Index
All Classes and Interfaces|All Packages|Constant Field Values|Serialized Form
A
- A - Variable in class net.sf.basedb.plugins.LowessNormalization.SpotData
- abort - Variable in class net.sf.basedb.clients.web.fileupload.FileUploadProgress
- ABORT - Static variable in class net.sf.basedb.core.signal.Signal
-
The ABORT signal, that requests that the receiver should clean up and die.
- ABORTING - Enum constant in enum class net.sf.basedb.core.Job.Status
-
The
Signal.ABORT
signal has been sent to the job, but it has not yet responded. - about - Variable in class net.sf.basedb.util.extensions.ExtensionBean
- about - Variable in class net.sf.basedb.util.extensions.manager.ExtensionsFile
- about - Variable in class net.sf.basedb.util.extensions.Registry.RegisteredExtension
- about - Variable in class net.sf.basedb.util.extensions.xml.PluginInfo
- About - Interface in net.sf.basedb.core.plugin
-
Get information, such as the name, version and authors, about a plugin.
- AboutBean - Class in net.sf.basedb.util.extensions
-
An implementation of the
About
interface, which complements all getter methods with setter methods. - AboutBean() - Constructor for class net.sf.basedb.util.extensions.AboutBean
-
Create a new empty about instance.
- AboutImpl - Class in net.sf.basedb.core.plugin
-
A simple implementation of the
About
interface. - AboutImpl(String, String, String, String, String, String, String) - Constructor for class net.sf.basedb.core.plugin.AboutImpl
-
Create a new about object without any min or max BASE version requirement.
- AboutImpl(String, String, String, String, String, String, String, String, String) - Constructor for class net.sf.basedb.core.plugin.AboutImpl
-
Create a new
About
object. - abs(String) - Method in class net.sf.basedb.core.dbengine.AbstractDbEngine
-
Return
ABS(<value>)
. - abs(String) - Method in interface net.sf.basedb.core.dbengine.DbEngine
-
Get the function call that takes the absolute of a value.
- abs(Expression) - Static method in class net.sf.basedb.core.query.Expressions
-
Calculate the absolute value of an expression: new expression = abs(e).
- AbsConverter - Class in net.sf.basedb.util.jep.convert
-
Convert
Abs
function to a Query APIExpression
. - AbsConverter() - Constructor for class net.sf.basedb.util.jep.convert.AbsConverter
- AbsExpression - Class in net.sf.basedb.core.query
-
Calculate the absolute value of an expression: abs(e).
- AbsExpression(Expression) - Constructor for class net.sf.basedb.core.query.AbsExpression
- ABSOLUTE - Enum constant in enum class net.sf.basedb.util.extensions.xml.PathType
-
Paths should be absolute paths from the root of the web server.
- AbsoluteProgressReporter - Interface in net.sf.basedb.core
-
This is interface is an extension to the
ProgressReporter
interface. - ABSORBED_DOSE - Static variable in class net.sf.basedb.core.Quantity
-
The id for the
Quantity
object representing absorbed dose. - AbstractAnalysisPlugin - Class in net.sf.basedb.core.plugin
-
This is a base class that is useful for all analysis type plugins.
- AbstractAnalysisPlugin() - Constructor for class net.sf.basedb.core.plugin.AbstractAnalysisPlugin
-
Create a new
AbstractAnalysisPlugin
. - AbstractBatcher - Class in net.sf.basedb.core
-
This is an abstract class for batchers that are connected to a single
DbControl
object. - AbstractBatcher() - Constructor for class net.sf.basedb.core.AbstractBatcher
-
Constructor for a batcher.
- AbstractBioAssaySetExporter - Class in net.sf.basedb.util.export.spotdata
-
An abstract superclass for all exporters that exports spot data from a bioassay set.
- AbstractBioAssaySetExporter() - Constructor for class net.sf.basedb.util.export.spotdata.AbstractBioAssaySetExporter
- AbstractCustomRequestHandler - Class in net.sf.basedb.clients.jobagent.handlers
-
Abstract base class for custom request handler implementations.
- AbstractCustomRequestHandler() - Constructor for class net.sf.basedb.clients.jobagent.handlers.AbstractCustomRequestHandler
- AbstractDataWriterFactory<T> - Class in net.sf.basedb.util.bfs
-
Abstract implementation of a data writer factory.
- AbstractDataWriterFactory(FilenameGenerator<T>) - Constructor for class net.sf.basedb.util.bfs.AbstractDataWriterFactory
-
Create a new factory that uses the given file name generator.
- AbstractDbEngine - Class in net.sf.basedb.core.dbengine
-
An abstract superclass with default implementations for most
DbEngine
methods. - AbstractDbEngine() - Constructor for class net.sf.basedb.core.dbengine.AbstractDbEngine
-
Create AbstractDbEngine.
- AbstractEntityQuery - Class in net.sf.basedb.core
-
An abstract implementation of the
EntityQuery
interface. - AbstractEntityQuery(Item, String, boolean) - Constructor for class net.sf.basedb.core.AbstractEntityQuery
-
Create a new query returning items of the specified item type using the default optional runtime filter.
- AbstractEntityQuery(Item, String, boolean, QueryRuntimeFilter) - Constructor for class net.sf.basedb.core.AbstractEntityQuery
-
Create a new query returning items of the specified type with a non-default optional runtime filter.
- AbstractEntityQuery(Item, Item, String, String, boolean, QueryRuntimeFilter) - Constructor for class net.sf.basedb.core.AbstractEntityQuery
-
Create a new query that may have different return type and root item type.
- AbstractExporterPlugin - Class in net.sf.basedb.core.plugin
-
An abstract base class for all exporter plugins that wish to implement the
ImmediateDownloadExporter
interface. - AbstractExporterPlugin() - Constructor for class net.sf.basedb.core.plugin.AbstractExporterPlugin
-
Create a new
AbstractExporterPlugin
. - AbstractFieldConverter - Class in net.sf.basedb.util.export.spotdata
-
Abstract helper class for implementing
ExportableFieldConverter
. - AbstractFieldConverter(DbControl, BioAssaySet) - Constructor for class net.sf.basedb.util.export.spotdata.AbstractFieldConverter
-
Creates a new field converter to be used with a specific bioassay set source.
- AbstractFilenameGenerator<T> - Class in net.sf.basedb.util.bfs
-
Abstract superclass for file names generator implementions that will help with ensuring that a generator creates unique file names.
- AbstractFilenameGenerator() - Constructor for class net.sf.basedb.util.bfs.AbstractFilenameGenerator
- AbstractFileUnpacker - Class in net.sf.basedb.util.zip
-
This is a base class for all plugins that wants to implement the
FileUnpacker
interface. - AbstractFileUnpacker() - Constructor for class net.sf.basedb.util.zip.AbstractFileUnpacker
- AbstractFlatFileImporter - Class in net.sf.basedb.plugins
-
An abstract base class for all importers that imports data from one or more flat files.
- AbstractFlatFileImporter() - Constructor for class net.sf.basedb.plugins.AbstractFlatFileImporter
- AbstractHqlQuery - Class in net.sf.basedb.core
-
An abstract implementation of the
HqlQuery
interface. - AbstractHqlQuery(String, String, boolean) - Constructor for class net.sf.basedb.core.AbstractHqlQuery
-
Create a new HQL query.
- AbstractIOSupport - Class in net.sf.basedb.plugins.executor
-
Abstract base class that is useful for plug-ins that need to implement the
IOSupport
interface and don't want to be visible as standalone plug-ins. - AbstractIOSupport() - Constructor for class net.sf.basedb.plugins.executor.AbstractIOSupport
- AbstractItemImporter<I extends BasicItem> - Class in net.sf.basedb.plugins.batchimport
-
An abstract base class for plug-ins that import items in batch.
- AbstractItemImporter() - Constructor for class net.sf.basedb.plugins.batchimport.AbstractItemImporter
- AbstractJepConversionFunction<T> - Class in net.sf.basedb.util.jep.convert
-
Abstract superclass implementing the
JepConversionFunction
interface. - AbstractJepConversionFunction() - Constructor for class net.sf.basedb.util.jep.convert.AbstractJepConversionFunction
- AbstractJspActionFactory<A extends Action> - Class in net.sf.basedb.clients.web.extensions
-
An abstract base class for action factories that may need to support adding scripts and stylesheets to the rendered JSP page.
- AbstractJspActionFactory() - Constructor for class net.sf.basedb.clients.web.extensions.AbstractJspActionFactory
-
Create a new factory instance.
- AbstractJspFactory - Class in net.sf.basedb.clients.web.extensions
-
An abstract BASE class for action and renderer factories.
- AbstractJspFactory() - Constructor for class net.sf.basedb.clients.web.extensions.AbstractJspFactory
-
Create a new factory instance.
- AbstractJspRendererFactory<A extends Action> - Class in net.sf.basedb.clients.web.extensions
-
An abstract base class for action factories that may need to support adding scripts and stylesheets to the rendered JSP page.
- AbstractJspRendererFactory() - Constructor for class net.sf.basedb.clients.web.extensions.AbstractJspRendererFactory
-
Create a new factory instance.
- AbstractListColumnBean<I,
V> - Class in net.sf.basedb.clients.web.extensions.list -
A simple bean-like implementation of the ListColumn interface.
- AbstractListColumnBean() - Constructor for class net.sf.basedb.clients.web.extensions.list.AbstractListColumnBean
- AbstractNodeLoader<I> - Class in net.sf.basedb.util.overview.loader
-
Abstract node loader implementation that does nothing/throws an exception.
- AbstractNodeLoader() - Constructor for class net.sf.basedb.util.overview.loader.AbstractNodeLoader
- AbstractOnSaveAction - Class in net.sf.basedb.clients.web.extensions.edit
-
Abstract base implementation of the OnSaveAction interface.
- AbstractOnSaveAction() - Constructor for class net.sf.basedb.clients.web.extensions.edit.AbstractOnSaveAction
-
Create a on-save action without a context
- AbstractOnSaveAction(JspContext) - Constructor for class net.sf.basedb.clients.web.extensions.edit.AbstractOnSaveAction
-
Create a on-save action with a jsp context.
- AbstractPlugin - Class in net.sf.basedb.core.plugin
-
This is an abstract base class useful for developing plugins.
- AbstractPlugin() - Constructor for class net.sf.basedb.core.plugin.AbstractPlugin
-
Create a new
AbstractPlugin
. - AbstractQuery - Class in net.sf.basedb.core
-
An abstract implementation of the
Query
interface. - AbstractQuery(String) - Constructor for class net.sf.basedb.core.AbstractQuery
-
Create a new query.
- AbstractQueryCache - Class in net.sf.basedb.core.hibernate
-
Abstract base class used to cache queries for a session.
- AbstractQueryCache() - Constructor for class net.sf.basedb.core.hibernate.AbstractQueryCache
- AbstractRenderer<A extends Action> - Class in net.sf.basedb.util.extensions
-
Abstract class that provides a default implementation of the deprecated
AbstractRenderer.render(Action)
method. - AbstractRenderer() - Constructor for class net.sf.basedb.util.extensions.AbstractRenderer
- AbstractResultList<I> - Class in net.sf.basedb.core
-
This is a list of the result from a query.
- AbstractResultList(long) - Constructor for class net.sf.basedb.core.AbstractResultList
- AbstractResultWriter - Class in net.sf.basedb.core.migrate
-
Abstract base implementation of a result writer that simply store the result set, writer, etc. that are needed later.
- AbstractResultWriter(ResultSet, int, Writer, char[]) - Constructor for class net.sf.basedb.core.migrate.AbstractResultWriter
-
Creates a new writer.
- AbstractSignalHandler - Class in net.sf.basedb.core.signal
-
An abstract base class for signal handler implementations.
- AbstractSignalHandler() - Constructor for class net.sf.basedb.core.signal.AbstractSignalHandler
-
Create a new signal handler, that initially doesn't support any signals at all.
- AbstractSignalHandler(Collection<Signal>) - Constructor for class net.sf.basedb.core.signal.AbstractSignalHandler
-
Create a new signal handler that supports the given signals.
- AbstractSignalReceiver - Class in net.sf.basedb.core.signal
-
Abstract base class that is useful when implementing signal receivers.
- AbstractSignalReceiver() - Constructor for class net.sf.basedb.core.signal.AbstractSignalReceiver
-
Create a new signal receiver.
- AbstractSignalTransporter - Class in net.sf.basedb.core.signal
-
Abstract base class that is useful when implementing signal transporters.
- AbstractSignalTransporter() - Constructor for class net.sf.basedb.core.signal.AbstractSignalTransporter
- AbstractSourceItemTransformer - Class in net.sf.basedb.util.listable
-
Abstract base class for source item transformers that can be useful for implementing some common functionality.
- AbstractSourceItemTransformer(Item, Item) - Constructor for class net.sf.basedb.util.listable.AbstractSourceItemTransformer
-
Create a new instance that transforms between the given source and target item types.
- AbstractSourceItemTransformerFactory - Class in net.sf.basedb.util.listable
-
Abstract base class for source item transformer factories that can be useful for implementing some common functionality.
- AbstractSourceItemTransformerFactory(Item, Item[], Item[]) - Constructor for class net.sf.basedb.util.listable.AbstractSourceItemTransformerFactory
-
Create a new instance supports transformation between the given source items and target item.
- AbstractSqlQuery - Class in net.sf.basedb.core
-
An abstract implementation of the
SqlQuery
interface. - AbstractSqlQuery(String) - Constructor for class net.sf.basedb.core.AbstractSqlQuery
- AbstractSqlQuery.CountWork - Class in net.sf.basedb.core
- ACCELERATION - Static variable in class net.sf.basedb.core.Quantity
-
The id for the
Quantity
object representing acceleration. - accept(File) - Method in class net.sf.basedb.util.OlderThanFileFilter
-
Accept files that are older than the specified last modified time.
- accept(File) - Method in class net.sf.basedb.util.RegexpFileFilter
-
Accept files with a name matching the regular expression
- accept(String) - Method in class net.sf.basedb.core.hibernate.SchemaGenerator.CollectSqlTarget
- Accept - Enum Class in net.sf.basedb.util.fileset
-
Return result from the
ValidationAction.acceptFile(net.sf.basedb.core.FileSetMember)
method. - Accept() - Constructor for enum class net.sf.basedb.util.fileset.Accept
- acceptDenied - Variable in class net.sf.basedb.util.overview.validator.NullNodeValidator
- acceptedFile - Variable in class net.sf.basedb.util.fileset.SingleFileValidationAction
- acceptFile(FileSetMember) - Method in class net.sf.basedb.util.fileset.SingleFileValidationAction
-
If the file has a file type matching the id given in the constructor it is accepted for immediate validation.
- acceptFile(FileSetMember) - Method in interface net.sf.basedb.util.fileset.ValidationAction
-
Check if the given file is handled by this validator implementation or not?
- acceptInsertIfNullReporterOnFeature - Variable in class net.sf.basedb.core.RawDataBatcher
-
If we should always accept inserts when the feature has a NULL reporter.
- acceptInsertIfNullReporterOnFeature(boolean) - Method in class net.sf.basedb.core.RawDataBatcher
-
Specify if inserts always should be accepted if there is a matching feature that has a NULL reporter.
- acceptMissing - Variable in class net.sf.basedb.util.overview.validator.NullNodeValidator
- AccessControlled - Interface in net.sf.basedb.core
-
This interface should be implemented by a class representing items which requires the logged in user to have permission to access them.
- AccountExpiredException - Exception in net.sf.basedb.core
-
This exception is thrown if you try to log in with an account that has expired.
- AccountExpiredException(String, Date) - Constructor for exception net.sf.basedb.core.AccountExpiredException
-
Creates a new
AccountExpiredException
. - aColumn - Static variable in class net.sf.basedb.util.importer.spotdata.MAParser
- ACT_AS_ANOTHER_USER - Enum constant in enum class net.sf.basedb.core.Permission
-
This permission allows a user act as another user using the
SessionControl.impersonateLogin(int, String)
method. - action - Variable in class net.sf.basedb.clients.web.extensions.list.RelatedItemExtensionColumn
- action - Variable in class net.sf.basedb.clients.web.taglib.table.Table
- Action - Interface in net.sf.basedb.util.extensions
-
An action is an object that is added to an
ExtensionPoint
by anExtension
. - Action() - Constructor for enum class net.sf.basedb.core.Transactional.Action
- actionClass - Variable in class net.sf.basedb.util.extensions.ExtensionPointBean
- actionClass - Variable in class net.sf.basedb.util.extensions.Registry.RegisteredExtensionPoint
- ActionClassEventFilter - Class in net.sf.basedb.util.extensions.events
-
Event filter that only passes on events to extension points with a given action class.
- ActionClassEventFilter(Class<? extends Action>) - Constructor for class net.sf.basedb.util.extensions.events.ActionClassEventFilter
-
Create a new action class filter.
- actionFactory - Variable in class net.sf.basedb.util.extensions.ExtensionBean
- actionFactory - Variable in class net.sf.basedb.util.extensions.Registry.RegisteredExtension
- ActionFactory<A extends Action> - Interface in net.sf.basedb.util.extensions
-
An action factory is an object which knows how to create
Action
:s. - actionId - Variable in class net.sf.basedb.clients.web.extensions.list.RelatedItemColumn.Specification
- ActionIterator<A extends Action> - Class in net.sf.basedb.util.extensions
-
Iterator for iterating over all actions that will be created by extensions after a call to
Registry.useExtensions(ClientContext, ExtensionsFilter, String...)
. - ActionIterator(Iterator<ExtensionContext<A>>) - Constructor for class net.sf.basedb.util.extensions.ActionIterator
- actions - Variable in class net.sf.basedb.clients.web.extensions.menu.FixedMenuItemFactory
- actions - Variable in class net.sf.basedb.clients.web.extensions.startpage.FixedStartPageFactory
- actions - Variable in class net.sf.basedb.clients.web.extensions.tabcontrol.FixedTabFactory
- actions - Variable in class net.sf.basedb.clients.web.extensions.toolbar.FixedButtonFactory
- actions - Variable in class net.sf.basedb.util.extensions.ActionIterator
- actions - Variable in class net.sf.basedb.util.extensions.debug.BeanActionFactory
- actions - Variable in class net.sf.basedb.util.extensions.debug.ProxyActionFactory
- active - Variable in class net.sf.basedb.clients.web.taglib.tab.TabControl
-
The ID attribute of the active tab.
- activeJobs - Variable in class net.sf.basedb.clients.jobagent.Agent
- activeProject - Variable in class net.sf.basedb.plugins.batchimport.AbstractItemImporter
- activeProject - Variable in class net.sf.basedb.plugins.batchimport.AnyToAnyImporter
- activeProjectId - Variable in class net.sf.basedb.core.AnnotationBatcher
- activeProjectId - Variable in class net.sf.basedb.core.data.JobData
- activeProjectId - Variable in class net.sf.basedb.core.SessionControl.LoginInfo
-
The id of the
ProjectData
object of the active project. - activeProjectName - Variable in class net.sf.basedb.core.SessionControl.LoginInfo
-
The name of the the active project.
- actualCatalog - Variable in class net.sf.basedb.core.ServiceSessionControl.SessionFactoryConfiguration
- actualParameters - Variable in class net.sf.basedb.util.jep.SimpleJepFunction
- actualSchema - Variable in class net.sf.basedb.core.ServiceSessionControl.SessionFactoryConfiguration
- AdaptiveNumberFormatter - Class in net.sf.basedb.util.formatter
-
Formats a number for output on a web page adapting thwe number of decimals depending on the order of magnitude of the value.
- AdaptiveNumberFormatter(int, boolean) - Constructor for class net.sf.basedb.util.formatter.AdaptiveNumberFormatter
-
Create a new number formatter.
- add(int, I) - Method in class net.sf.basedb.core.AbstractResultList
-
Not supported.
- add(int, T) - Method in class net.sf.basedb.core.UnmodifiableResultList
-
Not supported.
- add(E) - Method in class net.sf.basedb.util.Tree
-
Not supported.
- add(I) - Method in class net.sf.basedb.core.AbstractResultList
-
Not supported.
- add(Long, Long) - Method in class net.sf.basedb.core.DiskUsageStatistics.Summary
- add(Collection<? extends Integer>) - Method in class net.sf.basedb.core.ItemList
-
Add all items in the collection to this list.
- add(Iterator<? extends Listable>) - Method in class net.sf.basedb.core.ItemList
-
Add multiple items to this list in one go.
- add(K, V) - Method in class net.sf.basedb.util.Enumeration
- add(DerivedBioAssayData) - Method in class net.sf.basedb.core.DerivedBioAssay.FixDerivedBioAssayParentsRecursivelyAction
-
Register the given derived bioassay as one that has had it's parent items changed.
- add(SystemData) - Static method in class net.sf.basedb.core.SystemItems
-
Register a system item.
- add(ItemQuery<? extends Listable>) - Method in class net.sf.basedb.core.ItemList
-
Add all items that are returned by the query to this list.
- add(Listable) - Method in class net.sf.basedb.core.ItemList
-
Add an item to this list.
- add(Listable) - Method in class net.sf.basedb.core.ItemList.DelayedAdditionManager
- add(Expression, Expression) - Static method in class net.sf.basedb.core.query.Expressions
-
Add two expressions: new expression = e1 + e2.
- add(InheritSpecification) - Method in class net.sf.basedb.util.annotations.InheritAnnotationsManager.AnnotationTypeFilter
- add(LogEntry) - Method in class net.sf.basedb.util.extensions.logging.ExtensionsLog
-
Add a log entry.
- add(T) - Method in class net.sf.basedb.core.ItemResultList.ResultListListIterator
-
This operation is not supported.
- add(T) - Method in class net.sf.basedb.core.UnmodifiableResultList
-
Not supported.
- ADD - Enum constant in enum class net.sf.basedb.core.log.ChangeType
- ADD_ONLY - Enum constant in enum class net.sf.basedb.core.ItemList.SynchronizeOption
-
Synchronize the members by adding new items matching the filter.
- addAll(int, Collection<? extends I>) - Method in class net.sf.basedb.core.AbstractResultList
-
Not supported.
- addAll(int, Collection<? extends T>) - Method in class net.sf.basedb.core.UnmodifiableResultList
-
Not supported.
- addAll(Collection<? extends E>) - Method in class net.sf.basedb.util.Tree
-
Not supported.
- addAll(Collection<? extends I>) - Method in class net.sf.basedb.core.AbstractResultList
-
Not supported.
- addAll(Collection<? extends T>) - Method in class net.sf.basedb.core.UnmodifiableResultList
-
Not supported.
- addAll(ItemList) - Method in class net.sf.basedb.core.ItemList
-
Add all items from another item list to this list.
- addAll(ItemList.DelayedAdditionManager) - Method in class net.sf.basedb.core.ItemList.DelayedAdditionManager
- addAll(ReporterList) - Method in class net.sf.basedb.core.ReporterList
-
Add all reporters from another reporter list to this list.
- addAllItems(Collection<? extends Annotatable>) - Method in class net.sf.basedb.util.annotations.RunnableInheritAnnotationsManager
-
Add all items for processing.
- AddAllTransformer<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 APIExpression
. - AddConverter() - Constructor for class net.sf.basedb.util.jep.convert.AddConverter
- addData(SqlResultIterator, String...) - Method in class net.sf.basedb.util.plot.ScatterPlot
-
Add data to the plot.
- addData(SqlResultIterator, String, float, HistogramPlot.YAggregate, HistogramPlot.YAggregate) - Method in class net.sf.basedb.util.plot.HistogramPlot
-
Add data to the plot.
- addData(SqlResultIterator, Collection<PlotAnnotation>) - Method in class net.sf.basedb.util.plot.ScatterPlot
-
Add data to the plot.
- addData(SqlResultIterator, Collection<PlotAnnotation>, float, HistogramPlot.YAggregate, HistogramPlot.YAggregate) - Method in class net.sf.basedb.util.plot.HistogramPlot
-
Add data to the plot.
- addDataParser(DataParser) - Method in class net.sf.basedb.util.importer.spotdata.SynchronizedSpotDataParser
-
Adds a data parser.
- addDefaultItem(BasicItem) - Method in class net.sf.basedb.core.Project
-
Add an item as a default project item.
- addDefultRolesAndGroups(Session, UserData) - Static method in class net.sf.basedb.core.User
-
Add all groups and roles that has been marked as default to the user.
- addDirectory(File) - Method in class net.sf.basedb.util.extensions.manager.ExtensionsManager
-
Add a directory to this manager.
- addDynamicAttributes(StringBuilder) - Method in class net.sf.basedb.clients.web.taglib.StylableTag
- ADDED - Enum constant in enum class net.sf.basedb.core.AnnotationBatcher.Change
-
A new annotation was created.
- addedBytes - Variable in class net.sf.basedb.core.DataCube
- addedBytes - Variable in class net.sf.basedb.core.Experiment
- addEntity(Class) - Method in class net.sf.basedb.core.hibernate.NativeQueryWrapper
- addEntity(String) - Method in class net.sf.basedb.core.hibernate.NativeQueryWrapper
- addEntity(String, Class) - Method in class net.sf.basedb.core.hibernate.NativeQueryWrapper
- addEntity(String, Class, LockMode) - Method in class net.sf.basedb.core.hibernate.NativeQueryWrapper
- addEntity(String, String) - Method in class net.sf.basedb.core.hibernate.NativeQueryWrapper
- addEntity(String, String, LockMode) - Method in class net.sf.basedb.core.hibernate.NativeQueryWrapper
- addEntry(String, String...) - Method in class net.sf.basedb.util.bfs.MetadataModel.Section
-
Add a new entry to this section.
- addEntry(MetadataModel.SectionEntry) - Method in class net.sf.basedb.util.bfs.MetadataModel.Section
-
Add a new entry to this section.
- addEntry(Tree.Entry<E>) - Method in class net.sf.basedb.util.Tree
- addError(String) - Method in class net.sf.basedb.util.jep.FunctionSafeJep
-
Adds an error message to the "real" JEP parser.
- addErrorHandler(Class<? extends Throwable>, ErrorHandler) - Method in class net.sf.basedb.plugins.AbstractFlatFileImporter
-
Add an error handler for the specified class of error.
- addErrorHandler(Class<? extends Throwable>, ErrorHandler) - Method in class net.sf.basedb.util.error.ClassMapErrorHandler
-
Add an error handler for throwable:s of a specific class.
- addErrorMessage(ExtensionsFile, String) - Method in class net.sf.basedb.util.extensions.manager.ProcessResults
-
Adds a detailed message inidcating a failed operation to a file.
- addErrors(int) - Method in class net.sf.basedb.util.overview.Node
-
Add more errors to this node.
- addEventHandler(EventHandler) - Method in class net.sf.basedb.util.bfs.MultiEventHandler
-
Adds an event handler.
- addEventListeners(SessionEventListener...) - Method in class net.sf.basedb.core.hibernate.SessionWrapper
- addExperimentalFactor(AnnotationType) - Method in class net.sf.basedb.core.Experiment
-
Add an annotation type as an experimental factor to this experiment.
- addExperimentalFactorsAsAssayFields() - Method in class net.sf.basedb.util.export.spotdata.AbstractBioAssaySetExporter
-
Adds all experimental factors from the experiment that the source bioassay set belongs to as assay fields.
- addExperimentParameters(DbControl, Experiment, List<PluginParameter<?>>) - Method in class net.sf.basedb.plugins.RawDataFlatFileImporter
- AddExpression - Class in net.sf.basedb.core.query
-
Add two expressions: e1 + e2.
- AddExpression(Expression, Expression) - Constructor for class net.sf.basedb.core.query.AddExpression
- addExtendedProperties(Element, String) - Static method in class net.sf.basedb.core.HibernateUtil
-
Append <property> tags to the given class tag.
- addExtension(Registry.RegisteredExtension<A>) - Method in class net.sf.basedb.util.extensions.Registry.RegisteredExtensionPoint
-
Add an extension to this extension point.
- addExtensionsFile(ExtensionsFile) - Method in class net.sf.basedb.util.extensions.manager.ExtensionsManager
- addExtraColumns(List<TableColumn>, DbControl, BioAssaySet, String, String, String) - Static method in class net.sf.basedb.clients.web.DynamicUtil
- addExtraFile(String, String) - Method in class net.sf.basedb.util.export.spotdata.BfsExporter
-
Add information about an extra data file that is included as part of the BFS.
- addExtraFloat(DbControl, String) - Method in class net.sf.basedb.util.importer.spotdata.BaseFileInfo
-
Add information about an extra float value that appears in the BASEfile.
- addExtraFloatParser(ExtraFloatParser) - Method in class net.sf.basedb.util.importer.spotdata.BaseFileInfo.SpotSectionInfo
-
Add an extra value parser to this section.
- addFetch(String, String, String) - Method in class net.sf.basedb.core.hibernate.NativeQueryWrapper
- addFile(File) - Method in class net.sf.basedb.util.extensions.manager.ExtensionsManager
-
Add a file to the manager that is supposed to contain extensions.
- addFile(String, String) - Method in class net.sf.basedb.util.bfs.MetadataModel
-
Add an entry to the 'files' section.
- addFile(String, UploadedFile) - Method in class net.sf.basedb.clients.web.fileupload.FileUpload
-
Store information about an uploaded file.
- addFilename(String) - Method in class net.sf.basedb.util.bfs.AbstractFilenameGenerator
-
Add the file name to the list of already generated file names.
- addFilterConditions(Element, String, HibernateUtil.FilterConfigurator) - Static method in class net.sf.basedb.core.HibernateUtil
-
Add <filter> conditions to the given class tag.
- addFilteredColumn(String, String, boolean) - Method in class net.sf.basedb.clients.web.taglib.table.Table
- addFilterRows(int) - Method in class net.sf.basedb.core.ItemContext
-
Add filter rows to the table.
- addFix(Fix) - Method in class net.sf.basedb.util.overview.Failure
-
Add a suggested fix to this failure.
- addFormulaColumns(List<TableColumn>, DbControl, RawDataType, Formula.Type, IntensityTransform, String, String, boolean) - Static method in class net.sf.basedb.clients.web.DynamicUtil
- addFunctions(JEP, JepFunction...) - Static method in class net.sf.basedb.util.jep.Jep
- addGroup(Group) - Method in class net.sf.basedb.core.Group
-
Add a group as a member to this group.
- addHeaderColumns(int) - Method in class net.sf.basedb.clients.web.taglib.table.HeaderRow
- addHidden(String, String) - Method in class net.sf.basedb.clients.web.taglib.table.Table
- addIdAndStyles(StringBuilder, String...) - Method in class net.sf.basedb.clients.web.taglib.StylableTag
-
Add id, class and style attributes the the stringbuilder.
- addIfPresentIn(int, int, Collection<ItemList>) - Method in class net.sf.basedb.core.ItemList
-
Add items that are present in the specified number of lists to this list.
- addIfPresentIn(int, int, Collection<ReporterList>) - Method in class net.sf.basedb.core.ReporterList
-
Add reporters that are present in the specified number of lists to this list.
- addIgnore(File) - Method in class net.sf.basedb.util.extensions.manager.ExtensionsManager
-
Add a file to the ignore list.
- addIntersection(Collection<ItemList>) - Method in class net.sf.basedb.core.ItemList
-
Add items that are present in ALL OF the given lists to this list.
- addIntersection(Collection<ReporterList>) - Method in class net.sf.basedb.core.ReporterList
-
Add reporters that are present in ALL OF the given lists to this list.
- addItem(Annotatable) - Method in class net.sf.basedb.util.annotations.RunnableInheritAnnotationsManager
-
Add an item that should inherit annotations.
- addJoin(String, String) - Method in class net.sf.basedb.core.hibernate.NativeQueryWrapper
- addJoin(String, String, String) - Method in class net.sf.basedb.core.hibernate.NativeQueryWrapper
- addJoin(String, String, LockMode) - Method in class net.sf.basedb.core.hibernate.NativeQueryWrapper
- addManualSingleChange(ChangeType, Object) - Method in class net.sf.basedb.core.log.LoggingInterceptor
-
Adds a manual non-Hibernate change to the log system.
- addManualSingleChange(ChangeType, Object, Object, Object, String, Type) - Method in class net.sf.basedb.core.log.LoggingInterceptor
-
Adds a manual non-Hibernate change to the log system.
- addMeasurement(float) - Method in class net.sf.basedb.util.plot.HistogramPlot.HistogramBin
-
Add a measurement to this bin.
- addMember(File, DataFileType) - Method in class net.sf.basedb.core.FileSet
-
Add a file as a member to the file set.
- addMembers(Set<Integer>, ItemList.DelayedAdditionManager) - Method in class net.sf.basedb.core.ItemList
-
Add members to this list.
- addMembersMode - Variable in class net.sf.basedb.plugins.batchimport.AbstractItemImporter
- addMenuitem(String) - Method in class net.sf.basedb.clients.web.taglib.menu.Menu
- addMessage(ExtensionsFile, String) - Method in class net.sf.basedb.util.extensions.manager.ProcessResults
-
Adds a detailed message indicating a successful operation to a file.
- addMessage(ExtensionsFile, String, boolean) - Method in class net.sf.basedb.util.extensions.manager.ProcessResults
- addMoreColumnMappingParameters(List<PluginParameter<?>>) - Method in class net.sf.basedb.plugins.batchimport.AbstractItemImporter
-
Add column mapping parameters for item-specific properties.
- addMoreColumnMappingParameters(List<PluginParameter<?>>) - Method in class net.sf.basedb.plugins.batchimport.AnnotationTypeImporter
-
Adds column mappings for name and description.
- addMoreColumnMappingParameters(List<PluginParameter<?>>) - Method in class net.sf.basedb.plugins.batchimport.ArrayBatchImporter
-
Adds column mappings for name, description, protocol, robot, and array design
- addMoreColumnMappingParameters(List<PluginParameter<?>>) - Method in class net.sf.basedb.plugins.batchimport.ArrayDesignImporter
-
Adds column mappings for name, externalId, description, protocol, creation date, original quantity, pooled, parent and used quantity from parent.
- addMoreColumnMappingParameters(List<PluginParameter<?>>) - Method in class net.sf.basedb.plugins.batchimport.ArraySlideImporter
-
Adds column mappings for name, description, array batch, batch index, barcode and destroyed
- addMoreColumnMappingParameters(List<PluginParameter<?>>) - Method in class net.sf.basedb.plugins.batchimport.BioPlateImporter
-
Adds column mappings for name, description, plate type, plate geometry, barcode and freezer.
- addMoreColumnMappingParameters(List<PluginParameter<?>>) - Method in class net.sf.basedb.plugins.batchimport.BioSourceImporter
-
Adds column mappings for name, externalId and description.
- addMoreColumnMappingParameters(List<PluginParameter<?>>) - Method in class net.sf.basedb.plugins.batchimport.DerivedBioAssayImporter
-
Adds column mappings for name, internalId, subtype, description, protocol, hardware, software, parent, data files and permissions.
- addMoreColumnMappingParameters(List<PluginParameter<?>>) - Method in class net.sf.basedb.plugins.batchimport.ExtractImporter
-
Adds column mappings for name, externalId, description, protocol, creation date, original quantity, pooled, parent and used quantity from parent.
- addMoreColumnMappingParameters(List<PluginParameter<?>>) - Method in class net.sf.basedb.plugins.batchimport.FileImporter
-
Adds column mappings for name, externalId and description.
- addMoreColumnMappingParameters(List<PluginParameter<?>>) - Method in class net.sf.basedb.plugins.batchimport.KitImporter
-
Adds column mappings for name and description.
- addMoreColumnMappingParameters(List<PluginParameter<?>>) - Method in class net.sf.basedb.plugins.batchimport.PhysicalBioAssayImporter
-
Adds column mappings for name, externalId, description, protocol, creation date, original quantity, pooled, parent and used quantity from parent.
- addMoreColumnMappingParameters(List<PluginParameter<?>>) - Method in class net.sf.basedb.plugins.batchimport.RawBioAssayImporter
-
Adds column mappings for name, externalId, description, protocol, creation date, original quantity, pooled, parent and used quantity from parent.
- addMoreColumnMappingParameters(List<PluginParameter<?>>) - Method in class net.sf.basedb.plugins.batchimport.SampleImporter
-
Adds column mappings for name, externalId, description, protocol, creation date, original quantity, pooled, parent and used quantity from parent.
- addMoreColumnMappingParameters(List<PluginParameter<?>>) - Method in class net.sf.basedb.plugins.batchimport.TagImporter
-
Adds column mappings for name and description.
- addMoreErrorParameters(List<PluginParameter<?>>) - Method in class net.sf.basedb.plugins.batchimport.AbstractItemImporter
-
Add extra parameters to the "Error handling" section that the subclass needs.
- addMoreErrorParameters(List<PluginParameter<?>>) - Method in class net.sf.basedb.plugins.batchimport.PhysicalBioAssayImporter
- addMoreJobParameters(List<PluginParameter<?>>) - Method in class net.sf.basedb.plugins.batchimport.AbstractItemImporter
-
Add extra job parameters that the subclass needs.
- addMoreJobParameters(List<PluginParameter<?>>) - Method in class net.sf.basedb.plugins.batchimport.ArrayDesignImporter
-
Add parameter for "Data directory" directory where data files may be located.
- addMoreJobParameters(List<PluginParameter<?>>) - Method in class net.sf.basedb.plugins.batchimport.DerivedBioAssayImporter
-
Add parameter for "Data directory" directory where data files may be located.
- addMoreJobParameters(List<PluginParameter<?>>) - Method in class net.sf.basedb.plugins.batchimport.FileImporter
- addMoreJobParameters(List<PluginParameter<?>>) - Method in class net.sf.basedb.plugins.batchimport.RawBioAssayImporter
-
Add parameter for "Data directory" directory where data files may be located.
- addMoreParsingParameters(List<PluginParameter<?>>) - Method in class net.sf.basedb.plugins.batchimport.AbstractItemImporter
-
Add extra parameters to the "Parser settings" section that the subclass needs.
- addMoreParsingParameters(List<PluginParameter<?>>) - Method in class net.sf.basedb.plugins.batchimport.AnnotationTypeImporter
- addParameter(String, String) - Method in class net.sf.basedb.clients.web.fileupload.FileUpload
-
Store the value of a regular form field.
- addParameter(AnnotationType) - Method in class net.sf.basedb.core.Protocol
-
Add an annotation type as a parameter to this protocol.
- addParametersWithNamespace(List<PluginParameter<?>>, List<PluginParameter<?>>, String) - Method in class net.sf.basedb.plugins.executor.ExternalProgramExecutor
-
Add more parameters to a list of parameters with a different namespace.
