- GalExporter - Class in net.sf.basedb.plugins
-
Exports an array design with features to a GAL file.
- GalExporter() - Constructor for class net.sf.basedb.plugins.GalExporter
-
- gamma - Variable in class net.sf.basedb.core.data.SpotImagesData
-
- GB - Static variable in class net.sf.basedb.util.Values
-
- GENE_ID - Static variable in class net.sf.basedb.util.gtf.GtfInputStream.Attribute
-
- geneAveragesParameter - Variable in class net.sf.basedb.plugins.Base1PluginExecuter
-
If the data should be exported averaged per gene.
- geneIdIndex - Variable in class net.sf.basedb.util.gtf.GtfInputStream
-
- generateCFPlot(BioAssay, String, String) - Method in class net.sf.basedb.clients.web.servlet.PlotServlet
-
Generates a correction-factor plot, which is plotting the
MA-data for the parent together with the difference in M between
the parent and child.
- generateClass(String[]) - Method in class net.sf.basedb.clients.web.extensions.XJspCompiler
-
Called when a JSP page needs recompiling.
- generateDefaultName(FilePacker, Directory, Collection<Nameable>) - Method in class net.sf.basedb.plugins.PackedFileExporter
-
Generate a default name without a path for the packed file.
- generateDefaultPath(FilePacker, Directory, Collection<Nameable>) - Method in class net.sf.basedb.plugins.PackedFileExporter
-
Generate a default path for the packed file.
- generatedFiles - Variable in class net.sf.basedb.util.bfs.AbstractFilenameGenerator
-
- generateRandomId(int) - Static method in class net.sf.basedb.core.Application
-
Generate a random id.
- generateSignalMessage(Signal) - Method in class net.sf.basedb.core.signal.AbstractSignalTransporter
-
Generate a signal message string for the given signal.
- generateTitle(String, String) - Method in class net.sf.basedb.clients.web.ModeInfo
-
- generators - Variable in class net.sf.basedb.clients.web.extensions.plot.OverviewPlotBean
-
- GENERIC - Static variable in class net.sf.basedb.core.BioPlateEventType
-
The system ID for "Generic" event type.
- GENERIC - Static variable in class net.sf.basedb.core.Platform
-
The external id for the Generic
platform.
- GENERIC_EXTRAVALUE_DATA - Static variable in class net.sf.basedb.core.DataFileType
-
The external ID for the file type representing
generic analysed extra value data.
- GENERIC_PRINT_MAP - Static variable in class net.sf.basedb.core.DataFileType
-
The external ID for the file type representing
a generic print map (array design layout) of any type.
- GENERIC_RAW_DATA - Static variable in class net.sf.basedb.core.DataFileType
-
The external ID for the file type representing
a generic raw data file of any type.
- GENERIC_REPORTER_MAP - Static variable in class net.sf.basedb.core.DataFileType
-
The external ID for the file type representing
a generic reporter map (array design layout) of any type.
- GENERIC_SPOT_DATA - Static variable in class net.sf.basedb.core.DataFileType
-
The external ID for the file type representing
generic analysed spot data.
- GenericBaseDataWriterFactory<T> - Class in net.sf.basedb.util.bfs
-
Generic implementation of a data writer factory that create
files in the BASE file system.
- GenericBaseDataWriterFactory(DbControl, Directory, FilenameGenerator<T>) - Constructor for class net.sf.basedb.util.bfs.GenericBaseDataWriterFactory
-
Create a new factory that creates files in the given
directory.
- GenericDiskDataWriterFactory<T> - Class in net.sf.basedb.util.bfs
-
Generic implementation of a data writer factory that create
files on the local file system.
- GenericDiskDataWriterFactory(File, FilenameGenerator<T>) - Constructor for class net.sf.basedb.util.bfs.GenericDiskDataWriterFactory
-
Create a new factory that creates files in the given
directory.
- GenericExtraFileImporter - Class in net.sf.basedb.util.bfs
-
Extra file importer implementation that imports file to a specified
directory in the BASE file system.
- GenericExtraFileImporter(DbControl, Directory, boolean) - Constructor for class net.sf.basedb.util.bfs.GenericExtraFileImporter
-
Create a new extra file importer.
- GenericIntensityParser - Class in net.sf.basedb.util.importer.spotdata
-
Generic spot intensity parser implementation that
looks for 'intensity1', ..., 'intensityN' data columns for any
number of channels.
- GenericIntensityParser(int) - Constructor for class net.sf.basedb.util.importer.spotdata.GenericIntensityParser
-
Creates a new parser for the specified number of channels.
- GenericOverview - Class in net.sf.basedb.util.overview
-
Implementation for holding a generic overview of items.
- GenericOverview(DbControl, BasicItem, Project) - Constructor for class net.sf.basedb.util.overview.GenericOverview
-
Create a new generic overview.
- genericType - Variable in class net.sf.basedb.core.data.DataFileTypeData
-
- gensalt(int, SecureRandom) - Static method in class net.sf.basedb.util.bcrypt.BCrypt
-
Generate a salt for use with the BCrypt.hashpw() method
- gensalt(int) - Static method in class net.sf.basedb.util.bcrypt.BCrypt
-
Generate a salt for use with the BCrypt.hashpw() method
- gensalt() - Static method in class net.sf.basedb.util.bcrypt.BCrypt
-
Generate a salt for use with the BCrypt.hashpw() method,
selecting a reasonable default for the number of hashing
rounds to apply
- GENSALT_DEFAULT_LOG2_ROUNDS - Static variable in class net.sf.basedb.util.bcrypt.BCrypt
-
- geometricMean(Expression) - Static method in class net.sf.basedb.core.query.Aggregations
-
Calculates the geometric mean of all values for an expression: new expression =
EXP(AVG(LN(e))).
- GeometricMeanExpression - Class in net.sf.basedb.core.query
-
Calculates the geometric mean of an expression: EXP(AVG(LN(e)))
- GeometricMeanExpression(Expression) - Constructor for class net.sf.basedb.core.query.GeometricMeanExpression
-
- geometryQuery - Variable in class net.sf.basedb.plugins.batchimport.AbstractItemImporter
-
- get(DbControl) - Static method in class net.sf.basedb.clients.web.extensions.ExtensionsControl
-
Get an extension control object for managing the
installed extensions.
- get(String) - Method in class net.sf.basedb.clients.web.extensions.skin.ImageRemapper
-
Get the remapped image for the given source image.
- get(String) - Static method in class net.sf.basedb.clients.web.ModeInfo
-
- get(DbControl) - Static method in class net.sf.basedb.core.DerivedBioAssay.FixDerivedBioAssayParentsRecursivelyAction
-
Get an instance tht handles the fixes for the given DbControl.
- get(Object) - Method in class net.sf.basedb.core.ExtendedPropertyAccessor.GetterSetter
-
Get the value of the extended property.
- get(Class<T>, Serializable, LockMode) - Method in class net.sf.basedb.core.hibernate.SessionWrapper
-
- get(Class<T>, Serializable, LockOptions) - Method in class net.sf.basedb.core.hibernate.SessionWrapper
-
- get(Class<T>, Serializable) - Method in class net.sf.basedb.core.hibernate.SessionWrapper
-
- get(String, Serializable, LockMode) - Method in class net.sf.basedb.core.hibernate.SessionWrapper
-
Deprecated.
- get(String, Serializable, LockOptions) - Method in class net.sf.basedb.core.hibernate.SessionWrapper
-
- get(String, Serializable) - Method in class net.sf.basedb.core.hibernate.SessionWrapper
-
- get(Class, Serializable, LockMode) - Method in class net.sf.basedb.core.hibernate.StatelessSessionWrapper
-
- get(Class, Serializable) - Method in class net.sf.basedb.core.hibernate.StatelessSessionWrapper
-
- get(String, Serializable, LockMode) - Method in class net.sf.basedb.core.hibernate.StatelessSessionWrapper
-
- get(String, Serializable) - Method in class net.sf.basedb.core.hibernate.StatelessSessionWrapper
-
- get(int) - Method in class net.sf.basedb.core.ItemResultList
-
Get a BasicItem derived object.
- get(Class<E>, BasicData) - Method in class net.sf.basedb.core.ItemResultList
-
- get(DbControl, MeasuredBioMaterialData) - Static method in class net.sf.basedb.core.MeasuredBioMaterial.RemainingQuantityAction
-
- get(int, String) - Method in interface net.sf.basedb.core.query.SqlResultList
-
- get(int, int) - Method in interface net.sf.basedb.core.query.SqlResultList
-
- get(char) - Static method in enum net.sf.basedb.plugins.Base1PluginExecuter.Base1JobParameterType
-
- get(AnnotationUtil.AnnotatableWrapper) - Method in class net.sf.basedb.util.AnnotationUtil.Cache
-
- get(Object) - Method in class net.sf.basedb.util.ClassLocal
-
Get the object associated with the class of
the specified instance.
- get(Object) - Method in class net.sf.basedb.util.formatter.LookupFormatter
-
Get registered lookup value for a given key
- get(int) - Method in class net.sf.basedb.util.parser.FlatFileParser.Data
-
Get the value in the specified column.
- get(DbControl, ItemQuery<? extends E>...) - Static method in class net.sf.basedb.util.query.MultiQueryIterator
-
Create a new iterator for the given list of queries.
- getAbout() - Method in interface net.sf.basedb.util.extensions.Extension
-
Get information about the extensions.
- getAbout() - Method in class net.sf.basedb.util.extensions.ExtensionBean
-
- getAbout() - Method in class net.sf.basedb.util.extensions.manager.ExtensionsFile
-
Get information about the extensions in this file.
- getAbout() - Method in class net.sf.basedb.util.extensions.Registry.RegisteredExtension
-
- getAbout() - Method in class net.sf.basedb.util.extensions.xml.PluginInfo
-
Get information about the authors of the plug-in.
- getAbsolutePath(String) - Static method in class net.sf.basedb.core.File
-
Convert a relative path back to an absolute file path.
- getAbstract() - Method in class net.sf.basedb.core.data.ExperimentData
-
Get the abstract for this experiment.
- getAbstract() - Method in class net.sf.basedb.core.Experiment
-
Get the abstract text for the publication for this experiment.
- getAcceptedFile() - Method in class net.sf.basedb.util.fileset.SingleFileValidationAction
-
- getAction() - Method in class net.sf.basedb.clients.web.taglib.table.Table
-
- getAction() - Method in class net.sf.basedb.core.data.FileData
-
Get the value of the action variable for this FileData
object.
- getAction() - Method in class net.sf.basedb.core.File
-
- getActionClass() - Method in interface net.sf.basedb.util.extensions.ExtensionPoint
-
Get the class object that represents the type of action that
can be added to this extension point.
- getActionClass() - Method in class net.sf.basedb.util.extensions.ExtensionPointBean
-
- getActionClass() - Method in class net.sf.basedb.util.extensions.Registry.RegisteredExtensionPoint
-
- getActionFactory() - Method in interface net.sf.basedb.util.extensions.Extension
-
Get the factory class for creating actions.
- getActionFactory() - Method in class net.sf.basedb.util.extensions.ExtensionBean
-
- getActionFactory() - Method in class net.sf.basedb.util.extensions.Registry.RegisteredExtension
-
- getActions(InvokationContext<? super OnSaveAction>) - Method in class net.sf.basedb.clients.web.extensions.edit.DebugOnSaveActionFactory
-
- getActions(InvokationContext<? super ListColumnAction<I, V>>) - Method in class net.sf.basedb.clients.web.extensions.list.PropertyPathActionFactory
-
- getActions(InvokationContext<? super MenuItemAction>) - Method in class net.sf.basedb.clients.web.extensions.menu.FixedMenuItemFactory
-
- getActions(InvokationContext<? super MenuItemAction>) - Method in class net.sf.basedb.clients.web.extensions.menu.PermissionMenuItemFactory
-
- getActions(InvokationContext<? super OverviewPlotAction>) - Method in class net.sf.basedb.clients.web.extensions.plot.MAPlotFactory
-
- getActions(InvokationContext<? super SectionAction>) - Method in class net.sf.basedb.clients.web.extensions.section.IncludeContentSectionFactory
-
- getActions(InvokationContext<? super ServiceControllerAction>) - Method in class net.sf.basedb.clients.web.extensions.service.DummyService
-
- getActions(InvokationContext<? super SkinAction>) - Method in class net.sf.basedb.clients.web.extensions.skin.FixedSkinActionFactory
-
- getActions(InvokationContext<? super StartPageAction>) - Method in class net.sf.basedb.clients.web.extensions.startpage.FixedStartPageFactory
-
- getActions(InvokationContext<? super TabAction>) - Method in class net.sf.basedb.clients.web.extensions.tabcontrol.FixedTabFactory
-
- getActions(InvokationContext<? super TabAction>) - Method in class net.sf.basedb.clients.web.extensions.tabcontrol.IncludeContentTabFactory
-
- getActions(InvokationContext<? super ButtonAction>) - Method in class net.sf.basedb.clients.web.extensions.toolbar.FixedButtonFactory
-
- getActions(InvokationContext<? super ButtonAction>) - Method in class net.sf.basedb.clients.web.extensions.toolbar.PermissionButtonFactory
-
- getActions(InvokationContext<? super AuthenticationManager>) - Method in class net.sf.basedb.core.authentication.OldAuthenticationWrapperFactory
-
- getActions(InvokationContext<? super LogManagerFactory>) - Method in class net.sf.basedb.core.log.db.DbLogManagerFactory
-
- getActions(InvokationContext<? super CdfValidationAction>) - Method in class net.sf.basedb.util.affymetrix.CdfValidationFactory
-
- getActions(InvokationContext<? super CelValidationAction>) - Method in class net.sf.basedb.util.affymetrix.CelValidationFactory
-
- getActions(InvokationContext<? super A>) - Method in interface net.sf.basedb.util.extensions.ActionFactory
-
This method may be called one or several times for each request.
- getActions(InvokationContext<? super Action>) - Method in class net.sf.basedb.util.extensions.debug.BeanActionFactory
-
- getActions(InvokationContext<? super Action>) - Method in class net.sf.basedb.util.extensions.debug.ProxyActionFactory
-
- getActions() - Method in class net.sf.basedb.util.extensions.ExtensionContext
-
- getActions() - Method in class net.sf.basedb.util.extensions.ExtensionPointContext
-
Always null, since this is an extension point context.
- getActions() - Method in class net.sf.basedb.util.extensions.InvokationContext
-
Get the actions, or null if there is no current extension.
- getActions(InvokationContext<? super GtfValidationAction>) - Method in class net.sf.basedb.util.gtf.GtfValidationFactory
-
- getActions(InvokationContext<? super ValidationRuleAction>) - Method in class net.sf.basedb.util.overview.extensions.ReflectValidationRuleActionFactory
-
- getActions(InvokationContext<? super ConnectionManagerFactory>) - Method in class net.sf.basedb.util.uri.http.HttpConnectionManagerActionFactory
-
- getActive() - Method in class net.sf.basedb.clients.web.taglib.tab.TabControl
-
- getActiveProjectId() - Method in class net.sf.basedb.core.data.JobData
-
The ID of the project that should be made active when running this job.
- getActiveProjectId() - Method in class net.sf.basedb.core.Job
-
The ID of the project that should be made the active project while running
this job.
- getActiveProjectId() - Method in class net.sf.basedb.core.SessionControl
-
Get the id of the active project, or 0 if no project is active.
- getActiveProjectPermissions() - Method in class net.sf.basedb.core.SessionControl
-
Get the permissions that the logged in user has in the currently active project.
- getActiveRoles() - Method in class net.sf.basedb.core.SessionControl
-
Get the id of all active roles where the logged in user is a member.
- getActualCatalog() - Method in class net.sf.basedb.core.ServiceSessionControl.SessionFactoryConfiguration
-
The actual catalog that will be used by BASE.
- getActualSchema() - Method in class net.sf.basedb.core.ServiceSessionControl.SessionFactoryConfiguration
-
The actual schema that will be used by BASE.
- getActualUnit(DbControl) - Method in class net.sf.basedb.core.snapshot.AnnotationSnapshot
-
Get the unit that is most relevant for this annotation.
- getActualValues() - Method in class net.sf.basedb.core.snapshot.AnnotationSnapshot
-
Get the annotation values that are most relevant for this annotation.
- getActualValues(UnitConverter, Type) - Method in class net.sf.basedb.core.snapshot.AnnotationSnapshot
-
Get the annotations values, optionally converted to some specific unit
and type of values.
- getAddress() - Method in class net.sf.basedb.core.authentication.ExtraUserInformation
-
The postal address to the user.
- getAddress() - Method in class net.sf.basedb.core.data.UserData
-
Get the address for the user, or null if unknown.
- getAddress() - Method in class net.sf.basedb.core.User
-
Get the address for the user, or null if unknown.
- getAdvancedAssayField(String, boolean) - Method in class net.sf.basedb.util.export.spotdata.AdvancedFieldConverter
-
Convert an expression to an assay field.
- getAdvancedReporterField(String, boolean) - Method in class net.sf.basedb.util.export.spotdata.AdvancedFieldConverter
-
Convert an expression to a reporter field.
- getAdvancedSpotField(String, boolean) - Method in class net.sf.basedb.util.export.spotdata.AdvancedFieldConverter
-
Convert an expression to a spot field.
- getAffiliations() - Method in class net.sf.basedb.core.data.ExperimentData
-
Get the affiliations for this experiment.
- getAffiliations() - Method in class net.sf.basedb.core.Experiment
-
Get the affiliations for this experiment.
- getAge() - Method in class net.sf.basedb.core.DiskUsageStatistics.Summary
-
Get the age of this summary object since it was created in seconds.
- getAge() - Method in class net.sf.basedb.util.jobagent.JobAgentInfo
-
Get the age in milliseconds of this object.
- getAgent() - Method in class net.sf.basedb.clients.jobagent.handlers.AbstractCustomRequestHandler
-
- getAgent() - Method in class net.sf.basedb.clients.jobagent.slotmanager.InternalSlotManager
-
Get the job agent this slot manager belongs to.
- getAgentInfo(JobAgent) - Static method in class net.sf.basedb.core.JobAgent
-
Get a JobAgentInfo
for a job agent.
- getAlias() - Method in enum net.sf.basedb.core.Item
-
Get the alias for this item, which is used in queries,
- getAlias() - Method in class net.sf.basedb.core.query.AnnotationExpression
-
- getAlias() - Method in class net.sf.basedb.core.query.ExpressionSelect
-
- getAlias() - Method in interface net.sf.basedb.core.query.Select
-
Get the alias of the selected expression.
- getAlias() - Method in class net.sf.basedb.core.RealTable
-
Get the alias of this table.
- getAlias(BasicItem) - Method in class net.sf.basedb.core.RealTable
-
Get the alias of this table, using the ID of the item to make it
unique.
- getAlias(int) - Method in class net.sf.basedb.core.RealTable
-
Get the alias of this table, using the ID of the item to make it
unique.
- getAlias() - Method in enum net.sf.basedb.core.VirtualTable
-
Get the alias of this table.
- getAll() - Static method in class net.sf.basedb.core.ClonableProperty
-
Get a list containing cloned property representation for all static and
extended properties.
- getAllAnnotatableParentItems(DbControl, Annotatable, Filter<Annotatable>) - Static method in class net.sf.basedb.util.AnnotationUtil
-
Get all annotatable parent items for a given item.
- getAllAnnotatableParentItems(DbControl, Annotatable, Filter<Annotatable>, AnnotationUtil.Cache) - Static method in class net.sf.basedb.util.AnnotationUtil
-
Get all annotatable parent items for a given item.
- getAllAnnotationTypesWithInheritanceDisabled(DbControl) - Static method in class net.sf.basedb.core.AnnotationType
-
Load the IDs of all annotation types with the disable inheritance flag set.
- getAllCharsets() - Static method in class net.sf.basedb.core.Config
-
Get a set containing all character sets known to the current java virtual machine.
- getAllChildren(DbControl, Set<Integer>) - Method in class net.sf.basedb.util.overview.loader.ExtractLoader
-
- getAllColumnMappings() - Method in class net.sf.basedb.plugins.gtf.GtfReporterMapImporter
-
- getAllColumnMappings() - Method in class net.sf.basedb.plugins.PlateFlatFileImporter
-
- getAllColumnMappings(RawDataType) - Method in class net.sf.basedb.plugins.RawDataFlatFileImporter
-
Loads the column mappings if they hasn't been loaded already.
- getAllColumnMappings(boolean) - Method in class net.sf.basedb.plugins.ReporterFlatFileImporter
-
- getAllColumnMappings() - Method in class net.sf.basedb.plugins.ReporterMapFlatFileImporter
-
- getAllCurrentContexts(boolean, boolean) - Method in class net.sf.basedb.core.SessionControl
-
Get a list with the current default contexts.
- getAllExtended() - Method in class net.sf.basedb.core.data.RawData
-
- getAllItems() - Method in class net.sf.basedb.core.ItemList
-
Get a query that returns all items that can possibly be
members of this list.
- getAllMandatory() - Static method in class net.sf.basedb.core.ClonableProperty
-
Get a list with all mandatory properties that must be cloned.
- getAllMembers(DbControl, Set<Integer>) - Static method in class net.sf.basedb.core.User
-
Load the ID:s of all users that are direct members of
the specified groups.
- getAllMembers(Session, Collection<Integer>) - Static method in class net.sf.basedb.core.User
-
- getAllObjects() - Method in class net.sf.basedb.util.extensions.manager.ExtensionsFile
-
Get a list of all objects defined in this extensions
file.
- getAllowImmediateExecution() - Method in class net.sf.basedb.core.data.PluginDefinitionData
-
If the plugin is allowed to be immediately executed or if it
must be added to the job queue.
- getAllowImmediateExecution() - Method in class net.sf.basedb.core.PluginDefinition
-
If immediate execution of jobs are allowed or if they always must go through
the job queue.
- getAllowMultiple() - Method in class net.sf.basedb.core.data.ItemSubtypeFileTypeData
-
If multiple files of this type are allowed in a file set or not.
- getAllowMultiple() - Method in class net.sf.basedb.core.data.PlatformFileTypeData
-
If multiple files of this type are allowed in a file set or not.
- getAllowMultiple() - Method in class net.sf.basedb.core.ItemSubtypeFileType
-
Check if more than one file of this type is allowed in a file set or not.
- getAllowMultiple() - Method in class net.sf.basedb.core.PlatformFileType
-
Check if more than one file of this type is allowed in a file set or not.
- getAllowMultiple() - Method in interface net.sf.basedb.core.UsableDataFileType
-
A flag indicating if it is allowed to attach multiple files
or only a single one of the given type.
- getAllParentExtracts(DbControl, OverviewContext, PhysicalBioAssay) - Static method in class net.sf.basedb.util.overview.validator.PhysicalBioAssayValidator
-
Get all parent extracts that are associated with the given physical bioassay.
- getAllPermissions(Item, UserData, ItemKeyData, ProjectKeyData) - Method in class net.sf.basedb.core.InternalJobQueue.JobQueueKeyring
-
Return 0.
- getAllPermissions(Item, UserData, ItemKeyData, ProjectKeyData) - Method in class net.sf.basedb.core.InternalStorageController.StorageKeyring
-
Return 0.
- getAllPermissions(Item, UserData, ItemKeyData, ProjectKeyData) - Method in class net.sf.basedb.core.Job.SignalKeyring
-
Return 0.
- getAllPermissions(Item, UserData, ItemKeyData, ProjectKeyData) - Method in class net.sf.basedb.core.Keyring
-
- getAllPermissions(Item, UserData, ItemKeyData, ProjectKeyData) - Method in class net.sf.basedb.core.ServiceSessionControl.ServicesKeyring
-
Return 0.
- getAllPermissions(Item, UserData, ItemKeyData, ProjectKeyData) - Method in class net.sf.basedb.core.SessionControl
-
Get the combined permissions for an item of the specified type, owned by the specified
user and shared with the specified item and project keys.
- getAllPermissions(SharedData) - Method in class net.sf.basedb.core.SessionControl
-
- getAllResults() - Method in class net.sf.basedb.util.extensions.manager.ProcessResults
-
- getAllRoles() - Method in class net.sf.basedb.core.SessionControl
-
Get the id of all roles where the logged in user is a member.
- getAllRules(DbControl, GenericOverview) - Static method in class net.sf.basedb.util.overview.OverviewUtil
-
Get all static and extension validation rules grouped by relationship.
- getAlwaysGranted() - Method in class net.sf.basedb.core.plugin.Permissions
-
Get the permissions that the plugin always should be granted, even if
the logged in user doesn't have the permissions already.
- getAnalyzeTableSql(String, String, String) - Method in interface net.sf.basedb.core.dbengine.DbEngine
-
Generate SQL to update the index statistics for a table.
- getAnalyzeTableSql(String, String, String) - Method in class net.sf.basedb.core.dbengine.DefaultDbEngine
-
Return null.
- getAnalyzeTableSql(String, String, String) - Method in class net.sf.basedb.core.dbengine.MySQLEngine
-
Generate analyze table <catalog>.
- getAnalyzeTableSql(String, String, String) - Method in class net.sf.basedb.core.dbengine.PostgresDbEngine
-
Generate ANALYZE <schema>.
- getAndSetCurrentContext(SessionControl, Item, PageContext, ItemContext) - Static method in class net.sf.basedb.clients.web.Base
-
Same as: getAndSetCurrentContext(sc, itemType, "", pageContext, defaultContext, false)
.
- getAndSetCurrentContext(SessionControl, Item, PageContext, ItemContext, boolean) - Static method in class net.sf.basedb.clients.web.Base
-
Same as: getAndSetCurrentContext(sc, itemType, "", pageContext, defaultContext, resetTemporary)
.
- getAndSetCurrentContext(SessionControl, Item, String, PageContext, ItemContext) - Static method in class net.sf.basedb.clients.web.Base
-
Same as: getAndSetCurrentContext(sc, itemType, subContext, pageContext, defaultContext, false)
.
- getAndSetCurrentContext(SessionControl, Item, String, PageContext, ItemContext, boolean) - Static method in class net.sf.basedb.clients.web.Base
-
- getAndSetCurrentContext(SessionControl, Item, String, ServletRequest, ItemContext, boolean) - Static method in class net.sf.basedb.clients.web.Base
-
Get the current context and update it from request information if available.
- getAndSetReporterContext(SessionControl, PageContext) - Method in class net.sf.basedb.clients.web.ExperimentExplorer
-
Get and update the current settings for the reporter context.
- getAndSetSpotContext(SessionControl, PageContext) - Method in class net.sf.basedb.clients.web.ExperimentExplorer
-
Get and update the current settings for the spot context.
- getAnnotatable() - Method in class net.sf.basedb.util.AnnotationUtil.AnnotatableWrapper
-
The annotatable that we are wrapping.
- getAnnotatableItems() - Static method in class net.sf.basedb.core.Metadata
-
- getAnnotatableParents() - Method in interface net.sf.basedb.core.Annotatable
-
Get all parents objects which are annotatable and the logged in
user has read permission to.
- getAnnotatableParents() - Method in class net.sf.basedb.core.ArrayBatch
-
Get the array design.
- getAnnotatableParents() - Method in class net.sf.basedb.core.ArrayDesign
-
Get the plates, if any.
- getAnnotatableParents() - Method in class net.sf.basedb.core.ArraySlide
-
Get the array batch.
- getAnnotatableParents() - Method in class net.sf.basedb.core.BioAssay
-
Get the parent bioassay set, all parent bioassays and all parent
root raw bioassays.
- getAnnotatableParents() - Method in class net.sf.basedb.core.BioAssaySet
-
Get the parent bioassay set (if any) and the experiment.
- getAnnotatableParents() - Method in class net.sf.basedb.core.BioMaterial
-
- getAnnotatableParents() - Method in class net.sf.basedb.core.BioPlate
-
Get the freezer.
- getAnnotatableParents() - Method in class net.sf.basedb.core.DerivedBioAssay
-
Get the extract and parent bioassays or physical bioassays.
- getAnnotatableParents() - Method in class net.sf.basedb.core.Experiment
-
Always null.
- getAnnotatableParents() - Method in class net.sf.basedb.core.Extract
-
Get the tag and parent extracts.
- getAnnotatableParents() - Method in class net.sf.basedb.core.Hardware
-
- getAnnotatableParents() - Method in class net.sf.basedb.core.ItemList
-
Always returns null
- getAnnotatableParents() - Method in class net.sf.basedb.core.Kit
-
- getAnnotatableParents() - Method in class net.sf.basedb.core.MeasuredBioMaterial
-
Get the biosource or pooled samples and the bioplate
the biomaterial is located on.
- getAnnotatableParents(Collection<? extends MeasuredBioMaterial>) - Method in class net.sf.basedb.core.MeasuredBioMaterial
-
Get the annotable parents, possible only a given set of specific parents items.
- getAnnotatableParents() - Method in class net.sf.basedb.core.PhysicalBioAssay
-
Get the extracts and array slide.
- getAnnotatableParents(int, Extract) - Method in class net.sf.basedb.core.PhysicalBioAssay
-
Get the extracts, possible on a specific assay position or only a specific
extract, and the array slide.
- getAnnotatableParents(int, Collection<Extract>) - Method in class net.sf.basedb.core.PhysicalBioAssay
-
Get the extracts, possible on a specific assay position or only a given set of specific
extracts, and the array slide.
- getAnnotatableParents() - Method in class net.sf.basedb.core.Plate
-
Get the parent plates, if any.
- getAnnotatableParents() - Method in class net.sf.basedb.core.PluginConfiguration
-
- getAnnotatableParents() - Method in class net.sf.basedb.core.PluginDefinition
-
- getAnnotatableParents() - Method in class net.sf.basedb.core.Project
-
- getAnnotatableParents() - Method in class net.sf.basedb.core.Protocol
-
- getAnnotatableParents() - Method in class net.sf.basedb.core.RawBioAssay
-
Get the parent derived bioassay and extract, if any.
- getAnnotatableParents() - Method in class net.sf.basedb.core.RootRawBioAssay
-
Get the raw bioassay.
- getAnnotatableParents() - Method in class net.sf.basedb.core.Software
-
- getAnnotatableParents() - Method in class net.sf.basedb.core.Tag
-
- getAnnotatableParents() - Method in class net.sf.basedb.core.Well
-
Get the parent well, if any.
- getAnnotatableParents(DbControl, OverviewContext, Annotatable) - Static method in class net.sf.basedb.util.overview.OverviewUtil
-
Get all annotatable parent items for the given item.
- getAnnotatableParentWrappers(DbControl) - Method in class net.sf.basedb.util.AnnotationUtil.AnnotatableWrapper
-
Get all annotatable parents wrapped inside AnnotatableWrapper:s
- getAnnotation(AnnotationType) - Method in class net.sf.basedb.core.AnnotationSet
-
Get the
Annotation
object of the specified annotation type.
- getAnnotation(DbControl) - Method in class net.sf.basedb.core.snapshot.AnnotationSnapshot
-
- getAnnotation() - Method in class net.sf.basedb.util.overview.Fix
-
Get the annotation that needs to be edited for this fix.
- getAnnotationFormatter(SessionControl, Annotation, Unit) - Static method in class net.sf.basedb.clients.web.formatter.FormatterFactory
-
Get a formatter for nice formatting of annotation values, including units.
- getAnnotationGroup(short) - Method in class net.sf.basedb.clients.web.ExperimentExplorer.AnnotationSummary
-
Get the annotation group for the bioassay with the
give data cube column.
- getAnnotationGroups() - Method in class net.sf.basedb.clients.web.ExperimentExplorer.AnnotationSummary
-
Get all annotation groups that was found among the bioassays.
- getAnnotationId() - Method in class net.sf.basedb.core.snapshot.AnnotationSnapshot
-
- getAnnotationJoiner(JoinType) - Static method in class net.sf.basedb.core.HqlQueryJoiners
-
Get an annotation auto joiner.
- getAnnotationMessage() - Method in interface net.sf.basedb.core.AnnotatableProxy
-
A help message that should tell users how the proxied annotations
are used.
- getAnnotationMessage() - Method in interface net.sf.basedb.core.plugin.AnnotationSetterPlugin
-
Get a message that explains what the plug-in does with the annotations
it has.
- getAnnotationMessage() - Method in class net.sf.basedb.core.PluginConfiguration
-
Get a message explaining what the proxy does with the annotations.
- getAnnotationMessage() - Method in class net.sf.basedb.core.PluginDefinition
-
Get a message explaining what the proxy does with the annotations.
- getAnnotationMessage() - Method in class net.sf.basedb.plugins.ManualDerivedBioAssayCreator
-
- getAnnotationMessage() - Method in class net.sf.basedb.plugins.ManualTransformCreator
-
- getAnnotationMessage() - Method in class net.sf.basedb.plugins.RawDataFlatFileImporter
-
- getAnnotations(Annotation.Source) - Method in class net.sf.basedb.core.AnnotationSet
-
Get a query returning annotations with the specified source.
- getAnnotations() - Method in class net.sf.basedb.core.AnnotationSet
-
- getAnnotations() - Method in interface net.sf.basedb.core.data.AnnotatableData
-
Short-cut to all annotations belonging to this item.
- getAnnotations() - Method in class net.sf.basedb.core.data.AnnotatedData
-
- getAnnotations() - Method in class net.sf.basedb.core.data.AnnotationSetData
-
The annotations in this annotation set.
- getAnnotations() - Method in class net.sf.basedb.core.data.AnnotationTypeData
-
This is the inverse end.
- getAnnotations() - Method in class net.sf.basedb.core.data.BioAssayData
-
- getAnnotations() - Method in class net.sf.basedb.core.data.BioAssaySetData
-
- getAnnotations() - Method in class net.sf.basedb.core.data.PluginDefinitionData
-
- getAnnotations() - Method in class net.sf.basedb.core.data.ProjectData
-
- getAnnotations() - Method in class net.sf.basedb.core.data.RootRawBioAssayData
-
- getAnnotations() - Method in class net.sf.basedb.core.data.WellData
-
- getAnnotations() - Method in class net.sf.basedb.core.snapshot.AnnotationSetSnapshot
-
Get a list with the all annotations in this snapshot.
- getAnnotationSet() - Method in interface net.sf.basedb.core.Annotatable
-
Get the annotation set containing the annotations for this item.
- getAnnotationSet() - Method in class net.sf.basedb.core.AnnotatedItem
-
- getAnnotationSet() - Method in class net.sf.basedb.core.Annotation
-
Get the annotation set this annotation belongs to.
- getAnnotationSet() - Method in class net.sf.basedb.core.BioAssay
-
- getAnnotationSet() - Method in class net.sf.basedb.core.BioAssaySet
-
- getAnnotationSet() - Method in interface net.sf.basedb.core.data.AnnotatableData
-
Get the annotation set that holds the annotations for an item.
- getAnnotationSet() - Method in class net.sf.basedb.core.data.AnnotatedData
-
- getAnnotationSet() - Method in class net.sf.basedb.core.data.AnnotationData
-
Get the annotation set this annotation primarily belongs to.
- getAnnotationSet() - Method in class net.sf.basedb.core.data.BioAssayData
-
- getAnnotationSet() - Method in class net.sf.basedb.core.data.BioAssaySetData
-
- getAnnotationSet() - Method in class net.sf.basedb.core.data.PluginDefinitionData
-
- getAnnotationSet() - Method in class net.sf.basedb.core.data.ProjectData
-
- getAnnotationSet() - Method in class net.sf.basedb.core.data.RootRawBioAssayData
-
- getAnnotationSet() - Method in class net.sf.basedb.core.data.WellData
-
- getAnnotationSet() - Method in class net.sf.basedb.core.PluginDefinition
-
- getAnnotationSet() - Method in class net.sf.basedb.core.Project
-
- getAnnotationSet() - Method in class net.sf.basedb.core.RootRawBioAssay
-
- getAnnotationSet(DbControl) - Method in class net.sf.basedb.core.snapshot.AnnotationSetSnapshot
-
Get the annotation set this is a snapshot of.
- getAnnotationSet(DbControl) - Method in class net.sf.basedb.core.snapshot.AnnotationSnapshot
-
- getAnnotationSet() - Method in class net.sf.basedb.core.Well
-
- getAnnotationSetId() - Method in class net.sf.basedb.core.data.annotations.AnnotationLink
-
- getAnnotationSetId() - Method in class net.sf.basedb.core.snapshot.AnnotationSetSnapshot
-
Get the id of the annotation set this is a snapshot of.
- getAnnotationSetId() - Method in class net.sf.basedb.core.snapshot.AnnotationSnapshot
-
- getAnnotationSummary(DbControl, AnnotationType) - Method in class net.sf.basedb.clients.web.ExperimentExplorer
-
Get an AnnotationSummary object which can be used to calculate means
and other values for each annotation group.
- getAnnotationType() - Method in class net.sf.basedb.clients.web.ExperimentExplorer.AnnotationSummary
-
Get the annotation type this summary is based on.
- getAnnotationType() - Method in class net.sf.basedb.core.Annotation
-
Get the annotation type of this annotation.
- getAnnotationType() - Method in class net.sf.basedb.core.AnnotationBatcher.CurrentAnnotationInfo
-
Get the annotation type.
- getAnnotationType() - Method in class net.sf.basedb.core.data.AnnotationData
-
Get the type of this annotation.
- getAnnotationType() - Method in class net.sf.basedb.core.query.AnnotationExpression
-
- getAnnotationType() - Method in class net.sf.basedb.core.snapshot.AnnotationLoaderUtil
-
The annotation type that this loader load annotations from.
- getAnnotationType(DbControl) - Method in class net.sf.basedb.core.snapshot.AnnotationSnapshot
-
Get the annotation type.
- getAnnotationType() - Method in class net.sf.basedb.util.annotations.InheritSpecification
-
- getAnnotationType() - Method in class net.sf.basedb.util.export.spotdata.AnnotationAssayField
-
Get the configured annotation type.
- getAnnotationType() - Method in class net.sf.basedb.util.overview.Fix
-
Get the annotation type of the annotation that needs to be edited
for this fix.
- getAnnotationTypeId() - Method in class net.sf.basedb.core.data.annotations.AnnotationLink
-
- getAnnotationTypeId() - Method in class net.sf.basedb.core.snapshot.AnnotationSnapshot
-
Get the id of the annotation type.
- getAnnotationTypeIds() - Method in class net.sf.basedb.clients.web.ExperimentExplorer
-
Get the selected annotation types.
- getAnnotationTypes(DbControl, boolean) - Method in class net.sf.basedb.clients.web.ExperimentExplorer
-
Get the annotation types that are of interest in this experiment.
- getAnnotationTypes() - Method in interface net.sf.basedb.core.AnnotatableProxy
-
Get the annotation types that can be proxied.
- getAnnotationTypes(Item) - Method in class net.sf.basedb.core.AnnotationTypeCategory
-
Gets a query that returns the annotation types that are members of this category
- getAnnotationTypes() - Method in class net.sf.basedb.core.data.AnnotationTypeCategoryData
-
This is the inverse end.
- getAnnotationTypes() - Method in interface net.sf.basedb.core.plugin.AnnotationSetterPlugin
-
Create a query that returns the annotation types that can be used
by the current plug-in.
- getAnnotationTypes() - Method in class net.sf.basedb.core.PluginConfiguration
-
Get the annotation types that can be used by this configuration.
- getAnnotationTypes() - Method in class net.sf.basedb.core.PluginDefinition
-
Get the annotation types that can be used by this configuration.
- getAnnotationTypes() - Method in class net.sf.basedb.plugins.Base1PluginExecuter
-
Get the experimental factors connected to a experiment.
- getAnnotationTypes() - Method in class net.sf.basedb.plugins.ManualDerivedBioAssayCreator
-
Return a query that finds annotation types for bioassay sets.
- getAnnotationTypes() - Method in class net.sf.basedb.plugins.ManualTransformCreator
-
Return a query that finds annotation types for bioassay sets.
- getAnnotationTypes() - Method in class net.sf.basedb.plugins.RawDataFlatFileImporter
-
Return a query that finds annotation types for raw bioassays.
- getAnnotationTypesQuery(Item) - Static method in class net.sf.basedb.clients.web.Base
-
Get a query that returns all annotation types defined for a particular
item type.
- getAnnotationTypesQuery(Item, Boolean) - Static method in class net.sf.basedb.clients.web.Base
-
Get a query that returns all annotation types defined for a particular
item type and, optionally, with a specific protocol parameter setting.
- getAnnotationTypesQuery(AnnotatableProxy) - Static method in class net.sf.basedb.clients.web.Base
-
Get a query that returns all annotation types defined for a
AnnotatableProxy
item.
- getAnnotationValues() - Method in class net.sf.basedb.clients.web.ExperimentExplorer.AnnotationGroup
-
Get all annotation values in this annotation group.
- getAnnotationValues(DbControl, SnapshotManager, BioAssay, AnnotationType) - Static method in class net.sf.basedb.util.BioAssaySetUtil
-
Find the annotation values for a given annotation type on a bioassay.
- getAppId() - Method in class net.sf.basedb.core.data.SchemaVersionData
-
The ID of the application the schema version is valid for.
- getAppId() - Method in class net.sf.basedb.core.hibernate.SessionFactoryConfiguration
-
Deprecated.
Get the application id for schema versioning.
- getAppId() - Method in class net.sf.basedb.core.ServiceSessionControl.SessionFactoryConfiguration
-
Get the application id for schema versioning.
- getApproximateRowCountSql(String, String, String) - Method in class net.sf.basedb.core.dbengine.AbstractDbEngine
-
- getApproximateRowCountSql(String, String, String) - Method in interface net.sf.basedb.core.dbengine.DbEngine
-
Get an SQL statement that returns an approximate count for the number
of rows in the given table.
- getApproximateRowCountSql(String, String, String) - Method in class net.sf.basedb.core.dbengine.MySQLEngine
-
- getApproximateRowCountSql(String, String, String) - Method in class net.sf.basedb.core.dbengine.PostgresDbEngine
-
- getApproximateSize() - Method in class net.sf.basedb.core.hibernate.TypeWrapper
-
Get the number of bytes a single value for this type occupies
in a database (approximately).
- getArrayBatch() - Method in class net.sf.basedb.core.ArraySlide
-
Get the
ArrayBatch
item to which this slide belongs.
- getArrayBatch() - Method in class net.sf.basedb.core.data.ArraySlideData
-
Get the arrayBatch of this slide.
- getArrayBatches() - Method in class net.sf.basedb.core.ArrayDesign
-
Get a query that returns the batches for this design.
- getArrayBatches() - Method in class net.sf.basedb.core.data.ArrayDesignData
-
This is the inverse end.
- getArrayDesign() - Method in class net.sf.basedb.core.ArrayBatch
-
- getArrayDesign() - Method in class net.sf.basedb.core.ArrayDesignBlock
-
Get the ArrayDesign
that is linked with this block.
- getArrayDesign() - Method in class net.sf.basedb.core.ArrayDesignPlate
-
Gets this item's ArrayDesign
.
- getArrayDesign() - Method in class net.sf.basedb.core.data.ArrayBatchData
-
Get the array design item that was used for this batch.
- getArrayDesign() - Method in class net.sf.basedb.core.data.ArrayDesignBlockData
-
Used by Hibernate to link with ArrayDesign.
- getArrayDesign() - Method in class net.sf.basedb.core.data.ArrayDesignPlateData
-
Get the ArrayDesign
- getArrayDesign() - Method in class net.sf.basedb.core.data.RawBioAssayData
-
Get the array design used for the hybridization this raw bio assay comes from.
- getArrayDesign() - Method in class net.sf.basedb.core.DerivedBioAssay
-
Get the array design connected to this derived bioassay by
following the path from the physical bioassay to the array slide to
the array batch to the array design.
- getArrayDesign() - Method in class net.sf.basedb.core.FeatureBatcher
-
Get the array design this batcher is used for.
- getArrayDesign() - Method in class net.sf.basedb.core.RawBioAssay
-
- getArrayDesignBlock() - Method in class net.sf.basedb.core.data.FeatureData
-
Get the arraydesignblock of this feature.
- getArrayDesignBlock(DbControl, FeatureData) - Static method in class net.sf.basedb.core.Feature
-
Get the array design block from a feature.
- getArrayDesignBlocks() - Method in class net.sf.basedb.core.ArrayDesign
-
Get a query that returns the block of this array design.
- getArrayDesignBlocks() - Method in class net.sf.basedb.core.data.ArrayDesignData
-
This is the inverse end.
- getArrayDesignPlates() - Method in class net.sf.basedb.core.ArrayDesign
-
Get plate connections for this array design.
- getArrayDesigns() - Method in class net.sf.basedb.core.data.JobData
-
This is the inverse end.
- getArrayDesigns() - Method in class net.sf.basedb.core.data.PlateData
-
Used by Hibernate to link with the arraydesign for this plate.
- getArraySlide() - Method in class net.sf.basedb.core.data.PhysicalBioAssayData
-
Get the array slide.
- getArraySlide() - Method in class net.sf.basedb.core.PhysicalBioAssay
-
- getArraySlides() - Method in class net.sf.basedb.core.ArrayBatch
-
Get a query that returns the slides in this batch.
- getArraySlides() - Method in class net.sf.basedb.core.data.ArrayBatchData
-
This is the inverse end.
- getAssayAnnotationField(String, String) - Method in class net.sf.basedb.util.export.spotdata.AbstractFieldConverter
-
Get an assay annotation field.
- getAssayAnnotationsWriter() - Method in class net.sf.basedb.util.export.spotdata.BfsExporter
-
Get the writer were assay annotations should be printed.
- getAssayField(String, boolean) - Method in class net.sf.basedb.util.export.spotdata.AdvancedFieldConverter
-
- getAssayField(String, boolean) - Method in interface net.sf.basedb.util.export.spotdata.ExportableFieldConverter
-
Create an assay field for the given name.
- getAssayField(String, boolean) - Method in class net.sf.basedb.util.export.spotdata.StandardFieldConverter
-
Find an assay field.
- getAssayFields(DbControl, BioAssaySet) - Method in class net.sf.basedb.plugins.BfsExporterPlugin
-
- getAssayFields() - Method in class net.sf.basedb.util.export.spotdata.AbstractBioAssaySetExporter
-
Get the list of registered assay fields, in the order they were
registered.
- getAssayFields() - Method in class net.sf.basedb.util.export.spotdata.BaseFileExporter
-
- getAssayFields() - Method in class net.sf.basedb.util.export.spotdata.BfsExporter
-
- getAssayFields() - Method in class net.sf.basedb.util.importer.spotdata.BaseFileInfo.SpotSectionInfo
-
Get a list with all assay data fields, in the order they
appear in the file.
- getAssayIndex(short) - Method in class net.sf.basedb.util.export.spotdata.AbstractBioAssaySetExporter
-
Get the cached index value for an assay when you know the assay's column
number.
- getAssayPropertyField(String, String) - Method in class net.sf.basedb.util.export.spotdata.AbstractFieldConverter
-
Get a static assay property field, such as name, description or id.
- getAssays() - Method in class net.sf.basedb.util.importer.spotdata.BaseFileInfo.SpotSectionInfo
-
Get a list with the ID:s of all assays in the section,
in the order they appear in the data columns.
- getAssaysHaveParentAssaysMapping() - Method in class net.sf.basedb.util.importer.spotdata.BaseFileInfo
-
A flag that indicates if the BASEfile includes a mapping
from child to parent assays.
- getAssayValue(DbControl, BioAssay) - Method in class net.sf.basedb.util.export.spotdata.AnnotationAssayField
-
Return all annotation values that are related to the specified
bioassay, or null if not configured.
- getAssayValue(DbControl, BioAssay) - Method in interface net.sf.basedb.util.export.spotdata.AssayField
-
Get the values for the given bioassay.
- getAssayValue(DbControl, BioAssay) - Method in class net.sf.basedb.util.export.spotdata.AssayPropertyField
-
Return all values that are given by the specified property.
- getAssociatedDataFileType(DataFileType, boolean) - Method in class net.sf.basedb.core.ItemSubtype
-
Get information about a data file type that has been associated with this
item subtype.
- getAttribute(String) - Method in class net.sf.basedb.core.authentication.LoginRequest
-
Get the value of an extra attribute to use for the login request.
- getAttribute(String) - Method in class net.sf.basedb.util.extensions.AboutBean
-
- getAttribute(String) - Method in class net.sf.basedb.util.extensions.ClientContext
-
Get an attribute of the context.
- getAttribute(String) - Method in interface net.sf.basedb.util.extensions.ExtendedAbout
-
Get extra information
- getAttribute(String) - Method in class net.sf.basedb.util.extensions.ExtensionContext
-
- getAttribute(String) - Method in class net.sf.basedb.util.extensions.ExtensionPointContext
-
Always null, since this is an extension point context.
- getAttribute(String) - Method in class net.sf.basedb.util.extensions.InvokationContext
-
Get the value of an attribute that has been registered
for the extension.
- getAttribute(String, String) - Method in class net.sf.basedb.util.extensions.Registry
-
Get the value of a extra attribute for a registered extension
or extension point.
- getAttribute(String) - Method in class net.sf.basedb.util.extensions.Registry.RegisteredAbout
-
- getAttribute(NodeAttribute<T>) - Method in class net.sf.basedb.util.overview.Node
-
Get the value for a node attribute.
- getAttributeNames() - Method in class net.sf.basedb.util.extensions.AboutBean
-
- getAttributeNames() - Method in interface net.sf.basedb.util.extensions.ExtendedAbout
-
Get all extra attribute names.
- getAttributeNames() - Method in class net.sf.basedb.util.extensions.Registry.RegisteredAbout
-
- getAttributesString(Object) - Static method in class net.sf.basedb.clients.web.extensions.DynamicActionAttributeSupport
-
If the object implements DynamicActionAttributes interface,
get a string with all dynamic attributes, otherwise an empty string.
- getAuthenticationMethod() - Method in class net.sf.basedb.core.authentication.AuthenticatedUser
-
Get the authentication method that was used to verify the login.
- getAuthenticationMethod() - Method in class net.sf.basedb.core.data.SessionData
-
Get the authentication method used for this session.
- getAuthenticationMethod() - Method in class net.sf.basedb.core.Session
-
Get the authentication method that was used to login to
this session.
- getAuthenticationMethod() - Method in class net.sf.basedb.core.SessionControl
-
Get the method that was used to authenticate the currently
logged in user.
- getAuthenticator() - Static method in class net.sf.basedb.core.Application
-
- getAuthenticator(String) - Method in class net.sf.basedb.core.authentication.OldAuthenticationWrapperFactory
-
- getAuthors() - Method in class net.sf.basedb.core.data.ExperimentData
-
Get the authors for this experiment.
- getAuthors() - Method in class net.sf.basedb.core.Experiment
-
Get the authors of the publication for this experiment.
- getAutoCompress() - Method in class net.sf.basedb.core.data.DirectoryData
-
If files that are uploaded to this directory be compressed or not.
- getAutoCompress() - Method in class net.sf.basedb.core.data.MimeTypeData
-
If files of this MIME type should use auto-compression or not.
- getAutoCompress() - Method in class net.sf.basedb.core.Directory
-
If files that are uploaded to this directory should be
compressed or not.
- getAutoCompress() - Method in class net.sf.basedb.core.MimeType
-
If files of this MIME type should automatically be compressed
when they are uploaded to BASE.
- getAutoJoinType() - Method in class net.sf.basedb.core.query.ReporterListExpression
-
Get the join type for automatic joins.
- getAutoPermission() - Method in class net.sf.basedb.core.data.ProjectData
-
The permissions to use with automatic sharing to this
project.
- getAutoPermission() - Method in class net.sf.basedb.core.Project
-
The permissions to use when automatically sharing new items to
the project when it is the active project.
