean
 
setIcon(String) - Method in class net.sf.basedb.clients.web.extensions.menu.PermissionMenuItemFactory
Set the icon to use in all cases.
setIcon(String) - Method in class net.sf.basedb.clients.web.extensions.toolbar.ButtonBean
 
setIcon(String) - Method in class net.sf.basedb.clients.web.extensions.toolbar.FixedButtonFactory
 
setIcon(String) - Method in class net.sf.basedb.clients.web.extensions.toolbar.PermissionButtonFactory
Set the icon to use in all cases.
setIcon(String) - Method in class net.sf.basedb.clients.web.taglib.menu.Menuitem
 
setIcon(String) - Method in class net.sf.basedb.clients.web.taglib.menu.Submenu
 
setId(int) - Method in class net.sf.basedb.core.data.annotations.AnnotationLink
 
setId(int) - Method in class net.sf.basedb.core.data.BasicData
Set the id of the item.
setId(int) - Method in class net.sf.basedb.core.ItemContext
Set the ID of the current item in this context.
setId(String) - Method in class net.sf.basedb.clients.web.extensions.list.AbstractListColumnBean
 
setId(String) - Method in class net.sf.basedb.clients.web.extensions.list.PropertyPathActionFactory
 
setId(String) - Method in class net.sf.basedb.clients.web.extensions.login.LoginFormBean
 
setId(String) - Method in class net.sf.basedb.clients.web.extensions.menu.FixedMenuItemFactory
 
setId(String) - Method in class net.sf.basedb.clients.web.extensions.menu.MenuItemBean
 
setId(String) - Method in class net.sf.basedb.clients.web.extensions.menu.PermissionMenuItemFactory
 
setId(String) - Method in class net.sf.basedb.clients.web.extensions.plot.OverviewPlotBean
 
setId(String) - Method in class net.sf.basedb.clients.web.extensions.plot.PlotGeneratorBean
 
setId(String) - Method in class net.sf.basedb.clients.web.extensions.section.IncludeContentSectionFactory
 
setId(String) - Method in class net.sf.basedb.clients.web.extensions.section.SectionBean
 
setId(String) - Method in class net.sf.basedb.clients.web.extensions.skin.FixedSkinActionFactory
 
setId(String) - Method in class net.sf.basedb.clients.web.extensions.startpage.StartPageBean
 
setId(String) - Method in class net.sf.basedb.clients.web.extensions.tabcontrol.FixedTabFactory
 
setId(String) - Method in class net.sf.basedb.clients.web.extensions.tabcontrol.IncludeContentTabFactory
 
setId(String) - Method in class net.sf.basedb.clients.web.extensions.tabcontrol.TabBean
 
setId(String) - Method in class net.sf.basedb.clients.web.extensions.toolbar.ButtonBean
 
setId(String) - Method in class net.sf.basedb.clients.web.extensions.toolbar.FixedButtonFactory
 
setId(String) - Method in class net.sf.basedb.clients.web.extensions.toolbar.PermissionButtonFactory
Set the ID of the button.
setId(String) - Method in class net.sf.basedb.util.extensions.ExtensionBean
 
setId(String) - Method in class net.sf.basedb.util.extensions.ExtensionPointBean
 
setIdentifier(boolean) - Method in class net.sf.basedb.core.AnnotationType
 
setIdentifier(boolean) - Method in class net.sf.basedb.core.data.AnnotationTypeData
 
setIdentifierOnNewItem(DbControl, I, String) - Method in class net.sf.basedb.plugins.batchimport.AnnotationIdMethod
Set the annotation on a newly created item.
setIdentifierOnNewItem(DbControl, I, String) - Method in interface net.sf.basedb.plugins.batchimport.IdMethod
Set the ID on a newly created item when this is not done by other regular column mappers.
setIgnoredFile(File, boolean) - Method in class net.sf.basedb.util.extensions.manager.Settings
Mark the given file as ignored/not ignored by the extension system.
setIgnoreNonExistingColumns(boolean) - Method in class net.sf.basedb.util.parser.ColFunction
Set to TRUE to ignore non-existing columns.
setIgnoreNonExistingColumns(boolean) - Method in class net.sf.basedb.util.parser.FlatFileParser
Specify if trying to create a mapper with one of the FlatFileParser.getMapper(String) methods for an expression which references a non-existing column should result in an exception or be ignored.
setIgnoreRegexp(Pattern) - Method in class net.sf.basedb.util.parser.FlatFileParser
Set a regular expression that is used to match a line that should be ignored.
setIgnoreSubtypeFilter(boolean) - Method in class net.sf.basedb.core.ItemContext
Set a flag to indicate if the configured subtype should be ignored when configuring a query.
setImage(String) - Method in class net.sf.basedb.clients.web.taglib.Button
 
setImage(String) - Method in class net.sf.basedb.clients.web.taglib.Help
 
setImage(String) - Method in class net.sf.basedb.clients.web.taglib.Icon
 
setImage(String) - Method in class net.sf.basedb.clients.web.taglib.table.Button
 
setImage(String) - Method in class net.sf.basedb.clients.web.taglib.table.Label
 
setImage(String) - Method in class net.sf.basedb.clients.web.taglib.Zoom
 
setImage(String) - Method in class net.sf.basedb.core.data.PlateMappingData
 
setImage(String) - Method in class net.sf.basedb.core.PlateMapping
Set the name of a small image that is a graphical representation of the mapping.
setImageRemapDir(String) - Method in class net.sf.basedb.clients.web.extensions.skin.FixedSkinActionFactory
 
setImpersonated(boolean) - Method in class net.sf.basedb.core.data.SessionData
 
setInactive(boolean) - Method in class net.sf.basedb.core.data.KitData
 
setInactive(boolean) - Method in class net.sf.basedb.core.Kit
Set the inactive flag.
setInclude(int) - Method in class net.sf.basedb.core.data.ContextData
 
setInclude(int) - Method in class net.sf.basedb.core.data.ItemListSyncFilterData
 
setInclude(String) - Method in class net.sf.basedb.clients.web.extensions.section.IncludeContentSectionFactory
 
setInclude(String) - Method in class net.sf.basedb.clients.web.extensions.tabcontrol.IncludeContentTabFactory
 
setInclude(Collection<Include>) - Method in class net.sf.basedb.util.listable.TransformContext
 
setInclude(Set<Include>, String, Include) - Static method in class net.sf.basedb.clients.web.Base
Set include option if option parameter isn't null.
setIncludeDefault(boolean) - Method in class net.sf.basedb.core.FastAnnotationLoader
If the annotation type supports project-specific annotations this method can be used to control which values that are loaded.
setIncludeInherited(boolean) - Method in class net.sf.basedb.core.AnnotationRestriction.Options
 
setIncludePrimary(boolean) - Method in class net.sf.basedb.core.AnnotationRestriction.Options
 
setIncludes(Collection<Include>) - Method in class net.sf.basedb.core.AbstractEntityQuery
 
setIncludes(Collection<Include>) - Method in interface net.sf.basedb.core.query.EntityQuery
Clears the lists of includes and adds a new collection.
setIndex(float) - Method in class net.sf.basedb.util.extensions.ExtensionBean
 
setIndex(int) - Method in class net.sf.basedb.core.BioPlateEventParticipant
Set the index of the plate in this event.
setIndex(int) - Method in class net.sf.basedb.core.data.BioPlateEventParticipantData
 
setInheritedFrom(AnnotationData) - Method in class net.sf.basedb.core.data.AnnotationData
 
setInheritedFrom(AnnotationSnapshot) - Method in class net.sf.basedb.core.snapshot.AnnotationSnapshot
Set the primary annotation for an inherited annotation.
setInheritingAnnotations(Set<AnnotationData>) - Method in class net.sf.basedb.core.data.AnnotationData
 
setInitial(String) - Method in class net.sf.basedb.clients.web.taglib.HideableSection
 
setInputStream(InputStream) - Method in class net.sf.basedb.util.bfs.AnnotationParser
Set the input stream that should be parsed.
setInputStream(InputStream) - Method in class net.sf.basedb.util.bfs.DataParser
Set the input stream that should be parsed.
setInputStream(InputStream) - Method in class net.sf.basedb.util.bfs.MetadataParser
Set the input stream that should be parsed.
setInputStream(InputStream, String) - Method in class net.sf.basedb.util.parser.FlatFileParser
Set the input stream that will be parsed.
setInputStreamLocator(InputStreamLocator) - Method in class net.sf.basedb.util.importer.spotdata.BfsImporter
Set the input stream locator that is responsible for opening files that are referenced from the metadata file.
setInstalled() - Method in class net.sf.basedb.util.extensions.manager.ExtensionsFile.WriteableExtensionsFile
Mark the file as installed.
setInstalledFile(File) - Method in class net.sf.basedb.util.extensions.manager.Settings
Mark the given file as installed by the extension system.
setInstalledSchemaVersion(int) - Method in class net.sf.basedb.core.hibernate.SessionFactoryConfiguration
Deprecated.
Callback intended for BASE core to set the installed schema version.
setInteger(int, int) - Method in class net.sf.basedb.core.hibernate.QueryWrapper
Deprecated.
setInteger(String, int) - Method in class net.sf.basedb.core.hibernate.QueryWrapper
Deprecated.
setIntegerValues(List<Integer>) - Method in class net.sf.basedb.core.data.annotations.AnnotationLink
 
setIntensities(FlatFileParser.Data, float[], int) - Method in class net.sf.basedb.util.importer.spotdata.GenericIntensityParser
 
setIntensities(FlatFileParser.Data, float[], int) - Method in class net.sf.basedb.util.importer.spotdata.MAParser
 
setIntensities(FlatFileParser.Data, float[], int) - Method in interface net.sf.basedb.util.importer.spotdata.SpotIntensityParser
Extract the intensity values from the current data line for a single bioassay.
setIntensityTransform(int) - Method in class net.sf.basedb.core.data.BioAssaySetData
 
setIntensityTransform(IntensityTransform) - Method in class net.sf.basedb.core.BioAssaySet
Sets the transform used on the spot intensities before they were stored in the database.
setIntensityTransform(IntensityTransform) - Method in class net.sf.basedb.util.importer.spotdata.BaseFileImporter
Set the intensity transform that have been applied to the spot data in the file.
setInteractive(boolean) - Method in class net.sf.basedb.core.data.PluginDefinitionData
 
setInteractive(boolean) - Method in class net.sf.basedb.core.PluginDefinition
 
setInterfaceName(String) - Method in class net.sf.basedb.core.data.PluginTypeData
 
setInterfaceName(String) - Method in class net.sf.basedb.core.PluginType
The class name cannot be changed.
setInternalId(int) - Method in class net.sf.basedb.util.extensions.xml.PluginInfo
 
setInternalName(String) - Method in class net.sf.basedb.core.data.FileData
 
setInternalName(String) - Method in class net.sf.basedb.core.File
Set the internal name of this file.
setInterruptHandler(InterruptHandler) - Static method in class net.sf.basedb.core.signal.ThreadSignalHandler
Register an interrupt handler with the current thread.
setInterval(String) - Method in class net.sf.basedb.clients.web.extensions.service.DummyService
Set the interval between writes to stdout.
setItem(int, Item) - Method in class net.sf.basedb.core.snapshot.AnnotationSnapshot
 
setItem(Object) - Method in class net.sf.basedb.clients.web.taglib.extensions.Render
 
setItem(Object) - Method in class net.sf.basedb.clients.web.taglib.PropertyValue
 
setItem(Object) - Method in class net.sf.basedb.clients.web.taglib.table.ExtensionCells
 
setItem(String) - Method in class net.sf.basedb.clients.web.extensions.menu.PermissionMenuItemFactory
Set the item type to check the permission for.
setItem(String) - Method in class net.sf.basedb.clients.web.extensions.toolbar.PermissionButtonFactory
Set the item type to check the permission for.
setItem(Annotatable) - Method in class net.sf.basedb.core.AnnotationSet
Set the item this annotation set belongs to.
setItem(FileStoreEnabled) - Method in class net.sf.basedb.core.FileSet
Set the item this file set belongs to.
setItem(Item) - Method in class net.sf.basedb.clients.web.taglib.table.Table
 
setItem(Subtypable) - Method in class net.sf.basedb.clients.web.taglib.SubtypeSelector
 
setItemId(int) - Method in class net.sf.basedb.core.data.ChangeHistoryDetailData
 
setItemId(int) - Method in class net.sf.basedb.core.data.ContextData
 
setItemId(Integer) - Method in class net.sf.basedb.core.data.AnnotationSetData
 
setItemKey(ItemKeyData) - Method in interface net.sf.basedb.core.data.ShareableData
Set the ItemKeyData for the item.
setItemKey(ItemKeyData) - Method in class net.sf.basedb.core.data.SharedData
 
setItemKey(DbControl, ShareableData, ItemKey) - Static method in class net.sf.basedb.core.ShareableUtil
Set the item key of a ShareableData object.
setItemKey(ItemKey) - Method in interface net.sf.basedb.core.Shareable
Set the ItemKey for this item.
setItemKey(ItemKey) - Method in class net.sf.basedb.core.SharedItem
 
setItemKeys(Set<ItemKeyData>) - Method in class net.sf.basedb.core.data.GroupData
 
setItemKeys(Set<ItemKeyData>) - Method in class net.sf.basedb.core.data.UserData
 
setItemList(ItemListData) - Method in class net.sf.basedb.core.data.ItemListSyncFilterData
 
setItemPermission(Permission) - Method in class net.sf.basedb.core.AbstractEntityQuery
 
setItemPermission(Permission) - Method in class net.sf.basedb.core.ItemContext
Specify the permission the logged in user must have for items returned by a query.
setItemPermission(Permission) - Method in interface net.sf.basedb.core.query.EntityQuery
Only return items which the logged in user has the specified permission for.
setItemSubtype(ItemSubtypeData) - Method in class net.sf.basedb.core.data.AnnotationTypeCategoryData
 
setItemSubtype(ItemSubtypeData) - Method in class net.sf.basedb.core.data.BioMaterialData
 
setItemSubtype(ItemSubtypeData) - Method in class net.sf.basedb.core.data.BioPlateTypeData
 
setItemSubtype(ItemSubtypeData) - Method in class net.sf.basedb.core.data.ContextData
 
setItemSubtype(ItemSubtypeData) - Method in class net.sf.basedb.core.data.DerivedBioAssayData
 
setItemSubtype(ItemSubtypeData) - Method in class net.sf.basedb.core.data.FileData
 
setItemSubtype(ItemSubtypeData) - Method in class net.sf.basedb.core.data.HardwareData
 
setItemSubtype(ItemSubtypeData) - Method in class net.sf.basedb.core.data.ItemListData
 
setItemSubtype(ItemSubtypeData) - Method in class net.sf.basedb.core.data.ItemListSyncFilterData
 
setItemSubtype(ItemSubtypeData) - Method in class net.sf.basedb.core.data.ItemSubtypeFileTypeData
 
setItemSubtype(ItemSubtypeData) - Method in class net.sf.basedb.core.data.JobData
 
setItemSubtype(ItemSubtypeData) - Method in class net.sf.basedb.core.data.KitData
 
setItemSubtype(ItemSubtypeData) - Method in class net.sf.basedb.core.data.PhysicalBioAssayData
 
setItemSubtype(ItemSubtypeData) - Method in class net.sf.basedb.core.data.ProtocolData
 
setItemSubtype(ItemSubtypeData) - Method in class net.sf.basedb.core.data.SoftwareData
 
setItemSubtype(ItemSubtypeData) - Method in interface net.sf.basedb.core.data.SubtypableData
Set the subtype of the item.
setItemSubtype(ItemSubtypeData) - Method in class net.sf.basedb.core.data.TagData
 
setItemSubtype(ItemSubtype) - Method in class net.sf.basedb.core.AnnotationTypeCategory
Set the item subtype that is linked to this category of annotations.
setItemSubtype(ItemSubtype) - Method in class net.sf.basedb.core.BioMaterial
 
setItemSubtype(ItemSubtype) - Method in class net.sf.basedb.core.BioPlateType
Set the subtype that biomaterial items should have when placed on a plate with the bioplate type.
setItemSubtype(ItemSubtype) - Method in class net.sf.basedb.core.DerivedBioAssay
 
setItemSubtype(ItemSubtype) - Method in class net.sf.basedb.core.File
 
setItemSubtype(ItemSubtype) - Method in class net.sf.basedb.core.Hardware
 
setItemSubtype(ItemSubtype) - Method in class net.sf.basedb.core.ItemContext
Set a subtype to relate to this context.
setItemSubtype(ItemSubtype) - Method in class net.sf.basedb.core.ItemList
Set the subtype of items that can be members in this list.
setItemSubtype(ItemSubtype) - Method in class net.sf.basedb.core.ItemSubtype
Do nothing.
setItemSubtype(ItemSubtype) - Method in class net.sf.basedb.core.Job
 
setItemSubtype(ItemSubtype) - Method in class net.sf.basedb.core.Kit
 
setItemSubtype(ItemSubtype) - Method in class net.sf.basedb.core.PhysicalBioAssay
 
setItemSubtype(ItemSubtype) - Method in class net.sf.basedb.core.Protocol
 
setItemSubtype(ItemSubtype) - Method in class net.sf.basedb.core.Software
 
setItemSubtype(ItemSubtype) - Method in interface net.sf.basedb.core.Subtypable
Set the subtype on the item.
setItemSubtype(ItemSubtype) - Method in class net.sf.basedb.core.Tag
 
setItemSubtype(ItemSubtype) - Method in class net.sf.basedb.util.annotations.InheritSpecification
Set the subtype a parent item must have if annotations should be inherited from it.
setItemSubtypes(Set<ItemSubtypeFileTypeData>) - Method in class net.sf.basedb.core.data.DataFileTypeData
 
setItemtype(Item) - Method in class net.sf.basedb.clients.web.taglib.SubtypeSelector
 
setItemType(int) - Method in class net.sf.basedb.core.data.AnnotationSetData
 
setItemType(int) - Method in class net.sf.basedb.core.data.ChangeHistoryDetailData
 
setItemType(int) - Method in class net.sf.basedb.core.data.ContextData
 
setItemType(int) - Method in class net.sf.basedb.core.data.ContextIndex
 
setItemType(int) - Method in class net.sf.basedb.core.data.DataFileTypeData
 
setItemType(int) - Method in class net.sf.basedb.core.data.DiskUsageData
 
setItemType(int) - Method in class net.sf.basedb.core.data.FileSetData
 
setItemType(int) - Method in class net.sf.basedb.core.data.GuiContextData
 
setItemType(int) - Method in class net.sf.basedb.core.data.ItemSubtypeData
 
setItemType(int) - Method in class net.sf.basedb.core.data.RoleKeyData
 
setItemType(Item) - Method in class net.sf.basedb.core.DataFileType
 
setItemType(Item) - Method in class net.sf.basedb.core.query.QueryParameter
Changes the type of the parameter.
setItemTypes(Collection<Item>) - Method in class net.sf.basedb.core.AnnotationType
Enable the annotation type for all of the specified item and disable it for all other.
setItemTypes(Set<Integer>) - Method in class net.sf.basedb.core.data.AnnotationTypeData
 
setJarFile(String) - Method in class net.sf.basedb.core.data.PluginDefinitionData
 
setJarFile(String) - Method in class net.sf.basedb.core.data.PluginTypeData
 
setJarFile(String) - Method in class net.sf.basedb.core.PluginDefinition
The jar path cannot be changed.
setJarFile(String) - Method in class net.sf.basedb.core.PluginType
The jar path cannot be changed.
setJdbcBatchSize(Integer) - Method in class net.sf.basedb.core.hibernate.SessionWrapper
 
setJdbcBatchSize(Integer) - Method in class net.sf.basedb.core.hibernate.StatelessSessionWrapper
 
setJep(String) - Method in class net.sf.basedb.util.export.spotdata.JepDynamicField
Set the expression used to select data in the query.
setJob(JobData) - Method in class net.sf.basedb.core.data.ArrayDesignData
 
setJob(JobData) - Method in class net.sf.basedb.core.data.ChangeHistoryData
 
setJob(JobData) - Method in class net.sf.basedb.core.data.DerivedBioAssayData
 
setJob(JobData) - Method in class net.sf.basedb.core.data.ExtraValueData
 
setJob(JobData) - Method in class net.sf.basedb.core.data.MessageData
 
setJob(JobData) - Method in class net.sf.basedb.core.data.RawBioAssayData
 
setJob(JobData) - Method in class net.sf.basedb.core.data.TransformationData
 
setJob(JobData) - Method in class net.sf.basedb.core.Message
 
setJob(Job) - Method in class net.sf.basedb.core.DerivedBioAssay
Set the job on this derived bioassay that was used to create or import data for it.
setJob(Job) - Method in class net.sf.basedb.core.ExtraValue
Set the job that created the extra values.
setJob(Job) - Method in class net.sf.basedb.core.RawBioAssay
Set the job on this raw bioassay that was used to create or import data for it.
setJob(Job) - Method in class net.sf.basedb.core.Transformation
Set the job that executed this transformation.
setJobAgent(JobAgentData) - Method in class net.sf.basedb.core.data.JobAgentSettingsData
 
setJobAgent(JobAgent) - Method in class net.sf.basedb.core.Job
Set the job agent this job should run on.
setJobAgent(JobAgent) - Method in class net.sf.basedb.core.JobAgentSettings
 
setJobAgentId(Integer) - Method in class net.sf.basedb.core.data.JobData
 
setJobAgentSettings(Set<JobAgentSettingsData>) - Method in class net.sf.basedb.core.data.PluginDefinitionData
 
setJobId(Integer) - Method in class net.sf.basedb.core.data.ChangeHistoryData
 
setJobs(Set<JobData>) - Method in class net.sf.basedb.core.data.ExperimentData
 
setJspcontext(JspContext) - Method in class net.sf.basedb.clients.web.taglib.table.ColumnDef
 
setJspContext(JspContext) - Method in class net.sf.basedb.clients.web.extensions.edit.AbstractOnSaveAction
Get the JSP context of the current invokation.
setKeepSkippedLines(boolean) - Method in class net.sf.basedb.util.parser.FlatFileParser
If the FlatFileParser.nextData() and FlatFileParser.hasMoreData() methods should keep information of lines that was skipped because they matched the ignore pattern or could be interpreted as data lines.
setKeyId(int) - Method in class net.sf.basedb.core.data.keyring.KeyPermission
Set the id of the key.
setKeyId(int) - Method in class net.sf.basedb.core.data.keyring.PluginKeys
Sets the id of the RoleKey
setKeys(Set<RoleKeyData>) - Method in class net.sf.basedb.core.data.RoleData
 
setKit(KitData) - Method in class net.sf.basedb.core.data.BioMaterialEventData
 
setKit(KitData) - Method in class net.sf.basedb.core.data.BioPlateEventData
 
setKit(KitData) - Method in class net.sf.basedb.core.data.DerivedBioAssayData
 
setKit(Kit) - Method in class net.sf.basedb.core.BioMaterialEvent
Set the Kit that was used in this event.
setKit(Kit) - Method in class net.sf.basedb.core.BioPlateEvent
Set the Kit that was used in this event.
setKit(Kit) - Method in class net.sf.basedb.core.DerivedBioAssay
Set the Kit that was used when creating this bioassay.
setLabel(String) - Method in class net.sf.basedb.core.data.ParameterValueData
 
setLastModified(Date) - Method in class net.sf.basedb.util.uri.UriMetadata
 
setLastProcessResults(ProcessResults) - Method in class net.sf.basedb.util.extensions.manager.ExtensionsManager
Save the last process results so that they can be used later on.
setLastRemoteId(String) - Method in class net.sf.basedb.core.data.UserDeviceData
 
setLastSource(String) - Method in class net.sf.basedb.core.data.ReporterData
 
setLastSyncProperties(String) - Method in class net.sf.basedb.core.data.ItemListSyncFilterData
 
setLastUpdate(Date) - Method in class net.sf.basedb.core.data.AnnotationData
 
setLastUpdate(Date) - Method in class net.sf.basedb.core.data.FileData
 
setLastUpdate(Date) - Method in class net.sf.basedb.core.data.ReporterData
 
setLastUpdated() - Method in class net.sf.basedb.clients.jobagent.slotmanager.MasterSlotManager.RemoteSlot
 
setLastUsed(Date) - Method in class net.sf.basedb.core.data.UserDeviceData
 
setLatitude(Float) - Method in class net.sf.basedb.util.GeoLocation
 
setLayerNo(short) - Method in class net.sf.basedb.core.data.DataCubeLayerData
 
setLayerNo(short) - Method in class net.sf.basedb.core.DataCubeLayer
 
setLayers(Set<DataCubeLayerData>) - Method in class net.sf.basedb.core.data.DataCubeData
 
setLength(int) - Method in class net.sf.basedb.core.data.ReporterClonePropertyData
 
setLength(Long) - Method in class net.sf.basedb.util.uri.UriMetadata
 
setLevel(String) - Method in class net.sf.basedb.util.extensions.LoggingErrorHandlerFactory
Set the level of the error handler.
setLimit(int) - Method in class net.sf.basedb.core.signal.ProgressReporterSignalHandler
Set the percentage limit.
setLinkName(String) - Method in class net.sf.basedb.util.AnyToAnyLinkStatistics
 
setList(Collection<?>) - Method in class net.sf.basedb.clients.web.taglib.table.CellValue
 
setLocale(int, Locale) - Method in class net.sf.basedb.core.hibernate.QueryWrapper
Deprecated.
setLocale(String, Locale) - Method in class net.sf.basedb.core.hibernate.QueryWrapper
Deprecated.
setLocation(int) - Method in class net.sf.basedb.core.data.DiskUsageData
 
setLocation(int) - Method in class net.sf.basedb.core.data.FileData
 
setLocation(int) - Method in class net.sf.basedb.core.data.QuotaIndex
 
setLocation(String) - Method in class net.sf.basedb.core.data.SessionData
 
setLocation(String) - Method in class net.sf.basedb.core.data.UserDeviceData
 
setLocation(Location) - Method in class net.sf.basedb.core.File
Set the location of this File item.
setLocationLatitude(Float) - Method in class net.sf.basedb.core.data.SessionData
 
setLocationLatitude(Float) - Method in class net.sf.basedb.core.data.UserDeviceData
 
setLocationLongitude(Float) - Method in class net.sf.basedb.core.data.SessionData
 
setLocationLongitude(Float) - Method in class net.sf.basedb.core.data.UserDeviceData
 
setLocked(boolean) - Method in class net.sf.basedb.clients.web.taglib.table.Navigator
 
setLocked(boolean) - Method in class net.sf.basedb.core.data.ReporterCloneTemplateData
 
setLockMode(int) - Method in class net.sf.basedb.core.data.BioPlateTypeData
 
setLockMode(String, LockMode) - Method in class net.sf.basedb.core.hibernate.NativeQueryWrapper
 
setLockMode(String, LockMode) - Method in class net.sf.basedb.core.hibernate.QueryWrapper
 
setLockMode(LockModeType) - Method in class net.sf.basedb.core.hibernate.NativeQueryWrapper
 
setLockMode(LockModeType) - Method in class net.sf.basedb.core.hibernate.QueryWrapper
 
setLockMode(BioWell.LockMode) - Method in class net.sf.basedb.core.BioPlateType
Set the lock mode for wells on plates of this plate type.
setLockOptions(LockOptions) - Method in class net.sf.basedb.core.hibernate.NativeQueryWrapper
 
setLockOptions(LockOptions) - Method in class net.sf.basedb.core.hibernate.QueryWrapper
 
setLogarithmic(boolean) - Method in class net.sf.basedb.core.Coloring
Specify if we should take the logarithm of values before the color is generated or not.
setLogarithmic(boolean) - Method in class net.sf.basedb.core.data.ColoringData
 
setLogin(String) - Method in class net.sf.basedb.core.authentication.LoginRequest
Set the login name to use.
setLogin(String) - Method in class net.sf.basedb.core.data.UserData
 
setLogin(String) - Method in class net.sf.basedb.core.User
Set the login for the user account.
setLoginComment(String) - Method in class net.sf.basedb.core.data.SessionData
 
setLoginField(FieldInfo) - Method in class net.sf.basedb.clients.web.extensions.login.LoginFormBean
 
setLoginTime(Date) - Method in class net.sf.basedb.core.data.SessionData
 
setLogoutTime(Date) - Method in class net.sf.basedb.core.data.SessionData
 
setLong(int, long) - Method in class net.sf.basedb.core.hibernate.QueryWrapper
Deprecated.
setLong(String, long) - Method in class net.sf.basedb.core.hibernate.QueryWrapper
Deprecated.
setLongitude(Float) - Method in class net.sf.basedb.util.GeoLocation
 
setLongValues(List<Long>) - Method in class net.sf.basedb.core.data.annotations.AnnotationLink
 
setMainItemType(Item) - Method in class net.sf.basedb.core.ItemSubtype
 
setMainType(int) - Method in class net.sf.basedb.core.data.PluginDefinitionData
 
setMainType(Plugin.MainType) - Method in class net.sf.basedb.core.PluginDefinition
The type cannot be changed.
setMandatory(boolean) - Method in class net.sf.basedb.core.data.ReporterClonePropertyData
 
setMappings(short) - Method in class net.sf.basedb.core.data.VirtualDbData
 
setMasked(boolean) - Method in class net.sf.basedb.core.data.ParameterValueData
 
setMasterParser(AnnotationParser) - Method in class net.sf.basedb.util.importer.spotdata.SynchronizedSpotDataParser
Sets the master parser.
setMatchingSource(int) - Method in class net.sf.basedb.core.data.ItemListSyncFilterData
 
setMatchingTransformed(int) - Method in class net.sf.basedb.core.data.ItemListSyncFilterData
 
setMaxAge(int) - Method in class net.sf.basedb.core.DiskUsageStatistics
Set the max age in seconds for a disk usage summary object before it is reloaded from the database again.
setMaxBaseVersion(String) - Method in class net.sf.basedb.util.extensions.AboutBean
 
setMaxBytes(long) - Method in class net.sf.basedb.core.data.QuotaIndex
 
setMaxcharacters(int) - Method in class net.sf.basedb.clients.web.taglib.table.Cell
 
setMaxDataColumns(int) - Method in class net.sf.basedb.util.parser.FlatFileParser
Set the maximum number of columns a data line can contain in order for it to be counted as a data line.
setMaxheight(String) - Method in class net.sf.basedb.clients.web.taglib.table.Cell
 
setMaxLength(Integer) - Method in class net.sf.basedb.core.AnnotationType
Set the maximum allowed string length for a Type.STRING annotation.
setMaxMemory(Long) - Method in class net.sf.basedb.core.data.JobAgentSettingsData
 
setMaxMemory(Long) - Method in class net.sf.basedb.core.data.PluginDefinitionData
 
setMaxMemory(Long) - Method in class net.sf.basedb.core.JobAgentSettings
Set maximim amount of memory the plugin is allowed to use.
setMaxMemory(Long) - Method in class net.sf.basedb.core.PluginDefinition
Set the maximum amount of memory the plugin is allowed to use.
setMaxRandomSamples(int) - Method in class net.sf.basedb.util.AnyToAnyLinkStatistics.Options
Set the maximum number of items to use for gathering the statistics.
setMaxRawMappingsForSpot(int) - Method in class net.sf.basedb.core.data.DataCubeData
 
setMaxResults(int) - Method in class net.sf.basedb.core.AbstractQuery
 
setMaxResults(int) - Method in class net.sf.basedb.core.hibernate.NativeQueryWrapper
 
setMaxResults(int) - Method in class net.sf.basedb.core.hibernate.QueryWrapper
 
setMaxResults(int) - Method in interface net.sf.basedb.core.query.Query
Specify that the query should at most return the specified number of rows.
setMaxUnknownLines(int) - Method in class net.sf.basedb.util.parser.FlatFileParser
The number of unknown lines in a row that can be parsed by the parseHeaders method before it gives up.
setMaxValue(Float) - Method in class net.sf.basedb.core.Coloring
Set the value that represents the maximum value.
setMaxValue(Float) - Method in class net.sf.basedb.core.data.ColoringData
 
setMaxValueDouble(Double) - Method in class net.sf.basedb.core.AnnotationType
Set the maximum allowed value for a Type.FLOAT or Type.DOUBLE annotation.
setMaxValueLong(Long) - Method in class net.sf.basedb.core.AnnotationType
Set the maximum allowed value for an Type.INT or Type.LONG annotation.
setMaxwidth(String) - Method in class net.sf.basedb.clients.web.taglib.table.Cell
 
setMd5(String) - Method in class net.sf.basedb.core.data.FileData
 
setMd5(String) - Method in class net.sf.basedb.core.data.ItemListSyncFilterData
 
setMd5(String) - Method in class net.sf.basedb.util.uri.UriMetadata
 
setMd5AtLastSync(String) - Method in class net.sf.basedb.core.data.ItemListData
 
setMember(File, DataFileType) - Method in class net.sf.basedb.core.FileSet
Set a file of a given type as a member of this file set.
setMembers(Set<Integer>) - Method in class net.sf.basedb.core.data.ItemListData
 
setMembers(Set<FileSetMemberData>) - Method in class net.sf.basedb.core.data.FileSetData
 
setMemberType(int) - Method in class net.sf.basedb.core.data.ItemListData
 
setMemberType(Item) - Method in class net.sf.basedb.core.ItemList
 
setMenu(String) - Method in class net.sf.basedb.clients.web.taglib.Page
 
setMenuId(String) - Method in class net.sf.basedb.clients.web.extensions.menu.FixedMenuItemFactory
 
setMenuId(String) - Method in class net.sf.basedb.clients.web.extensions.menu.MenuItemBean
 
setMenuId(String) - Method in class net.sf.basedb.clients.web.extensions.menu.PermissionMenuItemFactory
 
setMessage(String) - Method in class net.sf.basedb.core.ItemContext
Set a message to be displayed by a client application as soon as it is appropriate to do so.
setMessagePrefix(String) - Method in class net.sf.basedb.util.ChainedProgressReporter
Set a message prefix that is pre-pended to message before it is sent to the master progress reporter.
setMessages(Set<MessageData>) - Method in class net.sf.basedb.core.data.JobData
 
setMessages(Set<MessageData>) - Method in class net.sf.basedb.core.data.UserData
 
setMetadataFromURI(UriMetadata) - Method in class net.sf.basedb.core.File
 
setMetadataParser(MetadataParser) - Method in class net.sf.basedb.util.importer.spotdata.BfsImporter
Set the metadata file parser.
setMetadataPrefix(String) - Method in class net.sf.basedb.util.basefile.BaseFileWriter
Change the metadata prefix string.
setMetadataWriter(MetadataWriter) - Method in class net.sf.basedb.util.export.spotdata.BfsExporter
Set the stream were the metadata should be written.
setMetaGrid(int, int) - Method in class net.sf.basedb.core.ArrayDesignBlock
Set the metagrid coordinates.
setMetaGridX(int) - Method in class net.sf.basedb.core.data.ArrayDesignBlockData
 
setMetaGridX(Integer) - Method in class net.sf.basedb.core.data.RawData
 
setMetaGridX(Integer) - Method in class net.sf.basedb.plugins.PrintMapFlatFileImporter.MetaBlock
 
setMetaGridY(int) - Method in class net.sf.basedb.core.data.ArrayDesignBlockData
 
setMetaGridY(Integer) - Method in class net.sf.basedb.core.data.RawData
 
setMetaGridY(Integer) - Method in class net.sf.basedb.plugins.PrintMapFlatFileImporter.MetaBlock
 
setMidValue(Float) - Method in class net.sf.basedb.core.Coloring
Set the value that represents the midpoint value.
setMidValue(Float) - Method in class net.sf.basedb.core.data.ColoringData
 
setMimeType(String) - Method in class net.sf.basedb.clients.web.util.ServletExportOutputStream
setMimeType(String) - Method in class net.sf.basedb.core.data.FileData
 
setMimeType(String) - Method in class net.sf.basedb.core.File
Set the mime type for this File item.
setMimeType(String) - Method in class net.sf.basedb.core.plugin.ExportOutputStream
Do nothing.
setMimeType(String) - Method in class net.sf.basedb.util.FileExportOutputStream
setMimeType(String) - Method in class net.sf.basedb.util.uri.UriMetadata
 
setMimeTypeAuto(String, ItemSubtype) - Method in class net.sf.basedb.core.File
Set the mime type automatically by checking the extension of the name.
setMinBaseVersion(String) - Method in class net.sf.basedb.util.extensions.AboutBean
 
setMinCount(int) - Method in class net.sf.basedb.util.AnyToAnyLinkStatistics.Options
Do not return information about links with a count that is less than this value.
setMinDataColumns(int) - Method in class net.sf.basedb.util.parser.FlatFileParser
Set the minimum number of columns a data line must contain in order for it to be counted as a data line.
setMinFraction(int) - Method in class net.sf.basedb.util.AnyToAnyLinkStatistics.Options
Do not return information about links if they are found on less than the specified fraction of samples.
setMinValue(Float) - Method in class net.sf.basedb.core.Coloring
Set the value that represents the minimum value.
setMinValue(Float) - Method in class net.sf.basedb.core.data.ColoringData
 
setMinValueDouble(Double) - Method in class net.sf.basedb.core.AnnotationType
Set the minimum allowed value for a Type.FLOAT or Type.DOUBLE annotation.
setMinValueLong(Long) - Method in class net.sf.basedb.core.AnnotationType
Set the minimum allowed value for an Type.INT or Type.LONG annotation.
setMode(boolean, boolean) - Method in class net.sf.basedb.util.basefile.BaseFileWriter
 
setMore(JSONObject, T) - Method in class net.sf.basedb.util.json.EnumConverter
Can be used by subclasses to set more properties on the JSON object.
setMore(JSONObject, T) - Method in class net.sf.basedb.util.json.NameableConverter
Can be used by subclasses to set more properties on the JSON object.
setMoreDynamicAttributes(Iterator<DynamicActionAttribute>) - Method in class net.sf.basedb.clients.web.taglib.StylableTag
 
setMultiple(boolean) - Method in class net.sf.basedb.clients.web.taglib.table.ColumnDef
 
setMultiple(boolean) - Method in class net.sf.basedb.plugins.executor.ParameterDefinition
Set if this parameter can have multiple values or only one.
setMultiplicity(int) - Method in class net.sf.basedb.core.AnnotationType
Set the multiplicity.
setMultiplicity(int) - Method in class net.sf.basedb.core.data.AnnotationTypeData
 
setMultiuserAccount(boolean) - Method in class net.sf.basedb.core.data.UserData
 
setMultiuserAccount(boolean) - Method in class net.sf.basedb.core.User
Sets if the user account is multiuser account.
setName(int) - Method in class net.sf.basedb.clients.web.taglib.Input
 
setName(String) - Method in class net.sf.basedb.clients.web.extensions.startpage.FixedStartPageFactory
 
setName(String) - Method in class net.sf.basedb.clients.web.extensions.startpage.StartPageBean
 
setName(String) - Method in class net.sf.basedb.clients.web.taglib.Input
 
setName(String) - Method in class net.sf.basedb.clients.web.taglib.table.Hidden
 
setName(String) - Method in class net.sf.basedb.core.AnyToAny
 
setName(String) - Method in class net.sf.basedb.core.authentication.ExtraUserInformation
 
setName(String) - Method in class net.sf.basedb.core.BioAssay
 
setName(String) - Method in class net.sf.basedb.core.BioAssaySet
 
setName(String) - Method in class net.sf.basedb.core.BioPlateEventType
 
setName(String) - Method in class net.sf.basedb.core.BioPlateType
 
setName(String) - Method in class net.sf.basedb.core.CommonItem
 
setName(String) - Method in class net.sf.basedb.core.data.AnyToAnyData
 
setName(String) - Method in class net.sf.basedb.core.data.BioAssayData
 
setName(String) - Method in class net.sf.basedb.core.data.BioAssaySetData
 
setName(String) - Method in class net.sf.basedb.core.data.BioPlateEventTypeData
 
setName(String) - Method in class net.sf.basedb.core.data.BioPlateTypeData
 
setName(String) - Method in class net.sf.basedb.core.data.ChangeHistoryData
 
setName(String) - Method in class net.sf.basedb.core.data.CommonData
 
setName(String) - Method in class net.sf.basedb.core.data.ContextData
 
setName(String) - Method in class net.sf.basedb.core.data.ContextIndex
 
setName(String) - Method in class net.sf.basedb.core.data.DataFileTypeData
 
setName(String) - Method in class net.sf.basedb.core.data.ExtraValueTypeData
 
setName(String) - Method in class net.sf.basedb.core.data.GroupData
 
setName(String) - Method in class net.sf.basedb.core.data.HelpData
 
setName(String) - Method in class net.sf.basedb.core.data.ItemListSyncFilterData
 
setName(String) - Method in class net.sf.basedb.core.data.ItemSubtypeData
 
setName(String) - Method in class net.sf.basedb.core.data.MessageData
 
setName(String) - Method in class net.sf.basedb.core.data.MimeTypeData
 
setName(String) - Method in interface net.sf.basedb.core.data.NameableData
Set the name of the item.
setName(String) - Method in class net.sf.basedb.core.data.NewsData
 
setName(String) - Method in class net.sf.basedb.core.data.PlateEventTypeData
 
setName(String) - Method in class net.sf.basedb.core.data.PlateGeometryData
 
setName(String) - Method in class net.sf.basedb.core.data.PlatformData
 
setName(String) - Method in class net.sf.basedb.core.data.PlatformVariantData
 
setName(String) - Method in class net.sf.basedb.core.data.PluginDefinitionData
 
setName(String) - Method in class net.sf.basedb.core.data.PluginTypeData
 
setName(String) - Method in class net.sf.basedb.core.data.ProjectData
 
setName(String) - Method in class net.sf.basedb.core.data.QuantityData
 
setName(String) - Method in class net.sf.basedb.core.data.QuotaData
 
setName(String) - Method in class net.sf.basedb.core.data.QuotaTypeData
 
setName(String) - Method in class net.sf.basedb.core.data.ReporterData
 
setName(String) - Method in class net.sf.basedb.core.data.ReporterTypeData
 
setName(String) - Method in class net.sf.basedb.core.data.RoleData
 
setName(String) - Method in class net.sf.basedb.core.data.RoleKeyData
 
setName(String) - Method in class net.sf.basedb.core.data.RootRawBioAssayData
 
setName(String) - Method in class net.sf.basedb.core.data.SettingData
 
setName(String) - Method in class net.sf.basedb.core.data.TransformationData
 
setName(String) - Method in class net.sf.basedb.core.data.UnitData
 
setName(String) - Method in class net.sf.basedb.core.data.UserData
 
setName(String) - Method in class net.sf.basedb.core.data.UserDeviceData
 
setName(String) - Method in class net.sf.basedb.core.data.VersionedParameter
 
setName(String) - Method in class net.sf.basedb.core.DataFileType
 
setName(String) - Method in class net.sf.basedb.core.Directory
 
setName(String) - Method in class net.sf.basedb.core.ExtraValueType
 
setName(String) - Method in class net.sf.basedb.core.File
 
setName(String) - Method in class net.sf.basedb.core.Group
 
setName(String) - Method in class net.sf.basedb.core.Help
 
setName(String) - Method in class net.sf.basedb.core.ItemSubtype
 
setName(String) - Method in class net.sf.basedb.core.Message
 
setName(String) - Method in class net.sf.basedb.core.MimeType
 
setName(String) - Method in interface net.sf.basedb.core.Nameable
Set the name of the item.
setName(String) - Method in class net.sf.basedb.core.News
 
setName(String) - Method in class net.sf.basedb.core.PlateEventType
 
setName(String) - Method in class net.sf.basedb.core.PlateGeometry
 
setName(String) - Method in class net.sf.basedb.core.Platform
 
setName(String) - Method in class net.sf.basedb.core.PlatformVariant
 
setName(String) - Method in class net.sf.basedb.core.PluginType
 
setName(String) - Method in class net.sf.basedb.core.Project
 
setName(String) - Method in class net.sf.basedb.core.Quantity
 
setName(String) - Method in class net.sf.basedb.core.Quota
 
setName(String) - Method in class net.sf.basedb.core.QuotaType
 
setName(String) - Method in class net.sf.basedb.core.RawDataType
Update the name.
setName(String) - Method in class net.sf.basedb.core.ReporterType
 
setName(String) - Method in class net.sf.basedb.core.Role
 
setName(String) - Method in class net.sf.basedb.core.RoleKey
 
setName(String) - Method in class net.sf.basedb.core.RootRawBioAssay
 
setName(String) - Method in class net.sf.basedb.core.Setting
Set the name for this setting.
setName(String) - Method in class net.sf.basedb.core.SyncFilter
 
setName(String) - Method in class net.sf.basedb.core.Transformation
 
setName(String) - Method in class net.sf.basedb.core.Unit
 
setName(String) - Method in class net.sf.basedb.core.User
 
setName(String) - Method in class net.sf.basedb.core.UserDevice
 
setName(String) - Method in class net.sf.basedb.plugins.executor.ParameterDefinition
Set the name of the parameter.
setName(String) - Method in class net.sf.basedb.util.extensions.AboutBean
 
setName(String) - Method in class net.sf.basedb.util.extensions.ExtensionPointBean
 
setName(String) - Method in class net.sf.basedb.util.importer.spotdata.BaseFileInfo.ChildBioAssay
Set the name of the child bioassay.
setName(NameableData, String) - Static method in class net.sf.basedb.core.NameableUtil
Set the name of a NameableData object.
setNeedResourcesPerExtension(boolean) - Method in class net.sf.basedb.clients.web.extensions.JspContext
Set a flag indicating that resources (eg. scripts and stylesheets) should be tracked per extension.
setNewAnnotations(AnnotationFlatFileImporter, AnnotationBatcher, boolean, boolean, boolean, boolean) - Method in class net.sf.basedb.plugins.AnnotationFlatFileImporter.NewAnnotations
Annotate the item with the annotation values from the file.
setNewitem(boolean) - Method in class net.sf.basedb.clients.web.taglib.Select
 
setNewsDate(Date) - Method in class net.sf.basedb.core.data.NewsData
 
setNewsDate(Date) - Method in class net.sf.basedb.core.News
Set the date that is shown in listings.
setNewValue(String) - Method in class net.sf.basedb.core.data.ChangeHistoryDetailData
 
setNextCommand(String) - Method in class net.sf.basedb.core.PluginRequest
Sets the next command in a configuration sequence.
setNode(String) - Method in class net.sf.basedb.core.data.JobData
 
setNoDuplicates(boolean) - Method in class net.sf.basedb.util.annotations.InheritSpecification
If this flag is set (default=true), only one annotation of the specified annotation type can be inherited.
setNoProject() - Method in class net.sf.basedb.core.snapshot.SnapshotManager
Revert to the default bahavior for loading project-specific annotations.
setNoskin(boolean) - Method in class net.sf.basedb.clients.web.taglib.Page
Set to TRUE to disable skins.
setNotabs(boolean) - Method in class net.sf.basedb.clients.web.taglib.tab.TabControl
 
setNotFound(boolean) - Method in class net.sf.basedb.util.extensions.xml.PluginInfo
 
setNotNullDate(Date, String) - Static method in class net.sf.basedb.core.DateUtil
Make a copy of a Date object.
setNotNullString(String, String, int) - Static method in class net.sf.basedb.core.StringUtil
Trim and check the length of a string.
setNullable(boolean) - Method in class net.sf.basedb.core.data.ReporterClonePropertyData
 
setNullableDate(Date, String) - Static method in class net.sf.basedb.core.DateUtil
Make a copy of a Date object.
setNullableString(String, String, int) - Static method in class net.sf.basedb.core.StringUtil
Trim and check the length of a string.
setNulltext(String) - Method in class net.sf.basedb.clients.web.taglib.PropertyValue
 
setNullValue(String) - Method in class net.sf.basedb.util.export.TableWriter
Change the null value string.
setNumArrays(int) - Method in class net.sf.basedb.core.ArrayDesign
Set the number of arrays on a single slide.
setNumArrays(int) - Method in class net.sf.basedb.core.data.ArrayDesignData
 
setNumberFormat(Formatter<Number>) - Method in class net.sf.basedb.util.excel.XlsxToCsvUtil
Set a formatter that is used for formatting cells with numeric values.
setNumColumns(int) - Method in class net.sf.basedb.clients.web.taglib.table.Table
 
setNumColumns(int) - Method in class net.sf.basedb.util.bfs.DataParser
Set the number of data columns that are expected to be found in this file.
setNumColumns(short) - Method in class net.sf.basedb.core.data.DataCubeData
 
setNumDbFeatures(int) - Method in class net.sf.basedb.core.data.ArrayDesignData
 
setNumDecimals(SessionControl, int) - Static method in class net.sf.basedb.clients.web.formatter.FormatterSettings
Set the number of decimals a number formatter should display.
setNumExtraValues(short) - Method in class net.sf.basedb.core.data.DataCubeData
 
setNumFileFeatures(int) - Method in class net.sf.basedb.core.ArrayDesign
Set the number of features that are stored in files.
setNumFileFeatures(int) - Method in class net.sf.basedb.core.data.ArrayDesignData
 
setNumFileReporters(int) - Method in class net.sf.basedb.core.BioAssaySet
Set the number of unique reporters for data that is stored in files.
setNumFileReporters(int) - Method in class net.sf.basedb.core.data.BioAssaySetData
 
setNumFileSpots(int) - Method in class net.sf.basedb.core.BioAssay
Set the number of spots that are stored in files.
setNumFileSpots(int) - Method in class net.sf.basedb.core.BioAssaySet
Set the number of spots that are stored in files.
setNumFileSpots(int) - Method in class net.sf.basedb.core.data.BioAssayData
 
setNumFileSpots(int) - Method in class net.sf.basedb.core.data.BioAssaySetData
 
setNumFileSpots(int) - Method in class net.sf.basedb.core.data.RawBioAssayData
 
setNumFileSpots(int) - Method in class net.sf.basedb.core.RawBioAssay
Set the number of spots that are stored in files.
setNumFileValues(int) - Method in class net.sf.basedb.core.data.ExtraValueData
 
setNumFileValues(int) - Method in class net.sf.basedb.core.ExtraValue
Set the number of extra values that are stored in files.
setNumFilters(short) - Method in class net.sf.basedb.core.data.DataCubeData
 
setNumLayers(short) - Method in class net.sf.basedb.core.data.DataCubeData
 
setNumPositions(int) - Method in class net.sf.basedb.core.data.DataCubeData
 
setNumPositions(int) - Method in class net.sf.basedb.core.DataCube
Set by the AbstractBatcher.close() method.
setNumReporters(int) - Method in class net.sf.basedb.core.data.BioAssaySetData
 
setNumSpots(int) - Method in class net.sf.basedb.core.data.BioAssayData
 
setNumSpots(int) - Method in class net.sf.basedb.core.data.BioAssaySetData
 
setNumValues(int) - Method in class net.sf.basedb.core.data.ExtraValueData
 
setNumValues(int) - Method in class net.sf.basedb.core.ExtraValue
Called from batcher when it is closed.
setObject(String, Object) - Method in class net.sf.basedb.core.ItemContext
Set a value.
setOldValue(String) - Method in class net.sf.basedb.core.data.ChangeHistoryDetailData
 
setOnClick(String) - Method in class net.sf.basedb.clients.web.extensions.toolbar.PermissionButtonFactory
 
setOnItem(Subtypable) - Method in class net.sf.basedb.core.ItemSubtype
Helper method for implementing the Subtypable.setItemSubtype(ItemSubtype) method.
setOpen(String) - Method in class net.sf.basedb.clients.web.taglib.menu.Menu
 
setOperator(int) - Method in class net.sf.basedb.core.data.PropertyFilterData
 
setOperator(Operator) - Method in class net.sf.basedb.core.PropertyFilter
Set the operator to use in the filter.
setOption(String, String) - Method in class net.sf.basedb.core.AnnotationType
Set an option.
setOption(String, String) - Method in class net.sf.basedb.plugins.executor.ParameterDefinition
Set the value for an option.
setOption(ValidationRuleAction, String, String) - Method in class net.sf.basedb.util.overview.ValidationOptions
Set an option for a validator rule.
setOptions(Map<String, String>) - Method in class net.sf.basedb.core.data.AnnotationTypeData
 
setOrAddFile(FileStoreEnabled, DataFileType, File) - Method in class net.sf.basedb.plugins.batchimport.AbstractItemImporter
Set or add a file to a file set.
setOrdinal(int) - Method in class net.sf.basedb.core.data.PlateEventTypeData
 
setOrdinal(int) - Method in class net.sf.basedb.core.PlateEventType
Set the order of this event in relation to the list of all events.
setOrganisation(String) - Method in class net.sf.basedb.core.authentication.ExtraUserInformation
 
setOrganisation(String) - Method in class net.sf.basedb.core.data.UserData
 
setOrganisation(String) - Method in class net.sf.basedb.core.User
Set the organisation this user works for, or null if unknown.
setOriginalBioMaterial(MeasuredBioMaterialData) - Method in class net.sf.basedb.core.data.BioWellData
 
setOriginalQuantity(Float) - Method in class net.sf.basedb.core.data.MeasuredBioMaterialData
 
setOriginalQuantity(Float) - Method in class net.sf.basedb.core.MeasuredBioMaterial
Set the original quantity of the biomaterial.
setOriginX(int) - Method in class net.sf.basedb.core.ArrayDesignBlock
Set the distance from the left edge of the slide to the top left spot in this block.
setOriginX(int) - Method in class net.sf.basedb.core.data.ArrayDesignBlockData
 
setOriginX(Integer) - Method in class net.sf.basedb.plugins.PrintMapFlatFileImporter.MetaBlock
 
setOriginY(int) - Method in class net.sf.basedb.core.ArrayDesignBlock
Set the distance from the top edge of the slide to the top left spot in this block.
setOriginY(int) - Method in class net.sf.basedb.core.data.ArrayDesignBlockData
 
setOriginY(Integer) - Method in class net.sf.basedb.plugins.PrintMapFlatFileImporter.MetaBlock
 
setOutputStream(OutputStream) - Method in class net.sf.basedb.util.zip.Bzip2FilePacker
Wrap the output stream in a GZIPOutputStream.
setOutputStream(OutputStream) - Method in interface net.sf.basedb.util.zip.FilePacker
The output stream that the compressed files should be written to.
setOutputStream(OutputStream) - Method in class net.sf.basedb.util.zip.GzipFilePacker
Wrap the output stream in a GZIPOutputStream.
setOutputStream(OutputStream) - Method in class net.sf.basedb.util.zip.TarFilePacker
Wrap the output stream in a TarOutputStream.
setOutputStream(OutputStream) - Method in class net.sf.basedb.util.zip.ZipFilePacker
Wrap the output stream in a ZipOutputStream.
setOverrideId(int) - Method in class net.sf.basedb.core.data.AnnotationData
 
setOverrideId(int) - Method in class net.sf.basedb.core.data.annotations.AnnotationLink
 
setOwner(OwnableData, User) - Static method in class net.sf.basedb.core.OwnableUtil
Set the owner of a OwnableData object.
setOwner(UserData) - Method in interface net.sf.basedb.core.data.OwnableData
Change the owner of the item.
setOwner(UserData) - Method in class net.sf.basedb.core.data.OwnedData
 
setOwner(DbControl, Set<OwnedItem>, User) - Static method in class net.sf.basedb.util.OwnableUtil
Change the owner of all specified items.
setOwner(DbControl, Item, Set<Integer>, User) - Static method in class net.sf.basedb.util.OwnableUtil
Change the owner of all specified items.
setOwner(User) - Method in interface net.sf.basedb.core.Ownable
Change the owner of the item.
setOwner(User) - Method in class net.sf.basedb.core.OwnedItem
 
setPage(int) - Method in class net.sf.basedb.clients.web.taglib.table.Navigator
 
setPage(int) - Method in class net.sf.basedb.core.data.ContextData
 
setPage(int) - Method in class net.sf.basedb.core.ItemContext
Set the current table page.
setPage(String) - Method in class net.sf.basedb.clients.web.taglib.table.Navigator
 
setPageContext(PageContext) - Method in class net.sf.basedb.clients.web.taglib.Head
 
setPageContext(PageContext) - Method in class net.sf.basedb.clients.web.taglib.Page
 
setPageContext(PageContext) - Method in class net.sf.basedb.clients.web.taglib.StylableTag
Reset the dynamic attributes to make sure old ones are not included in case the tag object is reused.
setPageContext(PageContext) - Method in class net.sf.basedb.clients.web.taglib.tab.Tab
Reset the dynamic attributes to make sure old ones are not included in case the tag object is reused.
setParameter(int, Object) - Method in class net.sf.basedb.core.hibernate.EntityQueryWrapper
 
setParameter(int, Object) - Method in class net.sf.basedb.core.hibernate.NativeQueryWrapper
 
setParameter(int, Object) - Method in class net.sf.basedb.core.hibernate.QueryWrapper
 
setParameter(int, Object, TemporalType) - Method in class net.sf.basedb.core.hibernate.NativeQueryWrapper
 
setParameter(int, Object, Type) - Method in class net.sf.basedb.core.hibernate.EntityQueryWrapper
 
setParameter(int, Object, Type) - Method in class net.sf.basedb.core.hibernate.NativeQueryWrapper
 
setParameter(int, Object, Type) - Method in class net.sf.basedb.core.hibernate.QueryWrapper
 
setParameter(int, Instant, TemporalType) - Method in class net.sf.basedb.core.hibernate.NativeQueryWrapper
 
setParameter(int, Instant, TemporalType) - Method in class net.sf.basedb.core.hibernate.QueryWrapper
 
setParameter(int, LocalDateTime, TemporalType) - Method in class net.sf.basedb.core.hibernate.NativeQueryWrapper
 
setParameter(int, LocalDateTime, TemporalType) - Method in class net.sf.basedb.core.hibernate.QueryWrapper
 
setParameter(int, OffsetDateTime, TemporalType) - Method in class net.sf.basedb.core.hibernate.NativeQueryWrapper
 
setParameter(int, OffsetDateTime, TemporalType) - Method in class net.sf.basedb.core.hibernate.QueryWrapper
 
setParameter(int, ZonedDateTime, TemporalType) - Method in class net.sf.basedb.core.hibernate.NativeQueryWrapper
 
setParameter(int, ZonedDateTime, TemporalType) - Method in class net.sf.basedb.core.hibernate.QueryWrapper
 
setParameter(int, Calendar, TemporalType) - Method in class net.sf.basedb.core.hibernate.NativeQueryWrapper
 
setParameter(int, Calendar, TemporalType) - Method in class net.sf.basedb.core.hibernate.QueryWrapper
 
setParameter(int, Date, TemporalType) - Method in class net.sf.basedb.core.hibernate.NativeQueryWrapper
 
setParameter(int, Date, TemporalType) - Method in class net.sf.basedb.core.hibernate.QueryWrapper
 
setParameter(int, P, TemporalType) - Method in class net.sf.basedb.core.hibernate.QueryWrapper
 
setParameter(String, boolean, Object, Type) - Method in class net.sf.basedb.core.AbstractQuery
 
setParameter(String, Object) - Method in class net.sf.basedb.core.hibernate.EntityQueryWrapper
 
setParameter(String, Object) - Method in class net.sf.basedb.core.hibernate.NativeQueryWrapper
 
setParameter(String, Object) - Method in class net.sf.basedb.core.hibernate.QueryWrapper
 
setParameter(String, Object) - Method in class net.sf.basedb.plugins.executor.ExternalProgramExecutor.RequestWrapper
 
setParameter(String, Object, TemporalType) - Method in class net.sf.basedb.core.hibernate.NativeQueryWrapper
 
setParameter(String, Object, Type) - Method in class net.sf.basedb.core.AbstractQuery
 
setParameter(String, Object, Type) - Method in interface net.sf.basedb.core.query.Query
Set the value of a query parameter.
setParameter(String, Object, Type) - Method in class net.sf.basedb.core.hibernate.EntityQueryWrapper
 
setParameter(String, Object, Type) - Method in class net.sf.basedb.core.hibernate.NativeQueryWrapper
 
setParameter(String, Object, Type) - Method in class net.sf.basedb.core.hibernate.QueryWrapper
 
setParameter(String, String) - Method in class net.sf.basedb.clients.web.extensions.AbstractJspFactory
Generic parameter setter metod.
setParameter(String, String) - Method in class net.sf.basedb.clients.web.extensions.ServletWrapper
Set the value of a servlet parameter.
setParameter(String, String) - Method in class net.sf.basedb.util.export.spotdata.BaseFileExporter
Add a parameter that is exported in the 'settings' section, which is the first section in the BASEfile.
setParameter(String, String) - Method in class net.sf.basedb.util.extensions.debug.BeanActionFactory
Set generic parameters.
setParameter(String, String) - Method in class net.sf.basedb.util.extensions.debug.ProxyActionFactory
Set generic parameters.
setParameter(String, String...) - Method in class net.sf.basedb.util.export.spotdata.BfsExporter
Add a parameter that is exported in the [parameters] section.
setParameter(String, Instant, TemporalType) - Method in class net.sf.basedb.core.hibernate.NativeQueryWrapper
 
setParameter(String, Instant, TemporalType) - Method in class net.sf.basedb.core.hibernate.QueryWrapper
 
setParameter(String, LocalDateTime, TemporalType) - Method in class net.sf.basedb.core.hibernate.NativeQueryWrapper
 
setParameter(String, LocalDateTime, TemporalType) - Method in class net.sf.basedb.core.hibernate.QueryWrapper
 
setParameter(String, OffsetDateTime, TemporalType) - Method in class net.sf.basedb.core.hibernate.NativeQueryWrapper
 
setParameter(String, OffsetDateTime, TemporalType) - Method in class net.sf.basedb.core.hibernate.QueryWrapper
 
setParameter(String, ZonedDateTime, TemporalType) - Method in class net.sf.basedb.core.hibernate.NativeQueryWrapper
 
setParameter(String, ZonedDateTime, TemporalType) - Method in class net.sf.basedb.core.hibernate.QueryWrapper
 
setParameter(String, Calendar, TemporalType) - Method in class net.sf.basedb.core.hibernate.NativeQueryWrapper
 
setParameter(String, Calendar, TemporalType) - Method in class net.sf.basedb.core.hibernate.QueryWrapper
 
setParameter(String, Date, TemporalType) - Method in class net.sf.basedb.core.hibernate.NativeQueryWrapper
 
setParameter(String, Date, TemporalType) - Method in class net.sf.basedb.core.hibernate.QueryWrapper
 
setParameter(String, P, TemporalType) - Method in class net.sf.basedb.core.hibernate.QueryWrapper
 
setParameter(Parameter<Instant>, Instant, TemporalType) - Method in class net.sf.basedb.core.hibernate.NativeQueryWrapper
 
setParameter(Parameter<Instant>, Instant, TemporalType) - Method in class net.sf.basedb.core.hibernate.QueryWrapper
 
setParameter(Parameter<LocalDateTime>, LocalDateTime, TemporalType) - Method in class net.sf.basedb.core.hibernate.NativeQueryWrapper
 
