Index (BASE 3.19.12 API documentation)

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

A

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

B

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

C

c - Variable in enum class net.sf.basedb.plugins.Base1PluginExecuter.Base1JobParameterType
CABINET - Static variable in class net.sf.basedb.core.Hardware: The id for the HardwareType object representing a cabinet.
cache - Variable in class net.sf.basedb.clients.web.ExperimentExplorer: The cache of reporter ids matching the current reporter filter.
cache - Static variable in class net.sf.basedb.core.DerivedBioAssay.FixDerivedBioAssayParentsRecursivelyAction
cache - Variable in class net.sf.basedb.core.hibernate.AbstractQueryCache
cache - Static variable in class net.sf.basedb.core.MeasuredBioMaterial.RemainingQuantityAction: We need a single action per DbControl and BioMaterial
cache - Variable in class net.sf.basedb.util.AnnotationUtil.AnnotatableWrapper
cache - Variable in class net.sf.basedb.util.bfs.BaseInputStreamLocator
cache - Variable in class net.sf.basedb.util.listable.TransformCache
cache - Variable in class net.sf.basedb.util.overview.cache.NodeCache
cache - Variable in class net.sf.basedb.util.StaticCache.CleanupTask
Cache() - Constructor for class net.sf.basedb.util.AnnotationUtil.Cache
cacheBase - Variable in class net.sf.basedb.clients.web.servlet.PlotServlet
cacheChildNodes(Node) - Method in class net.sf.basedb.util.overview.GenericOverview
cacheControl - Variable in class net.sf.basedb.clients.web.servlet.CacheControlFilter
cacheControl - Variable in class net.sf.basedb.clients.web.servlet.ImageRemapFilter
CacheControlFilter - Class in net.sf.basedb.clients.web.servlet: This is a filter that sets the "Cache-Control" header in the http response.
CacheControlFilter() - Constructor for class net.sf.basedb.clients.web.servlet.CacheControlFilter
cachedPaths - Variable in class net.sf.basedb.core.Metadata
cachedRssNews - Variable in class net.sf.basedb.clients.web.servlet.RssNewsFeed
CacheEntry(long, Set<Integer>) - Constructor for class net.sf.basedb.util.listable.TransformCache.CacheEntry
cacheFile - Variable in class net.sf.basedb.util.StreamCacher
cacheKey - Variable in class net.sf.basedb.util.overview.cache.DirectionalCacheKey
cacheKey - Variable in class net.sf.basedb.util.overview.cache.IndexedCacheKey
CacheKey(int, String) - Constructor for class net.sf.basedb.util.units.UnitCache.CacheKey
CacheKey(String, Item, Item, SyncFilter.SourceItemTransform, SortedSet<Integer>) - Constructor for class net.sf.basedb.util.listable.TransformCache.CacheKey
cacheNewNode(Object, Node, ChildNodeDirection) - Method in class net.sf.basedb.util.overview.node.NodeFactory: Store a node in the node cache if the current overview context supports caching.
cacheOut - Variable in class net.sf.basedb.util.StreamCacher
cacheQuery(String, Query<?>) - Method in class net.sf.basedb.core.hibernate.AbstractQueryCache: Cache a query.
cacheRegion - Variable in class net.sf.basedb.util.listable.SourceItemTransformerWithCache
cacheRegion - Variable in class net.sf.basedb.util.listable.SourceItemTransformerWithCache.TransformerWithCache
cacheRegion - Variable in class net.sf.basedb.util.listable.TransformCache.CacheKey
cacheReporterData() - Method in class net.sf.basedb.util.export.spotdata.AbstractBioAssaySetExporter: Loads and caches reporter data in an internal structure for quick access.
cacheResults - Variable in class net.sf.basedb.core.AbstractHqlQuery: If the results should be cached or not.
calculateBoxAndWhiskerStatistics(List<Float>) - Method in class net.sf.basedb.clients.web.servlet.ExperimentExplorerPlotServlet: Creates a box-and-whisker data holder for the given list of values.
calculateIntensities(RawData) - Method in interface net.sf.basedb.util.IntensityCalculator: Calculate intensities from a raw data spot.
calculateIntensities(RawData) - Method in class net.sf.basedb.util.IntensityCalculatorUtil.JepIntensityCalculatorImpl
calculateWeights(List<LowessNormalization.SpotData>, double, List<Double>) - Static method in class net.sf.basedb.plugins.LowessNormalization
CalendarButton - Class in net.sf.basedb.clients.web.taglib: A special button tag that is used to display a "Calendar" button that opens a popup for selecting a date and time.
CalendarButton() - Constructor for class net.sf.basedb.clients.web.taglib.CalendarButton
call() - Method in class net.sf.basedb.core.QueryExecutor.FutureItem
call() - Method in class net.sf.basedb.core.QueryExecutor.FutureResultSet
call() - Method in class net.sf.basedb.core.QueryExecutor.FutureScrollIterator
call() - Method in class net.sf.basedb.core.QueryExecutor.FutureUpdate
call() - Method in class net.sf.basedb.plugins.LowessNormalization.CallableWorker
CallableWorker(List<LowessNormalization.SpotData>, MACalculator, float, float, int, int) - Constructor for class net.sf.basedb.plugins.LowessNormalization.CallableWorker
calledFrom - Variable in class net.sf.basedb.util.StaticCache.State
canAdd(BioWell) - Method in enum class net.sf.basedb.core.BioWell.LockMode: Is it allowed to add (a different) biomaterial to the well?
canAdd(BioWellData) - Method in enum class net.sf.basedb.core.BioWell.LockMode
canAddBioMaterial() - Method in class net.sf.basedb.core.BioWell: Check if it is possible to add/change biomaterial in this well.
cancel() - Method in class net.sf.basedb.clients.jobagent.JobQueueChecker
cancel() - Method in interface net.sf.basedb.core.QueryExecutor.Cancelable
cancel() - Method in class net.sf.basedb.core.QueryExecutor.CancelableSession
cancel() - Method in class net.sf.basedb.core.QueryExecutor.CancelableStatelessSession
cancel() - Method in class net.sf.basedb.core.QueryExecutor.CancelableStatement
cancel() - Method in class net.sf.basedb.util.timer.ThreadTimerTask
CancelableSession(Session) - Constructor for class net.sf.basedb.core.QueryExecutor.CancelableSession
CancelableStatelessSession(StatelessSession) - Constructor for class net.sf.basedb.core.QueryExecutor.CancelableStatelessSession
CancelableStatement(Statement) - Constructor for class net.sf.basedb.core.QueryExecutor.CancelableStatement
cancelQuery() - Method in class net.sf.basedb.core.hibernate.SessionWrapper
cancelQuery() - Method in class net.sf.basedb.core.hibernate.StatelessSessionWrapper: Cancels the currently executing query in the same manner as Session.cancelQuery().
canClear(BioWell) - Method in enum class net.sf.basedb.core.BioWell.LockMode: Is it allowed to clear a well from biomaterial?
canClear(BioWellData) - Method in enum class net.sf.basedb.core.BioWell.LockMode
canClearBioMaterial() - Method in class net.sf.basedb.core.BioWell: Check if it is possible to clear the current biomaterial in this well.
canEnumerate - Variable in enum class net.sf.basedb.core.Type
canEnumerate() - Method in enum class net.sf.basedb.core.Type: If it makes sense to use values of this type as an enumeration to choose from.
canLogValues(String) - Method in class net.sf.basedb.core.log.EntityLogOptions: Check if it is allowed to log the old and new values of a modified property.
canUseColoring - Variable in enum class net.sf.basedb.core.Formula.Type
canUseColoring() - Method in enum class net.sf.basedb.core.Formula.Type: If a formula of this type can use coloring or not.
CAPACITANCE - Static variable in class net.sf.basedb.core.Quantity: The id for the Quantity object representing capacitance.
CaseExpression - Class in net.sf.basedb.core.query: An SQL case expression:
CaseExpression(Expression, WhenStatement...) - Constructor for class net.sf.basedb.core.query.CaseExpression
caseInsensitive - Variable in enum class net.sf.basedb.core.FeatureIdentificationMethod: If the feature identifiers may be affect by case sensitivity at the database level or not.
caseInsensitive - Variable in class net.sf.basedb.core.RawDataBatcher: If case should be ignored when comparing strings (external ID)
caseInsensitive() - Method in enum class net.sf.basedb.core.FeatureIdentificationMethod: Return TRUE if this identification method can be case insensitive.
caseInsensitiveComparison() - Method in interface net.sf.basedb.core.dbengine.DbEngine: If the database does case sensitive or case insensitive string comparison in expressions.
caseInsensitiveComparison() - Method in class net.sf.basedb.core.dbengine.DefaultDbEngine: Returns TRUE.
caseInsensitiveComparison() - Method in class net.sf.basedb.core.dbengine.MySQLEngine: Returns TRUE.
caseInsensitiveComparison() - Method in class net.sf.basedb.core.dbengine.PostgresDbEngine: Returns FALSE.
caseWhen(Expression, WhenStatement...) - Static method in class net.sf.basedb.core.query.Expressions: Create a conditional CASE-WHEN expression:
castToDate(String) - Method in class net.sf.basedb.core.dbengine.AbstractDbEngine
castToDate(String) - Method in interface net.sf.basedb.core.dbengine.DbEngine: Get a function that casts a date/timestamp to a date (eg. no time should be included in the result).
catalog - Variable in class net.sf.basedb.core.hibernate.SchemaExistsWork
catalog - Variable in class net.sf.basedb.core.hibernate.TableExistsWork
categories - Variable in class net.sf.basedb.core.data.AnnotationTypeData
categoryColumnMapping - Static variable in class net.sf.basedb.plugins.batchimport.AnnotationTypeImporter: Column mapping parameter for assigning annotation types to categories.
categoryMapper - Variable in class net.sf.basedb.plugins.batchimport.AnnotationTypeImporter
CdfFileReporterImporter - Class in net.sf.basedb.plugins: This plug-in can import probesets from Affymetrix CDF files as reporters.
CdfFileReporterImporter() - Constructor for class net.sf.basedb.plugins.CdfFileReporterImporter: Constructor should be empty.
CdfValidationAction - Class in net.sf.basedb.util.affymetrix: Action for validation of CDF files in a file set.
CdfValidationAction(DbControl, ArrayDesign) - Constructor for class net.sf.basedb.util.affymetrix.CdfValidationAction: Create a new action.
CdfValidationFactory - Class in net.sf.basedb.util.affymetrix: Action factory for creating CDF file validators.
CdfValidationFactory() - Constructor for class net.sf.basedb.util.affymetrix.CdfValidationFactory
CdfValidator - Class in net.sf.basedb.util.affymetrix: Helper class for working with Affymetrix CDF files.
CdfValidator() - Constructor for class net.sf.basedb.util.affymetrix.CdfValidator: Create a new instance.
Cell - Class in net.sf.basedb.clients.web.taglib.table: This tag defines a new cell in a row.
Cell() - Constructor for class net.sf.basedb.clients.web.taglib.table.Cell
cellClass - Variable in class net.sf.basedb.clients.web.extensions.list.AbstractListColumnBean
cellClass - Variable in class net.sf.basedb.clients.web.extensions.list.PropertyPathActionFactory
cellStyle - Variable in class net.sf.basedb.clients.web.extensions.list.AbstractListColumnBean
cellStyle - Variable in class net.sf.basedb.clients.web.extensions.list.PropertyPathActionFactory
CellStyleCreator - Class in net.sf.basedb.util.excel: Helper class for keeping track of formatting styles that has been created for given Excel worksheet.
CellStyleCreator(Workbook) - Constructor for class net.sf.basedb.util.excel.CellStyleCreator: Creates a new style creator for the given Excel workbook.
cellType - Variable in class net.sf.basedb.util.excel.XlsxToCsvUtil.CellTypeWithInfo
CellTypeWithInfo() - Constructor for class net.sf.basedb.util.excel.XlsxToCsvUtil.CellTypeWithInfo
CellValue - Class in net.sf.basedb.clients.web.taglib.table: This tag adds a value to a cell in a row.
CellValue() - Constructor for class net.sf.basedb.clients.web.taglib.table.CellValue
CelValidationAction - Class in net.sf.basedb.util.affymetrix: Action for validation of CEL files in a file set.
CelValidationAction(DbControl, RawBioAssay) - Constructor for class net.sf.basedb.util.affymetrix.CelValidationAction: Create a new action.
CelValidationFactory - Class in net.sf.basedb.util.affymetrix: Action factory for creating CEL file validators.
CelValidationFactory() - Constructor for class net.sf.basedb.util.affymetrix.CelValidationFactory
CelValidator - Class in net.sf.basedb.util.affymetrix: Helper class for working with Affymetrix CEL files.
CelValidator() - Constructor for class net.sf.basedb.util.affymetrix.CelValidator: Create a new instance.
cfg - Static variable in class net.sf.basedb.core.HibernateUtil: The Hibernate configuration, including all mappings.
cfg - Variable in class net.sf.basedb.core.MigrateRbaToDba.SubtypeMapping
CFResultIterator(SqlResultIterator, SqlResultIterator) - Constructor for class net.sf.basedb.clients.web.servlet.PlotServlet.CFResultIterator
CFSqlResult() - Constructor for class net.sf.basedb.clients.web.servlet.PlotServlet.CFSqlResult
ch - Variable in class net.sf.basedb.util.importer.spotdata.MatrixSpotIntensityEventHandler
ch - Variable in class net.sf.basedb.util.importer.spotdata.SerialSpotIntensityEventHandler
ch1 - Variable in class net.sf.basedb.plugins.LowessNormalization.SpotData
ch1 - Variable in class net.sf.basedb.plugins.MedianRatioNormalization.SpotData
ch2 - Variable in class net.sf.basedb.plugins.LowessNormalization.SpotData
ch2 - Variable in class net.sf.basedb.plugins.MedianRatioNormalization.SpotData
chain - Variable in class net.sf.basedb.util.AnnotationUtil.AnnotatableWrapper
chain - Variable in class net.sf.basedb.util.listable.SourceItemTransformerChain
CHAIN_ORDER - Static variable in class net.sf.basedb.core.SyncFilter
chained - Variable in class net.sf.basedb.core.Job.ProgressReporterImpl
ChainedFilter(List<QueryRuntimeFilter>) - Constructor for class net.sf.basedb.core.QueryRuntimeFilterFactory.ChainedFilter: Create a new ChainedFilter object.
ChainedFilter(QueryRuntimeFilter...) - Constructor for class net.sf.basedb.core.QueryRuntimeFilterFactory.ChainedFilter: Create a new ChainedFilter object.
chainedProgress - Variable in class net.sf.basedb.util.export.spotdata.BfsExporter
ChainedProgressReporter - Class in net.sf.basedb.util: An implementation of the ProgressReporter interface that chains to another progress reporter while recalculating the percentage values.
ChainedProgressReporter(ProgressReporter) - Constructor for class net.sf.basedb.util.ChainedProgressReporter: Create a new chained progress reporter.
Change(ChangeType) - Constructor for enum class net.sf.basedb.core.AnnotationBatcher.Change
ChangeHistory - Class in net.sf.basedb.core
ChangeHistory(ChangeHistoryDetailData) - Constructor for class net.sf.basedb.core.ChangeHistory
CHANGEHISTORY - Enum constant in enum class net.sf.basedb.core.Item: The item is a ChangeHistory entry.
CHANGEHISTORY_VALUES - Enum constant in enum class net.sf.basedb.core.Item: Virtual item representing the new and old values column in ChangeHistory which need special access permissions.
ChangeHistory.TransactionInfo - Class in net.sf.basedb.core: Holds information about a single transaction.
ChangeHistoryData - Class in net.sf.basedb.core.data: Represents the changes made in a single transaction.
ChangeHistoryData() - Constructor for class net.sf.basedb.core.data.ChangeHistoryData
ChangeHistoryDetailData - Class in net.sf.basedb.core.data: Represents a change (creation/update/deletion) made to a single entity in a transaction.
ChangeHistoryDetailData() - Constructor for class net.sf.basedb.core.data.ChangeHistoryDetailData
ChangeHistoryDetailLoader - Class in net.sf.basedb.clients.web.plugins: Data loader implementation for old and new values in the change history which are protected by special permissions.
