Index (BASE 2.17.2 API documentation)

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2.17.2: 2011-06-17

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A

A - Variable in class net.sf.basedb.plugins.LowessNormalization.SpotData
abort - Variable in class net.sf.basedb.clients.web.fileupload.FileUploadProgress
ABORT - Static variable in class net.sf.basedb.core.signal.Signal: The ABORT signal, that requests that the receiver should clean up and die.
about - Variable in class net.sf.basedb.clients.web.extensions.ExtensionsFile
about - Static variable in class net.sf.basedb.clients.web.plugins.SimpleExport: Plugin description
About - Interface in net.sf.basedb.core.plugin: Get information, such as the name, version and authors, about a plugin.
about - Static variable in class net.sf.basedb.plugins.AnnotationFlatFileImporter
about - Static variable in class net.sf.basedb.plugins.Base1PluginExecuter: Plugin description
about - Static variable in class net.sf.basedb.plugins.BaseFileExporterPlugin
about - Static variable in class net.sf.basedb.plugins.batchimport.ArrayBatchImporter
about - Static variable in class net.sf.basedb.plugins.batchimport.ArrayDesignImporter
about - Static variable in class net.sf.basedb.plugins.batchimport.ArraySlideImporter
about - Static variable in class net.sf.basedb.plugins.batchimport.BioPlateImporter
about - Static variable in class net.sf.basedb.plugins.batchimport.BioSourceImporter
about - Static variable in class net.sf.basedb.plugins.batchimport.ExtractImporter
about - Static variable in class net.sf.basedb.plugins.batchimport.HybridizationImporter
about - Static variable in class net.sf.basedb.plugins.batchimport.LabeledExtractImporter
about - Static variable in class net.sf.basedb.plugins.batchimport.RawBioAssayImporter
about - Static variable in class net.sf.basedb.plugins.batchimport.SampleImporter
about - Static variable in class net.sf.basedb.plugins.batchimport.ScanImporter
about - Static variable in class net.sf.basedb.plugins.BfsExporterPlugin
about - Static variable in class net.sf.basedb.plugins.BioAssaySetExporter: Deprecated.
about - Static variable in class net.sf.basedb.plugins.CdfFileReporterImporter: Plugin description
about - Static variable in class net.sf.basedb.plugins.executor.BaseFileExporterSupport
about - Static variable in class net.sf.basedb.plugins.executor.BaseFileImporterSupport
about - Static variable in class net.sf.basedb.plugins.executor.BfsExporterSupport
about - Static variable in class net.sf.basedb.plugins.executor.BfsImporterSupport
about - Static variable in class net.sf.basedb.plugins.executor.ExternalProgramExecutor
about - Static variable in class net.sf.basedb.plugins.executor.FileOnlyImporterSupport
about - Static variable in class net.sf.basedb.plugins.FormulaFilter: Plugin description
about - Static variable in class net.sf.basedb.plugins.GalExporter
about - Static variable in class net.sf.basedb.plugins.HelpExporter
about - Static variable in class net.sf.basedb.plugins.HelpImporter
about - Static variable in class net.sf.basedb.plugins.IlluminaRawDataImporter
about - Static variable in class net.sf.basedb.plugins.IntensityCalculatorPlugin: Plugin description
about - Static variable in class net.sf.basedb.plugins.JepExtraValueCalculator: Plugin description
about - Static variable in class net.sf.basedb.plugins.JepIntensityTransformer: Plugin description
about - Static variable in class net.sf.basedb.plugins.LowessNormalization: Plugin description
about - Static variable in class net.sf.basedb.plugins.MedianRatioNormalization: Plugin description
about - Static variable in class net.sf.basedb.plugins.PackedFileExporter
about - Static variable in class net.sf.basedb.plugins.PlateFlatFileImporter
about - Static variable in class net.sf.basedb.plugins.PlateMappingExporter
about - Static variable in class net.sf.basedb.plugins.PlateMappingImporter
about - Static variable in class net.sf.basedb.plugins.PluginConfigurationExporter
about - Static variable in class net.sf.basedb.plugins.PluginConfigurationImporter
about - Static variable in class net.sf.basedb.plugins.PrintMapFlatFileImporter
about - Static variable in class net.sf.basedb.plugins.RawDataFlatFileImporter
about - Static variable in class net.sf.basedb.plugins.ReporterFlatFileImporter
about - Static variable in class net.sf.basedb.plugins.ReporterMapFlatFileImporter
about - Static variable in class net.sf.basedb.plugins.SpotImageCreator: Plugin description
about - Static variable in class net.sf.basedb.plugins.TarFileUnpacker: Plugin description
about - Static variable in class net.sf.basedb.plugins.ZipFileUnpacker: Plugin description
about - Variable in class net.sf.basedb.util.extensions.ExtensionBean
about - Variable in class net.sf.basedb.util.extensions.Registry.RegisteredExtension
about - Variable in class net.sf.basedb.util.PluginInfo: The about information from the 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.
abs(String) - Method in class net.sf.basedb.core.dbengine.AbstractDbEngine: Return ABS(<value>).
abs(String) - Method in interface net.sf.basedb.core.dbengine.DbEngine: Get the function call that takes the absolute of a value.
abs(Expression) - Static method in class net.sf.basedb.core.query.Expressions: Calculate the absolute value of an expression: new expression = abs(e).
AbsConverter - Class in net.sf.basedb.util.jep.convert: Convert Abs function to a Query API Expression.
AbsConverter() - Constructor for class net.sf.basedb.util.jep.convert.AbsConverter
AbsExpression - Class in net.sf.basedb.core.query: Calculate the absolute value of an expression: abs(e).
AbsExpression(Expression) - Constructor for class net.sf.basedb.core.query.AbsExpression
AbsoluteProgressReporter - Interface in net.sf.basedb.core: This is interface is an extension to the ProgressReporter interface.
ABSORBED_DOSE - Static variable in class net.sf.basedb.core.Quantity: The id for the Quantity object representing absorbed dose.
AbstractAnalysisPlugin - Class in net.sf.basedb.core.plugin: This is a base class that is useful for all analysis type plugins.
AbstractAnalysisPlugin() - Constructor for class net.sf.basedb.core.plugin.AbstractAnalysisPlugin: Create a new AbstractAnalysisPlugin.
AbstractBatcher - Class in net.sf.basedb.core: This is an abstract class for batchers that are connected to a single DbControl object.
AbstractBatcher() - Constructor for class net.sf.basedb.core.AbstractBatcher: Constructor for a batcher.
AbstractBioAssaySetExporter - Class in net.sf.basedb.util.export.spotdata: An abstract superclass for all exporters that exports spot data from a bioassay set.
AbstractBioAssaySetExporter() - Constructor for class net.sf.basedb.util.export.spotdata.AbstractBioAssaySetExporter
AbstractCustomRequestHandler - Class in net.sf.basedb.clients.jobagent.handlers: Abstract base class for custom request handler implementations.
AbstractCustomRequestHandler() - Constructor for class net.sf.basedb.clients.jobagent.handlers.AbstractCustomRequestHandler
AbstractDataFileHandler - Class in net.sf.basedb.core.filehandler: This abstract class should, if possible, be used as a super-class for all classes implementing the DataFileValidator interface.
AbstractDataFileHandler() - Constructor for class net.sf.basedb.core.filehandler.AbstractDataFileHandler
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 - Class in net.sf.basedb.plugins.batchimport: An abstract base class for plug-ins that import items in batch.
AbstractItemImporter() - Constructor for class net.sf.basedb.plugins.batchimport.AbstractItemImporter
AbstractJepConversionFunction<T> - Class in net.sf.basedb.util.jep.convert: Abstract superclass implementing the JepConversionFunction interface.
AbstractJepConversionFunction() - Constructor for class net.sf.basedb.util.jep.convert.AbstractJepConversionFunction
AbstractJspActionFactory<A extends Action> - Class in net.sf.basedb.clients.web.extensions: An abstract base class for action factories that may need to support adding scripts and stylesheets to the rendered JSP page.
AbstractJspActionFactory() - Constructor for class net.sf.basedb.clients.web.extensions.AbstractJspActionFactory: Create a new factory instance.
AbstractJspFactory - Class in net.sf.basedb.clients.web.extensions: An abstract BASE class for action and renderer factories.
AbstractJspFactory() - Constructor for class net.sf.basedb.clients.web.extensions.AbstractJspFactory: Create a new factory instance.
AbstractJspRendererFactory<A extends Action> - Class in net.sf.basedb.clients.web.extensions: An abstract base class for action factories that may need to support adding scripts and stylesheets to the rendered JSP page.
AbstractJspRendererFactory() - Constructor for class net.sf.basedb.clients.web.extensions.AbstractJspRendererFactory: Create a new factory instance.
AbstractNodeLoader - Class in net.sf.basedb.util.overview.loader: Abstract node loader implementation that does nothing/throws an exception.
AbstractNodeLoader() - Constructor for class net.sf.basedb.util.overview.loader.AbstractNodeLoader
AbstractOnSaveAction - Class in net.sf.basedb.clients.web.extensions.edit: Abstract base implementation of the OnSaveAction interface.
AbstractOnSaveAction() - Constructor for class net.sf.basedb.clients.web.extensions.edit.AbstractOnSaveAction: Create a on-save action without a context
AbstractOnSaveAction(JspContext) - Constructor for class net.sf.basedb.clients.web.extensions.edit.AbstractOnSaveAction: Create a on-save action with a jsp context.
AbstractPlugin - Class in net.sf.basedb.core.plugin: This is an abstract base class useful for developing plugins.
AbstractPlugin() - Constructor for class net.sf.basedb.core.plugin.AbstractPlugin: Create a new AbstractPlugin.
AbstractQuery - Class in net.sf.basedb.core: An abstract implementation of the Query interface.
AbstractQuery(String) - Constructor for class net.sf.basedb.core.AbstractQuery: Create a new query.
AbstractQueryCache - Class in net.sf.basedb.core.hibernate: Abstract base class used to cache queries for a session.
AbstractQueryCache() - Constructor for class net.sf.basedb.core.hibernate.AbstractQueryCache
AbstractResultList - Class in net.sf.basedb.core: This is a list of the result from a query.
AbstractResultList(long) - Constructor for class net.sf.basedb.core.AbstractResultList
AbstractRPCClient - Class in net.sf.basedb.ws.client: Abstract class for RPCServiceClients in web services.
AbstractRPCClient(String, String) - Constructor for class net.sf.basedb.ws.client.AbstractRPCClient
AbstractRPCClient(String, String, ServiceFactory) - Constructor for class net.sf.basedb.ws.client.AbstractRPCClient
AbstractRPCService - Class in net.sf.basedb.ws.server: An abstract class for Web service classes to extend from.
AbstractRPCService() - Constructor for class net.sf.basedb.ws.server.AbstractRPCService
AbstractSignalHandler - Class in net.sf.basedb.core.signal: An abstract base class for signal handler implementations.
AbstractSignalHandler() - Constructor for class net.sf.basedb.core.signal.AbstractSignalHandler: Create a new signal handler, that initially doesn't support any signals at all.
AbstractSignalHandler(Collection<Signal>) - Constructor for class net.sf.basedb.core.signal.AbstractSignalHandler: Create a new signal handler that supports the given signals.
AbstractSignalReceiver - Class in net.sf.basedb.core.signal: Abstract base class that is useful when implementing signal receivers.
AbstractSignalReceiver() - Constructor for class net.sf.basedb.core.signal.AbstractSignalReceiver: Create a new signal receiver.
AbstractSignalTransporter - Class in net.sf.basedb.core.signal: Abstract base class that is useful when implementing signal transporters.
AbstractSignalTransporter() - Constructor for class net.sf.basedb.core.signal.AbstractSignalTransporter
AbstractSqlQuery - Class in net.sf.basedb.core: An abstract implementation of the SqlQuery interface.
AbstractSqlQuery(String) - Constructor for class net.sf.basedb.core.AbstractSqlQuery
abstractText - Variable in class net.sf.basedb.info.ExperimentInfo
ACCELERATION - Static variable in class net.sf.basedb.core.Quantity: The id for the Quantity object representing acceleration.
accept(File) - Method in class net.sf.basedb.util.OlderThanFileFilter: Accept files that are older than the specified last modified time.
accept(File) - Method in class net.sf.basedb.util.RegexpFileFilter: Accept files with a name matching the regular expression
acceptDenied - Variable in class net.sf.basedb.util.overview.validator.NullNodeValidator
acceptInsertIfNullReporterOnFeature - Variable in class net.sf.basedb.core.RawDataBatcher: If we should always accept inserts when the feature has a NULL reporter.
acceptInsertIfNullReporterOnFeature(boolean) - Method in class net.sf.basedb.core.RawDataBatcher: Specify if inserts always should be accepted if there is a matching feature that has a NULL reporter.
acceptMissing - Variable in class net.sf.basedb.util.overview.validator.NullNodeValidator
AccessControlled - Interface in net.sf.basedb.core: This interface should be implemented by a class representing items which requires the logged in user to have permission to access them.
AccountExpiredException - Exception in net.sf.basedb.core: This exception is thrown if you try to log in with an account that has expired.
AccountExpiredException(String, Date) - Constructor for exception net.sf.basedb.core.AccountExpiredException: Creates a new AccountExpiredException.
aColumn - Static variable in class net.sf.basedb.util.importer.spotdata.MAParser
action - Variable in class net.sf.basedb.clients.web.taglib.table.Table
action - Variable in class net.sf.basedb.core.data.FileData
Action - Interface in net.sf.basedb.util.extensions: An action is an object that is added to an ExtensionPoint by an Extension.
actionClass - Variable in class net.sf.basedb.util.extensions.ExtensionPointBean
actionClass - Variable in class net.sf.basedb.util.extensions.Registry.RegisteredExtensionPoint
ActionClassEventFilter - Class in net.sf.basedb.util.extensions.events: Event filter that only passes on events to extension points with a given action class.
ActionClassEventFilter(Class<? extends Action>) - Constructor for class net.sf.basedb.util.extensions.events.ActionClassEventFilter: Create a new action class filter.
ActionFactory<A extends Action> - Interface in net.sf.basedb.util.extensions: An action factory is an object which knows how to create Action:s.
actionFactory - Variable in class net.sf.basedb.util.extensions.ExtensionBean
actionFactory - Variable in class net.sf.basedb.util.extensions.Registry.RegisteredExtension
ActionIterator<A extends Action> - Class in net.sf.basedb.util.extensions: Iterator for iterating over all actions that will be created by extensions after a call to Registry.useExtensions(ClientContext, ExtensionsFilter, String...).
ActionIterator(Iterator<ExtensionContext<A>>) - Constructor for class net.sf.basedb.util.extensions.ActionIterator
actions - Variable in class net.sf.basedb.clients.web.extensions.menu.FixedMenuItemFactory
actions - Variable in class net.sf.basedb.clients.web.extensions.tabcontrol.FixedTabFactory
actions - Variable in class net.sf.basedb.clients.web.extensions.toolbar.FixedButtonFactory
actions - Variable in class net.sf.basedb.util.extensions.ActionIterator
actions - Variable in class net.sf.basedb.util.extensions.debug.BeanActionFactory
actions - Variable in class net.sf.basedb.util.extensions.debug.ProxyActionFactory
activate - Variable in class net.sf.basedb.clients.web.taglib.tab.Tab: A JavaScript method that is invoked when activating the tab.
active - Variable in class net.sf.basedb.clients.web.taglib.tab.TabControl: The ID attribute of the active tab.
activeJobs - Variable in class net.sf.basedb.clients.jobagent.Agent
activeProjectId - Variable in class net.sf.basedb.core.data.JobData
activeProjectId - Variable in class net.sf.basedb.core.SessionControl.LoginInfo: The id of the ProjectData object of the active project.
add(I) - Method in class net.sf.basedb.core.AbstractResultList: Not supported.
add(int, I) - Method in class net.sf.basedb.core.AbstractResultList: Not supported.
add(BioMaterial) - Method in class net.sf.basedb.core.BioMaterialList: Add a biomaterial to this list.
add(Iterator<? extends BioMaterial>) - Method in class net.sf.basedb.core.BioMaterialList: Add multiple biomaterials to this list in one go.
add(Long, Long) - Method in class net.sf.basedb.core.DiskUsageStatistics.Summary
add(T) - Method in class net.sf.basedb.core.ItemResultList.ResultListListIterator: This operation is not supported.
add(Expression, Expression) - Static method in class net.sf.basedb.core.query.Expressions: Add two expressions: new expression = e1 + e2.
add(SystemData) - Static method in class net.sf.basedb.core.SystemItems: Register a system item.
add(T) - Method in class net.sf.basedb.core.UnmodifiableResultList: Not supported.
add(int, T) - Method in class net.sf.basedb.core.UnmodifiableResultList: Not supported.
add(K, V) - Method in class net.sf.basedb.util.Enumeration
add(E) - Method in class net.sf.basedb.util.Tree: Not supported.
addAll(Collection<? extends I>) - Method in class net.sf.basedb.core.AbstractResultList: Not supported.
addAll(int, Collection<? extends I>) - Method in class net.sf.basedb.core.AbstractResultList: Not supported.
addAll(BioMaterialList) - Method in class net.sf.basedb.core.BioMaterialList: Add all items from another biomaterial list to this list.
addAll(ReporterList) - Method in class net.sf.basedb.core.ReporterList: Add all reporters from another reporter list to this list.
addAll(Collection<? extends T>) - Method in class net.sf.basedb.core.UnmodifiableResultList: Not supported.
addAll(int, Collection<? extends T>) - Method in class net.sf.basedb.core.UnmodifiableResultList: Not supported.
addAll(Collection<? extends E>) - Method in class net.sf.basedb.util.Tree: Not supported.
AddAllTransformer - 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
addAnnotations(DbControl, Node) - Method in class net.sf.basedb.util.overview.ExperimentOverview: Deprecated. Add annotations child node to an annotatable item.
addArrayBatch(DbControl, Node) - Method in class net.sf.basedb.util.overview.ExperimentOverview: Deprecated. Add an array batch child node to an array slide.
addArrayDesign(DbControl, Node) - Method in class net.sf.basedb.util.overview.ExperimentOverview: Deprecated. Add an array design child node to a raw bioassay or array batch.
addArrayDesignBlock(BlockInfo) - Method in class net.sf.basedb.core.ArrayDesign: Adds an ArrayDesignBlock to the array design.
addArraySlide(DbControl, Node) - Method in class net.sf.basedb.util.overview.ExperimentOverview: Deprecated. Add an array slide child node to a hybridization.
addAssayField(AssayField) - Method in class net.sf.basedb.util.export.spotdata.AbstractBioAssaySetExporter: Add information about an assay field that should be exported.
addAssayField(AssayField) - Method in class net.sf.basedb.util.export.spotdata.BaseFileExporter: Adds an assay field to the exported file.
addAssayField(AssayField) - Method in class net.sf.basedb.util.export.spotdata.BfsExporter
addAssayFields(Collection<? extends AssayField>) - Method in class net.sf.basedb.util.export.spotdata.BaseFileExporter: Add multiple assay fields in one go.
addAssayFields(Collection<? extends AssayField>) - Method in class net.sf.basedb.util.export.spotdata.BfsExporter: Add multiple assay fields in one go.
addAutoJoiner(AutoJoiner<?, ?>) - Method in class net.sf.basedb.core.AbstractQuery
addAutoJoiner(AutoJoiner<?, ?>) - Method in interface net.sf.basedb.core.query.Query
addBatcher(Batcher) - Method in class net.sf.basedb.core.DbControl: Add a Batcher to the batcher queue.
addBioSource(DbControl, Node) - Method in class net.sf.basedb.util.overview.ExperimentOverview: Deprecated. Add a biosource child node to a non-pooled sample.
addButton(String) - Method in class net.sf.basedb.clients.web.taglib.ButtonGroup
addBytes(long) - Method in class net.sf.basedb.core.DataCube
addBytes(long) - Method in class net.sf.basedb.core.DataCubeExtraValue
addBytes(long) - Method in class net.sf.basedb.core.DataCubeFilter
addBytes(long) - Method in class net.sf.basedb.core.DataCubeLayer
addBytes(long) - Method in class net.sf.basedb.core.Experiment
addCategory(AnnotationTypeCategory) - Method in class net.sf.basedb.core.AnnotationType: Add a category to this annotation type.
addChange(ChangeType, Object, Object[], Object[], String[], Type[]) - Method in class net.sf.basedb.core.log.LoggingInterceptor: If the log manager factory creates an entity logger, add information about the change to the internal list.
addChild(Node) - Method in class net.sf.basedb.util.overview.Node: Add a child node to this one.
addChild(E) - Method in class net.sf.basedb.util.Tree.Entry: Add a child to the node.
addChildAssay(BaseFileInfo.ChildBioAssay) - Method in class net.sf.basedb.util.importer.spotdata.BaseFileInfo: Add information about a child assay.
addChildBioAssaySets(BioAssaySetData, Set<BioAssaySetData>) - Method in class net.sf.basedb.core.BioAssaySet: Find all bioassaysets that are children to the specified parent (ie.
addChildElements(Map<QueryElement, Object>, QueryElement) - Method in class net.sf.basedb.core.AbstractQuery
addChildEntry(Tree.Entry<E>) - Method in class net.sf.basedb.util.Tree.Entry
addChildErrors(int) - Method in class net.sf.basedb.util.overview.Node: Add child errors to this node.
addChildReporter(Integer, Integer) - Method in class net.sf.basedb.util.importer.spotdata.BaseFileInfo: Add a child position/reporter mapping from the parsed BASEfile.
addChildWarnings(int) - Method in class net.sf.basedb.util.overview.Node: Add child warnings to this node.
addColumn(Mappings, Table, VirtualColumn) - Static method in class net.sf.basedb.core.HibernateUtil: Add a column to a table.
addColumnDef(ColumnDef) - Method in class net.sf.basedb.clients.web.taglib.table.Table
AddConverter - Class in net.sf.basedb.util.jep.convert: Convert Add function to a Query API Expression.
AddConverter() - Constructor for class net.sf.basedb.util.jep.convert.AddConverter
addData(SqlResultIterator, String, float, HistogramPlot.YAggregate, HistogramPlot.YAggregate) - Method in class net.sf.basedb.util.plot.HistogramPlot: Add data to the plot.
addData(SqlResultIterator, Collection<PlotAnnotation>, float, HistogramPlot.YAggregate, HistogramPlot.YAggregate) - Method in class net.sf.basedb.util.plot.HistogramPlot: Add data to the plot.
addData(SqlResultIterator, String...) - Method in class net.sf.basedb.util.plot.ScatterPlot: Add data to the plot.
addData(SqlResultIterator, Collection<PlotAnnotation>) - Method in class net.sf.basedb.util.plot.ScatterPlot: Add data to the plot.
addDataFiles(DbControl, Node) - Method in class net.sf.basedb.util.overview.ExperimentOverview: Deprecated. Add data files child node to a FileStoreEnabled item.
addDataParser(DataParser) - Method in class net.sf.basedb.util.importer.spotdata.SynchronizedSpotDataParser: Adds a data parser.
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.
addedBytes - Variable in class net.sf.basedb.core.DataCube
addedBytes - Variable in class net.sf.basedb.core.Experiment
addEntry(MetadataModel.SectionEntry) - Method in class net.sf.basedb.util.bfs.MetadataModel.Section: Add a new entry to this section.
addEntry(String, String...) - Method in class net.sf.basedb.util.bfs.MetadataModel.Section: Add a new entry to this section.
addEntry(Tree.Entry<E>) - Method in class net.sf.basedb.util.Tree
addError(String) - Method in class net.sf.basedb.util.jep.FunctionSafeJep: Adds an error message to the "real" JEP parser.
addErrorHandler(Class<? extends Throwable>, ErrorHandler) - Method in class net.sf.basedb.plugins.AbstractFlatFileImporter: Add an error handler for the specified class of error.
addErrorHandler(Class<? extends Throwable>, ErrorHandler) - Method in class net.sf.basedb.util.error.ClassMapErrorHandler: Add an error handler for throwable:s of a specific class.
addErrorMessage(ExtensionsFile, String) - Method in class net.sf.basedb.clients.web.extensions.ScanResults: Adds a detail message inidcating a failed operation to a file.
addErrors(int) - Method in class net.sf.basedb.util.overview.Node: Add more errors to this node.
addEventHandler(EventHandler) - Method in class net.sf.basedb.util.bfs.MultiEventHandler: Adds an event handler.
addExperimentalFactor(AnnotationType) - Method in class net.sf.basedb.core.Experiment: Add an annotation type as an experimental factor to this experiment.
addExperimentalFactors(DbControl, Node) - Method in class net.sf.basedb.util.overview.ExperimentOverview: Deprecated. Add experimental factors child node to the experiment node.
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.
addExtraColumns(List<TableColumn>, DbControl, BioAssaySet, String, String, String) - Static method in class net.sf.basedb.clients.web.DynamicUtil
addExtract(DbControl, Node, Extract) - Method in class net.sf.basedb.util.overview.ExperimentOverview: Deprecated. Add an extract child node to a non-pooled labeled extract.
addExtraFile(String, String) - Method in class net.sf.basedb.util.export.spotdata.BfsExporter: Add information about an extra data file that is included as part of the BFS.
addExtraFloat(DbControl, String) - Method in class net.sf.basedb.util.importer.spotdata.BaseFileInfo: Add information about an extra float value that appears in the BASEfile.
addExtraFloatParser(ExtraFloatParser) - Method in class net.sf.basedb.util.importer.spotdata.BaseFileInfo.SpotSectionInfo: Add an extra value parser to this section.
addFile(String, UploadedFile) - Method in class net.sf.basedb.clients.web.fileupload.FileUpload: Store information about an uploaded file.
addFile(String, String) - Method in class net.sf.basedb.util.bfs.MetadataModel: Add an entry to the 'files' section.
addFilename(String) - Method in class net.sf.basedb.util.bfs.AbstractFilenameGenerator: Add the file name to the list of already generated file names.
addFileType(DataFileType, boolean, PlatformVariant) - Method in class net.sf.basedb.core.Platform: Add a file type to this platform/variant.
addFileType(DataFileType, boolean) - Method in class net.sf.basedb.core.PlatformVariant: Add a file type to this platform variant.
addFilterConditions(Element, String) - Static method in class net.sf.basedb.core.HibernateUtil: Add <filter> conditions to the given class tag.
addFilteredColumn(String, boolean) - Method in class net.sf.basedb.clients.web.taglib.table.Table
addFix(Fix) - Method in class net.sf.basedb.util.overview.Failure: Add a suggested fix to this failure.
addFormulaColumns(List<TableColumn>, DbControl, RawDataType, Formula.Type, IntensityTransform, String, String, boolean) - Static method in class net.sf.basedb.clients.web.DynamicUtil
addFunctions(JEP, JepFunction...) - Static method in class net.sf.basedb.util.jep.Jep
addGroup(Group) - Method in class net.sf.basedb.core.Group: Add a group as a member to this group.
addHardware(DbControl, Node, String) - Method in class net.sf.basedb.util.overview.ExperimentOverview: Deprecated. Add a hardware child node to items with hardware (scanner, print robot, hyb.
addHeaderColumn(int) - Method in class net.sf.basedb.clients.web.taglib.table.Table
addHidden(String, String) - Method in class net.sf.basedb.clients.web.taglib.table.Table
addHybridization(DbControl, Node, Node) - Method in class net.sf.basedb.util.overview.ExperimentOverview: Deprecated. Add a hybridization child node to a scan.
addIfPresentIn(int, int, Collection<BioMaterialList>) - Method in class net.sf.basedb.core.BioMaterialList: Add items that are present in the specified number of lists to this list.
addIfPresentIn(int, int, Collection<ReporterList>) - Method in class net.sf.basedb.core.ReporterList: Add reporters that are present in the specified number of lists to this list.
addIgnore(File) - Method in class net.sf.basedb.clients.web.extensions.ExtensionsDirectory: Add a file to the ignore list.
addImage(DbControl, Node, Image) - Method in class net.sf.basedb.util.overview.ExperimentOverview: Deprecated. Add an image child node to the images folder.
addImages(DbControl, Node) - Method in class net.sf.basedb.util.overview.ExperimentOverview: Deprecated. Add images child node to a scan node.
addIntersection(Collection<BioMaterialList>) - Method in class net.sf.basedb.core.BioMaterialList: Add items that are present in ALL OF the given lists to this list.
addIntersection(Collection<ReporterList>) - Method in class net.sf.basedb.core.ReporterList: Add reporters that are present in ALL OF the given lists to this list.
addLabeledExtract(DbControl, Node, LabeledExtract) - Method in class net.sf.basedb.util.overview.ExperimentOverview: Deprecated. Add a labeled extract child node to the labeled extracts folder.
addLabeledExtracts(DbControl, Node, Node) - Method in class net.sf.basedb.util.overview.ExperimentOverview: Deprecated. Add labeled extracts child node to a hybridization node.
addMeasurement(float) - Method in class net.sf.basedb.util.plot.HistogramPlot.HistogramBin: Add a measurement to this bin.
addMembers(Set<BioMaterialData>) - Method in class net.sf.basedb.core.BioMaterialList: Add members to this list.
addMenuitem(String) - Method in class net.sf.basedb.clients.web.taglib.menu.Menu
addMessage(ExtensionsFile, String) - Method in class net.sf.basedb.clients.web.extensions.ScanResults: Adds a detail message indicating a successful operation to a file.
addMessage(ExtensionsFile, String, boolean) - Method in class net.sf.basedb.clients.web.extensions.ScanResults
addMoreColumnMappingParameters(List<PluginParameter<?>>) - Method in class net.sf.basedb.plugins.batchimport.AbstractItemImporter: Add column mapping parameters for item-specific properties.
addMoreColumnMappingParameters(List<PluginParameter<?>>) - Method in class net.sf.basedb.plugins.batchimport.ArrayBatchImporter: Adds column mappings for name, description, protocol, robot, and array design
addMoreColumnMappingParameters(List<PluginParameter<?>>) - Method in class net.sf.basedb.plugins.batchimport.ArrayDesignImporter: Adds column mappings for name, externalId, description, protocol, creation date, original quantity, pooled, parent and used quantity from parent.
addMoreColumnMappingParameters(List<PluginParameter<?>>) - Method in class net.sf.basedb.plugins.batchimport.ArraySlideImporter: Adds column mappings for name, description, array batch, batch index, barcode and destroyed
addMoreColumnMappingParameters(List<PluginParameter<?>>) - Method in class net.sf.basedb.plugins.batchimport.BioPlateImporter: Adds column mappings for name, description, plate type, plate geometry, barcode and freezer.
addMoreColumnMappingParameters(List<PluginParameter<?>>) - Method in class net.sf.basedb.plugins.batchimport.BioSourceImporter: Adds column mappings for name, externalId and description.
addMoreColumnMappingParameters(List<PluginParameter<?>>) - Method in class net.sf.basedb.plugins.batchimport.ExtractImporter: Adds column mappings for name, externalId, description, protocol, creation date, original quantity, pooled, parent and used quantity from parent.
addMoreColumnMappingParameters(List<PluginParameter<?>>) - Method in class net.sf.basedb.plugins.batchimport.HybridizationImporter: Adds column mappings for name, externalId, description, protocol, creation date, original quantity, pooled, parent and used quantity from parent.
addMoreColumnMappingParameters(List<PluginParameter<?>>) - Method in class net.sf.basedb.plugins.batchimport.LabeledExtractImporter: Adds column mappings for name, externalId, description, protocol, creation date, original quantity, pooled, parent and used quantity from parent.
addMoreColumnMappingParameters(List<PluginParameter<?>>) - Method in class net.sf.basedb.plugins.batchimport.RawBioAssayImporter: Adds column mappings for name, externalId, description, protocol, creation date, original quantity, pooled, parent and used quantity from parent.
addMoreColumnMappingParameters(List<PluginParameter<?>>) - Method in class net.sf.basedb.plugins.batchimport.SampleImporter: Adds column mappings for name, externalId, description, protocol, creation date, original quantity, pooled, parent and used quantity from parent.
addMoreColumnMappingParameters(List<PluginParameter<?>>) - Method in class net.sf.basedb.plugins.batchimport.ScanImporter: Adds column mappings for name, internalId, description, hybridization, protocol, hardware, image-file, image-name, image-format and image-description.
addMoreErrorParameters(List<PluginParameter<?>>) - Method in class net.sf.basedb.plugins.batchimport.AbstractItemImporter: Add extra parameters to the "Error handling" section that the subclass needs.
addMoreErrorParameters(List<PluginParameter<?>>) - Method in class net.sf.basedb.plugins.batchimport.HybridizationImporter
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.RawBioAssayImporter: Add parameter for "Data directory" directory where data files may be located.
addMoreJobParameters(List<PluginParameter<?>>) - Method in class net.sf.basedb.plugins.batchimport.ScanImporter: Add parameter for "Image directory" directory where image files may be located.
addMoreParsingParameters(List<PluginParameter<?>>) - Method in class net.sf.basedb.plugins.batchimport.AbstractItemImporter: Add extra parameters to the "Parser settings" section that the subclass needs.
addParameter(String, String) - Method in class net.sf.basedb.clients.web.fileupload.FileUpload: Store the value of a regular form field.
addParameter(AnnotationType) - Method in class net.sf.basedb.core.Protocol: Add an annotation type as a parameter to this protocol.
addParametersWithNamespace(List<PluginParameter<?>>, List<PluginParameter<?>>, String) - Method in class net.sf.basedb.plugins.executor.ExternalProgramExecutor: Add more parameters to a list of parameters with a different namespace.
addParticipant(BioPlate, String, int) - Method in class net.sf.basedb.core.BioPlateEvent: Add a bioplate as a participant in this event.
addPermissions(Group, Set<Permission>) - Method in class net.sf.basedb.core.GroupPermissions: Grant permissions to a group, keeping those that have already been set.
addPermissions(User, Set<Permission>) - Method in class net.sf.basedb.core.MultiPermissions: Grant permissions to a user, keeping those that have already been set.
addPermissions(Group, Set<Permission>) - Method in class net.sf.basedb.core.MultiPermissions: Grant permissions to a group, keeping those that have already been set.
addPermissions(Project, Set<Permission>) - Method in class net.sf.basedb.core.MultiPermissions: Grant permissions to a project, keeping those that have already been set.
addPermissions(Project, Set<Permission>) - Method in class net.sf.basedb.core.ProjectPermissions: Grant permissions to a project, keeping those that have already been set.
addPermissions(User, Set<Permission>) - Method in class net.sf.basedb.core.UserPermissions: Grant permissions to a user, keeping those that have already been set.
addPlate(Plate) - Method in class net.sf.basedb.core.ArrayDesign: Adds a single plate to the plate list.
addPlatform(DbControl, Node) - Method in class net.sf.basedb.util.overview.ExperimentOverview: Deprecated. Add a platform / variant child node to items with platform (raw bioassay and array design).
addPluginPermission(Session, int, Item, int, int) - Static method in class net.sf.basedb.core.Update
addPooledExtracts(DbControl, Node) - Method in class net.sf.basedb.util.overview.ExperimentOverview: Deprecated. Add extract child nodes that are the source extracts of a pooled extract.
addPooledLabeledExtracts(DbControl, Node) - Method in class net.sf.basedb.util.overview.ExperimentOverview: Deprecated. Add labeled extract child nodes that are the source labeled extracts of a pooled labeled extract
addPooledSamples(DbControl, Node) - Method in class net.sf.basedb.util.overview.ExperimentOverview: Deprecated. Add sample child nodes that are the source samples of a pooled sample.
addProtocol(DbControl, Node, Project.Default) - Method in class net.sf.basedb.util.overview.ExperimentOverview: Deprecated. Add a protocol child node to items with a protocol.
addProtocolParameters(DbControl, Node) - Method in class net.sf.basedb.util.overview.ExperimentOverview: Deprecated. Add protocol parameters child node to a protocol.
addRawBioAssay(RawBioAssay) - Method in class net.sf.basedb.core.Experiment: Add a raw bioassay to this experiment.
addRawBioAssay(DbControl, Node, RawBioAssay) - Method in class net.sf.basedb.util.overview.ExperimentOverview: Deprecated. Add a raw bioassay child node to the rawbioassays folder.
addRawBioAssayParameters(DbControl, RawBioAssay, List<PluginParameter<?>>) - Method in class net.sf.basedb.plugins.RawDataFlatFileImporter
addRawBioAssays(DbControl, Node) - Method in class net.sf.basedb.util.overview.ExperimentOverview: Deprecated. Add raw bioassays child node to the experiment node.
addRawDataColumns(List<TableColumn>, DbControl, RawDataType, String, String, String) - Static method in class net.sf.basedb.clients.web.DynamicUtil
addRawDataMappings(Configuration) - Static method in class net.sf.basedb.core.HibernateUtil: Generate additional mappings for the raw data types.
addRegistered(String, ExtensionsFile) - Method in class net.sf.basedb.clients.web.extensions.ExtensionsDirectory
addReplaceSection - Static variable in class net.sf.basedb.plugins.AnnotationFlatFileImporter
addReporter(ReporterData, Float) - Method in class net.sf.basedb.core.ReporterList: Add or update the score for a reporter.
addReporterColumns(List<TableColumn>, DbControl, String, String, String) - Static method in class net.sf.basedb.clients.web.DynamicUtil
addReporterField(DynamicField) - Method in class net.sf.basedb.util.export.spotdata.AbstractBioAssaySetExporter: Add information about a reporter field that should be exported.
addReporterField(DynamicField) - Method in class net.sf.basedb.util.export.spotdata.BaseFileExporter
addReporterField(DynamicField) - Method in class net.sf.basedb.util.export.spotdata.BfsExporter
addReporterFields(Collection<? extends DynamicField>) - Method in class net.sf.basedb.util.export.spotdata.BaseFileExporter: Add multiple reporter fields in one go.
addReporterFields(Collection<? extends DynamicField>) - Method in class net.sf.basedb.util.export.spotdata.BfsExporter: Add multiple reporter fields in one go.
addReporters(Set<Integer>) - Method in class net.sf.basedb.core.ReporterList
addResources(Vector<URL>, Enumeration<URL>) - Method in class net.sf.basedb.util.JarClassLoader
address - Variable in class net.sf.basedb.core.authentication.AuthenticationInformation: The postal address to the user.
address - Variable in class net.sf.basedb.core.data.UserData
addRoleKey(RoleKeyData) - Static method in class net.sf.basedb.core.SystemItems: Register a role key.
addRolePermissions(RoleData, Map<Item, Integer>) - Static method in class net.sf.basedb.core.Install: Add permissions for a role for specific item types.
addRow(String...) - Method in class net.sf.basedb.util.bfs.AnnotationModel: Add a row of data to the model.
addRow(String...) - Method in class net.sf.basedb.util.bfs.MatrixModel: Add a row of data to the model.
addSample(DbControl, Node, Sample) - Method in class net.sf.basedb.util.overview.ExperimentOverview: Deprecated. Add a sample child node to a non-pooled extract.
addScan(DbControl, Node) - Method in class net.sf.basedb.util.overview.ExperimentOverview: Deprecated. Add a scan child node to a raw bioassay.
addScript(String) - Method in class net.sf.basedb.clients.web.extensions.JspContext: Add an absolute reference to a script that should be included on the generated page with a <script> tag.
addScript(String) - Method in class net.sf.basedb.clients.web.taglib.table.Table
addSection(String) - Method in class net.sf.basedb.util.bfs.MetadataModel: Adds a new section to the model.
addSeries(HistogramPlot.HistogramSeries) - Method in class net.sf.basedb.util.plot.HistogramPlot.HistogramDataset
addSignal(Signal) - Method in class net.sf.basedb.core.signal.AbstractSignalHandler: Add a signal to the list of supported signals.
addSoftware(DbControl, Node) - Method in class net.sf.basedb.util.overview.ExperimentOverview: Deprecated. Add a software child node to a raw bioassay.
addSource(MeasuredBioMaterial, Float) - Method in class net.sf.basedb.core.BioMaterialEvent: Add a source biomaterial to this event or update the used quantity of an existing source.
addSpotColumns(List<TableColumn>, DbControl, int, IntensityTransform) - Static method in class net.sf.basedb.clients.web.DynamicUtil
addSpotField(DynamicField) - Method in class net.sf.basedb.util.export.spotdata.AbstractBioAssaySetExporter: Add information about a spot field that should be exported.
addSpotField(DynamicField) - Method in class net.sf.basedb.util.export.spotdata.BaseFileExporter
addSpotField(DynamicField) - Method in class net.sf.basedb.util.export.spotdata.BfsExporter: Add information about a spot field that should be exported.
addSpotFields(Collection<? extends DynamicField>) - Method in class net.sf.basedb.util.export.spotdata.BaseFileExporter: Add multiple spot fields in one go.
addSpotFields(Collection<? extends DynamicField>) - Method in class net.sf.basedb.util.export.spotdata.BfsExporter: Add multiple spot fields in one go.
addSpotIntensityParser(SpotIntensityParser) - Method in class net.sf.basedb.util.importer.spotdata.FirstPassSectionSpotsParser: Adds a spot intensity parser to the list of used parsers.
addSpotSectionInfo(int, BaseFileInfo.SpotSectionInfo) - Method in class net.sf.basedb.util.importer.spotdata.BaseFileInfo: Adds information about a 'spot' section.
addSqlFunctions(Configuration, DbEngine) - Static method in class net.sf.basedb.core.HibernateUtil: Add more SQL functions to HQL that are not present in a standard Hibernate installation.
addStaticMappings(Configuration) - Static method in class net.sf.basedb.core.HibernateUtil: Read all mapping files, which must be named Class.hbm.xml where class is the name of each class.
addStatistics(String, float) - Method in class net.sf.basedb.clients.web.ExperimentExplorer.AnnotationGroup: Add another statisitcal measurement to this group.
addStylesheet(String) - Method in class net.sf.basedb.clients.web.extensions.JspContext: Add an absolute reference to a CSS stylesheet that should be included on the generated page with a <link> tag.
addSymbol(String) - Method in class net.sf.basedb.core.Unit: Add a symbol to this unit.
addTab(TabAction) - Method in class net.sf.basedb.clients.web.taglib.tab.TabControl
addToBatch(D, PreparedStatement, List<BatchedPropertyInfo>) - Method in class net.sf.basedb.core.BasicBatcher: Add the data object to the batch represented by the prepared statement
addToDefaultRolesAndGroups() - Method in class net.sf.basedb.core.User: Add this user to the groups and roles that has been marked as default for new users.
addToList(BioMaterialList, Collection<? extends S>, CollectionTransformer<S, ? extends BioMaterial>) - Static method in class net.sf.basedb.util.biomaterial.ListUtil: Adds items to a biomaterial list.
addToUnlimited - Variable in class net.sf.basedb.plugins.AnnotationFlatFileImporter
addToUnlimitedParameter - Static variable in class net.sf.basedb.plugins.AnnotationFlatFileImporter
addTransferredBytes(long) - Method in class net.sf.basedb.clients.web.fileupload.FileUploadProgress: Adds a value to the number of transfered bytes.
addUnion(Collection<BioMaterialList>) - Method in class net.sf.basedb.core.BioMaterialList: Add items that are present in at least ONE OF the given lists to this list.
addUnion(Collection<ReporterList>) - Method in class net.sf.basedb.core.ReporterList: Add reporters that are present in at least ONE OF the given lists to this list.
addUsableUnit(Unit) - Method in class net.sf.basedb.core.AnnotationType: Add a unit to be used with this annotation type.
addUser(User) - Method in class net.sf.basedb.core.Group: Add a user as a member to this group.
addUser(User) - Method in class net.sf.basedb.core.Role: Assign this Role to a user.
addUsingItems(Set<ItemProxy>, Item, Query) - Method in class net.sf.basedb.core.BasicItem: Add items to the set of items using this one.
addUsingItems(Set<ItemProxy>, Query) - Method in class net.sf.basedb.core.BasicItem: Add items to the set of items using this one.
addValue(int, float) - Method in class net.sf.basedb.clients.web.ExperimentExplorer.AnnotationGroup: Add an intensity value to this group.
addValue(AnnotationType, Object, Unit, boolean) - Method in class net.sf.basedb.plugins.AnnotationFlatFileImporter.NewAnnotations: Add an annotation value.
addValueConverter(ValueConverter) - Method in class net.sf.basedb.util.extensions.xml.XmlLoader: Add a value converter to this loader
addWarnings(int) - Method in class net.sf.basedb.util.overview.Node: Add more warnings to this node.
adjustExistingItems(boolean, ProgressReporter, String, String) - Static method in class net.sf.basedb.core.Update: Adjust the existing items in the database to be compatible with the latest mappings.
adjustRanges() - Method in class net.sf.basedb.util.plot.HistogramPlot: Auto-size of the x and y range doesn't seem to work, so we have to do it manually.
ADMINISTRATOR - Static variable in class net.sf.basedb.core.Role: The id for the Role item representing adminstrators.
AdvancedFieldConverter - Class in net.sf.basedb.util.export.spotdata: Field converter implementation that gives more detailed control how fields are converted and used in the export.
AdvancedFieldConverter(DbControl, BioAssaySet) - Constructor for class net.sf.basedb.util.export.spotdata.AdvancedFieldConverter: Create a new advanced field converter.
affectedRows - Variable in class net.sf.basedb.core.hibernate.ExecuteUpdateWork
affiliations - Variable in class net.sf.basedb.core.data.ExperimentData
affiliations - Variable in class net.sf.basedb.info.ExperimentInfo
affyChip - Variable in class net.sf.basedb.core.data.ArrayDesignData
Affymetrix - Class in net.sf.basedb.core: Utility class for Affymetrix-specific functionality.
Affymetrix() - Constructor for class net.sf.basedb.core.Affymetrix
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.
AffymetrixFileHandler - Class in net.sf.basedb.core.filehandler: This class is used as a superclass for all Affymetrix-based validators and metadata readers.
AffymetrixFileHandler() - Constructor for class net.sf.basedb.core.filehandler.AffymetrixFileHandler
aFloat(float) - Static method in class net.sf.basedb.core.query.Expressions: Create a constant expression from a float.
AFTER_ENABLE - Static variable in class net.sf.basedb.clients.web.extensions.ExtensionsControl: This event is sent after an extension or extension point is enabled by ExtensionsControl.enableExtensionPoint(String, boolean), ExtensionsControl.enableExtension(String, boolean), or ExtensionsControl.enableAllInFile(String, boolean).
AFTER_REGISTRATION - Static variable in class net.sf.basedb.util.extensions.events.EventType: This event is sent after an extension or extension point has been registered with a registry.
AFTER_UPDATE - Static variable in class net.sf.basedb.util.extensions.events.EventType: This event is sent during an update of an existing extension point or extension.
afterCommit() - Method in class net.sf.basedb.core.log.db.DbLogManager
afterCommit() - Method in interface net.sf.basedb.core.log.LogManager: Called after a successful commit of changes to the database.
afterRollback() - Method in class net.sf.basedb.core.log.db.DbLogManager
afterRollback() - Method in interface net.sf.basedb.core.log.LogManager: Called after rollback.
afterTransactionCompletion(Transaction) - Method in class net.sf.basedb.core.log.LoggingInterceptor: Signals successful commit or rollback to the log manager.
Agent - Class in net.sf.basedb.clients.jobagent: This is the actual job agent application.
Agent(Properties) - Constructor for class net.sf.basedb.clients.jobagent.Agent: Create a new job agent.
agent - Variable in class net.sf.basedb.clients.jobagent.AgentSignalReceiver
agent - Variable in class net.sf.basedb.clients.jobagent.handlers.AbstractCustomRequestHandler
agent - Variable in class net.sf.basedb.clients.jobagent.handlers.DefaultRequestHandler
agent - Variable in class net.sf.basedb.clients.jobagent.handlers.InfoRequestHandler
agent - Variable in class net.sf.basedb.clients.jobagent.handlers.MultiProtocolRequestHandler
agent - Variable in class net.sf.basedb.clients.jobagent.handlers.PauseRequestHandler
agent - Variable in class net.sf.basedb.clients.jobagent.handlers.SignalRequestHandler
agent - Variable in class net.sf.basedb.clients.jobagent.handlers.StartRequestHandler
agent - Variable in class net.sf.basedb.clients.jobagent.handlers.StopRequestHandler
agent - Variable in class net.sf.basedb.clients.jobagent.JobQueueChecker
agent - Variable in class net.sf.basedb.clients.jobagent.JobRunner
agent - Variable in class net.sf.basedb.clients.jobagent.slotmanager.InternalSlotManager
agent - Variable in class net.sf.basedb.clients.jobagent.slotmanager.RemoteSlotManager
agent - Variable in class net.sf.basedb.core.Job.ProgressReporterImpl
AgentController - Class in net.sf.basedb.clients.jobagent: This is the command line controller class for the job agent application.
AgentController(Properties) - Constructor for class net.sf.basedb.clients.jobagent.AgentController: Create a new controller for controlling the job agent specified by the given properties.
agentInfo - Static variable in class net.sf.basedb.core.JobAgent
AgentSignalReceiver - Class in net.sf.basedb.clients.jobagent: Signal receiver implementation for job agents that is compatible with the SocketSignalReceiver.
AgentSignalReceiver(Agent) - Constructor for class net.sf.basedb.clients.jobagent.AgentSignalReceiver
agentVersionForJobQuery - Variable in class net.sf.basedb.clients.jobagent.JobQueueChecker: The job agent's version when the query was cached.
Aggregations - Class in net.sf.basedb.core.query: A factory class to create aggregate expressions.
Aggregations() - Constructor for class net.sf.basedb.core.query.Aggregations
aIndex - Variable in class net.sf.basedb.util.importer.spotdata.MAParser
ajaxEndRecord() - Method in class net.sf.basedb.clients.web.util.AjaxWriter: Deprecated. End the current record by printing the record separator string on a line by its own.
ajaxEscape(String) - Method in class net.sf.basedb.clients.web.util.AjaxWriter: Deprecated. Escape new line and carrige return characters in the input to the literal string '\n' and '\r' in the output.
ajaxPrintEntry(String, Object) - Method in class net.sf.basedb.clients.web.util.AjaxWriter: Deprecated. Print a record entry.
AjaxWriter - Class in net.sf.basedb.clients.web.util: Deprecated. In 2.17, we recommend using JSON for AJAX responses. Use classes from the org.json.simple.* package. See http://code.google.com/p/json-simple/ for more information and documentation.
AjaxWriter(Writer) - Constructor for class net.sf.basedb.clients.web.util.AjaxWriter: Deprecated. Create a new ajax writer that is writing it's output to the given writer.
alias - Variable in class net.sf.basedb.core.AnnotationRestriction
alias - Variable in enum net.sf.basedb.core.Item
alias - Variable in class net.sf.basedb.core.query.ExpressionSelect
alias(String) - Static method in class net.sf.basedb.core.query.Hql: Same as property(alias, null).
alias - Variable in class net.sf.basedb.core.query.HqlElementsExpression
alias - Variable in class net.sf.basedb.core.query.HqlIndexExpression
alias - Variable in class net.sf.basedb.core.query.HqlInnerJoin
alias - Variable in class net.sf.basedb.core.query.HqlLeftJoin
alias - Variable in class net.sf.basedb.core.query.HqlPropertyExpression
alias - Variable in class net.sf.basedb.core.query.HqlRightJoin
alias - Variable in class net.sf.basedb.core.query.HqlSizeExpression
alias - Variable in class net.sf.basedb.core.query.SqlColumnExpression
alias - Variable in class net.sf.basedb.core.RealTable: The alias to use in queries for this table.
alias - Variable in enum net.sf.basedb.core.VirtualTable: The alias to use in queries for this table.
alias - Variable in class net.sf.basedb.util.ssl.StaticKeyManager
ALIAS_REGEXP - Static variable in class net.sf.basedb.core.query.Hql: An alias can only contain the characters a-z, A-Z or 0-9.
ALIAS_REGEXP - Static variable in class net.sf.basedb.core.query.Selects: An alias can only contain the characters a-z, A-Z or 0-9.
aliasMapping - Static variable in enum net.sf.basedb.core.Item
align - Variable in class net.sf.basedb.clients.web.taglib.ButtonGroup: Optional align attribute
ALL - Static variable in enum net.sf.basedb.core.Include: A non-modifable collection containing all options.
ALL - Static variable in class net.sf.basedb.core.Keyring
all(Query) - Static method in class net.sf.basedb.core.query.Expressions: Create a subquery expression: ANY (subquery).
all - Static variable in class net.sf.basedb.core.RawDataTypes
all - Variable in class net.sf.basedb.util.plot.HistogramPlot.HistogramDataset
ALL_ITEM - Static variable in class net.sf.basedb.core.Keyring
allCharsets - Static variable in class net.sf.basedb.core.Config
allColumnMappings - Variable in class net.sf.basedb.plugins.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
AllEventsFilter - Class in net.sf.basedb.util.extensions.events: Event filter that passes all events.
AllEventsFilter() - Constructor for class net.sf.basedb.util.extensions.events.AllEventsFilter: Create a event type filter that passes all events.
allMustPass - Variable in class net.sf.basedb.util.extensions.events.CombiningEventFilter
allNodes - Variable in class net.sf.basedb.util.overview.ExperimentOverview: Deprecated.
allNodes - Variable in class net.sf.basedb.util.overview.GenericOverview
AllOfFilter<T> - Class in net.sf.basedb.util.filter: A filter implementation that accpets an object if all parent filters accepts it.
AllOfFilter(Collection<? extends Filter<? super T>>) - Constructor for class net.sf.basedb.util.filter.AllOfFilter: Create a new filter.
allow - Variable in class net.sf.basedb.core.signal.SocketSignalReceiver
ALLOW_ROOT_NODE - Static variable in class net.sf.basedb.util.overview.loader.BasicItemNodeLoader
allowAll - Variable in class net.sf.basedb.core.signal.SocketSignalReceiver
AllowAnyHostNameVerifyer - Class in net.sf.basedb.util.ssl: A simple implementation of a host name verifyer that allows all hosts.
AllowAnyHostNameVerifyer() - Constructor for class net.sf.basedb.util.ssl.AllowAnyHostNameVerifyer
allowAsRootNode - Variable in class net.sf.basedb.util.overview.loader.BasicItemNodeLoader
allowForward - Variable in class net.sf.basedb.core.signal.SocketSignalReceiver
allowImmediateDownload - Variable in class net.sf.basedb.core.PluginResponse
allowImmediateExecution - Variable in class net.sf.basedb.core.data.PluginDefinitionData
allowImmediateExecution - Variable in class net.sf.basedb.core.PluginConfigurationRequest
allowImmediateExecution - Variable in class net.sf.basedb.core.PluginRequest.RequestImpl
allowImmediateExecution - Variable in class net.sf.basedb.core.PluginResponse
allowMultiple - Variable in class net.sf.basedb.util.timer.ThreadTimerTask
allowRemotePause - Variable in class net.sf.basedb.clients.jobagent.Agent
allowRemoteStart - Variable in class net.sf.basedb.clients.jobagent.Agent
allowRemoteStop - Variable in class net.sf.basedb.clients.jobagent.Agent
allowRendererOverride() - Method in interface net.sf.basedb.util.extensions.ExtensionPoint: If an extension is allowed to override the renderer factory with an implementation of its own.
allowRendererOverride - Variable in class net.sf.basedb.util.extensions.ExtensionPointBean
allowRendererOverride() - Method in class net.sf.basedb.util.extensions.ExtensionPointBean
allowRendererOverride - Variable in class net.sf.basedb.util.extensions.Registry.RegisteredExtensionPoint
allowRendererOverride() - Method in class net.sf.basedb.util.extensions.Registry.RegisteredExtensionPoint
allowSaveParameters - Variable in enum net.sf.basedb.core.plugin.Response.Status
allowSaveParameters() - Method in enum net.sf.basedb.core.plugin.Response.Status
allowSubclass - Variable in class net.sf.basedb.util.filter.InstanceOfFilter
allowUse - Variable in class net.sf.basedb.util.jep.RawFunction
allProperties - Static variable in class net.sf.basedb.core.ExtendedProperties: A map from class name --> a list of extended properties of for that class.
allSame(Collection<Set<Permission>>) - Static method in class net.sf.basedb.core.MultiPermissions: Check if a collection of Set:s all contain the same permissions.
allSeries - Variable in class net.sf.basedb.util.plot.ScatterPlot
allVisible - Variable in class net.sf.basedb.clients.web.taglib.table.Table: "all" was specified for the columns attribute.
alphaToNumeric(String) - Static method in class net.sf.basedb.util.Coordinate: Convert an alphanumeric coordinate to a numeric coordinate, case is unimportent.
AlreadyLoggedInException - Exception in net.sf.basedb.core: This exception is thrown if you try to log in but are already logged in.
AlreadyLoggedInException(String) - Constructor for exception net.sf.basedb.core.AlreadyLoggedInException: Creates a new AlreadyLoggedInException.
ALTERNATE_PATH_MATCH - Static variable in class net.sf.basedb.clients.web.servlet.ExtensionsServlet: Alternatively the servlet is: /extensions/servlet and pathInfo is: /[jar-file-name]/[servlet-name]/optional/path/info
alwaysGranted - Variable in class net.sf.basedb.core.plugin.Permissions
AMP - Static variable in class net.sf.basedb.clients.web.util.HTML
AMPERSAND - Static variable in class net.sf.basedb.clients.web.util.HTML
AnalysisFilterPlugin - Interface in net.sf.basedb.core.plugin: This is a tagging interface that should be used by all analysis plug-ins that are filtering data only.
analyzeAfterBatchOperation() - Method in interface net.sf.basedb.core.dbengine.DbEngine: If TRUE, a batcher that inserts, updates or delets a lot of rows in a table should execute the SQL returned by DbEngine.getAnalyzeTableSql(String, String, String) for that table.
analyzeAfterBatchOperation() - Method in class net.sf.basedb.core.dbengine.DefaultDbEngine: Return false.
analyzeAfterBatchOperation() - Method in class net.sf.basedb.core.dbengine.MySQLEngine: Return true.
analyzeAfterBatchOperation() - Method in class net.sf.basedb.core.dbengine.PostgresDbEngine: Return true.
analyzeTable(String, String, String) - Method in class net.sf.basedb.core.AbstractBatcher: Update index statistics for a table.
and(Restriction...) - Static method in class net.sf.basedb.core.query.Restrictions: Combine one or more restrictions with AND: new restriction = r[0] AND r[1] AND ...
AndConverter - Class in net.sf.basedb.util.jep.convert: Convert the '&&' operator to a Query API Restriction.
AndConverter() - Constructor for class net.sf.basedb.util.jep.convert.AndConverter
AndRestriction - Class in net.sf.basedb.core.query: Combine one or more restrictions with AND: r[0] AND r[1] AND ...
AndRestriction(Restriction...) - Constructor for class net.sf.basedb.core.query.AndRestriction
ANGLE - Static variable in class net.sf.basedb.core.Quantity: The id for the Quantity object representing angle.
Annotatable - Interface in net.sf.basedb.core: This interface is implemented by all items which can be annotated.
ANNOTATABLE_FILTER - Static variable in class net.sf.basedb.core.QueryRuntimeFilterFactory
AnnotatableData - Interface in net.sf.basedb.core.data: An annotatable item is an item that can be annotated with name/value pairs.
annotatableItems - Static variable in class net.sf.basedb.core.Metadata
annotatableParents - Variable in class net.sf.basedb.util.overview.ExperimentOverview: Deprecated.
AnnotatableProxy - Interface in net.sf.basedb.core: This interface is implemented by items that can be used to hold annotations that are intended for other items.
AnnotatedData - Class in net.sf.basedb.core.data: This class extends the CommonData class and implements the AnnotatableData interface.
AnnotatedData() - Constructor for class net.sf.basedb.core.data.AnnotatedData
AnnotatedItem<D extends AnnotatedData> - Class in net.sf.basedb.core: This is a helper class for items that need to implement the Annotatable interface.
AnnotatedItem(D) - Constructor for class net.sf.basedb.core.AnnotatedItem
AnnotatedItemInfo - Class in net.sf.basedb.info
AnnotatedItemInfo() - Constructor for class net.sf.basedb.info.AnnotatedItemInfo
Annotation - Class in net.sf.basedb.core: This class represents an annotation.
Annotation(AnnotationData) - Constructor for class net.sf.basedb.core.Annotation
Annotation(AnnotationData, AnnotationSet) - Constructor for class net.sf.basedb.core.Annotation
annotation(AnnotationType, Formatter<?>) - Static method in class net.sf.basedb.util.export.spotdata.ExportableFieldFactory: Create an annotation assay field.
annotation(AnnotationType, String, Formatter<?>) - Static method in class net.sf.basedb.util.export.spotdata.ExportableFieldFactory: Create an annotation assay field, overriding the title of the annotation type.
Annotation.QueryRuntimeFilterImpl - Class in net.sf.basedb.core
Annotation.QueryRuntimeFilterImpl() - Constructor for class net.sf.basedb.core.Annotation.QueryRuntimeFilterImpl
ANNOTATION_INHERIT_FROM_DENIEDPARENT - Static variable in class net.sf.basedb.util.overview.Validator: Validator rule that checks if the logged in user has access to the parent item of an inherited annotation value.
ANNOTATION_INHERIT_FROM_NONPARENT - Static variable in class net.sf.basedb.util.overview.Validator: Validator rule that checks if an inherited annotation value is inherited from a parent item.
ANNOTATION_INHERIT_MULTIPLE - Static variable in class net.sf.basedb.util.overview.Validator: Validator rule that checks if two or more inherited annotations have the same annotation type.
ANNOTATION_INVALID_ITEM - Static variable in class net.sf.basedb.util.overview.Validator: Validator rule that checks if an annotation is not valid for the current item type.
ANNOTATION_INVALID_VALUE - Static variable in class net.sf.basedb.util.overview.Validator: Validator rule that checks if an annotation value is invalid according to annotation type specification.
ANNOTATION_IS_PARAMETER - Static variable in class net.sf.basedb.util.overview.Validator: Validator rule that checks if an annotation is a protocol parameter.
AnnotationAssayField - Class in net.sf.basedb.util.export.spotdata: Assay field implementation that exports the annotations of a bioassay.
AnnotationAssayField() - Constructor for class net.sf.basedb.util.export.spotdata.AnnotationAssayField: Create a new annotation field.
AnnotationBetweenRestriction - Class in net.sf.basedb.core: Restricts a query using annotation values between a low and high value.
AnnotationBetweenRestriction(AnnotationType, Object, Object, boolean) - Constructor for class net.sf.basedb.core.AnnotationBetweenRestriction: Deprecated. Use AnnotationBetweenRestriction.AnnotationBetweenRestriction(String, AnnotationType, Object, Object, boolean) instead with alias=null
AnnotationBetweenRestriction(String, AnnotationType, Object, Object, boolean) - Constructor for class net.sf.basedb.core.AnnotationBetweenRestriction: Create a new annotation restriction.
AnnotationData - Class in net.sf.basedb.core.data: This class holds information about an annotation
AnnotationData() - Constructor for class net.sf.basedb.core.data.AnnotationData
AnnotationFilter - Class in net.sf.basedb.core.snapshot: Filter implementation that finds the annotation snapshot for a given annotation.
AnnotationFilter() - Constructor for class net.sf.basedb.core.snapshot.AnnotationFilter: Create a filter that matches all annotations.
AnnotationFilter(Annotation) - Constructor for class net.sf.basedb.core.snapshot.AnnotationFilter: Create a filter that matches a specfic annotation.
AnnotationFlatFileImporter - Class in net.sf.basedb.plugins: Plug-in for importing annotations from simple text files.
AnnotationFlatFileImporter() - Constructor for class net.sf.basedb.plugins.AnnotationFlatFileImporter
AnnotationFlatFileImporter.AnnotationValue - Class in net.sf.basedb.plugins
AnnotationFlatFileImporter.AnnotationValue(Object, Unit) - Constructor for class net.sf.basedb.plugins.AnnotationFlatFileImporter.AnnotationValue
AnnotationFlatFileImporter.NewAnnotations - Class in net.sf.basedb.plugins: Internal cache for storing annotation values from the file for a single item.
AnnotationFlatFileImporter.NewAnnotations(Annotatable) - Constructor for class net.sf.basedb.plugins.AnnotationFlatFileImporter.NewAnnotations: Create a new cache for the specified item.
annotationId - Variable in class net.sf.basedb.core.snapshot.AnnotationFilter
annotationId - Variable in class net.sf.basedb.core.snapshot.AnnotationSnapshot
AnnotationInfo - Class in net.sf.basedb.info: An information class that holds information about annotation values for a given annotation type.
AnnotationInfo() - Constructor for class net.sf.basedb.info.AnnotationInfo: Creates information object with no properties set.
AnnotationInRestriction - Class in net.sf.basedb.core: Restricts a query using annotation values that exists in a set of given values.
AnnotationInRestriction(AnnotationType, boolean, Object...) - Constructor for class net.sf.basedb.core.AnnotationInRestriction: Deprecated. Use AnnotationInRestriction.AnnotationInRestriction(String, AnnotationType, boolean, Object[]) instead with alias=null
AnnotationInRestriction(String, AnnotationType, boolean, Object...) - Constructor for class net.sf.basedb.core.AnnotationInRestriction: Create a new annotation restriction.
AnnotationLoader - Class in net.sf.basedb.util.overview.loader: Node loader implementation for annotations.
AnnotationLoader() - Constructor for class net.sf.basedb.util.overview.loader.AnnotationLoader
AnnotationLogger - Class in net.sf.basedb.core.log.db: Logger for annotations that logs changes as updates to the parent item the annotations belong to.
AnnotationLogger() - Constructor for class net.sf.basedb.core.log.db.AnnotationLogger
AnnotationModel - Class in net.sf.basedb.util.bfs: A model container for BFS annotation files.
AnnotationModel() - Constructor for class net.sf.basedb.util.bfs.AnnotationModel: Create a new annotation model.
AnnotationNameGenerator - Class in net.sf.basedb.util.overview.node: Since an Annotation isn't Nameable we construct the name from the name of the annotation type, or from the value type if we are not allowed to access the annotation type.
AnnotationNameGenerator() - Constructor for class net.sf.basedb.util.overview.node.AnnotationNameGenerator
AnnotationParser - Class in net.sf.basedb.util.bfs: Parser implementation that parses a BFS annotation files.
AnnotationParser() - Constructor for class net.sf.basedb.util.bfs.AnnotationParser: Create a new annotation parser.
AnnotationRestriction - Class in net.sf.basedb.core: Base class for creating restrictions based on annotations.
AnnotationRestriction(String, AnnotationType, boolean) - Constructor for class net.sf.basedb.core.AnnotationRestriction: Create a new annotation restriction for an annotation type.
AnnotationRestriction(String, int, Type, boolean) - Constructor for class net.sf.basedb.core.AnnotationRestriction: Create a new annotation restriction given the id and value type of an annotation.
annotations - Variable in class net.sf.basedb.clients.web.servlet.ExperimentExplorerPlotServlet.ColumnKey
annotations - Variable in class net.sf.basedb.core.data.AnnotationSetData
annotations - Variable in class net.sf.basedb.core.data.AnnotationTypeData
Annotations - Class in net.sf.basedb.core.query: A factory class to create restrictions based on annotation values.
Annotations() - Constructor for class net.sf.basedb.core.query.Annotations
annotations - Variable in class net.sf.basedb.core.snapshot.AnnotationSetSnapshot
annotationSection - Static variable in class net.sf.basedb.core.plugin.AbstractPlugin: Section definition for grouping annotation options.
annotationSet - Variable in class net.sf.basedb.core.Annotation
AnnotationSet - Class in net.sf.basedb.core: An annotation set is the container for all annotations on an item.
AnnotationSet(AnnotationSetData) - Constructor for class net.sf.basedb.core.AnnotationSet: Regular constructor if the item is not known beforehand.
AnnotationSet(AnnotationSetData, Annotatable) - Constructor for class net.sf.basedb.core.AnnotationSet: Special constructor to avoid AnnotationSet.getItem() to hit the database when the item is known beforehand.
annotationSet - Variable in class net.sf.basedb.core.data.AnnotatedData
annotationSet - Variable in class net.sf.basedb.core.data.AnnotationData
annotationSet - Variable in class net.sf.basedb.core.data.BioAssayData
annotationSet - Variable in class net.sf.basedb.core.data.BioAssaySetData
annotationSet - Variable in class net.sf.basedb.core.data.PluginDefinitionData
annotationSet - Variable in class net.sf.basedb.core.data.WellData
annotationSet - Variable in class net.sf.basedb.util.overview.validator.ProtocolParameterValidator
AnnotationSet.QueryRuntimeFilterImpl - Class in net.sf.basedb.core
AnnotationSet.QueryRuntimeFilterImpl() - Constructor for class net.sf.basedb.core.AnnotationSet.QueryRuntimeFilterImpl
AnnotationSetData - Class in net.sf.basedb.core.data: This class holds information about a set of annotations.
AnnotationSetData() - Constructor for class net.sf.basedb.core.data.AnnotationSetData
annotationSetId - Variable in class net.sf.basedb.core.snapshot.AnnotationSetSnapshot
annotationSetId - Variable in class net.sf.basedb.core.snapshot.AnnotationSnapshot
AnnotationSetLogger - Class in net.sf.basedb.core.log.db: Logger for annotations sets that detects and logs changes to inherited anntations as updates to the parent item that are inheriting the annotations.
AnnotationSetLogger(boolean) - Constructor for class net.sf.basedb.core.log.db.AnnotationSetLogger
AnnotationSetSnapshot - Class in net.sf.basedb.core.snapshot: A snapshot of an annotation set that is used to store information as a file.
AnnotationSetSnapshot() - Constructor for class net.sf.basedb.core.snapshot.AnnotationSetSnapshot: Creates a new, empty snapshot.
AnnotationSetterPlugin - Interface in net.sf.basedb.core.plugin: This is a interface that should be implemented by plug-ins that are setting annotations on items thy create or work with.
AnnotationSimpleRestriction - Class in net.sf.basedb.core: Restricts a query using annotation values with a simple expression: annotation operator value.
AnnotationSimpleRestriction(AnnotationType, Operator, Object, boolean) - Constructor for class net.sf.basedb.core.AnnotationSimpleRestriction: Deprecated. Use AnnotationSimpleRestriction.AnnotationSimpleRestriction(String, AnnotationType, Operator, Object, boolean) instead with alias=null
AnnotationSimpleRestriction(String, AnnotationType, Operator, Object, boolean) - Constructor for class net.sf.basedb.core.AnnotationSimpleRestriction: Create a new annotation restriction using a simple expression: annotation operator value.
AnnotationSimpleRestriction(int, Type, Operator, Object, boolean) - Constructor for class net.sf.basedb.core.AnnotationSimpleRestriction: Deprecated. Use AnnotationSimpleRestriction.AnnotationSimpleRestriction(String, int, Type, Operator, Object, boolean) instead with alias=null
AnnotationSimpleRestriction(String, int, Type, Operator, Object, boolean) - Constructor for class net.sf.basedb.core.AnnotationSimpleRestriction: Creates a new annotation restriction for a specific valueType.
AnnotationSimpleRestriction(String, int, Type, Operator, List<Object>, boolean) - Constructor for class net.sf.basedb.core.AnnotationSimpleRestriction: Creates a new annotation restriction for a specific valueType.
AnnotationSnapshot - Class in net.sf.basedb.core.snapshot: Stores information about a single primary or inherited annotation or an inherited annotation set.
AnnotationSnapshot() - Constructor for class net.sf.basedb.core.snapshot.AnnotationSnapshot: Create a new, empty annotation snapshot.
annotationType - Variable in class net.sf.basedb.clients.web.ExperimentExplorer.AnnotationSummary
annotationType - Variable in class net.sf.basedb.clients.web.plugins.ExportedProperty
AnnotationType - Class in net.sf.basedb.core: Objects of this class defines an annotation type.
AnnotationType(AnnotationTypeData) - Constructor for class net.sf.basedb.core.AnnotationType
annotationType - Variable in class net.sf.basedb.core.data.AnnotationData
annotationType - Variable in class net.sf.basedb.util.overview.Fix
AnnotationTypeCategory - Class in net.sf.basedb.core: Objects of this class defines an annotation type category.
AnnotationTypeCategory(AnnotationTypeCategoryData) - Constructor for class net.sf.basedb.core.AnnotationTypeCategory
AnnotationTypeCategoryData - Class in net.sf.basedb.core.data: This data layer class holds information about annotation type categories.
AnnotationTypeCategoryData() - Constructor for class net.sf.basedb.core.data.AnnotationTypeCategoryData
AnnotationTypeClient - Class in net.sf.basedb.ws.client: Web service client for annotation types.
AnnotationTypeClient(SessionClient) - Constructor for class net.sf.basedb.ws.client.AnnotationTypeClient: Creates new AnnotationTypeClient object for an active session client.
AnnotationTypeData - Class in net.sf.basedb.core.data: This class holds information about an annotation type.
AnnotationTypeData() - Constructor for class net.sf.basedb.core.data.AnnotationTypeData
AnnotationTypeFilter - Class in net.sf.basedb.core.snapshot: Filter implementation that finds all annotation snapshots for a given annotation type.
AnnotationTypeFilter() - Constructor for class net.sf.basedb.core.snapshot.AnnotationTypeFilter: Create a filter that matches all annotation types.
AnnotationTypeFilter(AnnotationType) - Constructor for class net.sf.basedb.core.snapshot.AnnotationTypeFilter: Create a filter that matches a specfic annotation type.
annotationTypeId - Variable in class net.sf.basedb.core.AnnotationRestriction
annotationTypeId - Variable in class net.sf.basedb.core.snapshot.AnnotationSnapshot
annotationTypeId - Variable in class net.sf.basedb.core.snapshot.AnnotationTypeFilter
annotationTypeId - Variable in class net.sf.basedb.info.AnnotationInfo
annotationTypeIds - Variable in class net.sf.basedb.clients.web.ExperimentExplorer: The currently selected annotation types on the view page.
AnnotationTypeInfo - Class in net.sf.basedb.info: An information class that holds information about an AnnotationType.
AnnotationTypeInfo() - Constructor for class net.sf.basedb.info.AnnotationTypeInfo: Creates information object with no properties set.
annotationTypes - Variable in class net.sf.basedb.core.data.AnnotationTypeCategoryData
annotationTypeSection - Static variable in class net.sf.basedb.plugins.AnnotationFlatFileImporter: Section definition for grouping all mappings of columns to annotation types.
AnnotationTypeService - Class in net.sf.basedb.ws.server: Web service class for annotation types.
AnnotationTypeService() - Constructor for class net.sf.basedb.ws.server.AnnotationTypeService
AnnotationUtil - Class in net.sf.basedb.util: Utility class for working with annotations.
AnnotationUtil() - Constructor for class net.sf.basedb.util.AnnotationUtil
AnnotationUtil.AnnotatableWrapper - Class in net.sf.basedb.util: This wrapper class is needed because we need to keep track of the RawBioAssay.getArrayNum() property until we have loaded the Labeled Extracts of a Hybridization.
AnnotationUtil.AnnotatableWrapper(Annotatable, int) - Constructor for class net.sf.basedb.util.AnnotationUtil.AnnotatableWrapper
AnnotationValidator - Class in net.sf.basedb.util.overview.validator: Validator implementation for annotations.
AnnotationValidator() - Constructor for class net.sf.basedb.util.overview.validator.AnnotationValidator
annotationValues - Variable in class net.sf.basedb.clients.web.ExperimentExplorer.AnnotationGroup
AnnotationWriter - Class in net.sf.basedb.util.bfs
AnnotationWriter(Writer) - Constructor for class net.sf.basedb.util.bfs.AnnotationWriter
any(Query) - Static method in class net.sf.basedb.core.query.Expressions: Create a subquery expression: ANY (subquery).
AnyToAny - Class in net.sf.basedb.core: An any-to-any link is a named, directed link from one item to another item.
AnyToAny(AnyToAnyData) - Constructor for class net.sf.basedb.core.AnyToAny: Creates a new link item from the given data.
AnyToAny(AnyToAnyData, BasicItem) - Constructor for class net.sf.basedb.core.AnyToAny: Special constructor when the from item is known.
AnyToAnyData - Class in net.sf.basedb.core.data: Represents a link from one item to any other item.
AnyToAnyData() - Constructor for class net.sf.basedb.core.data.AnyToAnyData
AnyToAnyLoader - Class in net.sf.basedb.util.overview.loader: Node loader implementation for any-to-any links.
AnyToAnyLoader() - Constructor for class net.sf.basedb.util.overview.loader.AnyToAnyLoader
AnyToAnyNameGenerator - Class in net.sf.basedb.util.overview.node: Name generator for any-to-any links.
AnyToAnyNameGenerator() - Constructor for class net.sf.basedb.util.overview.node.AnyToAnyNameGenerator
AnyToAnyValidator - Class in net.sf.basedb.util.overview.validator: Validator implementation for any-to-any links.
AnyToAnyValidator() - Constructor for class net.sf.basedb.util.overview.validator.AnyToAnyValidator
append(String) - Method in class net.sf.basedb.core.Job.ProgressReporterImpl
append(String) - Method in interface net.sf.basedb.core.ProgressReporter: Append a message to the previous one.
append(String) - Method in class net.sf.basedb.core.signal.ProgressReporterSignalHandler
append(String) - Method in class net.sf.basedb.core.SimpleProgressReporter
append(String) - Method in class net.sf.basedb.util.ChainedProgressReporter
append(String) - Method in class net.sf.basedb.util.ConsoleProgressReporter
appendGroups(StringBuilder, DbControl, List<Expression>, int) - Method in class net.sf.basedb.core.AbstractQuery
appendHavings(StringBuilder, DbControl, List<Restriction>, int) - Method in class net.sf.basedb.core.AbstractQuery
appendJoins(StringBuilder, DbControl, List<Join>, boolean, int) - Method in class net.sf.basedb.core.AbstractQuery
appendOrders(StringBuilder, DbControl, List<Order>, int) - Method in class net.sf.basedb.core.AbstractQuery
appendPermissionOption(StringBuilder, Permission, Permission, String) - Method in class net.sf.basedb.clients.web.taglib.table.ColumnDef
appendProgress(Session, String) - Method in class net.sf.basedb.core.Job.ProgressReporterImpl
appendRestrictions(StringBuilder, DbControl, List<Restriction>, int) - Method in class net.sf.basedb.core.AbstractQuery
appendScripts(StringBuilder, boolean) - Method in class net.sf.basedb.clients.web.taglib.Head
appendSelects(StringBuilder, DbControl, List<Select>, int) - Method in class net.sf.basedb.core.AbstractQuery
appendStyles(StringBuilder, SessionControl, boolean) - Method in class net.sf.basedb.clients.web.taglib.Head
Application - Class in net.sf.basedb.core: This class represents the BASE application and is the starting point for all client applications.
Application() - Constructor for class net.sf.basedb.core.Application
Application.DbCleaner - Class in net.sf.basedb.core
Application.DbCleaner() - Constructor for class net.sf.basedb.core.Application.DbCleaner
Application.Pinger - Class in net.sf.basedb.core: A Pinger is an object that is used to protect another object from timing out by automatically pinging it.
Application.Pinger(SessionControl) - Constructor for class net.sf.basedb.core.Application.Pinger
Application.SecondaryStorageControllerTask - Class in net.sf.basedb.core
Application.SecondaryStorageControllerTask(SecondaryStorageController) - Constructor for class net.sf.basedb.core.Application.SecondaryStorageControllerTask
Application.SessionControlCacheCleaner - Class in net.sf.basedb.core
Application.SessionControlCacheCleaner() - Constructor for class net.sf.basedb.core.Application.SessionControlCacheCleaner
apply(List<Plate>, PlateType) - Method in class net.sf.basedb.core.PlateMapping: Apply this mapping to the given list of source plates and generate new plates of the specified type.
aquireLock(String, boolean, int) - Method in class net.sf.basedb.util.StaticCache: Aquire a read or write lock on a given cache entry.
AREA - Static variable in class net.sf.basedb.core.Quantity: The id for the Quantity object representing area.
arrangeData(int, short, Object[][], Object[]) - Method in class net.sf.basedb.util.export.spotdata.BfsExporter: Arrange the data that was returned by the query into the data writers array.
arrangeData(int, short, Object[][], Object[]) - Method in class net.sf.basedb.util.export.spotdata.MatrixBfsExporter: The column number is used to find the assay index.
arrangeData(int, short, Object[][], Object[]) - Method in class net.sf.basedb.util.export.spotdata.SerialBfsExporter: The column number is used to find the assay index.
array - Variable in class net.sf.basedb.util.ArrayIterator: The array to iterate.
ArrayBatch - Class in net.sf.basedb.core: This class represents the making of a new batch of microarray slides of a particular design.
ArrayBatch(ArrayBatchData) - Constructor for class net.sf.basedb.core.ArrayBatch
arrayBatch - Variable in class net.sf.basedb.core.data.ArraySlideData
arrayBatchColumnMapping - Static variable in class net.sf.basedb.plugins.batchimport.ArraySlideImporter
ArrayBatchData - Class in net.sf.basedb.core.data: This class represents the making of a new batch of microarray slides of a particular design.
ArrayBatchData() - Constructor for class net.sf.basedb.core.data.ArrayBatchData
arrayBatches - Variable in class net.sf.basedb.core.data.ArrayDesignData
ArrayBatchImporter - Class in net.sf.basedb.plugins.batchimport: Plug-in for importing array batch items in a batch.
ArrayBatchImporter() - Constructor for class net.sf.basedb.plugins.batchimport.ArrayBatchImporter
ArrayBatchLoader - Class in net.sf.basedb.util.overview.loader: Node loader implementation for array batches.
ArrayBatchLoader() - Constructor for class net.sf.basedb.util.overview.loader.ArrayBatchLoader
arrayBatchMapper - Variable in class net.sf.basedb.plugins.batchimport.ArraySlideImporter
ArrayBatchValidator - Class in net.sf.basedb.util.overview.validator: Validator implementation for array batch.
ArrayBatchValidator() - Constructor for class net.sf.basedb.util.overview.validator.ArrayBatchValidator
ArrayDesign - Class in net.sf.basedb.core: An array design is a description of the design of a microarray slide.
ArrayDesign(ArrayDesignData) - Constructor for class net.sf.basedb.core.ArrayDesign
arrayDesign - Variable in class net.sf.basedb.core.data.ArrayBatchData
arrayDesign - Variable in class net.sf.basedb.core.data.ArrayDesignBlockData
arrayDesign - Variable in class net.sf.basedb.core.data.ArrayDesignPlateData
arrayDesign - Variable in class net.sf.basedb.core.data.RawBioAssayData
arrayDesign - Variable in class net.sf.basedb.core.FeatureBatcher: The array design this batcher adds features to.
arrayDesign - Variable in class net.sf.basedb.core.RawDataBatcher: The array design the raw bioassay is connected to, if any.
arrayDesign - Variable in class net.sf.basedb.plugins.PrintMapFlatFileImporter
arrayDesign - Variable in class net.sf.basedb.plugins.ReporterMapFlatFileImporter
ArrayDesignBlock - Class in net.sf.basedb.core
ArrayDesignBlock(ArrayDesignBlockData) - Constructor for class net.sf.basedb.core.ArrayDesignBlock
arrayDesignBlock - Variable in class net.sf.basedb.core.data.FeatureData
ArrayDesignBlockData - Class in net.sf.basedb.core.data: This holds information about a block in an arraydesign.
ArrayDesignBlockData() - Constructor for class net.sf.basedb.core.data.ArrayDesignBlockData
arrayDesignBlocks - Variable in class net.sf.basedb.core.data.ArrayDesignData
ArrayDesignClient - Class in net.sf.basedb.ws.client: A web service client for array design in BASE.
ArrayDesignClient(SessionClient) - Constructor for class net.sf.basedb.ws.client.ArrayDesignClient: Creates a new client object for a session.
arrayDesignColumnMapping - Static variable in class net.sf.basedb.plugins.batchimport.ArrayBatchImporter
arrayDesignColumnMapping - Static variable in class net.sf.basedb.plugins.batchimport.RawBioAssayImporter
ArrayDesignData - Class in net.sf.basedb.core.data: This class holds information about an arrayDesign
ArrayDesignData() - Constructor for class net.sf.basedb.core.data.ArrayDesignData
arrayDesignData - Variable in class net.sf.basedb.core.FeatureBatcher: Just a copy of the data object for the array design.
arrayDesignHasBeenSet - Variable in class net.sf.basedb.core.RawBioAssay
arrayDesignId - Variable in class net.sf.basedb.info.RawBioAssayInfo
ArrayDesignImporter - Class in net.sf.basedb.plugins.batchimport: Plug-in for importing array design items in a batch.
ArrayDesignImporter() - Constructor for class net.sf.basedb.plugins.batchimport.ArrayDesignImporter
ArrayDesignInfo - Class in net.sf.basedb.info: Information class for a ArrayDesign in BASE.
ArrayDesignInfo() - Constructor for class net.sf.basedb.info.ArrayDesignInfo: Creates a new empty info object.
ArrayDesignLoader - Class in net.sf.basedb.util.overview.loader: Node loader implementation for array designs.
ArrayDesignLoader() - Constructor for class net.sf.basedb.util.overview.loader.ArrayDesignLoader
arrayDesignMapper - Variable in class net.sf.basedb.plugins.batchimport.ArrayBatchImporter
arrayDesignMapper - Variable in class net.sf.basedb.plugins.batchimport.RawBioAssayImporter
arrayDesignParameter - Variable in class net.sf.basedb.plugins.PrintMapFlatFileImporter
arrayDesignParameter - Variable in class net.sf.basedb.plugins.ReporterMapFlatFileImporter
ArrayDesignPlate - Class in net.sf.basedb.core
ArrayDesignPlate(ArrayDesignPlateData) - Constructor for class net.sf.basedb.core.ArrayDesignPlate
ArrayDesignPlateData - Class in net.sf.basedb.core.data: This class connects the ArrayDesign with its plates and adding an index to that connection.
ArrayDesignPlateData() - Constructor for class net.sf.basedb.core.data.ArrayDesignPlateData
arrayDesigns - Variable in class net.sf.basedb.core.data.PlateData
ArrayDesignService - Class in net.sf.basedb.ws.server: Web service class for ArrayDesign Provides services to access limited functionality in this class.
ArrayDesignService() - Constructor for class net.sf.basedb.ws.server.ArrayDesignService
arrayDesignType - Variable in class net.sf.basedb.plugins.PrintMapFlatFileImporter
arrayDesignType - Variable in class net.sf.basedb.plugins.ReporterMapFlatFileImporter
ArrayDesignValidator - Class in net.sf.basedb.util.overview.validator: Validator implementation for array designs.
ArrayDesignValidator() - Constructor for class net.sf.basedb.util.overview.validator.ArrayDesignValidator
arrayIndexColumnMapping - Static variable in class net.sf.basedb.plugins.batchimport.HybridizationImporter
arrayIndexColumnMapping - Static variable in class net.sf.basedb.plugins.batchimport.RawBioAssayImporter
arrayIndexMapper - Variable in class net.sf.basedb.plugins.batchimport.HybridizationImporter
arrayIndexMapper - Variable in class net.sf.basedb.plugins.batchimport.RawBioAssayImporter
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.
arrayNum - Variable in class net.sf.basedb.core.data.RawBioAssayData
arrayNum - Variable in class net.sf.basedb.util.AnnotationUtil.AnnotatableWrapper
ArraySlide - Class in net.sf.basedb.core: This class represents a physical microarray slide.
ArraySlide(ArraySlideData) - Constructor for class net.sf.basedb.core.ArraySlide
arraySlide - Variable in class net.sf.basedb.core.data.HybridizationData
arraySlideColumnMapping - Static variable in class net.sf.basedb.plugins.batchimport.HybridizationImporter
ArraySlideData - Class in net.sf.basedb.core.data: This class represents a phycsical microarray slide.
ArraySlideData() - Constructor for class net.sf.basedb.core.data.ArraySlideData
ArraySlideImporter - Class in net.sf.basedb.plugins.batchimport: Plug-in for importing array slide items in a batch.
ArraySlideImporter() - Constructor for class net.sf.basedb.plugins.batchimport.ArraySlideImporter
ArraySlideLoader - Class in net.sf.basedb.util.overview.loader: Node loader implementation for array slides.
ArraySlideLoader() - Constructor for class net.sf.basedb.util.overview.loader.ArraySlideLoader
arraySlideMapper - Variable in class net.sf.basedb.plugins.batchimport.HybridizationImporter
arraySlideQuery - Variable in class net.sf.basedb.plugins.batchimport.AbstractItemImporter
arraySlides - Variable in class net.sf.basedb.core.data.ArrayBatchData
ArraySlideValidator - Class in net.sf.basedb.util.overview.validator: Validator implementation for array slides.
ArraySlideValidator() - Constructor for class net.sf.basedb.util.overview.validator.ArraySlideValidator
asc(Expression) - Static method in class net.sf.basedb.core.query.Orders: Sort the result of a query in ascending order by the expression.
AscOrder - Class in net.sf.basedb.core.query: Sort the result of a query in ascending order by the expression.
AscOrder(Expression) - Constructor for class net.sf.basedb.core.query.AscOrder
asFloat - Variable in class net.sf.basedb.util.parser.ConstantMapper
asInteger - Variable in class net.sf.basedb.util.parser.ConstantMapper
assayAnnotationQuery - Variable in class net.sf.basedb.util.export.spotdata.AbstractFieldConverter
assayField(String, String, Type) - Method in class net.sf.basedb.plugins.BfsExporterPlugin
AssayField - Interface in net.sf.basedb.util.export.spotdata: Represents a bioassay field that is going to be exported.
assayFields - Variable in class net.sf.basedb.util.export.spotdata.AbstractBioAssaySetExporter
assayFields - Variable in class net.sf.basedb.util.importer.spotdata.BaseFileInfo.SpotSectionInfo
assayGroups - Variable in class net.sf.basedb.clients.web.ExperimentExplorer.AnnotationSummary
assayIndexMap - Variable in class net.sf.basedb.util.export.spotdata.AbstractBioAssaySetExporter
assayProperty(String, String, Type, Formatter<?>) - Static method in class net.sf.basedb.util.export.spotdata.ExportableFieldFactory: Create a property assay field.
AssayPropertyField - Class in net.sf.basedb.util.export.spotdata: Assay field implementation that exports a named property from a bioassay.
AssayPropertyField() - Constructor for class net.sf.basedb.util.export.spotdata.AssayPropertyField: Create a new annotation field.
assays - Variable in class net.sf.basedb.util.importer.spotdata.BaseFileInfo.SpotSectionInfo
assays - Variable in class net.sf.basedb.util.importer.spotdata.MatrixSpotIntensityEventHandler
assays - Variable in class net.sf.basedb.util.importer.spotdata.SerialSpotIntensityEventHandler
assaysHaveParentAssaysMapping - Variable in class net.sf.basedb.util.importer.spotdata.BaseFileInfo
assayWriter - Variable in class net.sf.basedb.util.export.spotdata.BfsExporter
associateFiles(DbControl, Transformation, Directory) - Method in class net.sf.basedb.plugins.Base1PluginExecuter
associationsSection - Static variable in class net.sf.basedb.plugins.IlluminaRawDataImporter: Section definition for grouping associations to other items: scan, software, protocol and experiment
ASTConstantConverter - Class in net.sf.basedb.util.jep.convert: Converts a constant node to an expression.
ASTConstantConverter() - Constructor for class net.sf.basedb.util.jep.convert.ASTConstantConverter
ASTFunNodeConverter - Class in net.sf.basedb.util.jep.convert: Converts a function node to an expression or restriction.
ASTFunNodeConverter() - Constructor for class net.sf.basedb.util.jep.convert.ASTFunNodeConverter
ASTVarNodeConverter - Class in net.sf.basedb.util.jep.convert: Converts a variable node to a parameter expression or null.
ASTVarNodeConverter() - Constructor for class net.sf.basedb.util.jep.convert.ASTVarNodeConverter
asXml() - Method in class net.sf.basedb.core.Presets: Convert the presets to an XML string.
at - Variable in class net.sf.basedb.util.export.spotdata.AnnotationAssayField
AT_OR_DOT - Static variable in class net.sf.basedb.clients.web.util.HTML
atBoundary - Variable in class net.sf.basedb.clients.web.fileupload.FileUpload.UploadStatus: TRUE if the FileUpload.checkBoundary(byte[], int, byte[], int) method finds that the line matches the boundary, FALSE otherwise.
atLastBoundary - Variable in class net.sf.basedb.clients.web.fileupload.FileUpload.UploadStatus: TRUE if the FileUpload.checkBoundary(byte[], int, byte[], int) method finds that the line matches the boundary + two extra dashes (--), FALSE otherwise.
attachesToItemType - Variable in enum net.sf.basedb.core.Project.Default
attachFile(DataSource, String) - Method in class net.sf.basedb.ws.server.AbstractRPCService: Attach a file to an OMElement so it can be sent with webservices.
ATTRIBUTE_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.
attributes - Variable in class net.sf.basedb.clients.web.taglib.Body: Any other attributes that is needed in the body tag.
attributes - Variable in class net.sf.basedb.util.extensions.ClientContext
attributes - Variable in class net.sf.basedb.util.extensions.Registry
authenticate(String, String) - Method in interface net.sf.basedb.core.authentication.Authenticator: Authenticates a user.
authenticate(String, String) - Method in class net.sf.basedb.core.authentication.POP3Authenticator: Authenticates a user against the POP3 server.
authenticate(String, String) - Method in class net.sf.basedb.core.authentication.SimpleAuthenticator: If login and password are equal the user is authenticated, otherwise an InvalidPasswordException is thrown.
authenticationDriver - Static variable in class net.sf.basedb.core.Application: The name of the external authenication class, if any.
AuthenticationException - Exception in net.sf.basedb.core.authentication: This exception can be thrown when an error occurs during the authentication.
AuthenticationException(String) - Constructor for exception net.sf.basedb.core.authentication.AuthenticationException: Create a new AuthenticationException object
AuthenticationException(Throwable) - Constructor for exception net.sf.basedb.core.authentication.AuthenticationException: Create a new AuthenticationException object
AuthenticationInformation - Class in net.sf.basedb.core.authentication: Objects of this class are returned by the Authenticator.authenticate(String,String) method and contains information about the authenticated user.
AuthenticationInformation(String, String) - Constructor for class net.sf.basedb.core.authentication.AuthenticationInformation: Creates a new AuthenticationInformation object without extra information.
AuthenticationInformation(String, String, String, String, String, String, String, String, String, String) - Constructor for class net.sf.basedb.core.authentication.AuthenticationInformation: Creates a new AuthenticationInformation object with extra information.
Authenticator - Interface in net.sf.basedb.core.authentication: This interface defines the methods that needs to be implemented by a class to be able to use it for external authentication against another database or directory service.
authors - Variable in class net.sf.basedb.core.data.ExperimentData
authors - Variable in class net.sf.basedb.info.ExperimentInfo
AUTO_INSTALL - Static variable in class net.sf.basedb.clients.web.extensions.Settings
autoAdjustHeight - Variable in class net.sf.basedb.clients.web.taglib.tab.TabControl: If tab height should be automatically adjusted or not.
AutoChildNodeLoader - Class in net.sf.basedb.util.overview.loader: Node loader implementation that automatically loads child nodes.
AutoChildNodeLoader(NodeLoader) - Constructor for class net.sf.basedb.util.overview.loader.AutoChildNodeLoader
autoCloseParsers - Variable in class net.sf.basedb.util.importer.spotdata.BfsImporter
autoCloseWriters - Variable in class net.sf.basedb.util.export.spotdata.BfsExporter
autoCompress - Variable in class net.sf.basedb.core.data.DirectoryData
autoCompress - Variable in class net.sf.basedb.core.data.MimeTypeData
autoCompressionEnabled() - Static method in class net.sf.basedb.core.Application: Check if auto-compression has been enabled or not.
AutoDetectFileFormat - Class in net.sf.basedb.util: This class has methods for autodetecting file formats.
AutoDetectFileFormat() - Constructor for class net.sf.basedb.util.AutoDetectFileFormat
AutoDetectFileFormat.IsImportableFilter - Class in net.sf.basedb.util: Filter implementation that filters a collection of ContextUtil.ContextResult:s by checking each plug-ins ability to import a given file.
AutoDetectFileFormat.IsImportableFilter(File, Filter<? super ContextUtil.ContextResult>) - Constructor for class net.sf.basedb.util.AutoDetectFileFormat.IsImportableFilter
AutoDetectingImporter - Interface in net.sf.basedb.core.plugin: This interface should be implemented by an import plugin that supports auto-detection of the file format.
autoInherit(DbControl, AnnotationType, boolean) - Method in class net.sf.basedb.core.AnnotationSet: Deprecated. In 2.15, use AnnotationSet.autoInherit(DbControl, Collection, SnapshotManager, boolean) instead since it has better performance
autoInherit(DbControl, Collection<AnnotationType>, SnapshotManager, boolean) - Method in class net.sf.basedb.core.AnnotationSet: Automatically inherit all annotations of one or more specified annotation types from parent items that are currntly missing from this annotation set This method will only consider parent items that the logged in user has access to with USE permission.
autoInstallTask - Static variable in class net.sf.basedb.clients.web.extensions.ExtensionsControl
autoJoin() - Method in class net.sf.basedb.core.AbstractQuery
AutoJoiner<Q extends Query,E extends QueryElement> - Interface in net.sf.basedb.core.query: An AutoJoiner is an object that automatically joins other tables in query depending on other query elements.
autoJoiners - Variable in class net.sf.basedb.core.AbstractQuery
autoJoinType - Variable in class net.sf.basedb.core.query.ReporterListExpression
autoLoadChildren - Variable in class net.sf.basedb.util.overview.loader.BasicItemNodeLoaderFactory
autoPermission - Variable in class net.sf.basedb.core.data.ProjectData
autoReload - Variable in class net.sf.basedb.util.units.UnitCache
autoShare - Variable in class net.sf.basedb.core.data.DirectoryData
autoShow - Variable in class net.sf.basedb.clients.web.taglib.table.Cell
autoUnloadPlugins - Static variable in class net.sf.basedb.core.Application: Allow automatic unload of plug-in JAR files or not.
autoUnloadPlugins() - Static method in class net.sf.basedb.core.Application: If external plug-in JAR files should automatically be unloaded if the are modified.
available() - Method in class net.sf.basedb.clients.web.fileupload.FileUpload.UploadStream
available() - Method in class net.sf.basedb.util.InputStreamCombiner
available() - Method in class net.sf.basedb.util.InputStreamSplitter
available() - Method in class net.sf.basedb.util.InputStreamTracker
averageMethod - Variable in class net.sf.basedb.clients.web.taglib.table.TableColumn
averageMethod - Variable in class net.sf.basedb.core.data.ExtraValueTypeData
averageMethod - Variable in class net.sf.basedb.core.data.FormulaData
averageMethod - Variable in class net.sf.basedb.core.ExtendedProperty
averageMethod - Variable in enum net.sf.basedb.core.IntensityTransform
averageMethod - Variable in class net.sf.basedb.util.export.spotdata.JepDynamicField
averageMethod - Variable in class net.sf.basedb.util.export.spotdata.SimpleDynamicField
averageOnReporter - Variable in class net.sf.basedb.util.export.spotdata.AbstractBioAssaySetExporter
avg - Variable in class net.sf.basedb.core.query.GeometricMeanExpression
avg - Variable in class net.sf.basedb.plugins.BioAssaySetExporter.QueryItem: Deprecated.