- addParent(DerivedBioAssay) - Method in class net.sf.basedb.core.DerivedBioAssay
-
Add a derived bioassay as a parent to this derived bioassay.
- addParticipant(BioPlate, String, int) - Method in class net.sf.basedb.core.BioPlateEvent
-
Add a bioplate as a participant in this event.
- addPermissions(Group, Set<Permission>) - Method in class net.sf.basedb.core.GroupPermissions
-
Grant permissions to a group, keeping those that have already been set.
- addPermissions(Group, Set<Permission>) - Method in class net.sf.basedb.core.MultiPermissions
-
Grant permissions to a group, keeping those that have already been set.
- addPermissions(Project, Set<Permission>) - Method in class net.sf.basedb.core.MultiPermissions
-
Grant permissions to a project, keeping those that have already been set.
- addPermissions(Project, Set<Permission>) - Method in class net.sf.basedb.core.ProjectPermissions
-
Grant permissions to a project, keeping those that have already been set.
- addPermissions(User, Set<Permission>) - Method in class net.sf.basedb.core.MultiPermissions
-
Grant permissions to a user, keeping those that have already been set.
- addPermissions(User, Set<Permission>) - Method in class net.sf.basedb.core.UserPermissions
-
Grant permissions to a user, keeping those that have already been set.
- addPhysicalBioAssay(PhysicalBioAssay) - Method in class net.sf.basedb.core.DerivedBioAssay
-
Add a physical bioassay as a parent to this derived bioassay.
- addPlate(Plate) - Method in class net.sf.basedb.core.ArrayDesign
-
Adds a single plate to the plate list.
- addQueryHint(String) - Method in class net.sf.basedb.core.hibernate.NativeQueryWrapper
- addQueryHint(String) - Method in class net.sf.basedb.core.hibernate.QueryWrapper
- addRawBioAssay(RawBioAssay) - Method in class net.sf.basedb.core.Experiment
-
Add a raw bioassay to this experiment.
- addRawBioAssayParameters(DbControl, RawBioAssay, List<PluginParameter<?>>) - Method in class net.sf.basedb.plugins.RawDataFlatFileImporter
- addRawDataColumns(List<TableColumn>, DbControl, RawDataType, String, String, String) - Static method in class net.sf.basedb.clients.web.DynamicUtil
- addRawDataMappings(MetadataSources) - Static method in class net.sf.basedb.core.HibernateUtil
-
Generate additional mappings for the raw data types.
- addReplaceSection - Static variable in class net.sf.basedb.plugins.AnnotationFlatFileImporter
- addReporter(ReporterData, Float) - Method in class net.sf.basedb.core.ReporterList
-
Add or update the score for a reporter.
- addReporterColumns(List<TableColumn>, DbControl, String, String, String) - Static method in class net.sf.basedb.clients.web.DynamicUtil
- addReporterColumns(List<TableColumn>, DbControl, ReporterCloneTemplate, String, String, String) - Static method in class net.sf.basedb.clients.web.DynamicUtil
- addReporterField(DynamicField) - Method in class net.sf.basedb.util.export.spotdata.AbstractBioAssaySetExporter
-
Add information about a reporter field that should be exported.
- addReporterField(DynamicField) - Method in class net.sf.basedb.util.export.spotdata.BaseFileExporter
- addReporterField(DynamicField) - Method in class net.sf.basedb.util.export.spotdata.BfsExporter
- addReporterFields(Collection<? extends DynamicField>) - Method in class net.sf.basedb.util.export.spotdata.BaseFileExporter
-
Add multiple reporter fields in one go.
- addReporterFields(Collection<? extends DynamicField>) - Method in class net.sf.basedb.util.export.spotdata.BfsExporter
-
Add multiple reporter fields in one go.
- addReporters(Set<Integer>) - Method in class net.sf.basedb.core.ReporterList
- addReportUriIfNeeded(String, FilterConfig) - Method in class net.sf.basedb.clients.web.servlet.ContentSecurityPolicyFilter
- addResources(Vector<URL>, Enumeration<URL>) - Method in class net.sf.basedb.util.JarClassLoader
- address - Variable in class net.sf.basedb.core.authentication.ExtraUserInformation
- address - Variable in class net.sf.basedb.core.data.UserData
- addRestriction(Restriction) - Method in class net.sf.basedb.core.ItemContext.RowRestrictions
- addRoleKey(RoleKeyData) - Static method in class net.sf.basedb.core.SystemItems
-
Register a role key.
- addRolePermissions(RoleData, Map<Item, Integer>) - Static method in class net.sf.basedb.core.Install
-
Add permissions for a role for specific item types.
- addRoot(String, Class) - Method in class net.sf.basedb.core.hibernate.NativeQueryWrapper
- addRoot(String, String) - Method in class net.sf.basedb.core.hibernate.NativeQueryWrapper
- addRow(String...) - Method in class net.sf.basedb.util.bfs.AnnotationModel
-
Add a row of data to the model.
- addRow(String...) - Method in class net.sf.basedb.util.bfs.MatrixModel
-
Add a row of data to the model.
- addScalar(String) - Method in class net.sf.basedb.core.hibernate.NativeQueryWrapper
- addScalar(String, Type) - Method in class net.sf.basedb.core.hibernate.NativeQueryWrapper
- addScript(String) - Method in class net.sf.basedb.clients.web.extensions.JspContext
-
Add an absolute reference to a script that should be included on the generated page with a
<script>
tag. - addScripts(Collection<String>) - Method in class net.sf.basedb.clients.web.extensions.JspContext
-
Add several scripts in one go.
- addSection(String) - Method in class net.sf.basedb.util.bfs.MetadataModel
-
Adds a new section to the model.
- addSeries(HistogramPlot.HistogramSeries) - Method in class net.sf.basedb.util.plot.HistogramPlot.HistogramDataset
- addSignal(Signal) - Method in class net.sf.basedb.core.signal.AbstractSignalHandler
-
Add a signal to the list of supported signals.
- addSource(BioMaterial) - Method in class net.sf.basedb.core.BioMaterialEvent
-
Add a biomaterial as a source to this event.
- addSpecification(InheritSpecification) - Method in class net.sf.basedb.util.annotations.RunnableInheritAnnotationsManager
-
Add a specification with rules for inheriting annotations.
- addSpotColumns(List<TableColumn>, DbControl, int, IntensityTransform) - Static method in class net.sf.basedb.clients.web.DynamicUtil
- addSpotField(DynamicField) - Method in class net.sf.basedb.util.export.spotdata.AbstractBioAssaySetExporter
-
Add information about a spot field that should be exported.
- addSpotField(DynamicField) - Method in class net.sf.basedb.util.export.spotdata.BaseFileExporter
- addSpotField(DynamicField) - Method in class net.sf.basedb.util.export.spotdata.BfsExporter
-
Add information about a spot field that should be exported.
- addSpotFields(Collection<? extends DynamicField>) - Method in class net.sf.basedb.util.export.spotdata.BaseFileExporter
-
Add multiple spot fields in one go.
- addSpotFields(Collection<? extends DynamicField>) - Method in class net.sf.basedb.util.export.spotdata.BfsExporter
-
Add multiple spot fields in one go.
- addSpotIntensityParser(SpotIntensityParser) - Method in class net.sf.basedb.util.importer.spotdata.FirstPassSectionSpotsParser
-
Adds a spot intensity parser to the list of used parsers.
- addSpotSectionInfo(int, BaseFileInfo.SpotSectionInfo) - Method in class net.sf.basedb.util.importer.spotdata.BaseFileInfo
-
Adds information about a 'spot' section.
- addSqlFunctions(SessionFactoryBuilder, DbEngine) - Static method in class net.sf.basedb.core.HibernateUtil
-
Add more SQL functions to HQL that are not present in a standard Hibernate installation.
- addStaticMappings(MetadataSources, HibernateUtil.FilterConfigurator) - Static method in class net.sf.basedb.core.HibernateUtil
-
Read all mapping files, which must be named
Class.hbm.xml
where class is the name of each class. - addStatistics(String, float) - Method in class net.sf.basedb.clients.web.ExperimentExplorer.AnnotationGroup
-
Add another statisitcal measurement to this group.
- addStylesheet(String) - Method in class net.sf.basedb.clients.web.extensions.JspContext
-
Add an absolute reference to a CSS stylesheet that should be included on the generated page with a
<link>
tag. - addStylesheets(Collection<String>) - Method in class net.sf.basedb.clients.web.extensions.JspContext
-
Add several stylesheets in one go.
- addSymbol(String) - Method in class net.sf.basedb.core.Unit
-
Add a symbol to this unit.
- addSynchronizedEntityClass(Class) - Method in class net.sf.basedb.core.hibernate.NativeQueryWrapper
- addSynchronizedEntityName(String) - Method in class net.sf.basedb.core.hibernate.NativeQueryWrapper
- addSynchronizedQuerySpace(String) - Method in class net.sf.basedb.core.hibernate.NativeQueryWrapper
- addTab(TabAction) - Method in class net.sf.basedb.clients.web.taglib.tab.TabControl
- addToBatch(D, PreparedStatement, List<BatchedPropertyInfo>) - Method in class net.sf.basedb.core.BasicBatcher
-
Add the data object to the batch represented by the prepared statement
- addToBatch(Object...) - Method in class net.sf.basedb.core.AnnotationBatcher.UpdateBatcher
-
Add a new entry to the batch.
- addToDefaultRolesAndGroups() - Method in class net.sf.basedb.core.User
-
Add this user to the groups and roles that has been marked as default for new users.
- addToUnlimited - Variable in class net.sf.basedb.plugins.AnnotationFlatFileImporter
- addToUnlimitedParameter - Static variable in class net.sf.basedb.plugins.AnnotationFlatFileImporter
- addTransactionalAction(TransactionalAction) - Method in class net.sf.basedb.core.DbControl
-
Add a transactional action to this DbControl.
- addTransferredBytes(long) - Method in class net.sf.basedb.clients.web.fileupload.FileUploadProgress
-
Adds a value to the number of transfered bytes.
- addUnion(Collection<ItemList>) - Method in class net.sf.basedb.core.ItemList
-
Add items that are present in at least ONE OF the given lists to this list.
- addUnion(Collection<ReporterList>) - Method in class net.sf.basedb.core.ReporterList
-
Add reporters that are present in at least ONE OF the given lists to this list.
- addURI(URI) - Method in class net.sf.basedb.util.extensions.manager.ExtensionsManager
-
Add an URI that points to an XML file containing definitions.
- addUsableUnit(Unit) - Method in class net.sf.basedb.core.AnnotationType
-
Add a unit to be used with this annotation type.
- addUsedQuantity(float) - Method in class net.sf.basedb.core.MeasuredBioMaterial.RemainingQuantityAction
-
Add some used quantity to what has currently been recorded.
- addUser(User) - Method in class net.sf.basedb.core.Group
-
Add a user as a member to this group.
- addUser(User) - Method in class net.sf.basedb.core.Role
-
Assign this
Role
to a user. - addUsingItems(Set<ItemProxy>, Item, Query<Integer>) - Method in class net.sf.basedb.core.BasicItem
-
Add items to the set of items using this one.
- addUsingItems(Set<ItemProxy>, Query<? extends BasicData>) - Method in class net.sf.basedb.core.BasicItem
-
Add items to the set of items using this one.
- addValue(int, float) - Method in class net.sf.basedb.clients.web.ExperimentExplorer.AnnotationGroup
-
Add an intensity value to this group.
- addValue(AnnotationType, Object, Unit, boolean) - Method in class net.sf.basedb.plugins.AnnotationFlatFileImporter.NewAnnotations
-
Add an annotation value.
- addValueConverter(ValueConverter) - Method in class net.sf.basedb.util.extensions.xml.XmlLoader
-
Add a value converter to this loader
- addWarnings(int) - Method in class net.sf.basedb.util.overview.Node
-
Add more warnings to this node.
- adjustExistingItems(ProgressReporter, int, String, String) - Static method in class net.sf.basedb.core.Update
-
Adjust the existing items in the database to be compatible with the latest mappings.
- adjustRanges() - Method in class net.sf.basedb.util.plot.HistogramPlot
-
Auto-size of the x and y range doesn't seem to work, so we have to do it manually.
- ADMINISTRATOR - Static variable in class net.sf.basedb.core.Role
-
The id for the
Role
item representing adminstrators. - AdvancedFieldConverter - Class in net.sf.basedb.util.export.spotdata
-
Field converter implementation that gives more detailed control how fields are converted and used in the export.
- AdvancedFieldConverter(DbControl, BioAssaySet) - Constructor for class net.sf.basedb.util.export.spotdata.AdvancedFieldConverter
-
Create a new advanced field converter.
- affiliations - Variable in class net.sf.basedb.core.data.ExperimentData
- AFFYMETRIX - Static variable in class net.sf.basedb.core.Platform
-
The external id for the
Affymetrix
platform. - AFFYMETRIX_CDF - Static variable in class net.sf.basedb.core.DataFileType
-
The external ID for the file type representing Affymetrix CDF files.
- AFFYMETRIX_CEL - Static variable in class net.sf.basedb.core.DataFileType
-
The external ID for the file type representing Affymetrix CEL files.
- AffymetrixUtil - Class in net.sf.basedb.util.affymetrix
-
Utility class with Affymetrix-related functionality.
- AffymetrixUtil() - Constructor for class net.sf.basedb.util.affymetrix.AffymetrixUtil
- aFloat(float) - Static method in class net.sf.basedb.core.query.Expressions
-
Create a constant expression from a float.
- AFTER_ENABLE - Static variable in class net.sf.basedb.clients.web.extensions.ExtensionsControl
-
This event is sent after an extension or extension point is enabled by
ExtensionsControl.enableExtensionPoint(String, boolean)
,ExtensionsControl.enableExtension(String, boolean)
, orExtensionsControl.enableAllInFile(String, boolean)
. - AFTER_REGISTRATION - Static variable in class net.sf.basedb.util.extensions.events.EventType
-
This event is sent after an extension or extension point has been registered with a registry.
- AFTER_UPDATE - Static variable in class net.sf.basedb.util.extensions.events.EventType
-
This event is sent during an update of an existing extension point or extension.
- afterCommit() - Method in class net.sf.basedb.core.log.db.DbLogManager
- afterCommit() - Method in interface net.sf.basedb.core.log.LogManager
-
Called after a successful commit of changes to the database.
- afterRollback() - Method in class net.sf.basedb.core.log.db.DbLogManager
- afterRollback() - Method in interface net.sf.basedb.core.log.LogManager
-
Called after rollback.
- afterTransactionCompletion(Transaction) - Method in class net.sf.basedb.core.log.LoggingInterceptor
-
Signals successful commit or rollback to the log manager.
- agent - Variable in class net.sf.basedb.clients.jobagent.AgentSignalReceiver
- agent - Variable in class net.sf.basedb.clients.jobagent.handlers.AbstractCustomRequestHandler
- agent - Variable in class net.sf.basedb.clients.jobagent.handlers.DefaultRequestHandler
- agent - Variable in class net.sf.basedb.clients.jobagent.handlers.InfoRequestHandler
- agent - Variable in class net.sf.basedb.clients.jobagent.handlers.MultiProtocolRequestHandler
- agent - Variable in class net.sf.basedb.clients.jobagent.handlers.PauseRequestHandler
- agent - Variable in class net.sf.basedb.clients.jobagent.handlers.SignalRequestHandler
- agent - Variable in class net.sf.basedb.clients.jobagent.handlers.StartRequestHandler
- agent - Variable in class net.sf.basedb.clients.jobagent.handlers.StopRequestHandler
- agent - Variable in class net.sf.basedb.clients.jobagent.JobQueueChecker
- agent - Variable in class net.sf.basedb.clients.jobagent.JobRunner
- agent - Variable in class net.sf.basedb.clients.jobagent.slotmanager.InternalSlotManager
- agent - Variable in class net.sf.basedb.clients.jobagent.slotmanager.RemoteSlotManager
- agent - Variable in class net.sf.basedb.core.Job.ProgressReporterImpl
- Agent - Class in net.sf.basedb.clients.jobagent
-
This is the actual job agent application.
- Agent(Properties) - Constructor for class net.sf.basedb.clients.jobagent.Agent
-
Create a new job agent.
- AgentController - Class in net.sf.basedb.clients.jobagent
-
This is the command line controller class for the job agent application.
- AgentController(Properties) - Constructor for class net.sf.basedb.clients.jobagent.AgentController
-
Create a new controller for controlling the job agent specified by the given properties.
- agentInfo - Static variable in class net.sf.basedb.core.JobAgent
- AgentSignalReceiver - Class in net.sf.basedb.clients.jobagent
-
Signal receiver implementation for job agents that is compatible with the
SocketSignalReceiver
. - AgentSignalReceiver(Agent) - Constructor for class net.sf.basedb.clients.jobagent.AgentSignalReceiver
- agentVersionForJobQuery - Variable in class net.sf.basedb.clients.jobagent.JobQueueChecker
-
The job agent's version when the query was cached.
- Aggregations - Class in net.sf.basedb.core.query
-
A factory class to create aggregate expressions.
- Aggregations() - Constructor for class net.sf.basedb.core.query.Aggregations
- aIndex - Variable in class net.sf.basedb.util.importer.spotdata.MAParser
- alias - Variable in class net.sf.basedb.core.AnnotationRestriction
- alias - Variable in enum class net.sf.basedb.core.Item
- alias - Variable in class net.sf.basedb.core.query.AnnotationExpression
- alias - Variable in class net.sf.basedb.core.query.AnnotationJoin
- alias - Variable in class net.sf.basedb.core.query.AnyToAnyRestriction
- alias - Variable in class net.sf.basedb.core.query.ExpressionSelect
- alias - Variable in class net.sf.basedb.core.query.HqlElementsExpression
- alias - Variable in class net.sf.basedb.core.query.HqlIndexExpression
- alias - Variable in class net.sf.basedb.core.query.HqlInnerJoin
- alias - Variable in class net.sf.basedb.core.query.HqlLeftJoin
- alias - Variable in class net.sf.basedb.core.query.HqlPropertyExpression
- alias - Variable in class net.sf.basedb.core.query.HqlRightJoin
- alias - Variable in class net.sf.basedb.core.query.HqlSizeExpression
- alias - Variable in class net.sf.basedb.core.query.SqlColumnExpression
- alias - Variable in class net.sf.basedb.core.RealTable
-
The alias to use in queries for this table.
- alias - Variable in enum class net.sf.basedb.core.VirtualTable
-
The alias to use in queries for this table.
- alias - Variable in class net.sf.basedb.util.ssl.StaticKeyManager
- alias(String) - Static method in class net.sf.basedb.core.query.Hql
-
Same as
property(alias, null)
. - ALIAS_REGEXP - Static variable in class net.sf.basedb.core.query.Hql
-
An alias can only contain the characters a-z, A-Z or 0-9.
- ALIAS_REGEXP - Static variable in class net.sf.basedb.core.query.Selects
-
An alias can only contain the characters a-z, A-Z or 0-9.
- aliasMapping - Static variable in enum class net.sf.basedb.core.Item
- ALIGNED_SEQUENCE - Static variable in class net.sf.basedb.core.File
-
The id for the
FileType
item representing a file containing aligned sequence data. - ALIGNMENT - Static variable in class net.sf.basedb.core.Protocol
-
The ID for the alignment protocol type, for example a protocol used when creating a
DerivedBioAssay
representing data that has been aligned against a reference genome. - ALIGNMENT - Static variable in class net.sf.basedb.core.Software
-
The id for the
SoftwareType
item representing software used for aligning sequenced data against a known reference database. - all - Static variable in class net.sf.basedb.core.RawDataTypes
- all - Variable in class net.sf.basedb.util.plot.HistogramPlot.HistogramDataset
- all(Query) - Static method in class net.sf.basedb.core.query.Expressions
-
Create a subquery expression:
ANY (subquery)
. - ALL - Enum constant in enum class net.sf.basedb.util.overview.node.ChildNodeDirection
- ALL - Static variable in enum class net.sf.basedb.core.Include
-
A non-modifable collection containing all options.
- ALL - Static variable in class net.sf.basedb.core.Keyring
- ALL_ITEM - Static variable in class net.sf.basedb.core.Keyring
- allCharsets - Static variable in class net.sf.basedb.core.Config
- allChildExtractsInChain - Variable in class net.sf.basedb.util.AnnotationUtil.AnnotatableWrapper
- allColumnMappings - Variable in class net.sf.basedb.plugins.gtf.GtfReporterMapImporter
- allColumnMappings - Variable in class net.sf.basedb.plugins.PlateFlatFileImporter
- allColumnMappings - Variable in class net.sf.basedb.plugins.RawDataFlatFileImporter
- allColumnMappings - Variable in class net.sf.basedb.plugins.ReporterFlatFileImporter
- allColumnMappings - Variable in class net.sf.basedb.plugins.ReporterMapFlatFileImporter
- allData - Variable in class net.sf.basedb.util.extensions.manager.processor.RegisterExtensionsProcessor
- AllEventsFilter - Class in net.sf.basedb.util.extensions.events
-
Event filter that passes all events.
- AllEventsFilter() - Constructor for class net.sf.basedb.util.extensions.events.AllEventsFilter
-
Create a event type filter that passes all events.
- allInsertBatchers - Variable in class net.sf.basedb.core.AnnotationBatcher
- allInsertBatchers - Variable in class net.sf.basedb.core.MigrateRbaToDba
- allModified - Variable in class net.sf.basedb.core.DerivedBioAssay.FixDerivedBioAssayParentsRecursivelyAction
- allMustPass - Variable in class net.sf.basedb.util.extensions.events.CombiningEventFilter
- allNodes - Variable in class net.sf.basedb.util.overview.GenericOverview
- allObjects - Variable in class net.sf.basedb.util.extensions.manager.ExtensionsFile
- AllOfFilter<T> - Class in net.sf.basedb.util.filter
-
A filter implementation that accpets an object if all parent filters accepts it.
- AllOfFilter(Collection<? extends Filter<? super T>>) - Constructor for class net.sf.basedb.util.filter.AllOfFilter
-
Create a new filter.
- allow - Variable in class net.sf.basedb.core.signal.SocketSignalReceiver
- ALLOW_ROOT_NODE - Static variable in class net.sf.basedb.util.overview.loader.BasicItemNodeLoader
- allowAll - Variable in class net.sf.basedb.core.signal.SocketSignalReceiver
- AllowAnyHostNameVerifyer - Class in net.sf.basedb.util.ssl
-
A simple implementation of a host name verifyer that allows all hosts.
- AllowAnyHostNameVerifyer() - Constructor for class net.sf.basedb.util.ssl.AllowAnyHostNameVerifyer
- allowAsRootNode - Variable in class net.sf.basedb.util.overview.loader.BasicItemNodeLoader
- allowColumnDrag() - Method in class net.sf.basedb.clients.web.taglib.table.Table
-
Can header columns be dragged for re-ordering?
- allowDoublingBack - Variable in class net.sf.basedb.clients.web.extensions.list.RelatedItemColumn.Specification
- allowedClients - Variable in class net.sf.basedb.core.SessionControl
- allowForward - Variable in class net.sf.basedb.core.signal.SocketSignalReceiver
- allowImmediateDownload - Variable in class net.sf.basedb.core.PluginResponse
- allowImmediateExecution - Variable in class net.sf.basedb.core.data.PluginDefinitionData
- allowImmediateExecution - Variable in class net.sf.basedb.core.PluginConfigurationRequest
- allowImmediateExecution - Variable in class net.sf.basedb.core.PluginRequest.RequestImpl
- allowImmediateExecution - Variable in class net.sf.basedb.core.PluginResponse
- allowMultiple - Variable in class net.sf.basedb.util.timer.ThreadTimerTask
- allowRemotePause - Variable in class net.sf.basedb.clients.jobagent.Agent
- allowRemoteStart - Variable in class net.sf.basedb.clients.jobagent.Agent
- allowRemoteStop - Variable in class net.sf.basedb.clients.jobagent.Agent
- allowRendererOverride - Variable in class net.sf.basedb.util.extensions.ExtensionPointBean
- allowRendererOverride - Variable in class net.sf.basedb.util.extensions.Registry.RegisteredExtensionPoint
- allowRendererOverride() - Method in interface net.sf.basedb.util.extensions.ExtensionPoint
-
If an extension is allowed to override the renderer factory with an implementation of its own.
- allowRendererOverride() - Method in class net.sf.basedb.util.extensions.ExtensionPointBean
- allowRendererOverride() - Method in class net.sf.basedb.util.extensions.Registry.RegisteredExtensionPoint
- allowSaveParameters - Variable in enum class net.sf.basedb.core.plugin.Response.Status
- allowSaveParameters() - Method in enum class net.sf.basedb.core.plugin.Response.Status
- allowSubclass - Variable in class net.sf.basedb.util.filter.InstanceOfFilter
- allowUnmodified - Variable in class net.sf.basedb.util.extensions.manager.filter.ValidAndNewOrModifiedFilter
- allowUse - Variable in class net.sf.basedb.util.jep.RawFunction
- allProjects - Variable in class net.sf.basedb.core.snapshot.SnapshotManager
- allProperties - Static variable in class net.sf.basedb.core.ExtendedProperties
-
A map from class name --> a list of extended properties of for that class.
- allSame(Collection<Set<Permission>>) - Static method in class net.sf.basedb.core.MultiPermissions
-
Check if a collection of
Set
:s all contain the same permissions. - allSeries - Variable in class net.sf.basedb.util.plot.ScatterPlot
- allSql - Variable in class net.sf.basedb.core.hibernate.SchemaGenerator.CollectSqlTarget
- allUpdateBatchers - Variable in class net.sf.basedb.core.AnnotationBatcher
- allUpdateBatchers - Variable in class net.sf.basedb.core.MigrateRbaToDba
- allVisible - Variable in class net.sf.basedb.clients.web.taglib.table.Table
-
"all" was specified for the columns attribute.
- alphaToNumeric(String) - Static method in class net.sf.basedb.util.Coordinate
-
Convert an alphanumeric coordinate to a numeric coordinate, case is unimportent.
- AlreadyLoggedInException - Exception in net.sf.basedb.core
-
This exception is thrown if you try to log in but are already logged in.
- AlreadyLoggedInException(String) - Constructor for exception net.sf.basedb.core.AlreadyLoggedInException
-
Creates a new
AlreadyLoggedInException
. - ALTERNATE_PATH_MATCH - Static variable in class net.sf.basedb.clients.web.servlet.ExtensionsServlet
-
Alternatively the servlet is: /extensions/servlet and pathInfo is: /[jar-file-name]/[servlet-name]/optional/path/info
- alwaysGranted - Variable in class net.sf.basedb.core.plugin.Permissions
- AMP - Static variable in class net.sf.basedb.clients.web.util.HTML
- AMPERSAND - Static variable in class net.sf.basedb.clients.web.util.HTML
- AnalysisFilterPlugin - Interface in net.sf.basedb.core.plugin
-
This is a tagging interface that should be used by all analysis plug-ins that are filtering data only.
- ANALYZE - Enum constant in enum class net.sf.basedb.core.plugin.Plugin.MainType
- analyzeAfterBatchOperation() - Method in interface net.sf.basedb.core.dbengine.DbEngine
-
If TRUE, a batcher that inserts, updates or delets a lot of rows in a table should execute the SQL returned by
DbEngine.getAnalyzeTableSql(String, String, String)
for that table. - analyzeAfterBatchOperation() - Method in class net.sf.basedb.core.dbengine.DefaultDbEngine
-
Return false.
- analyzeAfterBatchOperation() - Method in class net.sf.basedb.core.dbengine.MySQLEngine
-
Return true.
- analyzeAfterBatchOperation() - Method in class net.sf.basedb.core.dbengine.PostgresDbEngine
-
Return true.
- analyzeAfterImport - Variable in class net.sf.basedb.core.Migration
- analyzeTable(String, String, String) - Method in class net.sf.basedb.core.AbstractBatcher
-
Update index statistics for a table.
- analyzeUserAgent(String) - Static method in class net.sf.basedb.util.HttpUtil
-
Parse the User-Agent string from a HTTP request and return information about what it actually means.
- and(Restriction...) - Static method in class net.sf.basedb.core.query.Restrictions
-
Combine one or more restrictions with AND: new restriction = r[0] AND r[1] AND ...
- AND - Enum constant in enum class net.sf.basedb.core.Operator
- AndConverter - Class in net.sf.basedb.util.jep.convert
-
Convert the '&&' operator to a Query API
Restriction
. - AndConverter() - Constructor for class net.sf.basedb.util.jep.convert.AndConverter
- AndRestriction - Class in net.sf.basedb.core.query
-
Combine one or more restrictions with AND: r[0] AND r[1] AND ...
- AndRestriction(Restriction...) - Constructor for class net.sf.basedb.core.query.AndRestriction
- ANGLE - Static variable in class net.sf.basedb.core.Quantity
-
The id for the
Quantity
object representing angle. - Annotatable - Interface in net.sf.basedb.core
-
This interface is implemented by all items which can be annotated.
- ANNOTATABLE_FILTER - Static variable in class net.sf.basedb.core.QueryRuntimeFilterFactory
- AnnotatableData - Interface in net.sf.basedb.core.data
-
An annotatable item is an item that can be annotated with name/value pairs.
- AnnotatableFilter() - Constructor for class net.sf.basedb.core.QueryRuntimeFilterFactory.AnnotatableFilter
- annotatableItems - Static variable in class net.sf.basedb.core.Metadata
- AnnotatableProxy - Interface in net.sf.basedb.core
-
This interface is implemented by items that can be used to hold annotations that are intended for other items.
- AnnotatableWrapper(Annotatable, AnnotationUtil.AnnotatableWrapper) - Constructor for class net.sf.basedb.util.AnnotationUtil.AnnotatableWrapper
- AnnotatableWrapper(Annotatable, AnnotationUtil.Cache) - Constructor for class net.sf.basedb.util.AnnotationUtil.AnnotatableWrapper
- ANNOTATED - Enum constant in enum class net.sf.basedb.core.Include
-
Include items that have at least one annotation.
- AnnotatedData - Class in net.sf.basedb.core.data
-
This class extends the
CommonData
class and implements theAnnotatableData
interface. - AnnotatedData() - Constructor for class net.sf.basedb.core.data.AnnotatedData
- AnnotatedItem - Class in net.sf.basedb.core
-
This is a helper class for items that need to implement the
Annotatable
interface. - AnnotatedItem(AnnotatedData) - Constructor for class net.sf.basedb.core.AnnotatedItem
- annotation - Variable in class net.sf.basedb.util.overview.Fix
- annotation(AnnotationType, String, Formatter<?>) - Static method in class net.sf.basedb.util.export.spotdata.ExportableFieldFactory
-
Create an annotation assay field, overriding the title of the annotation type.
- annotation(AnnotationType, Formatter<?>) - Static method in class net.sf.basedb.util.export.spotdata.ExportableFieldFactory
-
Create an annotation assay field.
- Annotation - Class in net.sf.basedb.core
-
This class represents an annotation.
- Annotation(AnnotationData) - Constructor for class net.sf.basedb.core.Annotation
- Annotation(AnnotationData, AnnotationSet) - Constructor for class net.sf.basedb.core.Annotation
- ANNOTATION - Enum constant in enum class net.sf.basedb.core.Item
-
The item is an
Annotation
. - ANNOTATION - Enum constant in enum class net.sf.basedb.plugins.Base1PluginExecuter.Base1JobParameterType
- ANNOTATION_CLONE_OUTOFSYNC - Static variable in class net.sf.basedb.util.overview.Validator
-
Validator rule that checks if a cloned annotation value is in sync with the source annotation.
- ANNOTATION_CLONED_FROM_UNKNOWNPARENT - Static variable in class net.sf.basedb.util.overview.Validator
-
Validator rule that checks if a cloned annotation value has lost the reference to the parent item.
- ANNOTATION_INHERIT_FROM_DENIEDPARENT - Static variable in class net.sf.basedb.util.overview.Validator
-
Validator rule that checks if the logged in user has access to the parent item of an inherited annotation value.
- ANNOTATION_INHERIT_FROM_NONPARENT - Static variable in class net.sf.basedb.util.overview.Validator
-
Validator rule that checks if an inherited annotation value is inherited from a parent item.
- ANNOTATION_INHERIT_MULTIPLE - Static variable in class net.sf.basedb.util.overview.Validator
-
Validator rule that checks if two or more inherited annotations have the same annotation type.
- ANNOTATION_INVALID_ITEM - Static variable in class net.sf.basedb.util.overview.Validator
-
Validator rule that checks if an annotation is not valid for the current item type.
- ANNOTATION_INVALID_VALUE - Static variable in class net.sf.basedb.util.overview.Validator
-
Validator rule that checks if an annotation value is invalid according to annotation type specification.
- ANNOTATION_IS_PARAMETER - Static variable in class net.sf.basedb.util.overview.Validator
-
Validator rule that checks if an annotation is a protocol parameter.
- ANNOTATION_TOO_MANY_VALUES - Static variable in class net.sf.basedb.util.overview.Validator
-
Validator rule that checks if an annotation have more values than what the 'multiplicity' setting for the annotation type allow.
- Annotation.QueryRuntimeFilterImpl - Class in net.sf.basedb.core
- Annotation.Source - Enum Class in net.sf.basedb.core
-
The annotation source.
- AnnotationAssayField - Class in net.sf.basedb.util.export.spotdata
-
Assay field implementation that exports the annotations of a bioassay.
- AnnotationAssayField() - Constructor for class net.sf.basedb.util.export.spotdata.AnnotationAssayField
-
Create a new annotation field.
- AnnotationBatcher - Class in net.sf.basedb.core
-
Batcher implementation for adding, updating and removing multiple annotations to a large number of items in a single transaction while keeping the memory usage as low as possible.
- AnnotationBatcher(DbControl, Item) - Constructor for class net.sf.basedb.core.AnnotationBatcher
-
Create a new batcher instance.
- AnnotationBatcher(DbControl, Item, Integer) - Constructor for class net.sf.basedb.core.AnnotationBatcher
-
Create a new batcher instance.
- AnnotationBatcher(DbControl, Item, Project) - Constructor for class net.sf.basedb.core.AnnotationBatcher
-
Create a new batcher instance.
- AnnotationBatcher.Change - Enum Class in net.sf.basedb.core
-
A flag indicating what type of change that was made to an annotation as a result of calling
AnnotationBatcher.setValues(AnnotationType, List, Unit, boolean)
- AnnotationBatcher.CurrentAnnotationInfo - Class in net.sf.basedb.core
-
Holds information about an annotation for the current item.
- AnnotationBatcher.InsertBatcher - Class in net.sf.basedb.core
-
Batcher implementation for inserting into tables.
- AnnotationBatcher.UpdateBatcher - Class in net.sf.basedb.core
-
Batcher implementation for updating and deleting from tables.
- AnnotationBetweenRestriction - Class in net.sf.basedb.core
-
Restricts a query using annotation values between a low and high value.
- AnnotationBetweenRestriction(String, int, Type, Object, Object, boolean, boolean) - Constructor for class net.sf.basedb.core.AnnotationBetweenRestriction
-
Deprecated.
- AnnotationBetweenRestriction(String, AnnotationType, Object, Object, boolean, boolean) - Constructor for class net.sf.basedb.core.AnnotationBetweenRestriction
-
Deprecated.
- AnnotationBetweenRestriction(String, AnnotationType, Object, Object, AnnotationRestriction.Options) - Constructor for class net.sf.basedb.core.AnnotationBetweenRestriction
-
Create a new annotation restriction.
- AnnotationData - Class in net.sf.basedb.core.data
-
This class holds information about an annotation
- AnnotationData() - Constructor for class net.sf.basedb.core.data.AnnotationData
- AnnotationExpression - Class in net.sf.basedb.core.query
-
An expression representing the value of an annotation.
- AnnotationExpression(String, AnnotationType) - Constructor for class net.sf.basedb.core.query.AnnotationExpression
- AnnotationFilter - Class in net.sf.basedb.core.snapshot
-
Filter implementation that finds the annotation snapshot for a given annotation.
- AnnotationFilter() - Constructor for class net.sf.basedb.core.snapshot.AnnotationFilter
-
Create a filter that matches all annotations.
- AnnotationFilter(Annotation) - Constructor for class net.sf.basedb.core.snapshot.AnnotationFilter
-
Create a filter that matches a specfic annotation.
- AnnotationFlatFileImporter - Class in net.sf.basedb.plugins
-
Plug-in for importing annotations from simple text files.
- AnnotationFlatFileImporter() - Constructor for class net.sf.basedb.plugins.AnnotationFlatFileImporter
- AnnotationFlatFileImporter.AnnotationValue - Class in net.sf.basedb.plugins
- AnnotationFlatFileImporter.NewAnnotations - Class in net.sf.basedb.plugins
-
Internal cache for storing annotation values from the file for a single item.
- AnnotationGroup(int, Set<T>, int, Formatter<T>) - Constructor for class net.sf.basedb.clients.web.ExperimentExplorer.AnnotationGroup
- annotationId - Variable in class net.sf.basedb.clients.web.extensions.list.RelatedItemColumn.Specification
- annotationId - Variable in class net.sf.basedb.core.AnnotationBatcher.CurrentAnnotationInfo
- annotationId - Variable in class net.sf.basedb.core.FastAnnotationLoader.FastAnnotation
-
The ID of the annotation.
- annotationId - Variable in class net.sf.basedb.core.snapshot.AnnotationFilter
- annotationId - Variable in class net.sf.basedb.core.snapshot.AnnotationSnapshot
- AnnotationIdMethod - Class in net.sf.basedb.plugins.batchimport
-
Identification method implementation that can use an annotation for identifying items.
- AnnotationIdMethod(AnnotationType) - Constructor for class net.sf.basedb.plugins.batchimport.AnnotationIdMethod
-
Create a new id method.
- AnnotationInfo(int, int, int, int) - Constructor for class net.sf.basedb.core.ProjectSpecificAnnotationsManager.AnnotationInfo
- AnnotationInfo(int, int, int, int, int, int) - Constructor for class net.sf.basedb.core.ProjectSpecificAnnotationsManager.AnnotationInfo
- AnnotationInRestriction - Class in net.sf.basedb.core
-
Restricts a query using annotation values that exists in a set of given values.
- AnnotationInRestriction(String, AnnotationType, boolean, boolean, Object...) - Constructor for class net.sf.basedb.core.AnnotationInRestriction
-
Deprecated.
- AnnotationInRestriction(String, AnnotationType, AnnotationRestriction.Options, Object...) - Constructor for class net.sf.basedb.core.AnnotationInRestriction
-
Create a new annotation restriction.