ChangeHistoryDetailLoader(boolean) - Constructor for class net.sf.basedb.clients.web.plugins.ChangeHistoryDetailLoader
ChangeHistoryItemLoader - Class in net.sf.basedb.clients.web.plugins: Data loader implementation for loading the changed item.
ChangeHistoryItemLoader() - Constructor for class net.sf.basedb.clients.web.plugins.ChangeHistoryItemLoader
ChangeHistoryUtil - Class in net.sf.basedb.clients.web: Utility class for working with change history.
ChangeHistoryUtil() - Constructor for class net.sf.basedb.clients.web.ChangeHistoryUtil
changeHost(URI) - Method in class net.sf.basedb.util.uri.ConnectionParameters: If the connection parameters include a specific host:port or root path a new URI is created were the host:port is replaced and the root path is added to the URI path.
changeInfo - Variable in class net.sf.basedb.core.data.ChangeHistoryDetailData
changeReferenceFactorAndOffset(double, double) - Method in class net.sf.basedb.core.Unit: Changes the factor and offset used for converting values in this unit into the reference unit.
changeReferenceFactorAndOffset(SessionControl, Session, UnitData, double, double) - Static method in class net.sf.basedb.core.Unit
changes - Variable in class net.sf.basedb.core.log.LoggingInterceptor
changeType - Variable in class net.sf.basedb.core.data.ChangeHistoryDetailData
changeType - Variable in class net.sf.basedb.core.log.EntityDetails
changeType - Variable in class net.sf.basedb.core.log.ManualLogEntry
ChangeType - Enum Class in net.sf.basedb.core.log: Enumeration that represents the type of change that has happened.
ChangeType(int, String) - Constructor for enum class net.sf.basedb.core.log.ChangeType
ChangeTypeFormatter - Class in net.sf.basedb.core.log: Formatter implementation that converts an integer into it's ChangeType representation and the uses name() as the formatted value.
ChangeTypeFormatter() - Constructor for class net.sf.basedb.core.log.ChangeTypeFormatter: Create a new formatter.
ChangeTypeFormatter(String) - Constructor for class net.sf.basedb.core.log.ChangeTypeFormatter: Create a new formatter.
channel - Variable in class net.sf.basedb.core.RawDataProperty
channel(int) - Method in class net.sf.basedb.util.jep.ChannelFunction: Get the value of the specified channel of the current sql result.
channel(int) - Method in class net.sf.basedb.util.jep.RawChannelFunction: Get the value of the specified channel of the current sql result.
channel(int, String, Formatter<?>) - Static method in class net.sf.basedb.util.export.spotdata.ExportableFieldFactory: Create a simple dynamic field that exports the channel intensity of the given channel.
ChannelFunction - Class in net.sf.basedb.util.jep: A JEP function class that adds a ch(int) function to a JEP expression parser.
ChannelFunction() - Constructor for class net.sf.basedb.util.jep.ChannelFunction: Create a new instance of this function.
ChannelFunction(int[], IntensityTransform) - Constructor for class net.sf.basedb.util.jep.ChannelFunction: Create a new instance of this function which can be used to dynamically evaluate expressions.
channelIntensity(int) - Static method in class net.sf.basedb.core.VirtualColumn: Get a column that returns the intensity values for a channel.
channelParameters - Variable in class net.sf.basedb.plugins.JepIntensityTransformer
channelRaw(int) - Static method in class net.sf.basedb.core.VirtualColumn: Get a column that stores the raw spot value for a channel.
channels - Variable in class net.sf.basedb.core.data.FormulaData
channels - Variable in class net.sf.basedb.core.data.PlatformData
channels - Variable in class net.sf.basedb.core.data.PlatformVariantData
channels - Variable in class net.sf.basedb.core.RawDataType
channels - Variable in class net.sf.basedb.util.importer.spotdata.GenericIntensityParser
channels - Variable in class net.sf.basedb.util.importer.spotdata.SecondPassSectionSpotsParser
channelToIndex - Variable in class net.sf.basedb.util.jep.ChannelFunction
channelToIndex - Variable in class net.sf.basedb.util.jep.RawChannelFunction
CHAR_ESCAPE - Variable in class net.sf.basedb.core.migrate.postgres.PostgresResultWriterFactory
char64(char) - Static method in class net.sf.basedb.util.bcrypt.BCrypt: Look up the 3 bits base64-encoded by the specified character, range-checking againt conversion table
characterEncoding - Variable in class net.sf.basedb.clients.web.servlet.CharacterEncodingFilter
CharacterEncodingFilter - Class in net.sf.basedb.clients.web.servlet: This is a filter that sets the character encoding for both the request and the response.
CharacterEncodingFilter() - Constructor for class net.sf.basedb.clients.web.servlet.CharacterEncodingFilter
characterSetColumnMapping - Static variable in class net.sf.basedb.plugins.batchimport.FileImporter
characterSetMapper - Variable in class net.sf.basedb.plugins.batchimport.FileImporter
CHARGE - Static variable in class net.sf.basedb.core.Quantity: The id for the Quantity object representing electrical charge.
charset - Variable in class net.sf.basedb.clients.web.fileupload.FileUpload: The charset used for decoding header lines.
charset - Variable in class net.sf.basedb.core.data.FileData
charset - Variable in class net.sf.basedb.util.charset.CharsetDetector
charset - Variable in class net.sf.basedb.util.excel.XlsxToCsvUtil
charset - Variable in class net.sf.basedb.util.FileImportInputStream
charset - Variable in class net.sf.basedb.util.gtf.GtfInputStream
charset - Variable in class net.sf.basedb.util.uri.UriMetadata
CHARSET_PARAMETER - Static variable in class net.sf.basedb.plugins.util.Parameters: The name of the parameter that is created by Parameters.charsetParameter(String, String, String, boolean)
CharsetDetector - Class in net.sf.basedb.util.charset: Utility class for testing if a text stream can be parsed using a given character set.
CharsetDetector(Charset) - Constructor for class net.sf.basedb.util.charset.CharsetDetector: Create a detector for the given character set that only detects technical issues.
CharsetDetector(Charset, StringDetector) - Constructor for class net.sf.basedb.util.charset.CharsetDetector: Create a detector for the given character set that uses technical an content-based detection.
charsetParameter(String, String, String) - Static method in class net.sf.basedb.plugins.util.Parameters
charsetParameter(String, String, String, boolean) - Static method in class net.sf.basedb.plugins.util.Parameters: Parameter definition that asks for the character encoding used in the file that is imported.
CharsetTesterThread(Charset) - Constructor for class net.sf.basedb.core.File.CharsetTesterThread
charsetType - Static variable in class net.sf.basedb.plugins.util.Parameters: Enumerates all available character sets.
CharsetUtil - Class in net.sf.basedb.util.charset: Helper class for working with charsets and enabling the UTF-8 with fallback charsets: X-UTF-8_with_ISO-8859-1_fallback X-UTF-8_with_windows-1252_fallback
CharsetUtil() - Constructor for class net.sf.basedb.util.charset.CharsetUtil
charsetWithFallbacksType - Static variable in class net.sf.basedb.plugins.util.Parameters: Enumerates all available character sets and also inlcude fallback type.
chart - Variable in class net.sf.basedb.util.plot.HistogramPlot
chart - Variable in class net.sf.basedb.util.plot.ScatterPlot
checkAbortAndDelay() - Method in class net.sf.basedb.clients.web.fileupload.FileUpload: Check if upload has been aborted.
checkAllowedSource(BioMaterial, boolean) - Method in class net.sf.basedb.core.BioMaterialEvent: Check if the biomaterial is allowed as a source.
checkAndCreateTables() - Method in class net.sf.basedb.core.BioAssaySet
checkAndLoadClass(ClassLoader, String, boolean, Class<C>, Class<?>...) - Static method in class net.sf.basedb.util.ClassUtil: Check if a specified class exists and, optionally, if it has public no-argument constructor and implements a set of specific interfaces or superclasses.
checkBatchAnnotatableUsage(boolean, boolean) - Method in class net.sf.basedb.core.BasicItem: Annotatable items that are used with the AnnotationBatcher must not call Annotatable.getAnnotationSet() in the same transaction.
checkBioAssay(DbControl, int, int) - Method in class net.sf.basedb.util.importer.spotdata.BaseFileInfo: Checks that the bioassay with the given id exists in the database.
checkBioMaterialInWell(DbControl, OverviewContext, Node, Node) - Static method in class net.sf.basedb.util.overview.validator.BioPlateValidator: Check that the main type and subtype of the biomaterial is matching the requirements of the bioplate type.
checkBoundary(byte[], int, byte[], int) - Method in class net.sf.basedb.clients.web.fileupload.FileUpload: Check if the given line matches the boundary.
checkClass(Class<?>, boolean, Class<?>...) - Static method in class net.sf.basedb.util.ClassUtil: Check if a specified class has public no-argument constructor and implements a set of specific interfaces or superclasses.
checkClosed() - Method in class net.sf.basedb.util.extensions.manager.ExtensionsFile.WriteableExtensionsFile: Check if the file has been closed and throws an IllegalStateException if it has.
checkColumnMapping(String, boolean, String) - Method in class net.sf.basedb.plugins.AbstractFlatFileImporter: Check if a column mapping is a valid mapping expression and optionally if it is complex mapping.
checkColumnMapping(FlatFileParser, String, boolean, String) - Method in class net.sf.basedb.plugins.AbstractFlatFileImporter: Checks the syntax column mapping and verifies that the given file parser has found the columns that are used in the file.
checkContext(DbControl, ItemQuery<PluginDefinition>, ItemQuery<PluginConfiguration>, GuiContext, Object) - Static method in class net.sf.basedb.util.ContextUtil: Call the InteractivePlugin.isInContext(GuiContext, Object) method for all plug-ins returned by the queries.
checkCoordinate(MappingCoordinate, int, PlateGeometryData, boolean) - Method in class net.sf.basedb.core.PlateMapping: Checks that the coordinate is within the bouds given by the mapping and geometry.
checkDerivedBioAssaySubtype(DbControl, OverviewContext, Node, Node) - Static method in class net.sf.basedb.util.overview.validator.DerivedBioAssayValidator: Check the subtype of the derived bioassay that is the parent to a child derived bioassay.
checked - Variable in class net.sf.basedb.clients.web.taglib.Input: TRUE if the input element is checked.
checkEntity(IdentifiableData) - Method in class net.sf.basedb.core.hibernate.EntityQueryWrapper
checkEntityArray(Object[]) - Method in class net.sf.basedb.core.hibernate.EntityQueryWrapper
checkEntityCollection(Collection<?>) - Method in class net.sf.basedb.core.hibernate.EntityQueryWrapper
checkExperimentArrayDesign(DbControl, OverviewContext, Node, ArrayDesign) - Method in class net.sf.basedb.util.overview.validator.ArrayDesignValidator: Check if an experiment has used more than one array design.
checkExtractOnBioAssay(DbControl, OverviewContext, Node, Node) - Method in class net.sf.basedb.util.overview.validator.ExtractValidator
checkExtractSubtype(DbControl, OverviewContext, Node, Node) - Static method in class net.sf.basedb.util.overview.validator.DerivedBioAssayValidator: Check the subtype of the extract that is the linked with a derived bioassay.
checkExtractSubtype(DbControl, OverviewContext, Node, Node) - Static method in class net.sf.basedb.util.overview.validator.PhysicalBioAssayValidator: Check the subtype of the extract that is the parent to a physical bioassay.
checkExtractTag(DbControl, OverviewContext, Node, Node) - Static method in class net.sf.basedb.util.overview.validator.ExtractValidator: Check the tag of the child extract in relation to a parent extract.
checkForInvalidNumberOperation() - Method in class net.sf.basedb.core.dbengine.AbstractDbEngine: Returns FALSE.
checkForInvalidNumberOperation() - Method in interface net.sf.basedb.core.dbengine.DbEngine: If we need to check for invalid arguments to numerical functions to avoid exceptions from the database.
checkForInvalidNumberOperation() - Method in class net.sf.basedb.core.dbengine.PostgresDbEngine: Returns TRUE.
checkForJobs() - Method in class net.sf.basedb.clients.jobagent.JobQueueChecker
checkForSignals() - Method in class net.sf.basedb.core.signal.EnhancedThreadSignalHandler: If at least one signal has been received a SignalReceivedException is thrown.
checkForSignals() - Method in class net.sf.basedb.core.signal.ProgressReporterSignalHandler: If at least one signal has been received a SignalReceivedException is thrown.
checkIfDifferent(Object, Unit) - Method in class net.sf.basedb.core.Annotation: Check if the given value is different from the values already stored in this annotation.
checkIfDifferent(List<?>, Unit) - Method in class net.sf.basedb.core.Annotation: Check if the given values are different from the values already stored in this annotation.
checkIfReportersExists(FusionCDFData, ReporterBatcher, boolean, ReporterType, ProgressReporter) - Method in class net.sf.basedb.util.affymetrix.CdfValidator: Verify if probesets in a CDF file exists as reporters and optionally create those that doesn't exists.
checkImportable(SessionControl, PluginDefinition, PluginConfiguration, File, String, GuiContext, Object) - Static method in class net.sf.basedb.util.AutoDetectFileFormat
checkInstallation(DbControl, Collection<PluginInfo>) - Static method in class net.sf.basedb.core.PluginDefinition: Check the installation status of the given list of plug-ins.
checkInternalJobQueue() - Method in class net.sf.basedb.core.InternalJobQueue
checkInterrupted() - Static method in class net.sf.basedb.core.signal.ThreadSignalHandler: Utility method to check if the current thread has been interrupted and (may) throw a SignalException if it has.
checkInterval - Variable in class net.sf.basedb.clients.jobagent.Agent
checkItemType(Item) - Method in class net.sf.basedb.core.ItemSubtype: Check if this subtype can be used on items of the given type.
checkJdbcDriver(String, String, String) - Static method in class net.sf.basedb.core.HibernateUtil: Check that a JDBC driver is registered and try to load a driver if not.
checkLine(int, String) - Method in class net.sf.basedb.util.charset.SimpleStringDetector
checkLine(int, String) - Method in interface net.sf.basedb.util.charset.StringDetector: Check the given line.
checkLocked(String) - Method in class net.sf.basedb.core.Application.StartupOptions
checkLocked(String) - Method in class net.sf.basedb.core.ServiceSessionControl.SessionFactoryConfiguration: Check that the
checkMagicNumber(PushbackInputStream, byte[]) - Static method in class net.sf.basedb.util.FileUtil: Take a peek at an input stream and check if the first few bytes matches the bCheck parameter.
checkManualMembersAllowed() - Method in class net.sf.basedb.core.ItemList
checkMax(int, String, int) - Static method in class net.sf.basedb.core.IntegerUtil: Check that an integer is equal or lower than a maximum value.
checkMd5 - Variable in class net.sf.basedb.core.File.UploadStream: If the md5 should be checked or not.
checkMemberType(Collection<ItemList>) - Method in class net.sf.basedb.core.ItemList: Checks that the lists have the same member type as this list.
checkMemberType(Item) - Method in class net.sf.basedb.core.ItemList: Checks if the other type is the same type as the member type of this list.
checkMin(int, String, int) - Static method in class net.sf.basedb.core.IntegerUtil: Check that an integer is equal or greater than a minimum value.
checkMinMax(int, String, int, int) - Static method in class net.sf.basedb.core.IntegerUtil: Check that an integer is equal or between a minimum and a maximum value.
checkModified() - Method in class net.sf.basedb.util.extensions.manager.ExtensionsFile: Check if the underlying file has been modified since it was last processed.
