Index (BASE 3.19.10 API documentation)

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

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 - 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 - 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 in net.sf.basedb.util.fileset: Return result from the ValidationAction.acceptFile(net.sf.basedb.core.FileSetMember) method.
Accept() - Constructor for enum net.sf.basedb.util.fileset.Accept
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 - 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 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 - net.sf.basedb.core.log.ChangeType
ADD_ONLY - 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 - 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.
addFilterConditions(Element, String, HibernateUtil.FilterConfigurator) - Static method in class net.sf.basedb.core.HibernateUtil: Add <filter> conditions to the given class tag.
addFilteredColumn(String, String, boolean) - Method in class net.sf.basedb.clients.web.taglib.table.Table
addFilterRows(int) - Method in class net.sf.basedb.core.ItemContext: Add filter rows to the table.
addFix(Fix) - Method in class net.sf.basedb.util.overview.Failure: Add a suggested fix to this failure.
addFormulaColumns(List<TableColumn>, DbControl, RawDataType, Formula.Type, IntensityTransform, String, String, boolean) - Static method in class net.sf.basedb.clients.web.DynamicUtil
addFunctions(JEP, JepFunction...) - Static method in class net.sf.basedb.util.jep.Jep
addGroup(Group) - Method in class net.sf.basedb.core.Group: Add a group as a member to this group.
addHeaderColumns(int) - Method in class net.sf.basedb.clients.web.taglib.table.HeaderRow
addHidden(String, String) - Method in class net.sf.basedb.clients.web.taglib.table.Table
addIdAndStyles(StringBuilder, String...) - Method in class net.sf.basedb.clients.web.taglib.StylableTag: Add id, class and style attributes the the stringbuilder.
addIfPresentIn(int, int, Collection<ItemList>) - Method in class net.sf.basedb.core.ItemList: Add items that are present in the specified number of lists to this list.
addIfPresentIn(int, int, Collection<ReporterList>) - Method in class net.sf.basedb.core.ReporterList: Add reporters that are present in the specified number of lists to this list.
addIgnore(File) - Method in class net.sf.basedb.util.extensions.manager.ExtensionsManager: Add a file to the ignore list.
addIntersection(Collection<ItemList>) - Method in class net.sf.basedb.core.ItemList: Add items that are present in ALL OF the given lists to this list.
addIntersection(Collection<ReporterList>) - Method in class net.sf.basedb.core.ReporterList: Add reporters that are present in ALL OF the given lists to this list.
addItem(Annotatable) - Method in class net.sf.basedb.util.annotations.RunnableInheritAnnotationsManager: Add an item that should inherit annotations.
addJoin(String, String) - Method in class net.sf.basedb.core.hibernate.NativeQueryWrapper
addJoin(String, String, String) - Method in class net.sf.basedb.core.hibernate.NativeQueryWrapper
addJoin(String, String, LockMode) - Method in class net.sf.basedb.core.hibernate.NativeQueryWrapper
addManualSingleChange(ChangeType, Object) - Method in class net.sf.basedb.core.log.LoggingInterceptor: Adds a manual non-Hibernate change to the log system.
addManualSingleChange(ChangeType, Object, Object, Object, String, Type) - Method in class net.sf.basedb.core.log.LoggingInterceptor: Adds a manual non-Hibernate change to the log system.
addMeasurement(float) - Method in class net.sf.basedb.util.plot.HistogramPlot.HistogramBin: Add a measurement to this bin.
addMember(File, DataFileType) - Method in class net.sf.basedb.core.FileSet: Add a file as a member to the file set.
addMembers(Set<Integer>, ItemList.DelayedAdditionManager) - Method in class net.sf.basedb.core.ItemList: Add members to this list.
addMembersMode - Variable in class net.sf.basedb.plugins.batchimport.AbstractItemImporter
addMenuitem(String) - Method in class net.sf.basedb.clients.web.taglib.menu.Menu
addMessage(ExtensionsFile, String) - Method in class net.sf.basedb.util.extensions.manager.ProcessResults: Adds a detailed message indicating a successful operation to a file.
addMessage(ExtensionsFile, String, boolean) - Method in class net.sf.basedb.util.extensions.manager.ProcessResults
addMoreColumnMappingParameters(List<PluginParameter<?>>) - Method in class net.sf.basedb.plugins.batchimport.AbstractItemImporter: Add column mapping parameters for item-specific properties.
addMoreColumnMappingParameters(List<PluginParameter<?>>) - Method in class net.sf.basedb.plugins.batchimport.AnnotationTypeImporter: Adds column mappings for name and description.
addMoreColumnMappingParameters(List<PluginParameter<?>>) - Method in class net.sf.basedb.plugins.batchimport.ArrayBatchImporter: Adds column mappings for name, description, protocol, robot, and array design
addMoreColumnMappingParameters(List<PluginParameter<?>>) - Method in class net.sf.basedb.plugins.batchimport.ArrayDesignImporter: Adds column mappings for name, externalId, description, protocol, creation date, original quantity, pooled, parent and used quantity from parent.
addMoreColumnMappingParameters(List<PluginParameter<?>>) - Method in class net.sf.basedb.plugins.batchimport.ArraySlideImporter: Adds column mappings for name, description, array batch, batch index, barcode and destroyed
addMoreColumnMappingParameters(List<PluginParameter<?>>) - Method in class net.sf.basedb.plugins.batchimport.BioPlateImporter: Adds column mappings for name, description, plate type, plate geometry, barcode and freezer.
addMoreColumnMappingParameters(List<PluginParameter<?>>) - Method in class net.sf.basedb.plugins.batchimport.BioSourceImporter: Adds column mappings for name, externalId and description.
addMoreColumnMappingParameters(List<PluginParameter<?>>) - Method in class net.sf.basedb.plugins.batchimport.DerivedBioAssayImporter: Adds column mappings for name, internalId, subtype, description, protocol, hardware, software, parent, data files and permissions.
addMoreColumnMappingParameters(List<PluginParameter<?>>) - Method in class net.sf.basedb.plugins.batchimport.ExtractImporter: Adds column mappings for name, externalId, description, protocol, creation date, original quantity, pooled, parent and used quantity from parent.
addMoreColumnMappingParameters(List<PluginParameter<?>>) - Method in class net.sf.basedb.plugins.batchimport.FileImporter: Adds column mappings for name, externalId and description.
addMoreColumnMappingParameters(List<PluginParameter<?>>) - Method in class net.sf.basedb.plugins.batchimport.KitImporter: Adds column mappings for name and description.
addMoreColumnMappingParameters(List<PluginParameter<?>>) - Method in class net.sf.basedb.plugins.batchimport.PhysicalBioAssayImporter: Adds column mappings for name, externalId, description, protocol, creation date, original quantity, pooled, parent and used quantity from parent.
addMoreColumnMappingParameters(List<PluginParameter<?>>) - Method in class net.sf.basedb.plugins.batchimport.RawBioAssayImporter: Adds column mappings for name, externalId, description, protocol, creation date, original quantity, pooled, parent and used quantity from parent.
addMoreColumnMappingParameters(List<PluginParameter<?>>) - Method in class net.sf.basedb.plugins.batchimport.SampleImporter: Adds column mappings for name, externalId, description, protocol, creation date, original quantity, pooled, parent and used quantity from parent.
addMoreColumnMappingParameters(List<PluginParameter<?>>) - Method in class net.sf.basedb.plugins.batchimport.TagImporter: Adds column mappings for name and description.
addMoreErrorParameters(List<PluginParameter<?>>) - Method in class net.sf.basedb.plugins.batchimport.AbstractItemImporter: Add extra parameters to the "Error handling" section that the subclass needs.
addMoreErrorParameters(List<PluginParameter<?>>) - Method in class net.sf.basedb.plugins.batchimport.PhysicalBioAssayImporter
addMoreJobParameters(List<PluginParameter<?>>) - Method in class net.sf.basedb.plugins.batchimport.AbstractItemImporter: Add extra job parameters that the subclass needs.
addMoreJobParameters(List<PluginParameter<?>>) - Method in class net.sf.basedb.plugins.batchimport.ArrayDesignImporter: Add parameter for "Data directory" directory where data files may be located.
addMoreJobParameters(List<PluginParameter<?>>) - Method in class net.sf.basedb.plugins.batchimport.DerivedBioAssayImporter: Add parameter for "Data directory" directory where data files may be located.
addMoreJobParameters(List<PluginParameter<?>>) - Method in class net.sf.basedb.plugins.batchimport.FileImporter
addMoreJobParameters(List<PluginParameter<?>>) - Method in class net.sf.basedb.plugins.batchimport.RawBioAssayImporter: Add parameter for "Data directory" directory where data files may be located.
addMoreParsingParameters(List<PluginParameter<?>>) - Method in class net.sf.basedb.plugins.batchimport.AbstractItemImporter: Add extra parameters to the "Parser settings" section that the subclass needs.
addMoreParsingParameters(List<PluginParameter<?>>) - Method in class net.sf.basedb.plugins.batchimport.AnnotationTypeImporter
addParameter(String, String) - Method in class net.sf.basedb.clients.web.fileupload.FileUpload: Store the value of a regular form field.
addParameter(AnnotationType) - Method in class net.sf.basedb.core.Protocol: Add an annotation type as a parameter to this protocol.
addParametersWithNamespace(List<PluginParameter<?>>, List<PluginParameter<?>>, String) - Method in class net.sf.basedb.plugins.executor.ExternalProgramExecutor: Add more parameters to a list of parameters with a different namespace.
addParent(DerivedBioAssay) - Method in class net.sf.basedb.core.DerivedBioAssay: Add a derived bioassay as a parent to this derived bioassay.
addParticipant(BioPlate, String, int) - Method in class net.sf.basedb.core.BioPlateEvent: Add a bioplate as a participant in this event.
addPermissions(Group, Set<Permission>) - Method in class net.sf.basedb.core.GroupPermissions: Grant permissions to a group, keeping those that have already been set.
addPermissions(Group, Set<Permission>) - Method in class net.sf.basedb.core.MultiPermissions: Grant permissions to a group, keeping those that have already been set.
addPermissions(Project, Set<Permission>) - Method in class net.sf.basedb.core.MultiPermissions: Grant permissions to a project, keeping those that have already been set.
addPermissions(Project, Set<Permission>) - Method in class net.sf.basedb.core.ProjectPermissions: Grant permissions to a project, keeping those that have already been set.
addPermissions(User, Set<Permission>) - Method in class net.sf.basedb.core.MultiPermissions: Grant permissions to a user, keeping those that have already been set.
addPermissions(User, Set<Permission>) - Method in class net.sf.basedb.core.UserPermissions: Grant permissions to a user, keeping those that have already been set.
addPhysicalBioAssay(PhysicalBioAssay) - Method in class net.sf.basedb.core.DerivedBioAssay: Add a physical bioassay as a parent to this derived bioassay.
addPlate(Plate) - Method in class net.sf.basedb.core.ArrayDesign: Adds a single plate to the plate list.
addQueryHint(String) - Method in class net.sf.basedb.core.hibernate.NativeQueryWrapper
addQueryHint(String) - Method in class net.sf.basedb.core.hibernate.QueryWrapper
addRawBioAssay(RawBioAssay) - Method in class net.sf.basedb.core.Experiment: Add a raw bioassay to this experiment.
addRawBioAssayParameters(DbControl, RawBioAssay, List<PluginParameter<?>>) - Method in class net.sf.basedb.plugins.RawDataFlatFileImporter
addRawDataColumns(List<TableColumn>, DbControl, RawDataType, String, String, String) - Static method in class net.sf.basedb.clients.web.DynamicUtil
addRawDataMappings(MetadataSources) - Static method in class net.sf.basedb.core.HibernateUtil: Generate additional mappings for the raw data types.
addReplaceSection - Static variable in class net.sf.basedb.plugins.AnnotationFlatFileImporter
addReporter(ReporterData, Float) - Method in class net.sf.basedb.core.ReporterList: Add or update the score for a reporter.
addReporterColumns(List<TableColumn>, DbControl, String, String, String) - Static method in class net.sf.basedb.clients.web.DynamicUtil
addReporterColumns(List<TableColumn>, DbControl, ReporterCloneTemplate, String, String, String) - Static method in class net.sf.basedb.clients.web.DynamicUtil
addReporterField(DynamicField) - Method in class net.sf.basedb.util.export.spotdata.AbstractBioAssaySetExporter: Add information about a reporter field that should be exported.
addReporterField(DynamicField) - Method in class net.sf.basedb.util.export.spotdata.BaseFileExporter
addReporterField(DynamicField) - Method in class net.sf.basedb.util.export.spotdata.BfsExporter
addReporterFields(Collection<? extends DynamicField>) - Method in class net.sf.basedb.util.export.spotdata.BaseFileExporter: Add multiple reporter fields in one go.
addReporterFields(Collection<? extends DynamicField>) - Method in class net.sf.basedb.util.export.spotdata.BfsExporter: Add multiple reporter fields in one go.
addReporters(Set<Integer>) - Method in class net.sf.basedb.core.ReporterList
addReportUriIfNeeded(String, FilterConfig) - Method in class net.sf.basedb.clients.web.servlet.ContentSecurityPolicyFilter
addResources(Vector<URL>, Enumeration<URL>) - Method in class net.sf.basedb.util.JarClassLoader
address - Variable in class net.sf.basedb.core.authentication.ExtraUserInformation
address - Variable in class net.sf.basedb.core.data.UserData
addRestriction(Restriction) - Method in class net.sf.basedb.core.ItemContext.RowRestrictions
addRoleKey(RoleKeyData) - Static method in class net.sf.basedb.core.SystemItems: Register a role key.
addRolePermissions(RoleData, Map<Item, Integer>) - Static method in class net.sf.basedb.core.Install: Add permissions for a role for specific item types.
addRoot(String, Class) - Method in class net.sf.basedb.core.hibernate.NativeQueryWrapper
addRoot(String, String) - Method in class net.sf.basedb.core.hibernate.NativeQueryWrapper
addRow(String...) - Method in class net.sf.basedb.util.bfs.AnnotationModel: Add a row of data to the model.
addRow(String...) - Method in class net.sf.basedb.util.bfs.MatrixModel: Add a row of data to the model.
addScalar(String) - Method in class net.sf.basedb.core.hibernate.NativeQueryWrapper
addScalar(String, Type) - Method in class net.sf.basedb.core.hibernate.NativeQueryWrapper
addScript(String) - Method in class net.sf.basedb.clients.web.extensions.JspContext: Add an absolute reference to a script that should be included on the generated page with a <script> tag.
addScripts(Collection<String>) - Method in class net.sf.basedb.clients.web.extensions.JspContext: Add several scripts in one go.
addSection(String) - Method in class net.sf.basedb.util.bfs.MetadataModel: Adds a new section to the model.
addSeries(HistogramPlot.HistogramSeries) - Method in class net.sf.basedb.util.plot.HistogramPlot.HistogramDataset
addSignal(Signal) - Method in class net.sf.basedb.core.signal.AbstractSignalHandler: Add a signal to the list of supported signals.
addSource(BioMaterial) - Method in class net.sf.basedb.core.BioMaterialEvent: Add a biomaterial as a source to this event.
addSpecification(InheritSpecification) - Method in class net.sf.basedb.util.annotations.RunnableInheritAnnotationsManager: Add a specification with rules for inheriting annotations.
addSpotColumns(List<TableColumn>, DbControl, int, IntensityTransform) - Static method in class net.sf.basedb.clients.web.DynamicUtil
addSpotField(DynamicField) - Method in class net.sf.basedb.util.export.spotdata.AbstractBioAssaySetExporter: Add information about a spot field that should be exported.
addSpotField(DynamicField) - Method in class net.sf.basedb.util.export.spotdata.BaseFileExporter
addSpotField(DynamicField) - Method in class net.sf.basedb.util.export.spotdata.BfsExporter: Add information about a spot field that should be exported.
addSpotFields(Collection<? extends DynamicField>) - Method in class net.sf.basedb.util.export.spotdata.BaseFileExporter: Add multiple spot fields in one go.
addSpotFields(Collection<? extends DynamicField>) - Method in class net.sf.basedb.util.export.spotdata.BfsExporter: Add multiple spot fields in one go.
addSpotIntensityParser(SpotIntensityParser) - Method in class net.sf.basedb.util.importer.spotdata.FirstPassSectionSpotsParser: Adds a spot intensity parser to the list of used parsers.
addSpotSectionInfo(int, BaseFileInfo.SpotSectionInfo) - Method in class net.sf.basedb.util.importer.spotdata.BaseFileInfo: Adds information about a 'spot' section.
addSqlFunctions(SessionFactoryBuilder, DbEngine) - Static method in class net.sf.basedb.core.HibernateUtil: Add more SQL functions to HQL that are not present in a standard Hibernate installation.
addStaticMappings(MetadataSources, HibernateUtil.FilterConfigurator) - Static method in class net.sf.basedb.core.HibernateUtil: Read all mapping files, which must be named Class.hbm.xml where class is the name of each class.
addStatistics(String, float) - Method in class net.sf.basedb.clients.web.ExperimentExplorer.AnnotationGroup: Add another statisitcal measurement to this group.
addStylesheet(String) - Method in class net.sf.basedb.clients.web.extensions.JspContext: Add an absolute reference to a CSS stylesheet that should be included on the generated page with a <link> tag.
addStylesheets(Collection<String>) - Method in class net.sf.basedb.clients.web.extensions.JspContext: Add several stylesheets in one go.
addSymbol(String) - Method in class net.sf.basedb.core.Unit: Add a symbol to this unit.
addSynchronizedEntityClass(Class) - Method in class net.sf.basedb.core.hibernate.NativeQueryWrapper
addSynchronizedEntityName(String) - Method in class net.sf.basedb.core.hibernate.NativeQueryWrapper
addSynchronizedQuerySpace(String) - Method in class net.sf.basedb.core.hibernate.NativeQueryWrapper
addTab(TabAction) - Method in class net.sf.basedb.clients.web.taglib.tab.TabControl
addToBatch(D, PreparedStatement, List<BatchedPropertyInfo>) - Method in class net.sf.basedb.core.BasicBatcher: Add the data object to the batch represented by the prepared statement
addToBatch(Object...) - Method in class net.sf.basedb.core.AnnotationBatcher.UpdateBatcher: Add a new entry to the batch.
addToDefaultRolesAndGroups() - Method in class net.sf.basedb.core.User: Add this user to the groups and roles that has been marked as default for new users.
addToUnlimited - Variable in class net.sf.basedb.plugins.AnnotationFlatFileImporter
addToUnlimitedParameter - Static variable in class net.sf.basedb.plugins.AnnotationFlatFileImporter
addTransactionalAction(TransactionalAction) - Method in class net.sf.basedb.core.DbControl: Add a transactional action to this DbControl.
addTransferredBytes(long) - Method in class net.sf.basedb.clients.web.fileupload.FileUploadProgress: Adds a value to the number of transfered bytes.
addUnion(Collection<ItemList>) - Method in class net.sf.basedb.core.ItemList: Add items that are present in at least ONE OF the given lists to this list.
addUnion(Collection<ReporterList>) - Method in class net.sf.basedb.core.ReporterList: Add reporters that are present in at least ONE OF the given lists to this list.
addURI(URI) - Method in class net.sf.basedb.util.extensions.manager.ExtensionsManager: Add an URI that points to an XML file containing definitions.
addUsableUnit(Unit) - Method in class net.sf.basedb.core.AnnotationType: Add a unit to be used with this annotation type.
addUsedQuantity(float) - Method in class net.sf.basedb.core.MeasuredBioMaterial.RemainingQuantityAction: Add some used quantity to what has currently been recorded.
addUser(User) - Method in class net.sf.basedb.core.Group: Add a user as a member to this group.
addUser(User) - Method in class net.sf.basedb.core.Role: Assign this Role to a user.
addUsingItems(Set<ItemProxy>, Item, Query<Integer>) - Method in class net.sf.basedb.core.BasicItem: Add items to the set of items using this one.
addUsingItems(Set<ItemProxy>, Query<? extends BasicData>) - Method in class net.sf.basedb.core.BasicItem: Add items to the set of items using this one.
addValue(int, float) - Method in class net.sf.basedb.clients.web.ExperimentExplorer.AnnotationGroup: Add an intensity value to this group.
addValue(AnnotationType, Object, Unit, boolean) - Method in class net.sf.basedb.plugins.AnnotationFlatFileImporter.NewAnnotations: Add an annotation value.
addValueConverter(ValueConverter) - Method in class net.sf.basedb.util.extensions.xml.XmlLoader: Add a value converter to this loader
addWarnings(int) - Method in class net.sf.basedb.util.overview.Node: Add more warnings to this node.
adjustExistingItems(ProgressReporter, int, String, String) - Static method in class net.sf.basedb.core.Update: Adjust the existing items in the database to be compatible with the latest mappings.
adjustRanges() - Method in class net.sf.basedb.util.plot.HistogramPlot: Auto-size of the x and y range doesn't seem to work, so we have to do it manually.
ADMINISTRATOR - Static variable in class net.sf.basedb.core.Role: The id for the Role item representing adminstrators.
AdvancedFieldConverter - Class in net.sf.basedb.util.export.spotdata: Field converter implementation that gives more detailed control how fields are converted and used in the export.
AdvancedFieldConverter(DbControl, BioAssaySet) - Constructor for class net.sf.basedb.util.export.spotdata.AdvancedFieldConverter: Create a new advanced field converter.
affiliations - Variable in class net.sf.basedb.core.data.ExperimentData
AFFYMETRIX - Static variable in class net.sf.basedb.core.Platform: The external id for the Affymetrix platform.
AFFYMETRIX_CDF - Static variable in class net.sf.basedb.core.DataFileType: The external ID for the file type representing Affymetrix CDF files.
AFFYMETRIX_CEL - Static variable in class net.sf.basedb.core.DataFileType: The external ID for the file type representing Affymetrix CEL files.
AffymetrixUtil - Class in net.sf.basedb.util.affymetrix: Utility class with Affymetrix-related functionality.
AffymetrixUtil() - Constructor for class net.sf.basedb.util.affymetrix.AffymetrixUtil
aFloat(float) - Static method in class net.sf.basedb.core.query.Expressions: Create a constant expression from a float.
AFTER_ENABLE - Static variable in class net.sf.basedb.clients.web.extensions.ExtensionsControl: This event is sent after an extension or extension point is enabled by ExtensionsControl.enableExtensionPoint(String, boolean), ExtensionsControl.enableExtension(String, boolean), or ExtensionsControl.enableAllInFile(String, boolean).
AFTER_REGISTRATION - Static variable in class net.sf.basedb.util.extensions.events.EventType: This event is sent after an extension or extension point has been registered with a registry.
AFTER_UPDATE - Static variable in class net.sf.basedb.util.extensions.events.EventType: This event is sent during an update of an existing extension point or extension.
afterCommit() - Method in class net.sf.basedb.core.log.db.DbLogManager
afterCommit() - Method in interface net.sf.basedb.core.log.LogManager: Called after a successful commit of changes to the database.
afterRollback() - Method in class net.sf.basedb.core.log.db.DbLogManager
afterRollback() - Method in interface net.sf.basedb.core.log.LogManager: Called after rollback.
afterTransactionCompletion(Transaction) - Method in class net.sf.basedb.core.log.LoggingInterceptor: Signals successful commit or rollback to the log manager.
agent - Variable in class net.sf.basedb.clients.jobagent.AgentSignalReceiver
agent - Variable in class net.sf.basedb.clients.jobagent.handlers.AbstractCustomRequestHandler
agent - Variable in class net.sf.basedb.clients.jobagent.handlers.DefaultRequestHandler
agent - Variable in class net.sf.basedb.clients.jobagent.handlers.InfoRequestHandler
agent - Variable in class net.sf.basedb.clients.jobagent.handlers.MultiProtocolRequestHandler
agent - Variable in class net.sf.basedb.clients.jobagent.handlers.PauseRequestHandler
agent - Variable in class net.sf.basedb.clients.jobagent.handlers.SignalRequestHandler
agent - Variable in class net.sf.basedb.clients.jobagent.handlers.StartRequestHandler
agent - Variable in class net.sf.basedb.clients.jobagent.handlers.StopRequestHandler
agent - Variable in class net.sf.basedb.clients.jobagent.JobQueueChecker
agent - Variable in class net.sf.basedb.clients.jobagent.JobRunner
agent - Variable in class net.sf.basedb.clients.jobagent.slotmanager.InternalSlotManager
agent - Variable in class net.sf.basedb.clients.jobagent.slotmanager.RemoteSlotManager
agent - Variable in class net.sf.basedb.core.Job.ProgressReporterImpl
Agent - Class in net.sf.basedb.clients.jobagent: This is the actual job agent application.
Agent(Properties) - Constructor for class net.sf.basedb.clients.jobagent.Agent: Create a new job agent.
AgentController - Class in net.sf.basedb.clients.jobagent: This is the command line controller class for the job agent application.
AgentController(Properties) - Constructor for class net.sf.basedb.clients.jobagent.AgentController: Create a new controller for controlling the job agent specified by the given properties.
agentInfo - Static variable in class net.sf.basedb.core.JobAgent
AgentSignalReceiver - Class in net.sf.basedb.clients.jobagent: Signal receiver implementation for job agents that is compatible with the SocketSignalReceiver.
AgentSignalReceiver(Agent) - Constructor for class net.sf.basedb.clients.jobagent.AgentSignalReceiver
agentVersionForJobQuery - Variable in class net.sf.basedb.clients.jobagent.JobQueueChecker: The job agent's version when the query was cached.
Aggregations - Class in net.sf.basedb.core.query: A factory class to create aggregate expressions.
Aggregations() - Constructor for class net.sf.basedb.core.query.Aggregations
aIndex - Variable in class net.sf.basedb.util.importer.spotdata.MAParser
alias - Variable in class net.sf.basedb.core.AnnotationRestriction
alias - Variable in enum 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 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 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 - net.sf.basedb.util.overview.node.ChildNodeDirection
ALL - Static variable in enum net.sf.basedb.core.Include: A non-modifable collection containing all options.
ALL - Static variable in class net.sf.basedb.core.Keyring
ALL_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
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 net.sf.basedb.core.plugin.Response.Status
allowSaveParameters() - Method in enum net.sf.basedb.core.plugin.Response.Status
allowSubclass - Variable in class net.sf.basedb.util.filter.InstanceOfFilter
allowUnmodified - Variable in class net.sf.basedb.util.extensions.manager.filter.ValidAndNewOrModifiedFilter
allowUse - Variable in class net.sf.basedb.util.jep.RawFunction
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
allUpdateBatchers - Variable in class net.sf.basedb.core.AnnotationBatcher
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 - 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 - 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 - 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 - net.sf.basedb.core.Item: The item is an Annotation.
ANNOTATION - 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 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 in net.sf.basedb.core: A flag indicating what type of change that was made to an annotation as a result of calling AnnotationBatcher.setValues(AnnotationType, List, Unit, boolean)
AnnotationBatcher.CurrentAnnotationInfo - Class in net.sf.basedb.core: Holds information about an annotation for the current item.
AnnotationBatcher.InsertBatcher - Class in net.sf.basedb.core: Batcher implementation for inserting into tables.
AnnotationBatcher.UpdateBatcher - Class in net.sf.basedb.core: Batcher implementation for updating and deleting from tables.
AnnotationBetweenRestriction - Class in net.sf.basedb.core: Restricts a query using annotation values between a low and high value.
AnnotationBetweenRestriction(String, int, Type, Object, Object, boolean, boolean) - Constructor for class net.sf.basedb.core.AnnotationBetweenRestriction: Deprecated.
In 3.11, use AnnotationBetweenRestriction(String, AnnotationType, Object, Object, AnnotationRestriction.Options) instead
AnnotationBetweenRestriction(String, AnnotationType, Object, Object, boolean, boolean) - Constructor for class net.sf.basedb.core.AnnotationBetweenRestriction: Deprecated.
In 3.11, use AnnotationBetweenRestriction(String, AnnotationType, Object, Object, AnnotationRestriction.Options) instead
AnnotationBetweenRestriction(String, AnnotationType, Object, Object, AnnotationRestriction.Options) - Constructor for class net.sf.basedb.core.AnnotationBetweenRestriction: Create a new annotation restriction.
AnnotationData - Class in net.sf.basedb.core.data: This class holds information about an annotation
AnnotationData() - Constructor for class net.sf.basedb.core.data.AnnotationData
AnnotationExpression - Class in net.sf.basedb.core.query: An expression representing the value of an annotation.
AnnotationExpression(String, AnnotationType) - Constructor for class net.sf.basedb.core.query.AnnotationExpression
AnnotationFilter - Class in net.sf.basedb.core.snapshot: Filter implementation that finds the annotation snapshot for a given annotation.
AnnotationFilter() - Constructor for class net.sf.basedb.core.snapshot.AnnotationFilter: Create a filter that matches all annotations.
AnnotationFilter(Annotation) - Constructor for class net.sf.basedb.core.snapshot.AnnotationFilter: Create a filter that matches a specfic annotation.
AnnotationFlatFileImporter - Class in net.sf.basedb.plugins: Plug-in for importing annotations from simple text files.
AnnotationFlatFileImporter() - Constructor for class net.sf.basedb.plugins.AnnotationFlatFileImporter
AnnotationFlatFileImporter.AnnotationValue - Class in net.sf.basedb.plugins
AnnotationFlatFileImporter.NewAnnotations - Class in net.sf.basedb.plugins: Internal cache for storing annotation values from the file for a single item.
AnnotationGroup(int, Set<T>, int, Formatter<T>) - Constructor for class net.sf.basedb.clients.web.ExperimentExplorer.AnnotationGroup
annotationId - Variable in class net.sf.basedb.clients.web.extensions.list.RelatedItemColumn.Specification
annotationId - Variable in class net.sf.basedb.core.AnnotationBatcher.CurrentAnnotationInfo
annotationId - Variable in class net.sf.basedb.core.FastAnnotationLoader.FastAnnotation: The ID of the annotation.
annotationId - Variable in class net.sf.basedb.core.snapshot.AnnotationFilter
annotationId - Variable in class net.sf.basedb.core.snapshot.AnnotationSnapshot
AnnotationIdMethod - Class in net.sf.basedb.plugins.batchimport: Identification method implementation that can use an annotation for identifying items.
AnnotationIdMethod(AnnotationType) - Constructor for class net.sf.basedb.plugins.batchimport.AnnotationIdMethod: Create a new id method.
AnnotationInfo(int, int, int, int) - Constructor for class net.sf.basedb.core.ProjectSpecificAnnotationsManager.AnnotationInfo
AnnotationInfo(int, int, int, int, int, int) - Constructor for class net.sf.basedb.core.ProjectSpecificAnnotationsManager.AnnotationInfo
AnnotationInRestriction - Class in net.sf.basedb.core: Restricts a query using annotation values that exists in a set of given values.
AnnotationInRestriction(String, AnnotationType, boolean, boolean, Object...) - Constructor for class net.sf.basedb.core.AnnotationInRestriction: Deprecated.
In 3.11, use AnnotationInRestriction(String, AnnotationType, AnnotationRestriction.Options, Object...) instead
AnnotationInRestriction(String, AnnotationType, AnnotationRestriction.Options, Object...) - Constructor for class net.sf.basedb.core.AnnotationInRestriction: Create a new annotation restriction.
AnnotationJoin - Class in net.sf.basedb.core.query: Join annotations values to the query.
AnnotationJoin(JoinType, String, AnnotationType, String) - Constructor for class net.sf.basedb.core.query.AnnotationJoin
AnnotationJoiner(JoinType) - Constructor for class net.sf.basedb.core.HqlQueryJoiners.AnnotationJoiner
AnnotationLink - Class in net.sf.basedb.core.data.annotations: Class for mapping the "Annotations" table with shortcuts to all 'FooValues' tables.
AnnotationLink() - Constructor for class net.sf.basedb.core.data.annotations.AnnotationLink
AnnotationLoader - Class in net.sf.basedb.util.overview.loader: Node loader implementation for annotations.
AnnotationLoader() - Constructor for class net.sf.basedb.util.overview.loader.AnnotationLoader
AnnotationLoaderUtil - Class in net.sf.basedb.core.snapshot: Utility implementation for simple loading of primary annotations via SnapshotManager.
AnnotationLoaderUtil(DbControl, SnapshotManager, AnnotationType) - Constructor for class net.sf.basedb.core.snapshot.AnnotationLoaderUtil: Create a loder that uses the given snapshot manager to load annotations for a single annotation type.
AnnotationLoaderUtil(DbControl, SnapshotManager, AnnotationType, boolean, boolean) - Constructor for class net.sf.basedb.core.snapshot.AnnotationLoaderUtil: Create a loder that uses the given snapshot manager to load annotations for a single annotation type.
AnnotationLogger - Class in net.sf.basedb.core.log.db: Logger for annotations that logs changes as updates to the parent item the annotations belong to.
AnnotationLogger(DbLogManagerFactory) - Constructor for class net.sf.basedb.core.log.db.AnnotationLogger
AnnotationModel - Class in net.sf.basedb.util.bfs: A model container for BFS annotation files.
AnnotationModel() - Constructor for class net.sf.basedb.util.bfs.AnnotationModel: Create a new annotation model.
AnnotationNameGenerator - Class in net.sf.basedb.util.overview.node: Since an Annotation isn't Nameable we construct the name from the name of the annotation type, or from the value type if we are not allowed to access the annotation type.
AnnotationNameGenerator() - Constructor for class net.sf.basedb.util.overview.node.AnnotationNameGenerator
AnnotationParser - Class in net.sf.basedb.util.bfs: Parser implementation that parses a BFS annotation files.
AnnotationParser() - Constructor for class net.sf.basedb.util.bfs.AnnotationParser: Create a new annotation parser.
AnnotationRestriction - Class in net.sf.basedb.core: Base class for creating restrictions based on annotations.
AnnotationRestriction(String, int, Type, AnnotationRestriction.Options) - Constructor for class net.sf.basedb.core.AnnotationRestriction: Deprecated.
In 3.11
AnnotationRestriction(String, AnnotationType, AnnotationRestriction.Options) - Constructor for class net.sf.basedb.core.AnnotationRestriction: Create a new annotation restriction for an annotation type.
AnnotationRestriction.Options - Class in net.sf.basedb.core: Options that specify which annotations to consider when searching.
annotations - Variable in class net.sf.basedb.clients.web.servlet.ExperimentExplorerPlotServlet.ColumnKey
annotations - Variable in class net.sf.basedb.core.data.AnnotationSetData
annotations - Variable in class net.sf.basedb.core.data.AnnotationTypeData
annotations - Variable in class net.sf.basedb.core.snapshot.AnnotationSetSnapshot
Annotations - Class in net.sf.basedb.core.query: A factory class to create restrictions based on annotation values.
Annotations() - Constructor for class net.sf.basedb.core.query.Annotations
annotationSection - Static variable in class net.sf.basedb.core.plugin.AbstractPlugin: Section definition for grouping annotation options.
annotationSet - Variable in class net.sf.basedb.core.Annotation
annotationSet - Variable in class net.sf.basedb.core.data.AnnotatedData
annotationSet - Variable in class net.sf.basedb.core.data.AnnotationData
annotationSet - Variable in class net.sf.basedb.core.data.BioAssayData
annotationSet - Variable in class net.sf.basedb.core.data.BioAssaySetData
annotationSet - Variable in class net.sf.basedb.core.data.PluginDefinitionData
annotationSet - Variable in class net.sf.basedb.core.data.ProjectData
annotationSet - Variable in class net.sf.basedb.core.data.RootRawBioAssayData
annotationSet - Variable in class net.sf.basedb.core.data.WellData
annotationSet - Variable in class net.sf.basedb.core.ProjectSpecificAnnotationsManager.AnnotationInfo
annotationSet - Variable in class net.sf.basedb.util.overview.validator.ProtocolParameterValidator
AnnotationSet - Class in net.sf.basedb.core: An annotation set is the container for all annotations on an item.
AnnotationSet(AnnotationSetData) - Constructor for class net.sf.basedb.core.AnnotationSet: Regular constructor if the item is not known beforehand.
AnnotationSet(AnnotationSetData, Annotatable) - Constructor for class net.sf.basedb.core.AnnotationSet: Special constructor to avoid AnnotationSet.getItem() to hit the database when the item is known beforehand.
ANNOTATIONSET - 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.snapshot.AnnotationSetSnapshot
annotationSetId - Variable in class net.sf.basedb.core.snapshot.AnnotationSnapshot
AnnotationSetLogger - Class in net.sf.basedb.core.log.db: Logger for annotations sets that detects and logs changes to inherited anntations as updates to the parent item that are inheriting the annotations.
AnnotationSetLogger(DbLogManagerFactory) - Constructor for class net.sf.basedb.core.log.db.AnnotationSetLogger
AnnotationSetSnapshot - Class in net.sf.basedb.core.snapshot: A snapshot of an annotation set that is used to store information as a file.
AnnotationSetSnapshot() - Constructor for class net.sf.basedb.core.snapshot.AnnotationSetSnapshot: Creates a new, empty snapshot.
AnnotationSetSnapshot.SortByProjectComparator - Class in net.sf.basedb.core.snapshot: Comparator for sorting annotation snapshots so that project-specific annotations appear before default annotations.
AnnotationSetterPlugin - Interface in net.sf.basedb.core.plugin: This is a interface that should be implemented by plug-ins that are setting annotations on items thy create or work with.
AnnotationSimpleRestriction - Class in net.sf.basedb.core: Restricts a query using annotation values with a simple expression: annotation operator value.
AnnotationSimpleRestriction(String, int, Type, Operator, Object, boolean, boolean) - Constructor for class net.sf.basedb.core.AnnotationSimpleRestriction: Deprecated.
In 3.11, use AnnotationSimpleRestriction(String, AnnotationType, Operator, Object, AnnotationRestriction.Options) instead
AnnotationSimpleRestriction(String, int, Type, Operator, List<Object>, boolean, boolean) - Constructor for class net.sf.basedb.core.AnnotationSimpleRestriction: Deprecated.
In 3.11, use AnnotationSimpleRestriction(String, AnnotationType, Operator, List, AnnotationRestriction.Options) instead
AnnotationSimpleRestriction(String, AnnotationType, Operator, Object, boolean, boolean) - Constructor for class net.sf.basedb.core.AnnotationSimpleRestriction: Deprecated.
In 3.11, use AnnotationSimpleRestriction(String, AnnotationType, Operator, Object, AnnotationRestriction.Options) instead
AnnotationSimpleRestriction(String, AnnotationType, Operator, Object, AnnotationRestriction.Options) - Constructor for class net.sf.basedb.core.AnnotationSimpleRestriction: Create a new annotation restriction using a simple expression: annotation operator value.
AnnotationSimpleRestriction(String, AnnotationType, Operator, List<Object>, AnnotationRestriction.Options) - Constructor for class net.sf.basedb.core.AnnotationSimpleRestriction: Creates a new annotation restriction for a specific valueType.
AnnotationSnapshot - Class in net.sf.basedb.core.snapshot: Stores information about a single primary or inherited annotation or an inherited annotation set.
AnnotationSnapshot() - Constructor for class net.sf.basedb.core.snapshot.AnnotationSnapshot: Create a new, empty annotation snapshot.
AnnotationSnapshot.AnnotationTypeComparator - Class in net.sf.basedb.core.snapshot: Comparator implementation for sorting snapshots by name of annotation type.
AnnotationSnapshot.ProjectComparator - Class in net.sf.basedb.core.snapshot: Comparator implementation for sorting snapshots by name of project.
AnnotationSummary(ExperimentExplorer, DbControl, AnnotationType) - Constructor for class net.sf.basedb.clients.web.ExperimentExplorer.AnnotationSummary
annotationType - Variable in class net.sf.basedb.clients.web.ExperimentExplorer.AnnotationSummary
annotationType - Variable in class net.sf.basedb.clients.web.plugins.ExportedProperty
annotationType - Variable in class net.sf.basedb.core.AnnotationBatcher.CurrentAnnotationInfo
annotationType - Variable in class net.sf.basedb.core.AnnotationRestriction
annotationType - Variable in class net.sf.basedb.core.data.AnnotationData
annotationType - Variable in class net.sf.basedb.core.ProjectSpecificAnnotationsManager.AnnotationInfo
annotationType - Variable in class net.sf.basedb.core.query.AnnotationExpression
annotationType - Variable in class net.sf.basedb.core.query.AnnotationJoin
annotationType - Variable in class net.sf.basedb.plugins.batchimport.AnnotationIdMethod
annotationType - Variable in class net.sf.basedb.util.annotations.InheritSpecification
annotationType - Variable in class net.sf.basedb.util.overview.Fix
AnnotationType - Class in net.sf.basedb.core: Objects of this class defines an annotation type.
AnnotationType(AnnotationTypeData) - Constructor for class net.sf.basedb.core.AnnotationType
ANNOTATIONTYPE - 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 - 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 - 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 - 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
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 - 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 - 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 - 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 - 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
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
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 - 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 - 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 - 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 - 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 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 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 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 in net.sf.basedb.plugins
Base1PluginExecuter.JobParameter - Class in net.sf.basedb.plugins
base64_code - Static variable in class net.sf.basedb.util.bcrypt.BCrypt
baseBeginDataPart() - Method in class net.sf.basedb.util.basefile.BaseFileWriter: End the header part of the current section (by writing a single % on a line by itself) and start the data part.
baseBeginSection(String) - Method in class net.sf.basedb.util.basefile.BaseFileWriter: Start a new section in the BASEfile.
baseCompleted - Variable in class net.sf.basedb.core.SimpleAbsoluteProgressReporter
baseEndSection() - Method in class net.sf.basedb.util.basefile.BaseFileWriter: Ends the current section by writing an empty line.
baseEscape(String) - Method in class net.sf.basedb.util.basefile.BaseFileWriter: Escape new line and carrige return characters in the input to the literal string '\n' and '\r' in the output.
BaseException - Exception in net.sf.basedb.core: This is the base class for exceptions in BASE.
BaseException() - Constructor for exception net.sf.basedb.core.BaseException: Create a new BaseException object.
BaseException(String) - Constructor for exception net.sf.basedb.core.BaseException: Create a new BaseException object with the specified message
BaseException(String, Throwable) - Constructor for exception net.sf.basedb.core.BaseException: Create a new BaseException object with the specified message
BaseException(Throwable) - Constructor for exception net.sf.basedb.core.BaseException: Create a new BaseException object acting as a wrapper for another exception that caused the error.
BaseException(SQLException) - Constructor for exception net.sf.basedb.core.BaseException: Create a new BaseException object where the cause is an SQLException.
BASEFILE_MATRIX - Static variable in class net.sf.basedb.core.DataFileType: The external ID for the file type representing a matrix BASEFile.
BASEFILE_SERIAL - Static variable in class net.sf.basedb.core.DataFileType: The external ID for the file type representing a serial BASEFile.
BaseFileExporter - Class in net.sf.basedb.util.export.spotdata: A superclass for exporters that exports spot data to BASEfile format.
BaseFileExporter() - Constructor for class net.sf.basedb.util.export.spotdata.BaseFileExporter
BaseFileExporterPlugin - Class in net.sf.basedb.plugins: Exports bioassay set data as serial or matrix BASEfile:s.
BaseFileExporterPlugin() - Constructor for class net.sf.basedb.plugins.BaseFileExporterPlugin
BaseFileExporterPlugin.ExtendedDynamicField - Class in net.sf.basedb.plugins
BaseFileExporterSupport - Class in net.sf.basedb.plugins.executor: Exporter implementation for the external program executor that exports data to BASEfile format.
BaseFileExporterSupport() - Constructor for class net.sf.basedb.plugins.executor.BaseFileExporterSupport
BaseFileImporter - Class in net.sf.basedb.util.importer.spotdata: Imports spot data from a serial or matrix BASEfile.
BaseFileImporter() - Constructor for class net.sf.basedb.util.importer.spotdata.BaseFileImporter: Create a new importer object.
BaseFileImporter.RawDataProxy - Class in net.sf.basedb.util.importer.spotdata
BaseFileImporter.ReporterProxy - Class in net.sf.basedb.util.importer.spotdata
BaseFileImporterSupport - Class in net.sf.basedb.plugins.executor: Importer implementation for the external program executor that imports data from BASEfile format.
BaseFileImporterSupport() - Constructor for class net.sf.basedb.plugins.executor.BaseFileImporterSupport
BaseFileInfo - Class in net.sf.basedb.util.importer.spotdata: Collects information about a BASEfile as it gets parsed by a BaseFileImporter.
BaseFileInfo(FileWrapper) - Constructor for class net.sf.basedb.util.importer.spotdata.BaseFileInfo: The source file which should be a BASEfile.
BaseFileInfo.ChildBioAssay - Class in net.sf.basedb.util.importer.spotdata: Keeps information about a new child bioassay from the 'assays' section or 'spot' sections.
BaseFileInfo.SpotSectionInfo - Class in net.sf.basedb.util.importer.spotdata: Keeps information about headers and more in a 'spot' section.
BaseFileParser - Class in net.sf.basedb.util.basefile: Parser for serial and matrix BASEfile:s.
BaseFileParser() - Constructor for class net.sf.basedb.util.basefile.BaseFileParser: Creates a new parser object.
BaseFileSectionParser - Interface in net.sf.basedb.util.basefile: A section parser is responsible for parsing and collecting data that is found in a section in a serial or matrix BASEfile.
BaseFileWrapper - Class in net.sf.basedb.util.importer: File wrapper implementation for files that are located on the BASE file system.
BaseFileWrapper(File) - Constructor for class net.sf.basedb.util.importer.BaseFileWrapper
BaseFileWriter - Class in net.sf.basedb.util.basefile: Wraps a writer stream and provides methods for easier creation of BASEfiles.
BaseFileWriter(Writer) - Constructor for class net.sf.basedb.util.basefile.BaseFileWriter: Create a new BASEfile writer that is writing it's output to the given writer.
BaseInputStreamLocator - Class in net.sf.basedb.util.bfs: Input stream locator implementation that works with files within a given directory in the BASE file system.
BaseInputStreamLocator(DbControl, Directory) - Constructor for class net.sf.basedb.util.bfs.BaseInputStreamLocator: Create a new input stream locator.
basePrintData(Object...) - Method in class net.sf.basedb.util.basefile.BaseFileWriter: Print a data line to the BASEfile.
basePrintHeader(String, Object) - Method in class net.sf.basedb.util.basefile.BaseFileWriter: Prints a header in the BASEfile.
baseStyle - Variable in class net.sf.basedb.util.excel.CellStyleCreator
baseWriteBom() - Method in class net.sf.basedb.util.basefile.BaseFileWriter: Write the beginning-of-file marker (BASEfile) to the output.
basic - Static variable in class net.sf.basedb.core.Item.DefinedPermissions
BASIC_FILTER - Static variable in class net.sf.basedb.core.QueryRuntimeFilterFactory
BasicBatcher<D extends BatchableData> - Class in net.sf.basedb.core: This is an abstract class for batching functionallity.
BasicBatcher(Session, Class<D>, String) - Constructor for class net.sf.basedb.core.BasicBatcher: Constructor that initiate everything.
BasicChildItem - Class in net.sf.basedb.core: An abstract base class for all items which are child items to a BasicItem parent item.
BasicChildItem(BasicData) - Constructor for class net.sf.basedb.core.BasicChildItem
BasicData - Class in net.sf.basedb.core.data: This is the root superclass of all data classes.
BasicData() - Constructor for class net.sf.basedb.core.data.BasicData
BasicData2ItemPropertyPath(Item, Type) - Constructor for class net.sf.basedb.core.Metadata.BasicData2ItemPropertyPath
BasicFilter() - Constructor for class net.sf.basedb.core.QueryRuntimeFilterFactory.BasicFilter
BasicItem - Class in net.sf.basedb.core: This is the root superclass of all item classes.
BasicItem(BasicData) - Constructor for class net.sf.basedb.core.BasicItem: Create a new instance.
BasicItem2DataPropertyPath(Class<C>, Type) - Constructor for class net.sf.basedb.core.Metadata.BasicItem2DataPropertyPath
BasicItemFilter - Class in net.sf.basedb.util.overview.filter: A filter implementation that matches against the item that is attached to nodes.
BasicItemFilter(BasicItem) - Constructor for class net.sf.basedb.util.overview.filter.BasicItemFilter: Create a filter that finds nodes that has the given item attached to it.
BasicItemNodeLoader<I extends BasicItem> - Class in net.sf.basedb.util.overview.loader: Abstract class that is useful for all node loaders that works with BasicItem:s.
BasicItemNodeLoader(Object, boolean, NodeNameGenerator<I>) - Constructor for class net.sf.basedb.util.overview.loader.BasicItemNodeLoader: Create a new node loader.
BasicItemNodeLoaderFactory - Class in net.sf.basedb.util.overview.loader: Node loader factory implementation for BasicItem node loaders.
BasicItemNodeLoaderFactory() - Constructor for class net.sf.basedb.util.overview.loader.BasicItemNodeLoaderFactory: Creates a new factory.
BasicItemNodeValidatorFactory - Class in net.sf.basedb.util.overview.validator: Node validator factory implementation for BasicItem node validators.
BasicItemNodeValidatorFactory() - Constructor for class net.sf.basedb.util.overview.validator.BasicItemNodeValidatorFactory: Creates a new factory.
BasicItemToIdTransformer - Class in net.sf.basedb.util.collections: Collection transformer implementation that extracts the ID from BasicItem:s.
BasicItemToIdTransformer() - Constructor for class net.sf.basedb.util.collections.BasicItemToIdTransformer
BasicNodeValidator<I> - Class in net.sf.basedb.util.overview.validator: A simple node validation implementation that takes care of missing and denied access to items.
BasicNodeValidator(Validator, Validator) - Constructor for class net.sf.basedb.util.overview.validator.BasicNodeValidator: Creates a new validator.
BatchableData - Interface in net.sf.basedb.core.data: This is a tagging interface only.
BatchAndMapHolder(RawDataBatcher, RawDataType, FlatFileParser) - Constructor for class net.sf.basedb.plugins.IlluminaRawDataImporter.BatchAndMapHolder
batchCount - Variable in class net.sf.basedb.core.LogControl
batchDate - Variable in class net.sf.basedb.core.AnnotationBatcher
batchedExternalIds - Variable in class net.sf.basedb.core.ReporterBatcher: A set containing all batched but not yet flushed external reporter id:s.
BatchedPropertyInfo - Class in net.sf.basedb.core: Holds information about a batchable property.
BatchedPropertyInfo(String, int) - Constructor for class net.sf.basedb.core.BatchedPropertyInfo: Create a new extended property.
batcher - Variable in class net.sf.basedb.plugins.AnnotationFlatFileImporter
batcher - Variable in class net.sf.basedb.plugins.IlluminaRawDataImporter.BatchAndMapHolder
batcher - Variable in class net.sf.basedb.plugins.PrintMapFlatFileImporter
batcher - Variable in class net.sf.basedb.plugins.RawDataFlatFileImporter
batcher - Variable in class net.sf.basedb.plugins.ReporterFlatFileImporter
batcher - Variable in class net.sf.basedb.plugins.ReporterMapFlatFileImporter
Batcher - Interface in net.sf.basedb.core: The basic interface which all batchers must implement.
batchers - Variable in class net.sf.basedb.core.DbControl: A list of batchers that will be closed when DbControl is closed and will be flushed when commit is called.
batchIndex - Variable in class net.sf.basedb.core.data.ArraySlideData
batchQuery - Variable in class net.sf.basedb.plugins.batchimport.AbstractItemImporter
batchSize - Variable in class net.sf.basedb.core.AbstractBatcher: SQL command batch size.
batchSize - Variable in class net.sf.basedb.core.LogControl
BatchUtil - Class in net.sf.basedb.core: Utility class for batching information.
BatchUtil() - Constructor for class net.sf.basedb.core.BatchUtil
BCrypt - Class in net.sf.basedb.util.bcrypt: BCrypt implements OpenBSD-style Blowfish password hashing using the scheme described in "A Future-Adaptable Password Scheme" by Niels Provos and David Mazieres.
BCrypt() - Constructor for class net.sf.basedb.util.bcrypt.BCrypt
BCRYPT_SALT_LEN - Static variable in class net.sf.basedb.util.bcrypt.BCrypt
bean - Variable in class net.sf.basedb.util.extensions.debug.BeanActionFactory
BeanActionFactory - Class in net.sf.basedb.util.extensions.debug: Generic action factory class that can generate instances of actions if there exists a bean-like implementation of the action class.
BeanActionFactory() - Constructor for class net.sf.basedb.util.extensions.debug.BeanActionFactory: Creates a new proxy factory.
beanClassName - Variable in class net.sf.basedb.util.extensions.debug.BeanActionFactory
before - Variable in class net.sf.basedb.core.DbControl.SaveIf
BEFORE_DISABLE - Static variable in class net.sf.basedb.clients.web.extensions.ExtensionsControl: This event is sent before an extension or extension point is disabled by ExtensionsControl.enableExtensionPoint(String, boolean), ExtensionsControl.enableExtension(String, boolean), or ExtensionsControl.enableAllInFile(String, boolean).
BEFORE_UNREGISTRATION - Static variable in class net.sf.basedb.util.extensions.events.EventType: This event is sent before an extension point or extension is unregistered.
BEFORE_UPDATE - Static variable in class net.sf.basedb.util.extensions.events.EventType: This event is sent during an update of an existing extension point or extension.
beforeTransactionCompletion(Transaction) - Method in class net.sf.basedb.core.log.LoggingInterceptor: Flush remaining changes in the log control.
begin(DbControl) - Method in class net.sf.basedb.clients.web.plugins.SimpleExport
begin(DbControl) - Method in class net.sf.basedb.core.plugin.AbstractExporterPlugin: Called just before the export starts.
begin(DbControl) - Method in class net.sf.basedb.plugins.BaseFileExporterPlugin
begin(DbControl) - Method in class net.sf.basedb.plugins.BfsExporterPlugin
begin(DbControl) - Method in class net.sf.basedb.plugins.GalExporter
begin(DbControl) - Method in class net.sf.basedb.plugins.HelpExporter
begin(DbControl) - Method in class net.sf.basedb.plugins.PackedFileExporter
begin(DbControl) - Method in class net.sf.basedb.plugins.PlateMappingExporter
begin(DbControl) - Method in class net.sf.basedb.plugins.PluginConfigurationExporter
begin(ExtensionsManager, int) - Method in class net.sf.basedb.clients.web.extensions.LoadServletsProcessor
begin(ExtensionsManager, int) - Method in class net.sf.basedb.clients.web.extensions.UninstalledFileProcessor
begin(ExtensionsManager, int) - Method in interface net.sf.basedb.util.extensions.manager.ExtensionsFileProcessor: Called by the extensions manager before the processing starts.
begin(ExtensionsManager, int) - Method in class net.sf.basedb.util.extensions.manager.processor.DeleteResourcesProcessor
begin(ExtensionsManager, int) - Method in class net.sf.basedb.util.extensions.manager.processor.DisablePluginsProcessor
begin(ExtensionsManager, int) - Method in class net.sf.basedb.util.extensions.manager.processor.ExtractResourcesProcessor
begin(ExtensionsManager, int) - Method in class net.sf.basedb.util.extensions.manager.processor.IgnoreFileProcessor
begin(ExtensionsManager, int) - Method in class net.sf.basedb.util.extensions.manager.processor.MarkAsProcessedProcessor
begin(ExtensionsManager, int) - Method in class net.sf.basedb.util.extensions.manager.processor.PluginInstallationProcessor
begin(ExtensionsManager, int) - Method in class net.sf.basedb.util.extensions.manager.processor.RegisterExtensionsProcessor
begin(ExtensionsManager, int) - Method in class net.sf.basedb.util.extensions.manager.processor.ResetProcessor
begin(ExtensionsManager, int) - Method in class net.sf.basedb.util.extensions.manager.processor.UnregisterExtensionsProcessor
begin(FlatFileParser) - Method in class net.sf.basedb.plugins.AbstractFlatFileImporter: Called just before parsing of the file begins.
begin(FlatFileParser) - Method in class net.sf.basedb.plugins.AnnotationFlatFileImporter: Setup error handling and pre-load some of the configuration options.
begin(FlatFileParser) - Method in class net.sf.basedb.plugins.batchimport.AbstractItemImporter: Setup error handling and pre-load some of the configuration options.
begin(FlatFileParser) - Method in class net.sf.basedb.plugins.batchimport.AnyToAnyImporter: Setup error handling and pre-load some of the configuration options.
begin(FlatFileParser) - Method in class net.sf.basedb.plugins.IlluminaRawDataImporter
begin(FlatFileParser) - Method in class net.sf.basedb.plugins.PlateFlatFileImporter: Create a DbControl and a RawDataBatcher.
begin(FlatFileParser) - Method in class net.sf.basedb.plugins.PlateMappingImporter: Save reference to parser.
begin(FlatFileParser) - Method in class net.sf.basedb.plugins.PrintMapFlatFileImporter: Create a DbControl and a FeatureBatcher.
begin(FlatFileParser) - Method in class net.sf.basedb.plugins.RawDataFlatFileImporter: Prepare for importing the next file.
begin(FlatFileParser) - Method in class net.sf.basedb.plugins.ReporterFlatFileImporter: Create a DbControl and a ReporterBatcher.
begin(FlatFileParser) - Method in class net.sf.basedb.plugins.ReporterMapFlatFileImporter: Create a DbControl and a FeatureBatcher.
beginData() - Method in class net.sf.basedb.plugins.AbstractFlatFileImporter: Called by the parser after the headers have been parsed but before the first data line is parsed.
beginData() - Method in class net.sf.basedb.plugins.AnnotationFlatFileImporter: Setup column mapping.
beginData() - Method in class net.sf.basedb.plugins.batchimport.AbstractItemImporter: Setup column mapping.
beginData() - Method in class net.sf.basedb.plugins.batchimport.AnyToAnyImporter: Setup column mapping.
beginData() - Method in class net.sf.basedb.plugins.IlluminaRawDataImporter: Check column headers and map them to raw bioassays.
beginData() - Method in class net.sf.basedb.plugins.PlateFlatFileImporter: Initialise column Mapper:s.
beginData() - Method in class net.sf.basedb.plugins.PlateMappingImporter: Create a DbControl and a new PlateMapping.
beginData() - Method in class net.sf.basedb.plugins.RawDataFlatFileImporter: Initialise column Mapper:s.
beginData() - Method in class net.sf.basedb.plugins.ReporterFlatFileImporter: Initialise column Mapper:s.
beginData() - Method in class net.sf.basedb.plugins.ReporterMapFlatFileImporter: Initialise column Mapper:s.
beginDocument() - Method in interface net.sf.basedb.clients.web.plugins.ExportTemplate: Start writing the document.
beginDocument() - Method in class net.sf.basedb.clients.web.plugins.PlainTextTemplate: Do nothing.
beginDocument() - Method in class net.sf.basedb.clients.web.plugins.XlsxTemplate: Reset row and column to 0.
beginDocument() - Method in class net.sf.basedb.clients.web.plugins.XMLTemplate: Write XML start (<?
beginExport() - Method in class net.sf.basedb.util.export.spotdata.AbstractBioAssaySetExporter: Make preparations for the export.
beginExport() - Method in class net.sf.basedb.util.export.spotdata.BaseFileExporter: Prepare the export by adding all experimental factors as assay fields if no fields have been specified.
beginExport() - Method in class net.sf.basedb.util.export.spotdata.BfsExporter: Validates that all required properties has been set and initialises other things that are needed.
beginExport() - Method in class net.sf.basedb.util.export.spotdata.MatrixBaseFileExporter: Prepare the export by pre-loading some information and configure the queries that we are going to use.
beginExport() - Method in class net.sf.basedb.util.export.spotdata.SerialBaseFileExporter: Prepare the export by pre-loading some information and configure the queries that we are going to use.
beginItem(int) - Method in interface net.sf.basedb.clients.web.plugins.ExportTemplate: Start writing a new item.
beginItem(int) - Method in class net.sf.basedb.clients.web.plugins.PlainTextTemplate: Reset column number.
beginItem(int) - Method in class net.sf.basedb.clients.web.plugins.XlsxTemplate: Reset column number and create a new row.
beginItem(int) - Method in class net.sf.basedb.clients.web.plugins.XMLTemplate: Begin a new item element.
beginSection(BaseFileParser, FlatFileParser, List<String>) - Method in class net.sf.basedb.util.importer.spotdata.GenericIntensityParser
beginSection(BaseFileParser, FlatFileParser, List<String>) - Method in class net.sf.basedb.util.importer.spotdata.MAParser
beginSection(BaseFileParser, FlatFileParser, List<String>) - Method in interface net.sf.basedb.util.importer.spotdata.SpotIntensityParser: Prepare for parsing the data section.
beginTransaction() - Method in class net.sf.basedb.core.hibernate.SessionWrapper
beginTransaction() - Method in class net.sf.basedb.core.hibernate.StatelessSessionWrapper
belongsTo(AnnotationSet) - Method in class net.sf.basedb.core.Annotation: Check if this annotation belongs to the primaray annotations for a specified annotation set.
between(Expression, Expression, Expression) - Static method in class net.sf.basedb.core.query.Restrictions: Compare if one expression falls between two other expressions: new expression = low <= e AND e < high.
BETWEEN - 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 - net.sf.basedb.core.BioMaterialEvent.Type: An event of this type created a physical bioassay.
BIOASSAY - 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.
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 - 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 - net.sf.basedb.core.Item: The item is a BioMaterialEvent.
BioMaterialEvent.Type - Enum 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 - 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 - 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 - net.sf.basedb.core.Item: The item is a BioPlateEventParticipant
BioPlateEventParticipantData - Class in net.sf.basedb.core.data: Registers a plate as a participant in a bioplate event.
BioPlateEventParticipantData() - Constructor for class net.sf.basedb.core.data.BioPlateEventParticipantData
BioPlateEventType - Class in net.sf.basedb.core: The type of a bioplate event defines what happened in the event.
BioPlateEventType(BioPlateEventTypeData) - Constructor for class net.sf.basedb.core.BioPlateEventType
BIOPLATEEVENTTYPE - 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 - 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 - 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 - net.sf.basedb.core.Item: The item is a BioWell
BioWell.LockMode - Enum 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 - 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 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 - net.sf.basedb.core.Type: Boolean type.
BOOLEAN - Static variable in class net.sf.basedb.core.hibernate.TypeWrapper
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 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 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 net.sf.basedb.core.BioWell.LockMode: Is it allowed to add (a different) biomaterial to the well?
canAdd(BioWellData) - Method in enum net.sf.basedb.core.BioWell.LockMode
canAddBioMaterial() - Method in class net.sf.basedb.core.BioWell: Check if it is possible to add/change biomaterial in this well.
cancel() - Method in class net.sf.basedb.clients.jobagent.JobQueueChecker
cancel() - Method in interface net.sf.basedb.core.QueryExecutor.Cancelable
cancel() - Method in class net.sf.basedb.core.QueryExecutor.CancelableSession
cancel() - Method in class net.sf.basedb.core.QueryExecutor.CancelableStatelessSession
cancel() - Method in class net.sf.basedb.core.QueryExecutor.CancelableStatement
cancel() - Method in class net.sf.basedb.util.timer.ThreadTimerTask
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 net.sf.basedb.core.BioWell.LockMode: Is it allowed to clear a well from biomaterial?
canClear(BioWellData) - Method in enum net.sf.basedb.core.BioWell.LockMode
canClearBioMaterial() - Method in class net.sf.basedb.core.BioWell: Check if it is possible to clear the current biomaterial in this well.
canEnumerate - Variable in enum net.sf.basedb.core.Type
canEnumerate() - Method in enum net.sf.basedb.core.Type: If it makes sense to use values of this type as an enumeration to choose from.
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 net.sf.basedb.core.Formula.Type
canUseColoring() - Method in enum net.sf.basedb.core.Formula.Type: If a formula of this type can use coloring or not.
CAPACITANCE - Static variable in class net.sf.basedb.core.Quantity: The id for the Quantity object representing capacitance.
CaseExpression - Class in net.sf.basedb.core.query: An SQL case expression:
CaseExpression(Expression, WhenStatement...) - Constructor for class net.sf.basedb.core.query.CaseExpression
caseInsensitive - Variable in enum net.sf.basedb.core.FeatureIdentificationMethod: If the feature identifiers may be affect by case sensitivity at the database level or not.
caseInsensitive - Variable in class net.sf.basedb.core.RawDataBatcher: If case should be ignored when comparing strings (external ID)
caseInsensitive() - Method in enum 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
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.
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(ChangeType) - Constructor for enum net.sf.basedb.core.AnnotationBatcher.Change
ChangeHistory - Class in net.sf.basedb.core
ChangeHistory(ChangeHistoryDetailData) - Constructor for class net.sf.basedb.core.ChangeHistory
CHANGEHISTORY - net.sf.basedb.core.Item: The item is a ChangeHistory entry.
CHANGEHISTORY_VALUES - 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 in net.sf.basedb.core.log: Enumeration that represents the type of change that has happened.
ChangeType(int, String) - Constructor for enum 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 - 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 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 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
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 - 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 - 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 - 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 - 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 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 - net.sf.basedb.core.ExtraValue.CoordinateType: The extra values are attached to column coordinates only.
COLUMN - 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 - net.sf.basedb.core.Formula.Type: An arbitrary expression that specify one formula only.
COLUMN_EXTRA_FLOAT - net.sf.basedb.core.VirtualTable: Table that stores float column extra values.
COLUMN_EXTRA_INT - net.sf.basedb.core.VirtualTable: Table that stores integer column extra values.
COLUMN_EXTRA_STRING - 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 - net.sf.basedb.core.Formula.Type: An arbitraty expression that specify one formula only.
columnColumnMapping - Static variable in class net.sf.basedb.plugins.PlateFlatFileImporter
columnColumnMapping - Static variable in class net.sf.basedb.plugins.RawDataFlatFileImporter
columnColumnMapping - Static variable in class net.sf.basedb.plugins.ReporterMapFlatFileImporter
columnContent - Variable in class net.sf.basedb.clients.web.taglib.table.Table
columnCount - Variable in class net.sf.basedb.util.bfs.AnnotationWriter
columnCount - Variable in class net.sf.basedb.util.bfs.DataWriter
ColumnDef - Class in net.sf.basedb.clients.web.taglib.table: This tag defines a column in the table.
ColumnDef() - Constructor for class net.sf.basedb.clients.web.taglib.table.ColumnDef
ColumnDef.NullIterator<A,B> - Class in net.sf.basedb.clients.web.taglib.table: Iterator implementation that returns a single null value and nothing more.
columnFilter - Variable in class net.sf.basedb.clients.web.taglib.table.Table
columnFormatter - Variable in class net.sf.basedb.clients.web.taglib.table.Table
columnHeaders - Variable in class net.sf.basedb.plugins.AnnotationFlatFileImporter
columnHeaders - Variable in class net.sf.basedb.util.parser.ColFunction
columnHeaders - Variable in class net.sf.basedb.util.parser.FlatFileParser: List of the column names found by splitting the data header using the data splitter regexp.
ColumnHeaders - Class in net.sf.basedb.clients.web.taglib.table: Generate column headers for the columns that has been defined for this table.
ColumnHeaders() - Constructor for class net.sf.basedb.clients.web.taglib.table.ColumnHeaders
columnId - Variable in class net.sf.basedb.clients.web.taglib.table.Cell: The ID of the column to which this cell belongs.
columnIndex - Variable in class net.sf.basedb.util.bfs.AnnotationModel
ColumnInfo(String, String, Integer, int, boolean, boolean) - Constructor for class net.sf.basedb.core.dbengine.TableInfo.ColumnInfo: Create a new ColumnInfo object.
ColumnKey(Comparable<?>, String) - Constructor for class net.sf.basedb.clients.web.servlet.ExperimentExplorerPlotServlet.ColumnKey
columnMapper - Variable in class net.sf.basedb.plugins.PlateFlatFileImporter
columnMapper - Variable in class net.sf.basedb.plugins.RawDataFlatFileImporter
columnMapper - Variable in class net.sf.basedb.plugins.ReporterMapFlatFileImporter
ColumnMapper - Class in net.sf.basedb.util.parser: Returns the string found in the column given by the index set in the constructor.
ColumnMapper(int, String) - Constructor for class net.sf.basedb.util.parser.ColumnMapper: Create a new column mapper.
ColumnMapper(int, String, NumberFormat, boolean) - Constructor for class net.sf.basedb.util.parser.ColumnMapper: Deprecated.
In 3.15, use ColumnMapper(int, String, NumberFormat, Formatter, boolean) instead
ColumnMapper(int, String, NumberFormat, Formatter<Date>, boolean) - Constructor for class net.sf.basedb.util.parser.ColumnMapper: Create a new column mapper using a specific number or date format.
columnMappingParameterName - Variable in class net.sf.basedb.plugins.batchimport.PropertyIdMethod
columnName - Variable in class net.sf.basedb.core.Update.DropColumnChange
columnNo - Variable in class net.sf.basedb.core.data.DataCubeColumnData
columns - Variable in class net.sf.basedb.clients.web.taglib.table.Table: Which columns that should be visible and their order
columns - Variable in class net.sf.basedb.core.data.DataCubeData
columns - Variable in class net.sf.basedb.core.data.PlateGeometryData
columns - Variable in class net.sf.basedb.core.dbengine.TableInfo
columns - Variable in class net.sf.basedb.core.dbengine.TableInfo.IndexInfo
columns - Variable in class net.sf.basedb.core.dbengine.TableInfo.PrimaryKeyInfo
columns - Variable in class net.sf.basedb.core.ExtraValueJoin
columns - Variable in enum 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
commit() - Method in class net.sf.basedb.core.DbControl: Commit all changes made to items and close the connection to the database.
commit(Transaction) - Static method in class net.sf.basedb.core.HibernateUtil: Commit a transaction.
commitQueue - Variable in class net.sf.basedb.core.DbControl: A list of items that need special handling when commit is called.
COMMON - Static variable in class net.sf.basedb.clients.web.resources.Bundle: Resource bundle with strings that are used in lots and lots of places in the web gui.
commonCharsets - Static variable in class net.sf.basedb.core.Config
CommonData - Class in net.sf.basedb.core.data: This is a convenience class that extends the SharedData class and implements the NameableData and RemovableData interfaces.
CommonData() - Constructor for class net.sf.basedb.core.data.CommonData
commonDom - Static variable in class net.sf.basedb.core.PredefinedQuery: Holds the XML document containing the common queries.
CommonItem - Class in net.sf.basedb.core
CommonItem(CommonData) - Constructor for class net.sf.basedb.core.CommonItem
commonName - Variable in class net.sf.basedb.plugins.Base1PluginExecuter.JobParameter
commonQueryFile - Static variable in class net.sf.basedb.core.PredefinedQuery: The path to the query file with common queries.
CompactButtonRenderer - Class in net.sf.basedb.clients.web.extensions.toolbar: A compact renderer for toolbar button actions, which only only displays the icon.
CompactButtonRenderer(JspContext) - Constructor for class net.sf.basedb.clients.web.extensions.toolbar.CompactButtonRenderer
CompactButtonRendererFactory - Class in net.sf.basedb.clients.web.extensions.toolbar: Factory that create CompactButtonRenderer objects for rendering ButtonAction:s.
CompactButtonRendererFactory() - Constructor for class net.sf.basedb.clients.web.extensions.toolbar.CompactButtonRendererFactory
ComparableComparator<T extends Comparable<T>> - Class in net.sf.basedb.util: A comparator implemenation for any Comparable objects.
ComparableComparator() - Constructor for class net.sf.basedb.util.ComparableComparator
compare(String, String) - Method in class net.sf.basedb.util.StringLengthComparator
compare(URI, URI) - Method in class net.sf.basedb.util.extensions.manager.ExtensionsManager.JarFirstURIComparator
compare(RawDataType, RawDataType) - Method in class net.sf.basedb.core.RawDataTypes.NameComparator
compare(AnnotationSnapshot, AnnotationSnapshot) - Method in class net.sf.basedb.core.snapshot.AnnotationSetSnapshot.SortByProjectComparator
compare(AnnotationSnapshot, AnnotationSnapshot) - Method in class net.sf.basedb.core.snapshot.AnnotationSnapshot.AnnotationTypeComparator
compare(AnnotationSnapshot, AnnotationSnapshot) - Method in class net.sf.basedb.core.snapshot.AnnotationSnapshot.ProjectComparator
compare(T, T) - Method in class net.sf.basedb.util.ComparableComparator
compare(T, T) - Method in class net.sf.basedb.util.NameableComparator
compare(T, T) - Method in class net.sf.basedb.util.PriorityComparator
compare(T, T) - Method in class net.sf.basedb.util.ToStringComparator
compareByChainOrder() - Static method in class net.sf.basedb.core.SyncFilter: Create a comparator that sorts sync filters by: Filter group Source item type: BIOSOURCE, SAMPLE, EXTRACT, PHYSICALBIOASSAY, DERIVEDBIOASSAY, RAWBIOASSAY Type of transformation: PARENT_TO_CHILD, NONE, CHILD_TO_PARENT Name Source item must exists is sorted before source item must not exist Id
compareTo(ExperimentExplorer.AnnotationGroup) - Method in class net.sf.basedb.clients.web.ExperimentExplorer.AnnotationGroup
compareTo(ExperimentExplorerPlotServlet.ColumnKey) - Method in class net.sf.basedb.clients.web.servlet.ExperimentExplorerPlotServlet.ColumnKey: The ID of the key determines equality.
compareTo(ClonableProperty) - Method in class net.sf.basedb.core.ClonableProperty: Sort by title, but mandatory properties before non-madatory.
compareTo(KeyPermission) - Method in class net.sf.basedb.core.data.keyring.KeyPermission: Compare the keyId of this object to the keyId of another KeyPermission object.
compareTo(PluginKeys) - Method in class net.sf.basedb.core.data.keyring.PluginKeys: Compare the keyId of this object to the keyId of another PluginKeys object.
compareTo(ProjectPermission) - Method in class net.sf.basedb.core.data.keyring.ProjectPermission: Compare the projectId of this object to the projectId of another ProjectPermission object.
compareTo(TableInfo.ColumnInfo) - Method in class net.sf.basedb.core.dbengine.TableInfo.ColumnInfo
compareTo(ItemProxy) - Method in class net.sf.basedb.core.ItemProxy
compareTo(RawDataType) - Method in class net.sf.basedb.core.RawDataType: Compare the id:s of the raw data types.
compareTo(LowessNormalization.SpotData) - Method in class net.sf.basedb.plugins.LowessNormalization.SpotData: Sort by A in ascending order.
compareTo(MedianRatioNormalization.SpotData) - Method in class net.sf.basedb.plugins.MedianRatioNormalization.SpotData: Sort by ratio in ascending order.
compareTo(AnyToAnyLinkStatistics) - Method in class net.sf.basedb.util.AnyToAnyLinkStatistics: Sort items by count, linkName and targetType.
compareTo(ExtensionsFile) - Method in class net.sf.basedb.util.extensions.manager.ExtensionsFile
compareTo(Node) - Method in class net.sf.basedb.util.overview.Node
compareTo(PlotAnnotation) - Method in class net.sf.basedb.util.plot.PlotAnnotation
compareTo(UnitCache.CacheKey) - Method in class net.sf.basedb.util.units.UnitCache.CacheKey
compareWith(String) - Static method in class net.sf.basedb.core.Version: Compare the given version string, which should be of the form a.b or a.b.c, with the current BASE version.
compile(boolean, boolean) - Method in class net.sf.basedb.clients.web.extensions.XJspCompiler: Called when a JSP page needs recompiling.
compile(String, HttpServletRequest, HttpServletResponse) - Method in class net.sf.basedb.clients.web.servlet.CompileAll: Compile all files found in dir, recursively entering subdirectories.
CompileAll - Class in net.sf.basedb.clients.web.servlet: This servlet will scan for all files ending with .jsp and issue a request for them with the parameter jsp_precompile=true therby compiling all JSP files into servlets.
CompileAll() - Constructor for class net.sf.basedb.clients.web.servlet.CompileAll
completed - Variable in class net.sf.basedb.core.SimpleAbsoluteProgressReporter
complexMappings - Static variable in class net.sf.basedb.plugins.AbstractFlatFileImporter: Parameter that asks if complex column mappings should be enabled or not.
component - Variable in class net.sf.basedb.core.Metadata.ComponentPropertyPath
ComponentData - Interface in net.sf.basedb.core.data: Tagging interface that we need all componenets to implement so that we are able to export them properly using generic code.
ComponentPropertyPath(ComponentType, int, Type) - Constructor for class net.sf.basedb.core.Metadata.ComponentPropertyPath
CompoundMapper - Class in net.sf.basedb.util.parser: A compound mapper that gets its value by invoking multiple other mappers which are set in the constructor.
CompoundMapper(List<Mapper>) - Constructor for class net.sf.basedb.util.parser.CompoundMapper: Create a new compound mapper.
CompoundMapper(List<Mapper>, NumberFormat, boolean) - Constructor for class net.sf.basedb.util.parser.CompoundMapper: Create a new compound mapper, using a specific number formatter as it's parser.
CompoundMapper(List<Mapper>, NumberFormat, Formatter<Date>, boolean) - Constructor for class net.sf.basedb.util.parser.CompoundMapper: Create a new compound mapper, using a specific number formatter as it's parser.
compress - Variable in class net.sf.basedb.core.File.UploadStream: If the file should be compressed or not.
compress(ProgressReporter) - Method in class net.sf.basedb.core.File: Compress the file stored on the disk.
compressed - Variable in class net.sf.basedb.core.data.FileData
compressedSize - Variable in class net.sf.basedb.core.data.FileData
compressOrDecompress(ProgressReporter, boolean) - Method in class net.sf.basedb.core.File
condition - Variable in class net.sf.basedb.core.dbengine.TableInfo.IndexInfo
condition - Variable in class net.sf.basedb.core.HibernateUtil.DelayedFilterDef
condition - Variable in class net.sf.basedb.core.query.WhenStatement
conditionalExpression(Filter<? extends Query>, Expression, Expression) - Static method in class net.sf.basedb.core.query.Expressions: Create an expression that falls back to one of two expression depending on if the query passes a filter or not.
ConditionalQueryElement - Class in net.sf.basedb.core.query
ConditionalQueryElement(Filter<Query>, QueryElement, QueryElement) - Constructor for class net.sf.basedb.core.query.ConditionalQueryElement
conditionalRestriction(Filter<? extends Query>, Restriction, Restriction, boolean) - Static method in class net.sf.basedb.core.query.Restrictions: Create a restriction that falls back to one of two restrictions depending on if the query passes a filter or not.
config - Static variable in class net.sf.basedb.core.Config: Variable for holding the configuration properties.
config - Variable in class net.sf.basedb.core.hibernate.SchemaGenerator.CollectSqlTarget
config - Variable in class net.sf.basedb.core.plugin.ParameterValuesWrapper
config - Variable in class net.sf.basedb.util.ContextUtil.ContextResult
Config - Class in net.sf.basedb.core: Use this class to access the configuration settings for BASE.
Config() - Constructor for class net.sf.basedb.core.Config
configDir - Static variable in class net.sf.basedb.core.Config
configList - Static variable in class net.sf.basedb.plugins.PluginConfigurationExporter
configuration - Variable in class net.sf.basedb.core.ParameterValuesImpl
configuration - Variable in class net.sf.basedb.core.plugin.AbstractPlugin
configuration - Variable in class net.sf.basedb.plugins.gtf.DefaultConfigurationValues
ConfigurationException - Exception in net.sf.basedb.core: This exception is thrown by the Config class if there is a problem with finding or loading the configuration settings.
ConfigurationException(String) - Constructor for exception net.sf.basedb.core.ConfigurationException: Creates a new ConfigurationException.
ConfigurationException(String, Throwable) - Constructor for exception net.sf.basedb.core.ConfigurationException: Creates a new ConfigurationException with a cause.
configurationMap - Variable in class net.sf.basedb.plugins.PluginConfigurationImporter
configurationParameters - Variable in class net.sf.basedb.core.PluginRequest
configurations - Variable in class net.sf.basedb.core.data.PluginDefinitionData
configurationValues - Variable in class net.sf.basedb.core.data.PluginConfigurationData
configure() - Method in class net.sf.basedb.core.PluginConfiguration: Start the configuration sequence for a plugin.
configure(GuiContext) - Method in class net.sf.basedb.core.Job: Start the configuration sequence for a job.
configure(GuiContext, Request, Response) - Method in class net.sf.basedb.clients.web.plugins.SimpleExport
configure(GuiContext, Request, Response) - Method in interface net.sf.basedb.core.plugin.InteractivePlugin: Configure the plugin.
configure(GuiContext, Request, Response) - Method in class net.sf.basedb.plugins.AnnotationFlatFileImporter
configure(GuiContext, Request, Response) - Method in class net.sf.basedb.plugins.Base1PluginExecuter
configure(GuiContext, Request, Response) - Method in class net.sf.basedb.plugins.BaseFileExporterPlugin
configure(GuiContext, Request, Response) - Method in class net.sf.basedb.plugins.batchimport.AbstractItemImporter
configure(GuiContext, Request, Response) - Method in class net.sf.basedb.plugins.batchimport.AnnotationTypeImporter: Override this method so that we can make some extra parameter checks: A mapping for 'Value type' must be specified when 'create' or 'create+update' mode is used
configure(GuiContext, Request, Response) - Method in class net.sf.basedb.plugins.batchimport.AnyToAnyImporter
configure(GuiContext, Request, Response) - Method in class net.sf.basedb.plugins.BfsExporterPlugin
configure(GuiContext, Request, Response) - Method in class net.sf.basedb.plugins.CdfFileReporterImporter
configure(GuiContext, Request, Response) - Method in class net.sf.basedb.plugins.executor.BaseFileExporterSupport
configure(GuiContext, Request, Response) - Method in class net.sf.basedb.plugins.executor.BaseFileImporterSupport
configure(GuiContext, Request, Response) - Method in class net.sf.basedb.plugins.executor.BfsExporterSupport
configure(GuiContext, Request, Response) - Method in class net.sf.basedb.plugins.executor.BfsImporterSupport
configure(GuiContext, Request, Response) - Method in class net.sf.basedb.plugins.executor.ExternalProgramExecutor
configure(GuiContext, Request, Response) - Method in class net.sf.basedb.plugins.executor.FileOnlyImporterSupport
configure(GuiContext, Request, Response) - Method in class net.sf.basedb.plugins.FormulaFilter
configure(GuiContext, Request, Response) - Method in class net.sf.basedb.plugins.GalExporter
configure(GuiContext, Request, Response) - Method in class net.sf.basedb.plugins.gtf.GtfReporterMapImporter
configure(GuiContext, Request, Response) - Method in class net.sf.basedb.plugins.HelpExporter
configure(GuiContext, Request, Response) - Method in class net.sf.basedb.plugins.HelpImporter
configure(GuiContext, Request, Response) - Method in class net.sf.basedb.plugins.IlluminaRawDataImporter
configure(GuiContext, Request, Response) - Method in class net.sf.basedb.plugins.IntensityCalculatorPlugin: Store configuration settings for Request.COMMAND_CONFIGURE_PLUGIN, and Request.COMMAND_CONFIGURE_JOB.
configure(GuiContext, Request, Response) - Method in class net.sf.basedb.plugins.JepExtraValueCalculator
configure(GuiContext, Request, Response) - Method in class net.sf.basedb.plugins.JepIntensityTransformer
configure(GuiContext, Request, Response) - Method in class net.sf.basedb.plugins.LowessNormalization
configure(GuiContext, Request, Response) - Method in class net.sf.basedb.plugins.ManualDerivedBioAssayCreator
configure(GuiContext, Request, Response) - Method in class net.sf.basedb.plugins.ManualTransformCreator
configure(GuiContext, Request, Response) - Method in class net.sf.basedb.plugins.MedianRatioNormalization
configure(GuiContext, Request, Response) - Method in class net.sf.basedb.plugins.PackedFileExporter
configure(GuiContext, Request, Response) - Method in class net.sf.basedb.plugins.PlateFlatFileImporter: Store configuration settings for Request.COMMAND_CONFIGURE_PLUGIN and Request.COMMAND_CONFIGURE_JOB.
configure(GuiContext, Request, Response) - Method in class net.sf.basedb.plugins.PlateMappingExporter: Store configuration settings for Request.COMMAND_CONFIGURE_PLUGIN and Request.COMMAND_CONFIGURE_JOB.
configure(GuiContext, Request, Response) - Method in class net.sf.basedb.plugins.PlateMappingImporter: Store configuration settings for Request.COMMAND_CONFIGURE_PLUGIN and Request.COMMAND_CONFIGURE_JOB.
configure(GuiContext, Request, Response) - Method in class net.sf.basedb.plugins.PluginConfigurationExporter: Store configuration settings for Request.COMMAND_CONFIGURE_JOB.
configure(GuiContext, Request, Response) - Method in class net.sf.basedb.plugins.PluginConfigurationImporter
configure(GuiContext, Request, Response) - Method in class net.sf.basedb.plugins.PrintMapFlatFileImporter: Store configuration settings for Request.COMMAND_CONFIGURE_PLUGIN and Request.COMMAND_CONFIGURE_JOB.
configure(GuiContext, Request, Response) - Method in class net.sf.basedb.plugins.RawDataFlatFileImporter: Store configuration settings for Request.COMMAND_CONFIGURE_PLUGIN, RawDataFlatFileImporter.COMMAND_CONFIGURE_PARSER and Request.COMMAND_CONFIGURE_JOB.
configure(GuiContext, Request, Response) - Method in class net.sf.basedb.plugins.ReporterFlatFileImporter: Store configuration settings for Request.COMMAND_CONFIGURE_PLUGIN and Request.COMMAND_CONFIGURE_JOB.
configure(GuiContext, Request, Response) - Method in class net.sf.basedb.plugins.ReporterMapFlatFileImporter: Store configuration settings for Request.COMMAND_CONFIGURE_PLUGIN and Request.COMMAND_CONFIGURE_JOB.
configure(GuiContext, Request, Response) - Method in class net.sf.basedb.util.zip.AbstractFileUnpacker
CONFIGURE_IMPORT - Static variable in class net.sf.basedb.plugins.AnnotationFlatFileImporter
CONFIGURE_MAPPING - Static variable in class net.sf.basedb.plugins.AnnotationFlatFileImporter
CONFIGURE_OPTIONS - Static variable in class net.sf.basedb.plugins.batchimport.AbstractItemImporter
CONFIGURE_OPTIONS - Static variable in class net.sf.basedb.plugins.batchimport.AnyToAnyImporter
ConfigureByExample - Interface in net.sf.basedb.util.parser: This is a tagging interface for all plugins that use the FlatFileParser and wants easier configuration of the regular expressions used to parse the file.
configureExecutor - Variable in class net.sf.basedb.plugins.executor.BaseFileExporterSupport
configureExecutor - Variable in class net.sf.basedb.plugins.executor.BaseFileImporterSupport
configureExecutor - Variable in class net.sf.basedb.plugins.executor.BfsExporterSupport
configureExecutor - Variable in class net.sf.basedb.plugins.executor.BfsImporterSupport
configureExportImportPluginParameters - Variable in class net.sf.basedb.plugins.executor.ExternalProgramExecutor
configureExternalParameters - Variable in class net.sf.basedb.plugins.executor.ExternalProgramExecutor
configureImport - Variable in class net.sf.basedb.plugins.AnnotationFlatFileImporter
configureJob - Variable in class net.sf.basedb.clients.web.plugins.SimpleExport
configureJob - Variable in class net.sf.basedb.plugins.Base1PluginExecuter: Holds info about a job configuration request.
configureJob - Variable in class net.sf.basedb.plugins.BaseFileExporterPlugin
configureJob - Variable in class net.sf.basedb.plugins.BfsExporterPlugin
configureJob - Variable in class net.sf.basedb.plugins.CdfFileReporterImporter
configureJob - Variable in class net.sf.basedb.plugins.executor.BaseFileImporterSupport
configureJob - Variable in class net.sf.basedb.plugins.executor.BfsImporterSupport
configureJob - Variable in class net.sf.basedb.plugins.executor.ExternalProgramExecutor
configureJob - Variable in class net.sf.basedb.plugins.executor.FileOnlyImporterSupport
configureJob - Variable in class net.sf.basedb.plugins.FormulaFilter
configureJob - Variable in class net.sf.basedb.plugins.GalExporter
configureJob - Variable in class net.sf.basedb.plugins.gtf.GtfReporterMapImporter
configureJob - Variable in class net.sf.basedb.plugins.HelpExporter
configureJob - Variable in class net.sf.basedb.plugins.HelpImporter
configureJob - Variable in class net.sf.basedb.plugins.IlluminaRawDataImporter
configureJob - Variable in class net.sf.basedb.plugins.IntensityCalculatorPlugin
configureJob - Variable in class net.sf.basedb.plugins.JepExtraValueCalculator
configureJob - Variable in class net.sf.basedb.plugins.JepIntensityTransformer
configureJob - Variable in class net.sf.basedb.plugins.LowessNormalization
configureJob - Variable in class net.sf.basedb.plugins.ManualDerivedBioAssayCreator
configureJob - Variable in class net.sf.basedb.plugins.ManualTransformCreator
configureJob - Variable in class net.sf.basedb.plugins.MedianRatioNormalization
configureJob - Variable in class net.sf.basedb.plugins.PackedFileExporter
configureJob - Variable in class net.sf.basedb.plugins.PlateFlatFileImporter
configureJob - Variable in class net.sf.basedb.plugins.PlateMappingExporter
configureJob - Variable in class net.sf.basedb.plugins.PlateMappingImporter
configureJob - Variable in class net.sf.basedb.plugins.PluginConfigurationExporter
configureJob - Variable in class net.sf.basedb.plugins.PluginConfigurationImporter
configureJob - Variable in class net.sf.basedb.plugins.PrintMapFlatFileImporter
configureJob - Variable in class net.sf.basedb.plugins.RawDataFlatFileImporter
configureJob - Variable in class net.sf.basedb.plugins.ReporterFlatFileImporter
configureJob - Variable in class net.sf.basedb.plugins.ReporterMapFlatFileImporter
configureJob - Variable in class net.sf.basedb.util.zip.AbstractFileUnpacker
configureManual - Variable in class net.sf.basedb.plugins.Base1PluginExecuter: Holds information about a manual plugin configuration request.
configureMapping - Variable in class net.sf.basedb.plugins.AnnotationFlatFileImporter
configureOptions - Variable in class net.sf.basedb.plugins.batchimport.AbstractItemImporter
configureOptions - Variable in class net.sf.basedb.plugins.batchimport.AnyToAnyImporter
configureParser - Variable in class net.sf.basedb.plugins.AnnotationFlatFileImporter
configureParser - Variable in class net.sf.basedb.plugins.batchimport.AbstractItemImporter
configureParser - Variable in class net.sf.basedb.plugins.batchimport.AnyToAnyImporter
configureParser - Variable in class net.sf.basedb.plugins.RawDataFlatFileImporter
configurePlugin - Variable in class net.sf.basedb.plugins.Base1PluginExecuter: Holds information about a plugin configuration request.
configurePlugin - Variable in class net.sf.basedb.plugins.executor.ExternalProgramExecutor
configurePlugin - Variable in class net.sf.basedb.plugins.gtf.GtfReporterMapImporter
configurePlugin - Variable in class net.sf.basedb.plugins.ManualDerivedBioAssayCreator
configurePlugin - Variable in class net.sf.basedb.plugins.ManualTransformCreator
configurePlugin - Variable in class net.sf.basedb.plugins.PackedFileExporter
configurePlugin - Variable in class net.sf.basedb.plugins.PlateFlatFileImporter
configurePlugin - Variable in class net.sf.basedb.plugins.ReporterFlatFileImporter
configurePlugin - Variable in class net.sf.basedb.plugins.ReporterMapFlatFileImporter
configureQuery(DbControl, EntityQuery, boolean) - Method in class net.sf.basedb.core.ItemContext
configureQuery(DbControl, EntityQuery, ClientContext, boolean) - Method in class net.sf.basedb.core.ItemContext: Use the settings in this context to configure a query.
configureQuery(DbControl, SqlQuery, List<String>) - Method in class net.sf.basedb.core.ItemContext: Use the settings in this context to configure a dynamic query.
configureQuery(SqlQuery) - Method in interface net.sf.basedb.util.DynamicFilter: Configure the query before it is used.
configureQuery(SqlQuery) - Method in class net.sf.basedb.util.IncludeExcludeFilter: We need the position which is in column 2 (already selected).
configureRawDataType - Variable in class net.sf.basedb.plugins.RawDataFlatFileImporter
configureSelection - Variable in class net.sf.basedb.plugins.PluginConfigurationImporter
connect() - Method in class net.sf.basedb.util.jobagent.JobAgentConnection: Create a socket connection to the job agent.
connection() - Method in class net.sf.basedb.core.hibernate.StatelessSessionWrapper: Deprecated.
ConnectionClosedException - Exception in net.sf.basedb.core: This exception is thrown when trying to use a DbControl object that has been closed.
ConnectionClosedException() - Constructor for exception net.sf.basedb.core.ConnectionClosedException: Creates a new ConnectionClosedException.
ConnectionManager - Interface in net.sf.basedb.util.uri: A connection manager is used to access the contents and metadata about the resource pointed to by a given URI.
connectionManagerFactory - Variable in class net.sf.basedb.core.data.FileServerData
ConnectionManagerFactory - Interface in net.sf.basedb.util.uri: A connection manager factory is responsible for creating connection managers for some subset of URI:s that is supported.
ConnectionManagerUtil - Class in net.sf.basedb.util.uri: Collects utility methods related to connection managers.
ConnectionManagerUtil() - Constructor for class net.sf.basedb.util.uri.ConnectionManagerUtil
ConnectionParameters - Class in net.sf.basedb.util.uri: Connection parameters, such as username/password, that may be needed to connect to a server.
ConnectionParameters() - Constructor for class net.sf.basedb.util.uri.ConnectionParameters: Create a new empty parameters object.
connectTimeout - Variable in class net.sf.basedb.clients.jobagent.slotmanager.RemoteSlotManager
ConsoleProgressReporter - Class in net.sf.basedb.util: An implementation of the ProgressReporter interface that writes all messages to the standard console.
ConsoleProgressReporter() - Constructor for class net.sf.basedb.util.ConsoleProgressReporter
ConsoleProgressReporter(boolean) - Constructor for class net.sf.basedb.util.ConsoleProgressReporter
constant - Variable in class net.sf.basedb.util.parser.ConstantMapper
ConstantMapper - Class in net.sf.basedb.util.parser: A constant string mapper.
ConstantMapper(Float) - Constructor for class net.sf.basedb.util.parser.ConstantMapper
ConstantMapper(Integer) - Constructor for class net.sf.basedb.util.parser.ConstantMapper
ConstantMapper(String) - Constructor for class net.sf.basedb.util.parser.ConstantMapper: Create a constant mapper.
ConstantMapper(String, NumberFormat, boolean) - Constructor for class net.sf.basedb.util.parser.ConstantMapper: Create a constant mapper using a specific number formatter as it's parser.
ConstantMapper(String, NumberFormat, Formatter<Date>, boolean) - Constructor for class net.sf.basedb.util.parser.ConstantMapper: Create a constant mapper using a specific number formatter as it's parser.
ConstantMapper(Date, Formatter<Date>) - Constructor for class net.sf.basedb.util.parser.ConstantMapper
constructor - Variable in enum 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 - 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 - 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(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 net.sf.basedb.core.Type: Convert a number to the appropriate class.
convertString(Class, String) - Static method in class net.sf.basedb.util.extensions.debug.StringConverter
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 - 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 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 - 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 - net.sf.basedb.core.log.ChangeType
CREATE - net.sf.basedb.core.Permission: This permission allows a user create new items.
CREATE - net.sf.basedb.core.Transactional.Action: The item is a new item and is beeing saved to the database for the first time.