B

BACKSLASH - Static variable in class net.sf.basedb.clients.web.util.HTML
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.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.plugins.BioAssaySetExporter: Deprecated.
bas - Variable in class net.sf.basedb.util.jep.ExtraValueFunction
Base - Class in net.sf.basedb.clients.web: This class is used to collect some useful methods for the web client into a single place.
Base() - Constructor for class net.sf.basedb.clients.web.Base
base - Variable in class net.sf.basedb.core.query.LogExpression
base - Variable in class net.sf.basedb.core.query.PowerExpression
Base1FieldConverter - Class in net.sf.basedb.util.export.spotdata: Exportable field converter that support BASE 1 naming conventions.
Base1FieldConverter(DbControl, BioAssaySet) - Constructor for class net.sf.basedb.util.export.spotdata.Base1FieldConverter: Create a new converter for the given bioassay set.
Base1PluginExecuter - Class in net.sf.basedb.plugins: This plug-in executes a plug-in from the Base1 system.
Base1PluginExecuter() - Constructor for class net.sf.basedb.plugins.Base1PluginExecuter
Base1PluginExecuter.Base1JobParameterType - Enum in net.sf.basedb.plugins
Base1PluginExecuter.Base1JobParameterType(char) - Constructor for enum net.sf.basedb.plugins.Base1PluginExecuter.Base1JobParameterType
Base1PluginExecuter.JobParameter - Class in net.sf.basedb.plugins
Base1PluginExecuter.JobParameter(String...) - Constructor for class net.sf.basedb.plugins.Base1PluginExecuter.JobParameter
Base1PluginExecuter.JobParameter(Element) - Constructor for class net.sf.basedb.plugins.Base1PluginExecuter.JobParameter
BASE_VERSION - Static variable in class net.sf.basedb.clients.web.taglib.Page: The version of BASE.
baseBeginDataPart() - Method in class net.sf.basedb.util.basefile.BaseFileWriter: End the header part of the current section (by writing a single % on a line by itself) and start the data part.
baseBeginSection(String) - Method in class net.sf.basedb.util.basefile.BaseFileWriter: Start a new section in the BASEfile.
baseCompleted - Variable in class net.sf.basedb.core.SimpleAbsoluteProgressReporter
baseEndSection() - Method in class net.sf.basedb.util.basefile.BaseFileWriter: Ends the current section by writing an empty line.
baseEscape(String) - Method in class net.sf.basedb.util.basefile.BaseFileWriter: Escape new line and carrige return characters in the input to the literal string '\n' and '\r' in the output.
BaseException - Exception in net.sf.basedb.core: This is the base class for exceptions in BASE.
BaseException() - Constructor for exception net.sf.basedb.core.BaseException: Create a new BaseException object.
BaseException(String) - Constructor for exception net.sf.basedb.core.BaseException: Create a new BaseException object with the specified message
BaseException(String, Throwable) - Constructor for exception net.sf.basedb.core.BaseException: Create a new BaseException object with the specified message
BaseException(Throwable) - Constructor for exception net.sf.basedb.core.BaseException: Create a new BaseException object acting as a wrapper for another exception that caused the error.
BaseException(SQLException) - Constructor for exception net.sf.basedb.core.BaseException: Create a new BaseException object where the cause is an SQLException.
BASEFILE_MATRIX - Static variable in class net.sf.basedb.core.DataFileType: The external ID for the file type representing a matrix BASEFile.
BASEFILE_SERIAL - Static variable in class net.sf.basedb.core.DataFileType: The external ID for the file type representing a serial BASEFile.
BaseFileDataSource - Class in net.sf.basedb.ws.server
BaseFileDataSource(File) - Constructor for class net.sf.basedb.ws.server.BaseFileDataSource: Creates a new DataSourceObject for a file.
BaseFileExporter - Class in net.sf.basedb.util.export.spotdata: A superclass for exporters that exports spot data to BASEfile format.
BaseFileExporter() - Constructor for class net.sf.basedb.util.export.spotdata.BaseFileExporter
BaseFileExporterPlugin - Class in net.sf.basedb.plugins: Exports bioassay set data as serial or matrix BASEfile:s.
BaseFileExporterPlugin() - Constructor for class net.sf.basedb.plugins.BaseFileExporterPlugin
BaseFileExporterPlugin.ExtendedDynamicField - Class in net.sf.basedb.plugins
BaseFileExporterPlugin.ExtendedDynamicField(String, boolean, DynamicField) - Constructor for class net.sf.basedb.plugins.BaseFileExporterPlugin.ExtendedDynamicField
BaseFileExporterPlugin.ExtendedDynamicField(String, String, boolean, DynamicField) - Constructor for class net.sf.basedb.plugins.BaseFileExporterPlugin.ExtendedDynamicField
BaseFileExporterSupport - Class in net.sf.basedb.plugins.executor: Exporter implementation for the external program executor that exports data to BASEfile format.
BaseFileExporterSupport() - Constructor for class net.sf.basedb.plugins.executor.BaseFileExporterSupport
BaseFileImporter - Class in net.sf.basedb.util.importer.spotdata: Imports spot data from a serial or matrix BASEfile.
BaseFileImporter() - Constructor for class net.sf.basedb.util.importer.spotdata.BaseFileImporter: Create a new importer object.
BaseFileImporter.RawDataProxy - Class in net.sf.basedb.util.importer.spotdata
BaseFileImporter.RawDataProxy() - Constructor for class net.sf.basedb.util.importer.spotdata.BaseFileImporter.RawDataProxy
BaseFileImporter.ReporterProxy - Class in net.sf.basedb.util.importer.spotdata
BaseFileImporter.ReporterProxy() - Constructor for class net.sf.basedb.util.importer.spotdata.BaseFileImporter.ReporterProxy
BaseFileImporterSupport - Class in net.sf.basedb.plugins.executor: Importer implementation for the external program executor that imports data from BASEfile format.
BaseFileImporterSupport() - Constructor for class net.sf.basedb.plugins.executor.BaseFileImporterSupport
BaseFileInfo - Class in net.sf.basedb.util.importer.spotdata: Collects information about a BASEfile as it gets parsed by a BaseFileImporter.
BaseFileInfo(File) - Constructor for class net.sf.basedb.util.importer.spotdata.BaseFileInfo: Deprecated. In 2.16, use BaseFileInfo.BaseFileInfo(FileWrapper) instead
BaseFileInfo(FileWrapper) - Constructor for class net.sf.basedb.util.importer.spotdata.BaseFileInfo: The source file which should be a BASEfile.
BaseFileInfo.ChildBioAssay - Class in net.sf.basedb.util.importer.spotdata: Keeps information about a new child bioassay from the 'assays' section or 'spot' sections.
BaseFileInfo.ChildBioAssay() - Constructor for class net.sf.basedb.util.importer.spotdata.BaseFileInfo.ChildBioAssay: Create a new object.
BaseFileInfo.ChildBioAssay(int) - Constructor for class net.sf.basedb.util.importer.spotdata.BaseFileInfo.ChildBioAssay: Create a new object
BaseFileInfo.SpotSectionInfo - Class in net.sf.basedb.util.importer.spotdata: Keeps information about headers and more in a 'spot' section.
BaseFileInfo.SpotSectionInfo() - Constructor for class net.sf.basedb.util.importer.spotdata.BaseFileInfo.SpotSectionInfo: Creates a new object.
BaseFileParser - Class in net.sf.basedb.util.basefile: Parser for serial and matrix BASEfile:s.
BaseFileParser() - Constructor for class net.sf.basedb.util.basefile.BaseFileParser: Creates a new parser object.
BaseFileSectionParser - Interface in net.sf.basedb.util.basefile: A section parser is responsible for parsing and collecting data that is found in a section in a serial or matrix BASEfile.
BaseFileWrapper - Class in net.sf.basedb.util.importer: File wrapper implementation for files that are located on the BASE file system.
BaseFileWrapper(File) - Constructor for class net.sf.basedb.util.importer.BaseFileWrapper
BaseFileWriter - Class in net.sf.basedb.util.basefile: Wraps a writer stream and provides methods for easier creation of BASEfiles.
BaseFileWriter(Writer) - Constructor for class net.sf.basedb.util.basefile.BaseFileWriter: Create a new BASEfile writer that is writing it's output to the given writer.
BaseInputStreamLocator - Class in net.sf.basedb.util.bfs: Input stream locator implementation that works with files within a given directory in the BASE file system.
BaseInputStreamLocator(DbControl, Directory) - Constructor for class net.sf.basedb.util.bfs.BaseInputStreamLocator: Create a new input stream locator.
basePrintData(Object...) - Method in class net.sf.basedb.util.basefile.BaseFileWriter: Print a data line to the BASEfile.
basePrintHeader(String, Object) - Method in class net.sf.basedb.util.basefile.BaseFileWriter: Prints a header in the BASEfile.
baseWriteBom() - Method in class net.sf.basedb.util.basefile.BaseFileWriter: Write the beginning-of-file marker (BASEfile) to the output.
basic - Static variable in class net.sf.basedb.core.Item.DefinedPermissions
BASIC_FILTER - Static variable in class net.sf.basedb.core.QueryRuntimeFilterFactory
BasicBatcher<D extends BatchableData> - Class in net.sf.basedb.core: This is an abstract class for batching functionallity.
BasicBatcher(Session, Class<D>, String) - Constructor for class net.sf.basedb.core.BasicBatcher: Constructor that initiate everything.
BasicChildItem<D extends BasicData> - Class in net.sf.basedb.core: An abstract base class for all items which are child items to a BasicItem parent item.
BasicChildItem(D) - Constructor for class net.sf.basedb.core.BasicChildItem
BasicData - Class in net.sf.basedb.core.data: This is the root superclass of all data classes.
BasicData() - Constructor for class net.sf.basedb.core.data.BasicData
BasicItem<D extends BasicData> - Class in net.sf.basedb.core: This is the root superclass of all item classes.
BasicItem(D) - Constructor for class net.sf.basedb.core.BasicItem: Create a new instance.
BasicItemFilter - Class in net.sf.basedb.util.overview.filter: A filter implementation that matches against the item that is attached to nodes.
BasicItemFilter(BasicItem) - Constructor for class net.sf.basedb.util.overview.filter.BasicItemFilter: Create a filter that finds nodes that has the given item attached to it.
BasicItemInfo - Class in net.sf.basedb.info: Superclass for all transferable classes that transfer information about item-classes, ie. classes that are subclasses of BasicItem.
BasicItemInfo() - Constructor for class net.sf.basedb.info.BasicItemInfo
BasicItemNodeLoader - 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) - 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 - Class in net.sf.basedb.util.overview.validator: A simple node validation implementation that takes care of missing and denied access to items.
BasicNodeValidator(Validator, Validator) - Constructor for class net.sf.basedb.util.overview.validator.BasicNodeValidator: Creates a new validator.
BatchableData - Interface in net.sf.basedb.core.data: This is a tagging interface only.
batchedExternalIds - Variable in class net.sf.basedb.core.ReporterBatcher: A set containing all batched but not yet flushed external reporter id:s.
BatchedPropertyInfo - Class in net.sf.basedb.core: Holds information about a batchable property.
BatchedPropertyInfo(String, int) - Constructor for class net.sf.basedb.core.BatchedPropertyInfo: Create a new extended property.
Batcher - Interface in net.sf.basedb.core: The basic interface which all batchers must implement.
batcher - Variable in class net.sf.basedb.plugins.IlluminaRawDataImporter.BatchAndMapHolder
batcher - Variable in class net.sf.basedb.plugins.PrintMapFlatFileImporter
batcher - Variable in class net.sf.basedb.plugins.RawDataFlatFileImporter
batcher - Variable in class net.sf.basedb.plugins.ReporterFlatFileImporter
batcher - Variable in class net.sf.basedb.plugins.ReporterMapFlatFileImporter
batchers - Variable in class net.sf.basedb.core.DbControl: A list of batchers that will be closed when DbControl is closed and will be flushed when commit is called.
batchIndex - Variable in class net.sf.basedb.core.data.ArraySlideData
batchQuery - Variable in class net.sf.basedb.plugins.batchimport.AbstractItemImporter
batchSize - Variable in class net.sf.basedb.core.AbstractBatcher: SQL command batch size.
BatchUtil - Class in net.sf.basedb.core: Utility class for batching information.
BatchUtil() - Constructor for class net.sf.basedb.core.BatchUtil
bean - Variable in class net.sf.basedb.util.extensions.debug.BeanActionFactory
BeanActionFactory - Class in net.sf.basedb.util.extensions.debug: Generic action factory class that can generate instances of actions if there exists a bean-like implementation of the action class.
BeanActionFactory() - Constructor for class net.sf.basedb.util.extensions.debug.BeanActionFactory: Creates a new proxy factory.
beanClassName - Variable in class net.sf.basedb.util.extensions.debug.BeanActionFactory
before - Variable in class net.sf.basedb.core.DbControl.SaveIf
BEFORE_DISABLE - Static variable in class net.sf.basedb.clients.web.extensions.ExtensionsControl: This event is sent before an extension or extension point is disabled by ExtensionsControl.enableExtensionPoint(String, boolean), ExtensionsControl.enableExtension(String, boolean), or ExtensionsControl.enableAllInFile(String, boolean).
BEFORE_UNREGISTRATION - Static variable in class net.sf.basedb.util.extensions.events.EventType: This event is sent before an extension point or extension is unregistered.
BEFORE_UPDATE - Static variable in class net.sf.basedb.util.extensions.events.EventType: This event is sent during an update of an existing extension point or extension.
begin(DbControl) - Method in class net.sf.basedb.clients.web.plugins.SimpleExport
begin(DbControl) - Method in class net.sf.basedb.core.plugin.AbstractExporterPlugin: Called just before the export starts.
begin(FlatFileParser) - Method in class net.sf.basedb.plugins.AbstractFlatFileImporter: Called just before parsing of the file begins.
begin(FlatFileParser) - Method in class net.sf.basedb.plugins.AnnotationFlatFileImporter: Setup error handling and pre-load some of the configuration options.
begin(DbControl) - Method in class net.sf.basedb.plugins.BaseFileExporterPlugin
begin(FlatFileParser) - Method in class net.sf.basedb.plugins.batchimport.AbstractItemImporter: Setup error handling and pre-load some of the configuration options.
begin(DbControl) - Method in class net.sf.basedb.plugins.BfsExporterPlugin
begin(DbControl) - Method in class net.sf.basedb.plugins.BioAssaySetExporter: Deprecated.
begin(DbControl) - Method in class net.sf.basedb.plugins.GalExporter
begin(DbControl) - Method in class net.sf.basedb.plugins.HelpExporter
begin(FlatFileParser) - Method in class net.sf.basedb.plugins.IlluminaRawDataImporter
begin(DbControl) - Method in class net.sf.basedb.plugins.PackedFileExporter
begin(FlatFileParser) - Method in class net.sf.basedb.plugins.PlateFlatFileImporter: Create a DbControl and a RawDataBatcher.
begin(DbControl) - Method in class net.sf.basedb.plugins.PlateMappingExporter
begin(FlatFileParser) - Method in class net.sf.basedb.plugins.PlateMappingImporter: Save reference to parser.
begin(DbControl) - Method in class net.sf.basedb.plugins.PluginConfigurationExporter
begin(FlatFileParser) - Method in class net.sf.basedb.plugins.PrintMapFlatFileImporter: Create a DbControl and a FeatureBatcher.
begin(FlatFileParser) - Method in class net.sf.basedb.plugins.RawDataFlatFileImporter: Prepare for importing the next file.
begin(FlatFileParser) - Method in class net.sf.basedb.plugins.ReporterFlatFileImporter: Create a DbControl and a ReporterBatcher.
begin(FlatFileParser) - Method in class net.sf.basedb.plugins.ReporterMapFlatFileImporter: Create a DbControl and a FeatureBatcher.
beginData() - Method in class net.sf.basedb.plugins.AbstractFlatFileImporter: Called by the parser after the headers have been parsed but before the first data line is parsed.
beginData() - Method in class net.sf.basedb.plugins.AnnotationFlatFileImporter: Setup column mapping.
beginData() - Method in class net.sf.basedb.plugins.batchimport.AbstractItemImporter: Setup column mapping.
beginData() - Method in class net.sf.basedb.plugins.IlluminaRawDataImporter: Check column headers and map them to raw bioassays.
beginData() - Method in class net.sf.basedb.plugins.PlateFlatFileImporter: Initialise column Mapper:s.
beginData() - Method in class net.sf.basedb.plugins.PlateMappingImporter: Create a DbControl and a new PlateMapping.
beginData() - Method in class net.sf.basedb.plugins.RawDataFlatFileImporter: Initialise column Mapper:s.
beginData() - Method in class net.sf.basedb.plugins.ReporterFlatFileImporter: Initialise column Mapper:s.
beginData() - Method in class net.sf.basedb.plugins.ReporterMapFlatFileImporter: Initialise column Mapper:s.
beginDocument() - Method in interface net.sf.basedb.clients.web.plugins.ExportTemplate: Start writing the document.
beginDocument() - Method in class net.sf.basedb.clients.web.plugins.PlainTextTemplate: Do nothing.
beginDocument() - Method in class net.sf.basedb.clients.web.plugins.XMLTemplate: Write XML start (<?
beginExport() - Method in class net.sf.basedb.util.export.spotdata.AbstractBioAssaySetExporter: Make preparations for the export.
beginExport() - Method in class net.sf.basedb.util.export.spotdata.BaseFileExporter: Prepare the export by adding all experimental factors as assay fields if no fields have been specified.
beginExport() - Method in class net.sf.basedb.util.export.spotdata.BfsExporter: Validates that all required properties has been set and initialises other things that are needed.
beginExport() - Method in class net.sf.basedb.util.export.spotdata.MatrixBaseFileExporter: Prepare the export by pre-loading some information and configure the queries that we are going to use.
beginExport() - Method in class net.sf.basedb.util.export.spotdata.SerialBaseFileExporter: Prepare the export by pre-loading some information and configure the queries that we are going to use.
beginItem(int) - Method in interface net.sf.basedb.clients.web.plugins.ExportTemplate: Start writing a new item.
beginItem(int) - Method in class net.sf.basedb.clients.web.plugins.PlainTextTemplate: Reset column number.
beginItem(int) - Method in class net.sf.basedb.clients.web.plugins.XMLTemplate: Begin a new item element.
beginSection(BaseFileParser, FlatFileParser, List<String>) - Method in class net.sf.basedb.util.importer.spotdata.GenericIntensityParser
beginSection(BaseFileParser, FlatFileParser, List<String>) - Method in class net.sf.basedb.util.importer.spotdata.MAParser
beginSection(BaseFileParser, FlatFileParser, List<String>) - Method in interface net.sf.basedb.util.importer.spotdata.SpotIntensityParser: Prepare for parsing the data section.
beginTransaction() - Method in class net.sf.basedb.core.hibernate.SessionWrapper
beginTransaction() - Method in class net.sf.basedb.core.hibernate.StatelessSessionWrapper
belongsTo(AnnotationSet) - Method in class net.sf.basedb.core.Annotation: Check if this annotation belongs to the primaray annotations for a specified annotation set.
between(AnnotationType, Object, Object, boolean) - Static method in class net.sf.basedb.core.query.Annotations: Deprecated. Use Annotations.between(String, AnnotationType, Object, Object, boolean) instead with alias=null
between(String, AnnotationType, Object, Object, boolean) - Static method in class net.sf.basedb.core.query.Annotations: Create a restriction that searches for annotations between two given values on the root or a joined entity of a query.
between(Expression, Expression, Expression) - Static method in class net.sf.basedb.core.query.Restrictions: Compare if one expression falls between two other expressions: new expression = low <= e AND e < high.
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) - Constructor for class net.sf.basedb.core.query.BetweenRestriction
BFS_METADATA - Static variable in class net.sf.basedb.core.DataFileType: The external ID for the file type representing a BFS metadata file.
BfsExporter - Class in net.sf.basedb.util.export.spotdata: Base class for exporting spotdata to BFS format.
BfsExporter() - Constructor for class net.sf.basedb.util.export.spotdata.BfsExporter
BfsExporterPlugin - Class in net.sf.basedb.plugins: Exports bioassay set data to BFS format.
BfsExporterPlugin() - Constructor for class net.sf.basedb.plugins.BfsExporterPlugin
BfsExporterPlugin.ExtendedExportableField - Class in net.sf.basedb.plugins
BfsExporterPlugin.ExtendedExportableField(String, boolean, ExportableField) - Constructor for class net.sf.basedb.plugins.BfsExporterPlugin.ExtendedExportableField
BfsExporterPlugin.ExtendedExportableField(String, String, boolean, ExportableField) - Constructor for class net.sf.basedb.plugins.BfsExporterPlugin.ExtendedExportableField
BfsExporterSupport - Class in net.sf.basedb.plugins.executor: Exporter implementation for the external program executor that exports data to BFS format.
BfsExporterSupport() - Constructor for class net.sf.basedb.plugins.executor.BfsExporterSupport
BfsImporter - Class in net.sf.basedb.util.importer.spotdata: Imports spot data from a serial or matrix BFS.
BfsImporter() - Constructor for class net.sf.basedb.util.importer.spotdata.BfsImporter: Create a new importer object.
BfsImporter.ProgressEventHandler - Class in net.sf.basedb.util.importer.spotdata
BfsImporter.ProgressEventHandler(ProgressReporter, long) - Constructor for class net.sf.basedb.util.importer.spotdata.BfsImporter.ProgressEventHandler
BfsImporterSupport - Class in net.sf.basedb.plugins.executor: Importer implementation for the external program executor that imports data from BFS format.
BfsImporterSupport() - Constructor for class net.sf.basedb.plugins.executor.BfsImporterSupport
BfsParser - Interface in net.sf.basedb.util.bfs: Interface that it is recommended that all BFS parsers should implement.
bfsPrintComment(String) - Method in class net.sf.basedb.util.bfs.MetadataWriter: Prints one or more comment lines to the metadata file.
bfsPrintData(int, Object...) - Method in class net.sf.basedb.util.bfs.AnnotationWriter: Print a data line.
bfsPrintData(Object...) - Method in class net.sf.basedb.util.bfs.DataWriter: Print a data line.
bfsPrintEmptyLine(int) - Method in class net.sf.basedb.util.bfs.MetadataWriter: Print one or more empty lines to the metadata file.
bfsPrintHeaders(String...) - Method in class net.sf.basedb.util.bfs.AnnotationWriter: Print the header line.
bfsPrintSection(String, boolean, boolean) - Method in class net.sf.basedb.util.bfs.MetadataWriter: Start a new section.
bfsPrintValue(String, String...) - Method in class net.sf.basedb.util.bfs.MetadataWriter: Prints a section entry.
bfsPrintValue(String, T...) - Method in class net.sf.basedb.util.bfs.MetadataWriter: Prints a section entry.
bfsPrintValue(String, Formatter<T>, T...) - Method in class net.sf.basedb.util.bfs.MetadataWriter: Prints a section entry.
bindLimits(String, List<String>) - Method in class net.sf.basedb.core.AbstractSqlQuery: Parse the given SQL and add LIMIT and OFFSET parameters to it.
bins - Variable in class net.sf.basedb.util.plot.HistogramPlot.HistogramSeries
BioAssay - Class in net.sf.basedb.core: Represents the current intensities of raw data after some transformation has been applied to it.
BioAssay(BioAssayData) - Constructor for class net.sf.basedb.core.BioAssay: Creates a new bioassay item from the given data.
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.
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.util.export.spotdata.AbstractBioAssaySetExporter
bioAssays - Variable in class net.sf.basedb.util.export.spotdata.MatrixBaseFileExporter
bioAssays - Variable in class net.sf.basedb.util.export.spotdata.SerialBaseFileExporter
bioAssaySet - Variable in class net.sf.basedb.clients.web.ExperimentExplorer: The bioassay set we are exploring.
BioAssaySet - Class in net.sf.basedb.core: A bioassayset represents the current intensities of the raw data after some Transformation has been applied to it.
BioAssaySet(BioAssaySetData) - Constructor for class net.sf.basedb.core.BioAssaySet: Creates a new experiment item from the given data.
bioAssaySet - Variable in class net.sf.basedb.core.data.BioAssayData
bioAssaySet - Variable in class net.sf.basedb.core.data.ExtraValueData
bioAssaySet - Variable in class net.sf.basedb.core.DynamicPositionQuery
bioAssaySet - Variable in class net.sf.basedb.core.DynamicSpotQuery
bioAssaySet - Variable in class net.sf.basedb.core.FilterBatcher: The bioassayset this batcher inserts data for.
bioAssaySet - Variable in class net.sf.basedb.core.SpotBatcher: The bioassayset this batcher inserts data for.
BioAssaySetClient - Class in net.sf.basedb.ws.client: Web service client for BioAssaySetService in BASE.
BioAssaySetClient(SessionClient) - Constructor for class net.sf.basedb.ws.client.BioAssaySetClient: Creates new BioAssayClient for a session.
BioAssaySetData - Class in net.sf.basedb.core.data: This class holds information about a bioassayset.
BioAssaySetData() - Constructor for class net.sf.basedb.core.data.BioAssaySetData
BioAssaySetExporter - Class in net.sf.basedb.plugins: Deprecated. In 2.12. Use: SerialBaseFileExporter or MatrixBaseFileExporter for BASEfile export and the extension package at http://baseplugins.thep.lu.se/wiki/net.sf.basedb.mev for MeV export
BioAssaySetExporter() - Constructor for class net.sf.basedb.plugins.BioAssaySetExporter: Deprecated.
BioAssaySetExporter.QueryItem - Class in net.sf.basedb.plugins: Deprecated.
BioAssaySetExporter.QueryItem(String, String, String, String, Formula.AverageMethod) - Constructor for class net.sf.basedb.plugins.BioAssaySetExporter.QueryItem: Deprecated.
BioAssaySetExporter.QueryItemTitleComparator - Class in net.sf.basedb.plugins: Deprecated.
BioAssaySetExporter.QueryItemTitleComparator() - Constructor for class net.sf.basedb.plugins.BioAssaySetExporter.QueryItemTitleComparator: Deprecated.
BioAssaySetFilterUtil - Class in net.sf.basedb.util: This is a utility class for plugins that filters bioassay set data.
BioAssaySetFilterUtil() - Constructor for class net.sf.basedb.util.BioAssaySetFilterUtil
BioAssaySetInfo - Class in net.sf.basedb.info: Information class for bioassay set in BASE This class holds information that are useful when working with a bioassay set over Web Services.
BioAssaySetInfo() - Constructor for class net.sf.basedb.info.BioAssaySetInfo: Creates a new empty info object
bioAssaySetParameter - Variable in class net.sf.basedb.plugins.BioAssaySetExporter: Deprecated.
bioAssaySets - Variable in class net.sf.basedb.core.data.ExperimentData
BioAssaySetService - Class in net.sf.basedb.ws.server: Web service for BioAssaySet BioAssaySet.
BioAssaySetService() - Constructor for class net.sf.basedb.ws.server.BioAssaySetService
BioAssaySetUtil - Class in net.sf.basedb.util: This is a utility class for BioAssaySet.
BioAssaySetUtil() - Constructor for class net.sf.basedb.util.BioAssaySetUtil
bioAssaySpots - Variable in class net.sf.basedb.core.BioAssaySet: Stores the result of BioAssaySet.getSpotCount(int).
BioMaterial<D extends BioMaterialData> - Class in net.sf.basedb.core: This is the base class for for the four types of biomaterials: BioSource, Sample, Extract and LabeledExtract.
BioMaterial(D) - Constructor for class net.sf.basedb.core.BioMaterial
bioMaterial - Variable in class net.sf.basedb.core.data.BioMaterialEventData
bioMaterial - Variable in class net.sf.basedb.core.data.BioWellData
BioMaterialData - Class in net.sf.basedb.core.data: This class is the root class for biomaterials.
BioMaterialData() - Constructor for class net.sf.basedb.core.data.BioMaterialData
BioMaterialEvent - Class in net.sf.basedb.core: This class represents an event in the life of a MeasuredBioMaterial.
BioMaterialEvent(BioMaterialEventData) - Constructor for class net.sf.basedb.core.BioMaterialEvent
BioMaterialEvent.Type - Enum in net.sf.basedb.core: The type of the event.
BioMaterialEvent.Type(int, String) - Constructor for enum net.sf.basedb.core.BioMaterialEvent.Type
BioMaterialEventData - Class in net.sf.basedb.core.data: This class is used to register events for measured biomaterials.
BioMaterialEventData() - Constructor for class net.sf.basedb.core.data.BioMaterialEventData
BioMaterialEventLogger - Class in net.sf.basedb.core.log.db: Logger for biomaterial events that logs UPDATE:s to CREATION and HYBRIDIZATION events as updates to their parent biomaterial/hybridization.
BioMaterialEventLogger(boolean) - Constructor for class net.sf.basedb.core.log.db.BioMaterialEventLogger: Creates a new biomaterial event logger.
bioMaterialEvents - Variable in class net.sf.basedb.core.data.BioPlateEventParticipantData
BioMaterialList - Class in net.sf.basedb.core: This class represents a list of biomaterials.
BioMaterialList(BioMaterialListData) - Constructor for class net.sf.basedb.core.BioMaterialList
BioMaterialListData - Class in net.sf.basedb.core.data: This represents an arbitrary collection of biomaterials.
BioMaterialListData() - Constructor for class net.sf.basedb.core.data.BioMaterialListData
bioMaterials - Variable in class net.sf.basedb.core.data.BioMaterialListData
BioMaterialSourceEventData - Class in net.sf.basedb.core.data: This class is needed to be able to map the inverse relation MeasuredBioMaterialData.getSourceEvents() and still be able to filter in the used quantity or the source group property.
BioMaterialSourceEventData() - Constructor for class net.sf.basedb.core.data.BioMaterialSourceEventData
bioMaterialType - Variable in class net.sf.basedb.core.data.BioPlateTypeData
BioPlate - Class in net.sf.basedb.core: This class is represents physical bio-plates.
BioPlate(BioPlateData) - Constructor for class net.sf.basedb.core.BioPlate
bioPlate - Variable in class net.sf.basedb.core.data.BioPlateEventParticipantData
bioPlate - Variable in class net.sf.basedb.core.data.BioWellData
bioPlateColumnMapping - Static variable in class net.sf.basedb.plugins.batchimport.SampleImporter: Column mapping parameter for the bioplate
BioPlateData - Class in net.sf.basedb.core.data: This class holds information about a bioplate
BioPlateData() - Constructor for class net.sf.basedb.core.data.BioPlateData
BioPlateEvent - Class in net.sf.basedb.core: A bioplate event represents something that happened simultaneously to the biomaterial on one or more bioplates.
BioPlateEvent(BioPlateEventData) - Constructor for class net.sf.basedb.core.BioPlateEvent
BioPlateEventData - Class in net.sf.basedb.core.data: This class holds information about a bioplate event.
BioPlateEventData() - Constructor for class net.sf.basedb.core.data.BioPlateEventData
BioPlateEventParticipant - Class in net.sf.basedb.core: Holds information about a bioplate that is participating in a bioplate event.
BioPlateEventParticipant(BioPlateEventParticipantData) - Constructor for class net.sf.basedb.core.BioPlateEventParticipant
bioPlateEventParticipant - Variable in class net.sf.basedb.core.data.BioMaterialEventData
bioPlateEventParticipant - Variable in class net.sf.basedb.core.Hybridization
bioPlateEventParticipant - Variable in class net.sf.basedb.core.MeasuredBioMaterial
BioPlateEventParticipantData - Class in net.sf.basedb.core.data: Registers a plate as a participant in a bioplate event.
BioPlateEventParticipantData() - Constructor for class net.sf.basedb.core.data.BioPlateEventParticipantData
BioPlateEventType - Class in net.sf.basedb.core: The type of a bioplate event defines what happened in the event.
BioPlateEventType(BioPlateEventTypeData) - Constructor for class net.sf.basedb.core.BioPlateEventType
BioPlateEventTypeData - Class in net.sf.basedb.core.data: Each bioplate event must have a type that defines what happened.
BioPlateEventTypeData() - Constructor for class net.sf.basedb.core.data.BioPlateEventTypeData
BioPlateImporter - Class in net.sf.basedb.plugins.batchimport: Plug-in for importing bioplate items in a batch.
BioPlateImporter() - Constructor for class net.sf.basedb.plugins.batchimport.BioPlateImporter
bioPlateMapper - Variable in class net.sf.basedb.plugins.batchimport.ExtractImporter
bioPlateMapper - Variable in class net.sf.basedb.plugins.batchimport.LabeledExtractImporter
bioPlateMapper - Variable in class net.sf.basedb.plugins.batchimport.SampleImporter
bioPlateQuery - Variable in class net.sf.basedb.plugins.batchimport.AbstractItemImporter
bioPlates - Variable in class net.sf.basedb.core.data.BioPlateTypeData
BioPlateType - Class in net.sf.basedb.core: This class represents the type of a bio-plate.
BioPlateType(BioPlateTypeData) - Constructor for class net.sf.basedb.core.BioPlateType
bioPlateType - Variable in class net.sf.basedb.core.data.BioPlateData
bioPlateTypeColumnMapping - Static variable in class net.sf.basedb.plugins.batchimport.BioPlateImporter
BioPlateTypeData - Class in net.sf.basedb.core.data: This class holds information about a biomaterial plate type.
BioPlateTypeData() - Constructor for class net.sf.basedb.core.data.BioPlateTypeData
bioPlateTypeMapper - Variable in class net.sf.basedb.plugins.batchimport.BioPlateImporter
bioPlateTypeQuery - Variable in class net.sf.basedb.plugins.batchimport.AbstractItemImporter
BioSource - Class in net.sf.basedb.core: This class represent biosource items.
BioSource(BioSourceData) - Constructor for class net.sf.basedb.core.BioSource
BioSourceData - Class in net.sf.basedb.core.data: This represents a biosoruce which is the starting point of all biomaterials.
BioSourceData() - Constructor for class net.sf.basedb.core.data.BioSourceData
BioSourceImporter - Class in net.sf.basedb.plugins.batchimport: Plug-in for importing biosource items in a batch.
BioSourceImporter() - Constructor for class net.sf.basedb.plugins.batchimport.BioSourceImporter
BioSourceLoader - Class in net.sf.basedb.util.overview.loader: Node loader implementation for biosources.
BioSourceLoader() - Constructor for class net.sf.basedb.util.overview.loader.BioSourceLoader
bioSourceQuery - Variable in class net.sf.basedb.plugins.batchimport.AbstractItemImporter
BioSourceToSampleTransformer - Class in net.sf.basedb.util.biomaterial: Collection transformer that given a collection of biosources finds all samples that has the biosources as parents.
BioSourceToSampleTransformer(DbControl) - Constructor for class net.sf.basedb.util.biomaterial.BioSourceToSampleTransformer
BioSourceValidator - Class in net.sf.basedb.util.overview.validator: Validator implementation for biosources.
BioSourceValidator() - Constructor for class net.sf.basedb.util.overview.validator.BioSourceValidator
BioWell - Class in net.sf.basedb.core: A biowell is located on a BioPlate and contains a MeasuredBioMaterial.
BioWell(BioWellData) - Constructor for class net.sf.basedb.core.BioWell
bioWell - Variable in class net.sf.basedb.core.data.MeasuredBioMaterialData
BioWell.LockMode - Enum in net.sf.basedb.core: The lock mode for a well is determined by the plate's bio plate type.
BioWell.LockMode(int, String) - Constructor for enum net.sf.basedb.core.BioWell.LockMode
bioWellColColumnMapping - Static variable in class net.sf.basedb.plugins.batchimport.SampleImporter: Column mapping parameter for the biowell's column
bioWellColMapper - Variable in class net.sf.basedb.plugins.batchimport.ExtractImporter
bioWellColMapper - Variable in class net.sf.basedb.plugins.batchimport.LabeledExtractImporter
bioWellColMapper - Variable in class net.sf.basedb.plugins.batchimport.SampleImporter
BioWellData - Class in net.sf.basedb.core.data: This class holds information about a bio well on a bio plate.
BioWellData() - Constructor for class net.sf.basedb.core.data.BioWellData
bioWellRowColumnMapping - Static variable in class net.sf.basedb.plugins.batchimport.SampleImporter: Column mapping parameter for the biowell's row
bioWellRowMapper - Variable in class net.sf.basedb.plugins.batchimport.ExtractImporter
bioWellRowMapper - Variable in class net.sf.basedb.plugins.batchimport.LabeledExtractImporter
bioWellRowMapper - Variable in class net.sf.basedb.plugins.batchimport.SampleImporter
bioWells - Variable in class net.sf.basedb.core.data.BioPlateData
block - Variable in class net.sf.basedb.core.BlockInfo: The block number.
block - Variable in class net.sf.basedb.core.data.RawData
block - Variable in class net.sf.basedb.core.FeatureCoordinate
block - Variable in class net.sf.basedb.plugins.LowessNormalization.SpotData
block - Variable in class net.sf.basedb.plugins.MedianRatioNormalization.SpotData
block - Variable in class net.sf.basedb.plugins.PrintMapFlatFileImporter.MetaBlock
blockColumnMapping - Static variable in class net.sf.basedb.plugins.RawDataFlatFileImporter
blockColumnMapping - Static variable in class net.sf.basedb.plugins.ReporterMapFlatFileImporter
blockGroupParameter - Static variable in class net.sf.basedb.plugins.LowessNormalization
blockGroupParameter - Static variable in class net.sf.basedb.plugins.MedianRatioNormalization: Used with 2-channel data only
blockGroupSize - Variable in class net.sf.basedb.plugins.LowessNormalization.CallableWorker
BlockInfo - Class in net.sf.basedb.core: A BlockInfo object is used to represent the uniqe identifiers of an ArrayDesignBlock.
BlockInfo(int, int) - Constructor for class net.sf.basedb.core.BlockInfo: Create a new block info using the meta coordinates.
BlockInfo(int, int, int) - Constructor for class net.sf.basedb.core.BlockInfo: Create a new block info using meta coordinates.
blockMapper - Variable in class net.sf.basedb.plugins.RawDataFlatFileImporter
blockMapper - Variable in class net.sf.basedb.plugins.ReporterMapFlatFileImporter
blockNumber - Variable in class net.sf.basedb.core.data.ArrayDesignBlockData
blockNumber - Variable in enum net.sf.basedb.plugins.PrintMapFlatFileImporter.Section
blocks - Variable in class net.sf.basedb.core.ArrayDesign
blocks - Variable in class net.sf.basedb.plugins.PrintMapFlatFileImporter
blocks - Variable in class net.sf.basedb.plugins.ReporterMapFlatFileImporter
blockSizeX - Variable in class net.sf.basedb.core.data.ArrayDesignBlockData
blockSizeX - Variable in class net.sf.basedb.plugins.PrintMapFlatFileImporter.MetaBlock
blockSizeY - Variable in class net.sf.basedb.core.data.ArrayDesignBlockData
blockSizeY - Variable in class net.sf.basedb.plugins.PrintMapFlatFileImporter.MetaBlock
blueImageFile - Variable in class net.sf.basedb.core.data.SpotImagesData
Body - Class in net.sf.basedb.clients.web.taglib: This tag defines the body section of a page.
Body() - Constructor for class net.sf.basedb.clients.web.taglib.Body
BOF_EVENT - Static variable in class net.sf.basedb.util.bfs.MetadataParser: Event type that is issued when the beginning-of-file marker is found.
BOF_MARKER - Static variable in class net.sf.basedb.util.bfs.MetadataWriter
bofMarker - Variable in class net.sf.basedb.util.parser.FlatFileParser: The regular expression for matching the beginning-of-file marker
bofType - Variable in class net.sf.basedb.util.parser.FlatFileParser: The value that was captured by the bofMarker pattern.
BOOLEAN - Static variable in class net.sf.basedb.core.hibernate.TypeWrapper
BooleanFormatter - Class in net.sf.basedb.util.formatter: Formats a boolean value.
BooleanFormatter(BooleanFormatter.Type) - Constructor for class net.sf.basedb.util.formatter.BooleanFormatter: Create a new boolean formatter.
BooleanFormatter.Type - Enum in net.sf.basedb.util.formatter: Enum for holding the various types of boolean output.
BooleanFormatter.Type(String, String) - Constructor for enum net.sf.basedb.util.formatter.BooleanFormatter.Type
BooleanParameterType - Class in net.sf.basedb.core: This class represent a parameter type that is a boolean.
BooleanParameterType() - Constructor for class net.sf.basedb.core.BooleanParameterType: Create a new boolean parameter type, allowing null values.
BooleanParameterType(Boolean, boolean) - Constructor for class net.sf.basedb.core.BooleanParameterType: Create a new boolean parameter type.
BooleanParameterType(Boolean, boolean, int, Enumeration<Boolean, String>) - Constructor for class net.sf.basedb.core.BooleanParameterType
BooleanParameterValueData - Class in net.sf.basedb.core.data: Boolean parameter value.
BooleanParameterValueData() - Constructor for class net.sf.basedb.core.data.BooleanParameterValueData
BooleanParameterValueData(Boolean...) - Constructor for class net.sf.basedb.core.data.BooleanParameterValueData
BOTTOM - Static variable in class net.sf.basedb.clients.web.taglib.tab.TabControl: Tabs are at the bottom of the tab control.
boundary - Variable in class net.sf.basedb.clients.web.fileupload.FileUpload: The multipart/formdata boundary
buffer - Variable in class net.sf.basedb.clients.web.fileupload.FileUpload.UploadStream
BUFFER_SIZE - Static variable in class net.sf.basedb.util.FileUtil
build - Variable in class net.sf.basedb.core.data.SchemaVersionData
build - Static variable in class net.sf.basedb.core.Version
build - Variable in class net.sf.basedb.info.VersionInfo
buildDelete(String, Dialect) - Static method in class net.sf.basedb.core.BatchUtil: Build delete SQL string and put it in the SQL map.
buildDocument() - Method in class net.sf.basedb.core.Presets: Convert the presets to a XML document.
buildDom(Element) - Method in class net.sf.basedb.core.Presets.Preset: Add XML elements to the parent element for this preset's key-value pairs.
buildFilterSql() - Method in class net.sf.basedb.core.FilterBatcher: Builds the insert SQL statement.
buildInsert(String, Dialect) - Static method in class net.sf.basedb.core.BatchUtil: Build insert SQL string and put it in the SQL map.
buildInsertSelectSql(VirtualDb, VirtualTable, VirtualColumn[], String) - Static method in class net.sf.basedb.core.BatchUtil
buildInsertSelectSql(String) - Method in class net.sf.basedb.core.FilterBatcher: Build the INSERT INTO ...
buildInsertSelectSql(String) - Method in class net.sf.basedb.core.MappingBatcher: Build the INSERT INTO ...
buildInsertSelectSql(String) - Method in class net.sf.basedb.core.PositionBatcher: Build the INSERT INTO ...
buildInsertSelectSql(String) - Method in class net.sf.basedb.core.PositionExtraValueBatcher: Build the INSERT INTO ...
buildInsertSelectSql(String) - Method in class net.sf.basedb.core.SpotBatcher: Build the INSERT INTO ...
buildInsertSelectSql(String) - Method in class net.sf.basedb.core.SpotExtraValueBatcher: Build the INSERT INTO ...
buildInsertSql(VirtualDb, VirtualTable, VirtualColumn[], Object[]) - Static method in class net.sf.basedb.core.BatchUtil
buildLockRequest(LockOptions) - Method in class net.sf.basedb.core.hibernate.SessionWrapper
buildPositionSql() - Method in class net.sf.basedb.core.PositionBatcher: Builds the insert SQL statement.
buildRawMappingSql() - Method in class net.sf.basedb.core.MappingBatcher: Builds the insert SQL statement.
buildSpotSql() - Method in class net.sf.basedb.core.PositionExtraValueBatcher: Builds the insert SQL statement.
buildSpotSql() - Method in class net.sf.basedb.core.SpotBatcher: Builds the insert SQL statement.
buildSpotSql() - Method in class net.sf.basedb.core.SpotExtraValueBatcher: Builds the insert SQL statement.
buildUpdate(String, Dialect) - Static method in class net.sf.basedb.core.BatchUtil: Build update SQL string and put it in the SQL map.
Bundle - Class in net.sf.basedb.clients.web.resources: Declare the names of resource bundles used by the web client.
Bundle() - Constructor for class net.sf.basedb.clients.web.resources.Bundle
Button - Class in net.sf.basedb.clients.web.taglib: This tag is used to display a clickable button.
Button() - Constructor for class net.sf.basedb.clients.web.taglib.Button
Button - Class in net.sf.basedb.clients.web.taglib.table: This tag creates a button on a toolbar.
Button() - Constructor for class net.sf.basedb.clients.web.taglib.table.Button
ButtonAction - Interface in net.sf.basedb.clients.web.extensions.toolbar: Actions represented as buttons in a toolbar.
ButtonBean - Class in net.sf.basedb.clients.web.extensions.toolbar: A simple bean-like implementation of the ButtonAction interface.
ButtonBean() - Constructor for class net.sf.basedb.clients.web.extensions.toolbar.ButtonBean
buttonGroup - Variable in class net.sf.basedb.clients.web.taglib.Button
ButtonGroup - Class in net.sf.basedb.clients.web.taglib: This tag is used to display a clickable button.
ButtonGroup() - Constructor for class net.sf.basedb.clients.web.taglib.ButtonGroup
buttons - Variable in class net.sf.basedb.clients.web.taglib.ButtonGroup: The buttons in this group.
bytes - Variable in class net.sf.basedb.core.data.DataCubeData
bytes - Variable in class net.sf.basedb.core.data.DataCubeExtraValueData
bytes - Variable in class net.sf.basedb.core.data.DataCubeFilterData
bytes - Variable in class net.sf.basedb.core.data.DataCubeLayerData
bytes - Variable in class net.sf.basedb.core.data.DiskUsageData
bytes - Variable in class net.sf.basedb.core.data.ExperimentData
bytes - Variable in class net.sf.basedb.core.data.RawBioAssayData
bytes - Variable in class net.sf.basedb.core.FilterBatcher: The number of bytes this batcher has added to the experiment.
bytes - Variable in class net.sf.basedb.core.MappingBatcher: The number of bytes this batcher has added to the experiment.
bytes - Variable in class net.sf.basedb.core.PositionBatcher: The number of bytes this batcher has added to the data cube and experiment.
bytes - Variable in class net.sf.basedb.core.PositionExtraValueBatcher: The number of bytes this batcher has added to the experiment.
bytes - Variable in class net.sf.basedb.core.RawDataBatcher: The number of bytes the spot data is occupying on disk.
bytes - Variable in class net.sf.basedb.core.SpotBatcher: The number of bytes this batcher has added to the experiment.
bytes - Variable in class net.sf.basedb.core.SpotExtraValueBatcher: The number of bytes this batcher has added to the experiment.
BYTES_REGEXP - Static variable in class net.sf.basedb.util.Values
bytesPerRow - Variable in class net.sf.basedb.core.FilterBatcher: The number of bytes used by a single row.
bytesPerRow - Variable in class net.sf.basedb.core.MappingBatcher: The number of bytes used by a single row.
bytesPerRow - Variable in class net.sf.basedb.core.PositionBatcher: The number of bytes used by a single row.
bytesPerRow - Variable in class net.sf.basedb.core.PositionExtraValueBatcher: The number of bytes used by a single row.
bytesPerRow - Variable in class net.sf.basedb.core.SpotBatcher: The number of bytes used by a single row.
bytesPerRow - Variable in class net.sf.basedb.core.SpotExtraValueBatcher: The number of bytes used by a single row.
bzip - Variable in class net.sf.basedb.util.zip.Bzip2FilePacker
Bzip2FilePacker - Class in net.sf.basedb.util.zip: This class wraps the TarFilePacker in a BZIP2 stream, creating a tar.bz2 file.
Bzip2FilePacker() - Constructor for class net.sf.basedb.util.zip.Bzip2FilePacker: Create a new packer that compresses files with the BZIP2 format.

C

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

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

The cache of reporter ids matching the current reporter filter.

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

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

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

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

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

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

Deprecated.

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

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

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

cacheFile - Variable in class net.sf.basedb.util.StreamCacher

cacheKey - Variable in class net.sf.basedb.util.overview.cache.DirectionalCacheKey

cacheKey - Variable in class net.sf.basedb.util.overview.cache.IndexedCacheKey

cacheNewNode(Object, Node, ChildNodeDirection) - Method in class net.sf.basedb.util.overview.node.NodeFactory

Store a node in the node cache if the current overview context supports caching.

cacheOut - Variable in class net.sf.basedb.util.StreamCacher

cacheQuery(String, Query) - Method in class net.sf.basedb.core.hibernate.AbstractQueryCache

Cache a query.

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

Loads and caches reporter data in an internal structure for quick access.

cacheResults - Variable in class net.sf.basedb.core.AbstractHqlQuery

If the results should be cached or not.

calculateBoxAndWhiskerStatistics(List<Float>) - Method in class net.sf.basedb.clients.web.servlet.ExperimentExplorerPlotServlet

Creates a box-and-whisker data holder for the given list of values.

calculateIntensities(RawData) - Method in interface net.sf.basedb.util.IntensityCalculator

Calculate intensities from a raw data spot.

calculateIntensities(RawData) - Method in class net.sf.basedb.util.IntensityCalculatorUtil.JepIntensityCalculatorImpl

calculateWeights(List<LowessNormalization.SpotData>, double, List<Double>) - Static method in class net.sf.basedb.plugins.LowessNormalization

call() - Method in class net.sf.basedb.core.QueryExecutor.FutureItem

call() - Method in class net.sf.basedb.core.QueryExecutor.FutureResultSet

call() - Method in class net.sf.basedb.core.QueryExecutor.FutureScrollIterator

call() - Method in class net.sf.basedb.core.QueryExecutor.FutureUpdate

call() - Method in class net.sf.basedb.plugins.LowessNormalization.CallableWorker

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

To keep track of the code that created this DbControl.

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

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

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

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

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

canAddBioMaterial() - Method in class net.sf.basedb.core.BioWell

Check if it is possible to add/change biomaterial in this well.

cancel() - Method in class net.sf.basedb.clients.jobagent.JobQueueChecker

cancel() - Method in interface net.sf.basedb.core.QueryExecutor.Cancelable

cancel() - Method in class net.sf.basedb.core.QueryExecutor.CancelableSession

cancel() - Method in class net.sf.basedb.core.QueryExecutor.CancelableStatelessSession

cancel() - Method in class net.sf.basedb.core.QueryExecutor.CancelableStatement

cancel() - Method in class net.sf.basedb.util.timer.ThreadTimerTask

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

cancelQuery() - Method in class net.sf.basedb.core.hibernate.StatelessSessionWrapper

Cancels the currently executing query in the same manner as Session.cancelQuery().

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

Is it allowed to clear a well from biomaterial?

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

canClearBioMaterial() - Method in class net.sf.basedb.core.BioWell

Check if it is possible to clear the current biomaterial in this well.

canEnumerate - Variable in enum net.sf.basedb.core.Type

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

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

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

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

If a formula of this type can use coloring or not.

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

The id for the Quantity object representing capacitance.

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

An SQL case expression:

CASE
   WHEN r1 THEN e1
   WHEN r2 THEN e2
   ...CaseExpression(Expression, WhenStatement...) - 
Constructor for class net.sf.basedb.core.query.CaseExpression
 
caseInsensitive - 
Variable in enum net.sf.basedb.core.FeatureIdentificationMethod
If the feature identifiers may be affect by case sensitivity at the database
                level or not.
caseInsensitive() - 
Method in enum net.sf.basedb.core.FeatureIdentificationMethod
Return TRUE if this identification method can be case insensitive.
caseInsensitive - 
Variable in class net.sf.basedb.core.RawDataBatcher
If case should be ignored when comparing strings (external ID)
caseInsensitiveComparison() - 
Method in interface net.sf.basedb.core.dbengine.DbEngine
If the database does case sensitive or case insensitive string
                comparison in expressions.
caseInsensitiveComparison() - 
Method in class net.sf.basedb.core.dbengine.DefaultDbEngine
Returns TRUE.
caseInsensitiveComparison() - 
Method in class net.sf.basedb.core.dbengine.MySQLEngine
Returns TRUE.
caseInsensitiveComparison() - 
Method in class net.sf.basedb.core.dbengine.PostgresDbEngine
Returns FALSE.
caseWhen(Expression, WhenStatement...) - 
Static method in class net.sf.basedb.core.query.Expressions
Create a conditional CASE-WHEN expression:
                CASE
WHEN r1 THEN e1
WHEN r2 THEN e2
...
castToDate(String) - 
Method in class net.sf.basedb.core.dbengine.AbstractDbEngine
 
castToDate(String) - 
Method in interface net.sf.basedb.core.dbengine.DbEngine
Get a function that casts a date/timestamp to a date (eg. no time
                should be included in the result).
catalog - 
Variable in class net.sf.basedb.core.hibernate.TableExistsWork
 
categories - 
Variable in class net.sf.basedb.core.data.AnnotationTypeData
 
CDF_LINK_NAME - 
Static variable in class net.sf.basedb.core.Affymetrix
Deprecated. See DataFileType.AFFYMETRIX_CDF
cdfData - 
Variable in class net.sf.basedb.core.filehandler.CdfFileHandler
 
CdfFileHandler - Class in net.sf.basedb.core.filehandler
File handler that can validate and extract metadata from
        Affymetrix CDF files.
CdfFileHandler() - 
Constructor for class net.sf.basedb.core.filehandler.CdfFileHandler
 
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.
CEL_LINK_NAME - 
Static variable in class net.sf.basedb.core.Affymetrix
Deprecated. See DataFileType.AFFYMETRIX_CEL
celData - 
Variable in class net.sf.basedb.core.filehandler.CelFileHandler
 
CelFileHandler - Class in net.sf.basedb.core.filehandler
File handler that can validate and extract metadata from
        Affymetrix CEL files.
CelFileHandler() - 
Constructor for class net.sf.basedb.core.filehandler.CelFileHandler
 
Cell - Class in net.sf.basedb.clients.web.taglib.table
This tag defines a new cell in a row.
Cell() - 
Constructor for class net.sf.basedb.clients.web.taglib.table.Cell
 
CellValue - Class in net.sf.basedb.clients.web.taglib.table
This tag adds a value to a cell in a row.
CellValue() - 
Constructor for class net.sf.basedb.clients.web.taglib.table.CellValue
 
cfg - 
Variable in class net.sf.basedb.core.hibernate.SchemaGenerator
 
cfg - 
Static variable in class net.sf.basedb.core.HibernateUtil
The Hibernate configuration, including all mappings.
ch - 
Static variable in class net.sf.basedb.core.ItemContext
 
ch - 
Variable in class net.sf.basedb.util.importer.spotdata.MatrixSpotIntensityEventHandler
 
ch - 
Variable in class net.sf.basedb.util.importer.spotdata.SerialSpotIntensityEventHandler
 
ch1 - 
Variable in class net.sf.basedb.plugins.LowessNormalization.SpotData
 
ch1 - 
Variable in class net.sf.basedb.plugins.MedianRatioNormalization.SpotData
 
ch2 - 
Variable in class net.sf.basedb.plugins.LowessNormalization.SpotData
 
ch2 - 
Variable in class net.sf.basedb.plugins.MedianRatioNormalization.SpotData
 
chained - 
Variable in class net.sf.basedb.core.Job.ProgressReporterImpl
 
chainedProgress - 
Variable in class net.sf.basedb.util.export.spotdata.BfsExporter
 
ChainedProgressReporter - Class in net.sf.basedb.util
An implementation of the ProgressReporter interface that chains
        to another progress reporter while recalculating the percentage
        values.
ChainedProgressReporter(ProgressReporter) - 
Constructor for class net.sf.basedb.util.ChainedProgressReporter
Create a new chained progress reporter.
ChangeHistory - Class in net.sf.basedb.core
 
ChangeHistory(ChangeHistoryDetailData) - 
Constructor for class net.sf.basedb.core.ChangeHistory
 
ChangeHistoryData - Class in net.sf.basedb.core.data
Represents the changes made in a single transaction.
ChangeHistoryData() - 
Constructor for class net.sf.basedb.core.data.ChangeHistoryData
 
ChangeHistoryDetailData - Class in net.sf.basedb.core.data
Represents a change (creation/update/deletion) made to a
        single entity in a transaction.
ChangeHistoryDetailData() - 
Constructor for class net.sf.basedb.core.data.ChangeHistoryDetailData
 
ChangeHistoryUtil - Class in net.sf.basedb.clients.web
Utility class for working with change history.
ChangeHistoryUtil() - 
Constructor for class net.sf.basedb.clients.web.ChangeHistoryUtil
 
changeInfo - 
Variable in class net.sf.basedb.core.data.ChangeHistoryDetailData
 
changeReferenceFactorAndOffset(double, double) - 
Method in class net.sf.basedb.core.Unit
Changes the factor and offset used for converting values in this
                unit into the reference unit.
changes - 
Variable in class net.sf.basedb.core.log.LoggingInterceptor
 
changeType - 
Variable in class net.sf.basedb.core.data.ChangeHistoryDetailData
 
ChangeType - Enum in net.sf.basedb.core.log
Enumeration that representst the type of change that has happened.
ChangeType(int, String) - 
Constructor for enum net.sf.basedb.core.log.ChangeType
 
changeType - 
Variable in class net.sf.basedb.core.log.EntityDetails
 
channel - 
Variable in class net.sf.basedb.core.RawDataProperty
 
channel(int) - 
Static method in class net.sf.basedb.core.VirtualColumn
Deprecated. In 2.12. Use VirtualColumn.channelIntensity(int) or
                        VirtualColumn.channelRaw(int) instead. This method is forwarded
                        to VirtualColumn.channelIntensity(int) for maximum backwards
                        compatibility.
channel(int, String, Formatter<?>) - 
Static method in class net.sf.basedb.util.export.spotdata.ExportableFieldFactory
Create a simple dynamic field that exports the channel intensity
                of the given channel.
channel(int) - 
Method in class net.sf.basedb.util.jep.ChannelFunction
Get the value of the specified channel of the current sql result.
channel(int) - 
Method in class net.sf.basedb.util.jep.RawChannelFunction
Get the value of the specified channel of the current sql result.
ChannelFunction - Class in net.sf.basedb.util.jep
A JEP function class that adds a ch(int) function to a 
        JEP expression parser.
ChannelFunction() - 
Constructor for class net.sf.basedb.util.jep.ChannelFunction
Create a new instance of this function.
ChannelFunction(int[]) - 
Constructor for class net.sf.basedb.util.jep.ChannelFunction
Deprecated. In 2.12. Use ChannelFunction.ChannelFunction(int[], IntensityTransform)
                        instead. Using this constructor will disable the untransformation
                        of transformed values when JEP dynamic evalution is used.
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
 
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
 
CHARGE - 
Static variable in class net.sf.basedb.core.Quantity
The id for the Quantity object representing electrical charge.
charset - 
Variable in class net.sf.basedb.core.data.FileData
 
CHARSET - 
Static variable in class net.sf.basedb.plugins.AbstractFlatFileImporter
Deprecated. Use Parameters.CHARSET_PARAMETER
charset - 
Variable in class net.sf.basedb.util.FileImportInputStream
 
CHARSET_PARAMETER - 
Static variable in class net.sf.basedb.plugins.util.Parameters
The name of the parameter that is created by Parameters.charsetParameter(String, String, String)
charsetParameter(String, String, String) - 
Static method in class net.sf.basedb.plugins.util.Parameters
Parameter definition that asks for the character encoding used in the
                file that is imported.
charsetType - 
Static variable in class net.sf.basedb.plugins.AbstractFlatFileImporter
Deprecated. Use Parameters.charsetParameter(String, String, String)
charsetType - 
Static variable in class net.sf.basedb.plugins.util.Parameters
Enumerates all available character sets.
chart - 
Variable in class net.sf.basedb.util.plot.HistogramPlot
 
chart - 
Variable in class net.sf.basedb.util.plot.ScatterPlot
 
checkAbortAndDelay() - 
Method in class net.sf.basedb.clients.web.fileupload.FileUpload
Check if upload has been aborted.
checkAllowedSource(MeasuredBioMaterial) - 
Method in class net.sf.basedb.core.BioMaterialEvent
Check if the biomaterial is allowed as a source.
checkAndCreateTables() - 
Method in class net.sf.basedb.core.BioAssaySet
 
checkAndLoadClass(ClassLoader, String, boolean, Class<?>...) - 
Static method in class net.sf.basedb.util.ClassUtil
Check if a specified class exists and, optionally, if it has public no-argument
                constructor and implements a set of specific interfaces or superclasses.
checkBioAssay(DbControl, int, int) - 
Method in class net.sf.basedb.util.importer.spotdata.BaseFileInfo
Checks that the bioassay with the given id exists in the database.
checkBoundary(byte[], int, byte[], int) - 
Method in class net.sf.basedb.clients.web.fileupload.FileUpload
Check if the given line matches the boundary.
checkClass(Class<?>, boolean, Class<?>...) - 
Static method in class net.sf.basedb.util.ClassUtil
Check if a specified class has public no-argument
                constructor and implements a set of specific interfaces or superclasses.
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.
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(OverviewContext, Node, ArrayDesign) - 
Method in class net.sf.basedb.util.overview.validator.ArrayDesignValidator
Check if an experiment has used more than one array design.
checkForInvalidNumberOperation() - 
Method in class net.sf.basedb.core.dbengine.AbstractDbEngine
Returns FALSE.
checkForInvalidNumberOperation() - 
Method in interface net.sf.basedb.core.dbengine.DbEngine
If we need to check for invalid arguments to numerical
                functions to avoid exceptions from the database.
checkForInvalidNumberOperation() - 
Method in class net.sf.basedb.core.dbengine.PostgresDbEngine
Returns TRUE.
checkForJobs() - 
Method in class net.sf.basedb.clients.jobagent.JobQueueChecker
 
checkForSignals() - 
Method in class net.sf.basedb.core.signal.EnhancedThreadSignalHandler
If at least one signal has been received a SignalReceivedException
                is thrown.
checkForSignals() - 
Method in class net.sf.basedb.core.signal.ProgressReporterSignalHandler
If at least one signal has been received a SignalReceivedException
                is thrown.
checkIfReportersExists(FusionCDFData, ReporterBatcher, boolean, ReporterType, ProgressReporter) - 
Static method in class net.sf.basedb.core.Affymetrix
Verify that 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) - 
Method in class net.sf.basedb.util.PluginConfigInfo
Check the database if a configuration with the same name is already installed
                or not.
checkInstallation(DbControl) - 
Method in class net.sf.basedb.util.PluginInfo
Checks the database if this plug-in is installed or not.
checkInterrupted() - 
Method in class net.sf.basedb.core.plugin.AbstractPlugin
Deprecated. In 2.16, use ThreadSignalHandler.checkInterrupted() instead
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.
checkInterrupted() - 
Method in class net.sf.basedb.util.basefile.BaseFileParser
Deprecated. In 2.16, use ThreadSignalHandler.checkInterrupted() instead
checkInterrupted() - 
Method in class net.sf.basedb.util.export.spotdata.AbstractBioAssaySetExporter
Deprecated. In 2.16, use ThreadSignalHandler.checkInterrupted() instead
checkInterrupted() - 
Method in class net.sf.basedb.util.importer.spotdata.BaseFileImporter
Deprecated. In 2.16, use ThreadSignalHandler.checkInterrupted() instead
checkInterrupted() - 
Method in class net.sf.basedb.util.importer.spotdata.BfsImporter
Deprecated. In 2.16, use ThreadSignalHandler.checkInterrupted() instead
checkInterval - 
Variable in class net.sf.basedb.clients.jobagent.Agent
 
checkMagicNumber(PushbackInputStream, byte[]) - 
Static method in class net.sf.basedb.util.FileUtil
Take a peek at an input stream and check if the first few bytes
                matches the bCheck parameter.
checkMax(int, String, int) - 
Static method in class net.sf.basedb.core.IntegerUtil
Check that an integer is equal or lower than a maximum value.
checkMd5 - 
Variable in class net.sf.basedb.core.File.UploadStream
If the md5 should be checked or not.
checkMemberType(Item) - 
Method in class net.sf.basedb.core.BioMaterialList
Checks if the other type is the same type as the member type of
                this list.
checkMemberType(Collection<BioMaterialList>) - 
Method in class net.sf.basedb.core.BioMaterialList
Checks that the lists have the same member type as this list.
checkMin(int, String, int) - 
Static method in class net.sf.basedb.core.IntegerUtil
Check that an integer is equal or greater than a minimum value.
checkMinMax(int, String, int, int) - 
Static method in class net.sf.basedb.core.IntegerUtil
Check that an integer is equal or between a minimum and a maximum value.
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.Log2Function
 
checkNumberOfParameters(int) - 
Method in class net.sf.basedb.util.jep.MeanFunction
 
checkNumberOfParameters(int) - 
Method in class net.sf.basedb.util.jep.NotInReporterListFunction
 
checkNumberOfParameters(int) - 
Method in class net.sf.basedb.util.jep.PositionFunction
 
checkNumberOfParameters(int) - 
Method in class net.sf.basedb.util.jep.RawChannelFunction
 
checkNumberOfParameters(int) - 
Method in class net.sf.basedb.util.jep.RawFunction
 
checkNumberOfParameters(int) - 
Method in class net.sf.basedb.util.jep.ReporterFunction
 
checkNumberOfParameters(int) - 
Method in class net.sf.basedb.util.jep.ScoreFunction
 
checkNumberOfParameters(int) - 
Method in class net.sf.basedb.util.parser.ColFunction
 
checkNumberOfParameters(int) - 
Method in class net.sf.basedb.util.parser.DataNoFunction
 
checkNumberOfParameters(int) - 
Method in class net.sf.basedb.util.parser.LineNoFunction
 
checkPermission(Permission) - 
Method in class net.sf.basedb.clients.web.extensions.ExtensionsControl
 
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.
checkPermission(Permission) - 
Method in class net.sf.basedb.clients.web.util.NameablePluginAdaptor
 
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.Coloring
 
checkSameArrayDesign(Collection<RawBioAssay>, boolean) - 
Static method in class net.sf.basedb.util.IntensityCalculatorUtil
 
checkSuperclass - 
Variable in class net.sf.basedb.util.formatter.MultiFormatter
 
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
 
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)
childAssays - 
Variable in class net.sf.basedb.util.importer.spotdata.BaseFileInfo
 
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
 
childHasDifferentReporterPositionMapping - 
Variable in class net.sf.basedb.util.importer.spotdata.BaseFileInfo
 
childId - 
Variable in class net.sf.basedb.core.data.keyring.GroupGroups
 
ChildItem<D extends BasicData> - Class in net.sf.basedb.core
An abstract base class for all items which are child items to
        a Shareable parent item.
ChildItem(D) - 
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
 
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.GroupData
 
children - 
Variable in class net.sf.basedb.core.data.PlateData
 
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
 
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
 
CHP_LINK_NAME - 
Static variable in class net.sf.basedb.core.Affymetrix
Deprecated. See DataFileType
CIRCULAR_REFERENCE - 
Static variable in class net.sf.basedb.util.overview.Validator
Validator rule that checks for circular references among pooled items.
classes - 
Static variable in class net.sf.basedb.core.ExtendedProperties
A list with the name attribute of all classes found in
                the xml file.
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.PluginInfo
The classname of the plugin
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.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.Body
Optional class attribute
clazz - 
Variable in class net.sf.basedb.clients.web.taglib.Button
Optional class attribute
clazz - 
Variable in class net.sf.basedb.clients.web.taglib.ButtonGroup
Optional class attribute
clazz - 
Variable in class net.sf.basedb.clients.web.taglib.ExceptionCatcher
 
clazz - 
Variable in class net.sf.basedb.clients.web.taglib.Help
Optional class attribute
clazz - 
Variable in class net.sf.basedb.clients.web.taglib.HideableSection
Optional class attribute
clazz - 
Variable in class net.sf.basedb.clients.web.taglib.Icon
Optional class attribute
clazz - 
Variable in class net.sf.basedb.clients.web.taglib.menu.Menu
Optional class attribute
clazz - 
Variable in class net.sf.basedb.clients.web.taglib.Note
Optional class attribute
clazz - 
Variable in class net.sf.basedb.clients.web.taglib.path.Path
Optional class attribute
clazz - 
Variable in class net.sf.basedb.clients.web.taglib.path.PathElement
Optional class attribute
clazz - 
Variable in class net.sf.basedb.clients.web.taglib.Select
Optional class attribute
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.tab.TabControl
Optional class attribute.
clazz - 
Variable in class net.sf.basedb.clients.web.taglib.table.Button
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.ColumnDef
Optional class attribute
clazz - 
Variable in class net.sf.basedb.clients.web.taglib.table.Data
Optional class attribute
clazz - 
Variable in class net.sf.basedb.clients.web.taglib.table.Header
Optional class attribute
clazz - 
Variable in class net.sf.basedb.clients.web.taglib.table.Label
Optional class attribute
clazz - 
Variable in class net.sf.basedb.clients.web.taglib.table.Navigator
Optional class attribute
clazz - 
Variable in class net.sf.basedb.clients.web.taglib.table.Panel
Optional class attribute
clazz - 
Variable in class net.sf.basedb.clients.web.taglib.table.PresetSelector
Optional class attribute
clazz - 
Variable in class net.sf.basedb.clients.web.taglib.table.Row
Optional class attribute
clazz - 
Variable in class net.sf.basedb.clients.web.taglib.table.Table
Optional class attribute
clazz - 
Variable in class net.sf.basedb.clients.web.taglib.table.Toolbar
Optional class attribute
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.core.QueryExecutor.FutureScrollIterator
 
clazz - 
Variable in class net.sf.basedb.util.extensions.events.ActionClassEventFilter
 
clazz - 
Variable in class net.sf.basedb.util.filter.InstanceOfFilter
 
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() - 
Method in class net.sf.basedb.core.SessionControl
 
cleanUp(FileFilter) - 
Method in class net.sf.basedb.util.StaticCache
Remove all files that matches the specified filter from
                the cache.
cleanUpTask(FileFilter) - 
Method in class net.sf.basedb.util.StaticCache
Creates a task that cleans up this cache when it is 
                executed.
clear() - 
Method in class net.sf.basedb.core.AbstractResultList
Not supported.
clear() - 
Method in class net.sf.basedb.core.hibernate.SessionWrapper
 
clear(Session) - 
Static method in class net.sf.basedb.core.HibernateUtil
Clear the session of cached objects.
clear() - 
Method in class net.sf.basedb.core.UnmodifiableResultList
Not supported.
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.
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
 
clearFailures() - 
Method in class net.sf.basedb.util.overview.Node
Clear all warnings, errors on this node and on all child nodes.
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(String) - 
Method in class net.sf.basedb.core.ItemContext
Clear the recently used values list.
clearSources() - 
Method in class net.sf.basedb.core.BioMaterialEvent
Clear the sources collection and return the used quantities to
                the source biomaterials.
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 - Class in net.sf.basedb.core
This class represents a registered client application.
Client(ClientData) - 
Constructor for class net.sf.basedb.core.Client
 
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.plugins.HelpImporter
 
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
 
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(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(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, DbControl, Object) - 
Constructor for class net.sf.basedb.util.extensions.ClientContext
 
clientContext - 
Variable in class net.sf.basedb.util.extensions.ExtensionPointContext
 
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
 
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
 
clientId - 
Variable in class net.sf.basedb.core.SessionControl
The id of the ClientData. 0 = no client
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
 
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.
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.
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() - 
Static method in class net.sf.basedb.clients.web.extensions.service.Services
Stop all services.
close() - 
Method in class net.sf.basedb.clients.web.servlet.PlotServlet.CFResultIterator
 
close(int) - 
Method in class net.sf.basedb.clients.web.util.SimpleSignalProgressReporter
 
close() - 
Method in class net.sf.basedb.core.AbstractBatcher
 
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.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(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.
close() - 
Method in class net.sf.basedb.core.InternalJobQueue
Cleanup
close() - 
Method in class net.sf.basedb.core.InternalStorageController
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 interface net.sf.basedb.core.SecondaryStorageController
The core is now done with the storage controller.
close() - 
Method in class net.sf.basedb.core.SessionControl
Close this session control so it can't be used again.
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() - 
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(InputStream) - 
Static method in class net.sf.basedb.util.FileUtil
Close an input stream without throwing an exception.
close(OutputStream) - 
Static method in class net.sf.basedb.util.FileUtil
Close an output stream without throwing an exception.
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(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(ServerSocket) - 
Static method in class net.sf.basedb.util.SocketUtil
Close a server socket without throwing any exceptions.
close(Writer) - 
Static method in class net.sf.basedb.util.SocketUtil
Close a Writer without throwing any exceptions.
close(Reader) - 
Static method in class net.sf.basedb.util.SocketUtil
Close a Reader without throwing any exceptions.
close(InputStream) - 
Static method in class net.sf.basedb.util.SocketUtil
Close an InputStream without throwing any exceptions.
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.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() - 
Method in class net.sf.basedb.ws.server.TempFileDataSource.TempInputStream
 
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).
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.
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.
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.
ColFunction - Class in net.sf.basedb.util.parser
Adds a col() function to Jep.
ColFunction(Map<String, Integer>, NumberFormat) - 
Constructor for class net.sf.basedb.util.parser.ColFunction
 
ColFunction(List<String>, NumberFormat) - 
Constructor for class net.sf.basedb.util.parser.ColFunction
 
colFunction - 
Variable in class net.sf.basedb.util.parser.JepMapper
 
colIndex - 
Variable in class net.sf.basedb.clients.web.plugins.DynamicQueryWrapper
 
collections - 
Variable in class net.sf.basedb.util.NestedIterator
The array to iterate.
CollectionTransformer<S,D> - Interface in net.sf.basedb.util.collections
Allows a collection to be transformed by applying some operation to it.
colNum - 
Variable in class net.sf.basedb.clients.web.plugins.PlainTextTemplate
 
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 - 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(ColoringData, AccessControlled) - 
Constructor for class net.sf.basedb.core.Coloring
Create Coloring object which links to an existing item.
Coloring() - 
Constructor for class net.sf.basedb.core.Coloring
Create a new independent coloring object.
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
 
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.PresetSelector
Optional colspan attribute
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.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(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 - 
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.ReporterPropertyExpression
 
COLUMN - 
Static variable in class net.sf.basedb.core.VirtualColumn
This column stores the data cube column coordinate.
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.info.ExtendedPropertyInfo
 
column - 
Variable in class net.sf.basedb.plugins.LowessNormalization.SpotData
 
COLUMN_PREFIX - 
Static variable in class net.sf.basedb.clients.web.plugins.SimpleExport
 
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
 
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.
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
 
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) - 
Constructor for class net.sf.basedb.util.parser.ColumnMapper
Deprecated. Use ColumnMapper.ColumnMapper(int, String, NumberFormat, boolean)
ColumnMapper(int, String, NumberFormat, boolean) - 
Constructor for class net.sf.basedb.util.parser.ColumnMapper
Create a new column mapper using a specific number format.
columnMappingParameterName - 
Variable in class net.sf.basedb.plugins.batchimport.PropertyIdMethod
 
columnNo - 
Variable in class net.sf.basedb.core.data.DataCubeColumnData
 
Columns - Class in net.sf.basedb.clients.web.taglib.table
This tag is a place-holder for <tbl:header> tags.
Columns() - 
Constructor for class net.sf.basedb.clients.web.taglib.table.Columns
 
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.DynamicJoin
 
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.
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_BASEFILE - 
Static variable in class net.sf.basedb.plugins.BioAssaySetExporter
Deprecated.  
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.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<D extends CommonData> - Class in net.sf.basedb.core
 
CommonItem(D) - 
Constructor for class net.sf.basedb.core.CommonItem
 
CommonItemInfo - Class in net.sf.basedb.info
 
CommonItemInfo() - 
Constructor for class net.sf.basedb.info.CommonItemInfo
 
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(RawDataType, RawDataType) - 
Method in class net.sf.basedb.core.RawDataTypes.NameComparator
 
compare(BioAssaySetExporter.QueryItem, BioAssaySetExporter.QueryItem) - 
Method in class net.sf.basedb.plugins.BioAssaySetExporter.QueryItemTitleComparator
Deprecated.  
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(String, String) - 
Method in class net.sf.basedb.util.StringLengthComparator
 
compare(T, T) - 
Method in class net.sf.basedb.util.ToStringComparator
 
compareTo(ExperimentExplorer.AnnotationGroup) - 
Method in class net.sf.basedb.clients.web.ExperimentExplorer.AnnotationGroup
 
compareTo(ExtensionsFile) - 
Method in class net.sf.basedb.clients.web.extensions.ExtensionsFile
 
compareTo(ExperimentExplorerPlotServlet.ColumnKey) - 
Method in class net.sf.basedb.clients.web.servlet.ExperimentExplorerPlotServlet.ColumnKey
The ID of the key determines equality.
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(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(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
 
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.
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) - 
Constructor for class net.sf.basedb.util.parser.CompoundMapper
Deprecated. Use CompoundMapper.CompoundMapper(List, NumberFormat, boolean)
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.
compress(ProgressReporter) - 
Method in class net.sf.basedb.core.File
Compress the file stored on the disk.
compress - 
Variable in class net.sf.basedb.core.File.UploadStream
If the file should be compressed or not.
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.query.WhenStatement
 
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
 
config - 
Static variable in class net.sf.basedb.core.Config
Variable for holding the configuration properties.
config - 
Variable in class net.sf.basedb.core.plugin.ParameterValuesWrapper
 
config - 
Variable in class net.sf.basedb.util.ContextUtil.ContextResult
 
configDir - 
Static variable in class net.sf.basedb.core.Config
 
configList - 
Static variable in class net.sf.basedb.plugins.PluginConfigurationExporter
 
configs - 
Variable in class net.sf.basedb.util.PluginInfo
The list with belonging configurations
ConfigurableServiceFactory - Class in net.sf.basedb.ws.client
A service factory implementation that exposes the Options object.
ConfigurableServiceFactory() - 
Constructor for class net.sf.basedb.ws.client.ConfigurableServiceFactory
Create a new service factory that uses the default options.
ConfigurableServiceFactory(Options) - 
Constructor for class net.sf.basedb.ws.client.ConfigurableServiceFactory
Create a new service factory that uses the given options.
configuration - 
Variable in class net.sf.basedb.core.ParameterValuesImpl
 
configuration - 
Variable in class net.sf.basedb.core.plugin.AbstractPlugin
 
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.
configurationImportFile - 
Static variable in class net.sf.basedb.util.PluginInfo
The path in a jar-file to the file that holds 
                configurations to import
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(GuiContext, Request, Response) - 
Method in class net.sf.basedb.clients.web.plugins.SimpleExport
 
configure(GuiContext) - 
Method in class net.sf.basedb.core.Job
Start the configuration sequence for a job.
configure(GuiContext, Request, Response) - 
Method in interface net.sf.basedb.core.plugin.InteractivePlugin
Configure the plugin.
configure() - 
Method in class net.sf.basedb.core.PluginConfiguration
Start the configuration sequence for a 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.BfsExporterPlugin
 
configure(GuiContext, Request, Response) - 
Method in class net.sf.basedb.plugins.BioAssaySetExporter
Deprecated.  
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.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.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
 
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.BioAssaySetExporter
Deprecated.  
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.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.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
 
configureJobBasefile - 
Variable in class net.sf.basedb.plugins.BioAssaySetExporter
Deprecated.  
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
 
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.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.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(EntityQuery, boolean) - 
Method in class net.sf.basedb.core.ItemContext
Deprecated. Use ItemContext.configureQuery(DbControl, EntityQuery, boolean) instead
configureQuery(DbControl, EntityQuery, boolean) - 
Method in class net.sf.basedb.core.ItemContext
Use the settings in this context to configure a query.
configureQuery(DbControl, DynamicQuery, 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.SessionWrapper
Deprecated. 
connection() - 
Method in class net.sf.basedb.core.hibernate.StatelessSessionWrapper
 
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.
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(String) - 
Constructor for class net.sf.basedb.util.parser.ConstantMapper
Create a constant mapper.
ConstantMapper(String, NumberFormat) - 
Constructor for class net.sf.basedb.util.parser.ConstantMapper
Deprecated. Use ConstantMapper.ConstantMapper(String, NumberFormat, boolean)
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(Integer) - 
Constructor for class net.sf.basedb.util.parser.ConstantMapper
 
ConstantMapper(Float) - 
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
 
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.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.
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.renderer.PrefixSuffixRenderer
 
context - 
Variable in class net.sf.basedb.clients.web.extensions.ServletWrapper
 
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.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]
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
 
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
 
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.RssNewsFeed
 
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.ContextResult(SessionControl, PluginDefinition, PluginConfiguration, GuiContext, Object) - 
Constructor for class net.sf.basedb.util.ContextUtil.ContextResult
 
ContextUtil.ContextResult(PluginDefinition, PluginConfiguration, String) - 
Constructor for class net.sf.basedb.util.ContextUtil.ContextResult
Create a new warning-level result object.
ContextUtil.ContextResult(PluginDefinition, PluginConfiguration, Throwable) - 
Constructor for class net.sf.basedb.util.ContextUtil.ContextResult
Create a new error-level result object.
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().
ContextUtil.IsInContextFilter() - 
Constructor for class net.sf.basedb.util.ContextUtil.IsInContextFilter
 
continueAfterError - 
Variable in class net.sf.basedb.plugins.RawDataFlatFileImporter
 
continueLater(String, boolean) - 
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
 
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
 
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
 
convertTiffImage(RenderedImage, byte[]) - 
Method in class net.sf.basedb.core.SpotImages
Convert TIFF image from 16 bits to 8 bits if needed
convertToAbsolute(String) - 
Static method in class net.sf.basedb.core.PluginDefinition
Convert a relative plug-in path to an absolute path.
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.
convertToRelative(String) - 
Static method in class net.sf.basedb.core.PluginDefinition
Convert a plug-in path to a path relative to the plugins.dir
                setting in base.config.
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.
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
 
coordinateType - 
Variable in class net.sf.basedb.core.data.DataCubeExtraValueData
 
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(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(int) - 
Method in class net.sf.basedb.util.InputStreamSplitter
Write data to all output streams.
copy(byte[], int, int) - 
Method in class net.sf.basedb.util.InputStreamSplitter
Write data to all output streams.
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.
copyNotNulls(T[], T[]) - 
Static method in class net.sf.basedb.core.query.Restrictions
 
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.
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.
copySources - 
Variable in class net.sf.basedb.util.biomaterial.PooledChildrenTransformer
 
copySources - 
Variable in class net.sf.basedb.util.biomaterial.PooledParentsTransformer
 
copySubdirectories(DbControl, Directory, Directory, User) - 
Static method in class net.sf.basedb.core.Directory
This method copies a directory strucure to the destination directory.
copyTo - 
Variable in class net.sf.basedb.util.InputStreamSplitter
Streams to copy the data to.
count - 
Variable in class net.sf.basedb.clients.web.ExperimentExplorer.AnnotationGroup
 
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(Collection<BioMaterialList>, int, int) - 
Static method in class net.sf.basedb.core.BioMaterialList
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(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(DbControl) - 
Method in interface net.sf.basedb.core.query.Query
Count the number of items/rows that are returned by the query.
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 - 
Variable in class net.sf.basedb.util.plot.HistogramPlot.HistogramBin
 
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 or labeled extracts.
countChildren(boolean) - 
Method in class net.sf.basedb.core.LabeledExtract
Count the number of child labeled 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.
countImages() - 
Method in class net.sf.basedb.core.Scan
Counts all images that have been added to this scan.
countLabeledExtracts() - 
Method in class net.sf.basedb.core.Extract
Gets the number of LabeledExtract that are create from this item.
countLabeledExtracts() - 
Method in class net.sf.basedb.core.LabeledExtract
Counts all labeled extracts that have been created from this labeled extract.
countNotNulls(Object[]) - 
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.
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.Scan
Counts all raw bioassays that have been created from this scan.
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.
countScans() - 
Method in class net.sf.basedb.core.Hybridization
Counts all scans that have been created from this hybridization.
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.
cpuUsage - 
Variable in class net.sf.basedb.util.jobagent.JobAgentInfo
 
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(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.AnnotationParser
Utility method for creating an annotation parser for a file in the local
                file system.
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(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.AnnotationWriter
Utility method for creating an annotation writer to a file in the native
                file system.
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(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.DataParser
Utility method for creating a data parser for a file in the local
                file system.
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(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.DataWriter
Utility method for creating a data writer to a file in the native
                file system.
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(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.MetadataParser
Utility method for creating a metadata parser for a file in the local
                file system.
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(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(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_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
 
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, 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.
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.
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.
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.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.ExtractImporter
 
createColumnMappers(FlatFileParser, boolean) - 
Method in class net.sf.basedb.plugins.batchimport.HybridizationImporter
 
createColumnMappers(FlatFileParser, boolean) - 
Method in class net.sf.basedb.plugins.batchimport.LabeledExtractImporter
 
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.ScanImporter
 
createContext(SessionControl, PageContext) - 
Static method in class net.sf.basedb.clients.web.extensions.ExtensionsControl
Create a new JspContext object without an active DbControl.
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.
createCriteria(Class, String) - 
Method in class net.sf.basedb.core.hibernate.SessionWrapper
 
createCriteria(Class) - 
Method in class net.sf.basedb.core.hibernate.SessionWrapper
 
createCriteria(String, String) - 
Method in class net.sf.basedb.core.hibernate.SessionWrapper
 
createCriteria(String) - 
Method in class net.sf.basedb.core.hibernate.SessionWrapper
 
createCriteria(Class, String) - 
Method in class net.sf.basedb.core.hibernate.StatelessSessionWrapper
 
createCriteria(Class) - 
Method in class net.sf.basedb.core.hibernate.StatelessSessionWrapper
 
createCriteria(String, String) - 
Method in class net.sf.basedb.core.hibernate.StatelessSessionWrapper
 
createCriteria(String) - 
Method in class net.sf.basedb.core.hibernate.StatelessSessionWrapper
 
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, FileTypeData, String, String) - 
Static method in class net.sf.basedb.core.Install
Create a DataFileType.
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.
createDataWriter(Object, String) - 
Method in class net.sf.basedb.util.export.spotdata.BfsExporter
Utility method for calling creating a data writer.
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 ItemContext with settings for default
                visible columns and sort property.
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.
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.ExtractImporter
 
createdMapper - 
Variable in class net.sf.basedb.plugins.batchimport.HybridizationImporter
 
createdMapper - 
Variable in class net.sf.basedb.plugins.batchimport.LabeledExtractImporter
 
createdMapper - 
Variable in class net.sf.basedb.plugins.batchimport.SampleImporter
 
createDom(String, String) - 
Static method in class net.sf.basedb.util.XMLUtil
Create a new Document with root element and System id
                declaration.
createEngine(Dialect) - 
Static method in class net.sf.basedb.core.dbengine.EngineFactory
Create a new DbEngine object.
createExportedProperty(String, String, Metadata, Formatter) - 
Static method in class net.sf.basedb.clients.web.plugins.ExportedProperty
 
createExportedProperty(String, String, Metadata, Formatter) - 
Method in class net.sf.basedb.ws.server.ReporterService
 
createFactory(Element, ClassLoader, Class<F>) - 
Method in class net.sf.basedb.util.extensions.xml.XmlLoader
Create a new factory instance.
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.
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.
createFile(File, String) - 
Method in class net.sf.basedb.plugins.BfsExporterPlugin
 
createFile(DbControl, Directory, 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.
createFileType(String, String, String) - 
Static method in class net.sf.basedb.core.Install
Create a FileType.
createFilter(Object, String) - 
Method in class net.sf.basedb.core.hibernate.SessionWrapper
 
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
 
createFilterElement(String, String) - 
Static method in class net.sf.basedb.core.HibernateUtil
Create a <filter> tag using the given name and condition.
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.
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(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.ExperimentLoader
Create property-loading experiment nodes from a given rawbioassay node.
createForwardNode(DbControl, OverviewContext, Node) - 
Method in class net.sf.basedb.util.overview.loader.ExtractLoader
Create forward-loading extract nodes from a given parent sample
                of extract.
createForwardNode(Sample, DbControl, OverviewContext, Node) - 
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(Extract, DbControl, OverviewContext, Node) - 
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(DbControl, OverviewContext, Node) - 
Method in class net.sf.basedb.util.overview.loader.HybridizationLoader
Create forward-loading hybridization nodes from either a labeled extract or
                an array slide node.
createForwardNode(LabeledExtract, DbControl, OverviewContext, Node) - 
Method in class net.sf.basedb.util.overview.loader.HybridizationLoader
Create forward-loading hybridization nodes for the hybridizations 
                that has a given labeled extract as a source.
createForwardNode(ArraySlide, DbControl, OverviewContext, Node) - 
Method in class net.sf.basedb.util.overview.loader.HybridizationLoader
Create a forward-loading hybridization node from an array slide.
createForwardNode(DbControl, OverviewContext, Node) - 
Method in class net.sf.basedb.util.overview.loader.LabeledExtractLoader
Create forward-loading labeled extract nodes from a given parent extract
                or labeled extract node.
createForwardNode(Extract, DbControl, OverviewContext, Node) - 
Method in class net.sf.basedb.util.overview.loader.LabeledExtractLoader
Create forward-loading labeled extract nodes for the labeled extracts that 
                has a given extract as their parent.
createForwardNode(LabeledExtract, DbControl, OverviewContext, Node) - 
Method in class net.sf.basedb.util.overview.loader.LabeledExtractLoader
Create forward-loading labeled extract nodes for the (pooled) labeled extract that 
                has a given labeled extract among their parents.
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.RawBioAssayLoader
Create forward-loading raw bioassay nodes from a given scan 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(BioSource, DbControl, OverviewContext, Node) - 
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(Sample, DbControl, OverviewContext, Node) - 
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.
createForwardNode(DbControl, OverviewContext, Node) - 
Method in class net.sf.basedb.util.overview.loader.ScanLoader
Create forward-loading scan nodes from a given hybridization node.
createGroup(String, String, boolean, boolean, String) - 
Static method in class net.sf.basedb.core.Install
Create a Group.
createHardware(String, String, String, HardwareTypeData, UserData, ItemKeyData) - 
Static method in class net.sf.basedb.core.Install
Create a HardwareData.
createHardwareType(String, String, String) - 
Static method in class net.sf.basedb.core.Install
Create a HardwareType.
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) - 
Method in class net.sf.basedb.core.LogControl
Creates a Hibernate HQL query.
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.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.ExtractImporter
 
createItem(DbControl, FlatFileParser.Data) - 
Method in class net.sf.basedb.plugins.batchimport.HybridizationImporter
 
createItem(DbControl, FlatFileParser.Data) - 
Method in class net.sf.basedb.plugins.batchimport.LabeledExtractImporter
 
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.ScanImporter
 
createItemKey(String, Map<UserData, Integer>, Map<GroupData, Integer>) - 
Static method in class net.sf.basedb.core.Install
Create an ItemKey.
createItemNode(NodeFactory<I>, I, 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.ArrayBatchImporter
Calls ArrayBatch.getQuery().
createItemQuery() - 
Method in class net.sf.basedb.plugins.batchimport.ArrayDesignImporter
Calls Hybridization.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.ExtractImporter
Calls Extract.getQuery().
createItemQuery() - 
Method in class net.sf.basedb.plugins.batchimport.HybridizationImporter
Calls Hybridization.getQuery().
createItemQuery() - 
Method in class net.sf.basedb.plugins.batchimport.LabeledExtractImporter
Calls Extract.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.ScanImporter
Calls Scan.getQuery().
createJepExpression(DbControl, BioAssaySet, String, boolean) - 
Static method in class net.sf.basedb.util.BioAssaySetUtil
Deprecated. In 2.15, use BioAssaySetUtil.createJepExpression(DbControl, String, DynamicQuery)
                        instead. The 'allowRawIfMultipleMappings' parameter is replaced with an
                        option on the spot query: DynamicSpotQuery.setDisableRawJoinOnMergedData(boolean)
                        (it has no meaning on other queries)
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, BioAssaySet, String, boolean) - 
Static method in class net.sf.basedb.util.BioAssaySetUtil
Deprecated. In 2.15, use BioAssaySetUtil.createJepRestriction(DbControl, String, DynamicQuery)
                        instead. The 'allowRawIfMultipleMappings' parameter is replaced with an
                        option on the spot query: DynamicSpotQuery.setDisableRawJoinOnMergedData(boolean)
                        (it has no meaning on other queries)
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.
createKeyManagers(KeyStore, String, String, String) - 
Static method in class net.sf.basedb.util.ssl.SSLUtil
 
createKeyStore(InputStream, String, String, String) - 
Static method in class net.sf.basedb.util.ssl.SSLUtil
Create a key-store from the given input stream
createLabel(String, String, UserData, ItemKeyData) - 
Static method in class net.sf.basedb.core.Install
Create a Label.
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.
createLoginInfo(Session, UserData, String, boolean) - 
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
 
createMimeType(String, String, String, FileTypeData, 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.
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.
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.
createPluginConfigurations(String, boolean) - 
Static method in class net.sf.basedb.core.Install
Create PluginConfigurations from a XML file.
createPluginDefinition(String, String, ItemKeyData, boolean, Long, boolean) - 
Static method in class net.sf.basedb.core.Install
Create a PluginDefinition.
createPluginType(String, String, String, String) - 
Static method in class net.sf.basedb.core.Install
Create a PluginType.
createPropertyElement(ExtendedProperty) - 
Static method in class net.sf.basedb.core.HibernateUtil
Creates a <property> tag from an extended property
                definition.
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 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.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.HardwareLoader
 
createPropertyNode(DbControl, OverviewContext, Node) - 
Method in class net.sf.basedb.util.overview.loader.ImageLoader
 
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.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.SoftwareLoader
 
createProtocolType(String, String, String) - 
Static method in class net.sf.basedb.core.Install
Create a ProtocolType.
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(Session, String) - 
Static method in class net.sf.basedb.core.HibernateUtil
Create a Hibernate query.
createQuery(StatelessSession, String) - 
Static method in class net.sf.basedb.core.HibernateUtil
Create a Hibernate query using a stateless session.
createQuery(Item, String, Set<Include>) - 
Method in class net.sf.basedb.plugins.AnnotationFlatFileImporter
Create a query that return items of the specified type.
createQuery() - 
Method in class net.sf.basedb.util.biomaterial.BioSourceToSampleTransformer
Create a query for loading samples.
createQuery() - 
Method in class net.sf.basedb.util.biomaterial.ExtractToLabeledExtractTransformer
Create a query for loading labeled extracts.
createQuery() - 
Method in class net.sf.basedb.util.biomaterial.ExtractToSampleTransformer
Create a query for loading samples.
createQuery() - 
Method in class net.sf.basedb.util.biomaterial.LabeledExtractToExtractTransformer
Create a query for loading extracts.
createQuery() - 
Method in class net.sf.basedb.util.biomaterial.SampleToBioSourceTransformer
Create a query for loading biosources.
createQuery() - 
Method in class net.sf.basedb.util.biomaterial.SampleToExtractTransformer
Create a query for loading extracts.
createQuota(String, String, String, long) - 
Static method in class net.sf.basedb.core.Install
Create a Quota.
createQuotaType(String, String, String, boolean) - 
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.ExtractLoader
Create reverse-loading extract nodes from a labeled extract node
                or from a pooled extract.
createReverseNode(Extract, DbControl, OverviewContext, Node) - 
Method in class net.sf.basedb.util.overview.loader.ExtractLoader
Create reverse-loading extract nodes of a pooled extract.
createReverseNode(LabeledExtract, DbControl, OverviewContext, Node) - 
Method in class net.sf.basedb.util.overview.loader.ExtractLoader
Create a reverse-loading extract node from a labeled extract.
createReverseNode(DbControl, OverviewContext, Node) - 
Method in class net.sf.basedb.util.overview.loader.HybridizationLoader
Create a reverse-loading hybridization node from the scan node.
createReverseNode(DbControl, OverviewContext, Node) - 
Method in class net.sf.basedb.util.overview.loader.LabeledExtractLoader
Create reverse-loading labeled extract nodes from a hybridization node
                or from a pooled labeled extract.
createReverseNode(LabeledExtract, DbControl, OverviewContext, Node) - 
Method in class net.sf.basedb.util.overview.loader.LabeledExtractLoader
Create reverse-loading labeled extract nodes of a pooled labeled extract.
createReverseNode(Hybridization, DbControl, OverviewContext, Node) - 
Method in class net.sf.basedb.util.overview.loader.LabeledExtractLoader
Create reverse-loading labeled extract nodes from a hybridization.
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.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.SampleLoader
Create reverse-loading sample nodes from an extract node
                or from a pooled sample.
createReverseNode(Sample, DbControl, OverviewContext, Node) - 
Method in class net.sf.basedb.util.overview.loader.SampleLoader
Create reverse-loading samples nodes of a pooled sample.
createReverseNode(Extract, DbControl, OverviewContext, Node) - 
Method in class net.sf.basedb.util.overview.loader.SampleLoader
Create a reverse-loading sample node from an extract.
createReverseNode(DbControl, OverviewContext, Node) - 
Method in class net.sf.basedb.util.overview.loader.ScanLoader
Create a reverse-loading scan node from the raw bioassay node.
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 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
 
createSchemaVersion(int) - 
Static method in class net.sf.basedb.core.Install
Create the schema version.
createService(EndpointReference) - 
Method in class net.sf.basedb.ws.client.ConfigurableServiceFactory
 
createService(EndpointReference) - 
Method in interface net.sf.basedb.ws.client.ServiceFactory
Create a new RPCServiceClient object.
createSimpleEmail() - 
Static method in class net.sf.basedb.util.EmailUtil
Create a simple text email.
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, SoftwareTypeData, UserData, ItemKeyData) - 
Static method in class net.sf.basedb.core.Install
Create a Software.
createSoftwareType(String, String, String) - 
Static method in class net.sf.basedb.core.Install
Create a SoftwareType.
createSpotImages(File, int, int, int, int, int, float, float, File, File, File, ProgressReporter) - 
Method in class net.sf.basedb.core.SpotImages
Creates spot images with 8 bits per channel, from source images.
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.
createSqlQuery(Session, String) - 
Static method in class net.sf.basedb.core.HibernateUtil
Create a Hibernate SQL query.
createSqlQuery(StatelessSession, String) - 
Static method in class net.sf.basedb.core.HibernateUtil
Create a Hibernate SQL query using a stateless session.
createSqlQuery(String) - 
Method in class net.sf.basedb.core.LogControl
Creates a Hibernate SQL query.
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(boolean, ProgressReporter) - 
Static method in class net.sf.basedb.core.HibernateUtil
Create the all tables in the database.
createTables(boolean, ProgressReporter) - 
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.
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.
createTemporaryWorkingDirectory() - 
Method in class net.sf.basedb.plugins.executor.ExternalProgramExecutor
Create a temporary working directory in the local file
                system.
createTransformer(DbControl, Item, Item, boolean) - 
Static method in class net.sf.basedb.util.biomaterial.ListUtil
Create a transformer that can transform a collection with
                sourceItem:s into a collection with destinationItem:s
                by following parent/child paths.
createTrustManagers(KeyStore, String, String) - 
Static method in class net.sf.basedb.util.ssl.SSLUtil
 
createUnit(QuantityData, String, String, double, double, String, String...) - 
Static method in class net.sf.basedb.core.Install
Create a Unit.
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.
createXmlLoader() - 
Method in class net.sf.basedb.clients.web.extensions.ExtensionsDirectory
Creates a new XmlLoader and registers the ExtensionsDirectory.variableConverter
                and ExtensionsDirectory.pathConverter with it.
creationEvent - 
Variable in class net.sf.basedb.core.data.HybridizationData
 
creationEvent - 
Variable in class net.sf.basedb.core.data.MeasuredBioMaterialData
 
creationEvent - 
Variable in class net.sf.basedb.core.Hybridization
 
creationEvent - 
Variable in class net.sf.basedb.core.MeasuredBioMaterial
 
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
 
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 - 
Static variable in class net.sf.basedb.core.Quantity
The id for the Quantity object representing electric current.
current - 
Variable in class net.sf.basedb.util.NestedIterator
The current iterator.
currentAction - 
Variable in class net.sf.basedb.util.extensions.ActionIterator
 