- getAutoShare() - Method in class net.sf.basedb.core.data.DirectoryData
-
If new files and subdirectories should inherit the share permission
on this directory or not.
- getAutoShare() - Method in class net.sf.basedb.core.Directory
-
If new files and subdirectories that are created in this
directory automatically should be shared wtih the same
permissions as this directory.
- getAverageExpression(Expression) - Method in enum net.sf.basedb.core.Formula.AverageMethod
-
Given an expression, create an expression that takes the correct
average of it.
- getAverageMethod() - Method in class net.sf.basedb.clients.web.taglib.table.TableColumn
-
- getAverageMethod() - Method in class net.sf.basedb.core.data.ExtraValueTypeData
-
- getAverageMethod() - Method in class net.sf.basedb.core.data.FormulaData
-
- getAverageMethod() - Method in class net.sf.basedb.core.data.ReporterClonePropertyData
-
The code for the averate method to use when calculating averages.
- getAverageMethod() - Method in class net.sf.basedb.core.ExtendedProperty
-
Which method to use when calculating the average of a set of values.
- getAverageMethod() - Method in class net.sf.basedb.core.ExtraValueType
-
Get the average method for this extra value type.
- getAverageMethod() - Method in class net.sf.basedb.core.Formula
-
Get the average method for this formula.
- getAverageMethod() - Method in enum net.sf.basedb.core.IntensityTransform
-
Get the averaging method to use when averaging values
that has been transformed with the specified transformation.
- getAverageMethod() - Method in class net.sf.basedb.util.export.spotdata.JepDynamicField
-
Get the average method to use if the exporter is exporting
averaged data.
- getAverageMethod() - Method in class net.sf.basedb.util.export.spotdata.SimpleDynamicField
-
Get the average method to use if the exporter is exporting
averaged data.
- getAverageOnReporter() - Method in class net.sf.basedb.util.export.spotdata.AbstractBioAssaySetExporter
-
- getAverageOnReporter() - Method in class net.sf.basedb.util.export.spotdata.BaseFileExporter
-
- getAvg() - Method in class net.sf.basedb.core.query.GeometricMeanExpression
-
- getAwtColor() - Method in class net.sf.basedb.clients.web.ExperimentExplorer.AnnotationGroup
-
Get the AWT color object that corresponds to the HTML color string.
- getBarcode() - Method in class net.sf.basedb.core.ArraySlide
-
Get the barcode of the slide.
- getBarcode() - Method in class net.sf.basedb.core.BioPlate
-
Gets the barcode of this bio plate.
- getBarcode() - Method in class net.sf.basedb.core.data.ArraySlideData
-
Get the barcode of the slide.
- getBarcode() - Method in class net.sf.basedb.core.data.BioPlateData
-
Get the barcode for the bioplate.
- getBarcode() - Method in class net.sf.basedb.core.data.PlateData
-
Get the barcode for the plate.
- getBarcode() - Method in class net.sf.basedb.core.Plate
-
Get the barcode of this plate.
- getBaseFileParser() - Method in class net.sf.basedb.util.importer.spotdata.BaseFileImporter
-
Get the underlying parser for the BASEfile.
- getBaseFileWriter() - Method in class net.sf.basedb.util.export.spotdata.BaseFileExporter
-
Get the writer that writes the data to the file.
- getBaseVersion() - Method in class net.sf.basedb.clients.web.taglib.Page
-
- getBasicData() - Method in class net.sf.basedb.core.BasicItem
-
- getBatchIndex() - Method in class net.sf.basedb.core.ArraySlide
-
Get the index of this slide in the batch.
- getBatchIndex() - Method in class net.sf.basedb.core.data.ArraySlideData
-
Get the index of this slide in the batch.
- getBatchSize() - Method in class net.sf.basedb.core.AbstractBatcher
-
- getBatchSize() - Method in interface net.sf.basedb.core.Batcher
-
Get the current batch size of the batcher.
- getBestMatch(String, Collection<? extends String>) - Method in class net.sf.basedb.util.fuzzy.StringMatcher
-
Find the string that is most similar to a given string in a list of
strings.
- getBestPairs(Collection<? extends String>, Collection<? extends String>) - Method in class net.sf.basedb.util.fuzzy.StringMatcher
-
Match strings in two lists.
- getBFSSubtype() - Method in class net.sf.basedb.util.export.spotdata.BfsExporter
-
Get the BFS subtype.
- getBFSSubtype() - Method in class net.sf.basedb.util.export.spotdata.MatrixBfsExporter
-
- getBFSSubtype() - Method in class net.sf.basedb.util.export.spotdata.SerialBfsExporter
-
- getBin(int) - Method in class net.sf.basedb.util.plot.HistogramPlot.HistogramSeries
-
- getBioAssay(DbControl, short) - Method in class net.sf.basedb.clients.web.ExperimentExplorer
-
Get the bioassay with the specified column number in the
data cube.
- getBioAssays() - Method in class net.sf.basedb.core.BioAssaySet
-
Get a query returning the bioassays that are part of this
bioassayset.
- getBioAssays() - Method in class net.sf.basedb.core.data.BioAssaySetData
-
This is the inverse end.
- getBioAssays() - Method in class net.sf.basedb.core.data.RawBioAssayData
-
This is the inverse end.
- getBioAssays() - Method in class net.sf.basedb.util.export.spotdata.AbstractBioAssaySetExporter
-
Get a list with all bioassays in the source bioassay set.
- getBioAssaySet(DbControl) - Method in class net.sf.basedb.clients.web.ExperimentExplorer
-
Get the bioassay set that is currently beeing explored.
- getBioAssaySet() - Method in class net.sf.basedb.core.BioAssay
-
Get the bioassayset this bioassay belongs to.
- getBioAssaySet() - Method in class net.sf.basedb.core.data.BioAssayData
-
Get the bioassayset this bioassay belongs to.
- getBioAssaySet() - Method in class net.sf.basedb.core.data.ExtraValueData
-
Get the bioassayset this extra value belongs to.
- getBioAssaySet() - Method in class net.sf.basedb.core.ExtraValue
-
Get the bioassayset this extra value belongs to.
- getBioAssaySets() - Method in class net.sf.basedb.core.data.ExperimentData
-
This is the inverse end.
- getBioAssaySets() - Method in class net.sf.basedb.core.Experiment
-
Get a query that return all bioassaysets in this
experiment.
- getBioMaterial() - Method in class net.sf.basedb.core.BioMaterialEvent
-
- getBioMaterial() - Method in class net.sf.basedb.core.BioMaterialEventSource
-
Get the biomaterial that was used as a source in this event.
- getBioMaterial(PlateCoordinate) - Method in class net.sf.basedb.core.BioPlate
-
Get the biomaterial in the well at the given location.
- getBioMaterial() - Method in class net.sf.basedb.core.BioWell
-
- getBioMaterial() - Method in class net.sf.basedb.core.data.BioMaterialEventData
-
Get the biomaterial produced or affected by this event.
- getBioMaterial() - Method in class net.sf.basedb.core.data.BioMaterialEventSourceData
-
Get the parent biomaterial that was used in the event.
- getBioMaterial() - Method in class net.sf.basedb.core.data.BioWellData
-
- getBioMaterialEvents() - Method in class net.sf.basedb.core.BioPlateEvent
-
Get a query returning all biomaterial events linked to this
event.
- getBioMaterialEvents() - Method in class net.sf.basedb.core.data.BioPlateEventParticipantData
-
This is the inverse end.
- getBioMaterialType() - Method in class net.sf.basedb.core.BioPlateType
-
Get the biomaterial type that can be stored on plates of
this type.
- getBioMaterialType() - Method in class net.sf.basedb.core.BioWell
-
Get the type of biomaterial that is placed in this well.
- getBioMaterialType() - Method in class net.sf.basedb.core.data.BioPlateTypeData
-
If set, plates using this type can only hold the specific biomaterial
type (eg. samples, extracts or labeled extracts).
- getBioPlate() - Method in class net.sf.basedb.core.BioPlateEventParticipant
-
- getBioPlate() - Method in class net.sf.basedb.core.data.BioPlateEventParticipantData
-
The bioplate that is participating in the event.
- getBioPlate() - Method in class net.sf.basedb.core.data.BioWellData
-
The bioplate this well belongs to.
- getBioPlateEventParticipant() - Method in class net.sf.basedb.core.BioMaterialEvent
-
Get the bioplate event participant that is the master of this event.
- getBioPlateEventParticipant() - Method in class net.sf.basedb.core.data.BioMaterialEventData
-
Get the bioplate event that is the master event for this event.
- getBioPlates() - Method in class net.sf.basedb.core.BioPlateType
-
Creates a query that returns all bioplates that are using
this type.
- getBioPlates() - Method in class net.sf.basedb.core.data.BioPlateTypeData
-
The bioplates that use this type.
- getBioPlateType() - Method in class net.sf.basedb.core.BioPlate
-
- getBioPlateType() - Method in class net.sf.basedb.core.data.BioPlateData
-
Get the type of the bioplate.
- getBioWell(int, int) - Method in class net.sf.basedb.core.BioPlate
-
Gets bio well for specific location.
- getBioWell(PlateCoordinate) - Method in class net.sf.basedb.core.BioPlate
-
Gets bio well for specific location.
- getBioWell() - Method in class net.sf.basedb.core.data.MeasuredBioMaterialData
-
Get the bio well.
- getBioWell() - Method in class net.sf.basedb.core.MeasuredBioMaterial
-
Get the well this biomaterial is located in.
- getBioWells() - Method in class net.sf.basedb.core.BioPlate
-
Gets a query that returns all BioWell
s
on this plate.
- getBioWells() - Method in class net.sf.basedb.core.data.BioPlateData
-
The wells on this plate.
- getBlock() - Method in class net.sf.basedb.core.BlockInfo
-
Get the block number.
- getBlock() - Method in class net.sf.basedb.core.data.RawData
-
- getBlock() - Method in class net.sf.basedb.core.FeatureCoordinate
-
- getBlock() - Method in class net.sf.basedb.plugins.PrintMapFlatFileImporter.MetaBlock
-
- getBlockNumber() - Method in class net.sf.basedb.core.ArrayDesignBlock
-
Get the block number of this block.
- getBlockNumber() - Method in class net.sf.basedb.core.data.ArrayDesignBlockData
-
Get the block number of this block.
- getBlockNumber() - Method in enum net.sf.basedb.plugins.PrintMapFlatFileImporter.Section
-
- getBlockSizeX() - Method in class net.sf.basedb.core.ArrayDesignBlock
-
Get the number of columns in this block.
- getBlockSizeX() - Method in class net.sf.basedb.core.data.ArrayDesignBlockData
-
Get the maximum number of rows in this block.
- getBlockSizeX() - Method in class net.sf.basedb.plugins.PrintMapFlatFileImporter.MetaBlock
-
- getBlockSizeY() - Method in class net.sf.basedb.core.ArrayDesignBlock
-
Get the number of rows in this block.
- getBlockSizeY() - Method in class net.sf.basedb.core.data.ArrayDesignBlockData
-
Get the maximum number of columns in this block.
- getBlockSizeY() - Method in class net.sf.basedb.plugins.PrintMapFlatFileImporter.MetaBlock
-
- getBlueImageFile() - Method in class net.sf.basedb.core.data.SpotImagesData
-
The file used for the blue component in the spot images.
- getBlueImageFile() - Method in class net.sf.basedb.core.SpotImages
-
Get the file which was used for the blue channel in the
spot images.
- getBofType() - Method in class net.sf.basedb.util.parser.FlatFileParser
-
Get the value captured by the BOF marker regular expression.
- getBoolean(String) - Static method in class net.sf.basedb.core.Config
-
Get the configuration setting specified by key
as a boolean
value.
- getBoolean(String) - Method in class net.sf.basedb.plugins.Base1PluginExecuter
-
Creates a boolean from a string.
- getBoolean(String) - Static method in class net.sf.basedb.util.Values
-
Convert a string to a boolean. '0', 'no', 'false', '' and the null string are
converted to FALSE, all other values are converted to TRUE.
- getBoolean(String, boolean) - Static method in class net.sf.basedb.util.Values
-
Convert a string to a boolean.
- getBooleanAttribute(Element, String, boolean) - Static method in class net.sf.basedb.util.XmlUtil2
-
Get the value of an attribute as a boolean.
- getBooleanFormatter(SessionControl) - Static method in class net.sf.basedb.clients.web.formatter.FormatterFactory
-
Get the logged in user's formatter for boolean values.
- getBooleanOption(String, boolean) - Method in class net.sf.basedb.core.AnnotationType
-
Get an option and convert the value to a boolean.
- getBooleanValues() - Method in class net.sf.basedb.core.data.annotations.AnnotationLink
-
- getBuild() - Static method in class net.sf.basedb.core.Application
-
Get the build number.
- getBuild() - Method in class net.sf.basedb.core.data.SchemaVersionData
-
The build number.
- getBuild() - Static method in class net.sf.basedb.core.Version
-
Get the build version.
- getButtonclass() - Method in class net.sf.basedb.clients.web.taglib.Select
-
- getButtonicon() - Method in class net.sf.basedb.clients.web.taglib.Select
-
- getButtonstyle() - Method in class net.sf.basedb.clients.web.taglib.Select
-
- getButtontitle() - Method in class net.sf.basedb.clients.web.taglib.Select
-
- getByClassName(DbControl, String) - Static method in class net.sf.basedb.core.PluginDefinition
-
Get a PluginDefinition
item when you know the class name.
- getByExtension(DbControl, String) - Static method in class net.sf.basedb.core.MimeType
-
Get a MimeType
item when you know the file extension.
- getByExternalId(DbControl, String) - Static method in class net.sf.basedb.core.Client
-
Get a Client
item when you know the external ID.
- getByExternalId(DbControl, String) - Static method in class net.sf.basedb.core.DataFileType
-
Get a DataFileType
item when you know the external ID.
- getByExternalId(DbControl, String) - Static method in class net.sf.basedb.core.ExtraValueType
-
Get a ExtraValueType
when you know the external id.
- getByExternalId(DbControl, String) - Static method in class net.sf.basedb.core.JobAgent
-
Get a JobAgent
item when you know the external ID.
- getByExternalId(DbControl, String) - Static method in class net.sf.basedb.core.Platform
-
Get a Platform
item when you know the external ID.
- getByExternalId(DbControl, String) - Static method in class net.sf.basedb.core.PlatformVariant
-
Get a PlatformVariant
item when you know the external ID.
- getByExternalId(DbControl, String) - Static method in class net.sf.basedb.core.Reporter
-
- getByExternalId(DbControl, String, Experiment) - Static method in class net.sf.basedb.core.Reporter
-
Get a
ReporterData
object when you know the external id, possibly
using the cloned reporter annotations of the given experiment.
- getByExternalId(String) - Method in class net.sf.basedb.core.ReporterBatcher
-
Get a reporter when you know the external id.
- getByExternalId(String, boolean) - Method in class net.sf.basedb.core.ReporterBatcher
-
Get a reporter when you know the external id.
- getById(DbControl, int) - Static method in class net.sf.basedb.core.Annotation
-
Get an Annotation
item when you know the id.
- getById(DbControl, int) - Static method in class net.sf.basedb.core.AnnotationSet
-
Get an AnnotationSet
item when you know the id.
- getById(DbControl, int) - Static method in class net.sf.basedb.core.AnnotationType
-
Get an AnnotationType
item when you know the id.
- getById(DbControl, int) - Static method in class net.sf.basedb.core.AnnotationTypeCategory
-
Get an AnnotationTypeCategory
item when you know the id.
- getById(DbControl, int) - Static method in class net.sf.basedb.core.AnyToAny
-
Get an AnyToAny
link when you know the id.
- getById(DbControl, int) - Static method in class net.sf.basedb.core.ArrayBatch
-
Get a ArrayBatch
object when you know the ID.
- getById(DbControl, int) - Static method in class net.sf.basedb.core.ArrayDesign
-
Get an ArrayDesign
item when you know the ID.
- getById(DbControl, int) - Static method in class net.sf.basedb.core.ArrayDesignBlock
-
Get a ArrayDesignBlock
object when you know the ID.
- getById(DbControl, int) - Static method in class net.sf.basedb.core.ArrayDesignPlate
-
Get a ArrayDesignPlate
item when you know the id.
- getById(DbControl, int) - Static method in class net.sf.basedb.core.ArraySlide
-
Get a ArraySlide
object when you know the ID.
- getById(DbControl, int) - Static method in class net.sf.basedb.core.BioAssay
-
Get a BioAssay
item when you know the id.
- getById(DbControl, int) - Static method in class net.sf.basedb.core.BioAssaySet
-
Get a BioAssaySet
item when you know the id.
- getById(DbControl, int) - Static method in class net.sf.basedb.core.BioMaterial
-
Get a biomaterial item when you know the id.
- getById(DbControl, int) - Static method in class net.sf.basedb.core.BioMaterialEvent
-
Get a BioMaterialEvent
item when you know the id.
- getById(DbControl, int) - Static method in class net.sf.basedb.core.BioPlate
-
Gets a BioPlate when knowing the item's id
- getById(DbControl, int) - Static method in class net.sf.basedb.core.BioPlateEvent
-
Get a BioPlateEvent
item when you know the id.
- getById(DbControl, int) - Static method in class net.sf.basedb.core.BioPlateEventParticipant
-
Get a BioPlateEventParticipant
item when you know the id.
- getById(DbControl, int) - Static method in class net.sf.basedb.core.BioPlateEventType
-
Gets a BioPlate event type when knowing the item's id
- getById(DbControl, String) - Static method in class net.sf.basedb.core.BioPlateEventType
-
Gets a BioPlate event type when knowing the item's system id
- getById(DbControl, int) - Static method in class net.sf.basedb.core.BioPlateType
-
Gets a BioPlate type when knowing the item's id
- getById(DbControl, int) - Static method in class net.sf.basedb.core.BioSource
-
Get an BioSource
item when you know the id.
- getById(DbControl, int) - Static method in class net.sf.basedb.core.BioWell
-
Get a BioWell
item when you know the id.
- getById(DbControl, int) - Static method in class net.sf.basedb.core.ChangeHistory
-
Get a ChangeHistory
item when you know the ID.
- getById(DbControl, int) - Static method in class net.sf.basedb.core.Client
-
Get a Client
item when you know the ID.
- getById(DbControl, int) - Static method in class net.sf.basedb.core.ClientDefaultSetting
-
Get a ClientDefaultSetting
item when you know the ID.
- getById(DbControl, int) - Static method in class net.sf.basedb.core.DataCube
-
Get a VirtualDb
item when you know the id.
- getById(DbControl, int) - Static method in class net.sf.basedb.core.DataCubeColumn
-
Get a DataCubeColumn
item when you know the id.
- getById(DbControl, int) - Static method in class net.sf.basedb.core.DataCubeExtraValue
-
Get a DataCubeExtraValue
item when you know the id.
- getById(DbControl, int) - Static method in class net.sf.basedb.core.DataCubeFilter
-
Get a DataCubeFilter
item when you know the id.
- getById(DbControl, int) - Static method in class net.sf.basedb.core.DataCubeLayer
-
Get a DataCubeLayer
item when you know the id.
- getById(DbControl, int) - Static method in class net.sf.basedb.core.DataFileType
-
Get a DataFileType
object when you know the ID.
- getById(DbControl, int) - Static method in class net.sf.basedb.core.DerivedBioAssay
-
Get a DerivedBioAssay
item when you know the id.
- getById(DbControl, int) - Static method in class net.sf.basedb.core.Directory
-
Get a Directory
item when you know the ID.
- getById(DbControl, int) - Static method in class net.sf.basedb.core.Experiment
-
Get an Experiment
item when you know the id.
- getById(DbControl, int) - Static method in class net.sf.basedb.core.Extract
-
Get an Extract
item when you know the id.
- getById(DbControl, int) - Static method in class net.sf.basedb.core.ExtraValue
-
Get an ExtraValue
item when you know the id.
- getById(DbControl, int) - Static method in class net.sf.basedb.core.ExtraValueType
-
Get an ExtraValueType
object when you know the id.
- getById(DbControl, int) - Static method in class net.sf.basedb.core.File
-
Get a File
item when you know the id.
- getById(DbControl, int) - Static method in class net.sf.basedb.core.FileServer
-
Get a FileServer
item when you know the ID.
- getById(DbControl, int) - Static method in class net.sf.basedb.core.FileSet
-
Get a FileSet
item when you know the id.
- getById(DbControl, int) - Static method in class net.sf.basedb.core.FileSetMember
-
Get a FileSetMember
object when you know the ID.
- getById(DbControl, int) - Static method in class net.sf.basedb.core.Formula
-
Get a Formula
item when you know the ID.
- getById(DbControl, int) - Static method in class net.sf.basedb.core.GlobalDefaultSetting
-
Get a ClientDefaultSetting
item when you know the ID.
- getById(DbControl, int) - Static method in class net.sf.basedb.core.Group
-
Get a Group
item when you know the ID.
- getById(DbControl, int) - Static method in class net.sf.basedb.core.Hardware
-
Get a Hardware
item when you know the ID.
- getById(DbControl, int) - Static method in class net.sf.basedb.core.Help
-
Get a Help
item when you know the ID.
- getById - Variable in enum net.sf.basedb.core.Item
-
- getById(DbControl, int) - Method in enum net.sf.basedb.core.Item
-
Get the item of the type represented by this enumeration constant with
the specified id.
- getById(DbControl, int) - Static method in class net.sf.basedb.core.ItemKey
-
Get an ItemKey
item when you know the ID.
- getById(DbControl, int) - Static method in class net.sf.basedb.core.ItemList
-
Get an ItemList
item when you know the id.
- getById(DbControl, int) - Static method in class net.sf.basedb.core.ItemSubtype
-
Get an item subtype object when you know the ID.
- getById(DbControl, int) - Static method in class net.sf.basedb.core.ItemSubtypeFileType
-
Get a PlatformFileType
object when you know the ID.
- getById(DbControl, int) - Static method in class net.sf.basedb.core.Job
-
Get a Job
item when you know the id.
- getById(DbControl, int) - Static method in class net.sf.basedb.core.JobAgent
-
Get a JobAgent
object when you know the ID.
- getById(DbControl, int) - Static method in class net.sf.basedb.core.JobAgentSettings
-
Get a JobAgentSettings
item when you know the ID.
- getById(DbControl, int) - Static method in class net.sf.basedb.core.Kit
-
Get a Kit
item when you know the ID.
- getById(DbControl, int) - Static method in class net.sf.basedb.core.Message
-
Get a Message
item when you know the id.
- getById(DbControl, int) - Static method in class net.sf.basedb.core.MimeType
-
Get a MimeType
object when you know the ID.
- getById(DbControl, int) - Static method in class net.sf.basedb.core.News
-
Get a News
item when you know the ID.
- getById(DbControl, int) - Static method in class net.sf.basedb.core.PermissionTemplate
-
Get a permission template item when you know the id.
- getById(DbControl, int) - Static method in class net.sf.basedb.core.PhysicalBioAssay
-
Get a Hybridization
item when you know the id.
- getById(DbControl, int) - Static method in class net.sf.basedb.core.Plate
-
Get a Plate
item when you know the id.
- getById(DbControl, int) - Static method in class net.sf.basedb.core.PlateEvent
-
Get a PlateEvent
item when you know the id.
- getById(DbControl, int) - Static method in class net.sf.basedb.core.PlateEventType
-
Get a PlateEventType
item when you know the id.
- getById(DbControl, int) - Static method in class net.sf.basedb.core.PlateGeometry
-
Get a PlateGeometry
item when you know the id.
- getById(DbControl, int) - Static method in class net.sf.basedb.core.PlateMapping
-
Get a PlateMapping
item when you know the id.
- getById(DbControl, int) - Static method in class net.sf.basedb.core.PlateType
-
Get a PlateType
item when you know the id.
- getById(DbControl, int) - Static method in class net.sf.basedb.core.Platform
-
Get a Platform
object when you know the ID.
- getById(DbControl, int) - Static method in class net.sf.basedb.core.PlatformFileType
-
Get a PlatformFileType
object when you know the ID.
- getById(DbControl, int) - Static method in class net.sf.basedb.core.PlatformVariant
-
Get a PlatformVariant
object when you know the ID.
- getById(DbControl, int) - Static method in class net.sf.basedb.core.PluginConfiguration
-
Get a PluginConfiguration
item when you know the ID.
- getById(DbControl, int) - Static method in class net.sf.basedb.core.PluginDefinition
-
Get a PluginDefinition
item when you know the ID.
- getById(DbControl, int) - Static method in class net.sf.basedb.core.PluginType
-
Get a PluginType
object when you know the ID.
- getById(DbControl, int) - Static method in class net.sf.basedb.core.Project
-
Get a Project
item when you know the ID.
- getById(DbControl, int) - Static method in class net.sf.basedb.core.ProjectKey
-
Get a ProjectKey
item when you know the ID.
- getById(DbControl, int) - Static method in class net.sf.basedb.core.Protocol
-
Get a Protocol
item when you know the ID.
- getById(DbControl, int) - Static method in class net.sf.basedb.core.Quantity
-
Get a Quantity
object when you know the ID.
- getById(DbControl, int) - Static method in class net.sf.basedb.core.Quota
-
Get a Quota
item when you know the ID.
- getById(DbControl, int) - Static method in class net.sf.basedb.core.QuotaType
-
Get a QuotaType
object when you know the id.
- getById(DbControl, int) - Static method in class net.sf.basedb.core.RawBioAssay
-
Get a RawBioAssay
object when you know the id.
- getById(DbControl, int) - Static method in class net.sf.basedb.core.Reporter
-
- getById(DbControl, int, Experiment) - Static method in class net.sf.basedb.core.Reporter
-
Get a
ReporterData
object when you know the ID, possibly
using the cloned reporter annotations of the given experiment.
- getById(DbControl, int) - Static method in class net.sf.basedb.core.ReporterCloneTemplate
-
Get a reporter clone template item when you know the id.
- getById(DbControl, int) - Static method in class net.sf.basedb.core.ReporterList
-
Get a ReporterList
item when you know the ID.
- getById(DbControl, int) - Static method in class net.sf.basedb.core.ReporterType
-
Get a ReporterType
object when you know the ID.
- getById(DbControl, int) - Static method in class net.sf.basedb.core.Role
-
Get a Role
item when you know the ID.
- getById(DbControl, int) - Static method in class net.sf.basedb.core.RoleKey
-
Get a RoleKey
item when you know the ID.
- getById(DbControl, int) - Static method in class net.sf.basedb.core.RootRawBioAssay
-
Get a RootRawBioAssay
item when you know the id.
- getById(DbControl, int) - Static method in class net.sf.basedb.core.Sample
-
Get an Sample
item when you know the id.
- getById(DbControl, int) - Static method in class net.sf.basedb.core.Session
-
Get a Session
item when you know the ID.
- getById(DbControl, int) - Static method in class net.sf.basedb.core.Setting
-
Get a Setting
item when you know the ID.
- getById(DbControl, int) - Static method in class net.sf.basedb.core.Software
-
Get a Software
item when you know the ID.
- getById(DbControl, int) - Static method in class net.sf.basedb.core.SyncFilter
-
Get a SyncFilter
item when you know the id.
- getById(DbControl, int) - Static method in class net.sf.basedb.core.Tag
-
Get a Tag
item when you know the id.
- getById(DbControl, int) - Static method in class net.sf.basedb.core.Transformation
-
Get a Transformation
item when you know the id.
- getById(DbControl, int) - Static method in class net.sf.basedb.core.Unit
-
Get a Unit
object when you know the ID.
- getById(DbControl, int) - Static method in class net.sf.basedb.core.User
-
Get a User
item when you know the ID.
- getById(DbControl, int) - Static method in class net.sf.basedb.core.UserClientSetting
-
Get a UserClientSetting
item when you know the ID.
- getById(DbControl, int) - Static method in class net.sf.basedb.core.UserDefaultSetting
-
Get a UserDefaultSetting
item when you know the ID.
- getById(DbControl, int) - Static method in class net.sf.basedb.core.VirtualDb
-
Get a VirtualDb
item when you know the id.
- getById(DbControl, int) - Static method in class net.sf.basedb.core.Well
-
Get a Well
item when you know the id.
- getByInterfaceName(DbControl, String) - Static method in class net.sf.basedb.core.PluginType
-
Get a PluginType
object when you know the interface
name it represents.
- getByItemType(DbControl, Item) - Static method in class net.sf.basedb.core.RoleKey
-
Get a
RoleKey
item when you know the
Item
type.
- getByName(DbControl, BasicItem, String) - Static method in class net.sf.basedb.core.AnyToAny
-
Get an AnyToAny
link when you know the item
it is linking from and the name of the link.
- getByPath(DbControl, Path) - Static method in class net.sf.basedb.core.Directory
-
Get a Directory
item when you know the path.
- getByPath(DbControl, Path, boolean) - Static method in class net.sf.basedb.core.File
-
Get a File
item when you know the path.
- getBytes() - Method in class net.sf.basedb.core.data.DataCubeData
-
The number of bytes the analysed data in this cube occupies on disk.
- getBytes() - Method in class net.sf.basedb.core.data.DataCubeExtraValueData
-
The number of bytes the extra values data occupies on disk.
- getBytes() - Method in class net.sf.basedb.core.data.DataCubeFilterData
-
The number of bytes the analysed data in this cube occupies on disk.
- getBytes() - Method in class net.sf.basedb.core.data.DataCubeLayerData
-
The number of bytes the analysed data in this cube occupies on disk.
- getBytes() - Method in class net.sf.basedb.core.data.DiskUsageData
-
- getBytes() - Method in class net.sf.basedb.core.data.ExperimentData
-
The number of bytes the analysed data in this experiment occupies on disk.
- getBytes() - Method in class net.sf.basedb.core.data.RawBioAssayData
-
The number of bytes the raw data occupies on disk.
- getBytes() - Method in class net.sf.basedb.core.data.ReporterCloneTemplateData
-
The number of bytes the cloned reporter information uses in the
dynamic database.
- getBytes() - Method in class net.sf.basedb.core.DataCube
-
Gets the number of bytes the analysed data in this cube occupies on disk.
- getBytes() - Method in class net.sf.basedb.core.DataCubeExtraValue
-
Get the number of bytes the data stored in this layer occupies on disk.
- getBytes() - Method in class net.sf.basedb.core.DataCubeFilter
-
Get the number of bytes the data stored in this filter occupies on disk.
- getBytes() - Method in class net.sf.basedb.core.DataCubeLayer
-
Get the number of bytes the data stored in this layer occupies on disk.
- getBytes() - Method in interface net.sf.basedb.core.DiskConsumable
-
Get the absolute number of bytes this item uses.
- getBytes() - Method in class net.sf.basedb.core.DiskUsage
-
- getBytes() - Method in class net.sf.basedb.core.Experiment
-
- getBytes() - Method in class net.sf.basedb.core.File
-
- getBytes() - Method in class net.sf.basedb.core.RawBioAssay
-
- getBytes() - Method in class net.sf.basedb.core.ReporterCloneTemplate
-
Get the number of bytes the cloned reporter information use in
the database.
- getBytes() - Method in class net.sf.basedb.core.SpotImage
-
Get the number of bytes of the image.
- getBytesPerRow(RawDataType) - Method in enum net.sf.basedb.core.VirtualTable
-
- getBytesPerRow(Experiment) - Method in enum net.sf.basedb.core.VirtualTable
-
- getBytesPerRow(VirtualDb) - Method in enum net.sf.basedb.core.VirtualTable
-
Get the number of bytes a single row in the database occupies.
- getCachedDownloadStream() - Method in class net.sf.basedb.core.File
-
Get a (possible) cached stream for reading from the file.
- getCachedObject(Object) - Method in class net.sf.basedb.util.overview.GenericOverview
-
Retreive an object stored in the overview cache.
- getCachedObject(Object) - Method in interface net.sf.basedb.util.overview.OverviewContext
-
Retreive an object stored in the overview cache.
- getCachedQuery(String) - Method in class net.sf.basedb.core.hibernate.AbstractQueryCache
-
Get a cached query.
- getCacheKey(int) - Static method in class net.sf.basedb.core.snapshot.SnapshotManager
-
The static cache key under which the snapshot for the
annotation set with the given id is cached.
- getCacheMode() - Method in class net.sf.basedb.core.hibernate.QueryWrapper
-
- getCacheMode() - Method in class net.sf.basedb.core.hibernate.SessionWrapper
-
- getCacheRegion() - Method in class net.sf.basedb.core.hibernate.QueryWrapper
-
- getCacheSize() - Method in class net.sf.basedb.clients.web.ExperimentExplorer
-
The number of reporter id'd to cache.
- getCaseSensitiveVarchar(int) - Method in class net.sf.basedb.core.dbengine.AbstractDbEngine
-
Return null.
- getCaseSensitiveVarchar(int) - Method in interface net.sf.basedb.core.dbengine.DbEngine
-
Generate a column declaration that creates a case-sensitive
variable-length string column type.
- getCaseSensitiveVarchar(int) - Method in class net.sf.basedb.core.dbengine.MySQLEngine
-
Return varchar(length) CHARACTER SET utf8 COLLATE utf8_bin
.
- getCatalog() - Method in class net.sf.basedb.core.ServiceSessionControl
-
- getCatalogName(String, String) - Method in class net.sf.basedb.core.dbengine.AbstractDbEngine
-
Return the catalog name.
- getCatalogName(String, String) - Method in interface net.sf.basedb.core.dbengine.DbEngine
-
Get the catalog name to use for referencing the given catalog/schema
pair.
- getCatalogName(String, String) - Method in class net.sf.basedb.core.dbengine.MySQLEngine
-
Generates a catalog name by combining the catalog and
schema name (catalog_schema).
- getCategories() - Method in class net.sf.basedb.core.AnnotationType
-
Get a query that returns the categories an
annotation type belongs to.
- getCategories() - Method in class net.sf.basedb.core.data.AnnotationTypeData
-
Get the set that manages the categories of this annotation type.
- getCertificate(InputStream, String, String) - Static method in class net.sf.basedb.util.ssl.SSLUtil2
-
Get the certificate that is found in the given input stream.
- getCertificateChain(String) - Method in class net.sf.basedb.util.ssl.StaticKeyManager
-
- getChangeHistory() - Method in class net.sf.basedb.core.data.ChangeHistoryDetailData
-
Get the main history entry the details belong to.
- getChangeInfo() - Method in class net.sf.basedb.core.ChangeHistory
-
Get some additional free-text information about the change.
- getChangeInfo() - Method in class net.sf.basedb.core.data.ChangeHistoryDetailData
-
Get more information about this change.
- getChangesBy(User) - Static method in class net.sf.basedb.core.ChangeHistory
-
Get all changes made by the specified user.
- getChangesBy(Job) - Static method in class net.sf.basedb.core.ChangeHistory
-
Get all changes made by the specified job.
- getChangesIn(Session) - Static method in class net.sf.basedb.core.ChangeHistory
-
Get all changes made in the specified session.
- getChangeType() - Method in class net.sf.basedb.core.ChangeHistory
-
Get the type of change that was made.
- getChangeType() - Method in class net.sf.basedb.core.data.ChangeHistoryDetailData
-
The type of the change:
1 = create, 2 = update, 3 = delete
- getChangeType() - Method in class net.sf.basedb.core.log.EntityDetails
-
Was it a creation/update/deletion?
- getChangeType() - Method in class net.sf.basedb.core.log.ManualLogEntry
-
Get the change type.
- getChannel() - Method in class net.sf.basedb.core.RawDataProperty
-
Get the channel this property belongs to.
- getChannels() - Method in class net.sf.basedb.core.data.FormulaData
-
The number of required channels in the experiment to use this formula, or
0 if the number of channels doesn't matter.
- getChannels() - Method in class net.sf.basedb.core.data.PlatformData
-
The number of channels this platform uses.
- getChannels() - Method in class net.sf.basedb.core.data.PlatformVariantData
-
The number of channels this platform variant uses.
- getChannels() - Method in class net.sf.basedb.core.Formula
-
Get the number of channels required to be able to use this formula.
- getChannels() - Method in class net.sf.basedb.core.RawDataType
-
The number of channels in this raw data type.
- getCharacterSet() - Method in class net.sf.basedb.core.data.FileData
-
Get the character set used in this file (for text-files only).
- getCharacterSet() - Method in class net.sf.basedb.core.File
-
Get the character set used in this file (for text-files only).
- getCharacterSet() - Method in class net.sf.basedb.core.plugin.ImportInputStream
-
Get the character set used by the source if it is a text-file.
- getCharacterSet() - Method in class net.sf.basedb.util.FileImportInputStream
-
- getCharacterSet() - Method in class net.sf.basedb.util.importer.BaseFileWrapper
-
- getCharacterSet() - Method in class net.sf.basedb.util.importer.DiskFileWrapper
-
- getCharacterSet() - Method in interface net.sf.basedb.util.importer.FileWrapper
-
Get the character set used in the file.
- getCharacterSet() - Method in class net.sf.basedb.util.importer.spotdata.BaseFileInfo
-
Get the character set used by the file, or null if not known.
- getCharacterSet() - Method in class net.sf.basedb.util.uri.UriMetadata
-
Get the character set used by the resource.
- getCharset() - Static method in class net.sf.basedb.core.Config
-
Get the default character set to use when no other has been
specified.
- getCharset() - Method in class net.sf.basedb.plugins.AbstractFlatFileImporter
-
Get the character set the file uses.
- getCharset(Request) - Method in class net.sf.basedb.plugins.AbstractFlatFileImporter
-
Get the character set the file uses.
- getChart() - Method in class net.sf.basedb.util.plot.HistogramPlot
-
Get the underlying JFreeChar object.
- getChart() - Method in class net.sf.basedb.util.plot.ScatterPlot
-
Get the underlying JFreeChar object.
- getChild() - Method in class net.sf.basedb.util.importer.spotdata.BaseFileInfo.ChildBioAssay
-
Get the real child bioassay object once it has been created
and scheduled for saving into the database.
- getChild(String) - Method in class net.sf.basedb.util.overview.Node
-
Get the child node with a specific name.
- getChildAssay(int) - Method in class net.sf.basedb.util.importer.spotdata.BaseFileInfo
-
Get the child bioassay with the given id (from the BASEfile).
- getChildAssays() - Method in class net.sf.basedb.util.importer.spotdata.BaseFileInfo
-
Get information about all child bioassays referenced in the file.
- getChildColumns(short) - Method in class net.sf.basedb.util.importer.spotdata.BaseFileInfo
-
Get all child columns that have been mapped to the specified parent
column.
- getChildCreationEvents() - Method in class net.sf.basedb.core.BioMaterial
-
Get a query returning all events where this biomaterial has been used
as a source item.
- getChildCreationEvents() - Method in class net.sf.basedb.core.data.BioMaterialData
-
This is the inverse end.
- getChildDescriptionParameter(String, String, String) - Method in class net.sf.basedb.core.plugin.AbstractAnalysisPlugin
-
Create a plugin parameter that asks for the description of the child bioassay set.
- getChildErrors() - Method in class net.sf.basedb.util.overview.Node
-
Get the number of errors to children of this node.
- getChildExtracts() - Method in class net.sf.basedb.core.Extract
-
Creates a query that returns all child (pooled) extracts that
has this extracts as one of it's sources.
- getChildHasDifferentReporterPositionMapping() - Method in class net.sf.basedb.util.importer.spotdata.BaseFileInfo
-
A flag that indicates if the child data has a different position/reporter
mapping than the parent bioassay set.
- getChildId() - Method in class net.sf.basedb.core.data.keyring.GroupGroups
-
Get the id of the child group.
- getChildNameParameter(String, String, String) - Method in class net.sf.basedb.core.plugin.AbstractAnalysisPlugin
-
Create a plugin parameter that asks for the name of the child bioassay set.
- getChildNodeDirection() - Method in class net.sf.basedb.util.overview.Node
-
Get the direction to use when loading children of this node.
- getChildPlates() - Method in class net.sf.basedb.core.Plate
-
Get a query returning the child plates of this plate.
- getChildren() - Method in class net.sf.basedb.clients.web.ExperimentExplorer.InExpression
-
- getChildren() - Method in class net.sf.basedb.core.AnnotationRestriction
-
- getChildren() - Method in class net.sf.basedb.core.AnnotationSet.ProjectSpecificAnnotationsRestriction
-
- getChildren() - Method in class net.sf.basedb.core.data.BioAssayData
-
- getChildren() - Method in class net.sf.basedb.core.data.BioMaterialData
-
This is the inverse end.
- getChildren() - Method in class net.sf.basedb.core.data.DerivedBioAssayData
-
This is the inverse end.
- getChildren() - Method in class net.sf.basedb.core.data.GroupData
-
Get the set that manages which other groups are members of this group.
- getChildren() - Method in class net.sf.basedb.core.data.PlateData
-
The childs plates created by plate mappings.
- getChildren() - Method in class net.sf.basedb.core.DerivedBioAssay
-
Get all child derived bioassays.
- getChildren() - Method in class net.sf.basedb.core.DynamicJoin
-
- getChildren() - Method in class net.sf.basedb.core.DynamicRestriction
-
- getChildren() - Method in class net.sf.basedb.core.ExtraValueExpression
-
- getChildren() - Method in class net.sf.basedb.core.ExtraValueJoin
-
- getChildren() - Method in class net.sf.basedb.core.MeanRawDataPropertyExpression
-
- getChildren() - Method in class net.sf.basedb.core.query.AbsExpression
-
- getChildren() - Method in class net.sf.basedb.core.query.AddExpression
-
- getChildren() - Method in class net.sf.basedb.core.query.AndRestriction
-
- getChildren() - Method in class net.sf.basedb.core.query.AnnotationJoin
-
- getChildren() - Method in class net.sf.basedb.core.query.AnyToAnyRestriction
-
- getChildren() - Method in class net.sf.basedb.core.query.AscOrder
-
- getChildren() - Method in class net.sf.basedb.core.query.BetweenRestriction
-
- getChildren() - Method in class net.sf.basedb.core.query.BooleanExpression
-
- getChildren() - Method in class net.sf.basedb.core.query.CaseExpression
-
- getChildren() - Method in class net.sf.basedb.core.query.ConditionalQueryElement
-
- getChildren() - Method in class net.sf.basedb.core.query.CountExpression
-
- getChildren() - Method in class net.sf.basedb.core.query.DescOrder
-
- getChildren() - Method in class net.sf.basedb.core.query.DivideExpression
-
- getChildren() - Method in class net.sf.basedb.core.query.EqRestriction
-
- getChildren() - Method in class net.sf.basedb.core.query.ExpExpression
-
- getChildren() - Method in class net.sf.basedb.core.query.ExpressionSelect
-
- getChildren() - Method in class net.sf.basedb.core.query.FloatExpression
-
- getChildren() - Method in class net.sf.basedb.core.query.GeometricMeanExpression
-
- getChildren() - Method in class net.sf.basedb.core.query.GteqRestriction
-
- getChildren() - Method in class net.sf.basedb.core.query.GtRestriction
-
- getChildren() - Method in class net.sf.basedb.core.query.HqlElementsExpression
-
- getChildren() - Method in class net.sf.basedb.core.query.HqlEntityExpression
-
- getChildren() - Method in class net.sf.basedb.core.query.HqlEntityParameterExpression
-
- getChildren() - Method in class net.sf.basedb.core.query.HqlExpression
-
- getChildren() - Method in class net.sf.basedb.core.query.HqlIndexExpression
-
- getChildren() - Method in class net.sf.basedb.core.query.HqlInnerJoin
-
- getChildren() - Method in class net.sf.basedb.core.query.HqlLeftJoin
-
- getChildren() - Method in class net.sf.basedb.core.query.HqlPropertyExpression
-
- getChildren() - Method in class net.sf.basedb.core.query.HqlRightJoin
-
- getChildren() - Method in class net.sf.basedb.core.query.HqlSizeExpression
-
- getChildren() - Method in class net.sf.basedb.core.query.InRestriction
-
- getChildren() - Method in class net.sf.basedb.core.query.IntegerExpression
-
- getChildren() - Method in class net.sf.basedb.core.query.LikeRestriction
-
- getChildren() - Method in class net.sf.basedb.core.query.LogExpression
-
- getChildren() - Method in class net.sf.basedb.core.query.LteqRestriction
-
- getChildren() - Method in class net.sf.basedb.core.query.LtRestriction
-
- getChildren() - Method in class net.sf.basedb.core.query.MaxExpression
-
- getChildren() - Method in class net.sf.basedb.core.query.MeanExpression
-
- getChildren() - Method in class net.sf.basedb.core.query.MinExpression
-
- getChildren() - Method in class net.sf.basedb.core.query.MultiplyExpression
-
- getChildren() - Method in class net.sf.basedb.core.query.NegateExpression
-
- getChildren() - Method in class net.sf.basedb.core.query.NeqRestriction
-
- getChildren() - Method in class net.sf.basedb.core.query.NotRestriction
-
- getChildren() - Method in class net.sf.basedb.core.query.OrRestriction
-
- getChildren() - Method in class net.sf.basedb.core.query.ParameterExpression
-
- getChildren() - Method in class net.sf.basedb.core.query.PermissionRestriction
-
- getChildren() - Method in class net.sf.basedb.core.query.PowerExpression
-
- getChildren() - Method in class net.sf.basedb.core.query.QuadraticMeanExpression
-
- getChildren() - Method in interface net.sf.basedb.core.query.QueryElement
-
Get the children of this query element or null if it has no children.
- getChildren() - Method in class net.sf.basedb.core.query.ReporterListExpression
-
- getChildren() - Method in class net.sf.basedb.core.query.RlikeRestriction
-
- getChildren() - Method in class net.sf.basedb.core.query.SelectedExpression
-
- getChildren() - Method in class net.sf.basedb.core.query.SharedToRestriction
-
- getChildren() - Method in class net.sf.basedb.core.query.SqlColumnExpression
-
- getChildren() - Method in class net.sf.basedb.core.query.SqrtExpression
-
- getChildren() - Method in class net.sf.basedb.core.query.SubqueryExpression
-
- getChildren() - Method in class net.sf.basedb.core.query.SubtractExpression
-
- getChildren() - Method in class net.sf.basedb.core.query.SumExpression
-
- getChildren() - Method in class net.sf.basedb.core.query.ToDateExpression
-
- getChildren() - Method in class net.sf.basedb.core.query.VirtualColumnExpression
-
- getChildren() - Method in class net.sf.basedb.core.query.VirtualColumnExpression.WrappedExpression
-
- getChildren() - Method in class net.sf.basedb.core.RawBioAssayPropertyExpression
-
- getChildren() - Method in class net.sf.basedb.core.RawDataPropertyExpression
-
- getChildren() - Method in class net.sf.basedb.core.RealJoin
-
- getChildren() - Method in class net.sf.basedb.core.ReporterListJoin
-
- getChildren() - Method in class net.sf.basedb.core.ReporterPropertyExpression
-
- getChildren() - Method in class net.sf.basedb.util.overview.Node
-
Get all child nodes of this node.
- getChildren() - Method in class net.sf.basedb.util.Tree.Entry
-
Get the list of entries for the children to this node.
- getChildReporterPositions() - Method in class net.sf.basedb.util.importer.spotdata.BaseFileInfo
-
Get a map with all added child position/reporter mappings.
- getChildSamples() - Method in class net.sf.basedb.core.Sample
-
Creates a query that returns all child (pooled) samples that
has this sample as one of it's sources.
- getChildWarnings() - Method in class net.sf.basedb.util.overview.Node
-
Get the number of warnings to children of this node.
- getCircularRef(Node, BasicItem) - Static method in class net.sf.basedb.util.overview.OverviewUtil
-
Find the first parent node that has a reference to the given item.
- getClasses() - Static method in class net.sf.basedb.core.ExtendedProperties
-
Get a list with the name of all classes.
- getClassLoader() - Method in class net.sf.basedb.core.hibernate.SessionFactoryConfiguration
-
Deprecated.
Get the schema.
- getClassLoader() - Method in class net.sf.basedb.core.ServiceSessionControl.SessionFactoryConfiguration
-
Get the class loader used for accessing mapped classes.
- getClassLoader() - Method in class net.sf.basedb.util.extensions.ExtensionContext
-
The class loader is the class loader that loaded the action
factory of the extension.
- getClassLoader() - Method in class net.sf.basedb.util.extensions.ExtensionPointContext
-
The class loader is the class loader that loaded the action
class of the extension point.
- getClassLoader() - Method in class net.sf.basedb.util.extensions.InvokationContext
-
Get the class loader that is used for the given extension
or extension point.
- getClassLoader() - Method in class net.sf.basedb.util.extensions.manager.ExtensionsFile
-
Get the class loader used to load classes for the extension.
- getClassLoader() - Method in class net.sf.basedb.util.extensions.Registry.RegisteredExtension
-
- getClassLoader() - Method in class net.sf.basedb.util.extensions.Registry.RegisteredExtensionPoint
-
- getClassMapping(String) - Static method in class net.sf.basedb.core.HibernateUtil
-
- getClassMappings() - Static method in class net.sf.basedb.core.HibernateUtil
-
- getClassMetadata(String) - Static method in class net.sf.basedb.core.HibernateUtil
-
- getClassName() - Method in class net.sf.basedb.core.data.PluginDefinitionData
-
Get the class name of the Java class that implements this plugin.
- getClassName() - Method in class net.sf.basedb.core.PluginDefinition
-
Get the class name of the Java class that implements this plugin.
- getClassName() - Method in class net.sf.basedb.util.extensions.xml.PluginInfo
-
Get the class name of the plug-in.
- getClazz() - Method in class net.sf.basedb.clients.web.extensions.list.AbstractListColumnBean
-
- getClazz() - Method in interface net.sf.basedb.clients.web.extensions.list.ListColumnAction
-
Optional HTML class attribute that is used to style the column
through CSS.
- getClazz() - Method in class net.sf.basedb.clients.web.extensions.login.FieldInfo
-
Get a class attribute that can used to style the input field.
- getClazz() - Method in class net.sf.basedb.clients.web.extensions.menu.FixedMenuItemFactory
-
- getClazz() - Method in interface net.sf.basedb.clients.web.extensions.menu.MenuItemAction
-
Class attribute to add to the main menu tag.
- getClazz() - Method in class net.sf.basedb.clients.web.extensions.menu.MenuItemBean
-
- getClazz() - Method in class net.sf.basedb.clients.web.extensions.tabcontrol.FixedTabFactory
-
- getClazz() - Method in class net.sf.basedb.clients.web.extensions.tabcontrol.IncludeContentTabFactory.Tab
-
- getClazz() - Method in interface net.sf.basedb.clients.web.extensions.tabcontrol.TabAction
-
Class attribute of the main tab tag.
- getClazz() - Method in class net.sf.basedb.clients.web.extensions.tabcontrol.TabBean
-
- getClazz() - Method in interface net.sf.basedb.clients.web.extensions.toolbar.ButtonAction
-
Class attribute of the main button tag.
- getClazz() - Method in class net.sf.basedb.clients.web.extensions.toolbar.ButtonBean
-
- getClazz() - Method in class net.sf.basedb.clients.web.extensions.toolbar.FixedButtonFactory
-
- getClazz() - Method in class net.sf.basedb.clients.web.taglib.Body
-
- getClazz() - Method in class net.sf.basedb.clients.web.taglib.ExceptionCatcher
-
- getClazz() - Method in class net.sf.basedb.clients.web.taglib.StylableTag
-
- getClazz() - Method in class net.sf.basedb.clients.web.taglib.tab.Tab
-
- getClazz() - Method in class net.sf.basedb.clients.web.taglib.table.Button.ButtonActionWrapper
-
- getClazz() - Method in class net.sf.basedb.clients.web.taglib.table.Cell
-
- getClazz() - Method in class net.sf.basedb.clients.web.taglib.table.CellValue
-
- getClearState() - Method in class net.sf.basedb.core.PluginResponse
-
If set after a job configuration sequence, the saved state should
be cleared before starting the job.