CREATE_BIOMATERIAL - Static variable in class net.sf.basedb.core.BioPlateEventType: The system ID for "Create" event type.
createAgent(Properties) - Method in class net.sf.basedb.clients.jobagent.AgentController
createAllCopy(String) - Static method in class net.sf.basedb.core.ReporterCloneTemplate
createAnnotationType(String, String, Type, int, Object[], Item[], Map<String, String>, boolean, boolean, UserData, ItemKeyData) - Static method in class net.sf.basedb.core.Install: Create an AnnotationType.
createBean(Class<? extends Action>) - Method in class net.sf.basedb.util.extensions.debug.BeanActionFactory: Create the bean instance.
createBioPlateEventType(String, String, String) - Static method in class net.sf.basedb.core.Install: Create a BioPlateEventType.
createBioPlateType(String, String, Item, ItemSubtypeData, BioWell.LockMode) - Static method in class net.sf.basedb.core.Install: Create a BioPlateType.
createBlockHeaders(List<String>, ArrayDesign, Integer, List<ArrayDesignBlock>) - Method in class net.sf.basedb.plugins.GalExporter: Create header entries for each block in the array design.
createCache() - Static method in class net.sf.basedb.util.AnnotationUtil: Create a new cache object that can be used with AnnotationUtil.getAllAnnotatableParentItems(DbControl, Annotatable, Filter, Cache)
createChildBioAssays(DbControl, BioAssaySet, BaseFileInfo, boolean) - Method in class net.sf.basedb.util.importer.spotdata.BaseFileImporter: Helper method for creating new child bioassays using the information found in the BaseFileInfo object.
createChildBioAssaySet(DbControl, BaseFileInfo, Transformation, boolean) - Method in class net.sf.basedb.util.importer.spotdata.BaseFileImporter: Helper method for creating a child bioassay set using the information in the BaseFileInfo object.
createChildNodes(DbControl, OverviewContext, Node) - Method in interface net.sf.basedb.util.overview.extensions.ChildNodeLoaderAction: Create child nodes for the given parent node.
createChildPositionReporterMapping(BioAssaySet, BaseFileInfo, ProgressReporter) - Method in class net.sf.basedb.util.importer.spotdata.BaseFileImporter: Helper method for creating position/reporter mappings for the child bioassay set (which must be in a new datacube).
createChildRawDataMapping(BioAssaySet, BioAssaySet, BaseFileInfo, ProgressReporter) - Method in class net.sf.basedb.util.importer.spotdata.BaseFileImporter: Helper method for creating a rawdata mapping for the child bioassay set.
createClient(UserData, String, String, String, ItemKeyData) - Static method in class net.sf.basedb.core.Install: Create a Client.
createCloseableHttpClient(URI, ConnectionParameters) - Method in class net.sf.basedb.util.uri.http.HttpConnectionManager: Get a HttpClient object that has been configured to access the given URI.
createColumnMappers(FlatFileParser, boolean) - Method in class net.sf.basedb.plugins.batchimport.AbstractItemImporter: Create mappers that can be used to extract data values from the file that is currently being parsed by the ffp FlatFileParser.
createColumnMappers(FlatFileParser, boolean) - Method in class net.sf.basedb.plugins.batchimport.AnnotationTypeImporter
createColumnMappers(FlatFileParser, boolean) - Method in class net.sf.basedb.plugins.batchimport.ArrayBatchImporter
createColumnMappers(FlatFileParser, boolean) - Method in class net.sf.basedb.plugins.batchimport.ArrayDesignImporter
createColumnMappers(FlatFileParser, boolean) - Method in class net.sf.basedb.plugins.batchimport.ArraySlideImporter
createColumnMappers(FlatFileParser, boolean) - Method in class net.sf.basedb.plugins.batchimport.BioPlateImporter
createColumnMappers(FlatFileParser, boolean) - Method in class net.sf.basedb.plugins.batchimport.BioSourceImporter
createColumnMappers(FlatFileParser, boolean) - Method in class net.sf.basedb.plugins.batchimport.DerivedBioAssayImporter
createColumnMappers(FlatFileParser, boolean) - Method in class net.sf.basedb.plugins.batchimport.ExtractImporter
createColumnMappers(FlatFileParser, boolean) - Method in class net.sf.basedb.plugins.batchimport.FileImporter
createColumnMappers(FlatFileParser, boolean) - Method in class net.sf.basedb.plugins.batchimport.KitImporter
createColumnMappers(FlatFileParser, boolean) - Method in class net.sf.basedb.plugins.batchimport.PhysicalBioAssayImporter
createColumnMappers(FlatFileParser, boolean) - Method in class net.sf.basedb.plugins.batchimport.RawBioAssayImporter
createColumnMappers(FlatFileParser, boolean) - Method in class net.sf.basedb.plugins.batchimport.SampleImporter
createColumnMappers(FlatFileParser, boolean) - Method in class net.sf.basedb.plugins.batchimport.TagImporter
createConnectionManager(URI, ConnectionParameters) - Method in interface net.sf.basedb.util.uri.ConnectionManagerFactory: Create a new handler for accessing the resource at the given URI.
createConnectionManager(URI, ConnectionParameters) - Static method in class net.sf.basedb.util.uri.ConnectionManagerUtil: Utility method for creating a connection manager.
createConnectionManager(URI, ConnectionParameters) - Method in class net.sf.basedb.util.uri.http.HttpConnectionManagerFactory
createConnectionManager(File, ConnectionParameters) - Static method in class net.sf.basedb.util.uri.ConnectionManagerUtil: Utility method for creating a connection manager for a file item.
createContext(DbControl, PageContext) - Static method in class net.sf.basedb.clients.web.extensions.ExtensionsControl: Create a new JspContext object with an active DbControl.
createContext(DbControl, PageContext, GuiContext, Object) - Static method in class net.sf.basedb.clients.web.extensions.ExtensionsControl: 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.
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
createInstance(DbControl, PluginDefinition, String, boolean) - Method in class net.sf.basedb.plugins.executor.ExternalProgramExecutor: Create and initialize a plug-in instance for the given plug-in definition.
createItem(DbControl, FlatFileParser.Data) - Method in class net.sf.basedb.plugins.batchimport.AbstractItemImporter: Create a new item and populate it with data from the current line.
createItem(DbControl, FlatFileParser.Data) - Method in class net.sf.basedb.plugins.batchimport.AnnotationTypeImporter
createItem(DbControl, FlatFileParser.Data) - Method in class net.sf.basedb.plugins.batchimport.ArrayBatchImporter
createItem(DbControl, FlatFileParser.Data) - Method in class net.sf.basedb.plugins.batchimport.ArrayDesignImporter
createItem(DbControl, FlatFileParser.Data) - Method in class net.sf.basedb.plugins.batchimport.ArraySlideImporter
createItem(DbControl, FlatFileParser.Data) - Method in class net.sf.basedb.plugins.batchimport.BioPlateImporter
createItem(DbControl, FlatFileParser.Data) - Method in class net.sf.basedb.plugins.batchimport.BioSourceImporter
createItem(DbControl, FlatFileParser.Data) - Method in class net.sf.basedb.plugins.batchimport.DerivedBioAssayImporter
createItem(DbControl, FlatFileParser.Data) - Method in class net.sf.basedb.plugins.batchimport.ExtractImporter
createItem(DbControl, FlatFileParser.Data) - Method in class net.sf.basedb.plugins.batchimport.FileImporter
createItem(DbControl, FlatFileParser.Data) - Method in class net.sf.basedb.plugins.batchimport.KitImporter
createItem(DbControl, FlatFileParser.Data) - Method in class net.sf.basedb.plugins.batchimport.PhysicalBioAssayImporter
createItem(DbControl, FlatFileParser.Data) - Method in class net.sf.basedb.plugins.batchimport.RawBioAssayImporter
createItem(DbControl, FlatFileParser.Data) - Method in class net.sf.basedb.plugins.batchimport.SampleImporter
createItem(DbControl, FlatFileParser.Data) - Method in class net.sf.basedb.plugins.batchimport.TagImporter
createItemKey(String, Map<UserData, Integer>, Map<GroupData, Integer>) - Static method in class net.sf.basedb.core.Install: Create an ItemKey.
createItemNode(NodeFactory<? super S>, S, Object, boolean, Node, ChildNodeDirection) - Method in class net.sf.basedb.util.overview.loader.BasicItemNodeLoader: Create a new item node using the supplied node factory.
createItemQuery() - Method in class net.sf.basedb.plugins.batchimport.AbstractItemImporter: Create a new query that returns items of the importable type.
createItemQuery() - Method in class net.sf.basedb.plugins.batchimport.AnnotationTypeImporter: Calls AnnotationType.getQuery(Item).
createItemQuery() - Method in class net.sf.basedb.plugins.batchimport.ArrayBatchImporter: Calls ArrayBatch.getQuery().
createItemQuery() - Method in class net.sf.basedb.plugins.batchimport.ArrayDesignImporter: Calls PhysicalBioAssay.getQuery().
createItemQuery() - Method in class net.sf.basedb.plugins.batchimport.ArraySlideImporter: Calls ArraySlide.getQuery().
createItemQuery() - Method in class net.sf.basedb.plugins.batchimport.BioPlateImporter: Calls BioPlate.getQuery().
createItemQuery() - Method in class net.sf.basedb.plugins.batchimport.BioSourceImporter: Calls BioSource.getQuery().
createItemQuery() - Method in class net.sf.basedb.plugins.batchimport.DerivedBioAssayImporter: Calls DerivedBioAssay.getQuery().
createItemQuery() - Method in class net.sf.basedb.plugins.batchimport.ExtractImporter: Calls Extract.getQuery().
createItemQuery() - Method in class net.sf.basedb.plugins.batchimport.FileImporter: Calls File.getQuery().
createItemQuery() - Method in class net.sf.basedb.plugins.batchimport.KitImporter: Calls Kit.getQuery().
createItemQuery() - Method in class net.sf.basedb.plugins.batchimport.PhysicalBioAssayImporter: Calls PhysicalBioAssay.getQuery().
createItemQuery() - Method in class net.sf.basedb.plugins.batchimport.RawBioAssayImporter: Calls RawBioAssay.getQuery().
createItemQuery() - Method in class net.sf.basedb.plugins.batchimport.SampleImporter: Calls Sample.getQuery().
createItemQuery() - Method in class net.sf.basedb.plugins.batchimport.TagImporter: Calls Tag.getQuery().
createItemQuery(ItemList) - Method in class net.sf.basedb.plugins.batchimport.AbstractItemImporter: Create a new query that returns items that are members of the given list.
createItemSpecificFilter(String, Item, String, Element) - Method in class net.sf.basedb.core.HibernateUtil.FilterConfigurator: Item-specific filters are stored internally and registered later by HibernateUtil.FilterConfigurator.registerDelayedFilters(org.hibernate.boot.Metadata).
createItemSpecificFilterDef(String, Item, Element) - Method in class net.sf.basedb.core.HibernateUtil.FilterConfigurator: Clone the <filter-def> with the given name and insert a new item-specific <filter-def> definition into the document given by the <class> element.
createItemSubtype(Item, String, String, String, ItemSubtypeData...) - Static method in class net.sf.basedb.core.Install: Create an ItemSubtype.
createJepExpression(DbControl, String, DynamicQuery) - Static method in class net.sf.basedb.util.BioAssaySetUtil: Parse a JEP expression and create a restrictions that is suitable to be used in a dynamic query.
createJepExpressions(DbControl, RawDataType, String[]) - Static method in class net.sf.basedb.util.IntensityCalculatorUtil
createJepIntensityCalculator(DbControl, RawDataType, String...) - Static method in class net.sf.basedb.util.IntensityCalculatorUtil: Create an intensity calculator from mathematical expressions in strings.
createJepRestriction(DbControl, String, DynamicQuery) - Static method in class net.sf.basedb.util.BioAssaySetUtil: Parse a JEP expression and create a restrictions that is suitable to be used in a dynamic query.
createJobExecutor() - Method in class net.sf.basedb.clients.jobagent.Agent: Create a job executor and initialise it.
createJobQueueChecker() - Method in class net.sf.basedb.clients.jobagent.Agent: Create a job queue checker. and register it with the BASE core scheduler.
createJSON(JSONObject, DbControl, Annotation, Formatter<Object>, boolean) - Static method in class net.sf.basedb.clients.web.AnnotationUtil
createJsonForAnnotationTypeAndAnnotation(DbControl, AnnotationType, Annotation, Annotation, boolean, Set<AnnotationTypeCategory>) - Static method in class net.sf.basedb.clients.web.AnnotationUtil
createKeyManagers(KeyStore, String, String, String) - Static method in class net.sf.basedb.util.ssl.SSLUtil2
createKeyStore(InputStream, String, String, String) - Static method in class net.sf.basedb.util.ssl.SSLUtil2: Create a key-store from the given input stream
createLockedCopy() - Method in class net.sf.basedb.core.ReporterCloneTemplate: Create a deep clone of this template.
createLogFile(String) - Method in class net.sf.basedb.core.plugin.AbstractPlugin: Create a log file in the BASE file system for logging detailed information from a plug-in.
createLoggableString(LogControl, Item, int) - Method in class net.sf.basedb.core.log.db.AnyToAnyLogger
createLogger() - Method in class net.sf.basedb.util.extensions.logging.ExtensionsLog: Create a logger that adds messages to this log.
createLogger(String) - Static method in class net.sf.basedb.util.extensions.logging.ExtensionsLog: Create a logger that can add entries to the log for the given extension.
createLoginInfo(Session, UserData, String, boolean, AuthenticationMethod, int) - Method in class net.sf.basedb.core.SessionControl: Create a LoginInfo object and load all information that it needs.
createMappers(RawDataType, FlatFileParser) - Method in class net.sf.basedb.plugins.IlluminaRawDataImporter.BatchAndMapHolder
createMetadata(URI, HttpResponse) - Method in class net.sf.basedb.util.uri.http.HttpConnectionManager: Read metadata from the given http response and put the information in a UriMetadata object.
createMimeType(String, String, String, ItemSubtypeData, boolean) - Static method in class net.sf.basedb.core.Install: Create a MimeType.
createMissing - Variable in class net.sf.basedb.plugins.ReporterFlatFileImporter
createMissingNode(Node) - Method in class net.sf.basedb.util.overview.node.NodeFactory: Create a node representing a missing item.
createMode - Variable in class net.sf.basedb.plugins.batchimport.AbstractItemImporter
createMode - Variable in class net.sf.basedb.plugins.batchimport.AnyToAnyImporter
createNamedQuery(String) - Method in class net.sf.basedb.core.hibernate.SessionWrapper
createNamedQuery(String) - Method in class net.sf.basedb.core.hibernate.StatelessSessionWrapper
createNamedQuery(String, Class<R>) - Method in class net.sf.basedb.core.hibernate.StatelessSessionWrapper
createNamedQuery(String, Class<T>) - Method in class net.sf.basedb.core.hibernate.SessionWrapper
createNamedStoredProcedureQuery(String) - Method in class net.sf.basedb.core.hibernate.SessionWrapper
createNativeQuery(String) - Method in class net.sf.basedb.core.hibernate.SessionWrapper
createNativeQuery(String) - Method in class net.sf.basedb.core.hibernate.StatelessSessionWrapper
createNativeQuery(String, Class) - Method in class net.sf.basedb.core.hibernate.SessionWrapper
createNativeQuery(String, Class<R>) - Method in class net.sf.basedb.core.hibernate.StatelessSessionWrapper
createNativeQuery(String, String) - Method in class net.sf.basedb.core.hibernate.SessionWrapper
createNativeQuery(String, String) - Method in class net.sf.basedb.core.hibernate.StatelessSessionWrapper
createNews(String, String) - Static method in class net.sf.basedb.core.Install: Create a News.
createNode(I, Object, Node, ChildNodeDirection) - Method in class net.sf.basedb.util.overview.node.NodeFactory: Create a node representing an existing item.
createNode(I, String, String, Object, Node, ChildNodeDirection) - Method in class net.sf.basedb.util.overview.node.NodeFactory
createNodeLoader(Object) - Method in class net.sf.basedb.util.overview.loader.BasicItemNodeLoaderFactory: Create a new node loader for loading nodes for the specified item type.
createNodeLoader(K) - Method in interface net.sf.basedb.util.overview.loader.NodeLoaderFactory: Create a node loader that knows how to load nodes for items that are specified by the given key.
createNodeValidator(Object) - Method in class net.sf.basedb.util.overview.validator.BasicItemNodeValidatorFactory: Create a new node validator that can validate nodes with items of the specified item type.
createNodeValidator(K) - Method in interface net.sf.basedb.util.overview.validator.NodeValidatorFactory: Create a node validator that knows how to validate nodes for items that are specified by the given key.
createNotFoundItems - Variable in class net.sf.basedb.plugins.batchimport.AbstractItemImporter
createParameterMap() - Method in class net.sf.basedb.core.RequestInformation: Create a hash from parameter name to PluginParameter objects so that the RequestInformation.getParameter(String) method doesn't have to look in the list.
createPermissions - Variable in class net.sf.basedb.core.Job.SignalKeyring
createPlateGeometry(String, String, int, int) - Static method in class net.sf.basedb.core.Install: Create a PlateGeometry.
createPlateMapping(String, String, PlateGeometryData, int, PlateGeometryData, int, String, UserData, ItemKeyData) - Static method in class net.sf.basedb.core.Install: Create a PlateMapping.
createPlatform(String, String, String, boolean, String, int, Install.PlatformFT...) - Static method in class net.sf.basedb.core.Install: Create a Platform.
createPlatformVariant(PlatformData, String, String, String, boolean, String, int, Install.PlatformFT...) - Static method in class net.sf.basedb.core.Install: Create a PlatformVariant.
createPluginConfigurations(String, boolean) - Static method in class net.sf.basedb.core.Install: Create PluginConfigurations from a XML file.
createPluginDefinition(PluginInfo, ItemKey) - Static method in class net.sf.basedb.core.Install: Create a PluginDefinition.
createPluginDefinitions(String, ItemKey, boolean) - Static method in class net.sf.basedb.core.Install: Read plug-in definitions from the given file.
createPluginType(String, String, String, String) - Static method in class net.sf.basedb.core.Install: Create a PluginType.
createPooledReverseNode(Extract, DbControl, OverviewContext, Node) - Method in class net.sf.basedb.util.overview.loader.ExtractLoader: Create reverse-loading extract nodes of a pooled extract.
createPooledReverseNode(Sample, DbControl, OverviewContext, Node) - Method in class net.sf.basedb.util.overview.loader.SampleLoader: Create reverse-loading samples nodes of a sample with other sample(s) as parent items.
createPropertyElement(ExtendedProperty, Namespace) - Static method in class net.sf.basedb.core.HibernateUtil: Creates a <property> tag from an extended property definition.
createPropertyNode(BioPlateEvent, DbControl, OverviewContext, Node) - Method in class net.sf.basedb.util.overview.loader.BioPlateLoader: Create a property node(s) when the parent item is a bioplate event.
createPropertyNode(DbControl, OverviewContext, Node) - Method in class net.sf.basedb.util.overview.loader.AbstractNodeLoader
createPropertyNode(DbControl, OverviewContext, Node) - Method in class net.sf.basedb.util.overview.loader.AnnotationLoader
createPropertyNode(DbControl, OverviewContext, Node) - Method in class net.sf.basedb.util.overview.loader.AnyToAnyLoader
createPropertyNode(DbControl, OverviewContext, Node) - Method in class net.sf.basedb.util.overview.loader.ArrayDesignLoader: Create an array design property node from a raw bioassay or root raw bioassay node.
createPropertyNode(DbControl, OverviewContext, Node) - Method in class net.sf.basedb.util.overview.loader.AutoChildNodeLoader: Call the same method on the 'parent' node loader.
createPropertyNode(DbControl, OverviewContext, Node) - Method in class net.sf.basedb.util.overview.loader.BioPlateLoader: Create a bioplate property node from a biomaterial that is located on a plate or property nodes for each bioplate that is part of a bioplate event.
createPropertyNode(DbControl, OverviewContext, Node) - Method in class net.sf.basedb.util.overview.loader.DataFileLoader
createPropertyNode(DbControl, OverviewContext, Node) - Method in class net.sf.basedb.util.overview.loader.ExperimentalFactorLoader
createPropertyNode(DbControl, OverviewContext, Node) - Method in class net.sf.basedb.util.overview.loader.ExtensionChildNodeLoader: Call the same method on the 'parent' node loader.
createPropertyNode(DbControl, OverviewContext, Node) - Method in class net.sf.basedb.util.overview.loader.ExtractLoader: A property node is created when moving in the reverse direction so that we can load child extracts+physical bioassays with the ItemSubtype.getPushAnnotations() flag set.
createPropertyNode(DbControl, OverviewContext, Node) - Method in class net.sf.basedb.util.overview.loader.FileLoader
createPropertyNode(DbControl, OverviewContext, Node) - Method in class net.sf.basedb.util.overview.loader.HardwareLoader
createPropertyNode(DbControl, OverviewContext, Node) - Method in class net.sf.basedb.util.overview.loader.KitLoader
createPropertyNode(DbControl, OverviewContext, Node) - Method in interface net.sf.basedb.util.overview.loader.NodeLoader: Create a property node for the given parent node.
createPropertyNode(DbControl, OverviewContext, Node) - Method in class net.sf.basedb.util.overview.loader.NullNodeLoader
createPropertyNode(DbControl, OverviewContext, Node) - Method in class net.sf.basedb.util.overview.loader.PhysicalBioAssayLoader: A property node is created when moving in the reverse direction so that we can load child physical bioassays with the ItemSubtype.getPushAnnotations() flag set.
createPropertyNode(DbControl, OverviewContext, Node) - Method in class net.sf.basedb.util.overview.loader.PlatformLoader
createPropertyNode(DbControl, OverviewContext, Node) - Method in class net.sf.basedb.util.overview.loader.ProtocolLoader
createPropertyNode(DbControl, OverviewContext, Node) - Method in class net.sf.basedb.util.overview.loader.ProtocolParameterLoader
createPropertyNode(DbControl, OverviewContext, Node) - Method in class net.sf.basedb.util.overview.loader.SampleLoader: A property node is created when moving in the reverse direction so that we can load child samples+extracts with the ItemSubtype.getPushAnnotations() flag set.
createPropertyNode(DbControl, OverviewContext, Node) - Method in class net.sf.basedb.util.overview.loader.SoftwareLoader
createPropertyNode(DbControl, OverviewContext, Node) - Method in class net.sf.basedb.util.overview.loader.TagLoader
createPropertyNode(MeasuredBioMaterial, DbControl, OverviewContext, Node) - Method in class net.sf.basedb.util.overview.loader.BioPlateLoader: Create a property node when the parent item is a biomaterial.
createQuantity(String, String, String, String) - Static method in class net.sf.basedb.core.Install: Create a Quantity.
createQuery(String) - Method in class net.sf.basedb.core.hibernate.SessionWrapper: If the same query has been executed before, return the cached instance, otherwise create a new query from the parent session and cache it.
createQuery(String) - Method in class net.sf.basedb.core.hibernate.StatelessSessionWrapper: If the same query has been executed before, return the cached instance, otherwise create a new query from the parent session and cache it.
createQuery(String, Class<R>) - Method in class net.sf.basedb.core.hibernate.StatelessSessionWrapper
createQuery(String, Class<T>) - Method in class net.sf.basedb.core.hibernate.SessionWrapper
createQuery(CriteriaDelete) - Method in class net.sf.basedb.core.hibernate.SessionWrapper
createQuery(CriteriaDelete) - Method in class net.sf.basedb.core.hibernate.StatelessSessionWrapper
createQuery(CriteriaQuery<T>) - Method in class net.sf.basedb.core.hibernate.SessionWrapper
createQuery(CriteriaQuery<T>) - Method in class net.sf.basedb.core.hibernate.StatelessSessionWrapper
createQuery(CriteriaUpdate) - Method in class net.sf.basedb.core.hibernate.SessionWrapper
createQuery(CriteriaUpdate) - Method in class net.sf.basedb.core.hibernate.StatelessSessionWrapper
createQuery(Item, ItemList) - Method in class net.sf.basedb.plugins.AnnotationFlatFileImporter: Create a query that return items of the specified type.
createQuery(Item, ItemList) - Method in class net.sf.basedb.plugins.batchimport.AnyToAnyImporter: Create a query that return items of the specified type.
createQuery(Session, String) - Static method in class net.sf.basedb.core.HibernateUtil: Create a Hibernate query.
createQuery(Session, String, Class<R>) - Static method in class net.sf.basedb.core.HibernateUtil: Create a Hibernate query with a known return type.
createQuery(StatelessSession, String, Class<R>) - Static method in class net.sf.basedb.core.HibernateUtil: Create a Hibernate query using a stateless session and a known return type.
createQuota(String, String, String, long) - Static method in class net.sf.basedb.core.Install: Create a Quota.
createQuotaType(String, String, String) - Static method in class net.sf.basedb.core.Install: Create a QuotaType.
createReverseNode(DbControl, OverviewContext, Node) - Method in class net.sf.basedb.util.overview.loader.AbstractNodeLoader
createReverseNode(DbControl, OverviewContext, Node) - Method in class net.sf.basedb.util.overview.loader.ArrayBatchLoader: Create a reverse-loading array batch node from an array slide node.
createReverseNode(DbControl, OverviewContext, Node) - Method in class net.sf.basedb.util.overview.loader.ArrayDesignLoader: Create a reverse-loading array design node from an array batch node.
createReverseNode(DbControl, OverviewContext, Node) - Method in class net.sf.basedb.util.overview.loader.ArraySlideLoader: Create a reverse-loading array slide node from the hyrbidization node.
createReverseNode(DbControl, OverviewContext, Node) - Method in class net.sf.basedb.util.overview.loader.AutoChildNodeLoader: Call the same method on the 'parent' node loader.
createReverseNode(DbControl, OverviewContext, Node) - Method in class net.sf.basedb.util.overview.loader.BioSourceLoader: Create a reverse-loading biosource node from a sample node.
createReverseNode(DbControl, OverviewContext, Node) - Method in class net.sf.basedb.util.overview.loader.DerivedBioAssayLoader: Create a reverse-loading bioassay node from a cild bioassay node or a raw bioassay node.
createReverseNode(DbControl, OverviewContext, Node) - Method in class net.sf.basedb.util.overview.loader.ExtensionChildNodeLoader: Call the same method on the 'parent' node loader.
createReverseNode(DbControl, OverviewContext, Node) - Method in class net.sf.basedb.util.overview.loader.ExtractLoader: The parent node can be one of: Physical bioassay: Load the source extract(s) and return a folder-type node Extract: Load the parent extracts and return either a folder-type or item-type node depending on the number of parents Raw bioassay: Load the parent extract and return an item-type node Derived bioassay: Load the parent extract and return an item-type node
createReverseNode(DbControl, OverviewContext, Node) - Method in interface net.sf.basedb.util.overview.loader.NodeLoader: Create a reverse-loading (from child to parent) node for the given child node.
createReverseNode(DbControl, OverviewContext, Node) - Method in class net.sf.basedb.util.overview.loader.NullNodeLoader
createReverseNode(DbControl, OverviewContext, Node) - Method in class net.sf.basedb.util.overview.loader.PhysicalBioAssayLoader: Create a reverse-loading bioassay node from the derived bioassay node.
createReverseNode(DbControl, OverviewContext, Node) - Method in class net.sf.basedb.util.overview.loader.RawBioAssayLoader: Create a reverse-loading raw bioassay nodes from a given experiment node.
createReverseNode(DbControl, OverviewContext, Node) - Method in class net.sf.basedb.util.overview.loader.RootRawBioAssayLoader: Create a reverse-loading raw bioassay nodes from a given experiment node.
createReverseNode(DbControl, OverviewContext, Node) - Method in class net.sf.basedb.util.overview.loader.SampleLoader: Create reverse-loading sample nodes from an extract node or from a pooled sample.
createReverseNode(DerivedBioAssay, DbControl, OverviewContext, Node) - Method in class net.sf.basedb.util.overview.loader.DerivedBioAssayLoader: Create a reverse-loading bioassay node for the bioassay that is the parent to the given child bioassay.
createReverseNode(DerivedBioAssay, DbControl, OverviewContext, Node) - Method in class net.sf.basedb.util.overview.loader.ExtractLoader
createReverseNode(PhysicalBioAssay, DbControl, OverviewContext, Node) - Method in class net.sf.basedb.util.overview.loader.ExtractLoader: Create reverse-loading extract nodes from a physical bioassay.
createReverseNode(RawBioAssay, DbControl, OverviewContext, Node) - Method in class net.sf.basedb.util.overview.loader.DerivedBioAssayLoader: Create a reverse-loading bioassay node for the bioassay that is the parent to the given raw bioassay.
createReverseNode(RawBioAssay, DbControl, OverviewContext, Node) - Method in class net.sf.basedb.util.overview.loader.ExtractLoader
createRole(String, String, boolean, String) - Static method in class net.sf.basedb.core.Install: Create a Role.
createRoleKey(Item, String, String, Map<RoleData, Integer>) - Static method in class net.sf.basedb.core.Install: Create a RoleKey.
createRootBioAssaySet(DbControl, Experiment, Collection<RawBioAssay>, Job, Expression[], ProgressReporter) - Static method in class net.sf.basedb.util.IntensityCalculatorUtil: Create a root bioassayset for a given experiment and set of raw bioassays.
createRootBioAssaySet(DbControl, Experiment, Collection<RawBioAssay>, Job, IntensityCalculator, ProgressReporter) - Static method in class net.sf.basedb.util.IntensityCalculatorUtil: Create a root bioassayset for a given experiment and set of raw bioassays.
createRootNode(DbControl, BasicItem) - Method in class net.sf.basedb.util.overview.GenericOverview
createRootNode(DbControl, OverviewContext, I) - Method in class net.sf.basedb.util.overview.loader.AbstractNodeLoader
createRootNode(DbControl, OverviewContext, I) - Method in class net.sf.basedb.util.overview.loader.AutoChildNodeLoader: Call the same method on the 'parent' node loader.
createRootNode(DbControl, OverviewContext, I) - Method in class net.sf.basedb.util.overview.loader.BasicItemNodeLoader
createRootNode(DbControl, OverviewContext, I) - Method in class net.sf.basedb.util.overview.loader.ExtensionChildNodeLoader: Call the same method on the 'parent' node loader.
createRootNode(DbControl, OverviewContext, I) - Method in interface net.sf.basedb.util.overview.loader.NodeLoader: Create a root node for the given item.
createRootNode(DbControl, OverviewContext, I) - Method in class net.sf.basedb.util.overview.loader.NullNodeLoader
createRootNode(DbControl, OverviewContext, DerivedBioAssay) - Method in class net.sf.basedb.util.overview.loader.DerivedBioAssayLoader
createRootNode(DbControl, OverviewContext, RawBioAssay) - Method in class net.sf.basedb.util.overview.loader.RawBioAssayLoader
createSchemaVersion(int) - Static method in class net.sf.basedb.core.Install: Create the schema version.
createSessionFactoryConfiguration(String, String, int, ClassLoader) - Method in class net.sf.basedb.core.ServiceSessionControl: Create an object that can be used for collecting configuration options and other settings that are needed to create session factories for services.
createSimpleEmail() - Static method in class net.sf.basedb.util.EmailUtil: Create a simple text email.
createSingleParentReverseNode(Extract, DbControl, OverviewContext, Node) - Method in class net.sf.basedb.util.overview.loader.ExtractLoader: Create a reverse-loading extract node from an extract.
createSingleParentReverseNode(MeasuredBioMaterial, DbControl, OverviewContext, Node) - Method in class net.sf.basedb.util.overview.loader.SampleLoader: Create a reverse-loading sample node from an extract or sample.
createSlotManager() - Method in class net.sf.basedb.clients.jobagent.Agent: Create a slot manager and initialize it.
createSnapshot(DbControl, int) - Static method in class net.sf.basedb.core.AnnotationSet: Create a new annotation snapshot for the given annotation set.
createSoftware(String, String, String, ItemSubtypeData, UserData, ItemKeyData) - Static method in class net.sf.basedb.core.Install: Create a Software.
createSqlQuery(String) - Method in class net.sf.basedb.core.LogControl: Deprecated.
In 3.12. use LogControl.createSqlQuery(String, Class) instead
createSqlQuery(String, Class<R>) - Method in class net.sf.basedb.core.LogControl: Creates a Hibernate SQL query with a known return type.
createSqlQuery(Session, String) - Static method in class net.sf.basedb.core.HibernateUtil: Create a Hibernate SQL query.
createSqlQuery(Session, String, Class<R>) - Static method in class net.sf.basedb.core.HibernateUtil: Create a Hibernate SQL query with a known return type.
createSqlQuery(StatelessSession, String) - Static method in class net.sf.basedb.core.HibernateUtil: Create a Hibernate SQL query using a stateless session.
createSqlQuery(StatelessSession, String, Class<R>) - Static method in class net.sf.basedb.core.HibernateUtil: Create a Hibernate SQL query with a known return type using a stateless session.
createSQLQuery(String) - Method in class net.sf.basedb.core.hibernate.SessionWrapper: If the same query has been executed before, return the cached instance, otherwise create a new query from the parent session and cache it.
createSQLQuery(String) - Method in class net.sf.basedb.core.hibernate.StatelessSessionWrapper: If the same query has been executed before, return the cached instance, otherwise create a new query from the parent session and cache it.
createStandardHeaders(List<String>, ArrayDesign, List<ArrayDesignBlock>) - Method in class net.sf.basedb.plugins.GalExporter: Create the standard headers that are required by the GAL format or that are useful to have in the GAL file.
createStaticTables(SchemaGenerator.Mode, ProgressReporter) - Static method in class net.sf.basedb.core.HibernateUtil: Create the all tables in the database.
createStoredProcedureCall(String) - Method in class net.sf.basedb.core.hibernate.SessionWrapper
createStoredProcedureCall(String) - Method in class net.sf.basedb.core.hibernate.StatelessSessionWrapper
createStoredProcedureCall(String, Class...) - Method in class net.sf.basedb.core.hibernate.SessionWrapper
createStoredProcedureCall(String, Class...) - Method in class net.sf.basedb.core.hibernate.StatelessSessionWrapper
createStoredProcedureCall(String, String...) - Method in class net.sf.basedb.core.hibernate.SessionWrapper
createStoredProcedureCall(String, String...) - Method in class net.sf.basedb.core.hibernate.StatelessSessionWrapper
createStoredProcedureQuery(String) - Method in class net.sf.basedb.core.hibernate.SessionWrapper
createStoredProcedureQuery(String, Class...) - Method in class net.sf.basedb.core.hibernate.SessionWrapper
createStoredProcedureQuery(String, String...) - Method in class net.sf.basedb.core.hibernate.SessionWrapper
createStyle() - Method in class net.sf.basedb.util.excel.CellStyleCreator: Create a new cell style.
createTables(SchemaGenerator.Mode, ProgressReporter, String, String) - Static method in class net.sf.basedb.core.Install
createTables(VirtualTable...) - Method in class net.sf.basedb.core.VirtualDb: Create the real database tables for this virtual database.
createTag(String, String, ItemSubtypeData, UserData, ItemKeyData) - Static method in class net.sf.basedb.core.Install: Create a Tag.
createTargetTypeQuery(DbControl) - Method in class net.sf.basedb.clients.web.extensions.list.RelatedItemColumn.Specification
createTargetTypeRestriction(DbControl) - Method in class net.sf.basedb.clients.web.extensions.list.RelatedItemColumn.Specification
createTempCollection(CollectionTransformer<?, ?>) - Method in class net.sf.basedb.util.collections.MultiStepCollectionTransformer: Create a temporary collection that is suitable for holding an intermediary result.
createTempDirectory(String, String, File) - Static method in class net.sf.basedb.util.FileUtil: Creates a temporary directory.
createTempIdTable(Set<Integer>) - Method in class net.sf.basedb.core.DbControl: Create a temporary table for holding given list of ID values.
createTemporaryWorkingDirectory() - Method in class net.sf.basedb.plugins.executor.ExternalProgramExecutor: Create a temporary working directory in the local file system.
createTrustManagers(KeyStore, String, String) - Static method in class net.sf.basedb.util.ssl.SSLUtil2
createUnit(QuantityData, String, String, double, double, String, String...) - Static method in class net.sf.basedb.core.Install: Create a Unit.
createUpdateBatcher(Connection, String, int...) - Method in class net.sf.basedb.core.AnnotationBatcher
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 - 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.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
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 - 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 - 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 - 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 - 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 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 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 - 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 - 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 - 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 - 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 - 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 - 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 - net.sf.basedb.core.Type: The parameter is a date value.
DATE - Static variable in class net.sf.basedb.core.hibernate.TypeWrapper
DATE_FORMAT - Static variable in class net.sf.basedb.core.DateUtil
DATE_FORMAT - Static variable in class net.sf.basedb.core.log.EntityDetails
DATE_FORMAT_ERROR - Static variable in class net.sf.basedb.plugins.util.Parameters: The name of the parameter created by Parameters.dateFormatError(String, String, String, String...).
DATE_FORMAT_PARAMETER - Static variable in class net.sf.basedb.plugins.util.Parameters: The name of the parameter that is created by Parameters.dateFormatParameter(String, String, String)
DateCopyPropertyPath(Type) - Constructor for class net.sf.basedb.core.Metadata.DateCopyPropertyPath
dateFormat - Variable in class net.sf.basedb.core.migrate.DateWriter
dateFormat - Variable in class net.sf.basedb.core.migrate.postgres.PostgresResultWriterFactory: PostgreSQL uses 'yyyy-MM-dd' for dates.
dateFormat - Variable in class net.sf.basedb.core.migrate.TimestampWriter
dateFormat - Variable in class net.sf.basedb.util.excel.AutoFormatter
dateFormat - Variable in class net.sf.basedb.util.excel.XlsxToCsvUtil
dateFormat - Variable in class net.sf.basedb.util.formatter.DateFormatter
dateFormat - Variable in class net.sf.basedb.util.parser.ColFunction
dateFormat - Variable in class net.sf.basedb.util.parser.FlatFileParser: The default date formatter to use when creating mappers.
dateFormat - Variable in class net.sf.basedb.util.parser.JepMapper
dateFormatError(String, String, String, String...) - Static method in class net.sf.basedb.plugins.util.Parameters: Create the parameter for handling invalid dates/timestamps.
dateFormatErrorParameter - Static variable in class net.sf.basedb.plugins.AnnotationFlatFileImporter
DateFormatException - Exception in net.sf.basedb.core: This exception is thrown when parsing a string into a date failed.
DateFormatException(String) - Constructor for exception net.sf.basedb.core.DateFormatException: Creates a new DateFormatException.
DateFormatException(String, Throwable) - Constructor for exception net.sf.basedb.core.DateFormatException: Creates a new DateFormatException.
dateFormatParameter(String, String, String) - Static method in class net.sf.basedb.plugins.util.Parameters: Parameter definition that asks for the format used by date values when parsed from strings.
dateFormatter - Variable in class net.sf.basedb.plugins.AnnotationFlatFileImporter
dateFormatter - Variable in class net.sf.basedb.plugins.batchimport.AbstractItemImporter
dateFormatter - Variable in class net.sf.basedb.util.formatter.PropertyFilterFormatter
DateFormatter - Class in net.sf.basedb.util.formatter: Format a date for output in a client application.
DateFormatter(String) - Constructor for class net.sf.basedb.util.formatter.DateFormatter: Create a new date formatter.
DateFormatter(DateFormat) - Constructor for class net.sf.basedb.util.formatter.DateFormatter: Create a new date formatter.
DateParameterType - Class in net.sf.basedb.core: This class represent a parameter type that is a date.
DateParameterType() - Constructor for class net.sf.basedb.core.DateParameterType: Create a new date parameter type, allowing null values.
DateParameterType(Date, boolean) - Constructor for class net.sf.basedb.core.DateParameterType: Create a new date parameter type.
DateParameterType(Date, boolean, int, int, int, List<Date>) - Constructor for class net.sf.basedb.core.DateParameterType: Creates a new DateParameterType
DateParameterValueData - Class in net.sf.basedb.core.data: Date parameter value.
DateParameterValueData() - Constructor for class net.sf.basedb.core.data.DateParameterValueData
DateParameterValueData(Date...) - Constructor for class net.sf.basedb.core.data.DateParameterValueData
dateParser - Variable in class net.sf.basedb.util.parser.ColumnMapper
dateParser - Variable in class net.sf.basedb.util.parser.CompoundMapper
dateParser - Variable in class net.sf.basedb.util.parser.ConstantMapper
DATETIME_FORMAT - Static variable in class net.sf.basedb.core.log.EntityDetails
DateUtil - Class in net.sf.basedb.core: Utility methods that will make it easier to handle date values.
DateUtil() - Constructor for class net.sf.basedb.core.DateUtil
DateValue(Date, String) - Constructor for class net.sf.basedb.util.excel.ExcelValue.DateValue
DateWriter - Class in net.sf.basedb.core.migrate: Generic writer implementation that writes date values from a result set.
DateWriter(ResultSet, int, Writer, char[], FastDateFormat) - Constructor for class net.sf.basedb.core.migrate.DateWriter
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.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.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 - net.sf.basedb.util.extensions.logging.LogLevel
DEBUG - net.sf.basedb.util.extensions.LoggingErrorHandlerFactory.Level
debugEnabled - Static variable in class net.sf.basedb.core.AbstractEntityQuery: So we don't always have to call logParam.debug()
debugEnabled - Static variable in class net.sf.basedb.core.AbstractHqlQuery: So we don't always have to call logParam.debug()
debugEnabled - Static variable in class net.sf.basedb.core.AbstractQuery: So we don't always have to call logSql.debug()
debugEnabled - Static variable in class net.sf.basedb.core.BasicBatcher: So we don't always have to call logParam.debug()
debugEnabled - Static variable in class net.sf.basedb.core.BatchUtil: So we don't always have to call logSql.debug()
DebugOnSaveAction(JspContext) - Constructor for class net.sf.basedb.clients.web.extensions.edit.DebugOnSaveActionFactory.DebugOnSaveAction
DebugOnSaveActionFactory - Class in net.sf.basedb.clients.web.extensions.edit: On-save action factory that create actions that print a log message to System.out for all events.
DebugOnSaveActionFactory() - Constructor for class net.sf.basedb.clients.web.extensions.edit.DebugOnSaveActionFactory
DebugOnSaveActionFactory.DebugOnSaveAction - Class in net.sf.basedb.clients.web.extensions.edit
debugParamEnabled - Static variable in class net.sf.basedb.core.AbstractSqlQuery: So we don't always have to call logParam.debug()
debugSqlEnabled - Static variable in class net.sf.basedb.core.AbstractBatcher: So we don't always have to call logSql.debug()
debugSqlEnabled - Static variable in class net.sf.basedb.core.AbstractSqlQuery: So we don't always have to call logSql.debug()
debugSqlEnabled - Static variable in class net.sf.basedb.core.AnnotationRestriction: So we don't always have to call logSql.debug()
debugSqlEnabled - Static variable in class net.sf.basedb.core.RawDataBatcher: So we don't always have to call logSql.debug()
debugSqlEnabled - Static variable in class net.sf.basedb.core.VirtualDb: So we don't always have to call logSql.debug()
decapitalize(String) - Static method in class net.sf.basedb.core.StringUtil: Decapitalize the string by making sure the first character is lower-case.
decideOnFirst - Variable in class net.sf.basedb.util.formatter.MultiFormatter
DECIMAL_SEPARATOR_PARAMETER - Static variable in class net.sf.basedb.plugins.util.Parameters: The name of the parameter that is created by Parameters.decimalSeparatorParameter(String, String, String)
decimalSeparatorParameter(String, String, String) - Static method in class net.sf.basedb.plugins.util.Parameters: Parameter definition that asks for the decimal separator used by numeric values when parsed from strings.
decode(String) - Method in interface net.sf.basedb.util.encode.EncoderDecoder
decode(String) - Method in class net.sf.basedb.util.encode.IdentityEncoderDecoder
decode(String) - Method in class net.sf.basedb.util.encode.TabCrLfEncoderDecoder
decode(String) - Method in class net.sf.basedb.util.encode.ToSpaceEncoderDecoder
decode_base64(String, int) - Static method in class net.sf.basedb.util.bcrypt.BCrypt: Decode a string encoded using bcrypt's base64 scheme to a byte array.
decodeAll(Collection<String>, EncoderDecoder) - Static method in class net.sf.basedb.util.encode.EncodeUtil: Decode all strings in a collection.
decoder - Variable in class net.sf.basedb.util.bfs.AnnotationParser
decoder - Variable in class net.sf.basedb.util.bfs.DataParser
decoder - Variable in class net.sf.basedb.util.bfs.MetadataParser
decodeValue(String) - Method in class net.sf.basedb.util.bfs.AnnotationParser: Decode an encoded value.
decodeValue(String) - Method in class net.sf.basedb.util.bfs.DataParser: Decode an encoded value.
decodeValue(String) - Method in class net.sf.basedb.util.bfs.MetadataParser: Decode an encoded value.
decompress(ProgressReporter) - Method in class net.sf.basedb.core.File: Decompress the file stored on the disk.
deepCopy(Node) - Method in class net.sf.basedb.util.overview.Node: Create a deep copy of this node and all it's children.
deepCopyInternal(Node) - Method in class net.sf.basedb.util.overview.Node
DEFAULT - Static variable in class net.sf.basedb.clients.web.ModeInfo
DEFAULT - Static variable in class net.sf.basedb.core.Application.StartupOptions: Default startup options that will start BASE for normal operations using the options specified in "base.config".
DEFAULT - Static variable in class net.sf.basedb.core.Quota: The ID for the system default quota, which is assigned to new users unless another quota is specified.
DEFAULT_CHECK_INTERVAL - Static variable in class net.sf.basedb.clients.jobagent.Agent: The default check interval in seconds.
DEFAULT_DATE_FORMAT - Static variable in class net.sf.basedb.clients.web.formatter.FormatterSettings: The default date format for a date formatter = @value
DEFAULT_DATETIME_FORMAT - Static variable in class net.sf.basedb.clients.web.formatter.FormatterSettings: The default datetime format for a datetime formatter = @value
DEFAULT_ERROR - Static variable in class net.sf.basedb.plugins.util.Parameters: The name of the parameter created by Parameters.defaultError(String, String, String, String...).
DEFAULT_FILTER - Static variable in class net.sf.basedb.util.extensions.Registry: Default filter implementation for Registry.useExtensions(ClientContext, ExtensionsFilter, String...)
DEFAULT_JOB_EXECUTOR - Static variable in class net.sf.basedb.clients.jobagent.Agent: The default job executor to use if none has been specified in the configuration file.
DEFAULT_LOGIN - Static variable in class net.sf.basedb.clients.web.extensions.login.FieldInfo: This is the default login field.
DEFAULT_MAX_UNKNOWN_LINES - Static variable in class net.sf.basedb.util.parser.FlatFileParser: The default value for the number of unknown lines in a row that may be encountered by the parseHeaders method before it gives up.
DEFAULT_NAME - Static variable in class net.sf.basedb.core.ItemContext: This is the name of the default context which is automatically saved when a user is logging out.
DEFAULT_NUM_DECIMALS - Static variable in class net.sf.basedb.clients.web.formatter.FormatterSettings: The default number of decimals to display by a number formatter = @value
DEFAULT_PAGE_TITLE - Static variable in class net.sf.basedb.clients.web.taglib.Page: The default page title.
DEFAULT_PASSWORD - Static variable in class net.sf.basedb.clients.web.extensions.login.FieldInfo: This is the default password field.
DEFAULT_PORT - Static variable in class net.sf.basedb.core.JobAgent: The default port (47822) where job agents are listening for connections.
DEFAULT_SLOT_MANAGER - Static variable in class net.sf.basedb.clients.jobagent.Agent: The default slot manager to use if none has been specified in the configuration file.
DEFAULT_TIMEOUT - Static variable in class net.sf.basedb.clients.web.fileupload.FileUpload: The default timeout to use when waiting for the next data packet to arrive.
defaultArrayDesignFunction - Variable in class net.sf.basedb.plugins.batchimport.RawBioAssayImporter
DefaultConfigurationValues - Class in net.sf.basedb.plugins.gtf: Provides a default configuration values for GTF file parsing when none has been provided by the user.
DefaultConfigurationValues(ParameterValues) - Constructor for class net.sf.basedb.plugins.gtf.DefaultConfigurationValues
DefaultDbEngine - Class in net.sf.basedb.core.dbengine: A default DbEngine that is selected if no other can be found.
DefaultDbEngine() - Constructor for class net.sf.basedb.core.dbengine.DefaultDbEngine: Create DefaultDbEngine.
defaultDeleted(int, boolean) - Method in class net.sf.basedb.core.ProjectSpecificAnnotationsManager: A default annotation is being deleted in this transaction.
DefaultEntityLogger - Class in net.sf.basedb.core.log.db: Default logger for all entities that has been tagged with the LoggableData interface.
DefaultEntityLogger(DbLogManagerFactory) - Constructor for class net.sf.basedb.core.log.db.DefaultEntityLogger: Creates a new entity logger.
defaultError(String, String, String, String...) - Static method in class net.sf.basedb.plugins.util.Parameters: Create the default error handling parameter.
defaultErrorHandler - Variable in class net.sf.basedb.util.error.ClassMapErrorHandler
defaultErrorHandlerFactory - Variable in class net.sf.basedb.util.extensions.Registry
defaultErrorParameter - Static variable in class net.sf.basedb.plugins.AbstractFlatFileImporter
defaultErrorParameter - Static variable in class net.sf.basedb.plugins.AnnotationFlatFileImporter
DefaultFilter - Class in net.sf.basedb.util.extensions: A default filter implementation that enables all extensions and extension points and sorts the extensions based on the Extension.getIndex() values.
DefaultFilter() - Constructor for class net.sf.basedb.util.extensions.DefaultFilter: Create a new default filter.
defaultFirst - Variable in class net.sf.basedb.core.snapshot.AnnotationSnapshot.ProjectComparator
defaultFormat - Variable in class net.sf.basedb.clients.web.servlet.ExperimentExplorerPlotServlet
defaultFormat - Variable in class net.sf.basedb.clients.web.servlet.PlotServlet
defaultFormatter - Variable in class net.sf.basedb.util.formatter.MultiFormatter
defaultGuiContexts - Static variable in class net.sf.basedb.core.plugin.AbstractAnalysisPlugin: The default gui contexts where it makes sense to use an analysis plugin.
defaultHandler - Variable in class net.sf.basedb.clients.jobagent.handlers.MultiProtocolRequestHandler
defaultHardwareFunction - Variable in class net.sf.basedb.plugins.batchimport.ArrayBatchImporter
defaultHardwareFunction - Variable in class net.sf.basedb.plugins.batchimport.BioPlateImporter
defaultHardwareFunction - Variable in class net.sf.basedb.plugins.batchimport.DerivedBioAssayImporter
defaultHardwareFunction - Variable in class net.sf.basedb.plugins.batchimport.PhysicalBioAssayImporter
defaultHeight - Variable in class net.sf.basedb.clients.web.servlet.ExperimentExplorerPlotServlet
defaultHeight - Variable in class net.sf.basedb.clients.web.servlet.PlotServlet
defaultIds - Static variable in class net.sf.basedb.clients.web.taglib.Button
defaultImages - Static variable in class net.sf.basedb.clients.web.taglib.Button
DefaultItemFunction<T extends Nameable> - Class in net.sf.basedb.util.parser: JEP function that can be used to return the name of a default item in a project.
DefaultItemFunction(DbControl, Project, Item) - Constructor for class net.sf.basedb.util.parser.DefaultItemFunction: Create a new function instance.
defaultItems - Variable in class net.sf.basedb.clients.web.taglib.Select: The project default values.
defaultItems - Variable in class net.sf.basedb.core.data.ProjectData
defaultKeyManagers - Static variable in class net.sf.basedb.util.ssl.SSLUtil2
defaultLogger - Variable in class net.sf.basedb.core.log.db.DbLogManagerFactory
defaultMaxRecent - Static variable in class net.sf.basedb.clients.web.Base
defaultMimeType - Variable in class net.sf.basedb.clients.web.servlet.Download
defaultPlatformFunction - Variable in class net.sf.basedb.plugins.batchimport.ArrayDesignImporter
defaultPreset - Variable in class net.sf.basedb.core.Presets
defaultPriority - Variable in enum 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 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 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 - net.sf.basedb.core.log.ChangeType
DELETE - net.sf.basedb.core.Permission: This permission allows a user delete an item.
DELETE - 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 - 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 net.sf.basedb.core.Item
deletionOrder - Variable in enum 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 - 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 net.sf.basedb.core.Permission: Combine the given permission and convert to the integer deny value.
deny(Permission) - Static method in enum net.sf.basedb.core.Permission: Convert the given permission to the integer deny value.
deny(Permission...) - Static method in enum 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 net.sf.basedb.core.Permission
denyValue() - Method in enum 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 - 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 - 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.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.
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 - net.sf.basedb.core.Item: The item is a Directory.
DIRECTORY - 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 - 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 net.sf.basedb.core.BioMaterialEvent.Type
displayValue - Variable in enum net.sf.basedb.core.BioWell.LockMode
displayValue - Variable in enum net.sf.basedb.core.FeatureIdentificationMethod: Returned by the toString method.
displayValue - Variable in enum net.sf.basedb.core.Formula.AverageMethod
displayValue - Variable in enum net.sf.basedb.core.Formula.Parser
displayValue - Variable in enum net.sf.basedb.core.Formula.Type
displayValue - Variable in enum net.sf.basedb.core.IntensityTransform: Returned by the toString method.
displayValue - Variable in enum net.sf.basedb.core.Item
displayValue - Variable in enum net.sf.basedb.core.ItemContext.SortDirection: The string value of this direction.
displayValue - Variable in enum net.sf.basedb.core.Job.ExecutionTime
displayValue - Variable in enum net.sf.basedb.core.Job.Status
displayValue - Variable in enum net.sf.basedb.core.Job.Type
displayValue - Variable in enum net.sf.basedb.core.Location: Returned by the toString method.
displayValue - Variable in enum net.sf.basedb.core.Permission
displayValue - Variable in enum net.sf.basedb.core.plugin.Plugin.MainType
displayValue - Variable in enum net.sf.basedb.core.Type
displayValue - Variable in enum 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 - net.sf.basedb.core.Job.Status: The job has finished successfully.
DONE - net.sf.basedb.core.plugin.Response.Status
doneError(String) - Method in class net.sf.basedb.core.Job: Register the job as completed with an error.
doneError(String, Collection<? extends Throwable>) - Method in class net.sf.basedb.core.Job: Register the job as completed with an error.
doneError(String, Collection<? extends Throwable>, Date) - Method in class net.sf.basedb.core.Job: Register the job as completed with an error.
doneOk(String) - Method in class net.sf.basedb.core.Job: Register the job as successfully completed.
doneOk(String, Date) - Method in class net.sf.basedb.core.Job: Register the job as successfully completed.
doneWithItem(DbControl, I, int) - Method in class net.sf.basedb.plugins.batchimport.AbstractItemImporter: Called when the importer is finished with an item.
doneWithItem(DbControl, ArrayDesign, int) - Method in class net.sf.basedb.plugins.batchimport.ArrayDesignImporter: Validate data files if they have been set.
doneWithItem(DbControl, DerivedBioAssay, int) - Method in class net.sf.basedb.plugins.batchimport.DerivedBioAssayImporter: Validate data files if they have been set.
doneWithItem(DbControl, RawBioAssay, int) - Method in class net.sf.basedb.plugins.batchimport.RawBioAssayImporter: Validate data files if they have been set.
doPost(HttpServletRequest, HttpServletResponse) - Method in class net.sf.basedb.clients.web.servlet.CompileAll
doPost(HttpServletRequest, HttpServletResponse) - Method in class net.sf.basedb.clients.web.servlet.ContentSecurityPolicyReportServlet
doPost(HttpServletRequest, HttpServletResponse) - Method in class net.sf.basedb.clients.web.servlet.Download
doPost(HttpServletRequest, HttpServletResponse) - Method in class net.sf.basedb.clients.web.servlet.ExtensionsServlet
doPost(HttpServletRequest, HttpServletResponse) - Method in class net.sf.basedb.clients.web.servlet.PlotServlet: Forwards requests to PlotServlet.doGet(HttpServletRequest, HttpServletResponse)
doPost(HttpServletRequest, HttpServletResponse) - Method in class net.sf.basedb.clients.web.servlet.Upload
doRecursively(DbControl, Directory, Filter<? super Directory>, Filter<? super File>) - Static method in class net.sf.basedb.util.FileUtil: Do something recursively to all files and sub-directories in specified root directory.
doReturningWork(ReturningWork<T>) - Method in class net.sf.basedb.core.hibernate.SessionWrapper
doReturningWork(Session, ReturningWork<R>) - Static method in class net.sf.basedb.core.HibernateUtil: Execute some arbitrary JDBC code using the same database connection as the Hibernate session.
doStartTag() - Method in class net.sf.basedb.clients.web.taglib.Body
doStartTag() - Method in class net.sf.basedb.clients.web.taglib.Button
doStartTag() - Method in class net.sf.basedb.clients.web.taglib.ButtonGroup
doStartTag() - Method in class net.sf.basedb.clients.web.taglib.extensions.Render
doStartTag() - Method in class net.sf.basedb.clients.web.taglib.extensions.Scripts
doStartTag() - Method in class net.sf.basedb.clients.web.taglib.extensions.Stylesheets
doStartTag() - Method in class net.sf.basedb.clients.web.taglib.Head
doStartTag() - Method in class net.sf.basedb.clients.web.taglib.Help
doStartTag() - Method in class net.sf.basedb.clients.web.taglib.HideableSection
doStartTag() - Method in class net.sf.basedb.clients.web.taglib.Icon
doStartTag() - Method in class net.sf.basedb.clients.web.taglib.Input
doStartTag() - Method in class net.sf.basedb.clients.web.taglib.menu.Menu
doStartTag() - Method in class net.sf.basedb.clients.web.taglib.menu.Menuitem
doStartTag() - Method in class net.sf.basedb.clients.web.taglib.menu.Menuseparator
doStartTag() - Method in class net.sf.basedb.clients.web.taglib.menu.Submenu
doStartTag() - Method in class net.sf.basedb.clients.web.taglib.Page
doStartTag() - Method in class net.sf.basedb.clients.web.taglib.path.Path
doStartTag() - Method in class net.sf.basedb.clients.web.taglib.path.PathElement
doStartTag() - Method in class net.sf.basedb.clients.web.taglib.PropertyValue
doStartTag() - Method in class net.sf.basedb.clients.web.taglib.Select
doStartTag() - Method in class net.sf.basedb.clients.web.taglib.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 - 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 - net.sf.basedb.core.log.ChangeType
DOWNLOAD_IMMEDIATELY - net.sf.basedb.core.plugin.Response.Status
downloadable - Variable in enum 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.
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
enableFilter(String) - Method in class net.sf.basedb.core.hibernate.SessionWrapper
enableFilter(String) - Method in class net.sf.basedb.core.QueryRuntimeFilterManager: Enable a filter, unless it has already been enabled
enableFilter(Session, String) - Static method in class net.sf.basedb.core.HibernateUtil: Enable the filter with the given name.
enableFilters(DbControl) - Method in class net.sf.basedb.core.AbstractEntityQuery: Enable runtime query filters for the query.
enableFilters(QueryRuntimeFilterManager, EntityQuery, DbControl) - Method in class net.sf.basedb.core.Annotation.QueryRuntimeFilterImpl
enableFilters(QueryRuntimeFilterManager, EntityQuery, DbControl) - Method in class net.sf.basedb.core.AnnotationSet.QueryRuntimeFilterImpl
enableFilters(QueryRuntimeFilterManager, EntityQuery, DbControl) - Method in class net.sf.basedb.core.FileSet.QueryRuntimeFilterImpl
enableFilters(QueryRuntimeFilterManager, EntityQuery, DbControl) - Method in class net.sf.basedb.core.FileSetMember.QueryRuntimeFilterImpl
enableFilters(QueryRuntimeFilterManager, EntityQuery, DbControl) - Method in class net.sf.basedb.core.Group.QueryRuntimeFilterImpl
enableFilters(QueryRuntimeFilterManager, EntityQuery, DbControl) - Method in class net.sf.basedb.core.Message.QueryRuntimeFilterImpl
enableFilters(QueryRuntimeFilterManager, EntityQuery, DbControl) - Method in class net.sf.basedb.core.News.QueryRuntimeFilterImpl
enableFilters(QueryRuntimeFilterManager, EntityQuery, DbControl) - Method in class net.sf.basedb.core.Project.QueryRuntimeFilterImpl
enableFilters(QueryRuntimeFilterManager, EntityQuery, DbControl) - Method in interface net.sf.basedb.core.QueryRuntimeFilter: Enable the filters based on the options specified by the query and the logged in users permissions.
enableFilters(QueryRuntimeFilterManager, EntityQuery, DbControl) - Method in class net.sf.basedb.core.QueryRuntimeFilterFactory.AnnotatableFilter
enableFilters(QueryRuntimeFilterManager, EntityQuery, DbControl) - Method in class net.sf.basedb.core.QueryRuntimeFilterFactory.BasicFilter
enableFilters(QueryRuntimeFilterManager, EntityQuery, DbControl) - Method in class net.sf.basedb.core.QueryRuntimeFilterFactory.ChainedFilter: Call QueryRuntimeFilter.enableFilters(QueryRuntimeFilterManager, EntityQuery, DbControl) for each of the chained filters.
enableFilters(QueryRuntimeFilterManager, EntityQuery, DbControl) - Method in class net.sf.basedb.core.QueryRuntimeFilterFactory.ChildFilter
enableFilters(QueryRuntimeFilterManager, EntityQuery, DbControl) - Method in class net.sf.basedb.core.QueryRuntimeFilterFactory.DenyAllFilter
enableFilters(QueryRuntimeFilterManager, EntityQuery, DbControl) - Method in class net.sf.basedb.core.QueryRuntimeFilterFactory.OwnableFilter
enableFilters(QueryRuntimeFilterManager, EntityQuery, DbControl) - Method in class net.sf.basedb.core.QueryRuntimeFilterFactory.RemovableFilter
enableFilters(QueryRuntimeFilterManager, EntityQuery, DbControl) - Method in class net.sf.basedb.core.QueryRuntimeFilterFactory.ShareableFilter
enableFilters(QueryRuntimeFilterManager, EntityQuery, DbControl) - Method in class net.sf.basedb.core.Quota.QueryRuntimeFilterImpl
enableFilters(QueryRuntimeFilterManager, EntityQuery, DbControl) - Method in class net.sf.basedb.core.Role.QueryRuntimeFilterImpl
enableFilters(QueryRuntimeFilterManager, EntityQuery, DbControl) - Method in class net.sf.basedb.core.Session.QueryRuntimeFilterImpl
enableFilters(QueryRuntimeFilterManager, EntityQuery, DbControl) - Method in class net.sf.basedb.core.User.QueryRuntimeFilterImpl
enableFilters(QueryRuntimeFilterManager, EntityQuery, DbControl) - Method in class net.sf.basedb.core.UserDevice.QueryRuntimeFilterImpl
enableForItem(Item) - Method in class net.sf.basedb.core.AnnotationType: Enable this annotation type to be used for items of the specified type.
enablePropertyLink - Variable in class net.sf.basedb.clients.web.taglib.PropertyValue: A link to the property item or not.
enableViewDownload - Variable in class net.sf.basedb.clients.web.formatter.AutoLinkFormatter
enableViewDownload - Variable in class net.sf.basedb.clients.web.formatter.LinkedFileFormatter
encipher(int[], int) - Method in class net.sf.basedb.util.bcrypt.BCrypt: Blowfish encipher a single 64-bit block encoded as two 32-bit halves
encode(String) - Method in interface net.sf.basedb.util.encode.EncoderDecoder
encode(String) - Method in class net.sf.basedb.util.encode.IdentityEncoderDecoder
encode(String) - Method in class net.sf.basedb.util.encode.TabCrLfEncoderDecoder
encode(String) - Method in class net.sf.basedb.util.encode.ToSpaceEncoderDecoder
encode_base64(byte[], int) - Static method in class net.sf.basedb.util.bcrypt.BCrypt: Encode a byte array using bcrypt's slightly-modified base64 encoding scheme.
encodeAll(Collection<String>, EncoderDecoder) - Static method in class net.sf.basedb.util.encode.EncodeUtil: Encode all strings in a collection.
encodeAndJoin(Collection<String>, EncoderDecoder, String, boolean) - Static method in class net.sf.basedb.util.encode.EncodeUtil: Encode all strings in a collection and join them into a single string.
encoder - Variable in class net.sf.basedb.util.bfs.MetadataWriter
encoder - Variable in class net.sf.basedb.util.excel.XlsxToCsvUtil
encoder - Variable in class net.sf.basedb.util.export.TableWriter
EncoderDecoder - Interface in net.sf.basedb.util.encode: Interface for encoding and decoding strings to make them work in a certain context.
encodeTags(String) - Static method in class net.sf.basedb.clients.web.util.HTML: Scans a string for HTML tags and replaces all & with &, < with <, > with > 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 < and > 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 < and > 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.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
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 - 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 - 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.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.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 - net.sf.basedb.core.Job.Status: The job has finished with an error.
ERROR - net.sf.basedb.core.plugin.Response.Status
ERROR - net.sf.basedb.util.extensions.logging.LogLevel
ERROR - net.sf.basedb.util.extensions.LoggingErrorHandlerFactory.Level
ERROR - net.sf.basedb.util.overview.Severity: The rule generate errors.
ERROR_SECTION - Static variable in class net.sf.basedb.plugins.util.Parameters: The name of the parameter created by Parameters.errorSection(String, String).
errorClazz - Variable in class net.sf.basedb.clients.web.taglib.table.Cell: Optional class attribute for errors.
errorHandler - Variable in class net.sf.basedb.plugins.AbstractFlatFileImporter
errorHandler - Variable in class net.sf.basedb.plugins.AnnotationFlatFileImporter
errorHandler - Variable in class net.sf.basedb.plugins.batchimport.AbstractItemImporter
errorHandler - Variable in class net.sf.basedb.util.extensions.ExtensionPointContext
ErrorHandler - Interface in net.sf.basedb.util.error: An interface to make it easier to implement dynamic error handling.
ErrorHandler<A extends Action> - Interface in net.sf.basedb.util.extensions: Error handlers are created by the factory for each request/use of an extension point.
errorHandlerFactory - Variable in class net.sf.basedb.util.extensions.ExtensionPointBean
errorHandlerFactory - Variable in class net.sf.basedb.util.extensions.ExtensionPointContext
errorHandlerFactory - Variable in class net.sf.basedb.util.extensions.Registry.RegisteredExtensionPoint
ErrorHandlerFactory<A extends Action> - Interface in net.sf.basedb.util.extensions: Error handler factories are responsible for creating error handlers.
errorHandlers - Variable in class net.sf.basedb.util.error.ClassMapErrorHandler: Map of registered error handlers.
errorIfNotFound - Variable in class net.sf.basedb.plugins.PlateFlatFileImporter
errorIfNotFound - Variable in class net.sf.basedb.plugins.ReporterMapFlatFileImporter
errorList - Variable in class net.sf.basedb.core.PluginResponse
errorMessage - Variable in class net.sf.basedb.core.data.FileSetMemberData
errors - Variable in class net.sf.basedb.plugins.executor.ExternalProgramExecutor.ResponseWrapper
errors - Variable in class net.sf.basedb.util.fileset.ValidationRenderer
errorSection - Static variable in class net.sf.basedb.plugins.AbstractFlatFileImporter: Section definition for grouping error handling options.
errorSection - Static variable in class net.sf.basedb.plugins.util.Parameters: Section definition for grouping error handling options.
errorSection(String, String) - Static method in class net.sf.basedb.plugins.util.Parameters: Create a parameter starting an error section.
escape(String) - Method in class net.sf.basedb.clients.web.plugins.PlainTextTemplate: Replace newlines and tabs with a space.
escape(String) - Method in class net.sf.basedb.clients.web.plugins.XMLTemplate
ESCAPE - Variable in class net.sf.basedb.core.migrate.ByteArrayWriter
ESCAPE - Variable in class net.sf.basedb.core.migrate.TextWriter
estimated - Variable in class net.sf.basedb.clients.jobagent.slotmanager.Slot
estimatedExecutionTime - Variable in class net.sf.basedb.core.data.JobData
estimatedExecutionTime - Variable in class net.sf.basedb.core.PluginResponse
evaluate(Annotatable) - Method in class net.sf.basedb.clients.web.extensions.list.RawDataTypeFilter
evaluate(Annotatable) - Method in class net.sf.basedb.clients.web.extensions.list.SubtypeFilter
evaluate(Annotatable) - Method in class net.sf.basedb.util.annotations.InheritAnnotationsManager.UsableParentFilter
evaluate(EntityQuery) - Method in class net.sf.basedb.core.query.ReturnClassFilter: Returns TRUE if the EntityQuery.getItemType() returns an item type whose Item.getItemClass() is compatible with the specified class.
evaluate(AnnotationSnapshot) - Method in class net.sf.basedb.clients.web.util.ProjectSpecificInfoFilter: Evaluate the annotation snapshot and update the flags if the snapshot is a project-specific annotation and overrides a default value.
evaluate(AnnotationSnapshot) - Method in class net.sf.basedb.core.snapshot.AnnotationFilter
evaluate(AnnotationSnapshot) - Method in class net.sf.basedb.core.snapshot.AnnotationLoaderUtil
evaluate(AnnotationSnapshot) - Method in class net.sf.basedb.core.snapshot.AnnotationTypeFilter
evaluate(AnnotationSnapshot) - Method in class net.sf.basedb.core.snapshot.DisabledInheritanceFilter
evaluate(AnnotationSnapshot) - Method in class net.sf.basedb.core.snapshot.ProjectFilter
evaluate(AnnotationSnapshot) - Method in class net.sf.basedb.util.annotations.InheritAnnotationsManager.AnnotationTypeFilter
evaluate(AnnotationSnapshot) - Method in class net.sf.basedb.util.annotations.InheritSpecification
evaluate(ContextUtil.ContextResult) - Method in class net.sf.basedb.util.AutoDetectFileFormat.IsImportableFilter
evaluate(ContextUtil.ContextResult) - Method in class net.sf.basedb.util.ContextUtil.IsInContextFilter
evaluate(ExtensionsFile) - Method in class net.sf.basedb.clients.web.extensions.IgnoreFilter
evaluate(ExtensionsFile) - Method in class net.sf.basedb.clients.web.extensions.InstallFilter
evaluate(ExtensionsFile) - Method in class net.sf.basedb.clients.web.extensions.UninstallFilter
evaluate(ExtensionsFile) - Method in class net.sf.basedb.util.extensions.manager.filter.DeletedFilter
evaluate(ExtensionsFile) - Method in class net.sf.basedb.util.extensions.manager.filter.InstalledFilter
evaluate(ExtensionsFile) - Method in class net.sf.basedb.util.extensions.manager.filter.InvalidAndModifiedFilter
evaluate(ExtensionsFile) - Method in class net.sf.basedb.util.extensions.manager.filter.ValidAndNewOrModifiedFilter
evaluate(ExtensionsFile) - Method in class net.sf.basedb.util.extensions.manager.filter.WasProcessedFilter
evaluate(Node) - Method in class net.sf.basedb.util.overview.filter.BasicItemFilter
evaluate(Node) - Method in class net.sf.basedb.util.overview.filter.HasAttributeFilter
evaluate(Node) - Method in class net.sf.basedb.util.overview.filter.ItemTypeFilter
evaluate(Node) - Method in class net.sf.basedb.util.overview.filter.NodeTypeFilter
evaluate(HttpResponse) - Method in class net.sf.basedb.util.GeoLocation.ResponseFilter
evaluate(Element) - Method in class net.sf.basedb.util.extensions.xml.ExtensionPointFilter
evaluate(Element) - Method in class net.sf.basedb.util.extensions.xml.PluginDefinitionFilter
evaluate(T) - Method in class net.sf.basedb.util.filter.AllOfFilter
evaluate(T) - Method in class net.sf.basedb.util.filter.EqualsFilter
evaluate(T) - Method in interface net.sf.basedb.util.filter.Filter: Evaluate if the given object should pass the filter or not.
evaluate(T) - Method in class net.sf.basedb.util.filter.IdentityFilter
evaluate(T) - Method in class net.sf.basedb.util.filter.InstanceOfFilter
evaluate(T) - Method in class net.sf.basedb.util.filter.InverseFilter
evaluate(T) - Method in class net.sf.basedb.util.filter.NoneOfFilter
evaluate(T) - Method in class net.sf.basedb.util.filter.NotNullFilter
evaluate(T) - Method in class net.sf.basedb.util.filter.OneOfFilter
evaluate(T) - Method in class net.sf.basedb.util.filter.StaticFilter
evaluateFormula(Cell) - Method in class net.sf.basedb.util.excel.XlsxToCsvUtil.SheetInfo
evaluateFormulas - Variable in class net.sf.basedb.util.excel.XlsxToCsvUtil
evenodd - Variable in class net.sf.basedb.clients.web.taglib.table.Table: Keep track of which class to use for the next row.
event - Variable in class net.sf.basedb.core.data.BioMaterialEventSourceData
event - Variable in class net.sf.basedb.core.data.BioPlateEventParticipantData
eventDate - Variable in class net.sf.basedb.core.data.BioMaterialEventData
eventDate - Variable in class net.sf.basedb.core.data.BioPlateData
eventDate - Variable in class net.sf.basedb.core.data.BioPlateEventData
eventDate - Variable in class net.sf.basedb.core.data.PlateEventData
EventFilter - Interface in net.sf.basedb.util.extensions.events: A filter for events before they are sent to an EventHandler.
EventHandler - Interface in net.sf.basedb.util.bfs: Event handlers are used for reacting to various parsing events when parsing BFS files.
EventHandler - Interface in net.sf.basedb.util.extensions.events: An event handler receives events about things happening to extensions and extension points.
eventHandlers - Variable in class net.sf.basedb.util.extensions.Registry
eventParticipants - Variable in class net.sf.basedb.core.data.BioPlateData
events - Variable in class net.sf.basedb.core.data.BioPlateEventTypeData
events - Variable in class net.sf.basedb.core.data.MeasuredBioMaterialData
events - Variable in class net.sf.basedb.core.data.PlateData
eventType - Variable in class net.sf.basedb.core.data.BioMaterialEventData
eventType - Variable in class net.sf.basedb.core.data.BioPlateEventData
eventType - Variable in class net.sf.basedb.util.extensions.events.ExtensionEventFilter
EventType<T> - Class in net.sf.basedb.util.bfs: Defines an event type that is sent in event notifications to event handlers.
EventType - Class in net.sf.basedb.util.extensions.events: Represents different types of event.
EventType(String) - Constructor for class net.sf.basedb.util.bfs.EventType: Create a new event type object.
EventType(String) - Constructor for class net.sf.basedb.util.extensions.events.EventType: Create a new event type.
EventTypeFilter - Class in net.sf.basedb.util.extensions.events: Event filter that only passes on events of a specifiec event type.
EventTypeFilter(EventType) - Constructor for class net.sf.basedb.util.extensions.events.EventTypeFilter: Create a new event type filter.
eventTypes - Variable in class net.sf.basedb.core.data.PlateTypeData
EVERYONE - Static variable in class net.sf.basedb.core.Group: The id of the Everyone group where all users are (virtual) members.
EVERYONE - Static variable in class net.sf.basedb.core.Keyring
evict(Object) - Method in class net.sf.basedb.core.hibernate.SessionWrapper
evictData(Session, BasicData) - Static method in class net.sf.basedb.core.HibernateUtil: Remove a data item from the internal cache of Hibernate.
evictFromSecondLevelCacheIfModified - Variable in class net.sf.basedb.core.AnnotationBatcher
EvictPropertyPath(Type) - Constructor for class net.sf.basedb.core.Metadata.EvictPropertyPath
ExcelData(XlsxToCsvUtil.SheetInfo, int, int, int, String, String[], boolean, boolean, boolean) - Constructor for class net.sf.basedb.util.parser.FlatFileParser.ExcelData: Create a new data object.
excelFormatter - Variable in class net.sf.basedb.clients.web.plugins.ExportedProperty
ExcelFormatter<T,E> - Interface in net.sf.basedb.util.excel: Interface that is intended to be implemented by formatters that also want to support generating output for excel.
excelParsedLinesOffset - Variable in class net.sf.basedb.util.parser.FlatFileParser: The value of the parsedLines when the current Excel sheet is parsed.
excelSheet - Variable in class net.sf.basedb.util.parser.FlatFileParser: Excel sheet that is currently being parsed.
excelSheetName - Variable in class net.sf.basedb.util.parser.FlatFileParser: Name of the Excel sheet to parse if the file is an Excel file.
excelSheetParameter - Static variable in class net.sf.basedb.plugins.AbstractFlatFileImporter: Parameter definition for specifying the name of the sheet to use if the selected file is an Excel file.
ExcelValue<T> - Class in net.sf.basedb.util.excel: Represents a value and style format that should be written to a cell in an excel worksheet.
ExcelValue(T, String) - Constructor for class net.sf.basedb.util.excel.ExcelValue
ExcelValue.BlankValue<T> - Class in net.sf.basedb.util.excel: Represents a blank cell.
ExcelValue.BooleanValue - Class in net.sf.basedb.util.excel: Represents a cell with a numeric value.
ExcelValue.DateValue - Class in net.sf.basedb.util.excel: Represents a cell with a date value.
ExcelValue.IntValue - Class in net.sf.basedb.util.excel: Represents a cell with a numeric value without decimals.
ExcelValue.NumericValue - Class in net.sf.basedb.util.excel: Represents a cell with a numeric value.
ExcelValue.StringValue - Class in net.sf.basedb.util.excel: Represents a cell with a string value.
excelWorkbook - Variable in class net.sf.basedb.util.parser.FlatFileParser: Excel workbook that has been loaded.
exception - Variable in class net.sf.basedb.clients.web.fileupload.FileUploadProgress
exception - Variable in class net.sf.basedb.core.ItemContext
ExceptionCatcher - Class in net.sf.basedb.clients.web.taglib: This tag is a wrapper that catches any errors in it's body and outputs the error message.
ExceptionCatcher() - Constructor for class net.sf.basedb.clients.web.taglib.ExceptionCatcher
ExceptionInterruptHandler - Class in net.sf.basedb.core.signal: Interrupt handler implementation that always throw a SignalException.
ExceptionInterruptHandler(String) - Constructor for class net.sf.basedb.core.signal.ExceptionInterruptHandler
exclude - Variable in class net.sf.basedb.plugins.LowessNormalization.SpotData
exclude(Collection<Include>) - Method in class net.sf.basedb.core.AbstractEntityQuery
exclude(Collection<Include>) - Method in interface net.sf.basedb.core.query.EntityQuery
exclude(Include...) - Method in class net.sf.basedb.core.AbstractEntityQuery
exclude(Include...) - Method in interface net.sf.basedb.core.query.EntityQuery: Specify options for which items to exclude from the result.
excludeDefaultValues - Variable in class net.sf.basedb.core.AnnotationRestriction.Options
excludeDefaultValues() - Method in class net.sf.basedb.core.AnnotationRestriction.Options: Should default values (for project-specific annotation types) be excluded from the query or not.
excludeLimit - Variable in class net.sf.basedb.util.IncludeExcludeFilter
execDirectory - Variable in class net.sf.basedb.plugins.Base1PluginExecuter: This is the directory where the plugin will generate its output.
execNameParameter - Variable in class net.sf.basedb.plugins.Base1PluginExecuter: The name of the executable.
execPathParameter - Static variable in class net.sf.basedb.plugins.Base1PluginExecuter: The path to where the plug-in executer can find the executables.
executable - Variable in enum 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.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 - 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 - net.sf.basedb.core.Job.Status: The job is executing.
ExecutionTime(int, String, int, int) - Constructor for enum 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 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 - 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 - 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.
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 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 - 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 - 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
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 - 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 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 - 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 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 - 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 - 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 - 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 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 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 - net.sf.basedb.clients.web.extensions.fileviewer.FileViewerContext.Type: The context is a regular file listing context.
FILE - net.sf.basedb.core.Item: The item is a File.
FILE - 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 - 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 - 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 - 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
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 - 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
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 in net.sf.basedb.clients.web.extensions.fileviewer
FileViewerUtil - Class in net.sf.basedb.clients.web.extensions.fileviewer: Helper class for handling the "file-viewer" extension point.
FileViewerUtil(JspContext, FileViewerContext) - Constructor for class net.sf.basedb.clients.web.extensions.fileviewer.FileViewerUtil: Deprecated.
In 3.17, use FileViewerUtil.getOrCreate(JspContext, FileViewerContext) instead
FileWrapper - Interface in net.sf.basedb.util.importer: Wrapper around files that provide some basic information about the file.
fillText - Variable in class net.sf.basedb.clients.web.taglib.menu.Menu: Optional text to display to the far right of a horizontal menu
filter - Variable in class net.sf.basedb.core.query.ConditionalQueryElement
filter - Variable in class net.sf.basedb.util.extensions.manager.processor.ExtractResourcesProcessor
filter - Variable in class net.sf.basedb.util.extensions.Registry.RegisteredEventHandler
filter - Variable in class net.sf.basedb.util.extensions.xml.XmlLoader
filter - Variable in class net.sf.basedb.util.IncludeExcludeFilter
filter - Variable in class net.sf.basedb.util.StaticCache.CleanupTask
filter(Collection<? extends T>, Filter<? super T>) - Static method in class net.sf.basedb.util.filter.FilterUtil: Filter a collection and return a new collection with the objects that passes the Filter.evaluate(Object) method.
Filter<T> - Interface in net.sf.basedb.util.filter: A filter is something that selectes or rejects an object due to some property of it.
FILTER - 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.
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
FilterUtil - Class in net.sf.basedb.util.filter: Utility class for working with and using filters.
FilterUtil() - Constructor for class net.sf.basedb.util.filter.FilterUtil
fiMethod - Variable in class net.sf.basedb.core.FeatureBatcher
fiMethod - Variable in class net.sf.basedb.core.RawDataBatcher: The method to use for identifying features.
fiMethod - Variable in class net.sf.basedb.plugins.IlluminaRawDataImporter
finalizeRegistration(ExtensionsManager) - Method in class net.sf.basedb.util.extensions.manager.processor.IgnoreFileProcessor: Finalize the ignore registration.
finalizeRegistration(ExtensionsManager, boolean) - Method in class net.sf.basedb.util.extensions.manager.processor.RegisterExtensionsProcessor
find(Class<T>, Object) - Method in class net.sf.basedb.core.hibernate.SessionWrapper
find(Class<T>, Object, Map<String, Object>) - Method in class net.sf.basedb.core.hibernate.SessionWrapper
find(Class<T>, Object, LockModeType) - Method in class net.sf.basedb.core.hibernate.SessionWrapper
find(Class<T>, Object, LockModeType, Map<String, Object>) - Method in class net.sf.basedb.core.hibernate.SessionWrapper
find(Set<QuotaIndex>) - Method in class net.sf.basedb.core.data.QuotaIndex: Find the quota entry in the given set that correpsonds to the same quota type and location as this index.
find(DbControl, ItemQuery<I>, String) - Method in class net.sf.basedb.plugins.batchimport.AnnotationIdMethod: Find all items with property = identifier.
find(DbControl, ItemQuery<I>, String) - Method in class net.sf.basedb.plugins.batchimport.FallbackIdMethod: First, find items using the parent id method.
find(DbControl, ItemQuery<I>, String) - Method in class net.sf.basedb.plugins.batchimport.FileImporter.PathIdMethod
find(DbControl, ItemQuery<I>, String) - Method in interface net.sf.basedb.plugins.batchimport.IdMethod: Try to find items with this query method.
find(DbControl, ItemQuery<I>, String) - Method in class net.sf.basedb.plugins.batchimport.InternalIdMethod: Find the item with id = identifier
find(DbControl, ItemQuery<I>, String) - Method in class net.sf.basedb.plugins.batchimport.MultiPropertyIdMethod: Find all items with property[0] = identifier, or property[1] = identifier, ....
find(DbControl, ItemQuery<I>, String) - Method in class net.sf.basedb.plugins.batchimport.PropertyIdMethod: Find all items with property = identifier.
find(AnnotationSetSnapshot) - Method in class net.sf.basedb.core.snapshot.AnnotationLoaderUtil: Same as findAll but only return a boolean instead of the number of snapshots found.
find(AnnotationSetSnapshot, Filter<AnnotationSnapshot>) - Method in class net.sf.basedb.core.snapshot.AnnotationLoaderUtil: Same as findAll but only return a boolean instead of the number of snapshots found.
FIND_WHAT - Static variable in exception net.sf.basedb.core.ItemModifiedException: A pattern to extract the Xxxx and id parts from a string containing [net.sf.basedb.core.data.XxxxData#id].
findAll(Set<String>) - Method in class net.sf.basedb.core.dbengine.TableInfo: Find all indexes with the given set of columns.
findAll(AnnotationSetSnapshot) - Method in class net.sf.basedb.core.snapshot.AnnotationLoaderUtil: Find and load annotations from the given annotation set snapshot.
findAll(AnnotationSetSnapshot, Filter<AnnotationSnapshot>) - Method in class net.sf.basedb.core.snapshot.AnnotationLoaderUtil: Find and load annotations from the given annotation set snapshot using an optional extra filter.
findAll(Filter<? super Node>) - Method in class net.sf.basedb.util.overview.Node: Find all nodes in the parent chain that matches the given filter.
findAllDefaultData(Item, ItemSubtypeData, boolean) - Method in class net.sf.basedb.core.Project: Find all default items in this project of the given item type (required) and subtype (optional).
findAnnotations(DbControl, Annotatable, Filter<? super AnnotationSnapshot>, boolean) - Method in class net.sf.basedb.core.snapshot.SnapshotManager
findAnnotations(DbControl, Annotatable, Filter<? super AnnotationSnapshot>, boolean, boolean) - Method in class net.sf.basedb.core.snapshot.SnapshotManager: Utility method for calling getSnapshot and findAnnotations in one go.
findAnnotations(DbControl, AnnotationSetSnapshot, Filter<? super AnnotationSnapshot>, boolean) - Method in class net.sf.basedb.core.snapshot.SnapshotManager: Find annotations.
findAnnotations(DbControl, AnnotationSetSnapshot, Filter<? super AnnotationSnapshot>, boolean, boolean) - Method in class net.sf.basedb.core.snapshot.SnapshotManager: Search in a snapshot for all annotations matching a given filter.
findAnnotationTypeCategory(DbControl, IdMethod, String) - Method in class net.sf.basedb.plugins.batchimport.AbstractItemImporter: Find an annotation type category with a given identifier.
findArrayBatch(DbControl, IdMethod, String) - Method in class net.sf.basedb.plugins.batchimport.AbstractItemImporter: Find an array batch with a given identifier.
findArrayDesign(DbControl, IdMethod, String) - Method in class net.sf.basedb.plugins.batchimport.AbstractItemImporter: Find an array design with a given identifier.
findArraySlide(DbControl, IdMethod, String) - Method in class net.sf.basedb.plugins.batchimport.AbstractItemImporter: Find an array slide with a given identifier.
findBioAssay(List<DerivedBioAssay>, String) - Method in class net.sf.basedb.plugins.IlluminaRawDataImporter
findBioPlate(DbControl, IdMethod, String) - Method in class net.sf.basedb.plugins.batchimport.AbstractItemImporter: Find a bioplate with a given identifier.
findBioPlateType(DbControl, IdMethod, String) - Method in class net.sf.basedb.plugins.batchimport.AbstractItemImporter: Find a bioplate type with a given identifier.
findBioSource(DbControl, IdMethod, String) - Method in class net.sf.basedb.plugins.batchimport.AbstractItemImporter: Same as AbstractItemImporter.findBioSource(DbControl, IdMethod, String, ItemSubtype) with a null item subtype.
findBioSource(DbControl, IdMethod, String, ItemSubtype) - Method in class net.sf.basedb.plugins.batchimport.AbstractItemImporter: Find a biosource with a given identifier.
findBioWell(DbControl, BioPlate, String, String) - Method in class net.sf.basedb.plugins.batchimport.AbstractItemImporter: Find a well on a bioplate.
findChildren - Variable in class net.sf.basedb.core.BioAssaySet: Query to retrieve children for a bioassayset.
findClass(String) - Method in class net.sf.basedb.util.JarClassLoader
findClass(String) - Method in class net.sf.basedb.util.JarClassLoader.JarClassLoaderProxy
findColumn - Static variable in class net.sf.basedb.util.parser.FlatFileParser: Pattern used to find column mappings in a string, ie. abc \col\ def
findColumn(String) - Method in class net.sf.basedb.core.dbengine.TableInfo: Find information about a column with the given name.
findColumn(String) - Method in class net.sf.basedb.util.parser.ColFunction: Find column index by checking each column header against a regular expression.
findColumnHeaderIndex(String) - Method in class net.sf.basedb.util.parser.FlatFileParser: Find the index of a column header using a regular expression for pattern matching.
findConstructor(Class<I>, Object[]) - Static method in class net.sf.basedb.util.ClassUtil: Find a constructor for the specified class which takes parameters of the specified types taking superclasses and interfaces into account.
findDataFileType(DbControl, IdMethod, String) - Method in class net.sf.basedb.plugins.batchimport.AbstractItemImporter: Find a data file type with a given identifier.
findDefaultData(DbControl, String, boolean) - Method in class net.sf.basedb.core.Project
findDefaultData(Item, ItemSubtypeData, boolean) - Method in class net.sf.basedb.core.Project: Find a default item in this project of the given item type (required) and subtype (optional).
findDefaultItem() - Method in class net.sf.basedb.util.parser.DefaultItemFunction: Find a default item.
findDefaultItems(DbControl, Item, boolean) - Method in class net.sf.basedb.core.Project: Find the default items of the given item type.
findDefaultItems(DbControl, ItemSubtype, boolean) - Method in class net.sf.basedb.core.Project: Find the default (subtypable) items that has the given subtype.
findDefaultItemsOfRelatedSubtype(DbControl, ItemSubtype, Item) - Method in class net.sf.basedb.core.Project: Utility method for finding default items of the given relatedType.
findDefaultRelatedData(DbControl, Subtypable, Item, boolean) - Method in class net.sf.basedb.core.Project
findDerivedBioAssay(DbControl, IdMethod, String, ItemSubtype) - Method in class net.sf.basedb.plugins.batchimport.AbstractItemImporter: Find a derived bioassay with a given identifier.
findExtract(DbControl, IdMethod, String) - Method in class net.sf.basedb.plugins.batchimport.AbstractItemImporter: Same as AbstractItemImporter.findSample(DbControl, IdMethod, String, ItemSubtype) with a null subtype.
findExtract(DbControl, IdMethod, String, ItemSubtype) - Method in class net.sf.basedb.plugins.batchimport.AbstractItemImporter: Find an extract with a given identifier.
findFactory(URI) - Static method in class net.sf.basedb.util.uri.ConnectionManagerUtil: Find a factory for the given URI.
findFiles(File, FileFilter) - Static method in class net.sf.basedb.util.FileUtil: Find files matching a given filter in a directory.
findFileServer(DbControl, IdMethod, String) - Method in class net.sf.basedb.plugins.batchimport.AbstractItemImporter: Find a file server with a given identifier.
findFirstCommon(Collection<T>, Collection<T>, T) - Static method in class net.sf.basedb.util.ListUtil: Find the first entry in the master collection that is also present in the check collection.
findForeignKeyName(String, Set<String>, String) - Method in class net.sf.basedb.core.dbengine.TableInfo: Check if there is a foreign key with the same name or exactly the same set of columns referencing the same table.
findGeometry(DbControl, int, int) - Method in class net.sf.basedb.plugins.PlateMappingImporter
findHardware(DbControl, IdMethod, String) - Method in class net.sf.basedb.plugins.batchimport.AbstractItemImporter: Same as AbstractItemImporter.findHardware(DbControl, IdMethod, String, ItemSubtype) with a null item subtype.
findHardware(DbControl, IdMethod, String, ItemSubtype) - Method in class net.sf.basedb.plugins.batchimport.AbstractItemImporter: Find a hardware with a given identifier.
findHybridization(DbControl, IdMethod, String) - Method in class net.sf.basedb.plugins.batchimport.AbstractItemImporter: Find a hybridization with a given identifier.
findId - Static variable in class net.sf.basedb.clients.web.servlet.Download
findIndexName(String, Set<String>) - Method in class net.sf.basedb.core.dbengine.TableInfo: Check if there is an index with the same name or exactly the same set of columns.
findItemSubtype(DbControl, Item, FlatFileParser.Data) - Method in class net.sf.basedb.plugins.batchimport.AbstractItemImporter: Try to find subtype from the given file data.
findItemSubtype(DbControl, IdMethod, Item, String) - Method in class net.sf.basedb.plugins.batchimport.AbstractItemImporter: Find an item subtype with a given identifier.
findKit(DbControl, IdMethod, String, ItemSubtype) - Method in class net.sf.basedb.plugins.batchimport.AbstractItemImporter: Find a kit with a given identifier.
findLabeledExtract(DbControl, IdMethod, String) - Method in class net.sf.basedb.plugins.batchimport.AbstractItemImporter: Find a labled extract with a given identifier.
findMany - Static variable in class net.sf.basedb.clients.web.ModeInfo
findMaxBytes(Set<QuotaIndex>) - Method in class net.sf.basedb.core.data.QuotaIndex: Find the quota index entry in the given set and return the 'maxBytes' value.
findMethod(Class<?>, String, Class<?>...) - Static method in class net.sf.basedb.util.ClassUtil: Find a method in a clazz with the given name that takes the given list of arguments.
findOne - Static variable in class net.sf.basedb.clients.web.ModeInfo
findOtherUnit(Session, String) - Method in class net.sf.basedb.core.Unit: Find the unit with a given symbol that has the same quantity as this unit.
findParticipant(BioPlateData) - Method in class net.sf.basedb.core.BioPlateEvent: Find the participant object for the given bioplate.
findPermissionTemplate(DbControl, IdMethod, String) - Method in class net.sf.basedb.plugins.batchimport.AbstractItemImporter: Find a permission template with a given identifier.
findPhysicalBioAssay(DbControl, IdMethod, String, ItemSubtype) - Method in class net.sf.basedb.plugins.batchimport.AbstractItemImporter: Find a physical bioassay with a given identifier.
findPlateGeometry(DbControl, IdMethod, String) - Method in class net.sf.basedb.plugins.batchimport.AbstractItemImporter: Find a plate geometry with a given identifier.
findPlatform(DbControl, IdMethod, String) - Method in class net.sf.basedb.plugins.batchimport.AbstractItemImporter: Find a platform with a given identifier.
findPlugins(DbControl, GuiContext, File, String, PluginDefinition) - Static method in class net.sf.basedb.util.AutoDetectFileFormat: Find all plugins with configurations which can import the specified file.
findProjectSpecific - Variable in class net.sf.basedb.core.ProjectSpecificAnnotationsManager
findProjectSpecificAnnotation(Annotation, int) - Method in class net.sf.basedb.core.ProjectSpecificAnnotationsManager: Find a project-specific annotation for a given default annotation.
findProtocol(DbControl, IdMethod, String) - Method in class net.sf.basedb.plugins.batchimport.AbstractItemImporter: Same as AbstractItemImporter.findProtocol(DbControl, IdMethod, String, ItemSubtype) with a null item subtype.
findProtocol(DbControl, IdMethod, String, ItemSubtype) - Method in class net.sf.basedb.plugins.batchimport.AbstractItemImporter: Find a protocol with a given identifier.
findRange - Static variable in class net.sf.basedb.clients.web.servlet.Download
findRawDataType(DbControl, Platform, PlatformVariant, String) - Method in class net.sf.basedb.plugins.batchimport.AbstractItemImporter: Find a matching raw data type.
findReferencedItem(DbControl, IdMethod, ItemQuery<T>, String, int, boolean) - Method in class net.sf.basedb.plugins.batchimport.AbstractItemImporter: Find a referenced item.
findReferencedItemWithSubtype(DbControl, IdMethod, ItemQuery<T>, String, ItemSubtype, boolean) - Method in class net.sf.basedb.plugins.batchimport.AbstractItemImporter: Find a referenced item with a subtype.
findReporter - Variable in class net.sf.basedb.core.RawDataBatcher: A query to find reporters by the external id.
findReporter - Variable in class net.sf.basedb.core.ReporterBatcher: A query to find reporters by the external id.
findResource(String) - Method in class net.sf.basedb.util.JarClassLoader
findResource(String) - Method in class net.sf.basedb.util.JarClassLoader.JarClassLoaderProxy
findResources(String) - Method in class net.sf.basedb.util.JarClassLoader
findResources(String) - Method in class net.sf.basedb.util.JarClassLoader.JarClassLoaderProxy
findSample(DbControl, IdMethod, String) - Method in class net.sf.basedb.plugins.batchimport.AbstractItemImporter: Same as AbstractItemImporter.findSample(DbControl, IdMethod, String, ItemSubtype) with a null subtype.
findSample(DbControl, IdMethod, String, ItemSubtype) - Method in class net.sf.basedb.plugins.batchimport.AbstractItemImporter: Find a sample with a given identifier.
findSetterMethod(String, Class<?>) - Method in class net.sf.basedb.util.extensions.debug.BeanActionFactory: Find a setter method for the specified parameter.
findSoftware(DbControl, IdMethod, String) - Method in class net.sf.basedb.plugins.batchimport.AbstractItemImporter: Same as AbstractItemImporter.findSoftware(DbControl, IdMethod, String, ItemSubtype) with a null item subtype.
findSoftware(DbControl, IdMethod, String, ItemSubtype) - Method in class net.sf.basedb.plugins.batchimport.AbstractItemImporter: Find a software with a given identifier.
findTag(DbControl, IdMethod, String) - Method in class net.sf.basedb.plugins.batchimport.AbstractItemImporter: Same as AbstractItemImporter.findTag(DbControl, IdMethod, String, ItemSubtype) with a null item subtype.
findTag(DbControl, IdMethod, String, ItemSubtype) - Method in class net.sf.basedb.plugins.batchimport.AbstractItemImporter: Find a tag with a given identifier.
findTargetItem(String, String, FlatFileParser.Data) - Method in class net.sf.basedb.plugins.batchimport.AnyToAnyImporter
findUnit(int, String) - Method in class net.sf.basedb.util.units.UnitCache: Finds a unit with a given symbol for a given quantity.
findUnit(String, String) - Method in class net.sf.basedb.util.units.UnitCache: Finds a unit with a given symbol for a given quantity.
findUnit(DbControl, IdMethod, String) - Method in class net.sf.basedb.plugins.batchimport.AbstractItemImporter: Find a unit with a given identifier.
findUnit(Quantity, String) - Method in class net.sf.basedb.util.units.UnitCache: Finds a unit with a given symbol for a given quantity.
findUsers(String, QueryParameter...) - Method in class net.sf.basedb.core.AuthenticationContext: Find users in the database using a "free" restriction.
findValue(String, boolean, boolean) - Method in class net.sf.basedb.core.AnnotationType: This method should be used on enumerated string annotation types to find a matching predefined string value, optionally ignoring case and white-space.
findVariant(DbControl, Platform, IdMethod, String) - Method in class net.sf.basedb.plugins.batchimport.AbstractItemImporter: Find a platform variant with a given identifier.
findWell(int, int, int) - Method in class net.sf.basedb.plugins.PrintMapFlatFileImporter
findWhat(StaleStateException) - Static method in exception net.sf.basedb.core.ItemModifiedException
FINGERPRINT_LENGTH - Static variable in class net.sf.basedb.core.data.FileServerData
FINGERPRINT_LENGTH - Static variable in class net.sf.basedb.core.FileServer: The length of the SSH fingerprint that can be stored in the database.