- AnnotationJoin - Class in net.sf.basedb.core.query
-
Join annotations values to the query.
- AnnotationJoin(JoinType, String, AnnotationType, String) - Constructor for class net.sf.basedb.core.query.AnnotationJoin
- AnnotationJoiner(JoinType) - Constructor for class net.sf.basedb.core.HqlQueryJoiners.AnnotationJoiner
- AnnotationLink - Class in net.sf.basedb.core.data.annotations
-
Class for mapping the "Annotations" table with shortcuts to all 'FooValues' tables.
- AnnotationLink() - Constructor for class net.sf.basedb.core.data.annotations.AnnotationLink
- AnnotationLoader - Class in net.sf.basedb.util.overview.loader
-
Node loader implementation for annotations.
- AnnotationLoader() - Constructor for class net.sf.basedb.util.overview.loader.AnnotationLoader
- AnnotationLoaderUtil - Class in net.sf.basedb.core.snapshot
-
Utility implementation for simple loading of primary annotations via
SnapshotManager
. - AnnotationLoaderUtil(DbControl, SnapshotManager, AnnotationType) - Constructor for class net.sf.basedb.core.snapshot.AnnotationLoaderUtil
-
Create a loder that uses the given snapshot manager to load annotations for a single annotation type.
- AnnotationLoaderUtil(DbControl, SnapshotManager, AnnotationType, boolean, boolean) - Constructor for class net.sf.basedb.core.snapshot.AnnotationLoaderUtil
-
Create a loder that uses the given snapshot manager to load annotations for a single annotation type.
- AnnotationLogger - Class in net.sf.basedb.core.log.db
-
Logger for annotations that logs changes as updates to the parent item the annotations belong to.
- AnnotationLogger(DbLogManagerFactory) - Constructor for class net.sf.basedb.core.log.db.AnnotationLogger
- AnnotationModel - Class in net.sf.basedb.util.bfs
-
A model container for BFS annotation files.
- AnnotationModel() - Constructor for class net.sf.basedb.util.bfs.AnnotationModel
-
Create a new annotation model.
- AnnotationNameGenerator - Class in net.sf.basedb.util.overview.node
-
Since an Annotation isn't Nameable we construct the name from the name of the annotation type, or from the value type if we are not allowed to access the annotation type.
- AnnotationNameGenerator() - Constructor for class net.sf.basedb.util.overview.node.AnnotationNameGenerator
- AnnotationParser - Class in net.sf.basedb.util.bfs
-
Parser implementation that parses a BFS annotation files.
- AnnotationParser() - Constructor for class net.sf.basedb.util.bfs.AnnotationParser
-
Create a new annotation parser.
- AnnotationRestriction - Class in net.sf.basedb.core
-
Base class for creating restrictions based on annotations.
- AnnotationRestriction(String, int, Type, AnnotationRestriction.Options) - Constructor for class net.sf.basedb.core.AnnotationRestriction
-
Deprecated.In 3.11
- AnnotationRestriction(String, AnnotationType, AnnotationRestriction.Options) - Constructor for class net.sf.basedb.core.AnnotationRestriction
-
Create a new annotation restriction for an annotation type.
- AnnotationRestriction.Options - Class in net.sf.basedb.core
-
Options that specify which annotations to consider when searching.
- annotations - Variable in class net.sf.basedb.clients.web.servlet.ExperimentExplorerPlotServlet.ColumnKey
- annotations - Variable in class net.sf.basedb.core.data.AnnotationSetData
- annotations - Variable in class net.sf.basedb.core.data.AnnotationTypeData
- annotations - Variable in class net.sf.basedb.core.snapshot.AnnotationSetSnapshot
- Annotations - Class in net.sf.basedb.core.query
-
A factory class to create restrictions based on annotation values.
- Annotations() - Constructor for class net.sf.basedb.core.query.Annotations
- annotationSection - Static variable in class net.sf.basedb.core.plugin.AbstractPlugin
-
Section definition for grouping annotation options.
- annotationSet - Variable in class net.sf.basedb.core.Annotation
- annotationSet - Variable in class net.sf.basedb.core.data.AnnotatedData
- annotationSet - Variable in class net.sf.basedb.core.data.AnnotationData
- annotationSet - Variable in class net.sf.basedb.core.data.BioAssayData
- annotationSet - Variable in class net.sf.basedb.core.data.BioAssaySetData
- annotationSet - Variable in class net.sf.basedb.core.data.PluginDefinitionData
- annotationSet - Variable in class net.sf.basedb.core.data.ProjectData
- annotationSet - Variable in class net.sf.basedb.core.data.RootRawBioAssayData
- annotationSet - Variable in class net.sf.basedb.core.data.WellData
- annotationSet - Variable in class net.sf.basedb.core.ProjectSpecificAnnotationsManager.AnnotationInfo
- annotationSet - Variable in class net.sf.basedb.util.overview.validator.ProtocolParameterValidator
- AnnotationSet - Class in net.sf.basedb.core
-
An annotation set is the container for all annotations on an item.
- AnnotationSet(AnnotationSetData) - Constructor for class net.sf.basedb.core.AnnotationSet
-
Regular constructor if the item is not known beforehand.
- AnnotationSet(AnnotationSetData, Annotatable) - Constructor for class net.sf.basedb.core.AnnotationSet
-
Special constructor to avoid
AnnotationSet.getItem()
to hit the database when the item is known beforehand. - ANNOTATIONSET - Enum constant in enum class net.sf.basedb.core.Item
-
The item is an
AnnotationSet
. - AnnotationSet.ProjectSpecificAnnotationsRestriction - Class in net.sf.basedb.core
-
Restriction for matching project-specific annotations against the currently active project.
- AnnotationSet.QueryRuntimeFilterImpl - Class in net.sf.basedb.core
- AnnotationSetData - Class in net.sf.basedb.core.data
-
This class holds information about a set of annotations.
- AnnotationSetData() - Constructor for class net.sf.basedb.core.data.AnnotationSetData
- annotationSetId - Variable in class net.sf.basedb.core.AnnotationSet.ProjectSpecificAnnotationsRestriction
- annotationSetId - Variable in class net.sf.basedb.core.data.annotations.AnnotationLink
- annotationSetId - Variable in class net.sf.basedb.core.MigrateRbaToDba.Rba
- annotationSetId - Variable in class net.sf.basedb.core.snapshot.AnnotationSetSnapshot
- annotationSetId - Variable in class net.sf.basedb.core.snapshot.AnnotationSnapshot
- AnnotationSetLogger - Class in net.sf.basedb.core.log.db
-
Logger for annotations sets that detects and logs changes to inherited anntations as updates to the parent item that are inheriting the annotations.
- AnnotationSetLogger(DbLogManagerFactory) - Constructor for class net.sf.basedb.core.log.db.AnnotationSetLogger
- AnnotationSetSnapshot - Class in net.sf.basedb.core.snapshot
-
A snapshot of an annotation set that is used to store information as a file.
- AnnotationSetSnapshot() - Constructor for class net.sf.basedb.core.snapshot.AnnotationSetSnapshot
-
Creates a new, empty snapshot.
- AnnotationSetSnapshot.SortByProjectComparator - Class in net.sf.basedb.core.snapshot
-
Comparator for sorting annotation snapshots so that project-specific annotations appear before default annotations.
- AnnotationSetterPlugin - Interface in net.sf.basedb.core.plugin
-
This is a interface that should be implemented by plug-ins that are setting annotations on items thy create or work with.
- AnnotationSimpleRestriction - Class in net.sf.basedb.core
-
Restricts a query using annotation values with a simple expression:
annotation operator value
. - AnnotationSimpleRestriction(String, int, Type, Operator, Object, boolean, boolean) - Constructor for class net.sf.basedb.core.AnnotationSimpleRestriction
-
Deprecated.
- AnnotationSimpleRestriction(String, int, Type, Operator, List<Object>, boolean, boolean) - Constructor for class net.sf.basedb.core.AnnotationSimpleRestriction
-
Deprecated.
- AnnotationSimpleRestriction(String, AnnotationType, Operator, Object, boolean, boolean) - Constructor for class net.sf.basedb.core.AnnotationSimpleRestriction
-
Deprecated.
- AnnotationSimpleRestriction(String, AnnotationType, Operator, Object, AnnotationRestriction.Options) - Constructor for class net.sf.basedb.core.AnnotationSimpleRestriction
-
Create a new annotation restriction using a simple expression:
annotation operator value
. - AnnotationSimpleRestriction(String, AnnotationType, Operator, List<Object>, AnnotationRestriction.Options) - Constructor for class net.sf.basedb.core.AnnotationSimpleRestriction
-
Creates a new annotation restriction for a specific
valueType
. - AnnotationSnapshot - Class in net.sf.basedb.core.snapshot
-
Stores information about a single primary or inherited annotation or an inherited annotation set.
- AnnotationSnapshot() - Constructor for class net.sf.basedb.core.snapshot.AnnotationSnapshot
-
Create a new, empty annotation snapshot.
- AnnotationSnapshot.AnnotationTypeComparator - Class in net.sf.basedb.core.snapshot
-
Comparator implementation for sorting snapshots by name of annotation type.
- AnnotationSnapshot.ProjectComparator - Class in net.sf.basedb.core.snapshot
-
Comparator implementation for sorting snapshots by name of project.
- AnnotationSummary(ExperimentExplorer, DbControl, AnnotationType) - Constructor for class net.sf.basedb.clients.web.ExperimentExplorer.AnnotationSummary
- annotationType - Variable in class net.sf.basedb.clients.web.ExperimentExplorer.AnnotationSummary
- annotationType - Variable in class net.sf.basedb.clients.web.plugins.ExportedProperty
- annotationType - Variable in class net.sf.basedb.core.AnnotationBatcher.CurrentAnnotationInfo
- annotationType - Variable in class net.sf.basedb.core.AnnotationRestriction
- annotationType - Variable in class net.sf.basedb.core.data.AnnotationData
- annotationType - Variable in class net.sf.basedb.core.ProjectSpecificAnnotationsManager.AnnotationInfo
- annotationType - Variable in class net.sf.basedb.core.query.AnnotationExpression
- annotationType - Variable in class net.sf.basedb.core.query.AnnotationJoin
- annotationType - Variable in class net.sf.basedb.plugins.batchimport.AnnotationIdMethod
- annotationType - Variable in class net.sf.basedb.util.annotations.InheritSpecification
- annotationType - Variable in class net.sf.basedb.util.overview.Fix
- AnnotationType - Class in net.sf.basedb.core
-
Objects of this class defines an annotation type.
- AnnotationType(AnnotationTypeData) - Constructor for class net.sf.basedb.core.AnnotationType
- ANNOTATIONTYPE - Enum constant in enum class net.sf.basedb.core.Item
-
The item is an
AnnotationType
. - AnnotationType.RemoveInheritedAnnotationsAction - Class in net.sf.basedb.core
- AnnotationTypeCategory - Class in net.sf.basedb.core
-
Objects of this class defines an annotation type category.
- AnnotationTypeCategory(AnnotationTypeCategoryData) - Constructor for class net.sf.basedb.core.AnnotationTypeCategory
- ANNOTATIONTYPECATEGORY - Enum constant in enum class net.sf.basedb.core.Item
-
The item is an
AnnotationTypeCategory
. - AnnotationTypeCategoryData - Class in net.sf.basedb.core.data
-
This data layer class holds information about annotation type categories.
- AnnotationTypeCategoryData() - Constructor for class net.sf.basedb.core.data.AnnotationTypeCategoryData
- annotationTypeCategoryQuery - Variable in class net.sf.basedb.plugins.batchimport.AbstractItemImporter
- AnnotationTypeComparator(DbControl) - Constructor for class net.sf.basedb.core.snapshot.AnnotationSnapshot.AnnotationTypeComparator
- AnnotationTypeData - Class in net.sf.basedb.core.data
-
This class holds information about an annotation type.
- AnnotationTypeData() - Constructor for class net.sf.basedb.core.data.AnnotationTypeData
- AnnotationTypeEnumerationLoader - Class in net.sf.basedb.clients.web.plugins
-
Data loader implementation for loading the enumeration values collection of an annotation type.
- AnnotationTypeEnumerationLoader() - Constructor for class net.sf.basedb.clients.web.plugins.AnnotationTypeEnumerationLoader
- AnnotationTypeFilter - Class in net.sf.basedb.core.snapshot
-
Filter implementation that finds all annotation snapshots for a given annotation type.
- AnnotationTypeFilter() - Constructor for class net.sf.basedb.core.snapshot.AnnotationTypeFilter
-
Create a filter that matches all annotation types.
- AnnotationTypeFilter(Annotation.Source) - Constructor for class net.sf.basedb.util.annotations.InheritAnnotationsManager.AnnotationTypeFilter
- AnnotationTypeFilter(AnnotationType) - Constructor for class net.sf.basedb.core.snapshot.AnnotationTypeFilter
-
Create a filter that matches a specfic annotation type.
- annotationTypeId - Variable in class net.sf.basedb.core.AnnotationRestriction
- annotationTypeId - Variable in class net.sf.basedb.core.data.annotations.AnnotationLink
- annotationTypeId - Variable in class net.sf.basedb.core.snapshot.AnnotationSnapshot
- annotationTypeId - Variable in class net.sf.basedb.core.snapshot.AnnotationTypeFilter
- annotationTypeId - Variable in class net.sf.basedb.util.annotations.InheritSpecification
- annotationTypeIds - Variable in class net.sf.basedb.clients.web.ExperimentExplorer
-
The currently selected annotation types on the view page.
- annotationTypeIds - Variable in class net.sf.basedb.core.Annotation.QueryRuntimeFilterImpl
- AnnotationTypeImporter - Class in net.sf.basedb.plugins.batchimport
-
Plug-in for importing annotation type items in a batch.
- AnnotationTypeImporter() - Constructor for class net.sf.basedb.plugins.batchimport.AnnotationTypeImporter
- AnnotationTypeItemTypesLoader - Class in net.sf.basedb.clients.web.plugins
-
Data loader implementation for loading the item types collection of an annotation type.
- AnnotationTypeItemTypesLoader() - Constructor for class net.sf.basedb.clients.web.plugins.AnnotationTypeItemTypesLoader
- annotationTypes - Variable in class net.sf.basedb.core.data.AnnotationTypeCategoryData
- annotationTypes - Variable in class net.sf.basedb.util.annotations.InheritAnnotationsManager.AnnotationTypeFilter
- annotationTypeSection - Static variable in class net.sf.basedb.plugins.AnnotationFlatFileImporter
-
Section definition for grouping all mappings of columns to annotation types.
- AnnotationUtil - Class in net.sf.basedb.clients.web
-
Some utility functions for annotations.
- AnnotationUtil - Class in net.sf.basedb.util
-
Utility class for working with annotations.
- AnnotationUtil() - Constructor for class net.sf.basedb.clients.web.AnnotationUtil
- AnnotationUtil() - Constructor for class net.sf.basedb.util.AnnotationUtil
- AnnotationUtil.AnnotatableWrapper - Class in net.sf.basedb.util
-
This wrapper class is needed because we need to keep track of extracts linked with raw bioassays and derived bioassays until we have loaded the Extracts of a Physical Bioassay.
- AnnotationUtil.Cache - Class in net.sf.basedb.util
- AnnotationValidator - Class in net.sf.basedb.util.overview.validator
-
Validator implementation for annotations.
- AnnotationValidator() - Constructor for class net.sf.basedb.util.overview.validator.AnnotationValidator
- AnnotationValue(Object, Unit) - Constructor for class net.sf.basedb.plugins.AnnotationFlatFileImporter.AnnotationValue
- annotationValues - Variable in class net.sf.basedb.clients.web.ExperimentExplorer.AnnotationGroup
- AnnotationWriter - Class in net.sf.basedb.util.bfs
- AnnotationWriter(Writer) - Constructor for class net.sf.basedb.util.bfs.AnnotationWriter
- any - Variable in class net.sf.basedb.clients.web.extensions.fileviewer.FileViewerContext
- any(Query) - Static method in class net.sf.basedb.core.query.Expressions
-
Create a subquery expression:
ANY (subquery)
. - ANY_TO_ANY - Enum constant in enum class net.sf.basedb.clients.web.extensions.fileviewer.FileViewerContext.Type
-
The context is a list with any-to-any links from a parent item.
- AnyLinkColumn - Class in net.sf.basedb.clients.web.extensions.list
-
A column action implementation that finds an item linked with a any-to-any link.
- AnyLinkColumn(int, String, String, Item, Metadata.PropertyPath<BasicItem, ?>, FileViewerUtil) - Constructor for class net.sf.basedb.clients.web.extensions.list.AnyLinkColumn
- AnyLinkColumnActionFactory - Class in net.sf.basedb.clients.web.extensions.list
-
Action factory for adding columns to a table that display items that are linked with an any-to-any link.
- AnyLinkColumnActionFactory() - Constructor for class net.sf.basedb.clients.web.extensions.list.AnyLinkColumnActionFactory
- anyToAny(BasicItem) - Static method in class net.sf.basedb.clients.web.extensions.fileviewer.FileViewerContext
-
Creates an any-to-any listing context where files belong to a parent item.
- AnyToAny - Class in net.sf.basedb.core
-
An any-to-any link is a named, directed link from one item to another item.
- AnyToAny(AnyToAnyData) - Constructor for class net.sf.basedb.core.AnyToAny
-
Creates a new link item from the given data.
- AnyToAny(AnyToAnyData, BasicItem) - Constructor for class net.sf.basedb.core.AnyToAny
-
Special constructor when the from item is known.
- ANYTOANY - Enum constant in enum class net.sf.basedb.core.Item
-
The item is an
AnyToAny
link. - AnyToAny.FastLinkLoader<S extends BasicItem,
T extends BasicItem> - Class in net.sf.basedb.core -
Helper class for faster loading of any-to-any links between items.
- AnyToAnyData - Class in net.sf.basedb.core.data
-
Represents a link from one item to any other item.
- AnyToAnyData() - Constructor for class net.sf.basedb.core.data.AnyToAnyData
- AnyToAnyDataLoader - Class in net.sf.basedb.clients.web.plugins
-
Data loader implementation that load any-to-any links.
- AnyToAnyDataLoader(String, Item, Metadata.PropertyPath<BasicItem, ?>) - Constructor for class net.sf.basedb.clients.web.plugins.AnyToAnyDataLoader
-
Load links with the specified name and target type.
- AnyToAnyImporter - Class in net.sf.basedb.plugins.batchimport
-
Plug-in for importing any-to-any links from simple text files.
- AnyToAnyImporter() - Constructor for class net.sf.basedb.plugins.batchimport.AnyToAnyImporter
- AnyToAnyLinkStatistics - Class in net.sf.basedb.util
-
Class for holding statisics about any-to-any links between items.
- AnyToAnyLinkStatistics() - Constructor for class net.sf.basedb.util.AnyToAnyLinkStatistics
- AnyToAnyLinkStatistics.Options - Class in net.sf.basedb.util
-
Options to specify how the statistics should be generated.
- AnyToAnyLoader - Class in net.sf.basedb.util.overview.loader
-
Node loader implementation for any-to-any links.
- AnyToAnyLoader() - Constructor for class net.sf.basedb.util.overview.loader.AnyToAnyLoader
- AnyToAnyLogger - Class in net.sf.basedb.core.log.db
-
Logger for any-to-any links that logs changes as updates to the 'from' item.
- AnyToAnyLogger(DbLogManagerFactory) - Constructor for class net.sf.basedb.core.log.db.AnyToAnyLogger
- AnyToAnyNameGenerator - Class in net.sf.basedb.util.overview.node
-
Name generator for any-to-any links.
- AnyToAnyNameGenerator() - Constructor for class net.sf.basedb.util.overview.node.AnyToAnyNameGenerator
- AnyToAnyRestriction - Class in net.sf.basedb.core.query
-
Expression that can be used to filter on the existence or non-existence of a named any-to-any link.
- AnyToAnyRestriction(String, String, Item, boolean, EntityQuery) - Constructor for class net.sf.basedb.core.query.AnyToAnyRestriction
- AnyToAnyValidator - Class in net.sf.basedb.util.overview.validator
-
Validator implementation for any-to-any links.
- AnyToAnyValidator() - Constructor for class net.sf.basedb.util.overview.validator.AnyToAnyValidator
- append(String) - Method in class net.sf.basedb.core.Job.ProgressReporterImpl
- append(String) - Method in class net.sf.basedb.core.Migration.ProgressInputStream
- append(String) - Method in interface net.sf.basedb.core.ProgressReporter
-
Append a message to the previous one.
- append(String) - Method in class net.sf.basedb.core.signal.ProgressReporterSignalHandler
- append(String) - Method in class net.sf.basedb.core.SimpleProgressReporter
- append(String) - Method in class net.sf.basedb.util.ChainedProgressReporter
- append(String) - Method in class net.sf.basedb.util.ConsoleProgressReporter
- append(String) - Method in class net.sf.basedb.util.GeoLocation.ResponseFilter
- append(String) - Method in class net.sf.basedb.util.TransferRateProgressReporter
-
Forward the call to the parent if one exists.
- append(StringBuilder, String) - Method in class net.sf.basedb.util.GeoLocation
- appendFakeSources(Set<Integer>) - Method in class net.sf.basedb.util.listable.SourceItemTransformerChain
- appendGroups(StringBuilder, DbControl, List<Expression>, int) - Method in class net.sf.basedb.core.AbstractQuery
- appendHavings(StringBuilder, DbControl, List<Restriction>, int) - Method in class net.sf.basedb.core.AbstractQuery
- appendJoins(StringBuilder, DbControl, List<Join>, boolean, int) - Method in class net.sf.basedb.core.AbstractQuery
- appendLine(StringBuffer, String[], GtfInputStream.Attribute[]) - Method in class net.sf.basedb.util.gtf.GtfInputStream
-
Append columns to the buffer and separate each with a tab.
- appendList(StringBuilder, Collection<String>) - Method in class net.sf.basedb.core.dbengine.MySQLEngine
- appendList(StringBuilder, Collection<String>) - Method in class net.sf.basedb.core.dbengine.PostgresDbEngine
- appendListOfValues(StringBuilder, String, String) - Method in class net.sf.basedb.util.formatter.PropertyFilterFormatter
- appendOrders(StringBuilder, DbControl, List<Order>, int) - Method in class net.sf.basedb.core.AbstractQuery
- appendPermissionOption(StringBuilder, Permission, Permission, String) - Method in class net.sf.basedb.clients.web.taglib.table.ColumnDef
- appendProgress(Session, String) - Method in class net.sf.basedb.core.Job.ProgressReporterImpl
- appendRestrictions(StringBuilder, DbControl, List<Restriction>, int) - Method in class net.sf.basedb.core.AbstractQuery
- appendScripts(StringBuilder, JspContext) - Method in class net.sf.basedb.clients.web.taglib.Head
- appendSelects(StringBuilder, DbControl, List<Select>, int) - Method in class net.sf.basedb.core.AbstractQuery
- appendStyles(StringBuilder, String, boolean, JspContext) - Method in class net.sf.basedb.clients.web.taglib.Head
- appId - Variable in class net.sf.basedb.core.data.SchemaVersionData
- appId - Variable in class net.sf.basedb.core.ServiceSessionControl.SessionFactoryConfiguration
- Application - Class in net.sf.basedb.core
-
This class represents the BASE application and is the starting point for all client applications.
- Application() - Constructor for class net.sf.basedb.core.Application
- Application.DbCleaner - Class in net.sf.basedb.core
- Application.Pinger - Class in net.sf.basedb.core
-
A
Pinger
is an object that is used to protect another object from timing out by automatically pinging it. - Application.SessionControlCacheCleaner - Class in net.sf.basedb.core
- Application.StartupOptions - Class in net.sf.basedb.core
-
Startup optins when starting the BASE application.
- apply(List<Plate>, PlateType) - Method in class net.sf.basedb.core.PlateMapping
-
Apply this mapping to the given list of source plates and generate new plates of the specified type.
- applyGraph(RootGraph, GraphSemantic) - Method in class net.sf.basedb.core.hibernate.QueryWrapper
- approximateNumberOfRows - Variable in class net.sf.basedb.core.dbengine.TableInfo
- aquireLock(String, boolean, int) - Method in class net.sf.basedb.util.StaticCache
-
Aquire a read or write lock on a given cache entry.
- AREA - Static variable in class net.sf.basedb.core.Quantity
-
The id for the
Quantity
object representing area. - ARITHMETIC_MEAN - Enum constant in enum class net.sf.basedb.core.Formula.AverageMethod
- arrangeData(int, short, Object[][], Object[]) - Method in class net.sf.basedb.util.export.spotdata.BfsExporter
-
Arrange the data that was returned by the query into the data writers array.
- arrangeData(int, short, Object[][], Object[]) - Method in class net.sf.basedb.util.export.spotdata.MatrixBfsExporter
-
The column number is used to find the assay index.
- arrangeData(int, short, Object[][], Object[]) - Method in class net.sf.basedb.util.export.spotdata.SerialBfsExporter
-
The column number is used to find the assay index.
- ARRANGEMENT - Static variable in class net.sf.basedb.core.DerivedBioAssay
-
The id for the
DerivedBioAssayType
item representing sequenced data that has been aligned to a reference database. - array - Variable in class net.sf.basedb.util.ArrayIterator
-
The array to iterate.
- arrayBatch - Variable in class net.sf.basedb.core.data.ArraySlideData
- ArrayBatch - Class in net.sf.basedb.core
-
This class represents the making of a new batch of microarray slides of a particular design.
- ArrayBatch(ArrayBatchData) - Constructor for class net.sf.basedb.core.ArrayBatch
- ARRAYBATCH - Enum constant in enum class net.sf.basedb.core.Item
-
The item is an
ArrayBatch
. - arrayBatchColumnMapping - Static variable in class net.sf.basedb.plugins.batchimport.ArraySlideImporter
- ArrayBatchData - Class in net.sf.basedb.core.data
-
This class represents the making of a new batch of microarray slides of a particular design.
- ArrayBatchData() - Constructor for class net.sf.basedb.core.data.ArrayBatchData
- arrayBatches - Variable in class net.sf.basedb.core.data.ArrayDesignData
- ArrayBatchImporter - Class in net.sf.basedb.plugins.batchimport
-
Plug-in for importing array batch items in a batch.
- ArrayBatchImporter() - Constructor for class net.sf.basedb.plugins.batchimport.ArrayBatchImporter
- ArrayBatchLoader - Class in net.sf.basedb.util.overview.loader
-
Node loader implementation for array batches.
- ArrayBatchLoader() - Constructor for class net.sf.basedb.util.overview.loader.ArrayBatchLoader
- arrayBatchMapper - Variable in class net.sf.basedb.plugins.batchimport.ArraySlideImporter
- ArrayBatchValidator - Class in net.sf.basedb.util.overview.validator
-
Validator implementation for array batch.
- ArrayBatchValidator() - Constructor for class net.sf.basedb.util.overview.validator.ArrayBatchValidator
- arrayDesign - Variable in class net.sf.basedb.core.data.ArrayBatchData
- arrayDesign - Variable in class net.sf.basedb.core.data.ArrayDesignBlockData
- arrayDesign - Variable in class net.sf.basedb.core.data.ArrayDesignPlateData
- arrayDesign - Variable in class net.sf.basedb.core.data.RawBioAssayData
- arrayDesign - Variable in class net.sf.basedb.core.FeatureBatcher
-
The array design this batcher adds features to.
- arrayDesign - Variable in class net.sf.basedb.core.RawDataBatcher
-
The array design the raw bioassay is connected to, if any.
- arrayDesign - Variable in class net.sf.basedb.plugins.PrintMapFlatFileImporter
- arrayDesign - Variable in class net.sf.basedb.plugins.ReporterMapFlatFileImporter
- ArrayDesign - Class in net.sf.basedb.core
-
An array design is a description of the design of a microarray slide.
- ArrayDesign(ArrayDesignData) - Constructor for class net.sf.basedb.core.ArrayDesign
- ARRAYDESIGN - Enum constant in enum class net.sf.basedb.core.Item
-
The item is an
ArrayDesign
. - arrayDesignBlock - Variable in class net.sf.basedb.core.data.FeatureData
- ArrayDesignBlock - Class in net.sf.basedb.core
- ArrayDesignBlock(ArrayDesignBlockData) - Constructor for class net.sf.basedb.core.ArrayDesignBlock
- ARRAYDESIGNBLOCK - Enum constant in enum class net.sf.basedb.core.Item
-
The item is an
ArrayDesignBlock
. - ArrayDesignBlockData - Class in net.sf.basedb.core.data
-
This holds information about a block in an arraydesign.
- ArrayDesignBlockData() - Constructor for class net.sf.basedb.core.data.ArrayDesignBlockData
- arrayDesignBlocks - Variable in class net.sf.basedb.core.data.ArrayDesignData
- arrayDesignColumnMapping - Static variable in class net.sf.basedb.plugins.batchimport.ArrayBatchImporter
- arrayDesignColumnMapping - Static variable in class net.sf.basedb.plugins.batchimport.RawBioAssayImporter
- arrayDesignData - Variable in class net.sf.basedb.core.FeatureBatcher
-
Just a copy of the data object for the array design.
- ArrayDesignData - Class in net.sf.basedb.core.data
-
This class holds information about an arrayDesign
- ArrayDesignData() - Constructor for class net.sf.basedb.core.data.ArrayDesignData
- arrayDesignHasBeenSet - Variable in class net.sf.basedb.core.RawBioAssay
- arrayDesignId - Variable in class net.sf.basedb.core.MigrateRbaToDba.Rba
- ArrayDesignImporter - Class in net.sf.basedb.plugins.batchimport
-
Plug-in for importing array design items in a batch.
- ArrayDesignImporter() - Constructor for class net.sf.basedb.plugins.batchimport.ArrayDesignImporter
- arrayDesignLinkId - Variable in class net.sf.basedb.core.MigrateRbaToDba.Rba
- ArrayDesignLoader - Class in net.sf.basedb.util.overview.loader
-
Node loader implementation for array designs.
- ArrayDesignLoader() - Constructor for class net.sf.basedb.util.overview.loader.ArrayDesignLoader
- arrayDesignMapper - Variable in class net.sf.basedb.plugins.batchimport.ArrayBatchImporter
- arrayDesignMapper - Variable in class net.sf.basedb.plugins.batchimport.RawBioAssayImporter
- arrayDesignParameter - Variable in class net.sf.basedb.plugins.PrintMapFlatFileImporter
- arrayDesignParameter - Variable in class net.sf.basedb.plugins.ReporterMapFlatFileImporter
- ArrayDesignPlate - Class in net.sf.basedb.core
- ArrayDesignPlate(ArrayDesignPlateData) - Constructor for class net.sf.basedb.core.ArrayDesignPlate
- ARRAYDESIGNPLATE - Enum constant in enum class net.sf.basedb.core.Item
-
The item is a
ArrayDesignPlate
connecter. - ArrayDesignPlateData - Class in net.sf.basedb.core.data
-
This class connects the ArrayDesign with its plates and adding an index to that connection.
- ArrayDesignPlateData() - Constructor for class net.sf.basedb.core.data.ArrayDesignPlateData
- arrayDesigns - Variable in class net.sf.basedb.core.data.JobData
- arrayDesigns - Variable in class net.sf.basedb.core.data.PlateData
- arrayDesignType - Variable in class net.sf.basedb.plugins.PrintMapFlatFileImporter
- arrayDesignType - Variable in class net.sf.basedb.plugins.ReporterMapFlatFileImporter
- ArrayDesignValidator - Class in net.sf.basedb.util.overview.validator
-
Validator implementation for array designs.
- ArrayDesignValidator() - Constructor for class net.sf.basedb.util.overview.validator.ArrayDesignValidator
- ArrayIterator<E> - Class in net.sf.basedb.util
-
This class implements the
Iterator
interface for an array of objects. - ArrayIterator(E[]) - Constructor for class net.sf.basedb.util.ArrayIterator
-
Create a new
ArrayIterator
object. - arraySlide - Variable in class net.sf.basedb.core.data.PhysicalBioAssayData
- ArraySlide - Class in net.sf.basedb.core
-
This class represents a physical microarray slide.
- ArraySlide(ArraySlideData) - Constructor for class net.sf.basedb.core.ArraySlide
- ARRAYSLIDE - Enum constant in enum class net.sf.basedb.core.Item
-
The item is an
ArraySlide
. - arraySlideColumnMapping - Static variable in class net.sf.basedb.plugins.batchimport.PhysicalBioAssayImporter
- ArraySlideData - Class in net.sf.basedb.core.data
-
This class represents a phycsical microarray slide.
- ArraySlideData() - Constructor for class net.sf.basedb.core.data.ArraySlideData
- ArraySlideImporter - Class in net.sf.basedb.plugins.batchimport
-
Plug-in for importing array slide items in a batch.
- ArraySlideImporter() - Constructor for class net.sf.basedb.plugins.batchimport.ArraySlideImporter
- ArraySlideLoader - Class in net.sf.basedb.util.overview.loader
-
Node loader implementation for array slides.
- ArraySlideLoader() - Constructor for class net.sf.basedb.util.overview.loader.ArraySlideLoader
- arraySlideMapper - Variable in class net.sf.basedb.plugins.batchimport.PhysicalBioAssayImporter
- arraySlideQuery - Variable in class net.sf.basedb.plugins.batchimport.AbstractItemImporter
- arraySlides - Variable in class net.sf.basedb.core.data.ArrayBatchData
- ArraySlideValidator - Class in net.sf.basedb.util.overview.validator
-
Validator implementation for array slides.
- ArraySlideValidator() - Constructor for class net.sf.basedb.util.overview.validator.ArraySlideValidator
- asBoolean(Boolean) - Static method in class net.sf.basedb.util.excel.ExcelValue
-
Create a numeric cell value with boolean format.
- asc(Expression) - Static method in class net.sf.basedb.core.query.Orders
-
Sort the result of a query in ascending order by the expression.
- ASC - Enum constant in enum class net.sf.basedb.core.ItemContext.SortDirection
-
Items are sorted in ascending order.
- AscOrder - Class in net.sf.basedb.core.query
-
Sort the result of a query in ascending order by the expression.
- AscOrder(Expression) - Constructor for class net.sf.basedb.core.query.AscOrder
- asDate - Variable in class net.sf.basedb.util.parser.ConstantMapper
- asDate(Date, String) - Static method in class net.sf.basedb.util.excel.ExcelValue
-
Create a date cell value.
- asDouble - Variable in class net.sf.basedb.util.parser.ConstantMapper
- asEnumeration(Collection<String>) - Static method in class net.sf.basedb.util.charset.CharsetUtil
-
Convert charset names to an enumeration with display-friendly key/title pairs.
- asInt(Number) - Static method in class net.sf.basedb.util.excel.ExcelValue
-
Create a numeric cell value without any decimals.
- asJsonObject() - Method in class net.sf.basedb.clients.web.taglib.table.ColumnDef
-
Get a JSON representation of this column definition.
- asLong - Variable in class net.sf.basedb.util.parser.ConstantMapper
- asNumber(Number, int) - Static method in class net.sf.basedb.util.excel.ExcelValue
-
Create a numeric cell value and display a given number of decimals.
- asNumber(Number, String) - Static method in class net.sf.basedb.util.excel.ExcelValue
-
Create a numeric cell value with a custom numeric format.
- assayAnnotationQuery - Variable in class net.sf.basedb.util.export.spotdata.AbstractFieldConverter
- assayField(String, String, Type) - Method in class net.sf.basedb.plugins.BfsExporterPlugin
- AssayField - Interface in net.sf.basedb.util.export.spotdata
-
Represents a bioassay field that is going to be exported.
- assayFields - Variable in class net.sf.basedb.util.export.spotdata.AbstractBioAssaySetExporter
- assayFields - Variable in class net.sf.basedb.util.importer.spotdata.BaseFileInfo.SpotSectionInfo
- assayGroups - Variable in class net.sf.basedb.clients.web.ExperimentExplorer.AnnotationSummary
- assayIndexMap - Variable in class net.sf.basedb.util.export.spotdata.AbstractBioAssaySetExporter
- assayProperty(String, String, Type, Formatter<?>) - Static method in class net.sf.basedb.util.export.spotdata.ExportableFieldFactory
-
Create a property assay field.
- AssayPropertyField - Class in net.sf.basedb.util.export.spotdata
-
Assay field implementation that exports a named property from a bioassay.
- AssayPropertyField() - Constructor for class net.sf.basedb.util.export.spotdata.AssayPropertyField
-
Create a new annotation field.
- assays - Variable in class net.sf.basedb.util.importer.spotdata.BaseFileInfo.SpotSectionInfo
- assays - Variable in class net.sf.basedb.util.importer.spotdata.MatrixSpotIntensityEventHandler
- assays - Variable in class net.sf.basedb.util.importer.spotdata.SerialSpotIntensityEventHandler
- assaysHaveParentAssaysMapping - Variable in class net.sf.basedb.util.importer.spotdata.BaseFileInfo
- assayWriter - Variable in class net.sf.basedb.util.export.spotdata.BfsExporter
- associateFiles(DbControl, Transformation, Directory) - Method in class net.sf.basedb.plugins.Base1PluginExecuter
- associationsSection - Static variable in class net.sf.basedb.plugins.IlluminaRawDataImporter
-
Section definition for grouping associations to other items: scan, software, protocol and experiment
- asString(String) - Static method in class net.sf.basedb.util.excel.ExcelValue
-
Create a string cell value.
- ASTConstantConverter - Class in net.sf.basedb.util.jep.convert
-
Converts a constant node to an expression.
- ASTConstantConverter() - Constructor for class net.sf.basedb.util.jep.convert.ASTConstantConverter
- ASTFunNodeConverter - Class in net.sf.basedb.util.jep.convert
-
Converts a function node to an expression or restriction.
- ASTFunNodeConverter() - Constructor for class net.sf.basedb.util.jep.convert.ASTFunNodeConverter
- asTimestamp(Date, String) - Static method in class net.sf.basedb.util.excel.ExcelValue
-
Create a timestamp cell value.
- ASTVarNodeConverter - Class in net.sf.basedb.util.jep.convert
-
Converts a variable node to a parameter expression or null.
- ASTVarNodeConverter() - Constructor for class net.sf.basedb.util.jep.convert.ASTVarNodeConverter
- asXml() - Method in class net.sf.basedb.core.Presets
-
Convert the presets to an XML string.
