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All Classes All Packages

A

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

B

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

C

c - Variable in enum net.sf.basedb.plugins.Base1PluginExecuter.Base1JobParameterType
 
CABINET - Static variable in class net.sf.basedb.core.Hardware
The id for the HardwareType object representing a cabinet.
cache - Variable in class net.sf.basedb.clients.web.ExperimentExplorer
The cache of reporter ids matching the current reporter filter.
cache - Static variable in class net.sf.basedb.core.DerivedBioAssay.FixDerivedBioAssayParentsRecursivelyAction
 
cache - Variable in class net.sf.basedb.core.hibernate.AbstractQueryCache
 
cache - Static variable in class net.sf.basedb.core.MeasuredBioMaterial.RemainingQuantityAction
We need a single action per DbControl and BioMaterial
cache - Variable in class net.sf.basedb.util.AnnotationUtil.AnnotatableWrapper
 
cache - Variable in class net.sf.basedb.util.bfs.BaseInputStreamLocator
 
cache - Variable in class net.sf.basedb.util.listable.TransformCache
 
cache - Variable in class net.sf.basedb.util.overview.cache.NodeCache
 
cache - Variable in class net.sf.basedb.util.StaticCache.CleanupTask
 
Cache() - Constructor for class net.sf.basedb.util.AnnotationUtil.Cache
 
cacheBase - Variable in class net.sf.basedb.clients.web.servlet.PlotServlet
 
cacheChildNodes(Node) - Method in class net.sf.basedb.util.overview.GenericOverview
 
cacheControl - Variable in class net.sf.basedb.clients.web.servlet.CacheControlFilter
 
cacheControl - Variable in class net.sf.basedb.clients.web.servlet.ImageRemapFilter
 
CacheControlFilter - Class in net.sf.basedb.clients.web.servlet
This is a filter that sets the "Cache-Control" header in the http response.
CacheControlFilter() - Constructor for class net.sf.basedb.clients.web.servlet.CacheControlFilter
 
cachedPaths - Variable in class net.sf.basedb.core.Metadata
 
cachedRssNews - Variable in class net.sf.basedb.clients.web.servlet.RssNewsFeed
 
CacheEntry(long, Set<Integer>) - Constructor for class net.sf.basedb.util.listable.TransformCache.CacheEntry
 
cacheFile - Variable in class net.sf.basedb.util.StreamCacher
 
cacheKey - Variable in class net.sf.basedb.util.overview.cache.DirectionalCacheKey
 
cacheKey - Variable in class net.sf.basedb.util.overview.cache.IndexedCacheKey
 
CacheKey(int, String) - Constructor for class net.sf.basedb.util.units.UnitCache.CacheKey
 
CacheKey(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.
cacheReporterData() - Method in class net.sf.basedb.util.export.spotdata.AbstractBioAssaySetExporter
Loads and caches reporter data in an internal structure for quick access.
cacheResults - Variable in class net.sf.basedb.core.AbstractHqlQuery
If the results should be cached or not.
calculateBoxAndWhiskerStatistics(List<Float>) - Method in class net.sf.basedb.clients.web.servlet.ExperimentExplorerPlotServlet
Creates a box-and-whisker data holder for the given list of values.
calculateIntensities(RawData) - Method in interface net.sf.basedb.util.IntensityCalculator
Calculate intensities from a raw data spot.
calculateIntensities(RawData) - Method in class net.sf.basedb.util.IntensityCalculatorUtil.JepIntensityCalculatorImpl
 
calculateWeights(List<LowessNormalization.SpotData>, double, List<Double>) - Static method in class net.sf.basedb.plugins.LowessNormalization
 
CalendarButton - Class in net.sf.basedb.clients.web.taglib
A special button tag that is used to display a "Calendar" button that opens a popup for selecting a date and time.
CalendarButton() - Constructor for class net.sf.basedb.clients.web.taglib.CalendarButton
 
call() - Method in class net.sf.basedb.core.QueryExecutor.FutureItem
 
call() - Method in class net.sf.basedb.core.QueryExecutor.FutureResultSet
 
call() - Method in class net.sf.basedb.core.QueryExecutor.FutureScrollIterator
 
call() - Method in class net.sf.basedb.core.QueryExecutor.FutureUpdate
 
call() - Method in class net.sf.basedb.plugins.LowessNormalization.CallableWorker
 
CallableWorker(List<LowessNormalization.SpotData>, MACalculator, float, float, int, int) - Constructor for class net.sf.basedb.plugins.LowessNormalization.CallableWorker
 
calledFrom - Variable in class net.sf.basedb.util.StaticCache.State
 
canAdd(BioWell) - Method in enum net.sf.basedb.core.BioWell.LockMode
Is it allowed to add (a different) biomaterial to the well?
canAdd(BioWellData) - Method in enum net.sf.basedb.core.BioWell.LockMode
 
canAddBioMaterial() - Method in class net.sf.basedb.core.BioWell
Check if it is possible to add/change biomaterial in this well.
cancel() - Method in class net.sf.basedb.clients.jobagent.JobQueueChecker
 
cancel() - Method in interface net.sf.basedb.core.QueryExecutor.Cancelable
 
cancel() - Method in class net.sf.basedb.core.QueryExecutor.CancelableSession
 
cancel() - Method in class net.sf.basedb.core.QueryExecutor.CancelableStatelessSession
 
cancel() - Method in class net.sf.basedb.core.QueryExecutor.CancelableStatement
 
cancel() - Method in class net.sf.basedb.util.timer.ThreadTimerTask
 
CancelableSession(Session) - Constructor for class net.sf.basedb.core.QueryExecutor.CancelableSession
 
CancelableStatelessSession(StatelessSession) - Constructor for class net.sf.basedb.core.QueryExecutor.CancelableStatelessSession
 
CancelableStatement(Statement) - Constructor for class net.sf.basedb.core.QueryExecutor.CancelableStatement
 
cancelQuery() - Method in class net.sf.basedb.core.hibernate.SessionWrapper
 
cancelQuery() - Method in class net.sf.basedb.core.hibernate.StatelessSessionWrapper
Cancels the currently executing query in the same manner as Session.cancelQuery().
canClear(BioWell) - Method in enum net.sf.basedb.core.BioWell.LockMode
Is it allowed to clear a well from biomaterial?
canClear(BioWellData) - Method in enum net.sf.basedb.core.BioWell.LockMode
 
canClearBioMaterial() - Method in class net.sf.basedb.core.BioWell
Check if it is possible to clear the current biomaterial in this well.
canEnumerate - Variable in enum net.sf.basedb.core.Type
 
canEnumerate() - Method in enum net.sf.basedb.core.Type
If it makes sense to use values of this type as an enumeration to choose from.
canUseColoring - Variable in enum net.sf.basedb.core.Formula.Type
 
canUseColoring() - Method in enum net.sf.basedb.core.Formula.Type
If a formula of this type can use coloring or not.
CAPACITANCE - Static variable in class net.sf.basedb.core.Quantity
The id for the Quantity object representing capacitance.
CaseExpression - Class in net.sf.basedb.core.query
An SQL case expression:
CaseExpression(Expression, WhenStatement...) - Constructor for class net.sf.basedb.core.query.CaseExpression
 
caseInsensitive - Variable in enum net.sf.basedb.core.FeatureIdentificationMethod
If the feature identifiers may be affect by case sensitivity at the database level or not.
caseInsensitive - Variable in class net.sf.basedb.core.RawDataBatcher
If case should be ignored when comparing strings (external ID)
caseInsensitive() - Method in enum net.sf.basedb.core.FeatureIdentificationMethod
Return TRUE if this identification method can be case insensitive.
caseInsensitiveComparison() - Method in interface net.sf.basedb.core.dbengine.DbEngine
If the database does case sensitive or case insensitive string comparison in expressions.
caseInsensitiveComparison() - Method in class net.sf.basedb.core.dbengine.DefaultDbEngine
Returns TRUE.
caseInsensitiveComparison() - Method in class net.sf.basedb.core.dbengine.MySQLEngine
Returns TRUE.
caseInsensitiveComparison() - Method in class net.sf.basedb.core.dbengine.PostgresDbEngine
Returns FALSE.
caseWhen(Expression, WhenStatement...) - Static method in class net.sf.basedb.core.query.Expressions
Create a conditional CASE-WHEN expression:
castToDate(String) - Method in class net.sf.basedb.core.dbengine.AbstractDbEngine
 
castToDate(String) - Method in interface net.sf.basedb.core.dbengine.DbEngine
Get a function that casts a date/timestamp to a date (eg. no time should be included in the result).
catalog - Variable in class net.sf.basedb.core.hibernate.SchemaExistsWork
 
catalog - Variable in class net.sf.basedb.core.hibernate.TableExistsWork
 
categories - Variable in class net.sf.basedb.core.data.AnnotationTypeData
 
categoryColumnMapping - Static variable in class net.sf.basedb.plugins.batchimport.AnnotationTypeImporter
Column mapping parameter for assigning annotation types to categories.
categoryMapper - Variable in class net.sf.basedb.plugins.batchimport.AnnotationTypeImporter
 
CdfFileReporterImporter - Class in net.sf.basedb.plugins
This plug-in can import probesets from Affymetrix CDF files as reporters.
CdfFileReporterImporter() - Constructor for class net.sf.basedb.plugins.CdfFileReporterImporter
Constructor should be empty.
CdfValidationAction - Class in net.sf.basedb.util.affymetrix
Action for validation of CDF files in a file set.
CdfValidationAction(DbControl, ArrayDesign) - Constructor for class net.sf.basedb.util.affymetrix.CdfValidationAction
Create a new action.
CdfValidationFactory - Class in net.sf.basedb.util.affymetrix
Action factory for creating CDF file validators.
CdfValidationFactory() - Constructor for class net.sf.basedb.util.affymetrix.CdfValidationFactory
 
CdfValidator - Class in net.sf.basedb.util.affymetrix
Helper class for working with Affymetrix CDF files.
CdfValidator() - Constructor for class net.sf.basedb.util.affymetrix.CdfValidator
Create a new instance.
Cell - Class in net.sf.basedb.clients.web.taglib.table
This tag defines a new cell in a row.
Cell() - Constructor for class net.sf.basedb.clients.web.taglib.table.Cell
 
cellClass - Variable in class net.sf.basedb.clients.web.extensions.list.AbstractListColumnBean
 
cellClass - Variable in class net.sf.basedb.clients.web.extensions.list.PropertyPathActionFactory
 
cellStyle - Variable in class net.sf.basedb.clients.web.extensions.list.AbstractListColumnBean
 
cellStyle - Variable in class net.sf.basedb.clients.web.extensions.list.PropertyPathActionFactory
 
CellStyleCreator - Class in net.sf.basedb.util.excel
Helper class for keeping track of formatting styles that has been created for given Excel worksheet.
CellStyleCreator(Workbook) - Constructor for class net.sf.basedb.util.excel.CellStyleCreator
Creates a new style creator for the given Excel workbook.
cellType - Variable in class net.sf.basedb.util.excel.XlsxToCsvUtil.CellTypeWithInfo
 
CellTypeWithInfo() - Constructor for class net.sf.basedb.util.excel.XlsxToCsvUtil.CellTypeWithInfo
 
CellValue - Class in net.sf.basedb.clients.web.taglib.table
This tag adds a value to a cell in a row.
CellValue() - Constructor for class net.sf.basedb.clients.web.taglib.table.CellValue
 
CelValidationAction - Class in net.sf.basedb.util.affymetrix
Action for validation of CEL files in a file set.
CelValidationAction(DbControl, RawBioAssay) - Constructor for class net.sf.basedb.util.affymetrix.CelValidationAction
Create a new action.
CelValidationFactory - Class in net.sf.basedb.util.affymetrix
Action factory for creating CEL file validators.
CelValidationFactory() - Constructor for class net.sf.basedb.util.affymetrix.CelValidationFactory
 
CelValidator - Class in net.sf.basedb.util.affymetrix
Helper class for working with Affymetrix CEL files.
CelValidator() - Constructor for class net.sf.basedb.util.affymetrix.CelValidator
Create a new instance.
cfg - Static variable in class net.sf.basedb.core.HibernateUtil
The Hibernate configuration, including all mappings.
CFResultIterator(SqlResultIterator, SqlResultIterator) - Constructor for class net.sf.basedb.clients.web.servlet.PlotServlet.CFResultIterator
 
CFSqlResult() - Constructor for class net.sf.basedb.clients.web.servlet.PlotServlet.CFSqlResult
 
ch - Variable in class net.sf.basedb.util.importer.spotdata.MatrixSpotIntensityEventHandler
 
ch - Variable in class net.sf.basedb.util.importer.spotdata.SerialSpotIntensityEventHandler
 
ch1 - Variable in class net.sf.basedb.plugins.LowessNormalization.SpotData
 
ch1 - Variable in class net.sf.basedb.plugins.MedianRatioNormalization.SpotData
 
ch2 - Variable in class net.sf.basedb.plugins.LowessNormalization.SpotData
 
ch2 - Variable in class net.sf.basedb.plugins.MedianRatioNormalization.SpotData
 
chain - Variable in class net.sf.basedb.util.AnnotationUtil.AnnotatableWrapper
 
chain - Variable in class net.sf.basedb.util.listable.SourceItemTransformerChain
 
CHAIN_ORDER - Static variable in class net.sf.basedb.core.SyncFilter
 
chained - Variable in class net.sf.basedb.core.Job.ProgressReporterImpl
 
ChainedFilter(List<QueryRuntimeFilter>) - Constructor for class net.sf.basedb.core.QueryRuntimeFilterFactory.ChainedFilter
Create a new ChainedFilter object.
ChainedFilter(QueryRuntimeFilter...) - Constructor for class net.sf.basedb.core.QueryRuntimeFilterFactory.ChainedFilter
Create a new ChainedFilter object.
chainedProgress - Variable in class net.sf.basedb.util.export.spotdata.BfsExporter
 