- getClient(DbControl, ChangeHistory, boolean, boolean) - Static method in class net.sf.basedb.clients.web.ChangeHistoryUtil
-
Get the client application that was used to make the change in HTML format.
- getClient(DbControl) - Method in class net.sf.basedb.core.ChangeHistory
-
Load the client application that was used when the change was made.
- getClient() - Method in class net.sf.basedb.core.ClientDefaultSetting
-
Get the client application this setting is valid for.
- getClient() - Method in class net.sf.basedb.core.data.ChangeHistoryData
-
- getClient() - Method in class net.sf.basedb.core.data.ClientDefaultSettingData
-
Get the client application this setting is valid for.
- getClient() - Method in class net.sf.basedb.core.data.ContextData
-
Get the client which uses this context.
- getClient() - Method in class net.sf.basedb.core.data.ContextIndex
-
Get the client which uses this context.
- getClient() - Method in class net.sf.basedb.core.data.HelpData
-
Get the client for this help text.
- getClient() - Method in class net.sf.basedb.core.data.SessionData
-
Get the client application the user was using.
- getClient() - Method in class net.sf.basedb.core.data.UserClientSettingData
-
Get the client application this setting is valid for.
- getClient() - Method in class net.sf.basedb.core.Help
-
Get the client application this setting is valid for.
- getClient() - Method in class net.sf.basedb.core.Session
-
Get the client application the user was using in this session.
- getClient() - Method in class net.sf.basedb.core.UserClientSetting
-
Get the client application this setting is valid for.
- getClientAliases(String, Principal[]) - Method in class net.sf.basedb.util.ssl.StaticKeyManager
-
- getClientCertificate() - Method in class net.sf.basedb.core.data.FileServerData
-
Get the client certificate that we need to send to the server
to make the server accept our connection.
- getClientCertificate() - Method in class net.sf.basedb.core.FileServer
-
Get the client certificate that BASE should use to authenticate with the server
when connecting with https.
- getClientCertificate() - Method in class net.sf.basedb.util.uri.ConnectionParameters
-
Get the client certificate that BASE should use to authenticate with the server
when connecting using SSL.
- getClientCertificatePassword() - Method in class net.sf.basedb.core.data.FileServerData
-
Get the password that is used to unlock the client certificate.
- getClientCertificatePassword() - Method in class net.sf.basedb.core.FileServer
-
Get the password that is needed to unlock the client
certificate.
- getClientCertificatePassword() - Method in class net.sf.basedb.util.uri.ConnectionParameters
-
Get the password that is needed to unlock the client certificate.
- getClientContext() - Method in class net.sf.basedb.util.extensions.ExtensionContext
-
- getClientContext() - Method in class net.sf.basedb.util.extensions.ExtensionPointContext
-
- getClientContext() - Method in class net.sf.basedb.util.extensions.InvokationContext
-
- getClientDefaultSetting(String) - Method in class net.sf.basedb.core.SessionControl
-
- getClientId() - Method in class net.sf.basedb.core.ChangeHistory
-
Get the ID of the client application that was used to
make the change.
- getClientId() - Method in class net.sf.basedb.core.data.ChangeHistoryData
-
The ID of the client application the user used to make the change.
- getClientId() - Method in class net.sf.basedb.core.log.TransactionDetails
-
Get the ID of the client appliction that is used, or 0 if not known.
- getClientId() - Method in class net.sf.basedb.core.SessionControl
-
Get the id of the Client
application in use.
- getClientSettings() - Method in class net.sf.basedb.core.data.UserData
-
This is the inverse end.
- getClientSettings(Client) - Method in class net.sf.basedb.core.User
-
Get a query that returns the settings for the
specified client.
- getClientWithExternalId(String) - Method in class net.sf.basedb.core.SessionControl
-
- getClientX509Certificate() - Method in class net.sf.basedb.core.FileServer
-
Get the X.509 certificate for the client.
- getClonableProperties() - Method in class net.sf.basedb.core.ReporterCloneTemplate
-
Get a list with all clonable properties in this template.
- getClonableProperties(ReporterCloneTemplateData) - Static method in class net.sf.basedb.core.ReporterCloneTemplate
-
- getClonableProperty(String) - Method in class net.sf.basedb.core.ReporterCloneTemplate
-
Get information about a clonable property that is included in this template.
- getClone() - Method in class net.sf.basedb.util.annotations.InheritSpecification
-
- getClonedSelectSql(VirtualDb) - Static method in class net.sf.basedb.core.Reporter
-
Generate an SQL statement for selecting ALL reporter properties from a cloned
table.
- getCmd() - Method in class net.sf.basedb.clients.jobagent.CmdLine
-
Get the command parameter
- getCollected() - Method in class net.sf.basedb.util.listable.CollectExtracts
-
Get all extracts that has been collected.
- getCollectedChildren() - Method in class net.sf.basedb.util.listable.CollectExtracts
-
- getCollectedParents() - Method in class net.sf.basedb.util.listable.CollectExtracts
-
- getCollectionSeparatorParameter() - Method in class net.sf.basedb.clients.web.plugins.SimpleExport
-
- getColor() - Method in class net.sf.basedb.clients.web.ExperimentExplorer.AnnotationGroup
-
Get a color code for HTML that is as distinct as possible from
the color of the other groups.
- getColor(String) - Method in class net.sf.basedb.clients.web.servlet.ExperimentExplorerPlotServlet.ColumnKey
-
- getColor(float) - Method in class net.sf.basedb.util.ColorGenerator
-
Get the color for the value.
- getColorFormatter(SessionControl, Coloring, Formatter<Number>) - Static method in class net.sf.basedb.clients.web.formatter.FormatterFactory
-
Get a formatter that adds a color box to the display which is a visual representation
of the value.
- getColorGenerator(SessionControl, Coloring) - Static method in class net.sf.basedb.clients.web.Base
-
- getColoring() - Method in class net.sf.basedb.core.data.ExtraValueTypeData
-
Get the coloring information for this extra value type.
- getColoring() - Method in class net.sf.basedb.core.data.FormulaData
-
Get the coloring information for this formula.
- getColoring() - Method in class net.sf.basedb.core.ExtraValueType
-
Get coloring information for this extra value.
- getColoring() - Method in class net.sf.basedb.core.Formula
-
Get coloring information for this formula.
- getColspan() - Method in class net.sf.basedb.clients.web.taglib.table.Header
-
- getColumn() - Method in class net.sf.basedb.clients.web.taglib.table.Cell
-
- getColumn() - Method in class net.sf.basedb.core.BioWell
-
Gets the column index where this well is located.
- getColumn() - Method in class net.sf.basedb.core.data.BioWellData
-
The column coordinate of this well.
- getColumn() - Method in class net.sf.basedb.core.data.FeatureData
-
Get the column coordinate of the feature.
- getColumn() - Method in class net.sf.basedb.core.data.MappingCoordinate
-
Get the column number.
- getColumn() - Method in class net.sf.basedb.core.data.PlateCoordinate
-
Get the column number.
- getColumn() - Method in class net.sf.basedb.core.data.RawData
-
- getColumn() - Method in class net.sf.basedb.core.data.ReporterClonePropertyData
-
Get the name of database column.
- getColumn() - Method in class net.sf.basedb.core.data.WellData
-
The column coordinate of this well.
- getColumn() - Method in class net.sf.basedb.core.ExtendedProperty
-
Get the database column of the extended property.
- getColumn() - Method in class net.sf.basedb.core.FeatureCoordinate
-
- getColumn(String) - Static method in class net.sf.basedb.core.RawBioAssayPropertyExpression
-
- getColumn(RawDataType, String) - Static method in class net.sf.basedb.core.RawDataPropertyExpression
-
Get the database column name for the specified property of the
specified raw data type.
- getColumn(String) - Static method in class net.sf.basedb.core.ReporterPropertyExpression
-
- getColumn() - Method in class net.sf.basedb.core.VirtualColumn
-
Get the database column name of the column.
- getColumn() - Method in class net.sf.basedb.core.Well
-
Get the column coordinate of this well on the plate.
- getColumnContent() - Method in class net.sf.basedb.clients.web.taglib.table.Table
-
- getColumnCount() - Method in class net.sf.basedb.util.bfs.AnnotationModel
-
Get the number of column.
- getColumnCount() - Method in class net.sf.basedb.util.bfs.AnnotationWriter
-
Get the number of data columns.
- getColumnCount() - Method in class net.sf.basedb.util.bfs.DataWriter
-
Get the number of data columns.
- getColumnCount() - Method in class net.sf.basedb.util.bfs.MatrixModel
-
Get the number of columns.
- getColumnHeaderIndex(String) - Method in class net.sf.basedb.util.parser.FlatFileParser
-
Get the index of a column header with a given name.
- getColumnHeaders() - Method in class net.sf.basedb.util.parser.FlatFileParser
-
- getColumnIndex(String) - Method in class net.sf.basedb.util.bfs.AnnotationModel
-
Get the column index for a given header.
- getColumnMappingParameterName() - Method in class net.sf.basedb.plugins.batchimport.FallbackIdMethod
-
- getColumnMappingParameterName() - Method in class net.sf.basedb.plugins.batchimport.FileImporter.PathIdMethod
-
- getColumnMappingParameterName() - Method in interface net.sf.basedb.plugins.batchimport.IdMethod
-
- getColumnMappingParameterName() - Method in class net.sf.basedb.plugins.batchimport.InternalIdMethod
-
- getColumnMappingParameterName() - Method in class net.sf.basedb.plugins.batchimport.MultiPropertyIdMethod
-
- getColumnMappingParameterName() - Method in class net.sf.basedb.plugins.batchimport.PropertyIdMethod
-
- getColumnName(RawDataProperty, RawBioAssay) - Static method in class net.sf.basedb.plugins.IlluminaRawDataImporter
-
Convert a raw data property to a column name.
- getColumnNo() - Method in class net.sf.basedb.core.data.DataCubeColumnData
-
The column number of this column in the data cube.
- getColumnNo() - Method in class net.sf.basedb.core.DataCubeColumn
-
Get the number of this column.
- getColumnPrefixParameter() - Method in class net.sf.basedb.clients.web.plugins.SimpleExport
-
- getColumns() - Method in class net.sf.basedb.clients.web.taglib.table.Table
-
- getColumns() - Method in class net.sf.basedb.core.BioPlate
-
Get the number of rows on this plate.
- getColumns() - Method in class net.sf.basedb.core.data.DataCubeData
-
This is the inverse end.
- getColumns() - Method in class net.sf.basedb.core.data.PlateGeometryData
-
The number of rows in this geometry.
- getColumns() - Method in class net.sf.basedb.core.dbengine.TableInfo
-
Get information about the columns in the table.
- getColumns() - Method in class net.sf.basedb.core.dbengine.TableInfo.IndexInfo
-
- getColumns() - Method in class net.sf.basedb.core.dbengine.TableInfo.PrimaryKeyInfo
-
- getColumns() - Method in class net.sf.basedb.core.PlateGeometry
-
Get the number of columns in this geometry.
- getColumns(RawDataType) - Method in enum net.sf.basedb.core.VirtualTable
-
- getColumns(VirtualDb) - Method in enum net.sf.basedb.core.VirtualTable
-
Get all columns in this table.
- getColumns(Experiment) - Method in enum net.sf.basedb.core.VirtualTable
-
Get all columns in this table.
- getColumnsFile(TableInfo) - Method in class net.sf.basedb.core.Migration
-
Get the columns file for the given table.
- getCommand() - Method in class net.sf.basedb.core.plugin.NamespaceRequestWrapper
-
- getCommand() - Method in interface net.sf.basedb.core.plugin.Request
-
The command the plugin should execute.
- getCommand() - Method in class net.sf.basedb.core.PluginRequest
-
- getCommand() - Method in class net.sf.basedb.core.PluginRequest.RequestImpl
-
- getCommand() - Method in class net.sf.basedb.core.RequestInformation
-
Get the command this request information object is valid for.
- getCommand() - Method in class net.sf.basedb.plugins.executor.ExternalProgramExecutor.RequestWrapper
-
- getComment() - Method in class net.sf.basedb.core.authentication.LoginRequest
-
Get the comment to use.
- getComment() - Method in class net.sf.basedb.core.BioMaterialEvent
-
Get the comment about this event.
- getComment() - Method in class net.sf.basedb.core.data.BioMaterialEventData
-
Get the comment about this event.
- getComment() - Method in class net.sf.basedb.core.data.PlateEventData
-
Get the comment about this event.
- getComment() - Method in class net.sf.basedb.core.hibernate.QueryWrapper
-
- getComment() - Method in class net.sf.basedb.core.PlateEvent
-
Get the comment about this event.
- getCommonCharsets() - Static method in class net.sf.basedb.core.Config
-
Get a set containing the most common character sets used by text files.
- getCommonName() - Method in class net.sf.basedb.plugins.Base1PluginExecuter.JobParameter
-
- getCommonPrefix(Collection<String>) - Static method in class net.sf.basedb.core.StringUtil
-
Find the longest common prefix for a collection of strings.
- getCompleted() - Method in class net.sf.basedb.core.SimpleAbsoluteProgressReporter
-
Get completed number of ticks of the task.
- getCompressedSize() - Method in class net.sf.basedb.core.data.FileData
-
Get the size in bytes that this FileData
object
uses after compression.
- getCompressedSize() - Method in class net.sf.basedb.core.File
-
Get the compressed size of this file.
- getCondition() - Method in class net.sf.basedb.core.dbengine.TableInfo.IndexInfo
-
If a condition is specificed a partial index is
created for rows that matches the conditions.
- getCondition() - Method in class net.sf.basedb.core.query.WhenStatement
-
Get the condition of this statement.
- getConfigDirectory() - Static method in class net.sf.basedb.core.Config
-
Get the directory where the BASE configuration files are located.
- getConfigurationInstallOption(int) - Method in class net.sf.basedb.plugins.PluginConfigurationImporter
-
Returns if a configuration in a certain place/order in the XML-file should be imported
- getConfigurations() - Method in class net.sf.basedb.core.data.PluginDefinitionData
-
This is the inverse end.
- getConfigurationValues() - Method in class net.sf.basedb.core.data.PluginConfigurationData
-
Used by Hibernate to link with configuration values.
- getConfiguredColors(SessionControl) - Static method in class net.sf.basedb.clients.web.Base
-
- getConfiguredJobParameters() - Method in class net.sf.basedb.plugins.HelpImporter
-
- getConfiguredJobParameters() - Method in class net.sf.basedb.plugins.PluginConfigurationImporter
-
- getConfiguredQuery(DbControl, ItemContext, boolean, ItemQuery<T>, ModeInfo) - Static method in class net.sf.basedb.clients.web.Base
-
Configures a query.
- getConfiguredSelectionParameters() - Method in class net.sf.basedb.plugins.PluginConfigurationImporter
-
Gets request information to set which configuration to import
- getConfigureExecutorParameters(String) - Method in class net.sf.basedb.plugins.executor.BaseFileExporterSupport
-
- getConfigureExecutorParameters(String) - Method in class net.sf.basedb.plugins.executor.BaseFileImporterSupport
-
- getConfigureExecutorParameters(String) - Method in class net.sf.basedb.plugins.executor.BfsExporterSupport
-
- getConfigureExecutorParameters(String) - Method in class net.sf.basedb.plugins.executor.BfsImporterSupport
-
- getConfigureExecutorParameters(String) - Method in class net.sf.basedb.plugins.executor.FileOnlyImporterSupport
-
- getConfigureExportImportPluginParameters() - Method in class net.sf.basedb.plugins.executor.ExternalProgramExecutor
-
- getConfigureExternalParameters() - Method in class net.sf.basedb.plugins.executor.ExternalProgramExecutor
-
- getConfigureImportParameters(GuiContext) - Method in class net.sf.basedb.plugins.AnnotationFlatFileImporter
-
Step 3 of 3.
- getConfigureJobParameters(GuiContext) - Method in class net.sf.basedb.clients.web.plugins.SimpleExport
-
- getConfigureJobParameters() - Method in class net.sf.basedb.plugins.Base1PluginExecuter
-
Creates the information needed for job configuration and initiates the
parameters.
- getConfigureJobParameters(GuiContext, Boolean) - Method in class net.sf.basedb.plugins.BaseFileExporterPlugin
-
- getConfigureJobParameters(GuiContext) - Method in class net.sf.basedb.plugins.BfsExporterPlugin
-
- getConfigureJobParameters(GuiContext) - Method in class net.sf.basedb.plugins.CdfFileReporterImporter
-
- getConfigureJobParameters(String) - Method in class net.sf.basedb.plugins.executor.BaseFileImporterSupport
-
- getConfigureJobParameters(String) - Method in class net.sf.basedb.plugins.executor.BfsImporterSupport
-
- getConfigureJobParameters() - Method in class net.sf.basedb.plugins.executor.ExternalProgramExecutor
-
- getConfigureJobParameters(String) - Method in class net.sf.basedb.plugins.executor.FileOnlyImporterSupport
-
- getConfigureJobParameters(GuiContext) - Method in class net.sf.basedb.plugins.FormulaFilter
-
- getConfigureJobParameters(Boolean) - Method in class net.sf.basedb.plugins.GalExporter
-
- getConfigureJobParameters(Boolean) - Method in class net.sf.basedb.plugins.HelpExporter
-
- getConfigureJobParameters(GuiContext) - Method in class net.sf.basedb.plugins.IlluminaRawDataImporter
-
- getConfigureJobParameters() - Method in class net.sf.basedb.plugins.IntensityCalculatorPlugin
-
- getConfigureJobParameters() - Method in class net.sf.basedb.plugins.JepExtraValueCalculator
-
- getConfigureJobParameters(GuiContext) - Method in class net.sf.basedb.plugins.JepIntensityTransformer
-
- getConfigureJobParameters() - Method in class net.sf.basedb.plugins.LowessNormalization
-
- getConfigureJobParameters(GuiContext) - Method in class net.sf.basedb.plugins.ManualDerivedBioAssayCreator
-
- getConfigureJobParameters(GuiContext) - Method in class net.sf.basedb.plugins.ManualTransformCreator
-
- getConfigureJobParameters() - Method in class net.sf.basedb.plugins.MedianRatioNormalization
-
- getConfigureJobParameters(GuiContext, Boolean) - Method in class net.sf.basedb.plugins.PackedFileExporter
-
- getConfigureJobParameters(GuiContext) - Method in class net.sf.basedb.plugins.PlateFlatFileImporter
-
- getConfigureJobParameters(GuiContext, Boolean) - Method in class net.sf.basedb.plugins.PlateMappingExporter
-
- getConfigureJobParameters(GuiContext) - Method in class net.sf.basedb.plugins.PlateMappingImporter
-
- getConfigureJobParameters(Boolean) - Method in class net.sf.basedb.plugins.PluginConfigurationExporter
-
- getConfigureJobParameters(GuiContext) - Method in class net.sf.basedb.plugins.PrintMapFlatFileImporter
-
- getConfigureJobParameters(GuiContext) - Method in class net.sf.basedb.plugins.RawDataFlatFileImporter
-
- getConfigureJobParameters(GuiContext) - Method in class net.sf.basedb.plugins.ReporterFlatFileImporter
-
- getConfigureJobParameters(GuiContext) - Method in class net.sf.basedb.plugins.ReporterMapFlatFileImporter
-
- getConfigureJobParameters(GuiContext) - Method in class net.sf.basedb.util.zip.AbstractFileUnpacker
-
- getConfigureMappingParameters(GuiContext) - Method in class net.sf.basedb.plugins.AnnotationFlatFileImporter
-
Step 2 of 3.
- getConfigureOptionsParameters(GuiContext) - Method in class net.sf.basedb.plugins.batchimport.AbstractItemImporter
-
- getConfigureParserParameters(GuiContext, boolean) - Method in class net.sf.basedb.plugins.AnnotationFlatFileImporter
-
- getConfigureParserParameters(GuiContext, boolean) - Method in class net.sf.basedb.plugins.batchimport.AbstractItemImporter
-
- getConfigureParserParameters(RawDataType) - Method in class net.sf.basedb.plugins.RawDataFlatFileImporter
-
- getConfigurePluginParameters() - Method in class net.sf.basedb.plugins.Base1PluginExecuter
-
Creates the information needed for plugin configuration and initiates the
parameters.
- getConfigurePluginParameters() - Method in class net.sf.basedb.plugins.executor.ExternalProgramExecutor
-
- getConfigurePluginParameters(GuiContext) - Method in class net.sf.basedb.plugins.gtf.GtfReporterMapImporter
-
- getConfigurePluginParameters(GuiContext) - Method in class net.sf.basedb.plugins.ManualDerivedBioAssayCreator
-
- getConfigurePluginParameters(GuiContext) - Method in class net.sf.basedb.plugins.ManualTransformCreator
-
- getConfigurePluginParameters() - Method in class net.sf.basedb.plugins.PackedFileExporter
-
- getConfigurePluginParameters(GuiContext) - Method in class net.sf.basedb.plugins.PlateFlatFileImporter
-
- getConfigurePluginParameters(GuiContext) - Method in class net.sf.basedb.plugins.ReporterFlatFileImporter
-
- getConfigurePluginParameters(GuiContext) - Method in class net.sf.basedb.plugins.ReporterMapFlatFileImporter
-
- getConfigureRawDataTypeParameters() - Method in class net.sf.basedb.plugins.RawDataFlatFileImporter
-
- getConnection(Session) - Static method in class net.sf.basedb.core.HibernateUtil
-
Get the underlying JDBC connection from the Hibernate session.
- getConnection(Integer) - Method in class net.sf.basedb.core.JobAgent
-
Get a connection object for connecting to the job agent.
- getConnectionManagerFactory() - Method in class net.sf.basedb.core.data.FileServerData
-
Get the ID of the connection manager factory that should be
used to retreieve the file contents and metadata.
- getConnectionManagerFactoryId() - Method in class net.sf.basedb.core.FileServer
-
Get the ID of the connection manager factory that should be
used to access file contents and metadata.
- getConnectionManagerFactoryId() - Method in class net.sf.basedb.util.uri.ConnectionParameters
-
Get the connection manager factory that we should use to
access the file, or null to use auto-detection.
- getConnectionProperties() - Static method in class net.sf.basedb.core.HibernateUtil
-
Read database configuration properties from the base.config file
and map them to Hibernate settings.
- getConstructor() - Method in enum net.sf.basedb.core.Item
-
Get the default constructor for new objects of this type.
- getContact() - Method in class net.sf.basedb.core.data.PluginDefinitionData
-
Get contact information for the plugin.
- getContact() - Method in interface net.sf.basedb.core.plugin.About
-
Contact information to get more information about the plugin.
- getContact() - Method in class net.sf.basedb.core.plugin.AboutImpl
-
- getContact() - Method in class net.sf.basedb.core.PluginDefinition
-
Get contact information for the plugin.
- getContact() - Method in class net.sf.basedb.util.extensions.AboutBean
-
- getContact() - Method in class net.sf.basedb.util.extensions.Registry.RegisteredAbout
-
- getContent() - Method in class net.sf.basedb.clients.web.extensions.section.IncludeContentSectionFactory.Section
-
- getContent() - Method in interface net.sf.basedb.clients.web.extensions.section.SectionAction
-
Get the (HTML) contents of the section.
- getContent() - Method in class net.sf.basedb.clients.web.extensions.section.SectionBean
-
- getContent() - Method in class net.sf.basedb.clients.web.extensions.tabcontrol.FixedTabFactory
-
- getContent() - Method in class net.sf.basedb.clients.web.extensions.tabcontrol.IncludeContentTabFactory.Tab
-
- getContent() - Method in interface net.sf.basedb.clients.web.extensions.tabcontrol.TabAction
-
Get the (HTML) contents of the tab.
- getContent() - Method in class net.sf.basedb.clients.web.extensions.tabcontrol.TabBean
-
- getContent() - Method in class net.sf.basedb.clients.web.taglib.tab.Tab
-
- getContentLength(HttpResponse) - Static method in class net.sf.basedb.util.HttpUtil
-
Get the content length from the headers in the response.
- getContentStyle() - Method in class net.sf.basedb.clients.web.extensions.section.IncludeContentSectionFactory.Section
-
- getContentStyle() - Method in interface net.sf.basedb.clients.web.extensions.section.SectionAction
-
Extra CSS style attributes that will be added to the
style
attribute of the content section tag.
- getContentStyle() - Method in class net.sf.basedb.clients.web.extensions.section.SectionBean
-
- getContentstyle() - Method in class net.sf.basedb.clients.web.taglib.HideableSection
-
- getContentstyle() - Method in class net.sf.basedb.clients.web.taglib.tab.TabControl
-
- getContentType(HttpResponse) - Static method in class net.sf.basedb.util.HttpUtil
-
Get the content type of the content from the headers
in the response.
- getContext() - Method in class net.sf.basedb.clients.web.taglib.HideableSection
-
- getContext(int) - Method in class net.sf.basedb.core.SessionControl
-
Load a context without making it the current context.
- getContextId() - Method in class net.sf.basedb.core.ItemContext
-
Get the database ID of this context.
- getContextItem() - Method in class net.sf.basedb.core.data.JobData
-
The item type of the context that was active when configuring
this job. null = no context was known
- getContextMessage() - Method in class net.sf.basedb.util.ContextUtil.ContextResult
-
- getContextMessages(Collection<ContextUtil.ContextResult>, boolean, boolean) - Static method in class net.sf.basedb.util.ContextUtil
-
Get all messages from plug-in / configurations combinations that can't be used.
- getContextNames(Item) - Method in class net.sf.basedb.core.SessionControl
-
Same as: getContextNames(item, "")
- getContextNames(Item, String) - Method in class net.sf.basedb.core.SessionControl
-
Get a list with the names of all named contexts for a given item and
subcontext.
- getContexts() - Method in class net.sf.basedb.core.data.ClientData
-
This is the inverse end.
- getContexts() - Method in class net.sf.basedb.core.data.UserData
-
The saved contexts for the user.
- getContextType() - Method in class net.sf.basedb.core.data.GuiContextData
-
- getContextType() - Method in class net.sf.basedb.core.data.JobData
-
The context type that was active when configuring
this job. 0 = single item, 1 = list
- getConvertedValue(String, Method) - Method in class net.sf.basedb.util.extensions.xml.XmlLoader
-
- getConverter(PostfixMathCommandI, Operator) - Method in class net.sf.basedb.util.jep.convert.ASTFunNodeConverter
-
Get a converter by first checking the if one exists for the given function,
and then for the given operator symbol.
- getConverter(Object) - Static method in class net.sf.basedb.util.jep.convert.ConverterFactory
-
Get a converter for the specified built-in JEP object.
- getConverterByClass(Object) - Static method in class net.sf.basedb.util.jep.convert.ConverterFactory
-
Get a converter for the specified built-in JEP object by checking if
a converter has been registered for it's class.
- getConverters() - Static method in class net.sf.basedb.util.jep.convert.ConverterFactory
-
Get all registered converters.
- getCookie(HttpServletRequest, String) - Static method in class net.sf.basedb.clients.web.Base
-
Get the cookie with the specified name.
- getCookieValue(HttpServletRequest, String) - Static method in class net.sf.basedb.clients.web.Base
-
Get the value of the cookie with the specified name.
- getCoordinate() - Method in class net.sf.basedb.core.BioWell
-
Get a string representation of the coordinate for this well.
- getCoordinateType() - Method in class net.sf.basedb.core.data.DataCubeExtraValueData
-
If the extra value is a spot extra value, a position extra value
or a column extra value.
- getCoordinateType() - Method in class net.sf.basedb.core.DataCubeExtraValue
-
Get the coordinate type the extra values are attached to.
- getCoordinateType() - Method in class net.sf.basedb.core.ExtraValue
-
Get information about which coordinates in the data cube
the extra values are attached to.
- getCopyAnnotationsParmeter(String, String, Boolean) - Method in class net.sf.basedb.core.plugin.AbstractPlugin
-
Parameter definition that asks if annotations should be copied from the
plug-in definition/configuration to other items.
- getCopyright() - Method in class net.sf.basedb.core.data.PluginDefinitionData
-
Get a copyright notice for the plugin.
- getCopyright() - Method in interface net.sf.basedb.core.plugin.About
-
A copyright notice.
- getCopyright() - Method in class net.sf.basedb.core.plugin.AboutImpl
-
- getCopyright() - Method in class net.sf.basedb.core.PluginDefinition
-
Get a copyright notice for the plugin.
- getCopyright() - Method in class net.sf.basedb.util.extensions.AboutBean
-
- getCopyright() - Method in class net.sf.basedb.util.extensions.Registry.RegisteredAbout
-
- getCoreTimer() - Static method in class net.sf.basedb.core.Application
-
- getCount(int) - Method in class net.sf.basedb.clients.web.ExperimentExplorer.AnnotationGroup
-
Get the number of intensity values added to the specified channel.
- getCount() - Method in class net.sf.basedb.util.plot.HistogramPlot.HistogramBin
-
Get the number of values in this bin.
- getCountHqlQuery(DbControl) - Method in class net.sf.basedb.core.AbstractHqlQuery
-
Build the count query and set parameter values for it.
- getCountQuery(DbControl, boolean) - Method in class net.sf.basedb.core.AbstractQuery
-
Build the query string for returning the total count.
- getCountQuery(boolean) - Method in class net.sf.basedb.util.export.spotdata.BaseFileExporter
-
Get a configured query that counts the number of data lines that is about to
be written in a data section.
- getCpuUsage() - Method in class net.sf.basedb.core.JobAgent
-
Get the current CPU usage in percent of the server where the job agent is running.
- getCpuUsage() - Method in class net.sf.basedb.util.jobagent.JobAgentInfo
-
Get the CPU usage in percent.
- getCreated() - Method in class net.sf.basedb.clients.jobagent.slotmanager.MasterSlotManager.RemoteSlot
-
- getCreated() - Method in class net.sf.basedb.core.data.JobData
-
Get the date and time the job was created.
- getCreated() - Method in class net.sf.basedb.core.Job
-
Get the date and time the job was registered in the database.
- getCreateForeignKeySql(String, String, String, String, Set<String>, String, Set<String>) - Method in interface net.sf.basedb.core.dbengine.DbEngine
-
Generates SQL that creates a foreign key constraint between two tables.
- getCreateForeignKeySql(String, String, String, String, Set<String>, String, Set<String>) - Method in class net.sf.basedb.core.dbengine.DefaultDbEngine
-
- getCreateForeignKeySql(String, String, String, String, Set<String>, String, Set<String>) - Method in class net.sf.basedb.core.dbengine.MySQLEngine
-
Generate alter table schema.table add constraint name
foreign key (columns) references refTable (refColumns)
- getCreateForeignKeySql(String, String, String, String, Set<String>, String, Set<String>) - Method in class net.sf.basedb.core.dbengine.PostgresDbEngine
-
Generate alter table schema.table add constraint name
foreign key (columns) references refTable (refColumns)
- getCreateIndexSql(String, String, String, String, Set<String>, boolean) - Method in interface net.sf.basedb.core.dbengine.DbEngine
-
Generate SQL to create an index.
- getCreateIndexSql(String, String, String, String, Set<String>, boolean) - Method in class net.sf.basedb.core.dbengine.DefaultDbEngine
-
Generates
create [unique] index <name> on
<catalog>.
- getCreateIndexSql(String, String, String, String, Set<String>, boolean) - Method in class net.sf.basedb.core.dbengine.MySQLEngine
-
Generate alter table <catalog>.
- getCreateIndexSql(String, String, String, String, Set<String>, boolean) - Method in class net.sf.basedb.core.dbengine.PostgresDbEngine
-
Generate alter table <schema>.
- getCreatePartialIndexSql(String, String, String, String, Set<String>, String) - Method in class net.sf.basedb.core.dbengine.AbstractDbEngine
-
Default implementation returns a regular non-unique index.
- getCreatePartialIndexSql(String, String, String, String, Set<String>, String) - Method in interface net.sf.basedb.core.dbengine.DbEngine
-
Generate SQL to create a partial index.
- getCreatePartialIndexSql(String, String, String, String, Set<String>, String) - Method in class net.sf.basedb.core.dbengine.PostgresDbEngine
-
Creates a partial index which is the same as a regular index + 'WHERE [condition]';
- getCreatePrimaryKeySql(String, String, String, String, Set<String>) - Method in interface net.sf.basedb.core.dbengine.DbEngine
-
Generate SQL to create a primary key for a table.
- getCreatePrimaryKeySql(String, String, String, String, Set<String>) - Method in class net.sf.basedb.core.dbengine.DefaultDbEngine
-
- getCreatePrimaryKeySql(String, String, String, String, Set<String>) - Method in class net.sf.basedb.core.dbengine.MySQLEngine
-
Generate alter table catalog.table add primary key (columns)
- getCreatePrimaryKeySql(String, String, String, String, Set<String>) - Method in class net.sf.basedb.core.dbengine.PostgresDbEngine
-
Generate alter table schema.table add constraint name
primary key (columns)
.
- getCreateSchemaSql(String, String) - Method in interface net.sf.basedb.core.dbengine.DbEngine
-
Generate an SQL statement to create the given schema.
- getCreateSchemaSql(String, String) - Method in class net.sf.basedb.core.dbengine.DefaultDbEngine
-
Generate create schema <catalog>.
- getCreateSchemaSql(String, String) - Method in class net.sf.basedb.core.dbengine.MySQLEngine
-
Generate create schema <catalog>
.
- getCreateSchemaSql(String, String) - Method in class net.sf.basedb.core.dbengine.PostgresDbEngine
-
Generate create schema <schema>
.
- getCreationEvent() - Method in class net.sf.basedb.core.data.MeasuredBioMaterialData
-
Get the event that created this biomaterial.
- getCreationEvent() - Method in class net.sf.basedb.core.data.PhysicalBioAssayData
-
Get the event that created this bioassay.
- getCreationEvent() - Method in class net.sf.basedb.core.MeasuredBioMaterial
-
Get the event that represents the creation of this biomaterial.
- getCreationEvent() - Method in class net.sf.basedb.core.PhysicalBioAssay
-
Get the event that represents the creation of this hybridization.
- getCryptedPassword() - Method in class net.sf.basedb.core.data.PasswordData
-
Get the crypted password.
- getCubeNo() - Method in class net.sf.basedb.core.data.DataCubeData
-
The cube number of this cube in the virtual database.
- getCubeNo() - Method in class net.sf.basedb.core.DataCube
-
Get the number of this data cube.
- getCubes() - Method in class net.sf.basedb.core.data.VirtualDbData
-
The number of data cubes in the virtual database.
- getCubes() - Method in class net.sf.basedb.core.VirtualDb
-
Get the number of
DataCube
:s in this virtual database.
- getCurrent() - Method in class net.sf.basedb.clients.web.taglib.Select
-
- getCurrentBioAssaySet(DbControl) - Method in class net.sf.basedb.core.plugin.AbstractAnalysisPlugin
-
Get the current source bioassay set.
- getCurrentBioAssaySet(DbControl) - Method in class net.sf.basedb.plugins.executor.ExternalProgramExecutor
-
Get the bioassay set that is used as the source for the job.
- GetCurrentCatalogWork - Class in net.sf.basedb.core.hibernate
-
A work implementation that return the name of the current database catalog.
- GetCurrentCatalogWork() - Constructor for class net.sf.basedb.core.hibernate.GetCurrentCatalogWork
-
Create a new work item.
- getCurrentConfiguration(DbControl) - Method in class net.sf.basedb.core.plugin.AbstractPlugin
-
Get the plug-in configuration that this is currently in use or null.
- getCurrentConfigurationParameterValues(String) - Method in class net.sf.basedb.core.PluginRequest
-
Get the values that are currently stored in the plugin configuration
related to this request.
- getCurrentContext(Item) - Method in class net.sf.basedb.core.SessionControl
-
Same as: getCurrentContext(item, "", null)
.
- getCurrentContext(Item, String) - Method in class net.sf.basedb.core.SessionControl
-
Same as: getCurrentContext(item, subContext, null)
.
- getCurrentContext(Item, ItemContext) - Method in class net.sf.basedb.core.SessionControl
-
Same as: getCurrentContext(item, "", defaultContext)
.
- getCurrentContext(Item, String, ItemContext) - Method in class net.sf.basedb.core.SessionControl
-
Get the current context.
- getCurrentDerivedBioAssay(DbControl) - Method in class net.sf.basedb.core.plugin.AbstractAnalysisPlugin
-
Get the current source derived bioassay.
- getCurrentDirectory(DbControl) - Method in class net.sf.basedb.util.zip.AbstractFileUnpacker
-
Get the current directory or null there is no current or it can't be loaded.
- getCurrentExperiment(DbControl) - Method in class net.sf.basedb.core.plugin.AbstractAnalysisPlugin
-
Get the current experiment from information in the current context:
SessionControl.getCurrentContext(Item.EXPERIMENT)
.
- getCurrentFile() - Method in class net.sf.basedb.plugins.RawDataFlatFileImporter.FileIterator
-
- getCurrentFile(DbControl) - Method in class net.sf.basedb.util.zip.AbstractFileUnpacker
-
Get the current file or null there is no current or it can't be loaded.
- getCurrentFilename() - Method in class net.sf.basedb.clients.web.fileupload.FileUploadProgress
-
Get the name of the file that is currently beeing transferred.
- getCurrentItem() - Method in class net.sf.basedb.util.extensions.ClientContext
-
Get the currently active item.
- getCurrentJob(DbControl) - Method in class net.sf.basedb.core.plugin.AbstractPlugin
-
Get the job that is executing this plugin or null.
- getCurrentJobParameterValues(String) - Method in class net.sf.basedb.core.PluginRequest
-
Get the values that are currently stored in the job related to this
request.
- getCurrentLine() - Method in class net.sf.basedb.util.bfs.AnnotationParser
-
- getCurrentLine() - Method in interface net.sf.basedb.util.bfs.BfsParser
-
Get the current line number.
- getCurrentLine() - Method in class net.sf.basedb.util.bfs.DataParser
-
- getCurrentLine() - Method in class net.sf.basedb.util.bfs.MetadataParser
-
- getCurrentLine() - Method in class net.sf.basedb.util.importer.spotdata.SynchronizedSpotDataParser
-
- getCurrentLockMode(Object) - Method in class net.sf.basedb.core.hibernate.SessionWrapper
-
- getCurrentMapper() - Static method in class net.sf.basedb.clients.web.extensions.skin.ImageRemapperUtil
-
Get the current image remapper.
- getCurrentMatchingSource(DbControl) - Method in class net.sf.basedb.core.SyncFilter
-
Get the number of items that is currently matching this filter.
- getCurrentNodeName() - Method in class net.sf.basedb.util.overview.node.BioWellNameGenerator
-
- getCurrentOverview(SessionControl) - Static method in class net.sf.basedb.util.overview.OverviewUtil
-
Get the currently cached overview.
- getCurrentParameterValue(String) - Method in class net.sf.basedb.core.PluginRequest
-
- getCurrentParameterValues(String) - Method in class net.sf.basedb.core.PluginRequest
-
Get the values that are currently stored in the job or plugin configuration
related to this request.
- getCurrentPosition() - Method in class net.sf.basedb.util.importer.spotdata.PositionEventHandler
-
Get the current position.
- getCurrentRawBioAssay() - Method in class net.sf.basedb.plugins.RawDataFlatFileImporter.FileIterator
-
- getCurrentSection() - Method in class net.sf.basedb.util.basefile.BaseFileWriter
-
- getCurrentSection() - Method in class net.sf.basedb.util.bfs.MetadataWriter
-
Get the name of the current section.
- getCurrentSessionId() - Method in class net.sf.basedb.core.SessionControl
-
Get the id of the current user session, or 0 if no user is logged in.
- getCurrentTitlePrefix() - Method in class net.sf.basedb.util.overview.node.BioWellNameGenerator
-
- getCurrentValue() - Method in class net.sf.basedb.clients.web.taglib.table.ExtensionCells
-
Get the value for the current column and item.
- getCustomRequestHandlerClasses() - Method in class net.sf.basedb.clients.jobagent.Agent
-
- getData(DbControl, ExportedProperty, I) - Method in class net.sf.basedb.clients.web.extensions.list.ListColumnDataLoader
-
- getData(DbControl, ExportedProperty, AnnotationType) - Method in class net.sf.basedb.clients.web.plugins.AnnotationTypeEnumerationLoader
-
- getData(DbControl, ExportedProperty, AnnotationType) - Method in class net.sf.basedb.clients.web.plugins.AnnotationTypeItemTypesLoader
-
- getData(DbControl, ExportedProperty, BasicItem) - Method in class net.sf.basedb.clients.web.plugins.AnyToAnyDataLoader
-
- getData(DbControl, ExportedProperty, BioAssay) - Method in class net.sf.basedb.clients.web.plugins.BioAssayExperimentalFactorLoader
-
- getData(DbControl, ExportedProperty, ChangeHistory) - Method in class net.sf.basedb.clients.web.plugins.ChangeHistoryDetailLoader
-
- getData(DbControl, ExportedProperty, T) - Method in interface net.sf.basedb.clients.web.plugins.DataLoader
-
Get the value for the specified property.
- getData(DbControl, ExportedProperty, BasicData) - Method in class net.sf.basedb.clients.web.plugins.DataQueryWrapper
-
Uses a
Metadata
object to get the value of the specified property.
- getData(DbControl, ExportedProperty, SqlResult) - Method in class net.sf.basedb.clients.web.plugins.DynamicQueryWrapper
-
- getData(DbControl, ExportedProperty, FileStoreEnabled) - Method in class net.sf.basedb.clients.web.plugins.FileSetMemberLoader
-
- getData(DbControl, ExportedProperty, T) - Method in class net.sf.basedb.clients.web.plugins.ItemQueryLoader
-
- getData(DbControl, ExportedProperty, BasicItem) - Method in class net.sf.basedb.clients.web.plugins.ItemQueryWrapper
-
Uses a
Metadata
object to get the value of the specified property.
- getData(DbControl, ExportedProperty, BasicItem) - Method in class net.sf.basedb.clients.web.plugins.MapValueLoader
-
- getData(DbControl, ExportedProperty, MeasuredBioMaterial) - Method in class net.sf.basedb.clients.web.plugins.ParentBioMaterialEventSourceLoader
-
- getData(DbControl, ExportedProperty, PhysicalBioAssay) - Method in class net.sf.basedb.clients.web.plugins.ParentBioMaterialEventSourceLoaderFromBioAssay
-
- getData(DbControl, ExportedProperty, MeasuredBioMaterial) - Method in class net.sf.basedb.clients.web.plugins.ParentBioMaterialLoader
-
- getData(DbControl, ExportedProperty, Nameable) - Method in class net.sf.basedb.clients.web.plugins.PathLoader
-
- getData(DbControl, ExportedProperty, ReporterScore) - Method in class net.sf.basedb.clients.web.plugins.ReporterScoreQueryWrapper
-
Uses a
Metadata
object to get the value of the specified property.
- getData() - Method in class net.sf.basedb.core.AnnotatedItem
-
- getData() - Method in class net.sf.basedb.core.Annotation
-
- getData() - Method in class net.sf.basedb.core.AnnotationSet
-
- getData() - Method in class net.sf.basedb.core.AnnotationType
-
- getData() - Method in class net.sf.basedb.core.AnnotationTypeCategory
-
- getData() - Method in class net.sf.basedb.core.AnyToAny
-
- getData() - Method in class net.sf.basedb.core.ArrayBatch
-
- getData() - Method in class net.sf.basedb.core.ArrayDesign
-
- getData() - Method in class net.sf.basedb.core.ArrayDesignBlock
-
- getData() - Method in class net.sf.basedb.core.ArrayDesignPlate
-
- getData() - Method in class net.sf.basedb.core.ArraySlide
-
- getData() - Method in class net.sf.basedb.core.BasicItem
-
Get the
BasicData
object that holds all data for this item.
- getData() - Method in class net.sf.basedb.core.BioAssay
-
- getData() - Method in class net.sf.basedb.core.BioAssaySet
-
- getData() - Method in class net.sf.basedb.core.BioMaterial
-
- getData() - Method in class net.sf.basedb.core.BioMaterialEvent
-
- getData() - Method in class net.sf.basedb.core.BioPlate
-
- getData() - Method in class net.sf.basedb.core.BioPlateEvent
-
- getData() - Method in class net.sf.basedb.core.BioPlateEventParticipant
-
- getData() - Method in class net.sf.basedb.core.BioPlateEventType
-
- getData() - Method in class net.sf.basedb.core.BioPlateType
-
- getData() - Method in class net.sf.basedb.core.BioSource
-
- getData() - Method in class net.sf.basedb.core.BioWell
-
- getData() - Method in class net.sf.basedb.core.ChangeHistory
-
- getData() - Method in class net.sf.basedb.core.Client
-
- getData() - Method in class net.sf.basedb.core.ClientDefaultSetting
-
- getData() - Method in class net.sf.basedb.core.CommonItem
-
- getData() - Method in class net.sf.basedb.core.DataCube
-
- getData() - Method in class net.sf.basedb.core.DataCubeColumn
-
- getData() - Method in class net.sf.basedb.core.DataCubeExtraValue
-
- getData() - Method in class net.sf.basedb.core.DataCubeFilter
-
- getData() - Method in class net.sf.basedb.core.DataCubeLayer
-
- getData() - Method in class net.sf.basedb.core.DataFileType
-
- getData() - Method in class net.sf.basedb.core.DerivedBioAssay
-
- getData() - Method in class net.sf.basedb.core.Directory
-
- getData() - Method in class net.sf.basedb.core.DiskUsage
-
- getData() - Method in class net.sf.basedb.core.Experiment
-
- getData() - Method in class net.sf.basedb.core.Extract
-
- getData() - Method in class net.sf.basedb.core.ExtraValue
-
- getData() - Method in class net.sf.basedb.core.ExtraValueType
-
- getData() - Method in class net.sf.basedb.core.File
-
- getData() - Method in class net.sf.basedb.core.FileServer
-
- getData() - Method in class net.sf.basedb.core.FileSet
-
- getData() - Method in class net.sf.basedb.core.FileSetMember
-
- getData() - Method in class net.sf.basedb.core.Formula
-
- getData() - Method in class net.sf.basedb.core.GlobalDefaultSetting
-
- getData() - Method in class net.sf.basedb.core.Group
-
- getData() - Method in class net.sf.basedb.core.Hardware
-
- getData() - Method in class net.sf.basedb.core.Help
-
- getData(String, UserData, ClientData, boolean) - Method in class net.sf.basedb.core.ItemContext
-
Create a new database context object from this context.
- getData() - Method in class net.sf.basedb.core.ItemKey
-
- getData() - Method in class net.sf.basedb.core.ItemList
-
- getData() - Method in class net.sf.basedb.core.ItemSubtype
-
- getData() - Method in class net.sf.basedb.core.ItemSubtypeFileType
-
- getData() - Method in class net.sf.basedb.core.Job
-
- getData() - Method in class net.sf.basedb.core.JobAgent
-
- getData() - Method in class net.sf.basedb.core.JobAgentSettings
-
- getData() - Method in class net.sf.basedb.core.Kit
-
- getData() - Method in class net.sf.basedb.core.MeasuredBioMaterial
-
- getData() - Method in class net.sf.basedb.core.Message
-
- getData() - Method in class net.sf.basedb.core.MimeType
-
- getData() - Method in class net.sf.basedb.core.News
-
- getData() - Method in class net.sf.basedb.core.OwnedItem
-
- getData() - Method in class net.sf.basedb.core.PermissionTemplate
-
- getData() - Method in class net.sf.basedb.core.PhysicalBioAssay
-
- getData() - Method in class net.sf.basedb.core.Plate
-
- getData() - Method in class net.sf.basedb.core.PlateEvent
-
- getData() - Method in class net.sf.basedb.core.PlateEventType
-
- getData() - Method in class net.sf.basedb.core.PlateGeometry
-
- getData() - Method in class net.sf.basedb.core.PlateMapping
-
- getData() - Method in class net.sf.basedb.core.PlateType
-
- getData() - Method in class net.sf.basedb.core.Platform
-
- getData() - Method in class net.sf.basedb.core.PlatformFileType
-
- getData() - Method in class net.sf.basedb.core.PlatformVariant
-
- getData() - Method in class net.sf.basedb.core.PluginConfiguration
-
- getData() - Method in class net.sf.basedb.core.PluginDefinition
-
- getData() - Method in class net.sf.basedb.core.PluginType
-
- getData() - Method in class net.sf.basedb.core.Project
-
- getData() - Method in class net.sf.basedb.core.ProjectKey
-
- getData() - Method in class net.sf.basedb.core.PropertyFilter
-
Create a new database filter object from this filter.
- getData() - Method in class net.sf.basedb.core.Protocol
-
- getData() - Method in class net.sf.basedb.core.Quantity
-
- getData() - Method in class net.sf.basedb.core.Quota
-
- getData() - Method in class net.sf.basedb.core.QuotaType
-
- getData() - Method in class net.sf.basedb.core.RawBioAssay
-
- getData() - Method in class net.sf.basedb.core.ReporterCloneTemplate
-
- getData() - Method in class net.sf.basedb.core.ReporterList
-
- getData() - Method in class net.sf.basedb.core.ReporterScore
-
- getData() - Method in class net.sf.basedb.core.ReporterType
-
- getData() - Method in class net.sf.basedb.core.Role
-
- getData() - Method in class net.sf.basedb.core.RoleKey
-
- getData() - Method in class net.sf.basedb.core.RootRawBioAssay
-
- getData() - Method in class net.sf.basedb.core.Sample
-
- getData() - Method in class net.sf.basedb.core.Session
-
- getData() - Method in class net.sf.basedb.core.Setting
-
- getData() - Method in class net.sf.basedb.core.SharedItem
-
- getData() - Method in class net.sf.basedb.core.Software
-
- getData() - Method in class net.sf.basedb.core.SpotImages
-
- getData() - Method in class net.sf.basedb.core.SyncFilter
-
- getData() - Method in class net.sf.basedb.core.Tag
-
- getData() - Method in class net.sf.basedb.core.Transformation
-
- getData() - Method in class net.sf.basedb.core.Unit
-
- getData() - Method in class net.sf.basedb.core.User
-
- getData() - Method in class net.sf.basedb.core.UserClientSetting
-
- getData() - Method in class net.sf.basedb.core.UserDefaultSetting
-
- getData() - Method in class net.sf.basedb.core.VirtualDb
-
- getData() - Method in class net.sf.basedb.core.Well
-
- getData(int, int) - Method in class net.sf.basedb.util.bfs.AnnotationModel
-
Get the data element at a given row and column index.
- getData(int, String) - Method in class net.sf.basedb.util.bfs.AnnotationModel
-
Get the data element at a given row and column.
- getData(int, int) - Method in class net.sf.basedb.util.bfs.MatrixModel
-
Get the data element at a given row and column index.
- getData() - Method in class net.sf.basedb.util.importer.spotdata.SynchronizedSpotDataParser.SynchronizedData
-
Get the current data line, split into columns.
- getDatabaseVersionString() - Static method in class net.sf.basedb.core.Application
-
Gets the version of the database server
- getDataByName(Session, int, Item, String) - Static method in class net.sf.basedb.core.AnyToAny
-
Get an any-to-any link.
- getDataClass() - Method in enum net.sf.basedb.core.Item
-
Get the data object that is used to store information in the
database for items of this type.