- at - Variable in class net.sf.basedb.clients.web.extensions.list.RelatedItemAnnotationColumn
- at - Variable in class net.sf.basedb.core.AnnotationType.RemoveInheritedAnnotationsAction
- at - Variable in class net.sf.basedb.core.snapshot.AnnotationLoaderUtil
- at - Variable in class net.sf.basedb.util.export.spotdata.AnnotationAssayField
- AT_OR_DOT - Static variable in class net.sf.basedb.clients.web.util.HTML
- atBoundary - Variable in class net.sf.basedb.clients.web.fileupload.FileUpload.UploadStatus
-
TRUE if the
FileUpload.checkBoundary(byte[], int, byte[], int)
method finds that the line matches the boundary, FALSE otherwise. - atCommit - Variable in class net.sf.basedb.core.DropDynamicTableAction
- atComp - Variable in class net.sf.basedb.core.snapshot.AnnotationSnapshot.ProjectComparator
- atFilter - Variable in class net.sf.basedb.clients.web.extensions.list.RelatedItemAnnotationColumn
- atId - Variable in class net.sf.basedb.core.snapshot.AnnotationLoaderUtil
- atLastBoundary - Variable in class net.sf.basedb.clients.web.fileupload.FileUpload.UploadStatus
-
TRUE if the
FileUpload.checkBoundary(byte[], int, byte[], int)
method finds that the line matches the boundary + two extra dashes (--), FALSE otherwise. - atRollback - Variable in class net.sf.basedb.core.DropDynamicTableAction
- attribute - Variable in class net.sf.basedb.util.overview.filter.HasAttributeFilter
- Attribute(String, String) - Constructor for class net.sf.basedb.util.gtf.GtfInputStream.Attribute
- ATTRIBUTE_KEY - Static variable in class net.sf.basedb.clients.web.extensions.JspContext
-
The key that is used when storing a JspContext object in a request/page/session/etc. attribute.
- ATTRIBUTE_PATTERN - Variable in class net.sf.basedb.util.gtf.GtfInputStream
- AttributeKey(String, String) - Constructor for class net.sf.basedb.util.extensions.Registry.AttributeKey
- attributes - Variable in class net.sf.basedb.core.authentication.LoginRequest
- attributes - Variable in class net.sf.basedb.util.extensions.AboutBean
- attributes - Variable in class net.sf.basedb.util.extensions.ClientContext
- attributes - Variable in class net.sf.basedb.util.extensions.Registry
- attributes - Variable in class net.sf.basedb.util.extensions.Registry.RegisteredAbout
- attributes - Variable in class net.sf.basedb.util.gtf.GtfInputStream
- attributes - Variable in class net.sf.basedb.util.overview.Node
- authenticate() - Method in interface net.sf.basedb.core.authentication.AuthenticationManager
-
Try to authenticate a user given the login information passed to the factory in the
AuthenticationContext
. - authenticatedUser - Variable in class net.sf.basedb.core.SessionControl.UnverifiedDeviceInfo
- AuthenticatedUser - Class in net.sf.basedb.core.authentication
-
Objects of this class are returned by the
AuthenticationManager.authenticate()
method and contains information about the authenticated user. - AuthenticatedUser(AuthenticationMethod, String, String) - Constructor for class net.sf.basedb.core.authentication.AuthenticatedUser
-
Creates a new
AuthenticatedUser
object without any link to an existing user in BASE. - AuthenticatedUser(AuthenticationMethod, UserData) - Constructor for class net.sf.basedb.core.authentication.AuthenticatedUser
-
Creates a new
AuthenticatedUser
object with a link to an existing user in BASE. - AuthenticationContext - Class in net.sf.basedb.core
-
Gives authentication implementations limited access to the database.
- AuthenticationContext(SessionControl, Session, LoginRequest) - Constructor for class net.sf.basedb.core.AuthenticationContext
- AuthenticationException - Exception in net.sf.basedb.core.authentication
-
This exception can be thrown when an error occurs during the authentication.
- AuthenticationException(String) - Constructor for exception net.sf.basedb.core.authentication.AuthenticationException
-
Create a new
AuthenticationException
object - AuthenticationException(String, Throwable) - Constructor for exception net.sf.basedb.core.authentication.AuthenticationException
-
Create a new
AuthenticationException
object - AuthenticationException(Throwable) - Constructor for exception net.sf.basedb.core.authentication.AuthenticationException
-
Create a new
AuthenticationException
object - AuthenticationManager - Interface in net.sf.basedb.core.authentication
-
Action interface for external authentication.
- authenticationMethod - Variable in class net.sf.basedb.core.data.SessionData
- authenticationMethod - Variable in class net.sf.basedb.core.SessionControl.LoginInfo
-
The authentication method used to allow the user to login.
- AuthenticationMethod - Class in net.sf.basedb.core.authentication
-
Holds information about the method that was used to verify a user when logging in.
- AuthenticationMethod(String) - Constructor for class net.sf.basedb.core.authentication.AuthenticationMethod
- authors - Variable in class net.sf.basedb.core.data.ExperimentData
- AUTO - Enum constant in enum class net.sf.basedb.core.ReporterCloneBatcher.CloneSource
-
Select VIRTUAL if the experiment has position data in the virtual database, otherwise the RAW options used.
- AutoChildNodeLoader<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 class net.sf.basedb.core.IntensityTransform
- averageMethod - Variable in class net.sf.basedb.util.export.spotdata.JepDynamicField
- averageMethod - Variable in class net.sf.basedb.util.export.spotdata.SimpleDynamicField
- AverageMethod(int, String) - Constructor for enum class net.sf.basedb.core.Formula.AverageMethod
- averageOnReporter - Variable in class net.sf.basedb.util.export.spotdata.AbstractBioAssaySetExporter
- avg - Variable in class net.sf.basedb.core.query.GeometricMeanExpression
- avoid(Item, Set<Integer>) - Method in class net.sf.basedb.util.listable.TransformContext
-
Avoid collected items by removing them from the source set.
- avoiding - Variable in class net.sf.basedb.util.listable.TransformContext
B
- BACKSLASH - Static variable in class net.sf.basedb.clients.web.util.HTML
- BAM - Static variable in class net.sf.basedb.core.DataFileType
-
The external ID for the file type representing a BAM (Binary Sequence Alignment/Map) file.
- barcode - Variable in class net.sf.basedb.core.data.ArraySlideData
- barcode - Variable in class net.sf.basedb.core.data.BioPlateData
- barcode - Variable in class net.sf.basedb.core.data.PlateData
- BARCODE - Static variable in class net.sf.basedb.core.Tag
-
The ID for the BARCODE tag type.
- BARCODE - Static variable in class net.sf.basedb.plugins.batchimport.PropertyIdMethod
-
Use the barcode for finding items.
- barcodeColumnMapping - Static variable in class net.sf.basedb.plugins.batchimport.ArraySlideImporter
- barcodeColumnMapping - Static variable in class net.sf.basedb.plugins.batchimport.BioPlateImporter
- barcodeColumnMapping - Static variable in class net.sf.basedb.plugins.PlateFlatFileImporter
- barcodeExists(DbControl, String) - Static method in class net.sf.basedb.core.ArraySlide
-
Checks if a slide with the given barcode already exists in the database.
- barcodeMapper - Variable in class net.sf.basedb.plugins.batchimport.ArraySlideImporter
- barcodeMapper - Variable in class net.sf.basedb.plugins.batchimport.BioPlateImporter
- barcodeMapper - Variable in class net.sf.basedb.plugins.PlateFlatFileImporter
- bas - Variable in class net.sf.basedb.plugins.BaseFileExporterPlugin
- bas - Variable in class net.sf.basedb.plugins.BfsExporterPlugin
- bas - Variable in class net.sf.basedb.util.jep.ExtraValueFunction
- base - Variable in class net.sf.basedb.core.query.LogExpression
- base - Variable in class net.sf.basedb.core.query.PowerExpression
- Base - Class in net.sf.basedb.clients.web
-
This class is used to collect some useful methods for the web client into a single place.
- Base() - Constructor for class net.sf.basedb.clients.web.Base
- BASE_APP_ID - Static variable in class net.sf.basedb.core.data.SchemaVersionData
- BASE_VERSION - Static variable in class net.sf.basedb.clients.web.taglib.Page
-
The version of BASE.
- Base1FieldConverter - Class in net.sf.basedb.util.export.spotdata
-
Exportable field converter that support BASE 1 naming conventions.
- Base1FieldConverter(DbControl, BioAssaySet) - Constructor for class net.sf.basedb.util.export.spotdata.Base1FieldConverter
-
Create a new converter for the given bioassay set.
- Base1JobParameterType(char) - Constructor for enum class net.sf.basedb.plugins.Base1PluginExecuter.Base1JobParameterType
- Base1PluginExecuter - Class in net.sf.basedb.plugins
-
This plug-in executes a plug-in from the Base1 system.
- Base1PluginExecuter() - Constructor for class net.sf.basedb.plugins.Base1PluginExecuter
- Base1PluginExecuter.Base1JobParameterType - Enum Class in net.sf.basedb.plugins
- Base1PluginExecuter.JobParameter - Class in net.sf.basedb.plugins
- base64_code - Static variable in class net.sf.basedb.util.bcrypt.BCrypt
- baseBeginDataPart() - Method in class net.sf.basedb.util.basefile.BaseFileWriter
-
End the header part of the current section (by writing a single % on a line by itself) and start the data part.
- baseBeginSection(String) - Method in class net.sf.basedb.util.basefile.BaseFileWriter
-
Start a new section in the BASEfile.
- baseCompleted - Variable in class net.sf.basedb.core.SimpleAbsoluteProgressReporter
- baseEndSection() - Method in class net.sf.basedb.util.basefile.BaseFileWriter
-
Ends the current section by writing an empty line.
- baseEscape(String) - Method in class net.sf.basedb.util.basefile.BaseFileWriter
-
Escape new line and carrige return characters in the input to the literal string '\n' and '\r' in the output.
- BaseException - Exception in net.sf.basedb.core
-
This is the base class for exceptions in BASE.
- BaseException() - Constructor for exception net.sf.basedb.core.BaseException
-
Create a new
BaseException
object. - BaseException(String) - Constructor for exception net.sf.basedb.core.BaseException
-
Create a new
BaseException
object with the specifiedmessage
- BaseException(String, Throwable) - Constructor for exception net.sf.basedb.core.BaseException
-
Create a new
BaseException
object with the specifiedmessage
- BaseException(Throwable) - Constructor for exception net.sf.basedb.core.BaseException
-
Create a new
BaseException
object acting as a wrapper for another exception that caused the error. - BaseException(SQLException) - Constructor for exception net.sf.basedb.core.BaseException
-
Create a new
BaseException
object where the cause is an SQLException. - BASEFILE_MATRIX - Static variable in class net.sf.basedb.core.DataFileType
-
The external ID for the file type representing a matrix BASEFile.
- BASEFILE_SERIAL - Static variable in class net.sf.basedb.core.DataFileType
-
The external ID for the file type representing a serial BASEFile.
- BaseFileExporter - Class in net.sf.basedb.util.export.spotdata
-
A superclass for exporters that exports spot data to BASEfile format.
- BaseFileExporter() - Constructor for class net.sf.basedb.util.export.spotdata.BaseFileExporter
- BaseFileExporterPlugin - Class in net.sf.basedb.plugins
-
Exports bioassay set data as serial or matrix BASEfile:s.
- BaseFileExporterPlugin() - Constructor for class net.sf.basedb.plugins.BaseFileExporterPlugin
- BaseFileExporterPlugin.ExtendedDynamicField - Class in net.sf.basedb.plugins
- BaseFileExporterSupport - Class in net.sf.basedb.plugins.executor
-
Exporter implementation for the external program executor that exports data to BASEfile format.
- BaseFileExporterSupport() - Constructor for class net.sf.basedb.plugins.executor.BaseFileExporterSupport
- BaseFileImporter - Class in net.sf.basedb.util.importer.spotdata
-
Imports spot data from a serial or matrix BASEfile.
- BaseFileImporter() - Constructor for class net.sf.basedb.util.importer.spotdata.BaseFileImporter
-
Create a new importer object.
- BaseFileImporter.RawDataProxy - Class in net.sf.basedb.util.importer.spotdata
- BaseFileImporter.ReporterProxy - Class in net.sf.basedb.util.importer.spotdata
- BaseFileImporterSupport - Class in net.sf.basedb.plugins.executor
-
Importer implementation for the external program executor that imports data from BASEfile format.
- BaseFileImporterSupport() - Constructor for class net.sf.basedb.plugins.executor.BaseFileImporterSupport
- BaseFileInfo - Class in net.sf.basedb.util.importer.spotdata
-
Collects information about a BASEfile as it gets parsed by a
BaseFileImporter
. - BaseFileInfo(FileWrapper) - Constructor for class net.sf.basedb.util.importer.spotdata.BaseFileInfo
-
The source file which should be a BASEfile.
- BaseFileInfo.ChildBioAssay - Class in net.sf.basedb.util.importer.spotdata
-
Keeps information about a new child bioassay from the 'assays' section or 'spot' sections.
- BaseFileInfo.SpotSectionInfo - Class in net.sf.basedb.util.importer.spotdata
-
Keeps information about headers and more in a 'spot' section.
- BaseFileParser - Class in net.sf.basedb.util.basefile
-
Parser for serial and matrix BASEfile:s.
- BaseFileParser() - Constructor for class net.sf.basedb.util.basefile.BaseFileParser
-
Creates a new parser object.
- BaseFileSectionParser - Interface in net.sf.basedb.util.basefile
-
A section parser is responsible for parsing and collecting data that is found in a section in a serial or matrix BASEfile.
- BaseFileWrapper - Class in net.sf.basedb.util.importer
-
File wrapper implementation for files that are located on the BASE file system.
- BaseFileWrapper(File) - Constructor for class net.sf.basedb.util.importer.BaseFileWrapper
- BaseFileWriter - Class in net.sf.basedb.util.basefile
-
Wraps a writer stream and provides methods for easier creation of BASEfiles.
- BaseFileWriter(Writer) - Constructor for class net.sf.basedb.util.basefile.BaseFileWriter
-
Create a new BASEfile writer that is writing it's output to the given writer.
- BaseInputStreamLocator - Class in net.sf.basedb.util.bfs
-
Input stream locator implementation that works with files within a given directory in the BASE file system.
- BaseInputStreamLocator(DbControl, Directory) - Constructor for class net.sf.basedb.util.bfs.BaseInputStreamLocator
-
Create a new input stream locator.
- basePrintData(Object...) - Method in class net.sf.basedb.util.basefile.BaseFileWriter
-
Print a data line to the BASEfile.
- basePrintHeader(String, Object) - Method in class net.sf.basedb.util.basefile.BaseFileWriter
-
Prints a header in the BASEfile.
- baseStyle - Variable in class net.sf.basedb.util.excel.CellStyleCreator
- baseWriteBom() - Method in class net.sf.basedb.util.basefile.BaseFileWriter
-
Write the beginning-of-file marker (BASEfile) to the output.
- basic - Static variable in class net.sf.basedb.core.Item.DefinedPermissions
- BASIC_FILTER - Static variable in class net.sf.basedb.core.QueryRuntimeFilterFactory
- BasicBatcher<D extends BatchableData> - Class in net.sf.basedb.core
-
This is an abstract class for batching functionallity.
- BasicBatcher(Session, Class<D>, String) - Constructor for class net.sf.basedb.core.BasicBatcher
-
Constructor that initiate everything.
- BasicChildItem - Class in net.sf.basedb.core
-
An abstract base class for all items which are child items to a
BasicItem
parent item. - BasicChildItem(BasicData) - Constructor for class net.sf.basedb.core.BasicChildItem
- BasicData - Class in net.sf.basedb.core.data
-
This is the root superclass of all data classes.
- BasicData() - Constructor for class net.sf.basedb.core.data.BasicData
- BasicData2ItemPropertyPath(Item, Type) - Constructor for class net.sf.basedb.core.Metadata.BasicData2ItemPropertyPath
- BasicFilter() - Constructor for class net.sf.basedb.core.QueryRuntimeFilterFactory.BasicFilter
- BasicItem - Class in net.sf.basedb.core
-
This is the root superclass of all item classes.
- BasicItem(BasicData) - Constructor for class net.sf.basedb.core.BasicItem
-
Create a new instance.
- BasicItem2DataPropertyPath(Class<C>, Type) - Constructor for class net.sf.basedb.core.Metadata.BasicItem2DataPropertyPath
- BasicItemFilter - Class in net.sf.basedb.util.overview.filter
-
A filter implementation that matches against the item that is attached to nodes.
- BasicItemFilter(BasicItem) - Constructor for class net.sf.basedb.util.overview.filter.BasicItemFilter
-
Create a filter that finds nodes that has the given item attached to it.
- BasicItemNodeLoader<I extends BasicItem> - Class in net.sf.basedb.util.overview.loader
-
Abstract class that is useful for all node loaders that works with
BasicItem
:s. - BasicItemNodeLoader(Object, boolean, NodeNameGenerator<I>) - Constructor for class net.sf.basedb.util.overview.loader.BasicItemNodeLoader
-
Create a new node loader.
- BasicItemNodeLoaderFactory - Class in net.sf.basedb.util.overview.loader
-
Node loader factory implementation for
BasicItem
node loaders. - BasicItemNodeLoaderFactory() - Constructor for class net.sf.basedb.util.overview.loader.BasicItemNodeLoaderFactory
-
Creates a new factory.
- BasicItemNodeValidatorFactory - Class in net.sf.basedb.util.overview.validator
-
Node validator factory implementation for
BasicItem
node validators. - BasicItemNodeValidatorFactory() - Constructor for class net.sf.basedb.util.overview.validator.BasicItemNodeValidatorFactory
-
Creates a new factory.
- BasicItemToIdTransformer - Class in net.sf.basedb.util.collections
-
Collection transformer implementation that extracts the ID from
BasicItem
:s. - BasicItemToIdTransformer() - Constructor for class net.sf.basedb.util.collections.BasicItemToIdTransformer
- BasicNodeValidator<I> - Class in net.sf.basedb.util.overview.validator
-
A simple node validation implementation that takes care of missing and denied access to items.
- BasicNodeValidator(Validator, Validator) - Constructor for class net.sf.basedb.util.overview.validator.BasicNodeValidator
-
Creates a new validator.
- BatchableData - Interface in net.sf.basedb.core.data
-
This is a tagging interface only.
- BatchAndMapHolder(RawDataBatcher, RawDataType, FlatFileParser) - Constructor for class net.sf.basedb.plugins.IlluminaRawDataImporter.BatchAndMapHolder
- batchCount - Variable in class net.sf.basedb.core.LogControl
- batchDate - Variable in class net.sf.basedb.core.AnnotationBatcher
- batchedExternalIds - Variable in class net.sf.basedb.core.ReporterBatcher
-
A set containing all batched but not yet flushed external reporter id:s.
- BatchedPropertyInfo - Class in net.sf.basedb.core
-
Holds information about a batchable property.
- BatchedPropertyInfo(String, int) - Constructor for class net.sf.basedb.core.BatchedPropertyInfo
-
Create a new extended property.
- batcher - Variable in class net.sf.basedb.plugins.AnnotationFlatFileImporter
- batcher - Variable in class net.sf.basedb.plugins.IlluminaRawDataImporter.BatchAndMapHolder
- batcher - Variable in class net.sf.basedb.plugins.PrintMapFlatFileImporter
- batcher - Variable in class net.sf.basedb.plugins.RawDataFlatFileImporter
- batcher - Variable in class net.sf.basedb.plugins.ReporterFlatFileImporter
- batcher - Variable in class net.sf.basedb.plugins.ReporterMapFlatFileImporter
- Batcher - Interface in net.sf.basedb.core
-
The basic interface which all batchers must implement.
- batchers - Variable in class net.sf.basedb.core.DbControl
-
A list of batchers that will be closed when
DbControl
is closed and will be flushed when commit is called. - batchIndex - Variable in class net.sf.basedb.core.data.ArraySlideData
- batchQuery - Variable in class net.sf.basedb.plugins.batchimport.AbstractItemImporter
- batchSize - Variable in class net.sf.basedb.core.AbstractBatcher
-
SQL command batch size.
- batchSize - Variable in class net.sf.basedb.core.LogControl
- BatchUtil - Class in net.sf.basedb.core
-
Utility class for batching information.
- BatchUtil() - Constructor for class net.sf.basedb.core.BatchUtil
- BCrypt - Class in net.sf.basedb.util.bcrypt
-
BCrypt implements OpenBSD-style Blowfish password hashing using the scheme described in "A Future-Adaptable Password Scheme" by Niels Provos and David Mazieres.
- BCrypt() - Constructor for class net.sf.basedb.util.bcrypt.BCrypt
- BCRYPT_SALT_LEN - Static variable in class net.sf.basedb.util.bcrypt.BCrypt
- bean - Variable in class net.sf.basedb.util.extensions.debug.BeanActionFactory
- BeanActionFactory - Class in net.sf.basedb.util.extensions.debug
-
Generic action factory class that can generate instances of actions if there exists a bean-like implementation of the action class.
- BeanActionFactory() - Constructor for class net.sf.basedb.util.extensions.debug.BeanActionFactory
-
Creates a new proxy factory.
- beanClassName - Variable in class net.sf.basedb.util.extensions.debug.BeanActionFactory
- before - Variable in class net.sf.basedb.core.DbControl.SaveIf
- BEFORE_DISABLE - Static variable in class net.sf.basedb.clients.web.extensions.ExtensionsControl
-
This event is sent before an extension or extension point is disabled by
ExtensionsControl.enableExtensionPoint(String, boolean)
,ExtensionsControl.enableExtension(String, boolean)
, orExtensionsControl.enableAllInFile(String, boolean)
. - BEFORE_UNREGISTRATION - Static variable in class net.sf.basedb.util.extensions.events.EventType
-
This event is sent before an extension point or extension is unregistered.
- BEFORE_UPDATE - Static variable in class net.sf.basedb.util.extensions.events.EventType
-
This event is sent during an update of an existing extension point or extension.
- beforeTransactionCompletion(Transaction) - Method in class net.sf.basedb.core.log.LoggingInterceptor
-
Flush remaining changes in the log control.
- begin(DbControl) - Method in class net.sf.basedb.clients.web.plugins.SimpleExport
- begin(DbControl) - Method in class net.sf.basedb.core.plugin.AbstractExporterPlugin
-
Called just before the export starts.
- begin(DbControl) - Method in class net.sf.basedb.plugins.BaseFileExporterPlugin
- begin(DbControl) - Method in class net.sf.basedb.plugins.BfsExporterPlugin
- begin(DbControl) - Method in class net.sf.basedb.plugins.GalExporter
- begin(DbControl) - Method in class net.sf.basedb.plugins.HelpExporter
- begin(DbControl) - Method in class net.sf.basedb.plugins.PackedFileExporter
- begin(DbControl) - Method in class net.sf.basedb.plugins.PlateMappingExporter
- begin(DbControl) - Method in class net.sf.basedb.plugins.PluginConfigurationExporter
- begin(ExtensionsManager, int) - Method in class net.sf.basedb.clients.web.extensions.LoadServletsProcessor
- begin(ExtensionsManager, int) - Method in class net.sf.basedb.clients.web.extensions.UninstalledFileProcessor
- begin(ExtensionsManager, int) - Method in interface net.sf.basedb.util.extensions.manager.ExtensionsFileProcessor
-
Called by the extensions manager before the processing starts.
- begin(ExtensionsManager, int) - Method in class net.sf.basedb.util.extensions.manager.processor.DeleteResourcesProcessor
- begin(ExtensionsManager, int) - Method in class net.sf.basedb.util.extensions.manager.processor.DisablePluginsProcessor
- begin(ExtensionsManager, int) - Method in class net.sf.basedb.util.extensions.manager.processor.ExtractResourcesProcessor
- begin(ExtensionsManager, int) - Method in class net.sf.basedb.util.extensions.manager.processor.IgnoreFileProcessor
- begin(ExtensionsManager, int) - Method in class net.sf.basedb.util.extensions.manager.processor.MarkAsProcessedProcessor
- begin(ExtensionsManager, int) - Method in class net.sf.basedb.util.extensions.manager.processor.PluginInstallationProcessor
- begin(ExtensionsManager, int) - Method in class net.sf.basedb.util.extensions.manager.processor.RegisterExtensionsProcessor
- begin(ExtensionsManager, int) - Method in class net.sf.basedb.util.extensions.manager.processor.ResetProcessor
- begin(ExtensionsManager, int) - Method in class net.sf.basedb.util.extensions.manager.processor.UnregisterExtensionsProcessor
- begin(FlatFileParser) - Method in class net.sf.basedb.plugins.AbstractFlatFileImporter
-
Called just before parsing of the file begins.
- begin(FlatFileParser) - Method in class net.sf.basedb.plugins.AnnotationFlatFileImporter
-
Setup error handling and pre-load some of the configuration options.
- begin(FlatFileParser) - Method in class net.sf.basedb.plugins.batchimport.AbstractItemImporter
-
Setup error handling and pre-load some of the configuration options.
- begin(FlatFileParser) - Method in class net.sf.basedb.plugins.batchimport.AnyToAnyImporter
-
Setup error handling and pre-load some of the configuration options.
- begin(FlatFileParser) - Method in class net.sf.basedb.plugins.IlluminaRawDataImporter
- begin(FlatFileParser) - Method in class net.sf.basedb.plugins.PlateFlatFileImporter
-
Create a
DbControl
and aRawDataBatcher
. - 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 aFeatureBatcher
. - 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 aReporterBatcher
. - begin(FlatFileParser) - Method in class net.sf.basedb.plugins.ReporterMapFlatFileImporter
-
Create a
DbControl
and aFeatureBatcher
. - 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 newPlateMapping
. - beginData() - Method in class net.sf.basedb.plugins.RawDataFlatFileImporter
-
Initialise column
Mapper
:s. - beginData() - Method in class net.sf.basedb.plugins.ReporterFlatFileImporter
-
Initialise column
Mapper
:s. - beginData() - Method in class net.sf.basedb.plugins.ReporterMapFlatFileImporter
-
Initialise column
Mapper
:s. - beginDocument() - Method in interface net.sf.basedb.clients.web.plugins.ExportTemplate
-
Start writing the document.
- beginDocument() - Method in class net.sf.basedb.clients.web.plugins.PlainTextTemplate
-
Do nothing.
- beginDocument() - Method in class net.sf.basedb.clients.web.plugins.XlsxTemplate
-
Reset row and column to 0.
- beginDocument() - Method in class net.sf.basedb.clients.web.plugins.XMLTemplate
-
Write XML start (<?
- beginExport() - Method in class net.sf.basedb.util.export.spotdata.AbstractBioAssaySetExporter
-
Make preparations for the export.
- beginExport() - Method in class net.sf.basedb.util.export.spotdata.BaseFileExporter
-
Prepare the export by adding all experimental factors as assay fields if no fields have been specified.
- beginExport() - Method in class net.sf.basedb.util.export.spotdata.BfsExporter
-
Validates that all required properties has been set and initialises other things that are needed.
- beginExport() - Method in class net.sf.basedb.util.export.spotdata.MatrixBaseFileExporter
-
Prepare the export by pre-loading some information and configure the queries that we are going to use.
- beginExport() - Method in class net.sf.basedb.util.export.spotdata.SerialBaseFileExporter
-
Prepare the export by pre-loading some information and configure the queries that we are going to use.
- beginItem(int) - Method in interface net.sf.basedb.clients.web.plugins.ExportTemplate
-
Start writing a new item.
- beginItem(int) - Method in class net.sf.basedb.clients.web.plugins.PlainTextTemplate
-
Reset column number.
- beginItem(int) - Method in class net.sf.basedb.clients.web.plugins.XlsxTemplate
-
Reset column number and create a new row.
- beginItem(int) - Method in class net.sf.basedb.clients.web.plugins.XMLTemplate
-
Begin a new item element.
- beginSection(BaseFileParser, FlatFileParser, List<String>) - Method in class net.sf.basedb.util.importer.spotdata.GenericIntensityParser
- beginSection(BaseFileParser, FlatFileParser, List<String>) - Method in class net.sf.basedb.util.importer.spotdata.MAParser
- beginSection(BaseFileParser, FlatFileParser, List<String>) - Method in interface net.sf.basedb.util.importer.spotdata.SpotIntensityParser
-
Prepare for parsing the data section.
- beginTransaction() - Method in class net.sf.basedb.core.hibernate.SessionWrapper
- beginTransaction() - Method in class net.sf.basedb.core.hibernate.StatelessSessionWrapper
- belongsTo(AnnotationSet) - Method in class net.sf.basedb.core.Annotation
-
Check if this annotation belongs to the primaray annotations for a specified annotation set.
- between(Expression, Expression, Expression) - Static method in class net.sf.basedb.core.query.Restrictions
-
Compare if one expression falls between two other expressions: new expression = low <= e AND e < high.
- BETWEEN - Enum constant in enum class net.sf.basedb.core.Operator
- betweenInclusive(Expression, Expression, Expression) - Static method in class net.sf.basedb.core.query.Restrictions
-
Compare if one expression falls between two other expressions (inclusive): new expression = low <= e AND e <= high.
- BetweenRestriction - Class in net.sf.basedb.core.query
-
Compare if one expression falls between to other expressions: e BETWEEN low AND high.
- BetweenRestriction(Expression, Expression, Expression, boolean) - Constructor for class net.sf.basedb.core.query.BetweenRestriction
- bf_crypt_ciphertext - Static variable in class net.sf.basedb.util.bcrypt.BCrypt
- BFS_METADATA - Static variable in class net.sf.basedb.core.DataFileType
-
The external ID for the file type representing a BFS metadata file.
- BfsExporter - Class in net.sf.basedb.util.export.spotdata
-
Base class for exporting spotdata to BFS format.
- BfsExporter() - Constructor for class net.sf.basedb.util.export.spotdata.BfsExporter
- BfsExporterPlugin - Class in net.sf.basedb.plugins
-
Exports bioassay set data to BFS format.
- BfsExporterPlugin() - Constructor for class net.sf.basedb.plugins.BfsExporterPlugin
- BfsExporterPlugin.ExtendedExportableField - Class in net.sf.basedb.plugins
- BfsExporterSupport - Class in net.sf.basedb.plugins.executor
-
Exporter implementation for the external program executor that exports data to BFS format.
- BfsExporterSupport() - Constructor for class net.sf.basedb.plugins.executor.BfsExporterSupport
- BfsImporter - Class in net.sf.basedb.util.importer.spotdata
-
Imports spot data from a serial or matrix BFS.
- BfsImporter() - Constructor for class net.sf.basedb.util.importer.spotdata.BfsImporter
-
Create a new importer object.
- BfsImporter.ProgressEventHandler - Class in net.sf.basedb.util.importer.spotdata
- BfsImporterSupport - Class in net.sf.basedb.plugins.executor
-
Importer implementation for the external program executor that imports data from BFS format.
- BfsImporterSupport() - Constructor for class net.sf.basedb.plugins.executor.BfsImporterSupport
- BfsParser - Interface in net.sf.basedb.util.bfs
-
Interface that it is recommended that all BFS parsers should implement.
- bfsPrintComment(String) - Method in class net.sf.basedb.util.bfs.MetadataWriter
-
Prints one or more comment lines to the metadata file.
- bfsPrintData(int, Object...) - Method in class net.sf.basedb.util.bfs.AnnotationWriter
-
Print a data line.
- bfsPrintData(Object...) - Method in class net.sf.basedb.util.bfs.DataWriter
-
Print a data line.
- bfsPrintEmptyLine(int) - Method in class net.sf.basedb.util.bfs.MetadataWriter
-
Print one or more empty lines to the metadata file.
- bfsPrintHeaders(String...) - Method in class net.sf.basedb.util.bfs.AnnotationWriter
-
Print the header line.
- bfsPrintSection(String, boolean, boolean) - Method in class net.sf.basedb.util.bfs.MetadataWriter
-
Start a new section.
- bfsPrintValue(String, String...) - Method in class net.sf.basedb.util.bfs.MetadataWriter
-
Prints a section entry.
- bfsPrintValue(String, Formatter<T>, T...) - Method in class net.sf.basedb.util.bfs.MetadataWriter
-
Prints a section entry.
- bfsPrintValue(String, T...) - Method in class net.sf.basedb.util.bfs.MetadataWriter
-
Prints a section entry.
- BINARY_ESCAPE - Variable in class net.sf.basedb.core.migrate.postgres.PostgresResultWriterFactory
- bins - Variable in class net.sf.basedb.util.plot.HistogramPlot.HistogramSeries
- bioassay - Variable in class net.sf.basedb.core.data.ArraySlideData
- bioassay - Variable in class net.sf.basedb.core.data.BioMaterialEventData
- bioAssay - Variable in class net.sf.basedb.core.data.RawBioAssayData
- BioAssay - Class in net.sf.basedb.core
-
Represents the current intensities of raw data after some transformation has been applied to it.
- BioAssay(BioAssayData) - Constructor for class net.sf.basedb.core.BioAssay
-
Creates a new bioassay item from the given data.
- BIOASSAY - Enum constant in enum class net.sf.basedb.core.BioMaterialEvent.Type
-
An event of this type created a physical bioassay.
- BIOASSAY - Enum constant in enum class net.sf.basedb.core.Item
-
The item is a
BioAssay
- bioAssayColumnMapping - Static variable in class net.sf.basedb.plugins.batchimport.RawBioAssayImporter
- BioAssayData - Class in net.sf.basedb.core.data
-
This class holds information about a bioassay.
- BioAssayData() - Constructor for class net.sf.basedb.core.data.BioAssayData
- BioAssayExperimentalFactorLoader - Class in net.sf.basedb.clients.web.plugins
-
Data loader that gets annotation values for a bioassay including those that are present on the parent raw bioassay(s) without being directly inherited by the bioassay.
- BioAssayExperimentalFactorLoader() - Constructor for class net.sf.basedb.clients.web.plugins.BioAssayExperimentalFactorLoader
- BioAssayExperimentalFactorLoader(SnapshotManager) - Constructor for class net.sf.basedb.clients.web.plugins.BioAssayExperimentalFactorLoader
-
Creates an experimental factor loader that uses a specific snapshot manager for loading the annotation values.
- bioAssayId - Variable in class net.sf.basedb.core.MigrateRbaToDba.Rba
- bioAssayMapper - Variable in class net.sf.basedb.plugins.batchimport.RawBioAssayImporter
- bioAssays - Variable in class net.sf.basedb.clients.web.ExperimentExplorer
-
Maps a bioassays cube column number to it's id for fast loading by the
ExperimentExplorer.getBioAssay(DbControl, short)
method. - bioAssays - Variable in class net.sf.basedb.core.data.BioAssaySetData
- bioAssays - Variable in class net.sf.basedb.core.data.RawBioAssayData
- bioAssays - Variable in class net.sf.basedb.plugins.IlluminaRawDataImporter
- bioAssays - Variable in class net.sf.basedb.util.export.spotdata.AbstractBioAssaySetExporter
- bioAssays - Variable in class net.sf.basedb.util.export.spotdata.MatrixBaseFileExporter
- bioAssays - Variable in class net.sf.basedb.util.export.spotdata.SerialBaseFileExporter
- bioAssaySet - Variable in class net.sf.basedb.clients.web.ExperimentExplorer
-
The bioassay set we are exploring.
- bioAssaySet - Variable in class net.sf.basedb.core.data.BioAssayData
- bioAssaySet - Variable in class net.sf.basedb.core.data.ExtraValueData
- bioAssaySet - Variable in class net.sf.basedb.core.DynamicPositionQuery
- bioAssaySet - Variable in class net.sf.basedb.core.DynamicSpotQuery
- bioAssaySet - Variable in class net.sf.basedb.core.FilterBatcher
-
The bioassayset this batcher inserts data for.
- bioAssaySet - Variable in class net.sf.basedb.core.SpotBatcher
-
The bioassayset this batcher inserts data for.
- BioAssaySet - Class in net.sf.basedb.core
-
A bioassayset represents the current intensities of the raw data after some
Transformation
has been applied to it. - BioAssaySet(BioAssaySetData) - Constructor for class net.sf.basedb.core.BioAssaySet
-
Creates a new experiment item from the given data.
- BIOASSAYSET - Enum constant in enum class net.sf.basedb.core.Item
-
The item is a
BioAssaySet
- BioAssaySetData - Class in net.sf.basedb.core.data
-
This class holds information about a bioassayset.
- BioAssaySetData() - Constructor for class net.sf.basedb.core.data.BioAssaySetData
- BioAssaySetFilterUtil - Class in net.sf.basedb.util
-
This is a utility class for plugins that filters bioassay set data.
- BioAssaySetFilterUtil() - Constructor for class net.sf.basedb.util.BioAssaySetFilterUtil
- bioAssaySets - Variable in class net.sf.basedb.core.data.ExperimentData
- BioAssaySetUtil - Class in net.sf.basedb.util
-
This is a utility class for
BioAssaySet
. - BioAssaySetUtil() - Constructor for class net.sf.basedb.util.BioAssaySetUtil
- bioAssaySpots - Variable in class net.sf.basedb.core.BioAssaySet
-
Stores the result of
BioAssaySet.getSpotCount(int)
. - bioMaterial - Variable in class net.sf.basedb.core.data.BioMaterialEventData
- bioMaterial - Variable in class net.sf.basedb.core.data.BioMaterialEventSourceData
- bioMaterial - Variable in class net.sf.basedb.core.data.BioWellData
- bioMaterial - Variable in class net.sf.basedb.core.MeasuredBioMaterial.RemainingQuantityAction
- BioMaterial - Class in net.sf.basedb.core
- BioMaterial(BioMaterialData) - Constructor for class net.sf.basedb.core.BioMaterial
- BioMaterialData - Class in net.sf.basedb.core.data
-
This class is the root class for biomaterials.
- BioMaterialData() - Constructor for class net.sf.basedb.core.data.BioMaterialData
- BioMaterialEvent - Class in net.sf.basedb.core
-
This class represents an event in the life of a
MeasuredBioMaterial
. - BioMaterialEvent(BioMaterialEventData) - Constructor for class net.sf.basedb.core.BioMaterialEvent
- BIOMATERIALEVENT - Enum constant in enum class net.sf.basedb.core.Item
-
The item is a
BioMaterialEvent
. - BioMaterialEvent.Type - Enum Class in net.sf.basedb.core
-
The type of the event.
- BioMaterialEventData - Class in net.sf.basedb.core.data
-
This class is used to register events for measured biomaterials.