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
 
currentIndex - 
Variable in class net.sf.basedb.plugins.RawDataFlatFileImporter.FileIterator
 
currentPage - 
Variable in class net.sf.basedb.clients.web.taglib.table.Navigator
The current page.
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
 
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
 
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.Columns
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 - Variable in class net.sf.basedb.clients.web.taglib.table.Row: The parent <tbl:data> tag.
data - Variable in class net.sf.basedb.clients.web.taglib.table.Rows
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.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() - Method in class net.sf.basedb.util.parser.FlatFileParser.Data: The data line as an array of strings.
data - Variable in class net.sf.basedb.util.parser.LineNoFunction
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.
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.
dataClass - Variable in class net.sf.basedb.core.ScrollIterator
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 - 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 - 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.RawMappingQuery - Class in net.sf.basedb.core: Select data from Dynamic#RawParents table.
DataCube.RawMappingQuery(DataCube) - Constructor for class net.sf.basedb.core.DataCube.RawMappingQuery
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.
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.
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.
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.
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.RawBioAssayImporter
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 all files required by the platform are present 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.
DataFileHandler - Interface in net.sf.basedb.core.filehandler: This interface is the super-interface for all interfaces that are work on files of a specific DataFileType.
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
DataFileMetadataReader - Interface in net.sf.basedb.core.filehandler: This interface should be implemented by classes that are used to extract metadata from a file of a specific DataFileType.
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.
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
DataFileTypeInfo - Class in net.sf.basedb.info: This holds information about a DataFileType in BASE.
DataFileTypeInfo() - Constructor for class net.sf.basedb.info.DataFileTypeInfo
DataFileValidator - Interface in net.sf.basedb.core.filehandler: This interface should be implemented by classes that are used to validate a file of a specific DataFileType.
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.
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<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.
dataloader - Variable in class net.sf.basedb.clients.web.plugins.ExportedProperty
DataNoFunction - Class in net.sf.basedb.util.parser: Adds a dataNo() function to Jep.
DataNoFunction() - Constructor for class net.sf.basedb.util.parser.DataNoFunction
dataNoFunction - Variable in class net.sf.basedb.util.parser.JepMapper
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 - Class in net.sf.basedb.core: An implementation of the Query interface that returns data objects.
DataQuery(Class, 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, Item, String, String) - Constructor for class net.sf.basedb.core.DataQuery: Create a query that may have different return type and root entity.
DataQuery(Class, String, QueryRuntimeFilter) - Constructor for class net.sf.basedb.core.DataQuery: Create a new query for the specified item, using a non-default optional runtime filter.
DataQueryWrapper - Class in net.sf.basedb.clients.web.plugins: A query wrapper for DataQuery:s.
DataQueryWrapper(DbControl, DataQuery<BasicData>) - Constructor for class net.sf.basedb.clients.web.plugins.DataQueryWrapper: Create a new query wrapper.
DataResultIterator - Class in net.sf.basedb.core: Return the results of a DataQuery as an iterator.
DataResultIterator(ScrollIterator, SessionControl, Session, Class, 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.ColumnDef: The type of data in the property.
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<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.
dataWriterFactory - Variable in class net.sf.basedb.util.export.spotdata.BfsExporter
dataWriters - Variable in class net.sf.basedb.util.export.spotdata.BfsExporter
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.util.Values
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)
dateFormat - Variable in class net.sf.basedb.util.formatter.DateFormatter
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 - Class in net.sf.basedb.util.formatter: Format a date for output in a client application.
DateFormatter(DateFormat) - Constructor for class net.sf.basedb.util.formatter.DateFormatter: Create a new date formatter.
DateFormatter(String) - 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
DATETIME_FORMAT - Static variable in class net.sf.basedb.util.Values
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
DbControl - Class in net.sf.basedb.core: A DbControl object is the main object used for communicating with the database.
DbControl(SessionControl) - Constructor for class net.sf.basedb.core.DbControl: Create a new object.
DbControl.SaveIf - Class in net.sf.basedb.core
DbControl.SaveIf(BasicItem, boolean) - Constructor for class net.sf.basedb.core.DbControl.SaveIf
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 - Interface in net.sf.basedb.core.dbengine: Information about database-specific options that are not covered by the Hibernate Dialect objects.
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.
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.
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
dc - Variable in class net.sf.basedb.clients.web.formatter.SpotImageFormatter
dc - Variable in class net.sf.basedb.clients.web.plugins.DataQueryWrapper
dc - Variable in class net.sf.basedb.clients.web.plugins.DynamicQueryWrapper
dc - Variable in class net.sf.basedb.clients.web.plugins.ItemQueryWrapper
dc - Variable in class net.sf.basedb.clients.web.plugins.ReporterScoreQueryWrapper
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.core.AbstractBatcher: A reference to the current DbControl object.
dc - Variable in class net.sf.basedb.core.BasicItem: A reference to the current DbControl object.
dc - Variable in class net.sf.basedb.core.DiskUsageStatistics
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.ReporterScoreResultIterator: The DbControl that was used in the query.
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.BfsExporterPlugin
dc - Variable in class net.sf.basedb.plugins.BioAssaySetExporter: Deprecated.
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.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.biomaterial.BioSourceToSampleTransformer
dc - Variable in class net.sf.basedb.util.biomaterial.ExtractToLabeledExtractTransformer
dc - Variable in class net.sf.basedb.util.biomaterial.ExtractToSampleTransformer
dc - Variable in class net.sf.basedb.util.biomaterial.LabeledExtractToExtractTransformer
dc - Variable in class net.sf.basedb.util.biomaterial.PooledChildrenTransformer
dc - Variable in class net.sf.basedb.util.biomaterial.PooledParentsTransformer
dc - Variable in class net.sf.basedb.util.biomaterial.SampleToBioSourceTransformer
dc - Variable in class net.sf.basedb.util.biomaterial.SampleToExtractTransformer
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.export.spotdata.FieldConverter: Deprecated.
dc - Variable in class net.sf.basedb.util.extensions.ClientContext
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.overview.node.NodeFactory
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
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()
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
DebugOnSaveActionFactory.DebugOnSaveAction(JspContext) - Constructor for class net.sf.basedb.clients.web.extensions.edit.DebugOnSaveActionFactory.DebugOnSaveAction
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()
decideOnFirst - Variable in class net.sf.basedb.util.formatter.MultiFormatter
DECIMAL_SEPARATOR - Static variable in class net.sf.basedb.plugins.AbstractFlatFileImporter: Deprecated. Use Parameters.DECIMAL_SEPARATOR_PARAMETER
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.
decimalSeparatorType - Static variable in class net.sf.basedb.plugins.AbstractFlatFileImporter: Deprecated. Use Parameters.decimalSeparatorParameter(String, String, String)
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
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.Quota: The ID for the system default quota, which is assigned to new users unless another quota is specified.
DEFAULT_CACHE_SIZE - Static variable in class net.sf.basedb.clients.web.ExperimentExplorer: Deprecated. In 2.11, for performance reasons the cache always contains the full set of reporters
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_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_METHODS - Static variable in class net.sf.basedb.plugins.batchimport.PropertyIdMethod: Deprecated. In 2.16, due to possible problems with circular class initialization with the FallbackIdMethod class. This array is now empty.
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_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.
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.
DefaultEntityLogger - Class in net.sf.basedb.core.log.db: Default logger for all entities that has been tagged with the LoggableData interface.
DefaultEntityLogger(boolean) - 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.
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
defaultHeight - Variable in class net.sf.basedb.clients.web.servlet.ExperimentExplorerPlotServlet
defaultHeight - Variable in class net.sf.basedb.clients.web.servlet.PlotServlet
defaultImages - Static variable in class net.sf.basedb.clients.web.taglib.Button
defaultitem - Variable in class net.sf.basedb.clients.web.taglib.Select: The project default value
defaultKeyManagers - Static variable in class net.sf.basedb.util.ssl.SSLUtil
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
defaultPreset - Variable in class net.sf.basedb.core.Presets
defaultPriority - Variable in enum net.sf.basedb.core.Job.ExecutionTime
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
defaults - Variable in class net.sf.basedb.core.Project
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.SSLUtil
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.SSLUtil
defaultUnit - Variable in class net.sf.basedb.core.data.AnnotationTypeData
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.info.AnnotationTypeInfo
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
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
definedPermissions - Variable in enum net.sf.basedb.core.Item
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.
delayed - Variable in class net.sf.basedb.core.Job.JobSignalTransporter
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(D) - Method in class net.sf.basedb.core.BasicBatcher: Delete a data object.
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(Object) - Method in class net.sf.basedb.core.hibernate.SessionWrapper
delete(String, Object) - Method in class net.sf.basedb.core.hibernate.SessionWrapper
delete(Object) - Method in class net.sf.basedb.core.hibernate.StatelessSessionWrapper
delete(String, Object) - Method in class net.sf.basedb.core.hibernate.StatelessSessionWrapper
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(SessionControl, Collection<? extends Identifiable>, boolean, ProgressReporter) - Static method in class net.sf.basedb.core.Trashcan: Delete items permanently.
delete(DbControl, Item, Set<Integer>) - Static method in class net.sf.basedb.util.RemovableUtil
delete(String, int) - Method in class net.sf.basedb.util.StaticCache: Deletes an object from the cache.
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.
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
deleteData(Session, BasicData) - Static method in class net.sf.basedb.core.HibernateUtil: Delete a data item from the database.
deleteDir(File) - Method in class net.sf.basedb.plugins.Base1PluginExecuter: Deletes all files and sub directories under dir.
deleteEmptyDirectories(File, boolean) - Static method in class net.sf.basedb.util.FileUtil: Deletes all empty subdirectories and, optionally, also the root directory.
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.
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 change history entries that are linking to non-existing items.
deleteStrayLinks() - Static method in class net.sf.basedb.core.AnyToAny: Deprecated. Use AnyToAny.deleteStrayLinks(ProgressReporter) instead.
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.
deleteTempFile() - Method in class net.sf.basedb.ws.server.TempFileDataSource.TempInputStream: Delete the temp file if it exists and we know that only one stream is reading from it.
deleteUnusedItemKeys() - Static method in class net.sf.basedb.core.ItemKey: Delete all keys that are currently not used by any item.
deleteUnusedKeys() - Static method in class net.sf.basedb.core.ItemKey: Deprecated. Use ItemKey.deleteUnusedItemKeys() instead which returns the number of deleted keys
deleteUnusedKeys() - Static method in class net.sf.basedb.core.ProjectKey: Deprecated. Use ProjectKey.deleteUnusedProjectKeys() instead which returns the number of deleted keys
deleteUnusedProjectKeys() - Static method in class net.sf.basedb.core.ProjectKey: Delete all keys that are currently not used by any item.
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 - Variable in class net.sf.basedb.util.PluginInfo
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_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_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_HYBRIDIZATION - Static variable in class net.sf.basedb.util.overview.Validator: Validator rule that checks for denied access to hybridization.
DENIED_LABEL - Static variable in class net.sf.basedb.util.overview.Validator: Validator rule that checks for denied access to labels.
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_SCAN - Static variable in class net.sf.basedb.util.overview.Validator: Validator rule that checks for denied access to scans.
DENIED_SOFTWARE - Static variable in class net.sf.basedb.util.overview.Validator: Validator rule that checks for denied access to software.
DENSITY - Static variable in class net.sf.basedb.core.Quantity: The id for the Quantity object representing density.
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(Set<Permission>) - Static method in enum net.sf.basedb.core.Permission: Combine the given permission 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
denyValue - Variable in enum net.sf.basedb.core.Permission
denyValue() - Method in enum net.sf.basedb.core.Permission
depth - Variable in class net.sf.basedb.util.Tree.Entry
desc(Expression) - Static method in class net.sf.basedb.core.query.Orders: Sort the result of a query in descending order by the expression.
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.taglib.table.TableColumn
description - Variable in class net.sf.basedb.core.authentication.AuthenticationInformation: A description of the user.
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.FileTypeData
description - Variable in class net.sf.basedb.core.data.GroupData
description - Variable in class net.sf.basedb.core.data.HardwareTypeData
description - Variable in class net.sf.basedb.core.data.HelpData
description - Variable in class net.sf.basedb.core.data.ImageData
description - Variable in class net.sf.basedb.core.data.JobData
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.ProtocolTypeData
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.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.SoftwareTypeData
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.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.info.BioAssaySetInfo
description - Variable in class net.sf.basedb.info.CommonItemInfo
description - Variable in class net.sf.basedb.info.DataFileTypeInfo
description - Variable in class net.sf.basedb.info.ExtendedPropertyInfo
description - Variable in class net.sf.basedb.info.ProjectInfo
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.PluginConfigInfo: Description about the configuration
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.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.ExtractImporter
descriptionMapper - Variable in class net.sf.basedb.plugins.batchimport.HybridizationImporter
descriptionMapper - Variable in class net.sf.basedb.plugins.batchimport.LabeledExtractImporter
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.ScanImporter
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
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.CharacterEncodingFilter
destroy() - Method in class net.sf.basedb.clients.web.servlet.ExtensionsServlet
destroy() - Method in class net.sf.basedb.clients.web.servlet.StartStopServlet: Calls Application.stop().
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
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.ImageLogger
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
dialect - Variable in class net.sf.basedb.core.dbengine.TableInfo
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_LABEL - Static variable in class net.sf.basedb.util.overview.Validator: Validator rule that checks if a parent to a pooled labeled extract has the same lebel.
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.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
directories - Variable in class net.sf.basedb.core.Path: The directory part of the path.
directory - Variable in class net.sf.basedb.clients.web.extensions.ExtensionsFile
directory - Variable in class net.sf.basedb.clients.web.extensions.JspContext
directory - Variable in class net.sf.basedb.clients.web.extensions.Settings
directory - Variable in class net.sf.basedb.core.data.ExperimentData
directory - Variable in class net.sf.basedb.core.data.FileData
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.
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.
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.UserData
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.overview.validator.BasicItemNodeValidatorFactory
disabled - Variable in class net.sf.basedb.util.StaticCache
disabledClazz - Variable in class net.sf.basedb.clients.web.extensions.toolbar.PermissionButtonFactory
disabledExtensionPoints - Variable in class net.sf.basedb.clients.web.extensions.Settings
disabledExtensions - Variable in class net.sf.basedb.clients.web.extensions.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
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
disableFetchProfile(String) - Method in class net.sf.basedb.core.hibernate.SessionWrapper
disableFilter(String) - Method in class net.sf.basedb.core.hibernate.SessionWrapper
disableFilter(Session, String) - Static method in class net.sf.basedb.core.HibernateUtil: Disable the filter with the given name.
disableFilter(String) - Method in class net.sf.basedb.core.QueryRuntimeFilterManager: Disable a filter.
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.
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.
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.
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.
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.
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: Temporarily disconnect from the database.
disconnect() - Method in class net.sf.basedb.core.hibernate.SessionWrapper
disconnectSpotImages() - Method in class net.sf.basedb.core.SpotImages: Disconnects the generated spot image file from this item.
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 - 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 - Variable in class net.sf.basedb.core.DiskUsageStatistics.Summary
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.
DiskUsageStatistics.Summary() - Constructor for class net.sf.basedb.core.DiskUsageStatistics.Summary
DiskUsageStatistics.Summary(User) - Constructor for class net.sf.basedb.core.DiskUsageStatistics.Summary
DiskUsageStatistics.Summary(Group) - Constructor for class net.sf.basedb.core.DiskUsageStatistics.Summary
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
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
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.Image.Format: Returned by the toString method.
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
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
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.menu.Menu
doEndTag() - Method in class net.sf.basedb.clients.web.taglib.Note
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.Columns
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.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.PropertyFilter
doEndTag() - Method in class net.sf.basedb.clients.web.taglib.table.Row
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(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.
doExport() - Method in class net.sf.basedb.util.export.spotdata.AbstractBioAssaySetExporter: Run the export.
doFilter(ServletRequest, ServletResponse, FilterChain) - Method in class net.sf.basedb.clients.web.servlet.CharacterEncodingFilter
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
doGet(HttpServletRequest, HttpServletResponse) - Method in class net.sf.basedb.clients.web.servlet.ViewSpotImage
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.CdfFileReporterImporter
doImport(InputStream, ProgressReporter) - Method in class net.sf.basedb.plugins.HelpImporter
doImport(InputStream, ProgressReporter) - Method in class net.sf.basedb.plugins.PluginConfigurationImporter
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.
doInsert(RawData, String, String, boolean) - Method in class net.sf.basedb.core.RawDataBatcher: Do the actual insert.
doJdbcWork(Session, JdbcWork<R>) - Static method in class net.sf.basedb.core.HibernateUtil: Execute some arbitrary JDBC code using the same database connection as the Hibernate session.
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.
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.
doneOk(String) - 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, 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.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
doPost(HttpServletRequest, HttpServletResponse) - Method in class net.sf.basedb.clients.web.servlet.ViewSpotImage
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.
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.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.Note
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.Columns
doStartTag() - Method in class net.sf.basedb.clients.web.taglib.table.Data
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.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
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
doUpload(OutputStream, UploadedFile) - Method in class net.sf.basedb.clients.web.fileupload.FileUpload: Upload a single file section to the specified output stream
Download - Class in net.sf.basedb.clients.web.servlet
Download() - Constructor for class net.sf.basedb.clients.web.servlet.Download
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.
downloadable - Variable in enum net.sf.basedb.core.Location: If the file can be downloaded from this location.
downloadArrayDesignByType(int, String) - Method in class net.sf.basedb.ws.client.ArrayDesignClient: Downloads an arraydesign as a file, if it is stored as a file in BASE.
downloadArrayDesignByType(String, int, String) - Method in class net.sf.basedb.ws.server.ArrayDesignService: Returns array design file of a certain type, attached to an OMElement.
downloadBioAssaySet(int, String, String[], String[], boolean) - Method in class net.sf.basedb.ws.client.BioAssaySetClient: Deprecated. In 2.12. See BioAssaySetService.downloadBioAssaySet(String, int, String, String[], String[], Boolean) for more information. Use BioAssaySetClient.downloadDataFile(int, String) instead.
downloadBioAssaySet(String, int, String, String[], String[], Boolean) - Method in class net.sf.basedb.ws.server.BioAssaySetService: Deprecated. In 2.12. Spot data should not be exported dynamically. Instead, plug-ins should be used and attach the result to the bioassay set and the files can then be downloaded when needed. Use BioAssaySetService.downloadDataFile(String, int, String) instead.
downloadCache - Variable in class net.sf.basedb.core.File: Files that are EXTERNAL are cached locally per transaction
downloadDataFile(int, String) - Method in class net.sf.basedb.ws.client.BioAssaySetClient: Gets spot data as a file for a bioassay set if it is stored in a file in BASE.
downloadDataFile(String, int, String) - Method in class net.sf.basedb.ws.server.BioAssaySetService: Returns a data file of a certain type attached to an OMElement.
downloadImmediately(ExportOutputStream, ProgressReporter) - Method in class net.sf.basedb.core.PluginResponse
downloadRawDataByType(int, String) - Method in class net.sf.basedb.ws.client.RawBioAssayClient: Gets RawData as a file for a rawbioassay if it is stored in a file in BASE.
downloadRawDataByType(String, int, String) - Method in class net.sf.basedb.ws.server.RawBioAssayService: Returns a rawdata file of a certain type attached to an OMElement.
downloadReporters(ExtendedPropertyInfo[], QueryOptions) - Method in class net.sf.basedb.ws.client.ReporterClient: Downloads exported reporter properties to an input stream.
downloadReporters(String, ExtendedPropertyInfo[], QueryOptions) - Method in class net.sf.basedb.ws.server.ReporterService: Attach a file with exported reporter properties so it can be send through web services.
downloadReportersInList(int, ExtendedPropertyInfo[], QueryOptions) - Method in class net.sf.basedb.ws.client.ReporterClient: Gets an input stream for a file with info about reporters in a reporter list.
downloadReportersInList(String, int, ExtendedPropertyInfo[], QueryOptions) - Method in class net.sf.basedb.ws.server.ReporterService: Gets an input stream to exported data from a reporter list.
doWork(Work) - Method in class net.sf.basedb.core.hibernate.SessionWrapper
dropAllTables() - Method in class net.sf.basedb.core.VirtualDb: Drop all real database tables in this virtual database.
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.batchimport.AbstractItemImporter
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.XMLUtil.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
DUPLICATE_ARRAY_NUM - Static variable in class net.sf.basedb.util.overview.Validator: Validator rule that checks if the same sub-array index is used on more than one raw bioassay from the same scan.
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(Throwable) - Constructor for exception net.sf.basedb.clients.web.DuplicateWizardException: Create a new exception with a cause.
DuplicateWizardException(String, Throwable) - Constructor for exception net.sf.basedb.clients.web.DuplicateWizardException: Create a new exception with a cause and a message.
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
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, 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.
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.ExtraValueJoiner(JoinType) - Constructor for class net.sf.basedb.core.DynamicPositionQueryJoiners.ExtraValueJoiner
DynamicPositionQueryJoiners.ReporterJoiner - Class in net.sf.basedb.core: Joiner for reporters
DynamicPositionQueryJoiners.ReporterJoiner(JoinType) - Constructor for class net.sf.basedb.core.DynamicPositionQueryJoiners.ReporterJoiner
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.
DynamicQueryWrapper - Class in net.sf.basedb.clients.web.plugins: A query wrapper for DynamicQuery:s.
DynamicQueryWrapper(DbControl, DynamicQuery) - 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.
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.
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.
DynamicResultIterator.SqlResultImpl() - Constructor for class net.sf.basedb.core.DynamicResultIterator.SqlResultImpl
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.ExtraValueJoiner(JoinType) - Constructor for class net.sf.basedb.core.DynamicSpotQueryJoiners.ExtraValueJoiner
DynamicSpotQueryJoiners.RawDataJoiner - Class in net.sf.basedb.core: Joiner for raw data.
DynamicSpotQueryJoiners.RawDataJoiner(JoinType) - Constructor for class net.sf.basedb.core.DynamicSpotQueryJoiners.RawDataJoiner
DynamicSpotQueryJoiners.ReporterJoiner - Class in net.sf.basedb.core: Joiner for reporters
DynamicSpotQueryJoiners.ReporterJoiner(JoinType) - Constructor for class net.sf.basedb.core.DynamicSpotQueryJoiners.ReporterJoiner
DynamicSpotQueryJoiners.ReporterListJoiner - Class in net.sf.basedb.core: Joiner for reporter lists.
DynamicSpotQueryJoiners.ReporterListJoiner(JoinType) - Constructor for class net.sf.basedb.core.DynamicSpotQueryJoiners.ReporterListJoiner
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
DynamicUtil.SelectedInfo(List<String>, List<String>, List<TableColumn>) - Constructor for class net.sf.basedb.clients.web.DynamicUtil.SelectedInfo

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
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.AuthenticationInformation: The email address to the user.
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_STRING - Static variable in class net.sf.basedb.clients.web.fileupload.FileUpload
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.InternalStorageController.StorageKeyring
emptySet - Variable in class net.sf.basedb.core.InternalJobQueue.JobQueueKeyring
emptySet - Variable in class net.sf.basedb.core.InternalStorageController.StorageKeyring
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.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.toolbar.PermissionButtonFactory
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.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.clients.web.extensions.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.clients.web.extensions.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(Session, String) - Static method in class net.sf.basedb.core.HibernateUtil: Enable the filter with the given name.
enableFilter(String) - Method in class net.sf.basedb.core.QueryRuntimeFilterManager: Enable a filter, unless it has already been enabled
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.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.User.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.
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
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.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
encodeTags(String, Pattern) - Static method in class net.sf.basedb.clients.web.util.HTML
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.
end - Variable in class net.sf.basedb.clients.web.fileupload.FileUpload.UploadStream
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.BfsExporterPlugin
end(boolean) - Method in class net.sf.basedb.plugins.BioAssaySetExporter: Deprecated.
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 - Variable in class net.sf.basedb.util.ChainedProgressReporter
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.
endDate - Variable in class net.sf.basedb.core.data.NewsData
endDocument() - Method in interface net.sf.basedb.clients.web.plugins.ExportTemplate: End writing the document.
endDocument() - Method in class net.sf.basedb.clients.web.plugins.PlainTextTemplate: Do nothing.
endDocument() - 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.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
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.XMLTemplate: Write the current item element to the export stream.
endTime - Variable in class net.sf.basedb.clients.web.extensions.ScanResults
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.
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(EntityLogger, 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.
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.
EntityQuery - Interface in net.sf.basedb.core.query: This a HQL query that return enitities, ie. items.
EntityQueryWrapper - 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) - 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_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.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.ExperimentData
entryDate - Variable in class net.sf.basedb.core.data.ExtraValueTypeData
entryDate - Variable in class net.sf.basedb.core.data.FileTypeData
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.HardwareTypeData
entryDate - Variable in class net.sf.basedb.core.data.LabelData
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.ProtocolTypeData
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.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.ScanData
entryDate - Variable in class net.sf.basedb.core.data.SoftwareData
entryDate - Variable in class net.sf.basedb.core.data.SoftwareTypeData
entryDate - Variable in class net.sf.basedb.core.data.UserData
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.
enumeration - Variable in class net.sf.basedb.clients.web.taglib.table.ColumnDef
enumeration - Variable in class net.sf.basedb.core.ParameterType: List of allowed values.
enumeration - Variable in class net.sf.basedb.info.AnnotationTypeInfo
Enumeration<K,V> - Class in net.sf.basedb.util
Enumeration() - Constructor for class net.sf.basedb.util.Enumeration
Enumeration.Entry<K,V> - Class in net.sf.basedb.util
Enumeration.Entry(K, V) - Constructor for class net.sf.basedb.util.Enumeration.Entry
enumerationValues - Variable in class net.sf.basedb.core.data.AnnotationTypeData
enumOptions - Variable in class net.sf.basedb.plugins.Base1PluginExecuter.JobParameter
enumValues - Variable in class net.sf.basedb.info.AnnotationTypeInfo
eof() - Method in class net.sf.basedb.clients.web.fileupload.FileUpload: Check if the end of the upload has been reached or not.
eof - Variable in class net.sf.basedb.clients.web.fileupload.FileUpload.UploadStatus: TRUE if the end of the stream is reached, FALSE otherwise
ep - Variable in class net.sf.basedb.clients.web.formatter.ExtendedPropertyFormatter
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.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.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.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.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.toolbar.ToolbarUtil: ID:s for the toolbar extension point that appear on all pages that displays Shareable items.
eq(AnnotationType, Object, boolean) - Static method in class net.sf.basedb.core.query.Annotations: Deprecated. Use Annotations.eq(String, AnnotationType, Object, boolean) instead with alias=null
eq(String, AnnotationType, Object, boolean) - Static method in class net.sf.basedb.core.query.Annotations: Create a restriction that searches for annotations equal to a given value on the root or a joined entity of a query.
eq(Expression, Expression) - Static method in class net.sf.basedb.core.query.Restrictions: Compare if two expressions are equal: new restriction = e1 == e2.
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.ExtensionsFile
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.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.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.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.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.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 and property 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.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 have the same arrayNum.
equals(Object, Object) - Static method in class net.sf.basedb.util.EqualsHelper: Check if two objects are equal according to their equals implementation.
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.Registry.AttributeKey
equals(Object) - Method in class net.sf.basedb.util.jobagent.JobInfo
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.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
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.util.FileCopyRunnable
error(SAXParseException) - Method in class net.sf.basedb.util.XMLUtil.Validator: Errors thrown with a detailed error message.
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 - 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.
errorHandler - Variable in class net.sf.basedb.util.extensions.ExtensionPointContext
ErrorHandlerFactory<A extends Action> - Interface in net.sf.basedb.util.extensions: Error handler factories are responsible for creating error handlers.
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
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
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
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(AnnotationSnapshot) - Method in class net.sf.basedb.core.snapshot.AnnotationFilter
evaluate(AnnotationSnapshot) - Method in class net.sf.basedb.core.snapshot.AnnotationTypeFilter
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(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
evaluate(Node) - Method in class net.sf.basedb.util.overview.filter.BasicItemFilter
evaluate(Node) - Method in class net.sf.basedb.util.overview.filter.ItemTypeFilter
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.BioMaterialSourceEventData
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.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<T> - Class in net.sf.basedb.util.bfs: Defines an event type that is sent in event notifications to event handlers.
EventType(String) - Constructor for class net.sf.basedb.util.bfs.EventType: Create a new event type object.
EventType - Class in net.sf.basedb.util.extensions.events: Represents different types of event.
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.
exception - Variable in class net.sf.basedb.clients.web.fileupload.FileUploadProgress
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(Include...) - Method in class net.sf.basedb.core.AbstractEntityQuery
exclude(Collection<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.
exclude(Collection<Include>) - Method in interface net.sf.basedb.core.query.EntityQuery
exclude - Variable in class net.sf.basedb.plugins.LowessNormalization.SpotData
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.ExecuteUpdateWork: 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.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(ProgressReporter, String) - 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: Start the execution sequence for a job.
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(Query) - Static method in class net.sf.basedb.core.HibernateUtil: Exceute an update or delete query.
executeUpdate(PreparedStatement, SessionControl) - Static method in class net.sf.basedb.core.QueryExecutor: Execute a query by calling PreparedStatement.executeUpdate().
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.
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.clients.web.extensions.ExtensionsFile: Check if the file really exists on the disk.
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.
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) - Static method in class net.sf.basedb.util.JarClassLoader: Check if a class loader for the given JAR file exists.
exists - Variable in class net.sf.basedb.util.PluginConfigInfo
exists() - Method in class net.sf.basedb.util.PluginConfigInfo: If plug-in configuration with the same name already exists or not.
exists(String) - Method in class net.sf.basedb.util.StaticCache: Checks if a cache entry exists 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.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.TransformationData
experiment - Variable in class net.sf.basedb.core.data.VirtualDbData
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 - Static variable in class net.sf.basedb.core.QuotaType: The ID for experiments.
experiment - Variable in class net.sf.basedb.plugins.IlluminaRawDataImporter
experiment - Variable in class net.sf.basedb.util.overview.ExperimentOverview: Deprecated.
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
ExperimentClient - Class in net.sf.basedb.ws.client: Webservice client for Experiment.
ExperimentClient(SessionClient) - Constructor for class net.sf.basedb.ws.client.ExperimentClient: Creates a new client in active session
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
experimentDesign - Variable in class net.sf.basedb.info.ExperimentInfo
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.AnnotationGroup(int, Set<T>, int, Formatter<T>) - Constructor for class net.sf.basedb.clients.web.ExperimentExplorer.AnnotationGroup
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.AnnotationSummary(ExperimentExplorer, DbControl, AnnotationType) - Constructor for class net.sf.basedb.clients.web.ExperimentExplorer.AnnotationSummary
ExperimentExplorer.ReporterPositions - Class in net.sf.basedb.clients.web: Cache entry for a reporter with positions.
ExperimentExplorer.ReporterPositions(int, int[]) - Constructor for class net.sf.basedb.clients.web.ExperimentExplorer.ReporterPositions
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.
ExperimentExplorerPlotServlet.ColumnKey(Comparable, String) - Constructor for class net.sf.basedb.clients.web.servlet.ExperimentExplorerPlotServlet.ColumnKey
ExperimentInfo - Class in net.sf.basedb.info: Holds information about an Experiment item from BASE.
ExperimentInfo() - Constructor for class net.sf.basedb.info.ExperimentInfo: Creates an info-object with no properties set.
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
ExperimentOverview - Class in net.sf.basedb.util.overview: Deprecated. (In 2.10) Use GenericOverview instead
ExperimentOverview(Experiment, Project) - Constructor for class net.sf.basedb.util.overview.ExperimentOverview: Deprecated. Create a new overview for the experiment using defaults from the specified project.
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
ExperimentService - Class in net.sf.basedb.ws.server: Web Service class for Experiment
ExperimentService() - Constructor for class net.sf.basedb.ws.server.ExperimentService
experimentType - Variable in class net.sf.basedb.core.data.ExperimentData
experimentType - Variable in class net.sf.basedb.info.ExperimentInfo
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.UserData
explorer - Variable in class net.sf.basedb.clients.web.ExperimentExplorer.AnnotationSummary
exponent - Variable in class net.sf.basedb.core.query.PowerExpression
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
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.
exportBaseFileMatrix(BioAssaySet, File, Map<String, String>, List<String>, List<String>, Boolean) - Method in class net.sf.basedb.plugins.BioAssaySetExporter: Deprecated. In 2.11 and 2.12, use MatrixBaseFileExporter instead
exportBaseFileMatrix(BioAssaySet, File, Map<String, String>, List<String>, List<String>, Boolean, ProgressReporter) - Method in class net.sf.basedb.plugins.BioAssaySetExporter: Deprecated. In 2.12, use MatrixBaseFileExporter instead
exportBaseFileMatrix(BioAssaySet, OutputStream, Map<String, String>, List<String>, List<String>, boolean) - Method in class net.sf.basedb.plugins.BioAssaySetExporter: Deprecated. In 2.11 and 2.12, use MatrixBaseFileExporter instead.
exportBaseFileMatrix(BioAssaySet, OutputStream, Map<String, String>, List<String>, List<String>, boolean, ProgressReporter) - Method in class net.sf.basedb.plugins.BioAssaySetExporter: Deprecated. In 2.11 and 2.12, use MatrixBaseFileExporter instead.
exportBaseFileSectionAssays(PrintWriter, DbControl, BioAssaySet) - Method in class net.sf.basedb.plugins.BioAssaySetExporter: Deprecated.
exportBaseFileSectionHead(PrintWriter, Map<String, String>) - Method in class net.sf.basedb.plugins.BioAssaySetExporter: Deprecated.
exportBaseFileSectionSpots(PrintWriter, DbControl, BioAssaySet, DynamicSpotQuery, List<String>, List<String>, List<BioAssay>, Map<String, BioAssaySetExporter.QueryItem>, long, boolean, Map<Integer, String>, ProgressReporter) - Method in class net.sf.basedb.plugins.BioAssaySetExporter: Deprecated.
exportBaseFileSerial(BioAssaySet, File, Map<String, String>, List<String>, List<String>, Boolean) - Method in class net.sf.basedb.plugins.BioAssaySetExporter: Deprecated. In 2.11 and 2.12, use SerialBaseFileExporter instead.
exportBaseFileSerial(BioAssaySet, File, Map<String, String>, List<String>, List<String>, Boolean, ProgressReporter) - Method in class net.sf.basedb.plugins.BioAssaySetExporter: Deprecated. In 2.12, use SerialBaseFileExporter instead.
exportBaseFileSerial(BioAssaySet, OutputStream, Map<String, String>, List<String>, List<String>, boolean) - Method in class net.sf.basedb.plugins.BioAssaySetExporter: Deprecated. In 2.11 and 2.12, use SerialBaseFileExporter instead.
exportBaseFileSerial(BioAssaySet, OutputStream, Map<String, String>, List<String>, List<String>, boolean, ProgressReporter) - Method in class net.sf.basedb.plugins.BioAssaySetExporter: Deprecated. In 2.12, use SerialBaseFileExporter instead.
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, Unit, Formatter, DataLoader) - Constructor for class net.sf.basedb.clients.web.plugins.ExportedProperty
exporter - Variable in class net.sf.basedb.plugins.executor.ExternalProgramExecutor
exportGal(DbControl, ArrayDesign, PrintWriter, ProgressReporter) - Method in class net.sf.basedb.plugins.GalExporter: Deprecated. Use GalExporter.exportGal(DbControl, ArrayDesign, Integer, PrintWriter, ProgressReporter) instead
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.
exportMeV(BioAssaySet, OutputStream, ProgressReporter) - Method in class net.sf.basedb.plugins.BioAssaySetExporter: Deprecated. In 2.12, use extension package found at http://baseplugins.thep.lu.se/wiki/net.sf.basedb.mev instead
exportName - Variable in class net.sf.basedb.plugins.BioAssaySetExporter.QueryItem: Deprecated.
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.
exportPlainMatrix(BioAssaySet, OutputStream, ProgressReporter) - Method in class net.sf.basedb.plugins.BioAssaySetExporter: Deprecated. In 2.12, no direct replacement, write a subclass of AbstractBioAssaySetExporter instead
exportProperties(DbControl, ExportOutputStream, 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.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.core.query.AscOrder
expression - Variable in class net.sf.basedb.core.query.DescOrder
Expression - Interface in net.sf.basedb.core.query: An expression query element.
expression(String, String) - Static method in class net.sf.basedb.core.query.Hql
expression - Variable in class net.sf.basedb.core.query.HqlExpression: The restriction or expression as a string.
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 - 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
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.
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 - 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
extendedProperties - Variable in class net.sf.basedb.core.ReporterBatcher: The extended properties for reporters
extendedPropertiesFile - Static variable in class net.sf.basedb.core.Application: The path to the file containing extended properties.
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, 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.
ExtendedPropertyAccessor.GetterSetter(Class, String) - Constructor for class net.sf.basedb.core.ExtendedPropertyAccessor.GetterSetter: Create a new getter or setter.
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.
ExtendedPropertyInfo - Class in net.sf.basedb.info: Class to hold information about an extended property in Base ExtendedProperty.
ExtendedPropertyInfo() - Constructor for class net.sf.basedb.info.ExtendedPropertyInfo: Creates an object with no property set.
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.info.DataFileTypeInfo
Extension<A extends Action> - Interface in net.sf.basedb.util.extensions: Represents a concrete implementation of an extension to an extension point.
extension - Variable in class net.sf.basedb.util.extensions.ExtensionContext
EXTENSION_POINT_ID - Static variable in class net.sf.basedb.clients.web.extensions.service.Services
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.
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
extensionId - Variable in class net.sf.basedb.clients.web.extensions.service.DummyService
extensionIsRegistered(String) - Method in class net.sf.basedb.util.extensions.Registry: Checks if an extension is registered or not.
extensionPoint - Variable in class net.sf.basedb.util.extensions.ExtensionBean
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 - Variable in class net.sf.basedb.util.extensions.ExtensionPointContext
extensionPoint - Variable in class net.sf.basedb.util.extensions.Registry.RegisteredExtension
EXTENSIONPOINT_COMPARATOR - Static variable in class net.sf.basedb.util.extensions.Registry
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(ExtensionPoint) - Constructor for class net.sf.basedb.util.extensions.events.ExtensionPointEventFilter: Create a new extension point event filter.
ExtensionPointEventFilter(String) - Constructor for class net.sf.basedb.util.extensions.events.ExtensionPointEventFilter: Create a new extension point event filter
extensionPointIsRegistered(String) - Method in class net.sf.basedb.util.extensions.Registry: Checks if an extension point is registered or not.
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 - 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.Registry
extensions - Variable in class net.sf.basedb.util.extensions.Registry.RegisteredExtensionPoint
extensions - Variable in class net.sf.basedb.util.extensions.xml.XmlLoader
EXTENSIONS_URL - Static variable in class net.sf.basedb.clients.web.extensions.ExtensionsControl: The location where the extension system is looking for extensions.
EXTENSIONS_URL - Static variable in class net.sf.basedb.clients.web.extensions.XJspCompiler: The location where the extension system is looking for extensions.
ExtensionsControl - Class in net.sf.basedb.clients.web.extensions: Controller class for the extension system in the web client.
ExtensionsControl(Set<Permission>) - Constructor for class net.sf.basedb.clients.web.extensions.ExtensionsControl
ExtensionsControl.AutoInstallTask - Class in net.sf.basedb.clients.web.extensions: Task for starting an automatic check for new/updated/deleted extensions.
ExtensionsControl.AutoInstallTask() - Constructor for class net.sf.basedb.clients.web.extensions.ExtensionsControl.AutoInstallTask
extensionsDir - Static variable in class net.sf.basedb.clients.web.extensions.ExtensionsControl
extensionsDir - Variable in class net.sf.basedb.clients.web.extensions.ExtensionsDirectory
ExtensionsDirectory - Class in net.sf.basedb.clients.web.extensions: Represents a directory with extensions.
ExtensionsDirectory(File, File, String, String) - Constructor for class net.sf.basedb.clients.web.extensions.ExtensionsDirectory
ExtensionsFile - Class in net.sf.basedb.clients.web.extensions: Represents a single extensions XML file or a JAR file containing extensions.
ExtensionsFile(ExtensionsDirectory, File, File, XmlLoader) - Constructor for class net.sf.basedb.clients.web.extensions.ExtensionsFile: Create a new object.
ExtensionsFilter - Interface in net.sf.basedb.util.extensions: Allows extensions and extension points to be enabled/disabled and sorted externally.
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(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
ExtensionsServlet - Class in net.sf.basedb.clients.web.servlet: Servlet for starting the extension system when the web server starts.
ExtensionsServlet() - Constructor for class net.sf.basedb.clients.web.servlet.ExtensionsServlet
EXTERNAL_ID - Static variable in class net.sf.basedb.plugins.batchimport.PropertyIdMethod: Use the external ID for finding items.
externalClientId - Variable in class net.sf.basedb.core.SessionControl: The external id of the ClientData. null = no client
externalId - Variable in class net.sf.basedb.clients.jobagent.Agent
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.BioMaterialListData
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.JobAgentData
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.info.AnnotationTypeInfo
externalId - Variable in class net.sf.basedb.info.DataFileTypeInfo
externalId - Variable in class net.sf.basedb.info.ReporterListInfo
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.BioSourceImporter
externalIdMapper - Variable in class net.sf.basedb.plugins.batchimport.ExtractImporter
externalIdMapper - Variable in class net.sf.basedb.plugins.batchimport.LabeledExtractImporter
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.RequestWrapper(String, Request) - Constructor for class net.sf.basedb.plugins.executor.ExternalProgramExecutor.RequestWrapper
ExternalProgramExecutor.ResponseWrapper - Class in net.sf.basedb.plugins.executor
ExternalProgramExecutor.ResponseWrapper() - Constructor for class net.sf.basedb.plugins.executor.ExternalProgramExecutor.ResponseWrapper
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 - Class in net.sf.basedb.core: This class is used to represent extract items.
Extract(ExtractData) - Constructor for class net.sf.basedb.core.Extract
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.
ExtractData - Class in net.sf.basedb.core.data: This represents an extract.
ExtractData() - Constructor for class net.sf.basedb.core.data.ExtractData
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.ProtocolType: 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
extractMetadata(DbControl) - Method in class net.sf.basedb.core.filehandler.CdfFileHandler: Reads the number of probesets in the CDF file and stores it in ArrayDesign.getNumFileFeatures().
extractMetadata(DbControl) - Method in class net.sf.basedb.core.filehandler.CelFileHandler
extractMetadata(DbControl) - Method in interface net.sf.basedb.core.filehandler.DataFileMetadataReader: Extract metadata from the file(s) and write the metadata to the item passed to the DataFileHandler.setItem(net.sf.basedb.core.FileStoreEnabled) method.
extractMetadata(DbControl) - Method in class net.sf.basedb.core.FileSet.DataFileHandlerWrapper
extractQuery - Variable in class net.sf.basedb.plugins.batchimport.AbstractItemImporter
extractResources(boolean, ScanResults) - Method in class net.sf.basedb.clients.web.extensions.ExtensionsDirectory: Extract resources from JAR files.
extractResources(Pattern, String, boolean) - Method in class net.sf.basedb.clients.web.extensions.ExtensionsFile: Extract resources from a JAR file to a directory.
ExtractToLabeledExtractTransformer - Class in net.sf.basedb.util.biomaterial: Collection transformer that given a collection of extracts finds all labeled extracts that has the extracts as parents.
ExtractToLabeledExtractTransformer(DbControl) - Constructor for class net.sf.basedb.util.biomaterial.ExtractToLabeledExtractTransformer: Create a new Extract-to-labeled extract transformer.
ExtractToSampleTransformer - Class in net.sf.basedb.util.biomaterial: Collection transformer that given a collection of extracts finds their parent samples.
ExtractToSampleTransformer(DbControl) - Constructor for class net.sf.basedb.util.biomaterial.ExtractToSampleTransformer
ExtractValidator - Class in net.sf.basedb.util.overview.validator: Validator implementation for extracts.
ExtractValidator() - Constructor for class net.sf.basedb.util.overview.validator.ExtractValidator
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.
extraFileImporter - Variable in class net.sf.basedb.util.importer.spotdata.BfsImporter
extraFiles - Variable in class net.sf.basedb.util.export.spotdata.BfsExporter
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
extraNo - Variable in class net.sf.basedb.core.data.DataCubeExtraValueData
extraQuery - Variable in class net.sf.basedb.util.export.spotdata.AbstractFieldConverter
extraQuery - Variable in class net.sf.basedb.util.export.spotdata.FieldConverter: Deprecated.
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
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 - 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(ExtraValue) - Static method in class net.sf.basedb.core.query.Dynamic: Create an expression representing the extra value of a spot or position.
extraValue - Variable in class net.sf.basedb.core.SpotExtraValueBatcher: The extra value object which links the extra value type.
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(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.CoordinateType - Enum in net.sf.basedb.core: Defines which coordinates in the data cube the extra values are attached to.
ExtraValue.CoordinateType(int) - Constructor for enum net.sf.basedb.core.ExtraValue.CoordinateType
EXTRAVALUE_DATA - Static variable in class net.sf.basedb.core.FileType: The id for the FileType item representing a file containing analysed extra value data.
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, BioAssaySet) - Constructor for class net.sf.basedb.util.jep.ExtraValueFunction: Create a new instance of this function.
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.
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.
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.
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
 
Factories - Class in net.sf.basedb.ws.client
Utility class for keeping the default factory implementations.
Factories() - 
Constructor for class net.sf.basedb.ws.client.Factories
 
factorQuery - 
Variable in class net.sf.basedb.util.export.spotdata.AbstractFieldConverter
 
factoryKey - 
Variable in class net.sf.basedb.util.overview.loader.BasicItemNodeLoader
 
factoryParameters - 
Variable in class net.sf.basedb.util.extensions.xml.XmlLoader
 
failIfItemExists - 
Variable in class net.sf.basedb.plugins.batchimport.AbstractItemImporter
 
failIfMultipleArrayIndex - 
Variable in class net.sf.basedb.plugins.batchimport.HybridizationImporter
 
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
 
failIfNotFoundItems - 
Variable in class net.sf.basedb.plugins.batchimport.AbstractItemImporter
 
failIfNotFoundReference - 
Variable in class net.sf.basedb.plugins.batchimport.AbstractItemImporter
 
failIfNoUsePermissionToReference - 
Variable in class net.sf.basedb.plugins.batchimport.AbstractItemImporter
 
failIfNoWritePermissionToItem - 
Variable in class net.sf.basedb.plugins.batchimport.AbstractItemImporter
 
failIfTooManyValues - 
Variable in class net.sf.basedb.plugins.AnnotationFlatFileImporter
 
failIfUsed - 
Variable in class net.sf.basedb.plugins.ReporterFlatFileImporter
 
Failure - Class in net.sf.basedb.util.overview
Holds information about a failed validation.
Failure(Validator, Node) - 
Constructor for class net.sf.basedb.util.overview.Failure
Create a new validation failure.
Failure(Validator, Node, String) - 
Constructor for class net.sf.basedb.util.overview.Failure
Create a new validation failure with a detailed message.
Failure(Validator, 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.ExperimentOverview
Deprecated.  
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.
falseValue - 
Variable in enum net.sf.basedb.util.formatter.BooleanFormatter.Type
 
fatalError(SAXParseException) - 
Method in class net.sf.basedb.util.XMLUtil.Validator
Fatal errors thrown with a detailed error message.
fax - 
Variable in class net.sf.basedb.core.authentication.AuthenticationInformation
The fax number to the user.
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_EXTRACTION - 
Static variable in class net.sf.basedb.core.ProtocolType
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.SoftwareType
The id for the SoftwareType item representing the
                softwaretype "feature extraction software".
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, WellData) - 
Constructor for class net.sf.basedb.core.data.FeatureData
Create a new feature which is linked to a well.
FeatureData(ArrayDesignBlockData, ReporterData) - 
Constructor for class net.sf.basedb.core.data.FeatureData
Create a new feature which is linked to a reporter only.
featureDiameter - 
Variable in class net.sf.basedb.core.data.ArrayDesignBlockData
 
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.
featureMismatchErrorParameter - 
Static variable in class net.sf.basedb.plugins.IlluminaRawDataImporter
 
featureMismatchErrorParameter - 
Static variable in class net.sf.basedb.plugins.RawDataFlatFileImporter
 
featureQuery - 
Variable in class net.sf.basedb.plugins.batchimport.AbstractItemImporter
 
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
 
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.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
 
FieldConverter - Class in net.sf.basedb.util.export.spotdata
Deprecated. In 2.15. This implementation is Base1-specific. It 
                has been replaced with Base1FieldConverter
FieldConverter(DbControl, BioAssaySet) - 
Constructor for class net.sf.basedb.util.export.spotdata.FieldConverter
Deprecated. Create a new converter for the given bioassay set.
file - 
Variable in class net.sf.basedb.clients.web.extensions.ExtensionsFile
 
file - 
Variable in class net.sf.basedb.clients.web.extensions.Settings
 
file - 
Variable in class net.sf.basedb.core.data.FileSetMemberData
 
file - 
Variable in class net.sf.basedb.core.data.ImageData
 
file - 
Variable in class net.sf.basedb.core.data.ProtocolData
 
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 - 
Variable in class net.sf.basedb.core.File.UploadStream
The file to write to.
FILE - 
Static variable in class net.sf.basedb.core.QuotaType
The ID for the file.
file - 
Variable in class net.sf.basedb.util.AutoDetectFileFormat.IsImportableFilter
 
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 - 
Variable in class net.sf.basedb.ws.server.BaseFileDataSource
 
file - 
Variable in class net.sf.basedb.ws.server.TempFileDataSource.TempInputStream
 
File.Action - Enum in net.sf.basedb.core
A fileaction describes if a file should be moved to secondary storage 
                or brought back from it.
File.Action(int) - 
Constructor for enum net.sf.basedb.core.File.Action
Creates a new fileaction.
File.UploadStream - Class in net.sf.basedb.core
This class is used for uploading a file.
File.UploadStream(File, boolean, boolean, boolean) - 
Constructor for class net.sf.basedb.core.File.UploadStream
Create a new UploadStream and connect it to the
                        given file.
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.
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.
fileColumnMapping - 
Static variable in class net.sf.basedb.plugins.batchimport.ArrayDesignImporter
 
fileColumnMapping - 
Static variable in class net.sf.basedb.plugins.batchimport.RawBioAssayImporter
 
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
 
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
 
fileGui - 
Static variable in class net.sf.basedb.plugins.PackedFileExporter
 
fileId - 
Variable in class net.sf.basedb.util.importer.spotdata.BaseFileInfo.ChildBioAssay
 
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
 
fileMapper - 
Variable in class net.sf.basedb.plugins.batchimport.ArrayDesignImporter
 
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.clients.web.extensions.ScanResults
 
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.core.FileSet.DataFileHandlerWrapper
 
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
 
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
 
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.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.DataFileHandlerWrapper - Class in net.sf.basedb.core
Wraps a DataFileValidator and /or DataFileMetadataReader.
FileSet.DataFileHandlerWrapper(DataFileHandler, FileStoreEnabled) - 
Constructor for class net.sf.basedb.core.FileSet.DataFileHandlerWrapper
 
FileSet.QueryRuntimeFilterImpl - Class in net.sf.basedb.core
 
FileSet.QueryRuntimeFilterImpl() - 
Constructor for class net.sf.basedb.core.FileSet.QueryRuntimeFilterImpl
 
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.QueryRuntimeFilterImpl - Class in net.sf.basedb.core
 
FileSetMember.QueryRuntimeFilterImpl() - 
Constructor for class net.sf.basedb.core.FileSetMember.QueryRuntimeFilterImpl
 
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
 
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() - 
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
 
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.core.data.FileData
 
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.MimeTypeData
 
fileType - 
Variable in class net.sf.basedb.core.data.PlatformFileTypeData
 
FileType - Class in net.sf.basedb.core
This class is used to represent the type of
        File items in BASE.
FileType(FileTypeData) - 
Constructor for class net.sf.basedb.core.FileType
Creates a new filetype item from the given data.
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.RawBioAssayImporter
 
FileTypeData - Class in net.sf.basedb.core.data
This class hols information about the different filetyped
FileTypeData() - 
Constructor for class net.sf.basedb.core.data.FileTypeData
 
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.RawBioAssayImporter
 
fileTypeQuery - 
Variable in class net.sf.basedb.plugins.batchimport.AbstractItemImporter
 
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.SectionHeaders(String, String, String) - 
Constructor for class net.sf.basedb.clients.web.fileupload.FileUpload.SectionHeaders
 
FileUpload.UploadStatus - Class in net.sf.basedb.clients.web.fileupload
This class contains information about the read status on the ServletInputStream
FileUpload.UploadStatus() - 
Constructor for class net.sf.basedb.clients.web.fileupload.FileUpload.UploadStatus
Create a new UploadStatus object.
FileUpload.UploadStream - Class in net.sf.basedb.clients.web.fileupload
 
FileUpload.UploadStream() - 
Constructor for class net.sf.basedb.clients.web.fileupload.FileUpload.UploadStream
 
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
 
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 - 
Static variable in class net.sf.basedb.core.VirtualColumn
This column stores the data cube filter number.
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(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 - 
Variable in class net.sf.basedb.util.IncludeExcludeFilter
 
filter - 
Variable in class net.sf.basedb.util.StaticCache.CleanupTask
 
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
 
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.
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.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.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.
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
 
finalize() - 
Method in class net.sf.basedb.core.DbControl
Clean up if a bad client application forgot to close the connection.
finalize() - 
Method in class net.sf.basedb.core.SessionControl
Clean up if a bad client application forgets to logout.
finalize() - 
Method in class net.sf.basedb.util.StaticCache.LockSafeInputStream
 
finalize() - 
Method in class net.sf.basedb.util.StaticCache.LockSafeOutputStream
 
finalize() - 
Method in class net.sf.basedb.ws.server.TempFileDataSource.TempInputStream
 
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 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
Use getById method to find an item.
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_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].
findAnnotation(AnnotationType) - 
Method in class net.sf.basedb.core.AnnotationSet
Deprecated. Use AnnotationSet.findAnnotations(DbControl, AnnotationType, Boolean) instead
findAnnotations(DbControl, AnnotationType, Boolean) - 
Method in class net.sf.basedb.core.AnnotationSet
Find annotations of the specified annotation type among all annotations
                including the inherited annotations.
findAnnotations(DbControl, AnnotationSetSnapshot, Filter<? super AnnotationSnapshot>, boolean) - 
Method in class net.sf.basedb.core.snapshot.SnapshotManager
Search in a snapshot for all annotations of a specified annotation type.
findAnnotations(DbControl, Annotatable, Filter<? super AnnotationSnapshot>, boolean) - 
Method in class net.sf.basedb.core.snapshot.SnapshotManager
Utility method for calling getSnapshot and findAnnotations
                in one go.
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.
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
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
 
findColumn(String) - 
Method in class net.sf.basedb.util.parser.ColFunction
Find column index by checking each column header against a
                regular expression.
findColumn - 
Static variable in class net.sf.basedb.util.parser.FlatFileParser
Pattern used to find column mappings in a string, ie. abc \col\ def
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.
findDirtyCollections() - 
Method in class net.sf.basedb.core.log.EntityDetails
We must do this from the constructor since the "dirtyness" of a
                collection is reset after flush the SQL to the database, which is 
                completed before the rest of the logging is done.
findExtract(DbControl, IdMethod, String) - 
Method in class net.sf.basedb.plugins.batchimport.AbstractItemImporter
Find an extract with a given identifier.
findFeatureExtractionSoftware(DbControl, IdMethod, String) - 
Method in class net.sf.basedb.plugins.batchimport.AbstractItemImporter
Find a feature extraction software with a given identifier.
findFiles(File, FileFilter) - 
Static method in class net.sf.basedb.util.FileUtil
Find files matching a given filter in a directory.
findFreezer(DbControl, IdMethod, String) - 
Method in class net.sf.basedb.plugins.batchimport.AbstractItemImporter
Find a freezer with a given identifier.
findGeometry(DbControl, int, int) - 
Method in class net.sf.basedb.plugins.PlateMappingImporter
 
findHybridization(DbControl, IdMethod, String) - 
Method in class net.sf.basedb.plugins.batchimport.AbstractItemImporter
Find a hybridization with a given identifier.
findHybridizationStation(DbControl, IdMethod, String) - 
Method in class net.sf.basedb.plugins.batchimport.AbstractItemImporter
Find a hybridization station with a given identifier.
findId - 
Static variable in class net.sf.basedb.clients.web.servlet.Download
 
findImage(DbControl, Scan, File) - 
Method in class net.sf.basedb.plugins.batchimport.AbstractItemImporter
Find an image with given scan and file.
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.
findItemsSection - 
Static variable in class net.sf.basedb.plugins.AnnotationFlatFileImporter
 
findLabel(DbControl, IdMethod, String) - 
Method in class net.sf.basedb.plugins.batchimport.AbstractItemImporter
Find a label 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
 
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.
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, PluginDefinition) - 
Static method in class net.sf.basedb.util.AutoDetectFileFormat
Deprecated.  
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.
findPrintRobot(DbControl, IdMethod, String) - 
Method in class net.sf.basedb.plugins.batchimport.AbstractItemImporter
Find a print robot with a given identifier.
findProtocol(DbControl, IdMethod, String) - 
Method in class net.sf.basedb.plugins.batchimport.AbstractItemImporter
Same as AbstractItemImporter.findProtocol(DbControl, IdMethod, String, ProtocolType) with
                a null protocol type.
findProtocol(DbControl, IdMethod, String, ProtocolType) - 
Method in class net.sf.basedb.plugins.batchimport.AbstractItemImporter
Find a protocol with a given identifier.
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, boolean) - 
Method in class net.sf.basedb.plugins.batchimport.AbstractItemImporter
Find a referenced item.
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
 
findResources(String) - 
Method in class net.sf.basedb.util.JarClassLoader
 
findSample(DbControl, IdMethod, String) - 
Method in class net.sf.basedb.plugins.batchimport.AbstractItemImporter
Find a sample with a given identifier.
findScan(DbControl, IdMethod, String) - 
Method in class net.sf.basedb.plugins.batchimport.AbstractItemImporter
Find a scan with a given identifier.
findScanner(DbControl, IdMethod, String) - 
Method in class net.sf.basedb.plugins.batchimport.AbstractItemImporter
Find a scanner 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.
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(Quantity, String) - 
Method in class net.sf.basedb.util.units.UnitCache
Finds a unit with a given symbol for a given quantity.
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
 
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
 
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.
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, 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, FileSetMember) - 
Constructor for class net.sf.basedb.util.overview.Fix
 
Fix(String, BasicItem, DataFileType) - 
Constructor for class net.sf.basedb.util.overview.Fix
 
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.
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
 
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
 
FlatFileParser - Class in net.sf.basedb.util.parser
This class can be used to parse data from flat text files.
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.Data(int, int, String, String[], boolean, boolean) - 
Constructor for class net.sf.basedb.util.parser.FlatFileParser.Data
Create a new data object.
FlatFileParser.Line - Class in net.sf.basedb.util.parser
This class holds data about a line parsed by the FlatFileParser.parseHeaders() method.
FlatFileParser.Line(int, String, FlatFileParser.LineType) - 
Constructor for class net.sf.basedb.util.parser.FlatFileParser.Line
Create a new line object.
FlatFileParser.Line(int, String, String, FlatFileParser.LineType) - 
Constructor for class net.sf.basedb.util.parser.FlatFileParser.Line
Create a new section line object.
FlatFileParser.Line(int, String, String, String) - 
Constructor for class net.sf.basedb.util.parser.FlatFileParser.Line
Create a new header line object.
FlatFileParser.LineType - Enum in net.sf.basedb.util.parser
Represents the type of a line matched or unmatched by the parser.
FlatFileParser.LineType(String) - 
Constructor for enum net.sf.basedb.util.parser.FlatFileParser.LineType
 
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
 
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.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(Session) - 
Static method in class net.sf.basedb.core.HibernateUtil
Flush all changed objects 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.SpotBatcher
 
flush() - 
Method in class net.sf.basedb.core.SpotExtraValueBatcher
 
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.
flushUpdate() - 
Method in class net.sf.basedb.core.BasicBatcher
Flush the SQL insert command buffer.
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.clients.web.extensions.ScanResults
 
foreignKeys - 
Variable in class net.sf.basedb.core.dbengine.TableInfo
 
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(Number) - 
Method in class net.sf.basedb.clients.web.formatter.ColorFormatter
 
format(T) - 
Method in class net.sf.basedb.clients.web.formatter.ExtendedPropertyFormatter
 
format(Integer) - 
Method in class net.sf.basedb.clients.web.formatter.SpotImageFormatter
 
format(String) - 
Method in class net.sf.basedb.clients.web.formatter.StringFormatter
 
FORMAT - 
Static variable in class net.sf.basedb.clients.web.plugins.SimpleExport
 
format - 
Variable in class net.sf.basedb.core.data.ImageData
 
format(ExportableField) - 
Method in class net.sf.basedb.util.export.spotdata.ExportableFieldFormatter
 
format(Boolean) - 
Method in class net.sf.basedb.util.formatter.BooleanFormatter
 
format - 
Variable in class net.sf.basedb.util.formatter.DateFormatter
 
format(Date) - 
Method in class net.sf.basedb.util.formatter.DateFormatter
 
format(File) - 
Method in class net.sf.basedb.util.formatter.FilePathFormatter
 
format(T) - 
Method in interface net.sf.basedb.util.formatter.Formatter
Format a value by converting it to a string.
format(Identifiable) - 
Method in class net.sf.basedb.util.formatter.IdentifiableFormatter
 
format(Number) - 
Method in class net.sf.basedb.util.formatter.IntegerFormatter
 
format(T) - 
Method in class net.sf.basedb.util.formatter.LookupFormatter
 
format(Object) - 
Method in class net.sf.basedb.util.formatter.MultiFormatter
 
format(Nameable) - 
Method in class net.sf.basedb.util.formatter.NameableFormatter
 
format(Number) - 
Method in class net.sf.basedb.util.formatter.NumberFormatter
 
format(T) - 
Method in class net.sf.basedb.util.formatter.PrefixSuffixFormatter
 
format(T) - 
Method in class net.sf.basedb.util.formatter.ToStringFormatter
 
format(Integer) - 
Method in class net.sf.basedb.util.formatter.WellCoordinateFormatter
 
FORMAT_BASEFILE_MATRIX - 
Static variable in class net.sf.basedb.plugins.BaseFileExporterPlugin
 
FORMAT_BASEFILE_MATRIX - 
Static variable in class net.sf.basedb.plugins.BioAssaySetExporter
Deprecated.  
FORMAT_BASEFILE_SERIAL - 
Static variable in class net.sf.basedb.plugins.BaseFileExporterPlugin
 
FORMAT_BASEFILE_SERIAL - 
Static variable in class net.sf.basedb.plugins.BioAssaySetExporter
Deprecated.  
FORMAT_BASEFILES - 
Static variable in class net.sf.basedb.plugins.BioAssaySetExporter
Deprecated.  
FORMAT_MEV_TDMS - 
Static variable in class net.sf.basedb.plugins.BioAssaySetExporter
Deprecated.  
FORMAT_PLAIN_MATRIX - 
Static variable in class net.sf.basedb.plugins.BioAssaySetExporter
Deprecated.  
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.
formatDate(Date) - 
Static method in class net.sf.basedb.util.Values
Deprecated. Use a Formatter for dates instead
formatDateTime(Date) - 
Static method in class net.sf.basedb.util.Values
Deprecated. Use a Formatter for dates instead
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.
formatParameter - 
Variable in class net.sf.basedb.plugins.BioAssaySetExporter
Deprecated.  
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<T> - Interface in net.sf.basedb.util.formatter
A Formatter formats an object to a string suitable for
        output in a client application.
formatter - 
Variable in class net.sf.basedb.util.formatter.MultiFormatter
 
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.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(Date) - 
Static method in class net.sf.basedb.util.Values
Deprecated. Use a Formatter for dates instead
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
 
formName - 
Variable in class net.sf.basedb.clients.web.fileupload.UploadedFile
 
Formula - Class in net.sf.basedb.core
This class represents a formula.
Formula(FormulaData) - 
Constructor for class net.sf.basedb.core.Formula
 
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.AverageMethod - Enum in net.sf.basedb.core
The average method used for the values of this formula.
Formula.AverageMethod(int, String) - 
Constructor for enum net.sf.basedb.core.Formula.AverageMethod
 
Formula.Parser - Enum in net.sf.basedb.core
The parser used to parse the formula.
Formula.Parser(int, String) - 
Constructor for enum net.sf.basedb.core.Formula.Parser
 
Formula.Type - Enum in net.sf.basedb.core
The type of formula indicats in which situations it can be used.
Formula.Type(int, String, boolean, boolean, Type) - 
Constructor for enum net.sf.basedb.core.Formula.Type
 
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
 
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
 
formulaQuery - 
Variable in class net.sf.basedb.util.export.spotdata.FieldConverter
Deprecated.  
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
 
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.
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.HardwareType
The id for the HardwareType object representing a 
                freezer.
freezerQuery - 
Variable in class net.sf.basedb.plugins.batchimport.AbstractItemImporter
 
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
 
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.
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.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.File.Action
Get the File.Action 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.Image.Format
Get the Image.Format 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
 
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.SafeFunctionTable(FunctionSafeJep) - 
Constructor for class net.sf.basedb.util.jep.FunctionSafeJep.SafeFunctionTable
 
FunctionSafeJep.UnknownFunction - Class in net.sf.basedb.util.jep
Represents an unknown function that appears in an expression.
FunctionSafeJep.UnknownFunction(String) - 
Constructor for class net.sf.basedb.util.jep.FunctionSafeJep.UnknownFunction
 



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
 
gamma - 
Variable in class net.sf.basedb.core.data.SpotImagesData
 
GB - 
Static variable in class net.sf.basedb.util.Values
 
geneAveragesParameter - 
Variable in class net.sf.basedb.plugins.Base1PluginExecuter
If the data should be exported averaged per gene.
geneAveragesParameter - 
Variable in class net.sf.basedb.plugins.BioAssaySetExporter
Deprecated.  
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.
generateClass(String[]) - 
Method in class net.sf.basedb.clients.web.extensions.XJspCompiler
Called when a JSP page needs recompiling.
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
 
generateOverview(DbControl) - 
Method in class net.sf.basedb.util.overview.ExperimentOverview
Deprecated. Generates the overview and validation.
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.
generateTitle(String, String) - 
Method in class net.sf.basedb.clients.web.ModeInfo
 
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 - 
Static variable in class net.sf.basedb.core.RawDataTypes
 
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
 
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(DbControl) - 
Static method in class net.sf.basedb.clients.web.extensions.ExtensionsControl
Get an extension control object for managing the
                installed extensions.
get(String) - 
Static method in class net.sf.basedb.clients.web.ModeInfo
 
get(Object) - 
Method in class net.sf.basedb.core.ExtendedPropertyAccessor.GetterSetter
Get the value of the extended property.
get(Class, Serializable, LockMode) - 
Method in class net.sf.basedb.core.hibernate.SessionWrapper
Deprecated. 
get(Class, Serializable, LockOptions) - 
Method in class net.sf.basedb.core.hibernate.SessionWrapper
 
get(Class, Serializable) - 
Method in class net.sf.basedb.core.hibernate.SessionWrapper
 
get(String, Serializable, LockMode) - 
Method in class net.sf.basedb.core.hibernate.SessionWrapper
Deprecated. 
get(String, Serializable, LockOptions) - 
Method in class net.sf.basedb.core.hibernate.SessionWrapper
 
get(String, Serializable) - 
Method in class net.sf.basedb.core.hibernate.SessionWrapper
 
get(Class, Serializable, LockMode) - 
Method in class net.sf.basedb.core.hibernate.StatelessSessionWrapper
 
get(Class, Serializable) - 
Method in class net.sf.basedb.core.hibernate.StatelessSessionWrapper
 
get(String, Serializable, LockMode) - 
Method in class net.sf.basedb.core.hibernate.StatelessSessionWrapper
 
get(String, Serializable) - 
Method in class net.sf.basedb.core.hibernate.StatelessSessionWrapper
 
get(int) - 
Method in class net.sf.basedb.core.ItemResultList
Get a BasicItem derived object.
get(Class<E>, BasicData) - 
Method in class net.sf.basedb.core.ItemResultList
 
get(int, String) - 
Method in interface net.sf.basedb.core.query.SqlResultList
 
get(int, int) - 
Method in interface net.sf.basedb.core.query.SqlResultList
 
get(char) - 
Static method in enum net.sf.basedb.plugins.Base1PluginExecuter.Base1JobParameterType
 
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(int) - 
Method in class net.sf.basedb.util.parser.FlatFileParser.Data
Get the value in the specified column.
getAbout() - 
Method in class net.sf.basedb.clients.web.extensions.ExtensionsFile
Get information about this extensions file.
getAbout() - 
Method in class net.sf.basedb.clients.web.plugins.SimpleExport
 
getAbout() - 
Method in interface net.sf.basedb.core.plugin.Plugin
Get information about the plugin, such as
                name, version, authors, etc.
getAbout() - 
Method in class net.sf.basedb.plugins.AnnotationFlatFileImporter
 
getAbout() - 
Method in class net.sf.basedb.plugins.Base1PluginExecuter
 
getAbout() - 
Method in class net.sf.basedb.plugins.BaseFileExporterPlugin
 
getAbout() - 
Method in class net.sf.basedb.plugins.batchimport.ArrayBatchImporter
 
getAbout() - 
Method in class net.sf.basedb.plugins.batchimport.ArrayDesignImporter
 
getAbout() - 
Method in class net.sf.basedb.plugins.batchimport.ArraySlideImporter
 
getAbout() - 
Method in class net.sf.basedb.plugins.batchimport.BioPlateImporter
 
getAbout() - 
Method in class net.sf.basedb.plugins.batchimport.BioSourceImporter
 
getAbout() - 
Method in class net.sf.basedb.plugins.batchimport.ExtractImporter
 
getAbout() - 
Method in class net.sf.basedb.plugins.batchimport.HybridizationImporter
 
getAbout() - 
Method in class net.sf.basedb.plugins.batchimport.LabeledExtractImporter
 
getAbout() - 
Method in class net.sf.basedb.plugins.batchimport.RawBioAssayImporter
 
getAbout() - 
Method in class net.sf.basedb.plugins.batchimport.SampleImporter
 
getAbout() - 
Method in class net.sf.basedb.plugins.batchimport.ScanImporter
 
getAbout() - 
Method in class net.sf.basedb.plugins.BfsExporterPlugin
 
getAbout() - 
Method in class net.sf.basedb.plugins.BioAssaySetExporter
Deprecated.  
getAbout() - 
Method in class net.sf.basedb.plugins.CdfFileReporterImporter
 
getAbout() - 
Method in class net.sf.basedb.plugins.executor.BaseFileExporterSupport
 
getAbout() - 
Method in class net.sf.basedb.plugins.executor.BaseFileImporterSupport
 
getAbout() - 
Method in class net.sf.basedb.plugins.executor.BfsExporterSupport
 
getAbout() - 
Method in class net.sf.basedb.plugins.executor.BfsImporterSupport
 
getAbout() - 
Method in class net.sf.basedb.plugins.executor.ExternalProgramExecutor
 
getAbout() - 
Method in class net.sf.basedb.plugins.executor.FileOnlyImporterSupport
 
getAbout() - 
Method in class net.sf.basedb.plugins.FormulaFilter
 
getAbout() - 
Method in class net.sf.basedb.plugins.GalExporter
 
getAbout() - 
Method in class net.sf.basedb.plugins.HelpExporter
 
getAbout() - 
Method in class net.sf.basedb.plugins.HelpImporter
 
getAbout() - 
Method in class net.sf.basedb.plugins.IlluminaRawDataImporter
 
getAbout() - 
Method in class net.sf.basedb.plugins.IntensityCalculatorPlugin
 
getAbout() - 
Method in class net.sf.basedb.plugins.JepExtraValueCalculator
 
getAbout() - 
Method in class net.sf.basedb.plugins.JepIntensityTransformer
 
getAbout() - 
Method in class net.sf.basedb.plugins.LowessNormalization
 
getAbout() - 
Method in class net.sf.basedb.plugins.ManualTransformCreator
 
getAbout() - 
Method in class net.sf.basedb.plugins.MedianRatioNormalization
 
getAbout() - 
Method in class net.sf.basedb.plugins.PackedFileExporter
 
getAbout() - 
Method in class net.sf.basedb.plugins.PlateFlatFileImporter
 
getAbout() - 
Method in class net.sf.basedb.plugins.PlateMappingExporter
 
getAbout() - 
Method in class net.sf.basedb.plugins.PlateMappingImporter
 
getAbout() - 
Method in class net.sf.basedb.plugins.PluginConfigurationExporter
Returns information about this plugin
getAbout() - 
Method in class net.sf.basedb.plugins.PluginConfigurationImporter
 
getAbout() - 
Method in class net.sf.basedb.plugins.PrintMapFlatFileImporter
 
getAbout() - 
Method in class net.sf.basedb.plugins.RawDataFlatFileImporter
 
getAbout() - 
Method in class net.sf.basedb.plugins.ReporterFlatFileImporter
 
getAbout() - 
Method in class net.sf.basedb.plugins.ReporterMapFlatFileImporter
 
getAbout() - 
Method in class net.sf.basedb.plugins.SpotImageCreator
 
getAbout() - 
Method in class net.sf.basedb.plugins.TarFileUnpacker
 
getAbout() - 
Method in class net.sf.basedb.plugins.ZipFileUnpacker
 
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.Registry.RegisteredExtension
 
getAbout() - 
Method in class net.sf.basedb.util.PluginInfo
Gets the about information that is set for this plugin
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.
getAbstractText() - 
Method in class net.sf.basedb.info.ExperimentInfo
 
getAction() - 
Method in class net.sf.basedb.clients.web.taglib.table.Table
 
getAction() - 
Method in class net.sf.basedb.core.data.FileData
Get the value of the action variable for this FileData
                object.
getAction() - 
Method in class net.sf.basedb.core.File
Get the File.Action of this file.
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
 
getActions(InvokationContext<? super OnSaveAction>) - 
Method in class net.sf.basedb.clients.web.extensions.edit.DebugOnSaveActionFactory
 
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) - 
Method in class net.sf.basedb.clients.web.extensions.service.DummyService
 
getActions(InvokationContext) - 
Method in class net.sf.basedb.clients.web.extensions.tabcontrol.FixedTabFactory
 
getActions(InvokationContext) - 
Method in class net.sf.basedb.clients.web.extensions.tabcontrol.IncludeContentTabFactory
 
getActions(InvokationContext) - 
Method in class net.sf.basedb.clients.web.extensions.toolbar.FixedButtonFactory
 
getActions(InvokationContext) - 
Method in class net.sf.basedb.clients.web.extensions.toolbar.PermissionButtonFactory
 
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) - 
Method in class net.sf.basedb.util.extensions.debug.BeanActionFactory
 
getActions(InvokationContext) - 
Method in class net.sf.basedb.util.extensions.debug.ProxyActionFactory
 
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.
getActive() - 
Method in class net.sf.basedb.clients.web.taglib.tab.TabControl
 
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.
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.
getAffiliations() - 
Method in class net.sf.basedb.info.ExperimentInfo
 
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.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(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.
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() - 
Method in enum net.sf.basedb.core.VirtualTable
Get the alias of this table.
getAlign() - 
Method in class net.sf.basedb.clients.web.taglib.ButtonGroup
 
getAllAnnotatableParentItems(DbControl, Annotatable, Filter<Annotatable>) - 
Static method in class net.sf.basedb.util.AnnotationUtil
Get all annotatable parent items for a given item.
getAllBioMaterials() - 
Method in class net.sf.basedb.core.BioMaterialList
Get a query that returns all biomaterials that can possibly be 
                members of this list.
getAllCharsets() - 
Static method in class net.sf.basedb.core.Config
Get a set containing all character sets known to the current java virtual machine.
getAllColumnMappings() - 
Method in class net.sf.basedb.plugins.PlateFlatFileImporter
 
getAllColumnMappings(RawDataType) - 
Method in class net.sf.basedb.plugins.RawDataFlatFileImporter
Loads the column mappings if they hasn't been loaded already.
getAllColumnMappings(boolean) - 
Method in class net.sf.basedb.plugins.ReporterFlatFileImporter
 
getAllColumnMappings() - 
Method in class net.sf.basedb.plugins.ReporterMapFlatFileImporter
 
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
 
getAllInheritedAnnotations() - 
Method in class net.sf.basedb.core.AnnotationSet
Get a query that returns all inherited (directly and indirectly) annotations in
                this annotation set.
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
 
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.
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.InternalStorageController.StorageKeyring
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.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.
getAllPermissions(SharedData) - 
Method in class net.sf.basedb.core.SessionControl
Same as SessionControl.getAllPermissions(Item, UserData, ItemKeyData, ProjectKeyData)
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>.
getAnalyzeTableSql(String, String, String) - 
Method in class net.sf.basedb.core.dbengine.PostgresDbEngine
Generate ANALYZE <schema>.
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).
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.
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.
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 
                raw bioassays.
getAnnotatableParents() - 
Method in class net.sf.basedb.core.BioAssaySet
Get the parent bioassay set (if any).
getAnnotatableParents() - 
Method in class net.sf.basedb.core.BioPlate
Gets parent plates, always returns null
getAnnotatableParents() - 
Method in class net.sf.basedb.core.BioSource
Always null.
getAnnotatableParents() - 
Method in class net.sf.basedb.core.Extract
Get the sample or pooled extracts.
getAnnotatableParents() - 
Method in class net.sf.basedb.core.Hybridization
Get the labeled extracts and array slide.
getAnnotatableParents(int) - 
Method in class net.sf.basedb.core.Hybridization
Get the labeled extracts, possible on a specific array,
                and the array slide.
getAnnotatableParents() - 
Method in class net.sf.basedb.core.LabeledExtract
Get the extract or pooled labeled extracts.
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.Protocol
 
getAnnotatableParents() - 
Method in class net.sf.basedb.core.RawBioAssay
Get the scan, if any.
getAnnotatableParents() - 
Method in class net.sf.basedb.core.Sample
Get the biosource or pooled samples.
getAnnotatableParents() - 
Method in class net.sf.basedb.core.Scan
Get the hybridization.
getAnnotatableParents() - 
Method in class net.sf.basedb.core.Well
Get the parent well, if any.
getAnnotatableParents(Annotatable) - 
Method in class net.sf.basedb.util.overview.ExperimentOverview
Deprecated. Get all annotatatable parents, including parents of parents, 
                of the given annotatable item.
getAnnotatableParents(Annotatable, Annotatable) - 
Method in class net.sf.basedb.util.overview.ExperimentOverview
Deprecated.  
getAnnotatableParents(DbControl, OverviewContext, Annotatable) - 
Static method in class net.sf.basedb.util.overview.OverviewUtil
Get all annotatable parent items for the given item.
getAnnotatableParents(DbControl, OverviewContext, Annotatable, Annotatable) - 
Static method in class net.sf.basedb.util.overview.OverviewUtil
The internal implementation needs to keep track of the special case when we
                start with raw bioassay as the root item.
getAnnotatableParentWrappers() - 
Method in class net.sf.basedb.util.AnnotationUtil.AnnotatableWrapper
Get all annotatable parents wrapped inside AnnotatableWrapper:s
getAnnotation(AnnotationType) - 
Method in class net.sf.basedb.core.AnnotationSet
Get the Annotation object of the specified annotation type.
getAnnotation(DbControl) - 
Method in class net.sf.basedb.core.snapshot.AnnotationSnapshot
Get the annotation this is a snapshot of.
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.core.snapshot.AnnotationSnapshot
Get the id of the annotation this is a snapshot of.
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.ManualTransformCreator
 
getAnnotationMessage() - 
Method in class net.sf.basedb.plugins.RawDataFlatFileImporter
 
getAnnotations() - 
Method in class net.sf.basedb.core.AnnotationSet
Get a query that reurns all primary annotations in this annotation
                set.
getAnnotations() - 
Method in class net.sf.basedb.core.data.AnnotationSetData
The primary 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.snapshot.AnnotationSetSnapshot
Get a list with the all annotations in this snapshot.
getAnnotations(String, int, Integer[], boolean) - 
Method in class net.sf.basedb.ws.server.ArrayDesignService
Get the annotation values for one or more annotation types.
getAnnotations(String, int, Integer[], boolean) - 
Method in class net.sf.basedb.ws.server.BioAssaySetService
Get the annotation values for one or more annotation types.
getAnnotations(String, int, Integer[], boolean) - 
Method in class net.sf.basedb.ws.server.RawBioAssayService
Get the annotation values for one or more annotation types.
getAnnotations(DbControl, Annotatable, Integer[], boolean) - 
Method in class net.sf.basedb.ws.server.ServicesUtil
Load annotation values from an annotatable item.
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.WellData
 
getAnnotationSet() - 
Method in class net.sf.basedb.core.PluginDefinition
 
getAnnotationSet(DbControl) - 
Method in class net.sf.basedb.core.snapshot.AnnotationSetSnapshot
Get the annotation set this is a snapshot of.
getAnnotationSet(DbControl) - 
Method in class net.sf.basedb.core.snapshot.AnnotationSnapshot
Get the annotation set this annotation belongs to.
getAnnotationSet() - 
Method in class net.sf.basedb.core.Well
 
getAnnotationSetId() - 
Method in class net.sf.basedb.core.snapshot.AnnotationSetSnapshot
Get the id of the annotation set this is a snapshot of.
getAnnotationSetId() - 
Method in class net.sf.basedb.core.snapshot.AnnotationSnapshot
Get the id of the annotation set this annotation belongs to.
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.data.AnnotationData
Get the type of this annotation.
getAnnotationType(DbControl) - 
Method in class net.sf.basedb.core.snapshot.AnnotationSnapshot
Get the annotation type.
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.
getAnnotationTypeId() - 
Method in class net.sf.basedb.clients.web.ExperimentExplorer
Deprecated. In 2.14, use ExperimentExplorer.getAnnotationTypeIds() instead
getAnnotationTypeId() - 
Method in class net.sf.basedb.core.snapshot.AnnotationSnapshot
Get the id of the annotation type.
getAnnotationTypeId() - 
Method in class net.sf.basedb.info.AnnotationInfo
 
getAnnotationTypeIds() - 
Method in class net.sf.basedb.clients.web.ExperimentExplorer
Get the selected annotation types.
getAnnotationTypes(DbControl, boolean) - 
Method in class net.sf.basedb.clients.web.ExperimentExplorer
Get the annotation types that are of interest in this experiment.
getAnnotationTypes() - 
Method in interface net.sf.basedb.core.AnnotatableProxy
Get the annotation types that can be proxied.
getAnnotationTypes(Item) - 
Method in class net.sf.basedb.core.AnnotationTypeCategory
Gets a query that returns the annotation types that are members of this category
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.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(String, QueryOptions) - 
Method in class net.sf.basedb.ws.client.AnnotationTypeClient
Gets info about each projects that are available for the active session client.
getAnnotationTypes(String, String, QueryOptions) - 
Method in class net.sf.basedb.ws.server.AnnotationTypeService
Gets information about annotation types that are available
                for an active session.
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.
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.
getAnnotationValues() - 
Method in class net.sf.basedb.clients.web.ExperimentExplorer.AnnotationGroup
Get all annotation values in this annotation group.
getAnnotationValues(DbControl, BioAssay, AnnotationType) - 
Static method in class net.sf.basedb.util.BioAssaySetUtil
Deprecated. In BASE 2.14 due to performance problems, use 
                        BioAssaySetUtil.getAnnotationValues(DbControl, SnapshotManager, BioAssay, AnnotationType) 
                        instead
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.
getAnnotationValues(int, Integer[], boolean) - 
Method in class net.sf.basedb.ws.client.RawBioAssayClient
Get annotation values for one or more annotation types.
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.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.
getArrayDesign() - 
Method in class net.sf.basedb.core.Scan
Get the array design by connected to this scan following 
                the hybridization to the array slide to the array batch 
                to the array design.
getArrayDesign(int) - 
Method in class net.sf.basedb.ws.client.RawBioAssayClient
Returns information about the array design used in a rawbioassay
getArrayDesign(String, int) - 
Method in class net.sf.basedb.ws.server.RawBioAssayService
Gets information about the array design used in a rawbioassay.
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.
getArrayDesignId() - 
Method in class net.sf.basedb.info.RawBioAssayInfo
 
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.PlateData
Used by Hibernate to link with the arraydesign for this plate.
getArrayDesigns(QueryOptions) - 
Method in class net.sf.basedb.ws.client.ArrayDesignClient
Gets info about array designs that are available in the logged in session.
getArrayDesigns(String, QueryOptions) - 
Method in class net.sf.basedb.ws.server.ArrayDesignService
Gets an array with info about array designs 
                available for the active session.
getArrayNum() - 
Method in class net.sf.basedb.core.data.RawBioAssayData
The array number this raw bioassay is linked to on a multi-array 
                hybridization.
getArrayNum() - 
Method in class net.sf.basedb.core.RawBioAssay
Get the hybridization array number this raw bioassay is linked to.
getArrayNum(Annotatable, int) - 
Static method in class net.sf.basedb.util.AnnotationUtil.AnnotatableWrapper
Get the array num to use.
getArraySlide() - 
Method in class net.sf.basedb.core.data.HybridizationData
Get the array slide.
getArraySlide() - 
Method in class net.sf.basedb.core.Hybridization
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(DbControl, BioAssaySet) - 
Method in class net.sf.basedb.plugins.BfsExporterPlugin
 
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.
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.
getAttachesToItemType() - 
Method in enum net.sf.basedb.core.Project.Default
The item type an entry of this default type is usually attached to.
getAttribute(String) - 
Method in class net.sf.basedb.util.extensions.ClientContext
Get an attribute of the context.
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, String) - 
Method in class net.sf.basedb.util.extensions.Registry
Get the value of a extra attribute for a registered extension
                or extension point.
getAttributes() - 
Method in class net.sf.basedb.clients.web.taglib.Body
 
getAuthenticator() - 
Static method in class net.sf.basedb.core.Application
Get an object of the class that is used for external
                authentication.
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.
getAuthors() - 
Method in class net.sf.basedb.info.ExperimentInfo
 
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.
getAutoInstall() - 
Method in class net.sf.basedb.clients.web.extensions.ExtensionsControl
Get the auto-installation setting.
getAutoInstall() - 
Method in class net.sf.basedb.clients.web.extensions.Settings
Get the interval, in seconds, between automatic checks 
                for new/modified/deleted extensions.
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.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.
getBaseFileExtraQI(DbControl, BioAssaySet) - 
Method in class net.sf.basedb.plugins.BioAssaySetExporter
Deprecated.  
getBaseFileFormulaQI(DbControl, BioAssaySet) - 
Method in class net.sf.basedb.plugins.BioAssaySetExporter
Deprecated.  
getBaseFileParser() - 
Method in class net.sf.basedb.util.importer.spotdata.BaseFileImporter
Get the underlying parser for the BASEfile.
getBaseFileQIMap(DbControl, BioAssaySet) - 
Method in class net.sf.basedb.plugins.BioAssaySetExporter
Deprecated.  
getBaseFileRawQI(BioAssaySet) - 
Method in class net.sf.basedb.plugins.BioAssaySetExporter
Deprecated.  
getBaseFileReporterFields(DbControl, BioAssaySet, DynamicPositionQuery, Map<String, BioAssaySetExporter.QueryItem>, List<String>, boolean) - 
Method in class net.sf.basedb.plugins.BioAssaySetExporter
Deprecated.  
getBaseFileReporterQI() - 
Method in class net.sf.basedb.plugins.BioAssaySetExporter
Deprecated.  
getBaseFileSpotQI(BioAssaySet) - 
Method in class net.sf.basedb.plugins.BioAssaySetExporter
Deprecated.  
getBaseFileSpotSectionCount(DbControl, DynamicSpotQuery, boolean) - 
Method in class net.sf.basedb.plugins.BioAssaySetExporter
Deprecated.  
getBaseFileWriter() - 
Method in class net.sf.basedb.util.export.spotdata.BaseFileExporter
Get the writer that writes the data to the file.
getBaseVersion() - 
Method in class net.sf.basedb.clients.web.taglib.Page
 
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(DbControl) - 
Method in class net.sf.basedb.clients.web.ExperimentExplorer
Get the bioassay set that is currently beeing explored.
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.
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.
getBioAssaySets(int, QueryOptions) - 
Method in class net.sf.basedb.ws.client.ExperimentClient
Gets info about bioassay sets in an experiment
getBioAssaySets(String, int, QueryOptions) - 
Method in class net.sf.basedb.ws.server.ExperimentService
Gets information about the bioassay sets in an experiment.
getBioMaterial() - 
Method in class net.sf.basedb.core.BioMaterialEvent
Get the MeasuredBioMaterial that was affected or created by this event.
getBioMaterial(PlateCoordinate) - 
Method in class net.sf.basedb.core.BioPlate
Get the biomaterial in the well at the given location.
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.BioWellData
The MeasuredBioMaterialData used in this well.
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.
getBioMaterialLists() - 
Method in class net.sf.basedb.core.data.BioMaterialData
This is the inverse end.
getBioMaterialListsEnum(DbControl, Item, Collection<Include>) - 
Static method in class net.sf.basedb.clients.web.Base
Get available biomaterial lists as an Enumeration that is
                suitable to use in a column definition for a table.
getBioMaterials() - 
Method in class net.sf.basedb.core.data.BioMaterialListData
Get the set that manages which biomaterials are part of this list.
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.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.
getBioSource() - 
Method in class net.sf.basedb.core.Sample
Get the BioSource that is the parent of this sample.
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.
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.
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
 
getBlueImageFile() - 
Method in class net.sf.basedb.core.data.SpotImagesData
The file used for the blue component in the spot images.
getBlueImageFile() - 
Method in class net.sf.basedb.core.SpotImages
Get the file which was used for the blue channel in the
                spot images.
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.XMLUtil
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.
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.
getBuild() - 
Method in class net.sf.basedb.info.VersionInfo
 
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(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(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.
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.BioMaterialList
Get a BioMaterialList 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, String) - 
Static method in class net.sf.basedb.core.BioPlateEventType
Gets a BioPlate event type when knowing the item's system 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.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.FileType
Get a FileType 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.HardwareType
Get a HardwareType object 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) - 
Static method in class net.sf.basedb.core.Hybridization
Get a Hybridization item when you know the id.
getById(DbControl, int) - 
Static method in class net.sf.basedb.core.Image
Get an Image item when you know the id.
getById - 
Variable in enum net.sf.basedb.core.Item
 
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.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.Label
Get a Label item when you know the id.
getById(DbControl, int) - 
Static method in class net.sf.basedb.core.LabeledExtract
Get a LabeledExtract 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.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.ProtocolType
Get a ProtocolType object 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.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.Sample
Get an Sample item when you know the id.
getById(DbControl, int) - 
Static method in class net.sf.basedb.core.Scan
Get a Scan object 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.SoftwareType
Get a SoftwareType object 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.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(int) - 
Method in class net.sf.basedb.ws.client.AnnotationTypeClient
Get info about an annotation type when you know the ID.
getById(int) - 
Method in class net.sf.basedb.ws.client.ArrayDesignClient
Get info about an array design when you know the ID.
getById(int) - 
Method in class net.sf.basedb.ws.client.ExperimentClient
Get info about an experiment when you know the ID.
getById(int) - 
Method in class net.sf.basedb.ws.client.ProjectClient
Get info about a project when you know the ID.
getById(int) - 
Method in class net.sf.basedb.ws.client.RawBioAssayClient
Get info about a raw bioassay when you know the ID.
getById(String, int) - 
Method in class net.sf.basedb.ws.server.AnnotationTypeService
Get information about an annotation type that you know the ID of.
getById(String, int) - 
Method in class net.sf.basedb.ws.server.ArrayDesignService
Get information about an array design that you know the ID of.
getById(String, int) - 
Method in class net.sf.basedb.ws.server.ExperimentService
Get information about an experiment that you know the ID of.
getById(String, int) - 
Method in class net.sf.basedb.ws.server.ProjectService
Get information about a project that you know the ID of.
getById(String, int) - 
Method in class net.sf.basedb.ws.server.RawBioAssayService
Get information about a raw bioassay that you know the ID of.
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.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.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.SpotImage
Get the number of bytes of the image.
getBytesPerRow(RawDataType) - 
Method in enum net.sf.basedb.core.VirtualTable
Get the number of bytes a single row in the database occupies.
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.
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.SessionWrapper
 
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.
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.
getCdfFile(ArrayDesign) - 
Static method in class net.sf.basedb.core.Affymetrix
Deprecated. Use FileStoreUtil.getDataFile(DbControl, FileStoreEnabled, String)
                        with a data file type of DataFileType.AFFYMETRIX_CDF
                        instead
getCelFile(RawBioAssay) - 
Static method in class net.sf.basedb.core.Affymetrix
Deprecated.  
getCertificate(InputStream, String, String) - 
Static method in class net.sf.basedb.util.ssl.SSLUtil
Get the certificate that is found in the given input stream.
getCertificateChain(String) - 
Method in class net.sf.basedb.util.ssl.StaticKeyManager
 
getChallenge() - 
Method in class net.sf.basedb.core.SessionControl
Generate a new random string to be used for password encryption
                in the login method.
getChallenge() - 
Method in class net.sf.basedb.ws.client.SessionClient
Calling the getChallenge method.
getChallenge(String) - 
Method in class net.sf.basedb.ws.server.SessionService
Service for net.sf.basedb.core.SessionControl#getChallenge()
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(User) - 
Static method in class net.sf.basedb.core.ChangeHistory
Get all changes made by the specified user.
getChangesBy(Job) - 
Static method in class net.sf.basedb.core.ChangeHistory
Get all changes made by the specified job.
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?
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.
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.plugins.AbstractFlatFileImporter
Get the character set the file uses.
getCharset(Request) - 
Method in class net.sf.basedb.plugins.AbstractFlatFileImporter
Get the character set the file uses.
getCharsetParameter(String, String, String) - 
Method in class net.sf.basedb.plugins.AbstractFlatFileImporter
Deprecated. USe Parameters.charsetParameter(String, String, String)
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.
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.
getChildLabeledExtracts() - 
Method in class net.sf.basedb.core.LabeledExtract
Creates a query that returns all child (pooled) labeled extracts that
                has this labeled extracts as one of it's sources.
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.core.AnnotationRestriction
 
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.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.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.AscOrder
 
getChildren() - 
Method in class net.sf.basedb.core.query.BetweenRestriction
 
getChildren() - 
Method in class net.sf.basedb.core.query.CaseExpression
 
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.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.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.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.
getClasses() - 
Static method in class net.sf.basedb.core.ExtendedProperties
Get a list with the name of all classes.
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.PluginInfo
Gets the class name for the plugin
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.Button
 
getClazz() - 
Method in class net.sf.basedb.clients.web.taglib.ButtonGroup
 
getClazz() - 
Method in class net.sf.basedb.clients.web.taglib.ExceptionCatcher
 
getClazz() - 
Method in class net.sf.basedb.clients.web.taglib.Help
 
getClazz() - 
Method in class net.sf.basedb.clients.web.taglib.HideableSection
 
getClazz() - 
Method in class net.sf.basedb.clients.web.taglib.Icon
 
getClazz() - 
Method in class net.sf.basedb.clients.web.taglib.menu.Menu
 
getClazz() - 
Method in class net.sf.basedb.clients.web.taglib.Note
 
getClazz() - 
Method in class net.sf.basedb.clients.web.taglib.path.Path
 
getClazz() - 
Method in class net.sf.basedb.clients.web.taglib.path.PathElement
 
getClazz() - 
Method in class net.sf.basedb.clients.web.taglib.Select
 
getClazz() - 
Method in class net.sf.basedb.clients.web.taglib.tab.Tab
 
getClazz() - 
Method in class net.sf.basedb.clients.web.taglib.tab.TabControl
 
getClazz() - 
Method in class net.sf.basedb.clients.web.taglib.table.Button
 
getClazz() - 
Method in class net.sf.basedb.clients.web.taglib.table.Cell
 
getClazz() - 
Method in class net.sf.basedb.clients.web.taglib.table.ColumnDef
 
getClazz() - 
Method in class net.sf.basedb.clients.web.taglib.table.Data
 
getClazz() - 
Method in class net.sf.basedb.clients.web.taglib.table.Header
 
getClazz() - 
Method in class net.sf.basedb.clients.web.taglib.table.Label
 
getClazz() - 
Method in class net.sf.basedb.clients.web.taglib.table.Navigator
 
getClazz() - 
Method in class net.sf.basedb.clients.web.taglib.table.Panel
 
getClazz() - 
Method in class net.sf.basedb.clients.web.taglib.table.PresetSelector
 
getClazz() - 
Method in class net.sf.basedb.clients.web.taglib.table.Row
 
getClazz() - 
Method in class net.sf.basedb.clients.web.taglib.table.Table
 
getClazz() - 
Method in class net.sf.basedb.clients.web.taglib.table.Toolbar
 
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.
getClient(DbControl) - 
Method in class net.sf.basedb.core.ChangeHistory
Load the client application that was used when the change was made.
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.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.
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.
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.
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.InvokationContext
Get the client context that was passed to the 
                Registry.useExtensions(ClientContext, ExtensionsFilter, String...)
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.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 in use.
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.
getClientX509Certificate() - 
Method in class net.sf.basedb.core.FileServer
Get the X.509 certificate for the client.
getCmd() - 
Method in class net.sf.basedb.clients.jobagent.CmdLine
Get the command parameter
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(String) - 
Method in class net.sf.basedb.clients.web.servlet.ExperimentExplorerPlotServlet.ColumnKey
 
getColor(float) - 
Method in class net.sf.basedb.util.ColorGenerator
Get the color for the value.
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.PresetSelector
 