FINGERPRINT_PATTERN - Static variable in class net.sf.basedb.core.FileServer: Deprecated.
In 3.11, use FileServer.MD5_FINGERPRINT_PATTERN instead
FINGERPRINT_TYPE_MD5 - Static variable in class net.sf.basedb.core.FileServer: The fingerprint is a MD5 fingprint.
FINGERPRINT_TYPE_SHA256 - Static variable in class net.sf.basedb.core.FileServer: The fingerprint is a SHA256 fingprint.
fingerprintType - Variable in class net.sf.basedb.core.data.FileServerData
finish(Throwable) - Method in class net.sf.basedb.plugins.AbstractFlatFileImporter: Called once when all files has been imported or when exiting due to an error.
finish(Throwable) - Method in class net.sf.basedb.plugins.RawDataFlatFileImporter: Commit/rollback transaction if needed.
finishedFileSize - Variable in class net.sf.basedb.plugins.AbstractFlatFileImporter
firstAssayFieldIndex - Variable in class net.sf.basedb.util.importer.spotdata.BaseFileInfo.SpotSectionInfo
firstColumn - Variable in class net.sf.basedb.util.excel.XlsxToCsvUtil.SheetInfo
FirstPassSectionSpotsParser - Class in net.sf.basedb.util.importer.spotdata: Parses a 'spots' section of a BASEfile with bioassay set spot data.
FirstPassSectionSpotsParser(DbControl, BaseFileInfo, BioAssaySet) - Constructor for class net.sf.basedb.util.importer.spotdata.FirstPassSectionSpotsParser: Creates a new 'section spot' parser for the first pass.
firstResult - Variable in class net.sf.basedb.core.AbstractQuery: The index of the first result that should be returned by the query.
firstRow - Variable in class net.sf.basedb.util.excel.XlsxToCsvUtil.SheetInfo
fitFraction - Variable in class net.sf.basedb.plugins.LowessNormalization.CallableWorker
fitFractionParameter - Static variable in class net.sf.basedb.plugins.LowessNormalization
Fix - Class in net.sf.basedb.util.overview: Holds information about a suggested fix to a failure.
Fix(String, BasicItem) - Constructor for class net.sf.basedb.util.overview.Fix: Create a new suggested fix for an item.
Fix(String, BasicItem, Annotation) - Constructor for class net.sf.basedb.util.overview.Fix: Create a new suggested fix for the annotation of an item.
Fix(String, BasicItem, AnnotationType, boolean) - Constructor for class net.sf.basedb.util.overview.Fix: Create a new suggested fix for the annotation of an item.
Fix(String, BasicItem, DataFileType) - Constructor for class net.sf.basedb.util.overview.Fix
Fix(String, BasicItem, FileSetMember) - Constructor for class net.sf.basedb.util.overview.Fix
FixDerivedBioAssayParentsRecursivelyAction(DbControl) - Constructor for class net.sf.basedb.core.DerivedBioAssay.FixDerivedBioAssayParentsRecursivelyAction
FixedButtonFactory - Class in net.sf.basedb.clients.web.extensions.toolbar: A simple implementation of a toolbar button action factory that creates the same fixed button for all users not using any context information.
FixedButtonFactory() - Constructor for class net.sf.basedb.clients.web.extensions.toolbar.FixedButtonFactory: Create a new factory instance.
FixedMenuItemFactory - Class in net.sf.basedb.clients.web.extensions.menu: A simple implementation of a menu item action factory that creates the same fixed menu item for all users not using any context information.
FixedMenuItemFactory() - Constructor for class net.sf.basedb.clients.web.extensions.menu.FixedMenuItemFactory: Create a new factory instance.
FixedSkinActionFactory - Class in net.sf.basedb.clients.web.extensions.skin: A simple action factory implementation that always include the given skin on all pages.
FixedSkinActionFactory() - Constructor for class net.sf.basedb.clients.web.extensions.skin.FixedSkinActionFactory: Create a new factory instance.
FixedSkinActionFactory.MySkinAction - Class in net.sf.basedb.clients.web.extensions.skin
FixedStartPageFactory - Class in net.sf.basedb.clients.web.extensions.startpage: A simple start page action factory.
FixedStartPageFactory() - Constructor for class net.sf.basedb.clients.web.extensions.startpage.FixedStartPageFactory: Create a new factory instance.
FixedTabFactory - Class in net.sf.basedb.clients.web.extensions.tabcontrol: A simple implementation of a tab action factory that creates the same fixed tab for all users not using any context information.
FixedTabFactory() - Constructor for class net.sf.basedb.clients.web.extensions.tabcontrol.FixedTabFactory: Create a new factory instance.
fixes - Variable in class net.sf.basedb.util.overview.Failure
fixPaths(Presets.Preset) - Method in class net.sf.basedb.util.extensions.manager.Settings: Fix paths in older config files.
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 in net.sf.basedb.util.parser: Represents the type of a line matched or unmatched by the parser.
FLOAT - net.sf.basedb.core.Type: Float type.
FLOAT - 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.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 - net.sf.basedb.util.overview.Node.Type
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 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 - net.sf.basedb.core.Item: The item is a Formula
Formula.AverageMethod - Enum in net.sf.basedb.core: The average method used for the values of this formula.
Formula.Parser - Enum in net.sf.basedb.core: The parser used to parse the formula.
Formula.Type - Enum 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 - 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 - net.sf.basedb.core.query.QuerySection
fromClass(Class<?>) - Static method in enum 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 net.sf.basedb.core.Item: Get the Item object when you know the data class.
fromDataObject(BasicData) - Static method in enum net.sf.basedb.core.Item: Get the Item object when you have a data layer object.
fromDeniedInt(int) - Static method in enum 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 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 net.sf.basedb.core.Include: Convert an integer value to a set of includes.
fromInt(int) - Static method in enum net.sf.basedb.core.Permission: Convert an integer value to a set of granted permissions.
fromItemClass(Class<? extends BasicItem>) - Static method in enum 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 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
fromValue(int) - Static method in enum net.sf.basedb.core.BioMaterialEvent.Type: Get the BioMaterialEvent.Type object when you know the integer code.
fromValue(int) - Static method in enum net.sf.basedb.core.BioWell.LockMode: Get the Lock mode object when you know the integer code.
fromValue(int) - Static method in enum net.sf.basedb.core.ExtraValue.CoordinateType: Get the CoordinateType object when you know the integer code.
fromValue(int) - Static method in enum net.sf.basedb.core.FeatureIdentificationMethod: Get the FeatureIdentificationMethod object when you know the integer code.
fromValue(int) - Static method in enum net.sf.basedb.core.Formula.AverageMethod: Get the Formula.AverageMethod object when you know the integer code.
fromValue(int) - Static method in enum net.sf.basedb.core.Formula.Parser: Get the Formula.Parser object when you know the integer code.
fromValue(int) - Static method in enum net.sf.basedb.core.Formula.Type: Get the Formula.Type object when you know the integer code.
fromValue(int) - Static method in enum net.sf.basedb.core.IntensityTransform: Get the SpotDataTransform object when you know the integer code.
fromValue(int) - Static method in enum net.sf.basedb.core.Item: Get the Item object when you know the integer code.
fromValue(int) - Static method in enum net.sf.basedb.core.ItemContext.SortDirection: Get the SortDirection object when you know the integer code.
fromValue(int) - Static method in enum net.sf.basedb.core.Job.ExecutionTime: Get the Job.Status object when you know the integer code.
fromValue(int) - Static method in enum net.sf.basedb.core.Job.Status: Get the Job.Status object when you know the integer code.
fromValue(int) - Static method in enum net.sf.basedb.core.Job.Type: Get the Job.Status object when you know the integer code.
fromValue(int) - Static method in enum net.sf.basedb.core.Location: Get the Location object when you know the integer code.
fromValue(int) - Static method in enum net.sf.basedb.core.log.ChangeType: Get the change type corresponding to the given numerical value.
fromValue(int) - Static method in enum net.sf.basedb.core.Operator: Get the Operator object when you know the integer code.
fromValue(int) - Static method in enum net.sf.basedb.core.plugin.GuiContext.Type: Get the GuiContext.Type object when you know the integer code.
fromValue(int) - Static method in enum net.sf.basedb.core.plugin.Plugin.MainType
fromValue(int) - Static method in enum net.sf.basedb.core.Type: Get the Type object when you know the integer code.
fromValue(String) - Static method in enum 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 - 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
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 - 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 net.sf.basedb.plugins.Base1PluginExecuter.Base1JobParameterType
get(int) - Method in class net.sf.basedb.core.ItemResultList: Get a BasicItem derived object.
get(int) - Method in class net.sf.basedb.util.parser.FlatFileParser.Data: Deprecated.
In 3.15, use FlatFileParser.Data.getString(int) instead or one of the other getXxx() method to return a given data type directly
get(int, int) - Method in interface net.sf.basedb.core.query.SqlResultList
get(int, String) - Method in interface net.sf.basedb.core.query.SqlResultList
get(Class<E>, BasicData) - Method in class net.sf.basedb.core.ItemResultList
get(Class<T>, Serializable) - Method in class net.sf.basedb.core.hibernate.SessionWrapper
get(Class<T>, Serializable, LockMode) - Method in class net.sf.basedb.core.hibernate.SessionWrapper
get(Class<T>, Serializable, LockOptions) - Method in class net.sf.basedb.core.hibernate.SessionWrapper
get(Class, Serializable) - Method in class net.sf.basedb.core.hibernate.StatelessSessionWrapper
get(Class, Serializable, LockMode) - Method in class net.sf.basedb.core.hibernate.StatelessSessionWrapper
get(Object) - Method in class net.sf.basedb.core.ExtendedPropertyAccessor.GetterSetter: Get the value of the extended property.
get(Object) - Method in class net.sf.basedb.util.ClassLocal: Get the object associated with the class of the specified instance.
get(Object) - Method in class net.sf.basedb.util.formatter.LookupFormatter: Get registered lookup value for a given key
get(String) - Method in class net.sf.basedb.clients.web.extensions.skin.ImageRemapper: Get the remapped image for the given source image.
get(String) - Static method in class net.sf.basedb.clients.web.ModeInfo
get(String, Serializable) - Method in class net.sf.basedb.core.hibernate.SessionWrapper
get(String, Serializable) - Method in class net.sf.basedb.core.hibernate.StatelessSessionWrapper
get(String, Serializable, LockMode) - Method in class net.sf.basedb.core.hibernate.SessionWrapper
get(String, Serializable, LockMode) - Method in class net.sf.basedb.core.hibernate.StatelessSessionWrapper
get(String, Serializable, LockOptions) - Method in class net.sf.basedb.core.hibernate.SessionWrapper
get(JspContext) - Static method in class net.sf.basedb.clients.web.extensions.fileviewer.FileViewerUtil: Get an existing instance that is stored in the given JSP context.
get(DbControl) - Static method in class net.sf.basedb.clients.web.extensions.ExtensionsControl: Get an extension control object for managing the installed extensions.
get(DbControl) - Static method in class net.sf.basedb.core.DerivedBioAssay.FixDerivedBioAssayParentsRecursivelyAction: Get an instance tht handles the fixes for the given DbControl.
get(DbControl, MeasuredBioMaterialData) - Static method in class net.sf.basedb.core.MeasuredBioMaterial.RemainingQuantityAction
get(DbControl, ItemQuery<? extends E>...) - Static method in class net.sf.basedb.util.query.MultiQueryIterator: Create a new iterator for the given list of queries.
get(AnnotationUtil.AnnotatableWrapper) - Method in class net.sf.basedb.util.AnnotationUtil.Cache
get(TransformCache.CacheKey) - Method in class net.sf.basedb.util.listable.TransformCache: Get a cached entry if.
getAbout() - Method in interface net.sf.basedb.util.extensions.Extension: Get information about the extensions.
getAbout() - Method in class net.sf.basedb.util.extensions.ExtensionBean
getAbout() - Method in class net.sf.basedb.util.extensions.manager.ExtensionsFile: Get information about the extensions in this file.
getAbout() - Method in class net.sf.basedb.util.extensions.Registry.RegisteredExtension
getAbout() - Method in class net.sf.basedb.util.extensions.xml.PluginInfo: Get information about the authors of the plug-in.
getAbsolutePath(String) - Static method in class net.sf.basedb.core.File: Convert a relative path back to an absolute file path.
getAbstract() - Method in class net.sf.basedb.core.data.ExperimentData: Get the abstract for this experiment.
getAbstract() - Method in class net.sf.basedb.core.Experiment: Get the abstract text for the publication for this experiment.
getAcceptedFile() - Method in class net.sf.basedb.util.fileset.SingleFileValidationAction: Get the file that was last accepted by the SingleFileValidationAction.acceptFile(FileSetMember) method.
getAction() - Method in class net.sf.basedb.clients.web.taglib.table.Table
getActionClass() - Method in interface net.sf.basedb.util.extensions.ExtensionPoint: Get the class object that represents the type of action that can be added to this extension point.
getActionClass() - Method in class net.sf.basedb.util.extensions.ExtensionPointBean
getActionClass() - Method in class net.sf.basedb.util.extensions.Registry.RegisteredExtensionPoint
getActionFactory() - Method in interface net.sf.basedb.util.extensions.Extension: Get the factory class for creating actions.
getActionFactory() - Method in class net.sf.basedb.util.extensions.ExtensionBean
getActionFactory() - Method in class net.sf.basedb.util.extensions.Registry.RegisteredExtension
getActionId() - Method in class net.sf.basedb.clients.web.extensions.list.RelatedItemColumn.Specification: Get the action id from the expression.
getActions() - Method in class net.sf.basedb.util.extensions.ExtensionContext: Call Extension.getActionFactory() and then ActionFactory.getActions(InvokationContext) on the returned factory.
getActions() - Method in class net.sf.basedb.util.extensions.ExtensionPointContext: Always null, since this is an extension point context.
getActions() - Method in class net.sf.basedb.util.extensions.InvokationContext: Get the actions, or null if there is no current extension.
getActions(InvokationContext<? super A>) - Method in interface net.sf.basedb.util.extensions.ActionFactory: This method may be called one or several times for each request.
getActions(InvokationContext<? super OnSaveAction>) - Method in class net.sf.basedb.clients.web.extensions.edit.DebugOnSaveActionFactory
getActions(InvokationContext<? super ListColumnAction<I, V>>) - Method in class net.sf.basedb.clients.web.extensions.list.PropertyPathActionFactory
getActions(InvokationContext<? super ListColumnAction<Annotatable, Object>>) - Method in class net.sf.basedb.clients.web.extensions.list.RelatedItemColumnActionFactory
getActions(InvokationContext<? super ListColumnAction<BasicItem, Object>>) - Method in class net.sf.basedb.clients.web.extensions.list.AnyLinkColumnActionFactory
getActions(InvokationContext<? super LoginFormAction>) - Method in class net.sf.basedb.clients.web.extensions.login.PasswordLoginFormFactory
getActions(InvokationContext<? super MenuItemAction>) - Method in class net.sf.basedb.clients.web.extensions.menu.FixedMenuItemFactory
getActions(InvokationContext<? super MenuItemAction>) - Method in class net.sf.basedb.clients.web.extensions.menu.PermissionMenuItemFactory
getActions(InvokationContext<? super OverviewPlotAction>) - Method in class net.sf.basedb.clients.web.extensions.plot.MAPlotFactory
getActions(InvokationContext<? super SectionAction>) - Method in class net.sf.basedb.clients.web.extensions.section.IncludeContentSectionFactory
getActions(InvokationContext<? super ServiceControllerAction>) - Method in class net.sf.basedb.clients.web.extensions.service.DummyService
getActions(InvokationContext<? super SkinAction>) - Method in class net.sf.basedb.clients.web.extensions.skin.FixedSkinActionFactory
getActions(InvokationContext<? super StartPageAction>) - Method in class net.sf.basedb.clients.web.extensions.startpage.FixedStartPageFactory
getActions(InvokationContext<? super TabAction>) - Method in class net.sf.basedb.clients.web.extensions.tabcontrol.FixedTabFactory
getActions(InvokationContext<? super TabAction>) - Method in class net.sf.basedb.clients.web.extensions.tabcontrol.IncludeContentTabFactory
getActions(InvokationContext<? super ButtonAction>) - Method in class net.sf.basedb.clients.web.extensions.fileviewer.ViewAndDownloadActionFactory
getActions(InvokationContext<? super ButtonAction>) - Method in class net.sf.basedb.clients.web.extensions.toolbar.FixedButtonFactory
getActions(InvokationContext<? super ButtonAction>) - Method in class net.sf.basedb.clients.web.extensions.toolbar.PermissionButtonFactory
getActions(InvokationContext<? super LogManagerFactory>) - Method in class net.sf.basedb.core.log.db.DbLogManagerFactory
getActions(InvokationContext<? super CdfValidationAction>) - Method in class net.sf.basedb.util.affymetrix.CdfValidationFactory
getActions(InvokationContext<? super CelValidationAction>) - Method in class net.sf.basedb.util.affymetrix.CelValidationFactory
getActions(InvokationContext<? super Action>) - Method in class net.sf.basedb.util.extensions.debug.BeanActionFactory
getActions(InvokationContext<? super Action>) - Method in class net.sf.basedb.util.extensions.debug.ProxyActionFactory
getActions(InvokationContext<? super GtfValidationAction>) - Method in class net.sf.basedb.util.gtf.GtfValidationFactory
getActions(InvokationContext<? super ValidationRuleAction>) - Method in class net.sf.basedb.util.overview.extensions.ReflectValidationRuleActionFactory
getActions(InvokationContext<? super ConnectionManagerFactory>) - Method in class net.sf.basedb.util.uri.http.HttpConnectionManagerActionFactory
getActive() - Method in class net.sf.basedb.clients.web.taglib.tab.TabControl
getActive(DbControl) - Static method in class net.sf.basedb.core.Project: Get the currently active project if any.
getActiveProjectId() - Method in class net.sf.basedb.core.data.JobData: The ID of the project that should be made active when running this job.
getActiveProjectId() - Method in class net.sf.basedb.core.Job: The ID of the project that should be made the active project while running this job.
getActiveProjectId() - Method in class net.sf.basedb.core.SessionControl: Get the id of the active project, or 0 if no project is active.
getActiveProjectName() - Method in class net.sf.basedb.core.SessionControl: Get the name of the active project, or null if no project is active.
getActiveProjectPermissions() - Method in class net.sf.basedb.core.SessionControl: Get the permissions that the logged in user has in the currently active project.
getActiveRoles() - Method in class net.sf.basedb.core.SessionControl: Get the id of all active roles where the logged in user is a member.
getActualCatalog() - Method in class net.sf.basedb.core.ServiceSessionControl.SessionFactoryConfiguration: The actual catalog that will be used by BASE.
getActualSchema() - Method in class net.sf.basedb.core.ServiceSessionControl.SessionFactoryConfiguration: The actual schema that will be used by BASE.
getActualUnit(DbControl) - Method in class net.sf.basedb.core.snapshot.AnnotationSnapshot: Get the unit that is most relevant for this annotation.
getActualValues() - Method in class net.sf.basedb.core.snapshot.AnnotationSnapshot: Get the annotation values that are most relevant for this annotation.
getActualValues(UnitConverter, Type) - Method in class net.sf.basedb.core.snapshot.AnnotationSnapshot: Get the annotations values, optionally converted to some specific unit and type of values.
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 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 net.sf.basedb.core.VirtualTable: Get the alias of this table.
getAlias(int) - Method in class net.sf.basedb.core.RealTable: Get the alias of this table, using the ID of the item to make it unique.
getAlias(BasicItem) - Method in class net.sf.basedb.core.RealTable: Get the alias of this table, using the ID of the item to make it unique.
getAll() - Static method in class net.sf.basedb.core.ClonableProperty: Get a list containing cloned property representation for all static and extended properties.
getAllAnnotatableParentItems(DbControl, Annotatable, Filter<Annotatable>) - Static method in class net.sf.basedb.util.AnnotationUtil: Get all annotatable parent items for a given item.
getAllAnnotatableParentItems(DbControl, Annotatable, Filter<Annotatable>, AnnotationUtil.Cache) - Static method in class net.sf.basedb.util.AnnotationUtil: Get all annotatable parent items for a given item.
getAllAnnotationTypesWithInheritanceDisabled(DbControl) - Static method in class net.sf.basedb.core.AnnotationType: Load the IDs of all annotation types with the disable inheritance flag set.
getAllCharsets() - Static method in class net.sf.basedb.core.Config: Get a set containing all character sets known to the current java virtual machine.
getAllCharsets(boolean) - Static method in class net.sf.basedb.util.charset.CharsetUtil: Get all charsets that Config.getAllCharsets() returns and optionally include the fallback charsets.
getAllChildren(DbControl, Set<Integer>) - Method in class net.sf.basedb.util.overview.loader.ExtractLoader
getAllColumnMappings() - Method in class net.sf.basedb.plugins.gtf.GtfReporterMapImporter
getAllColumnMappings() - Method in class net.sf.basedb.plugins.PlateFlatFileImporter
getAllColumnMappings() - Method in class net.sf.basedb.plugins.ReporterMapFlatFileImporter
getAllColumnMappings(boolean) - Method in class net.sf.basedb.plugins.ReporterFlatFileImporter
getAllColumnMappings(RawDataType) - Method in class net.sf.basedb.plugins.RawDataFlatFileImporter: Loads the column mappings if they hasn't been loaded already.
getAllCurrentContexts(boolean, boolean) - Method in class net.sf.basedb.core.SessionControl: Get a list with the current default contexts.
getAllExtended() - Method in class net.sf.basedb.core.data.RawData
getAllItems() - Method in class net.sf.basedb.core.ItemList: Get a query that returns all items that can possibly be members of this list.
getAllMandatory() - Static method in class net.sf.basedb.core.ClonableProperty: Get a list with all mandatory properties that must be cloned.
getAllMembers(DbControl, Set<Integer>) - Static method in class net.sf.basedb.core.User: Load the ID:s of all users that are direct members of the specified groups.
getAllMembers(Session, Collection<Integer>) - Static method in class net.sf.basedb.core.User
getAllObjects() - Method in class net.sf.basedb.util.extensions.manager.ExtensionsFile: Get a list of all objects defined in this extensions file.
getAllowImmediateExecution() - Method in class net.sf.basedb.core.data.PluginDefinitionData: If the plugin is allowed to be immediately executed or if it must be added to the job queue.
getAllowImmediateExecution() - Method in class net.sf.basedb.core.PluginDefinition: If immediate execution of jobs are allowed or if they always must go through the job queue.
getAllowMultiple() - Method in class net.sf.basedb.core.data.ItemSubtypeFileTypeData: If multiple files of this type are allowed in a file set or not.
getAllowMultiple() - Method in class net.sf.basedb.core.data.PlatformFileTypeData: If multiple files of this type are allowed in a file set or not.
getAllowMultiple() - Method in class net.sf.basedb.core.ItemSubtypeFileType: Check if more than one file of this type is allowed in a file set or not.
getAllowMultiple() - Method in class net.sf.basedb.core.PlatformFileType: Check if more than one file of this type is allowed in a file set or not.
getAllowMultiple() - Method in interface net.sf.basedb.core.UsableDataFileType: A flag indicating if it is allowed to attach multiple files or only a single one of the given type.
getAllParentExtracts(DbControl, OverviewContext, PhysicalBioAssay) - Static method in class net.sf.basedb.util.overview.validator.PhysicalBioAssayValidator: Get all parent extracts that are associated with the given physical bioassay.
getAllPermissions(SharedData) - Method in class net.sf.basedb.core.SessionControl: Same as SessionControl.getAllPermissions(Item, UserData, ItemKeyData, ProjectKeyData)
getAllPermissions(Item, UserData, ItemKeyData, ProjectKeyData) - Method in class net.sf.basedb.core.InternalJobQueue.JobQueueKeyring: Return 0.
getAllPermissions(Item, UserData, ItemKeyData, ProjectKeyData) - Method in class net.sf.basedb.core.Job.SignalKeyring: Return 0.
getAllPermissions(Item, UserData, ItemKeyData, ProjectKeyData) - Method in class net.sf.basedb.core.Keyring
getAllPermissions(Item, UserData, ItemKeyData, ProjectKeyData) - Method in class net.sf.basedb.core.ServiceSessionControl.ServicesKeyring: Return 0.
getAllPermissions(Item, UserData, ItemKeyData, ProjectKeyData) - Method in class net.sf.basedb.core.SessionControl: Get the combined permissions for an item of the specified type, owned by the specified user and shared with the specified item and project keys.
getAllResults() - Method in class net.sf.basedb.util.extensions.manager.ProcessResults
getAllRoles() - Method in class net.sf.basedb.core.SessionControl: Get the id of all roles where the logged in user is a member.
getAllRules(DbControl, GenericOverview) - Static method in class net.sf.basedb.util.overview.OverviewUtil: Get all static and extension validation rules grouped by relationship.
getAllSamples(TransformContext, Set<Integer>) - Method in class net.sf.basedb.util.listable.PushToParentsTransformer
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, defaultContext, false).
getAndSetCurrentContext(SessionControl, Item, String, PageContext, ItemContext, boolean) - Static method in class net.sf.basedb.clients.web.Base
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, "", pageContext, defaultContext, false).
getAndSetCurrentContext(SessionControl, Item, PageContext, ItemContext, boolean) - Static method in class net.sf.basedb.clients.web.Base: Same as: getAndSetCurrentContext(sc, itemType, "", pageContext, 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 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 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 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.
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 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 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(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 net.sf.basedb.core.VirtualTable
getBytesPerRow(VirtualDb) - Method in enum 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.
getCell(int, int) - Method in class net.sf.basedb.util.excel.XlsxToCsvUtil.SheetInfo: Get the cell at the specified row and column.
getCellClass() - Method in class net.sf.basedb.clients.web.extensions.list.AbstractListColumnBean
getCellClass() - Method in interface net.sf.basedb.clients.web.extensions.list.ListColumnAction: Optional extra classes to add to table cell (td) tags for this column.
getCellStyle() - Method in class net.sf.basedb.clients.web.extensions.list.AbstractListColumnBean
getCellStyle() - Method in interface net.sf.basedb.clients.web.extensions.list.ListColumnAction: Optional extra style definition to add to table cell (td) tags for this column.
getCellStyle(String) - Method in class net.sf.basedb.util.excel.CellStyleCreator: Get the cell style for the given format string.
getCellStyleCreator() - Method in class net.sf.basedb.util.excel.XlsxTableWriter: Get the style creator that can be used for custom styling of cells.
getCellValueAsDate(Cell, Formatter<Date>, boolean) - Method in class net.sf.basedb.util.excel.XlsxToCsvUtil.SheetInfo: Get the cell value as a date.
getCellValueAsNumber(Cell, NumberFormat, boolean) - Method in class net.sf.basedb.util.excel.XlsxToCsvUtil.SheetInfo: Get the cell value as a number.
getCellValueAsString(Cell) - Method in class net.sf.basedb.util.excel.XlsxToCsvUtil.SheetInfo: Get the the cell value as a string.
getCertificate(InputStream, String, String) - Static method in class net.sf.basedb.util.ssl.SSLUtil2: Get the certificate that is found in the given input stream.
getCertificateChain(String) - Method in class net.sf.basedb.util.ssl.StaticKeyManager
getChangeHistory() - Method in class net.sf.basedb.core.data.ChangeHistoryDetailData: Get the main history entry the details belong to.
getChangeInfo() - Method in class net.sf.basedb.core.ChangeHistory: Get some additional free-text information about the change.
getChangeInfo() - Method in class net.sf.basedb.core.data.ChangeHistoryDetailData: Get more information about this change.
getChangesBy(Job) - Static method in class net.sf.basedb.core.ChangeHistory: Get all changes made by the specified job.
getChangesBy(User) - Static method in class net.sf.basedb.core.ChangeHistory: Get all changes made by the specified user.
getChangesIn(Session) - Static method in class net.sf.basedb.core.ChangeHistory: Get all changes made in the specified session.
getChangeType() - Method in class net.sf.basedb.core.ChangeHistory: Get the type of change that was made.
getChangeType() - Method in class net.sf.basedb.core.data.ChangeHistoryDetailData: The type of the change: 1 = create, 2 = update, 3 = delete
getChangeType() - Method in class net.sf.basedb.core.log.EntityDetails: Was it a creation/update/deletion?
getChangeType() - Method in class net.sf.basedb.core.log.ManualLogEntry: Get the change type.
getChannel() - Method in class net.sf.basedb.core.RawDataProperty: Get the channel this property belongs to.
getChannels() - Method in class net.sf.basedb.core.data.FormulaData: The number of required channels in the experiment to use this formula, or 0 if the number of channels doesn't matter.
getChannels() - Method in class net.sf.basedb.core.data.PlatformData: The number of channels this platform uses.
getChannels() - Method in class net.sf.basedb.core.data.PlatformVariantData: The number of channels this platform variant uses.
getChannels() - Method in class net.sf.basedb.core.Formula: Get the number of channels required to be able to use this formula.
getChannels() - Method in class net.sf.basedb.core.RawDataType: The number of channels in this raw data type.
getCharacterSet() - Method in class net.sf.basedb.core.data.FileData: Get the character set used in this file (for text-files only).
getCharacterSet() - Method in class net.sf.basedb.core.File: Get the character set used in this file (for text-files only).
getCharacterSet() - Method in class net.sf.basedb.core.plugin.ImportInputStream: Get the character set used by the source if it is a text-file.
getCharacterSet() - Method in class net.sf.basedb.util.FileImportInputStream: Calls File.getCharacterSet(), unless a character set was specified in the constructor.
getCharacterSet() - Method in class net.sf.basedb.util.importer.BaseFileWrapper
getCharacterSet() - Method in class net.sf.basedb.util.importer.DiskFileWrapper
getCharacterSet() - Method in interface net.sf.basedb.util.importer.FileWrapper: Get the character set used in the file.
getCharacterSet() - Method in class net.sf.basedb.util.importer.spotdata.BaseFileInfo: Get the character set used by the file, or null if not known.
getCharacterSet() - Method in class net.sf.basedb.util.uri.UriMetadata: Get the character set used by the resource.
getCharset() - Static method in class net.sf.basedb.core.Config: Get the default character set to use when no other has been specified.
getCharset() - Method in class net.sf.basedb.core.File.CharsetTesterThread
getCharset() - Method in class net.sf.basedb.plugins.AbstractFlatFileImporter: Get the character set the file uses.
getCharset() - Method in class net.sf.basedb.util.charset.CharsetDetector: Get the character set this detector is configured to use.
getCharset() - Method in class net.sf.basedb.util.excel.XlsxToCsvUtil: Get the current character set.
getCharset(String) - Static method in class net.sf.basedb.util.charset.CharsetUtil: Get a character set by name.
getCharset(Request) - Method in class net.sf.basedb.plugins.AbstractFlatFileImporter: Get the character set the file uses.
getChart() - Method in class net.sf.basedb.util.plot.HistogramPlot: Get the underlying JFreeChar object.
getChart() - Method in class net.sf.basedb.util.plot.ScatterPlot: Get the underlying JFreeChar object.
getChild() - Method in class net.sf.basedb.util.importer.spotdata.BaseFileInfo.ChildBioAssay: Get the real child bioassay object once it has been created and scheduled for saving into the database.
getChild(String) - Method in class net.sf.basedb.util.overview.Node: Get the child node with a specific name.
getChildAssay(int) - Method in class net.sf.basedb.util.importer.spotdata.BaseFileInfo: Get the child bioassay with the given id (from the BASEfile).
getChildAssays() - Method in class net.sf.basedb.util.importer.spotdata.BaseFileInfo: Get information about all child bioassays referenced in the file.
getChildColumns(short) - Method in class net.sf.basedb.util.importer.spotdata.BaseFileInfo: Get all child columns that have been mapped to the specified parent column.
getChildCreationEvents() - Method in class net.sf.basedb.core.BioMaterial: Get a query returning all events where this biomaterial has been used as a source item.
getChildCreationEvents() - Method in class net.sf.basedb.core.data.BioMaterialData: This is the inverse end.
getChildDescriptionParameter(String, String, String) - Method in class net.sf.basedb.core.plugin.AbstractAnalysisPlugin: Create a plugin parameter that asks for the description of the child bioassay set.
getChildErrors() - Method in class net.sf.basedb.util.overview.Node: Get the number of errors to children of this node.
getChildExtracts() - Method in class net.sf.basedb.core.Extract: Creates a query that returns all child (pooled) extracts that has this extracts as one of it's sources.
getChildHasDifferentReporterPositionMapping() - Method in class net.sf.basedb.util.importer.spotdata.BaseFileInfo: A flag that indicates if the child data has a different position/reporter mapping than the parent bioassay set.
getChildId() - Method in class net.sf.basedb.core.data.keyring.GroupGroups: Get the id of the child group.
getChildNameParameter(String, String, String) - Method in class net.sf.basedb.core.plugin.AbstractAnalysisPlugin: Create a plugin parameter that asks for the name of the child bioassay set.
getChildNodeDirection() - Method in class net.sf.basedb.util.overview.Node: Get the direction to use when loading children of this node.
getChildPlates() - Method in class net.sf.basedb.core.Plate: Get a query returning the child plates of this plate.
getChildren() - Method in class net.sf.basedb.clients.web.ExperimentExplorer.InExpression
getChildren() - Method in class net.sf.basedb.core.AnnotationRestriction
getChildren() - Method in class net.sf.basedb.core.AnnotationSet.ProjectSpecificAnnotationsRestriction
getChildren() - Method in class net.sf.basedb.core.data.BioAssayData: This is the inverse end to BioAssayData.getParents().
getChildren() - Method in class net.sf.basedb.core.data.BioMaterialData: This is the inverse end.
getChildren() - Method in class net.sf.basedb.core.data.DerivedBioAssayData: This is the inverse end.
getChildren() - Method in class net.sf.basedb.core.data.GroupData: Get the set that manages which other groups are members of this group.
getChildren() - Method in class net.sf.basedb.core.data.PlateData: The childs plates created by plate mappings.
getChildren() - Method in class net.sf.basedb.core.DerivedBioAssay: Get all child derived bioassays.
getChildren() - Method in class net.sf.basedb.core.DynamicJoin
getChildren() - Method in class net.sf.basedb.core.DynamicRestriction
getChildren() - Method in class net.sf.basedb.core.ExtraValueExpression
getChildren() - Method in class net.sf.basedb.core.ExtraValueJoin
getChildren() - Method in class net.sf.basedb.core.MeanRawDataPropertyExpression
getChildren() - Method in class net.sf.basedb.core.query.AbsExpression
getChildren() - Method in class net.sf.basedb.core.query.AddExpression
getChildren() - Method in class net.sf.basedb.core.query.AndRestriction
getChildren() - Method in class net.sf.basedb.core.query.AnnotationJoin
getChildren() - Method in class net.sf.basedb.core.query.AnyToAnyRestriction
getChildren() - Method in class net.sf.basedb.core.query.AscOrder
getChildren() - Method in class net.sf.basedb.core.query.BetweenRestriction
getChildren() - Method in class net.sf.basedb.core.query.BooleanExpression
getChildren() - Method in class net.sf.basedb.core.query.CaseExpression
getChildren() - Method in class net.sf.basedb.core.query.ConditionalQueryElement
getChildren() - Method in class net.sf.basedb.core.query.CountExpression
getChildren() - Method in class net.sf.basedb.core.query.DescOrder
getChildren() - Method in class net.sf.basedb.core.query.DivideExpression
getChildren() - Method in class net.sf.basedb.core.query.EqRestriction
getChildren() - Method in class net.sf.basedb.core.query.ExpExpression
getChildren() - Method in class net.sf.basedb.core.query.ExpressionSelect
getChildren() - Method in class net.sf.basedb.core.query.FloatExpression
getChildren() - Method in class net.sf.basedb.core.query.GeometricMeanExpression
getChildren() - Method in class net.sf.basedb.core.query.GteqRestriction
getChildren() - Method in class net.sf.basedb.core.query.GtRestriction
getChildren() - Method in class net.sf.basedb.core.query.HqlElementsExpression
getChildren() - Method in class net.sf.basedb.core.query.HqlEntityExpression
getChildren() - Method in class net.sf.basedb.core.query.HqlEntityParameterExpression
getChildren() - Method in class net.sf.basedb.core.query.HqlExpression
getChildren() - Method in class net.sf.basedb.core.query.HqlIndexExpression
getChildren() - Method in class net.sf.basedb.core.query.HqlInnerJoin
getChildren() - Method in class net.sf.basedb.core.query.HqlLeftJoin
getChildren() - Method in class net.sf.basedb.core.query.HqlPropertyExpression
getChildren() - Method in class net.sf.basedb.core.query.HqlRightJoin
getChildren() - Method in class net.sf.basedb.core.query.HqlSizeExpression
getChildren() - Method in class net.sf.basedb.core.query.IdListRestriction
getChildren() - Method in class net.sf.basedb.core.query.InRestriction
getChildren() - Method in class net.sf.basedb.core.query.IntegerExpression
getChildren() - Method in class net.sf.basedb.core.query.LikeRestriction
getChildren() - Method in class net.sf.basedb.core.query.LogExpression
getChildren() - Method in class net.sf.basedb.core.query.LteqRestriction
getChildren() - Method in class net.sf.basedb.core.query.LtRestriction
getChildren() - Method in class net.sf.basedb.core.query.MaxExpression
getChildren() - Method in class net.sf.basedb.core.query.MeanExpression
getChildren() - Method in class net.sf.basedb.core.query.MinExpression
getChildren() - Method in class net.sf.basedb.core.query.MultiplyExpression
getChildren() - Method in class net.sf.basedb.core.query.NegateExpression
getChildren() - Method in class net.sf.basedb.core.query.NeqRestriction
getChildren() - Method in class net.sf.basedb.core.query.NotRestriction
getChildren() - Method in class net.sf.basedb.core.query.OrRestriction
getChildren() - Method in class net.sf.basedb.core.query.ParameterExpression
getChildren() - Method in class net.sf.basedb.core.query.PermissionRestriction
getChildren() - Method in class net.sf.basedb.core.query.PowerExpression
getChildren() - Method in class net.sf.basedb.core.query.QuadraticMeanExpression
getChildren() - Method in interface net.sf.basedb.core.query.QueryElement: Get the children of this query element or null if it has no children.
getChildren() - Method in class net.sf.basedb.core.query.ReporterListExpression
getChildren() - Method in class net.sf.basedb.core.query.RlikeRestriction
getChildren() - Method in class net.sf.basedb.core.query.SelectedExpression
getChildren() - Method in class net.sf.basedb.core.query.SharedToRestriction
getChildren() - Method in class net.sf.basedb.core.query.SqlColumnExpression
getChildren() - Method in class net.sf.basedb.core.query.SqrtExpression
getChildren() - Method in class net.sf.basedb.core.query.SubqueryExpression
getChildren() - Method in class net.sf.basedb.core.query.SubtractExpression
getChildren() - Method in class net.sf.basedb.core.query.SumExpression
getChildren() - Method in class net.sf.basedb.core.query.ToDateExpression
getChildren() - Method in class net.sf.basedb.core.query.VirtualColumnExpression
getChildren() - Method in class net.sf.basedb.core.query.VirtualColumnExpression.WrappedExpression
getChildren() - Method in class net.sf.basedb.core.RawBioAssayPropertyExpression
getChildren() - Method in class net.sf.basedb.core.RawDataPropertyExpression
getChildren() - Method in class net.sf.basedb.core.RealJoin
getChildren() - Method in class net.sf.basedb.core.ReporterListJoin
getChildren() - Method in class net.sf.basedb.core.ReporterPropertyExpression
getChildren() - Method in class net.sf.basedb.util.overview.Node: Get all child nodes of this node.
getChildren() - Method in class net.sf.basedb.util.Tree.Entry: Get the list of entries for the children to this node.
getChildReporterPositions() - Method in class net.sf.basedb.util.importer.spotdata.BaseFileInfo: Get a map with all added child position/reporter mappings.
getChildSamples() - Method in class net.sf.basedb.core.Sample: Creates a query that returns all child (pooled) samples that has this sample as one of it's sources.
getChildWarnings() - Method in class net.sf.basedb.util.overview.Node: Get the number of warnings to children of this node.
getCircularRef(Node, BasicItem) - Static method in class net.sf.basedb.util.overview.OverviewUtil: Find the first parent node that has a reference to the given item.
getCity() - Method in class net.sf.basedb.util.GeoLocation
getClasses() - Static method in class net.sf.basedb.core.ExtendedProperties: Get a list with the name of all classes.
getClassLoader() - Method in class net.sf.basedb.core.hibernate.SessionFactoryConfiguration: Deprecated.

Get the schema.
getClassLoader() - Method in class net.sf.basedb.core.ServiceSessionControl.SessionFactoryConfiguration: Get the class loader used for accessing mapped classes.
getClassLoader() - Method in class net.sf.basedb.util.extensions.ExtensionContext: The class loader is the class loader that loaded the action factory of the extension.
getClassLoader() - Method in class net.sf.basedb.util.extensions.ExtensionPointContext: The class loader is the class loader that loaded the action class of the extension point.
getClassLoader() - Method in class net.sf.basedb.util.extensions.InvokationContext: Get the class loader that is used for the given extension or extension point.
getClassLoader() - Method in class net.sf.basedb.util.extensions.manager.ExtensionsFile: Get the class loader used to load classes for the extension.
getClassLoader() - Method in class net.sf.basedb.util.extensions.Registry.RegisteredExtension
getClassLoader() - Method in class net.sf.basedb.util.extensions.Registry.RegisteredExtensionPoint
getClassMapping(String) - Static method in class net.sf.basedb.core.HibernateUtil
getClassMappings() - Static method in class net.sf.basedb.core.HibernateUtil
getClassMetadata(String) - Static method in class net.sf.basedb.core.HibernateUtil
getClassName() - Method in class net.sf.basedb.core.data.PluginDefinitionData: Get the class name of the Java class that implements this plugin.
getClassName() - Method in class net.sf.basedb.core.PluginDefinition: Get the class name of the Java class that implements this plugin.
getClassName() - Method in class net.sf.basedb.util.extensions.xml.PluginInfo: Get the class name of the plug-in.
getClazz() - Method in class net.sf.basedb.clients.web.extensions.list.AbstractListColumnBean
getClazz() - Method in interface net.sf.basedb.clients.web.extensions.list.ListColumnAction: Optional HTML class attribute that is used to style the column through CSS.
getClazz() - Method in class net.sf.basedb.clients.web.extensions.login.FieldInfo: Get a class attribute that can used to style the input field.
getClazz() - Method in class net.sf.basedb.clients.web.extensions.menu.FixedMenuItemFactory
getClazz() - Method in interface net.sf.basedb.clients.web.extensions.menu.MenuItemAction: Class attribute to add to the main menu tag.
getClazz() - Method in class net.sf.basedb.clients.web.extensions.menu.MenuItemBean
getClazz() - Method in class net.sf.basedb.clients.web.extensions.tabcontrol.FixedTabFactory
getClazz() - Method in class net.sf.basedb.clients.web.extensions.tabcontrol.IncludeContentTabFactory.Tab
getClazz() - Method in interface net.sf.basedb.clients.web.extensions.tabcontrol.TabAction: Class attribute of the main tab tag.
getClazz() - Method in class net.sf.basedb.clients.web.extensions.tabcontrol.TabBean
getClazz() - Method in interface net.sf.basedb.clients.web.extensions.toolbar.ButtonAction: Class attribute of the main button tag.
getClazz() - Method in class net.sf.basedb.clients.web.extensions.toolbar.ButtonBean
getClazz() - Method in class net.sf.basedb.clients.web.extensions.toolbar.FixedButtonFactory
getClazz() - Method in class net.sf.basedb.clients.web.taglib.Body
getClazz() - Method in class net.sf.basedb.clients.web.taglib.ExceptionCatcher
getClazz() - Method in class net.sf.basedb.clients.web.taglib.StylableTag
getClazz() - Method in class net.sf.basedb.clients.web.taglib.tab.Tab
getClazz() - Method in class net.sf.basedb.clients.web.taglib.table.Button.ButtonActionWrapper
getClazz() - Method in class net.sf.basedb.clients.web.taglib.table.Cell
getClazz() - Method in class net.sf.basedb.clients.web.taglib.table.CellValue
getClearState() - Method in class net.sf.basedb.core.PluginResponse: If set after a job configuration sequence, the saved state should be cleared before starting the job.
getClient() - Method in class net.sf.basedb.core.ClientDefaultSetting: Get the client application this setting is valid for.
getClient() - Method in class net.sf.basedb.core.data.ChangeHistoryData
getClient() - Method in class net.sf.basedb.core.data.ClientDefaultSettingData: Get the client application this setting is valid for.
getClient() - Method in class net.sf.basedb.core.data.ContextData: Get the client which uses this context.
getClient() - Method in class net.sf.basedb.core.data.ContextIndex: Get the client which uses this context.
getClient() - Method in class net.sf.basedb.core.data.HelpData: Get the client for this help text.
getClient() - Method in class net.sf.basedb.core.data.SessionData: Get the client application the user was using.
getClient() - Method in class net.sf.basedb.core.data.UserClientSettingData: Get the client application this setting is valid for.
getClient() - Method in class net.sf.basedb.core.data.UserDeviceData: Get the client application this device is associated with.
getClient() - Method in class net.sf.basedb.core.Help: Get the client application this setting is valid for.
getClient() - Method in class net.sf.basedb.core.Session: Get the client application the user was using in this session.
getClient() - Method in class net.sf.basedb.core.UserClientSetting: Get the client application this setting is valid for.
getClient() - Method in class net.sf.basedb.core.UserDevice: Get the client application the user was using with this device.
getClient(DbControl) - Method in class net.sf.basedb.core.ChangeHistory: Load the client application that was used when the change was made.
getClient(DbControl) - Method in class net.sf.basedb.core.ChangeHistory.TransactionInfo: Load the client application that was used in the transaction.
getClient(DbControl, ChangeHistory, boolean, boolean) - Static method in class net.sf.basedb.clients.web.ChangeHistoryUtil: Get the client application that was used to make the change in HTML format.
getClientAliases(String, Principal[]) - Method in class net.sf.basedb.util.ssl.StaticKeyManager
getClientCertificate() - Method in class net.sf.basedb.core.data.FileServerData: Get the client certificate that we need to send to the server to make the server accept our connection.
getClientCertificate() - Method in class net.sf.basedb.core.FileServer: Get the client certificate that BASE should use to authenticate with the server when connecting with https.
getClientCertificate() - Method in class net.sf.basedb.util.uri.ConnectionParameters: Get the client certificate that BASE should use to authenticate with the server when connecting using SSL.
getClientCertificatePassword() - Method in class net.sf.basedb.core.data.FileServerData: Get the password that is used to unlock the client certificate.
getClientCertificatePassword() - Method in class net.sf.basedb.core.FileServer: Get the password that is needed to unlock the client certificate.
getClientCertificatePassword() - Method in class net.sf.basedb.util.uri.ConnectionParameters: Get the password that is needed to unlock the client certificate.
getClientContext() - Method in class net.sf.basedb.util.extensions.ExtensionContext
getClientContext() - Method in class net.sf.basedb.util.extensions.ExtensionPointContext
getClientContext() - Method in class net.sf.basedb.util.extensions.ExtensionsInvoker: Get the client context that is used by this invoker.
getClientContext() - Method in class net.sf.basedb.util.extensions.InvokationContext: Get the client context that was passed to the Registry.useExtensions(ClientContext, ExtensionsFilter, String...) method.
getClientDefaultSetting(String) - Method in class net.sf.basedb.core.SessionControl: Get the value of the ClientDefaultSetting with the specified name.
getClientId() - Method in class net.sf.basedb.core.ChangeHistory: Get the ID of the client application that was used to make the change.
getClientId() - Method in class net.sf.basedb.core.ChangeHistory.TransactionInfo: Get the ID of the client application that was used in the transaction.
getClientId() - Method in class net.sf.basedb.core.data.ChangeHistoryData: The ID of the client application the user used to make the change.
getClientId() - Method in class net.sf.basedb.core.log.TransactionDetails: Get the ID of the client appliction that is used, or 0 if not known.
getClientId() - Method in class net.sf.basedb.core.SessionControl: Get the id of the Client application that created this SessionControl.
getClientName() - Method in class net.sf.basedb.core.SessionControl: Get the name of the Client application that created this SessionControl.
getClientSettings() - Method in class net.sf.basedb.core.data.UserData: This is the inverse end.
getClientSettings(Client) - Method in class net.sf.basedb.core.User: Get a query that returns the settings for the specified client.
getClientWithExternalId(String) - Method in class net.sf.basedb.core.SessionControl
getClientX509Certificate() - Method in class net.sf.basedb.core.FileServer: Get the X.509 certificate for the client.
getClonableProperties() - Method in class net.sf.basedb.core.ReporterCloneTemplate: Get a list with all clonable properties in this template.
getClonableProperties(ReporterCloneTemplateData) - Static method in class net.sf.basedb.core.ReporterCloneTemplate
getClonableProperty(String) - Method in class net.sf.basedb.core.ReporterCloneTemplate: Get information about a clonable property that is included in this template.
getClone() - Method in class net.sf.basedb.util.annotations.InheritSpecification
getClonedSelectSql(VirtualDb) - Static method in class net.sf.basedb.core.Reporter: Generate an SQL statement for selecting ALL reporter properties from a cloned table.
getCmd() - Method in class net.sf.basedb.clients.jobagent.CmdLine: Get the command parameter
getCollected() - Method in class net.sf.basedb.util.listable.CollectExtracts: Get all extracts that has been collected.
getCollectedChildren() - Method in class net.sf.basedb.util.listable.CollectExtracts: Get child extracts that was collected by the CollectExtracts.collectChildrenOfCollected(boolean) and/or CollectExtracts.collectChildrenOfSource(boolean) collectors.
getCollectedParents() - Method in class net.sf.basedb.util.listable.CollectExtracts: Get parent extracts that was collected by the CollectExtracts.collectParentsOfSource(boolean) or CollectExtracts.collectParentsOfCollected(boolean) collector.
getCollectionFormatter() - Method in class net.sf.basedb.clients.web.extensions.list.AbstractListColumnBean
getCollectionFormatter() - Method in interface net.sf.basedb.clients.web.extensions.list.ListColumnAction: Get a formatter that is intended to format a collection of values that have been retrieved from this action.
getCollectionSeparatorParameter() - Method in class net.sf.basedb.clients.web.plugins.SimpleExport
getColor() - Method in class net.sf.basedb.clients.web.ExperimentExplorer.AnnotationGroup: Get a color code for HTML that is as distinct as possible from the color of the other groups.
getColor(float) - Method in class net.sf.basedb.util.ColorGenerator: Get the color for the value.
getColor(String) - Method in class net.sf.basedb.clients.web.servlet.ExperimentExplorerPlotServlet.ColumnKey
getColorFormatter(SessionControl, Coloring, Formatter<Number>) - Static method in class net.sf.basedb.clients.web.formatter.FormatterFactory: Get a formatter that adds a color box to the display which is a visual representation of the value.
getColorGenerator(SessionControl, Coloring) - Static method in class net.sf.basedb.clients.web.Base
getColoring() - Method in class net.sf.basedb.core.data.ExtraValueTypeData: Get the coloring information for this extra value type.
getColoring() - Method in class net.sf.basedb.core.data.FormulaData: Get the coloring information for this formula.
getColoring() - Method in class net.sf.basedb.core.ExtraValueType: Get coloring information for this extra value.
getColoring() - Method in class net.sf.basedb.core.Formula: Get coloring information for this formula.
getColspan() - Method in class net.sf.basedb.clients.web.taglib.table.Header
getColumn() - Method in class net.sf.basedb.clients.web.taglib.table.Cell
getColumn() - Method in class net.sf.basedb.core.BioWell: Gets the column index where this well is located.
getColumn() - Method in class net.sf.basedb.core.data.BioWellData: The column coordinate of this well.
getColumn() - Method in class net.sf.basedb.core.data.FeatureData: Get the column coordinate of the feature.
getColumn() - Method in class net.sf.basedb.core.data.MappingCoordinate: Get the column number.
getColumn() - Method in class net.sf.basedb.core.data.PlateCoordinate: Get the column number.
getColumn() - Method in class net.sf.basedb.core.data.RawData
getColumn() - Method in class net.sf.basedb.core.data.ReporterClonePropertyData: Get the name of database column.
getColumn() - Method in class net.sf.basedb.core.data.WellData: The column coordinate of this well.
getColumn() - Method in class net.sf.basedb.core.ExtendedProperty: Get the database column of the extended property.
getColumn() - Method in class net.sf.basedb.core.FeatureCoordinate
getColumn() - Method in class net.sf.basedb.core.VirtualColumn: Get the database column name of the column.
getColumn() - Method in class net.sf.basedb.core.Well: Get the column coordinate of this well on the plate.
getColumn(String) - Static method in class net.sf.basedb.core.RawBioAssayPropertyExpression
getColumn(String) - Static method in class net.sf.basedb.core.ReporterPropertyExpression
getColumn(RawDataType, String) - Static method in class net.sf.basedb.core.RawDataPropertyExpression: Get the database column name for the specified property of the specified raw data type.
getColumnContent() - Method in class net.sf.basedb.clients.web.taglib.table.Table
getColumnCount() - Method in class net.sf.basedb.util.bfs.AnnotationModel: Get the number of column.
getColumnCount() - Method in class net.sf.basedb.util.bfs.AnnotationWriter: Get the number of data columns.
getColumnCount() - Method in class net.sf.basedb.util.bfs.DataWriter: Get the number of data columns.
getColumnCount() - Method in class net.sf.basedb.util.bfs.MatrixModel: Get the number of columns.
getColumnFormatter(int) - Method in class net.sf.basedb.util.export.TableWriter
getColumnHeaderIndex(String) - Method in class net.sf.basedb.util.parser.FlatFileParser: Get the index of a column header with a given name.
getColumnHeaders() - Method in class net.sf.basedb.util.parser.FlatFileParser: Get all column headers that were found by splitting the line matching the FlatFileParser.setDataHeaderRegexp(Pattern) pattern using the FlatFileParser.setDataSplitterRegexp(Pattern) pattern.
getColumnIndex(String) - Method in class net.sf.basedb.util.bfs.AnnotationModel: Get the column index for a given header.
getColumnMappingParameterName() - Method in class net.sf.basedb.plugins.batchimport.AnnotationIdMethod
getColumnMappingParameterName() - Method in class net.sf.basedb.plugins.batchimport.FallbackIdMethod
getColumnMappingParameterName() - Method in class net.sf.basedb.plugins.batchimport.FileImporter.PathIdMethod
getColumnMappingParameterName() - Method in interface net.sf.basedb.plugins.batchimport.IdMethod
getColumnMappingParameterName() - Method in class net.sf.basedb.plugins.batchimport.InternalIdMethod
getColumnMappingParameterName() - Method in class net.sf.basedb.plugins.batchimport.MultiPropertyIdMethod
getColumnMappingParameterName() - Method in class net.sf.basedb.plugins.batchimport.PropertyIdMethod
getColumnName(RawDataProperty, RawBioAssay) - Static method in class net.sf.basedb.plugins.IlluminaRawDataImporter: Convert a raw data property to a column name.
getColumnNo() - Method in class net.sf.basedb.core.data.DataCubeColumnData: The column number of this column in the data cube.
getColumnNo() - Method in class net.sf.basedb.core.DataCubeColumn: Get the number of this column.
getColumnPrefixParameter() - Method in class net.sf.basedb.clients.web.plugins.SimpleExport
getColumnRestriction(PropertyFilter) - Method in interface net.sf.basedb.core.query.QueryFilterAction: Generate a restriction for the given filter.
getColumns() - Method in class net.sf.basedb.clients.web.taglib.table.Table
getColumns() - Method in class net.sf.basedb.core.BioPlate: Get the number of rows on this plate.
getColumns() - Method in class net.sf.basedb.core.data.DataCubeData: This is the inverse end.
getColumns() - Method in class net.sf.basedb.core.data.PlateGeometryData: The number of rows in this geometry.
getColumns() - Method in class net.sf.basedb.core.dbengine.TableInfo: Get information about the columns in the table.
getColumns() - Method in class net.sf.basedb.core.dbengine.TableInfo.IndexInfo
getColumns() - Method in class net.sf.basedb.core.dbengine.TableInfo.PrimaryKeyInfo
getColumns() - Method in class net.sf.basedb.core.PlateGeometry: Get the number of columns in this geometry.
getColumns(Experiment) - Method in enum net.sf.basedb.core.VirtualTable: Get all columns in this table.
getColumns(VirtualDb) - Method in enum net.sf.basedb.core.VirtualTable: Get all columns in this table.
getColumnSeparator() - Method in class net.sf.basedb.util.excel.XlsxToCsvUtil: Get the current column separator.
getColumnsFile(TableInfo) - Method in class net.sf.basedb.core.Migration: Get the columns file for the given table.
getColumnSubtitles() - Method in class net.sf.basedb.clients.web.taglib.table.Table
getCommand() - Method in class net.sf.basedb.core.plugin.NamespaceRequestWrapper
getCommand() - Method in interface net.sf.basedb.core.plugin.Request: The command the plugin should execute.
getCommand() - Method in class net.sf.basedb.core.PluginRequest: Get the command this request will issue to the plugin when PluginRequest.invoke() is called.
getCommand() - Method in class net.sf.basedb.core.PluginRequest.RequestImpl
getCommand() - Method in class net.sf.basedb.core.RequestInformation: Get the command this request information object is valid for.
getCommand() - Method in class net.sf.basedb.plugins.executor.ExternalProgramExecutor.RequestWrapper
getComment() - Method in class net.sf.basedb.core.authentication.LoginRequest: Get the comment to use.
getComment() - Method in class net.sf.basedb.core.BioMaterialEvent: Get the comment about this event.
getComment() - Method in class net.sf.basedb.core.data.BioMaterialEventData: Get the comment about this event.
getComment() - Method in class net.sf.basedb.core.data.PlateEventData: Get the comment about this event.
getComment() - Method in class net.sf.basedb.core.hibernate.QueryWrapper
getComment() - Method in class net.sf.basedb.core.PlateEvent: Get the comment about this event.
getCommonCharsets() - Static method in class net.sf.basedb.core.Config: Get a set containing the most common character sets used by text files.
getCommonName() - Method in class net.sf.basedb.plugins.Base1PluginExecuter.JobParameter
getCommonPrefix(Collection<String>) - Static method in class net.sf.basedb.core.StringUtil: Find the longest common prefix for a collection of strings.
getCompleted() - Method in class net.sf.basedb.core.SimpleAbsoluteProgressReporter: Get completed number of ticks of the task.
getCompressedSize() - Method in class net.sf.basedb.core.data.FileData: Get the size in bytes that this FileData object uses after compression.
getCompressedSize() - Method in class net.sf.basedb.core.File: Get the compressed size of this file.
getCondition() - Method in class net.sf.basedb.core.dbengine.TableInfo.IndexInfo: If a condition is specificed a partial index is created for rows that matches the conditions.
getCondition() - Method in class net.sf.basedb.core.query.WhenStatement: Get the condition of this statement.
getConfigDirectory() - Static method in class net.sf.basedb.core.Config: Get the directory where the BASE configuration files are located.
getConfigurationInstallOption(int) - Method in class net.sf.basedb.plugins.PluginConfigurationImporter: Returns if a configuration in a certain place/order in the XML-file should be imported
getConfigurations() - Method in class net.sf.basedb.core.data.PluginDefinitionData: This is the inverse end.
getConfigurationValues() - Method in class net.sf.basedb.core.data.PluginConfigurationData: Used by Hibernate to link with configuration values.
getConfigurationValues() - Method in class net.sf.basedb.core.hibernate.SchemaGenerator.CollectSqlTarget
getConfiguredColors(SessionControl) - Static method in class net.sf.basedb.clients.web.Base
getConfiguredJobParameters() - Method in class net.sf.basedb.plugins.HelpImporter
getConfiguredJobParameters() - Method in class net.sf.basedb.plugins.PluginConfigurationImporter
getConfiguredQuery(DbControl, ItemContext, boolean, ItemQuery<T>, ModeInfo) - Static method in class net.sf.basedb.clients.web.Base: Deprecated.
In 3.18, use Base.getConfiguredQuery(DbControl, ItemContext, ClientContext, boolean, ItemQuery, ModeInfo) instead
getConfiguredQuery(DbControl, ItemContext, ClientContext, boolean, ItemQuery<T>, ModeInfo) - Static method in class net.sf.basedb.clients.web.Base: Configures a query.
getConfiguredSelectionParameters() - Method in class net.sf.basedb.plugins.PluginConfigurationImporter: Gets request information to set which configuration to import
getConfigureExecutorParameters(String) - Method in class net.sf.basedb.plugins.executor.BaseFileExporterSupport
getConfigureExecutorParameters(String) - Method in class net.sf.basedb.plugins.executor.BaseFileImporterSupport
getConfigureExecutorParameters(String) - Method in class net.sf.basedb.plugins.executor.BfsExporterSupport
getConfigureExecutorParameters(String) - Method in class net.sf.basedb.plugins.executor.BfsImporterSupport
getConfigureExecutorParameters(String) - Method in class net.sf.basedb.plugins.executor.FileOnlyImporterSupport
getConfigureExportImportPluginParameters() - Method in class net.sf.basedb.plugins.executor.ExternalProgramExecutor
getConfigureExternalParameters() - Method in class net.sf.basedb.plugins.executor.ExternalProgramExecutor
getConfigureImportParameters(GuiContext) - Method in class net.sf.basedb.plugins.AnnotationFlatFileImporter: Step 3 of 3.
getConfigureJobParameters() - Method in class net.sf.basedb.plugins.Base1PluginExecuter: Creates the information needed for job configuration and initiates the parameters.
getConfigureJobParameters() - Method in class net.sf.basedb.plugins.executor.ExternalProgramExecutor
getConfigureJobParameters() - Method in class net.sf.basedb.plugins.IntensityCalculatorPlugin
getConfigureJobParameters() - Method in class net.sf.basedb.plugins.JepExtraValueCalculator
getConfigureJobParameters() - Method in class net.sf.basedb.plugins.LowessNormalization
getConfigureJobParameters() - Method in class net.sf.basedb.plugins.MedianRatioNormalization
getConfigureJobParameters(Boolean) - Method in class net.sf.basedb.plugins.GalExporter
getConfigureJobParameters(Boolean) - Method in class net.sf.basedb.plugins.HelpExporter
getConfigureJobParameters(Boolean) - Method in class net.sf.basedb.plugins.PluginConfigurationExporter
getConfigureJobParameters(String) - Method in class net.sf.basedb.plugins.executor.BaseFileImporterSupport
getConfigureJobParameters(String) - Method in class net.sf.basedb.plugins.executor.BfsImporterSupport
getConfigureJobParameters(String) - Method in class net.sf.basedb.plugins.executor.FileOnlyImporterSupport
getConfigureJobParameters(GuiContext) - Method in class net.sf.basedb.clients.web.plugins.SimpleExport
getConfigureJobParameters(GuiContext) - Method in class net.sf.basedb.plugins.BfsExporterPlugin
getConfigureJobParameters(GuiContext) - Method in class net.sf.basedb.plugins.CdfFileReporterImporter
getConfigureJobParameters(GuiContext) - Method in class net.sf.basedb.plugins.FormulaFilter
getConfigureJobParameters(GuiContext) - Method in class net.sf.basedb.plugins.IlluminaRawDataImporter
getConfigureJobParameters(GuiContext) - Method in class net.sf.basedb.plugins.JepIntensityTransformer
getConfigureJobParameters(GuiContext) - Method in class net.sf.basedb.plugins.ManualDerivedBioAssayCreator
getConfigureJobParameters(GuiContext) - Method in class net.sf.basedb.plugins.ManualTransformCreator
getConfigureJobParameters(GuiContext) - Method in class net.sf.basedb.plugins.PlateFlatFileImporter
getConfigureJobParameters(GuiContext) - Method in class net.sf.basedb.plugins.PlateMappingImporter
getConfigureJobParameters(GuiContext) - Method in class net.sf.basedb.plugins.PrintMapFlatFileImporter
getConfigureJobParameters(GuiContext) - Method in class net.sf.basedb.plugins.RawDataFlatFileImporter
getConfigureJobParameters(GuiContext) - Method in class net.sf.basedb.plugins.ReporterFlatFileImporter
getConfigureJobParameters(GuiContext) - Method in class net.sf.basedb.plugins.ReporterMapFlatFileImporter
getConfigureJobParameters(GuiContext) - Method in class net.sf.basedb.util.zip.AbstractFileUnpacker
getConfigureJobParameters(GuiContext, Boolean) - Method in class net.sf.basedb.plugins.BaseFileExporterPlugin
getConfigureJobParameters(GuiContext, Boolean) - Method in class net.sf.basedb.plugins.PackedFileExporter
getConfigureJobParameters(GuiContext, Boolean) - Method in class net.sf.basedb.plugins.PlateMappingExporter
getConfigureMappingParameters(GuiContext) - Method in class net.sf.basedb.plugins.AnnotationFlatFileImporter: Step 2 of 3.
getConfigureOptionsParameters(GuiContext) - Method in class net.sf.basedb.plugins.batchimport.AbstractItemImporter
getConfigureOptionsParameters(GuiContext) - Method in class net.sf.basedb.plugins.batchimport.AnyToAnyImporter
getConfigureParserParameters(GuiContext, boolean) - Method in class net.sf.basedb.plugins.AnnotationFlatFileImporter
getConfigureParserParameters(GuiContext, boolean) - Method in class net.sf.basedb.plugins.batchimport.AbstractItemImporter
getConfigureParserParameters(GuiContext, boolean) - Method in class net.sf.basedb.plugins.batchimport.AnyToAnyImporter
getConfigureParserParameters(RawDataType) - Method in class net.sf.basedb.plugins.RawDataFlatFileImporter
getConfigurePluginParameters() - Method in class net.sf.basedb.plugins.Base1PluginExecuter: Creates the information needed for plugin configuration and initiates the parameters.
getConfigurePluginParameters() - Method in class net.sf.basedb.plugins.executor.ExternalProgramExecutor
getConfigurePluginParameters() - Method in class net.sf.basedb.plugins.PackedFileExporter
getConfigurePluginParameters(GuiContext) - Method in class net.sf.basedb.plugins.gtf.GtfReporterMapImporter
getConfigurePluginParameters(GuiContext) - Method in class net.sf.basedb.plugins.ManualDerivedBioAssayCreator
getConfigurePluginParameters(GuiContext) - Method in class net.sf.basedb.plugins.ManualTransformCreator
getConfigurePluginParameters(GuiContext) - Method in class net.sf.basedb.plugins.PlateFlatFileImporter
getConfigurePluginParameters(GuiContext) - Method in class net.sf.basedb.plugins.ReporterFlatFileImporter
getConfigurePluginParameters(GuiContext) - Method in class net.sf.basedb.plugins.ReporterMapFlatFileImporter
getConfigureRawDataTypeParameters() - Method in class net.sf.basedb.plugins.RawDataFlatFileImporter
getConnection(Integer) - Method in class net.sf.basedb.core.JobAgent: Get a connection object for connecting to the job agent.
getConnection(Session) - Static method in class net.sf.basedb.core.HibernateUtil: Get the underlying JDBC connection from the Hibernate session.
getConnectionManagerFactory() - Method in class net.sf.basedb.core.data.FileServerData: Get the ID of the connection manager factory that should be used to retreieve the file contents and metadata.
getConnectionManagerFactoryId() - Method in class net.sf.basedb.core.FileServer: Get the ID of the connection manager factory that should be used to access file contents and metadata.
getConnectionManagerFactoryId() - Method in class net.sf.basedb.util.uri.ConnectionParameters: Get the connection manager factory that we should use to access the file, or null to use auto-detection.
getConnectionProperties() - Static method in class net.sf.basedb.core.HibernateUtil: Read database configuration properties from the base.config file and map them to Hibernate settings.
getConstructor() - Method in enum 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, "")
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
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(Item) - Method in class net.sf.basedb.core.SessionControl: Same as: getCurrentContext(item, "", 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, "", 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.
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 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.
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 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 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 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 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 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.
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.
getExportValue(RelatedItemHelper, Annotatable, SourceItemTransformer) - Method in class net.sf.basedb.clients.web.extensions.list.RelatedItemColumn: Alternate implementation for loading data.
getExportValue(RelatedItemHelper, Annotatable, SourceItemTransformer) - Method in class net.sf.basedb.clients.web.extensions.list.RelatedItemExtensionColumn
getExportValue(RelatedItemHelper, Annotatable, SourceItemTransformer) - Method in class net.sf.basedb.clients.web.extensions.list.RelatedItemMultiHopColumn
getExportValue(DbControl, I) - Method in class net.sf.basedb.clients.web.extensions.list.AbstractListColumnBean: This implementation simply forward to ListColumnAction.getValue(DbControl, Object).
getExportValue(DbControl, I) - Method in interface net.sf.basedb.clients.web.extensions.list.ListColumnAction: Get the value that should be used when exporting to a file.
getExportValue(DbControl, I) - Method in class net.sf.basedb.clients.web.extensions.list.PropertyPathActionFactory.PropertyPathAction
getExportValue(DbControl, Annotatable) - Method in class net.sf.basedb.clients.web.extensions.list.RelatedItemColumn: We finalize this implementation to make sure that the helper implementation always get a chance to re-cycle transactions.
getExpression() - Method in class net.sf.basedb.clients.web.extensions.list.RelatedItemColumn.Specification: Get the full expression that defines the targeted item and property.
getExpression() - Method in class net.sf.basedb.core.query.ExpressionSelect
getExpression() - Method in interface net.sf.basedb.core.query.Select: Get the expression object representing the selected expression.
getExpression() - Method in class net.sf.basedb.util.export.spotdata.SimpleDynamicField: Get the configured express.
getExpression(DbControl, DynamicQuery, BioAssaySet, boolean) - Method in class net.sf.basedb.plugins.BaseFileExporterPlugin.ExtendedDynamicField
getExpression(DbControl, DynamicQuery, BioAssaySet, boolean) - Method in interface net.sf.basedb.util.export.spotdata.DynamicField: Get an expression that selects the data that should be exported.
getExpression(DbControl, DynamicQuery, BioAssaySet, boolean) - Method in class net.sf.basedb.util.export.spotdata.JepDynamicField: Converts the configured JEP expression using the BioAssaySetUtil.createJepExpression(DbControl, String, DynamicQuery) method.
getExpression(DbControl, DynamicQuery, BioAssaySet, boolean) - Method in class net.sf.basedb.util.export.spotdata.SimpleDynamicField: Returns the configured expression.
getExpressions() - Method in class net.sf.basedb.core.IntensityFormula: Get the expressions used to calculate the intensities.
getExtended(String) - Method in class net.sf.basedb.core.authentication.ExtraUserInformation: Get an extended property value.
getExtended(String) - Method in interface net.sf.basedb.core.data.ExtendableData: Get the value of an extended property.
getExtended(String) - Method in class net.sf.basedb.core.data.RawData
getExtended(String) - Method in class net.sf.basedb.core.data.ReporterData
getExtended(String) - Method in class net.sf.basedb.core.data.UserData
getExtended(String) - Method in class net.sf.basedb.core.User: Gets an extended property with a certain name
getExtendedPropertyFiles() - Static method in class net.sf.basedb.core.Application: Get the path to the XML file containing extended properties.
getExtendedPropertyFormatter(SessionControl, ExtendedProperty) - Static method in class net.sf.basedb.clients.web.formatter.FormatterFactory: Get a formatter for an extended property.
getExtends() - Method in interface net.sf.basedb.util.extensions.Extension: Get the ID of the extension point this extension is extending.
getExtends() - Method in class net.sf.basedb.util.extensions.ExtensionBean
getExtends() - Method in class net.sf.basedb.util.extensions.Registry.RegisteredExtension
getExtension() - Method in class net.sf.basedb.clients.web.fileupload.UploadedFile: Get the extension of the original filename.
getExtension() - Method in class net.sf.basedb.core.data.DataFileTypeData: Get the extension that files of this type usually have.
getExtension() - Method in class net.sf.basedb.core.data.MimeTypeData: Get the extension for this MimeType item.
getExtension() - Method in class net.sf.basedb.core.DataFileType: Get the common file extension for data files of this type.
getExtension() - Method in class net.sf.basedb.core.MimeType: Get the extension for this MimeType item.
getExtension() - Method in class net.sf.basedb.util.extensions.ActionIterator: Get the extension that created the current action.
getExtension() - Method in class net.sf.basedb.util.extensions.ExtensionContext
getExtension() - Method in class net.sf.basedb.util.extensions.ExtensionPointContext: Always null, since this is an extension point context.
getExtension() - Method in class net.sf.basedb.util.extensions.InvokationContext: Get information about the extension.
getExtension(String) - Method in class net.sf.basedb.clients.web.extensions.ExtensionsControl: Get the extension with a given ID.
getExtension(String) - Method in class net.sf.basedb.util.extensions.Registry: Get the extension with a given ID.
getExtensionClassLoader() - Method in class net.sf.basedb.clients.web.extensions.XJspCompiler: Get a class loader that can load classes from the current web application as well as the extensions JAR file.
getExtensionColumns() - Method in class net.sf.basedb.clients.web.taglib.table.Table
getExtensionId() - Method in class net.sf.basedb.clients.web.extensions.list.RelatedItemColumn.Specification: Get the extension id from the expression.
getExtensionId() - Method in class net.sf.basedb.util.extensions.logging.ExtensionsLog: Get the extension id of the log.
getExtensionPoint() - Method in class net.sf.basedb.util.extensions.ActionIterator: Get the extension point that the current action belongs to.
getExtensionPoint() - Method in class net.sf.basedb.util.extensions.ExtensionContext
getExtensionPoint() - Method in class net.sf.basedb.util.extensions.ExtensionPointContext
getExtensionPoint() - Method in class net.sf.basedb.util.extensions.InvokationContext: Get information about the extension point.
getExtensionPoint() - Method in class net.sf.basedb.util.extensions.Registry.RegisteredExtension: Get the extension point this extension is registered with.
getExtensionPoint(String) - Method in class net.sf.basedb.clients.web.extensions.ExtensionsControl: Get the extension point with a given ID.
getExtensionPoint(String) - Method in class net.sf.basedb.util.extensions.Registry: Get the extension point with a given ID.
getExtensionPoints() - Method in class net.sf.basedb.clients.web.extensions.ExtensionsControl: Get an list returning all registered extension points.
getExtensionPoints() - Method in class net.sf.basedb.util.extensions.Registry: Get a list with all registered extension points.
getExtensionPoints() - Method in class net.sf.basedb.util.extensions.xml.XmlLoader: Get a list with all loaded extension points.
getExtensions() - Method in class net.sf.basedb.clients.web.extensions.ExtensionsControl: Get a list returning all registered extensions.
getExtensions() - Method in class net.sf.basedb.plugins.Bzip2FileUnpacker: Return a set containing the strings [ bz2 ].
getExtensions() - Method in class net.sf.basedb.plugins.GzipFileUnpacker: Return a set containing the strings [ gz ].
getExtensions() - Method in class net.sf.basedb.plugins.TarFileUnpacker: Return a set containing the strings [ tar, tar.gz, tgz, tar.bz2 ].
getExtensions() - Method in class net.sf.basedb.plugins.ZipFileUnpacker: Return a set containing the strings [ zip, jar ].
getExtensions() - Method in class net.sf.basedb.util.extensions.Registry: Get a list with all registered extensions.
getExtensions() - Method in class net.sf.basedb.util.extensions.Registry.RegisteredExtensionPoint: Get all extensions registered with this extension point.
getExtensions() - Method in class net.sf.basedb.util.extensions.xml.XmlLoader: Get a list with all loaded extensions.
getExtensions() - Method in interface net.sf.basedb.util.zip.FileUnpacker: Get the file extensions that this unpacker supports.
getExtensions(String) - Method in class net.sf.basedb.clients.web.extensions.ExtensionsControl: Get a list returning all registered extensions for a specific extension point.
getExtensions(String) - Method in class net.sf.basedb.util.extensions.Registry: Get a list with all registered extensions for a given extension point.
getExtensionsFile() - Method in class net.sf.basedb.util.extensions.manager.ExtensionsFile.WriteableExtensionsFile: Get the underlying extensions file (for readin information)
getExtensionsFile() - Method in class net.sf.basedb.util.extensions.manager.ProcessResults.FileResults
getExtensionsManager() - Static method in class net.sf.basedb.core.Application
getExternalClientId() - Method in class net.sf.basedb.core.SessionControl: Get the external id of the Client application that created this SessionControl.
getExternalId() - Method in class net.sf.basedb.core.AnnotationType: Get the external id of the annotation type.
getExternalId() - Method in class net.sf.basedb.core.authentication.AuthenticatedUser: Get the external id for the user.
getExternalId() - Method in class net.sf.basedb.core.BioMaterial: Get the external id of the biomaterial.
getExternalId() - Method in class net.sf.basedb.core.BioPlate: Gets the external id of this bio plate
getExternalId() - Method in class net.sf.basedb.core.Client: Get the external id for this Client item.
getExternalId() - Method in class net.sf.basedb.core.data.AnnotationTypeData: Get the external id for the biomaterial
getExternalId() - Method in class net.sf.basedb.core.data.BioMaterialData: Get the external id for the biomaterial
getExternalId() - Method in class net.sf.basedb.core.data.BioPlateData: Get the external id for the biomaterial
getExternalId() - Method in class net.sf.basedb.core.data.ClientData: Get the external id for this Client item.
getExternalId() - Method in class net.sf.basedb.core.data.DataFileTypeData: Get the external id for the item.
getExternalId() - Method in class net.sf.basedb.core.data.ExtraValueTypeData: Get the external id for this ExtraValueType item.
getExternalId() - Method in class net.sf.basedb.core.data.FeatureData: Get the external id for this FeatureData item.
getExternalId() - Method in class net.sf.basedb.core.data.HelpData: Get the external id for this Help item.
getExternalId() - Method in class net.sf.basedb.core.data.ItemListData: Get the external id for this ItemList item.
getExternalId() - Method in class net.sf.basedb.core.data.JobAgentData: Get the external ID for the job agent.
getExternalId() - Method in class net.sf.basedb.core.data.JobData: External ID of a job running on an external system.
getExternalId() - Method in class net.sf.basedb.core.data.PlatformData: Get the external id for the item.
getExternalId() - Method in class net.sf.basedb.core.data.PlatformVariantData: Get the external id for the item.
getExternalId() - Method in class net.sf.basedb.core.data.ProtocolData: Get the external id for the protocol.
getExternalId() - Method in class net.sf.basedb.core.data.ReporterData: Get the external id for this ReporterData item.
getExternalId() - Method in class net.sf.basedb.core.data.ReporterListData: Get the external id for this ReporterList item.
getExternalId() - Method in class net.sf.basedb.core.data.UserData: Get the external ID for the user account.
getExternalId() - Method in class net.sf.basedb.core.DataFileType: Get the external id for the data file type.
getExternalId() - Method in class net.sf.basedb.core.ExtraValueType: Get the external id for this ExtraValueType item.
getExternalId() - Method in class net.sf.basedb.core.Help: Get the external id for this Help item.
getExternalId() - Method in class net.sf.basedb.core.ItemList: Get the external id for this list.
getExternalId() - Method in class net.sf.basedb.core.Job: Get the external ID of a job running on an external server.
getExternalId() - Method in class net.sf.basedb.core.JobAgent: Get the external id for the job agent.
getExternalId() - Method in class net.sf.basedb.core.Platform: Get the external id for the platform.
getExternalId() - Method in class net.sf.basedb.core.PlatformVariant: Get the external id for the platform variant.
getExternalId() - Method in class net.sf.basedb.core.Protocol: Get the external id of the protocol.
getExternalId() - Method in class net.sf.basedb.core.RawDataBatcher.ReporterProxy
getExternalId() - Method in class net.sf.basedb.core.ReporterList: Get the external id for this ReporterList item.
getExternalId() - Method in class net.sf.basedb.core.User: Get the external id for the user account.
getExtract() - Method in class net.sf.basedb.core.data.DerivedBioAssayData: Get the extract that this bioassay is related to.
getExtract() - Method in class net.sf.basedb.core.DerivedBioAssay: Get the extract that is the parent of the data in this derived bioassay.
getExtract(Annotatable) - Static method in class net.sf.basedb.util.AnnotationUtil.AnnotatableWrapper: Get the extract to use.
getExtract(DerivedBioAssay) - Method in class net.sf.basedb.util.overview.loader.DerivedBioAssayLoader: Get the extract that is associated with the current derived bioassay
getExtract(RawBioAssay) - Method in class net.sf.basedb.util.overview.loader.RawBioAssayLoader: Get the extract that is associated with the current raw bioassay
getExtractChain(DbControl, Node) - Method in class net.sf.basedb.util.overview.loader.DerivedBioAssayLoader
getExtractChain(DbControl, Node) - Method in class net.sf.basedb.util.overview.loader.RawBioAssayLoader
getExtractChain(Node) - Method in class net.sf.basedb.util.overview.loader.ExtractLoader
getExtracts() - Method in class net.sf.basedb.core.Sample: Get a query that returns all extracts created from this sample.
getExtracts(int) - Method in class net.sf.basedb.core.PhysicalBioAssay: Get a query that returns extracts connected to this bioassay.
getExtraField() - Method in interface net.sf.basedb.clients.web.extensions.login.LoginFormAction: An optional extra field on the login form.
getExtraField() - Method in class net.sf.basedb.clients.web.extensions.login.LoginFormBean
getExtraFilesDirectory(DbControl, String) - Method in class net.sf.basedb.plugins.executor.BaseFileImporterSupport
getExtraFilesDirectory(DbControl, String) - Method in class net.sf.basedb.plugins.executor.BfsImporterSupport
getExtraFilesDirectory(DbControl, String) - Method in class net.sf.basedb.plugins.executor.FileOnlyImporterSupport
getExtraFloat(String) - Method in class net.sf.basedb.util.importer.spotdata.BaseFileInfo: Get the extra value type that has the given external id.
getExtraFloatParsers() - Method in class net.sf.basedb.util.importer.spotdata.BaseFileInfo.SpotSectionInfo: Get the list of extra value parsers that exists for this section.
getExtraInformation() - Method in class net.sf.basedb.core.authentication.AuthenticatedUser: Get extra information about the user.
getExtraNo() - Method in class net.sf.basedb.core.data.DataCubeExtraValueData: The number of this extra value in the data cube.
getExtraNo() - Method in class net.sf.basedb.core.DataCubeExtraValue: Get the extra value number.
getExtraNo() - Method in class net.sf.basedb.core.ExtraValue: Get the number in the data cube of the extra values.
getExtraValue() - Method in class net.sf.basedb.core.ExtraValueExpression
getExtraValue() - Method in class net.sf.basedb.core.SpotExtraValueBatcher: Get the extra value item representing all extra values.
getExtraValue(ExtraValueType) - Method in class net.sf.basedb.core.BioAssaySet: Get the extra value of the specified type in this bioassayset.
getExtraValueField(String, ExtraValue.CoordinateType, String) - Method in class net.sf.basedb.util.export.spotdata.AbstractFieldConverter: Get an extra value dynamic field.
getExtraValueFields(DbControl, BioAssaySet) - Method in class net.sf.basedb.plugins.BaseFileExporterPlugin
getExtraValueFields(DbControl, BioAssaySet) - Method in class net.sf.basedb.plugins.BfsExporterPlugin
getExtraValueJoiner(JoinType) - Static method in class net.sf.basedb.core.DynamicPositionQueryJoiners: Get a joiner instance for extra values for the specified join type.
getExtraValueJoiner(JoinType) - Static method in class net.sf.basedb.core.DynamicSpotQueryJoiners: Get a joiner instance for extra values for the specified join type.
getExtraValues() - Method in class net.sf.basedb.core.BioAssaySet: Get a query returning the extra values that are part of this bioassayset.
getExtraValues() - Method in class net.sf.basedb.core.data.BioAssaySetData: The extra values calculated for this bioassayset.
getExtraValues() - Method in class net.sf.basedb.core.data.DataCubeData: This is the inverse end.
getExtraValues() - Method in class net.sf.basedb.core.data.ExtraValueTypeData: This is the inverse end.
getExtraValueType() - Method in class net.sf.basedb.core.data.ExtraValueData: Get the type of this extra value.
getExtraValueType() - Method in class net.sf.basedb.core.ExtraValue: Get the type of the extra values.
getExtraValueTypes() - Method in class net.sf.basedb.core.BioAssaySet: Get a query returning all extra values types that are used in this bioassay set.
getFactories() - Static method in class net.sf.basedb.util.uri.ConnectionManagerUtil: Get a list with all connection manager factories.
getFactory(String) - Static method in class net.sf.basedb.util.uri.ConnectionManagerUtil: Get the connection manager factory with the given extension id.
getFactoryParameters(Object) - Method in class net.sf.basedb.util.extensions.xml.XmlLoader: Get a XML-like string representation of the parameters that was used to initialise a factory.
getFailures() - Method in class net.sf.basedb.util.overview.GenericOverview: Get a list containing all validation failures.
getFailureSummary() - Method in interface net.sf.basedb.util.overview.extensions.ValidationRuleAction: Get a short summary that is displayed when the validation fails
getFailureSummary() - Method in class net.sf.basedb.util.overview.Validator: Get a short summary that is displayed when the validation fails
getFallbackLocale(String, Locale) - Method in class net.sf.basedb.util.resources.Utf8PropertiesResourceBundleControl: We don't need a fallback locale.
getFastLoader(DbControl) - Method in class net.sf.basedb.core.AnnotationType: Create a loader that can be used for fast loading of annotation values for multiple items.
getFastLoader(DbControl, Item, String, Item) - Static method in class net.sf.basedb.core.AnyToAny: Create an optimized implementation for loading the target item of a given named link from multiple source items.
getFavicon() - Method in class net.sf.basedb.clients.web.extensions.skin.FixedSkinActionFactory
getFavicon() - Method in class net.sf.basedb.clients.web.extensions.skin.FixedSkinActionFactory.MySkinAction
getFavicon() - Method in interface net.sf.basedb.clients.web.extensions.skin.SkinAction: Get the full path to a favicon for the BASE site.
getFavicon() - Method in class net.sf.basedb.clients.web.taglib.Page
getFax() - Method in class net.sf.basedb.core.authentication.ExtraUserInformation: The fax number to the user.
getFax() - Method in class net.sf.basedb.core.data.UserData: Get the fax number to the user, or null if unknown.
getFax() - Method in class net.sf.basedb.core.User: Get the fax number to the user, or null if unknown.
getFeature() - Method in class net.sf.basedb.core.data.RawData: The feature this raw data is connected with.
getFeature(RawDataBatcher.FeatureProxy) - Method in class net.sf.basedb.core.RawDataBatcher.FeatureInfo
getFeatureBatcher(FeatureIdentificationMethod, Job) - Method in class net.sf.basedb.core.ArrayDesign: Get a feature batcher which can be used to add regular features to the array design.
getFeatureById(int) - Method in class net.sf.basedb.core.ArrayDesign: Get a feature when you know the id.
getFeatureById(int, boolean) - Method in class net.sf.basedb.core.ArrayDesign: Get a feature when you know the id.
getFeatureCoordinate(FeatureData) - Static method in class net.sf.basedb.core.Feature: Get the coordinate of the feature.
getFeatureDiameter() - Method in class net.sf.basedb.core.ArrayDesignBlock: Get the expected diameter of spots on the slide.
getFeatureDiameter() - Method in class net.sf.basedb.core.data.ArrayDesignBlockData: The expected diameter of spots.
getFeatureIdentificationMethod() - Method in class net.sf.basedb.core.ArrayDesign: Get the method used to identify features on this array design.
getFeatureIdentificationMethod() - Method in class net.sf.basedb.core.data.ArrayDesignData: The method to use for identiying features. 1 = COORDINATES, 2 = POSITION, 3 = FEATURE_ID
getFeatures() - Method in class net.sf.basedb.core.ArrayDesign: Get a query that returns the regular features of this array design.
getFeatures() - Method in class net.sf.basedb.core.data.ArrayDesignBlockData: Used by Hibernate to link with features.
getFetchSize() - Method in class net.sf.basedb.core.hibernate.QueryWrapper
getField() - Method in class net.sf.basedb.plugins.BfsExporterPlugin.ExtendedExportableField
getFile() - Method in class net.sf.basedb.clients.web.extensions.fileviewer.FileViewerContext: Get the current file.
getFile() - Method in interface net.sf.basedb.core.data.FileAttachableData: Get the file that is attached to the item.
getFile() - Method in class net.sf.basedb.core.data.FileSetMemberData: Get the file.
getFile() - Method in class net.sf.basedb.core.data.ProtocolData
getFile() - Method in interface net.sf.basedb.core.FileAttachable: Get the file that is attached to the item.
getFile() - Method in class net.sf.basedb.core.FileSetMember: Get the file this item is representing in the file set.
getFile() - Method in class net.sf.basedb.core.plugin.ExportOutputStream: If the export stream is going to a BASE File object, use this method to access it.
getFile() - Method in class net.sf.basedb.core.Protocol
getFile() - Method in class net.sf.basedb.util.extensions.manager.ExtensionsFile: Get the underlying file on the file system.
getFile() - Method in class net.sf.basedb.util.FileExportOutputStream
getFile(int) - Method in class net.sf.basedb.util.bfs.MetadataModel: Get the file entry with a given index.
getFile(String) - Method in class net.sf.basedb.clients.web.extensions.ExtensionsControl: Get information about an installed extensions file.
getFile(String) - Method in class net.sf.basedb.clients.web.fileupload.FileUpload: Get the file information for an uplodaded file.
getFile(String) - Method in class net.sf.basedb.util.bfs.BaseInputStreamLocator
getFile(String) - Method in class net.sf.basedb.util.bfs.MetadataModel: Get the file entry for a given key.
getFile(DbControl, Directory, String, boolean) - Static method in class net.sf.basedb.core.File: Get a File item when you know the directory and filename.
getFileByObjectKey(ObjectKey<?>) - Method in class net.sf.basedb.clients.web.extensions.ExtensionsControl: Find out which file the given object is defined in.
getFileByObjectKey(ObjectKey<?>) - Method in class net.sf.basedb.util.extensions.manager.ExtensionsManager: Find out which file the object with the given key was defined.
getFileByURI(String) - Method in class net.sf.basedb.util.extensions.manager.ExtensionsManager: Get the extension file that is located at the given URI.
getFileContext() - Method in class net.sf.basedb.clients.web.extensions.fileviewer.FileViewerUtil: Get the file context.
getFileCount() - Method in class net.sf.basedb.util.bfs.MetadataModel: Get the number of entries in the 'files' section.
getFileExtension() - Method in class net.sf.basedb.util.zip.Bzip2FilePacker
getFileExtension() - Method in interface net.sf.basedb.util.zip.FilePacker: Gets the extension that files, packed with this tool, should have, for example, zip or tar.gz Don't include the first dot!
getFileExtension() - Method in class net.sf.basedb.util.zip.GzipFilePacker
getFileExtension() - Method in class net.sf.basedb.util.zip.TarFilePacker
getFileExtension() - Method in class net.sf.basedb.util.zip.ZipFilePacker
getFileFormatParameter() - Static method in class net.sf.basedb.plugins.BaseFileExporterPlugin: Create a plug-in parameter that asks for the BASEFile subtype to use in the export.
getFileFormatParameter() - Static method in class net.sf.basedb.plugins.BfsExporterPlugin: Create a plug-in parameter that asks for the BFS subtype to use in the export.
getFileId() - Method in class net.sf.basedb.util.importer.spotdata.BaseFileInfo.ChildBioAssay: Get the id of the child bioassay as it appears in the BASEfile.
getFileIterator() - Method in class net.sf.basedb.plugins.AbstractFlatFileImporter: Get an iterator that returns the files to be imported.
getFileIterator() - Method in class net.sf.basedb.plugins.RawDataFlatFileImporter
getFileLinks(String, File, String) - Static method in class net.sf.basedb.clients.web.Base: Get view/download links for a file.
getFilename() - Method in class net.sf.basedb.clients.web.fileupload.UploadedFile: Get the original filename of the uploaded file.
getFilename() - Method in class net.sf.basedb.core.Path: Get the filename part of the path.
getFilename() - Method in class net.sf.basedb.core.plugin.ImportInputStream: Get the name of the source.
getFilename() - Method in class net.sf.basedb.util.bfs.AnnotationParser: Get the file name that this parser is reading from.
getFilename() - Method in class net.sf.basedb.util.bfs.AnnotationWriter: Get the file name that this writer is printing to.
getFilename() - Method in interface net.sf.basedb.util.bfs.BfsParser: Get the filename of the file that is being parsed.
getFilename() - Method in class net.sf.basedb.util.bfs.DataParser: Get the file name that this parser is reading from.
getFilename() - Method in class net.sf.basedb.util.bfs.DataWriter: Get the file name that this writer is printing to.
getFilename() - Method in class net.sf.basedb.util.bfs.MetadataParser: Get the file name that this writer is printing to.
getFilename() - Method in class net.sf.basedb.util.bfs.MetadataWriter: Get the file name that this writer is printing to.
getFilename() - Method in class net.sf.basedb.util.FileImportInputStream: Calls CommonItem.getName().
getFilename() - Method in class net.sf.basedb.util.importer.spotdata.SynchronizedSpotDataParser
getFileNameGeneratorParameter() - Static method in class net.sf.basedb.plugins.BfsExporterPlugin: Create a plug-in parameter that asks for the file name generation strategy.
getFileOnlyRawDataTypes() - Static method in class net.sf.basedb.core.RawDataTypes: Get the raw data types that are representations of file-only Platform:s.
getFiles() - Method in class net.sf.basedb.clients.web.extensions.ExtensionsControl: Get an list returning all XML/JAR files which contains installed extensions.
getFiles() - Method in class net.sf.basedb.core.data.DirectoryData: This is the inverse end.
getFiles() - Method in class net.sf.basedb.core.data.FileServerData: This is the inverse end.
getFiles() - Method in class net.sf.basedb.core.Directory: Get a query that return all files in this directory.
getFiles() - Method in class net.sf.basedb.core.FileServer: Get a query returning all files that has been registered with this server.
getFiles() - Method in class net.sf.basedb.util.extensions.manager.ExtensionsManager: Get a list of all extension files managed by this manager.
getFileServer() - Method in class net.sf.basedb.core.data.FileData: Get the associated FileServerData item.
getFileServer() - Method in class net.sf.basedb.core.File: Get the file server on which the external file is located.
getFileSet() - Method in class net.sf.basedb.core.ArrayDesign
getFileSet() - Method in class net.sf.basedb.core.BioAssaySet
getFileSet() - Method in class net.sf.basedb.core.data.ArrayDesignData
getFileSet() - Method in class net.sf.basedb.core.data.BioAssaySetData
getFileSet() - Method in class net.sf.basedb.core.data.DerivedBioAssayData
getFileSet() - Method in class net.sf.basedb.core.data.ExtraValueData
getFileSet() - Method in class net.sf.basedb.core.data.FileSetMemberData: Get the file set this file belongs to.
getFileSet() - Method in interface net.sf.basedb.core.data.FileStoreEnabledData: Get the file set attached to this item.
getFileSet() - Method in class net.sf.basedb.core.data.RawBioAssayData
getFileSet() - Method in class net.sf.basedb.core.DerivedBioAssay
getFileSet() - Method in class net.sf.basedb.core.ExtraValue
getFileSet() - Method in class net.sf.basedb.core.FileSetMember: Get the file set the file is a member of.
getFileSet() - Method in interface net.sf.basedb.core.FileStoreEnabled: Get the file set that collects all files that holds data for this item.
getFileSet() - Method in class net.sf.basedb.core.RawBioAssay
getFileSetMember() - Method in class net.sf.basedb.util.overview.Fix
getFileSetMembers() - Method in class net.sf.basedb.core.data.DataFileTypeData: This is the inverse end.
getFileSize() - Method in class net.sf.basedb.util.bfs.AnnotationParser: Get the size in bytes of the file that this parser is reading from.
getFileSize() - Method in interface net.sf.basedb.util.bfs.BfsParser: Get the size of the file that is being parsed.
getFileSize() - Method in class net.sf.basedb.util.bfs.DataParser: Get the size in bytes of the file that this parser is reading from.
getFileSize() - Method in class net.sf.basedb.util.bfs.MetadataParser: Get the size in bytes of the file that this parser is reading from.
getFileSize() - Method in class net.sf.basedb.util.importer.spotdata.SynchronizedSpotDataParser
getFileStoreEnabledItems() - Static method in class net.sf.basedb.core.Metadata: Get a set containing all FileStoreEnabled item types.
getFileType() - Method in class net.sf.basedb.clients.web.extensions.fileviewer.FileViewerContext: Get the current data file type.
getFileType() - Method in class net.sf.basedb.core.data.MimeTypeData: Get the associated ItemSubtypeData item.
getFileType() - Method in class net.sf.basedb.core.MimeType: Get the associated file subtype item.
getFileType(DataFileType, PlatformVariant, boolean) - Method in class net.sf.basedb.core.Platform: Get information about a file type that has been registered with this platform/variant.
getFileTypes() - Method in class net.sf.basedb.core.data.ItemSubtypeData: The file types that can be used on items of this subtype.
getFileTypes() - Method in class net.sf.basedb.core.data.PlatformData: The file types that can be used on this platform.
getFileTypes() - Method in class net.sf.basedb.core.data.PlatformVariantData: The additional file types that can be used on this platform variant.
getFileTypes(boolean) - Method in class net.sf.basedb.core.PlatformVariant: Get a query returning file types registered with this platform variant.
getFileTypes(PlatformVariant, boolean) - Method in class net.sf.basedb.core.Platform: Get the file types registered with this platform.
getFileValues(String) - Method in class net.sf.basedb.clients.web.fileupload.FileUpload: Get the file information for uplodaded files.
getFilltext() - Method in class net.sf.basedb.clients.web.taglib.menu.Menu
getFilterable() - Method in class net.sf.basedb.clients.web.taglib.table.TableColumn
getFilterAnnotationType(DbControl) - Method in class net.sf.basedb.clients.web.extensions.list.RelatedItemColumn.Specification
getFilterBatcher() - Method in class net.sf.basedb.core.BioAssaySet: Get a batcher used to insert the position/column coordinates that remain after some filter has been applied to the spot data of a bioassayset.