- BioMaterialEventData() - Constructor for class net.sf.basedb.core.data.BioMaterialEventData
- BioMaterialEventLogger - Class in net.sf.basedb.core.log.db
-
Logger for biomaterial events that logs UPDATE:s to CREATION and HYBRIDIZATION events as updates to their parent biomaterial/hybridization.
- BioMaterialEventLogger(DbLogManagerFactory) - Constructor for class net.sf.basedb.core.log.db.BioMaterialEventLogger
-
Creates a new biomaterial event logger.
- bioMaterialEvents - Variable in class net.sf.basedb.core.data.BioPlateEventParticipantData
- BioMaterialEventSource - Class in net.sf.basedb.core
-
Class for holding information about a parent biomaterial that was used in an event that created a child biomaterial or a physical bioassay.
- BioMaterialEventSource(DbControl, BioMaterialEventSourceData) - Constructor for class net.sf.basedb.core.BioMaterialEventSource
- BioMaterialEventSource.BioMaterialEventSourceTransformer - Class in net.sf.basedb.core
- BioMaterialEventSourceData - Class in net.sf.basedb.core.data
-
Data class for holding information about a parent biomaterial that was used in an event that created a child biomaterial or a physical bioassay.
- BioMaterialEventSourceData() - Constructor for class net.sf.basedb.core.data.BioMaterialEventSourceData
- BioMaterialEventSourceFormatter - Class in net.sf.basedb.clients.web.plugins
-
Formatter to handle
BioMaterialEventSource
items. - BioMaterialEventSourceFormatter() - Constructor for class net.sf.basedb.clients.web.plugins.BioMaterialEventSourceFormatter
-
Create a new formatter.
- BioMaterialEventSourceFormatter(String) - Constructor for class net.sf.basedb.clients.web.plugins.BioMaterialEventSourceFormatter
-
Create a new formatter.
- BioMaterialEventSourceTransformer() - Constructor for class net.sf.basedb.core.BioMaterialEventSource.BioMaterialEventSourceTransformer
- bioMaterialType - Variable in class net.sf.basedb.core.data.BioPlateTypeData
- bioPlate - Variable in class net.sf.basedb.core.data.BioPlateEventParticipantData
- bioPlate - Variable in class net.sf.basedb.core.data.BioWellData
- BioPlate - Class in net.sf.basedb.core
-
This class is represents physical bio-plates.
- BioPlate(BioPlateData) - Constructor for class net.sf.basedb.core.BioPlate
- BIOPLATE - Enum constant in enum class net.sf.basedb.core.Item
-
The item is a
BioPlate
- bioPlateColumnMapping - Static variable in class net.sf.basedb.plugins.batchimport.SampleImporter
-
Column mapping parameter for the bioplate
- BioPlateData - Class in net.sf.basedb.core.data
-
This class holds information about a bioplate
- BioPlateData() - Constructor for class net.sf.basedb.core.data.BioPlateData
- BioPlateEvent - Class in net.sf.basedb.core
-
A bioplate event represents something that happened simultaneously to the biomaterial on one or more bioplates.
- BioPlateEvent(BioPlateEventData) - Constructor for class net.sf.basedb.core.BioPlateEvent
- BIOPLATEEVENT - Enum constant in enum class net.sf.basedb.core.Item
-
The item is a
BioPlateEvent
- BioPlateEventData - Class in net.sf.basedb.core.data
-
This class holds information about a bioplate event.
- BioPlateEventData() - Constructor for class net.sf.basedb.core.data.BioPlateEventData
- BioPlateEventLoader - Class in net.sf.basedb.util.overview.loader
-
Node loader implementation for bioplate events.
- BioPlateEventLoader() - Constructor for class net.sf.basedb.util.overview.loader.BioPlateEventLoader
- bioPlateEventParticipant - Variable in class net.sf.basedb.core.data.BioMaterialEventData
- bioPlateEventParticipant - Variable in class net.sf.basedb.core.MeasuredBioMaterial
- bioPlateEventParticipant - Variable in class net.sf.basedb.core.PhysicalBioAssay
- BioPlateEventParticipant - Class in net.sf.basedb.core
-
Holds information about a bioplate that is participating in a bioplate event.
- BioPlateEventParticipant(BioPlateEventParticipantData) - Constructor for class net.sf.basedb.core.BioPlateEventParticipant
- BIOPLATEEVENTPARTICIPANT - Enum constant in enum class net.sf.basedb.core.Item
-
The item is a
BioPlateEventParticipant
- BioPlateEventParticipantData - Class in net.sf.basedb.core.data
-
Registers a plate as a participant in a bioplate event.
- BioPlateEventParticipantData() - Constructor for class net.sf.basedb.core.data.BioPlateEventParticipantData
- BioPlateEventType - Class in net.sf.basedb.core
-
The type of a bioplate event defines what happened in the event.
- BioPlateEventType(BioPlateEventTypeData) - Constructor for class net.sf.basedb.core.BioPlateEventType
- BIOPLATEEVENTTYPE - Enum constant in enum class net.sf.basedb.core.Item
-
The item is a
BioPlateEventType
- BioPlateEventTypeData - Class in net.sf.basedb.core.data
-
Each bioplate event must have a type that defines what happened.
- BioPlateEventTypeData() - Constructor for class net.sf.basedb.core.data.BioPlateEventTypeData
- BioPlateImporter - Class in net.sf.basedb.plugins.batchimport
-
Plug-in for importing bioplate items in a batch.
- BioPlateImporter() - Constructor for class net.sf.basedb.plugins.batchimport.BioPlateImporter
- BioPlateLoader - Class in net.sf.basedb.util.overview.loader
-
Node loader implementation for bioplates.
- BioPlateLoader() - Constructor for class net.sf.basedb.util.overview.loader.BioPlateLoader
- bioPlateMapper - Variable in class net.sf.basedb.plugins.batchimport.ExtractImporter
- bioPlateMapper - Variable in class net.sf.basedb.plugins.batchimport.SampleImporter
- BioPlateNameGenerator - Class in net.sf.basedb.util.overview.node
-
Name generator implementation for
BioPlate
items. - BioPlateNameGenerator(String, String) - Constructor for class net.sf.basedb.util.overview.node.BioPlateNameGenerator
-
Create a new name generator.
- bioPlateQuery - Variable in class net.sf.basedb.plugins.batchimport.AbstractItemImporter
- bioPlates - Variable in class net.sf.basedb.core.data.BioPlateTypeData
- bioPlateType - Variable in class net.sf.basedb.core.data.BioPlateData
- BioPlateType - Class in net.sf.basedb.core
-
This class represents the type of a bio-plate.
- BioPlateType(BioPlateTypeData) - Constructor for class net.sf.basedb.core.BioPlateType
- BIOPLATETYPE - Enum constant in enum class net.sf.basedb.core.Item
-
The item is a
BioPlateType
. - bioPlateTypeColumnMapping - Static variable in class net.sf.basedb.plugins.batchimport.BioPlateImporter
- BioPlateTypeData - Class in net.sf.basedb.core.data
-
This class holds information about a biomaterial plate type.
- BioPlateTypeData() - Constructor for class net.sf.basedb.core.data.BioPlateTypeData
- bioPlateTypeMapper - Variable in class net.sf.basedb.plugins.batchimport.BioPlateImporter
- bioPlateTypeQuery - Variable in class net.sf.basedb.plugins.batchimport.AbstractItemImporter
- BioPlateValidator - Class in net.sf.basedb.util.overview.validator
-
Validator implementation for bioplates.
- BioPlateValidator() - Constructor for class net.sf.basedb.util.overview.validator.BioPlateValidator
- BioSource - Class in net.sf.basedb.core
-
This class represent biosource items.
- BioSource(BioSourceData) - Constructor for class net.sf.basedb.core.BioSource
- BIOSOURCE - Enum constant in enum class net.sf.basedb.core.Item
-
The item is a
BioSource
. - BioSourceData - Class in net.sf.basedb.core.data
-
This represents a biosoruce which is the starting point of all biomaterials.
- BioSourceData() - Constructor for class net.sf.basedb.core.data.BioSourceData
- BioSourceImporter - Class in net.sf.basedb.plugins.batchimport
-
Plug-in for importing biosource items in a batch.
- BioSourceImporter() - Constructor for class net.sf.basedb.plugins.batchimport.BioSourceImporter
- BioSourceLoader - Class in net.sf.basedb.util.overview.loader
-
Node loader implementation for biosources.
- BioSourceLoader() - Constructor for class net.sf.basedb.util.overview.loader.BioSourceLoader
- bioSourceQuery - Variable in class net.sf.basedb.plugins.batchimport.AbstractItemImporter
- BioSourceToSampleTransformer - Class in net.sf.basedb.util.listable
-
Source item transformer that transform biosource items to their child samples.
- BioSourceToSampleTransformer() - Constructor for class net.sf.basedb.util.listable.BioSourceToSampleTransformer
- BioSourceValidator - Class in net.sf.basedb.util.overview.validator
-
Validator implementation for biosources.
- BioSourceValidator() - Constructor for class net.sf.basedb.util.overview.validator.BioSourceValidator
- bioWell - Variable in class net.sf.basedb.core.data.MeasuredBioMaterialData
- BioWell - Class in net.sf.basedb.core
-
A biowell is located on a
BioPlate
and contains aMeasuredBioMaterial
. - BioWell(BioWellData) - Constructor for class net.sf.basedb.core.BioWell
- BIOWELL - Enum constant in enum class net.sf.basedb.core.Item
-
The item is a
BioWell
- BioWell.LockMode - Enum Class in net.sf.basedb.core
-
The lock mode for a well is determined by the plate's bio plate type.
- bioWellColColumnMapping - Static variable in class net.sf.basedb.plugins.batchimport.SampleImporter
-
Column mapping parameter for the biowell's column
- bioWellColMapper - Variable in class net.sf.basedb.plugins.batchimport.ExtractImporter
- bioWellColMapper - Variable in class net.sf.basedb.plugins.batchimport.SampleImporter
- BioWellData - Class in net.sf.basedb.core.data
-
This class holds information about a bio well on a bio plate.
- BioWellData() - Constructor for class net.sf.basedb.core.data.BioWellData
- BioWellLoader - Class in net.sf.basedb.util.overview.loader
-
Node loader implementation that load biomaterial on a bioplate.
- BioWellLoader() - Constructor for class net.sf.basedb.util.overview.loader.BioWellLoader
- BioWellNameGenerator - Class in net.sf.basedb.util.overview.node
-
Name generator implementation for biomaterial items that are located on a biowell.
- BioWellNameGenerator() - Constructor for class net.sf.basedb.util.overview.node.BioWellNameGenerator
-
Create a new biowell name generator.
- bioWellRowColumnMapping - Static variable in class net.sf.basedb.plugins.batchimport.SampleImporter
-
Column mapping parameter for the biowell's row
- bioWellRowMapper - Variable in class net.sf.basedb.plugins.batchimport.ExtractImporter
- bioWellRowMapper - Variable in class net.sf.basedb.plugins.batchimport.SampleImporter
- bioWells - Variable in class net.sf.basedb.core.data.BioPlateData
- BlankValue() - Constructor for class net.sf.basedb.util.excel.ExcelValue.BlankValue
- block - Variable in class net.sf.basedb.core.BlockInfo
-
The block number.
- block - Variable in class net.sf.basedb.core.data.RawData
- block - Variable in class net.sf.basedb.core.FeatureCoordinate
- block - Variable in class net.sf.basedb.plugins.LowessNormalization.SpotData
- block - Variable in class net.sf.basedb.plugins.MedianRatioNormalization.SpotData
- block - Variable in class net.sf.basedb.plugins.PrintMapFlatFileImporter.MetaBlock
- BLOCK - Enum constant in enum class net.sf.basedb.plugins.PrintMapFlatFileImporter.Section
- blockColumnMapping - Static variable in class net.sf.basedb.plugins.RawDataFlatFileImporter
- blockColumnMapping - Static variable in class net.sf.basedb.plugins.ReporterMapFlatFileImporter
- blockGroupParameter - Static variable in class net.sf.basedb.plugins.LowessNormalization
- blockGroupParameter - Static variable in class net.sf.basedb.plugins.MedianRatioNormalization
-
Used with 2-channel data only
- blockGroupSize - Variable in class net.sf.basedb.plugins.LowessNormalization.CallableWorker
- BlockInfo - Class in net.sf.basedb.core
-
A
BlockInfo
object is used to represent the uniqe identifiers of anArrayDesignBlock
. - BlockInfo(int, int) - Constructor for class net.sf.basedb.core.BlockInfo
-
Create a new block info using the meta coordinates.
- BlockInfo(int, int, int) - Constructor for class net.sf.basedb.core.BlockInfo
-
Create a new block info using meta coordinates.
- blockMapper - Variable in class net.sf.basedb.plugins.RawDataFlatFileImporter
- blockMapper - Variable in class net.sf.basedb.plugins.ReporterMapFlatFileImporter
- blockNumber - Variable in class net.sf.basedb.core.data.ArrayDesignBlockData
- blockNumber - Variable in enum class net.sf.basedb.plugins.PrintMapFlatFileImporter.Section
- blocks - Variable in class net.sf.basedb.core.ArrayDesign
- blocks - Variable in class net.sf.basedb.plugins.PrintMapFlatFileImporter
- blocks - Variable in class net.sf.basedb.plugins.ReporterMapFlatFileImporter
- blockSizeX - Variable in class net.sf.basedb.core.data.ArrayDesignBlockData
- blockSizeX - Variable in class net.sf.basedb.plugins.PrintMapFlatFileImporter.MetaBlock
- blockSizeY - Variable in class net.sf.basedb.core.data.ArrayDesignBlockData
- blockSizeY - Variable in class net.sf.basedb.plugins.PrintMapFlatFileImporter.MetaBlock
- BLOWFISH_NUM_ROUNDS - Static variable in class net.sf.basedb.util.bcrypt.BCrypt
- Body - Class in net.sf.basedb.clients.web.taglib
-
This tag defines the body section of a page.
- Body() - Constructor for class net.sf.basedb.clients.web.taglib.Body
- BOF_EVENT - Static variable in class net.sf.basedb.util.bfs.MetadataParser
-
Event type that is issued when the beginning-of-file marker is found.
- BOF_MARKER - Static variable in class net.sf.basedb.util.bfs.MetadataWriter
- bofMarker - Variable in class net.sf.basedb.util.parser.FlatFileParser
-
The regular expression for matching the beginning-of-file marker
- bofType - Variable in class net.sf.basedb.util.parser.FlatFileParser
-
The value that was captured by the bofMarker pattern.
- bool(boolean) - Static method in class net.sf.basedb.core.query.Expressions
-
Create a constant expression from a boolean.
- bool(Restriction) - Static method in class net.sf.basedb.core.query.Expressions
-
Create a boolean expression view of a restriction.
- BOOLEAN - Enum constant in enum class net.sf.basedb.core.Type
-
Boolean type.
- BOOLEAN - Static variable in class net.sf.basedb.core.hibernate.TypeWrapper
- BOOLEAN_FORMAT - Static variable in class net.sf.basedb.clients.web.plugins.SimpleExport
- BooleanExpression - Class in net.sf.basedb.core.query
-
A constant boolean expression.
- BooleanExpression(boolean) - Constructor for class net.sf.basedb.core.query.BooleanExpression
- BooleanExpression(Restriction) - Constructor for class net.sf.basedb.core.query.BooleanExpression
- BooleanFormatter - Class in net.sf.basedb.util.formatter
-
Formats a boolean value.
- BooleanFormatter(BooleanFormatter.Type) - Constructor for class net.sf.basedb.util.formatter.BooleanFormatter
-
Create a new boolean formatter.
- BooleanFormatter.Type - Enum Class in net.sf.basedb.util.formatter
-
Enum for holding the various types of boolean output.
- BooleanParameterType - Class in net.sf.basedb.core
-
This class represent a parameter type that is a boolean.
- BooleanParameterType() - Constructor for class net.sf.basedb.core.BooleanParameterType
-
Create a new boolean parameter type, allowing null values.
- BooleanParameterType(Boolean, boolean) - Constructor for class net.sf.basedb.core.BooleanParameterType
-
Create a new boolean parameter type.
- BooleanParameterType(Boolean, boolean, int, Enumeration<Boolean, String>) - Constructor for class net.sf.basedb.core.BooleanParameterType
- BooleanParameterValueData - Class in net.sf.basedb.core.data
-
Boolean parameter value.
- BooleanParameterValueData() - Constructor for class net.sf.basedb.core.data.BooleanParameterValueData
- BooleanParameterValueData(Boolean...) - Constructor for class net.sf.basedb.core.data.BooleanParameterValueData
- BooleanValue(boolean) - Constructor for class net.sf.basedb.util.excel.ExcelValue.BooleanValue
- BooleanWriter - Class in net.sf.basedb.core.migrate
-
Database-independent writer implementation that writes boolean values from a result set.
- BooleanWriter(ResultSet, int, Writer, char[]) - Constructor for class net.sf.basedb.core.migrate.BooleanWriter
- BOTTOM - Static variable in class net.sf.basedb.clients.web.taglib.tab.TabControl
-
Tabs are at the bottom of the tab control.
- boundary - Variable in class net.sf.basedb.clients.web.fileupload.FileUpload
-
The multipart/formdata boundary
- breakCircularReferences(Set<ItemProxy>) - Method in class net.sf.basedb.core.BasicItem
-
Break references to items that may lead to circular references.
- breakCircularReferences(Set<ItemProxy>) - Method in class net.sf.basedb.core.DerivedBioAssay
-
Any parent bioassays found among the given items are removed from this item.
- breakCircularReferences(Set<ItemProxy>) - Method in class net.sf.basedb.core.MeasuredBioMaterial
-
Any parent items found among the given items are removed from the creation event of this item.
- breakCircularReferences(Set<ItemProxy>) - Method in class net.sf.basedb.core.User
-
If the home directory is found among the items, set it to null.
- breakCircularReferences(SessionControl, Set<Identifiable>) - Static method in class net.sf.basedb.core.Trashcan
- buffer - Variable in class net.sf.basedb.clients.web.fileupload.FileUpload.UploadStream
- buffer - Variable in class net.sf.basedb.util.gtf.GtfInputStream
- BUFFER_SIZE - Static variable in class net.sf.basedb.util.FileUtil
- build - Variable in class net.sf.basedb.core.data.SchemaVersionData
- build - Static variable in class net.sf.basedb.core.Version
- buildDelete(String, Dialect) - Static method in class net.sf.basedb.core.BatchUtil
-
Build delete SQL string and put it in the SQL map.
- buildDocument() - Method in class net.sf.basedb.core.Presets
-
Convert the presets to a XML document.
- buildDom(Element) - Method in class net.sf.basedb.core.Presets.Preset
-
Add XML elements to the parent element for this preset's key-value pairs.
- buildFilterSql() - Method in class net.sf.basedb.core.FilterBatcher
-
Builds the insert SQL statement.
- buildInsert(String, Dialect) - Static method in class net.sf.basedb.core.BatchUtil
-
Build insert SQL string and put it in the SQL map.
- buildInsertSelectSql(String) - Method in class net.sf.basedb.core.FilterBatcher
-
Build the INSERT INTO ...
- buildInsertSelectSql(String) - Method in class net.sf.basedb.core.MappingBatcher
-
Build the INSERT INTO ...
- buildInsertSelectSql(String) - Method in class net.sf.basedb.core.PositionBatcher
-
Build the INSERT INTO ...
- buildInsertSelectSql(String) - Method in class net.sf.basedb.core.PositionExtraValueBatcher
-
Build the INSERT INTO ...
- buildInsertSelectSql(String) - Method in class net.sf.basedb.core.SpotBatcher
-
Build the INSERT INTO ...
- buildInsertSelectSql(String) - Method in class net.sf.basedb.core.SpotExtraValueBatcher
-
Build the INSERT INTO ...
- buildInsertSelectSql(VirtualDb, VirtualTable, VirtualColumn[], String) - Static method in class net.sf.basedb.core.BatchUtil
- buildInsertSql() - Method in class net.sf.basedb.core.ReporterCloneBatcher
-
Builds the insert SQL statement.
- buildInsertSql(VirtualDb, VirtualTable, VirtualColumn[], Object[]) - Static method in class net.sf.basedb.core.BatchUtil
- buildLockRequest(LockOptions) - Method in class net.sf.basedb.core.hibernate.SessionWrapper
- buildPositionSql() - Method in class net.sf.basedb.core.PositionBatcher
-
Builds the insert SQL statement.
- buildPropertyAccess(Class, String) - Method in class net.sf.basedb.core.ExtendedPropertyAccessor
- buildRawMappingSql() - Method in class net.sf.basedb.core.MappingBatcher
-
Builds the insert SQL statement.
- buildRawSelectQuery() - Method in class net.sf.basedb.core.ReporterCloneBatcher
- buildSelectQuery() - Method in class net.sf.basedb.core.ReporterCloneBatcher
-
Builds a query that select all reporter properties that should be cloned from the real reporter table.
- buildSessionFactory(ServiceSessionControl.SessionFactoryConfiguration) - Method in class net.sf.basedb.core.ServiceSessionControl
-
Create a session factory for the given configuration.
- buildSpotSql() - Method in class net.sf.basedb.core.PositionExtraValueBatcher
-
Builds the insert SQL statement.
- buildSpotSql() - Method in class net.sf.basedb.core.SpotBatcher
-
Builds the insert SQL statement.
- buildSpotSql() - Method in class net.sf.basedb.core.SpotExtraValueBatcher
-
Builds the insert SQL statement.
- buildUpdate(String, Dialect) - Static method in class net.sf.basedb.core.BatchUtil
-
Build update SQL string and put it in the SQL map.
- bulletlist - Variable in class net.sf.basedb.clients.web.taglib.table.CellValue
- Bundle - Class in net.sf.basedb.clients.web.resources
-
Declare the names of resource bundles used by the web client.
- Bundle() - Constructor for class net.sf.basedb.clients.web.resources.Bundle
- Button - Class in net.sf.basedb.clients.web.taglib
-
This tag is used to display a clickable button.
- Button - Class in net.sf.basedb.clients.web.taglib.table
-
This tag creates a button on a toolbar.
- Button() - Constructor for class net.sf.basedb.clients.web.taglib.Button
- Button() - Constructor for class net.sf.basedb.clients.web.taglib.table.Button
- Button.ButtonActionWrapper - Class in net.sf.basedb.clients.web.taglib.table
- ButtonAction - Interface in net.sf.basedb.clients.web.extensions.toolbar
-
Actions represented as buttons in a toolbar.
- ButtonActionWrapper() - Constructor for class net.sf.basedb.clients.web.taglib.table.Button.ButtonActionWrapper
- ButtonBean - Class in net.sf.basedb.clients.web.extensions.toolbar
-
A simple bean-like implementation of the
ButtonAction
interface. - ButtonBean() - Constructor for class net.sf.basedb.clients.web.extensions.toolbar.ButtonBean
- buttonclass - Variable in class net.sf.basedb.clients.web.taglib.Select
- buttonGroup - Variable in class net.sf.basedb.clients.web.taglib.Button
- ButtonGroup - Class in net.sf.basedb.clients.web.taglib
-
This tag is used to group buttons together (horizontally) and make them all have the same size.
- ButtonGroup() - Constructor for class net.sf.basedb.clients.web.taglib.ButtonGroup
- buttonicon - Variable in class net.sf.basedb.clients.web.taglib.Select
- buttons - Variable in class net.sf.basedb.clients.web.taglib.ButtonGroup
-
The buttons in this group.
- buttonstyle - Variable in class net.sf.basedb.clients.web.taglib.Select
- buttonTag - Variable in class net.sf.basedb.clients.web.extensions.toolbar.CompactButtonRenderer
- buttonTag - Variable in class net.sf.basedb.clients.web.extensions.toolbar.CompactButtonRendererFactory
- buttontitle - Variable in class net.sf.basedb.clients.web.taglib.Select
- byId(Class<T>) - Method in class net.sf.basedb.core.hibernate.SessionWrapper
- byId(String) - Method in class net.sf.basedb.core.hibernate.SessionWrapper
- byMultipleIds(Class<T>) - Method in class net.sf.basedb.core.hibernate.SessionWrapper
- byMultipleIds(String) - Method in class net.sf.basedb.core.hibernate.SessionWrapper
- byNaturalId(Class<T>) - Method in class net.sf.basedb.core.hibernate.SessionWrapper
- byNaturalId(String) - Method in class net.sf.basedb.core.hibernate.SessionWrapper
- bySimpleNaturalId(Class<T>) - Method in class net.sf.basedb.core.hibernate.SessionWrapper
- bySimpleNaturalId(String) - Method in class net.sf.basedb.core.hibernate.SessionWrapper
- ByteArrayWriter - Class in net.sf.basedb.core.migrate
-
Generic writer implementation that writes byte-array values from a result set.
- ByteArrayWriter(ResultSet, int, Writer, char[], char[][]) - Constructor for class net.sf.basedb.core.migrate.ByteArrayWriter
- bytes - Variable in class net.sf.basedb.core.data.DataCubeData
- bytes - Variable in class net.sf.basedb.core.data.DataCubeExtraValueData
- bytes - Variable in class net.sf.basedb.core.data.DataCubeFilterData
- bytes - Variable in class net.sf.basedb.core.data.DataCubeLayerData
- bytes - Variable in class net.sf.basedb.core.data.DiskUsageData
- bytes - Variable in class net.sf.basedb.core.data.ExperimentData
- bytes - Variable in class net.sf.basedb.core.data.RawBioAssayData
- bytes - Variable in class net.sf.basedb.core.data.ReporterCloneTemplateData
- bytes - Variable in class net.sf.basedb.core.FilterBatcher
-
The number of bytes this batcher has added to the experiment.
- bytes - Variable in class net.sf.basedb.core.MappingBatcher
-
The number of bytes this batcher has added to the experiment.
- bytes - Variable in class net.sf.basedb.core.PositionBatcher
-
The number of bytes this batcher has added to the data cube and experiment.
- bytes - Variable in class net.sf.basedb.core.PositionExtraValueBatcher
-
The number of bytes this batcher has added to the experiment.
- bytes - Variable in class net.sf.basedb.core.RawDataBatcher
-
The number of bytes the spot data is occupying on disk.
- bytes - Variable in class net.sf.basedb.core.SpotBatcher
-
The number of bytes this batcher has added to the experiment.
- bytes - Variable in class net.sf.basedb.core.SpotExtraValueBatcher
-
The number of bytes this batcher has added to the experiment.
- BYTES_REGEXP - Static variable in class net.sf.basedb.util.Values
- bytesPerRow - Variable in class net.sf.basedb.core.FilterBatcher
-
The number of bytes used by a single row.
- bytesPerRow - Variable in class net.sf.basedb.core.MappingBatcher
-
The number of bytes used by a single row.
- bytesPerRow - Variable in class net.sf.basedb.core.PositionBatcher
-
The number of bytes used by a single row.
- bytesPerRow - Variable in class net.sf.basedb.core.PositionExtraValueBatcher
-
The number of bytes used by a single row.
- bytesPerRow - Variable in class net.sf.basedb.core.ReporterCloneBatcher
-
The number of bytes used by a single row.
- bytesPerRow - Variable in class net.sf.basedb.core.SpotBatcher
-
The number of bytes used by a single row.
- bytesPerRow - Variable in class net.sf.basedb.core.SpotExtraValueBatcher
-
The number of bytes used by a single row.
- bzip - Variable in class net.sf.basedb.util.zip.Bzip2FilePacker
- Bzip2FilePacker - Class in net.sf.basedb.util.zip
-
This class wraps the
TarFilePacker
in a BZIP2 stream, creating a tar.bz2 file. - Bzip2FilePacker() - Constructor for class net.sf.basedb.util.zip.Bzip2FilePacker
-
Create a new packer that compresses files with the BZIP2 format.
- Bzip2FileUnpacker - Class in net.sf.basedb.plugins
-
A plugin for unpacking a bzip2 compressed file to the BASE file system.
- Bzip2FileUnpacker() - Constructor for class net.sf.basedb.plugins.Bzip2FileUnpacker
C
- c - Variable in enum class net.sf.basedb.plugins.Base1PluginExecuter.Base1JobParameterType
- CABINET - Static variable in class net.sf.basedb.core.Hardware
-
The id for the
HardwareType
object representing a cabinet. - cache - Variable in class net.sf.basedb.clients.web.ExperimentExplorer
-
The cache of reporter ids matching the current reporter filter.
- cache - Static variable in class net.sf.basedb.core.DerivedBioAssay.FixDerivedBioAssayParentsRecursivelyAction
- cache - Variable in class net.sf.basedb.core.hibernate.AbstractQueryCache
- cache - Static variable in class net.sf.basedb.core.MeasuredBioMaterial.RemainingQuantityAction
-
We need a single action per DbControl and BioMaterial
- cache - Variable in class net.sf.basedb.util.AnnotationUtil.AnnotatableWrapper
- cache - Variable in class net.sf.basedb.util.bfs.BaseInputStreamLocator
- cache - Variable in class net.sf.basedb.util.listable.TransformCache
- cache - Variable in class net.sf.basedb.util.overview.cache.NodeCache
- cache - Variable in class net.sf.basedb.util.StaticCache.CleanupTask
- Cache() - Constructor for class net.sf.basedb.util.AnnotationUtil.Cache
- cacheBase - Variable in class net.sf.basedb.clients.web.servlet.PlotServlet
- cacheChildNodes(Node) - Method in class net.sf.basedb.util.overview.GenericOverview
- cacheControl - Variable in class net.sf.basedb.clients.web.servlet.CacheControlFilter
- cacheControl - Variable in class net.sf.basedb.clients.web.servlet.ImageRemapFilter
- CacheControlFilter - Class in net.sf.basedb.clients.web.servlet
-
This is a filter that sets the "Cache-Control" header in the http response.
- CacheControlFilter() - Constructor for class net.sf.basedb.clients.web.servlet.CacheControlFilter
- cachedPaths - Variable in class net.sf.basedb.core.Metadata
- cachedRssNews - Variable in class net.sf.basedb.clients.web.servlet.RssNewsFeed
- CacheEntry(long, Set<Integer>) - Constructor for class net.sf.basedb.util.listable.TransformCache.CacheEntry
- cacheFile - Variable in class net.sf.basedb.util.StreamCacher
- cacheKey - Variable in class net.sf.basedb.util.overview.cache.DirectionalCacheKey
- cacheKey - Variable in class net.sf.basedb.util.overview.cache.IndexedCacheKey
- CacheKey(int, String) - Constructor for class net.sf.basedb.util.units.UnitCache.CacheKey
- CacheKey(String, Item, Item, SyncFilter.SourceItemTransform, SortedSet<Integer>) - Constructor for class net.sf.basedb.util.listable.TransformCache.CacheKey
- cacheNewNode(Object, Node, ChildNodeDirection) - Method in class net.sf.basedb.util.overview.node.NodeFactory
-
Store a node in the node cache if the current overview context supports caching.
- cacheOut - Variable in class net.sf.basedb.util.StreamCacher
- cacheQuery(String, Query<?>) - Method in class net.sf.basedb.core.hibernate.AbstractQueryCache
-
Cache a query.
- cacheRegion - Variable in class net.sf.basedb.util.listable.SourceItemTransformerWithCache
- cacheRegion - Variable in class net.sf.basedb.util.listable.SourceItemTransformerWithCache.TransformerWithCache
- cacheRegion - Variable in class net.sf.basedb.util.listable.TransformCache.CacheKey
- cacheReporterData() - Method in class net.sf.basedb.util.export.spotdata.AbstractBioAssaySetExporter
-
Loads and caches reporter data in an internal structure for quick access.
- cacheResults - Variable in class net.sf.basedb.core.AbstractHqlQuery
-
If the results should be cached or not.
- calculateBoxAndWhiskerStatistics(List<Float>) - Method in class net.sf.basedb.clients.web.servlet.ExperimentExplorerPlotServlet
-
Creates a box-and-whisker data holder for the given list of values.
- calculateIntensities(RawData) - Method in interface net.sf.basedb.util.IntensityCalculator
-
Calculate intensities from a raw data spot.
- calculateIntensities(RawData) - Method in class net.sf.basedb.util.IntensityCalculatorUtil.JepIntensityCalculatorImpl
- calculateWeights(List<LowessNormalization.SpotData>, double, List<Double>) - Static method in class net.sf.basedb.plugins.LowessNormalization
- CalendarButton - Class in net.sf.basedb.clients.web.taglib
-
A special button tag that is used to display a "Calendar" button that opens a popup for selecting a date and time.
- CalendarButton() - Constructor for class net.sf.basedb.clients.web.taglib.CalendarButton
- call() - Method in class net.sf.basedb.core.QueryExecutor.FutureItem
- call() - Method in class net.sf.basedb.core.QueryExecutor.FutureResultSet
- call() - Method in class net.sf.basedb.core.QueryExecutor.FutureScrollIterator
- call() - Method in class net.sf.basedb.core.QueryExecutor.FutureUpdate
- call() - Method in class net.sf.basedb.plugins.LowessNormalization.CallableWorker
- CallableWorker(List<LowessNormalization.SpotData>, MACalculator, float, float, int, int) - Constructor for class net.sf.basedb.plugins.LowessNormalization.CallableWorker
- calledFrom - Variable in class net.sf.basedb.util.StaticCache.State
- canAdd(BioWell) - Method in enum class net.sf.basedb.core.BioWell.LockMode
-
Is it allowed to add (a different) biomaterial to the well?
- canAdd(BioWellData) - Method in enum class net.sf.basedb.core.BioWell.LockMode
- canAddBioMaterial() - Method in class net.sf.basedb.core.BioWell
-
Check if it is possible to add/change biomaterial in this well.
- cancel() - Method in class net.sf.basedb.clients.jobagent.JobQueueChecker
- cancel() - Method in interface net.sf.basedb.core.QueryExecutor.Cancelable
- cancel() - Method in class net.sf.basedb.core.QueryExecutor.CancelableSession
- cancel() - Method in class net.sf.basedb.core.QueryExecutor.CancelableStatelessSession
- cancel() - Method in class net.sf.basedb.core.QueryExecutor.CancelableStatement
- cancel() - Method in class net.sf.basedb.util.timer.ThreadTimerTask
- CancelableSession(Session) - Constructor for class net.sf.basedb.core.QueryExecutor.CancelableSession
- CancelableStatelessSession(StatelessSession) - Constructor for class net.sf.basedb.core.QueryExecutor.CancelableStatelessSession
- CancelableStatement(Statement) - Constructor for class net.sf.basedb.core.QueryExecutor.CancelableStatement
- cancelQuery() - Method in class net.sf.basedb.core.hibernate.SessionWrapper
- cancelQuery() - Method in class net.sf.basedb.core.hibernate.StatelessSessionWrapper
-
Cancels the currently executing query in the same manner as
Session.cancelQuery()
. - canClear(BioWell) - Method in enum class net.sf.basedb.core.BioWell.LockMode
-
Is it allowed to clear a well from biomaterial?
- canClear(BioWellData) - Method in enum class net.sf.basedb.core.BioWell.LockMode
- canClearBioMaterial() - Method in class net.sf.basedb.core.BioWell
-
Check if it is possible to clear the current biomaterial in this well.
- canEnumerate - Variable in enum class net.sf.basedb.core.Type
- canEnumerate() - Method in enum class net.sf.basedb.core.Type
-
If it makes sense to use values of this type as an enumeration to choose from.
- canLogValues(String) - Method in class net.sf.basedb.core.log.EntityLogOptions
-
Check if it is allowed to log the old and new values of a modified property.
- canUseColoring - Variable in enum class net.sf.basedb.core.Formula.Type
- canUseColoring() - Method in enum class net.sf.basedb.core.Formula.Type
-
If a formula of this type can use coloring or not.
- CAPACITANCE - Static variable in class net.sf.basedb.core.Quantity
-
The id for the
Quantity
object representing capacitance. - CaseExpression - Class in net.sf.basedb.core.query
-
An SQL case expression:
- CaseExpression(Expression, WhenStatement...) - Constructor for class net.sf.basedb.core.query.CaseExpression
- caseInsensitive - Variable in enum class net.sf.basedb.core.FeatureIdentificationMethod
-
If the feature identifiers may be affect by case sensitivity at the database level or not.
- caseInsensitive - Variable in class net.sf.basedb.core.RawDataBatcher
-
If case should be ignored when comparing strings (external ID)
- caseInsensitive() - Method in enum class net.sf.basedb.core.FeatureIdentificationMethod
-
Return TRUE if this identification method can be case insensitive.
- caseInsensitiveComparison() - Method in interface net.sf.basedb.core.dbengine.DbEngine
-
If the database does case sensitive or case insensitive string comparison in expressions.
- caseInsensitiveComparison() - Method in class net.sf.basedb.core.dbengine.DefaultDbEngine
-
Returns TRUE.
- caseInsensitiveComparison() - Method in class net.sf.basedb.core.dbengine.MySQLEngine
-
Returns TRUE.
- caseInsensitiveComparison() - Method in class net.sf.basedb.core.dbengine.PostgresDbEngine
-
Returns FALSE.
- caseWhen(Expression, WhenStatement...) - Static method in class net.sf.basedb.core.query.Expressions
-
Create a conditional
CASE-WHEN
expression: - castToDate(String) - Method in class net.sf.basedb.core.dbengine.AbstractDbEngine
- castToDate(String) - Method in interface net.sf.basedb.core.dbengine.DbEngine
-
Get a function that casts a date/timestamp to a date (eg. no time should be included in the result).
- catalog - Variable in class net.sf.basedb.core.hibernate.SchemaExistsWork
- catalog - Variable in class net.sf.basedb.core.hibernate.TableExistsWork
- categories - Variable in class net.sf.basedb.core.data.AnnotationTypeData
- categoryColumnMapping - Static variable in class net.sf.basedb.plugins.batchimport.AnnotationTypeImporter
-
Column mapping parameter for assigning annotation types to categories.
- categoryMapper - Variable in class net.sf.basedb.plugins.batchimport.AnnotationTypeImporter
- CdfFileReporterImporter - Class in net.sf.basedb.plugins
-
This plug-in can import probesets from Affymetrix CDF files as reporters.
- CdfFileReporterImporter() - Constructor for class net.sf.basedb.plugins.CdfFileReporterImporter
-
Constructor should be empty.
- CdfValidationAction - Class in net.sf.basedb.util.affymetrix
-
Action for validation of CDF files in a file set.
- CdfValidationAction(DbControl, ArrayDesign) - Constructor for class net.sf.basedb.util.affymetrix.CdfValidationAction
-
Create a new action.
- CdfValidationFactory - Class in net.sf.basedb.util.affymetrix
-
Action factory for creating CDF file validators.