- getDataClassName(Object) - Static method in class net.sf.basedb.core.log.EntityDetails
-
- getDataCube() - Method in class net.sf.basedb.core.BioAssaySet
-
Get the data cube this biossayset stores it's data in.
- getDataCube() - Method in class net.sf.basedb.core.data.DataCubeColumnData
-
Get the data cube this column belongs to.
- getDataCube() - Method in class net.sf.basedb.core.data.DataCubeExtraValueData
-
Get the data cube this filter belongs to.
- getDataCube() - Method in class net.sf.basedb.core.data.DataCubeFilterData
-
Get the data cube this filter belongs to.
- getDataCube() - Method in class net.sf.basedb.core.data.DataCubeLayerData
-
Get the data cube this layer belongs to.
- getDataCube() - Method in class net.sf.basedb.core.DataCubeColumn
-
Get the data cube this layer belongs to.
- getDataCube() - Method in class net.sf.basedb.core.DataCubeExtraValue
-
Get the data cube this extra value belongs to.
- getDataCube() - Method in class net.sf.basedb.core.DataCubeFilter
-
Get the data cube this filter belongs to.
- getDataCube() - Method in class net.sf.basedb.core.DataCubeLayer
-
Get the data cube this layer belongs to.
- getDataCube() - Method in class net.sf.basedb.core.DynamicQuery
-
- getDataCube() - Method in class net.sf.basedb.core.ExtraValue
-
- getDataCubeColumn() - Method in class net.sf.basedb.core.BioAssay
-
Get the DataCubeColumn
object where this bioassay
store it's data.
- getDataCubeColumn() - Method in class net.sf.basedb.core.data.BioAssayData
-
Get the column this bioassay stores it's data in.
- getDataCubeColumnNo() - Method in class net.sf.basedb.core.BioAssay
-
Get the column coordinate in the data cube that this bioassay
stores it's data in.
- getDataCubeExtraValue() - Method in class net.sf.basedb.core.data.ExtraValueData
-
Get the data cube extra value where the extra values are stored.
- getDataCubeExtraValue() - Method in class net.sf.basedb.core.ExtraValue
-
- getDataCubeFilter() - Method in class net.sf.basedb.core.BioAssaySet
-
Get the data cube filter this biossayset uses to filter spot data.
- getDataCubeFilter() - Method in class net.sf.basedb.core.data.BioAssaySetData
-
Get the filter used by this bioassayset.
- getDataCubeFilterNo() - Method in class net.sf.basedb.core.BioAssaySet
-
Get the number of the filter that this bioassayset is using, or 0 if
no filter is used.
- getDataCubeLayer() - Method in class net.sf.basedb.core.BioAssaySet
-
Get the data cube layer this biossayset stores it's data in.
- getDataCubeLayer() - Method in class net.sf.basedb.core.data.BioAssaySetData
-
Get the layer this bioassayset stores it's data in.
- getDataCubeLayerNo() - Method in class net.sf.basedb.core.BioAssay
-
Get the layer coordinate in the data cube that this bioassay stores it's data in.
- getDataCubeLayerNo() - Method in class net.sf.basedb.core.BioAssaySet
-
Get the layer coordinate in the data cube that this bioassayset stores it's data in.
- getDataCubeNo() - Method in class net.sf.basedb.core.BioAssay
-
Get the number of the data cube this bioassay stores it's data in.
- getDataCubeNo() - Method in class net.sf.basedb.core.BioAssaySet
-
Get the number of the data cube this bioassayset stores it's data in.
- getDataCubeNo() - Method in class net.sf.basedb.core.DataCubeColumn
-
Get the number of the data cube this layer belongs to.
- getDataCubeNo() - Method in class net.sf.basedb.core.DataCubeExtraValue
-
Get the number of the data cube this extra value belongs to.
- getDataCubeNo() - Method in class net.sf.basedb.core.DataCubeFilter
-
Get the number of the data cube this filter belongs to.
- getDataCubeNo() - Method in class net.sf.basedb.core.DataCubeLayer
-
Get the number of the data cube this layer belongs to.
- getDataCubeNo() - Method in class net.sf.basedb.core.ExtraValue
-
Get the number of the data cube the extra values are stored in.
- getDataCubes() - Method in class net.sf.basedb.core.data.VirtualDbData
-
This is the inverse end.
- getDataFile(DbControl, FileStoreEnabled, String, boolean) - Static method in class net.sf.basedb.core.FileStoreUtil
-
Get the file of the given data file type in the
FileStoreEnabled
item's file set assuming that at most
one file exists.
- getDataFile(TableInfo) - Method in class net.sf.basedb.core.Migration
-
Get the data file for the given table.
- getDataFile(TableInfo, boolean) - Method in class net.sf.basedb.core.Migration
-
Get the data file for the given table.
- getDataFileColumns(Item, String) - Static method in class net.sf.basedb.clients.web.Base
-
Get a query returning all data file types that are needed to display
file set members for the given columns.
- getDataFiles(DbControl, FileStoreEnabled, String, boolean) - Static method in class net.sf.basedb.core.FileStoreUtil
-
Get the file of the given data file type in the
FileStoreEnabled
item's file set.
- getDataFileType() - Method in class net.sf.basedb.core.data.FileSetMemberData
-
Get the type of this file.
- getDataFileType() - Method in class net.sf.basedb.core.data.FileTypeIndex
-
- getDataFileType() - Method in class net.sf.basedb.core.data.ItemSubtypeFileTypeData
-
Get the file type.
- getDataFileType() - Method in class net.sf.basedb.core.data.PlatformFileTypeData
-
Get the file type.
- getDataFileType() - Method in class net.sf.basedb.core.FileSetMember
-
Get the type of the file.
- getDataFileType() - Method in class net.sf.basedb.core.ItemSubtypeFileType
-
Get the type of the file.
- getDataFileType() - Method in class net.sf.basedb.core.PlatformFileType
-
Get the type of the file.
- getDataFileType() - Method in interface net.sf.basedb.core.UsableDataFileType
-
Get the data file type the information applies to.
- getDataFileType() - Method in class net.sf.basedb.util.overview.Fix
-
- getDataFileTypes(Item, FileStoreEnabled, Platform, PlatformVariant, ItemSubtype) - Static method in class net.sf.basedb.clients.web.Base
-
Get a query that returns all data file types for a specific
platform/variant/subtype that can be used on a given item type.
- getDataFileTypes() - Method in class net.sf.basedb.core.ItemSubtype
-
Get a query returning the data file types that have been
associated with this subtype.
- getDataSeparator() - Method in class net.sf.basedb.util.export.TableWriter
-
The data separator string is written between
each data column in the output.
- getDatatype() - Method in class net.sf.basedb.clients.web.taglib.table.ColumnDef
-
- getDatatype() - Method in class net.sf.basedb.clients.web.taglib.table.TableColumn
-
- getDataValue(Object) - Static method in class net.sf.basedb.core.Values
-
Convert an item values to a data value.
- getDataValues(List<?>) - Static method in class net.sf.basedb.core.Values
-
Convert a list of item values to data values.
- getDataWriterFactory() - Method in class net.sf.basedb.util.export.spotdata.BfsExporter
-
Get the factory that creates data writers.
- getDate(HttpResponse, String, Date) - Static method in class net.sf.basedb.util.HttpUtil
-
- getDate(String[], Formatter<Date>) - Static method in class net.sf.basedb.util.Values
-
- getDateFormat(SessionControl) - Static method in class net.sf.basedb.clients.web.formatter.FormatterSettings
-
Get format string for a date formatter.
- getDateFormat() - Method in class net.sf.basedb.util.formatter.DateFormatter
-
Get access to the underlying
DateFormat
object
used for formatting and parsing dates.
- getDateFormatter(SessionControl) - Static method in class net.sf.basedb.clients.web.formatter.FormatterFactory
-
Get the logged in user's date formatter.
- getDateTimeFormat(SessionControl) - Static method in class net.sf.basedb.clients.web.formatter.FormatterSettings
-
Get format string for a datetime formatter.
- getDateTimeFormatter(SessionControl) - Static method in class net.sf.basedb.clients.web.formatter.FormatterFactory
-
Get the logged in user's datetime formatter.
- getDateValues() - Method in class net.sf.basedb.core.data.annotations.AnnotationLink
-
- getDbcontrol() - Method in class net.sf.basedb.clients.web.taglib.PropertyValue
-
- getDbControl() - Method in class net.sf.basedb.core.AbstractBatcher
-
Get the
DbControl
object that currently manages this batcher.
- getDbControl() - Method in class net.sf.basedb.core.BasicItem
-
Get the
DbControl
object that currently manages this item.
- getDbControl() - Method in class net.sf.basedb.util.export.spotdata.AbstractBioAssaySetExporter
-
Get the current DbControl.
- getDbControl() - Method in class net.sf.basedb.util.export.spotdata.AbstractFieldConverter
-
Get the DbControl to use for database access.
- getDbControl() - Method in class net.sf.basedb.util.extensions.ClientContext
-
Get the current DbControl.
- getDbControl() - Method in class net.sf.basedb.util.importer.spotdata.BaseFileImporter
-
Get the current DbControl.
- getDbControl() - Method in class net.sf.basedb.util.importer.spotdata.BfsImporter
-
Get the current DbControl.
- getDbControl() - Method in class net.sf.basedb.util.listable.TransformContext
-
Get the DbControl to use in this transformation context.
- getDbControl() - Method in class net.sf.basedb.util.units.UnitCache
-
Get the DbControl that is currently used for database access.
- getDbEngine() - Static method in class net.sf.basedb.core.HibernateUtil
-
Get the database engine.
- getDecimalSeparator() - Method in class net.sf.basedb.plugins.AbstractFlatFileImporter
-
Get the decimal separator used by numbers in the file.
- getDecimalSeparator() - Method in class net.sf.basedb.plugins.IlluminaRawDataImporter
-
- getDefault() - Method in class net.sf.basedb.core.Presets
-
Get the default preset.
- getDefaultAnnotation() - Method in class net.sf.basedb.core.Annotation
-
Get the default annotation that this project-specific annotation is overriding.
- getDefaultClazz(int) - Method in class net.sf.basedb.clients.web.taglib.Body
-
- getDefaultErrorHandlerFactory() - Method in class net.sf.basedb.clients.web.extensions.ExtensionsControl
-
Get the default error handling factory.
- getDefaultErrorHandlerFactory() - Method in class net.sf.basedb.util.extensions.Registry
-
Get the default error handler factory.
- getDefaultFileExtension() - Method in interface net.sf.basedb.clients.web.plugins.ExportTemplate
-
Get the default file extension to give to files generated by this template.
- getDefaultFileExtension() - Method in class net.sf.basedb.clients.web.plugins.PlainTextTemplate
-
- getDefaultFileExtension() - Method in class net.sf.basedb.clients.web.plugins.XMLTemplate
-
- getDefaultId(String) - Method in class net.sf.basedb.clients.web.taglib.Button
-
- getDefaultImage(String) - Method in class net.sf.basedb.clients.web.taglib.Button
-
- getDefaultItemFunction(Item) - Method in class net.sf.basedb.plugins.batchimport.AbstractItemImporter
-
- getDefaultItems() - Method in class net.sf.basedb.core.data.ProjectData
-
The default items to use in this project
- getDefaultItems(DbControl) - Method in class net.sf.basedb.core.Project
-
Get a list with all default items added to this project.
- getDefaultItems(DbControl, Item) - Method in class net.sf.basedb.core.Project
-
Get a list with all default items of a given item type
added to this project.
- getDefaultKeyManagers() - Static method in class net.sf.basedb.util.ssl.SSLUtil2
-
Get the default keys manages as configured in the base.config file by
ssl.keystore.* settings.
- getDefaultNumberFormat() - Method in class net.sf.basedb.util.parser.FlatFileParser
-
Get the default number format.
- getDefaultPriority() - Method in enum net.sf.basedb.core.Job.ExecutionTime
-
The default thread priority to use when executing jobs in
with this execution time.
- getDefaultRawDataType() - Method in class net.sf.basedb.core.Project
-
Gets the default raw data type for this project.
- getDefaultReporterContext() - Method in class net.sf.basedb.clients.web.ExperimentExplorer
-
Get the default reporter context that is used to initialise the actual context.
- getDefaultSelects() - Method in class net.sf.basedb.core.AbstractSqlQuery
-
- getDefaultSelects() - Method in class net.sf.basedb.core.DataCube.RawMappingQuery
-
- getDefaultSelects() - Method in class net.sf.basedb.core.DynamicExtraValueQuery
-
Default selection: column, position, extraValue
- getDefaultSelects() - Method in class net.sf.basedb.core.DynamicPositionQuery
-
Default selection: position
- getDefaultSelects() - Method in class net.sf.basedb.core.DynamicRawDataQuery
-
No default selection.
- getDefaultSelects() - Method in class net.sf.basedb.core.DynamicReporterQuery
-
No default selection.
- getDefaultSelects() - Method in class net.sf.basedb.core.DynamicSpotQuery
-
Default selection: column, postion, ch1, ch2, ...
- getDefaultSetting(String) - Method in class net.sf.basedb.core.Client
-
Get the default setting with the specified name.
- getDefaultSettings() - Method in class net.sf.basedb.core.Client
-
Get a query that will return all default settings for this client.
- getDefaultSettings() - Method in class net.sf.basedb.core.data.ClientData
-
This is the inverse end.
- getDefaultSettings() - Method in class net.sf.basedb.core.data.UserData
-
This is the inverse end.
- getDefaultSettings() - Method in class net.sf.basedb.core.User
-
Get a query that returns all default settings for this user.
- getDefaultSeverity() - Method in interface net.sf.basedb.util.overview.extensions.ValidationRuleAction
-
Get the default severity level.
- getDefaultSeverity() - Method in class net.sf.basedb.util.overview.Validator
-
Get the default severity level.
- getDefaultSlots() - Method in enum net.sf.basedb.core.Job.ExecutionTime
-
The default number of execution slots available for jobs with
this execution time in the internal job queue.
- getDefaultSpotContext() - Method in class net.sf.basedb.clients.web.ExperimentExplorer
-
Get the default spot context that is used to initialise the actual context.
- getDefaultSystemId(Item) - Static method in class net.sf.basedb.core.Hardware
-
Get the system id for the hardware subtype that should be used on an item
that doesn't have a subtype.
- getDefaultSystemId(Item) - Static method in class net.sf.basedb.core.Kit
-
Get the system id for the kit subtype that should be used on an item
that doesn't have a subtype.
- getDefaultSystemId(Item) - Static method in class net.sf.basedb.core.Protocol
-
Get the system id for the protocol subtype that should be used on an item
that doesn't have a subtype.
- getDefaultSystemId(Item) - Static method in class net.sf.basedb.core.Software
-
Get the system id for the software subtype that should be used on an item
that doesn't have a subtype.
- getDefaultTrustManagers() - Static method in class net.sf.basedb.util.ssl.SSLUtil2
-
Get the default trust manages as configured in the base.config file by
ssl.truststore.* settings.
- getDefaultUnit() - Method in class net.sf.basedb.core.AnnotationBatcher.CurrentAnnotationInfo
-
Get the default unit for the annotation type.
- getDefaultUnit() - Method in class net.sf.basedb.core.AnnotationType
-
Get the default unit for this annotation type.
- getDefaultUnit() - Method in class net.sf.basedb.core.data.AnnotationTypeData
-
Get the unit used to store annotation values for this type.
- getDefaultValue() - Method in class net.sf.basedb.core.AnnotationType
-
Get the recommended default value for new annotations of this annotation type.
- getDefaultValue() - Method in class net.sf.basedb.core.data.AnnotationTypeData
-
The default value of new annotations.
- getDefaultValue() - Method in class net.sf.basedb.core.ParameterType
-
Get the default value.
- getDefaultValue() - Method in class net.sf.basedb.core.PluginParameter
-
Get the default value for this parameter or null if no
default has been specified
- getDefaultValue() - Method in class net.sf.basedb.core.query.ParameterExpression
-
Get the default value of the parameter.
- getDefaultValue() - Method in class net.sf.basedb.plugins.Base1PluginExecuter.JobParameter
-
- getDefaultValue() - Method in class net.sf.basedb.plugins.executor.ParameterDefinition
-
Get the default value for this parameter.
- getDefaultValue() - Method in class net.sf.basedb.util.formatter.LookupFormatter
-
Get the default value.
- getDefinedPermissions() - Method in enum net.sf.basedb.core.Item
-
Get the permissions which are meaningful to assign to an item
if this type.
- getDelegateFirst() - Method in class net.sf.basedb.util.JarClassLoader
-
If this class loader delegates to the parent class loader
before or after trying to find the class by itself.
- getDeletePropertyOrder(Class<? extends BatchableData>) - Static method in class net.sf.basedb.core.BatchUtil
-
Get the order of properties in the delete SQL.
- getDeletePropertyOrder(String) - Static method in class net.sf.basedb.core.BatchUtil
-
Get the order of properties in the delete SQL.
- getDeleteSql(Class<? extends BatchableData>) - Static method in class net.sf.basedb.core.BatchUtil
-
Get the SQL that deletes a new row of the specified class.
- getDeleteSql(String) - Static method in class net.sf.basedb.core.BatchUtil
-
Get the SQL that deletes a new row of the specified class.
- getDeletionOrder() - Method in enum net.sf.basedb.core.Item
-
Get a value indicating the deletion order.
- getDenied() - Method in class net.sf.basedb.core.data.keyring.PluginKeys
-
Get the denied permissions.
- getDenied() - Method in class net.sf.basedb.core.data.PluginPermission
-
The plugin's permission can be set to always be used or only if the user has it already.
- getDenied(RoleKey) - Method in class net.sf.basedb.core.PluginDefinition
-
Get the permissions that have been denied to this plugin.
- getDeniedItemFix(DbControl, Node, Node) - Method in class net.sf.basedb.util.overview.validator.BasicNodeValidator
-
Subclasses should override this method if they have a suggessted fix
for an access denied problem.
- getDeniedNodeName(Node) - Method in class net.sf.basedb.util.overview.node.AnnotationNameGenerator
-
- getDeniedNodeName(Node) - Method in class net.sf.basedb.util.overview.node.AnyToAnyNameGenerator
-
- getDeniedNodeName(Node) - Method in class net.sf.basedb.util.overview.node.BioWellNameGenerator
-
- getDeniedNodeName(Node) - Method in class net.sf.basedb.util.overview.node.FileSetMemberNameGenerator
-
- getDeniedNodeName(Node) - Method in class net.sf.basedb.util.overview.node.ItemListMemberNameGenerator
-
- getDeniedNodeName(Node) - Method in class net.sf.basedb.util.overview.node.NameableNameGenerator
-
- getDeniedNodeName(Node) - Method in interface net.sf.basedb.util.overview.node.NodeNameGenerator
-
Generate a name for a node when the item exists, but
the current user doesn't have permission to access read
the item.
- getDeniedNodeTitle(Node) - Method in class net.sf.basedb.util.overview.node.AnnotationNameGenerator
-
- getDeniedNodeTitle(Node) - Method in class net.sf.basedb.util.overview.node.AnyToAnyNameGenerator
-
- getDeniedNodeTitle(Node) - Method in class net.sf.basedb.util.overview.node.BioWellNameGenerator
-
- getDeniedNodeTitle(Node) - Method in class net.sf.basedb.util.overview.node.FileSetMemberNameGenerator
-
- getDeniedNodeTitle(Node) - Method in class net.sf.basedb.util.overview.node.ItemListMemberNameGenerator
-
- getDeniedNodeTitle(Node) - Method in class net.sf.basedb.util.overview.node.NameableNameGenerator
-
- getDeniedNodeTitle(Node) - Method in interface net.sf.basedb.util.overview.node.NodeNameGenerator
-
Generate a title for a node when the item exists, but
the current user doesn't have permission to access read
the item.
- getDependingLists() - Method in class net.sf.basedb.core.ItemList
-
Get a query that return all item lists that are used
by synchronization filters in this list.
- getDepth() - Method in class net.sf.basedb.util.Tree.Entry
-
Get the depth of this entry within the tree.
- getDerivedBioAssays() - Method in class net.sf.basedb.core.data.ExtractData
-
This is the inverse end.
- getDerivedBioAssays() - Method in class net.sf.basedb.core.data.JobData
-
This is the inverse end.
- getDerivedBioAssays() - Method in class net.sf.basedb.core.data.PhysicalBioAssayData
-
This is the inverse end.
- getDerivedBioAssays() - Method in class net.sf.basedb.core.PhysicalBioAssay
-
Get a query that returns all derived bioassay created from this
physical bioassay.
- getDescription() - Method in class net.sf.basedb.clients.jobagent.Agent
-
Get the agent.description
configuration value.
- getDescription() - Method in interface net.sf.basedb.clients.web.extensions.plot.OverviewPlotAction
-
A description of the overview plots.
- getDescription() - Method in class net.sf.basedb.clients.web.extensions.plot.OverviewPlotBean
-
- getDescription() - Method in class net.sf.basedb.clients.web.extensions.startpage.FixedStartPageFactory
-
- getDescription() - Method in interface net.sf.basedb.clients.web.extensions.startpage.StartPageAction
-
Get an optional description of the start page.
- getDescription() - Method in class net.sf.basedb.clients.web.extensions.startpage.StartPageBean
-
- getDescription() - Method in class net.sf.basedb.clients.web.taglib.table.TableColumn
-
- getDescription() - Method in class net.sf.basedb.core.AnyToAny
-
- getDescription() - Method in class net.sf.basedb.core.authentication.ExtraUserInformation
-
A description of the user.
- getDescription() - Method in class net.sf.basedb.core.BioAssay
-
- getDescription() - Method in class net.sf.basedb.core.BioAssaySet
-
- getDescription() - Method in class net.sf.basedb.core.BioPlateEventType
-
- getDescription() - Method in class net.sf.basedb.core.BioPlateType
-
- getDescription() - Method in class net.sf.basedb.core.CommonItem
-
- getDescription() - Method in class net.sf.basedb.core.data.AnyToAnyData
-
- getDescription() - Method in class net.sf.basedb.core.data.BioAssayData
-
- getDescription() - Method in class net.sf.basedb.core.data.BioAssaySetData
-
- getDescription() - Method in class net.sf.basedb.core.data.BioPlateEventTypeData
-
- getDescription() - Method in class net.sf.basedb.core.data.BioPlateTypeData
-
- getDescription() - Method in class net.sf.basedb.core.data.CommonData
-
- getDescription() - Method in class net.sf.basedb.core.data.DataFileTypeData
-
- getDescription() - Method in class net.sf.basedb.core.data.ExtraValueTypeData
-
- getDescription() - Method in class net.sf.basedb.core.data.GroupData
-
- getDescription() - Method in class net.sf.basedb.core.data.HelpData
-
- getDescription() - Method in class net.sf.basedb.core.data.ItemListSyncFilterData
-
- getDescription() - Method in class net.sf.basedb.core.data.ItemSubtypeData
-
- getDescription() - Method in class net.sf.basedb.core.data.MessageData
-
- getDescription() - Method in class net.sf.basedb.core.data.MimeTypeData
-
- getDescription() - Method in interface net.sf.basedb.core.data.NameableData
-
Get the description for the item.
- getDescription() - Method in class net.sf.basedb.core.data.NewsData
-
- getDescription() - Method in class net.sf.basedb.core.data.ParameterValueData
-
Get the description of the parameter.
- getDescription() - Method in class net.sf.basedb.core.data.PlateEventTypeData
-
- getDescription() - Method in class net.sf.basedb.core.data.PlateGeometryData
-
- getDescription() - Method in class net.sf.basedb.core.data.PlatformData
-
- getDescription() - Method in class net.sf.basedb.core.data.PlatformVariantData
-
- getDescription() - Method in class net.sf.basedb.core.data.PluginDefinitionData
-
Get a description of the plugin.
- getDescription() - Method in class net.sf.basedb.core.data.PluginTypeData
-
- getDescription() - Method in class net.sf.basedb.core.data.ProjectData
-
- getDescription() - Method in class net.sf.basedb.core.data.QuantityData
-
- getDescription() - Method in class net.sf.basedb.core.data.QuotaData
-
- getDescription() - Method in class net.sf.basedb.core.data.QuotaTypeData
-
- getDescription() - Method in class net.sf.basedb.core.data.ReporterClonePropertyData
-
Get a description of the property.
- getDescription() - Method in class net.sf.basedb.core.data.ReporterData
-
- getDescription() - Method in class net.sf.basedb.core.data.ReporterTypeData
-
- getDescription() - Method in class net.sf.basedb.core.data.RoleData
-
- getDescription() - Method in class net.sf.basedb.core.data.RoleKeyData
-
Get the description for the item.
- getDescription() - Method in class net.sf.basedb.core.data.RootRawBioAssayData
-
- getDescription() - Method in class net.sf.basedb.core.data.TransformationData
-
- getDescription() - Method in class net.sf.basedb.core.data.UnitData
-
- getDescription() - Method in class net.sf.basedb.core.data.UserData
-
- getDescription() - Method in class net.sf.basedb.core.DataFileType
-
- getDescription() - Method in class net.sf.basedb.core.Directory
-
- getDescription() - Method in class net.sf.basedb.core.ExtendedProperty
-
Get a description of the extended property.
- getDescription() - Method in class net.sf.basedb.core.ExtraValueType
-
- getDescription() - Method in class net.sf.basedb.core.Group
-
- getDescription() - Method in class net.sf.basedb.core.Help
-
- getDescription() - Method in class net.sf.basedb.core.IntensityFormula
-
Get a description of the intensity formula.
- getDescription() - Method in class net.sf.basedb.core.ItemSubtype
-
- getDescription() - Method in class net.sf.basedb.core.Message
-
- getDescription() - Method in class net.sf.basedb.core.MimeType
-
- getDescription() - Method in interface net.sf.basedb.core.Nameable
-
Get the description for the item.
- getDescription() - Method in class net.sf.basedb.core.News
-
- getDescription() - Method in class net.sf.basedb.core.ParameterInfo
-
- getDescription() - Method in class net.sf.basedb.core.PlateEventType
-
- getDescription() - Method in class net.sf.basedb.core.PlateGeometry
-
- getDescription() - Method in class net.sf.basedb.core.Platform
-
- getDescription() - Method in class net.sf.basedb.core.PlatformVariant
-
- getDescription() - Method in interface net.sf.basedb.core.plugin.About
-
A description of the plugin and what it does.
- getDescription() - Method in class net.sf.basedb.core.plugin.AboutImpl
-
- getDescription() - Method in class net.sf.basedb.core.PluginParameter
-
Get a description of the parameter.
- getDescription() - Method in class net.sf.basedb.core.PluginType
-
- getDescription() - Method in class net.sf.basedb.core.Project
-
- getDescription() - Method in class net.sf.basedb.core.Quantity
-
- getDescription() - Method in class net.sf.basedb.core.Quota
-
- getDescription() - Method in class net.sf.basedb.core.QuotaType
-
- getDescription() - Method in class net.sf.basedb.core.RawDataType
-
Get a description of this raw data type.
- getDescription() - Method in class net.sf.basedb.core.ReporterType
-
- getDescription() - Method in class net.sf.basedb.core.RequestInformation
-
Get a description of the request.
- getDescription() - Method in class net.sf.basedb.core.Role
-
- getDescription() - Method in class net.sf.basedb.core.RoleKey
-
- getDescription() - Method in class net.sf.basedb.core.RootRawBioAssay
-
- getDescription() - Method in class net.sf.basedb.core.signal.Signal
-
Get the description of the what the signal means and how
receivers should behave when the signal is sent to them
- getDescription() - Method in class net.sf.basedb.core.SyncFilter
-
- getDescription() - Method in class net.sf.basedb.core.Transformation
-
- getDescription() - Method in class net.sf.basedb.core.Unit
-
- getDescription() - Method in class net.sf.basedb.core.User
-
- getDescription() - Method in class net.sf.basedb.plugins.executor.ParameterDefinition
-
Get a description/help text about this parameter.
- getDescription() - Method in class net.sf.basedb.util.extensions.AboutBean
-
- getDescription() - Method in interface net.sf.basedb.util.extensions.ExtensionPoint
-
Get a description of the extension point.
- getDescription() - Method in class net.sf.basedb.util.extensions.ExtensionPointBean
-
- getDescription() - Method in class net.sf.basedb.util.extensions.Registry.RegisteredAbout
-
- getDescription() - Method in class net.sf.basedb.util.extensions.Registry.RegisteredExtensionPoint
-
- getDescription() - Method in class net.sf.basedb.util.jep.convert.AbsConverter
-
- getDescription() - Method in class net.sf.basedb.util.jep.convert.AbstractJepConversionFunction
-
- getDescription() - Method in class net.sf.basedb.util.jep.convert.AddConverter
-
- getDescription() - Method in class net.sf.basedb.util.jep.convert.AndConverter
-
- getDescription() - Method in class net.sf.basedb.util.jep.convert.DivideConverter
-
- getDescription() - Method in class net.sf.basedb.util.jep.convert.EqualsConverter
-
- getDescription() - Method in class net.sf.basedb.util.jep.convert.ExpConverter
-
- getDescription() - Method in class net.sf.basedb.util.jep.convert.GreaterConverter
-
- getDescription() - Method in class net.sf.basedb.util.jep.convert.GreaterEqualsConverter
-
- getDescription() - Method in class net.sf.basedb.util.jep.convert.IfConverter
-
- getDescription() - Method in interface net.sf.basedb.util.jep.convert.JepConversionFunction
-
Get a short description of the function or operator
- getDescription() - Method in class net.sf.basedb.util.jep.convert.LessConverter
-
- getDescription() - Method in class net.sf.basedb.util.jep.convert.LessEqualsConverter
-
- getDescription() - Method in class net.sf.basedb.util.jep.convert.LogarithmConverter
-
- getDescription() - Method in class net.sf.basedb.util.jep.convert.MultiplyConverter
-
- getDescription() - Method in class net.sf.basedb.util.jep.convert.NaturalLogarithmConverter
-
- getDescription() - Method in class net.sf.basedb.util.jep.convert.NotConverter
-
- getDescription() - Method in class net.sf.basedb.util.jep.convert.NotEqualsConverter
-
- getDescription() - Method in class net.sf.basedb.util.jep.convert.OrConverter
-
- getDescription() - Method in class net.sf.basedb.util.jep.convert.SquareRootConverter
-
- getDescription() - Method in class net.sf.basedb.util.jep.convert.SubtractConverter
-
- getDescription() - Method in class net.sf.basedb.util.jep.convert.UMinusConverter
-
- getDescription() - Method in interface net.sf.basedb.util.overview.extensions.ValidationRuleAction
-
Get a lengthier description of the validation that takes place
- getDescription() - Method in class net.sf.basedb.util.overview.Validator
-
Get a lengthier description of the validation that takes place
- getDescription() - Method in interface net.sf.basedb.util.uri.ConnectionManagerFactory
-
Get a longer description that can be used by client applications to
show more information about the capabilities of the factory to
the users.
- getDescription() - Method in class net.sf.basedb.util.uri.http.HttpConnectionManagerFactory
-
- getDescription() - Method in class net.sf.basedb.util.zip.Bzip2FilePacker
-
- getDescription() - Method in interface net.sf.basedb.util.zip.FilePacker
-
Get a short description of this file format that is suitable for display in
selection list boxes.
- getDescription() - Method in class net.sf.basedb.util.zip.GzipFilePacker
-
- getDescription() - Method in class net.sf.basedb.util.zip.TarFilePacker
-
- getDescription() - Method in class net.sf.basedb.util.zip.ZipFilePacker
-
- getDescriptor() - Method in class net.sf.basedb.util.overview.Failure
-
- getDestinationCount() - Method in class net.sf.basedb.core.data.PlateMappingData
-
The produced number of destination plates.
- getDestinationCount() - Method in class net.sf.basedb.core.PlateMapping
-
Get the number of produced destination plates.
- getDestinationGeometry() - Method in class net.sf.basedb.core.data.PlateMappingData
-
The required geometry of destination plates in this mapping.
- getDestinationGeometry() - Method in class net.sf.basedb.core.PlateMapping
-
- getDestinationIndex() - Method in class net.sf.basedb.core.data.PlateData
-
If the plate was created by a plate mapping, this is the index
of this plate in the list of created plates.
- getDestinationIndex() - Method in class net.sf.basedb.core.Plate
-
If the plate was created by a plate mapping, this is the index
of this plate in the list of created plates.
- getDetail() - Method in exception net.sf.basedb.clients.web.WebException
-
Get the detailed description of the error message.
- getDetails() - Method in class net.sf.basedb.core.data.ChangeHistoryData
-
This is the inverse end.
- getDetails() - Method in class net.sf.basedb.core.data.PlateMappingData
-
For each destination coordinate we can get the source coordinate.
- getDialect() - Static method in class net.sf.basedb.core.HibernateUtil
-
Get the database dialect.
- getDifference() - Method in interface net.sf.basedb.core.DiskConsumable
-
Get the number of bytes this items now is using compared to when it was
loaded from the database.
- getDifference() - Method in class net.sf.basedb.core.Experiment
-
- getDifference() - Method in class net.sf.basedb.core.File
-
Always 0.
- getDifference() - Method in class net.sf.basedb.core.RawBioAssay
-
Always 0.
- getDirection() - Method in class net.sf.basedb.clients.web.taglib.table.Table
-
- getDirectionImage(ItemContext.SortDirection) - Method in class net.sf.basedb.clients.web.taglib.table.Table
-
Get sort direction <img> element for the given direction.
- getDirectory() - Method in class net.sf.basedb.core.data.ExperimentData
-
Get the associated
DirectoryData
item directory where
it is recommended for plugins to save files related to the experiment.
- getDirectory() - Method in class net.sf.basedb.core.data.FileData
-
- getDirectory() - Method in class net.sf.basedb.core.Experiment
-
Get the associated directory where it is recommended that plugins
store files that are related to this experiment.
- getDirectory() - Method in class net.sf.basedb.core.File
-
- getDirectory(int) - Method in class net.sf.basedb.core.Path
-
Get the name of the i:th directory on the path, starting with 0.
- getDirectory(DbControl, Path) - Method in class net.sf.basedb.plugins.batchimport.FileImporter
-
- getDirectory(DbControl, Path) - Method in class net.sf.basedb.plugins.TarFileUnpacker
-
Get the directory for the specified path.
- getDirectory(Path) - Method in class net.sf.basedb.util.zip.ZipUnpacker
-
Get the directory for the specified path.
- getDirectoryCount() - Method in class net.sf.basedb.core.Path
-
Get the number of directories on the path.
- getDirectoryParameter(String, String) - Method in class net.sf.basedb.util.zip.AbstractFileUnpacker
-
Get a plugin parameter that asks for the directory where the
unpacked files are stored.
- getDirectoryTree(DbControl, Directory) - Static method in class net.sf.basedb.util.FileUtil
-
Get the complete tree of sub-directories from a given directory.
- getDirty(int) - Method in class net.sf.basedb.core.log.EntityDetails
-
- getDisableInheritance() - Method in class net.sf.basedb.core.AnnotationType
-
If this flag is set, annotations of this type can't be inherited
to child items.
- getDisableInheritance() - Method in class net.sf.basedb.core.data.AnnotationTypeData
-
If this flag is set, annotation of this type can't be inherited.
- getDisableinproject() - Method in class net.sf.basedb.clients.web.taglib.table.PresetSelector
-
- getDisableLogOfValues() - Method in class net.sf.basedb.core.AnnotationType
-
If this flag is set, the change history logging will not include
actual annotation values.
- getDisableLogOfValues() - Method in class net.sf.basedb.core.data.AnnotationTypeData
-
If this flag is set, logging of actual annotation values should not
be done in the change history.
- getDisableManualMembers() - Method in class net.sf.basedb.core.data.ItemListData
-
If set, manually adding/removing members is disabled
- getDisableManualMembers() - Method in class net.sf.basedb.core.ItemList
-
If this flag is set manual modification of members is disabled.
- getDisableothers() - Method in class net.sf.basedb.clients.web.taglib.table.PresetSelector
-
- getDisableownedby() - Method in class net.sf.basedb.clients.web.taglib.table.PresetSelector
-
- getDisableRawJoinOnMergedData() - Method in class net.sf.basedb.core.DynamicSpotQuery
-
- getDisableremoved() - Method in class net.sf.basedb.clients.web.taglib.table.PresetSelector
-
- getDisablesharedto() - Method in class net.sf.basedb.clients.web.taglib.table.PresetSelector
-
- getDisableSyncFilters() - Method in class net.sf.basedb.core.data.ItemListData
-
If set, syncing members with sync filter is disabled
- getDisableSyncFilters() - Method in class net.sf.basedb.core.ItemList
-
If this flag is set synchronization of members with sync filters is disabled.
- getDiskConsumableItems() - Static method in class net.sf.basedb.core.Metadata
-
- getDiskUsage() - Method in interface net.sf.basedb.core.data.DiskConsumableData
-
- getDiskUsage() - Method in class net.sf.basedb.core.data.ExperimentData
-
- getDiskUsage() - Method in class net.sf.basedb.core.data.FileData
-
- getDiskUsage() - Method in class net.sf.basedb.core.data.RawBioAssayData
-
- getDiskUsage(UserData, QuotaTypeData, Location) - Method in class net.sf.basedb.core.DbControl
-
Get the disk usage for the specified user at the specified
location and quota type.
- getDiskUsage(GroupData, QuotaTypeData, Location) - Method in class net.sf.basedb.core.DbControl
-
Get the disk usage for the specified group at the specified
location and quota type.
- getDiskUsage(QuotaType, Location) - Method in class net.sf.basedb.core.Group
-
Get the used number of bytes for the specified quota type and location.
- getDiskUsage(QuotaType, Location) - Method in class net.sf.basedb.core.User
-
Get the used number of bytes for the specified quota type and location.
- getDisplayAsList() - Method in class net.sf.basedb.core.AnnotationType
-
Check if the enumeration values should be displayed as a selection list
or as radio buttons/checkboxes by the client application.
- getDisplayName() - Method in interface net.sf.basedb.util.uri.ConnectionManagerFactory
-
Get a short string that is suitable for use in selection lists, etc.
- getDisplayName() - Method in class net.sf.basedb.util.uri.http.HttpConnectionManagerFactory
-
- getDisplaySymbol() - Method in class net.sf.basedb.core.data.UnitData
-
The symbol to display together with values of this unit.
- getDisplaySymbol() - Method in class net.sf.basedb.core.Unit
-
Get the display symbol to use when displaying values with this
unit.
- getDoctype() - Method in class net.sf.basedb.clients.web.taglib.Page
-
- getDomainOrder() - Method in class net.sf.basedb.util.plot.HistogramPlot.HistogramDataset
-
- getDouble(String) - Method in class net.sf.basedb.util.parser.ColumnMapper
-
- getDouble(String) - Static method in class net.sf.basedb.util.Values
-
Convert a string to a double.
- getDouble(String, double) - Static method in class net.sf.basedb.util.Values
-
Convert a string to a double.
- getDouble(String, Double) - Static method in class net.sf.basedb.util.Values
-
- getDouble(String[]) - Static method in class net.sf.basedb.util.Values
-
Convert an array of strings to an array of Double:s.
- getDoubleFormatter(SessionControl) - Static method in class net.sf.basedb.clients.web.formatter.FormatterFactory
-
Get the logged in user's number formatter for double values.
- getDoubleOption(String, Double) - Method in class net.sf.basedb.core.AnnotationType
-
Get an option and convert the value to a double.
- getDoubleValues() - Method in class net.sf.basedb.core.data.annotations.AnnotationLink
-
- getDownloadStream(long) - Method in class net.sf.basedb.core.File
-
Get an InputStream
that can be used
to download the physical file for this file item.
- getDragcolumns() - Method in class net.sf.basedb.clients.web.taglib.table.Table
-
- getDropForeignKeySql(String, String, String, String) - Method in interface net.sf.basedb.core.dbengine.DbEngine
-
Generate SQL to drop a foreign key constraint.
- getDropForeignKeySql(String, String, String, String) - Method in class net.sf.basedb.core.dbengine.DefaultDbEngine
-
Generate alter table <catalog>.
- getDropForeignKeySql(String, String, String, String) - Method in class net.sf.basedb.core.dbengine.MySQLEngine
-
Generate alter table <catalog>.
- getDropForeignKeySql(String, String, String, String) - Method in class net.sf.basedb.core.dbengine.PostgresDbEngine
-
Generate alter table <schema>.
- getDropIndexSql(String, String, String, String, boolean) - Method in interface net.sf.basedb.core.dbengine.DbEngine
-
Generate SQL to drop an index.
- getDropIndexSql(String, String, String, String, boolean) - Method in class net.sf.basedb.core.dbengine.DefaultDbEngine
-
Generate drop index <catalog>.
- getDropIndexSql(String, String, String, String, boolean) - Method in class net.sf.basedb.core.dbengine.MySQLEngine
-
Generate drop index <name> on <catalog>.
- getDropIndexSql(String, String, String, String, boolean) - Method in class net.sf.basedb.core.dbengine.PostgresDbEngine
-
Generate alter table <schema>.
- getDropPrimaryKey(String, String, String, String) - Method in interface net.sf.basedb.core.dbengine.DbEngine
-
Generate SQL that drops the primary key from a table.
- getDropPrimaryKey(String, String, String, String) - Method in class net.sf.basedb.core.dbengine.DefaultDbEngine
-
- getDropPrimaryKey(String, String, String, String) - Method in class net.sf.basedb.core.dbengine.MySQLEngine
-
Generate alter table catalog.table drop primary key
- getDropPrimaryKey(String, String, String, String) - Method in class net.sf.basedb.core.dbengine.PostgresDbEngine
-
Generate alter table schema.table drop constraint name
- getDynamicActionAttributes() - Method in class net.sf.basedb.clients.web.extensions.AbstractJspFactory
-
- getDynamicActionAttributes() - Method in interface net.sf.basedb.clients.web.extensions.DynamicActionAttributes
-
Get an iterator that return all dynamic attributes.
- getDynamicActionAttributes() - Method in class net.sf.basedb.clients.web.extensions.DynamicActionAttributeSupport
-
- getDynamicActionAttributes() - Method in class net.sf.basedb.clients.web.extensions.skin.FixedSkinActionFactory.MySkinAction
-
- getDynamicActionAttributes() - Method in class net.sf.basedb.clients.web.taglib.StylableTag
-
- getDynamicActionAttributes() - Method in class net.sf.basedb.clients.web.taglib.tab.Tab
-
- getDynamicActionAttributes() - Method in class net.sf.basedb.clients.web.taglib.table.Button.ButtonActionWrapper
-
- getDynamicAttribute(String) - Method in class net.sf.basedb.clients.web.taglib.StylableTag
-
Get the dynamic attribute for the given name
- getDynamicCatalog() - Static method in class net.sf.basedb.core.Application
-
Get the name of the dynamic catalog.
- getDynamicExpression(DbControl, String) - Static method in class net.sf.basedb.core.ItemContext
-
- getDynamicExpression(DbControl, SqlQuery, String) - Static method in class net.sf.basedb.core.ItemContext
-
- getDynamicQuery() - Static method in class net.sf.basedb.core.Reporter
-
Get a dynamic query object configured to retrieve reporter information.
- getDynamicQuery(Experiment) - Static method in class net.sf.basedb.core.Reporter
-
Get a dynamic query object configured to retrieve reporter
information from either the master reporter table or a
cloned reporter table in the given experiment.
- getDynamicRawData() - Method in class net.sf.basedb.core.RawBioAssay
-
Get a dynamic query that returns the raw data of this raw bioassay.
- getDynamicRestriction(DbControl) - Method in class net.sf.basedb.core.PropertyFilter
-
- getDynamicRestriction(DbControl, SqlQuery) - Method in class net.sf.basedb.core.PropertyFilter
-
- getDynamicSchema() - Static method in class net.sf.basedb.core.Application
-
Get the name of the dynamic schema.
- getDynamicSelect(DbControl, String) - Static method in class net.sf.basedb.core.ItemContext
-
- getDynamicSelect(DbControl, SqlQuery, String) - Static method in class net.sf.basedb.core.ItemContext
-
- getEffectiveFilter() - Method in class net.sf.basedb.core.ItemContext.PropertyFilterPair
-
- getEffectiveMaxMemory() - Method in class net.sf.basedb.core.JobAgentSettings
-
Get the effective maximum amount of memory the plugin is allowed to use.
- getEffectivePriority(Job) - Method in class net.sf.basedb.core.JobAgentSettings
-
Get the effective priority for the specified job, when the priority boost is
taken into account.
- getElementClass() - Method in class net.sf.basedb.core.DynamicPositionQueryJoiners.ExtraValueJoiner
-
- getElementClass() - Method in class net.sf.basedb.core.DynamicPositionQueryJoiners.ReporterJoiner
-
- getElementClass() - Method in class net.sf.basedb.core.DynamicPositionQueryJoiners.ReporterListJoiner
-
- getElementClass() - Method in class net.sf.basedb.core.DynamicRawDataQuery.RawBioAssayJoiner
-
- getElementClass() - Method in class net.sf.basedb.core.DynamicRawDataQuery.ReporterJoiner
-
- getElementClass() - Method in class net.sf.basedb.core.DynamicRawDataQuery.ReporterListJoiner
-
- getElementClass() - Method in class net.sf.basedb.core.DynamicReporterQuery.MasterReporterJoiner
-
- getElementClass() - Method in class net.sf.basedb.core.DynamicReporterQuery.ReporterListJoiner
-
- getElementClass() - Method in class net.sf.basedb.core.DynamicSpotQueryJoiners.ExtraValueJoiner
-
- getElementClass() - Method in class net.sf.basedb.core.DynamicSpotQueryJoiners.RawDataJoiner
-
- getElementClass() - Method in class net.sf.basedb.core.DynamicSpotQueryJoiners.ReporterJoiner
-
- getElementClass() - Method in class net.sf.basedb.core.DynamicSpotQueryJoiners.ReporterListJoiner
-
- getElementClass() - Method in class net.sf.basedb.core.HqlQueryJoiners.AnnotationJoiner
-
- getElementClass() - Method in class net.sf.basedb.core.HqlQueryJoiners.ReporterListJoiner
-
- getElementClass() - Method in interface net.sf.basedb.core.query.AutoJoiner
-
The type of the query element the implementation works for.
- getEmail() - Method in class net.sf.basedb.core.authentication.ExtraUserInformation
-
- getEmail() - Method in class net.sf.basedb.core.data.PluginDefinitionData
-
Get an email address that can be used to get more information about the plugin.
- getEmail() - Method in class net.sf.basedb.core.data.UserData
-
Get the email address to the user, or null if unknown.
- getEmail() - Method in interface net.sf.basedb.core.plugin.About
-
An email adress to get more information about the plugin.
- getEmail() - Method in class net.sf.basedb.core.plugin.AboutImpl
-
- getEmail() - Method in class net.sf.basedb.core.PluginDefinition
-
Get an email address that can be used to get more information about the plugin.
- getEmail() - Method in class net.sf.basedb.core.User
-
Get the email address to the user.
- getEmail() - Method in class net.sf.basedb.util.extensions.AboutBean
-
- getEmail() - Method in class net.sf.basedb.util.extensions.Registry.RegisteredAbout
-
- getEnabledFilter(String) - Method in class net.sf.basedb.core.hibernate.SessionWrapper
-
- getEnabledItems() - Method in class net.sf.basedb.core.AnnotationType
-
Get the
Item
types this annotation type is enabled for.
- getEnableDownloadLink() - Method in class net.sf.basedb.clients.web.taglib.PropertyValue
-
- getEnableEditLink() - Method in class net.sf.basedb.clients.web.taglib.PropertyValue
-
- getEnablePropertyLink() - Method in class net.sf.basedb.clients.web.taglib.PropertyValue
-
- getEncodedName(Nameable, boolean) - Static method in class net.sf.basedb.clients.web.Base
-
- getEncoder() - Method in class net.sf.basedb.util.export.TableWriter
-
Get the current default encoder for this writer.
- getEndDate() - Method in class net.sf.basedb.core.data.NewsData
-
Get the last day this news item should be shown.
- getEndDate() - Method in class net.sf.basedb.core.News
-
Get the end date and time for this news item to be published.
- getEnded() - Method in class net.sf.basedb.core.data.JobData
-
Get the date and time the job was ended or null if the job hasn't ended.
- getEnded() - Method in class net.sf.basedb.core.Job
-
Get the date and time the job ended.
- getEndTime() - Method in class net.sf.basedb.util.extensions.manager.ProcessResults
-
Get the end time of the scan as a millisecond value.
- getEndX() - Method in class net.sf.basedb.util.plot.HistogramPlot.HistogramBin
-
- getEndX(int, int) - Method in class net.sf.basedb.util.plot.HistogramPlot.HistogramDataset
-
- getEndXValue(int, int) - Method in class net.sf.basedb.util.plot.HistogramPlot.HistogramDataset
-
- getEndY(int, int) - Method in class net.sf.basedb.util.plot.HistogramPlot.HistogramDataset
-
- getEndYValue(int, int) - Method in class net.sf.basedb.util.plot.HistogramPlot.HistogramDataset
-
- getEntity() - Method in class net.sf.basedb.core.log.EntityDetails
-
Get the entity that was changed.
- getEntityLogger(LogManager, Object) - Method in class net.sf.basedb.core.log.db.DbLogManagerFactory
-
If a special logger has been registered for the class of the given
entity, use that logger, otherwise use the default logger.
- getEntityLogger(LogManager, Object) - Method in interface net.sf.basedb.core.log.LogManagerFactory
-
Get/create an entity logger for logging changes to the given entity.
- getEntityLogOptions(Object) - Static method in class net.sf.basedb.core.log.EntityLogOptions
-
Get the logging options for the given entity.
- getEntityLogOptionsForClass(Class<?>) - Static method in class net.sf.basedb.core.log.EntityLogOptions
-
Get the logging options for the given class of entities.
- getEntityName(Object) - Method in class net.sf.basedb.core.hibernate.SessionWrapper
-
- getEntityName() - Method in class net.sf.basedb.core.RawDataType
-
- getEntriesByKey(K) - Method in class net.sf.basedb.util.Enumeration
-
Get a list with all entries that equals the given key.
- getEntriesByValue(V) - Method in class net.sf.basedb.util.Enumeration
-
Get a list with all entries that equals the given value.
- getEntry(int) - Method in class net.sf.basedb.util.bfs.MetadataModel.Section
-
Get the entry in this section with the given index.
- getEntry(String) - Method in class net.sf.basedb.util.bfs.MetadataModel.Section
-
Get the first entry in this section with a given key.
- getEntry(int) - Method in class net.sf.basedb.util.Enumeration
-
- getEntry(E) - Method in class net.sf.basedb.util.Tree
-
Get the entry for an arbitrary node.
- getEntryCount() - Method in class net.sf.basedb.util.bfs.MetadataModel.Section
-
Get the number of entries in this section.
- getEntryDate() - Method in class net.sf.basedb.core.AnnotationType
-
- getEntryDate() - Method in class net.sf.basedb.core.AnnotationTypeCategory
-
- getEntryDate() - Method in class net.sf.basedb.core.ArrayBatch
-
- getEntryDate() - Method in class net.sf.basedb.core.ArrayDesign
-
- getEntryDate() - Method in class net.sf.basedb.core.ArraySlide
-
- getEntryDate() - Method in class net.sf.basedb.core.BioMaterialEvent
-
Get the date this event was added to the database.