ChainedProgressReporter - Class in net.sf.basedb.util
An implementation of the ProgressReporter interface that chains to another progress reporter while recalculating the percentage values.
ChainedProgressReporter(ProgressReporter) - Constructor for class net.sf.basedb.util.ChainedProgressReporter
Create a new chained progress reporter.
Change(ChangeType) - Constructor for enum net.sf.basedb.core.AnnotationBatcher.Change
 
ChangeHistory - Class in net.sf.basedb.core
 
ChangeHistory(ChangeHistoryDetailData) - Constructor for class net.sf.basedb.core.ChangeHistory
 
CHANGEHISTORY - net.sf.basedb.core.Item
The item is a ChangeHistory entry.
CHANGEHISTORY_VALUES - net.sf.basedb.core.Item
Virtual item representing the new and old values column in ChangeHistory which need special access permissions.
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
 
ChangeHistoryUtil - Class in net.sf.basedb.clients.web
Utility class for working with change history.
ChangeHistoryUtil() - Constructor for class net.sf.basedb.clients.web.ChangeHistoryUtil
 
changeHost(URI) - Method in class net.sf.basedb.util.uri.ConnectionParameters
If the connection parameters include a specific host:port or root path a new URI is created were the host:port is replaced and the root path is added to the URI path.
changeInfo - Variable in class net.sf.basedb.core.data.ChangeHistoryDetailData
 
changeReferenceFactorAndOffset(double, double) - Method in class net.sf.basedb.core.Unit
Changes the factor and offset used for converting values in this unit into the reference unit.
changeReferenceFactorAndOffset(SessionControl, Session, UnitData, double, double) - Static method in class net.sf.basedb.core.Unit
 
changes - Variable in class net.sf.basedb.core.log.LoggingInterceptor
 
changeType - Variable in class net.sf.basedb.core.data.ChangeHistoryDetailData
 
changeType - Variable in class net.sf.basedb.core.log.EntityDetails
 
changeType - Variable in class net.sf.basedb.core.log.ManualLogEntry
 
ChangeType - Enum in net.sf.basedb.core.log
Enumeration that represents the type of change that has happened.
ChangeType(int, String) - Constructor for enum net.sf.basedb.core.log.ChangeType
 
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.
checkEntity(IdentifiableData) - Method in class net.sf.basedb.core.hibernate.EntityQueryWrapper
 
checkEntityArray(Object[]) - Method in class net.sf.basedb.core.hibernate.EntityQueryWrapper
 
checkEntityCollection(Collection<?>) - Method in class net.sf.basedb.core.hibernate.EntityQueryWrapper
 
checkExperimentArrayDesign(DbControl, OverviewContext, Node, ArrayDesign) - Method in class net.sf.basedb.util.overview.validator.ArrayDesignValidator
Check if an experiment has used more than one array design.
checkExtractOnBioAssay(DbControl, OverviewContext, Node, Node) - Method in class net.sf.basedb.util.overview.validator.ExtractValidator
 
checkExtractSubtype(DbControl, OverviewContext, Node, Node) - Static method in class net.sf.basedb.util.overview.validator.DerivedBioAssayValidator
Check the subtype of the extract that is the linked with a derived bioassay.
checkExtractSubtype(DbControl, OverviewContext, Node, Node) - Static method in class net.sf.basedb.util.overview.validator.PhysicalBioAssayValidator
Check the subtype of the extract that is the parent to a physical bioassay.
checkExtractTag(DbControl, OverviewContext, Node, Node) - Static method in class net.sf.basedb.util.overview.validator.ExtractValidator
Check the tag of the child extract in relation to a parent extract.
checkForInvalidNumberOperation() - Method in class net.sf.basedb.core.dbengine.AbstractDbEngine
Returns FALSE.
checkForInvalidNumberOperation() - Method in interface net.sf.basedb.core.dbengine.DbEngine
If we need to check for invalid arguments to numerical functions to avoid exceptions from the database.
checkForInvalidNumberOperation() - Method in class net.sf.basedb.core.dbengine.PostgresDbEngine
Returns TRUE.
checkForJobs() - Method in class net.sf.basedb.clients.jobagent.JobQueueChecker
 
checkForSignals() - Method in class net.sf.basedb.core.signal.EnhancedThreadSignalHandler
If at least one signal has been received a SignalReceivedException is thrown.
checkForSignals() - Method in class net.sf.basedb.core.signal.ProgressReporterSignalHandler
If at least one signal has been received a SignalReceivedException is thrown.
checkIfDifferent(Object, Unit) - Method in class net.sf.basedb.core.Annotation
Check if the given value is different from the values already stored in this annotation.
checkIfDifferent(List<?>, Unit) - Method in class net.sf.basedb.core.Annotation
Check if the given values are different from the values already stored in this annotation.
checkIfReportersExists(FusionCDFData, ReporterBatcher, boolean, ReporterType, ProgressReporter) - Method in class net.sf.basedb.util.affymetrix.CdfValidator
Verify if probesets in a CDF file exists as reporters and optionally create those that doesn't exists.
checkImportable(SessionControl, PluginDefinition, PluginConfiguration, File, String, GuiContext, Object) - Static method in class net.sf.basedb.util.AutoDetectFileFormat
 
checkInstallation(DbControl, Collection<PluginInfo>) - Static method in class net.sf.basedb.core.PluginDefinition
Check the installation status of the given list of plug-ins.
checkInternalJobQueue() - Method in class net.sf.basedb.core.InternalJobQueue
 
checkInterrupted() - Static method in class net.sf.basedb.core.signal.ThreadSignalHandler
Utility method to check if the current thread has been interrupted and (may) throw a SignalException if it has.
checkInterval - Variable in class net.sf.basedb.clients.jobagent.Agent
 
checkItemType(Item) - Method in class net.sf.basedb.core.ItemSubtype
Check if this subtype can be used on items of the given type.
checkJdbcDriver(String, String, String) - Static method in class net.sf.basedb.core.HibernateUtil
Check that a JDBC driver is registered and try to load a driver if not.
checkLine(int, String) - Method in class net.sf.basedb.util.charset.SimpleStringDetector
 
checkLine(int, String) - Method in interface net.sf.basedb.util.charset.StringDetector
Check the given line.
checkLocked(String) - Method in class net.sf.basedb.core.Application.StartupOptions
 
checkLocked(String) - Method in class net.sf.basedb.core.ServiceSessionControl.SessionFactoryConfiguration
Check that the
checkMagicNumber(PushbackInputStream, byte[]) - Static method in class net.sf.basedb.util.FileUtil
Take a peek at an input stream and check if the first few bytes matches the bCheck parameter.
checkManualMembersAllowed() - Method in class net.sf.basedb.core.ItemList
 
checkMax(int, String, int) - Static method in class net.sf.basedb.core.IntegerUtil
Check that an integer is equal or lower than a maximum value.
checkMd5 - Variable in class net.sf.basedb.core.File.UploadStream
If the md5 should be checked or not.
checkMemberType(Collection<ItemList>) - Method in class net.sf.basedb.core.ItemList
Checks that the lists have the same member type as this list.
checkMemberType(Item) - Method in class net.sf.basedb.core.ItemList
Checks if the other type is the same type as the member type of this list.
checkMin(int, String, int) - Static method in class net.sf.basedb.core.IntegerUtil
Check that an integer is equal or greater than a minimum value.
checkMinMax(int, String, int, int) - Static method in class net.sf.basedb.core.IntegerUtil
Check that an integer is equal or between a minimum and a maximum value.
checkModified() - Method in class net.sf.basedb.util.extensions.manager.ExtensionsFile
Check if the underlying file has been modified since it was last processed.
checkNext - Variable in class net.sf.basedb.core.DynamicResultIterator
 
checkNext - Variable in class net.sf.basedb.util.extensions.ActionIterator
 
checkNumberOfParameters(int) - Method in class net.sf.basedb.util.jep.ChannelFunction
 
checkNumberOfParameters(int) - Method in class net.sf.basedb.util.jep.ExtraValueFunction
 
checkNumberOfParameters(int) - Method in class net.sf.basedb.util.jep.FunctionSafeJep.UnknownFunction
 
checkNumberOfParameters(int) - Method in class net.sf.basedb.util.jep.InReporterListFunction
 
checkNumberOfParameters(int) - Method in class net.sf.basedb.util.jep.LeftFunction
 
checkNumberOfParameters(int) - Method in class net.sf.basedb.util.jep.Log2Function
 
checkNumberOfParameters(int) - Method in class net.sf.basedb.util.jep.MeanFunction
 
checkNumberOfParameters(int) - Method in class net.sf.basedb.util.jep.NotInReporterListFunction
 
checkNumberOfParameters(int) - Method in class net.sf.basedb.util.jep.PositionFunction
 
checkNumberOfParameters(int) - Method in class net.sf.basedb.util.jep.RawChannelFunction
 
checkNumberOfParameters(int) - Method in class net.sf.basedb.util.jep.RawFunction
 
checkNumberOfParameters(int) - Method in class net.sf.basedb.util.jep.ReporterFunction
 
checkNumberOfParameters(int) - Method in class net.sf.basedb.util.jep.ScoreFunction
 
checkNumberOfParameters(int) - Method in class net.sf.basedb.util.jep.SimpleJepFunction
 
checkNumberOfParameters(int) - Method in class net.sf.basedb.util.parser.ColFunction
 
checkNumberOfParameters(int) - Method in class net.sf.basedb.util.parser.DataNoFunction
 
checkNumberOfParameters(int) - Method in class net.sf.basedb.util.parser.DefaultItemFunction
 
checkNumberOfParameters(int) - Method in class net.sf.basedb.util.parser.LineNoFunction
 
checkParentBioSourceSubtype(DbControl, OverviewContext, Node, Node) - Static method in class net.sf.basedb.util.overview.validator.SampleValidator
Check the subtype of the biosurce that is the parent to a sample.
checkParentExtractSubtype(DbControl, OverviewContext, Node, Node) - Static method in class net.sf.basedb.util.overview.validator.ExtractValidator
Check the subtype of the extract that is the parent to another extract.
checkParentSampleSubtype(DbControl, OverviewContext, Node, Node) - Static method in class net.sf.basedb.util.overview.validator.ExtractValidator
Check the subtype of the sample that is the parent to an extract.
checkParentSampleSubtype(DbControl, OverviewContext, Node, Node) - Static method in class net.sf.basedb.util.overview.validator.SampleValidator
Check the subtype of the sample that is the parent to another sample.
checkPassword(String, String) - Static method in class net.sf.basedb.core.User
Check the plain-text password against the crypted password.
checkPermission(Permission) - Method in class net.sf.basedb.clients.web.extensions.ExtensionsControl
 
checkPermission(Permission) - Method in interface net.sf.basedb.core.AccessControlled
Check if the logged in user has the desired permission on the item, otherwise throw an exception.
checkPermission(Permission) - Method in class net.sf.basedb.core.BasicBatcher
Checks if the logged in user has the specified permission on this item.
checkPermission(Permission) - Method in class net.sf.basedb.core.BasicItem
Checks if the logged in user has the specified permission on this item.
checkPermission(Permission) - Method in class net.sf.basedb.core.BioMaterialEventSource
 
checkPermission(Permission) - Method in class net.sf.basedb.core.Coloring
 
checkPermission(Permission, String) - Method in class net.sf.basedb.clients.web.extensions.ExtensionsControl
For checking the permission and adding a custom message to the PermissionDeniedException if the required permission is missing.
checkPhysicalBioAssaySubtype(DbControl, OverviewContext, Node, Node) - Static method in class net.sf.basedb.util.overview.validator.DerivedBioAssayValidator
Check the subtype of the physical bioassay that is the parent to a derived bioassay.
checkpw(String, String) - Static method in class net.sf.basedb.util.bcrypt.BCrypt
Check that a plaintext password matches a previously hashed one
checkSameArrayDesign(Collection<RawBioAssay>, boolean) - Static method in class net.sf.basedb.util.IntensityCalculatorUtil
 
checkSuperclass - Variable in class net.sf.basedb.util.formatter.MultiFormatter
 
checkSyncFiltersAllowed() - Method in class net.sf.basedb.core.ItemList
 
checkTimeoutOnRemoteSlots() - Method in class net.sf.basedb.clients.jobagent.slotmanager.MasterSlotManager
Check the remote slots to see if they have timed out.
checkUniqueFields(String, String) - Method in class net.sf.basedb.plugins.executor.BaseFileExporterSupport
 
checkUniqueFields(String, String) - Method in class net.sf.basedb.plugins.executor.BfsExporterSupport
 
checkUnsafeScriptableUsage(Extension<?>) - Method in class net.sf.basedb.clients.web.extensions.ExtensionsControl
Checks if the given extension may violate the 'Content Security Policy' for the server.
checkUnsafeScriptableUsage(ExtensionsFile) - Method in class net.sf.basedb.clients.web.extensions.ExtensionsControl
Checks if the given extensions file contain any extensions that may violate the 'Content Security Policy' for the server.
checkUnsafeScriptableUsageInternal(Extension<?>) - Method in class net.sf.basedb.clients.web.extensions.ExtensionsControl
 
checkValues - Variable in class net.sf.basedb.core.ParameterType
 
child - Variable in class net.sf.basedb.clients.web.servlet.PlotServlet.CFResultIterator
 
child - Variable in class net.sf.basedb.clients.web.servlet.PlotServlet.CFSqlResult
 
child - Variable in class net.sf.basedb.core.QueryRuntimeFilterFactory.ChildFilter
The item type of the child item.
child - Variable in class net.sf.basedb.util.importer.spotdata.BaseFileInfo.ChildBioAssay
 
child - Variable in class net.sf.basedb.util.importer.spotdata.SecondPassSectionSpotsParser
 