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.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(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.
getColumn(String) - 
Static method in class net.sf.basedb.core.ReporterPropertyExpression
 
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() - 
Method in class net.sf.basedb.info.ExtendedPropertyInfo
 
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.
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.FallbackIdMethod
 
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
 
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(RawDataType) - 
Method in enum net.sf.basedb.core.VirtualTable
Get all columns in this 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.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.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.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.
getConfigurations() - 
Method in class net.sf.basedb.util.PluginInfo
Gets information about the configurations that come together with the plugin in the jar.
getConfigurationsPath() - 
Method in class net.sf.basedb.util.PluginInfo
The path inside a jar to the xml-file that holds 
                the pluginconfigurations that can be imported.
getConfigurationValues() - 
Method in class net.sf.basedb.core.data.PluginConfigurationData
Used by Hibernate to link with configuration values.
getConfigureBasefileParameters(GuiContext) - 
Method in class net.sf.basedb.plugins.BioAssaySetExporter
Deprecated.  
getConfiguredColors(SessionControl) - 
Static method in class net.sf.basedb.clients.web.Base
 
getConfiguredItemQuery(ItemQuery<T>, QueryOptions) - 
Method in class net.sf.basedb.ws.server.ServicesUtil
Put options and restriction on a item query and returns it
getConfiguredJobParameters() - 
Method in class net.sf.basedb.plugins.HelpImporter
 
getConfiguredJobParameters() - 
Method in class net.sf.basedb.plugins.PluginConfigurationImporter
 
getConfiguredQuery(ItemContext, boolean, ItemQuery<T>, ModeInfo) - 
Static method in class net.sf.basedb.clients.web.Base
Deprecated. Use Base.getConfiguredQuery(DbControl, ItemContext, boolean, ItemQuery, ModeInfo)
                        instead
getConfiguredQuery(DbControl, ItemContext, 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(GuiContext) - 
Method in class net.sf.basedb.clients.web.plugins.SimpleExport
 
getConfigureJobParameters() - 
Method in class net.sf.basedb.plugins.Base1PluginExecuter
Creates the information needed for job configuration and initiates the 
                parameters.
getConfigureJobParameters(GuiContext, Boolean) - 
Method in class net.sf.basedb.plugins.BaseFileExporterPlugin
 
getConfigureJobParameters(GuiContext) - 
Method in class net.sf.basedb.plugins.BfsExporterPlugin
 
getConfigureJobParameters(GuiContext, Boolean) - 
Method in class net.sf.basedb.plugins.BioAssaySetExporter
Deprecated.  
getConfigureJobParameters(GuiContext) - 
Method in class net.sf.basedb.plugins.CdfFileReporterImporter
 
getConfigureJobParameters(String) - 
Method in class net.sf.basedb.plugins.executor.BaseFileImporterSupport
 
getConfigureJobParameters(String) - 
Method in class net.sf.basedb.plugins.executor.BfsImporterSupport
 
getConfigureJobParameters() - 
Method in class net.sf.basedb.plugins.executor.ExternalProgramExecutor
 
getConfigureJobParameters(String) - 
Method in class net.sf.basedb.plugins.executor.FileOnlyImporterSupport
 
getConfigureJobParameters(GuiContext) - 
Method in class net.sf.basedb.plugins.FormulaFilter
 
getConfigureJobParameters(Boolean) - 
Method in class net.sf.basedb.plugins.GalExporter
 
getConfigureJobParameters(Boolean) - 
Method in class net.sf.basedb.plugins.HelpExporter
 
getConfigureJobParameters(GuiContext) - 
Method in class net.sf.basedb.plugins.IlluminaRawDataImporter
 
getConfigureJobParameters() - 
Method in class net.sf.basedb.plugins.IntensityCalculatorPlugin
 
getConfigureJobParameters() - 
Method in class net.sf.basedb.plugins.JepExtraValueCalculator
 
getConfigureJobParameters(GuiContext) - 
Method in class net.sf.basedb.plugins.JepIntensityTransformer
 
getConfigureJobParameters() - 
Method in class net.sf.basedb.plugins.LowessNormalization
 
getConfigureJobParameters(GuiContext) - 
Method in class net.sf.basedb.plugins.ManualTransformCreator
 
getConfigureJobParameters() - 
Method in class net.sf.basedb.plugins.MedianRatioNormalization
 
getConfigureJobParameters(GuiContext, Boolean) - 
Method in class net.sf.basedb.plugins.PackedFileExporter
 
getConfigureJobParameters(GuiContext) - 
Method in class net.sf.basedb.plugins.PlateFlatFileImporter
 
getConfigureJobParameters(GuiContext, Boolean) - 
Method in class net.sf.basedb.plugins.PlateMappingExporter
 
getConfigureJobParameters(GuiContext) - 
Method in class net.sf.basedb.plugins.PlateMappingImporter
 
getConfigureJobParameters(Boolean) - 
Method in class net.sf.basedb.plugins.PluginConfigurationExporter
 
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
 
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
 
getConfigureParserParameters(GuiContext, boolean) - 
Method in class net.sf.basedb.plugins.AnnotationFlatFileImporter
 
getConfigureParserParameters(GuiContext, boolean) - 
Method in class net.sf.basedb.plugins.batchimport.AbstractItemImporter
 
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(GuiContext) - 
Method in class net.sf.basedb.plugins.ManualTransformCreator
 
getConfigurePluginParameters() - 
Method in class net.sf.basedb.plugins.PackedFileExporter
 
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(Session) - 
Static method in class net.sf.basedb.core.HibernateUtil
Get the underlying JDBC connection from the Hibernate session.
getConnection(Integer) - 
Method in class net.sf.basedb.core.JobAgent
Get a connection object for connecting to the job agent.
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.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
 
getContentType(HttpResponse) - 
Static method in class net.sf.basedb.util.HttpUtil
Get the content type of the content from the headers 
                in the response.
getContentType() - 
Method in class net.sf.basedb.ws.server.BaseFileDataSource
 
getContentType() - 
Method in class net.sf.basedb.ws.server.TempFileDataSource
Get the supplied MIME type, if any.
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(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.
getConverter(Object) - 
Static method in class net.sf.basedb.util.jep.convert.ConverterFactory
Get a converter for the specified built-in JEP object.
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(int) - 
Method in class net.sf.basedb.clients.web.ExperimentExplorer.AnnotationGroup
Get the number of intensity values added to the specified channel.
getCount() - 
Method in class net.sf.basedb.util.plot.HistogramPlot.HistogramBin
Get the number of values in this bin.
getCountHqlQuery(DbControl) - 
Method in class net.sf.basedb.core.AbstractHqlQuery
Build the count query and set parameter values for it.
getCountQuery(DbControl, boolean) - 
Method in class net.sf.basedb.core.AbstractQuery
Build the query string for returning the total count.
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.
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.
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>.
getCreateIndexSql(String, String, String, String, Set<String>, boolean) - 
Method in class net.sf.basedb.core.dbengine.MySQLEngine
Generate ALTER TABLE <catalog>.
getCreateIndexSql(String, String, String, String, Set<String>, boolean) - 
Method in class net.sf.basedb.core.dbengine.PostgresDbEngine
Generate ALTER TABLE <schema>.
getCreationEvent() - 
Method in class net.sf.basedb.core.data.HybridizationData
Get the event that created this hybidization.
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.Hybridization
Get the event that represents the creation of this hybridization.
getCreationEvent() - 
Method in class net.sf.basedb.core.MeasuredBioMaterial
Get the event that represents the creation of this biomaterial.
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.
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, ItemContext) - 
Method in class net.sf.basedb.core.SessionControl
Same as: getCurrentContext(item, "", defaultContext).
getCurrentContext(Item, String, ItemContext) - 
Method in class net.sf.basedb.core.SessionControl
Get the current context.
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.
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).
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
 
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
 
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.
getCustomRequestHandlerClasses() - 
Method in class net.sf.basedb.clients.jobagent.Agent
 
getData(ExportedProperty, BioAssay) - 
Method in class net.sf.basedb.clients.web.plugins.BioAssayExperimentalFactorLoader
 
getData(ExportedProperty, T) - 
Method in interface net.sf.basedb.clients.web.plugins.DataLoader
Get the value for the specified property.
getData(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(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(ExportedProperty, FileStoreEnabled) - 
Method in class net.sf.basedb.clients.web.plugins.FileSetMemberLoader
 
getData(ExportedProperty, BasicItem<?>) - 
Method in class net.sf.basedb.clients.web.plugins.ItemQueryLoader
 
getData(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(ExportedProperty, MeasuredBioMaterial<?>) - 
Method in class net.sf.basedb.clients.web.plugins.ParentBioMaterialLoader
 
getData(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() - 
Method in class net.sf.basedb.clients.web.taglib.table.Columns
 
getData() - 
Method in class net.sf.basedb.clients.web.taglib.table.Row
 
getData() - 
Method in class net.sf.basedb.clients.web.taglib.table.Rows
 
getData() - 
Method in class net.sf.basedb.core.BasicItem
Get the BasicData object that holds all data for this item.
getData(String, UserData, ClientData, boolean) - 
Method in class net.sf.basedb.core.ItemContext
Create a new database context object from this context.
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.ReporterScore
 
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, String) - 
Method in class net.sf.basedb.util.bfs.AnnotationModel
Get the data element at a given row and column.
getData(int, int) - 
Method in class net.sf.basedb.util.bfs.MatrixModel
Get the data element at a given row and column index.
getData() - 
Method in class net.sf.basedb.util.importer.spotdata.SynchronizedSpotDataParser.SynchronizedData
Get the current data line, split into columns.
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.
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) - 
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.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.PlatformFileType
Get the type of the file.
getDataFileType() - 
Method in class net.sf.basedb.util.overview.Fix
 
getDataFileTypes(Item, FileStoreEnabled, Platform, PlatformVariant) - 
Static method in class net.sf.basedb.clients.web.Base
Get a query that returns all data file types for a specific
                platform/variant that can be used on a given item type.
getDataFileTypes(int, QueryOptions) - 
Method in class net.sf.basedb.ws.client.ArrayDesignClient
Gets the datafile types that is used to store an array design.
getDataFileTypes(int, QueryOptions) - 
Method in class net.sf.basedb.ws.client.BioAssaySetClient
Returns information about data file types that are used storing
                spot data for a bioassay set.
getDataFileTypes(int, QueryOptions) - 
Method in class net.sf.basedb.ws.client.RawBioAssayClient
Returns information about data file types that are used storing
                raw data for a raw bioassay.
getDataFileTypes(String, int, QueryOptions) - 
Method in class net.sf.basedb.ws.server.ArrayDesignService
Returns information objects for each DataFileType represented in the FileSet
                of an ArrayDesign
getDataFileTypes(String, int, QueryOptions) - 
Method in class net.sf.basedb.ws.server.BioAssaySetService
Returns information objects for each DataFileType represented in the FileSet
                of a BioAssaySet.
getDataFileTypes(String, int, QueryOptions) - 
Method in class net.sf.basedb.ws.server.RawBioAssayService
Returns information objects for each DataFileType represented in the FileSet
                of a RawBioAssay.
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(HttpResponse, String, Date) - 
Static method in class net.sf.basedb.util.HttpUtil
 
getDate(String) - 
Static method in class net.sf.basedb.util.Values
Deprecated. Use a Formatter for dates instead
getDate(String, Date) - 
Static method in class net.sf.basedb.util.Values
Deprecated. Use a Formatter for dates instead
getDate(String[]) - 
Static method in class net.sf.basedb.util.Values
Deprecated. Use a Formatter for dates instead
getDate(String[], Formatter<Date>) - 
Static method in class net.sf.basedb.util.Values
 
getDateFormat(SessionControl) - 
Static method in class net.sf.basedb.clients.web.formatter.FormatterSettings
Get format string for a date formatter.
getDateFormat() - 
Method in class net.sf.basedb.util.formatter.DateFormatter
Get access to the underlying DateFormat object
                used for formatting and parsing dates.
getDateFormatter(SessionControl) - 
Static method in class net.sf.basedb.clients.web.formatter.FormatterFactory
Get the logged in user's date formatter.
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.
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.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
 
getDecimalSeparatorParameter(String, String, String) - 
Method in class net.sf.basedb.plugins.AbstractFlatFileImporter
Deprecated. Use Parameters.decimalSeparatorParameter(String, String, String)
getDefault() - 
Method in class net.sf.basedb.core.Presets
Get the default preset.
getDefaultData(DbControl, Project.Default) - 
Method in class net.sf.basedb.core.Project
Gets the project's default item as a data object.
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.
getDefaultImage(String) - 
Method in class net.sf.basedb.clients.web.taglib.Button
 
getDefaultitem() - 
Method in class net.sf.basedb.clients.web.taglib.Select
 
getDefaultItem(DbControl, Project.Default) - 
Method in class net.sf.basedb.core.Project
Gets the project's default item of a certain itemType defined in defaultType.
getDefaultKeyManagers() - 
Static method in class net.sf.basedb.util.ssl.SSLUtil
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.
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, ...
getDefaultServiceFactory() - 
Static method in class net.sf.basedb.ws.client.Factories
Get the default service factory that is used when creating
                SessionClient objects when no factory has been specified
                in the constructor.
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 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.
getDefaultTrustManagers() - 
Static method in class net.sf.basedb.util.ssl.SSLUtil
Get the default trust manages as configured in the base.config file by
                ssl.truststore.* settings.
getDefaultType(Item, Item) - 
Static method in class net.sf.basedb.core.Project
Get the project default entry that is used to attach item of a
                given itemType to attachesToType.
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.info.AnnotationTypeInfo
 
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.
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(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.FileSetMemberNameGenerator
 
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.FileSetMemberNameGenerator
 
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.
getDepth() - 
Method in class net.sf.basedb.util.Tree.Entry
Get the depth of this entry within the tree.
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.taglib.table.TableColumn
 
getDescription() - 
Method in class net.sf.basedb.clients.web.util.NameablePluginAdaptor
 
getDescription() - 
Method in class net.sf.basedb.core.AnyToAny
 
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.FileTypeData
 
getDescription() - 
Method in class net.sf.basedb.core.data.GroupData
 
getDescription() - 
Method in class net.sf.basedb.core.data.HardwareTypeData
 
getDescription() - 
Method in class net.sf.basedb.core.data.HelpData
 
getDescription() - 
Method in class net.sf.basedb.core.data.ImageData
 
getDescription() - 
Method in class net.sf.basedb.core.data.JobData
 
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.ProtocolTypeData
 
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.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.SoftwareTypeData
 
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.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.FileType
 
getDescription() - 
Method in class net.sf.basedb.core.Group
 
getDescription() - 
Method in class net.sf.basedb.core.HardwareType
 
getDescription() - 
Method in class net.sf.basedb.core.Help
 
getDescription() - 
Method in class net.sf.basedb.core.Image
 
getDescription() - 
Method in class net.sf.basedb.core.IntensityFormula
Get a description of the intensity formula.
getDescription() - 
Method in class net.sf.basedb.core.Job
 
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.PluginDefinition
Get a description of the plugin.
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.ProtocolType
 
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.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.SoftwareType
 
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.info.BioAssaySetInfo
 
getDescription() - 
Method in class net.sf.basedb.info.CommonItemInfo
 
getDescription() - 
Method in class net.sf.basedb.info.DataFileTypeInfo
 
getDescription() - 
Method in class net.sf.basedb.info.ExtendedPropertyInfo
 
getDescription() - 
Method in interface net.sf.basedb.info.NameableInfo
Gets the description of the info object
getDescription() - 
Method in class net.sf.basedb.info.ProjectInfo
 
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 class net.sf.basedb.util.overview.Validator
Get a lengthier description of the validation that takes place
getDescription() - 
Method in class net.sf.basedb.util.PluginConfigInfo
Gets the description of the configuration
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.
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.taglib.table.Table
 
getDirectionImage() - 
Method in class net.sf.basedb.clients.web.taglib.table.Table
 
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.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.
getDisableinproject() - 
Method in class net.sf.basedb.clients.web.taglib.table.PresetSelector
 
getDisableothers() - 
Method in class net.sf.basedb.clients.web.taglib.table.PresetSelector
 
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
 
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(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(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(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.
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.
getDomainOrder() - 
Method in class net.sf.basedb.util.plot.HistogramPlot.HistogramDataset
 
getDouble(String) - 
Method in class net.sf.basedb.util.parser.ColumnMapper
 
getDouble(String) - 
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
Convert a string to a double.
getDouble(String, Double) - 
Static method in class net.sf.basedb.util.Values
 
getDouble(String[]) - 
Static method in class net.sf.basedb.util.Values
Convert an array of strings to an array of Double:s.
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.
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.
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>.
getDropIndexSql(String, String, String, String, boolean) - 
Method in class net.sf.basedb.core.dbengine.MySQLEngine
Generate DROP INDEX <name> ON <catalog>.
getDropIndexSql(String, String, String, String, boolean) - 
Method in class net.sf.basedb.core.dbengine.PostgresDbEngine
Generate ALTER TABLE <schema>.
getDynamicCatalog() - 
Static method in class net.sf.basedb.core.Application
Get the name of the dynamic catalog.
getDynamicExpression(DbControl, 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.
getDynamicRawData() - 
Method in class net.sf.basedb.core.RawBioAssay
Get a dynamic query that returns the raw data of this raw bioassay.
getDynamicRestriction(DbControl) - 
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, String) - 
Static method in class net.sf.basedb.core.ItemContext
Same as ItemContext.getDynamicExpression(DbControl, String) but generates
                a select object instead.
getEffectiveFilter() - 
Method in class net.sf.basedb.core.ItemContext.PropertyFilterPair
 
getEffectiveJarPath() - 
Method in class net.sf.basedb.core.JobAgentSettings
Get the effective path to the JAR file that contains the plugin implementation.
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.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.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.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
 
getEncodedName(Nameable, boolean, String) - 
Static method in class net.sf.basedb.clients.web.Base
Deprecated. Use Base.getLinkedName(String, Nameable, boolean, boolean) instead
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.clients.web.extensions.ScanResults
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.
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() - 
Method in class net.sf.basedb.core.log.EntityDetails
Get the entity logger that handles the logging for this
                event.
getEntityLogger(LogManager, Object) - 
Method in interface net.sf.basedb.core.log.LogManagerFactory
Get/create an entity logger for logging changes to the given entity.
getEntityMode() - 
Method in class net.sf.basedb.core.hibernate.SessionWrapper
 
getEntityName(Object) - 
Method in class net.sf.basedb.core.hibernate.SessionWrapper
 
getEntityName() - 
Method in class net.sf.basedb.core.RawDataType
 
getEntry(int) - 
Method in class net.sf.basedb.util.bfs.MetadataModel.Section
Get the entry in this section with the given index.
getEntry(String) - 
Method in class net.sf.basedb.util.bfs.MetadataModel.Section
Get the first entry in this section with a given key.
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.
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.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.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.ExperimentData
 
getEntryDate() - 
Method in class net.sf.basedb.core.data.ExtraValueTypeData
 
getEntryDate() - 
Method in class net.sf.basedb.core.data.FileTypeData
 
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.HardwareTypeData
 
getEntryDate() - 
Method in class net.sf.basedb.core.data.LabelData
 
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.ProtocolTypeData
 
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.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.ScanData
 
getEntryDate() - 
Method in class net.sf.basedb.core.data.SoftwareData
 
getEntryDate() - 
Method in class net.sf.basedb.core.data.SoftwareTypeData
 
getEntryDate() - 
Method in class net.sf.basedb.core.data.UserData
 
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.FileType
 
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.HardwareType
 
getEntryDate() - 
Method in class net.sf.basedb.core.Hybridization
 
getEntryDate() - 
Method in class net.sf.basedb.core.Label
 
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.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.ProtocolType
 
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.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.Scan
 
getEntryDate() - 
Method in class net.sf.basedb.core.Software
 
getEntryDate() - 
Method in class net.sf.basedb.core.SoftwareType
 
getEntryDate() - 
Method in class net.sf.basedb.core.User
 
getEnum() - 
Method in class net.sf.basedb.clients.web.taglib.table.ColumnDef
 
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
 
getEnumValues() - 
Method in class net.sf.basedb.info.AnnotationTypeInfo
 
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(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() - 
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(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.
getEvent() - 
Method in class net.sf.basedb.core.BioPlateEventParticipant
Get the BioPlateEvent.
getEvent() - 
Method in class net.sf.basedb.core.data.BioMaterialSourceEventData
 
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.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.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.
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.
getException() - 
Method in class net.sf.basedb.clients.web.fileupload.FileUploadProgress
Get the exception that caused the upload to fail.
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.
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
 
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(ServletRequest, 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(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, 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.
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.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.ReporterList
Get the experiment this reporter list 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() - 
Method in class net.sf.basedb.util.overview.ExperimentOverview
Deprecated. Get the experiment of this overview.
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.
getExperimentalFactors(DbControl, BioAssaySet) - 
Method in class net.sf.basedb.plugins.BioAssaySetExporter
Deprecated.  
getExperimentalFactors(int, QueryOptions) - 
Method in class net.sf.basedb.ws.client.ExperimentClient
Gets info about the experimental factors for an experiment.
getExperimentalFactors(String, int, QueryOptions) - 
Method in class net.sf.basedb.ws.server.ExperimentService
Gets an array with information objects for each
                experimental factor in an 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.
getExperimentDesign() - 
Method in class net.sf.basedb.info.ExperimentInfo
 
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.
getExperiments(QueryOptions) - 
Method in class net.sf.basedb.ws.client.ExperimentClient
Gets info about experiments that are available in the logged in session.
getExperiments(String, QueryOptions) - 
Method in class net.sf.basedb.ws.server.ExperimentService
Gets an array with info about experiments 
                available for the active session.
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.
getExperimentType() - 
Method in class net.sf.basedb.info.ExperimentInfo
 
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.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.
getExportFormats() - 
Method in class net.sf.basedb.ws.client.BioAssaySetClient
Deprecated. In 2.12. Use BioAssaySetClient.getDataFileTypes(int, QueryOptions) instead.
getExportFormats(String) - 
Method in class net.sf.basedb.ws.server.BioAssaySetService
Deprecated. In 2.12. Use BioAssaySetService.getDataFileTypes(String, int, QueryOptions)
                        instead
getExportName() - 
Method in class net.sf.basedb.plugins.BioAssaySetExporter.QueryItem
Deprecated.  
getExportproperty() - 
Method in class net.sf.basedb.clients.web.taglib.table.ColumnDef
 
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(DbControl, DynamicQuery, BioAssaySet, boolean) - 
Method in class net.sf.basedb.plugins.BaseFileExporterPlugin.ExtendedDynamicField
 
getExpression(DbControl, DynamicQuery, boolean) - 
Method in class net.sf.basedb.plugins.BioAssaySetExporter.QueryItem
Deprecated.  
getExpression(DbControl, DynamicQuery, boolean, Formula.AverageMethod) - 
Method in class net.sf.basedb.plugins.BioAssaySetExporter.QueryItem
Deprecated.  
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.
getExpression() - 
Method in class net.sf.basedb.util.export.spotdata.SimpleDynamicField
Get the configured express.
getExpressions() - 
Method in class net.sf.basedb.core.IntensityFormula
Get the expressions used to calculate the intensities.
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
getExtendedProperties() - 
Method in class net.sf.basedb.ws.client.ReporterClient
Gets the extended properties, for reporters, through web services.
getExtendedProperties() - 
Method in class net.sf.basedb.ws.server.ReporterService
Gets information about each extended property for reporters.
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(String) - 
Method in class net.sf.basedb.clients.web.extensions.ExtensionsControl
Get the extension with a given ID.
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.info.DataFileTypeInfo
 
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.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.
getExtensionDirectory() - 
Method in class net.sf.basedb.clients.web.extensions.ExtensionsDirectory
Get the file object representing the directory where
                extensions are installed.
getExtensionPoint(String) - 
Method in class net.sf.basedb.clients.web.extensions.ExtensionsControl
Get the extension point with a given ID.
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(String) - 
Method in class net.sf.basedb.util.extensions.Registry
Get the extension point with a given ID.
getExtensionPoint() - 
Method in class net.sf.basedb.util.extensions.Registry.RegisteredExtension
Get the extension point this extension is registered with.
getExtensionPoints() - 
Method in class net.sf.basedb.clients.web.extensions.ExtensionsControl
Get an iterator returning all registered extension points.
getExtensionPoints() - 
Method in class net.sf.basedb.clients.web.extensions.ExtensionsFile
Get an iterator returning all extension points that
                are defined by this file.
getExtensionPoints() - 
Method in class net.sf.basedb.util.extensions.Registry
Get an iterator returning 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 an iterator returning all registered extensions.
getExtensions(String) - 
Method in class net.sf.basedb.clients.web.extensions.ExtensionsControl
Get an iterator returning all registered extensions for a
                specific extension point.
getExtensions() - 
Method in class net.sf.basedb.clients.web.extensions.ExtensionsFile
Get an iterator returning all extensions that
                are defined by this file.
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 an iterator returning all registered extensions.
getExtensions(String) - 
Method in class net.sf.basedb.util.extensions.Registry
Get an iterator returning all registered extensions
                for a given extension point.
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.
getExternalClientId() - 
Method in class net.sf.basedb.core.SessionControl
Get the external id of the Client application in use.
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.BioMaterial
Get the external id of the biomaterial.
getExternalId() - 
Method in class net.sf.basedb.core.BioMaterialList
Get the external id for this list.
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.BioMaterialListData
Get the external id for this ReporterList item.
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.JobAgentData
Get the external ID for the job agent.
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.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.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.
getExternalId() - 
Method in class net.sf.basedb.info.AnnotationTypeInfo
 
getExternalId() - 
Method in class net.sf.basedb.info.DataFileTypeInfo
 
getExternalId() - 
Method in class net.sf.basedb.info.ReporterListInfo
 
getExtract() - 
Method in class net.sf.basedb.core.LabeledExtract
Get the Extract that is the parent of this labeled extract.
getExtracts() - 
Method in class net.sf.basedb.core.Sample
Get a query that returns all extracts created from this sample.
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.
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(ExtraValueType) - 
Method in class net.sf.basedb.core.BioAssaySet
Get the extra value of the specified type in this bioassayset.
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.
getExtraValueField(String, ExtraValue.CoordinateType, String) - 
Method in class net.sf.basedb.util.export.spotdata.AbstractFieldConverter
Get an extra value dynamic field.
getExtraValueField(String, ExtraValue.CoordinateType, String) - 
Method in class net.sf.basedb.util.export.spotdata.FieldConverter
Deprecated. Find an extra value with the given external id and coordinate type and
                create a dynamic field from it using exportTitle as the title.
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.
getFactoryParameters(Object) - 
Method in class net.sf.basedb.clients.web.extensions.ExtensionsFile
Get a XML-like string representation of the parameters that was
                used to initialise a factory.
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.ExperimentOverview
Deprecated. Get all failures generated by validation rules.
getFailures() - 
Method in class net.sf.basedb.util.overview.GenericOverview
Get a list containing all validation failures.
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.
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.
getFeatureBatcher() - 
Method in class net.sf.basedb.core.ArrayDesign
Deprecated. Use ArrayDesign.getFeatureBatcher(FeatureIdentificationMethod, Job) instead
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.
getField() - 
Method in class net.sf.basedb.plugins.BfsExporterPlugin.ExtendedExportableField
 
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.extensions.ExtensionsDirectory
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() - 
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.ImageData
 
getFile() - 
Method in class net.sf.basedb.core.data.ProtocolData
 
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.
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.Image
 
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(String) - 
Method in class net.sf.basedb.util.bfs.BaseInputStreamLocator
 
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.util.bfs.MetadataModel
Get the file entry for a given key.
getFile() - 
Method in class net.sf.basedb.util.FileExportOutputStream
 
getFileByExtensionId(String) - 
Method in class net.sf.basedb.clients.web.extensions.ExtensionsControl
Get information about the file a given extension or extension
                point is defined in.
getFileByExtensionId(String) - 
Method in class net.sf.basedb.clients.web.extensions.ExtensionsDirectory
Get information about the file a given extension or extension
                point is defined in.
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 iterator returning all XML/JAR files which contains installed
                extensions.
getFiles() - 
Method in class net.sf.basedb.clients.web.extensions.ExtensionsDirectory
Get an iterator returning all XML/JAR files which contains installed
                extensions.
getFiles() - 
Method in class net.sf.basedb.clients.web.extensions.ScanResults
Get all extension files that was handled in the last scan.
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.
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.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.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.core.data.FileData
Get the associated FileTypeData item.
getFileType() - 
Method in class net.sf.basedb.core.data.FileTypeIndex
 
getFileType() - 
Method in class net.sf.basedb.core.data.MimeTypeData
Get the associated FileTypeData item.
getFileType() - 
Method in class net.sf.basedb.core.File
Get the associated FileType item.
getFileType() - 
Method in class net.sf.basedb.core.MimeType
Get the associated FileType item.
getFileType(DataFileType, PlatformVariant) - 
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.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(PlatformVariant, boolean) - 
Method in class net.sf.basedb.core.Platform
Get the file types registered with this platform.
getFileTypes(boolean) - 
Method in class net.sf.basedb.core.PlatformVariant
Get a query returning file types registered with this platform
                variant.
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
 
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.
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
 
getFilterRestriction(String, DbControl, EntityQuery) - 
Method in class net.sf.basedb.core.ItemContext
Create a restriction from a property filter.
getFilters() - 
Method in class net.sf.basedb.core.data.DataCubeData
This is the inverse end.
getFirstAssayFieldIndex() - 
Method in class net.sf.basedb.util.importer.spotdata.BaseFileInfo.SpotSectionInfo
The index of the first data column that contains assay data.
getFirstMatching(DbControl, ItemQuery<T>, String, PropertyFilter) - 
Static method in class net.sf.basedb.clients.web.Base
 
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 interface net.sf.basedb.core.query.Query
The number of the row the query should start returning.
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(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
 
getFloat(String) - 
Static method in class net.sf.basedb.util.Values
Convert a string to an float.
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(String[]) - 
Static method in class net.sf.basedb.util.Values
Convert an array of strings to an array of Float:s.
getFloatOption(String, Float) - 
Method in class net.sf.basedb.core.AnnotationType
Get an option and convert the value to a float.
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, SessionImplementor) - 
Method in class net.sf.basedb.core.ExtendedPropertyAccessor.GetterSetter
Get the value of the extended property.
getFormat() - 
Method in class net.sf.basedb.core.data.ImageData
Get the format of the file. 0 = unknown, 1 = TIFF, 2 = JPEG
getFormat() - 
Method in class net.sf.basedb.core.Image
Get the format of this image.
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.
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(String) - 
Method in class net.sf.basedb.clients.web.taglib.table.Table
 
getFormatter() - 
Method in class net.sf.basedb.clients.web.taglib.table.TableColumn
 
getFormatter(Formatter<T>) - 
Method in class net.sf.basedb.core.Unit
Create a formatter for formatting values with this unit.
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
 
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.
getFormulaField(String, String) - 
Method in class net.sf.basedb.util.export.spotdata.FieldConverter
Deprecated. Find a formula with the given name and create a dynamic field from it
                using exportTitle as the title.
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 freezer associated with 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
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.
getFullPermissionNames(Identifiable) - 
Static method in class net.sf.basedb.clients.web.PermissionUtil
 
getFullPermissionNames(Set<Permission>) - 
Static method in class net.sf.basedb.clients.web.PermissionUtil
Create a comma-separated string with "readable" permission names.
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.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.parser.ColFunction
 
getFunctionName() - 
Method in class net.sf.basedb.util.parser.DataNoFunction
 
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.
getGamma() - 
Method in class net.sf.basedb.core.data.SpotImagesData
The gamma correction value.
getGamma() - 
Method in class net.sf.basedb.core.SpotImages
Get the gamma correction value.
getGenericDataFiles(DbControl, FileStoreEnabled, String) - 
Static method in class net.sf.basedb.core.FileStoreUtil
Get all files with a specific generic FileType in a given item's file
                set.
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(Class, String) - 
Method in class net.sf.basedb.core.ExtendedPropertyAccessor
Create a Getter object for the specified class and
                property.
getGlobalSignalId(SignalHandler) - 
Method in class net.sf.basedb.core.signal.AbstractSignalReceiver
Generate a signal ID string.
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.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.
getGreenImageFile() - 
Method in class net.sf.basedb.core.data.SpotImagesData
The file used for the green component in the spot images.
getGreenImageFile() - 
Method in class net.sf.basedb.core.SpotImages
Get the file which was used for the green channel in the
                spot images.
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.InternalStorageController.StorageKeyring
Return empty set.
getGroups(boolean) - 
Method in class net.sf.basedb.core.Keyring
 
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.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.
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.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.ExtractImporter
 
getGuiContexts() - 
Method in class net.sf.basedb.plugins.batchimport.HybridizationImporter
 
getGuiContexts() - 
Method in class net.sf.basedb.plugins.batchimport.LabeledExtractImporter
 
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.ScanImporter
 
getGuiContexts() - 
Method in class net.sf.basedb.plugins.BfsExporterPlugin
 
getGuiContexts() - 
Method in class net.sf.basedb.plugins.BioAssaySetExporter
Deprecated.  
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.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.HardwareTypeData
This is the inverse end.
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.HardwareType
Get a query that returns all hardware of this type
getHardware() - 
Method in class net.sf.basedb.core.PlateEvent
Get the Hardware that was used in this event.
getHardwareType() - 
Method in class net.sf.basedb.core.data.HardwareData
 
getHardwareType() - 
Method in class net.sf.basedb.core.Hardware
Get the associated HardwareType item.
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(String) - 
Method in class net.sf.basedb.core.RawBioAssay
Get the value for the raw data header with the specified name.
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.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 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.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.Help
 
getHelpid() - 
Method in class net.sf.basedb.clients.web.taglib.tab.Tab
 
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.
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
 
getHighestScoreIdx(double[][]) - 
Method in class net.sf.basedb.util.fuzzy.StringMatcher
 
getHighlight() - 
Method in class net.sf.basedb.clients.web.taglib.table.Row
 
getHistoryOf(BasicItem) - 
Static method in class net.sf.basedb.core.ChangeHistory
Get the change history for a given item.
getHome(Extension) - 
Method in class net.sf.basedb.clients.web.extensions.JspContext
Get the URL to the home directory for a given extension.
getHome() - 
Method in class net.sf.basedb.util.extensions.xml.PathConverter
Get the value of the home path.
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.
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.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.
getHttpClient() - 
Method in class net.sf.basedb.core.File
Get a HttpClient object that has been configured to download this file.
getHybridization() - 
Method in class net.sf.basedb.core.ArraySlide
Get the Hybridization item which was used on this slide.
getHybridization() - 
Method in class net.sf.basedb.core.BioMaterialEvent
Get the Hybridization that was created by this event.
getHybridization() - 
Method in class net.sf.basedb.core.data.ArraySlideData
Get the hybridization
getHybridization() - 
Method in class net.sf.basedb.core.data.BioMaterialEventData
Get the hybridization that was created by this event.
getHybridization() - 
Method in class net.sf.basedb.core.data.ScanData
Get the hybridization.
getHybridization() - 
Method in class net.sf.basedb.core.Scan
Get the Hybridization this scan is created from.
getHybridizations() - 
Method in class net.sf.basedb.core.LabeledExtract
Get a query that returns all hybridizations created from this 
                labeled extract.
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.Note
 
getIcon() - 
Method in class net.sf.basedb.clients.web.taglib.table.Button
 
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 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.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(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(BasicItem) - 
Method in class net.sf.basedb.clients.web.plugins.ItemQueryWrapper
Calls BasicItem.getId()
getId(T) - 
Method in interface net.sf.basedb.clients.web.plugins.QueryWrapper
Get the ID of the specified item.
getId(ReporterScore) - 
Method in class net.sf.basedb.clients.web.plugins.ReporterScoreQueryWrapper
Calls BasicData.getId().
getId() - 
Method in class net.sf.basedb.clients.web.taglib.table.TableColumn
 
getId() - 
Method in class net.sf.basedb.clients.web.util.NameablePluginAdaptor
 
getId() - 
Method in class net.sf.basedb.core.BasicItem
 
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.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(String) - 
Static method in class net.sf.basedb.core.SystemItems
Get the numeric id for an item when you know the system id.
getId() - 
Method in class net.sf.basedb.info.BasicItemInfo
 
getId() - 
Method in class net.sf.basedb.plugins.BaseFileExporterPlugin.ExtendedDynamicField
 
getId() - 
Method in class net.sf.basedb.plugins.BfsExporterPlugin.ExtendedExportableField
 
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 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 class net.sf.basedb.ws.client.SessionClient
Gets the id of the session.
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
getIdentifier(Object) - 
Method in class net.sf.basedb.core.hibernate.SessionWrapper
 
getIdFromPath(DbControl, Path) - 
Static method in class net.sf.basedb.core.Directory
Get the id of a directory when you know the path.
getIdMethod(String) - 
Method in class net.sf.basedb.plugins.batchimport.AbstractItemImporter
Get the id method to use for finding items.
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.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.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.HybridizationImporter
Useable methods are:
                
                PropertyIdMethod.NAME
                InternalIdMethod.INTERNAL_ID
                FallbackIdMethod.NAME_OR_ID
                
getIdMethods() - 
Method in class net.sf.basedb.plugins.batchimport.LabeledExtractImporter
Useable methods are:
                
                PropertyIdMethod.NAME
                PropertyIdMethod.EXTERNAL_ID
                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.ScanImporter
Useable methods are:
                
                PropertyIdMethod.NAME
                InternalIdMethod.INTERNAL_ID
                FallbackIdMethod.NAME_OR_ID
                
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.
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.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.
getImage() - 
Method in class net.sf.basedb.core.SpotImage
Get the image as an array of bytes.
getImagealign() - 
Method in class net.sf.basedb.clients.web.taglib.table.Button
 
getImages() - 
Method in class net.sf.basedb.core.data.ScanData
This is the inverse end.
getImages() - 
Method in class net.sf.basedb.core.Scan
Get a query that returns all images for this scan.
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
 
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.ItemContext
Get a Set object to specify Include options for 
                a query.
getIncludeInProject() - 
Method in class net.sf.basedb.info.QueryOptions
Gets if items in the project that is currently active should be included.
getIncludeMine() - 
Method in class net.sf.basedb.info.QueryOptions
Gets if items of logged in user should be included
getIncludeNotRemoved() - 
Method in class net.sf.basedb.info.QueryOptions
Include not removed items
getIncludeOthers() - 
Method in class net.sf.basedb.info.QueryOptions
Gets if other users' item should be included in the query
getIncludeShared() - 
Method in class net.sf.basedb.info.QueryOptions
Gets if items shared to the logged in user should 
                be included or not
getIndex(String) - 
Method in class net.sf.basedb.clients.web.servlet.PlotServlet.CFResultIterator
 
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(String) - 
Method in class net.sf.basedb.core.DynamicResultIterator
 
getIndex(String, String[], Comparator<String>) - 
Method in class net.sf.basedb.core.Metadata
 
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() - 
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
 
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.
getInherited() - 
Method in class net.sf.basedb.core.data.AnnotationSetData
Annotations that are inherited from other annotation sets.
getInheritedAnnotations() - 
Method in class net.sf.basedb.core.AnnotationSet
Get a query that returns directly inherited annotations in this annotation set.
getInheritedAnnotationSets() - 
Method in class net.sf.basedb.core.AnnotationSet
Get a query that returns all inherited annotation sets in this annotation set.
getInheritedSets() - 
Method in class net.sf.basedb.core.data.AnnotationSetData
Annotation sets from which this set should inherit all annotations.
getInheritingAnnotationSets() - 
Method in class net.sf.basedb.core.AnnotationSet
Get a query that returns all annotation sets inheriting from this annotation set.
getInheritingSets() - 
Method in class net.sf.basedb.core.data.AnnotationData
The annotation sets which inherit this annotation.
getInheritingSets() - 
Method in class net.sf.basedb.core.data.AnnotationSetData
Annotation sets inherting annotations from this set.
getInitial() - 
Method in class net.sf.basedb.clients.web.taglib.HideableSection
 
getInitializedFlatFileParser() - 
Method in class net.sf.basedb.plugins.AbstractFlatFileImporter
Create and initialise a flat file parser by setting all regular expressions
                and other options.
getInitializedFlatFileParser() - 
Method in class net.sf.basedb.plugins.AnnotationFlatFileImporter
 
getInitializedFlatFileParser(ParameterValues) - 
Method in class net.sf.basedb.plugins.AnnotationFlatFileImporter
 
getInitializedFlatFileParser(InputStream, String) - 
Method in class net.sf.basedb.plugins.Base1PluginExecuter
Creates a FlatFileParser for a plugin configuration file.
getInitializedFlatFileParser() - 
Method in class net.sf.basedb.plugins.batchimport.AbstractItemImporter
 
getInitializedFlatFileParser(ParameterValues) - 
Method in class net.sf.basedb.plugins.batchimport.AbstractItemImporter
 
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.util.basefile.BaseFileParser
Creates a FlatFileParser for parsing a BASEfile.
getInitParameter(String) - 
Method in class net.sf.basedb.clients.web.extensions.ServletWrapper
 
getInitParameterNames() - 
Method in class net.sf.basedb.clients.web.extensions.ServletWrapper
 
getInputStream(UploadedFile) - 
Method in class net.sf.basedb.clients.web.fileupload.FileUpload
Get an input stream for reading from the current file section.
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.core.SpotImage
Get an InputStream of the image.
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(File) - 
Static method in class net.sf.basedb.util.FileUtil
Get a buffered InputStream object reading from
                the specified 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(String, int) - 
Method in class net.sf.basedb.util.StaticCache
Get a lock-safe input stream.
getInputStream() - 
Method in class net.sf.basedb.ws.server.BaseFileDataSource
 
getInputStream() - 
Method in class net.sf.basedb.ws.server.TempFileDataSource
Get an InputStream that deletes the source file as soon
                as the end of file is reached or close() is called.
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.
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.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.
getInstance() - 
Static method in class net.sf.basedb.util.jep.Log2Function
Get the singleton instance of this function.
getInt(int) - 
Method in class net.sf.basedb.clients.web.servlet.PlotServlet.CFSqlResult
 
getInt(String) - 
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.Config
Get the configuration setting specified by key as an integer value.
getInt(int) - 
Method in class net.sf.basedb.core.DynamicResultIterator.SqlResultImpl
 
getInt(String) - 
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.core.IntegerUtil
Get the int value of an String.
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(int) - 
Method in interface net.sf.basedb.core.query.SqlResult
Get the value of the specified column as 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
 
getInt(String) - 
Static method in class net.sf.basedb.util.Values
Convert a string to an integer.
getInt(String, int) - 
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.
getIntAttribute(Element, String, int) - 
Static method in class net.sf.basedb.util.XMLUtil
Get the value of an attribute as an integer.
getInteger(String, Integer) - 
Static method in class net.sf.basedb.util.Values
 
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.
getIntensityField(String) - 
Method in class net.sf.basedb.util.export.spotdata.FieldConverter
Deprecated. 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.
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(Extension) - 
Static method in class net.sf.basedb.clients.web.extensions.service.Services
 
getItem(DbControl, ChangeHistory, boolean, boolean) - 
Static method in class net.sf.basedb.clients.web.ChangeHistoryUtil
Get the item that was changed in HTML format.
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(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() - 
Method in class net.sf.basedb.core.ContextKey
 
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() - 
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.filehandler.AbstractDataFileHandler
Get the itemt that was set by AbstractDataFileHandler.setItem(FileStoreEnabled)
getItem() - 
Method in class net.sf.basedb.core.FileSet
Get the item this file set belongs to.
getItem(DbControl) - 
Method in class net.sf.basedb.core.ItemProxy
 
getItem() - 
Method in class net.sf.basedb.core.plugin.GuiContext
 
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.core.snapshot.AnnotationSnapshot
Get the item that this annotation belongs to.
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(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.
getItemClass() - 
Method in enum net.sf.basedb.core.Item
Get the class object that is used to handle items of this type.
getItemCount(int) - 
Method in class net.sf.basedb.util.plot.HistogramPlot.HistogramDataset
 
getItemCount() - 
Method in class net.sf.basedb.util.plot.HistogramPlot.HistogramSeries
 
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.
getItemId() - 
Method in class net.sf.basedb.core.snapshot.AnnotationSnapshot
Get the id of the item this annotation belongs 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.InternalStorageController.StorageKeyring
Return empty set.
getItemKeys(Permission) - 
Method in class net.sf.basedb.core.Keyring
 
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.SessionControl
Get the id of all item keys where the logged in user has the
                requested permission.
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(Item) - 
Method in class net.sf.basedb.core.MultiPermissions
Get all items of a specific item type.
getItems(Collection<Item>) - 
Method in class net.sf.basedb.core.MultiPermissions
Get all items of specific item types.
getItems() - 
Method in class net.sf.basedb.core.ParameterType
Get the list of values to choose from.
getItems(Item, int, int, Permission) - 
Method in class net.sf.basedb.core.Project
Deprecated. Use Project.getItems(Item, int, int, Permission, Set) instead
getItems(Item, int, int, Permission, Set<Include>) - 
Method in class net.sf.basedb.core.Project
 
getItems(Set<Item>, int, int, Permission, Set<Include>) - 
Method in class net.sf.basedb.core.Project
Deprecated. In 2.15, use Project.getItems(Set, int, int, Permission, Set, Restriction)
                        instead
getItems(Set<Item>, int, int, Permission, Set<Include>, Restriction) - 
Method in class net.sf.basedb.core.Project
Load the items in a project.
getItems(DbControl, Item, int, int) - 
Static method in class net.sf.basedb.core.Trashcan
 
getItems(DbControl, Set<Item>, int, int) - 
Static method in class net.sf.basedb.core.Trashcan
Load all items flagged for deletion that are owned by the logged in user.
getItems(Item, int, int, Permission) - 
Method in class net.sf.basedb.core.User
 
getItems(Set<Item>, int, int, Permission) - 
Method in class net.sf.basedb.core.User
Deprecated. In 2.15, use User.getItems(Set, int, int, Permission, Restriction) instead
getItems(Set<Item>, int, int, Permission, Restriction) - 
Method in class net.sf.basedb.core.User
Load the items owned by this user.
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.
getItemType() - 
Method in class net.sf.basedb.core.AbstractEntityQuery
 
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.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 enum net.sf.basedb.core.Project.Default
 
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.core.snapshot.AnnotationSnapshot
Get the item type of the item this annotation belongs 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.
getItemTypes() - 
Method in class net.sf.basedb.info.AnnotationTypeInfo
 
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.
getJarPath() - 
Method in class net.sf.basedb.core.data.JobAgentSettingsData
Get the path to the JAR file where the plugin class is located.
getJarPath() - 
Method in class net.sf.basedb.core.data.PluginDefinitionData
Get the path to the JAR file where the plugin class is located.
getJarPath() - 
Method in class net.sf.basedb.core.data.PluginTypeData
Get the path to the JAR file where the interface class is located.
getJarPath() - 
Method in class net.sf.basedb.core.JobAgentSettings
Get the path to the JAR file that contains the plugin implementation.
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.
getJarPath() - 
Method in class net.sf.basedb.util.PluginInfo
Gets the name of the jar file holding this plugin
getJarPathInDatabase() - 
Method in class net.sf.basedb.util.PluginInfo
Gets the jar path of the already installed plugin.
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.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.DynamicQuery
Create custom JEP function that can be used with the current
                query.
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(DbControl, ChangeHistory, boolean, boolean) - 
Static method in class net.sf.basedb.clients.web.ChangeHistoryUtil
Get the job that made the change in HTML format.
getJob() - 
Method in class net.sf.basedb.core.ArrayDesign
Get the job that imported features to this array design.
getJob(DbControl) - 
Method in class net.sf.basedb.core.ChangeHistory
Load the job that was executing when the change was made.
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.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.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 imported data to this raw bioassay.
getJob() - 
Method in class net.sf.basedb.core.Transformation
Get the job that executed this transformation.
getJobAgent(DbControl) - 
Method in class net.sf.basedb.clients.jobagent.Agent
Get the JobAgent item corresponding to this agent.
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.
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.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.
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.
getJobs() - 
Method in class net.sf.basedb.util.jobagent.JobAgentInfo
Deprecated. Use JobAgentInfo.getJobInfo() instead
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.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.
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(int) - 
Method in class net.sf.basedb.util.bfs.MetadataModel.Section
Get the key of the entry at the given index.
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(int) - 
Method in class net.sf.basedb.util.Enumeration
 
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
 
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.util.QueryParameters
Get all keys that are present in the query string.
getLabel() - 
Method in class net.sf.basedb.core.data.LabeledExtractData
The label compound used to label the extract.
getLabel() - 
Method in class net.sf.basedb.core.data.ParameterValueData
Get the label of the parameter.
getLabel() - 
Method in class net.sf.basedb.core.LabeledExtract
Get the Label compound used for labeling the extract.
getLabel() - 
Method in class net.sf.basedb.core.ParameterInfo
 
getLabel() - 
Method in class net.sf.basedb.core.PluginParameter
Get the label of the parameter.
getLabeledExtracts() - 
Method in class net.sf.basedb.core.Extract
Get a query that returns all labeled extracts created from this extract.
getLabeledExtracts(int) - 
Method in class net.sf.basedb.core.Hybridization
Get a query that returns labeled extracts connected to
                this hybridization.
getLabeledExtracts() - 
Method in class net.sf.basedb.core.Label
Get a query that returns all labeled extracts labeled
                with this label.
getLastAccess() - 
Method in class net.sf.basedb.core.SessionControl
Get the time this object last was accessed.
getLastChallenge() - 
Method in class net.sf.basedb.core.SessionControl
Get the last challenge generated.
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(HttpResponse) - 
Static method in class net.sf.basedb.util.HttpUtil
Get the date the content was last modified from the headers 
                in the response.
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.
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
 
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.
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.info.ExtendedPropertyInfo
 
getLength() - 
Method in class net.sf.basedb.util.FileImportInputStream
Calls File.getSize() to get the file size.
getLimit() - 
Method in class net.sf.basedb.core.signal.ProgressReporterSignalHandler
Get the percentage limit where signal checking becomes disabled.
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
 
getLinkedFile(String, File, boolean, boolean, boolean, String) - 
Static method in class net.sf.basedb.clients.web.Base
 
getLinkedName(String, Nameable, boolean, boolean) - 
Static method in class net.sf.basedb.clients.web.Base
 
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
 
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 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.
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
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.
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.
getLogger() - 
Static method in class net.sf.basedb.core.Application
Get the BASE core logger.
getLogin() - 
Method in class net.sf.basedb.clients.jobagent.Agent
Get the agent.user configuration value.
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.
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.
getLogManagerFactory() - 
Static method in class net.sf.basedb.core.Application
Get the log manager factory, or null if not enabled.
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(String, long) - 
Static method in class net.sf.basedb.core.Config
Get the configuration setting specified by key as a long value.
getLong(HttpResponse, String, Long) - 
Static method in class net.sf.basedb.util.HttpUtil
 
getLong(String) - 
Static method in class net.sf.basedb.util.Values
Convert a string to a long.
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(String[]) - 
Static method in class net.sf.basedb.util.Values
Convert an array of strings to an array of Long:s.
getLongFormatter(SessionControl) - 
Static method in class net.sf.basedb.clients.web.formatter.FormatterFactory
Get the logged in user's formatter for long numbers.
getLongOption(String, Long) - 
Method in class net.sf.basedb.core.AnnotationType
Get an option and convert the value to a long.
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.
getMainHqlQuery(DbControl) - 
Method in class net.sf.basedb.core.AbstractHqlQuery
Build the main query and set parameter values for it.
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.
getMaintenance() - 
Method in class net.sf.basedb.info.VersionInfo
 
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.BioAssaySetExporter
Deprecated.  
getMainType() - 
Method in class net.sf.basedb.plugins.CdfFileReporterImporter
 
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.plugins.SpotImageCreator
 
getMainType() - 
Method in class net.sf.basedb.util.zip.AbstractFileUnpacker
 
getMajor() - 
Static method in class net.sf.basedb.core.Version
Get the major version.
getMajor() - 
Method in class net.sf.basedb.info.VersionInfo
 
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(FlatFileParser, String, Integer, Mapper) - 
Method in class net.sf.basedb.plugins.AbstractFlatFileImporter
Get a mapper for the specified flat file parser.
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
Create a mapper object that maps an expression string to a value.
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.
getMatchingReporters(DbControl) - 
Method in class net.sf.basedb.clients.web.ExperimentExplorer
Get the number of reporters matching the current reporter
                filter.
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.
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.
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 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.File
Get the MD5 hash of the file contents, or null if not known.
getMd5Password() - 
Method in class net.sf.basedb.core.data.PasswordData
Get the MD5 encrypted password.
getMean(int) - 
Method in class net.sf.basedb.clients.web.ExperimentExplorer.AnnotationGroup
Get the mean of the intensity values for the given channel.
getMean() - 
Method in class net.sf.basedb.util.plot.HistogramPlot.HistogramBin
Get the mean of all values in this bin.
getMember() - 
Method in class net.sf.basedb.core.ExtendedPropertyAccessor.GetterSetter
Always return null.
getMember(String) - 
Method in class net.sf.basedb.core.filehandler.AbstractDataFileHandler
Get the file set member of a specific DataFileType.
getMember(DataFileType) - 
Method in class net.sf.basedb.core.FileSet
Get the member of the given type.
getMemberBioMaterials() - 
Method in class net.sf.basedb.core.BioMaterialList
Get a query that returns all biomaterials that are
                members of 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.FileSet
Get the members of this file set.
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 FileType.
getMemberType() - 
Method in class net.sf.basedb.core.BioMaterialList
Get the item type of members on this list.
getMemberType() - 
Method in class net.sf.basedb.core.data.BioMaterialListData
Get the type of (biomaterial) items this list can hold.
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(String) - 
Method in class net.sf.basedb.plugins.executor.ExternalProgramExecutor.ResponseWrapper
 
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.
getMessages() - 
Method in class net.sf.basedb.clients.web.extensions.ScanResults.FileResults
A list of detailed messages, indicating the results of
                        individual operation on this file.
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.
getMessagestyle() - 
Method in class net.sf.basedb.clients.web.taglib.Note
 
getMetaColumn() - 
Method in class net.sf.basedb.core.FeatureCoordinate
 
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.
getMetadataReader() - 
Method in class net.sf.basedb.core.DataFileType
Create a new instance of the DataFileMetadataReader class specified
                by DataFileType.getMetadataReaderClass().
getMetadataReaderClass() - 
Method in class net.sf.basedb.core.data.DataFileTypeData
Get the class name of the Java class that extracts metadata from
                this file type.
getMetadataReaderClass() - 
Method in class net.sf.basedb.core.DataFileType
Get the class name of the Java class that is used to extract metadata from files of
                this type.
getMetadataReaderJarPath() - 
Method in class net.sf.basedb.core.data.DataFileTypeData
Get the path to the JAR file where the validator class is located.
getMetadataReaderJarPath() - 
Method in class net.sf.basedb.core.DataFileType
Get the path to the JAR file where the meta data reader class is located.
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
 
getMetaRow() - 
Method in class net.sf.basedb.core.FeatureCoordinate
 
getMethod() - 
Method in class net.sf.basedb.core.ExtendedPropertyAccessor.GetterSetter
Always return null.
getMethod() - 
Method in class net.sf.basedb.plugins.batchimport.FallbackIdMethod
 
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(Item) - 
Method in class net.sf.basedb.util.overview.ExperimentOverview
Deprecated. Get the annotation types that have the 'Required for MIAME' flag
                set to true and is enabled for the specified item type.
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.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(DbControl, String, String) - 
Static method in class net.sf.basedb.core.MimeType
Get the MIME type of a given file name or extension.
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.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
 
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 class net.sf.basedb.util.PluginInfo
Gets the lowest version of BASE that the plugin is compatible with
getMinor() - 
Static method in class net.sf.basedb.core.Version
Get the minor version.
getMinor() - 
Method in class net.sf.basedb.info.VersionInfo
 
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(Node) - 
Method in class net.sf.basedb.util.overview.validator.AnnotationValidator
 
getMissingItemFix(Node) - 
Method in class net.sf.basedb.util.overview.validator.AnyToAnyValidator
 
getMissingItemFix(Node) - 
Method in class net.sf.basedb.util.overview.validator.ArrayBatchValidator
The suggested fix is to add an array batch to the
                slide.
getMissingItemFix(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(Node) - 
Method in class net.sf.basedb.util.overview.validator.ArraySlideValidator
The suggested fix is to add an array slide to the
                hybridization.
getMissingItemFix(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(Node) - 
Method in class net.sf.basedb.util.overview.validator.BioSourceValidator
 
getMissingItemFix(Node) - 
Method in class net.sf.basedb.util.overview.validator.DataFileValidator
 
getMissingItemFix(Node) - 
Method in class net.sf.basedb.util.overview.validator.ExperimentalFactorValidator
 
getMissingItemFix(Node) - 
Method in class net.sf.basedb.util.overview.validator.ExperimentValidator
 
getMissingItemFix(Node) - 
Method in class net.sf.basedb.util.overview.validator.ExtractValidator
The suggested fix is to add a parent extract to the 
                labled extract or one or more extracts to the pooled extract.
getMissingItemFix(Node) - 
Method in class net.sf.basedb.util.overview.validator.HardwareValidator
 
getMissingItemFix(Node) - 
Method in class net.sf.basedb.util.overview.validator.HybridizationValidator
 
getMissingItemFix(Node) - 
Method in class net.sf.basedb.util.overview.validator.LabeledExtractValidator
The suggested fix is to add a source labeled extracts to the 
                either the hybridization or the pooled labeled extract.
getMissingItemFix(Node) - 
Method in class net.sf.basedb.util.overview.validator.PlatformValidator
 
getMissingItemFix(Node) - 
Method in class net.sf.basedb.util.overview.validator.ProtocolParameterValidator
 
getMissingItemFix(Node) - 
Method in class net.sf.basedb.util.overview.validator.ProtocolValidator
 
getMissingItemFix(Node) - 
Method in class net.sf.basedb.util.overview.validator.RawBioAssayValidator
 
getMissingItemFix(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(Node) - 
Method in class net.sf.basedb.util.overview.validator.ScanValidator
 
getMissingItemFix(Node) - 
Method in class net.sf.basedb.util.overview.validator.SoftwareValidator
 
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.FileSetMemberNameGenerator
 
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.FileSetMemberNameGenerator
 
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.
getMultiplicity() - 
Method in class net.sf.basedb.info.AnnotationTypeInfo
 
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.ExtensionsFile
Get the name of the file.
getName() - 
Method in class net.sf.basedb.clients.web.ModeInfo
 
getName(BasicItem) - 
Method in class net.sf.basedb.clients.web.taglib.Select
 
getName() - 
Method in class net.sf.basedb.clients.web.taglib.table.Hidden
 
getName() - 
Method in class net.sf.basedb.clients.web.util.NameablePluginAdaptor
 
getName() - 
Method in class net.sf.basedb.core.AnyToAny
 
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.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.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.FileTypeData
 
getName() - 
Method in class net.sf.basedb.core.data.GroupData
 
getName() - 
Method in class net.sf.basedb.core.data.HardwareTypeData
 
getName() - 
Method in class net.sf.basedb.core.data.HelpData
 
getName() - 
Method in class net.sf.basedb.core.data.ImageData
 
getName() - 
Method in class net.sf.basedb.core.data.JobData
 
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.ProtocolTypeData
 
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.SettingData
Used by Hibernate to link with setting name.
getName() - 
Method in class net.sf.basedb.core.data.SoftwareTypeData
 
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.UserData
 
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.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.FileType
 
getName() - 
Method in class net.sf.basedb.core.Group
 
getName() - 
Method in class net.sf.basedb.core.HardwareType
 
getName() - 
Method in class net.sf.basedb.core.Help
 
getName() - 
Method in class net.sf.basedb.core.Image
 
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.Job
 
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.PluginDefinition
Get the name of the plugin.
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 enum net.sf.basedb.core.Project.Default
 
getName() - 
Method in class net.sf.basedb.core.Project
 
getName() - 
Method in class net.sf.basedb.core.ProtocolType
 
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.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.SoftwareType
 
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.VirtualColumn
Get the name of the column.
getName() - 
Method in class net.sf.basedb.info.BioAssaySetInfo
 
getName() - 
Method in class net.sf.basedb.info.CommonItemInfo
 
getName() - 
Method in class net.sf.basedb.info.DataFileTypeInfo
 
getName() - 
Method in class net.sf.basedb.info.ExtendedPropertyInfo
 
getName() - 
Method in interface net.sf.basedb.info.NameableInfo
Get the name of the info object
getName() - 
Method in class net.sf.basedb.info.ProjectInfo
 
getName() - 
Method in class net.sf.basedb.info.QueryParameter
Get the parameter name.
getName() - 
Method in class net.sf.basedb.plugins.Base1PluginExecuter.JobParameter
 
getName() - 
Method in class net.sf.basedb.plugins.BioAssaySetExporter.QueryItem
Deprecated.  
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.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.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.PluginConfigInfo
Gets the configuration's name
getName() - 
Method in class net.sf.basedb.util.resources.ResourceBundleWrapper
Get the base name of the resource bundle.
getName() - 
Method in class net.sf.basedb.ws.server.BaseFileDataSource
 
getNamedParameters() - 
Method in class net.sf.basedb.core.hibernate.QueryWrapper
 
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(DbControl, AnnotationType, AnnotationSet) - 
Static method in class net.sf.basedb.core.Annotation
Create a new annotation.
getNew(DbControl, Annotatable) - 
Static method in class net.sf.basedb.core.AnnotationSet
Create a new annotation set for the specified item.
getNew(DbControl, Type) - 
Static method in class net.sf.basedb.core.AnnotationType
Create a new AnnotationType item.
getNew(DbControl) - 
Static method in class net.sf.basedb.core.AnnotationTypeCategory
Creates a new AnnotationTypeCategory item.
getNew(DbControl, BasicItem, BasicItem, String, boolean) - 
Static method in class net.sf.basedb.core.AnyToAny
Create a new AnyToAny link
getNew(DbControl, ArrayDesign) - 
Static method in class net.sf.basedb.core.ArrayBatch
Create a new ArrayBatch item.
getNew(DbControl, boolean) - 
Static method in class net.sf.basedb.core.ArrayDesign
Deprecated. Use ArrayDesign.getNew(DbControl, Platform) instead
getNew(DbControl, Platform) - 
Static method in class net.sf.basedb.core.ArrayDesign
Create a new ArrayDesign item for a given platform.
getNew(DbControl, PlatformVariant) - 
Static method in class net.sf.basedb.core.ArrayDesign
Create a new ArrayDesign item for a given platform
                variant.
getNew(DbControl, ArrayDesign, BlockInfo) - 
Static method in class net.sf.basedb.core.ArrayDesignBlock
 
getNew(DbControl, ArrayBatch) - 
Static method in class net.sf.basedb.core.ArraySlide
Create a new ArraySlide item.
getNew(DbControl, BioAssaySet, DataCubeColumn) - 
Static method in class net.sf.basedb.core.BioAssay
Create a new BioAssay item.
getNew(DbControl, Transformation, DataCubeLayer) - 
Static method in class net.sf.basedb.core.BioAssaySet
Create a new BioAssaySet 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, Item) - 
Static method in class net.sf.basedb.core.BioMaterialList
Create a new BioMaterialList item.
getNew(DbControl, PlateGeometry) - 
Static method in class net.sf.basedb.core.BioPlate
Deprecated. In 2.16, use BioPlate.getNew(DbControl, PlateGeometry, BioPlateType) instead
                Will try to find a bioplate type that is not locked to a specific biomaterial
                type. If not found an exception is thrown.
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, BioPlateEventType) - 
Static method in class net.sf.basedb.core.BioPlateEvent
Create a new BioPlateEvent item.
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, String) - 
Static method in class net.sf.basedb.core.BioPlateEventType
Creates a new bioplate event type.
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, String) - 
Static method in class net.sf.basedb.core.Client
Create a new Client item.
getNew(DbControl, Client, String, String) - 
Static method in class net.sf.basedb.core.ClientDefaultSetting
Create a new ClientDefaultSetting item.
getNew(DbControl, VirtualDb) - 
Static method in class net.sf.basedb.core.DataCube
Create a new DataCube item.
getNew(DbControl, DataCube) - 
Static method in class net.sf.basedb.core.DataCubeColumn
Create a new DataCubeColumn item.
getNew(DbControl, DataCube, Type, ExtraValue.CoordinateType) - 
Static method in class net.sf.basedb.core.DataCubeExtraValue
Create a new DataCubeExtraValue 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, String, Item) - 
Static method in class net.sf.basedb.core.DataFileType
Create a new data file type.
getNew(DbControl, Directory) - 
Static method in class net.sf.basedb.core.Directory
Create a new Directory item.
getNew(DbControl, Path) - 
Static method in class net.sf.basedb.core.Directory
Create a new or existing Directory from a path.
getNew(DbControl, RawDataType) - 
Static method in class net.sf.basedb.core.Experiment
Create a new Experiment item.
getNew(DbControl) - 
Static method in class net.sf.basedb.core.Extract
Create a new Extract 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, BioAssaySet, ExtraValueType, DataCubeExtraValue, Job) - 
Static method in class net.sf.basedb.core.ExtraValue
Create a new ExtraValue item.
getNew(DbControl, String, Type) - 
Static method in class net.sf.basedb.core.ExtraValueType
Create a new ExtraValue item.
getNew(DbControl, ArrayDesign) - 
Static method in class net.sf.basedb.core.FeatureBatcher
Create a new batcher for regular features.
getNew(DbControl, Directory) - 
Static method in class net.sf.basedb.core.File
Create a new File item.
getNew(DbControl) - 
Static method in class net.sf.basedb.core.FileServer
Create a new FileServer item.
getNew(DbControl, FileStoreEnabled) - 
Static method in class net.sf.basedb.core.FileSet
Create a new file set for the specified 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) - 
Static method in class net.sf.basedb.core.Formula
Create a new Formula item.
getNew(DbControl, String, String) - 
Static method in class net.sf.basedb.core.GlobalDefaultSetting
Create a new GlobalDefaultSetting item.
getNew(DbControl) - 
Static method in class net.sf.basedb.core.Group
Create a new Group item.
getNew(DbControl, HardwareType) - 
Static method in class net.sf.basedb.core.Hardware
Create a new Hardware item.
getNew(DbControl) - 
Static method in class net.sf.basedb.core.HardwareType
Create a new HardwareType item.
getNew(DbControl, Client, String) - 
Static method in class net.sf.basedb.core.Help
Create a new Help item.
getNew(DbControl) - 
Static method in class net.sf.basedb.core.Hybridization
Create a new Hybridization item.
getNew(DbControl, BioPlateEventParticipant) - 
Static method in class net.sf.basedb.core.Hybridization
Create a new Hybridization item as part of a
                master bioplate event.
getNew(DbControl, Scan) - 
Static method in class net.sf.basedb.core.Image
Create a new Image item.
getNew(DbControl, PluginDefinition, PluginConfiguration) - 
Static method in class net.sf.basedb.core.Job
Deprecated. Use Job.getNew(DbControl, PluginDefinition, PluginConfiguration, Experiment)
                        instead
getNew(DbControl, PluginDefinition, PluginConfiguration, Experiment) - 
Static method in class net.sf.basedb.core.Job
Create a new Job item.
getNew(DbControl, String) - 
Static method in class net.sf.basedb.core.JobAgent
Create a new JobAgent item.
getNew(DbControl, JobAgent, PluginDefinition) - 
Static method in class net.sf.basedb.core.JobAgentSettings
Create a new JobAgentSettings item.
getNew(DbControl) - 
Static method in class net.sf.basedb.core.Label
Create a new Label item.
getNew(DbControl, Label) - 
Static method in class net.sf.basedb.core.LabeledExtract
Create a new LabeledExtract item.
getNew(DbControl, Label, BioPlateEventParticipant) - 
Static method in class net.sf.basedb.core.LabeledExtract
Create a new LabeledExtract item as part
                of a master bioplate event.
getNew(DbControl, User, String, User, Job) - 
Static method in class net.sf.basedb.core.Message
Create a new Message item.
getNew(DbControl) - 
Static method in class net.sf.basedb.core.MimeType
Create a new MimeType item.
getNew(DbControl, Date, Date) - 
Static method in class net.sf.basedb.core.News
Create a new News item.
getNew(DbControl) - 
Static method in class net.sf.basedb.core.PermissionTemplate
Create a new permission template item.
getNew(DbControl, PlateType) - 
Static method in class net.sf.basedb.core.Plate
Create a new Plate item.
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.PlateEventType
Create a new PlateEventType item.
getNew(DbControl, int, int) - 
Static method in class net.sf.basedb.core.PlateGeometry
Create a new PlateGeometry item.
getNew(DbControl, PlateGeometry, int, PlateGeometry, int) - 
Static method in class net.sf.basedb.core.PlateMapping
Create a new PlateMapping item.
getNew(DbControl, PlateGeometry) - 
Static method in class net.sf.basedb.core.PlateType
Create a new PlateType item.
getNew(DbControl, String, int) - 
Static method in class net.sf.basedb.core.Platform
Create a new file-only platform.
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, Platform, PlatformVariant, DataFileType, boolean) - 
Static method in class net.sf.basedb.core.PlatformFileType
Create a new item linking a file type to a platform/variant.
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, PluginDefinition) - 
Static method in class net.sf.basedb.core.PluginConfiguration
Create a new PluginConfiguration item.
getNew(DbControl, String, String, boolean) - 
Static method in class net.sf.basedb.core.PluginDefinition
Create a new PluginDefinition item.
getNew(DbControl, String, String) - 
Static method in class net.sf.basedb.core.PluginType
Create a new PluginType item.
getNew(DbControl) - 
Static method in class net.sf.basedb.core.Project
Create a new Project item.
getNew(DbControl, ProtocolType) - 
Static method in class net.sf.basedb.core.Protocol
Create a new Protocol item.
getNew(DbControl) - 
Static method in class net.sf.basedb.core.ProtocolType
Create a new FileType item.
getNew(DbControl, String) - 
Static method in class net.sf.basedb.core.Quantity
Create a new Quantity item.
getNew(DbControl, long) - 
Static method in class net.sf.basedb.core.Quota
Create a new Quota item.
getNew(DbControl, RawDataType) - 
Static method in class net.sf.basedb.core.RawBioAssay
Deprecated. Use RawBioAssay.getNew(DbControl, Platform, RawDataType) or
                        RawBioAssay.getNew(DbControl, PlatformVariant, RawDataType) instead.
                        This method will set the platform to Platform.GENERIC.
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, RawDataType) - 
Static method in class net.sf.basedb.core.RawBioAssay
Create a new raw bioassay for a specific platform variant.
getNew(DbControl, RawBioAssay, FeatureIdentificationMethod) - 
Static method in class net.sf.basedb.core.RawDataBatcher
Create a new batcher for raw data.
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.ReporterBatcher
Create a new batcher for reporters.
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, BioPlateEventParticipant) - 
Static method in class net.sf.basedb.core.Sample
Create a new Sample item as part of a
                master bioplate event.
getNew(DbControl, Hybridization) - 
Static method in class net.sf.basedb.core.Scan
Create a new Scan item.
getNew(DbControl, SoftwareType) - 
Static method in class net.sf.basedb.core.Software
Create a new Software item.
getNew(DbControl, RawBioAssay) - 
Static method in class net.sf.basedb.core.SpotImages
Create a new Image item.
getNew(DbControl, Experiment, Job) - 
Static method in class net.sf.basedb.core.Transformation
Create a new Transformation item.
getNew(DbControl, Quantity, String) - 
Static method in class net.sf.basedb.core.Unit
Create a new Unit item.
getNew(DbControl, String, String) - 
Static method in class net.sf.basedb.core.User
Create a new User item.
getNew(DbControl, User, Client, String, String) - 
Static method in class net.sf.basedb.core.UserClientSetting
Create a new UserClientSetting item.
getNew(DbControl, User, String, String) - 
Static method in class net.sf.basedb.core.UserDefaultSetting
Create a new UserDefaultSetting item.
getNew(DbControl) - 
Static method in class net.sf.basedb.core.VirtualDb
Create a new DynamicTables item.
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.
getNewHybridizationEvent(DbControl, Hybridization, BioPlateEventParticipant) - 
Static method in class net.sf.basedb.core.BioMaterialEvent
Create a new BioMaterialEvent of the BioMaterialEvent.Type.HYBRIDIZATION
                type.
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, 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.
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.
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.
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, User, String, User, Job) - 
Static method in class net.sf.basedb.core.Message
Create a new Message from the system.
getNextAutoScanTime() - 
Method in class net.sf.basedb.clients.web.extensions.ExtensionsControl
Get the next scheduled time for automatic scanning.
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(T, String) - 
Method in interface net.sf.basedb.util.bfs.FilenameGenerator
Get the next file name.
getNextFilename(Object, String) - 
Method in class net.sf.basedb.util.bfs.SequenceFilenameGenerator
 
getNextFilename(Object, String) - 
Method in class net.sf.basedb.util.bfs.SuggestedFilenameGenerator
 
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.
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(K) - 
Method in class net.sf.basedb.util.overview.cache.NodeCache
 
getNode(String) - 
Method in class net.sf.basedb.util.overview.ExperimentOverview
Deprecated. Get the node with the given ID.
getNode() - 
Method in class net.sf.basedb.util.overview.Failure
Get the node that failed validation.
getNode(String) - 
Method in class net.sf.basedb.util.overview.GenericOverview
Get the node with the given ID.
getNode() - 
Method in class net.sf.basedb.util.Tree.Entry
Get the node element object.
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<I>, NodeNameGenerator<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(OverviewContext) - 
Method in class net.sf.basedb.util.overview.loader.BasicItemNodeLoader
Get the node loader factory used by the current context.
getNodeLoaderFactory() - 
Method in interface net.sf.basedb.util.overview.OverviewContext
Get the node loader factory that is used to create node loaders.
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(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.
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(FileSetMember, Node) - 
Method in class net.sf.basedb.util.overview.node.FileSetMemberNameGenerator
 
getNodeTitle(LabeledExtract, Node) - 
Method in class net.sf.basedb.util.overview.node.LabeledExtractNameGenerator
The base of the title is generated by the superclass.
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.
getNodeType() - 
Method in class net.sf.basedb.util.overview.Node
Get the node type of this node.
getNodeValidator(OverviewContext) - 
Method in class net.sf.basedb.util.overview.loader.BasicItemNodeLoader
Get the default node validator for nodes of this type.
getNodeValidator() - 
Method in class net.sf.basedb.util.overview.node.NodeFactory
Get the node validator that is used by this factory.
getNodeValidatorFactory() - 
Method in class net.sf.basedb.util.overview.GenericOverview
Get the current node validator factory.
getNodeValidatorFactory(OverviewContext) - 
Method in class net.sf.basedb.util.overview.loader.BasicItemNodeLoader
Get the node validator factory used by the current context.
getNodeValidatorFactory() - 
Method in interface net.sf.basedb.util.overview.OverviewContext
Get the node validator factory that is used to create node validators.
getNonCorePluginDirectory() - 
Static method in class net.sf.basedb.core.Application
Get the directory where non-core plugins are located and installed
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.clients.web.util.AjaxWriter
Deprecated. The null value string is written to the output instead of
                null data values.
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.
getNumArrays() - 
Method in class net.sf.basedb.core.data.HybridizationData
The number of arrays that was hybridized.
getNumArrays() - 
Method in class net.sf.basedb.core.Hybridization
Get the number of arrays that on the 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(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.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.parser.ColFunction
 
getNumberOfParameters() - 
Method in class net.sf.basedb.util.parser.DataNoFunction
 
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.
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.
getNumDbFeatures() - 
Method in class net.sf.basedb.info.ArrayDesignInfo
 
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(SessionControl) - 
Static method in class net.sf.basedb.clients.web.formatter.FormatterSettings
Get the number of decimals a number formatter should display.
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(boolean, boolean, boolean, boolean) method because of an
                        error (too many values).
getNumErrorFiles() - 
Method in class net.sf.basedb.clients.web.extensions.ScanResults
The number of extension files that could not be completely loaded
                because of an error.
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.
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.
getNumFeatures(DbControl) - 
Method in class net.sf.basedb.core.ArrayDesign
Deprecated. Use ArrayDesign.getNumDbFeatures() and/or ArrayDesign.getNumFileFeatures()
                        instead
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.
getNumFileFeatures() - 
Method in class net.sf.basedb.info.ArrayDesignInfo
 
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.
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.
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.
getNumPlates() - 
Method in class net.sf.basedb.core.ArrayDesign
The number of plates connected to this array design.
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.
getNumPositions(DbControl, ReporterData) - 
Method in class net.sf.basedb.clients.web.ExperimentExplorer
Deprecated. In 2.11 for performance reasons, use ExperimentExplorer.getNumPositions(DbControl, int)
                        instead
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.
getNumPropertyFilters() - 
Method in class net.sf.basedb.core.ItemContext
Get the number of property filters stored in this
                context.
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(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(String) - 
Method in class net.sf.basedb.core.ItemContext
Get the number of recently used value in the list.
getNumRemoved() - 
Method in class net.sf.basedb.plugins.AnnotationFlatFileImporter.NewAnnotations
Number of annotations that was removed by the call to the
                        AnnotationFlatFileImporter.NewAnnotations.setNewAnnotations(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(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.
getNumReporters() - 
Method in class net.sf.basedb.info.BioAssaySetInfo
 
getNumReportersNotFound() - 
Method in class net.sf.basedb.core.RawDataBatcher
Get the number of reporters that was not found.
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(boolean, boolean, boolean, boolean) method.
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.
getNumSpots() - 
Method in class net.sf.basedb.info.BioAssaySetInfo
 
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.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(String) - 
Method in class net.sf.basedb.core.ItemContext
Get an object.
getObject(int) - 
Method in interface net.sf.basedb.core.query.SqlResult
Get the value of the specified column as an object.
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.
getOnActivate() - 
Method in class net.sf.basedb.clients.web.extensions.tabcontrol.FixedTabFactory
 
getOnActivate() - 
Method in class net.sf.basedb.clients.web.extensions.tabcontrol.IncludeContentTabFactory.Tab
 
getOnActivate() - 
Method in interface net.sf.basedb.clients.web.extensions.tabcontrol.TabAction
A javascript action that is executed when activating the tab.
getOnActivate() - 
Method in class net.sf.basedb.clients.web.extensions.tabcontrol.TabBean
 
getOnActivate() - 
Method in class net.sf.basedb.clients.web.taglib.tab.Tab
 
getOnchange() - 
Method in class net.sf.basedb.clients.web.taglib.Select
 
getOnchange() - 
Method in class net.sf.basedb.clients.web.taglib.table.PresetSelector
 
getOnClick() - 
Method in class net.sf.basedb.clients.web.extensions.menu.FixedMenuItemFactory
 
getOnClick() - 
Method in interface net.sf.basedb.clients.web.extensions.menu.MenuItemAction
A javascript action that is executed when the user clicks the menu.
getOnClick() - 
Method in class net.sf.basedb.clients.web.extensions.menu.MenuItemBean
 
getOnClick() - 
Method in interface net.sf.basedb.clients.web.extensions.toolbar.ButtonAction
A javascript action that is executed when the user clicks on 
                the button.
getOnClick() - 
Method in class net.sf.basedb.clients.web.extensions.toolbar.ButtonBean
 
getOnClick() - 
Method in class net.sf.basedb.clients.web.extensions.toolbar.FixedButtonFactory
 
getOnclick() - 
Method in class net.sf.basedb.clients.web.taglib.Button
 
getOnClick() - 
Method in class net.sf.basedb.clients.web.taglib.Help
 
getOnclick() - 
Method in class net.sf.basedb.clients.web.taglib.Icon
 
getOnclick() - 
Method in class net.sf.basedb.clients.web.taglib.menu.Menuitem
 
getOnclick() - 
Method in class net.sf.basedb.clients.web.taglib.table.Button
 
getOnClick() - 
Method in class net.sf.basedb.clients.web.taglib.table.Button
 
getOnkeypress() - 
Method in class net.sf.basedb.clients.web.taglib.Body
 
getOnload() - 
Method in class net.sf.basedb.clients.web.taglib.Body
 
getOnselect() - 
Method in class net.sf.basedb.clients.web.taglib.Select
 
getOntoggle() - 
Method in class net.sf.basedb.clients.web.taglib.HideableSection
 
getOnunload() - 
Method in class net.sf.basedb.clients.web.taglib.Body
 
getOnValidate() - 
Method in class net.sf.basedb.clients.web.extensions.tabcontrol.FixedTabFactory
 
getOnValidate() - 
Method in class net.sf.basedb.clients.web.extensions.tabcontrol.IncludeContentTabFactory.Tab
 
getOnValidate() - 
Method in interface net.sf.basedb.clients.web.extensions.tabcontrol.TabAction
A javascript action that is executed when validating form
                data on the tab.
getOnValidate() - 
Method in class net.sf.basedb.clients.web.extensions.tabcontrol.TabBean
 
getOnValidate() - 
Method in class net.sf.basedb.clients.web.taglib.tab.Tab
 
getOpen() - 
Method in class net.sf.basedb.clients.web.taglib.menu.Menu
 
getOperation(String) - 
Method in class net.sf.basedb.ws.client.AbstractRPCClient
 
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>.
getOptimizeTableSql(String, String, String) - 
Method in class net.sf.basedb.core.dbengine.PostgresDbEngine
Generate VACUUM FULL <schema>.
getOption(String) - 
Method in class net.sf.basedb.clients.jobagent.CmdLine
Get the value for the specified option
getOption(String, String) - 
Method in class net.sf.basedb.clients.jobagent.CmdLine
Get the value for an 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(Validator, 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.
getOptions() - 
Method in class net.sf.basedb.ws.client.ConfigurableServiceFactory
Get the currently active options that are used by the 
                ConfigurableServiceFactory.createService(EndpointReference) method.
getOrderInXml() - 
Method in class net.sf.basedb.util.PluginConfigInfo
Gets in wich order the configuration comes in the import file.
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.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(Group) - 
Method in class net.sf.basedb.core.GroupPermissions
Get the original permissions for a group if this object was created with the
                GroupPermissions.GroupPermissions(ItemKey) constructor.
getOriginalPermissions() - 
Method in class net.sf.basedb.core.GroupPermissions
Get the internal representation of the original permissions.
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.ProjectPermissions(ProjectKey) constructor.
getOriginalPermissions() - 
Method in class net.sf.basedb.core.ProjectPermissions
Get the internal representation of the original permissions.
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.UserPermissions(ItemKey) constructor.
getOriginalPermissions() - 
Method in class net.sf.basedb.core.UserPermissions
Get the internal representation of the original permissions.
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(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(File) - 
Static method in class net.sf.basedb.util.FileUtil
Get a buffered OutputStream object writing to
                the specified file.
getOutputStream(String, int) - 
Method in class net.sf.basedb.util.StaticCache
Get a lock-safe output stream.
getOutputStream() - 
Method in class net.sf.basedb.ws.server.BaseFileDataSource
 
getOverview(Experiment, Project) - 
Static method in class net.sf.basedb.util.overview.ExperimentOverview
Deprecated. (In 2.10) Use OverviewUtil.getNewOrCurrentOverview(DbControl, BasicItem, Project) instead
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
 
getOwnerId() - 
Method in class net.sf.basedb.info.OwnedItemInfo
 
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(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.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.
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.
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(int) - 
Method in class net.sf.basedb.core.PluginConfiguration
Get the names of all configuration values in a specific version.
getParameterNames() - 
Method in interface net.sf.basedb.core.query.Query
Get a set with the names for all parameters in this
                query.
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.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.
getParameters() - 
Method in class net.sf.basedb.info.QueryOptions
Get the parameters used in this query.
getParametersFromBaseFile(File) - 
Method in class net.sf.basedb.plugins.Base1PluginExecuter
Get the data from the configuration file.
getParameterType(String) - 
Method in class net.sf.basedb.core.AbstractQuery
Get the type of the parameter, or null if not known.
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, List<?>) - 
Method in class net.sf.basedb.plugins.PluginConfigurationImporter
Gets the ParameterType to use with a class.
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.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.
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, int) - 
Method in class net.sf.basedb.core.PluginConfiguration
Get the values of a configuration parameter in a specific version.
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.core.PluginRequest.RequestImpl
 
getParameterValues(String) - 
Method in class net.sf.basedb.plugins.executor.ExternalProgramExecutor.RequestWrapper
 
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.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.
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.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.
getParentPlates() - 
Method in class net.sf.basedb.core.Plate
Get a query returning the parent plates of this plate.
getParentProperties(DbControl, BioAssay, String) - 
Static method in class net.sf.basedb.util.BioAssaySetUtil
Deprecated. In 2.15, use BioAssaySetUtil.getParentProperties(DbControl, BioAssay, Metadata.PropertyPath) instead
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.
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.GroupData
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.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.
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.PlatformFileType
 
getParentType() - 
Method in class net.sf.basedb.core.PlatformVariant
 
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.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.parser.FlatFileParser
Get the number of parsed lines 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.
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.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.
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(ParameterValues, String) - 
Method in class net.sf.basedb.plugins.AnnotationFlatFileImporter
 
getPattern(ParameterValues, String) - 
Method in class net.sf.basedb.plugins.batchimport.AbstractItemImporter
 
getPattern(String, int, int) - 
Method in class net.sf.basedb.util.export.spotdata.AdvancedFieldConverter
 
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.
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.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(int) - 
Static method in class net.sf.basedb.clients.web.PermissionUtil
Translate a given integer to a set of permissions.
getPermissions() - 
Method in class net.sf.basedb.clients.web.util.NameablePluginAdaptor
 
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.Coloring
 
getPermissions() - 
Method in class net.sf.basedb.core.data.PluginDefinitionData
Get a map containing the rolekey and the permissions for this plugin.
getPermissions(Group) - 
Method in class net.sf.basedb.core.GroupPermissions
Get the permissions for a group.
getPermissions(User) - 
Method in class net.sf.basedb.core.ItemKey
Get the permissions for a user.
getPermissions(Group) - 
Method in class net.sf.basedb.core.ItemKey
Get the permissions for a group.
getPermissions(User) - 
Method in class net.sf.basedb.core.MultiPermissions
Get the permissions for a user.
getPermissions(Group) - 
Method in class net.sf.basedb.core.MultiPermissions
Get the permissions for a group.
getPermissions(Project) - 
Method in class net.sf.basedb.core.MultiPermissions
Get the permissions for a project.
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(User) - 
Method in class net.sf.basedb.core.Project
Get the permissions for a user in this project.
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.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.UserPermissions
Get the permissions for a user.
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.BioAssaySetExporter
Deprecated. 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.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.plugins.SpotImageCreator
Request write access to RawBioAssay:s, create and write access to File:s,
                use access to FileType:s and Directory:s.
getPermissions() - 
Method in class net.sf.basedb.util.zip.AbstractFileUnpacker
Request create and write access to File:s and Directory:s.
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.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.
getPlate(int) - 
Method in class net.sf.basedb.core.ArrayDesign
Get a Plate from a given position.
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.
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.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.
getPlatformId() - 
Method in class net.sf.basedb.info.RawBioAssayInfo
 
getPlatformProxy() - 
Method in class net.sf.basedb.core.RawDataType
Needed to make RawBioAssay.setRawDataType(RawDataType)
                backwards compatible.
getPlatformRawDataType(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(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.
getPlugin(DbControl) - 
Method in class net.sf.basedb.core.ChangeHistory
Load the plug-in that made the change.
getPlugin() - 
Method in class net.sf.basedb.core.data.ChangeHistoryData
 
getPlugin() - 
Method in class net.sf.basedb.core.PluginRequest
Get the plugin object.
getPluginClass() - 
Method in class net.sf.basedb.util.PluginConfigInfo
Gets the class name of the plugin that this configuration is ment for
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.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.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
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.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.
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(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() - 
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.RoleKey
 
getPluginPermissions(Item) - 
Method in class net.sf.basedb.core.SessionControl
Get all plugin-specific permissions for the specified item type.
getPluginPermissions() - 
Method in class net.sf.basedb.core.User
Make sure plug-ins always has at least read access to the logged in user.
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.
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.
getPoolingEvents() - 
Method in class net.sf.basedb.core.MeasuredBioMaterial
Get a query that returns all events where this biomaterial
                has been used as a source.
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(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.
getPosition(DbControl, ReporterData, int) - 
Method in class net.sf.basedb.clients.web.ExperimentExplorer
Deprecated. In 2.11 for performance reasons, use ExperimentExplorer.getPosition(DbControl, int, int)
                        instead
getPosition() - 
Method in class net.sf.basedb.core.ArrayDesignPlate
Gets the position of this item.
getPosition() - 
Method in class net.sf.basedb.core.data.ArrayDesignPlateData
Get the index.
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.plugins.Base1PluginExecuter.JobParameter
 
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, String...) - 
Static method in class net.sf.basedb.core.HibernateUtil
Get a predefined HQL query.
getPredefinedQuery(StatelessSession, String) - 
Static method in class net.sf.basedb.core.HibernateUtil
Get a predefined HQL query using the stateless session.
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.
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.
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
getPrimaryLocationFilter() - 
Method in class net.sf.basedb.plugins.AbstractFlatFileImporter
Deprecated. In 2.16. Since files can now be references to external URL:s
                        this filter no longer makes sense. Plug-ins should not use the location
                        to filter files.
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
 
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.
getProgressReporter(ProgressReporter) - 
Method in class net.sf.basedb.core.Job
Get a progress reporter that reports progress by updating the information
                in 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.
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.
getProject(DbControl) - 
Method in class net.sf.basedb.core.ChangeHistory
Load the project that was active when the change was made.
getProject() - 
Method in class net.sf.basedb.core.data.ChangeHistoryData
 
getProject() - 
Method in class net.sf.basedb.util.overview.ExperimentOverview
Deprecated. Get the project of this overview (may be null).
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.
getProjectDefaultItem(DbControl, Project, Project.Default) - 
Static method in class net.sf.basedb.util.overview.OverviewUtil
Get the project default item for a given project and type of item.
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.ChangeHistory
Get the ID of the project that was active when the change
                was made.
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.
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.InternalStorageController.StorageKeyring
Return empty set.
getProjectKeys(Permission) - 
Method in class net.sf.basedb.core.Keyring
 
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.SessionControl
Get the id of all project keys where the logged in user has the
                requested permission.
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.InternalStorageController.StorageKeyring
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.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.
getProjects(QueryOptions) - 
Method in class net.sf.basedb.ws.client.ProjectClient
Gets info about each projects that are available for the active session client.
getProjects(String, QueryOptions) - 
Method in class net.sf.basedb.ws.server.ProjectService
Gets information about projects that are available
                for an active session.
getProperties(String) - 
Static method in class net.sf.basedb.core.ExtendedProperties
Get a list of extended properties for the specified class.
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.
getProperty(String) - 
Method in class net.sf.basedb.clients.jobagent.Agent
Get a configuration property.
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(String, String) - 
Static method in class net.sf.basedb.core.ExtendedProperties
Find an extended property in a given class.
getProperty() - 
Method in class net.sf.basedb.core.PropertyFilter
Get the name of the property this filter is used on.
getProperty(String) - 
Method in class net.sf.basedb.core.RawDataType
 
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.
getPropertyFilter(String) - 
Static method in class net.sf.basedb.core.FileType
Create a PropertyFilter object that can be used to
                filter files by their file type: file.fileType = FileType
getPropertyFilter(String, boolean) - 
Static method in class net.sf.basedb.core.FileType
Create a PropertyFilter object that can be used to
                filter files by their file type: file.fileType = FileType
getPropertyFilter(String) - 
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.ItemContext
Get a collection of all property filters stored in this context.
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.
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.
getPropertyValue(BasicItem, String) - 
Static method in class net.sf.basedb.core.Metadata
Deprecated. In 2.15, use Metadata.getPropertyPath(String, boolean) instead
getPropertyValue(DbControl, C, String) - 
Method in class net.sf.basedb.core.Metadata
Deprecated. In 2.15, use Metadata.getPropertyPath(String, boolean) instead
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.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.data.ScanData
Get the protocol used while scanning.
getProtocol() - 
Method in class net.sf.basedb.core.Hybridization
Get the protocol from the creation event.
getProtocol() - 
Method in class net.sf.basedb.core.MeasuredBioMaterial
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.RawBioAssay
Get the Protocol used while analysing the scanned images.
getProtocol() - 
Method in class net.sf.basedb.core.Scan
Get the Protocol used to create this scan.
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.
getProtocols() - 
Method in class net.sf.basedb.core.data.ProtocolTypeData
This is the inverse end.
getProtocols() - 
Method in class net.sf.basedb.core.ProtocolType
Get a query that returns all protocols of this type
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.data.ProtocolData
Get the associated ProtocolTypeData item.
getProtocolType() - 
Method in class net.sf.basedb.core.PlateEventType
Get the associated ProtocolType item.
getProtocolType() - 
Method in class net.sf.basedb.core.Protocol
Get the associated ProtocolType item.
getProxy(int) - 
Static method in class net.sf.basedb.core.Reporter
Get a proxy reporter object.
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.
getPublication() - 
Method in class net.sf.basedb.info.ExperimentInfo
 
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.
getPublicationDate() - 
Method in class net.sf.basedb.info.ExperimentInfo
 
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.
getPubMedId() - 
Method in class net.sf.basedb.info.ExperimentInfo
 
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.
getQuality() - 
Method in class net.sf.basedb.core.data.SpotImagesData
The quality setting for the spot images.
getQuality() - 
Method in class net.sf.basedb.core.SpotImages
Get the quality used for the jpeg compression.
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() - 
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(Item) - 
Static method in class net.sf.basedb.core.AnnotationType
Get a ItemQuery that returns annotation types.
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(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() - 
Static method in class net.sf.basedb.core.ArraySlide
Get a ItemQuery object configured
                to retrieve array slides.
getQuery(BioAssaySet) - 
Static method in class net.sf.basedb.core.BioAssay
Get a query configured to retrieve bioassays in
                a given bioassayset.
getQuery(Experiment) - 
Static method in class net.sf.basedb.core.BioAssaySet
Get a query configured to retrieve bioassaysets for
                a given experiment.
getQuery(Transformation) - 
Static method in class net.sf.basedb.core.BioAssaySet
Get a query configured to retrieve bioassaysets 
                created by a given transformation.
getQuery(MeasuredBioMaterial) - 
Static method in class net.sf.basedb.core.BioMaterialEvent
Get a query that returns events for a biomaterial.
getQuery() - 
Static method in class net.sf.basedb.core.BioMaterialList
Get a query that returns biomaterial lists.
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(BioPlateEvent) - 
Static method in class net.sf.basedb.core.BioPlateEventParticipant
Get a query configured to return all participants for a bioplate 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() - 
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(BioPlate) - 
Static method in class net.sf.basedb.core.BioWell
Get a query configured to retrieve wells for a plate.
getQuery() - 
Static method in class net.sf.basedb.core.Client
Get a new query object for this class.
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() - 
Static method in class net.sf.basedb.core.DataFileType
Get a query configured to retrieve DataFileType 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(Platform, PlatformVariant, Item, FileType) - 
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() - 
Static method in class net.sf.basedb.core.Directory
Get a query configured to retrieve directories.
getQuery(User, Group) - 
Static method in class net.sf.basedb.core.DiskUsage
Get a query configured to retrieve disk usage for the specified user.
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(BioAssaySet) - 
Static method in class net.sf.basedb.core.ExtraValue
Get a query configured to retrieve extra values in a given bioassayset.
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(FileSet) - 
Static method in class net.sf.basedb.core.FileSetMember
Get a query configured to retrieve FileSetMember items.
getQuery() - 
Static method in class net.sf.basedb.core.FileType
Get a query configured to retrieve FileType items.
getQuery() - 
Static method in class net.sf.basedb.core.Formula
Get a new query object for this class.
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() - 
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() - 
Static method in class net.sf.basedb.core.HardwareType
Get a query configured to retrieve hardware types.
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() - 
Static method in class net.sf.basedb.core.Hybridization
Get a query that returns hybridizations.
getQuery(Scan) - 
Static method in class net.sf.basedb.core.Image
Get a query configured to retrieve 
                images for the specified scan.
getQuery() - 
Method in class net.sf.basedb.core.ItemContext
 
getQuery() - 
Static method in class net.sf.basedb.core.Job
Get a query configured to retrieve getQuery() - 
Static method in class net.sf.basedb.core.JobAgent
Get an ItemQuery that returns job agents.
getQuery(JobAgent) - 
Static method in class net.sf.basedb.core.JobAgentSettings
Get a query configured to retrieve settings for the specified agent.
getQuery(PluginDefinition) - 
Static method in class net.sf.basedb.core.JobAgentSettings
Get a query configured to retrieve settings for the specified plugin.
getQuery() - 
Static method in class net.sf.basedb.core.Label
Get a query that returns labels.
getQuery() - 
Static method in class net.sf.basedb.core.LabeledExtract
Get a query that returns labeled extracts.
getQuery(User) - 
Static method in class net.sf.basedb.core.Message
Get a query configured to retrieve messages for the specified user.
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.Plate
Get a query that returns plates.
getQuery(Plate) - 
Static method in class net.sf.basedb.core.PlateEvent
Get a query configured to retrieve plate events for the specified 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() - 
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(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() - 
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(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() - 
Static method in class net.sf.basedb.core.PluginDefinition
Get a query that returns plugin definitions.
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() - 
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.ProtocolType
Get a query configured to retrieve protocol types.
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.ReporterList
Get a new query object for this class.
getQuery(ReporterList) - 
Static method in class net.sf.basedb.core.ReporterScore
Get a query object configured to retrieve reporters.
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.Sample
Get a query that returns samples.
getQuery() - 
Static method in class net.sf.basedb.core.Scan
Get a query that returns scans.
getQuery(User) - 
Static method in class net.sf.basedb.core.Session
Get a query configured to retrieve sessions for the specified user.
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.SoftwareType
Get a query configured to retrieve software types.
getQuery(Experiment) - 
Static method in class net.sf.basedb.core.Transformation
Get a query configured to retrieve transformations for
                a given experiment.
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() - 
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(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) - 
Static method in class net.sf.basedb.core.UserDefaultSetting
Get a query configured to retrieve default settings for a user.
getQuery(Plate) - 
Static method in class net.sf.basedb.core.Well
Get a query configured to retrieve wells for a plate.
getQuery(Item) - 
Static method in class net.sf.basedb.util.biomaterial.ListUtil
Get a query that returns all biomaterials that can possibly be 
                members of this list.
getQueryAlias() - 
Method in class net.sf.basedb.plugins.BioAssaySetExporter.QueryItem
Deprecated.  
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.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.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.
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.
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.DefaultDbEngine
Put quotes (") around the name.
getQuotedName(String) - 
Method in class net.sf.basedb.core.dbengine.MySQLEngine
Put quotes (`) around the name.
getQuotedName(String) - 
Method in class net.sf.basedb.core.dbengine.PostgresDbEngine
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.SpotImagesData
Get the scan that produced this image.
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(DbControl, RawData) - 
Static method in class net.sf.basedb.core.RawDataUtil
Get the raw bioassay the raw data belongs to.
getRawBioAssay() - 
Method in class net.sf.basedb.core.SpotImages
Get the raw bioassay the spot images 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.ExperimentData
A set that manages which raw bioassays are available in the experiment.
getRawBioAssays() - 
Method in class net.sf.basedb.core.data.ScanData
This is the inverse end.
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.Scan
Get a query that returns all raw bioassays created from this 
                scan.
getRawBioAssays(int, QueryOptions) - 
Method in class net.sf.basedb.ws.client.ExperimentClient
Gets info about raw bioassays used in an experiment.
getRawBioAssays(QueryOptions) - 
Method in class net.sf.basedb.ws.client.RawBioAssayClient
Gets info about raw bioassays that are available in the logged in session.
getRawBioAssays(String, int, QueryOptions) - 
Method in class net.sf.basedb.ws.server.ExperimentService
Gets an array with information objects for each
                rawbioassay in an experiment.
getRawBioAssays(String, QueryOptions) - 
Method in class net.sf.basedb.ws.server.RawBioAssayService
Gets an array with info about raw bioassays
                available for the active session.
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() - 
Method in class net.sf.basedb.core.RawBioAssay
Deprecated. Use RawBioAssay.getRawDataBatcher(FeatureIdentificationMethod, Job) instead
getRawDataBatcher(FeatureIdentificationMethod) - 
Method in class net.sf.basedb.core.RawBioAssay
Deprecated. Use RawBioAssay.getRawDataBatcher(FeatureIdentificationMethod, Job)
                instead.
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.
getRawdataProperty(String, String) - 
Method in class net.sf.basedb.util.export.spotdata.FieldConverter
Deprecated. 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.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.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.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(String) - 
Static method in class net.sf.basedb.core.RawDataTypes
Get a information about a raw data type.
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.
getRawDataTypeFiles() - 
Static method in class net.sf.basedb.core.Application
Get the path to the XML file containing raw data type definitions.
getRawDataTypeId() - 
Method in class net.sf.basedb.info.RawBioAssayInfo
 