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.
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 net.sf.basedb.util.extensions.logging.LogLevel: Get the icon that represents this log level.
getId() - Method in class net.sf.basedb.clients.jobagent.Agent: Get the agent.id configuration value.
getId() - Method in class net.sf.basedb.clients.jobagent.slotmanager.Slot: Get the id of the slot.
getId() - Method in class net.sf.basedb.clients.web.ExperimentExplorer.AnnotationGroup: The ID of the group.
getId() - Method in class net.sf.basedb.clients.web.extensions.list.AbstractListColumnBean
getId() - Method in interface net.sf.basedb.clients.web.extensions.list.ListColumnAction: ID attribute of the column.
getId() - Method in interface net.sf.basedb.clients.web.extensions.login.LoginFormAction: Get the ID of this login form.
getId() - Method in class net.sf.basedb.clients.web.extensions.login.LoginFormBean
getId() - Method in class net.sf.basedb.clients.web.extensions.login.PasswordLoginFormFactory
getId() - Method in class net.sf.basedb.clients.web.extensions.menu.FixedMenuItemFactory
getId() - Method in interface net.sf.basedb.clients.web.extensions.menu.MenuItemAction: ID attribute of the main menu tag.
getId() - Method in class net.sf.basedb.clients.web.extensions.menu.MenuItemBean
getId() - Method in interface net.sf.basedb.clients.web.extensions.plot.OverviewPlotAction: The ID of the overview plots.
getId() - Method in class net.sf.basedb.clients.web.extensions.plot.OverviewPlotBean
getId() - Method in interface net.sf.basedb.clients.web.extensions.plot.PlotGenerator: Get the ID of the image.
getId() - Method in class net.sf.basedb.clients.web.extensions.plot.PlotGeneratorBean
getId() - Method in class net.sf.basedb.clients.web.extensions.section.IncludeContentSectionFactory.Section
getId() - Method in interface net.sf.basedb.clients.web.extensions.section.SectionAction: ID attribute of the main section tag.
getId() - Method in class net.sf.basedb.clients.web.extensions.section.SectionBean
getId() - Method in class net.sf.basedb.clients.web.extensions.skin.FixedSkinActionFactory
getId() - Method in class net.sf.basedb.clients.web.extensions.skin.FixedSkinActionFactory.MySkinAction
getId() - Method in interface net.sf.basedb.clients.web.extensions.skin.SkinAction: Get the ID of the extension.
getId() - Method in class net.sf.basedb.clients.web.extensions.startpage.FixedStartPageFactory
getId() - Method in interface net.sf.basedb.clients.web.extensions.startpage.StartPageAction: Get the ID of the the action.
getId() - Method in class net.sf.basedb.clients.web.extensions.startpage.StartPageBean
getId() - Method in class net.sf.basedb.clients.web.extensions.tabcontrol.FixedTabFactory
getId() - Method in class net.sf.basedb.clients.web.extensions.tabcontrol.IncludeContentTabFactory.Tab
getId() - Method in interface net.sf.basedb.clients.web.extensions.tabcontrol.TabAction: ID attribute of the main tab tag.
getId() - Method in class net.sf.basedb.clients.web.extensions.tabcontrol.TabBean
getId() - Method in interface net.sf.basedb.clients.web.extensions.toolbar.ButtonAction: ID attribute of the main button tag.
getId() - Method in class net.sf.basedb.clients.web.extensions.toolbar.ButtonBean
getId() - Method in class net.sf.basedb.clients.web.extensions.toolbar.FixedButtonFactory
getId() - Method in class net.sf.basedb.clients.web.taglib.Button
getId() - Method in class net.sf.basedb.clients.web.taglib.table.Button.ButtonActionWrapper
getId() - Method in class net.sf.basedb.clients.web.taglib.table.TableColumn
getId() - Method in class net.sf.basedb.core.BasicItem
getId() - Method in class net.sf.basedb.core.data.annotations.AnnotationLink
getId() - Method in class net.sf.basedb.core.data.BasicData: Get the id of the item.
getId() - Method in interface net.sf.basedb.core.data.IdentifiableData: Get the id for the item.
getId() - Method in class net.sf.basedb.core.data.UserData: We must override this method because the id must be the same as the id for the password.
getId() - Method in interface net.sf.basedb.core.Identifiable: Get the id for the item.
getId() - Method in class net.sf.basedb.core.ItemContext: Get the ID of the current item in this context.
getId() - Method in class net.sf.basedb.core.ItemProxy
getId() - Method in class net.sf.basedb.core.ParameterValuesImpl
getId() - Method in class net.sf.basedb.core.plugin.NamespaceParameterValuesWrapper
getId() - Method in interface net.sf.basedb.core.plugin.ParameterValues: Get the ID of the job or configuration the parameters comes from.
getId() - Method in class net.sf.basedb.core.plugin.ParameterValuesWrapper: Get the ID of either the job or the configuration, depending in the preferJob parameter that was set when creating this object.
getId() - Method in class net.sf.basedb.core.RawDataBatcher.FeatureProxy
getId() - Method in class net.sf.basedb.core.RawDataBatcher.ReporterProxy
getId() - Method in class net.sf.basedb.core.RawDataType: Get the id of this raw data type.
getId() - Method in class net.sf.basedb.core.SessionControl: Get the id of this SessionControl.
getId() - Method in class net.sf.basedb.core.signal.Signal: Get the signal ID.
getId() - Method in class net.sf.basedb.core.snapshot.AnnotationLoaderUtil: The ID of the annotation type that this loader load annotations from.
getId() - Method in class net.sf.basedb.plugins.BaseFileExporterPlugin.ExtendedDynamicField
getId() - Method in class net.sf.basedb.plugins.BfsExporterPlugin.ExtendedExportableField
getId() - Method in class net.sf.basedb.plugins.gtf.DefaultConfigurationValues
getId() - Method in interface net.sf.basedb.util.extensions.Extension: Get the ID of the extension.
getId() - Method in class net.sf.basedb.util.extensions.ExtensionBean
getId() - Method in interface net.sf.basedb.util.extensions.ExtensionPoint: Get the ID of the extension point.
getId() - Method in class net.sf.basedb.util.extensions.ExtensionPointBean
getId() - Method in class net.sf.basedb.util.extensions.Registry.RegisteredExtension
getId() - Method in class net.sf.basedb.util.extensions.Registry.RegisteredExtensionPoint
getId() - Method in class net.sf.basedb.util.importer.spotdata.BaseFileImporter.RawDataProxy
getId() - Method in class net.sf.basedb.util.importer.spotdata.BaseFileImporter.ReporterProxy
getId() - Method in class net.sf.basedb.util.importer.spotdata.ExtraFloatParser: Get the external id of the extra value type.
getId() - Method in interface net.sf.basedb.util.overview.extensions.ValidationRuleAction: Get the unique ID of this validation rule.
getId() - Method in class net.sf.basedb.util.overview.Node: Get a unique ID for this node.
getId() - Method in class net.sf.basedb.util.overview.Validator: Get the unique ID of this validator.
getId() - Method in interface net.sf.basedb.util.uri.ConnectionManagerFactory: Get the ID of this connection manager factory.
getId() - Method in class net.sf.basedb.util.uri.http.HttpConnectionManagerFactory
getId(String) - Static method in class net.sf.basedb.core.SystemItems: Get the numeric id for an item when you know the system id.
getId(BasicItem) - Method in class net.sf.basedb.clients.web.plugins.ItemQueryWrapper: Calls BasicItem.getId()
getId(BasicData) - Method in class net.sf.basedb.clients.web.plugins.DataQueryWrapper: Calls BasicData.getId()
getId(SqlResult) - Method in class net.sf.basedb.clients.web.plugins.DynamicQueryWrapper: Keeps a counter which is incremented at each call to this method.
getId(ReporterScore) - Method in class net.sf.basedb.clients.web.plugins.ReporterScoreQueryWrapper: Calls BasicData.getId().
getId(T) - Method in interface net.sf.basedb.clients.web.plugins.QueryWrapper: Get the ID of the specified item.
getIdentifier(Object) - Method in class net.sf.basedb.core.hibernate.SessionWrapper
getIdentifier(FeatureData) - Method in enum net.sf.basedb.core.FeatureIdentificationMethod: Get the feature identifier for this method.
getIdentifier(RawData, String) - Method in enum net.sf.basedb.core.FeatureIdentificationMethod: Get a feature identifier using this method
getIdFromPath(DbControl, Path) - Static method in class net.sf.basedb.core.Directory: Get the id of a directory when you know the path.
getIdHqlQuery(DbControl) - Method in class net.sf.basedb.core.AbstractHqlQuery: Build the ID query and set parameter values for it.
getIdMethod(DbControl, String) - Method in class net.sf.basedb.plugins.batchimport.AbstractItemImporter: Get the id method to use for finding items.
getIdMethod(DbControl, String) - Method in class net.sf.basedb.plugins.batchimport.FileImporter: We need to initialize the PathIdMethod when this is called.
getIdMethod(DbControl, Item, String) - Method in class net.sf.basedb.plugins.AnnotationFlatFileImporter
getIdMethod(DbControl, Item, String) - Method in class net.sf.basedb.plugins.batchimport.AnyToAnyImporter
getIdMethods() - Method in class net.sf.basedb.plugins.batchimport.AbstractItemImporter: Get an array with all identification methods that can be used to find items.
getIdMethods() - Method in class net.sf.basedb.plugins.batchimport.AnnotationTypeImporter: Useable methods are: PropertyIdMethod.NAME PropertyIdMethod.EXTERNAL_ID InternalIdMethod.INTERNAL_ID FallbackIdMethod.NAME_OR_ID
getIdMethods() - Method in class net.sf.basedb.plugins.batchimport.ArrayBatchImporter: Useable methods are: PropertyIdMethod.NAME InternalIdMethod.INTERNAL_ID FallbackIdMethod.NAME_OR_ID
getIdMethods() - Method in class net.sf.basedb.plugins.batchimport.ArrayDesignImporter: Useable methods are: PropertyIdMethod.NAME InternalIdMethod.INTERNAL_ID FallbackIdMethod.NAME_OR_ID
getIdMethods() - Method in class net.sf.basedb.plugins.batchimport.ArraySlideImporter: Useable methods are: PropertyIdMethod.NAME PropertyIdMethod.BARCODE InternalIdMethod.INTERNAL_ID FallbackIdMethod.NAME_OR_ID
getIdMethods() - Method in class net.sf.basedb.plugins.batchimport.BioPlateImporter: Useable methods are: PropertyIdMethod.NAME PropertyIdMethod.BARCODE InternalIdMethod.INTERNAL_ID FallbackIdMethod.NAME_OR_ID
getIdMethods() - Method in class net.sf.basedb.plugins.batchimport.BioSourceImporter: Useable methods are: PropertyIdMethod.NAME PropertyIdMethod.EXTERNAL_ID InternalIdMethod.INTERNAL_ID FallbackIdMethod.NAME_OR_ID
getIdMethods() - Method in class net.sf.basedb.plugins.batchimport.DerivedBioAssayImporter: Useable methods are: PropertyIdMethod.NAME InternalIdMethod.INTERNAL_ID FallbackIdMethod.NAME_OR_ID
getIdMethods() - Method in class net.sf.basedb.plugins.batchimport.ExtractImporter: Useable methods are: PropertyIdMethod.NAME PropertyIdMethod.EXTERNAL_ID InternalIdMethod.INTERNAL_ID FallbackIdMethod.NAME_OR_ID
getIdMethods() - Method in class net.sf.basedb.plugins.batchimport.FileImporter: Useable methods are: FileImporter.PathIdMethod InternalIdMethod.INTERNAL_ID
getIdMethods() - Method in class net.sf.basedb.plugins.batchimport.KitImporter: Useable methods are: PropertyIdMethod.NAME InternalIdMethod.INTERNAL_ID FallbackIdMethod.NAME_OR_ID
getIdMethods() - Method in class net.sf.basedb.plugins.batchimport.PhysicalBioAssayImporter: Useable methods are: PropertyIdMethod.NAME InternalIdMethod.INTERNAL_ID FallbackIdMethod.NAME_OR_ID
getIdMethods() - Method in class net.sf.basedb.plugins.batchimport.RawBioAssayImporter: Useable methods are: PropertyIdMethod.NAME InternalIdMethod.INTERNAL_ID FallbackIdMethod.NAME_OR_ID
getIdMethods() - Method in class net.sf.basedb.plugins.batchimport.SampleImporter: Useable methods are: PropertyIdMethod.NAME PropertyIdMethod.EXTERNAL_ID InternalIdMethod.INTERNAL_ID FallbackIdMethod.NAME_OR_ID
getIdMethods() - Method in class net.sf.basedb.plugins.batchimport.TagImporter: Useable methods are: PropertyIdMethod.NAME InternalIdMethod.INTERNAL_ID FallbackIdMethod.NAME_OR_ID
getIdMethods(DbControl, Item) - Method in class net.sf.basedb.plugins.AnnotationFlatFileImporter
getIdMethods(DbControl, Item) - Static method in class net.sf.basedb.plugins.batchimport.AnnotationIdMethod: Get identification methods that are based on annotations.
getIdMethods(DbControl, Item) - Method in class net.sf.basedb.plugins.batchimport.AnyToAnyImporter
getIdPrefix() - Method in class net.sf.basedb.clients.web.taglib.StylableTag: Optional prefix to include in the 'id' attribute.
getIdPrefix() - Method in class net.sf.basedb.clients.web.taglib.table.ColumnDef
getIdQuery(DbControl, boolean) - Method in class net.sf.basedb.core.AbstractQuery: Build a query string that is identical to the main query but only return the ID values.
getIgnoredFiles() - Method in class net.sf.basedb.clients.web.extensions.ExtensionsControl: Get files that are currently ignored.
getIgnoredFiles() - Method in class net.sf.basedb.util.extensions.manager.Settings: Get a list with all files that are ignored.
getIgnoredFiles(boolean) - Method in class net.sf.basedb.util.extensions.manager.ExtensionsManager: Get all ignored files.
getIgnoredLines() - Method in class net.sf.basedb.util.parser.FlatFileParser: Get the number of lines that the last call to FlatFileParser.nextData() or FlatFileParser.hasMoreData() ignored because they matched the ignore regular expression.
getIgnoredSql() - Method in class net.sf.basedb.core.hibernate.SchemaGenerator: Get a list with the SQL statements that was ignored in the last run.
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.
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.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 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, 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.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.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.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.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.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
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.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 net.sf.basedb.core.query.JoinType
getJoinProperty() - Method in class net.sf.basedb.core.query.ReporterListExpression
getJspContext() - Method in class net.sf.basedb.clients.web.extensions.edit.AbstractOnSaveAction: Set the JSP context of the current invokation.
getJspContext() - Method in class net.sf.basedb.clients.web.extensions.fileviewer.FileViewerUtil: Get the JSP context.
getJspPage() - Method in class net.sf.basedb.core.RequestInformation: The name of the jsp page to use for displaying the input form for requesting parameters.
getKey() - Method in class net.sf.basedb.util.bfs.MetadataModel.SectionEntry: Get the key of the entry.
getKey() - Method in class net.sf.basedb.util.Enumeration.Entry
getKey() - Method in class net.sf.basedb.util.fuzzy.StringMatcher.FuzzyMatch: Get the key string.
getKey() - Method in class net.sf.basedb.util.StaticCache.LockEntry
getKey(int) - Method in class net.sf.basedb.util.bfs.MetadataModel.Section: Get the key of the entry at the given index.
getKey(int) - Method in class net.sf.basedb.util.Enumeration
getKey(String, Item, Item, SyncFilter.SourceItemTransform, Set<Integer>) - Static method in class net.sf.basedb.util.listable.TransformCache
getKey(Item, Item, SyncFilter.SourceItemTransform, Set<Integer>) - Static method in class net.sf.basedb.util.listable.TransformCache: Get a key that is able to identify a given transformation.
getKeyId() - Method in class net.sf.basedb.core.data.keyring.KeyPermission: Get the id of the key.
getKeyId() - Method in class net.sf.basedb.core.data.keyring.PluginKeys: Gets the id of the RoleKey
getKeys() - Method in class net.sf.basedb.core.data.RoleData: This is the inverse end.
getKeys() - Method in class net.sf.basedb.core.Presets.Preset: Get all keys in this preset.
getKeys() - Method in class net.sf.basedb.util.QueryParameters: Get all keys that are present in the query string.
getKit() - Method in class net.sf.basedb.core.BioMaterialEvent: Get the Kit that was used in this event.
getKit() - Method in class net.sf.basedb.core.BioPlateEvent: Get the Kit that was used in this event.
getKit() - Method in class net.sf.basedb.core.data.BioMaterialEventData: Get the kit used in this event.
getKit() - Method in class net.sf.basedb.core.data.BioPlateEventData: Get the kit used in this event.
getKit() - Method in class net.sf.basedb.core.data.DerivedBioAssayData: Get the kit used to create this bioassay set.
getKit() - Method in class net.sf.basedb.core.DerivedBioAssay: Get the Kit that was used when creating this bioassay.
getLabel() - Method in class net.sf.basedb.core.data.ParameterValueData: Get the label of the parameter.
getLabel() - Method in class net.sf.basedb.core.ParameterInfo
getLabel() - Method in class net.sf.basedb.core.PluginParameter: Get the label of the parameter.
getLastAccess() - Method in class net.sf.basedb.core.SessionControl: Get the time this object last was accessed.
getLastColumn() - Method in class net.sf.basedb.util.excel.XlsxToCsvUtil.SheetInfo: Get the column number for the last column that contains data.
getLastError() - Method in class net.sf.basedb.util.extensions.Registry.RegisteredExtension
getLastError() - Method in class net.sf.basedb.util.extensions.Registry.RegisteredExtensionPoint
getLastExtensionError(String) - Method in class net.sf.basedb.clients.web.extensions.ExtensionsControl: Get information about the last error that happened when rendering an extension.
getLastExtensionError(String) - Method in class net.sf.basedb.util.extensions.Registry: Get information about the last error that happened when rendering an extension.
getLastExtensionPointError(String) - Method in class net.sf.basedb.clients.web.extensions.ExtensionsControl: Get information about the last error that happened when rendering an extension point.
getLastExtensionPointError(String) - Method in class net.sf.basedb.util.extensions.Registry: Get information about the last error that happened when rendering an extension point.
getLastGuiContext() - Method in class net.sf.basedb.core.Job: Get the gui-context that was active when this job was created.
getLastModified() - Method in class net.sf.basedb.util.uri.UriMetadata: Get the date and time the resource was last modified.
getLastModified(HttpResponse) - Static method in class net.sf.basedb.util.HttpUtil: Get the date the content was last modified from the headers in the response.
getLastProcessResults() - Method in class net.sf.basedb.util.extensions.manager.ExtensionsManager: Get the results of the last processing.
getLastRemoteId() - Method in class net.sf.basedb.core.data.UserDeviceData: Get the remote id (=ip address) of the last login from this device.
getLastRemoteId() - Method in class net.sf.basedb.core.UserDevice: Get the remote ID of the host the user used for this device the last time.
getLastRow() - Method in class net.sf.basedb.util.excel.XlsxToCsvUtil.SheetInfo: Get the row number for the last row that contains data.
getLastScanResults() - Method in class net.sf.basedb.clients.web.extensions.ExtensionsControl: Get the results of the last scan (manual or automatic).
getLastSource() - Method in class net.sf.basedb.core.data.ReporterData: Get the source that was used when this reporter was last updated.
getLastSyncMatchingSource() - Method in class net.sf.basedb.core.SyncFilter: Get the number of source items that matched this particular filter during the last synchronization.
getLastSyncMatchingTransformed() - Method in class net.sf.basedb.core.SyncFilter: Get the number of transformed items that matched this particular filter during the last synchronization.
getLastSyncProperties() - Method in class net.sf.basedb.core.data.ItemListSyncFilterData: A string representation of properties that was affecting that last filter during the last sync.
getLastUpdate() - Method in class net.sf.basedb.core.Annotation: Get the date and time the values in this annotation was last updated.
getLastUpdate() - Method in class net.sf.basedb.core.data.AnnotationData: Get the date and time the values in this annotation was last updated.
getLastUpdate() - Method in class net.sf.basedb.core.data.FileData: Get the date and time the actual file data was last updated.
getLastUpdate() - Method in class net.sf.basedb.core.data.ReporterData: Get the date and time the information about this reporter last was updated.
getLastUpdate() - Method in class net.sf.basedb.core.File: Get the date and time the actual file data was last updated.
getLastUpdated() - Method in class net.sf.basedb.clients.jobagent.slotmanager.MasterSlotManager.RemoteSlot
getLastUsed() - Method in class net.sf.basedb.core.data.UserDeviceData: Get the date and time the user last logged in from this device.
getLastUsed() - Method in class net.sf.basedb.core.UserDevice: Get the date and time the user last used this device.
getLatitude() - Method in class net.sf.basedb.util.GeoLocation
getLayerNo() - Method in class net.sf.basedb.core.data.DataCubeLayerData: The layer number of this layer in the data cube.
getLayerNo() - Method in class net.sf.basedb.core.DataCubeLayer: Get the number of this layer.
getLayers() - Method in class net.sf.basedb.core.data.DataCubeData: This is the inverse end.
getLeftTableAlias(Query) - Method in class net.sf.basedb.core.RealJoin
getLeftTableColumn() - Method in class net.sf.basedb.core.RealJoin
getLength() - Method in class net.sf.basedb.core.data.ReporterClonePropertyData: The maximum length of string value types.
getLength() - Method in class net.sf.basedb.core.ExtendedProperty: Get the maximum allowed length of the property value.
getLength() - Method in class net.sf.basedb.core.plugin.ImportInputStream: Get the length of the stream in number of bytes.
getLength() - Method in class net.sf.basedb.util.FileImportInputStream: Calls File.getSize() to get the file size.
getLength() - Method in class net.sf.basedb.util.uri.UriMetadata: Get the length in bytes of the resource.
getLevel() - Method in class net.sf.basedb.util.extensions.logging.LogEntry: The level of the log entry.
getLimit() - Method in class net.sf.basedb.core.signal.ProgressReporterSignalHandler: Get the percentage limit where signal checking becomes disabled.
getLimitHandler() - Method in class net.sf.basedb.core.AbstractSqlQuery: Get a handler for adding LIMIT and OFFSET parameters to an SQL statement.
getLine(int) - Method in class net.sf.basedb.util.parser.FlatFileParser: Get the line with the specified number.
getLineCount() - Method in class net.sf.basedb.util.bfs.MetadataWriter: Get the number of lines that has been written to this file so far, including all comment lines, empty lines, sections headers, etc.
getLineCount() - Method in class net.sf.basedb.util.parser.FlatFileParser: Get the number of lines that the FlatFileParser.parseHeaders() method parsed.
getLines() - Method in class net.sf.basedb.util.parser.FlatFileParser: Get the lines read by FlatFileParser.parseHeaders().
getLink(String, String, Item, int, boolean) - Static method in class net.sf.basedb.clients.web.Base
getLink(String, String, Item, int, boolean, String) - Static method in class net.sf.basedb.clients.web.Base
getLink(String, Nameable, Integer, boolean, boolean, boolean, boolean) - Static method in class net.sf.basedb.clients.web.ChangeHistoryUtil
getLink(S) - Method in class net.sf.basedb.core.AnyToAny.FastLinkLoader: Get the any-to-any link.
getLinkedFile(String, File, boolean, boolean, boolean, String) - Static method in class net.sf.basedb.clients.web.Base
getLinkedItem(DbControl, BasicItem) - Method in class net.sf.basedb.clients.web.plugins.AnyToAnyDataLoader: Get the item that is linked to by this any-to-any link definition.
getLinkedName(String, Nameable, boolean, boolean) - Static method in class net.sf.basedb.clients.web.Base
getLinkName() - Method in class net.sf.basedb.core.AnyToAny.FastLinkLoader: The link name.
getLinkName() - Method in class net.sf.basedb.util.AnyToAnyLinkStatistics: Get the name of the link.
getLinksFrom(BasicItem) - Static method in class net.sf.basedb.core.AnyToAny: Get a query that returns all links linking from the specified item.
getLinksTo(BasicItem) - Static method in class net.sf.basedb.core.AnyToAny: Get a query that returns all links linking to the specified item.
getList() - Method in class net.sf.basedb.clients.web.taglib.table.CellValue
getListableItems() - Static method in class net.sf.basedb.core.Metadata: Get a set containing all Listable item types.
getListableItems(Item, SyncFilter.SourceItemTransform) - Static method in class net.sf.basedb.util.listable.ListableUtil: Get all item types that can have the specified relation to the with the given item type.
getListMemberType() - Method in class net.sf.basedb.core.SyncFilter
getLobHelper() - Method in class net.sf.basedb.core.hibernate.SessionWrapper
getLocale() - Static method in class net.sf.basedb.core.Config: Get the default locale configured for the server.
getLocale() - Method in class net.sf.basedb.core.SessionControl: Get the locale that is curently assigned to this session control.
getLocale() - Method in class net.sf.basedb.util.resources.ResourceBundleWrapper: Get the actual locale used by the bundle, which may be a different locale from the one that was used to load it.
getLocalHost() - Static method in class net.sf.basedb.util.SocketUtil: Get the local address of the local host.
getLocalSignalHandlerId(SignalHandler) - Method in class net.sf.basedb.core.signal.AbstractSignalReceiver: Get the local signal handler id of the given signal handler.
getLocation() - Method in class net.sf.basedb.core.data.DiskUsageData: Get the location of the DiskConsumable item.
getLocation() - Method in class net.sf.basedb.core.data.FileData: Get the Location of this FileData
getLocation() - Method in class net.sf.basedb.core.data.QuotaIndex
getLocation() - Method in class net.sf.basedb.core.data.SessionData: Get the location of the user (if known).
getLocation() - Method in class net.sf.basedb.core.data.UserDeviceData: Get the location of the user (if known).
getLocation() - Method in interface net.sf.basedb.core.DiskConsumable: Get the Location the items is stored at.
getLocation() - Method in class net.sf.basedb.core.DiskUsage: Get the location of the DiskConsumable item.
getLocation() - Method in class net.sf.basedb.core.Experiment: Always Location.PRIMARY.
getLocation() - Method in class net.sf.basedb.core.File
getLocation() - Method in class net.sf.basedb.core.RawBioAssay: Always Location.PRIMARY.
getLocation() - Method in class net.sf.basedb.core.Session: Get the location of the host the user used for this session.
getLocation() - Method in class net.sf.basedb.core.UserDevice: Get the last known location of the device.
getLocation(AuthenticationMethod) - Method in class net.sf.basedb.core.SessionControl
getLocationFromIp(String) - Static method in class net.sf.basedb.util.GeoLocation: Try to convert the given ip address to a location.
getLocationLatitude() - Method in class net.sf.basedb.core.data.SessionData: Get the location latitude of the user (if known).
getLocationLatitude() - Method in class net.sf.basedb.core.data.UserDeviceData: Get the location latitude of the user (if known).
getLocationLatitude() - Method in class net.sf.basedb.core.Session: Get the location latitude of the host the user used for this session.
getLocationLatitude() - Method in class net.sf.basedb.core.UserDevice: Get the last known location latitude of the device.
getLocationLongitude() - Method in class net.sf.basedb.core.data.SessionData: Get the location longitude of the user (if known).
getLocationLongitude() - Method in class net.sf.basedb.core.data.UserDeviceData: Get the location longitude of the user (if known).
getLocationLongitude() - Method in class net.sf.basedb.core.Session: Get the location longitude of the host the user used for this session.
getLocationLongitude() - Method in class net.sf.basedb.core.UserDevice: Get the last known location longitude of the device.
getLockMode() - Method in class net.sf.basedb.core.BioPlateType: Get the lock mode for wells located on plates of this plate type.
getLockMode() - Method in class net.sf.basedb.core.BioWell: Get the lock mode of this well.
getLockMode() - Method in class net.sf.basedb.core.data.BioPlateTypeData: A flag indicating if plates with this type have locked wells or not. 0 = not locked; 1 = locked-after-move; 2 = locked-after-add; 3=locked-after-create
getLockMode() - Method in class net.sf.basedb.core.hibernate.QueryWrapper
getLockMode(Object) - Method in class net.sf.basedb.core.hibernate.SessionWrapper
getLockOptions() - Method in class net.sf.basedb.core.hibernate.QueryWrapper
getLog(String, boolean) - Static method in class net.sf.basedb.util.extensions.logging.ExtensionsLog: Get the service log for the given extension.
getLogChangeType() - Method in enum 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 net.sf.basedb.core.IntensityTransform: Get a MA calculator implementation that is suitable for calculating MA-values for the given source data type.
getMainHqlQuery(DbControl, Class<R>) - Method in class net.sf.basedb.core.AbstractHqlQuery: Build the main query and set parameter values for it.
getMainItemType() - Method in class net.sf.basedb.core.ItemSubtype: Get the main item type that the subtype belongs to.
getMainQuery(DbControl, boolean) - Method in class net.sf.basedb.core.AbstractQuery: Build the main query string.
getMaintenance() - Static method in class net.sf.basedb.core.Version: Get the maintentance version.
getMaintenanceVersion() - Static method in class net.sf.basedb.core.Application: Get the maintenance version.
getMainType() - Method in class net.sf.basedb.clients.web.plugins.SimpleExport
getMainType() - Method in class net.sf.basedb.core.data.PluginDefinitionData: Get the main type of plugin.
getMainType() - Method in class net.sf.basedb.core.plugin.AbstractAnalysisPlugin
getMainType() - Method in class net.sf.basedb.core.plugin.AbstractExporterPlugin
getMainType() - Method in interface net.sf.basedb.core.plugin.Plugin: Get the type of the plugin.
getMainType() - Method in class net.sf.basedb.core.PluginDefinition: Get the type of plugin.
getMainType() - Method in class net.sf.basedb.plugins.AbstractFlatFileImporter: Return Plugin.MainType.IMPORT.
getMainType() - Method in class net.sf.basedb.plugins.BfsExporterPlugin
getMainType() - Method in class net.sf.basedb.plugins.CdfFileReporterImporter
getMainType() - Method in class net.sf.basedb.plugins.CloneReportersPlugin
getMainType() - Method in class net.sf.basedb.plugins.executor.BaseFileExporterSupport
getMainType() - Method in class net.sf.basedb.plugins.executor.BaseFileImporterSupport
getMainType() - Method in class net.sf.basedb.plugins.executor.BfsExporterSupport
getMainType() - Method in class net.sf.basedb.plugins.executor.BfsImporterSupport
getMainType() - Method in class net.sf.basedb.plugins.executor.FileOnlyImporterSupport
getMainType() - Method in class net.sf.basedb.plugins.HelpImporter
getMainType() - Method in class net.sf.basedb.plugins.IntensityCalculatorPlugin: Returns the main plugin type this plugin belongs to.
getMainType() - Method in class net.sf.basedb.plugins.PluginConfigurationImporter
getMainType() - Method in class net.sf.basedb.util.zip.AbstractFileUnpacker
getMajor() - Static method in class net.sf.basedb.core.Version: Get the major version.
getMajorVersion() - Static method in class net.sf.basedb.core.Application: Get the major version.
getManualConfigureParameters() - Method in class net.sf.basedb.plugins.Base1PluginExecuter: Creates the information needed for manual configuration and initiates the parameters.
getMapper(String) - Method in class net.sf.basedb.util.parser.FlatFileParser: Get a mapper using the default number format.
getMapper(String, boolean) - Method in class net.sf.basedb.util.parser.FlatFileParser: Get a mapper using the default number format.
getMapper(String, NumberFormat) - Method in class net.sf.basedb.util.parser.FlatFileParser: Get a mapper using a specific number format.
getMapper(String, NumberFormat, boolean) - Method in class net.sf.basedb.util.parser.FlatFileParser
getMapper(String, NumberFormat, boolean, JepFunction...) - Method in class net.sf.basedb.util.parser.FlatFileParser
getMapper(String, NumberFormat, Formatter<Date>, boolean, JepFunction...) - Method in class net.sf.basedb.util.parser.FlatFileParser: Create a mapper object that maps an expression string to a value.
getMapper(String, Formatter<Date>, boolean) - Method in class net.sf.basedb.util.parser.FlatFileParser: Get a mapper using the specified date format.
getMapper(String, JepFunction...) - Method in class net.sf.basedb.util.parser.FlatFileParser
getMapper(FlatFileParser, String, Integer, Mapper) - Method in class net.sf.basedb.plugins.AbstractFlatFileImporter
getMapper(FlatFileParser, String, Integer, Mapper, JepFunction...) - Method in class net.sf.basedb.plugins.AbstractFlatFileImporter: Get a mapper for the specified flat file parser.
getMapping() - Static method in class net.sf.basedb.core.HibernateUtil
getMappingBatcher() - Method in class net.sf.basedb.core.BioAssaySet: Get a batcher used to insert mappings to raw data.
getMappingBatcher() - Method in class net.sf.basedb.core.DataCube
getMappings() - Method in class net.sf.basedb.core.data.VirtualDbData: The number of cube mappings in the virtual database.
getMappings() - Method in class net.sf.basedb.core.VirtualDb: Get the number of DataCubeMapping:s in this virtual database.
getMasterReporterJoiner(JoinType) - Static method in class net.sf.basedb.core.DynamicReporterQuery: Get a joiner instance for joining the master reporter table when the root query is against the cloned reporters table.
getMatching(DbControl) - Method in class net.sf.basedb.core.SyncFilter
getMatchingReporters(DbControl) - Method in class net.sf.basedb.clients.web.ExperimentExplorer: Get the number of reporters matching the current reporter filter.
getMatchingSource() - Method in class net.sf.basedb.core.data.ItemListSyncFilterData: The number of matching source items during that last sync.
getMatchingTransformed() - Method in class net.sf.basedb.core.data.ItemListSyncFilterData: The number of matching items after the transform during that last sync.
getMax() - Method in class net.sf.basedb.util.plot.HistogramPlot.HistogramBin: Get the maximum of all values in this bin.
getMaxAge() - Method in class net.sf.basedb.core.DiskUsageStatistics: Get the max age in seconds for a disk usage summary object before it is reloaded from the database again.
getMaxBaseVersion() - Method in interface net.sf.basedb.core.plugin.About: Get the maximum BASE version were to plug-in no longer is expected to work.
getMaxBaseVersion() - Method in class net.sf.basedb.core.plugin.AboutImpl
getMaxBaseVersion() - Method in class net.sf.basedb.util.extensions.AboutBean
getMaxBaseVersion() - Method in class net.sf.basedb.util.extensions.Registry.RegisteredAbout
getMaxBytes() - Method in class net.sf.basedb.core.data.QuotaIndex
getMaxEntries() - Method in class net.sf.basedb.util.extensions.logging.ExtensionsLog: Get the max number of entries to keep in the log.
getMaxLength() - Method in class net.sf.basedb.core.AnnotationType: Get the maximum allowed string length for a Type.STRING annotation.
getMaxLength() - Method in class net.sf.basedb.core.StringParameterType: Get the max length of the parameter.
getMaxMemory() - Method in class net.sf.basedb.core.data.JobAgentSettingsData: The max amount of memory the plugin can use.
getMaxMemory() - Method in class net.sf.basedb.core.data.PluginDefinitionData: The max amount of memory the plugin can use.
getMaxMemory() - Method in class net.sf.basedb.core.JobAgentSettings: Get the maximum amount of memory the plugin is allowed to use.
getMaxMemory() - Method in class net.sf.basedb.core.PluginDefinition: Get the maximum amount of memory the plugins is allowed to use.
getMaxParametersInQuery() - Method in class net.sf.basedb.core.dbengine.AbstractDbEngine: Returns 10000.
getMaxParametersInQuery() - Method in interface net.sf.basedb.core.dbengine.DbEngine: Get the maximum number of parameters that can be used in a prepared statement for a query.
getMaxProjectPermission() - Method in class net.sf.basedb.core.Keyring: Get the max project permission within the currently active project.
getMaxRandomSamples() - Method in class net.sf.basedb.util.AnyToAnyLinkStatistics.Options
getMaxRawMappingsForSpot() - Method in class net.sf.basedb.core.BioAssaySet: Get the number of mappings to raw data spots for the spot with the most number of mappings.
getMaxRawMappingsForSpot() - Method in class net.sf.basedb.core.data.DataCubeData: The maximum number of raw data spots a single spot in this data cube is mapped to.
getMaxRawMappingsForSpot() - Method in class net.sf.basedb.core.DataCube: Get the number of mappings to raw data spots for the spot with the most number of mappings.
getMaxRecent(SessionControl) - Static method in class net.sf.basedb.clients.web.Base: Get the setting for the maximum number of recently used items to save.
getMaxResults() - Method in class net.sf.basedb.core.AbstractQuery
getMaxResults() - Method in class net.sf.basedb.core.hibernate.QueryWrapper
getMaxResults() - Method in interface net.sf.basedb.core.query.Query: The maximum number of rows returned by the query.
getMaxUrlLength() - Method in class net.sf.basedb.clients.web.taglib.Page
getMaxValue() - Method in class net.sf.basedb.core.Coloring: Get the value that represents the maximum value.
getMaxValue() - Method in class net.sf.basedb.core.data.ColoringData: The value for the ax endpoint color.
getMaxValueDouble() - Method in class net.sf.basedb.core.AnnotationType: Get the maximum allowed value for a Type.FLOAT or Type.DOUBLE annotation.
getMaxValueLong() - Method in class net.sf.basedb.core.AnnotationType: Get the maximum allowed value for an Type.INT or Type.LONG annotation.
getMaxY(int) - Method in class net.sf.basedb.util.plot.HistogramPlot.HistogramSeries
getMaxY(HistogramPlot.HistogramBin) - Method in enum net.sf.basedb.util.plot.HistogramPlot.YAggregate
getMaybeGranted() - Method in class net.sf.basedb.core.plugin.Permissions: Get the permissions that the plugin should be granted only if the logged in user already have the permissions.
getMd5() - Method in class net.sf.basedb.core.data.FileData: Get the MD5 hash of the file contents.
getMd5() - Method in class net.sf.basedb.core.data.ItemListSyncFilterData: Get the MD5 hash of the concatenated ID values.
getMd5() - Method in class net.sf.basedb.core.File: Get the MD5 hash of the file contents, or null if not known.
getMd5() - Method in class net.sf.basedb.util.uri.UriMetadata: Get the MD5 checksum of the resource.
getMd5AtLastSync() - Method in class net.sf.basedb.core.data.ItemListData: Get the MD5 hash of the concatenated ID values from the last sync.
getMean() - Method in class net.sf.basedb.util.plot.HistogramPlot.HistogramBin: Get the mean of all values in this bin.
getMean(int) - Method in class net.sf.basedb.clients.web.ExperimentExplorer.AnnotationGroup: Get the mean of the intensity values for the given channel.
getMember() - Method in class net.sf.basedb.clients.web.extensions.fileviewer.FileViewerContext: Get the current file set member information for the file.
getMember() - Method in class net.sf.basedb.core.ExtendedPropertyAccessor.GetterSetter: Always return null.
getMember() - Method in class net.sf.basedb.util.fileset.ValidatingFileSetMember: Get the file set member that this proxy represents.
getMember(DataFileType) - Method in class net.sf.basedb.core.FileSet: Get the member of the given type assuming that there is only a single member of that type.
getMemberRestriction() - Method in class net.sf.basedb.core.ItemList: Get a restriction that mathces members in this list.
getMembers() - Method in class net.sf.basedb.core.data.FileSetData: The members of this file set.
getMembers() - Method in class net.sf.basedb.core.data.ItemListData: Get the set that manages which items that are part of this list.
getMembers() - Method in class net.sf.basedb.core.FileSet: Get the members of this file set.
getMembers() - Method in class net.sf.basedb.core.ItemList: Get a query that returns all items that are members of this list.
getMembers(String) - Method in class net.sf.basedb.core.FileSet: Get a query that returns all members in a file set with a specific generic ItemSubtype.
getMembers(DataFileType) - Method in class net.sf.basedb.core.FileSet: Get a query that returns all members in a file set with a specific DataFileType.
getMemberType() - Method in class net.sf.basedb.core.data.ItemListData: Get the type of items this list can hold.
getMemberType() - Method in class net.sf.basedb.core.ItemList: Get the item type of members on this list.
getMemberTypes() - Method in class net.sf.basedb.core.FileSet: Get a query that return the DataFileType for all members of this file set.
getMenu() - Method in class net.sf.basedb.clients.web.taglib.Page
getMenuId() - Method in class net.sf.basedb.clients.web.extensions.menu.FixedMenuItemFactory
getMenuId() - Method in interface net.sf.basedb.clients.web.extensions.menu.MenuItemAction: The ID of the menu where this menu item belongs, or null if it belongs to the top-level menu.
getMenuId() - Method in class net.sf.basedb.clients.web.extensions.menu.MenuItemBean
getMessage() - Method in class net.sf.basedb.core.ItemContext: Get a message that should be displayed by a client application as soon as it is appropriate to do so.
getMessage() - Method in class net.sf.basedb.core.PluginResponse: Get the return message from the plugin.
getMessage() - Method in class net.sf.basedb.core.SimpleProgressReporter: Get the last progress message this progress reporter should display.
getMessage() - Method in class net.sf.basedb.plugins.executor.ExternalProgramExecutor.ResponseWrapper
getMessage() - Method in class net.sf.basedb.util.extensions.logging.LogEntry: Get the log message.
getMessage() - Method in class net.sf.basedb.util.fileset.ValidatingFileSetMember: Get the error message if the file failed validation.
getMessage() - Method in class net.sf.basedb.util.overview.Failure: Get a message explaining the failure.
getMessage() - Method in class net.sf.basedb.util.overview.Fix: Get a message explaining what needs to be fixed.
getMessage(String) - Method in class net.sf.basedb.plugins.executor.ExternalProgramExecutor.ResponseWrapper
getMessages() - Method in class net.sf.basedb.core.data.JobData: This is the inverse end.
getMessages() - Method in class net.sf.basedb.core.data.UserData: This is the inverse end.
getMessages() - Method in class net.sf.basedb.core.User: Get a query that returns all messages for the user.
getMessages() - Method in class net.sf.basedb.util.extensions.manager.ProcessResults.FileResults: A list of detailed messages, indicating the results of individual operation on this file.
getMetaColumn() - Method in class net.sf.basedb.core.FeatureCoordinate
getMetadata() - Method in interface net.sf.basedb.util.uri.ConnectionManager: Get metadata about the resource.
getMetadata() - Method in class net.sf.basedb.util.uri.http.HttpConnectionManager
getMetadata(ObjectKey<M>) - Method in class net.sf.basedb.util.extensions.manager.ExtensionsFile: Get metadata registered for a given given key.
getMetadataKeysOfClass(Class<T>) - Method in class net.sf.basedb.util.extensions.manager.ExtensionsFile: Get a list of all metadata defined in this extensions file that are keyed with the specified class or interface.
getMetadataParser() - Method in class net.sf.basedb.util.importer.spotdata.BfsImporter
getMetadataPrefix() - Method in class net.sf.basedb.util.basefile.BaseFileWriter: The metadata prefix is written to the beginning of each line that is not a data line.
getMetadataSources() - Method in class net.sf.basedb.core.ServiceSessionControl.SessionFactoryConfiguration: Get an object for registering mapped entity classes.
getMetadataWriter() - Method in class net.sf.basedb.util.export.spotdata.BfsExporter: Get the writer were metadata should be printed.
getMetaGridX() - Method in class net.sf.basedb.core.ArrayDesignBlock: Get the column coordinate of this block.
getMetaGridX() - Method in class net.sf.basedb.core.BlockInfo: Get the row or x meta coordinate.
getMetaGridX() - Method in class net.sf.basedb.core.data.ArrayDesignBlockData: Get the row coordinate of this block.
getMetaGridX() - Method in class net.sf.basedb.core.data.RawData
getMetaGridX() - Method in class net.sf.basedb.plugins.PrintMapFlatFileImporter.MetaBlock
getMetaGridY() - Method in class net.sf.basedb.core.ArrayDesignBlock: Get the row coordinate of this block.
getMetaGridY() - Method in class net.sf.basedb.core.BlockInfo: Get the column or y meta coordinate.
getMetaGridY() - Method in class net.sf.basedb.core.data.ArrayDesignBlockData: Get the column coordinate of this block.
getMetaGridY() - Method in class net.sf.basedb.core.data.RawData
getMetaGridY() - Method in class net.sf.basedb.plugins.PrintMapFlatFileImporter.MetaBlock
getMetamodel() - Method in class net.sf.basedb.core.hibernate.SessionWrapper
getMetaRow() - Method in class net.sf.basedb.core.FeatureCoordinate
getMethod() - Method in class net.sf.basedb.core.authentication.AuthenticationMethod: Get the name of the authentication method.
getMethod() - Method in class net.sf.basedb.core.ExtendedPropertyAccessor.GetterSetter: Always return null.
getMethod() - Method in class net.sf.basedb.plugins.batchimport.AnnotationIdMethod
getMethod() - Method in class net.sf.basedb.plugins.batchimport.FallbackIdMethod
getMethod() - Method in class net.sf.basedb.plugins.batchimport.FileImporter.PathIdMethod
getMethod() - Method in interface net.sf.basedb.plugins.batchimport.IdMethod: The name of this method, which should be unique among the methods that can be used at a given time.
getMethod() - Method in class net.sf.basedb.plugins.batchimport.InternalIdMethod
getMethod() - Method in class net.sf.basedb.plugins.batchimport.MultiPropertyIdMethod
getMethod() - Method in class net.sf.basedb.plugins.batchimport.PropertyIdMethod
getMethod(Class<?>, String, Class<?>) - Method in class net.sf.basedb.util.extensions.debug.BeanActionFactory: Get a method with a specific name with optionally, takes a single parameter of given type.
getMethodName() - Method in class net.sf.basedb.core.ExtendedPropertyAccessor.GetterSetter: Always return null.
getMethodName(String, String) - Method in class net.sf.basedb.util.extensions.debug.BeanActionFactory: Convert the parameter name to a method name.
getMiameAnnotationTypes(DbControl, OverviewContext, Item) - Static method in class net.sf.basedb.util.overview.OverviewUtil: Get all annotation types that has been marked as "Required for MIAME".
getMidValue() - Method in class net.sf.basedb.core.Coloring: Get the value that represents the midpoint value.
getMidValue() - Method in class net.sf.basedb.core.data.ColoringData: The value for the midpoint color.
getMillisecondsSinceStart() - Method in class net.sf.basedb.clients.web.fileupload.FileUploadProgress: Get the number of milliseconds since the start of the upload.
getMimeType() - Method in class net.sf.basedb.clients.web.fileupload.UploadedFile: Get the MIME type of the uploaded file.
getMimeType() - Method in interface net.sf.basedb.clients.web.plugins.ExportTemplate: Get the MIME type to assign to files generated by this template.
getMimeType() - Method in class net.sf.basedb.clients.web.plugins.PlainTextTemplate
getMimeType() - Method in class net.sf.basedb.clients.web.plugins.XlsxTemplate
getMimeType() - Method in class net.sf.basedb.clients.web.plugins.XMLTemplate
getMimeType() - Method in class net.sf.basedb.core.data.FileData: Get the mime type of this FileData item.
getMimeType() - Method in class net.sf.basedb.core.File: The mimetype of this File.
getMimeType() - Method in class net.sf.basedb.core.plugin.ImportInputStream: Get the MIME type of the source.
getMimeType() - Method in class net.sf.basedb.util.FileImportInputStream: Calls File.getMimeType().
getMimeType() - Method in class net.sf.basedb.util.uri.UriMetadata: Get the MIME type of the resource.
getMimeType() - Method in class net.sf.basedb.util.zip.Bzip2FilePacker
getMimeType() - Method in interface net.sf.basedb.util.zip.FilePacker: Gets the MIME type to give compressed files from this packer
getMimeType() - Method in class net.sf.basedb.util.zip.GzipFilePacker
getMimeType() - Method in class net.sf.basedb.util.zip.TarFilePacker
getMimeType() - Method in class net.sf.basedb.util.zip.ZipFilePacker
getMimeType(DbControl, String, String) - Static method in class net.sf.basedb.core.MimeType: Get the MIME type of a given file name or extension.
getMimeTypes() - Method in class net.sf.basedb.plugins.Bzip2FileUnpacker: Return a set containing the strings [ application/x-bzip2 ].
getMimeTypes() - Method in class net.sf.basedb.plugins.GzipFileUnpacker: Return a set containing the strings [ application/x-gzip ].
getMimeTypes() - Method in class net.sf.basedb.plugins.TarFileUnpacker: Return a set containing the strings [ application/x-tar, application/x-gzip, application/x-bzip2 ].
getMimeTypes() - Method in class net.sf.basedb.plugins.ZipFileUnpacker: Return a set containing the strings [ application/zip, application/java-archive ].
getMimeTypes() - Method in interface net.sf.basedb.util.zip.FileUnpacker: Get the MIME type for the file formats this unpacker supports.
getMin() - Method in class net.sf.basedb.util.plot.HistogramPlot.HistogramBin: Get the minumum of all values in this bin.
getMinBaseVersion() - Method in interface net.sf.basedb.core.plugin.About: Get the minimum BASE version that the plug-in requires.
getMinBaseVersion() - Method in class net.sf.basedb.core.plugin.AboutImpl
getMinBaseVersion() - Method in class net.sf.basedb.util.extensions.AboutBean
getMinBaseVersion() - Method in class net.sf.basedb.util.extensions.Registry.RegisteredAbout
getMinCount() - Method in class net.sf.basedb.util.AnyToAnyLinkStatistics.Options
getMinFraction() - Method in class net.sf.basedb.util.AnyToAnyLinkStatistics.Options
getMinor() - Static method in class net.sf.basedb.core.Version: Get the minor version.
getMinorVersion() - Static method in class net.sf.basedb.core.Application: Get the minor version.
getMinValue() - Method in class net.sf.basedb.core.Coloring: Get the value that represents the minimum value.
getMinValue() - Method in class net.sf.basedb.core.data.ColoringData: The value for the minimum endpoint color.
getMinValueDouble() - Method in class net.sf.basedb.core.AnnotationType: Get the minumum allowed value for a Type.FLOAT or Type.DOUBLE annotation.
getMinValueLong() - Method in class net.sf.basedb.core.AnnotationType: Get the minumum allowed value for an Type.INT or Type.LONG annotation.
getMinY(int) - Method in class net.sf.basedb.util.plot.HistogramPlot.HistogramSeries
getMinY(HistogramPlot.HistogramBin) - Method in enum 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.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 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.
getNamedNativeQuery(String) - Method in class net.sf.basedb.core.hibernate.SessionWrapper
getNamedNativeQuery(String) - Method in class net.sf.basedb.core.hibernate.StatelessSessionWrapper
getNamedParameters() - Method in class net.sf.basedb.core.hibernate.QueryWrapper: Deprecated.
getNamedProcedureCall(String) - Method in class net.sf.basedb.core.hibernate.SessionWrapper
getNamedProcedureCall(String) - Method in class net.sf.basedb.core.hibernate.StatelessSessionWrapper
getNamedQuery(String) - Method in class net.sf.basedb.core.hibernate.SessionWrapper: If the same query has been executed before, return the cached instance, otherwise create a new query from the parent session and cache it.
getNamedQuery(String) - Method in class net.sf.basedb.core.hibernate.StatelessSessionWrapper: If the same query has been executed before, return the cached instance, otherwise create a new query from the parent session and cache it.
getNew(String) - Static method in class net.sf.basedb.core.Reporter: Get a new instance of a reporter, and setting the external ID.
getNew(DbControl) - Static method in class net.sf.basedb.core.AnnotationTypeCategory: Creates a new AnnotationTypeCategory item.
getNew(DbControl) - Static method in class net.sf.basedb.core.BioPlateType: Creates a new bioplate type.
getNew(DbControl) - Static method in class net.sf.basedb.core.BioSource: Create a new BioSource item.
getNew(DbControl) - Static method in class net.sf.basedb.core.Extract: Create a new Extract item.
getNew(DbControl) - Static method in class net.sf.basedb.core.FileServer: Create a new FileServer item.
getNew(DbControl) - Static method in class net.sf.basedb.core.Formula: Create a new Formula item.
getNew(DbControl) - Static method in class net.sf.basedb.core.Group: Create a new Group item.
getNew(DbControl) - Static method in class net.sf.basedb.core.Hardware: Create a new Hardware item.
getNew(DbControl) - Static method in class net.sf.basedb.core.Kit: Create a new Kit item.
getNew(DbControl) - Static method in class net.sf.basedb.core.MimeType: Create a new MimeType item.
getNew(DbControl) - Static method in class net.sf.basedb.core.PermissionTemplate: Create a new permission template item.
getNew(DbControl) - Static method in class net.sf.basedb.core.PhysicalBioAssay: Create a new PhysicalBioAssay item.
getNew(DbControl) - Static method in class net.sf.basedb.core.Project: Create a new Project item.
getNew(DbControl) - Static method in class net.sf.basedb.core.Protocol: Create a new Protocol item.
getNew(DbControl) - Static method in class net.sf.basedb.core.ReporterBatcher: Create a new batcher for reporters.
getNew(DbControl) - Static method in class net.sf.basedb.core.ReporterCloneTemplate: Create a new reporter clone template item.
getNew(DbControl) - Static method in class net.sf.basedb.core.ReporterList: Create a new ReporterList item.
getNew(DbControl) - Static method in class net.sf.basedb.core.ReporterType: Create a new ReporterType item.
getNew(DbControl) - Static method in class net.sf.basedb.core.Role: Create a new Role item.
getNew(DbControl) - Static method in class net.sf.basedb.core.Sample: Create a new Sample item.
getNew(DbControl) - Static method in class net.sf.basedb.core.Software: Create a new Software item.
getNew(DbControl) - Static method in class net.sf.basedb.core.Tag: Create a new Tag item.
getNew(DbControl) - Static method in class net.sf.basedb.core.VirtualDb: Create a new DynamicTables item.
getNew(DbControl, boolean, Job) - Static method in class net.sf.basedb.core.DerivedBioAssay: Create a new parent-less derived bioassay.
getNew(DbControl, int, int) - Static method in class net.sf.basedb.core.PlateGeometry: Create a new PlateGeometry item.
getNew(DbControl, long) - Static method in class net.sf.basedb.core.Quota: Create a new Quota item.
getNew(DbControl, String) - Static method in class net.sf.basedb.core.BioPlateEventType: Creates a new bioplate event type.
getNew(DbControl, String) - Static method in class net.sf.basedb.core.Client: Create a new Client item.
getNew(DbControl, String) - Static method in class net.sf.basedb.core.JobAgent: Create a new JobAgent item.
getNew(DbControl, String) - Static method in class net.sf.basedb.core.Quantity: Create a new Quantity item.
getNew(DbControl, String, int) - Static method in class net.sf.basedb.core.Platform: Create a new file-only platform.
getNew(DbControl, String, String) - Static method in class net.sf.basedb.core.GlobalDefaultSetting: Create a new GlobalDefaultSetting item.
getNew(DbControl, String, String) - Static method in class net.sf.basedb.core.PluginType: Create a new PluginType item.
getNew(DbControl, String, String) - Static method in class net.sf.basedb.core.User: Create a new User item.
getNew(DbControl, String, String, boolean) - Static method in class net.sf.basedb.core.PluginDefinition: Create a new PluginDefinition item.
getNew(DbControl, String, Item) - Static method in class net.sf.basedb.core.DataFileType: Create a new data file type.
getNew(DbControl, String, RawDataType) - Static method in class net.sf.basedb.core.Platform: Create a new platform which may optionally import data into the database.
getNew(DbControl, String, Type) - Static method in class net.sf.basedb.core.ExtraValueType: Create a new ExtraValue item.
getNew(DbControl, Date, Date) - Static method in class net.sf.basedb.core.News: Create a new News item.
getNew(DbControl, Annotatable) - Static method in class net.sf.basedb.core.AnnotationSet: Create a new annotation set for the specified item.
getNew(DbControl, ArrayBatch) - Static method in class net.sf.basedb.core.ArraySlide: Create a new ArraySlide item.
getNew(DbControl, ArrayDesign) - Static method in class net.sf.basedb.core.ArrayBatch: Create a new ArrayBatch item.
getNew(DbControl, ArrayDesign) - Static method in class net.sf.basedb.core.FeatureBatcher: Create a new batcher for regular features.
getNew(DbControl, ArrayDesign, BlockInfo) - Static method in class net.sf.basedb.core.ArrayDesignBlock
getNew(DbControl, BasicItem, BasicItem, String, boolean) - Static method in class net.sf.basedb.core.AnyToAny: Create a new AnyToAny link
getNew(DbControl, BioAssaySet, DataCubeColumn) - Static method in class net.sf.basedb.core.BioAssay: Create a new BioAssay item.
getNew(DbControl, BioAssaySet, ExtraValueType, DataCubeExtraValue, Job) - Static method in class net.sf.basedb.core.ExtraValue: Create a new ExtraValue item.
getNew(DbControl, BioPlateEventParticipant) - Static method in class net.sf.basedb.core.Extract: Create a new Extract item as part of a master bioplate event.
getNew(DbControl, BioPlateEventParticipant) - Static method in class net.sf.basedb.core.PhysicalBioAssay: Create a new PhysicalBioAssay item as part of a master bioplate event.
getNew(DbControl, BioPlateEventParticipant) - Static method in class net.sf.basedb.core.Sample: Create a new Sample item as part of a master bioplate event.
getNew(DbControl, BioPlateEvent, BioPlate) - Static method in class net.sf.basedb.core.BioPlateEventParticipant: Creates a new participant for the given event and bioplate.
getNew(DbControl, BioPlateEventType) - Static method in class net.sf.basedb.core.BioPlateEvent: Create a new BioPlateEvent item.
getNew(DbControl, Client, String) - Static method in class net.sf.basedb.core.Help: Create a new Help item.
getNew(DbControl, Client, String, String) - Static method in class net.sf.basedb.core.ClientDefaultSetting: Create a new ClientDefaultSetting item.
getNew(DbControl, DataCube) - Static method in class net.sf.basedb.core.DataCubeColumn: Create a new DataCubeColumn item.
getNew(DbControl, DataCube) - Static method in class net.sf.basedb.core.DataCubeFilter: Create a new DataCubeFilter item.
getNew(DbControl, DataCube) - Static method in class net.sf.basedb.core.DataCubeLayer: Create a new DataCubeLayer item.
getNew(DbControl, DataCube, Type, ExtraValue.CoordinateType) - Static method in class net.sf.basedb.core.DataCubeExtraValue: Create a new DataCubeExtraValue item.
getNew(DbControl, DerivedBioAssay, Job) - Static method in class net.sf.basedb.core.DerivedBioAssay: Create a new child derived bioassay from a parent derived bioassay.
getNew(DbControl, Directory) - Static method in class net.sf.basedb.core.Directory: Create a new Directory item.
getNew(DbControl, Directory) - Static method in class net.sf.basedb.core.File: Create a new File item.
getNew(DbControl, Experiment, Job) - Static method in class net.sf.basedb.core.Transformation: Create a new Transformation item.
getNew(DbControl, FileSet, File, DataFileType) - Static method in class net.sf.basedb.core.FileSetMember: Create a new member in a file set.
getNew(DbControl, FileStoreEnabled) - Static method in class net.sf.basedb.core.FileSet: Create a new file set for the specified item.
getNew(DbControl, Item) - Static method in class net.sf.basedb.core.ItemList: Create a new ItemList item.
getNew(DbControl, Item) - Static method in class net.sf.basedb.core.ItemSubtype: Create a new item subtype item.
getNew(DbControl, ItemSubtype, DataFileType) - Static method in class net.sf.basedb.core.ItemSubtypeFileType: Create a new item linking a file type to an item subtype.
getNew(DbControl, JobAgent, PluginDefinition) - Static method in class net.sf.basedb.core.JobAgentSettings: Create a new JobAgentSettings item.
getNew(DbControl, MeasuredBioMaterial) - Static method in class net.sf.basedb.core.BioMaterialEvent: Create a new BioMaterialEvent of the BioMaterialEvent.Type.OTHER type.
getNew(DbControl, MeasuredBioMaterial, BioPlateEventParticipant) - Static method in class net.sf.basedb.core.BioMaterialEvent: Create a new BioMaterialEvent of the BioMaterialEvent.Type.OTHER type that is linked with a master BioPlateEventParticipant.
getNew(DbControl, Path) - Static method in class net.sf.basedb.core.Directory: Create a new or existing Directory from a path.
getNew(DbControl, PhysicalBioAssay, Job) - Static method in class net.sf.basedb.core.DerivedBioAssay: Create a new (root) derived bioassay from a physical bioassay.
getNew(DbControl, PlateGeometry) - Static method in class net.sf.basedb.core.PlateType: Create a new PlateType item.
getNew(DbControl, PlateGeometry, int, PlateGeometry, int) - Static method in class net.sf.basedb.core.PlateMapping: Create a new PlateMapping item.
getNew(DbControl, PlateGeometry, BioPlateType) - Static method in class net.sf.basedb.core.BioPlate: Creates a new bioplate with a specific plate geometry and type.
getNew(DbControl, Plate, PlateEventType) - Static method in class net.sf.basedb.core.PlateEvent: Create a new PlateEvent item.
getNew(DbControl, PlateType) - Static method in class net.sf.basedb.core.Plate: Create a new Plate item.
getNew(DbControl, PlateType) - Static method in class net.sf.basedb.core.PlateEventType: Create a new PlateEventType item.
getNew(DbControl, Platform) - Static method in class net.sf.basedb.core.ArrayDesign: Create a new ArrayDesign item for a given platform.
getNew(DbControl, Platform, String) - Static method in class net.sf.basedb.core.PlatformVariant: Create a new variant of a platform.
getNew(DbControl, Platform, String, int) - Static method in class net.sf.basedb.core.PlatformVariant: Create a new file-only variant of a platform.
getNew(DbControl, Platform, String, RawDataType) - Static method in class net.sf.basedb.core.PlatformVariant: Create a new platform variant which may optionally import data into the database.
getNew(DbControl, Platform, PlatformVariant, DataFileType) - Static method in class net.sf.basedb.core.PlatformFileType: Create a new item linking a file type to a platform/variant.
getNew(DbControl, Platform, RawDataType) - Static method in class net.sf.basedb.core.RawBioAssay: Create a new raw bioassay for a specific platform and/or raw data type.
getNew(DbControl, PlatformVariant) - Static method in class net.sf.basedb.core.ArrayDesign: Create a new ArrayDesign item for a given platform variant.
getNew(DbControl, PlatformVariant, RawDataType) - Static method in class net.sf.basedb.core.RawBioAssay: Create a new raw bioassay for a specific platform variant.
getNew(DbControl, PluginDefinition) - Static method in class net.sf.basedb.core.PluginConfiguration: Create a new PluginConfiguration item.
getNew(DbControl, PluginDefinition, PluginConfiguration, Experiment) - Static method in class net.sf.basedb.core.Job: Create a new Job item.
getNew(DbControl, Quantity, String) - Static method in class net.sf.basedb.core.Unit: Create a new Unit item.
getNew(DbControl, RawBioAssay, FeatureIdentificationMethod) - Static method in class net.sf.basedb.core.RawDataBatcher: Create a new batcher for raw data.
getNew(DbControl, RawDataType) - Static method in class net.sf.basedb.core.Experiment: Create a new Experiment item.
getNew(DbControl, Transformation, DataCubeLayer) - Static method in class net.sf.basedb.core.BioAssaySet: Create a new BioAssaySet item.
getNew(DbControl, Type) - Static method in class net.sf.basedb.core.AnnotationType: Create a new AnnotationType item.
getNew(DbControl, User, String, String) - Static method in class net.sf.basedb.core.UserDefaultSetting: Create a new UserDefaultSetting item.
getNew(DbControl, User, String, User, Job) - Static method in class net.sf.basedb.core.Message: Create a new Message item.
getNew(DbControl, User, Client, String, String) - Static method in class net.sf.basedb.core.UserClientSetting: Create a new UserClientSetting item.
getNew(DbControl, VirtualDb) - Static method in class net.sf.basedb.core.DataCube: Create a new DataCube item.
getNewBioAssayEvent(DbControl, PhysicalBioAssay, BioPlateEventParticipant) - Static method in class net.sf.basedb.core.BioMaterialEvent: Create a new BioMaterialEvent of the BioMaterialEvent.Type.BIOASSAY type.
getNewChildren() - Method in class net.sf.basedb.util.overview.Node: Get all new children to this node.
getNewCreationEvent(DbControl, MeasuredBioMaterial, BioPlateEventParticipant) - Static method in class net.sf.basedb.core.BioMaterialEvent: Create a new BioMaterialEvent of the BioMaterialEvent.Type.CREATION type (creation event).
getNewFile(boolean) - Method in class net.sf.basedb.core.File: Get a new random file path.
getNewImageRemapperIfNeeded(ServletContext) - Static method in class net.sf.basedb.clients.web.extensions.skin.ImageRemapperUtil: Get a new image remapper if it is needed, otherwise null.
getNewInherited(DbControl, AnnotationSet, AnnotationData, boolean) - Static method in class net.sf.basedb.core.Annotation: Create a new inherited or cloned annotation.
getNewOrCurrentOverview(DbControl, BasicItem, Project) - Static method in class net.sf.basedb.util.overview.OverviewUtil: Get the current overview or create a new overview.
getNewOrExisting(DbControl, BasicItem, String, BasicItem, boolean) - Static method in class net.sf.basedb.core.AnyToAny: Get a new or existing AnyToAny link.
getNewOrExisting(DbControl, ProjectPermissions) - Static method in class net.sf.basedb.core.ProjectKey: Create a new or load an existing ProjectKey when you have a combination of project/permission values.
getNewOrExisting(DbControl, UserPermissions, GroupPermissions) - Static method in class net.sf.basedb.core.ItemKey: Create a new or load an existing ItemKey when you have a combination of user/group/permission values.
getNewOrExistingId(Session, Map<ProjectData, Integer>) - Static method in class net.sf.basedb.core.ProjectKey: Find the ID of an existing key with exactly the same project/permission combination.
getNewOrExistingKey(Session, Map<UserData, Integer>, Map<GroupData, Integer>) - Static method in class net.sf.basedb.core.ItemKey: Find the ID of an existing key with exactly the same user/group/permission combination.
getNewOverview(DbControl, BasicItem, Project) - Static method in class net.sf.basedb.util.overview.OverviewUtil: Create a new overview for the given item and project.
getNewParameterVersion() - Method in class net.sf.basedb.core.PluginConfiguration: Increase the version number once per transaction.
getNewPrimary(DbControl, AnnotationSet, AnnotationTypeData) - Static method in class net.sf.basedb.core.Annotation: Create a new primary annotation.
getNewsDate() - Method in class net.sf.basedb.core.data.NewsData: Get the news date of this news item.
getNewsDate() - Method in class net.sf.basedb.core.News: Get the date that is shown in listings.
getNewsFeed(String, boolean) - Method in class net.sf.basedb.clients.web.servlet.RssNewsFeed: Generate the XML string for the news feed.
getNewStream() - Method in class net.sf.basedb.util.StreamCacher: Get a new stream that appears to be reading from the start of the master stream.
getNewSystemMessage(DbControl, UserData, String, UserData, JobData) - Static method in class net.sf.basedb.core.Message: Create a new Message from the system.
getNewValue() - Method in class net.sf.basedb.core.ChangeHistory: Get the new value of the property had immediately after this change.
getNewValue() - Method in class net.sf.basedb.core.data.ChangeHistoryDetailData: Get the new value after the change.
getNewValue() - Method in class net.sf.basedb.core.log.ManualLogEntry: New value after the change.
getNewValues() - Method in class net.sf.basedb.core.AnnotationBatcher.CurrentAnnotationInfo: Get the new annotation values.
getNextColumnId() - Method in class net.sf.basedb.clients.web.taglib.table.ExtensionCells: This is called by the Cell taglib when the next extension column is about to be processed.
getNextColumnNo() - Method in class net.sf.basedb.core.DataCube: Generate the next available column number.
getNextCommand() - Method in class net.sf.basedb.core.PluginResponse: Get the next command sent via Response.Status.CONTINUE.
getNextCubeNo() - Method in class net.sf.basedb.core.VirtualDb: Generate the next available cube number.
getNextEntry(TarInputStream) - Static method in class net.sf.basedb.util.zip.TarUtil: Get the next entry from a TAR input stream.
getNextExtraValueNo() - Method in class net.sf.basedb.core.DataCube: Generate the next available extra value number.
getNextFilename(Object, String) - Method in class net.sf.basedb.util.bfs.SequenceFilenameGenerator
getNextFilename(Object, String) - Method in class net.sf.basedb.util.bfs.SuggestedFilenameGenerator
getNextFilename(T, String) - Method in interface net.sf.basedb.util.bfs.FilenameGenerator: Get the next file name.
getNextFileNumber() - Method in class net.sf.basedb.util.bfs.SequenceFilenameGenerator: Get the next file number.
getNextFilterNo() - Method in class net.sf.basedb.core.DataCube: Generate the next available filter number.
getNextLayerNo() - Method in class net.sf.basedb.core.DataCube: Generate the next available layer number.
getNextLine() - Method in class net.sf.basedb.util.gtf.GtfInputStream: Read the next line from the GTF file and split on tab character.
getNextRequest() - Method in class net.sf.basedb.core.PluginResponse: Get a PluginRequest object that handles the next request, if status is Response.Status.CONTINUE.
getNextRowClass() - Method in class net.sf.basedb.clients.web.taglib.table.Table
getNode() - Method in class net.sf.basedb.core.data.JobData: The name of the node where the job is executing.
getNode() - Method in class net.sf.basedb.core.Job: Get the name of the node where the job is executing.
getNode() - Method in class net.sf.basedb.util.overview.Failure: Get the node that failed validation.
getNode() - Method in class net.sf.basedb.util.Tree.Entry: Get the node element object.
getNode(String) - Method in class net.sf.basedb.util.overview.GenericOverview: Get the node with the given ID.
getNode(K) - Method in class net.sf.basedb.util.overview.cache.NodeCache
getNodeCache() - Method in class net.sf.basedb.util.overview.GenericOverview: This overview implementation doesn't currently support node caching.
getNodeCache() - Method in interface net.sf.basedb.util.overview.OverviewContext: Get the current node cache.
getNodeFactory(DbControl, OverviewContext) - Method in class net.sf.basedb.util.overview.loader.BasicItemNodeLoader: Get a node factory that can be used to create item nodes.
getNodeFactory(DbControl, OverviewContext, NodeValidator<? super I>, NodeNameGenerator<? super I>) - Method in class net.sf.basedb.util.overview.loader.BasicItemNodeLoader: Get a node factory that can be used to create item nodes using a non-default name generator and validator.
getNodeLoader(OverviewContext, Object) - Method in class net.sf.basedb.util.overview.loader.BasicItemNodeLoader: Get a node loader for a specific item type using the current context's node loader factory.
getNodeLoaderFactory() - Method in class net.sf.basedb.util.overview.GenericOverview: Get the current node loader factory.
getNodeLoaderFactory() - Method in interface net.sf.basedb.util.overview.OverviewContext: Get the node loader factory that is used to create node loaders.
getNodeLoaderFactory(OverviewContext) - Method in class net.sf.basedb.util.overview.loader.BasicItemNodeLoader: Get the node loader factory used by the current context.
getNodeName(I, Node) - Method in class net.sf.basedb.util.overview.node.NameableNameGenerator
getNodeName(I, Node) - Method in interface net.sf.basedb.util.overview.node.NodeNameGenerator: Generate a name for the new node that is about to be created.
getNodeName(Annotation, Node) - Method in class net.sf.basedb.util.overview.node.AnnotationNameGenerator
getNodeName(AnyToAny, Node) - Method in class net.sf.basedb.util.overview.node.AnyToAnyNameGenerator
getNodeName(FileSetMember, Node) - Method in class net.sf.basedb.util.overview.node.FileSetMemberNameGenerator
getNodeName(Listable, Node) - Method in class net.sf.basedb.util.overview.node.ItemListMemberNameGenerator
getNodeName(MeasuredBioMaterial, Node) - Method in class net.sf.basedb.util.overview.node.BioWellNameGenerator
getNodeNameGenerator() - Method in class net.sf.basedb.util.overview.loader.BasicItemNodeLoader: Get the name generator that is used by this loader.
getNodeTitle(I, Node) - Method in class net.sf.basedb.util.overview.node.NameableNameGenerator
getNodeTitle(I, Node) - Method in interface net.sf.basedb.util.overview.node.NodeNameGenerator: Generate a title for the new node that is about to be created.
getNodeTitle(Annotation, Node) - Method in class net.sf.basedb.util.overview.node.AnnotationNameGenerator
getNodeTitle(AnyToAny, Node) - Method in class net.sf.basedb.util.overview.node.AnyToAnyNameGenerator
getNodeTitle(BioPlate, Node) - Method in class net.sf.basedb.util.overview.node.BioPlateNameGenerator: The base of the title is generated by the superclass.
getNodeTitle(Extract, Node) - Method in class net.sf.basedb.util.overview.node.ExtractNameGenerator: The base of the title is generated by the superclass.
getNodeTitle(FileSetMember, Node) - Method in class net.sf.basedb.util.overview.node.FileSetMemberNameGenerator
getNodeTitle(Listable, Node) - Method in class net.sf.basedb.util.overview.node.ItemListMemberNameGenerator
getNodeTitle(MeasuredBioMaterial, Node) - Method in class net.sf.basedb.util.overview.node.BioWellNameGenerator
getNodeType() - Method in class net.sf.basedb.util.overview.Node: Get the node type of this node.
getNodeValidator() - Method in class net.sf.basedb.util.overview.node.NodeFactory: Get the node validator that is used by this factory.
getNodeValidator(OverviewContext) - Method in class net.sf.basedb.util.overview.loader.BasicItemNodeLoader: Get the default node validator for nodes of this type.
getNodeValidatorFactory() - Method in class net.sf.basedb.util.overview.GenericOverview: Get the current node validator factory.
getNodeValidatorFactory() - Method in interface net.sf.basedb.util.overview.OverviewContext: Get the node validator factory that is used to create node validators.
getNodeValidatorFactory(OverviewContext) - Method in class net.sf.basedb.util.overview.loader.BasicItemNodeLoader: Get the node validator factory used by the current context.
getNoDuplicates() - Method in class net.sf.basedb.util.annotations.InheritSpecification
getNoSkin() - Method in class net.sf.basedb.clients.web.taglib.Page
getNotNull() - Method in class net.sf.basedb.core.ParameterType: Check if the parameter can be null.
getNulltext() - Method in class net.sf.basedb.clients.web.taglib.PropertyValue
getNullValue() - Method in class net.sf.basedb.util.export.TableWriter: The null value string is written to the output instead of null data values.
getNumAcceptedWithNullReporterOnFeature() - Method in class net.sf.basedb.core.RawDataBatcher: Get the number of accepted inserts because of features with a NULL reporter.
getNumAnnotations() - Method in class net.sf.basedb.plugins.AnnotationFlatFileImporter.NewAnnotations: The total numer of annotation values that has been added to this cache.
getNumArrays() - Method in class net.sf.basedb.core.ArrayDesign: Get the number of arrays on a single slide.
getNumArrays() - Method in class net.sf.basedb.core.data.ArrayDesignData: The number of arrays on a single slide.
getNumberFormat() - Method in class net.sf.basedb.plugins.AbstractFlatFileImporter: Get a number formatter that is able to parse numbers with the specified decimal separator.
getNumberFormat() - Method in class net.sf.basedb.util.excel.XlsxToCsvUtil: Get the formatter that is used for formatting cells with numeric values.
getNumberFormat(char, char) - Static method in class net.sf.basedb.util.NumberFormatUtil
getNumberFormatter(SessionControl) - Static method in class net.sf.basedb.clients.web.formatter.FormatterFactory: Get the logged in user's number formatter for float values.
getNumberOfParameters() - Method in class net.sf.basedb.util.jep.ChannelFunction
getNumberOfParameters() - Method in class net.sf.basedb.util.jep.ExtraValueFunction
getNumberOfParameters() - Method in class net.sf.basedb.util.jep.FunctionSafeJep.UnknownFunction
getNumberOfParameters() - Method in class net.sf.basedb.util.jep.InReporterListFunction
getNumberOfParameters() - Method in class net.sf.basedb.util.jep.LeftFunction
getNumberOfParameters() - Method in class net.sf.basedb.util.jep.Log2Function
getNumberOfParameters() - Method in class net.sf.basedb.util.jep.MeanFunction
getNumberOfParameters() - Method in class net.sf.basedb.util.jep.NotInReporterListFunction
getNumberOfParameters() - Method in class net.sf.basedb.util.jep.PositionFunction
getNumberOfParameters() - Method in class net.sf.basedb.util.jep.RawChannelFunction
getNumberOfParameters() - Method in class net.sf.basedb.util.jep.RawFunction
getNumberOfParameters() - Method in class net.sf.basedb.util.jep.ReporterFunction
getNumberOfParameters() - Method in class net.sf.basedb.util.jep.ScoreFunction
getNumberOfParameters() - Method in class net.sf.basedb.util.jep.SimpleJepFunction
getNumberOfParameters() - Method in class net.sf.basedb.util.parser.ColFunction
getNumberOfParameters() - Method in class net.sf.basedb.util.parser.DataNoFunction
getNumberOfParameters() - Method in class net.sf.basedb.util.parser.DefaultItemFunction
getNumberOfParameters() - Method in class net.sf.basedb.util.parser.LineNoFunction
getNumBioAssays() - Method in class net.sf.basedb.clients.web.ExperimentExplorer: Get the number of bioassays in the bioassayset.
getNumBytes(FlatFileParser) - Method in class net.sf.basedb.plugins.AbstractFlatFileImporter: Get the number of bytes read from the file.
getNumBytes(FlatFileParser) - Method in class net.sf.basedb.plugins.gtf.GtfReporterImporter: Get the number of bytes read from the original file.
getNumBytes(FlatFileParser) - Method in class net.sf.basedb.plugins.gtf.GtfReporterMapImporter: Get the number of bytes read from the original file.
getNumChildren() - Method in class net.sf.basedb.util.Tree.Entry: Get the number of children added to this node.
getNumColumns() - Method in class net.sf.basedb.core.data.DataCubeData: The number of columns in this data cube.
getNumColumns() - Method in class net.sf.basedb.core.DataCube: Get the number of columns created in this data cube.
getNumDbFeatures() - Method in class net.sf.basedb.core.ArrayDesign: Get the number of features on this array design that are stored in the database.
getNumDbFeatures() - Method in class net.sf.basedb.core.data.ArrayDesignData: The number of features on this array design that are stored in the database.
getNumDbSpots() - Method in class net.sf.basedb.core.RawBioAssay: Get the number of spots on this raw bioassay that are stored in the database.
getNumDecimals(Number) - Method in class net.sf.basedb.util.formatter.AdaptiveNumberFormatter
getNumDecimals(SessionControl) - Static method in class net.sf.basedb.clients.web.formatter.FormatterSettings: Get the number of decimals a number formatter should display.
getNumDeleted() - Method in class net.sf.basedb.util.extensions.manager.ExtensionsManager: Get the number of deleted files that was found in the last call to ExtensionsManager.scanForChanges().
getNumDeleted() - Method in class net.sf.basedb.util.extensions.manager.processor.DeleteResourcesProcessor: Get the total number of resources that was deleted.
getNumEntries() - Method in class net.sf.basedb.util.extensions.logging.ExtensionsLog: Get the current number of entries in the log.
getNumError() - Method in class net.sf.basedb.clients.web.extensions.LoadServletsProcessor: Get the number of files that was had an error.
getNumError() - Method in class net.sf.basedb.plugins.AnnotationFlatFileImporter.NewAnnotations: Number of annotations that was couldn't be set by the call to the AnnotationFlatFileImporter.NewAnnotations.setNewAnnotations(AnnotationFlatFileImporter, AnnotationBatcher, boolean, boolean, boolean, boolean) method because of an error (too many values).
getNumError() - Method in class net.sf.basedb.util.extensions.manager.processor.DeleteResourcesProcessor: Get the number of files that was had an error.
getNumError() - Method in class net.sf.basedb.util.extensions.manager.processor.DisablePluginsProcessor: Get the number of files that was had an error.
getNumError() - Method in class net.sf.basedb.util.extensions.manager.processor.ExtractResourcesProcessor: Get the number of files that was had an error.
getNumError() - Method in class net.sf.basedb.util.extensions.manager.processor.PluginInstallationProcessor: Get the number of files that was had an error.
getNumError() - Method in class net.sf.basedb.util.extensions.manager.processor.RegisterExtensionsProcessor: Get the number of files that was had an error.
getNumError() - Method in class net.sf.basedb.util.extensions.manager.processor.UnregisterExtensionsProcessor: Get the number of files that was had an error.
getNumErrorFiles() - Method in class net.sf.basedb.util.extensions.manager.ProcessResults: The number of extension files that could not be completely loaded because of an error.
getNumErrors() - Method in class net.sf.basedb.util.extensions.logging.ExtensionsLog: Get the current number of error entries in the log.
getNumErrors() - Method in class net.sf.basedb.util.overview.Node: Get the number of errors on this node.
getNumExtensions() - Method in class net.sf.basedb.util.extensions.ExtensionsInvoker: Get the number of enabled extensions in this invokation.
getNumExtracted() - Method in class net.sf.basedb.util.extensions.manager.processor.ExtractResourcesProcessor: Get the total number of resources that was extracts.
getNumExtraValues() - Method in class net.sf.basedb.core.data.DataCubeData: The number of extra values in this data cube.
getNumExtraValues() - Method in class net.sf.basedb.core.DataCube: Get the number of extra values created for this data cube.
getNumFileFeatures() - Method in class net.sf.basedb.core.ArrayDesign: Get the number of features on this array design that are stored inside files.
getNumFileFeatures() - Method in class net.sf.basedb.core.data.ArrayDesignData: The number of features on this array design that are stored inside files.
getNumFileReporters() - Method in class net.sf.basedb.core.BioAssaySet: Get the number of unique reporters for data that is stored in files.
getNumFileReporters() - Method in class net.sf.basedb.core.data.BioAssaySetData: The number of unique reporters as stored in files in this bioassayset.
getNumFiles() - Method in class net.sf.basedb.clients.web.extensions.LoadServletsProcessor: Get the number of files that was successfully processed.
getNumFiles() - Method in class net.sf.basedb.clients.web.extensions.UninstalledFileProcessor: Get the number of files that was processed.
getNumFiles() - Method in class net.sf.basedb.util.extensions.manager.processor.DeleteResourcesProcessor: Get the number of files that was successfully processed.
getNumFiles() - Method in class net.sf.basedb.util.extensions.manager.processor.DisablePluginsProcessor: Get the number of files that was successfully processed.
getNumFiles() - Method in class net.sf.basedb.util.extensions.manager.processor.ExtractResourcesProcessor: Get the number of files that was successfully processed.
getNumFiles() - Method in class net.sf.basedb.util.extensions.manager.processor.IgnoreFileProcessor: Get the number of files that was processed.
getNumFiles() - Method in class net.sf.basedb.util.extensions.manager.processor.MarkAsProcessedProcessor: Get the number of files that was processed.
getNumFiles() - Method in class net.sf.basedb.util.extensions.manager.processor.PluginInstallationProcessor: Get the number of files that was successfully processed.
getNumFiles() - Method in class net.sf.basedb.util.extensions.manager.processor.RegisterExtensionsProcessor: Get the number of files that was successfully processed.
getNumFiles() - Method in class net.sf.basedb.util.extensions.manager.processor.ResetProcessor: Get the number of files that was processed.
getNumFiles() - Method in class net.sf.basedb.util.extensions.manager.processor.UnregisterExtensionsProcessor: Get the number of files that was successfully processed.
getNumFileSpots() - Method in class net.sf.basedb.core.BioAssay: Get the number of spots that are stored in files.
getNumFileSpots() - Method in class net.sf.basedb.core.BioAssaySet: Get the number of spots that are stored in files.
getNumFileSpots() - Method in class net.sf.basedb.core.data.BioAssayData: The number of unique spots in this bioassayset.
getNumFileSpots() - Method in class net.sf.basedb.core.data.BioAssaySetData: The number of unique spots in this bioassayset.
getNumFileSpots() - Method in class net.sf.basedb.core.data.RawBioAssayData: The number of spots on this raw bioassay that are stored inside files.
getNumFileSpots() - Method in class net.sf.basedb.core.RawBioAssay: Get the number of spots on this raw bioassay that are stored inside files.
getNumFileValues() - Method in class net.sf.basedb.core.data.ExtraValueData: The number of extra values that are stored in files.
getNumFileValues() - Method in class net.sf.basedb.core.ExtraValue: Get the number of values that are stored in files.
getNumFilteredColumns() - Method in class net.sf.basedb.clients.web.taglib.table.Table
getNumFilters() - Method in class net.sf.basedb.core.data.DataCubeData: The number of filters in this data cube.
getNumFilters() - Method in class net.sf.basedb.core.DataCube: Get the number of filters created for this data cube.
getNumFormulas() - Method in class net.sf.basedb.core.Formula: Get the number of expression defined by this formula.
getNumIgnored() - Method in class net.sf.basedb.util.extensions.manager.ExtensionsManager: Get the number of ignored files that was found in the last call to ExtensionsManager.scanForChanges().
getNumLayers() - Method in class net.sf.basedb.core.data.DataCubeData: The number of layers in this data cube.
getNumLayers() - Method in class net.sf.basedb.core.DataCube: Get the number of layers created in this data cube.
getNumLines() - Method in class net.sf.basedb.util.gtf.GtfInputStream: Get the number of lines parsed so far.
getNumMembers(DataFileType) - Method in class net.sf.basedb.core.FileSet: Get the number of members in the file set of the specified type.
getNumModified() - Method in class net.sf.basedb.util.extensions.manager.ExtensionsManager: Get the number of modified files that was found in the last call to ExtensionsManager.scanForChanges().
getNumNew() - Method in class net.sf.basedb.util.extensions.manager.ExtensionsManager: Get the number of new files that was found in the last call to ExtensionsManager.scanForChanges().
getNumPlates() - Method in class net.sf.basedb.core.ArrayDesign: The number of plates connected to this array design.
getNumPlugins() - Method in class net.sf.basedb.util.extensions.manager.processor.DisablePluginsProcessor: Get the total number of plug-in installed or updated by the processor.
getNumPlugins() - Method in class net.sf.basedb.util.extensions.manager.processor.PluginInstallationProcessor: Get the total number of plug-in installed or updated by the processor.
getNumPositions() - Method in class net.sf.basedb.core.data.DataCubeData: The number of positions in this data cube.
getNumPositions() - Method in class net.sf.basedb.core.DataCube: Get the number of positions created in this data cube.
getNumPositions(DbControl, int) - Method in class net.sf.basedb.clients.web.ExperimentExplorer: Get the number of unique positions the reporter of the specifed index is present in among all the bioassays in the bioassay set.
getNumPropertyFilters() - Method in class net.sf.basedb.core.ItemContext: Get the total number of property filters stored in this context.
getNumPropertyFilters(int) - Method in class net.sf.basedb.core.ItemContext: Get the number of property filters stored in this context for the given filter row.
getNumRead() - Method in class net.sf.basedb.util.InputStreamSplitter: Get the number of bytes that has been read or skipped from the input stream.
getNumRead() - Method in class net.sf.basedb.util.InputStreamTracker: Get the number of bytes read or skipped from the input stream.
getNumRecent(String) - Method in class net.sf.basedb.core.ItemContext: Get the number of recently used value in the list.
getNumRecent(Item) - Method in class net.sf.basedb.core.ItemContext: Get the number of recently used items in the list.
getNumRecent(Item, String) - Method in class net.sf.basedb.core.ItemContext: Get the number of recently used items in a list with a sublist.
getNumRecent(Item, ItemSubtype) - Method in class net.sf.basedb.core.ItemContext: Get the number of recently used items in the list.
getNumRegistered() - Method in class net.sf.basedb.util.extensions.manager.processor.RegisterExtensionsProcessor: Get the number of extensions + extension points that was registered.
getNumRemoved() - Method in class net.sf.basedb.plugins.AnnotationFlatFileImporter.NewAnnotations: Number of annotations that was removed by the call to the AnnotationFlatFileImporter.NewAnnotations.setNewAnnotations(AnnotationFlatFileImporter, AnnotationBatcher, boolean, boolean, boolean, boolean) method.
getNumReplaced() - Method in class net.sf.basedb.plugins.AnnotationFlatFileImporter.NewAnnotations: Number of annotations that was replaced by the call to the AnnotationFlatFileImporter.NewAnnotations.setNewAnnotations(AnnotationFlatFileImporter, AnnotationBatcher, boolean, boolean, boolean, boolean) method.
getNumReporters() - Method in class net.sf.basedb.clients.web.ExperimentExplorer: Get the total number of unique reporters found in the bioassayset.
getNumReporters() - Method in class net.sf.basedb.core.BioAssaySet: Get the number of unique reporters among all bioassays in this bioassayset.
getNumReporters() - Method in class net.sf.basedb.core.data.BioAssaySetData: The number of unique reporters in this bioassayset.
getNumReportersNotFound() - Method in class net.sf.basedb.core.RawDataBatcher: Get the number of reporters that was not found.
getNumServlets() - Method in class net.sf.basedb.clients.web.extensions.LoadServletsProcessor: Get the total number of servlets found during the last processing.
getNumSet() - Method in class net.sf.basedb.plugins.AnnotationFlatFileImporter.NewAnnotations: Number of annotations that was set (=added or replaced) by the call to the AnnotationFlatFileImporter.NewAnnotations.setNewAnnotations(AnnotationFlatFileImporter, AnnotationBatcher, boolean, boolean, boolean, boolean) method.
getNumSheets() - Method in class net.sf.basedb.util.excel.XlsxToCsvUtil: Get the number of sheets in the workbook.
getNumSkippedLines() - Method in class net.sf.basedb.util.parser.FlatFileParser: Get the number of lines that the last call to FlatFileParser.nextData() or FlatFileParser.hasMoreData() ignored because they matched the ignore regular expression or couldn't be interpreted as data lines.
getNumSkippedMissingFeature() - Method in class net.sf.basedb.core.RawDataBatcher: Get the number of skipped inserts because of a missing feature.
getNumSpots() - Method in class net.sf.basedb.clients.web.ExperimentExplorer: Get the total number of spots in the bioassayset.
getNumSpots() - Method in class net.sf.basedb.core.BioAssay: Get the number of spots in this bioassay.
getNumSpots() - Method in class net.sf.basedb.core.BioAssaySet: Get the number of spots in all bioassays in this bioassayset.
getNumSpots() - Method in class net.sf.basedb.core.data.BioAssayData: The number of unique spots in this bioassay.
getNumSpots() - Method in class net.sf.basedb.core.data.BioAssaySetData: The number of unique spots in this bioassayset.
getNumStatements() - Method in class net.sf.basedb.core.hibernate.SchemaGenerator.CollectSqlTarget
getNumUniqueTranscriptIds() - Method in class net.sf.basedb.util.gtf.GtfInputStream: Get the number of unique transcript ids found so far.
getNumUnmodified() - Method in class net.sf.basedb.util.extensions.manager.ExtensionsManager: Get the number of unmodified files that was found in the last call to ExtensionsManager.scanForChanges().
getNumUnregistered() - Method in class net.sf.basedb.util.extensions.manager.processor.RegisterExtensionsProcessor: Get the number of extensions + extension points that was unregistered.
getNumUnregistered() - Method in class net.sf.basedb.util.extensions.manager.processor.UnregisterExtensionsProcessor: Get the number of extensions + extension points that was unregistered.
getNumValues() - Method in class net.sf.basedb.core.data.ExtraValueData: The number of extra values that have been inserted.
getNumValues() - Method in class net.sf.basedb.core.ExtraValue: Get the number of extra values inserted.
getNumValues(String) - Method in class net.sf.basedb.util.QueryParameters: Get the number of values for a key.
getNumWarnings() - Method in class net.sf.basedb.util.extensions.logging.ExtensionsLog: Get the current number of warning entries in the log.
getNumWarnings() - Method in class net.sf.basedb.util.overview.Node: Get the number of warnings on this node.
getObject(int) - Method in class net.sf.basedb.clients.web.servlet.PlotServlet.CFSqlResult
getObject(int) - Method in class net.sf.basedb.core.DynamicResultIterator.SqlResultImpl
getObject(int) - Method in interface net.sf.basedb.core.query.SqlResult: Get the value of the specified column as an object.
getObject(String) - Method in class net.sf.basedb.core.ItemContext: Get an object.
getObjectForKey(ObjectKey<O>) - Method in class net.sf.basedb.clients.web.extensions.ExtensionsControl: Get the object that was registered for the given key.
getObjectForKey(ObjectKey<O>) - Method in class net.sf.basedb.util.extensions.manager.ExtensionsFile: Get the object that was registered for the given key.
getObjectsOfClass(Class<T>) - Method in class net.sf.basedb.util.extensions.manager.ExtensionsFile: Get a list of all objects defined in this extensions file that are of the specified class or interface.
getOldItem(SessionControl, T, int) - Static method in class net.sf.basedb.clients.web.Base: Get the old item that is stored in the SessionControl:s session setting itemType.item.
getOldValue() - Method in class net.sf.basedb.core.ChangeHistory: Get the old value of the property had before this change.
getOldValue() - Method in class net.sf.basedb.core.data.ChangeHistoryDetailData: Get the previous value before the change.
getOldValue() - Method in class net.sf.basedb.core.log.ManualLogEntry: Old value before the change.
getOldValues() - Method in class net.sf.basedb.core.AnnotationBatcher.CurrentAnnotationInfo: Get the old annotation values.
getOldValues() - Method in class net.sf.basedb.core.data.ParameterValueData: Get the old values that has been replaced by new values in this session.
getOpen() - Method in class net.sf.basedb.clients.web.taglib.menu.Menu
getOperator() - Method in class net.sf.basedb.core.data.PropertyFilterData: Get the operator used for this filter.
getOperator() - Method in class net.sf.basedb.core.PropertyFilter: Get the operator to use in the filter.
getOperators() - Static method in class net.sf.basedb.util.jep.Jep: Get a list of built-in operators supported by the Jep.jepToExpression(JEP) and Jep.jepToRestriction(JEP) converter.
getOptimizeTableSql(String, String, String) - Method in interface net.sf.basedb.core.dbengine.DbEngine: Generate SQL to optimize a table.
getOptimizeTableSql(String, String, String) - Method in class net.sf.basedb.core.dbengine.DefaultDbEngine: Return null.
getOptimizeTableSql(String, String, String) - Method in class net.sf.basedb.core.dbengine.MySQLEngine: Generate optimize table <catalog>.<table>.
getOptimizeTableSql(String, String, String) - Method in class net.sf.basedb.core.dbengine.PostgresDbEngine: Generate VACUUM FULL <schema>.<table>.