checkNext - Variable in class net.sf.basedb.core.DynamicResultIterator
checkNext - Variable in class net.sf.basedb.util.extensions.ActionIterator
checkNumberOfParameters(int) - Method in class net.sf.basedb.util.jep.ChannelFunction
checkNumberOfParameters(int) - Method in class net.sf.basedb.util.jep.ExtraValueFunction
checkNumberOfParameters(int) - Method in class net.sf.basedb.util.jep.FunctionSafeJep.UnknownFunction
checkNumberOfParameters(int) - Method in class net.sf.basedb.util.jep.InReporterListFunction
checkNumberOfParameters(int) - Method in class net.sf.basedb.util.jep.LeftFunction
checkNumberOfParameters(int) - Method in class net.sf.basedb.util.jep.Log2Function
checkNumberOfParameters(int) - Method in class net.sf.basedb.util.jep.MeanFunction
checkNumberOfParameters(int) - Method in class net.sf.basedb.util.jep.NotInReporterListFunction
checkNumberOfParameters(int) - Method in class net.sf.basedb.util.jep.PositionFunction
checkNumberOfParameters(int) - Method in class net.sf.basedb.util.jep.RawChannelFunction
checkNumberOfParameters(int) - Method in class net.sf.basedb.util.jep.RawFunction
checkNumberOfParameters(int) - Method in class net.sf.basedb.util.jep.ReporterFunction
checkNumberOfParameters(int) - Method in class net.sf.basedb.util.jep.ScoreFunction
checkNumberOfParameters(int) - Method in class net.sf.basedb.util.jep.SimpleJepFunction
checkNumberOfParameters(int) - Method in class net.sf.basedb.util.parser.ColFunction
checkNumberOfParameters(int) - Method in class net.sf.basedb.util.parser.DataNoFunction
checkNumberOfParameters(int) - Method in class net.sf.basedb.util.parser.DefaultItemFunction
checkNumberOfParameters(int) - Method in class net.sf.basedb.util.parser.LineNoFunction
checkParentBioSourceSubtype(DbControl, OverviewContext, Node, Node) - Static method in class net.sf.basedb.util.overview.validator.SampleValidator: Check the subtype of the biosurce that is the parent to a sample.
checkParentExtractSubtype(DbControl, OverviewContext, Node, Node) - Static method in class net.sf.basedb.util.overview.validator.ExtractValidator: Check the subtype of the extract that is the parent to another extract.
checkParentSampleSubtype(DbControl, OverviewContext, Node, Node) - Static method in class net.sf.basedb.util.overview.validator.ExtractValidator: Check the subtype of the sample that is the parent to an extract.
checkParentSampleSubtype(DbControl, OverviewContext, Node, Node) - Static method in class net.sf.basedb.util.overview.validator.SampleValidator: Check the subtype of the sample that is the parent to another sample.
checkPassword(String, String) - Static method in class net.sf.basedb.core.User: Check the plain-text password against the crypted password.
checkPermission(Permission) - Method in class net.sf.basedb.clients.web.extensions.ExtensionsControl
checkPermission(Permission) - Method in interface net.sf.basedb.core.AccessControlled: Check if the logged in user has the desired permission on the item, otherwise throw an exception.
checkPermission(Permission) - Method in class net.sf.basedb.core.BasicBatcher: Checks if the logged in user has the specified permission on this item.
checkPermission(Permission) - Method in class net.sf.basedb.core.BasicItem: Checks if the logged in user has the specified permission on this item.
checkPermission(Permission) - Method in class net.sf.basedb.core.BioMaterialEventSource
checkPermission(Permission) - Method in class net.sf.basedb.core.Coloring
checkPermission(Permission, String) - Method in class net.sf.basedb.clients.web.extensions.ExtensionsControl: For checking the permission and adding a custom message to the PermissionDeniedException if the required permission is missing.
checkPhysicalBioAssaySubtype(DbControl, OverviewContext, Node, Node) - Static method in class net.sf.basedb.util.overview.validator.DerivedBioAssayValidator: Check the subtype of the physical bioassay that is the parent to a derived bioassay.
checkpw(String, String) - Static method in class net.sf.basedb.util.bcrypt.BCrypt: Check that a plaintext password matches a previously hashed one
checkSameArrayDesign(Collection<RawBioAssay>, boolean) - Static method in class net.sf.basedb.util.IntensityCalculatorUtil
checkSuperclass - Variable in class net.sf.basedb.util.formatter.MultiFormatter
checkSyncFiltersAllowed() - Method in class net.sf.basedb.core.ItemList
checkTimeoutOnRemoteSlots() - Method in class net.sf.basedb.clients.jobagent.slotmanager.MasterSlotManager: Check the remote slots to see if they have timed out.
checkUniqueFields(String, String) - Method in class net.sf.basedb.plugins.executor.BaseFileExporterSupport
checkUniqueFields(String, String) - Method in class net.sf.basedb.plugins.executor.BfsExporterSupport
checkUnsafeScriptableUsage(Extension<?>) - Method in class net.sf.basedb.clients.web.extensions.ExtensionsControl: Checks if the given extension may violate the 'Content Security Policy' for the server.
checkUnsafeScriptableUsage(ExtensionsFile) - Method in class net.sf.basedb.clients.web.extensions.ExtensionsControl: Checks if the given extensions file contain any extensions that may violate the 'Content Security Policy' for the server.
checkUnsafeScriptableUsageInternal(Extension<?>) - Method in class net.sf.basedb.clients.web.extensions.ExtensionsControl
checkValues - Variable in class net.sf.basedb.core.ParameterType
child - Variable in class net.sf.basedb.clients.web.servlet.PlotServlet.CFResultIterator
child - Variable in class net.sf.basedb.clients.web.servlet.PlotServlet.CFSqlResult
child - Variable in class net.sf.basedb.core.QueryRuntimeFilterFactory.ChildFilter: The item type of the child item.
child - Variable in class net.sf.basedb.util.importer.spotdata.BaseFileInfo.ChildBioAssay
child - Variable in class net.sf.basedb.util.importer.spotdata.SecondPassSectionSpotsParser
CHILD_DESCRIPTION - Static variable in class net.sf.basedb.core.plugin.AbstractAnalysisPlugin: The name of the parameter that asks for the description of the child bioassay set.
CHILD_DESCRIPTION - Static variable in class net.sf.basedb.plugins.util.Parameters: The name of the parameter that asks is created by Parameters.childDescriptionParameter(String, String, String)
CHILD_NAME - Static variable in class net.sf.basedb.core.plugin.AbstractAnalysisPlugin: The name of the parameter that asks for the name of the child bioassay set.
CHILD_NAME - Static variable in class net.sf.basedb.plugins.util.Parameters: The name of the parameter that is created by Parameters.childNameParameter(String, String, String)
CHILD_TO_PARENT - Enum constant in enum class net.sf.basedb.core.SyncFilter.SourceItemTransform: Source items are transformed to parent items.
CHILD_TO_PARENT - Static variable in class net.sf.basedb.util.listable.ToBioSourceSourceItemTransformerFactory
CHILD_TO_PARENT - Static variable in class net.sf.basedb.util.listable.ToDerivedBioAssaySourceItemTransformerFactory
CHILD_TO_PARENT - Static variable in class net.sf.basedb.util.listable.ToExtractSourceItemTransformerFactory
CHILD_TO_PARENT - Static variable in class net.sf.basedb.util.listable.ToPhysicalBioAssaySourceItemTransformerFactory
CHILD_TO_PARENT - Static variable in class net.sf.basedb.util.listable.ToRawBioAssaySourceItemTransformerFactory
CHILD_TO_PARENT - Static variable in class net.sf.basedb.util.listable.ToSampleSourceItemTransformerFactory
childAssays - Variable in class net.sf.basedb.util.importer.spotdata.BaseFileInfo
ChildBioAssay() - Constructor for class net.sf.basedb.util.importer.spotdata.BaseFileInfo.ChildBioAssay: Create a new object.
ChildBioAssay(int) - Constructor for class net.sf.basedb.util.importer.spotdata.BaseFileInfo.ChildBioAssay: Create a new object
childCreationEvents - Variable in class net.sf.basedb.core.data.BioMaterialData
childDescriptionParameter(String, String, String) - Static method in class net.sf.basedb.plugins.util.Parameters: Create a plugin parameter that asks for the description of the child bioassay set.
childErrors - Variable in class net.sf.basedb.util.overview.Node
ChildFilter(Item, Item) - Constructor for class net.sf.basedb.core.QueryRuntimeFilterFactory.ChildFilter: Create a new ChildFilter object.
childHasDifferentReporterPositionMapping - Variable in class net.sf.basedb.util.importer.spotdata.BaseFileInfo
childId - Variable in class net.sf.basedb.core.data.keyring.GroupGroups
ChildItem - Class in net.sf.basedb.core: An abstract base class for all items which are child items to a Shareable parent item.
ChildItem(BasicData) - Constructor for class net.sf.basedb.core.ChildItem
childIterator - Variable in class net.sf.basedb.util.Tree.EntryIterator: An iterator over the children of the root entry.
childNameParameter(String, String, String) - Static method in class net.sf.basedb.plugins.util.Parameters: Create a plugin parameter that asks for the name of the child bioassay set.
ChildNodeDirection - Enum Class in net.sf.basedb.util.overview.node: Represents the direction to use for loading child nodes in a tree.
ChildNodeDirection(boolean, boolean, boolean) - Constructor for enum class net.sf.basedb.util.overview.node.ChildNodeDirection
ChildNodeLoaderAction - Interface in net.sf.basedb.util.overview.extensions: Load and create child nodes for a given parent node.
children - Variable in class net.sf.basedb.core.data.BioAssayData
children - Variable in class net.sf.basedb.core.data.BioMaterialData
children - Variable in class net.sf.basedb.core.data.DerivedBioAssayData
children - Variable in class net.sf.basedb.core.data.GroupData
children - Variable in class net.sf.basedb.core.data.PlateData
children - Variable in class net.sf.basedb.util.listable.CollectExtracts
children - Variable in class net.sf.basedb.util.overview.Node
children - Variable in class net.sf.basedb.util.Tree.Entry
childrenLoaded - Variable in class net.sf.basedb.util.overview.Node
childReporterPositions - Variable in class net.sf.basedb.util.importer.spotdata.BaseFileInfo
childToParent - Variable in class net.sf.basedb.util.listable.AbstractSourceItemTransformerFactory
childToParentChain(List<SourceItemTransformer>, Item, Item, boolean) - Static method in class net.sf.basedb.util.listable.ToExtractSourceItemTransformerFactory: Utility method for creating the transformer chain from child items up to extracts.
childWarnings - Variable in class net.sf.basedb.util.overview.Node
chIndex - Variable in class net.sf.basedb.util.importer.spotdata.MatrixSpotIntensityEventHandler
chIndex - Variable in class net.sf.basedb.util.importer.spotdata.SerialSpotIntensityEventHandler
chooseClientAlias(String[], Principal[], Socket) - Method in class net.sf.basedb.util.ssl.StaticKeyManager
chooseServerAlias(String, Principal[], Socket) - Method in class net.sf.basedb.util.ssl.StaticKeyManager
CIRCULAR_REFERENCE - Static variable in class net.sf.basedb.util.overview.Validator: Validator rule that checks for circular references among pooled items.
CircularRefInfo(DbControl, Identifiable) - Constructor for class net.sf.basedb.core.Trashcan.CircularRefInfo
city - Variable in class net.sf.basedb.util.GeoLocation
classes - Static variable in class net.sf.basedb.core.ExtendedProperties: A list with the name attribute of all classes found in the xml file.
classLoader - Variable in class net.sf.basedb.core.ServiceSessionControl.SessionFactoryConfiguration
classLoader - Variable in class net.sf.basedb.util.extensions.Registry.RegisteredExtension
classLoader - Variable in class net.sf.basedb.util.extensions.Registry.RegisteredExtensionPoint
classLoaders - Variable in class net.sf.basedb.util.extensions.xml.XmlLoader
classLoaders - Static variable in class net.sf.basedb.util.JarClassLoader: A map of all loaded class loaders.
ClassLocal<E> - Class in net.sf.basedb.util: This class is a similar to the JDK ThreadLocal class, but stores one object per class instead of one object per thread.
ClassLocal() - Constructor for class net.sf.basedb.util.ClassLocal: Create a new ClassLocal object.
ClassMapErrorHandler - Class in net.sf.basedb.util.error: Error handler that allows the registration of one or more error handler for subclasses to Throwable.
ClassMapErrorHandler(ErrorHandler) - Constructor for class net.sf.basedb.util.error.ClassMapErrorHandler: Create a new ClassMapErrorHandler.
classMetadata - Variable in class net.sf.basedb.core.Metadata
className - Variable in class net.sf.basedb.core.data.PluginDefinitionData
className - Variable in class net.sf.basedb.util.extensions.manager.PluginInfoKey
className - Variable in class net.sf.basedb.util.extensions.xml.PluginInfo
classNameToPath(String) - Method in class net.sf.basedb.util.JarClassLoader: Convert a class name to a file path.
classPath - Variable in class net.sf.basedb.util.JarClassLoader: Contains mappings from class names to the JAR file in which the class implementation can be found.
ClassUtil - Class in net.sf.basedb.util: Utility class for Class objects.
ClassUtil() - Constructor for class net.sf.basedb.util.ClassUtil
clazz - Variable in class net.sf.basedb.clients.web.extensions.list.AbstractListColumnBean
clazz - Variable in class net.sf.basedb.clients.web.extensions.list.PropertyPathActionFactory
clazz - Variable in class net.sf.basedb.clients.web.extensions.login.FieldInfo
clazz - Variable in class net.sf.basedb.clients.web.extensions.menu.FixedMenuItemFactory
clazz - Variable in class net.sf.basedb.clients.web.extensions.menu.MenuItemBean
clazz - Variable in class net.sf.basedb.clients.web.extensions.tabcontrol.FixedTabFactory
clazz - Variable in class net.sf.basedb.clients.web.extensions.tabcontrol.IncludeContentTabFactory
clazz - Variable in class net.sf.basedb.clients.web.extensions.tabcontrol.TabBean
clazz - Variable in class net.sf.basedb.clients.web.extensions.toolbar.ButtonBean
clazz - Variable in class net.sf.basedb.clients.web.extensions.toolbar.FixedButtonFactory
clazz - Variable in class net.sf.basedb.clients.web.taglib.ExceptionCatcher
clazz - Variable in class net.sf.basedb.clients.web.taglib.StylableTag
clazz - Variable in class net.sf.basedb.clients.web.taglib.tab.Tab: Optional class attribute.
clazz - Variable in class net.sf.basedb.clients.web.taglib.table.Cell: Optional class attribute
clazz - Variable in class net.sf.basedb.clients.web.taglib.table.CellValue
clazz - Variable in class net.sf.basedb.core.ExtendedPropertyAccessor.GetterSetter
clazz - Variable in class net.sf.basedb.core.Metadata.BasicItem2DataPropertyPath
clazz - Variable in class net.sf.basedb.core.Metadata
clazz - Variable in class net.sf.basedb.core.Metadata.NoopPropertyPath
clazz - Variable in class net.sf.basedb.core.ParameterType: The class of allowed parameter values.
clazz - Variable in class net.sf.basedb.core.QueryExecutor.FutureItem
clazz - Variable in class net.sf.basedb.util.extensions.events.ActionClassEventFilter
clazz - Variable in class net.sf.basedb.util.filter.InstanceOfFilter
clean() - Method in class net.sf.basedb.util.listable.TransformCache
clean(AnnotationBatcher.UpdateBatcher) - Method in class net.sf.basedb.core.MigrateRbaToDba.Rba: Remove links to from the raw bioassay to annotations, files, etc.
cleanable - Variable in class net.sf.basedb.core.DbControl.State
cleanable - Variable in class net.sf.basedb.util.StaticCache.LockSafeInputStream
cleanable - Variable in class net.sf.basedb.util.StaticCache.LockSafeOutputStream
cleanContextFromProperty(Session, Item, String, String, boolean) - Static method in class net.sf.basedb.core.Update
cleaner - Static variable in class net.sf.basedb.core.Application: For keeping track of objects that need to be cleaned up.
cleanSessionControlCache(boolean) - Static method in class net.sf.basedb.core.Application: Clean the cache from unused SessionControl objects.
cleanUp() - Method in class net.sf.basedb.core.DbControl: Clear and close all objects.
cleanUp(FileFilter) - Method in class net.sf.basedb.util.StaticCache: Remove all files that matches the specified filter from the cache.
cleanupProjectSpecificAnnotations() - Static method in class net.sf.basedb.core.ProjectSpecificAnnotationsManager: Delete project-specific annotations that belong to projects that no longer exists.
cleanUpTask(FileFilter) - Method in class net.sf.basedb.util.StaticCache: Creates a task that cleans up this cache when it is executed.