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(DbControl, Item) - 
Method in class net.sf.basedb.core.ItemContext
Get all recently used items of the specified type.
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, int) - 
Method in class net.sf.basedb.core.ItemContext
 
getRecent(DbControl, Item, String, int) - 
Method in class net.sf.basedb.core.ItemContext
 
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
 
getRecentSettingName(String) - 
Method in class net.sf.basedb.core.ItemContext
 
getRecordSeparator() - 
Method in class net.sf.basedb.clients.web.util.AjaxWriter
Deprecated. The record separator is written to the output on a single
                line between each record.
getRedefinedColumnName(String, String) - 
Method in class net.sf.basedb.util.basefile.BaseFileParser
Get the redefined column name for a section.
getRedImageFile() - 
Method in class net.sf.basedb.core.data.SpotImagesData
The file used for the red component in the spot images.
getRedImageFile() - 
Method in class net.sf.basedb.core.SpotImages
Get the file which was used for the red channel in the
                spot images.
getRefColumns() - 
Method in class net.sf.basedb.core.dbengine.TableInfo.ForeignKeyInfo
 
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
 
getRegistered(ExtensionsFile) - 
Method in class net.sf.basedb.clients.web.extensions.ExtensionsDirectory
 
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.
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.InternalStorageController.StorageKeyring
Never reload since everything is static.
getReload() - 
Method in class net.sf.basedb.core.Keyring
 
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.
getRemoteId() - 
Method in class net.sf.basedb.ws.server.AbstractRPCService
Gets the remote id to identify connection with.
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.
getRemoteSlot(String) - 
Method in class net.sf.basedb.clients.jobagent.slotmanager.MasterSlotManager
Get the remote slot with the given id.
getRemovableItems() - 
Static method in class net.sf.basedb.core.Metadata
Get a set containing all Removable item types.
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(InvokationContext) - 
Method in class net.sf.basedb.clients.web.extensions.toolbar.CompactButtonRendererFactory
 
getRenderer(InvokationContext) - 
Method in class net.sf.basedb.clients.web.extensions.toolbar.ToolbarButtonRendererFactory
 
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.
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
 
getReporter(DbControl, int) - 
Method in class net.sf.basedb.clients.web.ExperimentExplorer
Get the reporter for the specified index.
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(boolean) - 
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.
getReporterAnnotationsWriter() - 
Method in class net.sf.basedb.util.export.spotdata.BfsExporter
Get the writer were reporter annotations should be printed.
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) - 
Method in class net.sf.basedb.util.export.spotdata.FieldConverter
Deprecated. Convert a reporter field.
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.
getReporterIndex() - 
Method in class net.sf.basedb.clients.web.ExperimentExplorer
Get the index of the current reporter.
getReporterIndex(DbControl, ReporterData) - 
Method in class net.sf.basedb.clients.web.ExperimentExplorer
Deprecated. This method is a helper for other deprecated methods.
                        Do not use it in non-deprecated methods.
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.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.
getReporterLists(int, QueryOptions) - 
Method in class net.sf.basedb.ws.client.ExperimentClient
Gets info about reporter lists in an experiment.
getReporterLists(String, int, QueryOptions) - 
Method in class net.sf.basedb.ws.server.ExperimentService
Gets an array with information objects for each reporter list used 
                in an Experiment.
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.
getReporterProperty(String, String) - 
Method in class net.sf.basedb.util.export.spotdata.FieldConverter
Deprecated. Find an extended reporter property with the given name and create
                a dynamic field from it using exportTitle as the title.
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.
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).
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(DbControl, ReporterData) - 
Static method in class net.sf.basedb.core.Reporter
Get the reporter type item from a reporter data object.
getReporterType(String) - 
Method in class net.sf.basedb.plugins.ReporterFlatFileImporter
 
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() - 
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.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.BfsExporterPlugin
 
getRequestInformation(GuiContext, String) - 
Method in class net.sf.basedb.plugins.BioAssaySetExporter
Deprecated.  
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.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.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.
getRequiresConfiguration() - 
Method in class net.sf.basedb.core.data.PluginDefinitionData
If the plugin requires a configurations or not.
getResource(String) - 
Method in class net.sf.basedb.util.JarClassLoader
 
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.
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() - 
Method in class net.sf.basedb.util.resources.ResourceBundleWrapper
Get access to the underlying resource bundle.
getResources(String) - 
Method in class net.sf.basedb.util.JarClassLoader
 
getResourcesDirectory() - 
Method in class net.sf.basedb.clients.web.extensions.ExtensionsDirectory
Get the file object representing the directory where
                resource files are extracted.
getResourcesUrl() - 
Method in class net.sf.basedb.clients.web.extensions.ExtensionsDirectory
Get the URL that points to the resources directory when accessed
                through the web server.
getResourcesUrl(ExtensionsFile) - 
Method in class net.sf.basedb.clients.web.extensions.ExtensionsDirectory
Get the URL that points to the resources directory for a specific
                extensions file when accessed through the web server.
getResponseImpl() - 
Method in class net.sf.basedb.core.PluginResponse
Get a new reponse object.
getRestriction(Expression, Expression) - 
Method in enum net.sf.basedb.core.Operator
 
getRestriction(Expression, Expression[]) - 
Method in enum net.sf.basedb.core.Operator
 
getRestriction() - 
Method in class net.sf.basedb.core.PropertyFilter
Deprecated. Use PropertyFilter.getRestriction(DbControl, EntityQuery) instead
getRestriction(DbControl) - 
Method in class net.sf.basedb.core.PropertyFilter
Deprecated. Use PropertyFilter.getRestriction(DbControl, EntityQuery) instead
getRestriction(DbControl, EntityQuery) - 
Method in class net.sf.basedb.core.PropertyFilter
Create a restriction from the filter.
getRestriction() - 
Method in class net.sf.basedb.info.QueryOptions
Gets the restriction for this QueryOptions
getRestrictionPrefix() - 
Method in class net.sf.basedb.info.QueryOptions
Gets the prefix used with the restriction/expression
                in this object.
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() - 
Method in class net.sf.basedb.core.hibernate.ExecuteUpdateWork
 
getResult() - 
Method in interface net.sf.basedb.core.hibernate.JdbcWork
Get the result of the work.
getResult() - 
Method in class net.sf.basedb.core.hibernate.MultiUpdateWork
 
getResult() - 
Method in class net.sf.basedb.core.hibernate.ResultSetWork
 
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.
getResult() - 
Method in class net.sf.basedb.core.hibernate.TableExistsWork
 
getResult() - 
Method in class net.sf.basedb.core.hibernate.TableInfoWork
 
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.clients.web.extensions.ScanResults
Get the results for a specific extensions file.
getReturnAliases() - 
Method in class net.sf.basedb.core.hibernate.QueryWrapper
 
getReturnType() - 
Method in class net.sf.basedb.core.ExtendedPropertyAccessor.GetterSetter
Always return null.
getReturnTypes() - 
Method in class net.sf.basedb.core.hibernate.QueryWrapper
 
getReverseDirection() - 
Method in class net.sf.basedb.clients.web.taglib.table.Table
 
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.InternalStorageController.StorageKeyring
 
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.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.InternalStorageController.StorageKeyring
Return empty set.
getRoles() - 
Method in class net.sf.basedb.core.Keyring
 
getRoles() - 
Method in class net.sf.basedb.core.SessionControl
Get the id of all roles where the logged in user is a member.
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.
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.ExperimentOverview
Deprecated. Get the root node (ie. the experiment node).
getRootNode() - 
Method in class net.sf.basedb.util.overview.GenericOverview
Get the root node.
getRootTable() - 
Method in class net.sf.basedb.core.DynamicQuery
 
getRootTable() - 
Method in class net.sf.basedb.core.DynamicRawDataQuery
 
getRootTable() - 
Method in class net.sf.basedb.core.DynamicReporterQuery
 
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.
getRootUrl() - 
Method in class net.sf.basedb.clients.web.extensions.ExtensionsDirectory
Get the URL that points to the root directory when accessed
                through the web server.
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.
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.
getRowId(int) - 
Method in class net.sf.basedb.util.bfs.AnnotationModel
Get the row id for a given row.
getRowIndex(int) - 
Method in class net.sf.basedb.util.bfs.AnnotationModel
Get the row index for a given row id.
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.
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
 
getSample() - 
Method in class net.sf.basedb.core.Extract
Get the Sample that is the parent of this extract.
getSamples() - 
Method in class net.sf.basedb.core.BioSource
Get a query that returns all samples created from this biosource.
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.
getScan() - 
Method in class net.sf.basedb.core.data.ImageData
Get the scan that produced this image.
getScan() - 
Method in class net.sf.basedb.core.data.RawBioAssayData
Get the scan.
getScan() - 
Method in class net.sf.basedb.core.Image
Get the scan this image belongs to.
getScan() - 
Method in class net.sf.basedb.core.RawBioAssay
Get the Scan this raw bioassay is created from.
getScanner() - 
Method in class net.sf.basedb.core.data.ScanData
Get the hardware, ie. scanner, used to scan the images.
getScanner() - 
Method in class net.sf.basedb.core.Scan
Get the Hardware (scanner) used to create this scan.
getScans() - 
Method in class net.sf.basedb.core.data.HybridizationData
This is the inverse end.
getScans() - 
Method in class net.sf.basedb.core.Hybridization
Get a query that returns all scans created from this 
                hybridization.
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.info.VersionInfo
 
getSchemaValidatedXML(URL, String...) - 
Static method in class net.sf.basedb.util.XMLUtil
Validate an XML file using XML schemas.
getSchemaValidatedXML(InputStream, String, String...) - 
Static method in class net.sf.basedb.util.XMLUtil
Validate an XML input stream 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(Session) - 
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(ReporterData) - 
Method in class net.sf.basedb.core.ReporterList
Get the score for the specified reporter.
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.
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
 
getSecondaryLocation() - 
Method in class net.sf.basedb.core.data.QuotaTypeData
If this quota type can use disk quota in the secondary location or not.
getSecondaryStorageController() - 
Static method in class net.sf.basedb.core.Application
Get an object of the class that is used for seconary storage handling.
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(String) - 
Method in class net.sf.basedb.util.basefile.BaseFileParser
The number of times we have seen a certain section in the
                file.
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.
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
 
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.
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.
getService() - 
Method in class net.sf.basedb.ws.client.AbstractRPCClient
 
getServiceFactory() - 
Method in class net.sf.basedb.ws.client.AbstractRPCClient
Get the factory that is used to create RPCServiceClient
                objects for this web service.
getServlet(String) - 
Method in class net.sf.basedb.clients.web.extensions.ExtensionsFile
Get a servlet that has been defined in this JAR file.
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.
getServletsUrl(ExtensionsFile) - 
Method in class net.sf.basedb.clients.web.extensions.ExtensionsDirectory
Get the URL that points to the servlet directory for a specific
                extensions file when accessed through the web server.
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(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.
getSession(DbControl) - 
Method in class net.sf.basedb.core.ChangeHistory
Load the session in which the change was made.
getSession() - 
Method in class net.sf.basedb.core.data.ChangeHistoryData
 
getSession(EntityMode) - 
Method in class net.sf.basedb.core.hibernate.SessionWrapper
 
getSession() - 
Method in class net.sf.basedb.core.LogControl
 
getSessionControl() - 
Method in class net.sf.basedb.clients.jobagent.Agent
Get a session control with the configured user logged in.
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 new or existing SessionControl object
                given a ServletRequest instance.
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(String, String) - 
Static method in class net.sf.basedb.core.Application
Get an existing SessionControl object if you know
                the id.
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) - 
Method in class net.sf.basedb.ws.server.AbstractRPCService
Gets the SessionControl for a given session ID.
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.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.
getSessionSetting(String) - 
Method in class net.sf.basedb.core.SessionControl
Get the value of a session setting with the specified name.
getSessionTimeOut() - 
Method in class net.sf.basedb.ws.client.SessionClient
Gets how long time it takes before
                the session timeout.
getSessionTimeOut() - 
Method in class net.sf.basedb.ws.server.SessionService
Gets the time in minutes when a session 
                is automatically logged out.
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(Class, String) - 
Method in class net.sf.basedb.core.ExtendedPropertyAccessor
Create a Setter object for the specified class and
                property.
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.
getSettings() - 
Method in class net.sf.basedb.core.data.ContextData
Get a map for other settings.
getSettings(PluginDefinition, boolean) - 
Method in class net.sf.basedb.core.JobAgent
Get the settings for the specified plugin.
getSettings(Job) - 
Method in class net.sf.basedb.core.JobAgent
Get the settings for the plugin that is used for the specified job.
getSettings() - 
Method in class net.sf.basedb.core.JobAgent
Get a query that returns all plugin-specific settings for this job agent.
getSeverity(Validator) - 
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.Image
 
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.SpotImages
 
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.InternalStorageController.StorageKeyring
Return 0.
getSharedPermissions(ShareableData) - 
Method in class net.sf.basedb.core.Keyring
 
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.
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 enum net.sf.basedb.core.Project.Default
 
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
 
getSignal(String) - 
Static method in class net.sf.basedb.core.signal.Signal
Get the signal with a given ID.
getSignal() - 
Method in exception net.sf.basedb.core.signal.UnsupportedSignalException
Get the signal that is not supported.
getSignalHandler() - 
Method in class net.sf.basedb.clients.web.plugins.SimpleExport
 
getSignalHandler(String) - 
Method in class net.sf.basedb.core.signal.AbstractSignalReceiver
Get the signal handler with a given ID.
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.BioAssaySetExporter
Deprecated.  
getSignalHandler() - 
Method in class net.sf.basedb.plugins.CdfFileReporterImporter
 
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.plugins.SpotImageCreator
 
getSignalHandler() - 
Method in class net.sf.basedb.util.zip.AbstractFileUnpacker
 
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.BioMaterialList
Get the number of members in this list.
getSize() - 
Method in class net.sf.basedb.core.data.BioMaterialListData
The number of biomaterials in the list.
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.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.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(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.
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.
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(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.ExecutionTime) - 
Method in class net.sf.basedb.clients.jobagent.slotmanager.InternalSlotManager
Get a slot for a job with the given estimated execution time.
getSlot() - 
Method in class net.sf.basedb.clients.jobagent.slotmanager.MasterSlotManager.RemoteSlot
 
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() - 
Method in class net.sf.basedb.util.jobagent.JobInfo
Get the slot the job is using on the job agent.
getSlotManagerClass(String) - 
Method in class net.sf.basedb.clients.jobagent.Agent
Get the class object for the configured slot manager.
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.
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.data.SoftwareTypeData
This is the inverse end.
getSoftware() - 
Method in class net.sf.basedb.core.RawBioAssay
Get the Software used while analysing the scanned images.
getSoftware() - 
Method in class net.sf.basedb.core.SoftwareType
Get a query that returns all software of this type
getSoftwareType() - 
Method in class net.sf.basedb.core.data.SoftwareData
 
getSoftwareType() - 
Method in class net.sf.basedb.core.Software
Get the associated SoftwareType item.
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.
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.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.data.TransformationData
Get the source bioassayset for the transformation.
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.
getSourceBioMaterials() - 
Method in class net.sf.basedb.core.data.BioMaterialEventData
This is the inverse end.
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.
getSourceEvents() - 
Method in class net.sf.basedb.core.data.MeasuredBioMaterialData
This is the inverse end.
getSourceFile() - 
Method in class net.sf.basedb.util.importer.spotdata.BaseFileImporter
Deprecated. In 2.16, use BaseFileImporter.getSourceFileWrapper() instead
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.
getSourceGroup(MeasuredBioMaterial) - 
Method in class net.sf.basedb.core.BioMaterialEvent
Get the source group of the biomaterial
getSourceGroup() - 
Method in class net.sf.basedb.core.data.BioMaterialSourceEventData
 
getSourceGroup() - 
Method in class net.sf.basedb.core.data.UsedQuantity
This column was previously used as a 'dummy' value for making
                sure that links were not deleted when the used quantity was
                null.
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.
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 the source biomaterials and the used quantity for
                this event.
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
 
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) - 
Method in class net.sf.basedb.util.export.spotdata.FieldConverter
Deprecated. Convert a spot field.
getSpotField(String, boolean) - 
Method in class net.sf.basedb.util.export.spotdata.StandardFieldConverter
Find a spot dynamic field.
getSpotFields(BioAssaySet) - 
Method in class net.sf.basedb.plugins.BaseFileExporterPlugin
 
getSpotFields(BioAssaySet) - 
Method in class net.sf.basedb.plugins.BfsExporterPlugin
 
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
 
getSpotImage(RawData) - 
Method in class net.sf.basedb.core.SpotImages
Get a spot as a PNG image.
getSpotImages() - 
Method in class net.sf.basedb.core.data.RawBioAssayData
Get the settings used for generating spot images for this raw bio assay.
getSpotImages() - 
Method in class net.sf.basedb.core.RawBioAssay
Get the SpotImages item used to generate spot images
                for this raw bioassay.
getSpotImages(List<RawData>) - 
Method in class net.sf.basedb.core.SpotImages
Get a list of spot PNG images from a list of RawData.
getSpotImagesFile() - 
Method in class net.sf.basedb.core.data.SpotImagesData
The file containing the spot images.
getSpotImagesFile() - 
Method in class net.sf.basedb.core.SpotImages
Get the file which holds the spot images.
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(DbControl, ReporterData, int, List<TableColumn>) - 
Method in class net.sf.basedb.clients.web.ExperimentExplorer
Deprecated. In 2.11. For performance reasons, use ExperimentExplorer.getSpotQuery(DbControl, int, int, List) instead
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.
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).
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
Deprecated. Use RawBioAssay.getNumDbSpots() or RawBioAssay.getNumFileSpots()
                        instead. This method first checks the database and if not 0, it
                        returns that value, otherwise it returns the number of file spots
getSpotSectionInfo(int) - 
Method in class net.sf.basedb.util.importer.spotdata.BaseFileInfo
Get information about a spot section.
getSpotsize() - 
Method in class net.sf.basedb.core.data.SpotImagesData
The size of the spots.
getSpotsize() - 
Method in class net.sf.basedb.core.SpotImages
Get the size of the spots in pixels.
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
 
getSSLSocketFactory() - 
Method in class net.sf.basedb.core.FileServer
Get a socket factory that can be used to create SSL connections to the given
                server.
getSSLSocketFactory() - 
Static method in class net.sf.basedb.util.ssl.SSLUtil
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.SSLUtil
Create a SSL socket factory that optionally uses the given trusted server certificate
                and client certificate.
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.clients.web.extensions.ScanResults
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.
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.
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
 
getStatistics() - 
Method in class net.sf.basedb.core.hibernate.SessionWrapper
 
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.clients.web.extensions.ScanResults.FileResults
A short status message indicating the completed
                        results on this file.
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.
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.
getString(int) - 
Method in class net.sf.basedb.clients.web.servlet.PlotServlet.CFSqlResult
 
getString(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.core.Config
Get the configuration setting specified by key as a String value.
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(boolean) - 
Method in enum net.sf.basedb.util.formatter.BooleanFormatter.Type
 
getString(HttpResponse, String, String) - 
Static method in class net.sf.basedb.util.HttpUtil
 
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...) - 
Method in class net.sf.basedb.util.resources.ResourceBundleWrapper
Get a string value from the bundle.
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, String) - 
Static method in class net.sf.basedb.util.Values
Convert a string to a string.
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
 
getStringFormatter(SessionControl) - 
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.
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.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.Body
 
getStyle() - 
Method in class net.sf.basedb.clients.web.taglib.Button
 
getStyle() - 
Method in class net.sf.basedb.clients.web.taglib.ButtonGroup
 
getStyle() - 
Method in class net.sf.basedb.clients.web.taglib.Help
 
getStyle() - 
Method in class net.sf.basedb.clients.web.taglib.HideableSection
 
getStyle() - 
Method in class net.sf.basedb.clients.web.taglib.Icon
 
getStyle() - 
Method in class net.sf.basedb.clients.web.taglib.menu.Menu
 
getStyle() - 
Method in class net.sf.basedb.clients.web.taglib.menu.Menuitem
 
getStyle() - 
Method in class net.sf.basedb.clients.web.taglib.menu.Menuseparator
 
getStyle() - 
Method in class net.sf.basedb.clients.web.taglib.menu.Submenu
 
getStyle() - 
Method in class net.sf.basedb.clients.web.taglib.Note
 
getStyle() - 
Method in class net.sf.basedb.clients.web.taglib.path.Path
 
getStyle() - 
Method in class net.sf.basedb.clients.web.taglib.path.PathElement
 
getStyle() - 
Method in class net.sf.basedb.clients.web.taglib.Select
 
getStyle() - 
Method in class net.sf.basedb.clients.web.taglib.tab.Tab
 
getStyle() - 
Method in class net.sf.basedb.clients.web.taglib.tab.TabControl
 
getStyle() - 
Method in class net.sf.basedb.clients.web.taglib.table.Button
 
getStyle() - 
Method in class net.sf.basedb.clients.web.taglib.table.Cell
 
getStyle() - 
Method in class net.sf.basedb.clients.web.taglib.table.ColumnDef
 
getStyle() - 
Method in class net.sf.basedb.clients.web.taglib.table.Data
 
getStyle() - 
Method in class net.sf.basedb.clients.web.taglib.table.Header
 
getStyle() - 
Method in class net.sf.basedb.clients.web.taglib.table.Label
 
getStyle() - 
Method in class net.sf.basedb.clients.web.taglib.table.Navigator
 
getStyle() - 
Method in class net.sf.basedb.clients.web.taglib.table.Panel
 
getStyle() - 
Method in class net.sf.basedb.clients.web.taglib.table.PresetSelector
 
getStyle() - 
Method in class net.sf.basedb.clients.web.taglib.table.Row
 
getStyle() - 
Method in class net.sf.basedb.clients.web.taglib.table.Table
 
getStyle() - 
Method in class net.sf.basedb.clients.web.taglib.table.Toolbar
 
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.
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.clients.web.taglib.table.Table
 
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
 
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.
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(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() - 
Method in class net.sf.basedb.plugins.BaseFileExporterPlugin
 
getSuccessMessage(int) - 
Method in class net.sf.basedb.plugins.batchimport.AbstractItemImporter
 
getSuccessMessage() - 
Method in class net.sf.basedb.plugins.BfsExporterPlugin
 
getSuccessMessage() - 
Method in class net.sf.basedb.plugins.BioAssaySetExporter
Deprecated.  
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(int) - 
Method in class net.sf.basedb.plugins.IlluminaRawDataImporter
 
getSuccessMessage() - 
Method in class net.sf.basedb.plugins.PackedFileExporter
 
getSuccessMessage(int) - 
Method in class net.sf.basedb.plugins.PlateFlatFileImporter
Return x plates inserted.
getSuccessMessage() - 
Method in class net.sf.basedb.plugins.PlateMappingExporter
 
getSuccessMessage(int) - 
Method in class net.sf.basedb.plugins.PlateMappingImporter
Return Platemapping 'name' created.
getSuccessMessage() - 
Method in class net.sf.basedb.plugins.PluginConfigurationExporter
 
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() - 
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(int) - 
Method in class net.sf.basedb.clients.web.ExperimentExplorer.AnnotationGroup
Get the sum of intensities for the specified channel.
getSum() - 
Method in class net.sf.basedb.util.plot.HistogramPlot.HistogramBin
Get the sum of all values in this bin.
getSummary() - 
Method in class net.sf.basedb.clients.web.extensions.ScanResults
Get a summary of the scan results as a textual description.
getSummary(User) - 
Method in class net.sf.basedb.core.DiskUsageStatistics
Get a summary of the disk usage for the specified user.
getSummary(Group) - 
Method in class net.sf.basedb.core.DiskUsageStatistics
Get a summary of the disk usage for the specified group.
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.
getSupportsConfigurations() - 
Method in class net.sf.basedb.core.data.PluginDefinitionData
If the plugin supports configurations or not.
getSwitch() - 
Method in class net.sf.basedb.clients.web.taglib.tab.TabControl
 
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.
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.FileTypeData
 
getSystemId() - 
Method in class net.sf.basedb.core.data.GroupData
 
getSystemId() - 
Method in class net.sf.basedb.core.data.HardwareTypeData
 
getSystemId() - 
Method in class net.sf.basedb.core.data.ProtocolTypeData
 
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 class net.sf.basedb.core.data.SoftwareTypeData
 
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.FileType
 
getSystemId() - 
Method in class net.sf.basedb.core.Group
 
getSystemId() - 
Method in class net.sf.basedb.core.HardwareType
 
getSystemId() - 
Method in class net.sf.basedb.core.ProtocolType
 
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 class net.sf.basedb.core.SoftwareType
 
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
 
getTable() - 
Method in class net.sf.basedb.clients.web.taglib.table.Columns
 
getTable() - 
Method in class net.sf.basedb.clients.web.taglib.table.Data
 
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.clients.web.taglib.table.Toolbar
 
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.
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.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.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
 
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.data.ChangeHistoryData
Get the time of the change.
getTime(int) - 
Method in class net.sf.basedb.util.timer.PerformanceTimer
Get the current time of a timer.
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.
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.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.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.menu.Menuitem
 
getTitle() - 
Method in class net.sf.basedb.clients.web.taglib.menu.Submenu
 
getTitle() - 
Method in class net.sf.basedb.clients.web.taglib.Note
 
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
 
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 exception net.sf.basedb.clients.web.WebException
Get the title of the error message.
getTitle() - 
Method in class net.sf.basedb.core.data.ExperimentData
Get the title for this experiment.
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.info.ExperimentInfo
 
getTitle() - 
Method in class net.sf.basedb.info.ExtendedPropertyInfo
 
getTitle() - 
Method in class net.sf.basedb.plugins.BaseFileExporterPlugin.ExtendedDynamicField
 
getTitle() - 
Method in class net.sf.basedb.plugins.batchimport.FallbackIdMethod
 
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.plugins.BioAssaySetExporter.QueryItem
Deprecated.  
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 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.
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.
getToolParameters(List<String>) - 
Method in class net.sf.basedb.plugins.ManualTransformCreator
 
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
 
getTooltip() - 
Method in class net.sf.basedb.clients.web.taglib.table.ColumnDef
 
getTooltip() - 
Method in class net.sf.basedb.clients.web.taglib.table.Label
 
getTotal() - 
Method in class net.sf.basedb.core.DiskUsageStatistics.Summary
Get the total disk usage in bytes
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.
getTotal() - 
Method in class net.sf.basedb.core.SimpleAbsoluteProgressReporter
Get the end point of the task.
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
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.
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.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.
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.menu.Menu
 
getType() - 
Method in class net.sf.basedb.clients.web.util.NameablePluginAdaptor
 
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.BioMaterialList
 
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.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.FileType
 
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.HardwareType
 
getType() - 
Method in class net.sf.basedb.core.Help
 
getType() - 
Method in class net.sf.basedb.core.Hybridization
 
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.Image
 
getType() - 
Method in class net.sf.basedb.core.ItemKey
 
getType() - 
Method in class net.sf.basedb.core.ItemProxy
 
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.Label
 
getType() - 
Method in class net.sf.basedb.core.LabeledExtract
 
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.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 enum net.sf.basedb.core.Project.Default
 
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.ProtocolType
 
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.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.Sample
 
getType() - 
Method in class net.sf.basedb.core.Scan
 
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.SoftwareType
 
getType() - 
Method in class net.sf.basedb.core.SpotImages
 
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.VirtualDb
 
getType() - 
Method in class net.sf.basedb.core.Well
 
getType() - 
Method in class net.sf.basedb.info.QueryParameter
Get the parameter type.
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
 
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 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(String) - 
Method in class net.sf.basedb.core.Quantity
Get a a unit by symbol, also checking among the aliases.
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.
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.
getUnitConverter(Unit) - 
Method in class net.sf.basedb.core.Annotation
Get a converter for converting the values in this annotation to
                a specific unit.
getUnitFormatter(Formatter<T>, Unit) - 
Method in class net.sf.basedb.core.Annotation
Wrap a parent formatter with a formatter for units.
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(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
 
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.
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.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(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.
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() - 
Method in class net.sf.basedb.ws.client.SessionClient
Gets the URL of the session
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.
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(MeasuredBioMaterial) - 
Method in class net.sf.basedb.core.BioMaterialEvent
Get the quantity that was used by this event for the specified biomaterial.
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.BioMaterialSourceEventData
 
getUsedQuantity() - 
Method in class net.sf.basedb.core.data.UsedQuantity
Get the used quantity.
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.
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(DbControl, ChangeHistory, boolean, boolean) - 
Static method in class net.sf.basedb.clients.web.ChangeHistoryUtil
Get the user that made the change in HTML format.
getUser() - 
Method in class net.sf.basedb.core.BioMaterialEvent
Get the User that is responsible for this event.
getUser(DbControl) - 
Method in class net.sf.basedb.core.ChangeHistory
Load the user that made the change.
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.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.
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.
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.ChangeHistory
Get the ID of the user that made the change.
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.
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.InternalStorageController.StorageKeyring
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.
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 hybridization 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
                PlatformFileType:s using this file type
                
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:
                
                LabeledExtract:s created from this 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
                SpotImages using this file
                
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.FileType
Get all:
                
                File:s of this type
                
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:
                
                Scan:s with this hardware
                ArrayBatch:s with this hardware
                BioMaterial:s and Hybridization:s with this hardware
                Plate:s with this hardware
                
getUsingItems() - 
Method in class net.sf.basedb.core.HardwareType
Get all:
                
                Hardware:s if this type
                
getUsingItems() - 
Method in class net.sf.basedb.core.Hybridization
Get all:
                
                Scan:s created from this hybridization
                
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.Job
Get the transformation and raw bioassays using this job.
getUsingItems() - 
Method in class net.sf.basedb.core.Label
Get all:
                
                LabeledExtract:s labeled with this label
                
getUsingItems() - 
Method in class net.sf.basedb.core.LabeledExtract
Get all:
                
                Hybridization:s created from this labeled extract
                
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.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 Hybridization:s using this protocol
                a Plate:s using this protocol
                an ArrayBatch:s using this protocol
                a Scan:s using this protocol
                a RawBioAssay:s using this protocol
                
getUsingItems() - 
Method in class net.sf.basedb.core.ProtocolType
Get all:
                
                Protocol:s of this type
                PlateEventType:s using this protocol type
                
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.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.Scan
Get all:
                
                RawBioAssay:s created from this scan
                
getUsingItems() - 
Method in class net.sf.basedb.core.Software
Get all:
                
                RawBioAssay:s created with this software
                
getUsingItems() - 
Method in class net.sf.basedb.core.SoftwareType
Get all:
                
                Software of this type
                
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(InputStream, URL) - 
Static method in class net.sf.basedb.util.XMLUtil
Deprecated. Use XMLUtil.getValidatedXML(InputStream, URL, String) instead
getValidatedXml(URL, URL) - 
Static method in class net.sf.basedb.util.XMLUtil
Load and validate an XML file against a DTD, and return it as a
                Document object.
getValidatedXml(String, URL) - 
Static method in class net.sf.basedb.util.XMLUtil
 
getValidatedXML(InputStream, URL, String) - 
Static method in class net.sf.basedb.util.XMLUtil
Validate an InputStream against a DTD file 
                and return it as a Document
getValidationError() - 
Method in class net.sf.basedb.clients.web.extensions.ExtensionsFile
Get more information about the error that caused the validation
                to fail.
getValidationOptions() - 
Method in class net.sf.basedb.util.overview.ExperimentOverview
Deprecated. Get the validation options currently in use.
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.ExperimentOverview
Deprecated. (In 2.10) Use OverviewUtil.getValidationPresets(SessionControl) instead
getValidationPresets(SessionControl) - 
Static method in class net.sf.basedb.util.overview.OverviewUtil
Get the validation options presets for the currently logged in user.
getValidator() - 
Method in class net.sf.basedb.core.DataFileType
Create a new instance of the DataFileValidator class specified
                by DataFileType.getValidatorClass().
getValidator() - 
Method in class net.sf.basedb.util.overview.Failure
Get the validation rule that failed.
getValidatorClass() - 
Method in class net.sf.basedb.core.data.DataFileTypeData
Get the class name of the Java class that is the validator for
                this file type.
getValidatorClass() - 
Method in class net.sf.basedb.core.DataFileType
Get the class name of the Java class that is used to validate the files of
                this type.
getValidatorJarPath() - 
Method in class net.sf.basedb.core.data.DataFileTypeData
Get the path to the JAR file where the validator class is located.
getValidatorJarPath() - 
Method in class net.sf.basedb.core.DataFileType
Get the path to the JAR file where the validator class is located.
getValidators() - 
Static method in class net.sf.basedb.util.overview.ExperimentOverview
Deprecated. (In 2.10) Use OverviewUtil.getValidators() instead
getValidators() - 
Static method in class net.sf.basedb.util.overview.OverviewUtil
Get all validation rules grouped by relattionship.
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 
                        CoordinateTypegetValue() - 
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.File.Action
Get the integer value that is used when storing an File.Action 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.Image.Format
Get the integer value that is used when storing an Image.Format to 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(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, Collection<C>) - 
Method in class net.sf.basedb.core.Metadata.CollectionPropertyPath
 
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, Date) - 
Method in class net.sf.basedb.core.Metadata.DateCopyPropertyPath
 
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, IdentifiableData) - 
Method in class net.sf.basedb.core.Metadata.IdentifierPropertyPath
 
getValue(DbControl, Map) - 
Method in class net.sf.basedb.core.Metadata.MapPropertyPath
 
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, ReporterScore) - 
Method in class net.sf.basedb.core.Metadata.ReporterScore2DataPropertyPath
 
getValue() - 
Method in enum net.sf.basedb.core.Operator
Get the integer value that is used when storing an operator in the database.
getValue(String) - 
Method in class net.sf.basedb.core.ParameterValuesImpl
 
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(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() - 
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.info.QueryParameter
Set the parameter value.
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(int) - 
Method in class net.sf.basedb.util.bfs.MetadataModel.Section
Get the value of the entry at the given index.
getValue(String) - 
Method in class net.sf.basedb.util.bfs.MetadataModel.Section
Get the value of the first entry with a given key.
getValue() - 
Method in class net.sf.basedb.util.bfs.MetadataModel.SectionEntry
Get the value of the entry.
getValue(T, T, T) - 
Method in class net.sf.basedb.util.Diff3
Get the correct value to set on the newItem object.
getValue() - 
Method in class net.sf.basedb.util.Enumeration.Entry
 
getValue(int) - 
Method in class net.sf.basedb.util.Enumeration
 
getValue() - 
Method in class net.sf.basedb.util.fuzzy.StringMatcher.FuzzyMatch
Get the value string.
getValue(FlatFileParser.Data, int) - 
Method in class net.sf.basedb.util.importer.spotdata.ExtraFloatParser
Get the extra value from the data.
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(FlatFileParser.Data) - 
Method in class net.sf.basedb.util.parser.ColumnMapper
Get the value in the data objects column with the index specified
                in the constructor.
getValue(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.
getValue(FlatFileParser.Data) - 
Method in class net.sf.basedb.util.parser.ConstantMapper
 
getValue(FlatFileParser.Data) - 
Method in class net.sf.basedb.util.parser.CropStringMapper
Use the parent mapper to get the string value.
getValue(FlatFileParser.Data) - 
Method in class net.sf.basedb.util.parser.JepMapper
 
getValue(FlatFileParser.Data) - 
Method in interface net.sf.basedb.util.parser.Mapper
Get the value for the line of data.
getValue(FlatFileParser.Data) - 
Method in class net.sf.basedb.util.parser.NullIfExceptionMapper
 
getValue(String) - 
Method in class net.sf.basedb.util.QueryParameters
Get the (single) value for a key.
getValueAsObject() - 
Method in class net.sf.basedb.core.PropertyFilter
Get the value as an object of the correct type.
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.
getValueList(Element, Class) - 
Method in class net.sf.basedb.plugins.PluginConfigurationImporter
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(Unit) - 
Method in class net.sf.basedb.core.Annotation
Get the values for this annotation in a specific unit.
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(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() - 
Method in class net.sf.basedb.core.snapshot.AnnotationSnapshot
Get the annotation values.
getValues(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.
getValues() - 
Method in class net.sf.basedb.info.AnnotationInfo
 
getValues() - 
Method in class net.sf.basedb.plugins.executor.ProgramParameter
Get the values for this parameter.
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(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.util.bfs.MetadataModel.Section
Get the values of the first entry with a given key.
getValues() - 
Method in class net.sf.basedb.util.bfs.MetadataModel.SectionEntry
Get all values.
getValues(Map<String, List<String>>, String) - 
Method in class net.sf.basedb.util.jobagent.JobAgentInfo
 
getValues() - 
Method in class net.sf.basedb.util.plot.PlotAnnotation
The values that falls into this annotation.
getValues(String) - 
Method in class net.sf.basedb.util.QueryParameters
Get all values for a key.
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(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
 
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.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.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.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.info.AnnotationInfo
 
getValueType() - 
Method in class net.sf.basedb.info.AnnotationTypeInfo
 
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.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.
getVariantProxy() - 
Method in class net.sf.basedb.core.RawDataType
Needed to make RawBioAssay.setRawDataType(RawDataType)
                backwards compatible.
getVariantRawDataType(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.clients.web.util.NameablePluginAdaptor
 
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.info.BasicItemInfo
 
getVersion() - 
Method in class net.sf.basedb.util.extensions.AboutBean
 
getVersion() - 
Method in class net.sf.basedb.util.extensions.Registry.RegisteredAbout
 
getVersion() - 
Method in class net.sf.basedb.ws.client.SessionClient
 
getVersion() - 
Method in class net.sf.basedb.ws.server.SessionService
Return information about which Base version is in use.
getVersionInDatabase() - 
Method in class net.sf.basedb.util.PluginInfo
Get which version of this plugin that is installed in BASE.
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.
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 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
 
getVirtualDb() - 
Method in class net.sf.basedb.core.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(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.
getVirtualTable() - 
Method in class net.sf.basedb.core.ExtraValue
 
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(DbControl, FeatureData) - 
Static method in class net.sf.basedb.core.Feature
Get the well from a feature.
getWell(int, int) - 
Method in class net.sf.basedb.core.Plate
Get the well on the specified plate coordinate.
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.clients.web.taglib.tab.TabControl
 
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.
getWorkingDirectory() - 
Method in class net.sf.basedb.plugins.executor.ExternalProgramExecutor
Get the current working directory were data files for the
                external program are stored.
getX() - 
Method in class net.sf.basedb.core.data.RawData
 
getX(int, int) - 
Method in class net.sf.basedb.util.plot.HistogramPlot.HistogramDataset
 
getX() - 
Method in class net.sf.basedb.util.plot.HistogramPlot.TempSeries
 
getXml(String, URL, boolean) - 
Static method in class net.sf.basedb.util.XMLUtil
Parse a string containing XML, optionally validating it against a DTD, 
                and return it as a Document object.
getXOffset() - 
Method in class net.sf.basedb.core.data.SpotImagesData
Get the x-axis offset.
getXOffset() - 
Method in class net.sf.basedb.core.SpotImages
Get the X-axis offset used to convert data coordinates to image
                pixel values: xPixel = (xData - xOffset) / xScale.
getXScale() - 
Method in class net.sf.basedb.core.data.SpotImagesData
Get the x-axis scale.
getXScale() - 
Method in class net.sf.basedb.core.SpotImages
Get the X-axis scale factor used to convert data coordinates to image
                pixel values: xPixel = (xData - xOffset) / xScale.
getXValue(int, int) - 
Method in class net.sf.basedb.util.plot.HistogramPlot.HistogramDataset
 
getY() - 
Method in class net.sf.basedb.core.data.RawData
 
getY(int, int) - 
Method in class net.sf.basedb.util.plot.HistogramPlot.HistogramDataset
 
getY() - 
Method in class net.sf.basedb.util.plot.HistogramPlot.TempSeries
 
getYOffset() - 
Method in class net.sf.basedb.core.data.SpotImagesData
The y-axis offset.
getYOffset() - 
Method in class net.sf.basedb.core.SpotImages
Get the Y-axis offset used to convert data coordinates to image
                pixel values: yPixel = (yData - yOffset) / yScale.
getYScale() - 
Method in class net.sf.basedb.core.data.SpotImagesData
Get the y-axis scale.
getYScale() - 
Method in class net.sf.basedb.core.SpotImages
Get the Y-axis scale factor used to convert data coordinates to image
                pixel values: yPixel = (yData - yOffset) / yScale.
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
 
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
 
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.
grant(Set<Permission>) - 
Static method in enum net.sf.basedb.core.Permission
Combine the given permission 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
 
greenImageFile - 
Variable in class net.sf.basedb.core.data.SpotImagesData
 
group(Expression) - 
Method in class net.sf.basedb.core.AbstractEntityQuery
Not supported.
group(Expression) - 
Method in class net.sf.basedb.core.AbstractQuery
 
group - 
Variable in class net.sf.basedb.core.data.DiskUsageData
 
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(Expression) - 
Method in interface net.sf.basedb.core.query.Query
Add an expression query element to the group list.
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.
Group.QueryRuntimeFilterImpl() - 
Constructor for class net.sf.basedb.core.Group.QueryRuntimeFilterImpl
 
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 - 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.
groupPermissions - 
Variable in class net.sf.basedb.core.GroupPermissions
 
groupPermissions - 
Variable in class net.sf.basedb.core.MultiPermissions
 
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 - 
Static variable in class net.sf.basedb.clients.web.util.HTML
 
gt(AnnotationType, Object, boolean) - 
Static method in class net.sf.basedb.core.query.Annotations
Deprecated. Use Annotations.gt(String, AnnotationType, Object, boolean) instead with alias=null
gt(String, AnnotationType, Object, boolean) - 
Static method in class net.sf.basedb.core.query.Annotations
Create a restriction that searches for annotations
                greater than a given value on the root or a joined entity of a 
                query.
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.
gteq(AnnotationType, Object, boolean) - 
Static method in class net.sf.basedb.core.query.Annotations
Deprecated. Use Annotations.gteq(String, AnnotationType, Object, boolean) instead with alias=null
gteq(String, AnnotationType, Object, boolean) - 
Static method in class net.sf.basedb.core.query.Annotations
Create a restriction that searches for annotations
                greater than or equal to a given value on the root or a joined entity of a 
                query.
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.
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
 
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
 
GuiContext.Type(int) - 
Constructor for enum net.sf.basedb.core.plugin.GuiContext.Type
 
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.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.ExtractImporter
 
guiContexts - 
Static variable in class net.sf.basedb.plugins.batchimport.HybridizationImporter
 
guiContexts - 
Static variable in class net.sf.basedb.plugins.batchimport.LabeledExtractImporter
 
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.ScanImporter
 
guiContexts - 
Static variable in class net.sf.basedb.plugins.BfsExporterPlugin
 
guiContexts - 
Static variable in class net.sf.basedb.plugins.BioAssaySetExporter
Deprecated.  
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.



H

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(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.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
 
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.
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(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(String, Throwable) - 
Method in class net.sf.basedb.util.extensions.ExtensionContext
 
handleError(A, String, Throwable) - 
Method in class net.sf.basedb.util.extensions.ExtensionContext
 
handleError(String, Throwable) - 
Method in class net.sf.basedb.util.extensions.ExtensionPointContext
 
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, ExtensionPoint<?>, Extension<?>) - 
Method in class net.sf.basedb.clients.web.extensions.service.ServicesEventHandler
 
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, Object, BfsParser) - 
Method in class net.sf.basedb.util.bfs.MetadataModel
 
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, 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.
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.
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
 
handleHeader(EventHandler, String[]) - 
Method in class net.sf.basedb.util.bfs.AnnotationParser
Handle the header-found event.
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.core.FileSet.DataFileHandlerWrapper
 
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(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
 
handleSection(EventHandler, String) - 
Method in class net.sf.basedb.util.bfs.MetadataParser
Handle the new section event.
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.HardwareTypeData
 
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.
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.HybridizationImporter
 
hardwareColumnMapping - 
Static variable in class net.sf.basedb.plugins.batchimport.ScanImporter
 
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
 
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.HybridizationImporter
 
hardwareMapper - 
Variable in class net.sf.basedb.plugins.batchimport.ScanImporter
 
hardwareType - 
Variable in class net.sf.basedb.core.data.HardwareData
 
HardwareType - Class in net.sf.basedb.core
This class is used to represent the type of
        Hardware items in BASE.
HardwareType(HardwareTypeData) - 
Constructor for class net.sf.basedb.core.HardwareType
Creates a hardwaretype item.
HardwareTypeData - Class in net.sf.basedb.core.data
This class holds information about a hardwaretype.
HardwareTypeData() - 
Constructor for class net.sf.basedb.core.data.HardwareTypeData
 
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() - 
Method in class net.sf.basedb.clients.web.fileupload.FileUploadProgress
Check if the upload has been requested to be aborted.
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.
hasAnnotation(AnnotationType) - 
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, AnnotationType, boolean, boolean) - 
Constructor for class net.sf.basedb.core.HasAnnotationRestriction
Create a new restriction that checks if an item has been annotatated
                or not.
HasAnnotationRestriction(String, int, boolean, boolean) - 
Constructor for class net.sf.basedb.core.HasAnnotationRestriction
 
hasArrayDesign() - 
Method in class net.sf.basedb.core.RawBioAssay
Check if this raw bioassay is connected to an array design or not.
hasAutoJoined - 
Variable in class net.sf.basedb.core.AbstractQuery
 
hasBeenAnnotatated - 
Variable in class net.sf.basedb.core.HasAnnotationRestriction
 
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.clients.web.extensions.Settings
 
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.
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.
hasCheck - 
Variable in class net.sf.basedb.clients.web.ModeInfo
 
hasCheck() - 
Method in class net.sf.basedb.clients.web.ModeInfo
 
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.
hasConfigurations() - 
Method in class net.sf.basedb.util.PluginInfo
 
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
 
hasDifferentVersion() - 
Method in class net.sf.basedb.util.PluginInfo
Has the plug-in a version number that differ from what is stored in
                the database.
hasDisabledRawJoin() - 
Method in class net.sf.basedb.core.DynamicSpotQuery
Check if joining to raw data has been disabled.
hasDownloadableData(int) - 
Method in class net.sf.basedb.ws.client.ArrayDesignClient
Gets if data in an array design can be downloaded as a file or not.
hasDownloadableData(int) - 
Method in class net.sf.basedb.ws.client.BioAssaySetClient
Returns if a bioassay set has spot data in the form of files that 
                can be downloaded or not.
hasDownloadableData(int) - 
Method in class net.sf.basedb.ws.client.RawBioAssayClient
Returns if a rawbioassay has raw data that can be downloaded or not.
hasDownloadableData(String, int) - 
Method in class net.sf.basedb.ws.server.ArrayDesignService
Gets if the arraydesign files can be downloaded or not.
hasDownloadableData(String, int) - 
Method in class net.sf.basedb.ws.server.BioAssaySetService
Checks if the files has been attached to bioassay set.
hasDownloadableData(String, int) - 
Method in class net.sf.basedb.ws.server.RawBioAssayService
Gets if the rawdata files can be downloaded or not.
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.clients.web.extensions.ExtensionsFile
 
hasError() - 
Method in class net.sf.basedb.clients.web.extensions.ExtensionsFile
If there was an error when registering the extensions in this file.
hasError - 
Variable in class net.sf.basedb.clients.web.extensions.ScanResults.FileResults
 
hasError() - 
Method in class net.sf.basedb.clients.web.extensions.ScanResults.FileResults
If there was an error in this file or not.
hasError - 
Variable in class net.sf.basedb.clients.web.extensions.ScanResults
 
hasError() - 
Method in class net.sf.basedb.clients.web.extensions.ScanResults
Check if the scan was successful or not.
hasError - 
Variable in class net.sf.basedb.plugins.executor.ExternalProgramExecutor.ResponseWrapper
 
hasError() - 
Method in class net.sf.basedb.plugins.executor.ExternalProgramExecutor.ResponseWrapper
 
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.
hasExternalId(Item) - 
Method in class net.sf.basedb.plugins.AnnotationFlatFileImporter
Check if the current item has an 'externalId' property.
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.
hasFeatures - 
Variable in class net.sf.basedb.core.data.ArrayDesignData
 
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.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() - 
Method in class net.sf.basedb.clients.web.extensions.ExtensionsFile
 
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.ContextKey
Calculate the hash code for the object.
hashCode - 
Variable in class net.sf.basedb.core.data.BasicData
Stores the hash code of the item.
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 - 
Variable in class net.sf.basedb.core.DynamicJoin
 
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 - 
Variable in class net.sf.basedb.core.query.AndRestriction
 
hashCode() - 
Method in class net.sf.basedb.core.query.AndRestriction
 
hashCode() - 
Method in class net.sf.basedb.core.query.AscOrder
 
hashCode() - 
Method in class net.sf.basedb.core.query.BetweenRestriction
 
hashCode - 
Variable in class net.sf.basedb.core.query.CaseExpression
 
hashCode() - 
Method in class net.sf.basedb.core.query.CaseExpression
 
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 - 
Variable in class net.sf.basedb.core.query.InRestriction
 
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 - 
Variable in class net.sf.basedb.core.query.OrRestriction
 
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.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(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.
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.Registry.AttributeKey
 
hashCode() - 
Method in class net.sf.basedb.util.jobagent.JobInfo
 
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.units.UnitCache.CacheKey
From the Object class
                        ---------------------
hasHiddenMembers() - 
Method in class net.sf.basedb.core.Group
Does this group have hidden members?
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
 
hasLineNo - 
Variable in class net.sf.basedb.util.parser.JepMapper
 
hasMember(DataFileType) - 
Method in class net.sf.basedb.core.FileSet
Check if the file set contains a 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() - 
Method in class net.sf.basedb.clients.web.servlet.PlotServlet.CFResultIterator
 
hasNext() - 
Method in class net.sf.basedb.core.DataResultIterator
 
hasNext - 
Variable in class net.sf.basedb.core.DynamicResultIterator
 
hasNext() - 
Method in class net.sf.basedb.core.DynamicResultIterator
 
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 - 
Variable in class net.sf.basedb.util.extensions.ActionIterator
 
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.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(Permission) - 
Method in class net.sf.basedb.clients.web.extensions.ExtensionsControl
 
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
 
hasPermission(Permission) - 
Method in class net.sf.basedb.clients.web.util.NameablePluginAdaptor
 
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.Coloring
 
hasPermission(int, Permission) - 
Static method in enum net.sf.basedb.core.Permission
Checks if the given Permission is granted by the 
                permissions code.
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.
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.
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.
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.
hasSecondaryLocation() - 
Method in class net.sf.basedb.core.QuotaType
Check if items using quota from this quota type can be stored
                in the secondary location or not.
hasSecondaryStorage() - 
Static method in class net.sf.basedb.core.Application
Checks if the server has configured a secondary storage or not.
hasSignalTransporter() - 
Method in class net.sf.basedb.core.Job
Checks if a signal transporter has been registered for this job or not.
hasSpotImages() - 
Method in class net.sf.basedb.core.RawBioAssay
Check if spot images exists for this raw bioassay or not.
hasSystemPermission(Permission) - 
Method in class net.sf.basedb.core.SessionControl
Check if the logged in user has the specified system permission.
hasTable - 
Variable in class net.sf.basedb.core.hibernate.TableExistsWork
 
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
 
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.
hasValidated - 
Variable in class net.sf.basedb.clients.web.extensions.ExtensionsFile
 
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.
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 - 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 - 
Variable in class net.sf.basedb.util.parser.FlatFileParser
The regular expression for matching a header line.
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.
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.
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 - 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() - 
Constructor for class net.sf.basedb.clients.web.taglib.Help
 
Help - Class in net.sf.basedb.core
This class is used to represent a help text for
        a client application.
Help(HelpData) - 
Constructor for class net.sf.basedb.core.Help
Creates a new help item
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
 
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.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
 
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.
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
 
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 - 
Variable in class net.sf.basedb.core.PluginParameter
If the parameter should be hidden from user input or not.
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
 
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
 
histogram - 
Variable in class net.sf.basedb.util.plot.HistogramPlot
 
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.HistogramBin(float, float) - 
Constructor for class net.sf.basedb.util.plot.HistogramPlot.HistogramBin
Create a new HistogramBin.
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.HistogramDataset() - 
Constructor for class net.sf.basedb.util.plot.HistogramPlot.HistogramDataset
 
HistogramPlot.HistogramSeries - Class in net.sf.basedb.util.plot
Collects information about one histogram series.
HistogramPlot.HistogramSeries(String, float[], float[], float, HistogramPlot.YAggregate, float, float) - 
Constructor for class net.sf.basedb.util.plot.HistogramPlot.HistogramSeries
Create a new HistogramSeries.
HistogramPlot.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.
HistogramPlot.TempSeries - Class in net.sf.basedb.util.plot
Helper class for storing histogram data that needs to split into
                different annotations.
HistogramPlot.TempSeries(String, int, boolean) - 
Constructor for class net.sf.basedb.util.plot.HistogramPlot.TempSeries
 
HistogramPlot.YAggregate - Enum in net.sf.basedb.util.plot
Defines what to to plot on the y axis in a histogram plot.
HistogramPlot.YAggregate() - 
Constructor for enum net.sf.basedb.util.plot.HistogramPlot.YAggregate
 
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 - 
Static variable in class net.sf.basedb.core.Directory
The id for the Directory item representing
                the home directory.
home - 
Variable in class net.sf.basedb.util.extensions.xml.PathConverter
 
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.authentication.POP3Authenticator
The address or IP-number to the POP3 host.
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
 
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)
        
        Throws an UnsupportedOperationException if 
        Query.getQueryType() isn't QueryType.HQL.
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.
HqlPropertyExpression(String, String) - 
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.ReporterListJoiner - Class in net.sf.basedb.core
Joiner for reporter lists.
HqlQueryJoiners.ReporterListJoiner(JoinType) - 
Constructor for class net.sf.basedb.core.HqlQueryJoiners.ReporterListJoiner
 
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.path.PathElement
URL to the linked page.
hSession - 
Variable in class net.sf.basedb.core.DbControl
The Hibernate session.
hStatelessSession - 
Variable in class net.sf.basedb.core.DbControl
A Hibernate stateless session.
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
The Hibernate transaction.
HTTP_DATE_FORMAT - 
Static variable in class net.sf.basedb.util.HttpUtil
 
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.BioPlateEventType
The system ID for "Hybridization" event type.
hybridization - 
Variable in class net.sf.basedb.core.data.ArraySlideData
 
hybridization - 
Variable in class net.sf.basedb.core.data.BioMaterialEventData
 
hybridization - 
Variable in class net.sf.basedb.core.data.ScanData
 
Hybridization - Class in net.sf.basedb.core
A hybridization is a representation of the process of hybridizing
        one or more LabeledExtract:s on an ArraySlide.
Hybridization(HybridizationData) - 
Constructor for class net.sf.basedb.core.Hybridization
 
HYBRIDIZATION - 
Static variable in class net.sf.basedb.core.ProtocolType
The ID for the hybridization protocol type, for example a protocol
                used when creating a Hybridization from a set of
                LabeledExtract:s.
HYBRIDIZATION_STATION - 
Static variable in class net.sf.basedb.core.HardwareType
The id for the HardwareType object representing a 
                hybridization station.
hybridizationColumnMapping - 
Static variable in class net.sf.basedb.plugins.batchimport.ScanImporter
 
HybridizationData - Class in net.sf.basedb.core.data
This class holds information about an hybridization.
HybridizationData() - 
Constructor for class net.sf.basedb.core.data.HybridizationData
 
HybridizationImporter - Class in net.sf.basedb.plugins.batchimport
Plug-in for importing hybridization items in a batch.
HybridizationImporter() - 
Constructor for class net.sf.basedb.plugins.batchimport.HybridizationImporter
 
HybridizationLoader - Class in net.sf.basedb.util.overview.loader
Node loader implementation for hybridizations.
HybridizationLoader() - 
Constructor for class net.sf.basedb.util.overview.loader.HybridizationLoader
 
hybridizationMapper - 
Variable in class net.sf.basedb.plugins.batchimport.ScanImporter
 
HybridizationValidator - Class in net.sf.basedb.util.overview.validator
Validator implementation for hybridizations.
HybridizationValidator() - 
Constructor for class net.sf.basedb.util.overview.validator.HybridizationValidator
 
hybStationQuery - 
Variable in class net.sf.basedb.plugins.batchimport.AbstractItemImporter
 



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 - 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
 
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 class net.sf.basedb.clients.web.taglib.Note
The filename of an optional icon that should be displayed with the error message.
iconAbsolute - 
Variable in class net.sf.basedb.clients.web.taglib.menu.Menuitem
 
iconAbsolute - 
Variable in class net.sf.basedb.clients.web.taglib.menu.Submenu
 
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.plot.OverviewPlotBean
 
id - 
Variable in class net.sf.basedb.clients.web.extensions.plot.PlotGeneratorBean
 
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.formatter.SpotImageFormatter
 
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.authentication.AuthenticationInformation
A unique id for the user in the authentication system.
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.query.HqlEntityExpression
 
id - 
Variable in class net.sf.basedb.core.RawDataType
 
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.info.BasicItemInfo
 
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.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.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.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.ws.client.SessionClient
 
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.batchimport.AbstractItemImporter
 
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.
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.
idMapper - 
Variable in class net.sf.basedb.plugins.batchimport.AbstractItemImporter
 
idMapper - 
Variable in class net.sf.basedb.plugins.ReporterFlatFileImporter
 
idMapping - 
Variable in class net.sf.basedb.plugins.batchimport.AbstractItemImporter
 
idMethod - 
Variable in class net.sf.basedb.plugins.batchimport.AbstractItemImporter
 
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
 
ignore - 
Variable in class net.sf.basedb.clients.web.extensions.ExtensionsDirectory
 
ignore - 
Variable in class net.sf.basedb.util.parser.FlatFileParser
The regular expression for matching a comment line.
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.
ignoredLines - 
Variable in class net.sf.basedb.util.parser.FlatFileParser
Number of ignored lines in the FlatFileParser.nextData() method.
ignoreFilename - 
Variable in class net.sf.basedb.util.FileExportOutputStream
 
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.
IlluminaRawDataImporter.BatchAndMapHolder(RawDataBatcher, RawDataType, FlatFileParser) - 
Constructor for class net.sf.basedb.plugins.IlluminaRawDataImporter.BatchAndMapHolder
 
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.core.data.PlateMappingData
 
IMAGE - 
Static variable in class net.sf.basedb.core.FileType
The id for the FileType item representing an
                image file.
Image - Class in net.sf.basedb.core
An image represents a single image produced by a Scan.
Image(ImageData) - 
Constructor for class net.sf.basedb.core.Image
 
image - 
Variable in class net.sf.basedb.core.SpotImage
 
Image.Format - Enum in net.sf.basedb.core
This enumeration is used to indicate the type of image.
Image.Format(int, String) - 
Constructor for enum net.sf.basedb.core.Image.Format
 
IMAGE_EXTENSION - 
Static variable in class net.sf.basedb.clients.web.util.HTML
 
imageAlign - 
Variable in class net.sf.basedb.clients.web.taglib.table.Button
LEFT or RIGTH;
ImageData - Class in net.sf.basedb.core.data
This class holds information about an image produced by scanning a
        hybridization.
ImageData() - 
Constructor for class net.sf.basedb.core.data.ImageData
 
imageDescriptionColumnMapping - 
Static variable in class net.sf.basedb.plugins.batchimport.ScanImporter
 
imageDescriptionMapper - 
Variable in class net.sf.basedb.plugins.batchimport.ScanImporter
 
imageFileColumnMapping - 
Static variable in class net.sf.basedb.plugins.batchimport.ScanImporter
 
imageFileMapper - 
Variable in class net.sf.basedb.plugins.batchimport.ScanImporter
 
imageFormatColumnMapping - 
Static variable in class net.sf.basedb.plugins.batchimport.ScanImporter
 
imageFormatMapper - 
Variable in class net.sf.basedb.plugins.batchimport.ScanImporter
 
ImageLoader - Class in net.sf.basedb.util.overview.loader
Node loader implementation for scan images.
ImageLoader() - 
Constructor for class net.sf.basedb.util.overview.loader.ImageLoader
 
ImageLogger - Class in net.sf.basedb.core.log.db
Logger for images that logs changes as
        updates to the scan they belong to.
ImageLogger(boolean) - 
Constructor for class net.sf.basedb.core.log.db.ImageLogger
Creates a new image logger.
imageNameColumnMapping - 
Static variable in class net.sf.basedb.plugins.batchimport.ScanImporter
 
imageNameMapper - 
Variable in class net.sf.basedb.plugins.batchimport.ScanImporter
 
imagePreviewColumnMapping - 
Static variable in class net.sf.basedb.plugins.batchimport.ScanImporter
 
imagePreviewMapper - 
Variable in class net.sf.basedb.plugins.batchimport.ScanImporter
 
images - 
Variable in class net.sf.basedb.core.data.ScanData
 
imagesDirectory - 
Variable in class net.sf.basedb.plugins.batchimport.ScanImporter
 
imgClass - 
Variable in class net.sf.basedb.clients.web.formatter.SpotImageFormatter
 
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(Ownable, 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.
impersonateLogin(Ownable, String) - 
Method in class net.sf.basedb.core.SessionControl
Log in as the owner of the specified item.
importableFileTypes - 
Variable in class net.sf.basedb.plugins.ManualTransformCreator
 
importAll - 
Variable in class net.sf.basedb.plugins.PluginConfigurationImporter
 
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
 
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.fileupload.FileUpload
The stream coming from the browser.
in(AnnotationType, boolean, Object...) - 
Static method in class net.sf.basedb.core.query.Annotations
Deprecated. Use Annotations.in(String, AnnotationType, boolean, Object[])
                        instead with alias=null
in(String, AnnotationType, boolean, Object...) - 
Static method in class net.sf.basedb.core.query.Annotations
Create a restriction that searches for annotations
                on the root or a joined entity
                equal to any value in a list of given values.
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 - 
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.
include - 
Variable in class net.sf.basedb.clients.web.extensions.tabcontrol.IncludeContentTabFactory
 
include(Include...) - 
Method in class net.sf.basedb.core.AbstractEntityQuery
 
include(Collection<Include>) - 
Method in class net.sf.basedb.core.AbstractEntityQuery
 
include - 
Variable in class net.sf.basedb.core.data.ContextData
 
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.
include - 
Variable in class net.sf.basedb.core.ItemContext
 
include(Include...) - 
Method in interface net.sf.basedb.core.query.EntityQuery
Specify options for which items to include in the result.
include(Collection<Include>) - 
Method in interface net.sf.basedb.core.query.EntityQuery
 
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
 
IncludeContentTabFactory.Tab(JspContext) - 
Constructor for class net.sf.basedb.clients.web.extensions.tabcontrol.IncludeContentTabFactory.Tab
 
IncludeExcludeFilter - Class in net.sf.basedb.util
 
IncludeExcludeFilter(DbControl, BioAssaySet, List<BioAssay>, Restriction, Integer, Integer) - 
Constructor for class net.sf.basedb.util.IncludeExcludeFilter
 
includeInheriting - 
Variable in class net.sf.basedb.core.AnnotationRestriction
 
includeInProject - 
Variable in class net.sf.basedb.info.QueryOptions
Include items from the active project.
includeLimit - 
Variable in class net.sf.basedb.util.IncludeExcludeFilter
 
includeMine - 
Variable in class net.sf.basedb.info.QueryOptions
Include items that belongs to the logged in user.
includeNotRemoved - 
Variable in class net.sf.basedb.info.QueryOptions
 
includeOthers - 
Variable in class net.sf.basedb.info.QueryOptions
Include items that belong to other users.
includes - 
Variable in class net.sf.basedb.core.AbstractEntityQuery
Flags specifying which items to include.
includeShared - 
Variable in class net.sf.basedb.info.QueryOptions
Include items, shared to the logged in user.
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.
incoming - 
Variable in class net.sf.basedb.util.jobagent.JobAgentServerConnection.RequestHandlerThread
 
INCORRECT_ARRAY_NUM - 
Static variable in class net.sf.basedb.util.overview.Validator
Validator rule that checks if the sub-array index on a raw bioassay
                or labeled extract is between 1 and the number of sub-arrays on the 
                hybridization.
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_NUM_LABELEDEXTRACTS - 
Static variable in class net.sf.basedb.util.overview.Validator
Validator rule that checks if the number of labeled extracts
                attached to a hybridization matches the number of channels in the
                experiment.
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_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.
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.core.data.BioPlateEventParticipantData
 
index - 
Variable in class net.sf.basedb.core.Metadata.ComponentPropertyPath
 
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 - 
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.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_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 - 
Static variable in class net.sf.basedb.core.VirtualColumn
Used in constructor to tell that the column should be indexed.
indexed - 
Variable in class net.sf.basedb.core.VirtualColumn
If the column should be indexed or not.
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
 
indexes - 
Variable in class net.sf.basedb.core.dbengine.TableInfo
 
indexMapper - 
Variable in class net.sf.basedb.plugins.batchimport.ArraySlideImporter
 
indexOf(Object) - 
Method in class net.sf.basedb.core.ItemResultList
 
info - 
Variable in class net.sf.basedb.core.hibernate.TableInfoWork
 
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
 
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
 
inheritAnnotation(Annotation) - 
Method in class net.sf.basedb.core.AnnotationSet
Inherit an annotation.
inheritAnnotationSet(AnnotationSet) - 
Method in class net.sf.basedb.core.AnnotationSet
Inherit an annotation set.
inherited - 
Variable in class net.sf.basedb.core.data.AnnotationSetData
 
inherited - 
Variable in class net.sf.basedb.core.snapshot.AnnotationSnapshot
 
inheritedSets - 
Variable in class net.sf.basedb.core.data.AnnotationSetData
 
inheritingSets - 
Variable in class net.sf.basedb.core.data.AnnotationData
 
inheritingSets - 
Variable in class net.sf.basedb.core.data.AnnotationSetData
 
init(String) - 
Method in class net.sf.basedb.clients.jobagent.AgentSignalReceiver
Initialise the receiver.
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(ExtensionsDirectory, ServletContext) - 
Static method in class net.sf.basedb.clients.web.extensions.ExtensionsControl
Initialise the extension system.
init(Registry, Settings) - 
Static method in class net.sf.basedb.clients.web.extensions.service.Services
Initialise and start the installed services.
init(JspCompilationContext, JspServletWrapper) - 
Method in class net.sf.basedb.clients.web.extensions.XJspCompiler
Initialises the compiler.
init(FilterConfig) - 
Method in class net.sf.basedb.clients.web.servlet.CharacterEncodingFilter
 
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.ExtensionsServlet
 
init() - 
Method in class net.sf.basedb.clients.web.servlet.PlotServlet
 
init() - 
Method in class net.sf.basedb.clients.web.servlet.RssNewsFeed
 
init() - 
Method in class net.sf.basedb.clients.web.servlet.StartStopServlet
Calls Application.start().
init(String) - 
Method in class net.sf.basedb.clients.web.util.SimpleSignalProgressReporter
Nothing need to be initilized.
init(String) - 
Method in interface net.sf.basedb.core.authentication.Authenticator
Initialises the object.
init(String) - 
Method in class net.sf.basedb.core.authentication.POP3Authenticator
Initialises the object.
init(String) - 
Method in class net.sf.basedb.core.authentication.SimpleAuthenticator
There is nothing to initialise.
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(String) - 
Method in class net.sf.basedb.core.InternalStorageController
 
init(String) - 
Method in class net.sf.basedb.core.Job.JobSignalTransporter
 
init() - 
Static method in class net.sf.basedb.core.Keyring
 
init() - 
Static method in class net.sf.basedb.core.Metadata
 
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() - 
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(String) - 
Method in interface net.sf.basedb.core.SecondaryStorageController
Initialises the object.
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(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 and annotation sets.
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(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() - 
Static method in class net.sf.basedb.util.EmailUtil
 
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.
initAutoInstaller() - 
Static method in class net.sf.basedb.clients.web.extensions.ExtensionsControl
Initialise the automatic installation task.
initBean(Class<? extends Action>) - 
Method in class net.sf.basedb.util.extensions.debug.BeanActionFactory
Create the bean object.
initBeanWithReflection(Object, Element) - 
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(boolean, 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.
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
 
initialValue(Object) - 
Method in class net.sf.basedb.util.ClassLocal
Subclasses may override this to initialize the object
                stored for that class.
initInherited(AnnotationData) - 
Method in class net.sf.basedb.core.snapshot.AnnotationSnapshot
Initialize the snapshot with information from the given
                inherited annotation.
initInherited(AnnotationSetData) - 
Method in class net.sf.basedb.core.snapshot.AnnotationSnapshot
Initialize the snapshot with information from the given
                inherited annotation set.
initInherited(AnnotationSnapshot) - 
Method in class net.sf.basedb.core.snapshot.AnnotationSnapshot
Initializes this snapshot as an inherited annotation
                with complete data from another primary annotation
                snapshot.
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.
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.FileType
 
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.HardwareType
If this is a system hardware type, delete and create permissions are revoked.
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.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.ProtocolType
If this is a system protocol type, delete and create permissions are revoked.
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.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.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.SoftwareType
 
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.
initPlatforms() - 
Static method in class net.sf.basedb.core.RawDataTypes
Load file-only platforms and create raw data types for them.
initPrimary(AnnotationData) - 
Method in class net.sf.basedb.core.snapshot.AnnotationSnapshot
Initialize the snapshot with information from the given
                primary annotation.
initProxy(Class<? extends Action>) - 
Method in class net.sf.basedb.util.extensions.debug.ProxyActionFactory
Initialise the proxy class.
initQuery(ItemQuery<T>, String, String) - 
Method in class net.sf.basedb.util.overview.ExperimentOverview
Deprecated. Set include options and sorting order for a query.
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>, 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 interface net.sf.basedb.util.overview.OverviewContext
Initialise a query with "global options" and optionally a sort
                order.
initReferenceQuery(DbControl, IdMethod, ItemQuery<T>) - 
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.
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.
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, OutputStream...) - 
Constructor for class net.sf.basedb.util.InputStreamSplitter
Create a new input stream splitter.
InputStreamSplitter(InputStream, boolean, boolean, 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.
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
 
inSameJarFile - 
Variable in class net.sf.basedb.util.PluginInfo
 
inSameJarFile() - 
Method in class net.sf.basedb.util.PluginInfo
If the plug-in is already installed in the same or a different JAR file.
insert(D) - 
Method in class net.sf.basedb.core.BasicBatcher
Insert a data object.
insert(FeatureData) - 
Method in class net.sf.basedb.core.FeatureBatcher
Set the position number and add the feature to the insert queue.
insert(short, int) - 
Method in class net.sf.basedb.core.FilterBatcher
Insert a column/position coordinate that passed the filter.
insert(AbstractSqlQuery) - 
Method in class net.sf.basedb.core.FilterBatcher
Insert column/position coordinates using a query.
insert(Object) - 
Method in class net.sf.basedb.core.hibernate.StatelessSessionWrapper
 
insert(String, Object) - 
Method in class net.sf.basedb.core.hibernate.StatelessSessionWrapper
 
insert(short, int, RawData) - 
Method in class net.sf.basedb.core.MappingBatcher
Link a spot to a raw data.
insert(AbstractSqlQuery) - 
Method in class net.sf.basedb.core.MappingBatcher
Insert mapping to raw spots using a query.
insert(int, ReporterData) - 
Method in class net.sf.basedb.core.PositionBatcher
Link a position to a reporter.
insert(AbstractSqlQuery) - 
Method in class net.sf.basedb.core.PositionBatcher
Insert position/reporter links using a query.
insert(int, I) - 
Method in class net.sf.basedb.core.PositionExtraValueBatcher
Insert an extra value for a given position coordinate.
insert(AbstractSqlQuery) - 
Method in class net.sf.basedb.core.PositionExtraValueBatcher
Insert position extra values using a query.
insert(RawData) - 
Method in class net.sf.basedb.core.RawDataBatcher
 
insert(RawData, String) - 
Method in class net.sf.basedb.core.RawDataBatcher
Deprecated. Use RawDataBatcher.insert(RawData, String, String) instead
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.
insert(short, int, float...) - 
Method in class net.sf.basedb.core.SpotBatcher
Insert intensities for a given column/position coordinate.
insert(AbstractSqlQuery) - 
Method in class net.sf.basedb.core.SpotBatcher
Insert spot intensities using a query.
insert(short, int, I) - 
Method in class net.sf.basedb.core.SpotExtraValueBatcher
Insert an extra value for a given column/position coordinate.
insert(AbstractSqlQuery) - 
Method in class net.sf.basedb.core.SpotExtraValueBatcher
Insert extra values using a query.
insertable - 
Variable in class net.sf.basedb.core.ExtendedProperty
 
insertable - 
Variable in class net.sf.basedb.info.ExtendedPropertyInfo
 
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.
insertPropertyOrder - 
Variable in class net.sf.basedb.core.BasicBatcher
 
insertSql - 
Variable in class net.sf.basedb.core.BasicBatcher
 
insertStatement - 
Variable in class net.sf.basedb.core.BasicBatcher
 
insideImage(float, float, int, int, int) - 
Method in class net.sf.basedb.core.SpotImages
Check if entire spot is inside the soure image.
inspectSchemaGenerationSQL(String, Dialect, boolean) - 
Method in class net.sf.basedb.core.dbengine.AbstractDbEngine
Remove "not null" constraints from "alter table ... add column"
                statements that doesn't supply a default value for the new column
                when updating.
inspectSchemaGenerationSQL(String, Dialect, boolean) - 
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.
inspectSchemaGenerationSQL(String, Dialect, boolean) - 
Method in class net.sf.basedb.core.dbengine.PostgresDbEngine
Skip all "create index" statements since Hibernate doesn't generate those
                with unique names.
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.PlatformFT - Class in net.sf.basedb.core
 
Install.PlatformFT(DataFileTypeData, boolean) - 
Constructor for class net.sf.basedb.core.Install.PlatformFT
 
installAndUpdateExtensions(boolean) - 
Method in class net.sf.basedb.clients.web.extensions.ExtensionsControl
Perform a manual scan for new/updated/deleted extensions.
installAndUpdateExtensions(Registry, ServletContext, boolean, boolean) - 
Method in class net.sf.basedb.clients.web.extensions.ExtensionsDirectory
Scan the directory for new/modified/deleted extension files
                and perform neccesary changed in the registry.
installedExtensions - 
Variable in class net.sf.basedb.clients.web.extensions.ExtensionsDirectory
 
installedFiles - 
Variable in class net.sf.basedb.clients.web.extensions.ExtensionsDirectory
 
installHelpTexts(Client, boolean, InputStream) - 
Method in class net.sf.basedb.plugins.HelpImporter
Deprecated. Use HelpImporter.installHelpTexts(Client, boolean, InputStream, String) instead
installHelpTexts(Client, boolean, InputStream, String) - 
Method in class net.sf.basedb.plugins.HelpImporter
This method installs the helptexts from an inputstream.
installUnits(String, boolean) - 
Static method in class net.sf.basedb.core.Install
 
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.
INTEGER - 
Static variable in class net.sf.basedb.core.hibernate.TypeWrapper
 
integer(int) - 
Static method in class net.sf.basedb.core.query.Expressions
Create a constant expression from an integer.
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.
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
 
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.
IntensityCalculatorUtil.JepIntensityCalculatorImpl(JEP[], RawFunction, MeanFunction) - 
Constructor for class net.sf.basedb.util.IntensityCalculatorUtil.JepIntensityCalculatorImpl
 
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_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.
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.JobQueueKeyring() - 
Constructor for class net.sf.basedb.core.InternalJobQueue.JobQueueKeyring
 
InternalJobQueue.JobRunner - Class in net.sf.basedb.core
Encapsulates the running of a job in a separate thread.
InternalJobQueue.JobRunner(JobData, Job.ExecutionTime) - 
Constructor for class net.sf.basedb.core.InternalJobQueue.JobRunner
 
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
 
InternalStorageController - Class in net.sf.basedb.core
A simple implementation of a secondary storage controller which just moves
        files to another directory.
InternalStorageController() - 
Constructor for class net.sf.basedb.core.InternalStorageController
Create the storage controller.
InternalStorageController.StorageKeyring - Class in net.sf.basedb.core
Our own keyring containing the permissions we need to move the files.
InternalStorageController.StorageKeyring() - 
Constructor for class net.sf.basedb.core.InternalStorageController.StorageKeyring
 
InterruptHandler - Interface in net.sf.basedb.core.signal
An interface for handling thread interrupts.
interruptHandler - 
Static variable in class net.sf.basedb.core.signal.ThreadSignalHandler
Keep per-thread interupt handlers.
intersection(Collection<BioMaterialList>) - 
Static method in class net.sf.basedb.core.BioMaterialList
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
 
INV_LN2 - 
Static variable in class net.sf.basedb.plugins.LowessNormalization.SpotData
 
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...).
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(Throwable) - 
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.
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(String) - 
Constructor for exception net.sf.basedb.core.authentication.InvalidPasswordException
Create a new InvalidPasswordException object
InvalidPasswordException(String, String) - 
Constructor for exception net.sf.basedb.core.authentication.InvalidPasswordException
Create a new InvalidPasswordException object
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.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
        DataFileValidator has detected that a related
        file is invalid.
InvalidRelationException() - 
Constructor for exception net.sf.basedb.core.InvalidRelationException
Create a new InvalidRelationException object.
InvalidRelationException(Throwable) - 
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.
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(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
 
invokeBlocking(String, Object[], Class[]) - 
Method in class net.sf.basedb.ws.client.AbstractRPCClient
 
invokeBlocking(String, Class<T>, Object...) - 
Method in class net.sf.basedb.ws.client.AbstractRPCClient
 
invokeBlocking(String, Object...) - 
Method in class net.sf.basedb.ws.client.AbstractRPCClient
 
invokeFileBlocking(String, Object...) - 
Method in class net.sf.basedb.ws.client.AbstractRPCClient
 
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
 
isAffyChip() - 
Method in class net.sf.basedb.core.ArrayDesign
Deprecated. Use ArrayDesign.isPlatform(String) instead with
                        Platform.AFFYMETRIX as the parameter
isAffyChip() - 
Method in class net.sf.basedb.core.data.ArrayDesignData
Deprecated. Has been replaced by platform
isAffymetrix(FileStoreEnabled) - 
Method in class net.sf.basedb.core.filehandler.AffymetrixFileHandler
Check if the item is using the affymetrix platform.
isAffymetrix - 
Variable in class net.sf.basedb.core.RawDataType
 
isAffymetrix() - 
Method in class net.sf.basedb.core.RawDataType
Deprecated. Use RawDataType.getPlatform(DbControl) and compare
                        the external ID with Platform.AFFYMETRIX
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
 
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.Well
 
isAnnotated - 
Variable in class net.sf.basedb.info.AnnotatedItemInfo
 
isAnnotated() - 
Method in class net.sf.basedb.info.AnnotatedItemInfo
 
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.
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.
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.
isChildrenLoaded() - 
Method in class net.sf.basedb.util.overview.Node
 
isClosed - 
Variable in class net.sf.basedb.clients.jobagent.handlers.MultiProtocolRequestHandler
 
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 - 
Variable in class net.sf.basedb.core.DbControl
Is the connection closed or not?
isClosed() - 
Method in class net.sf.basedb.core.DbControl
Check if the connection to the database has been closed.
isClosed - 
Variable in class net.sf.basedb.core.DynamicResultIterator
 
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 - 
Variable in class net.sf.basedb.core.ScrollIterator
 
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.
isCollection - 
Variable in class net.sf.basedb.clients.web.taglib.table.ColumnDef
If the property is a collection or not.
isCollection() - 
Method in class net.sf.basedb.clients.web.taglib.table.ColumnDef
 
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 - 
Variable in class net.sf.basedb.core.DbControl
If Hibernate is connected to the database or not.
isConnected() - 
Method in class net.sf.basedb.core.DbControl
Checks if there is an active connection to the database or not.
isConnected() - 
Method in class net.sf.basedb.core.hibernate.SessionWrapper
 
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
 
isDefault - 
Variable in class net.sf.basedb.core.data.GroupData
 
isDefault() - 
Method in class net.sf.basedb.core.data.GroupData
If this group should be assigned to new users by default or not.
isDefault - 
Variable in class net.sf.basedb.core.data.RoleData
 
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.
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.
isDenied() - 
Method in class net.sf.basedb.util.PluginInfo
If the currently logged in user has write permission to the (installed) plug-in
                or not.
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.UserData
Check if this account is disabled or enabled.
isDisabled() - 
Method in class net.sf.basedb.core.User
Check if this account has been disabled.
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.
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(ExtensionPoint) - 
Method in class net.sf.basedb.clients.web.extensions.ExtensionsControl
Check if an extension point is enabled of disabled.
isEnabled(Extension) - 
Method in class net.sf.basedb.clients.web.extensions.ExtensionsControl
Check if an extension is enabled of disabled.
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(ExtensionPoint) - 
Method in class net.sf.basedb.clients.web.extensions.Settings
 
isEnabled(Extension) - 
Method in class net.sf.basedb.clients.web.extensions.Settings
 
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.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
 
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(ExtensionPoint<?>) - 
Method in class net.sf.basedb.util.extensions.DefaultFilter
 
isEnabled(Extension<?>) - 
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(Extension<?>) - 
Method in interface net.sf.basedb.util.extensions.ExtensionsFilter
Check if an extension is enabled or disabled.
isEnabled(ExtensionPoint<?>) - 
Method in class net.sf.basedb.util.extensions.SingleExtensionFilter
 
isEnabled(Extension<?>) - 
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() - 
Method in class net.sf.basedb.core.AnnotationType
Check if this annotation type provides a list of predefined allowed values.
isEnumeration - 
Variable in class net.sf.basedb.core.data.AnnotationTypeData
 
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.
isEnumeration() - 
Method in class net.sf.basedb.info.AnnotationTypeInfo
 
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.
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.
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.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.
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.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.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.
isIconabsolute() - 
Method in class net.sf.basedb.clients.web.taglib.menu.Menuitem
 
isIconabsolute() - 
Method in class net.sf.basedb.clients.web.taglib.menu.Submenu
 
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(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(InputStream) - 
Method in class net.sf.basedb.plugins.CdfFileReporterImporter
 
isImportable(InputStream) - 
Method in class net.sf.basedb.plugins.HelpImporter
 
isImportable(FlatFileParser) - 
Method in class net.sf.basedb.plugins.IlluminaRawDataImporter
Check that the first line contains the text "Illumina"
isImportable(InputStream) - 
Method in class net.sf.basedb.plugins.PluginConfigurationImporter
 
isImportable(FlatFileParser) - 
Method in class net.sf.basedb.plugins.PrintMapFlatFileImporter
Check that the file is a TAM or MwBr file.
isIncluded(Include...) - 
Method in class net.sf.basedb.core.AbstractEntityQuery
 
isIncluded(Collection<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
isIncluded(Collection<Include>) - 
Method in interface net.sf.basedb.core.query.EntityQuery
 
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 and that the logged in user has 
                permission to use the current experiment.
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) - 
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.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.BfsExporterPlugin
 
isInContext(GuiContext, Object) - 
Method in class net.sf.basedb.plugins.BioAssaySetExporter
Deprecated.  
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.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.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 isn't an affy design.
isInContext() - 
Method in class net.sf.basedb.util.ContextUtil.ContextResult
If the context check was successful and generate no warnings or error.
isInContext(GuiContext, Object) - 
Method in class net.sf.basedb.util.zip.AbstractFileUnpacker
 
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.
isInherited(AnnotationSet) - 
Method in class net.sf.basedb.core.AnnotationSet
Check if an annotation set is inherited or not by this annotation set.
isInherited() - 
Method in class net.sf.basedb.core.snapshot.AnnotationSnapshot
Is this annotation a primary or inherited annotation?
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
 
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.
isInsertable() - 
Method in class net.sf.basedb.info.ExtendedPropertyInfo
 
isInstalled - 
Variable in class net.sf.basedb.util.PluginInfo
 
isInstalled() - 
Method in class net.sf.basedb.util.PluginInfo
If the plug-in is already installed in BASE.
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.clients.web.extensions.ExtensionsFile
 
isJar() - 
Method in class net.sf.basedb.clients.web.extensions.ExtensionsFile
If the file name ends with '.jar' the file is considered a JAR file.
isLastChild(E) - 
Method in class net.sf.basedb.util.Tree.Entry
Check if the specified object is the last child to this node.
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.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.
isMember(AnnotationTypeCategory) - 
Method in class net.sf.basedb.core.AnnotationType
Checks if the annotation type is a member of a category.
isMember(User) - 
Method in class net.sf.basedb.core.Group
Checks if a user is a member of this group.
isMember(Group) - 
Method in class net.sf.basedb.core.Group
Checks if a group 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(Role) - 
Method in class net.sf.basedb.core.SessionControl
Check if the logged in user is a member of the specified role.
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.
isMetadataReader - 
Variable in class net.sf.basedb.core.FileSet.DataFileHandlerWrapper
 
isModified() - 
Method in class net.sf.basedb.clients.web.extensions.ExtensionsFile
Check if the file has been modified since the last call to
                ExtensionsFile.resetModified().
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.
isNew() - 
Method in class net.sf.basedb.clients.web.extensions.ExtensionsFile
If the file is a new file not previously registered with the
                extension system.
isNewitem() - 
Method in class net.sf.basedb.clients.web.taglib.Select
 
isNotPartOf(ReporterList) - 
Static method in class net.sf.basedb.core.query.Dynamic
 
isNotPartOf(String, String, ReporterList) - 
Static method in class net.sf.basedb.core.query.Hql
 
isNullable - 
Variable in class net.sf.basedb.core.dbengine.TableInfo.ColumnInfo
 
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.
isNullable() - 
Method in class net.sf.basedb.info.ExtendedPropertyInfo
 
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().
isOpen() - 
Method in class net.sf.basedb.core.hibernate.SessionWrapper
 
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.
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
 
isParameter(AnnotationType) - 
Method in class net.sf.basedb.core.Protocol
Check if the annotation type is a parameter to this protocol.
isParameter(Annotation) - 
Method in class net.sf.basedb.core.Protocol
Check if the annotation is 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(ReporterList) - 
Static method in class net.sf.basedb.core.query.Dynamic
 
isPartOf(String, String, ReporterList) - 
Static method in class net.sf.basedb.core.query.Hql
 
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.
isPooled() - 
Method in class net.sf.basedb.core.data.MeasuredBioMaterialData
If the biomaterial was created by pooling other biomaterials of the same type
                or not.
isPooled() - 
Method in class net.sf.basedb.core.MeasuredBioMaterial
Check if this biomaterial was created by pooling or not.
isPreview() - 
Method in class net.sf.basedb.core.data.ImageData
A boolean value indicating if this image is a preview image
                or the full-sized image.
isPreview() - 
Method in class net.sf.basedb.core.Image
A boolean value indicating if this image is a preview image
                or the full-sized image.
isPrimaryKey() - 
Method in class net.sf.basedb.core.VirtualColumn
If the column is part of the primary key or not.
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(Protocol) - 
Method in class net.sf.basedb.core.AnnotationType
Check if this annotation type is a parameter to the specified protocol.
isProtocolParameter - 
Variable in class net.sf.basedb.core.data.AnnotationTypeData
 
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() - 
Method in class net.sf.basedb.info.AnnotationTypeInfo
 
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 class net.sf.basedb.core.hibernate.QueryWrapper
 
isReadOnly(Object) - 
Method in class net.sf.basedb.core.hibernate.SessionWrapper
 
isReadonly() - 
Method in interface net.sf.basedb.core.query.Query
If this query is readonly and cannot be structurally modified.
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.data.BioAssaySetData
 
isRemoved() - 
Method in class net.sf.basedb.core.data.BioPlateEventTypeData
 
isRemoved() - 
Method in class net.sf.basedb.core.data.BioPlateTypeData
 
isRemoved() - 
Method in class net.sf.basedb.core.data.CommonData
 
isRemoved() - 
Method in class net.sf.basedb.core.data.DataFileTypeData
 
isRemoved() - 
Method in class net.sf.basedb.core.data.ExtraValueTypeData
 
isRemoved() - 
Method in class net.sf.basedb.core.data.GroupData
 
isRemoved() - 
Method in class net.sf.basedb.core.data.HardwareTypeData
 
isRemoved() - 
Method in class net.sf.basedb.core.data.ImageData
 
isRemoved() - 
Method in class net.sf.basedb.core.data.JobData
 
isRemoved() - 
Method in class net.sf.basedb.core.data.MessageData
 
isRemoved() - 
Method in class net.sf.basedb.core.data.MimeTypeData
 
isRemoved() - 
Method in class net.sf.basedb.core.data.NewsData
 
isRemoved() - 
Method in class net.sf.basedb.core.data.PlateEventTypeData
 
isRemoved() - 
Method in class net.sf.basedb.core.data.PlateGeometryData
 
isRemoved() - 
Method in class net.sf.basedb.core.data.PlatformData
 
isRemoved() - 
Method in class net.sf.basedb.core.data.PlatformVariantData
 
isRemoved() - 
Method in class net.sf.basedb.core.data.PluginDefinitionData
 
isRemoved() - 
Method in class net.sf.basedb.core.data.PluginTypeData
 
isRemoved() - 
Method in class net.sf.basedb.core.data.ProjectData
 
isRemoved() - 
Method in class net.sf.basedb.core.data.ProtocolTypeData
 
isRemoved() - 
Method in class net.sf.basedb.core.data.QuantityData
 
isRemoved() - 
Method in class net.sf.basedb.core.data.QuotaData
 
isRemoved() - 
Method in interface net.sf.basedb.core.data.RemovableData
Check if the removed flag is set for this item.
isRemoved() - 
Method in class net.sf.basedb.core.data.ReporterTypeData
 
isRemoved() - 
Method in class net.sf.basedb.core.data.RoleData
 
isRemoved() - 
Method in class net.sf.basedb.core.data.TransformationData
 
isRemoved() - 
Method in class net.sf.basedb.core.data.UnitData
 
isRemoved() - 
Method in class net.sf.basedb.core.data.UserData
 
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.HardwareType
 
isRemoved() - 
Method in class net.sf.basedb.core.Image
 
isRemoved() - 
Method in class net.sf.basedb.core.Job
 
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.ProtocolType
 
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.PlatformFileTypeData
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 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.
isRequiredForMiame() - 
Method in class net.sf.basedb.info.AnnotationTypeInfo
 
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.
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().
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() - 
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 variable in class net.sf.basedb.core.Application
If BASE is running or not.
isRunning() - 
Static method in class net.sf.basedb.core.Application
Check if BASE is running.
isRunning - 
Variable in class net.sf.basedb.core.Application.SecondaryStorageControllerTask
 
isRunning - 
Variable in class net.sf.basedb.util.timer.PerformanceTimer
 
isRunning(int) - 
Method in class net.sf.basedb.util.timer.PerformanceTimer
Check if a timer is running or not.
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
 
isShared - 
Variable in class net.sf.basedb.info.SharedItemInfo
 
isShared() - 
Method in class net.sf.basedb.info.SharedItemInfo
 
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.taglib.table.ColumnDef
 
isSortedby(String) - 
Method in class net.sf.basedb.clients.web.taglib.table.Table
 
isStateless() - 
Method in class net.sf.basedb.core.AbstractHqlQuery
If queries are using the stateless Hibernate session or the regular
                session.
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.FileType
 
isSystemItem() - 
Method in class net.sf.basedb.core.Group
 
isSystemItem() - 
Method in class net.sf.basedb.core.HardwareType
 
isSystemItem() - 
Method in class net.sf.basedb.core.ProtocolType
 
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 class net.sf.basedb.core.SoftwareType
 
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.
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.FallbackIdMethod
 
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() - 
Method 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.IndexInfo
 
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.
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.
isUpdateable() - 
Method in class net.sf.basedb.info.ExtendedPropertyInfo
 
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.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 LabeledExtract:s has been created from this item
                no Extract:s has been created from 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.FileType
Check if:
                
                any file has been assigned this type
                
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 Scan 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.HardwareType
Check if:
                
                A Hardware of this type exists
                
isUsed() - 
Method in class net.sf.basedb.core.Hybridization
Check that:
                
                No Scan:s use the hybridization
                
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.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.Label
Check if:
                
                Some LabeledExtract:s are labeled with this label
                
isUsed() - 
Method in class net.sf.basedb.core.LabeledExtract
Check that:
                
                no Hybridization:s has been created from this item
                no LabeledExtract:s has been created from this item
                
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.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 Scan
                a RawBioAssay
                
isUsed() - 
Method in class net.sf.basedb.core.ProtocolType
Check if:
                
                A Protocol of this type exists
                A PlateEventType is linked to this protocol type
                
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.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.Scan
Check if:
                
                A RawBioAssay has been created from this scan
                
isUsed() - 
Method in class net.sf.basedb.core.Software
Check if:
                
                a RawBioAssay was created with this software
                
isUsed() - 
Method in class net.sf.basedb.core.SoftwareType
Check if:
                
                there are any Software using this type
                
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(Hybridization) - 
Method in class net.sf.basedb.core.ArraySlide
Checks if this array design is used by a different hybridization
                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.
isUsingInternalAuthentication() - 
Static method in class net.sf.basedb.core.Application
Check if BASE is using internal or external authentication.
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.clients.web.extensions.ExtensionsFile
 
isValid() - 
Method in class net.sf.basedb.clients.web.extensions.ExtensionsFile
Checks if the file is a valid extensions definition file.
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.
isValidator - 
Variable in class net.sf.basedb.core.FileSet.DataFileHandlerWrapper
 
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.
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.
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.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.Note
 
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
 
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
 
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
 
ITEM - 
Static variable in class net.sf.basedb.clients.web.extensions.toolbar.ToolbarUtil
 
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.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.filehandler.AbstractDataFileHandler
 
item - 
Variable in class net.sf.basedb.core.FileSet.DataFileHandlerWrapper
 
item - 
Variable in class net.sf.basedb.core.FileSet
The item this file set belongs to.
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 - 
Variable in class net.sf.basedb.core.plugin.GuiContext
 
item(Item) - 
Static method in class net.sf.basedb.core.plugin.GuiContext
Shortcut to create a single-item context.
item - 
Variable in class net.sf.basedb.core.query.HqlEntityExpression
 
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.DefinedPermissions - Class in net.sf.basedb.core
Helper class to make it easier to set up the defined permissions.
Item.DefinedPermissions() - 
Constructor for class net.sf.basedb.core.Item.DefinedPermissions
 
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.
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(Item, String, String) - 
Constructor for class net.sf.basedb.core.ItemContext
Create a new empty context.
ItemContext(ContextData) - 
Constructor for class net.sf.basedb.core.ItemContext
Create a new context from a loaded database object.
ItemContext.PropertyFilterPair - Class in net.sf.basedb.core
Holds a pair of filter.
ItemContext.PropertyFilterPair() - 
Constructor for class net.sf.basedb.core.ItemContext.PropertyFilterPair
 
ItemContext.SortDirection - Enum in net.sf.basedb.core
Enumeration used to specify the sort direction.
ItemContext.SortDirection(int, String) - 
Constructor for enum net.sf.basedb.core.ItemContext.SortDirection
Creates a new 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.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.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
 
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
 
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
 
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
 
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.
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<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.
itemQuery - 
Variable in class net.sf.basedb.plugins.AnnotationFlatFileImporter
 
itemQuery - 
Variable in class net.sf.basedb.plugins.batchimport.AbstractItemImporter
 
ItemQueryLoader - 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(DbControl, 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.ResultListIterator(Iterator<? extends BasicData>, Class<T>) - 
Constructor for class net.sf.basedb.core.ItemResultList.ResultListIterator
 
ItemResultList.ResultListListIterator<T extends BasicItem> - Class in net.sf.basedb.core
Inner class to implement the iterator returned by
                the ItemResultList.listIterator() method.
ItemResultList.ResultListListIterator(ListIterator<? extends BasicData>, Class<T>) - 
Constructor for class net.sf.basedb.core.ItemResultList.ResultListListIterator
 
items - 
Variable in class net.sf.basedb.core.MultiPermissions
 
items - 
Variable in class net.sf.basedb.core.ParameterType
List of allowed values.
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.plugins.XMLTemplate
 
itemType - 
Variable in class net.sf.basedb.clients.web.taglib.table.Table
 
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.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.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 enum net.sf.basedb.core.Project.Default
 
itemType - 
Variable in class net.sf.basedb.core.query.HqlEntityParameterExpression
 
itemType - 
Variable in class net.sf.basedb.core.query.QueryParameter
 
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.util.overview.filter.BasicItemFilter
 
itemType - 
Variable in class net.sf.basedb.util.overview.filter.ItemTypeFilter
 
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.
itemTypes - 
Variable in class net.sf.basedb.core.data.AnnotationTypeData
 
itemTypes - 
Variable in class net.sf.basedb.info.AnnotationTypeInfo
 
iterate() - 
Method in class net.sf.basedb.clients.web.plugins.DataQueryWrapper
Calls DataQuery.iterate(DbControl)
iterate() - 
Method in class net.sf.basedb.clients.web.plugins.DynamicQueryWrapper
Calls AbstractSqlQuery.iterate(DbControl)
iterate() - 
Method in class net.sf.basedb.clients.web.plugins.ItemQueryWrapper
Calls ItemQuery.iterate(DbControl)
iterate() - 
Method in interface net.sf.basedb.clients.web.plugins.QueryWrapper
Get the ResultIterator for the query.
iterate() - 
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() - 
Method in class net.sf.basedb.core.hibernate.QueryWrapper
 
iterate(DbControl) - 
Method in class net.sf.basedb.core.ItemQuery
Execute the query and return the results as an iterator.
iterate(DbControl) - 
Method in class net.sf.basedb.core.ReporterScoreQuery
Execute the query and return the results as an iterator.
iterate() - 
Method in class net.sf.basedb.util.extensions.ExtensionsInvoker
Create an iterator that iterates over all Action:s created
                by the extensions.
iterations - 
Variable in class net.sf.basedb.plugins.LowessNormalization.CallableWorker
 
iterator() - 
Method in class net.sf.basedb.core.ItemResultList
 
iterator - 
Variable in class net.sf.basedb.core.ItemResultList.ResultListIterator
 
iterator - 
Variable in class net.sf.basedb.core.ItemResultList.ResultListListIterator
 
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 - 
Variable in class net.sf.basedb.util.extensions.ActionIterator
 
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.JarInfo - Class in net.sf.basedb.util
 
JarClassLoader.JarInfo(File) - 
Constructor for class net.sf.basedb.util.JarClassLoader.JarInfo
 
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.
jarInDatabase - 
Variable in class net.sf.basedb.util.PluginInfo
 
jarLoader - 
Variable in class net.sf.basedb.clients.web.extensions.ExtensionsFile
 
jarPath - 
Variable in class net.sf.basedb.core.data.JobAgentSettingsData
 
jarPath - 
Variable in class net.sf.basedb.core.data.PluginDefinitionData
 
jarPath - 
Variable in class net.sf.basedb.core.data.PluginTypeData
 
jarPath - 
Variable in class net.sf.basedb.util.PluginInfo
The path to the jarfile the plugin is located in.
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.
JdbcWork<R> - Interface in net.sf.basedb.core.hibernate
An extension to Hibernate's Work API which adds functionality
        for returning a value as a result from the work.
jep - 
Variable in class net.sf.basedb.plugins.BioAssaySetExporter.QueryItem
Deprecated.  
jep(String, String, Formula.AverageMethod, Formatter<?>) - 
Static method in class net.sf.basedb.util.export.spotdata.ExportableFieldFactory
Deprecated. In 2.15, use ExportableFieldFactory.jep(String, String, Type, net.sf.basedb.core.Formula.AverageMethod, Formatter)
                instead
jep(String, String, Type, Formula.AverageMethod, Formatter<?>) - 
Static method in class net.sf.basedb.util.export.spotdata.ExportableFieldFactory
Create a JEP dynamic field.
jep - 
Variable in class net.sf.basedb.util.export.spotdata.JepDynamicField
 
jep - 
Variable in class net.sf.basedb.util.jep.FunctionSafeJep.SafeFunctionTable
 
Jep - Class in net.sf.basedb.util.jep
Utility class for parsing mathematical expressions.
Jep() - 
Constructor for class net.sf.basedb.util.jep.Jep
 
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.
JepIntensityTransformer - Class in net.sf.basedb.plugins
This plugin transform channel intensities using mathematical formulas
        entered by the user.
JepIntensityTransformer() - 
Constructor for class net.sf.basedb.plugins.JepIntensityTransformer
Constructor should be empty.
JepMapper - Class in net.sf.basedb.util.parser
A mapper that uses Jep to calculate the final value.
JepMapper(String, List<String>) - 
Constructor for class net.sf.basedb.util.parser.JepMapper
Create a new JepMapper.
JepMapper(String, List<String>, NumberFormat) - 
Constructor for class net.sf.basedb.util.parser.JepMapper
 
JepMapper(String, List<String>, NumberFormat, boolean) - 
Constructor for class net.sf.basedb.util.parser.JepMapper
 
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.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 - 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 - 
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.ExecutionTime - Enum in net.sf.basedb.core
A rough estimate of the execution time of a job.
Job.ExecutionTime(int, String, int, int) - 
Constructor for enum net.sf.basedb.core.Job.ExecutionTime
 
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.JobSignalTransporter(SignalTransporter) - 
Constructor for class net.sf.basedb.core.Job.JobSignalTransporter
 
Job.ProgressReporterImpl - Class in net.sf.basedb.core
Implements the ProgressReporter interface and
                stores the percentage completed for the current job.
Job.ProgressReporterImpl(Job, String, JobAgent, ProgressReporter) - 
Constructor for class net.sf.basedb.core.Job.ProgressReporterImpl
 
Job.Status - Enum in net.sf.basedb.core
The status of a job.
Job.Status(int, String, boolean) - 
Constructor for enum net.sf.basedb.core.Job.Status
 
Job.Type - Enum in net.sf.basedb.core
The type of job.
Job.Type(int, String) - 
Constructor for enum net.sf.basedb.core.Job.Type
 
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 - 
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.ListenerThread(ServerSocketChannel, RequestHandler, Logger) - 
Constructor for class net.sf.basedb.util.jobagent.JobAgentServerConnection.ListenerThread
 
JobAgentServerConnection.RequestHandlerThread - Class in net.sf.basedb.util.jobagent
This class is used for forwarding requests to a RequestHandler.
JobAgentServerConnection.RequestHandlerThread(Socket, RequestHandler, Logger) - 
Constructor for class net.sf.basedb.util.jobagent.JobAgentServerConnection.RequestHandlerThread
 
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
 
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 - Class in net.sf.basedb.core.data
This class holds information about a job.
JobData() - 
Constructor for class net.sf.basedb.core.data.JobData
 
jobData - 
Variable in class net.sf.basedb.core.InternalJobQueue.JobRunner
 
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.
jobDone(InternalJobQueue.JobRunner) - 
Method in class net.sf.basedb.core.InternalJobQueue
Called from a InternalJobQueue.JobRunner when it has finished 
                executing the job.
jobExecutor - 
Variable in class net.sf.basedb.clients.jobagent.Agent
 
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.
jobExecutor - 
Variable in class net.sf.basedb.clients.jobagent.JobRunner
 
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(Job, Job.ExecutionTime) - 
Constructor for class net.sf.basedb.util.jobagent.JobInfo
Create a new JobInfo object.
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.
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.
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
 
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.
jobs - 
Variable in class net.sf.basedb.core.data.ExperimentData
 
jobs - 
Variable in class net.sf.basedb.util.jobagent.JobAgentInfo
 
join(Join) - 
Method in class net.sf.basedb.core.AbstractQuery
 
Join - Interface in net.sf.basedb.core.query
A join query element.
join(Join) - 
Method in interface net.sf.basedb.core.query.Query
Add a join query element to the join list.
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.
joinAlias - 
Variable in class net.sf.basedb.core.query.ReporterListExpression
 
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.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, ReporterPropertyExpression) - 
Method in class net.sf.basedb.core.DynamicPositionQueryJoiners.ReporterJoiner
 
joinIfNeeded(DynamicSpotQuery, ExtraValueExpression) - 
Method in class net.sf.basedb.core.DynamicSpotQueryJoiners.ExtraValueJoiner
 
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(DynamicSpotQuery, ReporterListExpression) - 
Method in class net.sf.basedb.core.DynamicSpotQueryJoiners.ReporterListJoiner
 
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.
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
 
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.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.DynamicSpotQuery
Join information about reporters in the query.
joins - 
Variable in class net.sf.basedb.core.AbstractQuery
List of joins added to the query.
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.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.ReporterListJoiner
 
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
 
joinType - 
Variable in class net.sf.basedb.core.RealJoin
 
joinType - 
Variable in class net.sf.basedb.core.ReporterListJoin
 
jsEnum - 
Variable in class net.sf.basedb.clients.web.taglib.table.ColumnDef
Options for enum.
jspContext - 
Variable in class net.sf.basedb.clients.web.extensions.edit.AbstractOnSaveAction
 
JspContext - Class in net.sf.basedb.clients.web.extensions
Context object for the web application.
JspContext(ExtensionsDirectory, SessionControl, DbControl, PageContext, GuiContext, Object) - 
Constructor for class net.sf.basedb.clients.web.extensions.JspContext
 
jspContext - 
Variable in class net.sf.basedb.clients.web.extensions.tabcontrol.IncludeContentTabFactory.Tab
 
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<D extends KeyData> - Class in net.sf.basedb.core
This is the base class for keys.
Key(D) - 
Constructor for class net.sf.basedb.core.Key
 
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.StaticCache.LockSafeInputStream
 
key - 
Variable in class net.sf.basedb.util.StaticCache.LockSafeOutputStream
 
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 - 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 - 
Variable in class net.sf.basedb.core.SessionControl.LoginInfo
The Keyring of the logged in user.
Keyring.ReloadTask - Class in net.sf.basedb.core
 
Keyring.ReloadTask() - 
Constructor for class net.sf.basedb.core.Keyring.ReloadTask
 
keys - 
Variable in class net.sf.basedb.core.data.RoleData
 
keyStore - 
Variable in class net.sf.basedb.util.ssl.StaticKeyManager
 
knownFiles - 
Variable in class net.sf.basedb.plugins.executor.ExternalProgramExecutor
Files that are known to exists in the working directory.