- getEntryDate() - Method in class net.sf.basedb.core.BioPlate
-
- getEntryDate() - Method in class net.sf.basedb.core.BioPlateEvent
-
- getEntryDate() - Method in class net.sf.basedb.core.BioSource
-
- getEntryDate() - Method in class net.sf.basedb.core.Client
-
- getEntryDate() - Method in class net.sf.basedb.core.data.AnnotationTypeCategoryData
-
- getEntryDate() - Method in class net.sf.basedb.core.data.AnnotationTypeData
-
- getEntryDate() - Method in class net.sf.basedb.core.data.ArrayBatchData
-
- getEntryDate() - Method in class net.sf.basedb.core.data.ArrayDesignData
-
- getEntryDate() - Method in class net.sf.basedb.core.data.ArraySlideData
-
- getEntryDate() - Method in class net.sf.basedb.core.data.BioMaterialEventData
-
- getEntryDate() - Method in class net.sf.basedb.core.data.BioPlateData
-
- getEntryDate() - Method in class net.sf.basedb.core.data.BioPlateEventData
-
- getEntryDate() - Method in class net.sf.basedb.core.data.BioSourceData
-
- getEntryDate() - Method in class net.sf.basedb.core.data.ClientData
-
- getEntryDate() - Method in class net.sf.basedb.core.data.DerivedBioAssayData
-
- getEntryDate() - Method in class net.sf.basedb.core.data.ExperimentData
-
- getEntryDate() - Method in class net.sf.basedb.core.data.ExtraValueTypeData
-
- getEntryDate() - Method in class net.sf.basedb.core.data.FormulaData
-
- getEntryDate() - Method in class net.sf.basedb.core.data.GroupData
-
- getEntryDate() - Method in class net.sf.basedb.core.data.HardwareData
-
- getEntryDate() - Method in class net.sf.basedb.core.data.ItemSubtypeData
-
- getEntryDate() - Method in class net.sf.basedb.core.data.KitData
-
- getEntryDate() - Method in class net.sf.basedb.core.data.MimeTypeData
-
- getEntryDate() - Method in class net.sf.basedb.core.data.NewsData
-
- getEntryDate() - Method in class net.sf.basedb.core.data.PlateData
-
- getEntryDate() - Method in class net.sf.basedb.core.data.PlateEventData
-
Get the date this event was added to the database.
- getEntryDate() - Method in class net.sf.basedb.core.data.PlateGeometryData
-
- getEntryDate() - Method in class net.sf.basedb.core.data.PlateMappingData
-
- getEntryDate() - Method in class net.sf.basedb.core.data.PlateTypeData
-
- getEntryDate() - Method in class net.sf.basedb.core.data.PluginConfigurationData
-
- getEntryDate() - Method in class net.sf.basedb.core.data.PluginDefinitionData
-
- getEntryDate() - Method in class net.sf.basedb.core.data.PluginTypeData
-
- getEntryDate() - Method in class net.sf.basedb.core.data.ProjectData
-
- getEntryDate() - Method in class net.sf.basedb.core.data.ProtocolData
-
- getEntryDate() - Method in class net.sf.basedb.core.data.QuotaTypeData
-
- getEntryDate() - Method in class net.sf.basedb.core.data.RawBioAssayData
-
- getEntryDate() - Method in interface net.sf.basedb.core.data.RegisteredData
-
Get the date this item was added to the database.
- getEntryDate() - Method in class net.sf.basedb.core.data.ReporterCloneTemplateData
-
- getEntryDate() - Method in class net.sf.basedb.core.data.ReporterData
-
- getEntryDate() - Method in class net.sf.basedb.core.data.ReporterListData
-
- getEntryDate() - Method in class net.sf.basedb.core.data.ReporterTypeData
-
- getEntryDate() - Method in class net.sf.basedb.core.data.RoleData
-
- getEntryDate() - Method in class net.sf.basedb.core.data.SoftwareData
-
- getEntryDate() - Method in class net.sf.basedb.core.data.TagData
-
- getEntryDate() - Method in class net.sf.basedb.core.data.UserData
-
- getEntryDate() - Method in class net.sf.basedb.core.DerivedBioAssay
-
- getEntryDate() - Method in class net.sf.basedb.core.Experiment
-
- getEntryDate() - Method in class net.sf.basedb.core.ExtraValueType
-
- getEntryDate() - Method in class net.sf.basedb.core.Formula
-
- getEntryDate() - Method in class net.sf.basedb.core.Group
-
- getEntryDate() - Method in class net.sf.basedb.core.Hardware
-
- getEntryDate() - Method in class net.sf.basedb.core.ItemSubtype
-
- getEntryDate() - Method in class net.sf.basedb.core.Kit
-
- getEntryDate() - Method in class net.sf.basedb.core.MeasuredBioMaterial
-
- getEntryDate() - Method in class net.sf.basedb.core.MimeType
-
- getEntryDate() - Method in class net.sf.basedb.core.News
-
- getEntryDate() - Method in class net.sf.basedb.core.PhysicalBioAssay
-
- getEntryDate() - Method in class net.sf.basedb.core.Plate
-
- getEntryDate() - Method in class net.sf.basedb.core.PlateEvent
-
Get the date this event was added to the database.
- getEntryDate() - Method in class net.sf.basedb.core.PlateGeometry
-
- getEntryDate() - Method in class net.sf.basedb.core.PlateMapping
-
- getEntryDate() - Method in class net.sf.basedb.core.PlateType
-
- getEntryDate() - Method in class net.sf.basedb.core.PluginConfiguration
-
- getEntryDate() - Method in class net.sf.basedb.core.PluginDefinition
-
- getEntryDate() - Method in class net.sf.basedb.core.PluginType
-
- getEntryDate() - Method in class net.sf.basedb.core.Project
-
- getEntryDate() - Method in class net.sf.basedb.core.Protocol
-
- getEntryDate() - Method in class net.sf.basedb.core.QuotaType
-
- getEntryDate() - Method in class net.sf.basedb.core.RawBioAssay
-
- getEntryDate() - Method in interface net.sf.basedb.core.Registered
-
Get the date that the item was registered in the database.
- getEntryDate() - Method in class net.sf.basedb.core.ReporterCloneTemplate
-
- getEntryDate() - Method in class net.sf.basedb.core.ReporterList
-
- getEntryDate() - Method in class net.sf.basedb.core.ReporterType
-
- getEntryDate() - Method in class net.sf.basedb.core.Role
-
- getEntryDate() - Method in class net.sf.basedb.core.Software
-
- getEntryDate() - Method in class net.sf.basedb.core.Tag
-
- getEntryDate() - Method in class net.sf.basedb.core.User
-
- getEnumeration() - Method in class net.sf.basedb.clients.web.extensions.list.AbstractListColumnBean
-
- getEnumeration() - Method in interface net.sf.basedb.clients.web.extensions.list.ListColumnAction
-
Get an enumeration of possible values that can be found in the
column.
- getEnumeration() - Method in class net.sf.basedb.clients.web.taglib.table.ColumnDef
-
- getEnumeration() - Method in class net.sf.basedb.core.ParameterType
-
Get the list of values to choose from as an enumeration.
- getEnumerationValues() - Method in class net.sf.basedb.core.data.AnnotationTypeData
-
The allowed values if this is an enumeration.
- getEnumOptions() - Method in class net.sf.basedb.plugins.Base1PluginExecuter.JobParameter
-
- getError() - Method in class net.sf.basedb.core.SimpleProgressReporter
-
Get error that happened while processing some action that
was reported via this progress reporter.
- getError() - Method in class net.sf.basedb.util.ContextUtil.ContextResult
-
Get the exception that caused the error, or null if this is a
warning-level object.
- getError() - Method in class net.sf.basedb.util.FileCopyRunnable
-
Get the exception that was thrown when executing the file copy
operation.
- getErrorclazz() - Method in class net.sf.basedb.clients.web.taglib.table.Cell
-
- getErrorHandler(String, ErrorHandler) - Method in class net.sf.basedb.plugins.AbstractFlatFileImporter
-
- getErrorHandler(InvokationContext<? extends A>) - Method in interface net.sf.basedb.util.extensions.ErrorHandlerFactory
-
Get an error handler for the current context.
- getErrorHandler() - Method in class net.sf.basedb.util.extensions.ExtensionContext
-
- getErrorHandler() - Method in class net.sf.basedb.util.extensions.ExtensionPointContext
-
- getErrorHandler() - Method in class net.sf.basedb.util.extensions.InvokationContext
-
Get the error handler used in this context.
- getErrorHandler(InvokationContext<? extends Action>) - Method in class net.sf.basedb.util.extensions.LoggingErrorHandlerFactory
-
- getErrorHandler(InvokationContext<? extends Action>) - Method in class net.sf.basedb.util.extensions.RethrowErrorHandlerFactory
-
- getErrorHandlerFactory() - Method in interface net.sf.basedb.util.extensions.ExtensionPoint
-
Get the error handler factory that should be used with this
extension point.
- getErrorHandlerFactory() - Method in class net.sf.basedb.util.extensions.ExtensionPointBean
-
- getErrorHandlerFactory() - Method in class net.sf.basedb.util.extensions.Registry.RegisteredExtensionPoint
-
- getErrorList() - Method in class net.sf.basedb.core.PluginResponse
-
- getErrorMessage() - Method in class net.sf.basedb.core.data.FileSetMemberData
-
The error message if the file validation failed.
- getErrorMessage() - Method in class net.sf.basedb.core.FileSetMember
-
Get the error message if the validation failed.
- getErrorOption(String) - Method in class net.sf.basedb.plugins.AbstractFlatFileImporter
-
Get the value for an error handling parameter.
- getErrors() - Method in class net.sf.basedb.plugins.executor.ExternalProgramExecutor.ResponseWrapper
-
- getEstimatedExecutionTime() - Method in class net.sf.basedb.clients.jobagent.slotmanager.Slot
-
Get the estimated execution time for this slot.
- getEstimatedExecutionTime() - Method in class net.sf.basedb.core.data.JobData
-
Get the estimated execution time of the job.
0 = <1 minute, 1 = 1 - 10 minutes, 2 = <1 hour, 3 = >1 hour
- getEstimatedExecutionTime() - Method in class net.sf.basedb.core.Job
-
Get the estimated execution time of the job.
- getEstimatedExecutionTime() - Method in class net.sf.basedb.core.PluginResponse
-
Get the estimated execution time of the job.
- getEvent() - Method in class net.sf.basedb.core.BioMaterialEventSource
-
Get the event that this information belongs to.
- getEvent() - Method in class net.sf.basedb.core.BioPlateEventParticipant
-
- getEvent() - Method in class net.sf.basedb.core.data.BioMaterialEventSourceData
-
Get the event that created something from the parent biomaterial.
- getEvent() - Method in class net.sf.basedb.core.data.BioPlateEventParticipantData
-
The bioplate event.
- getEvent(PlateEventType) - Method in class net.sf.basedb.core.Plate
-
Get the event for the specified event type.
- getEventDate() - Method in class net.sf.basedb.core.BioMaterialEvent
-
Get the date this event was done in the lab.
- getEventDate() - Method in class net.sf.basedb.core.BioPlate
-
Get the date this plate was created.
- getEventDate() - Method in class net.sf.basedb.core.BioPlateEvent
-
Get the date this event was done in the lab.
- getEventDate() - Method in class net.sf.basedb.core.data.BioMaterialEventData
-
Get the date this event happened in the lab.
- getEventDate() - Method in class net.sf.basedb.core.data.BioPlateData
-
Get the date this plate was created in the lab.
- getEventDate() - Method in class net.sf.basedb.core.data.BioPlateEventData
-
Get the date this event happened in the lab.
- getEventDate() - Method in class net.sf.basedb.core.data.PlateEventData
-
Get the date this event happened in the lab.
- getEventDate() - Method in class net.sf.basedb.core.PlateEvent
-
Get the date this event was done in the lab.
- getEventParticipants() - Method in class net.sf.basedb.core.data.BioPlateData
-
This is the inverse end.
- getEvents() - Method in class net.sf.basedb.core.BioPlate
-
Get a query returning events that this plate has been a part of.
- getEvents() - Method in class net.sf.basedb.core.data.BioPlateEventTypeData
-
This is the inverse end.
- getEvents() - Method in class net.sf.basedb.core.data.MeasuredBioMaterialData
-
This is the inverse end.
- getEvents() - Method in class net.sf.basedb.core.data.PlateData
-
The event for this plate.
- getEvents() - Method in class net.sf.basedb.core.MeasuredBioMaterial
-
Get a query that returns all events for this biomaterial.
- getEvents() - Method in class net.sf.basedb.core.Plate
-
Get a query that returns all event types for this plate type.
- getEventSource(BioMaterial) - Method in class net.sf.basedb.core.BioMaterialEvent
-
Get information about a biomaterial used as a source to this event.
- getEventSources() - Method in class net.sf.basedb.core.BioMaterialEvent
-
Create a special query that return BioMaterialEventSource objects.
- getEventSources(DbControl, int) - Method in class net.sf.basedb.core.BioMaterialEvent
-
Utility method for finding all sources on a given bioassay
position.
- getEventType() - Method in class net.sf.basedb.core.BioMaterialEvent
-
Get the type of event.
- getEventType() - Method in class net.sf.basedb.core.BioPlateEvent
-
Get the event type of this event.
- getEventType() - Method in class net.sf.basedb.core.data.BioMaterialEventData
-
Get the type of event, 1=creation event, 2=hybridization event, 3=other event
- getEventType() - Method in class net.sf.basedb.core.data.BioPlateEventData
-
The type of the event.
- getEventTypes() - Method in class net.sf.basedb.core.data.PlateTypeData
-
The event types defined for this plate type.
- getEventTypes() - Method in class net.sf.basedb.core.PlateType
-
Get a query that returns all event types for this plate type.
- getException() - Method in class net.sf.basedb.clients.web.fileupload.FileUploadProgress
-
Get the exception that caused the upload to fail.
- getExcludeReportersParameters(DbControl) - Method in class net.sf.basedb.plugins.LowessNormalization
-
- getExecDirectory() - Method in class net.sf.basedb.plugins.Base1PluginExecuter
-
Get the exec directory as a java.io.File.
- getExecLine() - Method in class net.sf.basedb.plugins.Base1PluginExecuter
-
- getExecuteCommand() - Method in class net.sf.basedb.core.data.JobData
-
The command to send to the plug-in when starting to
execute it.
- getExecuteCommand() - Method in class net.sf.basedb.core.Job
-
The command to send to the plug-in when starting to
execute it.
- getExecutionRequest(ProgressReporter) - Method in class net.sf.basedb.core.PluginResponse
-
- getExecutor() - Method in class net.sf.basedb.plugins.executor.AbstractIOSupport
-
Get the external program executor that invoked the plug-in.
- getExernalPluginParameters(DbControl, BioAssaySet) - Method in class net.sf.basedb.plugins.executor.ExternalProgramExecutor
-
- getExistingSessionControl(PageContext, boolean) - Static method in class net.sf.basedb.clients.web.Base
-
Get an existing
SessionControl
object
given a
PageContext
and optionally check that a user is logged in.
- getExistingSessionControl(ServletRequest, boolean) - Static method in class net.sf.basedb.clients.web.Base
-
Get a session control for the BASE web client "net.sf.basedb.clients.web".
- getExistingSessionControl(ServletRequest, String, boolean) - Static method in class net.sf.basedb.clients.web.Base
-
Get an existing
SessionControl
object
given a
ServletRequest
object and optionally check that a user is logged in.
- getExistingSessionControl(PageContext, Permission, Item) - Static method in class net.sf.basedb.clients.web.Base
-
Get an existing
SessionControl
object given
a
PageContext
and check for generic (role-based)
permission to an item type.
- getExistingSessionControl(ServletRequest, Permission, Item) - Static method in class net.sf.basedb.clients.web.Base
-
Get an existing
SessionControl
object given
a
ServletRequest
and check for generic (role-based)
permission to an item type.
- getExpectedHardwareSubtype(DbControl, BasicItem) - Method in class net.sf.basedb.util.overview.validator.HardwareValidator
-
Get the subtype of the associated hardware that we expect for the given
parent item.
- getExpectedKitSubtype(DbControl, BasicItem, boolean) - Method in class net.sf.basedb.util.overview.validator.KitValidator
-
Get the subtype of the associated kit that we expect for the given
parent item.
- getExpectedProtocolSubtype(DbControl, BasicItem) - Method in class net.sf.basedb.util.overview.validator.ProtocolValidator
-
Get the subtype of the associated protocol that we expect for the given
parent item.
- getExpectedSoftwareSubtype(DbControl, BasicItem) - Method in class net.sf.basedb.util.overview.validator.SoftwareValidator
-
Get the subtype of the associated software that we expect for the given
parent item.
- getExpectedTagSubtype(DbControl, BasicItem) - Method in class net.sf.basedb.util.overview.validator.TagValidator
-
Get the subtype of the associated tag that we expect for the given
parent item.
- getExperiment(DbControl) - Method in class net.sf.basedb.clients.web.ExperimentExplorer
-
Get the experiment that is currently beeing explored.
- getExperiment() - Method in class net.sf.basedb.core.BioAssay
-
Get the experiment this bioassay belongs to.
- getExperiment() - Method in class net.sf.basedb.core.BioAssaySet
-
Get the experiment this bioassayset belongs to.
- getExperiment() - Method in class net.sf.basedb.core.data.BioAssaySetData
-
Get the experiment this bioassayset belongs to.
- getExperiment() - Method in class net.sf.basedb.core.data.JobData
-
The experiment this job is a part of.
- getExperiment() - Method in class net.sf.basedb.core.data.ReporterListData
-
Get the experiment this reporter list belongs to.
- getExperiment() - Method in class net.sf.basedb.core.data.RootRawBioAssayData
-
Get the experiment this root raw bioassay belongs to.
- getExperiment() - Method in class net.sf.basedb.core.data.TransformationData
-
Get the experiment this bioassayset belongs to.
- getExperiment() - Method in class net.sf.basedb.core.data.VirtualDbData
-
Get the experiment that stores it's data in this virtual database.
- getExperiment() - Method in class net.sf.basedb.core.DataCube
-
Get the experiment this data cube belongs to.
- getExperiment() - Method in class net.sf.basedb.core.ExtraValue
-
Get the experiment this extra value belongs to.
- getExperiment() - Method in class net.sf.basedb.core.Job
-
Get the experiment this job is a part of.
- getExperiment() - Method in class net.sf.basedb.core.ReporterCloneBatcher
-
Get the current experiment this batcher is used with.
- getExperiment() - Method in class net.sf.basedb.core.ReporterList
-
Get the experiment this reporter list belongs to.
- getExperiment() - Method in class net.sf.basedb.core.RootRawBioAssay
-
Get the experiment this root raw bioassay belongs to.
- getExperiment() - Method in class net.sf.basedb.core.Transformation
-
Get the experiment this transformation belongs to.
- getExperiment() - Method in class net.sf.basedb.core.VirtualDb
-
Get the experiment this set of tables stores data for.
- getExperimentalFactorField(String, String) - Method in class net.sf.basedb.util.export.spotdata.AbstractFieldConverter
-
Get an experimental factor assay field.
- getExperimentalFactors() - Method in class net.sf.basedb.core.data.ExperimentData
-
The annotation types which describes the experimental factors for this experiment.
- getExperimentalFactors() - Method in class net.sf.basedb.core.Experiment
-
Get a query that returns all annotation types used as experimental factors
for this experiment.
- getExperimentDesign() - Method in class net.sf.basedb.core.data.ExperimentData
-
Get the experimental design for this experiment.
- getExperimentDesign() - Method in class net.sf.basedb.core.Experiment
-
Get the a text describing the experimental design.
- getExperiments() - Method in class net.sf.basedb.core.data.AnnotationTypeData
-
This is the inverse end.
- getExperiments() - Method in class net.sf.basedb.core.data.RawBioAssayData
-
This is the inverse end.
- getExperiments() - Method in class net.sf.basedb.core.RawBioAssay
-
Get a query that returns all experiments where this raw bioassay is used.
- getExperimentType() - Method in class net.sf.basedb.core.data.ExperimentData
-
Get the experimental type for this experiment.
- getExperimentType() - Method in class net.sf.basedb.core.Experiment
-
Get the a text describing the experiment type.
- getExpirationDate() - Method in class net.sf.basedb.core.data.KitData
-
Get expiration date for the kit.
- getExpirationDate() - Method in class net.sf.basedb.core.data.UserData
-
Get the expiration date for this user account, or null if no expiration date
is set.
- getExpirationDate() - Method in class net.sf.basedb.core.Kit
-
Get the expiration date of the kit.
- getExpirationDate() - Method in class net.sf.basedb.core.User
-
Get the expire date of the account.
- getExplorer(BioAssaySet) - Static method in class net.sf.basedb.clients.web.ExperimentExplorer
-
Get the existing experiment explorer for a bioassayset or create a new
one if none exist yet.
- getExportable() - Method in class net.sf.basedb.clients.web.taglib.table.TableColumn
-
- getExportableFields(DbControl, BioAssaySet) - Method in class net.sf.basedb.plugins.BaseFileExporterPlugin
-
- getExportableFields(DbControl, BioAssaySet) - Method in class net.sf.basedb.plugins.BfsExporterPlugin
-
- getExporter(DbControl, boolean, boolean) - Method in class net.sf.basedb.plugins.executor.ExternalProgramExecutor
-
Get an instance of the exporter plug-in.
- getExportFormatter() - Method in class net.sf.basedb.clients.web.extensions.list.AbstractListColumnBean
-
- getExportFormatter() - Method in interface net.sf.basedb.clients.web.extensions.list.ListColumnAction
-
Get a formatter that converts the exported value to a string that is written
to the file.
- getExportProperty() - Method in class net.sf.basedb.clients.web.extensions.list.AbstractListColumnBean
-
- getExportProperty() - Method in interface net.sf.basedb.clients.web.extensions.list.ListColumnAction
-
Override the default property when this column is used for exporting.
- getExportproperty() - Method in class net.sf.basedb.clients.web.taglib.table.ColumnDef
-
- getExportValue(DbControl, I) - Method in class net.sf.basedb.clients.web.extensions.list.AbstractListColumnBean
-
- getExportValue(DbControl, I) - Method in interface net.sf.basedb.clients.web.extensions.list.ListColumnAction
-
Get the value that should be used when exporting to a file.
- getExpression() - Method in class net.sf.basedb.core.query.ExpressionSelect
-
- getExpression() - Method in interface net.sf.basedb.core.query.Select
-
Get the expression object representing the selected expression.
- getExpression(DbControl, DynamicQuery, BioAssaySet, boolean) - Method in class net.sf.basedb.plugins.BaseFileExporterPlugin.ExtendedDynamicField
-
- getExpression(DbControl, DynamicQuery, BioAssaySet, boolean) - Method in interface net.sf.basedb.util.export.spotdata.DynamicField
-
Get an expression that selects the data that should be exported.
- getExpression(DbControl, DynamicQuery, BioAssaySet, boolean) - Method in class net.sf.basedb.util.export.spotdata.JepDynamicField
-
- getExpression(DbControl, DynamicQuery, BioAssaySet, boolean) - Method in class net.sf.basedb.util.export.spotdata.SimpleDynamicField
-
Returns the configured expression.
- getExpression() - Method in class net.sf.basedb.util.export.spotdata.SimpleDynamicField
-
Get the configured express.
- getExpressions() - Method in class net.sf.basedb.core.IntensityFormula
-
Get the expressions used to calculate the intensities.
- getExtended(String) - Method in class net.sf.basedb.core.authentication.ExtraUserInformation
-
Get an extended property value.
- getExtended(String) - Method in interface net.sf.basedb.core.data.ExtendableData
-
Get the value of an extended property.
- getExtended(String) - Method in class net.sf.basedb.core.data.RawData
-
- getExtended(String) - Method in class net.sf.basedb.core.data.ReporterData
-
- getExtended(String) - Method in class net.sf.basedb.core.data.UserData
-
- getExtended(String) - Method in class net.sf.basedb.core.User
-
Gets an extended property with a certain name
- getExtendedPropertyFiles() - Static method in class net.sf.basedb.core.Application
-
Get the path to the XML file containing extended properties.
- getExtendedPropertyFormatter(SessionControl, ExtendedProperty) - Static method in class net.sf.basedb.clients.web.formatter.FormatterFactory
-
Get a formatter for an extended property.
- getExtends() - Method in interface net.sf.basedb.util.extensions.Extension
-
Get the ID of the extension point this extension is extending.
- getExtends() - Method in class net.sf.basedb.util.extensions.ExtensionBean
-
- getExtends() - Method in class net.sf.basedb.util.extensions.Registry.RegisteredExtension
-
- getExtension(String) - Method in class net.sf.basedb.clients.web.extensions.ExtensionsControl
-
Get the extension with a given ID.
- getExtension() - Method in class net.sf.basedb.clients.web.fileupload.UploadedFile
-
Get the extension of the original filename.
- getExtension() - Method in class net.sf.basedb.core.data.DataFileTypeData
-
Get the extension that files of this type usually have.
- getExtension() - Method in class net.sf.basedb.core.data.MimeTypeData
-
Get the extension for this MimeType
item.
- getExtension() - Method in class net.sf.basedb.core.DataFileType
-
Get the common file extension for data files of this type.
- getExtension() - Method in class net.sf.basedb.core.MimeType
-
Get the extension for this MimeType
item.
- getExtension() - Method in class net.sf.basedb.util.extensions.ActionIterator
-
Get the extension that created the current action.
- getExtension() - Method in class net.sf.basedb.util.extensions.ExtensionContext
-
- getExtension() - Method in class net.sf.basedb.util.extensions.ExtensionPointContext
-
Always null, since this is an extension point context.
- getExtension() - Method in class net.sf.basedb.util.extensions.InvokationContext
-
Get information about the extension.
- getExtension(String) - Method in class net.sf.basedb.util.extensions.Registry
-
Get the extension with a given ID.
- getExtensionClassLoader() - Method in class net.sf.basedb.clients.web.extensions.XJspCompiler
-
Get a class loader that can load classes from the current web application
as well as the extensions JAR file.
- getExtensionColumns() - Method in class net.sf.basedb.clients.web.taglib.table.Table
-
- getExtensionPoint(String) - Method in class net.sf.basedb.clients.web.extensions.ExtensionsControl
-
Get the extension point with a given ID.
- getExtensionPoint() - Method in class net.sf.basedb.util.extensions.ActionIterator
-
Get the extension point that the current action
belongs to.
- getExtensionPoint() - Method in class net.sf.basedb.util.extensions.ExtensionContext
-
- getExtensionPoint() - Method in class net.sf.basedb.util.extensions.ExtensionPointContext
-
- getExtensionPoint() - Method in class net.sf.basedb.util.extensions.InvokationContext
-
Get information about the extension point.
- getExtensionPoint(String) - Method in class net.sf.basedb.util.extensions.Registry
-
Get the extension point with a given ID.
- getExtensionPoint() - Method in class net.sf.basedb.util.extensions.Registry.RegisteredExtension
-
Get the extension point this extension is registered with.
- getExtensionPoints() - Method in class net.sf.basedb.clients.web.extensions.ExtensionsControl
-
Get an list returning all registered extension points.
- getExtensionPoints() - Method in class net.sf.basedb.util.extensions.Registry
-
Get a list with all registered extension points.
- getExtensionPoints() - Method in class net.sf.basedb.util.extensions.xml.XmlLoader
-
Get a list with all loaded extension points.
- getExtensions() - Method in class net.sf.basedb.clients.web.extensions.ExtensionsControl
-
Get a list returning all registered extensions.
- getExtensions(String) - Method in class net.sf.basedb.clients.web.extensions.ExtensionsControl
-
Get a list returning all registered extensions for a
specific extension point.
- getExtensions() - Method in class net.sf.basedb.plugins.Bzip2FileUnpacker
-
Return a set containing the strings [ bz2 ].
- getExtensions() - Method in class net.sf.basedb.plugins.GzipFileUnpacker
-
Return a set containing the strings [ gz ].
- getExtensions() - Method in class net.sf.basedb.plugins.TarFileUnpacker
-
Return a set containing the strings [ tar, tar.gz, tgz, tar.bz2 ].
- getExtensions() - Method in class net.sf.basedb.plugins.ZipFileUnpacker
-
Return a set containing the strings [ zip, jar ].
- getExtensions() - Method in class net.sf.basedb.util.extensions.Registry
-
Get a list with all registered extensions.
- getExtensions(String) - Method in class net.sf.basedb.util.extensions.Registry
-
Get a list with all registered extensions
for a given extension point.
- getExtensions() - Method in class net.sf.basedb.util.extensions.Registry.RegisteredExtensionPoint
-
Get all extensions registered with this extension point.
- getExtensions() - Method in class net.sf.basedb.util.extensions.xml.XmlLoader
-
Get a list with all loaded extensions.
- getExtensions() - Method in interface net.sf.basedb.util.zip.FileUnpacker
-
Get the file extensions that this unpacker supports.
- getExtensionsFile() - Method in class net.sf.basedb.util.extensions.manager.ExtensionsFile.WriteableExtensionsFile
-
Get the underlying extensions file (for readin information)
- getExtensionsFile() - Method in class net.sf.basedb.util.extensions.manager.ProcessResults.FileResults
-
- getExtensionsManager() - Static method in class net.sf.basedb.core.Application
-
- getExternalClientId() - Method in class net.sf.basedb.core.SessionControl
-
Get the external id of the Client
application in use.
- getExternalId() - Method in class net.sf.basedb.core.AnnotationType
-
Get the external id of the annotation type.
- getExternalId() - Method in class net.sf.basedb.core.authentication.AuthenticatedUser
-
Get the external id for the user.
- getExternalId() - Method in class net.sf.basedb.core.BioMaterial
-
Get the external id of the biomaterial.
- getExternalId() - Method in class net.sf.basedb.core.BioPlate
-
Gets the external id of this bio plate
- getExternalId() - Method in class net.sf.basedb.core.Client
-
Get the external id for this Client
item.
- getExternalId() - Method in class net.sf.basedb.core.data.AnnotationTypeData
-
Get the external id for the biomaterial
- getExternalId() - Method in class net.sf.basedb.core.data.BioMaterialData
-
Get the external id for the biomaterial
- getExternalId() - Method in class net.sf.basedb.core.data.BioPlateData
-
Get the external id for the biomaterial
- getExternalId() - Method in class net.sf.basedb.core.data.ClientData
-
Get the external id for this Client
item.
- getExternalId() - Method in class net.sf.basedb.core.data.DataFileTypeData
-
Get the external id for the item.
- getExternalId() - Method in class net.sf.basedb.core.data.ExtraValueTypeData
-
Get the external id for this ExtraValueType
item.
- getExternalId() - Method in class net.sf.basedb.core.data.FeatureData
-
Get the external id for this FeatureData
item.
- getExternalId() - Method in class net.sf.basedb.core.data.HelpData
-
Get the external id for this Help
item.
- getExternalId() - Method in class net.sf.basedb.core.data.ItemListData
-
Get the external id for this ItemList
item.
- getExternalId() - Method in class net.sf.basedb.core.data.JobAgentData
-
Get the external ID for the job agent.
- getExternalId() - Method in class net.sf.basedb.core.data.JobData
-
External ID of a job running on an external system.
- getExternalId() - Method in class net.sf.basedb.core.data.PlatformData
-
Get the external id for the item.
- getExternalId() - Method in class net.sf.basedb.core.data.PlatformVariantData
-
Get the external id for the item.
- getExternalId() - Method in class net.sf.basedb.core.data.ProtocolData
-
Get the external id for the protocol.
- getExternalId() - Method in class net.sf.basedb.core.data.ReporterData
-
Get the external id for this ReporterData
item.
- getExternalId() - Method in class net.sf.basedb.core.data.ReporterListData
-
Get the external id for this ReporterList
item.
- getExternalId() - Method in class net.sf.basedb.core.data.UserData
-
Get the external ID for the user account.
- getExternalId() - Method in class net.sf.basedb.core.DataFileType
-
Get the external id for the data file type.
- getExternalId() - Method in class net.sf.basedb.core.ExtraValueType
-
Get the external id for this ExtraValueType
item.
- getExternalId() - Method in class net.sf.basedb.core.Help
-
Get the external id for this Help
item.
- getExternalId() - Method in class net.sf.basedb.core.ItemList
-
Get the external id for this list.
- getExternalId() - Method in class net.sf.basedb.core.Job
-
Get the external ID of a job running on an external server.
- getExternalId() - Method in class net.sf.basedb.core.JobAgent
-
Get the external id for the job agent.
- getExternalId() - Method in class net.sf.basedb.core.Platform
-
Get the external id for the platform.
- getExternalId() - Method in class net.sf.basedb.core.PlatformVariant
-
Get the external id for the platform variant.
- getExternalId() - Method in class net.sf.basedb.core.Protocol
-
Get the external id of the protocol.
- getExternalId() - Method in class net.sf.basedb.core.RawDataBatcher.ReporterProxy
-
- getExternalId() - Method in class net.sf.basedb.core.ReporterList
-
Get the external id for this ReporterList
item.
- getExternalId() - Method in class net.sf.basedb.core.User
-
Get the external id for the user account.
- getExtract() - Method in class net.sf.basedb.core.data.DerivedBioAssayData
-
Get the extract that this bioassay is related to.
- getExtract() - Method in class net.sf.basedb.core.DerivedBioAssay
-
Get the extract that is the parent of the data in this
derived bioassay.
- getExtract(Annotatable) - Static method in class net.sf.basedb.util.AnnotationUtil.AnnotatableWrapper
-
Get the extract to use.
- getExtract(DerivedBioAssay) - Method in class net.sf.basedb.util.overview.loader.DerivedBioAssayLoader
-
Get the extract that is associated with the current derived bioassay
- getExtractChain(DbControl, Node) - Method in class net.sf.basedb.util.overview.loader.DerivedBioAssayLoader
-
- getExtractChain(Node) - Method in class net.sf.basedb.util.overview.loader.ExtractLoader
-
- getExtractChain(DbControl, Node) - Method in class net.sf.basedb.util.overview.loader.RawBioAssayLoader
-
- getExtracts(int) - Method in class net.sf.basedb.core.PhysicalBioAssay
-
Get a query that returns extracts connected to
this bioassay.
- getExtracts() - Method in class net.sf.basedb.core.Sample
-
Get a query that returns all extracts created from this sample.
- getExtraFilesDirectory(DbControl, String) - Method in class net.sf.basedb.plugins.executor.BaseFileImporterSupport
-
- getExtraFilesDirectory(DbControl, String) - Method in class net.sf.basedb.plugins.executor.BfsImporterSupport
-
- getExtraFilesDirectory(DbControl, String) - Method in class net.sf.basedb.plugins.executor.FileOnlyImporterSupport
-
- getExtraFloat(String) - Method in class net.sf.basedb.util.importer.spotdata.BaseFileInfo
-
Get the extra value type that has the given external id.
- getExtraFloatParsers() - Method in class net.sf.basedb.util.importer.spotdata.BaseFileInfo.SpotSectionInfo
-
Get the list of extra value parsers that exists for
this section.
- getExtraInformation() - Method in class net.sf.basedb.core.authentication.AuthenticatedUser
-
Get extra information about the user.
- getExtraNo() - Method in class net.sf.basedb.core.data.DataCubeExtraValueData
-
The number of this extra value in the data cube.
- getExtraNo() - Method in class net.sf.basedb.core.DataCubeExtraValue
-
Get the extra value number.
- getExtraNo() - Method in class net.sf.basedb.core.ExtraValue
-
Get the number in the data cube of the extra values.
- getExtraValue(ExtraValueType) - Method in class net.sf.basedb.core.BioAssaySet
-
Get the extra value of the specified type in this bioassayset.
- getExtraValue() - Method in class net.sf.basedb.core.ExtraValueExpression
-
- getExtraValue() - Method in class net.sf.basedb.core.SpotExtraValueBatcher
-
Get the extra value item representing all extra values.
- getExtraValueField(String, ExtraValue.CoordinateType, String) - Method in class net.sf.basedb.util.export.spotdata.AbstractFieldConverter
-
Get an extra value dynamic field.
- getExtraValueFields(DbControl, BioAssaySet) - Method in class net.sf.basedb.plugins.BaseFileExporterPlugin
-
- getExtraValueFields(DbControl, BioAssaySet) - Method in class net.sf.basedb.plugins.BfsExporterPlugin
-
- getExtraValueJoiner(JoinType) - Static method in class net.sf.basedb.core.DynamicPositionQueryJoiners
-
Get a joiner instance for extra values for the specified join type.
- getExtraValueJoiner(JoinType) - Static method in class net.sf.basedb.core.DynamicSpotQueryJoiners
-
Get a joiner instance for extra values for the specified join type.
- getExtraValues() - Method in class net.sf.basedb.core.BioAssaySet
-
Get a query returning the extra values that are part of this
bioassayset.
- getExtraValues() - Method in class net.sf.basedb.core.data.BioAssaySetData
-
The extra values calculated for this bioassayset.
- getExtraValues() - Method in class net.sf.basedb.core.data.DataCubeData
-
This is the inverse end.
- getExtraValues() - Method in class net.sf.basedb.core.data.ExtraValueTypeData
-
This is the inverse end.
- getExtraValueType() - Method in class net.sf.basedb.core.data.ExtraValueData
-
Get the type of this extra value.
- getExtraValueType() - Method in class net.sf.basedb.core.ExtraValue
-
Get the type of the extra values.
- getExtraValueTypes() - Method in class net.sf.basedb.core.BioAssaySet
-
Get a query returning all extra values types that are used in
this bioassay set.
- getFactories() - Static method in class net.sf.basedb.util.uri.ConnectionManagerUtil
-
Get a list with all connection manager factories.
- getFactory(String) - Static method in class net.sf.basedb.util.uri.ConnectionManagerUtil
-
Get the connection manager factory with the given extension id.
- getFactoryParameters(Object) - Method in class net.sf.basedb.util.extensions.xml.XmlLoader
-
Get a XML-like string representation of the parameters that was
used to initialise a factory.
- getFailures() - Method in class net.sf.basedb.util.overview.GenericOverview
-
Get a list containing all validation failures.
- getFailureSummary() - Method in interface net.sf.basedb.util.overview.extensions.ValidationRuleAction
-
Get a short summary that is displayed when the validation fails
- getFailureSummary() - Method in class net.sf.basedb.util.overview.Validator
-
Get a short summary that is displayed when the validation fails
- getFallbackLocale(String, Locale) - Method in class net.sf.basedb.util.resources.Utf8PropertiesResourceBundleControl
-
We don't need a fallback locale.
- getFavicon() - Method in class net.sf.basedb.clients.web.extensions.skin.FixedSkinActionFactory
-
- getFavicon() - Method in class net.sf.basedb.clients.web.extensions.skin.FixedSkinActionFactory.MySkinAction
-
- getFavicon() - Method in interface net.sf.basedb.clients.web.extensions.skin.SkinAction
-
Get the full path to a favicon for the BASE site.
- getFavicon() - Method in class net.sf.basedb.clients.web.taglib.Page
-
- getFax() - Method in class net.sf.basedb.core.authentication.ExtraUserInformation
-
The fax number to the user.
- getFax() - Method in class net.sf.basedb.core.data.UserData
-
Get the fax number to the user, or null if unknown.
- getFax() - Method in class net.sf.basedb.core.User
-
Get the fax number to the user, or null if unknown.
- getFeature() - Method in class net.sf.basedb.core.data.RawData
-
The feature this raw data is connected with.
- getFeature(RawDataBatcher.FeatureProxy) - Method in class net.sf.basedb.core.RawDataBatcher.FeatureInfo
-
- getFeatureBatcher(FeatureIdentificationMethod, Job) - Method in class net.sf.basedb.core.ArrayDesign
-
Get a feature batcher which can be used to add regular features to the
array design.
- getFeatureById(int) - Method in class net.sf.basedb.core.ArrayDesign
-
Get a feature when you know the id.
- getFeatureById(int, boolean) - Method in class net.sf.basedb.core.ArrayDesign
-
Get a feature when you know the id.
- getFeatureCoordinate(FeatureData) - Static method in class net.sf.basedb.core.Feature
-
Get the coordinate of the feature.
- getFeatureDiameter() - Method in class net.sf.basedb.core.ArrayDesignBlock
-
Get the expected diameter of spots on the slide.
- getFeatureDiameter() - Method in class net.sf.basedb.core.data.ArrayDesignBlockData
-
The expected diameter of spots.
- getFeatureIdentificationMethod() - Method in class net.sf.basedb.core.ArrayDesign
-
Get the method used to identify features on this array design.
- getFeatureIdentificationMethod() - Method in class net.sf.basedb.core.data.ArrayDesignData
-
The method to use for identiying features.
1 = COORDINATES, 2 = POSITION, 3 = FEATURE_ID
- getFeatures() - Method in class net.sf.basedb.core.ArrayDesign
-
Get a query that returns the regular features of this array design.
- getFeatures() - Method in class net.sf.basedb.core.data.ArrayDesignBlockData
-
Used by Hibernate to link with features.
- getFetchSize() - Method in class net.sf.basedb.core.hibernate.QueryWrapper
-
- getField() - Method in class net.sf.basedb.plugins.BfsExporterPlugin.ExtendedExportableField
-
- getFile(String) - Method in class net.sf.basedb.clients.web.extensions.ExtensionsControl
-
Get information about an installed extensions file.
- getFile(String) - Method in class net.sf.basedb.clients.web.fileupload.FileUpload
-
Get the file information for an uplodaded file.
- getFile() - Method in interface net.sf.basedb.core.data.FileAttachableData
-
Get the file that is attached to the item.
- getFile() - Method in class net.sf.basedb.core.data.FileSetMemberData
-
Get the file.
- getFile() - Method in class net.sf.basedb.core.data.ProtocolData
-
- getFile(DbControl, Directory, String, boolean) - Static method in class net.sf.basedb.core.File
-
Get a File
item when you know the directory and filename.
- getFile() - Method in interface net.sf.basedb.core.FileAttachable
-
Get the file that is attached to the item.
- getFile() - Method in class net.sf.basedb.core.FileSetMember
-
Get the file this item is representing in the file set.
- getFile() - Method in class net.sf.basedb.core.plugin.ExportOutputStream
-
If the export stream is going to a BASE
File
object,
use this method to access it.
- getFile() - Method in class net.sf.basedb.core.Protocol
-
- getFile(String) - Method in class net.sf.basedb.util.bfs.BaseInputStreamLocator
-
- getFile(int) - Method in class net.sf.basedb.util.bfs.MetadataModel
-
Get the file entry with a given index.
- getFile(String) - Method in class net.sf.basedb.util.bfs.MetadataModel
-
Get the file entry for a given key.
- getFile() - Method in class net.sf.basedb.util.extensions.manager.ExtensionsFile
-
Get the underlying file on the file system.
- getFile() - Method in class net.sf.basedb.util.FileExportOutputStream
-
- getFileByObjectKey(ObjectKey<?>) - Method in class net.sf.basedb.clients.web.extensions.ExtensionsControl
-
Find out which file the given object is defined in.
- getFileByObjectKey(ObjectKey<?>) - Method in class net.sf.basedb.util.extensions.manager.ExtensionsManager
-
Find out which file the object with the given key was defined.
- getFileByURI(String) - Method in class net.sf.basedb.util.extensions.manager.ExtensionsManager
-
Get the extension file that is located at the given URI.
- getFileCount() - Method in class net.sf.basedb.util.bfs.MetadataModel
-
Get the number of entries in the 'files' section.
- getFileExtension() - Method in class net.sf.basedb.util.zip.Bzip2FilePacker
-
- getFileExtension() - Method in interface net.sf.basedb.util.zip.FilePacker
-
Gets the extension that files, packed with this tool, should have,
for example, zip
or tar.gz
Don't include the first
dot!
- getFileExtension() - Method in class net.sf.basedb.util.zip.GzipFilePacker
-
- getFileExtension() - Method in class net.sf.basedb.util.zip.TarFilePacker
-
- getFileExtension() - Method in class net.sf.basedb.util.zip.ZipFilePacker
-
- getFileFormatParameter() - Static method in class net.sf.basedb.plugins.BaseFileExporterPlugin
-
Create a plug-in parameter that asks for the BASEFile subtype to use in
the export.
- getFileFormatParameter() - Static method in class net.sf.basedb.plugins.BfsExporterPlugin
-
Create a plug-in parameter that asks for the BFS subtype to use in
the export.
- getFileId() - Method in class net.sf.basedb.util.importer.spotdata.BaseFileInfo.ChildBioAssay
-
Get the id of the child bioassay as it appears in the
BASEfile.
- getFileIterator() - Method in class net.sf.basedb.plugins.AbstractFlatFileImporter
-
Get an iterator that returns the files to be imported.
- getFileIterator() - Method in class net.sf.basedb.plugins.RawDataFlatFileImporter
-
- getFileLinks(String, File, String) - Static method in class net.sf.basedb.clients.web.Base
-
Get view/download links for a file.
- getFilename() - Method in class net.sf.basedb.clients.web.fileupload.UploadedFile
-
Get the original filename of the uploaded file.
- getFilename() - Method in class net.sf.basedb.core.Path
-
Get the filename part of the path.
- getFilename() - Method in class net.sf.basedb.core.plugin.ImportInputStream
-
Get the name of the source.
- getFilename() - Method in class net.sf.basedb.util.bfs.AnnotationParser
-
Get the file name that this parser is reading from.
- getFilename() - Method in class net.sf.basedb.util.bfs.AnnotationWriter
-
Get the file name that this writer is printing to.
- getFilename() - Method in interface net.sf.basedb.util.bfs.BfsParser
-
Get the filename of the file that is being parsed.
- getFilename() - Method in class net.sf.basedb.util.bfs.DataParser
-
Get the file name that this parser is reading from.
- getFilename() - Method in class net.sf.basedb.util.bfs.DataWriter
-
Get the file name that this writer is printing to.
- getFilename() - Method in class net.sf.basedb.util.bfs.MetadataParser
-
Get the file name that this writer is printing to.
- getFilename() - Method in class net.sf.basedb.util.bfs.MetadataWriter
-
Get the file name that this writer is printing to.
- getFilename() - Method in class net.sf.basedb.util.FileImportInputStream
-
- getFilename() - Method in class net.sf.basedb.util.importer.spotdata.SynchronizedSpotDataParser
-
- getFileNameGeneratorParameter() - Static method in class net.sf.basedb.plugins.BfsExporterPlugin
-
Create a plug-in parameter that asks for the file name generation strategy.
- getFileOnlyRawDataTypes() - Static method in class net.sf.basedb.core.RawDataTypes
-
Get the raw data types that are representations of file-only
Platform
:s.
- getFiles() - Method in class net.sf.basedb.clients.web.extensions.ExtensionsControl
-
Get an list returning all XML/JAR files which contains installed
extensions.
- getFiles() - Method in class net.sf.basedb.core.data.DirectoryData
-
This is the inverse end.
- getFiles() - Method in class net.sf.basedb.core.data.FileServerData
-
This is the inverse end.
- getFiles() - Method in class net.sf.basedb.core.Directory
-
Get a query that return all files in this directory.
- getFiles() - Method in class net.sf.basedb.core.FileServer
-
Get a query returning all files that has been registered with this
server.
- getFiles() - Method in class net.sf.basedb.util.extensions.manager.ExtensionsManager
-
Get a list of all extension files managed by this manager.
- getFileServer() - Method in class net.sf.basedb.core.data.FileData
-
- getFileServer() - Method in class net.sf.basedb.core.File
-
Get the file server on which the external file is located.
- getFileSet() - Method in class net.sf.basedb.core.ArrayDesign
-
- getFileSet() - Method in class net.sf.basedb.core.BioAssaySet
-
- getFileSet() - Method in class net.sf.basedb.core.data.ArrayDesignData
-
- getFileSet() - Method in class net.sf.basedb.core.data.BioAssaySetData
-
- getFileSet() - Method in class net.sf.basedb.core.data.DerivedBioAssayData
-
- getFileSet() - Method in class net.sf.basedb.core.data.ExtraValueData
-
- getFileSet() - Method in class net.sf.basedb.core.data.FileSetMemberData
-
Get the file set this file belongs to.
- getFileSet() - Method in interface net.sf.basedb.core.data.FileStoreEnabledData
-
Get the file set attached to this item.
- getFileSet() - Method in class net.sf.basedb.core.data.RawBioAssayData
-
- getFileSet() - Method in class net.sf.basedb.core.DerivedBioAssay
-
- getFileSet() - Method in class net.sf.basedb.core.ExtraValue
-
- getFileSet() - Method in class net.sf.basedb.core.FileSetMember
-
Get the file set the file is a member of.
- getFileSet() - Method in interface net.sf.basedb.core.FileStoreEnabled
-
Get the file set that collects all files that holds data
for this item.
- getFileSet() - Method in class net.sf.basedb.core.RawBioAssay
-
- getFileSetMember() - Method in class net.sf.basedb.util.overview.Fix
-
- getFileSetMembers() - Method in class net.sf.basedb.core.data.DataFileTypeData
-
This is the inverse end.
- getFileSize() - Method in class net.sf.basedb.util.bfs.AnnotationParser
-
Get the size in bytes of the file that this parser is reading from.
- getFileSize() - Method in interface net.sf.basedb.util.bfs.BfsParser
-
Get the size of the file that is being parsed.
- getFileSize() - Method in class net.sf.basedb.util.bfs.DataParser
-
Get the size in bytes of the file that this parser is reading from.
- getFileSize() - Method in class net.sf.basedb.util.bfs.MetadataParser
-
Get the size in bytes of the file that this parser is reading from.
- getFileSize() - Method in class net.sf.basedb.util.importer.spotdata.SynchronizedSpotDataParser
-
- getFileStoreEnabledItems() - Static method in class net.sf.basedb.core.Metadata
-
- getFileType() - Method in class net.sf.basedb.core.data.MimeTypeData
-
- getFileType() - Method in class net.sf.basedb.core.MimeType
-
Get the associated file subtype item.
- getFileType(DataFileType, PlatformVariant, boolean) - Method in class net.sf.basedb.core.Platform
-
Get information about a file type that has been registered with this
platform/variant.
- getFileTypes() - Method in class net.sf.basedb.core.data.ItemSubtypeData
-
The file types that can be used on items of this subtype.
- getFileTypes() - Method in class net.sf.basedb.core.data.PlatformData
-
The file types that can be used on this platform.
- getFileTypes() - Method in class net.sf.basedb.core.data.PlatformVariantData
-
The additional file types that can be used on this platform variant.
- getFileTypes(PlatformVariant, boolean) - Method in class net.sf.basedb.core.Platform
-
Get the file types registered with this platform.
- getFileTypes(boolean) - Method in class net.sf.basedb.core.PlatformVariant
-
Get a query returning file types registered with this platform
variant.
- getFileValues(String) - Method in class net.sf.basedb.clients.web.fileupload.FileUpload
-
Get the file information for uplodaded files.
- getFilltext() - Method in class net.sf.basedb.clients.web.taglib.menu.Menu
-
- getFilterable() - Method in class net.sf.basedb.clients.web.taglib.table.TableColumn
-
- getFilterBatcher() - Method in class net.sf.basedb.core.BioAssaySet
-
Get a batcher used to insert the position/column coordinates that remain
after some filter has been applied to the spot data of a bioassayset.
- getFilterNo() - Method in class net.sf.basedb.core.data.DataCubeFilterData
-
The number of this filter in the data cube.
- getFilterNo() - Method in class net.sf.basedb.core.DataCubeFilter
-
Get the number of this filter.
- getFilterProperty() - Method in class net.sf.basedb.clients.web.extensions.list.AbstractListColumnBean
-
- getFilterProperty() - Method in interface net.sf.basedb.clients.web.extensions.list.ListColumnAction
-
Override the default property when this column is used for filtering.