CHILD_DESCRIPTION - Static variable in class net.sf.basedb.core.plugin.AbstractAnalysisPlugin
The name of the parameter that asks for the description of the child bioassay set.
CHILD_DESCRIPTION - Static variable in class net.sf.basedb.plugins.util.Parameters
The name of the parameter that asks is created by Parameters.childDescriptionParameter(String, String, String)
CHILD_NAME - Static variable in class net.sf.basedb.core.plugin.AbstractAnalysisPlugin
The name of the parameter that asks for the name of the child bioassay set.
CHILD_NAME - Static variable in class net.sf.basedb.plugins.util.Parameters
The name of the parameter that is created by Parameters.childNameParameter(String, String, String)
CHILD_TO_PARENT - net.sf.basedb.core.SyncFilter.SourceItemTransform
Source items are transformed to parent items.
CHILD_TO_PARENT - Static variable in class net.sf.basedb.util.listable.ToBioSourceSourceItemTransformerFactory
 
CHILD_TO_PARENT - Static variable in class net.sf.basedb.util.listable.ToDerivedBioAssaySourceItemTransformerFactory
 
CHILD_TO_PARENT - Static variable in class net.sf.basedb.util.listable.ToExtractSourceItemTransformerFactory
 
CHILD_TO_PARENT - Static variable in class net.sf.basedb.util.listable.ToPhysicalBioAssaySourceItemTransformerFactory
 
CHILD_TO_PARENT - Static variable in class net.sf.basedb.util.listable.ToRawBioAssaySourceItemTransformerFactory
 
CHILD_TO_PARENT - Static variable in class net.sf.basedb.util.listable.ToSampleSourceItemTransformerFactory
 
childAssays - Variable in class net.sf.basedb.util.importer.spotdata.BaseFileInfo
 
ChildBioAssay() - Constructor for class net.sf.basedb.util.importer.spotdata.BaseFileInfo.ChildBioAssay
Create a new object.
ChildBioAssay(int) - Constructor for class net.sf.basedb.util.importer.spotdata.BaseFileInfo.ChildBioAssay
Create a new object
childCreationEvents - Variable in class net.sf.basedb.core.data.BioMaterialData
 
childDescriptionParameter(String, String, String) - Static method in class net.sf.basedb.plugins.util.Parameters
Create a plugin parameter that asks for the description of the child bioassay set.
childErrors - Variable in class net.sf.basedb.util.overview.Node
 
ChildFilter(Item, Item) - Constructor for class net.sf.basedb.core.QueryRuntimeFilterFactory.ChildFilter
Create a new ChildFilter object.
childHasDifferentReporterPositionMapping - Variable in class net.sf.basedb.util.importer.spotdata.BaseFileInfo
 
childId - Variable in class net.sf.basedb.core.data.keyring.GroupGroups
 
ChildItem - Class in net.sf.basedb.core
An abstract base class for all items which are child items to a Shareable parent item.
ChildItem(BasicData) - Constructor for class net.sf.basedb.core.ChildItem
 
childIterator - Variable in class net.sf.basedb.util.Tree.EntryIterator
An iterator over the children of the root entry.
childNameParameter(String, String, String) - Static method in class net.sf.basedb.plugins.util.Parameters
Create a plugin parameter that asks for the name of the child bioassay set.
ChildNodeDirection - Enum in net.sf.basedb.util.overview.node
Represents the direction to use for loading child nodes in a tree.
ChildNodeDirection(boolean, boolean, boolean) - Constructor for enum net.sf.basedb.util.overview.node.ChildNodeDirection
 
ChildNodeLoaderAction - Interface in net.sf.basedb.util.overview.extensions
Load and create child nodes for a given parent node.
children - Variable in class net.sf.basedb.core.data.BioAssayData
 
children - Variable in class net.sf.basedb.core.data.BioMaterialData
 
children - Variable in class net.sf.basedb.core.data.DerivedBioAssayData
 
children - Variable in class net.sf.basedb.core.data.GroupData
 
children - Variable in class net.sf.basedb.core.data.PlateData
 
children - Variable in class net.sf.basedb.util.listable.CollectExtracts
 
children - Variable in class net.sf.basedb.util.overview.Node
 
children - Variable in class net.sf.basedb.util.Tree.Entry
 
childrenLoaded - Variable in class net.sf.basedb.util.overview.Node
 
childReporterPositions - Variable in class net.sf.basedb.util.importer.spotdata.BaseFileInfo
 
childToParent - Variable in class net.sf.basedb.util.listable.AbstractSourceItemTransformerFactory
 
childToParentChain(List<SourceItemTransformer>, Item, Item) - Static method in class net.sf.basedb.util.listable.ToExtractSourceItemTransformerFactory
Utility method for creating the transformer chain from child items up to extracts.
childWarnings - Variable in class net.sf.basedb.util.overview.Node
 
chIndex - Variable in class net.sf.basedb.util.importer.spotdata.MatrixSpotIntensityEventHandler
 
chIndex - Variable in class net.sf.basedb.util.importer.spotdata.SerialSpotIntensityEventHandler
 
chooseClientAlias(String[], Principal[], Socket) - Method in class net.sf.basedb.util.ssl.StaticKeyManager
 
chooseServerAlias(String, Principal[], Socket) - Method in class net.sf.basedb.util.ssl.StaticKeyManager
 
CIRCULAR_REFERENCE - Static variable in class net.sf.basedb.util.overview.Validator
Validator rule that checks for circular references among pooled items.
CircularRefInfo(DbControl, Identifiable) - Constructor for class net.sf.basedb.core.Trashcan.CircularRefInfo
 
city - Variable in class net.sf.basedb.util.GeoLocation
 
classes - Static variable in class net.sf.basedb.core.ExtendedProperties
A list with the name attribute of all classes found in the xml file.
classLoader - Variable in class net.sf.basedb.core.ServiceSessionControl.SessionFactoryConfiguration
 
classLoader - Variable in class net.sf.basedb.util.extensions.Registry.RegisteredExtension
 
classLoader - Variable in class net.sf.basedb.util.extensions.Registry.RegisteredExtensionPoint
 
classLoaders - Variable in class net.sf.basedb.util.extensions.xml.XmlLoader
 
classLoaders - Static variable in class net.sf.basedb.util.JarClassLoader
A map of all loaded class loaders.
ClassLocal<E> - Class in net.sf.basedb.util
This class is a similar to the JDK ThreadLocal class, but stores one object per class instead of one object per thread.
ClassLocal() - Constructor for class net.sf.basedb.util.ClassLocal
Create a new ClassLocal object.
ClassMapErrorHandler - Class in net.sf.basedb.util.error
Error handler that allows the registration of one or more error handler for subclasses to Throwable.
ClassMapErrorHandler(ErrorHandler) - Constructor for class net.sf.basedb.util.error.ClassMapErrorHandler
Create a new ClassMapErrorHandler.
classMetadata - Variable in class net.sf.basedb.core.Metadata
 
className - Variable in class net.sf.basedb.core.data.PluginDefinitionData
 
className - Variable in class net.sf.basedb.util.extensions.manager.PluginInfoKey
 
className - Variable in class net.sf.basedb.util.extensions.xml.PluginInfo
 
classNameToPath(String) - Method in class net.sf.basedb.util.JarClassLoader
Convert a class name to a file path.
classPath - Variable in class net.sf.basedb.util.JarClassLoader
Contains mappings from class names to the JAR file in which the class implementation can be found.
ClassUtil - Class in net.sf.basedb.util
Utility class for Class objects.
ClassUtil() - Constructor for class net.sf.basedb.util.ClassUtil
 
clazz - Variable in class net.sf.basedb.clients.web.extensions.list.AbstractListColumnBean
 
clazz - Variable in class net.sf.basedb.clients.web.extensions.list.PropertyPathActionFactory
 
clazz - Variable in class net.sf.basedb.clients.web.extensions.login.FieldInfo
 
clazz - Variable in class net.sf.basedb.clients.web.extensions.menu.FixedMenuItemFactory
 
clazz - Variable in class net.sf.basedb.clients.web.extensions.menu.MenuItemBean
 
clazz - Variable in class net.sf.basedb.clients.web.extensions.tabcontrol.FixedTabFactory
 
clazz - Variable in class net.sf.basedb.clients.web.extensions.tabcontrol.IncludeContentTabFactory
 
clazz - Variable in class net.sf.basedb.clients.web.extensions.tabcontrol.TabBean
 
clazz - Variable in class net.sf.basedb.clients.web.extensions.toolbar.ButtonBean
 
clazz - Variable in class net.sf.basedb.clients.web.extensions.toolbar.FixedButtonFactory
 
clazz - Variable in class net.sf.basedb.clients.web.taglib.ExceptionCatcher
 
clazz - Variable in class net.sf.basedb.clients.web.taglib.StylableTag
 
clazz - Variable in class net.sf.basedb.clients.web.taglib.tab.Tab
Optional class attribute.
clazz - Variable in class net.sf.basedb.clients.web.taglib.table.Cell
Optional class attribute
clazz - Variable in class net.sf.basedb.clients.web.taglib.table.CellValue
 
clazz - Variable in class net.sf.basedb.core.ExtendedPropertyAccessor.GetterSetter
 
clazz - Variable in class net.sf.basedb.core.Metadata.BasicItem2DataPropertyPath
 
clazz - Variable in class net.sf.basedb.core.Metadata
 
clazz - Variable in class net.sf.basedb.core.Metadata.NoopPropertyPath
 
clazz - Variable in class net.sf.basedb.core.ParameterType
The class of allowed parameter values.
clazz - Variable in class net.sf.basedb.core.QueryExecutor.FutureItem
 
clazz - Variable in class net.sf.basedb.util.extensions.events.ActionClassEventFilter
 
clazz - Variable in class net.sf.basedb.util.filter.InstanceOfFilter
 
clean() - Method in class net.sf.basedb.util.listable.TransformCache
 
cleanable - Variable in class net.sf.basedb.core.DbControl.State
 
cleanable - Variable in class net.sf.basedb.util.StaticCache.LockSafeInputStream
 
cleanable - Variable in class net.sf.basedb.util.StaticCache.LockSafeOutputStream
 
cleanContextFromProperty(Session, Item, String, String, boolean) - Static method in class net.sf.basedb.core.Update
 
cleaner - Static variable in class net.sf.basedb.core.Application
For keeping track of objects that need to be cleaned up.
cleanSessionControlCache(boolean) - Static method in class net.sf.basedb.core.Application
Clean the cache from unused SessionControl objects.
cleanUp() - Method in class net.sf.basedb.core.DbControl
Clear and close all objects.
cleanUp(FileFilter) - Method in class net.sf.basedb.util.StaticCache
Remove all files that matches the specified filter from the cache.
cleanupProjectSpecificAnnotations() - Static method in class net.sf.basedb.core.ProjectSpecificAnnotationsManager
Delete project-specific annotations that belong to projects that no longer exists.
cleanUpTask(FileFilter) - Method in class net.sf.basedb.util.StaticCache
Creates a task that cleans up this cache when it is executed.
CleanupTask(StaticCache, FileFilter) - Constructor for class net.sf.basedb.util.StaticCache.CleanupTask
 
clear() - Method in class net.sf.basedb.core.AbstractResultList
Not supported.
clear() - Method in class net.sf.basedb.core.hibernate.SessionWrapper
 
clear() - Method in class net.sf.basedb.core.snapshot.SnapshotManager
Clear the manager from all memory-cached information.
clear() - Method in class net.sf.basedb.core.UnmodifiableResultList
Not supported.
clear() - Method in class net.sf.basedb.util.AnnotationUtil.Cache
Clear all information from the cache.
clear() - Method in class net.sf.basedb.util.formatter.LookupFormatter
Remove all registered lookup entries.
clear() - Method in class net.sf.basedb.util.Tree
Clear all elements except the root element.
clear(Session) - Static method in class net.sf.basedb.core.HibernateUtil
Clear the session of cached objects.
clearAllRecent() - Method in class net.sf.basedb.core.ItemContext
Clear all recently used values lists.
clearDbControlCache() - Method in class net.sf.basedb.core.SessionControl
 
clearError() - Method in class net.sf.basedb.util.extensions.ActionIterator
Clear any error that has been registered for the current action.
clearError() - Method in class net.sf.basedb.util.extensions.ExtensionContext
 
clearError() - Method in class net.sf.basedb.util.extensions.ExtensionPointContext
 
clearError() - Method in class net.sf.basedb.util.extensions.InvokationContext
Clear the registered error for the current extension or extension point.
clearError() - Method in class net.sf.basedb.util.extensions.Registry.RegisteredExtension
 
clearError() - Method in class net.sf.basedb.util.extensions.Registry.RegisteredExtensionPoint
 
clearErrorList(JEP) - Static method in class net.sf.basedb.util.jep.Jep
This is a workaround for a bug in the JEP error handling.
clearErrors - Variable in class net.sf.basedb.util.extensions.ExtensionsInvoker
 
clearExecuteCommand() - Method in class net.sf.basedb.core.Job
Reset the currently stored execution command to force a plug-in to restart from the beginning instead of at the stored breakpoint.
clearFailures() - Method in class net.sf.basedb.util.overview.Node
Clear all warnings, errors on this node and on all child nodes.
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.plugins.HelpImporter
 
Client - Class in net.sf.basedb.core
This class represents a registered client application.
Client(ClientData) - Constructor for class net.sf.basedb.core.Client
 
CLIENT - net.sf.basedb.core.Item
The item is an Client.
CLIENT_RUNTIME_FILTER - Static variable in class net.sf.basedb.core.UserClientSetting
This filter will only return items if the logged in user has generic read permission to clients.
clientCertificate - Variable in class net.sf.basedb.core.data.FileServerData
 
clientCertificate - Variable in class net.sf.basedb.util.uri.ConnectionParameters
 
clientCertificatePassword - Variable in class net.sf.basedb.util.uri.ConnectionParameters
 
clientContext - Variable in class net.sf.basedb.util.extensions.ExtensionPointContext
 