L

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 - 
Variable in class net.sf.basedb.core.data.LabeledExtractData
 
label - 
Variable in class net.sf.basedb.core.data.ParameterValueData
 
Label - Class in net.sf.basedb.core
This class represents a labelling compund.
Label(LabelData) - 
Constructor for class net.sf.basedb.core.Label
 
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.
labelColumnMapping - 
Static variable in class net.sf.basedb.plugins.batchimport.LabeledExtractImporter
 
LabelData - Class in net.sf.basedb.core.data
This represents a labeling compund use to label extracts.
LabelData() - 
Constructor for class net.sf.basedb.core.data.LabelData
 
LabeledExtract - Class in net.sf.basedb.core
This class is used to represent labeled extract items.
LabeledExtract(LabeledExtractData) - 
Constructor for class net.sf.basedb.core.LabeledExtract
 
LabeledExtractData - Class in net.sf.basedb.core.data
This represents a labeled extract.
LabeledExtractData() - 
Constructor for class net.sf.basedb.core.data.LabeledExtractData
 
LabeledExtractImporter - Class in net.sf.basedb.plugins.batchimport
Plug-in for importing labled extract items in a batch.
LabeledExtractImporter() - 
Constructor for class net.sf.basedb.plugins.batchimport.LabeledExtractImporter
 
LabeledExtractLoader - Class in net.sf.basedb.util.overview.loader
Node loader implementation for labeled extracts.
LabeledExtractLoader() - 
Constructor for class net.sf.basedb.util.overview.loader.LabeledExtractLoader
 
LabeledExtractNameGenerator - Class in net.sf.basedb.util.overview.node
Name generator implementation for LabeledExtract
        items.
LabeledExtractNameGenerator(String, String) - 
Constructor for class net.sf.basedb.util.overview.node.LabeledExtractNameGenerator
Create a new name generator.
labeledExtractQuery - 
Variable in class net.sf.basedb.plugins.batchimport.AbstractItemImporter
 
LabeledExtractToExtractTransformer - Class in net.sf.basedb.util.biomaterial
Collection transformer that given a collection of labeled extracts finds
        their parent extract.
LabeledExtractToExtractTransformer(DbControl) - 
Constructor for class net.sf.basedb.util.biomaterial.LabeledExtractToExtractTransformer
 
LabeledExtractValidator - Class in net.sf.basedb.util.overview.validator
Validator implementation for labeled extracts.
LabeledExtractValidator() - 
Constructor for class net.sf.basedb.util.overview.validator.LabeledExtractValidator
 
LABELING - 
Static variable in class net.sf.basedb.core.ProtocolType
The ID for the labeling protocol type, for example a protocol
                used when creating a LabeledExtract from
                an Extract.
labelMapper - 
Variable in class net.sf.basedb.plugins.batchimport.LabeledExtractImporter
 
labelQuery - 
Variable in class net.sf.basedb.plugins.batchimport.AbstractItemImporter
 
lastAccess - 
Variable in class net.sf.basedb.core.SessionControl
The time of the last access to this object.
lastChallenge - 
Variable in class net.sf.basedb.core.SessionControl
The last generated challenge for password encryption.
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
 
lastIdentifier - 
Variable in class net.sf.basedb.plugins.batchimport.AbstractItemImporter
 
lastIndexOf(Object) - 
Method in class net.sf.basedb.core.ItemResultList
 
lastItem - 
Variable in class net.sf.basedb.plugins.batchimport.AbstractItemImporter
 
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.ExtensionsFile
 
lastModified - 
Variable in class net.sf.basedb.clients.web.extensions.XJspCompiler
 
lastModified - 
Variable in class net.sf.basedb.util.JarClassLoader.JarInfo
 
lastProtocolNode - 
Variable in class net.sf.basedb.util.overview.validator.ProtocolParameterValidator
 
lastReset - 
Static variable in class net.sf.basedb.clients.web.servlet.RssNewsFeed
 
lastScanResults - 
Static variable in class net.sf.basedb.clients.web.extensions.ExtensionsControl
 
lastSource - 
Variable in class net.sf.basedb.core.data.ReporterData
The source of the last update
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
 
lastUpdated - 
Variable in class net.sf.basedb.clients.jobagent.slotmanager.MasterSlotManager.RemoteSlot
 
lastValue - 
Variable in class net.sf.basedb.core.Job.ProgressReporterImpl
 
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
 
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 - 
Variable in class net.sf.basedb.core.RealJoin
 
left - 
Variable in class net.sf.basedb.core.ReporterListJoin
 
leftColumn - 
Variable in class net.sf.basedb.core.RealJoin
 
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.
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.ExtendedProperty
 
LENGTH - 
Static variable in class net.sf.basedb.core.Quantity
The id for the Quantity object representing length.
length - 
Variable in class net.sf.basedb.info.ExtendedPropertyInfo
 
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.LoggingErrorHandlerFactory
 
like(AnnotationType, Object, boolean) - 
Static method in class net.sf.basedb.core.query.Annotations
Deprecated. Use Annotations.like(String, AnnotationType, Object, boolean) instead with alias=null
like(String, AnnotationType, Object, boolean) - 
Static method in class net.sf.basedb.core.query.Annotations
Create a restriction that searches for annotations
                matching a given value on the root or a joined entity of a 
                query.
like(Expression, Expression) - 
Static method in class net.sf.basedb.core.query.Restrictions
Check if one expression matches another: e1 LIKE e2
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 ....
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() - 
Method in class net.sf.basedb.util.parser.FlatFileParser.Data
The entire line as it was read from the input stream.
line - 
Variable in class net.sf.basedb.util.parser.FlatFileParser.Line
 
line() - 
Method in class net.sf.basedb.util.parser.FlatFileParser.Line
The entire line as it was read from the input stream.
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() - 
Method in class net.sf.basedb.util.parser.FlatFileParser.Data
The line number of the data in the input stream.
lineNo - 
Variable in class net.sf.basedb.util.parser.FlatFileParser.Line
 
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
 
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.importer.spotdata.SecondPassSectionSpotsParser
 
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.
linkers - 
Variable in class net.sf.basedb.core.ExtendedProperty
 
LIST - 
Static variable in class net.sf.basedb.clients.web.extensions.toolbar.ToolbarUtil
 
list - 
Variable in class net.sf.basedb.clients.web.taglib.table.CellValue
 
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(Item) - 
Static method in class net.sf.basedb.core.plugin.GuiContext
Shortcut to create a list context.
listener - 
Variable in class net.sf.basedb.core.signal.SocketSignalReceiver
 
listener - 
Variable in class net.sf.basedb.util.jobagent.JobAgentServerConnection
 
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
 
lists - 
Variable in class net.sf.basedb.core.data.BioMaterialData
 
listToInfo(List<? extends ToTransferable<T>>, Class<T>) - 
Method in class net.sf.basedb.ws.server.ServicesUtil
Convert a list of objects to an array of Transferable objects
                objects.
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.biomaterial
Utility class for working with biomaterials.
ListUtil() - 
Constructor for class net.sf.basedb.util.biomaterial.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).
load(Class, Serializable, LockMode) - 
Method in class net.sf.basedb.core.hibernate.SessionWrapper
Deprecated. 
load(Class, Serializable, LockOptions) - 
Method in class net.sf.basedb.core.hibernate.SessionWrapper
 
load(Class, Serializable) - 
Method in class net.sf.basedb.core.hibernate.SessionWrapper
 
load(Object, Serializable) - 
Method in class net.sf.basedb.core.hibernate.SessionWrapper
 
load(String, Serializable, LockMode) - 
Method in class net.sf.basedb.core.hibernate.SessionWrapper
Deprecated. 
load(String, Serializable, LockOptions) - 
Method in class net.sf.basedb.core.hibernate.SessionWrapper
 
load(String, 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.
loadAbout(Element) - 
Method in class net.sf.basedb.util.extensions.xml.XmlLoader
Load information in an <about> tag.
loadCdfFile(File) - 
Static method in class net.sf.basedb.core.Affymetrix
Deprecated. Use AffymetrixFileHandler.loadCdfFile(File) instead
loadCdfFile(File) - 
Method in class net.sf.basedb.core.filehandler.AffymetrixFileHandler
Load a CDF file using the Affymetric Fusion SDK.
loadCelFile(File) - 
Static method in class net.sf.basedb.core.Affymetrix
Deprecated. Use AffymetrixFileHandler.loadCdfFile(File) instead
loadCelFile(File) - 
Method in class net.sf.basedb.core.filehandler.AffymetrixFileHandler
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 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.
loadConfigurationsForPlugin(Document, String) - 
Static method in class net.sf.basedb.util.PluginConfigInfo
Loads PluginConfigInfo objects from xml-document for a plugin.
loadContext(SessionControl, int, ItemContext) - 
Static method in class net.sf.basedb.clients.web.Base
 
loadContext(int) - 
Method in class net.sf.basedb.core.SessionControl
Load a context and make it the current context.
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(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.
loadData(Class<T>, Query) - 
Static method in class net.sf.basedb.core.HibernateUtil
Load a data item from the database using a query.
loadData(Class<T>, Query, StatelessSession, SessionControl) - 
Static method in class net.sf.basedb.core.QueryExecutor
Executes a Hibernate query on a stateless session.
loadDefinitions(boolean, ScanResults) - 
Method in class net.sf.basedb.clients.web.extensions.ExtensionsDirectory
Load the extension definitions from XML files.
loadDiskUsage(Query) - 
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.clients.web.extensions.ExtensionsFile
 
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() - 
Method in class net.sf.basedb.clients.web.extensions.ExtensionsFile
Load the extension definitions from the XML or JAR file.
loadExtensions(Document, ClassLoader, About) - 
Method in class net.sf.basedb.util.extensions.xml.XmlLoader
Create extensions from an XML document.
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.
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 hybridization node that is related to the given array slide node.
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.ExtractLoader
Loads the pooled extracts and labled extracts that has been created from
                this extract.
loadForwardChildNodes(DbControl, OverviewContext, Node) - 
Method in class net.sf.basedb.util.overview.loader.HybridizationLoader
Load forward-loading child nodes:
                
                Scans: ScanLoader.createForwardNode(DbControl, OverviewContext, Node)
                Array slide in reverse direction (if the parent node is a labeled extract):
                        ArraySlideLoader.createReverseNode(DbControl, OverviewContext, Node)
                Labeled extracts in reverse direction (if the parent node is the array slide):
                        LabeledExtractLoader.createReverseNode(DbControl, OverviewContext, Node)
                
loadForwardChildNodes(DbControl, OverviewContext, Node) - 
Method in class net.sf.basedb.util.overview.loader.LabeledExtractLoader
Loads the hybridizations and labeled extracts that has been created from
                this labeled extract.
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.
loadForwardChildNodes(DbControl, OverviewContext, Node) - 
Method in class net.sf.basedb.util.overview.loader.ScanLoader
Loads all raw bioassay nodes that are children of the given scan node.
loadFrom(String) - 
Method in class net.sf.basedb.core.Presets
Load presets from an XML string.
loadFrom(InputStream, String) - 
Method in class net.sf.basedb.core.Presets
Load presets from a stream.
loadFromJar(File) - 
Static method in class net.sf.basedb.util.PluginInfo
Gets a list with PluginInfo objects, one for every plugin listed 
                in the base-plugins.xml file, which is located in the jar-file's META-INF 
                directory.
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.
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(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(Class<T>, Query, SessionControl) - 
Static method in class net.sf.basedb.core.HibernateUtil
Scroll through the result of a query using an iterator.
loadIterator(Class<T>, Query, StatelessSession, SessionControl) - 
Static method in class net.sf.basedb.core.QueryExecutor
Executes a Hibernate query that returns an iterator on a stateless session.
loadJar() - 
Method in class net.sf.basedb.clients.web.extensions.ExtensionsFile
Load extensions from a validated JAR file.
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.
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(Class<T>, Query, 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.
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.
loadPluginInformation(String, String, boolean) - 
Method in class net.sf.basedb.core.PluginDefinition
Load a plugin and copy all information, ie. plugin.about(), 
                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.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.BioSourceLoader
Loads property nodes of an array design.
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)
                
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.HybridizationLoader
Loads property nodes of a hybridization.
loadPropertyChildNodes(DbControl, OverviewContext, Node) - 
Method in class net.sf.basedb.util.overview.loader.LabeledExtractLoader
Loads property nodes of a labeled extract.
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.SampleLoader
Loads property nodes of a sample.
loadPropertyChildNodes(DbControl, OverviewContext, Node) - 
Method in class net.sf.basedb.util.overview.loader.ScanLoader
Loads property nodes of a scan.
loadRawDataTypes(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.ExperimentLoader
Loads the raw bioassay nodes that are part of this experiment
loadReverseChildNodes(DbControl, OverviewContext, Node) - 
Method in class net.sf.basedb.util.overview.loader.ExtractLoader
If the extract is a pooled extract, loads the parent extracts that
                it was pooled from.
loadReverseChildNodes(DbControl, OverviewContext, Node) - 
Method in class net.sf.basedb.util.overview.loader.HybridizationLoader
Load reverse child nodes:
                
                Labeled extracts: LabeledExtractLoader.createReverseNode(DbControl, OverviewContext, Node)
                Array slide: ArraySlideLoader.createReverseNode(DbControl, OverviewContext, Node)
                
loadReverseChildNodes(DbControl, OverviewContext, Node) - 
Method in class net.sf.basedb.util.overview.loader.LabeledExtractLoader
If the labeled extract is a pooled labeled extract, loads the labeled extracts
                it was pooled from.
loadReverseChildNodes(DbControl, OverviewContext, Node) - 
Method in class net.sf.basedb.util.overview.loader.RawBioAssayLoader
Loads the scan 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.
loadReverseChildNodes(DbControl, OverviewContext, Node) - 
Method in class net.sf.basedb.util.overview.loader.ScanLoader
Loads the hybridization node that is the parent of this scan.
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(ServletContext, boolean, ScanResults) - 
Method in class net.sf.basedb.clients.web.extensions.ExtensionsDirectory
Load servlet definitions from JAR files.
loadServlets(ServletContext) - 
Method in class net.sf.basedb.clients.web.extensions.ExtensionsFile
Load servlet definitions from a JAR file.
loadServlets(Document, ClassLoader) - 
Method in class net.sf.basedb.clients.web.extensions.ServletLoader
Load the servlet definitions from an XML document.
loadTiffImage(File, int) - 
Method in class net.sf.basedb.core.SpotImages
Loads a TIFF file and returns a RenderedOp.
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.
loadXml() - 
Method in class net.sf.basedb.clients.web.extensions.ExtensionsFile
Load extensions from a validated XML file.
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.
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.
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 - 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.
locator - 
Variable in class net.sf.basedb.util.importer.spotdata.BfsImporter
 
lock(Object, LockMode) - 
Method in class net.sf.basedb.core.hibernate.SessionWrapper
Deprecated. 
lock(String, Object, LockMode) - 
Method in class net.sf.basedb.core.hibernate.SessionWrapper
Deprecated. 
lock() - 
Method in class net.sf.basedb.util.Enumeration
 
lock - 
Variable in class net.sf.basedb.util.StaticCache.LockSafeInputStream
 
lock - 
Variable in class net.sf.basedb.util.StaticCache.LockSafeOutputStream
 
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.util.Enumeration
 
lockedColumns - 
Variable in class net.sf.basedb.util.bfs.DataWriter
 
lockMode - 
Variable in class net.sf.basedb.core.data.BioPlateTypeData
 
locks - 
Variable in class net.sf.basedb.util.StaticCache
 
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.ExtensionsDirectory
 
log - 
Static variable in class net.sf.basedb.clients.web.extensions.ExtensionsFile
 
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 - 
Static variable in class net.sf.basedb.clients.web.fileupload.FileUpload
Debug file upload.
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.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.InternalStorageController
Log storage 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(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(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 - 
Static variable in class net.sf.basedb.core.PredefinedQuery
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 - 
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.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(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 - 
Variable in class net.sf.basedb.util.ColorGenerator
 
log - 
Static variable in class net.sf.basedb.util.extensions.LoggingErrorHandlerFactory
 
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.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.XMLUtil
Log core events.
log10(Expression) - 
Static method in class net.sf.basedb.core.query.Expressions
Calculate the 10-based logarithm of an expression: new expression = log10(e).
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 - 
Static variable in class net.sf.basedb.util.jep.Log2Function
The natural logarithm of 2.
log2(Number) - 
Method in class net.sf.basedb.util.jep.Log2Function
Calculate the 2-based logarithm of the argument.
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.
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(ChangeHistoryDetailData) - 
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.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).
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.ImageLogger
 
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.
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 - 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
 
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.
logger - 
Static variable in class net.sf.basedb.clients.web.util.SimpleSignalProgressReporter
Log signals processing.
logger - 
Variable in class net.sf.basedb.core.log.EntityDetails
 
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.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.
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, LogManagerFactory) - 
Constructor for class net.sf.basedb.core.log.LoggingInterceptor
Creates a new interceptor.
login - 
Variable in class net.sf.basedb.clients.jobagent.Agent
 
login - 
Variable in class net.sf.basedb.core.authentication.AuthenticationInformation
The login for the user.
login - 
Variable in class net.sf.basedb.core.data.UserData
 
login(Keyring) - 
Method in class net.sf.basedb.core.PluginSessionControl
 
login(String, String, String, boolean) - 
Method in class net.sf.basedb.core.PluginSessionControl
 
login(Keyring) - 
Method in class net.sf.basedb.core.SessionControl
 
login(String, String, String, boolean) - 
Method in class net.sf.basedb.core.SessionControl
Log in to BASE.
login(String, String, String, boolean) - 
Method in class net.sf.basedb.ws.client.SessionClient
Login to BASE
login(String, String, String, String, boolean) - 
Method in class net.sf.basedb.ws.server.SessionService
Service to login to BASE
loginComment - 
Variable in class net.sf.basedb.core.data.SessionData
 
loginInfo - 
Variable in class net.sf.basedb.core.SessionControl
Login information for the logged in user.
loginIsUsed(DbControl, String) - 
Static method in class net.sf.basedb.core.User
Check if a login name already exists in the database
loginTime - 
Variable in class net.sf.basedb.core.data.SessionData
 
logManager - 
Variable in class net.sf.basedb.core.log.LoggingInterceptor
 
LogManager - Interface in net.sf.basedb.core.log
Manages the logging of changes made in a single transaction.
logManagerFactory - 
Static variable in class net.sf.basedb.core.Application
The log manager factory currently in use (may be null)
logManagerFactory - 
Variable in class net.sf.basedb.core.log.LoggingInterceptor
 
LogManagerFactory - Interface in net.sf.basedb.core.log
A log manager factory handles the creation of log managers and
        entity loggers.
logManagerFactoryDriver - 
Static variable in class net.sf.basedb.core.Application
The name of the log manager factory class, if any.
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.
logout() - 
Method in class net.sf.basedb.ws.client.SessionClient
Logs out from BASE
logout(String) - 
Method in class net.sf.basedb.ws.server.SessionService
Service to logout from 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.
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.
LogUtil - Class in net.sf.basedb.core
Utility class for LOG4J logging.
LogUtil() - 
Constructor for class net.sf.basedb.core.LogUtil
 
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.
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
 
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.CallableWorker(List<LowessNormalization.SpotData>, float, float, int, int) - 
Constructor for class net.sf.basedb.plugins.LowessNormalization.CallableWorker
 
LowessNormalization.SpotData - Class in net.sf.basedb.plugins
 
LowessNormalization.SpotData(short, int, float, float, int, boolean) - 
Constructor for class net.sf.basedb.plugins.LowessNormalization.SpotData
 
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 - 
Static variable in class net.sf.basedb.clients.web.util.HTML
 
lt(AnnotationType, Object, boolean) - 
Static method in class net.sf.basedb.core.query.Annotations
Deprecated. Use Annotations.lt(String, AnnotationType, Object, boolean) instead with alias=null
lt(String, AnnotationType, Object, boolean) - 
Static method in class net.sf.basedb.core.query.Annotations
Create a restriction that searches for annotations
                less than a given value on the root or a joined entity of a 
                query.
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.
lteq(AnnotationType, Object, boolean) - 
Static method in class net.sf.basedb.core.query.Annotations
Deprecated. Use Annotations.lteq(String, AnnotationType, Object, boolean) instead with alias=null
lteq(String, AnnotationType, Object, boolean) - 
Static method in class net.sf.basedb.core.query.Annotations
Create a restriction that searches for annotations
                less than or equal to a given value on the root or a joined entity of a 
                query.
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.
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
 
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
 
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
 
maintenance - 
Variable in class net.sf.basedb.info.VersionInfo
 
mainType - 
Variable in class net.sf.basedb.core.data.PluginDefinitionData
 
major - 
Static variable in class net.sf.basedb.core.Version
 
major - 
Variable in class net.sf.basedb.info.VersionInfo
 
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.
manifest - 
Variable in class net.sf.basedb.util.JarClassLoader.JarInfo
 
manipulateDocument(Document) - 
Static method in class net.sf.basedb.core.HibernateUtil
Some XML files require manipulation by us before they are registered.
manualScan - 
Variable in class net.sf.basedb.clients.web.extensions.ScanResults
 
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.util.formatter.LookupFormatter
 
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.
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 - 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
 
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
 
mappings - 
Static variable in class net.sf.basedb.core.HibernateUtil
The mappings related to a configuration.
mappingSection - 
Static variable in class net.sf.basedb.plugins.AbstractFlatFileImporter
Section definition for grouping all column mapping expressions
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
 
markSupported() - 
Method in class net.sf.basedb.clients.web.fileupload.FileUpload.UploadStream
Not supported.
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.
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.StreamCacher
 
masterParser - 
Variable in class net.sf.basedb.util.importer.spotdata.SynchronizedSpotDataParser
 
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.RemoteSlot(Slot) - 
Constructor for class net.sf.basedb.clients.jobagent.slotmanager.MasterSlotManager.RemoteSlot
 
MasterSlotManager.RemoteSlotRequestHandler - Class in net.sf.basedb.clients.jobagent.slotmanager
Request handler implementation that accepts requests for slots
                from remote hosts.
MasterSlotManager.RemoteSlotRequestHandler(MasterSlotManager) - 
Constructor for class net.sf.basedb.clients.jobagent.slotmanager.MasterSlotManager.RemoteSlotRequestHandler
 
MasterSlotManager.RemoteSlotTimeoutChecker - Class in net.sf.basedb.clients.jobagent.slotmanager
Task that is scheduled at regular intervals to check for
                timed out slots.
MasterSlotManager.RemoteSlotTimeoutChecker(MasterSlotManager) - 
Constructor for class net.sf.basedb.clients.jobagent.slotmanager.MasterSlotManager.RemoteSlotTimeoutChecker
 
matcher - 
Variable in class net.sf.basedb.util.fuzzy.StringMatcher
 
matchingReporters - 
Variable in class net.sf.basedb.clients.web.ExperimentExplorer
Number of reporter that match the reporter search.
MATRIX_BASEFILE - 
Static variable in class net.sf.basedb.ws.server.BioAssaySetService
 
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(Expression) - 
Static method in class net.sf.basedb.core.query.Aggregations
Calculates the maximum value of an expression: new expression = MAX(e)
max - 
Variable in class net.sf.basedb.util.plot.HistogramPlot.HistogramBin
 
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_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.DataFileTypeData
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.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.DataFileType
The maximum length of the class names 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_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_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.BioMaterialList
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.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.BioMaterialListData
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.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.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.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_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_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_JARPATH_LENGTH - 
Static variable in class net.sf.basedb.core.data.DataFileTypeData
 
MAX_JARPATH_LENGTH - 
Static variable in class net.sf.basedb.core.data.JobAgentSettingsData
 
MAX_JARPATH_LENGTH - 
Static variable in class net.sf.basedb.core.data.PluginDefinitionData
 
MAX_JARPATH_LENGTH - 
Static variable in class net.sf.basedb.core.data.PluginTypeData
 
MAX_JARPATH_LENGTH - 
Static variable in class net.sf.basedb.core.DataFileType
The maximum length of the jar paths that can be stored in the database.
MAX_JARPATH_LENGTH - 
Static variable in class net.sf.basedb.core.JobAgentSettings
The maximum length of the jar path that can be stored in the database.
MAX_JARPATH_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_JARPATH_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_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_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_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_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_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_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_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_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
 
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.
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
 
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.
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.
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
 
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.File.UploadStream
The md5 sum calculater.
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
 
md5Password - 
Variable in class net.sf.basedb.core.data.PasswordData
 
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 - 
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.
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<D extends MeasuredBioMaterialData> - Class in net.sf.basedb.core
This class is the base class for measured biomaterial items.
MeasuredBioMaterial(D) - 
Constructor for class net.sf.basedb.core.MeasuredBioMaterial
 
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
 
MedianRatioNormalization.SpotData(int, float, float, int) - 
Constructor for class net.sf.basedb.plugins.MedianRatioNormalization.SpotData
 
medianRatioSection - 
Static variable in class net.sf.basedb.plugins.MedianRatioNormalization
Section for normalization options
member - 
Variable in class net.sf.basedb.util.overview.Fix
 
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.filehandler.AbstractDataFileHandler
 
memberType - 
Variable in class net.sf.basedb.core.data.BioMaterialListData
 
MENU - 
Static variable in class net.sf.basedb.clients.web.resources.Bundle
Resource bundle with string that are used in the menu.
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 - 
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.
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
 
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
 
MenuItemAction.MenuType() - 
Constructor for enum net.sf.basedb.clients.web.extensions.menu.MenuItemAction.MenuType
 
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.
MenuItemBean(MenuItemAction.MenuType, String, String, String, String, String, String, String, boolean, boolean) - 
Constructor for class net.sf.basedb.clients.web.extensions.menu.MenuItemBean
Create a new initialised 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
 
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(Object) - 
Method in class net.sf.basedb.core.hibernate.SessionWrapper
 
merge(String, Object) - 
Method in class net.sf.basedb.core.hibernate.SessionWrapper
 
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(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(Integer...) - 
Static method in enum net.sf.basedb.core.Permission
Merges a list of integer permission values.
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.
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.UserPermissions
Merge the permissions for all users from the given item key with the permissions 
                in this object.
mergeColorImages() - 
Method in class net.sf.basedb.core.SpotImages
Merge the three color images into a single image.
message - 
Variable in class net.sf.basedb.core.ItemContext
 
Message - Class in net.sf.basedb.core
This class represents a message.
Message(MessageData) - 
Constructor for class net.sf.basedb.core.Message
 
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.overview.Failure
 
message - 
Variable in class net.sf.basedb.util.overview.Fix
 
MessageData - Class in net.sf.basedb.core.data
This class holds information about messages.
MessageData() - 
Constructor for class net.sf.basedb.core.data.MessageData
 
messages - 
Variable in class net.sf.basedb.clients.web.extensions.ScanResults.FileResults
 
messages - 
Variable in class net.sf.basedb.core.data.JobData
 
messages - 
Variable in class net.sf.basedb.core.data.UserData
 
messageStyle - 
Variable in class net.sf.basedb.clients.web.taglib.Note
Optional style attribute for the message section
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.BasicBatcher
Hibernate metadata for the batchable object.
metaData - 
Static variable in class net.sf.basedb.core.Feature
 
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 - 
Variable in class net.sf.basedb.core.Metadata.EntityPropertyPath
 
metaData - 
Static variable in class net.sf.basedb.core.Reporter
 
metadata - 
Variable in class net.sf.basedb.util.export.spotdata.AssayPropertyField
 
metaData - 
Variable in class net.sf.basedb.util.jep.RawFunction
 
metaData - 
Variable in class net.sf.basedb.util.jep.ReporterFunction
 
Metadata.BasicData2ItemPropertyPath<C extends BasicData,V extends BasicItem<C>> - Class in net.sf.basedb.core
Property path implementation that converts a BasicData object
                to a BasicItem.
Metadata.BasicData2ItemPropertyPath(Item, Type) - 
Constructor for class net.sf.basedb.core.Metadata.BasicData2ItemPropertyPath
 
Metadata.BasicItem2DataPropertyPath<C extends BasicItem<V>,V extends BasicData> - Class in net.sf.basedb.core
Property path implementation that converts a BasicItem to a BasicData
                object.
Metadata.BasicItem2DataPropertyPath(Class<C>, Type) - 
Constructor for class net.sf.basedb.core.Metadata.BasicItem2DataPropertyPath
 
Metadata.CollectionPropertyPath<C> - Class in net.sf.basedb.core
Property path implementation which wraps a collection inside an unmodifiable
                collection.
Metadata.CollectionPropertyPath(Type) - 
Constructor for class net.sf.basedb.core.Metadata.CollectionPropertyPath
 
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.CombinedPropertyPath(List<Metadata.PropertyPath>) - 
Constructor for class net.sf.basedb.core.Metadata.CombinedPropertyPath
 
Metadata.ComponentPropertyPath<C,V> - Class in net.sf.basedb.core
Property path implementation which gets a value from a component.
Metadata.ComponentPropertyPath(ComponentType, int, Type) - 
Constructor for class net.sf.basedb.core.Metadata.ComponentPropertyPath
 
Metadata.DateCopyPropertyPath - Class in net.sf.basedb.core
Property path implementation clones a Date.
Metadata.DateCopyPropertyPath(Type) - 
Constructor for class net.sf.basedb.core.Metadata.DateCopyPropertyPath
 
Metadata.EntityPropertyPath<C,V> - Class in net.sf.basedb.core
Property path implementation which gets a value from an entity.
Metadata.EntityPropertyPath(ClassMetadata, String, Type) - 
Constructor for class net.sf.basedb.core.Metadata.EntityPropertyPath
 
Metadata.EvictPropertyPath<C> - Class in net.sf.basedb.core
Property path implementation that evicts the selected item from
                the Hibernate first-level cache.
Metadata.EvictPropertyPath(Type) - 
Constructor for class net.sf.basedb.core.Metadata.EvictPropertyPath
 
Metadata.IdentifierPropertyPath - Class in net.sf.basedb.core
Property path implementation which gets the id from an entity.
Metadata.IdentifierPropertyPath(Type) - 
Constructor for class net.sf.basedb.core.Metadata.IdentifierPropertyPath
 
Metadata.MapPropertyPath - Class in net.sf.basedb.core
Property path implementation which wraps a map inside an unmodifiable
                map.
Metadata.MapPropertyPath(Type) - 
Constructor for class net.sf.basedb.core.Metadata.MapPropertyPath
 
Metadata.NoopPropertyPath<C> - Class in net.sf.basedb.core
Property path implementation that does nothing.
Metadata.NoopPropertyPath(Class<C>, Type) - 
Constructor for class net.sf.basedb.core.Metadata.NoopPropertyPath
 
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.
Metadata.ReporterScore2DataPropertyPath(Type) - 
Constructor for class net.sf.basedb.core.Metadata.ReporterScore2DataPropertyPath
 
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.Section(String) - 
Constructor for class net.sf.basedb.util.bfs.MetadataModel.Section
Create a new section.
MetadataModel.SectionEntry - Class in net.sf.basedb.util.bfs
Holds information about a section entry.
MetadataModel.SectionEntry(String, String) - 
Constructor for class net.sf.basedb.util.bfs.MetadataModel.SectionEntry
Create a new single-valued section entry.
MetadataModel.SectionEntry(String, String...) - 
Constructor for class net.sf.basedb.util.bfs.MetadataModel.SectionEntry
Create a new section entry with an array of values.
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.
metadataParser - 
Variable in class net.sf.basedb.util.importer.spotdata.BfsImporter
 
metadataPrefix - 
Variable in class net.sf.basedb.util.basefile.BaseFileWriter
 
metadataReaderClass - 
Variable in class net.sf.basedb.core.data.DataFileTypeData
 
metadataReaderJarPath - 
Variable in class net.sf.basedb.core.data.DataFileTypeData
 
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.
metadataWriter - 
Variable in class net.sf.basedb.util.export.spotdata.BfsExporter
 
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.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
 
methodParameter - 
Static variable in class net.sf.basedb.plugins.MedianRatioNormalization
List of median normalization methods.
MEV - 
Static variable in class net.sf.basedb.ws.server.BioAssaySetService
 
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.
miameAnnotations - 
Variable in class net.sf.basedb.util.overview.ExperimentOverview
Deprecated.  
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
 
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 - 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 - 
Variable in class net.sf.basedb.ws.server.TempFileDataSource
 
MimeTypeData - Class in net.sf.basedb.core.data
This class holds information about mimetypes
MimeTypeData() - 
Constructor for class net.sf.basedb.core.data.MimeTypeData
 
mimeTypes - 
Static variable in class net.sf.basedb.plugins.TarFileUnpacker
 
mimeTypes - 
Static variable in class net.sf.basedb.plugins.ZipFileUnpacker
 
min(Expression) - 
Static method in class net.sf.basedb.core.query.Aggregations
Calculates the minimum value of an expression: new expression = MIN(e)
min - 
Variable in class net.sf.basedb.util.plot.HistogramPlot.HistogramBin
 
minBaseVersion - 
Variable in class net.sf.basedb.util.PluginInfo
The BASE version that the plugin at least requires
minChannelsParameter - 
Variable in class net.sf.basedb.plugins.Base1PluginExecuter
The minimum number of channels.
minColor - 
Variable in class net.sf.basedb.util.ColorGenerator
 
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
 
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
 
minIntensityParameter - 
Variable in class net.sf.basedb.plugins.MedianRatioNormalization
 
minor - 
Static variable in class net.sf.basedb.core.Version
 
minor - 
Variable in class net.sf.basedb.info.VersionInfo
 
minValue - 
Variable in class net.sf.basedb.core.data.ColoringData
 
minValue - 
Variable in class net.sf.basedb.util.ColorGenerator
 
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_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_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_HARDWARE - 
Static variable in class net.sf.basedb.util.overview.Validator
Validator rule that checks for missing hardware.
MISSING_HYBRIDIZATION - 
Static variable in class net.sf.basedb.util.overview.Validator
Validator rule that checks for missing hybridization.
MISSING_LABELED_EXTRACT - 
Static variable in class net.sf.basedb.util.overview.Validator
Validator rule that checks for missing labeled extract.
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_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_SCAN - 
Static variable in class net.sf.basedb.util.overview.Validator
Validator rule that checks for missing scan.
MISSING_SOFTWARE - 
Static variable in class net.sf.basedb.util.overview.Validator
Validator rule that checks for missing software.
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
 
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.SessionControl.SettingInfo
If the setting has been modified while the user was logged in or not
MOMENTUM - 
Static variable in class net.sf.basedb.core.Quantity
The id for the Quantity object representing momentum.
MOVE - 
Static variable in class net.sf.basedb.core.BioPlateEventType
The system ID for "Move" event type.
moveToPrimary(int) - 
Method in class net.sf.basedb.core.InternalStorageController
 
moveToSecondary(int) - 
Method in class net.sf.basedb.core.InternalStorageController
 
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.
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.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.
multipleArrayIndexErrorParameter - 
Static variable in class net.sf.basedb.plugins.batchimport.HybridizationImporter
 
multipleItemsFoundErrorParameter - 
Static variable in class net.sf.basedb.plugins.AnnotationFlatFileImporter
 
multipleItemsFoundErrorParameter - 
Static variable in class net.sf.basedb.plugins.batchimport.AbstractItemImporter
 
multipleReferencesFoundErrorParameter - 
Static variable in class net.sf.basedb.plugins.batchimport.AbstractItemImporter
 
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.
multiplicity - 
Variable in class net.sf.basedb.info.AnnotationTypeInfo
 
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.
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
 
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.clients.web.util.AjaxWriter
Deprecated.  
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.ServletWrapper
 
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.table.Hidden
The name of the element.
name - 
Variable in class net.sf.basedb.core.authentication.AuthenticationInformation
The full name of the user.
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.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.FileTypeData
 
name - 
Variable in class net.sf.basedb.core.data.GroupData
 
name - 
Variable in class net.sf.basedb.core.data.HardwareTypeData
 
name - 
Variable in class net.sf.basedb.core.data.HelpData
 
name - 
Variable in class net.sf.basedb.core.data.ImageData
 
name - 
Variable in class net.sf.basedb.core.data.JobData
 
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.ProtocolTypeData
 
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.SettingData
 
name - 
Variable in class net.sf.basedb.core.data.SoftwareTypeData
 
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.VersionedParameter
The name of the parameter.
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.IntensityFormula
 
name - 
Variable in class net.sf.basedb.core.ItemContext
 
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 enum net.sf.basedb.core.Project.Default
 
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.signal.Signal
 
name - 
Variable in class net.sf.basedb.core.VirtualColumn
The name of the column.
name - 
Variable in class net.sf.basedb.info.BioAssaySetInfo
 
name - 
Variable in class net.sf.basedb.info.CommonItemInfo
 
name - 
Variable in class net.sf.basedb.info.DataFileTypeInfo
 
name - 
Variable in class net.sf.basedb.info.ExtendedPropertyInfo
 
name - 
Variable in class net.sf.basedb.info.ProjectInfo
 
name - 
Variable in class net.sf.basedb.info.QueryParameter
 
name - 
Variable in class net.sf.basedb.plugins.Base1PluginExecuter.JobParameter
 
NAME - 
Static variable in class net.sf.basedb.plugins.batchimport.PropertyIdMethod
Use the name for finding items.
name - 
Variable in class net.sf.basedb.plugins.BioAssaySetExporter.QueryItem
Deprecated.  
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.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.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.overview.Node
 
name - 
Variable in class net.sf.basedb.util.parser.ColumnMapper
 
name - 
Variable in class net.sf.basedb.util.parser.FlatFileParser.Line
 
name() - 
Method in class net.sf.basedb.util.parser.FlatFileParser.Line
The name of the header if the line is a header 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.PluginConfigInfo
The name of the configuration
name - 
Variable in class net.sf.basedb.util.resources.ResourceBundleWrapper
 
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_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.
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.
NameableInfo - Interface in net.sf.basedb.info
 
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.
NameablePluginAdaptor - Class in net.sf.basedb.clients.web.util
This class wraps a Nameable object around a 
        PluginDefinition.
NameablePluginAdaptor(PluginDefinition) - 
Constructor for class net.sf.basedb.clients.web.util.NameablePluginAdaptor
 
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
 
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.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.ExtractImporter
 
nameMapper - 
Variable in class net.sf.basedb.plugins.batchimport.HybridizationImporter
 
nameMapper - 
Variable in class net.sf.basedb.plugins.batchimport.LabeledExtractImporter
 
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.ScanImporter
 
nameMapper - 
Variable in class net.sf.basedb.plugins.PlateFlatFileImporter
 
nameMapper - 
Variable in class net.sf.basedb.plugins.ReporterFlatFileImporter
 
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
 
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
 
needSynchronize - 
Variable in class net.sf.basedb.core.BioPlateEvent
 
needToParseNumeric - 
Variable in class net.sf.basedb.util.parser.ConstantMapper
 
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(AnnotationType, Object, boolean) - 
Static method in class net.sf.basedb.core.query.Annotations
Deprecated. Use Annotations.neq(String, AnnotationType, Object, boolean) instead with alias=null
neq(String, AnnotationType, Object, boolean) - 
Static method in class net.sf.basedb.core.query.Annotations
Create a restriction that searches for annotations
                not equal to a given value on the root or a joined entity of a 
                query.
neq(Expression, Expression) - 
Static method in class net.sf.basedb.core.query.Restrictions
Compare if two expressions are inequal: new restriction = e1 <> e2.
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.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.service - package net.sf.basedb.clients.web.extensions.service
 
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
This package is a taglib for generating a fancy 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
This package defines a framework for supporting user authentication
from external databases and directory services.
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.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.filehandler - package net.sf.basedb.core.filehandler
 
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.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.info - package net.sf.basedb.info

        This package contains pure data-holder classes which are used
        for transporting information about items in the database.
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.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.basefile - package net.sf.basedb.util.basefile
 
net.sf.basedb.util.bfs - package net.sf.basedb.util.bfs
 
net.sf.basedb.util.biomaterial - package net.sf.basedb.util.biomaterial
 
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.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.xml - package net.sf.basedb.util.extensions.xml
 
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.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.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.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.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.units - package net.sf.basedb.util.units
 
net.sf.basedb.util.zip - package net.sf.basedb.util.zip
 
net.sf.basedb.ws.client - package net.sf.basedb.ws.client
 
net.sf.basedb.ws.server - package net.sf.basedb.ws.server
 
NEW_SCHEMA_VERSION - 
Static variable in class net.sf.basedb.core.Install
The schema version to give to new installations.
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(BioAssay) - 
Method in class net.sf.basedb.core.BioAssaySet
Create a new BioAssay in this bioassayset using a 
                single parent.
newBioAssay(Collection<BioAssay>) - 
Method in class net.sf.basedb.core.BioAssaySet
Create a new BioAssay with links to multiple parent
                bioassays.
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
 
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.
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) - 
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, Well) - 
Method in class net.sf.basedb.core.FeatureBatcher
Create a new feature.
newFeature(ArrayDesignBlock, ReporterData) - 
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.
newHardware() - 
Method in class net.sf.basedb.core.HardwareType
Create a new Hardware item of this type.
newHelp(String) - 
Method in class net.sf.basedb.core.Client
Create a new help text for this client.
newImage() - 
Method in class net.sf.basedb.core.Scan
Create a new Image for this scan.
newInstance() - 
Method in class net.sf.basedb.core.PluginDefinition
Get an unitialized instance of the plugin.
newInstance(String) - 
Method in class net.sf.basedb.core.PluginDefinition
 
newInstance(Class<P>, String) - 
Method in class net.sf.basedb.core.PluginDefinition
Get an unitialized instance of the plugin implementation.
newInstance(Class<P>, String, SessionControl, PluginConfiguration, Job) - 
Method in class net.sf.basedb.core.PluginDefinition
Get an initialized instance of the plugin implementation.
newInstance(String, String, boolean) - 
Method in class net.sf.basedb.core.PluginDefinition
Create a new object instance of the given class.
newInstance(String) - 
Static method in class net.sf.basedb.util.JarClassLoader
Get a new class loader for the specified jar file.
newInstance() - 
Static method in class net.sf.basedb.util.MD5
 
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() - 
Method in class net.sf.basedb.core.PluginConfiguration
Deprecated. Use PluginConfiguration.newJob(Experiment) instead
newJob(Experiment) - 
Method in class net.sf.basedb.core.PluginConfiguration
Create a new Job for this plugin configuration.
newLabeledExtract(Label, Float) - 
Method in class net.sf.basedb.core.Extract
Create a new LabeledExtract from this extract.
newLabeledExtract(Label, Float, BioPlateEventParticipant) - 
Method in class net.sf.basedb.core.Extract
Create a new LabeledExtract from this extract as
                part of a master bioplate event.
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
 
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.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.
newProtocol() - 
Method in class net.sf.basedb.core.ProtocolType
Create a new Protocol item of this type.
newRawBioAssay(RawDataType) - 
Method in class net.sf.basedb.core.Scan
Deprecated. Use RawBioAssay.getNew(DbControl, Platform, RawDataType)
                        or RawBioAssay.getNew(DbControl, PlatformVariant, RawDataType) instead
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.
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.QueryRuntimeFilterImpl - Class in net.sf.basedb.core
 
News.QueryRuntimeFilterImpl() - 
Constructor for class net.sf.basedb.core.News.QueryRuntimeFilterImpl
 
newSample() - 
Method in class net.sf.basedb.core.BioSource
Create a new Sample from this biosource.
newScan() - 
Method in class net.sf.basedb.core.Hybridization
Create a new Scan from this hybridization.
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(Interceptor) - 
Static method in class net.sf.basedb.core.HibernateUtil
Create a new Hibernate session, optionally with an interceptor.
newSession(String) - 
Method in class net.sf.basedb.ws.server.SessionService
Creates a new session control.
newSessionControl(String, String, String) - 
Static method in class net.sf.basedb.core.Application
Create a new SessionControl object.
newSoftware() - 
Method in class net.sf.basedb.core.SoftwareType
Create a new Software item of this type.
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.
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.
newVariant(String) - 
Method in class net.sf.basedb.core.Platform
Create a new PlatformVariant of this platform.
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 - 
Variable in class net.sf.basedb.clients.web.servlet.PlotServlet.CFResultIterator
 
next() - 
Method in class net.sf.basedb.clients.web.servlet.PlotServlet.CFResultIterator
 
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.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.Tree.ElementIterator
 
next - 
Variable in class net.sf.basedb.util.Tree.EntryIterator
The next element to return.
next() - 
Method in class net.sf.basedb.util.Tree.EntryIterator
 
nextAutoScan - 
Static variable in class net.sf.basedb.clients.web.extensions.ExtensionsControl
 
nextBioAssay - 
Variable in class net.sf.basedb.util.export.spotdata.SerialBaseFileExporter
 
nextBuffer - 
Variable in class net.sf.basedb.clients.web.fileupload.FileUpload.UploadStream
 
nextCommand - 
Variable in class net.sf.basedb.core.PluginResponse
 
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 - 
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.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
 
nextIndex() - 
Method in class net.sf.basedb.core.ItemResultList.ResultListListIterator
 
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
 
nextReport - 
Variable in class net.sf.basedb.util.importer.spotdata.BfsImporter.ProgressEventHandler
 
nextSection() - 
Method in class net.sf.basedb.util.bfs.MetadataParser
Parse to the next section in the metadata file.
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.parser.FlatFileParser
Get the next line that matches the section 
                regular expression.
nextStream() - 
Method in class net.sf.basedb.util.InputStreamCombiner
 
nextToken(String) - 
Method in class net.sf.basedb.util.jep.FunctionSafeJep.SafeFunctionTable
Get the next token in the parser.
niceFormat(String) - 
Static method in class net.sf.basedb.clients.web.util.HTML
A convenience method for doing encodeTags(in, SAFE_TAGS),
                scanForLinks(in, "_new") 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, "_new") 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.
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.
NO_CANCELBUTTON - 
Static variable in class net.sf.basedb.clients.web.ModeInfo
 
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.
node - 
Variable in class net.sf.basedb.util.overview.Failure
 
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, ChildNodeDirection) - 
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(Node, Node) - 
Constructor for class net.sf.basedb.util.overview.Node
Make a copy of a node
node - 
Variable in class net.sf.basedb.util.Tree.Entry
 
Node.Type - Enum in net.sf.basedb.util.overview
The type of node.
Node.Type() - 
Constructor for enum net.sf.basedb.util.overview.Node.Type
 
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.
NodeValidator<I> - Interface in net.sf.basedb.util.overview.validator
A node validator is responsible for checking the "validity" of
        a node.
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.
nonCorePluginDirectory - 
Static variable in class net.sf.basedb.core.Application
The directory where non-core plugins are located/installed.
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.
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 hybridization.
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_LABEL - 
Static variable in class net.sf.basedb.util.overview.Validator
Validator rule that checks if a hybridization has more than one
                labeled extract with the same label.
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.
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>) - 
Method in class net.sf.basedb.plugins.LowessNormalization.CallableWorker
Normalize the spot data.
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.
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.
normalize1ch(DbControl, BioAssaySet, Job, float, float, float, boolean, ProgressReporter) - 
Method in class net.sf.basedb.plugins.MedianRatioNormalization
Normalise the source bioassay set using MEDIAN-RATIO normalization.
not(Restriction) - 
Static method in class net.sf.basedb.core.query.Restrictions
Negate a restriction: new restriction = NOT r
NOT_COMPACT - 
Static variable in class net.sf.basedb.clients.web.ModeInfo
 
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
 
Note - Class in net.sf.basedb.clients.web.taglib
This tag is used to display small notes on a BASE web page.
Note() - 
Constructor for class net.sf.basedb.clients.web.taglib.Note
 
NOTE_TYPE_ERROR - 
Static variable in class net.sf.basedb.clients.web.taglib.Note
 
NOTE_TYPE_INFORMATION - 
Static variable in class net.sf.basedb.clients.web.taglib.Note
 
NOTE_TYPE_QUESTION - 
Static variable in class net.sf.basedb.clients.web.taglib.Note
 
NOTE_TYPE_WARNING - 
Static variable in class net.sf.basedb.clients.web.taglib.Note
 
NotEqualsConverter - Class in net.sf.basedb.util.jep.convert
Convert the '!
NotEqualsConverter() - 
Constructor for class net.sf.basedb.util.jep.convert.NotEqualsConverter
 
notifyThread - 
Variable in class net.sf.basedb.clients.web.util.SimpleSignalProgressReporter
 
notifyThread - 
Variable in class net.sf.basedb.core.signal.AbstractSignalReceiver
 
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_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.
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
 
noWritePermissionToItemErrorParameter - 
Static variable in class net.sf.basedb.plugins.batchimport.AbstractItemImporter
 
nullable - 
Variable in class net.sf.basedb.core.ExtendedProperty
 
NULLABLE - 
Static variable in class net.sf.basedb.core.VirtualColumn
Used in constructor to tell that the column should be nullable.
nullable - 
Variable in class net.sf.basedb.core.VirtualColumn
If the column should be nullable or not.
nullable - 
Variable in class net.sf.basedb.info.ExtendedPropertyInfo
 
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
 
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.
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(Restriction...) - 
Static method in class net.sf.basedb.core.query.Restrictions
Combine one or more restrictions with AND 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.util.AjaxWriter
Deprecated.  
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.FilePathFormatter
 
nullValue - 
Variable in class net.sf.basedb.util.formatter.IdentifiableFormatter
 
nullValue - 
Variable in class net.sf.basedb.util.formatter.NameableFormatter
 
NUM_SPOT_IMAGES - 
Static variable in class net.sf.basedb.core.SpotImages
The number of spot images to place side by side in each file.
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
 
numArrays - 
Variable in class net.sf.basedb.core.data.HybridizationData
 
numArraysColumnMapping - 
Static variable in class net.sf.basedb.plugins.batchimport.ArrayDesignImporter
 
numArraysColumnMapping - 
Static variable in class net.sf.basedb.plugins.batchimport.HybridizationImporter
 
numArraysMapper - 
Variable in class net.sf.basedb.plugins.batchimport.ArrayDesignImporter
 
numArraysMapper - 
Variable in class net.sf.basedb.plugins.batchimport.HybridizationImporter
 
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.IlluminaRawDataImporter
 
numberFormat - 
Variable in class net.sf.basedb.plugins.RawDataFlatFileImporter
 
numberFormat - 
Variable in class net.sf.basedb.plugins.ReporterFlatFileImporter
 
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
 
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
 
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
 
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, 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.
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.
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.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
 
numDataColumnsType - 
Static variable in class net.sf.basedb.plugins.AbstractFlatFileImporter
 
numDbFeatures - 
Variable in class net.sf.basedb.info.ArrayDesignInfo
 
numDecimals - 
Variable in class net.sf.basedb.util.formatter.NumberFormatter
 
numDeleted - 
Variable in class net.sf.basedb.plugins.ReporterFlatFileImporter
 
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.
numericToAlpha(int) - 
Static method in class net.sf.basedb.util.Coordinate
Convert a numeric coordinate to an alphanumeric coordinate.
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
 
numErrorFiles - 
Variable in class net.sf.basedb.clients.web.extensions.ScanResults
 
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
 
numFileFeatures - 
Variable in class net.sf.basedb.info.ArrayDesignInfo
 
numFileReporters - 
Variable in class net.sf.basedb.core.data.BioAssaySetData
 
numFiles - 
Variable in class net.sf.basedb.plugins.PackedFileExporter
 
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
 
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
 
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.plugins.AnnotationFlatFileImporter
 
numLayers - 
Variable in class net.sf.basedb.core.data.DataCubeData
 
numMultiLines - 
Variable in class net.sf.basedb.plugins.batchimport.AbstractItemImporter
 
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
 
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.
numRemoved - 
Variable in class net.sf.basedb.plugins.AnnotationFlatFileImporter.NewAnnotations
 
numRemoved - 
Variable in class net.sf.basedb.plugins.AnnotationFlatFileImporter
 
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
 
numReporters - 
Variable in class net.sf.basedb.info.BioAssaySetInfo
 
numReportersNotFound - 
Variable in class net.sf.basedb.core.RawDataBatcher
The number of reporters that was not found.
numSelected - 
Variable in class net.sf.basedb.plugins.PluginConfigurationExporter
 
numSet - 
Variable in class net.sf.basedb.plugins.AnnotationFlatFileImporter.NewAnnotations
 
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
 
numSpots - 
Variable in class net.sf.basedb.info.BioAssaySetInfo
 
numStreams - 
Variable in class net.sf.basedb.ws.server.TempFileDataSource
 
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
 
numUpdated - 
Variable in class net.sf.basedb.plugins.batchimport.AbstractItemImporter
 
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.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
 
objects - 
Variable in class net.sf.basedb.core.ItemContext
 
objects - 
Variable in class net.sf.basedb.util.ClassLocal
 
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.
oldFile - 
Variable in class net.sf.basedb.util.importer.spotdata.BaseFileImporter
 
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.
onActivate - 
Variable in class net.sf.basedb.clients.web.extensions.tabcontrol.FixedTabFactory
 
onActivate - 
Variable in class net.sf.basedb.clients.web.extensions.tabcontrol.IncludeContentTabFactory
 
onActivate - 
Variable in class net.sf.basedb.clients.web.extensions.tabcontrol.TabBean
 
onAdd(BioWellData, MeasuredBioMaterialData) - 
Method in enum net.sf.basedb.core.BioWell.LockMode
Called when biomaterial is added to a well.
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.File
 
onAfterCommit() - 
Method in class net.sf.basedb.core.Job.JobSignalTransporter
 
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.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
 
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.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.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(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(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(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.BioMaterial
On delete action: issue an update to decrease the size of all 
                BioMaterialList:s this is a member of.
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.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.Hybridization
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.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.Project
 
onBeforeCommit(Transactional.Action) - 
Method in class net.sf.basedb.core.RawBioAssay
Delete raw data if it exists.
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.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.
onChange - 
Variable in class net.sf.basedb.clients.web.taglib.Select
JavaScript statement.
onChange - 
Variable in class net.sf.basedb.clients.web.taglib.table.PresetSelector
 
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.menu.FixedMenuItemFactory
 
onClick - 
Variable in class net.sf.basedb.clients.web.extensions.menu.MenuItemBean
 
onClick - 
Variable in class net.sf.basedb.clients.web.extensions.menu.PermissionMenuItemFactory
 
onClick - 
Variable in class net.sf.basedb.clients.web.extensions.toolbar.ButtonBean
 
onClick - 
Variable in class net.sf.basedb.clients.web.extensions.toolbar.FixedButtonFactory
 
onClick - 
Variable in class net.sf.basedb.clients.web.extensions.toolbar.PermissionButtonFactory
 
onClick - 
Variable in class net.sf.basedb.clients.web.taglib.Button
JavaScript statement.
onClick - 
Variable in class net.sf.basedb.clients.web.taglib.Help
Optional JavaScript statement.
onClick - 
Variable in class net.sf.basedb.clients.web.taglib.Icon
An optional JavaScript statement.
onclick - 
Variable in class net.sf.basedb.clients.web.taglib.menu.Menuitem
Javascript statment to execute when the user clicks the menu.
onClick - 
Variable in class net.sf.basedb.clients.web.taglib.table.Button
A JavaScript statement that is executet when the button is clicked.
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.
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.
onKeyPress - 
Variable in class net.sf.basedb.clients.web.taglib.Body
A JavaScript statement that is put into the onkeypress attribute
                of the body tag.
onLoad - 
Variable in class net.sf.basedb.clients.web.taglib.Body
A JavaScript statement that is put into the onload attribute
                of the body tag.
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.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
 
onSelect - 
Variable in class net.sf.basedb.clients.web.taglib.Select
JavaScript statement.
onToggle - 
Variable in class net.sf.basedb.clients.web.taglib.HideableSection
Javascript to call when showing/hiding section
onUnload - 
Variable in class net.sf.basedb.clients.web.taglib.Body
A JavaScript statement that is put into the onunload attribute
                of the body tag.
onValidate - 
Variable in class net.sf.basedb.clients.web.extensions.tabcontrol.FixedTabFactory
 
onValidate - 
Variable in class net.sf.basedb.clients.web.extensions.tabcontrol.IncludeContentTabFactory
 
onValidate - 
Variable in class net.sf.basedb.clients.web.extensions.tabcontrol.TabBean
 
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.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 - Enum in net.sf.basedb.core
 
Operator(int, String, String, boolean, boolean) - 
Constructor for enum net.sf.basedb.core.Operator
 
operator - 
Variable in class net.sf.basedb.core.PropertyFilter
 
operator - 
Variable in class net.sf.basedb.core.query.SubqueryExpression
 
operators - 
Static variable in class net.sf.basedb.util.jep.Jep
 
optionalBooleanType - 
Static variable in class net.sf.basedb.plugins.AnnotationFlatFileImporter
 
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.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.data.AnnotationTypeData
 
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 - 
Variable in class net.sf.basedb.ws.client.ConfigurableServiceFactory
 
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] ...
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 - Interface in net.sf.basedb.core.query
An ordering query element.
order(Order) - 
Method in interface net.sf.basedb.core.query.Query
Add an ordering query element to the orderby list.
orderInXml - 
Variable in class net.sf.basedb.util.PluginConfigInfo
In which place the configuration comes in the file.
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.AuthenticationInformation
The organisation of the user.
organisation - 
Variable in class net.sf.basedb.core.data.UserData
 
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.LabeledExtractImporter
 
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
 
os - 
Variable in class net.sf.basedb.ws.server.BaseFileDataSource
 
OTHER - 
Static variable in class net.sf.basedb.core.HardwareType
The id for the HardwareType object representing something
                else.
out - 
Variable in class net.sf.basedb.clients.jobagent.executors.ProcessJobExecutor.StreamRedirector
 
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.
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 - 
Static variable in class net.sf.basedb.core.plugin.AbstractExporterPlugin
Parameter name for the AbstractExporterPlugin.getOverwriteParameter(String, String) parameter.
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.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_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.
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() - 
Constructor for class net.sf.basedb.core.OwnableUtil
 
OwnableUtil - Class in net.sf.basedb.util
 
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<D extends OwnedData> - Class in net.sf.basedb.core
This class inherits from the BasicItem
        class and implements the Ownable interface.
OwnedItem(D) - 
Constructor for class net.sf.basedb.core.OwnedItem
 
OwnedItemInfo - Class in net.sf.basedb.info
 
OwnedItemInfo() - 
Constructor for class net.sf.basedb.info.OwnedItemInfo
 
owner - 
Variable in class net.sf.basedb.core.data.OwnedData
 
ownerId - 
Variable in class net.sf.basedb.core.InternalJobQueue.JobRunner
 
ownerId - 
Variable in class net.sf.basedb.info.OwnedItemInfo
 



P

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 ZipEntry 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
 
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.Note
The parent <base:page> tag.
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 - 
Variable in class net.sf.basedb.clients.web.taglib.table.Table
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_TYPE_DEFAULT - 
Static variable in class net.sf.basedb.clients.web.taglib.Page
This is the default page type.
PAGE_TYPE_FRAMESET - 
Static variable in class net.sf.basedb.clients.web.taglib.Page
The page is a frameset.
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, Type) - 
Static method in class net.sf.basedb.core.query.Expressions
Create an expression for a typed parameter without a default value.
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_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 - 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.
parameterDefinition - 
Variable in class net.sf.basedb.plugins.executor.ProgramParameter
 
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 - 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
 
parameterInfo - 
Variable in class net.sf.basedb.core.PluginRequest
 
parameterMap - 
Variable in class net.sf.basedb.core.RequestInformation
 
parameterName - 
Variable in class net.sf.basedb.clients.web.plugins.ItemQueryLoader
 
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.info.QueryOptions
 
parameters - 
Variable in class net.sf.basedb.plugins.executor.ExternalProgramExecutor.RequestWrapper
 
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
 
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
 
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>) - 
Constructor for class net.sf.basedb.core.ParameterType
 
parameterTypes - 
Variable in class net.sf.basedb.core.ParameterValuesImpl
 
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(PluginDefinition) - 
Constructor for class net.sf.basedb.core.ParameterValuesImpl
Empty parameter values
ParameterValuesImpl(Job, boolean) - 
Constructor for class net.sf.basedb.core.ParameterValuesImpl
 
ParameterValuesImpl(PluginConfiguration, int, boolean) - 
Constructor for class net.sf.basedb.core.ParameterValuesImpl
 
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.QueryRuntimeFilterFactory.ChildFilter
The item type of the parent item.
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.filter.InverseFilter
 
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.overview.loader.AutoChildNodeLoader
 
parent - 
Variable in class net.sf.basedb.util.overview.Node
 
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.Tree.Entry
 
ParentBioMaterialLoader - Class in net.sf.basedb.clients.web.plugins
This class get data from the parents to a MeasuredBioMaterial
ParentBioMaterialLoader() - 
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.SampleImporter
Column mapping parameter for the parent (biosource OR pooled 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.util.overview.validator.ProtocolParameterValidator
 
parentItemNode - 
Variable in class net.sf.basedb.util.overview.validator.ProtocolParameterValidator
 
parentMapper - 
Variable in class net.sf.basedb.plugins.batchimport.ExtractImporter
 
parentMapper - 
Variable in class net.sf.basedb.plugins.batchimport.HybridizationImporter
 
parentMapper - 
Variable in class net.sf.basedb.plugins.batchimport.LabeledExtractImporter
 
parentMapper - 
Variable in class net.sf.basedb.plugins.batchimport.SampleImporter
 
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.GroupData
 
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
 
parentSet - 
Variable in class net.sf.basedb.core.data.PlateData
 
parse(DbControl, Metadata, String, String, boolean, Formatter, boolean, DataLoader) - 
Static method in class net.sf.basedb.clients.web.plugins.ExportedProperty
 
parse(InputStream, String) - 
Method in class net.sf.basedb.util.basefile.BaseFileParser
Parse the given input stream.
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.
parseAnswer(String) - 
Static method in class net.sf.basedb.util.jobagent.JobAgentConnection
Utility method for parsing a 'typical' answer from a job agent.
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(String) - 
Method in class net.sf.basedb.plugins.batchimport.AbstractItemImporter
Parse a string to a date using the date format specified by the 
                'Date format' parameter.
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.XMLUtil.Validator
 
parsedLines - 
Variable in class net.sf.basedb.util.parser.FlatFileParser
The total number of lines 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...
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
 
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.ColorFormatter
 
parseString(String) - 
Method in class net.sf.basedb.clients.web.formatter.ExtendedPropertyFormatter
 
parseString(String) - 
Method in class net.sf.basedb.clients.web.formatter.SpotImageFormatter
Not supported.
parseString(String) - 
Method in class net.sf.basedb.clients.web.formatter.StringFormatter
 
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, NumberFormat) - 
Method in class net.sf.basedb.core.ExtendedProperty
Deprecated. Use ExtendedProperty.parseString(String, NumberFormat, boolean) instead
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) - 
Method in enum net.sf.basedb.core.Type
Parse a string and return a value of the correct type.
parseString(String, NumberFormat) - 
Method in enum net.sf.basedb.core.Type
Deprecated. Use Type.parseString(String, NumberFormat, boolean) instead
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) - 
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.DateFormatter
 
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.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.NumberFormatter
 
parseString(String) - 
Method in class net.sf.basedb.util.formatter.PrefixSuffixFormatter
 
parseString(String) - 
Method in class net.sf.basedb.util.formatter.ToStringFormatter
 
parseString(String) - 
Method in class net.sf.basedb.util.formatter.WellCoordinateFormatter
 
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.
parseXml(String, boolean) - 
Static method in class net.sf.basedb.plugins.executor.ParameterDefinition
Parse an XML document containing parameter definitions.
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.data.FileServerData
 
password - 
Variable in class net.sf.basedb.core.data.UserData
 
password - 
Variable in class net.sf.basedb.util.ssl.StaticKeyManager
 
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
 
Path - Class in net.sf.basedb.clients.web.taglib.path
This tag defines a navigation path.
Path() - 
Constructor for class net.sf.basedb.clients.web.taglib.path.Path
 
path - 
Variable in class net.sf.basedb.clients.web.taglib.path.PathElement
The parent Path.
path - 
Variable in class net.sf.basedb.core.InternalStorageController
The path to the directory where the secondary storage is located.
path - 
Variable in class net.sf.basedb.core.Metadata.CombinedPropertyPath
 
Path - Class in net.sf.basedb.core
This class is used represent the path to a Directory
        or File item.
Path(String, Path.Type) - 
Constructor for class net.sf.basedb.core.Path
Create a new Path object by parsing the given string.
Path(String, String[], String) - 
Constructor for class net.sf.basedb.core.Path
Create a new Path object.
Path(Path, String) - 
Constructor for class net.sf.basedb.core.Path
Create a new Path object.
Path.Type - Enum in net.sf.basedb.core
An enum that describes what type the path is
Path.Type() - 
Constructor for enum net.sf.basedb.core.Path.Type
 
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.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)
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.
pathComparator - 
Static variable in class net.sf.basedb.clients.web.servlet.CompileAll
 
pathConverter - 
Variable in class net.sf.basedb.clients.web.extensions.ExtensionsDirectory
 
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
 
pathInfo - 
Variable in class net.sf.basedb.clients.web.extensions.RequestWrapper
 
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.
pathType - 
Variable in class net.sf.basedb.core.PathParameterType
 
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
 
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.
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
 
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 - 
Static variable in class net.sf.basedb.clients.web.util.HTML
 
percent - 
Variable in class net.sf.basedb.core.signal.ProgressReporterSignalHandler
The current percentage status.
percent - 
Variable in class net.sf.basedb.core.SimpleProgressReporter
 
percentComplete - 
Variable in class net.sf.basedb.core.data.JobData
 
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.
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(ProgressReporter) - 
Method in class net.sf.basedb.plugins.BfsExporterPlugin
 
performExport(ExportOutputStream, ProgressReporter) - 
Method in class net.sf.basedb.plugins.BioAssaySetExporter
Deprecated.  
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
 
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 - 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(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.
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.
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.
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 - 
Variable in class net.sf.basedb.core.InternalStorageController.StorageKeyring
 
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
 
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.BioAssaySetExporter
Deprecated.  
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.plugins.SpotImageCreator
 
permissions - 
Static variable in class net.sf.basedb.util.zip.AbstractFileUnpacker
 
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
 
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.AuthenticationInformation
The phone number to the user.
phone - 
Variable in class net.sf.basedb.core.data.UserData
 
ping() - 
Method in class net.sf.basedb.core.Application.Pinger
Ping the SessionControl by updating the last access time:
                        SessionControl.updateLastAccess()
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.
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.
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.
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 - 
Static variable in class net.sf.basedb.core.FileType
The id for the FileType item representing a
                plate file.
Plate - Class in net.sf.basedb.core
This class is represents physical plates.
Plate(PlateData) - 
Constructor for class net.sf.basedb.core.Plate
 
PLATE_MAPPING - 
Static variable in class net.sf.basedb.core.FileType
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
 
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(boolean) - 
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
 
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
 
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
 
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 - 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 - 
Variable in class net.sf.basedb.plugins.PlateFlatFileImporter
 
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 - 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 - 
Variable in class net.sf.basedb.core.RawDataType
 
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.
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
 
platformId - 
Variable in class net.sf.basedb.info.RawBioAssayInfo
 
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.
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.CFResultIterator(SqlResultIterator, SqlResultIterator) - 
Constructor for class net.sf.basedb.clients.web.servlet.PlotServlet.CFResultIterator
 
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
PlotServlet.CFSqlResult() - 
Constructor for class net.sf.basedb.clients.web.servlet.PlotServlet.CFSqlResult
 
plugin - 
Variable in class net.sf.basedb.clients.web.util.NameablePluginAdaptor
 
plugin - 
Variable in class net.sf.basedb.core.data.ChangeHistoryData
 
plugin - 
Variable in class net.sf.basedb.core.ParameterValuesImpl
 
Plugin - Interface in net.sf.basedb.core.plugin
This interface must be implemented by all plugins to BASE.
plugin - 
Variable in class net.sf.basedb.core.PluginRequest
 
plugin - 
Variable in class net.sf.basedb.util.ContextUtil.ContextResult
 
Plugin.MainType - Enum in net.sf.basedb.core.plugin
 
Plugin.MainType(int, String) - 
Constructor for enum net.sf.basedb.core.plugin.Plugin.MainType
 
pluginClass - 
Variable in class net.sf.basedb.util.PluginConfigInfo
The plugin the configuration can be use with
PluginConfigInfo - Class in net.sf.basedb.util
This class should be used to keep information about a plugin configuration 
 that is loaded from an XML-file.
PluginConfigInfo(String, String, String) - 
Constructor for class net.sf.basedb.util.PluginConfigInfo
Constructor to create a new instance with information for a plugin configuration.
pluginConfiguration - 
Variable in class net.sf.basedb.core.data.JobData
 
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 - 
Variable in class net.sf.basedb.core.PluginRequest
 
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 - Class in net.sf.basedb.core
A plugin definition represents the executable plugin.
PluginDefinition(PluginDefinitionData) - 
Constructor for class net.sf.basedb.core.PluginDefinition
 
pluginDefinition - 
Variable in class net.sf.basedb.core.PluginRequest
 
PluginDefinitionData - Class in net.sf.basedb.core.data
This class represent an installed plugin.
PluginDefinitionData() - 
Constructor for class net.sf.basedb.core.data.PluginDefinitionData
 
pluginDefinitionId - 
Variable in class net.sf.basedb.core.data.keyring.PluginKeys
 
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(SessionControl, Plugin, String, PluginConfiguration, ParameterValuesImpl, Job, ParameterValuesImpl, PluginDefinition) - 
Constructor for class net.sf.basedb.core.PluginExecutionRequest
 
PluginExecutionRequest(PluginRequest<? extends Plugin>, String) - 
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
A PluginInfo object is used to keep information about 
        external plugin located in a jar file.
PluginInfo(String, String, String, About, List<PluginConfigInfo>) - 
Constructor for class net.sf.basedb.util.PluginInfo
Creates a new PluginInfo object.
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
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() - 
Constructor for class net.sf.basedb.core.data.PluginPermission
 
PluginPermission(int, int) - 
Constructor for class net.sf.basedb.core.data.PluginPermission
 
PluginPermission - Class in net.sf.basedb.core
 
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(SessionControl, P, String, PluginConfiguration, ParameterValuesImpl, Job, ParameterValuesImpl, PluginDefinition) - 
Constructor for class net.sf.basedb.core.PluginRequest
 
PluginRequest(PluginRequest<? extends P>, String) - 
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.
PluginRequest.RequestImpl(boolean) - 
Constructor for class net.sf.basedb.core.PluginRequest.RequestImpl
 
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.
PluginResponse.ResponseImpl() - 
Constructor for class net.sf.basedb.core.PluginResponse.ResponseImpl
 
plugins - 
Variable in class net.sf.basedb.core.data.JobAgentData
 
plugins - 
Variable in class net.sf.basedb.core.data.PluginTypeData
 
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.
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
 
pluginVersion - 
Variable in class net.sf.basedb.util.PluginInfo
The version of this plug-in
PLUS - 
Static variable in class net.sf.basedb.clients.web.util.HTML
 
pm - 
Variable in class net.sf.basedb.plugins.PlateMappingImporter
 
pooled - 
Variable in class net.sf.basedb.core.data.MeasuredBioMaterialData
 
PooledChildrenTransformer<I extends MeasuredBioMaterial> - Class in net.sf.basedb.util.biomaterial
Collection transformer that given a collection of biomaterials
        finds all pooled children (of the same type).
PooledChildrenTransformer(DbControl, boolean, ItemQuery<I>) - 
Constructor for class net.sf.basedb.util.biomaterial.PooledChildrenTransformer
 
pooledColumnMapping - 
Static variable in class net.sf.basedb.plugins.batchimport.SampleImporter
Column mapping parameter for the pooled property.
pooledMapper - 
Variable in class net.sf.basedb.plugins.batchimport.ExtractImporter
 
pooledMapper - 
Variable in class net.sf.basedb.plugins.batchimport.LabeledExtractImporter
 
pooledMapper - 
Variable in class net.sf.basedb.plugins.batchimport.SampleImporter
 
PooledParentsTransformer<I extends MeasuredBioMaterial> - Class in net.sf.basedb.util.biomaterial
Collection transformer that given a collection of (pooled) 
        biomaterials finds all parents (of the same type).
PooledParentsTransformer(DbControl, boolean, ItemQuery<I>) - 
Constructor for class net.sf.basedb.util.biomaterial.PooledParentsTransformer
 
POOLING - 
Static variable in class net.sf.basedb.core.ProtocolType
The ID for the pooling protocol type, for example a protocol
                used when creating a biomaterial item (Sample,
                Extract or LabeledExtract)
                from a set of other biomaterial items.
POP3Authenticator - Class in net.sf.basedb.core.authentication
This class is an example implementation of the Authenticator
        interface that authenticates a user against a POP3 server.
POP3Authenticator() - 
Constructor for class net.sf.basedb.core.authentication.POP3Authenticator
Create a new POP3Authenticator object.
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.authentication.POP3Authenticator
The POP3 port to use.
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
 
pos - 
Variable in class net.sf.basedb.util.parser.ColumnMapper
 
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.FeatureData
 
position - 
Variable in class net.sf.basedb.core.data.RawData
 
POSITION - 
Static variable in class net.sf.basedb.core.VirtualColumn
This column stores the data cube position coordinate.
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
 
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.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.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 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.
postMissingItem(DbControl, OverviewContext, Node, Node) - 
Method in class net.sf.basedb.util.overview.validator.BasicNodeValidator
Do nothing.
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.DataFileValidator
 
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.HardwareValidator
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.LabeledExtractValidator
 
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.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.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.
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
 
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.LabeledExtractValidator
 
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.
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 - 
Static variable in class net.sf.basedb.core.Quantity
The id for the Quantity object representing power.
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_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
 
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 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.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.info.QueryOptions
The prefix that represent a root alias in 
                a query.
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, 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.
preloaded - 
Variable in class net.sf.basedb.core.RawDataBatcher
Holds info about the features of an array design.
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 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
 
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(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(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<? 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) - 
Method in class net.sf.basedb.clients.web.extensions.service.DummyService
 
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 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<? 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.
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 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
Return the original query, unmodified.
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.
presets - 
Variable in class net.sf.basedb.clients.web.extensions.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 - 
Variable in class net.sf.basedb.core.Presets
 
Presets.Preset - Class in net.sf.basedb.core
Represents a single preset.
Presets.Preset() - 
Constructor for class net.sf.basedb.core.Presets.Preset
 
Presets.Preset(String) - 
Constructor for class net.sf.basedb.core.Presets.Preset
 
Presets.Preset(Element) - 
Constructor for class net.sf.basedb.core.Presets.Preset
Load preset name and key-value pairs from XML Document.
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 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
 
preview - 
Variable in class net.sf.basedb.core.data.ImageData
 
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_KEY - 
Static variable in class net.sf.basedb.core.VirtualColumn
Used in constructor to tell that the column is part of the primary key.
primaryKey - 
Variable in class net.sf.basedb.core.VirtualColumn
If the column should be part of the primary key or not.
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_MAP - 
Static variable in class net.sf.basedb.core.FileType
The id for the FileType item representing a
                print map file.
PRINT_ROBOT - 
Static variable in class net.sf.basedb.core.HardwareType
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.ProtocolType
The ID for the printing protocol type, for example a protocol
                used when printing a batch of array slides using a print robot.
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.FormatType() - 
Constructor for enum net.sf.basedb.plugins.PrintMapFlatFileImporter.FormatType
 
PrintMapFlatFileImporter.MetaBlock - Class in net.sf.basedb.plugins
 
PrintMapFlatFileImporter.MetaBlock(int) - 
Constructor for class net.sf.basedb.plugins.PrintMapFlatFileImporter.MetaBlock
 
PrintMapFlatFileImporter.Section - Enum in net.sf.basedb.plugins
 
PrintMapFlatFileImporter.Section(String) - 
Constructor for enum net.sf.basedb.plugins.PrintMapFlatFileImporter.Section
 
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.
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.
ProcessJobExecutor.StreamRedirector(Reader, Writer) - 
Constructor for class net.sf.basedb.clients.jobagent.executors.ProcessJobExecutor.StreamRedirector
 
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.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.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
 
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.
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 - Class in net.sf.basedb.core
This class is used to represent projects.
Project(ProjectData) - 
Constructor for class net.sf.basedb.core.Project
 
project - 
Variable in class net.sf.basedb.util.overview.ExperimentOverview
Deprecated.  
project - 
Variable in class net.sf.basedb.util.overview.GenericOverview
 
Project.Default - Enum in net.sf.basedb.core
 
Project.Default(String, String, Item, String, Item) - 
Constructor for enum net.sf.basedb.core.Project.Default
 
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.
Project.QueryRuntimeFilterImpl() - 
Constructor for class net.sf.basedb.core.Project.QueryRuntimeFilterImpl
 
ProjectClient - Class in net.sf.basedb.ws.client
Web service client for project in BASE.
ProjectClient(SessionClient) - 
Constructor for class net.sf.basedb.ws.client.ProjectClient
Creates new ProjectClient object for an active session client.
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
 
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.Keyring
The active project's ID.
projectId - 
Variable in class net.sf.basedb.core.log.TransactionDetails
 
ProjectInfo - Class in net.sf.basedb.info
Holds information about a project in BASE
        It can only keep simple objects that can be handled
        by Web Services.
ProjectInfo() - 
Constructor for class net.sf.basedb.info.ProjectInfo
Creates a new empty info object
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
 
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 - 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.
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.
projectKeySet - 
Variable in class net.sf.basedb.core.SharedItem
 
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 - 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.
projectPermissions - 
Variable in class net.sf.basedb.core.ProjectPermissions
 
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
 
ProjectService - Class in net.sf.basedb.ws.server
Web service class for Project
        Project.
ProjectService() - 
Constructor for class net.sf.basedb.ws.server.ProjectService
 
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.XMLTemplate
 
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
 
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(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 - 
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.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_REGEXP - 
Static variable in class net.sf.basedb.core.query.Hql
A property can only contain the characters a-zA-Z0-9, period(.) 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() - 
Constructor for class net.sf.basedb.clients.web.taglib.table.PropertyFilter
 
PropertyFilter - Class in net.sf.basedb.core
Used to store filter settings in the current context.
PropertyFilter(String) - 
Constructor for class net.sf.basedb.core.PropertyFilter
Create a new filter for a property.
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.
PropertyFilter(String, PropertyFilterData) - 
Constructor for class net.sf.basedb.core.PropertyFilter
Create a new filter from a loaded database object.
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
 
propertyFilters - 
Variable in class net.sf.basedb.core.data.ContextData
 
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.
propertyPath - 
Variable in class net.sf.basedb.clients.web.plugins.ExportedProperty
 
propertyPath - 
Variable in class net.sf.basedb.util.export.spotdata.AssayPropertyField
 
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.PlateEventData
 
protocol - 
Variable in class net.sf.basedb.core.data.RawBioAssayData
 
protocol - 
Variable in class net.sf.basedb.core.data.ScanData
 
PROTOCOL - 
Static variable in class net.sf.basedb.core.FileType
The id for the FileType item representing a
                protocol.
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 - 
Variable in class net.sf.basedb.plugins.IlluminaRawDataImporter
 
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.RawBioAssay
 
protocolHasBeenSet - 
Variable in class net.sf.basedb.core.Scan
 
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.ExtractImporter
 
protocolMapper - 
Variable in class net.sf.basedb.plugins.batchimport.HybridizationImporter
 
protocolMapper - 
Variable in class net.sf.basedb.plugins.batchimport.LabeledExtractImporter
 
protocolMapper - 
Variable in class net.sf.basedb.plugins.batchimport.RawBioAssayImporter
 
protocolMapper - 
Variable in class net.sf.basedb.plugins.batchimport.SampleImporter
 
protocolMapper - 
Variable in class net.sf.basedb.plugins.batchimport.ScanImporter
 
protocolParameter - 
Variable in class net.sf.basedb.info.AnnotationTypeInfo
 
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
 
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
 
protocols - 
Variable in class net.sf.basedb.core.data.ProtocolTypeData
 
protocolType - 
Variable in class net.sf.basedb.core.data.PlateEventTypeData
 
protocolType - 
Variable in class net.sf.basedb.core.data.ProtocolData
 
ProtocolType - Class in net.sf.basedb.core
This class is used to represent the type of the
        Protocol items in BASE.
ProtocolType(ProtocolTypeData) - 
Constructor for class net.sf.basedb.core.ProtocolType
Creates a new protocoltype item.
ProtocolTypeData - Class in net.sf.basedb.core.data
 
ProtocolTypeData() - 
Constructor for class net.sf.basedb.core.data.ProtocolTypeData
 
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.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.
ps - 
Variable in class net.sf.basedb.core.QueryExecutor.FutureResultSet
 
ps - 
Variable in class net.sf.basedb.core.QueryExecutor.FutureUpdate
 
publication - 
Variable in class net.sf.basedb.core.data.ExperimentData
 
publication - 
Variable in class net.sf.basedb.info.ExperimentInfo
 
publicationDate - 
Variable in class net.sf.basedb.core.data.ExperimentData
 
publicationDate - 
Variable in class net.sf.basedb.info.ExperimentInfo
 
pubMedId - 
Variable in class net.sf.basedb.core.data.ExperimentData
 
pubMedId - 
Variable in class net.sf.basedb.info.ExperimentInfo
 
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

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
 
quality - 
Variable in class net.sf.basedb.core.data.SpotImagesData
 
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.
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
 
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.ReporterScoreQueryWrapper
 
query - 
Variable in class net.sf.basedb.core.hibernate.QueryWrapper
 
query - 
Variable in class net.sf.basedb.core.ItemContext
 
Query - Interface in net.sf.basedb.core.query
This defines the simplest form of a relational query.
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.biomaterial.PooledChildrenTransformer
 
query - 
Variable in class net.sf.basedb.util.biomaterial.PooledParentsTransformer
 
query - 
Variable in class net.sf.basedb.util.units.UnitCache
 
queryAlias - 
Variable in class net.sf.basedb.plugins.BioAssaySetExporter.QueryItem
Deprecated.  
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.CancelableSession(Session) - 
Constructor for class net.sf.basedb.core.QueryExecutor.CancelableSession
 
QueryExecutor.CancelableStatelessSession - Class in net.sf.basedb.core
Cancels a query running in a stateless Hibernate session.
QueryExecutor.CancelableStatelessSession(StatelessSession) - 
Constructor for class net.sf.basedb.core.QueryExecutor.CancelableStatelessSession
 
QueryExecutor.CancelableStatement - Class in net.sf.basedb.core
Cancels a statement by calling Statement.cancel().
QueryExecutor.CancelableStatement(Statement) - 
Constructor for class net.sf.basedb.core.QueryExecutor.CancelableStatement
 
QueryExecutor.FutureItem<T> - Class in net.sf.basedb.core
 
QueryExecutor.FutureItem(Class<T>, Query) - 
Constructor for class net.sf.basedb.core.QueryExecutor.FutureItem
 
QueryExecutor.FutureResultSet - Class in net.sf.basedb.core
A callable implementation the calls PreparedStatement.executeQuery()
QueryExecutor.FutureResultSet(PreparedStatement) - 
Constructor for class net.sf.basedb.core.QueryExecutor.FutureResultSet
 
QueryExecutor.FutureScrollIterator<T> - Class in net.sf.basedb.core
Calls Query.scroll(ScrollMode) and returns the result as a
                ScrollIterator.
QueryExecutor.FutureScrollIterator(Class<T>, Query) - 
Constructor for class net.sf.basedb.core.QueryExecutor.FutureScrollIterator
 
QueryExecutor.FutureUpdate - Class in net.sf.basedb.core
A callable implementation the calls PreparedStatement.executeUpdate()
QueryExecutor.FutureUpdate(PreparedStatement) - 
Constructor for class net.sf.basedb.core.QueryExecutor.FutureUpdate
 
queryFile - 
Static variable in class net.sf.basedb.core.Application
The path to the file containing predefined queries.
QueryOptions - Class in net.sf.basedb.info
This class holds information to configure 
        itemqueries in webservices with.
QueryOptions() - 
Constructor for class net.sf.basedb.info.QueryOptions
An empty constructor.
QueryOptions(Boolean, Boolean, Boolean, Boolean, String, String) - 
Constructor for class net.sf.basedb.info.QueryOptions
Constructor where the parameters is set from start.
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.
QueryParameter - Class in net.sf.basedb.info
Hold information about a single parameter to a query.
QueryParameter() - 
Constructor for class net.sf.basedb.info.QueryParameter
Create a new empty query parameter.
QueryParameter(String, String, String) - 
Constructor for class net.sf.basedb.info.QueryParameter
Create a new query parameter.
QueryParameter(String, Integer) - 
Constructor for class net.sf.basedb.info.QueryParameter
Useful constructor to create a parmeter where the value is an integer.
QueryParameter(String, Float) - 
Constructor for class net.sf.basedb.info.QueryParameter
Useful constructor to create a parmeter where the value is a float.
QueryParameter(String, String) - 
Constructor for class net.sf.basedb.info.QueryParameter
Useful constructor to create a parmeter where the value is a string.
QueryParameters - Class in net.sf.basedb.util
Utiltity class for parsing string values in the form of 
        HTTP request query parameters:
        
        key1=value1&key2=value2...
QueryParameters(String) - 
Constructor for class net.sf.basedb.util.QueryParameters
 
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.AnnotatableFilter() - 
Constructor for class net.sf.basedb.core.QueryRuntimeFilterFactory.AnnotatableFilter
 
QueryRuntimeFilterFactory.BasicFilter - Class in net.sf.basedb.core
An optional default filter for BasicItem:s that are not
                Ownable or Shareable.
QueryRuntimeFilterFactory.BasicFilter() - 
Constructor for class net.sf.basedb.core.QueryRuntimeFilterFactory.BasicFilter
 
QueryRuntimeFilterFactory.ChainedFilter - Class in net.sf.basedb.core
Chains one or more filters into a single filter.
QueryRuntimeFilterFactory.ChainedFilter(List<QueryRuntimeFilter>) - 
Constructor for class net.sf.basedb.core.QueryRuntimeFilterFactory.ChainedFilter
Create a new ChainedFilter object.
QueryRuntimeFilterFactory.ChainedFilter(QueryRuntimeFilter...) - 
Constructor for class net.sf.basedb.core.QueryRuntimeFilterFactory.ChainedFilter
Create a new ChainedFilter object.
QueryRuntimeFilterFactory.ChildFilter - Class in net.sf.basedb.core
An optional filter that can be used by BasicItem:s to replace
                the QueryRuntimeFilterFactory.BasicFilter.
QueryRuntimeFilterFactory.ChildFilter(Item, Item) - 
Constructor for class net.sf.basedb.core.QueryRuntimeFilterFactory.ChildFilter
Create a new ChildFilter object.
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.DenyAllFilter() - 
Constructor for class net.sf.basedb.core.QueryRuntimeFilterFactory.DenyAllFilter
 
QueryRuntimeFilterFactory.OwnableFilter - Class in net.sf.basedb.core
An optional default filter for Ownable items that are not
                Shareable.
QueryRuntimeFilterFactory.OwnableFilter() - 
Constructor for class net.sf.basedb.core.QueryRuntimeFilterFactory.OwnableFilter
 
QueryRuntimeFilterFactory.RemovableFilter - Class in net.sf.basedb.core
A required filter for Removable items.
QueryRuntimeFilterFactory.RemovableFilter() - 
Constructor for class net.sf.basedb.core.QueryRuntimeFilterFactory.RemovableFilter
 
QueryRuntimeFilterFactory.ShareableFilter - Class in net.sf.basedb.core
An optional default filter for Shareable items.
QueryRuntimeFilterFactory.ShareableFilter() - 
Constructor for class net.sf.basedb.core.QueryRuntimeFilterFactory.ShareableFilter
 
QueryRuntimeFilterManager - Class in net.sf.basedb.core
This class manages the enabling/disabling of QueryRuntimeFilter:s.
QueryRuntimeFilterManager(DbControl) - 
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<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 - Class in net.sf.basedb.core.hibernate
A simple wrapper around hibernate queries which simply forwards 
        all calls to a parent query.
QueryWrapper(Query) - 
Constructor for class net.sf.basedb.core.hibernate.QueryWrapper
 
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.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.
Quota.QueryRuntimeFilterImpl() - 
Constructor for class net.sf.basedb.core.Quota.QueryRuntimeFilterImpl
 
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.
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 - 
Static variable in class net.sf.basedb.clients.web.util.HTML
 
quote(String) - 
Static method in class net.sf.basedb.core.HibernateUtil
Quote a string with the default quote type for the current database engine.