- getFilterproperty() - Method in class net.sf.basedb.clients.web.taglib.table.ColumnDef
-
- getFilterRestriction(String, DbControl, EntityQuery) - Method in class net.sf.basedb.core.ItemContext
-
Create a restriction from a property filter on filter row 0.
- getFilterRestriction(String, int, DbControl, EntityQuery) - Method in class net.sf.basedb.core.ItemContext
-
Create a restriction from a property filter on the given filter row.
- getFilterrows() - Method in class net.sf.basedb.clients.web.taglib.table.Table
-
- getFilterRows() - Method in class net.sf.basedb.core.ItemContext
-
Get the number of filter rows to display on the list page.
- getFilterRows() - Method in class net.sf.basedb.core.SyncFilter
-
Get the number of filter rows in this filter.
- getFilters() - Method in class net.sf.basedb.core.data.DataCubeData
-
This is the inverse end.
- getFingerprintType() - Method in class net.sf.basedb.core.data.FileServerData
-
Get the type of SSH fingerprint.
- getFingerprintType() - Method in class net.sf.basedb.core.FileServer
-
Get the type of the SSH fingerprint.
- getFirst(ExtensionsInvoker<ConnectionManagerFactory>) - Static method in class net.sf.basedb.util.uri.ConnectionManagerUtil
-
Get the first factory returned by the invoker.
- getFirstAssayFieldIndex() - Method in class net.sf.basedb.util.importer.spotdata.BaseFileInfo.SpotSectionInfo
-
The index of the first data column that contains assay data.
- getFirstMatching(DbControl, ItemQuery<T>, String, PropertyFilter) - Static method in class net.sf.basedb.clients.web.Base
-
- getFirstNode(Filter<? super Node>) - Method in class net.sf.basedb.util.overview.Node
-
Find the first node (including this) that matches
a filter.
- getFirstNull(Object[]) - Static method in class net.sf.basedb.core.query.Expressions
-
Test if there is null in the array.
- getFirstNull(Object[]) - Static method in class net.sf.basedb.core.query.Restrictions
-
Test if there is null in the array.
- getFirstParent(Filter<? super Node>) - Method in class net.sf.basedb.util.overview.Node
-
Find the first parent node that matches a filter.
- getFirstResult() - Method in class net.sf.basedb.core.AbstractQuery
-
- getFirstResult() - Method in class net.sf.basedb.core.hibernate.QueryWrapper
-
- getFirstResult() - Method in interface net.sf.basedb.core.query.Query
-
The number of the row the query should start returning.
- getFixes() - Method in class net.sf.basedb.util.overview.Failure
-
Get a list of suggested fixes.
- getFkColumns() - Method in class net.sf.basedb.core.dbengine.TableInfo.ForeignKeyInfo
-
- getFloat(int) - Method in class net.sf.basedb.clients.web.servlet.PlotServlet.CFSqlResult
-
- getFloat(int) - Method in class net.sf.basedb.core.DynamicResultIterator.SqlResultImpl
-
- getFloat(int) - Method in interface net.sf.basedb.core.query.SqlResult
-
Get the value of the specified column as a float.
- getFloat(FlatFileParser.Data) - Method in class net.sf.basedb.util.parser.ColumnMapper
-
- getFloat(FlatFileParser.Data) - Method in class net.sf.basedb.util.parser.CompoundMapper
-
- getFloat(FlatFileParser.Data) - Method in class net.sf.basedb.util.parser.ConstantMapper
-
- getFloat(FlatFileParser.Data) - Method in class net.sf.basedb.util.parser.CropStringMapper
-
- getFloat(FlatFileParser.Data) - Method in class net.sf.basedb.util.parser.JepMapper
-
- getFloat(FlatFileParser.Data) - Method in interface net.sf.basedb.util.parser.Mapper
-
Get the value for the line of data as a float.
- getFloat(FlatFileParser.Data) - Method in class net.sf.basedb.util.parser.NullIfExceptionMapper
-
- getFloat(String) - Static method in class net.sf.basedb.util.Values
-
Convert a string to an float.
- getFloat(String, float) - Static method in class net.sf.basedb.util.Values
-
Convert a string to an integer.
- getFloat(String, Float) - Static method in class net.sf.basedb.util.Values
-
- getFloat(String[]) - Static method in class net.sf.basedb.util.Values
-
Convert an array of strings to an array of Float:s.
- getFloatOption(String, Float) - Method in class net.sf.basedb.core.AnnotationType
-
Get an option and convert the value to a float.
- getFloatValues() - Method in class net.sf.basedb.core.data.annotations.AnnotationLink
-
- getFlushMode() - Method in class net.sf.basedb.core.hibernate.QueryWrapper
-
- getFlushMode() - Method in class net.sf.basedb.core.hibernate.SessionWrapper
-
- getForeignKeys() - Method in class net.sf.basedb.core.dbengine.TableInfo
-
Get information about the foreign keys in the table.
- getForInsert(Object, Map, SessionImplementor) - Method in class net.sf.basedb.core.ExtendedPropertyAccessor.GetterSetter
-
Get the value of the extended property.
- getFormatName() - Method in class net.sf.basedb.plugins.Bzip2FileUnpacker
-
- getFormatName() - Method in class net.sf.basedb.plugins.GzipFileUnpacker
-
- getFormatName() - Method in class net.sf.basedb.plugins.TarFileUnpacker
-
- getFormatName() - Method in class net.sf.basedb.plugins.ZipFileUnpacker
-
- getFormatName() - Method in interface net.sf.basedb.util.zip.FileUnpacker
-
Get the name of the compressed file format this unpacker supports.
- getFormatParameter() - Method in class net.sf.basedb.clients.web.plugins.SimpleExport
-
- getFormats(String) - Method in class net.sf.basedb.util.resources.Utf8PropertiesResourceBundleControl
-
This control only handle property files.
- getFormattedAndSortedFilters(Collection<PropertyFilter>, Formatter<PropertyFilter>) - Static method in class net.sf.basedb.core.SyncFilter
-
Utility method for formatting and sorting a list of property filters.
- getFormatter() - Method in class net.sf.basedb.clients.web.extensions.list.AbstractListColumnBean
-
- getFormatter() - Method in interface net.sf.basedb.clients.web.extensions.list.ListColumnAction
-
Get a formatter that converts the current value to a string that is displayed
in the column.
- getFormatter(InvokationContext, String) - Method in class net.sf.basedb.clients.web.extensions.list.PropertyPathActionFactory
-
Create a formatter instance that should be used for the online table.
- getFormatter() - Method in class net.sf.basedb.clients.web.taglib.table.Cell
-
- getFormatter() - Method in class net.sf.basedb.clients.web.taglib.table.ColumnDef
-
- getFormatter(String) - Method in class net.sf.basedb.clients.web.taglib.table.Table
-
- getFormatter() - Method in class net.sf.basedb.clients.web.taglib.table.TableColumn
-
- getFormatter(Formatter<T>) - Method in class net.sf.basedb.core.Unit
-
Create a formatter for formatting values with this unit.
- getFormatter() - Method in class net.sf.basedb.plugins.BaseFileExporterPlugin.ExtendedDynamicField
-
- getFormatter() - Method in class net.sf.basedb.util.export.spotdata.AnnotationAssayField
-
- getFormatter() - Method in class net.sf.basedb.util.export.spotdata.AssayPropertyField
-
- getFormatter() - Method in interface net.sf.basedb.util.export.spotdata.ExportableField
-
Get a formatter that converts the values in this field to strings.
- getFormatter() - Method in class net.sf.basedb.util.export.spotdata.JepDynamicField
-
- getFormatter() - Method in class net.sf.basedb.util.export.spotdata.SimpleDynamicField
-
- getFormName() - Method in class net.sf.basedb.clients.web.fileupload.UploadedFile
-
Get the name of the form field that this file was selected in.
- getFormula(int) - Method in class net.sf.basedb.core.Formula
-
Get an expression.
- getFormulaField(String, String) - Method in class net.sf.basedb.util.export.spotdata.AbstractFieldConverter
-
Get a formula dynamic field.
- getFormulaFields(DbControl, BioAssaySet) - Method in class net.sf.basedb.plugins.BaseFileExporterPlugin
-
- getFormulaFields(DbControl, BioAssaySet) - Method in class net.sf.basedb.plugins.BfsExporterPlugin
-
- getFormulaFormatter(SessionControl, Formula) - Static method in class net.sf.basedb.clients.web.formatter.FormatterFactory
-
Get a formatter that knows how to format results from formulas.
- getFormulas() - Method in class net.sf.basedb.core.data.FormulaData
-
Get the list of formulas.
- getFormulas() - Method in class net.sf.basedb.core.Formula
-
Get all expressions as an unmodifiable list.
- getFormulaType() - Method in class net.sf.basedb.core.Formula
-
Get the type of formula.
- getFreeWells() - Method in class net.sf.basedb.core.BioPlate
-
Get the number of free wells on this plate.
- getFreeWells() - Method in class net.sf.basedb.core.data.BioPlateData
-
Get the number of wells that are free on the bioplate.
- getFreezer() - Method in class net.sf.basedb.core.BioPlate
-
Gets the storage location of this bio plate
- getFreezer() - Method in class net.sf.basedb.core.data.BioPlateData
-
Get the hardware, ie. freezer where the plate is kept.
- getFriends() - Method in class net.sf.basedb.core.SessionControl
-
Get the id of all friends to logged in user.
- getFrom() - Method in class net.sf.basedb.core.AnyToAny
-
Get the item this link is linking from.
- getFrom() - Method in class net.sf.basedb.core.data.MessageData
-
The name of the user this message is from.
- getFrom() - Method in class net.sf.basedb.core.Message
-
Get the name of the sender of this message.
- getFromId() - Method in class net.sf.basedb.core.AnyToAny
-
Get the ID of the item this link is linking from.
- getFromId() - Method in class net.sf.basedb.core.data.AnyToAnyData
-
The ID of the item we are linking from.
- getFromId() - Method in class net.sf.basedb.core.data.MessageData
-
The id of the user if this message was from a real user.
- getFromType() - Method in class net.sf.basedb.core.AnyToAny
-
Get the type of the item this link is linking from.
- getFromType() - Method in class net.sf.basedb.core.data.AnyToAnyData
-
The type code of the item we are linking from.
- getFullClass(String...) - Method in class net.sf.basedb.clients.web.taglib.CalendarButton
-
Make sure that "auto-init" is added to the class
attribute.
- getFullClass(String...) - Method in class net.sf.basedb.clients.web.taglib.StylableTag
-
Get the full class (eg. main and subclass) as a single
string.
- getFullPermissionNames(Identifiable) - Static method in class net.sf.basedb.clients.web.PermissionUtil
-
- getFullPermissionNames(Set<Permission>, String) - Static method in class net.sf.basedb.clients.web.PermissionUtil
-
Create a comma-separated string with "readable" permission names.
- getFullQuotedTableName(DbEngine) - Method in class net.sf.basedb.core.dbengine.TableInfo
-
Get the fully quialified and quoted table name using
the quoting rules from the given DBEngine
- getFunctionName() - Method in class net.sf.basedb.util.jep.ChannelFunction
-
- getFunctionName() - Method in class net.sf.basedb.util.jep.ExtraValueFunction
-
- getFunctionName() - Method in class net.sf.basedb.util.jep.InReporterListFunction
-
- getFunctionName() - Method in interface net.sf.basedb.util.jep.JepFunction
-
Get the name of this function.
- getFunctionName() - Method in class net.sf.basedb.util.jep.LeftFunction
-
- getFunctionName() - Method in class net.sf.basedb.util.jep.Log2Function
-
- getFunctionName() - Method in class net.sf.basedb.util.jep.MeanFunction
-
- getFunctionName() - Method in class net.sf.basedb.util.jep.NotInReporterListFunction
-
- getFunctionName() - Method in class net.sf.basedb.util.jep.PositionFunction
-
- getFunctionName() - Method in class net.sf.basedb.util.jep.RawChannelFunction
-
- getFunctionName() - Method in class net.sf.basedb.util.jep.RawFunction
-
- getFunctionName() - Method in class net.sf.basedb.util.jep.ReporterFunction
-
- getFunctionName() - Method in class net.sf.basedb.util.jep.ScoreFunction
-
- getFunctionName() - Method in class net.sf.basedb.util.jep.SimpleJepFunction
-
- getFunctionName() - Method in class net.sf.basedb.util.parser.ColFunction
-
- getFunctionName() - Method in class net.sf.basedb.util.parser.DataNoFunction
-
- getFunctionName() - Method in class net.sf.basedb.util.parser.DefaultItemFunction
-
- getFunctionName() - Method in class net.sf.basedb.util.parser.LineNoFunction
-
- getFunctions() - Static method in class net.sf.basedb.util.jep.Jep
-
- getFutureResult(Callable<T>, QueryExecutor.Cancelable, SessionControl) - Static method in class net.sf.basedb.core.QueryExecutor
-
Run the callable and wait for the result.
- getGamma() - Method in class net.sf.basedb.core.data.SpotImagesData
-
The gamma correction value.
- getGamma() - Method in class net.sf.basedb.core.SpotImages
-
Get the gamma correction value.
- getGenericDataFiles(DbControl, FileStoreEnabled, String) - Static method in class net.sf.basedb.core.FileStoreUtil
-
Get all files with a specific generic
ItemSubtype
in a given item's file
set.
- getGenericMembers(DbControl, FileStoreEnabled, String) - Static method in class net.sf.basedb.core.FileStoreUtil
-
Get all file members with a specific generic
ItemSubtype
in a given item's file
set.
- getGenericPlatformFileTypes(DbControl, FileStoreEnabled, String) - Static method in class net.sf.basedb.core.FileStoreUtil
-
Get a list of all platform file types that has the specified generic
ItemSubtype
.
- getGenericType() - Method in class net.sf.basedb.core.data.DataFileTypeData
-
Get the generic file type of files with this member type.
- getGenericType() - Method in class net.sf.basedb.core.DataFileType
-
Get the generic file type for this data file type.
- getGetter() - Method in class net.sf.basedb.core.ExtendedPropertyAccessor.GetterSetter
-
- getGlobalSignalId(SignalHandler) - Method in class net.sf.basedb.core.signal.AbstractSignalReceiver
-
Generate a signal ID string.
- getGlobalSignalId() - Method in class net.sf.basedb.core.signal.AbstractSignalTransporter
-
- getGlobalSignalId(SignalHandler) - Method in class net.sf.basedb.core.signal.SocketSignalReceiver
-
Override ID generation so we can add proxy information if needed.
- getGranted() - Method in class net.sf.basedb.core.data.keyring.PluginKeys
-
Get the granted permissions.
- getGranted() - Method in class net.sf.basedb.core.data.PluginPermission
-
The permissions for the plugin
- getGranted(RoleKey) - Method in class net.sf.basedb.core.PluginDefinition
-
Get the permissions that have been granted to this plugin.
- getGreenImageFile() - Method in class net.sf.basedb.core.data.SpotImagesData
-
The file used for the green component in the spot images.
- getGreenImageFile() - Method in class net.sf.basedb.core.SpotImages
-
Get the file which was used for the green channel in the
spot images.
- getGroup() - Method in class net.sf.basedb.core.data.DiskUsageData
-
- getGroup() - Method in class net.sf.basedb.core.DiskUsage
-
Get the group that owns the
DiskConsumable
item or
null
if ther is none.
- getGroupId() - Method in class net.sf.basedb.core.data.keyring.GroupKeys
-
Get the id of the group.
- getGroupId() - Method in class net.sf.basedb.core.data.keyring.GroupProjects
-
Get the id of the group.
- getGroupId() - Method in class net.sf.basedb.core.data.keyring.UserGroups
-
Get the id of the group.
- getGroupIds(Permission) - Method in class net.sf.basedb.core.ItemKey
-
Get the ID:s of all groups that have the specified permission in this item key.
- getGroupPermissions() - Method in class net.sf.basedb.core.GroupPermissions
-
Get the internal representation of the permissions.
- getGroups() - Method in class net.sf.basedb.core.data.ItemKeyData
-
Get the map that manages which groups that have permissions
for this key.
- getGroups() - Method in class net.sf.basedb.core.data.ProjectData
-
Get the map that manages which users are members of this project
and their permissions.
- getGroups() - Method in class net.sf.basedb.core.data.UserData
-
This is the inverse end.
- getGroups() - Method in class net.sf.basedb.core.Group
-
Get a query that returns the groups that
are members of this group.
- getGroups() - Method in class net.sf.basedb.core.InternalJobQueue.JobQueueKeyring
-
Return empty set.
- getGroups() - Method in class net.sf.basedb.core.InternalStorageController.StorageKeyring
-
Return empty set.
- getGroups() - Method in class net.sf.basedb.core.Job.SignalKeyring
-
Return empty set.
- getGroups(boolean) - Method in class net.sf.basedb.core.Keyring
-
- getGroups() - Method in class net.sf.basedb.core.MultiPermissions
-
Get a query that returns all groups appearing in at least one of
the item keys.
- getGroups() - Method in class net.sf.basedb.core.Project
-
Get a query that returns the groups that
are members of this project.
- getGroups() - Method in class net.sf.basedb.core.ServiceSessionControl.ServicesKeyring
-
Return empty set.
- getGroups() - Method in class net.sf.basedb.core.SessionControl
-
Get the id of all groups where the logged in user is a member, directly or indirectly.
- getGroups() - Method in class net.sf.basedb.core.User
-
Get a query that returns the groups where this user is a
member.
- getGroupsRecursive(DbControl, Set<Integer>) - Static method in class net.sf.basedb.core.Group
-
Load all groups withing groups.
- getGroupsRecursive(Session, Collection<Integer>) - Static method in class net.sf.basedb.core.Group
-
- getGuiContext() - Method in class net.sf.basedb.clients.web.extensions.JspContext
-
- getGuiContext() - Method in class net.sf.basedb.core.PluginConfigurationRequest
-
Get the context of the client application when this configuration request
was created.
- getGuiContexts() - Method in class net.sf.basedb.clients.web.plugins.SimpleExport
-
- getGuiContexts() - Method in class net.sf.basedb.core.data.PluginDefinitionData
-
The item code for all items where it makes sense to use the
plugin in a client application.
- getGuiContexts() - Method in class net.sf.basedb.core.plugin.AbstractAnalysisPlugin
-
- getGuiContexts() - Method in interface net.sf.basedb.core.plugin.InteractivePlugin
-
Get a set containing all items that the plugin handles.
- getGuiContexts() - Method in class net.sf.basedb.core.PluginDefinition
-
Get the
Item
types where it makes sense to use this plugin
for a client application.
- getGuiContexts() - Method in class net.sf.basedb.plugins.AnnotationFlatFileImporter
-
This plug-in works in list context of all
Annotatable
items,
except bioassay sets, bioassays and wells because they are not standalone
items.
- getGuiContexts() - Method in class net.sf.basedb.plugins.BaseFileExporterPlugin
-
- getGuiContexts() - Method in class net.sf.basedb.plugins.batchimport.AnnotationTypeImporter
-
- getGuiContexts() - Method in class net.sf.basedb.plugins.batchimport.ArrayBatchImporter
-
- getGuiContexts() - Method in class net.sf.basedb.plugins.batchimport.ArrayDesignImporter
-
- getGuiContexts() - Method in class net.sf.basedb.plugins.batchimport.ArraySlideImporter
-
- getGuiContexts() - Method in class net.sf.basedb.plugins.batchimport.BioPlateImporter
-
- getGuiContexts() - Method in class net.sf.basedb.plugins.batchimport.BioSourceImporter
-
- getGuiContexts() - Method in class net.sf.basedb.plugins.batchimport.DerivedBioAssayImporter
-
- getGuiContexts() - Method in class net.sf.basedb.plugins.batchimport.ExtractImporter
-
- getGuiContexts() - Method in class net.sf.basedb.plugins.batchimport.FileImporter
-
- getGuiContexts() - Method in class net.sf.basedb.plugins.batchimport.HybridizationImporter
-
Deprecated.
- getGuiContexts() - Method in class net.sf.basedb.plugins.batchimport.KitImporter
-
- getGuiContexts() - Method in class net.sf.basedb.plugins.batchimport.LabeledExtractImporter
-
Deprecated.
- getGuiContexts() - Method in class net.sf.basedb.plugins.batchimport.PhysicalBioAssayImporter
-
- getGuiContexts() - Method in class net.sf.basedb.plugins.batchimport.RawBioAssayImporter
-
- getGuiContexts() - Method in class net.sf.basedb.plugins.batchimport.SampleImporter
-
- getGuiContexts() - Method in class net.sf.basedb.plugins.batchimport.ScanImporter
-
Deprecated.
- getGuiContexts() - Method in class net.sf.basedb.plugins.BfsExporterPlugin
-
- getGuiContexts() - Method in class net.sf.basedb.plugins.CdfFileReporterImporter
-
- getGuiContexts() - Method in class net.sf.basedb.plugins.executor.AbstractIOSupport
-
- getGuiContexts() - Method in class net.sf.basedb.plugins.FormulaFilter
-
- getGuiContexts() - Method in class net.sf.basedb.plugins.GalExporter
-
- getGuiContexts() - Method in class net.sf.basedb.plugins.HelpExporter
-
- getGuiContexts() - Method in class net.sf.basedb.plugins.HelpImporter
-
- getGuiContexts() - Method in class net.sf.basedb.plugins.IlluminaRawDataImporter
-
- getGuiContexts() - Method in class net.sf.basedb.plugins.IntensityCalculatorPlugin
-
- getGuiContexts() - Method in class net.sf.basedb.plugins.JepExtraValueCalculator
-
- getGuiContexts() - Method in class net.sf.basedb.plugins.JepIntensityTransformer
-
- getGuiContexts() - Method in class net.sf.basedb.plugins.ManualDerivedBioAssayCreator
-
- getGuiContexts() - Method in class net.sf.basedb.plugins.PackedFileExporter
-
- getGuiContexts() - Method in class net.sf.basedb.plugins.PlateFlatFileImporter
-
- getGuiContexts() - Method in class net.sf.basedb.plugins.PlateMappingExporter
-
Return a set containing the context:s [PLATEMAPPING, ITEM].
- getGuiContexts() - Method in class net.sf.basedb.plugins.PlateMappingImporter
-
Return a set containing the context:s [PLATEMAPPING, LIST].
- getGuiContexts() - Method in class net.sf.basedb.plugins.PluginConfigurationExporter
-
- getGuiContexts() - Method in class net.sf.basedb.plugins.PluginConfigurationImporter
-
- getGuiContexts() - Method in class net.sf.basedb.plugins.PrintMapFlatFileImporter
-
- getGuiContexts() - Method in class net.sf.basedb.plugins.RawDataFlatFileImporter
-
- getGuiContexts() - Method in class net.sf.basedb.plugins.ReporterFlatFileImporter
-
Return a set containing the context:s [REPORTER, LIST],
[REPORTERLIST, ITEM], [REPORTERSCORE, LIST].
- getGuiContexts() - Method in class net.sf.basedb.plugins.ReporterMapFlatFileImporter
-
Return a set containing the element [ARRAYDESIGN, ITEM].
- getGuiContexts() - Method in class net.sf.basedb.util.zip.AbstractFileUnpacker
-
- getGuiTitle() - Method in class net.sf.basedb.plugins.BaseFileExporterPlugin.ExtendedDynamicField
-
- getGuiTitle() - Method in class net.sf.basedb.plugins.BfsExporterPlugin.ExtendedExportableField
-
- getHandlerId() - Method in class net.sf.basedb.core.signal.AbstractSignalTransporter
-
Get the local handler ID part of the signal URI.
- getHardware() - Method in class net.sf.basedb.core.BioMaterialEvent
-
Get the
Hardware
that was used in this event.
- getHardware() - Method in class net.sf.basedb.core.BioPlateEvent
-
Get the
Hardware
that was used in this event.
- getHardware() - Method in class net.sf.basedb.core.data.BioMaterialEventData
-
Get the hardware used in this event
- getHardware() - Method in class net.sf.basedb.core.data.BioPlateEventData
-
Get the hardware used in this event
- getHardware() - Method in class net.sf.basedb.core.data.DerivedBioAssayData
-
Get the hardware used to create this bioassay set.
- getHardware() - Method in class net.sf.basedb.core.data.PlateEventData
-
Get the hardware used in this event.
- getHardware() - Method in class net.sf.basedb.core.DerivedBioAssay
-
Get the
Hardware
that was used when
creating this bioassay set.
- getHardware() - Method in class net.sf.basedb.core.PlateEvent
-
Get the
Hardware
that was used in this event.
- getHasData() - Method in class net.sf.basedb.core.data.RawBioAssayData
-
If the raw bioassay has data or not.
- getHasFeatures() - Method in class net.sf.basedb.core.data.ArrayDesignData
-
If the array design has features or not.
- getHashString(String) - Static method in class net.sf.basedb.util.MD5
-
Calculates the MD5 hash of an UTF-8 encoded string.
- getHashString(MessageDigest) - Static method in class net.sf.basedb.util.MD5
-
- getHeader(String) - Method in class net.sf.basedb.core.RawBioAssay
-
Get the value for the raw data header with the specified name.
- getHeader(int) - Method in class net.sf.basedb.util.bfs.AnnotationModel
-
Get the column header for a given column index.
- getHeader(String) - Method in class net.sf.basedb.util.parser.FlatFileParser
-
Get the value of the header with the specified name.
- getHeaderAttribute(String, Pattern) - Method in class net.sf.basedb.clients.web.fileupload.FileUpload
-
- getHeaderNames() - Method in class net.sf.basedb.core.RawBioAssay
-
Get the names of all raw data headers.
- getHeaderNames() - Method in class net.sf.basedb.util.parser.FlatFileParser
-
- getHeaders() - Method in class net.sf.basedb.core.data.RawBioAssayData
-
File headers from the raw data file.
- getHeaders() - Method in class net.sf.basedb.util.bfs.AnnotationModel
-
Get all column headers.
- getHeight() - Method in interface net.sf.basedb.clients.web.extensions.plot.PlotGenerator
-
Get the height of the generated image.
- getHeight() - Method in class net.sf.basedb.clients.web.extensions.plot.PlotGeneratorBean
-
- getHeight() - Method in class net.sf.basedb.core.AnnotationType
-
Get the recommended height in characters a client application should use
to render an input field for annotations of this annotation type.
- getHeight() - Method in class net.sf.basedb.core.data.AnnotationTypeData
-
The recommended height (lines) to display input fields for this
annotation in client applications.
- getHeight() - Method in class net.sf.basedb.core.ParameterType
-
Get the height of the input field for the parameter in the GUI.
- getHelp() - Method in interface net.sf.basedb.clients.web.extensions.login.LoginFormAction
-
Optional help text that is displayed on the login form to aid the
user when logging in.
- getHelp() - Method in class net.sf.basedb.clients.web.extensions.login.LoginFormBean
-
- getHelp() - Method in class net.sf.basedb.core.Client
-
Get a query that will return all help texts for this client.
- getHelpByExternalId(DbControl, String, boolean) - Method in class net.sf.basedb.core.Client
-
Get a Help
item when you know the external ID.
- getHelpId() - Method in class net.sf.basedb.clients.web.extensions.tabcontrol.FixedTabFactory
-
- getHelpId() - Method in class net.sf.basedb.clients.web.extensions.tabcontrol.IncludeContentTabFactory.Tab
-
- getHelpId() - Method in interface net.sf.basedb.clients.web.extensions.tabcontrol.TabAction
-
The external id of a help text that the user can display
to get more information about how to use the information
in this tab.
- getHelpId() - Method in class net.sf.basedb.clients.web.extensions.tabcontrol.TabBean
-
- getHelpid() - Method in class net.sf.basedb.clients.web.taglib.Help
-
- getHelpid() - Method in class net.sf.basedb.clients.web.taglib.tab.Tab
-
- getHelpId() - Method in class net.sf.basedb.clients.web.taglib.tab.Tab
-
- getHelpTexts() - Method in class net.sf.basedb.core.data.ClientData
-
This is the inverse end.
- getHibernateConfig() - Method in class net.sf.basedb.core.hibernate.SessionFactoryConfiguration
-
Deprecated.
Get the underlying Hibernate configuration instance.
- getHibernateSession() - Method in class net.sf.basedb.core.DbControl
-
Get the underlying Hibernate session.
- getHibernateType() - Method in class net.sf.basedb.core.hibernate.TypeWrapper
-
Get the underlying Hibernate type.
- getHibernateType() - Method in class net.sf.basedb.core.Metadata.BasicData2ItemPropertyPath
-
- getHibernateType() - Method in class net.sf.basedb.core.Metadata.BasicItem2DataPropertyPath
-
- getHibernateType() - Method in class net.sf.basedb.core.Metadata.CollectionPropertyPath
-
- getHibernateType() - Method in class net.sf.basedb.core.Metadata.CombinedPropertyPath
-
- getHibernateType() - Method in class net.sf.basedb.core.Metadata.ComponentPropertyPath
-
- getHibernateType() - Method in class net.sf.basedb.core.Metadata.DateCopyPropertyPath
-
- getHibernateType() - Method in class net.sf.basedb.core.Metadata.EntityPropertyPath
-
- getHibernateType() - Method in class net.sf.basedb.core.Metadata.EvictPropertyPath
-
- getHibernateType() - Method in class net.sf.basedb.core.Metadata.IdentifierPropertyPath
-
- getHibernateType() - Method in class net.sf.basedb.core.Metadata.MapPropertyPath
-
- getHibernateType() - Method in class net.sf.basedb.core.Metadata.NoopPropertyPath
-
- getHibernateType() - Method in interface net.sf.basedb.core.Metadata.PropertyPath
-
Get type information about the value that is returned by this path.
- getHibernateType() - Method in class net.sf.basedb.core.Metadata.ReporterScore2DataPropertyPath
-
- getHiddenFilteredColumns() - Method in class net.sf.basedb.clients.web.taglib.table.Table
-
- getHiddenMembers() - Method in class net.sf.basedb.core.data.GroupData
-
A flag indicating if members of the group should be hidden
to each other or not.
- getHideClazz() - Method in class net.sf.basedb.clients.web.extensions.section.IncludeContentSectionFactory.Section
-
- getHideClazz() - Method in interface net.sf.basedb.clients.web.extensions.section.SectionAction
-
Additional class attribute of the main section tag that is used
when the section is hidden.
- getHideClazz() - Method in class net.sf.basedb.clients.web.extensions.section.SectionBean
-
- getHideclazz() - Method in class net.sf.basedb.clients.web.taglib.HideableSection
-
- getHighestScoreIdx(double[][]) - Method in class net.sf.basedb.util.fuzzy.StringMatcher
-
- getHighlight() - Method in class net.sf.basedb.clients.web.taglib.table.Row
-
- getHistoryOf(BasicItem) - Static method in class net.sf.basedb.core.ChangeHistory
-
Get the history for a given item.
- getHome(Extension<?>) - Method in class net.sf.basedb.clients.web.extensions.JspContext
-
Get the URL to the home directory for a given extension.
- getHome() - Method in class net.sf.basedb.util.extensions.xml.PathConverter
-
Get the value of the home path.
- getHomeDirectory() - Method in class net.sf.basedb.core.data.UserData
-
Get the home directory for this user.
- getHomeDirectory() - Method in class net.sf.basedb.core.User
-
- getHomeUrl(String) - Static method in class net.sf.basedb.clients.web.extensions.ExtensionsControl
-
Get the URL to the home directory of extension with the
given ID.
- getHost() - Method in class net.sf.basedb.core.data.FileServerData
-
Get the name:port of the actual host to use for all files
using this server (overrides the host specified in the file url)
- getHost() - Method in class net.sf.basedb.core.FileServer
-
Get the name:port of the host that should override the host:port
in the file url for files using this file server.
- getHost() - Method in class net.sf.basedb.util.uri.ConnectionParameters
-
Get the host:port that should override the host:port
specified by the file URI.
- getHostName() - Static method in class net.sf.basedb.core.Application
-
Get the host name of the server running BASE.
- getHref() - Method in class net.sf.basedb.clients.web.taglib.path.PathElement
-
- getHTML(ButtonAction, boolean, boolean) - Method in class net.sf.basedb.clients.web.extensions.toolbar.ToolbarButtonRenderer
-
Generate the HTML that is needed to create a toolbar button.
- getIcon() - Method in class net.sf.basedb.clients.web.extensions.menu.FixedMenuItemFactory
-
- getIcon() - Method in interface net.sf.basedb.clients.web.extensions.menu.MenuItemAction
-
Get an absolute reference to an image that will be displayed in the menu.
- getIcon() - Method in class net.sf.basedb.clients.web.extensions.menu.MenuItemBean
-
- getIcon() - Method in interface net.sf.basedb.clients.web.extensions.toolbar.ButtonAction
-
Get a reference to an image that will be displayed in the menu.
- getIcon() - Method in class net.sf.basedb.clients.web.extensions.toolbar.ButtonBean
-
- getIcon() - Method in class net.sf.basedb.clients.web.extensions.toolbar.FixedButtonFactory
-
- getIcon() - Method in class net.sf.basedb.clients.web.taglib.menu.Menuitem
-
- getIcon() - Method in class net.sf.basedb.clients.web.taglib.menu.Submenu
-
- getIcon() - Method in class net.sf.basedb.clients.web.taglib.table.Button.ButtonActionWrapper
-
- getId() - Method in class net.sf.basedb.clients.jobagent.Agent
-
Get the agent.id
configuration value.
- getId() - Method in class net.sf.basedb.clients.jobagent.slotmanager.Slot
-
Get the id of the slot.
- getId() - Method in class net.sf.basedb.clients.web.ExperimentExplorer.AnnotationGroup
-
The ID of the group.
- getId() - Method in class net.sf.basedb.clients.web.extensions.list.AbstractListColumnBean
-
- getId() - Method in interface net.sf.basedb.clients.web.extensions.list.ListColumnAction
-
ID attribute of the column.
- getId() - Method in class net.sf.basedb.clients.web.extensions.menu.FixedMenuItemFactory
-
- getId() - Method in interface net.sf.basedb.clients.web.extensions.menu.MenuItemAction
-
ID attribute of the main menu tag.
- getId() - Method in class net.sf.basedb.clients.web.extensions.menu.MenuItemBean
-
- getId() - Method in interface net.sf.basedb.clients.web.extensions.plot.OverviewPlotAction
-
The ID of the overview plots.
- getId() - Method in class net.sf.basedb.clients.web.extensions.plot.OverviewPlotBean
-
- getId() - Method in interface net.sf.basedb.clients.web.extensions.plot.PlotGenerator
-
Get the ID of the image.
- getId() - Method in class net.sf.basedb.clients.web.extensions.plot.PlotGeneratorBean
-
- getId() - Method in class net.sf.basedb.clients.web.extensions.section.IncludeContentSectionFactory.Section
-
- getId() - Method in interface net.sf.basedb.clients.web.extensions.section.SectionAction
-
ID attribute of the main section tag.
- getId() - Method in class net.sf.basedb.clients.web.extensions.section.SectionBean
-
- getId() - Method in class net.sf.basedb.clients.web.extensions.skin.FixedSkinActionFactory
-
- getId() - Method in class net.sf.basedb.clients.web.extensions.skin.FixedSkinActionFactory.MySkinAction
-
- getId() - Method in interface net.sf.basedb.clients.web.extensions.skin.SkinAction
-
Get the ID of the extension.
- getId() - Method in class net.sf.basedb.clients.web.extensions.startpage.FixedStartPageFactory
-
- getId() - Method in interface net.sf.basedb.clients.web.extensions.startpage.StartPageAction
-
Get the ID of the the action.
- getId() - Method in class net.sf.basedb.clients.web.extensions.startpage.StartPageBean
-
- getId() - Method in class net.sf.basedb.clients.web.extensions.tabcontrol.FixedTabFactory
-
- getId() - Method in class net.sf.basedb.clients.web.extensions.tabcontrol.IncludeContentTabFactory.Tab
-
- getId() - Method in interface net.sf.basedb.clients.web.extensions.tabcontrol.TabAction
-
ID attribute of the main tab tag.
- getId() - Method in class net.sf.basedb.clients.web.extensions.tabcontrol.TabBean
-
- getId() - Method in interface net.sf.basedb.clients.web.extensions.toolbar.ButtonAction
-
ID attribute of the main button tag.
- getId() - Method in class net.sf.basedb.clients.web.extensions.toolbar.ButtonBean
-
- getId() - Method in class net.sf.basedb.clients.web.extensions.toolbar.FixedButtonFactory
-
- getId(BasicData) - Method in class net.sf.basedb.clients.web.plugins.DataQueryWrapper
-
- getId(SqlResult) - Method in class net.sf.basedb.clients.web.plugins.DynamicQueryWrapper
-
Keeps a counter which is incremented at each call to this method.
- getId(BasicItem) - Method in class net.sf.basedb.clients.web.plugins.ItemQueryWrapper
-
- getId(T) - Method in interface net.sf.basedb.clients.web.plugins.QueryWrapper
-
Get the ID of the specified item.
- getId(ReporterScore) - Method in class net.sf.basedb.clients.web.plugins.ReporterScoreQueryWrapper
-
- getId() - Method in class net.sf.basedb.clients.web.taglib.Button
-
- getId() - Method in class net.sf.basedb.clients.web.taglib.table.Button.ButtonActionWrapper
-
- getId() - Method in class net.sf.basedb.clients.web.taglib.table.TableColumn
-
- getId() - Method in class net.sf.basedb.core.BasicItem
-
- getId() - Method in class net.sf.basedb.core.data.annotations.AnnotationLink
-
- getId() - Method in class net.sf.basedb.core.data.BasicData
-
Get the id of the item.
- getId() - Method in interface net.sf.basedb.core.data.IdentifiableData
-
Get the id for the item.
- getId() - Method in class net.sf.basedb.core.data.UserData
-
We must override this method because the id must be the same as the
id for the password.
- getId() - Method in interface net.sf.basedb.core.Identifiable
-
Get the id for the item.
- getId() - Method in class net.sf.basedb.core.ItemContext
-
Get the ID of the current item in this context.
- getId() - Method in class net.sf.basedb.core.ItemProxy
-
- getId() - Method in class net.sf.basedb.core.ParameterValuesImpl
-
- getId() - Method in class net.sf.basedb.core.plugin.NamespaceParameterValuesWrapper
-
- getId() - Method in interface net.sf.basedb.core.plugin.ParameterValues
-
Get the ID of the job or configuration the parameters
comes from.
- getId() - Method in class net.sf.basedb.core.plugin.ParameterValuesWrapper
-
Get the ID of either the job or the configuration, depending in the
preferJob
parameter that was set when creating this object.
- getId() - Method in class net.sf.basedb.core.RawDataBatcher.FeatureProxy
-
- getId() - Method in class net.sf.basedb.core.RawDataBatcher.ReporterProxy
-
- getId() - Method in class net.sf.basedb.core.RawDataType
-
Get the id of this raw data type.
- getId() - Method in class net.sf.basedb.core.SessionControl
-
Get the id of this SessionControl
.
- getId() - Method in class net.sf.basedb.core.signal.Signal
-
Get the signal ID.
- getId() - Method in class net.sf.basedb.core.snapshot.AnnotationLoaderUtil
-
The ID of the annotation type that this loader load annotations from.
- getId(String) - Static method in class net.sf.basedb.core.SystemItems
-
Get the numeric id for an item when you know the system id.
- getId() - Method in class net.sf.basedb.plugins.BaseFileExporterPlugin.ExtendedDynamicField
-
- getId() - Method in class net.sf.basedb.plugins.BfsExporterPlugin.ExtendedExportableField
-
- getId() - Method in class net.sf.basedb.plugins.gtf.DefaultConfigurationValues
-
- getId() - Method in interface net.sf.basedb.util.extensions.Extension
-
Get the ID of the extension.
- getId() - Method in class net.sf.basedb.util.extensions.ExtensionBean
-
- getId() - Method in interface net.sf.basedb.util.extensions.ExtensionPoint
-
Get the ID of the extension point.
- getId() - Method in class net.sf.basedb.util.extensions.ExtensionPointBean
-
- getId() - Method in class net.sf.basedb.util.extensions.Registry.RegisteredExtension
-
- getId() - Method in class net.sf.basedb.util.extensions.Registry.RegisteredExtensionPoint
-
- getId() - Method in class net.sf.basedb.util.importer.spotdata.BaseFileImporter.RawDataProxy
-
- getId() - Method in class net.sf.basedb.util.importer.spotdata.BaseFileImporter.ReporterProxy
-
- getId() - Method in class net.sf.basedb.util.importer.spotdata.ExtraFloatParser
-
Get the external id of the extra value type.
- getId() - Method in interface net.sf.basedb.util.overview.extensions.ValidationRuleAction
-
Get the unique ID of this validation rule.
- getId() - Method in class net.sf.basedb.util.overview.Node
-
Get a unique ID for this node.
- getId() - Method in class net.sf.basedb.util.overview.Validator
-
Get the unique ID of this validator.
- getId() - Method in interface net.sf.basedb.util.uri.ConnectionManagerFactory
-
Get the ID of this connection manager factory.
- getId() - Method in class net.sf.basedb.util.uri.http.HttpConnectionManagerFactory
-
- getIdentifier(FeatureData) - Method in enum net.sf.basedb.core.FeatureIdentificationMethod
-
Get the feature identifier for this method.
- getIdentifier(RawData, String) - Method in enum net.sf.basedb.core.FeatureIdentificationMethod
-
Get a feature identifier using this method
- getIdentifier(Object) - Method in class net.sf.basedb.core.hibernate.SessionWrapper
-
- getIdFromPath(DbControl, Path) - Static method in class net.sf.basedb.core.Directory
-
Get the id of a directory when you know the path.
- getIdHqlQuery(DbControl) - Method in class net.sf.basedb.core.AbstractHqlQuery
-
Build the ID query and set parameter values for it.
- getIdMethod(String) - Method in class net.sf.basedb.plugins.batchimport.AbstractItemImporter
-
Get the id method to use for finding items.
- getIdMethods() - Method in class net.sf.basedb.plugins.batchimport.AbstractItemImporter
-
Get an array with all identification methods that can be used to find
items.
- getIdMethods() - Method in class net.sf.basedb.plugins.batchimport.AnnotationTypeImporter
-
- getIdMethods() - Method in class net.sf.basedb.plugins.batchimport.ArrayBatchImporter
-
- getIdMethods() - Method in class net.sf.basedb.plugins.batchimport.ArrayDesignImporter
-
- getIdMethods() - Method in class net.sf.basedb.plugins.batchimport.ArraySlideImporter
-
- getIdMethods() - Method in class net.sf.basedb.plugins.batchimport.BioPlateImporter
-
- getIdMethods() - Method in class net.sf.basedb.plugins.batchimport.BioSourceImporter
-
- getIdMethods() - Method in class net.sf.basedb.plugins.batchimport.DerivedBioAssayImporter
-
- getIdMethods() - Method in class net.sf.basedb.plugins.batchimport.ExtractImporter
-
- getIdMethods() - Method in class net.sf.basedb.plugins.batchimport.FileImporter
-
- getIdMethods() - Method in class net.sf.basedb.plugins.batchimport.HybridizationImporter
-
Deprecated.
- getIdMethods() - Method in class net.sf.basedb.plugins.batchimport.KitImporter
-
- getIdMethods() - Method in class net.sf.basedb.plugins.batchimport.LabeledExtractImporter
-
Deprecated.
- getIdMethods() - Method in class net.sf.basedb.plugins.batchimport.PhysicalBioAssayImporter
-
- getIdMethods() - Method in class net.sf.basedb.plugins.batchimport.RawBioAssayImporter
-
- getIdMethods() - Method in class net.sf.basedb.plugins.batchimport.SampleImporter
-
- getIdMethods() - Method in class net.sf.basedb.plugins.batchimport.ScanImporter
-
Deprecated.
- getIdPrefix() - Method in class net.sf.basedb.clients.web.taglib.StylableTag
-
Optional prefix to include in the 'id' attribute.
- getIdPrefix() - Method in class net.sf.basedb.clients.web.taglib.table.ColumnDef
-
- getIdQuery(DbControl, boolean) - Method in class net.sf.basedb.core.AbstractQuery
-
Build a query string that is identical to the main query but only return the ID values.
- getIgnoredFiles() - Method in class net.sf.basedb.clients.web.extensions.ExtensionsControl
-
Get files that are currently ignored.
- getIgnoredFiles(boolean) - Method in class net.sf.basedb.util.extensions.manager.ExtensionsManager
-
Get all ignored files.
- getIgnoredFiles() - Method in class net.sf.basedb.util.extensions.manager.Settings
-
Get a list with all files that are ignored.
- getIgnoredLines() - Method in class net.sf.basedb.util.parser.FlatFileParser
-
- getIgnoredSql() - Method in class net.sf.basedb.core.hibernate.SchemaGenerator
-
Get a list with the SQL statements that was ignored in the last run.
- getImage() - Method in class net.sf.basedb.clients.web.taglib.Button
-
- getImage() - Method in class net.sf.basedb.clients.web.taglib.Help
-
- getImage() - Method in class net.sf.basedb.clients.web.taglib.Icon
-
- getImage() - Method in class net.sf.basedb.clients.web.taglib.table.Button
-
- getImage() - Method in class net.sf.basedb.clients.web.taglib.table.Label
-
- getImage() - Method in class net.sf.basedb.clients.web.taglib.Zoom
-
- getImage() - Method in class net.sf.basedb.core.data.PlateMappingData
-
An optional name of a small image with a graphical representation of the mapping.
- getImage() - Method in class net.sf.basedb.core.PlateMapping
-
Get the name of a small image that is a graphical representation of the mapping.
- getImage() - Method in class net.sf.basedb.core.SpotImage
-
Get the image as an array of bytes.
- getImageRemapDir() - Method in class net.sf.basedb.clients.web.extensions.skin.FixedSkinActionFactory
-
- getImpersonated() - Method in class net.sf.basedb.core.data.SessionData
-
Check if another user is acting as the user of this session.
- getImpersonated() - Method in class net.sf.basedb.core.Session
-
Check if another user was acting as the user of this session.
- getImpersonatedSessionControl(Job) - Method in class net.sf.basedb.clients.jobagent.Agent
-
Get a session control where the owner of the job has been impersonated and
the active project has been set if needed.
- getImplementingItems(Class<?>) - Static method in class net.sf.basedb.core.Metadata
-
Get all
Item
:s implementing/extinding the specified
interface/class.
- getImporter(DbControl, boolean, boolean) - Method in class net.sf.basedb.plugins.executor.ExternalProgramExecutor
-
Get an instance of the importer plug-in.
- getImportFileType() - Method in class net.sf.basedb.plugins.ManualTransformCreator
-
- getInactiveRoles() - Method in class net.sf.basedb.core.Keyring
-
- getInactiveRoles() - Method in class net.sf.basedb.core.SessionControl
-
Get the id of all inactive roles where the logged in user is a member.
- getInclude() - Method in class net.sf.basedb.core.data.ContextData
-
Flags for specifying include options to an entity query.
- getInclude() - Method in class net.sf.basedb.core.data.ItemListSyncFilterData
-
Flags for specifying include options to an entity query.
- getInclude() - Method in class net.sf.basedb.core.ItemContext
-
Get a
Set
object to specify
Include
options for
a query.
- getInclude() - Method in class net.sf.basedb.util.listable.TransformContext
-
Include options when executing queries to find
parent/child items.
- getIndex(String) - Method in class net.sf.basedb.clients.web.servlet.PlotServlet.CFResultIterator
-
- getIndex() - Method in class net.sf.basedb.core.BioPlateEventParticipant
-
Get the index of the plate in this event.
- getIndex() - Method in class net.sf.basedb.core.data.BioPlateEventParticipantData
-
Get the index of this plate in the event.
- getIndex(String) - Method in class net.sf.basedb.core.DynamicResultIterator
-
- getIndex(String) - Method in class net.sf.basedb.core.log.EntityDetails
-
Get the array index of the given property.
- getIndex(String, String[], Comparator<String>) - Method in class net.sf.basedb.core.Metadata
-
- getIndex(String) - Method in interface net.sf.basedb.core.query.SqlResultIterator
-
Get the index number of a selected column.
- getIndex(String) - Method in class net.sf.basedb.util.bfs.MetadataModel.Section
-
Get the index of the first entry with the given key.
- getIndex() - Method in interface net.sf.basedb.util.extensions.Extension
-
The extensions in an extension point are by default ordered by their
index value.
- getIndex() - Method in class net.sf.basedb.util.extensions.ExtensionBean
-
- getIndex() - Method in class net.sf.basedb.util.extensions.Registry.RegisteredExtension
-
- getIndexes() - Method in class net.sf.basedb.core.dbengine.TableInfo
-
Get information about the indexes in the table.
- getInfo() - Method in class net.sf.basedb.clients.jobagent.AgentController
-
Get info about running job agent by sending an info request to the agents remote control
service.
- getInfo() - Method in class net.sf.basedb.core.JobAgent
-
Get info about the running job agent.
- getInfo(boolean) - Method in class net.sf.basedb.util.jobagent.JobAgentConnection
-
Send an info
or status
request to the job agent.
- getInheritedAnnotation(DbControl) - Method in class net.sf.basedb.core.snapshot.AnnotationSnapshot
-
Get the parent annotation this annotation is inherited from.
- getInheritedAnnotationColumns(String) - Static method in class net.sf.basedb.clients.web.Base
-
Get a query returning all annotation types that are needed to display
inherited annotations for the given columns.
- getInheritedAnnotationId() - Method in class net.sf.basedb.core.snapshot.AnnotationSnapshot
-
Get the ID of the annotation this annotation is inherited from.
- getInheritedAnnotationSet(DbControl) - Method in class net.sf.basedb.core.snapshot.AnnotationSnapshot
-
Get the annotation set this annotation is inherited from.
- getInheritedAnnotationSetId() - Method in class net.sf.basedb.core.snapshot.AnnotationSnapshot
-
Get the ID of the annotation set this annotation is inherited from.
- getInheritedAnnotationSets() - Method in class net.sf.basedb.core.AnnotationSet
-
- getInheritedFrom() - Method in class net.sf.basedb.core.Annotation
-
Get the parent annotation if this is an inherited or cloned
annotation.
- getInheritedFrom() - Method in class net.sf.basedb.core.data.AnnotationData
-
The parent annotation if this is an inherited or cloned annotation.
- getInheritedFrom() - Method in class net.sf.basedb.core.snapshot.AnnotationSnapshot
-
Get a snapshot for the annotation this is inherited from.
- getInheritingAnnotations() - Method in class net.sf.basedb.core.data.AnnotationData
-
Other annotations which inherit this annotation.
- getInheritingAnnotationSets() - Method in class net.sf.basedb.core.AnnotationSet
-
- getInitial() - Method in class net.sf.basedb.clients.web.taglib.HideableSection
-
- getInitializedFlatFileParser() - Method in class net.sf.basedb.plugins.AbstractFlatFileImporter
-
Create and initialise a flat file parser by setting all regular expressions
and other options.
- getInitializedFlatFileParser() - Method in class net.sf.basedb.plugins.AnnotationFlatFileImporter
-
- getInitializedFlatFileParser(ParameterValues) - Method in class net.sf.basedb.plugins.AnnotationFlatFileImporter
-
- getInitializedFlatFileParser(InputStream, String) - Method in class net.sf.basedb.plugins.Base1PluginExecuter
-
- getInitializedFlatFileParser() - Method in class net.sf.basedb.plugins.batchimport.AbstractItemImporter
-
- getInitializedFlatFileParser(ParameterValues) - Method in class net.sf.basedb.plugins.batchimport.AbstractItemImporter
-
- getInitializedFlatFileParser() - Method in class net.sf.basedb.plugins.IlluminaRawDataImporter
-
Create a FlatFileParser that can parse Illumina data files:
Data splitter: (,|\t)
Header regexp: (.+)=(.*?)