CleanupTask(StaticCache, FileFilter) - Constructor for class net.sf.basedb.util.StaticCache.CleanupTask
clear() - Method in class net.sf.basedb.core.AbstractResultList: Not supported.
clear() - Method in class net.sf.basedb.core.hibernate.SessionWrapper
clear() - Method in class net.sf.basedb.core.snapshot.SnapshotManager: Clear the manager from all memory-cached information.
clear() - Method in class net.sf.basedb.core.UnmodifiableResultList: Not supported.
clear() - Method in class net.sf.basedb.util.AnnotationUtil.Cache: Clear all information from the cache.
clear() - Method in class net.sf.basedb.util.formatter.LookupFormatter: Remove all registered lookup entries.
clear() - Method in class net.sf.basedb.util.Tree: Clear all elements except the root element.
clear(Session) - Static method in class net.sf.basedb.core.HibernateUtil: Clear the session of cached objects.
clearAllRecent() - Method in class net.sf.basedb.core.ItemContext: Clear all recently used values lists.
clearDbControlCache() - Method in class net.sf.basedb.core.SessionControl
clearError() - Method in class net.sf.basedb.util.extensions.ActionIterator: Clear any error that has been registered for the current action.
clearError() - Method in class net.sf.basedb.util.extensions.ExtensionContext
clearError() - Method in class net.sf.basedb.util.extensions.ExtensionPointContext
clearError() - Method in class net.sf.basedb.util.extensions.InvokationContext: Clear the registered error for the current extension or extension point.
clearError() - Method in class net.sf.basedb.util.extensions.Registry.RegisteredExtension
clearError() - Method in class net.sf.basedb.util.extensions.Registry.RegisteredExtensionPoint
clearErrorList(JEP) - Static method in class net.sf.basedb.util.jep.Jep: This is a workaround for a bug in the JEP error handling.
clearErrors - Variable in class net.sf.basedb.util.extensions.ExtensionsInvoker
clearExecuteCommand() - Method in class net.sf.basedb.core.Job: Reset the currently stored execution command to force a plug-in to restart from the beginning instead of at the stored breakpoint.
clearFailures() - Method in class net.sf.basedb.util.overview.Node: Clear all warnings, errors on this node and on all child nodes.
clearLog() - Method in class net.sf.basedb.util.extensions.logging.ExtensionsLog: Clear the log.
clearRecent(String) - Method in class net.sf.basedb.core.ItemContext: Clear the recently used values list.
clearRecent(Item) - Method in class net.sf.basedb.core.ItemContext: Clear the recently used items list from items of the specified type.
clearRecent(Item, String) - Method in class net.sf.basedb.core.ItemContext: Clear the recently used items sublist from items of the specified type.
clearRecent(Item, ItemSubtype) - Method in class net.sf.basedb.core.ItemContext: Clear the recently used items list from items of the specified type.
clearSources() - Method in class net.sf.basedb.core.BioMaterialEvent: Clear the sources collection and return the used quantities to the source biomaterials.
clearSourcesExcept(BioMaterial) - Method in class net.sf.basedb.core.BioMaterialEvent: Clear the sources collection and return the used quantities to the source biomaterials, except for the given biomaterial.
clearState - Variable in class net.sf.basedb.core.PluginResponse
clearUsableUnits() - Method in class net.sf.basedb.core.AnnotationType: Clear all units.
clearValueConverters() - Method in class net.sf.basedb.util.extensions.xml.XmlLoader: Remove all value converters.
client - Variable in class net.sf.basedb.core.data.ChangeHistoryData
client - Variable in class net.sf.basedb.core.data.ClientDefaultSettingData
client - Variable in class net.sf.basedb.core.data.ContextData
client - Variable in class net.sf.basedb.core.data.ContextIndex
client - Variable in class net.sf.basedb.core.data.HelpData
client - Variable in class net.sf.basedb.core.data.SessionData
client - Variable in class net.sf.basedb.core.data.UserClientSettingData
client - Variable in class net.sf.basedb.core.data.UserDeviceData
client - Variable in class net.sf.basedb.core.SessionControl: Information about the ClientData that created this SessionControl.
client - Variable in class net.sf.basedb.plugins.HelpImporter
Client - Class in net.sf.basedb.core: This class represents a registered client application.
Client(ClientData) - Constructor for class net.sf.basedb.core.Client
CLIENT - Enum constant in enum class net.sf.basedb.core.Item: The item is an Client.
CLIENT_RUNTIME_FILTER - Static variable in class net.sf.basedb.core.UserClientSetting: This filter will only return items if the logged in user has generic read permission to clients.
clientCertificate - Variable in class net.sf.basedb.core.data.FileServerData
clientCertificate - Variable in class net.sf.basedb.util.uri.ConnectionParameters
clientCertificatePassword - Variable in class net.sf.basedb.util.uri.ConnectionParameters
clientContext - Variable in class net.sf.basedb.util.extensions.ExtensionPointContext
clientContext - Variable in class net.sf.basedb.util.extensions.ExtensionsInvoker
ClientContext - Class in net.sf.basedb.util.extensions: Keeps information about the current context in the client application that extensions can use to decide what actions to generate.
ClientContext() - Constructor for class net.sf.basedb.util.extensions.ClientContext: Create a new context with no session or current item.
ClientContext(DbControl) - Constructor for class net.sf.basedb.util.extensions.ClientContext: Create a new context with a DbControl.
ClientContext(DbControl, Object) - Constructor for class net.sf.basedb.util.extensions.ClientContext: Create a new context with a DbControl and item.
ClientContext(SessionControl) - Constructor for class net.sf.basedb.util.extensions.ClientContext: Create a new context with a session and no DbControl.
ClientContext(SessionControl, Object) - Constructor for class net.sf.basedb.util.extensions.ClientContext: Create a new context with a session and item but no DbControl.
ClientContext(SessionControl, DbControl, Object) - Constructor for class net.sf.basedb.util.extensions.ClientContext
ClientData - Class in net.sf.basedb.core.data: This class holds information about a client.
ClientData() - Constructor for class net.sf.basedb.core.data.ClientData
ClientDefaultSetting - Class in net.sf.basedb.core: This class is used to represent a setting for specific client application.
ClientDefaultSetting(ClientDefaultSettingData) - Constructor for class net.sf.basedb.core.ClientDefaultSetting
CLIENTDEFAULTSETTING - Enum constant in enum class net.sf.basedb.core.Item: The item is an ClientDefaultSetting.
ClientDefaultSettingData - Class in net.sf.basedb.core.data
ClientDefaultSettingData() - Constructor for class net.sf.basedb.core.data.ClientDefaultSettingData
clientDefaultSettings - Variable in class net.sf.basedb.core.SessionControl: Stores name and value from ClientDefaultSettingData.
clientId - Variable in class net.sf.basedb.core.data.ChangeHistoryData
clientId - Variable in class net.sf.basedb.core.log.TransactionDetails
ClientInfo(int, String, String) - Constructor for class net.sf.basedb.core.SessionControl.ClientInfo
clientItem - Static variable in class net.sf.basedb.plugins.HelpExporter
clientItem - Static variable in class net.sf.basedb.plugins.HelpImporter
clientParameter - Variable in class net.sf.basedb.plugins.HelpExporter
clientParameter - Variable in class net.sf.basedb.plugins.HelpImporter
clientPassword - Variable in class net.sf.basedb.core.data.FileServerData
clientSettings - Variable in class net.sf.basedb.core.data.UserData
clientType - Variable in class net.sf.basedb.plugins.HelpExporter
clonableProperty(ClonableProperty) - Static method in class net.sf.basedb.core.VirtualColumn: Get a virtual column view of a cloned reporter property.
ClonableProperty - Class in net.sf.basedb.core: Represents a reporter property that can be cloned to a per-experiment table in the dynamic database.
ClonableProperty(String, String, String, String, Type, int, boolean, Formula.AverageMethod, boolean) - Constructor for class net.sf.basedb.core.ClonableProperty: Create a cloned property representation of a static property.
ClonableProperty(String, ReporterClonePropertyData) - Constructor for class net.sf.basedb.core.ClonableProperty: Create a cloned property representation of a data-layer object.
ClonableProperty(ExtendedProperty) - Constructor for class net.sf.basedb.core.ClonableProperty: Create a cloned property representation of an extended property
ClonableReporterQuery - Interface in net.sf.basedb.core: An interface that indicates that a query may be used together with cloned reporter information.
CLONAL_AMPLIFICATION - Static variable in class net.sf.basedb.core.PhysicalBioAssay: The id for the PhysicalBioAssayType item representing a flow cell.
clone - Variable in class net.sf.basedb.util.annotations.InheritSpecification
cloneCachedNode(Object, Node, ChildNodeDirection) - Method in class net.sf.basedb.util.overview.node.NodeFactory: Clones a cached node if the current context supports caching and another node with the given cache key already exists.
CLONED - Enum constant in enum class net.sf.basedb.core.Annotation.Source: The annotation is an inherited annotation with a local copy of the values at the time the copy was made.
CLONED_REPORTERS - Enum constant in enum class net.sf.basedb.core.VirtualTable: Table that holds cloned reporter information for an experiment.
cloneParameter(PluginParameter<T>, T) - Static method in class net.sf.basedb.plugins.util.Parameters: Clone a plug-in parameter but give it a different default value.
cloneParameterWithDefaultValue(PluginParameter<T>) - Method in class net.sf.basedb.core.plugin.AbstractPlugin: Clone a plug-in parameter and set the default value to the value that is already stored in the job or configuration parameters.
cloneReporters(ReporterCloneBatcher.CloneSource, ReporterCloneTemplate, ProgressReporter) - Method in class net.sf.basedb.core.ReporterCloneBatcher: Create a reporter clone table in the dynamic database for this experiment and populate it with the current reporter annotations for all reporters that are part of the experiment.
CloneReportersPlugin - Class in net.sf.basedb.plugins: A plug-in that clone reporter annotations to an experiment.
CloneReportersPlugin() - Constructor for class net.sf.basedb.plugins.CloneReportersPlugin
CloneSource() - Constructor for enum class net.sf.basedb.core.ReporterCloneBatcher.CloneSource
close() - Method in class net.sf.basedb.clients.jobagent.executors.DummyJobExecutor
close() - Method in class net.sf.basedb.clients.jobagent.executors.ProcessJobExecutor
close() - Method in class net.sf.basedb.clients.jobagent.executors.ThreadJobExecutor
close() - Method in class net.sf.basedb.clients.jobagent.handlers.AbstractCustomRequestHandler
close() - Method in interface net.sf.basedb.clients.jobagent.handlers.CustomRequestHandler: This method is called at when the agent is stopped.
close() - Method in class net.sf.basedb.clients.jobagent.handlers.MultiProtocolRequestHandler: Close this handler.
close() - Method in interface net.sf.basedb.clients.jobagent.JobExecutor: This method is called at when the agent is stopped or paused.
close() - Method in class net.sf.basedb.clients.jobagent.slotmanager.InternalSlotManager
close() - Method in class net.sf.basedb.clients.jobagent.slotmanager.MasterSlotManager
close() - Method in class net.sf.basedb.clients.jobagent.slotmanager.RemoteSlotManager
close() - Method in interface net.sf.basedb.clients.jobagent.slotmanager.SlotManager: This method is called when the job agent is shutting down.
close() - Static method in class net.sf.basedb.clients.web.extensions.ExtensionsControl: Shut down the extensions system.
close() - Method in class net.sf.basedb.clients.web.extensions.list.RelatedItemHelper
close() - Static method in class net.sf.basedb.clients.web.extensions.service.Services: Stop all services.
close() - Method in class net.sf.basedb.clients.web.plugins.PlainTextTemplate: Do nothing.
close() - Method in class net.sf.basedb.clients.web.plugins.XlsxTemplate: Dispose and close workbook.
close() - Method in class net.sf.basedb.clients.web.plugins.XMLTemplate: Do nothing.
close() - Method in class net.sf.basedb.clients.web.servlet.PlotServlet.CFResultIterator
close() - Method in class net.sf.basedb.core.AbstractBatcher
close() - Method in class net.sf.basedb.core.AnnotationBatcher.InsertBatcher: Close the batcher.
close() - Method in class net.sf.basedb.core.AnnotationBatcher.UpdateBatcher: Close the batcher.
close() - Method in interface net.sf.basedb.core.Batcher: Flush the batcher and close it.
close() - Method in class net.sf.basedb.core.DataResultIterator: From the ResultIterator interface ---------------------------------
close() - Method in class net.sf.basedb.core.DbControl: Close the connection to the database.
close() - Method in class net.sf.basedb.core.DynamicResultIterator: From the ResultIterator interface ---------------------------------
close() - Method in class net.sf.basedb.core.File.CharsetTesterThread: The file has been uploaded.
close() - Method in class net.sf.basedb.core.File.UploadStream: Close the stream and register the size and location with the file item.
close() - Method in class net.sf.basedb.core.hibernate.SessionWrapper
close() - Method in class net.sf.basedb.core.hibernate.StatelessSessionWrapper
close() - Method in class net.sf.basedb.core.InternalJobQueue: Cleanup
close() - Method in class net.sf.basedb.core.ItemResultIterator: From the ResultIterator interface ---------------------------------
close() - Method in class net.sf.basedb.core.plugin.ExportOutputStream
close() - Method in interface net.sf.basedb.core.query.ResultIterator: Close the iterator and immediately release all resources associated with it.
close() - Method in class net.sf.basedb.core.ReporterScoreResultIterator: From the ResultIterator interface ---------------------------------
close() - Method in class net.sf.basedb.core.ScrollIterator: Close the results and return resources.
close() - Method in class net.sf.basedb.core.SessionControl: Close this session control so it can't be used again.
close() - Method in class net.sf.basedb.util.bfs.AnnotationParser
close() - Method in interface net.sf.basedb.util.bfs.BfsParser: Close the parser and relase underlying system resources that are associated with it.
close() - Method in class net.sf.basedb.util.bfs.DataParser
close() - Method in class net.sf.basedb.util.bfs.MetadataParser
close() - Method in class net.sf.basedb.util.excel.XlsxTableWriter: Closes the workbook unless it was supplied in the constructor from an external source.
close() - Method in class net.sf.basedb.util.excel.XlsxToCsvUtil: Closes the current workbook.
close() - Method in class net.sf.basedb.util.excel.XlsxToCsvUtil.WorkbookStream
close() - Method in class net.sf.basedb.util.extensions.manager.ExtensionsFile.WriteableExtensionsFile: Close the writeable file.
close() - Method in class net.sf.basedb.util.gtf.GtfInputStream
close() - Method in class net.sf.basedb.util.importer.spotdata.SynchronizedSpotDataParser
close() - Method in class net.sf.basedb.util.InputStreamCombiner: Closes all underlying streams.
close() - Method in class net.sf.basedb.util.InputStreamSplitter
close() - Method in class net.sf.basedb.util.InputStreamTracker
close() - Method in class net.sf.basedb.util.jobagent.JobAgentConnection: Close the connection to the job agent.
close() - Method in class net.sf.basedb.util.jobagent.JobAgentServerConnection: Stop listening for incoming connections.
close() - Method in class net.sf.basedb.util.StaticCache.LockSafeInputStream
close() - Method in class net.sf.basedb.util.StaticCache.LockSafeOutputStream
close() - Method in class net.sf.basedb.util.StreamCacher: Close the master stream and remove the cached file data.
close() - Method in class net.sf.basedb.util.uri.CloseResourceInputStream: Make sure the client connection manager is closed when the file has been completely downloaded.
close() - Method in class net.sf.basedb.util.zip.Bzip2FilePacker: Finish the BZIP stream.
close() - Method in interface net.sf.basedb.util.zip.FilePacker: End the packing and close.
close() - Method in class net.sf.basedb.util.zip.GzipFilePacker: Finish the GZIP stream.
close() - Method in class net.sf.basedb.util.zip.TarFilePacker: Finish the TAR file.
close() - Method in class net.sf.basedb.util.zip.ZipFilePacker: Finish the ZIP file.
close(int) - Method in class net.sf.basedb.clients.web.util.SimpleSignalProgressReporter
close(int) - Method in class net.sf.basedb.core.signal.AbstractSignalReceiver: Close this signal receiver.
close(int) - Method in class net.sf.basedb.core.signal.LocalSignalReceiver
close(int) - Method in interface net.sf.basedb.core.signal.SignalReceiver: Close the receiver.
close(int) - Method in class net.sf.basedb.core.signal.SocketSignalReceiver: Close this receiver and the socket it is listening on.
close(Closeable) - Static method in class net.sf.basedb.util.FileUtil: Close a Closeable without throwing an exception.
close(InputStream) - Static method in class net.sf.basedb.util.FileUtil: Close an input stream without throwing an exception.
close(InputStream) - Static method in class net.sf.basedb.util.SocketUtil: Close an InputStream without throwing any exceptions.
close(OutputStream) - Static method in class net.sf.basedb.util.FileUtil: Close an output stream without throwing an exception.
close(Reader) - Static method in class net.sf.basedb.util.SocketUtil: Close a Reader without throwing any exceptions.
close(Writer) - Static method in class net.sf.basedb.util.SocketUtil: Close a Writer without throwing any exceptions.
close(AutoCloseable) - Static method in class net.sf.basedb.util.FileUtil: Close a AutoCloseable without throwing an exception.
close(ServerSocket) - Static method in class net.sf.basedb.util.SocketUtil: Close a server socket without throwing any exceptions.
close(Socket) - Static method in class net.sf.basedb.util.SocketUtil: Close a socket without throwing any exceptions.
close(ServerSocketChannel) - Static method in class net.sf.basedb.util.SocketUtil: Close a server socket channel without throwing any exceptions.
close(Session) - Static method in class net.sf.basedb.core.HibernateUtil: Close a session.
close(StatelessSession) - Static method in class net.sf.basedb.core.HibernateUtil: Close a statless session.
closed - Variable in class net.sf.basedb.core.File.UploadStream: If this file closed or not.
closed - Variable in class net.sf.basedb.core.SessionControl: If the session control has been closed it can no longer be used.
closed - Variable in class net.sf.basedb.util.StaticCache.LockSafeInputStream
closed - Variable in class net.sf.basedb.util.StaticCache.LockSafeOutputStream
closeJobExecutor() - Method in class net.sf.basedb.clients.jobagent.Agent: Close the job executor.
closeJobQueueChecker() - Method in class net.sf.basedb.clients.jobagent.Agent: Close the job queue checker.
closeLogFile() - Method in class net.sf.basedb.core.plugin.AbstractPlugin: Close the log file created by AbstractPlugin.createLogFile(String).