- CdfValidationFactory() - Constructor for class net.sf.basedb.util.affymetrix.CdfValidationFactory
- CdfValidator - Class in net.sf.basedb.util.affymetrix
-
Helper class for working with Affymetrix CDF files.
- CdfValidator() - Constructor for class net.sf.basedb.util.affymetrix.CdfValidator
-
Create a new instance.
- Cell - Class in net.sf.basedb.clients.web.taglib.table
-
This tag defines a new cell in a row.
- Cell() - Constructor for class net.sf.basedb.clients.web.taglib.table.Cell
- cellClass - Variable in class net.sf.basedb.clients.web.extensions.list.AbstractListColumnBean
- cellClass - Variable in class net.sf.basedb.clients.web.extensions.list.PropertyPathActionFactory
- cellStyle - Variable in class net.sf.basedb.clients.web.extensions.list.AbstractListColumnBean
- cellStyle - Variable in class net.sf.basedb.clients.web.extensions.list.PropertyPathActionFactory
- CellStyleCreator - Class in net.sf.basedb.util.excel
-
Helper class for keeping track of formatting styles that has been created for given Excel worksheet.
- CellStyleCreator(Workbook) - Constructor for class net.sf.basedb.util.excel.CellStyleCreator
-
Creates a new style creator for the given Excel workbook.
- cellType - Variable in class net.sf.basedb.util.excel.XlsxToCsvUtil.CellTypeWithInfo
- CellTypeWithInfo() - Constructor for class net.sf.basedb.util.excel.XlsxToCsvUtil.CellTypeWithInfo
- CellValue - Class in net.sf.basedb.clients.web.taglib.table
-
This tag adds a value to a cell in a row.
- CellValue() - Constructor for class net.sf.basedb.clients.web.taglib.table.CellValue
- CelValidationAction - Class in net.sf.basedb.util.affymetrix
-
Action for validation of CEL files in a file set.
- CelValidationAction(DbControl, RawBioAssay) - Constructor for class net.sf.basedb.util.affymetrix.CelValidationAction
-
Create a new action.
- CelValidationFactory - Class in net.sf.basedb.util.affymetrix
-
Action factory for creating CEL file validators.
- CelValidationFactory() - Constructor for class net.sf.basedb.util.affymetrix.CelValidationFactory
- CelValidator - Class in net.sf.basedb.util.affymetrix
-
Helper class for working with Affymetrix CEL files.
- CelValidator() - Constructor for class net.sf.basedb.util.affymetrix.CelValidator
-
Create a new instance.
- cfg - Static variable in class net.sf.basedb.core.HibernateUtil
-
The Hibernate configuration, including all mappings.
- cfg - Variable in class net.sf.basedb.core.MigrateRbaToDba.SubtypeMapping
- CFResultIterator(SqlResultIterator, SqlResultIterator) - Constructor for class net.sf.basedb.clients.web.servlet.PlotServlet.CFResultIterator
- CFSqlResult() - Constructor for class net.sf.basedb.clients.web.servlet.PlotServlet.CFSqlResult
- ch - Variable in class net.sf.basedb.util.importer.spotdata.MatrixSpotIntensityEventHandler
- ch - Variable in class net.sf.basedb.util.importer.spotdata.SerialSpotIntensityEventHandler
- ch1 - Variable in class net.sf.basedb.plugins.LowessNormalization.SpotData
- ch1 - Variable in class net.sf.basedb.plugins.MedianRatioNormalization.SpotData
- ch2 - Variable in class net.sf.basedb.plugins.LowessNormalization.SpotData
- ch2 - Variable in class net.sf.basedb.plugins.MedianRatioNormalization.SpotData
- chain - Variable in class net.sf.basedb.util.AnnotationUtil.AnnotatableWrapper
- chain - Variable in class net.sf.basedb.util.listable.SourceItemTransformerChain
- CHAIN_ORDER - Static variable in class net.sf.basedb.core.SyncFilter
- chained - Variable in class net.sf.basedb.core.Job.ProgressReporterImpl
- ChainedFilter(List<QueryRuntimeFilter>) - Constructor for class net.sf.basedb.core.QueryRuntimeFilterFactory.ChainedFilter
-
Create a new
ChainedFilter
object. - ChainedFilter(QueryRuntimeFilter...) - Constructor for class net.sf.basedb.core.QueryRuntimeFilterFactory.ChainedFilter
-
Create a new
ChainedFilter
object. - chainedProgress - Variable in class net.sf.basedb.util.export.spotdata.BfsExporter
- ChainedProgressReporter - Class in net.sf.basedb.util
-
An implementation of the ProgressReporter interface that chains to another progress reporter while recalculating the percentage values.
- ChainedProgressReporter(ProgressReporter) - Constructor for class net.sf.basedb.util.ChainedProgressReporter
-
Create a new chained progress reporter.
- Change(ChangeType) - Constructor for enum class net.sf.basedb.core.AnnotationBatcher.Change
- ChangeHistory - Class in net.sf.basedb.core
- ChangeHistory(ChangeHistoryDetailData) - Constructor for class net.sf.basedb.core.ChangeHistory
- CHANGEHISTORY - Enum constant in enum class net.sf.basedb.core.Item
-
The item is a
ChangeHistory
entry. - CHANGEHISTORY_VALUES - Enum constant in enum class net.sf.basedb.core.Item
-
Virtual item representing the new and old values column in
ChangeHistory
which need special access permissions. - ChangeHistory.TransactionInfo - Class in net.sf.basedb.core
-
Holds information about a single transaction.
- ChangeHistoryData - Class in net.sf.basedb.core.data
-
Represents the changes made in a single transaction.
- ChangeHistoryData() - Constructor for class net.sf.basedb.core.data.ChangeHistoryData
- ChangeHistoryDetailData - Class in net.sf.basedb.core.data
-
Represents a change (creation/update/deletion) made to a single entity in a transaction.
- ChangeHistoryDetailData() - Constructor for class net.sf.basedb.core.data.ChangeHistoryDetailData
- ChangeHistoryDetailLoader - Class in net.sf.basedb.clients.web.plugins
-
Data loader implementation for old and new values in the change history which are protected by special permissions.
- ChangeHistoryDetailLoader(boolean) - Constructor for class net.sf.basedb.clients.web.plugins.ChangeHistoryDetailLoader
- ChangeHistoryItemLoader - Class in net.sf.basedb.clients.web.plugins
-
Data loader implementation for loading the changed item.
- ChangeHistoryItemLoader() - Constructor for class net.sf.basedb.clients.web.plugins.ChangeHistoryItemLoader
- ChangeHistoryUtil - Class in net.sf.basedb.clients.web
-
Utility class for working with change history.
- ChangeHistoryUtil() - Constructor for class net.sf.basedb.clients.web.ChangeHistoryUtil
- changeHost(URI) - Method in class net.sf.basedb.util.uri.ConnectionParameters
-
If the connection parameters include a specific host:port or root path a new URI is created were the host:port is replaced and the root path is added to the URI path.
- changeInfo - Variable in class net.sf.basedb.core.data.ChangeHistoryDetailData
- changeReferenceFactorAndOffset(double, double) - Method in class net.sf.basedb.core.Unit
-
Changes the factor and offset used for converting values in this unit into the reference unit.
- changeReferenceFactorAndOffset(SessionControl, Session, UnitData, double, double) - Static method in class net.sf.basedb.core.Unit
- changes - Variable in class net.sf.basedb.core.log.LoggingInterceptor
- changeType - Variable in class net.sf.basedb.core.data.ChangeHistoryDetailData
- changeType - Variable in class net.sf.basedb.core.log.EntityDetails
- changeType - Variable in class net.sf.basedb.core.log.ManualLogEntry
- ChangeType - Enum Class in net.sf.basedb.core.log
-
Enumeration that represents the type of change that has happened.
- ChangeType(int, String) - Constructor for enum class net.sf.basedb.core.log.ChangeType
- ChangeTypeFormatter - Class in net.sf.basedb.core.log
-
Formatter implementation that converts an integer into it's ChangeType representation and the uses name() as the formatted value.
- ChangeTypeFormatter() - Constructor for class net.sf.basedb.core.log.ChangeTypeFormatter
-
Create a new formatter.
- ChangeTypeFormatter(String) - Constructor for class net.sf.basedb.core.log.ChangeTypeFormatter
-
Create a new formatter.
- channel - Variable in class net.sf.basedb.core.RawDataProperty
- channel(int) - Method in class net.sf.basedb.util.jep.ChannelFunction
-
Get the value of the specified channel of the current sql result.
- channel(int) - Method in class net.sf.basedb.util.jep.RawChannelFunction
-
Get the value of the specified channel of the current sql result.
- channel(int, String, Formatter<?>) - Static method in class net.sf.basedb.util.export.spotdata.ExportableFieldFactory
-
Create a simple dynamic field that exports the channel intensity of the given channel.
- ChannelFunction - Class in net.sf.basedb.util.jep
-
A JEP function class that adds a
ch(int)
function to a JEP expression parser. - ChannelFunction() - Constructor for class net.sf.basedb.util.jep.ChannelFunction
-
Create a new instance of this function.
- ChannelFunction(int[], IntensityTransform) - Constructor for class net.sf.basedb.util.jep.ChannelFunction
-
Create a new instance of this function which can be used to dynamically evaluate expressions.
- channelIntensity(int) - Static method in class net.sf.basedb.core.VirtualColumn
-
Get a column that returns the intensity values for a channel.
- channelParameters - Variable in class net.sf.basedb.plugins.JepIntensityTransformer
- channelRaw(int) - Static method in class net.sf.basedb.core.VirtualColumn
-
Get a column that stores the raw spot value for a channel.
- channels - Variable in class net.sf.basedb.core.data.FormulaData
- channels - Variable in class net.sf.basedb.core.data.PlatformData
- channels - Variable in class net.sf.basedb.core.data.PlatformVariantData
- channels - Variable in class net.sf.basedb.core.RawDataType
- channels - Variable in class net.sf.basedb.util.importer.spotdata.GenericIntensityParser
- channels - Variable in class net.sf.basedb.util.importer.spotdata.SecondPassSectionSpotsParser
- channelToIndex - Variable in class net.sf.basedb.util.jep.ChannelFunction
- channelToIndex - Variable in class net.sf.basedb.util.jep.RawChannelFunction
- CHAR_ESCAPE - Variable in class net.sf.basedb.core.migrate.postgres.PostgresResultWriterFactory
- char64(char) - Static method in class net.sf.basedb.util.bcrypt.BCrypt
-
Look up the 3 bits base64-encoded by the specified character, range-checking againt conversion table
- characterEncoding - Variable in class net.sf.basedb.clients.web.servlet.CharacterEncodingFilter
- CharacterEncodingFilter - Class in net.sf.basedb.clients.web.servlet
-
This is a filter that sets the character encoding for both the request and the response.
- CharacterEncodingFilter() - Constructor for class net.sf.basedb.clients.web.servlet.CharacterEncodingFilter
- characterSetColumnMapping - Static variable in class net.sf.basedb.plugins.batchimport.FileImporter
- characterSetMapper - Variable in class net.sf.basedb.plugins.batchimport.FileImporter
- CHARGE - Static variable in class net.sf.basedb.core.Quantity
-
The id for the
Quantity
object representing electrical charge. - charset - Variable in class net.sf.basedb.clients.web.fileupload.FileUpload
-
The charset used for decoding header lines.
- charset - Variable in class net.sf.basedb.core.data.FileData
- charset - Variable in class net.sf.basedb.util.charset.CharsetDetector
- charset - Variable in class net.sf.basedb.util.excel.XlsxToCsvUtil
- charset - Variable in class net.sf.basedb.util.FileImportInputStream
- charset - Variable in class net.sf.basedb.util.gtf.GtfInputStream
- charset - Variable in class net.sf.basedb.util.uri.UriMetadata
- CHARSET_PARAMETER - Static variable in class net.sf.basedb.plugins.util.Parameters
-
The name of the parameter that is created by
Parameters.charsetParameter(String, String, String, boolean)
- CharsetDetector - Class in net.sf.basedb.util.charset
-
Utility class for testing if a text stream can be parsed using a given character set.
- CharsetDetector(Charset) - Constructor for class net.sf.basedb.util.charset.CharsetDetector
-
Create a detector for the given character set that only detects technical issues.
- CharsetDetector(Charset, StringDetector) - Constructor for class net.sf.basedb.util.charset.CharsetDetector
-
Create a detector for the given character set that uses technical an content-based detection.
- charsetParameter(String, String, String) - Static method in class net.sf.basedb.plugins.util.Parameters
- charsetParameter(String, String, String, boolean) - Static method in class net.sf.basedb.plugins.util.Parameters
-
Parameter definition that asks for the character encoding used in the file that is imported.
- CharsetTesterThread(Charset) - Constructor for class net.sf.basedb.core.File.CharsetTesterThread
- charsetType - Static variable in class net.sf.basedb.plugins.util.Parameters
-
Enumerates all available character sets.
- CharsetUtil - Class in net.sf.basedb.util.charset
-
Helper class for working with charsets and enabling the UTF-8 with fallback charsets: X-UTF-8_with_ISO-8859-1_fallback X-UTF-8_with_windows-1252_fallback
- CharsetUtil() - Constructor for class net.sf.basedb.util.charset.CharsetUtil
- charsetWithFallbacksType - Static variable in class net.sf.basedb.plugins.util.Parameters
-
Enumerates all available character sets and also inlcude fallback type.
- chart - Variable in class net.sf.basedb.util.plot.HistogramPlot
- chart - Variable in class net.sf.basedb.util.plot.ScatterPlot
- checkAbortAndDelay() - Method in class net.sf.basedb.clients.web.fileupload.FileUpload
-
Check if upload has been aborted.
- checkAllowedSource(BioMaterial, boolean) - Method in class net.sf.basedb.core.BioMaterialEvent
-
Check if the biomaterial is allowed as a source.
- checkAndCreateTables() - Method in class net.sf.basedb.core.BioAssaySet
- checkAndLoadClass(ClassLoader, String, boolean, Class<C>, Class<?>...) - Static method in class net.sf.basedb.util.ClassUtil
-
Check if a specified class exists and, optionally, if it has public no-argument constructor and implements a set of specific interfaces or superclasses.
- checkBatchAnnotatableUsage(boolean, boolean) - Method in class net.sf.basedb.core.BasicItem
-
Annotatable items that are used with the
AnnotationBatcher
must not callAnnotatable.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 theboundary
. - checkClass(Class<?>, boolean, Class<?>...) - Static method in class net.sf.basedb.util.ClassUtil
-
Check if a specified class has public no-argument constructor and implements a set of specific interfaces or superclasses.
- checkClosed() - Method in class net.sf.basedb.util.extensions.manager.ExtensionsFile.WriteableExtensionsFile
-
Check if the file has been closed and throws an IllegalStateException if it has.
- checkColumnMapping(String, boolean, String) - Method in class net.sf.basedb.plugins.AbstractFlatFileImporter
-
Check if a column mapping is a valid mapping expression and optionally if it is complex mapping.
- checkColumnMapping(FlatFileParser, String, boolean, String) - Method in class net.sf.basedb.plugins.AbstractFlatFileImporter
-
Checks the syntax column mapping and verifies that the given file parser has found the columns that are used in the file.
- checkContext(DbControl, ItemQuery<PluginDefinition>, ItemQuery<PluginConfiguration>, GuiContext, Object) - Static method in class net.sf.basedb.util.ContextUtil
-
Call the
InteractivePlugin.isInContext(GuiContext, Object)
method for all plug-ins returned by the queries. - checkCoordinate(MappingCoordinate, int, PlateGeometryData, boolean) - Method in class net.sf.basedb.core.PlateMapping
-
Checks that the coordinate is within the bouds given by the mapping and geometry.
- checkDerivedBioAssaySubtype(DbControl, OverviewContext, Node, Node) - Static method in class net.sf.basedb.util.overview.validator.DerivedBioAssayValidator
-
Check the subtype of the derived bioassay that is the parent to a child derived bioassay.
- checked - Variable in class net.sf.basedb.clients.web.taglib.Input
-
TRUE if the input element is checked.
- checkEntity(IdentifiableData) - Method in class net.sf.basedb.core.hibernate.EntityQueryWrapper
- checkEntityArray(Object[]) - Method in class net.sf.basedb.core.hibernate.EntityQueryWrapper
- checkEntityCollection(Collection<?>) - Method in class net.sf.basedb.core.hibernate.EntityQueryWrapper
- checkExperimentArrayDesign(DbControl, OverviewContext, Node, ArrayDesign) - Method in class net.sf.basedb.util.overview.validator.ArrayDesignValidator
-
Check if an experiment has used more than one array design.
- checkExtractOnBioAssay(DbControl, OverviewContext, Node, Node) - Method in class net.sf.basedb.util.overview.validator.ExtractValidator
- checkExtractSubtype(DbControl, OverviewContext, Node, Node) - Static method in class net.sf.basedb.util.overview.validator.DerivedBioAssayValidator
-
Check the subtype of the extract that is the linked with a derived bioassay.
- checkExtractSubtype(DbControl, OverviewContext, Node, Node) - Static method in class net.sf.basedb.util.overview.validator.PhysicalBioAssayValidator
-
Check the subtype of the extract that is the parent to a physical bioassay.
- checkExtractTag(DbControl, OverviewContext, Node, Node) - Static method in class net.sf.basedb.util.overview.validator.ExtractValidator
-
Check the tag of the child extract in relation to a parent extract.
- checkForInvalidNumberOperation() - Method in class net.sf.basedb.core.dbengine.AbstractDbEngine
-
Returns FALSE.
- checkForInvalidNumberOperation() - Method in interface net.sf.basedb.core.dbengine.DbEngine
-
If we need to check for invalid arguments to numerical functions to avoid exceptions from the database.
- checkForInvalidNumberOperation() - Method in class net.sf.basedb.core.dbengine.PostgresDbEngine
-
Returns TRUE.
- checkForJobs() - Method in class net.sf.basedb.clients.jobagent.JobQueueChecker
- checkForSignals() - Method in class net.sf.basedb.core.signal.EnhancedThreadSignalHandler
-
If at least one signal has been received a
SignalReceivedException
is thrown. - checkForSignals() - Method in class net.sf.basedb.core.signal.ProgressReporterSignalHandler
-
If at least one signal has been received a
SignalReceivedException
is thrown. - checkIfDifferent(Object, Unit) - Method in class net.sf.basedb.core.Annotation
-
Check if the given value is different from the values already stored in this annotation.
- checkIfDifferent(List<?>, Unit) - Method in class net.sf.basedb.core.Annotation
-
Check if the given values are different from the values already stored in this annotation.
- checkIfReportersExists(FusionCDFData, ReporterBatcher, boolean, ReporterType, ProgressReporter) - Method in class net.sf.basedb.util.affymetrix.CdfValidator
-
Verify if probesets in a CDF file exists as reporters and optionally create those that doesn't exists.
- checkImportable(SessionControl, PluginDefinition, PluginConfiguration, File, String, GuiContext, Object) - Static method in class net.sf.basedb.util.AutoDetectFileFormat
- checkInstallation(DbControl, Collection<PluginInfo>) - Static method in class net.sf.basedb.core.PluginDefinition
-
Check the installation status of the given list of plug-ins.
- checkInternalJobQueue() - Method in class net.sf.basedb.core.InternalJobQueue
- checkInterrupted() - Static method in class net.sf.basedb.core.signal.ThreadSignalHandler
-
Utility method to check if the current thread has been interrupted and (may) throw a SignalException if it has.
- checkInterval - Variable in class net.sf.basedb.clients.jobagent.Agent
- checkItemType(Item) - Method in class net.sf.basedb.core.ItemSubtype
-
Check if this subtype can be used on items of the given type.
- checkJdbcDriver(String, String, String) - Static method in class net.sf.basedb.core.HibernateUtil
-
Check that a JDBC driver is registered and try to load a driver if not.
- checkLine(int, String) - Method in class net.sf.basedb.util.charset.SimpleStringDetector
- checkLine(int, String) - Method in interface net.sf.basedb.util.charset.StringDetector
-
Check the given line.
- checkLocked(String) - Method in class net.sf.basedb.core.Application.StartupOptions
- checkLocked(String) - Method in class net.sf.basedb.core.ServiceSessionControl.SessionFactoryConfiguration
-
Check that the
- checkMagicNumber(PushbackInputStream, byte[]) - Static method in class net.sf.basedb.util.FileUtil
-
Take a peek at an input stream and check if the first few bytes matches the bCheck parameter.
- checkManualMembersAllowed() - Method in class net.sf.basedb.core.ItemList
- checkMax(int, String, int) - Static method in class net.sf.basedb.core.IntegerUtil
-
Check that an integer is equal or lower than a maximum value.
- checkMd5 - Variable in class net.sf.basedb.core.File.UploadStream
-
If the md5 should be checked or not.
- checkMemberType(Collection<ItemList>) - Method in class net.sf.basedb.core.ItemList
-
Checks that the lists have the same member type as this list.
- checkMemberType(Item) - Method in class net.sf.basedb.core.ItemList
-
Checks if the other type is the same type as the member type of this list.
- checkMin(int, String, int) - Static method in class net.sf.basedb.core.IntegerUtil
-
Check that an integer is equal or greater than a minimum value.
- checkMinMax(int, String, int, int) - Static method in class net.sf.basedb.core.IntegerUtil
-
Check that an integer is equal or between a minimum and a maximum value.
- checkModified() - Method in class net.sf.basedb.util.extensions.manager.ExtensionsFile
-
Check if the underlying file has been modified since it was last processed.
- checkNext - Variable in class net.sf.basedb.core.DynamicResultIterator
- checkNext - Variable in class net.sf.basedb.util.extensions.ActionIterator
- checkNumberOfParameters(int) - Method in class net.sf.basedb.util.jep.ChannelFunction
- checkNumberOfParameters(int) - Method in class net.sf.basedb.util.jep.ExtraValueFunction
- checkNumberOfParameters(int) - Method in class net.sf.basedb.util.jep.FunctionSafeJep.UnknownFunction
- checkNumberOfParameters(int) - Method in class net.sf.basedb.util.jep.InReporterListFunction
- checkNumberOfParameters(int) - Method in class net.sf.basedb.util.jep.LeftFunction
- checkNumberOfParameters(int) - Method in class net.sf.basedb.util.jep.Log2Function
- checkNumberOfParameters(int) - Method in class net.sf.basedb.util.jep.MeanFunction
- checkNumberOfParameters(int) - Method in class net.sf.basedb.util.jep.NotInReporterListFunction
- checkNumberOfParameters(int) - Method in class net.sf.basedb.util.jep.PositionFunction
- checkNumberOfParameters(int) - Method in class net.sf.basedb.util.jep.RawChannelFunction
- checkNumberOfParameters(int) - Method in class net.sf.basedb.util.jep.RawFunction
- checkNumberOfParameters(int) - Method in class net.sf.basedb.util.jep.ReporterFunction
- checkNumberOfParameters(int) - Method in class net.sf.basedb.util.jep.ScoreFunction
- checkNumberOfParameters(int) - Method in class net.sf.basedb.util.jep.SimpleJepFunction
- checkNumberOfParameters(int) - Method in class net.sf.basedb.util.parser.ColFunction
- checkNumberOfParameters(int) - Method in class net.sf.basedb.util.parser.DataNoFunction
- checkNumberOfParameters(int) - Method in class net.sf.basedb.util.parser.DefaultItemFunction
- checkNumberOfParameters(int) - Method in class net.sf.basedb.util.parser.LineNoFunction
- checkParentBioSourceSubtype(DbControl, OverviewContext, Node, Node) - Static method in class net.sf.basedb.util.overview.validator.SampleValidator
-
Check the subtype of the biosurce that is the parent to a sample.
- checkParentExtractSubtype(DbControl, OverviewContext, Node, Node) - Static method in class net.sf.basedb.util.overview.validator.ExtractValidator
-
Check the subtype of the extract that is the parent to another extract.
- checkParentSampleSubtype(DbControl, OverviewContext, Node, Node) - Static method in class net.sf.basedb.util.overview.validator.ExtractValidator
-
Check the subtype of the sample that is the parent to an extract.
- checkParentSampleSubtype(DbControl, OverviewContext, Node, Node) - Static method in class net.sf.basedb.util.overview.validator.SampleValidator
-
Check the subtype of the sample that is the parent to another sample.
- checkPassword(String, String) - Static method in class net.sf.basedb.core.User
-
Check the plain-text password against the crypted password.
- checkPermission(Permission) - Method in class net.sf.basedb.clients.web.extensions.ExtensionsControl
- checkPermission(Permission) - Method in interface net.sf.basedb.core.AccessControlled
-
Check if the logged in user has the desired permission on the item, otherwise throw an exception.
- checkPermission(Permission) - Method in class net.sf.basedb.core.BasicBatcher
-
Checks if the logged in user has the specified permission on this item.
- checkPermission(Permission) - Method in class net.sf.basedb.core.BasicItem
-
Checks if the logged in user has the specified permission on this item.
- checkPermission(Permission) - Method in class net.sf.basedb.core.BioMaterialEventSource
- checkPermission(Permission) - Method in class net.sf.basedb.core.Coloring
- checkPermission(Permission, String) - Method in class net.sf.basedb.clients.web.extensions.ExtensionsControl
-
For checking the permission and adding a custom message to the PermissionDeniedException if the required permission is missing.
- checkPhysicalBioAssaySubtype(DbControl, OverviewContext, Node, Node) - Static method in class net.sf.basedb.util.overview.validator.DerivedBioAssayValidator
-
Check the subtype of the physical bioassay that is the parent to a derived bioassay.
- checkpw(String, String) - Static method in class net.sf.basedb.util.bcrypt.BCrypt
-
Check that a plaintext password matches a previously hashed one
- checkSameArrayDesign(Collection<RawBioAssay>, boolean) - Static method in class net.sf.basedb.util.IntensityCalculatorUtil
- checkSuperclass - Variable in class net.sf.basedb.util.formatter.MultiFormatter
- checkSyncFiltersAllowed() - Method in class net.sf.basedb.core.ItemList
- checkTimeoutOnRemoteSlots() - Method in class net.sf.basedb.clients.jobagent.slotmanager.MasterSlotManager
-
Check the remote slots to see if they have timed out.
- checkUniqueFields(String, String) - Method in class net.sf.basedb.plugins.executor.BaseFileExporterSupport
- checkUniqueFields(String, String) - Method in class net.sf.basedb.plugins.executor.BfsExporterSupport
- checkUnsafeScriptableUsage(Extension<?>) - Method in class net.sf.basedb.clients.web.extensions.ExtensionsControl
-
Checks if the given extension may violate the 'Content Security Policy' for the server.
- checkUnsafeScriptableUsage(ExtensionsFile) - Method in class net.sf.basedb.clients.web.extensions.ExtensionsControl
-
Checks if the given extensions file contain any extensions that may violate the 'Content Security Policy' for the server.
- checkUnsafeScriptableUsageInternal(Extension<?>) - Method in class net.sf.basedb.clients.web.extensions.ExtensionsControl
- checkValues - Variable in class net.sf.basedb.core.ParameterType
- child - Variable in class net.sf.basedb.clients.web.servlet.PlotServlet.CFResultIterator
- child - Variable in class net.sf.basedb.clients.web.servlet.PlotServlet.CFSqlResult
- child - Variable in class net.sf.basedb.core.QueryRuntimeFilterFactory.ChildFilter
-
The item type of the child item.
- child - Variable in class net.sf.basedb.util.importer.spotdata.BaseFileInfo.ChildBioAssay
- child - Variable in class net.sf.basedb.util.importer.spotdata.SecondPassSectionSpotsParser
- CHILD_DESCRIPTION - Static variable in class net.sf.basedb.core.plugin.AbstractAnalysisPlugin
-
The name of the parameter that asks for the description of the child bioassay set.
- CHILD_DESCRIPTION - Static variable in class net.sf.basedb.plugins.util.Parameters
-
The name of the parameter that asks is created by
Parameters.childDescriptionParameter(String, String, String)
- CHILD_NAME - Static variable in class net.sf.basedb.core.plugin.AbstractAnalysisPlugin
-
The name of the parameter that asks for the name of the child bioassay set.
- CHILD_NAME - Static variable in class net.sf.basedb.plugins.util.Parameters
-
The name of the parameter that is created by
Parameters.childNameParameter(String, String, String)
- CHILD_TO_PARENT - Enum constant in enum class net.sf.basedb.core.SyncFilter.SourceItemTransform
-
Source items are transformed to parent items.
- CHILD_TO_PARENT - Static variable in class net.sf.basedb.util.listable.ToBioSourceSourceItemTransformerFactory
- CHILD_TO_PARENT - Static variable in class net.sf.basedb.util.listable.ToDerivedBioAssaySourceItemTransformerFactory
- CHILD_TO_PARENT - Static variable in class net.sf.basedb.util.listable.ToExtractSourceItemTransformerFactory
- CHILD_TO_PARENT - Static variable in class net.sf.basedb.util.listable.ToPhysicalBioAssaySourceItemTransformerFactory
- CHILD_TO_PARENT - Static variable in class net.sf.basedb.util.listable.ToRawBioAssaySourceItemTransformerFactory
- CHILD_TO_PARENT - Static variable in class net.sf.basedb.util.listable.ToSampleSourceItemTransformerFactory
- childAssays - Variable in class net.sf.basedb.util.importer.spotdata.BaseFileInfo
- ChildBioAssay() - Constructor for class net.sf.basedb.util.importer.spotdata.BaseFileInfo.ChildBioAssay
-
Create a new object.
- ChildBioAssay(int) - Constructor for class net.sf.basedb.util.importer.spotdata.BaseFileInfo.ChildBioAssay
-
Create a new object
- childCreationEvents - Variable in class net.sf.basedb.core.data.BioMaterialData
- childDescriptionParameter(String, String, String) - Static method in class net.sf.basedb.plugins.util.Parameters
-
Create a plugin parameter that asks for the description of the child bioassay set.
- childErrors - Variable in class net.sf.basedb.util.overview.Node
- ChildFilter(Item, Item) - Constructor for class net.sf.basedb.core.QueryRuntimeFilterFactory.ChildFilter
-
Create a new
ChildFilter
object. - childHasDifferentReporterPositionMapping - Variable in class net.sf.basedb.util.importer.spotdata.BaseFileInfo
- childId - Variable in class net.sf.basedb.core.data.keyring.GroupGroups
- ChildItem - Class in net.sf.basedb.core
-
An abstract base class for all items which are child items to a
Shareable
parent item. - ChildItem(BasicData) - Constructor for class net.sf.basedb.core.ChildItem
- childIterator - Variable in class net.sf.basedb.util.Tree.EntryIterator
-
An iterator over the children of the root entry.
- childNameParameter(String, String, String) - Static method in class net.sf.basedb.plugins.util.Parameters
-
Create a plugin parameter that asks for the name of the child bioassay set.
- ChildNodeDirection - Enum Class in net.sf.basedb.util.overview.node
-
Represents the direction to use for loading child nodes in a tree.
- ChildNodeDirection(boolean, boolean, boolean) - Constructor for enum class net.sf.basedb.util.overview.node.ChildNodeDirection
- ChildNodeLoaderAction - Interface in net.sf.basedb.util.overview.extensions
-
Load and create child nodes for a given parent node.
- children - Variable in class net.sf.basedb.core.data.BioAssayData
- children - Variable in class net.sf.basedb.core.data.BioMaterialData
- children - Variable in class net.sf.basedb.core.data.DerivedBioAssayData
- children - Variable in class net.sf.basedb.core.data.GroupData
- children - Variable in class net.sf.basedb.core.data.PlateData
- children - Variable in class net.sf.basedb.util.listable.CollectExtracts
- children - Variable in class net.sf.basedb.util.overview.Node
- children - Variable in class net.sf.basedb.util.Tree.Entry
- childrenLoaded - Variable in class net.sf.basedb.util.overview.Node
- childReporterPositions - Variable in class net.sf.basedb.util.importer.spotdata.BaseFileInfo
- childToParent - Variable in class net.sf.basedb.util.listable.AbstractSourceItemTransformerFactory
- childToParentChain(List<SourceItemTransformer>, Item, Item, boolean) - Static method in class net.sf.basedb.util.listable.ToExtractSourceItemTransformerFactory
-
Utility method for creating the transformer chain from child items up to extracts.
- childWarnings - Variable in class net.sf.basedb.util.overview.Node
- chIndex - Variable in class net.sf.basedb.util.importer.spotdata.MatrixSpotIntensityEventHandler
- chIndex - Variable in class net.sf.basedb.util.importer.spotdata.SerialSpotIntensityEventHandler
- chooseClientAlias(String[], Principal[], Socket) - Method in class net.sf.basedb.util.ssl.StaticKeyManager
- chooseServerAlias(String, Principal[], Socket) - Method in class net.sf.basedb.util.ssl.StaticKeyManager
- CIRCULAR_REFERENCE - Static variable in class net.sf.basedb.util.overview.Validator
-
Validator rule that checks for circular references among pooled items.
- CircularRefInfo(DbControl, Identifiable) - Constructor for class net.sf.basedb.core.Trashcan.CircularRefInfo
- city - Variable in class net.sf.basedb.util.GeoLocation
- classes - Static variable in class net.sf.basedb.core.ExtendedProperties
-
A list with the
name
attribute of all classes found in the xml file. - classLoader - Variable in class net.sf.basedb.core.ServiceSessionControl.SessionFactoryConfiguration
- classLoader - Variable in class net.sf.basedb.util.extensions.Registry.RegisteredExtension
- classLoader - Variable in class net.sf.basedb.util.extensions.Registry.RegisteredExtensionPoint
- classLoaders - Variable in class net.sf.basedb.util.extensions.xml.XmlLoader
- classLoaders - Static variable in class net.sf.basedb.util.JarClassLoader
-
A map of all loaded class loaders.
- ClassLocal<E> - Class in net.sf.basedb.util
-
This class is a similar to the JDK
ThreadLocal
class, but stores one object per class instead of one object per thread. - ClassLocal() - Constructor for class net.sf.basedb.util.ClassLocal
-
Create a new
ClassLocal
object. - ClassMapErrorHandler - Class in net.sf.basedb.util.error
-
Error handler that allows the registration of one or more error handler for subclasses to
Throwable
. - ClassMapErrorHandler(ErrorHandler) - Constructor for class net.sf.basedb.util.error.ClassMapErrorHandler
-
Create a new
ClassMapErrorHandler
. - classMetadata - Variable in class net.sf.basedb.core.Metadata
- className - Variable in class net.sf.basedb.core.data.PluginDefinitionData
- className - Variable in class net.sf.basedb.util.extensions.manager.PluginInfoKey
- className - Variable in class net.sf.basedb.util.extensions.xml.PluginInfo
- classNameToPath(String) - Method in class net.sf.basedb.util.JarClassLoader
-
Convert a class name to a file path.
- classPath - Variable in class net.sf.basedb.util.JarClassLoader
-
Contains mappings from class names to the JAR file in which the class implementation can be found.
- ClassUtil - Class in net.sf.basedb.util
-
Utility class for
Class
objects. - ClassUtil() - Constructor for class net.sf.basedb.util.ClassUtil
- clazz - Variable in class net.sf.basedb.clients.web.extensions.list.AbstractListColumnBean
- clazz - Variable in class net.sf.basedb.clients.web.extensions.list.PropertyPathActionFactory
- clazz - Variable in class net.sf.basedb.clients.web.extensions.login.FieldInfo
- clazz - Variable in class net.sf.basedb.clients.web.extensions.menu.FixedMenuItemFactory
- clazz - Variable in class net.sf.basedb.clients.web.extensions.menu.MenuItemBean
- clazz - Variable in class net.sf.basedb.clients.web.extensions.tabcontrol.FixedTabFactory
- clazz - Variable in class net.sf.basedb.clients.web.extensions.tabcontrol.IncludeContentTabFactory
- clazz - Variable in class net.sf.basedb.clients.web.extensions.tabcontrol.TabBean
- clazz - Variable in class net.sf.basedb.clients.web.extensions.toolbar.ButtonBean
- clazz - Variable in class net.sf.basedb.clients.web.extensions.toolbar.FixedButtonFactory
- clazz - Variable in class net.sf.basedb.clients.web.taglib.ExceptionCatcher
- clazz - Variable in class net.sf.basedb.clients.web.taglib.StylableTag
- clazz - Variable in class net.sf.basedb.clients.web.taglib.tab.Tab
-
Optional
class
attribute. - clazz - Variable in class net.sf.basedb.clients.web.taglib.table.Cell
-
Optional
class
attribute - clazz - Variable in class net.sf.basedb.clients.web.taglib.table.CellValue
- clazz - Variable in class net.sf.basedb.core.ExtendedPropertyAccessor.GetterSetter
- clazz - Variable in class net.sf.basedb.core.Metadata.BasicItem2DataPropertyPath
- clazz - Variable in class net.sf.basedb.core.Metadata
- clazz - Variable in class net.sf.basedb.core.Metadata.NoopPropertyPath
- clazz - Variable in class net.sf.basedb.core.ParameterType
-
The class of allowed parameter values.
- clazz - Variable in class net.sf.basedb.core.QueryExecutor.FutureItem
- clazz - Variable in class net.sf.basedb.util.extensions.events.ActionClassEventFilter
- clazz - Variable in class net.sf.basedb.util.filter.InstanceOfFilter
- clean() - Method in class net.sf.basedb.util.listable.TransformCache
- clean(AnnotationBatcher.UpdateBatcher) - Method in class net.sf.basedb.core.MigrateRbaToDba.Rba
-
Remove links to from the raw bioassay to annotations, files, etc.
- cleanable - Variable in class net.sf.basedb.core.DbControl.State
- cleanable - Variable in class net.sf.basedb.util.StaticCache.LockSafeInputStream
- cleanable - Variable in class net.sf.basedb.util.StaticCache.LockSafeOutputStream
- cleanContextFromProperty(Session, Item, String, String, boolean) - Static method in class net.sf.basedb.core.Update
- cleaner - Static variable in class net.sf.basedb.core.Application
-
For keeping track of objects that need to be cleaned up.
- cleanSessionControlCache(boolean) - Static method in class net.sf.basedb.core.Application
-
Clean the cache from unused
SessionControl
objects. - cleanUp() - Method in class net.sf.basedb.core.DbControl
-
Clear and close all objects.
- cleanUp(FileFilter) - Method in class net.sf.basedb.util.StaticCache
-
Remove all files that matches the specified filter from the cache.