- getInitializedFlatFileParser() - Method in class net.sf.basedb.plugins.PlateMappingImporter
-
- getInitializedFlatFileParser() - Method in class net.sf.basedb.plugins.PrintMapFlatFileImporter
-
- getInitializedFlatFileParser(InputStream, String) - Method in class net.sf.basedb.util.basefile.BaseFileParser
-
- getInitParameter(String) - Method in class net.sf.basedb.clients.web.extensions.ServletWrapper
-
- getInitParameterNames() - Method in class net.sf.basedb.clients.web.extensions.ServletWrapper
-
- getInputStream(UploadedFile) - Method in class net.sf.basedb.clients.web.fileupload.FileUpload
-
Get an input stream for reading from the current file section.
- getInputStream() - Method in class net.sf.basedb.clients.web.fileupload.UploadedFile
-
Get an input stream for uploading the file.
- getInputStream(File) - Method in class net.sf.basedb.core.Migration
-
Get a stream for reading from the given file.
- getInputStream() - Method in class net.sf.basedb.core.SpotImage
-
Get an InputStream
of the image.
- getInputStream(String) - Method in class net.sf.basedb.util.bfs.BaseInputStreamLocator
-
Finds and opens an input stream to the file with the given filename.
- getInputStream(String) - Method in class net.sf.basedb.util.bfs.DiskInputStreamLocator
-
Finds and opens an input stream to the file with the given filename.
- getInputStream(String) - Method in interface net.sf.basedb.util.bfs.InputStreamLocator
-
Create an input stream that reads data from the given named
resource.
- getInputStream(File) - Static method in class net.sf.basedb.util.FileUtil
-
Get a buffered InputStream
object reading from
the specified file.
- getInputStream() - Method in class net.sf.basedb.util.importer.BaseFileWrapper
-
- getInputStream() - Method in class net.sf.basedb.util.importer.DiskFileWrapper
-
- getInputStream() - Method in interface net.sf.basedb.util.importer.FileWrapper
-
Get an input stream that reads data from the file.
- getInputStream(String, int) - Method in class net.sf.basedb.util.StaticCache
-
Get a lock-safe input stream.
- getInputStream() - Method in interface net.sf.basedb.util.uri.ConnectionManager
-
Get an InputStream for reading the contents of the resource.
- getInputStream() - Method in class net.sf.basedb.util.uri.http.HttpConnectionManager
-
- getInputStream(long) - Method in class net.sf.basedb.util.uri.http.HttpConnectionManager
-
- getInputStream(long) - Method in interface net.sf.basedb.util.uri.ResumableConnectionManager
-
Get an InputStream for reading the contents of the resource.
- getInsertAutoIncrementSql(PersistentClass) - Method in interface net.sf.basedb.core.dbengine.DbEngine
-
Return a SQL fragment that can be used in an INSERT INTO statement
to generate an ID for new rows.
- getInsertAutoIncrementSql(PersistentClass) - Method in class net.sf.basedb.core.dbengine.DefaultDbEngine
-
- getInsertAutoIncrementSql(PersistentClass) - Method in class net.sf.basedb.core.dbengine.MySQLEngine
-
- getInsertAutoIncrementSql(PersistentClass) - Method in class net.sf.basedb.core.dbengine.PostgresDbEngine
-
- getInsertPropertyOrder(Class<? extends BatchableData>) - Static method in class net.sf.basedb.core.BatchUtil
-
Get the order of properties in the insert SQL.
- getInsertPropertyOrder(String) - Static method in class net.sf.basedb.core.BatchUtil
-
Get the order of properties in the insert SQL.
- getInsertSql(Class<? extends BatchableData>) - Static method in class net.sf.basedb.core.BatchUtil
-
Get the SQL that inserts a new row of the specified class.
- getInsertSql(String) - Static method in class net.sf.basedb.core.BatchUtil
-
Get the SQL that inserts a new row of the specified class.
- getInstalledFiles() - Method in class net.sf.basedb.util.extensions.manager.Settings
-
Get a list with all files that are installed.
- getInstalledSchemaVersion() - Method in class net.sf.basedb.core.hibernate.SessionFactoryConfiguration
-
Deprecated.
Get the schema version that was installed prior to updating it.
- getInstalledSchemaVersion() - Method in class net.sf.basedb.core.ServiceSessionControl.SessionFactoryConfiguration
-
Get the currently installed version of the schema or
0 if not installed.
- getInstallMode() - Method in class net.sf.basedb.core.ServiceSessionControl.SessionFactoryConfiguration
-
Get the installation mode that BASE will use when creating the session
factory.
- getInstance(String) - Static method in class net.sf.basedb.core.authentication.AuthenticationMethod
-
Get an instance of this class for the given authentication method.
- getInstance(Class<I>) - Static method in class net.sf.basedb.core.Metadata
-
Get the metadata instance for the specified type of item.
- getInstance(Class<I>, String) - Static method in class net.sf.basedb.core.Metadata
-
Get the metadata instance for the item with the specified
entity name.
- getInstance(String) - Static method in class net.sf.basedb.util.JarClassLoader
-
Get a class loader for the specified JAR file.
- getInstance(String, boolean) - Static method in class net.sf.basedb.util.JarClassLoader
-
Get a class loader for the specified JAR file, optionally unloading an the old
one if the JAR file has been modified.
- getInstance() - Static method in class net.sf.basedb.util.jep.Log2Function
-
Get the singleton instance of this function.
- getInt(int) - Method in class net.sf.basedb.clients.web.servlet.PlotServlet.CFSqlResult
-
- getInt(String) - Static method in class net.sf.basedb.core.Config
-
Get the configuration setting specified by key
as an integer value.
- getInt(String, int) - Static method in class net.sf.basedb.core.Config
-
Get the configuration setting specified by key
as an integer value.
- getInt(int) - Method in class net.sf.basedb.core.DynamicResultIterator.SqlResultImpl
-
- getInt(String) - Static method in class net.sf.basedb.core.IntegerUtil
-
Get the int value of an String
.
- getInt(String, int) - Static method in class net.sf.basedb.core.IntegerUtil
-
Get the int value of an String
.
- getInt(Integer) - Static method in class net.sf.basedb.core.IntegerUtil
-
Get the value of an Integer
.
- getInt(Integer, int) - Static method in class net.sf.basedb.core.IntegerUtil
-
Get the value of an Integer
.
- getInt(int) - Method in interface net.sf.basedb.core.query.SqlResult
-
Get the value of the specified column as an integer.
- getInt(FlatFileParser.Data) - Method in class net.sf.basedb.util.parser.ColumnMapper
-
- getInt(FlatFileParser.Data) - Method in class net.sf.basedb.util.parser.CompoundMapper
-
- getInt(FlatFileParser.Data) - Method in class net.sf.basedb.util.parser.ConstantMapper
-
- getInt(FlatFileParser.Data) - Method in class net.sf.basedb.util.parser.CropStringMapper
-
- getInt(FlatFileParser.Data) - Method in class net.sf.basedb.util.parser.JepMapper
-
- getInt(FlatFileParser.Data) - Method in interface net.sf.basedb.util.parser.Mapper
-
Get the value for the line of data as an integer.
- getInt(FlatFileParser.Data) - Method in class net.sf.basedb.util.parser.NullIfExceptionMapper
-
- getInt(String) - Static method in class net.sf.basedb.util.Values
-
Convert a string to an integer.
- getInt(String, int) - Static method in class net.sf.basedb.util.Values
-
Convert a string to an integer.
- getInt(String[]) - Static method in class net.sf.basedb.util.Values
-
Convert an array of strings to an array of Integer:s.
- getIntAttribute(Element, String, int) - Static method in class net.sf.basedb.util.XmlUtil2
-
Get the value of an attribute as an integer.
- getInteger(String, Integer) - Static method in class net.sf.basedb.util.Values
-
- getIntegerValues() - Method in class net.sf.basedb.core.data.annotations.AnnotationLink
-
- getIntensityField(String, String) - Method in class net.sf.basedb.util.export.spotdata.AbstractFieldConverter
-
Create a dynamic field for spot intensity if the field name has
the pattern 'Ch X' where 'X' is a channel number between 1
and the number of channels in the raw data type used by the
source bioassay set.
- getIntensityField(String, String) - Method in class net.sf.basedb.util.export.spotdata.Base1FieldConverter
-
Create a dynamic field for spot intensity if the field name has
the pattern 'intensityX' where 'X' is a channel number between 1
and the number of channels in the raw data type used by the
source bioassay set.
- getIntensityFormula(String) - Method in class net.sf.basedb.core.RawDataType
-
- getIntensityFormulas() - Method in class net.sf.basedb.core.RawDataType
-
- getIntensityTransform() - Method in class net.sf.basedb.core.BioAssaySet
-
Get information about in what way the spot intensities has been
transformed before they were stored in the database.
- getIntensityTransform() - Method in class net.sf.basedb.core.data.BioAssaySetData
-
A flag indicating how the spot intensities has been transformed
before it was stored in the database:
0 = no transformation; 1 = 2-log; 2 = 10-log
- getIntensityTransform() - Method in class net.sf.basedb.core.DynamicQuery
-
Get the intensity transform that was used to store spot intensities
for the root bioassay set in this query.
- getIntensityTransform() - Method in class net.sf.basedb.util.importer.spotdata.BaseFileImporter
-
Get the intensity transform
- getInterfaceName() - Method in class net.sf.basedb.core.data.PluginTypeData
-
Get the interface name a plugin must implement to be of this type.
- getInterfaceName() - Method in class net.sf.basedb.core.PluginType
-
Get the class name of the Java class that implements this plugin.
- getInterfaces(Class<?>) - Static method in class net.sf.basedb.util.ClassUtil
-
Get all interfaces a class implements, including those implemented
by superclasses.
- getInternalId() - Method in class net.sf.basedb.core.authentication.AuthenticatedUser
-
Get the internal id for the user (0 if not known)
- getInternalId() - Method in class net.sf.basedb.util.extensions.xml.PluginInfo
-
Get the internal if of this plug-in.
- getInternalName() - Method in class net.sf.basedb.core.data.FileData
-
Get the internal name accosiated with this file.
- getInternalName() - Method in class net.sf.basedb.core.File
-
Get the internal name of this file.
- getIntFormatter(SessionControl) - Static method in class net.sf.basedb.clients.web.formatter.FormatterFactory
-
Get the logged in user's formatter for integral numbers.
- getIntOption(String, Integer) - Method in class net.sf.basedb.core.AnnotationType
-
Get an option and convert the value to an integer.
- getInvoker(Extension<ServiceControllerAction>) - Static method in class net.sf.basedb.clients.web.extensions.service.Services
-
- getInvoker(DbControl) - Method in class net.sf.basedb.core.FileSet
-
- getInvoker(ClientContext, ExtensionsFilter) - Static method in class net.sf.basedb.util.uri.ConnectionManagerUtil
-
Get an invoker for using the connection manager factory extensions.
- getItem(DbControl, ChangeHistory, boolean, boolean) - Static method in class net.sf.basedb.clients.web.ChangeHistoryUtil
-
Get the item that was changed in HTML format.
- getItem() - Method in class net.sf.basedb.clients.web.taglib.PropertyValue
-
- getItem() - Method in class net.sf.basedb.clients.web.taglib.table.Table
-
- getItem() - Method in class net.sf.basedb.core.AnnotationSet
-
Get the item this annotation set belongs to.
- getItem(DbControl) - Method in class net.sf.basedb.core.AnnotationSet
-
Get the item this annotation set belongs to using a specific
DbControl for database access.
- getItem(DbControl) - Method in class net.sf.basedb.core.ChangeHistory
-
Load the item that was changed.
- getItem() - Method in class net.sf.basedb.core.ContextKey
-
- getItem(Class<I>, BasicData, Object...) - Method in class net.sf.basedb.core.DbControl
-
Get an item object for a known data object, using the cache if
possible.
- getItem() - Method in class net.sf.basedb.core.DiskUsage
-
Get the item this disk usage holds information for
- getItem() - Method in class net.sf.basedb.core.FileSet
-
Get the item this file set belongs to.
- getItem(DbControl) - Method in class net.sf.basedb.core.ItemProxy
-
- getItem() - Method in class net.sf.basedb.core.log.ManualLogEntry
-
Get the item this log entry is related to.
- getItem() - Method in class net.sf.basedb.core.plugin.GuiContext
-
- getItem(DbControl) - Method in class net.sf.basedb.core.snapshot.AnnotationSetSnapshot
-
Get item the annotations belong to.
- getItem(DbControl) - Method in class net.sf.basedb.core.snapshot.AnnotationSnapshot
-
- getItem() - Method in class net.sf.basedb.util.overview.Fix
-
Get the item that needs to be edited for this fix.
- getItem() - Method in class net.sf.basedb.util.overview.Node
-
Get the item that is related to this node.
- getItem(DbControl) - Method in class net.sf.basedb.util.overview.Node
-
Get the item that is related to this node and make sure that it is
loaded with the current DbControl.
- getItemClass() - Method in enum net.sf.basedb.core.Item
-
Get the class object that is used to handle items of this type.
- getItemCount(int) - Method in class net.sf.basedb.util.plot.HistogramPlot.HistogramDataset
-
- getItemCount() - Method in class net.sf.basedb.util.plot.HistogramPlot.HistogramSeries
-
- getItemForSubtypes() - Method in class net.sf.basedb.plugins.batchimport.AbstractItemImporter
-
Does the importer want to use item subtypes when importing?
- getItemForSubtypes() - Method in class net.sf.basedb.plugins.batchimport.BioSourceImporter
-
- getItemForSubtypes() - Method in class net.sf.basedb.plugins.batchimport.DerivedBioAssayImporter
-
- getItemForSubtypes() - Method in class net.sf.basedb.plugins.batchimport.ExtractImporter
-
- getItemForSubtypes() - Method in class net.sf.basedb.plugins.batchimport.FileImporter
-
- getItemForSubtypes() - Method in class net.sf.basedb.plugins.batchimport.KitImporter
-
- getItemForSubtypes() - Method in class net.sf.basedb.plugins.batchimport.PhysicalBioAssayImporter
-
- getItemForSubtypes() - Method in class net.sf.basedb.plugins.batchimport.SampleImporter
-
- getItemId() - Method in class net.sf.basedb.core.AnnotationBatcher.CurrentAnnotationInfo
-
Get the id of the current item.
- getItemId() - Method in class net.sf.basedb.core.AnnotationSet
-
Get the ID of the item this annotation set belongs to.
- getItemId() - Method in class net.sf.basedb.core.ChangeHistory
-
Get the ID of the item that was changed.
- getItemId() - Method in class net.sf.basedb.core.data.AnnotationSetData
-
The ID if the item this annotation set is associated with.
- getItemId() - Method in class net.sf.basedb.core.data.ChangeHistoryDetailData
-
The ID of the item that was changed
- getItemId() - Method in class net.sf.basedb.core.data.ContextData
-
Get the current item ID or 0 if no item is current.
- getItemId() - Method in class net.sf.basedb.core.snapshot.AnnotationSetSnapshot
-
Get the ID of the item the annotations in this snapshot
belong to.
- getItemId() - Method in class net.sf.basedb.core.snapshot.AnnotationSnapshot
-
- getItemKey() - Method in interface net.sf.basedb.core.data.ShareableData
-
- getItemKey() - Method in class net.sf.basedb.core.data.SharedData
-
- getItemKey() - Method in interface net.sf.basedb.core.Shareable
-
Get the
ItemKey
that is used to share this item to users
and groups.
- getItemKey() - Method in class net.sf.basedb.core.SharedItem
-
- getItemKeyId() - Method in class net.sf.basedb.core.SessionControl
-
Get the id of the
ItemKey
that new items should be shared to
according to the settings in the currently active project.
- getItemKeys() - Method in class net.sf.basedb.core.data.GroupData
-
This is the inverse end.
- getItemKeys() - Method in class net.sf.basedb.core.data.UserData
-
This is the inverse end.
- getItemKeys() - Method in class net.sf.basedb.core.InternalJobQueue.JobQueueKeyring
-
Return empty set.
- getItemKeys() - Method in class net.sf.basedb.core.InternalStorageController.StorageKeyring
-
Return empty set.
- getItemKeys() - Method in class net.sf.basedb.core.Job.SignalKeyring
-
Return empty set.
- getItemKeys(Permission) - Method in class net.sf.basedb.core.Keyring
-
- getItemKeys() - Method in class net.sf.basedb.core.ServiceSessionControl.ServicesKeyring
-
Return empty set.
- getItemKeys() - Method in class net.sf.basedb.core.SessionControl
-
Get the id of all item keys where the logged in user has read permission.
- getItemKeys(Permission) - Method in class net.sf.basedb.core.SessionControl
-
Get the id of all item keys where the logged in user has the
requested permission.
- getItemList() - Method in class net.sf.basedb.core.data.ItemListSyncFilterData
-
Get the item list this sync filter belongs to.
- getItemList() - Method in class net.sf.basedb.core.SyncFilter
-
Get the item list this filter belongs to.
- getItemListsEnum(DbControl, Item, Collection<Include>) - Static method in class net.sf.basedb.clients.web.Base
-
Get available item lists as an Enumeration that is
suitable to use in a column definition for a table.
- getItemPermission() - Method in class net.sf.basedb.core.AbstractEntityQuery
-
- getItemPermission() - Method in class net.sf.basedb.core.ItemContext
-
The permission the logged in user must have for items returned
by a query.
- getItemPermission() - Method in interface net.sf.basedb.core.query.EntityQuery
-
The logged in user's permission on the items returned by this query.
- getItems() - Method in class net.sf.basedb.core.MultiPermissions
-
Returns the items that are handled within this class.
- getItems(Item) - Method in class net.sf.basedb.core.MultiPermissions
-
Get all items of a specific item type.
- getItems(Collection<Item>) - Method in class net.sf.basedb.core.MultiPermissions
-
Get all items of specific item types.
- getItems() - Method in class net.sf.basedb.core.ParameterType
-
Get the list of values to choose from.
- getItems(Item, int, int, Permission, Set<Include>) - Method in class net.sf.basedb.core.Project
-
- getItems(Set<Item>, int, int, Permission, Set<Include>, Restriction) - Method in class net.sf.basedb.core.Project
-
Load the items in a project.
- getItems(DbControl, Item, int, int) - Static method in class net.sf.basedb.core.Trashcan
-
- getItems(DbControl, Set<Item>, int, int) - Static method in class net.sf.basedb.core.Trashcan
-
- getItems(DbControl, Set<Item>, int, int, Restriction) - Static method in class net.sf.basedb.core.Trashcan
-
Load all items flagged for deletion that are owned by or removed
by the logged in user.
- getItems(Item, int, int, Permission) - Method in class net.sf.basedb.core.User
-
- getItems(Set<Item>, int, int, Permission, Restriction) - Method in class net.sf.basedb.core.User
-
Load the items owned by this user.
- getItems(DbControl, ItemQuery<T>, Restriction...) - Method in class net.sf.basedb.plugins.IlluminaRawDataImporter
-
Sort the items by name and add USE permission filter to the query.
- getItemSubtype() - Method in class net.sf.basedb.core.BioMaterial
-
- getItemSubtype() - Method in class net.sf.basedb.core.BioPlateType
-
Get the subtype that biomaterial items should have when placed
on a plate with this bioplate type.
- getItemSubtype() - Method in class net.sf.basedb.core.data.BioMaterialData
-
- getItemSubtype() - Method in class net.sf.basedb.core.data.BioPlateTypeData
-
Get the subtype of biomaterials that can be placed on plates of this type.
- getItemSubtype() - Method in class net.sf.basedb.core.data.DerivedBioAssayData
-
- getItemSubtype() - Method in class net.sf.basedb.core.data.FileData
-
- getItemSubtype() - Method in class net.sf.basedb.core.data.HardwareData
-
- getItemSubtype() - Method in class net.sf.basedb.core.data.ItemListData
-
Get the subtype of items that can be members in this list.
- getItemSubtype() - Method in class net.sf.basedb.core.data.ItemSubtypeFileTypeData
-
Get the item subtype.
- getItemSubtype() - Method in class net.sf.basedb.core.data.JobData
-
- getItemSubtype() - Method in class net.sf.basedb.core.data.KitData
-
- getItemSubtype() - Method in class net.sf.basedb.core.data.PhysicalBioAssayData
-
- getItemSubtype() - Method in class net.sf.basedb.core.data.ProtocolData
-
- getItemSubtype() - Method in class net.sf.basedb.core.data.SoftwareData
-
- getItemSubtype() - Method in interface net.sf.basedb.core.data.SubtypableData
-
Get the subtype of the item.
- getItemSubtype() - Method in class net.sf.basedb.core.data.TagData
-
- getItemSubtype() - Method in class net.sf.basedb.core.DerivedBioAssay
-
- getItemSubtype() - Method in class net.sf.basedb.core.Extract
-
- getItemSubtype() - Method in class net.sf.basedb.core.File
-
- getItemSubtype() - Method in class net.sf.basedb.core.Hardware
-
- getItemSubtype() - Method in class net.sf.basedb.core.ItemList
-
Get the subtype of items that can be members in this list.
- getItemSubtype() - Method in class net.sf.basedb.core.ItemSubtype
-
- getItemSubtype() - Method in class net.sf.basedb.core.ItemSubtypeFileType
-
Get the item subtype.
- getItemSubtype() - Method in class net.sf.basedb.core.Job
-
- getItemSubtype() - Method in class net.sf.basedb.core.Kit
-
- getItemSubtype() - Method in class net.sf.basedb.core.MeasuredBioMaterial
-
- getItemSubtype() - Method in class net.sf.basedb.core.PhysicalBioAssay
-
- getItemSubtype() - Method in class net.sf.basedb.core.Protocol
-
- getItemSubtype() - Method in class net.sf.basedb.core.Sample
-
- getItemSubtype() - Method in class net.sf.basedb.core.Software
-
- getItemSubtype() - Method in interface net.sf.basedb.core.Subtypable
-
Get the subtype of the item.
- getItemSubtype() - Method in class net.sf.basedb.core.Tag
-
- getItemSubtype() - Method in class net.sf.basedb.util.annotations.InheritSpecification
-
- getItemSubtypes() - Method in class net.sf.basedb.core.data.DataFileTypeData
-
The subtypes that this file type can be used with.
- getItemSubtypes() - Method in class net.sf.basedb.core.DataFileType
-
Get a query returning the item subtypes that files of this type
can be used on.
- getItemType() - Method in class net.sf.basedb.core.AbstractEntityQuery
-
- getItemType() - Method in class net.sf.basedb.core.AnnotationBatcher.CurrentAnnotationInfo
-
Get the item type of the item.
- getItemType() - Method in class net.sf.basedb.core.AnnotationSet
-
Get the
Item
type of the item this annotation set belongs to.
- getItemType() - Method in class net.sf.basedb.core.ChangeHistory
-
Get the type of the item that was changed.
- getItemType() - Method in class net.sf.basedb.core.data.AnnotationSetData
-
Get the item type this annotation set is associated with.
- getItemType() - Method in class net.sf.basedb.core.data.ChangeHistoryDetailData
-
The type code of the item that was changed.
- getItemType() - Method in class net.sf.basedb.core.data.ContextData
-
Get the item type this context is valid for.
- getItemType() - Method in class net.sf.basedb.core.data.ContextIndex
-
- getItemType() - Method in class net.sf.basedb.core.data.DataFileTypeData
-
The item type this file type can be associated with.
- getItemType() - Method in class net.sf.basedb.core.data.DiskUsageData
-
Get the item type this annotation set is associated with.
- getItemType() - Method in class net.sf.basedb.core.data.FileSetData
-
Get the item type this file set is associated with.
- getItemType() - Method in class net.sf.basedb.core.data.GuiContextData
-
- getItemType() - Method in class net.sf.basedb.core.data.ItemSubtypeData
-
Get the item type this subtype can be applied to.
- getItemType() - Method in class net.sf.basedb.core.data.RoleKeyData
-
Get the code for the type of items this role key applies to.
- getItemType() - Method in class net.sf.basedb.core.DataFileType
-
Get the type of item files of this type can be used on.
- getItemType() - Method in class net.sf.basedb.core.DataResultIterator
-
Get the type of items contained in this list.
- getItemType() - Method in class net.sf.basedb.core.DiskUsage
-
Get the
Item
type of the item this annotation set belongs to.
- getItemType() - Method in class net.sf.basedb.core.FileSet
-
Get the
Item
type of the item this file set belongs to.
- getItemType() - Method in class net.sf.basedb.core.ItemContext
-
Get the type of item this object is storing context for.
- getItemType() - Method in class net.sf.basedb.core.ItemResultIterator
-
Get the type of items contained in this list.
- getItemType() - Method in class net.sf.basedb.core.ItemResultList
-
Get the type of items contained in this list.
- getItemType() - Method in class net.sf.basedb.core.plugin.Permissions
-
Get the item type the permissions are valid for.
- getItemType() - Method in interface net.sf.basedb.core.query.EntityQuery
-
The type of items the query returns.
- getItemType() - Method in class net.sf.basedb.core.query.HqlEntityParameterExpression
-
Get the type of entites that are accepted by the parameter.
- getItemType() - Method in class net.sf.basedb.core.query.QueryParameter
-
The parameter should be an entity of the given item type.
- getItemType() - Method in class net.sf.basedb.core.ReporterScoreResultIterator
-
Get the type of items contained in this list.
- getItemType() - Method in class net.sf.basedb.core.RoleKey
-
Get the
Item
type for the type of items this role key applies to.
- getItemType() - Method in class net.sf.basedb.core.snapshot.AnnotationSetSnapshot
-
Get the item type of the item the annotations in this snapshot
belong to.
- getItemType() - Method in class net.sf.basedb.core.snapshot.AnnotationSnapshot
-
- getItemType() - Method in class net.sf.basedb.util.overview.Node
-
Get the item type of the item that this node related to this node.
- getItemTypes() - Method in class net.sf.basedb.core.data.AnnotationTypeData
-
The item code for all items this annotation type can be applied to.
- getItemValue(DbControl, Object) - Static method in class net.sf.basedb.core.Values
-
Convert a a data value to a item value.
- getItemValues(DbControl, List<?>) - Static method in class net.sf.basedb.core.Values
-
Convert a list of data values to item values.
- getJarFile() - Method in class net.sf.basedb.core.data.PluginDefinitionData
-
Get the file name of the JAR file where the plugin class is located.
- getJarFile() - Method in class net.sf.basedb.core.data.PluginTypeData
-
Get the file name of the JAR file where the plugin class is located.
- getJarFile() - Method in class net.sf.basedb.core.PluginDefinition
-
Get the name of the JAR file that contains this plug-in.
- getJarFile() - Method in class net.sf.basedb.core.PluginType
-
Get the name of the JAR file that contains this plug-in.
- getJarPath() - Method in class net.sf.basedb.core.PluginDefinition
-
Get the path to the JAR file that contains the plugin class file.
- getJarPath() - Method in class net.sf.basedb.core.PluginType
-
Get the path to the JAR file that contains the plugin class file.
- getJdbcFetchSize() - Static method in class net.sf.basedb.core.HibernateUtil
-
The number of rows to load at a time when reading
from the database.
- getJep() - Method in class net.sf.basedb.util.export.spotdata.JepDynamicField
-
Get the configured JEP expression.
- getJepExpression() - Method in class net.sf.basedb.clients.web.taglib.table.TableColumn
-
- getJepFunctions(DbControl, boolean) - Method in class net.sf.basedb.core.DataCube.RawMappingQuery
-
No JEP functions can be used with this type of query.
- getJepFunctions(DbControl, boolean) - Method in class net.sf.basedb.core.DynamicExtraValueQuery
-
- getJepFunctions(DbControl, boolean) - Method in class net.sf.basedb.core.DynamicPositionQuery
-
- getJepFunctions(DbControl, boolean) - Method in class net.sf.basedb.core.DynamicQuery
-
Create custom JEP function that can be used with the current
query.
- getJepFunctions(DbControl, boolean) - Method in class net.sf.basedb.core.DynamicSpotQuery
-
- getJob(DbControl, ChangeHistory, boolean, boolean) - Static method in class net.sf.basedb.clients.web.ChangeHistoryUtil
-
Get the job that made the change in HTML format.
- getJob() - Method in class net.sf.basedb.core.ArrayDesign
-
Get the job that imported features to this array design.
- getJob(DbControl) - Method in class net.sf.basedb.core.ChangeHistory
-
Load the job that was executing when the change was made.
- getJob() - Method in class net.sf.basedb.core.data.ArrayDesignData
-
Get the job that was used to import features to this array desing
- getJob() - Method in class net.sf.basedb.core.data.ChangeHistoryData
-
- getJob() - Method in class net.sf.basedb.core.data.DerivedBioAssayData
-
Get the job used to create this bioassay set.
- getJob() - Method in class net.sf.basedb.core.data.ExtraValueData
-
Get the job that was used to execute this calculate this extra value.
- getJob() - Method in class net.sf.basedb.core.data.MessageData
-
If this message is a message about a job completion (or failure)
this property contains a reference to that job.
- getJob() - Method in class net.sf.basedb.core.data.RawBioAssayData
-
Get the job that was used to import raw data to this raw bioassay
- getJob() - Method in class net.sf.basedb.core.data.TransformationData
-
Get the job that was used to execute this transformation
- getJob() - Method in class net.sf.basedb.core.DerivedBioAssay
-
Get the job that created this bioassay.
- getJob() - Method in class net.sf.basedb.core.ExtraValue
-
Get the job that created the extra values.
- getJob() - Method in class net.sf.basedb.core.InternalJobQueue.JobRunner
-
Get the job.
- getJob() - Method in class net.sf.basedb.core.Message
-
Get the
Job
this message is about.
- getJob() - Method in class net.sf.basedb.core.ParameterValuesImpl
-
- getJob() - Method in class net.sf.basedb.core.plugin.NamespaceParameterValuesWrapper
-
- getJob() - Method in interface net.sf.basedb.core.plugin.ParameterValues
-
Get the job that we are executing/configuring.
- getJob() - Method in class net.sf.basedb.core.plugin.ParameterValuesWrapper
-
- getJob() - Method in class net.sf.basedb.core.PluginRequest
-
Get the job for the request or null if we are not configuring/executing a job.
- getJob() - Method in class net.sf.basedb.core.RawBioAssay
-
Get the job that imported data to this raw bioassay.
- getJob() - Method in class net.sf.basedb.core.Transformation
-
Get the job that executed this transformation.
- getJob() - Method in class net.sf.basedb.plugins.gtf.DefaultConfigurationValues
-
- getJobAgent(DbControl) - Method in class net.sf.basedb.clients.jobagent.Agent
-
Get the
JobAgent
item corresponding to this agent.
- getJobAgent() - Method in class net.sf.basedb.core.data.JobAgentSettingsData
-
The job agent these settings belong to.
- getJobAgent() - Method in class net.sf.basedb.core.Job
-
Get the job agent this job should run on, is running on or
was running on.
- getJobAgent() - Method in class net.sf.basedb.core.JobAgentSettings
-
Get the job agent that owns these settings.
- getJobAgentId() - Method in class net.sf.basedb.core.data.JobData
-
The ID of the job agent this job should run/is running/was running on.
- getJobAgentSettings() - Method in class net.sf.basedb.core.data.PluginDefinitionData
-
This is the inverse end.
- getJobExecutorClass(String) - Method in class net.sf.basedb.clients.jobagent.Agent
-
Get the class object for the configured job executor.
- getJobId() - Method in class net.sf.basedb.core.ChangeHistory
-
Get the ID of the job that was executing when the change was made
- getJobId() - Method in class net.sf.basedb.core.data.ChangeHistoryData
-
The ID of the job that was making the changes.
- getJobId() - Method in class net.sf.basedb.core.log.TransactionDetails
-
Get the ID of the currently running job or 0 if no job is running.
- getJobId() - Method in class net.sf.basedb.core.SessionControl
-
Get the id of the job that is currently running with this
session control.
- getJobId() - Method in class net.sf.basedb.util.jobagent.JobInfo
-
Get the ID of the job.
- getJobInfo() - Method in class net.sf.basedb.util.jobagent.JobAgentInfo
-
Get detailed information about the running jobs.
- getJobName() - Method in class net.sf.basedb.core.log.TransactionDetails
-
Utility method for loading the name of the currently executing job.
- getJobOrConfigurationValue(String) - Method in class net.sf.basedb.core.plugin.AbstractPlugin
-
Get the value for a job or configuration parameter.
- getJobParameterObjectsFromXML(String, boolean) - Method in class net.sf.basedb.plugins.Base1PluginExecuter
-
- getJobParameters() - Method in class net.sf.basedb.plugins.Base1PluginExecuter
-
Reads the configuration file an creates the parameters found there.
- getJobParametersFromXML(String, boolean) - Method in class net.sf.basedb.plugins.Base1PluginExecuter
-
- getJobs() - Method in class net.sf.basedb.core.data.ExperimentData
-
This is the inverse end.
- getJobs() - Method in class net.sf.basedb.core.PluginConfiguration
-
Get a query that returns the jobs
using this plugin configuration.
- getJobSessionControl(Job) - Method in class net.sf.basedb.core.SessionControl
-
Create a new session control for executing a job.
- getJobType() - Method in class net.sf.basedb.core.Job
-
Get the type of job, ie. if it is a job executed by a plugin
or not.
- getJoinAlias() - Method in class net.sf.basedb.core.ExtraValue
-
The alias used when joining this extra value into a query.
- getJoinAlias() - Method in class net.sf.basedb.core.query.AnnotationExpression
-
- getJoinAlias() - Method in class net.sf.basedb.core.query.ReporterListExpression
-
- getJoinExpression() - Method in enum net.sf.basedb.core.query.JoinType
-
- getJoinProperty() - Method in class net.sf.basedb.core.query.ReporterListExpression
-
- getJspContext() - Method in class net.sf.basedb.clients.web.extensions.edit.AbstractOnSaveAction
-
Set the JSP context of the current invokation.
- getJspPage() - Method in class net.sf.basedb.core.RequestInformation
-
The name of the jsp page to use for displaying the input form for
requesting parameters.
- getKey(int) - Method in class net.sf.basedb.util.bfs.MetadataModel.Section
-
Get the key of the entry at the given index.
- getKey() - Method in class net.sf.basedb.util.bfs.MetadataModel.SectionEntry
-
Get the key of the entry.
- getKey() - Method in class net.sf.basedb.util.Enumeration.Entry
-
- getKey(int) - Method in class net.sf.basedb.util.Enumeration
-
- getKey() - Method in class net.sf.basedb.util.fuzzy.StringMatcher.FuzzyMatch
-
Get the key string.
- getKey() - Method in class net.sf.basedb.util.StaticCache.LockEntry
-
- getKeyId() - Method in class net.sf.basedb.core.data.keyring.KeyPermission
-
Get the id of the key.
- getKeyId() - Method in class net.sf.basedb.core.data.keyring.PluginKeys
-
Gets the id of the RoleKey
- getKeys() - Method in class net.sf.basedb.core.data.RoleData
-
This is the inverse end.
- getKeys() - Method in class net.sf.basedb.core.Presets.Preset
-
Get all keys in this preset.
- getKeys() - Method in class net.sf.basedb.util.QueryParameters
-
Get all keys that are present in the query string.
- getKit() - Method in class net.sf.basedb.core.BioMaterialEvent
-
Get the
Kit
that was used in this event.
- getKit() - Method in class net.sf.basedb.core.BioPlateEvent
-
Get the
Kit
that was used in this event.
- getKit() - Method in class net.sf.basedb.core.data.BioMaterialEventData
-
Get the kit used in this event.
- getKit() - Method in class net.sf.basedb.core.data.BioPlateEventData
-
Get the kit used in this event.
- getKit() - Method in class net.sf.basedb.core.data.DerivedBioAssayData
-
Get the kit used to create this bioassay set.
- getKit() - Method in class net.sf.basedb.core.DerivedBioAssay
-
Get the
Kit
that was used when creating this bioassay.
- getLabel() - Method in class net.sf.basedb.core.data.ParameterValueData
-
Get the label of the parameter.
- getLabel() - Method in class net.sf.basedb.core.ParameterInfo
-
- getLabel() - Method in class net.sf.basedb.core.PluginParameter
-
Get the label of the parameter.
- getLastAccess() - Method in class net.sf.basedb.core.SessionControl
-
Get the time this object last was accessed.
- getLastError() - Method in class net.sf.basedb.util.extensions.Registry.RegisteredExtension
-
- getLastError() - Method in class net.sf.basedb.util.extensions.Registry.RegisteredExtensionPoint
-
- getLastExtensionError(String) - Method in class net.sf.basedb.clients.web.extensions.ExtensionsControl
-
Get information about the last error that happened
when rendering an extension.
- getLastExtensionError(String) - Method in class net.sf.basedb.util.extensions.Registry
-
Get information about the last error that happened
when rendering an extension.
- getLastExtensionPointError(String) - Method in class net.sf.basedb.clients.web.extensions.ExtensionsControl
-
Get information about the last error that happened
when rendering an extension point.
- getLastExtensionPointError(String) - Method in class net.sf.basedb.util.extensions.Registry
-
Get information about the last error that happened
when rendering an extension point.
- getLastGuiContext() - Method in class net.sf.basedb.core.Job
-
Get the gui-context that was active when this job was created.
- getLastModified(HttpResponse) - Static method in class net.sf.basedb.util.HttpUtil
-
Get the date the content was last modified from the headers
in the response.
- getLastModified() - Method in class net.sf.basedb.util.uri.UriMetadata
-
Get the date and time the resource was last modified.
- getLastProcessResults() - Method in class net.sf.basedb.util.extensions.manager.ExtensionsManager
-
Get the results of the last processing.
- getLastScanResults() - Method in class net.sf.basedb.clients.web.extensions.ExtensionsControl
-
Get the results of the last scan (manual or automatic).
- getLastSource() - Method in class net.sf.basedb.core.data.ReporterData
-
Get the source that was used when this reporter
was last updated.
- getLastSyncMatchingSource() - Method in class net.sf.basedb.core.SyncFilter
-
Get the number of source items that matched this particular filter during the last
synchronization.
- getLastSyncMatchingTransformed() - Method in class net.sf.basedb.core.SyncFilter
-
Get the number of transformed items that matched this particular filter during the last
synchronization.
- getLastUpdate() - Method in class net.sf.basedb.core.Annotation
-
Get the date and time the values in this annotation was last
updated.
- getLastUpdate() - Method in class net.sf.basedb.core.data.AnnotationData
-
Get the date and time the values in this annotation was last updated.
- getLastUpdate() - Method in class net.sf.basedb.core.data.FileData
-
Get the date and time the actual file data was last updated.
- getLastUpdate() - Method in class net.sf.basedb.core.data.ReporterData
-
Get the date and time the information about this reporter
last was updated.
- getLastUpdate() - Method in class net.sf.basedb.core.File
-
Get the date and time the actual file data was last updated.
- getLastUpdated() - Method in class net.sf.basedb.clients.jobagent.slotmanager.MasterSlotManager.RemoteSlot
-
- getLayerNo() - Method in class net.sf.basedb.core.data.DataCubeLayerData
-
The layer number of this layer in the data cube.
- getLayerNo() - Method in class net.sf.basedb.core.DataCubeLayer
-
Get the number of this layer.
- getLayers() - Method in class net.sf.basedb.core.data.DataCubeData
-
This is the inverse end.
- getLeftTableAlias(Query) - Method in class net.sf.basedb.core.RealJoin
-
- getLeftTableColumn() - Method in class net.sf.basedb.core.RealJoin
-
- getLength() - Method in class net.sf.basedb.core.data.ReporterClonePropertyData
-
The maximum length of string value types.
- getLength() - Method in class net.sf.basedb.core.ExtendedProperty
-
Get the maximum allowed length of the property value.
- getLength() - Method in class net.sf.basedb.core.plugin.ImportInputStream
-
Get the length of the stream in number of bytes.
- getLength() - Method in class net.sf.basedb.util.FileImportInputStream
-
- getLength() - Method in class net.sf.basedb.util.uri.UriMetadata
-
Get the length in bytes of the resource.
- getLimit() - Method in class net.sf.basedb.core.signal.ProgressReporterSignalHandler
-
Get the percentage limit where signal checking becomes disabled.
- getLimitHandler() - Method in class net.sf.basedb.core.AbstractSqlQuery
-
Get a handler for adding LIMIT and OFFSET parameters to
an SQL statement.
- getLine(int) - Method in class net.sf.basedb.util.parser.FlatFileParser
-
Get the line with the specified number.
- getLineCount() - Method in class net.sf.basedb.util.bfs.MetadataWriter
-
Get the number of lines that has been written to this
file so far, including all comment lines, empty lines,
sections headers, etc.
- getLineCount() - Method in class net.sf.basedb.util.parser.FlatFileParser
-
- getLines() - Method in class net.sf.basedb.util.parser.FlatFileParser
-
- getLink(String, String, Item, int, boolean) - Static method in class net.sf.basedb.clients.web.Base
-
- getLink(String, String, Item, int, boolean, String) - Static method in class net.sf.basedb.clients.web.Base
-
- getLink(String, Nameable, Integer, boolean, boolean, boolean, boolean) - Static method in class net.sf.basedb.clients.web.ChangeHistoryUtil
-
- getLinkedFile(String, File, boolean, boolean, boolean, String) - Static method in class net.sf.basedb.clients.web.Base
-
- getLinkedItem(DbControl, BasicItem) - Method in class net.sf.basedb.clients.web.plugins.AnyToAnyDataLoader
-
Get the item that is linked to by this any-to-any link definition.
- getLinkedName(String, Nameable, boolean, boolean) - Static method in class net.sf.basedb.clients.web.Base
-
- getLinksFrom(BasicItem) - Static method in class net.sf.basedb.core.AnyToAny
-
Get a query that returns all links linking from the specified item.
- getLinksTo(BasicItem) - Static method in class net.sf.basedb.core.AnyToAny
-
Get a query that returns all links linking to the specified item.
- getList() - Method in class net.sf.basedb.clients.web.taglib.table.CellValue
-
- getListableItems() - Static method in class net.sf.basedb.core.Metadata
-
Get a set containing all
Listable
item types.
- getListableItems(Item, SyncFilter.SourceItemTransform) - Static method in class net.sf.basedb.util.listable.ListableUtil
-
Get all item types that can have the specified relation to the
with the given item type.
- getListMemberType() - Method in class net.sf.basedb.core.SyncFilter
-
- getLobHelper() - Method in class net.sf.basedb.core.hibernate.SessionWrapper
-
- getLocale() - Static method in class net.sf.basedb.core.Config
-
Get the default locale configured for the server.
- getLocale() - Method in class net.sf.basedb.core.SessionControl
-
Get the locale that is curently assigned to this session control.
- getLocale() - Method in class net.sf.basedb.util.resources.ResourceBundleWrapper
-
Get the actual locale used by the bundle, which may be a different
locale from the one that was used to load it.
- getLocalHost() - Static method in class net.sf.basedb.util.SocketUtil
-
Get the local address of the local host.
- getLocalSignalHandlerId(SignalHandler) - Method in class net.sf.basedb.core.signal.AbstractSignalReceiver
-
Get the local signal handler id of the given signal handler.
- getLocation() - Method in class net.sf.basedb.core.data.DiskUsageData
-
- getLocation() - Method in class net.sf.basedb.core.data.FileData
-
- getLocation() - Method in class net.sf.basedb.core.data.QuotaIndex
-
- getLocation() - Method in interface net.sf.basedb.core.DiskConsumable
-
Get the
Location
the items is stored at.
- getLocation() - Method in class net.sf.basedb.core.DiskUsage
-
- getLocation() - Method in class net.sf.basedb.core.Experiment
-
- getLocation() - Method in class net.sf.basedb.core.File
-
- getLocation() - Method in class net.sf.basedb.core.RawBioAssay
-
- getLockMode() - Method in class net.sf.basedb.core.BioPlateType
-
Get the lock mode for wells located on plates of this plate type.
- getLockMode() - Method in class net.sf.basedb.core.BioWell
-
Get the lock mode of this well.
- getLockMode() - Method in class net.sf.basedb.core.data.BioPlateTypeData
-
A flag indicating if plates with this type have locked wells or not.
0 = not locked; 1 = locked-after-move; 2 = locked-after-add; 3=locked-after-create
- getLockOptions() - Method in class net.sf.basedb.core.hibernate.QueryWrapper
-
- getLogChangeType() - Method in enum net.sf.basedb.core.AnnotationBatcher.Change
-
- getLogControl() - Method in class net.sf.basedb.core.DbControl
-
Get the log controller for this db control.
- getLogControl() - Method in class net.sf.basedb.core.log.db.DbLogManager
-
- getLogControl() - Method in interface net.sf.basedb.core.log.LogManager
-
Get the log controller that is used in this transaction.
- getLoggedInUserId() - Method in class net.sf.basedb.core.SessionControl
-
Get the id of the logged in user, or 0 if no user is logged in.
- getLogger() - Static method in class net.sf.basedb.core.Application
-
Get the BASE core logger.
- getLoggingInterceptor() - Method in class net.sf.basedb.core.DbControl
-
Get the logging interceptor for this db control.
- getLogin() - Method in class net.sf.basedb.clients.jobagent.Agent
-
Get the agent.user
configuration value.
- getLogin() - Method in class net.sf.basedb.core.authentication.AuthenticatedUser
-
Get the login string for the user.
- getLogin() - Method in class net.sf.basedb.core.authentication.LoginRequest
-
Get the login name to use.
- getLogin() - Method in class net.sf.basedb.core.data.UserData
-
Get the login for the user account.
- getLogin() - Method in class net.sf.basedb.core.User
-
Get the login for the user account.
- getLoginComment() - Method in class net.sf.basedb.core.data.SessionData
-
Get the login comment.
- getLoginComment() - Method in class net.sf.basedb.core.Session
-
Get the login comment.
- getLoginField() - Method in interface net.sf.basedb.clients.web.extensions.login.LoginFormAction
-
Get attributes for the login field on the form.
- getLoginField() - Method in class net.sf.basedb.clients.web.extensions.login.LoginFormBean
-
- getLogInfo() - Method in class net.sf.basedb.core.log.ManualLogEntry
-
Get information about the log entry.
- getLoginRequest() - Method in class net.sf.basedb.core.AuthenticationContext
-
Get the login request information.
- getLoginTime() - Method in class net.sf.basedb.core.data.SessionData
-
Get the date and time the user logged in.
- getLoginTime() - Method in class net.sf.basedb.core.Session
-
Get the date and time the user logged in.
- getLogManager(LogControl) - Method in class net.sf.basedb.core.log.db.DbLogManagerFactory
-
- getLogManager(LogControl) - Method in interface net.sf.basedb.core.log.LogManagerFactory
-
Get/create a log manager to log events in a given transaction.
- getLogoutTime() - Method in class net.sf.basedb.core.data.SessionData
-
Get the date and time the user logged out.
- getLogoutTime() - Method in class net.sf.basedb.core.Session
-
Get the date and time the user logged out.
- getLong(String, long) - Static method in class net.sf.basedb.core.Config
-
Get the configuration setting specified by key
as a long value.
- getLong(HttpResponse, String, Long) - Static method in class net.sf.basedb.util.HttpUtil
-
- getLong(String) - Static method in class net.sf.basedb.util.Values
-
Convert a string to a long.
- getLong(String, long) - Static method in class net.sf.basedb.util.Values
-
Convert a string to an long.
- getLong(String, Long) - Static method in class net.sf.basedb.util.Values
-
Convert a string to an long.
- getLong(String[]) - Static method in class net.sf.basedb.util.Values
-
Convert an array of strings to an array of Long:s.
- getLongFormatter(SessionControl) - Static method in class net.sf.basedb.clients.web.formatter.FormatterFactory
-
Get the logged in user's formatter for long numbers.
- getLongOption(String, Long) - Method in class net.sf.basedb.core.AnnotationType
-
Get an option and convert the value to a long.
- getLongValues() - Method in class net.sf.basedb.core.data.annotations.AnnotationLink
-
- getLowerLimit() - Method in class net.sf.basedb.core.DoubleParameterType
-
Get the lowst valid value of the parameter.
- getLowerLimit() - Method in class net.sf.basedb.core.FloatParameterType
-
Get the lowst valid value of the parameter.
- getLowerLimit() - Method in class net.sf.basedb.core.IntegerParameterType
-
Get the lowest valid value of the parameter.
- getLowerLimit() - Method in class net.sf.basedb.core.LongParameterType
-
Get the lowest valid value of the parameter.
- getMACalculator() - Method in enum net.sf.basedb.core.IntensityTransform
-
Get a MA calculator implementation that is suitable for calculating
MA-values for the given source data type.
- getMainHqlQuery(DbControl) - Method in class net.sf.basedb.core.AbstractHqlQuery
-
Build the main query and set parameter values for it.
- getMainItemType() - Method in class net.sf.basedb.core.ItemSubtype
-
Get the main item type that the subtype belongs to.
- getMainQuery(DbControl, boolean) - Method in class net.sf.basedb.core.AbstractQuery
-
Build the main query string.
- getMaintenance() - Static method in class net.sf.basedb.core.Version
-
Get the maintentance version.
- getMaintenanceVersion() - Static method in class net.sf.basedb.core.Application
-
Get the maintenance version.
- getMainType() - Method in class net.sf.basedb.clients.web.plugins.SimpleExport
-
- getMainType() - Method in class net.sf.basedb.core.data.PluginDefinitionData
-
Get the main type of plugin.
- getMainType() - Method in class net.sf.basedb.core.plugin.AbstractAnalysisPlugin
-
- getMainType() - Method in class net.sf.basedb.core.plugin.AbstractExporterPlugin
-
- getMainType() - Method in interface net.sf.basedb.core.plugin.Plugin
-
Get the type of the plugin.
- getMainType() - Method in class net.sf.basedb.core.PluginDefinition
-
Get the type of plugin.
- getMainType() - Method in class net.sf.basedb.plugins.AbstractFlatFileImporter
-
- getMainType() - Method in class net.sf.basedb.plugins.BfsExporterPlugin
-
- getMainType() - Method in class net.sf.basedb.plugins.CdfFileReporterImporter
-
- getMainType() - Method in class net.sf.basedb.plugins.CloneReportersPlugin
-
- getMainType() - Method in class net.sf.basedb.plugins.executor.BaseFileExporterSupport
-
- getMainType() - Method in class net.sf.basedb.plugins.executor.BaseFileImporterSupport
-
- getMainType() - Method in class net.sf.basedb.plugins.executor.BfsExporterSupport
-
- getMainType() - Method in class net.sf.basedb.plugins.executor.BfsImporterSupport
-
- getMainType() - Method in class net.sf.basedb.plugins.executor.FileOnlyImporterSupport
-
- getMainType() - Method in class net.sf.basedb.plugins.HelpImporter
-
- getMainType() - Method in class net.sf.basedb.plugins.IntensityCalculatorPlugin
-
Returns the main plugin type this plugin belongs to.
- getMainType() - Method in class net.sf.basedb.plugins.PluginConfigurationImporter
-
- getMainType() - Method in class net.sf.basedb.plugins.SpotImageCreator
-
- getMainType() - Method in class net.sf.basedb.util.zip.AbstractFileUnpacker
-
- getMajor() - Static method in class net.sf.basedb.core.Version
-
Get the major version.