setParameter(Parameter<LocalDateTime>, LocalDateTime, TemporalType) - Method in class net.sf.basedb.core.hibernate.QueryWrapper
 
setParameter(Parameter<OffsetDateTime>, OffsetDateTime, TemporalType) - Method in class net.sf.basedb.core.hibernate.NativeQueryWrapper
 
setParameter(Parameter<OffsetDateTime>, OffsetDateTime, TemporalType) - Method in class net.sf.basedb.core.hibernate.QueryWrapper
 
setParameter(Parameter<ZonedDateTime>, ZonedDateTime, TemporalType) - Method in class net.sf.basedb.core.hibernate.NativeQueryWrapper
 
setParameter(Parameter<ZonedDateTime>, ZonedDateTime, TemporalType) - Method in class net.sf.basedb.core.hibernate.QueryWrapper
 
setParameter(Parameter<Calendar>, Calendar, TemporalType) - Method in class net.sf.basedb.core.hibernate.NativeQueryWrapper
 
setParameter(Parameter<Calendar>, Calendar, TemporalType) - Method in class net.sf.basedb.core.hibernate.QueryWrapper
 
setParameter(Parameter<Date>, Date, TemporalType) - Method in class net.sf.basedb.core.hibernate.NativeQueryWrapper
 
setParameter(Parameter<Date>, Date, TemporalType) - Method in class net.sf.basedb.core.hibernate.QueryWrapper
 
setParameter(Parameter<P>, P) - Method in class net.sf.basedb.core.hibernate.NativeQueryWrapper
 
setParameter(Parameter<T>, T) - Method in class net.sf.basedb.core.hibernate.EntityQueryWrapper
 
setParameter(Parameter<T>, T) - Method in class net.sf.basedb.core.hibernate.QueryWrapper
 
setParameter(QueryParameter<P>, P) - Method in class net.sf.basedb.core.hibernate.NativeQueryWrapper
 
setParameter(QueryParameter<P>, P, TemporalType) - Method in class net.sf.basedb.core.hibernate.NativeQueryWrapper
 
setParameter(QueryParameter<P>, P, TemporalType) - Method in class net.sf.basedb.core.hibernate.QueryWrapper
 
setParameter(QueryParameter<P>, P, Type) - Method in class net.sf.basedb.core.hibernate.EntityQueryWrapper
 
setParameter(QueryParameter<P>, P, Type) - Method in class net.sf.basedb.core.hibernate.NativeQueryWrapper
 
setParameter(QueryParameter<P>, P, Type) - Method in class net.sf.basedb.core.hibernate.QueryWrapper
 
setParameter(QueryParameter<T>, T) - Method in class net.sf.basedb.core.hibernate.EntityQueryWrapper
 
setParameter(QueryParameter<T>, T) - Method in class net.sf.basedb.core.hibernate.QueryWrapper
 
setParameterDefinition(ParameterDefinition) - Method in class net.sf.basedb.plugins.executor.ProgramParameter
 
setParameterList(int, Object[]) - Method in class net.sf.basedb.core.hibernate.QueryWrapper
Deprecated.
setParameterList(int, Object[], Type) - Method in class net.sf.basedb.core.hibernate.QueryWrapper
Deprecated.
setParameterList(int, Collection) - Method in class net.sf.basedb.core.hibernate.QueryWrapper
Deprecated.
setParameterList(int, Collection, Type) - Method in class net.sf.basedb.core.hibernate.QueryWrapper
Deprecated.
setParameterList(String, Object[]) - Method in class net.sf.basedb.core.hibernate.EntityQueryWrapper
 
setParameterList(String, Object[]) - Method in class net.sf.basedb.core.hibernate.NativeQueryWrapper
 
setParameterList(String, Object[]) - Method in class net.sf.basedb.core.hibernate.QueryWrapper
 
setParameterList(String, Object[], Type) - Method in class net.sf.basedb.core.hibernate.EntityQueryWrapper
 
setParameterList(String, Object[], Type) - Method in class net.sf.basedb.core.hibernate.NativeQueryWrapper
 
setParameterList(String, Object[], Type) - Method in class net.sf.basedb.core.hibernate.QueryWrapper
 
setParameterList(String, Collection) - Method in class net.sf.basedb.core.hibernate.EntityQueryWrapper
 
setParameterList(String, Collection) - Method in class net.sf.basedb.core.hibernate.NativeQueryWrapper
 
setParameterList(String, Collection) - Method in class net.sf.basedb.core.hibernate.QueryWrapper
 
setParameterList(String, Collection, Type) - Method in class net.sf.basedb.core.hibernate.EntityQueryWrapper
 
setParameterList(String, Collection, Type) - Method in class net.sf.basedb.core.hibernate.NativeQueryWrapper
 
setParameterList(String, Collection, Type) - Method in class net.sf.basedb.core.hibernate.QueryWrapper
 
setParameterList(QueryParameter<P>, Collection<P>) - Method in class net.sf.basedb.core.hibernate.EntityQueryWrapper
 
setParameterList(QueryParameter<P>, Collection<P>) - Method in class net.sf.basedb.core.hibernate.NativeQueryWrapper
 
setParameterList(QueryParameter<P>, Collection<P>) - Method in class net.sf.basedb.core.hibernate.QueryWrapper
 
setParameters(Object[], Type[]) - Method in class net.sf.basedb.core.hibernate.QueryWrapper
Deprecated.
setParameters(PreparedStatement) - Method in class net.sf.basedb.core.AbstractSqlQuery.CountWork
 
setParameters(PreparedStatement) - Method in class net.sf.basedb.core.hibernate.ExecuteUpdateWork
This method should be overridden by subclasses that needs to set parameters on the statement that is going to be executed.
setParameters(PreparedStatement) - Method in class net.sf.basedb.core.hibernate.ResultSetWork
This method should be overridden by subclasses that needs to set parameters on the statement that is going to be executed.
setParameters(PreparedStatement, List<String>, int) - Method in class net.sf.basedb.core.AbstractSqlQuery
Set parameter values on a prepared statement.
setParameters(Map<String, ParameterValueData<?>>) - Method in class net.sf.basedb.core.data.JobData
 
setParameters(Set<AnnotationTypeData>) - Method in class net.sf.basedb.core.data.ProtocolData
 
setParameters(Query<?>, Map<String, QueryParameter>) - Method in class net.sf.basedb.core.AbstractHqlQuery
Set parameter values on a query.
setParameterValue(String, Object) - Method in class net.sf.basedb.core.PluginRequest
Set the value of a request parameter to a single value.
setParameterValue(String, String, String, ParameterType<?>, Object) - Method in class net.sf.basedb.core.Job
Set the value of a configuration parameter.
setParameterValue(String, ParameterType<?>, Object) - Method in class net.sf.basedb.core.Job
Set the value of a configuration parameter.
setParameterValue(PreparedStatement, int, Object, Type) - Method in class net.sf.basedb.core.AbstractSqlQuery
Set a parameter value on a prepared statement.
setParameterValues(String, String, String, ParameterType<?>, List<?>) - Method in class net.sf.basedb.core.Job
Set the value of a configuration parameter.
setParameterValues(String, String, String, ParameterType<?>, List<?>) - Method in class net.sf.basedb.core.PluginConfiguration
Set a configuration parameter.
setParameterValues(String, List<?>) - Method in class net.sf.basedb.core.PluginRequest
Set the value of a request parameter to a list of values.
setParameterValues(String, ParameterType<?>, List<?>) - Method in class net.sf.basedb.core.Job
Set the value of a configuration parameter.
setParameterValues(String, ParameterType<?>, List<?>) - Method in class net.sf.basedb.core.PluginConfiguration
Set a configuration parameter.
setParameterValues2(List<Element>) - Method in class net.sf.basedb.core.PluginConfiguration
Sets parameters for a PluginConfiguration from the elements in a xml configurations file.
setParameterValuesInternal(String, String, String, ParameterType<?>, List<?>, boolean) - Method in class net.sf.basedb.core.Job
Set the values of a configuration parameter.
setParameterValuesInternal(String, String, String, ParameterType<?>, List<?>, boolean) - Method in class net.sf.basedb.core.PluginConfiguration
Set the values of a configuration parameter.
setParameterVersion(int) - Method in class net.sf.basedb.core.data.JobData
 
setParameterVersion(int) - Method in class net.sf.basedb.core.data.PluginConfigurationData
 
setParent(BioMaterialData) - Method in class net.sf.basedb.core.data.MeasuredBioMaterialData
 
setParent(DirectoryData) - Method in class net.sf.basedb.core.data.DirectoryData
 
setParent(WellData) - Method in class net.sf.basedb.core.data.WellData
 
setParent(Directory) - Method in class net.sf.basedb.core.Directory
Set the parent directory of this directory.
setParent(Well) - Method in class net.sf.basedb.core.Well
Set the parent well.
setParent(Renderer<? super A>) - Method in class net.sf.basedb.clients.web.extensions.renderer.PrefixSuffixRenderer
 
setParent(Renderer<? super A>) - Method in interface net.sf.basedb.util.extensions.WrappingRenderer
Set a parent renderer.
setParentBioAssay(DerivedBioAssayData) - Method in class net.sf.basedb.core.data.RawBioAssayData
 
setParentBioAssay(DerivedBioAssay) - Method in class net.sf.basedb.core.RawBioAssay
Set the DerivedBioAssay this raw bioassay is created from.
setParentExtract(ExtractData) - Method in class net.sf.basedb.core.data.RawBioAssayData
 
setParentExtract(Extract) - Method in class net.sf.basedb.core.RawBioAssay
Set the Extract this raw bioassay is created from.
setParentFilter(Filter<? super AnnotationSnapshot>) - Method in class net.sf.basedb.core.snapshot.DisabledInheritanceFilter
Set a parent filter that must also be passed in order for the this filter to pass an annotation.
setParentHasNullReporter(boolean) - Method in class net.sf.basedb.util.importer.spotdata.BaseFileInfo
Set a flag indicating that at least one position in the parent bioassay set has a null reporter.
setParentHasZeroReporter(boolean) - Method in class net.sf.basedb.util.importer.spotdata.BaseFileInfo
Set a flag indicating that at least one position in the parent bioassay set has a reporter with ID=0.
setParentId(int) - Method in class net.sf.basedb.core.data.keyring.GroupGroups
Set the id of the parent group.
setParents(Map<PlateData, Integer>) - Method in class net.sf.basedb.core.data.PlateData
 
setParents(Set<Integer>) - Method in class net.sf.basedb.util.importer.spotdata.BaseFileInfo.ChildBioAssay
Set the parents for this child.
setParents(Set<BioAssayData>) - Method in class net.sf.basedb.core.data.BioAssayData
 
setParents(Set<DerivedBioAssayData>) - Method in class net.sf.basedb.core.data.DerivedBioAssayData
 
setParents(Set<GroupData>) - Method in class net.sf.basedb.core.data.GroupData
 
setParents(Set<ItemSubtypeData>) - Method in class net.sf.basedb.core.data.ItemSubtypeData
 
setParentSet(Set<PlateData>) - Method in class net.sf.basedb.core.data.PlateData
 
setParentType(Integer) - Method in class net.sf.basedb.core.data.MeasuredBioMaterialData
 
setParseAllExcelSheets(boolean) - Method in class net.sf.basedb.util.parser.FlatFileParser
If this flag is set and the source file is an Excel file, then all sheets will be parsed unless a named sheet specified.
setParser(int) - Method in class net.sf.basedb.core.data.FormulaData
 
setParser(Formula.Parser) - Method in class net.sf.basedb.core.Formula
Set the parser used to convert the formula to an expression or restriction.
setParticipants(Set<BioPlateEventParticipantData>) - Method in class net.sf.basedb.core.data.BioPlateEventData
 
setPassword(String) - Method in class net.sf.basedb.core.authentication.LoginRequest
Set the password to use.
setPassword(String) - Method in class net.sf.basedb.core.data.FileServerData
 
setPassword(String) - Method in class net.sf.basedb.core.FileServer
Set the password to use when authenticating with the file server.
setPassword(String) - Method in class net.sf.basedb.core.User
Set the password.
setPassword(String) - Method in class net.sf.basedb.util.uri.ConnectionParameters
 
setPassword(String) - Method in interface net.sf.basedb.util.zip.FilePacker
Set the password to use for encrypting the archive.
setPassword(String) - Method in class net.sf.basedb.util.zip.ZipFilePacker
 
setPassword(PasswordData) - Method in class net.sf.basedb.core.data.UserData
 
setPasswordField(FieldInfo) - Method in class net.sf.basedb.clients.web.extensions.login.LoginFormBean
 
setPause(String, String, Serializable) - Method in interface net.sf.basedb.core.plugin.Response
A plug-in can call this method to notify the core that it has been paused.
setPause(String, String, Serializable) - Method in class net.sf.basedb.core.PluginResponse.ResponseImpl
 
setPause(String, String, Serializable) - Method in class net.sf.basedb.plugins.executor.ExternalProgramExecutor.ResponseWrapper
 
setPercentComplete(int) - Method in class net.sf.basedb.core.data.JobData
 
setPermanentEntityParameter(String, BasicItem) - Method in class net.sf.basedb.core.AbstractHqlQuery
 
setPermanentEntityParameter(String, BasicItem) - Method in interface net.sf.basedb.core.query.HqlQuery
Permanently set the value of an entity parameter.
setPermanentParameter(String, Object, Type) - Method in class net.sf.basedb.core.AbstractQuery
 
setPermanentParameter(String, Object, Type) - Method in interface net.sf.basedb.core.query.Query
Permanently set the value of a query parameter.
setPermission(int) - Method in class net.sf.basedb.core.data.keyring.KeyPermission
Set the permission.
setPermission(int) - Method in class net.sf.basedb.core.data.keyring.ProjectPermission
Set the permission.
setPermissions - Variable in class net.sf.basedb.plugins.PluginConfigurationImporter
 
setPermissions(Map<RoleKeyData, PluginPermission>) - Method in class net.sf.basedb.core.data.PluginDefinitionData
 
setPermissions(Group, Set<Permission>) - Method in class net.sf.basedb.core.GroupPermissions
Grant permissions to a group.
setPermissions(Group, Set<Permission>) - Method in class net.sf.basedb.core.MultiPermissions
Grant permissions to a group.
setPermissions(Group, Set<Permission>) - Method in class net.sf.basedb.core.Project
Grant a group permissions to this project.
setPermissions(Item, int, ItemKeyData, ProjectKeyData) - Static method in class net.sf.basedb.core.Install
 
setPermissions(Project, Set<Permission>) - Method in class net.sf.basedb.core.MultiPermissions
Grant permissions to a project.
setPermissions(Project, Set<Permission>) - Method in class net.sf.basedb.core.ProjectPermissions
Grant permissions to a project.
setPermissions(RoleKey, Set<Permission>, Set<Permission>) - Method in class net.sf.basedb.core.PluginDefinition
Sets the permissions for this plugin.
setPermissions(Role, Set<Permission>) - Method in class net.sf.basedb.core.RoleKey
Grant permissions to a role.
setPermissions(User, Set<Permission>) - Method in class net.sf.basedb.core.MultiPermissions
Grant permissions to a user.
setPermissions(User, Set<Permission>) - Method in class net.sf.basedb.core.Project
Grant a user permissions to this project.
setPermissions(User, Set<Permission>) - Method in class net.sf.basedb.core.UserPermissions
Grant permissions to a user.
setPermissionsParameter - Static variable in class net.sf.basedb.plugins.PluginConfigurationImporter
 
setPermissionTemplate(PermissionTemplateData) - Method in class net.sf.basedb.core.data.ProjectData
 
setPermissionTemplate(PermissionTemplate) - Method in class net.sf.basedb.core.Project
Set the permission template that should be used to share new items when this project is active.
setPhone(String) - Method in class net.sf.basedb.core.authentication.ExtraUserInformation
 
setPhone(String) - Method in class net.sf.basedb.core.data.UserData
 
setPhone(String) - Method in class net.sf.basedb.core.User
Set the phone number to the user, or null if unknown.
setPhysicalBioAssay(PhysicalBioAssayData) - Method in class net.sf.basedb.core.data.ArraySlideData
 
setPhysicalBioAssay(PhysicalBioAssayData) - Method in class net.sf.basedb.core.data.BioMaterialEventData
 
setPhysicalBioAssay(PhysicalBioAssay) - Method in class net.sf.basedb.core.BioMaterialEvent
Set the hybidization that was created by this event.
setPhysicalBioAssays(Set<PhysicalBioAssayData>) - Method in class net.sf.basedb.core.data.DerivedBioAssayData
 
setPlaceHolder(String) - Method in class net.sf.basedb.clients.web.extensions.login.FieldInfo
 
setPlate(int) - Method in class net.sf.basedb.core.data.MappingCoordinate
Set the plate number.
setPlate(PlateData) - Method in class net.sf.basedb.core.data.ArrayDesignPlateData
 
setPlate(PlateData) - Method in class net.sf.basedb.core.data.PlateEventData
 
setPlate(PlateData) - Method in class net.sf.basedb.core.data.WellData
 
setPlate(Plate) - Method in class net.sf.basedb.core.PlateEvent
Set the plate owning this event.
setPlateEvents(Set<PlateEventData>) - Method in class net.sf.basedb.core.data.PlateEventTypeData
 
setPlateEventType(PlateEventTypeData) - Method in class net.sf.basedb.core.data.PlateEventData
 
setPlateEventType(PlateEventType) - Method in class net.sf.basedb.core.PlateEvent
Set the plate event type of this event.
setPlateGeometry(PlateGeometryData) - Method in class net.sf.basedb.core.data.BioPlateData
 
setPlateGeometry(PlateGeometryData) - Method in class net.sf.basedb.core.data.PlateTypeData
 
setPlateGeometry(PlateGeometry) - Method in class net.sf.basedb.core.BioPlate
 
setPlateGeometry(PlateGeometry) - Method in class net.sf.basedb.core.PlateType
Set the plate geometry of this plate type.
setPlateList(List<Plate>) - Method in class net.sf.basedb.core.ArrayDesign
Set the list of plates to be used by this array design.
setPlateMapping(PlateMappingData) - Method in class net.sf.basedb.core.data.PlateData
 
setPlates(Set<ArrayDesignPlateData>) - Method in class net.sf.basedb.core.data.ArrayDesignData
 
setPlates(Set<PlateData>) - Method in class net.sf.basedb.core.data.PlateTypeData
 
setPlateType(PlateTypeData) - Method in class net.sf.basedb.core.data.PlateData
 
setPlateType(PlateTypeData) - Method in class net.sf.basedb.core.data.PlateEventTypeData
 
setPlateType(PlateType) - Method in class net.sf.basedb.core.Plate
Set the plate type of this plate.
setPlateType(PlateType) - Method in class net.sf.basedb.core.PlateEventType
Set the plate type owning this event type.
setPlateTypes(Set<PlateTypeData>) - Method in class net.sf.basedb.core.data.PlateGeometryData
 
setPlatform(PlatformData) - Method in class net.sf.basedb.core.data.ArrayDesignData
 
setPlatform(PlatformData) - Method in class net.sf.basedb.core.data.PlatformFileTypeData
 
setPlatform(PlatformData) - Method in class net.sf.basedb.core.data.PlatformVariantData
 
setPlatform(PlatformData) - Method in class net.sf.basedb.core.data.RawBioAssayData
 
setPlatform(Platform) - Method in class net.sf.basedb.core.ArrayDesign
Set the platform of the array design.
setPlatform(Platform) - Method in class net.sf.basedb.core.PlatformVariant
 
setPlatform(Platform, RawDataType) - Method in class net.sf.basedb.core.RawBioAssay
Set the platform and raw data type of the raw bioassay.
setPlatforms(Set<PlatformFileTypeData>) - Method in class net.sf.basedb.core.data.DataFileTypeData
 
setPlotGenerators(PlotGenerator[]) - Method in class net.sf.basedb.clients.web.extensions.plot.OverviewPlotBean
 
setPlotServler(String) - Method in class net.sf.basedb.clients.web.extensions.plot.MAPlotFactory
 
setPlugin(PluginDefinitionData) - Method in class net.sf.basedb.core.data.ChangeHistoryData
 
setPluginConfiguration(PluginConfigurationData) - Method in class net.sf.basedb.core.data.JobData
 
setPluginConfiguration(PluginConfiguration) - Method in class net.sf.basedb.core.Job
Set the plugin configuration of this job.
setPluginDefinition(PluginDefinitionData) - Method in class net.sf.basedb.core.data.JobAgentSettingsData
 
setPluginDefinition(PluginDefinitionData) - Method in class net.sf.basedb.core.data.JobData
 
setPluginDefinition(PluginDefinitionData) - Method in class net.sf.basedb.core.data.PluginConfigurationData
 
setPluginDefinition(PluginDefinition) - Method in class net.sf.basedb.core.Job
Set the plugin configuration of this job.
setPluginDefinition(PluginDefinition) - Method in class net.sf.basedb.core.JobAgentSettings
 
setPluginDefinition(PluginDefinition) - Method in class net.sf.basedb.core.PluginConfiguration
The definition cannot be changed.
setPluginDefinitionId(int) - Method in class net.sf.basedb.core.data.keyring.PluginKeys
Sets the PluginDefinition:s ID
setPluginId(Integer) - Method in class net.sf.basedb.core.data.ChangeHistoryData
 
setPlugins(Map<PluginDefinitionData, JobAgentSettingsData>) - Method in class net.sf.basedb.core.data.JobAgentData
 
setPlugins(Set<PluginDefinitionData>) - Method in class net.sf.basedb.core.data.PluginTypeData
 
setPluginTypes(Set<PluginTypeData>) - Method in class net.sf.basedb.core.data.PluginDefinitionData
 
setPluginVersion(String) - Method in class net.sf.basedb.core.data.JobData
 
setPluginVersion(String) - Method in class net.sf.basedb.core.Job
Set the version of the plugin that executes the job.
setPort(Integer) - Method in class net.sf.basedb.core.data.JobAgentData
 
setPort(Integer) - Method in class net.sf.basedb.core.JobAgent
Set the port the job agent is listening on.
setPosition(int) - Method in class net.sf.basedb.core.BioMaterialEventSource
 
setPosition(int) - Method in class net.sf.basedb.core.data.ArrayDesignPlateData
 
setPosition(int) - Method in class net.sf.basedb.core.data.BioMaterialEventSourceData
 
setPosition(int) - Method in class net.sf.basedb.core.data.FeatureData
This method was private until 2.6.
setPosition(int) - Method in class net.sf.basedb.core.data.RawData
This method was private before 2.6.
setPosition(String) - Method in class net.sf.basedb.clients.web.taglib.tab.TabControl
 
setPosition(String) - Method in class net.sf.basedb.core.BioPlate
Set the position within the "storage location" for this bioplate.
setPosition(String) - Method in class net.sf.basedb.core.data.BioPlateData
 
setPositionIndex(int) - Method in class net.sf.basedb.clients.web.ExperimentExplorer
Set the index of the curren position.
setPositionIndex(int) - Method in class net.sf.basedb.util.importer.spotdata.BaseFileInfo.SpotSectionInfo
Set the column index of the 'position' data column.
setPrefix(String) - Method in class net.sf.basedb.clients.web.taglib.table.CellValue
 
setPrefix(String) - Method in class net.sf.basedb.util.bfs.SequenceFilenameGenerator
Set the prefix that is used for file name generation.
setPrefixAndSuffix(String, String) - Method in class net.sf.basedb.clients.web.extensions.fileviewer.FileViewerUtil
Sets a prefix and suffix string to use before and after the list of actions.
setPrepared(String, JobAgent) - Method in class net.sf.basedb.core.Job
Set the job's status to Job.Status.PREPARED.
setPrintRobot(HardwareData) - Method in class net.sf.basedb.core.data.ArrayBatchData
 
setPrintRobot(Hardware) - Method in class net.sf.basedb.core.ArrayBatch
Set the print robot used for this array batch.
setPriority(int) - Method in class net.sf.basedb.core.data.JobData
 
setPriority(int) - Method in class net.sf.basedb.core.Job
Set the priority of the job.
setPriorityBoost(int) - Method in class net.sf.basedb.core.data.JobAgentSettingsData
 
setPriorityBoost(int) - Method in class net.sf.basedb.core.JobAgentSettings
Set the priority boost given to jobs executed by this plugin.
setProducts(Set<BioAssaySetData>) - Method in class net.sf.basedb.core.data.TransformationData
 
setProgress(int, String) - Method in class net.sf.basedb.core.Job
Set the progress of the job.
setProgress(int, String) - Method in class net.sf.basedb.util.export.spotdata.AbstractBioAssaySetExporter
Update the progress of the export.
setProgress(int, String) - Method in class net.sf.basedb.util.importer.spotdata.BaseFileImporter
Update the progress of the export.
setProgress(int, String) - Method in class net.sf.basedb.util.importer.spotdata.BfsImporter
Update the progress of the export.
setProgress(long, String) - Method in class net.sf.basedb.util.basefile.BaseFileParser
Update the progress of the parsing.
setProgressReporter(AbsoluteProgressReporter) - Method in class net.sf.basedb.util.basefile.BaseFileParser
Set a progress reporter that will be used to report how the parsing is progressing.
setProgressReporter(Job.ProgressReporterImpl) - Method in class net.sf.basedb.core.PluginConfigurationRequest
 
setProgressReporter(Job.ProgressReporterImpl) - Method in class net.sf.basedb.core.PluginExecutionRequest
Initialise a progress reporter that the plugin can use to store progress information in the database.
setProgressReporter(ProgressReporter) - Method in class net.sf.basedb.util.annotations.RunnableInheritAnnotationsManager
Set the progress reporter to use for reporting progress.
setProgressReporter(ProgressReporter) - Method in class net.sf.basedb.util.export.spotdata.AbstractBioAssaySetExporter
Set the progress reporter that is used to report progress.
setProgressReporter(ProgressReporter) - Method in class net.sf.basedb.util.importer.spotdata.BaseFileImporter
Set the progress reporter that is used to report progress.
setProgressReporter(ProgressReporter) - Method in class net.sf.basedb.util.importer.spotdata.BfsImporter
Set the progress reporter that is used to report progress.
setProject(ProjectData) - Method in class net.sf.basedb.core.data.ChangeHistoryData
 
setProject(Project) - Method in class net.sf.basedb.core.FastAnnotationLoader
If the annotation type supports project-specific annotations this method can be used to control which values that are loaded.
setProject(Project) - Method in class net.sf.basedb.core.snapshot.SnapshotManager
When a project is set, the snapshot manager will only search for project-specific annotations explicitely belonging to that project (or default values if project == null).
setProjectAnnotations(boolean) - Method in class net.sf.basedb.core.AnnotationType
If this flag is set, annotation values can be set per project.
setProjectAnnotations(boolean) - Method in class net.sf.basedb.core.data.AnnotationTypeData
 
setProjectDefaults(Map<String, String>) - Method in class net.sf.basedb.core.data.ProjectData
 
setProjectDefaults(Project) - Method in class net.sf.basedb.core.ArrayBatch
Set print robot and protocol from project default settings.
setProjectDefaults(Project) - Method in class net.sf.basedb.core.BasicItem
This method is called before inserting new items into the database to allow items to propagate default values from the active project.
setProjectDefaults(Project) - Method in class net.sf.basedb.core.BioMaterialEvent
Set protocol and hardware from project default settings.
setProjectDefaults(Project) - Method in class net.sf.basedb.core.DerivedBioAssay
Set protocol, hardware and software from project default settings.
setProjectDefaults(Project) - Method in class net.sf.basedb.core.RawBioAssay
Set software, protocol and array design from project default settings.
setProjectId(int) - Method in class net.sf.basedb.core.Annotation
Set the project that this annotation value should belong to.
setProjectId(int) - Method in class net.sf.basedb.core.data.AnnotationData
 
setProjectId(int) - Method in class net.sf.basedb.core.data.annotations.AnnotationLink
 
setProjectId(int) - Method in class net.sf.basedb.core.data.keyring.ProjectKeys
Set the id of the project.
setProjectId(int) - Method in class net.sf.basedb.core.data.keyring.ProjectPermission
Set the id of the project.
setProjectId(Integer) - Method in class net.sf.basedb.core.data.ChangeHistoryData
 
setProjectKey(ProjectKeyData) - Method in interface net.sf.basedb.core.data.ShareableData
Set the ProjectKeyData for the item.
setProjectKey(ProjectKeyData) - Method in class net.sf.basedb.core.data.SharedData
 
setProjectKey(ShareableData, ProjectKey) - Static method in class net.sf.basedb.core.ShareableUtil
Set the project key of a ShareableData object.
setProjectKey(ProjectKey) - Method in interface net.sf.basedb.core.Shareable
Set the ProjectKey for this item.
setProjectKey(ProjectKey) - Method in class net.sf.basedb.core.SharedItem
 
setProjectKeys(Set<ProjectKeyData>) - Method in class net.sf.basedb.core.data.ProjectData
 
setProjects(Map<ProjectData, Integer>) - Method in class net.sf.basedb.core.data.ProjectKeyData
 
setProjects(Set<ProjectData>) - Method in class net.sf.basedb.core.data.GroupData
 
setProjects(Set<ProjectData>) - Method in class net.sf.basedb.core.data.PermissionTemplateData
 
setProjects(Set<ProjectData>) - Method in class net.sf.basedb.core.data.UserData
 
setPrompt(String) - Method in class net.sf.basedb.clients.web.extensions.login.FieldInfo
 
setProperties(Object) - Method in class net.sf.basedb.core.hibernate.NativeQueryWrapper
 
setProperties(Object) - Method in class net.sf.basedb.core.hibernate.QueryWrapper
 
setProperties(Map) - Method in class net.sf.basedb.core.hibernate.NativeQueryWrapper
 
setProperties(Map) - Method in class net.sf.basedb.core.hibernate.QueryWrapper
 
setProperties(Map<String, ReporterClonePropertyData>) - Method in class net.sf.basedb.core.data.ReporterCloneTemplateData
 
setProperty(String) - Method in class net.sf.basedb.clients.web.extensions.list.AbstractListColumnBean
 
setProperty(String) - Method in class net.sf.basedb.clients.web.extensions.list.PropertyPathActionFactory
 
setProperty(String) - Method in class net.sf.basedb.clients.web.taglib.PropertyValue
 
setProperty(String) - Method in class net.sf.basedb.clients.web.taglib.table.ColumnDef
 
setProperty(String) - Method in class net.sf.basedb.util.export.spotdata.AssayPropertyField
Set the property that should be exported.
setProperty(String, Object) - Method in class net.sf.basedb.core.hibernate.SessionWrapper
 
setProperty(String, String) - Static method in class net.sf.basedb.core.Config
Programatically set a configuration property that overrides a configuration setting in the base.config file.
setProperty(String, String) - Method in class net.sf.basedb.util.extensions.xml.PluginInfo
 
setPropertyFilter(PropertyFilter) - Method in class net.sf.basedb.core.ItemContext
Set a property filter.
setPropertyFilters(Map<String, PropertyFilterData>) - Method in class net.sf.basedb.core.data.ContextData
 
setPropertyFilters(Map<String, PropertyFilterData>) - Method in class net.sf.basedb.core.data.ItemListSyncFilterData
 
setPropertyInspector(Filter<String>) - Method in class net.sf.basedb.core.ItemContext
Set a filter for this context that is used to inspect which properties that are allowed to be used in queries.
setPropertyValue(D, String, Object) - Method in class net.sf.basedb.core.BasicBatcher
Set a protected property value on a data object using Hibernate built-in reflection methods.
setProtocol(ProtocolData) - Method in class net.sf.basedb.core.data.ArrayBatchData
 
setProtocol(ProtocolData) - Method in class net.sf.basedb.core.data.BioMaterialEventData
 
setProtocol(ProtocolData) - Method in class net.sf.basedb.core.data.BioPlateEventData
 
setProtocol(ProtocolData) - Method in class net.sf.basedb.core.data.DerivedBioAssayData
 
setProtocol(ProtocolData) - Method in class net.sf.basedb.core.data.PlateEventData
 
setProtocol(ProtocolData) - Method in class net.sf.basedb.core.data.RawBioAssayData
 
setProtocol(Protocol) - Method in class net.sf.basedb.core.ArrayBatch
Set the Protocol used for printing the arrays.
setProtocol(Protocol) - Method in class net.sf.basedb.core.BioMaterialEvent
Set the Protocol that describes the procedure used in this event.
setProtocol(Protocol) - Method in class net.sf.basedb.core.BioPlateEvent
Set the Protocol that describes the procedure used in this event.
setProtocol(Protocol) - Method in class net.sf.basedb.core.DerivedBioAssay
Set the Protocol that describes the procedure used when creating this bioassay set.
setProtocol(Protocol) - Method in class net.sf.basedb.core.PlateEvent
Set the protocol that was followed in this event.
setProtocol(Protocol) - Method in class net.sf.basedb.core.RawBioAssay
Set the Protocol used while analysing the scanned images.
setProtocolParameter(boolean) - Method in class net.sf.basedb.core.AnnotationType
Specify if this annotation type should be used as a protocol parameter or as a regular annotation type
setProtocolParameter(boolean) - Method in class net.sf.basedb.core.data.AnnotationTypeData
 
setProtocols(Set<ProtocolData>) - Method in class net.sf.basedb.core.data.AnnotationTypeData
 
setProtocolType(ItemSubtypeData) - Method in class net.sf.basedb.core.data.PlateEventTypeData
 
setProtocolType(ItemSubtype) - Method in class net.sf.basedb.core.PlateEventType
Set the protocol type of this PlateTypeEvent item.
setPublic(boolean) - Method in class net.sf.basedb.core.data.ContextData
 
setPublication(String) - Method in class net.sf.basedb.core.data.ExperimentData
 
setPublication(String) - Method in class net.sf.basedb.core.Experiment
Set publication text.
setPublicationDate(Date) - Method in class net.sf.basedb.core.data.ExperimentData
 
setPublicationDate(Date) - Method in class net.sf.basedb.core.Experiment
Set the date this experiment was published.
setPubMedId(String) - Method in class net.sf.basedb.core.data.ExperimentData
 
setPubMedId(String) - Method in class net.sf.basedb.core.Experiment
Set the PubMed ID of the publication.
setPushAnnotations(boolean) - Method in class net.sf.basedb.core.data.ItemSubtypeData
 
setPushAnnotations(boolean) - Method in class net.sf.basedb.core.ItemSubtype
 
setQuantity(QuantityData) - Method in class net.sf.basedb.core.data.AnnotationTypeData
 
setQuantity(QuantityData) - Method in class net.sf.basedb.core.data.UnitData
 
setQuantity(QuantityData) - Method in class net.sf.basedb.core.data.UnitSymbolData
 
setQuantity(Quantity) - Method in class net.sf.basedb.core.Unit
 
setQuery(Query) - Method in class net.sf.basedb.core.ItemContext
 
setQuota(QuotaData) - Method in class net.sf.basedb.core.data.GroupData
 
setQuota(QuotaData) - Method in class net.sf.basedb.core.data.UserData
 
setQuota(Quota) - Method in class net.sf.basedb.core.Group
Set the quota for the group.
setQuota(Quota) - Method in class net.sf.basedb.core.User
Set the quota for the user.
setQuotaGroup(GroupData) - Method in class net.sf.basedb.core.data.UserData
 
setQuotaGroup(Group) - Method in class net.sf.basedb.core.User
Set the group whose quota should be checked for disk consuming items.
setQuotaType(QuotaTypeData) - Method in class net.sf.basedb.core.data.DiskUsageData
 
setQuotaType(QuotaTypeData) - Method in class net.sf.basedb.core.data.QuotaIndex
 
setQuotaValue(QuotaType, Location, long) - Method in class net.sf.basedb.core.Quota
Set the quota for the specified type, location and size.
setQuotaValues(Set<QuotaIndex>) - Method in class net.sf.basedb.core.data.QuotaData
 
setRange(int, int) - Method in class net.sf.basedb.util.ChainedProgressReporter
Set the range to use for the percentage values.
setRawBioAssay(RawBioAssayData) - Method in class net.sf.basedb.core.data.RawData
 
setRawBioAssay(RawBioAssayData) - Method in class net.sf.basedb.core.data.RootRawBioAssayData
 
setRawBioAssays(Set<RawBioAssayData>) - Method in class net.sf.basedb.core.data.DerivedBioAssayData
 
setRawBioAssays(Set<RawBioAssayData>) - Method in class net.sf.basedb.core.data.ExperimentData
 
setRawBioAssays(Set<RawBioAssayData>) - Method in class net.sf.basedb.core.data.ExtractData
 
setRawBioAssays(Set<RawBioAssayData>) - Method in class net.sf.basedb.core.data.JobData
 
setRawData(RawData) - Method in class net.sf.basedb.util.jep.MeanFunction
Set a new raw data object that will be used the next time the JEP expression is evaluated.
setRawData(RawData) - Method in class net.sf.basedb.util.jep.RawFunction
Set a new raw data object that will be used the next time the JEP expression is evaluated.
setRawDataType(String) - Method in class net.sf.basedb.core.data.ExperimentData
 
setRawDataType(String) - Method in class net.sf.basedb.core.data.FormulaData
 
setRawDataType(String) - Method in class net.sf.basedb.core.data.ItemListData
 
setRawDataType(String) - Method in class net.sf.basedb.core.data.PlatformData
 
setRawDataType(String) - Method in class net.sf.basedb.core.data.PlatformVariantData
 
setRawDataType(String) - Method in class net.sf.basedb.core.data.RawBioAssayData
 
setRawDataType(RawDataType) - Method in class net.sf.basedb.core.Experiment
Set the raw data type.
setRawDataType(RawDataType) - Method in class net.sf.basedb.core.Formula
Set the raw data type this formula can be used on.
setRawDataType(RawDataType) - Method in class net.sf.basedb.core.ItemList
Set the raw data type of raw bioassays that can be members in this list.
setRawDataType(RawDataType) - Method in class net.sf.basedb.core.Platform
Set the raw data type.
setRawDataType(RawDataType) - Method in class net.sf.basedb.core.PlatformVariant
Set the raw data type.
setRawParents(Set<RawBioAssayData>) - Method in class net.sf.basedb.core.data.BioAssayData
 
setRawSources(Collection<RawBioAssay>) - Method in class net.sf.basedb.core.Transformation
Set the raw bioassay sources used in this transformation.
setRawSources(Set<RawBioAssayData>) - Method in class net.sf.basedb.core.data.TransformationData
 
setRead(boolean) - Method in class net.sf.basedb.core.data.MessageData
 
setRead(boolean) - Method in class net.sf.basedb.core.Message
Set read status of the message.
setReadOnly(boolean) - Method in class net.sf.basedb.core.hibernate.NativeQueryWrapper
 
setReadOnly(boolean) - Method in class net.sf.basedb.core.hibernate.QueryWrapper
 
setReadOnly(Object, boolean) - Method in class net.sf.basedb.core.hibernate.SessionWrapper
 
setRecent(String, String, int) - Method in class net.sf.basedb.core.ItemContext
Add a value to the list of recently used values for the specified key.
setRecent(String, List<String>) - Method in class net.sf.basedb.core.ItemContext
 
setRecent(List<? extends BasicItem>) - Method in class net.sf.basedb.clients.web.taglib.Select
 
setRecent(BasicItem, int) - Method in class net.sf.basedb.core.ItemContext
Deprecated.
In 3.15, use ItemContext.setRecent(Item, BasicItem, int) which support 'null' entries
setRecent(BasicItem, String, int) - Method in class net.sf.basedb.core.ItemContext
Deprecated.
In 3.15, use ItemContext.setRecent(Item, BasicItem, String, int) which support 'null' entries
setRecent(BasicItem, ItemSubtype, int) - Method in class net.sf.basedb.core.ItemContext
Deprecated.
In 3.15, use ItemContext.setRecent(Item, BasicItem, ItemSubtype, int) which support 'null' entries
setRecent(Item, BasicItem, int) - Method in class net.sf.basedb.core.ItemContext
Add an item to the "recently used items" list.
setRecent(Item, BasicItem, String, int) - Method in class net.sf.basedb.core.ItemContext
Add an item to the "recently used items" list.
setRecent(Item, BasicItem, ItemSubtype, int) - Method in class net.sf.basedb.core.ItemContext
Add an item to the "recently used items" list when used for a specific item subtype.
setRedefinedColumnName(String, String, String) - Method in class net.sf.basedb.util.basefile.BaseFileParser
Redefined a column name for a specified section.
setReferenceFactor(double) - Method in class net.sf.basedb.core.data.UnitData
 
setReferenceOffset(double) - Method in class net.sf.basedb.core.data.UnitData
 
setReferenceUnit(String) - Method in class net.sf.basedb.core.data.QuantityData
 
setReferenceUnit(String) - Method in class net.sf.basedb.core.Quantity
Sets the reference unit.
setRegion(String) - Method in class net.sf.basedb.util.GeoLocation
 
setRelatedSubtype(ItemSubtype) - Method in class net.sf.basedb.core.ItemSubtype
Set a subtype that is related to this subtype.
setRelatedSubtypes(Map<Integer, ItemSubtypeData>) - Method in class net.sf.basedb.core.data.ItemSubtypeData
 
setReload(boolean) - Method in class net.sf.basedb.core.Keyring
 
setRemainingQuantity(Float) - Method in class net.sf.basedb.core.data.MeasuredBioMaterialData
 
setRemember(boolean) - Method in class net.sf.basedb.clients.web.taglib.tab.TabControl
 
setRememberLast(String) - Method in class net.sf.basedb.util.extensions.LoggingErrorHandlerFactory
Set a flag indicating if errors should be remembered by the registry.
setRememberLastLogin(boolean) - Method in class net.sf.basedb.clients.web.extensions.login.LoginFormBean
 
setRemoteId(String) - Method in class net.sf.basedb.core.data.SessionData
 
setRemove(boolean) - Method in class net.sf.basedb.util.annotations.InheritSpecification
Set a flag to remove all inherited annotations of the specified annotation type.
setRemoved(boolean) - Method in class net.sf.basedb.core.BioAssaySet
 
setRemoved(boolean) - Method in class net.sf.basedb.core.BioPlateEventType
 
setRemoved(boolean) - Method in class net.sf.basedb.core.BioPlateType
 
setRemoved(boolean) - Method in class net.sf.basedb.core.CommonItem
 
setRemoved(boolean) - Method in class net.sf.basedb.core.DataFileType
 
setRemoved(boolean) - Method in class net.sf.basedb.core.Directory
 
setRemoved(boolean) - Method in class net.sf.basedb.core.ExtraValueType
 
setRemoved(boolean) - Method in class net.sf.basedb.core.Group
 
setRemoved(boolean) - Method in class net.sf.basedb.core.ItemSubtype
 
setRemoved(boolean) - Method in class net.sf.basedb.core.Message
 
setRemoved(boolean) - Method in class net.sf.basedb.core.MimeType
 
setRemoved(boolean) - Method in class net.sf.basedb.core.News
 
setRemoved(boolean) - Method in class net.sf.basedb.core.PlateEventType
 
setRemoved(boolean) - Method in class net.sf.basedb.core.PlateGeometry
 
setRemoved(boolean) - Method in class net.sf.basedb.core.Platform
 
setRemoved(boolean) - Method in class net.sf.basedb.core.PlatformVariant
 
setRemoved(boolean) - Method in class net.sf.basedb.core.PluginDefinition
 
setRemoved(boolean) - Method in class net.sf.basedb.core.PluginType
 
setRemoved(boolean) - Method in class net.sf.basedb.core.Project
 
setRemoved(boolean) - Method in class net.sf.basedb.core.Quantity
 
setRemoved(boolean) - Method in class net.sf.basedb.core.Quota
 
setRemoved(boolean) - Method in interface net.sf.basedb.core.Removable
Set the removed flag for this item.
setRemoved(boolean) - Method in class net.sf.basedb.core.ReporterType
 
setRemoved(boolean) - Method in class net.sf.basedb.core.Role
 
setRemoved(boolean) - Method in class net.sf.basedb.core.Transformation
 
setRemoved(boolean) - Method in class net.sf.basedb.core.Unit
 
setRemoved(boolean) - Method in class net.sf.basedb.core.User
 
setRemoved(DbControl, Item, Set<Integer>, boolean) - Static method in class net.sf.basedb.util.RemovableUtil
 
setRemovedBy(Integer) - Method in class net.sf.basedb.core.data.BioAssaySetData
 
setRemovedBy(Integer) - Method in class net.sf.basedb.core.data.BioPlateEventTypeData
 
setRemovedBy(Integer) - Method in class net.sf.basedb.core.data.BioPlateTypeData
 
setRemovedBy(Integer) - Method in class net.sf.basedb.core.data.CommonData
 
setRemovedBy(Integer) - Method in class net.sf.basedb.core.data.DataFileTypeData
 
setRemovedBy(Integer) - Method in class net.sf.basedb.core.data.ExtraValueTypeData
 
setRemovedBy(Integer) - Method in class net.sf.basedb.core.data.GroupData
 
setRemovedBy(Integer) - Method in class net.sf.basedb.core.data.ItemSubtypeData
 
setRemovedBy(Integer) - Method in class net.sf.basedb.core.data.MessageData
 
setRemovedBy(Integer) - Method in class net.sf.basedb.core.data.MimeTypeData
 
setRemovedBy(Integer) - Method in class net.sf.basedb.core.data.NewsData
 
setRemovedBy(Integer) - Method in class net.sf.basedb.core.data.PlateEventTypeData
 
setRemovedBy(Integer) - Method in class net.sf.basedb.core.data.PlateGeometryData
 
setRemovedBy(Integer) - Method in class net.sf.basedb.core.data.PlatformData
 
setRemovedBy(Integer) - Method in class net.sf.basedb.core.data.PlatformVariantData
 
setRemovedBy(Integer) - Method in class net.sf.basedb.core.data.PluginDefinitionData
 
setRemovedBy(Integer) - Method in class net.sf.basedb.core.data.PluginTypeData
 
setRemovedBy(Integer) - Method in class net.sf.basedb.core.data.ProjectData
 
setRemovedBy(Integer) - Method in class net.sf.basedb.core.data.QuantityData
 
setRemovedBy(Integer) - Method in class net.sf.basedb.core.data.QuotaData
 
setRemovedBy(Integer) - Method in interface net.sf.basedb.core.data.RemovableData
Set the ID of the user that removed this item or null to restore the item.
setRemovedBy(Integer) - Method in class net.sf.basedb.core.data.ReporterTypeData
 
setRemovedBy(Integer) - Method in class net.sf.basedb.core.data.RoleData
 
setRemovedBy(Integer) - Method in class net.sf.basedb.core.data.TransformationData
 
setRemovedBy(Integer) - Method in class net.sf.basedb.core.data.UnitData
 
setRemovedBy(Integer) - Method in class net.sf.basedb.core.data.UserData
 
setRemovedFlag(Removable, boolean) - Static method in class net.sf.basedb.util.RemovableUtil
 
setRemoveJobWhenFinished(boolean) - Method in class net.sf.basedb.core.data.JobData
 
setRemoveJobWhenFinished(boolean) - Method in class net.sf.basedb.core.Job
Set if the job should be deleted after it has finished successfully.
setRenderer(Renderer<?>) - Method in class net.sf.basedb.clients.web.taglib.extensions.Render
 
setRendererFactory(RendererFactory<? super A>) - Method in class net.sf.basedb.util.extensions.ExtensionBean
 
setRendererFactory(RendererFactory<? super A>) - Method in class net.sf.basedb.util.extensions.ExtensionPointBean
 
setReplaceExisting(boolean) - Method in class net.sf.basedb.util.annotations.InheritSpecification
If this flag is set (default=false), existing inherited annotations of the specified annotation type are removed before inheriting new ones.
setReporter(ReporterData) - Method in class net.sf.basedb.core.data.FeatureData
 
setReporter(ReporterData) - Method in class net.sf.basedb.core.data.RawData
 
setReporter(ReporterData) - Method in class net.sf.basedb.core.data.ReporterListScoreData
 
setReporter(ReporterData) - Method in class net.sf.basedb.core.data.WellData
 
setReporter(ReporterData) - Method in class net.sf.basedb.core.Well
Set the reporter of this well.
setReporter(ReporterData) - Method in class net.sf.basedb.util.jep.ReporterFunction
Set a new reporter object that will be used the next time the JEP expression is evaluated.
setReporterAnnotationsWriter(AnnotationWriter) - Method in class net.sf.basedb.util.export.spotdata.BfsExporter
Set the stream were reporter annotations should be written.
setReporterCloneTemplate(ReporterCloneTemplateData) - Method in class net.sf.basedb.core.data.VirtualDbData
 
setReporterId(int) - Method in class net.sf.basedb.core.data.ReporterListScoreData
 
setReporterIndex(int) - Method in class net.sf.basedb.clients.web.ExperimentExplorer
Set the index of the currently viewed reporter.
setReporterList(ReporterListData) - Method in class net.sf.basedb.core.data.ReporterListScoreData
 
setReporterLists(Set<ReporterListData>) - Method in class net.sf.basedb.core.data.ExperimentData
 
setReporterListScores(Map<Integer, ReporterListScoreData>) - Method in class net.sf.basedb.core.data.ReporterListData
 
setReporterListScores(Set<ReporterListScoreData>) - Method in class net.sf.basedb.core.data.ReporterData
 
setReporters(Set<ReporterData>) - Method in class net.sf.basedb.core.data.ReporterTypeData
This is the inverse end.
setReporterType(ReporterData, ReporterType) - Static method in class net.sf.basedb.core.Reporter
Set the reporter type on a reporter data object.
setReporterType(ReporterTypeData) - Method in class net.sf.basedb.core.data.ReporterData
 
setRequired(boolean) - Method in class net.sf.basedb.clients.web.taglib.Select
 
setRequired(boolean) - Method in class net.sf.basedb.core.data.ItemSubtypeFileTypeData
 
setRequired(boolean) - Method in class net.sf.basedb.core.data.PlatformFileTypeData
 
setRequired(boolean) - Method in class net.sf.basedb.core.ItemSubtypeFileType
Set the required flag for this file type.
setRequired(boolean) - Method in class net.sf.basedb.core.PlatformFileType
Set the required flag for this file type.
setRequired(boolean) - Method in class net.sf.basedb.plugins.executor.ParameterDefinition
Set if this parameter should be a required or optional parameter.
setRequiredForMiame(boolean) - Method in class net.sf.basedb.core.AnnotationType
Set if an annotation of this annotation type is required for an item to be compliant with the MIAME recommendation.
setRequiredForMiame(boolean) - Method in class net.sf.basedb.core.data.AnnotationTypeData
 
setRequiresConfiguration(boolean) - Method in class net.sf.basedb.core.data.PluginDefinitionData
 
setRequiresConfiguration(boolean) - Method in class net.sf.basedb.core.PluginDefinition
 
setResetClassLoader(boolean) - Method in class net.sf.basedb.util.extensions.manager.processor.ResetProcessor
This flag controls if the class loader should be reset or not.
setResetErrorFlag(boolean) - Method in class net.sf.basedb.util.extensions.manager.processor.ResetProcessor
This flag controls if the error flag should be reset or not.
setResponseFilter(Filter<HttpResponse>) - Method in class net.sf.basedb.util.uri.http.HttpConnectionManager
Set a filter that will inspect the response before an input stream is returned to the calling code.
setRestrictionParameters(NativeQuery<?>) - Method in class net.sf.basedb.core.AnnotationBetweenRestriction
 
setRestrictionParameters(NativeQuery<?>) - Method in class net.sf.basedb.core.AnnotationInRestriction
 
setRestrictionParameters(NativeQuery<?>) - Method in class net.sf.basedb.core.AnnotationRestriction
Set the value for all parameters defined in the SQL fragment returned by AnnotationRestriction.getRestrictionSql(Query, DbControl).
setRestrictionParameters(NativeQuery<?>) - Method in class net.sf.basedb.core.AnnotationSimpleRestriction
 
setRestrictionParameters(NativeQuery<?>) - Method in class net.sf.basedb.core.HasAnnotationRestriction
 
setResult(boolean, String) - Method in class net.sf.basedb.util.fileset.ValidatingFileSetMember
Set the result of the validation for this file.
setResult(SqlResult, SqlResult) - Method in class net.sf.basedb.clients.web.servlet.PlotServlet.CFSqlResult
 
setResultIntensityTransform(Integer) - Method in class net.sf.basedb.core.data.FormulaData
 
setResultIntensityTransform(IntensityTransform) - Method in class net.sf.basedb.core.Formula
Sets the transform that this formula generates.
setResultSetMapping(String) - Method in class net.sf.basedb.core.hibernate.NativeQueryWrapper
 
setResultTransformer(ResultTransformer) - Method in class net.sf.basedb.core.hibernate.QueryWrapper
Deprecated.
setResyncCloned(boolean) - Method in class net.sf.basedb.util.annotations.InheritSpecification
 
setReturnKeys(boolean) - Method in class net.sf.basedb.util.resources.ResourceBundleWrapper
Set a flag indicating that the various getString() methods should always return the key instead of trying to find a value for it.
setReturnTotalCount(boolean) - Method in class net.sf.basedb.core.AbstractQuery
 
setReturnTotalCount(boolean) - Method in interface net.sf.basedb.core.query.Query
Specify if the query should return a count for the total number of items that would have been returned if the Query.setFirstResult(int) and Query.setMaxResults(int) had been disabled, or if the results are loaded by an iterator where the number of rows not are known beforehand.
setRole(String) - Method in class net.sf.basedb.core.BioPlateEventParticipant
Set the role that the plate has in this event.
setRole(String) - Method in class net.sf.basedb.core.data.BioPlateEventParticipantData
 
setRoleId(int) - Method in class net.sf.basedb.core.data.keyring.RoleKeys
Set the id of the role.
setRoleId(int) - Method in class net.sf.basedb.core.data.keyring.UserRoles
Set the id of the role.
setRoleInactive(int, boolean) - Method in class net.sf.basedb.core.Keyring
Set a roles as inactive (or active).
setRoleInactive(int, boolean) - Method in class net.sf.basedb.core.SessionControl
Set a role as active or inactive.
setRoles(Map<RoleData, Integer>) - Method in class net.sf.basedb.core.data.RoleKeyData
 
setRoles(Set<RoleData>) - Method in class net.sf.basedb.core.data.UserData
 
setRoot(boolean) - Method in class net.sf.basedb.core.data.DerivedBioAssayData
 
setRoot(String) - Method in class net.sf.basedb.util.extensions.xml.PathConverter
Set the value of the root path.
setRootDerivedBioAssays(Set<DerivedBioAssayData>) - Method in class net.sf.basedb.core.data.PhysicalBioAssayData
 
setRootPath(String) - Method in class net.sf.basedb.core.data.FileServerData
 
setRootPath(String) - Method in class net.sf.basedb.core.FileServer
Set the root path that should be added to all URI:s when used with this file server.
setRootPath(String) - Method in class net.sf.basedb.util.uri.ConnectionParameters
 
setRootRawBioAssays(Map<RawBioAssayData, RootRawBioAssayData>) - Method in class net.sf.basedb.core.data.ExperimentData
 
setRow(int) - Method in class net.sf.basedb.clients.web.taglib.table.PropertyFilter
 
setRow(int) - Method in class net.sf.basedb.core.data.BioWellData
 
setRow(int) - Method in class net.sf.basedb.core.data.FeatureData
 
setRow(int) - Method in class net.sf.basedb.core.data.MappingCoordinate
Set the row number.
setRow(int) - Method in class net.sf.basedb.core.data.PlateCoordinate
Set the row number.
setRow(int) - Method in class net.sf.basedb.core.data.WellData
 
setRow(Integer) - Method in class net.sf.basedb.core.data.RawData
 
setRowIndex(int) - Method in class net.sf.basedb.core.PropertyFilter
Only used internally when removing filter rows
setRows(int) - Method in class net.sf.basedb.core.data.PlateGeometryData
 
setRows(int) - Method in class net.sf.basedb.core.PlateGeometry
The number of rows cannot be changed, used at object creation only.
setRowSeparator(String) - Method in class net.sf.basedb.util.excel.XlsxToCsvUtil
Set the row separator.
setRowsperpage(int) - Method in class net.sf.basedb.clients.web.taglib.table.Navigator
 
setRowsperpage(String) - Method in class net.sf.basedb.clients.web.taglib.table.Navigator
 
setRowsPerPage(int) - Method in class net.sf.basedb.core.data.ContextData
 
setRowsPerPage(int) - Method in class net.sf.basedb.core.ItemContext
Set the number of rows the current table page should show.
setSafeResources(String, boolean) - Static method in class net.sf.basedb.clients.web.servlet.ContentSecurityPolicyFilter
Set a flag indicating if resources from the given extension JAR file are should use the regular policy or the 'unsafe-resources' policy.
setSampleSize(int) - Method in class net.sf.basedb.util.AnyToAnyLinkStatistics
 
setSc(SessionControl) - Method in class net.sf.basedb.clients.web.taglib.Page
Set the session control to use in this request.
setSc(SessionControl) - Method in class net.sf.basedb.clients.web.taglib.table.Table
 
setScheduled(String, JobAgent) - Method in class net.sf.basedb.core.Job
Set the job's status to Job.Status.WAITING.
setScheduled(Date) - Method in class net.sf.basedb.core.data.JobData
 
setSchemaVersion(int) - Method in class net.sf.basedb.core.data.SchemaVersionData
 
setSchemaVersion(String, int) - Method in class net.sf.basedb.core.hibernate.SessionFactoryConfiguration
Deprecated.
Set the schema version of the current configuration.
setSchemaVersion(Session, int) - Static method in class net.sf.basedb.core.Update
 
setSchemaVersion(Session, String, int, int) - Static method in class net.sf.basedb.core.Update
Update the database with a new schema version number.
setSchemaVersionInTransaction(Session, int) - Static method in class net.sf.basedb.core.Update
Update the schema version version number using a new transaction.
setScore(Float) - Method in class net.sf.basedb.core.data.ReporterListScoreData
 
setScript(String) - Method in class net.sf.basedb.clients.web.extensions.AbstractJspFactory
Add a reference to a javascript file to the factory.
setScripts(String) - Method in class net.sf.basedb.clients.web.taglib.Head
 
setSection(String) - Method in class net.sf.basedb.core.BioPlate
Set the section within the "storage location" for this bioplate.
setSection(String) - Method in class net.sf.basedb.core.data.BioPlateData
 
setSectionParser(String, BaseFileSectionParser) - Method in class net.sf.basedb.util.basefile.BaseFileParser
Adds a section parser.
setSectionRegexp(Pattern) - Method in class net.sf.basedb.util.parser.FlatFileParser
Set a regular expression that can be matched against the section line.
setSelectdefault(boolean) - Method in class net.sf.basedb.clients.web.taglib.Select
 
setSelectrecent(boolean) - Method in class net.sf.basedb.clients.web.taglib.Select
 
setSender(UserData) - Method in class net.sf.basedb.core.Message
 
setSendMessage(boolean) - Method in class net.sf.basedb.core.data.JobData
 
setSendMessage(boolean) - Method in class net.sf.basedb.core.Job
Set if a message should be sent to owner when the job finishes.
setSendMessagesAsEmail(boolean) - Method in class net.sf.basedb.core.data.UserData
 
setSendMessagesAsEmail(boolean) - Method in class net.sf.basedb.core.User
Set a flag indicating that all messages should also be sent as email.
setSeparator(String) - Method in class net.sf.basedb.clients.web.taglib.table.CellValue
 
setSerializable(int, Serializable) - Method in class net.sf.basedb.core.hibernate.QueryWrapper
Deprecated.
setSerializable(String, Serializable) - Method in class net.sf.basedb.core.hibernate.QueryWrapper
Deprecated.
setServer(String) - Method in class net.sf.basedb.core.data.JobAgentData
 
setServer(String) - Method in class net.sf.basedb.core.data.JobData
 
setServer(String) - Method in class net.sf.basedb.core.JobAgent
Set the name/IP of the server where the job agent is running.
setServerCertificate(byte[]) - Method in class net.sf.basedb.core.data.FileServerData
 
setServerCertificate(byte[]) - Method in class net.sf.basedb.core.FileServer
Set the public server certificate so that BASE can trust https connections to the server.
setServerCertificate(byte[]) - Method in class net.sf.basedb.util.uri.ConnectionParameters
 
setServletContext(ServletContext) - Method in class net.sf.basedb.clients.web.extensions.ServletWrapper
Set the servlet context from the web application.
setSession(SessionData) - Method in class net.sf.basedb.core.data.ChangeHistoryData
 
setSessionId(int) - Method in class net.sf.basedb.core.data.ChangeHistoryData
 
setSessions(Set<SessionData>) - Method in class net.sf.basedb.core.data.ClientData
 
setSessions(Set<SessionData>) - Method in class net.sf.basedb.core.data.UserData
 
setSessions(Set<SessionData>) - Method in class net.sf.basedb.core.data.UserDeviceData
 
setSessionSetting(String, Object) - Method in class net.sf.basedb.core.SessionControl
Set the value of a session setting.
setSetting(String, String) - Method in class net.sf.basedb.core.ItemContext
Set a value.
setSetting(String, String) - Method in class net.sf.basedb.core.Presets.Preset
Set a value for the specified setting.
setSetting(String, String, String) - Method in class net.sf.basedb.clients.web.extensions.ExtensionsControl
Set a configuration setting for an extension.
setSetting(String, String, String) - Method in class net.sf.basedb.util.extensions.manager.Settings
Set a configuration setting for an extension.
setSettings(Map<String, String>) - Method in class net.sf.basedb.core.data.ContextData
 
setSeverity(ValidationRuleAction, Severity) - Method in class net.sf.basedb.util.overview.ValidationOptions
Set a severity level for the specified validation rule.
setShort(int, short) - Method in class net.sf.basedb.core.hibernate.QueryWrapper
Deprecated.
setShort(String, short) - Method in class net.sf.basedb.core.hibernate.QueryWrapper
Deprecated.
setShortName(String) - Method in class net.sf.basedb.core.AnnotationTypeCategory
Set the short name.
setShortName(String) - Method in class net.sf.basedb.core.data.AnnotationTypeCategoryData
 
setShow(String) - Method in class net.sf.basedb.clients.web.taglib.table.ColumnDef
 
setShowclazz(String) - Method in class net.sf.basedb.clients.web.taglib.HideableSection
 
setShowClazz(String) - Method in class net.sf.basedb.clients.web.extensions.section.IncludeContentSectionFactory
 
setShowClazz(String) - Method in class net.sf.basedb.clients.web.extensions.section.SectionBean
 
setSignalReceiver(SignalReceiver) - Method in class net.sf.basedb.clients.jobagent.executors.ThreadJobExecutor
 
setSignalTransporter(Class<? extends SignalTransporter>, String) - Method in class net.sf.basedb.core.Job
Set information needed to create a signal transporter object that can be used to send signals to the plug-in that is currently executing this job.
setSignalTransporter(String) - Method in class net.sf.basedb.core.data.JobData
 