ClientContext - Class in net.sf.basedb.util.extensions
Keeps information about the current context in the client application that extensions can use to decide what actions to generate.
ClientContext() - Constructor for class net.sf.basedb.util.extensions.ClientContext
Create a new context with no session or current item.
ClientContext(DbControl) - Constructor for class net.sf.basedb.util.extensions.ClientContext
Create a new context with a DbControl.
ClientContext(DbControl, Object) - Constructor for class net.sf.basedb.util.extensions.ClientContext
Create a new context with a DbControl and item.
ClientContext(SessionControl) - Constructor for class net.sf.basedb.util.extensions.ClientContext
Create a new context with a session and no DbControl.
ClientContext(SessionControl, Object) - Constructor for class net.sf.basedb.util.extensions.ClientContext
Create a new context with a session and item but no DbControl.
ClientContext(SessionControl, DbControl, Object) - Constructor for class net.sf.basedb.util.extensions.ClientContext
 
ClientData - Class in net.sf.basedb.core.data
This class holds information about a client.
ClientData() - Constructor for class net.sf.basedb.core.data.ClientData
 
ClientDefaultSetting - Class in net.sf.basedb.core
This class is used to represent a setting for specific client application.
ClientDefaultSetting(ClientDefaultSettingData) - Constructor for class net.sf.basedb.core.ClientDefaultSetting
 
CLIENTDEFAULTSETTING - net.sf.basedb.core.Item
The item is an ClientDefaultSetting.
ClientDefaultSettingData - Class in net.sf.basedb.core.data
 
ClientDefaultSettingData() - Constructor for class net.sf.basedb.core.data.ClientDefaultSettingData
 
clientDefaultSettings - Variable in class net.sf.basedb.core.SessionControl
Stores name and value from ClientDefaultSettingData.
clientId - Variable in class net.sf.basedb.core.data.ChangeHistoryData
 
clientId - Variable in class net.sf.basedb.core.log.TransactionDetails
 
clientId - Variable in class net.sf.basedb.core.SessionControl
The id of the ClientData. 0 = no client
clientItem - Static variable in class net.sf.basedb.plugins.HelpExporter
 
clientItem - Static variable in class net.sf.basedb.plugins.HelpImporter
 
clientParameter - Variable in class net.sf.basedb.plugins.HelpExporter
 
clientParameter - Variable in class net.sf.basedb.plugins.HelpImporter
 
clientPassword - Variable in class net.sf.basedb.core.data.FileServerData
 
clientSettings - Variable in class net.sf.basedb.core.data.UserData
 
clientType - Variable in class net.sf.basedb.plugins.HelpExporter
 
clonableProperty(ClonableProperty) - Static method in class net.sf.basedb.core.VirtualColumn
Get a virtual column view of a cloned reporter property.
ClonableProperty - Class in net.sf.basedb.core
Represents a reporter property that can be cloned to a per-experiment table in the dynamic database.
ClonableProperty(String, String, String, String, Type, int, boolean, Formula.AverageMethod, boolean) - Constructor for class net.sf.basedb.core.ClonableProperty
Create a cloned property representation of a static property.
ClonableProperty(String, ReporterClonePropertyData) - Constructor for class net.sf.basedb.core.ClonableProperty
Create a cloned property representation of a data-layer object.
ClonableProperty(ExtendedProperty) - Constructor for class net.sf.basedb.core.ClonableProperty
Create a cloned property representation of an extended property
ClonableReporterQuery - Interface in net.sf.basedb.core
An interface that indicates that a query may be used together with cloned reporter information.
CLONAL_AMPLIFICATION - Static variable in class net.sf.basedb.core.PhysicalBioAssay
The id for the PhysicalBioAssayType item representing a flow cell.
clone - Variable in class net.sf.basedb.util.annotations.InheritSpecification
 
cloneCachedNode(Object, Node, ChildNodeDirection) - Method in class net.sf.basedb.util.overview.node.NodeFactory
Clones a cached node if the current context supports caching and another node with the given cache key already exists.
CLONED - net.sf.basedb.core.Annotation.Source
The annotation is an inherited annotation with a local copy of the values at the time the copy was made.
CLONED_REPORTERS - net.sf.basedb.core.VirtualTable
Table that holds cloned reporter information for an experiment.
cloneParameter(PluginParameter<T>, T) - Static method in class net.sf.basedb.plugins.util.Parameters
Clone a plug-in parameter but give it a different default value.
cloneParameterWithDefaultValue(PluginParameter<T>) - Method in class net.sf.basedb.core.plugin.AbstractPlugin
Clone a plug-in parameter and set the default value to the value that is already stored in the job or configuration parameters.
cloneReporters(ReporterCloneBatcher.CloneSource, ReporterCloneTemplate, ProgressReporter) - Method in class net.sf.basedb.core.ReporterCloneBatcher
Create a reporter clone table in the dynamic database for this experiment and populate it with the current reporter annotations for all reporters that are part of the experiment.
CloneReportersPlugin - Class in net.sf.basedb.plugins
A plug-in that clone reporter annotations to an experiment.
CloneReportersPlugin() - Constructor for class net.sf.basedb.plugins.CloneReportersPlugin
 
CloneSource() - Constructor for enum net.sf.basedb.core.ReporterCloneBatcher.CloneSource
 
close() - Method in class net.sf.basedb.clients.jobagent.executors.DummyJobExecutor
 
close() - Method in class net.sf.basedb.clients.jobagent.executors.ProcessJobExecutor
 
close() - Method in class net.sf.basedb.clients.jobagent.executors.ThreadJobExecutor
 
close() - Method in class net.sf.basedb.clients.jobagent.handlers.AbstractCustomRequestHandler
 
close() - Method in interface net.sf.basedb.clients.jobagent.handlers.CustomRequestHandler
This method is called at when the agent is stopped.
close() - Method in class net.sf.basedb.clients.jobagent.handlers.MultiProtocolRequestHandler
Close this handler.
close() - Method in interface net.sf.basedb.clients.jobagent.JobExecutor
This method is called at when the agent is stopped or paused.
close() - Method in class net.sf.basedb.clients.jobagent.slotmanager.InternalSlotManager
 
close() - Method in class net.sf.basedb.clients.jobagent.slotmanager.MasterSlotManager
 
close() - Method in class net.sf.basedb.clients.jobagent.slotmanager.RemoteSlotManager
 
close() - Method in interface net.sf.basedb.clients.jobagent.slotmanager.SlotManager
This method is called when the job agent is shutting down.
close() - Static method in class net.sf.basedb.clients.web.extensions.ExtensionsControl
Shut down the extensions system.
close() - Method in class net.sf.basedb.clients.web.extensions.list.RelatedItemHelper
 
close() - Static method in class net.sf.basedb.clients.web.extensions.service.Services
Stop all services.
close() - Method in class net.sf.basedb.clients.web.plugins.PlainTextTemplate
Do nothing.
close() - Method in class net.sf.basedb.clients.web.plugins.XlsxTemplate
Dispose and close workbook.
close() - Method in class net.sf.basedb.clients.web.plugins.XMLTemplate
Do nothing.
close() - Method in class net.sf.basedb.clients.web.servlet.PlotServlet.CFResultIterator
 
close() - Method in class net.sf.basedb.core.AbstractBatcher
 
close() - Method in class net.sf.basedb.core.AnnotationBatcher.InsertBatcher
Close the batcher.
close() - Method in class net.sf.basedb.core.AnnotationBatcher.UpdateBatcher
Close the batcher.
close() - Method in interface net.sf.basedb.core.Batcher
Flush the batcher and close it.
close() - Method in class net.sf.basedb.core.DataResultIterator
From the ResultIterator interface ---------------------------------
close() - Method in class net.sf.basedb.core.DbControl
Close the connection to the database.
close() - Method in class net.sf.basedb.core.DynamicResultIterator
From the ResultIterator interface ---------------------------------
close() - Method in class net.sf.basedb.core.File.CharsetTesterThread
The file has been uploaded.
close() - Method in class net.sf.basedb.core.File.UploadStream
Close the stream and register the size and location with the file item.
close() - Method in class net.sf.basedb.core.hibernate.SessionWrapper
 
close() - Method in class net.sf.basedb.core.hibernate.StatelessSessionWrapper
 
close() - Method in class net.sf.basedb.core.InternalJobQueue
Cleanup
close() - Method in class net.sf.basedb.core.ItemResultIterator
From the ResultIterator interface ---------------------------------
close() - Method in class net.sf.basedb.core.plugin.ExportOutputStream
 
close() - Method in interface net.sf.basedb.core.query.ResultIterator
Close the iterator and immediately release all resources associated with it.
close() - Method in class net.sf.basedb.core.ReporterScoreResultIterator
From the ResultIterator interface ---------------------------------
close() - Method in class net.sf.basedb.core.ScrollIterator
Close the results and return resources.
close() - Method in class net.sf.basedb.core.SessionControl
Close this session control so it can't be used again.
close() - Method in class net.sf.basedb.util.bfs.AnnotationParser
 
close() - Method in interface net.sf.basedb.util.bfs.BfsParser
Close the parser and relase underlying system resources that are associated with it.
close() - Method in class net.sf.basedb.util.bfs.DataParser
 
close() - Method in class net.sf.basedb.util.bfs.MetadataParser
 
close() - Method in class net.sf.basedb.util.excel.XlsxTableWriter
Closes the workbook unless it was supplied in the constructor from an external source.
close() - Method in class net.sf.basedb.util.excel.XlsxToCsvUtil
Closes the current workbook.
close() - Method in class net.sf.basedb.util.excel.XlsxToCsvUtil.WorkbookStream
 
close() - Method in class net.sf.basedb.util.extensions.manager.ExtensionsFile.WriteableExtensionsFile
Close the writeable file.
close() - Method in class net.sf.basedb.util.gtf.GtfInputStream
 
close() - Method in class net.sf.basedb.util.importer.spotdata.SynchronizedSpotDataParser
 
close() - Method in class net.sf.basedb.util.InputStreamCombiner
Closes all underlying streams.
close() - Method in class net.sf.basedb.util.InputStreamSplitter
 
close() - Method in class net.sf.basedb.util.InputStreamTracker
 
close() - Method in class net.sf.basedb.util.jobagent.JobAgentConnection
Close the connection to the job agent.
close() - Method in class net.sf.basedb.util.jobagent.JobAgentServerConnection
Stop listening for incoming connections.
close() - Method in class net.sf.basedb.util.StaticCache.LockSafeInputStream
 
close() - Method in class net.sf.basedb.util.StaticCache.LockSafeOutputStream
 
close() - Method in class net.sf.basedb.util.StreamCacher
Close the master stream and remove the cached file data.
close() - Method in class net.sf.basedb.util.uri.CloseResourceInputStream
Make sure the client connection manager is closed when the file has been completely downloaded.
close() - Method in class net.sf.basedb.util.zip.Bzip2FilePacker
Finish the BZIP stream.
close() - Method in interface net.sf.basedb.util.zip.FilePacker
End the packing and close.
close() - Method in class net.sf.basedb.util.zip.GzipFilePacker
Finish the GZIP stream.
close() - Method in class net.sf.basedb.util.zip.TarFilePacker
Finish the TAR file.
close() - Method in class net.sf.basedb.util.zip.ZipFilePacker
Finish the ZIP file.
close(int) - Method in class net.sf.basedb.clients.web.util.SimpleSignalProgressReporter
 
close(int) - Method in class net.sf.basedb.core.signal.AbstractSignalReceiver
Close this signal receiver.
close(int) - Method in class net.sf.basedb.core.signal.LocalSignalReceiver
 
close(int) - Method in interface net.sf.basedb.core.signal.SignalReceiver
Close the receiver.
close(int) - Method in class net.sf.basedb.core.signal.SocketSignalReceiver
Close this receiver and the socket it is listening on.
close(Closeable) - Static method in class net.sf.basedb.util.FileUtil
Close a Closeable without throwing an exception.
close(InputStream) - Static method in class net.sf.basedb.util.FileUtil
Close an input stream without throwing an exception.
close(InputStream) - Static method in class net.sf.basedb.util.SocketUtil
Close an InputStream without throwing any exceptions.
close(OutputStream) - Static method in class net.sf.basedb.util.FileUtil
Close an output stream without throwing an exception.
close(Reader) - Static method in class net.sf.basedb.util.SocketUtil
Close a Reader without throwing any exceptions.
close(Writer) - Static method in class net.sf.basedb.util.SocketUtil
Close a Writer without throwing any exceptions.
close(AutoCloseable) - Static method in class net.sf.basedb.util.FileUtil
Close a AutoCloseable without throwing an exception.
close(ServerSocket) - Static method in class net.sf.basedb.util.SocketUtil
Close a server socket without throwing any exceptions.
close(Socket) - Static method in class net.sf.basedb.util.SocketUtil
Close a socket without throwing any exceptions.
close(ServerSocketChannel) - Static method in class net.sf.basedb.util.SocketUtil
Close a server socket channel without throwing any exceptions.
close(Session) - Static method in class net.sf.basedb.core.HibernateUtil
Close a session.
close(StatelessSession) - Static method in class net.sf.basedb.core.HibernateUtil
Close a statless session.
closed - Variable in class net.sf.basedb.core.File.UploadStream
If this file closed or not.
closed - Variable in class net.sf.basedb.core.SessionControl
If the session control has been closed it can no longer be used.
closed - Variable in class net.sf.basedb.util.StaticCache.LockSafeInputStream
 
closed - Variable in class net.sf.basedb.util.StaticCache.LockSafeOutputStream
 
closeJobExecutor() - Method in class net.sf.basedb.clients.jobagent.Agent
Close the job executor.
closeJobQueueChecker() - Method in class net.sf.basedb.clients.jobagent.Agent
Close the job queue checker.
closeLogFile() - Method in class net.sf.basedb.core.plugin.AbstractPlugin
Close the log file created by AbstractPlugin.createLogFile(String).
CloseMyDbControl(RelatedItemHelper) - Constructor for class net.sf.basedb.clients.web.extensions.list.RelatedItemHelper.CloseMyDbControl
 