CloseMyDbControl(RelatedItemHelper) - Constructor for class net.sf.basedb.clients.web.extensions.list.RelatedItemHelper.CloseMyDbControl
CloseResourceInputStream - Class in net.sf.basedb.util.uri: Inputstream filter that closes a given resource whenever the parent input stream is closed.
CloseResourceInputStream(InputStream, Closeable) - Constructor for class net.sf.basedb.util.uri.CloseResourceInputStream: Create a new stream.
closeResultSet(ResultSet, String) - Method in class net.sf.basedb.core.AbstractSqlQuery: Close the result set without throwing an exception.
closeServer() - Method in class net.sf.basedb.clients.jobagent.Agent: Close the service listener.
closeSlotManager() - Method in class net.sf.basedb.clients.jobagent.Agent: Close the slot manager.
closeStatement(Statement, String) - Method in class net.sf.basedb.core.AbstractSqlQuery: Close the statement without throwing an exception.
closeTimeout - Variable in class net.sf.basedb.clients.jobagent.Agent: Timeout to wait for jobs to act on the ABORT signal when stopping.
closeTimeout - Variable in class net.sf.basedb.core.InternalJobQueue: Timeout to wait for jobs to act on the ABORT signal when shutting down BASE.
CLUSTER_GENERATION - Static variable in class net.sf.basedb.core.Kit: The ID for the cluster generation (in a flow cell) kit type, for example a protocol used when creating a PhysicalBioAssay.
CLUSTER_GENERATION - Static variable in class net.sf.basedb.core.Protocol: The ID for the cluster generation (in a flow cell) protocol type, for example a protocol used when creating a PhysicalBioAssay.
CLUSTER_GENERATOR - Static variable in class net.sf.basedb.core.Hardware: The id for the HardwareType object representing a cluster generator station.
cmap - Variable in class net.sf.basedb.util.AnnotationUtil.Cache
cmd - Variable in class net.sf.basedb.clients.jobagent.CmdLine
CmdLine - Class in net.sf.basedb.clients.jobagent: Utility class for parsing command line arguments.
CmdLine(String[]) - Constructor for class net.sf.basedb.clients.jobagent.CmdLine: Create a new object for parsing the command line.
coalesce(String...) - Static method in class net.sf.basedb.core.StringUtil: Return the first non-null value (or null if all values are null).
colFunction - Variable in class net.sf.basedb.util.parser.JepMapper
ColFunction - Class in net.sf.basedb.util.parser: Adds a col() function to Jep.
ColFunction(List<String>, NumberFormat) - Constructor for class net.sf.basedb.util.parser.ColFunction
ColFunction(List<String>, NumberFormat, Formatter<Date>) - Constructor for class net.sf.basedb.util.parser.ColFunction
ColFunction(Map<String, Integer>, NumberFormat) - Constructor for class net.sf.basedb.util.parser.ColFunction
ColFunction(Map<String, Integer>, NumberFormat, Formatter<Date>) - Constructor for class net.sf.basedb.util.parser.ColFunction
colIndex - Variable in class net.sf.basedb.clients.web.plugins.DynamicQueryWrapper
collect(Item, Set<Integer>) - Method in class net.sf.basedb.util.listable.TransformContext: Store collected items for later use if collecting has been enabled.
CollectChildren(boolean, boolean) - Constructor for class net.sf.basedb.util.listable.CollectExtracts.CollectChildren
collectChildrenOfCollected(boolean) - Method in class net.sf.basedb.util.listable.CollectExtracts: The created transformer collect the ID:s of all child extracts to the already collected extracts and store them in the CollectExtracts.getCollectedChildren().
collectChildrenOfSource(boolean) - Method in class net.sf.basedb.util.listable.CollectExtracts: The created transformer collect the ID:s of all child extracts to the source extracts and store them in the CollectExtracts.getCollectedChildren().
collected - Variable in class net.sf.basedb.util.listable.CollectExtracts
collectedByItemType - Variable in class net.sf.basedb.util.listable.TransformContext
collectedExtracts - Variable in class net.sf.basedb.util.listable.CollectedExtractsToDerivedBioAssayTransformer
collectedExtracts - Variable in class net.sf.basedb.util.listable.CollectedExtractsToRawBioAssayTransformer
collectedExtracts - Variable in class net.sf.basedb.util.listable.DerivedBioAssayToRawBioAssayTransformer
collectedExtracts - Variable in class net.sf.basedb.util.listable.ExtractToParentExtractTransformer
collectedExtracts - Variable in class net.sf.basedb.util.listable.PhysicalBioAssayToDerivedBioAssayTransformer
CollectedExtractsToDerivedBioAssayTransformer - Class in net.sf.basedb.util.listable: Source item transformer implementation that transform collected extract items to derived bioassays.
CollectedExtractsToDerivedBioAssayTransformer(CollectExtracts) - Constructor for class net.sf.basedb.util.listable.CollectedExtractsToDerivedBioAssayTransformer: Create a new collected extracts to derived bioassay transformer.
CollectedExtractsToDerivedBioAssayTransformer(CollectExtracts, boolean) - Constructor for class net.sf.basedb.util.listable.CollectedExtractsToDerivedBioAssayTransformer: Create a new collected extracts to derived bioassay transformer.
CollectedExtractsToRawBioAssayTransformer - Class in net.sf.basedb.util.listable: Source item transformer implementation that transform collected extract items to raw bioassays.
CollectedExtractsToRawBioAssayTransformer(CollectExtracts) - Constructor for class net.sf.basedb.util.listable.CollectedExtractsToRawBioAssayTransformer: Create a new collected extracts to derived bioassay transformer.
CollectExtracts - Class in net.sf.basedb.util.listable: Collect extracts seen on derived bioassays and raw bioassays that has been loaded by other transformers.
CollectExtracts() - Constructor for class net.sf.basedb.util.listable.CollectExtracts: Create a new derived bioassay to physical bioassay transformer.
CollectExtracts.CollectChildren - Class in net.sf.basedb.util.listable: Transformer implementation that collect the child extracts from the source or collected extracts.
CollectExtracts.CollectFromDerivedBioAssays - Class in net.sf.basedb.util.listable: Transformer implementation that given a set of derived bioassays load their linked extracts and store that in the parent class.
CollectExtracts.CollectFromExtracts - Class in net.sf.basedb.util.listable: Transformer implementation that store the given set of extracts in the parent class.
CollectExtracts.CollectFromRawBioAssays - Class in net.sf.basedb.util.listable: Transformer implementation that given a set of raw bioassays load their linked extracts and store that in the parent class.
CollectExtracts.CollectParents - Class in net.sf.basedb.util.listable: Transformer implementation that collect the parent extracts from the source or collected extracts.
CollectExtracts.ResetCollected - Class in net.sf.basedb.util.listable: Transformer implementation that reset the collected extracts before forwarding the call to the parent transformer.
collectFromDerivedBioAssays(boolean) - Method in class net.sf.basedb.util.listable.CollectExtracts: The created transformer collect the ID:s of all extracts linked from the source derived bioassays and then return the same set of derived bioassays again.
CollectFromDerivedBioAssays(boolean) - Constructor for class net.sf.basedb.util.listable.CollectExtracts.CollectFromDerivedBioAssays
collectFromExtracts() - Method in class net.sf.basedb.util.listable.CollectExtracts: The created transformer collect the ID:s of all extracts in the source collection and return same set of extracts again.
CollectFromExtracts() - Constructor for class net.sf.basedb.util.listable.CollectExtracts.CollectFromExtracts
collectFromRawBioAssays() - Method in class net.sf.basedb.util.listable.CollectExtracts: The created transformer collect the ID:s of all extracts linked from the source raw bioassays and then return the same set of raw bioassays again.
CollectFromRawBioAssays() - Constructor for class net.sf.basedb.util.listable.CollectExtracts.CollectFromRawBioAssays
collecting - Variable in class net.sf.basedb.util.listable.TransformContext
COLLECTION_SEPARATOR - Static variable in class net.sf.basedb.clients.web.plugins.SimpleExport
collectionFormatter - Variable in class net.sf.basedb.clients.web.extensions.list.AbstractListColumnBean
CollectionFormatter - Class in net.sf.basedb.util.formatter: Formatter implementation that formats a collection of values to a string by concatenating the values with a given separator.
CollectionFormatter(String, boolean, Formatter<? super I>) - Constructor for class net.sf.basedb.util.formatter.CollectionFormatter
CollectionFormatter(Formatter<? super I>) - Constructor for class net.sf.basedb.util.formatter.CollectionFormatter: Create a collection formatting using ", " as separator and skipping null values.
CollectionPropertyPath(Type) - Constructor for class net.sf.basedb.core.Metadata.CollectionPropertyPath
collections - Variable in class net.sf.basedb.util.NestedIterator: The array to iterate.
collectionSeparator - Variable in class net.sf.basedb.clients.web.plugins.PlainTextTemplate
collectionSeparator - Variable in class net.sf.basedb.clients.web.plugins.XlsxTemplate
CollectionTransformer<S,D> - Interface in net.sf.basedb.util.collections: Allows a collection to be transformed by applying some operation to it.
CollectParents(boolean, boolean) - Constructor for class net.sf.basedb.util.listable.CollectExtracts.CollectParents
collectParentsOfCollected(boolean) - Method in class net.sf.basedb.util.listable.CollectExtracts: The created transformer collect the ID:s of all parent extracts to the already collected extracts and store them in the CollectExtracts.getCollectedParents().
collectParentsOfSource(boolean) - Method in class net.sf.basedb.util.listable.CollectExtracts: The created transformer collect the ID:s of all parent extracts to the source extracts and store them in the CollectExtracts.getCollectedParents().
CollectSqlTarget() - Constructor for class net.sf.basedb.core.hibernate.SchemaGenerator.CollectSqlTarget
CollectSqlTarget(DbEngine, Dialect, SchemaGenerator.Mode, Connection) - Constructor for class net.sf.basedb.core.hibernate.SchemaGenerator.CollectSqlTarget
colNo - Variable in class net.sf.basedb.util.excel.XlsxTableWriter
colNum - Variable in class net.sf.basedb.clients.web.plugins.PlainTextTemplate
colNum - Variable in class net.sf.basedb.clients.web.plugins.XlsxTemplate
colOffset - Variable in class net.sf.basedb.util.parser.FlatFileParser.ExcelData
color - Variable in class net.sf.basedb.clients.web.ExperimentExplorer.AnnotationGroup
ColorFormatter - Class in net.sf.basedb.clients.web.formatter: Formatter that adds a small colored box next to a value.
ColorFormatter(ColorGenerator, Formatter<Number>) - Constructor for class net.sf.basedb.clients.web.formatter.ColorFormatter: Create a new color formatter.
colorGen - Variable in class net.sf.basedb.clients.web.formatter.ColorFormatter
ColorGenerator - Class in net.sf.basedb.util: This class is used to generate colors for numerical values.
ColorGenerator(Color, Color, Color, float, float, float, boolean) - Constructor for class net.sf.basedb.util.ColorGenerator: Create a new color generator.
coloring - Variable in class net.sf.basedb.core.data.ExtraValueTypeData
coloring - Variable in class net.sf.basedb.core.data.FormulaData
coloring - Variable in class net.sf.basedb.core.ExtraValueType
coloring - Variable in class net.sf.basedb.core.Formula
Coloring - Class in net.sf.basedb.core: This class keeps coloring information for items which can be colored when values are displayed in a client application.
Coloring() - Constructor for class net.sf.basedb.core.Coloring: Create a new independent coloring object.
Coloring(ColoringData, AccessControlled) - Constructor for class net.sf.basedb.core.Coloring: Create Coloring object which links to an existing item.
ColoringData - Class in net.sf.basedb.core.data: Hold coloring information.
ColoringData() - Constructor for class net.sf.basedb.core.data.ColoringData
ColoringData(boolean, boolean, Float, Float, Float) - Constructor for class net.sf.basedb.core.data.ColoringData
COLORS - Static variable in class net.sf.basedb.clients.web.ExperimentExplorer: Predefined colors for annotation groups
colspan - Variable in class net.sf.basedb.clients.web.taglib.table.Header
column - Variable in class net.sf.basedb.clients.web.extensions.list.ListColumnDataLoader
column - Variable in class net.sf.basedb.core.data.BioWellData
column - Variable in class net.sf.basedb.core.data.FeatureData
column - Variable in class net.sf.basedb.core.data.MappingCoordinate: The column number.
column - Variable in class net.sf.basedb.core.data.PlateCoordinate: The column number.
column - Variable in class net.sf.basedb.core.data.RawData
column - Variable in class net.sf.basedb.core.data.ReporterClonePropertyData
column - Variable in class net.sf.basedb.core.data.WellData
column - Variable in class net.sf.basedb.core.DynamicRestriction
column - Variable in class net.sf.basedb.core.ExtendedProperty
column - Variable in class net.sf.basedb.core.ExtraValueExpression
column - Variable in class net.sf.basedb.core.FeatureCoordinate: The column of this feature.
column - Variable in class net.sf.basedb.core.query.SqlColumnExpression
column - Variable in class net.sf.basedb.core.query.VirtualColumnExpression
column - Variable in class net.sf.basedb.core.RawBioAssayPropertyExpression
column - Variable in class net.sf.basedb.core.ReporterPropertyExpression
column - Variable in class net.sf.basedb.core.VirtualColumn: The column name in the database of the column.
column - Variable in class net.sf.basedb.plugins.LowessNormalization.SpotData
column(VirtualColumn) - Static method in class net.sf.basedb.core.query.Dynamic: Create an expression representing a column in the root table: expression = rootAlias.columnName.
column(VirtualTable, VirtualColumn) - Static method in class net.sf.basedb.core.query.Dynamic: Create an expression representing a column in a table: expression = tableAlias.columnName.
COLUMN - Enum constant in enum class net.sf.basedb.core.ExtraValue.CoordinateType: The extra values are attached to column coordinates only.
COLUMN - Enum constant in enum class net.sf.basedb.core.VirtualTable: Table that maps columns coordinates in a data cube to raw bioassays.
COLUMN - Static variable in class net.sf.basedb.core.VirtualColumn: This column stores the data cube column coordinate.
COLUMN_EXPRESSION - Enum constant in enum class net.sf.basedb.core.Formula.Type: An arbitrary expression that specify one formula only.
COLUMN_EXTRA_FLOAT - Enum constant in enum class net.sf.basedb.core.VirtualTable: Table that stores float column extra values.