setSize(int) - Method in class net.sf.basedb.core.data.ItemListData
 
setSize(int) - Method in class net.sf.basedb.core.data.PhysicalBioAssayData
 
setSize(int) - Method in class net.sf.basedb.core.data.ReporterListData
 
setSize(int) - Method in class net.sf.basedb.core.PhysicalBioAssay
Set the size of the bioassay.
setSize(long) - Method in class net.sf.basedb.core.data.FileData
 
setSizeAtLastSync(int) - Method in class net.sf.basedb.core.data.ItemListData
 
setSkip(boolean) - Method in class net.sf.basedb.clients.web.taglib.table.Hidden
 
setSmartenum(boolean) - Method in class net.sf.basedb.clients.web.taglib.table.ColumnDef
 
setSnapshotInvalid() - Method in class net.sf.basedb.core.AnnotationSet
Mark the snapshot (if it exists) of this annotation set as invalid.
setSnapshotManager(SnapshotManager) - Method in class net.sf.basedb.util.export.spotdata.AbstractBioAssaySetExporter
Set's the snapshot manager that should be used to load annotation values.
setSnapshotManager(SnapshotManager) - Method in class net.sf.basedb.util.export.spotdata.AbstractFieldConverter
Set a snapshot manager that should be used with annotation-based fields.
setSnapshotManager(SnapshotManager) - Method in class net.sf.basedb.util.export.spotdata.AnnotationAssayField
Set the snapshot manager that should be used to load annotation values.
setSoftware(SoftwareData) - Method in class net.sf.basedb.core.data.DerivedBioAssayData
 
setSoftware(SoftwareData) - Method in class net.sf.basedb.core.data.RawBioAssayData
 
setSoftware(Software) - Method in class net.sf.basedb.core.DerivedBioAssay
Set the Software that was used when creating this bioassay set.
setSoftware(Software) - Method in class net.sf.basedb.core.RawBioAssay
Set the Software used while analysing the scanned images.
setSortable(boolean) - Method in class net.sf.basedb.clients.web.extensions.list.AbstractListColumnBean
 
setSortable(boolean) - Method in class net.sf.basedb.clients.web.taglib.table.ColumnDef
 
setSortable(String) - Method in class net.sf.basedb.clients.web.extensions.list.PropertyPathActionFactory
 
setSortby(String) - Method in class net.sf.basedb.clients.web.taglib.table.Table
 
setSortDirection(int) - Method in class net.sf.basedb.core.data.ContextData
 
setSortDirection(ItemContext.SortDirection) - Method in class net.sf.basedb.core.ItemContext
Set the sort direction (ascending or descending) of the current listing.
setSortproperty(String) - Method in class net.sf.basedb.clients.web.taglib.table.ColumnDef
 
setSortProperty(String) - Method in class net.sf.basedb.clients.web.extensions.list.AbstractListColumnBean
 
setSortProperty(String) - Method in class net.sf.basedb.clients.web.extensions.list.PropertyPathActionFactory
 
setSortProperty(String) - Method in class net.sf.basedb.core.data.ContextData
 
setSortProperty(String) - Method in class net.sf.basedb.core.ItemContext
Set the name of the property that the current listing is sorted by.
setSource(int) - Method in class net.sf.basedb.core.data.AnnotationData
 
setSource(int) - Method in class net.sf.basedb.core.data.annotations.AnnotationLink
 
setSource(BioAssaySet) - Method in class net.sf.basedb.core.Transformation
Set the source bioassayset.
setSource(BioAssaySet) - Method in class net.sf.basedb.util.export.spotdata.AbstractBioAssaySetExporter
Set the bioassay set that is used as a source for the spot data.
setSource(BioMaterial) - Method in class net.sf.basedb.core.BioMaterialEvent
Set a single parent item for this event.
setSource(BioAssaySetData) - Method in class net.sf.basedb.core.data.TransformationData
 
setSourceCoordinate(MappingCoordinate, MappingCoordinate) - Method in class net.sf.basedb.core.PlateMapping
Set the source coordinate for a given destination coordinate.
setSourceCount(int) - Method in class net.sf.basedb.core.data.PlateMappingData
 
setSourceCount(int) - Method in class net.sf.basedb.core.PlateMapping
Set the number of source plates.
setSourceFileWrapper(FileWrapper) - Method in class net.sf.basedb.util.importer.spotdata.BaseFileImporter
Set the source BASEfile to import data from.
setSourceGeometry(PlateGeometryData) - Method in class net.sf.basedb.core.data.PlateMappingData
 
setSourceGeometry(PlateGeometry) - Method in class net.sf.basedb.core.PlateMapping
Set the source geometry.
setSourceIntensityTransform(Integer) - Method in class net.sf.basedb.core.data.FormulaData
 
setSourceIntensityTransform(IntensityTransform) - Method in class net.sf.basedb.core.Formula
Sets the transform that is required on spot data if this formula should generate the correct result.
setSourceItemMustExist(boolean) - Method in class net.sf.basedb.core.SyncFilter
 
setSourceItemTransform(int) - Method in class net.sf.basedb.core.data.ItemListSyncFilterData
 
setSourceItemType(int) - Method in class net.sf.basedb.core.data.ItemListSyncFilterData
 
setSourceMustExist(boolean) - Method in class net.sf.basedb.core.data.ItemListSyncFilterData
 
setSources(Map<BioMaterialData, BioMaterialEventSourceData>) - Method in class net.sf.basedb.core.data.BioMaterialEventData
 
setSpacingX(int) - Method in class net.sf.basedb.core.ArrayDesignBlock
Set the x spacing between the spots in the slide.
setSpacingX(int) - Method in class net.sf.basedb.core.data.ArrayDesignBlockData
 
setSpacingX(Integer) - Method in class net.sf.basedb.plugins.PrintMapFlatFileImporter.MetaBlock
 
setSpacingY(int) - Method in class net.sf.basedb.core.ArrayDesignBlock
Set the y spacing between the spots in the slide.
setSpacingY(int) - Method in class net.sf.basedb.core.data.ArrayDesignBlockData
 
setSpacingY(Integer) - Method in class net.sf.basedb.plugins.PrintMapFlatFileImporter.MetaBlock
 
setSpecialLogger(Class<? extends LoggableData>, EntityLogger) - Method in class net.sf.basedb.core.log.db.DbLogManagerFactory
Register a special logger for entities of the given class.
setSpotIntensityParser(SpotIntensityParser) - Method in class net.sf.basedb.util.importer.spotdata.BaseFileInfo.SpotSectionInfo
Set the spot intensity parser for the section.
setSpots(int) - Method in class net.sf.basedb.core.data.RawBioAssayData
 
setSqlResult(SqlResult) - Method in class net.sf.basedb.util.jep.ChannelFunction
Set a new SqlResult object that will be used the next time the JEP expression is evaluated.
setSqlResult(SqlResult) - Method in class net.sf.basedb.util.jep.ExtraValueFunction
Set a new SqlResult object that will be used the next time the JEP expression is evaluated.
setSqlResult(SqlResult) - Method in class net.sf.basedb.util.jep.RawChannelFunction
Set a new SqlResult object that will be used the next time the JEP expression is evaluated.
setSqlResult(SqlResult) - Method in class net.sf.basedb.util.jep.ScoreFunction
Set a new SqlResult object that will be used the next time the JEP expression is evaluated.
setSshFingerprint(String) - Method in class net.sf.basedb.core.data.FileServerData
 
setSshFingerprint(String) - Method in class net.sf.basedb.core.FileServer
Set the SSH fingerprint for the server.
setSshFingerprint(String) - Method in class net.sf.basedb.util.uri.ConnectionParameters
 
setSshPrivateKey(byte[]) - Method in class net.sf.basedb.core.data.FileServerData
 
setSshPrivateKey(byte[]) - Method in class net.sf.basedb.core.FileServer
Set the private that BASE should use to authenticate with the server when connecting with SSH.
setSshPrivateKey(byte[]) - Method in class net.sf.basedb.util.uri.ConnectionParameters
 
setSshPrivateKeyFormat(String) - Method in class net.sf.basedb.core.data.FileServerData
 
setSshPrivateKeyFormat(String) - Method in class net.sf.basedb.core.FileServer
Set the format of the SSH private key.
setSshPrivateKeyFormat(String) - Method in class net.sf.basedb.util.uri.ConnectionParameters
 
setSshPrivateKeyPassword(String) - Method in class net.sf.basedb.core.data.FileServerData
 
setSshPrivateKeyPassword(String) - Method in class net.sf.basedb.core.FileServer
Set the password that is needed to unlock the SSH private key.
setSshPrivateKeyPassword(String) - Method in class net.sf.basedb.util.uri.ConnectionParameters
 
setStackTrace(String) - Method in class net.sf.basedb.core.data.JobData
 
setStartDate(Date) - Method in class net.sf.basedb.core.data.NewsData
 
setStartDate(Date) - Method in class net.sf.basedb.core.News
Set the start date and time for this item to be published.
setStarted(Class<? extends SignalTransporter>, String) - Method in class net.sf.basedb.core.Job.ProgressReporterImpl
 
setStarted(Date) - Method in class net.sf.basedb.core.data.JobData
 
setStatus(int) - Method in class net.sf.basedb.core.data.JobData
 
setStatus(ExtensionsFile, String) - Method in class net.sf.basedb.util.extensions.manager.ProcessResults
Sets a short overall status message for an entire file.
setStatusMessage(String) - Method in class net.sf.basedb.core.data.JobData
 
setSticky(boolean) - Method in class net.sf.basedb.core.data.NewsData
 
setSticky(boolean) - Method in class net.sf.basedb.core.News
Set the sticky flag for this news item.
setStickyheaders(String) - Method in class net.sf.basedb.clients.web.taglib.table.Table
 
setStorageType(ItemSubtypeData) - Method in class net.sf.basedb.core.data.BioPlateTypeData
 
setStorageType(ItemSubtype) - Method in class net.sf.basedb.core.BioPlateType
Set the subtype of storage location where plates of this type are usually stored.
setString(int, String) - Method in class net.sf.basedb.core.hibernate.QueryWrapper
Deprecated.
setString(String, String) - Method in class net.sf.basedb.core.hibernate.QueryWrapper
Deprecated.
setStringValues(List<String>) - Method in class net.sf.basedb.core.data.annotations.AnnotationLink
 
setStyle(String) - Method in class net.sf.basedb.clients.web.extensions.list.AbstractListColumnBean
 
setStyle(String) - Method in class net.sf.basedb.clients.web.extensions.list.PropertyPathActionFactory
 
setStyle(String) - Method in class net.sf.basedb.clients.web.extensions.login.FieldInfo
 
setStyle(String) - Method in class net.sf.basedb.clients.web.extensions.menu.FixedMenuItemFactory
 
setStyle(String) - Method in class net.sf.basedb.clients.web.extensions.menu.MenuItemBean
 
setStyle(String) - Method in class net.sf.basedb.clients.web.extensions.menu.PermissionMenuItemFactory
Set the style to use in all cases.
setStyle(String) - Method in class net.sf.basedb.clients.web.extensions.section.IncludeContentSectionFactory
 
setStyle(String) - Method in class net.sf.basedb.clients.web.extensions.section.SectionBean
 
setStyle(String) - Method in class net.sf.basedb.clients.web.extensions.tabcontrol.FixedTabFactory
 
setStyle(String) - Method in class net.sf.basedb.clients.web.extensions.tabcontrol.IncludeContentTabFactory
 
setStyle(String) - Method in class net.sf.basedb.clients.web.extensions.tabcontrol.TabBean
 
setStyle(String) - Method in class net.sf.basedb.clients.web.extensions.toolbar.ButtonBean
 
setStyle(String) - Method in class net.sf.basedb.clients.web.extensions.toolbar.FixedButtonFactory
 
setStyle(String) - Method in class net.sf.basedb.clients.web.extensions.toolbar.PermissionButtonFactory
Set the style to use in all cases.
setStyle(String) - Method in class net.sf.basedb.clients.web.taglib.StylableTag
 
setStyle(String) - Method in class net.sf.basedb.clients.web.taglib.tab.Tab
 
setStyle(String) - Method in class net.sf.basedb.clients.web.taglib.table.Cell
 
setStyle(String) - Method in class net.sf.basedb.clients.web.taglib.table.CellValue
 
setStyles(String) - Method in class net.sf.basedb.clients.web.taglib.Head
 
setStylesheet(String) - Method in class net.sf.basedb.clients.web.extensions.AbstractJspFactory
Add a reference to a CSS stylesheet file to the factory.
setSubCategories(Set<AnnotationTypeCategoryData>) - Method in class net.sf.basedb.core.data.ItemSubtypeData
 
setSubCategoriesAnnotationType(AnnotationType) - Method in class net.sf.basedb.core.ItemSubtype
Set an annotation type to use for dividing into sub-categories when mapping to annotation type categories.
setSubCategoriesAnnotationType(AnnotationTypeData) - Method in class net.sf.basedb.core.data.ItemSubtypeData
 
setSubcategory(AnnotationTypeCategory) - Method in class net.sf.basedb.clients.web.taglib.SubtypeSelector
 
setSubCategory(AnnotationTypeCategory, ItemContext.AddFilter) - Method in class net.sf.basedb.core.ItemContext
Set a sub-category to relate to this context.
setSubCategory(AnnotationTypeCategoryData) - Method in class net.sf.basedb.core.data.ContextData
 
setSubCategoryValues(List<?>) - Method in class net.sf.basedb.core.AnnotationTypeCategory
Set the list of values that should be used to match sub-categories.
setSubCategoryValues(ParameterValueData<?>) - Method in class net.sf.basedb.core.data.AnnotationTypeCategoryData
 
setSubclass(String) - Method in class net.sf.basedb.clients.web.taglib.StylableTag
 
setSubclass(String) - Method in class net.sf.basedb.clients.web.taglib.table.Cell
 
setSubcontext(String) - Method in class net.sf.basedb.clients.web.taglib.table.Table
 
setSubContext(String) - Method in class net.sf.basedb.core.data.ContextData
 
setSubContext(String) - Method in class net.sf.basedb.core.data.ContextIndex
 
setSubContext(String) - Method in class net.sf.basedb.core.data.JobData
 
setSubdirectories(Set<DirectoryData>) - Method in class net.sf.basedb.core.data.DirectoryData
 
setSubid(String) - Method in class net.sf.basedb.clients.web.taglib.menu.Submenu
 
setSubmenuId(String) - Method in class net.sf.basedb.clients.web.extensions.menu.FixedMenuItemFactory
 
setSubmenuId(String) - Method in class net.sf.basedb.clients.web.extensions.menu.MenuItemBean
 
setSubmenuId(String) - Method in class net.sf.basedb.clients.web.extensions.menu.PermissionMenuItemFactory
 
setSubtitle(String) - Method in class net.sf.basedb.clients.web.extensions.list.AbstractListColumnBean
 
setSubtitle(String) - Method in class net.sf.basedb.clients.web.extensions.list.PropertyPathActionFactory
 
setSubtitle(String) - Method in class net.sf.basedb.clients.web.taglib.table.ColumnDef
 
setSubtype(String) - Method in class net.sf.basedb.util.bfs.MetadataModel
Set the subtype of the BFS.
setSubtype(String) - Method in class net.sf.basedb.util.bfs.MetadataWriter
Set the BFS subtype for this writer.
setSubtypes(List<ItemSubtype>) - Method in class net.sf.basedb.clients.web.taglib.SubtypeSelector
 
setSuffix(String) - Method in class net.sf.basedb.clients.web.taglib.table.CellValue
 
setSuffix(String) - Method in class net.sf.basedb.util.bfs.SequenceFilenameGenerator
Set the suffix that is used for file name generation.
setSuggestedJobName(String) - Method in interface net.sf.basedb.core.plugin.Response
A plug-in may call this method on it's job configuration phase to suggest a name for the job.
setSuggestedJobName(String) - Method in class net.sf.basedb.core.PluginResponse.ResponseImpl
 
setSuggestedJobName(String) - Method in class net.sf.basedb.plugins.executor.ExternalProgramExecutor.ResponseWrapper
 
setSummary(String) - Method in class net.sf.basedb.util.extensions.manager.ProcessResults
Set a summary of the results.
setSupportsConfigurations(boolean) - Method in class net.sf.basedb.core.data.PluginDefinitionData
 
setSupportsConfigurations(boolean) - Method in class net.sf.basedb.core.PluginDefinition
 
setSupportsDeviceVerification(boolean) - Method in class net.sf.basedb.core.Client
 
setSupportsDeviceVerification(boolean) - Method in class net.sf.basedb.core.data.ClientData
 
setSymbol(String) - Method in class net.sf.basedb.core.data.ReporterData
 
setSymbol(String) - Method in class net.sf.basedb.core.data.UnitSymbolData
 
setSymbols(Set<String>) - Method in class net.sf.basedb.core.Unit
Set the symbols that should be registered for this unit.
setSymbols(Set<UnitSymbolData>) - Method in class net.sf.basedb.core.data.QuantityData
 
setSymbols(Set<UnitSymbolData>) - Method in class net.sf.basedb.core.data.UnitData
 
setSyncContext(ItemContext, SyncFilter.SourceItemTransform) - Method in class net.sf.basedb.core.SyncFilter
Copy filters and other settings from the given context to this synchronization filter.
setSyncDate(Date) - Method in class net.sf.basedb.core.data.ItemListData
 
setSyncFilters(Set<ItemListSyncFilterData>) - Method in class net.sf.basedb.core.data.ItemListData
 
setSystemId(String) - Method in class net.sf.basedb.core.BioPlateEventType
 
setSystemId(String) - Method in class net.sf.basedb.core.data.BioPlateEventTypeData
 
setSystemId(String) - Method in class net.sf.basedb.core.data.DirectoryData
 
setSystemId(String) - Method in class net.sf.basedb.core.data.GroupData
 
setSystemId(String) - Method in class net.sf.basedb.core.data.ItemSubtypeData
 
setSystemId(String) - Method in class net.sf.basedb.core.data.QuantityData
 
setSystemId(String) - Method in class net.sf.basedb.core.data.QuotaData
 
setSystemId(String) - Method in class net.sf.basedb.core.data.QuotaTypeData
 
setSystemId(String) - Method in class net.sf.basedb.core.data.RoleData
 
setSystemId(String) - Method in class net.sf.basedb.core.data.UserData
 
setTabcontrol(String) - Method in class net.sf.basedb.clients.web.taglib.Help
 
setTabindex(int) - Method in class net.sf.basedb.clients.web.taglib.Button
 
setTabindex(int) - Method in class net.sf.basedb.clients.web.taglib.Help
 
setTabindex(int) - Method in class net.sf.basedb.clients.web.taglib.Icon
 
setTabindex(int) - Method in class net.sf.basedb.clients.web.taglib.Input
 
setTabindex(int) - Method in class net.sf.basedb.clients.web.taglib.Select
 
setTabindex(int) - Method in class net.sf.basedb.clients.web.taglib.tab.Tab
 
setTabindex(int) - Method in class net.sf.basedb.clients.web.taglib.table.Button
 
setTabindex(int) - Method in class net.sf.basedb.clients.web.taglib.Zoom
 
setTabIndex(int) - Method in class net.sf.basedb.clients.web.extensions.tabcontrol.TabBean
 
setTabIndex(int) - Method in class net.sf.basedb.clients.web.extensions.toolbar.ButtonBean
 
setTabIndex(int) - Method in class net.sf.basedb.clients.web.extensions.toolbar.FixedButtonFactory
 
setTabIndex(String) - Method in class net.sf.basedb.clients.web.extensions.tabcontrol.FixedTabFactory
 
setTabIndex(String) - Method in class net.sf.basedb.clients.web.extensions.tabcontrol.IncludeContentTabFactory
 
setTable(String) - Method in class net.sf.basedb.clients.web.taglib.SubtypeSelector
 
setTag(TagData) - Method in class net.sf.basedb.core.data.ExtractData
 
setTag(Tag) - Method in class net.sf.basedb.core.Extract
Set the tag that was applied to this extract in order to be able to distinguish it from other extracts on a physical bioassay.
setTarget(ScriptTargetOutput) - Method in class net.sf.basedb.core.hibernate.DbIndexWork
Set a target for receiving information about SQL statements that are needed to create missing foreign keys and indexes.
setTargetType(Item) - Method in class net.sf.basedb.util.AnyToAnyLinkStatistics
 
setTemporary(boolean) - Method in class net.sf.basedb.core.PropertyFilter
Set or clear a flag indicating that this filter is temporary filter.
setText(int, String) - Method in class net.sf.basedb.core.hibernate.QueryWrapper
Deprecated.
setText(String, String) - Method in class net.sf.basedb.core.hibernate.QueryWrapper
Deprecated.
setTextarea(String) - Method in class net.sf.basedb.clients.web.taglib.CalendarButton
 
setTextarea(String) - Method in class net.sf.basedb.clients.web.taglib.Zoom
 
setTextValues(List<String>) - Method in class net.sf.basedb.core.data.annotations.AnnotationLink
 
setTheId(int) - Method in class net.sf.basedb.core.RawDataBatcher.FeatureProxy
 
setTheId(int) - Method in class net.sf.basedb.util.importer.spotdata.BaseFileImporter.RawDataProxy
 
setTheId(int) - Method in class net.sf.basedb.util.importer.spotdata.BaseFileImporter.ReporterProxy
 
setTheId(int, String) - Method in class net.sf.basedb.core.RawDataBatcher.ReporterProxy
 
setThousandsSeparator(SessionControl, Character) - Static method in class net.sf.basedb.clients.web.formatter.FormatterSettings
Set the separator character to use as a "thousands" separator in large numbers.
setTime(int, Date) - Method in class net.sf.basedb.core.hibernate.QueryWrapper
Deprecated.
setTime(String, Date) - Method in class net.sf.basedb.core.hibernate.QueryWrapper
Deprecated.
setTime(Date) - Method in class net.sf.basedb.core.data.ChangeHistoryData
 
setTimeout(int) - Method in class net.sf.basedb.core.hibernate.NativeQueryWrapper
 
setTimeout(int) - Method in class net.sf.basedb.core.hibernate.QueryWrapper
 
setTimeout(int) - Method in class net.sf.basedb.util.uri.http.HttpConnectionManager
Set a timeout in seconds to allocate for the request to return (not including downloading of data).
setTimeSent(Date) - Method in class net.sf.basedb.core.data.MessageData
 
setTimestamp(int, Date) - Method in class net.sf.basedb.core.hibernate.QueryWrapper
Deprecated.
setTimestamp(String, Date) - Method in class net.sf.basedb.core.hibernate.QueryWrapper
Deprecated.
setTimestampFormat(Formatter<Date>) - Method in class net.sf.basedb.util.excel.XlsxToCsvUtil
Set a date formatter to use for formatting cells with timestamp-like values.
setTimestampValues(List<Date>) - Method in class net.sf.basedb.core.data.annotations.AnnotationLink
 
setTimstampFormat(String) - Method in class net.sf.basedb.util.excel.AutoFormatter
Set the data format template to use for timestamp values.
Setting - Class in net.sf.basedb.core
This is the base class for all setting items.
Setting(SettingData) - Constructor for class net.sf.basedb.core.Setting
 
SETTING - Enum constant in enum class net.sf.basedb.core.Item
The item is an Setting.
SettingData - Class in net.sf.basedb.core.data
 
SettingData() - Constructor for class net.sf.basedb.core.data.SettingData
 
SettingInfo(String, boolean) - Constructor for class net.sf.basedb.core.SessionControl.SettingInfo
 
settings - Variable in class net.sf.basedb.clients.jobagent.JobRunner
 
settings - Static variable in class net.sf.basedb.clients.web.extensions.ExtensionsControl
 
settings - Variable in class net.sf.basedb.clients.web.extensions.service.ServicesEventHandler
 
settings - Variable in class net.sf.basedb.core.data.ContextData
 
settings - Variable in class net.sf.basedb.core.ItemContext
 
settings - Variable in class net.sf.basedb.core.Presets.Preset
The key-value pairs in this preset.
settings - Variable in class net.sf.basedb.util.extensions.manager.ExtensionsManager
 
settings - Variable in class net.sf.basedb.util.extensions.manager.filter.InstalledFilter
 
settings - Variable in class net.sf.basedb.util.extensions.manager.Settings
 
Settings - Class in net.sf.basedb.util.extensions.manager
Class for keeping settings for the extensions system.
Settings(ExtensionsManager, File) - Constructor for class net.sf.basedb.util.extensions.manager.Settings
Create a new Settings object.
setTitle(String) - Method in class net.sf.basedb.clients.web.extensions.list.AbstractListColumnBean
 
setTitle(String) - Method in class net.sf.basedb.clients.web.extensions.list.PropertyPathActionFactory
 
setTitle(String) - Method in class net.sf.basedb.clients.web.extensions.menu.FixedMenuItemFactory
 
setTitle(String) - Method in class net.sf.basedb.clients.web.extensions.menu.MenuItemBean
 
setTitle(String) - Method in class net.sf.basedb.clients.web.extensions.menu.PermissionMenuItemFactory
Set the title of the menu item in all cases.
setTitle(String) - Method in class net.sf.basedb.clients.web.extensions.plot.OverviewPlotBean
 
setTitle(String) - Method in class net.sf.basedb.clients.web.extensions.plot.PlotGeneratorBean
 
setTitle(String) - Method in class net.sf.basedb.clients.web.extensions.section.IncludeContentSectionFactory
 
setTitle(String) - Method in class net.sf.basedb.clients.web.extensions.section.SectionBean
 
setTitle(String) - Method in class net.sf.basedb.clients.web.extensions.tabcontrol.FixedTabFactory
 
setTitle(String) - Method in class net.sf.basedb.clients.web.extensions.tabcontrol.IncludeContentTabFactory
 
setTitle(String) - Method in class net.sf.basedb.clients.web.extensions.tabcontrol.TabBean
 
setTitle(String) - Method in class net.sf.basedb.clients.web.extensions.toolbar.ButtonBean
 
setTitle(String) - Method in class net.sf.basedb.clients.web.extensions.toolbar.FixedButtonFactory
 
setTitle(String) - Method in class net.sf.basedb.clients.web.extensions.toolbar.PermissionButtonFactory
Set the title of the button in all cases.
setTitle(String) - Method in class net.sf.basedb.clients.web.taglib.Button
 
setTitle(String) - Method in class net.sf.basedb.clients.web.taglib.CalendarButton
The title attribute now goes into the calendar popup dialog instead.
setTitle(String) - Method in class net.sf.basedb.clients.web.taglib.HideableSection
 
setTitle(String) - Method in class net.sf.basedb.clients.web.taglib.Input
 
setTitle(String) - Method in class net.sf.basedb.clients.web.taglib.menu.Menuitem
 
setTitle(String) - Method in class net.sf.basedb.clients.web.taglib.menu.Submenu
 
setTitle(String) - Method in class net.sf.basedb.clients.web.taglib.Page
 
setTitle(String) - Method in class net.sf.basedb.clients.web.taglib.path.PathElement
 
setTitle(String) - Method in class net.sf.basedb.clients.web.taglib.tab.Tab
 
setTitle(String) - Method in class net.sf.basedb.clients.web.taglib.table.Button
 
setTitle(String) - Method in class net.sf.basedb.clients.web.taglib.table.ColumnDef
 
setTitle(String) - Method in class net.sf.basedb.clients.web.taglib.table.Label
 
setTitle(String) - Method in class net.sf.basedb.clients.web.taglib.table.Table
 
setTitle(String) - Method in class net.sf.basedb.clients.web.taglib.Zoom
 
setTitle(String) - Method in class net.sf.basedb.core.data.ExperimentData
 
setTitle(String) - Method in class net.sf.basedb.core.data.ReporterClonePropertyData
 
setTitle(String) - Method in class net.sf.basedb.core.Experiment
Set the title for the publication of this experiment.
setTitle(String) - Method in class net.sf.basedb.util.export.spotdata.AnnotationAssayField
Set a custom title for the assay field.
setTitle(String) - Method in class net.sf.basedb.util.export.spotdata.AssayPropertyField
Set the title of the exported property.
setTitle(String) - Method in class net.sf.basedb.util.export.spotdata.JepDynamicField
Set the column header title.
setTitle(String) - Method in class net.sf.basedb.util.export.spotdata.SimpleDynamicField
Set the column header title.
setTo(BasicItem) - Method in class net.sf.basedb.core.AnyToAny
Set the destination item of the link.
setTo(UserData) - Method in class net.sf.basedb.core.data.MessageData
 
setTo(UserData) - Method in class net.sf.basedb.core.Message
Set the user this message should be sent to.
setToId(int) - Method in class net.sf.basedb.core.data.AnyToAnyData
 
setToken(String) - Method in class net.sf.basedb.core.data.UserDeviceData
 
setTooltip(String) - Method in class net.sf.basedb.clients.web.extensions.list.AbstractListColumnBean
 
setTooltip(String) - Method in class net.sf.basedb.clients.web.extensions.list.PropertyPathActionFactory
 
setTooltip(String) - Method in class net.sf.basedb.clients.web.extensions.login.FieldInfo
 
setTooltip(String) - Method in class net.sf.basedb.clients.web.extensions.menu.FixedMenuItemFactory
 
setTooltip(String) - Method in class net.sf.basedb.clients.web.extensions.menu.MenuItemBean
 
setTooltip(String) - Method in class net.sf.basedb.clients.web.extensions.menu.PermissionMenuItemFactory
Set the tooltip of the menu item in all cases.
setTooltip(String) - Method in class net.sf.basedb.clients.web.extensions.tabcontrol.FixedTabFactory
 
setTooltip(String) - Method in class net.sf.basedb.clients.web.extensions.tabcontrol.IncludeContentTabFactory
 
setTooltip(String) - Method in class net.sf.basedb.clients.web.extensions.tabcontrol.TabBean
 
setTooltip(String) - Method in class net.sf.basedb.clients.web.extensions.toolbar.ButtonBean
 
setTooltip(String) - Method in class net.sf.basedb.clients.web.extensions.toolbar.FixedButtonFactory
 
setTooltip(String) - Method in class net.sf.basedb.clients.web.extensions.toolbar.PermissionButtonFactory
Set the tooltip of the button in all cases.
setTooltip(String) - Method in class net.sf.basedb.clients.web.taglib.Button
 
setTooltip(String) - Method in class net.sf.basedb.clients.web.taglib.Help
 
setTooltip(String) - Method in class net.sf.basedb.clients.web.taglib.Icon
 
setTooltip(String) - Method in class net.sf.basedb.clients.web.taglib.menu.Menuitem
 
setTooltip(String) - Method in class net.sf.basedb.clients.web.taglib.menu.Submenu
 
setTooltip(String) - Method in class net.sf.basedb.clients.web.taglib.path.PathElement
 
setTooltip(String) - Method in class net.sf.basedb.clients.web.taglib.PropertyValue
 
setTooltip(String) - Method in class net.sf.basedb.clients.web.taglib.tab.Tab
 
setTooltip(String) - Method in class net.sf.basedb.clients.web.taglib.table.Button
 
setTooltip(String) - Method in class net.sf.basedb.clients.web.taglib.table.ColumnDef
 
setTooltip(String) - Method in class net.sf.basedb.clients.web.taglib.table.Label
 
setTooltip(String) - Method in class net.sf.basedb.clients.web.taglib.Zoom
 
setTotalrows(int) - Method in class net.sf.basedb.clients.web.taglib.table.Navigator
 
setTotalrows(long) - Method in class net.sf.basedb.clients.web.taglib.table.Navigator
 
setTotalrows(String) - Method in class net.sf.basedb.clients.web.taglib.table.Navigator
 
setToType(int) - Method in class net.sf.basedb.core.data.AnyToAnyData
 
setTransferredBytes(long) - Method in class net.sf.basedb.clients.web.fileupload.FileUploadProgress
Sets the number of transferred bytes.
setTransformation(TransformationData) - Method in class net.sf.basedb.core.data.BioAssaySetData
 
setTransformation(Transformation) - Method in class net.sf.basedb.core.BioAssaySet
Set the transformation that created this bioassayset.
setTransformation(Transformation) - Method in class net.sf.basedb.util.importer.spotdata.BaseFileImporter
Set the destination transformation.
setTransformation(Transformation) - Method in class net.sf.basedb.util.importer.spotdata.BfsImporter
Set the destination transformation.
setTransformations(Set<TransformationData>) - Method in class net.sf.basedb.core.data.BioAssaySetData
 
setTransformations(Set<TransformationData>) - Method in class net.sf.basedb.core.data.ExperimentData
 
setTransformations(Set<TransformationData>) - Method in class net.sf.basedb.core.data.JobData
 
setTransformations(Set<TransformationData>) - Method in class net.sf.basedb.core.data.RawBioAssayData
 
setTray(String) - Method in class net.sf.basedb.core.BioPlate
Set the tray within the "storage location" for this bioplate.
setTray(String) - Method in class net.sf.basedb.core.data.BioPlateData
 
setTrimQuotes(boolean) - Method in class net.sf.basedb.util.parser.FlatFileParser
Set if quotes around each data value should be removed or not.
setTrimWhiteSpace(boolean) - Method in class net.sf.basedb.util.parser.FlatFileParser
Set a flag indicating if white-space should be trimmed from start and end of data values.
setTrusted(boolean) - Method in class net.sf.basedb.core.data.PluginDefinitionData
 
setTrusted(boolean) - Method in class net.sf.basedb.core.PluginDefinition
Set if this plugin should be trusted or not.
setTrusted(Boolean) - Method in class net.sf.basedb.core.data.JobAgentSettingsData
 
setTrusted(Boolean) - Method in class net.sf.basedb.core.JobAgentSettings
Set the trusted flag for this plugin.
setType(int) - Method in class net.sf.basedb.core.data.FormulaData
 
setType(int) - Method in class net.sf.basedb.core.data.JobData
 
setType(String) - Method in class net.sf.basedb.clients.web.extensions.menu.FixedMenuItemFactory
 
setType(String) - Method in class net.sf.basedb.clients.web.extensions.menu.PermissionMenuItemFactory
Set the type of menu.
setType(String) - Method in class net.sf.basedb.clients.web.taglib.Input
 
setType(String) - Method in class net.sf.basedb.clients.web.taglib.menu.Menu
 
setType(String) - Method in class net.sf.basedb.clients.web.taglib.Page
 
setType(String) - Method in class net.sf.basedb.plugins.executor.ParameterDefinition
Set the type of the parameter.
setType(MenuItemAction.MenuType) - Method in class net.sf.basedb.clients.web.extensions.menu.FixedMenuItemFactory
 
setType(MenuItemAction.MenuType) - Method in class net.sf.basedb.clients.web.extensions.menu.MenuItemBean
 
setType(MenuItemAction.MenuType) - Method in class net.sf.basedb.clients.web.extensions.menu.PermissionMenuItemFactory
Set the type of the menu.
setType(Plugin.MainType) - Method in class net.sf.basedb.util.extensions.xml.PluginInfo
 
setType(Type) - Method in class net.sf.basedb.core.query.QueryParameter
Changes the type of the parameter.
setType(Type) - Method in class net.sf.basedb.util.export.spotdata.AssayPropertyField
Set the data type of the exported property.
setType(Type) - Method in class net.sf.basedb.util.export.spotdata.JepDynamicField
Set the data type of the exported field.
setType(Type) - Method in class net.sf.basedb.util.export.spotdata.SimpleDynamicField
Set the data type of the exported field.
setUninstalled() - Method in class net.sf.basedb.util.extensions.manager.ExtensionsFile.WriteableExtensionsFile
Mark the file as uninstalled.
setUninstalledFile(File) - Method in class net.sf.basedb.util.extensions.manager.Settings
Mark the given file as uninstalled.
setUnit(UnitData) - Method in class net.sf.basedb.core.data.AnnotationData
 
setUnit(UnitData) - Method in class net.sf.basedb.core.data.PropertyFilterData
 
setUnit(UnitData) - Method in class net.sf.basedb.core.data.UnitSymbolData
 
setUnit(Unit) - Method in class net.sf.basedb.clients.web.taglib.table.ColumnDef
 
setUnit(Unit) - Method in class net.sf.basedb.core.PropertyFilter
Sets the unit the values for the property are stored in the database.
setUnits(Set<UnitData>) - Method in class net.sf.basedb.core.data.QuantityData
 
setUnselectedtext(String) - Method in class net.sf.basedb.clients.web.taglib.Select
 
setUpdateSource(String) - Method in class net.sf.basedb.core.ReporterBatcher
Set the source that was used when updating the reporters.
setUpErrorHandling() - Method in class net.sf.basedb.plugins.AbstractFlatFileImporter
Initialise the error handling system.
setUpErrorHandling() - Method in class net.sf.basedb.plugins.AnnotationFlatFileImporter
Don't use AbstractFlatFileImporter to handle errors.
setUpErrorHandling() - Method in class net.sf.basedb.plugins.batchimport.AbstractItemImporter
Don't use AbstractFlatFileImporter to handle errors.
setUrl(String) - Method in class net.sf.basedb.clients.web.extensions.plot.PlotGeneratorBean
 
setUrl(String) - Method in class net.sf.basedb.clients.web.extensions.startpage.FixedStartPageFactory
 
setUrl(String) - Method in class net.sf.basedb.clients.web.extensions.startpage.StartPageBean
 
setUrl(String) - Method in class net.sf.basedb.clients.web.taglib.menu.Menuitem
 
setUrl(String) - Method in class net.sf.basedb.core.authentication.ExtraUserInformation
 
setUrl(String) - Method in class net.sf.basedb.core.data.FileData
 
setUrl(String) - Method in class net.sf.basedb.core.data.PluginDefinitionData
 
setUrl(String) - Method in class net.sf.basedb.core.data.UserData
 
setUrl(String) - Method in class net.sf.basedb.core.PluginDefinition
Set the URL to a web page with more information about the plug-in.
setUrl(String) - Method in class net.sf.basedb.core.User
Set the URL to the user's homepage, or null if unknown.
setUrl(String) - Method in class net.sf.basedb.util.extensions.AboutBean
 
setUrl(String, boolean) - Method in class net.sf.basedb.core.File
Set the URL to an external file that should represent this file object.
setUrl(String, UriMetadata) - Method in class net.sf.basedb.core.File
Set the URL to an external file that should represent this file object and update the metadata without going to the remote server.
setUsableUnits(Set<UnitData>) - Method in class net.sf.basedb.core.data.AnnotationTypeData
 
setUseClonedReporters(boolean) - Method in interface net.sf.basedb.core.ClonableReporterQuery
Set if cloned reporters should be used by default or not.
setUseClonedReporters(boolean) - Method in class net.sf.basedb.core.DynamicQuery
Set if cloned reporters should be used by default or not.
setUseClonedReporters(boolean) - Method in class net.sf.basedb.core.DynamicReporterQuery
Set if cloned reporters should be used by default or not.
setUseDeviceVerification(boolean) - Method in class net.sf.basedb.core.data.UserData
 
setUseDeviceVerification(boolean) - Method in class net.sf.basedb.core.User
Enable or disable device verification for this user account.
setUsedQuantity(Float) - Method in class net.sf.basedb.core.BioMaterialEvent
Set the used quantity.
setUsedQuantity(Float) - Method in class net.sf.basedb.core.BioMaterialEventSource
Set the quantity that was used from the source biomaterial by the event.
setUsedQuantity(Float) - Method in class net.sf.basedb.core.data.BioMaterialEventData
 
setUsedQuantity(Float) - Method in class net.sf.basedb.core.data.BioMaterialEventSourceData
 
setUsedUnits(Set<AnnotationTypeData>) - Method in class net.sf.basedb.core.data.UnitData
 
setUseInternalJobQueue(boolean) - Method in class net.sf.basedb.core.data.PluginDefinitionData
 
setUseInternalJobQueue(boolean) - Method in class net.sf.basedb.core.PluginDefinition
Set if the plug-in can use the internal job queue or not.
setUseNullIfEmpty(boolean) - Method in class net.sf.basedb.util.parser.FlatFileParser
Specify if null values should be returned instead of empty strings for columns that doesn't contain any value.
setUseNullIfException(boolean) - Method in class net.sf.basedb.util.parser.FlatFileParser
Specify if null should be returned if a (numeric) value can't be parsed.
setUseNullIfNull(boolean) - Method in class net.sf.basedb.util.parser.FlatFileParser
Specify if null values should be returned for strings having the value "NULL" (ignoring case).
setUseNullLoaderIfNotFound(boolean) - Method in class net.sf.basedb.util.overview.loader.BasicItemNodeLoaderFactory
Set a flag that determines if a NullNodeLoader should be used or if an ItemNotFoundException should be thrown if no registered node loader is found for a specific key.
setUsePermissions(boolean) - Method in class net.sf.basedb.core.data.PluginDefinitionData
 
setUsePermissions(boolean) - Method in class net.sf.basedb.core.PluginDefinition
 
setUser(UserData) - Method in class net.sf.basedb.core.data.BioMaterialEventData
 
setUser(UserData) - Method in class net.sf.basedb.core.data.ChangeHistoryData
 
setUser(UserData) - Method in class net.sf.basedb.core.data.ContextData
 
setUser(UserData) - Method in class net.sf.basedb.core.data.DiskUsageData
 
setUser(UserData) - Method in class net.sf.basedb.core.data.PasswordData
 
setUser(UserData) - Method in class net.sf.basedb.core.data.PlateEventData
 
setUser(UserData) - Method in class net.sf.basedb.core.data.SessionData
 
setUser(UserData) - Method in class net.sf.basedb.core.data.UserClientSettingData
 
setUser(UserData) - Method in class net.sf.basedb.core.data.UserDefaultSettingData
 
setUser(UserData) - Method in class net.sf.basedb.core.data.UserDeviceData
 
setUser(User) - Method in class net.sf.basedb.core.UserClientSetting
Set the user this setting is valid for.
setUser(User) - Method in class net.sf.basedb.core.UserDefaultSetting
Set the user this setting is valid for.
setUserAgent(String) - Method in class net.sf.basedb.core.data.UserDeviceData
 
setUserClientSetting(String, String) - Method in class net.sf.basedb.core.SessionControl
Set the value of a UserClientSetting.
setUserDefaultSetting(String, String) - Method in class net.sf.basedb.core.SessionControl
Set the value of a UserDefaultSetting.
setUserId(int) - Method in class net.sf.basedb.core.authentication.LoginRequest
Set the user id to use.
setUserId(int) - Method in class net.sf.basedb.core.data.ChangeHistoryData
 
setUserId(int) - Method in class net.sf.basedb.core.data.keyring.UserGroups
Set the id of the user.
setUserId(int) - Method in class net.sf.basedb.core.data.keyring.UserKeys
Set the id of the user.
setUserId(int) - Method in class net.sf.basedb.core.data.keyring.UserProjects
Set the id of the user.
setUserId(int) - Method in class net.sf.basedb.core.data.keyring.UserRoles
Set the id of the user.
setUsername(String) - Method in class net.sf.basedb.core.data.FileServerData
 
setUsername(String) - Method in class net.sf.basedb.core.FileServer
Set the username that is required to authenticate with the file server.
setUsername(String) - Method in class net.sf.basedb.util.uri.ConnectionParameters
 
setUsers(Map<UserData, Integer>) - Method in class net.sf.basedb.core.data.ItemKeyData
 
setUsers(Map<UserData, Integer>) - Method in class net.sf.basedb.core.data.ProjectData
 
setUsers(Set<UserData>) - Method in class net.sf.basedb.core.data.GroupData
 
setUsers(Set<UserData>) - Method in class net.sf.basedb.core.data.RoleData
 
setUserSettings(Set<UserClientSettingData>) - Method in class net.sf.basedb.core.data.ClientData
 
setUseSeparateConnections(boolean) - Method in class net.sf.basedb.core.hibernate.SessionFactoryConfiguration
Deprecated.
Set to TRUE to use connections separate from BASE connections.
setUseSeparateConnections(boolean) - Method in class net.sf.basedb.core.ServiceSessionControl.SessionFactoryConfiguration
Set to TRUE to use connections separate from BASE connections.
setUsingColors(boolean) - Method in class net.sf.basedb.core.Coloring
Specifiy if colors should be used when displaying values for this item or not.
setUsingColors(boolean) - Method in class net.sf.basedb.core.data.ColoringData
 
setUsingTo(boolean) - Method in class net.sf.basedb.core.AnyToAny
If this link counts as using the destination item.
setUsingTo(boolean) - Method in class net.sf.basedb.core.data.AnyToAnyData
 
setUsNullValidatorIfNotFound(boolean) - Method in class net.sf.basedb.util.overview.validator.BasicItemNodeValidatorFactory
Set a flag that determines if a NullNodeValidator should be used or if an ItemNotFoundException should be thrown if no registered node validator is found for a specific key.
setValid(Boolean) - Method in class net.sf.basedb.core.data.FileSetMemberData
 
setValid(Boolean, String) - Method in class net.sf.basedb.core.FileSetMember
Set the validation status of this member.
setValue(int) - Method in class net.sf.basedb.clients.web.taglib.Input
 
setValue(Object) - Method in class net.sf.basedb.clients.web.taglib.table.Cell
 
setValue(Object) - Method in class net.sf.basedb.clients.web.taglib.table.CellValue
 
setValue(Object) - Method in class net.sf.basedb.core.query.QueryParameter
Change the value of the parameter.
setValue(String) - Method in class net.sf.basedb.clients.web.taglib.Input
 
setValue(String) - Method in class net.sf.basedb.clients.web.taglib.table.Hidden
 
setValue(String) - Method in class net.sf.basedb.core.data.PropertyFilterData
 
setValue(String) - Method in class net.sf.basedb.core.data.SettingData
 
setValue(String) - Method in class net.sf.basedb.core.PropertyFilter
Set the value to use in the filter.
setValue(String) - Method in class net.sf.basedb.core.Setting
Set the value for this setting.
setValue(String, ParameterType<T>, T) - Method in class net.sf.basedb.core.ParameterValuesImpl
 
setValue(String, ParameterType<T>, T) - Method in class net.sf.basedb.core.plugin.NamespaceParameterValuesWrapper
 
setValue(String, ParameterType<T>, T) - Method in interface net.sf.basedb.core.plugin.ParameterValues
Set a single value for a parameter.
setValue(String, ParameterType<T>, T) - Method in class net.sf.basedb.core.plugin.ParameterValuesWrapper
Set the value on either the job or configuration, depending in the preferJob parameter that was set when creating this object.
setValue(String, ParameterType<T>, T) - Method in class net.sf.basedb.plugins.gtf.DefaultConfigurationValues
 
setValue(AnnotationType, Object, Unit, boolean) - Method in class net.sf.basedb.core.AnnotationBatcher
Add, update or delete a single-valued annotation.
setValueId(int) - Method in class net.sf.basedb.core.data.annotations.AnnotationLink
 
setValueIfDifferent(Object, Unit) - Method in class net.sf.basedb.core.Annotation
Set the value of the annotation, replacing any previous values if they are different.
setValues(String, ParameterType<T>, List<T>) - Method in class net.sf.basedb.core.ParameterValuesImpl
 
setValues(String, ParameterType<T>, List<T>) - Method in class net.sf.basedb.core.plugin.NamespaceParameterValuesWrapper
 
setValues(String, ParameterType<T>, List<T>) - Method in interface net.sf.basedb.core.plugin.ParameterValues
Set a list of values for a parameter.
setValues(String, ParameterType<T>, List<T>) - Method in class net.sf.basedb.core.plugin.ParameterValuesWrapper
Set the value on either the job or configuration, depending in the preferJob parameter that was set when creating this object.
setValues(String, ParameterType<T>, List<T>) - Method in class net.sf.basedb.plugins.gtf.DefaultConfigurationValues
 
setValues(List<?>) - Method in class net.sf.basedb.core.AnnotationType
Set the list of allowed values for an enumerated annotation type.
setValues(List<?>) - Method in class net.sf.basedb.plugins.executor.ProgramParameter
 
setValues(List<Boolean>) - Method in class net.sf.basedb.core.data.BooleanParameterValueData
 
setValues(List<Double>) - Method in class net.sf.basedb.core.data.DoubleParameterValueData
 
setValues(List<Float>) - Method in class net.sf.basedb.core.data.FloatParameterValueData
 
setValues(List<Integer>) - Method in class net.sf.basedb.core.data.IntegerParameterValueData
 
setValues(List<Long>) - Method in class net.sf.basedb.core.data.LongParameterValueData
 
setValues(List<String>) - Method in class net.sf.basedb.core.data.StringParameterValueData
 
setValues(List<String>) - Method in class net.sf.basedb.core.data.TextParameterValueData
 
setValues(List<Date>) - Method in class net.sf.basedb.core.data.DateParameterValueData
 
setValues(List<Date>) - Method in class net.sf.basedb.core.data.TimestampParameterValueData
 
setValues(List<BasicData>) - Method in class net.sf.basedb.core.data.ItemParameterValueData
 
setValues(List<T>) - Method in class net.sf.basedb.core.data.ParameterValueData
Set values of this parameter.
setValues(AnnotationType, List<?>, Unit, boolean) - Method in class net.sf.basedb.core.AnnotationBatcher
Add, update or delete annotation values for the current item.
setValues(ParameterValueData<?>) - Method in class net.sf.basedb.core.data.AnnotationData
 
setValuesIfDifferent(List<?>, Unit) - Method in class net.sf.basedb.core.Annotation
Set the values of the annotation, replacing any previous values if they are different.
setValueType(int) - Method in class net.sf.basedb.core.data.AnnotationTypeData
 
setValueType(int) - Method in class net.sf.basedb.core.data.DataCubeExtraValueData
 
setValueType(int) - Method in class net.sf.basedb.core.data.ExtraValueTypeData
 
setValueType(int) - Method in class net.sf.basedb.core.data.PropertyFilterData
 
setValueType(int) - Method in class net.sf.basedb.core.data.ReporterClonePropertyData
 
setValueType(Integer) - Method in class net.sf.basedb.core.data.FormulaData
 
setValueType(String) - Method in class net.sf.basedb.clients.web.extensions.list.PropertyPathActionFactory
 
setValueType(Type) - Method in class net.sf.basedb.clients.web.extensions.list.AbstractListColumnBean
 
setValueType(Type) - Method in class net.sf.basedb.clients.web.taglib.table.ColumnDef
 
setValueType(Type) - Method in class net.sf.basedb.core.DataCubeExtraValue
Set the value type.
setValueType(Type) - Method in class net.sf.basedb.core.ExtraValueType
Set the value type for this extra value type.
setValueType(Type) - Method in class net.sf.basedb.core.Formula
Set the type of the values that this formula produces.
setValueType(Type) - Method in class net.sf.basedb.core.PropertyFilter
Set the type of the property.
setVariable(String, String) - Method in class net.sf.basedb.util.extensions.xml.VariableConverter
Set the value of a variable.
setVariant(PlatformVariantData) - Method in class net.sf.basedb.core.data.ArrayDesignData
 
setVariant(PlatformVariantData) - Method in class net.sf.basedb.core.data.FileTypeIndex
 
setVariant(PlatformVariantData) - Method in class net.sf.basedb.core.data.PlatformFileTypeData
 
setVariant(PlatformVariantData) - Method in class net.sf.basedb.core.data.RawBioAssayData
 
setVariant(PlatformVariant) - Method in class net.sf.basedb.core.ArrayDesign
Set the platform and variant of the array design.
setVariant(PlatformVariant, RawDataType) - Method in class net.sf.basedb.core.RawBioAssay
Set the platform and variant of the raw bioassay.
setVariants(Set<PlatformVariantData>) - Method in class net.sf.basedb.core.data.PlatformData
 
setVerified(boolean) - Method in class net.sf.basedb.core.data.UserDeviceData
 
setVerifyOnly(boolean) - Method in class net.sf.basedb.core.authentication.LoginRequest
Set a flag to indicate if the login request should only verify the login parameters and not do a full login.
setVersion(int) - Method in class net.sf.basedb.core.data.BasicData
Set the version of the item.
setVersion(int) - Method in class net.sf.basedb.core.data.VersionedParameter
 
setVersion(String) - Method in class net.sf.basedb.util.extensions.AboutBean
 
setVersionString(String) - Method in class net.sf.basedb.core.data.HardwareData
 
setVersionString(String) - Method in class net.sf.basedb.core.data.PluginDefinitionData
 
setVersionString(String) - Method in class net.sf.basedb.core.data.SoftwareData
 
setVersionString(String) - Method in class net.sf.basedb.core.Hardware
Set the versionstring for this Hardware item.
setVersionString(String) - Method in class net.sf.basedb.core.PluginDefinition
Update version information for this plug-in.
setVersionString(String) - Method in class net.sf.basedb.core.Software
Set the versionstring for this Software item.
setVertical(boolean) - Method in class net.sf.basedb.clients.web.taglib.ButtonGroup
 
setVirtualDb(VirtualDbData) - Method in class net.sf.basedb.core.data.DataCubeData
 
setVirtualDb(VirtualDbData) - Method in class net.sf.basedb.core.data.ExperimentData
 
setVirtualDb(VirtualDb) - Method in class net.sf.basedb.core.DataCube
Set the experiment.
setVisible(boolean) - Method in class net.sf.basedb.clients.web.extensions.menu.FixedMenuItemFactory
 
setVisible(boolean) - Method in class net.sf.basedb.clients.web.extensions.menu.MenuItemBean
 
setVisible(boolean) - Method in class net.sf.basedb.clients.web.extensions.tabcontrol.FixedTabFactory
 
setVisible(boolean) - Method in class net.sf.basedb.clients.web.extensions.tabcontrol.IncludeContentTabFactory
 
setVisible(boolean) - Method in class net.sf.basedb.clients.web.extensions.tabcontrol.TabBean
 
setVisible(boolean) - Method in class net.sf.basedb.clients.web.extensions.toolbar.ButtonBean
 
setVisible(boolean) - Method in class net.sf.basedb.clients.web.extensions.toolbar.FixedButtonFactory
 
setVisible(boolean) - Method in class net.sf.basedb.clients.web.taglib.Button
 
setVisible(boolean) - Method in class net.sf.basedb.clients.web.taglib.Help
 
setVisible(boolean) - Method in class net.sf.basedb.clients.web.taglib.HideableSection
 
setVisible(boolean) - Method in class net.sf.basedb.clients.web.taglib.Icon
 
setVisible(boolean) - Method in class net.sf.basedb.clients.web.taglib.Input
 
setVisible(boolean) - Method in class net.sf.basedb.clients.web.taglib.menu.Menuitem
 
setVisible(boolean) - Method in class net.sf.basedb.clients.web.taglib.menu.Menuseparator
 
setVisible(boolean) - Method in class net.sf.basedb.clients.web.taglib.menu.Submenu
 
setVisible(boolean) - Method in class net.sf.basedb.clients.web.taglib.path.PathElement
 
setVisible(boolean) - Method in class net.sf.basedb.clients.web.taglib.Select
 
setVisible(boolean) - Method in class net.sf.basedb.clients.web.taglib.tab.Tab
 
setVisible(boolean) - Method in class net.sf.basedb.clients.web.taglib.table.Button
 
setVisible(boolean) - Method in class net.sf.basedb.clients.web.taglib.table.Cell
 
setVisible(boolean) - Method in class net.sf.basedb.clients.web.taglib.table.Header
 
setVisible(boolean) - Method in class net.sf.basedb.clients.web.taglib.table.Label
 
setVisible(boolean) - Method in class net.sf.basedb.clients.web.taglib.table.Navigator
 
setVisible(boolean) - Method in class net.sf.basedb.clients.web.taglib.table.Panel
 
setVisible(boolean) - Method in class net.sf.basedb.clients.web.taglib.table.PresetSelector
 
setVisible(boolean) - Method in class net.sf.basedb.clients.web.taglib.table.Row
 
setVisible(boolean) - Method in class net.sf.basedb.clients.web.taglib.table.Toolbar
 
setVisible(boolean) - Method in class net.sf.basedb.clients.web.taglib.Zoom
 
setVisible(String) - Method in class net.sf.basedb.clients.web.extensions.menu.FixedMenuItemFactory
 
setVisible(String) - Method in class net.sf.basedb.clients.web.extensions.tabcontrol.FixedTabFactory
 
setVisible(String) - Method in class net.sf.basedb.clients.web.extensions.tabcontrol.IncludeContentTabFactory
 
setVisible(String) - Method in class net.sf.basedb.clients.web.extensions.toolbar.FixedButtonFactory
 
setVisiblePermission(String) - Method in class net.sf.basedb.clients.web.extensions.menu.PermissionMenuItemFactory
Set the minimum permission that is required to make the menu item visible.
setVisiblePermission(String) - Method in class net.sf.basedb.clients.web.extensions.toolbar.PermissionButtonFactory
Set the minimum permission that is required to make the button visible.
setWarnings(int) - Method in class net.sf.basedb.util.overview.Node
Set the number of warnings that was found while validating this node.
setWell(WellData) - Method in class net.sf.basedb.core.data.FeatureData
 
setWells(Map<PlateCoordinate, WellData>) - Method in class net.sf.basedb.core.data.PlateData
 
setWidth(int) - Method in class net.sf.basedb.clients.web.extensions.plot.PlotGeneratorBean
 
setWidth(int) - Method in class net.sf.basedb.clients.web.taglib.table.Form
 
setWidth(int) - Method in class net.sf.basedb.core.AnnotationType
Set the recommended width in characters a client application should use to render an input field for annotations of this annotation type.
setWidth(int) - Method in class net.sf.basedb.core.data.AnnotationTypeData
 
setWidth(String) - Method in class net.sf.basedb.clients.web.extensions.plot.MAPlotFactory
 
setWorkerThread() - Method in class net.sf.basedb.core.signal.EnhancedThreadSignalHandler
Set the worker thread to the current thread.
setWorkerThread(Thread) - Method in class net.sf.basedb.core.signal.ThreadSignalHandler
Set the worker thread that should be interrupted when a signal is receiver.
setWrapper(WrappingRenderer<?>) - Method in class net.sf.basedb.clients.web.taglib.extensions.Render
 
setWriteProtected(boolean) - Method in class net.sf.basedb.core.data.FileData
 
setWriteProtected(boolean) - Method in class net.sf.basedb.core.File
Set the write protected flag for this file.
setWriter(BaseFileWriter) - Method in class net.sf.basedb.util.export.spotdata.BaseFileExporter
Set the stream were the exported data should be written.
setWriteTrailingColumns(boolean) - Method in class net.sf.basedb.util.excel.XlsxToCsvUtil
 
setX(Float) - Method in class net.sf.basedb.core.data.RawData
 
setY(Float) - Method in class net.sf.basedb.core.data.RawData
 
severities - Variable in class net.sf.basedb.util.overview.ValidationOptions
Maps Validator ID to severity.
Severity - Enum Class in net.sf.basedb.util.overview
Severity levels for a validation rule.
Severity(String) - Constructor for enum class net.sf.basedb.util.overview.Severity
 
sf - Static variable in class net.sf.basedb.core.HibernateUtil
The single SessionFactory.
SHA256_FINGERPRINT_PATTERN - Static variable in class net.sf.basedb.core.FileServer
Pattern that matches a SSH SHa256 fingerprint in BASE64 encoding (padding is optional).
SHARE_TO_EVERYONE - Enum constant in enum class net.sf.basedb.core.Permission
This permission allows a user to share an item to the Group.EVERYONE group.
shareable - Static variable in class net.sf.basedb.core.Item.DefinedPermissions
 
Shareable - Interface in net.sf.basedb.core
An Shareable item is an item which can be shared to other User:s, Group:s and Project:s.
shareable_annotatable - Static variable in class net.sf.basedb.core.Item.DefinedPermissions
 
SHAREABLE_FILTER - Static variable in class net.sf.basedb.core.QueryRuntimeFilterFactory
 
ShareableData - Interface in net.sf.basedb.core.data
A shareable item is an item which can be shared to other users, groups or projects.
ShareableFilter() - Constructor for class net.sf.basedb.core.QueryRuntimeFilterFactory.ShareableFilter
 
shareableItems - Static variable in class net.sf.basedb.core.Metadata
 
ShareableUtil - Class in net.sf.basedb.core
Utility methods that will make it easier to implement the Shareable interface, including data validation.
ShareableUtil - Class in net.sf.basedb.util
 
ShareableUtil() - Constructor for class net.sf.basedb.core.ShareableUtil
 
ShareableUtil() - Constructor for class net.sf.basedb.util.ShareableUtil
 
SHARED - Enum constant in enum class net.sf.basedb.core.Include
Include items shared to the logged in user.
SharedData - Class in net.sf.basedb.core.data
This class extends the OwnedData class and implements the ShareableData interface.
SharedData() - Constructor for class net.sf.basedb.core.data.SharedData
 
SharedItem - Class in net.sf.basedb.core
This class inherits from the OwnedItem class and implements the Shareable interface.
SharedItem(SharedData) - Constructor for class net.sf.basedb.core.SharedItem
 
sharedTo - Variable in class net.sf.basedb.core.query.SharedToRestriction
 
sharedTo(boolean, Restriction, Restriction, Restriction) - Static method in class net.sf.basedb.core.query.Hql
A special restriction that works on Shareable items.
SharedToRestriction - Class in net.sf.basedb.core.query
A special restriction that works on Shareable items.
SharedToRestriction(boolean, Restriction, Restriction, Restriction) - Constructor for class net.sf.basedb.core.query.SharedToRestriction
 
shareRecursively(DbControl, Directory) - Static method in class net.sf.basedb.core.ShareableUtil
Share all files and sub-directories in the given directory with the same permissions.
sheet - Variable in class net.sf.basedb.clients.web.plugins.XlsxTemplate
 
sheet - Variable in class net.sf.basedb.util.excel.XlsxTableWriter
 
sheet - Variable in class net.sf.basedb.util.excel.XlsxToCsvUtil.SheetInfo
 
sheet - Variable in class net.sf.basedb.util.parser.FlatFileParser.ExcelData
 
SheetInfo(Sheet) - Constructor for class net.sf.basedb.util.excel.XlsxToCsvUtil.SheetInfo
 
sheetNames - Variable in class net.sf.basedb.util.excel.XlsxToCsvUtil
 
sheets - Variable in class net.sf.basedb.util.excel.XlsxToCsvUtil
 
SHORT - Enum constant in enum class net.sf.basedb.core.Job.ExecutionTime
The job shouldn't take more than 10 minutes to execute.
SHORT - Static variable in class net.sf.basedb.core.hibernate.TypeWrapper
 
SHORTEST - Enum constant in enum class net.sf.basedb.core.Job.ExecutionTime
The job is fast and should not take more than a minute to execute.
shortName - Variable in class net.sf.basedb.core.data.AnnotationTypeCategoryData
 