CloseResourceInputStream - Class in net.sf.basedb.util.uri
Inputstream filter that closes a given resource whenever the parent input stream is closed.
CloseResourceInputStream(InputStream, Closeable) - Constructor for class net.sf.basedb.util.uri.CloseResourceInputStream
Create a new stream.
closeResultSet(ResultSet, String) - Method in class net.sf.basedb.core.AbstractSqlQuery
Close the result set without throwing an exception.
closeServer() - Method in class net.sf.basedb.clients.jobagent.Agent
Close the service listener.
closeSlotManager() - Method in class net.sf.basedb.clients.jobagent.Agent
Close the slot manager.
closeStatement(Statement, String) - Method in class net.sf.basedb.core.AbstractSqlQuery
Close the statement without throwing an exception.
closeTimeout - Variable in class net.sf.basedb.clients.jobagent.Agent
Timeout to wait for jobs to act on the ABORT signal when stopping.
closeTimeout - Variable in class net.sf.basedb.core.InternalJobQueue
Timeout to wait for jobs to act on the ABORT signal when shutting down BASE.
CLUSTER_GENERATION - Static variable in class net.sf.basedb.core.Kit
The ID for the cluster generation (in a flow cell) kit type, for example a protocol used when creating a PhysicalBioAssay.
CLUSTER_GENERATION - Static variable in class net.sf.basedb.core.Protocol
The ID for the cluster generation (in a flow cell) protocol type, for example a protocol used when creating a PhysicalBioAssay.
CLUSTER_GENERATOR - Static variable in class net.sf.basedb.core.Hardware
The id for the HardwareType object representing a cluster generator station.
cmap - Variable in class net.sf.basedb.util.AnnotationUtil.Cache
 
cmd - Variable in class net.sf.basedb.clients.jobagent.CmdLine
 
CmdLine - Class in net.sf.basedb.clients.jobagent
Utility class for parsing command line arguments.
CmdLine(String[]) - Constructor for class net.sf.basedb.clients.jobagent.CmdLine
Create a new object for parsing the command line.
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
 
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
 
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.
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
 
COLLECTION_SEPARATOR - Static variable in class net.sf.basedb.clients.web.plugins.SimpleExport
 
CollectionFormatter<I> - Class in net.sf.basedb.util.formatter
Formatter implementation that formats a collection of values to a string by concatenating the values with a given separator.
CollectionFormatter(String, boolean, Formatter<? super I>) - Constructor for class net.sf.basedb.util.formatter.CollectionFormatter
 
CollectionFormatter(Formatter<? super I>) - Constructor for class net.sf.basedb.util.formatter.CollectionFormatter
Create a collection formatting using ", " as separator and skipping null values.
CollectionPropertyPath(Type) - Constructor for class net.sf.basedb.core.Metadata.CollectionPropertyPath
 
collections - Variable in class net.sf.basedb.util.NestedIterator
The array to iterate.
collectionSeparator - Variable in class net.sf.basedb.clients.web.plugins.PlainTextTemplate
 
collectionSeparator - Variable in class net.sf.basedb.clients.web.plugins.XlsxTemplate
 
CollectionTransformer<S,​D> - Interface in net.sf.basedb.util.collections
Allows a collection to be transformed by applying some operation to it.
CollectParents(boolean, boolean) - Constructor for class net.sf.basedb.util.listable.CollectExtracts.CollectParents
 
collectParentsOfCollected(boolean) - Method in class net.sf.basedb.util.listable.CollectExtracts
The created transformer collect the ID:s of all parent extracts to the already collected extracts and store them in the CollectExtracts.getCollectedParents().
collectParentsOfSource(boolean) - Method in class net.sf.basedb.util.listable.CollectExtracts
The created transformer collect the ID:s of all parent extracts to the source extracts and store them in the CollectExtracts.getCollectedParents().
CollectSqlTarget() - Constructor for class net.sf.basedb.core.hibernate.SchemaGenerator.CollectSqlTarget
 
CollectSqlTarget(DbEngine, Dialect, SchemaGenerator.Mode, Connection) - Constructor for class net.sf.basedb.core.hibernate.SchemaGenerator.CollectSqlTarget
 
colNo - Variable in class net.sf.basedb.util.excel.XlsxTableWriter
 
colNum - Variable in class net.sf.basedb.clients.web.plugins.PlainTextTemplate
 
colNum - Variable in class net.sf.basedb.clients.web.plugins.XlsxTemplate
 
colOffset - Variable in class net.sf.basedb.util.parser.FlatFileParser.ExcelData
 
color - Variable in class net.sf.basedb.clients.web.ExperimentExplorer.AnnotationGroup
 
ColorFormatter - Class in net.sf.basedb.clients.web.formatter
Formatter that adds a small colored box next to a value.
ColorFormatter(ColorGenerator, Formatter<Number>) - Constructor for class net.sf.basedb.clients.web.formatter.ColorFormatter
Create a new color formatter.
colorGen - Variable in class net.sf.basedb.clients.web.formatter.ColorFormatter
 
ColorGenerator - Class in net.sf.basedb.util
This class is used to generate colors for numerical values.
ColorGenerator(Color, Color, Color, float, float, float, boolean) - Constructor for class net.sf.basedb.util.ColorGenerator
Create a new color generator.
coloring - Variable in class net.sf.basedb.core.data.ExtraValueTypeData
 
coloring - Variable in class net.sf.basedb.core.data.FormulaData
 
coloring - Variable in class net.sf.basedb.core.ExtraValueType
 
coloring - Variable in class net.sf.basedb.core.Formula
 
Coloring - Class in net.sf.basedb.core
This class keeps coloring information for items which can be colored when values are displayed in a client application.
Coloring() - Constructor for class net.sf.basedb.core.Coloring
Create a new independent coloring object.
Coloring(ColoringData, AccessControlled) - Constructor for class net.sf.basedb.core.Coloring
Create Coloring object which links to an existing item.
ColoringData - Class in net.sf.basedb.core.data
Hold coloring information.
ColoringData() - Constructor for class net.sf.basedb.core.data.ColoringData
 
ColoringData(boolean, boolean, Float, Float, Float) - Constructor for class net.sf.basedb.core.data.ColoringData
 
COLORS - Static variable in class net.sf.basedb.clients.web.ExperimentExplorer
Predefined colors for annotation groups
colspan - Variable in class net.sf.basedb.clients.web.taglib.table.Header
 
column - Variable in class net.sf.basedb.clients.web.extensions.list.ListColumnDataLoader
 
column - Variable in class net.sf.basedb.core.data.BioWellData
 
column - Variable in class net.sf.basedb.core.data.FeatureData
 
column - Variable in class net.sf.basedb.core.data.MappingCoordinate
The column number.
column - Variable in class net.sf.basedb.core.data.PlateCoordinate
The column number.
column - Variable in class net.sf.basedb.core.data.RawData
 
column - Variable in class net.sf.basedb.core.data.ReporterClonePropertyData
 
column - Variable in class net.sf.basedb.core.data.WellData
 
column - Variable in class net.sf.basedb.core.DynamicRestriction
 
column - Variable in class net.sf.basedb.core.ExtendedProperty
 
column - Variable in class net.sf.basedb.core.ExtraValueExpression
 
column - Variable in class net.sf.basedb.core.FeatureCoordinate
The column of this feature.
column - Variable in class net.sf.basedb.core.query.SqlColumnExpression
 
column - Variable in class net.sf.basedb.core.query.VirtualColumnExpression
 
column - Variable in class net.sf.basedb.core.RawBioAssayPropertyExpression
 
column - Variable in class net.sf.basedb.core.ReporterPropertyExpression
 
column - Variable in class net.sf.basedb.core.VirtualColumn
The column name in the database of the column.
column - Variable in class net.sf.basedb.plugins.LowessNormalization.SpotData
 
column(VirtualColumn) - Static method in class net.sf.basedb.core.query.Dynamic
Create an expression representing a column in the root table: expression = rootAlias.columnName.
column(VirtualTable, VirtualColumn) - Static method in class net.sf.basedb.core.query.Dynamic
Create an expression representing a column in a table: expression = tableAlias.columnName.
COLUMN - net.sf.basedb.core.ExtraValue.CoordinateType
The extra values are attached to column coordinates only.
COLUMN - net.sf.basedb.core.VirtualTable
Table that maps columns coordinates in a data cube to raw bioassays.
COLUMN - Static variable in class net.sf.basedb.core.VirtualColumn
This column stores the data cube column coordinate.
COLUMN_EXPRESSION - net.sf.basedb.core.Formula.Type
An arbitrary expression that specify one formula only.
COLUMN_EXTRA_FLOAT - net.sf.basedb.core.VirtualTable
Table that stores float column extra values.
COLUMN_EXTRA_INT - net.sf.basedb.core.VirtualTable
Table that stores integer column extra values.
COLUMN_EXTRA_STRING - net.sf.basedb.core.VirtualTable
Table that stores string column extra values.
COLUMN_PREFIX - Static variable in class net.sf.basedb.clients.web.plugins.SimpleExport
 
COLUMN_RESTRICTION - net.sf.basedb.core.Formula.Type
An arbitraty expression that specify one formula only.
columnColumnMapping - Static variable in class net.sf.basedb.plugins.PlateFlatFileImporter
 
columnColumnMapping - Static variable in class net.sf.basedb.plugins.RawDataFlatFileImporter
 
columnColumnMapping - Static variable in class net.sf.basedb.plugins.ReporterMapFlatFileImporter
 
columnContent - Variable in class net.sf.basedb.clients.web.taglib.table.Table
 
columnCount - Variable in class net.sf.basedb.util.bfs.AnnotationWriter
 
columnCount - Variable in class net.sf.basedb.util.bfs.DataWriter
 
ColumnDef - Class in net.sf.basedb.clients.web.taglib.table
This tag defines a column in the table.
ColumnDef() - Constructor for class net.sf.basedb.clients.web.taglib.table.ColumnDef
 
ColumnDef.NullIterator<A,​B> - Class in net.sf.basedb.clients.web.taglib.table
Iterator implementation that returns a single null value and nothing more.
columnFilter - Variable in class net.sf.basedb.clients.web.taglib.table.Table
 
columnFormatter - Variable in class net.sf.basedb.clients.web.taglib.table.Table
 
columnHeaders - Variable in class net.sf.basedb.plugins.AnnotationFlatFileImporter
 
columnHeaders - Variable in class net.sf.basedb.util.parser.ColFunction
 
columnHeaders - Variable in class net.sf.basedb.util.parser.FlatFileParser
List of the column names found by splitting the data header using the data splitter regexp.
ColumnHeaders - Class in net.sf.basedb.clients.web.taglib.table
Generate column headers for the columns that has been defined for this table.
ColumnHeaders() - Constructor for class net.sf.basedb.clients.web.taglib.table.ColumnHeaders
 
columnId - Variable in class net.sf.basedb.clients.web.taglib.table.Cell
The ID of the column to which this cell belongs.
columnIndex - Variable in class net.sf.basedb.util.bfs.AnnotationModel
 
ColumnInfo(String, String, Integer, int, boolean, boolean) - Constructor for class net.sf.basedb.core.dbengine.TableInfo.ColumnInfo
Create a new ColumnInfo object.
ColumnKey(Comparable<?>, String) - Constructor for class net.sf.basedb.clients.web.servlet.ExperimentExplorerPlotServlet.ColumnKey
 
columnMapper - Variable in class net.sf.basedb.plugins.PlateFlatFileImporter
 
columnMapper - Variable in class net.sf.basedb.plugins.RawDataFlatFileImporter
 
columnMapper - Variable in class net.sf.basedb.plugins.ReporterMapFlatFileImporter
 
ColumnMapper - Class in net.sf.basedb.util.parser
Returns the string found in the column given by the index set in the constructor.
ColumnMapper(int, String) - Constructor for class net.sf.basedb.util.parser.ColumnMapper
Create a new column mapper.
ColumnMapper(int, String, NumberFormat, boolean) - Constructor for class net.sf.basedb.util.parser.ColumnMapper
ColumnMapper(int, String, NumberFormat, Formatter<Date>, boolean) - Constructor for class net.sf.basedb.util.parser.ColumnMapper
Create a new column mapper using a specific number or date format.
columnMappingParameterName - Variable in class net.sf.basedb.plugins.batchimport.PropertyIdMethod
 
columnName - Variable in class net.sf.basedb.core.Update.DropColumnChange
 
columnNo - Variable in class net.sf.basedb.core.data.DataCubeColumnData
 
columns - Variable in class net.sf.basedb.clients.web.taglib.table.Table
Which columns that should be visible and their order
columns - Variable in class net.sf.basedb.core.data.DataCubeData
 
columns - Variable in class net.sf.basedb.core.data.PlateGeometryData
 
columns - Variable in class net.sf.basedb.core.dbengine.TableInfo
 
columns - Variable in class net.sf.basedb.core.dbengine.TableInfo.IndexInfo
 
columns - Variable in class net.sf.basedb.core.dbengine.TableInfo.PrimaryKeyInfo
 
columns - Variable in class net.sf.basedb.core.ExtraValueJoin
 
columns - Variable in enum net.sf.basedb.core.VirtualTable
The columns in the table.
columns() - Method in class net.sf.basedb.util.parser.FlatFileParser.Data
The number of columns as determined by the FlatFileParser.setDataSplitterRegexp(Pattern) regular expression.
columnSeparator - Variable in class net.sf.basedb.util.excel.XlsxToCsvUtil
 
columnSubtitle - Variable in class net.sf.basedb.clients.web.taglib.table.Table
 
ColumnSubtitles - Class in net.sf.basedb.clients.web.taglib.table
Generate column subtitle header for the columns that has been defined for this table.
ColumnSubtitles() - Constructor for class net.sf.basedb.clients.web.taglib.table.ColumnSubtitles
 