R

r - 
Variable in class net.sf.basedb.clients.web.util.AjaxWriter
Deprecated.  
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
 
ratio - 
Variable in class net.sf.basedb.plugins.MedianRatioNormalization.SpotData
 
raw - 
Static variable in class net.sf.basedb.core.ItemContext
 
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_DATA - 
Static variable in class net.sf.basedb.core.FileType
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.SpotImagesData
 
rawBioAssay - 
Variable in class net.sf.basedb.core.DynamicRawDataQuery
 
RawBioAssay - Class in net.sf.basedb.core
A rawbioassay represents the raw data generated from a single
        Scan.
RawBioAssay(RawBioAssayData) - 
Constructor for class net.sf.basedb.core.RawBioAssay
 
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_ID - 
Static variable in class net.sf.basedb.core.VirtualColumn
This column stores the id of a raw bioassay.
RawBioAssayClient - Class in net.sf.basedb.ws.client
Webservice client for RawBioAssay.
RawBioAssayClient(SessionClient) - 
Constructor for class net.sf.basedb.ws.client.RawBioAssayClient
Creates a new object for a session.
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
 
rawBioAssayData - 
Variable in class net.sf.basedb.core.RawDataBatcher
Just a copy of the data object for the raw bioassay.
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
 
RawBioAssayInfo - Class in net.sf.basedb.info
An information class that holds information about an 
        RawBioAssay in BASE.
RawBioAssayInfo() - 
Constructor for class net.sf.basedb.info.RawBioAssayInfo
Creates information object with 
                no properties set.
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
 
rawBioAssays - 
Variable in class net.sf.basedb.core.data.ExperimentData
 
rawBioAssays - 
Variable in class net.sf.basedb.core.data.ScanData
 
rawBioAssays - 
Variable in class net.sf.basedb.plugins.IlluminaRawDataImporter
 
rawBioAssays - 
Variable in class net.sf.basedb.plugins.RawDataFlatFileImporter.FileIterator
 
RawBioAssayService - Class in net.sf.basedb.ws.server
Web service class for 
        RawBioAssay
RawBioAssayService() - 
Constructor for class net.sf.basedb.ws.server.RawBioAssayService
 
rawBioAssaysParameter - 
Variable in class net.sf.basedb.plugins.IntensityCalculatorPlugin
 
rawBioAssaysType - 
Variable in class net.sf.basedb.plugins.IntensityCalculatorPlugin
 
RawBioAssayValidator - Class in net.sf.basedb.util.overview.validator
Validator implementation for raw bioassays.
RawBioAssayValidator() - 
Constructor for class net.sf.basedb.util.overview.validator.RawBioAssayValidator
 
rawCh - 
Static variable in class net.sf.basedb.core.ItemContext
 
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 - 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(String) - 
Static method in class net.sf.basedb.core.query.Dynamic
Create an expression representing a property of a raw data spot.
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(String, String, Formula.AverageMethod, Formatter<?>) - 
Static method in class net.sf.basedb.util.export.spotdata.ExportableFieldFactory
Deprecated. In 2.15, use ExportableFieldFactory.rawData(String, String, Type, net.sf.basedb.core.Formula.AverageMethod, Formatter)
                        instead
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 - 
Variable in class net.sf.basedb.util.jep.MeanFunction
 
rawData - 
Variable in class net.sf.basedb.util.jep.RawFunction
 
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
 
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
 
RawDataFlatFileImporter.FileIterator(List<RawBioAssay>, List<File>) - 
Constructor for class net.sf.basedb.plugins.RawDataFlatFileImporter.FileIterator
 
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
 
rawDataType - 
Variable in class net.sf.basedb.clients.web.formatter.SpotImageFormatter
 
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.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 - Class in net.sf.basedb.core
This class holds information about a raw data type.
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.
RawDataType(String, String, String, int, boolean, PlatformData, PlatformVariantData, boolean, String, List<RawDataProperty>, List<IntensityFormula>) - 
Constructor for class net.sf.basedb.core.RawDataType
 
rawDataType - 
Variable in class net.sf.basedb.util.jep.RawFunction
 
rawDataTypeColumnMapping - 
Static variable in class net.sf.basedb.plugins.batchimport.RawBioAssayImporter
 
rawDataTypeId - 
Variable in class net.sf.basedb.info.RawBioAssayInfo
 
rawDataTypeMapper - 
Variable in class net.sf.basedb.plugins.batchimport.RawBioAssayImporter
 
rawDataTypeParameter - 
Variable in class net.sf.basedb.plugins.RawDataFlatFileImporter
 
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 - 
Static variable in class net.sf.basedb.core.RawDataTypes
A map from raw data type name --> RawDataType.
RawDataTypes.NameComparator - Class in net.sf.basedb.core
Comparator implementation that sorts raw data types
                according to their name.
RawDataTypes.NameComparator() - 
Constructor for class net.sf.basedb.core.RawDataTypes.NameComparator
 
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.
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
 
rawSources - 
Variable in class net.sf.basedb.core.data.TransformationData
 
rba - 
Variable in class net.sf.basedb.plugins.IlluminaRawDataImporter.BatchAndMapHolder
 
read() - 
Method in class net.sf.basedb.clients.web.fileupload.FileUpload.UploadStream
 
read(byte[], int, int) - 
Method in class net.sf.basedb.clients.web.fileupload.FileUpload.UploadStream
 
read(byte[]) - 
Method in class net.sf.basedb.clients.web.fileupload.FileUpload.UploadStream
 
read - 
Static variable in class net.sf.basedb.core.Item.DefinedPermissions
 
read(InputStream) - 
Static method in class net.sf.basedb.util.FileUtil
Read from the input stream until the end is reached.
read(byte[], int, int) - 
Method in class net.sf.basedb.util.InputStreamCombiner
 
read(byte[]) - 
Method in class net.sf.basedb.util.InputStreamCombiner
 
read() - 
Method in class net.sf.basedb.util.InputStreamCombiner
 
read() - 
Method in class net.sf.basedb.util.InputStreamSplitter
 
read(byte[], int, int) - 
Method in class net.sf.basedb.util.InputStreamSplitter
 
read(byte[]) - 
Method in class net.sf.basedb.util.InputStreamSplitter
 
read() - 
Method in class net.sf.basedb.util.InputStreamTracker
 
read(byte[], int, int) - 
Method in class net.sf.basedb.util.InputStreamTracker
 
read(byte[]) - 
Method in class net.sf.basedb.util.InputStreamTracker
 
read(Socket, boolean) - 
Static method in class net.sf.basedb.util.SocketUtil
Read input from a socket.
read(String, OutputStream, int) - 
Method in class net.sf.basedb.util.StaticCache
Read binary information from the cache.
read(String, int) - 
Method in class net.sf.basedb.util.StaticCache
Get an input stream for reading binary information from the cache.
read() - 
Method in class net.sf.basedb.ws.server.TempFileDataSource.TempInputStream
 
read(byte[]) - 
Method in class net.sf.basedb.ws.server.TempFileDataSource.TempInputStream
 
read(byte[], int, int) - 
Method in class net.sf.basedb.ws.server.TempFileDataSource.TempInputStream
 
readData(DbControl, DynamicSpotQuery, BioAssay) - 
Method in class net.sf.basedb.plugins.LowessNormalization
 
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() - 
Method in class net.sf.basedb.util.StaticCache.LockEntry
 
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.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
 
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.
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.
RealJoin(JoinType, VirtualTable, RealTable, VirtualColumn) - 
Constructor for class net.sf.basedb.core.RealJoin
Create a new join to 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(BasicItem) - 
Method in class net.sf.basedb.core.DbControl
Deprecated. Use DbControl.reattachItem(BasicItem, boolean) instead
reattachItem(T, boolean) - 
Method in class net.sf.basedb.core.DbControl
Reattach a detached item from this DbControl.
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
Reconnects to the database after a DbControl.disconnect().
reconnect() - 
Method in class net.sf.basedb.core.hibernate.SessionWrapper
Deprecated. 
reconnect(Connection) - 
Method in class net.sf.basedb.core.hibernate.SessionWrapper
 
recordSeparator - 
Variable in class net.sf.basedb.clients.web.util.AjaxWriter
Deprecated.  
recursive - 
Variable in class net.sf.basedb.util.OlderThanFileFilter
 
redefinedColumnNames - 
Variable in class net.sf.basedb.util.basefile.BaseFileParser
 
redImageFile - 
Variable in class net.sf.basedb.core.data.SpotImagesData
 
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
 
refName - 
Variable in class net.sf.basedb.core.dbengine.TableInfo.ForeignKeyInfo
 
refresh(Object, LockMode) - 
Method in class net.sf.basedb.core.hibernate.SessionWrapper
Deprecated. 
refresh(Object, LockOptions) - 
Method in class net.sf.basedb.core.hibernate.SessionWrapper
 
refresh(Object) - 
Method in class net.sf.basedb.core.hibernate.SessionWrapper
 
refresh(Object, LockMode) - 
Method in class net.sf.basedb.core.hibernate.StatelessSessionWrapper
 
refresh(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) - 
Method in class net.sf.basedb.core.hibernate.StatelessSessionWrapper
 
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.
refreshSession(String) - 
Method in class net.sf.basedb.ws.client.SessionClient
Refresh a session to prevent a timeout.
refreshSession(String) - 
Method in class net.sf.basedb.ws.server.SessionService
Refresh a session so the time for logging out will be reset.
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.
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<? extends NodeValidator<? extends BasicItem>>) - 
Method in class net.sf.basedb.util.overview.validator.BasicItemNodeValidatorFactory
Register a node loader implementation that you are sure fulfills the
                requirements.
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.
Registered - Interface in net.sf.basedb.core
Items that implements this interface has their registration
        date stored in the database.
RegisteredData - Interface in net.sf.basedb.core.data
Adds the date an item was registered in the database.
registerEditTab(Registry, String, String) - 
Static method in class net.sf.basedb.clients.web.extensions.edit.EditUtil
 
registerEventHandler(EventHandler, EventFilter) - 
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>) - 
Method in class net.sf.basedb.util.extensions.Registry
Register an extension.
registerExtensionPoint(ExtensionPoint<A>) - 
Method in class net.sf.basedb.util.extensions.Registry
Register an extension point.
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, boolean) - 
Method in class net.sf.basedb.clients.web.extensions.ExtensionsFile
Register all extension points with a registry.
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(Registry, boolean, ScanResults) - 
Method in class net.sf.basedb.clients.web.extensions.ExtensionsDirectory
Register extensions with the registry.
registerExtensions(Registry, boolean) - 
Method in class net.sf.basedb.clients.web.extensions.ExtensionsFile
Register all extensions with a registry.
registerExtensions(Registry, boolean) - 
Method in class net.sf.basedb.util.extensions.xml.XmlLoader
Register all loaded extensions with a registry.
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
 
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.
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 - 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.AttributeKey(String, String) - 
Constructor for class net.sf.basedb.util.extensions.Registry.AttributeKey
 
Registry.RegisteredAbout - Class in net.sf.basedb.util.extensions
 
Registry.RegisteredAbout(About) - 
Constructor for class net.sf.basedb.util.extensions.Registry.RegisteredAbout
Create a new registered about by copying the
                        information from the parameter.
Registry.RegisteredExtension<A extends Action> - Class in net.sf.basedb.util.extensions
Internal representation of an extension.
Registry.RegisteredExtension(Extension<A>, Registry.RegisteredExtensionPoint<? super A>) - 
Constructor for class net.sf.basedb.util.extensions.Registry.RegisteredExtension
Create a new registered extension by copying the
                        information from the parameter.
Registry.RegisteredExtensionPoint<A extends Action> - Class in net.sf.basedb.util.extensions
Internal representation of an extension point.
Registry.RegisteredExtensionPoint(ExtensionPoint<A>) - 
Constructor for class net.sf.basedb.util.extensions.Registry.RegisteredExtensionPoint
Create a new registered extension point by copying the
                        information from the parameter.
releaseRemoteSlot(String) - 
Method in class net.sf.basedb.clients.jobagent.slotmanager.MasterSlotManager
Release the remote slot with the given id.
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.
remainingQuantity - 
Variable in class net.sf.basedb.core.data.MeasuredBioMaterialData
 
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
 
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.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
 
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.
RemoteSlotManager.RemoteSlotPinger(RemoteSlotManager) - 
Constructor for class net.sf.basedb.clients.jobagent.slotmanager.RemoteSlotManager.RemoteSlotPinger
 
remoteSlots - 
Variable in class net.sf.basedb.clients.jobagent.slotmanager.MasterSlotManager
 
remoteSlots - 
Variable in class net.sf.basedb.clients.jobagent.slotmanager.RemoteSlotManager
 
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.
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() - 
Method in class net.sf.basedb.clients.web.servlet.PlotServlet.CFResultIterator
Not supported.
remove(int) - 
Method in class net.sf.basedb.core.AbstractResultList
Not supported.
remove(Object) - 
Method in class net.sf.basedb.core.AbstractResultList
Not supported.
remove(BioMaterial) - 
Method in class net.sf.basedb.core.BioMaterialList
Remove a biomaterial from the list.
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(int) - 
Method in class net.sf.basedb.core.UnmodifiableResultList
Not supported.
remove(Object) - 
Method in class net.sf.basedb.core.UnmodifiableResultList
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(int) - 
Method in class net.sf.basedb.util.Enumeration
 
remove() - 
Method in class net.sf.basedb.util.extensions.ActionIterator
Not supported.
remove(Object) - 
Method in class net.sf.basedb.util.formatter.LookupFormatter
Remove an entry from the lookup map.
remove() - 
Method in class net.sf.basedb.util.NestedIterator
This operation is not supported.
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(Object) - 
Method in class net.sf.basedb.util.Tree
Not supported.
removeAll(Collection<?>) - 
Method in class net.sf.basedb.core.AbstractResultList
Not supported.
removeAll(BioMaterialList) - 
Method in class net.sf.basedb.core.BioMaterialList
Remove all items from this list that are present
                in the other list.
removeAll(ReporterList) - 
Method in class net.sf.basedb.core.ReporterList
Remove all reporters from this list that are present
                in the other list.
removeAll(Collection<?>) - 
Method in class net.sf.basedb.core.UnmodifiableResultList
Not supported.
removeAll(Collection<?>) - 
Method in class net.sf.basedb.util.Tree
Not supported.
removeAllMembers() - 
Method in class net.sf.basedb.core.FileSet
Remove all members in a file set.
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 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.Well
 
removeAnyToAnyLinkedTo(DbControl, ItemQuery<AnyToAny>, boolean) - 
Static method in class net.sf.basedb.util.RemovableUtil
 
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.
removed - 
Variable in class net.sf.basedb.core.data.BioAssaySetData
 
removed - 
Variable in class net.sf.basedb.core.data.BioPlateEventTypeData
 
removed - 
Variable in class net.sf.basedb.core.data.BioPlateTypeData
 
removed - 
Variable in class net.sf.basedb.core.data.CommonData
 
removed - 
Variable in class net.sf.basedb.core.data.DataFileTypeData
 
removed - 
Variable in class net.sf.basedb.core.data.ExtraValueTypeData
 
removed - 
Variable in class net.sf.basedb.core.data.GroupData
 
removed - 
Variable in class net.sf.basedb.core.data.HardwareTypeData
 
removed - 
Variable in class net.sf.basedb.core.data.ImageData
 
removed - 
Variable in class net.sf.basedb.core.data.JobData
 
removed - 
Variable in class net.sf.basedb.core.data.MessageData
 
removed - 
Variable in class net.sf.basedb.core.data.MimeTypeData
 
removed - 
Variable in class net.sf.basedb.core.data.NewsData
 
removed - 
Variable in class net.sf.basedb.core.data.PlateEventTypeData
 
removed - 
Variable in class net.sf.basedb.core.data.PlateGeometryData
 
removed - 
Variable in class net.sf.basedb.core.data.PlatformData
 
removed - 
Variable in class net.sf.basedb.core.data.PlatformVariantData
 
removed - 
Variable in class net.sf.basedb.core.data.PluginDefinitionData
 
removed - 
Variable in class net.sf.basedb.core.data.PluginTypeData
 
removed - 
Variable in class net.sf.basedb.core.data.ProjectData
 
removed - 
Variable in class net.sf.basedb.core.data.ProtocolTypeData
 
removed - 
Variable in class net.sf.basedb.core.data.QuantityData
 
removed - 
Variable in class net.sf.basedb.core.data.QuotaData
 
removed - 
Variable in class net.sf.basedb.core.data.ReporterTypeData
 
removed - 
Variable in class net.sf.basedb.core.data.RoleData
 
removed - 
Variable in class net.sf.basedb.core.data.TransformationData
 
removed - 
Variable in class net.sf.basedb.core.data.UnitData
 
removed - 
Variable in class net.sf.basedb.core.data.UserData
 
removed - 
Variable in class net.sf.basedb.plugins.Base1PluginExecuter.JobParameter
 
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.
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.
removeFileType(DataFileType) - 
Method in class net.sf.basedb.core.PlatformVariant
Remove a file type from this platform variant.
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<BioMaterialList>) - 
Method in class net.sf.basedb.core.BioMaterialList
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.clients.web.extensions.ExtensionsDirectory
Remove a file from the ignore list.
removeInheritedAnnotation(Annotation) - 
Method in class net.sf.basedb.core.AnnotationSet
Remove an inherited an annotation.
removeInheritedAnnotationSet(AnnotationSet) - 
Method in class net.sf.basedb.core.AnnotationSet
Remove an inherited an annotation set.
removeIntersection(Collection<BioMaterialList>) - 
Method in class net.sf.basedb.core.BioMaterialList
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.
removeJobWhenFinished - 
Variable in class net.sf.basedb.core.data.JobData
 
removeMember(DataFileType) - 
Method in class net.sf.basedb.core.FileSet
Remove the member of the given type.
removeMembers(Set<BioMaterialData>) - 
Method in class net.sf.basedb.core.BioMaterialList
Remove members from this list
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.
removeParticipant(BioPlate) - 
Method in class net.sf.basedb.core.BioPlateEvent
Remove the given bioplate from this event.
removePropertyFilter(String) - 
Method in class net.sf.basedb.core.ItemContext
Remove a property filter.
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.
removeRegistered(String, ExtensionsFile) - 
Method in class net.sf.basedb.clients.web.extensions.ExtensionsDirectory
 
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
 
removeResources() - 
Method in class net.sf.basedb.clients.web.extensions.ExtensionsFile
Remove all extracted resources.
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.
removeSource(MeasuredBioMaterial) - 
Method in class net.sf.basedb.core.BioMaterialEvent
Remove a biomaterial used as a source.
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.
removeUnion(Collection<BioMaterialList>) - 
Method in class net.sf.basedb.core.BioMaterialList
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(A) - 
Method in class net.sf.basedb.clients.web.extensions.renderer.PrefixSuffixRenderer
 
render(ServiceControllerAction) - 
Method in class net.sf.basedb.clients.web.extensions.service.StartServiceRenderer
Calls ServiceControllerAction.start() on the service.
render(ServiceControllerAction) - 
Method in class net.sf.basedb.clients.web.extensions.service.StopServiceRenderer
Calls ServiceControllerAction.stop() on the service.
render(ButtonAction) - 
Method in class net.sf.basedb.clients.web.extensions.toolbar.CompactButtonRenderer
Generates a linked icon: 
                


                If the button isn't visible nothing is generated.
render(ButtonAction) - 
Method in class net.sf.basedb.clients.web.extensions.toolbar.ToolbarButtonRenderer
Generates a toolbar button.
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
 
render(TabAction) - 
Method in class net.sf.basedb.clients.web.taglib.tab.TabControl
 
render(Renderer<A>) - 
Method in class net.sf.basedb.util.extensions.ExtensionsInvoker
Render all actions using a specific renderer.
render(A) - 
Method in interface net.sf.basedb.util.extensions.Renderer
Render the action in the client application.
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.
rep - 
Static variable in class net.sf.basedb.core.ItemContext
 
rep - 
Variable in class net.sf.basedb.util.extensions.Registry.RegisteredExtension
 
REPLACE_VALUE - 
Static variable in class net.sf.basedb.core.ExtendedPropertyLinker
 
replaceExisting - 
Variable in class net.sf.basedb.plugins.AnnotationFlatFileImporter
 
replaceExistingParameter - 
Static variable in class net.sf.basedb.plugins.AnnotationFlatFileImporter
 
replaceValues(List<?>) - 
Method in class net.sf.basedb.core.data.DateParameterValueData
Overrides the parent method since we want to get rid of the
                time part of the date.
replaceValues(List<?>) - 
Method in class net.sf.basedb.core.data.ParameterValueData
Replace the values in the database with the new
                values in the specified list.
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 - 
Static variable in class net.sf.basedb.core.FileType
The id for the FileType item representing a
                reporter file.
reporter(String) - 
Static method in class net.sf.basedb.core.query.Dynamic
Create an expression representing a property of a reporter.
Reporter - Class in net.sf.basedb.core
This is an utilitiy class for reporters.
Reporter() - 
Constructor for class net.sf.basedb.core.Reporter
 
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(String, String, Formula.AverageMethod, Formatter<?>) - 
Static method in class net.sf.basedb.util.export.spotdata.ExportableFieldFactory
Deprecated. In 2.15, use ExportableFieldFactory.reporter(String, String, Type, net.sf.basedb.core.Formula.AverageMethod, Formatter)
                        instead
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 - 
Variable in class net.sf.basedb.util.jep.ReporterFunction
 
REPORTER_ID - 
Static variable in class net.sf.basedb.core.VirtualColumn
This column stores the id of a reporter.
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.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.FileType
The id for the FileType item representing a
                reporter map file.
ReporterBatcher - Class in net.sf.basedb.core
Batcher class for reporters.
ReporterBatcher(DbControl) - 
Constructor for class net.sf.basedb.core.ReporterBatcher
 
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
 
reporterCache - 
Variable in class net.sf.basedb.util.export.spotdata.AbstractBioAssaySetExporter
 
ReporterClient - Class in net.sf.basedb.ws.client
Web service client for reporter.
ReporterClient(SessionClient) - 
Constructor for class net.sf.basedb.ws.client.ReporterClient
Creates a new instance of ReporterClient used together with a SessionClient
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(String, String, Type, Formula.AverageMethod) - 
Method in class net.sf.basedb.plugins.BaseFileExporterPlugin
 
reporterField - 
Variable in class net.sf.basedb.plugins.BfsExporterPlugin.ExtendedExportableField
 
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) function to a 
        JEP expression parser.
ReporterFunction() - 
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
 
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
 
reporterList - 
Variable in class net.sf.basedb.core.data.ReporterListScoreData
 
reporterList - 
Variable in class net.sf.basedb.core.query.ReporterListExpression
 
ReporterList - Class in net.sf.basedb.core
 
ReporterList(ReporterListData) - 
Constructor for class net.sf.basedb.core.ReporterList
 
reporterList - 
Variable in class net.sf.basedb.core.ReporterListJoin
 
reporterList - 
Variable in class net.sf.basedb.plugins.ReporterFlatFileImporter
 
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, JoinType) - 
Constructor for class net.sf.basedb.core.query.ReporterListExpression
Create a new expression for the specified reporter list.
ReporterListExpression(ReporterList, String, String, String, JoinType) - 
Constructor for class net.sf.basedb.core.query.ReporterListExpression
 
ReporterListInfo - Class in net.sf.basedb.info
Info class to hold information about 
        ReporterList object.
ReporterListInfo() - 
Constructor for class net.sf.basedb.info.ReporterListInfo
 
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) - 
Constructor for class net.sf.basedb.core.ReporterListJoin
Create a new join using the root entity table as the left table.
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
 
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
 
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
 
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(DbControl, 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
 
ReporterService - Class in net.sf.basedb.ws.server
Services for Reporters in Base.
ReporterService() - 
Constructor for class net.sf.basedb.ws.server.ReporterService
Empty constructor
reporterType - 
Variable in class net.sf.basedb.core.data.ReporterData
 
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 - 
Variable in class net.sf.basedb.plugins.ReporterFlatFileImporter
 
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
 
request - 
Variable in class net.sf.basedb.core.plugin.ParameterValuesWrapper
 
Request - Interface in net.sf.basedb.core.plugin
Pass request information to a plugin.
request - 
Variable in class net.sf.basedb.core.PluginResponse
 
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.
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
 
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(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.PlatformFileTypeData
 
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.RawDataFlatFileImporter
 
requiredColumnMapping - 
Static variable in class net.sf.basedb.plugins.ReporterFlatFileImporter
 
requiredColumnMapping - 
Static variable in class net.sf.basedb.plugins.ReporterMapFlatFileImporter
 
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
 
requiredForMiame - 
Variable in class net.sf.basedb.info.AnnotationTypeInfo
 
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
 
requiresConfiguration() - 
Method in class net.sf.basedb.clients.web.plugins.SimpleExport
 
requiresConfiguration - 
Variable in class net.sf.basedb.core.data.PluginDefinitionData
 
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.BfsExporterPlugin
 
requiresConfiguration() - 
Method in class net.sf.basedb.plugins.BioAssaySetExporter
Deprecated.  
requiresConfiguration() - 
Method in class net.sf.basedb.plugins.CdfFileReporterImporter
 
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.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.plugins.SpotImageCreator
 
requiresConfiguration() - 
Method in class net.sf.basedb.util.zip.AbstractFileUnpacker
Returns FALSE.
rescaleColors(RenderedOp, boolean, boolean, boolean) - 
Method in class net.sf.basedb.core.SpotImages
Rescale the colors of the images so we use the whole 16-bit color range.
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.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(Response.Status) - 
Method in class net.sf.basedb.core.PluginResponse
 
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.InputStreamSplitter
 
reset() - 
Method in class net.sf.basedb.util.InputStreamTracker
 
reset(DbControl) - 
Method in class net.sf.basedb.util.overview.ExperimentOverview
Deprecated. Reset the overview, regenerate the entire structure and revalidate
                everything.
reset(DbControl) - 
Method in class net.sf.basedb.util.overview.GenericOverview
Reset the overview and re-create the root node.
reset(int) - 
Method in class net.sf.basedb.util.timer.PerformanceTimer
Reset a timer.
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.
resetIgnore() - 
Method in class net.sf.basedb.clients.web.extensions.ExtensionsDirectory
Clears all files that has been added to the 
                ExtensionsDirectory.ignore set.
resetMetadata(DbControl) - 
Method in class net.sf.basedb.core.filehandler.CdfFileHandler
Reset ArrayDesign.getNumFileFeatures() to 0.
resetMetadata(DbControl) - 
Method in class net.sf.basedb.core.filehandler.CelFileHandler
Reset the number of file spots to 0, and remove all headers.
resetMetadata(DbControl) - 
Method in interface net.sf.basedb.core.filehandler.DataFileMetadataReader
Reset all metadata that this class normally can set.
resetMetadata(DbControl) - 
Method in class net.sf.basedb.core.FileSet.DataFileHandlerWrapper
 
resetModified() - 
Method in class net.sf.basedb.clients.web.extensions.ExtensionsFile
Resets the remembered timestamp and size attributes of the file.
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.XMLUtil.Validator
This method is called when the parser wants a reference to the
                        DTD file.
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.
resourcesDir - 
Variable in class net.sf.basedb.clients.web.extensions.ExtensionsDirectory
 
resourcesDir - 
Variable in class net.sf.basedb.clients.web.extensions.ExtensionsFile
 
resourcesUrl - 
Variable in class net.sf.basedb.clients.web.extensions.ExtensionsDirectory
 
response - 
Variable in class net.sf.basedb.clients.web.util.ServletExportOutputStream
 
Response - Interface in net.sf.basedb.core.plugin
The response interface used by the core.
response - 
Variable in class net.sf.basedb.core.PluginResponse
 
Response.Status - Enum in net.sf.basedb.core.plugin
 
Response.Status(boolean) - 
Constructor for enum net.sf.basedb.core.plugin.Response.Status
 
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.
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.
restriction - 
Variable in class net.sf.basedb.info.QueryOptions
A restriction to set on
                the query.
restrictions - 
Variable in class net.sf.basedb.core.AbstractQuery
List of restrictions added to the query.
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
 
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
result - 
Variable in class net.sf.basedb.core.hibernate.ResultSetWork
 
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.
results - 
Variable in class net.sf.basedb.core.DynamicResultIterator
The results of the query.
results - 
Variable in class net.sf.basedb.core.ScrollIterator
 
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.
retainAll(Collection<?>) - 
Method in class net.sf.basedb.core.AbstractResultList
Not supported.
retainAll(BioMaterialList) - 
Method in class net.sf.basedb.core.BioMaterialList
Remove all items from this list that are NOT present
                in the other list.
retainAll(ReporterList) - 
Method in class net.sf.basedb.core.ReporterList
Remove all reporters from this list that are NOT present
                in the other list.
retainAll(Collection<?>) - 
Method in class net.sf.basedb.core.UnmodifiableResultList
Not supported.
retainAll(Collection<?>) - 
Method in class net.sf.basedb.util.Tree
Not supported.
retainIfPresentIn(int, int, Collection<BioMaterialList>) - 
Method in class net.sf.basedb.core.BioMaterialList
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<BioMaterialList>) - 
Method in class net.sf.basedb.core.BioMaterialList
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<BioMaterialData>) - 
Method in class net.sf.basedb.core.BioMaterialList
Keep only specified members in this list
retainReporters(Set<Integer>) - 
Method in class net.sf.basedb.core.ReporterList
 
retainUnion(Collection<BioMaterialList>) - 
Method in class net.sf.basedb.core.BioMaterialList
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) - 
Method in class net.sf.basedb.core.Job
Deprecated. Use Job.retry(boolean, boolean) instead
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.
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.
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
 
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.
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.
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
 
robotQuery - 
Variable in class net.sf.basedb.plugins.batchimport.AbstractItemImporter
 
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.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.
Role.QueryRuntimeFilterImpl() - 
Constructor for class net.sf.basedb.core.Role.QueryRuntimeFilterImpl
 
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
 
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 - 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.
roleKeys - 
Static variable in class net.sf.basedb.core.SystemItems
An array to hold mappings for RoleKeyData:
                RoleKeyData.itemType --> RoleKeyData.id
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.
root - 
Variable in class net.sf.basedb.clients.web.formatter.SpotImageFormatter
 
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 - 
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
 
rootAlias - 
Variable in class net.sf.basedb.core.AbstractHqlQuery
The alias for the root table.
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.ExperimentOverview
Deprecated.  
rootNode - 
Variable in class net.sf.basedb.util.overview.GenericOverview
 
rootTable - 
Variable in class net.sf.basedb.core.DynamicQuery
 
rootTable - 
Variable in class net.sf.basedb.core.DynamicRawDataQuery
 
rootTable - 
Variable in class net.sf.basedb.core.DynamicReporterQuery
 
rootType - 
Variable in class net.sf.basedb.core.AbstractEntityQuery
The root item type we start with in the query. eq.
rootUrl - 
Variable in class net.sf.basedb.clients.web.extensions.ExtensionsDirectory
 
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
 
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.
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
 
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
 
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
 
rows - 
Variable in class net.sf.basedb.core.data.PlateGeometryData
 
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
 
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
 
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.clients.web.extensions.ExtensionsControl.AutoInstallTask
 
run() - 
Method in class net.sf.basedb.core.Application.DbCleaner
 
run() - 
Method in class net.sf.basedb.core.Application.SecondaryStorageControllerTask
 
run() - 
Method in class net.sf.basedb.core.Application.SessionControlCacheCleaner
 
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.InternalStorageController
Check the database for files for waiting to be moved.
run() - 
Method in class net.sf.basedb.core.Keyring.ReloadTask
 
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() - 
Method in class net.sf.basedb.core.PluginExecutionRequest
 
run() - 
Method in interface net.sf.basedb.core.SecondaryStorageController
Run the storage controller.
run() - 
Method in class net.sf.basedb.core.signal.SocketSignalReceiver.ListenerThread
 
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.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.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.plugins.SpotImageCreator
 
run() - 
Method in class net.sf.basedb.util.FileCopyRunnable
 
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.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() - 
Method in class net.sf.basedb.util.jobagent.JobAgentServerConnection.ListenerThread
 
run() - 
Method in class net.sf.basedb.util.jobagent.JobAgentServerConnection.RequestHandlerThread
 
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.LineNoFunction
 
run() - 
Method in class net.sf.basedb.util.StaticCache.CleanupTask
 
run() - 
Method in class net.sf.basedb.util.timer.ThreadTimerTask
 
run(Request, Response, ProgressReporter) - 
Method in class net.sf.basedb.util.zip.AbstractFileUnpacker
 
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.
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.Annotation
This filter gives everybody read permission to annotations.
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.Image
This filter will only return items if the logged in user has
                generic read permission to scans.
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.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.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.
rwLock - 
Variable in class net.sf.basedb.util.StaticCache.LockEntry
 



S

s - 
Variable in class net.sf.basedb.core.QueryExecutor.CancelableStatement
 
SAFE_TAGS - 
Static variable in class net.sf.basedb.clients.web.util.HTML
This pattern is a list of HTML tags considered "safe".
safeToDrop(TableInfo.IndexInfo) - 
Method in class net.sf.basedb.core.dbengine.TableInfo
It is safe to drop an index if it is not a foreign key, a primary key
                index or a unique column.
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
 
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
 
SampleToBioSourceTransformer - Class in net.sf.basedb.util.biomaterial
Collection transformer that given a collection of samples finds
        their parent biosources.
SampleToBioSourceTransformer(DbControl) - 
Constructor for class net.sf.basedb.util.biomaterial.SampleToBioSourceTransformer
 
SampleToExtractTransformer - Class in net.sf.basedb.util.biomaterial
Collection transformer that given a collection of samples finds
        child extracts which has the samples as parents.
SampleToExtractTransformer(DbControl) - 
Constructor for class net.sf.basedb.util.biomaterial.SampleToExtractTransformer
Create a new Sample-to-extract transformer.
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.ProtocolType
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.clients.web.extensions.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.
saveIfQueue - 
Variable in class net.sf.basedb.core.DbControl
Lists items that are saved only if the parent item is also saved.
saveImage(ZipOutputStream, String, RenderedImage, float) - 
Method in class net.sf.basedb.core.SpotImages
Saving an image as jpeg and putting it in a zip file
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(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
 
saveParameters(DbControl, GuiContext) - 
Method in class net.sf.basedb.core.PluginRequest
Save all parameters that have got values in this request/response session.
saveParameters(DbControl) - 
Method in class net.sf.basedb.core.PluginResponse
Save all parameters that has been configured during the configuration sequence to
                the database.
saveSettings() - 
Method in class net.sf.basedb.clients.web.extensions.ExtensionsControl
Save the settings.
saveSettings(Session, Query, Map<String, SessionControl.SettingInfo>, Class<I>, UserData, ClientData) - 
Method in class net.sf.basedb.core.SessionControl
Save settings when a user logs out.
saveTo - 
Variable in class net.sf.basedb.core.plugin.AbstractExporterPlugin
 
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.ExperimentOverview
Deprecated. In 2.10, use OverviewUtil.saveValidationPresets(SessionControl) instead
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.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.InternalStorageController
The 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.extensions.ClientContext
 
scale - 
Variable in class net.sf.basedb.util.ChainedProgressReporter
 
scan - 
Variable in class net.sf.basedb.core.data.ImageData
 
scan - 
Variable in class net.sf.basedb.core.data.RawBioAssayData
 
Scan - Class in net.sf.basedb.core
A scan represents the scanning of a Hybridization by
        some scanner.
Scan(ScanData) - 
Constructor for class net.sf.basedb.core.Scan
 
scan - 
Variable in class net.sf.basedb.plugins.IlluminaRawDataImporter
 
scanColumnMapping - 
Static variable in class net.sf.basedb.plugins.batchimport.RawBioAssayImporter
 
ScanData - Class in net.sf.basedb.core.data
This class holds information about an scan.
ScanData() - 
Constructor for class net.sf.basedb.core.data.ScanData
 
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, 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, 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.
scanForNewAndUpdated(boolean, ScanResults) - 
Method in class net.sf.basedb.clients.web.extensions.ExtensionsDirectory
Scan for new extensions.
ScanImporter - Class in net.sf.basedb.plugins.batchimport
Plug-in for importing scan items in a batch.
ScanImporter() - 
Constructor for class net.sf.basedb.plugins.batchimport.ScanImporter
 
ScanLoader - Class in net.sf.basedb.util.overview.loader
Node loader implementation for scans.
ScanLoader() - 
Constructor for class net.sf.basedb.util.overview.loader.ScanLoader
 
scanMapper - 
Variable in class net.sf.basedb.plugins.batchimport.RawBioAssayImporter
 
scanner - 
Variable in class net.sf.basedb.core.data.ScanData
 
SCANNER - 
Static variable in class net.sf.basedb.core.HardwareType
The id for the HardwareType object representing a
                scanner.
scannerHasBeenSet - 
Variable in class net.sf.basedb.core.Scan
 
scannerQuery - 
Variable in class net.sf.basedb.plugins.batchimport.AbstractItemImporter
 
SCANNING - 
Static variable in class net.sf.basedb.core.ProtocolType
The ID for the scanning protocol type, for example a protocol
                used for scanning the microarray slide after an experiment.
scanQuery - 
Variable in class net.sf.basedb.plugins.batchimport.AbstractItemImporter
 
ScanResults - Class in net.sf.basedb.clients.web.extensions
Holds information about the results of a scan for new/deleted/updated
        extensions.
ScanResults(boolean, boolean) - 
Constructor for class net.sf.basedb.clients.web.extensions.ScanResults
Create a new scan results object.
ScanResults.FileResults - Class in net.sf.basedb.clients.web.extensions
Scan results for a single XML or JAR file.
ScanResults.FileResults() - 
Constructor for class net.sf.basedb.clients.web.extensions.ScanResults.FileResults
 
scans - 
Variable in class net.sf.basedb.core.data.HybridizationData
 
ScanValidator - Class in net.sf.basedb.util.overview.validator
Validator implementation for scans.
ScanValidator() - 
Constructor for class net.sf.basedb.util.overview.validator.ScanValidator
 
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.
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
 
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
 
scheduleAtFixedRate(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
 
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.TableExistsWork
 
schema - 
Variable in class net.sf.basedb.info.VersionInfo
 
schemaFileURL - 
Static variable in class net.sf.basedb.clients.web.extensions.ServletLoader
The URL pointing to the servlets.xsd schema.
schemaFileURL - 
Static variable in class net.sf.basedb.util.extensions.xml.XmlLoader
The URL pointing to the extensions.xsd schema.
SchemaGenerator - Class in net.sf.basedb.core.hibernate
Replaces the Hibernate SchemaExport and SchemaUpdate tools.
SchemaGenerator(Configuration, Dialect, DbEngine, boolean, ProgressReporter) - 
Constructor for class net.sf.basedb.core.hibernate.SchemaGenerator
Create a new schema generator.
schemaVersion - 
Variable in class net.sf.basedb.core.data.SchemaVersionData
 
schemaVersion - 
Static variable in class net.sf.basedb.core.Install
 
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(ReporterList) - 
Static method in class net.sf.basedb.core.query.Dynamic
 
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.
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
 
script - 
Variable in class net.sf.basedb.clients.web.taglib.tab.TabControl
JavaScript for initialising the tabcontrol
script - 
Variable in class net.sf.basedb.clients.web.taglib.table.Table
 
scripts - 
Variable in class net.sf.basedb.clients.web.extensions.AbstractJspFactory
 
scripts - 
Variable in class net.sf.basedb.clients.web.extensions.JspContext
 
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
 
scripts - 
Variable in class net.sf.basedb.clients.web.taglib.Head
A comma-separated list of JavaScript filenames.
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(Class<E>, ScrollableResults) - 
Constructor for class net.sf.basedb.core.ScrollIterator
 
searchMapping - 
Variable in class net.sf.basedb.plugins.AnnotationFlatFileImporter
 
searchParameterType - 
Variable in class net.sf.basedb.plugins.AnnotationFlatFileImporter
 
searchProperty - 
Variable in class net.sf.basedb.plugins.AnnotationFlatFileImporter
 
secondaryLocation - 
Variable in class net.sf.basedb.core.data.QuotaTypeData
 
SecondaryStorageController - Interface in net.sf.basedb.core
This interface defines the methods that needs to be implemented 
        by a class to be able to use it as a controller for seconday storage.
secondaryStorageDriver - 
Static variable in class net.sf.basedb.core.Application
The name of the secondary storage controller class, if any.
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.plugins.PrintMapFlatFileImporter
 
SECTION - 
Static variable in class net.sf.basedb.util.importer.spotdata.FirstPassSectionSpotsParser
The section of the BASEfile this parser can parse, eg.
section - 
Variable in class net.sf.basedb.util.parser.FlatFileParser
The regular expression for matching the fist line of a section.
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.
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.
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
 
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
 
Select - Class in net.sf.basedb.clients.web.taglib
This tag is used to display a selection list of items.
Select() - 
Constructor for class net.sf.basedb.clients.web.taglib.Select
 
select(Select) - 
Method in class net.sf.basedb.core.AbstractEntityQuery
Not supported.
select(Select) - 
Method in class net.sf.basedb.core.AbstractQuery
 
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(ExtraValue, String) - 
Static method in class net.sf.basedb.core.query.Dynamic
Select an extra value.
select(Select) - 
Method in interface net.sf.basedb.core.query.Query
Add a selection query element to the selection list.
Select - Interface in net.sf.basedb.core.query
A selection query element.
select - 
Variable in class net.sf.basedb.core.query.SelectedExpression
 
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
 
selectedProperties - 
Variable in class net.sf.basedb.clients.web.DynamicUtil.SelectedInfo
 
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.
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.
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, BufferedWriter, BufferedReader) - 
Method in class net.sf.basedb.core.authentication.POP3Authenticator
Send cmd to the out buffer.
send(Signal) - 
Method in class net.sf.basedb.core.Job.JobSignalTransporter
 
send(String, Signal) - 
Method in class net.sf.basedb.core.signal.LocalSignalReceiver
Send the signal to a registered handler.
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.
send(String) - 
Method in class net.sf.basedb.util.jobagent.JobAgentConnection
Send a remote control command to the job agent.
send(Socket, String, boolean) - 
Static method in class net.sf.basedb.util.SocketUtil
Send output to a socket.
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.
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.
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(Signal) - 
Method in class net.sf.basedb.clients.web.util.SimpleSignalProgressReporter
Deprecated. 
sendToAll(SignalSender) - 
Method in class net.sf.basedb.clients.web.util.SimpleSignalProgressReporter
 
sendToAll(Signal) - 
Method in class net.sf.basedb.core.signal.AbstractSignalReceiver
Deprecated. In 2.16, use AbstractSignalReceiver.sendToAll(SignalSender) instead
sendToAll(SignalSender) - 
Method in class net.sf.basedb.core.signal.AbstractSignalReceiver
 
sendToAll(Signal) - 
Method in interface net.sf.basedb.core.signal.SignalReceiver
Deprecated. In 2.16, use SignalReceiver.sendToAll(SignalSender) instead
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
 
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.
SERIAL_BASEFILE - 
Static variable in class net.sf.basedb.ws.server.BioAssaySetService
 
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.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.servlet.ViewSpotImage
 
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.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.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.Note
 
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.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.Columns
 
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.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.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 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.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.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.UsedQuantity
 
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.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.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.info.AnnotationInfo
 
serialVersionUID - 
Static variable in class net.sf.basedb.info.AnnotationTypeInfo
 
serialVersionUID - 
Static variable in class net.sf.basedb.info.ArrayDesignInfo
 
serialVersionUID - 
Static variable in class net.sf.basedb.info.BioAssaySetInfo
 
serialVersionUID - 
Static variable in class net.sf.basedb.info.DataFileTypeInfo
 
serialVersionUID - 
Static variable in class net.sf.basedb.info.ExperimentInfo
 
serialVersionUID - 
Static variable in class net.sf.basedb.info.ExtendedPropertyInfo
 
serialVersionUID - 
Static variable in class net.sf.basedb.info.ProjectInfo
 
serialVersionUID - 
Static variable in class net.sf.basedb.info.RawBioAssayInfo
 
serialVersionUID - 
Static variable in class net.sf.basedb.info.ReporterListInfo
 
serialVersionUID - 
Static variable in class net.sf.basedb.info.VersionInfo
 
serialVersionUID - 
Static variable in class net.sf.basedb.plugins.BioAssaySetExporter.QueryItemTitleComparator
Deprecated.  
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
 
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(HttpServletRequest, HttpServletResponse) - 
Method in class net.sf.basedb.clients.web.extensions.ServletWrapper
Service a request to the wrapped servlet.
service - 
Static variable in class net.sf.basedb.core.QueryExecutor
 
ServiceControllerAction - Interface in net.sf.basedb.clients.web.extensions.service
Action for controlling services installed under the extensions system.
serviceFactory - 
Variable in class net.sf.basedb.ws.client.AbstractRPCClient
 
serviceFactory - 
Static variable in class net.sf.basedb.ws.client.Factories
 
ServiceFactory - Interface in net.sf.basedb.ws.client
Interface that should be implemented by classes that can
        create RPCServiceClient objects.
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
 
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(Settings) - 
Constructor for class net.sf.basedb.clients.web.extensions.service.ServicesEventHandler
 
ServicesUtil - Class in net.sf.basedb.ws.server
A utility class for common methods in the web services.
ServicesUtil() - 
Constructor for class net.sf.basedb.ws.server.ServicesUtil
 
serviceUrl - 
Variable in class net.sf.basedb.ws.client.AbstractRPCClient
 
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
 
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.
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.ExtensionsFile
 
servlets - 
Variable in class net.sf.basedb.clients.web.extensions.ServletLoader
 
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
 
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.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 - 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 - 
Variable in class net.sf.basedb.ws.client.AnnotationTypeClient
 
session - 
Variable in class net.sf.basedb.ws.client.ArrayDesignClient
 
session - 
Variable in class net.sf.basedb.ws.client.BioAssaySetClient
 
session - 
Variable in class net.sf.basedb.ws.client.ExperimentClient
 
session - 
Variable in class net.sf.basedb.ws.client.ProjectClient
 
session - 
Variable in class net.sf.basedb.ws.client.RawBioAssayClient
 
session - 
Variable in class net.sf.basedb.ws.client.ReporterClient
 
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.
SessionClient - Class in net.sf.basedb.ws.client
Client for handling sessions.
SessionClient(String, String, String) - 
Constructor for class net.sf.basedb.ws.client.SessionClient
Creates a new SessionClient using the default service factory.
SessionClient(String, String, String, ServiceFactory) - 
Constructor for class net.sf.basedb.ws.client.SessionClient
Creates a new SessionClient using a specific service factory.
sessionControl - 
Static variable in class net.sf.basedb.core.Install
 
SessionControl - Class in net.sf.basedb.core
This class handles user sessions.
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(String, String, boolean, String) - 
Constructor for class net.sf.basedb.core.SessionControl
Creates a new SessionControl object.
SessionControl.LoginInfo - Class in net.sf.basedb.core
Internal class to hold information about the logged in user.
SessionControl.LoginInfo() - 
Constructor for class net.sf.basedb.core.SessionControl.LoginInfo
 
SessionControl.LoginInfo(SessionControl.LoginInfo) - 
Constructor for class net.sf.basedb.core.SessionControl.LoginInfo
 
SessionControl.SettingInfo - Class in net.sf.basedb.core
Internal class to hold information about a setting
SessionControl.SettingInfo(String, boolean) - 
Constructor for class net.sf.basedb.core.SessionControl.SettingInfo
 
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
 
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
 
SessionService - Class in net.sf.basedb.ws.server
Web service class for Session in BASE 
        Session
SessionService() - 
Constructor for class net.sf.basedb.ws.server.SessionService
 
sessionSettings - 
Variable in class net.sf.basedb.core.SessionControl.LoginInfo
Stores name and value of session settings.
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(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(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.
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
 
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.
setAbstractText(String) - 
Method in class net.sf.basedb.info.ExperimentInfo
 
setAction(String) - 
Method in class net.sf.basedb.clients.web.taglib.table.Table
 
setAction(int) - 
Method in class net.sf.basedb.core.data.FileData
 
setAction(File.Action) - 
Method in class net.sf.basedb.core.File
Set the action of this File item.
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
 
setActivate(String) - 
Method in class net.sf.basedb.clients.web.taglib.tab.Tab
 
setActive(String) - 
Method in class net.sf.basedb.clients.web.taglib.tab.TabControl
 
setActive(int) - 
Method in class net.sf.basedb.ws.client.ProjectClient
Sets a project to be active.
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.
setActiveProject(String, int) - 
Method in class net.sf.basedb.ws.server.ProjectService
Sets a project active
setActiveProjectId(int) - 
Method in class net.sf.basedb.core.data.JobData
 
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.
setAffiliations(String) - 
Method in class net.sf.basedb.info.ExperimentInfo
 
setAffyChip(boolean) - 
Method in class net.sf.basedb.core.data.ArrayDesignData
Deprecated. Has been replaced by platform
setAlign(String) - 
Method in class net.sf.basedb.clients.web.taglib.ButtonGroup
 
setAllowImmediateExecution(boolean) - 
Method in class net.sf.basedb.core.data.PluginDefinitionData
 
setAllowImmediateExecution(boolean) - 
Method in class net.sf.basedb.core.PluginDefinition
 
setAllowRendererOverrider(boolean) - 
Method in class net.sf.basedb.util.extensions.ExtensionPointBean
 
setAnnotated(boolean) - 
Method in class net.sf.basedb.info.AnnotatedItemInfo
 
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(Map<AnnotationTypeData, AnnotationData>) - 
Method in class net.sf.basedb.core.data.AnnotationSetData
 
setAnnotations(Set<AnnotationData>) - 
Method in class net.sf.basedb.core.data.AnnotationTypeData
 
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.WellData
 
setAnnotationType(AnnotationTypeData) - 
Method in class net.sf.basedb.core.data.AnnotationData
 
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.
setAnnotationTypeId(int) - 
Method in class net.sf.basedb.clients.web.ExperimentExplorer
Deprecated. In 2.14, use ExperimentExplorer.setAnnotationTypeIds(Collection) instead
setAnnotationTypeId(int) - 
Method in class net.sf.basedb.info.AnnotationInfo
 
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
 
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(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
 
setArrayDesign(ArrayDesign) - 
Method in class net.sf.basedb.core.RawBioAssay
Set the ArrayDesign this raw data uses.
setArrayDesignBlock(ArrayDesignBlockData) - 
Method in class net.sf.basedb.core.data.FeatureData
 
setArrayDesignBlocks(Set<ArrayDesignBlockData>) - 
Method in class net.sf.basedb.core.data.ArrayDesignData
 
setArrayDesignId(int) - 
Method in class net.sf.basedb.info.RawBioAssayInfo
 
setArrayDesigns(Set<ArrayDesignPlateData>) - 
Method in class net.sf.basedb.core.data.PlateData
 
setArrayNum(int) - 
Method in class net.sf.basedb.core.data.RawBioAssayData
 
setArrayNum(int) - 
Method in class net.sf.basedb.core.RawBioAssay
Set the hybridization array number this raw bioassay is linked to.
setArraySlide(ArraySlideData) - 
Method in class net.sf.basedb.core.data.HybridizationData
 
setArraySlide(ArraySlide) - 
Method in class net.sf.basedb.core.Hybridization
Set the ArraySlide this hybridization is using.
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, Object) - 
Method in class net.sf.basedb.util.extensions.Registry
Set an extra attribute on a registered extension or extension point.
setAttributes(String) - 
Method in class net.sf.basedb.clients.web.taglib.Body
 
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.
setAuthors(String) - 
Method in class net.sf.basedb.info.ExperimentInfo
 
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.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.
setAutoheight(boolean) - 
Method in class net.sf.basedb.clients.web.taglib.tab.TabControl
 
setAutoInstall(int) - 
Method in class net.sf.basedb.clients.web.extensions.ExtensionsControl
Change the auto-installation setting.
setAutoInstall(int) - 
Method in class net.sf.basedb.clients.web.extensions.Settings
Change the interval, in seconds, between automatic checks 
                for new/modified/deleted extensions.
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.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(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
 
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.
setBase1Password(String) - 
Method in class net.sf.basedb.core.User
Set the encrypted password from BASE 1.
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
 
setBigDecimal(String, BigDecimal) - 
Method in class net.sf.basedb.core.hibernate.QueryWrapper
 
setBigInteger(int, BigInteger) - 
Method in class net.sf.basedb.core.hibernate.QueryWrapper
 
setBigInteger(String, BigInteger) - 
Method in class net.sf.basedb.core.hibernate.QueryWrapper
 
setBinary(int, byte[]) - 
Method in class net.sf.basedb.core.hibernate.QueryWrapper
 
setBinary(String, byte[]) - 
Method in class net.sf.basedb.core.hibernate.QueryWrapper
 
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(BioAssaySetData) - 
Method in class net.sf.basedb.core.data.BioAssayData
 
setBioAssaySet(BioAssaySetData) - 
Method in class net.sf.basedb.core.data.ExtraValueData
 
setBioAssaySet(BioAssaySet) - 
Method in class net.sf.basedb.core.ExtraValue
Set the bioassayset.
setBioAssaySets(Set<BioAssaySetData>) - 
Method in class net.sf.basedb.core.data.ExperimentData
 
setBioMaterial(MeasuredBioMaterial) - 
Method in class net.sf.basedb.core.BioMaterialEvent
Set the biomaterial that was affected or created by this event.
setBioMaterial(MeasuredBioMaterialData) - 
Method in class net.sf.basedb.core.data.BioMaterialEventData
 
setBioMaterial(MeasuredBioMaterialData) - 
Method in class net.sf.basedb.core.data.BioWellData
 
setBioMaterialEvents(Set<BioMaterialEventData>) - 
Method in class net.sf.basedb.core.data.BioPlateEventParticipantData
 
setBioMaterialLists(Set<BioMaterialListData>) - 
Method in class net.sf.basedb.core.data.BioMaterialData
 
setBioMaterials(Set<BioMaterialData>) - 
Method in class net.sf.basedb.core.data.BioMaterialListData
 
setBioMaterialType(Item) - 
Method in class net.sf.basedb.core.BioPlateType
Set the type of biomaterial that can be stored on plates with
                this type.
setBioMaterialType(Integer) - 
Method in class net.sf.basedb.core.data.BioPlateTypeData
 
setBioPlate(BioPlateData) - 
Method in class net.sf.basedb.core.data.BioPlateEventParticipantData
 
setBioPlate(BioPlateData) - 
Method in class net.sf.basedb.core.data.BioWellData
 
setBioPlateEventParticipant(BioPlateEventParticipantData) - 
Method in class net.sf.basedb.core.data.BioMaterialEventData
 
setBioPlateEventParticipant(BioPlateEventParticipant) - 
Method in class net.sf.basedb.core.Hybridization
 
setBioPlateEventParticipant(BioPlateEventParticipant) - 
Method in class net.sf.basedb.core.MeasuredBioMaterial
 
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
 
setBioSource(BioSource) - 
Method in class net.sf.basedb.core.Sample
Set the BioSource item that is the parent
                of this sample.
setBioWell(BioWellData) - 
Method in class net.sf.basedb.core.data.MeasuredBioMaterialData
 
setBioWell(BioWell) - 
Method in class net.sf.basedb.core.MeasuredBioMaterial
Sets the BioWell where this biomaterial is located.
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
 
setBlueImageFile(FileData) - 
Method in class net.sf.basedb.core.data.SpotImagesData
 
setBlueImageFile(File) - 
Method in class net.sf.basedb.core.SpotImages
 
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
 
setBoolean(String, boolean) - 
Method in class net.sf.basedb.core.hibernate.QueryWrapper
 
setBuild(int) - 
Method in class net.sf.basedb.core.data.SchemaVersionData
 
setBuild(int) - 
Method in class net.sf.basedb.info.VersionInfo
 
setByte(int, byte) - 
Method in class net.sf.basedb.core.hibernate.QueryWrapper
 
setByte(String, byte) - 
Method in class net.sf.basedb.core.hibernate.QueryWrapper
 
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
 
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.QueryWrapper
 
setCacheMode(CacheMode) - 
Method in class net.sf.basedb.core.hibernate.SessionWrapper
 
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.
setCacheSize(int) - 
Method in class net.sf.basedb.clients.web.ExperimentExplorer
Deprecated. In 2.11. For performance reasons the full reporter set
                        is always cached.
setCalendar(int, Calendar) - 
Method in class net.sf.basedb.core.hibernate.QueryWrapper
 
setCalendar(String, Calendar) - 
Method in class net.sf.basedb.core.hibernate.QueryWrapper
 
setCalendarDate(int, Calendar) - 
Method in class net.sf.basedb.core.hibernate.QueryWrapper
 
setCalendarDate(String, Calendar) - 
Method in class net.sf.basedb.core.hibernate.QueryWrapper
 
setCategories(Set<AnnotationTypeCategoryData>) - 
Method in class net.sf.basedb.core.data.AnnotationTypeData
 
setCdfFile(ArrayDesign, File) - 
Static method in class net.sf.basedb.core.Affymetrix
Deprecated. Use FileStoreUtil.setDataFile(DbControl, FileStoreEnabled, String, File)
                        instead with DataFileType.AFFYMETRIX_CDF as the file
                        type
setCelFile(RawBioAssay, File) - 
Static method in class net.sf.basedb.core.Affymetrix
Deprecated. Use FileStoreUtil.setDataFile(DbControl, FileStoreEnabled, String, File)
                        instead with DataFileType.AFFYMETRIX_CEL as the file
                        type
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
 
setCharacter(String, char) - 
Method in class net.sf.basedb.core.hibernate.QueryWrapper
 
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)
setChild(BioAssay) - 
Method in class net.sf.basedb.util.importer.spotdata.BaseFileInfo.ChildBioAssay
Set the real child bioassay object.
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<MeasuredBioMaterialData>) - 
Method in class net.sf.basedb.core.data.BioMaterialData
 
setChildren(Set<GroupData>) - 
Method in class net.sf.basedb.core.data.GroupData
 
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.
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.
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.Body
 
setClazz(String) - 
Method in class net.sf.basedb.clients.web.taglib.Button
 
setClazz(String) - 
Method in class net.sf.basedb.clients.web.taglib.ButtonGroup
 
setClazz(String) - 
Method in class net.sf.basedb.clients.web.taglib.ExceptionCatcher
 
setClazz(String) - 
Method in class net.sf.basedb.clients.web.taglib.Help
 
setClazz(String) - 
Method in class net.sf.basedb.clients.web.taglib.HideableSection
 
setClazz(String) - 
Method in class net.sf.basedb.clients.web.taglib.Icon
 
setClazz(String) - 
Method in class net.sf.basedb.clients.web.taglib.menu.Menu
 
setClazz(String) - 
Method in class net.sf.basedb.clients.web.taglib.Note
 
setClazz(String) - 
Method in class net.sf.basedb.clients.web.taglib.path.Path
 
setClazz(String) - 
Method in class net.sf.basedb.clients.web.taglib.path.PathElement
 
setClazz(String) - 
Method in class net.sf.basedb.clients.web.taglib.Select
 
setClazz(String) - 
Method in class net.sf.basedb.clients.web.taglib.tab.Tab
 
setClazz(String) - 
Method in class net.sf.basedb.clients.web.taglib.tab.TabControl
 
setClazz(String) - 
Method in class net.sf.basedb.clients.web.taglib.table.Button
 
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.ColumnDef
 
setClazz(String) - 
Method in class net.sf.basedb.clients.web.taglib.table.Data
 
setClazz(String) - 
Method in class net.sf.basedb.clients.web.taglib.table.Header
 
setClazz(String) - 
Method in class net.sf.basedb.clients.web.taglib.table.Label
 
setClazz(String) - 
Method in class net.sf.basedb.clients.web.taglib.table.Navigator
 
setClazz(String) - 
Method in class net.sf.basedb.clients.web.taglib.table.Panel
 
setClazz(String) - 
Method in class net.sf.basedb.clients.web.taglib.table.PresetSelector
 
setClazz(String) - 
Method in class net.sf.basedb.clients.web.taglib.table.Row
 
setClazz(String) - 
Method in class net.sf.basedb.clients.web.taglib.table.Table
 
setClazz(String) - 
Method in class net.sf.basedb.clients.web.taglib.table.Toolbar
 
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.
setClient(Client) - 
Method in class net.sf.basedb.core.ClientDefaultSetting
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(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.
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.
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.
setClientId(Integer) - 
Method in class net.sf.basedb.core.data.ChangeHistoryData
 
setClientSettings(Set<UserClientSettingData>) - 
Method in class net.sf.basedb.core.data.UserData
 
setCollection(boolean) - 
Method in class net.sf.basedb.clients.web.taglib.table.ColumnDef
 
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(String) - 
Method in class net.sf.basedb.clients.web.taglib.table.PresetSelector
 
setColumn(String) - 
Method in class net.sf.basedb.clients.web.taglib.table.Cell
 
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(Integer) - 
Method in class net.sf.basedb.core.data.RawData
 
setColumn(int) - 
Method in class net.sf.basedb.core.data.WellData
 
setColumn(String) - 
Method in class net.sf.basedb.info.ExtendedPropertyInfo
 
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, String) - 
Method in class net.sf.basedb.clients.web.taglib.table.Table
 
setColumnNo(short) - 
Method in class net.sf.basedb.core.data.DataCubeColumnData
 
setColumnNo(short) - 
Method in class net.sf.basedb.core.DataCubeColumn
 
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
 
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.
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.QueryWrapper
 
setComment(String) - 
Method in class net.sf.basedb.core.PlateEvent
Set the comment about this event.
setCompressed(boolean) - 
Method in class net.sf.basedb.core.data.FileData
 
setCompressedSize(long) - 
Method in class net.sf.basedb.core.data.FileData
 
setConfigurationProperties(Configuration) - 
Static method in class net.sf.basedb.core.HibernateUtil
Read database configuration properties from the base.config file
                and add those to the Hibernate configuration.
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
 
setContact(String) - 
Method in class net.sf.basedb.core.data.PluginDefinitionData
 
setContact(String) - 
Method in class net.sf.basedb.core.PluginDefinition
The contact information cannot be changed.
setContact(String) - 
Method in class net.sf.basedb.util.extensions.AboutBean
 
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
 
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
 
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(Set<ContextData>) - 
Method in class net.sf.basedb.core.data.ClientData
 
setContexts(Map<ContextIndex, ContextData>) - 
Method in class net.sf.basedb.core.data.UserData
 
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
 
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
The copyright notice cannot be changed.
setCopyright(String) - 
Method in class net.sf.basedb.util.extensions.AboutBean
 
setCounting(boolean) - 
Method in class net.sf.basedb.core.AbstractQuery
Set the counting status of the query.
setCreated(Date) - 
Method in class net.sf.basedb.core.data.JobData
 
setCreationEvent(BioMaterialEventData) - 
Method in class net.sf.basedb.core.data.HybridizationData
 
setCreationEvent(BioMaterialEventData) - 
Method in class net.sf.basedb.core.data.MeasuredBioMaterialData
 
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.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.parser.ColFunction
 
setCurNumberOfParameters(int) - 
Method in class net.sf.basedb.util.parser.DataNoFunction
 
setCurNumberOfParameters(int) - 
Method in class net.sf.basedb.util.parser.LineNoFunction
 
setCurrent(BasicItem) - 
Method in class net.sf.basedb.clients.web.taglib.Select
 
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.
setData(String[]) - 
Method in class net.sf.basedb.util.importer.spotdata.SynchronizedSpotDataParser.SynchronizedData
 
setData(FlatFileParser.Data) - 
Method in class net.sf.basedb.util.parser.ColFunction
 
setData(FlatFileParser.Data) - 
Method in class net.sf.basedb.util.parser.DataNoFunction
 
setData(FlatFileParser.Data) - 
Method in class net.sf.basedb.util.parser.JepMapper
 
setData(FlatFileParser.Data) - 
Method in class net.sf.basedb.util.parser.LineNoFunction
 
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(DataCubeColumn) - 
Method in class net.sf.basedb.core.BioAssay
 
setDataCubeColumn(DataCubeColumnData) - 
Method in class net.sf.basedb.core.data.BioAssayData
 
setDataCubeExtraValue(DataCubeExtraValueData) - 
Method in class net.sf.basedb.core.data.ExtraValueData
 
setDataCubeExtraValue(DataCubeExtraValue) - 
Method in class net.sf.basedb.core.ExtraValue
 
setDataCubeFilter(DataCubeFilter) - 
Method in class net.sf.basedb.core.BioAssaySet
 
setDataCubeFilter(DataCubeFilterData) - 
Method in class net.sf.basedb.core.data.BioAssaySetData
 
setDataCubeLayer(DataCubeLayer) - 
Method in class net.sf.basedb.core.BioAssaySet
 
setDataCubeLayer(DataCubeLayerData) - 
Method in class net.sf.basedb.core.data.BioAssaySetData
 
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.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
 
setDate(String, Date) - 
Method in class net.sf.basedb.core.hibernate.QueryWrapper
 
setDateFormat(SessionControl, String) - 
Static method in class net.sf.basedb.clients.web.formatter.FormatterSettings
Set the format string for a date formatter.
setDateTimeFormat(SessionControl, String) - 
Static method in class net.sf.basedb.clients.web.formatter.FormatterSettings
Set the format string for a datetime formatter.
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
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.
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
 
setDefaultItem(DbControl, BasicItem, Project.Default) - 
Method in class net.sf.basedb.core.Project
Sets item as default for project.
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
 
setDefaultServiceFactory(ServiceFactory) - 
Static method in class net.sf.basedb.ws.client.Factories
Set the default service factory that is used when creating
                SessionClient objects when no factory has been specified
                in the constructor.
setDefaultSettings(Set<ClientDefaultSettingData>) - 
Method in class net.sf.basedb.core.data.ClientData
 
setDefaultSettings(Set<UserDefaultSettingData>) - 
Method in class net.sf.basedb.core.data.UserData
 
setDefaultUnit(Unit) - 
Method in class net.sf.basedb.core.AnnotationType
Set the default unit to use for this annotation type.
setDefaultUnit(UnitData) - 
Method in class net.sf.basedb.core.data.AnnotationTypeData
 
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.info.AnnotationTypeInfo
 
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.
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
 
setDescription(String) - 
Method in class net.sf.basedb.clients.web.extensions.plot.OverviewPlotBean
 
setDescription(String) - 
Method in class net.sf.basedb.clients.web.util.NameablePluginAdaptor
Ignored.
setDescription(String) - 
Method in class net.sf.basedb.core.AnyToAny
 
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.FileTypeData
 
setDescription(String) - 
Method in class net.sf.basedb.core.data.GroupData
 
setDescription(String) - 
Method in class net.sf.basedb.core.data.HardwareTypeData
 
setDescription(String) - 
Method in class net.sf.basedb.core.data.HelpData
 
setDescription(String) - 
Method in class net.sf.basedb.core.data.ImageData
 
setDescription(String) - 
Method in class net.sf.basedb.core.data.JobData
 
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.ProtocolTypeData
 
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.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.SoftwareTypeData
 
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.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.FileType
 
setDescription(String) - 
Method in class net.sf.basedb.core.Group
 
setDescription(String) - 
Method in class net.sf.basedb.core.HardwareType
 
setDescription(String) - 
Method in class net.sf.basedb.core.Help
 
setDescription(String) - 
Method in class net.sf.basedb.core.Image
 
setDescription(String) - 
Method in class net.sf.basedb.core.Job
 
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(NameableData, String) - 
Static method in class net.sf.basedb.core.NameableUtil
Set the description of a NameableData object.
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.PluginDefinition
The description cannot be changed.
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.ProtocolType
 
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.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.SoftwareType
 
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.info.BioAssaySetInfo
 
setDescription(String) - 
Method in class net.sf.basedb.info.CommonItemInfo
 
setDescription(String) - 
Method in class net.sf.basedb.info.DataFileTypeInfo
 
setDescription(String) - 
Method in class net.sf.basedb.info.ExtendedPropertyInfo
 
setDescription(String) - 
Method in interface net.sf.basedb.info.NameableInfo
Sets the description of an info object.
setDescription(String) - 
Method in class net.sf.basedb.info.ProjectInfo
 
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
 
setDescriptionInternal(String) - 
Method in class net.sf.basedb.core.PluginDefinition
The description cannot be changed.
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(Set<ChangeHistoryDetailData>) - 
Method in class net.sf.basedb.core.data.ChangeHistoryData
 
setDetails(Map<MappingCoordinate, MappingCoordinate>) - 
Method in class net.sf.basedb.core.data.PlateMappingData
 
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.
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.UserData
 
setDisabled(boolean) - 
Method in class net.sf.basedb.core.User
Disables or enables the account.
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.
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.
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.
setDisableinproject(boolean) - 
Method in class net.sf.basedb.clients.web.taglib.table.PresetSelector
 
setDisableothers(boolean) - 
Method in class net.sf.basedb.clients.web.taglib.table.PresetSelector
 
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
 
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.
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.
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) - 
Method in interface net.sf.basedb.core.plugin.Response
This will end the job execution and report it as a success.
setDone(String, Job.ExecutionTime) - 
Method in class net.sf.basedb.core.PluginResponse.ResponseImpl
 
setDone(String) - 
Method in class net.sf.basedb.core.PluginResponse.ResponseImpl
 
setDone(String, Job.ExecutionTime) - 
Method in class net.sf.basedb.plugins.executor.ExternalProgramExecutor.ResponseWrapper
 
setDone(String) - 
Method in class net.sf.basedb.plugins.executor.ExternalProgramExecutor.ResponseWrapper
 
setDouble(int, double) - 
Method in class net.sf.basedb.core.hibernate.QueryWrapper
 
setDouble(String, double) - 
Method in class net.sf.basedb.core.hibernate.QueryWrapper
 
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
 
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
 
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
The email address cannot be changed.
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(String) - 
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(String) - 
Method in class net.sf.basedb.clients.web.extensions.toolbar.FixedButtonFactory
 
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
 
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.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.clients.web.extensions.ScanResults
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
 
setEntity(String, Object) - 
Method in class net.sf.basedb.core.hibernate.EntityQueryWrapper
 
setEntity(int, Object) - 
Method in class net.sf.basedb.core.hibernate.QueryWrapper
 
setEntity(String, Object) - 
Method in class net.sf.basedb.core.hibernate.QueryWrapper
 
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.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.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.ExperimentData
 
setEntryDate(Date) - 
Method in class net.sf.basedb.core.data.ExtraValueTypeData
 
setEntryDate(Date) - 
Method in class net.sf.basedb.core.data.FileTypeData
 
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.HardwareTypeData
 
setEntryDate(Date) - 
Method in class net.sf.basedb.core.data.LabelData
 
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.ProtocolTypeData
 
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.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.ScanData
 
setEntryDate(Date) - 
Method in class net.sf.basedb.core.data.SoftwareData
 
setEntryDate(Date) - 
Method in class net.sf.basedb.core.data.SoftwareTypeData
 
setEntryDate(Date) - 
Method in class net.sf.basedb.core.data.UserData
 
setEnum(String) - 
Method in class net.sf.basedb.clients.web.taglib.table.ColumnDef
 
setEnumeration(Enumeration<String, String>) - 
Method in class net.sf.basedb.clients.web.taglib.table.ColumnDef
 
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(boolean) - 
Method in class net.sf.basedb.info.AnnotationTypeInfo
 
setEnumerationValues(ParameterValueData<?>) - 
Method in class net.sf.basedb.core.data.AnnotationTypeData
 
setEnumValues(String[]) - 
Method in class net.sf.basedb.info.AnnotationTypeInfo
 
setError(boolean) - 
Method in class net.sf.basedb.clients.web.extensions.ExtensionsFile
Sets the error status.
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, Throwable) - 
Method in class net.sf.basedb.core.PluginResponse
Set a singe error message.
setError(String, List<? extends Throwable>) - 
Method in class net.sf.basedb.plugins.executor.ExternalProgramExecutor.ResponseWrapper
 
setError(Throwable) - 
Method in class net.sf.basedb.util.extensions.ActionIterator
Register an error for the current action.
setError(String, Throwable) - 
Method in class net.sf.basedb.util.extensions.ActionIterator
Register an error with a message for the current action.
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
 
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
 
setEvent(BioMaterialEventData) - 
Method in class net.sf.basedb.core.data.BioMaterialSourceEventData
 
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.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.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(Set<BioPlateEventData>) - 
Method in class net.sf.basedb.core.data.BioPlateEventTypeData
 
setEvents(Set<BioMaterialEventData>) - 
Method in class net.sf.basedb.core.data.MeasuredBioMaterialData
 
setEvents(Map<PlateEventTypeData, PlateEventData>) - 
Method in class net.sf.basedb.core.data.PlateData
 
setEventType(BioPlateEventType) - 
Method in class net.sf.basedb.core.BioPlateEvent
 
setEventType(int) - 
Method in class net.sf.basedb.core.data.BioMaterialEventData
 
setEventType(BioPlateEventTypeData) - 
Method in class net.sf.basedb.core.data.BioPlateEventData
 
setEventTypes(Set<PlateEventTypeData>) - 
Method in class net.sf.basedb.core.data.PlateTypeData
 
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.
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(Experiment) - 
Method in class net.sf.basedb.core.BioAssaySet
Set the experiment.
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.TransformationData
 
setExperiment(ExperimentData) - 
Method in class net.sf.basedb.core.data.VirtualDbData
 
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.
setExperimentDesign(String) - 
Method in class net.sf.basedb.info.ExperimentInfo
 
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.
setExperimentType(String) - 
Method in class net.sf.basedb.info.ExperimentInfo
 
setExpirationDate(Date) - 
Method in class net.sf.basedb.core.data.UserData
 
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.taglib.table.ColumnDef
 
setExportproperty(String) - 
Method in class net.sf.basedb.clients.web.taglib.table.ColumnDef
 
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 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
setExtends(String) - 
Method in class net.sf.basedb.util.extensions.ExtensionBean
 
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.
setExtension(String) - 
Method in class net.sf.basedb.info.DataFileTypeInfo
 
setExtensions(ExtensionsInvoker) - 
Method in class net.sf.basedb.clients.web.taglib.extensions.Render
 
setExtensions(ExtensionsInvoker<TabAction>) - 
Method in class net.sf.basedb.clients.web.taglib.tab.TabControl
 
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.BioMaterialList
Set the external id for this list.
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.BioMaterialListData
 
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.JobAgentData
 
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.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.
setExternalId(String) - 
Method in class net.sf.basedb.info.AnnotationTypeInfo
 
setExternalId(String) - 
Method in class net.sf.basedb.info.DataFileTypeInfo
 
setExternalId(String) - 
Method in class net.sf.basedb.info.ReporterListInfo
 
setExtract(Extract, Float) - 
Method in class net.sf.basedb.core.LabeledExtract
Set the Extract item that is the parent
                of this labeled extract.
setExtraFileImporter(ExtraFileImporter) - 
Method in class net.sf.basedb.util.importer.spotdata.BfsImporter
 
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.
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.QueryWrapper
 
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.ImageData
 
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(FileSetMember) - 
Method in class net.sf.basedb.core.filehandler.AbstractDataFileHandler
 
setFile(FileSetMember) - 
Method in interface net.sf.basedb.core.filehandler.DataFileHandler
Set the file that is part of the file set with a DataFileType
                that is using this file handler.
setFile(FileSetMember) - 
Method in class net.sf.basedb.core.FileSet.DataFileHandlerWrapper
 
setFile(File) - 
Method in class net.sf.basedb.core.Image
 
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.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(FileTypeData) - 
Method in class net.sf.basedb.core.data.FileData
 
setFileType(DataFileTypeData) - 
Method in class net.sf.basedb.core.data.FileTypeIndex
 
setFileType(FileTypeData) - 
Method in class net.sf.basedb.core.data.MimeTypeData
 
setFileType(FileType) - 
Method in class net.sf.basedb.core.File
Set the filetype of this File item.
setFileType(FileType) - 
Method in class net.sf.basedb.core.MimeType
Set the filetype of this item.
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
 
setFilterable(boolean) - 
Method in class net.sf.basedb.clients.web.taglib.table.ColumnDef
 
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
 
setFilters(Set<DataCubeFilterData>) - 
Method in class net.sf.basedb.core.data.DataCubeData
 
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.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
 
setFloat(String, float) - 
Method in class net.sf.basedb.core.hibernate.QueryWrapper
 
setFlushMode(FlushMode) - 
Method in class net.sf.basedb.core.hibernate.QueryWrapper
 
setFlushMode(FlushMode) - 
Method in class net.sf.basedb.core.hibernate.SessionWrapper
 
setForceStop(boolean) - 
Method in class net.sf.basedb.core.signal.ThreadSignalHandler
Call this method with a true value to make the signal handler
                use Thread.stop(Throwable) instead of Thread.interrupt().
setFormat(int) - 
Method in class net.sf.basedb.core.data.ImageData
 
setFormat(Image.Format) - 
Method in class net.sf.basedb.core.Image
Set the format of the image.
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.
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(Hardware) - 
Method in class net.sf.basedb.core.BioPlate
Sets the freezer where this bio plate is stored
setFreezer(HardwareData) - 
Method in class net.sf.basedb.core.data.BioPlateData
 
setFrom(BasicItem) - 
Method in class net.sf.basedb.core.AnyToAny
 
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.
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
 
setGamma(float) - 
Method in class net.sf.basedb.core.data.SpotImagesData
 
setGamma(float) - 
Method in class net.sf.basedb.core.SpotImages
 
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 FileType.
setGenericType(FileTypeData) - 
Method in class net.sf.basedb.core.data.DataFileTypeData
 
setGenericType(FileType) - 
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
 
setGreenImageFile(FileData) - 
Method in class net.sf.basedb.core.data.SpotImagesData
 
setGreenImageFile(File) - 
Method in class net.sf.basedb.core.SpotImages
 
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(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(HardwareData) - 
Method in class net.sf.basedb.core.data.BioMaterialEventData
 
setHardware(HardwareData) - 
Method in class net.sf.basedb.core.data.BioPlateEventData
 
setHardware(Set<HardwareData>) - 
Method in class net.sf.basedb.core.data.HardwareTypeData
 
setHardware(HardwareData) - 
Method in class net.sf.basedb.core.data.PlateEventData
 
setHardware(Hardware) - 
Method in class net.sf.basedb.core.PlateEvent
Set the Hardware that was used in this event.
setHardwareType(HardwareTypeData) - 
Method in class net.sf.basedb.core.data.HardwareData
 
setHardwareType(HardwareType) - 
Method in class net.sf.basedb.core.Hardware
Set the HardwareType of this Hardware item.
setHasData(boolean) - 
Method in class net.sf.basedb.core.data.RawBioAssayData
 
setHasFeatures(boolean) - 
Method in class net.sf.basedb.core.data.ArrayDesignData
 
setHeader(RawBioAssay, String, String) - 
Method in class net.sf.basedb.core.filehandler.CelFileHandler
 
setHeader(String, String) - 
Method in class net.sf.basedb.core.RawBioAssay
Set the value for a raw data header.
setHeaderRegexp(Pattern) - 
Method in class net.sf.basedb.util.parser.FlatFileParser
Set a regular expression that can be matched against a header.
setHeaders(Map<String, String>) - 
Method in class net.sf.basedb.core.data.RawBioAssayData
 
setHeaders(String...) - 
Method in class net.sf.basedb.util.bfs.AnnotationModel
Set the column headers.
setHeight(String) - 
Method in class net.sf.basedb.clients.web.extensions.plot.MAPlotFactory
 
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
 
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
 
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
 
setHelpTexts(Set<HelpData>) - 
Method in class net.sf.basedb.core.data.ClientData
 
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
 
setHightligh(String) - 
Method in class net.sf.basedb.clients.web.taglib.table.Row
 
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.
setHref(String) - 
Method in class net.sf.basedb.clients.web.taglib.path.PathElement
 
setHybridization(Hybridization) - 
Method in class net.sf.basedb.core.BioMaterialEvent
Set the hybidization that was created by this event.
setHybridization(HybridizationData) - 
Method in class net.sf.basedb.core.data.ArraySlideData
 
setHybridization(HybridizationData) - 
Method in class net.sf.basedb.core.data.BioMaterialEventData
 
setHybridization(HybridizationData) - 
Method in class net.sf.basedb.core.data.ScanData
 
setHybridization(Hybridization) - 
Method in class net.sf.basedb.core.Scan
Set the ArraySlide this hybridization is using.
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
 
setIcon(String) - 
Method in class net.sf.basedb.clients.web.taglib.Note
 
setIconabsolute(boolean) - 
Method in class net.sf.basedb.clients.web.taglib.menu.Menuitem
 
setIconabsolute(boolean) - 
Method in class net.sf.basedb.clients.web.taglib.menu.Submenu
 
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.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(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(int) - 
Method in class net.sf.basedb.info.BasicItemInfo
 
setId(String) - 
Method in class net.sf.basedb.util.extensions.ExtensionBean
 
setId(String) - 
Method in class net.sf.basedb.util.extensions.ExtensionPointBean
 
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.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.
setImagealign(String) - 
Method in class net.sf.basedb.clients.web.taglib.table.Button
 
setImages(Set<ImageData>) - 
Method in class net.sf.basedb.core.data.ScanData
 
setImgClass(String) - 
Method in class net.sf.basedb.clients.web.formatter.SpotImageFormatter
Sets the class attribute for the generated <img> tag
                that displays the spot image.
setImpersonated(boolean) - 
Method in class net.sf.basedb.core.data.SessionData
 
setInclude(Set<Include>, String, Include) - 
Static method in class net.sf.basedb.clients.web.Base
Set include option if option parameter isn't null.
setInclude(String) - 
Method in class net.sf.basedb.clients.web.extensions.tabcontrol.IncludeContentTabFactory
 
setInclude(int) - 
Method in class net.sf.basedb.core.data.ContextData
 
setIncludeInProject(boolean) - 
Method in class net.sf.basedb.info.QueryOptions
Sets if items in currently active project should be included.
setIncludeMine(boolean) - 
Method in class net.sf.basedb.info.QueryOptions
Sets if the logged in user's items should be included or not.
setIncludeNotRemoved(boolean) - 
Method in class net.sf.basedb.info.QueryOptions
Sets if not removed items should be included
setIncludeOthers(boolean) - 
Method in class net.sf.basedb.info.QueryOptions
Sets if other users' items should be included.
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.
setIncludeShared(boolean) - 
Method in class net.sf.basedb.info.QueryOptions
Sets if items shared to logged in user should be included.
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
 
setIndex(float) - 
Method in class net.sf.basedb.util.extensions.ExtensionBean
 
setInherited(Set<AnnotationData>) - 
Method in class net.sf.basedb.core.data.AnnotationSetData
 
setInheritedSets(Set<AnnotationSetData>) - 
Method in class net.sf.basedb.core.data.AnnotationSetData
 
setInheritingSets(Set<AnnotationSetData>) - 
Method in class net.sf.basedb.core.data.AnnotationData
 
setInheritingSets(Set<AnnotationSetData>) - 
Method in class net.sf.basedb.core.data.AnnotationSetData
 
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) - 
Method in class net.sf.basedb.util.parser.FlatFileParser
Deprecated. Use FlatFileParser.setInputStream(InputStream, String) instead
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.
setInsertable(boolean) - 
Method in class net.sf.basedb.info.ExtendedPropertyInfo
 
setInteger(int, int) - 
Method in class net.sf.basedb.core.hibernate.QueryWrapper
 
setInteger(String, int) - 
Method in class net.sf.basedb.core.hibernate.QueryWrapper
 
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(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(int) - 
Method in class net.sf.basedb.core.data.BioAssaySetData
 
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.
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(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(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(Item) - 
Method in class net.sf.basedb.clients.web.taglib.table.Table
 
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.filehandler.AbstractDataFileHandler
 
setItem(FileStoreEnabled) - 
Method in interface net.sf.basedb.core.filehandler.DataFileHandler
Sets the item that we are currently working with.
setItem(FileStoreEnabled) - 
Method in class net.sf.basedb.core.FileSet
Set the item this file set belongs to.
setItem(int, Item) - 
Method in class net.sf.basedb.core.snapshot.AnnotationSnapshot
 
setItemId(Integer) - 
Method in class net.sf.basedb.core.data.AnnotationSetData
 
setItemId(int) - 
Method in class net.sf.basedb.core.data.ChangeHistoryDetailData
 
setItemId(int) - 
Method in class net.sf.basedb.core.data.ContextData
 
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(ItemKey) - 
Method in interface net.sf.basedb.core.Shareable
Set the ItemKey for this item.
setItemKey(ShareableData, ItemKey) - 
Static method in class net.sf.basedb.core.ShareableUtil
Deprecated. Use ShareableUtil.setItemKey(DbControl, ShareableData, ItemKey) instead
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 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
 
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.
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.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(Set<Integer>) - 
Method in class net.sf.basedb.core.data.AnnotationTypeData
 
setItemTypes(String[]) - 
Method in class net.sf.basedb.info.AnnotationTypeInfo
 
setJarPath(String) - 
Method in class net.sf.basedb.core.data.JobAgentSettingsData
 
setJarPath(String) - 
Method in class net.sf.basedb.core.data.PluginDefinitionData
 
setJarPath(String) - 
Method in class net.sf.basedb.core.data.PluginTypeData
 
setJarPath(String) - 
Method in class net.sf.basedb.core.JobAgentSettings
Set the path to the JAR file that contains the plugin implementation.
setJarPath(String) - 
Method in class net.sf.basedb.core.PluginDefinition
The jar path cannot be changed.
setJarPath(String) - 
Method in class net.sf.basedb.core.PluginType
The jar path cannot be changed.
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.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(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.Message
 
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.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
 
setLabel(LabelData) - 
Method in class net.sf.basedb.core.data.LabeledExtractData
 
setLabel(String) - 
Method in class net.sf.basedb.core.data.ParameterValueData
 
setLabel(Label) - 
Method in class net.sf.basedb.core.LabeledExtract
Set the Label that was used to label the extract.
setLastScanResults(ScanResults) - 
Static method in class net.sf.basedb.clients.web.extensions.ExtensionsControl
 
setLastSource(String) - 
Method in class net.sf.basedb.core.data.ReporterData
 
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
 
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.info.ExtendedPropertyInfo
 
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.
setList(Iterable<?>) - 
Method in class net.sf.basedb.clients.web.taglib.table.CellValue
 
setLocale(int, Locale) - 
Method in class net.sf.basedb.core.hibernate.QueryWrapper
 
setLocale(String, Locale) - 
Method in class net.sf.basedb.core.hibernate.QueryWrapper
 
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(Location) - 
Method in class net.sf.basedb.core.File
Set the location of this File item.
setLocked(boolean) - 
Method in class net.sf.basedb.clients.web.taglib.table.Navigator
 
setLockMode(BioWell.LockMode) - 
Method in class net.sf.basedb.core.BioPlateType
Set the lock mode for wells on plates of this plate type.
setLockMode(int) - 
Method in class net.sf.basedb.core.data.BioPlateTypeData
 
setLockMode(String, LockMode) - 
Method in class net.sf.basedb.core.hibernate.QueryWrapper
 
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.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
 
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
 
setLong(String, long) - 
Method in class net.sf.basedb.core.hibernate.QueryWrapper
 
setMaintenance(String) - 
Method in class net.sf.basedb.info.VersionInfo
 
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.
setMajor(String) - 
Method in class net.sf.basedb.info.VersionInfo
 
setMappings(short) - 
Method in class net.sf.basedb.core.data.VirtualDbData
 
setMasterParser(AnnotationParser) - 
Method in class net.sf.basedb.util.importer.spotdata.SynchronizedSpotDataParser
Sets the master parser.
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.
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.
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.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
 
setMd5Password(String) - 
Method in class net.sf.basedb.core.data.PasswordData
 
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(Map<DataFileTypeData, FileSetMemberData>) - 
Method in class net.sf.basedb.core.data.FileSetData
 
setMemberType(Item) - 
Method in class net.sf.basedb.core.BioMaterialList
 
setMemberType(int) - 
Method in class net.sf.basedb.core.data.BioMaterialListData
 
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.
setMessages(Set<MessageData>) - 
Method in class net.sf.basedb.core.data.JobData
 
setMessages(Set<MessageData>) - 
Method in class net.sf.basedb.core.data.UserData
 
setMessagestyle(String) - 
Method in class net.sf.basedb.clients.web.taglib.Note
 
setMetadataFromHttpResponse(HttpResponse) - 
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.
setMetadataReaderClass(String) - 
Method in class net.sf.basedb.core.data.DataFileTypeData
 
setMetadataReaderClass(String) - 
Method in class net.sf.basedb.core.DataFileType
Set the class name of the Java class that is used to extract metadata from files of
                this type.
setMetadataReaderJarPath(String) - 
Method in class net.sf.basedb.core.data.DataFileTypeData
 
setMetadataReaderJarPath(String) - 
Method in class net.sf.basedb.core.DataFileType
Set the path to the JAR file where the meta data reader class is located.
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)
setMimeTypeAuto(String, FileType) - 
Method in class net.sf.basedb.core.File
Set the mime type automatically by checking the extension of the
                name.
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.
setMinor(String) - 
Method in class net.sf.basedb.info.VersionInfo
 
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
 
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
 
setMultiplicity(int) - 
Method in class net.sf.basedb.info.AnnotationTypeInfo
 
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(String) - 
Method in class net.sf.basedb.clients.web.taglib.table.Hidden
 
setName(String) - 
Method in class net.sf.basedb.clients.web.util.NameablePluginAdaptor
Ignored.
setName(String) - 
Method in class net.sf.basedb.core.AnyToAny
 
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.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.FileTypeData
 
setName(String) - 
Method in class net.sf.basedb.core.data.GroupData
 
setName(String) - 
Method in class net.sf.basedb.core.data.HardwareTypeData
 
setName(String) - 
Method in class net.sf.basedb.core.data.HelpData
 
setName(String) - 
Method in class net.sf.basedb.core.data.ImageData
 
setName(String) - 
Method in class net.sf.basedb.core.data.JobData
 
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.ProtocolTypeData
 
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.SettingData
 
setName(String) - 
Method in class net.sf.basedb.core.data.SoftwareTypeData
 
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.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.FileType
 
setName(String) - 
Method in class net.sf.basedb.core.Group
 
setName(String) - 
Method in class net.sf.basedb.core.HardwareType
 
setName(String) - 
Method in class net.sf.basedb.core.Help
 
setName(String) - 
Method in class net.sf.basedb.core.Image
 
setName(String) - 
Method in class net.sf.basedb.core.Job
 
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(NameableData, String) - 
Static method in class net.sf.basedb.core.NameableUtil
Set the name of a NameableData object.
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.PluginDefinition
The name cannot be changed.
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.ProtocolType
 
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.Setting
Set the name for this setting.
setName(String) - 
Method in class net.sf.basedb.core.SoftwareType
 
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.info.BioAssaySetInfo
 
setName(String) - 
Method in class net.sf.basedb.info.CommonItemInfo
 
setName(String) - 
Method in class net.sf.basedb.info.DataFileTypeInfo
 
setName(String) - 
Method in class net.sf.basedb.info.ExtendedPropertyInfo
 
setName(String) - 
Method in interface net.sf.basedb.info.NameableInfo
Set the info object's name
setName(String) - 
Method in class net.sf.basedb.info.ProjectInfo
 
setName(String) - 
Method in class net.sf.basedb.info.QueryParameter
Set the parameter name.
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.
setNameInternal(String) - 
Method in class net.sf.basedb.core.PluginDefinition
The name cannot be changed.
setNewAnnotations(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.
setNextCommand(String) - 
Method in class net.sf.basedb.core.PluginRequest
Sets the next command in a configuration sequence.
setNotabs(boolean) - 
Method in class net.sf.basedb.clients.web.taglib.tab.TabControl
 
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.info.ExtendedPropertyInfo
 
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.clients.web.util.AjaxWriter
Deprecated. Change the null value string.
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
 
setNumArrays(int) - 
Method in class net.sf.basedb.core.data.HybridizationData
 
setNumArrays(int) - 
Method in class net.sf.basedb.core.Hybridization
Set the number of arrays on a single slide.
setNumColumns(short) - 
Method in class net.sf.basedb.core.data.DataCubeData
 
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.
setNumDbFeatures(int) - 
Method in class net.sf.basedb.core.data.ArrayDesignData
 
setNumDbFeatures(int) - 
Method in class net.sf.basedb.info.ArrayDesignInfo
 
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
 
setNumFileFeatures(int) - 
Method in class net.sf.basedb.info.ArrayDesignInfo
 
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
 
setNumReporters(int) - 
Method in class net.sf.basedb.info.BioAssaySetInfo
 
setNumSpots(int) - 
Method in class net.sf.basedb.core.data.BioAssayData
 
setNumSpots(int) - 
Method in class net.sf.basedb.core.data.BioAssaySetData
 
setNumSpots(int) - 
Method in class net.sf.basedb.info.BioAssaySetInfo
 
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.
setOnActivate(String) - 
Method in class net.sf.basedb.clients.web.extensions.tabcontrol.FixedTabFactory
 
setOnActivate(String) - 
Method in class net.sf.basedb.clients.web.extensions.tabcontrol.IncludeContentTabFactory
 
setOnActivate(String) - 
Method in class net.sf.basedb.clients.web.extensions.tabcontrol.TabBean
 
setOnchange(String) - 
Method in class net.sf.basedb.clients.web.taglib.Select
 
setOnchange(String) - 
Method in class net.sf.basedb.clients.web.taglib.table.PresetSelector
 
setOnClick(String) - 
Method in class net.sf.basedb.clients.web.extensions.menu.FixedMenuItemFactory
 
setOnClick(String) - 
Method in class net.sf.basedb.clients.web.extensions.menu.MenuItemBean
 
setOnClick(String) - 
Method in class net.sf.basedb.clients.web.extensions.menu.PermissionMenuItemFactory
Set the javascript action to call when the menu is clicked.
setOnClick(String) - 
Method in class net.sf.basedb.clients.web.extensions.toolbar.ButtonBean
 
setOnClick(String) - 
Method in class net.sf.basedb.clients.web.extensions.toolbar.FixedButtonFactory
 
setOnClick(String) - 
Method in class net.sf.basedb.clients.web.extensions.toolbar.PermissionButtonFactory
 
setOnclick(String) - 
Method in class net.sf.basedb.clients.web.taglib.Button
 
setOnClick(String) - 
Method in class net.sf.basedb.clients.web.taglib.Help
 
setOnclick(String) - 
Method in class net.sf.basedb.clients.web.taglib.Icon
 
setOnclick(String) - 
Method in class net.sf.basedb.clients.web.taglib.menu.Menuitem
 
setOnclick(String) - 
Method in class net.sf.basedb.clients.web.taglib.table.Button
 
setOnkeypress(String) - 
Method in class net.sf.basedb.clients.web.taglib.Body
 
setOnload(String) - 
Method in class net.sf.basedb.clients.web.taglib.Body
 
setOnselect(String) - 
Method in class net.sf.basedb.clients.web.taglib.Select
 
setOntoggle(String) - 
Method in class net.sf.basedb.clients.web.taglib.HideableSection
 
setOnunload(String) - 
Method in class net.sf.basedb.clients.web.taglib.Body
 
setOnValidate(String) - 
Method in class net.sf.basedb.clients.web.extensions.tabcontrol.FixedTabFactory
 
setOnValidate(String) - 
Method in class net.sf.basedb.clients.web.extensions.tabcontrol.IncludeContentTabFactory
 
setOnValidate(String) - 
Method in class net.sf.basedb.clients.web.extensions.tabcontrol.TabBean
 
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(Validator, 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
 
setOptions(Options) - 
Method in class net.sf.basedb.ws.client.ConfigurableServiceFactory
Set the options to use when creating new RPCServiceClient
                objects with ConfigurableServiceFactory.createService(EndpointReference).
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.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.
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(User) - 
Method in interface net.sf.basedb.core.Ownable
Change the owner of the item.
setOwner(OwnableData, User) - 
Static method in class net.sf.basedb.core.OwnableUtil
Set the owner of a OwnableData object.
setOwner(User) - 
Method in class net.sf.basedb.core.OwnedItem
 
setOwner(DbControl, Item, Set<Integer>, User) - 
Static method in class net.sf.basedb.util.OwnableUtil
Change the owner of all specified items.
setOwner(DbControl, Set<OwnedItem>, User) - 
Static method in class net.sf.basedb.util.OwnableUtil
Change the owner of all specified items.
setOwnerId(int) - 
Method in class net.sf.basedb.info.OwnedItemInfo
 
setPage(String) - 
Method in class net.sf.basedb.clients.web.taglib.table.Navigator
 
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.
setPageContext(PageContext) - 
Method in class net.sf.basedb.clients.web.taglib.Page
 
setParameter(String, String) - 
Method in class net.sf.basedb.clients.web.extensions.ServletWrapper
Set the value of a servlet parameter.
setParameter(String, boolean, Object, Type) - 
Method in class net.sf.basedb.core.AbstractQuery
 
setParameter(String, Object, Type) - 
Method in class net.sf.basedb.core.AbstractQuery
 
setParameter(int, Object) - 
Method in class net.sf.basedb.core.hibernate.EntityQueryWrapper
 
setParameter(String, Object) - 
Method in class net.sf.basedb.core.hibernate.EntityQueryWrapper
 
setParameter(int, Object, Type) - 
Method in class net.sf.basedb.core.hibernate.EntityQueryWrapper
 
setParameter(String, Object, Type) - 
Method in class net.sf.basedb.core.hibernate.EntityQueryWrapper
 
setParameter(int, Object) - 
Method in class net.sf.basedb.core.hibernate.QueryWrapper
 
setParameter(String, Object) - 
Method in class net.sf.basedb.core.hibernate.QueryWrapper
 
setParameter(int, Object, Type) - 
Method in class net.sf.basedb.core.hibernate.QueryWrapper
 
setParameter(String, Object, Type) - 
Method in class net.sf.basedb.core.hibernate.QueryWrapper
 
setParameter(String, Object, Type) - 
Method in interface net.sf.basedb.core.query.Query
Set the value of a query parameter.
setParameter(String, Object) - 
Method in class net.sf.basedb.plugins.executor.ExternalProgramExecutor.RequestWrapper
 