COLUMN_EXTRA_INT - Enum constant in enum class net.sf.basedb.core.VirtualTable: Table that stores integer column extra values.
COLUMN_EXTRA_STRING - Enum constant in enum class net.sf.basedb.core.VirtualTable: Table that stores string column extra values.
COLUMN_PREFIX - Static variable in class net.sf.basedb.clients.web.plugins.SimpleExport
COLUMN_RESTRICTION - Enum constant in enum class net.sf.basedb.core.Formula.Type: An arbitraty expression that specify one formula only.
columnColumnMapping - Static variable in class net.sf.basedb.plugins.PlateFlatFileImporter
columnColumnMapping - Static variable in class net.sf.basedb.plugins.RawDataFlatFileImporter
columnColumnMapping - Static variable in class net.sf.basedb.plugins.ReporterMapFlatFileImporter
columnContent - Variable in class net.sf.basedb.clients.web.taglib.table.Table
columnCount - Variable in class net.sf.basedb.util.bfs.AnnotationWriter
columnCount - Variable in class net.sf.basedb.util.bfs.DataWriter
ColumnDef - Class in net.sf.basedb.clients.web.taglib.table: This tag defines a column in the table.
ColumnDef() - Constructor for class net.sf.basedb.clients.web.taglib.table.ColumnDef
ColumnDef.NullIterator<A,B> - Class in net.sf.basedb.clients.web.taglib.table: Iterator implementation that returns a single null value and nothing more.
columnFilter - Variable in class net.sf.basedb.clients.web.taglib.table.Table
columnFormatter - Variable in class net.sf.basedb.clients.web.taglib.table.Table
columnHeaders - Variable in class net.sf.basedb.plugins.AnnotationFlatFileImporter
columnHeaders - Variable in class net.sf.basedb.util.parser.ColFunction
columnHeaders - Variable in class net.sf.basedb.util.parser.FlatFileParser: List of the column names found by splitting the data header using the data splitter regexp.
ColumnHeaders - Class in net.sf.basedb.clients.web.taglib.table: Generate column headers for the columns that has been defined for this table.
ColumnHeaders() - Constructor for class net.sf.basedb.clients.web.taglib.table.ColumnHeaders
columnId - Variable in class net.sf.basedb.clients.web.taglib.table.Cell: The ID of the column to which this cell belongs.
columnIndex - Variable in class net.sf.basedb.util.bfs.AnnotationModel
ColumnInfo(String, String, Integer, int, boolean, boolean) - Constructor for class net.sf.basedb.core.dbengine.TableInfo.ColumnInfo: Create a new ColumnInfo object.
ColumnKey(Comparable<?>, String) - Constructor for class net.sf.basedb.clients.web.servlet.ExperimentExplorerPlotServlet.ColumnKey
columnMapper - Variable in class net.sf.basedb.plugins.PlateFlatFileImporter
columnMapper - Variable in class net.sf.basedb.plugins.RawDataFlatFileImporter
columnMapper - Variable in class net.sf.basedb.plugins.ReporterMapFlatFileImporter
ColumnMapper - Class in net.sf.basedb.util.parser: Returns the string found in the column given by the index set in the constructor.
ColumnMapper(int, String) - Constructor for class net.sf.basedb.util.parser.ColumnMapper: Create a new column mapper.
ColumnMapper(int, String, NumberFormat, boolean) - Constructor for class net.sf.basedb.util.parser.ColumnMapper: Deprecated.
In 3.15, use ColumnMapper(int, String, NumberFormat, Formatter, boolean) instead
ColumnMapper(int, String, NumberFormat, Formatter<Date>, boolean) - Constructor for class net.sf.basedb.util.parser.ColumnMapper: Create a new column mapper using a specific number or date format.
columnMappingParameterName - Variable in class net.sf.basedb.plugins.batchimport.PropertyIdMethod
columnName - Variable in class net.sf.basedb.core.Update.DropColumnChange
columnNo - Variable in class net.sf.basedb.core.data.DataCubeColumnData
columns - Variable in class net.sf.basedb.clients.web.taglib.table.Table: Which columns that should be visible and their order
columns - Variable in class net.sf.basedb.core.data.DataCubeData
columns - Variable in class net.sf.basedb.core.data.PlateGeometryData
columns - Variable in class net.sf.basedb.core.dbengine.TableInfo
columns - Variable in class net.sf.basedb.core.dbengine.TableInfo.IndexInfo
columns - Variable in class net.sf.basedb.core.dbengine.TableInfo.PrimaryKeyInfo
columns - Variable in class net.sf.basedb.core.ExtraValueJoin
columns - Variable in enum class net.sf.basedb.core.VirtualTable: The columns in the table.
columns() - Method in class net.sf.basedb.util.parser.FlatFileParser.Data: The number of columns as determined by the FlatFileParser.setDataSplitterRegexp(Pattern) regular expression.
columnSeparator - Variable in class net.sf.basedb.util.excel.XlsxToCsvUtil
columnSubtitle - Variable in class net.sf.basedb.clients.web.taglib.table.Table
ColumnSubtitles - Class in net.sf.basedb.clients.web.taglib.table: Generate column subtitle header for the columns that has been defined for this table.
ColumnSubtitles() - Constructor for class net.sf.basedb.clients.web.taglib.table.ColumnSubtitles
CombinedPropertyPath(List<Metadata.PropertyPath>) - Constructor for class net.sf.basedb.core.Metadata.CombinedPropertyPath
CombiningEventFilter - Class in net.sf.basedb.util.extensions.events: Event filter that only passes on events based on multiple other event filters.
CombiningEventFilter(Collection<EventFilter>, boolean) - Constructor for class net.sf.basedb.util.extensions.events.CombiningEventFilter: Create a new combining event filter.
command - Variable in class net.sf.basedb.core.PluginRequest
command - Variable in class net.sf.basedb.core.RequestInformation
command - Variable in class net.sf.basedb.plugins.executor.ExternalProgramExecutor.RequestWrapper
COMMAND_CONFIGURE_EXTERNAL_PARAMETERS - Static variable in class net.sf.basedb.plugins.executor.ExternalProgramExecutor
COMMAND_CONFIGURE_IO_JOB - Static variable in interface net.sf.basedb.plugins.executor.IOSupport: This command is sent to import and export plug-ins in the job configuration sequence: InteractivePlugin.getRequestInformation(GuiContext, String) and InteractivePlugin.configure(GuiContext, Request, Response)
COMMAND_CONFIGURE_IO_PLUGIN - Static variable in interface net.sf.basedb.plugins.executor.IOSupport: This command is sent to import and export plug-ins in the plug-in configuration sequence: InteractivePlugin.getRequestInformation(GuiContext, String) and InteractivePlugin.configure(GuiContext, Request, Response)
COMMAND_CONFIGURE_JOB - Static variable in interface net.sf.basedb.core.plugin.Request: This should be the first command to use when setting the plugin's job parameters.
COMMAND_CONFIGURE_PARSER - Static variable in class net.sf.basedb.plugins.RawDataFlatFileImporter
COMMAND_CONFIGURE_PLUGIN - Static variable in interface net.sf.basedb.core.plugin.Request: This should be the first command to use when setting the plugin's configuration.
COMMAND_EXECUTE - Static variable in interface net.sf.basedb.core.plugin.Request: This command will tell the plugin to start its execution.
COMMAND_EXECUTE_IO_JOB - Static variable in interface net.sf.basedb.plugins.executor.IOSupport: This command is sent to import and export plug-ins in the job execution sequence: Plugin.run(Request, Response, ProgressReporter)
COMMAND_MANUAL_CONFIG - Static variable in class net.sf.basedb.plugins.Base1PluginExecuter: This command is used if the user decides to configure the plugin by hand.
COMMAND_SELECT_CONFIGURATIONS - Static variable in class net.sf.basedb.plugins.PluginConfigurationImporter
commandHandlers - Variable in class net.sf.basedb.clients.jobagent.handlers.DefaultRequestHandler
comment - Variable in class net.sf.basedb.core.authentication.LoginRequest
comment - Variable in class net.sf.basedb.core.data.BioMaterialEventData
comment - Variable in class net.sf.basedb.core.data.PlateEventData
comment - Variable in class net.sf.basedb.core.MigrateRbaToDba.LineMapping
commit() - Method in class net.sf.basedb.core.DbControl: Commit all changes made to items and close the connection to the database.
commit(Transaction) - Static method in class net.sf.basedb.core.HibernateUtil: Commit a transaction.
commitQueue - Variable in class net.sf.basedb.core.DbControl: A list of items that need special handling when commit is called.
COMMON - Static variable in class net.sf.basedb.clients.web.resources.Bundle: Resource bundle with strings that are used in lots and lots of places in the web gui.
commonCharsets - Static variable in class net.sf.basedb.core.Config
CommonData - Class in net.sf.basedb.core.data: This is a convenience class that extends the SharedData class and implements the NameableData and RemovableData interfaces.
CommonData() - Constructor for class net.sf.basedb.core.data.CommonData
commonDom - Static variable in class net.sf.basedb.core.PredefinedQuery: Holds the XML document containing the common queries.
CommonItem - Class in net.sf.basedb.core
CommonItem(CommonData) - Constructor for class net.sf.basedb.core.CommonItem
commonName - Variable in class net.sf.basedb.plugins.Base1PluginExecuter.JobParameter
commonQueryFile - Static variable in class net.sf.basedb.core.PredefinedQuery: The path to the query file with common queries.
CompactButtonRenderer - Class in net.sf.basedb.clients.web.extensions.toolbar: A compact renderer for toolbar button actions, which only only displays the icon.
CompactButtonRenderer(JspContext) - Constructor for class net.sf.basedb.clients.web.extensions.toolbar.CompactButtonRenderer
CompactButtonRendererFactory - Class in net.sf.basedb.clients.web.extensions.toolbar: Factory that create CompactButtonRenderer objects for rendering ButtonAction:s.
CompactButtonRendererFactory() - Constructor for class net.sf.basedb.clients.web.extensions.toolbar.CompactButtonRendererFactory
ComparableComparator<T extends Comparable<T>> - Class in net.sf.basedb.util: A comparator implemenation for any Comparable objects.
ComparableComparator() - Constructor for class net.sf.basedb.util.ComparableComparator
compare(String, String) - Method in class net.sf.basedb.util.StringLengthComparator
compare(URI, URI) - Method in class net.sf.basedb.util.extensions.manager.ExtensionsManager.JarFirstURIComparator
compare(RawDataType, RawDataType) - Method in class net.sf.basedb.core.RawDataTypes.NameComparator
compare(AnnotationSnapshot, AnnotationSnapshot) - Method in class net.sf.basedb.core.snapshot.AnnotationSetSnapshot.SortByProjectComparator
compare(AnnotationSnapshot, AnnotationSnapshot) - Method in class net.sf.basedb.core.snapshot.AnnotationSnapshot.AnnotationTypeComparator
compare(AnnotationSnapshot, AnnotationSnapshot) - Method in class net.sf.basedb.core.snapshot.AnnotationSnapshot.ProjectComparator
compare(T, T) - Method in class net.sf.basedb.util.ComparableComparator
compare(T, T) - Method in class net.sf.basedb.util.NameableComparator
compare(T, T) - Method in class net.sf.basedb.util.PriorityComparator
compare(T, T) - Method in class net.sf.basedb.util.ToStringComparator
compareByChainOrder() - Static method in class net.sf.basedb.core.SyncFilter: Create a comparator that sorts sync filters by: Filter group Source item type: BIOSOURCE, SAMPLE, EXTRACT, PHYSICALBIOASSAY, DERIVEDBIOASSAY, RAWBIOASSAY Type of transformation: PARENT_TO_CHILD, NONE, CHILD_TO_PARENT Name Source item must exists is sorted before source item must not exist Id
compareTo(ExperimentExplorer.AnnotationGroup) - Method in class net.sf.basedb.clients.web.ExperimentExplorer.AnnotationGroup
compareTo(ExperimentExplorerPlotServlet.ColumnKey) - Method in class net.sf.basedb.clients.web.servlet.ExperimentExplorerPlotServlet.ColumnKey: The ID of the key determines equality.
compareTo(ClonableProperty) - Method in class net.sf.basedb.core.ClonableProperty: Sort by title, but mandatory properties before non-madatory.
compareTo(KeyPermission) - Method in class net.sf.basedb.core.data.keyring.KeyPermission: Compare the keyId of this object to the keyId of another KeyPermission object.
compareTo(PluginKeys) - Method in class net.sf.basedb.core.data.keyring.PluginKeys: Compare the keyId of this object to the keyId of another PluginKeys object.
compareTo(ProjectPermission) - Method in class net.sf.basedb.core.data.keyring.ProjectPermission: Compare the projectId of this object to the projectId of another ProjectPermission object.
compareTo(TableInfo.ColumnInfo) - Method in class net.sf.basedb.core.dbengine.TableInfo.ColumnInfo
compareTo(ItemProxy) - Method in class net.sf.basedb.core.ItemProxy
compareTo(RawDataType) - Method in class net.sf.basedb.core.RawDataType: Compare the id:s of the raw data types.
compareTo(LowessNormalization.SpotData) - Method in class net.sf.basedb.plugins.LowessNormalization.SpotData: Sort by A in ascending order.
compareTo(MedianRatioNormalization.SpotData) - Method in class net.sf.basedb.plugins.MedianRatioNormalization.SpotData: Sort by ratio in ascending order.
compareTo(AnyToAnyLinkStatistics) - Method in class net.sf.basedb.util.AnyToAnyLinkStatistics: Sort items by count, linkName and targetType.
compareTo(ExtensionsFile) - Method in class net.sf.basedb.util.extensions.manager.ExtensionsFile
compareTo(Node) - Method in class net.sf.basedb.util.overview.Node
compareTo(PlotAnnotation) - Method in class net.sf.basedb.util.plot.PlotAnnotation
compareTo(UnitCache.CacheKey) - Method in class net.sf.basedb.util.units.UnitCache.CacheKey
compareWith(String) - Static method in class net.sf.basedb.core.Version: Compare the given version string, which should be of the form a.b or a.b.c, with the current BASE version.
compile(boolean, boolean) - Method in class net.sf.basedb.clients.web.extensions.XJspCompiler: Called when a JSP page needs recompiling.
compile(String, HttpServletRequest, HttpServletResponse) - Method in class net.sf.basedb.clients.web.servlet.CompileAll: Compile all files found in dir, recursively entering subdirectories.
CompileAll - Class in net.sf.basedb.clients.web.servlet: This servlet will scan for all files ending with .jsp and issue a request for them with the parameter jsp_precompile=true therby compiling all JSP files into servlets.
CompileAll() - Constructor for class net.sf.basedb.clients.web.servlet.CompileAll
completed - Variable in class net.sf.basedb.core.SimpleAbsoluteProgressReporter
complexMappings - Static variable in class net.sf.basedb.plugins.AbstractFlatFileImporter: Parameter that asks if complex column mappings should be enabled or not.
component - Variable in class net.sf.basedb.core.Metadata.ComponentPropertyPath
ComponentData - Interface in net.sf.basedb.core.data: Tagging interface that we need all componenets to implement so that we are able to export them properly using generic code.
ComponentPropertyPath(ComponentType, int, Type) - Constructor for class net.sf.basedb.core.Metadata.ComponentPropertyPath
CompoundMapper - Class in net.sf.basedb.util.parser: A compound mapper that gets its value by invoking multiple other mappers which are set in the constructor.
CompoundMapper(List<Mapper>) - Constructor for class net.sf.basedb.util.parser.CompoundMapper: Create a new compound mapper.
CompoundMapper(List<Mapper>, NumberFormat, boolean) - Constructor for class net.sf.basedb.util.parser.CompoundMapper: Create a new compound mapper, using a specific number formatter as it's parser.
CompoundMapper(List<Mapper>, NumberFormat, Formatter<Date>, boolean) - Constructor for class net.sf.basedb.util.parser.CompoundMapper: Create a new compound mapper, using a specific number formatter as it's parser.
compress - Variable in class net.sf.basedb.core.File.UploadStream: If the file should be compressed or not.
compress(ProgressReporter) - Method in class net.sf.basedb.core.File: Compress the file stored on the disk.
compressed - Variable in class net.sf.basedb.core.data.FileData
compressedSize - Variable in class net.sf.basedb.core.data.FileData
compressOrDecompress(ProgressReporter, boolean) - Method in class net.sf.basedb.core.File
condition - Variable in class net.sf.basedb.core.dbengine.TableInfo.IndexInfo
condition - Variable in class net.sf.basedb.core.HibernateUtil.DelayedFilterDef
condition - Variable in class net.sf.basedb.core.query.WhenStatement
conditionalExpression(Filter<? extends Query>, Expression, Expression) - Static method in class net.sf.basedb.core.query.Expressions: Create an expression that falls back to one of two expression depending on if the query passes a filter or not.