getOption(String) - Method in class net.sf.basedb.clients.jobagent.CmdLine: Get the value for the specified option
getOption(String) - Method in class net.sf.basedb.core.AnnotationType: Get an option.
getOption(String) - Method in class net.sf.basedb.plugins.executor.ParameterDefinition: Get the value for an option.
getOption(String, String) - Method in class net.sf.basedb.clients.jobagent.CmdLine: Get the value for an option.
getOption(ValidationRuleAction, String, String) - Method in class net.sf.basedb.util.overview.ValidationOptions: Get the configured option for a validator rule.
getOptionalFilter(Item) - Static method in class net.sf.basedb.core.QueryRuntimeFilterFactory: Get the default optional runtime filter for the speicified item type.
getOptions() - Method in class net.sf.basedb.core.data.AnnotationTypeData: Additional options depending on the value type.
getOptions() - Method in class net.sf.basedb.plugins.Base1PluginExecuter.JobParameter
getOptions() - Method in class net.sf.basedb.plugins.executor.ParameterDefinition: Get the names of other options that are defined for this parmeter.
getOrCreate(JspContext, FileViewerContext) - Static method in class net.sf.basedb.clients.web.extensions.fileviewer.FileViewerUtil: Get an existing instance or create a new instance.
getOrdinal() - Method in class net.sf.basedb.core.data.PlateEventTypeData: The ordinal of this event type among all event types defined for the plate type.
getOrdinal() - Method in class net.sf.basedb.core.PlateEventType: Get the order of this event among the list of events.
getOrganisation() - Method in class net.sf.basedb.core.authentication.ExtraUserInformation: The organisation of the user.
getOrganisation() - Method in class net.sf.basedb.core.data.UserData: Get the organisation this user works for, or null if unknown.
getOrganisation() - Method in class net.sf.basedb.core.User: Get the organisation this user works for, or null if unknown.
getOriginalBioMaterial() - Method in class net.sf.basedb.core.BioWell: Get the original biomaterial that was placed in this biowell.
getOriginalBioMaterial() - Method in class net.sf.basedb.core.data.BioWellData: The MeasuredBioMaterialData used in this well.
getOriginalPermissions() - Method in class net.sf.basedb.core.GroupPermissions: Get the internal representation of the original permissions.
getOriginalPermissions() - Method in class net.sf.basedb.core.ProjectPermissions: Get the internal representation of the original permissions.
getOriginalPermissions() - Method in class net.sf.basedb.core.UserPermissions: Get the internal representation of the original permissions.
getOriginalPermissions(Group) - Method in class net.sf.basedb.core.GroupPermissions: Get the original permissions for a group if this object was created with the GroupPermissions(ItemKey) constructor.
getOriginalPermissions(Project) - Method in class net.sf.basedb.core.ProjectPermissions: Get the original permissions for a project if this object was created with the ProjectPermissions(ProjectKey) constructor.
getOriginalPermissions(User) - Method in class net.sf.basedb.core.UserPermissions: Get the original permissions for a user if this object was created with the UserPermissions(ItemKey) constructor.
getOriginalQuantity() - Method in class net.sf.basedb.core.data.MeasuredBioMaterialData: Get the original quantity of the biomaterial.
getOriginalQuantity() - Method in class net.sf.basedb.core.MeasuredBioMaterial: Get the original quantity of the biomaterial.
getOriginX() - Method in class net.sf.basedb.core.ArrayDesignBlock: Get the distance from the left edge of the slide to the top left spot in the block.
getOriginX() - Method in class net.sf.basedb.core.data.ArrayDesignBlockData: Get the distance from the left edge of the slide to the top left spot in the block.
getOriginX() - Method in class net.sf.basedb.plugins.PrintMapFlatFileImporter.MetaBlock
getOriginY() - Method in class net.sf.basedb.core.ArrayDesignBlock: Get the distance from the top edge of the slide to the top left spot in the block.
getOriginY() - Method in class net.sf.basedb.core.data.ArrayDesignBlockData: Get the distance from the top edge of the slide to the top left spot in the block.
getOriginY() - Method in class net.sf.basedb.plugins.PrintMapFlatFileImporter.MetaBlock
getOut() - Method in class net.sf.basedb.clients.web.extensions.JspContext: Get a writer object that can be used to return generated text to the response that is sent back to the browser.
getOutputStream(File) - Method in class net.sf.basedb.core.Migration: Get a stream for writing to the given file.
getOutputStream(File) - Static method in class net.sf.basedb.util.FileUtil: Get a buffered OutputStream object writing to the specified file.
getOutputStream(String) - Method in class net.sf.basedb.util.bfs.AbstractDataWriterFactory: Create an output stream for writing to a file with the given filename.
getOutputStream(String) - Method in class net.sf.basedb.util.bfs.GenericBaseDataWriterFactory: Create a new file in the data directory with the given file name.
getOutputStream(String) - Method in class net.sf.basedb.util.bfs.GenericDiskDataWriterFactory: Create a new file in the data directory with the given file name.
getOutputStream(String, int) - Method in class net.sf.basedb.util.StaticCache: Get a lock-safe output stream.
getOverrideId() - Method in class net.sf.basedb.core.data.AnnotationData: The ID of the default annotation that this project-specific annotation is overriding. 0 for default annotations.
getOverrideId() - Method in class net.sf.basedb.core.data.annotations.AnnotationLink
getOverrideId() - Method in class net.sf.basedb.core.snapshot.AnnotationSnapshot: Get the id of the default annotation that this project-specific annotation is overriding.
getOverwrite() - Method in class net.sf.basedb.core.plugin.AbstractExporterPlugin: Get the configured value for the overwrite parameter.
getOverwrite() - Method in class net.sf.basedb.util.zip.AbstractFileUnpacker: If existing file should be overwritten or not.
getOverwriteAnnotationsParameters(String, String, Boolean) - Method in class net.sf.basedb.core.plugin.AbstractPlugin: Parameter definition that asks if copied annotations should overwrite existing annotations or not.
getOverwriteParameter(String, String) - Method in class net.sf.basedb.core.plugin.AbstractExporterPlugin: Get a plugin parameter that asks if existing files can be overwritten or not.
getOverwriteParameter(String, String) - Method in class net.sf.basedb.util.zip.AbstractFileUnpacker: Get a plugin parameter that asks if existing files should be overwritten or not.
getOwnableItems() - Static method in class net.sf.basedb.core.Metadata: Get a set containing all Ownable item types.
getOwner() - Method in interface net.sf.basedb.core.data.OwnableData: Get the UserData that is the owner of the item.
getOwner() - Method in class net.sf.basedb.core.data.OwnedData
getOwner() - Method in interface net.sf.basedb.core.Ownable: Get the User that is the owner of the item.
getOwner() - Method in class net.sf.basedb.core.OwnedItem
getPacker() - Method in class net.sf.basedb.plugins.PackedFileExporter: Get the FilePacker that has been configured in the current configuration.
getPacker(String) - Method in class net.sf.basedb.plugins.PackedFileExporter: Create a FilePacker from the given class.
getPage() - Method in class net.sf.basedb.clients.web.taglib.table.Navigator
getPage() - Method in class net.sf.basedb.clients.web.taglib.table.Table
getPage() - Method in class net.sf.basedb.core.data.ContextData: Get the current page number, starting at 0.
getPage() - Method in class net.sf.basedb.core.ItemContext: Get the current table page.
getPageContext() - Method in class net.sf.basedb.clients.web.extensions.JspContext: Get the JSP Page context object for the current request.
getPageType() - Method in class net.sf.basedb.clients.web.ModeInfo
getPageType() - Method in exception net.sf.basedb.clients.web.WebException: Get the page type to display the error message in.
getParameter(int) - Method in class net.sf.basedb.core.hibernate.QueryWrapper
getParameter(int, Class<T>) - Method in class net.sf.basedb.core.hibernate.QueryWrapper
getParameter(String) - Method in class net.sf.basedb.clients.web.extensions.AbstractJspFactory: Get a generic parameter value.
getParameter(String) - Method in class net.sf.basedb.clients.web.fileupload.FileUpload: Get the value for a form field.
getParameter(String) - Method in class net.sf.basedb.core.hibernate.QueryWrapper
getParameter(String) - Method in class net.sf.basedb.core.RequestInformation: Get the plugin parameter with the specified name.
getParameter(String) - Method in class net.sf.basedb.util.export.spotdata.BaseFileExporter: Get the current value of a 'settings' parameter.
getParameter(String) - Method in class net.sf.basedb.util.export.spotdata.BfsExporter: Get the current value of a parameter.
getParameter(String, Class<T>) - Method in class net.sf.basedb.core.hibernate.QueryWrapper
getParameterClass() - Method in class net.sf.basedb.core.ParameterType: Get the class a value must have to match this parameter type.
getParameterDefinition() - Method in class net.sf.basedb.plugins.executor.ProgramParameter: Get the definition of this parameter.
getParameterDefinitions(boolean) - Method in class net.sf.basedb.plugins.executor.ExternalProgramExecutor: Get the current program parameter definitions.
getParameterInfo(String) - Method in class net.sf.basedb.core.Job: Get extra information about a parameter.
getParameterInfo(String) - Method in class net.sf.basedb.core.PluginConfiguration: Get extra information about a parameter in the latest version.
getParameterInfo(String, int) - Method in class net.sf.basedb.core.PluginConfiguration: Get extra information about a parameter in a specific version.
getParameterMetadata() - Method in class net.sf.basedb.core.hibernate.QueryWrapper
getParameterName(String) - Method in class net.sf.basedb.util.extensions.debug.ProxyActionFactory: Convert a method name to a parameter name.
getParameterNames() - Method in class net.sf.basedb.clients.web.fileupload.FileUpload: Get the names for all fields used in the form, excluding file input fields.
getParameterNames() - Method in class net.sf.basedb.core.AbstractQuery
getParameterNames() - Method in class net.sf.basedb.core.Job: Get the names of all parameters for the job.
getParameterNames() - Method in class net.sf.basedb.core.PluginConfiguration: Get the names of all configuration values in the latest version.
getParameterNames() - Method in interface net.sf.basedb.core.query.Query: Get a set with the names for all parameters in this query.
getParameterNames(int) - Method in class net.sf.basedb.core.PluginConfiguration: Get the names of all configuration values in a specific version.
getParameters() - Method in class net.sf.basedb.core.AbstractQuery: Get all query parameters.
getParameters() - Method in class net.sf.basedb.core.data.JobData: The parameters for this job.
getParameters() - Method in class net.sf.basedb.core.data.ProtocolData: This set manages the parameters for this protcol.
getParameters() - Method in class net.sf.basedb.core.hibernate.QueryWrapper
getParameters() - Method in class net.sf.basedb.core.Protocol: Get a query that returns all annotation types used as parameters for this protocol.
getParameters() - Method in class net.sf.basedb.core.RequestInformation: Get a list containing the information about the parameters needed for the current request.
getParametersFromBaseFile(File) - Method in class net.sf.basedb.plugins.Base1PluginExecuter: Get the data from the configuration file.
getParameterType() - Method in class net.sf.basedb.core.PluginParameter: Get the parameter type, which tells the client application the data type and allowed values for the parameter.
getParameterType(Class<T>, List<?>) - Method in class net.sf.basedb.core.PluginConfiguration: Gets the ParameterType to use with a class.
getParameterType(String) - Method in class net.sf.basedb.core.AbstractQuery: Get the type of the parameter, or null if not known.
getParameterValue(int) - Method in class net.sf.basedb.core.hibernate.QueryWrapper
getParameterValue(String) - Method in class net.sf.basedb.core.AbstractQuery: Get the value of the named parameter.
getParameterValue(String) - Method in class net.sf.basedb.core.hibernate.QueryWrapper
getParameterValue(String) - Method in class net.sf.basedb.core.Job: Get the value of a named parameter.
getParameterValue(String) - Method in class net.sf.basedb.core.plugin.NamespaceRequestWrapper
getParameterValue(String) - Method in interface net.sf.basedb.core.plugin.Request: Get the value for the parameter with the specified name.
getParameterValue(String) - Method in class net.sf.basedb.core.PluginRequest.RequestImpl
getParameterValue(String) - Method in class net.sf.basedb.plugins.executor.ExternalProgramExecutor.RequestWrapper
getParameterValue(String, Class<?>) - Method in class net.sf.basedb.util.extensions.debug.ProxyActionFactory: Get the value of a parameter.
getParameterValue(Parameter<T>) - Method in class net.sf.basedb.core.hibernate.QueryWrapper
getParameterValues() - Method in class net.sf.basedb.core.Job: Get the configuration parameters as a ParameterValues object.
getParameterValues(int) - Method in class net.sf.basedb.core.PluginConfiguration: Get the configuration parameters as a ParameterValues object.
getParameterValues(String) - Method in class net.sf.basedb.clients.web.fileupload.FileUpload: Get an array of values for a form field.
getParameterValues(String) - Method in class net.sf.basedb.core.Job: Get the values of a named parameter.
getParameterValues(String) - Method in class net.sf.basedb.core.plugin.NamespaceRequestWrapper
getParameterValues(String) - Method in interface net.sf.basedb.core.plugin.Request: Get the values for the parameter with the specified name.
getParameterValues(String) - Method in class net.sf.basedb.core.PluginConfiguration: Get the values of a configuration parameter in the latest version.
getParameterValues(String) - Method in class net.sf.basedb.core.PluginRequest.RequestImpl
getParameterValues(String) - Method in class net.sf.basedb.plugins.executor.ExternalProgramExecutor.RequestWrapper
getParameterValues(String, int) - Method in class net.sf.basedb.core.PluginConfiguration: Get the values of a configuration parameter in a specific version.
getParameterValuesImpl() - Method in class net.sf.basedb.core.Job: Get a write-protected ParameterValuesImpl object.
getParameterValuesImpl(int) - Method in class net.sf.basedb.core.PluginConfiguration: Get a write-protected ParameterValuesImpl object so a job can read the paremeters.
getParameterVersion() - Method in class net.sf.basedb.core.data.JobData: Get the parameter version of the configuration used for this job.
getParameterVersion() - Method in class net.sf.basedb.core.data.PluginConfigurationData: Get the current/latest parameter version.
getParameterVersion() - Method in class net.sf.basedb.core.Job: Get the version number of the configuration parameters used for this job.
getParameterVersion() - Method in class net.sf.basedb.core.PluginConfiguration: Get the latest version number of the parameters.
getParent() - Method in class net.sf.basedb.clients.web.extensions.renderer.PrefixSuffixRenderer
getParent() - Method in class net.sf.basedb.core.data.DirectoryData: Get the parent directory of this directory.
getParent() - Method in class net.sf.basedb.core.data.MeasuredBioMaterialData: Get the parent biomaterial.
getParent() - Method in class net.sf.basedb.core.data.WellData: If the plate was created from a PlateMappingData this property points to the well on the source plate used in the mapping.
getParent() - Method in class net.sf.basedb.core.Directory: Get the parent directory of this directory.
getParent() - Method in class net.sf.basedb.core.MeasuredBioMaterial: Get the parent biomaterial if there is a single parent item only.
getParent() - Method in class net.sf.basedb.core.Path: Get the parent path.
getParent() - Method in class net.sf.basedb.core.Well: Get the parent well.
getParent() - Method in interface net.sf.basedb.util.extensions.WrappingRenderer: Get the current parent renderer.
getParent() - Method in class net.sf.basedb.util.overview.Node: Get the parent of this node.
getParent() - Method in class net.sf.basedb.util.Tree.Entry: Get the entry for the parent node.
getParentBioAssay() - Method in class net.sf.basedb.core.data.RawBioAssayData: Get the derived bioassay that this raw bioassay has been created from.
getParentBioAssay() - Method in class net.sf.basedb.core.RawBioAssay: Get the DerivedBioAssay this raw bioassay is created from.
getParentExtract() - Method in class net.sf.basedb.core.data.RawBioAssayData: Get the derived bioassay that this raw bioassay has been created from.
getParentExtract() - Method in class net.sf.basedb.core.RawBioAssay: Get the Extract this raw bioassay is created from.
getParentFileSets() - Method in class net.sf.basedb.core.ArrayDesign: There are no parent file sets.
getParentFileSets() - Method in class net.sf.basedb.core.BioAssaySet: Get the file set from the parent bioassay set if it exists.
getParentFileSets() - Method in class net.sf.basedb.core.DerivedBioAssay
getParentFileSets() - Method in class net.sf.basedb.core.ExtraValue: Get the file set from the parent bioassay set if it exists.
getParentFileSets() - Method in interface net.sf.basedb.core.FileStoreEnabled: Get the file sets of parent item(s) that are related to the current item.
getParentFileSets() - Method in class net.sf.basedb.core.RawBioAssay: Get the file set from the array design, if it exists.
getParentHasNullReporter() - Method in class net.sf.basedb.util.importer.spotdata.BaseFileInfo: A flag that indicates if at least one position in the parent bioassay set has a null reporter or not.
getParentHasZeroReporter() - Method in class net.sf.basedb.util.importer.spotdata.BaseFileInfo: A flag that indicates if at least one position in the parent bioassay set has a reporter with ID=0.
getParentId() - Method in class net.sf.basedb.core.data.keyring.GroupGroups: Get the id of the parent group.
getParentInformation(DbControl, Node) - Method in class net.sf.basedb.util.overview.validator.ProtocolParameterValidator: Load parent item information from the current protocol node.
getParentItem() - Method in class net.sf.basedb.clients.web.extensions.fileviewer.FileViewerContext: If the context has a parent item this method returns it.
getParentPlates() - Method in class net.sf.basedb.core.Plate: Get a query returning the parent plates of this plate.
getParentProperties(DbControl, BioAssay, Metadata.PropertyPath<RawBioAssay, ?>) - Static method in class net.sf.basedb.util.BioAssaySetUtil: Find the values of parent properties for a given bioassay.
getParentQuery() - Method in class net.sf.basedb.core.hibernate.NativeQueryWrapper: Get the underlying parent query from Hibernate.
getParents() - Method in class net.sf.basedb.core.BioAssay: Get a query for loading the parents bioassays to this bioassay.
getParents() - Method in class net.sf.basedb.core.data.BioAssayData: Get a set that manages the parent bioassays the data in this bioassay is based on.
getParents() - Method in class net.sf.basedb.core.data.DerivedBioAssayData: A set that manages the parent bioassays that this derived bioassay related to.
getParents() - Method in class net.sf.basedb.core.data.GroupData: This is the inverse end.
getParents() - Method in class net.sf.basedb.core.data.ItemSubtypeData: This is the inverse end.
getParents() - Method in class net.sf.basedb.core.data.PlateData: If the plate was created by a PlateMappingData the source plates are kept here.
getParents() - Method in class net.sf.basedb.core.DerivedBioAssay: Get all parent derived bioassays.
getParents() - Method in class net.sf.basedb.util.importer.spotdata.BaseFileInfo.ChildBioAssay: Get the parent assays of this child.
getParentSession() - Method in class net.sf.basedb.core.hibernate.SessionWrapper: Get the underlying parent session from Hibernate.
getParentSession() - Method in class net.sf.basedb.core.hibernate.StatelessSessionWrapper: Get the underlying parent session from Hibernate.
getParentSet() - Method in class net.sf.basedb.core.data.PlateData: Duplicate of PlateData.getParents() but with a set instead of a map.
getParentSubtypes() - Method in class net.sf.basedb.core.ItemSubtype: Get a query returning all subtypes that have a relation to this subtype.
getParentSubtypes(DbControl, Subtypable, Item) - Static method in class net.sf.basedb.core.ItemSubtype: Utility method for locating all subtypes that have a relationship to the subtype of the given item.
getParentType() - Method in class net.sf.basedb.core.BasicChildItem: Get the type of item that is the parent of this item.
getParentType() - Method in class net.sf.basedb.core.data.MeasuredBioMaterialData: Get the type of the parent item.
getParentType() - Method in class net.sf.basedb.core.ItemSubtypeFileType
getParentType() - Method in class net.sf.basedb.core.MeasuredBioMaterial: Get the item type of the parent biomaterial.
getParentType() - Method in class net.sf.basedb.core.PlatformFileType
getParentType() - Method in class net.sf.basedb.core.PlatformVariant
getParseAllExcelSheets() - Method in class net.sf.basedb.util.parser.FlatFileParser
getParsedBytes() - Method in class net.sf.basedb.util.bfs.AnnotationParser
getParsedBytes() - Method in interface net.sf.basedb.util.bfs.BfsParser: Get the number of parsed bytes so far.
getParsedBytes() - Method in class net.sf.basedb.util.bfs.DataParser
getParsedBytes() - Method in class net.sf.basedb.util.bfs.MetadataParser
getParsedBytes() - Method in class net.sf.basedb.util.charset.CharsetDetector: Get the number of bytes that the last test operation parsed.
getParsedBytes() - Method in class net.sf.basedb.util.importer.spotdata.SynchronizedSpotDataParser
getParsedBytes() - Method in class net.sf.basedb.util.parser.FlatFileParser: Get the number of parsed bytes so far.
getParsedCharacters() - Method in class net.sf.basedb.util.parser.FlatFileParser: Get the number of parsed characters so far.
getParsedDataLines() - Method in class net.sf.basedb.util.parser.FlatFileParser: Get the number of parsed data lines so far in the current section.
getParsedLines() - Method in class net.sf.basedb.util.charset.CharsetDetector
getParsedLines() - Method in class net.sf.basedb.util.parser.FlatFileParser: Get the number of parsed lines so far.
getParsedSections() - Method in class net.sf.basedb.util.parser.FlatFileParser: Get the number of found sections so far.
getParser() - Method in class net.sf.basedb.core.data.FormulaData: Which parser to use to convert the formula to an expression or restriction. 1 = JEP
getParser() - Method in class net.sf.basedb.core.Formula: Get the parser that converts the formula to an expresion or restriction.
getParser() - Method in class net.sf.basedb.util.importer.spotdata.SynchronizedSpotDataParser.SynchronizedData: The underlying parser.
getParsingFailure() - Method in class net.sf.basedb.util.charset.CharsetDetector: If the last test failed, get the exception that was thrown by the parser.
getParticipant(BioPlate) - Method in class net.sf.basedb.core.BioPlateEvent: Get the participant object representing the given bioplate in this event.
getParticipants() - Method in class net.sf.basedb.core.BioPlateEvent: Get a query returning all participants in the event.
getParticipants() - Method in class net.sf.basedb.core.data.BioPlateEventData: This is the inverse end.
getPassword() - Method in class net.sf.basedb.clients.jobagent.Agent: Get the agent.password configuration value.
getPassword() - Method in class net.sf.basedb.core.authentication.LoginRequest: Get the password to use.
getPassword() - Method in class net.sf.basedb.core.data.FileServerData: Get the password that is used to login to the server.
getPassword() - Method in class net.sf.basedb.core.data.UserData: Get the PasswordData object which allows you to change the password for the user.
getPassword() - Method in class net.sf.basedb.core.FileServer: Get the password that is used when authenticating with the file server.
getPassword() - Method in class net.sf.basedb.util.uri.ConnectionParameters: Get the password that should be used to authenticate the user.
getPasswordField() - Method in interface net.sf.basedb.clients.web.extensions.login.LoginFormAction: Get attributes for the password field on the form.
getPasswordField() - Method in class net.sf.basedb.clients.web.extensions.login.LoginFormBean
getPasswordField() - Method in class net.sf.basedb.clients.web.extensions.login.PasswordLoginFormFactory
getPasswordParameter() - Method in interface net.sf.basedb.util.zip.FilePacker: The default implementation return a parameter asking for a password.
getPasswordParameter() - Method in class net.sf.basedb.util.zip.ZipFilePacker: Get the encyption password parameter.
getPath() - Method in class net.sf.basedb.core.Directory: Get the complete path to this directory.
getPath() - Method in class net.sf.basedb.core.File: Get the complete path of this file.
getPath() - Method in class net.sf.basedb.core.Metadata.BasicData2ItemPropertyPath
getPath() - Method in class net.sf.basedb.core.Metadata.BasicItem2DataPropertyPath
getPath() - Method in class net.sf.basedb.core.Metadata.CollectionPropertyPath
getPath() - Method in class net.sf.basedb.core.Metadata.CombinedPropertyPath
getPath() - Method in class net.sf.basedb.core.Metadata.ComponentPropertyPath
getPath() - Method in class net.sf.basedb.core.Metadata.DateCopyPropertyPath
getPath() - Method in class net.sf.basedb.core.Metadata.EntityPropertyPath
getPath() - Method in class net.sf.basedb.core.Metadata.EvictPropertyPath
getPath() - Method in class net.sf.basedb.core.Metadata.IdentifierPropertyPath
getPath() - Method in class net.sf.basedb.core.Metadata.MapPropertyPath
getPath() - Method in class net.sf.basedb.core.Metadata.NoopPropertyPath
getPath() - Method in interface net.sf.basedb.core.Metadata.PropertyPath: Get the path that this object represents.
getPath() - Method in class net.sf.basedb.core.Metadata.ReporterScore2DataPropertyPath
getPathInfo() - Method in class net.sf.basedb.clients.web.extensions.RequestWrapper: From the HttpServletRequestInterface ------------------------------------
getPathType() - Method in class net.sf.basedb.core.PathParameterType: Get the type of the path to ask for.
getPattern(String) - Method in class net.sf.basedb.plugins.AbstractFlatFileImporter
getPattern(String, int, int) - Method in class net.sf.basedb.util.export.spotdata.AdvancedFieldConverter
getPattern(ParameterValues, String) - Method in class net.sf.basedb.plugins.AbstractFlatFileImporter
getPercent() - Method in class net.sf.basedb.core.SimpleProgressReporter: Get the last percentage completed of the task.
getPercentComplete() - Method in class net.sf.basedb.core.data.JobData: If the job is running, how many percent has been completed.
getPercentComplete() - Method in class net.sf.basedb.core.Job: An estimate of the percentage of the work currently completed by an executing job.
getPercentile(List<? extends Number>, int) - Method in class net.sf.basedb.clients.web.servlet.ExperimentExplorerPlotServlet: Calculates the percentile values from a sorted list of values.
getPermanentSelects() - Method in class net.sf.basedb.core.AbstractQuery: Get all permanent selects.
getPermission() - Method in class net.sf.basedb.core.data.keyring.KeyPermission: Get the permission.
getPermission() - Method in class net.sf.basedb.core.data.keyring.ProjectPermission: Get the permission.
getPermissionCode(Set<Permission>) - Static method in class net.sf.basedb.clients.web.PermissionUtil: Translate the given set of permissions to an integer code that can be used to later recreate the set again.
getPermissionForUse() - Method in class net.sf.basedb.core.ChildItem: Get the permission that is required on the parent item that gives use permission on the child item.
getPermissionForWriteDeleteAndCreate() - Method in class net.sf.basedb.core.BasicChildItem: Get the permission that is required on the parent item that gives write, delete and create permission on the child item.
getPermissionForWriteDeleteAndCreate() - Method in class net.sf.basedb.core.BioAssay: USE permission is enough to be able to manage bioassays.
getPermissionForWriteDeleteAndCreate() - Method in class net.sf.basedb.core.BioAssaySet: USE permission is enough to be able to manage bioassay sets.
getPermissionForWriteDeleteAndCreate() - Method in class net.sf.basedb.core.ChildItem: Get the permission that is required on the parent item that gives write, delete and create permission on the child item.
getPermissionForWriteDeleteAndCreate() - Method in class net.sf.basedb.core.DataCube: USE permission is enough to be able to manage data cubes.
getPermissionForWriteDeleteAndCreate() - Method in class net.sf.basedb.core.DataCubeColumn: USE permission is enough to be able to manage data cubes.
getPermissionForWriteDeleteAndCreate() - Method in class net.sf.basedb.core.DataCubeExtraValue: USE permission is enough to be able to manage data cubes.
getPermissionForWriteDeleteAndCreate() - Method in class net.sf.basedb.core.DataCubeFilter: USE permission is enough to be able to manage data cubes.
getPermissionForWriteDeleteAndCreate() - Method in class net.sf.basedb.core.DataCubeLayer: USE permission is enough to be able to manage data cubes.
getPermissionForWriteDeleteAndCreate() - Method in class net.sf.basedb.core.ExtraValue: USE permission is enough to be able to manage extra values.
getPermissionForWriteDeleteAndCreate() - Method in class net.sf.basedb.core.RootRawBioAssay: WRITE permission is required to be able to manage root raw bioassays.
getPermissionForWriteDeleteAndCreate() - Method in class net.sf.basedb.core.Transformation: USE permission is enough to be able to manage transformations.
getPermissionForWriteDeleteAndCreate() - Method in class net.sf.basedb.core.VirtualDb: USE permission is enough to be able to manage virtual db.
getPermissionGroups() - Static method in class net.sf.basedb.clients.web.PermissionUtil
getPermissions() - Method in class net.sf.basedb.clients.web.extensions.ExtensionsControl
getPermissions() - Method in interface net.sf.basedb.core.AccessControlled: Get the logged in user's permissions on the item.
getPermissions() - Method in class net.sf.basedb.core.BasicBatcher
getPermissions() - Method in class net.sf.basedb.core.BasicItem
getPermissions() - Method in class net.sf.basedb.core.BioMaterialEventSource
getPermissions() - Method in class net.sf.basedb.core.Coloring
getPermissions() - Method in class net.sf.basedb.core.data.PluginDefinitionData: Get a map containing the rolekey and the permissions for this plugin.
getPermissions() - Method in class net.sf.basedb.core.plugin.AbstractPlugin: Return null, which gives the plugin the same permissions as the logged in user.
getPermissions() - Method in interface net.sf.basedb.core.plugin.Plugin: Get the permissions this plugin requires to function as expected.
getPermissions() - Method in class net.sf.basedb.plugins.AnnotationFlatFileImporter: Request read access to File:s, read access to annotation types and write access to all annotatable items.
getPermissions() - Method in class net.sf.basedb.plugins.Base1PluginExecuter
getPermissions() - Method in class net.sf.basedb.plugins.BaseFileExporterPlugin: Request create and write access to File:s and Directory:s and read access to Experiment:s and User:s.
getPermissions() - Method in class net.sf.basedb.plugins.CdfFileReporterImporter: Request create and write access to Reporter:s and read access to File:s ArrayDesign:s, ReporterType:s, Platform:s and DataFileType:s
getPermissions() - Method in class net.sf.basedb.plugins.CloneReportersPlugin: Request write permission to Experiment:s and Reporter clone templates and read permission to reporters.
getPermissions() - Method in class net.sf.basedb.plugins.FormulaFilter: Request use access to Experiment:s and read access to Job:s and ReporterLists.
getPermissions() - Method in class net.sf.basedb.plugins.GalExporter: Request create and write access to File:s, Directory:s and ArrayDesign:s read access to User:s and forced read access to DataFileType:s.
getPermissions() - Method in class net.sf.basedb.plugins.HelpExporter: Request create and write access to File:s and Directory:s and read access to Client:s and User:s.
getPermissions() - Method in class net.sf.basedb.plugins.HelpImporter: Request write access to Client:s and read access to File:s.
getPermissions() - Method in class net.sf.basedb.plugins.IntensityCalculatorPlugin: Request use access to Experiment:s and read access to RawBioAssay:s, ArrayDesign:s, Formulas:s, Job:s and and Reporter:s.
getPermissions() - Method in class net.sf.basedb.plugins.JepExtraValueCalculator: Request use access to Experiment:s and ExtraValueType:s and read access to Job:s.
getPermissions() - Method in class net.sf.basedb.plugins.JepIntensityTransformer: Request use access to Experiment:s and read access to Job:s.
getPermissions() - Method in class net.sf.basedb.plugins.LowessNormalization: Request use access to Experiment:s and read access to Job:s.
getPermissions() - Method in class net.sf.basedb.plugins.MedianRatioNormalization: Request use access to Experiment:s and read access to Job:s.
getPermissions() - Method in class net.sf.basedb.plugins.PackedFileExporter: Request create and delete access to File:s and Directory:s.
getPermissions() - Method in class net.sf.basedb.plugins.PlateFlatFileImporter: Request create access to Plate:s, use access to PlateType:s and read access to Reporter:s, PlateGeometry:s and File:s.
getPermissions() - Method in class net.sf.basedb.plugins.PlateMappingExporter: Request create and write access to File:s and Directory:s and read access to PlateMapping:s and PlateGeometries.
getPermissions() - Method in class net.sf.basedb.plugins.PlateMappingImporter: Request create and write access to PlateMapping:s, create and use access to PlateGeometries and read access to File:s.
getPermissions() - Method in class net.sf.basedb.plugins.PluginConfigurationExporter: Request create and write access to File:s and Directory:s and read access to PluginConfigurations:s, PluginDefinition:s and User:s.
getPermissions() - Method in class net.sf.basedb.plugins.PrintMapFlatFileImporter: Request write access to ArrayDesign:s, read access to Plate:s, Reporter:s, DataFileType:s, Platform:s and File:s.
getPermissions() - Method in class net.sf.basedb.plugins.RawDataFlatFileImporter: Request write access to RawBioAssay:s and read access to ArrayDesign:s, File:s, Reporter:s, Platform:s and DataFileType:s
getPermissions() - Method in class net.sf.basedb.plugins.ReporterFlatFileImporter: Request create, write and delete access to Reporter:s, write access to ReporterList:s and read access to File:s and ReporterType:s.
getPermissions() - Method in class net.sf.basedb.plugins.ReporterMapFlatFileImporter: Request write access to ArrayDesign:s, read access to Reporter:s, DataFileType:s, Platform:s and File:s.
getPermissions() - Method in class net.sf.basedb.util.zip.AbstractFileUnpacker: Request create and write access to File:s and Directory:s.
getPermissions(int) - Static method in class net.sf.basedb.clients.web.PermissionUtil: Translate a given integer to a set of permissions.
getPermissions(Group) - Method in class net.sf.basedb.core.GroupPermissions: Get the permissions for a group.
getPermissions(Group) - Method in class net.sf.basedb.core.ItemKey: Get the permissions for a group.
getPermissions(Group) - Method in class net.sf.basedb.core.MultiPermissions: Get the permissions for a group.
getPermissions(Group) - Method in class net.sf.basedb.core.Project: Get the permissions for a group in this project.
getPermissions(Project) - Method in class net.sf.basedb.core.MultiPermissions: Get the permissions for a project.
getPermissions(Project) - Method in class net.sf.basedb.core.ProjectKey: Get the permissions for a project.
getPermissions(Project) - Method in class net.sf.basedb.core.ProjectPermissions: Get the permissions for a project.
getPermissions(Role) - Method in class net.sf.basedb.core.RoleKey: Get the permissions for a role.
getPermissions(User) - Method in class net.sf.basedb.core.ItemKey: Get the permissions for a user.
getPermissions(User) - Method in class net.sf.basedb.core.MultiPermissions: Get the permissions for a user.
getPermissions(User) - Method in class net.sf.basedb.core.Project: Get the permissions for a user in this project.
getPermissions(User) - Method in class net.sf.basedb.core.UserPermissions: Get the permissions for a user.
getPermissionTemplate() - Method in class net.sf.basedb.core.data.ProjectData: A permission template can be used to set default permissions when this project is active.
getPermissionTemplate() - Method in class net.sf.basedb.core.Project: Get the permission template that is used to share new items when this project is active.
getPhone() - Method in class net.sf.basedb.core.authentication.ExtraUserInformation: The phone number to the user.
getPhone() - Method in class net.sf.basedb.core.data.UserData: Get the phone number to the user, or null if unknown.
getPhone() - Method in class net.sf.basedb.core.User: Get the phone number to the user, or null if unknown.
getPhysicalBioAssay() - Method in class net.sf.basedb.core.ArraySlide: Get the PhysicalBioAssay item which was used on this slide.
getPhysicalBioAssay() - Method in class net.sf.basedb.core.BioMaterialEvent: Get the PhysicalBioAssay that was created by this event.
getPhysicalBioAssay() - Method in class net.sf.basedb.core.data.ArraySlideData: Get the bioassay.
getPhysicalBioAssay() - Method in class net.sf.basedb.core.data.BioMaterialEventData: Get the physical bioassay that was created by this event.
getPhysicalBioAssays() - Method in class net.sf.basedb.core.data.DerivedBioAssayData: A set that manages the parent physical bioassays that this derived bioassay is related to.
getPhysicalBioAssays() - Method in class net.sf.basedb.core.DerivedBioAssay: Get a query that returns the physical bioassays used to create this derived bioassay.
getPhysicalBioAssays() - Method in class net.sf.basedb.core.Extract: Get a query that returns all bioassays created from this extract.
getPhysicalBioAssays(DbControl, OverviewContext, DerivedBioAssay) - Static method in class net.sf.basedb.util.overview.validator.PhysicalBioAssayValidator: Get all physical bioassays that are parents to the given derived bioassay.
getPlaceHolder() - Method in class net.sf.basedb.clients.web.extensions.login.FieldInfo: Get a placeholder text that is displayed in the field when it is empty.
getPlainConnection() - Static method in class net.sf.basedb.core.HibernateUtil
getPlate() - Method in class net.sf.basedb.core.ArrayDesignPlate: Gets the Plate that belongs to this item.
getPlate() - Method in class net.sf.basedb.core.BioWell: Get the BioPlate this biowell belongs to.
getPlate() - Method in class net.sf.basedb.core.data.ArrayDesignPlateData: Get the Plate.
getPlate() - Method in class net.sf.basedb.core.data.MappingCoordinate: Get the plate number.
getPlate() - Method in class net.sf.basedb.core.data.PlateEventData: The plate this event belongs to.
getPlate() - Method in class net.sf.basedb.core.data.WellData: The plate this well belongs to.
getPlate() - Method in class net.sf.basedb.core.PlateEvent: Get the Plate this event belongs to.
getPlate() - Method in class net.sf.basedb.core.Well: Get the Plate this event belongs to.
getPlate(int) - Method in class net.sf.basedb.core.ArrayDesign: Get a Plate from a given position.
getPlateCoordinate() - Method in class net.sf.basedb.core.BioWell: Get the plate coordinate representation of the coordinate for this well.
getPlateEvents() - Method in class net.sf.basedb.core.data.PlateEventTypeData: This is the inverse end.
getPlateEventType() - Method in class net.sf.basedb.core.data.PlateEventData: The event type of this event.
getPlateEventType() - Method in class net.sf.basedb.core.PlateEvent: Get the PlateEventType of this event.
getPlateGeometry() - Method in class net.sf.basedb.core.BioPlate: Get the PlateGeometry of this bioplate.
getPlateGeometry() - Method in class net.sf.basedb.core.data.BioPlateData: The geometry of this plate type.
getPlateGeometry() - Method in class net.sf.basedb.core.data.PlateTypeData: The geometry of this plate type.
getPlateGeometry() - Method in class net.sf.basedb.core.PlateType: Get the PlateGeometry of this plate type.
getPlateMapping() - Method in class net.sf.basedb.core.data.PlateData: If this plate was created by a plate mapping, it is linked here.
getPlateMapping() - Method in class net.sf.basedb.core.Plate: Get the PlateMapping used to create this plate.
getPlatePosition(Plate) - Method in class net.sf.basedb.core.ArrayDesign: Get the position of a Plate in this array design.
getPlates() - Method in class net.sf.basedb.core.ArrayDesign: Get a query that returns the plates that are used by this arraydesign.
getPlates() - Method in class net.sf.basedb.core.data.ArrayDesignData: The plates this design is made from.
getPlates() - Method in class net.sf.basedb.core.data.PlateTypeData: The plates of this type.
getPlates() - Method in class net.sf.basedb.core.PlateType: Get a query that returns all plates of this plate type.
getPlateType() - Method in class net.sf.basedb.core.data.PlateData: The plate type of this plate.
getPlateType() - Method in class net.sf.basedb.core.data.PlateEventTypeData: The plate type this event type belongs to.
getPlateType() - Method in class net.sf.basedb.core.Plate: Get the PlateType of this plate.
getPlateType() - Method in class net.sf.basedb.core.PlateEventType: Get the PlateType this event type belongs to.
getPlateTypes() - Method in class net.sf.basedb.core.data.PlateGeometryData: This is the invers end.
getPlateTypes() - Method in class net.sf.basedb.core.PlateGeometry: Get a query returning all plate types using this geometry.
getPlatform() - Method in class net.sf.basedb.core.ArrayDesign
getPlatform() - Method in class net.sf.basedb.core.BioAssaySet
getPlatform() - Method in class net.sf.basedb.core.data.ArrayDesignData: Get the platform this raw bioassay uses
getPlatform() - Method in class net.sf.basedb.core.data.PlatformFileTypeData: Get the platform.
getPlatform() - Method in class net.sf.basedb.core.data.PlatformVariantData: The parent platform of this variant.
getPlatform() - Method in class net.sf.basedb.core.data.RawBioAssayData: Get the platform this raw bioassay uses.
getPlatform() - Method in class net.sf.basedb.core.DerivedBioAssay
getPlatform() - Method in class net.sf.basedb.core.ExtraValue
getPlatform() - Method in interface net.sf.basedb.core.FileStoreEnabled: Get the platform the item is related to.
getPlatform() - Method in class net.sf.basedb.core.PlatformFileType: Get the platform.
getPlatform() - Method in class net.sf.basedb.core.PlatformVariant: Get that platform this is a variant of.
getPlatform() - Method in class net.sf.basedb.core.RawBioAssay
getPlatform(DbControl) - Method in class net.sf.basedb.core.RawDataType: Get the platform that this raw data type is associated with.
getPlatformRawDataType(Session, String) - Static method in class net.sf.basedb.core.RawDataTypes
getPlatforms() - Method in class net.sf.basedb.core.data.DataFileTypeData: This is the inverse end.
getPlatforms() - Method in class net.sf.basedb.core.DataFileType: Get a query that returns all platforms/variants that are using this file type.
getPlotGenerators() - Method in interface net.sf.basedb.clients.web.extensions.plot.OverviewPlotAction: The plot generates that contains information for each image that is generated.
getPlotGenerators() - Method in class net.sf.basedb.clients.web.extensions.plot.OverviewPlotBean
getPlugin() - Method in class net.sf.basedb.core.data.ChangeHistoryData
getPlugin() - Method in class net.sf.basedb.core.PluginRequest: Get the plugin object.
getPlugin(DbControl) - Method in class net.sf.basedb.core.ChangeHistory: Load the plug-in that made the change.
getPlugin(DbControl) - Method in class net.sf.basedb.core.ChangeHistory.TransactionInfo: Load the plug-in that was executing the transaction.
getPlugin(DbControl, ChangeHistory, boolean, boolean) - Static method in class net.sf.basedb.clients.web.ChangeHistoryUtil: Get the plug-in that made the change in HTML format.
getPluginConfiguration() - Method in class net.sf.basedb.core.data.JobData: The plugin configuration for the plugin.
getPluginConfiguration() - Method in class net.sf.basedb.core.Job: Get the PluginConfiguration defining the plugin this job should execute.
getPluginConfiguration() - Method in class net.sf.basedb.core.ParameterValuesImpl
getPluginConfiguration() - Method in class net.sf.basedb.core.plugin.NamespaceParameterValuesWrapper
getPluginConfiguration() - Method in interface net.sf.basedb.core.plugin.ParameterValues: Get the configuration that we are using/configuring.
getPluginConfiguration() - Method in class net.sf.basedb.core.plugin.ParameterValuesWrapper
getPluginConfiguration() - Method in class net.sf.basedb.plugins.gtf.DefaultConfigurationValues
getPluginConfiguration() - Method in class net.sf.basedb.util.ContextUtil.ContextResult: Get the plugin configuration that was checked, or null.
getPluginConfigurations() - Method in class net.sf.basedb.core.PluginDefinition: Get a query that returns the configurations for this plugin definition.
getPluginDefinition() - Method in class net.sf.basedb.core.data.JobAgentSettingsData: The plugin these settings are used for.
getPluginDefinition() - Method in class net.sf.basedb.core.data.JobData: The plugin that executes the job.
getPluginDefinition() - Method in class net.sf.basedb.core.data.PluginConfigurationData: Get the plugin definition for this configuration.
getPluginDefinition() - Method in class net.sf.basedb.core.Job: Get the PluginConfiguration defining the plugin this job should execute.
getPluginDefinition() - Method in class net.sf.basedb.core.JobAgentSettings: Get the plugin that these settings are used for.
getPluginDefinition() - Method in class net.sf.basedb.core.ParameterValuesImpl
getPluginDefinition() - Method in class net.sf.basedb.core.plugin.NamespaceParameterValuesWrapper
getPluginDefinition() - Method in interface net.sf.basedb.core.plugin.ParameterValues: Get the plugin that we are executing/configuring.
getPluginDefinition() - Method in class net.sf.basedb.core.plugin.ParameterValuesWrapper: Get the PluginDefinition of either the job or the configuration, depending in the preferJob parameter that was set when creating this object.
getPluginDefinition() - Method in class net.sf.basedb.core.PluginConfiguration: Get the plugin definition for this configuration.
getPluginDefinition() - Method in class net.sf.basedb.plugins.gtf.DefaultConfigurationValues
getPluginDefinition() - Method in class net.sf.basedb.util.ContextUtil.ContextResult: Get the plugin definition that was checked.
getPluginDefinitionId() - Method in class net.sf.basedb.core.data.keyring.PluginKeys: Gets the id of the plugin
getPluginDefinitions() - Method in class net.sf.basedb.util.extensions.xml.XmlLoader: Get a list with all loaded plug-in definitions.
getPluginDirectory(DbControl, String) - Method in class net.sf.basedb.plugins.Base1PluginExecuter: Get a directory
getPluginId() - Method in class net.sf.basedb.core.ChangeHistory: Get the ID of the plug-in that was making the change.
getPluginId() - Method in class net.sf.basedb.core.ChangeHistory.TransactionInfo: Get the ID of the plug-in that was executing the transaction.
getPluginId() - Method in class net.sf.basedb.core.data.ChangeHistoryData: The ID of the plug-in that was making the changes.
getPluginId() - Method in class net.sf.basedb.core.log.TransactionDetails: Get the ID of the currently running plug-in or 0 if no plug-in is running.
getPluginId() - Method in class net.sf.basedb.core.SessionControl: Get the id of the plug-in that is currently running with this session control.
getPluginName() - Method in class net.sf.basedb.core.log.TransactionDetails: Utility method for loading the name of the currently executing plugin.
getPluginName() - Method in class net.sf.basedb.core.SessionControl: Get the name of the plug-in that is currently running with this session control.
getPluginParameter() - Method in class net.sf.basedb.plugins.Base1PluginExecuter.JobParameter
getPluginPermissions() - Method in class net.sf.basedb.core.Annotation
getPluginPermissions() - Method in class net.sf.basedb.core.AnnotationSet
getPluginPermissions() - Method in class net.sf.basedb.core.AnyToAny
getPluginPermissions() - Method in class net.sf.basedb.core.BasicBatcher
getPluginPermissions() - Method in class net.sf.basedb.core.BasicChildItem
getPluginPermissions() - Method in class net.sf.basedb.core.BasicItem
getPluginPermissions() - Method in class net.sf.basedb.core.ChildItem
getPluginPermissions() - Method in class net.sf.basedb.core.FeatureBatcher
getPluginPermissions() - Method in class net.sf.basedb.core.FileSet
getPluginPermissions() - Method in class net.sf.basedb.core.FileSetMember
getPluginPermissions() - Method in class net.sf.basedb.core.ItemKey
getPluginPermissions() - Method in class net.sf.basedb.core.Project: Make sure plug-ins always has at least read access to the active project.
getPluginPermissions() - Method in class net.sf.basedb.core.ProjectKey
getPluginPermissions() - Method in class net.sf.basedb.core.RawDataBatcher
getPluginPermissions() - Method in class net.sf.basedb.core.ReporterCloneTemplate
getPluginPermissions() - Method in class net.sf.basedb.core.RoleKey
getPluginPermissions() - Method in class net.sf.basedb.core.User: Make sure plug-ins always has at least read access to the logged in user.
getPluginPermissions(Item) - Method in class net.sf.basedb.core.Keyring: Get the active plugin's permissions to an unspecified item of a certain Item type.
getPluginPermissions(Item) - Method in class net.sf.basedb.core.SessionControl: Get all plugin-specific permissions for the specified item type.
getPlugins() - Method in class net.sf.basedb.core.data.JobAgentData: The plugins that can be executed by this job agent.
getPlugins() - Method in class net.sf.basedb.core.data.PluginTypeData: The plugin implementing this interface.
getPlugins() - Method in class net.sf.basedb.core.PluginType: Get a query that returns the plugin definitions which implements this type.
getPluginsDir() - Method in class net.sf.basedb.clients.web.extensions.XJspCompiler: Get the path to the plug-in directory from BASE.
getPluginsDirectory() - Static method in class net.sf.basedb.core.Application: Get the directory where plug-ins and extensions must be installed.
getPluginSessionControl(PluginDefinition, Job) - Method in class net.sf.basedb.core.PluginSessionControl: Create a new session control for executing a plugin using the same parent as this session control has.
getPluginSessionControl(PluginDefinition, Job) - Method in class net.sf.basedb.core.SessionControl: Create a new session control for executing a plugin.
getPluginTypes() - Method in class net.sf.basedb.core.data.PluginDefinitionData: The plugin types of this plugin, ie. all interfaces that it implements.
getPluginTypes() - Method in class net.sf.basedb.core.PluginDefinition: Get a query that returns the plugin types for this plugin definition.
getPluginVersion() - Method in class net.sf.basedb.core.data.JobData: Get the version of the plugin used to execute this job at the time the job was executed or registered.
getPluginVersion() - Method in class net.sf.basedb.core.Job: Get the version of the plugin used to execute this job at the time the job was executed or registered.
getPort() - Method in class net.sf.basedb.clients.jobagent.Agent: Get the agent.port configuration value.
getPort() - Method in class net.sf.basedb.core.data.JobAgentData: The port the job agent is listening on. null if it doesn't listen.
getPort() - Method in class net.sf.basedb.core.JobAgent: Get the port the job agent is listening on.
getPosition() - Method in class net.sf.basedb.core.ArrayDesignPlate: Gets the position of this item.
getPosition() - Method in class net.sf.basedb.core.BioMaterialEventSource: Get the position that the source biomaterial was used on in the event.
getPosition() - Method in class net.sf.basedb.core.BioPlate: Get the position within the "storage location" for this bioplate.
getPosition() - Method in class net.sf.basedb.core.data.ArrayDesignPlateData: Get the index.
getPosition() - Method in class net.sf.basedb.core.data.BioMaterialEventSourceData: Get the position of the parent biomaterial as it was used in the event.
getPosition() - Method in class net.sf.basedb.core.data.BioPlateData: Get the position in the storage location were the bioplate is stored.
getPosition() - Method in class net.sf.basedb.core.data.FeatureData: Get the position number of the feature.
getPosition() - Method in class net.sf.basedb.core.data.RawData
getPosition() - Method in class net.sf.basedb.core.RawDataBatcher.FeatureInfo
getPosition() - Method in class net.sf.basedb.plugins.Base1PluginExecuter.JobParameter
getPosition(DbControl, int, int) - Method in class net.sf.basedb.clients.web.ExperimentExplorer: Get the position number of the position specified by the given reporter and position index.
getPositionBatcher() - Method in class net.sf.basedb.core.BioAssaySet: Get a batcher that links position coordinates to reporters for the data cube this bioassayset uses.
getPositionBatcher() - Method in class net.sf.basedb.core.DataCube
getPositionData() - Method in class net.sf.basedb.core.BioAssaySet: Get a query that returns position data for the data cube where this bioassayset is located.
getPositionExtraValueBatcher(Class<I>, ExtraValueType, Job) - Method in class net.sf.basedb.core.BioAssaySet: Get a batcher that is used to insert extra values per position of the specified type.
getPositionIndex() - Method in class net.sf.basedb.clients.web.ExperimentExplorer: Get the index of the current position.
getPositionIndex() - Method in class net.sf.basedb.util.importer.spotdata.BaseFileInfo.SpotSectionInfo: The index of the 'position' data column.
getPredefinedQuery(Session, String) - Static method in class net.sf.basedb.core.HibernateUtil: Get a predefined HQL query.
getPredefinedQuery(Session, String, Class<R>, String...) - Static method in class net.sf.basedb.core.HibernateUtil: Get a predefined HQL query with a known return type.
getPredefinedQuery(Session, String, String...) - Static method in class net.sf.basedb.core.HibernateUtil: Get a predefined HQL query.
getPredefinedQuery(StatelessSession, String, Class<R>) - Static method in class net.sf.basedb.core.HibernateUtil: Get a predefined HQL query with a known return type using the stateless session.
getPredefinedSQLQuery(Session, String, Class<R>, String...) - Static method in class net.sf.basedb.core.HibernateUtil: Get a predefined SQL query with a known return type.
getPredefinedSQLQuery(Session, String, String...) - Static method in class net.sf.basedb.core.HibernateUtil: Get a predefined SQL query.
getPredefinedSQLQuery(StatelessSession, String) - Static method in class net.sf.basedb.core.HibernateUtil: Get a predefined SQL query using the stateless session.
getPredefinedSQLQuery(StatelessSession, String, Class<R>) - Static method in class net.sf.basedb.core.HibernateUtil: Get a predefined SQL query with a known return type using the stateless session.
getPrefix() - Method in class net.sf.basedb.clients.web.taglib.table.CellValue
getPrefix() - Method in class net.sf.basedb.util.bfs.SequenceFilenameGenerator: Get the prefix that is used for file name generation.
getPrefixedStream(XlsxToCsvUtil.SheetInfo) - Method in class net.sf.basedb.util.excel.XlsxToCsvUtil.WorkbookStream: Create a combined stream by adding a "prefix": [sheet-name] and then the regular CSV stream for the given worksheet.
getPreset(String) - Method in class net.sf.basedb.core.Presets: Get a named preset.
getPreviousState() - Method in class net.sf.basedb.core.log.EntityDetails: Get an array with the previous state of the entity.
getPrimaryKey() - Method in class net.sf.basedb.core.dbengine.TableInfo: Get information about the primary key of the table
getPrintRobot() - Method in class net.sf.basedb.core.ArrayBatch: Get the print robot used for printing the arrays.
getPrintRobot() - Method in class net.sf.basedb.core.data.ArrayBatchData: Get the hardware used for creating this batch.
getPriority() - Method in class net.sf.basedb.core.data.JobData: The jobs priority.
getPriority() - Method in class net.sf.basedb.core.Job: Get the priority of the job.
getPriorityBoost() - Method in class net.sf.basedb.core.data.JobAgentSettingsData: The priority boost for this plugin.
getPriorityBoost() - Method in class net.sf.basedb.core.JobAgentSettings: Get the priority boost given to jobs executed by this plugin.
getPrivateKey(String) - Method in class net.sf.basedb.util.ssl.StaticKeyManager
getProcessResults() - Method in class net.sf.basedb.util.extensions.manager.processor.DisablePluginsProcessor
getProcessResults() - Method in class net.sf.basedb.util.extensions.manager.processor.PluginInstallationProcessor
getProcessResults() - Method in class net.sf.basedb.util.extensions.manager.processor.RegisterExtensionsProcessor
getProducer() - Method in class net.sf.basedb.core.hibernate.QueryWrapper
getProducts() - Method in class net.sf.basedb.core.data.TransformationData: This is the inverse end.
getProducts() - Method in class net.sf.basedb.core.Transformation: Get a query that return all bioassaysets created by this transformation.
getProgramParameters() - Method in class net.sf.basedb.plugins.executor.ExternalProgramExecutor: Get all program parameters and their values.
getProgress() - Method in class net.sf.basedb.clients.web.fileupload.FileUpload: Get progress information about the upload.
getProgress(FlatFileParser) - Method in class net.sf.basedb.plugins.AbstractFlatFileImporter: Get the progress of import as a percentage value.
getProgress(FlatFileParser) - Method in class net.sf.basedb.plugins.AnnotationFlatFileImporter: Overriding default implementation since we want file parsing to only use 'progressParser'% and the remaining 'progressDatabase'% for storing to the database.
getProgressReporter() - Method in class net.sf.basedb.util.export.spotdata.AbstractBioAssaySetExporter: Get the progress reporter
getProgressReporter() - Method in class net.sf.basedb.util.importer.spotdata.BaseFileImporter: Get the progress reporter.
getProgressReporter() - Method in class net.sf.basedb.util.importer.spotdata.BfsImporter: Get the progress reporter.
getProgressReporter(ProgressReporter) - Method in class net.sf.basedb.core.Job: Get a progress reporter that reports progress by updating the information in the database.
getProject() - Method in class net.sf.basedb.core.Annotation: Get the project that this project-specific annotation belongs to.
getProject() - Method in class net.sf.basedb.core.data.ChangeHistoryData
getProject() - Method in class net.sf.basedb.util.overview.GenericOverview: Get the project of this overview is using for validating against project defaults (may be null).
getProject() - Method in interface net.sf.basedb.util.overview.OverviewContext: Get the project the overview is using as the "current" project.
getProject(DbControl) - Method in class net.sf.basedb.core.ChangeHistory: Load the project that was active when the change was made.
getProject(DbControl) - Method in class net.sf.basedb.core.ChangeHistory.TransactionInfo: Load the project that was active during the transaction.
getProject(DbControl) - Method in class net.sf.basedb.core.snapshot.AnnotationSnapshot: Get the project that a project-specific annotation belongs to.
getProject(DbControl, ChangeHistory, boolean, boolean) - Static method in class net.sf.basedb.clients.web.ChangeHistoryUtil: Get the project that was active when the change was made in HTML format.
getProjectAnnotation(AnnotationType, Project) - Method in class net.sf.basedb.core.AnnotationSet: Get a value for a project-specific annotation using the specified project instead of the currently active project.
getProjectAnnotations() - Method in class net.sf.basedb.core.AnnotationType: If this flag is set, annotation values can be set per project.
getProjectAnnotations() - Method in class net.sf.basedb.core.data.AnnotationTypeData: If this flag is set, annotation values can be set per project.
getProjectAnnotations(Annotation.Source, Project) - Method in class net.sf.basedb.core.AnnotationSet: Get a query returning annotations with the specified source and belonging to the specified project (or default values if projectId=0).
getProjectDefaultPlatform(DbControl) - Method in class net.sf.basedb.plugins.batchimport.AbstractItemImporter: Get the default platform of the currently active project.
getProjectDefaultRawDataType(DbControl) - Method in class net.sf.basedb.plugins.batchimport.AbstractItemImporter: Get the default raw data type of the currently active project.
getProjectDefaults() - Method in class net.sf.basedb.core.data.ProjectData: Gets the default values
getProjectDefaultVariant(DbControl) - Method in class net.sf.basedb.plugins.batchimport.AbstractItemImporter: Get the default platform variant of the currently active project.
getProjectId() - Method in class net.sf.basedb.core.Annotation: Get the ID of the project that this project-specicif annotation belongs to.
getProjectId() - Method in class net.sf.basedb.core.AnnotationBatcher.CurrentAnnotationInfo: Get the id of the project this annotation belong to.
getProjectId() - Method in class net.sf.basedb.core.ChangeHistory: Get the ID of the project that was active when the change was made.
getProjectId() - Method in class net.sf.basedb.core.ChangeHistory.TransactionInfo: Get the ID of the project that was active during the transaction.
getProjectId() - Method in class net.sf.basedb.core.data.AnnotationData: The ID of the project that this annotation belongs to. 0 is used for default annotations.
getProjectId() - Method in class net.sf.basedb.core.data.annotations.AnnotationLink
getProjectId() - Method in class net.sf.basedb.core.data.ChangeHistoryData: The ID of the project that was active when the changes were made.
getProjectId() - Method in class net.sf.basedb.core.data.keyring.ProjectKeys: Get the id of the project.
getProjectId() - Method in class net.sf.basedb.core.data.keyring.ProjectPermission: Get the id of the project.
getProjectId() - Method in class net.sf.basedb.core.log.TransactionDetails: Get the ID of the currently active project, or 0 if no project is active.
getProjectId() - Method in class net.sf.basedb.core.snapshot.AnnotationSnapshot: Get the id of the project that this project-specific annotation belongs to.
getProjectIds(Permission) - Method in class net.sf.basedb.core.ProjectKey: Get the ID:s of all projects that are shared with this project key having the specified permission.
getProjectKey() - Method in interface net.sf.basedb.core.data.ShareableData: Get the ProjectKeyData for the item.
getProjectKey() - Method in class net.sf.basedb.core.data.SharedData
getProjectKey() - Method in interface net.sf.basedb.core.Shareable: Get the ProjectKey that is used to share this item to projects.
getProjectKey() - Method in class net.sf.basedb.core.SharedItem
getProjectKeyId() - Method in class net.sf.basedb.core.SessionControl: Get the id of the ProjectKey that can be used to share an item to the active project with full permission, or 0 if no project is active or the logged in user only has read permission to the active project.
getProjectKeys() - Method in class net.sf.basedb.core.data.ProjectData: This is the inverse end.
getProjectKeys() - Method in class net.sf.basedb.core.InternalJobQueue.JobQueueKeyring: Return empty set.
getProjectKeys() - Method in class net.sf.basedb.core.Job.SignalKeyring: Return empty set.
getProjectKeys() - Method in class net.sf.basedb.core.ServiceSessionControl.ServicesKeyring: Return empty set.
getProjectKeys() - Method in class net.sf.basedb.core.SessionControl: Get the id of all project keys where the logged in user has read permission.
getProjectKeys(Permission) - Method in class net.sf.basedb.core.Keyring
getProjectKeys(Permission) - Method in class net.sf.basedb.core.SessionControl: Get the id of all project keys where the logged in user has the requested permission.
getProjectName() - Method in class net.sf.basedb.core.log.TransactionDetails: Utility method for loading the name of the currently active project.
getProjectName(int) - Method in class net.sf.basedb.core.log.TransactionDetails: Get the name of the project with the given id.
getProjectName(DbControl) - Method in class net.sf.basedb.core.snapshot.AnnotationSnapshot: Get the name of project if the annotation is a project-specific value.
getProjectPermission(Project) - Method in class net.sf.basedb.core.SessionControl
getProjectPermissions() - Method in class net.sf.basedb.core.ProjectPermissions: Get the internal representation of the permissions.
getProjects() - Method in class net.sf.basedb.core.data.GroupData: This is the inverse end.
getProjects() - Method in class net.sf.basedb.core.data.PermissionTemplateData: This is the inverse end.
getProjects() - Method in class net.sf.basedb.core.data.ProjectKeyData: Get the map that manages which projects that have permissions for this key.
getProjects() - Method in class net.sf.basedb.core.data.UserData: This is the inverse end.
getProjects() - Method in class net.sf.basedb.core.Group: Get a query that returns the projects that this group is a member of.
getProjects() - Method in class net.sf.basedb.core.InternalJobQueue.JobQueueKeyring: Return empty map.
getProjects() - Method in class net.sf.basedb.core.Job.SignalKeyring: Return empty map.
getProjects() - Method in class net.sf.basedb.core.Keyring
getProjects() - Method in class net.sf.basedb.core.MultiPermissions: Get a query that returns all projects appearing in at least one of the project keys.
getProjects() - Method in class net.sf.basedb.core.PermissionTemplate: Get a query that returns all projects that use this permission template.
getProjects() - Method in class net.sf.basedb.core.ServiceSessionControl.ServicesKeyring: Return empty map.
getProjects() - Method in class net.sf.basedb.core.SessionControl: Get the id of all projects where the logged in user is a member, directly or indirectly.
getProjects() - Method in class net.sf.basedb.core.User: Get a query that returns the projects where this user is a member.
getProjectSpecificAnnotationsManager() - Method in class net.sf.basedb.core.DbControl: Get the manager used for handling project specific annotations in this transaction.
getPrompt() - Method in class net.sf.basedb.clients.web.extensions.login.FieldInfo: Get the prompt that is associated with the field.
getProperties() - Method in class net.sf.basedb.core.data.ReporterCloneTemplateData: Get the map that manages cloned properties.
getProperties() - Method in class net.sf.basedb.core.hibernate.SessionWrapper
getProperties() - Method in class net.sf.basedb.core.log.EntityDetails: Get an array with the names of all properties.
getProperties() - Method in class net.sf.basedb.core.RawDataType: Get a list of RawDataProperty:s with definitions for the extra properties that has been defined for this raw data type.
getProperties(String) - Static method in class net.sf.basedb.core.ExtendedProperties: Get a list of extended properties for the specified class.
getProperties(String, boolean) - Static method in class net.sf.basedb.core.ExtendedProperties: Get a list of extended properties for the specified class.
getProperty() - Method in class net.sf.basedb.clients.web.extensions.list.AbstractListColumnBean
getProperty() - Method in interface net.sf.basedb.clients.web.extensions.list.ListColumnAction: The property name for referencing data in the column.
getProperty() - Method in class net.sf.basedb.clients.web.extensions.list.RelatedItemColumn.Specification: Get the property from the expression.
getProperty() - Method in class net.sf.basedb.clients.web.taglib.PropertyValue
getProperty() - Method in class net.sf.basedb.clients.web.taglib.table.ColumnDef
getProperty() - Method in class net.sf.basedb.clients.web.taglib.table.TableColumn
getProperty() - Method in class net.sf.basedb.core.PropertyFilter: Get the name of the property this filter is used on.
getProperty() - Method in class net.sf.basedb.plugins.batchimport.PropertyIdMethod
getProperty() - Method in class net.sf.basedb.util.export.spotdata.AssayPropertyField: Get the configured property.
getProperty(String) - Method in class net.sf.basedb.clients.jobagent.Agent: Get a configuration property.
getProperty(String) - Method in class net.sf.basedb.core.RawDataType
getProperty(String) - Method in class net.sf.basedb.util.extensions.xml.PluginInfo
getProperty(String, String) - Static method in class net.sf.basedb.core.ExtendedProperties: Find an extended property in a given class.
getPropertyAccessStrategy() - Method in class net.sf.basedb.core.ExtendedPropertyAccessor.GetterSetter
getPropertyFilter(String) - Method in class net.sf.basedb.core.ItemContext: Get a filter for a property on filter row 0.
getPropertyFilter(String, int) - Method in class net.sf.basedb.core.ItemContext: Get a filter for a property.
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 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 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 net.sf.basedb.core.Item: Get a query returning items of this type.
getQuery() - Method in class net.sf.basedb.core.ItemContext
getQuery() - Static method in class net.sf.basedb.core.ItemList: Get a query that returns item lists.
getQuery() - Static method in class net.sf.basedb.core.Job: Get a query configured to retrieve jobs.
getQuery() - Static method in class net.sf.basedb.core.JobAgent: Get an ItemQuery that returns job agents.
getQuery() - Static method in class net.sf.basedb.core.Kit: Get a query configured to retrieve kits.
getQuery() - Static method in class net.sf.basedb.core.MimeType: Get a query configured to retrieve MIME types.
getQuery() - Static method in class net.sf.basedb.core.News: Get a query configured to retrieve news.
getQuery() - Static method in class net.sf.basedb.core.PermissionTemplate: Get a query that returns permission templates.
getQuery() - Static method in class net.sf.basedb.core.PhysicalBioAssay: Get a query that returns physical bioassays.
getQuery() - Static method in class net.sf.basedb.core.Plate: Get a query that returns plates.
getQuery() - Static method in class net.sf.basedb.core.PlateGeometry: Get a query configured to retrieve plate geometries.
getQuery() - Static method in class net.sf.basedb.core.PlateMapping: Get a query that returns plate mappings.
getQuery() - Static method in class net.sf.basedb.core.PlateType: Get a query that returns plate types.
getQuery() - Static method in class net.sf.basedb.core.Platform: Get a query configured to retrieve Platform items.
getQuery() - Static method in class net.sf.basedb.core.PlatformVariant: Get a query configured to retrieve PlatformVariant items.
getQuery() - Static method in class net.sf.basedb.core.PluginConfiguration: Get a query configured to retrieve plugin configurations.
getQuery() - Static method in class net.sf.basedb.core.PluginDefinition: Get a query that returns plugin definitions.
getQuery() - Static method in class net.sf.basedb.core.PluginType: Get a query configured to retrieve plugin types.
getQuery() - Static method in class net.sf.basedb.core.Project: Get a query configured to retrieve projects.
getQuery() - Static method in class net.sf.basedb.core.Protocol: Get a query configured to retrieve protocols.
getQuery() - Static method in class net.sf.basedb.core.Quantity: Get a query configured to retrieve quantities.
getQuery() - Static method in class net.sf.basedb.core.Quota: Get a query configured to retrieve quota.
getQuery() - Static method in class net.sf.basedb.core.QuotaType: Get a query configured to retrieve QuotaType.
getQuery() - Static method in class net.sf.basedb.core.RawBioAssay: Get a query configured to retrieve raw bioassays.
getQuery() - Static method in class net.sf.basedb.core.Reporter: Get a query object configured to retrieve reporters.
getQuery() - Static method in class net.sf.basedb.core.ReporterCloneTemplate: Get a query that returns reporter clone templates.
getQuery() - Static method in class net.sf.basedb.core.ReporterList: Get a new query object for this class.
getQuery() - Static method in class net.sf.basedb.core.ReporterType: Get a query configured to retrieve reporter types.
getQuery() - Static method in class net.sf.basedb.core.Role: Get a ItemQuery object configured to retrieve Role items.
getQuery() - Static method in class net.sf.basedb.core.RoleKey: Get a query object configured to retrieve role keys.
getQuery() - Static method in class net.sf.basedb.core.RootRawBioAssay: Get a query configured to retrieve raw bioassays.
getQuery() - Static method in class net.sf.basedb.core.Sample: Get a query that returns samples.
getQuery() - Static method in class net.sf.basedb.core.Software: Get a query configured to retrieve software.
getQuery() - Static method in class net.sf.basedb.core.Tag: Get a query that returns tags.
getQuery() - Static method in class net.sf.basedb.core.Unit: Get a query configured to retrieve units.
getQuery() - Static method in class net.sf.basedb.core.User: Get a query configured to retrieve users.
getQuery(Collection<RawBioAssay>) - Static method in class net.sf.basedb.core.DynamicRawDataQuery: Create a new dynamic query for raw data.
getQuery(ArrayDesign) - Static method in class net.sf.basedb.core.ArrayDesignBlock: Get a query configured to retrieve array design blocks for the specified array design.
getQuery(ArrayDesign) - Static method in class net.sf.basedb.core.ArrayDesignPlate: Get a query that returns ArrayDesignPlates connections for the specified array design.
getQuery(BioAssaySet) - Static method in class net.sf.basedb.core.BioAssay: Get a query configured to retrieve bioassays in a given bioassayset.
getQuery(BioAssaySet) - Static method in class net.sf.basedb.core.ExtraValue: Get a query configured to retrieve extra values in a given bioassayset.
getQuery(BioAssaySet) - Static method in class net.sf.basedb.core.Transformation: Get a query configured to retrieve transformations using the given bioassayset as source.
getQuery(BioMaterial) - Static method in class net.sf.basedb.core.BioMaterialEventSource: Get a query returning event information where a given biomaterial has been used as a source.
getQuery(BioMaterialEvent) - Static method in class net.sf.basedb.core.BioMaterialEventSource: Get a query returning source information for a given (creation) event.
getQuery(BioPlate) - Static method in class net.sf.basedb.core.BioPlateEventParticipant: Get a query configured to return all event participants for a bioplate.
getQuery(BioPlate) - Static method in class net.sf.basedb.core.BioWell: Get a query configured to retrieve wells for a plate.
getQuery(BioPlateEvent) - Static method in class net.sf.basedb.core.BioPlateEventParticipant: Get a query configured to return all participants for a bioplate event.
getQuery(Client) - Static method in class net.sf.basedb.core.ClientDefaultSetting: Get a query object configured to retrieve default settings for the specified client application.
getQuery(Client) - Static method in class net.sf.basedb.core.Help: Get a query configured to retrieve help texts for the specified client application.
getQuery(DataFileType) - Static method in class net.sf.basedb.core.ItemSubtypeFileType: Get the item subtype types that have been registered for a specific data file type.
getQuery(Experiment) - Static method in class net.sf.basedb.core.BioAssaySet: Get a query configured to retrieve bioassaysets for a given experiment.
getQuery(Experiment) - Static method in class net.sf.basedb.core.Transformation: Get a query configured to retrieve transformations for a given experiment.
getQuery(FileSet) - Static method in class net.sf.basedb.core.FileSetMember: Get a query configured to retrieve FileSetMember items.
getQuery(FileStoreEnabled) - Static method in class net.sf.basedb.core.DataFileType: Get a query configured to retrieve DataFileType:s that can be used on a given item.
getQuery(Formula.Type, RawDataType, IntensityTransform) - Static method in class net.sf.basedb.core.Formula: Get a query that return formulas that can be used with the specified raw data type.
getQuery(Item) - Static method in class net.sf.basedb.core.AnnotationType: Get a ItemQuery that returns annotation types.
getQuery(Item) - Static method in class net.sf.basedb.core.ItemSubtype: Get a query configured to retrieve item types.
getQuery(ItemList) - Static method in class net.sf.basedb.core.SyncFilter: Get a query configured to retrieve sync filters for the specified item list.
getQuery(ItemSubtype) - Static method in class net.sf.basedb.core.ItemSubtypeFileType: Get the file types that have been registered for a specific item subtype.
getQuery(JobAgent) - Static method in class net.sf.basedb.core.JobAgentSettings: Get a query configured to retrieve settings for the specified agent.
getQuery(MeasuredBioMaterial) - Static method in class net.sf.basedb.core.BioMaterialEvent: Get a query that returns events for a biomaterial.
getQuery(Plate) - Static method in class net.sf.basedb.core.PlateEvent: Get a query configured to retrieve plate events for the specified plate.
getQuery(Plate) - Static method in class net.sf.basedb.core.Well: Get a query configured to retrieve wells for a plate.
getQuery(PlateType) - Static method in class net.sf.basedb.core.PlateEventType: Get a query configured to retrieve event types for the specified plate type
getQuery(Platform, PlatformVariant, boolean) - Static method in class net.sf.basedb.core.PlatformFileType: Get the file types that have been registered for a specific platform and variant.
getQuery(Platform, PlatformVariant, Item, ItemSubtype) - Static method in class net.sf.basedb.core.DataFileType: Get a query to retrieve DataFileType:s that can be used on specific platform/variant for a given item and/or generic file type.
getQuery(GuiContext, String) - Static method in class net.sf.basedb.core.PluginConfiguration: Get a query that returns all plugins configurations related to a specified GUI context and implementing a certain interface.
getQuery(GuiContext, String) - Static method in class net.sf.basedb.core.PluginDefinition: Get a query that returns all plugins related to a specified GUI context and implementing a certain interface.
getQuery(PluginDefinition) - Static method in class net.sf.basedb.core.JobAgentSettings: Get a query configured to retrieve settings for the specified plugin.
getQuery(RawBioAssay) - Static method in class net.sf.basedb.core.DynamicRawDataQuery: Create a new dynamic query for raw data.
getQuery(ReporterList) - Static method in class net.sf.basedb.core.ReporterScore: Get a query object configured to retrieve reporters.
getQuery(Transformation) - Static method in class net.sf.basedb.core.BioAssaySet: Get a query configured to retrieve bioassaysets created by a given transformation.
getQuery(User) - Static method in class net.sf.basedb.core.Message: Get a query configured to retrieve messages for the specified user.
getQuery(User) - Static method in class net.sf.basedb.core.Session: Get a query configured to retrieve sessions for the specified user.
getQuery(User) - Static method in class net.sf.basedb.core.UserDefaultSetting: Get a query configured to retrieve default settings for a user.
getQuery(User) - Static method in class net.sf.basedb.core.UserDevice: Get a query configured to retrieve devices for the specified user.
getQuery(User, Client) - Static method in class net.sf.basedb.core.UserClientSetting: Get a query configured to retrieve client specific settings for a user.
getQuery(User, Group) - Static method in class net.sf.basedb.core.DiskUsage: Get a query configured to retrieve disk usage for the specified user.
getQueryClass() - Method in class net.sf.basedb.core.DynamicPositionQueryJoiners.ExtraValueJoiner
getQueryClass() - Method in class net.sf.basedb.core.DynamicPositionQueryJoiners.ReporterJoiner
getQueryClass() - Method in class net.sf.basedb.core.DynamicPositionQueryJoiners.ReporterListJoiner
getQueryClass() - Method in class net.sf.basedb.core.DynamicRawDataQuery.RawBioAssayJoiner
getQueryClass() - Method in class net.sf.basedb.core.DynamicRawDataQuery.ReporterJoiner
getQueryClass() - Method in class net.sf.basedb.core.DynamicRawDataQuery.ReporterListJoiner
getQueryClass() - Method in class net.sf.basedb.core.DynamicReporterQuery.MasterReporterJoiner
getQueryClass() - Method in class net.sf.basedb.core.DynamicReporterQuery.ReporterListJoiner
getQueryClass() - Method in class net.sf.basedb.core.DynamicSpotQueryJoiners.ExtraValueJoiner
getQueryClass() - Method in class net.sf.basedb.core.DynamicSpotQueryJoiners.RawDataJoiner
getQueryClass() - Method in class net.sf.basedb.core.DynamicSpotQueryJoiners.ReporterJoiner
getQueryClass() - Method in class net.sf.basedb.core.DynamicSpotQueryJoiners.ReporterListJoiner
getQueryClass() - Method in class net.sf.basedb.core.HqlQueryJoiners.AnnotationJoiner
getQueryClass() - Method in class net.sf.basedb.core.HqlQueryJoiners.ReporterListJoiner
getQueryClass() - Method in interface net.sf.basedb.core.query.AutoJoiner: The type of the query the implementation works for.
getQueryFile() - Static method in class net.sf.basedb.core.Application: Get the path to the XML file containing predefined queries for SQL and HQL.
getQueryOptions() - Method in class net.sf.basedb.core.hibernate.QueryWrapper: Deprecated.
getQueryParameter(String) - Method in class net.sf.basedb.core.AbstractQuery
getQueryParameter(String) - Method in interface net.sf.basedb.core.query.Query: Get parameter information for the parameter with given name.
getQueryPropertyInspector() - Method in class net.sf.basedb.core.VirtualDb: Return a filter that can be used to check that a query is only using cloned reporter properties for sorting, filtering, etc.
getQueryRestriction() - Method in interface net.sf.basedb.core.query.QueryFilterAction: Generate a restriction for the entire query after all column and row filters has been processed.
getQueryReturns() - Method in class net.sf.basedb.core.hibernate.NativeQueryWrapper: Deprecated.
getQuerySection() - Method in class net.sf.basedb.core.AbstractQuery
getQuerySection() - Method in interface net.sf.basedb.core.query.Query: Get the current section of the query that is beeing built.
getQueryString() - Method in class net.sf.basedb.core.hibernate.QueryWrapper
getQueryString(String, String...) - Static method in class net.sf.basedb.core.PredefinedQuery: Get the query string for the predefined query with the specified name.
getQueryType() - Method in class net.sf.basedb.core.AbstractEntityQuery
getQueryType() - Method in class net.sf.basedb.core.AbstractHqlQuery
getQueryType() - Method in class net.sf.basedb.core.AbstractSqlQuery
getQueryType() - Method in interface net.sf.basedb.core.query.Query: Get the type of query.
getQuota() - Method in class net.sf.basedb.core.data.GroupData: Get the quota object which holds quota information for this group.
getQuota() - Method in class net.sf.basedb.core.data.UserData: Get the quota object which holds quota information for this user.
getQuota() - Method in class net.sf.basedb.core.Group: Get the Quota that applies to the group.
getQuota() - Method in class net.sf.basedb.core.User: Get the Quota that applies to the user.
getQuotaGroup() - Method in class net.sf.basedb.core.data.UserData: Get the group this user is sharing quota with, or null if this user only has it's own quota.
getQuotaGroup() - Method in class net.sf.basedb.core.User: Get the Group whose Quota also applies to the user.
getQuotaType() - Method in class net.sf.basedb.core.data.DiskUsageData: Get the QuotaTypeData for this DiskUsageData.
getQuotaType() - Method in class net.sf.basedb.core.data.QuotaIndex
getQuotaType() - Method in class net.sf.basedb.core.DiskUsage: Get the QuotaType the DiskConsumable item is using.
getQuotaTypes() - Method in class net.sf.basedb.core.DiskUsageStatistics: Get the list of quota types that are registered for DiskConsumable items.
getQuotaTypeSystemId() - Method in interface net.sf.basedb.core.DiskConsumable: Get the QuotaType system id of this item.
getQuotaTypeSystemId() - Method in class net.sf.basedb.core.Experiment: Always QuotaType.EXPERIMENT.
getQuotaTypeSystemId() - Method in class net.sf.basedb.core.File: Always QuotaType.FILE.
getQuotaTypeSystemId() - Method in class net.sf.basedb.core.RawBioAssay: Always QuotaType.RAW_DATA.
getQuotaValue(QuotaType, Location) - Method in class net.sf.basedb.core.Quota: Get the quota for the specified type and location.
getQuotaValues() - Method in class net.sf.basedb.core.data.QuotaData
getQuotedName(String) - Method in class net.sf.basedb.core.dbengine.AbstractDbEngine: Put quotes (") around the name.
getQuotedName(String) - Method in interface net.sf.basedb.core.dbengine.DbEngine: Quote the name with the database specific quote character.
getQuotedName(String) - Method in class net.sf.basedb.core.dbengine.MySQLEngine: Put quotes (`) around the name.
getRawBioAssay() - Method in class net.sf.basedb.core.data.RawData: The raw bioassay this raw data spot belongs to.
getRawBioAssay() - Method in class net.sf.basedb.core.data.RootRawBioAssayData: Get the raw bioassay root raw bioassay is derived from.
getRawBioAssay() - Method in class net.sf.basedb.core.DynamicRawDataQuery
getRawBioAssay() - Method in class net.sf.basedb.core.RawDataBatcher: Get the raw bioassay this batcher is used for.
getRawBioAssay() - Method in class net.sf.basedb.core.RootRawBioAssay: Get the raw bioassay this root raw bioassay is representing.
getRawBioAssay(DbControl, RawData) - Static method in class net.sf.basedb.core.RawDataUtil: Get the raw bioassay the raw data belongs to.
getRawBioAssayData - Static variable in class net.sf.basedb.core.RawDataUtil: Method for calling RawData.getRawBioAssay()
getRawBioAssayQuery(Experiment) - Method in class net.sf.basedb.plugins.RawDataFlatFileImporter: Get a query that returns all raw bioassays which it may be possible to import raw data to for the given experiment.
getRawBioAssays() - Method in class net.sf.basedb.core.BioAssay
getRawBioAssays() - Method in class net.sf.basedb.core.data.DerivedBioAssayData: This is the inverse end.
getRawBioAssays() - Method in class net.sf.basedb.core.data.ExperimentData: Duplicates the mapping ExperimentData.getRootRawBioAssays().
getRawBioAssays() - Method in class net.sf.basedb.core.data.ExtractData: This is the inverse end.
getRawBioAssays() - Method in class net.sf.basedb.core.data.JobData: This is the inverse end.
getRawBioAssays() - Method in class net.sf.basedb.core.DerivedBioAssay
getRawBioAssays() - Method in class net.sf.basedb.core.Experiment: Get a query that returns the raw bioassays used in this experiment.
getRawBioAssays() - Method in class net.sf.basedb.core.Extract: Get a query that returns all raw bioassays created from this extract.
getRawData() - Method in class net.sf.basedb.core.RawBioAssay: Get a query that returns the raw data of this raw bioassay.
getRawData() - Method in class net.sf.basedb.util.jep.MeanFunction: Get the current raw data object used when evaluating the JEP expression.
getRawData() - Method in class net.sf.basedb.util.jep.RawFunction: Get the current raw data object used when evaluating the JEP expression.
getRawDataBatcher(FeatureIdentificationMethod, Job) - Method in class net.sf.basedb.core.RawBioAssay: Get a raw data batcher object which can be used to add raw data to the raw bioassay.
getRawDataById(int) - Method in class net.sf.basedb.core.RawBioAssay: Get a raw data spot when you know the id.
getRawDataById(int, boolean) - Method in class net.sf.basedb.core.RawBioAssay: Get a raw data spot when you know the id.
getRawDataById(DbControl, int) - Method in class net.sf.basedb.core.RawDataType
getRawdataFields(BioAssaySet) - Method in class net.sf.basedb.plugins.BaseFileExporterPlugin
getRawdataFields(BioAssaySet) - Method in class net.sf.basedb.plugins.BfsExporterPlugin
getRawDataJoiner(JoinType) - Static method in class net.sf.basedb.core.DynamicSpotQueryJoiners: Get a joiner instance for raw data for the specified join type.
getRawDataProperty(String, String) - Method in class net.sf.basedb.util.export.spotdata.AbstractFieldConverter: Find an extended raw data property with the given name and create a dynamic field from it using exportTitle as the title.
getRawDataType() - Method in class net.sf.basedb.clients.web.extensions.list.RelatedItemColumn.Specification
getRawDataType() - Method in class net.sf.basedb.core.BioAssay: Get the raw data type the experiment uses for the raw data.
getRawDataType() - Method in class net.sf.basedb.core.BioAssaySet: Get the raw data type this experiment uses for the raw data.
getRawDataType() - Method in class net.sf.basedb.core.data.ExperimentData: Get the name of the raw data type used in this experiment.
getRawDataType() - Method in class net.sf.basedb.core.data.FormulaData: The name of raw data type this formula can be used on, or null if it can be used on any raw data type.
getRawDataType() - Method in class net.sf.basedb.core.data.ItemListData: Get the raw data type of raw bioassays that can be members in this list.
getRawDataType() - Method in class net.sf.basedb.core.data.PlatformData: The raw data type this platform is locked to, or null.
getRawDataType() - Method in class net.sf.basedb.core.data.PlatformVariantData: The raw data type this platform variant is locked to, or null.
getRawDataType() - Method in class net.sf.basedb.core.data.RawBioAssayData: Get the name of the raw data type used by this raw bio assay.
getRawDataType() - Method in class net.sf.basedb.core.DataCube: Get the raw data type this experiment uses for the raw data.
getRawDataType() - Method in class net.sf.basedb.core.DynamicRawDataQuery
getRawDataType() - Method in class net.sf.basedb.core.Experiment: Get the raw data type this experiment uses for the raw data.
getRawDataType() - Method in class net.sf.basedb.core.ExtraValue: Get the raw data type the experiment uses for the raw data.
getRawDataType() - Method in class net.sf.basedb.core.Formula: Get the raw data type this formula can be used on.
getRawDataType() - Method in class net.sf.basedb.core.ItemList: Get the raw data type of raw bioassays that can be members in this list.
getRawDataType() - Method in class net.sf.basedb.core.Platform: Get the raw data type this platform is locked to.
getRawDataType() - Method in class net.sf.basedb.core.PlatformVariant: Get the raw data type this platform variant is locked to.
getRawDataType() - Method in class net.sf.basedb.core.RawBioAssay: Get the raw data type this raw bioassay uses for the raw data.
getRawDataType() - Method in class net.sf.basedb.core.VirtualDb: Get the raw data type the experiment uses for the raw data.
getRawDataType() - Method in class net.sf.basedb.util.jep.RawFunction: Get the raw data type this function uses.
getRawDataType(String) - Static method in class net.sf.basedb.core.RawDataTypes: Get a information about a raw data type.
getRawDataTypeFiles() - Static method in class net.sf.basedb.core.Application: Get the path to the XML file containing raw data type definitions.
getRawDataTypes() - Static method in class net.sf.basedb.core.RawDataTypes: Get a collection with all raw data types that has been defined.
getRawParents() - Method in class net.sf.basedb.core.data.BioAssayData: Get a set that manages the raw parent bioassays the data in this bioassay is based on.
getRawSources() - Method in class net.sf.basedb.core.data.TransformationData: Get the source raw bioassays for the transformation.
getRawSources() - Method in class net.sf.basedb.core.Transformation: Get a query that returns the raw bioassay sources used by this transformation.
getRealTable() - Method in class net.sf.basedb.core.RawDataType
getReceivedSignals() - Method in class net.sf.basedb.core.signal.DelegatingSignalHandler: Get the list of received signals.
getReceivedSignals() - Method in class net.sf.basedb.core.signal.EnhancedThreadSignalHandler: Get the list of received signals.
getReceivedSignals() - Method in class net.sf.basedb.core.signal.ProgressReporterSignalHandler: Get the list of received signals.
getReceiverId() - Method in class net.sf.basedb.core.signal.AbstractSignalReceiver: Get the receiver ID that was passed to the AbstractSignalReceiver.init(String) method.
getReceiverId() - Method in class net.sf.basedb.core.signal.AbstractSignalTransporter: Get the receiverId part of the signal URI.
getRecent() - Method in class net.sf.basedb.clients.web.taglib.Select
getRecent(String) - Method in class net.sf.basedb.core.ItemContext: Get all recently used values for the specified key.
getRecent(String, int) - Method in class net.sf.basedb.core.ItemContext
getRecent(DbControl, Item) - Method in class net.sf.basedb.core.ItemContext: Get all recently used items of the specified type.
getRecent(DbControl, Item, int) - Method in class net.sf.basedb.core.ItemContext
getRecent(DbControl, Item, String) - Method in class net.sf.basedb.core.ItemContext: Get all recently used items of the specified type in a given sublist.
getRecent(DbControl, Item, String, int) - Method in class net.sf.basedb.core.ItemContext
getRecent(DbControl, Item, ItemSubtype) - Method in class net.sf.basedb.core.ItemContext: Get all recently used items of the specified type.
getRecentSettingName(String) - Method in class net.sf.basedb.core.ItemContext
getRedefinedColumnName(String, String) - Method in class net.sf.basedb.util.basefile.BaseFileParser: Get the redefined column name for a section.
getRefColumns() - Method in class net.sf.basedb.core.dbengine.TableInfo.ForeignKeyInfo
getReference(Class<T>, Object) - Method in class net.sf.basedb.core.hibernate.SessionWrapper
getReferenceFactor() - Method in class net.sf.basedb.core.data.UnitData: Factor that controls how this unit relates to the reference unit of the quantity.
getReferenceFactor() - Method in class net.sf.basedb.core.Unit: Get the factor that is used for converting values in this unit into the reference unit of the quantity.
getReferenceOffset() - Method in class net.sf.basedb.core.data.UnitData: An offset that controls how this unit relates to the reference unit of the quantity.
getReferenceOffset() - Method in class net.sf.basedb.core.Unit: Get the offset that is used for converting values in this unit into the reference unit of the quantity.
getReferenceUnit() - Method in class net.sf.basedb.core.data.QuantityData: The reference unit that all units of must relate to.
getReferenceUnit() - Method in class net.sf.basedb.core.Quantity: The reference unit describes the unit that all other units must relate to.
getRefName() - Method in class net.sf.basedb.core.dbengine.TableInfo.ForeignKeyInfo
getRegion() - Method in class net.sf.basedb.util.GeoLocation
getRegistry() - Method in class net.sf.basedb.util.extensions.ExtensionContext
getRegistry() - Method in class net.sf.basedb.util.extensions.ExtensionPointContext
getRegistry() - Method in class net.sf.basedb.util.extensions.InvokationContext: Get the registry where this invokation originated from.
getRegistry() - Method in class net.sf.basedb.util.extensions.manager.ExtensionsManager: Get the registry in which all extensions that are managed by this manager are stored.
getRegistryBuilder() - Method in class net.sf.basedb.core.ServiceSessionControl.SessionFactoryConfiguration: Get the registry for collecting configuration options.
getRelatedItems(Annotatable, SourceItemTransformer) - Method in class net.sf.basedb.clients.web.extensions.list.RelatedItemColumn: Get all parent or child items to the requested item that matches the specified filter.
getRelatedItems(Item) - Static method in class net.sf.basedb.core.ItemSubtype: Get a list with (subtypable) items that are related to the given item (which should also be subtypable).
getRelatedSubtype(DbControl, Subtypable, Item...) - Static method in class net.sf.basedb.core.ItemSubtype: Utility method for locating a subtype that is related to the subtype of a given item.
getRelatedSubtype(DbControl, Subtypable, Item, int) - Static method in class net.sf.basedb.core.ItemSubtype: Same as ItemSubtype.getRelatedSubtype(DbControl, Subtypable, Item, int, int) with the same id for the last two parameters.
getRelatedSubtype(DbControl, Subtypable, Item, int, int) - Static method in class net.sf.basedb.core.ItemSubtype: Utility method for loading a subtype that is related to the subtype of the given item.
getRelatedSubtype(Item) - Method in class net.sf.basedb.core.ItemSubtype: Get a related subtype of another item type.
getRelatedSubtypes() - Method in class net.sf.basedb.core.data.ItemSubtypeData
getRelatedSubtypes() - Method in class net.sf.basedb.core.ItemSubtype: Get a query returning all subtypes that are related to this subtype.
getRelativePath(File) - Static method in class net.sf.basedb.core.File: Get the relative path of the specified file from the base upload directory and convert directory separator to forward slash.
getReload() - Method in class net.sf.basedb.core.InternalJobQueue.JobQueueKeyring: Never reload since everything is static.
getReload() - Method in class net.sf.basedb.core.Job.SignalKeyring: Never reload since everything is static.
getReload() - Method in class net.sf.basedb.core.Keyring
getReload() - Method in class net.sf.basedb.core.ServiceSessionControl.ServicesKeyring: Never reload since everything is static.
getRemainingQuantity() - Method in class net.sf.basedb.core.data.MeasuredBioMaterialData: Get the remaining quantity of the biomaterial.
getRemainingQuantity() - Method in class net.sf.basedb.core.MeasuredBioMaterial: Get the remaining quantity of the biomaterial.
getRemoteAddresses(String) - Method in class net.sf.basedb.clients.jobagent.Agent: Split the string at commas and try to create an InetAddress for each part.
getRemoteId() - Method in class net.sf.basedb.core.data.SessionData: Get the login comment.
getRemoteId() - Method in class net.sf.basedb.core.Session: Get the remote ID of the host the user used for this session.
getRemoteId() - Method in class net.sf.basedb.core.SessionControl: Get the remote id that was passed to the Application.newSessionControl(String,String,String) method when creating this object.
getRemoteSlot(String) - Method in class net.sf.basedb.clients.jobagent.slotmanager.MasterSlotManager: Get the remote slot with the given id.
getRemoteSlot(Job.ExecutionTime) - Method in class net.sf.basedb.clients.jobagent.slotmanager.MasterSlotManager: Create a slot for a job on a remote job agent with the specified estimated execution time.
getRemovableItems() - Static method in class net.sf.basedb.core.Metadata: Get a set containing all Removable item types.
getRemove() - Method in class net.sf.basedb.util.annotations.InheritSpecification
getRemovedBy() - Method in class net.sf.basedb.core.BioAssaySet
getRemovedBy() - Method in class net.sf.basedb.core.BioPlateEventType
getRemovedBy() - Method in class net.sf.basedb.core.BioPlateType
getRemovedBy() - Method in class net.sf.basedb.core.CommonItem
getRemovedBy() - Method in class net.sf.basedb.core.data.BioAssaySetData
getRemovedBy() - Method in class net.sf.basedb.core.data.BioPlateEventTypeData
getRemovedBy() - Method in class net.sf.basedb.core.data.BioPlateTypeData
getRemovedBy() - Method in class net.sf.basedb.core.data.CommonData
getRemovedBy() - Method in class net.sf.basedb.core.data.DataFileTypeData
getRemovedBy() - Method in class net.sf.basedb.core.data.ExtraValueTypeData
getRemovedBy() - Method in class net.sf.basedb.core.data.GroupData
getRemovedBy() - Method in class net.sf.basedb.core.data.ItemSubtypeData
getRemovedBy() - Method in class net.sf.basedb.core.data.MessageData
getRemovedBy() - Method in class net.sf.basedb.core.data.MimeTypeData
getRemovedBy() - Method in class net.sf.basedb.core.data.NewsData
getRemovedBy() - Method in class net.sf.basedb.core.data.PlateEventTypeData
getRemovedBy() - Method in class net.sf.basedb.core.data.PlateGeometryData
getRemovedBy() - Method in class net.sf.basedb.core.data.PlatformData
getRemovedBy() - Method in class net.sf.basedb.core.data.PlatformVariantData
getRemovedBy() - Method in class net.sf.basedb.core.data.PluginDefinitionData
getRemovedBy() - Method in class net.sf.basedb.core.data.PluginTypeData
getRemovedBy() - Method in class net.sf.basedb.core.data.ProjectData
getRemovedBy() - Method in class net.sf.basedb.core.data.QuantityData
getRemovedBy() - Method in class net.sf.basedb.core.data.QuotaData
getRemovedBy() - Method in interface net.sf.basedb.core.data.RemovableData: Get the ID of the user that removed this item.