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.export.spotdata.BfsExporter
Add a parameter that is exported in the [parameters] section.
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.
setParameterDefinition(ParameterDefinition) - 
Method in class net.sf.basedb.plugins.executor.ProgramParameter
 
setParameterList(String, Collection) - 
Method in class net.sf.basedb.core.hibernate.EntityQueryWrapper
 
setParameterList(String, Object[]) - 
Method in class net.sf.basedb.core.hibernate.EntityQueryWrapper
 
setParameterList(String, Collection, Type) - 
Method in class net.sf.basedb.core.hibernate.EntityQueryWrapper
 
setParameterList(String, Object[], Type) - 
Method in class net.sf.basedb.core.hibernate.EntityQueryWrapper
 
setParameterList(String, Collection) - 
Method in class net.sf.basedb.core.hibernate.QueryWrapper
 
setParameterList(String, Object[]) - 
Method in class net.sf.basedb.core.hibernate.QueryWrapper
 
setParameterList(String, Collection, Type) - 
Method in class net.sf.basedb.core.hibernate.QueryWrapper
 
setParameterList(String, Object[], Type) - 
Method in class net.sf.basedb.core.hibernate.QueryWrapper
 
setParameters(Query, Map<String, QueryParameter>) - 
Method in class net.sf.basedb.core.AbstractHqlQuery
Set parameter values on a query.
setParameters(PreparedStatement, List<String>) - 
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(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(Object[], Type[]) - 
Method in class net.sf.basedb.core.hibernate.QueryWrapper
 
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(QueryParameter[]) - 
Method in class net.sf.basedb.info.QueryOptions
Set the parmeters to use in this query.
setParameterValue(PreparedStatement, int, Object, Type) - 
Method in class net.sf.basedb.core.AbstractSqlQuery
Set a parameter value on a prepared statement.
setParameterValue(String, ParameterType<?>, Object) - 
Method in class net.sf.basedb.core.Job
Set the value of a configuration parameter.
setParameterValue(String, String, String, ParameterType<?>, Object) - 
Method in class net.sf.basedb.core.Job
Set the value of a configuration parameter.
setParameterValue(String, Object) - 
Method in class net.sf.basedb.core.PluginRequest
Set the value of a request parameter to a single value.
setParameterValues(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.Job
Set the value of a configuration parameter.
setParameterValues(String, ParameterType<?>, List<?>) - 
Method in class net.sf.basedb.core.PluginConfiguration
Set 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.
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(Renderer<? super A>) - 
Method in class net.sf.basedb.clients.web.extensions.renderer.PrefixSuffixRenderer
 
setParent(DirectoryData) - 
Method in class net.sf.basedb.core.data.DirectoryData
 
setParent(BioMaterialData) - 
Method in class net.sf.basedb.core.data.MeasuredBioMaterialData
 
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 interface net.sf.basedb.util.extensions.WrappingRenderer
Set a parent renderer.
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(Set<BioAssayData>) - 
Method in class net.sf.basedb.core.data.BioAssayData
 
setParents(Set<GroupData>) - 
Method in class net.sf.basedb.core.data.GroupData
 
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.
setParentSet(Set<PlateData>) - 
Method in class net.sf.basedb.core.data.PlateData
 
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.data.FileServerData
 
setPassword(PasswordData) - 
Method in class net.sf.basedb.core.data.UserData
 
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.
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(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(Item, int, ItemKeyData, ProjectKeyData) - 
Static method in class net.sf.basedb.core.Install
 
setPermissions(User, Set<Permission>) - 
Method in class net.sf.basedb.core.MultiPermissions
Grant permissions to a user.
setPermissions(Group, Set<Permission>) - 
Method in class net.sf.basedb.core.MultiPermissions
Grant permissions to a group.
setPermissions(Project, Set<Permission>) - 
Method in class net.sf.basedb.core.MultiPermissions
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(User, Set<Permission>) - 
Method in class net.sf.basedb.core.Project
Grant a user permissions to this project.
setPermissions(Group, Set<Permission>) - 
Method in class net.sf.basedb.core.Project
Grant a group permissions to this project.
setPermissions(Project, Set<Permission>) - 
Method in class net.sf.basedb.core.ProjectPermissions
Grant permissions to a project.
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.UserPermissions
Grant permissions to a user.
setPermissions - 
Variable in class net.sf.basedb.plugins.PluginConfigurationImporter
 
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.data.UserData
 
setPhone(String) - 
Method in class net.sf.basedb.core.User
Set the phone number to the user, or null if unknown.
setPlate(PlateData) - 
Method in class net.sf.basedb.core.data.ArrayDesignPlateData
 
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.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(PlateGeometry) - 
Method in class net.sf.basedb.core.BioPlate
 
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.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(Platform) - 
Method in class net.sf.basedb.core.ArrayDesign
Set the platform of the array design.
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.PlatformVariant
 
setPlatform(Platform, RawDataType) - 
Method in class net.sf.basedb.core.RawBioAssay
Set the platform and raw data type of the raw bioassay.
setPlatformId(int) - 
Method in class net.sf.basedb.info.RawBioAssayInfo
 
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
 
setPluginConf(List, PluginConfiguration) - 
Method in class net.sf.basedb.plugins.PluginConfigurationImporter
Sets parameters for a PluginConfiguration
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
 
setPooled(boolean) - 
Method in class net.sf.basedb.core.data.MeasuredBioMaterialData
 
setPooled(boolean) - 
Method in class net.sf.basedb.core.MeasuredBioMaterial
Specify if this biomaterial was created by pooling or not.
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(String) - 
Method in class net.sf.basedb.clients.web.taglib.tab.TabControl
 
setPosition(int) - 
Method in class net.sf.basedb.core.data.ArrayDesignPlateData
 
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.
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.
setPrepared(String) - 
Method in class net.sf.basedb.core.Job
Deprecated. Use Job.setPrepared(String, JobAgent) instead
setPrepared(String, JobAgent) - 
Method in class net.sf.basedb.core.Job
Set the job's status to Job.Status.PREPARED.
setPreview(boolean) - 
Method in class net.sf.basedb.core.data.ImageData
 
setPreview(boolean) - 
Method in class net.sf.basedb.core.Image
Set a flag indicating if this image is a preview image
                or the full-sized image.
setPrintRobot(Hardware) - 
Method in class net.sf.basedb.core.ArrayBatch
Set the print robot used for this array batch.
setPrintRobot(HardwareData) - 
Method in class net.sf.basedb.core.data.ArrayBatchData
 
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(long, String) - 
Method in class net.sf.basedb.util.basefile.BaseFileParser
Update the progress of the parsing.
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.
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(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(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
 
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(Map<String, String>) - 
Method in class net.sf.basedb.core.data.ProjectData
 
setProjectDefaults(Project) - 
Method in class net.sf.basedb.core.RawBioAssay
Set software, protocol and array design from project default settings.
setProjectDefaults(Project) - 
Method in class net.sf.basedb.core.Scan
Set scanner and protocol from project default settings.
setProjectId(Integer) - 
Method in class net.sf.basedb.core.data.ChangeHistoryData
 
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.
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(ProjectKey) - 
Method in interface net.sf.basedb.core.Shareable
Set the ProjectKey for this item.
setProjectKey(ShareableData, ProjectKey) - 
Static method in class net.sf.basedb.core.ShareableUtil
Set the project key of a ShareableData object.
setProjectKey(ProjectKey) - 
Method in class net.sf.basedb.core.SharedItem
 
setProjectKeys(Set<ProjectKeyData>) - 
Method in class net.sf.basedb.core.data.ProjectData
 
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(Map<ProjectData, Integer>) - 
Method in class net.sf.basedb.core.data.ProjectKeyData
 
setProjects(Set<ProjectData>) - 
Method in class net.sf.basedb.core.data.UserData
 
setProperties(Object) - 
Method in class net.sf.basedb.core.hibernate.QueryWrapper
 
setProperties(Map) - 
Method in class net.sf.basedb.core.hibernate.QueryWrapper
 
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, 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) - 
Method in class net.sf.basedb.util.export.spotdata.AssayPropertyField
Set the property that should be exported.
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
 
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(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(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.PlateEventData
 
setProtocol(ProtocolData) - 
Method in class net.sf.basedb.core.data.RawBioAssayData
 
setProtocol(ProtocolData) - 
Method in class net.sf.basedb.core.data.ScanData
 
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.
setProtocol(Protocol) - 
Method in class net.sf.basedb.core.Scan
Set the Protocol used to create this scan.
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
 
setProtocolParameter(boolean) - 
Method in class net.sf.basedb.info.AnnotationTypeInfo
 
setProtocols(Set<ProtocolData>) - 
Method in class net.sf.basedb.core.data.AnnotationTypeData
 
setProtocols(Set<ProtocolData>) - 
Method in class net.sf.basedb.core.data.ProtocolTypeData
 
setProtocolType(ProtocolTypeData) - 
Method in class net.sf.basedb.core.data.PlateEventTypeData
 
setProtocolType(ProtocolTypeData) - 
Method in class net.sf.basedb.core.data.ProtocolData
 
setProtocolType(ProtocolType) - 
Method in class net.sf.basedb.core.PlateEventType
Set the protocol type of this PlateTypeEvent item.
setProtocolType(ProtocolType) - 
Method in class net.sf.basedb.core.Protocol
Set the protocol type of this Protocol 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.
setPublication(String) - 
Method in class net.sf.basedb.info.ExperimentInfo
 
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.
setPublicationDate(Date) - 
Method in class net.sf.basedb.info.ExperimentInfo
 
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.
setPubMedId(String) - 
Method in class net.sf.basedb.info.ExperimentInfo
 
setQuality(float) - 
Method in class net.sf.basedb.core.data.SpotImagesData
 
setQuality(float) - 
Method in class net.sf.basedb.core.SpotImages
 
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(Map<QuotaIndex, Long>) - 
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.SpotImagesData
 
setRawBioAssay(RawBioAssay) - 
Method in class net.sf.basedb.core.SpotImages
Set the raw bioassay the spot images belongs to.
setRawBioAssays(Set<RawBioAssayData>) - 
Method in class net.sf.basedb.core.data.ExperimentData
 
setRawBioAssays(Set<RawBioAssayData>) - 
Method in class net.sf.basedb.core.data.ScanData
 
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.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.Platform
Set the raw data type.
setRawDataType(RawDataType) - 
Method in class net.sf.basedb.core.PlatformVariant
Set the raw data type.
setRawDataType(RawDataType) - 
Method in class net.sf.basedb.core.RawBioAssay
Deprecated. Use RawBioAssay.setPlatform(Platform, RawDataType) or 
                        RawBioAssay.setVariant(PlatformVariant, RawDataType) instead
setRawDataTypeId(String) - 
Method in class net.sf.basedb.info.RawBioAssayInfo
 
setRawParents(Set<RawBioAssayData>) - 
Method in class net.sf.basedb.core.data.BioAssayData
 
setRawSources(Set<RawBioAssayData>) - 
Method in class net.sf.basedb.core.data.TransformationData
 
setRawSources(Collection<RawBioAssay>) - 
Method in class net.sf.basedb.core.Transformation
Set the raw bioassay sources used in this transformation.
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.QueryWrapper
 
setReadOnly(Object, boolean) - 
Method in class net.sf.basedb.core.hibernate.SessionWrapper
 
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
Add an item to the "recently used items" list.
setRecent(BasicItem, String, int) - 
Method in class net.sf.basedb.core.ItemContext
Add an item to the "recently used items" list.
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
 
setRecordSeparator(String) - 
Method in class net.sf.basedb.clients.web.util.AjaxWriter
Deprecated. Change the record separator string.
setRedefinedColumnName(String, String, String) - 
Method in class net.sf.basedb.util.basefile.BaseFileParser
Redefined a column name for a specified section.
setRedImageFile(FileData) - 
Method in class net.sf.basedb.core.data.SpotImagesData
 
setRedImageFile(File) - 
Method in class net.sf.basedb.core.SpotImages
 
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.
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.
setRemoteId(String) - 
Method in class net.sf.basedb.core.data.SessionData
 
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.data.BioAssaySetData
 
setRemoved(boolean) - 
Method in class net.sf.basedb.core.data.BioPlateEventTypeData
 
setRemoved(boolean) - 
Method in class net.sf.basedb.core.data.BioPlateTypeData
 
setRemoved(boolean) - 
Method in class net.sf.basedb.core.data.CommonData
 
setRemoved(boolean) - 
Method in class net.sf.basedb.core.data.DataFileTypeData
 
setRemoved(boolean) - 
Method in class net.sf.basedb.core.data.ExtraValueTypeData
 
setRemoved(boolean) - 
Method in class net.sf.basedb.core.data.GroupData
 
setRemoved(boolean) - 
Method in class net.sf.basedb.core.data.HardwareTypeData
 
setRemoved(boolean) - 
Method in class net.sf.basedb.core.data.ImageData
 
setRemoved(boolean) - 
Method in class net.sf.basedb.core.data.JobData
 
setRemoved(boolean) - 
Method in class net.sf.basedb.core.data.MessageData
 
setRemoved(boolean) - 
Method in class net.sf.basedb.core.data.MimeTypeData
 
setRemoved(boolean) - 
Method in class net.sf.basedb.core.data.NewsData
 
setRemoved(boolean) - 
Method in class net.sf.basedb.core.data.PlateEventTypeData
 
setRemoved(boolean) - 
Method in class net.sf.basedb.core.data.PlateGeometryData
 
setRemoved(boolean) - 
Method in class net.sf.basedb.core.data.PlatformData
 
setRemoved(boolean) - 
Method in class net.sf.basedb.core.data.PlatformVariantData
 
setRemoved(boolean) - 
Method in class net.sf.basedb.core.data.PluginDefinitionData
 
setRemoved(boolean) - 
Method in class net.sf.basedb.core.data.PluginTypeData
 
setRemoved(boolean) - 
Method in class net.sf.basedb.core.data.ProjectData
 
setRemoved(boolean) - 
Method in class net.sf.basedb.core.data.ProtocolTypeData
 
setRemoved(boolean) - 
Method in class net.sf.basedb.core.data.QuantityData
 
setRemoved(boolean) - 
Method in class net.sf.basedb.core.data.QuotaData
 
setRemoved(boolean) - 
Method in interface net.sf.basedb.core.data.RemovableData
Set the removed flag for this item.
setRemoved(boolean) - 
Method in class net.sf.basedb.core.data.ReporterTypeData
 
setRemoved(boolean) - 
Method in class net.sf.basedb.core.data.RoleData
 
setRemoved(boolean) - 
Method in class net.sf.basedb.core.data.TransformationData
 
setRemoved(boolean) - 
Method in class net.sf.basedb.core.data.UnitData
 
setRemoved(boolean) - 
Method in class net.sf.basedb.core.data.UserData
 
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.HardwareType
 
setRemoved(boolean) - 
Method in class net.sf.basedb.core.Image
 
setRemoved(boolean) - 
Method in class net.sf.basedb.core.Job
 
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.ProtocolType
 
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
 
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
 
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.
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(Set<ReporterListScoreData>) - 
Method in class net.sf.basedb.core.data.ReporterData
 
setReporterListScores(Map<Integer, ReporterListScoreData>) - 
Method in class net.sf.basedb.core.data.ReporterListData
 
setReporters(Set<ReporterData>) - 
Method in class net.sf.basedb.core.data.ReporterTypeData
This is the inverse end.
setReporterType(ReporterTypeData) - 
Method in class net.sf.basedb.core.data.ReporterData
 
setReporterType(ReporterData, ReporterType) - 
Static method in class net.sf.basedb.core.Reporter
Set the reporter type on a reporter data object.
setRequired(boolean) - 
Method in class net.sf.basedb.clients.web.taglib.Select
 
setRequired(boolean) - 
Method in class net.sf.basedb.core.data.PlatformFileTypeData
 
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
 
setRequiredForMiame(boolean) - 
Method in class net.sf.basedb.info.AnnotationTypeInfo
 
setRequiresConfiguration(boolean) - 
Method in class net.sf.basedb.core.data.PluginDefinitionData
 
setRequiresConfiguration(boolean) - 
Method in class net.sf.basedb.core.PluginDefinition
 
setRestriction(String) - 
Method in class net.sf.basedb.info.QueryOptions
Sets restriction for these query options.
setRestrictionParameters(SQLQuery) - 
Method in class net.sf.basedb.core.AnnotationBetweenRestriction
 
setRestrictionParameters(SQLQuery) - 
Method in class net.sf.basedb.core.AnnotationInRestriction
 
setRestrictionParameters(SQLQuery) - 
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(SQLQuery) - 
Method in class net.sf.basedb.core.AnnotationSimpleRestriction
 
setRestrictionParameters(SQLQuery) - 
Method in class net.sf.basedb.core.HasAnnotationRestriction
 
setRestrictionPrefix(String) - 
Method in class net.sf.basedb.info.QueryOptions
Sets the prefix to use in restrictions or expression
setRestrictionWithPrefix(String, String) - 
Method in class net.sf.basedb.info.QueryOptions
Sets both the restriction and the prefix with it.
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.
setResultTransformer(ResultTransformer) - 
Method in class net.sf.basedb.core.hibernate.QueryWrapper
 
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.
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(String) - 
Method in class net.sf.basedb.util.extensions.xml.PathConverter
Set the value of the root path.
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(Integer) - 
Method in class net.sf.basedb.core.data.RawData
 
setRow(int) - 
Method in class net.sf.basedb.core.data.WellData
 
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.
setRowsperpage(String) - 
Method in class net.sf.basedb.clients.web.taglib.table.Navigator
 
setRowsperpage(int) - 
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.
setSample(Sample, Float) - 
Method in class net.sf.basedb.core.Extract
Set the Sample item that is the parent
                of this extract.
setSc(SessionControl) - 
Method in class net.sf.basedb.clients.web.taglib.table.Table
 
setScan(ScanData) - 
Method in class net.sf.basedb.core.data.ImageData
 
setScan(ScanData) - 
Method in class net.sf.basedb.core.data.RawBioAssayData
 
setScan(Scan) - 
Method in class net.sf.basedb.core.Image
Set the scan this image belongs to.
setScan(Scan) - 
Method in class net.sf.basedb.core.RawBioAssay
Set the Scan this raw bioassay is created from.
setScanner(HardwareData) - 
Method in class net.sf.basedb.core.data.ScanData
 
setScanner(Hardware) - 
Method in class net.sf.basedb.core.Scan
Set the Hardware (scanner) used to create this scan.
setScans(Set<ScanData>) - 
Method in class net.sf.basedb.core.data.HybridizationData
 
setScheduled(Date) - 
Method in class net.sf.basedb.core.data.JobData
 
setSchema(int) - 
Method in class net.sf.basedb.info.VersionInfo
 
setSchemaVersion(int) - 
Method in class net.sf.basedb.core.data.SchemaVersionData
 
setSchemaVersion(Session, 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
 
setSecondaryLocation(boolean) - 
Method in class net.sf.basedb.core.data.QuotaTypeData
 
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(User) - 
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
 
setSerializable(String, Serializable) - 
Method in class net.sf.basedb.core.hibernate.QueryWrapper
 
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.
setServiceFactory(ServiceFactory) - 
Method in class net.sf.basedb.ws.client.AbstractRPCClient
Sets the factory that is used to create RPCServiceClient
                objects for this web service.
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
 
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.
setSettings(Map<String, String>) - 
Method in class net.sf.basedb.core.data.ContextData
 
setSeverity(Validator, Severity) - 
Method in class net.sf.basedb.util.overview.ValidationOptions
Set a severity level for the specified validation rule.
setShared(boolean) - 
Method in class net.sf.basedb.info.SharedItemInfo
 
setShort(int, short) - 
Method in class net.sf.basedb.core.hibernate.QueryWrapper
 
setShort(String, short) - 
Method in class net.sf.basedb.core.hibernate.QueryWrapper
 
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
 
setSignalReceiver(SignalReceiver) - 
Method in class net.sf.basedb.clients.jobagent.executors.ThreadJobExecutor
 
setSignalTransporter(String) - 
Method in class net.sf.basedb.core.data.JobData
 
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.
setSingleValue(Object) - 
Method in class net.sf.basedb.core.data.DateParameterValueData
Overrides the parent method since we want to get rid of the
                time part of the date.
setSingleValue(Object) - 
Method in class net.sf.basedb.core.data.ParameterValueData
Replace the current list with a single new value.
setSize(int) - 
Method in class net.sf.basedb.core.data.BioMaterialListData
 
setSize(long) - 
Method in class net.sf.basedb.core.data.FileData
 
setSize(int) - 
Method in class net.sf.basedb.core.data.ReporterListData
 
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.RawBioAssayData
 
setSoftware(Set<SoftwareData>) - 
Method in class net.sf.basedb.core.data.SoftwareTypeData
 
setSoftware(Software) - 
Method in class net.sf.basedb.core.RawBioAssay
Set the Software used while analysing the scanned images.
setSoftwareType(SoftwareTypeData) - 
Method in class net.sf.basedb.core.data.SoftwareData
 
setSoftwareType(SoftwareType) - 
Method in class net.sf.basedb.core.Software
Set the SoftwareType of this Software item.
setSortable(boolean) - 
Method in class net.sf.basedb.clients.web.taglib.table.ColumnDef
 
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.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(MeasuredBioMaterial, Float) - 
Method in class net.sf.basedb.core.BioMaterialEvent
Set a single source.
setSource(BioAssaySetData) - 
Method in class net.sf.basedb.core.data.TransformationData
 
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.
setSourceBioMaterials(Set<MeasuredBioMaterialData>) - 
Method in class net.sf.basedb.core.data.BioMaterialEventData
 
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.
setSourceEvents(Set<BioMaterialSourceEventData>) - 
Method in class net.sf.basedb.core.data.MeasuredBioMaterialData
 
setSourceFile(File) - 
Method in class net.sf.basedb.util.importer.spotdata.BaseFileImporter
Deprecated. In 2.16, use BaseFileImporter.setSourceFileWrapper(FileWrapper) instead
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.
setSourceGroup(MeasuredBioMaterial, int) - 
Method in class net.sf.basedb.core.BioMaterialEvent
Set the source group for a biomaterial that was used as a source in this event.
setSourceGroup(int) - 
Method in class net.sf.basedb.core.data.BioMaterialSourceEventData
 
setSourceGroup(int) - 
Method in class net.sf.basedb.core.data.UsedQuantity
 
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.
setSources(Map<MeasuredBioMaterialData, UsedQuantity>) - 
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, EntityLogger) - 
Method in class net.sf.basedb.core.log.db.DbLogManagerFactory
Register a special logger for entities of the given class.
setSpotImages(SpotImagesData) - 
Method in class net.sf.basedb.core.data.RawBioAssayData
 
setSpotImagesFile(FileData) - 
Method in class net.sf.basedb.core.data.SpotImagesData
 
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
 
setSpotsize(int) - 
Method in class net.sf.basedb.core.data.SpotImagesData
 
setSpotsize(int) - 
Method in class net.sf.basedb.core.SpotImages
 
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.
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(Date) - 
Method in class net.sf.basedb.core.data.JobData
 
setStarted(Class<? extends SignalTransporter>, String) - 
Method in class net.sf.basedb.core.Job.ProgressReporterImpl
 
setStatus(ExtensionsFile, String) - 
Method in class net.sf.basedb.clients.web.extensions.ScanResults
Sets the short status message for an entire file.
setStatus(int) - 
Method in class net.sf.basedb.core.data.JobData
 
setStatusMessage(String) - 
Method in class net.sf.basedb.core.data.JobData
 
setString(int, String) - 
Method in class net.sf.basedb.core.hibernate.QueryWrapper
 
setString(String, String) - 
Method in class net.sf.basedb.core.hibernate.QueryWrapper
 
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.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.Body
 
setStyle(String) - 
Method in class net.sf.basedb.clients.web.taglib.Button
 
setStyle(String) - 
Method in class net.sf.basedb.clients.web.taglib.ButtonGroup
 
setStyle(String) - 
Method in class net.sf.basedb.clients.web.taglib.Help
 
setStyle(String) - 
Method in class net.sf.basedb.clients.web.taglib.HideableSection
 
setStyle(String) - 
Method in class net.sf.basedb.clients.web.taglib.Icon
 
setStyle(String) - 
Method in class net.sf.basedb.clients.web.taglib.menu.Menu
 
setStyle(String) - 
Method in class net.sf.basedb.clients.web.taglib.menu.Menuitem
 
setStyle(String) - 
Method in class net.sf.basedb.clients.web.taglib.menu.Menuseparator
 
setStyle(String) - 
Method in class net.sf.basedb.clients.web.taglib.menu.Submenu
 
setStyle(String) - 
Method in class net.sf.basedb.clients.web.taglib.Note
 
setStyle(String) - 
Method in class net.sf.basedb.clients.web.taglib.path.Path
 
setStyle(String) - 
Method in class net.sf.basedb.clients.web.taglib.path.PathElement
 
setStyle(String) - 
Method in class net.sf.basedb.clients.web.taglib.Select
 
setStyle(String) - 
Method in class net.sf.basedb.clients.web.taglib.tab.Tab
 
setStyle(String) - 
Method in class net.sf.basedb.clients.web.taglib.tab.TabControl
 
setStyle(String) - 
Method in class net.sf.basedb.clients.web.taglib.table.Button
 
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.ColumnDef
 
setStyle(String) - 
Method in class net.sf.basedb.clients.web.taglib.table.Data
 
setStyle(String) - 
Method in class net.sf.basedb.clients.web.taglib.table.Header
 
setStyle(String) - 
Method in class net.sf.basedb.clients.web.taglib.table.Label
 
setStyle(String) - 
Method in class net.sf.basedb.clients.web.taglib.table.Navigator
 
setStyle(String) - 
Method in class net.sf.basedb.clients.web.taglib.table.Panel
 
setStyle(String) - 
Method in class net.sf.basedb.clients.web.taglib.table.PresetSelector
 
setStyle(String) - 
Method in class net.sf.basedb.clients.web.taglib.table.Row
 
setStyle(String) - 
Method in class net.sf.basedb.clients.web.taglib.table.Table
 
setStyle(String) - 
Method in class net.sf.basedb.clients.web.taglib.table.Toolbar
 
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.
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
 
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.clients.web.extensions.ScanResults
 
setSupportsConfigurations(boolean) - 
Method in class net.sf.basedb.core.data.PluginDefinitionData
 
setSupportsConfigurations(boolean) - 
Method in class net.sf.basedb.core.PluginDefinition
 
setSwitch(String) - 
Method in class net.sf.basedb.clients.web.taglib.tab.TabControl
 
setSymbol(String) - 
Method in class net.sf.basedb.core.data.ReporterData
 
setSymbol(String) - 
Method in class net.sf.basedb.core.data.UnitSymbolData
 
setSymbols(Set<UnitSymbolData>) - 
Method in class net.sf.basedb.core.data.QuantityData
 
setSymbols(Set<UnitSymbolData>) - 
Method in class net.sf.basedb.core.data.UnitData
 
setSymbols(Set<String>) - 
Method in class net.sf.basedb.core.Unit
Set the symbols that should be registered for this unit.
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.FileTypeData
 
setSystemId(String) - 
Method in class net.sf.basedb.core.data.GroupData
 
setSystemId(String) - 
Method in class net.sf.basedb.core.data.HardwareTypeData
 
setSystemId(String) - 
Method in class net.sf.basedb.core.data.ProtocolTypeData
 
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.SoftwareTypeData
 
setSystemId(String) - 
Method in class net.sf.basedb.core.data.UserData
 
setTabcontrol(String) - 
Method in class net.sf.basedb.clients.web.taglib.Help
 
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
 
setText(String, String) - 
Method in class net.sf.basedb.core.hibernate.QueryWrapper
 
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
 
setTime(Date) - 
Method in class net.sf.basedb.core.data.ChangeHistoryData
 
setTime(int, Date) - 
Method in class net.sf.basedb.core.hibernate.QueryWrapper
 
setTime(String, Date) - 
Method in class net.sf.basedb.core.hibernate.QueryWrapper
 
setTimeout(int) - 
Method in class net.sf.basedb.core.hibernate.QueryWrapper
 
setTimeSent(Date) - 
Method in class net.sf.basedb.core.data.MessageData
 
setTimestamp(int, Date) - 
Method in class net.sf.basedb.core.hibernate.QueryWrapper
 
setTimestamp(String, Date) - 
Method in class net.sf.basedb.core.hibernate.QueryWrapper
 
Setting<D extends SettingData> - Class in net.sf.basedb.core
This is the base class for all setting items.
Setting(D) - 
Constructor for class net.sf.basedb.core.Setting
 
SettingData - Class in net.sf.basedb.core.data
 
SettingData() - 
Constructor for class net.sf.basedb.core.data.SettingData
 
settings - 
Variable in class net.sf.basedb.clients.jobagent.JobRunner
 
settings - 
Static variable in class net.sf.basedb.clients.web.extensions.ExtensionsControl
 
settings - 
Static variable in class net.sf.basedb.clients.web.extensions.service.Services
 
settings - 
Variable in class net.sf.basedb.clients.web.extensions.service.ServicesEventHandler
 
Settings - Class in net.sf.basedb.clients.web.extensions
Class for keeping settings for the extensions system.
Settings(ExtensionsDirectory, File) - 
Constructor for class net.sf.basedb.clients.web.extensions.Settings
Create a new Settings object.
settings - 
Variable in class net.sf.basedb.clients.web.extensions.Settings
 
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.
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.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.HideableSection
 
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.Note
 
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.core.data.ExperimentData
 
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.info.ExperimentInfo
 
setTitle(String) - 
Method in class net.sf.basedb.info.ExtendedPropertyInfo
 
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(User) - 
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
 
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
 
setTotalrows(String) - 
Method in class net.sf.basedb.clients.web.taglib.table.Navigator
 
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
 
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(Transformation) - 
Method in class net.sf.basedb.core.BioAssaySet
Set the transformation that created this bioassayset.
setTransformation(TransformationData) - 
Method in class net.sf.basedb.core.data.BioAssaySetData
 
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.RawBioAssayData
 
setTrimQuotes(boolean) - 
Method in class net.sf.basedb.util.parser.FlatFileParser
Set if quotes around each data value should be removed or not.
setTrusted(Boolean) - 
Method in class net.sf.basedb.core.data.JobAgentSettingsData
 
setTrusted(boolean) - 
Method in class net.sf.basedb.core.data.PluginDefinitionData
 
setTrusted(Boolean) - 
Method in class net.sf.basedb.core.JobAgentSettings
Set the trusted flag for this plugin.
setTrusted(boolean) - 
Method in class net.sf.basedb.core.PluginDefinition
Set if this plugin should be trusted or not.
setType(MenuItemAction.MenuType) - 
Method in class net.sf.basedb.clients.web.extensions.menu.FixedMenuItemFactory
 
setType(String) - 
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(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.menu.Menu
 
setType(String) - 
Method in class net.sf.basedb.clients.web.taglib.Note
 
setType(String) - 
Method in class net.sf.basedb.clients.web.taglib.Page
 
setType(int) - 
Method in class net.sf.basedb.core.data.FormulaData
 
setType(int) - 
Method in class net.sf.basedb.core.data.JobData
 
setType(Type) - 
Method in class net.sf.basedb.core.query.QueryParameter
Changes the type of the parameter.
setType(String) - 
Method in class net.sf.basedb.info.QueryParameter
Set the parameter type.
setType(String) - 
Method in class net.sf.basedb.plugins.executor.ParameterDefinition
Set 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.
setUnit(Unit) - 
Method in class net.sf.basedb.clients.web.taglib.table.ColumnDef
 
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.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
 
setUpdateable(boolean) - 
Method in class net.sf.basedb.info.ExtendedPropertyInfo
 
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.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, boolean) - 
Method in class net.sf.basedb.core.File
Set the URL to an external file that should represent this file
                object.
setUrl(String) - 
Method in class net.sf.basedb.core.PluginDefinition
The URL cannot be changed.
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
 
setUsableUnits(Set<UnitData>) - 
Method in class net.sf.basedb.core.data.AnnotationTypeData
 
setUsedQuantity(Float) - 
Method in class net.sf.basedb.core.BioMaterialEvent
Set the used quantity.
setUsedQuantity(Float) - 
Method in class net.sf.basedb.core.data.BioMaterialEventData
 
setUsedQuantity(Float) - 
Method in class net.sf.basedb.core.data.BioMaterialSourceEventData
 
setUsedQuantity(Float) - 
Method in class net.sf.basedb.core.data.UsedQuantity
 
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(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.
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.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.
setUsers(Set<UserData>) - 
Method in class net.sf.basedb.core.data.GroupData
 
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.RoleData
 
setUserSettings(Set<UserClientSettingData>) - 
Method in class net.sf.basedb.core.data.ClientData
 
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.FileSet.DataFileHandlerWrapper
 
setValid(Boolean, String) - 
Method in class net.sf.basedb.core.FileSetMember
Set the validation status of this member.
setValidate(String) - 
Method in class net.sf.basedb.clients.web.taglib.tab.Tab
 
setValidatorClass(String) - 
Method in class net.sf.basedb.core.data.DataFileTypeData
 
setValidatorClass(String) - 
Method in class net.sf.basedb.core.DataFileType
Set the class name of the Java class that is used to validate the files of
                this type.
setValidatorJarPath(String) - 
Method in class net.sf.basedb.core.data.DataFileTypeData
 
setValidatorJarPath(String) - 
Method in class net.sf.basedb.core.DataFileType
Set the path to the JAR file where the validator class is located.
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(String) - 
Method in class net.sf.basedb.clients.web.taglib.table.Hidden
 
setValue(Object) - 
Method in class net.sf.basedb.core.Annotation
 
setValue(Object, Unit) - 
Method in class net.sf.basedb.core.Annotation
Set the value of the annotation, replacing any previous values.
setValue(String) - 
Method in class net.sf.basedb.core.data.PropertyFilterData
 
setValue(String) - 
Method in class net.sf.basedb.core.data.SettingData
 
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) - 
Method in class net.sf.basedb.core.PropertyFilter
Set the value to use in the filter.
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.core.Setting
Set the value for this setting.
setValue(String) - 
Method in class net.sf.basedb.info.QueryParameter
Set the parameter name.
setValues(List<?>) - 
Method in class net.sf.basedb.core.Annotation
 
setValues(List<?>, Unit) - 
Method in class net.sf.basedb.core.Annotation
Set the values of the annotation, replacing any previous values.
setValues(List<?>) - 
Method in class net.sf.basedb.core.AnnotationType
Set the list of allowed values for an enumerated annotation type.
setValues(ParameterValueData<?>) - 
Method in class net.sf.basedb.core.data.AnnotationData
 
setValues(List<Boolean>) - 
Method in class net.sf.basedb.core.data.BooleanParameterValueData
 
setValues(List<Date>) - 
Method in class net.sf.basedb.core.data.DateParameterValueData
 
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<BasicData>) - 
Method in class net.sf.basedb.core.data.ItemParameterValueData
 
setValues(List<Long>) - 
Method in class net.sf.basedb.core.data.LongParameterValueData
 
setValues(List<T>) - 
Method in class net.sf.basedb.core.data.ParameterValueData
Set values of this parameter.
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.TimestampParameterValueData
 
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[]) - 
Method in class net.sf.basedb.info.AnnotationInfo
 
setValues(List<?>) - 
Method in class net.sf.basedb.plugins.executor.ProgramParameter
 
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(Integer) - 
Method in class net.sf.basedb.core.data.FormulaData
 
setValueType(int) - 
Method in class net.sf.basedb.core.data.PropertyFilterData
 
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.
setValueType(String) - 
Method in class net.sf.basedb.info.AnnotationInfo
 
setValueType(String) - 
Method in class net.sf.basedb.info.AnnotationTypeInfo
 
setVariable(String, String) - 
Method in class net.sf.basedb.util.extensions.xml.VariableConverter
Set the value of a variable.
setVariant(PlatformVariant) - 
Method in class net.sf.basedb.core.ArrayDesign
Set the platform and variant of the array design.
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, 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
 
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(int) - 
Method in class net.sf.basedb.info.BasicItemInfo
 
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
The version cannot be changed.
setVersionString(String) - 
Method in class net.sf.basedb.core.Software
Set the versionstring for this Software item.
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(String) - 
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(String) - 
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(String) - 
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(String) - 
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.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.Note
 
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
 
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(String) - 
Method in class net.sf.basedb.clients.web.extensions.plot.MAPlotFactory
 
setWidth(int) - 
Method in class net.sf.basedb.clients.web.extensions.plot.PlotGeneratorBean
 
setWidth(String) - 
Method in class net.sf.basedb.clients.web.taglib.tab.TabControl
 
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
 
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.
setX(Float) - 
Method in class net.sf.basedb.core.data.RawData
 
setXOffset(int) - 
Method in class net.sf.basedb.core.data.SpotImagesData
 
setXOffset(int) - 
Method in class net.sf.basedb.core.SpotImages
 
setXScale(int) - 
Method in class net.sf.basedb.core.data.SpotImagesData
 
setXScale(int) - 
Method in class net.sf.basedb.core.SpotImages
 
setY(Float) - 
Method in class net.sf.basedb.core.data.RawData
 
setYOffset(int) - 
Method in class net.sf.basedb.core.data.SpotImagesData
 
setYOffset(int) - 
Method in class net.sf.basedb.core.SpotImages
 
setYScale(int) - 
Method in class net.sf.basedb.core.data.SpotImagesData
 
setYScale(int) - 
Method in class net.sf.basedb.core.SpotImages
 
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.
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_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.
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() - 
Constructor for class net.sf.basedb.core.ShareableUtil
 
ShareableUtil - Class in net.sf.basedb.util
 
ShareableUtil() - 
Constructor for class net.sf.basedb.util.ShareableUtil
 
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<D extends SharedData> - Class in net.sf.basedb.core
This class inherits from the OwnedItem
        class and implements the Shareable interface.
SharedItem(D) - 
Constructor for class net.sf.basedb.core.SharedItem
 
SharedItemInfo - Class in net.sf.basedb.info
 
SharedItemInfo() - 
Constructor for class net.sf.basedb.info.SharedItemInfo
 
sharedTo(boolean, Restriction, Restriction, Restriction) - 
Static method in class net.sf.basedb.core.query.Hql
A special restriction that works on Shareable items.
sharedTo - 
Variable in class net.sf.basedb.core.query.SharedToRestriction
 
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.
SHORT - 
Static variable in class net.sf.basedb.core.hibernate.TypeWrapper
 
shortName - 
Variable in enum net.sf.basedb.core.Project.Default
 
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.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
 
showInitially - 
Variable in class net.sf.basedb.clients.web.taglib.HideableSection
If the section should be shown or hidden to start with.
SHUTDOWN - 
Static variable in class net.sf.basedb.core.signal.Signal
The SHUTDOWN signal, that requests that the receiver should
                clean up and die.
shutdown(HttpClient) - 
Static method in class net.sf.basedb.util.HttpUtil
Safely shuts down a http client and it's connection manager
                without trowing an exception.
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 - 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
 
signal - 
Variable in class net.sf.basedb.core.signal.SimpleSignalSender
 
signal - 
Variable in exception net.sf.basedb.core.signal.UnsupportedSignalException
 
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(Throwable) - 
Constructor for exception net.sf.basedb.core.signal.SignalException
 
SignalException(String, 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 - Interface in net.sf.basedb.core.signal
A signal handler is an object that is able to receive and act on signals.
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.BioAssaySetExporter
Deprecated.  
signalHandler - 
Variable in class net.sf.basedb.plugins.CdfFileReporterImporter
 
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.plugins.SpotImageCreator
 
signalHandler - 
Variable in class net.sf.basedb.util.zip.AbstractFileUnpacker
 
signalHandlerURI - 
Variable in class net.sf.basedb.core.signal.AbstractSignalTransporter
 
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(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.
SignalReceivedException(List<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.
simple(Expression, String, Formula.AverageMethod, Formatter<?>) - 
Static method in class net.sf.basedb.util.export.spotdata.ExportableFieldFactory
Deprecated. In 2.15, use ExportableFieldFactory.simple(Expression, String, Type, net.sf.basedb.core.Formula.AverageMethod, Formatter) 
                        instead
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.
SimpleAuthenticator - Class in net.sf.basedb.core.authentication
This class is an example implementation of the Authenticator
        interface that authenticates everyone as long as the login is the same
        as the password.
SimpleAuthenticator() - 
Constructor for class net.sf.basedb.core.authentication.SimpleAuthenticator
Create a new SimpleAuthenticator object.
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
 
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.
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(Extension) - 
Constructor for class net.sf.basedb.util.extensions.SingleExtensionFilter
Create a filter that enables the given 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.
size - 
Variable in class net.sf.basedb.clients.web.extensions.ExtensionsFile
 
size - 
Variable in class net.sf.basedb.core.data.BioMaterialListData
 
size - 
Variable in class net.sf.basedb.core.data.FileData
 
size - 
Variable in class net.sf.basedb.core.data.ReporterListData
 
size - 
Variable in class net.sf.basedb.core.dbengine.TableInfo.ColumnInfo
 
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.ProjectPermissions
Get the number of entries.
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.
size() - 
Method in class net.sf.basedb.core.UserPermissions
Get the number of entries.
size - 
Variable in class net.sf.basedb.core.VirtualColumn
The size of the column if it is a string.
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 - 
Variable in class net.sf.basedb.util.JarClassLoader.JarInfo
 
size(String) - 
Method in class net.sf.basedb.util.StaticCache
Checks the size (in bytes) of a cache entry.
size() - 
Method in class net.sf.basedb.util.Tree
 
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.
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.
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.
slot - 
Variable in class net.sf.basedb.clients.jobagent.slotmanager.MasterSlotManager.RemoteSlot
 
Slot - Class in net.sf.basedb.clients.jobagent.slotmanager
Represents a slot that has been assigned to a job.
Slot(Job.ExecutionTime) - 
Constructor for class net.sf.basedb.clients.jobagent.slotmanager.Slot
Create a new slot and automatically assign an id to
                it.
Slot(String, Job.ExecutionTime) - 
Constructor for class net.sf.basedb.clients.jobagent.slotmanager.Slot
Create a new slot.
slot - 
Variable in class net.sf.basedb.core.InternalJobQueue.JobRunner
 
slot - 
Variable in class net.sf.basedb.util.jobagent.JobInfo
 
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 - 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.
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
 
snapshots - 
Variable in class net.sf.basedb.core.snapshot.SnapshotManager
 
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.
SocketSignalReceiver.ListenerThread(ServerSocketChannel) - 
Constructor for class net.sf.basedb.core.signal.SocketSignalReceiver.ListenerThread
 
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.RawBioAssayData
 
software - 
Variable in class net.sf.basedb.core.data.SoftwareTypeData
 
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 - 
Variable in class net.sf.basedb.plugins.IlluminaRawDataImporter
 
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.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.RawBioAssayImporter
 
softwareType - 
Variable in class net.sf.basedb.core.data.SoftwareData
 
SoftwareType - Class in net.sf.basedb.core
This class is used to represent the type of
        Software items in BASE.
SoftwareType(SoftwareTypeData) - 
Constructor for class net.sf.basedb.core.SoftwareType
Creates a new softwaretype.
SoftwareTypeData - Class in net.sf.basedb.core.data
This class holds information about a softwaretype.
SoftwareTypeData() - 
Constructor for class net.sf.basedb.core.data.SoftwareTypeData
 
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.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).
sortbyMultiple - 
Variable in class net.sf.basedb.clients.web.taglib.table.Table
 
sortChildren(Comparator<? super Node>) - 
Method in class net.sf.basedb.util.overview.Node
Sorts the list of child nodes.
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
 
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.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.core.data.TransformationData
 
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.export.spotdata.FieldConverter
Deprecated.  
SOURCE_BIOASSAYS - 
Static variable in class net.sf.basedb.core.plugin.AbstractAnalysisPlugin
 
SOURCE_BIOASSAYSET - 
Static variable in class net.sf.basedb.core.plugin.AbstractAnalysisPlugin
 
sourceBioAssaySetType - 
Static variable in class net.sf.basedb.core.plugin.AbstractAnalysisPlugin
The parameter type for the source bioassay set.
sourceBioMaterials - 
Variable in class net.sf.basedb.core.data.BioMaterialEventData
 
sourceColumnMapper - 
Variable in class net.sf.basedb.plugins.PlateMappingImporter
 
sourceCount - 
Variable in class net.sf.basedb.core.data.PlateMappingData
 
sourceEvents - 
Variable in class net.sf.basedb.core.data.MeasuredBioMaterialData
 
sourceFile - 
Variable in class net.sf.basedb.util.importer.spotdata.BaseFileImporter
 
sourceGeometry - 
Variable in class net.sf.basedb.core.data.PlateMappingData
 
sourceGroup - 
Variable in class net.sf.basedb.core.data.BioMaterialSourceEventData
 
sourceGroup - 
Variable in class net.sf.basedb.core.data.UsedQuantity
 
sourceIntensityTransform - 
Variable in class net.sf.basedb.core.data.FormulaData
 
sourceParameter - 
Variable in class net.sf.basedb.core.plugin.AbstractAnalysisPlugin
The source parameter.
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.
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
 
specialLoggers - 
Variable in class net.sf.basedb.core.log.db.DbLogManagerFactory
 
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_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.FileType
The id for the FileType item representing a
                file containing analysed spot data.
SPOT_IMAGES - 
Static variable in class net.sf.basedb.core.FileType
The id for the FileType item representing a
                spot images file.
spotBatcher - 
Variable in class net.sf.basedb.core.BioAssaySet
The one and only spot batcher for this bioassayset.
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.
spotBatcher - 
Variable in class net.sf.basedb.util.importer.spotdata.MatrixSpotIntensityEventHandler
 
spotBatcher - 
Variable in class net.sf.basedb.util.importer.spotdata.SerialSpotIntensityEventHandler
 
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
 
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
 
SpotImage - Class in net.sf.basedb.core
Holds the image information about a single spot image
        in PNG format.
SpotImage(byte[]) - 
Constructor for class net.sf.basedb.core.SpotImage
Constructor that takes the image as a byte array.
SpotImageCreator - Class in net.sf.basedb.plugins
 
SpotImageCreator() - 
Constructor for class net.sf.basedb.plugins.SpotImageCreator
 
SpotImageFormatter - Class in net.sf.basedb.clients.web.formatter
 
SpotImageFormatter(DbControl, RawDataType, String) - 
Constructor for class net.sf.basedb.clients.web.formatter.SpotImageFormatter
 
spotImages - 
Variable in class net.sf.basedb.core.data.RawBioAssayData
 
SpotImages - Class in net.sf.basedb.core
Holds settings for creating small spot iamges from 1-3
        image files and the raw data information for a single raw bioassay.
SpotImages(SpotImagesData) - 
Constructor for class net.sf.basedb.core.SpotImages
 
SpotImagesData - Class in net.sf.basedb.core.data
This class holds information about the settiings used to generate spot images
        for a raw bio assay.
SpotImagesData() - 
Constructor for class net.sf.basedb.core.data.SpotImagesData
 
spotImagesFile - 
Variable in class net.sf.basedb.core.data.SpotImagesData
 
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
 
spotsize - 
Variable in class net.sf.basedb.core.data.SpotImagesData
 
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.hibernate.ExecuteUpdateWork
 
sql - 
Variable in class net.sf.basedb.core.hibernate.ResultSetWork
 
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.
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
 
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(Expression) - 
Static method in class net.sf.basedb.core.query.Expressions
Calculate the square root of an expression: new expression = sqrt(e).
sqrt - 
Variable in class net.sf.basedb.core.query.QuadraticMeanExpression
 
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
 
ssc - 
Variable in class net.sf.basedb.core.Application.SecondaryStorageControllerTask
 
ssl - 
Static variable in class net.sf.basedb.util.EmailUtil
 
SSLUtil - Class in net.sf.basedb.util.ssl
Utility class for working with SSL connections.
SSLUtil() - 
Constructor for class net.sf.basedb.util.ssl.SSLUtil
 
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() - 
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(Extension) - 
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.
start - 
Variable in class net.sf.basedb.clients.web.fileupload.FileUpload.UploadStream
 
start() - 
Static method in class net.sf.basedb.core.Application
Starts the BASE application.
start(boolean) - 
Static method in class net.sf.basedb.core.Application
Starts the BASE application.
start(boolean, boolean, Boolean) - 
Static method in class net.sf.basedb.core.Application
Starts the BASE application.
start(String, String) - 
Method in class net.sf.basedb.core.Job
Deprecated. Use Job.start(String, String, JobAgent) instead
start(String, String, JobAgent) - 
Method in class net.sf.basedb.core.Job
Register the job as started.
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 - 
Variable in class net.sf.basedb.util.ChainedProgressReporter
 
start(int) - 
Method in class net.sf.basedb.util.timer.PerformanceTimer
Start the timer with the given index.
startActive - 
Variable in class net.sf.basedb.clients.web.taglib.tab.TabControl
The real ID of the tab that is initially active.
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
 
startJob(Job, JobAgentSettings) - 
Method in class net.sf.basedb.clients.jobagent.Agent
Start a job.
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 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.extensions.ScanResults
 
startTime - 
Variable in class net.sf.basedb.clients.web.fileupload.FileUploadProgress
 
startX - 
Variable in class net.sf.basedb.util.plot.HistogramPlot.HistogramBin
 
state - 
Variable in class net.sf.basedb.core.log.EntityDetails
 
stateless - 
Variable in class net.sf.basedb.core.AbstractHqlQuery
If the query should be executed in a stateless session or not.
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
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.CleanupTask(StaticCache, FileFilter) - 
Constructor for class net.sf.basedb.util.StaticCache.CleanupTask
 
StaticCache.LockEntry - Class in net.sf.basedb.util
Keeps track of a locked cached entry.
StaticCache.LockEntry(ReadWriteLock, String) - 
Constructor for class net.sf.basedb.util.StaticCache.LockEntry
 
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.LockSafeInputStream(InputStream, StaticCache.LockEntry) - 
Constructor for class net.sf.basedb.util.StaticCache.LockSafeInputStream
 
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.LockSafeOutputStream(OutputStream, StaticCache.LockEntry) - 
Constructor for class net.sf.basedb.util.StaticCache.LockSafeOutputStream
 
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.
staticIgnore - 
Variable in class net.sf.basedb.clients.web.extensions.ExtensionsDirectory
 
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
statistics - 
Variable in class net.sf.basedb.clients.web.ExperimentExplorer.AnnotationGroup
 
status - 
Variable in class net.sf.basedb.clients.web.extensions.ScanResults.FileResults
 
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
 
statusMessage - 
Variable in class net.sf.basedb.core.data.JobData
 
steps - 
Variable in class net.sf.basedb.util.collections.MultiStepCollectionTransformer
 
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(Extension) - 
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.
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.
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.
store(String, Object, int) - 
Method in class net.sf.basedb.util.StaticCache
Store a serializable object in the cache.
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.
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.
STRING - 
Static variable in class net.sf.basedb.core.hibernate.TypeWrapper
 
string(String) - 
Static method in class net.sf.basedb.core.query.Expressions
Create a constant expression from a string.
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(Type, Object) - 
Constructor for class net.sf.basedb.util.extensions.debug.StringConverter
 
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
 
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.
StringMatcher.FuzzyMatch(String, String, double) - 
Constructor for class net.sf.basedb.util.fuzzy.StringMatcher.FuzzyMatch
 
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
 
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
 
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.
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.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.Body
Optional style attribute
style - 
Variable in class net.sf.basedb.clients.web.taglib.Button
Optional style attribute
style - 
Variable in class net.sf.basedb.clients.web.taglib.ButtonGroup
Optional style attribute
style - 
Variable in class net.sf.basedb.clients.web.taglib.Help
Optional style attribute
style - 
Variable in class net.sf.basedb.clients.web.taglib.HideableSection
Optional style attribute
style - 
Variable in class net.sf.basedb.clients.web.taglib.Icon
Optional style attribute
style - 
Variable in class net.sf.basedb.clients.web.taglib.menu.Menu
Optional style attribute
style - 
Variable in class net.sf.basedb.clients.web.taglib.menu.Menuitem
Optional style attribute
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.menu.Submenu
Optional style attribute
style - 
Variable in class net.sf.basedb.clients.web.taglib.Note
Optional style attribute
style - 
Variable in class net.sf.basedb.clients.web.taglib.path.Path
Optional style attribute
style - 
Variable in class net.sf.basedb.clients.web.taglib.path.PathElement
Optional style attribute
style - 
Variable in class net.sf.basedb.clients.web.taglib.Select
Optional style attribute
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.tab.TabControl
Optional style attribute
style - 
Variable in class net.sf.basedb.clients.web.taglib.table.Button
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.ColumnDef
Optional style attribute
style - 
Variable in class net.sf.basedb.clients.web.taglib.table.Data
Optional style attribute
style - 
Variable in class net.sf.basedb.clients.web.taglib.table.Header
Optional style attribute
style - 
Variable in class net.sf.basedb.clients.web.taglib.table.Label
Optional style attribute
style - 
Variable in class net.sf.basedb.clients.web.taglib.table.Navigator
Optional style attribute
style - 
Variable in class net.sf.basedb.clients.web.taglib.table.Panel
Optional style attribute
style - 
Variable in class net.sf.basedb.clients.web.taglib.table.PresetSelector
Optional style attribute
style - 
Variable in class net.sf.basedb.clients.web.taglib.table.Row
Optional style attribute
style - 
Variable in class net.sf.basedb.clients.web.taglib.table.Table
Optional style attribute
style - 
Variable in class net.sf.basedb.clients.web.taglib.table.Toolbar
Optional style attribute
styles - 
Variable in class net.sf.basedb.clients.web.taglib.Head
A comma-separated list of stylesheets filenames.
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
 
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
 
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
 
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".
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.
subtype - 
Variable in class net.sf.basedb.util.bfs.MetadataModel
 
subtype - 
Variable in class net.sf.basedb.util.bfs.MetadataWriter
 
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
 
successMessage - 
Variable in class net.sf.basedb.clients.web.plugins.SimpleExport
 
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 - 
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(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 - 
Variable in class net.sf.basedb.util.plot.HistogramPlot.HistogramBin
 
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.clients.web.extensions.ScanResults
 
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(PluginType) - 
Method in class net.sf.basedb.core.PluginDefinition
Check if a plugin implements the interface specified by the plugin
                type.
supports(String) - 
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() - 
Method in class net.sf.basedb.clients.web.plugins.SimpleExport
 
supportsConfigurations - 
Variable in class net.sf.basedb.core.data.PluginDefinitionData
 
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.BfsExporterPlugin
 
supportsConfigurations() - 
Method in class net.sf.basedb.plugins.BioAssaySetExporter
Deprecated.  
supportsConfigurations() - 
Method in class net.sf.basedb.plugins.CdfFileReporterImporter
 
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.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.plugins.SpotImageCreator
 
supportsConfigurations() - 
Method in class net.sf.basedb.util.zip.AbstractFileUnpacker
Returns FALSE.
supportsExtraInformation() - 
Method in interface net.sf.basedb.core.authentication.Authenticator
Should return TRUE or FALSE depending on if the authentication
                server returns additional information about the user.
supportsExtraInformation() - 
Method in class net.sf.basedb.core.authentication.POP3Authenticator
Always return FALSE.
supportsExtraInformation() - 
Method in class net.sf.basedb.core.authentication.SimpleAuthenticator
Always return FALSE.
supportUnits() - 
Method in class net.sf.basedb.core.AnnotationType
Checks if this annotation types support units.
switchtab - 
Variable in class net.sf.basedb.clients.web.taglib.tab.TabControl
The JavaScript method to call to change tabs.
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
 
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
 
synchronizeAllBioMaterialEvents() - 
Method in class net.sf.basedb.core.BioPlateEvent
Synchronize all properties on the child biomaterial
                events that are related to this event.
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.
SynchronizedSpotDataParser.SynchronizedData(BfsParser) - 
Constructor for class net.sf.basedb.util.importer.spotdata.SynchronizedSpotDataParser.SynchronizedData
 
synchronizeProperties(BioMaterialEventData, BioPlateEventParticipantData) - 
Method in class net.sf.basedb.core.BioPlateEvent
Synchronize all related properties between this event and the
                biomaterial event.
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.FileTypeData
 
systemId - 
Variable in class net.sf.basedb.core.data.GroupData
 
systemId - 
Variable in class net.sf.basedb.core.data.HardwareTypeData
 
systemId - 
Variable in class net.sf.basedb.core.data.ProtocolTypeData
 
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.SoftwareTypeData
 
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
 



T

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
 
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.
table - 
Variable in class net.sf.basedb.clients.web.taglib.table.Button
The parent <tbl:table> tag.
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.Columns
 
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.Header
The parent <tbl:table> tag.
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 - 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
 
table - 
Variable in class net.sf.basedb.clients.web.taglib.table.Toolbar
The parent <tbl:table> tag.
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
 
tableAlias - 
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.
TableColumn(String, String, String, Type, String, String) - 
Constructor for class net.sf.basedb.clients.web.taglib.table.TableColumn
Deprecated.  
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
 
tableColumn - 
Variable in class net.sf.basedb.core.query.ReporterListExpression
 
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
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.ColumnInfo(String, String, Integer, int, boolean, boolean) - 
Constructor for class net.sf.basedb.core.dbengine.TableInfo.ColumnInfo
Create a new ColumnInfo object.
TableInfo.ForeignKeyInfo - Class in net.sf.basedb.core.dbengine
Holds information about a foreign key of a table.
TableInfo.ForeignKeyInfo(String, String) - 
Constructor for class net.sf.basedb.core.dbengine.TableInfo.ForeignKeyInfo
Create a new ForeignKeyInfo object.
TableInfo.IndexInfo - Class in net.sf.basedb.core.dbengine
Holds information about an index in a table.
TableInfo.IndexInfo(String, boolean) - 
Constructor for class net.sf.basedb.core.dbengine.TableInfo.IndexInfo
Create a new IndexInfo object.
TableInfo.PrimaryKeyInfo - Class in net.sf.basedb.core.dbengine
Holds information about the primary key of a table.
TableInfo.PrimaryKeyInfo(String, Set<String>) - 
Constructor for class net.sf.basedb.core.dbengine.TableInfo.PrimaryKeyInfo
Create a new PrimaryKeyInfo object.
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.RealTable
The unquoted table name.
tableName - 
Variable in enum net.sf.basedb.core.Type
 
tablePrintData(Object...) - 
Method in class net.sf.basedb.util.export.TableWriter
Print a data line to the parent writer using the
                default encoder.
tablePrintData(EncoderDecoder, Object...) - 
Method in class net.sf.basedb.util.export.TableWriter
Print a data 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_REGEXP - 
Static variable in class net.sf.basedb.clients.web.util.HTML
This pattern can be used to fins HTML tags.
takeOwnership() - 
Method in interface net.sf.basedb.core.Ownable
Take ownership of the item.
takeOwnership() - 
Method in class net.sf.basedb.core.OwnedItem
 
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
 
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.
TempFileDataSource - Class in net.sf.basedb.ws.server
A DataSource implementation for temporary files.
TempFileDataSource(File, String) - 
Constructor for class net.sf.basedb.ws.server.TempFileDataSource
 
TempFileDataSource.TempInputStream - Class in net.sf.basedb.ws.server
An InputStream implementation that deletes the source file
                once the entire stream has been read (=any of the read()
                methods return -1) or when close() is called.
TempFileDataSource.TempInputStream(InputStream, File) - 
Constructor for class net.sf.basedb.ws.server.TempFileDataSource.TempInputStream
 
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 - 
Static variable in class net.sf.basedb.core.PropertyFilter
Flag to use for temporary filters.
temporary - 
Variable in class net.sf.basedb.core.PropertyFilter
 
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.
testTransactions() - 
Static method in class net.sf.basedb.core.HibernateUtil
 
TEXT - 
Static variable in class net.sf.basedb.core.hibernate.TypeWrapper
 
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
 
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.
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.
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
 
ThreadJobExecutor.ShutdownHook(SignalReceiver) - 
Constructor for class net.sf.basedb.clients.jobagent.executors.ThreadJobExecutor.ShutdownHook
 
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
 
time - 
Variable in class net.sf.basedb.core.data.ChangeHistoryData
 
TIME - 
Static variable in class net.sf.basedb.core.Quantity
The id for the Quantity object representing time.
TIME_FORMAT - 
Static variable in class net.sf.basedb.util.Values
 
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
 
timeoutChecker - 
Variable in class net.sf.basedb.clients.jobagent.slotmanager.MasterSlotManager
 
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 - 
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)
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
 
title - 
Variable in class net.sf.basedb.clients.web.ExperimentExplorer.AnnotationGroup
 
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.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.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.Note
The title of the note.
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 exception net.sf.basedb.clients.web.WebException
The title of the error message.
title - 
Variable in class net.sf.basedb.core.data.ExperimentData
 
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.info.ExperimentInfo
 
title - 
Variable in class net.sf.basedb.info.ExtendedPropertyInfo
 
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.plugins.BioAssaySetExporter.QueryItem
Deprecated.  
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
 
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(T[]) - 
Method in class net.sf.basedb.core.ItemResultList
 
toArray() - 
Method in class net.sf.basedb.util.Tree
Not supported.
toArray(T[]) - 
Method in class net.sf.basedb.util.Tree
Not supported.
toChangeHistoryData() - 
Method in class net.sf.basedb.core.log.TransactionDetails
Convert the information about the transaction to a
                ChangeHistoryData object.
toChangeHistoryDetailData(boolean) - 
Method in class net.sf.basedb.core.log.EntityDetails
Create a new ChangeHistoryDetailData object from the information
                in this object assuming that the entity is a subclass of
                BasicData.
toChangeHistoryDetailData(BasicData, ChangeType, boolean) - 
Method in class net.sf.basedb.core.log.EntityDetails
Create a new ChangeHistoryDetailData object using a mix of the information
                in this object, and the given parameters.
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
 
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(T) - 
Method in class net.sf.basedb.util.jep.convert.AbstractJepConversionFunction
 
toExpression(Node) - 
Method in class net.sf.basedb.util.jep.convert.AddConverter
Convert to expression by calling Expressions.add(Expression, Expression).
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.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(Number) - 
Method in class net.sf.basedb.util.jep.convert.FloatConverter
Convert to expression by calling Expressions.aFloat(float).
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(Integer) - 
Method in class net.sf.basedb.util.jep.convert.IntegerConverter
Convert to expression by calling Expressions.integer(int).
toExpression(T) - 
Method in interface net.sf.basedb.util.jep.convert.JepConversionFunction
Convert the object to an expression.
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(String) - 
Method in class net.sf.basedb.util.jep.convert.StringConverter
Convert to expression by calling Expressions.string(String).
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.
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
 
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.
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 in the table.
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.ManualTransformCreator
 
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.
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.
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(Query, DbControl) - 
Method in class net.sf.basedb.core.AnnotationRestriction
 
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.AscOrder
 
toQl(Query, DbControl) - 
Method in class net.sf.basedb.core.query.BetweenRestriction
 
toQl(Query, DbControl) - 
Method in class net.sf.basedb.core.query.CaseExpression
 
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.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.PowerExpression
 
toQl(Query, DbControl) - 
Method in class net.sf.basedb.core.query.QuadraticMeanExpression
 
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 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.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
 
toReferenceUnit(double) - 
Method in class net.sf.basedb.core.Unit
Convert a value from this unit to the reference unit.
toRestriction(T) - 
Method in class net.sf.basedb.util.jep.convert.AbstractJepConversionFunction
 
toRestriction(Node) - 
Method in class net.sf.basedb.util.jep.convert.AndConverter
Convert to restriction by calling Restrictions.and(Restriction[]).
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.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(T) - 
Method in interface net.sf.basedb.util.jep.convert.JepConversionFunction
Convert the object to a restriction.
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.
TORGUE - 
Static variable in class net.sf.basedb.core.Quantity
The id for the Quantity object representing torque.
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.servlet.ExperimentExplorerPlotServlet.ColumnKey
 
toString() - 
Method in class net.sf.basedb.core.AbstractQuery
 
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.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.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.UsedQuantity
Convert the value to a string.
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 enum net.sf.basedb.core.Image.Format
 
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.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.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.AscOrder
 
toString() - 
Method in class net.sf.basedb.core.query.BetweenRestriction
 
toString() - 
Method in class net.sf.basedb.core.query.CaseExpression
 
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.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.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 class net.sf.basedb.info.VersionInfo
Combine the versions to a string: major.minor.maintenance (build; schema)
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.FallbackIdMethod
 
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.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.Registry.RegisteredExtension
 
toString() - 
Method in class net.sf.basedb.util.extensions.Registry.RegisteredExtensionPoint
 
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.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.Node
 
toString() - 
Method in enum net.sf.basedb.util.overview.Severity
 
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 - 
Static variable in class net.sf.basedb.core.QuotaType
The ID for the total quota.
total - 
Variable in class net.sf.basedb.core.SimpleAbsoluteProgressReporter
 
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.
toTransferable(AnnotatedItemInfo) - 
Method in class net.sf.basedb.core.AnnotatedItem
 
toTransferable(AnnotationTypeInfo) - 
Method in class net.sf.basedb.core.AnnotationType
 
toTransferable(ArrayDesignInfo) - 
Method in class net.sf.basedb.core.ArrayDesign
 
toTransferable(BasicItemInfo) - 
Method in class net.sf.basedb.core.BasicItem
 
toTransferable(BioAssaySetInfo) - 
Method in class net.sf.basedb.core.BioAssaySet
 
toTransferable(CommonItemInfo) - 
Method in class net.sf.basedb.core.CommonItem
 
toTransferable(DataFileTypeInfo) - 
Method in class net.sf.basedb.core.DataFileType
 
toTransferable(ExperimentInfo) - 
Method in class net.sf.basedb.core.Experiment
 
toTransferable(ExtendedPropertyInfo) - 
Method in class net.sf.basedb.core.ExtendedProperty
 
toTransferable(OwnedItemInfo) - 
Method in class net.sf.basedb.core.OwnedItem
 
toTransferable(ProjectInfo) - 
Method in class net.sf.basedb.core.Project
 
toTransferable(RawBioAssayInfo) - 
Method in class net.sf.basedb.core.RawBioAssay
 
toTransferable(ReporterListInfo) - 
Method in class net.sf.basedb.core.ReporterList
 
toTransferable(SharedItemInfo) - 
Method in class net.sf.basedb.core.SharedItem
 
ToTransferable<T extends Transferable> - Interface in net.sf.basedb.info
This interface should be implemented by classes that can
        convert (parts of) it's internal state into a Transferable 
        object.
toTransferable(T) - 
Method in interface net.sf.basedb.info.ToTransferable
Transfer the internal state to a transferable object.
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.XMLUtil
Convert a Document to xml.
toXmlFragment(boolean) - 
Method in class net.sf.basedb.plugins.executor.ParameterDefinition
Render this parameter definition as an XML fragment.
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.
Transactional.Action() - 
Constructor for enum net.sf.basedb.core.Transactional.Action
 
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(SessionControl) - 
Constructor for class net.sf.basedb.core.log.TransactionDetails
Creates a new transaction details object with information from 
                given session control
transactionDetails - 
Variable in class net.sf.basedb.core.LogControl
 
transactionPerFile - 
Variable in class net.sf.basedb.plugins.RawDataFlatFileImporter
 
Transferable - Interface in net.sf.basedb.info
Tagging interface for objects that support some kind of
        transfer mechanism between virtual machines or between Java
        and another programming language.
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)
transferredBytes - 
Variable in class net.sf.basedb.clients.web.fileupload.FileUploadProgress
 
transform - 
Variable in class net.sf.basedb.core.DynamicQuery
 
transform(Collection<? extends BioSource>, Collection<? super Sample>) - 
Method in class net.sf.basedb.util.biomaterial.BioSourceToSampleTransformer
Add all samples that are children to any of the biosources in the
                source collection.
transform(Collection<? extends Extract>, Collection<? super LabeledExtract>) - 
Method in class net.sf.basedb.util.biomaterial.ExtractToLabeledExtractTransformer
Add all labeled extracts that are children to any of the extracts in the
                source collection.
transform(Collection<? extends Extract>, Collection<? super Sample>) - 
Method in class net.sf.basedb.util.biomaterial.ExtractToSampleTransformer
Add all samples that are parents to any of the extracts in the
                source collection.
transform(Collection<? extends LabeledExtract>, Collection<? super Extract>) - 
Method in class net.sf.basedb.util.biomaterial.LabeledExtractToExtractTransformer
Add all samples that are parents to any of the extracts in the
                source collection.
transform(Collection<? extends I>, Collection<? super I>) - 
Method in class net.sf.basedb.util.biomaterial.PooledChildrenTransformer
 
transform(Collection<? extends I>, Collection<? super I>) - 
Method in class net.sf.basedb.util.biomaterial.PooledParentsTransformer
 
transform(Collection<? extends Sample>, Collection<? super BioSource>) - 
Method in class net.sf.basedb.util.biomaterial.SampleToBioSourceTransformer
Add all biosources that are parents to any of the samples in the
                source collection.
transform(Collection<? extends Sample>, Collection<? super Extract>) - 
Method in class net.sf.basedb.util.biomaterial.SampleToExtractTransformer
Add all extracts that are children to any of the samples in the
                source collection.
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 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(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 - 
Variable in class net.sf.basedb.util.importer.spotdata.BaseFileImporter
 
transform - 
Variable in class net.sf.basedb.util.jep.ChannelFunction
 
transformation - 
Variable in class net.sf.basedb.core.data.BioAssaySetData
 
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 - 
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_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.RawBioAssayData
 
translatePermissionsToString(Set<Permission>) - 
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
 
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 - 
Variable in class net.sf.basedb.util.Tree.Entry
 
Tree.ElementIterator - Class in net.sf.basedb.util
An iterator that return elements for each node.
Tree.ElementIterator(Iterator<Tree.Entry<E>>) - 
Constructor for class net.sf.basedb.util.Tree.ElementIterator
 
Tree.Entry<E> - Class in net.sf.basedb.util
Represents an entry for a node in the tree.
Tree.Entry(Tree<E>, E, Tree.Entry<E>) - 
Constructor for class net.sf.basedb.util.Tree.Entry
 
Tree.EntryIterator - Class in net.sf.basedb.util
An iterator that return entries for each node.
Tree.EntryIterator(Tree.Entry<E>) - 
Constructor for class net.sf.basedb.util.Tree.EntryIterator
Create an iterator that starts at the specified entry.
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.
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.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.menu.Menu
If it is a vertical or horizontal menu.
type - 
Variable in class net.sf.basedb.clients.web.taglib.Note
The type of note.
type - 
Variable in class net.sf.basedb.clients.web.taglib.Page
The type of the current page.
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.BioMaterialList
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 - 
Variable in class net.sf.basedb.core.data.FormulaData
 
type - 
Variable in class net.sf.basedb.core.data.JobData
 
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 - 
Variable in class net.sf.basedb.core.dbengine.TableInfo.ColumnInfo
 
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 - 
Variable in class net.sf.basedb.core.ExtendedProperty
 
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.FileType
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.HardwareType
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.Hybridization
The type of item represented by this class.
TYPE - 
Static variable in class net.sf.basedb.core.Image
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 - 
Variable in class net.sf.basedb.core.ItemProxy
 
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.Label
The type of item represented by this class.
TYPE - 
Static variable in class net.sf.basedb.core.LabeledExtract
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 - 
Variable in class net.sf.basedb.core.Path
The type of the path.
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.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 - 
Variable in class net.sf.basedb.core.plugin.GuiContext
 
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 - 
Variable in class net.sf.basedb.core.PluginParameter
Information of the parameter type.
TYPE - 
Static variable in class net.sf.basedb.core.PluginType
The type of item represented by this class.
type - 
Variable in enum net.sf.basedb.core.Project.Default
 
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.ProtocolType
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 - 
Variable in class net.sf.basedb.core.query.QueryParameter
 
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.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.Sample
The type of item represented by this class.
TYPE - 
Static variable in class net.sf.basedb.core.Scan
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.SoftwareType
The type of item represented by this class.
TYPE - 
Static variable in class net.sf.basedb.core.SpotImages
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 - Enum in net.sf.basedb.core
This class defines constants for supported value types in BASE.
Type(TypeWrapper, int, Class<?>, String, String, String, boolean, boolean, boolean) - 
Constructor for enum net.sf.basedb.core.Type
 
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.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.
type - 
Variable in class net.sf.basedb.info.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.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.
typeFromLength(Integer) - 
Static method in class net.sf.basedb.core.StringParameterType
 
types - 
Variable in class net.sf.basedb.core.log.EntityDetails
 
TypeWrapper<T extends org.hibernate.type.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) - 
Constructor for class net.sf.basedb.core.hibernate.TypeWrapper
 
typeWrapper - 
Variable in enum net.sf.basedb.core.Type
 
typeWrapper - 
Variable in class net.sf.basedb.core.VirtualColumn
The data type of the column.



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
 
UNDEFINED - 
Static variable in class net.sf.basedb.core.Quota
Quota is is not defined.
union(Collection<BioMaterialList>) - 
Static method in class net.sf.basedb.core.BioMaterialList
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.
unique - 
Variable in class net.sf.basedb.plugins.batchimport.MultiPropertyIdMethod
 
unique - 
Variable in class net.sf.basedb.plugins.batchimport.PropertyIdMethod
 
uniqueKeys - 
Variable in class net.sf.basedb.util.bfs.MetadataWriter
 
uniqueResult() - 
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 - 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 - 
Variable in class net.sf.basedb.plugins.AnnotationFlatFileImporter.AnnotationValue
 
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.
UnitCache.CacheKey(int, String) - 
Constructor for class net.sf.basedb.util.units.UnitCache.CacheKey
 
UnitConverter - Interface in net.sf.basedb.util.units
Interface for converting values between two units.
UnitData - Class in net.sf.basedb.core.data
This class holds information units.
UnitData() - 
Constructor for class net.sf.basedb.core.data.UnitData
 
units - 
Variable in class net.sf.basedb.core.data.QuantityData
 
units - 
Variable in class net.sf.basedb.util.units.UnitCache
 
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
 
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.
unload(String) - 
Static method in class net.sf.basedb.util.JarClassLoader
Unload the class loader for the given JAR file.
UnmodifiableResultList<T> - Class in net.sf.basedb.core
 
UnmodifiableResultList(List<T>, long) - 
Constructor for class net.sf.basedb.core.UnmodifiableResultList
 
unpack(DbControl, Directory, InputStream, boolean, AbsoluteProgressReporter) - 
Method in class net.sf.basedb.plugins.TarFileUnpacker
 
unpack(DbControl, Directory, InputStream, boolean, AbsoluteProgressReporter) - 
Method in class net.sf.basedb.plugins.ZipFileUnpacker
Use the ZipUnpacker to unpack the file.
unpack(DbControl, Directory, InputStream, 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, 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
 
unregisterAll(Registry) - 
Method in class net.sf.basedb.clients.web.extensions.ExtensionsFile
Unregister all extensions and extension points.
unregisterDeleted(Registry, ScanResults) - 
Method in class net.sf.basedb.clients.web.extensions.ExtensionsDirectory
Unregister extensions/extension points that no longer
                exists.
unregisterEventHandler(EventHandler) - 
Method in class net.sf.basedb.util.extensions.Registry
Unregisters an event handler.
unregisterExtension(String) - 
Method in class net.sf.basedb.util.extensions.Registry
Unregister an extension.
unregisterExtensionPoint(String) - 
Method in class net.sf.basedb.util.extensions.Registry
Unregister an extension point.
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.
unregisterFileOnlyRawDataType(RawDataType) - 
Static method in class net.sf.basedb.core.RawDataTypes
 
unregisterMissing(Registry) - 
Method in class net.sf.basedb.clients.web.extensions.ExtensionsFile
Unregister extensions and extension points that have been removed
                from this package after an update.
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.clients.web.plugins.PlainTextTemplate
 
unsafe - 
Static variable in class net.sf.basedb.plugins.GalExporter
 
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(Throwable) - 
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.
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(Throwable) - 
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.
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(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.
unTransform(double) - 
Method in enum net.sf.basedb.core.IntensityTransform
Un-transform a transformed intensity value back to a
                regular 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.
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.
update(D) - 
Method in class net.sf.basedb.core.BasicBatcher
Update a data object.
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 - 
Variable in class net.sf.basedb.core.hibernate.SchemaGenerator
 
update(Object) - 
Method in class net.sf.basedb.core.hibernate.SessionWrapper
 
update(String, 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.StatelessSessionWrapper
 
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 - 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(About) - 
Method in class net.sf.basedb.util.extensions.Registry.RegisteredAbout
Update the registered information.
update(Extension<A>) - 
Method in class net.sf.basedb.util.extensions.Registry.RegisteredExtension
Update the registered information.
update(ExtensionPoint<A>) - 
Method in class net.sf.basedb.util.extensions.Registry.RegisteredExtensionPoint
Update the registered information.
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.
updateable - 
Variable in class net.sf.basedb.core.ExtendedProperty
 
updateable - 
Variable in class net.sf.basedb.info.ExtendedPropertyInfo
 
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, ProgressReporter) - 
Method in class net.sf.basedb.core.RawBioAssay
Deprecated. Use RawBioAssay.updateArrayDesign(ArrayDesign, FeatureIdentificationMethod, ProgressReporter)
                instead
updateArrayDesign(ArrayDesign, FeatureIdentificationMethod, ProgressReporter) - 
Method in class net.sf.basedb.core.RawBioAssay
Set the ArrayDesign this raw data uses.
updateCount - 
Variable in class net.sf.basedb.core.BasicBatcher
 
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.ExperimentOverview
Deprecated. Updates the failure count (warnings and errors) on all nodes.
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, 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
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, 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, Extract, FlatFileParser.Data) - 
Method in class net.sf.basedb.plugins.batchimport.ExtractImporter
 
updateItem(DbControl, Hybridization, FlatFileParser.Data) - 
Method in class net.sf.basedb.plugins.batchimport.HybridizationImporter
 
updateItem(DbControl, LabeledExtract, FlatFileParser.Data) - 
Method in class net.sf.basedb.plugins.batchimport.LabeledExtractImporter
 
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, Scan, FlatFileParser.Data) - 
Method in class net.sf.basedb.plugins.batchimport.ScanImporter
 
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.
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, ArrayDesign, FlatFileParser.Data, int) - 
Method in class net.sf.basedb.plugins.batchimport.ArrayDesignImporter
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, Hybridization, FlatFileParser.Data, int) - 
Method in class net.sf.basedb.plugins.batchimport.HybridizationImporter
Add parent labeled extracts and the used quantities
updateMultiLineItem(DbControl, LabeledExtract, FlatFileParser.Data, int) - 
Method in class net.sf.basedb.plugins.batchimport.LabeledExtractImporter
If the labeled extract is pooled, add the parent labeled extract.
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.
updateMultiLineItem(DbControl, Scan, FlatFileParser.Data, int) - 
Method in class net.sf.basedb.plugins.batchimport.ScanImporter
 
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
 
updateToSchemaVersion10(SessionControl) - 
Static method in class net.sf.basedb.core.Update
Load all plugins and call PluginDefinition.loadPluginInformation(String, String, boolean)
                for each one so that the PluginDefinition.supportsConfigurations() and
                PluginDefinition.requiresConfiguration() return correct values.
updateToSchemaVersion19(Session) - 
Static method in class net.sf.basedb.core.Update
Set JobData.getParameterVersion and PluginConfigurationData.getParameterVersion
                to 1 if they have null values.
updateToSchemaVersion2(Session) - 
Static method in class net.sf.basedb.core.Update
Set Jobs.project_id to 0 for all old jobs with a null value in this column.
updateToSchemaVersion24(Session) - 
Static method in class net.sf.basedb.core.Update
Move FileValues to ItemValues.
updateToSchemaVersion25(Session) - 
Static method in class net.sf.basedb.core.Update
Set the itemType property on all DiskUsageData items.
updateToSchemaVersion28(SessionControl) - 
Static method in class net.sf.basedb.core.Update
Find the number of raw mappings for the spot with the maximum number
                for each data cube
updateToSchemaVersion30(Session) - 
Static method in class net.sf.basedb.core.Update
Vefify and update the remaining quantity of all biomaterials.
updateToSchemaVersion31(Session) - 
Static method in class net.sf.basedb.core.Update
Set the writeProtected flag on all files with a null value to false.
updateToSchemaVersion35(Session) - 
Static method in class net.sf.basedb.core.Update
Check and update the file size and MD5 on existing file items since
                they may be incorrect
updateToSchemaVersion38(Session) - 
Static method in class net.sf.basedb.core.Update
Set the experiment for jobs that belong to a single transformation.
updateToSchemaVersion39(Session) - 
Static method in class net.sf.basedb.core.Update
Remove AnyToAny links created by older versions of Base1PluginExecuter
updateToSchemaVersion4(Session) - 
Static method in class net.sf.basedb.core.Update
Find the unique index on HelpTextData.externalId and remove it.
updateToSchemaVersion42(Session) - 
Static method in class net.sf.basedb.core.Update
Has been replaced with Update.updateToSchemaVersion44(SessionControl)
updateToSchemaVersion43(Session) - 
Static method in class net.sf.basedb.core.Update
Update property filter on 'guiContexts.itemType' to '$ctx.itemType'
updateToSchemaVersion44(SessionControl) - 
Static method in class net.sf.basedb.core.Update

                Set a platform for array designs and raw bioassays
                Change experiment raw data type if it is "affymetrix" to "platform.affymetrix"
                Change project default raw data type if it is "affymetrix" to "platform.affymetrix"
                Move CEL and CDF files into FileSet:s
                Remove filters on ArrayDesign.isAffyChip property
                Add READ permission to PLATFORM and DATAFILETYPE for all plug-ins
                        working with ARRAYDESIGN or RAWBIOASSAY
                
updateToSchemaVersion45(Session) - 
Static method in class net.sf.basedb.core.Update
Update useInternalJobQueue for plug-ins.
updateToSchemaVersion49(Session) - 
Static method in class net.sf.basedb.core.Update
Find the unique index on Feature (row, column and block) and remove it.
updateToSchemaVersion51(Session) - 
Static method in class net.sf.basedb.core.Update
Change all plug-ins with an absolute JAR path to relative 
                paths.
updateToSchemaVersion56(Session) - 
Static method in class net.sf.basedb.core.Update
Count the number of reporters in existing reporter lists.
updateToSchemaVersion57(Session) - 
Static method in class net.sf.basedb.core.Update
Grant Permission.SELECT_JOBAGENT permission to
                administrators, power users and job agent roles.
updateToSchemaVersion60(Session) - 
Static method in class net.sf.basedb.core.Update
Update incorrect quota values for experiments.
updateToSchemaVersion7(Session) - 
Static method in class net.sf.basedb.core.Update
Set RawBioAssays.has_data to true or false depending on the number of spots.
updateToSchemaVersion76(Session, ProgressReporter) - 
Static method in class net.sf.basedb.core.Update
Sets the AnnotationSetData.getItemId() for
                all annotation sets with a null value.
updateToSchemaVersion77(Session) - 
Static method in class net.sf.basedb.core.Update
Try to set the value type for as many formulas as possible.
updateToSchemaVersion79(Session) - 
Static method in class net.sf.basedb.core.Update
Set sort_property in Contexts table to null if it contains a literal string 'null'.
updateToSchemaVersion80(Session) - 
Static method in class net.sf.basedb.core.Update
Set the plate type for all existing bio plates to "Storage plate".
updateToSchemaVersion84(Session) - 
Static method in class net.sf.basedb.core.Update
Set the scheduled data for existing jobs.
updateToSchemaVersion85(Session) - 
Static method in class net.sf.basedb.core.Update
Change the date type for the DateValues.values column,.
updateToSchemaVersion86(Session) - 
Static method in class net.sf.basedb.core.Update
Remove all context settings with a name ending with '.recent' that has
                at least one colon (:) in the value.
updateToSchemaVersion90(Session) - 
Static method in class net.sf.basedb.core.Update
Calculate the value for BioPlateData.getFreeWells() for all existing bioplates.
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
 
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.
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, FileType).
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.
uploadStream - 
Variable in class net.sf.basedb.core.File
A stream for uploading a physical 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.
url - 
Variable in class net.sf.basedb.clients.web.extensions.plot.PlotGeneratorBean
 
url - 
Variable in class net.sf.basedb.core.authentication.AuthenticationInformation
An URL to the user homepage (or similar).
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 - 
Variable in class net.sf.basedb.ws.client.SessionClient
 
URL_REGEXP - 
Static variable in class net.sf.basedb.clients.web.util.HTML
This pattern can be used to find URL:s.
urlEncode(String) - 
Static method in class net.sf.basedb.clients.web.util.HTML
Encode URL-unsafe characters in a string.
usableUnits - 
Variable in class net.sf.basedb.core.data.AnnotationTypeData
 
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.
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.
usedColumnsParameter - 
Variable in class net.sf.basedb.plugins.BioAssaySetExporter
Deprecated.  
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.
usedFieldsParameter - 
Variable in class net.sf.basedb.plugins.BioAssaySetExporter
Deprecated.  
usedFiles - 
Variable in class net.sf.basedb.util.bfs.AbstractDataWriterFactory
 
usedHybArrays - 
Variable in class net.sf.basedb.util.overview.ExperimentOverview
Deprecated.  
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.BioMaterialSourceEventData
 
UsedQuantity - Class in net.sf.basedb.core.data
Hibernate will not save entries in the sources map BioMaterialEventData.getSources()
        where the element is null, so we have to use a composite element instead.
UsedQuantity() - 
Constructor for class net.sf.basedb.core.data.UsedQuantity
Used by Hibernate to create an instance.
UsedQuantity(Float, int) - 
Constructor for class net.sf.basedb.core.data.UsedQuantity
Create a new instance.
usedQuantity - 
Variable in class net.sf.basedb.core.data.UsedQuantity
The used quantity value.
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.HybridizationImporter
 
usedQuantityMapper - 
Variable in class net.sf.basedb.plugins.batchimport.LabeledExtractImporter
 
usedQuantityMapper - 
Variable in class net.sf.basedb.plugins.batchimport.SampleImporter
 
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, String...) - 
Static method in class net.sf.basedb.clients.web.extensions.ExtensionsControl
Use extensions from one or more extension points.
useExtensions(JspContext, ExtensionsFilter, String...) - 
Static method in class net.sf.basedb.clients.web.extensions.ExtensionsControl
 
useExtensions(JspContext) - 
Static method in class net.sf.basedb.clients.web.extensions.toolbar.ToolbarUtil
Use toolbar extensions for a given gui context.
useExtensions(ClientContext, ExtensionsFilter, String...) - 
Method in class net.sf.basedb.util.extensions.Registry
Use extensions from one or more extension points.
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.
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 - 
Static variable in class net.sf.basedb.core.Role
The id for the Role item representing regular users.
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.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.
User.QueryRuntimeFilterImpl() - 
Constructor for class net.sf.basedb.core.User.QueryRuntimeFilterImpl
 
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.
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
 
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
 
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.
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.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
 
userPermissions - 
Variable in class net.sf.basedb.core.MultiPermissions
 
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.
userPermissions - 
Variable in class net.sf.basedb.core.UserPermissions
 
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
 
useSmartFeatureMismatchHandling - 
Variable in class net.sf.basedb.plugins.IlluminaRawDataImporter
 
usesTo - 
Variable in class net.sf.basedb.core.data.AnyToAnyData
 
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.
utf8 - 
Variable in class net.sf.basedb.clients.web.servlet.RssNewsFeed
 
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
 
util - 
Variable in class net.sf.basedb.ws.server.AbstractRPCService
 



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.
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.clients.web.extensions.ExtensionsFile
 
validate - 
Variable in class net.sf.basedb.clients.web.taglib.tab.Tab
A JavaScript method that validates the tab content.
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() - 
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.DataFileType
Check that the validator and meta data reader classes implement the
                correct interfaces.
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 postion 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(DbControl) - 
Method in class net.sf.basedb.core.filehandler.CdfFileHandler
Check that the array design is using the Affymetrix platform 
                (Platform.AFFYMETRIX) and that the file selected
                as the CDF file really is a CDF file.
validate(DbControl) - 
Method in class net.sf.basedb.core.filehandler.CelFileHandler
Check that the raw bioassay is using the Affymetrix platform 
                (Platform.AFFYMETRIX) and that the file selected
                as the CEL file really is a CEL file.
validate(DbControl) - 
Method in interface net.sf.basedb.core.filehandler.DataFileValidator
Validate the file(s) that has been added to this validator
                with the DataFileHandler.setFile(net.sf.basedb.core.FileSetMember)
                method.
validate(DbControl) - 
Method in class net.sf.basedb.core.FileSet.DataFileHandlerWrapper
 
validate(DbControl, boolean) - 
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() - 
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(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(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(Object) - 
Method in enum net.sf.basedb.core.Type
Check if an object is a value of the correct type.
validate(List<?>) - 
Method in enum net.sf.basedb.core.Type
Check if a list of values contain only objects of the correct type.
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
 
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(RawBioAssay, ArrayDesign, boolean) - 
Static method in class net.sf.basedb.core.Affymetrix
Check if the CEL file on the raw bioassay matches the CDF file on the
                array design.
validateCelAndCdf(FusionCELData, FusionCDFData, String) - 
Static method in class net.sf.basedb.core.Affymetrix
 
validateCelAndCdf(FusionCELData, FusionCDFData, String) - 
Static method in class net.sf.basedb.core.filehandler.CelFileHandler
 
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.
validateJar() - 
Method in class net.sf.basedb.clients.web.extensions.ExtensionsFile
Try to validate a JAR file with extensions.
validateKey(String) - 
Method in class net.sf.basedb.util.StaticCache
 
validateLabeledExtractOnHyb(DbControl, OverviewContext, Node, Node) - 
Method in class net.sf.basedb.util.overview.validator.LabeledExtractValidator
 
validatePooledLabeledExtract(DbControl, OverviewContext, Node, Node) - 
Method in class net.sf.basedb.util.overview.validator.LabeledExtractValidator
 
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(String, Boolean) - 
Method in class net.sf.basedb.core.BooleanParameterType
Always validate.
validateValue(String, Date) - 
Method in class net.sf.basedb.core.DateParameterType
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(Object) - 
Method in class net.sf.basedb.core.ExtendedProperty
Check if an object is valid according to the specifications of this property.
validateValue(String, File) - 
Method in class net.sf.basedb.core.FileParameterType
Always validate.
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, T) - 
Method in class net.sf.basedb.core.ItemParameterType
Check if the value is in the list of allowed values.
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, T) - 
Method in class net.sf.basedb.core.ParameterType
Validate a value.
validateValue(String, String) - 
Method in class net.sf.basedb.core.PathParameterType
Checks if the value is a valif Path value.
validateValue() - 
Method in class net.sf.basedb.core.query.QueryParameter
Validate the parameter value using the type information if
                it has been provided.
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.TimestampParameterType
Always validate.
validateXml() - 
Method in class net.sf.basedb.clients.web.extensions.ExtensionsFile
Try to validate an XML file with extensions.
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.
validationError - 
Variable in class net.sf.basedb.clients.web.extensions.ExtensionsFile
 
validationOptions - 
Variable in class net.sf.basedb.util.overview.ExperimentOverview
Deprecated.  
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.
validator - 
Variable in class net.sf.basedb.util.overview.Failure
 
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.
validatorClass - 
Variable in class net.sf.basedb.core.data.DataFileTypeData
 
validatorJarPath - 
Variable in class net.sf.basedb.core.data.DataFileTypeData
 
validators - 
Static variable in class net.sf.basedb.util.overview.OverviewUtil
 
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.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 enum net.sf.basedb.core.FeatureIdentificationMethod
The integer value of this method.
value - 
Variable in enum net.sf.basedb.core.File.Action
The integer value of this fileaction.
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.Image.Format
The integer value of this format.
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.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.info.QueryParameter
 
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.fuzzy.StringMatcher.FuzzyMatch
 
value - 
Variable in class net.sf.basedb.util.parser.FlatFileParser.Line
 
value() - 
Method in class net.sf.basedb.util.parser.FlatFileParser.Line
The value of the header if the line is a header line.
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
 
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.File.Action
Maps the integer that is stored in the database with an fileaction.
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.Image.Format
Maps the integer that is stored in the database with an fileaction.
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.menu.MenuItemAction.MenuType
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.File.Action
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.Image.Format
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.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.Project.Default
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.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.xml.PathType
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() - 
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 - 
Variable in class net.sf.basedb.core.AnnotationInRestriction
 
values - 
Variable in class net.sf.basedb.core.AnnotationSimpleRestriction
 
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 - 
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() - 
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.File.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.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.Image.Format
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.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 - 
Variable in class net.sf.basedb.core.ParameterInfo
 
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.Project.Default
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 - 
Variable in class net.sf.basedb.core.snapshot.AnnotationSnapshot
 
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 - Class in net.sf.basedb.core
Utility class to handle the conversion between data objects and
        item objects.
Values() - 
Constructor for class net.sf.basedb.core.Values
 
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 - 
Variable in class net.sf.basedb.info.AnnotationInfo
 
values - 
Variable in class net.sf.basedb.plugins.AnnotationFlatFileImporter.NewAnnotations
 
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 - 
Variable in class net.sf.basedb.plugins.executor.ProgramParameter
 
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 - 
Variable in class net.sf.basedb.util.bfs.MetadataModel.SectionEntry
 
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.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 - 
Variable in class net.sf.basedb.util.plot.PlotAnnotation
 
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.util.Values
 
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 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.SpotExtraValueBatcher
The type of values to insert.
valueType - 
Variable in class net.sf.basedb.info.AnnotationInfo
 
valueType - 
Variable in class net.sf.basedb.info.AnnotationTypeInfo
 
valueType - 
Variable in class net.sf.basedb.plugins.batchimport.MultiPropertyIdMethod
 
valueType - 
Variable in class net.sf.basedb.plugins.batchimport.PropertyIdMethod
 
VARIABLE - 
Static variable in class net.sf.basedb.util.extensions.xml.VariableConverter
 
variableConverter - 
Variable in class net.sf.basedb.clients.web.extensions.ExtensionsDirectory
 
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.
verify(String, SSLSocket) - 
Method in class net.sf.basedb.util.ssl.AllowAnyHostNameVerifyer
 
verify(String, X509Certificate) - 
Method in class net.sf.basedb.util.ssl.AllowAnyHostNameVerifyer
 
verify(String, String[], String[]) - 
Method in class net.sf.basedb.util.ssl.AllowAnyHostNameVerifyer
 
verify(String, SSLSession) - 
Method in class net.sf.basedb.util.ssl.AllowAnyHostNameVerifyer
 
verifyColumns - 
Variable in class net.sf.basedb.plugins.IlluminaRawDataImporter
 
verifyUserExternal(Session, String, String) - 
Method in class net.sf.basedb.core.SessionControl
Verify the user with external authentication.
verifyUserInternal(Session, String, String, boolean) - 
Method in class net.sf.basedb.core.SessionControl
Check that the user exists and verify the password using
                internal authentication.
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 - Class in net.sf.basedb.core
Get information about the BASE version.
Version() - 
Constructor for class net.sf.basedb.core.Version
 
version - 
Variable in class net.sf.basedb.info.BasicItemInfo
 
version - 
Variable in class net.sf.basedb.util.extensions.AboutBean
 
version - 
Variable in class net.sf.basedb.util.extensions.Registry.RegisteredAbout
 
versionCompatible(String) - 
Static method in class net.sf.basedb.util.PluginInfo
Gets if a version is compatible with current 
                major.minor-version of BASE
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.
versionInDatabase - 
Variable in class net.sf.basedb.util.PluginInfo
 
VersionInfo - Class in net.sf.basedb.info
Information about the version the BASE server is running.
VersionInfo() - 
Constructor for class net.sf.basedb.info.VersionInfo
Creates a new empty info object
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
 
ViewSpotImage - Class in net.sf.basedb.clients.web.servlet
 
ViewSpotImage() - 
Constructor for class net.sf.basedb.clients.web.servlet.ViewSpotImage
 
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) - 
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
 
VirtualColumnExpression.WrappedExpression(String) - 
Constructor for class net.sf.basedb.core.query.VirtualColumnExpression.WrappedExpression
 
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 - 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.
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.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.Note
If the note should be visible or not.
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.
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
 
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
 
warning(SAXParseException) - 
Method in class net.sf.basedb.util.XMLUtil.Validator
Ignore 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.
wasForceUpdate() - 
Method in class net.sf.basedb.clients.web.extensions.ScanResults
 
wasManual() - 
Method in class net.sf.basedb.clients.web.extensions.ScanResults
 
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
 
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
 
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.tab.TabControl
The width of the tab control.
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.
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.
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 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.
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(byte[], int, int) - 
Method in class net.sf.basedb.core.File.UploadStream
 
write(byte[]) - 
Method in class net.sf.basedb.core.File.UploadStream
 
write(int) - 
Method in class net.sf.basedb.core.File.UploadStream
Writes the specified byte to this buffered output stream.
write - 
Static variable in class net.sf.basedb.core.Item.DefinedPermissions
 
write(byte[], int, int) - 
Method in class net.sf.basedb.core.plugin.ExportOutputStream
 
write(byte[]) - 
Method in class net.sf.basedb.core.plugin.ExportOutputStream
 
write(int) - 
Method in class net.sf.basedb.core.plugin.ExportOutputStream
 
write(String, InputStream, int) - 
Method in class net.sf.basedb.util.StaticCache
Store binary information in the cache.
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.
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.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.XMLTemplate
Add collection values to the current item element.
writeColumnFilters() - 
Method in class net.sf.basedb.clients.web.taglib.table.Table
 
writeColumns() - 
Method in class net.sf.basedb.clients.web.taglib.table.Table
 
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.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.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.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
 
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.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.
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.



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
 
xgetFeatureBatcher(FeatureIdentificationMethod) - 
Method in class net.sf.basedb.core.ArrayDesign
Deprecated. Use ArrayDesign.getFeatureBatcher(FeatureIdentificationMethod, Job)
                        instead
xgetQuery(Formula.Type, RawDataType) - 
Static method in class net.sf.basedb.core.Formula
Deprecated. In 2.12. Use Formula.getQuery(Type, RawDataType, IntensityTransform) instead
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
 
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
 
xmlFile - 
Static variable in class net.sf.basedb.util.PluginInfo
The name of a XML-file that holds information 
                about each plugin class in the jar file.
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.XMLUtil
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.
XMLUtil - Class in net.sf.basedb.util
This class contains some useful methods for handling
        XML documents.
XMLUtil() - 
Constructor for class net.sf.basedb.util.XMLUtil
 
XMLUtil.Validator - Class in net.sf.basedb.util
This class is used to handle callbacks from the XML parser.
XMLUtil.Validator(String, URL) - 
Constructor for class net.sf.basedb.util.XMLUtil.Validator
Create a new instance of this class.
xOffset - 
Variable in class net.sf.basedb.core.data.SpotImagesData
 
xScale - 
Variable in class net.sf.basedb.core.data.SpotImagesData
 
xtra(Integer) - 
Method in class net.sf.basedb.util.jep.ExtraValueFunction
Get the value of the specified extra value of the current sql result.



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
 
yColumnMapping - 
Static variable in class net.sf.basedb.plugins.RawDataFlatFileImporter
 
yMapper - 
Variable in class net.sf.basedb.plugins.RawDataFlatFileImporter
 
yOffset - 
Variable in class net.sf.basedb.core.data.SpotImagesData
 
yScale - 
Variable in class net.sf.basedb.core.data.SpotImagesData
 
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.


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