ShortWriter - Class in net.sf.basedb.core.migrate
Database-independent writer implementation that writes short values from a result set.
ShortWriter(ResultSet, int, Writer, char[]) - Constructor for class net.sf.basedb.core.migrate.ShortWriter
 
shouldManageNamespaces() - Method in class net.sf.basedb.core.hibernate.SchemaGenerator.CollectSqlTarget
 
shouldSend(EventType, ExtensionPoint<?>, Extension<?>) - Method in class net.sf.basedb.util.extensions.events.ActionClassEventFilter
 
shouldSend(EventType, ExtensionPoint<?>, Extension<?>) - Method in class net.sf.basedb.util.extensions.events.AllEventsFilter
 
shouldSend(EventType, ExtensionPoint<?>, Extension<?>) - Method in class net.sf.basedb.util.extensions.events.CombiningEventFilter
 
shouldSend(EventType, ExtensionPoint<?>, Extension<?>) - Method in interface net.sf.basedb.util.extensions.events.EventFilter
Determine if the event should be sent to the event handler or not.
shouldSend(EventType, ExtensionPoint<?>, Extension<?>) - Method in class net.sf.basedb.util.extensions.events.EventTypeFilter
 
shouldSend(EventType, ExtensionPoint<?>, Extension<?>) - Method in class net.sf.basedb.util.extensions.events.ExtensionEventFilter
 
shouldSend(EventType, ExtensionPoint<?>, Extension<?>) - Method in class net.sf.basedb.util.extensions.events.ExtensionPointEventFilter
 
show - Variable in class net.sf.basedb.clients.web.taglib.table.ColumnDef
If the column should be visible or not.
show - Variable in class net.sf.basedb.clients.web.taglib.table.TableColumn
 
showChangeHistoryTab(SessionControl) - Static method in class net.sf.basedb.clients.web.ChangeHistoryUtil
Check if the "Change history" tab should be visible for the current user or not.
showClass - Variable in class net.sf.basedb.clients.web.taglib.HideableSection
 
showClazz - Variable in class net.sf.basedb.clients.web.extensions.section.IncludeContentSectionFactory
 
showClazz - Variable in class net.sf.basedb.clients.web.extensions.section.SectionBean
 
showInitially - Variable in class net.sf.basedb.clients.web.taglib.HideableSection
If the section should be shown or hidden to start with.
shutdown(CloseableHttpClient) - Static method in class net.sf.basedb.util.HttpUtil
Safely shuts down a http client and it's connection manager without trowing an exception.
SHUTDOWN - Static variable in class net.sf.basedb.core.signal.Signal
The SHUTDOWN signal, that requests that the receiver should clean up and die.
ShutdownHook(SignalReceiver) - Constructor for class net.sf.basedb.clients.jobagent.executors.ThreadJobExecutor.ShutdownHook
 
ShutdownSignalSender - Class in net.sf.basedb.core.signal
A signal sender implementation that is used by the system when shutting down.
ShutdownSignalSender() - Constructor for class net.sf.basedb.core.signal.ShutdownSignalSender
 
signal - Variable in class net.sf.basedb.core.signal.ExtensionSignalTransporter.SendSignalRenderer
 
signal - Variable in class net.sf.basedb.core.signal.SimpleSignalSender
 
signal - Variable in exception net.sf.basedb.core.signal.UnsupportedSignalException
 
Signal - Class in net.sf.basedb.core.signal
Represents a signal that can be sent to a class implementing the SignalTarget interface.
Signal(String, String, String) - Constructor for class net.sf.basedb.core.signal.Signal
 
SignalException - Exception in net.sf.basedb.core.signal
Base class for all signal exceptions.
SignalException() - Constructor for exception net.sf.basedb.core.signal.SignalException
 
SignalException(String) - Constructor for exception net.sf.basedb.core.signal.SignalException
 
SignalException(String, Throwable) - Constructor for exception net.sf.basedb.core.signal.SignalException
 
SignalException(Throwable) - Constructor for exception net.sf.basedb.core.signal.SignalException
 
signalHandler - Variable in class net.sf.basedb.clients.jobagent.executors.ProcessJobExecutor
 
signalHandler - Variable in class net.sf.basedb.clients.web.plugins.SimpleExport
 
signalHandler - Variable in class net.sf.basedb.plugins.AbstractFlatFileImporter
 
signalHandler - Variable in class net.sf.basedb.plugins.Base1PluginExecuter
 
signalHandler - Variable in class net.sf.basedb.plugins.BaseFileExporterPlugin
 
signalHandler - Variable in class net.sf.basedb.plugins.BfsExporterPlugin
 
signalHandler - Variable in class net.sf.basedb.plugins.CdfFileReporterImporter
 
signalHandler - Variable in class net.sf.basedb.plugins.CloneReportersPlugin
 
signalHandler - Variable in class net.sf.basedb.plugins.executor.ExternalProgramExecutor
 
signalHandler - Variable in class net.sf.basedb.plugins.FormulaFilter
 
signalHandler - Variable in class net.sf.basedb.plugins.GalExporter
 
signalHandler - Variable in class net.sf.basedb.plugins.HelpExporter
 
signalHandler - Variable in class net.sf.basedb.plugins.HelpImporter
 
signalHandler - Variable in class net.sf.basedb.plugins.IntensityCalculatorPlugin
 
signalHandler - Variable in class net.sf.basedb.plugins.JepExtraValueCalculator
 
signalHandler - Variable in class net.sf.basedb.plugins.JepIntensityTransformer
 
signalHandler - Variable in class net.sf.basedb.plugins.LowessNormalization
 
signalHandler - Variable in class net.sf.basedb.plugins.MedianRatioNormalization
 
signalHandler - Variable in class net.sf.basedb.plugins.PackedFileExporter
 
signalHandler - Variable in class net.sf.basedb.plugins.PlateMappingExporter
 
signalHandler - Variable in class net.sf.basedb.plugins.PluginConfigurationExporter
 
signalHandler - Variable in class net.sf.basedb.plugins.PluginConfigurationImporter
 
signalHandler - Variable in class net.sf.basedb.util.zip.AbstractFileUnpacker
 
SignalHandler - Interface in net.sf.basedb.core.signal
A signal handler is an object that is able to receive and act on signals.
signalHandlerURI - Variable in class net.sf.basedb.core.signal.AbstractSignalTransporter
 
SignalKeyring() - Constructor for class net.sf.basedb.core.Job.SignalKeyring
 
SignalReceivedException - Exception in net.sf.basedb.core.signal
This exception can be thrown by signal handlers when one or more signal has been received.
SignalReceivedException(List<Signal>) - Constructor for exception net.sf.basedb.core.signal.SignalReceivedException
Create a new SignalReceivedException when multiple signals has been received.
SignalReceivedException(Signal) - Constructor for exception net.sf.basedb.core.signal.SignalReceivedException
Create a new UnsupportedSignalException.
SignalReceivedException(Signal...) - Constructor for exception net.sf.basedb.core.signal.SignalReceivedException
Create a new SignalReceivedException when multiple signals has been received.
signalReceiver - Variable in class net.sf.basedb.clients.jobagent.Agent
 
signalReceiver - Variable in class net.sf.basedb.clients.jobagent.executors.ProcessJobExecutor
 
signalReceiver - Variable in class net.sf.basedb.clients.jobagent.executors.ThreadJobExecutor.ShutdownHook
 
signalReceiver - Variable in class net.sf.basedb.clients.jobagent.executors.ThreadJobExecutor
 
signalReceiver - Variable in class net.sf.basedb.clients.jobagent.handlers.SignalRequestHandler
 
signalReceiver - Static variable in class net.sf.basedb.core.InternalJobQueue
Use the local signal receiver only.
signalReceiver - Variable in class net.sf.basedb.core.PluginExecutionRequest
 
SignalReceiver - Interface in net.sf.basedb.core.signal
A signal receiver is a class that knows how to receive a Signal from a SignalTransporter and how to distribute this to a SignalHandler.
SignalRequestHandler - Class in net.sf.basedb.clients.jobagent.handlers
This is a request handler for the signal commands.
SignalRequestHandler(Agent) - Constructor for class net.sf.basedb.clients.jobagent.handlers.SignalRequestHandler
 
signals - Variable in class net.sf.basedb.core.signal.AbstractSignalTransporter
 
signals - Static variable in class net.sf.basedb.core.signal.Signal
Holds all registered signals.
signals - Variable in exception net.sf.basedb.core.signal.SignalReceivedException
 
SignalSender - Interface in net.sf.basedb.core.signal
A signal sender is responsible for sending a signal to a signal handler.
SignalTarget - Interface in net.sf.basedb.core.signal
This interface should be implemented by classes that are able to receive Signal:s.
signalTransporter - Variable in class net.sf.basedb.core.data.JobData
 
signalTransporter - Variable in class net.sf.basedb.core.Job
 
SignalTransporter - Interface in net.sf.basedb.core.signal
A signal transporter is a class that knows how to send a signal to a specific SignalReceiver implementation.
silent - Variable in class net.sf.basedb.core.hibernate.DbIndexWork
 
simple(Expression, String, Type, Formula.AverageMethod, Formatter<?>) - Static method in class net.sf.basedb.util.export.spotdata.ExportableFieldFactory
Create a simple dynamic field.
SimpleAbsoluteProgressReporter - Class in net.sf.basedb.core
This is a simple implementation of the AbsoluteProgressReporter interface, which simply remembers that last values.
SimpleAbsoluteProgressReporter(ProgressReporter, long) - Constructor for class net.sf.basedb.core.SimpleAbsoluteProgressReporter
Create a new absolute progress reporter.
SimpleDynamicField - Class in net.sf.basedb.util.export.spotdata
Represents an exported data field.
SimpleDynamicField() - Constructor for class net.sf.basedb.util.export.spotdata.SimpleDynamicField
Create a new object.
SimpleErrorHandler - Class in net.sf.basedb.util.error
A simple error handler that either ignores all errors or re-throws them.
SimpleErrorHandler(boolean) - Constructor for class net.sf.basedb.util.error.SimpleErrorHandler
Create a new simple error handler.
SimpleExport - Class in net.sf.basedb.clients.web.plugins
Export plugin for exporting data from table listings in the web client.
SimpleExport() - Constructor for class net.sf.basedb.clients.web.plugins.SimpleExport
 
SimpleJepFunction - Class in net.sf.basedb.util.jep
A simple base class for registering a JEP function by name and number of parameters.
SimpleJepFunction(String, int) - Constructor for class net.sf.basedb.util.jep.SimpleJepFunction
 
SimpleProgressReporter - Class in net.sf.basedb.core
This is a simple implementation of the ProgressReporter interface, which simply remembers that last values.
SimpleProgressReporter(ProgressReporter) - Constructor for class net.sf.basedb.core.SimpleProgressReporter
Create a new simple progress reporter.
SimpleSignalProgressReporter - Class in net.sf.basedb.clients.web.util
This class can be used to report progress and hold signal receiver for those export plugins that download immediately.
SimpleSignalProgressReporter(ProgressReporter) - Constructor for class net.sf.basedb.clients.web.util.SimpleSignalProgressReporter
 
SimpleSignalSender - Class in net.sf.basedb.core.signal
A signal sender implementation that sends a specific signal to all handlers that supports it.
SimpleSignalSender(Signal) - Constructor for class net.sf.basedb.core.signal.SimpleSignalSender
Create a new signal sender.
SimpleStringDetector - Class in net.sf.basedb.util.charset
A simple string detector implementation that works with two strings.
SimpleStringDetector(String, String) - Constructor for class net.sf.basedb.util.charset.SimpleStringDetector
 
SINGLE_QUOTE - Static variable in class net.sf.basedb.clients.web.util.HTML
 
SingleExtensionFilter - Class in net.sf.basedb.util.extensions
A filter implementation that enables a single extension and disables all other.
SingleExtensionFilter(String) - Constructor for class net.sf.basedb.util.extensions.SingleExtensionFilter
Create a filter that enables the extension with the given ID and disables all others.
SingleExtensionFilter(Extension<?>) - Constructor for class net.sf.basedb.util.extensions.SingleExtensionFilter
Create a filter that enables the given extension and disables all other.
SingleFileValidationAction - Class in net.sf.basedb.util.fileset
Base class for validators that works on single files of a known data file type.
SingleFileValidationAction(String) - Constructor for class net.sf.basedb.util.fileset.SingleFileValidationAction
Create a new instance.
size - Variable in class net.sf.basedb.core.data.FileData
 
size - Variable in class net.sf.basedb.core.data.ItemListData
 
size - Variable in class net.sf.basedb.core.data.PhysicalBioAssayData
 
size - Variable in class net.sf.basedb.core.data.ReporterListData
 
size - Variable in class net.sf.basedb.core.dbengine.TableInfo.ColumnInfo
 
size - Variable in class net.sf.basedb.core.hibernate.TypeWrapper
 
size - Variable in class net.sf.basedb.core.log.EntityLogOptions
 
size - Variable in class net.sf.basedb.core.MigrateRbaToDba.Itemlist
 
size - Variable in class net.sf.basedb.core.VirtualColumn
The size of the column if it is a string.
size - Variable in class net.sf.basedb.util.JarClassLoader.JarInfo
 
size() - Method in class net.sf.basedb.clients.web.extensions.skin.ImageRemapper
Get the number of remapped images.
size() - Method in class net.sf.basedb.core.AnyToAny.FastLinkLoader
Number of items that matches.
size() - Method in class net.sf.basedb.core.GroupPermissions
Get the number of entries.
size() - Method in class net.sf.basedb.core.ItemResultList
 
size() - Method in class net.sf.basedb.core.Presets.Preset
Get the number of settings in the preset.
size() - Method in class net.sf.basedb.core.ProjectPermissions
Get the number of entries.
size() - Method in class net.sf.basedb.core.UserPermissions
Get the number of entries.
size() - Method in class net.sf.basedb.util.Enumeration
 
size() - Method in class net.sf.basedb.util.formatter.LookupFormatter
Get the number of registered lookup entries.
size() - Method in class net.sf.basedb.util.Tree
 
size(String) - Method in class net.sf.basedb.util.StaticCache
Checks the size (in bytes) of a cache entry.
size(String, String) - Static method in class net.sf.basedb.core.query.Hql
Create a size expression for a property that is a collection of values.
sizeAtLastSync - Variable in class net.sf.basedb.core.data.ItemListData
 
sizeColumnMapping - Static variable in class net.sf.basedb.plugins.batchimport.PhysicalBioAssayImporter
 
sizeMapper - Variable in class net.sf.basedb.plugins.batchimport.PhysicalBioAssayImporter
 
sizeOf(Object) - Method in enum class net.sf.basedb.core.Type
Get the size in bytes an object of this type requires when stored in the database.
SkinAction - Interface in net.sf.basedb.clients.web.extensions.skin
Action for adding skins to BASE.
skinActions - Variable in class net.sf.basedb.clients.web.taglib.Page
 
skinContext - Variable in class net.sf.basedb.clients.web.taglib.Page
 
skip - Variable in class net.sf.basedb.clients.web.taglib.table.Hidden
If the hidden element should be included or not.
skip(long) - Method in class net.sf.basedb.util.InputStreamCombiner
 
skip(long) - Method in class net.sf.basedb.util.InputStreamSplitter
 
skip(long) - Method in class net.sf.basedb.util.InputStreamTracker
 
skipInsertIfMissingFeature - Variable in class net.sf.basedb.core.RawDataBatcher
If inserts that can't find a matching feature should be skipped or generate an error.
skipInsertIfMissingFeature(boolean) - Method in class net.sf.basedb.core.RawDataBatcher
Specify if the insert method should skip the insert if a feature for the spot can't be found.
skipNull - Variable in class net.sf.basedb.util.formatter.CollectionFormatter
 
skippedLast - Variable in class net.sf.basedb.plugins.batchimport.AbstractItemImporter
 
skippedLines - Variable in class net.sf.basedb.plugins.AbstractFlatFileImporter
 
skippedLines - Variable in class net.sf.basedb.util.parser.FlatFileParser
List for keeping ignored and unknown lines in the FlatFileParser.nextData() method.
skipRepeatedTranscriptIds - Variable in class net.sf.basedb.util.gtf.GtfInputStream
 
SLIDES - Enum constant in enum class net.sf.basedb.plugins.PrintMapFlatFileImporter.Section
 
slot - Variable in class net.sf.basedb.clients.jobagent.slotmanager.MasterSlotManager.RemoteSlot
 
slot - Variable in class net.sf.basedb.core.InternalJobQueue.JobRunner
 
slot - Variable in class net.sf.basedb.util.jobagent.JobInfo
 
Slot - Class in net.sf.basedb.clients.jobagent.slotmanager
Represents a slot that has been assigned to a job.
Slot(String, Job.ExecutionTime) - Constructor for class net.sf.basedb.clients.jobagent.slotmanager.Slot
Create a new slot.
Slot(Job.ExecutionTime) - Constructor for class net.sf.basedb.clients.jobagent.slotmanager.Slot
Create a new slot and automatically assign an id to it.
slotManager - Variable in class net.sf.basedb.clients.jobagent.Agent
 
SlotManager - Interface in net.sf.basedb.clients.jobagent.slotmanager
A slot manager is responsible for slot assigment to jobs.
slotManagerClass - Variable in class net.sf.basedb.clients.jobagent.Agent
 
SMART_IMAGES - Static variable in class net.sf.basedb.clients.web.util.HTML
This flag is used in HTML.scanForLinks(String,int) when you want to create links for images with a <img> tag instead of an <a> tag.
smartEnum - Variable in class net.sf.basedb.clients.web.taglib.table.ColumnDef
 
snapshotIsInvalid - Variable in class net.sf.basedb.core.AnnotationSet
Flag to indicate if this annotation set has been modified and the snapshot must be removed.
snapshotManager - Variable in class net.sf.basedb.clients.web.ExperimentExplorer
The snapshot manager that loads annotation values.
snapshotManager - Variable in class net.sf.basedb.clients.web.plugins.BioAssayExperimentalFactorLoader
 
snapshotManager - Variable in class net.sf.basedb.util.annotations.InheritAnnotationsManager
 
snapshotManager - Variable in class net.sf.basedb.util.export.spotdata.AbstractBioAssaySetExporter
 
snapshotManager - Variable in class net.sf.basedb.util.export.spotdata.AbstractFieldConverter
 
snapshotManager - Variable in class net.sf.basedb.util.export.spotdata.AnnotationAssayField
 
snapshotManager - Variable in class net.sf.basedb.util.overview.GenericOverview
 
SnapshotManager - Class in net.sf.basedb.core.snapshot
Manager for annotation snapshots.
SnapshotManager() - Constructor for class net.sf.basedb.core.snapshot.SnapshotManager
Create a new snapshot manager.
snapshots - Variable in class net.sf.basedb.core.snapshot.AnnotationLoaderUtil
 
snapshots - Variable in class net.sf.basedb.core.snapshot.SnapshotManager
 
snapshotsToDelete - Variable in class net.sf.basedb.core.AnnotationBatcher
 
socket - Variable in class net.sf.basedb.core.signal.SocketSignalReceiver.ListenerThread
 
socket - Variable in class net.sf.basedb.util.jobagent.JobAgentServerConnection.ListenerThread
 
SocketSignalReceiver - Class in net.sf.basedb.core.signal
A signal receiver implementation that listens on a socket for incoming signals.
SocketSignalReceiver() - Constructor for class net.sf.basedb.core.signal.SocketSignalReceiver
Create a new socket signal receiver.
SocketSignalReceiver.ListenerThread - Class in net.sf.basedb.core.signal
This class is used for listening to the specified socket for incoming connections.
SocketSignalTransporter - Class in net.sf.basedb.core.signal
 
SocketSignalTransporter() - Constructor for class net.sf.basedb.core.signal.SocketSignalTransporter
Create a new socket signal transporter.
SocketUtil - Class in net.sf.basedb.util
This class contains some useful methods when working with sockets.
SocketUtil() - Constructor for class net.sf.basedb.util.SocketUtil
 
software - Variable in class net.sf.basedb.core.data.DerivedBioAssayData
 
software - Variable in class net.sf.basedb.core.data.RawBioAssayData
 
software - Variable in class net.sf.basedb.plugins.IlluminaRawDataImporter
 
Software - Class in net.sf.basedb.core
This class is used to represent individual software items and information about them.
Software(SoftwareData) - Constructor for class net.sf.basedb.core.Software
Creates a new software item.
SOFTWARE - Enum constant in enum class net.sf.basedb.core.Item
The item is a Software.
softwareColumnMapping - Static variable in class net.sf.basedb.plugins.batchimport.DerivedBioAssayImporter
 
softwareColumnMapping - Static variable in class net.sf.basedb.plugins.batchimport.RawBioAssayImporter
 
SoftwareData - Class in net.sf.basedb.core.data
This class holds information about a software.
SoftwareData() - Constructor for class net.sf.basedb.core.data.SoftwareData
 
softwareHasBeenSet - Variable in class net.sf.basedb.core.DerivedBioAssay
 
softwareHasBeenSet - Variable in class net.sf.basedb.core.RawBioAssay
 
softwareId - Variable in class net.sf.basedb.core.MigrateRbaToDba.Rba
 
SoftwareLoader - Class in net.sf.basedb.util.overview.loader
Node loader implementation for software.
SoftwareLoader() - Constructor for class net.sf.basedb.util.overview.loader.SoftwareLoader
 
softwareMapper - Variable in class net.sf.basedb.plugins.batchimport.DerivedBioAssayImporter
 
softwareMapper - Variable in class net.sf.basedb.plugins.batchimport.RawBioAssayImporter
 
softwareQuery - Variable in class net.sf.basedb.plugins.batchimport.AbstractItemImporter
 
SoftwareValidator - Class in net.sf.basedb.util.overview.validator
Validator implementation for software.
SoftwareValidator() - Constructor for class net.sf.basedb.util.overview.validator.SoftwareValidator
 
sort(List<? extends InvokationContext<?>>) - Method in class net.sf.basedb.util.extensions.DefaultFilter
 
sort(List<? extends InvokationContext<?>>) - Method in interface net.sf.basedb.util.extensions.ExtensionsFilter
Sort a list of invoked extensions according to some property.
sort(List<? extends InvokationContext<?>>) - Method in class net.sf.basedb.util.extensions.SingleExtensionFilter
Do nothing since the list should contain only a single extension.
sortable - Variable in class net.sf.basedb.clients.web.extensions.list.AbstractListColumnBean
 
sortable - Variable in class net.sf.basedb.clients.web.extensions.list.PropertyPathActionFactory
 
sortable - Variable in class net.sf.basedb.clients.web.taglib.table.ColumnDef
If the column is sortable or not
sortable - Variable in class net.sf.basedb.clients.web.taglib.table.TableColumn
 
sortby - Variable in class net.sf.basedb.clients.web.taglib.table.Table
The column to sort by.
sortBy(Expression) - Method in enum class net.sf.basedb.core.ItemContext.SortDirection
Create an order expression that can be used with queries: Query.order(Order).
sortByAnnotationType(DbControl) - Static method in class net.sf.basedb.core.snapshot.AnnotationSnapshot
Create a comparator for sorting annotation snapshots by the name of the annotation type.
sortByProject(DbControl, boolean) - Static method in class net.sf.basedb.core.snapshot.AnnotationSnapshot
Create a comparator for sorting annotation snapshots by the name of the project.
SortByProjectComparator() - Constructor for class net.sf.basedb.core.snapshot.AnnotationSetSnapshot.SortByProjectComparator
 
sortChildren(Comparator<? super Node>) - Method in class net.sf.basedb.util.overview.Node
Sorts the list of child nodes.
sortColumns - Variable in class net.sf.basedb.clients.web.taglib.table.Table
 
sortDirection - Variable in class net.sf.basedb.clients.web.taglib.table.Table
ASC or DESC
sortDirection - Variable in class net.sf.basedb.core.data.ContextData
 
sortDirection - Variable in class net.sf.basedb.core.ItemContext
 
SortDirection(int, String) - Constructor for enum class net.sf.basedb.core.ItemContext.SortDirection
Creates a new direction.
sortKeys() - Method in class net.sf.basedb.util.Enumeration
This method will sort the enumration on the keys using Collections.sort(List, Comparator).
sortProperty - Variable in class net.sf.basedb.clients.web.extensions.list.AbstractListColumnBean
 
sortProperty - Variable in class net.sf.basedb.clients.web.extensions.list.PropertyPathActionFactory
 
sortProperty - Variable in class net.sf.basedb.clients.web.taglib.table.ColumnDef
Optional property used for sorting.
sortProperty - Variable in class net.sf.basedb.core.data.ContextData
 
sortProperty - Variable in class net.sf.basedb.core.ItemContext
 
sortValues() - Method in class net.sf.basedb.util.Enumeration
This method will sort the enumration on the values using Collections.sort(List, Comparator).
source - Variable in class net.sf.basedb.clients.web.extensions.DynamicActionAttributeSupport
 
source - Variable in class net.sf.basedb.core.data.AnnotationData
 
source - Variable in class net.sf.basedb.core.data.annotations.AnnotationLink
 
source - Variable in class net.sf.basedb.core.data.TransformationData
 
source - Variable in class net.sf.basedb.core.snapshot.AnnotationSnapshot
 
source - Variable in class net.sf.basedb.util.annotations.InheritAnnotationsManager.AnnotationTypeFilter
 
source - Variable in class net.sf.basedb.util.export.spotdata.AbstractBioAssaySetExporter
 
source - Variable in class net.sf.basedb.util.export.spotdata.AbstractFieldConverter
 
source - Variable in class net.sf.basedb.util.listable.AbstractSourceItemTransformer
 
source - Variable in class net.sf.basedb.util.listable.SourceItemTransformerChain
 
Source() - Constructor for enum class net.sf.basedb.core.Annotation.Source
 
SOURCE - Enum constant in enum class net.sf.basedb.plugins.PrintMapFlatFileImporter.Section
 
SOURCE_BIOASSAYS - Static variable in class net.sf.basedb.core.plugin.AbstractAnalysisPlugin
 
SOURCE_BIOASSAYSET - Static variable in class net.sf.basedb.core.plugin.AbstractAnalysisPlugin
 
SOURCE_DERIVEDBIOASSAY - Static variable in class net.sf.basedb.core.plugin.AbstractAnalysisPlugin
 
sourceBioAssaySetParameter - Variable in class net.sf.basedb.core.plugin.AbstractAnalysisPlugin
The source parameter for bioassay set.
sourceBioAssaySetType - Static variable in class net.sf.basedb.core.plugin.AbstractAnalysisPlugin
The parameter type for the source bioassay set.
sourceColumnMapper - Variable in class net.sf.basedb.plugins.PlateMappingImporter
 
sourceCount - Variable in class net.sf.basedb.core.data.PlateMappingData
 
sourceDerivedBioAssayParameter - Variable in class net.sf.basedb.core.plugin.AbstractAnalysisPlugin
The source parameter for derived bioassay.
sourceDerivedBioAssayType - Static variable in class net.sf.basedb.core.plugin.AbstractAnalysisPlugin
The parameter type for the source derived bioassay.
sourceFile - Variable in class net.sf.basedb.util.importer.spotdata.BaseFileImporter
 
sourceGeometry - Variable in class net.sf.basedb.core.data.PlateMappingData
 
sourceIdHash - Variable in class net.sf.basedb.util.listable.TransformCache.CacheKey
 
sourceIntensityTransform - Variable in class net.sf.basedb.core.data.FormulaData
 
sourceItemTransform - Variable in class net.sf.basedb.core.data.ItemListSyncFilterData
 
SourceItemTransform() - Constructor for enum class net.sf.basedb.core.SyncFilter.SourceItemTransform
 
SourceItemTransformer - Interface in net.sf.basedb.util.listable
Implementations are responsible for transforming a set of source item ID:s into a set of related target item ID:s.
SourceItemTransformerChain - Class in net.sf.basedb.util.listable
Chains together one or more source item transformers.
SourceItemTransformerChain(List<SourceItemTransformer>) - Constructor for class net.sf.basedb.util.listable.SourceItemTransformerChain
Create a new source item transformer chain.
SourceItemTransformerFactory - Interface in net.sf.basedb.util.listable
A source item transformer factory is responsible for creating SourceItemTransformer:s that can transform between the supported SourceItemTransformerFactory.getSupportedSourceItems(SyncFilter.SourceItemTransform) to the specified SourceItemTransformerFactory.getTargetItem().
SourceItemTransformerWithCache - Class in net.sf.basedb.util.listable
This is a wrapper transformer factory that can be applied to any other factory in order to provide support for caching.
SourceItemTransformerWithCache(SourceItemTransformerFactory) - Constructor for class net.sf.basedb.util.listable.SourceItemTransformerWithCache
Create a new source item transformer chain.
SourceItemTransformerWithCache(SourceItemTransformerFactory, String) - Constructor for class net.sf.basedb.util.listable.SourceItemTransformerWithCache
 
SourceItemTransformerWithCache.TransformerWithCache - Class in net.sf.basedb.util.listable
 
sourceItemType - Variable in class net.sf.basedb.core.data.ItemListSyncFilterData
 
sourceMustExist - Variable in class net.sf.basedb.core.data.ItemListSyncFilterData
 
sourcePlateMapper - Variable in class net.sf.basedb.plugins.PlateMappingImporter
 
sourceRowMapper - Variable in class net.sf.basedb.plugins.PlateMappingImporter
 
sources - Variable in class net.sf.basedb.core.data.BioMaterialEventData
 
sourceSubSetParameter - Variable in class net.sf.basedb.core.plugin.AbstractAnalysisPlugin
The bioAssays subset parameter.
sourceType - Variable in class net.sf.basedb.clients.web.extensions.list.RelatedItemColumn.Specification
 
sourceType - Variable in class net.sf.basedb.util.listable.TransformCache.CacheKey
 
SPACE - Static variable in class net.sf.basedb.clients.web.util.HTML
 
spacingX - Variable in class net.sf.basedb.core.data.ArrayDesignBlockData
 
spacingX - Variable in class net.sf.basedb.plugins.PrintMapFlatFileImporter.MetaBlock
 
spacingY - Variable in class net.sf.basedb.core.data.ArrayDesignBlockData
 
spacingY - Variable in class net.sf.basedb.plugins.PrintMapFlatFileImporter.MetaBlock
 
spec - Variable in class net.sf.basedb.clients.web.extensions.list.RelatedItemColumn
 
specialLoggers - Variable in class net.sf.basedb.core.log.db.DbLogManagerFactory
 
SpecialQuery<C> - Class in net.sf.basedb.core
A special HQL query implementation that can return almost any kind of object.
SpecialQuery(String, String, String, Transformer<C, ?>) - Constructor for class net.sf.basedb.core.SpecialQuery
 
Specification() - Constructor for class net.sf.basedb.clients.web.extensions.list.RelatedItemColumn.Specification
 
specifications - Variable in class net.sf.basedb.util.annotations.InheritAnnotationsManager
 
specifications - Variable in class net.sf.basedb.util.annotations.RunnableInheritAnnotationsManager
 
spiParser - Variable in class net.sf.basedb.util.importer.spotdata.BaseFileInfo.SpotSectionInfo
 
splitHeader - Static variable in class net.sf.basedb.plugins.IlluminaRawDataImporter
A column header must be like: extendedpropertyname-arrayname
splitter - Variable in class net.sf.basedb.util.StreamCacher
 
splitValueWithUnit(String) - Static method in class net.sf.basedb.util.units.UnitUtil
Splits a value with an optional unit.
SPOT - Enum constant in enum class net.sf.basedb.core.ExtraValue.CoordinateType
The extra values are attached to spots.
SPOT - Enum constant in enum class net.sf.basedb.core.VirtualTable
Table that stores spot intensities for each spot in a data cube.
SPOT_ALL - Static variable in class net.sf.basedb.clients.web.ExperimentExplorer
Special value to use in the ExperimentExplorer.setPositionIndex(int) method to show all positions.
SPOT_AVG - Static variable in class net.sf.basedb.clients.web.ExperimentExplorer
Special value to use in the ExperimentExplorer.setPositionIndex(int) method to calculate the average for each bioassay.
SPOT_DATA - Static variable in class net.sf.basedb.core.File
The id for the FileType item representing a file containing analysed spot data.
SPOT_EXTRA_FLOAT - Enum constant in enum class net.sf.basedb.core.VirtualTable
Table that stores float spot extra values.
SPOT_EXTRA_INT - Enum constant in enum class net.sf.basedb.core.VirtualTable
Table that stores integer spot extra values.
SPOT_EXTRA_STRING - Enum constant in enum class net.sf.basedb.core.VirtualTable
Table that stores string spot extra values.
spotBatcher - Variable in class net.sf.basedb.core.BioAssaySet
The one and only spot batcher for this bioassayset.
spotBatcher - Variable in class net.sf.basedb.util.importer.spotdata.MatrixSpotIntensityEventHandler
 
spotBatcher - Variable in class net.sf.basedb.util.importer.spotdata.SerialSpotIntensityEventHandler
 
SpotBatcher - Class in net.sf.basedb.core
Batcher class for per-spot intensity values for bioassaysets.
SpotBatcher(DbControl, BioAssaySet) - Constructor for class net.sf.basedb.core.SpotBatcher
Create a new spot batcher for a bioassayset.
spotCount - Variable in class net.sf.basedb.util.export.spotdata.BfsExporter
 
spotCount - Variable in class net.sf.basedb.util.export.spotdata.MatrixBaseFileExporter
 
spotCount - Variable in class net.sf.basedb.util.export.spotdata.SerialBaseFileExporter
 
SpotData(int, float, float, int, MACalculator) - Constructor for class net.sf.basedb.plugins.MedianRatioNormalization.SpotData
 
SpotData(short, int, float, float, int, boolean, MACalculator) - Constructor for class net.sf.basedb.plugins.LowessNormalization.SpotData
 
SPOTDATA - Enum constant in enum class net.sf.basedb.core.Item
Representing spot data, not an actual item.
SpotExtraValueBatcher<I> - Class in net.sf.basedb.core
Batcher class for per-spot extra values.
SpotExtraValueBatcher(DbControl, ExtraValue) - Constructor for class net.sf.basedb.core.SpotExtraValueBatcher
Create a new spot batcher for a bioassayset.
spotExtraValueBatchers - Variable in class net.sf.basedb.core.BioAssaySet
Cache of already created spot extra value batchers.
spotFields - Variable in class net.sf.basedb.util.export.spotdata.AbstractBioAssaySetExporter
 
SpotIntensityParser - Interface in net.sf.basedb.util.importer.spotdata
A spot intensity parser is responsible for parsing and extracting spot intensity data on a row-by-row basis from a BASEfile.
spotIntensityParsers - Variable in class net.sf.basedb.util.importer.spotdata.FirstPassSectionSpotsParser
 
spotQuery - Variable in class net.sf.basedb.util.export.spotdata.MatrixBaseFileExporter
 
spotQuery - Variable in class net.sf.basedb.util.export.spotdata.SerialBaseFileExporter
 
spots - Variable in class net.sf.basedb.core.data.RawBioAssayData
 
spotSectionInfo - Variable in class net.sf.basedb.util.importer.spotdata.BaseFileInfo
 
SpotSectionInfo() - Constructor for class net.sf.basedb.util.importer.spotdata.BaseFileInfo.SpotSectionInfo
Creates a new object.
spotSize - Variable in class net.sf.basedb.plugins.PrintMapFlatFileImporter
 
spotSql - Variable in class net.sf.basedb.core.SpotBatcher
The statement that inserts spot data.
spotSqlStatement - Variable in class net.sf.basedb.core.SpotBatcher
The SQL string for the SpotBatcher.spotSql statement.
sql - Variable in class net.sf.basedb.core.AnnotationBatcher.InsertBatcher
 
sql - Variable in class net.sf.basedb.core.AnnotationBatcher.UpdateBatcher
 
sql - Variable in class net.sf.basedb.core.FastAnnotationLoader.FastIterator
 
sql - Variable in class net.sf.basedb.core.hibernate.ExecuteUpdateWork
 
sql - Variable in class net.sf.basedb.core.hibernate.ResultSetWork
 
SQL - Enum constant in enum class net.sf.basedb.core.query.QueryType
The query is using Structured Query Language.
SqlColumnExpression - Class in net.sf.basedb.core.query
An expression representing the column in a database tabe: alias.column.
SqlColumnExpression(String, String) - Constructor for class net.sf.basedb.core.query.SqlColumnExpression
 
sqlDeletes - Static variable in class net.sf.basedb.core.BatchUtil
Mapping classes/entity names to SQL deletes.
sqlInserts - Static variable in class net.sf.basedb.core.BatchUtil
Mapping classes/entity names to SQL inserts.
SqlQuery - Interface in net.sf.basedb.core.query
This is a query that is using SQL as the query language.
sqlResult - Variable in class net.sf.basedb.core.DynamicResultIterator
 
SqlResult - Interface in net.sf.basedb.core.query
This interface represents a single row in the results of a SqlQuery.
SqlResultImpl() - Constructor for class net.sf.basedb.core.DynamicResultIterator.SqlResultImpl
 
SqlResultIterator - Interface in net.sf.basedb.core.query
Return the result of a SqlQuery as an iterator.
SqlResultList<I> - Interface in net.sf.basedb.core.query
 
SqlStatement(String) - Constructor for class net.sf.basedb.core.hibernate.SchemaGenerator.SqlStatement
 
SqlStatement(String, String) - Constructor for class net.sf.basedb.core.hibernate.SchemaGenerator.SqlStatement
 
sqlSymbol - Variable in enum class net.sf.basedb.core.Operator
 
sqlType - Variable in class net.sf.basedb.core.dbengine.TableInfo.ColumnInfo
 
sqlType - Variable in class net.sf.basedb.core.hibernate.TypeWrapper
 
sqlType - Variable in class net.sf.basedb.core.PositionExtraValueBatcher
The sql type code of the value to insert.
sqlType - Variable in class net.sf.basedb.core.SpotExtraValueBatcher
The sql type code of the value to insert.
sqlTypeCode - Variable in class net.sf.basedb.core.BatchedPropertyInfo
 
sqlUpdates - Static variable in class net.sf.basedb.core.BatchUtil
Mapping classes/entity names to SQL updates.
sqrt - Variable in class net.sf.basedb.core.query.QuadraticMeanExpression
 
sqrt(Expression) - Static method in class net.sf.basedb.core.query.Expressions
Calculate the square root of an expression: new expression = sqrt(e).
SqrtExpression - Class in net.sf.basedb.core.query
 
SqrtExpression(Expression) - Constructor for class net.sf.basedb.core.query.SqrtExpression
 
squaredSum - Variable in class net.sf.basedb.util.plot.HistogramPlot.HistogramBin
 
SquareRootConverter - Class in net.sf.basedb.util.jep.convert
Convert SquareRoot function to a Query API Expression.
SquareRootConverter() - Constructor for class net.sf.basedb.util.jep.convert.SquareRootConverter
 
sshFingerprint - Variable in class net.sf.basedb.core.data.FileServerData
 
sshFingerprint - Variable in class net.sf.basedb.util.uri.ConnectionParameters
 
sshPrivateKey - Variable in class net.sf.basedb.core.data.FileServerData
 
sshPrivateKey - Variable in class net.sf.basedb.util.uri.ConnectionParameters
 
sshPrivateKeyFormat - Variable in class net.sf.basedb.core.data.FileServerData
 
sshPrivateKeyFormat - Variable in class net.sf.basedb.util.uri.ConnectionParameters
 
sshPrivateKeyPassword - Variable in class net.sf.basedb.core.data.FileServerData
 
sshPrivateKeyPassword - Variable in class net.sf.basedb.util.uri.ConnectionParameters
 
ssl - Static variable in class net.sf.basedb.util.EmailUtil
 
SSLUtil2 - Class in net.sf.basedb.util.ssl
Utility class for working with SSL connections.
SSLUtil2() - Constructor for class net.sf.basedb.util.ssl.SSLUtil2
 
stacktrace - Variable in class net.sf.basedb.core.DbControl.State
 
stackTrace - Variable in class net.sf.basedb.core.data.JobData
 
stackTraceToImage(Throwable, int, int) - Static method in class net.sf.basedb.util.error.ThrowableUtil
Prints as much of a stacktrace as possible to an image.
stackTraceToString(Throwable) - Static method in class net.sf.basedb.util.error.ThrowableUtil
Convert a stacktrace to a string that is usually printed with the Throwable.printStackTrace() method.
StandardFieldConverter - Class in net.sf.basedb.util.export.spotdata
Default field converter implementation that works mainly by checking names and/or external id values of formulas, extra values, experimental factors etc.
StandardFieldConverter(DbControl, BioAssaySet) - Constructor for class net.sf.basedb.util.export.spotdata.StandardFieldConverter
Create a new standard field converter.
start - Variable in class net.sf.basedb.clients.web.fileupload.FileUpload.UploadStream
 
start - Variable in class net.sf.basedb.util.ChainedProgressReporter
 
start() - Method in class net.sf.basedb.clients.jobagent.Agent
Start the job agent.
start() - Method in class net.sf.basedb.clients.web.extensions.service.DummyService
 
start() - Method in interface net.sf.basedb.clients.web.extensions.service.ServiceControllerAction
Start the service if it is not already running.
start() - Static method in class net.sf.basedb.core.Application
Starts the BASE application.
start() - Method in class net.sf.basedb.plugins.AbstractFlatFileImporter
Called once before starting the import.
start() - Method in class net.sf.basedb.plugins.RawDataFlatFileImporter
Prepare for the import.
start(boolean) - Static method in class net.sf.basedb.core.Application
Deprecated.
In BASE 3.18; use Application.start(StartupOptions) instead
start(int) - Method in class net.sf.basedb.util.timer.PerformanceTimer
Start the timer with the given index.
start(String, String, String, JobAgent, Date) - Method in class net.sf.basedb.core.Job
Register the job as started.
start(String, String, JobAgent) - Method in class net.sf.basedb.core.Job
Register the job as started.
start(String, String, JobAgent, Date) - Method in class net.sf.basedb.core.Job
 
start(Application.StartupOptions) - Static method in class net.sf.basedb.core.Application
Starts the BASE application.
start(Extension<ServiceControllerAction>) - Static method in class net.sf.basedb.clients.web.extensions.service.Services
Start services as a result of an administrator has installed a new extension or updated/enabled an existing on.
startAgent() - Method in class net.sf.basedb.clients.jobagent.AgentController
Start the agent this controller is controlling.
startDate - Variable in class net.sf.basedb.core.data.NewsData
 
started - Variable in class net.sf.basedb.core.data.JobData
 
startIndex - Variable in class net.sf.basedb.core.FastAnnotationLoader.FastIterator
 
startJob(Job, JobAgentSettings) - Method in class net.sf.basedb.clients.jobagent.Agent
Start a job.
StartPageAction - Interface in net.sf.basedb.clients.web.extensions.startpage
Action for selecting the start page that should be displayed after logging in to BASE.
StartPageBean - Class in net.sf.basedb.clients.web.extensions.startpage
A simple bean-like implementation of the StartPageAction interface.
StartPageBean() - Constructor for class net.sf.basedb.clients.web.extensions.startpage.StartPageBean
 
StartRequestHandler - Class in net.sf.basedb.clients.jobagent.handlers
This is a request handler for the start command.
StartRequestHandler(Agent) - Constructor for class net.sf.basedb.clients.jobagent.handlers.StartRequestHandler
 
StartServiceRenderer - Class in net.sf.basedb.clients.web.extensions.service
A renderer that starts the service of a ServiceControllerAction.
StartServiceRenderer() - Constructor for class net.sf.basedb.clients.web.extensions.service.StartServiceRenderer
 
StartStopServlet - Class in net.sf.basedb.clients.web.servlet
Servlet listener for starting BASE when the web server is started and stopping BASE when the web server is stopped.
StartStopServlet() - Constructor for class net.sf.basedb.clients.web.servlet.StartStopServlet
 
startTime - Variable in class net.sf.basedb.clients.web.fileupload.FileUploadProgress
 
startTime - Variable in class net.sf.basedb.util.extensions.manager.ProcessResults
 
startTime - Variable in class net.sf.basedb.util.TransferRateProgressReporter
 
StartupOptions() - Constructor for class net.sf.basedb.core.Application.StartupOptions
 
startX - Variable in class net.sf.basedb.util.plot.HistogramPlot.HistogramBin
 
state - Variable in class net.sf.basedb.core.DbControl
The state is holding Hibernate database connections and transaction.
state - Variable in class net.sf.basedb.core.log.EntityDetails
 
state - Variable in class net.sf.basedb.core.PluginRequest
 
state - Variable in class net.sf.basedb.core.PluginResponse
 
state - Variable in class net.sf.basedb.util.StaticCache.LockSafeInputStream
 
state - Variable in class net.sf.basedb.util.StaticCache.LockSafeOutputStream
 
State() - Constructor for class net.sf.basedb.core.DbControl.State
 
State(Closeable, StaticCache.LockEntry, boolean) - Constructor for class net.sf.basedb.util.StaticCache.State
 
stateless - Variable in class net.sf.basedb.core.AbstractHqlQuery
If the query should be executed in a stateless session or not.
statelessSession - Variable in class net.sf.basedb.core.AnnotationBatcher
 
StatelessSessionWrapper - Class in net.sf.basedb.core.hibernate
Wrapper around stateless Hibernate sessions that includes a query cache.
StatelessSessionWrapper(StatelessSession) - Constructor for class net.sf.basedb.core.hibernate.StatelessSessionWrapper
Creates a new session wrapper
statement - Variable in class net.sf.basedb.core.AnnotationBatcher.InsertBatcher
 
statement - Variable in class net.sf.basedb.core.AnnotationBatcher.UpdateBatcher
 
statements - Variable in class net.sf.basedb.core.hibernate.MultiUpdateWork
 
staticCache - Static variable in class net.sf.basedb.core.Application
Cache for static data.
StaticCache - Class in net.sf.basedb.util
A cache for storing data to files on the file system.
StaticCache(File) - Constructor for class net.sf.basedb.util.StaticCache
Creates a new static cache.
StaticCache.CleanupTask - Class in net.sf.basedb.util
A timer task that clean up the cache when it is executed.
StaticCache.LockEntry - Class in net.sf.basedb.util
Keeps track of a locked cached entry.
StaticCache.LockSafeInputStream - Class in net.sf.basedb.util
A lock-safe input stream that releases the associated read lock when the stream is closed.
StaticCache.LockSafeOutputStream - Class in net.sf.basedb.util
A lock-safe output stream that releases the associated write lock when the stream is closed.
StaticCache.State - Class in net.sf.basedb.util
Inner class for performing the actual release of locks and closing of streams (in/out).
StaticFilter<T> - Class in net.sf.basedb.util.filter
A filter implementation that either rejects or accepts all object (including null).
StaticFilter(boolean) - Constructor for class net.sf.basedb.util.filter.StaticFilter
Create a new filter.
StaticKeyManager - Class in net.sf.basedb.util.ssl
A key manager implementation that always selects a specified keystore entry.
StaticKeyManager(KeyStore, String, String) - Constructor for class net.sf.basedb.util.ssl.StaticKeyManager
Create a new key manager
staticRules - Static variable in class net.sf.basedb.util.overview.OverviewUtil
 
statistics - Variable in class net.sf.basedb.clients.web.ExperimentExplorer.AnnotationGroup
 
status - Variable in class net.sf.basedb.clients.web.fileupload.FileUpload
The status of the upload.
status - Variable in class net.sf.basedb.core.data.JobData
 
status - Variable in class net.sf.basedb.core.PluginResponse
 
status - Variable in class net.sf.basedb.util.extensions.manager.ProcessResults.FileResults
 
Status(boolean) - Constructor for enum class net.sf.basedb.core.plugin.Response.Status
 
Status(int, String, boolean) - Constructor for enum class net.sf.basedb.core.Job.Status
 
STATUS - Static variable in class net.sf.basedb.core.signal.Signal
The STATUS signal, that requests that the receiver should update the status on the system.
statusMessage - Variable in class net.sf.basedb.core.data.JobData
 
STDEV - Enum constant in enum class net.sf.basedb.util.plot.HistogramPlot.YAggregate
Plot the standard deviation of all y-values for spots falling into each bin.
steps - Variable in class net.sf.basedb.util.collections.MultiStepCollectionTransformer
 
sticky - Variable in class net.sf.basedb.core.data.NewsData
 
stickyCol - Variable in class net.sf.basedb.clients.web.taglib.table.Table
The id of a column that is "sticky".
stickyHeaders - Variable in class net.sf.basedb.clients.web.taglib.table.Table
If sticky headers is enabled or not.
stop() - Method in class net.sf.basedb.clients.jobagent.Agent
Stop the job agent.
stop() - Method in class net.sf.basedb.clients.web.extensions.service.DummyService
 
stop() - Method in interface net.sf.basedb.clients.web.extensions.service.ServiceControllerAction
Stop the service if it is running.
stop() - Method in class net.sf.basedb.core.Application.Pinger
Stop this pinger.
stop() - Static method in class net.sf.basedb.core.Application
Stops the BASE application.
stop(int) - Method in class net.sf.basedb.util.timer.PerformanceTimer
Stop a running timer.
stop(Extension<ServiceControllerAction>) - Static method in class net.sf.basedb.clients.web.extensions.service.Services
Start services as a result of an administrator has uninstalled an extension or is updating/disabling an existing on.
stopAgent() - Method in class net.sf.basedb.clients.jobagent.AgentController
Stop a running job agent by sending a stop request to the agents remote control service.
stopAll() - Method in class net.sf.basedb.util.timer.PerformanceTimer
Stop all running timers
stopPinger(Application.Pinger) - Static method in class net.sf.basedb.core.Application
 
StopRequestHandler - Class in net.sf.basedb.clients.jobagent.handlers
This is a request handler for the stop command.
StopRequestHandler(Agent) - Constructor for class net.sf.basedb.clients.jobagent.handlers.StopRequestHandler
Create a new stop request handler.
StopServiceRenderer - Class in net.sf.basedb.clients.web.extensions.service
A renderer that stops the service of a ServiceControllerAction.
StopServiceRenderer() - Constructor for class net.sf.basedb.clients.web.extensions.service.StopServiceRenderer
 
stopStart(int, int) - Method in class net.sf.basedb.util.timer.PerformanceTimer
Start one timer and stop another.
STORAGE_SIZE - Static variable in class net.sf.basedb.core.Quantity
The id for the Quantity object representing storage sizes.
storageType - Variable in class net.sf.basedb.core.data.BioPlateTypeData
 
store(String, Object, int) - Method in class net.sf.basedb.util.StaticCache
Store a serializable object in the cache.
store(TransformCache.CacheKey, Set<Integer>) - Method in class net.sf.basedb.util.listable.TransformCache
Store a new entry into the cache.
storeAttributes(ItemContext, String) - Method in class net.sf.basedb.util.extensions.ClientContext
Store all attributes that has been set on this context to the given ItemContext instance.
storeCurrentValuesAsOld(List<T>) - Method in class net.sf.basedb.core.data.ParameterValueData
Store the current values as old values, except if there are no current values or if old values have already been stored.
storePropertyFilters(Map<String, PropertyFilterData>) - Method in class net.sf.basedb.core.ItemContext
Store the current property filters and save them in the give filterData map.
storeValue(ParameterValues, Request, PluginParameter<T>) - Method in class net.sf.basedb.core.plugin.AbstractPlugin
Copy a parameter value from a Request to a ParameterValues object.
storeValue(ParameterValues, PluginParameter<T>, T) - Method in class net.sf.basedb.core.plugin.AbstractPlugin
Store a value in a ParameterValues object.
storeValues(ParameterValues, Request, PluginParameter<T>) - Method in class net.sf.basedb.core.plugin.AbstractPlugin
Copy a list of parameter values from a Request to a ParameterValues object.
strategy - Variable in class net.sf.basedb.core.ExtendedPropertyAccessor.GetterSetter
 
stream - Variable in class net.sf.basedb.util.StaticCache.State
 
stream() - Method in class net.sf.basedb.core.hibernate.QueryWrapper
 
StreamCacher - Class in net.sf.basedb.util
Caches the contents of a stream to a local temporary file.
StreamCacher(InputStream) - Constructor for class net.sf.basedb.util.StreamCacher
Create a new stream cacher for reading from the given master stream.
StreamCacher(InputStream, File) - Constructor for class net.sf.basedb.util.StreamCacher
Create a new stream cacher for reading from the given master stream.
StreamRedirector(Reader, Writer) - Constructor for class net.sf.basedb.clients.jobagent.executors.ProcessJobExecutor.StreamRedirector
 
streamtoword(byte[], int[]) - Static method in class net.sf.basedb.util.bcrypt.BCrypt
Cycically extract a word of key material
string(String) - Static method in class net.sf.basedb.core.query.Expressions
Create a constant expression from a string.
STRING - Enum constant in enum class net.sf.basedb.core.Type
String type where maximum length allowed is 255 characters.
STRING - Enum constant in enum class net.sf.basedb.plugins.Base1PluginExecuter.Base1JobParameterType
 
STRING - Static variable in class net.sf.basedb.core.hibernate.TypeWrapper
 
STRING_TOO_LONG_ERROR - Static variable in class net.sf.basedb.plugins.util.Parameters
STRING_TYPE - Static variable in class net.sf.basedb.core.dbengine.TableInfo
 
StringConverter - Class in net.sf.basedb.util.extensions.debug
Convert strings to other data types.
StringConverter - Class in net.sf.basedb.util.jep.convert
Convert a String constant to a Query API Expression.
StringConverter() - Constructor for class net.sf.basedb.util.jep.convert.StringConverter
 
StringConverter(Type, Object) - Constructor for class net.sf.basedb.util.extensions.debug.StringConverter
 
StringDetector - Interface in net.sf.basedb.util.charset
Interface for checking if a text line in a file seems to be decoded correctly with the current character set.
StringFormatter - Class in net.sf.basedb.clients.web.formatter
Format a string for output on a web page.
StringFormatter() - Constructor for class net.sf.basedb.clients.web.formatter.StringFormatter
Create a new string formatter.
StringLengthComparator - Class in net.sf.basedb.util
A comparator implementation for strings that sorts them according to their length.
StringLengthComparator() - Constructor for class net.sf.basedb.util.StringLengthComparator
Create a new string length comparator instance.
stringMapping - Static variable in enum class net.sf.basedb.core.Type
 
stringMapping - Static variable in enum class net.sf.basedb.plugins.PrintMapFlatFileImporter.Section
 
StringMatcher - Class in net.sf.basedb.util.fuzzy
A wrapper class for fuzzy string matching using the SecondString package.
StringMatcher() - Constructor for class net.sf.basedb.util.fuzzy.StringMatcher
Create a new matcher using the default fuzzy matching algorithm: Level2JaroWinkler.
StringMatcher(StringDistance) - Constructor for class net.sf.basedb.util.fuzzy.StringMatcher
Create a new matcher using a specific fuzzy matching algorithm.
StringMatcher.FuzzyMatch - Class in net.sf.basedb.util.fuzzy
Wrapper that holds information about a fuzzy match.
StringParameterType - Class in net.sf.basedb.core
This class represent a parameter type that is a string.
StringParameterType() - Constructor for class net.sf.basedb.core.StringParameterType
Create a new string parameter type, setting the max length to 255 and nulls are allowed.
StringParameterType(Integer, String, boolean) - Constructor for class net.sf.basedb.core.StringParameterType
Create a new string parameter type.
StringParameterType(Integer, String, boolean, int, int, int) - Constructor for class net.sf.basedb.core.StringParameterType
 
StringParameterType(Integer, String, boolean, int, int, int, List<String>) - Constructor for class net.sf.basedb.core.StringParameterType
 
StringParameterType(Integer, String, boolean, int, int, int, Enumeration<String, String>) - Constructor for class net.sf.basedb.core.StringParameterType
 
StringParameterType(Integer, String, boolean, int, int, int, Enumeration<String, String>, boolean) - Constructor for class net.sf.basedb.core.StringParameterType
 
StringParameterValueData - Class in net.sf.basedb.core.data
String parameter value.
StringParameterValueData() - Constructor for class net.sf.basedb.core.data.StringParameterValueData
 
StringParameterValueData(String...) - Constructor for class net.sf.basedb.core.data.StringParameterValueData
 
stringTooLongError(String, String, String, String...) - Static method in class net.sf.basedb.plugins.util.Parameters
Create the parameter for handling too long strings.
stringTooLongErrorParameter - Static variable in class net.sf.basedb.plugins.AbstractFlatFileImporter
 
stringTooLongErrorParameter - Static variable in class net.sf.basedb.plugins.AnnotationFlatFileImporter
 
StringTooLongException - Exception in net.sf.basedb.core
This exception is thrown when an item's field or a parameter which must be shorter than a specified length exceeds that length.
StringTooLongException() - Constructor for exception net.sf.basedb.core.StringTooLongException
Create a new StringTooLongException object.
StringTooLongException(String, String, int) - Constructor for exception net.sf.basedb.core.StringTooLongException
Create a new StringTooLongException object.
StringUtil - Class in net.sf.basedb.core
Utility methods that will make it easier to implement data validation for string attributes.
StringUtil() - Constructor for class net.sf.basedb.core.StringUtil
 
stringValue - Variable in enum class net.sf.basedb.core.Type
 
StringValue(String) - Constructor for class net.sf.basedb.util.excel.ExcelValue.StringValue
 
stripMarkup(CharSequence) - Static method in class net.sf.basedb.clients.web.util.HTML
Remove all HTML markup in a string and return what is left.
StylableTag - Class in net.sf.basedb.clients.web.taglib
Generic tag class for tags that want to support id, class and style of the main html object they use.
StylableTag(String) - Constructor for class net.sf.basedb.clients.web.taglib.StylableTag
Create a new stylable tag.
style - Variable in class net.sf.basedb.clients.web.extensions.list.AbstractListColumnBean
 
style - Variable in class net.sf.basedb.clients.web.extensions.list.PropertyPathActionFactory
 
style - Variable in class net.sf.basedb.clients.web.extensions.login.FieldInfo
 
style - Variable in class net.sf.basedb.clients.web.extensions.menu.FixedMenuItemFactory
 
style - Variable in class net.sf.basedb.clients.web.extensions.menu.MenuItemBean
 
style - Variable in class net.sf.basedb.clients.web.extensions.section.IncludeContentSectionFactory
 
style - Variable in class net.sf.basedb.clients.web.extensions.section.SectionBean
 
style - Variable in class net.sf.basedb.clients.web.extensions.tabcontrol.FixedTabFactory
 
style - Variable in class net.sf.basedb.clients.web.extensions.tabcontrol.IncludeContentTabFactory
 
style - Variable in class net.sf.basedb.clients.web.extensions.tabcontrol.TabBean
 
style - Variable in class net.sf.basedb.clients.web.extensions.toolbar.ButtonBean
 
style - Variable in class net.sf.basedb.clients.web.extensions.toolbar.FixedButtonFactory
 
style - Variable in class net.sf.basedb.clients.web.taglib.menu.Menuseparator
Optional style attribute
style - Variable in class net.sf.basedb.clients.web.taglib.StylableTag
 
style - Variable in class net.sf.basedb.clients.web.taglib.tab.Tab
Optional style attribute
style - Variable in class net.sf.basedb.clients.web.taglib.table.Cell
Optional style attribute
style - Variable in class net.sf.basedb.clients.web.taglib.table.CellValue
 
styleCreator - Variable in class net.sf.basedb.clients.web.plugins.XlsxTemplate
 
styleCreator - Variable in class net.sf.basedb.util.excel.XlsxTableWriter
 
styles - Variable in class net.sf.basedb.clients.web.taglib.Head
A comma-separated list of stylesheets filenames.
styles - Variable in class net.sf.basedb.util.excel.CellStyleCreator
 
stylesheets - Variable in class net.sf.basedb.clients.web.extensions.AbstractJspFactory
 
stylesheets - Variable in class net.sf.basedb.clients.web.extensions.JspContext
 
Stylesheets - Class in net.sf.basedb.clients.web.taglib.extensions
Tag for creating <link> tags to stylesheets from a JspContext.
Stylesheets() - Constructor for class net.sf.basedb.clients.web.taglib.extensions.Stylesheets
 
subCategories - Variable in class net.sf.basedb.core.data.ItemSubtypeData
 
subCategoriesType - Variable in class net.sf.basedb.core.data.ItemSubtypeData
 
subCategory - Variable in class net.sf.basedb.core.data.ContextData
 
subCategory - Variable in class net.sf.basedb.core.ItemContext
 
subCategoryValues - Variable in class net.sf.basedb.core.data.AnnotationTypeCategoryData
 
subclass - Variable in class net.sf.basedb.clients.web.taglib.StylableTag
 
subclass - Variable in class net.sf.basedb.clients.web.taglib.table.Cell
More classes.
subcontext - Variable in class net.sf.basedb.clients.web.taglib.table.Table
 
subContext - Variable in class net.sf.basedb.core.ContextKey
 
subContext - Variable in class net.sf.basedb.core.data.ContextData
 
subContext - Variable in class net.sf.basedb.core.data.ContextIndex
 
subContext - Variable in class net.sf.basedb.core.data.JobData
 
subContext - Variable in class net.sf.basedb.core.ItemContext
 
subContext - Variable in class net.sf.basedb.core.plugin.GuiContext
 
SubContext - Class in net.sf.basedb.clients.web
Helper class for changing the current subcontext.
SubContext(String) - Constructor for class net.sf.basedb.clients.web.SubContext
Create an instance that doesn't change the current item context.
SubContext(String, ItemSubtype, AnnotationTypeCategory, ItemContext.AddFilter) - Constructor for class net.sf.basedb.clients.web.SubContext
Create an instance that changes the current item context.
SUBCONTEXT - Static variable in class net.sf.basedb.clients.web.extensions.list.RelatedItemExtensionColumn
The named subcontext to use when using the extensions.
SUBDIR_FORMAT - Static variable in class net.sf.basedb.core.File
 
subdirectories - Variable in class net.sf.basedb.core.data.DirectoryData
 
subId - Variable in class net.sf.basedb.clients.web.taglib.menu.Submenu
The ID of the submenu.
subList(int, int) - Method in class net.sf.basedb.core.ItemResultList
 
Submenu - Class in net.sf.basedb.clients.web.taglib.menu
This tag defines a menu item inside a drop-down menu.
Submenu() - Constructor for class net.sf.basedb.clients.web.taglib.menu.Submenu
 
SUBMENU - Enum constant in enum class net.sf.basedb.clients.web.extensions.menu.MenuItemAction.MenuType
A menu item that opens a submenu.
submenuId - Variable in class net.sf.basedb.clients.web.extensions.menu.FixedMenuItemFactory
 
submenuId - Variable in class net.sf.basedb.clients.web.extensions.menu.MenuItemBean
 
submenuId - Variable in class net.sf.basedb.clients.web.extensions.menu.PermissionMenuItemFactory
 
subquery - Variable in class net.sf.basedb.core.query.SubqueryExpression
 
SubqueryExpression - Class in net.sf.basedb.core.query
Expression that returns the result of a query as it's value.
SubqueryExpression(String, Query) - Constructor for class net.sf.basedb.core.query.SubqueryExpression
 
SUBSTANCE - Static variable in class net.sf.basedb.core.Quantity
The id for the Quantity object representing "amount of substance".
subtitle - Variable in class net.sf.basedb.clients.web.extensions.list.AbstractListColumnBean
 
subtitle - Variable in class net.sf.basedb.clients.web.extensions.list.PropertyPathActionFactory
 
subtitle - Variable in class net.sf.basedb.clients.web.taglib.table.ColumnDef
The subtitle of the column.
subtract(Expression, Expression) - Static method in class net.sf.basedb.core.query.Expressions
Subtract one expression from another: new expression = e1 - e2.
SubtractConverter - Class in net.sf.basedb.util.jep.convert
Convert Subtract function to a Query API Expression.
SubtractConverter() - Constructor for class net.sf.basedb.util.jep.convert.SubtractConverter
 