CombinedPropertyPath(List<Metadata.PropertyPath>) - Constructor for class net.sf.basedb.core.Metadata.CombinedPropertyPath
 
CombiningEventFilter - Class in net.sf.basedb.util.extensions.events
Event filter that only passes on events based on multiple other event filters.
CombiningEventFilter(Collection<EventFilter>, boolean) - Constructor for class net.sf.basedb.util.extensions.events.CombiningEventFilter
Create a new combining event filter.
command - Variable in class net.sf.basedb.core.PluginRequest
 
command - Variable in class net.sf.basedb.core.RequestInformation
 
command - Variable in class net.sf.basedb.plugins.executor.ExternalProgramExecutor.RequestWrapper
 
COMMAND_CONFIGURE_EXTERNAL_PARAMETERS - Static variable in class net.sf.basedb.plugins.executor.ExternalProgramExecutor
 
COMMAND_CONFIGURE_IO_JOB - Static variable in interface net.sf.basedb.plugins.executor.IOSupport
This command is sent to import and export plug-ins in the job configuration sequence: InteractivePlugin.getRequestInformation(GuiContext, String) and InteractivePlugin.configure(GuiContext, Request, Response)
COMMAND_CONFIGURE_IO_PLUGIN - Static variable in interface net.sf.basedb.plugins.executor.IOSupport
This command is sent to import and export plug-ins in the plug-in configuration sequence: InteractivePlugin.getRequestInformation(GuiContext, String) and InteractivePlugin.configure(GuiContext, Request, Response)
COMMAND_CONFIGURE_JOB - Static variable in interface net.sf.basedb.core.plugin.Request
This should be the first command to use when setting the plugin's job parameters.
COMMAND_CONFIGURE_PARSER - Static variable in class net.sf.basedb.plugins.RawDataFlatFileImporter
 
COMMAND_CONFIGURE_PLUGIN - Static variable in interface net.sf.basedb.core.plugin.Request
This should be the first command to use when setting the plugin's configuration.
COMMAND_EXECUTE - Static variable in interface net.sf.basedb.core.plugin.Request
This command will tell the plugin to start its execution.
COMMAND_EXECUTE_IO_JOB - Static variable in interface net.sf.basedb.plugins.executor.IOSupport
This command is sent to import and export plug-ins in the job execution sequence: Plugin.run(Request, Response, ProgressReporter)
COMMAND_MANUAL_CONFIG - Static variable in class net.sf.basedb.plugins.Base1PluginExecuter
This command is used if the user decides to configure the plugin by hand.
COMMAND_SELECT_CONFIGURATIONS - Static variable in class net.sf.basedb.plugins.PluginConfigurationImporter
 
commandHandlers - Variable in class net.sf.basedb.clients.jobagent.handlers.DefaultRequestHandler
 
comment - Variable in class net.sf.basedb.core.authentication.LoginRequest
 
comment - Variable in class net.sf.basedb.core.data.BioMaterialEventData
 
comment - Variable in class net.sf.basedb.core.data.PlateEventData
 
commit() - Method in class net.sf.basedb.core.DbControl
Commit all changes made to items and close the connection to the database.
commit(Transaction) - Static method in class net.sf.basedb.core.HibernateUtil
Commit a transaction.
commitQueue - Variable in class net.sf.basedb.core.DbControl
A list of items that need special handling when commit is called.
COMMON - Static variable in class net.sf.basedb.clients.web.resources.Bundle
Resource bundle with strings that are used in lots and lots of places in the web gui.
commonCharsets - Static variable in class net.sf.basedb.core.Config
 
CommonData - Class in net.sf.basedb.core.data
This is a convenience class that extends the SharedData class and implements the NameableData and RemovableData interfaces.
CommonData() - Constructor for class net.sf.basedb.core.data.CommonData
 
commonDom - Static variable in class net.sf.basedb.core.PredefinedQuery
Holds the XML document containing the common queries.
CommonItem - Class in net.sf.basedb.core
 
CommonItem(CommonData) - Constructor for class net.sf.basedb.core.CommonItem
 
commonName - Variable in class net.sf.basedb.plugins.Base1PluginExecuter.JobParameter
 
commonQueryFile - Static variable in class net.sf.basedb.core.PredefinedQuery
The path to the query file with common queries.
CompactButtonRenderer - Class in net.sf.basedb.clients.web.extensions.toolbar
A compact renderer for toolbar button actions, which only only displays the icon.
CompactButtonRenderer(JspContext) - Constructor for class net.sf.basedb.clients.web.extensions.toolbar.CompactButtonRenderer
 
CompactButtonRendererFactory - Class in net.sf.basedb.clients.web.extensions.toolbar
Factory that create CompactButtonRenderer objects for rendering ButtonAction:s.
CompactButtonRendererFactory() - Constructor for class net.sf.basedb.clients.web.extensions.toolbar.CompactButtonRendererFactory
 
ComparableComparator<T extends Comparable<T>> - Class in net.sf.basedb.util
A comparator implemenation for any Comparable objects.
ComparableComparator() - Constructor for class net.sf.basedb.util.ComparableComparator
 
compare(String, String) - Method in class net.sf.basedb.util.StringLengthComparator
 
compare(URI, URI) - Method in class net.sf.basedb.util.extensions.manager.ExtensionsManager.JarFirstURIComparator
 
compare(RawDataType, RawDataType) - Method in class net.sf.basedb.core.RawDataTypes.NameComparator
 
compare(AnnotationSnapshot, AnnotationSnapshot) - Method in class net.sf.basedb.core.snapshot.AnnotationSetSnapshot.SortByProjectComparator
 
compare(AnnotationSnapshot, AnnotationSnapshot) - Method in class net.sf.basedb.core.snapshot.AnnotationSnapshot.AnnotationTypeComparator
 
compare(T, T) - Method in class net.sf.basedb.util.ComparableComparator
 
compare(T, T) - Method in class net.sf.basedb.util.NameableComparator
 
compare(T, T) - Method in class net.sf.basedb.util.PriorityComparator
 
compare(T, T) - Method in class net.sf.basedb.util.ToStringComparator
 
compareByChainOrder() - Static method in class net.sf.basedb.core.SyncFilter
Create a comparator that sorts sync filters by: Filter group Source item type: BIOSOURCE, SAMPLE, EXTRACT, PHYSICALBIOASSAY, DERIVEDBIOASSAY, RAWBIOASSAY Type of transformation: PARENT_TO_CHILD, NONE, CHILD_TO_PARENT Name Source item must exists is sorted before source item must not exist Id
compareTo(ExperimentExplorer.AnnotationGroup) - Method in class net.sf.basedb.clients.web.ExperimentExplorer.AnnotationGroup
 
compareTo(ExperimentExplorerPlotServlet.ColumnKey) - Method in class net.sf.basedb.clients.web.servlet.ExperimentExplorerPlotServlet.ColumnKey
The ID of the key determines equality.
compareTo(ClonableProperty) - Method in class net.sf.basedb.core.ClonableProperty
Sort by title, but mandatory properties before non-madatory.
compareTo(KeyPermission) - Method in class net.sf.basedb.core.data.keyring.KeyPermission
Compare the keyId of this object to the keyId of another KeyPermission object.
compareTo(PluginKeys) - Method in class net.sf.basedb.core.data.keyring.PluginKeys
Compare the keyId of this object to the keyId of another PluginKeys object.
compareTo(ProjectPermission) - Method in class net.sf.basedb.core.data.keyring.ProjectPermission
Compare the projectId of this object to the projectId of another ProjectPermission object.
compareTo(TableInfo.ColumnInfo) - Method in class net.sf.basedb.core.dbengine.TableInfo.ColumnInfo
 
compareTo(ItemProxy) - Method in class net.sf.basedb.core.ItemProxy
 
compareTo(RawDataType) - Method in class net.sf.basedb.core.RawDataType
Compare the id:s of the raw data types.
compareTo(LowessNormalization.SpotData) - Method in class net.sf.basedb.plugins.LowessNormalization.SpotData
Sort by A in ascending order.
compareTo(MedianRatioNormalization.SpotData) - Method in class net.sf.basedb.plugins.MedianRatioNormalization.SpotData
Sort by ratio in ascending order.
compareTo(AnyToAnyLinkStatistics) - Method in class net.sf.basedb.util.AnyToAnyLinkStatistics
Sort items by count, linkName and targetType.
compareTo(ExtensionsFile) - Method in class net.sf.basedb.util.extensions.manager.ExtensionsFile
 
compareTo(Node) - Method in class net.sf.basedb.util.overview.Node
 
compareTo(PlotAnnotation) - Method in class net.sf.basedb.util.plot.PlotAnnotation
 
compareTo(UnitCache.CacheKey) - Method in class net.sf.basedb.util.units.UnitCache.CacheKey
 
compareWith(String) - Static method in class net.sf.basedb.core.Version
Compare the given version string, which should be of the form a.b or a.b.c, with the current BASE version.
compile(boolean, boolean) - Method in class net.sf.basedb.clients.web.extensions.XJspCompiler
Called when a JSP page needs recompiling.
compile(String, HttpServletRequest, HttpServletResponse) - Method in class net.sf.basedb.clients.web.servlet.CompileAll
Compile all files found in dir, recursively entering subdirectories.
CompileAll - Class in net.sf.basedb.clients.web.servlet
This servlet will scan for all files ending with .jsp and issue a request for them with the parameter jsp_precompile=true therby compiling all JSP files into servlets.
CompileAll() - Constructor for class net.sf.basedb.clients.web.servlet.CompileAll
 
completed - Variable in class net.sf.basedb.core.SimpleAbsoluteProgressReporter
 
complexMappings - Static variable in class net.sf.basedb.plugins.AbstractFlatFileImporter
Parameter that asks if complex column mappings should be enabled or not.
component - Variable in class net.sf.basedb.core.Metadata.ComponentPropertyPath
 
ComponentData - Interface in net.sf.basedb.core.data
Tagging interface that we need all componenets to implement so that we are able to export them properly using generic code.
ComponentPropertyPath(ComponentType, int, Type) - Constructor for class net.sf.basedb.core.Metadata.ComponentPropertyPath
 
CompoundMapper - Class in net.sf.basedb.util.parser
A compound mapper that gets its value by invoking multiple other mappers which are set in the constructor.
CompoundMapper(List<Mapper>) - Constructor for class net.sf.basedb.util.parser.CompoundMapper
Create a new compound mapper.
CompoundMapper(List<Mapper>, NumberFormat, boolean) - Constructor for class net.sf.basedb.util.parser.CompoundMapper
Create a new compound mapper, using a specific number formatter as it's parser.
CompoundMapper(List<Mapper>, NumberFormat, Formatter<Date>, boolean) - Constructor for class net.sf.basedb.util.parser.CompoundMapper
Create a new compound mapper, using a specific number formatter as it's parser.
compress - Variable in class net.sf.basedb.core.File.UploadStream
If the file should be compressed or not.
compress(ProgressReporter) - Method in class net.sf.basedb.core.File
Compress the file stored on the disk.
compressed - Variable in class net.sf.basedb.core.data.FileData
 
compressedSize - Variable in class net.sf.basedb.core.data.FileData
 
compressOrDecompress(ProgressReporter, boolean) - Method in class net.sf.basedb.core.File
 
condition - Variable in class net.sf.basedb.core.dbengine.TableInfo.IndexInfo
 
condition - Variable in class net.sf.basedb.core.HibernateUtil.DelayedFilterDef
 
condition - Variable in class net.sf.basedb.core.query.WhenStatement
 
conditionalExpression(Filter<? extends Query>, Expression, Expression) - Static method in class net.sf.basedb.core.query.Expressions
Create an expression that falls back to one of two expression depending on if the query passes a filter or not.
ConditionalQueryElement - Class in net.sf.basedb.core.query
 
ConditionalQueryElement(Filter<Query>, QueryElement, QueryElement) - Constructor for class net.sf.basedb.core.query.ConditionalQueryElement
 
conditionalRestriction(Filter<? extends Query>, Restriction, Restriction, boolean) - Static method in class net.sf.basedb.core.query.Restrictions
Create a restriction that falls back to one of two restrictions depending on if the query passes a filter or not.
config - Static variable in class net.sf.basedb.core.Config
Variable for holding the configuration properties.
config - Variable in class net.sf.basedb.core.hibernate.SchemaGenerator.CollectSqlTarget
 
config - Variable in class net.sf.basedb.core.plugin.ParameterValuesWrapper
 
config - Variable in class net.sf.basedb.util.ContextUtil.ContextResult
 
Config - Class in net.sf.basedb.core
Use this class to access the configuration settings for BASE.
Config() - Constructor for class net.sf.basedb.core.Config
 
configDir - Static variable in class net.sf.basedb.core.Config
 
configList - Static variable in class net.sf.basedb.plugins.PluginConfigurationExporter
 
configuration - Variable in class net.sf.basedb.core.ParameterValuesImpl
 
configuration - Variable in class net.sf.basedb.core.plugin.AbstractPlugin
 
configuration - Variable in class net.sf.basedb.plugins.gtf.DefaultConfigurationValues
 