ConditionalQueryElement - Class in net.sf.basedb.core.query
ConditionalQueryElement(Filter<Query>, QueryElement, QueryElement) - Constructor for class net.sf.basedb.core.query.ConditionalQueryElement
conditionalRestriction(Filter<? extends Query>, Restriction, Restriction, boolean) - Static method in class net.sf.basedb.core.query.Restrictions: Create a restriction that falls back to one of two restrictions depending on if the query passes a filter or not.
config - Static variable in class net.sf.basedb.core.Config: Variable for holding the configuration properties.
config - Variable in class net.sf.basedb.core.hibernate.SchemaGenerator.CollectSqlTarget
config - Variable in class net.sf.basedb.core.plugin.ParameterValuesWrapper
config - Variable in class net.sf.basedb.util.ContextUtil.ContextResult
Config - Class in net.sf.basedb.core: Use this class to access the configuration settings for BASE.
Config() - Constructor for class net.sf.basedb.core.Config
configDir - Static variable in class net.sf.basedb.core.Config
configList - Static variable in class net.sf.basedb.plugins.PluginConfigurationExporter
configuration - Variable in class net.sf.basedb.core.ParameterValuesImpl
configuration - Variable in class net.sf.basedb.core.plugin.AbstractPlugin
configuration - Variable in class net.sf.basedb.plugins.gtf.DefaultConfigurationValues
ConfigurationException - Exception in net.sf.basedb.core: This exception is thrown by the Config class if there is a problem with finding or loading the configuration settings.
ConfigurationException(String) - Constructor for exception net.sf.basedb.core.ConfigurationException: Creates a new ConfigurationException.
ConfigurationException(String, Throwable) - Constructor for exception net.sf.basedb.core.ConfigurationException: Creates a new ConfigurationException with a cause.
configurationMap - Variable in class net.sf.basedb.plugins.PluginConfigurationImporter
configurationParameters - Variable in class net.sf.basedb.core.PluginRequest
configurations - Variable in class net.sf.basedb.core.data.PluginDefinitionData
configurationValues - Variable in class net.sf.basedb.core.data.PluginConfigurationData
configure() - Method in class net.sf.basedb.core.PluginConfiguration: Start the configuration sequence for a plugin.
configure(GuiContext) - Method in class net.sf.basedb.core.Job: Start the configuration sequence for a job.
configure(GuiContext, Request, Response) - Method in class net.sf.basedb.clients.web.plugins.SimpleExport
configure(GuiContext, Request, Response) - Method in interface net.sf.basedb.core.plugin.InteractivePlugin: Configure the plugin.
configure(GuiContext, Request, Response) - Method in class net.sf.basedb.plugins.AnnotationFlatFileImporter
configure(GuiContext, Request, Response) - Method in class net.sf.basedb.plugins.Base1PluginExecuter
configure(GuiContext, Request, Response) - Method in class net.sf.basedb.plugins.BaseFileExporterPlugin
configure(GuiContext, Request, Response) - Method in class net.sf.basedb.plugins.batchimport.AbstractItemImporter
configure(GuiContext, Request, Response) - Method in class net.sf.basedb.plugins.batchimport.AnnotationTypeImporter: Override this method so that we can make some extra parameter checks: A mapping for 'Value type' must be specified when 'create' or 'create+update' mode is used
configure(GuiContext, Request, Response) - Method in class net.sf.basedb.plugins.batchimport.AnyToAnyImporter
configure(GuiContext, Request, Response) - Method in class net.sf.basedb.plugins.BfsExporterPlugin
configure(GuiContext, Request, Response) - Method in class net.sf.basedb.plugins.CdfFileReporterImporter
configure(GuiContext, Request, Response) - Method in class net.sf.basedb.plugins.executor.BaseFileExporterSupport
configure(GuiContext, Request, Response) - Method in class net.sf.basedb.plugins.executor.BaseFileImporterSupport
configure(GuiContext, Request, Response) - Method in class net.sf.basedb.plugins.executor.BfsExporterSupport
configure(GuiContext, Request, Response) - Method in class net.sf.basedb.plugins.executor.BfsImporterSupport
configure(GuiContext, Request, Response) - Method in class net.sf.basedb.plugins.executor.ExternalProgramExecutor
configure(GuiContext, Request, Response) - Method in class net.sf.basedb.plugins.executor.FileOnlyImporterSupport
configure(GuiContext, Request, Response) - Method in class net.sf.basedb.plugins.FormulaFilter
configure(GuiContext, Request, Response) - Method in class net.sf.basedb.plugins.GalExporter
configure(GuiContext, Request, Response) - Method in class net.sf.basedb.plugins.gtf.GtfReporterMapImporter
configure(GuiContext, Request, Response) - Method in class net.sf.basedb.plugins.HelpExporter
configure(GuiContext, Request, Response) - Method in class net.sf.basedb.plugins.HelpImporter
configure(GuiContext, Request, Response) - Method in class net.sf.basedb.plugins.IlluminaRawDataImporter
configure(GuiContext, Request, Response) - Method in class net.sf.basedb.plugins.IntensityCalculatorPlugin: Store configuration settings for Request.COMMAND_CONFIGURE_PLUGIN, and Request.COMMAND_CONFIGURE_JOB.
configure(GuiContext, Request, Response) - Method in class net.sf.basedb.plugins.JepExtraValueCalculator
configure(GuiContext, Request, Response) - Method in class net.sf.basedb.plugins.JepIntensityTransformer
configure(GuiContext, Request, Response) - Method in class net.sf.basedb.plugins.LowessNormalization
configure(GuiContext, Request, Response) - Method in class net.sf.basedb.plugins.ManualDerivedBioAssayCreator
configure(GuiContext, Request, Response) - Method in class net.sf.basedb.plugins.ManualTransformCreator
configure(GuiContext, Request, Response) - Method in class net.sf.basedb.plugins.MedianRatioNormalization
configure(GuiContext, Request, Response) - Method in class net.sf.basedb.plugins.PackedFileExporter
configure(GuiContext, Request, Response) - Method in class net.sf.basedb.plugins.PlateFlatFileImporter: Store configuration settings for Request.COMMAND_CONFIGURE_PLUGIN and Request.COMMAND_CONFIGURE_JOB.
configure(GuiContext, Request, Response) - Method in class net.sf.basedb.plugins.PlateMappingExporter: Store configuration settings for Request.COMMAND_CONFIGURE_PLUGIN and Request.COMMAND_CONFIGURE_JOB.
configure(GuiContext, Request, Response) - Method in class net.sf.basedb.plugins.PlateMappingImporter: Store configuration settings for Request.COMMAND_CONFIGURE_PLUGIN and Request.COMMAND_CONFIGURE_JOB.
configure(GuiContext, Request, Response) - Method in class net.sf.basedb.plugins.PluginConfigurationExporter: Store configuration settings for Request.COMMAND_CONFIGURE_JOB.
configure(GuiContext, Request, Response) - Method in class net.sf.basedb.plugins.PluginConfigurationImporter
configure(GuiContext, Request, Response) - Method in class net.sf.basedb.plugins.PrintMapFlatFileImporter: Store configuration settings for Request.COMMAND_CONFIGURE_PLUGIN and Request.COMMAND_CONFIGURE_JOB.
configure(GuiContext, Request, Response) - Method in class net.sf.basedb.plugins.RawDataFlatFileImporter: Store configuration settings for Request.COMMAND_CONFIGURE_PLUGIN, RawDataFlatFileImporter.COMMAND_CONFIGURE_PARSER and Request.COMMAND_CONFIGURE_JOB.
configure(GuiContext, Request, Response) - Method in class net.sf.basedb.plugins.ReporterFlatFileImporter: Store configuration settings for Request.COMMAND_CONFIGURE_PLUGIN and Request.COMMAND_CONFIGURE_JOB.
configure(GuiContext, Request, Response) - Method in class net.sf.basedb.plugins.ReporterMapFlatFileImporter: Store configuration settings for Request.COMMAND_CONFIGURE_PLUGIN and Request.COMMAND_CONFIGURE_JOB.
configure(GuiContext, Request, Response) - Method in class net.sf.basedb.util.zip.AbstractFileUnpacker
CONFIGURE_IMPORT - Static variable in class net.sf.basedb.plugins.AnnotationFlatFileImporter
CONFIGURE_MAPPING - Static variable in class net.sf.basedb.plugins.AnnotationFlatFileImporter
CONFIGURE_OPTIONS - Static variable in class net.sf.basedb.plugins.batchimport.AbstractItemImporter
CONFIGURE_OPTIONS - Static variable in class net.sf.basedb.plugins.batchimport.AnyToAnyImporter
ConfigureByExample - Interface in net.sf.basedb.util.parser: This is a tagging interface for all plugins that use the FlatFileParser and wants easier configuration of the regular expressions used to parse the file.
configureExecutor - Variable in class net.sf.basedb.plugins.executor.BaseFileExporterSupport
configureExecutor - Variable in class net.sf.basedb.plugins.executor.BaseFileImporterSupport
configureExecutor - Variable in class net.sf.basedb.plugins.executor.BfsExporterSupport
configureExecutor - Variable in class net.sf.basedb.plugins.executor.BfsImporterSupport
configureExportImportPluginParameters - Variable in class net.sf.basedb.plugins.executor.ExternalProgramExecutor
configureExternalParameters - Variable in class net.sf.basedb.plugins.executor.ExternalProgramExecutor
configureImport - Variable in class net.sf.basedb.plugins.AnnotationFlatFileImporter
configureJob - Variable in class net.sf.basedb.clients.web.plugins.SimpleExport
configureJob - Variable in class net.sf.basedb.plugins.Base1PluginExecuter: Holds info about a job configuration request.
configureJob - Variable in class net.sf.basedb.plugins.BaseFileExporterPlugin
configureJob - Variable in class net.sf.basedb.plugins.BfsExporterPlugin
configureJob - Variable in class net.sf.basedb.plugins.CdfFileReporterImporter
configureJob - Variable in class net.sf.basedb.plugins.executor.BaseFileImporterSupport
configureJob - Variable in class net.sf.basedb.plugins.executor.BfsImporterSupport
configureJob - Variable in class net.sf.basedb.plugins.executor.ExternalProgramExecutor
configureJob - Variable in class net.sf.basedb.plugins.executor.FileOnlyImporterSupport
configureJob - Variable in class net.sf.basedb.plugins.FormulaFilter
configureJob - Variable in class net.sf.basedb.plugins.GalExporter
configureJob - Variable in class net.sf.basedb.plugins.gtf.GtfReporterMapImporter
configureJob - Variable in class net.sf.basedb.plugins.HelpExporter
configureJob - Variable in class net.sf.basedb.plugins.HelpImporter
configureJob - Variable in class net.sf.basedb.plugins.IlluminaRawDataImporter
configureJob - Variable in class net.sf.basedb.plugins.IntensityCalculatorPlugin
configureJob - Variable in class net.sf.basedb.plugins.JepExtraValueCalculator
configureJob - Variable in class net.sf.basedb.plugins.JepIntensityTransformer
configureJob - Variable in class net.sf.basedb.plugins.LowessNormalization
configureJob - Variable in class net.sf.basedb.plugins.ManualDerivedBioAssayCreator
configureJob - Variable in class net.sf.basedb.plugins.ManualTransformCreator
configureJob - Variable in class net.sf.basedb.plugins.MedianRatioNormalization
configureJob - Variable in class net.sf.basedb.plugins.PackedFileExporter
configureJob - Variable in class net.sf.basedb.plugins.PlateFlatFileImporter
configureJob - Variable in class net.sf.basedb.plugins.PlateMappingExporter
configureJob - Variable in class net.sf.basedb.plugins.PlateMappingImporter
configureJob - Variable in class net.sf.basedb.plugins.PluginConfigurationExporter
configureJob - Variable in class net.sf.basedb.plugins.PluginConfigurationImporter
configureJob - Variable in class net.sf.basedb.plugins.PrintMapFlatFileImporter
configureJob - Variable in class net.sf.basedb.plugins.RawDataFlatFileImporter
configureJob - Variable in class net.sf.basedb.plugins.ReporterFlatFileImporter
configureJob - Variable in class net.sf.basedb.plugins.ReporterMapFlatFileImporter
configureJob - Variable in class net.sf.basedb.util.zip.AbstractFileUnpacker
configureManual - Variable in class net.sf.basedb.plugins.Base1PluginExecuter: Holds information about a manual plugin configuration request.
configureMapping - Variable in class net.sf.basedb.plugins.AnnotationFlatFileImporter
configureOptions - Variable in class net.sf.basedb.plugins.batchimport.AbstractItemImporter
configureOptions - Variable in class net.sf.basedb.plugins.batchimport.AnyToAnyImporter
configureParser - Variable in class net.sf.basedb.plugins.AnnotationFlatFileImporter
configureParser - Variable in class net.sf.basedb.plugins.batchimport.AbstractItemImporter
configureParser - Variable in class net.sf.basedb.plugins.batchimport.AnyToAnyImporter
configureParser - Variable in class net.sf.basedb.plugins.RawDataFlatFileImporter
configurePlugin - Variable in class net.sf.basedb.plugins.Base1PluginExecuter: Holds information about a plugin configuration request.
configurePlugin - Variable in class net.sf.basedb.plugins.executor.ExternalProgramExecutor
configurePlugin - Variable in class net.sf.basedb.plugins.gtf.GtfReporterMapImporter
configurePlugin - Variable in class net.sf.basedb.plugins.ManualDerivedBioAssayCreator
configurePlugin - Variable in class net.sf.basedb.plugins.ManualTransformCreator
configurePlugin - Variable in class net.sf.basedb.plugins.PackedFileExporter
configurePlugin - Variable in class net.sf.basedb.plugins.PlateFlatFileImporter
configurePlugin - Variable in class net.sf.basedb.plugins.ReporterFlatFileImporter
configurePlugin - Variable in class net.sf.basedb.plugins.ReporterMapFlatFileImporter
configureQuery(DbControl, EntityQuery, boolean) - Method in class net.sf.basedb.core.ItemContext
configureQuery(DbControl, EntityQuery, ClientContext, boolean) - Method in class net.sf.basedb.core.ItemContext: Use the settings in this context to configure a query.
configureQuery(DbControl, SqlQuery, List<String>) - Method in class net.sf.basedb.core.ItemContext: Use the settings in this context to configure a dynamic query.
configureQuery(SqlQuery) - Method in interface net.sf.basedb.util.DynamicFilter: Configure the query before it is used.
configureQuery(SqlQuery) - Method in class net.sf.basedb.util.IncludeExcludeFilter: We need the position which is in column 2 (already selected).
configureRawDataType - Variable in class net.sf.basedb.plugins.RawDataFlatFileImporter
configureSelection - Variable in class net.sf.basedb.plugins.PluginConfigurationImporter
connect() - Method in class net.sf.basedb.util.jobagent.JobAgentConnection: Create a socket connection to the job agent.
connection() - Method in class net.sf.basedb.core.hibernate.StatelessSessionWrapper: Deprecated.
ConnectionClosedException - Exception in net.sf.basedb.core: This exception is thrown when trying to use a DbControl object that has been closed.
ConnectionClosedException() - Constructor for exception net.sf.basedb.core.ConnectionClosedException: Creates a new ConnectionClosedException.
ConnectionManager - Interface in net.sf.basedb.util.uri: A connection manager is used to access the contents and metadata about the resource pointed to by a given URI.
connectionManagerFactory - Variable in class net.sf.basedb.core.data.FileServerData
ConnectionManagerFactory - Interface in net.sf.basedb.util.uri: A connection manager factory is responsible for creating connection managers for some subset of URI:s that is supported.
ConnectionManagerUtil - Class in net.sf.basedb.util.uri: Collects utility methods related to connection managers.
ConnectionManagerUtil() - Constructor for class net.sf.basedb.util.uri.ConnectionManagerUtil
ConnectionParameters - Class in net.sf.basedb.util.uri: Connection parameters, such as username/password, that may be needed to connect to a server.