SubtractExpression - Class in net.sf.basedb.core.query
Subtract one expression from another: e1 - e2.
SubtractExpression(Expression, Expression) - Constructor for class net.sf.basedb.core.query.SubtractExpression
 
subTreeIterator - Variable in class net.sf.basedb.util.Tree.EntryIterator
An iterator over the subtree for each child of the root entry.
Subtypable - Interface in net.sf.basedb.core
A subtypable item is an item that can have a subtype.
SubtypableData - Interface in net.sf.basedb.core.data
A subtypable item is an item that can have a subtype.
subtypableItems - Static variable in class net.sf.basedb.core.Metadata
 
SubtypableRelatedItems - Annotation Interface in net.sf.basedb.core
Annotation that can be used by Subtypable items to tell about related items.
subtype - Variable in class net.sf.basedb.clients.web.extensions.list.RelatedItemColumn.Specification
 
subtype - Variable in class net.sf.basedb.clients.web.extensions.list.SubtypeFilter
 
subtype - Variable in class net.sf.basedb.clients.web.SubContext
 
subtype - Variable in class net.sf.basedb.core.data.AnnotationTypeCategoryData
 
subtype - Variable in class net.sf.basedb.core.data.BioMaterialData
 
subtype - Variable in class net.sf.basedb.core.data.BioPlateTypeData
 
subtype - Variable in class net.sf.basedb.core.data.ContextData
 
subtype - Variable in class net.sf.basedb.core.data.DerivedBioAssayData
 
subtype - Variable in class net.sf.basedb.core.data.FileData
 
subtype - Variable in class net.sf.basedb.core.data.HardwareData
 
subtype - Variable in class net.sf.basedb.core.data.ItemListData
 
subtype - Variable in class net.sf.basedb.core.data.ItemListSyncFilterData
 
subtype - Variable in class net.sf.basedb.core.data.ItemSubtypeFileTypeData
 
subtype - Variable in class net.sf.basedb.core.data.JobData
 
subtype - Variable in class net.sf.basedb.core.data.KitData
 
subtype - Variable in class net.sf.basedb.core.data.PhysicalBioAssayData
 
subtype - Variable in class net.sf.basedb.core.data.ProtocolData
 
subtype - Variable in class net.sf.basedb.core.data.SoftwareData
 
subtype - Variable in class net.sf.basedb.core.data.TagData
 
subtype - Variable in class net.sf.basedb.core.Install.ItemSubtypeFT
 
subtype - Variable in class net.sf.basedb.core.ItemContext
 
subtype - Variable in class net.sf.basedb.util.annotations.InheritSpecification
 
subtype - Variable in class net.sf.basedb.util.bfs.MetadataModel
 
subtype - Variable in class net.sf.basedb.util.bfs.MetadataWriter
 
subtype - Variable in class net.sf.basedb.util.parser.DefaultItemFunction
 
SUBTYPE - Static variable in class net.sf.basedb.util.export.spotdata.MatrixBaseFileExporter
 
SUBTYPE - Static variable in class net.sf.basedb.util.export.spotdata.MatrixBfsExporter
 
SUBTYPE - Static variable in class net.sf.basedb.util.export.spotdata.SerialBaseFileExporter
 
SUBTYPE - Static variable in class net.sf.basedb.util.export.spotdata.SerialBfsExporter
 
subtypeColumnMapping - Static variable in class net.sf.basedb.plugins.batchimport.AbstractItemImporter
 
SubtypeFilter - Class in net.sf.basedb.clients.web.extensions.list
Filter implementation that accept (annotatable) items of a given subtype.
SubtypeFilter(ItemSubtype) - Constructor for class net.sf.basedb.clients.web.extensions.list.SubtypeFilter
 
subtypeId - Variable in class net.sf.basedb.core.MigrateRbaToDba.Itemlist
 
subtypeId - Variable in class net.sf.basedb.core.MigrateRbaToDba.LineMapping
 
subtypeId - Variable in class net.sf.basedb.core.MigrateRbaToDba.Rba
 
subtypeMapper - Variable in class net.sf.basedb.plugins.batchimport.AbstractItemImporter
 
SubtypeMapping(File) - Constructor for class net.sf.basedb.core.MigrateRbaToDba.SubtypeMapping
 
subtypeName - Variable in class net.sf.basedb.clients.web.extensions.list.RelatedItemColumn.Specification
 
subtypeQuery - Variable in class net.sf.basedb.plugins.batchimport.AbstractItemImporter
 
subtypes - Variable in class net.sf.basedb.clients.web.taglib.SubtypeSelector
 
SubtypeSelector - Class in net.sf.basedb.clients.web.taglib
This tag defines a selectable list of subtypes.
SubtypeSelector() - Constructor for class net.sf.basedb.clients.web.taglib.SubtypeSelector
 
successMessage - Variable in class net.sf.basedb.clients.web.plugins.SimpleExport
 
suffix - Variable in class net.sf.basedb.clients.web.extensions.fileviewer.FileViewerUtil
 
suffix - Variable in class net.sf.basedb.clients.web.extensions.renderer.PrefixSuffixRenderer
 
suffix - Variable in class net.sf.basedb.clients.web.taglib.table.CellValue
 
suffix - Static variable in class net.sf.basedb.core.Version
 
suffix - Variable in class net.sf.basedb.util.bfs.SequenceFilenameGenerator
 
suffix - Variable in class net.sf.basedb.util.formatter.PrefixSuffixFormatter
 
SuggestedFilenameGenerator - Class in net.sf.basedb.util.bfs
File name generator implementation that uses the suggested file name.
SuggestedFilenameGenerator() - Constructor for class net.sf.basedb.util.bfs.SuggestedFilenameGenerator
 
suggestedJobName - Variable in class net.sf.basedb.core.PluginResponse
 
sum - Variable in class net.sf.basedb.clients.web.ExperimentExplorer.AnnotationGroup
 
sum - Variable in class net.sf.basedb.util.plot.HistogramPlot.HistogramBin
 
sum(Expression) - Static method in class net.sf.basedb.core.query.Aggregations
Calculates the sum of all values of an expression: new expression = SUM(e)
SUM - Enum constant in enum class net.sf.basedb.util.plot.HistogramPlot.YAggregate
Plot the sum of all y-values for spots falling into each bin.
sumArrays(int[], int[]) - Static method in class net.sf.basedb.util.RemovableUtil
 
SumExpression - Class in net.sf.basedb.core.query
Calculates the sum of an expression: SUM(e)
SumExpression(Expression) - Constructor for class net.sf.basedb.core.query.SumExpression
 
summaries - Variable in class net.sf.basedb.core.DiskUsageStatistics
 
summary - Variable in class net.sf.basedb.util.extensions.manager.ProcessResults
 
Summary() - Constructor for class net.sf.basedb.core.DiskUsageStatistics.Summary
 
Summary(Group) - Constructor for class net.sf.basedb.core.DiskUsageStatistics.Summary
 
Summary(User) - Constructor for class net.sf.basedb.core.DiskUsageStatistics.Summary
 
summaryCache - Variable in class net.sf.basedb.clients.web.ExperimentExplorer
Caches annotation summaries.
SUPERVISOR - Static variable in class net.sf.basedb.core.Role
The id for the Role item representing supervisors.
supportColumnAliasInGroupBy() - Method in class net.sf.basedb.core.dbengine.AbstractDbEngine
Returns FALSE.
supportColumnAliasInGroupBy() - Method in interface net.sf.basedb.core.dbengine.DbEngine
If the current database supports column aliases in the group by part of a query or not.
supportColumnAliasInGroupBy() - Method in class net.sf.basedb.core.dbengine.MySQLEngine
Returns TRUE.
supportColumnAliasInGroupBy() - Method in class net.sf.basedb.core.dbengine.PostgresDbEngine
Returns TRUE.
supportColumnAliasInHaving() - Method in class net.sf.basedb.core.dbengine.AbstractDbEngine
Returns FALSE.
supportColumnAliasInHaving() - Method in interface net.sf.basedb.core.dbengine.DbEngine
If the current database supports column aliases in the order by part of a query or not.
supportColumnAliasInHaving() - Method in class net.sf.basedb.core.dbengine.MySQLEngine
Returns TRUE.
supportColumnAliasInHaving() - Method in class net.sf.basedb.core.dbengine.PostgresDbEngine
Returns FALSE.
supportColumnAliasInOrderBy() - Method in class net.sf.basedb.core.dbengine.AbstractDbEngine
Returns FALSE.
supportColumnAliasInOrderBy() - Method in interface net.sf.basedb.core.dbengine.DbEngine
If the current database supports column aliases in the order by part of a query or not.
supportColumnAliasInOrderBy() - Method in class net.sf.basedb.core.dbengine.MySQLEngine
Returns TRUE.
supportColumnAliasInOrderBy() - Method in class net.sf.basedb.core.dbengine.PostgresDbEngine
Returns TRUE.
supported - Variable in class net.sf.basedb.core.signal.AbstractSignalHandler
Holds the supported signals.
supported - Static variable in class net.sf.basedb.core.signal.ThreadSignalHandler
 
supports(String) - Method in class net.sf.basedb.core.PluginDefinition
Check if a plugin implements the interface specified by the plugin type.
supports(URI) - Method in interface net.sf.basedb.util.uri.ConnectionManagerFactory
Check if the given factory knows how to create a handler for the given URI.
supports(URI) - Method in class net.sf.basedb.util.uri.http.HttpConnectionManagerFactory
 
supports(PluginType) - Method in class net.sf.basedb.core.PluginDefinition
Check if a plugin implements the interface specified by the plugin type.
supports(Signal) - Method in class net.sf.basedb.core.signal.AbstractSignalHandler
 
supports(Signal) - Method in class net.sf.basedb.core.signal.DelegatingSignalHandler
Check if at least one handler has been registered for the given signal.
supports(Signal) - Method in interface net.sf.basedb.core.signal.SignalHandler
Check if a given signal is supported.
supportsAverage - Variable in enum class net.sf.basedb.core.Formula.Type
 
supportsAverage() - Method in enum class net.sf.basedb.core.Formula.Type
If a formula of this type can be used in an average expression or not.
supportsColumnAlias(DbEngine) - Method in enum class net.sf.basedb.core.query.QuerySection
If the current database supports column aliases in that part of the query.
supportsColumnAliasInWhere() - Method in class net.sf.basedb.core.dbengine.AbstractDbEngine
Returns FALSE.
supportsColumnAliasInWhere() - Method in interface net.sf.basedb.core.dbengine.DbEngine
If the current database supports column aliases in the where part of a query or not.
supportsColumnAliasInWhere() - Method in class net.sf.basedb.core.dbengine.MySQLEngine
Returns FALSE.
supportsColumnAliasInWhere() - Method in class net.sf.basedb.core.dbengine.PostgresDbEngine
Returns FALSE.
supportsConfigurations - Variable in class net.sf.basedb.core.data.PluginDefinitionData
 
supportsConfigurations() - Method in class net.sf.basedb.clients.web.plugins.SimpleExport
 
supportsConfigurations() - Method in class net.sf.basedb.core.plugin.AbstractPlugin
Returns TRUE, since that is how the plugins used to work before this method was introduced.
supportsConfigurations() - Method in interface net.sf.basedb.core.plugin.Plugin
Return TRUE if the plugin supports different configurations when executing a job.
supportsConfigurations() - Method in class net.sf.basedb.core.PluginDefinition
Check if the plugin supports configurations or not when executing a job.
supportsConfigurations() - Method in class net.sf.basedb.plugins.AnnotationFlatFileImporter
 
supportsConfigurations() - Method in class net.sf.basedb.plugins.Base1PluginExecuter
 
supportsConfigurations() - Method in class net.sf.basedb.plugins.BaseFileExporterPlugin
 
supportsConfigurations() - Method in class net.sf.basedb.plugins.batchimport.AbstractItemImporter
 
supportsConfigurations() - Method in class net.sf.basedb.plugins.batchimport.AnyToAnyImporter
 
supportsConfigurations() - Method in class net.sf.basedb.plugins.BfsExporterPlugin
 
supportsConfigurations() - Method in class net.sf.basedb.plugins.CdfFileReporterImporter
 
supportsConfigurations() - Method in class net.sf.basedb.plugins.CloneReportersPlugin
 
supportsConfigurations() - Method in class net.sf.basedb.plugins.executor.AbstractIOSupport
 
supportsConfigurations() - Method in class net.sf.basedb.plugins.executor.ExternalProgramExecutor
 
supportsConfigurations() - Method in class net.sf.basedb.plugins.FormulaFilter
 
supportsConfigurations() - Method in class net.sf.basedb.plugins.GalExporter
 
supportsConfigurations() - Method in class net.sf.basedb.plugins.HelpExporter
 
supportsConfigurations() - Method in class net.sf.basedb.plugins.HelpImporter
 
supportsConfigurations() - Method in class net.sf.basedb.plugins.IlluminaRawDataImporter
 
supportsConfigurations() - Method in class net.sf.basedb.plugins.IntensityCalculatorPlugin
 
supportsConfigurations() - Method in class net.sf.basedb.plugins.JepExtraValueCalculator
 
supportsConfigurations() - Method in class net.sf.basedb.plugins.JepIntensityTransformer
 
supportsConfigurations() - Method in class net.sf.basedb.plugins.LowessNormalization
 
supportsConfigurations() - Method in class net.sf.basedb.plugins.ManualDerivedBioAssayCreator
 
supportsConfigurations() - Method in class net.sf.basedb.plugins.ManualTransformCreator
 
supportsConfigurations() - Method in class net.sf.basedb.plugins.MedianRatioNormalization
 
supportsConfigurations() - Method in class net.sf.basedb.plugins.PackedFileExporter
 
supportsConfigurations() - Method in class net.sf.basedb.plugins.PlateFlatFileImporter
 
supportsConfigurations() - Method in class net.sf.basedb.plugins.PlateMappingExporter
 
supportsConfigurations() - Method in class net.sf.basedb.plugins.PlateMappingImporter
 
supportsConfigurations() - Method in class net.sf.basedb.plugins.PluginConfigurationExporter
Always false
supportsConfigurations() - Method in class net.sf.basedb.plugins.PluginConfigurationImporter
 
supportsConfigurations() - Method in class net.sf.basedb.plugins.PrintMapFlatFileImporter
 
supportsConfigurations() - Method in class net.sf.basedb.plugins.RawDataFlatFileImporter
 
supportsConfigurations() - Method in class net.sf.basedb.plugins.ReporterFlatFileImporter
 
supportsConfigurations() - Method in class net.sf.basedb.plugins.ReporterMapFlatFileImporter
 
supportsConfigurations() - Method in class net.sf.basedb.util.zip.AbstractFileUnpacker
Returns FALSE.
supportsDeviceVerification - Variable in class net.sf.basedb.core.data.ClientData
 
supportsEncryption() - Method in interface net.sf.basedb.util.zip.FilePacker
Does the packer support encryption or not?
supportsEncryption() - Method in class net.sf.basedb.util.zip.ZipFilePacker
Encryption is supported.
supportsGetQuery() - Method in enum class net.sf.basedb.core.Item
Check if Item.getQuery() is supported by this item type.
supportsPushAnnotations(Item) - Static method in class net.sf.basedb.core.ItemSubtype
Check if the given item type has support for pushing annotations to the parent item or not.
SupportsPushAnnotations - Annotation Interface in net.sf.basedb.core
Annotation (java) that can be used by Subtypable items to enable/disable support for pushing annotations (BASE) to parent items.
supportUnits() - Method in class net.sf.basedb.core.AnnotationType
Checks if this annotation types support units.
symbol - Variable in class net.sf.basedb.core.data.ReporterData
 
symbol - Variable in class net.sf.basedb.core.data.UnitSymbolData
 
symbol - Variable in enum class net.sf.basedb.core.Operator
 
symbol - Variable in class net.sf.basedb.util.units.UnitCache.CacheKey
 
SYMBOL - Static variable in class net.sf.basedb.core.ClonableProperty
The property name of the "static" property ReporterData.getSymbol()
symbolColumnMapping - Static variable in class net.sf.basedb.plugins.ReporterFlatFileImporter
 
symbolMapper - Variable in class net.sf.basedb.plugins.ReporterFlatFileImporter
 
symbols - Variable in class net.sf.basedb.core.data.QuantityData
 
symbols - Variable in class net.sf.basedb.core.data.UnitData
 
syncDate - Variable in class net.sf.basedb.core.data.ItemListData
 
SyncFilter - Class in net.sf.basedb.core
Holds information about a synchronization filter used by an item list.
SyncFilter(ItemListSyncFilterData) - Constructor for class net.sf.basedb.core.SyncFilter
 
SYNCFILTER - Enum constant in enum class net.sf.basedb.core.Item
The item is a SyncFilter
SyncFilter.SourceItemTransform - Enum Class in net.sf.basedb.core
 
syncFilters - Variable in class net.sf.basedb.core.data.ItemListData
 
synchronize(Set<Integer>, Set<Integer>) - Method in enum class net.sf.basedb.core.ItemList.SynchronizeOption
Synchronize the existing members with the items matching the current filter context.
synchronizeAllBioMaterialEvents() - Method in class net.sf.basedb.core.BioPlateEvent
Synchronize all properties on the child biomaterial events that are related to this event.
SynchronizedData(BfsParser) - Constructor for class net.sf.basedb.util.importer.spotdata.SynchronizedSpotDataParser.SynchronizedData
 
SynchronizedSpotDataParser - Class in net.sf.basedb.util.importer.spotdata
A parser that synchronizes the parsing of multiple underlying data parsers and a master reporter annotations parser.
SynchronizedSpotDataParser() - Constructor for class net.sf.basedb.util.importer.spotdata.SynchronizedSpotDataParser
Create a new synchronized data parser.
SynchronizedSpotDataParser.SynchronizedData - Class in net.sf.basedb.util.importer.spotdata
This class holds information that is sent to the event handler when SynchronizedSpotDataParser.DATA_EVENT:s are sent.
SynchronizeOption() - Constructor for enum class net.sf.basedb.core.ItemList.SynchronizeOption
 
synchronizeProperties(BioMaterialEventData, BioPlateEventParticipantData) - Method in class net.sf.basedb.core.BioPlateEvent
Synchronize all related properties between this event and the biomaterial event.
SYSTEM - Enum constant in enum class net.sf.basedb.core.Item
Not an item as susch.
systemCreated - Variable in class net.sf.basedb.core.Message
 
SystemData - Interface in net.sf.basedb.core.data
A system item is an item which has an additional id in the form of string.
systemId - Variable in class net.sf.basedb.core.data.BioPlateEventTypeData
 
systemId - Variable in class net.sf.basedb.core.data.DirectoryData
 
systemId - Variable in class net.sf.basedb.core.data.GroupData
 
systemId - Variable in class net.sf.basedb.core.data.ItemSubtypeData
 
systemId - Variable in class net.sf.basedb.core.data.QuantityData
 
systemId - Variable in class net.sf.basedb.core.data.QuotaData
 
systemId - Variable in class net.sf.basedb.core.data.QuotaTypeData
 
systemId - Variable in class net.sf.basedb.core.data.RoleData
 
systemId - Variable in class net.sf.basedb.core.data.UserData
 
systemIds - Static variable in class net.sf.basedb.core.SystemItems
A map from system id --> numeric id
SystemItem - Interface in net.sf.basedb.core
A SystemItem is an item which has an additional systemwide unique id in the form of string.
SystemItems - Class in net.sf.basedb.core
This class is used to map the system id of all SystemData items to the numerical internal id in the current installation.
SystemItems() - Constructor for class net.sf.basedb.core.SystemItems
 
systemPermissions - Variable in class net.sf.basedb.core.InternalJobQueue.JobQueueKeyring
 
systemPermissions - Variable in class net.sf.basedb.core.ServiceSessionControl.ServicesKeyring
 

T

t - Variable in class net.sf.basedb.util.extensions.logging.LogEntry
 
Tab - Class in net.sf.basedb.clients.web.taglib.tab
This tag defines the title and contents of a single tab inside a tab control.
Tab() - Constructor for class net.sf.basedb.clients.web.taglib.tab.Tab
 
Tab(InvokationContext<? super TabAction>) - Constructor for class net.sf.basedb.clients.web.extensions.tabcontrol.IncludeContentTabFactory.Tab
 
TabAction - Interface in net.sf.basedb.clients.web.extensions.tabcontrol
Action that inserts a new tab in a tabcontrol.
TabBean - Class in net.sf.basedb.clients.web.extensions.tabcontrol
A simple bean-like implementation of the TabAction interface.
TabBean() - Constructor for class net.sf.basedb.clients.web.extensions.tabcontrol.TabBean
 
tabcontrol - Variable in class net.sf.basedb.clients.web.taglib.Help
The tabcontrol ID to get the help id from.
TabControl - Class in net.sf.basedb.clients.web.taglib.tab
This is the main tag for the tab control.
TabControl() - Constructor for class net.sf.basedb.clients.web.taglib.tab.TabControl
 
TabCrLfEncoderDecoder - Class in net.sf.basedb.util.encode
Symmetrical encoder/decoder implementation that replaces newline, carriage return, tab and backslash with \n, \r, \t and \\.
TabCrLfEncoderDecoder(boolean) - Constructor for class net.sf.basedb.util.encode.TabCrLfEncoderDecoder
Creates a new encoder/decoder.
tabIndex - Variable in class net.sf.basedb.clients.web.extensions.tabcontrol.FixedTabFactory
 
tabIndex - Variable in class net.sf.basedb.clients.web.extensions.tabcontrol.IncludeContentTabFactory
 
tabIndex - Variable in class net.sf.basedb.clients.web.extensions.tabcontrol.TabBean
 
tabIndex - Variable in class net.sf.basedb.clients.web.extensions.toolbar.ButtonBean
 
tabIndex - Variable in class net.sf.basedb.clients.web.extensions.toolbar.FixedButtonFactory
 
tabIndex - Variable in class net.sf.basedb.clients.web.taglib.Button
 
tabIndex - Variable in class net.sf.basedb.clients.web.taglib.Help
 
tabIndex - Variable in class net.sf.basedb.clients.web.taglib.Icon
 
tabIndex - Variable in class net.sf.basedb.clients.web.taglib.Input
 
tabIndex - Variable in class net.sf.basedb.clients.web.taglib.Select
 
tabIndex - Variable in class net.sf.basedb.clients.web.taglib.tab.Tab
 
tabIndex - Variable in class net.sf.basedb.clients.web.taglib.table.Button
 
tabIndex - Variable in class net.sf.basedb.clients.web.taglib.Zoom
 
table - Variable in class net.sf.basedb.clients.web.taglib.SubtypeSelector
 
table - Variable in class net.sf.basedb.clients.web.taglib.table.Cell
The parent <tbl:table> tag.
table - Variable in class net.sf.basedb.clients.web.taglib.table.ColumnDef
The parent <tbl:table> tag.
table - Variable in class net.sf.basedb.clients.web.taglib.table.ColumnHeaders
 
table - Variable in class net.sf.basedb.clients.web.taglib.table.ColumnSubtitles
 
table - Variable in class net.sf.basedb.clients.web.taglib.table.Data
The parent <tbl:table> tag.
table - Variable in class net.sf.basedb.clients.web.taglib.table.Form
 
table - Variable in class net.sf.basedb.clients.web.taglib.table.Headers
 
table - Variable in class net.sf.basedb.clients.web.taglib.table.Hidden
The parent <tbl:table> tag.
table - Variable in class net.sf.basedb.clients.web.taglib.table.Label
The parent <tbl:table> tag.
table - Variable in class net.sf.basedb.clients.web.taglib.table.Navigator
The parent <tbl:table> tag.
table - Variable in class net.sf.basedb.clients.web.taglib.table.PresetSelector
The parent <tbl:table> tag.
table - Variable in class net.sf.basedb.clients.web.taglib.table.PropertyFilter
The parent <tbl:table> tag.
table - Variable in class net.sf.basedb.clients.web.taglib.table.Row
The parent <tbl:table> tag.
table - Variable in class net.sf.basedb.clients.web.taglib.table.Rows
 
table - Variable in class net.sf.basedb.core.BasicBatcher
The table where items of this type are stored.
table - Variable in class net.sf.basedb.core.dbengine.TableInfo
 
table - Variable in class net.sf.basedb.core.DynamicRestriction
 
table - Variable in class net.sf.basedb.core.hibernate.TableExistsWork
 
table - Variable in class net.sf.basedb.core.hibernate.TableInfoWork
 
table - Variable in class net.sf.basedb.core.query.VirtualColumnExpression
 
table - Variable in class net.sf.basedb.core.RawDataType
 
Table - Class in net.sf.basedb.clients.web.taglib.table
This is the main tag for the table.
Table() - Constructor for class net.sf.basedb.clients.web.taglib.table.Table
 
tableAlias - Variable in class net.sf.basedb.core.query.ReporterListExpression
 
tableColumn - Variable in class net.sf.basedb.core.query.ReporterListExpression
 
TableColumn - Class in net.sf.basedb.clients.web.taglib.table
Column properties class used to define table columns.
Example use in a jsp page:
TableColumn(String, String, String, Type, String, String, String, boolean, boolean, boolean, Formula.AverageMethod, Formatter<?>) - Constructor for class net.sf.basedb.clients.web.taglib.table.TableColumn
 
tableEncode(String) - Method in class net.sf.basedb.util.export.TableWriter
Encode the given string with the default encoder.
tableExists(String, Session) - Static method in class net.sf.basedb.core.HibernateUtil
Check if table in the dynamic database exists.
TableExistsWork - Class in net.sf.basedb.core.hibernate
A work implementation that checks if a given table exists in the database or not.
TableExistsWork(String, String, String) - Constructor for class net.sf.basedb.core.hibernate.TableExistsWork
Create a new work item.
TableInfo - Class in net.sf.basedb.core.dbengine
Holds minimal but useful information about a table in the database.
TableInfo(Table) - Constructor for class net.sf.basedb.core.dbengine.TableInfo
 
TableInfo(Table, DatabaseMetaData) - Constructor for class net.sf.basedb.core.dbengine.TableInfo
Deprecated.
TableInfo(Table, DatabaseMetaData, String, String) - Constructor for class net.sf.basedb.core.dbengine.TableInfo
Create table info by reading JDBC metadata from the current database
TableInfo(Table, Dialect) - Constructor for class net.sf.basedb.core.dbengine.TableInfo
Create table info by reading the Hibernate mappings.
TableInfo.ColumnInfo - Class in net.sf.basedb.core.dbengine
Holds information about a single column in a table.
TableInfo.ForeignKeyInfo - Class in net.sf.basedb.core.dbengine
Holds information about a foreign key of a table.
TableInfo.IndexInfo - Class in net.sf.basedb.core.dbengine
Holds information about an index in a table.
TableInfo.PrimaryKeyInfo - Class in net.sf.basedb.core.dbengine
Holds information about the primary key of a table.
TableInfoWork - Class in net.sf.basedb.core.hibernate
A work implementation that loads database metadata for a table and returns it as a TableInfo object.
TableInfoWork(Table) - Constructor for class net.sf.basedb.core.hibernate.TableInfoWork
Create a new work item.
tableName - Variable in class net.sf.basedb.core.DropDynamicTableAction
 
tableName - Variable in class net.sf.basedb.core.RealTable
The unquoted table name.
tableName - Variable in enum class net.sf.basedb.core.Type
 
tableName - Variable in class net.sf.basedb.core.Update.DropColumnChange
 
tablePrintData(Object...) - Method in class net.sf.basedb.util.export.TableWriter
Print a data line to the parent writer using the default encoder and column formatters.
tablePrintData(EncoderDecoder, Object...) - Method in class net.sf.basedb.util.export.TableWriter
Print a data line to the parent writer.
tablePrintData(EncoderDecoder, Map<Integer, Formatter<?>>, Object...) - Method in class net.sf.basedb.util.excel.XlsxTableWriter
 
tablePrintData(EncoderDecoder, Map<Integer, Formatter<?>>, Object...) - Method in class net.sf.basedb.util.export.TableWriter
Print a data line to the parent writer.
tablePrintHeaders(Object...) - Method in class net.sf.basedb.util.excel.XlsxTableWriter
 
tablePrintHeaders(Object...) - Method in class net.sf.basedb.util.export.TableWriter
Print a header line to the parent writer.
TableWriter - Class in net.sf.basedb.util.export
Wraps a writer stream and provides methods for easier writing of tabular data.
TableWriter(Writer) - Constructor for class net.sf.basedb.util.export.TableWriter
Create a new table writer that is writing it's output to the given writer.
tabs - Variable in class net.sf.basedb.clients.web.taglib.tab.TabControl
The HTML for the tabs.
tag - Variable in class net.sf.basedb.core.data.ExtractData
 
tag - Variable in class net.sf.basedb.util.overview.validator.ExtractValidator.TagPosition
 
Tag - Class in net.sf.basedb.core
This class represents a tag.
Tag(TagData) - Constructor for class net.sf.basedb.core.Tag
 
TAG - Enum constant in enum class net.sf.basedb.core.Item
The item is a Tag.
TAG_REGEXP - Static variable in class net.sf.basedb.clients.web.util.HTML
This pattern can be used to fins HTML tags.
tagColumnMapping - Static variable in class net.sf.basedb.plugins.batchimport.ExtractImporter
 
TagData - Class in net.sf.basedb.core.data
This represents a tag that is used to mark an extract so that it can be tracked on physical bioassays.
TagData() - Constructor for class net.sf.basedb.core.data.TagData
 
tagElements - Variable in class net.sf.basedb.util.formatter.PropertyFilterFormatter
 
TAGGED_PARENT - Static variable in class net.sf.basedb.util.overview.Validator
Validator rule that checks if the parent to a non-tagged extract has a tag.
TagImporter - Class in net.sf.basedb.plugins.batchimport
Plug-in for importing tag items in a batch.
TagImporter() - Constructor for class net.sf.basedb.plugins.batchimport.TagImporter
 
TagLoader - Class in net.sf.basedb.util.overview.loader
Node loader implementation for tags.
TagLoader() - Constructor for class net.sf.basedb.util.overview.loader.TagLoader
 
tagMapper - Variable in class net.sf.basedb.plugins.batchimport.ExtractImporter
 
TagPosition(Tag, int) - Constructor for class net.sf.basedb.util.overview.validator.ExtractValidator.TagPosition
 
tagQuery - Variable in class net.sf.basedb.plugins.batchimport.AbstractItemImporter
 
TagValidator - Class in net.sf.basedb.util.overview.validator
Validator implementation for tags.
TagValidator() - Constructor for class net.sf.basedb.util.overview.validator.TagValidator
 
takeOwnership() - Method in interface net.sf.basedb.core.Ownable
Take ownership of the item.
takeOwnership() - Method in class net.sf.basedb.core.OwnedItem
 
TAM - Enum constant in enum class net.sf.basedb.plugins.PrintMapFlatFileImporter.FormatType
 
tar - Variable in class net.sf.basedb.util.zip.TarFilePacker
 
TarFilePacker - Class in net.sf.basedb.util.zip
This class packs files into a TAR archive.
TarFilePacker() - Constructor for class net.sf.basedb.util.zip.TarFilePacker
Creates a new TarFilePacker.
TarFileUnpacker - Class in net.sf.basedb.plugins
A plugin for unpacking tar, gzipped tar and bzipped tar files to the BASE file system.
TarFileUnpacker() - Constructor for class net.sf.basedb.plugins.TarFileUnpacker
 
target - Variable in class net.sf.basedb.core.hibernate.DbIndexWork
 
target - Variable in class net.sf.basedb.util.listable.AbstractSourceItemTransformer
 
target - Variable in class net.sf.basedb.util.listable.AbstractSourceItemTransformerFactory
 
target - Variable in class net.sf.basedb.util.listable.SourceItemTransformerChain
 
TARGET - Enum constant in enum class net.sf.basedb.plugins.PrintMapFlatFileImporter.Section
 
targetIdMapper - Variable in class net.sf.basedb.plugins.batchimport.AnyToAnyImporter
 
targetItemIdColumnMapping - Static variable in class net.sf.basedb.plugins.batchimport.AnyToAnyImporter
 
targetItemQueries - Variable in class net.sf.basedb.plugins.batchimport.AnyToAnyImporter
 
targetItemTypeColumnMapping - Static variable in class net.sf.basedb.plugins.batchimport.AnyToAnyImporter
 
targetList - Variable in class net.sf.basedb.util.listable.TransformCache.CacheEntry
 
targetNotFoundErrorParameter - Static variable in class net.sf.basedb.plugins.batchimport.AnyToAnyImporter
 
targets - Variable in class net.sf.basedb.core.AnyToAny.FastLinkLoader
 
targetType - Variable in class net.sf.basedb.clients.web.extensions.list.AnyLinkColumn
 
targetType - Variable in class net.sf.basedb.clients.web.extensions.list.RelatedItemColumn.Specification
 
targetType - Variable in class net.sf.basedb.util.AnyToAnyLinkStatistics
 
targetType - Variable in class net.sf.basedb.util.listable.TransformCache.CacheKey
 
targetTypeMapper - Variable in class net.sf.basedb.plugins.batchimport.AnyToAnyImporter
 
TarUtil - Class in net.sf.basedb.util.zip
Contains utility functions for TAR archives.
TarUtil() - Constructor for class net.sf.basedb.util.zip.TarUtil
 
task - Variable in class net.sf.basedb.util.timer.ThreadTimerTask
 
tc - Variable in class net.sf.basedb.clients.web.taglib.tab.Tab
The parent TabControl object.
TEMPERATURE - Static variable in class net.sf.basedb.core.Quantity
The id for the Quantity object representing temperature.
TEMPLATE - Static variable in class net.sf.basedb.core.Directory
The id for the Directory item representing the template directory.
temporary - Variable in class net.sf.basedb.core.ItemContext.PropertyFilterPair
 
temporary - Variable in class net.sf.basedb.core.PropertyFilter
 
TEMPORARY - Enum constant in enum class net.sf.basedb.core.ItemContext.AddFilter
Add as temporary filter.
TEMPORARY - Static variable in class net.sf.basedb.core.PropertyFilter
Flag to use for temporary filters.
temporaryJoin(Join) - Method in class net.sf.basedb.core.AbstractQuery
 
temporaryJoins - Variable in class net.sf.basedb.core.AbstractQuery
Tempoarary joins, that are automatically cleared after each build.
temporarySelect(Select) - Method in class net.sf.basedb.core.AbstractQuery
 
temporarySelects - Variable in class net.sf.basedb.core.AbstractQuery
Tempoarary selections, that are automatically cleared after each build.
TempSeries(String, int, boolean) - Constructor for class net.sf.basedb.util.plot.HistogramPlot.TempSeries
 
testFixChildren() - Method in class net.sf.basedb.core.DerivedBioAssay
 
testIt(InputStream) - Method in class net.sf.basedb.util.charset.CharsetDetector
Test if the given input stream can be parsed with the configured character set.
testIt(InputStream, long, int) - Method in class net.sf.basedb.util.charset.CharsetDetector
Test if the given input stream can be parsed with the configured character set.
testTransactions() - Static method in class net.sf.basedb.core.HibernateUtil
 
TEXT - Enum constant in enum class net.sf.basedb.core.Type
Text blob type.
TEXT - Enum constant in enum class net.sf.basedb.plugins.Base1PluginExecuter.Base1JobParameterType
 
TEXT - Static variable in class net.sf.basedb.core.hibernate.TypeWrapper
 
textarea - Variable in class net.sf.basedb.clients.web.taglib.Zoom
 
textLength(CharSequence) - Static method in class net.sf.basedb.clients.web.util.HTML
Counts the length of a string ignoring all characters in HTML markup tags.
TextParameterValueData - Class in net.sf.basedb.core.data
Text parameter value.
TextParameterValueData() - Constructor for class net.sf.basedb.core.data.TextParameterValueData
 
TextParameterValueData(String...) - Constructor for class net.sf.basedb.core.data.TextParameterValueData
 
TextWriter - Class in net.sf.basedb.core.migrate
Generic writer implementation that writes string values from a result set.
TextWriter(ResultSet, int, Writer, char[], char[][]) - Constructor for class net.sf.basedb.core.migrate.TextWriter
 
theAbstract - Variable in class net.sf.basedb.core.data.ExperimentData
 
theInstance - Static variable in class net.sf.basedb.util.jep.Log2Function
The one and only instance of this function.
thenMatch - Variable in class net.sf.basedb.util.charset.SimpleStringDetector
 
THERMAL_CONDUCTIVITY - Static variable in class net.sf.basedb.core.Quantity
The id for the Quantity object representing thermal conductivity.
thetaJoinConditions - Variable in class net.sf.basedb.core.AbstractQuery
Temporary list to hold theta join conditions if needed by the database.
thread - Variable in class net.sf.basedb.core.File.CharsetTesterThread
 
ThreadJobExecutor - Class in net.sf.basedb.clients.jobagent.executors
This is a job executor which executes jobs in the current thread.
ThreadJobExecutor() - Constructor for class net.sf.basedb.clients.jobagent.executors.ThreadJobExecutor
 
ThreadJobExecutor.ShutdownHook - Class in net.sf.basedb.clients.jobagent.executors
 
ThreadSignalHandler - Class in net.sf.basedb.core.signal
An implementation of a signal handler that uses the Thread class to communicate signals back to the SignalTarget.
ThreadSignalHandler() - Constructor for class net.sf.basedb.core.signal.ThreadSignalHandler
Create a new thread signal handler.
ThreadSignalHandler(Thread) - Constructor for class net.sf.basedb.core.signal.ThreadSignalHandler
Create a new thread signal handler.
ThreadTimerTask - Class in net.sf.basedb.util.timer
Class for forcing the execution of a TimerTask in a new thread.
ThreadTimerTask(TimerTask, boolean) - Constructor for class net.sf.basedb.util.timer.ThreadTimerTask
Create a new threaded timer task.
throwable - Variable in class net.sf.basedb.util.ContextUtil.ContextResult
 
ThrowableUtil - Class in net.sf.basedb.util.error
Utility class for working with Throwable:s.
ThrowableUtil() - Constructor for class net.sf.basedb.util.error.ThrowableUtil
 
TICK_INTERVAL - Variable in class net.sf.basedb.core.Migration.ProgressInputStream
 
time - Variable in class net.sf.basedb.core.data.ChangeHistoryData
 
time - Variable in class net.sf.basedb.util.extensions.manager.ProcessResults.FileResults
 
TIME - Static variable in class net.sf.basedb.core.Quantity
The id for the Quantity object representing time.
timeout - Variable in class net.sf.basedb.clients.jobagent.AgentController
 
timeout - Variable in class net.sf.basedb.clients.web.fileupload.FileUpload
The timeout in milliseconds that we wait for more data to arrive.
timeout - Variable in class net.sf.basedb.util.jobagent.JobAgentConnection
 
timeout - Variable in class net.sf.basedb.util.listable.TransformCache.CacheEntry
 
timeout - Variable in class net.sf.basedb.util.uri.http.HttpConnectionManager
 
timeoutChecker - Variable in class net.sf.basedb.clients.jobagent.slotmanager.MasterSlotManager
 
timeoutInMillis - Variable in class net.sf.basedb.util.listable.TransformCache
 
TimeoutTimer(HttpGet) - Constructor for class net.sf.basedb.util.uri.http.HttpConnectionManager.TimeoutTimer
 
timer - Variable in class net.sf.basedb.clients.web.extensions.service.DummyService
 
timer - Static variable in class net.sf.basedb.core.Application
The core timer which schedules events.
timer - Variable in class net.sf.basedb.util.timer.Scheduler
 
timers - Variable in class net.sf.basedb.util.timer.PerformanceTimer
 
timeSent - Variable in class net.sf.basedb.core.data.MessageData
 
timestamp - Variable in class net.sf.basedb.util.extensions.logging.LogEntry
 
TIMESTAMP - Enum constant in enum class net.sf.basedb.core.Type
The parameter is a date+time value.
TIMESTAMP - Static variable in class net.sf.basedb.core.hibernate.TypeWrapper
 
TIMESTAMP_FORMAT - Static variable in class net.sf.basedb.core.DateUtil
 
TIMESTAMP_FORMAT_PARAMETER - Static variable in class net.sf.basedb.plugins.util.Parameters
The name of the parameter that is created by Parameters.timestampFormatParameter(String, String, String)
timestampFormat - Variable in class net.sf.basedb.core.migrate.postgres.PostgresResultWriterFactory
PostgreSQL uses 'yyyy-MM-dd HH:mm:ss' for timestamps.
timestampFormat - Variable in class net.sf.basedb.util.excel.AutoFormatter
 
timestampFormat - Variable in class net.sf.basedb.util.excel.XlsxToCsvUtil
 
timestampFormat - Variable in class net.sf.basedb.util.parser.FlatFileParser
The default timestamp format to use when creating mappers.
timestampFormatParameter(String, String, String) - Static method in class net.sf.basedb.plugins.util.Parameters
Parameter definition that asks for the format used by timestamp values when parsed from strings.
timestampFormatter - Variable in class net.sf.basedb.plugins.AnnotationFlatFileImporter
 
TimestampParameterType - Class in net.sf.basedb.core
This class represent a parameter type that is a timestamp.
TimestampParameterType() - Constructor for class net.sf.basedb.core.TimestampParameterType
Create a new timestamp parameter type, allowing null values.
TimestampParameterType(Date, boolean) - Constructor for class net.sf.basedb.core.TimestampParameterType
Create a new timestamp parameter type.
TimestampParameterType(Date, boolean, int, int, int, List<Date>) - Constructor for class net.sf.basedb.core.TimestampParameterType
Creates a new TimestampParameterType
TimestampParameterValueData - Class in net.sf.basedb.core.data
Date+time parameter value.
TimestampParameterValueData() - Constructor for class net.sf.basedb.core.data.TimestampParameterValueData
 
TimestampParameterValueData(Date...) - Constructor for class net.sf.basedb.core.data.TimestampParameterValueData
 
TimestampWriter - Class in net.sf.basedb.core.migrate
Generic writer implementation that writes timestamp values from a result set.
TimestampWriter(ResultSet, int, Writer, char[], FastDateFormat) - Constructor for class net.sf.basedb.core.migrate.TimestampWriter
 
title - Variable in class net.sf.basedb.clients.web.ExperimentExplorer.AnnotationGroup
 
title - Variable in class net.sf.basedb.clients.web.extensions.list.AbstractListColumnBean
 
title - Variable in class net.sf.basedb.clients.web.extensions.list.PropertyPathActionFactory
 
title - Variable in class net.sf.basedb.clients.web.extensions.menu.FixedMenuItemFactory
 
title - Variable in class net.sf.basedb.clients.web.extensions.menu.MenuItemBean
 
title - Variable in class net.sf.basedb.clients.web.extensions.plot.OverviewPlotBean
 
title - Variable in class net.sf.basedb.clients.web.extensions.plot.PlotGeneratorBean
 
title - Variable in class net.sf.basedb.clients.web.extensions.section.IncludeContentSectionFactory
 
title - Variable in class net.sf.basedb.clients.web.extensions.section.SectionBean
 
title - Variable in class net.sf.basedb.clients.web.extensions.tabcontrol.FixedTabFactory
 
title - Variable in class net.sf.basedb.clients.web.extensions.tabcontrol.IncludeContentTabFactory
 
title - Variable in class net.sf.basedb.clients.web.extensions.tabcontrol.TabBean
 
title - Variable in class net.sf.basedb.clients.web.extensions.toolbar.ButtonBean
 
title - Variable in class net.sf.basedb.clients.web.extensions.toolbar.FixedButtonFactory
 
title - Variable in class net.sf.basedb.clients.web.plugins.ExportedProperty
 
title - Variable in class net.sf.basedb.clients.web.servlet.ExperimentExplorerPlotServlet.ColumnKey
 
title - Variable in class net.sf.basedb.clients.web.taglib.Button
The title of the button.
title - Variable in class net.sf.basedb.clients.web.taglib.HideableSection
The title of the section.
title - Variable in class net.sf.basedb.clients.web.taglib.Input
An optional title.
title - Variable in class net.sf.basedb.clients.web.taglib.menu.Menuitem
The title of the menu item.
title - Variable in class net.sf.basedb.clients.web.taglib.menu.Submenu
The title of the menu item.
title - Variable in class net.sf.basedb.clients.web.taglib.Page
The title of the page.
title - Variable in class net.sf.basedb.clients.web.taglib.path.PathElement
The title of the menu item.
title - Variable in class net.sf.basedb.clients.web.taglib.tab.Tab
The title of the tab.
title - Variable in class net.sf.basedb.clients.web.taglib.table.Button
An optional title text on the button.
title - Variable in class net.sf.basedb.clients.web.taglib.table.ColumnDef
The title of the column.
title - Variable in class net.sf.basedb.clients.web.taglib.table.Label
An optional title text on the button.
title - Variable in class net.sf.basedb.clients.web.taglib.table.Table
An optional title of the table.
title - Variable in class net.sf.basedb.clients.web.taglib.table.TableColumn
 
title - Variable in class net.sf.basedb.clients.web.taglib.Zoom
 
title - Variable in exception net.sf.basedb.clients.web.WebException
The title of the error message.
title - Static variable in class net.sf.basedb.core.Application
The title of the server.
title - Variable in class net.sf.basedb.core.data.ExperimentData
 
title - Variable in class net.sf.basedb.core.data.ReporterClonePropertyData
 
title - Variable in class net.sf.basedb.core.ExtendedProperty
 
title - Variable in class net.sf.basedb.core.IntensityFormula
 
title - Variable in class net.sf.basedb.core.RequestInformation
 
title - Variable in class net.sf.basedb.plugins.batchimport.FallbackIdMethod
 
title - Variable in class net.sf.basedb.plugins.batchimport.InternalIdMethod
 
title - Variable in class net.sf.basedb.plugins.batchimport.MultiPropertyIdMethod
 
title - Variable in class net.sf.basedb.plugins.batchimport.PropertyIdMethod
 
title - Variable in class net.sf.basedb.util.export.spotdata.AnnotationAssayField
 
title - Variable in class net.sf.basedb.util.export.spotdata.AssayPropertyField
 
title - Variable in class net.sf.basedb.util.export.spotdata.JepDynamicField
 
title - Variable in class net.sf.basedb.util.export.spotdata.SimpleDynamicField
 
title - Variable in class net.sf.basedb.util.overview.Node
 
title - Variable in class net.sf.basedb.util.overview.Validator
 
title - Variable in enum class net.sf.basedb.util.parser.FlatFileParser.LineType
 
titlePrefix - Variable in class net.sf.basedb.util.overview.node.NameableNameGenerator
 
titleTemplate - Variable in class net.sf.basedb.clients.web.ModeInfo
 
tls - Static variable in class net.sf.basedb.util.EmailUtil
 
tmpTable - Variable in class net.sf.basedb.core.query.IdListRestriction
 
to - Variable in class net.sf.basedb.core.AnyToAny
 
to - Variable in class net.sf.basedb.core.data.MessageData
 
toAlpha - Variable in class net.sf.basedb.util.formatter.WellCoordinateFormatter
 
toArray() - Method in class net.sf.basedb.core.ItemResultList
 
toArray() - Method in class net.sf.basedb.util.Tree
Not supported.
toArray(Collection<T>, JsonConverter<? super T>) - Static method in class net.sf.basedb.util.json.JsonUtil
Convert a collection of objects to an array with JSON-compatible objects.
toArray(Iterator<T>, JsonConverter<? super T>) - Static method in class net.sf.basedb.util.json.JsonUtil
Convert all objects returned by the iterator to an array with JSON-compatible objects.
toArray(T[]) - Method in class net.sf.basedb.core.ItemResultList
 
toArray(T[]) - Method in class net.sf.basedb.util.Tree
Not supported.
ToBioSourceSourceItemTransformerFactory - Class in net.sf.basedb.util.listable
Transformer factory implementation for transforming to biosources.
ToBioSourceSourceItemTransformerFactory() - Constructor for class net.sf.basedb.util.listable.ToBioSourceSourceItemTransformerFactory
 
toChangeDetails(boolean, boolean) - Method in class net.sf.basedb.core.log.EntityDetails
Create a list of ChangeHistoryDetailData objects from the information in this object assuming that the entity is a subclass of BasicData.
toChangeDetails(Item, int, String, ChangeType, boolean, boolean) - Method in class net.sf.basedb.core.log.EntityDetails
Create a list of ChangeHistoryDetailData objects using a mix of the information in this object, and the given parameters.
toChangeHistoryData() - Method in class net.sf.basedb.core.log.TransactionDetails
Convert the information about the transaction to a ChangeHistoryData object.
toData() - Method in class net.sf.basedb.core.ClonableProperty
Create a data-layer reprsentation of the cloned property.
toDate(Expression) - Static method in class net.sf.basedb.core.query.Expressions
Get the date part from a date or timestamp expression.
ToDateExpression - Class in net.sf.basedb.core.query
Get the date part of a date or timestamp epxression.
ToDateExpression(Expression) - Constructor for class net.sf.basedb.core.query.ToDateExpression
 
ToDerivedBioAssaySourceItemTransformerFactory - Class in net.sf.basedb.util.listable
Transformer factory implementation for transforming to derived bioassays.
ToDerivedBioAssaySourceItemTransformerFactory() - Constructor for class net.sf.basedb.util.listable.ToDerivedBioAssaySourceItemTransformerFactory
 
toDescription() - Method in class net.sf.basedb.clients.web.extensions.ServletWrapperKey
 
toDescription() - Method in class net.sf.basedb.util.extensions.manager.ExtensionKey
 
toDescription() - Method in class net.sf.basedb.util.extensions.manager.ExtensionPointKey
 
toDescription() - Method in class net.sf.basedb.util.extensions.manager.FactoryParametersKey
 
toDescription() - Method in interface net.sf.basedb.util.extensions.manager.ObjectKey
Get a string description of the key that is suitable for use in (error) messages to users.
toDescription() - Method in class net.sf.basedb.util.extensions.manager.PluginInfoKey
 
toExcelValue(Boolean) - Method in class net.sf.basedb.util.formatter.BooleanFormatter
 
toExcelValue(Integer) - Method in class net.sf.basedb.util.formatter.WellCoordinateFormatter
 
toExcelValue(Number) - Method in class net.sf.basedb.util.formatter.AdaptiveNumberFormatter
 
toExcelValue(Number) - Method in class net.sf.basedb.util.formatter.IntegerFormatter
 
toExcelValue(Number) - Method in class net.sf.basedb.util.formatter.NumberFormatFormatter
 
toExcelValue(Number) - Method in class net.sf.basedb.util.formatter.NumberFormatter
 
toExcelValue(Object) - Method in class net.sf.basedb.util.excel.AutoFormatter
 
toExcelValue(Object) - Method in class net.sf.basedb.util.formatter.MultiFormatter
 
toExcelValue(String) - Method in class net.sf.basedb.clients.web.formatter.NiceFormatter
No escaping is needed.
toExcelValue(String) - Method in class net.sf.basedb.clients.web.formatter.StringFormatter
No escaping is needed.
toExcelValue(Date) - Method in class net.sf.basedb.util.formatter.DateFormatter
 
toExcelValue(T) - Method in interface net.sf.basedb.util.excel.ExcelFormatter
Convert and format the given value to an Excel value.
toExcelValue(T) - Method in class net.sf.basedb.util.excel.WrappedFormatter
 
toExcelValue(T) - Method in class net.sf.basedb.util.formatter.ToStringFormatter
 
toExpression(Integer) - Method in class net.sf.basedb.util.jep.convert.IntegerConverter
Convert to expression by calling Expressions.integer(int).
toExpression(Number) - Method in class net.sf.basedb.util.jep.convert.FloatConverter
Convert to expression by calling Expressions.aFloat(float).
toExpression(String) - Method in class net.sf.basedb.util.jep.convert.StringConverter
Convert to expression by calling Expressions.string(String).
toExpression(ASTConstant) - Method in class net.sf.basedb.util.jep.convert.ASTConstantConverter
Get the value from the constant node and check the ConverterFactory for a registered converter for the class and use it.
toExpression(ASTFunNode) - Method in class net.sf.basedb.util.jep.convert.ASTFunNodeConverter
Get the PostfixMathCommandI object from the function node and delegate conversion to JepExpressionFunction if that interface is implemented.
toExpression(ASTVarNode) - Method in class net.sf.basedb.util.jep.convert.ASTVarNodeConverter
Converts a JEP variable to a parameter.
toExpression(Node) - Method in class net.sf.basedb.util.jep.ChannelFunction
Use the Dynamic.column(VirtualColumn) method to create an expression referencing a channel intensity.
toExpression(Node) - Method in class net.sf.basedb.util.jep.convert.AbsConverter
Convert to expression by calling Expressions.abs(Expression).
toExpression(Node) - Method in class net.sf.basedb.util.jep.convert.AddConverter
Convert to expression by calling Expressions.add(Expression, Expression).
toExpression(Node) - Method in class net.sf.basedb.util.jep.convert.DivideConverter
Convert to expression by calling Expressions.divide(Expression, Expression).
toExpression(Node) - Method in class net.sf.basedb.util.jep.convert.ExpConverter
Convert to expression by calling Expressions.exp(Expression).
toExpression(Node) - Method in class net.sf.basedb.util.jep.convert.IfConverter
toExpression(Node) - Method in class net.sf.basedb.util.jep.convert.LogarithmConverter
Convert to expression by calling Expressions.log10(Expression).
toExpression(Node) - Method in class net.sf.basedb.util.jep.convert.MultiplyConverter
Convert to expression by calling Expressions.multiply(Expression, Expression).
toExpression(Node) - Method in class net.sf.basedb.util.jep.convert.NaturalLogarithmConverter
Convert to expression by calling Expressions.ln(Expression).
toExpression(Node) - Method in class net.sf.basedb.util.jep.convert.SquareRootConverter
Convert to expression by calling Expressions.sqrt(Expression).
toExpression(Node) - Method in class net.sf.basedb.util.jep.convert.SubtractConverter
Convert to expression by calling Expressions.subtract(Expression, Expression).
toExpression(Node) - Method in class net.sf.basedb.util.jep.convert.UMinusConverter
 
toExpression(Node) - Method in class net.sf.basedb.util.jep.ExtraValueFunction
Use the Dynamic.extraValue(ExtraValue) method to create an expression referencing an extra value.
toExpression(Node) - Method in interface net.sf.basedb.util.jep.JepExpressionFunction
Convert this function to an Expression that can be used in a query.
toExpression(Node) - Method in class net.sf.basedb.util.jep.Log2Function
Use the Expressions.log2(Expression) method to create an expression taking the 2-based logarithm of the argument.
toExpression(Node) - Method in class net.sf.basedb.util.jep.MeanFunction
Use the Dynamic.meanRawData(String) method to create an expression for the mean of the given raw data property.
toExpression(Node) - Method in class net.sf.basedb.util.jep.PositionFunction
Use the Dynamic.column(VirtualColumn) method to create an expression referencing a position.
toExpression(Node) - Method in class net.sf.basedb.util.jep.RawChannelFunction
Use the Dynamic.column(VirtualColumn) method to create an expression referencing a channel intensity.
toExpression(Node) - Method in class net.sf.basedb.util.jep.RawFunction
Use the Dynamic.rawData(String) method to create an expression referencing a raw data property.
toExpression(Node) - Method in class net.sf.basedb.util.jep.ReporterFunction
Use the Dynamic.reporter(String) method to create an expression referencing a reporter property.
toExpression(Node) - Method in class net.sf.basedb.util.jep.ScoreFunction
Use the Dynamic.score(ReporterList) method to create an expression referencing the score of a reporter in the reporter list.
toExpression(T) - Method in class net.sf.basedb.util.jep.convert.AbstractJepConversionFunction
Convert to a restriction and then use Expressions.bool(Restriction) to create a boolean expression.
toExpression(T) - Method in interface net.sf.basedb.util.jep.convert.JepConversionFunction
Convert the object to an expression.
ToExtractSourceItemTransformerFactory - Class in net.sf.basedb.util.listable
Transformer factory implementation for transforming to extracts.
ToExtractSourceItemTransformerFactory() - Constructor for class net.sf.basedb.util.listable.ToExtractSourceItemTransformerFactory
 
ToExtractSourceItemTransformerFactory(boolean) - Constructor for class net.sf.basedb.util.listable.ToExtractSourceItemTransformerFactory
 
toFile(String) - Method in class net.sf.basedb.util.extensions.manager.Settings
A file is typically stored under the absolute path, but if it matches the plug-ins directory we replace it with {plugins.dir}.
toHex(Color) - Static method in class net.sf.basedb.util.ColorGenerator
Generate a hex color string from a Color object.
toId - Variable in class net.sf.basedb.core.data.AnyToAnyData
 
toInt(Set<Include>) - Static method in enum class net.sf.basedb.core.Include
 
token - Variable in class net.sf.basedb.core.data.UserDeviceData
 
tokenize(String, String, boolean) - Static method in class net.sf.basedb.core.StringUtil
Tokenize a string by splitting it at positions matching the regular expression, optionally ignoring matches that are inside quotes.
tokenize(String, String, boolean, boolean) - Static method in class net.sf.basedb.core.StringUtil
Tokenize a string by splitting it at positions matching the regular expression.
toKey(File) - Method in class net.sf.basedb.util.extensions.manager.Settings
A file is typically stored under the absolute path, but if it matches the plug-ins directory we replace it with {plugins.dir}.
toLoggableString(Type, Object) - Static method in class net.sf.basedb.core.log.EntityDetails
 
toMd5(SortedSet<Integer>) - Static method in class net.sf.basedb.core.SyncFilter
Calculate the MD5 sum of all all ID values in the collection.
TOOL - Enum constant in enum class net.sf.basedb.plugins.PrintMapFlatFileImporter.Section
 
toolbar - Variable in class net.sf.basedb.clients.web.taglib.table.Button
The parent <tbl:toolbar> tag.
toolbar - Variable in class net.sf.basedb.clients.web.taglib.table.Label
The parent <tbl:toolbar> tag.
Toolbar - Class in net.sf.basedb.clients.web.taglib.table
This tag creates a toolbar.
Toolbar() - Constructor for class net.sf.basedb.clients.web.taglib.table.Toolbar
 
TOOLBAR_ITEMS - Static variable in class net.sf.basedb.clients.web.extensions.toolbar.ToolbarUtil
An array containing all items that we are registering an extension point for.
ToolbarButtonRenderer - Class in net.sf.basedb.clients.web.extensions.toolbar
A renderer for toolbar button actions, which displays the action as a toolbar button.
ToolbarButtonRenderer() - Constructor for class net.sf.basedb.clients.web.extensions.toolbar.ToolbarButtonRenderer
Create a new "standalone" toolbar button renderer.
ToolbarButtonRenderer(JspContext) - Constructor for class net.sf.basedb.clients.web.extensions.toolbar.ToolbarButtonRenderer
Create a new toolbar button renderer.
ToolbarButtonRendererFactory - Class in net.sf.basedb.clients.web.extensions.toolbar
Factory that create ToolbarButtonRenderer objects for rendering ButtonAction:s.
ToolbarButtonRendererFactory() - Constructor for class net.sf.basedb.clients.web.extensions.toolbar.ToolbarButtonRendererFactory
 
ToolbarUtil - Class in net.sf.basedb.clients.web.extensions.toolbar
Utility class for toolbar extension points.
ToolbarUtil() - Constructor for class net.sf.basedb.clients.web.extensions.toolbar.ToolbarUtil
 
toolParameters - Variable in class net.sf.basedb.plugins.ManualDerivedBioAssayCreator
 
toolParameters - Variable in class net.sf.basedb.plugins.ManualTransformCreator
 
tooltip - Variable in class net.sf.basedb.clients.web.extensions.list.AbstractListColumnBean
 
tooltip - Variable in class net.sf.basedb.clients.web.extensions.list.PropertyPathActionFactory
 
tooltip - Variable in class net.sf.basedb.clients.web.extensions.login.FieldInfo
 
tooltip - Variable in class net.sf.basedb.clients.web.extensions.menu.FixedMenuItemFactory
 
tooltip - Variable in class net.sf.basedb.clients.web.extensions.menu.MenuItemBean
 
tooltip - Variable in class net.sf.basedb.clients.web.extensions.tabcontrol.FixedTabFactory
 
tooltip - Variable in class net.sf.basedb.clients.web.extensions.tabcontrol.IncludeContentTabFactory
 
tooltip - Variable in class net.sf.basedb.clients.web.extensions.tabcontrol.TabBean
 
tooltip - Variable in class net.sf.basedb.clients.web.extensions.toolbar.ButtonBean
 
tooltip - Variable in class net.sf.basedb.clients.web.extensions.toolbar.FixedButtonFactory
 
tooltip - Variable in class net.sf.basedb.clients.web.taglib.Button
An optional tooltip.
tooltip - Variable in class net.sf.basedb.clients.web.taglib.Help
Optional tooltip.
tooltip - Variable in class net.sf.basedb.clients.web.taglib.Icon
An optional tooltip.
tooltip - Variable in class net.sf.basedb.clients.web.taglib.menu.Menuitem
A tooltip explaining the menu item.
tooltip - Variable in class net.sf.basedb.clients.web.taglib.menu.Submenu
A tooltip explaining the menu item.
tooltip - Variable in class net.sf.basedb.clients.web.taglib.path.PathElement
A tooltip explaining the link.
tooltip - Variable in class net.sf.basedb.clients.web.taglib.PropertyValue
An optional tooltip.
tooltip - Variable in class net.sf.basedb.clients.web.taglib.tab.Tab
A popup tooltip text.
tooltip - Variable in class net.sf.basedb.clients.web.taglib.table.Button
An optional tooltip that will show when the mouse is over the button.
tooltip - Variable in class net.sf.basedb.clients.web.taglib.table.ColumnDef
A tooltip with explaining text.
tooltip - Variable in class net.sf.basedb.clients.web.taglib.table.Label
An optional tooltip that will show when the mouse is over the button.
tooltip - Variable in class net.sf.basedb.clients.web.taglib.Zoom
Optional tooltip.
tooManyValuesErrorParameter - Static variable in class net.sf.basedb.plugins.AnnotationFlatFileImporter
 