- cleanupProjectSpecificAnnotations() - Static method in class net.sf.basedb.core.ProjectSpecificAnnotationsManager
-
Delete project-specific annotations that belong to projects that no longer exists.
- cleanUpTask(FileFilter) - Method in class net.sf.basedb.util.StaticCache
-
Creates a task that cleans up this cache when it is executed.
- CleanupTask(StaticCache, FileFilter) - Constructor for class net.sf.basedb.util.StaticCache.CleanupTask
- clear() - Method in class net.sf.basedb.core.AbstractResultList
-
Not supported.
- clear() - Method in class net.sf.basedb.core.hibernate.SessionWrapper
- clear() - Method in class net.sf.basedb.core.snapshot.SnapshotManager
-
Clear the manager from all memory-cached information.
- clear() - Method in class net.sf.basedb.core.UnmodifiableResultList
-
Not supported.
- clear() - Method in class net.sf.basedb.util.AnnotationUtil.Cache
-
Clear all information from the cache.
- clear() - Method in class net.sf.basedb.util.formatter.LookupFormatter
-
Remove all registered lookup entries.
- clear() - Method in class net.sf.basedb.util.Tree
-
Clear all elements except the root element.
- clear(Session) - Static method in class net.sf.basedb.core.HibernateUtil
-
Clear the session of cached objects.
- clearAllRecent() - Method in class net.sf.basedb.core.ItemContext
-
Clear all recently used values lists.
- clearDbControlCache() - Method in class net.sf.basedb.core.SessionControl
- clearError() - Method in class net.sf.basedb.util.extensions.ActionIterator
-
Clear any error that has been registered for the current action.
- clearError() - Method in class net.sf.basedb.util.extensions.ExtensionContext
- clearError() - Method in class net.sf.basedb.util.extensions.ExtensionPointContext
- clearError() - Method in class net.sf.basedb.util.extensions.InvokationContext
-
Clear the registered error for the current extension or extension point.
- clearError() - Method in class net.sf.basedb.util.extensions.Registry.RegisteredExtension
- clearError() - Method in class net.sf.basedb.util.extensions.Registry.RegisteredExtensionPoint
- clearErrorList(JEP) - Static method in class net.sf.basedb.util.jep.Jep
-
This is a workaround for a bug in the JEP error handling.
- clearErrors - Variable in class net.sf.basedb.util.extensions.ExtensionsInvoker
- clearExecuteCommand() - Method in class net.sf.basedb.core.Job
-
Reset the currently stored execution command to force a plug-in to restart from the beginning instead of at the stored breakpoint.
- clearFailures() - Method in class net.sf.basedb.util.overview.Node
-
Clear all warnings, errors on this node and on all child nodes.
- clearLog() - Method in class net.sf.basedb.util.extensions.logging.ExtensionsLog
-
Clear the log.
- clearRecent(String) - Method in class net.sf.basedb.core.ItemContext
-
Clear the recently used values list.
- clearRecent(Item) - Method in class net.sf.basedb.core.ItemContext
-
Clear the recently used items list from items of the specified type.
- clearRecent(Item, String) - Method in class net.sf.basedb.core.ItemContext
-
Clear the recently used items sublist from items of the specified type.
- clearRecent(Item, ItemSubtype) - Method in class net.sf.basedb.core.ItemContext
-
Clear the recently used items list from items of the specified type.
- clearSources() - Method in class net.sf.basedb.core.BioMaterialEvent
-
Clear the sources collection and return the used quantities to the source biomaterials.
- clearSourcesExcept(BioMaterial) - Method in class net.sf.basedb.core.BioMaterialEvent
-
Clear the sources collection and return the used quantities to the source biomaterials, except for the given biomaterial.
- clearState - Variable in class net.sf.basedb.core.PluginResponse
- clearUsableUnits() - Method in class net.sf.basedb.core.AnnotationType
-
Clear all units.
- clearValueConverters() - Method in class net.sf.basedb.util.extensions.xml.XmlLoader
-
Remove all value converters.
- client - Variable in class net.sf.basedb.core.data.ChangeHistoryData
- client - Variable in class net.sf.basedb.core.data.ClientDefaultSettingData
- client - Variable in class net.sf.basedb.core.data.ContextData
- client - Variable in class net.sf.basedb.core.data.ContextIndex
- client - Variable in class net.sf.basedb.core.data.HelpData
- client - Variable in class net.sf.basedb.core.data.SessionData
- client - Variable in class net.sf.basedb.core.data.UserClientSettingData
- client - Variable in class net.sf.basedb.core.data.UserDeviceData
- client - Variable in class net.sf.basedb.core.SessionControl
-
Information about the
ClientData
that created this SessionControl. - client - Variable in class net.sf.basedb.plugins.HelpImporter
- Client - Class in net.sf.basedb.core
-
This class represents a registered client application.
- Client(ClientData) - Constructor for class net.sf.basedb.core.Client
- CLIENT - Enum constant in enum class net.sf.basedb.core.Item
-
The item is an
Client
. - CLIENT_RUNTIME_FILTER - Static variable in class net.sf.basedb.core.UserClientSetting
-
This filter will only return items if the logged in user has generic read permission to clients.
- clientCertificate - Variable in class net.sf.basedb.core.data.FileServerData
- clientCertificate - Variable in class net.sf.basedb.util.uri.ConnectionParameters
- clientCertificatePassword - Variable in class net.sf.basedb.util.uri.ConnectionParameters
- clientContext - Variable in class net.sf.basedb.util.extensions.ExtensionPointContext
- clientContext - Variable in class net.sf.basedb.util.extensions.ExtensionsInvoker
- ClientContext - Class in net.sf.basedb.util.extensions
-
Keeps information about the current context in the client application that extensions can use to decide what actions to generate.
- ClientContext() - Constructor for class net.sf.basedb.util.extensions.ClientContext
-
Create a new context with no session or current item.
- ClientContext(DbControl) - Constructor for class net.sf.basedb.util.extensions.ClientContext
-
Create a new context with a DbControl.
- ClientContext(DbControl, Object) - Constructor for class net.sf.basedb.util.extensions.ClientContext
-
Create a new context with a DbControl and item.
- ClientContext(SessionControl) - Constructor for class net.sf.basedb.util.extensions.ClientContext
-
Create a new context with a session and no DbControl.
- ClientContext(SessionControl, Object) - Constructor for class net.sf.basedb.util.extensions.ClientContext
-
Create a new context with a session and item but no DbControl.
- ClientContext(SessionControl, DbControl, Object) - Constructor for class net.sf.basedb.util.extensions.ClientContext
- ClientData - Class in net.sf.basedb.core.data
-
This class holds information about a client.
- ClientData() - Constructor for class net.sf.basedb.core.data.ClientData
- ClientDefaultSetting - Class in net.sf.basedb.core
-
This class is used to represent a setting for specific client application.
- ClientDefaultSetting(ClientDefaultSettingData) - Constructor for class net.sf.basedb.core.ClientDefaultSetting
- CLIENTDEFAULTSETTING - Enum constant in enum class net.sf.basedb.core.Item
-
The item is an
ClientDefaultSetting
. - ClientDefaultSettingData - Class in net.sf.basedb.core.data
- ClientDefaultSettingData() - Constructor for class net.sf.basedb.core.data.ClientDefaultSettingData
- clientDefaultSettings - Variable in class net.sf.basedb.core.SessionControl
-
Stores name and value from
ClientDefaultSettingData
. - clientId - Variable in class net.sf.basedb.core.data.ChangeHistoryData
- clientId - Variable in class net.sf.basedb.core.log.TransactionDetails
- ClientInfo(int, String, String) - Constructor for class net.sf.basedb.core.SessionControl.ClientInfo
- clientItem - Static variable in class net.sf.basedb.plugins.HelpExporter
- clientItem - Static variable in class net.sf.basedb.plugins.HelpImporter
- clientParameter - Variable in class net.sf.basedb.plugins.HelpExporter
- clientParameter - Variable in class net.sf.basedb.plugins.HelpImporter
- clientPassword - Variable in class net.sf.basedb.core.data.FileServerData
- clientSettings - Variable in class net.sf.basedb.core.data.UserData
- clientType - Variable in class net.sf.basedb.plugins.HelpExporter
- clonableProperty(ClonableProperty) - Static method in class net.sf.basedb.core.VirtualColumn
-
Get a virtual column view of a cloned reporter property.
- ClonableProperty - Class in net.sf.basedb.core
-
Represents a reporter property that can be cloned to a per-experiment table in the dynamic database.
- ClonableProperty(String, String, String, String, Type, int, boolean, Formula.AverageMethod, boolean) - Constructor for class net.sf.basedb.core.ClonableProperty
-
Create a cloned property representation of a static property.
- ClonableProperty(String, ReporterClonePropertyData) - Constructor for class net.sf.basedb.core.ClonableProperty
-
Create a cloned property representation of a data-layer object.
- ClonableProperty(ExtendedProperty) - Constructor for class net.sf.basedb.core.ClonableProperty
-
Create a cloned property representation of an extended property
- ClonableReporterQuery - Interface in net.sf.basedb.core
-
An interface that indicates that a query may be used together with cloned reporter information.
- CLONAL_AMPLIFICATION - Static variable in class net.sf.basedb.core.PhysicalBioAssay
-
The id for the
PhysicalBioAssayType
item representing a flow cell. - clone - Variable in class net.sf.basedb.util.annotations.InheritSpecification
- cloneCachedNode(Object, Node, ChildNodeDirection) - Method in class net.sf.basedb.util.overview.node.NodeFactory
-
Clones a cached node if the current context supports caching and another node with the given cache key already exists.
- CLONED - Enum constant in enum class net.sf.basedb.core.Annotation.Source
-
The annotation is an inherited annotation with a local copy of the values at the time the copy was made.
- CLONED_REPORTERS - Enum constant in enum class net.sf.basedb.core.VirtualTable
-
Table that holds cloned reporter information for an experiment.
- cloneParameter(PluginParameter<T>, T) - Static method in class net.sf.basedb.plugins.util.Parameters
-
Clone a plug-in parameter but give it a different default value.
- cloneParameterWithDefaultValue(PluginParameter<T>) - Method in class net.sf.basedb.core.plugin.AbstractPlugin
-
Clone a plug-in parameter and set the default value to the value that is already stored in the job or configuration parameters.
- cloneReporters(ReporterCloneBatcher.CloneSource, ReporterCloneTemplate, ProgressReporter) - Method in class net.sf.basedb.core.ReporterCloneBatcher
-
Create a reporter clone table in the dynamic database for this experiment and populate it with the current reporter annotations for all reporters that are part of the experiment.
- CloneReportersPlugin - Class in net.sf.basedb.plugins
-
A plug-in that clone reporter annotations to an experiment.
- CloneReportersPlugin() - Constructor for class net.sf.basedb.plugins.CloneReportersPlugin
- CloneSource() - Constructor for enum class net.sf.basedb.core.ReporterCloneBatcher.CloneSource
- close() - Method in class net.sf.basedb.clients.jobagent.executors.DummyJobExecutor
- close() - Method in class net.sf.basedb.clients.jobagent.executors.ProcessJobExecutor
- close() - Method in class net.sf.basedb.clients.jobagent.executors.ThreadJobExecutor
- close() - Method in class net.sf.basedb.clients.jobagent.handlers.AbstractCustomRequestHandler
- close() - Method in interface net.sf.basedb.clients.jobagent.handlers.CustomRequestHandler
-
This method is called at when the agent is stopped.
- close() - Method in class net.sf.basedb.clients.jobagent.handlers.MultiProtocolRequestHandler
-
Close this handler.
- close() - Method in interface net.sf.basedb.clients.jobagent.JobExecutor
-
This method is called at when the agent is stopped or paused.
- close() - Method in class net.sf.basedb.clients.jobagent.slotmanager.InternalSlotManager
- close() - Method in class net.sf.basedb.clients.jobagent.slotmanager.MasterSlotManager
- close() - Method in class net.sf.basedb.clients.jobagent.slotmanager.RemoteSlotManager
- close() - Method in interface net.sf.basedb.clients.jobagent.slotmanager.SlotManager
-
This method is called when the job agent is shutting down.
- close() - Static method in class net.sf.basedb.clients.web.extensions.ExtensionsControl
-
Shut down the extensions system.
- close() - Method in class net.sf.basedb.clients.web.extensions.list.RelatedItemHelper
- close() - Static method in class net.sf.basedb.clients.web.extensions.service.Services
-
Stop all services.
- close() - Method in class net.sf.basedb.clients.web.plugins.PlainTextTemplate
-
Do nothing.
- close() - Method in class net.sf.basedb.clients.web.plugins.XlsxTemplate
-
Dispose and close workbook.
- close() - Method in class net.sf.basedb.clients.web.plugins.XMLTemplate
-
Do nothing.
- close() - Method in class net.sf.basedb.clients.web.servlet.PlotServlet.CFResultIterator
- close() - Method in class net.sf.basedb.core.AbstractBatcher
- close() - Method in class net.sf.basedb.core.AnnotationBatcher.InsertBatcher
-
Close the batcher.
- close() - Method in class net.sf.basedb.core.AnnotationBatcher.UpdateBatcher
-
Close the batcher.
- close() - Method in interface net.sf.basedb.core.Batcher
-
Flush the batcher and close it.
- close() - Method in class net.sf.basedb.core.DataResultIterator
-
From the ResultIterator interface ---------------------------------
- close() - Method in class net.sf.basedb.core.DbControl
-
Close the connection to the database.
- close() - Method in class net.sf.basedb.core.DynamicResultIterator
-
From the ResultIterator interface ---------------------------------
- close() - Method in class net.sf.basedb.core.File.CharsetTesterThread
-
The file has been uploaded.
- close() - Method in class net.sf.basedb.core.File.UploadStream
-
Close the stream and register the size and location with the file item.
- close() - Method in class net.sf.basedb.core.hibernate.SessionWrapper
- close() - Method in class net.sf.basedb.core.hibernate.StatelessSessionWrapper
- close() - Method in class net.sf.basedb.core.InternalJobQueue
-
Cleanup
- close() - Method in class net.sf.basedb.core.ItemResultIterator
-
From the ResultIterator interface ---------------------------------
- close() - Method in class net.sf.basedb.core.plugin.ExportOutputStream
- close() - Method in interface net.sf.basedb.core.query.ResultIterator
-
Close the iterator and immediately release all resources associated with it.
- close() - Method in class net.sf.basedb.core.ReporterScoreResultIterator
-
From the ResultIterator interface ---------------------------------
- close() - Method in class net.sf.basedb.core.ScrollIterator
-
Close the results and return resources.
- close() - Method in class net.sf.basedb.core.SessionControl
-
Close this session control so it can't be used again.
- close() - Method in class net.sf.basedb.util.bfs.AnnotationParser
- close() - Method in interface net.sf.basedb.util.bfs.BfsParser
-
Close the parser and relase underlying system resources that are associated with it.
- close() - Method in class net.sf.basedb.util.bfs.DataParser
- close() - Method in class net.sf.basedb.util.bfs.MetadataParser
- close() - Method in class net.sf.basedb.util.excel.XlsxTableWriter
-
Closes the workbook unless it was supplied in the constructor from an external source.
- close() - Method in class net.sf.basedb.util.excel.XlsxToCsvUtil
-
Closes the current workbook.
- close() - Method in class net.sf.basedb.util.excel.XlsxToCsvUtil.WorkbookStream
- close() - Method in class net.sf.basedb.util.extensions.manager.ExtensionsFile.WriteableExtensionsFile
-
Close the writeable file.
- close() - Method in class net.sf.basedb.util.gtf.GtfInputStream
- close() - Method in class net.sf.basedb.util.importer.spotdata.SynchronizedSpotDataParser
- close() - Method in class net.sf.basedb.util.InputStreamCombiner
-
Closes all underlying streams.
- close() - Method in class net.sf.basedb.util.InputStreamSplitter
- close() - Method in class net.sf.basedb.util.InputStreamTracker
- close() - Method in class net.sf.basedb.util.jobagent.JobAgentConnection
-
Close the connection to the job agent.
- close() - Method in class net.sf.basedb.util.jobagent.JobAgentServerConnection
-
Stop listening for incoming connections.
- close() - Method in class net.sf.basedb.util.StaticCache.LockSafeInputStream
- close() - Method in class net.sf.basedb.util.StaticCache.LockSafeOutputStream
- close() - Method in class net.sf.basedb.util.StreamCacher
-
Close the master stream and remove the cached file data.
- close() - Method in class net.sf.basedb.util.uri.CloseResourceInputStream
-
Make sure the client connection manager is closed when the file has been completely downloaded.
- close() - Method in class net.sf.basedb.util.zip.Bzip2FilePacker
-
Finish the BZIP stream.
- close() - Method in interface net.sf.basedb.util.zip.FilePacker
-
End the packing and close.
- close() - Method in class net.sf.basedb.util.zip.GzipFilePacker
-
Finish the GZIP stream.
- close() - Method in class net.sf.basedb.util.zip.TarFilePacker
-
Finish the TAR file.
- close() - Method in class net.sf.basedb.util.zip.ZipFilePacker
-
Finish the ZIP file.
- close(int) - Method in class net.sf.basedb.clients.web.util.SimpleSignalProgressReporter
- close(int) - Method in class net.sf.basedb.core.signal.AbstractSignalReceiver
-
Close this signal receiver.
- close(int) - Method in class net.sf.basedb.core.signal.LocalSignalReceiver
- close(int) - Method in interface net.sf.basedb.core.signal.SignalReceiver
-
Close the receiver.
- close(int) - Method in class net.sf.basedb.core.signal.SocketSignalReceiver
-
Close this receiver and the socket it is listening on.
- close(Closeable) - Static method in class net.sf.basedb.util.FileUtil
-
Close a
Closeable
without throwing an exception. - close(InputStream) - Static method in class net.sf.basedb.util.FileUtil
-
Close an input stream without throwing an exception.
- close(InputStream) - Static method in class net.sf.basedb.util.SocketUtil
-
Close an
InputStream
without throwing any exceptions. - close(OutputStream) - Static method in class net.sf.basedb.util.FileUtil
-
Close an output stream without throwing an exception.
- close(Reader) - Static method in class net.sf.basedb.util.SocketUtil
-
Close a
Reader
without throwing any exceptions. - close(Writer) - Static method in class net.sf.basedb.util.SocketUtil
-
Close a
Writer
without throwing any exceptions. - close(AutoCloseable) - Static method in class net.sf.basedb.util.FileUtil
-
Close a
AutoCloseable
without throwing an exception. - close(ServerSocket) - Static method in class net.sf.basedb.util.SocketUtil
-
Close a server socket without throwing any exceptions.
- close(Socket) - Static method in class net.sf.basedb.util.SocketUtil
-
Close a socket without throwing any exceptions.
- close(ServerSocketChannel) - Static method in class net.sf.basedb.util.SocketUtil
-
Close a server socket channel without throwing any exceptions.
- close(Session) - Static method in class net.sf.basedb.core.HibernateUtil
-
Close a session.
- close(StatelessSession) - Static method in class net.sf.basedb.core.HibernateUtil
-
Close a statless session.
- closed - Variable in class net.sf.basedb.core.File.UploadStream
-
If this file closed or not.
- closed - Variable in class net.sf.basedb.core.SessionControl
-
If the session control has been closed it can no longer be used.
- closed - Variable in class net.sf.basedb.util.StaticCache.LockSafeInputStream
- closed - Variable in class net.sf.basedb.util.StaticCache.LockSafeOutputStream
- closeJobExecutor() - Method in class net.sf.basedb.clients.jobagent.Agent
-
Close the job executor.
- closeJobQueueChecker() - Method in class net.sf.basedb.clients.jobagent.Agent
-
Close the job queue checker.
- closeLogFile() - Method in class net.sf.basedb.core.plugin.AbstractPlugin
-
Close the log file created by
AbstractPlugin.createLogFile(String)
. - CloseMyDbControl(RelatedItemHelper) - Constructor for class net.sf.basedb.clients.web.extensions.list.RelatedItemHelper.CloseMyDbControl
- CloseResourceInputStream - Class in net.sf.basedb.util.uri
-
Inputstream filter that closes a given resource whenever the parent input stream is closed.
- CloseResourceInputStream(InputStream, Closeable) - Constructor for class net.sf.basedb.util.uri.CloseResourceInputStream
-
Create a new stream.
- closeResultSet(ResultSet, String) - Method in class net.sf.basedb.core.AbstractSqlQuery
-
Close the result set without throwing an exception.
- closeServer() - Method in class net.sf.basedb.clients.jobagent.Agent
-
Close the service listener.
- closeSlotManager() - Method in class net.sf.basedb.clients.jobagent.Agent
-
Close the slot manager.
- closeStatement(Statement, String) - Method in class net.sf.basedb.core.AbstractSqlQuery
-
Close the statement without throwing an exception.
- closeTimeout - Variable in class net.sf.basedb.clients.jobagent.Agent
-
Timeout to wait for jobs to act on the ABORT signal when stopping.
- closeTimeout - Variable in class net.sf.basedb.core.InternalJobQueue
-
Timeout to wait for jobs to act on the ABORT signal when shutting down BASE.
- CLUSTER_GENERATION - Static variable in class net.sf.basedb.core.Kit
-
The ID for the cluster generation (in a flow cell) kit type, for example a protocol used when creating a
PhysicalBioAssay
. - CLUSTER_GENERATION - Static variable in class net.sf.basedb.core.Protocol
-
The ID for the cluster generation (in a flow cell) protocol type, for example a protocol used when creating a
PhysicalBioAssay
. - CLUSTER_GENERATOR - Static variable in class net.sf.basedb.core.Hardware
-
The id for the
HardwareType
object representing a cluster generator station. - cmap - Variable in class net.sf.basedb.util.AnnotationUtil.Cache
- cmd - Variable in class net.sf.basedb.clients.jobagent.CmdLine
- CmdLine - Class in net.sf.basedb.clients.jobagent
-
Utility class for parsing command line arguments.
- CmdLine(String[]) - Constructor for class net.sf.basedb.clients.jobagent.CmdLine
-
Create a new object for parsing the command line.
- coalesce(String...) - Static method in class net.sf.basedb.core.StringUtil
-
Return the first non-null value (or null if all values are null).
- colFunction - Variable in class net.sf.basedb.util.parser.JepMapper
- ColFunction - Class in net.sf.basedb.util.parser
-
Adds a
col()
function to Jep. - ColFunction(List<String>, NumberFormat) - Constructor for class net.sf.basedb.util.parser.ColFunction
- ColFunction(List<String>, NumberFormat, Formatter<Date>) - Constructor for class net.sf.basedb.util.parser.ColFunction
- ColFunction(Map<String, Integer>, NumberFormat) - Constructor for class net.sf.basedb.util.parser.ColFunction
- ColFunction(Map<String, Integer>, NumberFormat, Formatter<Date>) - Constructor for class net.sf.basedb.util.parser.ColFunction
- colIndex - Variable in class net.sf.basedb.clients.web.plugins.DynamicQueryWrapper
- collect(Item, Set<Integer>) - Method in class net.sf.basedb.util.listable.TransformContext
-
Store collected items for later use if collecting has been enabled.
- CollectChildren(boolean, boolean) - Constructor for class net.sf.basedb.util.listable.CollectExtracts.CollectChildren
- collectChildrenOfCollected(boolean) - Method in class net.sf.basedb.util.listable.CollectExtracts
-
The created transformer collect the ID:s of all child extracts to the already collected extracts and store them in the
CollectExtracts.getCollectedChildren()
. - collectChildrenOfSource(boolean) - Method in class net.sf.basedb.util.listable.CollectExtracts
-
The created transformer collect the ID:s of all child extracts to the source extracts and store them in the
CollectExtracts.getCollectedChildren()
. - collected - Variable in class net.sf.basedb.util.listable.CollectExtracts
- collectedByItemType - Variable in class net.sf.basedb.util.listable.TransformContext
- collectedExtracts - Variable in class net.sf.basedb.util.listable.CollectedExtractsToDerivedBioAssayTransformer
- collectedExtracts - Variable in class net.sf.basedb.util.listable.CollectedExtractsToRawBioAssayTransformer
- collectedExtracts - Variable in class net.sf.basedb.util.listable.DerivedBioAssayToRawBioAssayTransformer
- collectedExtracts - Variable in class net.sf.basedb.util.listable.ExtractToParentExtractTransformer
- collectedExtracts - Variable in class net.sf.basedb.util.listable.PhysicalBioAssayToDerivedBioAssayTransformer
- CollectedExtractsToDerivedBioAssayTransformer - Class in net.sf.basedb.util.listable
-
Source item transformer implementation that transform collected extract items to derived bioassays.
- CollectedExtractsToDerivedBioAssayTransformer(CollectExtracts) - Constructor for class net.sf.basedb.util.listable.CollectedExtractsToDerivedBioAssayTransformer
-
Create a new collected extracts to derived bioassay transformer.
- CollectedExtractsToDerivedBioAssayTransformer(CollectExtracts, boolean) - Constructor for class net.sf.basedb.util.listable.CollectedExtractsToDerivedBioAssayTransformer
-
Create a new collected extracts to derived bioassay transformer.
- CollectedExtractsToRawBioAssayTransformer - Class in net.sf.basedb.util.listable
-
Source item transformer implementation that transform collected extract items to raw bioassays.
- CollectedExtractsToRawBioAssayTransformer(CollectExtracts) - Constructor for class net.sf.basedb.util.listable.CollectedExtractsToRawBioAssayTransformer
-
Create a new collected extracts to derived bioassay transformer.
- CollectExtracts - Class in net.sf.basedb.util.listable
-
Collect extracts seen on derived bioassays and raw bioassays that has been loaded by other transformers.
- CollectExtracts() - Constructor for class net.sf.basedb.util.listable.CollectExtracts
-
Create a new derived bioassay to physical bioassay transformer.
- CollectExtracts.CollectChildren - Class in net.sf.basedb.util.listable
-
Transformer implementation that collect the child extracts from the source or collected extracts.
- CollectExtracts.CollectFromDerivedBioAssays - Class in net.sf.basedb.util.listable
-
Transformer implementation that given a set of derived bioassays load their linked extracts and store that in the parent class.
- CollectExtracts.CollectFromExtracts - Class in net.sf.basedb.util.listable
-
Transformer implementation that store the given set of extracts in the parent class.
- CollectExtracts.CollectFromRawBioAssays - Class in net.sf.basedb.util.listable
-
Transformer implementation that given a set of raw bioassays load their linked extracts and store that in the parent class.
- CollectExtracts.CollectParents - Class in net.sf.basedb.util.listable
-
Transformer implementation that collect the parent extracts from the source or collected extracts.
- CollectExtracts.ResetCollected - Class in net.sf.basedb.util.listable
-
Transformer implementation that reset the collected extracts before forwarding the call to the parent transformer.
- collectFromDerivedBioAssays(boolean) - Method in class net.sf.basedb.util.listable.CollectExtracts
-
The created transformer collect the ID:s of all extracts linked from the source derived bioassays and then return the same set of derived bioassays again.
- CollectFromDerivedBioAssays(boolean) - Constructor for class net.sf.basedb.util.listable.CollectExtracts.CollectFromDerivedBioAssays
- collectFromExtracts() - Method in class net.sf.basedb.util.listable.CollectExtracts
-
The created transformer collect the ID:s of all extracts in the source collection and return same set of extracts again.
- CollectFromExtracts() - Constructor for class net.sf.basedb.util.listable.CollectExtracts.CollectFromExtracts
- collectFromRawBioAssays() - Method in class net.sf.basedb.util.listable.CollectExtracts
-
The created transformer collect the ID:s of all extracts linked from the source raw bioassays and then return the same set of raw bioassays again.
- CollectFromRawBioAssays() - Constructor for class net.sf.basedb.util.listable.CollectExtracts.CollectFromRawBioAssays
- collecting - Variable in class net.sf.basedb.util.listable.TransformContext
- COLLECTION_SEPARATOR - Static variable in class net.sf.basedb.clients.web.plugins.SimpleExport
- collectionFormatter - Variable in class net.sf.basedb.clients.web.extensions.list.AbstractListColumnBean
- CollectionFormatter<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 - Enum constant in enum class net.sf.basedb.core.ExtraValue.CoordinateType
-
The extra values are attached to column coordinates only.
- COLUMN - Enum constant in enum class net.sf.basedb.core.VirtualTable
-
Table that maps columns coordinates in a data cube to raw bioassays.
- COLUMN - Static variable in class net.sf.basedb.core.VirtualColumn
-
This column stores the data cube column coordinate.
- COLUMN_EXPRESSION - Enum constant in enum class net.sf.basedb.core.Formula.Type
-
An arbitrary expression that specify one formula only.
- COLUMN_EXTRA_FLOAT - Enum constant in enum class net.sf.basedb.core.VirtualTable
-
Table that stores float column extra values.
- COLUMN_EXTRA_INT - Enum constant in enum class net.sf.basedb.core.VirtualTable
-
Table that stores integer column extra values.
- COLUMN_EXTRA_STRING - Enum constant in enum class net.sf.basedb.core.VirtualTable
-
Table that stores string column extra values.
- COLUMN_PREFIX - Static variable in class net.sf.basedb.clients.web.plugins.SimpleExport
- COLUMN_RESTRICTION - Enum constant in enum class net.sf.basedb.core.Formula.Type
-
An arbitraty expression that specify one formula only.
- columnColumnMapping - Static variable in class net.sf.basedb.plugins.PlateFlatFileImporter
- columnColumnMapping - Static variable in class net.sf.basedb.plugins.RawDataFlatFileImporter
- columnColumnMapping - Static variable in class net.sf.basedb.plugins.ReporterMapFlatFileImporter
- columnContent - Variable in class net.sf.basedb.clients.web.taglib.table.Table
- columnCount - Variable in class net.sf.basedb.util.bfs.AnnotationWriter
- columnCount - Variable in class net.sf.basedb.util.bfs.DataWriter
- ColumnDef - Class in net.sf.basedb.clients.web.taglib.table
-
This tag defines a column in the table.
- ColumnDef() - Constructor for class net.sf.basedb.clients.web.taglib.table.ColumnDef
- ColumnDef.NullIterator<A,
B> - Class in net.sf.basedb.clients.web.taglib.table -
Iterator implementation that returns a single null value and nothing more.
- columnFilter - Variable in class net.sf.basedb.clients.web.taglib.table.Table
- columnFormatter - Variable in class net.sf.basedb.clients.web.taglib.table.Table
- columnHeaders - Variable in class net.sf.basedb.plugins.AnnotationFlatFileImporter
- columnHeaders - Variable in class net.sf.basedb.util.parser.ColFunction
- columnHeaders - Variable in class net.sf.basedb.util.parser.FlatFileParser
-
List of the column names found by splitting the data header using the data splitter regexp.
- ColumnHeaders - Class in net.sf.basedb.clients.web.taglib.table
-
Generate column headers for the columns that has been defined for this table.
- ColumnHeaders() - Constructor for class net.sf.basedb.clients.web.taglib.table.ColumnHeaders
- columnId - Variable in class net.sf.basedb.clients.web.taglib.table.Cell
-
The ID of the column to which this cell belongs.
- columnIndex - Variable in class net.sf.basedb.util.bfs.AnnotationModel
- ColumnInfo(String, String, Integer, int, boolean, boolean) - Constructor for class net.sf.basedb.core.dbengine.TableInfo.ColumnInfo
-
Create a new ColumnInfo object.
- ColumnKey(Comparable<?>, String) - Constructor for class net.sf.basedb.clients.web.servlet.ExperimentExplorerPlotServlet.ColumnKey
- columnMapper - Variable in class net.sf.basedb.plugins.PlateFlatFileImporter
- columnMapper - Variable in class net.sf.basedb.plugins.RawDataFlatFileImporter
- columnMapper - Variable in class net.sf.basedb.plugins.ReporterMapFlatFileImporter
- ColumnMapper - Class in net.sf.basedb.util.parser
-
Returns the string found in the column given by the index set in the constructor.
- ColumnMapper(int, String) - Constructor for class net.sf.basedb.util.parser.ColumnMapper
-
Create a new column mapper.
- ColumnMapper(int, String, NumberFormat, boolean) - Constructor for class net.sf.basedb.util.parser.ColumnMapper
-
Deprecated.In 3.15, use
ColumnMapper(int, String, NumberFormat, Formatter, boolean)
instead - ColumnMapper(int, String, NumberFormat, Formatter<Date>, boolean) - Constructor for class net.sf.basedb.util.parser.ColumnMapper
-
Create a new column mapper using a specific number or date format.
- columnMappingParameterName - Variable in class net.sf.basedb.plugins.batchimport.PropertyIdMethod
- columnName - Variable in class net.sf.basedb.core.Update.DropColumnChange
- columnNo - Variable in class net.sf.basedb.core.data.DataCubeColumnData
- columns - Variable in class net.sf.basedb.clients.web.taglib.table.Table
-
Which columns that should be visible and their order
- columns - Variable in class net.sf.basedb.core.data.DataCubeData
- columns - Variable in class net.sf.basedb.core.data.PlateGeometryData
- columns - Variable in class net.sf.basedb.core.dbengine.TableInfo
- columns - Variable in class net.sf.basedb.core.dbengine.TableInfo.IndexInfo
- columns - Variable in class net.sf.basedb.core.dbengine.TableInfo.PrimaryKeyInfo
- columns - Variable in class net.sf.basedb.core.ExtraValueJoin
- columns - Variable in enum class net.sf.basedb.core.VirtualTable
-
The columns in the table.
- columns() - Method in class net.sf.basedb.util.parser.FlatFileParser.Data
-
The number of columns as determined by the
FlatFileParser.setDataSplitterRegexp(Pattern)
regular expression. - columnSeparator - Variable in class net.sf.basedb.util.excel.XlsxToCsvUtil
- columnSubtitle - Variable in class net.sf.basedb.clients.web.taglib.table.Table
- ColumnSubtitles - Class in net.sf.basedb.clients.web.taglib.table
-
Generate column subtitle header for the columns that has been defined for this table.
- ColumnSubtitles() - Constructor for class net.sf.basedb.clients.web.taglib.table.ColumnSubtitles
- CombinedPropertyPath(List<Metadata.PropertyPath>) - Constructor for class net.sf.basedb.core.Metadata.CombinedPropertyPath
- CombiningEventFilter - Class in net.sf.basedb.util.extensions.events
-
Event filter that only passes on events based on multiple other event filters.
- CombiningEventFilter(Collection<EventFilter>, boolean) - Constructor for class net.sf.basedb.util.extensions.events.CombiningEventFilter
-
Create a new combining event filter.
- command - Variable in class net.sf.basedb.core.PluginRequest
- command - Variable in class net.sf.basedb.core.RequestInformation
- command - Variable in class net.sf.basedb.plugins.executor.ExternalProgramExecutor.RequestWrapper
- COMMAND_CONFIGURE_EXTERNAL_PARAMETERS - Static variable in class net.sf.basedb.plugins.executor.ExternalProgramExecutor
- COMMAND_CONFIGURE_IO_JOB - Static variable in interface net.sf.basedb.plugins.executor.IOSupport
-
This command is sent to import and export plug-ins in the job configuration sequence:
InteractivePlugin.getRequestInformation(GuiContext, String)
andInteractivePlugin.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)
andInteractivePlugin.configure(GuiContext, Request, Response)
- COMMAND_CONFIGURE_JOB - Static variable in interface net.sf.basedb.core.plugin.Request
-
This should be the first command to use when setting the plugin's job parameters.
- COMMAND_CONFIGURE_PARSER - Static variable in class net.sf.basedb.plugins.RawDataFlatFileImporter
- COMMAND_CONFIGURE_PLUGIN - Static variable in interface net.sf.basedb.core.plugin.Request
-
This should be the first command to use when setting the plugin's configuration.
- COMMAND_EXECUTE - Static variable in interface net.sf.basedb.core.plugin.Request
-
This command will tell the plugin to start its execution.
- COMMAND_EXECUTE_IO_JOB - Static variable in interface net.sf.basedb.plugins.executor.IOSupport
-
This command is sent to import and export plug-ins in the job execution sequence:
Plugin.run(Request, Response, ProgressReporter)
- COMMAND_MANUAL_CONFIG - Static variable in class net.sf.basedb.plugins.Base1PluginExecuter
-
This command is used if the user decides to configure the plugin by hand.
- COMMAND_SELECT_CONFIGURATIONS - Static variable in class net.sf.basedb.plugins.PluginConfigurationImporter
- commandHandlers - Variable in class net.sf.basedb.clients.jobagent.handlers.DefaultRequestHandler
- comment - Variable in class net.sf.basedb.core.authentication.LoginRequest
- comment - Variable in class net.sf.basedb.core.data.BioMaterialEventData
- comment - Variable in class net.sf.basedb.core.data.PlateEventData
- comment - Variable in class net.sf.basedb.core.MigrateRbaToDba.LineMapping
- commit() - Method in class net.sf.basedb.core.DbControl
-
Commit all changes made to items and close the connection to the database.
- commit(Transaction) - Static method in class net.sf.basedb.core.HibernateUtil
-
Commit a transaction.
- commitQueue - Variable in class net.sf.basedb.core.DbControl
-
A list of items that need special handling when commit is called.
- COMMON - Static variable in class net.sf.basedb.clients.web.resources.Bundle
-
Resource bundle with strings that are used in lots and lots of places in the web gui.
- commonCharsets - Static variable in class net.sf.basedb.core.Config
- CommonData - Class in net.sf.basedb.core.data
-
This is a convenience class that extends the
SharedData
class and implements theNameableData
andRemovableData
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 renderingButtonAction
:s. - CompactButtonRendererFactory() - Constructor for class net.sf.basedb.clients.web.extensions.toolbar.CompactButtonRendererFactory
- ComparableComparator<T extends Comparable<T>> - Class in net.sf.basedb.util
-
A comparator implemenation for any Comparable objects.