ConfigurationException - Exception in net.sf.basedb.core
This exception is thrown by the Config class if there is a problem with finding or loading the configuration settings.
ConfigurationException(String) - Constructor for exception net.sf.basedb.core.ConfigurationException
Creates a new ConfigurationException.
ConfigurationException(String, Throwable) - Constructor for exception net.sf.basedb.core.ConfigurationException
Creates a new ConfigurationException with a cause.
configurationMap - Variable in class net.sf.basedb.plugins.PluginConfigurationImporter
 
configurationParameters - Variable in class net.sf.basedb.core.PluginRequest
 
configurations - Variable in class net.sf.basedb.core.data.PluginDefinitionData
 
configurationValues - Variable in class net.sf.basedb.core.data.PluginConfigurationData
 
configure() - Method in class net.sf.basedb.core.PluginConfiguration
Start the configuration sequence for a plugin.
configure(GuiContext) - Method in class net.sf.basedb.core.Job
Start the configuration sequence for a job.
configure(GuiContext, Request, Response) - Method in class net.sf.basedb.clients.web.plugins.SimpleExport
 
configure(GuiContext, Request, Response) - Method in interface net.sf.basedb.core.plugin.InteractivePlugin
Configure the plugin.
configure(GuiContext, Request, Response) - Method in class net.sf.basedb.plugins.AnnotationFlatFileImporter
 
configure(GuiContext, Request, Response) - Method in class net.sf.basedb.plugins.Base1PluginExecuter
 
configure(GuiContext, Request, Response) - Method in class net.sf.basedb.plugins.BaseFileExporterPlugin
 
configure(GuiContext, Request, Response) - Method in class net.sf.basedb.plugins.batchimport.AbstractItemImporter
 
configure(GuiContext, Request, Response) - Method in class net.sf.basedb.plugins.batchimport.AnnotationTypeImporter
Override this method so that we can make some extra parameter checks: A mapping for 'Value type' must be specified when 'create' or 'create+update' mode is used
configure(GuiContext, Request, Response) - Method in class net.sf.basedb.plugins.batchimport.AnyToAnyImporter
 
configure(GuiContext, Request, Response) - Method in class net.sf.basedb.plugins.BfsExporterPlugin
 
configure(GuiContext, Request, Response) - Method in class net.sf.basedb.plugins.CdfFileReporterImporter
 
configure(GuiContext, Request, Response) - Method in class net.sf.basedb.plugins.executor.BaseFileExporterSupport
 
configure(GuiContext, Request, Response) - Method in class net.sf.basedb.plugins.executor.BaseFileImporterSupport
 
configure(GuiContext, Request, Response) - Method in class net.sf.basedb.plugins.executor.BfsExporterSupport
 
configure(GuiContext, Request, Response) - Method in class net.sf.basedb.plugins.executor.BfsImporterSupport
 
configure(GuiContext, Request, Response) - Method in class net.sf.basedb.plugins.executor.ExternalProgramExecutor
 
configure(GuiContext, Request, Response) - Method in class net.sf.basedb.plugins.executor.FileOnlyImporterSupport
 
configure(GuiContext, Request, Response) - Method in class net.sf.basedb.plugins.FormulaFilter
 
configure(GuiContext, Request, Response) - Method in class net.sf.basedb.plugins.GalExporter
 
configure(GuiContext, Request, Response) - Method in class net.sf.basedb.plugins.gtf.GtfReporterMapImporter
 
configure(GuiContext, Request, Response) - Method in class net.sf.basedb.plugins.HelpExporter
 
configure(GuiContext, Request, Response) - Method in class net.sf.basedb.plugins.HelpImporter
 
configure(GuiContext, Request, Response) - Method in class net.sf.basedb.plugins.IlluminaRawDataImporter
 
configure(GuiContext, Request, Response) - Method in class net.sf.basedb.plugins.IntensityCalculatorPlugin
configure(GuiContext, Request, Response) - Method in class net.sf.basedb.plugins.JepExtraValueCalculator
 
configure(GuiContext, Request, Response) - Method in class net.sf.basedb.plugins.JepIntensityTransformer
 
configure(GuiContext, Request, Response) - Method in class net.sf.basedb.plugins.LowessNormalization
 
configure(GuiContext, Request, Response) - Method in class net.sf.basedb.plugins.ManualDerivedBioAssayCreator
 
configure(GuiContext, Request, Response) - Method in class net.sf.basedb.plugins.ManualTransformCreator
 
configure(GuiContext, Request, Response) - Method in class net.sf.basedb.plugins.MedianRatioNormalization
 
configure(GuiContext, Request, Response) - Method in class net.sf.basedb.plugins.PackedFileExporter
 
configure(GuiContext, Request, Response) - Method in class net.sf.basedb.plugins.PlateFlatFileImporter
configure(GuiContext, Request, Response) - Method in class net.sf.basedb.plugins.PlateMappingExporter
configure(GuiContext, Request, Response) - Method in class net.sf.basedb.plugins.PlateMappingImporter
configure(GuiContext, Request, Response) - Method in class net.sf.basedb.plugins.PluginConfigurationExporter
Store configuration settings for Request.COMMAND_CONFIGURE_JOB.
configure(GuiContext, Request, Response) - Method in class net.sf.basedb.plugins.PluginConfigurationImporter
 
configure(GuiContext, Request, Response) - Method in class net.sf.basedb.plugins.PrintMapFlatFileImporter
configure(GuiContext, Request, Response) - Method in class net.sf.basedb.plugins.RawDataFlatFileImporter
configure(GuiContext, Request, Response) - Method in class net.sf.basedb.plugins.ReporterFlatFileImporter
configure(GuiContext, Request, Response) - Method in class net.sf.basedb.plugins.ReporterMapFlatFileImporter
configure(GuiContext, Request, Response) - Method in class net.sf.basedb.util.zip.AbstractFileUnpacker
 
CONFIGURE_IMPORT - Static variable in class net.sf.basedb.plugins.AnnotationFlatFileImporter
 
CONFIGURE_MAPPING - Static variable in class net.sf.basedb.plugins.AnnotationFlatFileImporter
 
CONFIGURE_OPTIONS - Static variable in class net.sf.basedb.plugins.batchimport.AbstractItemImporter
 
CONFIGURE_OPTIONS - Static variable in class net.sf.basedb.plugins.batchimport.AnyToAnyImporter
 
ConfigureByExample - Interface in net.sf.basedb.util.parser
This is a tagging interface for all plugins that use the FlatFileParser and wants easier configuration of the regular expressions used to parse the file.
configureExecutor - Variable in class net.sf.basedb.plugins.executor.BaseFileExporterSupport
 
configureExecutor - Variable in class net.sf.basedb.plugins.executor.BaseFileImporterSupport
 
configureExecutor - Variable in class net.sf.basedb.plugins.executor.BfsExporterSupport
 
configureExecutor - Variable in class net.sf.basedb.plugins.executor.BfsImporterSupport
 
configureExportImportPluginParameters - Variable in class net.sf.basedb.plugins.executor.ExternalProgramExecutor
 
configureExternalParameters - Variable in class net.sf.basedb.plugins.executor.ExternalProgramExecutor
 
configureImport - Variable in class net.sf.basedb.plugins.AnnotationFlatFileImporter
 
configureJob - Variable in class net.sf.basedb.clients.web.plugins.SimpleExport
 
configureJob - Variable in class net.sf.basedb.plugins.Base1PluginExecuter
Holds info about a job configuration request.
configureJob - Variable in class net.sf.basedb.plugins.BaseFileExporterPlugin
 
configureJob - Variable in class net.sf.basedb.plugins.BfsExporterPlugin
 
configureJob - Variable in class net.sf.basedb.plugins.CdfFileReporterImporter
 
configureJob - Variable in class net.sf.basedb.plugins.executor.BaseFileImporterSupport
 
configureJob - Variable in class net.sf.basedb.plugins.executor.BfsImporterSupport
 
configureJob - Variable in class net.sf.basedb.plugins.executor.ExternalProgramExecutor
 
configureJob - Variable in class net.sf.basedb.plugins.executor.FileOnlyImporterSupport
 
configureJob - Variable in class net.sf.basedb.plugins.FormulaFilter
 
configureJob - Variable in class net.sf.basedb.plugins.GalExporter
 
configureJob - Variable in class net.sf.basedb.plugins.gtf.GtfReporterMapImporter
 
configureJob - Variable in class net.sf.basedb.plugins.HelpExporter
 
configureJob - Variable in class net.sf.basedb.plugins.HelpImporter
 
configureJob - Variable in class net.sf.basedb.plugins.IlluminaRawDataImporter
 
configureJob - Variable in class net.sf.basedb.plugins.IntensityCalculatorPlugin
 
configureJob - Variable in class net.sf.basedb.plugins.JepExtraValueCalculator
 
configureJob - Variable in class net.sf.basedb.plugins.JepIntensityTransformer
 
configureJob - Variable in class net.sf.basedb.plugins.LowessNormalization
 
configureJob - Variable in class net.sf.basedb.plugins.ManualDerivedBioAssayCreator
 
configureJob - Variable in class net.sf.basedb.plugins.ManualTransformCreator
 
configureJob - Variable in class net.sf.basedb.plugins.MedianRatioNormalization
 
configureJob - Variable in class net.sf.basedb.plugins.PackedFileExporter
 
configureJob - Variable in class net.sf.basedb.plugins.PlateFlatFileImporter
 
configureJob - Variable in class net.sf.basedb.plugins.PlateMappingExporter
 
configureJob - Variable in class net.sf.basedb.plugins.PlateMappingImporter
 
configureJob - Variable in class net.sf.basedb.plugins.PluginConfigurationExporter
 
configureJob - Variable in class net.sf.basedb.plugins.PluginConfigurationImporter
 
configureJob - Variable in class net.sf.basedb.plugins.PrintMapFlatFileImporter
 
configureJob - Variable in class net.sf.basedb.plugins.RawDataFlatFileImporter
 
configureJob - Variable in class net.sf.basedb.plugins.ReporterFlatFileImporter
 
configureJob - Variable in class net.sf.basedb.plugins.ReporterMapFlatFileImporter
 
configureJob - Variable in class net.sf.basedb.util.zip.AbstractFileUnpacker
 
configureManual - Variable in class net.sf.basedb.plugins.Base1PluginExecuter
Holds information about a manual plugin configuration request.
configureMapping - Variable in class net.sf.basedb.plugins.AnnotationFlatFileImporter
 
configureOptions - Variable in class net.sf.basedb.plugins.batchimport.AbstractItemImporter
 
configureOptions - Variable in class net.sf.basedb.plugins.batchimport.AnyToAnyImporter
 
configureParser - Variable in class net.sf.basedb.plugins.AnnotationFlatFileImporter
 
configureParser - Variable in class net.sf.basedb.plugins.batchimport.AbstractItemImporter
 
configureParser - Variable in class net.sf.basedb.plugins.batchimport.AnyToAnyImporter
 
configureParser - Variable in class net.sf.basedb.plugins.RawDataFlatFileImporter
 
configurePlugin - Variable in class net.sf.basedb.plugins.Base1PluginExecuter
Holds information about a plugin configuration request.
configurePlugin - Variable in class net.sf.basedb.plugins.executor.ExternalProgramExecutor
 
configurePlugin - Variable in class net.sf.basedb.plugins.gtf.GtfReporterMapImporter
 
configurePlugin - Variable in class net.sf.basedb.plugins.ManualDerivedBioAssayCreator
 
configurePlugin - Variable in class net.sf.basedb.plugins.ManualTransformCreator
 
configurePlugin - Variable in class net.sf.basedb.plugins.PackedFileExporter
 
configurePlugin - Variable in class net.sf.basedb.plugins.PlateFlatFileImporter
 
configurePlugin - Variable in class net.sf.basedb.plugins.ReporterFlatFileImporter
 
configurePlugin - Variable in class net.sf.basedb.plugins.ReporterMapFlatFileImporter
 
configureQuery(DbControl, EntityQuery, boolean) - Method in class net.sf.basedb.core.ItemContext
 
configureQuery(DbControl, EntityQuery, ClientContext, boolean) - Method in class net.sf.basedb.core.ItemContext
Use the settings in this context to configure a query.
configureQuery(DbControl, SqlQuery, List<String>) - Method in class net.sf.basedb.core.ItemContext
Use the settings in this context to configure a dynamic query.
configureQuery(SqlQuery) - Method in interface net.sf.basedb.util.DynamicFilter
Configure the query before it is used.
configureQuery(SqlQuery) - Method in class net.sf.basedb.util.IncludeExcludeFilter
We need the position which is in column 2 (already selected).
configureRawDataType - Variable in class net.sf.basedb.plugins.RawDataFlatFileImporter
 
configureSelection - Variable in class net.sf.basedb.plugins.PluginConfigurationImporter
 
connect() - Method in class net.sf.basedb.util.jobagent.JobAgentConnection
Create a socket connection to the job agent.
connection() - Method in class net.sf.basedb.core.hibernate.StatelessSessionWrapper
Deprecated.
ConnectionClosedException - Exception in net.sf.basedb.core
This exception is thrown when trying to use a DbControl object that has been closed.
ConnectionClosedException() - Constructor for exception net.sf.basedb.core.ConnectionClosedException
Creates a new ConnectionClosedException.
ConnectionManager - Interface in net.sf.basedb.util.uri
A connection manager is used to access the contents and metadata about the resource pointed to by a given URI.
connectionManagerFactory - Variable in class net.sf.basedb.core.data.FileServerData
 
ConnectionManagerFactory - Interface in net.sf.basedb.util.uri
A connection manager factory is responsible for creating connection managers for some subset of URI:s that is supported.
ConnectionManagerUtil - Class in net.sf.basedb.util.uri
Collects utility methods related to connection managers.
ConnectionManagerUtil() - Constructor for class net.sf.basedb.util.uri.ConnectionManagerUtil
 