TOP - Static variable in class net.sf.basedb.clients.web.taglib.tab.TabControl
Tabs are at the top of the tab control.
ToPhysicalBioAssaySourceItemTransformerFactory - Class in net.sf.basedb.util.listable
Transformer factory implementation for transforming to physical bioassays.
ToPhysicalBioAssaySourceItemTransformerFactory() - Constructor for class net.sf.basedb.util.listable.ToPhysicalBioAssaySourceItemTransformerFactory
 
toPluginParameter(DbControl, BioAssaySet) - Method in class net.sf.basedb.plugins.executor.ParameterDefinition
Convert this parameter definition to a PluginParameter object.
toQl(DbControl) - Method in class net.sf.basedb.core.AbstractQuery
 
toQl(DbControl) - Method in interface net.sf.basedb.core.query.Query
Generate the query string that is going to be sent to the underlying query system (eg.
toQl(Query, DbControl) - Method in class net.sf.basedb.clients.web.ExperimentExplorer.InExpression
 
toQl(Query, DbControl) - Method in class net.sf.basedb.core.AnnotationRestriction
 
toQl(Query, DbControl) - Method in class net.sf.basedb.core.AnnotationSet.ProjectSpecificAnnotationsRestriction
 
toQl(Query, DbControl) - Method in class net.sf.basedb.core.DynamicJoin
 
toQl(Query, DbControl) - Method in class net.sf.basedb.core.DynamicRestriction
 
toQl(Query, DbControl) - Method in class net.sf.basedb.core.ExtraValueExpression
 
toQl(Query, DbControl) - Method in class net.sf.basedb.core.ExtraValueJoin
 
toQl(Query, DbControl) - Method in class net.sf.basedb.core.MeanRawDataPropertyExpression
 
toQl(Query, DbControl) - Method in class net.sf.basedb.core.query.AbsExpression
 
toQl(Query, DbControl) - Method in class net.sf.basedb.core.query.AddExpression
 
toQl(Query, DbControl) - Method in class net.sf.basedb.core.query.AndRestriction
 
toQl(Query, DbControl) - Method in class net.sf.basedb.core.query.AnnotationJoin
 
toQl(Query, DbControl) - Method in class net.sf.basedb.core.query.AnyToAnyRestriction
 
toQl(Query, DbControl) - Method in class net.sf.basedb.core.query.AscOrder
 
toQl(Query, DbControl) - Method in class net.sf.basedb.core.query.BetweenRestriction
 
toQl(Query, DbControl) - Method in class net.sf.basedb.core.query.BooleanExpression
 
toQl(Query, DbControl) - Method in class net.sf.basedb.core.query.CaseExpression
 
toQl(Query, DbControl) - Method in class net.sf.basedb.core.query.ConditionalQueryElement
 
toQl(Query, DbControl) - Method in class net.sf.basedb.core.query.CountExpression
 
toQl(Query, DbControl) - Method in class net.sf.basedb.core.query.DescOrder
 
toQl(Query, DbControl) - Method in class net.sf.basedb.core.query.DivideExpression
 
toQl(Query, DbControl) - Method in class net.sf.basedb.core.query.EqRestriction
 
toQl(Query, DbControl) - Method in class net.sf.basedb.core.query.ExpExpression
 
toQl(Query, DbControl) - Method in class net.sf.basedb.core.query.ExpressionSelect
 
toQl(Query, DbControl) - Method in class net.sf.basedb.core.query.FloatExpression
 
toQl(Query, DbControl) - Method in class net.sf.basedb.core.query.GeometricMeanExpression
 
toQl(Query, DbControl) - Method in class net.sf.basedb.core.query.GteqRestriction
 
toQl(Query, DbControl) - Method in class net.sf.basedb.core.query.GtRestriction
 
toQl(Query, DbControl) - Method in class net.sf.basedb.core.query.HqlElementsExpression
 
toQl(Query, DbControl) - Method in class net.sf.basedb.core.query.HqlEntityExpression
 
toQl(Query, DbControl) - Method in class net.sf.basedb.core.query.HqlEntityParameterExpression
 
toQl(Query, DbControl) - Method in class net.sf.basedb.core.query.HqlExpression
 
toQl(Query, DbControl) - Method in class net.sf.basedb.core.query.HqlIndexExpression
 
toQl(Query, DbControl) - Method in class net.sf.basedb.core.query.HqlInnerJoin
 
toQl(Query, DbControl) - Method in class net.sf.basedb.core.query.HqlLeftJoin
 
toQl(Query, DbControl) - Method in class net.sf.basedb.core.query.HqlPropertyExpression
 
toQl(Query, DbControl) - Method in class net.sf.basedb.core.query.HqlRightJoin
 
toQl(Query, DbControl) - Method in class net.sf.basedb.core.query.HqlSizeExpression
 
toQl(Query, DbControl) - Method in class net.sf.basedb.core.query.IdListRestriction
 
toQl(Query, DbControl) - Method in class net.sf.basedb.core.query.InRestriction
 
toQl(Query, DbControl) - Method in class net.sf.basedb.core.query.IntegerExpression
 
toQl(Query, DbControl) - Method in class net.sf.basedb.core.query.LikeRestriction
 
toQl(Query, DbControl) - Method in class net.sf.basedb.core.query.LogExpression
 
toQl(Query, DbControl) - Method in class net.sf.basedb.core.query.LteqRestriction
 
toQl(Query, DbControl) - Method in class net.sf.basedb.core.query.LtRestriction
 
toQl(Query, DbControl) - Method in class net.sf.basedb.core.query.MaxExpression
 
toQl(Query, DbControl) - Method in class net.sf.basedb.core.query.MeanExpression
 
toQl(Query, DbControl) - Method in class net.sf.basedb.core.query.MinExpression
 
toQl(Query, DbControl) - Method in class net.sf.basedb.core.query.MultiplyExpression
 
toQl(Query, DbControl) - Method in class net.sf.basedb.core.query.NegateExpression
 
toQl(Query, DbControl) - Method in class net.sf.basedb.core.query.NeqRestriction
 
toQl(Query, DbControl) - Method in class net.sf.basedb.core.query.NotRestriction
 
toQl(Query, DbControl) - Method in class net.sf.basedb.core.query.OrRestriction
 
toQl(Query, DbControl) - Method in class net.sf.basedb.core.query.ParameterExpression
 
toQl(Query, DbControl) - Method in class net.sf.basedb.core.query.PermissionRestriction
 
toQl(Query, DbControl) - Method in class net.sf.basedb.core.query.PowerExpression
 
toQl(Query, DbControl) - Method in class net.sf.basedb.core.query.QuadraticMeanExpression
 
toQl(Query, DbControl) - Method in interface net.sf.basedb.core.query.QueryElement
Create a query language string of the query element.
toQl(Query, DbControl) - Method in class net.sf.basedb.core.query.ReporterListExpression
 
toQl(Query, DbControl) - Method in class net.sf.basedb.core.query.RlikeRestriction
 
toQl(Query, DbControl) - Method in class net.sf.basedb.core.query.SelectedExpression
 
toQl(Query, DbControl) - Method in class net.sf.basedb.core.query.SharedToRestriction
 
toQl(Query, DbControl) - Method in class net.sf.basedb.core.query.SqlColumnExpression
 
toQl(Query, DbControl) - Method in class net.sf.basedb.core.query.SqrtExpression
 
toQl(Query, DbControl) - Method in class net.sf.basedb.core.query.SubqueryExpression
 
toQl(Query, DbControl) - Method in class net.sf.basedb.core.query.SubtractExpression
 
toQl(Query, DbControl) - Method in class net.sf.basedb.core.query.SumExpression
 
toQl(Query, DbControl) - Method in class net.sf.basedb.core.query.ToDateExpression
 
toQl(Query, DbControl) - Method in class net.sf.basedb.core.query.VirtualColumnExpression
 
toQl(Query, DbControl) - Method in class net.sf.basedb.core.query.VirtualColumnExpression.WrappedExpression
 
toQl(Query, DbControl) - Method in class net.sf.basedb.core.RawBioAssayPropertyExpression
 
toQl(Query, DbControl) - Method in class net.sf.basedb.core.RawDataPropertyExpression
 
toQl(Query, DbControl) - Method in class net.sf.basedb.core.RealJoin
 
toQl(Query, DbControl) - Method in class net.sf.basedb.core.ReporterListJoin
 
toQl(Query, DbControl) - Method in class net.sf.basedb.core.ReporterPropertyExpression
 
ToRawBioAssaySourceItemTransformerFactory - Class in net.sf.basedb.util.listable
Transformer factory implementation for transforming to raw bioassays.
ToRawBioAssaySourceItemTransformerFactory() - Constructor for class net.sf.basedb.util.listable.ToRawBioAssaySourceItemTransformerFactory
 
toReferenceUnit(double) - Method in class net.sf.basedb.core.Unit
Convert a value from this unit to the reference unit.
toRestriction(ASTFunNode) - Method in class net.sf.basedb.util.jep.convert.ASTFunNodeConverter
Get the PostfixMathCommandI object from the function node and delegate conversion to JepRestrictionFunction if that interface is implemented.
toRestriction(Node) - Method in class net.sf.basedb.util.jep.convert.AndConverter
Convert to restriction by calling Restrictions.and(Restriction[]).
toRestriction(Node) - Method in class net.sf.basedb.util.jep.convert.EqualsConverter
Convert to restriction by calling Restrictions.eq(Expression, Expression).
toRestriction(Node) - Method in class net.sf.basedb.util.jep.convert.GreaterConverter
toRestriction(Node) - Method in class net.sf.basedb.util.jep.convert.GreaterEqualsConverter
toRestriction(Node) - Method in class net.sf.basedb.util.jep.convert.LessConverter
toRestriction(Node) - Method in class net.sf.basedb.util.jep.convert.LessEqualsConverter
toRestriction(Node) - Method in class net.sf.basedb.util.jep.convert.NotConverter
Convert to restriction by calling Restrictions.not(Restriction).
toRestriction(Node) - Method in class net.sf.basedb.util.jep.convert.NotEqualsConverter
toRestriction(Node) - Method in class net.sf.basedb.util.jep.convert.OrConverter
Convert to restriction by calling Restrictions.or(Restriction[]).
toRestriction(Node) - Method in class net.sf.basedb.util.jep.InReporterListFunction
Use the Dynamic.isPartOf(ReporterList) method to create a restriction checking that a reporter is found in the reporter list.
toRestriction(Node) - Method in interface net.sf.basedb.util.jep.JepRestrictionFunction
Convert this function to a Restriction that can be used in a query.
toRestriction(Node) - Method in class net.sf.basedb.util.jep.NotInReporterListFunction
Use the Dynamic.isNotPartOf(ReporterList) method to create a restriction checking that a reporter isn't found in the reporter list.
toRestriction(T) - Method in class net.sf.basedb.util.jep.convert.AbstractJepConversionFunction
 
toRestriction(T) - Method in interface net.sf.basedb.util.jep.convert.JepConversionFunction
Convert the object to a restriction.
TORGUE - Static variable in class net.sf.basedb.core.Quantity
The id for the Quantity object representing torque.
ToSampleSourceItemTransformerFactory - Class in net.sf.basedb.util.listable
Transformer factory implementation for transforming to samples.
ToSampleSourceItemTransformerFactory() - Constructor for class net.sf.basedb.util.listable.ToSampleSourceItemTransformerFactory
 
ToSampleSourceItemTransformerFactory(boolean) - Constructor for class net.sf.basedb.util.listable.ToSampleSourceItemTransformerFactory
 
ToSpaceEncoderDecoder - Class in net.sf.basedb.util.encode
Encoder implementation that replaces newline, carriage return, tab and backslash with a space.
ToSpaceEncoderDecoder() - Constructor for class net.sf.basedb.util.encode.ToSpaceEncoderDecoder
 
toString() - Method in class net.sf.basedb.clients.jobagent.slotmanager.Slot
 
toString() - Method in class net.sf.basedb.clients.web.extensions.service.DummyService
 
toString() - Method in class net.sf.basedb.clients.web.extensions.ServletWrapperKey
 
toString() - Method in class net.sf.basedb.clients.web.extensions.skin.ImageRemapper
 
toString() - Method in class net.sf.basedb.clients.web.ModeInfo.ModeContext
 
toString() - Method in class net.sf.basedb.clients.web.ModeInfo
 
toString() - Method in class net.sf.basedb.clients.web.servlet.ExperimentExplorerPlotServlet.ColumnKey
 
toString() - Method in class net.sf.basedb.core.AbstractQuery
 
toString() - Method in class net.sf.basedb.core.AnnotationBetweenRestriction
 
toString() - Method in class net.sf.basedb.core.authentication.AuthenticationMethod
 
toString() - Method in class net.sf.basedb.core.BasicItem
 
toString() - Method in enum class net.sf.basedb.core.BioMaterialEvent.Type
 
toString() - Method in enum class net.sf.basedb.core.BioWell.LockMode
 
toString() - Method in class net.sf.basedb.core.BlockInfo
Get the coordinate as [number;metaGridX,metaGridY]
toString() - Method in class net.sf.basedb.core.BooleanParameterType
 
toString() - Method in class net.sf.basedb.core.ClonableProperty
 
toString() - Method in class net.sf.basedb.core.data.BasicData
The string will look like ClassName[id=55] or ClassName[new].
toString() - Method in class net.sf.basedb.core.data.BooleanParameterValueData
 
toString() - Method in class net.sf.basedb.core.data.DateParameterValueData
 
toString() - Method in class net.sf.basedb.core.data.DoubleParameterValueData
 
toString() - Method in class net.sf.basedb.core.data.FloatParameterValueData
 
toString() - Method in class net.sf.basedb.core.data.IntegerParameterValueData
 
toString() - Method in class net.sf.basedb.core.data.LongParameterValueData
 
toString() - Method in class net.sf.basedb.core.data.MappingCoordinate
Get the coordinate as [plate, row, column]
toString() - Method in class net.sf.basedb.core.data.PlateCoordinate
Get the coordinate as [row, column]
toString() - Method in class net.sf.basedb.core.data.QuotaIndex
 
toString() - Method in class net.sf.basedb.core.data.ReporterListScoreData
 
toString() - Method in class net.sf.basedb.core.data.StringParameterValueData
 
toString() - Method in class net.sf.basedb.core.data.TextParameterValueData
 
toString() - Method in class net.sf.basedb.core.data.TimestampParameterValueData
 
toString() - Method in class net.sf.basedb.core.data.VersionedParameter
Convert the value to a string.
toString() - Method in class net.sf.basedb.core.DateParameterType
 
toString() - Method in class net.sf.basedb.core.dbengine.TableInfo.ColumnInfo
 
toString() - Method in class net.sf.basedb.core.dbengine.TableInfo.ForeignKeyInfo
 
toString() - Method in class net.sf.basedb.core.dbengine.TableInfo.IndexInfo
 
toString() - Method in class net.sf.basedb.core.dbengine.TableInfo.PrimaryKeyInfo
 
toString() - Method in class net.sf.basedb.core.DoubleParameterType
 
toString() - Method in class net.sf.basedb.core.DynamicJoin
 
toString() - Method in class net.sf.basedb.core.DynamicRestriction
 
toString() - Method in class net.sf.basedb.core.ExtraValueExpression
 
toString() - Method in class net.sf.basedb.core.ExtraValueJoin
 
toString() - Method in class net.sf.basedb.core.FeatureCoordinate
Get the coordinate as [block, row, column] or [metarow, metacolumn, row, column]
toString() - Method in enum class net.sf.basedb.core.FeatureIdentificationMethod
 
toString() - Method in class net.sf.basedb.core.FileParameterType
 
toString() - Method in class net.sf.basedb.core.FloatParameterType
 
toString() - Method in enum class net.sf.basedb.core.Formula.AverageMethod
 
toString() - Method in enum class net.sf.basedb.core.Formula.Parser
 
toString() - Method in enum class net.sf.basedb.core.Formula.Type
 
toString() - Method in class net.sf.basedb.core.IntegerParameterType
 
toString() - Method in enum class net.sf.basedb.core.IntensityTransform
 
toString() - Method in enum class net.sf.basedb.core.Item
 
toString() - Method in enum class net.sf.basedb.core.ItemContext.SortDirection
 
toString() - Method in class net.sf.basedb.core.ItemParameterType
 
toString() - Method in class net.sf.basedb.core.ItemProxy
 
toString() - Method in enum class net.sf.basedb.core.Job.ExecutionTime
 
toString() - Method in enum class net.sf.basedb.core.Job.Status
 
toString() - Method in enum class net.sf.basedb.core.Job.Type
 
toString() - Method in enum class net.sf.basedb.core.Location
 
toString() - Method in class net.sf.basedb.core.LongParameterType
 
toString() - Method in class net.sf.basedb.core.MeanRawDataPropertyExpression
 
toString() - Method in class net.sf.basedb.core.Metadata.BasicData2ItemPropertyPath
 
toString() - Method in class net.sf.basedb.core.Metadata.BasicItem2DataPropertyPath
 
toString() - Method in class net.sf.basedb.core.Metadata.CollectionPropertyPath
 
toString() - Method in class net.sf.basedb.core.Metadata.CombinedPropertyPath
 
toString() - Method in class net.sf.basedb.core.Metadata.ComponentPropertyPath
 
toString() - Method in class net.sf.basedb.core.Metadata.DateCopyPropertyPath
 
toString() - Method in class net.sf.basedb.core.Metadata.EntityPropertyPath
 
toString() - Method in class net.sf.basedb.core.Metadata.EvictPropertyPath
 
toString() - Method in class net.sf.basedb.core.Metadata.IdentifierPropertyPath
 
toString() - Method in class net.sf.basedb.core.Metadata.MapPropertyPath
 
toString() - Method in class net.sf.basedb.core.Metadata.NoopPropertyPath
 
toString() - Method in class net.sf.basedb.core.Metadata.ReporterScore2DataPropertyPath
 
toString() - Method in class net.sf.basedb.core.Metadata
 
toString() - Method in class net.sf.basedb.core.MigrateRbaToDba.Rba
 
toString() - Method in enum class net.sf.basedb.core.Operator
 
toString() - Method in class net.sf.basedb.core.PasswordParameterType
 
toString() - Method in class net.sf.basedb.core.Path
Get the string representation of the path.
toString() - Method in class net.sf.basedb.core.PathParameterType
 
toString() - Method in enum class net.sf.basedb.core.Permission
 
toString() - Method in class net.sf.basedb.core.plugin.GuiContext
 
toString() - Method in class net.sf.basedb.core.plugin.Permissions
 
toString() - Method in enum class net.sf.basedb.core.plugin.Plugin.MainType
 
toString() - Method in class net.sf.basedb.core.PluginParameter
 
toString() - Method in class net.sf.basedb.core.ProjectSpecificAnnotationsManager.AnnotationInfo
 
toString() - Method in class net.sf.basedb.core.PropertyFilter
 
toString() - Method in class net.sf.basedb.core.query.AbsExpression
 
toString() - Method in class net.sf.basedb.core.query.AddExpression
 
toString() - Method in class net.sf.basedb.core.query.AndRestriction
 
toString() - Method in class net.sf.basedb.core.query.AnnotationJoin
 
toString() - Method in class net.sf.basedb.core.query.AnyToAnyRestriction
 
toString() - Method in class net.sf.basedb.core.query.AscOrder
 
toString() - Method in class net.sf.basedb.core.query.BetweenRestriction
 
toString() - Method in class net.sf.basedb.core.query.BooleanExpression
 
toString() - Method in class net.sf.basedb.core.query.CaseExpression
 
toString() - Method in class net.sf.basedb.core.query.ConditionalQueryElement
 
toString() - Method in class net.sf.basedb.core.query.CountExpression
 
toString() - Method in class net.sf.basedb.core.query.DescOrder
 
toString() - Method in class net.sf.basedb.core.query.DivideExpression
 
toString() - Method in class net.sf.basedb.core.query.EqRestriction
 
toString() - Method in class net.sf.basedb.core.query.ExpExpression
 
toString() - Method in class net.sf.basedb.core.query.ExpressionSelect
 
toString() - Method in class net.sf.basedb.core.query.FloatExpression
 
toString() - Method in class net.sf.basedb.core.query.GeometricMeanExpression
 
toString() - Method in class net.sf.basedb.core.query.GteqRestriction
 
toString() - Method in class net.sf.basedb.core.query.GtRestriction
 
toString() - Method in class net.sf.basedb.core.query.HqlElementsExpression
 
toString() - Method in class net.sf.basedb.core.query.HqlEntityExpression
 
toString() - Method in class net.sf.basedb.core.query.HqlEntityParameterExpression
 
toString() - Method in class net.sf.basedb.core.query.HqlExpression
Returns the expression field.
toString() - Method in class net.sf.basedb.core.query.HqlIndexExpression
 
toString() - Method in class net.sf.basedb.core.query.HqlInnerJoin
 
toString() - Method in class net.sf.basedb.core.query.HqlLeftJoin
 
toString() - Method in class net.sf.basedb.core.query.HqlPropertyExpression
 
toString() - Method in class net.sf.basedb.core.query.HqlRightJoin
 
toString() - Method in class net.sf.basedb.core.query.HqlSizeExpression
 
toString() - Method in class net.sf.basedb.core.query.IdListRestriction
 
toString() - Method in class net.sf.basedb.core.query.InRestriction
 
toString() - Method in class net.sf.basedb.core.query.IntegerExpression
 
toString() - Method in class net.sf.basedb.core.query.LikeRestriction
 
toString() - Method in class net.sf.basedb.core.query.LogExpression
 
toString() - Method in class net.sf.basedb.core.query.LteqRestriction
 
toString() - Method in class net.sf.basedb.core.query.LtRestriction
 
toString() - Method in class net.sf.basedb.core.query.MaxExpression
 
toString() - Method in class net.sf.basedb.core.query.MeanExpression
 
toString() - Method in class net.sf.basedb.core.query.MinExpression
 
toString() - Method in class net.sf.basedb.core.query.MultiplyExpression
 
toString() - Method in class net.sf.basedb.core.query.NegateExpression
 
toString() - Method in class net.sf.basedb.core.query.NeqRestriction
 
toString() - Method in class net.sf.basedb.core.query.NotRestriction
 
toString() - Method in class net.sf.basedb.core.query.OrRestriction
 
toString() - Method in class net.sf.basedb.core.query.ParameterExpression
 
toString() - Method in class net.sf.basedb.core.query.PowerExpression
 
toString() - Method in class net.sf.basedb.core.query.QuadraticMeanExpression
 
toString() - Method in class net.sf.basedb.core.query.QueryParameter
 
toString() - Method in class net.sf.basedb.core.query.ReporterListExpression
 
toString() - Method in class net.sf.basedb.core.query.RlikeRestriction
 
toString() - Method in class net.sf.basedb.core.query.SelectedExpression
 
toString() - Method in class net.sf.basedb.core.query.SharedToRestriction
 
toString() - Method in class net.sf.basedb.core.query.SqlColumnExpression
 
toString() - Method in class net.sf.basedb.core.query.SqrtExpression
 
toString() - Method in class net.sf.basedb.core.query.SubqueryExpression
 
toString() - Method in class net.sf.basedb.core.query.SubtractExpression
 
toString() - Method in class net.sf.basedb.core.query.SumExpression
 
toString() - Method in class net.sf.basedb.core.query.ToDateExpression
 
toString() - Method in class net.sf.basedb.core.query.VirtualColumnExpression
 
toString() - Method in class net.sf.basedb.core.query.WhenStatement
 
toString() - Method in class net.sf.basedb.core.RawBioAssayPropertyExpression
 
toString() - Method in class net.sf.basedb.core.RawDataPropertyExpression
 
toString() - Method in class net.sf.basedb.core.RawDataType
 
toString() - Method in class net.sf.basedb.core.RealJoin
 
toString() - Method in class net.sf.basedb.core.ReporterListJoin
 
toString() - Method in class net.sf.basedb.core.ReporterPropertyExpression
 
toString() - Method in class net.sf.basedb.core.SessionControl.MainContext
 
toString() - Method in class net.sf.basedb.core.SessionControl.SettingInfo
 
toString() - Method in class net.sf.basedb.core.signal.Signal
 
toString() - Method in class net.sf.basedb.core.signal.SimpleSignalSender
 
toString() - Method in class net.sf.basedb.core.StringParameterType
 
toString() - Method in class net.sf.basedb.core.TimestampParameterType
 
toString() - Method in enum class net.sf.basedb.core.Type
 
toString() - Method in enum class net.sf.basedb.plugins.Base1PluginExecuter.Base1JobParameterType
 
toString() - Method in class net.sf.basedb.plugins.Base1PluginExecuter.JobParameter
 
toString() - Method in class net.sf.basedb.plugins.batchimport.AnnotationIdMethod
 
toString() - Method in class net.sf.basedb.plugins.batchimport.FallbackIdMethod
 
toString() - Method in class net.sf.basedb.plugins.batchimport.FileImporter.PathIdMethod
 
toString() - Method in class net.sf.basedb.plugins.batchimport.InternalIdMethod
 
toString() - Method in class net.sf.basedb.plugins.batchimport.MultiPropertyIdMethod
 
toString() - Method in class net.sf.basedb.plugins.batchimport.PropertyIdMethod
 
toString() - Method in class net.sf.basedb.plugins.PrintMapFlatFileImporter.MetaBlock
 
toString() - Method in class net.sf.basedb.util.AnnotationUtil.AnnotatableWrapper
 
toString() - Method in class net.sf.basedb.util.AnnotationUtil.Cache
 
toString() - Method in class net.sf.basedb.util.AnyToAnyLinkStatistics
 
toString() - Method in class net.sf.basedb.util.bfs.EventType
 
toString() - Method in class net.sf.basedb.util.collections.MultiStepCollectionTransformer
 
toString() - Method in class net.sf.basedb.util.export.spotdata.AnnotationAssayField
 
toString() - Method in class net.sf.basedb.util.export.spotdata.AssayPropertyField
 
toString() - Method in class net.sf.basedb.util.export.spotdata.JepDynamicField
 
toString() - Method in class net.sf.basedb.util.export.spotdata.SimpleDynamicField
 
toString() - Method in class net.sf.basedb.util.extensions.events.EventType
 
toString() - Method in class net.sf.basedb.util.extensions.ExtensionBean
 
toString() - Method in class net.sf.basedb.util.extensions.ExtensionPointBean
 
toString() - Method in class net.sf.basedb.util.extensions.logging.LogEntry
 
toString() - Method in class net.sf.basedb.util.extensions.manager.ExtensionKey
 
toString() - Method in class net.sf.basedb.util.extensions.manager.ExtensionPointKey
 
toString() - Method in class net.sf.basedb.util.extensions.manager.ExtensionsFile
 
toString() - Method in class net.sf.basedb.util.extensions.manager.FactoryParametersKey
 
toString() - Method in class net.sf.basedb.util.extensions.manager.PluginInfoKey
 
toString() - Method in class net.sf.basedb.util.extensions.Registry.RegisteredExtension
 
toString() - Method in class net.sf.basedb.util.extensions.Registry.RegisteredExtensionPoint
 
toString() - Method in class net.sf.basedb.util.extensions.xml.ExtensionPointFilter
 
toString() - Method in class net.sf.basedb.util.GeoLocation
 
toString() - Method in class net.sf.basedb.util.gtf.GtfInputStream.Attribute
 
toString() - Method in class net.sf.basedb.util.JarClassLoader
 
toString() - Method in class net.sf.basedb.util.jobagent.JobAgentInfo
Convert the information to a string that is suitable for sening as an answer to a JobAgentConnection object.
toString() - Method in class net.sf.basedb.util.jobagent.JobInfo
Convert the information to a string that is suitable for sening as an answer to a JobAgentConnection object.
toString() - Method in class net.sf.basedb.util.listable.TransformCache.CacheKey
 
toString() - Method in class net.sf.basedb.util.overview.Failure
 
toString() - Method in class net.sf.basedb.util.overview.Fix
 
toString() - Method in class net.sf.basedb.util.overview.loader.AutoChildNodeLoader
 
toString() - Method in class net.sf.basedb.util.overview.loader.ExtensionChildNodeLoader
 
toString() - Method in class net.sf.basedb.util.overview.Node
 
toString() - Method in enum class net.sf.basedb.util.overview.Severity
 
toString() - Method in class net.sf.basedb.util.overview.validator.ExtensionNodeValidator
 
toString() - Method in class net.sf.basedb.util.parser.ColumnMapper
 
toString() - Method in class net.sf.basedb.util.parser.CompoundMapper
 
toString() - Method in class net.sf.basedb.util.parser.ConstantMapper
 
toString() - Method in class net.sf.basedb.util.parser.FlatFileParser.Data
 
toString() - Method in class net.sf.basedb.util.parser.FlatFileParser.Line
 
toString() - Method in enum class net.sf.basedb.util.parser.FlatFileParser.LineType
 
toString() - Method in class net.sf.basedb.util.parser.JepMapper
 
toString() - Method in class net.sf.basedb.util.resources.ResourceBundleWrapper
 
toString() - Method in class net.sf.basedb.util.StaticCache.LockEntry
 
toString() - Method in class net.sf.basedb.util.StaticCache.LockSafeInputStream
 
toString() - Method in class net.sf.basedb.util.StaticCache.LockSafeOutputStream
 
toString() - Method in class net.sf.basedb.util.timer.PerformanceTimer
Print out time information about each timer.
ToStringComparator<T> - Class in net.sf.basedb.util
An implementation of the Comparator interface which uses the result of the toString method to compare the objects.
ToStringComparator(boolean) - Constructor for class net.sf.basedb.util.ToStringComparator
Create a new comparator.
toStringFormatter - Static variable in class net.sf.basedb.clients.web.taglib.table.CellValue
 
ToStringFormatter<T> - Class in net.sf.basedb.util.formatter
A generic formatter that simply formats objects by calling the toString() method.
ToStringFormatter() - Constructor for class net.sf.basedb.util.formatter.ToStringFormatter
Create a new integer formatter.
toStrings(Collection<T>, Formatter<T>) - Static method in class net.sf.basedb.util.Values
Convert a collection of objects to an array of strings.
total - Variable in class net.sf.basedb.core.SimpleAbsoluteProgressReporter
 
TOTAL - Static variable in class net.sf.basedb.core.QuotaType
The ID for the total quota.
totalBytes - Variable in class net.sf.basedb.clients.web.fileupload.FileUploadProgress
 
totalBytes - Variable in class net.sf.basedb.core.File.UploadStream
Number of bytes written to the stream.
totalBytes - Variable in class net.sf.basedb.plugins.PackedFileExporter
 
totalBytes - Variable in class net.sf.basedb.util.importer.spotdata.BfsImporter.ProgressEventHandler
 
totalBytes - Variable in class net.sf.basedb.util.importer.spotdata.FirstPassSectionSpotsParser
 
totalBytes - Variable in class net.sf.basedb.util.importer.spotdata.SectionReporterListParser
 
totalCount - Variable in class net.sf.basedb.core.AbstractResultList
 
totalCount - Variable in class net.sf.basedb.core.BasicBatcher
 
totalCount - Variable in class net.sf.basedb.core.DataResultIterator
The total number of items.
totalCount - Variable in class net.sf.basedb.core.DynamicResultIterator
The total number of items.
totalCount - Variable in class net.sf.basedb.core.ItemResultIterator
The total number of items.
totalCount - Variable in class net.sf.basedb.core.ReporterScoreResultIterator
The total number of items.
totalCount - Variable in class net.sf.basedb.core.UnmodifiableResultList
 
totalFileSize - Variable in class net.sf.basedb.plugins.AbstractFlatFileImporter
 
totalFileSize - Variable in class net.sf.basedb.plugins.RawDataFlatFileImporter
 
totalInsertCount - Variable in class net.sf.basedb.core.FilterBatcher
The total number of inserts done by this batcher.
totalInsertCount - Variable in class net.sf.basedb.core.MappingBatcher
The total number of inserts done by this batcher.
totalInsertCount - Variable in class net.sf.basedb.core.PositionBatcher
The total number of inserts done by this batcher.
totalInsertCount - Variable in class net.sf.basedb.core.PositionExtraValueBatcher
The total number of inserts done by this batcher.
totalInsertCount - Variable in class net.sf.basedb.core.SpotBatcher
The total number of inserts done by this batcher.
totalInsertCount - Variable in class net.sf.basedb.core.SpotExtraValueBatcher
The total number of inserts done by this batcher.
totalMemory - Variable in class net.sf.basedb.util.jobagent.JobAgentInfo
 
totalRows - Variable in class net.sf.basedb.clients.web.taglib.table.Navigator
The total number of rows.
toType - Variable in class net.sf.basedb.core.AnyToAny.FastLinkLoader
 
toType - Variable in class net.sf.basedb.core.data.AnyToAnyData
 
toUnit(double, Unit) - Method in class net.sf.basedb.core.Unit
Convert a value from this unit to another unit.
toURLString(String) - Method in class net.sf.basedb.core.Path
Get this Path's URL-string encoded with a given character encoding.
toXml() - Method in class net.sf.basedb.plugins.Base1PluginExecuter.JobParameter
 
toXml(Document) - Static method in class net.sf.basedb.util.XmlUtil2
Convert a Document to xml.
toXmlFragment(boolean) - Method in class net.sf.basedb.plugins.executor.ParameterDefinition
Render this parameter definition as an XML fragment.
trace(String) - Method in class net.sf.basedb.util.extensions.logging.ExtensionsLogger
Log a TRACE message with the related SLF4J logger.
trace(String, Throwable) - Method in class net.sf.basedb.util.extensions.logging.ExtensionsLogger
Log a TRACE message with an optional stacktrace.
TRACE - Enum constant in enum class net.sf.basedb.util.extensions.logging.LogLevel
 
TRACE - Enum constant in enum class net.sf.basedb.util.extensions.LoggingErrorHandlerFactory.Level
 
tracker - Variable in class net.sf.basedb.plugins.gtf.GtfReporterImporter
Needed for progress reporting since reading from the source will produce less bytes when wrapped.
tracker - Variable in class net.sf.basedb.plugins.gtf.GtfReporterMapImporter
Needed for progress reporting since reading from the source will produce less bytes when wrapped.
tracker - Variable in class net.sf.basedb.util.parser.FlatFileParser
For keeping track of the number of bytes parsed.
Transactional - Interface in net.sf.basedb.core
This interface is a tagging interface for items that wants to be notified before a transaction is committed or after it has been completed or rollbacked.
Transactional.Action - Enum Class in net.sf.basedb.core
Enumeration constants used to tell the item what is going on in the core.
TransactionalAction - Interface in net.sf.basedb.core
Interface that define hooks for callbacks during transaction commit and rollback.
transactionalActions - Variable in class net.sf.basedb.core.DbControl
List of actions that should be performed when the transaction commits or rollbacks.
transactionDetails - Variable in class net.sf.basedb.core.LogControl
 
TransactionDetails - Class in net.sf.basedb.core.log
Holds information about the curren transaction, such as the logged in user, the active project, the plug-in that is executing, etc.
TransactionDetails(LogControl, SessionControl) - Constructor for class net.sf.basedb.core.log.TransactionDetails
Creates a new transaction details object with information from given session control
TransactionInfo(ChangeHistoryData) - Constructor for class net.sf.basedb.core.ChangeHistory.TransactionInfo
 
transactionPerFile - Variable in class net.sf.basedb.plugins.RawDataFlatFileImporter
 
TRANSCRIPT_ID - Static variable in class net.sf.basedb.util.gtf.GtfInputStream.Attribute
 
transcriptIdIndex - Variable in class net.sf.basedb.util.gtf.GtfInputStream
 
transcriptIds - Variable in class net.sf.basedb.util.gtf.GtfInputStream
 
transferIsComplete() - Method in class net.sf.basedb.clients.web.fileupload.FileUploadProgress
Checks if the transfer is complete or not.
transferRate - Variable in class net.sf.basedb.clients.web.fileupload.FileUpload
The maximum transefer rate (bytes/second)
TransferRateProgressReporter - Class in net.sf.basedb.util
A progress reporter implementation that has a "side-effect" that limits the transfer rate.
TransferRateProgressReporter(AbsoluteProgressReporter, int) - Constructor for class net.sf.basedb.util.TransferRateProgressReporter
Create a new progress reporter.
TransferRateProgressReporter(AbsoluteProgressReporter, int, int) - Constructor for class net.sf.basedb.util.TransferRateProgressReporter
Create a new progress reporter.
transferredBytes - Variable in class net.sf.basedb.clients.web.fileupload.FileUploadProgress
 
transform - Variable in class net.sf.basedb.core.DynamicQuery
 
transform - Variable in class net.sf.basedb.util.importer.spotdata.BaseFileImporter
 
transform - Variable in class net.sf.basedb.util.jep.ChannelFunction
 
transform - Variable in class net.sf.basedb.util.listable.SourceItemTransformerWithCache.TransformerWithCache
 
transform - Variable in class net.sf.basedb.util.listable.TransformCache.CacheKey
 
transform(double) - Method in enum class net.sf.basedb.core.IntensityTransform
Transform a "normal" intensity value to the transformed value.
transform(Collection<? extends I>, Collection<? super I>) - Method in class net.sf.basedb.util.collections.AddAllTransformer
Add all elements of the source collection to the destination collection.
transform(Collection<? extends I>, Collection<? super I>) - Method in class net.sf.basedb.util.collections.RemoveAllTransformer
Remove all elements in the source collection from the destination collection.
transform(Collection<? extends BasicItem>, Collection<? super Integer>) - Method in class net.sf.basedb.util.collections.BasicItemToIdTransformer
Put the ID of each BasicItem in the source collection into the destination collection.
transform(Collection<? extends S>, Collection<? super D>) - Method in interface net.sf.basedb.util.collections.CollectionTransformer
Transform the source collection and store the changes in the destination collection.
transform(Collection<? extends S>, Collection<? super D>) - Method in class net.sf.basedb.util.collections.MultiStepCollectionTransformer
Transform the source collection into the destination collection by applying all intermediate transformers specified in the constructor.
transform(DbControl, F) - Method in interface net.sf.basedb.util.transform.Transformer
Transform the given object into another object.
transform(DbControl, BioMaterialEventSourceData) - Method in class net.sf.basedb.core.BioMaterialEventSource.BioMaterialEventSourceTransformer
 
transform(Expression) - Method in enum class net.sf.basedb.core.IntensityTransform
Transform an expression representing a "normal" intensity value so that it represents the transformed intensity value.
transform(TransformContext, Set<Integer>) - Method in class net.sf.basedb.util.listable.BioSourceToSampleTransformer
Load the ID of all samples that are immediate children to the given set of biosources.
transform(TransformContext, Set<Integer>) - Method in class net.sf.basedb.util.listable.CollectedExtractsToDerivedBioAssayTransformer
 
transform(TransformContext, Set<Integer>) - Method in class net.sf.basedb.util.listable.CollectedExtractsToRawBioAssayTransformer
 
transform(TransformContext, Set<Integer>) - Method in class net.sf.basedb.util.listable.CollectExtracts.CollectChildren
 
transform(TransformContext, Set<Integer>) - Method in class net.sf.basedb.util.listable.CollectExtracts.CollectFromDerivedBioAssays
 
transform(TransformContext, Set<Integer>) - Method in class net.sf.basedb.util.listable.CollectExtracts.CollectFromExtracts
 
transform(TransformContext, Set<Integer>) - Method in class net.sf.basedb.util.listable.CollectExtracts.CollectFromRawBioAssays
 
transform(TransformContext, Set<Integer>) - Method in class net.sf.basedb.util.listable.CollectExtracts.CollectParents
 
transform(TransformContext, Set<Integer>) - Method in class net.sf.basedb.util.listable.CollectExtracts.ResetCollected
 
transform(TransformContext, Set<Integer>) - Method in class net.sf.basedb.util.listable.DerivedBioAssayToChildDerivedBioAssayTransformer
 
transform(TransformContext, Set<Integer>) - Method in class net.sf.basedb.util.listable.DerivedBioAssayToParentDerivedBioAssayTransformer
 
transform(TransformContext, Set<Integer>) - Method in class net.sf.basedb.util.listable.DerivedBioAssayToPhysicalBioAssayTransformer
 
transform(TransformContext, Set<Integer>) - Method in class net.sf.basedb.util.listable.DerivedBioAssayToRawBioAssayTransformer
 
transform(TransformContext, Set<Integer>) - Method in class net.sf.basedb.util.listable.ExtractToChildExtractTransformer
 
transform(TransformContext, Set<Integer>) - Method in class net.sf.basedb.util.listable.ExtractToParentExtractTransformer
 
transform(TransformContext, Set<Integer>) - Method in class net.sf.basedb.util.listable.ExtractToPhysicalBioAssayTransformer
 
transform(TransformContext, Set<Integer>) - Method in class net.sf.basedb.util.listable.ExtractToSampleTransformer
Load the ID of all samples that are immediate parents to the given set of extracts.
transform(TransformContext, Set<Integer>) - Method in class net.sf.basedb.util.listable.PhysicalBioAssayToDerivedBioAssayTransformer
 
transform(TransformContext, Set<Integer>) - Method in class net.sf.basedb.util.listable.PhysicalBioAssayToExtractTransformer
 
transform(TransformContext, Set<Integer>) - Method in class net.sf.basedb.util.listable.PushToParentsTransformer
 
transform(TransformContext, Set<Integer>) - Method in class net.sf.basedb.util.listable.RawBioAssayToDerivedBioAssayTransformer
 
transform(TransformContext, Set<Integer>) - Method in class net.sf.basedb.util.listable.RestrictionTransformer
 
transform(TransformContext, Set<Integer>) - Method in class net.sf.basedb.util.listable.SampleToBioSourceTransformer
Load the ID of all biosources that are immediate parents to the given set of samples.
transform(TransformContext, Set<Integer>) - Method in class net.sf.basedb.util.listable.SampleToChildSampleTransformer
 
transform(TransformContext, Set<Integer>) - Method in class net.sf.basedb.util.listable.SampleToExtractTransformer
Load the ID of all extracts that are immediate children to the given set of samples.
transform(TransformContext, Set<Integer>) - Method in class net.sf.basedb.util.listable.SampleToParentSampleTransformer
 
transform(TransformContext, Set<Integer>) - Method in interface net.sf.basedb.util.listable.SourceItemTransformer
Transform the given set of source item ID:s into a set of target item ID:s
transform(TransformContext, Set<Integer>) - Method in class net.sf.basedb.util.listable.SourceItemTransformerChain
Transform the source items into target items by invoking each step in the transformer chain.
transform(TransformContext, Set<Integer>) - Method in class net.sf.basedb.util.listable.SourceItemTransformerWithCache.TransformerWithCache
If a cache exists check if it has data for this transform already.
TRANSFORM_ORDER - Static variable in class net.sf.basedb.core.SyncFilter
 
transformation - Variable in class net.sf.basedb.core.data.BioAssaySetData
 
transformation - Variable in class net.sf.basedb.util.importer.spotdata.BaseFileImporter
 
transformation - Variable in class net.sf.basedb.util.importer.spotdata.BfsImporter
 
transformation - Variable in class net.sf.basedb.util.importer.spotdata.SectionReporterListParser
 
Transformation - Class in net.sf.basedb.core
A transformation represents an analysis step for an Experiment.
Transformation(TransformationData) - Constructor for class net.sf.basedb.core.Transformation
Creates a new experiment item from the given data.
TRANSFORMATION - Enum constant in enum class net.sf.basedb.core.Item
The item is a Transformation
TRANSFORMATION_NAME - Static variable in class net.sf.basedb.core.plugin.AbstractAnalysisPlugin
The name of the parameter that asks for the name of the transformation.
TRANSFORMATION_NAME - Static variable in class net.sf.basedb.plugins.util.Parameters
The name of the parameter that asks created by Parameters.transformationNameParameter(String, String, String)
TransformationData - Class in net.sf.basedb.core.data
This class holds information about a transformation.
TransformationData() - Constructor for class net.sf.basedb.core.data.TransformationData
 
transformationNameParameter(String, String, String) - Static method in class net.sf.basedb.plugins.util.Parameters
Create a plugin parameter that asks for the name of the transformation.
transformations - Variable in class net.sf.basedb.core.data.BioAssaySetData
 
transformations - Variable in class net.sf.basedb.core.data.ExperimentData
 
transformations - Variable in class net.sf.basedb.core.data.JobData
 
transformations - Variable in class net.sf.basedb.core.data.RawBioAssayData
 
TransformCache - Class in net.sf.basedb.util.listable
A simple cache implementation for holding the result of source item to target item transformation.
TransformCache(int) - Constructor for class net.sf.basedb.util.listable.TransformCache
Creates a new cache with the specified timeout.
TransformCache.CacheEntry - Class in net.sf.basedb.util.listable
 
TransformCache.CacheKey - Class in net.sf.basedb.util.listable
 
transformContext - Variable in class net.sf.basedb.clients.web.extensions.list.RelatedItemHelper
 
transformContext - Variable in class net.sf.basedb.core.PropertyFilter
 
TransformContext - Class in net.sf.basedb.util.listable
Transformation context that can be used to keep track of vital information when doing multi-step transformations.
TransformContext(DbControl) - Constructor for class net.sf.basedb.util.listable.TransformContext
Creates a new transformation context that will use the given DbControl for database access.
transformer - Variable in class net.sf.basedb.clients.web.extensions.list.RelatedItemColumn
 
transformer - Variable in class net.sf.basedb.core.SpecialQuery
 
transformer - Variable in class net.sf.basedb.util.listable.RestrictionTransformer
 
transformer - Variable in class net.sf.basedb.util.listable.SourceItemTransformerWithCache.TransformerWithCache
 
Transformer<T,F> - Interface in net.sf.basedb.util.transform
 
TransformerWithCache(SourceItemTransformer, SyncFilter.SourceItemTransform, String) - Constructor for class net.sf.basedb.util.listable.SourceItemTransformerWithCache.TransformerWithCache
 
translatePermissionsToString(Set<Permission>, String) - Static method in class net.sf.basedb.clients.web.PermissionUtil
 
transporter - Variable in class net.sf.basedb.core.Job.JobSignalTransporter
 
Trashcan - Class in net.sf.basedb.core
This class contains functionality to manage items that have been marked for deletion.
Trashcan() - Constructor for class net.sf.basedb.core.Trashcan
 
Trashcan.CircularRefInfo - Class in net.sf.basedb.core
Helper class for holding information about a single item, other items using it and other information that is relevant for resolving circular references.
tray - Variable in class net.sf.basedb.core.data.BioPlateData
 
trayColumnMapping - Static variable in class net.sf.basedb.plugins.batchimport.BioPlateImporter
 
trayMapper - Variable in class net.sf.basedb.plugins.batchimport.BioPlateImporter
 
tree - Variable in class net.sf.basedb.util.Tree.Entry
 
Tree<E> - Class in net.sf.basedb.util
 
Tree(E) - Constructor for class net.sf.basedb.util.Tree
Create a new tree with the with the default initial capacity (16).
Tree(E, int) - Constructor for class net.sf.basedb.util.Tree
Create a new tree with the with the specified initial capacity.
Tree.ElementIterator - Class in net.sf.basedb.util
An iterator that return elements for each node.
Tree.Entry<E> - Class in net.sf.basedb.util
Represents an entry for a node in the tree.
Tree.EntryIterator - Class in net.sf.basedb.util
An iterator that return entries for each node.
trim(String, int) - Static method in class net.sf.basedb.util.Values
Trim a string to a maximum length.
trimQuotes - Variable in class net.sf.basedb.util.parser.FlatFileParser
If quotes should be trimmed from data values or not.
trimQuotes(String[]) - Method in class net.sf.basedb.util.parser.FlatFileParser
Remove enclosing quotes (" or ') around all columns.
trimQuotesParameter - Static variable in class net.sf.basedb.plugins.AbstractFlatFileImporter
Parameter definition that asks if quotes around quoted values should be removed or not.
trimString(String, int) - Static method in class net.sf.basedb.core.StringUtil
Trim a string to a maximum length.
trimString(String, int) - Static method in class net.sf.basedb.util.Values
Trims long strings to a maximum of maxLength characters.
trimStringMiddle(String, int) - Static method in class net.sf.basedb.core.StringUtil
Trim a string to a maximum length.
trimWhiteSpace - Variable in class net.sf.basedb.util.parser.FlatFileParser.Data
 
trimWhiteSpace - Variable in class net.sf.basedb.util.parser.FlatFileParser
If white space should be trimmed from data values or not.
TRUE - Static variable in class net.sf.basedb.core.migrate.BooleanWriter
 
TRUE - Static variable in class net.sf.basedb.util.excel.ExcelValue
 
TRUE_FALSE - Enum constant in enum class net.sf.basedb.util.formatter.BooleanFormatter.Type
Display true/false.
TRUE_FALSE_CAPS - Enum constant in enum class net.sf.basedb.util.formatter.BooleanFormatter.Type
Display TRUE/FALSE
trueValue - Variable in enum class net.sf.basedb.util.formatter.BooleanFormatter.Type
 
truncate(Date) - Static method in class net.sf.basedb.core.DateUtil
Truncate the given date so that only the date part remains.
trusted - Variable in class net.sf.basedb.core.data.JobAgentSettingsData
 
trusted - Variable in class net.sf.basedb.core.data.PluginDefinitionData
 
tryGetDirectoryPath - Variable in class net.sf.basedb.clients.web.taglib.Select
 
type - Variable in class net.sf.basedb.clients.web.extensions.fileviewer.FileViewerContext
 
type - Variable in class net.sf.basedb.clients.web.extensions.menu.FixedMenuItemFactory
 
type - Variable in class net.sf.basedb.clients.web.extensions.menu.MenuItemBean
 
type - Variable in class net.sf.basedb.clients.web.extensions.menu.PermissionMenuItemFactory
 
type - Variable in class net.sf.basedb.clients.web.taglib.Input
The type of input.
type - Variable in class net.sf.basedb.clients.web.taglib.menu.Menu
If it is a vertical or horizontal menu.
type - Variable in class net.sf.basedb.clients.web.taglib.Page
The type of the current page.
type - Variable in class net.sf.basedb.core.data.FormulaData
 
type - Variable in class net.sf.basedb.core.data.JobData
 
type - Variable in class net.sf.basedb.core.dbengine.TableInfo.ColumnInfo
 
type - Variable in class net.sf.basedb.core.ExtendedProperty
 
type - Variable in class net.sf.basedb.core.FastAnnotationLoader
 
type - Variable in class net.sf.basedb.core.ItemProxy
 
type - Variable in class net.sf.basedb.core.Path
The type of the path.
type - Variable in class net.sf.basedb.core.plugin.GuiContext
 
type - Variable in class net.sf.basedb.core.PluginParameter
Information of the parameter type.
type - Variable in class net.sf.basedb.core.query.QueryParameter
 
type - Variable in class net.sf.basedb.plugins.Base1PluginExecuter.JobParameter
 
type - Variable in class net.sf.basedb.plugins.executor.ParameterDefinition
 
type - Variable in class net.sf.basedb.util.export.spotdata.AssayPropertyField
 
type - Variable in class net.sf.basedb.util.export.spotdata.JepDynamicField
 
type - Variable in class net.sf.basedb.util.export.spotdata.SimpleDynamicField
 
type - Variable in class net.sf.basedb.util.extensions.debug.StringConverter
 
type - Variable in class net.sf.basedb.util.extensions.events.EventTypeFilter
 
type - Variable in class net.sf.basedb.util.extensions.xml.PluginInfo
 
type - Variable in class net.sf.basedb.util.formatter.BooleanFormatter
 
type - Variable in class net.sf.basedb.util.overview.Node
 
type - Variable in class net.sf.basedb.util.parser.FlatFileParser.Line
 
type() - Method in class net.sf.basedb.util.parser.FlatFileParser.Line
The type of the line as determined by the FlatFileParser.parseHeaders() method.
Type - Enum Class in net.sf.basedb.core
This class defines constants for supported value types in BASE.
Type() - Constructor for enum class net.sf.basedb.clients.web.extensions.fileviewer.FileViewerContext.Type
 
Type() - Constructor for enum class net.sf.basedb.core.Path.Type
 
Type() - Constructor for enum class net.sf.basedb.util.overview.Node.Type
 
Type(int) - Constructor for enum class net.sf.basedb.core.plugin.GuiContext.Type
 
Type(int, String) - Constructor for enum class net.sf.basedb.core.BioMaterialEvent.Type
 
Type(int, String) - Constructor for enum class net.sf.basedb.core.Job.Type
 
Type(int, String, boolean, boolean, Type) - Constructor for enum class net.sf.basedb.core.Formula.Type
 
Type(String, String) - Constructor for enum class net.sf.basedb.util.formatter.BooleanFormatter.Type
 
Type(TypeWrapper<?>, int, Class<?>, String, String, String, boolean, boolean, boolean, boolean) - Constructor for enum class net.sf.basedb.core.Type
 
TYPE - Static variable in class net.sf.basedb.core.Annotation
The type of item represented by this class.
TYPE - Static variable in class net.sf.basedb.core.AnnotationSet
The type of item represented by this class.
TYPE - Static variable in class net.sf.basedb.core.AnnotationType
The type of item represented by this class.
TYPE - Static variable in class net.sf.basedb.core.AnnotationTypeCategory
The type of item represented by this class.
TYPE - Static variable in class net.sf.basedb.core.AnyToAny
The type of item represented by this class.
TYPE - Static variable in class net.sf.basedb.core.ArrayBatch
The type of item represented by this class.
TYPE - Static variable in class net.sf.basedb.core.ArrayDesign
The type of item represented by this class.
TYPE - Static variable in class net.sf.basedb.core.ArrayDesignBlock
The type of item represented by this class.
TYPE - Static variable in class net.sf.basedb.core.ArrayDesignPlate
The type of item represented by this class.
TYPE - Static variable in class net.sf.basedb.core.ArraySlide
The type of item represented by this class.
TYPE - Static variable in class net.sf.basedb.core.BioAssay
The type of item represented by this class.
TYPE - Static variable in class net.sf.basedb.core.BioAssaySet
The type of item represented by this class.
TYPE - Static variable in class net.sf.basedb.core.BioMaterialEvent
The type of item represented by this class.
TYPE - Static variable in class net.sf.basedb.core.BioPlate
The type of item represented by this class.
TYPE - Static variable in class net.sf.basedb.core.BioPlateEvent
The type of item represented by this class.
TYPE - Static variable in class net.sf.basedb.core.BioPlateEventParticipant
The type of item represented by this class.
TYPE - Static variable in class net.sf.basedb.core.BioPlateEventType
The type of item represented by this class.
TYPE - Static variable in class net.sf.basedb.core.BioPlateType
The type of item represented by this class.
TYPE - Static variable in class net.sf.basedb.core.BioSource
The type of item represented by this class.
TYPE - Static variable in class net.sf.basedb.core.BioWell
The type of item represented by this class.
TYPE - Static variable in class net.sf.basedb.core.ChangeHistory
The type of item represented by this class.
TYPE - Static variable in class net.sf.basedb.core.Client
The type of item represented by this class.
TYPE - Static variable in class net.sf.basedb.core.ClientDefaultSetting
The type of item represented by this class.
TYPE - Static variable in class net.sf.basedb.core.DataCube
The type of item represented by this class.
TYPE - Static variable in class net.sf.basedb.core.DataCubeColumn
The type of item represented by this class.
TYPE - Static variable in class net.sf.basedb.core.DataCubeExtraValue
The type of item represented by this class.
TYPE - Static variable in class net.sf.basedb.core.DataCubeFilter
The type of item represented by this class.
TYPE - Static variable in class net.sf.basedb.core.DataCubeLayer
The type of item represented by this class.
TYPE - Static variable in class net.sf.basedb.core.DataFileType
The type of item represented by this class.
TYPE - Static variable in class net.sf.basedb.core.DerivedBioAssay
The type of item represented by this class.
TYPE - Static variable in class net.sf.basedb.core.Directory
The type of item represented by this class.
TYPE - Static variable in class net.sf.basedb.core.DiskUsage
The type of item represented by this class.
TYPE - Static variable in class net.sf.basedb.core.Experiment
The type of item represented by this class.
TYPE - Static variable in class net.sf.basedb.core.Extract
The type of item represented by this class.
TYPE - Static variable in class net.sf.basedb.core.ExtraValue
The type of item represented by this class.
TYPE - Static variable in class net.sf.basedb.core.ExtraValueType
The type of item represented by this class.
TYPE - Static variable in class net.sf.basedb.core.File
The type of item represented by this class.
TYPE - Static variable in class net.sf.basedb.core.FileServer
The type of item represented by this class.
TYPE - Static variable in class net.sf.basedb.core.FileSet
The type of item represented by this class.
TYPE - Static variable in class net.sf.basedb.core.FileSetMember
The type of item represented by this class.
TYPE - Static variable in class net.sf.basedb.core.Formula
The type of item represented by this class.
TYPE - Static variable in class net.sf.basedb.core.GlobalDefaultSetting
The type of item represented by this class.
TYPE - Static variable in class net.sf.basedb.core.Group
The type of item represented by this class.
TYPE - Static variable in class net.sf.basedb.core.Hardware
The type of item represented by this class.
TYPE - Static variable in class net.sf.basedb.core.Help
The type of item represented by this class.
TYPE - Static variable in class net.sf.basedb.core.ItemKey
The type of item represented by this class.
TYPE - Static variable in class net.sf.basedb.core.ItemList
The type of item represented by this class.
TYPE - Static variable in class net.sf.basedb.core.ItemSubtype
The type of item represented by this class.
TYPE - Static variable in class net.sf.basedb.core.ItemSubtypeFileType
The type of item represented by this class.
TYPE - Static variable in class net.sf.basedb.core.Job
The type of item represented by this class.
TYPE - Static variable in class net.sf.basedb.core.JobAgent
The type of item represented by this class.
TYPE - Static variable in class net.sf.basedb.core.JobAgentSettings
The type of item represented by this class.
TYPE - Static variable in class net.sf.basedb.core.Kit
The type of item represented by this class.
TYPE - Static variable in class net.sf.basedb.core.Message
The type of item represented by this class.
TYPE - Static variable in class net.sf.basedb.core.MimeType
The type of item represented by this class.
TYPE - Static variable in class net.sf.basedb.core.News
The type of item represented by this class.
TYPE - Static variable in class net.sf.basedb.core.PermissionTemplate
The type of item represented by this class.
TYPE - Static variable in class net.sf.basedb.core.PhysicalBioAssay
The type of item represented by this class.
TYPE - Static variable in class net.sf.basedb.core.Plate
The type of item represented by this class.
TYPE - Static variable in class net.sf.basedb.core.PlateEvent
The type of item represented by this class.
TYPE - Static variable in class net.sf.basedb.core.PlateEventType
The type of item represented by this class.
TYPE - Static variable in class net.sf.basedb.core.PlateGeometry
The type of item represented by this class.
TYPE - Static variable in class net.sf.basedb.core.PlateMapping
The type of item represented by this class.
TYPE - Static variable in class net.sf.basedb.core.PlateType
The type of item represented by this class.
TYPE - Static variable in class net.sf.basedb.core.Platform
The type of item represented by this class.
TYPE - Static variable in class net.sf.basedb.core.PlatformFileType
The type of item represented by this class.
TYPE - Static variable in class net.sf.basedb.core.PlatformVariant
The type of item represented by this class.
TYPE - Static variable in class net.sf.basedb.core.PluginConfiguration
The type of item represented by this class.
TYPE - Static variable in class net.sf.basedb.core.PluginDefinition
The type of item represented by this class.
TYPE - Static variable in class net.sf.basedb.core.PluginType
The type of item represented by this class.
TYPE - Static variable in class net.sf.basedb.core.Project
The type of item represented by this class.
TYPE - Static variable in class net.sf.basedb.core.ProjectKey
The type of item represented by this class.
TYPE - Static variable in class net.sf.basedb.core.Protocol
The type of item represented by this class.
TYPE - Static variable in class net.sf.basedb.core.Quantity
The type of item represented by this class.
TYPE - Static variable in class net.sf.basedb.core.Quota
The type of item represented by this class.
TYPE - Static variable in class net.sf.basedb.core.QuotaType
The type of item represented by this class.
TYPE - Static variable in class net.sf.basedb.core.RawBioAssay
The type of item represented by this class.
TYPE - Static variable in class net.sf.basedb.core.ReporterCloneTemplate
The type of item represented by this class.
TYPE - Static variable in class net.sf.basedb.core.ReporterList
The type of item represented by this class.
TYPE - Static variable in class net.sf.basedb.core.ReporterType
The type of item represented by this class.
TYPE - Static variable in class net.sf.basedb.core.Role
The type of item represented by this class.
TYPE - Static variable in class net.sf.basedb.core.RoleKey
The type of item represented by this class.
TYPE - Static variable in class net.sf.basedb.core.RootRawBioAssay
The type of item represented by this class.
TYPE - Static variable in class net.sf.basedb.core.Sample
The type of item represented by this class.
TYPE - Static variable in class net.sf.basedb.core.Session
The type of item represented by this class.
TYPE - Static variable in class net.sf.basedb.core.Setting
The type of item represented by this class.
TYPE - Static variable in class net.sf.basedb.core.Software
The type of item represented by this class.
TYPE - Static variable in class net.sf.basedb.core.SyncFilter
The type of item represented by this class.
TYPE - Static variable in class net.sf.basedb.core.Tag
The type of item represented by this class.
TYPE - Static variable in class net.sf.basedb.core.Transformation
The type of item represented by this class.
TYPE - Static variable in class net.sf.basedb.core.Unit
The type of item represented by this class.
TYPE - Static variable in class net.sf.basedb.core.User
The type of item represented by this class.
TYPE - Static variable in class net.sf.basedb.core.UserClientSetting
The type of item represented by this class.
TYPE - Static variable in class net.sf.basedb.core.UserDefaultSetting
The type of item represented by this class.
TYPE - Static variable in class net.sf.basedb.core.UserDevice
The type of item represented by this class.
TYPE - Static variable in class net.sf.basedb.core.VirtualDb
The type of item represented by this class.
TYPE - Static variable in class net.sf.basedb.core.Well
The type of item represented by this class.
typeFromLength(Integer) - Static method in class net.sf.basedb.core.StringParameterType
 
types - Variable in class net.sf.basedb.core.log.EntityDetails
 
typeWrapper - Variable in enum class net.sf.basedb.core.Type
 
typeWrapper - Variable in class net.sf.basedb.core.VirtualColumn
The data type of the column.
TypeWrapper<T extends Type> - Class in net.sf.basedb.core.hibernate
Wrapper class for Hibernate types that will try to "hide" issues with the redesign of the type system in Hibernate that is going on in Hibernate 3.5.2 --> Hibernate 3.6.
TypeWrapper(T, int) - Constructor for class net.sf.basedb.core.hibernate.TypeWrapper
 

U

UMinusConverter - Class in net.sf.basedb.util.jep.convert
Convert UMinus function to a Query API Expression.
UMinusConverter() - Constructor for class net.sf.basedb.util.jep.convert.UMinusConverter
 
UNCONFIGURED - Enum constant in enum class net.sf.basedb.core.Job.Status
The job hasn't been configured yet.
UNDEFINED - Static variable in class net.sf.basedb.core.Quota
Quota is is not defined.
UninstalledFileProcessor - Class in net.sf.basedb.clients.web.extensions
File processor implementation that finalizes the uninstallation of an extensions file by removing it from the settings.
UninstalledFileProcessor(ProcessResults) - Constructor for class net.sf.basedb.clients.web.extensions.UninstalledFileProcessor
 