getRemovedBy() - Method in class net.sf.basedb.core.data.ReporterTypeData
getRemovedBy() - Method in class net.sf.basedb.core.data.RoleData
getRemovedBy() - Method in class net.sf.basedb.core.data.TransformationData
getRemovedBy() - Method in class net.sf.basedb.core.data.UnitData
getRemovedBy() - Method in class net.sf.basedb.core.data.UserData
getRemovedBy() - Method in class net.sf.basedb.core.DataFileType
getRemovedBy() - Method in class net.sf.basedb.core.Directory
getRemovedBy() - Method in class net.sf.basedb.core.ExtraValueType
getRemovedBy() - Method in class net.sf.basedb.core.Group
getRemovedBy() - Method in class net.sf.basedb.core.ItemSubtype
getRemovedBy() - Method in class net.sf.basedb.core.Message
getRemovedBy() - Method in class net.sf.basedb.core.MimeType
getRemovedBy() - Method in class net.sf.basedb.core.News
getRemovedBy() - Method in class net.sf.basedb.core.PlateEventType
getRemovedBy() - Method in class net.sf.basedb.core.PlateGeometry
getRemovedBy() - Method in class net.sf.basedb.core.Platform
getRemovedBy() - Method in class net.sf.basedb.core.PlatformVariant
getRemovedBy() - Method in class net.sf.basedb.core.PluginType
getRemovedBy() - Method in class net.sf.basedb.core.Project
getRemovedBy() - Method in class net.sf.basedb.core.Quantity
getRemovedBy() - Method in class net.sf.basedb.core.Quota
getRemovedBy() - Method in interface net.sf.basedb.core.Removable: Get the user that flagged this item for removal.
getRemovedBy() - Method in class net.sf.basedb.core.ReporterType
getRemovedBy() - Method in class net.sf.basedb.core.Role
getRemovedBy() - Method in class net.sf.basedb.core.Transformation
getRemovedBy() - Method in class net.sf.basedb.core.Unit
getRemovedBy() - Method in class net.sf.basedb.core.User
getRemoveJobWhenFinished() - Method in class net.sf.basedb.core.data.JobData: If the core should delete the job when it's finished successfully.
getRemoveJobWhenFinished() - Method in class net.sf.basedb.core.Job: If the job should flagged for deletion after it's done successfully.
getRenderer() - Method in class net.sf.basedb.util.extensions.ActionIterator: Gets the renderer for the current action.
getRenderer() - Method in class net.sf.basedb.util.extensions.ExtensionContext: If the extension point allows it and this extension specifies a renderer factory, create a new renderer from it.
getRenderer() - Method in class net.sf.basedb.util.extensions.ExtensionPointContext: If the extension point defines a renderer factory, creates a new renderer unless one already exists.
getRenderer() - Method in class net.sf.basedb.util.extensions.InvokationContext: Get the renderer, if any.
getRenderer(InvokationContext<? extends A>) - Method in interface net.sf.basedb.util.extensions.RendererFactory: Get a renderer for a given context.
getRenderer(InvokationContext<? extends ButtonAction>) - Method in class net.sf.basedb.clients.web.extensions.toolbar.CompactButtonRendererFactory
getRenderer(InvokationContext<? extends ButtonAction>) - Method in class net.sf.basedb.clients.web.extensions.toolbar.ToolbarButtonRendererFactory
getRendererFactory() - Method in interface net.sf.basedb.util.extensions.Extension: Get an optional factory class for creating renderers for the actions.
getRendererFactory() - Method in class net.sf.basedb.util.extensions.ExtensionBean
getRendererFactory() - Method in interface net.sf.basedb.util.extensions.ExtensionPoint: This is an optional factory for creating Renderer instances.
getRendererFactory() - Method in class net.sf.basedb.util.extensions.ExtensionPointBean
getRendererFactory() - Method in class net.sf.basedb.util.extensions.Registry.RegisteredExtension
getRendererFactory() - Method in class net.sf.basedb.util.extensions.Registry.RegisteredExtensionPoint
getReplaceExisting() - Method in class net.sf.basedb.util.annotations.InheritSpecification
getReporter() - Method in class net.sf.basedb.core.data.FeatureData: Get the reporter of the feature.
getReporter() - Method in class net.sf.basedb.core.data.RawData: The reporter this raw data is connected with.
getReporter() - Method in class net.sf.basedb.core.data.ReporterListScoreData: Get the reporter.
getReporter() - Method in class net.sf.basedb.core.data.WellData: The reporter used in this well.
getReporter() - Method in class net.sf.basedb.core.ReporterScore: Get the reporter.
getReporter() - Method in class net.sf.basedb.core.Well: Get the reporter in this well.
getReporter() - Method in class net.sf.basedb.util.jep.ReporterFunction: Get the current reporter object used when evaluating the JEP expression.
getReporter(boolean) - Method in class net.sf.basedb.core.Well: Get the reporter in this well.
getReporter(DbControl, int) - Method in class net.sf.basedb.clients.web.ExperimentExplorer: Get the reporter for the specified index.
getReporter(RawDataBatcher.ReporterProxy) - Method in class net.sf.basedb.core.RawDataBatcher.FeatureInfo
getReporterAnnotationsWriter() - Method in class net.sf.basedb.util.export.spotdata.BfsExporter: Get the writer were reporter annotations should be printed.
getReporterCloneBatcher(DbControl) - Method in class net.sf.basedb.core.Experiment: Get a batcher for managing cloned reporter information for this experiment.
getReporterCloneTemplate() - Method in class net.sf.basedb.core.data.VirtualDbData: Get the template used for creating the cloned reporter table in this virtual database, or null if there is no cloned reporter information.
getReporterCloneTemplate() - Method in class net.sf.basedb.core.VirtualDb: Get the reporter clone template that is active in the current virtual database.
getReporterField(String, boolean) - Method in class net.sf.basedb.util.export.spotdata.AdvancedFieldConverter
getReporterField(String, boolean) - Method in class net.sf.basedb.util.export.spotdata.Base1FieldConverter: Convert a reporter field.
getReporterField(String, boolean) - Method in interface net.sf.basedb.util.export.spotdata.ExportableFieldConverter: Create a reporter dynamic field for the given name.
getReporterField(String, boolean) - Method in class net.sf.basedb.util.export.spotdata.StandardFieldConverter: Find a reporter dynamic field.
getReporterFields() - Method in class net.sf.basedb.plugins.BaseFileExporterPlugin
getReporterFields() - Static method in class net.sf.basedb.plugins.BfsExporterPlugin
getReporterFields() - Method in class net.sf.basedb.util.export.spotdata.AbstractBioAssaySetExporter: Get the list of registered reporter fields, in the order they were registered.
getReporterFields() - Method in class net.sf.basedb.util.export.spotdata.BaseFileExporter
getReporterFields() - Method in class net.sf.basedb.util.export.spotdata.BfsExporter
getReporterId() - Method in class net.sf.basedb.core.data.ReporterListScoreData: The id of the reporter.
getReporterId(int) - Method in class net.sf.basedb.clients.web.ExperimentExplorer: Get the reporter id for the specified index.
getReporterIndex() - Method in class net.sf.basedb.clients.web.ExperimentExplorer: Get the index of the current reporter.
getReporterJoiner(JoinType) - Static method in class net.sf.basedb.core.DynamicPositionQueryJoiners: Get a joiner instance for reporters for the specified join type.
getReporterJoiner(JoinType) - Static method in class net.sf.basedb.core.DynamicSpotQueryJoiners: Get a joiner instance for reporters for the specified join type.
getReporterList() - Method in class net.sf.basedb.core.data.ReporterListScoreData: The reporter list this reporter and score belongs to.
getReporterList() - Method in class net.sf.basedb.core.query.ReporterListExpression: Get the reporter list.
getReporterListJoiner(JoinType) - Static method in class net.sf.basedb.core.DynamicPositionQueryJoiners: Get a joiner instance for reporter lists for the specified join type.
getReporterListJoiner(JoinType) - Static method in class net.sf.basedb.core.DynamicReporterQuery: Get a joiner instance for reporter lists for the specified join type.
getReporterListJoiner(JoinType) - Static method in class net.sf.basedb.core.DynamicSpotQueryJoiners: Get a joiner instance for raw data for the specified join type.
getReporterListJoiner(JoinType) - Static method in class net.sf.basedb.core.HqlQueryJoiners: Get a joiner instance for raw data for the specified join type.
getReporterLists() - Method in class net.sf.basedb.core.data.ExperimentData: This is the inverse end.
getReporterListScores() - Method in class net.sf.basedb.core.data.ReporterData: The lists this reporter is used in.
getReporterListScores() - Method in class net.sf.basedb.core.data.ReporterListData: The list of reporters and their scores.
getReporterListsEnum(DbControl) - Static method in class net.sf.basedb.clients.web.Base
getReporterProperty(String, String) - Method in class net.sf.basedb.util.export.spotdata.AbstractFieldConverter: Get a static or extended reporter property field, such as name, description or id.
getReporterQuery() - Method in class net.sf.basedb.util.export.spotdata.AbstractBioAssaySetExporter: Get a configured query for position data that returns all fields that has been registered with AbstractBioAssaySetExporter.addReporterField(DynamicField).
getReporterQuery(DbControl, List<String>) - Method in class net.sf.basedb.clients.web.ExperimentExplorer: Get a query returning the reporter data used by the reporter search page.
getReporters() - Method in class net.sf.basedb.core.ArrayDesign: Get a query that returns the reporters on this array design.
getReporters() - Method in class net.sf.basedb.core.data.ReporterTypeData: This is the inverse end.
getReporters() - Method in class net.sf.basedb.core.Plate: Get a query that returns the reporters on this plate.
getReporters() - Method in class net.sf.basedb.core.RawBioAssay: Get a query that returns the reporters on this raw bioassay.
getReporterScores() - Method in class net.sf.basedb.core.ReporterList: Get a query returning ReporterScore objects.
getReporterType() - Method in class net.sf.basedb.core.data.ReporterData: Get the ReporterTypeData of this the reporter.
getReporterType(String) - Method in class net.sf.basedb.plugins.ReporterFlatFileImporter
getReporterType(DbControl, ReporterData) - Static method in class net.sf.basedb.core.Reporter: Get the reporter type item from a reporter data object.
getRequestInformation() - Method in class net.sf.basedb.core.PluginConfigurationRequest: Get the request information object containing information about the parameters needed for the plugin.
getRequestInformation(GuiContext, String) - Method in class net.sf.basedb.clients.web.plugins.SimpleExport
getRequestInformation(GuiContext, String) - Method in interface net.sf.basedb.core.plugin.InteractivePlugin: This method will return the RequestInformation for a given command, i.e.
getRequestInformation(GuiContext, String) - Method in class net.sf.basedb.plugins.AnnotationFlatFileImporter
getRequestInformation(GuiContext, String) - Method in class net.sf.basedb.plugins.Base1PluginExecuter
getRequestInformation(GuiContext, String) - Method in class net.sf.basedb.plugins.BaseFileExporterPlugin
getRequestInformation(GuiContext, String) - Method in class net.sf.basedb.plugins.batchimport.AbstractItemImporter
getRequestInformation(GuiContext, String) - Method in class net.sf.basedb.plugins.batchimport.AnyToAnyImporter
getRequestInformation(GuiContext, String) - Method in class net.sf.basedb.plugins.BfsExporterPlugin
getRequestInformation(GuiContext, String) - Method in class net.sf.basedb.plugins.CdfFileReporterImporter
getRequestInformation(GuiContext, String) - Method in class net.sf.basedb.plugins.executor.BaseFileExporterSupport
getRequestInformation(GuiContext, String) - Method in class net.sf.basedb.plugins.executor.BaseFileImporterSupport
getRequestInformation(GuiContext, String) - Method in class net.sf.basedb.plugins.executor.BfsExporterSupport
getRequestInformation(GuiContext, String) - Method in class net.sf.basedb.plugins.executor.BfsImporterSupport
getRequestInformation(GuiContext, String) - Method in class net.sf.basedb.plugins.executor.ExternalProgramExecutor
getRequestInformation(GuiContext, String) - Method in class net.sf.basedb.plugins.executor.FileOnlyImporterSupport
getRequestInformation(GuiContext, String) - Method in class net.sf.basedb.plugins.FormulaFilter
getRequestInformation(GuiContext, String) - Method in class net.sf.basedb.plugins.GalExporter
getRequestInformation(GuiContext, String) - Method in class net.sf.basedb.plugins.gtf.GtfReporterMapImporter
getRequestInformation(GuiContext, String) - Method in class net.sf.basedb.plugins.HelpExporter
getRequestInformation(GuiContext, String) - Method in class net.sf.basedb.plugins.HelpImporter
getRequestInformation(GuiContext, String) - Method in class net.sf.basedb.plugins.IlluminaRawDataImporter
getRequestInformation(GuiContext, String) - Method in class net.sf.basedb.plugins.IntensityCalculatorPlugin: The Request.COMMAND_CONFIGURE_PLUGIN command will not ask for any parameters.
getRequestInformation(GuiContext, String) - Method in class net.sf.basedb.plugins.JepExtraValueCalculator
getRequestInformation(GuiContext, String) - Method in class net.sf.basedb.plugins.JepIntensityTransformer
getRequestInformation(GuiContext, String) - Method in class net.sf.basedb.plugins.LowessNormalization
getRequestInformation(GuiContext, String) - Method in class net.sf.basedb.plugins.ManualDerivedBioAssayCreator
getRequestInformation(GuiContext, String) - Method in class net.sf.basedb.plugins.ManualTransformCreator
getRequestInformation(GuiContext, String) - Method in class net.sf.basedb.plugins.MedianRatioNormalization
getRequestInformation(GuiContext, String) - Method in class net.sf.basedb.plugins.PackedFileExporter
getRequestInformation(GuiContext, String) - Method in class net.sf.basedb.plugins.PlateFlatFileImporter: The Request.COMMAND_CONFIGURE_PLUGIN command will ask for parser regular expressions and column mappings.
getRequestInformation(GuiContext, String) - Method in class net.sf.basedb.plugins.PlateMappingExporter
getRequestInformation(GuiContext, String) - Method in class net.sf.basedb.plugins.PlateMappingImporter
getRequestInformation(GuiContext, String) - Method in class net.sf.basedb.plugins.PluginConfigurationExporter
getRequestInformation(GuiContext, String) - Method in class net.sf.basedb.plugins.PluginConfigurationImporter
getRequestInformation(GuiContext, String) - Method in class net.sf.basedb.plugins.PrintMapFlatFileImporter: The Request.COMMAND_CONFIGURE_PLUGIN command will ask for parser regular expressions and column mappings.
getRequestInformation(GuiContext, String) - Method in class net.sf.basedb.plugins.RawDataFlatFileImporter: The Request.COMMAND_CONFIGURE_PLUGIN command will ask for what type of rawdata to import.
getRequestInformation(GuiContext, String) - Method in class net.sf.basedb.plugins.ReporterFlatFileImporter: The Request.COMMAND_CONFIGURE_PLUGIN command will ask for parser regular expressions, column mappings and the reporter type.
getRequestInformation(GuiContext, String) - Method in class net.sf.basedb.plugins.ReporterMapFlatFileImporter: The Request.COMMAND_CONFIGURE_PLUGIN command will ask for parser regular expressions and column mappings.
getRequestInformation(GuiContext, String) - Method in class net.sf.basedb.util.zip.AbstractFileUnpacker
getRequiredFilter(Item) - Static method in class net.sf.basedb.core.QueryRuntimeFilterFactory: Get the required runtime filter for the speicified item type.
getRequiredHeader(FlatFileParser, String, String, String) - Method in class net.sf.basedb.util.basefile.BaseFileParser: Get the value of a required header.
getRequiredHeader(FlatFileParser, String, String, String, String) - Method in class net.sf.basedb.util.basefile.BaseFileParser: Get the value of a header as a list of sub-values.
getRequiredIndex(List<String>, String, String, String, int, String) - Method in class net.sf.basedb.util.basefile.BaseFileParser: Get the index of value in a list of values or throw an exception if the value is not found.
getRequiredString(String, String) - Static method in class net.sf.basedb.core.Config: Get a required configuration setting.
getRequiresConfiguration() - Method in class net.sf.basedb.core.data.PluginDefinitionData: If the plugin requires a configurations or not.
getResetClassLoader() - Method in class net.sf.basedb.util.extensions.manager.processor.ResetProcessor
getResetrrorFlag() - Method in class net.sf.basedb.util.extensions.manager.processor.ResetProcessor
getResource(String) - Method in class net.sf.basedb.util.JarClassLoader
getResourceBundle() - Method in class net.sf.basedb.util.resources.ResourceBundleWrapper: Get access to the underlying resource bundle.
getResourceBundle(String, Locale) - Static method in class net.sf.basedb.util.resources.ResourceBundleFactory: Same as getResouceBundle(name, locale, null).
getResourceBundle(String, Locale, ClassLoader) - Static method in class net.sf.basedb.util.resources.ResourceBundleFactory: Get a resource bundle for the given locale.
getResourceBundle(String, SessionControl) - Static method in class net.sf.basedb.util.resources.ResourceBundleFactory: Same as getResouceBundle(name, sc, null).
getResourceBundle(String, SessionControl, ClassLoader) - Static method in class net.sf.basedb.util.resources.ResourceBundleFactory: Get a resource bundle for the given session control.
getResources(String) - Method in class net.sf.basedb.util.JarClassLoader
getResponseImpl() - Method in class net.sf.basedb.core.PluginResponse: Get a new reponse object.
getRestriction() - Method in class net.sf.basedb.core.ItemContext.QueryRestrictions
getRestriction(DbControl, EntityQuery) - Method in class net.sf.basedb.core.PropertyFilter: Create a restriction from the filter.
getRestriction(DbControl, EntityQuery, ClientContext) - Method in class net.sf.basedb.core.PropertyFilter: Create a restriction from the filter.
getRestriction(Expression, Expression) - Method in enum net.sf.basedb.core.Operator
getRestriction(Expression, Expression[]) - Method in enum 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 net.sf.basedb.core.ItemContext.SortDirection: Get the reverse sort direction.
getRole() - Method in class net.sf.basedb.core.BioPlateEventParticipant: Get the role that the plate has in this event.
getRole() - Method in class net.sf.basedb.core.data.BioPlateEventParticipantData: Get the role of the plate in the event.
getRoleId() - Method in class net.sf.basedb.core.data.keyring.RoleKeys: Get the id of the role.
getRoleId() - Method in class net.sf.basedb.core.data.keyring.UserRoles: Get the id of the role.
getRoleKeyId(Item) - Static method in class net.sf.basedb.core.SystemItems: Get the numeric id for a RoleKey when you know the Item type of the RoleKey.
getRolePermissions(Item) - Method in class net.sf.basedb.core.InternalJobQueue.JobQueueKeyring: Return Permission.ACT_AS_ANOTHER_USER if itemType = Item.SYSTEM, 0 otherwise.
getRolePermissions(Item) - Method in class net.sf.basedb.core.Job.SignalKeyring: Return Permission.WRITE if itemType = Item.JOB, Permission.READ if Item.USER and Permission.CREATE if Item.MESSAGE or 0 otherwise.
getRolePermissions(Item) - Method in class net.sf.basedb.core.Keyring: Get the logged in user's permission to an unspecified item of a certain Item type.
getRolePermissions(Item) - Method in class net.sf.basedb.core.ServiceSessionControl.ServicesKeyring: Return Permission.ACT_AS_ANOTHER_USER if itemType = Item.SYSTEM, 0 otherwise.
getRolePermissions(Item) - Method in class net.sf.basedb.core.SessionControl: Get all role-based permissions for the specified type of items.
getRoles() - Method in class net.sf.basedb.core.data.RoleKeyData: Get the map that manages which roles that have permissions for this key.
getRoles() - Method in class net.sf.basedb.core.data.UserData: This is the inverse end.
getRoles() - Method in class net.sf.basedb.core.InternalJobQueue.JobQueueKeyring: Return empty set.
getRoles() - Method in class net.sf.basedb.core.Job.SignalKeyring: Return empty set.
getRoles() - Method in class net.sf.basedb.core.Keyring
getRoles() - Method in class net.sf.basedb.core.ServiceSessionControl.ServicesKeyring: Return empty set.
getRoles() - Method in class net.sf.basedb.core.SessionControl: Deprecated.
In 3.11, use SessionControl.getAllRoles() or SessionControl.getActiveRoles() instead
getRoles() - Method in class net.sf.basedb.core.User: Get a query that returns the roles where this user is a member.
getRoot() - Method in class net.sf.basedb.clients.web.extensions.JspContext: Get the URL to the web application root as a string.
getRoot() - Method in class net.sf.basedb.clients.web.taglib.menu.Menu
getRoot() - Method in class net.sf.basedb.clients.web.taglib.Page
getRoot() - Method in class net.sf.basedb.clients.web.taglib.path.Path
getRoot() - Method in class net.sf.basedb.clients.web.taglib.PropertyValue
getRoot() - Method in class net.sf.basedb.util.extensions.xml.PathConverter: Get the value of the root path.
getRootAlias() - Method in class net.sf.basedb.core.AbstractHqlQuery: The alias of the item that is the root of this query.
getRootAlias() - Method in class net.sf.basedb.core.DynamicQuery: The alias of the item that is returned by this query.
getRootAlias() - Method in class net.sf.basedb.core.DynamicRawDataQuery: The alias of the item that is returned by this query.
getRootAlias() - Method in class net.sf.basedb.core.DynamicReporterQuery: The alias of the item that is returned by this query.
getRootAlias() - Method in interface net.sf.basedb.core.query.Query: The alias of the root-entity in the FROM part.
getRootDerivedBioAssays() - Method in class net.sf.basedb.core.data.PhysicalBioAssayData: This is the inverse end with an extra restriction
getRootDerivedBioAssays() - Method in class net.sf.basedb.core.PhysicalBioAssay: Get a query that returns all root derived bioassay created from this physical bioassay.
getRootEntry() - Method in class net.sf.basedb.util.Tree: Get the entry for the root node.
getRootItem() - Method in class net.sf.basedb.util.overview.GenericOverview: Get the root item of this overview.
getRootNode() - Method in class net.sf.basedb.util.overview.GenericOverview: Get the root node.
getRootPath() - Method in class net.sf.basedb.core.data.FileServerData: Get the root path that must be added to all URI:s using this file server.
getRootPath() - Method in class net.sf.basedb.core.FileServer
getRootPath() - Method in class net.sf.basedb.util.uri.ConnectionParameters: Get the root path that must be added to all URI:s used with these connection parameters.
getRootPath(DbControl) - Method in class net.sf.basedb.plugins.batchimport.FileImporter
getRootRawBioAssay(RawBioAssay) - Method in class net.sf.basedb.core.Experiment: Get the root raw bioassay that represents the given raw bioassay in this experiment.
getRootRawBioAssays() - Method in class net.sf.basedb.core.BioAssay
getRootRawBioAssays() - Method in class net.sf.basedb.core.data.ExperimentData: Manages which raw bioassays are available in the experiment.
getRootRawBioAssays() - Method in class net.sf.basedb.core.Experiment: Get a query that returns the root raw bioassays used in this experiment.
getRootTable() - Method in class net.sf.basedb.core.DynamicQuery
getRootTable() - Method in class net.sf.basedb.core.DynamicRawDataQuery
getRootTransformations() - Method in class net.sf.basedb.core.Experiment: Get a query that return all root transformations in this experiment.
getRootType() - Method in class net.sf.basedb.core.AbstractEntityQuery
getRootType() - Method in interface net.sf.basedb.core.query.EntityQuery: The type of items that is the root of the query.
getRow() - Method in class net.sf.basedb.clients.web.taglib.table.PropertyFilter
getRow() - Method in class net.sf.basedb.core.BioWell: Gets the row index where this well is located.
getRow() - Method in class net.sf.basedb.core.data.BioWellData: The row coordinate of this well.
getRow() - Method in class net.sf.basedb.core.data.FeatureData: Get the row coordinate of the feature.
getRow() - Method in class net.sf.basedb.core.data.MappingCoordinate: Get the row number.
getRow() - Method in class net.sf.basedb.core.data.PlateCoordinate: Get the row number.
getRow() - Method in class net.sf.basedb.core.data.RawData
getRow() - Method in class net.sf.basedb.core.data.WellData: The row coordinate of this well.
getRow() - Method in class net.sf.basedb.core.FeatureCoordinate
getRow() - Method in class net.sf.basedb.core.Well: Get the row coordinate of this well on the plate.
getRow(int) - Method in class net.sf.basedb.core.ItemContext.QueryRestrictions
getRowById(int) - Method in class net.sf.basedb.util.bfs.AnnotationModel
getRowByIndex(int) - Method in class net.sf.basedb.util.bfs.AnnotationModel
getRowByIndex(int) - Method in class net.sf.basedb.util.bfs.MatrixModel
getRowCount() - Method in class net.sf.basedb.util.bfs.AnnotationModel: Get the number of rows.
getRowCount() - Method in class net.sf.basedb.util.bfs.MatrixModel: Get the number of rows.
getRowCount(DbEngine, Connection, boolean) - Method in class net.sf.basedb.core.dbengine.TableInfo: Count the number of rows in the table.
getRowId(int) - Method in class net.sf.basedb.util.bfs.AnnotationModel: Get the row id for a given row.
getRowIndex() - Method in class net.sf.basedb.core.PropertyFilter: Get the filter row index this filter is part of.
getRowIndex(int) - Method in class net.sf.basedb.util.bfs.AnnotationModel: Get the row index for a given row id.
getRowRestriction() - Method in class net.sf.basedb.core.ItemContext.RowRestrictions
getRowRestriction(int) - Method in interface net.sf.basedb.core.query.QueryFilterAction: Generate a restriction for the given filter row.
getRows() - Method in class net.sf.basedb.core.BioPlate: Get the number of rows on this plate.
getRows() - Method in class net.sf.basedb.core.data.PlateGeometryData: The number of rows in this geometry.
getRows() - Method in class net.sf.basedb.core.PlateGeometry: Get the number of rows in this geometry.
getRowSelectionForLimitHandler() - Method in class net.sf.basedb.core.AbstractSqlQuery: Get a RowSelection object to be used with a LimitHandler so that it can modify and add parameters to the SQL.
getRowSeparator() - Method in class net.sf.basedb.util.excel.XlsxToCsvUtil: Get the current row separator.
getRowsperpage() - Method in class net.sf.basedb.clients.web.taglib.table.Navigator
getRowsPerPage() - Method in class net.sf.basedb.core.data.ContextData: Get the number of rows that are displayed on each table page.
getRowsPerPage() - Method in class net.sf.basedb.core.ItemContext: Get the number of rows the current table page is displaying.
getRunningJobs() - Method in class net.sf.basedb.clients.jobagent.Agent: Get a set containing the ID:s of the jobs that are currently beeing executed by this job agent.
getSafeRawDataType(String) - Static method in class net.sf.basedb.core.RawDataTypes: Get a information about a raw data type or throw an exception if the raw data type is not found.
getSameUnitsParameter() - Method in class net.sf.basedb.clients.web.plugins.SimpleExport
getSamples() - Method in class net.sf.basedb.core.BioSource: Get a query that returns all samples created from this biosource.
getSampleSize() - Method in class net.sf.basedb.util.AnyToAnyLinkStatistics: Get the number of items that was sampled to generated the statistics.
getSaveAsParameter(String, String, String, boolean) - Method in class net.sf.basedb.core.plugin.AbstractExporterPlugin: Get a plugin parameter that asks for the path to a file where the exported data should be saved.
getSaveAsPath(DbControl) - Method in class net.sf.basedb.core.plugin.AbstractExporterPlugin: Get the configured path where the exported data should be saved.
getSaveTo() - Method in class net.sf.basedb.core.plugin.AbstractExporterPlugin: Get the file object that the current export is writing to.
getSc() - Method in class net.sf.basedb.clients.web.taglib.table.Table
getScale(SessionControl) - Static method in class net.sf.basedb.clients.web.Base: Get the display scale setting.
getScheduled() - Method in class net.sf.basedb.core.data.JobData: Get the date and time the job was scheduled to the job queue, or null if it hasn't been scheduled yet.
getScheduled() - Method in class net.sf.basedb.core.Job: Get the date and time the job was scheduled to the job queue.
getScheduler() - Static method in class net.sf.basedb.core.Application: Get a scheduler that can be used for registering TimerTask for executions.
getSchema() - Method in class net.sf.basedb.core.hibernate.SessionFactoryConfiguration: Deprecated.

Get the schema.
getSchema() - Method in class net.sf.basedb.core.ServiceSessionControl.SessionFactoryConfiguration: Get the schema.
getSchemaName(String, String) - Method in class net.sf.basedb.core.dbengine.AbstractDbEngine: Return the schema name.
getSchemaName(String, String) - Method in interface net.sf.basedb.core.dbengine.DbEngine: Get the schema name to use for referencing the given catalog/schema pair.
getSchemaName(String, String) - Method in class net.sf.basedb.core.dbengine.MySQLEngine: Return null.
getSchemaValidatedXML(InputStream, String, String...) - Static method in class net.sf.basedb.util.XmlUtil2: Validate an XML input stream using XML schemas.
getSchemaValidatedXML(URL, String...) - Static method in class net.sf.basedb.util.XmlUtil2: Validate an XML file using XML schemas.
getSchemaVersion() - Static method in class net.sf.basedb.core.Application: Get the current database schema version number.
getSchemaVersion() - Method in class net.sf.basedb.core.data.SchemaVersionData: The current schema version.
getSchemaVersion() - Method in class net.sf.basedb.core.hibernate.SessionFactoryConfiguration: Deprecated.

Get the schema version of the current configuration.
getSchemaVersion() - Method in class net.sf.basedb.core.ServiceSessionControl.SessionFactoryConfiguration: Get the schema version of the current configuration.
getSchemaVersion(Session, String) - Static method in class net.sf.basedb.core.Update
getSchemaVersionInTransaction(Session, String) - Static method in class net.sf.basedb.core.Update: Get the current schema version number as it is stored in the database.
getScore() - Method in class net.sf.basedb.core.data.ReporterListScoreData: Get the score for the reporter, or null if no score has been set.
getScore() - Method in class net.sf.basedb.core.ReporterScore: Get the score for this reporter or null if no score has been set.
getScore() - Method in class net.sf.basedb.util.fuzzy.StringMatcher.FuzzyMatch: Get the similarity score of the key/value strings.
getScore(String, String) - Method in class net.sf.basedb.util.fuzzy.StringMatcher: Get the similarity score of two strings.
getScore(ReporterData) - Method in class net.sf.basedb.core.ReporterList: Get the score for the specified reporter.
getScripts() - Method in class net.sf.basedb.clients.web.extensions.AbstractJspFactory: Get a set with all script references.
getScripts() - Method in class net.sf.basedb.clients.web.extensions.JspContext: Get all scripts that has been added to this context.
getScripts() - Method in class net.sf.basedb.clients.web.taglib.Head
getScripts(String) - Method in class net.sf.basedb.clients.web.extensions.JspContext: Get all scripts that has been added to this context by the given extension
getScriptSourceInput() - Method in class net.sf.basedb.core.hibernate.SchemaGenerator.CollectSqlTarget
getScriptTargetOutput() - Method in class net.sf.basedb.core.hibernate.SchemaGenerator.CollectSqlTarget
getSection() - Method in class net.sf.basedb.core.BioPlate: Get the section within the "storage location" for this bioplate.
getSection() - Method in class net.sf.basedb.core.data.BioPlateData: Get the section in the storage location were the bioplate is stored.
getSection(int) - Method in class net.sf.basedb.util.bfs.MetadataModel: Get the section at a given index.
getSection(String) - Method in class net.sf.basedb.util.bfs.MetadataModel: Get the first section with a given name.
getSectionCount() - Method in class net.sf.basedb.util.bfs.MetadataModel: Get the number of sections.
getSectionCount() - Method in class net.sf.basedb.util.bfs.MetadataWriter: Get the number of sections that has been written to this file so far.
getSectionCount(String) - Method in class net.sf.basedb.util.basefile.BaseFileParser: The number of times we have seen a certain section in the file.
getSectionParser(String) - Method in class net.sf.basedb.util.basefile.BaseFileParser: Get the parser that is currently registered for a section.
getSelectdefault() - Method in class net.sf.basedb.clients.web.taglib.Select
getSelected() - Method in class net.sf.basedb.core.ItemContext: Get a Set object to specify the ID:s of all items that are currently selected.
getSelectedColumns(ItemContext, List<TableColumn>, boolean) - Static method in class net.sf.basedb.clients.web.DynamicUtil
getSelectrecent() - Method in class net.sf.basedb.clients.web.taglib.Select
getSelects() - Method in class net.sf.basedb.core.AbstractQuery: Get all non-permanent selects.
getSender() - Method in class net.sf.basedb.core.Message: Get the user that sent this message.
getSendMessage() - Method in class net.sf.basedb.core.data.JobData: If the core should send a message to the owner when the job is finished or not.
getSendMessage() - Method in class net.sf.basedb.core.Job: If a message should be sent to the owner once the job has finished or not.
getSendMessagesAsEmail() - Method in class net.sf.basedb.core.data.UserData: If this flag is set, all messages to this user are sent as an email also, but only if: the server admin has configured an outgoing smtp server and the user has supplied a valid email address.
getSendMessagesAsEmail() - Method in class net.sf.basedb.core.User: If this flag has been set, messges to the user is also sent as an email.
getSeparator() - Method in class net.sf.basedb.clients.web.taglib.path.Path
getSeparator() - Method in class net.sf.basedb.clients.web.taglib.table.CellValue
getSeriesCount() - Method in class net.sf.basedb.util.plot.HistogramPlot.HistogramDataset
getSeriesKey(int) - Method in class net.sf.basedb.util.plot.HistogramPlot.HistogramDataset
getServer() - Method in class net.sf.basedb.core.data.JobAgentData: Get the server name or ip that this jobagent is running on.
getServer() - Method in class net.sf.basedb.core.data.JobData: The name of the server where the job is executing.
getServer() - Method in class net.sf.basedb.core.Job: Get the name of the server where the job is executing.
getServer() - Method in class net.sf.basedb.core.JobAgent: Get the name or IP-adress of the server were the job agent is running.
getServerAliases(String, Principal[]) - Method in class net.sf.basedb.util.ssl.StaticKeyManager
getServerAndNode() - Method in class net.sf.basedb.core.Job: Utility method for getting both the server and node as a single string (for display purposes).
getServerCertificate() - Method in class net.sf.basedb.core.data.FileServerData: Get the public server certificate indicating that we should trust https connections to the server.
getServerCertificate() - Method in class net.sf.basedb.core.FileServer: Get the public server certificate that indicates that we should only trust the server if it can present a certificate that matches this.
getServerCertificate() - Method in class net.sf.basedb.util.uri.ConnectionParameters: Get the public server certificate that indicates that we should only trust the server if it can present a certificate that matches this.
getServerInfo() - Method in class net.sf.basedb.core.File
getServerName() - Method in class net.sf.basedb.clients.jobagent.Agent: Get the host name of the server where the job agent is running.
getServerName() - Method in class net.sf.basedb.clients.web.taglib.Page
getServerX509Certificate() - Method in class net.sf.basedb.core.FileServer: Get the X.509 certificate for the server.
getServletContext() - Method in class net.sf.basedb.clients.web.extensions.ServletWrapper
getServletName() - Method in class net.sf.basedb.clients.web.extensions.ServletWrapper
getServletPath() - Method in class net.sf.basedb.clients.web.extensions.RequestWrapper
getServlets() - Method in class net.sf.basedb.clients.web.extensions.ServletLoader: Get a list with all loaded servlet definitions.
getServletUrl(String, String) - Static method in class net.sf.basedb.clients.web.extensions.ExtensionsControl: Get the base URL for servlets in the extension with the given ID.
getSession() - Method in class net.sf.basedb.core.data.ChangeHistoryData
getSession() - Method in class net.sf.basedb.core.hibernate.SessionWrapper: Deprecated.
getSession() - Method in class net.sf.basedb.core.LogControl
getSession(DbControl) - Method in class net.sf.basedb.core.ChangeHistory: Load the session in which the change was made.
getSession(DbControl) - Method in class net.sf.basedb.core.ChangeHistory.TransactionInfo: Load the session in which the change was made.
getSession(DbControl, ChangeHistory, boolean, boolean) - Static method in class net.sf.basedb.clients.web.ChangeHistoryUtil: Get the session in which the changes was made in HTML format.
getSessionControl() - Method in class net.sf.basedb.clients.jobagent.Agent: Get a session control with the configured user logged in.
getSessionControl() - Method in class net.sf.basedb.clients.web.taglib.Page
getSessionControl() - Method in class net.sf.basedb.core.AbstractBatcher: Get the SessionControl object that manages this item.
getSessionControl() - Method in class net.sf.basedb.core.BasicItem: Get the SessionControl object that manages this item.
getSessionControl() - Method in class net.sf.basedb.core.DbControl: Get the SessionControl object that owns this DbControl object.
getSessionControl() - Method in class net.sf.basedb.core.PluginRequest
getSessionControl() - Method in class net.sf.basedb.util.extensions.ClientContext: Get the current session control.
getSessionControl(String, String, String, boolean) - Static method in class net.sf.basedb.core.Application: Get an existing SessionControl object if you know the id.
getSessionControl(PageContext, boolean) - Static method in class net.sf.basedb.clients.web.Base: Get a new or existing SessionControl object given a PageContext.
getSessionControl(ServletRequest, boolean) - Static method in class net.sf.basedb.clients.web.Base: Get a session control for the BASE web client "net.sf.basedb.clients.web".
getSessionControl(ServletRequest, String, boolean) - Static method in class net.sf.basedb.clients.web.Base: Get a new or existing SessionControl object given a ServletRequest instance.
getSessionFactory() - Method in class net.sf.basedb.core.hibernate.SessionWrapper
getSessionFactory() - Static method in class net.sf.basedb.core.HibernateUtil: Get the configured session factory.
getSessionId() - Method in class net.sf.basedb.core.ChangeHistory: Get the ID of the session in which the change was made.
getSessionId() - Method in class net.sf.basedb.core.ChangeHistory.TransactionInfo: Get the ID of the session the transaction.
getSessionId() - Method in class net.sf.basedb.core.data.ChangeHistoryData: The ID of the session in which the changes happened.
getSessionId() - Method in class net.sf.basedb.core.log.TransactionDetails: Get the ID of the session or 0 if no user is logged in.
getSessions() - Method in class net.sf.basedb.core.data.ClientData: This is the invers end.
getSessions() - Method in class net.sf.basedb.core.data.UserData: This is the inverse end.
getSessions() - Method in class net.sf.basedb.core.data.UserDeviceData: This is the inverse end but we do not map with inverse="true" cascade="delete" since we want Hibernate to set SessionData.device_id = null instead of deleting sessions.
getSessions() - Method in class net.sf.basedb.core.UserDevice: Get a query for loading login session from this device.
getSessionSetting(String) - Method in class net.sf.basedb.core.SessionControl: Get the value of a session setting with the specified name.
getSet(Map<String, Set<String>>, String) - Method in class net.sf.basedb.clients.web.extensions.JspContext: Get the Set that is stored under the given key.
getSetParameterMethod(Class<?>) - Method in class net.sf.basedb.util.extensions.xml.XmlLoader: Check if the bean class has a setParameter(String, String) method and return it's reference if it has.
getSetter() - Method in class net.sf.basedb.core.ExtendedPropertyAccessor.GetterSetter
getSetterMethod(Class<?>, String) - Method in class net.sf.basedb.util.extensions.xml.XmlLoader: Get the setter method for a given tag name.
getSetterMethodNameFromTag(String) - Method in class net.sf.basedb.util.extensions.xml.XmlLoader: Convert the tag name to a setter method name.
getSetting(String) - Method in class net.sf.basedb.core.ItemContext: Get a value.
getSetting(String) - Method in class net.sf.basedb.core.Presets.Preset: Get the value for the setting with the specified name.
getSetting(String, String) - Method in class net.sf.basedb.clients.web.extensions.ExtensionsControl: Get a configuration setting for an extension.
getSetting(String, String) - Method in class net.sf.basedb.core.ItemContext: Get a value from the settings or the default value if no current value exists.
getSetting(String, String) - Method in class net.sf.basedb.util.extensions.manager.Settings: Get a configuration setting for an extension.
getSettings() - Method in class net.sf.basedb.core.data.ContextData: Get a map for other settings.
getSettings() - Method in class net.sf.basedb.core.JobAgent: Get a query that returns all plugin-specific settings for this job agent.
getSettings() - Method in class net.sf.basedb.util.extensions.manager.ExtensionsManager: Get the settings for the extension manager.
getSettings(Job) - Method in class net.sf.basedb.core.JobAgent: Get the settings for the plugin that is used for the specified job.
getSettings(PluginDefinition, boolean) - Method in class net.sf.basedb.core.JobAgent: Get the settings for the specified plugin.
getSettingsForExtension(String) - Method in class net.sf.basedb.util.extensions.manager.Settings: Get a preset containing settings for the given extesion.
getSeverity(ValidationRuleAction) - Method in class net.sf.basedb.util.overview.ValidationOptions: Get the severity level for the specified validator rule.
getShareableItems() - Static method in class net.sf.basedb.core.Metadata: Get a set containing all Shareable item types.
getSharedParent() - Method in class net.sf.basedb.core.ArrayDesignBlock
getSharedParent() - Method in class net.sf.basedb.core.ArrayDesignPlate
getSharedParent() - Method in class net.sf.basedb.core.BioAssay: Get the experiment.
getSharedParent() - Method in class net.sf.basedb.core.BioAssaySet: Get the experiment.
getSharedParent() - Method in class net.sf.basedb.core.BioMaterialEvent
getSharedParent() - Method in class net.sf.basedb.core.BioPlateEventParticipant
getSharedParent() - Method in class net.sf.basedb.core.BioWell
getSharedParent() - Method in class net.sf.basedb.core.ChildItem: Get the shareable parent item of this child item.
getSharedParent() - Method in class net.sf.basedb.core.DataCube: Get the experiment.
getSharedParent() - Method in class net.sf.basedb.core.DataCubeColumn: Get the experiment.
getSharedParent() - Method in class net.sf.basedb.core.DataCubeExtraValue: Get the experiment.
getSharedParent() - Method in class net.sf.basedb.core.DataCubeFilter: Get the experiment.
getSharedParent() - Method in class net.sf.basedb.core.DataCubeLayer: Get the experiment.
getSharedParent() - Method in class net.sf.basedb.core.ExtraValue: Get the experiment.
getSharedParent() - Method in class net.sf.basedb.core.Help
getSharedParent() - Method in class net.sf.basedb.core.JobAgentSettings
getSharedParent() - Method in class net.sf.basedb.core.PlateEvent
getSharedParent() - Method in class net.sf.basedb.core.PlateEventType
getSharedParent() - Method in class net.sf.basedb.core.RootRawBioAssay: Get the experiment.
getSharedParent() - Method in class net.sf.basedb.core.SyncFilter
getSharedParent() - Method in class net.sf.basedb.core.Transformation: Get the experiment.
getSharedParent() - Method in class net.sf.basedb.core.VirtualDb: Get the experiment.
getSharedParent() - Method in class net.sf.basedb.core.Well
getSharedPermissions(ShareableData) - Method in class net.sf.basedb.core.InternalJobQueue.JobQueueKeyring: Return 0.
getSharedPermissions(ShareableData) - Method in class net.sf.basedb.core.Job.SignalKeyring: Return 0.
getSharedPermissions(ShareableData) - Method in class net.sf.basedb.core.Keyring
getSharedPermissions(ShareableData) - Method in class net.sf.basedb.core.ServiceSessionControl.ServicesKeyring: Return 0.
getSharedPermissions(ShareableData) - Method in class net.sf.basedb.core.SessionControl: Get the shared permissions for a ShareableData object.
getSharedTo(DbControl, SharedItem) - Static method in class net.sf.basedb.util.ShareableUtil: Gets a list with the projects, groups and users(in that order) that an item is shared to.
getShareToEveryOneKey(DbControl, Permission) - Static method in class net.sf.basedb.core.ItemKey: Get a key that can be used to share items to the EVERYONE group with the given permissions.
getSheet() - Method in class net.sf.basedb.util.excel.XlsxTableWriter: Get the current sheet in the workbook.
getSheetAsCsv(int) - Method in class net.sf.basedb.util.excel.XlsxToCsvUtil: Convert the given sheet to an CSV InputStream.
getSheetAsCsv(String) - Method in class net.sf.basedb.util.excel.XlsxToCsvUtil: Convert the given named sheet to a CSV InputStream.
getSheetNames() - Method in class net.sf.basedb.util.excel.XlsxToCsvUtil: Get the names of the sheets in the workbook.
getShort(int) - Method in class net.sf.basedb.clients.web.servlet.PlotServlet.CFSqlResult
getShort(int) - Method in class net.sf.basedb.core.DynamicResultIterator.SqlResultImpl
getShort(int) - Method in interface net.sf.basedb.core.query.SqlResult: Get the value of the specified column as a short.
getShortEntityName(String) - Static method in class net.sf.basedb.core.HibernateUtil: Removes the package name part of a class name and any ending 'Data'.
getShortName() - Method in class net.sf.basedb.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 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 net.sf.basedb.core.Type: Get the type of this parameter as specified by the java.sql.Types class.
getSqlTypeCode() - Method in class net.sf.basedb.core.BatchedPropertyInfo: Get the sql type code as defined by Types.
getSqrt() - Method in class net.sf.basedb.core.query.QuadraticMeanExpression
getSshFingerprint() - Method in class net.sf.basedb.core.data.FileServerData: Get the fingerprint of the SSH public key for the server that must be verified when (if) it is accessed via the SSH protocol.
getSshFingerprint() - Method in class net.sf.basedb.core.FileServer
getSshFingerprint() - Method in class net.sf.basedb.util.uri.ConnectionParameters: Get the SSH fingerprint of the server.
getSshPrivateKey() - Method in class net.sf.basedb.core.data.FileServerData: Get the SSH private key that we need to send to the server to make the server accept our connection.
getSshPrivateKey() - Method in class net.sf.basedb.core.FileServer: Get the private key that BASE should use to authenticate with the server when connecting with SSH.
getSshPrivateKey() - Method in class net.sf.basedb.util.uri.ConnectionParameters: Get the private key that should be used to authenticate with the server when connecting using SSH.
getSshPrivateKeyFormat() - Method in class net.sf.basedb.core.data.FileServerData: Get the private key format.
getSshPrivateKeyFormat() - Method in class net.sf.basedb.core.FileServer: Get the format of the SSH private key.
getSshPrivateKeyFormat() - Method in class net.sf.basedb.util.uri.ConnectionParameters: Get the format of the SSH private key (if known).
getSshPrivateKeyPassword() - Method in class net.sf.basedb.core.data.FileServerData: Get the password that is used to unlock the SSH private key.
getSshPrivateKeyPassword() - Method in class net.sf.basedb.core.FileServer: Get the password that is needed to unlock the SSH private key.
getSshPrivateKeyPassword() - Method in class net.sf.basedb.util.uri.ConnectionParameters: Get the password that is needed to unlock the SSH private key.
getSSLContext(byte[], byte[], String) - Static method in class net.sf.basedb.util.ssl.SSLUtil2: Create a SSL context that optionally uses the given trusted server certificate and client certificate.
getSSLSocketFactory() - Static method in class net.sf.basedb.util.ssl.SSLUtil2: Get a SSL Socket Factory object that is used to create SSL sockets.
getSSLSocketFactory(byte[], byte[], String) - Static method in class net.sf.basedb.util.ssl.SSLUtil2: Create a SSL socket factory that optionally uses the given trusted server certificate and client certificate.
getSSLSocketFactory2() - Method in class net.sf.basedb.core.FileServer: Get a socket factory that can be used to create SSL connections to the given server.
getStacktrace() - Method in class net.sf.basedb.util.extensions.logging.LogEntry: Get the stacktrace of the log entry.
getStackTrace() - Method in class net.sf.basedb.core.data.JobData: Get the stack trace in case of an error
getStackTrace() - Method in class net.sf.basedb.core.Job: Get the stack trace in case the job ended with an error
getStartDate() - Method in class net.sf.basedb.core.data.NewsData: Get the first day this news item should be shown.
getStartDate() - Method in class net.sf.basedb.core.News: Get the start date and time for this news item to be published.
getStarted() - Method in class net.sf.basedb.core.data.JobData: Get the date and time the job was started or null if the job hasn't been started.
getStarted() - Method in class net.sf.basedb.core.Job: Get the date and time the job was started.
getStartTime() - Method in class net.sf.basedb.util.extensions.manager.ProcessResults: Get the start time of the scan as a millisecond value.
getStartX() - Method in class net.sf.basedb.util.plot.HistogramPlot.HistogramBin
getStartX(int, int) - Method in class net.sf.basedb.util.plot.HistogramPlot.HistogramDataset
getStartXValue(int, int) - Method in class net.sf.basedb.util.plot.HistogramPlot.HistogramDataset
getStartY(int, int) - Method in class net.sf.basedb.util.plot.HistogramPlot.HistogramDataset
getStartYValue(int, int) - Method in class net.sf.basedb.util.plot.HistogramPlot.HistogramDataset
getState() - Method in class net.sf.basedb.core.log.EntityDetails: Get an array with the current state of the entity.
getState() - Method in class net.sf.basedb.core.plugin.NamespaceRequestWrapper
getState() - Method in interface net.sf.basedb.core.plugin.Request: Get state information that was previously saved by Response.setPause(String, String, java.io.Serializable) or Response.setContinue(String, java.io.Serializable).
getState() - Method in class net.sf.basedb.core.PluginRequest.RequestImpl
getState() - Method in class net.sf.basedb.core.PluginResponse: Get the state information that the plug-in wants to save until it is restarted again.
getState() - Method in class net.sf.basedb.plugins.executor.ExternalProgramExecutor.RequestWrapper
getStatelessSession() - Method in class net.sf.basedb.core.DbControl: Get a stateless Hibernate session using the same database connection as the regular session.
getStaticCache() - Static method in class net.sf.basedb.core.Application: Get the static cache mananger.
getStaticRules() - Static method in class net.sf.basedb.util.overview.OverviewUtil: Get all static (built-in) validation rules grouped by relationship.
getStatistics() - Method in class net.sf.basedb.core.hibernate.SessionWrapper
getStatistics(String) - Method in class net.sf.basedb.clients.web.ExperimentExplorer.AnnotationGroup: Get the sum of all values added with the ExperimentExplorer.AnnotationGroup.addStatistics(String, float) method with the given key.
getStatistics(DbControl) - Static method in class net.sf.basedb.core.DiskUsage
getStatus() - Method in class net.sf.basedb.clients.jobagent.AgentController: Get status info about running job agent by sending an info request to the agents r emote control service.
getStatus() - Method in class net.sf.basedb.core.data.JobData: Get the status of the job. 1 = waiting, 2 = running, 3 = completed ok, 4 = error
getStatus() - Method in class net.sf.basedb.core.Job: Get the status of the job.
getStatus() - Method in class net.sf.basedb.core.PluginResponse: Get the status of the response.
getStatus() - Method in class net.sf.basedb.util.extensions.manager.ProcessResults.FileResults: A short status message indicating the completed results on this file.
getStatusMessage() - Method in class net.sf.basedb.core.data.JobData: Get a status message.
getStatusMessage() - Method in class net.sf.basedb.core.Job: Get a message about the current status of the job.
getStdev() - Method in class net.sf.basedb.util.plot.HistogramPlot.HistogramBin: Get the standard deviation of all values in this bin.
getStickyCol() - Method in class net.sf.basedb.clients.web.taglib.table.Table
getStorageType() - Method in class net.sf.basedb.core.BioPlateType: Get the subtype of storage location where plates of this type are usually stored.
getStorageType() - Method in class net.sf.basedb.core.data.BioPlateTypeData: Get the subtype of storage location where plates of this type are usually stored.
getStream(String) - Method in class net.sf.basedb.util.extensions.manager.ExtensionsFile: Get an input stream for reading the resource specified by the given path
getString(boolean) - Method in enum 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 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.
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.
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 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.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 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 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 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 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 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 net.sf.basedb.core.ExtraValue.CoordinateType: Get the integer value that is used when storing a CoordinateType in the database.
getValue() - Method in enum 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 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 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 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 net.sf.basedb.core.Include
getValue() - Method in enum net.sf.basedb.core.IntensityTransform: Get the integer value that is used when storing a transform in the database.
getValue() - Method in enum net.sf.basedb.core.Item: Get the integer value that is used when storing an item to the database.
getValue() - Method in enum net.sf.basedb.core.ItemContext.SortDirection: Get the integer value that is used when storing an location to the database.
getValue() - Method in enum 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 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 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 net.sf.basedb.core.Location: Get the integer value that is used when storing an location to the database.
getValue() - Method in enum net.sf.basedb.core.log.ChangeType: Get the numerical value for this change type.
getValue() - Method in enum net.sf.basedb.core.Operator: Get the integer value that is used when storing an operator in the database.
getValue() - Method in enum 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 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 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 net.sf.basedb.core.Type: Get the class of objects that can be used as values for this type.
getValueCount() - Method in class net.sf.basedb.util.bfs.MetadataModel.SectionEntry: Get the number of values in the entry.
getValueCount() - Method in class net.sf.basedb.util.bfs.MetadataWriter: Get the number of values that has been written to the current section so far.
getValueId() - Method in class net.sf.basedb.core.data.annotations.AnnotationLink
getValueList2(Element, Class<T>) - Method in class net.sf.basedb.core.PluginConfiguration: Gets the list of values for a parameter from the XML-file.
getValues() - Method in class net.sf.basedb.core.Annotation: Get the values this annotation contains.
getValues() - Method in class net.sf.basedb.core.AnnotationType: Get the list of allowed values if this annotation type is an enumeration.
getValues() - Method in class net.sf.basedb.core.data.AnnotationData: The values of this annotation.
getValues() - Method in class net.sf.basedb.core.data.BooleanParameterValueData
getValues() - Method in class net.sf.basedb.core.data.DateParameterValueData
getValues() - Method in class net.sf.basedb.core.data.DoubleParameterValueData
getValues() - Method in class net.sf.basedb.core.data.FloatParameterValueData
getValues() - Method in class net.sf.basedb.core.data.IntegerParameterValueData
getValues() - Method in class net.sf.basedb.core.data.ItemParameterValueData
getValues() - Method in class net.sf.basedb.core.data.LongParameterValueData
getValues() - Method in class net.sf.basedb.core.data.ParameterValueData: Get values of this parameter.
getValues() - Method in class net.sf.basedb.core.data.StringParameterValueData
getValues() - Method in class net.sf.basedb.core.data.TextParameterValueData
getValues() - Method in class net.sf.basedb.core.data.TimestampParameterValueData
getValues() - Method in class net.sf.basedb.core.ExtraValue: Get a query returning the extra values.
getValues() - Method in class net.sf.basedb.core.ParameterInfo
getValues() - Method in class net.sf.basedb.core.snapshot.AnnotationLoaderUtil: Get the values from the last annotation found when calling AnnotationLoaderUtil.find(AnnotationSetSnapshot)
getValues() - Method in class net.sf.basedb.plugins.executor.ProgramParameter: Get the values for this parameter.
getValues() - Method in class net.sf.basedb.util.bfs.MetadataModel.SectionEntry: Get all values.
getValues() - Method in class net.sf.basedb.util.plot.PlotAnnotation: The values that falls into this annotation.
getValues(int) - Method in class net.sf.basedb.util.bfs.MetadataModel.Section: Get the values of the entry at the given index.
getValues(String) - Method in class net.sf.basedb.core.ParameterValuesImpl
getValues(String) - Method in class net.sf.basedb.core.plugin.NamespaceParameterValuesWrapper
getValues(String) - Method in interface net.sf.basedb.core.plugin.ParameterValues: Get a List of values for a specific parameter.
getValues(String) - Method in class net.sf.basedb.core.plugin.ParameterValuesWrapper: Get the values of the parameter with the specified name.
getValues(String) - Method in class net.sf.basedb.plugins.gtf.DefaultConfigurationValues
getValues(String) - Method in class net.sf.basedb.util.bfs.MetadataModel.Section: Get the values of the first entry with a given key.
getValues(String) - Method in class net.sf.basedb.util.QueryParameters: Get all values for a key.
getValues(String, String) - Method in class net.sf.basedb.util.bfs.MetadataModel: Utility method for getting the values of the first entry in the first section that matches the given section and key name.
getValues(Map<String, List<String>>, String) - Method in class net.sf.basedb.util.jobagent.JobAgentInfo
getValues(Unit) - Method in class net.sf.basedb.core.Annotation: Get the values for this annotation in a specific unit.
getValuesAsObjects() - Method in class net.sf.basedb.core.PropertyFilter: Splits the value string at each "|" and creates a list with objects from the substrings that were found.
getValuesAsObjects(String, Unit, boolean) - Method in class net.sf.basedb.core.PropertyFilter
getValuesAsObjects(Unit, boolean) - Method in class net.sf.basedb.core.PropertyFilter: Same as PropertyFilter.getValueAsObject(Unit, boolean) but the filter string is first split at each "|".
getValueSeparator() - Method in class net.sf.basedb.core.PropertyFilter
getValuesOrMask() - Method in class net.sf.basedb.core.ParameterInfo: Utility method for getting the values or a mask (*****) if the ParameterInfo.isMasked() flag is set.
getValuesOrMask(String) - Method in class net.sf.basedb.core.ParameterInfo: Utility method for getting the values or a mask if the ParameterInfo.isMasked() flag is set.
getValuesVersion() - Method in class net.sf.basedb.core.Annotation: Get the version number of the item keeping the values.
getValueType() - Method in class net.sf.basedb.clients.web.extensions.list.AbstractListColumnBean
getValueType() - Method in interface net.sf.basedb.clients.web.extensions.list.ListColumnAction: The data type of the values that are referenced by the property.
getValueType() - Method in class net.sf.basedb.clients.web.taglib.table.ColumnDef
getValueType() - Method in class net.sf.basedb.core.Annotation: Get the value type for this annotation type.
getValueType() - Method in class net.sf.basedb.core.AnnotationBatcher.CurrentAnnotationInfo: Shortcut to AnnotationType.getValueType().
getValueType() - Method in class net.sf.basedb.core.AnnotationType: Get the value type for this annotation type.
getValueType() - Method in class net.sf.basedb.core.data.AnnotationTypeData: The code for the value type.
getValueType() - Method in class net.sf.basedb.core.data.BooleanParameterValueData
getValueType() - Method in class net.sf.basedb.core.data.DataCubeExtraValueData: The type of value, ie. int, float or string.
getValueType() - Method in class net.sf.basedb.core.data.DateParameterValueData
getValueType() - Method in class net.sf.basedb.core.data.DoubleParameterValueData
getValueType() - Method in class net.sf.basedb.core.data.ExtraValueTypeData: The code for the value type.
getValueType() - Method in class net.sf.basedb.core.data.FloatParameterValueData
getValueType() - Method in class net.sf.basedb.core.data.FormulaData: The code for the value type. null = not known or doesn't care.
getValueType() - Method in class net.sf.basedb.core.data.IntegerParameterValueData
getValueType() - Method in class net.sf.basedb.core.data.ItemParameterValueData
getValueType() - Method in class net.sf.basedb.core.data.LongParameterValueData
getValueType() - Method in class net.sf.basedb.core.data.ParameterValueData: Get the type of parameter values that are store in this parameter.
getValueType() - Method in class net.sf.basedb.core.data.PropertyFilterData: Get the type of value user for this filter.
getValueType() - Method in class net.sf.basedb.core.data.ReporterClonePropertyData: The code for the value type.
getValueType() - Method in class net.sf.basedb.core.data.StringParameterValueData
getValueType() - Method in class net.sf.basedb.core.data.TextParameterValueData
getValueType() - Method in class net.sf.basedb.core.data.TimestampParameterValueData
getValueType() - Method in class net.sf.basedb.core.DataCubeExtraValue: Get the value type of the extra values.
getValueType() - Method in class net.sf.basedb.core.ExtraValue: Get the type of values.
getValueType() - Method in class net.sf.basedb.core.ExtraValueType: Get the value type for this extra value type.
getValueType() - Method in class net.sf.basedb.core.Formula: Get the type of values that this formula produces.
getValueType() - Method in enum 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 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 - 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 net.sf.basedb.core.Permission: Combine the given permission and convert to the integer grant value.
grant(Permission) - Static method in enum net.sf.basedb.core.Permission: Convert the given permission to the integer grant value.
grant(Permission...) - Static method in enum 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 net.sf.basedb.core.Permission
grantValue() - Method in enum 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 - 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 - 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 - 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 - 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 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 - net.sf.basedb.core.Item: The item is a Hardware.
hardwareColumnMapping - Static variable in class net.sf.basedb.plugins.batchimport.ArrayBatchImporter
hardwareColumnMapping - Static variable in class net.sf.basedb.plugins.batchimport.BioPlateImporter
hardwareColumnMapping - Static variable in class net.sf.basedb.plugins.batchimport.DerivedBioAssayImporter
hardwareColumnMapping - Static variable in class net.sf.basedb.plugins.batchimport.PhysicalBioAssayImporter
HardwareData - Class in net.sf.basedb.core.data: This class holds information about a Hardware.
HardwareData() - Constructor for class net.sf.basedb.core.data.HardwareData
hardwareHasBeenSet - Variable in class net.sf.basedb.core.BioMaterialEvent
hardwareHasBeenSet - Variable in class net.sf.basedb.core.DerivedBioAssay
HardwareLoader - Class in net.sf.basedb.util.overview.loader: Node loader implementation for hardware.
HardwareLoader() - Constructor for class net.sf.basedb.util.overview.loader.HardwareLoader
hardwareMapper - Variable in class net.sf.basedb.plugins.batchimport.ArrayBatchImporter
hardwareMapper - Variable in class net.sf.basedb.plugins.batchimport.BioPlateImporter
hardwareMapper - Variable in class net.sf.basedb.plugins.batchimport.DerivedBioAssayImporter
hardwareMapper - Variable in class net.sf.basedb.plugins.batchimport.PhysicalBioAssayImporter
hardwareQuery - Variable in class net.sf.basedb.plugins.batchimport.AbstractItemImporter
HardwareValidator - Class in net.sf.basedb.util.overview.validator: Validator implementation for hardware.
HardwareValidator() - Constructor for class net.sf.basedb.util.overview.validator.HardwareValidator
HAS_CANCELBUTTON - Static variable in class net.sf.basedb.clients.web.ModeInfo
HAS_CHECK - Static variable in class net.sf.basedb.clients.web.ModeInfo
HAS_CLOSEBUTTON - Static variable in class net.sf.basedb.clients.web.ModeInfo
HAS_EDITLINK - Static variable in class net.sf.basedb.clients.web.ModeInfo
HAS_FILTER - Static variable in class net.sf.basedb.clients.web.ModeInfo
HAS_ICONS - Static variable in class net.sf.basedb.clients.web.ModeInfo
HAS_NAVIGATOR - Static variable in class net.sf.basedb.clients.web.ModeInfo
HAS_OKBUTTON - Static variable in class net.sf.basedb.clients.web.ModeInfo
HAS_PROPERTYLINK - Static variable in class net.sf.basedb.clients.web.ModeInfo
HAS_RADIO - Static variable in class net.sf.basedb.clients.web.ModeInfo
HAS_TOOLBAR - Static variable in class net.sf.basedb.clients.web.ModeInfo
hasAborted - Variable in class net.sf.basedb.core.signal.ThreadSignalHandler: If TRUE, at least one ABORT signal has been recieved.
hasAborted() - Method in class net.sf.basedb.clients.web.fileupload.FileUploadProgress: Check if the upload has been requested to be aborted.
hasActiveValidator(DbControl) - Method in class net.sf.basedb.core.DataFileType: Check if there is at least one extension that claims to support validation of files of this type.
hasAllRequiredFiles() - Method in class net.sf.basedb.core.FileSet: Checks if this file set contains a file for each DataFileType that is required according to what has been specified by the Platform and PlatformVariant.
hasAnnotatableItem - Variable in class net.sf.basedb.core.MultiPermissions
hasAnnotatableItem() - Method in class net.sf.basedb.core.MultiPermissions: Is any of the items to share an annotatable item?
hasAnnotation(AnnotationType, Annotation.Source) - Method in class net.sf.basedb.core.AnnotationSet: Check if the annotation set contains an annotation of the specified type.
HasAnnotationRestriction - Class in net.sf.basedb.core: Restricts a query by the presence of absence of an annotation.
HasAnnotationRestriction(String, int, boolean, boolean, boolean) - Constructor for class net.sf.basedb.core.HasAnnotationRestriction: Deprecated.
In 3.11, use HasAnnotationRestriction(String, AnnotationType, boolean, AnnotationRestriction.Options) instead
HasAnnotationRestriction(String, AnnotationType, boolean, boolean, boolean) - Constructor for class net.sf.basedb.core.HasAnnotationRestriction: Deprecated.
In 3.11, use HasAnnotationRestriction(String, AnnotationType, boolean, AnnotationRestriction.Options) instead
HasAnnotationRestriction(String, AnnotationType, boolean, AnnotationRestriction.Options) - Constructor for class net.sf.basedb.core.HasAnnotationRestriction: Create a new restriction that checks if an item has been annotatated or not.
hasArrayDesign() - Method in class net.sf.basedb.core.RawBioAssay: Check if this raw bioassay is connected to an array design or not.
hasAttribute(NodeAttribute<?>) - Method in class net.sf.basedb.util.overview.Node: Check if the node has a value for the given attribute.
HasAttributeFilter - Class in net.sf.basedb.util.overview.filter: A filter implementation that checks if a value for a given attribute exists on a node.
HasAttributeFilter(NodeAttribute<?>) - Constructor for class net.sf.basedb.util.overview.filter.HasAttributeFilter: Create a filter that finds nodes that has value for the given attribute.
HasAttributeFilter(NodeAttribute<?>, Object) - Constructor for class net.sf.basedb.util.overview.filter.HasAttributeFilter: Create a filter that finds nodes that has a specific value for the given attribute.
hasAutoJoined - Variable in class net.sf.basedb.core.AbstractQuery
hasBeenAccepted - Variable in class net.sf.basedb.util.fileset.ValidatingFileSetMember
hasBeenAccepted() - Method in class net.sf.basedb.util.fileset.ValidatingFileSetMember: Has this member been accepted for validation by at least one validator?
hasBeenAnnotatated - Variable in class net.sf.basedb.core.HasAnnotationRestriction
hasBeenCalledFromAnnotationBatcher - Variable in class net.sf.basedb.core.BasicItem
hasBeenCalledFromGetAnnotationSet - Variable in class net.sf.basedb.core.BasicItem
hasBeenUsed - Variable in class net.sf.basedb.core.AnnotationBatcher.CurrentAnnotationInfo
hasBeenUsed() - Method in class net.sf.basedb.core.BioWell: If the original biomaterial in this well has been moved to another plate (eg. for final storage in a freezer).
hasBom - Variable in class net.sf.basedb.util.basefile.BaseFileWriter
hasCancelButton - Variable in class net.sf.basedb.clients.web.ModeInfo
hasCancelButton() - Method in class net.sf.basedb.clients.web.ModeInfo
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 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.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.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
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 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
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 - 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 - 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 - 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 - 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 - net.sf.basedb.util.plot.HistogramPlot.YAggregate: Plot a high/low bar for each bin with the maximum and minimum values.
HILOSTDEV - 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 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 - 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 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 - 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 - 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.
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 - 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 - net.sf.basedb.core.Operator
IN_PROJECT - 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 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 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 - net.sf.basedb.util.extensions.logging.LogLevel
INFO - 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 - 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 - 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 - 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 - 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 - 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 - net.sf.basedb.core.plugin.Plugin.MainType
INTENSITY_EXPRESSION - net.sf.basedb.core.Formula.Type: The formula represents an intensity measurement expression.
INTENSITY_TRANSFORMATION - 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 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 net.sf.basedb.core.IntensityTransform: Creates a new intensity transform.
interactive - Variable in class net.sf.basedb.core.data.PluginDefinitionData
InteractivePlugin - Interface in net.sf.basedb.core.plugin: An interactive plugin is a Plugin that supports interactive configuration in a user session.
interfaceName - Variable in class net.sf.basedb.core.data.PluginTypeData
INTERNAL - Static variable in class net.sf.basedb.core.authentication.AuthenticationMethod: This is special-case internal login used by job queue, etc.
INTERNAL_ID - Static variable in class net.sf.basedb.plugins.batchimport.InternalIdMethod: Use the internal ID for finding items.
internalFile - Variable in class net.sf.basedb.core.File: The path to the internal file.
internalId - Variable in class net.sf.basedb.core.authentication.AuthenticatedUser
internalId - Variable in class net.sf.basedb.util.extensions.xml.PluginInfo
internalIdColumnMapping - Static variable in class net.sf.basedb.plugins.AnnotationFlatFileImporter
internalIdColumnMapping - Static variable in class net.sf.basedb.plugins.batchimport.AbstractItemImporter
InternalIdMethod - Class in net.sf.basedb.plugins.batchimport: Identification method implementation that finds an item by using the getById() method.
InternalIdMethod(String, String) - Constructor for class net.sf.basedb.plugins.batchimport.InternalIdMethod: Create a new id method.
internalJobQueue - Static variable in class net.sf.basedb.core.Application: The internal job queue reference if it is enabled.
InternalJobQueue - Class in net.sf.basedb.core: A simple implementation of a job queue that executes jobs in order of priority and longest waiting time.
InternalJobQueue() - Constructor for class net.sf.basedb.core.InternalJobQueue: Create the job queue.
InternalJobQueue.JobQueueKeyring - Class in net.sf.basedb.core: Our own keyring containing the permissions we need to execute the jobs.
InternalJobQueue.JobRunner - Class in net.sf.basedb.core: Encapsulates the running of a job in a separate thread.
internalName - Variable in class net.sf.basedb.core.data.FileData
internalPrintBofMarker() - Method in class net.sf.basedb.util.bfs.MetadataWriter: Prints the beginning-of-file marker.
internalPrintComment(String) - Method in class net.sf.basedb.util.bfs.MetadataWriter: Print a single-line comment.
internalPrintSection(String) - Method in class net.sf.basedb.util.bfs.MetadataWriter: Prints a section header assuming that the name has already been encoded.
internalPrintValue(String, String) - Method in class net.sf.basedb.util.bfs.MetadataWriter: Prints a section entry assuming that the key and value has already been encoded.
InternalSlotManager - Class in net.sf.basedb.clients.jobagent.slotmanager: The internal slot manager assigns slot to jobs based on their estimated execution time.
InternalSlotManager() - Constructor for class net.sf.basedb.clients.jobagent.slotmanager.InternalSlotManager
interruptHandler - Static variable in class net.sf.basedb.core.signal.ThreadSignalHandler: Keep per-thread interupt handlers.
InterruptHandler - Interface in net.sf.basedb.core.signal: An interface for handling thread interrupts.
intersect(IdListRestriction) - Method in class net.sf.basedb.core.query.IdListRestriction: Merge this id list with another list.
intersection(Collection<ItemList>, ItemList.DelayedAdditionManager) - Static method in class net.sf.basedb.core.ItemList: Create a set with the intersection of the items in the given lists.
intersection(Collection<ReporterList>) - Static method in class net.sf.basedb.core.ReporterList: Create a set with the intersection of the reporter ID:s in the given lists.
interval - Variable in class net.sf.basedb.clients.web.extensions.service.DummyService
interval - Variable in class net.sf.basedb.util.ProgressInputStream
IntValue(Number) - Constructor for class net.sf.basedb.util.excel.ExcelValue.IntValue
INV_LN10x2 - Static variable in class net.sf.basedb.util.ma.MACalculator
INV_LN2 - Static variable in class net.sf.basedb.plugins.LowessNormalization.SpotData
INV_LN2 - Static variable in class net.sf.basedb.util.ma.MACalculator
INV_LOG10_2 - Static variable in class net.sf.basedb.util.ma.Log10MACalculator
INV_LOG2_10x2 - Static variable in class net.sf.basedb.util.ma.Log2MACalculator
invalid - Static variable in class net.sf.basedb.core.Path: A regexp checking for invalid characters.
INVALID_CHARACTERS - Static variable in class net.sf.basedb.core.Path: These characters are not valid within a file or directory name: "~\\/:;*?<>|\""
INVALID_USE_OF_NULL_ERROR - Static variable in class net.sf.basedb.plugins.util.Parameters: The name of the parameter created by Parameters.invalidUseOfNullError(String, String, String, String...).
InvalidAndModifiedFilter - Class in net.sf.basedb.util.extensions.manager.filter: Filter implementation for extension files that allow modified but invalid files to pass.
InvalidAndModifiedFilter() - Constructor for class net.sf.basedb.util.extensions.manager.filter.InvalidAndModifiedFilter: Create a new filter.
InvalidAnnotationException - Exception in net.sf.basedb.core
InvalidAnnotationException() - Constructor for exception net.sf.basedb.core.InvalidAnnotationException: Create a new InvalidAnnotationException object.
InvalidAnnotationException(String) - Constructor for exception net.sf.basedb.core.InvalidAnnotationException: Create a new InvalidAnnotationException object with the specified message.
InvalidAnnotationException(AnnotationType, Item) - Constructor for exception net.sf.basedb.core.InvalidAnnotationException: Create a new InvalidAnnotationException object when the annotation type cannot be used for the specified item type.
invalidColumnsErrorParameter - Static variable in class net.sf.basedb.plugins.IlluminaRawDataImporter
InvalidDataException - Exception in net.sf.basedb.core: Exceptions of this type are thrown when invalid data is encountered.
InvalidDataException() - Constructor for exception net.sf.basedb.core.InvalidDataException: Create a new InvalidDataException object.
InvalidDataException(String) - Constructor for exception net.sf.basedb.core.InvalidDataException: Create a new InvalidDataException object with the specified message.
InvalidDataException(String, Throwable) - Constructor for exception net.sf.basedb.core.InvalidDataException: Create a new InvalidDataException object with the specified message.
InvalidDataException(Throwable) - Constructor for exception net.sf.basedb.core.InvalidDataException: Create a new InvalidDataException object.
invalidEnumErrorParameter - Static variable in class net.sf.basedb.plugins.AnnotationFlatFileImporter
InvalidPasswordException - Exception in net.sf.basedb.core.authentication: This exception can be thrown when the password is invalid.
InvalidPasswordException - Exception in net.sf.basedb.core: Exceptions of this type are thrown when user tries to log in, but the password is incorrect.
InvalidPasswordException(String) - Constructor for exception net.sf.basedb.core.authentication.InvalidPasswordException: Create a new InvalidPasswordException object
InvalidPasswordException(String) - Constructor for exception net.sf.basedb.core.InvalidPasswordException: Create a new InvalidPasswordException object with the specified message
InvalidPasswordException(String, String) - Constructor for exception net.sf.basedb.core.authentication.InvalidPasswordException: Create a new InvalidPasswordException object
InvalidPasswordException(String, Throwable) - Constructor for exception net.sf.basedb.core.InvalidPasswordException: Create a new InvalidPasswordException object with the specified message
InvalidPathException - Exception in net.sf.basedb.core: This exception is thrown when BASE is trying to parse a path which is invalid.
InvalidPathException(String) - Constructor for exception net.sf.basedb.core.InvalidPathException: Create a new InvalidPathException object.
InvalidRelationException - Exception in net.sf.basedb.core: Exceptions of this type are thrown when a ValidationAction has detected that a file related to the main file is invalid.
InvalidRelationException() - Constructor for exception net.sf.basedb.core.InvalidRelationException: Create a new InvalidRelationException object.
InvalidRelationException(String) - Constructor for exception net.sf.basedb.core.InvalidRelationException: Create a new InvalidRelationException object with the specified message.
InvalidRelationException(String, Throwable) - Constructor for exception net.sf.basedb.core.InvalidRelationException: Create a new InvalidRelationException object with the specified message.
InvalidRelationException(Throwable) - Constructor for exception net.sf.basedb.core.InvalidRelationException: Create a new InvalidRelationException object.
invalidUseOfNullError(String, String, String, String...) - Static method in class net.sf.basedb.plugins.util.Parameters: Create the parameter for handling required but missing values.
invalidUseOfNullErrorParameter - Static variable in class net.sf.basedb.plugins.AbstractFlatFileImporter
InvalidUseOfNullException - Exception in net.sf.basedb.core: This exception is thrown when an object field or a parameter that mustn't be null is set to null.
InvalidUseOfNullException() - Constructor for exception net.sf.basedb.core.InvalidUseOfNullException: Create a new InvalidUseOfNullException object.
InvalidUseOfNullException(String) - Constructor for exception net.sf.basedb.core.InvalidUseOfNullException: Create a new InvalidUseOfNullException object.
invariantEquals(List<?>, List<?>) - Static method in class net.sf.basedb.util.EqualsHelper: Checks if two lists contains equal elements disregarding their positions in the array.
invariantEquals(T[], T[]) - Static method in class net.sf.basedb.util.EqualsHelper: Checks if two arrays contains equal elements disregarding their positions in the array.
InverseFilter<T> - Class in net.sf.basedb.util.filter: A filter implementation that negates the result of a parent filter.
InverseFilter(Filter<? super T>) - Constructor for class net.sf.basedb.util.filter.InverseFilter
INVLN2 - Static variable in class net.sf.basedb.util.ColorGenerator: Constant holding the value of 1 / ln(2).
InvokationContext<A extends Action> - Class in net.sf.basedb.util.extensions: Keeps contextual information about a single invokation of extensions.
InvokationContext() - Constructor for class net.sf.basedb.util.extensions.InvokationContext
invoke() - Method in class net.sf.basedb.core.PluginConfigurationRequest
invoke() - Method in class net.sf.basedb.core.PluginExecutionRequest
invoke() - Method in class net.sf.basedb.core.PluginRequest: Invoke the plugin and let it do it's work.
invoke(Object, Method, Object[]) - Method in class net.sf.basedb.util.extensions.debug.ProxyActionFactory
IOSupport - Interface in net.sf.basedb.plugins.executor: This interface is a tagging interface that should be implemented by export and import plug-ins that knows how to cooperate with the external program executor.
ip - Variable in class net.sf.basedb.core.signal.SocketSignalReceiver
IS_COMPACT - Static variable in class net.sf.basedb.clients.web.ModeInfo
isAcceptableParent(Annotatable) - Method in class net.sf.basedb.util.annotations.InheritSpecification: Checks if the parent item has a subtype matching the subtype (if any) in this specification.
isAcceptedByValidator(ValidationAction) - Method in class net.sf.basedb.util.fileset.ValidatingFileSetMember: Check if the member is accepted by the given validator.
isAffymetrix(FileStoreEnabled) - Static method in class net.sf.basedb.util.affymetrix.AffymetrixUtil: Check if the item is using the affymetrix platform.
isAllowedControl(InetAddress, String) - Method in class net.sf.basedb.clients.jobagent.Agent: Check if the computer specified by the given address is allowed to control this job agent.
isAllowedHost(InetAddress) - Method in class net.sf.basedb.core.signal.SocketSignalReceiver: Checks if the specified remote host is allowed to send signals to this receiver.
isAllowedImmediateExecution() - Method in class net.sf.basedb.core.plugin.NamespaceRequestWrapper
isAllowedImmediateExecution() - Method in interface net.sf.basedb.core.plugin.Request: If this plugin has been allowed immediate execution or not.
isAllowedImmediateExecution() - Method in class net.sf.basedb.core.PluginRequest.RequestImpl
isAllowedImmediateExecution() - Method in class net.sf.basedb.plugins.executor.ExternalProgramExecutor.RequestWrapper
isAllowedToUseClient(String) - Method in class net.sf.basedb.core.SessionControl: Checks if this session control can be used by the given client application.
isAnExcelFile(InputStream) - Static method in class net.sf.basedb.util.excel.XlsxToCsvUtil: Check if the given stream is an Excel file by looking at the first few bytes.
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 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
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 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 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 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 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 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.
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?
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 net.sf.basedb.core.Operator
isListOperator() - Method in enum 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 net.sf.basedb.core.Operator
isNegationOperator() - Method in enum 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 net.sf.basedb.core.Type
isNumerical() - Method in enum 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 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 net.sf.basedb.core.Type
isTemporal() - Method in enum 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 net.sf.basedb.core.Type
isText() - Method in enum 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 net.sf.basedb.core.IntensityTransform: If the intensities are transformed or not.
isTransformed() - Method in enum 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.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.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(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 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 net.sf.basedb.core.Item
ITEM - net.sf.basedb.core.plugin.GuiContext.Type
ITEM - 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 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 net.sf.basedb.core.Item
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.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 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.
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 - 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.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 - Class in net.sf.basedb.core: This class represents a list of items.
ItemList(ItemListData) - Constructor for class net.sf.basedb.core.ItemList
ITEMLIST - 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 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 - 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 - 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.table.Table
itemType - Variable in class net.sf.basedb.core.AnnotationBatcher.CurrentAnnotationInfo
itemType - Variable in class net.sf.basedb.core.AnnotationBatcher
itemType - Variable in class net.sf.basedb.core.data.AnnotationSetData
itemType - Variable in class net.sf.basedb.core.data.ChangeHistoryDetailData
itemType - Variable in class net.sf.basedb.core.data.ContextData
itemType - Variable in class net.sf.basedb.core.data.ContextIndex
itemType - Variable in class net.sf.basedb.core.data.DataFileTypeData
itemType - Variable in class net.sf.basedb.core.data.DiskUsageData
itemType - Variable in class net.sf.basedb.core.data.FileSetData
itemType - Variable in class net.sf.basedb.core.data.GuiContextData
itemType - Variable in class net.sf.basedb.core.data.ItemSubtypeData
itemType - Variable in class net.sf.basedb.core.data.RoleKeyData
itemType - Variable in class net.sf.basedb.core.DataResultIterator: The type of items returned by the query.
itemType - Variable in class net.sf.basedb.core.HibernateUtil.DelayedFilterDef
itemType - Variable in class net.sf.basedb.core.ItemContext
itemType - Variable in class net.sf.basedb.core.ItemResultIterator: The type of items returned by the query.
itemType - Variable in class net.sf.basedb.core.ItemResultList: The type of items returned by the query.
itemType - Variable in class net.sf.basedb.core.Metadata.BasicData2ItemPropertyPath
itemType - Variable in class net.sf.basedb.core.plugin.Permissions
itemType - Variable in class net.sf.basedb.core.query.HqlEntityParameterExpression
itemType - Variable in class net.sf.basedb.core.query.PermissionRestriction
itemType - Variable in class net.sf.basedb.core.query.QueryParameter
itemType - Variable in class net.sf.basedb.core.QueryRuntimeFilterManager
itemType - Variable in class net.sf.basedb.core.ReporterScoreResultIterator: The type of items returned by the query.
itemType - Variable in class net.sf.basedb.core.snapshot.AnnotationSetSnapshot
itemType - Variable in class net.sf.basedb.core.snapshot.AnnotationSnapshot
itemType - Variable in class net.sf.basedb.plugins.AnnotationFlatFileImporter
itemType - Variable in class net.sf.basedb.plugins.batchimport.AnyToAnyImporter
itemType - Variable in class net.sf.basedb.util.listable.PushToParentsTransformer
itemType - Variable in class net.sf.basedb.util.overview.filter.BasicItemFilter
itemType - Variable in class net.sf.basedb.util.overview.filter.ItemTypeFilter
itemType - Variable in class net.sf.basedb.util.parser.DefaultItemFunction
ItemTypeFilter - Class in net.sf.basedb.util.overview.filter: A filter implementation that mathces item types on nodes.
ItemTypeFilter(Item) - Constructor for class net.sf.basedb.util.overview.filter.ItemTypeFilter: Create a filter that finds nodes that has an attached item of the given item type.
ItemTypeFormatter - Class in net.sf.basedb.util.formatter: Formatter implementation that converts an integer into it's Item representation and the uses name() as the formatted value.
ItemTypeFormatter() - Constructor for class net.sf.basedb.util.formatter.ItemTypeFormatter: Create a new formatter.
ItemTypeFormatter(String) - Constructor for class net.sf.basedb.util.formatter.ItemTypeFormatter: Create a new formatter.
itemTypes - Variable in class net.sf.basedb.core.data.AnnotationTypeData
itemTypesColumnMapping - Static variable in class net.sf.basedb.plugins.batchimport.AnnotationTypeImporter: Column mapping parameter for "Item types".
itemTypesMapper - Variable in class net.sf.basedb.plugins.batchimport.AnnotationTypeImporter
iterate() - Method in class net.sf.basedb.core.hibernate.QueryWrapper: Deprecated.
iterate() - Method in class net.sf.basedb.util.extensions.ExtensionsInvoker: Create an iterator that iterates over all Action:s created by the extensions.
iterate(DbControl) - Method in class net.sf.basedb.clients.web.plugins.DataQueryWrapper: Calls DataQuery.iterate(DbControl)
iterate(DbControl) - Method in class net.sf.basedb.clients.web.plugins.DynamicQueryWrapper: Calls AbstractSqlQuery.iterate(DbControl)
iterate(DbControl) - Method in class net.sf.basedb.clients.web.plugins.ItemQueryWrapper: Calls ItemQuery.iterate(DbControl)
iterate(DbControl) - Method in interface net.sf.basedb.clients.web.plugins.QueryWrapper: Get the ResultIterator for the query.
iterate(DbControl) - Method in class net.sf.basedb.clients.web.plugins.ReporterScoreQueryWrapper: Calls ReporterScoreQuery.iterate(DbControl)
iterate(DbControl) - Method in class net.sf.basedb.core.AbstractSqlQuery: Execute the query.
iterate(DbControl) - Method in class net.sf.basedb.core.DataQuery: Execute the query and return the results as an iterator.
iterate(DbControl) - Method in class net.sf.basedb.core.ItemQuery: Execute the query and return the results as an iterator.
iterate(DbControl) - Method in interface net.sf.basedb.core.query.SqlQuery
iterate(DbControl) - Method in class net.sf.basedb.core.ReporterScoreQuery: Execute the query and return the results as an iterator.
iterations - Variable in class net.sf.basedb.plugins.LowessNormalization.CallableWorker
iterator - Variable in class net.sf.basedb.core.ItemResultList.ResultListIterator
iterator - Variable in class net.sf.basedb.core.ItemResultList.ResultListListIterator
iterator - Variable in class net.sf.basedb.util.extensions.ActionIterator
iterator() - Method in class net.sf.basedb.core.ItemResultList
iterator() - Method in class net.sf.basedb.core.Presets: Iterate over all named presets.
iterator() - Method in class net.sf.basedb.core.Presets.Preset: Iterate over all settings.
iterator() - Method in class net.sf.basedb.util.extensions.ExtensionsInvoker
iterator() - Method in class net.sf.basedb.util.Tree
iterParameter - Static variable in class net.sf.basedb.plugins.LowessNormalization

J

JarClassLoader - Class in net.sf.basedb.util: A class loader implementation that loads classes from JAR files.
JarClassLoader(String) - Constructor for class net.sf.basedb.util.JarClassLoader: Create a new JAR file class loader.
JarClassLoader.JarClassLoaderProxy - Class in net.sf.basedb.util: A proxy class loader is typically needed when one extension depends on another extension.
JarClassLoader.JarInfo - Class in net.sf.basedb.util
JarClassLoaderProxy(String) - Constructor for class net.sf.basedb.util.JarClassLoader.JarClassLoaderProxy: Creates a proxy class loader for the given JAR file.
jarFile - Variable in class net.sf.basedb.clients.web.extensions.ServletWrapperKey
jarFile - Variable in class net.sf.basedb.core.data.PluginDefinitionData
jarFile - Variable in class net.sf.basedb.core.data.PluginTypeData
jarFile - Variable in class net.sf.basedb.util.JarClassLoader.JarInfo
jarFiles - Variable in class net.sf.basedb.util.JarClassLoader: For keeping track of jar files listed by Class-Path entry in the manifest file.
JarFirstURIComparator() - Constructor for class net.sf.basedb.util.extensions.manager.ExtensionsManager.JarFirstURIComparator
JarInfo(File) - Constructor for class net.sf.basedb.util.JarClassLoader.JarInfo
jarLoader - Variable in class net.sf.basedb.util.extensions.manager.ExtensionsFile
jarPath - Variable in class net.sf.basedb.util.JarClassLoader.JarClassLoaderProxy
jarSize - Variable in class net.sf.basedb.util.JarClassLoader: The size of the JAR file.
jarTimeStamp - Variable in class net.sf.basedb.util.JarClassLoader: The timestamp of the JAR file.
javaBin - Variable in class net.sf.basedb.clients.jobagent.executors.ProcessJobExecutor
javaScriptEncode(String) - Static method in class net.sf.basedb.clients.web.util.HTML: Escape a string to make it safe for use in a JavaScript statement.
jdbcFetchSize - Static variable in class net.sf.basedb.core.HibernateUtil: Number of rows to load at a time when iterating over a result set.
jep - Variable in class net.sf.basedb.util.export.spotdata.JepDynamicField
jep - Variable in class net.sf.basedb.util.jep.FunctionSafeJep.SafeFunctionTable
jep(String, String, Type, Formula.AverageMethod, Formatter<?>) - Static method in class net.sf.basedb.util.export.spotdata.ExportableFieldFactory: Create a JEP dynamic field.
Jep - Class in net.sf.basedb.util.jep: Utility class for parsing mathematical expressions.
Jep() - Constructor for class net.sf.basedb.util.jep.Jep
JEP - net.sf.basedb.core.Formula.Parser: Use the JEP parser.
JepConversionFunction<T> - Interface in net.sf.basedb.util.jep.convert: Convert a built-in JEP function or operation to a Query API Expression or Restriction.
JepDynamicField - Class in net.sf.basedb.util.export.spotdata: A dynamic field implementation that uses a JEP expression to generate the expression that is needed to select the data.
JepDynamicField() - Constructor for class net.sf.basedb.util.export.spotdata.JepDynamicField: Create a new object.
jepErrorList - Static variable in class net.sf.basedb.util.jep.Jep
jepExpression - Variable in class net.sf.basedb.clients.web.taglib.table.TableColumn
JepExpressionFunction - Interface in net.sf.basedb.util.jep: This interface should be implemented by JEP functions that can also be converted into an Expression that can be used in queries.
JepExtraValueCalculator - Class in net.sf.basedb.plugins: This plugin caluclates extra values from a bioassayset using mathematical formulas entered by the user.
JepExtraValueCalculator() - Constructor for class net.sf.basedb.plugins.JepExtraValueCalculator
JepFunction - Interface in net.sf.basedb.util.jep: This interface should be implemented by objects that can perform some kind of calculation for a JEP expression.
JepIntensityCalculatorImpl(JEP[], RawFunction, MeanFunction) - Constructor for class net.sf.basedb.util.IntensityCalculatorUtil.JepIntensityCalculatorImpl
JepIntensityTransformer - Class in net.sf.basedb.plugins: This plugin transform channel intensities using mathematical formulas entered by the user.
JepIntensityTransformer() - Constructor for class net.sf.basedb.plugins.JepIntensityTransformer: Constructor should be empty.
JepMapper - Class in net.sf.basedb.util.parser: A mapper that uses Jep to calculate the final value.
JepMapper(String, List<String>) - Constructor for class net.sf.basedb.util.parser.JepMapper: Create a new JepMapper.
JepMapper(String, List<String>, NumberFormat) - Constructor for class net.sf.basedb.util.parser.JepMapper: Deprecated.
In 3.15, use JepMapper(String, List, NumberFormat, Formatter, boolean, JepFunction...) instead
JepMapper(String, List<String>, NumberFormat, boolean) - Constructor for class net.sf.basedb.util.parser.JepMapper: Deprecated.
In 3.15, use JepMapper(String, List, NumberFormat, Formatter, boolean, JepFunction...) instead
JepMapper(String, List<String>, NumberFormat, boolean, JepFunction...) - Constructor for class net.sf.basedb.util.parser.JepMapper: Deprecated.
In 3.15, use JepMapper(String, List, NumberFormat, Formatter, boolean, JepFunction...) instead
JepMapper(String, List<String>, NumberFormat, Formatter<Date>, boolean, JepFunction...) - Constructor for class net.sf.basedb.util.parser.JepMapper
JepRestrictionFunction - Interface in net.sf.basedb.util.jep: This interface should be implemented by JEP functions that can also be converted into a Restriction that can be used in queries.
jeps - Variable in class net.sf.basedb.util.IntensityCalculatorUtil.JepIntensityCalculatorImpl
jepToExpression(JEP) - Static method in class net.sf.basedb.util.jep.Jep: Convert a JEP expression to a Query API Expression.
jepToRestriction(JEP) - Static method in class net.sf.basedb.util.jep.Jep: Convert a JEP expression to a Query API Restriction.
job - Variable in class net.sf.basedb.clients.jobagent.JobRunner
job - Variable in class net.sf.basedb.core.data.ArrayDesignData
job - Variable in class net.sf.basedb.core.data.ChangeHistoryData
job - Variable in class net.sf.basedb.core.data.DerivedBioAssayData
job - Variable in class net.sf.basedb.core.data.ExtraValueData
job - Variable in class net.sf.basedb.core.data.MessageData
job - Variable in class net.sf.basedb.core.data.RawBioAssayData
job - Variable in class net.sf.basedb.core.data.TransformationData
job - Variable in class net.sf.basedb.core.Job.ProgressReporterImpl
job - Variable in class net.sf.basedb.core.ParameterValuesImpl
job - Variable in class net.sf.basedb.core.plugin.AbstractPlugin
job - Variable in class net.sf.basedb.core.plugin.ParameterValuesWrapper
job - Variable in class net.sf.basedb.core.PluginRequest
job - Variable in class net.sf.basedb.core.Transformation
Job - Class in net.sf.basedb.core: This class represents the execution of a job.
Job(JobData) - Constructor for class net.sf.basedb.core.Job
JOB - net.sf.basedb.core.Item: The item is a Job
Job.ExecutionTime - Enum 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 in net.sf.basedb.core: The status of a job.
Job.Type - Enum 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 - 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 - 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.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 - 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 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 in net.sf.basedb.core.query: An enumeration used to specify the type of join.
JoinType(String) - Constructor for enum 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, 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 - 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 - 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 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 - 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 - 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.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
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.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 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.
linkAttributes(ClientContext) - Method in class net.sf.basedb.util.extensions.ClientContext: Link this context to the other context with respect to attributes.
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
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
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 - 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.
