2.17.2: 2011-06-17
A B C D E F G H I J K L M N O P Q R S T U V W X Y Z

A

A - Variable in class net.sf.basedb.plugins.LowessNormalization.SpotData
 
abort - Variable in class net.sf.basedb.clients.web.fileupload.FileUploadProgress
 
ABORT - Static variable in class net.sf.basedb.core.signal.Signal
The ABORT signal, that requests that the receiver should clean up and die.
about - 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<I extends BasicItem> - Class in net.sf.basedb.plugins.batchimport
An abstract base class for plug-ins that import items in batch.
AbstractItemImporter() - Constructor for class net.sf.basedb.plugins.batchimport.AbstractItemImporter
 
AbstractJepConversionFunction<T> - Class in net.sf.basedb.util.jep.convert
Abstract superclass implementing the JepConversionFunction interface.
AbstractJepConversionFunction() - Constructor for class net.sf.basedb.util.jep.convert.AbstractJepConversionFunction
 
AbstractJspActionFactory<A extends Action> - Class in net.sf.basedb.clients.web.extensions
An abstract base class for action factories that may need to support adding scripts and stylesheets to the rendered JSP page.
AbstractJspActionFactory() - Constructor for class net.sf.basedb.clients.web.extensions.AbstractJspActionFactory
Create a new factory instance.
AbstractJspFactory - Class in net.sf.basedb.clients.web.extensions
An abstract BASE class for action and renderer factories.
AbstractJspFactory() - Constructor for class net.sf.basedb.clients.web.extensions.AbstractJspFactory
Create a new factory instance.
AbstractJspRendererFactory<A extends Action> - Class in net.sf.basedb.clients.web.extensions
An abstract base class for action factories that may need to support adding scripts and stylesheets to the rendered JSP page.
AbstractJspRendererFactory() - Constructor for class net.sf.basedb.clients.web.extensions.AbstractJspRendererFactory
Create a new factory instance.
AbstractNodeLoader<I> - Class in net.sf.basedb.util.overview.loader
Abstract node loader implementation that does nothing/throws an exception.
AbstractNodeLoader() - Constructor for class net.sf.basedb.util.overview.loader.AbstractNodeLoader
 
AbstractOnSaveAction - Class in net.sf.basedb.clients.web.extensions.edit
Abstract base implementation of the OnSaveAction interface.
AbstractOnSaveAction() - Constructor for class net.sf.basedb.clients.web.extensions.edit.AbstractOnSaveAction
Create a on-save action without a context
AbstractOnSaveAction(JspContext) - Constructor for class net.sf.basedb.clients.web.extensions.edit.AbstractOnSaveAction
Create a on-save action with a jsp context.
AbstractPlugin - Class in net.sf.basedb.core.plugin
This is an abstract base class useful for developing plugins.
AbstractPlugin() - Constructor for class net.sf.basedb.core.plugin.AbstractPlugin
Create a new AbstractPlugin.
AbstractQuery - Class in net.sf.basedb.core
An abstract implementation of the Query interface.
AbstractQuery(String) - Constructor for class net.sf.basedb.core.AbstractQuery
Create a new query.
AbstractQueryCache - Class in net.sf.basedb.core.hibernate
Abstract base class used to cache queries for a session.
AbstractQueryCache() - Constructor for class net.sf.basedb.core.hibernate.AbstractQueryCache
 
AbstractResultList<I> - Class in net.sf.basedb.core
This is a list of the result from a query.
AbstractResultList(long) - Constructor for class net.sf.basedb.core.AbstractResultList
 
AbstractRPCClient - Class in net.sf.basedb.ws.client
Abstract class for RPCServiceClients in web services.
AbstractRPCClient(String, String) - Constructor for class net.sf.basedb.ws.client.AbstractRPCClient
 
AbstractRPCClient(String, String, ServiceFactory) - Constructor for class net.sf.basedb.ws.client.AbstractRPCClient
 
AbstractRPCService - Class in net.sf.basedb.ws.server
An abstract class for Web service classes to extend from.
AbstractRPCService() - Constructor for class net.sf.basedb.ws.server.AbstractRPCService
 
AbstractSignalHandler - Class in net.sf.basedb.core.signal
An abstract base class for signal handler implementations.
AbstractSignalHandler() - Constructor for class net.sf.basedb.core.signal.AbstractSignalHandler
Create a new signal handler, that initially doesn't support any signals at all.
AbstractSignalHandler(Collection<Signal>) - Constructor for class net.sf.basedb.core.signal.AbstractSignalHandler
Create a new signal handler that supports the given signals.
AbstractSignalReceiver - Class in net.sf.basedb.core.signal
Abstract base class that is useful when implementing signal receivers.
AbstractSignalReceiver() - Constructor for class net.sf.basedb.core.signal.AbstractSignalReceiver
Create a new signal receiver.
AbstractSignalTransporter - Class in net.sf.basedb.core.signal
Abstract base class that is useful when implementing signal transporters.
AbstractSignalTransporter() - Constructor for class net.sf.basedb.core.signal.AbstractSignalTransporter
 
AbstractSqlQuery - Class in net.sf.basedb.core
An abstract implementation of the SqlQuery interface.
AbstractSqlQuery(String) - Constructor for class net.sf.basedb.core.AbstractSqlQuery
 
abstractText - Variable in class net.sf.basedb.info.ExperimentInfo
 
ACCELERATION - Static variable in class net.sf.basedb.core.Quantity
The id for the Quantity object representing acceleration.
accept(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<I> - Class in net.sf.basedb.util.collections
Collection transformer implementation that adds all elements in the source collection to the destination collection.
AddAllTransformer() - Constructor for class net.sf.basedb.util.collections.AddAllTransformer
 