UninstallFilter - Class in net.sf.basedb.clients.web.extensions
Filter implementation that selects only those extensions that was selected for uninstallation by the user in the gui.
UninstallFilter(HttpServletRequest) - Constructor for class net.sf.basedb.clients.web.extensions.UninstallFilter
 
union(Collection<ItemList>, ItemList.DelayedAdditionManager) - Static method in class net.sf.basedb.core.ItemList
Create a set with the union of the items in the given lists.
union(Collection<ReporterList>) - Static method in class net.sf.basedb.core.ReporterList
Create a set with the union of the reporter ID:s in the given lists.
union(IdListRestriction) - Method in class net.sf.basedb.core.query.IdListRestriction
Merge this id list with another list.
unique - Variable in class net.sf.basedb.core.VirtualColumn
If the column must contain unique values or not.
unique - Variable in class net.sf.basedb.plugins.batchimport.MultiPropertyIdMethod
 
unique - Variable in class net.sf.basedb.plugins.batchimport.PropertyIdMethod
 
UNIQUE - Static variable in class net.sf.basedb.core.VirtualColumn
Used in constructor to tell that the column must contain only unique values.
uniqueKeys - Variable in class net.sf.basedb.util.bfs.MetadataWriter
 
uniqueRandom() - Method in class net.sf.basedb.core.DbControl
Generate a random string value that is unique for the given transaction.
uniqueRandoms - Variable in class net.sf.basedb.core.DbControl
Holds random strings that must be unique within a transaction.
uniqueResult() - Method in class net.sf.basedb.core.hibernate.QueryWrapper
 
uniqueResultOptional() - Method in class net.sf.basedb.core.hibernate.QueryWrapper
 
unit - Variable in class net.sf.basedb.clients.web.plugins.ExportedProperty
 
unit - Variable in class net.sf.basedb.clients.web.taglib.table.ColumnDef
 
unit - Variable in class net.sf.basedb.core.data.AnnotationData
 
unit - Variable in class net.sf.basedb.core.data.PropertyFilterData
 
unit - Variable in class net.sf.basedb.core.data.UnitSymbolData
 
unit - Variable in class net.sf.basedb.core.PropertyFilter
 
unit - Variable in class net.sf.basedb.core.snapshot.AnnotationLoaderUtil
 
unit - Variable in class net.sf.basedb.plugins.AnnotationFlatFileImporter.AnnotationValue
 
Unit - Class in net.sf.basedb.core
This class is used to represent a specific unit that can be used with annotations.
Unit(UnitData) - Constructor for class net.sf.basedb.core.Unit
Creates a unit item.
UNIT - Enum constant in enum class net.sf.basedb.core.Item
The item is a Unit.
unitCache - Variable in class net.sf.basedb.plugins.AnnotationFlatFileImporter
 
UnitCache - Class in net.sf.basedb.util.units
Helper class for optimized lookup of units by symbol.
UnitCache() - Constructor for class net.sf.basedb.util.units.UnitCache
Create a new unit cache.
UnitCache(DbControl) - Constructor for class net.sf.basedb.util.units.UnitCache
Create a new unit cache which is ready to be used immediately.
UnitCache.CacheKey - Class in net.sf.basedb.util.units
Units are cached by (quantity,symbol) combination.
UnitConverter - Interface in net.sf.basedb.util.units
Interface for converting values between two units.
unitConvertes - Variable in class net.sf.basedb.core.AnnotationBatcher
 
UnitData - Class in net.sf.basedb.core.data
This class holds information units.
UnitData() - Constructor for class net.sf.basedb.core.data.UnitData
 
unitId - Variable in class net.sf.basedb.core.AnnotationBatcher.CurrentAnnotationInfo
 
unitId - Variable in class net.sf.basedb.core.FastAnnotationLoader.FastAnnotation
The ID of the unit that has been selected for this annotation.
unitId - Variable in class net.sf.basedb.core.snapshot.AnnotationSnapshot
 
unitQuery - Variable in class net.sf.basedb.plugins.batchimport.AbstractItemImporter
 
units - Variable in class net.sf.basedb.core.data.QuantityData
 
units - Variable in class net.sf.basedb.util.units.UnitCache
 
unitSymbol - Variable in class net.sf.basedb.core.snapshot.AnnotationLoaderUtil
 
UnitSymbolData - Class in net.sf.basedb.core.data
This class holds information the symbol that are used with units.
UnitSymbolData() - Constructor for class net.sf.basedb.core.data.UnitSymbolData
 
UnitUtil - Class in net.sf.basedb.util.units
A utility class for working with Unit:s.
UnitUtil() - Constructor for class net.sf.basedb.util.units.UnitUtil
 
UNKNOWN - Enum constant in enum class net.sf.basedb.util.parser.FlatFileParser.LineType
The parsed line is of an unknown type.
UnknownFunction(String) - Constructor for class net.sf.basedb.util.jep.FunctionSafeJep.UnknownFunction
 
unknownLines - Variable in class net.sf.basedb.util.parser.FlatFileParser
Number of unknown lines in the FlatFileParser.nextData() method.
UnknownLoginException - Exception in net.sf.basedb.core.authentication
This exception can be thrown when the login is unknown to the authentication server.
UnknownLoginException(String) - Constructor for exception net.sf.basedb.core.authentication.UnknownLoginException
Create a new UnknownLoginException object
UnknownLoginException(String, String) - Constructor for exception net.sf.basedb.core.authentication.UnknownLoginException
Create a new UnknownLoginException object
UNLIMITED - Static variable in class net.sf.basedb.core.Quota
Quota is unlimited.
unlinkAllFrom(DbControl, BasicItem) - Static method in class net.sf.basedb.core.AnyToAny
Delete all links linking from the specified item.
unlinkFrom(DbControl, BasicItem, String) - Static method in class net.sf.basedb.core.AnyToAny
 
unlinkJobs() - Method in class net.sf.basedb.core.Experiment
Unlink jobs from this experiment that are references from other items NOT PART of the experiment.
unload() - Static method in class net.sf.basedb.core.BatchUtil
Unload all settings.
unload() - Static method in class net.sf.basedb.core.Config
Unload all settings.
unload() - Static method in class net.sf.basedb.core.ExtendedProperties
Unload all settings.
unload() - Static method in class net.sf.basedb.core.HibernateUtil
Unload all settings.
unload() - Static method in class net.sf.basedb.core.Keyring
Unload all settings.
unload() - Static method in class net.sf.basedb.core.Metadata
Unload all settings.
unload() - Static method in class net.sf.basedb.core.PredefinedQuery
Unload all settings.
unload() - Static method in class net.sf.basedb.core.QueryExecutor
 
unload() - Static method in class net.sf.basedb.core.QueryRuntimeFilterFactory
Unload all settings.
unload() - Static method in class net.sf.basedb.core.RawDataTypes
Unload all settings.
unload() - Static method in class net.sf.basedb.core.RawDataUtil
Unload all settings.
unload() - Static method in class net.sf.basedb.core.SystemItems
Unload all settings.
unload() - Static method in class net.sf.basedb.util.EmailUtil
Unload all settings.
UNLOCKED - Enum constant in enum class net.sf.basedb.core.BioWell.LockMode
The well is not locked.
UnmodifiableResultList<T> - Class in net.sf.basedb.core
 
UnmodifiableResultList(List<T>, long) - Constructor for class net.sf.basedb.core.UnmodifiableResultList
 
unpack(DbControl, Directory, InputStream, File, boolean, AbsoluteProgressReporter) - Method in class net.sf.basedb.plugins.Bzip2FileUnpacker
 
unpack(DbControl, Directory, InputStream, File, boolean, AbsoluteProgressReporter) - Method in class net.sf.basedb.plugins.GzipFileUnpacker
 
unpack(DbControl, Directory, InputStream, File, boolean, AbsoluteProgressReporter) - Method in class net.sf.basedb.plugins.TarFileUnpacker
 
unpack(DbControl, Directory, InputStream, File, boolean, AbsoluteProgressReporter) - Method in class net.sf.basedb.plugins.ZipFileUnpacker
Use the ZipUnpacker to unpack the file.
unpack(DbControl, Directory, InputStream, File, boolean, AbsoluteProgressReporter) - Method in interface net.sf.basedb.util.zip.FileUnpacker
Unpack the given input stream into a BASE directory.
UNPACK_DIRECTORY - Static variable in class net.sf.basedb.util.zip.AbstractFileUnpacker
The name of the parameter that asks for the directory where the unpacked files are stored.
unpackType - Static variable in class net.sf.basedb.util.zip.AbstractFileUnpacker
The parameter type for unpack directory.
unpackZipFile(Directory, ZipInputStream, File, boolean, AbsoluteProgressReporter) - Method in class net.sf.basedb.util.zip.ZipUnpacker
Unpack a zip file.
unregisterAgent() - Method in class net.sf.basedb.clients.jobagent.AgentController
 
unregisterAllObjects(ExtensionsFile) - Method in class net.sf.basedb.util.extensions.manager.ExtensionsManager
Unregister all objects know in the file.
unregisterEventHandler(EventHandler) - Method in class net.sf.basedb.util.extensions.Registry
Unregisters an event handler.
unregisterEventHandlers(ClassLoader) - Method in class net.sf.basedb.util.extensions.Registry
Unregister all event handlers that was loaded by the given class loader.
unregisterExtension(String) - Method in class net.sf.basedb.util.extensions.Registry
Unregister an extension.
unregisterExtension(ExtensionsFile.WriteableExtensionsFile, Extension<?>, Registry) - Method in class net.sf.basedb.util.extensions.manager.processor.UnregisterExtensionsProcessor
Unregister the given extension including factory metadata etc.
unregisterExtension(RegisterExtensionsProcessor.FileData, Extension<?>, Registry) - Method in class net.sf.basedb.util.extensions.manager.processor.RegisterExtensionsProcessor
Unregister the given extension if it is not included in the new file data information.
unregisterExtensionPoint(String) - Method in class net.sf.basedb.util.extensions.Registry
Unregister an extension point.
unregisterExtensionPoint(ExtensionsFile.WriteableExtensionsFile, ExtensionPoint<?>, Registry) - Method in class net.sf.basedb.util.extensions.manager.processor.UnregisterExtensionsProcessor
Unregister the given extension point including factory metadata etc.
unregisterExtensionPoint(RegisterExtensionsProcessor.FileData, ExtensionPoint<?>, Registry) - Method in class net.sf.basedb.util.extensions.manager.processor.RegisterExtensionsProcessor
Unregister the given extension point if it is not included in the new file data information.
unregisterExtensionPoints(Registry) - Method in class net.sf.basedb.util.extensions.xml.XmlLoader
Unregister all loaded extension points from a registry.
unregisterExtensions(Registry) - Method in class net.sf.basedb.util.extensions.xml.XmlLoader
Unregister all loaded extensions from a registry.
UnregisterExtensionsProcessor - Class in net.sf.basedb.util.extensions.manager.processor
Extensions file processor implementation that unregisters all extension points and extensions.
UnregisterExtensionsProcessor(ProcessResults) - Constructor for class net.sf.basedb.util.extensions.manager.processor.UnregisterExtensionsProcessor
Create a new processor.
unregisterFactory(ExtensionsFile.WriteableExtensionsFile, Object) - Method in class net.sf.basedb.util.extensions.manager.processor.UnregisterExtensionsProcessor
 
unregisterFactory(RegisterExtensionsProcessor.FileData, Object) - Method in class net.sf.basedb.util.extensions.manager.processor.RegisterExtensionsProcessor
 
unregisterFileOnlyRawDataType(RawDataType) - Static method in class net.sf.basedb.core.RawDataTypes
 
unregisterMetadata(ObjectKey<M>) - Method in class net.sf.basedb.util.extensions.manager.ExtensionsFile.WriteableExtensionsFile
Unregister metadata about an object.
unregisterObject(ObjectKey<?>, ExtensionsFile) - Method in class net.sf.basedb.util.extensions.manager.ExtensionsManager
Unregister an object.
unregisterObject(ObjectKey<O>) - Method in class net.sf.basedb.util.extensions.manager.ExtensionsFile.WriteableExtensionsFile
Unregister an object that was "defined" by this extensions file.
unregisterProtocols(String...) - Method in class net.sf.basedb.clients.jobagent.handlers.MultiProtocolRequestHandler
Unregister a handler for one or more protocols.
unregisterRequestHandler(String...) - Method in class net.sf.basedb.clients.jobagent.Agent
Unregister one or more protocols.
unregisterSignalHandler(SignalHandler) - Method in class net.sf.basedb.clients.web.util.SimpleSignalProgressReporter
 
unregisterSignalHandler(SignalHandler) - Method in class net.sf.basedb.core.signal.AbstractSignalReceiver
Unregister a signal handler.
unregisterSignalHandler(SignalHandler) - Method in class net.sf.basedb.core.signal.DelegatingSignalHandler
Unregister a signal handler.
unregisterSignalHandler(SignalHandler) - Method in interface net.sf.basedb.core.signal.SignalReceiver
Unregister a signal handler from this receiever.
UNRESTRICTED - Static variable in class net.sf.basedb.core.Quota
The ID for the unrestricted quota, which gives users unlimited disk space.
unsafe - Static variable in class net.sf.basedb.plugins.GalExporter
 
UNSAFE - Static variable in class net.sf.basedb.clients.web.plugins.PlainTextTemplate
 
UNSAFE_INLINE_SCRIPTS_ARE_ALLOWED - Static variable in class net.sf.basedb.clients.web.servlet.ContentSecurityPolicyFilter
 
unsafeResources - Static variable in class net.sf.basedb.clients.web.servlet.ContentSecurityPolicyFilter
 
unsafeResourcesPolicy - Variable in class net.sf.basedb.clients.web.servlet.ContentSecurityPolicyFilter
 
UnsafeScriptable - Annotation Interface in net.sf.basedb.clients.web.extensions
Annotation to be used on an Action interface to mark it as a possible candidate for generating unsafe inline javascripts.
UnsavedItemException - Exception in net.sf.basedb.core
This exception is thrown when trying to use an item that has not been saved to the database in places where this is required.
UnsavedItemException() - Constructor for exception net.sf.basedb.core.UnsavedItemException
Create a new UnsavedItemException object.
UnsavedItemException(String) - Constructor for exception net.sf.basedb.core.UnsavedItemException
Create a new UnsavedItemException object with the specified message.
UnsavedItemException(String, Throwable) - Constructor for exception net.sf.basedb.core.UnsavedItemException
Create a new UnsavedItemException object with the specified message.
UnsavedItemException(Throwable) - Constructor for exception net.sf.basedb.core.UnsavedItemException
Create a new UnsavedItemException object.
unselectedText - Variable in class net.sf.basedb.clients.web.taglib.Select
Text to display that for the "unselected" option
UnsupportedFileFormatException - Exception in net.sf.basedb.core
Thrown when an import plug-in is forced to use a file that is not of the correct format.
UnsupportedFileFormatException() - Constructor for exception net.sf.basedb.core.UnsupportedFileFormatException
Create a new UnsupportedFileFormatException object.
UnsupportedFileFormatException(String) - Constructor for exception net.sf.basedb.core.UnsupportedFileFormatException
Create a new UnsupportedFileFormatException object with the specified message.
UnsupportedFileFormatException(String, Throwable) - Constructor for exception net.sf.basedb.core.UnsupportedFileFormatException
Create a new UnsupportedFileFormatException object with the specified message.
UnsupportedFileFormatException(Throwable) - Constructor for exception net.sf.basedb.core.UnsupportedFileFormatException
Create a new UnsupportedFileFormatException object.
UnsupportedSignalException - Exception in net.sf.basedb.core.signal
This exception is thrown by signal handlers and others that doesn't support a given signal.
UnsupportedSignalException(Signal) - Constructor for exception net.sf.basedb.core.signal.UnsupportedSignalException
Create a new UnsupportedSignalException.
UnsupportedSignalException(Signal, String) - Constructor for exception net.sf.basedb.core.signal.UnsupportedSignalException
Create a new UnsupportedSignalException with a custom message.
unTransform(double) - Method in enum class net.sf.basedb.core.IntensityTransform
Un-transform a transformed intensity value back to a regular intensity value.
unTransform(Expression) - Method in enum class net.sf.basedb.core.IntensityTransform
Un-transform an expression representing a transformed intensity value so that it represents a raw intensity value.
untransformIntensities - Variable in class net.sf.basedb.core.VirtualColumn
 
untransformIntensities() - Method in class net.sf.basedb.core.VirtualColumn
A flag indicating if transformed intensity valus belonging to a bioassay set should be untransformed as part of a query.
unverifiedDeviceInfo - Variable in class net.sf.basedb.core.SessionControl
Temporary login information before a device is verified.
UnverifiedDeviceInfo() - Constructor for class net.sf.basedb.core.SessionControl.UnverifiedDeviceInfo
 
unwrap() - Method in class net.sf.basedb.util.overview.cache.DirectionalCacheKey
Get the original cache key passed to the constructor.
unwrap() - Method in class net.sf.basedb.util.overview.cache.IndexedCacheKey
Get the original cache key passed to the constructor.
unwrap(Class<T>) - Method in class net.sf.basedb.core.hibernate.QueryWrapper
 
unwrap(Class<T>) - Method in class net.sf.basedb.core.hibernate.SessionWrapper
 
unwrapIfProxy(Session, BasicData) - Static method in class net.sf.basedb.core.HibernateUtil
If the given data object is a proxy, load the real data object instead.
update(D) - Method in class net.sf.basedb.core.BasicBatcher
Update a data object.
update(Object) - Method in class net.sf.basedb.core.hibernate.SessionWrapper
 
update(Object) - Method in class net.sf.basedb.core.hibernate.StatelessSessionWrapper
 
update(String, Object) - Method in class net.sf.basedb.core.hibernate.SessionWrapper
 
update(String, Object) - Method in class net.sf.basedb.core.hibernate.StatelessSessionWrapper
 
update(FeatureData) - Method in class net.sf.basedb.core.FeatureBatcher
Always throws a PermissionDeniedException, since a feature cannot be modifed once it has been created.
update(RawData) - Method in class net.sf.basedb.core.RawDataBatcher
Always throws a PermissionDeniedException, since raw data cannot be modifed once it has been created.
update(About) - Method in class net.sf.basedb.util.extensions.Registry.RegisteredAbout
Update the registered information.
update(Extension<A>, ClassLoader) - Method in class net.sf.basedb.util.extensions.Registry.RegisteredExtension
Update the registered information.
update(ExtensionPoint<A>, ClassLoader) - Method in class net.sf.basedb.util.extensions.Registry.RegisteredExtensionPoint
Update the registered information.
Update - Class in net.sf.basedb.core
This class contains static methods used to update items already in the database.
Update() - Constructor for class net.sf.basedb.core.Update
 
UPDATE - Enum constant in enum class net.sf.basedb.core.hibernate.SchemaGenerator.Mode
Updating an existing installation.
UPDATE - Enum constant in enum class net.sf.basedb.core.log.ChangeType
 
UPDATE - Enum constant in enum class net.sf.basedb.core.Transactional.Action
The item is an existing item which is beeing updated.
UPDATE_INTERVAL - Static variable in class net.sf.basedb.core.Job.ProgressReporterImpl
Number of miliseconds between updates to the database.
UPDATE_PERCENT - Static variable in class net.sf.basedb.core.Job.ProgressReporterImpl
Min percentage difference between updates to the database.
Update.DropColumnChange - Class in net.sf.basedb.core
Action that drops a column in a table.
Update.SchemaChange - Class in net.sf.basedb.core
Action that need to make some change to the database schem after the main transaction in Update.adjustExistingItems(ProgressReporter, int, String, String) has finished.
updateable - Variable in class net.sf.basedb.core.ExtendedProperty
 
updateAnnotations - Variable in class net.sf.basedb.core.AnnotationBatcher
 
updateAnnotations(DbControl, Annotatable, Annotatable, HttpServletRequest) - Static method in class net.sf.basedb.clients.web.Base
Update annotations on an item taking concurrent modifications into account.
updateArrayDesign(ArrayDesign, FeatureIdentificationMethod, ProgressReporter) - Method in class net.sf.basedb.core.RawBioAssay
Set the ArrayDesign this raw data uses.
UpdateBatcher(Connection, String, int...) - Constructor for class net.sf.basedb.core.AnnotationBatcher.UpdateBatcher
Prepare a new batcher for the given SQL statement.
updateCount - Variable in class net.sf.basedb.core.BasicBatcher
 
UPDATED - Enum constant in enum class net.sf.basedb.core.AnnotationBatcher.Change
An existing annotation was updated.
updateData(Session, BasicData) - Static method in class net.sf.basedb.core.HibernateUtil
Update an existing data object in the database.
updateDatabase(ProgressReporter, String, String) - Static method in class net.sf.basedb.core.Update
Update the database by modifying existing items to follow new requirements.
updatedBytes - Variable in class net.sf.basedb.core.Experiment
 
updateDiskUsage(BasicItem) - Method in class net.sf.basedb.core.DbControl
Update the disk usage information for a DiskConsumable item.
updateEntry(AnnotationBatcher.UpdateBatcher) - Method in class net.sf.basedb.core.MigrateRbaToDba.Itemlist
Update the item list entry.
updateExisting - Variable in class net.sf.basedb.plugins.ReporterFlatFileImporter
 
updateExistingItems - Variable in class net.sf.basedb.plugins.batchimport.AbstractItemImporter
 
updateFailureCountOnNodes() - Method in class net.sf.basedb.util.overview.GenericOverview
Updates the failure count (warnings and errors) on all nodes.
updateFiles(DbControl, FileStoreEnabled, HttpServletRequest, boolean, ItemContext, int) - Static method in class net.sf.basedb.clients.web.Base
Update files that are associated with a FileStoreEnabled item.
updateFreeWells(int) - Method in class net.sf.basedb.core.data.BioPlateData
Update the number of free wells with the given difference
updateFreeWells(BioPlateData, int) - Method in class net.sf.basedb.core.MeasuredBioMaterial
 
updateIndexes - Variable in class net.sf.basedb.core.hibernate.DbIndexWork
 
updateItem(DbControl, I, FlatFileParser.Data) - Method in class net.sf.basedb.plugins.batchimport.AbstractItemImporter
Update an item with data from the current line.
updateItem(DbControl, AnnotationType, FlatFileParser.Data) - Method in class net.sf.basedb.plugins.batchimport.AnnotationTypeImporter
 
updateItem(DbControl, ArrayBatch, FlatFileParser.Data) - Method in class net.sf.basedb.plugins.batchimport.ArrayBatchImporter
 
updateItem(DbControl, ArrayDesign, FlatFileParser.Data) - Method in class net.sf.basedb.plugins.batchimport.ArrayDesignImporter
 
updateItem(DbControl, ArraySlide, FlatFileParser.Data) - Method in class net.sf.basedb.plugins.batchimport.ArraySlideImporter
 
updateItem(DbControl, BioPlate, FlatFileParser.Data) - Method in class net.sf.basedb.plugins.batchimport.BioPlateImporter
 
updateItem(DbControl, BioSource, FlatFileParser.Data) - Method in class net.sf.basedb.plugins.batchimport.BioSourceImporter
 
updateItem(DbControl, DerivedBioAssay, FlatFileParser.Data) - Method in class net.sf.basedb.plugins.batchimport.DerivedBioAssayImporter
 
updateItem(DbControl, Extract, FlatFileParser.Data) - Method in class net.sf.basedb.plugins.batchimport.ExtractImporter
 
updateItem(DbControl, File, FlatFileParser.Data) - Method in class net.sf.basedb.plugins.batchimport.FileImporter
 
updateItem(DbControl, Kit, FlatFileParser.Data) - Method in class net.sf.basedb.plugins.batchimport.KitImporter
 
updateItem(DbControl, PhysicalBioAssay, FlatFileParser.Data) - Method in class net.sf.basedb.plugins.batchimport.PhysicalBioAssayImporter
 
updateItem(DbControl, RawBioAssay, FlatFileParser.Data) - Method in class net.sf.basedb.plugins.batchimport.RawBioAssayImporter
 
updateItem(DbControl, Sample, FlatFileParser.Data) - Method in class net.sf.basedb.plugins.batchimport.SampleImporter
 
updateItem(DbControl, Tag, FlatFileParser.Data) - Method in class net.sf.basedb.plugins.batchimport.TagImporter
 
updateItemLists(Connection, Map<Integer, Integer>) - Method in class net.sf.basedb.core.MigrateRbaToDba
Update item lists with raw bioassays to item lists with derived bioassays.
updateItemSubtype(DbControl, Subtypable, FlatFileParser.Data) - Method in class net.sf.basedb.plugins.batchimport.AbstractItemImporter
If a mapping for item subtype has been specified or if a single subtype was selected for item identification in this job, this method is will update the subtype on the item.
updateItemTable - Variable in class net.sf.basedb.core.AnnotationBatcher
 
updateKeys(DbControl) - Method in class net.sf.basedb.core.MultiPermissions
Generate the new keys and update all items with the new keys.
updateKeys(DbControl, boolean) - Method in class net.sf.basedb.core.MultiPermissions
Generate the new keys and update all items with the new keys.
updateLastAccess() - Method in class net.sf.basedb.core.AbstractBatcher
Update the last access time so the session control doesn't get cleaned up.
updateLastAccess() - Method in class net.sf.basedb.core.SessionControl
Update the time this object last was accessed.
updateMode - Variable in class net.sf.basedb.plugins.batchimport.AbstractItemImporter
 
updateMode - Variable in class net.sf.basedb.plugins.batchimport.AnyToAnyImporter
 
updateMultiLineItem(DbControl, I, FlatFileParser.Data, int) - Method in class net.sf.basedb.plugins.batchimport.AbstractItemImporter
Update an item with data from a multi-line entry.
updateMultiLineItem(DbControl, AnnotationType, FlatFileParser.Data, int) - Method in class net.sf.basedb.plugins.batchimport.AnnotationTypeImporter
 
updateMultiLineItem(DbControl, ArrayDesign, FlatFileParser.Data, int) - Method in class net.sf.basedb.plugins.batchimport.ArrayDesignImporter
Add data files
updateMultiLineItem(DbControl, DerivedBioAssay, FlatFileParser.Data, int) - Method in class net.sf.basedb.plugins.batchimport.DerivedBioAssayImporter
Add data files
updateMultiLineItem(DbControl, Extract, FlatFileParser.Data, int) - Method in class net.sf.basedb.plugins.batchimport.ExtractImporter
If the sample is pooled, add the parent sample.
updateMultiLineItem(DbControl, PhysicalBioAssay, FlatFileParser.Data, int) - Method in class net.sf.basedb.plugins.batchimport.PhysicalBioAssayImporter
Add parent extracts and the used quantities
updateMultiLineItem(DbControl, RawBioAssay, FlatFileParser.Data, int) - Method in class net.sf.basedb.plugins.batchimport.RawBioAssayImporter
Add data files
updateMultiLineItem(DbControl, Sample, FlatFileParser.Data, int) - Method in class net.sf.basedb.plugins.batchimport.SampleImporter
If the sample is pooled, add the parent sample.
updateOverrideId - Variable in class net.sf.basedb.core.AnnotationBatcher
 
updatePermissions(DbControl, Shareable, FlatFileParser.Data, boolean) - Method in class net.sf.basedb.plugins.batchimport.AbstractItemImporter
If a mapping for a permission template has been specified for the job, this method is automatically called.
updateProgress(Session, int, String) - Method in class net.sf.basedb.core.Job.ProgressReporterImpl
 
updatePropertyOrder - Variable in class net.sf.basedb.core.BasicBatcher
 
updateRemainingQuantity(DbControl, MeasuredBioMaterialData, Float) - Static method in class net.sf.basedb.core.MeasuredBioMaterial
Update the remaining quantity of a biomaterial.
updateSource - Variable in class net.sf.basedb.core.ReporterBatcher
A string to hold the name of the source, used to update the reporters.
updateSql - Variable in class net.sf.basedb.core.BasicBatcher
 
updateStatement - Variable in class net.sf.basedb.core.BasicBatcher
 
updateToSchemaVersion101(Session) - Static method in class net.sf.basedb.core.Update
Remove duplicate file set members.
updateToSchemaVersion102(Session) - Static method in class net.sf.basedb.core.Update
Add unique index on FileSetMembers(fileset_id,datafiletype_id,file_id)
updateToSchemaVersion110(Session, int) - Static method in class net.sf.basedb.core.Update
Move derived bioassay parent items to different tables.
updateToSchemaVersion111(Session, ProgressReporter) - Static method in class net.sf.basedb.core.Update
Remove annotation sets that have no annotation values and no inherited annotations.
updateToSchemaVersion112(Session, ProgressReporter) - Static method in class net.sf.basedb.core.Update
Ensure that parent_id and parent_type in BioMaterials table is correct when compared to BioMaterialEventSources2 table.
updateToSchemaVersion114(Session, ProgressReporter) - Static method in class net.sf.basedb.core.Update
Ensure that old log entries for annotation changes use the same text format that is used after this update.
updateToSchemaVersion120(Session) - Static method in class net.sf.basedb.core.Update
Transfer existing biomaterial lists to item lists.
updateToSchemaVersion121(Session) - Static method in class net.sf.basedb.core.Update
Remove all '0' members from item lists and decrease the size of the list with 1 where it is found.
updateToSchemaVersion122(Session) - Static method in class net.sf.basedb.core.Update
Move all entries from the "ExperimentRawBioAssays" table to "RootRawBioAssays".
updateToSchemaVersion123(Session) - Static method in class net.sf.basedb.core.Update
Convert all entries from the "InheritedAnnotationSets" table to entries in the "InheritedAnnotations" table.
updateToSchemaVersion124(Session) - Static method in class net.sf.basedb.core.Update
Inherited annotations in the "InheritedAnnotations" table must be converted to entries in the "Annotations" table with source=1 (INHERITED)
updateToSchemaVersion125(Session) - Static method in class net.sf.basedb.core.Update
Experimental factors in existing experiments are inherited to the RootRawBioAssayData items from the RawBioAssayData parents.
updateToSchemaVersion126(Session) - Static method in class net.sf.basedb.core.Update
Fix the conversion formula for Fahrenheit.
updateToSchemaVersion131(Session, ProgressReporter) - Static method in class net.sf.basedb.core.Update
Fix the old_values for date annotations in the change history.
updateToSchemaVersion132(Session, ProgressReporter) - Static method in class net.sf.basedb.core.Update
Delete annotation entries that have no values.
updateToSchemaVersion136(Session, ProgressReporter) - Static method in class net.sf.basedb.core.Update
Update the Jobs table by splitting the server value into a server+node value for all entries that contain '[..]'.
updateToSchemaVersion144(Session, int) - Static method in class net.sf.basedb.core.Update
Update the Files table by setting location=0 (offline) on all files with location=2 (secondary), remove the 'action' column and all stored contexts using the 'action' column.
updateToSchemaVersion147(Session, int) - Static method in class net.sf.basedb.core.Update
 
updateToSchemaVersion151(Session, int, ProgressReporter) - Static method in class net.sf.basedb.core.Update
 
updateToSchemaVersion154(Session, int, ProgressReporter) - Static method in class net.sf.basedb.core.Update
 
updateURLMetadata() - Method in class net.sf.basedb.core.File
If this is an external file, try to update the metadata.
upload(InputStream, boolean) - Method in class net.sf.basedb.core.File
Upload a physical file for this file item.
upload(InputStream, boolean, Boolean) - Method in class net.sf.basedb.core.File
Upload a physical file for this file item.
Upload - Class in net.sf.basedb.clients.web.servlet
The upload servlet is used to handle single file uploads.
Upload() - Constructor for class net.sf.basedb.clients.web.servlet.Upload
 
UploadAbortedException - Exception in net.sf.basedb.clients.web.fileupload
 
UploadAbortedException() - Constructor for exception net.sf.basedb.clients.web.fileupload.UploadAbortedException
 
uploadCompressed - Variable in class net.sf.basedb.core.File
If the next upload should use compression or not.
uploadCompressed() - Method in class net.sf.basedb.core.File
Return the result of auto-compress check from the last call to File.setMimeTypeAuto(String, ItemSubtype).
UploadedFile - Class in net.sf.basedb.clients.web.fileupload
Objects of this class can be used to get information about an uploaded file and save the file to a directory in the filesystem.
UploadedFile(FileUpload, String, String, String) - Constructor for class net.sf.basedb.clients.web.fileupload.UploadedFile
Create a new UploadedFile object.
uploadFiles(DbControl, Directory, File, FileFilter, boolean, ProgressReporter) - Static method in class net.sf.basedb.util.FileUtil
Upload multiple files to BASE.
UploadStatus() - Constructor for class net.sf.basedb.clients.web.fileupload.FileUpload.UploadStatus
Create a new UploadStatus object.
uploadStream - Variable in class net.sf.basedb.core.File
A stream for uploading a physical file.
UploadStream() - Constructor for class net.sf.basedb.clients.web.fileupload.FileUpload.UploadStream
 
UploadStream(File, boolean, boolean, boolean, boolean) - Constructor for class net.sf.basedb.core.File.UploadStream
Create a new UploadStream and connect it to the given file.
upperLimit - Variable in class net.sf.basedb.core.DoubleParameterType
The upper limit of the parameter.
upperLimit - Variable in class net.sf.basedb.core.FloatParameterType
The upper limit of the parameter.
upperLimit - Variable in class net.sf.basedb.core.IntegerParameterType
The upper limit of the parameter.
upperLimit - Variable in class net.sf.basedb.core.LongParameterType
The upper limit of the parameter.
uri - Variable in class net.sf.basedb.util.extensions.manager.ExtensionsFile
 
uri - Variable in class net.sf.basedb.util.uri.http.HttpConnectionManager
 
uri - Variable in class net.sf.basedb.util.uri.UriMetadata
 
UriMetadata - Class in net.sf.basedb.util.uri
Holds metadata about the data referenced by given URI.
UriMetadata(URI) - Constructor for class net.sf.basedb.util.uri.UriMetadata
Create an empty metadata object for the given URI.
url - Variable in class net.sf.basedb.clients.web.extensions.plot.PlotGeneratorBean
 
url - Variable in class net.sf.basedb.clients.web.extensions.startpage.FixedStartPageFactory
 
url - Variable in class net.sf.basedb.clients.web.extensions.startpage.StartPageBean
 
url - Variable in class net.sf.basedb.core.authentication.ExtraUserInformation
 
url - Variable in class net.sf.basedb.core.data.FileData
 
url - Variable in class net.sf.basedb.core.data.PluginDefinitionData
 
url - Variable in class net.sf.basedb.core.data.UserData
 
url - Variable in class net.sf.basedb.core.ExtendedPropertyLinker
 
url - Variable in class net.sf.basedb.core.plugin.AboutImpl
 
url - Variable in class net.sf.basedb.util.extensions.AboutBean
 
url - Variable in class net.sf.basedb.util.extensions.Registry.RegisteredAbout
 
URL_REGEXP - Static variable in class net.sf.basedb.clients.web.util.HTML
This pattern can be used to find URL:s.
urlColumnMapping - Static variable in class net.sf.basedb.plugins.batchimport.FileImporter
 
urlEncode(String) - Static method in class net.sf.basedb.clients.web.util.HTML
Encode URL-unsafe characters in a string.
urlMapper - Variable in class net.sf.basedb.plugins.batchimport.FileImporter
 
UsableDataFileType - Interface in net.sf.basedb.core
Utility interface for collecting information about data file requirements when used on a certain platform/variant or item subtype.
UsableParentFilter() - Constructor for class net.sf.basedb.util.annotations.InheritAnnotationsManager.UsableParentFilter
 
usableUnitColumnMapping - Static variable in class net.sf.basedb.plugins.batchimport.AnnotationTypeImporter
Column mapping parameter for "Usable unit".
usableUnitMapper - Variable in class net.sf.basedb.plugins.batchimport.AnnotationTypeImporter
 
usableUnits - Variable in class net.sf.basedb.core.data.AnnotationTypeData
 
USE - Enum constant in enum class net.sf.basedb.core.Permission
This permission allows a user to use/link to an item.
useAutoDetection() - Method in interface net.sf.basedb.util.uri.ConnectionManagerFactory
Does this factory support auto-detection if an URI is supported or not?
useAutoDetection() - Method in class net.sf.basedb.util.uri.http.HttpConnectionManagerFactory
 
useBase2ColumnNames(int) - Method in class net.sf.basedb.util.importer.spotdata.BaseFileImporter
Reconfigure the parser to use BASE 2 column names instead of BASE 1 column names.
useBulletList() - Method in class net.sf.basedb.core.snapshot.AnnotationLoaderUtil
When displaying annotations with multiple values, should use a bullet list be used or a simple comma-separated list.
useCloned - Variable in class net.sf.basedb.core.ReporterPropertyExpression
 
useCloned(ClonableReporterQuery) - Method in class net.sf.basedb.core.ReporterPropertyExpression
Check if this reporter property should use the cloned reporter for the given query or not.
useClonedReporters - Variable in class net.sf.basedb.core.DynamicQuery
 
useClonedReporters - Variable in class net.sf.basedb.core.DynamicReporterQuery
 
useClonedReporters() - Method in interface net.sf.basedb.core.ClonableReporterQuery
Checks if this query is using cloned reporter or not by default.
useClonedReporters() - Method in class net.sf.basedb.core.DynamicQuery
Checks if this query is using cloned reporter or not by default.
useClonedReporters() - Method in class net.sf.basedb.core.DynamicReporterQuery
Checks if this query is using cloned reporter or not by default.
useCollectedAsSource - Variable in class net.sf.basedb.util.listable.CollectExtracts.CollectChildren
 
useCollectedAsSource - Variable in class net.sf.basedb.util.listable.CollectExtracts.CollectParents
 
useColors - Variable in class net.sf.basedb.core.data.ColoringData
 
usedColumnsParameter - Variable in class net.sf.basedb.plugins.Base1PluginExecuter
The reporter fields that should be exported as a tab separated string of column headers.
useDeviceVerification - Variable in class net.sf.basedb.core.data.UserData
 
usedFeatures - Variable in class net.sf.basedb.core.RawDataBatcher
Keep track of the used features to make sure that no more than raw data spot references the same feature.
usedFieldsParameter - Variable in class net.sf.basedb.plugins.Base1PluginExecuter
The spot fields that should be exported as a tab separated string of column headers.
usedFiles - Variable in class net.sf.basedb.util.bfs.AbstractDataWriterFactory
 
usedIds - Variable in class net.sf.basedb.util.bfs.AnnotationParser
 
usedIds - Variable in class net.sf.basedb.util.bfs.AnnotationWriter
 
useDifference() - Method in interface net.sf.basedb.core.DiskConsumable
If this item reports the difference in used bytes or the absolute number.
useDifference() - Method in class net.sf.basedb.core.Experiment
TRUE if the experiment has been saved to the database, FALSE otherwise.
useDifference() - Method in class net.sf.basedb.core.File
Always FALSE.
useDifference() - Method in class net.sf.basedb.core.RawBioAssay
Always FALSE.
usedKeys - Variable in class net.sf.basedb.util.bfs.MetadataWriter
 
usedMemory - Variable in class net.sf.basedb.util.jobagent.JobAgentInfo
 
usedQuantity - Variable in class net.sf.basedb.core.data.BioMaterialEventData
 
usedQuantity - Variable in class net.sf.basedb.core.data.BioMaterialEventSourceData
 
usedQuantity - Variable in class net.sf.basedb.core.MeasuredBioMaterial.RemainingQuantityAction
 
usedQuantityColumnMapping - Static variable in class net.sf.basedb.plugins.batchimport.SampleImporter
Column mapping parameter for the used quantity from the parent.
usedQuantityMapper - Variable in class net.sf.basedb.plugins.batchimport.ExtractImporter
 
usedQuantityMapper - Variable in class net.sf.basedb.plugins.batchimport.PhysicalBioAssayImporter
 
usedQuantityMapper - Variable in class net.sf.basedb.plugins.batchimport.SampleImporter
 
UsedQuantityMapper - Class in net.sf.basedb.plugins.batchimport
A special mapper for "Used quantity" values.
UsedQuantityMapper(Mapper) - Constructor for class net.sf.basedb.plugins.batchimport.UsedQuantityMapper
 
usedSections - Variable in class net.sf.basedb.util.bfs.MetadataWriter
 
usedSlots - Variable in class net.sf.basedb.clients.jobagent.slotmanager.InternalSlotManager
 
usedSlots - Variable in class net.sf.basedb.core.InternalJobQueue
The current number of threads executing in each slot.
usedUnits - Variable in class net.sf.basedb.core.data.UnitData
 
useEditExtensions(JspContext) - Static method in class net.sf.basedb.clients.web.extensions.edit.EditUtil
Use edit-dialog extensions for a given gui context.
useExtensions(String, JspContext) - Static method in class net.sf.basedb.clients.web.extensions.edit.EditUtil
 
useExtensions(JspContext) - Static method in class net.sf.basedb.clients.web.extensions.list.ListColumnUtil
 
useExtensions(JspContext) - Static method in class net.sf.basedb.clients.web.extensions.toolbar.ToolbarUtil
Use toolbar extensions for a given gui context.
useExtensions(JspContext, String...) - Static method in class net.sf.basedb.clients.web.extensions.ExtensionsControl
Use extensions from one or more extension points.
useExtensions(JspContext, ExtensionsFilter) - Static method in class net.sf.basedb.clients.web.extensions.list.ListColumnUtil
Use list column extensions for a given gui context.
useExtensions(JspContext, ExtensionsFilter, String...) - Static method in class net.sf.basedb.clients.web.extensions.ExtensionsControl
 
useExtensions(ClientContext, ExtensionsFilter, String...) - Method in class net.sf.basedb.util.extensions.Registry
Use extensions from one or more extension points.
useExtensions(ExtensionsFilter) - Static method in class net.sf.basedb.core.ServicesUtil
Create an extensions invoker for the services extensions.
useIncludeSpot() - Method in interface net.sf.basedb.util.DynamicFilter
If the includeSpot method must be called for each spot or not.
useIncludeSpot() - Method in class net.sf.basedb.util.IncludeExcludeFilter
Always true.
useInDistinctCount - Variable in class net.sf.basedb.core.query.ExpressionSelect
 
useInDistinctCount() - Method in class net.sf.basedb.core.query.ExpressionSelect
 
useInDistinctCount() - Method in interface net.sf.basedb.core.query.Select
If this expression should be use in count distinct queries or not.
useInternalJobQueue - Variable in class net.sf.basedb.core.data.PluginDefinitionData
 
useJavaSysMon - Static variable in class net.sf.basedb.clients.jobagent.handlers.InfoRequestHandler
 
useNewLine - Variable in class net.sf.basedb.util.ConsoleProgressReporter
 
useNullIfException - Variable in class net.sf.basedb.util.parser.FlatFileParser
If null should be returned if a (numeric) value can't be parsed.
useNullIfReporterNotFound - Variable in class net.sf.basedb.core.RawDataBatcher
If we should use the null reporter if a reporter isn't found.
useNullIfReporterNotFound(boolean) - Method in class net.sf.basedb.core.RawDataBatcher
Specify if the insert method should use a null reporter if a reporter with the given external ID isn't found.
useNullLoader - Variable in class net.sf.basedb.util.overview.loader.BasicItemNodeLoaderFactory
 
useNullLoaderIfNotFound() - Method in class net.sf.basedb.util.overview.loader.BasicItemNodeLoaderFactory
Get the null loader setting.
useNullValidator - Variable in class net.sf.basedb.util.overview.validator.BasicItemNodeValidatorFactory
 
useNullValidatorIfNotFound() - Method in class net.sf.basedb.util.overview.validator.BasicItemNodeValidatorFactory
Get the null validator setting.
useOnSaveExtensions(JspContext) - Static method in class net.sf.basedb.clients.web.extensions.edit.EditUtil
Use on-save extensions for a given gui context.
usePathInfo - Variable in class net.sf.basedb.clients.web.servlet.Download
 
usePermissions - Variable in class net.sf.basedb.core.data.PluginDefinitionData
 
usePluginPermissions - Variable in class net.sf.basedb.core.Keyring
If the running plugin should use specific permissions or not.
usePrefixForNull - Variable in class net.sf.basedb.util.formatter.PrefixSuffixFormatter
 
useProjectAnnotations - Variable in class net.sf.basedb.core.AnnotationBatcher.CurrentAnnotationInfo
 
user - Variable in class net.sf.basedb.core.data.BioMaterialEventData
 
user - Variable in class net.sf.basedb.core.data.ChangeHistoryData
 
user - Variable in class net.sf.basedb.core.data.ContextData
 
user - Variable in class net.sf.basedb.core.data.DiskUsageData
 
user - Variable in class net.sf.basedb.core.data.PasswordData
 
user - Variable in class net.sf.basedb.core.data.PlateEventData
 
user - Variable in class net.sf.basedb.core.data.SessionData
 
user - Variable in class net.sf.basedb.core.data.UserClientSettingData
 
user - Variable in class net.sf.basedb.core.data.UserDefaultSettingData
 
user - Variable in class net.sf.basedb.core.data.UserDeviceData
 
User - Class in net.sf.basedb.core
This class is used to represent a user in BASE.
User(UserData) - Constructor for class net.sf.basedb.core.User
 
USER - Enum constant in enum class net.sf.basedb.core.Item
The item is a User.
USER - Static variable in class net.sf.basedb.core.Role
The id for the Role item representing regular users.
USER_RUNTIME_FILTER - Static variable in class net.sf.basedb.core.UserClientSetting
This filter will only return items if the logged in user has generic read permission to users.
User.QueryRuntimeFilterImpl - Class in net.sf.basedb.core
A runtime filter implementation that limits a query to only return users which are members of at least one group where the logged in user is also a member unless the logged in user has generic read permission.
userAgent - Variable in class net.sf.basedb.core.data.UserDeviceData
 
userAgentAnalyzer - Static variable in class net.sf.basedb.util.HttpUtil
 
USERCLIENT_RUNTIME_FILTER - Static variable in class net.sf.basedb.core.UserClientSetting
This filter will only return items if the logged in user has generic read permission to users and clients.
UserClientSetting - Class in net.sf.basedb.core
This class is used to represent a setting valid for a specific user using a specific client application.
UserClientSetting(UserClientSettingData) - Constructor for class net.sf.basedb.core.UserClientSetting
 
USERCLIENTSETTING - Enum constant in enum class net.sf.basedb.core.Item
The item is an UserClientSetting.
UserClientSettingData - Class in net.sf.basedb.core.data
 
UserClientSettingData() - Constructor for class net.sf.basedb.core.data.UserClientSettingData
 
userClientSettings - Variable in class net.sf.basedb.core.SessionControl.LoginInfo
Stores name and value from UserClientSettingData.
UserData - Class in net.sf.basedb.core.data
This class holds information about a user.
UserData() - Constructor for class net.sf.basedb.core.data.UserData
 
UserDefaultSetting - Class in net.sf.basedb.core
This class is used to represent a setting valid for a specific user using any client application.
UserDefaultSetting(UserDefaultSettingData) - Constructor for class net.sf.basedb.core.UserDefaultSetting
 
USERDEFAULTSETTING - Enum constant in enum class net.sf.basedb.core.Item
The item is an UserDefaultSetting.
UserDefaultSettingData - Class in net.sf.basedb.core.data
 
UserDefaultSettingData() - Constructor for class net.sf.basedb.core.data.UserDefaultSettingData
 
userDefaultSettings - Variable in class net.sf.basedb.core.SessionControl.LoginInfo
Stores name and value from UserDefaultSettingData.
UserDevice - Class in net.sf.basedb.core
A user device represents a verified device a user may use for accessing BASE.
UserDevice(UserDeviceData) - Constructor for class net.sf.basedb.core.UserDevice
 
USERDEVICE - Enum constant in enum class net.sf.basedb.core.Item
The item is an UserDevice.
UserDevice.QueryRuntimeFilterImpl - Class in net.sf.basedb.core
A runtime filter implementation that limits a query to only return devices for the currently logged in user unless the logged in user has generic read permission.
UserDeviceData - Class in net.sf.basedb.core.data
This class holds information about a verified user device.
UserDeviceData() - Constructor for class net.sf.basedb.core.data.UserDeviceData
 
userEmail - Variable in class net.sf.basedb.core.SessionControl.UnverifiedDeviceInfo
 
userFilesDir - Variable in class net.sf.basedb.util.extensions.manager.Settings
 
userFilesDirectory - Static variable in class net.sf.basedb.core.Application
The directory where uploaded files are stored.
UserGroups - Class in net.sf.basedb.core.data.keyring
Class for mapping the UserGroups table.
UserGroups() - Constructor for class net.sf.basedb.core.data.keyring.UserGroups
Create a new UserGroups object.
userId - Variable in class net.sf.basedb.core.authentication.LoginRequest
 
userId - Variable in class net.sf.basedb.core.data.ChangeHistoryData
 
userId - Variable in class net.sf.basedb.core.data.keyring.UserGroups
 
userId - Variable in class net.sf.basedb.core.data.keyring.UserKeys
 
userId - Variable in class net.sf.basedb.core.data.keyring.UserProjects
 
userId - Variable in class net.sf.basedb.core.data.keyring.UserRoles
 
userId - Variable in class net.sf.basedb.core.Keyring
The logged in user's ID.
userId - Variable in class net.sf.basedb.core.log.TransactionDetails
 
userId - Variable in class net.sf.basedb.core.SessionControl.LoginInfo
The id of the UserData object for the logged in user.
UserKeys - Class in net.sf.basedb.core.data.keyring
Class for mapping the UserKeys table.
UserKeys() - Constructor for class net.sf.basedb.core.data.keyring.UserKeys
Create a new UserKeys object.
userlogin - Variable in class net.sf.basedb.core.Path
The userlogin part of the path.
userLogin - Variable in class net.sf.basedb.core.SessionControl.LoginInfo
The login property of the logged in user.
username - Variable in class net.sf.basedb.core.data.FileServerData
 
username - Variable in class net.sf.basedb.util.uri.ConnectionParameters
 
userName - Variable in class net.sf.basedb.core.log.TransactionDetails
 
userName - Variable in class net.sf.basedb.core.SessionControl.LoginInfo
The name property of the logged in user.
userName - Variable in class net.sf.basedb.core.SessionControl.UnverifiedDeviceInfo
 
userPermissions - Variable in class net.sf.basedb.core.MultiPermissions
 
userPermissions - Variable in class net.sf.basedb.core.UserPermissions
 
UserPermissions - Class in net.sf.basedb.core
This class is used to specify permissions to share an item to users.
UserPermissions() - Constructor for class net.sf.basedb.core.UserPermissions
Create a new empty object.
UserPermissions(ItemKey) - Constructor for class net.sf.basedb.core.UserPermissions
Create a new object, and initialise it with the permissions from a ItemKey.
UserProjects - Class in net.sf.basedb.core.data.keyring
Class for mapping the UserProjects table.
UserProjects() - Constructor for class net.sf.basedb.core.data.keyring.UserProjects
Create a new UserProjects object.
UserRoles - Class in net.sf.basedb.core.data.keyring
Class for mapping the UserRoles table.
UserRoles() - Constructor for class net.sf.basedb.core.data.keyring.UserRoles
Create a new UserRoles object.
users - Variable in class net.sf.basedb.core.data.GroupData
 
users - Variable in class net.sf.basedb.core.data.ItemKeyData
 
users - Variable in class net.sf.basedb.core.data.ProjectData
 
users - Variable in class net.sf.basedb.core.data.RoleData
 
users - Variable in class net.sf.basedb.core.Keyring
Holds the ID of all users which are members of at least one of the groups that the logged in user is also a member of.
users - Variable in class net.sf.basedb.core.query.SharedToRestriction
 
userSettings - Variable in class net.sf.basedb.core.data.ClientData
 
useSavePointToContinueTransactionFromSqlFailure() - Method in class net.sf.basedb.core.dbengine.AbstractDbEngine
 
useSavePointToContinueTransactionFromSqlFailure() - Method in interface net.sf.basedb.core.dbengine.DbEngine
If the underlying database need to create a savepoint before executing an SQL statement that results in an error in order to be able to continue using the same transaction for other SQL queries.
useSavePointToContinueTransactionFromSqlFailure() - Method in class net.sf.basedb.core.dbengine.PostgresDbEngine
 
useSeparateConnections - Variable in class net.sf.basedb.core.ServiceSessionControl.SessionFactoryConfiguration
 
useSeparateConnections() - Method in class net.sf.basedb.core.hibernate.SessionFactoryConfiguration
Deprecated.
Should the session factory be configured to use separate connections or is piggy-backed sessions required?
useSeparateConnections() - Method in class net.sf.basedb.core.ServiceSessionControl.SessionFactoryConfiguration
Should the session factory be configured to use separate connections or is piggy-backed sessions required?
useSmartFeatureMismatchHandling - Variable in class net.sf.basedb.plugins.IlluminaRawDataImporter
 
usesTo - Variable in class net.sf.basedb.core.data.AnyToAnyData
 
useSuffixForNull - Variable in class net.sf.basedb.util.formatter.PrefixSuffixFormatter
 
useThetaJoin() - Method in class net.sf.basedb.core.dbengine.AbstractDbEngine
Most databases doesn't.
useThetaJoin() - Method in interface net.sf.basedb.core.dbengine.DbEngine
If the database uses theta join or ansi join.
useThetaJoin() - Method in class net.sf.basedb.core.dbengine.MySQLEngine
Always false.
useThetaJoin() - Method in class net.sf.basedb.core.dbengine.PostgresDbEngine
Always false.
useThetaJoin(QueryType) - Static method in class net.sf.basedb.core.HibernateUtil
Check if theta joins or ANSI joins are used by the database.
usingItems - Variable in class net.sf.basedb.core.Trashcan.CircularRefInfo
 
utf8 - Variable in class net.sf.basedb.clients.web.servlet.RssNewsFeed
 
UTF8_WITH_FALLBACK - Static variable in class net.sf.basedb.util.charset.CharsetUtil
The provider that is providing the UTF-8 with fallback characeter sets.
Utf8PropertiesResourceBundleControl - Class in net.sf.basedb.util.resources
ResourceBundle.Control implementation that open property files in UTF-8 format instead of ISO-8859-1 format.
Utf8PropertiesResourceBundleControl() - Constructor for class net.sf.basedb.util.resources.Utf8PropertiesResourceBundleControl
 
utf8Tester - Variable in class net.sf.basedb.core.File.UploadStream
 

V

valid - Variable in class net.sf.basedb.core.data.FileSetMemberData
 
valid - Static variable in class net.sf.basedb.core.dbengine.AbstractDbEngine
A regexp checking for invalid characters.
valid - Static variable in class net.sf.basedb.core.ExtendedProperty
A regexp checking for invalid characters.
validActions(A[]) - Method in class net.sf.basedb.util.extensions.ActionIterator
Check that the actions array is a not-null, non-empty array and contains actions of a type that is compatible with the ExtensionPoint.getActionClass() class.
ValidAndNewOrModifiedFilter - Class in net.sf.basedb.util.extensions.manager.filter
Filter implementation for extension files that allow valid and new or modified files to pass.
ValidAndNewOrModifiedFilter(boolean) - Constructor for class net.sf.basedb.util.extensions.manager.filter.ValidAndNewOrModifiedFilter
Create a new filter.
ValidAndNewOrModifiedFilter(boolean, Filter<ExtensionsFile>) - Constructor for class net.sf.basedb.util.extensions.manager.filter.ValidAndNewOrModifiedFilter
Create a new filter.
Validatable - Interface in net.sf.basedb.core
This interface is a tagging interface for items that needs case 2 validation.
validate() - Method in class net.sf.basedb.core.BasicItem
This method is called on each Validatable item before is saved to the database.
validate() - Method in class net.sf.basedb.core.Coloring
Check that all values has been specified and that minValue <= midValue >= maxValue.
validate() - Method in class net.sf.basedb.core.Formula
 
validate() - Method in class net.sf.basedb.core.News
Check that startDate is before newsDate is before endDate.
validate() - Method in class net.sf.basedb.util.export.spotdata.AbstractBioAssaySetExporter
Validate that all required options has been set and that other options have sensible values.
validate() - Method in class net.sf.basedb.util.export.spotdata.BfsExporter
 
validate() - Method in class net.sf.basedb.util.extensions.manager.ExtensionsFile
Validate the XML file with the extension definitions.
validate(D) - Method in class net.sf.basedb.core.BasicBatcher
Validate the data, since no validation is possible in set methods of the data object.
validate(Object) - Method in enum class net.sf.basedb.core.Type
Check if an object is a value of the correct type.
validate(String, Object) - Method in class net.sf.basedb.core.ParameterType
Check if a value is valid according to the settings of this parameter type.
validate(String, List<?>) - Method in class net.sf.basedb.core.ParameterType
Check if a list of values contain invalid values.
validate(List<?>) - Method in enum class net.sf.basedb.core.Type
Check if a list of values contain only objects of the correct type.
validate(FeatureData) - Method in class net.sf.basedb.core.FeatureBatcher
Validate all properties for the feature object: The data object is not null An array design block has been specfied The position number is > 0 The external id is not null or too long The feature identification is unique The data object belongs to the correct array design The reporter match the well's reporter if a well has been specified
validate(RawData) - Method in class net.sf.basedb.core.RawDataBatcher
Validate all properties for the raw data object: The data object is not null The data object belongs to the correct raw bioassay The position value is > 0 All of the extra properties using the ExtendedProperty.validateValue(Object) method
validate(ReporterData) - Method in class net.sf.basedb.core.ReporterBatcher
Validate all properties for the reporter object: The data object is not null The name or external id is not null or too long The description or symbol is not too long All of the extendable properties using the ExtendedProperty.validateValue(Object) method
validate(DbControl) - Method in class net.sf.basedb.core.FileSet
Validate the files in this file set.
validate(Formula) - Method in enum class net.sf.basedb.core.Formula.Type
 
validate(ValidationAction) - Method in class net.sf.basedb.util.fileset.ValidationRenderer
 
VALIDATE_IMMEDIATELY - Enum constant in enum class net.sf.basedb.util.fileset.Accept
The file is handled by the validator and should be validated immediately.
VALIDATE_LATER - Enum constant in enum class net.sf.basedb.util.fileset.Accept
The file is handled by the validator but should not be validated until all files in the file set has been asked for acception.
validateAndExtractMetadata() - Method in class net.sf.basedb.util.affymetrix.CdfValidationAction
 
validateAndExtractMetadata() - Method in class net.sf.basedb.util.affymetrix.CelValidationAction
 
validateAndExtractMetadata() - Method in interface net.sf.basedb.util.fileset.ValidationAction
Validate and extract metadata from the file(s) that has been added to this validator.
validateAndExtractMetadata() - Method in class net.sf.basedb.util.gtf.GtfValidationAction
 
validateAnnotationValue(Object) - Method in class net.sf.basedb.core.AnnotationType
Validate an annotation value assuming that the value is in the default unit.
validateAnnotationValue(Object, Unit) - Method in class net.sf.basedb.core.AnnotationType
Validate an annotation value that can be in a different unit than the default unit.
validateCelAndCdf(FusionCELData, FusionCDFData, String) - Method in class net.sf.basedb.util.affymetrix.CelValidator
Check if the loaded CEL and CDF files matches.
validateCelAndCdf(RawBioAssay, ArrayDesign, boolean) - Static method in class net.sf.basedb.util.affymetrix.AffymetrixUtil
Check if the CEL file on the raw bioassay matches the CDF file on the array design.
validateConfiguration() - Method in class net.sf.basedb.clients.jobagent.Agent
Validate that all required configuration parameters have been specified.
validatedDom - Variable in class net.sf.basedb.clients.web.extensions.ServletLoader
 
validatedDom - Variable in class net.sf.basedb.util.extensions.xml.XmlLoader
 
validateFeatures(DbControl, ArrayDesign, FeatureIdentificationMethod, boolean, ProgressReporter) - Method in class net.sf.basedb.core.RawBioAssay
Validate that the features/reporters of the raw data matches the features/reporter on the array design.
validateKey(String) - Method in class net.sf.basedb.util.StaticCache
 
validateMapping(DbControl) - Method in class net.sf.basedb.core.MigrateRbaToDba.SubtypeMapping
 
validateMapping(DbControl, List<String>) - Method in class net.sf.basedb.core.MigrateRbaToDba.LineMapping
 
validateRequestParameters(List<PluginParameter<?>>, Request) - Method in class net.sf.basedb.core.plugin.AbstractPlugin
Validate the parameter values in a request against a list of plugin parameter definitions.
validateValue() - Method in class net.sf.basedb.core.query.QueryParameter
Validate the parameter value using the type information if it has been provided.
validateValue(Object) - Method in class net.sf.basedb.core.ExtendedProperty
Check if an object is valid according to the specifications of this property.
validateValue(String, Boolean) - Method in class net.sf.basedb.core.BooleanParameterType
Always validate.
validateValue(String, Double) - Method in class net.sf.basedb.core.DoubleParameterType
Checks if the value is within the range given by the upper and lower limits if those are given.
validateValue(String, Float) - Method in class net.sf.basedb.core.FloatParameterType
Checks if the value is within the range given by the upper and lower limits if those are given.
validateValue(String, Integer) - Method in class net.sf.basedb.core.IntegerParameterType
Checks if the value is within the range given by the upper and lower limits if those are given.
validateValue(String, Long) - Method in class net.sf.basedb.core.LongParameterType
Checks if the value is within the range given by the upper and lower limits if those are given.
validateValue(String, String) - Method in class net.sf.basedb.core.PathParameterType
Checks if the value is a valif Path value.
validateValue(String, String) - Method in class net.sf.basedb.core.StringParameterType
Checks if the value is a String object and shorter than the maximum length.
validateValue(String, Date) - Method in class net.sf.basedb.core.DateParameterType
Always validate.
validateValue(String, Date) - Method in class net.sf.basedb.core.TimestampParameterType
Always validate.
validateValue(String, File) - Method in class net.sf.basedb.core.FileParameterType
Always validate.
validateValue(String, T) - Method in class net.sf.basedb.core.ItemParameterType
Check if the value is in the list of allowed values.
validateValue(String, T) - Method in class net.sf.basedb.core.ParameterType
Validate a value.
validateXmlFile(InputStream, String) - Method in class net.sf.basedb.clients.web.extensions.ServletLoader
Validate an XML file against the servlet definition schema.
validateXmlFile(InputStream, String) - Method in class net.sf.basedb.util.extensions.xml.XmlLoader
Validate an XML file against the extensions definition schema.
ValidatingFileSetMember - Class in net.sf.basedb.util.fileset
This class is a proxy used for holding information about a file set member that is currently undergoing validation.
ValidatingFileSetMember(FileSetMember) - Constructor for class net.sf.basedb.util.fileset.ValidatingFileSetMember
Create a new instance for the given real member file.
ValidationAction - Interface in net.sf.basedb.util.fileset
Action for validating and metadata extraction from files in a file set.
validationError - Variable in class net.sf.basedb.util.extensions.manager.ExtensionsFile
 
validationOptions - Variable in class net.sf.basedb.util.overview.GenericOverview
 