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 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 net.sf.basedb.util.overview.node.ChildNodeDirection
loadForward() - Method in enum 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 net.sf.basedb.util.overview.node.ChildNodeDirection
loadProperty() - Method in enum net.sf.basedb.util.overview.node.ChildNodeDirection
loadPropertyChildNodes(DbControl, OverviewContext, Node) - Method in class net.sf.basedb.util.overview.loader.AbstractNodeLoader: Load property-type child nodes.
loadPropertyChildNodes(DbControl, OverviewContext, Node) - Method in class net.sf.basedb.util.overview.loader.AnyToAnyLoader: Loads property nodes of an any-to-any node.
loadPropertyChildNodes(DbControl, OverviewContext, Node) - Method in class net.sf.basedb.util.overview.loader.ArrayBatchLoader: Loads property nodes of an array batch.
loadPropertyChildNodes(DbControl, OverviewContext, Node) - Method in class net.sf.basedb.util.overview.loader.ArrayDesignLoader: Loads property nodes of an array design.
loadPropertyChildNodes(DbControl, OverviewContext, Node) - Method in class net.sf.basedb.util.overview.loader.ArraySlideLoader: Loads property nodes of an array slide.
loadPropertyChildNodes(DbControl, OverviewContext, Node) - Method in class net.sf.basedb.util.overview.loader.BioPlateEventLoader: Loads property nodes of an event.
loadPropertyChildNodes(DbControl, OverviewContext, Node) - Method in class net.sf.basedb.util.overview.loader.BioPlateLoader: Load the freezer node.
loadPropertyChildNodes(DbControl, OverviewContext, Node) - Method in class net.sf.basedb.util.overview.loader.BioSourceLoader: Loads property nodes of an array design.
loadPropertyChildNodes(DbControl, OverviewContext, Node) - Method in class net.sf.basedb.util.overview.loader.DataFileLoader: Loads property nodes of files.
loadPropertyChildNodes(DbControl, OverviewContext, Node) - Method in class net.sf.basedb.util.overview.loader.DerivedBioAssayLoader: Loads property nodes of a derived bioassay set.
loadPropertyChildNodes(DbControl, OverviewContext, Node) - Method in class net.sf.basedb.util.overview.loader.ExperimentLoader: Load property nodes for an experiment: Experimental factors: ExperimentalFactorLoader.createPropertyNode(DbControl, OverviewContext, Node) Annotations: AnnotationLoader.createPropertyNode(DbControl, OverviewContext, Node)
loadPropertyChildNodes(DbControl, OverviewContext, Node) - Method in class net.sf.basedb.util.overview.loader.ExtractLoader: Loads property nodes of an extract.
loadPropertyChildNodes(DbControl, OverviewContext, Node) - Method in class net.sf.basedb.util.overview.loader.FileLoader: Loads annotations for the given file node.
loadPropertyChildNodes(DbControl, OverviewContext, Node) - Method in class net.sf.basedb.util.overview.loader.HardwareLoader: Loads annotations and hardware parameters for the given hardware node.
loadPropertyChildNodes(DbControl, OverviewContext, Node) - Method in class net.sf.basedb.util.overview.loader.ItemListLoader: Loads property nodes of a item list.
loadPropertyChildNodes(DbControl, OverviewContext, Node) - Method in class net.sf.basedb.util.overview.loader.KitLoader: Loads annotations for the given kit node.
loadPropertyChildNodes(DbControl, OverviewContext, Node) - Method in class net.sf.basedb.util.overview.loader.PhysicalBioAssayLoader: Loads property nodes of a physical bioassay.
loadPropertyChildNodes(DbControl, OverviewContext, Node) - Method in class net.sf.basedb.util.overview.loader.ProtocolLoader: Loads annotations and protocol parameters for the given protocol node.
loadPropertyChildNodes(DbControl, OverviewContext, Node) - Method in class net.sf.basedb.util.overview.loader.RawBioAssayLoader: Load property nodes for a raw bioassay: Annotations: AnnotationLoader.createPropertyNode(DbControl, OverviewContext, Node) Data files: DataFileLoader.createPropertyNode(DbControl, OverviewContext, Node) Platform: PlatformLoader.createPropertyNode(DbControl, OverviewContext, Node) Protocol: ProtocolLoader.createPropertyNode(DbControl, OverviewContext, Node) Software: SoftwareLoader.createPropertyNode(DbControl, OverviewContext, Node) Array design: ArrayDesignLoader.createPropertyNode(DbControl, OverviewContext, Node)
loadPropertyChildNodes(DbControl, OverviewContext, Node) - Method in class net.sf.basedb.util.overview.loader.RootRawBioAssayLoader: Load property nodes for a raw bioassay: Annotations: AnnotationLoader.createPropertyNode(DbControl, OverviewContext, Node) Data files: DataFileLoader.createPropertyNode(DbControl, OverviewContext, Node) Platform: PlatformLoader.createPropertyNode(DbControl, OverviewContext, Node) Protocol: ProtocolLoader.createPropertyNode(DbControl, OverviewContext, Node) Software: SoftwareLoader.createPropertyNode(DbControl, OverviewContext, Node) Array design: ArrayDesignLoader.createPropertyNode(DbControl, OverviewContext, Node)
loadPropertyChildNodes(DbControl, OverviewContext, Node) - Method in class net.sf.basedb.util.overview.loader.SampleLoader: Loads property nodes of a sample.
loadPropertyChildNodes(DbControl, OverviewContext, Node) - Method in class net.sf.basedb.util.overview.loader.SoftwareLoader: Loads annotations and software parameters for the given software node.
loadPropertyChildNodes(DbControl, OverviewContext, Node) - Method in class net.sf.basedb.util.overview.loader.TagLoader: Loads annotations and tag parameters for the given tag node.
loadRawDataTypes(Set<String>, Document, String) - Static method in class net.sf.basedb.core.RawDataTypes: Load the raw data types and put the information in the RawDataTypes.rawDataTypes map.
loadRawDataTypesFile() - Static method in class net.sf.basedb.core.RawDataTypes: Load and parse the file with raw data types.
loadRecent(DbControl, Item, String) - Method in class net.sf.basedb.core.ItemContext
loadRecent(DbControl, Item, String, int) - Method in class net.sf.basedb.core.ItemContext
loadReverse - Variable in enum net.sf.basedb.util.overview.node.ChildNodeDirection
loadReverse() - Method in enum net.sf.basedb.util.overview.node.ChildNodeDirection
loadReverseChildNodes(DbControl, OverviewContext, Node) - Method in class net.sf.basedb.util.overview.loader.AbstractNodeLoader: Load reverse-loading child nodes.
loadReverseChildNodes(DbControl, OverviewContext, Node) - Method in class net.sf.basedb.util.overview.loader.ArrayBatchLoader: Loads the array design node that is the parent of this array batch.
loadReverseChildNodes(DbControl, OverviewContext, Node) - Method in class net.sf.basedb.util.overview.loader.ArraySlideLoader: Loads the array batch node that is the parent of this array slide.
loadReverseChildNodes(DbControl, OverviewContext, Node) - Method in class net.sf.basedb.util.overview.loader.BioSourceLoader: A biosource usually don't have any reverse child nodes.
loadReverseChildNodes(DbControl, OverviewContext, Node) - Method in class net.sf.basedb.util.overview.loader.DerivedBioAssayLoader: Loads the parent bioassay or the parent physical bioassay.
loadReverseChildNodes(DbControl, OverviewContext, Node) - Method in class net.sf.basedb.util.overview.loader.ExperimentLoader: Loads the root raw bioassay nodes that are part of this experiment
loadReverseChildNodes(DbControl, OverviewContext, Node) - Method in class net.sf.basedb.util.overview.loader.ExtractLoader: Load either the parent sample or extract(s) and child extracts+physical bioassays with a subtype that has ItemSubtype.getPushAnnotations() flag set.
loadReverseChildNodes(DbControl, OverviewContext, Node) - Method in class net.sf.basedb.util.overview.loader.PhysicalBioAssayLoader: Load reverse child nodes: Extracts: ExtractLoader.createReverseNode(DbControl, OverviewContext, Node) Array slide: ArraySlideLoader.createReverseNode(DbControl, OverviewContext, Node)
loadReverseChildNodes(DbControl, OverviewContext, Node) - Method in class net.sf.basedb.util.overview.loader.RawBioAssayLoader: Loads the derived bioassay node that this raw bioassay is created from.
loadReverseChildNodes(DbControl, OverviewContext, Node) - Method in class net.sf.basedb.util.overview.loader.RootRawBioAssayLoader: Loads the derived bioassay node that this raw bioassay is created from.
loadReverseChildNodes(DbControl, OverviewContext, Node) - Method in class net.sf.basedb.util.overview.loader.SampleLoader: If the sample is a pooled sample, loads the parent samples that it was pooled from.
loadRoleKeys(Session) - Method in class net.sf.basedb.core.Keyring: Load all RoleKey:s for the logged in user and put the result in Keyring.rolePermissions
loadRoles(Session) - Method in class net.sf.basedb.core.Keyring: Loads role membership for the user and put that information in the Keyring.roles variable.
loadServletClass(String, ClassLoader) - Method in class net.sf.basedb.clients.web.extensions.ServletLoader: Load the servlet class.
loadServlets(Document, ClassLoader) - Method in class net.sf.basedb.clients.web.extensions.ServletLoader: Load the servlet definitions from an XML document.
LoadServletsProcessor - Class in net.sf.basedb.clients.web.extensions: Processor implementation that define servlets based on what it can find in the META-INF/servlets.xml file.
LoadServletsProcessor(ServletContext, ProcessResults) - Constructor for class net.sf.basedb.clients.web.extensions.LoadServletsProcessor
loadState(ClassLoader) - Method in class net.sf.basedb.core.Job: Load the saved state from the cache.
loadUserClientSettings(Session, int, int) - Method in class net.sf.basedb.core.SessionControl: Load users client-specific settings.
loadUserDefaultSettings(Session, int) - Method in class net.sf.basedb.core.SessionControl: Load users default settings.
loadUsers(Session) - Method in class net.sf.basedb.core.Keyring: Load all users which are member of at least one group where the logged in user is also a member and put that information in the Keyring.users variable.
loadXmlFile(InputStream, String, ClassLoader, boolean) - Method in class net.sf.basedb.clients.web.extensions.ServletLoader: Load a servlet definition XML file.
loadXmlFile(InputStream, String, ClassLoader, boolean) - Method in class net.sf.basedb.util.extensions.xml.XmlLoader: Load an extensions definition XML file.
loadXmlFile2(InputStream, String) - Static method in class net.sf.basedb.core.PluginConfiguration: Load a configurations xml file from the given stream.
LOCAL_HOST - Static variable in class net.sf.basedb.util.SocketUtil
locale - Static variable in class net.sf.basedb.core.Config
LocalSignalReceiver - Class in net.sf.basedb.core.signal: A signal receiver implementation that can receive signals from the local virtual machine only.
LocalSignalReceiver() - Constructor for class net.sf.basedb.core.signal.LocalSignalReceiver: Create a new local signal receiver.
LocalSignalTransporter - Class in net.sf.basedb.core.signal: A signal transporter implementation that can transport signals within the local virtual machine only.
LocalSignalTransporter() - Constructor for class net.sf.basedb.core.signal.LocalSignalTransporter: Create a new signal transporter instance.
localVersion - Variable in class net.sf.basedb.clients.web.taglib.Head
location - Variable in class net.sf.basedb.core.data.DiskUsageData
location - Variable in class net.sf.basedb.core.data.FileData
location - Variable in class net.sf.basedb.core.data.QuotaIndex
location - Variable in class net.sf.basedb.core.data.SessionData
location - Variable in class net.sf.basedb.core.data.UserDeviceData
location - Variable in class net.sf.basedb.core.SessionControl: Location of the remote IP.
Location - Enum 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 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 - net.sf.basedb.core.BioWell.LockMode: It is allowed to add biomaterial once to the well.
LOCKED_AFTER_CREATE - 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 - 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 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 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 - 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 - net.sf.basedb.core.IntensityTransform: Spot intensities are stored as base-2 logged values
LOG2 - Static variable in class net.sf.basedb.util.jep.Log2Function: The natural logarithm of 2.
Log2Function - Class in net.sf.basedb.util.jep: A JEP function class that adds a log2(expression) function to a JEP expression parser.
Log2Function() - Constructor for class net.sf.basedb.util.jep.Log2Function: Create a new instance of this function.
Log2MACalculator - Class in net.sf.basedb.util.ma: MA calculator for log2-transformed spot intensity values.
Log2MACalculator() - Constructor for class net.sf.basedb.util.ma.Log2MACalculator
LogarithmConverter - Class in net.sf.basedb.util.jep.convert: Convert Logarithm function to a Query API Expression.
LogarithmConverter() - Constructor for class net.sf.basedb.util.jep.convert.LogarithmConverter
logarithmic - Variable in class net.sf.basedb.core.data.ColoringData
logChangeDetails(Collection<ChangeHistoryDetailData>, EntityDetails) - Method in class net.sf.basedb.core.log.db.DbLogManager: Log the given details to the database.
logChangeDetails(ChangeHistoryDetailData, EntityDetails) - Method in class net.sf.basedb.core.log.db.DbLogManager: Log the given details to the database.
logChanges(LogManager, EntityDetails) - Method in class net.sf.basedb.core.log.db.AnnotationLogger
logChanges(LogManager, EntityDetails) - Method in class net.sf.basedb.core.log.db.AnnotationSetLogger
logChanges(LogManager, EntityDetails) - Method in class net.sf.basedb.core.log.db.AnyToAnyLogger
logChanges(LogManager, EntityDetails) - Method in class net.sf.basedb.core.log.db.BioMaterialEventLogger
logChanges(LogManager, EntityDetails) - Method in class net.sf.basedb.core.log.db.DefaultEntityLogger: Creates a new ChangeHistoryDetailData and saves it to DbLogManager.logChangeDetails(ChangeHistoryDetailData, EntityDetails).
logChanges(LogManager, EntityDetails) - Method in class net.sf.basedb.core.log.db.FileSetMemberLogger
logChanges(LogManager, EntityDetails) - Method in class net.sf.basedb.core.log.db.ManualEntryLogger
logChanges(LogManager, EntityDetails) - Method in class net.sf.basedb.core.log.db.PlateEventLogger
logChanges(LogManager, EntityDetails) - Method in interface net.sf.basedb.core.log.EntityLogger: Called when changes has been detected to an entity.
logChangeType - Variable in enum 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 Type 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 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
loginTime - Variable in class net.sf.basedb.core.data.SessionData
logInvoker - Variable in class net.sf.basedb.core.log.LoggingInterceptor
LogLevel - Enum in net.sf.basedb.util.extensions.logging: The level of the log message.
LogLevel(String) - Constructor for enum 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 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 - net.sf.basedb.core.Job.ExecutionTime: The job takes more than 1 hour to execute.
LONG - 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 - 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 - 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
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 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.plugins.PlateMappingExporter
MAPPING - 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
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
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 - net.sf.basedb.core.Formula.AverageMethod
MAX - 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 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 - 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 - 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 - 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 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 net.sf.basedb.clients.web.extensions.menu.MenuItemAction.MenuType
merge(Integer...) - Static method in enum 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 - 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
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 - 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 - net.sf.basedb.core.Formula.AverageMethod
MIN - 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 - 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.core.hibernate.SchemaGenerator.CollectSqlTarget
mode - Variable in class net.sf.basedb.core.hibernate.SchemaGenerator
Mode(boolean, boolean) - Constructor for enum net.sf.basedb.core.hibernate.SchemaGenerator.Mode
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
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 - 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.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.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 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 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 - 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 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 - 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_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 - 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 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 - net.sf.basedb.core.FeatureIdentificationMethod: None, because the array design is a file-only platform.
NONE - net.sf.basedb.core.Formula.AverageMethod
NONE - net.sf.basedb.core.IntensityTransform: No transformation has been applied to the spot intensities.
NONE - net.sf.basedb.core.SyncFilter.SourceItemTransform: No transformation of source items is done.
NONE - 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 - net.sf.basedb.core.Operator
NOT_ANNOTATED - 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 - 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 - 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 - 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 - net.sf.basedb.core.Operator
NotLoggable - Annotation Type in net.sf.basedb.core.data: Getter methods that are annotated with this annotation should not trigger a log entry even if their values have changed.
notLoggableProperties - Variable in class net.sf.basedb.core.log.EntityLogOptions
NotLoggedInException - Exception in net.sf.basedb.core: This exception is thrown if you try to perform a function that requires a user to be logged in without beeing logged in.
NotLoggedInException() - Constructor for exception net.sf.basedb.core.NotLoggedInException: Creates a new NotLoggedInException.
notNull - Variable in class net.sf.basedb.core.ParameterType: If the parameter can be null or not.
NotNullFilter<T> - Class in net.sf.basedb.util.filter: A filter implementation that rejects all null objects.
NotNullFilter(boolean) - Constructor for class net.sf.basedb.util.filter.NotNullFilter: Create a new filter.
NotRestriction - Class in net.sf.basedb.core.query: Negate a restriction: NOT r
NotRestriction(Restriction) - Constructor for class net.sf.basedb.core.query.NotRestriction
noUsePermissionToReferenceErrorParameter - Static variable in class net.sf.basedb.plugins.batchimport.AbstractItemImporter
noUsePermissionToTargetErrorParameter - Static variable in class net.sf.basedb.plugins.batchimport.AnyToAnyImporter
noWritePermissionToItemErrorParameter - Static variable in class net.sf.basedb.plugins.batchimport.AbstractItemImporter
noWritePermissionToItemErrorParameter - Static variable in class net.sf.basedb.plugins.batchimport.AnyToAnyImporter
NULL_ESCAPE - Variable in class net.sf.basedb.core.migrate.AbstractResultWriter
NULL_ESCAPE - Variable in class net.sf.basedb.core.migrate.postgres.PostgresResultWriterFactory: PostgreSQL uses "\N" for null values.
nullable - Variable in class net.sf.basedb.core.data.ReporterClonePropertyData
nullable - Variable in class net.sf.basedb.core.ExtendedProperty
nullable - Variable in class net.sf.basedb.core.VirtualColumn: If the column should be nullable or not.
NULLABLE - Static variable in class net.sf.basedb.core.ClonableProperty
NULLABLE - Static variable in class net.sf.basedb.core.VirtualColumn: Used in constructor to tell that the column should be nullable.
nullIfException - Variable in class net.sf.basedb.plugins.IlluminaRawDataImporter
nullIfException - Variable in class net.sf.basedb.plugins.RawDataFlatFileImporter
nullIfException - Variable in class net.sf.basedb.plugins.ReporterFlatFileImporter
nullIfException - Variable in class net.sf.basedb.util.parser.ColumnMapper
nullIfException - Variable in class net.sf.basedb.util.parser.CompoundMapper
nullIfException - Variable in class net.sf.basedb.util.parser.ConstantMapper
NullIfExceptionMapper - Class in net.sf.basedb.util.parser: A mapper that returns null if there is an exception when parsing the input data.
NullIfExceptionMapper(Mapper) - Constructor for class net.sf.basedb.util.parser.NullIfExceptionMapper: Create a new CropStringMapper.
nullIfMissingReporter - Variable in class net.sf.basedb.plugins.IlluminaRawDataImporter
nullifyClonedReferences - Variable in class net.sf.basedb.core.AnnotationBatcher
nullIsEmptyString - Variable in class net.sf.basedb.util.encode.TabCrLfEncoderDecoder
nullIsNull - Variable in class net.sf.basedb.util.parser.FlatFileParser.Data
nullIsNull - Variable in class net.sf.basedb.util.parser.FlatFileParser: If null should be returned for the string NULL (ignoring case) or not.
NullIterator() - Constructor for class net.sf.basedb.clients.web.taglib.table.ColumnDef.NullIterator
NullNodeLoader<I> - Class in net.sf.basedb.util.overview.loader: A node loader implementation that doesn't load any nodes.
NullNodeLoader() - Constructor for class net.sf.basedb.util.overview.loader.NullNodeLoader
NullNodeValidator<I> - Class in net.sf.basedb.util.overview.validator: A node validator implementation that accepts all nodes, except missing items and denied access items (depending on configuration).
NullNodeValidator() - Constructor for class net.sf.basedb.util.overview.validator.NullNodeValidator: Create a new validator with default settings.
NullNodeValidator(boolean, boolean) - Constructor for class net.sf.basedb.util.overview.validator.NullNodeValidator: Created a new validator that accepts denied and/or missing nodes.
nullSafeAnd(Collection<? extends Restriction>) - Static method in class net.sf.basedb.core.query.Restrictions: Combine one or more restrictions with AND: new restriction = r[0] AND r[1] AND ...
nullSafeAnd(Restriction...) - Static method in class net.sf.basedb.core.query.Restrictions: Combine one or more restrictions with AND ignoring null elements.
nullSafeOr(Collection<? extends Restriction>) - Static method in class net.sf.basedb.core.query.Restrictions: Combine one or more restrictions with OR ignoring null elements.
nullSafeOr(Restriction...) - Static method in class net.sf.basedb.core.query.Restrictions: Combine one or more restrictions with OR ignoring null elements.
nullText - Variable in class net.sf.basedb.clients.web.taglib.PropertyValue: What to show if the value is null.
nullValue - Variable in class net.sf.basedb.clients.web.plugins.BioMaterialEventSourceFormatter
nullValue - Variable in class net.sf.basedb.core.log.ChangeTypeFormatter
nullValue - Variable in class net.sf.basedb.util.export.spotdata.ExportableFieldFormatter
nullValue - Variable in class net.sf.basedb.util.export.TableWriter
nullValue - Variable in class net.sf.basedb.util.formatter.EnumFormatter
nullValue - Variable in class net.sf.basedb.util.formatter.FilePathFormatter
nullValue - Variable in class net.sf.basedb.util.formatter.IdentifiableFormatter
nullValue - Variable in class net.sf.basedb.util.formatter.ItemTypeFormatter
nullValue - Variable in class net.sf.basedb.util.formatter.NameableFormatter
nullValue - Variable in class net.sf.basedb.util.formatter.ValueTypeFormatter
numAcceptedWithNullReporterOnFeature - Variable in class net.sf.basedb.core.RawDataBatcher: The number of accepted inserts were the feature had a NULL reporter
numAddedToList - Variable in class net.sf.basedb.plugins.ReporterFlatFileImporter
numAnnotations - Variable in class net.sf.basedb.plugins.AnnotationFlatFileImporter.NewAnnotations
numAnnotations - Variable in class net.sf.basedb.plugins.AnnotationFlatFileImporter
numArrays - Variable in class net.sf.basedb.core.data.ArrayDesignData
numArraysColumnMapping - Static variable in class net.sf.basedb.plugins.batchimport.ArrayDesignImporter
numArraysMapper - Variable in class net.sf.basedb.plugins.batchimport.ArrayDesignImporter
NUMBER_FORMAT_ERROR - Static variable in class net.sf.basedb.plugins.util.Parameters: The name of the parameter created by Parameters.numberFormatError(String, String, String, String...).
NUMBER_OUT_OF_RANGE_ERROR - Static variable in class net.sf.basedb.plugins.util.Parameters: The name of the parameter created by Parameters.numberOutOfRangeError(String, String, String, String...).
numberFormat - Variable in class net.sf.basedb.plugins.AnnotationFlatFileImporter
numberFormat - Variable in class net.sf.basedb.plugins.batchimport.AnnotationTypeImporter
numberFormat - Variable in class net.sf.basedb.util.excel.XlsxToCsvUtil
numberFormat - Variable in class net.sf.basedb.util.parser.ColFunction
numberFormat - Variable in class net.sf.basedb.util.parser.FlatFileParser: The default number formatter to use for creating mappers.
numberFormat - Variable in class net.sf.basedb.util.parser.JepMapper
numberFormat(int) - Static method in class net.sf.basedb.util.excel.ExcelValue: Creates a format string for formatting numbers with the given number of decimals (between 0 and 15).
numberFormatError(String, String, String, String...) - Static method in class net.sf.basedb.plugins.util.Parameters: Create the parameter for handling invalid numbers.
numberFormatErrorParameter - Static variable in class net.sf.basedb.plugins.AbstractFlatFileImporter
numberFormatErrorParameter - Static variable in class net.sf.basedb.plugins.AnnotationFlatFileImporter
NumberFormatFormatter - Class in net.sf.basedb.util.formatter: Formatter implementation for numeric values that simply wrap a NumberFormat instance.
NumberFormatFormatter(NumberFormat) - Constructor for class net.sf.basedb.util.formatter.NumberFormatFormatter: Create a new number formatter.
numberFormatter - Variable in class net.sf.basedb.clients.web.formatter.ColorFormatter
NumberFormatter - Class in net.sf.basedb.util.formatter: Formats a number for output on a web page.
NumberFormatter(int, boolean) - Constructor for class net.sf.basedb.util.formatter.NumberFormatter: Create a new number formatter.
NumberFormatUtil - Class in net.sf.basedb.util: Utility class for working with NumberFormat object.
NumberFormatUtil() - Constructor for class net.sf.basedb.util.NumberFormatUtil
numberOfRows - Variable in class net.sf.basedb.core.dbengine.TableInfo
numberOutOfRangeError(String, String, String, String...) - Static method in class net.sf.basedb.plugins.util.Parameters: Create the parameter for handling numeric values that are outside the allowed range.
numberOutOfRangeErrorParameter - Static variable in class net.sf.basedb.plugins.AbstractFlatFileImporter
numberOutOfRangeErrorParameter - Static variable in class net.sf.basedb.plugins.AnnotationFlatFileImporter
NumberOutOfRangeException - Exception in net.sf.basedb.core: This exception is thrown when an item's field or a parameter that only accepts numeric values within a certain range are passed a value outside that range.
NumberOutOfRangeException() - Constructor for exception net.sf.basedb.core.NumberOutOfRangeException: Create a new NumberOutOfRangeException object.
NumberOutOfRangeException(String) - Constructor for exception net.sf.basedb.core.NumberOutOfRangeException
NumberOutOfRangeException(String, double, double, boolean) - Constructor for exception net.sf.basedb.core.NumberOutOfRangeException: Create a new NumberOutOfRangeException object when the parameter is less than a minimum or greater than a maximum value.
NumberOutOfRangeException(String, double, double, double) - Constructor for exception net.sf.basedb.core.NumberOutOfRangeException: Create a new NumberOutOfRangeException object when the parameter is outside both a minimum and a maximum allowed value.
NumberOutOfRangeException(String, long, long, boolean) - Constructor for exception net.sf.basedb.core.NumberOutOfRangeException: Create a new NumberOutOfRangeException object when the parameter is less than a minimum or greater than a maximum value.
NumberOutOfRangeException(String, long, long, long) - Constructor for exception net.sf.basedb.core.NumberOutOfRangeException: Create a new NumberOutOfRangeException object when the parameter is outside both a minimum and a maximum allowed value.
numBlocks - Variable in class net.sf.basedb.plugins.PrintMapFlatFileImporter
numBlocks - Variable in class net.sf.basedb.plugins.ReporterMapFlatFileImporter
numChannels - Variable in class net.sf.basedb.core.SpotBatcher: The number of channels used in the raw data type of the experiment where the bioassayset belongs.
numChildren() - Method in class net.sf.basedb.util.overview.Node: Get the number of child nodes in this node.
numColumns - Variable in class net.sf.basedb.clients.web.taglib.table.HeaderRow
numColumns - Variable in class net.sf.basedb.core.data.DataCubeData
numColumns - Variable in class net.sf.basedb.util.bfs.AnnotationParser
numColumns - Variable in class net.sf.basedb.util.bfs.DataParser
numColumns - Variable in class net.sf.basedb.util.bfs.MatrixModel
numCreated - Variable in class net.sf.basedb.plugins.batchimport.AbstractItemImporter
numCreated - Variable in class net.sf.basedb.plugins.batchimport.AnyToAnyImporter
numDataColumnsType - Static variable in class net.sf.basedb.plugins.AbstractFlatFileImporter
numDecimals - Variable in class net.sf.basedb.util.formatter.NumberFormatter
numDeleted - Variable in class net.sf.basedb.plugins.ReporterFlatFileImporter
numDeleted - Variable in class net.sf.basedb.util.extensions.manager.ExtensionsManager
numDeleted - Variable in class net.sf.basedb.util.extensions.manager.processor.DeleteResourcesProcessor
numElements - Variable in class net.sf.basedb.clients.web.taglib.path.Path: Keeps track of the number of path elements so separators can be added.
numEntries - Variable in class net.sf.basedb.util.extensions.logging.ExtensionsLog
numericToAlpha(int) - Static method in class net.sf.basedb.util.Coordinate: Convert a numeric coordinate to an alphanumeric coordinate.
NumericValue(Number, String) - Constructor for class net.sf.basedb.util.excel.ExcelValue.NumericValue
numError - Variable in class net.sf.basedb.clients.web.extensions.LoadServletsProcessor
numError - Variable in class net.sf.basedb.plugins.AnnotationFlatFileImporter.NewAnnotations
numError - Variable in class net.sf.basedb.plugins.AnnotationFlatFileImporter
numError - Variable in class net.sf.basedb.plugins.batchimport.AbstractItemImporter
numError - Variable in class net.sf.basedb.util.extensions.manager.processor.DeleteResourcesProcessor
numError - Variable in class net.sf.basedb.util.extensions.manager.processor.DisablePluginsProcessor
numError - Variable in class net.sf.basedb.util.extensions.manager.processor.ExtractResourcesProcessor
numError - Variable in class net.sf.basedb.util.extensions.manager.processor.PluginInstallationProcessor
numError - Variable in class net.sf.basedb.util.extensions.manager.processor.RegisterExtensionsProcessor
numError - Variable in class net.sf.basedb.util.extensions.manager.processor.UnregisterExtensionsProcessor
numErrorFiles - Variable in class net.sf.basedb.util.extensions.manager.ProcessResults
numErrors - Variable in class net.sf.basedb.util.extensions.logging.ExtensionsLog
numErrors - Variable in class net.sf.basedb.util.overview.Node
numExisted - Variable in class net.sf.basedb.plugins.batchimport.AbstractItemImporter
numExists - Variable in class net.sf.basedb.plugins.ReporterFlatFileImporter
numExported - Variable in class net.sf.basedb.plugins.GalExporter
numExported - Variable in class net.sf.basedb.plugins.HelpExporter
numExported - Variable in class net.sf.basedb.plugins.PluginConfigurationExporter
numExtraValues - Variable in class net.sf.basedb.core.data.DataCubeData
numFeatures - Variable in class net.sf.basedb.plugins.PrintMapFlatFileImporter
numFeatures - Variable in class net.sf.basedb.plugins.ReporterMapFlatFileImporter
numFileReporters - Variable in class net.sf.basedb.core.data.BioAssaySetData
numFiles - Variable in class net.sf.basedb.clients.web.extensions.LoadServletsProcessor
numFiles - Variable in class net.sf.basedb.clients.web.extensions.UninstalledFileProcessor
numFiles - Variable in class net.sf.basedb.plugins.PackedFileExporter
numFiles - Variable in class net.sf.basedb.util.extensions.manager.processor.DeleteResourcesProcessor
numFiles - Variable in class net.sf.basedb.util.extensions.manager.processor.DisablePluginsProcessor
numFiles - Variable in class net.sf.basedb.util.extensions.manager.processor.ExtractResourcesProcessor
numFiles - Variable in class net.sf.basedb.util.extensions.manager.processor.IgnoreFileProcessor
numFiles - Variable in class net.sf.basedb.util.extensions.manager.processor.MarkAsProcessedProcessor
numFiles - Variable in class net.sf.basedb.util.extensions.manager.processor.PluginInstallationProcessor
numFiles - Variable in class net.sf.basedb.util.extensions.manager.processor.RegisterExtensionsProcessor
numFiles - Variable in class net.sf.basedb.util.extensions.manager.processor.ResetProcessor
numFiles - Variable in class net.sf.basedb.util.extensions.manager.processor.UnregisterExtensionsProcessor
numFileSpots - Variable in class net.sf.basedb.core.data.BioAssayData
numFileSpots - Variable in class net.sf.basedb.core.data.BioAssaySetData
numFileValues - Variable in class net.sf.basedb.core.data.ExtraValueData
numFilteredColumns - Variable in class net.sf.basedb.clients.web.taglib.table.Table
numFilterRows - Variable in class net.sf.basedb.clients.web.taglib.table.Table: Number of filter rows in the table.
numFilterRows - Variable in class net.sf.basedb.core.ItemContext
numFilterRows - Variable in class net.sf.basedb.core.SyncFilter
numFilters - Variable in class net.sf.basedb.core.data.DataCubeData
numHeaderColumns - Variable in class net.sf.basedb.clients.web.taglib.table.Table
numHeaderColumns() - Method in class net.sf.basedb.clients.web.taglib.table.Table
numIgnored - Variable in class net.sf.basedb.util.extensions.manager.ExtensionsManager
numImported - Variable in class net.sf.basedb.plugins.HelpImporter
numInserted - Variable in class net.sf.basedb.plugins.IlluminaRawDataImporter
numInserted - Variable in class net.sf.basedb.plugins.ReporterFlatFileImporter
numItemNotFound - Variable in class net.sf.basedb.plugins.AnnotationFlatFileImporter
numItems - Variable in class net.sf.basedb.core.AnnotationBatcher
numItems - Variable in class net.sf.basedb.plugins.AnnotationFlatFileImporter
numLayers - Variable in class net.sf.basedb.core.data.DataCubeData
numLines - Variable in class net.sf.basedb.core.Migration.ProgressInputStream
numModified - Variable in class net.sf.basedb.util.extensions.manager.ExtensionsManager
numMultiLines - Variable in class net.sf.basedb.plugins.batchimport.AbstractItemImporter
numNew - Variable in class net.sf.basedb.util.extensions.manager.ExtensionsManager
numNewChildren() - Method in class net.sf.basedb.util.overview.Node: Get the number of new children added to this node since the last call to Node.getNewChildren().
numNotFound - Variable in class net.sf.basedb.plugins.batchimport.AbstractItemImporter
numNotFound - Variable in class net.sf.basedb.plugins.ReporterFlatFileImporter
numParameters - Variable in class net.sf.basedb.util.jep.ChannelFunction
numParameters - Variable in class net.sf.basedb.util.jep.ExtraValueFunction
numParameters - Variable in class net.sf.basedb.util.jep.InReporterListFunction
numParameters - Variable in class net.sf.basedb.util.jep.MeanFunction
numParameters - Variable in class net.sf.basedb.util.jep.NotInReporterListFunction
numParameters - Variable in class net.sf.basedb.util.jep.RawChannelFunction
numParameters - Variable in class net.sf.basedb.util.jep.RawFunction
numParameters - Variable in class net.sf.basedb.util.jep.ReporterFunction
numParameters - Variable in class net.sf.basedb.util.jep.ScoreFunction
numParameters - Variable in class net.sf.basedb.util.jep.SimpleJepFunction
numParameters - Variable in class net.sf.basedb.util.parser.DefaultItemFunction
numPlates - Variable in class net.sf.basedb.plugins.PlateFlatFileImporter
numPositions - Variable in class net.sf.basedb.core.data.DataCubeData
numRawBioAssays - Variable in class net.sf.basedb.plugins.IlluminaRawDataImporter
numRead - Variable in class net.sf.basedb.util.InputStreamSplitter
numRead - Variable in class net.sf.basedb.util.InputStreamTracker: The number of bytes that has been read from the underlying input stream so far.
numReadAtMark - Variable in class net.sf.basedb.util.InputStreamTracker: The number of bytes that had been read when InputStreamTracker.mark(int) was called.
numRegistered - Variable in class net.sf.basedb.util.extensions.manager.processor.RegisterExtensionsProcessor
numRemoved - Variable in class net.sf.basedb.plugins.AnnotationFlatFileImporter.NewAnnotations
numRemoved - Variable in class net.sf.basedb.plugins.AnnotationFlatFileImporter
numRemoved - Variable in class net.sf.basedb.plugins.batchimport.AnyToAnyImporter
numReplaced - Variable in class net.sf.basedb.plugins.AnnotationFlatFileImporter.NewAnnotations
numReplaced - Variable in class net.sf.basedb.plugins.AnnotationFlatFileImporter
numReporters - Variable in class net.sf.basedb.core.data.BioAssaySetData
numReportersNotFound - Variable in class net.sf.basedb.core.RawDataBatcher: The number of reporters that was not found.
numReturned - Variable in class net.sf.basedb.util.query.MultiQueryIterator
numRows(long) - Method in class net.sf.basedb.core.Migration
numRowsFormat - Variable in class net.sf.basedb.core.Migration
numSelected - Variable in class net.sf.basedb.plugins.PluginConfigurationExporter
numServlets - Variable in class net.sf.basedb.clients.web.extensions.LoadServletsProcessor
numSet - Variable in class net.sf.basedb.plugins.AnnotationFlatFileImporter.NewAnnotations
numSkipped - Variable in class net.sf.basedb.plugins.batchimport.AnyToAnyImporter
numSkippedMissingFeature - Variable in class net.sf.basedb.core.RawDataBatcher: The number of skipped inserts due to missing feature
numSpots - Variable in class net.sf.basedb.core.data.BioAssayData
numSpots - Variable in class net.sf.basedb.core.data.BioAssaySetData
numStatements - Variable in class net.sf.basedb.core.hibernate.SchemaGenerator.CollectSqlTarget
numTabs - Variable in class net.sf.basedb.clients.web.taglib.tab.TabControl: The number of tabs.
numTotal - Variable in class net.sf.basedb.plugins.HelpImporter
numTotalExtracted - Variable in class net.sf.basedb.util.extensions.manager.processor.ExtractResourcesProcessor
numTotalPlugins - Variable in class net.sf.basedb.util.extensions.manager.processor.DisablePluginsProcessor
numTotalPlugins - Variable in class net.sf.basedb.util.extensions.manager.processor.PluginInstallationProcessor
numUnmodified - Variable in class net.sf.basedb.util.extensions.manager.ExtensionsManager
numUnregistered - Variable in class net.sf.basedb.util.extensions.manager.processor.RegisterExtensionsProcessor
numUnregistered - Variable in class net.sf.basedb.util.extensions.manager.processor.UnregisterExtensionsProcessor
numUpdated - Variable in class net.sf.basedb.plugins.batchimport.AbstractItemImporter
numUpdated - Variable in class net.sf.basedb.plugins.batchimport.AnyToAnyImporter
numUpdated - Variable in class net.sf.basedb.plugins.HelpImporter
numUpdated - Variable in class net.sf.basedb.plugins.ReporterFlatFileImporter
numUsed - Variable in class net.sf.basedb.plugins.ReporterFlatFileImporter
numValues - Variable in class net.sf.basedb.core.data.ExtraValueData
numVisibleColumns() - Method in class net.sf.basedb.clients.web.taglib.table.Table
numWarnings - Variable in class net.sf.basedb.util.extensions.logging.ExtensionsLog
numWarnings - Variable in class net.sf.basedb.util.overview.Node
numWells - Variable in class net.sf.basedb.plugins.PlateFlatFileImporter

O

object - Variable in class net.sf.basedb.util.filter.EqualsFilter
object - Variable in class net.sf.basedb.util.filter.IdentityFilter
objectCache - Variable in class net.sf.basedb.util.overview.GenericOverview
ObjectKey<O> - Interface in net.sf.basedb.util.extensions.manager: Instances of object keys should be something that uniquely identifies an object that has been defined by an extension.
objectMetadata - Variable in class net.sf.basedb.util.extensions.manager.ExtensionsFile
objects - Variable in class net.sf.basedb.core.ItemContext
objects - Variable in class net.sf.basedb.util.ClassLocal
OFF - net.sf.basedb.util.extensions.LoggingErrorHandlerFactory.Level
OFFLINE - 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 net.sf.basedb.core.BioWell.LockMode: Called when biomaterial is added to a well.
onAfterCommit() - Method in class net.sf.basedb.clients.web.extensions.list.RelatedItemHelper.CloseMyDbControl
onAfterCommit() - Method in class net.sf.basedb.core.AnnotationType.RemoveInheritedAnnotationsAction
onAfterCommit() - Method in class net.sf.basedb.core.DerivedBioAssay.FixDerivedBioAssayParentsRecursivelyAction
onAfterCommit() - Method in class net.sf.basedb.core.DropDynamicTableAction
onAfterCommit() - Method in class net.sf.basedb.core.ItemList.DelayedAdditionManager
onAfterCommit() - Method in class net.sf.basedb.core.Job.JobSignalTransporter
onAfterCommit() - Method in class net.sf.basedb.core.MeasuredBioMaterial.RemainingQuantityAction
onAfterCommit() - Method in class net.sf.basedb.core.ProjectSpecificAnnotationsManager
onAfterCommit() - Method in class net.sf.basedb.core.ServiceSessionControl.FlushSessionAction
onAfterCommit() - Method in interface net.sf.basedb.core.TransactionalAction: Called after a successful commit.
onAfterCommit(Transactional.Action) - Method in class net.sf.basedb.core.BasicItem: This method is called on each Transactional object after a successful commit to the database.
onAfterCommit(Transactional.Action) - Method in class net.sf.basedb.core.Experiment: Remove old reporter clone table after a successful commit.
onAfterCommit(Transactional.Action) - Method in class net.sf.basedb.core.File
onAfterCommit(Transactional.Action) - Method in class net.sf.basedb.core.Job: If the Signal.ABORT signal is waiting to be sent send it.
onAfterCommit(Transactional.Action) - Method in class net.sf.basedb.core.Message: Send the message as an email if requested by the user.
onAfterCommit(Transactional.Action) - Method in class net.sf.basedb.core.Platform: Register file-only platforms as raw data type after insert and unregister after delete.
onAfterCommit(Transactional.Action) - Method in class net.sf.basedb.core.PlatformVariant: Register file-only platforms as raw data type after insert and unregister after delete.
onAfterCommit(Transactional.Action) - Method in class net.sf.basedb.core.PluginConfiguration: Reset parameter version so that adding new parameters will increase the version the next time.
onAfterCommit(Transactional.Action) - Method in class net.sf.basedb.core.VirtualDb: Remove all dynamic tables if action == Action.DELETE
onAfterInsert() - Method in class net.sf.basedb.core.Annotation
onAfterInsert() - Method in class net.sf.basedb.core.BasicItem: This method is called on all items directly after Hibernate has inserted it into the database.
onAfterInsert() - Method in class net.sf.basedb.core.BioPlateEventType
onAfterInsert() - Method in class net.sf.basedb.core.PluginDefinition
onBeforeClose() - Method in class net.sf.basedb.core.AbstractBatcher: Let a subclass cleanup itself before the connection to the database is closed.
onBeforeClose() - Method in class net.sf.basedb.core.AnnotationBatcher
onBeforeClose() - Method in class net.sf.basedb.core.BasicBatcher: Close all open SQL statements.
onBeforeClose() - Method in class net.sf.basedb.core.FeatureBatcher: Set the hasFeature flag on the array design if features has been added.
onBeforeClose() - Method in class net.sf.basedb.core.FilterBatcher: Close open SQL statements.
onBeforeClose() - Method in class net.sf.basedb.core.MappingBatcher: Update bytes on data cube and close open SQL statements.
onBeforeClose() - Method in class net.sf.basedb.core.PositionBatcher: Update bytes and max position on the datacube and close open SQL statements.
onBeforeClose() - Method in class net.sf.basedb.core.PositionExtraValueBatcher: Update disk usage and close open SQL statements
onBeforeClose() - Method in class net.sf.basedb.core.RawDataBatcher: Update the spot count and disk usage on the raw bioassay.
onBeforeClose() - Method in class net.sf.basedb.core.ReporterCloneBatcher: Update disk usage and close open SQL statements.
onBeforeClose() - Method in class net.sf.basedb.core.SpotBatcher: Update disk usage and close open SQL statements
onBeforeClose() - Method in class net.sf.basedb.core.SpotExtraValueBatcher: Update disk usage and close open SQL statements
onBeforeCommit() - Method in class net.sf.basedb.clients.web.extensions.list.RelatedItemHelper.CloseMyDbControl
onBeforeCommit() - Method in class net.sf.basedb.core.AnnotationType.RemoveInheritedAnnotationsAction
onBeforeCommit() - Method in class net.sf.basedb.core.DerivedBioAssay.FixDerivedBioAssayParentsRecursivelyAction
onBeforeCommit() - Method in class net.sf.basedb.core.DropDynamicTableAction
onBeforeCommit() - Method in class net.sf.basedb.core.ItemList.DelayedAdditionManager
onBeforeCommit() - Method in class net.sf.basedb.core.MeasuredBioMaterial.RemainingQuantityAction
onBeforeCommit() - Method in class net.sf.basedb.core.ProjectSpecificAnnotationsManager
onBeforeCommit() - Method in class net.sf.basedb.core.ServiceSessionControl.FlushSessionAction
onBeforeCommit() - Method in interface net.sf.basedb.core.TransactionalAction: This method is called before the commit is about to happen.
onBeforeCommit(D, Transactional.Action) - Method in class net.sf.basedb.core.BasicBatcher: Called after the object has been validated just before the SQL is added to the batch queue.
onBeforeCommit(ReporterData, Transactional.Action) - Method in class net.sf.basedb.core.ReporterBatcher: Set the last update date to today's date and change the last source of update.
onBeforeCommit(Transactional.Action) - Method in class net.sf.basedb.core.Annotation: Nullify links to this annotation from cloned annotations when this annotation is deleted (since the cloned annotation should not be deleted).
onBeforeCommit(Transactional.Action) - Method in class net.sf.basedb.core.AnnotationSet: Remove the cached snapshot if needed.
onBeforeCommit(Transactional.Action) - Method in class net.sf.basedb.core.AnyToAny: We may have to set the AnyToAny.getFromId() and/or AnyToAny.getToId() values if those items are also created in the same transaction.
onBeforeCommit(Transactional.Action) - Method in class net.sf.basedb.core.BasicItem: This method is called on each Transactional item and on all items if the action is Transactional.Action.CREATE or Transactional.Action.DELETE before a commit is issued to the database.
onBeforeCommit(Transactional.Action) - Method in class net.sf.basedb.core.BioAssay
onBeforeCommit(Transactional.Action) - Method in class net.sf.basedb.core.BioAssaySet: On creation, count the number of spots and reporters in the bioassays attached to this bioassayset.
onBeforeCommit(Transactional.Action) - Method in class net.sf.basedb.core.BioMaterialEvent: Return used guantity to biomaterials on delete action.
onBeforeCommit(Transactional.Action) - Method in class net.sf.basedb.core.BioPlate
onBeforeCommit(Transactional.Action) - Method in class net.sf.basedb.core.BioPlateEvent
onBeforeCommit(Transactional.Action) - Method in class net.sf.basedb.core.BioPlateEventParticipant
onBeforeCommit(Transactional.Action) - Method in class net.sf.basedb.core.DataCube: Delete data and update disk usage information on the experiment if action == Action.DELETE
onBeforeCommit(Transactional.Action) - Method in class net.sf.basedb.core.DataCubeExtraValue: Delete data and update disk usage information on the experiment if action == Action.DELETE
onBeforeCommit(Transactional.Action) - Method in class net.sf.basedb.core.DataCubeFilter: Delete data and update disk usage information on the experiment if action == Action.DELETE
onBeforeCommit(Transactional.Action) - Method in class net.sf.basedb.core.DataCubeLayer: Delete data and update disk usage information on the experiment if action == Action.DELETE
onBeforeCommit(Transactional.Action) - Method in class net.sf.basedb.core.DerivedBioAssay: Automatically try to assign an extract from parent items at creation time.
onBeforeCommit(Transactional.Action) - Method in class net.sf.basedb.core.Experiment
onBeforeCommit(Transactional.Action) - Method in class net.sf.basedb.core.File
onBeforeCommit(Transactional.Action) - Method in class net.sf.basedb.core.Group: Set group to null in disk usage where this group is referenced.
onBeforeCommit(Transactional.Action) - Method in class net.sf.basedb.core.Job: Set's the project id to the currently active project.
onBeforeCommit(Transactional.Action) - Method in class net.sf.basedb.core.MeasuredBioMaterial: Make sure the creation event is created at the same time this item is created and that source biomaterials get their used quantities back if this item is deleted.
onBeforeCommit(Transactional.Action) - Method in class net.sf.basedb.core.OwnedItem: Overrides the BasicItem.onBeforeCommit(Transactional.Action) method.
onBeforeCommit(Transactional.Action) - Method in class net.sf.basedb.core.PhysicalBioAssay: Make sure the creation event is created at the same time this item is created and that source biomaterials get their used quantities back if this item is deleted.
onBeforeCommit(Transactional.Action) - Method in class net.sf.basedb.core.Project
onBeforeCommit(Transactional.Action) - Method in class net.sf.basedb.core.RawBioAssay: Delete raw data if it exists.
onBeforeCommit(Transactional.Action) - Method in class net.sf.basedb.core.SharedItem: If a project is active, automatically share the new item according to the settings of that project, unless a project or item key has been explicitely set (including null).
onBeforeCommit(Transactional.Action) - Method in class net.sf.basedb.core.Transformation: Delete the product bioassaysets when deleting this transction.
onBeforeCommit(Transactional.Action) - Method in class net.sf.basedb.core.Unit: Set property filters that use this unit to null when the unit is deleted.
onClear(BioWellData, MeasuredBioMaterialData) - Method in enum 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 - 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 in net.sf.basedb.core
Operator(int, String, String, boolean, boolean, boolean) - Constructor for enum 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 - 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 - 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 - net.sf.basedb.core.BioMaterialEvent.Type: An event of this type affected a single biomaterial in some way.
OTHER - net.sf.basedb.core.Job.Type: The job is executed by some other program.
OTHER - 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 - net.sf.basedb.core.Include: Include items owned by other users.
out - Variable in class net.sf.basedb.clients.jobagent.executors.ProcessJobExecutor.StreamRedirector
out - Variable in class net.sf.basedb.clients.web.plugins.XlsxTemplate
out - Variable in class net.sf.basedb.core.plugin.ExportOutputStream
out - Variable in class net.sf.basedb.util.export.spotdata.BaseFileExporter
out - Variable in class net.sf.basedb.util.export.spotdata.MatrixBaseFileExporter
out - Variable in class net.sf.basedb.util.export.spotdata.SerialBaseFileExporter
out - Variable in class net.sf.basedb.util.FileCopyRunnable
overridden - Static variable in class net.sf.basedb.core.Config: Properties that has been programmatically overridden.
override - Variable in class net.sf.basedb.clients.web.util.ProjectSpecificInfoFilter
overrideId - Variable in class net.sf.basedb.core.AnnotationBatcher.CurrentAnnotationInfo
overrideId - Variable in class net.sf.basedb.core.data.AnnotationData
overrideId - Variable in class net.sf.basedb.core.data.annotations.AnnotationLink
overrideId - Variable in class net.sf.basedb.core.FastAnnotationLoader.FastAnnotation: The ID of the default annotation this value is overriding.
overrideId - Variable in class net.sf.basedb.core.snapshot.AnnotationSnapshot
overridesDefaultAnnotation() - Method in class net.sf.basedb.clients.web.util.ProjectSpecificInfoFilter: Check if the override flag is set.
OverviewContext - Interface in net.sf.basedb.util.overview: Interface that should be implemented by overview generating classes.
OverviewPlotAction - Interface in net.sf.basedb.clients.web.extensions.plot: Action for generating overview plots for a bioassay set.
OverviewPlotBean - Class in net.sf.basedb.clients.web.extensions.plot: A simple bean-like implementation of the OverviewPlotAction interface.
OverviewPlotBean() - Constructor for class net.sf.basedb.clients.web.extensions.plot.OverviewPlotBean
OverviewUtil - Class in net.sf.basedb.util.overview: Utility class for the overview generation functionality.
OverviewUtil() - Constructor for class net.sf.basedb.util.overview.OverviewUtil
overwrite - Variable in class net.sf.basedb.plugins.HelpImporter
overwrite - Variable in class net.sf.basedb.util.bfs.GenericExtraFileImporter
OVERWRITE - Static variable in class net.sf.basedb.core.plugin.AbstractExporterPlugin: Parameter name for the AbstractExporterPlugin.getOverwriteParameter(String, String) parameter.
OVERWRITE - Static variable in class net.sf.basedb.util.zip.AbstractFileUnpacker: The name of the parameter that asks if existing files should be overwritten or not.
OVERWRITE_ANNOTATIONS - Static variable in class net.sf.basedb.core.plugin.AbstractPlugin: The name of the parameter that asks if annotations should be overwritten or not.
overWriteParameter - Variable in class net.sf.basedb.plugins.HelpImporter
overwriteType - Static variable in class net.sf.basedb.core.plugin.AbstractExporterPlugin
ownable - Static variable in class net.sf.basedb.core.Item.DefinedPermissions
Ownable - Interface in net.sf.basedb.core: An Ownable item is an item which has a User as its owner.
ownable_annotatable - Static variable in class net.sf.basedb.core.Item.DefinedPermissions
OWNABLE_FILTER - Static variable in class net.sf.basedb.core.QueryRuntimeFilterFactory
OwnableData - Interface in net.sf.basedb.core.data: An ownable item is an item which has an owner.
OwnableFilter() - Constructor for class net.sf.basedb.core.QueryRuntimeFilterFactory.OwnableFilter
ownableItems - Static variable in class net.sf.basedb.core.Metadata
OwnableUtil - Class in net.sf.basedb.core: Utility methods that will make it easier to implement the Ownable interface, including data validation.
OwnableUtil - Class in net.sf.basedb.util
OwnableUtil() - Constructor for class net.sf.basedb.core.OwnableUtil
OwnableUtil() - Constructor for class net.sf.basedb.util.OwnableUtil
OwnedData - Class in net.sf.basedb.core.data: This class extends the BasicData class and implements the OwnableData interface.
OwnedData() - Constructor for class net.sf.basedb.core.data.OwnedData
OwnedItem - Class in net.sf.basedb.core: This class inherits from the BasicItem class and implements the Ownable interface.
OwnedItem(OwnedData) - Constructor for class net.sf.basedb.core.OwnedItem
owner - Variable in class net.sf.basedb.core.data.OwnedData
ownerId - Variable in class net.sf.basedb.core.InternalJobQueue.JobRunner

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 - 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, boolean, DataLoader) - Static method in class net.sf.basedb.clients.web.plugins.ExportedProperty
parse(Item, String) - Static method in class net.sf.basedb.clients.web.extensions.list.RelatedItemColumn.Specification
parse(EventHandler) - Method in class net.sf.basedb.util.bfs.AnnotationParser: Parse the input stream and notify the specified event handler with events.
parse(EventHandler) - Method in class net.sf.basedb.util.bfs.DataParser: Parse the input stream and notify the specified event handler with events.
parse(EventHandler) - Method in class net.sf.basedb.util.bfs.MetadataParser: Parse the input stream and notify the specified event handler with events.
parse(EventHandler) - Method in class net.sf.basedb.util.importer.spotdata.SynchronizedSpotDataParser: Begin parsing and issue events to the given event handler.
parseAllExcelSheets - Variable in class net.sf.basedb.util.parser.FlatFileParser: Flag to indicate if only a single (=false) or all (=true) Excel sheets should be parsed in one go.
parseAnswer(String) - Static method in class net.sf.basedb.util.jobagent.JobAgentConnection: Utility method for parsing a 'typical' answer from a job agent.
parseAttributes(String) - Method in class net.sf.basedb.util.gtf.GtfInputStream: Parse attributes from the given template string.
parseBuildNumber(String) - Static method in class net.sf.basedb.core.Version: Find the first digits in a string and return those as the build number.
parseBytes(String, Long) - Static method in class net.sf.basedb.util.Values: Parses a string containing the number of bytes formatted as the Values.formatBytes(Long) method.
parseDate() - Method in class net.sf.basedb.util.parser.ConstantMapper
parseDate(String) - Method in class net.sf.basedb.plugins.batchimport.AbstractItemImporter: Deprecated.
In 3.15, use FlatFileParser.getDateMapper(String) or FlatFileParser.getTimestampMapper(String) and Mapper.getDate(FlatFileParser.Data) instead
parsedBytes - Variable in class net.sf.basedb.util.charset.CharsetDetector
parsedCharacters - Variable in class net.sf.basedb.util.parser.FlatFileParser: The total number of parsed characters so far.
parsedDataLines - Variable in class net.sf.basedb.util.parser.FlatFileParser: The number of data lines parsed in the current section so far.
parsedFile - Variable in class net.sf.basedb.util.XmlUtil2.Validator
parsedLines - Variable in class net.sf.basedb.util.charset.CharsetDetector
parsedLines - Variable in class net.sf.basedb.util.parser.FlatFileParser: The total number of lines parsed so far.
parsedSections - Variable in class net.sf.basedb.util.parser.FlatFileParser: The number of sections parsed so far.
parseException - Variable in class net.sf.basedb.util.parser.ConstantMapper
parseHeaders() - Method in class net.sf.basedb.util.parser.FlatFileParser: Start parsing the input stream.
parseInitParameters(String) - Method in class net.sf.basedb.core.signal.SocketSignalReceiver: Parse the initialisation parameters.
parseNumeric() - Method in class net.sf.basedb.util.parser.ConstantMapper
parseParameters(String, List<String>) - Method in class net.sf.basedb.core.AbstractSqlQuery: Parse the given SQL and find named parameters.
parseQueryString(String) - Static method in class net.sf.basedb.util.QueryParameters: Parses a string in HTTP query format (key1=value1&key2=value2...) and returns it as a QueryParameters object.
parser - Variable in class net.sf.basedb.core.data.FormulaData
parser - Variable in class net.sf.basedb.util.importer.spotdata.BaseFileImporter
parser - Variable in class net.sf.basedb.util.importer.spotdata.SynchronizedSpotDataParser.SynchronizedData
parser - Variable in class net.sf.basedb.util.parser.ColumnMapper
parser - Variable in class net.sf.basedb.util.parser.CompoundMapper
parser - Variable in class net.sf.basedb.util.parser.ConstantMapper
parser - Variable in class net.sf.basedb.util.parser.JepMapper
Parser(int, String) - Constructor for enum 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 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 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 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 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 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 Type 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() - Method in annotation type net.sf.basedb.util.extensions.xml.PathSetter: The type of path that should be generated.
PathType - Enum in net.sf.basedb.util.extensions.xml: Specify the type of paths.
PathType() - Constructor for enum 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 - 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 - 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 in net.sf.basedb.core: This enumeration defined constants for permissions.
Permission(int, int, String) - Constructor for enum 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 - 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 - 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 - 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 - 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 - 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 - 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 - 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 - 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 - 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 - 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
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 - 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 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 - 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 - 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 - 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 - net.sf.basedb.core.ExtraValue.CoordinateType: The extra values are attached to position coordinates only.
POSITION - net.sf.basedb.core.FeatureIdentificationMethod: Use position number.
POSITION - 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 - net.sf.basedb.core.VirtualTable: Table that stores float position extra values.
POSITION_EXTRA_INT - net.sf.basedb.core.VirtualTable: Table that stores integer position extra values.
POSITION_EXTRA_STRING - 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 - 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 - net.sf.basedb.core.Annotation.Source: The annotation is a primary annotation.
PRIMARY - 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 in net.sf.basedb.plugins
PrintMapFlatFileImporter.MetaBlock - Class in net.sf.basedb.plugins
PrintMapFlatFileImporter.Section - Enum 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.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 - 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 - 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.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 - 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 Type 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 - 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
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 - 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 - 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 in net.sf.basedb.core.query: Indicates which part of a query that is currently beeing built.
QuerySection() - Constructor for enum net.sf.basedb.core.query.QuerySection
QueryType - Enum in net.sf.basedb.core.query: A type representing the language of the query.
QueryType() - Constructor for enum 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 - 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 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 - 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 - 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 - 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 - 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.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 - 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
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 - 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 net.sf.basedb.core.Type: Read a value of this type to the input stream.
readWorkbook(InputStream) - Method in class net.sf.basedb.util.excel.XlsxToCsvUtil: Read an Excel workbook from the stream.
RealJoin - Class in net.sf.basedb.core: Represents a join from one virtual table in the dynamic database to a table in the regular database or between two tables in the regular database.
RealJoin(JoinType, RealTable, RealTable, String) - Constructor for class net.sf.basedb.core.RealJoin: Create a new join between two regular tables.
RealJoin(JoinType, VirtualTable, RealTable, VirtualColumn) - Constructor for class net.sf.basedb.core.RealJoin: Create a new join between a virtual and a regular table.
realTable - Variable in class net.sf.basedb.core.RawDataType
RealTable - Class in net.sf.basedb.core: This class defines constants that are used to specify a table in the regular (non-dynamic) database while doing analysis with dynamic queries.
RealTable(String, String) - Constructor for class net.sf.basedb.core.RealTable: Creates a new table.
reattachItem(T, boolean) - Method in class net.sf.basedb.core.DbControl: Reattach a detached item from this DbControl.
recalculateFreeWells(ProgressReporter) - Static method in class net.sf.basedb.core.Update: Vefify and update the free wells of all bioplates.
recalculateRemainingQuantity(ProgressReporter) - Static method in class net.sf.basedb.core.Update: Vefify and update the remaining quantity of all biomaterials.
received - Variable in class net.sf.basedb.core.signal.DelegatingSignalHandler: List holding received signals.
received - Variable in class net.sf.basedb.core.signal.EnhancedThreadSignalHandler
received - Variable in class net.sf.basedb.core.signal.ProgressReporterSignalHandler
receiverId - Variable in class net.sf.basedb.core.signal.AbstractSignalReceiver
receiverId - Variable in class net.sf.basedb.core.signal.LocalSignalReceiver
receivers - Static variable in class net.sf.basedb.core.signal.LocalSignalReceiver: Holds all registered signal receivers.
recent - Variable in class net.sf.basedb.clients.web.taglib.Select: List of recently used items.
reconnect() - Method in class net.sf.basedb.core.DbControl: Deprecated.
In 3.12. Applications should use separate DbControl instead.
reconnect(Connection) - Method in class net.sf.basedb.core.hibernate.SessionWrapper
recursive - Variable in class net.sf.basedb.util.OlderThanFileFilter
recycle(DbControl, Annotatable) - Method in class net.sf.basedb.clients.web.extensions.list.RelatedItemHelper: Re-cycle transactions if needed and re-load the given item in the new transaction.
redefinedColumnNames - Variable in class net.sf.basedb.util.basefile.BaseFileParser
REF_SEQ_GTF - Static variable in class net.sf.basedb.core.DataFileType: The external ID for the file type representing a GTF reference file that define the features on an array design that we are interested in.
refColumns - Variable in class net.sf.basedb.core.dbengine.TableInfo.ForeignKeyInfo
referenceFactor - Variable in class net.sf.basedb.core.data.UnitData
referenceNotFoundErrorParameter - Static variable in class net.sf.basedb.plugins.batchimport.AbstractItemImporter
referenceOffset - Variable in class net.sf.basedb.core.data.UnitData
referenceUnit - Variable in class net.sf.basedb.core.data.QuantityData
ReflectValidationRuleActionFactory - Class in net.sf.basedb.util.overview.extensions: Factory implementation for validation rule actions that uses reflection to access the value of a public static field and return that as the validation rule.
ReflectValidationRuleActionFactory() - Constructor for class net.sf.basedb.util.overview.extensions.ReflectValidationRuleActionFactory
refName - Variable in class net.sf.basedb.core.dbengine.TableInfo.ForeignKeyInfo
refresh(Object) - Method in class net.sf.basedb.core.hibernate.SessionWrapper
refresh(Object) - Method in class net.sf.basedb.core.hibernate.StatelessSessionWrapper
refresh(Object, Map<String, Object>) - Method in class net.sf.basedb.core.hibernate.SessionWrapper
refresh(Object, LockModeType) - Method in class net.sf.basedb.core.hibernate.SessionWrapper
refresh(Object, LockModeType, Map<String, Object>) - Method in class net.sf.basedb.core.hibernate.SessionWrapper
refresh(Object, LockMode) - Method in class net.sf.basedb.core.hibernate.SessionWrapper
refresh(Object, LockMode) - Method in class net.sf.basedb.core.hibernate.StatelessSessionWrapper
refresh(Object, LockOptions) - Method in class net.sf.basedb.core.hibernate.SessionWrapper
refresh(String, Object) - Method in class net.sf.basedb.core.hibernate.SessionWrapper
refresh(String, Object) - Method in class net.sf.basedb.core.hibernate.StatelessSessionWrapper
refresh(String, Object, LockMode) - Method in class net.sf.basedb.core.hibernate.StatelessSessionWrapper
refresh(String, Object, LockOptions) - Method in class net.sf.basedb.core.hibernate.SessionWrapper
refresh(Session, BasicData) - Static method in class net.sf.basedb.core.HibernateUtil: Reload the data from the database for a given entity.
refreshItem(BasicItem) - Method in class net.sf.basedb.core.DbControl: Reload the item from the database.
regexp - Variable in class net.sf.basedb.core.ExtendedPropertyLinker
regexp - Variable in class net.sf.basedb.core.query.RlikeRestriction
RegexpFileFilter - Class in net.sf.basedb.util: An implementation of the FileFilter interface that filter files and directories based on regular expressions.
RegexpFileFilter(String, String) - Constructor for class net.sf.basedb.util.RegexpFileFilter: Create a new file filter from a string regular expressions.
RegexpFileFilter(Pattern, Pattern) - Constructor for class net.sf.basedb.util.RegexpFileFilter: Create a new file filter from patterns.
region - Variable in class net.sf.basedb.util.GeoLocation
register(Registry, String, String) - Static method in class net.sf.basedb.clients.web.extensions.list.ListColumnUtil
register(Registry, String, String) - Static method in class net.sf.basedb.clients.web.extensions.toolbar.ToolbarUtil
registerAgent() - Method in class net.sf.basedb.clients.jobagent.AgentController
registerCheckedNodeLoader(Object, Class<? extends NodeLoader<? extends BasicItem>>) - Method in class net.sf.basedb.util.overview.loader.BasicItemNodeLoaderFactory: Register a node loader implementation that you are sure fulfills the requirements.
registerCheckedNodeValidator(Object, Class<?>) - Method in class net.sf.basedb.util.overview.validator.BasicItemNodeValidatorFactory: Register a node loader implementation that you are sure fulfills the requirements.
registerCleanup(Object, Runnable) - Static method in class net.sf.basedb.core.Application: Register an action that needs to be performed when the monitored object becomes unreachable.
registerConverter(Object, JepConversionFunction<?>) - Static method in class net.sf.basedb.util.jep.convert.ConverterFactory: Add a converter for a specific object.
registerCustomRequestHandlers(MultiProtocolRequestHandler) - Method in class net.sf.basedb.clients.jobagent.Agent
registerDefaultNodeLoaders() - Method in class net.sf.basedb.util.overview.loader.BasicItemNodeLoaderFactory: Registers default item node loaders from BioSource to Experiment, etc.
registerDefaultNodeValidators() - Method in class net.sf.basedb.util.overview.validator.BasicItemNodeValidatorFactory: Registers default item node validators from BioSource to Experiment, etc.
registerDelayedFilters(Metadata) - Method in class net.sf.basedb.core.HibernateUtil.FilterConfigurator: Register all filters that has been stored by HibernateUtil.FilterConfigurator.createItemSpecificFilter(String, Item, String, Element)
Registered - Interface in net.sf.basedb.core: Items that implements this interface has their registration date stored in the database.
RegisteredAbout(About) - Constructor for class net.sf.basedb.util.extensions.Registry.RegisteredAbout: Create a new registered about by copying the information from the parameter.
registeredColumnMapping - Static variable in class net.sf.basedb.plugins.batchimport.AbstractItemImporter: Column mapping parameter for the item registration date.
RegisteredData - Interface in net.sf.basedb.core.data: Adds the date an item was registered in the database.
RegisteredEventHandler(EventHandler, EventFilter, ClassLoader) - Constructor for class net.sf.basedb.util.extensions.Registry.RegisteredEventHandler
RegisteredExtension(Extension<A>, Registry.RegisteredExtensionPoint<? super A>, ClassLoader) - Constructor for class net.sf.basedb.util.extensions.Registry.RegisteredExtension: Create a new registered extension by copying the information from the parameter.
RegisteredExtensionPoint(ExtensionPoint<A>, ClassLoader) - Constructor for class net.sf.basedb.util.extensions.Registry.RegisteredExtensionPoint: Create a new registered extension point by copying the information from the parameter.
registerEditTab(Registry, String, String) - Static method in class net.sf.basedb.clients.web.extensions.edit.EditUtil
registeredMapper - Variable in class net.sf.basedb.plugins.batchimport.AnnotationTypeImporter
registeredMapper - Variable in class net.sf.basedb.plugins.batchimport.ArrayBatchImporter
registeredMapper - Variable in class net.sf.basedb.plugins.batchimport.ArrayDesignImporter
registeredMapper - Variable in class net.sf.basedb.plugins.batchimport.ArraySlideImporter
registeredMapper - Variable in class net.sf.basedb.plugins.batchimport.BioPlateImporter
registeredMapper - Variable in class net.sf.basedb.plugins.batchimport.BioSourceImporter
registeredMapper - Variable in class net.sf.basedb.plugins.batchimport.DerivedBioAssayImporter
registeredMapper - Variable in class net.sf.basedb.plugins.batchimport.ExtractImporter
registeredMapper - Variable in class net.sf.basedb.plugins.batchimport.KitImporter
registeredMapper - Variable in class net.sf.basedb.plugins.batchimport.PhysicalBioAssayImporter
registeredMapper - Variable in class net.sf.basedb.plugins.batchimport.RawBioAssayImporter
registeredMapper - Variable in class net.sf.basedb.plugins.batchimport.SampleImporter
registeredMapper - Variable in class net.sf.basedb.plugins.batchimport.TagImporter
registerEventHandler(EventHandler, EventFilter, ClassLoader) - Method in class net.sf.basedb.util.extensions.Registry: Register an event handler for responding to events happening to extension points and extensions in the registry.
registerExtension(Extension<A>, ClassLoader) - Method in class net.sf.basedb.util.extensions.Registry: Register an extension.
registerExtensionPoint(ExtensionPoint<A>, ClassLoader) - Method in class net.sf.basedb.util.extensions.Registry: Register an extension point.
registerExtensionPoints(RegisterExtensionsProcessor.FileData, Registry, boolean) - Method in class net.sf.basedb.util.extensions.manager.processor.RegisterExtensionsProcessor
registerExtensionPoints(Registry) - Static method in class net.sf.basedb.clients.web.extensions.edit.EditUtil: Registers tabcontrol and on-save extension points with the given registry.
registerExtensionPoints(Registry) - Static method in class net.sf.basedb.clients.web.extensions.list.ListColumnUtil
registerExtensionPoints(Registry) - Static method in class net.sf.basedb.clients.web.extensions.toolbar.ToolbarUtil
registerExtensionPoints(Registry, boolean) - Method in class net.sf.basedb.util.extensions.xml.XmlLoader: Register all loaded extension points with a registry.
registerExtensions(RegisterExtensionsProcessor.FileData, ExtensionsManager, boolean) - Method in class net.sf.basedb.util.extensions.manager.processor.RegisterExtensionsProcessor
registerExtensions(Registry, boolean) - Method in class net.sf.basedb.util.extensions.xml.XmlLoader: Register all loaded extensions with a registry.
RegisterExtensionsProcessor - Class in net.sf.basedb.util.extensions.manager.processor: Extension file processor implementation that will load the extension definitions from each file and register them with the registry that is managed by the manager.
RegisterExtensionsProcessor(XmlLoader, ProcessResults) - Constructor for class net.sf.basedb.util.extensions.manager.processor.RegisterExtensionsProcessor: Create a new processor.
RegisterExtensionsProcessor.FileData - Class in net.sf.basedb.util.extensions.manager.processor: Keep track of the extension points and extensions found in a file.
registerFactory(RegisterExtensionsProcessor.FileData, Object) - Method in class net.sf.basedb.util.extensions.manager.processor.RegisterExtensionsProcessor: Register factory parameters for the given factory instance.
registerFileOnlyRawDataType(RawDataType) - Static method in class net.sf.basedb.core.RawDataTypes
registerFormatter(Class<? extends T>, Formatter<T>) - Method in class net.sf.basedb.util.formatter.MultiFormatter: Register a formatter for the specified class.
registerHandler(RequestHandler, String...) - Method in class net.sf.basedb.clients.jobagent.handlers.DefaultRequestHandler
registerMetadata(ObjectKey<M>, M) - Method in class net.sf.basedb.util.extensions.manager.ExtensionsFile.WriteableExtensionsFile: Register metadata about an object.
registerNodeLoader(Object, Class<? extends NodeLoader<? extends BasicItem>>) - Method in class net.sf.basedb.util.overview.loader.BasicItemNodeLoaderFactory: Register a node loader implementation.
registerNodeValidator(Item, Class<? extends NodeValidator<? extends BasicItem>>) - Method in class net.sf.basedb.util.overview.validator.BasicItemNodeValidatorFactory: Register a node validator implementation.
registerObject(ObjectKey<?>, ExtensionsFile) - Method in class net.sf.basedb.util.extensions.manager.ExtensionsManager: Register an object as defined by the given extensions file.
registerObject(ObjectKey<O>, O) - Method in class net.sf.basedb.util.extensions.manager.ExtensionsFile.WriteableExtensionsFile: Register an object as "defined" by this extensions file.
registerOnSave(Registry, String, String, RethrowErrorHandlerFactory) - Static method in class net.sf.basedb.clients.web.extensions.edit.EditUtil
registerParameters(List<PluginParameter<?>>) - Method in class net.sf.basedb.core.PluginRequest: Keep track of all parameters so that we can save label and description in the ParameterValuesImpl.saveParameters(Job, Map) method.
registerProtocols(RequestHandler, String...) - Method in class net.sf.basedb.clients.jobagent.handlers.MultiProtocolRequestHandler: Register a handler for one or more protocols.
registerRequestHandler(RequestHandler, String...) - Method in class net.sf.basedb.clients.jobagent.Agent: Register a request handler for one or more protocols.
registerSignal(String, String, String) - Static method in class net.sf.basedb.core.signal.Signal: Register a signal.
registerSignalHandler(SignalHandler) - Method in class net.sf.basedb.clients.web.util.SimpleSignalProgressReporter: This return null when there is no need for a global id.
registerSignalHandler(SignalHandler) - Method in class net.sf.basedb.core.signal.AbstractSignalReceiver: Register a signal handler with this receiver.
registerSignalHandler(SignalHandler) - Method in class net.sf.basedb.core.signal.DelegatingSignalHandler: Register a signal handler to delegate to.
registerSignalHandler(SignalHandler) - Method in interface net.sf.basedb.core.signal.SignalReceiver: Register a signal handler with this receiver.
registerSignalReceiver(SignalReceiver) - Method in class net.sf.basedb.core.PluginExecutionRequest: Register a signal receiver that will receive signals for this job.
registry - Static variable in class net.sf.basedb.clients.web.extensions.ExtensionsControl
registry - Variable in class net.sf.basedb.util.extensions.ExtensionPointContext
registry - Variable in class net.sf.basedb.util.extensions.manager.ExtensionsManager
Registry - Class in net.sf.basedb.util.extensions: A registry for keeping track of extensions points and installed extensions.
Registry() - Constructor for class net.sf.basedb.util.extensions.Registry: Create a new empty registry.
Registry.AttributeKey - Class in net.sf.basedb.util.extensions: Identifies attribute.
Registry.RegisteredAbout - Class in net.sf.basedb.util.extensions
Registry.RegisteredEventHandler - Class in net.sf.basedb.util.extensions
Registry.RegisteredExtension<A extends Action> - Class in net.sf.basedb.util.extensions: Internal representation of an extension.
Registry.RegisteredExtensionPoint<A extends Action> - Class in net.sf.basedb.util.extensions: Internal representation of an extension point.
registryBuilder - Variable in class net.sf.basedb.core.ServiceSessionControl.SessionFactoryConfiguration
RelatedItemAnnotationColumn - Class in net.sf.basedb.clients.web.extensions.list: Related item column that load annotation values from the parent or child items.
RelatedItemAnnotationColumn(DbControl, int, RelatedItemColumn.Specification, RelatedItemHelper, AnnotationType) - Constructor for class net.sf.basedb.clients.web.extensions.list.RelatedItemAnnotationColumn
RelatedItemColumn - Class in net.sf.basedb.clients.web.extensions.list: A column action implementation that finds a parent or child item of a given subtype and then get an annotation or other property value from it.
RelatedItemColumn(DbControl, int, RelatedItemColumn.Specification, RelatedItemHelper) - Constructor for class net.sf.basedb.clients.web.extensions.list.RelatedItemColumn
RelatedItemColumn.Specification - Class in net.sf.basedb.clients.web.extensions.list: Represents a specification for loading a related parent or child item.
RelatedItemColumnActionFactory - Class in net.sf.basedb.clients.web.extensions.list: Action factory for adding columns to a table that pull data from a parent or child item from an arbitrary location up or down the chain of linked items.
RelatedItemColumnActionFactory() - Constructor for class net.sf.basedb.clients.web.extensions.list.RelatedItemColumnActionFactory
RelatedItemErrorColumn - Class in net.sf.basedb.clients.web.extensions.list: Related item column that displays an error message.
RelatedItemErrorColumn(int, RelatedItemColumn.Specification, RelatedItemHelper, String) - Constructor for class net.sf.basedb.clients.web.extensions.list.RelatedItemErrorColumn
RelatedItemExtensionColumn - Class in net.sf.basedb.clients.web.extensions.list: Related item column that get values from an extension.
RelatedItemExtensionColumn(DbControl, int, RelatedItemColumn.Specification, RelatedItemHelper, ListColumnAction<Annotatable, ?>) - Constructor for class net.sf.basedb.clients.web.extensions.list.RelatedItemExtensionColumn
RelatedItemHelper - Class in net.sf.basedb.clients.web.extensions.list: Helper class for storing request-scoped objects that may be useful to re-use between multiple columns.
RelatedItemHelper(SessionControl, JspContext, boolean) - Constructor for class net.sf.basedb.clients.web.extensions.list.RelatedItemHelper
RelatedItemHelper.CloseMyDbControl - Class in net.sf.basedb.clients.web.extensions.list
RelatedItemListColumn - Class in net.sf.basedb.clients.web.extensions.list: Related item column that get the item lists that the parent or child item is a member of.
RelatedItemListColumn(DbControl, int, RelatedItemColumn.Specification, Filter<? super ItemList>, RelatedItemHelper) - Constructor for class net.sf.basedb.clients.web.extensions.list.RelatedItemListColumn
RelatedItemMultiHopColumn - Class in net.sf.basedb.clients.web.extensions.list: Related item column that get values from multiple hops betweeen child->parent->child.
RelatedItemMultiHopColumn(DbControl, int, RelatedItemColumn.Specification, RelatedItemHelper, RelatedItemColumn) - Constructor for class net.sf.basedb.clients.web.extensions.list.RelatedItemMultiHopColumn
RelatedItemPropertyColumn - Class in net.sf.basedb.clients.web.extensions.list: Related item column that get values from parent or child items by specifying a "property path".
RelatedItemPropertyColumn(DbControl, int, RelatedItemColumn.Specification, RelatedItemHelper, Metadata.PropertyPath<? super Annotatable, ?>) - Constructor for class net.sf.basedb.clients.web.extensions.list.RelatedItemPropertyColumn
relatedItems - Static variable in class net.sf.basedb.core.ItemSubtype
relatedSubtypes - Variable in class net.sf.basedb.core.data.ItemSubtypeData
release() - Method in class net.sf.basedb.core.hibernate.SchemaGenerator.CollectSqlTarget
releaseRemoteSlot(String) - Method in class net.sf.basedb.clients.jobagent.slotmanager.MasterSlotManager: Release the remote slot with the given id.
releaseSavepoint(Connection, Savepoint, String) - Method in class net.sf.basedb.core.AbstractSqlQuery: Release the given savepoint.
releaseSlot(Slot) - Method in class net.sf.basedb.clients.jobagent.slotmanager.InternalSlotManager
releaseSlot(Slot) - Method in class net.sf.basedb.clients.jobagent.slotmanager.RemoteSlotManager
releaseSlot(Slot) - Method in interface net.sf.basedb.clients.jobagent.slotmanager.SlotManager: Called by the job agent when the job has finished exeuting.
reload - Variable in class net.sf.basedb.core.Keyring: TRUE if the Timer has signaled that it is time to reload the information.
reload() - Method in class net.sf.basedb.core.Keyring: Reload all permission information
reloadPermissions() - Method in class net.sf.basedb.core.SessionControl: Tell the core to reload the logged in users permission the next time the client application needs to check the permissions.
reloadSettings(boolean, boolean) - Method in class net.sf.basedb.core.SessionControl: Reloads user- and client-specific settings.
ReloadTask() - Constructor for class net.sf.basedb.core.Keyring.ReloadTask
remainingQuantity - Variable in class net.sf.basedb.core.data.MeasuredBioMaterialData
RemainingQuantityAction(DbControl, MeasuredBioMaterialData) - Constructor for class net.sf.basedb.core.MeasuredBioMaterial.RemainingQuantityAction
remapAllTo(ImageRemapper, String) - Static method in class net.sf.basedb.clients.web.extensions.skin.ImageRemapperUtil: Scan the given url for images (png and gif) and remap them.
remapDir - Variable in class net.sf.basedb.clients.web.extensions.skin.FixedSkinActionFactory
remapImages(ImageRemapper) - Method in class net.sf.basedb.clients.web.extensions.skin.FixedSkinActionFactory.MySkinAction
remapImages(ImageRemapper) - Method in interface net.sf.basedb.clients.web.extensions.skin.SkinAction: Remap images to another location.
remember - Variable in class net.sf.basedb.clients.web.taglib.tab.TabControl: If it should try to remember the last active tab on the page
rememberLast - Variable in class net.sf.basedb.util.extensions.LoggingErrorHandlerFactory
rememberLastLogin - Variable in class net.sf.basedb.clients.web.extensions.login.LoginFormBean
rememberLastLogin() - Method in interface net.sf.basedb.clients.web.extensions.login.LoginFormAction: If TRUE, the browser is asked to remember the last login used.
rememberLastLogin() - Method in class net.sf.basedb.clients.web.extensions.login.LoginFormBean
rememberLastLogin() - Method in class net.sf.basedb.clients.web.extensions.login.PasswordLoginFormFactory
remote - Variable in class net.sf.basedb.clients.jobagent.Agent
remoteHost - Variable in class net.sf.basedb.clients.jobagent.slotmanager.RemoteSlotManager
remoteId - Variable in class net.sf.basedb.core.data.SessionData
remoteId - Variable in class net.sf.basedb.core.data.UserDeviceData
remoteId - Variable in class net.sf.basedb.core.SessionControl: The remote IP.
remotePort - Variable in class net.sf.basedb.clients.jobagent.slotmanager.RemoteSlotManager
remoteRequestHandler - Variable in class net.sf.basedb.clients.jobagent.slotmanager.MasterSlotManager
RemoteSlot(Slot) - Constructor for class net.sf.basedb.clients.jobagent.slotmanager.MasterSlotManager.RemoteSlot
RemoteSlotManager - Class in net.sf.basedb.clients.jobagent.slotmanager: Slot manager implementation that requests slots from another job agent.
RemoteSlotManager() - Constructor for class net.sf.basedb.clients.jobagent.slotmanager.RemoteSlotManager
RemoteSlotManager.RemoteSlotPinger - Class in net.sf.basedb.clients.jobagent.slotmanager: Task that is scheduled at regular intervals to send ping commands to the remote host.
RemoteSlotPinger(RemoteSlotManager) - Constructor for class net.sf.basedb.clients.jobagent.slotmanager.RemoteSlotManager.RemoteSlotPinger
RemoteSlotRequestHandler(MasterSlotManager) - Constructor for class net.sf.basedb.clients.jobagent.slotmanager.MasterSlotManager.RemoteSlotRequestHandler
remoteSlots - Variable in class net.sf.basedb.clients.jobagent.slotmanager.MasterSlotManager
remoteSlots - Variable in class net.sf.basedb.clients.jobagent.slotmanager.RemoteSlotManager
RemoteSlotTimeoutChecker(MasterSlotManager) - Constructor for class net.sf.basedb.clients.jobagent.slotmanager.MasterSlotManager.RemoteSlotTimeoutChecker
Removable - Interface in net.sf.basedb.core: A Removable item is an item that can be flagged as removed.
REMOVABLE_FILTER - Static variable in class net.sf.basedb.core.QueryRuntimeFilterFactory
RemovableData - Interface in net.sf.basedb.core.data: A removable item is an item that can be flagged as removed.
RemovableFilter() - Constructor for class net.sf.basedb.core.QueryRuntimeFilterFactory.RemovableFilter
removableItems - Static variable in class net.sf.basedb.core.Metadata
RemovableUtil - Class in net.sf.basedb.util
RemovableUtil() - Constructor for class net.sf.basedb.util.RemovableUtil
remove - Variable in class net.sf.basedb.util.annotations.InheritSpecification
remove() - Method in class net.sf.basedb.clients.web.servlet.PlotServlet.CFResultIterator: Not supported.
remove() - Method in class net.sf.basedb.core.DataResultIterator: Not supported.
remove() - Method in class net.sf.basedb.core.DynamicResultIterator: Not supported.
remove() - Method in class net.sf.basedb.core.ItemResultIterator: Not supported.
remove() - Method in class net.sf.basedb.core.ItemResultList.ResultListIterator: This operation is not supported.
remove() - Method in class net.sf.basedb.core.ItemResultList.ResultListListIterator: This operation is not supported.
remove() - Method in class net.sf.basedb.core.ReporterScoreResultIterator: Not supported.
remove() - Method in class net.sf.basedb.core.ScrollIterator: Not supported.
remove() - Method in class net.sf.basedb.plugins.RawDataFlatFileImporter.FileIterator
remove() - Method in class net.sf.basedb.util.ArrayIterator: This operation is not supported.
remove() - Method in class net.sf.basedb.util.extensions.ActionIterator: Not supported.
remove() - Method in class net.sf.basedb.util.NestedIterator: This operation is not supported.
remove() - Method in class net.sf.basedb.util.query.MultiQueryIterator
remove() - Method in class net.sf.basedb.util.Tree.ElementIterator: Not supported.
remove() - Method in class net.sf.basedb.util.Tree.EntryIterator: Not supported.
remove(int) - Method in class net.sf.basedb.core.AbstractResultList: Not supported.
remove(int) - Method in class net.sf.basedb.core.UnmodifiableResultList: Not supported.
remove(int) - Method in class net.sf.basedb.util.Enumeration
remove(Object) - Method in class net.sf.basedb.core.AbstractResultList: Not supported.
remove(Object) - Method in class net.sf.basedb.core.hibernate.SessionWrapper
remove(Object) - Method in class net.sf.basedb.core.UnmodifiableResultList: Not supported.
remove(Object) - Method in class net.sf.basedb.util.formatter.LookupFormatter: Remove an entry from the lookup map.
remove(Object) - Method in class net.sf.basedb.util.Tree: Not supported.
remove(Listable) - Method in class net.sf.basedb.core.ItemList.DelayedAdditionManager
remove(Listable) - Method in class net.sf.basedb.core.ItemList: Deprecated.
In 3.15, use ItemList.removeItem(Listable item) instead
remove(IdListRestriction) - Method in class net.sf.basedb.core.query.IdListRestriction: Merge this id list with another list by removing ids that are found in the other list.
REMOVE - net.sf.basedb.core.log.ChangeType
REMOVE_ONLY - net.sf.basedb.core.ItemList.SynchronizeOption: Synchronize the members by removing items that doesn't match the filter.
removeAll(Collection<?>) - Method in class net.sf.basedb.core.AbstractResultList: Not supported.
removeAll(Collection<?>) - Method in class net.sf.basedb.core.UnmodifiableResultList: Not supported.
removeAll(Collection<?>) - Method in class net.sf.basedb.util.Tree: Not supported.
removeAll(ItemList) - Method in class net.sf.basedb.core.ItemList: Remove all items from this list that are present in the other list.
removeAll(ItemList.DelayedAdditionManager) - Method in class net.sf.basedb.core.ItemList.DelayedAdditionManager
removeAll(ReporterList) - Method in class net.sf.basedb.core.ReporterList: Remove all reporters from this list that are present in the other list.
removeAllInherited(AnnotationSet) - Method in class net.sf.basedb.core.AnnotationSet: Utility method to stop inheriting all annotations in the given annotation set.
removeAllMembers() - Method in class net.sf.basedb.core.FileSet: Remove all members in a file set.
removeAllOfType(DataFileType) - Method in class net.sf.basedb.core.FileSet: Remove all member files of the given type.
removeAllOfTypeExcept(DataFileType, File) - Method in class net.sf.basedb.core.FileSet: Remove all member files of the given type.
removeAllPropertyFilters() - Method in class net.sf.basedb.core.ItemContext: Remove all property filter from this context.
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 - 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
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 - 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 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 - 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 - 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 - 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 - 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 net.sf.basedb.core.hibernate.SchemaGenerator.Mode
requireEmptyDatabase() - Method in enum 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
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 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 - 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 - 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 - 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 - 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 - 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 - net.sf.basedb.core.Item: The item is a RootRawBioAssay.
RootRawBioAssayData - Class in net.sf.basedb.core.data: This class holds the link between experiments and raw bioassays including an annotation set that is representing the experimental factor values.
RootRawBioAssayData() - Constructor for class net.sf.basedb.core.data.RootRawBioAssayData
RootRawBioAssayLoader - Class in net.sf.basedb.util.overview.loader: Node loader implementation for root raw bioassays.
RootRawBioAssayLoader() - Constructor for class net.sf.basedb.util.overview.loader.RootRawBioAssayLoader
rootRawBioAssays - Variable in class net.sf.basedb.core.data.ExperimentData
rootTable - Variable in class net.sf.basedb.core.DynamicQuery
rootTable - Variable in class net.sf.basedb.core.DynamicRawDataQuery
rootType - Variable in class net.sf.basedb.core.AbstractEntityQuery: The root item type we start with in the query. eq.
row - Variable in class net.sf.basedb.clients.web.taglib.table.PropertyFilter
row - Variable in class net.sf.basedb.core.data.BioWellData
row - Variable in class net.sf.basedb.core.data.FeatureData
row - Variable in class net.sf.basedb.core.data.MappingCoordinate: The row number.
row - Variable in class net.sf.basedb.core.data.PlateCoordinate: The row number.
row - Variable in class net.sf.basedb.core.data.RawData
row - Variable in class net.sf.basedb.core.data.WellData
row - Variable in class net.sf.basedb.core.FeatureCoordinate: The row of this feature.
Row - Class in net.sf.basedb.clients.web.taglib.table: This tag defines a new row in the table.
Row() - Constructor for class net.sf.basedb.clients.web.taglib.table.Row
rowclass - Static variable in class net.sf.basedb.clients.web.taglib.table.Table: The class names for even and odd row respectively.
rowColumnMapping - Static variable in class net.sf.basedb.plugins.PlateFlatFileImporter
rowColumnMapping - Static variable in class net.sf.basedb.plugins.RawDataFlatFileImporter
rowColumnMapping - Static variable in class net.sf.basedb.plugins.ReporterMapFlatFileImporter
rowIdList - Variable in class net.sf.basedb.core.ItemContext.RowRestrictions
rowIndex - Variable in class net.sf.basedb.core.ItemContext.RowRestrictions
rowIndex - Variable in class net.sf.basedb.core.PropertyFilter
rowIndex - Variable in class net.sf.basedb.util.bfs.AnnotationModel
rowMapper - Variable in class net.sf.basedb.plugins.PlateFlatFileImporter
rowMapper - Variable in class net.sf.basedb.plugins.RawDataFlatFileImporter
rowMapper - Variable in class net.sf.basedb.plugins.ReporterMapFlatFileImporter
rowNo - Variable in class net.sf.basedb.util.excel.XlsxTableWriter
rowNum - Variable in class net.sf.basedb.clients.web.plugins.XlsxTemplate
rowOffset - Variable in class net.sf.basedb.util.parser.FlatFileParser.ExcelData
rowRestrictions - Variable in class net.sf.basedb.core.ItemContext.QueryRestrictions
RowRestrictions(int) - Constructor for class net.sf.basedb.core.ItemContext.RowRestrictions
rows - Variable in class net.sf.basedb.core.data.PlateGeometryData
Rows - Class in net.sf.basedb.clients.web.taglib.table: This tag is a place-holder for <tbl:row> tags.
Rows() - Constructor for class net.sf.basedb.clients.web.taglib.table.Rows
rowSeparator - Variable in class net.sf.basedb.util.excel.XlsxToCsvUtil
rowsPerPage - Variable in class net.sf.basedb.clients.web.taglib.table.Navigator: The number of rows to display on a single page.
rowsPerPage - Variable in class net.sf.basedb.core.data.ContextData
rowsPerPage - Variable in class net.sf.basedb.core.ItemContext
rs - Variable in class net.sf.basedb.core.migrate.AbstractResultWriter
RssNewsFeed - Class in net.sf.basedb.clients.web.servlet: A servlet that generates a RSS feed from the public news on the BASE server.
RssNewsFeed() - Constructor for class net.sf.basedb.clients.web.servlet.RssNewsFeed
rule - Variable in class net.sf.basedb.util.overview.extensions.ReflectValidationRuleActionFactory
rule - Variable in class net.sf.basedb.util.overview.Failure
ruleDenied - Variable in class net.sf.basedb.util.overview.validator.BasicNodeValidator
ruleMissing - Variable in class net.sf.basedb.util.overview.validator.BasicNodeValidator
run() - Method in class net.sf.basedb.clients.jobagent.executors.ProcessJobExecutor.StreamRedirector
run() - Method in class net.sf.basedb.clients.jobagent.executors.ThreadJobExecutor.ShutdownHook
run() - Method in class net.sf.basedb.clients.jobagent.JobQueueChecker
run() - Method in class net.sf.basedb.clients.jobagent.JobRunner: Find a free slot to use and then pass control to the JobExecutor.executeJob(SessionControl, Agent, Job, JobAgentSettings, Job.ExecutionTime) method.
run() - Method in class net.sf.basedb.clients.jobagent.slotmanager.MasterSlotManager.RemoteSlotTimeoutChecker
run() - Method in class net.sf.basedb.clients.jobagent.slotmanager.RemoteSlotManager.RemoteSlotPinger
run() - Method in class net.sf.basedb.core.Application.DbCleaner
run() - Method in class net.sf.basedb.core.Application.SessionControlCacheCleaner
run() - Method in class net.sf.basedb.core.DbControl.State
run() - Method in class net.sf.basedb.core.File.CharsetTesterThread: Runs in a separate thread.
run() - Method in class net.sf.basedb.core.InternalJobQueue.JobRunner: Execute the job.
run() - Method in class net.sf.basedb.core.InternalJobQueue: Check the database for jobs that are waiting to be executed.
run() - Method in class net.sf.basedb.core.Keyring.ReloadTask
run() - Method in class net.sf.basedb.core.PluginExecutionRequest
run() - Method in class net.sf.basedb.core.signal.SocketSignalReceiver.ListenerThread
run() - Method in class net.sf.basedb.util.annotations.RunnableInheritAnnotationsManager
run() - Method in class net.sf.basedb.util.FileCopyRunnable
run() - Method in class net.sf.basedb.util.jobagent.JobAgentServerConnection.ListenerThread
run() - Method in class net.sf.basedb.util.jobagent.JobAgentServerConnection.RequestHandlerThread
run() - Method in class net.sf.basedb.util.StaticCache.CleanupTask
run() - Method in class net.sf.basedb.util.StaticCache.State
run() - Method in class net.sf.basedb.util.timer.ThreadTimerTask
run() - Method in class net.sf.basedb.util.uri.http.HttpConnectionManager.TimeoutTimer
run(Stack) - Method in class net.sf.basedb.util.jep.ChannelFunction
run(Stack) - Method in class net.sf.basedb.util.jep.ExtraValueFunction
run(Stack) - Method in class net.sf.basedb.util.jep.FunctionSafeJep.UnknownFunction
run(Stack) - Method in class net.sf.basedb.util.jep.InReporterListFunction
run(Stack) - Method in class net.sf.basedb.util.jep.LeftFunction
run(Stack) - Method in class net.sf.basedb.util.jep.Log2Function
run(Stack) - Method in class net.sf.basedb.util.jep.MeanFunction
run(Stack) - Method in class net.sf.basedb.util.jep.NotInReporterListFunction
run(Stack) - Method in class net.sf.basedb.util.jep.PositionFunction
run(Stack) - Method in class net.sf.basedb.util.jep.RawChannelFunction
run(Stack) - Method in class net.sf.basedb.util.jep.RawFunction
run(Stack) - Method in class net.sf.basedb.util.jep.ReporterFunction
run(Stack) - Method in class net.sf.basedb.util.jep.ScoreFunction
run(Stack) - Method in class net.sf.basedb.util.jep.SimpleJepFunction
run(Stack) - Method in class net.sf.basedb.util.parser.ColFunction
run(Stack) - Method in class net.sf.basedb.util.parser.DataNoFunction
run(Stack) - Method in class net.sf.basedb.util.parser.DefaultItemFunction
run(Stack) - Method in class net.sf.basedb.util.parser.LineNoFunction
run(Request, Response, ProgressReporter) - Method in class net.sf.basedb.core.plugin.AbstractExporterPlugin: Checks the AbstractExporterPlugin.SAVE_AS parameter for the path to save the exported data.
run(Request, Response, ProgressReporter) - Method in interface net.sf.basedb.core.plugin.Plugin: Run the plugin.
run(Request, Response, ProgressReporter) - Method in class net.sf.basedb.plugins.AbstractFlatFileImporter: Implements the Request.COMMAND_EXECUTE command.
run(Request, Response, ProgressReporter) - Method in class net.sf.basedb.plugins.Base1PluginExecuter
run(Request, Response, ProgressReporter) - Method in class net.sf.basedb.plugins.BfsExporterPlugin
run(Request, Response, ProgressReporter) - Method in class net.sf.basedb.plugins.CdfFileReporterImporter
run(Request, Response, ProgressReporter) - Method in class net.sf.basedb.plugins.CloneReportersPlugin
run(Request, Response, ProgressReporter) - Method in class net.sf.basedb.plugins.executor.AbstractIOSupport: Accepts the IOSupport.COMMAND_EXECUTE_IO_JOB command.
run(Request, Response, ProgressReporter) - Method in class net.sf.basedb.plugins.executor.ExternalProgramExecutor
run(Request, Response, ProgressReporter) - Method in class net.sf.basedb.plugins.FormulaFilter
run(Request, Response, ProgressReporter) - Method in class net.sf.basedb.plugins.HelpImporter
run(Request, Response, ProgressReporter) - Method in class net.sf.basedb.plugins.IntensityCalculatorPlugin
run(Request, Response, ProgressReporter) - Method in class net.sf.basedb.plugins.JepExtraValueCalculator
run(Request, Response, ProgressReporter) - Method in class net.sf.basedb.plugins.JepIntensityTransformer
run(Request, Response, ProgressReporter) - Method in class net.sf.basedb.plugins.LowessNormalization
run(Request, Response, ProgressReporter) - Method in class net.sf.basedb.plugins.ManualDerivedBioAssayCreator
run(Request, Response, ProgressReporter) - Method in class net.sf.basedb.plugins.ManualTransformCreator
run(Request, Response, ProgressReporter) - Method in class net.sf.basedb.plugins.MedianRatioNormalization
run(Request, Response, ProgressReporter) - Method in class net.sf.basedb.plugins.PluginConfigurationImporter
run(Request, Response, ProgressReporter) - Method in class net.sf.basedb.util.zip.AbstractFileUnpacker
RUN_PLUGIN - 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 - net.sf.basedb.core.Item: The item is a Sample.
SampleData - Class in net.sf.basedb.core.data: This represents a sample.
SampleData() - Constructor for class net.sf.basedb.core.data.SampleData
SampleImporter - Class in net.sf.basedb.plugins.batchimport: Plug-in for importing sample items in a batch.
SampleImporter() - Constructor for class net.sf.basedb.plugins.batchimport.SampleImporter
SampleLoader - Class in net.sf.basedb.util.overview.loader: Node loader implementation for samples.
SampleLoader() - Constructor for class net.sf.basedb.util.overview.loader.SampleLoader
sampleQuery - Variable in class net.sf.basedb.plugins.batchimport.AbstractItemImporter
sampleSize - Variable in class net.sf.basedb.util.AnyToAnyLinkStatistics
SampleToBioSourceTransformer - Class in net.sf.basedb.util.listable: Source item transformer that transform sample items to their parent biosources.