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<I> - Class in net.sf.basedb.util.overview.loader
Node loader implementation that automatically loads child nodes.
AutoChildNodeLoader(NodeLoader<I>) - Constructor for class net.sf.basedb.util.overview.loader.AutoChildNodeLoader
 
autoCloseParsers - Variable in class net.sf.basedb.util.importer.spotdata.BfsImporter
 
autoCloseWriters - Variable in class net.sf.basedb.util.export.spotdata.BfsExporter
 
autoCompress - Variable in class net.sf.basedb.core.data.DirectoryData
 
autoCompress - Variable in class net.sf.basedb.core.data.MimeTypeData
 
autoCompressionEnabled() - Static method in class net.sf.basedb.core.Application
Check if auto-compression has been enabled or not.
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<I extends BasicItem> - Class in net.sf.basedb.util.overview.loader
Abstract class that is useful for all node loaders that works with BasicItem:s.
BasicItemNodeLoader(Object, boolean, NodeNameGenerator<I>) - Constructor for class net.sf.basedb.util.overview.loader.BasicItemNodeLoader
Create a new node loader.
BasicItemNodeLoaderFactory - Class in net.sf.basedb.util.overview.loader
Node loader factory implementation for BasicItem node loaders.
BasicItemNodeLoaderFactory() - Constructor for class net.sf.basedb.util.overview.loader.BasicItemNodeLoaderFactory
Creates a new factory.
BasicItemNodeValidatorFactory - Class in net.sf.basedb.util.overview.validator
Node validator factory implementation for BasicItem node validators.
BasicItemNodeValidatorFactory() - Constructor for class net.sf.basedb.util.overview.validator.BasicItemNodeValidatorFactory
Creates a new factory.
BasicItemToIdTransformer - Class in net.sf.basedb.util.collections
Collection transformer implementation that extracts the ID from BasicItem:s.
BasicItemToIdTransformer() - Constructor for class net.sf.basedb.util.collections.BasicItemToIdTransformer
 
BasicNodeValidator<I> - Class in net.sf.basedb.util.overview.validator
A simple node validation implementation that takes care of missing and denied access to items.
BasicNodeValidator(Validator, Validator) - Constructor for class net.sf.basedb.util.overview.validator.BasicNodeValidator
Creates a new validator.
BatchableData - Interface in net.sf.basedb.core.data
This is a tagging interface only.
batchedExternalIds - Variable in class net.sf.basedb.core.ReporterBatcher
A set containing all batched but not yet flushed external reporter id:s.
BatchedPropertyInfo - Class in net.sf.basedb.core
Holds information about a batchable property.
BatchedPropertyInfo(String, int) - Constructor for class net.sf.basedb.core.BatchedPropertyInfo
Create a new extended property.
Batcher - Interface in net.sf.basedb.core
The basic interface which all batchers must implement.
batcher - Variable in class net.sf.basedb.plugins.IlluminaRawDataImporter.BatchAndMapHolder
 
batcher - Variable in class net.sf.basedb.plugins.PrintMapFlatFileImporter
 
batcher - Variable in class net.sf.basedb.plugins.RawDataFlatFileImporter
 
batcher - Variable in class net.sf.basedb.plugins.ReporterFlatFileImporter
 
batcher - Variable in class net.sf.basedb.plugins.ReporterMapFlatFileImporter
 
batchers - Variable in class net.sf.basedb.core.DbControl
A list of batchers that will be closed when DbControl is closed and will be flushed when commit is called.
batchIndex - Variable in class net.sf.basedb.core.data.ArraySlideData
 
batchQuery - Variable in class net.sf.basedb.plugins.batchimport.AbstractItemImporter
 
batchSize - Variable in class net.sf.basedb.core.AbstractBatcher
SQL command batch size.
BatchUtil - Class in net.sf.basedb.core
Utility class for batching information.
BatchUtil() - Constructor for class net.sf.basedb.core.BatchUtil
 
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<I extends BasicData> - Class in net.sf.basedb.core
An implementation of the Query interface that returns data objects.
DataQuery(Class<I>, String) - Constructor for class net.sf.basedb.core.DataQuery
Create a new query for the specified item, using the default optional runtime filter.
DataQuery(Class<I>, Item, String, String) - Constructor for class net.sf.basedb.core.DataQuery
Create a query that may have different return type and root entity.
DataQuery(Class<I>, 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<I extends BasicData> - Class in net.sf.basedb.core
Return the results of a DataQuery as an iterator.
DataResultIterator(ScrollIterator<I>, SessionControl, Session, Class<I>, long) - Constructor for class net.sf.basedb.core.DataResultIterator
 
dataSeparator - Variable in class net.sf.basedb.util.export.TableWriter
 
dataSplitter - Variable in class net.sf.basedb.util.parser.FlatFileParser
The regular expression for splitting a data line.
dataSplitterRegexpParameter - Static variable in class net.sf.basedb.plugins.AbstractFlatFileImporter
Parameter definition that asks for the regular expression that splits a data line into individual columns.
dataType - Variable in class net.sf.basedb.clients.web.taglib.table.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