ValidationOptions - Class in net.sf.basedb.util.overview
Stores all validation options (ie. validator -- severity) combinations.
ValidationOptions() - Constructor for class net.sf.basedb.util.overview.ValidationOptions
Create a new ValidationOptions object.
ValidationOptions(Presets.Preset) - Constructor for class net.sf.basedb.util.overview.ValidationOptions
Create a new ValidationOptions object and load settings from a preset.
ValidationRenderer - Class in net.sf.basedb.util.fileset
Renderer implementation for validating the members of a file set.
ValidationRenderer(List<ValidatingFileSetMember>, List<Throwable>) - Constructor for class net.sf.basedb.util.fileset.ValidationRenderer
Create a new renderer instance.
ValidationRuleAction - Interface in net.sf.basedb.util.overview.extensions
The same as a Validator.
validator - Variable in class net.sf.basedb.util.affymetrix.CdfValidationAction
 
validator - Variable in class net.sf.basedb.util.affymetrix.CelValidationAction
 
validator - Variable in class net.sf.basedb.util.overview.node.NodeFactory
 
Validator - Class in net.sf.basedb.util.overview
Placeholder for a validation rule.
Validator(String, String, String, String, Severity) - Constructor for class net.sf.basedb.util.overview.Validator
Create a new validator.
Validator(String, URL) - Constructor for class net.sf.basedb.util.XmlUtil2.Validator
Create a new instance of this class.
validators - Variable in class net.sf.basedb.util.overview.validator.BasicItemNodeValidatorFactory
 
validKey - Static variable in class net.sf.basedb.util.StaticCache
 
value - Variable in class net.sf.basedb.clients.web.extensions.DynamicActionAttribute
 
value - Variable in class net.sf.basedb.clients.web.taglib.Input
The value of the input element.
value - Variable in class net.sf.basedb.clients.web.taglib.table.Cell
The value to display.
value - Variable in class net.sf.basedb.clients.web.taglib.table.CellValue
The value to display.
value - Variable in class net.sf.basedb.clients.web.taglib.table.Hidden
The value of the element.
value - Variable in class net.sf.basedb.core.AnnotationSimpleRestriction
 
value - Variable in enum class net.sf.basedb.core.BioMaterialEvent.Type
 
value - Variable in enum class net.sf.basedb.core.BioWell.LockMode
The integer value of this lock mode.
value - Variable in class net.sf.basedb.core.data.PropertyFilterData
 
value - Variable in class net.sf.basedb.core.data.SettingData
 
value - Variable in class net.sf.basedb.core.DynamicRestriction
 
value - Variable in enum class net.sf.basedb.core.ExtraValue.CoordinateType
The integer value of this coordinate type.
value - Variable in class net.sf.basedb.core.FastAnnotationLoader.FastAnnotation
The value.
value - Variable in enum class net.sf.basedb.core.FeatureIdentificationMethod
The integer value of this method.
value - Variable in enum class net.sf.basedb.core.Formula.AverageMethod
 
value - Variable in enum class net.sf.basedb.core.Formula.Parser
 
value - Variable in enum class net.sf.basedb.core.Formula.Type
 
value - Variable in enum class net.sf.basedb.core.Include
 
value - Variable in enum class net.sf.basedb.core.IntensityTransform
The integer value of this transform.
value - Variable in enum class net.sf.basedb.core.Item
 
value - Variable in enum class net.sf.basedb.core.ItemContext.SortDirection
The integer value of this direction.
value - Variable in enum class net.sf.basedb.core.Job.ExecutionTime
 
value - Variable in enum class net.sf.basedb.core.Job.Status
 
value - Variable in enum class net.sf.basedb.core.Job.Type
 
value - Variable in enum class net.sf.basedb.core.Location
The integer value of this location.
value - Variable in enum class net.sf.basedb.core.log.ChangeType
 
value - Variable in enum class net.sf.basedb.core.Operator
 
value - Variable in enum class net.sf.basedb.core.plugin.GuiContext.Type
 
value - Variable in enum class net.sf.basedb.core.plugin.Plugin.MainType
 
value - Variable in class net.sf.basedb.core.PropertyFilter
 
value - Variable in class net.sf.basedb.core.query.BooleanExpression
 
value - Variable in class net.sf.basedb.core.query.FloatExpression
 
value - Variable in class net.sf.basedb.core.query.IntegerExpression
 
value - Variable in class net.sf.basedb.core.query.QueryParameter
 
value - Variable in class net.sf.basedb.core.query.WhenStatement
 
value - Variable in class net.sf.basedb.core.SessionControl.SettingInfo
The value of the setting, null indicates removal
value - Variable in enum class net.sf.basedb.core.Type
 
value - Variable in class net.sf.basedb.plugins.AnnotationFlatFileImporter.AnnotationValue
 
value - Variable in class net.sf.basedb.util.bfs.MetadataModel.SectionEntry
 
value - Variable in class net.sf.basedb.util.Enumeration.Entry
 
value - Variable in class net.sf.basedb.util.excel.ExcelValue
 
value - Variable in class net.sf.basedb.util.fuzzy.StringMatcher.FuzzyMatch
 
value - Variable in class net.sf.basedb.util.gtf.GtfInputStream.Attribute
 
value - Variable in class net.sf.basedb.util.overview.filter.HasAttributeFilter
 
value - Variable in class net.sf.basedb.util.parser.FlatFileParser.Line
 
value() - Element in annotation interface net.sf.basedb.core.SubtypableRelatedItems
 
value() - Method in class net.sf.basedb.util.parser.FlatFileParser.Line
The value of the header if the line is a header line.
value(String) - Method in class net.sf.basedb.util.formatter.PropertyFilterFormatter
 
value_separator - Static variable in class net.sf.basedb.core.PropertyFilter
The string/characters used as a separator in a string with more then one filter values.
VALUE_WITH_UNIT - Static variable in class net.sf.basedb.util.units.UnitUtil
Pattern for checking if a string is a numeric value with an optional unit.
valueCache - Variable in class net.sf.basedb.util.extensions.debug.ProxyActionFactory
 
valueClass - Variable in enum class net.sf.basedb.core.Type
 
ValueConverter - Interface in net.sf.basedb.util.extensions.xml
Interface for classes that wants to inspect/convert parameters from the XML file before they are passed to factory setter methods.
valueCount - Variable in class net.sf.basedb.util.bfs.MetadataWriter
 
valueFormatter - Variable in class net.sf.basedb.clients.web.formatter.ExtendedPropertyFormatter
 
valueId - Variable in class net.sf.basedb.core.AnnotationBatcher.CurrentAnnotationInfo
 
valueId - Variable in class net.sf.basedb.core.data.annotations.AnnotationLink
 
valueIds - Variable in class net.sf.basedb.core.AnnotationBatcher
 
valueIndex - Variable in class net.sf.basedb.util.importer.spotdata.ExtraFloatParser
 
valueMapping - Static variable in enum class net.sf.basedb.core.BioMaterialEvent.Type
Maps the integer that is stored in the database.
valueMapping - Static variable in enum class net.sf.basedb.core.BioWell.LockMode
Maps an integer to a lock mode.
valueMapping - Static variable in enum class net.sf.basedb.core.ExtraValue.CoordinateType
Maps the integer that is stored in the database with an fileaction.
valueMapping - Static variable in enum class net.sf.basedb.core.FeatureIdentificationMethod
Maps an integer to a location.
valueMapping - Static variable in enum class net.sf.basedb.core.Formula.AverageMethod
Maps the integer that is stored in the database.
valueMapping - Static variable in enum class net.sf.basedb.core.Formula.Parser
Maps the integer that is stored in the database.
valueMapping - Static variable in enum class net.sf.basedb.core.Formula.Type
Maps the integer that is stored in the database.
valueMapping - Static variable in enum class net.sf.basedb.core.IntensityTransform
Maps an integer to a transform.
valueMapping - Static variable in enum class net.sf.basedb.core.Item
 
valueMapping - Static variable in enum class net.sf.basedb.core.ItemContext.SortDirection
Maps an integer to a sort direction.
valueMapping - Static variable in enum class net.sf.basedb.core.Job.ExecutionTime
Maps the integer that is stored in the database.
valueMapping - Static variable in enum class net.sf.basedb.core.Job.Status
Maps the integer that is stored in the database.
valueMapping - Static variable in enum class net.sf.basedb.core.Job.Type
Maps the integer that is stored in the database.
valueMapping - Static variable in enum class net.sf.basedb.core.Location
Maps an integer to a location.
valueMapping - Static variable in enum class net.sf.basedb.core.Operator
 
valueMapping - Static variable in enum class net.sf.basedb.core.plugin.GuiContext.Type
Maps the integer that is stored in the database.
valueMapping - Static variable in enum class net.sf.basedb.core.plugin.Plugin.MainType
Maps an integer to a type.
valueMapping - Static variable in enum class net.sf.basedb.core.Type
 
valueOf(String) - Static method in enum class net.sf.basedb.clients.web.extensions.fileviewer.FileViewerContext.Type
Returns the enum constant of this class with the specified name.
valueOf(String) - Static method in enum class net.sf.basedb.clients.web.extensions.menu.MenuItemAction.MenuType
Returns the enum constant of this class with the specified name.
valueOf(String) - Static method in enum class net.sf.basedb.core.Annotation.Source
Returns the enum constant of this class with the specified name.
valueOf(String) - Static method in enum class net.sf.basedb.core.AnnotationBatcher.Change
Returns the enum constant of this class with the specified name.
valueOf(String) - Static method in enum class net.sf.basedb.core.BioMaterialEvent.Type
Returns the enum constant of this class with the specified name.
valueOf(String) - Static method in enum class net.sf.basedb.core.BioWell.LockMode
Returns the enum constant of this class with the specified name.
valueOf(String) - Static method in enum class net.sf.basedb.core.ExtraValue.CoordinateType
Returns the enum constant of this class with the specified name.
valueOf(String) - Static method in enum class net.sf.basedb.core.FeatureIdentificationMethod
Returns the enum constant of this class with the specified name.
valueOf(String) - Static method in enum class net.sf.basedb.core.Formula.AverageMethod
Returns the enum constant of this class with the specified name.
valueOf(String) - Static method in enum class net.sf.basedb.core.Formula.Parser
Returns the enum constant of this class with the specified name.
valueOf(String) - Static method in enum class net.sf.basedb.core.Formula.Type
Returns the enum constant of this class with the specified name.
valueOf(String) - Static method in enum class net.sf.basedb.core.hibernate.SchemaGenerator.Mode
Returns the enum constant of this class with the specified name.
valueOf(String) - Static method in enum class net.sf.basedb.core.Include
Returns the enum constant of this class with the specified name.
valueOf(String) - Static method in enum class net.sf.basedb.core.IntensityTransform
Returns the enum constant of this class with the specified name.
valueOf(String) - Static method in enum class net.sf.basedb.core.Item
Returns the enum constant of this class with the specified name.
valueOf(String) - Static method in enum class net.sf.basedb.core.ItemContext.AddFilter
Returns the enum constant of this class with the specified name.
valueOf(String) - Static method in enum class net.sf.basedb.core.ItemContext.SortDirection
Returns the enum constant of this class with the specified name.
valueOf(String) - Static method in enum class net.sf.basedb.core.ItemList.SynchronizeOption
Returns the enum constant of this class with the specified name.
valueOf(String) - Static method in enum class net.sf.basedb.core.Job.ExecutionTime
Returns the enum constant of this class with the specified name.
valueOf(String) - Static method in enum class net.sf.basedb.core.Job.Status
Returns the enum constant of this class with the specified name.
valueOf(String) - Static method in enum class net.sf.basedb.core.Job.Type
Returns the enum constant of this class with the specified name.
valueOf(String) - Static method in enum class net.sf.basedb.core.Location
Returns the enum constant of this class with the specified name.
valueOf(String) - Static method in enum class net.sf.basedb.core.log.ChangeType
Returns the enum constant of this class with the specified name.
valueOf(String) - Static method in enum class net.sf.basedb.core.Operator
Returns the enum constant of this class with the specified name.
valueOf(String) - Static method in enum class net.sf.basedb.core.Path.Type
Returns the enum constant of this class with the specified name.
valueOf(String) - Static method in enum class net.sf.basedb.core.Permission
Returns the enum constant of this class with the specified name.
valueOf(String) - Static method in enum class net.sf.basedb.core.plugin.GuiContext.Type
Returns the enum constant of this class with the specified name.
valueOf(String) - Static method in enum class net.sf.basedb.core.plugin.Plugin.MainType
Returns the enum constant of this class with the specified name.
valueOf(String) - Static method in enum class net.sf.basedb.core.plugin.Response.Status
Returns the enum constant of this class with the specified name.
valueOf(String) - Static method in enum class net.sf.basedb.core.query.JoinType
Returns the enum constant of this class with the specified name.
valueOf(String) - Static method in enum class net.sf.basedb.core.query.QuerySection
Returns the enum constant of this class with the specified name.
valueOf(String) - Static method in enum class net.sf.basedb.core.query.QueryType
Returns the enum constant of this class with the specified name.
valueOf(String) - Static method in enum class net.sf.basedb.core.ReporterCloneBatcher.CloneSource
Returns the enum constant of this class with the specified name.
valueOf(String) - Static method in enum class net.sf.basedb.core.SyncFilter.SourceItemTransform
Returns the enum constant of this class with the specified name.
valueOf(String) - Static method in enum class net.sf.basedb.core.Transactional.Action
Returns the enum constant of this class with the specified name.
valueOf(String) - Static method in enum class net.sf.basedb.core.Type
Returns the enum constant of this class with the specified name.
valueOf(String) - Static method in enum class net.sf.basedb.core.VirtualTable
Returns the enum constant of this class with the specified name.
valueOf(String) - Static method in enum class net.sf.basedb.plugins.Base1PluginExecuter.Base1JobParameterType
Returns the enum constant of this class with the specified name.
valueOf(String) - Static method in enum class net.sf.basedb.plugins.PrintMapFlatFileImporter.FormatType
Returns the enum constant of this class with the specified name.
valueOf(String) - Static method in enum class net.sf.basedb.plugins.PrintMapFlatFileImporter.Section
Returns the enum constant of this class with the specified name.
valueOf(String) - Static method in enum class net.sf.basedb.util.extensions.logging.LogLevel
Returns the enum constant of this class with the specified name.
valueOf(String) - Static method in enum class net.sf.basedb.util.extensions.LoggingErrorHandlerFactory.Level
Returns the enum constant of this class with the specified name.
valueOf(String) - Static method in enum class net.sf.basedb.util.extensions.xml.PathType
Returns the enum constant of this class with the specified name.
valueOf(String) - Static method in enum class net.sf.basedb.util.fileset.Accept
Returns the enum constant of this class with the specified name.
valueOf(String) - Static method in enum class net.sf.basedb.util.formatter.BooleanFormatter.Type
Returns the enum constant of this class with the specified name.
valueOf(String) - Static method in enum class net.sf.basedb.util.overview.node.ChildNodeDirection
Returns the enum constant of this class with the specified name.
valueOf(String) - Static method in enum class net.sf.basedb.util.overview.Node.Type
Returns the enum constant of this class with the specified name.
valueOf(String) - Static method in enum class net.sf.basedb.util.overview.Severity
Returns the enum constant of this class with the specified name.
valueOf(String) - Static method in enum class net.sf.basedb.util.parser.FlatFileParser.LineType
Returns the enum constant of this class with the specified name.
valueOf(String) - Static method in enum class net.sf.basedb.util.plot.HistogramPlot.YAggregate
Returns the enum constant of this class with the specified name.
values - Variable in class net.sf.basedb.core.AnnotationBatcher.CurrentAnnotationInfo
 
values - Variable in class net.sf.basedb.core.AnnotationInRestriction
 
values - Variable in class net.sf.basedb.core.AnnotationSimpleRestriction
 
values - Variable in class net.sf.basedb.core.data.AnnotationData
 
values - Variable in class net.sf.basedb.core.data.BooleanParameterValueData
 
values - Variable in class net.sf.basedb.core.data.DateParameterValueData
 
values - Variable in class net.sf.basedb.core.data.DoubleParameterValueData
 
values - Variable in class net.sf.basedb.core.data.FloatParameterValueData
 
values - Variable in class net.sf.basedb.core.data.IntegerParameterValueData
 
values - Variable in class net.sf.basedb.core.data.ItemParameterValueData
 
values - Variable in class net.sf.basedb.core.data.LongParameterValueData
 
values - Variable in class net.sf.basedb.core.data.StringParameterValueData
 
values - Variable in class net.sf.basedb.core.data.TextParameterValueData
 
values - Variable in class net.sf.basedb.core.data.TimestampParameterValueData
 
values - Variable in class net.sf.basedb.core.ParameterInfo
 
values - Variable in class net.sf.basedb.core.snapshot.AnnotationSnapshot
 
values - Variable in class net.sf.basedb.plugins.AnnotationFlatFileImporter.NewAnnotations
 
values - Variable in class net.sf.basedb.plugins.executor.ProgramParameter
 
values - Variable in class net.sf.basedb.util.bfs.MetadataModel.SectionEntry
 
values - Variable in class net.sf.basedb.util.plot.PlotAnnotation
 
values() - Static method in enum class net.sf.basedb.clients.web.extensions.fileviewer.FileViewerContext.Type
Returns an array containing the constants of this enum class, in the order they are declared.
values() - Static method in enum class net.sf.basedb.clients.web.extensions.menu.MenuItemAction.MenuType
Returns an array containing the constants of this enum class, in the order they are declared.
values() - Static method in enum class net.sf.basedb.core.Annotation.Source
Returns an array containing the constants of this enum class, in the order they are declared.
values() - Static method in enum class net.sf.basedb.core.AnnotationBatcher.Change
Returns an array containing the constants of this enum class, in the order they are declared.
values() - Static method in enum class net.sf.basedb.core.BioMaterialEvent.Type
Returns an array containing the constants of this enum class, in the order they are declared.
values() - Static method in enum class net.sf.basedb.core.BioWell.LockMode
Returns an array containing the constants of this enum class, in the order they are declared.
values() - Static method in enum class net.sf.basedb.core.ExtraValue.CoordinateType
Returns an array containing the constants of this enum class, in the order they are declared.
values() - Static method in enum class net.sf.basedb.core.FeatureIdentificationMethod
Returns an array containing the constants of this enum class, in the order they are declared.
values() - Static method in enum class net.sf.basedb.core.Formula.AverageMethod
Returns an array containing the constants of this enum class, in the order they are declared.
values() - Static method in enum class net.sf.basedb.core.Formula.Parser
Returns an array containing the constants of this enum class, in the order they are declared.
values() - Static method in enum class net.sf.basedb.core.Formula.Type
Returns an array containing the constants of this enum class, in the order they are declared.
values() - Static method in enum class net.sf.basedb.core.hibernate.SchemaGenerator.Mode
Returns an array containing the constants of this enum class, in the order they are declared.
values() - Static method in enum class net.sf.basedb.core.Include
Returns an array containing the constants of this enum class, in the order they are declared.
values() - Static method in enum class net.sf.basedb.core.IntensityTransform
Returns an array containing the constants of this enum class, in the order they are declared.
values() - Static method in enum class net.sf.basedb.core.Item
Returns an array containing the constants of this enum class, in the order they are declared.
values() - Static method in enum class net.sf.basedb.core.ItemContext.AddFilter
Returns an array containing the constants of this enum class, in the order they are declared.
values() - Static method in enum class net.sf.basedb.core.ItemContext.SortDirection
Returns an array containing the constants of this enum class, in the order they are declared.
values() - Static method in enum class net.sf.basedb.core.ItemList.SynchronizeOption
Returns an array containing the constants of this enum class, in the order they are declared.
values() - Static method in enum class net.sf.basedb.core.Job.ExecutionTime
Returns an array containing the constants of this enum class, in the order they are declared.
values() - Static method in enum class net.sf.basedb.core.Job.Status
Returns an array containing the constants of this enum class, in the order they are declared.
values() - Static method in enum class net.sf.basedb.core.Job.Type
Returns an array containing the constants of this enum class, in the order they are declared.
values() - Static method in enum class net.sf.basedb.core.Location
Returns an array containing the constants of this enum class, in the order they are declared.
values() - Static method in enum class net.sf.basedb.core.log.ChangeType
Returns an array containing the constants of this enum class, in the order they are declared.
values() - Static method in enum class net.sf.basedb.core.Operator
Returns an array containing the constants of this enum class, in the order they are declared.
values() - Static method in enum class net.sf.basedb.core.Path.Type
Returns an array containing the constants of this enum class, in the order they are declared.
values() - Static method in enum class net.sf.basedb.core.Permission
Returns an array containing the constants of this enum class, in the order they are declared.
values() - Static method in enum class net.sf.basedb.core.plugin.GuiContext.Type
Returns an array containing the constants of this enum class, in the order they are declared.
values() - Static method in enum class net.sf.basedb.core.plugin.Plugin.MainType
Returns an array containing the constants of this enum class, in the order they are declared.
values() - Static method in enum class net.sf.basedb.core.plugin.Response.Status
Returns an array containing the constants of this enum class, in the order they are declared.
values() - Static method in enum class net.sf.basedb.core.query.JoinType
Returns an array containing the constants of this enum class, in the order they are declared.
values() - Static method in enum class net.sf.basedb.core.query.QuerySection
Returns an array containing the constants of this enum class, in the order they are declared.
values() - Static method in enum class net.sf.basedb.core.query.QueryType
Returns an array containing the constants of this enum class, in the order they are declared.
values() - Static method in enum class net.sf.basedb.core.ReporterCloneBatcher.CloneSource
Returns an array containing the constants of this enum class, in the order they are declared.
values() - Static method in enum class net.sf.basedb.core.SyncFilter.SourceItemTransform
Returns an array containing the constants of this enum class, in the order they are declared.
values() - Static method in enum class net.sf.basedb.core.Transactional.Action
Returns an array containing the constants of this enum class, in the order they are declared.
values() - Static method in enum class net.sf.basedb.core.Type
Returns an array containing the constants of this enum class, in the order they are declared.
values() - Static method in enum class net.sf.basedb.core.VirtualTable
Returns an array containing the constants of this enum class, in the order they are declared.
values() - Static method in enum class net.sf.basedb.plugins.Base1PluginExecuter.Base1JobParameterType
Returns an array containing the constants of this enum class, in the order they are declared.
values() - Static method in enum class net.sf.basedb.plugins.PrintMapFlatFileImporter.FormatType
Returns an array containing the constants of this enum class, in the order they are declared.
values() - Static method in enum class net.sf.basedb.plugins.PrintMapFlatFileImporter.Section
Returns an array containing the constants of this enum class, in the order they are declared.
values() - Static method in enum class net.sf.basedb.util.extensions.logging.LogLevel
Returns an array containing the constants of this enum class, in the order they are declared.
values() - Static method in enum class net.sf.basedb.util.extensions.LoggingErrorHandlerFactory.Level
Returns an array containing the constants of this enum class, in the order they are declared.
values() - Static method in enum class net.sf.basedb.util.extensions.xml.PathType
Returns an array containing the constants of this enum class, in the order they are declared.
values() - Static method in enum class net.sf.basedb.util.fileset.Accept
Returns an array containing the constants of this enum class, in the order they are declared.
values() - Static method in enum class net.sf.basedb.util.formatter.BooleanFormatter.Type
Returns an array containing the constants of this enum class, in the order they are declared.
values() - Static method in enum class net.sf.basedb.util.overview.node.ChildNodeDirection
Returns an array containing the constants of this enum class, in the order they are declared.
values() - Static method in enum class net.sf.basedb.util.overview.Node.Type
Returns an array containing the constants of this enum class, in the order they are declared.
values() - Static method in enum class net.sf.basedb.util.overview.Severity
Returns an array containing the constants of this enum class, in the order they are declared.
values() - Static method in enum class net.sf.basedb.util.parser.FlatFileParser.LineType
Returns an array containing the constants of this enum class, in the order they are declared.
values() - Static method in enum class net.sf.basedb.util.plot.HistogramPlot.YAggregate
Returns an array containing the constants of this enum class, in the order they are declared.
Values - Class in net.sf.basedb.core
Utility class to handle the conversion between data objects and item objects.
Values - Class in net.sf.basedb.util
This class contains a set of static methods that may be useful for handling strings, ints and other values.
Values() - Constructor for class net.sf.basedb.core.Values
 
Values() - Constructor for class net.sf.basedb.util.Values
 
valuesPermissions - Variable in class net.sf.basedb.core.ChangeHistory
 
valueType - Variable in class net.sf.basedb.clients.web.extensions.list.AbstractListColumnBean
 
valueType - Variable in class net.sf.basedb.clients.web.extensions.list.PropertyPathActionFactory
 
valueType - Variable in class net.sf.basedb.clients.web.taglib.table.ColumnDef
The type of data in the property.
valueType - Variable in class net.sf.basedb.core.AnnotationBatcher.CurrentAnnotationInfo
 
valueType - Variable in class net.sf.basedb.core.AnnotationRestriction
 
valueType - Variable in class net.sf.basedb.core.data.AnnotationTypeData
 
valueType - Variable in class net.sf.basedb.core.data.DataCubeExtraValueData
 
valueType - Variable in class net.sf.basedb.core.data.ExtraValueTypeData
 
valueType - Variable in class net.sf.basedb.core.data.FormulaData
 
valueType - Variable in class net.sf.basedb.core.data.PropertyFilterData
 
valueType - Variable in class net.sf.basedb.core.data.ReporterClonePropertyData
 
valueType - Variable in enum class net.sf.basedb.core.Formula.Type
 
valueType - Variable in class net.sf.basedb.core.ParameterInfo
 
valueType - Variable in class net.sf.basedb.core.ParameterType
The matching type of parameter values (can be null)
valueType - Variable in class net.sf.basedb.core.PositionExtraValueBatcher
The type of values to insert.
valueType - Variable in class net.sf.basedb.core.PropertyFilter
 
valueType - Variable in class net.sf.basedb.core.query.ParameterExpression
 
valueType - Variable in class net.sf.basedb.core.snapshot.AnnotationLoaderUtil
 
valueType - Variable in class net.sf.basedb.core.snapshot.AnnotationSnapshot
 
valueType - Variable in class net.sf.basedb.core.SpotExtraValueBatcher
The type of values to insert.
valueType - Variable in class net.sf.basedb.plugins.batchimport.MultiPropertyIdMethod
 
valueType - Variable in class net.sf.basedb.plugins.batchimport.PropertyIdMethod
 
valueTypeColumnMapping - Static variable in class net.sf.basedb.plugins.batchimport.AnnotationTypeImporter
Column mapping parameter for the annotation value type
ValueTypeFormatter - Class in net.sf.basedb.util.formatter
Formatter implementation that converts an integer into it's Type representation and the uses name() as the formatted value.
ValueTypeFormatter() - Constructor for class net.sf.basedb.util.formatter.ValueTypeFormatter
Create a new formatter.
ValueTypeFormatter(String) - Constructor for class net.sf.basedb.util.formatter.ValueTypeFormatter
Create a new formatter.
valueTypeMapper - Variable in class net.sf.basedb.plugins.batchimport.AnnotationTypeImporter
 
VARIABLE - Static variable in class net.sf.basedb.util.extensions.xml.VariableConverter
 
variableConverter - Variable in class net.sf.basedb.clients.web.extensions.WebClientRegisterExtensionsProcessor
 
VariableConverter - Class in net.sf.basedb.util.extensions.xml
A value converter that can be used on all setter methods that has been annotated with the VariableSetter annotation.
VariableConverter() - Constructor for class net.sf.basedb.util.extensions.xml.VariableConverter
Create a new variable converter.
variables - Variable in class net.sf.basedb.util.extensions.xml.VariableConverter
 
VariableSetter - Annotation Interface in net.sf.basedb.util.extensions.xml
Indicates that a factory setter method which takes a string as it's input will have the value scanned by a VariableConverter before the setter method is invoked.
variant - Variable in class net.sf.basedb.core.data.ArrayDesignData
 
variant - Variable in class net.sf.basedb.core.data.FileTypeIndex
 
variant - Variable in class net.sf.basedb.core.data.PlatformFileTypeData
 
variant - Variable in class net.sf.basedb.core.data.RawBioAssayData
 
variant - Variable in class net.sf.basedb.core.RawDataType
 
variantColumnMapping - Static variable in class net.sf.basedb.plugins.batchimport.ArrayDesignImporter
 
variantColumnMapping - Static variable in class net.sf.basedb.plugins.batchimport.RawBioAssayImporter
 
variantId - Variable in class net.sf.basedb.core.MigrateRbaToDba.LineMapping
 
variantId - Variable in class net.sf.basedb.core.MigrateRbaToDba.Rba
 
variantMapper - Variable in class net.sf.basedb.plugins.batchimport.ArrayDesignImporter
 
variantMapper - Variable in class net.sf.basedb.plugins.batchimport.RawBioAssayImporter
 
variantQuery - Variable in class net.sf.basedb.plugins.batchimport.AbstractItemImporter
 
variants - Variable in class net.sf.basedb.core.data.PlatformData
 
vdb - Variable in class net.sf.basedb.core.DynamicJoin
 
vdb - Variable in class net.sf.basedb.core.ExtraValueJoin
 
VELOCITY - Static variable in class net.sf.basedb.core.Quantity
The id for the Quantity object representing velocity.
verificationCode - Variable in class net.sf.basedb.core.SessionControl.UnverifiedDeviceInfo
 
verificationCode - Variable in class net.sf.basedb.core.User
 
verifiedEmail - Variable in class net.sf.basedb.core.User
 
verify(String, SSLSession) - Method in class net.sf.basedb.util.ssl.AllowAnyHostNameVerifyer
 
verifyBaseVersion(About, boolean) - Method in class net.sf.basedb.util.extensions.xml.XmlLoader
 
verifyColumns - Variable in class net.sf.basedb.plugins.IlluminaRawDataImporter
 
verifyDevice(String, boolean) - Method in class net.sf.basedb.core.SessionControl
Call this method to verify a device.
verifyOnly - Variable in class net.sf.basedb.core.authentication.LoginRequest
 
verifyRootLoginAndPassword(String, String) - Static method in class net.sf.basedb.core.Update
Verify the root user login and password.
verifySchemaVersion - Variable in class net.sf.basedb.core.Application.StartupOptions
 
verifySchemaVersion - Variable in enum class net.sf.basedb.core.hibernate.SchemaGenerator.Mode
 
verifySchemaVersion() - Method in enum class net.sf.basedb.core.hibernate.SchemaGenerator.Mode
Does this installation mode require a check against the schema version of the intalled database or not?
verifySchemaVersion(boolean) - Method in class net.sf.basedb.core.Application.StartupOptions
Set to FALSE when starting a new installation or upgrade.
verifyUserExternal(Session, LoginRequest, List<AuthenticationManager>) - Method in class net.sf.basedb.core.SessionControl
Verify the user with external authentication.
verifyUserInternal(LoginRequest) - Method in class net.sf.basedb.core.AuthenticationContext
Check that the user exists and verify the password using internal authentication.
verifyUserInternal(Session, LoginRequest) - Method in class net.sf.basedb.core.SessionControl
Verify the user with internal authentication.
version - Variable in class net.sf.basedb.core.AnnotationBatcher.CurrentAnnotationInfo
 
version - Variable in class net.sf.basedb.core.data.BasicData
 
version - Variable in class net.sf.basedb.core.data.PluginDefinitionData
 
version - Variable in class net.sf.basedb.core.data.VersionedParameter
The version of the parameter.
version - Variable in class net.sf.basedb.core.MigrateRbaToDba.Rba
 
version - Variable in class net.sf.basedb.core.plugin.AboutImpl
 
version - Variable in class net.sf.basedb.util.extensions.AboutBean
 
version - Variable in class net.sf.basedb.util.extensions.Registry.RegisteredAbout
 
Version - Class in net.sf.basedb.core
Get information about the BASE version.
Version() - Constructor for class net.sf.basedb.core.Version
 
VERSION - Static variable in class net.sf.basedb.core.ClonableProperty
The property name of the "static" property BasicData.getVersion().
VersionedParameter - Class in net.sf.basedb.core.data
The key to a plugin configuration parameter.
VersionedParameter() - Constructor for class net.sf.basedb.core.data.VersionedParameter
Used by Hibernate to create an instance.
VersionedParameter(String, int) - Constructor for class net.sf.basedb.core.data.VersionedParameter
Create a new instance.
versionNumberParameter - Variable in class net.sf.basedb.plugins.Base1PluginExecuter
The version number of the plug-in.
versionString - Variable in class net.sf.basedb.core.data.HardwareData
 
versionString - Variable in class net.sf.basedb.core.data.SoftwareData
 
vertical - Variable in class net.sf.basedb.clients.web.taglib.ButtonGroup
If the buttons should be vertically grouped.
vetoAuthenticatedUser(UserData, AuthenticatedUser) - Method in interface net.sf.basedb.core.authentication.AuthenticationManager
This method is called if there are multiple installed external authentication managers and at least one of them accepted the user in the AuthenticationManager.authenticate() method.
VIEW - Enum constant in enum class net.sf.basedb.core.log.ChangeType
 
ViewAndDownloadActionFactory - Class in net.sf.basedb.clients.web.extensions.fileviewer
Facotry for creating the "View" and "Download" actions in file lists.
ViewAndDownloadActionFactory() - Constructor for class net.sf.basedb.clients.web.extensions.fileviewer.ViewAndDownloadActionFactory
 
VIRTUAL - Enum constant in enum class net.sf.basedb.core.ReporterCloneBatcher.CloneSource
Use the position-to-reporter mapping in the experiment.
VirtualColumn - Class in net.sf.basedb.core
This class is used to define columns in the virtual tables in the dynamic part of the database that are storing analysed data.
VirtualColumn(String, String, TypeWrapper<?>, int, boolean, boolean, boolean, boolean, boolean) - Constructor for class net.sf.basedb.core.VirtualColumn
Create a new virtual column.
VirtualColumnExpression - Class in net.sf.basedb.core.query
 
VirtualColumnExpression(VirtualTable, VirtualColumn) - Constructor for class net.sf.basedb.core.query.VirtualColumnExpression
 
VirtualColumnExpression.WrappedExpression - Class in net.sf.basedb.core.query
 
virtualDb - Variable in class net.sf.basedb.core.data.DataCubeData
 
virtualDb - Variable in class net.sf.basedb.core.data.ExperimentData
 
virtualDb - Variable in class net.sf.basedb.core.DynamicQuery
 
virtualDb - Variable in class net.sf.basedb.core.DynamicReporterQuery
 
virtualDb - Variable in class net.sf.basedb.core.ReporterCloneBatcher
 
VirtualDb - Class in net.sf.basedb.core
A virtual database represents the set of tables in the dynamic database used by a single experiment to store it's analysed data.
VirtualDb(VirtualDbData) - Constructor for class net.sf.basedb.core.VirtualDb
Creates a new experiment item from the given data.
VIRTUALDB - Enum constant in enum class net.sf.basedb.core.Item
The item is a VirtualDb
VirtualDbData - Class in net.sf.basedb.core.data
This class holds information about a virtual database in the dynamic part of Base.
VirtualDbData() - Constructor for class net.sf.basedb.core.data.VirtualDbData
 
VirtualTable - Enum Class in net.sf.basedb.core
This enumeration defines constants that are used to specify different virtual tables in the dynamic part of the database used for analysis.
VirtualTable(String, String, VirtualColumn...) - Constructor for enum class net.sf.basedb.core.VirtualTable
Creates a new virtual table.
virtualTableExists(VirtualDb, VirtualTable) - Static method in class net.sf.basedb.core.HibernateUtil
Check if a table exists in the dynamic database or not.
visible - Variable in class net.sf.basedb.clients.web.extensions.menu.FixedMenuItemFactory
 
visible - Variable in class net.sf.basedb.clients.web.extensions.menu.MenuItemBean
 
visible - Variable in class net.sf.basedb.clients.web.extensions.tabcontrol.FixedTabFactory
 
visible - Variable in class net.sf.basedb.clients.web.extensions.tabcontrol.IncludeContentTabFactory
 
visible - Variable in class net.sf.basedb.clients.web.extensions.tabcontrol.TabBean
 
visible - Variable in class net.sf.basedb.clients.web.extensions.toolbar.ButtonBean
 
visible - Variable in class net.sf.basedb.clients.web.extensions.toolbar.FixedButtonFactory
 
visible - Variable in class net.sf.basedb.clients.web.taglib.Button
If the button should be visible or not.
visible - Variable in class net.sf.basedb.clients.web.taglib.Help
If the help icon should be visible or not.
visible - Variable in class net.sf.basedb.clients.web.taglib.HideableSection
If the section should be visible or not.
visible - Variable in class net.sf.basedb.clients.web.taglib.Icon
If the icon should be visible or not.
visible - Variable in class net.sf.basedb.clients.web.taglib.Input
If the input should be visible or not.
visible - Variable in class net.sf.basedb.clients.web.taglib.menu.Menuitem
If the menu item is visible.
visible - Variable in class net.sf.basedb.clients.web.taglib.menu.Menuseparator
If the separator is visible.
visible - Variable in class net.sf.basedb.clients.web.taglib.menu.Submenu
If the menu item is visible.
visible - Variable in class net.sf.basedb.clients.web.taglib.path.PathElement
 
visible - Variable in class net.sf.basedb.clients.web.taglib.Select
If the select list should be visible or not.
visible - Variable in class net.sf.basedb.clients.web.taglib.tab.Tab
If the tab should be visible or not.
visible - Variable in class net.sf.basedb.clients.web.taglib.table.Button
If the button should be visible or not.
visible - Variable in class net.sf.basedb.clients.web.taglib.table.Cell
If the cell should be visible or not.
visible - Variable in class net.sf.basedb.clients.web.taglib.table.Header
If the header should be visible or not.
visible - Variable in class net.sf.basedb.clients.web.taglib.table.Label
If the button should be visible or not.
visible - Variable in class net.sf.basedb.clients.web.taglib.table.Navigator
If the navigator bar should be visible or not.
visible - Variable in class net.sf.basedb.clients.web.taglib.table.Panel
If the panel should be visible or not.
visible - Variable in class net.sf.basedb.clients.web.taglib.table.PresetSelector
If the preset selector should be visible or not.
visible - Variable in class net.sf.basedb.clients.web.taglib.table.Row
If the row should be visible or not.
visible - Variable in class net.sf.basedb.clients.web.taglib.table.Toolbar
If the toolbar should be visible or not.
visible - Variable in class net.sf.basedb.clients.web.taglib.Zoom
If the zoom icon should be visible or not.
visibleColumns - Variable in class net.sf.basedb.clients.web.taglib.table.Table
The ID of all visible columns, sorted by the order they should appear.
visiblePermission - Variable in class net.sf.basedb.clients.web.extensions.menu.PermissionMenuItemFactory
 
visiblePermission - Variable in class net.sf.basedb.clients.web.extensions.toolbar.PermissionButtonFactory
 
visibleProperties - Static variable in class net.sf.basedb.core.ExtendedProperties
A map from class name --> a list of extended properties of for that class.
vLeft - Variable in class net.sf.basedb.core.RealJoin
 
vLeftColumn - Variable in class net.sf.basedb.core.RealJoin
 
VOLUME - Static variable in class net.sf.basedb.core.Quantity
The id for the Quantity object representing volume.

W

wait - Variable in class net.sf.basedb.clients.jobagent.executors.DummyJobExecutor
 
WAITING - Enum constant in enum class net.sf.basedb.core.Job.Status
The job is waiting to be started.
warn(String) - Method in class net.sf.basedb.util.extensions.logging.ExtensionsLogger
Log a WARNING message.
warn(String, String, String) - Static method in class net.sf.basedb.clients.web.taglib.DeprecationLogger
Log a warning for using the given taglib and attribute.
warn(String, Throwable) - Method in class net.sf.basedb.util.extensions.logging.ExtensionsLogger
Log a WARNING message with an optional stacktrace.
WARN - Enum constant in enum class net.sf.basedb.util.extensions.LoggingErrorHandlerFactory.Level
 
warning(SAXParseException) - Method in class net.sf.basedb.util.XmlUtil2.Validator
Ignore warnings
WARNING - Enum constant in enum class net.sf.basedb.util.extensions.logging.LogLevel
 
WARNING - Enum constant in enum class net.sf.basedb.util.overview.Severity
The rule generate warnings.
was - Variable in enum class net.sf.basedb.core.log.ChangeType
 
was(String) - Method in enum class net.sf.basedb.core.log.ChangeType
Create a string for display purposes that explains what has happened to the what.
wasModified - Variable in class net.sf.basedb.util.extensions.manager.ExtensionsFile
 
wasModified() - Method in class net.sf.basedb.util.extensions.manager.ExtensionsFile
Check if the file was modified when the last call to ExtensionsFile.checkModified() was made.
WasProcessedFilter - Class in net.sf.basedb.util.extensions.manager.filter
Filter implementation that passes all extension files that has been processed according to the information in the given ProcessResults object.
WasProcessedFilter(ProcessResults) - Constructor for class net.sf.basedb.util.extensions.manager.filter.WasProcessedFilter
 
WEBCLIENT_ID - Static variable in class net.sf.basedb.clients.web.Base
The external ID of the web client application.
WebClientRegisterExtensionsProcessor - Class in net.sf.basedb.clients.web.extensions
A subclass to the regular extensions processor that adds information about various paths (eg. home path, servlet path) on the web client as variables in the XmlLoader that is used to process the definition files.
WebClientRegisterExtensionsProcessor(String, String, String, ProcessResults) - Constructor for class net.sf.basedb.clients.web.extensions.WebClientRegisterExtensionsProcessor
 
WebException - Exception in net.sf.basedb.clients.web
This exception can be thrown on any JSP page in BASE.
WebException(String, String, String) - Constructor for exception net.sf.basedb.clients.web.WebException
Create a new WebException.
WebException(String, String, String, Object...) - Constructor for exception net.sf.basedb.clients.web.WebException
Create a new WebException.
weightedLeastSquaresRegression(List<LowessNormalization.SpotData>, List<Double>) - Static method in class net.sf.basedb.plugins.LowessNormalization
 
well - Variable in class net.sf.basedb.core.data.FeatureData
 
Well - Class in net.sf.basedb.core
A well is located on a Plate and contains a ReporterData.
Well(WellData) - Constructor for class net.sf.basedb.core.Well
 
WELL - Enum constant in enum class net.sf.basedb.core.Item
The item is a Well.
WellCoordinateFormatter - Class in net.sf.basedb.util.formatter
Formats an internal well coordinate to an external coordinate.
WellCoordinateFormatter(boolean) - Constructor for class net.sf.basedb.util.formatter.WellCoordinateFormatter
Create a well coordinate formatter.
WellData - Class in net.sf.basedb.core.data
This class holds information about a well on a plate.
WellData() - Constructor for class net.sf.basedb.core.data.WellData
 
wells - Variable in class net.sf.basedb.core.data.PlateData
 
what - Variable in class net.sf.basedb.util.Diff3
 
WhenStatement - Class in net.sf.basedb.core.query
Create a WHEN statement to be used in a CaseExpression.
WhenStatement(Restriction, Expression) - Constructor for class net.sf.basedb.core.query.WhenStatement
Create a new WhenStatement
whenStatements - Variable in class net.sf.basedb.core.query.CaseExpression
 
WHERE - Enum constant in enum class net.sf.basedb.core.query.QuerySection
 
WHICH_ITEMS - Static variable in class net.sf.basedb.clients.web.plugins.SimpleExport
 
WHICH_PROPERTIES - Static variable in class net.sf.basedb.clients.web.plugins.SimpleExport
 
width - Variable in class net.sf.basedb.clients.web.extensions.plot.MAPlotFactory
 
width - Variable in class net.sf.basedb.clients.web.extensions.plot.PlotGeneratorBean
 
width - Variable in class net.sf.basedb.clients.web.taglib.table.Form
 
width - Variable in class net.sf.basedb.core.data.AnnotationTypeData
 
width - Variable in class net.sf.basedb.core.ParameterType
Width of the input field for the parameter in the GUI.
withPrefix(String, String) - Method in class net.sf.basedb.clients.web.extensions.list.RelatedItemColumn.Specification
Return prefix+string if string is not null or the empty string otherwise.
work - Variable in class net.sf.basedb.core.hibernate.SavePointWork
 
workbook - Variable in class net.sf.basedb.clients.web.plugins.XlsxTemplate
 
workbook - Variable in class net.sf.basedb.util.excel.CellStyleCreator
 
workbook - Variable in class net.sf.basedb.util.excel.XlsxTableWriter
 
workbook - Variable in class net.sf.basedb.util.excel.XlsxToCsvUtil
 
WorkbookStream() - Constructor for class net.sf.basedb.util.excel.XlsxToCsvUtil.WorkbookStream
 
workDir - Variable in class net.sf.basedb.plugins.executor.ExternalProgramExecutor
Temporary working directory at runtime.
workerThread - Variable in class net.sf.basedb.core.signal.EnhancedThreadSignalHandler
The worker thread that should be interrupted when a signal is received.
workerThread - Variable in class net.sf.basedb.core.signal.ThreadSignalHandler
The worker thread that should be interrupted when Signal.ABORT is received.
wrap(Logger) - Method in class net.sf.basedb.util.extensions.logging.ExtensionsLogger
Wrap a generic SLF4J logger with this logger.
wrapForReset(SourceItemTransformer) - Method in class net.sf.basedb.util.listable.CollectExtracts
Wraps the parent transformer with a ResetCollected transformer the first time this method is called.
wrapInputStream(InputStream) - Method in class net.sf.basedb.plugins.AbstractFlatFileImporter
This method is called before the parser starts reading from the input stream.
wrapInputStream(InputStream) - Method in class net.sf.basedb.plugins.gtf.GtfReporterImporter
Wrap the input stream with a GtfInputStream.
wrapInputStream(InputStream) - Method in class net.sf.basedb.plugins.gtf.GtfReporterMapImporter
Wrap the input stream with a GtfInputStream.
wrapInputStream(InputStream) - Method in interface net.sf.basedb.util.parser.WrappedConfigureByExample
Wrap an input stream within another stream, for example, a gzip input stream.
WrappedConfigureByExample - Interface in net.sf.basedb.util.parser
This is an extension to the ConfigureByExample interface that allows a plug-in to wrap an input stream with another stream.
WrappedExpression(String) - Constructor for class net.sf.basedb.core.query.VirtualColumnExpression.WrappedExpression
 
WrappedFormatter<T> - Class in net.sf.basedb.util.excel
Excel formatter implementation that uses the value from any parent formatter and creates a string cell value.
WrappedFormatter(Formatter<T>) - Constructor for class net.sf.basedb.util.excel.WrappedFormatter
 
wrapper - Variable in class net.sf.basedb.clients.web.taglib.extensions.Render
 
WrappingRenderer<A extends Action> - Interface in net.sf.basedb.util.extensions
An extension to the regular renderer interface intended for renderers that wants to wrap an existing renderer to give the result their own touch.
write - Static variable in class net.sf.basedb.core.Item.DefinedPermissions
 
write() - Method in class net.sf.basedb.core.migrate.BooleanWriter
 
write() - Method in class net.sf.basedb.core.migrate.ByteArrayWriter
 
write() - Method in class net.sf.basedb.core.migrate.DateWriter
 
write() - Method in class net.sf.basedb.core.migrate.DoubleWriter
 
write() - Method in class net.sf.basedb.core.migrate.FloatWriter
 
write() - Method in class net.sf.basedb.core.migrate.IntegerWriter
 
write() - Method in class net.sf.basedb.core.migrate.LongWriter
 
write() - Method in interface net.sf.basedb.core.migrate.ResultWriter
Write the current data.
write() - Method in class net.sf.basedb.core.migrate.ShortWriter
 
write() - Method in class net.sf.basedb.core.migrate.TextWriter
 
write() - Method in class net.sf.basedb.core.migrate.TimestampWriter
 
write(byte[]) - Method in class net.sf.basedb.core.File.UploadStream
 
write(byte[]) - Method in class net.sf.basedb.core.plugin.ExportOutputStream
 
write(byte[], int, int) - Method in class net.sf.basedb.core.File.CharsetTesterThread
Runs in the main thread.
write(byte[], int, int) - Method in class net.sf.basedb.core.File.UploadStream
 
write(byte[], int, int) - Method in class net.sf.basedb.core.plugin.ExportOutputStream
 
write(char[]) - Method in class net.sf.basedb.util.excel.XlsxTableWriter
 
write(char[], int, int) - Method in class net.sf.basedb.util.excel.XlsxTableWriter
 
write(int) - Method in class net.sf.basedb.core.File.CharsetTesterThread
Runs in the main thread.
write(int) - Method in class net.sf.basedb.core.File.UploadStream
Writes the specified byte to this buffered output stream.
write(int) - Method in class net.sf.basedb.core.plugin.ExportOutputStream
 
write(int) - Method in class net.sf.basedb.util.excel.XlsxTableWriter
 
write(String) - Method in class net.sf.basedb.util.excel.XlsxTableWriter
 
write(String, int) - Method in class net.sf.basedb.util.StaticCache
Get an output stream that can be used to write binary information to the cache.
write(String, int, int) - Method in class net.sf.basedb.util.excel.XlsxTableWriter
 
write(String, InputStream, int) - Method in class net.sf.basedb.util.StaticCache
Store binary information in the cache.
WRITE - Enum constant in enum class net.sf.basedb.core.Permission
This permission allows a user update the information about an item.
WriteableExtensionsFile(ExtensionsFile) - Constructor for class net.sf.basedb.util.extensions.manager.ExtensionsFile.WriteableExtensionsFile
Creates a new writeable extensions file.
writeableFile - Variable in class net.sf.basedb.util.extensions.manager.processor.RegisterExtensionsProcessor.FileData
 
writeAnnotations(ExportedProperty, List<?>, String) - Method in interface net.sf.basedb.clients.web.plugins.ExportTemplate
Write annotation values.
writeAnnotations(ExportedProperty, List<?>, String) - Method in class net.sf.basedb.clients.web.plugins.PlainTextTemplate
Join the annotation values into a single string with a comma.
writeAnnotations(ExportedProperty, List<?>, String) - Method in class net.sf.basedb.clients.web.plugins.XlsxTemplate
Join the annotation values into a single string with a comma.
writeAnnotations(ExportedProperty, List<?>, String) - Method in class net.sf.basedb.clients.web.plugins.XMLTemplate
Add annotation values to the current item element.
writeCollection(ExportedProperty, Collection<?>) - Method in interface net.sf.basedb.clients.web.plugins.ExportTemplate
Write the values in a collection
writeCollection(ExportedProperty, Collection<?>) - Method in class net.sf.basedb.clients.web.plugins.PlainTextTemplate
Writes a collection of values.
writeCollection(ExportedProperty, Collection<?>) - Method in class net.sf.basedb.clients.web.plugins.XlsxTemplate
Writes a collection of values.
writeCollection(ExportedProperty, Collection<?>) - Method in class net.sf.basedb.clients.web.plugins.XMLTemplate
Add collection values to the current item element.
writeColumnFilters(int) - Method in class net.sf.basedb.clients.web.taglib.table.Table
 
writeColumns() - Method in class net.sf.basedb.clients.web.taglib.table.Table
 
writeColumnSubtitles(StringBuilder) - Method in class net.sf.basedb.clients.web.taglib.table.Table
 
writeData(Object, boolean) - Method in class net.sf.basedb.util.excel.XlsxTableWriter
Write the data to the next cell.
writeDataHeader(PrintWriter) - Method in class net.sf.basedb.plugins.GalExporter
Write the data header.
writeFeature(PrintWriter, FeatureData, ArrayDesignBlock) - Method in class net.sf.basedb.plugins.GalExporter
Write feature data.
writeHeaders() - Method in interface net.sf.basedb.clients.web.plugins.ExportTemplate
Write headers.
writeHeaders() - Method in class net.sf.basedb.clients.web.plugins.PlainTextTemplate
Write the headers on a single line.
writeHeaders() - Method in class net.sf.basedb.clients.web.plugins.XlsxTemplate
Write the headers on a single row.
writeHeaders() - Method in class net.sf.basedb.clients.web.plugins.XMLTemplate
Write property and annotation definitions.
writeHeaders(PrintWriter, List<String>) - Method in class net.sf.basedb.plugins.GalExporter
Write the headers of the GAL file, including the two first lines with the "ATF 1.0" line and the second line with the number of header lines and the number of data columns.
writeLock() - Method in class net.sf.basedb.util.extensions.manager.ExtensionsFile
Try to aquire a write-lock.
writeLock() - Method in class net.sf.basedb.util.StaticCache.LockEntry
 
writeMissingFeature(PrintWriter, FeatureCoordinate) - Method in class net.sf.basedb.plugins.GalExporter
Write a missing features.
writeObject(ObjectOutputStream) - Method in class net.sf.basedb.clients.web.taglib.extensions.Render
 
writeObject(ObjectOutputStream) - Method in class net.sf.basedb.clients.web.taglib.extensions.Scripts
 
writeObject(ObjectOutputStream) - Method in class net.sf.basedb.clients.web.taglib.extensions.Stylesheets
 
writeObject(ObjectOutputStream) - Method in class net.sf.basedb.clients.web.taglib.table.ExtensionCells
 
writeObject(ObjectOutputStream) - Method in class net.sf.basedb.core.data.ContextIndex
 
writeObject(ObjectOutputStream) - Method in class net.sf.basedb.core.data.FileTypeIndex
 
writeObject(ObjectOutputStream) - Method in class net.sf.basedb.core.data.QuotaIndex
 
writeObject(ObjectOutputStream) - Method in class net.sf.basedb.core.data.ReporterListScoreData
 
writeObject(ObjectOutputStream) - Method in class net.sf.basedb.core.log.LoggingInterceptor
 
writeObject(ObjectOutputStream) - Method in class net.sf.basedb.core.snapshot.AnnotationSetSnapshot
 
writeObject(ObjectOutputStream) - Method in class net.sf.basedb.core.snapshot.AnnotationSnapshot
 
writeObject(ObjectOutputStream) - Method in class net.sf.basedb.util.jep.FunctionSafeJep.SafeFunctionTable
 
writePermissions - Variable in class net.sf.basedb.core.Job.SignalKeyring
 
writeProperty(ExportedProperty, Object) - Method in interface net.sf.basedb.clients.web.plugins.ExportTemplate
Write the specified property values.
writeProperty(ExportedProperty, Object) - Method in class net.sf.basedb.clients.web.plugins.PlainTextTemplate
Write the data object.
writeProperty(ExportedProperty, Object) - Method in class net.sf.basedb.clients.web.plugins.XlsxTemplate
Write the data object.
writeProperty(ExportedProperty, Object) - Method in class net.sf.basedb.clients.web.plugins.XMLTemplate
Add the property value to the current item element.
writeProtected - Variable in class net.sf.basedb.core.data.FileData
 
writeProtected - Variable in class net.sf.basedb.core.ParameterValuesImpl
The configuration should only be writeable when configuring the job, not while executing a job.
writer - Variable in class net.sf.basedb.core.migrate.AbstractResultWriter
 
writeTo(OutputStream) - Method in class net.sf.basedb.clients.web.fileupload.UploadedFile
Upload the file and write the data to the specified output stream.
writeTo(OutputStream) - Method in class net.sf.basedb.core.Presets
Write the prestes to a stream as an XML file.
writeTo(Cell, CellStyleCreator) - Method in class net.sf.basedb.util.excel.ExcelValue.BlankValue
 
writeTo(Cell, CellStyleCreator) - Method in class net.sf.basedb.util.excel.ExcelValue.BooleanValue
 
writeTo(Cell, CellStyleCreator) - Method in class net.sf.basedb.util.excel.ExcelValue.DateValue
 
writeTo(Cell, CellStyleCreator) - Method in class net.sf.basedb.util.excel.ExcelValue.IntValue
 
writeTo(Cell, CellStyleCreator) - Method in class net.sf.basedb.util.excel.ExcelValue.NumericValue
 
writeTo(Cell, CellStyleCreator) - Method in class net.sf.basedb.util.excel.ExcelValue.StringValue
 
writeTo(Cell, CellStyleCreator) - Method in class net.sf.basedb.util.excel.ExcelValue
Write the value to the given cell and apply a format to it with the help of the style creator.
writeTrailingColumns - Variable in class net.sf.basedb.util.excel.XlsxToCsvUtil
 
writeValue(Serializable, ObjectOutputStream) - Method in enum class net.sf.basedb.core.Type
Write a value of this type to the output stream.

X

x - Variable in class net.sf.basedb.core.data.RawData
 
x - Variable in class net.sf.basedb.util.plot.HistogramPlot.TempSeries
 
xColumnMapping - Static variable in class net.sf.basedb.plugins.RawDataFlatFileImporter
 
XJspCompiler - Class in net.sf.basedb.clients.web.extensions
Class that enabled compilation of custom JSP pages that are part of an extension that uses classes from the extension JAR file (eg. a JAR file in the /WEB-INF/extensions directory).
XJspCompiler() - Constructor for class net.sf.basedb.clients.web.extensions.XJspCompiler
 
XLSX_MIME_TYPE - Static variable in class net.sf.basedb.util.excel.XlsxToCsvUtil
The MIME type for Excel workbook files.
XlsxTableWriter - Class in net.sf.basedb.util.excel
This is a simple wrapper for the TableWriter class to make it create an Excel workbook instead of a CSV file.
XlsxTableWriter(String) - Constructor for class net.sf.basedb.util.excel.XlsxTableWriter
Create a new workbook with a single worksheet.
XlsxTableWriter(Workbook, String) - Constructor for class net.sf.basedb.util.excel.XlsxTableWriter
Add a sheet to the given Excel workbook.
XlsxTemplate - Class in net.sf.basedb.clients.web.plugins
Template implementation that exports data to Excel format (xlsx).
XlsxTemplate(OutputStream, List<ExportedProperty>, Item, long, String) - Constructor for class net.sf.basedb.clients.web.plugins.XlsxTemplate
Create a new template.
XlsxToCsvUtil - Class in net.sf.basedb.util.excel
Utility class for converting Excel worksheets to CSV-formatted InputStreams.
XlsxToCsvUtil() - Constructor for class net.sf.basedb.util.excel.XlsxToCsvUtil
Create a new instance using defult settings.
XlsxToCsvUtil.CellTypeWithInfo - Class in net.sf.basedb.util.excel
 
XlsxToCsvUtil.SheetInfo - Class in net.sf.basedb.util.excel
Represents a single sheet in a workbook.
XlsxToCsvUtil.WorkbookStream - Class in net.sf.basedb.util.excel
Input stream implementation that combines streams from all sheets in the current workbook.
xMapper - Variable in class net.sf.basedb.plugins.RawDataFlatFileImporter
 
xmlFile - Variable in class net.sf.basedb.plugins.HelpImporter
 
xmlFile - Variable in class net.sf.basedb.plugins.PluginConfigurationImporter
 
xmlFileParameter - Static variable in class net.sf.basedb.plugins.PluginConfigurationImporter
 
XmlLoader - Class in net.sf.basedb.util.extensions.xml
Loads extension points and extensions from extension definition XML files.
XmlLoader() - Constructor for class net.sf.basedb.util.extensions.xml.XmlLoader
Create a new XML loader instance.
xmlOut - Variable in class net.sf.basedb.clients.web.plugins.XMLTemplate
 
xmlOut - Variable in class net.sf.basedb.util.extensions.xml.XmlLoader
 
xmlParserClass - Static variable in class net.sf.basedb.util.XmlUtil2
The parser class we are using.
XMLTemplate - Class in net.sf.basedb.clients.web.plugins
A XML template that exports data in a simple one-level XML format.
XMLTemplate(Writer, List<ExportedProperty>, Item) - Constructor for class net.sf.basedb.clients.web.plugins.XMLTemplate
Create a new template.
XmlUtil2 - Class in net.sf.basedb.util
This class contains some useful methods for handling XML documents using JDOM2.
XmlUtil2() - Constructor for class net.sf.basedb.util.XmlUtil2
 
XmlUtil2.Validator - Class in net.sf.basedb.util
This class is used to handle callbacks from the XML parser.
xtFile - Variable in class net.sf.basedb.util.extensions.manager.ExtensionsFile.WriteableExtensionsFile
 
xtFile - Variable in class net.sf.basedb.util.extensions.manager.ProcessResults.FileResults
 
xtFiles - Variable in class net.sf.basedb.util.extensions.manager.ExtensionsManager
 
xtId - Variable in class net.sf.basedb.clients.web.extensions.skin.FixedSkinActionFactory.MySkinAction
 
xtManager - Static variable in class net.sf.basedb.core.Application
Manager for the extensions system.
xtra(Integer) - Method in class net.sf.basedb.util.jep.ExtraValueFunction
Get the value of the specified extra value of the current sql result.
xtValidators - Variable in class net.sf.basedb.util.overview.validator.ExtensionNodeValidator
 
xtVersions - Static variable in class net.sf.basedb.clients.web.taglib.Head
 

Y

y - Variable in class net.sf.basedb.core.data.RawData
 
y - Variable in class net.sf.basedb.util.plot.HistogramPlot.TempSeries
 
yAggregate - Variable in class net.sf.basedb.util.plot.HistogramPlot.HistogramSeries
 
YAggregate() - Constructor for enum class net.sf.basedb.util.plot.HistogramPlot.YAggregate
 
yColumnMapping - Static variable in class net.sf.basedb.plugins.RawDataFlatFileImporter
 
YES_NO - Enum constant in enum class net.sf.basedb.util.formatter.BooleanFormatter.Type
Display yes/no.
yMapper - Variable in class net.sf.basedb.plugins.RawDataFlatFileImporter
 
ywRangeFactor - Static variable in class net.sf.basedb.plugins.LowessNormalization
 

Z

ZERO - Static variable in class net.sf.basedb.core.DiskUsageStatistics
 
ZERO_SET - Static variable in class net.sf.basedb.core.AbstractHqlQuery
 
ZERO_SET - Static variable in class net.sf.basedb.core.QueryRuntimeFilterFactory
 
zip - Variable in class net.sf.basedb.util.zip.ZipFilePacker
 
ZIP_FILE - Static variable in class net.sf.basedb.util.zip.AbstractFileUnpacker
The name of the parameter that asks for the file that is going to be unpacked.
ZipFilePacker - Class in net.sf.basedb.util.zip
This class packs files into a ZIP archive.
ZipFilePacker() - Constructor for class net.sf.basedb.util.zip.ZipFilePacker
Create a new packer that compresses files with the zip format.
zipFileType - Static variable in class net.sf.basedb.util.zip.AbstractFileUnpacker
The parameter type for file to unpack.
ZipFileUnpacker - Class in net.sf.basedb.plugins
A plugin for unpacking zip and jar file on the BASE file system.
ZipFileUnpacker() - Constructor for class net.sf.basedb.plugins.ZipFileUnpacker
 
ZipUnpacker - Class in net.sf.basedb.util.zip
This class can be used to unpack zip files into the BASE directory structure.
ZipUnpacker(DbControl) - Constructor for class net.sf.basedb.util.zip.ZipUnpacker
Create a new zip unpacker.
Zoom - Class in net.sf.basedb.clients.web.taglib
This tag is used to make it easier to add zoom features on a BASE web page.
Zoom() - Constructor for class net.sf.basedb.clients.web.taglib.Zoom
 
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