SampleToBioSourceTransformer() - Constructor for class net.sf.basedb.util.listable.SampleToBioSourceTransformer
SampleToBioSourceTransformer(boolean) - Constructor for class net.sf.basedb.util.listable.SampleToBioSourceTransformer: Create a new sample to biosource transformer that only load parent biosources to sample that has a subtype with "push annotations" set.
SampleToChildSampleTransformer - Class in net.sf.basedb.util.listable: Source item transformer implementation that transform sample items to their child sample items.
SampleToChildSampleTransformer(boolean) - Constructor for class net.sf.basedb.util.listable.SampleToChildSampleTransformer: Create a new sample to child sample transformer.
SampleToChildSampleTransformer(boolean, boolean) - Constructor for class net.sf.basedb.util.listable.SampleToChildSampleTransformer: Create a new sample to child sample transformer that only load children that has a subtype with "push annotations" set.
SampleToExtractTransformer - Class in net.sf.basedb.util.listable: Source item transformer that transform sample items to their child extract.
SampleToExtractTransformer() - Constructor for class net.sf.basedb.util.listable.SampleToExtractTransformer
SampleToParentSampleTransformer - Class in net.sf.basedb.util.listable: Source item transformer implementation that transform sample items to their parent sample items.
SampleToParentSampleTransformer(boolean) - Constructor for class net.sf.basedb.util.listable.SampleToParentSampleTransformer: Create a new sample to parent sample transformer.
SampleToParentSampleTransformer(boolean, boolean) - Constructor for class net.sf.basedb.util.listable.SampleToParentSampleTransformer: Create a new sample to parent sample transformer that only load parents to samples that has a subtype with "push annotations" set.
SampleValidator - Class in net.sf.basedb.util.overview.validator: Validator implementation for sample.
SampleValidator() - Constructor for class net.sf.basedb.util.overview.validator.SampleValidator
SAMPLING - Static variable in class net.sf.basedb.core.Kit: The ID for the sampling kit type, for example a kit used when creating a Sample from a BioSource.
SAMPLING - Static variable in class net.sf.basedb.core.Protocol: The ID for the sampling protocol type, for example a protocol used when creating a Sample from a BioSource.
save() - Method in class net.sf.basedb.util.extensions.manager.Settings: Save the settings to disk.
save(Object) - Method in class net.sf.basedb.core.hibernate.SessionWrapper
save(String, Object) - Method in class net.sf.basedb.core.hibernate.SessionWrapper
SAVE_AS - Static variable in class net.sf.basedb.core.plugin.AbstractExporterPlugin: Parameter name for the AbstractExporterPlugin.getSaveAsParameter(String, String, String, boolean) parameter.
saveAllCurrentContexts(Session, UserData, ClientData) - Method in class net.sf.basedb.core.SessionControl
saveAllUserSettings(Session) - Method in class net.sf.basedb.core.SessionControl: Saves all user settings.
saveCurrentContextAs(Item, String, boolean, boolean) - Method in class net.sf.basedb.core.SessionControl: Same as: saveCurrentContextAs(item, "", 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 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 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 - 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 - net.sf.basedb.core.query.QuerySection
SELECT_FILTER - Static variable in class net.sf.basedb.clients.web.ModeInfo
SELECT_JOBAGENT - 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 - 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.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.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 - 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.SettingInfo - Class in net.sf.basedb.core: Internal class to hold information about a setting
SessionControl.UnverifiedDeviceInfo - Class in net.sf.basedb.core: Class for storing temporary device information for a user that has been authenticated but before a device has been verified.
SessionControlCacheCleaner() - Constructor for class net.sf.basedb.core.Application.SessionControlCacheCleaner
SessionData - Class in net.sf.basedb.core.data: This class holds information about a session.
SessionData() - Constructor for class net.sf.basedb.core.data.SessionData
SessionFactoryConfiguration - Class in net.sf.basedb.core.hibernate: Deprecated.
In 3.8, use ServiceSessionControl.createSessionFactoryConfiguration(String, String, int, ClassLoader) instead
SessionFactoryConfiguration(String, ClassLoader) - Constructor for class net.sf.basedb.core.hibernate.SessionFactoryConfiguration: Deprecated.

Create a configuration instance.
SessionFactoryConfiguration(String, String, int, ClassLoader) - Constructor for class net.sf.basedb.core.ServiceSessionControl.SessionFactoryConfiguration
sessionId - Variable in class net.sf.basedb.core.data.ChangeHistoryData
sessionId - Variable in class net.sf.basedb.core.log.TransactionDetails
sessionId - Variable in class net.sf.basedb.core.SessionControl.LoginInfo: The id of the SessionData.
sessions - Variable in class net.sf.basedb.core.data.ClientData
sessions - Variable in class net.sf.basedb.core.data.UserData
sessions - Variable in class net.sf.basedb.core.data.UserDeviceData
sessionSettings - Variable in class net.sf.basedb.core.SessionControl: Stores name and value of session settings.
sessionWithOptions() - Method in class net.sf.basedb.core.hibernate.SessionWrapper
SessionWrapper - Class in net.sf.basedb.core.hibernate: Wrapper around Hibernate sessions that includes a query cache.
SessionWrapper(Session) - Constructor for class net.sf.basedb.core.hibernate.SessionWrapper: Creates a new session wrapper
set(int, I) - Method in class net.sf.basedb.core.AbstractResultList: Not supported.
set(int, T) - Method in class net.sf.basedb.core.UnmodifiableResultList: Not supported.
set(Object, E) - Method in class net.sf.basedb.util.ClassLocal: Store an object and associate it with the class of the specified instance.
set(Object, Object, SessionFactoryImplementor) - Method in class net.sf.basedb.core.ExtendedPropertyAccessor.GetterSetter: Set the value of the extended property.
set(T) - Method in class net.sf.basedb.core.ItemResultList.ResultListListIterator: This operation is not supported.
SET_OWNER - net.sf.basedb.core.Permission: This permission allows a user change the owner of an item.
SET_PERMISSION - 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.
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 net.sf.basedb.plugins.PrintMapFlatFileImporter.Section
setBlockSizeX(int) - Method in class net.sf.basedb.core.ArrayDesignBlock: Set the number of columns in this block.
setBlockSizeX(int) - Method in class net.sf.basedb.core.data.ArrayDesignBlockData
setBlockSizeX(Integer) - Method in class net.sf.basedb.plugins.PrintMapFlatFileImporter.MetaBlock
setBlockSizeY(int) - Method in class net.sf.basedb.core.ArrayDesignBlock: Set the number of rows in this block.
setBlockSizeY(int) - Method in class net.sf.basedb.core.data.ArrayDesignBlockData
setBlockSizeY(Integer) - Method in class net.sf.basedb.plugins.PrintMapFlatFileImporter.MetaBlock
setBlockValue(PrintMapFlatFileImporter.MetaBlock, FlatFileParser.Line) - Method in class net.sf.basedb.plugins.PrintMapFlatFileImporter
setBofMarkerRegexp(Pattern) - Method in class net.sf.basedb.util.parser.FlatFileParser: Set a regular expression that maches a beginning-of-file marker.
setBoolean(int, boolean) - Method in class net.sf.basedb.core.hibernate.QueryWrapper: Deprecated.
setBoolean(String, boolean) - Method in class net.sf.basedb.core.hibernate.QueryWrapper: Deprecated.
setBooleanValues(List<Boolean>) - Method in class net.sf.basedb.core.data.annotations.AnnotationLink
setBuild(int) - Method in class net.sf.basedb.core.data.SchemaVersionData
setBulletlist(boolean) - Method in class net.sf.basedb.clients.web.taglib.table.CellValue
setButtonclass(String) - Method in class net.sf.basedb.clients.web.taglib.Select
setButtonicon(String) - Method in class net.sf.basedb.clients.web.taglib.Select
setButtonstyle(String) - Method in class net.sf.basedb.clients.web.taglib.Select
setButtonTag(String) - Method in class net.sf.basedb.clients.web.extensions.toolbar.CompactButtonRenderer: Set the HTML tag to use for the "button".
setButtonTag(String) - Method in class net.sf.basedb.clients.web.extensions.toolbar.CompactButtonRendererFactory: Set the HTML tag to use for the "button".
setButtontitle(String) - Method in class net.sf.basedb.clients.web.taglib.Select
setByte(int, byte) - Method in class net.sf.basedb.core.hibernate.QueryWrapper: Deprecated.
setByte(String, byte) - Method in class net.sf.basedb.core.hibernate.QueryWrapper: Deprecated.
setBytes(long) - Method in class net.sf.basedb.core.data.DataCubeData
setBytes(long) - Method in class net.sf.basedb.core.data.DataCubeExtraValueData
setBytes(long) - Method in class net.sf.basedb.core.data.DataCubeFilterData
setBytes(long) - Method in class net.sf.basedb.core.data.DataCubeLayerData
setBytes(long) - Method in class net.sf.basedb.core.data.DiskUsageData
setBytes(long) - Method in class net.sf.basedb.core.data.ExperimentData
setBytes(long) - Method in class net.sf.basedb.core.data.RawBioAssayData
setBytes(long) - Method in class net.sf.basedb.core.data.ReporterCloneTemplateData
setCacheable(boolean) - Method in class net.sf.basedb.core.hibernate.NativeQueryWrapper
setCacheable(boolean) - Method in class net.sf.basedb.core.hibernate.QueryWrapper
setCachedObject(Object, Object) - Method in class net.sf.basedb.util.overview.GenericOverview: Store an auxilliary object in the overview cache.
setCachedObject(Object, Object) - Method in interface net.sf.basedb.util.overview.OverviewContext: Store an auxilliary object in the overview cache.
setCacheMode(CacheMode) - Method in class net.sf.basedb.core.hibernate.NativeQueryWrapper
setCacheMode(CacheMode) - Method in class net.sf.basedb.core.hibernate.QueryWrapper
setCacheMode(CacheMode) - Method in class net.sf.basedb.core.hibernate.SessionWrapper
setCacheRegion(String) - Method in class net.sf.basedb.core.hibernate.NativeQueryWrapper
setCacheRegion(String) - Method in class net.sf.basedb.core.hibernate.QueryWrapper
setCacheResult(boolean) - Method in class net.sf.basedb.core.AbstractHqlQuery
setCacheResult(boolean) - Method in interface net.sf.basedb.core.query.HqlQuery: Specify if the query results should be cached or not.
setCalendar(int, Calendar) - Method in class net.sf.basedb.core.hibernate.QueryWrapper: Deprecated.
setCalendar(String, Calendar) - Method in class net.sf.basedb.core.hibernate.QueryWrapper: Deprecated.
setCalendarDate(int, Calendar) - Method in class net.sf.basedb.core.hibernate.QueryWrapper: Deprecated.
setCalendarDate(String, Calendar) - Method in class net.sf.basedb.core.hibernate.QueryWrapper: Deprecated.
setCategories(Set<AnnotationTypeCategoryData>) - Method in class net.sf.basedb.core.data.AnnotationTypeData
setCellClass(String) - Method in class net.sf.basedb.clients.web.extensions.list.AbstractListColumnBean
setCellClass(String) - Method in class net.sf.basedb.clients.web.extensions.list.PropertyPathActionFactory
setCellStyle(String) - Method in class net.sf.basedb.clients.web.extensions.list.AbstractListColumnBean
setCellStyle(String) - Method in class net.sf.basedb.clients.web.extensions.list.PropertyPathActionFactory
setChangeHistory(ChangeHistoryData) - Method in class net.sf.basedb.core.data.ChangeHistoryDetailData
setChangeInfo(String) - Method in class net.sf.basedb.core.data.ChangeHistoryDetailData
setChangeType(int) - Method in class net.sf.basedb.core.data.ChangeHistoryDetailData
setChannels(int) - Method in class net.sf.basedb.core.data.FormulaData
setChannels(int) - Method in class net.sf.basedb.core.data.PlatformData
setChannels(int) - Method in class net.sf.basedb.core.data.PlatformVariantData
setChannels(int) - Method in class net.sf.basedb.core.Formula: Set the number of channels that are required to use this formula.
setChannels(int) - Method in class net.sf.basedb.core.Platform: Set the number of channels for a file-only platform.
setChannels(int) - Method in class net.sf.basedb.core.PlatformVariant: Set the number of channels for a file-only platform variant.
setCharacter(int, char) - Method in class net.sf.basedb.core.hibernate.QueryWrapper: Deprecated.
setCharacter(String, char) - Method in class net.sf.basedb.core.hibernate.QueryWrapper: Deprecated.
setCharacterSet(String) - Method in class net.sf.basedb.clients.web.util.ServletExportOutputStream: Calls ServletResponse.setCharacterEncoding(String)
setCharacterSet(String) - Method in class net.sf.basedb.core.data.FileData
setCharacterSet(String) - Method in class net.sf.basedb.core.File: Set the character set used in this file (for text-files only).
setCharacterSet(String) - Method in class net.sf.basedb.core.plugin.ExportOutputStream: Do nothing should be overridden by subclasses.
setCharacterSet(String) - Method in class net.sf.basedb.util.FileExportOutputStream: Calls File.setCharacterSet(String)
setCharacterSet(String) - Method in class net.sf.basedb.util.uri.UriMetadata
setCharset(Charset) - Method in class net.sf.basedb.util.excel.XlsxToCsvUtil: Set the character set to use for the text.
setChecked(boolean) - Method in class net.sf.basedb.clients.web.taglib.Input
setChild(BioAssay) - Method in class net.sf.basedb.util.importer.spotdata.BaseFileInfo.ChildBioAssay: Set the real child bioassay object.
setChildCreationEvents(Set<BioMaterialEventSourceData>) - Method in class net.sf.basedb.core.data.BioMaterialData
setChildHasDifferentReporterPositionMapping(boolean) - Method in class net.sf.basedb.util.importer.spotdata.BaseFileInfo: Set a flag that indicates if the child data has a different position/reporter mapping than the parent bioassay set.
setChildId(int) - Method in class net.sf.basedb.core.data.keyring.GroupGroups: Set the id of the child group.
setChildren(Set<BioAssayData>) - Method in class net.sf.basedb.core.data.BioAssayData
setChildren(Set<DerivedBioAssayData>) - Method in class net.sf.basedb.core.data.DerivedBioAssayData
setChildren(Set<GroupData>) - Method in class net.sf.basedb.core.data.GroupData
setChildren(Set<MeasuredBioMaterialData>) - Method in class net.sf.basedb.core.data.BioMaterialData
setChildren(Set<PlateData>) - Method in class net.sf.basedb.core.data.PlateData
setChildrenLoaded() - Method in class net.sf.basedb.util.overview.Node: Sets a flag to indicate that all children has been loaded.
setCity(String) - Method in class net.sf.basedb.util.GeoLocation
setClassName(String) - Method in class net.sf.basedb.core.data.PluginDefinitionData
setClassName(String) - Method in class net.sf.basedb.core.PluginDefinition: The class name cannot be changed.
setClassName(String) - Method in class net.sf.basedb.util.extensions.xml.PluginInfo
setClazz(String) - Method in class net.sf.basedb.clients.web.extensions.list.AbstractListColumnBean
setClazz(String) - Method in class net.sf.basedb.clients.web.extensions.list.PropertyPathActionFactory
setClazz(String) - Method in class net.sf.basedb.clients.web.extensions.login.FieldInfo
setClazz(String) - Method in class net.sf.basedb.clients.web.extensions.menu.FixedMenuItemFactory
setClazz(String) - Method in class net.sf.basedb.clients.web.extensions.menu.MenuItemBean
setClazz(String) - Method in class net.sf.basedb.clients.web.extensions.tabcontrol.FixedTabFactory
setClazz(String) - Method in class net.sf.basedb.clients.web.extensions.tabcontrol.IncludeContentTabFactory
setClazz(String) - Method in class net.sf.basedb.clients.web.extensions.tabcontrol.TabBean
setClazz(String) - Method in class net.sf.basedb.clients.web.extensions.toolbar.ButtonBean
setClazz(String) - Method in class net.sf.basedb.clients.web.extensions.toolbar.FixedButtonFactory
setClazz(String) - Method in class net.sf.basedb.clients.web.extensions.toolbar.PermissionButtonFactory: Set the class to use in all cases.
setClazz(String) - Method in class net.sf.basedb.clients.web.taglib.ExceptionCatcher
setClazz(String) - Method in class net.sf.basedb.clients.web.taglib.StylableTag
setClazz(String) - Method in class net.sf.basedb.clients.web.taglib.tab.Tab
setClazz(String) - Method in class net.sf.basedb.clients.web.taglib.table.Cell
setClazz(String) - Method in class net.sf.basedb.clients.web.taglib.table.CellValue
setClearErrors(boolean) - Method in class net.sf.basedb.util.extensions.ExtensionsInvoker: Set a flag to indicate if existing errors should be cleared before an action is rendered.
setClearState() - Method in interface net.sf.basedb.core.plugin.Response: This can be used in the configuration phase of a plug-in to clear the stored state and nextCommand information.
setClearState() - Method in class net.sf.basedb.core.PluginResponse.ResponseImpl
setClearState() - Method in class net.sf.basedb.plugins.executor.ExternalProgramExecutor.ResponseWrapper
setClient(Client) - Method in class net.sf.basedb.core.ClientDefaultSetting: Set the client application this setting is valid for.
setClient(Client) - Method in class net.sf.basedb.core.Help: Set the client application this setting is valid for.
setClient(Client) - Method in class net.sf.basedb.core.UserClientSetting: Set the client application this setting is valid for.
setClient(ClientData) - Method in class net.sf.basedb.core.data.ChangeHistoryData
setClient(ClientData) - Method in class net.sf.basedb.core.data.ClientDefaultSettingData
setClient(ClientData) - Method in class net.sf.basedb.core.data.ContextData
setClient(ClientData) - Method in class net.sf.basedb.core.data.ContextIndex
setClient(ClientData) - Method in class net.sf.basedb.core.data.HelpData
setClient(ClientData) - Method in class net.sf.basedb.core.data.SessionData
setClient(ClientData) - Method in class net.sf.basedb.core.data.UserClientSettingData
setClient(ClientData) - Method in class net.sf.basedb.core.data.UserDeviceData
setClientCertificate(byte[]) - Method in class net.sf.basedb.core.data.FileServerData
setClientCertificate(byte[]) - Method in class net.sf.basedb.core.FileServer: Set the client certificate that BASE should use to authenticate with the server when connecting with https.
setClientCertificate(byte[]) - Method in class net.sf.basedb.util.uri.ConnectionParameters
setClientCertificatePassword(String) - Method in class net.sf.basedb.core.data.FileServerData
setClientCertificatePassword(String) - Method in class net.sf.basedb.core.FileServer: Set the password that is needed to unlock the client certificate.
setClientCertificatePassword(String) - Method in class net.sf.basedb.util.uri.ConnectionParameters
setClientId(Integer) - Method in class net.sf.basedb.core.data.ChangeHistoryData
setClientSettings(Set<UserClientSettingData>) - Method in class net.sf.basedb.core.data.UserData
setClone(boolean) - Method in class net.sf.basedb.util.annotations.InheritSpecification: Set a flag to inherit annotations by cloning the original values.
setCollecting() - Method in class net.sf.basedb.util.listable.TransformContext: Shortcut for enabling 'collecting' and disabling 'avoiding'.
setCollecting(boolean) - Method in class net.sf.basedb.util.listable.TransformContext: Enable/disable collecting of all source items that the transformers in this context are using.
setCollectionFormatter(Formatter<Collection<? super V>>) - Method in class net.sf.basedb.clients.web.extensions.list.AbstractListColumnBean
setColor(String) - Method in class net.sf.basedb.clients.web.ExperimentExplorer.AnnotationGroup: Sets the color for this annotation group.
setColor(String, Color) - Method in class net.sf.basedb.clients.web.servlet.ExperimentExplorerPlotServlet.ColumnKey
setColoring(ColoringData) - Method in class net.sf.basedb.core.data.ExtraValueTypeData
setColoring(ColoringData) - Method in class net.sf.basedb.core.data.FormulaData
setColorsAuto() - Method in class net.sf.basedb.clients.web.ExperimentExplorer.AnnotationSummary: Arranges the colors of the groups in the order they are returned by the ExperimentExplorer.AnnotationSummary.getAnnotationGroups() set.
setColspan(int) - Method in class net.sf.basedb.clients.web.taglib.table.Header
setColumn(int) - Method in class net.sf.basedb.core.data.BioWellData
setColumn(int) - Method in class net.sf.basedb.core.data.FeatureData
setColumn(int) - Method in class net.sf.basedb.core.data.MappingCoordinate: Set the location.
setColumn(int) - Method in class net.sf.basedb.core.data.PlateCoordinate: Set the location.
setColumn(int) - Method in class net.sf.basedb.core.data.WellData
setColumn(Integer) - Method in class net.sf.basedb.core.data.RawData
setColumn(String) - Method in class net.sf.basedb.clients.web.taglib.table.Cell
setColumn(String) - Method in class net.sf.basedb.core.data.ReporterClonePropertyData
setColumnContent(String, String) - Method in class net.sf.basedb.clients.web.taglib.table.Table
setColumnCount(int) - Method in class net.sf.basedb.util.bfs.DataWriter: Set the number of data columns.
setColumnFilter(String, int, String) - Method in class net.sf.basedb.clients.web.taglib.table.Table
setColumnFormatter(int, Formatter<?>) - Method in class net.sf.basedb.util.export.TableWriter: Set a data formatter for a given column.
setColumnNo(short) - Method in class net.sf.basedb.core.data.DataCubeColumnData
setColumnNo(short) - Method in class net.sf.basedb.core.DataCubeColumn
setColumns(int) - Method in class net.sf.basedb.core.data.PlateGeometryData
setColumns(int) - Method in class net.sf.basedb.core.PlateGeometry: The number of columns cannot be changed, used at object creation only.
setColumns(String) - Method in class net.sf.basedb.clients.web.taglib.table.Table
setColumns(Set<DataCubeColumnData>) - Method in class net.sf.basedb.core.data.DataCubeData
setColumnSeparator(String) - Method in class net.sf.basedb.util.excel.XlsxToCsvUtil: Set the column separator.
setComment(String) - Method in class net.sf.basedb.core.authentication.LoginRequest: Set the comment to use.
setComment(String) - Method in class net.sf.basedb.core.BioMaterialEvent: Set the comment about this event.
setComment(String) - Method in class net.sf.basedb.core.data.BioMaterialEventData
setComment(String) - Method in class net.sf.basedb.core.data.PlateEventData
setComment(String) - Method in class net.sf.basedb.core.hibernate.NativeQueryWrapper
setComment(String) - Method in class net.sf.basedb.core.hibernate.QueryWrapper
setComment(String) - Method in class net.sf.basedb.core.PlateEvent: Set the comment about this event.
setCompleted() - Method in class net.sf.basedb.util.uri.http.HttpConnectionManager.TimeoutTimer
setCompressed(boolean) - Method in class net.sf.basedb.core.data.FileData
setCompressedSize(long) - Method in class net.sf.basedb.core.data.FileData
setCondition(String) - Method in class net.sf.basedb.core.dbengine.TableInfo.IndexInfo
setConfigurations(Set<PluginConfigurationData>) - Method in class net.sf.basedb.core.data.PluginDefinitionData
setConfigurationValues(Map<VersionedParameter, ParameterValueData<?>>) - Method in class net.sf.basedb.core.data.PluginConfigurationData
setConfigured(PluginResponse) - Method in class net.sf.basedb.core.Job.ProgressReporterImpl
setConnectionManagerFactory(String) - Method in class net.sf.basedb.core.data.FileServerData
setConnectionManagerFactoryId(String) - Method in class net.sf.basedb.core.FileServer: Set the ID of the connection manager factory.
setConnectionManagerFactoryId(String) - Method in class net.sf.basedb.util.uri.ConnectionParameters
setContact(String) - Method in class net.sf.basedb.core.data.PluginDefinitionData
setContact(String) - Method in class net.sf.basedb.core.PluginDefinition: Set contact information for this plug-in.
setContact(String) - Method in class net.sf.basedb.util.extensions.AboutBean
setContent(String) - Method in class net.sf.basedb.clients.web.extensions.section.SectionBean
setContent(String) - Method in class net.sf.basedb.clients.web.extensions.tabcontrol.FixedTabFactory
setContent(String) - Method in class net.sf.basedb.clients.web.extensions.tabcontrol.TabBean
setContentLength(long) - Method in class net.sf.basedb.clients.web.util.ServletExportOutputStream: Calls ServletResponse.setContentLength(int)
setContentLength(long) - Method in class net.sf.basedb.core.plugin.ExportOutputStream: Do nothing.
setContentLength(long) - Method in class net.sf.basedb.util.FileExportOutputStream: Ignored.
setContentstyle(String) - Method in class net.sf.basedb.clients.web.taglib.HideableSection
setContentstyle(String) - Method in class net.sf.basedb.clients.web.taglib.tab.TabControl
setContentStyle(String) - Method in class net.sf.basedb.clients.web.extensions.section.IncludeContentSectionFactory
setContentStyle(String) - Method in class net.sf.basedb.clients.web.extensions.section.SectionBean
setContext(JspContext) - Method in class net.sf.basedb.clients.web.taglib.extensions.Render
setContext(JspContext) - Method in class net.sf.basedb.clients.web.taglib.extensions.Scripts
setContext(JspContext) - Method in class net.sf.basedb.clients.web.taglib.extensions.Stylesheets
setContext(ItemContext) - Method in class net.sf.basedb.clients.web.taglib.HideableSection
setContext(ClientContext) - Method in class net.sf.basedb.core.signal.ExtensionSignalTransporter
setContextClassLoader() - Method in class net.sf.basedb.clients.web.extensions.XJspCompiler: Sets the context class loader if this JSP page is an extension JSP page and if the extensions JAR file has been modified since the last time the class loader was set.
setContextItem(Integer) - Method in class net.sf.basedb.core.data.JobData
setContexts(Map<ContextIndex, ContextData>) - Method in class net.sf.basedb.core.data.UserData
setContexts(Set<ContextData>) - Method in class net.sf.basedb.core.data.ClientData
setContextType(int) - Method in class net.sf.basedb.core.data.GuiContextData
setContextType(Integer) - Method in class net.sf.basedb.core.data.JobData
setContinue(String) - Method in interface net.sf.basedb.core.plugin.Response: This method will continue the configuration or execution of the job with a new command to the plugin.
setContinue(String) - Method in class net.sf.basedb.core.PluginResponse.ResponseImpl
setContinue(String) - Method in class net.sf.basedb.plugins.executor.ExternalProgramExecutor.ResponseWrapper
setContinue(String, Serializable) - Method in interface net.sf.basedb.core.plugin.Response: Can be used by an executing job to also store state information that will be restored when the job is starting up again.
setContinue(String, Serializable) - Method in class net.sf.basedb.core.PluginResponse.ResponseImpl
setContinue(String, Serializable) - Method in class net.sf.basedb.plugins.executor.ExternalProgramExecutor.ResponseWrapper
setCoordinateType(int) - Method in class net.sf.basedb.core.data.DataCubeExtraValueData
setCoordinateType(ExtraValue.CoordinateType) - Method in class net.sf.basedb.core.DataCubeExtraValue: Set the coordinate type.
setCopyright(String) - Method in class net.sf.basedb.core.data.PluginDefinitionData
setCopyright(String) - Method in class net.sf.basedb.core.PluginDefinition: Update copyright information about this plug-in.
setCopyright(String) - Method in class net.sf.basedb.util.extensions.AboutBean
setCopyToStdout(boolean) - Method in class net.sf.basedb.util.extensions.logging.ExtensionsLog: Enable or disable copies of log entries to standard output.
setCount(int) - Method in class net.sf.basedb.util.AnyToAnyLinkStatistics
setCounting(boolean) - Method in class net.sf.basedb.core.AbstractQuery: Set the counting status of the query.
setCountry(String) - Method in class net.sf.basedb.util.GeoLocation
setCreated(Date) - Method in class net.sf.basedb.core.data.JobData
setCreationEvent(BioMaterialEventData) - Method in class net.sf.basedb.core.data.MeasuredBioMaterialData
setCreationEvent(BioMaterialEventData) - Method in class net.sf.basedb.core.data.PhysicalBioAssayData
setCryptedPassword(String) - Method in class net.sf.basedb.core.data.PasswordData: Set the encrypted password.
setCubeNo(short) - Method in class net.sf.basedb.core.data.DataCubeData
setCubeNo(short) - Method in class net.sf.basedb.core.DataCube
setCubes(short) - Method in class net.sf.basedb.core.data.VirtualDbData
setCurNumberOfParameters(int) - Method in class net.sf.basedb.util.jep.ChannelFunction
setCurNumberOfParameters(int) - Method in class net.sf.basedb.util.jep.ExtraValueFunction
setCurNumberOfParameters(int) - Method in class net.sf.basedb.util.jep.FunctionSafeJep.UnknownFunction
setCurNumberOfParameters(int) - Method in class net.sf.basedb.util.jep.InReporterListFunction
setCurNumberOfParameters(int) - Method in class net.sf.basedb.util.jep.LeftFunction
setCurNumberOfParameters(int) - Method in class net.sf.basedb.util.jep.Log2Function
setCurNumberOfParameters(int) - Method in class net.sf.basedb.util.jep.MeanFunction
setCurNumberOfParameters(int) - Method in class net.sf.basedb.util.jep.NotInReporterListFunction
setCurNumberOfParameters(int) - Method in class net.sf.basedb.util.jep.PositionFunction: Can't be changed.
setCurNumberOfParameters(int) - Method in class net.sf.basedb.util.jep.RawChannelFunction
setCurNumberOfParameters(int) - Method in class net.sf.basedb.util.jep.RawFunction
setCurNumberOfParameters(int) - Method in class net.sf.basedb.util.jep.ReporterFunction
setCurNumberOfParameters(int) - Method in class net.sf.basedb.util.jep.ScoreFunction
setCurNumberOfParameters(int) - Method in class net.sf.basedb.util.jep.SimpleJepFunction
setCurNumberOfParameters(int) - Method in class net.sf.basedb.util.parser.ColFunction
setCurNumberOfParameters(int) - Method in class net.sf.basedb.util.parser.DataNoFunction
setCurNumberOfParameters(int) - Method in class net.sf.basedb.util.parser.DefaultItemFunction
setCurNumberOfParameters(int) - Method in class net.sf.basedb.util.parser.LineNoFunction
setCurrent(BasicItem) - Method in class net.sf.basedb.clients.web.taglib.Select
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.
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.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
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
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
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.
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
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.BioMaterialData
setItemSubtype(ItemSubtypeData) - Method in class net.sf.basedb.core.data.BioPlateTypeData
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.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.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.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(int) - Method in class net.sf.basedb.core.data.AnnotationSetData
setItemType(int) - Method in class net.sf.basedb.core.data.ChangeHistoryDetailData
setItemType(int) - Method in class net.sf.basedb.core.data.ContextData
setItemType(int) - Method in class net.sf.basedb.core.data.ContextIndex
setItemType(int) - Method in class net.sf.basedb.core.data.DataFileTypeData
setItemType(int) - Method in class net.sf.basedb.core.data.DiskUsageData
setItemType(int) - Method in class net.sf.basedb.core.data.FileSetData
setItemType(int) - Method in class net.sf.basedb.core.data.GuiContextData
setItemType(int) - Method in class net.sf.basedb.core.data.ItemSubtypeData
setItemType(int) - Method in class net.sf.basedb.core.data.RoleKeyData
setItemType(Item) - Method in class net.sf.basedb.core.DataFileType
setItemType(Item) - Method in class net.sf.basedb.core.query.QueryParameter: Changes the type of the parameter.
setItemTypes(Collection<Item>) - Method in class net.sf.basedb.core.AnnotationType: Enable the annotation type for all of the specified item and disable it for all other.
setItemTypes(Set<Integer>) - Method in class net.sf.basedb.core.data.AnnotationTypeData
setJarFile(String) - Method in class net.sf.basedb.core.data.PluginDefinitionData
setJarFile(String) - Method in class net.sf.basedb.core.data.PluginTypeData
setJarFile(String) - Method in class net.sf.basedb.core.PluginDefinition: The jar path cannot be changed.
setJarFile(String) - Method in class net.sf.basedb.core.PluginType: The jar path cannot be changed.
setJdbcBatchSize(Integer) - Method in class net.sf.basedb.core.hibernate.SessionWrapper
setJdbcBatchSize(Integer) - Method in class net.sf.basedb.core.hibernate.StatelessSessionWrapper
setJep(String) - Method in class net.sf.basedb.util.export.spotdata.JepDynamicField: Set the expression used to select data in the query.
setJob(JobData) - Method in class net.sf.basedb.core.data.ArrayDesignData
setJob(JobData) - Method in class net.sf.basedb.core.data.ChangeHistoryData
setJob(JobData) - Method in class net.sf.basedb.core.data.DerivedBioAssayData
setJob(JobData) - Method in class net.sf.basedb.core.data.ExtraValueData
setJob(JobData) - Method in class net.sf.basedb.core.data.MessageData
setJob(JobData) - Method in class net.sf.basedb.core.data.RawBioAssayData
setJob(JobData) - Method in class net.sf.basedb.core.data.TransformationData
setJob(JobData) - Method in class net.sf.basedb.core.Message
setJob(Job) - Method in class net.sf.basedb.core.DerivedBioAssay: Set the job on this derived bioassay that was used to create or import data for it.
setJob(Job) - Method in class net.sf.basedb.core.ExtraValue: Set the job that created the extra values.
setJob(Job) - Method in class net.sf.basedb.core.RawBioAssay: Set the job on this raw bioassay that was used to create or import data for it.
setJob(Job) - Method in class net.sf.basedb.core.Transformation: Set the job that executed this transformation.
setJobAgent(JobAgentData) - Method in class net.sf.basedb.core.data.JobAgentSettingsData
setJobAgent(JobAgent) - Method in class net.sf.basedb.core.Job: Set the job agent this job should run on.
setJobAgent(JobAgent) - Method in class net.sf.basedb.core.JobAgentSettings
setJobAgentId(Integer) - Method in class net.sf.basedb.core.data.JobData
setJobAgentSettings(Set<JobAgentSettingsData>) - Method in class net.sf.basedb.core.data.PluginDefinitionData
setJobId(Integer) - Method in class net.sf.basedb.core.data.ChangeHistoryData
setJobs(Set<JobData>) - Method in class net.sf.basedb.core.data.ExperimentData
setJspcontext(JspContext) - Method in class net.sf.basedb.clients.web.taglib.table.ColumnDef
setJspContext(JspContext) - Method in class net.sf.basedb.clients.web.extensions.edit.AbstractOnSaveAction: Get the JSP context of the current invokation.
setKeepSkippedLines(boolean) - Method in class net.sf.basedb.util.parser.FlatFileParser: If the FlatFileParser.nextData() and FlatFileParser.hasMoreData() methods should keep information of lines that was skipped because they matched the ignore pattern or could be interpreted as data lines.
setKeyId(int) - Method in class net.sf.basedb.core.data.keyring.KeyPermission: Set the id of the key.
setKeyId(int) - Method in class net.sf.basedb.core.data.keyring.PluginKeys: Sets the id of the RoleKey
setKeys(Set<RoleKeyData>) - Method in class net.sf.basedb.core.data.RoleData
setKit(KitData) - Method in class net.sf.basedb.core.data.BioMaterialEventData
setKit(KitData) - Method in class net.sf.basedb.core.data.BioPlateEventData
setKit(KitData) - Method in class net.sf.basedb.core.data.DerivedBioAssayData
setKit(Kit) - Method in class net.sf.basedb.core.BioMaterialEvent: Set the Kit that was used in this event.
setKit(Kit) - Method in class net.sf.basedb.core.BioPlateEvent: Set the Kit that was used in this event.
setKit(Kit) - Method in class net.sf.basedb.core.DerivedBioAssay: Set the Kit that was used when creating this bioassay.
setLabel(String) - Method in class net.sf.basedb.core.data.ParameterValueData
setLastModified(Date) - Method in class net.sf.basedb.util.uri.UriMetadata
setLastProcessResults(ProcessResults) - Method in class net.sf.basedb.util.extensions.manager.ExtensionsManager: Save the last process results so that they can be used later on.
setLastRemoteId(String) - Method in class net.sf.basedb.core.data.UserDeviceData
setLastSource(String) - Method in class net.sf.basedb.core.data.ReporterData
setLastSyncProperties(String) - Method in class net.sf.basedb.core.data.ItemListSyncFilterData
setLastUpdate(Date) - Method in class net.sf.basedb.core.data.AnnotationData
setLastUpdate(Date) - Method in class net.sf.basedb.core.data.FileData
setLastUpdate(Date) - Method in class net.sf.basedb.core.data.ReporterData
setLastUpdated() - Method in class net.sf.basedb.clients.jobagent.slotmanager.MasterSlotManager.RemoteSlot
setLastUsed(Date) - Method in class net.sf.basedb.core.data.UserDeviceData
setLatitude(Float) - Method in class net.sf.basedb.util.GeoLocation
setLayerNo(short) - Method in class net.sf.basedb.core.data.DataCubeLayerData
setLayerNo(short) - Method in class net.sf.basedb.core.DataCubeLayer
setLayers(Set<DataCubeLayerData>) - Method in class net.sf.basedb.core.data.DataCubeData
setLength(int) - Method in class net.sf.basedb.core.data.ReporterClonePropertyData
setLength(Long) - Method in class net.sf.basedb.util.uri.UriMetadata
setLevel(String) - Method in class net.sf.basedb.util.extensions.LoggingErrorHandlerFactory: Set the level of the error handler.
setLimit(int) - Method in class net.sf.basedb.core.signal.ProgressReporterSignalHandler: Set the percentage limit.
setLinkName(String) - Method in class net.sf.basedb.util.AnyToAnyLinkStatistics
setList(Collection<?>) - Method in class net.sf.basedb.clients.web.taglib.table.CellValue
setLocale(int, Locale) - Method in class net.sf.basedb.core.hibernate.QueryWrapper: Deprecated.
setLocale(String, Locale) - Method in class net.sf.basedb.core.hibernate.QueryWrapper: Deprecated.
setLocation(int) - Method in class net.sf.basedb.core.data.DiskUsageData
setLocation(int) - Method in class net.sf.basedb.core.data.FileData
setLocation(int) - Method in class net.sf.basedb.core.data.QuotaIndex
setLocation(String) - Method in class net.sf.basedb.core.data.SessionData
setLocation(String) - Method in class net.sf.basedb.core.data.UserDeviceData
setLocation(Location) - Method in class net.sf.basedb.core.File: Set the location of this File item.
setLocationLatitude(Float) - Method in class net.sf.basedb.core.data.SessionData
setLocationLatitude(Float) - Method in class net.sf.basedb.core.data.UserDeviceData
setLocationLongitude(Float) - Method in class net.sf.basedb.core.data.SessionData
setLocationLongitude(Float) - Method in class net.sf.basedb.core.data.UserDeviceData
setLocked(boolean) - Method in class net.sf.basedb.clients.web.taglib.table.Navigator
setLocked(boolean) - Method in class net.sf.basedb.core.data.ReporterCloneTemplateData
setLockMode(int) - Method in class net.sf.basedb.core.data.BioPlateTypeData
setLockMode(String, LockMode) - Method in class net.sf.basedb.core.hibernate.NativeQueryWrapper
setLockMode(String, LockMode) - Method in class net.sf.basedb.core.hibernate.QueryWrapper
setLockMode(LockModeType) - Method in class net.sf.basedb.core.hibernate.NativeQueryWrapper
setLockMode(LockModeType) - Method in class net.sf.basedb.core.hibernate.QueryWrapper
setLockMode(BioWell.LockMode) - Method in class net.sf.basedb.core.BioPlateType: Set the lock mode for wells on plates of this plate type.
setLockOptions(LockOptions) - Method in class net.sf.basedb.core.hibernate.NativeQueryWrapper
setLockOptions(LockOptions) - Method in class net.sf.basedb.core.hibernate.QueryWrapper
setLogarithmic(boolean) - Method in class net.sf.basedb.core.Coloring: Specify if we should take the logarithm of values before the color is generated or not.
setLogarithmic(boolean) - Method in class net.sf.basedb.core.data.ColoringData
setLogin(String) - Method in class net.sf.basedb.core.authentication.LoginRequest: Set the login name to use.
setLogin(String) - Method in class net.sf.basedb.core.data.UserData
setLogin(String) - Method in class net.sf.basedb.core.User: Set the login for the user account.
setLoginComment(String) - Method in class net.sf.basedb.core.data.SessionData
setLoginField(FieldInfo) - Method in class net.sf.basedb.clients.web.extensions.login.LoginFormBean
setLoginTime(Date) - Method in class net.sf.basedb.core.data.SessionData
setLogoutTime(Date) - Method in class net.sf.basedb.core.data.SessionData
setLong(int, long) - Method in class net.sf.basedb.core.hibernate.QueryWrapper: Deprecated.
setLong(String, long) - Method in class net.sf.basedb.core.hibernate.QueryWrapper: Deprecated.
setLongitude(Float) - Method in class net.sf.basedb.util.GeoLocation
setLongValues(List<Long>) - Method in class net.sf.basedb.core.data.annotations.AnnotationLink
setMainItemType(Item) - Method in class net.sf.basedb.core.ItemSubtype
setMainType(int) - Method in class net.sf.basedb.core.data.PluginDefinitionData
setMainType(Plugin.MainType) - Method in class net.sf.basedb.core.PluginDefinition: The type cannot be changed.
setMandatory(boolean) - Method in class net.sf.basedb.core.data.ReporterClonePropertyData
setMappings(short) - Method in class net.sf.basedb.core.data.VirtualDbData
setMasked(boolean) - Method in class net.sf.basedb.core.data.ParameterValueData
setMasterParser(AnnotationParser) - Method in class net.sf.basedb.util.importer.spotdata.SynchronizedSpotDataParser: Sets the master parser.
setMatchingSource(int) - Method in class net.sf.basedb.core.data.ItemListSyncFilterData
setMatchingTransformed(int) - Method in class net.sf.basedb.core.data.ItemListSyncFilterData
setMaxAge(int) - Method in class net.sf.basedb.core.DiskUsageStatistics: Set the max age in seconds for a disk usage summary object before it is reloaded from the database again.
setMaxBaseVersion(String) - Method in class net.sf.basedb.util.extensions.AboutBean
setMaxBytes(long) - Method in class net.sf.basedb.core.data.QuotaIndex
setMaxcharacters(int) - Method in class net.sf.basedb.clients.web.taglib.table.Cell
setMaxDataColumns(int) - Method in class net.sf.basedb.util.parser.FlatFileParser: Set the maximum number of columns a data line can contain in order for it to be counted as a data line.
setMaxheight(String) - Method in class net.sf.basedb.clients.web.taglib.table.Cell
setMaxLength(Integer) - Method in class net.sf.basedb.core.AnnotationType: Set the maximum allowed string length for a Type.STRING annotation.
setMaxMemory(Long) - Method in class net.sf.basedb.core.data.JobAgentSettingsData
setMaxMemory(Long) - Method in class net.sf.basedb.core.data.PluginDefinitionData
setMaxMemory(Long) - Method in class net.sf.basedb.core.JobAgentSettings: Set maximim amount of memory the plugin is allowed to use.
setMaxMemory(Long) - Method in class net.sf.basedb.core.PluginDefinition: Set the maximum amount of memory the plugin is allowed to use.
setMaxRandomSamples(int) - Method in class net.sf.basedb.util.AnyToAnyLinkStatistics.Options: Set the maximum number of items to use for gathering the statistics.
setMaxRawMappingsForSpot(int) - Method in class net.sf.basedb.core.data.DataCubeData
setMaxResults(int) - Method in class net.sf.basedb.core.AbstractQuery
setMaxResults(int) - Method in class net.sf.basedb.core.hibernate.NativeQueryWrapper
setMaxResults(int) - Method in class net.sf.basedb.core.hibernate.QueryWrapper
setMaxResults(int) - Method in interface net.sf.basedb.core.query.Query: Specify that the query should at most return the specified number of rows.
setMaxUnknownLines(int) - Method in class net.sf.basedb.util.parser.FlatFileParser: The number of unknown lines in a row that can be parsed by the parseHeaders method before it gives up.
setMaxValue(Float) - Method in class net.sf.basedb.core.Coloring: Set the value that represents the maximum value.
setMaxValue(Float) - Method in class net.sf.basedb.core.data.ColoringData
setMaxValueDouble(Double) - Method in class net.sf.basedb.core.AnnotationType: Set the maximum allowed value for a Type.FLOAT or Type.DOUBLE annotation.
setMaxValueLong(Long) - Method in class net.sf.basedb.core.AnnotationType: Set the maximum allowed value for an Type.INT or Type.LONG annotation.
setMaxwidth(String) - Method in class net.sf.basedb.clients.web.taglib.table.Cell
setMd5(String) - Method in class net.sf.basedb.core.data.FileData
setMd5(String) - Method in class net.sf.basedb.core.data.ItemListSyncFilterData
setMd5(String) - Method in class net.sf.basedb.util.uri.UriMetadata
setMd5AtLastSync(String) - Method in class net.sf.basedb.core.data.ItemListData
setMember(File, DataFileType) - Method in class net.sf.basedb.core.FileSet: Set a file of a given type as a member of this file set.
setMembers(Set<Integer>) - Method in class net.sf.basedb.core.data.ItemListData
setMembers(Set<FileSetMemberData>) - Method in class net.sf.basedb.core.data.FileSetData
setMemberType(int) - Method in class net.sf.basedb.core.data.ItemListData
setMemberType(Item) - Method in class net.sf.basedb.core.ItemList
setMenu(String) - Method in class net.sf.basedb.clients.web.taglib.Page
setMenuId(String) - Method in class net.sf.basedb.clients.web.extensions.menu.FixedMenuItemFactory
setMenuId(String) - Method in class net.sf.basedb.clients.web.extensions.menu.MenuItemBean
setMenuId(String) - Method in class net.sf.basedb.clients.web.extensions.menu.PermissionMenuItemFactory
setMessage(String) - Method in class net.sf.basedb.core.ItemContext: Set a message to be displayed by a client application as soon as it is appropriate to do so.
setMessagePrefix(String) - Method in class net.sf.basedb.util.ChainedProgressReporter: Set a message prefix that is pre-pended to message before it is sent to the master progress reporter.
setMessages(Set<MessageData>) - Method in class net.sf.basedb.core.data.JobData
setMessages(Set<MessageData>) - Method in class net.sf.basedb.core.data.UserData
setMetadataFromURI(UriMetadata) - Method in class net.sf.basedb.core.File
setMetadataParser(MetadataParser) - Method in class net.sf.basedb.util.importer.spotdata.BfsImporter: Set the metadata file parser.
setMetadataPrefix(String) - Method in class net.sf.basedb.util.basefile.BaseFileWriter: Change the metadata prefix string.
setMetadataWriter(MetadataWriter) - Method in class net.sf.basedb.util.export.spotdata.BfsExporter: Set the stream were the metadata should be written.
setMetaGrid(int, int) - Method in class net.sf.basedb.core.ArrayDesignBlock: Set the metagrid coordinates.
setMetaGridX(int) - Method in class net.sf.basedb.core.data.ArrayDesignBlockData
setMetaGridX(Integer) - Method in class net.sf.basedb.core.data.RawData
setMetaGridX(Integer) - Method in class net.sf.basedb.plugins.PrintMapFlatFileImporter.MetaBlock
setMetaGridY(int) - Method in class net.sf.basedb.core.data.ArrayDesignBlockData
setMetaGridY(Integer) - Method in class net.sf.basedb.core.data.RawData
setMetaGridY(Integer) - Method in class net.sf.basedb.plugins.PrintMapFlatFileImporter.MetaBlock
setMidValue(Float) - Method in class net.sf.basedb.core.Coloring: Set the value that represents the midpoint value.
setMidValue(Float) - Method in class net.sf.basedb.core.data.ColoringData
setMimeType(String) - Method in class net.sf.basedb.clients.web.util.ServletExportOutputStream: Calls ServletResponse.setContentType(String)
setMimeType(String) - Method in class net.sf.basedb.core.data.FileData
setMimeType(String) - Method in class net.sf.basedb.core.File: Set the mime type for this File item.
setMimeType(String) - Method in class net.sf.basedb.core.plugin.ExportOutputStream: Do nothing.
setMimeType(String) - Method in class net.sf.basedb.util.FileExportOutputStream: Calls File.setMimeType(String)
setMimeType(String) - Method in class net.sf.basedb.util.uri.UriMetadata
setMimeTypeAuto(String, ItemSubtype) - Method in class net.sf.basedb.core.File: Set the mime type automatically by checking the extension of the name.
setMinBaseVersion(String) - Method in class net.sf.basedb.util.extensions.AboutBean
setMinCount(int) - Method in class net.sf.basedb.util.AnyToAnyLinkStatistics.Options: Do not return information about links with a count that is less than this value.
setMinDataColumns(int) - Method in class net.sf.basedb.util.parser.FlatFileParser: Set the minimum number of columns a data line must contain in order for it to be counted as a data line.
setMinFraction(int) - Method in class net.sf.basedb.util.AnyToAnyLinkStatistics.Options: Do not return information about links if they are found on less than the specified fraction of samples.
setMinValue(Float) - Method in class net.sf.basedb.core.Coloring: Set the value that represents the minimum value.
setMinValue(Float) - Method in class net.sf.basedb.core.data.ColoringData
setMinValueDouble(Double) - Method in class net.sf.basedb.core.AnnotationType: Set the minimum allowed value for a Type.FLOAT or Type.DOUBLE annotation.
setMinValueLong(Long) - Method in class net.sf.basedb.core.AnnotationType: Set the minimum allowed value for an Type.INT or Type.LONG annotation.
setMode(boolean, boolean) - Method in class net.sf.basedb.util.basefile.BaseFileWriter
setMore(JSONObject, T) - Method in class net.sf.basedb.util.json.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.
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.
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.
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
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 - 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 in net.sf.basedb.util.overview: Severity levels for a validation rule.
Severity(String) - Constructor for enum 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 - 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 - 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 - 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 - net.sf.basedb.core.Job.ExecutionTime: The job is fast and should not take more than a minute to execute.
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.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 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 - 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 - 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
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 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 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 net.sf.basedb.core.Annotation.Source
SOURCE - 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 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 - net.sf.basedb.core.ExtraValue.CoordinateType: The extra values are attached to spots.
SPOT - 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 - net.sf.basedb.core.VirtualTable: Table that stores float spot extra values.
SPOT_EXTRA_INT - net.sf.basedb.core.VirtualTable: Table that stores integer spot extra values.
SPOT_EXTRA_STRING - 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 - 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 - 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 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 net.sf.basedb.core.plugin.Response.Status
Status(int, String, boolean) - Constructor for enum 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 - 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 - net.sf.basedb.core.Type: String type where maximum length allowed is 255 characters.
STRING - net.sf.basedb.plugins.Base1PluginExecuter.Base1JobParameterType
STRING - Static variable in class net.sf.basedb.core.hibernate.TypeWrapper
STRING_TOO_LONG_ERROR - Static variable in class net.sf.basedb.plugins.util.Parameters: The name of the parameter created by Parameters.stringTooLongError(String, String, String, String...).
STRING_TYPE - Static variable in class net.sf.basedb.core.dbengine.TableInfo
StringConverter - Class in net.sf.basedb.util.extensions.debug: Convert strings to other data types.
StringConverter - Class in net.sf.basedb.util.jep.convert: Convert a String constant to a Query API Expression.
StringConverter() - Constructor for class net.sf.basedb.util.jep.convert.StringConverter
StringConverter(Type, Object) - Constructor for class net.sf.basedb.util.extensions.debug.StringConverter
StringDetector - Interface in net.sf.basedb.util.charset: Interface for checking if a text line in a file seems to be decoded correctly with the current character set.
StringFormatter - Class in net.sf.basedb.clients.web.formatter: Format a string for output on a web page.
StringFormatter() - Constructor for class net.sf.basedb.clients.web.formatter.StringFormatter: Create a new string formatter.
StringLengthComparator - Class in net.sf.basedb.util: A comparator implementation for strings that sorts them according to their length.
StringLengthComparator() - Constructor for class net.sf.basedb.util.StringLengthComparator: Create a new string length comparator instance.
stringMapping - Static variable in enum net.sf.basedb.core.Type
stringMapping - Static variable in enum 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 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
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 - 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 - 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 Type 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.core.data.BioMaterialData
subtype - Variable in class net.sf.basedb.core.data.BioPlateTypeData
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.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.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
subtypeMapper - Variable in class net.sf.basedb.plugins.batchimport.AbstractItemImporter
subtypeName - Variable in class net.sf.basedb.clients.web.extensions.list.RelatedItemColumn.Specification
subtypeQuery - Variable in class net.sf.basedb.plugins.batchimport.AbstractItemImporter
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 - 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 net.sf.basedb.core.Formula.Type
supportsAverage() - Method in enum 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 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 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 Type 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 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 - net.sf.basedb.core.Item: The item is a SyncFilter
SyncFilter.SourceItemTransform - Enum in net.sf.basedb.core
syncFilters - Variable in class net.sf.basedb.core.data.ItemListData
synchronize(Set<Integer>, Set<Integer>) - Method in enum 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 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 - 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.table.Cell: The parent <tbl:table> tag.
table - Variable in class net.sf.basedb.clients.web.taglib.table.ColumnDef: The parent <tbl:table> tag.
table - Variable in class net.sf.basedb.clients.web.taglib.table.ColumnHeaders
table - Variable in class net.sf.basedb.clients.web.taglib.table.ColumnSubtitles
table - Variable in class net.sf.basedb.clients.web.taglib.table.Data: The parent <tbl:table> tag.
table - Variable in class net.sf.basedb.clients.web.taglib.table.Form
table - Variable in class net.sf.basedb.clients.web.taglib.table.Headers
table - Variable in class net.sf.basedb.clients.web.taglib.table.Hidden: The parent <tbl:table> tag.
table - Variable in class net.sf.basedb.clients.web.taglib.table.Label: The parent <tbl:table> tag.
table - Variable in class net.sf.basedb.clients.web.taglib.table.Navigator: The parent <tbl:table> tag.
table - Variable in class net.sf.basedb.clients.web.taglib.table.PresetSelector: The parent <tbl:table> tag.
table - Variable in class net.sf.basedb.clients.web.taglib.table.PropertyFilter: The parent <tbl:table> tag.
table - Variable in class net.sf.basedb.clients.web.taglib.table.Row: The parent <tbl:table> tag.
table - Variable in class net.sf.basedb.clients.web.taglib.table.Rows
table - Variable in class net.sf.basedb.core.BasicBatcher: The table where items of this type are stored.
table - Variable in class net.sf.basedb.core.dbengine.TableInfo
table - Variable in class net.sf.basedb.core.DynamicRestriction
table - Variable in class net.sf.basedb.core.hibernate.TableExistsWork
table - Variable in class net.sf.basedb.core.hibernate.TableInfoWork
table - Variable in class net.sf.basedb.core.query.VirtualColumnExpression
table - Variable in class net.sf.basedb.core.RawDataType
Table - Class in net.sf.basedb.clients.web.taglib.table: This is the main tag for the table.
Table() - Constructor for class net.sf.basedb.clients.web.taglib.table.Table
tableAlias - Variable in class net.sf.basedb.core.query.ReporterListExpression
tableColumn - Variable in class net.sf.basedb.core.query.ReporterListExpression
TableColumn - Class in net.sf.basedb.clients.web.taglib.table: Column properties class used to define table columns.
Example use in a jsp page:
TableColumn(String, String, String, Type, String, String, String, boolean, boolean, boolean, Formula.AverageMethod, Formatter<?>) - Constructor for class net.sf.basedb.clients.web.taglib.table.TableColumn
tableEncode(String) - Method in class net.sf.basedb.util.export.TableWriter: Encode the given string with the default encoder.
tableExists(String, Session) - Static method in class net.sf.basedb.core.HibernateUtil: Check if table in the dynamic database exists.
TableExistsWork - Class in net.sf.basedb.core.hibernate: A work implementation that checks if a given table exists in the database or not.
TableExistsWork(String, String, String) - Constructor for class net.sf.basedb.core.hibernate.TableExistsWork: Create a new work item.
TableInfo - Class in net.sf.basedb.core.dbengine: Holds minimal but useful information about a table in the database.
TableInfo(Table) - Constructor for class net.sf.basedb.core.dbengine.TableInfo
TableInfo(Table, DatabaseMetaData) - Constructor for class net.sf.basedb.core.dbengine.TableInfo: Deprecated.
In 3.14, use TableInfo(Table, DatabaseMetaData, String, String) instead
TableInfo(Table, DatabaseMetaData, String, String) - Constructor for class net.sf.basedb.core.dbengine.TableInfo: Create table info by reading JDBC metadata from the current database
TableInfo(Table, Dialect) - Constructor for class net.sf.basedb.core.dbengine.TableInfo: Create table info by reading the Hibernate mappings.
TableInfo.ColumnInfo - Class in net.sf.basedb.core.dbengine: Holds information about a single column in a table.
TableInfo.ForeignKeyInfo - Class in net.sf.basedb.core.dbengine: Holds information about a foreign key of a table.
TableInfo.IndexInfo - Class in net.sf.basedb.core.dbengine: Holds information about an index in a table.
TableInfo.PrimaryKeyInfo - Class in net.sf.basedb.core.dbengine: Holds information about the primary key of a table.
TableInfoWork - Class in net.sf.basedb.core.hibernate: A work implementation that loads database metadata for a table and returns it as a TableInfo object.
TableInfoWork(Table) - Constructor for class net.sf.basedb.core.hibernate.TableInfoWork: Create a new work item.
tableName - Variable in class net.sf.basedb.core.DropDynamicTableAction
tableName - Variable in class net.sf.basedb.core.RealTable: The unquoted table name.
tableName - Variable in enum 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 - 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 - 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 - 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 - 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 - net.sf.basedb.core.Type: Text blob type.
TEXT - 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 - 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 net.sf.basedb.util.parser.FlatFileParser.LineType
titlePrefix - Variable in class net.sf.basedb.util.overview.node.NameableNameGenerator
titleTemplate - Variable in class net.sf.basedb.clients.web.ModeInfo
tls - Static variable in class net.sf.basedb.util.EmailUtil
tmpTable - Variable in class net.sf.basedb.core.query.IdListRestriction
to - Variable in class net.sf.basedb.core.AnyToAny
to - Variable in class net.sf.basedb.core.data.MessageData
toAlpha - Variable in class net.sf.basedb.util.formatter.WellCoordinateFormatter
toArray() - Method in class net.sf.basedb.core.ItemResultList
toArray() - Method in class net.sf.basedb.util.Tree: Not supported.
toArray(Collection<T>, JsonConverter<? super T>) - Static method in class net.sf.basedb.util.json.JsonUtil: Convert a collection of objects to an array with JSON-compatible objects.
toArray(Iterator<T>, JsonConverter<? super T>) - Static method in class net.sf.basedb.util.json.JsonUtil: Convert all objects returned by the iterator to an array with JSON-compatible objects.
toArray(T[]) - Method in class net.sf.basedb.core.ItemResultList
toArray(T[]) - Method in class net.sf.basedb.util.Tree: Not supported.
ToBioSourceSourceItemTransformerFactory - Class in net.sf.basedb.util.listable: Transformer factory implementation for transforming to biosources.
ToBioSourceSourceItemTransformerFactory() - Constructor for class net.sf.basedb.util.listable.ToBioSourceSourceItemTransformerFactory
toChangeDetails(boolean, boolean) - Method in class net.sf.basedb.core.log.EntityDetails: Create a list of ChangeHistoryDetailData objects from the information in this object assuming that the entity is a subclass of BasicData.
toChangeDetails(Item, int, String, ChangeType, boolean, boolean) - Method in class net.sf.basedb.core.log.EntityDetails: Create a list of ChangeHistoryDetailData objects using a mix of the information in this object, and the given parameters.
toChangeHistoryData() - Method in class net.sf.basedb.core.log.TransactionDetails: Convert the information about the transaction to a ChangeHistoryData object.
toData() - Method in class net.sf.basedb.core.ClonableProperty: Create a data-layer reprsentation of the cloned property.
toDate(Expression) - Static method in class net.sf.basedb.core.query.Expressions: Get the date part from a date or timestamp expression.
ToDateExpression - Class in net.sf.basedb.core.query: Get the date part of a date or timestamp epxression.
ToDateExpression(Expression) - Constructor for class net.sf.basedb.core.query.ToDateExpression
ToDerivedBioAssaySourceItemTransformerFactory - Class in net.sf.basedb.util.listable: Transformer factory implementation for transforming to derived bioassays.
ToDerivedBioAssaySourceItemTransformerFactory() - Constructor for class net.sf.basedb.util.listable.ToDerivedBioAssaySourceItemTransformerFactory
toDescription() - Method in class net.sf.basedb.clients.web.extensions.ServletWrapperKey
toDescription() - Method in class net.sf.basedb.util.extensions.manager.ExtensionKey
toDescription() - Method in class net.sf.basedb.util.extensions.manager.ExtensionPointKey
toDescription() - Method in class net.sf.basedb.util.extensions.manager.FactoryParametersKey
toDescription() - Method in interface net.sf.basedb.util.extensions.manager.ObjectKey: Get a string description of the key that is suitable for use in (error) messages to users.
toDescription() - Method in class net.sf.basedb.util.extensions.manager.PluginInfoKey
toExcelValue(Boolean) - Method in class net.sf.basedb.util.formatter.BooleanFormatter
toExcelValue(Integer) - Method in class net.sf.basedb.util.formatter.WellCoordinateFormatter
toExcelValue(Number) - Method in class net.sf.basedb.util.formatter.AdaptiveNumberFormatter
toExcelValue(Number) - Method in class net.sf.basedb.util.formatter.IntegerFormatter
toExcelValue(Number) - Method in class net.sf.basedb.util.formatter.NumberFormatFormatter
toExcelValue(Number) - Method in class net.sf.basedb.util.formatter.NumberFormatter
toExcelValue(Object) - Method in class net.sf.basedb.util.excel.AutoFormatter
toExcelValue(Object) - Method in class net.sf.basedb.util.formatter.MultiFormatter
toExcelValue(String) - Method in class net.sf.basedb.clients.web.formatter.NiceFormatter: No escaping is needed.
toExcelValue(String) - Method in class net.sf.basedb.clients.web.formatter.StringFormatter: No escaping is needed.
toExcelValue(Date) - Method in class net.sf.basedb.util.formatter.DateFormatter
toExcelValue(T) - Method in interface net.sf.basedb.util.excel.ExcelFormatter: Convert and format the given value to an Excel value.
toExcelValue(T) - Method in class net.sf.basedb.util.excel.WrappedFormatter
toExcelValue(T) - Method in class net.sf.basedb.util.formatter.ToStringFormatter
toExpression(Integer) - Method in class net.sf.basedb.util.jep.convert.IntegerConverter: Convert to expression by calling Expressions.integer(int).
toExpression(Number) - Method in class net.sf.basedb.util.jep.convert.FloatConverter: Convert to expression by calling Expressions.aFloat(float).
toExpression(String) - Method in class net.sf.basedb.util.jep.convert.StringConverter: Convert to expression by calling Expressions.string(String).
toExpression(ASTConstant) - Method in class net.sf.basedb.util.jep.convert.ASTConstantConverter: Get the value from the constant node and check the ConverterFactory for a registered converter for the class and use it.
toExpression(ASTFunNode) - Method in class net.sf.basedb.util.jep.convert.ASTFunNodeConverter: Get the PostfixMathCommandI object from the function node and delegate conversion to JepExpressionFunction if that interface is implemented.
toExpression(ASTVarNode) - Method in class net.sf.basedb.util.jep.convert.ASTVarNodeConverter: Converts a JEP variable to a parameter.
toExpression(Node) - Method in class net.sf.basedb.util.jep.ChannelFunction: Use the Dynamic.column(VirtualColumn) method to create an expression referencing a channel intensity.
toExpression(Node) - Method in class net.sf.basedb.util.jep.convert.AbsConverter: Convert to expression by calling Expressions.abs(Expression).
toExpression(Node) - Method in class net.sf.basedb.util.jep.convert.AddConverter: Convert to expression by calling Expressions.add(Expression, Expression).
toExpression(Node) - Method in class net.sf.basedb.util.jep.convert.DivideConverter: Convert to expression by calling Expressions.divide(Expression, Expression).
toExpression(Node) - Method in class net.sf.basedb.util.jep.convert.ExpConverter: Convert to expression by calling Expressions.exp(Expression).
toExpression(Node) - Method in class net.sf.basedb.util.jep.convert.IfConverter: Convert to expression by calling Expressions.caseWhen(Expression, net.sf.basedb.core.query.WhenStatement[]).
toExpression(Node) - Method in class net.sf.basedb.util.jep.convert.LogarithmConverter: Convert to expression by calling Expressions.log10(Expression).
toExpression(Node) - Method in class net.sf.basedb.util.jep.convert.MultiplyConverter: Convert to expression by calling Expressions.multiply(Expression, Expression).
toExpression(Node) - Method in class net.sf.basedb.util.jep.convert.NaturalLogarithmConverter: Convert to expression by calling Expressions.ln(Expression).
toExpression(Node) - Method in class net.sf.basedb.util.jep.convert.SquareRootConverter: Convert to expression by calling Expressions.sqrt(Expression).
toExpression(Node) - Method in class net.sf.basedb.util.jep.convert.SubtractConverter: Convert to expression by calling Expressions.subtract(Expression, Expression).
toExpression(Node) - Method in class net.sf.basedb.util.jep.convert.UMinusConverter
toExpression(Node) - Method in class net.sf.basedb.util.jep.ExtraValueFunction: Use the Dynamic.extraValue(ExtraValue) method to create an expression referencing an extra value.
toExpression(Node) - Method in interface net.sf.basedb.util.jep.JepExpressionFunction: Convert this function to an Expression that can be used in a query.
toExpression(Node) - Method in class net.sf.basedb.util.jep.Log2Function: Use the Expressions.log2(Expression) method to create an expression taking the 2-based logarithm of the argument.
toExpression(Node) - Method in class net.sf.basedb.util.jep.MeanFunction: Use the Dynamic.meanRawData(String) method to create an expression for the mean of the given raw data property.
toExpression(Node) - Method in class net.sf.basedb.util.jep.PositionFunction: Use the Dynamic.column(VirtualColumn) method to create an expression referencing a position.
toExpression(Node) - Method in class net.sf.basedb.util.jep.RawChannelFunction: Use the Dynamic.column(VirtualColumn) method to create an expression referencing a channel intensity.
toExpression(Node) - Method in class net.sf.basedb.util.jep.RawFunction: Use the Dynamic.rawData(String) method to create an expression referencing a raw data property.
toExpression(Node) - Method in class net.sf.basedb.util.jep.ReporterFunction: Use the Dynamic.reporter(String) method to create an expression referencing a reporter property.
toExpression(Node) - Method in class net.sf.basedb.util.jep.ScoreFunction: Use the Dynamic.score(ReporterList) method to create an expression referencing the score of a reporter in the reporter list.
toExpression(T) - Method in class net.sf.basedb.util.jep.convert.AbstractJepConversionFunction: Convert to a restriction and then use Expressions.bool(Restriction) to create a boolean expression.
toExpression(T) - Method in interface net.sf.basedb.util.jep.convert.JepConversionFunction: Convert the object to an expression.
ToExtractSourceItemTransformerFactory - Class in net.sf.basedb.util.listable: Transformer factory implementation for transforming to extracts.
ToExtractSourceItemTransformerFactory() - Constructor for class net.sf.basedb.util.listable.ToExtractSourceItemTransformerFactory
ToExtractSourceItemTransformerFactory(boolean) - Constructor for class net.sf.basedb.util.listable.ToExtractSourceItemTransformerFactory
toFile(String) - Method in class net.sf.basedb.util.extensions.manager.Settings: A file is typically stored under the absolute path, but if it matches the plug-ins directory we replace it with {plugins.dir}.
toHex(Color) - Static method in class net.sf.basedb.util.ColorGenerator: Generate a hex color string from a Color object.
toId - Variable in class net.sf.basedb.core.data.AnyToAnyData
toInt(Set<Include>) - Static method in enum 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 - net.sf.basedb.plugins.PrintMapFlatFileImporter.Section
toolbar - Variable in class net.sf.basedb.clients.web.taglib.table.Button: The parent <tbl:toolbar> tag.
toolbar - Variable in class net.sf.basedb.clients.web.taglib.table.Label: The parent <tbl:toolbar> tag.
Toolbar - Class in net.sf.basedb.clients.web.taglib.table: This tag creates a toolbar.
Toolbar() - Constructor for class net.sf.basedb.clients.web.taglib.table.Toolbar
TOOLBAR_ITEMS - Static variable in class net.sf.basedb.clients.web.extensions.toolbar.ToolbarUtil: An array containing all items that we are registering an extension point for.
ToolbarButtonRenderer - Class in net.sf.basedb.clients.web.extensions.toolbar: A renderer for toolbar button actions, which displays the action as a toolbar button.
ToolbarButtonRenderer() - Constructor for class net.sf.basedb.clients.web.extensions.toolbar.ToolbarButtonRenderer: Create a new "standalone" toolbar button renderer.
ToolbarButtonRenderer(JspContext) - Constructor for class net.sf.basedb.clients.web.extensions.toolbar.ToolbarButtonRenderer: Create a new toolbar button renderer.
ToolbarButtonRendererFactory - Class in net.sf.basedb.clients.web.extensions.toolbar: Factory that create ToolbarButtonRenderer objects for rendering ButtonAction:s.
ToolbarButtonRendererFactory() - Constructor for class net.sf.basedb.clients.web.extensions.toolbar.ToolbarButtonRendererFactory
ToolbarUtil - Class in net.sf.basedb.clients.web.extensions.toolbar: Utility class for toolbar extension points.
ToolbarUtil() - Constructor for class net.sf.basedb.clients.web.extensions.toolbar.ToolbarUtil
toolParameters - Variable in class net.sf.basedb.plugins.ManualDerivedBioAssayCreator
toolParameters - Variable in class net.sf.basedb.plugins.ManualTransformCreator
tooltip - Variable in class net.sf.basedb.clients.web.extensions.list.AbstractListColumnBean
tooltip - Variable in class net.sf.basedb.clients.web.extensions.list.PropertyPathActionFactory
tooltip - Variable in class net.sf.basedb.clients.web.extensions.login.FieldInfo
tooltip - Variable in class net.sf.basedb.clients.web.extensions.menu.FixedMenuItemFactory
tooltip - Variable in class net.sf.basedb.clients.web.extensions.menu.MenuItemBean
tooltip - Variable in class net.sf.basedb.clients.web.extensions.tabcontrol.FixedTabFactory
tooltip - Variable in class net.sf.basedb.clients.web.extensions.tabcontrol.IncludeContentTabFactory
tooltip - Variable in class net.sf.basedb.clients.web.extensions.tabcontrol.TabBean
tooltip - Variable in class net.sf.basedb.clients.web.extensions.toolbar.ButtonBean
tooltip - Variable in class net.sf.basedb.clients.web.extensions.toolbar.FixedButtonFactory
tooltip - Variable in class net.sf.basedb.clients.web.taglib.Button: An optional tooltip.
tooltip - Variable in class net.sf.basedb.clients.web.taglib.Help: Optional tooltip.
tooltip - Variable in class net.sf.basedb.clients.web.taglib.Icon: An optional tooltip.
tooltip - Variable in class net.sf.basedb.clients.web.taglib.menu.Menuitem: A tooltip explaining the menu item.
tooltip - Variable in class net.sf.basedb.clients.web.taglib.menu.Submenu: A tooltip explaining the menu item.
tooltip - Variable in class net.sf.basedb.clients.web.taglib.path.PathElement: A tooltip explaining the link.
tooltip - Variable in class net.sf.basedb.clients.web.taglib.PropertyValue: An optional tooltip.
tooltip - Variable in class net.sf.basedb.clients.web.taglib.tab.Tab: A popup tooltip text.
tooltip - Variable in class net.sf.basedb.clients.web.taglib.table.Button: An optional tooltip that will show when the mouse is over the button.
tooltip - Variable in class net.sf.basedb.clients.web.taglib.table.ColumnDef: A tooltip with explaining text.
tooltip - Variable in class net.sf.basedb.clients.web.taglib.table.Label: An optional tooltip that will show when the mouse is over the button.
tooltip - Variable in class net.sf.basedb.clients.web.taglib.Zoom: Optional tooltip.
tooManyValuesErrorParameter - Static variable in class net.sf.basedb.plugins.AnnotationFlatFileImporter
TOP - Static variable in class net.sf.basedb.clients.web.taglib.tab.TabControl: Tabs are at the top of the tab control.
ToPhysicalBioAssaySourceItemTransformerFactory - Class in net.sf.basedb.util.listable: Transformer factory implementation for transforming to physical bioassays.
ToPhysicalBioAssaySourceItemTransformerFactory() - Constructor for class net.sf.basedb.util.listable.ToPhysicalBioAssaySourceItemTransformerFactory
toPluginParameter(DbControl, BioAssaySet) - Method in class net.sf.basedb.plugins.executor.ParameterDefinition: Convert this parameter definition to a PluginParameter object.
toQl(DbControl) - Method in class net.sf.basedb.core.AbstractQuery
toQl(DbControl) - Method in interface net.sf.basedb.core.query.Query: Generate the query string that is going to be sent to the underlying query system (eg.
toQl(Query, DbControl) - Method in class net.sf.basedb.clients.web.ExperimentExplorer.InExpression
toQl(Query, DbControl) - Method in class net.sf.basedb.core.AnnotationRestriction
toQl(Query, DbControl) - Method in class net.sf.basedb.core.AnnotationSet.ProjectSpecificAnnotationsRestriction
toQl(Query, DbControl) - Method in class net.sf.basedb.core.DynamicJoin
toQl(Query, DbControl) - Method in class net.sf.basedb.core.DynamicRestriction
toQl(Query, DbControl) - Method in class net.sf.basedb.core.ExtraValueExpression
toQl(Query, DbControl) - Method in class net.sf.basedb.core.ExtraValueJoin
toQl(Query, DbControl) - Method in class net.sf.basedb.core.MeanRawDataPropertyExpression
toQl(Query, DbControl) - Method in class net.sf.basedb.core.query.AbsExpression
toQl(Query, DbControl) - Method in class net.sf.basedb.core.query.AddExpression
toQl(Query, DbControl) - Method in class net.sf.basedb.core.query.AndRestriction
toQl(Query, DbControl) - Method in class net.sf.basedb.core.query.AnnotationJoin
toQl(Query, DbControl) - Method in class net.sf.basedb.core.query.AnyToAnyRestriction
toQl(Query, DbControl) - Method in class net.sf.basedb.core.query.AscOrder
toQl(Query, DbControl) - Method in class net.sf.basedb.core.query.BetweenRestriction
toQl(Query, DbControl) - Method in class net.sf.basedb.core.query.BooleanExpression
toQl(Query, DbControl) - Method in class net.sf.basedb.core.query.CaseExpression
toQl(Query, DbControl) - Method in class net.sf.basedb.core.query.ConditionalQueryElement
toQl(Query, DbControl) - Method in class net.sf.basedb.core.query.CountExpression
toQl(Query, DbControl) - Method in class net.sf.basedb.core.query.DescOrder
toQl(Query, DbControl) - Method in class net.sf.basedb.core.query.DivideExpression
toQl(Query, DbControl) - Method in class net.sf.basedb.core.query.EqRestriction
toQl(Query, DbControl) - Method in class net.sf.basedb.core.query.ExpExpression
toQl(Query, DbControl) - Method in class net.sf.basedb.core.query.ExpressionSelect
toQl(Query, DbControl) - Method in class net.sf.basedb.core.query.FloatExpression
toQl(Query, DbControl) - Method in class net.sf.basedb.core.query.GeometricMeanExpression
toQl(Query, DbControl) - Method in class net.sf.basedb.core.query.GteqRestriction
toQl(Query, DbControl) - Method in class net.sf.basedb.core.query.GtRestriction
toQl(Query, DbControl) - Method in class net.sf.basedb.core.query.HqlElementsExpression
toQl(Query, DbControl) - Method in class net.sf.basedb.core.query.HqlEntityExpression
toQl(Query, DbControl) - Method in class net.sf.basedb.core.query.HqlEntityParameterExpression
toQl(Query, DbControl) - Method in class net.sf.basedb.core.query.HqlExpression
toQl(Query, DbControl) - Method in class net.sf.basedb.core.query.HqlIndexExpression
toQl(Query, DbControl) - Method in class net.sf.basedb.core.query.HqlInnerJoin
toQl(Query, DbControl) - Method in class net.sf.basedb.core.query.HqlLeftJoin
toQl(Query, DbControl) - Method in class net.sf.basedb.core.query.HqlPropertyExpression
toQl(Query, DbControl) - Method in class net.sf.basedb.core.query.HqlRightJoin
toQl(Query, DbControl) - Method in class net.sf.basedb.core.query.HqlSizeExpression
toQl(Query, DbControl) - Method in class net.sf.basedb.core.query.IdListRestriction
toQl(Query, DbControl) - Method in class net.sf.basedb.core.query.InRestriction
toQl(Query, DbControl) - Method in class net.sf.basedb.core.query.IntegerExpression
toQl(Query, DbControl) - Method in class net.sf.basedb.core.query.LikeRestriction
toQl(Query, DbControl) - Method in class net.sf.basedb.core.query.LogExpression
toQl(Query, DbControl) - Method in class net.sf.basedb.core.query.LteqRestriction
toQl(Query, DbControl) - Method in class net.sf.basedb.core.query.LtRestriction
toQl(Query, DbControl) - Method in class net.sf.basedb.core.query.MaxExpression
toQl(Query, DbControl) - Method in class net.sf.basedb.core.query.MeanExpression
toQl(Query, DbControl) - Method in class net.sf.basedb.core.query.MinExpression
toQl(Query, DbControl) - Method in class net.sf.basedb.core.query.MultiplyExpression
toQl(Query, DbControl) - Method in class net.sf.basedb.core.query.NegateExpression
toQl(Query, DbControl) - Method in class net.sf.basedb.core.query.NeqRestriction
toQl(Query, DbControl) - Method in class net.sf.basedb.core.query.NotRestriction
toQl(Query, DbControl) - Method in class net.sf.basedb.core.query.OrRestriction
toQl(Query, DbControl) - Method in class net.sf.basedb.core.query.ParameterExpression
toQl(Query, DbControl) - Method in class net.sf.basedb.core.query.PermissionRestriction
toQl(Query, DbControl) - Method in class net.sf.basedb.core.query.PowerExpression
toQl(Query, DbControl) - Method in class net.sf.basedb.core.query.QuadraticMeanExpression
toQl(Query, DbControl) - Method in interface net.sf.basedb.core.query.QueryElement: Create a query language string of the query element.
toQl(Query, DbControl) - Method in class net.sf.basedb.core.query.ReporterListExpression
toQl(Query, DbControl) - Method in class net.sf.basedb.core.query.RlikeRestriction
toQl(Query, DbControl) - Method in class net.sf.basedb.core.query.SelectedExpression
toQl(Query, DbControl) - Method in class net.sf.basedb.core.query.SharedToRestriction
toQl(Query, DbControl) - Method in class net.sf.basedb.core.query.SqlColumnExpression
toQl(Query, DbControl) - Method in class net.sf.basedb.core.query.SqrtExpression
toQl(Query, DbControl) - Method in class net.sf.basedb.core.query.SubqueryExpression
toQl(Query, DbControl) - Method in class net.sf.basedb.core.query.SubtractExpression
toQl(Query, DbControl) - Method in class net.sf.basedb.core.query.SumExpression
toQl(Query, DbControl) - Method in class net.sf.basedb.core.query.ToDateExpression
toQl(Query, DbControl) - Method in class net.sf.basedb.core.query.VirtualColumnExpression
toQl(Query, DbControl) - Method in class net.sf.basedb.core.query.VirtualColumnExpression.WrappedExpression
toQl(Query, DbControl) - Method in class net.sf.basedb.core.RawBioAssayPropertyExpression
toQl(Query, DbControl) - Method in class net.sf.basedb.core.RawDataPropertyExpression
toQl(Query, DbControl) - Method in class net.sf.basedb.core.RealJoin
toQl(Query, DbControl) - Method in class net.sf.basedb.core.ReporterListJoin
toQl(Query, DbControl) - Method in class net.sf.basedb.core.ReporterPropertyExpression
ToRawBioAssaySourceItemTransformerFactory - Class in net.sf.basedb.util.listable: Transformer factory implementation for transforming to raw bioassays.
ToRawBioAssaySourceItemTransformerFactory() - Constructor for class net.sf.basedb.util.listable.ToRawBioAssaySourceItemTransformerFactory
toReferenceUnit(double) - Method in class net.sf.basedb.core.Unit: Convert a value from this unit to the reference unit.
toRestriction(ASTFunNode) - Method in class net.sf.basedb.util.jep.convert.ASTFunNodeConverter: Get the PostfixMathCommandI object from the function node and delegate conversion to JepRestrictionFunction if that interface is implemented.
toRestriction(Node) - Method in class net.sf.basedb.util.jep.convert.AndConverter: Convert to restriction by calling Restrictions.and(Restriction[]).
toRestriction(Node) - Method in class net.sf.basedb.util.jep.convert.EqualsConverter: Convert to restriction by calling Restrictions.eq(Expression, Expression).
toRestriction(Node) - Method in class net.sf.basedb.util.jep.convert.GreaterConverter: Convert to restriction by calling Restrictions.gt(net.sf.basedb.core.query.Expression, net.sf.basedb.core.query.Expression).
toRestriction(Node) - Method in class net.sf.basedb.util.jep.convert.GreaterEqualsConverter: Convert to restriction by calling Restrictions.gteq(net.sf.basedb.core.query.Expression, net.sf.basedb.core.query.Expression).
toRestriction(Node) - Method in class net.sf.basedb.util.jep.convert.LessConverter: Convert to restriction by calling Restrictions.lt(net.sf.basedb.core.query.Expression, net.sf.basedb.core.query.Expression).
toRestriction(Node) - Method in class net.sf.basedb.util.jep.convert.LessEqualsConverter: Convert to restriction by calling Restrictions.lteq(net.sf.basedb.core.query.Expression, net.sf.basedb.core.query.Expression).
toRestriction(Node) - Method in class net.sf.basedb.util.jep.convert.NotConverter: Convert to restriction by calling Restrictions.not(Restriction).
toRestriction(Node) - Method in class net.sf.basedb.util.jep.convert.NotEqualsConverter: Convert to restriction by calling Restrictions.neq(net.sf.basedb.core.query.Expression, net.sf.basedb.core.query.Expression).
toRestriction(Node) - Method in class net.sf.basedb.util.jep.convert.OrConverter: Convert to restriction by calling Restrictions.or(Restriction[]).
toRestriction(Node) - Method in class net.sf.basedb.util.jep.InReporterListFunction: Use the Dynamic.isPartOf(ReporterList) method to create a restriction checking that a reporter is found in the reporter list.
toRestriction(Node) - Method in interface net.sf.basedb.util.jep.JepRestrictionFunction: Convert this function to a Restriction that can be used in a query.
toRestriction(Node) - Method in class net.sf.basedb.util.jep.NotInReporterListFunction: Use the Dynamic.isNotPartOf(ReporterList) method to create a restriction checking that a reporter isn't found in the reporter list.
toRestriction(T) - Method in class net.sf.basedb.util.jep.convert.AbstractJepConversionFunction
toRestriction(T) - Method in interface net.sf.basedb.util.jep.convert.JepConversionFunction: Convert the object to a restriction.
TORGUE - Static variable in class net.sf.basedb.core.Quantity: The id for the Quantity object representing torque.
ToSampleSourceItemTransformerFactory - Class in net.sf.basedb.util.listable: Transformer factory implementation for transforming to samples.
ToSampleSourceItemTransformerFactory() - Constructor for class net.sf.basedb.util.listable.ToSampleSourceItemTransformerFactory
ToSampleSourceItemTransformerFactory(boolean) - Constructor for class net.sf.basedb.util.listable.ToSampleSourceItemTransformerFactory
ToSpaceEncoderDecoder - Class in net.sf.basedb.util.encode: Encoder implementation that replaces newline, carriage return, tab and backslash with a space.
ToSpaceEncoderDecoder() - Constructor for class net.sf.basedb.util.encode.ToSpaceEncoderDecoder
toString() - Method in class net.sf.basedb.clients.jobagent.slotmanager.Slot
toString() - Method in class net.sf.basedb.clients.web.extensions.service.DummyService
toString() - Method in class net.sf.basedb.clients.web.extensions.ServletWrapperKey
toString() - Method in class net.sf.basedb.clients.web.extensions.skin.ImageRemapper
toString() - Method in class net.sf.basedb.clients.web.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 net.sf.basedb.core.BioMaterialEvent.Type
toString() - Method in enum 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 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 net.sf.basedb.core.Formula.AverageMethod
toString() - Method in enum net.sf.basedb.core.Formula.Parser
toString() - Method in enum net.sf.basedb.core.Formula.Type
toString() - Method in class net.sf.basedb.core.IntegerParameterType
toString() - Method in enum net.sf.basedb.core.IntensityTransform
toString() - Method in enum net.sf.basedb.core.Item
toString() - Method in enum 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 net.sf.basedb.core.Job.ExecutionTime
toString() - Method in enum net.sf.basedb.core.Job.Status
toString() - Method in enum net.sf.basedb.core.Job.Type
toString() - Method in enum 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 enum 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 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 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.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 net.sf.basedb.core.Type
toString() - Method in enum 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 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 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 - net.sf.basedb.util.extensions.logging.LogLevel
TRACE - 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 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 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 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 - 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 - net.sf.basedb.util.formatter.BooleanFormatter.Type: Display true/false.
trueValue - Variable in enum 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 in net.sf.basedb.core: This class defines constants for supported value types in BASE.
Type() - Constructor for enum net.sf.basedb.clients.web.extensions.fileviewer.FileViewerContext.Type
Type() - Constructor for enum net.sf.basedb.core.Path.Type
Type() - Constructor for enum net.sf.basedb.util.overview.Node.Type
Type(int) - Constructor for enum net.sf.basedb.core.plugin.GuiContext.Type
Type(int, String) - Constructor for enum net.sf.basedb.core.BioMaterialEvent.Type
Type(int, String) - Constructor for enum net.sf.basedb.core.Job.Type
Type(int, String, boolean, boolean, Type) - Constructor for enum net.sf.basedb.core.Formula.Type
Type(String, String) - Constructor for enum net.sf.basedb.util.formatter.BooleanFormatter.Type
Type(TypeWrapper<?>, int, Class<?>, String, String, String, boolean, boolean, boolean, boolean) - Constructor for enum 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 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 - 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 - 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 - 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 - 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 Type 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 net.sf.basedb.core.IntensityTransform: Un-transform a transformed intensity value back to a regular intensity value.
unTransform(Expression) - Method in enum 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 - net.sf.basedb.core.hibernate.SchemaGenerator.Mode: Updating an existing installation.
UPDATE - net.sf.basedb.core.log.ChangeType
UPDATE - 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 - 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.
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
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
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 - 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 - 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 - 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 - 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 - 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 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 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 net.sf.basedb.core.Formula.Type
validate(ValidationAction) - Method in class net.sf.basedb.util.fileset.ValidationRenderer
VALIDATE_IMMEDIATELY - net.sf.basedb.util.fileset.Accept: The file is handled by the validator and should be validated immediately.
VALIDATE_LATER - 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
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 net.sf.basedb.core.BioMaterialEvent.Type
value - Variable in enum 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 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 net.sf.basedb.core.FeatureIdentificationMethod: The integer value of this method.
value - Variable in enum net.sf.basedb.core.Formula.AverageMethod
value - Variable in enum net.sf.basedb.core.Formula.Parser
value - Variable in enum net.sf.basedb.core.Formula.Type
value - Variable in enum net.sf.basedb.core.Include
value - Variable in enum net.sf.basedb.core.IntensityTransform: The integer value of this transform.
value - Variable in enum net.sf.basedb.core.Item
value - Variable in enum net.sf.basedb.core.ItemContext.SortDirection: The integer value of this direction.
value - Variable in enum net.sf.basedb.core.Job.ExecutionTime
value - Variable in enum net.sf.basedb.core.Job.Status
value - Variable in enum net.sf.basedb.core.Job.Type
value - Variable in enum net.sf.basedb.core.Location: The integer value of this location.
value - Variable in enum net.sf.basedb.core.log.ChangeType
value - Variable in enum net.sf.basedb.core.Operator
value - Variable in enum net.sf.basedb.core.plugin.GuiContext.Type
value - Variable in enum 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 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() - Method in annotation type 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 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 net.sf.basedb.core.BioMaterialEvent.Type: Maps the integer that is stored in the database.
valueMapping - Static variable in enum net.sf.basedb.core.BioWell.LockMode: Maps an integer to a lock mode.
valueMapping - Static variable in enum net.sf.basedb.core.ExtraValue.CoordinateType: Maps the integer that is stored in the database with an fileaction.
valueMapping - Static variable in enum net.sf.basedb.core.FeatureIdentificationMethod: Maps an integer to a location.
valueMapping - Static variable in enum net.sf.basedb.core.Formula.AverageMethod: Maps the integer that is stored in the database.
valueMapping - Static variable in enum net.sf.basedb.core.Formula.Parser: Maps the integer that is stored in the database.
valueMapping - Static variable in enum net.sf.basedb.core.Formula.Type: Maps the integer that is stored in the database.
valueMapping - Static variable in enum net.sf.basedb.core.IntensityTransform: Maps an integer to a transform.
valueMapping - Static variable in enum net.sf.basedb.core.Item
valueMapping - Static variable in enum net.sf.basedb.core.ItemContext.SortDirection: Maps an integer to a sort direction.
valueMapping - Static variable in enum net.sf.basedb.core.Job.ExecutionTime: Maps the integer that is stored in the database.
valueMapping - Static variable in enum net.sf.basedb.core.Job.Status: Maps the integer that is stored in the database.
valueMapping - Static variable in enum net.sf.basedb.core.Job.Type: Maps the integer that is stored in the database.
valueMapping - Static variable in enum net.sf.basedb.core.Location: Maps an integer to a location.
valueMapping - Static variable in enum net.sf.basedb.core.Operator
valueMapping - Static variable in enum net.sf.basedb.core.plugin.GuiContext.Type: Maps the integer that is stored in the database.
valueMapping - Static variable in enum net.sf.basedb.core.plugin.Plugin.MainType: Maps an integer to a type.
valueMapping - Static variable in enum net.sf.basedb.core.Type
valueOf(String) - Static method in enum net.sf.basedb.clients.web.extensions.fileviewer.FileViewerContext.Type: Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum net.sf.basedb.clients.web.extensions.menu.MenuItemAction.MenuType: Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum net.sf.basedb.core.Annotation.Source: Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum net.sf.basedb.core.AnnotationBatcher.Change: Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum net.sf.basedb.core.BioMaterialEvent.Type: Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum net.sf.basedb.core.BioWell.LockMode: Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum net.sf.basedb.core.ExtraValue.CoordinateType: Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum net.sf.basedb.core.FeatureIdentificationMethod: Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum net.sf.basedb.core.Formula.AverageMethod: Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum net.sf.basedb.core.Formula.Parser: Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum net.sf.basedb.core.Formula.Type: Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum net.sf.basedb.core.hibernate.SchemaGenerator.Mode: Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum net.sf.basedb.core.Include: Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum net.sf.basedb.core.IntensityTransform: Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum net.sf.basedb.core.Item: Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum net.sf.basedb.core.ItemContext.SortDirection: Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum net.sf.basedb.core.ItemList.SynchronizeOption: Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum net.sf.basedb.core.Job.ExecutionTime: Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum net.sf.basedb.core.Job.Status: Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum net.sf.basedb.core.Job.Type: Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum net.sf.basedb.core.Location: Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum net.sf.basedb.core.log.ChangeType: Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum net.sf.basedb.core.Operator: Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum net.sf.basedb.core.Path.Type: Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum net.sf.basedb.core.Permission: Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum net.sf.basedb.core.plugin.GuiContext.Type: Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum net.sf.basedb.core.plugin.Plugin.MainType: Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum net.sf.basedb.core.plugin.Response.Status: Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum net.sf.basedb.core.query.JoinType: Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum net.sf.basedb.core.query.QuerySection: Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum net.sf.basedb.core.query.QueryType: Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum net.sf.basedb.core.ReporterCloneBatcher.CloneSource: Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum net.sf.basedb.core.SyncFilter.SourceItemTransform: Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum net.sf.basedb.core.Transactional.Action: Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum net.sf.basedb.core.Type: Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum net.sf.basedb.core.VirtualTable: Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum net.sf.basedb.plugins.Base1PluginExecuter.Base1JobParameterType: Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum net.sf.basedb.plugins.PrintMapFlatFileImporter.FormatType: Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum net.sf.basedb.plugins.PrintMapFlatFileImporter.Section: Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum net.sf.basedb.util.extensions.logging.LogLevel: Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum net.sf.basedb.util.extensions.LoggingErrorHandlerFactory.Level: Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum net.sf.basedb.util.extensions.xml.PathType: Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum net.sf.basedb.util.fileset.Accept: Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum net.sf.basedb.util.formatter.BooleanFormatter.Type: Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum net.sf.basedb.util.overview.node.ChildNodeDirection: Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum net.sf.basedb.util.overview.Node.Type: Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum net.sf.basedb.util.overview.Severity: Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum net.sf.basedb.util.parser.FlatFileParser.LineType: Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum net.sf.basedb.util.plot.HistogramPlot.YAggregate: Returns the enum constant of this type 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 net.sf.basedb.clients.web.extensions.fileviewer.FileViewerContext.Type: Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum net.sf.basedb.clients.web.extensions.menu.MenuItemAction.MenuType: Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum net.sf.basedb.core.Annotation.Source: Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum net.sf.basedb.core.AnnotationBatcher.Change: Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum net.sf.basedb.core.BioMaterialEvent.Type: Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum net.sf.basedb.core.BioWell.LockMode: Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum net.sf.basedb.core.ExtraValue.CoordinateType: Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum net.sf.basedb.core.FeatureIdentificationMethod: Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum net.sf.basedb.core.Formula.AverageMethod: Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum net.sf.basedb.core.Formula.Parser: Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum net.sf.basedb.core.Formula.Type: Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum net.sf.basedb.core.hibernate.SchemaGenerator.Mode: Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum net.sf.basedb.core.Include: Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum net.sf.basedb.core.IntensityTransform: Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum net.sf.basedb.core.Item: Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum net.sf.basedb.core.ItemContext.SortDirection: Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum net.sf.basedb.core.ItemList.SynchronizeOption: Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum net.sf.basedb.core.Job.ExecutionTime: Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum net.sf.basedb.core.Job.Status: Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum net.sf.basedb.core.Job.Type: Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum net.sf.basedb.core.Location: Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum net.sf.basedb.core.log.ChangeType: Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum net.sf.basedb.core.Operator: Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum net.sf.basedb.core.Path.Type: Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum net.sf.basedb.core.Permission: Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum net.sf.basedb.core.plugin.GuiContext.Type: Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum net.sf.basedb.core.plugin.Plugin.MainType: Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum net.sf.basedb.core.plugin.Response.Status: Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum net.sf.basedb.core.query.JoinType: Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum net.sf.basedb.core.query.QuerySection: Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum net.sf.basedb.core.query.QueryType: Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum net.sf.basedb.core.ReporterCloneBatcher.CloneSource: Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum net.sf.basedb.core.SyncFilter.SourceItemTransform: Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum net.sf.basedb.core.Transactional.Action: Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum net.sf.basedb.core.Type: Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum net.sf.basedb.core.VirtualTable: Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum net.sf.basedb.plugins.Base1PluginExecuter.Base1JobParameterType: Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum net.sf.basedb.plugins.PrintMapFlatFileImporter.FormatType: Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum net.sf.basedb.plugins.PrintMapFlatFileImporter.Section: Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum net.sf.basedb.util.extensions.logging.LogLevel: Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum net.sf.basedb.util.extensions.LoggingErrorHandlerFactory.Level: Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum net.sf.basedb.util.extensions.xml.PathType: Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum net.sf.basedb.util.fileset.Accept: Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum net.sf.basedb.util.formatter.BooleanFormatter.Type: Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum net.sf.basedb.util.overview.node.ChildNodeDirection: Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum net.sf.basedb.util.overview.Node.Type: Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum net.sf.basedb.util.overview.Severity: Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum net.sf.basedb.util.parser.FlatFileParser.LineType: Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum net.sf.basedb.util.plot.HistogramPlot.YAggregate: Returns an array containing the constants of this enum type, 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 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 Type 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
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 net.sf.basedb.core.hibernate.SchemaGenerator.Mode
verifySchemaVersion() - Method in enum 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.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 - 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 - 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 - 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 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 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 - 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 - net.sf.basedb.util.extensions.LoggingErrorHandlerFactory.Level
warning(SAXParseException) - Method in class net.sf.basedb.util.XmlUtil2.Validator: Ignore warnings
WARNING - net.sf.basedb.util.extensions.logging.LogLevel
WARNING - net.sf.basedb.util.overview.Severity: The rule generate warnings.
was - Variable in enum net.sf.basedb.core.log.ChangeType
was(String) - Method in enum 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 - 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 - 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 - 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 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 net.sf.basedb.util.plot.HistogramPlot.YAggregate
yColumnMapping - Static variable in class net.sf.basedb.plugins.RawDataFlatFileImporter
YES_NO - 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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