- ComparableComparator() - Constructor for class net.sf.basedb.util.ComparableComparator
- compare(String, String) - Method in class net.sf.basedb.util.StringLengthComparator
- compare(URI, URI) - Method in class net.sf.basedb.util.extensions.manager.ExtensionsManager.JarFirstURIComparator
- compare(RawDataType, RawDataType) - Method in class net.sf.basedb.core.RawDataTypes.NameComparator
- compare(AnnotationSnapshot, AnnotationSnapshot) - Method in class net.sf.basedb.core.snapshot.AnnotationSetSnapshot.SortByProjectComparator
- compare(AnnotationSnapshot, AnnotationSnapshot) - Method in class net.sf.basedb.core.snapshot.AnnotationSnapshot.AnnotationTypeComparator
- compare(AnnotationSnapshot, AnnotationSnapshot) - Method in class net.sf.basedb.core.snapshot.AnnotationSnapshot.ProjectComparator
- compare(T, T) - Method in class net.sf.basedb.util.ComparableComparator
- compare(T, T) - Method in class net.sf.basedb.util.NameableComparator
- compare(T, T) - Method in class net.sf.basedb.util.PriorityComparator
- compare(T, T) - Method in class net.sf.basedb.util.ToStringComparator
- compareByChainOrder() - Static method in class net.sf.basedb.core.SyncFilter
-
Create a comparator that sorts sync filters by: Filter group Source item type: BIOSOURCE, SAMPLE, EXTRACT, PHYSICALBIOASSAY, DERIVEDBIOASSAY, RAWBIOASSAY Type of transformation: PARENT_TO_CHILD, NONE, CHILD_TO_PARENT Name Source item must exists is sorted before source item must not exist Id
- compareTo(ExperimentExplorer.AnnotationGroup) - Method in class net.sf.basedb.clients.web.ExperimentExplorer.AnnotationGroup
- compareTo(ExperimentExplorerPlotServlet.ColumnKey) - Method in class net.sf.basedb.clients.web.servlet.ExperimentExplorerPlotServlet.ColumnKey
-
The ID of the key determines equality.
- compareTo(ClonableProperty) - Method in class net.sf.basedb.core.ClonableProperty
-
Sort by title, but mandatory properties before non-madatory.
- compareTo(KeyPermission) - Method in class net.sf.basedb.core.data.keyring.KeyPermission
-
Compare the keyId of this object to the keyId of another
KeyPermission
object. - compareTo(PluginKeys) - Method in class net.sf.basedb.core.data.keyring.PluginKeys
-
Compare the keyId of this object to the keyId of another
PluginKeys
object. - compareTo(ProjectPermission) - Method in class net.sf.basedb.core.data.keyring.ProjectPermission
-
Compare the projectId of this object to the projectId of another
ProjectPermission
object. - compareTo(TableInfo.ColumnInfo) - Method in class net.sf.basedb.core.dbengine.TableInfo.ColumnInfo
- compareTo(ItemProxy) - Method in class net.sf.basedb.core.ItemProxy
- compareTo(RawDataType) - Method in class net.sf.basedb.core.RawDataType
-
Compare the id:s of the raw data types.
- compareTo(LowessNormalization.SpotData) - Method in class net.sf.basedb.plugins.LowessNormalization.SpotData
-
Sort by A in ascending order.
- compareTo(MedianRatioNormalization.SpotData) - Method in class net.sf.basedb.plugins.MedianRatioNormalization.SpotData
-
Sort by ratio in ascending order.
- compareTo(AnyToAnyLinkStatistics) - Method in class net.sf.basedb.util.AnyToAnyLinkStatistics
-
Sort items by count, linkName and targetType.
- compareTo(ExtensionsFile) - Method in class net.sf.basedb.util.extensions.manager.ExtensionsFile
- compareTo(Node) - Method in class net.sf.basedb.util.overview.Node
- compareTo(PlotAnnotation) - Method in class net.sf.basedb.util.plot.PlotAnnotation
- compareTo(UnitCache.CacheKey) - Method in class net.sf.basedb.util.units.UnitCache.CacheKey
- compareWith(String) - Static method in class net.sf.basedb.core.Version
-
Compare the given version string, which should be of the form a.b or a.b.c, with the current BASE version.
- compile(boolean, boolean) - Method in class net.sf.basedb.clients.web.extensions.XJspCompiler
-
Called when a JSP page needs recompiling.
- compile(String, HttpServletRequest, HttpServletResponse) - Method in class net.sf.basedb.clients.web.servlet.CompileAll
-
Compile all files found in dir, recursively entering subdirectories.
- CompileAll - Class in net.sf.basedb.clients.web.servlet
-
This servlet will scan for all files ending with .jsp and issue a request for them with the parameter
jsp_precompile=true
therby compiling all JSP files into servlets. - CompileAll() - Constructor for class net.sf.basedb.clients.web.servlet.CompileAll
- completed - Variable in class net.sf.basedb.core.SimpleAbsoluteProgressReporter
- complexMappings - Static variable in class net.sf.basedb.plugins.AbstractFlatFileImporter
-
Parameter that asks if complex column mappings should be enabled or not.
- component - Variable in class net.sf.basedb.core.Metadata.ComponentPropertyPath
- ComponentData - Interface in net.sf.basedb.core.data
-
Tagging interface that we need all componenets to implement so that we are able to export them properly using generic code.
- ComponentPropertyPath(ComponentType, int, Type) - Constructor for class net.sf.basedb.core.Metadata.ComponentPropertyPath
- CompoundMapper - Class in net.sf.basedb.util.parser
-
A compound mapper that gets its value by invoking multiple other mappers which are set in the constructor.
- CompoundMapper(List<Mapper>) - Constructor for class net.sf.basedb.util.parser.CompoundMapper
-
Create a new compound mapper.
- CompoundMapper(List<Mapper>, NumberFormat, boolean) - Constructor for class net.sf.basedb.util.parser.CompoundMapper
-
Create a new compound mapper, using a specific number formatter as it's parser.
- CompoundMapper(List<Mapper>, NumberFormat, Formatter<Date>, boolean) - Constructor for class net.sf.basedb.util.parser.CompoundMapper
-
Create a new compound mapper, using a specific number formatter as it's parser.
- compress - Variable in class net.sf.basedb.core.File.UploadStream
-
If the file should be compressed or not.
- compress(ProgressReporter) - Method in class net.sf.basedb.core.File
-
Compress the file stored on the disk.
- compressed - Variable in class net.sf.basedb.core.data.FileData
- compressedSize - Variable in class net.sf.basedb.core.data.FileData
- compressOrDecompress(ProgressReporter, boolean) - Method in class net.sf.basedb.core.File
- condition - Variable in class net.sf.basedb.core.dbengine.TableInfo.IndexInfo
- condition - Variable in class net.sf.basedb.core.HibernateUtil.DelayedFilterDef
- condition - Variable in class net.sf.basedb.core.query.WhenStatement
- conditionalExpression(Filter<? extends Query>, Expression, Expression) - Static method in class net.sf.basedb.core.query.Expressions
-
Create an expression that falls back to one of two expression depending on if the query passes a filter or not.
- ConditionalQueryElement - Class in net.sf.basedb.core.query
- ConditionalQueryElement(Filter<Query>, QueryElement, QueryElement) - Constructor for class net.sf.basedb.core.query.ConditionalQueryElement
- conditionalRestriction(Filter<? extends Query>, Restriction, Restriction, boolean) - Static method in class net.sf.basedb.core.query.Restrictions
-
Create a restriction that falls back to one of two restrictions depending on if the query passes a filter or not.
- config - Static variable in class net.sf.basedb.core.Config
-
Variable for holding the configuration properties.
- config - Variable in class net.sf.basedb.core.hibernate.SchemaGenerator.CollectSqlTarget
- config - Variable in class net.sf.basedb.core.plugin.ParameterValuesWrapper
- config - Variable in class net.sf.basedb.util.ContextUtil.ContextResult
- Config - Class in net.sf.basedb.core
-
Use this class to access the configuration settings for BASE.
- Config() - Constructor for class net.sf.basedb.core.Config
- configDir - Static variable in class net.sf.basedb.core.Config
- configList - Static variable in class net.sf.basedb.plugins.PluginConfigurationExporter
- configuration - Variable in class net.sf.basedb.core.ParameterValuesImpl
- configuration - Variable in class net.sf.basedb.core.plugin.AbstractPlugin
- configuration - Variable in class net.sf.basedb.plugins.gtf.DefaultConfigurationValues
- ConfigurationException - Exception in net.sf.basedb.core
-
This exception is thrown by the
Config
class if there is a problem with finding or loading the configuration settings. - ConfigurationException(String) - Constructor for exception net.sf.basedb.core.ConfigurationException
-
Creates a new
ConfigurationException
. - ConfigurationException(String, Throwable) - Constructor for exception net.sf.basedb.core.ConfigurationException
-
Creates a new
ConfigurationException
with a cause. - configurationMap - Variable in class net.sf.basedb.plugins.PluginConfigurationImporter
- configurationParameters - Variable in class net.sf.basedb.core.PluginRequest
- configurations - Variable in class net.sf.basedb.core.data.PluginDefinitionData
- configurationValues - Variable in class net.sf.basedb.core.data.PluginConfigurationData
- configure() - Method in class net.sf.basedb.core.PluginConfiguration
-
Start the configuration sequence for a plugin.
- configure(GuiContext) - Method in class net.sf.basedb.core.Job
-
Start the configuration sequence for a job.
- configure(GuiContext, Request, Response) - Method in class net.sf.basedb.clients.web.plugins.SimpleExport
- configure(GuiContext, Request, Response) - Method in interface net.sf.basedb.core.plugin.InteractivePlugin
-
Configure the plugin.
- configure(GuiContext, Request, Response) - Method in class net.sf.basedb.plugins.AnnotationFlatFileImporter
- configure(GuiContext, Request, Response) - Method in class net.sf.basedb.plugins.Base1PluginExecuter
- configure(GuiContext, Request, Response) - Method in class net.sf.basedb.plugins.BaseFileExporterPlugin
- configure(GuiContext, Request, Response) - Method in class net.sf.basedb.plugins.batchimport.AbstractItemImporter
- configure(GuiContext, Request, Response) - Method in class net.sf.basedb.plugins.batchimport.AnnotationTypeImporter
-
Override this method so that we can make some extra parameter checks: A mapping for 'Value type' must be specified when 'create' or 'create+update' mode is used
- configure(GuiContext, Request, Response) - Method in class net.sf.basedb.plugins.batchimport.AnyToAnyImporter
- configure(GuiContext, Request, Response) - Method in class net.sf.basedb.plugins.BfsExporterPlugin
- configure(GuiContext, Request, Response) - Method in class net.sf.basedb.plugins.CdfFileReporterImporter
- configure(GuiContext, Request, Response) - Method in class net.sf.basedb.plugins.executor.BaseFileExporterSupport
- configure(GuiContext, Request, Response) - Method in class net.sf.basedb.plugins.executor.BaseFileImporterSupport
- configure(GuiContext, Request, Response) - Method in class net.sf.basedb.plugins.executor.BfsExporterSupport
- configure(GuiContext, Request, Response) - Method in class net.sf.basedb.plugins.executor.BfsImporterSupport
- configure(GuiContext, Request, Response) - Method in class net.sf.basedb.plugins.executor.ExternalProgramExecutor
- configure(GuiContext, Request, Response) - Method in class net.sf.basedb.plugins.executor.FileOnlyImporterSupport
- configure(GuiContext, Request, Response) - Method in class net.sf.basedb.plugins.FormulaFilter
- configure(GuiContext, Request, Response) - Method in class net.sf.basedb.plugins.GalExporter
- configure(GuiContext, Request, Response) - Method in class net.sf.basedb.plugins.gtf.GtfReporterMapImporter
- configure(GuiContext, Request, Response) - Method in class net.sf.basedb.plugins.HelpExporter
- configure(GuiContext, Request, Response) - Method in class net.sf.basedb.plugins.HelpImporter
- configure(GuiContext, Request, Response) - Method in class net.sf.basedb.plugins.IlluminaRawDataImporter
- configure(GuiContext, Request, Response) - Method in class net.sf.basedb.plugins.IntensityCalculatorPlugin
-
Store configuration settings for
Request.COMMAND_CONFIGURE_PLUGIN
, andRequest.COMMAND_CONFIGURE_JOB
. - configure(GuiContext, Request, Response) - Method in class net.sf.basedb.plugins.JepExtraValueCalculator
- configure(GuiContext, Request, Response) - Method in class net.sf.basedb.plugins.JepIntensityTransformer
- configure(GuiContext, Request, Response) - Method in class net.sf.basedb.plugins.LowessNormalization
- configure(GuiContext, Request, Response) - Method in class net.sf.basedb.plugins.ManualDerivedBioAssayCreator
- configure(GuiContext, Request, Response) - Method in class net.sf.basedb.plugins.ManualTransformCreator
- configure(GuiContext, Request, Response) - Method in class net.sf.basedb.plugins.MedianRatioNormalization
- configure(GuiContext, Request, Response) - Method in class net.sf.basedb.plugins.PackedFileExporter
- configure(GuiContext, Request, Response) - Method in class net.sf.basedb.plugins.PlateFlatFileImporter
-
Store configuration settings for
Request.COMMAND_CONFIGURE_PLUGIN
andRequest.COMMAND_CONFIGURE_JOB
. - configure(GuiContext, Request, Response) - Method in class net.sf.basedb.plugins.PlateMappingExporter
-
Store configuration settings for
Request.COMMAND_CONFIGURE_PLUGIN
andRequest.COMMAND_CONFIGURE_JOB
. - configure(GuiContext, Request, Response) - Method in class net.sf.basedb.plugins.PlateMappingImporter
-
Store configuration settings for
Request.COMMAND_CONFIGURE_PLUGIN
andRequest.COMMAND_CONFIGURE_JOB
. - configure(GuiContext, Request, Response) - Method in class net.sf.basedb.plugins.PluginConfigurationExporter
-
Store configuration settings for
Request.COMMAND_CONFIGURE_JOB
. - configure(GuiContext, Request, Response) - Method in class net.sf.basedb.plugins.PluginConfigurationImporter
- configure(GuiContext, Request, Response) - Method in class net.sf.basedb.plugins.PrintMapFlatFileImporter
-
Store configuration settings for
Request.COMMAND_CONFIGURE_PLUGIN
andRequest.COMMAND_CONFIGURE_JOB
. - configure(GuiContext, Request, Response) - Method in class net.sf.basedb.plugins.RawDataFlatFileImporter
-
Store configuration settings for
Request.COMMAND_CONFIGURE_PLUGIN
,RawDataFlatFileImporter.COMMAND_CONFIGURE_PARSER
andRequest.COMMAND_CONFIGURE_JOB
. - configure(GuiContext, Request, Response) - Method in class net.sf.basedb.plugins.ReporterFlatFileImporter
-
Store configuration settings for
Request.COMMAND_CONFIGURE_PLUGIN
andRequest.COMMAND_CONFIGURE_JOB
. - configure(GuiContext, Request, Response) - Method in class net.sf.basedb.plugins.ReporterMapFlatFileImporter
-
Store configuration settings for
Request.COMMAND_CONFIGURE_PLUGIN
andRequest.COMMAND_CONFIGURE_JOB
. - configure(GuiContext, Request, Response) - Method in class net.sf.basedb.util.zip.AbstractFileUnpacker
- CONFIGURE_IMPORT - Static variable in class net.sf.basedb.plugins.AnnotationFlatFileImporter
- CONFIGURE_MAPPING - Static variable in class net.sf.basedb.plugins.AnnotationFlatFileImporter
- CONFIGURE_OPTIONS - Static variable in class net.sf.basedb.plugins.batchimport.AbstractItemImporter
- CONFIGURE_OPTIONS - Static variable in class net.sf.basedb.plugins.batchimport.AnyToAnyImporter
- ConfigureByExample - Interface in net.sf.basedb.util.parser
-
This is a tagging interface for all plugins that use the
FlatFileParser
and wants easier configuration of the regular expressions used to parse the file. - configureExecutor - Variable in class net.sf.basedb.plugins.executor.BaseFileExporterSupport
- configureExecutor - Variable in class net.sf.basedb.plugins.executor.BaseFileImporterSupport
- configureExecutor - Variable in class net.sf.basedb.plugins.executor.BfsExporterSupport
- configureExecutor - Variable in class net.sf.basedb.plugins.executor.BfsImporterSupport
- configureExportImportPluginParameters - Variable in class net.sf.basedb.plugins.executor.ExternalProgramExecutor
- configureExternalParameters - Variable in class net.sf.basedb.plugins.executor.ExternalProgramExecutor
- configureImport - Variable in class net.sf.basedb.plugins.AnnotationFlatFileImporter
- configureJob - Variable in class net.sf.basedb.clients.web.plugins.SimpleExport
- configureJob - Variable in class net.sf.basedb.plugins.Base1PluginExecuter
-
Holds info about a job configuration request.
- configureJob - Variable in class net.sf.basedb.plugins.BaseFileExporterPlugin
- configureJob - Variable in class net.sf.basedb.plugins.BfsExporterPlugin
- configureJob - Variable in class net.sf.basedb.plugins.CdfFileReporterImporter
- configureJob - Variable in class net.sf.basedb.plugins.executor.BaseFileImporterSupport
- configureJob - Variable in class net.sf.basedb.plugins.executor.BfsImporterSupport
- configureJob - Variable in class net.sf.basedb.plugins.executor.ExternalProgramExecutor
- configureJob - Variable in class net.sf.basedb.plugins.executor.FileOnlyImporterSupport
- configureJob - Variable in class net.sf.basedb.plugins.FormulaFilter
- configureJob - Variable in class net.sf.basedb.plugins.GalExporter
- configureJob - Variable in class net.sf.basedb.plugins.gtf.GtfReporterMapImporter
- configureJob - Variable in class net.sf.basedb.plugins.HelpExporter
- configureJob - Variable in class net.sf.basedb.plugins.HelpImporter
- configureJob - Variable in class net.sf.basedb.plugins.IlluminaRawDataImporter
- configureJob - Variable in class net.sf.basedb.plugins.IntensityCalculatorPlugin
- configureJob - Variable in class net.sf.basedb.plugins.JepExtraValueCalculator
- configureJob - Variable in class net.sf.basedb.plugins.JepIntensityTransformer
- configureJob - Variable in class net.sf.basedb.plugins.LowessNormalization
- configureJob - Variable in class net.sf.basedb.plugins.ManualDerivedBioAssayCreator
- configureJob - Variable in class net.sf.basedb.plugins.ManualTransformCreator
- configureJob - Variable in class net.sf.basedb.plugins.MedianRatioNormalization
- configureJob - Variable in class net.sf.basedb.plugins.PackedFileExporter
- configureJob - Variable in class net.sf.basedb.plugins.PlateFlatFileImporter
- configureJob - Variable in class net.sf.basedb.plugins.PlateMappingExporter
- configureJob - Variable in class net.sf.basedb.plugins.PlateMappingImporter
- configureJob - Variable in class net.sf.basedb.plugins.PluginConfigurationExporter
- configureJob - Variable in class net.sf.basedb.plugins.PluginConfigurationImporter
- configureJob - Variable in class net.sf.basedb.plugins.PrintMapFlatFileImporter
- configureJob - Variable in class net.sf.basedb.plugins.RawDataFlatFileImporter
- configureJob - Variable in class net.sf.basedb.plugins.ReporterFlatFileImporter
- configureJob - Variable in class net.sf.basedb.plugins.ReporterMapFlatFileImporter
- configureJob - Variable in class net.sf.basedb.util.zip.AbstractFileUnpacker
- configureManual - Variable in class net.sf.basedb.plugins.Base1PluginExecuter
-
Holds information about a manual plugin configuration request.
- configureMapping - Variable in class net.sf.basedb.plugins.AnnotationFlatFileImporter
- configureOptions - Variable in class net.sf.basedb.plugins.batchimport.AbstractItemImporter
- configureOptions - Variable in class net.sf.basedb.plugins.batchimport.AnyToAnyImporter
- configureParser - Variable in class net.sf.basedb.plugins.AnnotationFlatFileImporter
- configureParser - Variable in class net.sf.basedb.plugins.batchimport.AbstractItemImporter
- configureParser - Variable in class net.sf.basedb.plugins.batchimport.AnyToAnyImporter
- configureParser - Variable in class net.sf.basedb.plugins.RawDataFlatFileImporter
- configurePlugin - Variable in class net.sf.basedb.plugins.Base1PluginExecuter
-
Holds information about a plugin configuration request.
- configurePlugin - Variable in class net.sf.basedb.plugins.executor.ExternalProgramExecutor
- configurePlugin - Variable in class net.sf.basedb.plugins.gtf.GtfReporterMapImporter
- configurePlugin - Variable in class net.sf.basedb.plugins.ManualDerivedBioAssayCreator
- configurePlugin - Variable in class net.sf.basedb.plugins.ManualTransformCreator
- configurePlugin - Variable in class net.sf.basedb.plugins.PackedFileExporter
- configurePlugin - Variable in class net.sf.basedb.plugins.PlateFlatFileImporter
- configurePlugin - Variable in class net.sf.basedb.plugins.ReporterFlatFileImporter
- configurePlugin - Variable in class net.sf.basedb.plugins.ReporterMapFlatFileImporter
- configureQuery(DbControl, EntityQuery, boolean) - Method in class net.sf.basedb.core.ItemContext
- configureQuery(DbControl, EntityQuery, ClientContext, boolean) - Method in class net.sf.basedb.core.ItemContext
-
Use the settings in this context to configure a query.
- configureQuery(DbControl, SqlQuery, List<String>) - Method in class net.sf.basedb.core.ItemContext
-
Use the settings in this context to configure a dynamic query.
- configureQuery(SqlQuery) - Method in interface net.sf.basedb.util.DynamicFilter
-
Configure the query before it is used.
- configureQuery(SqlQuery) - Method in class net.sf.basedb.util.IncludeExcludeFilter
-
We need the position which is in column 2 (already selected).
- configureRawDataType - Variable in class net.sf.basedb.plugins.RawDataFlatFileImporter
- configureSelection - Variable in class net.sf.basedb.plugins.PluginConfigurationImporter
- connect() - Method in class net.sf.basedb.util.jobagent.JobAgentConnection
-
Create a socket connection to the job agent.
- connection() - Method in class net.sf.basedb.core.hibernate.StatelessSessionWrapper
-
Deprecated.
- ConnectionClosedException - Exception in net.sf.basedb.core
-
This exception is thrown when trying to use a
DbControl
object that has been closed. - ConnectionClosedException() - Constructor for exception net.sf.basedb.core.ConnectionClosedException
-
Creates a new
ConnectionClosedException
. - ConnectionManager - Interface in net.sf.basedb.util.uri
-
A connection manager is used to access the contents and metadata about the resource pointed to by a given URI.
- connectionManagerFactory - Variable in class net.sf.basedb.core.data.FileServerData
- ConnectionManagerFactory - Interface in net.sf.basedb.util.uri
-
A connection manager factory is responsible for creating connection managers for some subset of URI:s that is supported.
- ConnectionManagerUtil - Class in net.sf.basedb.util.uri
-
Collects utility methods related to connection managers.
- ConnectionManagerUtil() - Constructor for class net.sf.basedb.util.uri.ConnectionManagerUtil
- ConnectionParameters - Class in net.sf.basedb.util.uri
-
Connection parameters, such as username/password, that may be needed to connect to a server.
- ConnectionParameters() - Constructor for class net.sf.basedb.util.uri.ConnectionParameters
-
Create a new empty parameters object.
- connectTimeout - Variable in class net.sf.basedb.clients.jobagent.slotmanager.RemoteSlotManager
- ConsoleProgressReporter - Class in net.sf.basedb.util
-
An implementation of the ProgressReporter interface that writes all messages to the standard console.
- ConsoleProgressReporter() - Constructor for class net.sf.basedb.util.ConsoleProgressReporter
- ConsoleProgressReporter(boolean) - Constructor for class net.sf.basedb.util.ConsoleProgressReporter
- constant - Variable in class net.sf.basedb.util.parser.ConstantMapper
- ConstantMapper - Class in net.sf.basedb.util.parser
-
A constant string mapper.
- ConstantMapper(Float) - Constructor for class net.sf.basedb.util.parser.ConstantMapper
- ConstantMapper(Integer) - Constructor for class net.sf.basedb.util.parser.ConstantMapper
- ConstantMapper(String) - Constructor for class net.sf.basedb.util.parser.ConstantMapper
-
Create a constant mapper.
- ConstantMapper(String, NumberFormat, boolean) - Constructor for class net.sf.basedb.util.parser.ConstantMapper
-
Create a constant mapper using a specific number formatter as it's parser.
- ConstantMapper(String, NumberFormat, Formatter<Date>, boolean) - Constructor for class net.sf.basedb.util.parser.ConstantMapper
-
Create a constant mapper using a specific number formatter as it's parser.
- ConstantMapper(Date, Formatter<Date>) - Constructor for class net.sf.basedb.util.parser.ConstantMapper
- constructor - Variable in enum class net.sf.basedb.core.Item
- contact - Variable in class net.sf.basedb.core.data.PluginDefinitionData
- contact - Variable in class net.sf.basedb.core.plugin.AboutImpl
- contact - Variable in class net.sf.basedb.util.extensions.AboutBean
- contact - Variable in class net.sf.basedb.util.extensions.Registry.RegisteredAbout
- contains(Object) - Method in class net.sf.basedb.core.hibernate.SessionWrapper
- contains(Object) - Method in class net.sf.basedb.core.ItemResultList
- contains(Object) - Method in class net.sf.basedb.util.Tree
- contains(String, Object) - Method in class net.sf.basedb.core.hibernate.SessionWrapper
- contains(AnnotationUtil.AnnotatableWrapper) - Method in class net.sf.basedb.util.AnnotationUtil.Cache
- containsAll(Collection<?>) - Method in class net.sf.basedb.core.AbstractResultList
- containsAll(Collection<?>) - Method in class net.sf.basedb.core.UnmodifiableResultList
- containsAll(Collection<?>) - Method in class net.sf.basedb.util.Tree
- containsKey(Object) - Method in class net.sf.basedb.util.formatter.LookupFormatter
-
Checks if a given key has been registered.
- containsKey(Object) - Method in class net.sf.basedb.util.jep.FunctionSafeJep.SafeFunctionTable
-
If the key is already registered, return TRUE.
- content - Variable in class net.sf.basedb.clients.web.extensions.section.SectionBean
- content - Variable in class net.sf.basedb.clients.web.extensions.tabcontrol.FixedTabFactory
- content - Variable in class net.sf.basedb.clients.web.extensions.tabcontrol.TabBean
- content - Variable in class net.sf.basedb.clients.web.taglib.tab.TabControl
-
The HTML for the contents of the tabs.
- ContentSecurityPolicyFilter - Class in net.sf.basedb.clients.web.servlet
-
This is a filter that sets the "Content-Security-Policy" header in the http response.
- ContentSecurityPolicyFilter() - Constructor for class net.sf.basedb.clients.web.servlet.ContentSecurityPolicyFilter
- ContentSecurityPolicyReportServlet - Class in net.sf.basedb.clients.web.servlet
-
This is a servlet for posting reports from "Content-Security-Policy" violations.
- ContentSecurityPolicyReportServlet() - Constructor for class net.sf.basedb.clients.web.servlet.ContentSecurityPolicyReportServlet
- contentStyle - Variable in class net.sf.basedb.clients.web.extensions.section.IncludeContentSectionFactory
- contentStyle - Variable in class net.sf.basedb.clients.web.extensions.section.SectionBean
- contentStyle - Variable in class net.sf.basedb.clients.web.taglib.HideableSection
-
Optional
style
attribute for the content section - contentStyle - Variable in class net.sf.basedb.clients.web.taglib.tab.TabControl
-
Optional
style
attribute for the content section - context - Variable in class net.sf.basedb.clients.web.extensions.LoadServletsProcessor
- context - Variable in class net.sf.basedb.clients.web.extensions.renderer.PrefixSuffixRenderer
- context - Variable in class net.sf.basedb.clients.web.extensions.ServletWrapper
- context - Variable in class net.sf.basedb.clients.web.extensions.tabcontrol.IncludeContentTabFactory.Tab
- context - Variable in class net.sf.basedb.clients.web.extensions.toolbar.CompactButtonRenderer
- context - Variable in class net.sf.basedb.clients.web.extensions.toolbar.ToolbarButtonRenderer
- context - Variable in class net.sf.basedb.clients.web.taglib.extensions.Render
- context - Variable in class net.sf.basedb.clients.web.taglib.extensions.Scripts
- context - Variable in class net.sf.basedb.clients.web.taglib.extensions.Stylesheets
- context - Variable in class net.sf.basedb.clients.web.taglib.HideableSection
- context - Variable in class net.sf.basedb.core.PluginConfigurationRequest
- context - Variable in class net.sf.basedb.core.signal.ExtensionSignalTransporter
- context - Variable in class net.sf.basedb.util.overview.node.NodeFactory
- CONTEXT_BIOASSAYS - Static variable in class net.sf.basedb.core.plugin.AbstractAnalysisPlugin
-
GuiContext = [Item.BIOASSAY, GuiContext.Type.LIST]
- CONTEXT_BIOASSAYSET - Static variable in class net.sf.basedb.core.plugin.AbstractAnalysisPlugin
-
GuiContext = [Item.BIOASSAYSET, GuiContext.Type.ITEM]
- CONTEXT_DERIVEDBIOASSAY - Static variable in class net.sf.basedb.core.plugin.AbstractAnalysisPlugin
-
GuiContext = [Item.DERIVEDBIOASSAY, GuiContext.Type.ITEM]
- CONTEXT_RELATIVE - Enum constant in enum class net.sf.basedb.util.extensions.xml.PathType
-
Paths should be relative to the web application context.
- ContextData - Class in net.sf.basedb.core.data
-
This class holds context information to help client applications with storing common settings for tables.
- ContextData() - Constructor for class net.sf.basedb.core.data.ContextData
- contextDestroyed(ServletContextEvent) - Method in class net.sf.basedb.clients.web.servlet.StartStopServlet
- contextId - Variable in class net.sf.basedb.core.ItemContext
- ContextIndex - Class in net.sf.basedb.core.data
- ContextIndex() - Constructor for class net.sf.basedb.core.data.ContextIndex
- ContextIndex(ClientData, int, String, String) - Constructor for class net.sf.basedb.core.data.ContextIndex
- contextInitialized(ServletContextEvent) - Method in class net.sf.basedb.clients.web.servlet.StartStopServlet
- contextItem - Variable in class net.sf.basedb.core.data.JobData
- ContextKey - Class in net.sf.basedb.core
- ContextKey(Item, String) - Constructor for class net.sf.basedb.core.ContextKey
-
Create a new ContextKey object from
Item
and it's subcontext. - contextMessage - Variable in class net.sf.basedb.util.ContextUtil.ContextResult
- contextPath - Variable in class net.sf.basedb.clients.web.servlet.ImageRemapFilter
- contextPath - Variable in class net.sf.basedb.clients.web.servlet.RssNewsFeed
- ContextResult(PluginDefinition, PluginConfiguration, String) - Constructor for class net.sf.basedb.util.ContextUtil.ContextResult
-
Create a new warning-level result object.
- ContextResult(PluginDefinition, PluginConfiguration, Throwable) - Constructor for class net.sf.basedb.util.ContextUtil.ContextResult
-
Create a new error-level result object.
- ContextResult(SessionControl, PluginDefinition, PluginConfiguration, GuiContext, Object) - Constructor for class net.sf.basedb.util.ContextUtil.ContextResult
- contexts - Variable in class net.sf.basedb.core.data.ClientData
- contexts - Variable in class net.sf.basedb.core.data.UserData
- contexts - Variable in class net.sf.basedb.util.extensions.ExtensionsInvoker
- contextType - Variable in class net.sf.basedb.core.data.GuiContextData
- contextType - Variable in class net.sf.basedb.core.data.JobData
- ContextUtil - Class in net.sf.basedb.util
-
A class with utility methods for plug-ins.
- ContextUtil() - Constructor for class net.sf.basedb.util.ContextUtil
- ContextUtil.ContextResult - Class in net.sf.basedb.util
-
Class for holding the result of a call to the
InteractivePlugin.isInContext(GuiContext, Object)
method. - ContextUtil.IsInContextFilter - Class in net.sf.basedb.util
-
Filter implementation that works on collections of
ContextUtil.ContextResult
:s and return only those that return true fromContextUtil.ContextResult.isInContext()
. - CONTINUE - Enum constant in enum class net.sf.basedb.core.plugin.Response.Status
- continueAfterError - Variable in class net.sf.basedb.plugins.RawDataFlatFileImporter
- continueLater(String, boolean, Serializable) - Method in class net.sf.basedb.core.Job
-
This method is used to indicate that a job had to be aborted due to a system shutdown.
- continueWithNextFileAfterError(Throwable) - Method in class net.sf.basedb.plugins.AbstractFlatFileImporter
-
If the importer should continue with the next file after an error.
- continueWithNextFileAfterError(Throwable) - Method in class net.sf.basedb.plugins.RawDataFlatFileImporter
-
We will continue if: The file is not of the correct format, eg. t =
UnsupportedFileFormatException
. - Controlled - Interface in net.sf.basedb.core
-
This is the base tagging interface for items that needs special attention by the
DbControl
object whenDbControl.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 APIExpression
orRestriction
objects. - ConverterFactory() - Constructor for class net.sf.basedb.util.jep.convert.ConverterFactory
- converters - Variable in class net.sf.basedb.util.extensions.xml.XmlLoader
- converters - Static variable in class net.sf.basedb.util.jep.convert.ConverterFactory
- convertJavaDateFormatToExcelFormat(String) - Static method in class net.sf.basedb.util.excel.CellStyleCreator
-
Converts a Java date format string to the corresponding Excel date format string.
- convertNumber(Number) - Method in enum class net.sf.basedb.core.Type
-
Convert a number to the appropriate class.
- convertString(Class, String) - Static method in class net.sf.basedb.util.extensions.debug.StringConverter
- convertToNull(String) - Method in class net.sf.basedb.util.parser.FlatFileParser
- convertToReferenceUnit(double) - Method in class net.sf.basedb.util.units.IdentityUnitConverter
- convertToReferenceUnit(double) - Method in class net.sf.basedb.util.units.LinearUnitConverter
-
value(ref) = value(specific) * factor + offset
- convertToReferenceUnit(double) - Method in interface net.sf.basedb.util.units.UnitConverter
-
Convert a value from the specific unit to the reference unit.
- convertToSpecificUnit(double) - Method in class net.sf.basedb.util.units.IdentityUnitConverter
- convertToSpecificUnit(double) - Method in class net.sf.basedb.util.units.LinearUnitConverter
-
value(specific) = (value(ref) - offset) / factor
- convertToSpecificUnit(double) - Method in interface net.sf.basedb.util.units.UnitConverter
-
Convert a value from the reference unit to the specific unit.
- convertValue(String, Class<?>) - Method in class net.sf.basedb.util.extensions.debug.BeanActionFactory
-
Convert a string value to another type.
- convertValues(AnnotationType, List<?>, Unit) - Method in class net.sf.basedb.core.Annotation
- convertValueToUnit(Session, String, String, Unit) - Method in class net.sf.basedb.core.PropertyFilter
-
Converts a string to a numeric value with the correct unit.
- Coordinate - Class in net.sf.basedb.util
-
Util class for coordinate transformations in base.
- Coordinate() - Constructor for class net.sf.basedb.util.Coordinate
- COORDINATES - Enum constant in enum class net.sf.basedb.core.FeatureIdentificationMethod
-
Use coordinates (block, metaGridX, metaGridY, row, column)
- coordinateType - Variable in class net.sf.basedb.core.data.DataCubeExtraValueData
- CoordinateType(int) - Constructor for enum class net.sf.basedb.core.ExtraValue.CoordinateType
- copy(byte[], int, int) - Method in class net.sf.basedb.util.InputStreamSplitter
-
Write data to all output streams.
- copy(int) - Method in class net.sf.basedb.util.InputStreamSplitter
-
Write data to all output streams.
- copy(InputStream, OutputStream) - Static method in class net.sf.basedb.util.FileUtil
-
Copy from the input stream to the output stream until end of file is reached.
- copy(InputStream, OutputStream, AbsoluteProgressReporter) - Static method in class net.sf.basedb.util.FileUtil
-
Copy from the input stream to the output stream until end of file is reached.
- copy(Reader, Writer) - Static method in class net.sf.basedb.util.FileUtil
-
Copy from the reader to the writer until end of file is reached.
- copy(Reader, Writer, AbsoluteProgressReporter) - Static method in class net.sf.basedb.util.FileUtil
-
Copy from the reader to the writer until end of file is reached.
- copy(Date) - Static method in class net.sf.basedb.core.DateUtil
-
Get a copy of the date.
- copy(File, File) - Method in class net.sf.basedb.plugins.Base1PluginExecuter
-
Copies the content from a File to a directory on the file system.
- copy(About, boolean) - Method in class net.sf.basedb.util.extensions.AboutBean
-
Copy information from antoher
About
object to this one. - COPY_ANNOTATIONS - Static variable in class net.sf.basedb.core.plugin.AbstractPlugin
-
The name of the parameter that asks if annotations should be copied or not.
- copyFrom(Annotatable, boolean) - Method in class net.sf.basedb.core.AnnotationSet
-
Copy annotations from another annotatable item to this annotation set.
- copyFrom(ItemContext, boolean) - Method in class net.sf.basedb.core.ItemContext
-
Copy settings from another context to this context.
- copyFromSyncFilter(ItemListSyncFilterData) - Method in class net.sf.basedb.core.ItemContext
- copyMetadata(FusionCDFData, ArrayDesign) - Method in class net.sf.basedb.util.affymetrix.CdfValidator
-
Copy metadata from the CDF file to the array design.
- copyMetadata(FusionCELData, RawBioAssay) - Method in class net.sf.basedb.util.affymetrix.CelValidator
-
Copy metadata from the CEL file to the raw bioassay.
- copyNotNulls(Collection<? extends T>, T[]) - Static method in class net.sf.basedb.core.query.Restrictions
- copyNotNulls(T[], T[]) - Static method in class net.sf.basedb.core.query.Restrictions
- copyObjectsAndTemporaryFilters(ItemContext) - Method in class net.sf.basedb.core.ItemContext
-
Copies all objects and temporary filters from this context to another context.
- copyParametersFrom(Job) - Method in class net.sf.basedb.core.Job
-
Copy all parameter values from another job.
- copyParametersFrom(PluginConfiguration) - Method in class net.sf.basedb.core.PluginConfiguration
-
Copy all parameter values from another plugin configuration.
- copyPermissions(DbControl, Shareable, Shareable) - Static method in class net.sf.basedb.core.ShareableUtil
-
Copy permissions from one item to another.
- copyProperties(File, File) - Static method in class net.sf.basedb.util.zip.PackUtil
-
Copy certain properties from the archive file to the unpacked file.
- copyRedefinedColumnNames(BaseFileParser) - Method in class net.sf.basedb.util.basefile.BaseFileParser
-
Copy redefined column names from the given parser into this parser
AnnotationBetweenRestriction(String, AnnotationType, Object, Object, AnnotationRestriction.Options)
instead