ConnectionParameters - Class in net.sf.basedb.util.uri
Connection parameters, such as username/password, that may be needed to connect to a server.
ConnectionParameters() - Constructor for class net.sf.basedb.util.uri.ConnectionParameters
Create a new empty parameters object.
connectTimeout - Variable in class net.sf.basedb.clients.jobagent.slotmanager.RemoteSlotManager
 
ConsoleProgressReporter - Class in net.sf.basedb.util
An implementation of the ProgressReporter interface that writes all messages to the standard console.
ConsoleProgressReporter() - Constructor for class net.sf.basedb.util.ConsoleProgressReporter
 
ConsoleProgressReporter(boolean) - Constructor for class net.sf.basedb.util.ConsoleProgressReporter
 
constant - Variable in class net.sf.basedb.util.parser.ConstantMapper
 
ConstantMapper - Class in net.sf.basedb.util.parser
A constant string mapper.
ConstantMapper(Float) - Constructor for class net.sf.basedb.util.parser.ConstantMapper
 
ConstantMapper(Integer) - Constructor for class net.sf.basedb.util.parser.ConstantMapper
 
ConstantMapper(String) - Constructor for class net.sf.basedb.util.parser.ConstantMapper
Create a constant mapper.
ConstantMapper(String, NumberFormat, boolean) - Constructor for class net.sf.basedb.util.parser.ConstantMapper
Create a constant mapper using a specific number formatter as it's parser.
ConstantMapper(String, NumberFormat, Formatter<Date>, boolean) - Constructor for class net.sf.basedb.util.parser.ConstantMapper
Create a constant mapper using a specific number formatter as it's parser.
ConstantMapper(Date, Formatter<Date>) - Constructor for class net.sf.basedb.util.parser.ConstantMapper
 
constructor - Variable in enum net.sf.basedb.core.Item
 
contact - Variable in class net.sf.basedb.core.data.PluginDefinitionData
 
contact - Variable in class net.sf.basedb.core.plugin.AboutImpl
 
contact - Variable in class net.sf.basedb.util.extensions.AboutBean
 
contact - Variable in class net.sf.basedb.util.extensions.Registry.RegisteredAbout
 
contains(Object) - Method in class net.sf.basedb.core.hibernate.SessionWrapper
 
contains(Object) - Method in class net.sf.basedb.core.ItemResultList
 
contains(Object) - Method in class net.sf.basedb.util.Tree
 
contains(String, Object) - Method in class net.sf.basedb.core.hibernate.SessionWrapper
 
contains(AnnotationUtil.AnnotatableWrapper) - Method in class net.sf.basedb.util.AnnotationUtil.Cache
 
containsAll(Collection<?>) - Method in class net.sf.basedb.core.AbstractResultList
 
containsAll(Collection<?>) - Method in class net.sf.basedb.core.UnmodifiableResultList
 
containsAll(Collection<?>) - Method in class net.sf.basedb.util.Tree
 
containsKey(Object) - Method in class net.sf.basedb.util.formatter.LookupFormatter
Checks if a given key has been registered.
containsKey(Object) - Method in class net.sf.basedb.util.jep.FunctionSafeJep.SafeFunctionTable
If the key is already registered, return TRUE.
content - Variable in class net.sf.basedb.clients.web.extensions.section.SectionBean
 
content - Variable in class net.sf.basedb.clients.web.extensions.tabcontrol.FixedTabFactory
 
content - Variable in class net.sf.basedb.clients.web.extensions.tabcontrol.TabBean
 
content - Variable in class net.sf.basedb.clients.web.taglib.tab.TabControl
The HTML for the contents of the tabs.
ContentSecurityPolicyFilter - Class in net.sf.basedb.clients.web.servlet
This is a filter that sets the "Content-Security-Policy" header in the http response.
ContentSecurityPolicyFilter() - Constructor for class net.sf.basedb.clients.web.servlet.ContentSecurityPolicyFilter
 
ContentSecurityPolicyReportServlet - Class in net.sf.basedb.clients.web.servlet
This is a servlet for posting reports from "Content-Security-Policy" violations.
ContentSecurityPolicyReportServlet() - Constructor for class net.sf.basedb.clients.web.servlet.ContentSecurityPolicyReportServlet
 
contentStyle - Variable in class net.sf.basedb.clients.web.extensions.section.IncludeContentSectionFactory
 
contentStyle - Variable in class net.sf.basedb.clients.web.extensions.section.SectionBean
 
contentStyle - Variable in class net.sf.basedb.clients.web.taglib.HideableSection
Optional style attribute for the content section
contentStyle - Variable in class net.sf.basedb.clients.web.taglib.tab.TabControl
Optional style attribute for the content section
context - Variable in class net.sf.basedb.clients.web.extensions.LoadServletsProcessor
 
context - Variable in class net.sf.basedb.clients.web.extensions.renderer.PrefixSuffixRenderer
 
context - Variable in class net.sf.basedb.clients.web.extensions.ServletWrapper
 
context - Variable in class net.sf.basedb.clients.web.extensions.tabcontrol.IncludeContentTabFactory.Tab
 
context - Variable in class net.sf.basedb.clients.web.extensions.toolbar.CompactButtonRenderer
 
context - Variable in class net.sf.basedb.clients.web.extensions.toolbar.ToolbarButtonRenderer
 
context - Variable in class net.sf.basedb.clients.web.taglib.extensions.Render
 
context - Variable in class net.sf.basedb.clients.web.taglib.extensions.Scripts
 
context - Variable in class net.sf.basedb.clients.web.taglib.extensions.Stylesheets
 
context - Variable in class net.sf.basedb.clients.web.taglib.HideableSection
 
context - Variable in class net.sf.basedb.core.PluginConfigurationRequest
 
context - Variable in class net.sf.basedb.core.signal.ExtensionSignalTransporter
 
context - Variable in class net.sf.basedb.util.overview.node.NodeFactory
 
CONTEXT_BIOASSAYS - Static variable in class net.sf.basedb.core.plugin.AbstractAnalysisPlugin
GuiContext = [Item.BIOASSAY, GuiContext.Type.LIST]
CONTEXT_BIOASSAYSET - Static variable in class net.sf.basedb.core.plugin.AbstractAnalysisPlugin
GuiContext = [Item.BIOASSAYSET, GuiContext.Type.ITEM]
CONTEXT_DERIVEDBIOASSAY - Static variable in class net.sf.basedb.core.plugin.AbstractAnalysisPlugin
GuiContext = [Item.DERIVEDBIOASSAY, GuiContext.Type.ITEM]
CONTEXT_RELATIVE - net.sf.basedb.util.extensions.xml.PathType
Paths should be relative to the web application context.
ContextData - Class in net.sf.basedb.core.data
This class holds context information to help client applications with storing common settings for tables.
ContextData() - Constructor for class net.sf.basedb.core.data.ContextData
 
contextDestroyed(ServletContextEvent) - Method in class net.sf.basedb.clients.web.servlet.StartStopServlet
 
contextId - Variable in class net.sf.basedb.core.ItemContext
 
ContextIndex - Class in net.sf.basedb.core.data
 
ContextIndex() - Constructor for class net.sf.basedb.core.data.ContextIndex
 
ContextIndex(ClientData, int, String, String) - Constructor for class net.sf.basedb.core.data.ContextIndex
 
contextInitialized(ServletContextEvent) - Method in class net.sf.basedb.clients.web.servlet.StartStopServlet
 
contextItem - Variable in class net.sf.basedb.core.data.JobData
 
ContextKey - Class in net.sf.basedb.core
 
ContextKey(Item, String) - Constructor for class net.sf.basedb.core.ContextKey
Create a new ContextKey object from Item and it's subcontext.
contextMessage - Variable in class net.sf.basedb.util.ContextUtil.ContextResult
 
contextPath - Variable in class net.sf.basedb.clients.web.servlet.ImageRemapFilter
 
contextPath - Variable in class net.sf.basedb.clients.web.servlet.RssNewsFeed
 
ContextResult(PluginDefinition, PluginConfiguration, String) - Constructor for class net.sf.basedb.util.ContextUtil.ContextResult
Create a new warning-level result object.
ContextResult(PluginDefinition, PluginConfiguration, Throwable) - Constructor for class net.sf.basedb.util.ContextUtil.ContextResult
Create a new error-level result object.
ContextResult(SessionControl, PluginDefinition, PluginConfiguration, GuiContext, Object) - Constructor for class net.sf.basedb.util.ContextUtil.ContextResult
 
contexts - Variable in class net.sf.basedb.core.data.ClientData
 
contexts - Variable in class net.sf.basedb.core.data.UserData
 
contexts - Variable in class net.sf.basedb.util.extensions.ExtensionsInvoker
 
contextType - Variable in class net.sf.basedb.core.data.GuiContextData
 
contextType - Variable in class net.sf.basedb.core.data.JobData
 
ContextUtil - Class in net.sf.basedb.util
A class with utility methods for plug-ins.
ContextUtil() - Constructor for class net.sf.basedb.util.ContextUtil
 
ContextUtil.ContextResult - Class in net.sf.basedb.util
Class for holding the result of a call to the InteractivePlugin.isInContext(GuiContext, Object) method.
ContextUtil.IsInContextFilter - Class in net.sf.basedb.util
Filter implementation that works on collections of ContextUtil.ContextResult:s and return only those that return true from ContextUtil.ContextResult.isInContext().
CONTINUE - net.sf.basedb.core.plugin.Response.Status
 
continueAfterError - Variable in class net.sf.basedb.plugins.RawDataFlatFileImporter
 
continueLater(String, boolean, Serializable) - Method in class net.sf.basedb.core.Job
This method is used to indicate that a job had to be aborted due to a system shutdown.
continueWithNextFileAfterError(Throwable) - Method in class net.sf.basedb.plugins.AbstractFlatFileImporter
If the importer should continue with the next file after an error.
continueWithNextFileAfterError(Throwable) - Method in class net.sf.basedb.plugins.RawDataFlatFileImporter
We will continue if: The file is not of the correct format, eg. t = UnsupportedFileFormatException.
Controlled - Interface in net.sf.basedb.core
This is the base tagging interface for items that needs special attention by the DbControl object when DbControl.commit() is called.
convert(String) - Method in class net.sf.basedb.util.extensions.debug.StringConverter
 
convert(String, Method) - Method in class net.sf.basedb.util.extensions.xml.PathConverter
 
convert(String, Method) - Method in interface net.sf.basedb.util.extensions.xml.ValueConverter
Convert a value.
convert(String, Method) - Method in class net.sf.basedb.util.extensions.xml.VariableConverter
 
convert(T) - Method in class net.sf.basedb.util.json.IdentityConverter
 
convert(T) - Method in interface net.sf.basedb.util.json.JsonConverter
Convert the given object to a JSON-compatible object.
convert(T) - Method in class net.sf.basedb.util.json.NameableConverter
 
converter - Variable in class net.sf.basedb.core.snapshot.AnnotationLoaderUtil
 
converter - Static variable in class net.sf.basedb.util.extensions.debug.StringConverter
 
ConverterFactory - Class in net.sf.basedb.util.jep.convert
Keep JepConversionFunction objects for converting built-in JEP object to Query API Expression or Restriction objects.
ConverterFactory() - Constructor for class net.sf.basedb.util.jep.convert.ConverterFactory
 
converters - Variable in class net.sf.basedb.util.extensions.xml.XmlLoader
 
converters - Static variable in class net.sf.basedb.util.jep.convert.ConverterFactory
 
convertJavaDateFormatToExcelFormat(String) - Static method in class net.sf.basedb.util.excel.CellStyleCreator
Converts a Java date format string to the corresponding Excel date format string.
convertNumber(Number) - Method in enum net.sf.basedb.core.Type
Convert a number to the appropriate class.
convertString(Class, String) - Static method in class net.sf.basedb.util.extensions.debug.StringConverter
 
convertToNull(String) - Method in class net.sf.basedb.util.parser.FlatFileParser
 
convertToReferenceUnit(double) - Method in class net.sf.basedb.util.units.IdentityUnitConverter
 
convertToReferenceUnit(double) - Method in class net.sf.basedb.util.units.LinearUnitConverter
value(ref) = value(specific) * factor + offset
convertToReferenceUnit(double) - Method in interface net.sf.basedb.util.units.UnitConverter
Convert a value from the specific unit to the reference unit.
convertToSpecificUnit(double) - Method in class net.sf.basedb.util.units.IdentityUnitConverter
 
convertToSpecificUnit(double) - Method in class net.sf.basedb.util.units.LinearUnitConverter
value(specific) = (value(ref) - offset) / factor
convertToSpecificUnit(double) - Method in interface net.sf.basedb.util.units.UnitConverter
Convert a value from the reference unit to the specific unit.
convertValue(String, Class<?>) - Method in class net.sf.basedb.util.extensions.debug.BeanActionFactory
Convert a string value to another type.
convertValues(AnnotationType, List<?>, Unit) - Method in class net.sf.basedb.core.Annotation
 
convertValueToUnit(Session, String, String, Unit) - Method in class net.sf.basedb.core.PropertyFilter
Converts a string to a numeric value with the correct unit.
Coordinate - Class in net.sf.basedb.util
Util class for coordinate transformations in base.
Coordinate() - Constructor for class net.sf.basedb.util.Coordinate
 
COORDINATES - net.sf.basedb.core.FeatureIdentificationMethod
Use coordinates (block, metaGridX, metaGridY, row, column)
coordinateType - Variable in class net.sf.basedb.core.data.DataCubeExtraValueData
 
CoordinateType(int) - Constructor for enum net.sf.basedb.core.ExtraValue.CoordinateType
 
copy(byte[], int, int) - Method in class net.sf.basedb.util.InputStreamSplitter
Write data to all output streams.
copy(int) - Method in class net.sf.basedb.util.InputStreamSplitter
Write data to all output streams.
copy(InputStream, OutputStream) - Static method in class net.sf.basedb.u