ConnectionParameters() - Constructor for class net.sf.basedb.util.uri.ConnectionParameters: Create a new empty parameters object.
connectTimeout - Variable in class net.sf.basedb.clients.jobagent.slotmanager.RemoteSlotManager
ConsoleProgressReporter - Class in net.sf.basedb.util: An implementation of the ProgressReporter interface that writes all messages to the standard console.
ConsoleProgressReporter() - Constructor for class net.sf.basedb.util.ConsoleProgressReporter
ConsoleProgressReporter(boolean) - Constructor for class net.sf.basedb.util.ConsoleProgressReporter
constant - Variable in class net.sf.basedb.util.parser.ConstantMapper
ConstantMapper - Class in net.sf.basedb.util.parser: A constant string mapper.
ConstantMapper(Float) - Constructor for class net.sf.basedb.util.parser.ConstantMapper
ConstantMapper(Integer) - Constructor for class net.sf.basedb.util.parser.ConstantMapper
ConstantMapper(String) - Constructor for class net.sf.basedb.util.parser.ConstantMapper: Create a constant mapper.
ConstantMapper(String, NumberFormat, boolean) - Constructor for class net.sf.basedb.util.parser.ConstantMapper: Create a constant mapper using a specific number formatter as it's parser.
ConstantMapper(String, NumberFormat, Formatter<Date>, boolean) - Constructor for class net.sf.basedb.util.parser.ConstantMapper: Create a constant mapper using a specific number formatter as it's parser.
ConstantMapper(Date, Formatter<Date>) - Constructor for class net.sf.basedb.util.parser.ConstantMapper
constructor - Variable in enum class net.sf.basedb.core.Item
contact - Variable in class net.sf.basedb.core.data.PluginDefinitionData
contact - Variable in class net.sf.basedb.core.plugin.AboutImpl
contact - Variable in class net.sf.basedb.util.extensions.AboutBean
contact - Variable in class net.sf.basedb.util.extensions.Registry.RegisteredAbout
contains(Object) - Method in class net.sf.basedb.core.hibernate.SessionWrapper
contains(Object) - Method in class net.sf.basedb.core.ItemResultList
contains(Object) - Method in class net.sf.basedb.util.Tree
contains(String, Object) - Method in class net.sf.basedb.core.hibernate.SessionWrapper
contains(AnnotationUtil.AnnotatableWrapper) - Method in class net.sf.basedb.util.AnnotationUtil.Cache
containsAll(Collection<?>) - Method in class net.sf.basedb.core.AbstractResultList
containsAll(Collection<?>) - Method in class net.sf.basedb.core.UnmodifiableResultList
containsAll(Collection<?>) - Method in class net.sf.basedb.util.Tree
containsKey(Object) - Method in class net.sf.basedb.util.formatter.LookupFormatter: Checks if a given key has been registered.
containsKey(Object) - Method in class net.sf.basedb.util.jep.FunctionSafeJep.SafeFunctionTable: If the key is already registered, return TRUE.
content - Variable in class net.sf.basedb.clients.web.extensions.section.SectionBean
content - Variable in class net.sf.basedb.clients.web.extensions.tabcontrol.FixedTabFactory
content - Variable in class net.sf.basedb.clients.web.extensions.tabcontrol.TabBean
content - Variable in class net.sf.basedb.clients.web.taglib.tab.TabControl: The HTML for the contents of the tabs.
ContentSecurityPolicyFilter - Class in net.sf.basedb.clients.web.servlet: This is a filter that sets the "Content-Security-Policy" header in the http response.
ContentSecurityPolicyFilter() - Constructor for class net.sf.basedb.clients.web.servlet.ContentSecurityPolicyFilter
ContentSecurityPolicyReportServlet - Class in net.sf.basedb.clients.web.servlet: This is a servlet for posting reports from "Content-Security-Policy" violations.
ContentSecurityPolicyReportServlet() - Constructor for class net.sf.basedb.clients.web.servlet.ContentSecurityPolicyReportServlet
contentStyle - Variable in class net.sf.basedb.clients.web.extensions.section.IncludeContentSectionFactory
contentStyle - Variable in class net.sf.basedb.clients.web.extensions.section.SectionBean
contentStyle - Variable in class net.sf.basedb.clients.web.taglib.HideableSection: Optional style attribute for the content section
contentStyle - Variable in class net.sf.basedb.clients.web.taglib.tab.TabControl: Optional style attribute for the content section
context - Variable in class net.sf.basedb.clients.web.extensions.LoadServletsProcessor
context - Variable in class net.sf.basedb.clients.web.extensions.renderer.PrefixSuffixRenderer
context - Variable in class net.sf.basedb.clients.web.extensions.ServletWrapper
context - Variable in class net.sf.basedb.clients.web.extensions.tabcontrol.IncludeContentTabFactory.Tab
context - Variable in class net.sf.basedb.clients.web.extensions.toolbar.CompactButtonRenderer
context - Variable in class net.sf.basedb.clients.web.extensions.toolbar.ToolbarButtonRenderer
context - Variable in class net.sf.basedb.clients.web.taglib.extensions.Render
context - Variable in class net.sf.basedb.clients.web.taglib.extensions.Scripts
context - Variable in class net.sf.basedb.clients.web.taglib.extensions.Stylesheets
context - Variable in class net.sf.basedb.clients.web.taglib.HideableSection
context - Variable in class net.sf.basedb.core.PluginConfigurationRequest
context - Variable in class net.sf.basedb.core.signal.ExtensionSignalTransporter
context - Variable in class net.sf.basedb.util.overview.node.NodeFactory
CONTEXT_BIOASSAYS - Static variable in class net.sf.basedb.core.plugin.AbstractAnalysisPlugin: GuiContext = [Item.BIOASSAY, GuiContext.Type.LIST]
CONTEXT_BIOASSAYSET - Static variable in class net.sf.basedb.core.plugin.AbstractAnalysisPlugin: GuiContext = [Item.BIOASSAYSET, GuiContext.Type.ITEM]
CONTEXT_DERIVEDBIOASSAY - Static variable in class net.sf.basedb.core.plugin.AbstractAnalysisPlugin: GuiContext = [Item.DERIVEDBIOASSAY, GuiContext.Type.ITEM]
CONTEXT_RELATIVE - Enum constant in enum class net.sf.basedb.util.extensions.xml.PathType: Paths should be relative to the web application context.
ContextData - Class in net.sf.basedb.core.data: This class holds context information to help client applications with storing common settings for tables.
ContextData() - Constructor for class net.sf.basedb.core.data.ContextData
contextDestroyed(ServletContextEvent) - Method in class net.sf.basedb.clients.web.servlet.StartStopServlet
contextId - Variable in class net.sf.basedb.core.ItemContext
ContextIndex - Class in net.sf.basedb.core.data
ContextIndex() - Constructor for class net.sf.basedb.core.data.ContextIndex
ContextIndex(ClientData, int, String, String) - Constructor for class net.sf.basedb.core.data.ContextIndex
contextInitialized(ServletContextEvent) - Method in class net.sf.basedb.clients.web.servlet.StartStopServlet
contextItem - Variable in class net.sf.basedb.core.data.JobData
ContextKey - Class in net.sf.basedb.core
ContextKey(Item, String) - Constructor for class net.sf.basedb.core.ContextKey: Create a new ContextKey object from Item and it's subcontext.
contextMessage - Variable in class net.sf.basedb.util.ContextUtil.ContextResult
contextPath - Variable in class net.sf.basedb.clients.web.servlet.ImageRemapFilter
contextPath - Variable in class net.sf.basedb.clients.web.servlet.RssNewsFeed
ContextResult(PluginDefinition, PluginConfiguration, String) - Constructor for class net.sf.basedb.util.ContextUtil.ContextResult: Create a new warning-level result object.
ContextResult(PluginDefinition, PluginConfiguration, Throwable) - Constructor for class net.sf.basedb.util.ContextUtil.ContextResult: Create a new error-level result object.
ContextResult(SessionControl, PluginDefinition, PluginConfiguration, GuiContext, Object) - Constructor for class net.sf.basedb.util.ContextUtil.ContextResult
contexts - Variable in class net.sf.basedb.core.data.ClientData
contexts - Variable in class net.sf.basedb.core.data.UserData
contexts - Variable in class net.sf.basedb.util.extensions.ExtensionsInvoker
contextType - Variable in class net.sf.basedb.core.data.GuiContextData
contextType - Variable in class net.sf.basedb.core.data.JobData
ContextUtil - Class in net.sf.basedb.util: A class with utility methods for plug-ins.
ContextUtil() - Constructor for class net.sf.basedb.util.ContextUtil
ContextUtil.ContextResult - Class in net.sf.basedb.util: Class for holding the result of a call to the InteractivePlugin.isInContext(GuiContext, Object) method.
ContextUtil.IsInContextFilter - Class in net.sf.basedb.util: Filter implementation that works on collections of ContextUtil.ContextResult:s and return only those that return true from ContextUtil.ContextResult.isInContext().
CONTINUE - Enum constant in enum class net.sf.basedb.core.plugin.Response.Status
continueAfterError - Variable in class net.sf.basedb.plugins.RawDataFlatFileImporter
continueLater(String, boolean, Serializable) - Method in class net.sf.basedb.core.Job: This method is used to indicate that a job had to be aborted due to a system shutdown.
continueWithNextFileAfterError(Throwable) - Method in class net.sf.basedb.plugins.AbstractFlatFileImporter: If the importer should continue with the next file after an error.
continueWithNextFileAfterError(Throwable) - Method in class net.sf.basedb.plugins.RawDataFlatFileImporter: We will continue if: The file is not of the correct format, eg. t = UnsupportedFileFormatException.
Controlled - Interface in net.sf.basedb.core: This is the base tagging interface for items that needs special attention by the DbControl object when DbControl.commit() is called.
convert(String) - Method in class net.sf.basedb.util.extensions.debug.StringConverter
convert(String, Method) - Method in class net.sf.basedb.util.extensions.xml.PathConverter
convert(String, Method) - Method in interface net.sf.basedb.util.extensions.xml.ValueConverter: Convert a value.
convert(String, Method) - Method in class net.sf.basedb.util.extensions.xml.VariableConverter
convert(T) - Method in class net.sf.basedb.util.json.IdentityConverter
convert(T) - Method in interface net.sf.basedb.util.json.JsonConverter: Convert the given object to a JSON-compatible object.
convert(T) - Method in class net.sf.basedb.util.json.NameableConverter
converter - Variable in class net.sf.basedb.core.snapshot.AnnotationLoaderUtil
converter - Static variable in class net.sf.basedb.util.extensions.debug.StringConverter
ConverterFactory - Class in net.sf.basedb.util.jep.convert: Keep JepConversionFunction objects for converting built-in JEP object to Query API Expression or Restriction objects.
ConverterFactory() - Constructor for class net.sf.basedb.util.jep.convert.ConverterFactory
converters - Variable in class net.sf.basedb.util.extensions.xml.XmlLoader
converters - Static variable in class net.sf.basedb.util.jep.convert.ConverterFactory
convertJavaDateFormatToExcelFormat(String) - Static method in class net.sf.basedb.util.excel.CellStyleCreator: Converts a Java date format string to the corresponding Excel date format string.
convertNumber(Number) - Method in enum class net.sf.basedb.core.Type: Convert a number to the appropriate class.
convertString(Class, String) - Static method in class net.sf.basedb.util.extensions.debug.StringConverter
convertToNull(String) - Method in class net.sf.basedb.util.parser.FlatFileParser
convertToReferenceUnit(double) - Method in class net.sf.basedb.util.units.IdentityUnitConverter
convertToReferenceUnit(double) - Method in class net.sf.basedb.util.units.LinearUnitConverter: value(ref) = value(specific) * factor + offset
convertToReferenceUnit(double) - Method in interface net.sf.basedb.util.units.UnitConverter: Convert a value from the specific unit to the reference unit.
convertToSpecificUnit(double) - Method in class net.sf.basedb.util.units.IdentityUnitConverter
convertToSpecificUnit(double) - Method in class net.sf.basedb.util.units.LinearUnitConverter: value(specific) = (value(ref) - offset) / factor
convertToSpecificUnit(double) - Method in interface net.sf.basedb.util.units.UnitConverter: Convert a value from the reference unit to the specific unit.
convertValue(String, Class<?>) - Method in class net.sf.basedb.util.extensions.debug.BeanActionFactory: Convert a string value to another type.
convertValues(AnnotationType, List<?>, Unit) - Method in class net.sf.basedb.core.Annotation
convertValueToUnit(Session, String, String, Unit) - Method in class net.sf.basedb.core.PropertyFilter: Converts a string to a numeric value with the correct unit.
Coordinate - Class in net.sf.basedb.util: Util class for coordinate transformations in base.
Coordinate() - Constructor for class net.sf.basedb.util.Coordinate
COORDINATES - Enum constant in enum class net.sf.basedb.core.FeatureIdentificationMethod: Use coordinates (block, metaGridX, metaGridY, row, column)
coordinateType - Variable in class net.sf.basedb.core.data.DataCubeExtraValueData
CoordinateType(int) - Constructor for enum class net.sf.basedb.core.ExtraValue.CoordinateType
copy(byte[], int, int) - Method in class net.sf.basedb.util.InputStreamSplitter: Write data to all output streams.
copy(int) - Method in class net.sf.basedb.util.InputStreamSplitter: Write data to all output streams.
copy(InputStream, OutputStream) - Static method in class net.sf.basedb.util.FileUtil: Copy from the input stream to the output stream until end of file is reached.
copy(InputStream, OutputStream, AbsoluteProgressReporter) - Static method in class net.sf.basedb.util.FileUtil: Copy from the input stream to the output stream until end of file is reached.
copy(Reader, Writer) - Static method in class net.sf.basedb.util.FileUtil: Copy from the reader to the writer until end of file is reached.
copy(Reader, Writer, AbsoluteProgressReporter) - Static method in class net.sf.basedb.util.FileUtil: Copy from the reader to the writer until end of file is reached.
copy(Date) - Static method in class net.sf.basedb.core.DateUtil: Get a copy of the date.
copy(File, File) - Method in class net.sf.basedb.plugins.Base1PluginExecuter: Copies the content from a File to a directory on the file system.
copy(About, boolean) - Method in class net.sf.basedb.util.extensions.AboutBean: Copy information from antoher About object to this one.
COPY_ANNOTATIONS - Static variable in class net.sf.basedb.core.plugin.AbstractPlugin: The name of the parameter that asks if annotations should be copied or not.
copyFrom(Annotatable, boolean) - Method in class net.sf.basedb.core.AnnotationSet: Copy annotations from another annotatable item to this annotation set.
copyFrom(ItemContext, boolean) - Method in class net.sf.basedb.core.ItemContext: Copy settings from another context to this context.
copyFromSyncFilter(ItemListSyncFilterData) - Method in class net.sf.basedb.core.ItemContext
copyMetadata(FusionCDFData, ArrayDesign) - Method in class net.sf.basedb.util.affymetrix.CdfValidator: Copy metadata from the CDF file to the array design.
copyMetadata(FusionCELData, RawBioAssay) - Method in class net.sf.basedb.util.affymetrix.CelValidator: Copy metadata from the CEL file to the raw bioassay.
copyNotNulls(Collection<? extends T>, T[]) - Static method in class net.sf.basedb.core.query.Restrictions
copyNotNulls(T[], T[]) - Static method in class net.sf.basedb.core.query.Restrictions
copyObjectsAndTemporaryFilters(ItemContext) - Method in class net.sf.basedb.core.ItemContext: Copies all objects and temporary filters from this context to another context.
copyParametersFrom(Job) - Method in class net.sf.basedb.core.Job: Copy all parameter values from another job.
copyParametersFrom(PluginConfiguration) - Method in class net.sf.basedb.core.PluginConfiguration: Copy all parameter values from another plugin configuration.
copyPermissions(DbControl, Shareable, Shareable) - Static method in class net.sf.basedb.core.ShareableUtil: Copy permissions from one item to another.
copyProperties(File, File) - Static method in class net.sf.basedb.util.zip.PackUtil: Copy certain properties from the archive file to the unpacked file.
copyRedefinedColumnNames(BaseFileParser) - Method in class net.sf.basedb.util.basefile.BaseFileParser: Copy redefined column names from the given parser into this parser