- getMajorVersion() - Static method in class net.sf.basedb.core.Application
-
Get the major version.
- getManualConfigureParameters() - Method in class net.sf.basedb.plugins.Base1PluginExecuter
-
Creates the information needed for manual configuration and initiates the
parameters.
- getMapper(FlatFileParser, String, Integer, Mapper) - Method in class net.sf.basedb.plugins.AbstractFlatFileImporter
-
- getMapper(FlatFileParser, String, Integer, Mapper, JepFunction...) - Method in class net.sf.basedb.plugins.AbstractFlatFileImporter
-
Get a mapper for the specified flat file parser.
- getMapper(String) - Method in class net.sf.basedb.util.parser.FlatFileParser
-
Get a mapper using the default number format.
- getMapper(String, JepFunction...) - Method in class net.sf.basedb.util.parser.FlatFileParser
-
- getMapper(String, boolean) - Method in class net.sf.basedb.util.parser.FlatFileParser
-
Get a mapper using the default number format.
- getMapper(String, NumberFormat) - Method in class net.sf.basedb.util.parser.FlatFileParser
-
Get a mapper using a specific number format.
- getMapper(String, NumberFormat, boolean) - Method in class net.sf.basedb.util.parser.FlatFileParser
-
- getMapper(String, NumberFormat, boolean, JepFunction...) - Method in class net.sf.basedb.util.parser.FlatFileParser
-
Create a mapper object that maps an expression string to a value.
- getMapping() - Static method in class net.sf.basedb.core.HibernateUtil
-
- getMappingBatcher() - Method in class net.sf.basedb.core.BioAssaySet
-
Get a batcher used to insert mappings to raw data.
- getMappingBatcher() - Method in class net.sf.basedb.core.DataCube
-
- getMappings() - Method in class net.sf.basedb.core.data.VirtualDbData
-
The number of cube mappings in the virtual database.
- getMappings() - Method in class net.sf.basedb.core.VirtualDb
-
Get the number of DataCubeMapping:s in this virtual database.
- getMasterReporterJoiner(JoinType) - Static method in class net.sf.basedb.core.DynamicReporterQuery
-
Get a joiner instance for joining the master reporter table
when the root query is against the cloned reporters table.
- getMatching(DbControl) - Method in class net.sf.basedb.core.SyncFilter
-
- getMatchingReporters(DbControl) - Method in class net.sf.basedb.clients.web.ExperimentExplorer
-
Get the number of reporters matching the current reporter
filter.
- getMatchingSource() - Method in class net.sf.basedb.core.data.ItemListSyncFilterData
-
The number of matching source items during that last sync.
- getMatchingTransformed() - Method in class net.sf.basedb.core.data.ItemListSyncFilterData
-
The number of matching items after the transform during that last sync.
- getMax() - Method in class net.sf.basedb.util.plot.HistogramPlot.HistogramBin
-
Get the maximum of all values in this bin.
- getMaxAge() - Method in class net.sf.basedb.core.DiskUsageStatistics
-
Get the max age in seconds for a disk usage summary
object before it is reloaded from the database again.
- getMaxBaseVersion() - Method in interface net.sf.basedb.core.plugin.About
-
Get the maximum BASE version were to plug-in no longer is
expected to work.
- getMaxBaseVersion() - Method in class net.sf.basedb.core.plugin.AboutImpl
-
- getMaxBaseVersion() - Method in class net.sf.basedb.util.extensions.AboutBean
-
- getMaxBaseVersion() - Method in class net.sf.basedb.util.extensions.Registry.RegisteredAbout
-
- getMaxBytes() - Method in class net.sf.basedb.core.data.QuotaIndex
-
- getMaxLength() - Method in class net.sf.basedb.core.AnnotationType
-
Get the maximum allowed string length for a
Type.STRING
annotation.
- getMaxLength() - Method in class net.sf.basedb.core.StringParameterType
-
Get the max length of the parameter.
- getMaxMemory() - Method in class net.sf.basedb.core.data.JobAgentSettingsData
-
The max amount of memory the plugin can use.
- getMaxMemory() - Method in class net.sf.basedb.core.data.PluginDefinitionData
-
The max amount of memory the plugin can use.
- getMaxMemory() - Method in class net.sf.basedb.core.JobAgentSettings
-
Get the maximum amount of memory the plugin is allowed to use.
- getMaxMemory() - Method in class net.sf.basedb.core.PluginDefinition
-
Get the maximum amount of memory the plugins is allowed to use.
- getMaxParametersInQuery() - Method in class net.sf.basedb.core.dbengine.AbstractDbEngine
-
Returns 10000.
- getMaxParametersInQuery() - Method in interface net.sf.basedb.core.dbengine.DbEngine
-
Get the maximum number of parameters that can be used in a prepared
statement for a query.
- getMaxProjectPermission() - Method in class net.sf.basedb.core.Keyring
-
Get the max project permission within the currently active project.
- getMaxRawMappingsForSpot() - Method in class net.sf.basedb.core.BioAssaySet
-
Get the number of mappings to raw data spots for the spot with
the most number of mappings.
- getMaxRawMappingsForSpot() - Method in class net.sf.basedb.core.data.DataCubeData
-
The maximum number of raw data spots a single spot in this data cube
is mapped to.
- getMaxRawMappingsForSpot() - Method in class net.sf.basedb.core.DataCube
-
Get the number of mappings to raw data spots for the spot with
the most number of mappings.
- getMaxRecent(SessionControl) - Static method in class net.sf.basedb.clients.web.Base
-
Get the setting for the maximum number of recently used items
to save.
- getMaxResults() - Method in class net.sf.basedb.core.AbstractQuery
-
- getMaxResults() - Method in class net.sf.basedb.core.hibernate.QueryWrapper
-
- getMaxResults() - Method in interface net.sf.basedb.core.query.Query
-
The maximum number of rows returned by the query.
- getMaxUrlLength() - Method in class net.sf.basedb.clients.web.taglib.Page
-
- getMaxValue() - Method in class net.sf.basedb.core.Coloring
-
Get the value that represents the maximum value.
- getMaxValue() - Method in class net.sf.basedb.core.data.ColoringData
-
The value for the ax endpoint color.
- getMaxValueDouble() - Method in class net.sf.basedb.core.AnnotationType
-
- getMaxValueLong() - Method in class net.sf.basedb.core.AnnotationType
-
- getMaxY(int) - Method in class net.sf.basedb.util.plot.HistogramPlot.HistogramSeries
-
- getMaxY(HistogramPlot.HistogramBin) - Method in enum net.sf.basedb.util.plot.HistogramPlot.YAggregate
-
- getMaybeGranted() - Method in class net.sf.basedb.core.plugin.Permissions
-
Get the permissions that the plugin should be granted only if the
logged in user already have the permissions.
- getMd5() - Method in class net.sf.basedb.core.data.FileData
-
Get the MD5 hash of the file contents.
- getMd5() - Method in class net.sf.basedb.core.data.ItemListSyncFilterData
-
Get the MD5 hash of the concatenated ID values.
- getMd5() - Method in class net.sf.basedb.core.File
-
Get the MD5 hash of the file contents, or null if not known.
- getMd5() - Method in class net.sf.basedb.util.uri.UriMetadata
-
Get the MD5 checksum of the resource.
- getMean(int) - Method in class net.sf.basedb.clients.web.ExperimentExplorer.AnnotationGroup
-
Get the mean of the intensity values for the given channel.
- getMean() - Method in class net.sf.basedb.util.plot.HistogramPlot.HistogramBin
-
Get the mean of all values in this bin.
- getMember() - Method in class net.sf.basedb.core.ExtendedPropertyAccessor.GetterSetter
-
Always return null.
- getMember(DataFileType) - Method in class net.sf.basedb.core.FileSet
-
Get the member of the given type assuming that there
is only a single member of that type.
- getMember() - Method in class net.sf.basedb.util.fileset.ValidatingFileSetMember
-
Get the file set member that this proxy represents.
- getMembers() - Method in class net.sf.basedb.core.data.FileSetData
-
The members of this file set.
- getMembers() - Method in class net.sf.basedb.core.data.ItemListData
-
Get the set that manages which items that are part of this list.
- getMembers() - Method in class net.sf.basedb.core.FileSet
-
Get the members of this file set.
- getMembers(String) - Method in class net.sf.basedb.core.FileSet
-
Get a query that returns all members in a file set with a specific
generic
ItemSubtype
.
- getMembers(DataFileType) - Method in class net.sf.basedb.core.FileSet
-
Get a query that returns all members in a file set with a specific
DataFileType
.
- getMembers() - Method in class net.sf.basedb.core.ItemList
-
Get a query that returns all items that are members of this list.
- getMemberType() - Method in class net.sf.basedb.core.data.ItemListData
-
Get the type of items this list can hold.
- getMemberType() - Method in class net.sf.basedb.core.ItemList
-
Get the item type of members on this list.
- getMemberTypes() - Method in class net.sf.basedb.core.FileSet
-
Get a query that return the
DataFileType
for all members
of this file set.
- getMenu() - Method in class net.sf.basedb.clients.web.taglib.Page
-
- getMenuId() - Method in class net.sf.basedb.clients.web.extensions.menu.FixedMenuItemFactory
-
- getMenuId() - Method in interface net.sf.basedb.clients.web.extensions.menu.MenuItemAction
-
The ID of the menu where this menu item belongs, or null if
it belongs to the top-level menu.
- getMenuId() - Method in class net.sf.basedb.clients.web.extensions.menu.MenuItemBean
-
- getMessage() - Method in class net.sf.basedb.core.ItemContext
-
Get a message that should be displayed by a client application as
soon as it is appropriate to do so.
- getMessage() - Method in class net.sf.basedb.core.PluginResponse
-
Get the return message from the plugin.
- getMessage() - Method in class net.sf.basedb.core.SimpleProgressReporter
-
Get the last progress message this progress reporter should display.
- getMessage() - Method in class net.sf.basedb.plugins.executor.ExternalProgramExecutor.ResponseWrapper
-
- getMessage(String) - Method in class net.sf.basedb.plugins.executor.ExternalProgramExecutor.ResponseWrapper
-
- getMessage() - Method in class net.sf.basedb.util.fileset.ValidatingFileSetMember
-
Get the error message if the file failed validation.
- getMessage() - Method in class net.sf.basedb.util.overview.Failure
-
Get a message explaining the failure.
- getMessage() - Method in class net.sf.basedb.util.overview.Fix
-
Get a message explaining what needs to be fixed.
- getMessages() - Method in class net.sf.basedb.core.data.JobData
-
This is the inverse end.
- getMessages() - Method in class net.sf.basedb.core.data.UserData
-
This is the inverse end.
- getMessages() - Method in class net.sf.basedb.core.User
-
Get a query that returns all messages for the user.
- getMessages() - Method in class net.sf.basedb.util.extensions.manager.ProcessResults.FileResults
-
A list of detailed messages, indicating the results of
individual operation on this file.
- getMetaColumn() - Method in class net.sf.basedb.core.FeatureCoordinate
-
- getMetadata(ObjectKey<M>) - Method in class net.sf.basedb.util.extensions.manager.ExtensionsFile
-
Get metadata registered for a given given key.
- getMetadata() - Method in interface net.sf.basedb.util.uri.ConnectionManager
-
Get metadata about the resource.
- getMetadata() - Method in class net.sf.basedb.util.uri.http.HttpConnectionManager
-
- getMetadataKeysOfClass(Class<T>) - Method in class net.sf.basedb.util.extensions.manager.ExtensionsFile
-
Get a list of all metadata defined in this extensions
file that are keyed with the specified class or interface.
- getMetadataParser() - Method in class net.sf.basedb.util.importer.spotdata.BfsImporter
-
- getMetadataPrefix() - Method in class net.sf.basedb.util.basefile.BaseFileWriter
-
The metadata prefix is written to the beginning of
each line that is not a data line.
- getMetadataSources() - Method in class net.sf.basedb.core.ServiceSessionControl.SessionFactoryConfiguration
-
Get an object for registering mapped entity classes.
- getMetadataWriter() - Method in class net.sf.basedb.util.export.spotdata.BfsExporter
-
Get the writer were metadata should be printed.
- getMetaGridX() - Method in class net.sf.basedb.core.ArrayDesignBlock
-
Get the column coordinate of this block.
- getMetaGridX() - Method in class net.sf.basedb.core.BlockInfo
-
Get the row or x meta coordinate.
- getMetaGridX() - Method in class net.sf.basedb.core.data.ArrayDesignBlockData
-
Get the row coordinate of this block.
- getMetaGridX() - Method in class net.sf.basedb.core.data.RawData
-
- getMetaGridX() - Method in class net.sf.basedb.plugins.PrintMapFlatFileImporter.MetaBlock
-
- getMetaGridY() - Method in class net.sf.basedb.core.ArrayDesignBlock
-
Get the row coordinate of this block.
- getMetaGridY() - Method in class net.sf.basedb.core.BlockInfo
-
Get the column or y meta coordinate.
- getMetaGridY() - Method in class net.sf.basedb.core.data.ArrayDesignBlockData
-
Get the column coordinate of this block.
- getMetaGridY() - Method in class net.sf.basedb.core.data.RawData
-
- getMetaGridY() - Method in class net.sf.basedb.plugins.PrintMapFlatFileImporter.MetaBlock
-
- getMetaRow() - Method in class net.sf.basedb.core.FeatureCoordinate
-
- getMethod() - Method in class net.sf.basedb.core.authentication.AuthenticationMethod
-
Get the name of the authentication method.
- getMethod() - Method in class net.sf.basedb.core.ExtendedPropertyAccessor.GetterSetter
-
Always return null.
- getMethod() - Method in class net.sf.basedb.plugins.batchimport.FallbackIdMethod
-
- getMethod() - Method in class net.sf.basedb.plugins.batchimport.FileImporter.PathIdMethod
-
- getMethod() - Method in interface net.sf.basedb.plugins.batchimport.IdMethod
-
The name of this method, which should be unique among the methods that
can be used at a given time.
- getMethod() - Method in class net.sf.basedb.plugins.batchimport.InternalIdMethod
-
- getMethod() - Method in class net.sf.basedb.plugins.batchimport.MultiPropertyIdMethod
-
- getMethod() - Method in class net.sf.basedb.plugins.batchimport.PropertyIdMethod
-
- getMethod(Class<?>, String, Class<?>) - Method in class net.sf.basedb.util.extensions.debug.BeanActionFactory
-
Get a method with a specific name with optionally, takes
a single parameter of given type.
- getMethodName() - Method in class net.sf.basedb.core.ExtendedPropertyAccessor.GetterSetter
-
Always return null.
- getMethodName(String, String) - Method in class net.sf.basedb.util.extensions.debug.BeanActionFactory
-
Convert the parameter name to a method name.
- getMiameAnnotationTypes(DbControl, OverviewContext, Item) - Static method in class net.sf.basedb.util.overview.OverviewUtil
-
Get all annotation types that has been marked as "Required for MIAME".
- getMidValue() - Method in class net.sf.basedb.core.Coloring
-
Get the value that represents the midpoint value.
- getMidValue() - Method in class net.sf.basedb.core.data.ColoringData
-
The value for the midpoint color.
- getMillisecondsSinceStart() - Method in class net.sf.basedb.clients.web.fileupload.FileUploadProgress
-
Get the number of milliseconds since the start of the upload.
- getMimeType() - Method in class net.sf.basedb.clients.web.fileupload.UploadedFile
-
Get the MIME type of the uploaded file.
- getMimeType() - Method in interface net.sf.basedb.clients.web.plugins.ExportTemplate
-
Get the MIME type to assign to files generated by this template.
- getMimeType() - Method in class net.sf.basedb.clients.web.plugins.PlainTextTemplate
-
- getMimeType() - Method in class net.sf.basedb.clients.web.plugins.XMLTemplate
-
- getMimeType() - Method in class net.sf.basedb.core.data.FileData
-
Get the mime type of this FileData
item.
- getMimeType() - Method in class net.sf.basedb.core.File
-
The mimetype of this File
.
- getMimeType(DbControl, String, String) - Static method in class net.sf.basedb.core.MimeType
-
Get the MIME type of a given file name or extension.
- getMimeType() - Method in class net.sf.basedb.core.plugin.ImportInputStream
-
Get the MIME type of the source.
- getMimeType() - Method in class net.sf.basedb.util.FileImportInputStream
-
- getMimeType() - Method in class net.sf.basedb.util.uri.UriMetadata
-
Get the MIME type of the resource.
- getMimeType() - Method in class net.sf.basedb.util.zip.Bzip2FilePacker
-
- getMimeType() - Method in interface net.sf.basedb.util.zip.FilePacker
-
Gets the MIME type to give compressed files from this packer
- getMimeType() - Method in class net.sf.basedb.util.zip.GzipFilePacker
-
- getMimeType() - Method in class net.sf.basedb.util.zip.TarFilePacker
-
- getMimeType() - Method in class net.sf.basedb.util.zip.ZipFilePacker
-
- getMimeTypes() - Method in class net.sf.basedb.plugins.Bzip2FileUnpacker
-
Return a set containing the strings [ application/x-bzip2 ].
- getMimeTypes() - Method in class net.sf.basedb.plugins.GzipFileUnpacker
-
Return a set containing the strings [ application/x-gzip ].
- getMimeTypes() - Method in class net.sf.basedb.plugins.TarFileUnpacker
-
Return a set containing the strings [ application/x-tar, application/x-gzip,
application/x-bzip2 ].
- getMimeTypes() - Method in class net.sf.basedb.plugins.ZipFileUnpacker
-
Return a set containing the strings [ application/zip, application/java-archive ].
- getMimeTypes() - Method in interface net.sf.basedb.util.zip.FileUnpacker
-
Get the MIME type for the file formats this unpacker supports.
- getMin() - Method in class net.sf.basedb.util.plot.HistogramPlot.HistogramBin
-
Get the minumum of all values in this bin.
- getMinBaseVersion() - Method in interface net.sf.basedb.core.plugin.About
-
Get the minimum BASE version that the plug-in requires.
- getMinBaseVersion() - Method in class net.sf.basedb.core.plugin.AboutImpl
-
- getMinBaseVersion() - Method in class net.sf.basedb.util.extensions.AboutBean
-
- getMinBaseVersion() - Method in class net.sf.basedb.util.extensions.Registry.RegisteredAbout
-
- getMinor() - Static method in class net.sf.basedb.core.Version
-
Get the minor version.
- getMinorVersion() - Static method in class net.sf.basedb.core.Application
-
Get the minor version.
- getMinValue() - Method in class net.sf.basedb.core.Coloring
-
Get the value that represents the minimum value.
- getMinValue() - Method in class net.sf.basedb.core.data.ColoringData
-
The value for the minimum endpoint color.
- getMinValueDouble() - Method in class net.sf.basedb.core.AnnotationType
-
- getMinValueLong() - Method in class net.sf.basedb.core.AnnotationType
-
- getMinY(int) - Method in class net.sf.basedb.util.plot.HistogramPlot.HistogramSeries
-
- getMinY(HistogramPlot.HistogramBin) - Method in enum net.sf.basedb.util.plot.HistogramPlot.YAggregate
-
- getMissingDataFileTypes() - Method in class net.sf.basedb.core.FileSet
-
Get a query that is returning all file types that
have been marked as required by the associated platform but has no member
in this file set.
- getMissingItemFix(DbControl, Node) - Method in class net.sf.basedb.util.overview.validator.AnnotationValidator
-
- getMissingItemFix(DbControl, Node) - Method in class net.sf.basedb.util.overview.validator.AnyToAnyValidator
-
- getMissingItemFix(DbControl, Node) - Method in class net.sf.basedb.util.overview.validator.ArrayBatchValidator
-
The suggested fix is to add an array batch to the
slide.
- getMissingItemFix(DbControl, Node) - Method in class net.sf.basedb.util.overview.validator.ArrayDesignValidator
-
The suggested fix is to add an array design to the
raw bioassay.
- getMissingItemFix(DbControl, Node) - Method in class net.sf.basedb.util.overview.validator.ArraySlideValidator
-
The suggested fix is to add an array slide to the
bioassay.
- getMissingItemFix(DbControl, Node) - Method in class net.sf.basedb.util.overview.validator.BasicNodeValidator
-
Subclasses should override this method if they have a suggessted fix
for a missing item problem.
- getMissingItemFix(DbControl, Node) - Method in class net.sf.basedb.util.overview.validator.BioPlateValidator
-
- getMissingItemFix(DbControl, Node) - Method in class net.sf.basedb.util.overview.validator.BioSourceValidator
-
- getMissingItemFix(DbControl, Node) - Method in class net.sf.basedb.util.overview.validator.DataFileValidator
-
- getMissingItemFix(DbControl, Node) - Method in class net.sf.basedb.util.overview.validator.DerivedBioAssayValidator
-
- getMissingItemFix(DbControl, Node) - Method in class net.sf.basedb.util.overview.validator.ExperimentalFactorValidator
-
- getMissingItemFix(DbControl, Node) - Method in class net.sf.basedb.util.overview.validator.ExperimentValidator
-
- getMissingItemFix(DbControl, Node) - Method in class net.sf.basedb.util.overview.validator.ExtractValidator
-
The suggested fix is to add parent extracts to the physical
bioassay or one or more extracts to the pooled extract.
- getMissingItemFix(DbControl, Node) - Method in class net.sf.basedb.util.overview.validator.HardwareValidator
-
- getMissingItemFix(DbControl, Node) - Method in class net.sf.basedb.util.overview.validator.KitValidator
-
- getMissingItemFix(DbControl, Node) - Method in class net.sf.basedb.util.overview.validator.PhysicalBioAssayValidator
-
- getMissingItemFix(DbControl, Node) - Method in class net.sf.basedb.util.overview.validator.PlatformValidator
-
- getMissingItemFix(DbControl, Node) - Method in class net.sf.basedb.util.overview.validator.ProtocolParameterValidator
-
- getMissingItemFix(DbControl, Node) - Method in class net.sf.basedb.util.overview.validator.ProtocolValidator
-
- getMissingItemFix(DbControl, Node) - Method in class net.sf.basedb.util.overview.validator.RawBioAssayValidator
-
- getMissingItemFix(DbControl, Node) - Method in class net.sf.basedb.util.overview.validator.SampleValidator
-
The suggested fix is to add a parent sample to the extract
or one or more samples to the pooled sample.
- getMissingItemFix(DbControl, Node) - Method in class net.sf.basedb.util.overview.validator.SoftwareValidator
-
- getMissingItemFix(DbControl, Node) - Method in class net.sf.basedb.util.overview.validator.TagValidator
-
- getMissingNodeName(Node) - Method in class net.sf.basedb.util.overview.node.AnnotationNameGenerator
-
- getMissingNodeName(Node) - Method in class net.sf.basedb.util.overview.node.AnyToAnyNameGenerator
-
- getMissingNodeName(Node) - Method in class net.sf.basedb.util.overview.node.BioWellNameGenerator
-
- getMissingNodeName(Node) - Method in class net.sf.basedb.util.overview.node.FileSetMemberNameGenerator
-
- getMissingNodeName(Node) - Method in class net.sf.basedb.util.overview.node.ItemListMemberNameGenerator
-
- getMissingNodeName(Node) - Method in class net.sf.basedb.util.overview.node.NameableNameGenerator
-
- getMissingNodeName(Node) - Method in interface net.sf.basedb.util.overview.node.NodeNameGenerator
-
Generate a name for a node when the item is missing.
- getMissingNodeTitle(Node) - Method in class net.sf.basedb.util.overview.node.AnnotationNameGenerator
-
- getMissingNodeTitle(Node) - Method in class net.sf.basedb.util.overview.node.AnyToAnyNameGenerator
-
- getMissingNodeTitle(Node) - Method in class net.sf.basedb.util.overview.node.BioWellNameGenerator
-
- getMissingNodeTitle(Node) - Method in class net.sf.basedb.util.overview.node.FileSetMemberNameGenerator
-
- getMissingNodeTitle(Node) - Method in class net.sf.basedb.util.overview.node.ItemListMemberNameGenerator
-
- getMissingNodeTitle(Node) - Method in class net.sf.basedb.util.overview.node.NameableNameGenerator
-
- getMissingNodeTitle(Node) - Method in interface net.sf.basedb.util.overview.node.NodeNameGenerator
-
Generate a title for a node when the item is missing.
- getModifiedProperties(String, String, String) - Method in class net.sf.basedb.core.log.EntityDetails
-
Get all modified properties as a string, separating each
property name with the given separator.
- getMultiPermissions(DbControl, Item, Set<Integer>) - Static method in class net.sf.basedb.util.ShareableUtil
-
- getMultiplicity() - Method in class net.sf.basedb.core.AnnotationType
-
Get the multiplicity.
- getMultiplicity() - Method in class net.sf.basedb.core.data.AnnotationTypeData
-
How many values are allowed for this annotations of this type. 0 = no limit
- getMultiplicity() - Method in class net.sf.basedb.core.ParameterType
-
Get how many values that can be tied to this
parameter. 0 is unlimited values and 1 is default.
- getName() - Method in class net.sf.basedb.clients.jobagent.Agent
-
Get the agent.name
configuration value.
- getName() - Method in class net.sf.basedb.clients.web.extensions.DynamicActionAttribute
-
Get the name of the dynamic attribute.
- getName() - Method in class net.sf.basedb.clients.web.extensions.startpage.FixedStartPageFactory
-
- getName() - Method in interface net.sf.basedb.clients.web.extensions.startpage.StartPageAction
-
Get the name of the start page.
- getName() - Method in class net.sf.basedb.clients.web.extensions.startpage.StartPageBean
-
- getName() - Method in class net.sf.basedb.clients.web.ModeInfo
-
- getName(BasicItem) - Method in class net.sf.basedb.clients.web.taglib.Select
-
- getName() - Method in class net.sf.basedb.clients.web.taglib.table.Hidden
-
- getName() - Method in class net.sf.basedb.core.AnyToAny
-
- getName() - Method in class net.sf.basedb.core.authentication.ExtraUserInformation
-
The full name of the user.
- getName() - Method in class net.sf.basedb.core.BatchedPropertyInfo
-
Get the name of the property.
- getName() - Method in class net.sf.basedb.core.BioAssay
-
- getName() - Method in class net.sf.basedb.core.BioAssaySet
-
- getName() - Method in class net.sf.basedb.core.BioPlateEventType
-
- getName() - Method in class net.sf.basedb.core.BioPlateType
-
- getName() - Method in class net.sf.basedb.core.CommonItem
-
- getName() - Method in class net.sf.basedb.core.data.AnyToAnyData
-
- getName() - Method in class net.sf.basedb.core.data.BioAssayData
-
- getName() - Method in class net.sf.basedb.core.data.BioAssaySetData
-
- getName() - Method in class net.sf.basedb.core.data.BioPlateEventTypeData
-
- getName() - Method in class net.sf.basedb.core.data.BioPlateTypeData
-
- getName() - Method in class net.sf.basedb.core.data.ClientDefaultSettingData
-
Used by Hibernate to link with setting name.
- getName() - Method in class net.sf.basedb.core.data.CommonData
-
- getName() - Method in class net.sf.basedb.core.data.ContextData
-
Get the name of this Context
item.
- getName() - Method in class net.sf.basedb.core.data.ContextIndex
-
Get the name of this Context
item.
- getName() - Method in class net.sf.basedb.core.data.DataFileTypeData
-
- getName() - Method in class net.sf.basedb.core.data.DirectoryData
-
Get the name of the item.
- getName() - Method in class net.sf.basedb.core.data.ExtraValueTypeData
-
- getName() - Method in class net.sf.basedb.core.data.FileData
-
Get the name of the item.
- getName() - Method in class net.sf.basedb.core.data.GlobalDefaultSettingData
-
Used by Hibernate to link with setting name.
- getName() - Method in class net.sf.basedb.core.data.GroupData
-
- getName() - Method in class net.sf.basedb.core.data.HelpData
-
- getName() - Method in class net.sf.basedb.core.data.ItemListSyncFilterData
-
- getName() - Method in class net.sf.basedb.core.data.ItemSubtypeData
-
Get the name of the subtype which must be unique for subtypes related to a given item type.
- getName() - Method in class net.sf.basedb.core.data.MessageData
-
- getName() - Method in class net.sf.basedb.core.data.MimeTypeData
-
- getName() - Method in interface net.sf.basedb.core.data.NameableData
-
Get the name of the item.
- getName() - Method in class net.sf.basedb.core.data.NewsData
-
- getName() - Method in class net.sf.basedb.core.data.PlateEventTypeData
-
- getName() - Method in class net.sf.basedb.core.data.PlateGeometryData
-
- getName() - Method in class net.sf.basedb.core.data.PlatformData
-
- getName() - Method in class net.sf.basedb.core.data.PlatformVariantData
-
- getName() - Method in class net.sf.basedb.core.data.PluginDefinitionData
-
Get the name of the plugin.
- getName() - Method in class net.sf.basedb.core.data.PluginTypeData
-
- getName() - Method in class net.sf.basedb.core.data.ProjectData
-
- getName() - Method in class net.sf.basedb.core.data.QuantityData
-
- getName() - Method in class net.sf.basedb.core.data.QuotaData
-
- getName() - Method in class net.sf.basedb.core.data.QuotaTypeData
-
- getName() - Method in class net.sf.basedb.core.data.ReporterData
-
- getName() - Method in class net.sf.basedb.core.data.ReporterTypeData
-
- getName() - Method in class net.sf.basedb.core.data.RoleData
-
- getName() - Method in class net.sf.basedb.core.data.RoleKeyData
-
Get the name of the role key.
- getName() - Method in class net.sf.basedb.core.data.RootRawBioAssayData
-
- getName() - Method in class net.sf.basedb.core.data.SettingData
-
Used by Hibernate to link with setting name.
- getName() - Method in class net.sf.basedb.core.data.TransformationData
-
- getName() - Method in class net.sf.basedb.core.data.UnitData
-
- getName() - Method in class net.sf.basedb.core.data.UserClientSettingData
-
Used by Hibernate to link with setting name.
- getName() - Method in class net.sf.basedb.core.data.UserData
-
- getName() - Method in class net.sf.basedb.core.data.UserDefaultSettingData
-
Used by Hibernate to link with setting name.
- getName() - Method in class net.sf.basedb.core.data.VersionedParameter
-
Get the parameter name.
- getName() - Method in class net.sf.basedb.core.DataFileType
-
- getName() - Method in class net.sf.basedb.core.dbengine.TableInfo.ColumnInfo
-
- getName() - Method in class net.sf.basedb.core.dbengine.TableInfo.ForeignKeyInfo
-
- getName() - Method in class net.sf.basedb.core.dbengine.TableInfo.IndexInfo
-
- getName() - Method in class net.sf.basedb.core.dbengine.TableInfo.PrimaryKeyInfo
-
- getName() - Method in class net.sf.basedb.core.Directory
-
- getName() - Method in class net.sf.basedb.core.ExtendedProperty
-
Get the name of the extended property.
- getName() - Method in class net.sf.basedb.core.ExtraValueType
-
- getName() - Method in class net.sf.basedb.core.Group
-
- getName() - Method in class net.sf.basedb.core.Help
-
- getName() - Method in class net.sf.basedb.core.IntensityFormula
-
Get the name of the intensity formula.
- getName() - Method in class net.sf.basedb.core.ItemContext
-
Get the name of this context.
- getName() - Method in class net.sf.basedb.core.ItemSubtype
-
- getName() - Method in class net.sf.basedb.core.Message
-
- getName() - Method in class net.sf.basedb.core.MimeType
-
- getName() - Method in interface net.sf.basedb.core.Nameable
-
Get the name of the item.
- getName() - Method in class net.sf.basedb.core.News
-
- getName() - Method in class net.sf.basedb.core.PlateEventType
-
- getName() - Method in class net.sf.basedb.core.PlateGeometry
-
- getName() - Method in class net.sf.basedb.core.Platform
-
- getName() - Method in class net.sf.basedb.core.PlatformVariant
-
- getName() - Method in interface net.sf.basedb.core.plugin.About
-
The name of the plugin.
- getName() - Method in class net.sf.basedb.core.plugin.AboutImpl
-
- getName() - Method in class net.sf.basedb.core.PluginParameter
-
Get the parameter name.
- getName() - Method in class net.sf.basedb.core.PluginType
-
- getName() - Method in class net.sf.basedb.core.Presets.Preset
-
Get the name of this preset.
- getName() - Method in class net.sf.basedb.core.Project
-
- getName() - Method in class net.sf.basedb.core.Quantity
-
- getName() - Method in class net.sf.basedb.core.query.HqlEntityParameterExpression
-
Get the name of the parameter.
- getName() - Method in class net.sf.basedb.core.query.ParameterExpression
-
Get the name of the parameter.
- getName() - Method in class net.sf.basedb.core.query.QueryParameter
-
Get the name of the parameter.
- getName() - Method in class net.sf.basedb.core.Quota
-
- getName() - Method in class net.sf.basedb.core.QuotaType
-
- getName() - Method in class net.sf.basedb.core.RawDataType
-
Get the name of this raw data type.
- getName() - Method in class net.sf.basedb.core.ReporterType
-
- getName() - Method in class net.sf.basedb.core.Role
-
- getName() - Method in class net.sf.basedb.core.RoleKey
-
- getName() - Method in class net.sf.basedb.core.RootRawBioAssay
-
- getName() - Method in class net.sf.basedb.core.Setting
-
Get the name of this setting.
- getName() - Method in class net.sf.basedb.core.signal.Signal
-
Get the short name of the signal.
- getName() - Method in class net.sf.basedb.core.SyncFilter
-
- getName() - Method in class net.sf.basedb.core.Transformation
-
- getName() - Method in class net.sf.basedb.core.Unit
-
- getName() - Method in class net.sf.basedb.core.User
-
- getName() - Method in class net.sf.basedb.core.VirtualColumn
-
Get the name of the column.
- getName() - Method in class net.sf.basedb.plugins.Base1PluginExecuter.JobParameter
-
- getName() - Method in class net.sf.basedb.plugins.executor.ParameterDefinition
-
Get the name of the parameter.
- getName() - Method in enum net.sf.basedb.plugins.PrintMapFlatFileImporter.Section
-
- getName() - Method in class net.sf.basedb.util.bfs.MetadataModel.Section
-
Get the name of the section.
- getName() - Method in class net.sf.basedb.util.ContextUtil.ContextResult
-
Get the name of the plug-in configuration or, if the configuration is null,
of the plug-in definition
- getName() - Method in class net.sf.basedb.util.extensions.AboutBean
-
- getName() - Method in interface net.sf.basedb.util.extensions.ExtensionPoint
-
Get the name of the extension point.
- getName() - Method in class net.sf.basedb.util.extensions.ExtensionPointBean
-
- getName(Extension<?>) - Static method in class net.sf.basedb.util.extensions.ExtensionsUtil
-
Get the name of the extension.
- getName() - Method in class net.sf.basedb.util.extensions.manager.ExtensionsFile
-
Get the name of the file.
- getName() - Method in class net.sf.basedb.util.extensions.Registry.RegisteredAbout
-
- getName() - Method in class net.sf.basedb.util.extensions.Registry.RegisteredExtensionPoint
-
- getName() - Method in class net.sf.basedb.util.importer.BaseFileWrapper
-
- getName() - Method in class net.sf.basedb.util.importer.DiskFileWrapper
-
- getName() - Method in interface net.sf.basedb.util.importer.FileWrapper
-
Get the name of the file.
- getName() - Method in class net.sf.basedb.util.importer.spotdata.BaseFileInfo.ChildBioAssay
-
Get the name of the child bioassay.
- getName() - Method in class net.sf.basedb.util.importer.spotdata.BaseFileInfo
-
Get the name of the file.
- getName() - Method in class net.sf.basedb.util.jep.convert.AbsConverter
-
- getName() - Method in class net.sf.basedb.util.jep.convert.AbstractJepConversionFunction
-
- getName() - Method in class net.sf.basedb.util.jep.convert.AddConverter
-
- getName() - Method in class net.sf.basedb.util.jep.convert.AndConverter
-
- getName() - Method in class net.sf.basedb.util.jep.convert.DivideConverter
-
- getName() - Method in class net.sf.basedb.util.jep.convert.EqualsConverter
-
- getName() - Method in class net.sf.basedb.util.jep.convert.ExpConverter
-
- getName() - Method in class net.sf.basedb.util.jep.convert.GreaterConverter
-
- getName() - Method in class net.sf.basedb.util.jep.convert.GreaterEqualsConverter
-
- getName() - Method in class net.sf.basedb.util.jep.convert.IfConverter
-
- getName() - Method in interface net.sf.basedb.util.jep.convert.JepConversionFunction
-
Get the name of the function or the symbol of the operator
- getName() - Method in class net.sf.basedb.util.jep.convert.LessConverter
-
- getName() - Method in class net.sf.basedb.util.jep.convert.LessEqualsConverter
-
- getName() - Method in class net.sf.basedb.util.jep.convert.LogarithmConverter
-
- getName() - Method in class net.sf.basedb.util.jep.convert.MultiplyConverter
-
- getName() - Method in class net.sf.basedb.util.jep.convert.NaturalLogarithmConverter
-
- getName() - Method in class net.sf.basedb.util.jep.convert.NotConverter
-
- getName() - Method in class net.sf.basedb.util.jep.convert.NotEqualsConverter
-
- getName() - Method in class net.sf.basedb.util.jep.convert.OrConverter
-
- getName() - Method in class net.sf.basedb.util.jep.convert.SquareRootConverter
-
- getName() - Method in class net.sf.basedb.util.jep.convert.SubtractConverter
-
- getName() - Method in class net.sf.basedb.util.jep.convert.UMinusConverter
-
- getName() - Method in class net.sf.basedb.util.overview.Node
-
Get the name of this node.
- getName() - Method in class net.sf.basedb.util.plot.HistogramPlot.HistogramSeries
-
- getName() - Method in class net.sf.basedb.util.plot.PlotAnnotation
-
The name of the annotation, which will be used as a label in the image.
- getName() - Method in class net.sf.basedb.util.resources.ResourceBundleWrapper
-
Get the base name of the resource bundle.
- getNamedParameters() - Method in class net.sf.basedb.core.hibernate.QueryWrapper
-
- getNamedProcedureCall(String) - Method in class net.sf.basedb.core.hibernate.SessionWrapper
-
- getNamedProcedureCall(String) - Method in class net.sf.basedb.core.hibernate.StatelessSessionWrapper
-
- getNamedQuery(String) - Method in class net.sf.basedb.core.hibernate.SessionWrapper
-
If the same query has been executed before, return the cached
instance, otherwise create a new query from the parent session
and cache it.
- getNamedQuery(String) - Method in class net.sf.basedb.core.hibernate.StatelessSessionWrapper
-
If the same query has been executed before, return the cached
instance, otherwise create a new query from the parent session
and cache it.
- getNew(DbControl, Annotatable) - Static method in class net.sf.basedb.core.AnnotationSet
-
Create a new annotation set for the specified item.
- getNew(DbControl, Type) - Static method in class net.sf.basedb.core.AnnotationType
-
Create a new AnnotationType
item.
- getNew(DbControl) - Static method in class net.sf.basedb.core.AnnotationTypeCategory
-
Creates a new AnnotationTypeCategory
item.
- getNew(DbControl, BasicItem, BasicItem, String, boolean) - Static method in class net.sf.basedb.core.AnyToAny
-
Create a new AnyToAny
link
- getNew(DbControl, ArrayDesign) - Static method in class net.sf.basedb.core.ArrayBatch
-
Create a new ArrayBatch
item.
- getNew(DbControl, Platform) - Static method in class net.sf.basedb.core.ArrayDesign
-
Create a new ArrayDesign
item for a given platform.
- getNew(DbControl, PlatformVariant) - Static method in class net.sf.basedb.core.ArrayDesign
-
Create a new ArrayDesign
item for a given platform
variant.
- getNew(DbControl, ArrayDesign, BlockInfo) - Static method in class net.sf.basedb.core.ArrayDesignBlock
-
- getNew(DbControl, ArrayBatch) - Static method in class net.sf.basedb.core.ArraySlide
-
Create a new ArraySlide
item.
- getNew(DbControl, BioAssaySet, DataCubeColumn) - Static method in class net.sf.basedb.core.BioAssay
-
Create a new BioAssay
item.
- getNew(DbControl, Transformation, DataCubeLayer) - Static method in class net.sf.basedb.core.BioAssaySet
-
Create a new BioAssaySet
item.
- getNew(DbControl, MeasuredBioMaterial) - Static method in class net.sf.basedb.core.BioMaterialEvent
-
- getNew(DbControl, MeasuredBioMaterial, BioPlateEventParticipant) - Static method in class net.sf.basedb.core.BioMaterialEvent
-
- getNew(DbControl, PlateGeometry, BioPlateType) - Static method in class net.sf.basedb.core.BioPlate
-
Creates a new bioplate with a specific plate geometry and type.
- getNew(DbControl, BioPlateEventType) - Static method in class net.sf.basedb.core.BioPlateEvent
-
Create a new BioPlateEvent
item.
- getNew(DbControl, BioPlateEvent, BioPlate) - Static method in class net.sf.basedb.core.BioPlateEventParticipant
-
Creates a new participant for the given event and bioplate.
- getNew(DbControl, String) - Static method in class net.sf.basedb.core.BioPlateEventType
-
Creates a new bioplate event type.
- getNew(DbControl) - Static method in class net.sf.basedb.core.BioPlateType
-
Creates a new bioplate type.
- getNew(DbControl) - Static method in class net.sf.basedb.core.BioSource
-
Create a new BioSource
item.
- getNew(DbControl, String) - Static method in class net.sf.basedb.core.Client
-
Create a new Client
item.
- getNew(DbControl, Client, String, String) - Static method in class net.sf.basedb.core.ClientDefaultSetting
-
Create a new ClientDefaultSetting
item.
- getNew(DbControl, VirtualDb) - Static method in class net.sf.basedb.core.DataCube
-
Create a new DataCube
item.
- getNew(DbControl, DataCube) - Static method in class net.sf.basedb.core.DataCubeColumn
-
Create a new DataCubeColumn
item.
- getNew(DbControl, DataCube, Type, ExtraValue.CoordinateType) - Static method in class net.sf.basedb.core.DataCubeExtraValue
-
Create a new DataCubeExtraValue
item.
- getNew(DbControl, DataCube) - Static method in class net.sf.basedb.core.DataCubeFilter
-
Create a new DataCubeFilter
item.
- getNew(DbControl, DataCube) - Static method in class net.sf.basedb.core.DataCubeLayer
-
Create a new DataCubeLayer
item.
- getNew(DbControl, String, Item) - Static method in class net.sf.basedb.core.DataFileType
-
Create a new data file type.
- getNew(DbControl, boolean, Job) - Static method in class net.sf.basedb.core.DerivedBioAssay
-
Create a new parent-less derived bioassay.
- getNew(DbControl, PhysicalBioAssay, Job) - Static method in class net.sf.basedb.core.DerivedBioAssay
-
Create a new (root) derived bioassay from a physical bioassay.
- getNew(DbControl, DerivedBioAssay, Job) - Static method in class net.sf.basedb.core.DerivedBioAssay
-
Create a new child derived bioassay from a parent derived bioassay.
- getNew(DbControl, Directory) - Static method in class net.sf.basedb.core.Directory
-
Create a new Directory
item.
- getNew(DbControl, Path) - Static method in class net.sf.basedb.core.Directory
-
Create a new or existing Directory
from a path.
- getNew(DbControl, RawDataType) - Static method in class net.sf.basedb.core.Experiment
-
Create a new Experiment
item.
- getNew(DbControl) - Static method in class net.sf.basedb.core.Extract
-
Create a new Extract
item.
- getNew(DbControl, BioPlateEventParticipant) - Static method in class net.sf.basedb.core.Extract
-
Create a new Extract
item as part
of a master bioplate event.
- getNew(DbControl, BioAssaySet, ExtraValueType, DataCubeExtraValue, Job) - Static method in class net.sf.basedb.core.ExtraValue
-
Create a new ExtraValue
item.
- getNew(DbControl, String, Type) - Static method in class net.sf.basedb.core.ExtraValueType
-
Create a new ExtraValue
item.
- getNew(DbControl, ArrayDesign) - Static method in class net.sf.basedb.core.FeatureBatcher
-
Create a new batcher for regular features.
- getNew(DbControl, Directory) - Static method in class net.sf.basedb.core.File
-
Create a new File
item.
- getNew(DbControl) - Static method in class net.sf.basedb.core.FileServer
-
Create a new FileServer
item.
- getNew(DbControl, FileStoreEnabled) - Static method in class net.sf.basedb.core.FileSet
-
Create a new file set for the specified item.
- getNew(DbControl, FileSet, File, DataFileType) - Static method in class net.sf.basedb.core.FileSetMember
-
Create a new member in a file set.
- getNew(DbControl) - Static method in class net.sf.basedb.core.Formula
-
Create a new Formula
item.
- getNew(DbControl, String, String) - Static method in class net.sf.basedb.core.GlobalDefaultSetting
-
Create a new GlobalDefaultSetting
item.
- getNew(DbControl) - Static method in class net.sf.basedb.core.Group
-
Create a new Group
item.
- getNew(DbControl) - Static method in class net.sf.basedb.core.Hardware
-
Create a new Hardware
item.
- getNew(DbControl, Client, String) - Static method in class net.sf.basedb.core.Help
-
Create a new Help
item.
- getNew(DbControl, Item) - Static method in class net.sf.basedb.core.ItemList
-
Create a new ItemList
item.
- getNew(DbControl, Item) - Static method in class net.sf.basedb.core.ItemSubtype
-
Create a new item subtype item.
- getNew(DbControl, ItemSubtype, DataFileType) - Static method in class net.sf.basedb.core.ItemSubtypeFileType
-
Create a new item linking a file type to an item subtype.
- getNew(DbControl, PluginDefinition, PluginConfiguration, Experiment) - Static method in class net.sf.basedb.core.Job
-
Create a new Job
item.
- getNew(DbControl, String) - Static method in class net.sf.basedb.core.JobAgent
-
Create a new JobAgent
item.
- getNew(DbControl, JobAgent, PluginDefinition) - Static method in class net.sf.basedb.core.JobAgentSettings
-
Create a new JobAgentSettings
item.
- getNew(DbControl) - Static method in class net.sf.basedb.core.Kit
-
Create a new Kit
item.
- getNew(DbControl, User, String, User, Job) - Static method in class net.sf.basedb.core.Message
-
Create a new Message
item.
- getNew(DbControl) - Static method in class net.sf.basedb.core.MimeType
-
Create a new MimeType
item.
- getNew(DbControl, Date, Date) - Static method in class net.sf.basedb.core.News
-
Create a new News
item.
- getNew(DbControl) - Static method in class net.sf.basedb.core.PermissionTemplate
-
Create a new permission template item.
- getNew(DbControl) - Static method in class net.sf.basedb.core.PhysicalBioAssay
-
Create a new PhysicalBioAssay
item.
- getNew(DbControl, BioPlateEventParticipant) - Static method in class net.sf.basedb.core.PhysicalBioAssay
-
Create a new PhysicalBioAssay
item as part of a
master bioplate event.
- getNew(DbControl, PlateType) - Static method in class net.sf.basedb.core.Plate
-
Create a new Plate
item.
- getNew(DbControl, Plate, PlateEventType) - Static method in class net.sf.basedb.core.PlateEvent
-
Create a new PlateEvent
item.
- getNew(DbControl, PlateType) - Static method in class net.sf.basedb.core.PlateEventType
-
Create a new PlateEventType
item.
- getNew(DbControl, int, int) - Static method in class net.sf.basedb.core.PlateGeometry
-
Create a new PlateGeometry
item.
- getNew(DbControl, PlateGeometry, int, PlateGeometry, int) - Static method in class net.sf.basedb.core.PlateMapping
-
Create a new PlateMapping
item.
- getNew(DbControl, PlateGeometry) - Static method in class net.sf.basedb.core.PlateType
-
Create a new PlateType
item.
- getNew(DbControl, String, int) - Static method in class net.sf.basedb.core.Platform
-
Create a new file-only platform.
- getNew(DbControl, String, RawDataType) - Static method in class net.sf.basedb.core.Platform
-
Create a new platform which may optionally import data into the database.
- getNew(DbControl, Platform, PlatformVariant, DataFileType) - Static method in class net.sf.basedb.core.PlatformFileType
-
Create a new item linking a file type to a platform/variant.
- getNew(DbControl, Platform, String) - Static method in class net.sf.basedb.core.PlatformVariant
-
Create a new variant of a platform.
- getNew(DbControl, Platform, String, int) - Static method in class net.sf.basedb.core.PlatformVariant
-
Create a new file-only variant of a platform.
- getNew(DbControl, Platform, String, RawDataType) - Static method in class net.sf.basedb.core.PlatformVariant
-
Create a new platform variant which may optionally import data
into the database.
- getNew(DbControl, PluginDefinition) - Static method in class net.sf.basedb.core.PluginConfiguration
-
Create a new PluginConfiguration
item.
- getNew(DbControl, String, String, boolean) - Static method in class net.sf.basedb.core.PluginDefinition
-
Create a new PluginDefinition
item.
- getNew(DbControl, String, String) - Static method in class net.sf.basedb.core.PluginType
-
Create a new PluginType
item.
- getNew(DbControl) - Static method in class net.sf.basedb.core.Project
-
Create a new Project
item.
- getNew(DbControl) - Static method in class net.sf.basedb.core.Protocol
-
Create a new Protocol
item.
- getNew(DbControl, String) - Static method in class net.sf.basedb.core.Quantity
-
Create a new Quantity
item.
- getNew(DbControl, long) - Static method in class net.sf.basedb.core.Quota
-
Create a new Quota
item.
- getNew(DbControl, Platform, RawDataType) - Static method in class net.sf.basedb.core.RawBioAssay
-
Create a new raw bioassay for a specific platform and/or raw data type.
- getNew(DbControl, PlatformVariant, RawDataType) - Static method in class net.sf.basedb.core.RawBioAssay
-
Create a new raw bioassay for a specific platform variant.
- getNew(DbControl, RawBioAssay, FeatureIdentificationMethod) - Static method in class net.sf.basedb.core.RawDataBatcher
-
Create a new batcher for raw data.
- getNew(String) - Static method in class net.sf.basedb.core.Reporter
-
Get a new instance of a reporter, and setting the external ID.
- getNew(DbControl) - Static method in class net.sf.basedb.core.ReporterBatcher
-
Create a new batcher for reporters.
- getNew(DbControl) - Static method in class net.sf.basedb.core.ReporterCloneTemplate
-
Create a new reporter clone template item.
- getNew(DbControl) - Static method in class net.sf.basedb.core.ReporterList
-
Create a new ReporterList
item.
- getNew(DbControl) - Static method in class net.sf.basedb.core.ReporterType
-
Create a new ReporterType
item.
- getNew(DbControl) - Static method in class net.sf.basedb.core.Role
-
Create a new Role
item.
- getNew(DbControl) - Static method in class net.sf.basedb.core.Sample
-
Create a new Sample
item.
- getNew(DbControl, BioPlateEventParticipant) - Static method in class net.sf.basedb.core.Sample
-
Create a new Sample
item as part of a
master bioplate event.
- getNew(DbControl) - Static method in class net.sf.basedb.core.Software
-
Create a new Software
item.
- getNew(DbControl, RawBioAssay) - Static method in class net.sf.basedb.core.SpotImages
-
Create a new Image
item.
- getNew(DbControl) - Static method in class net.sf.basedb.core.Tag
-
Create a new Tag
item.
- getNew(DbControl, Experiment, Job) - Static method in class net.sf.basedb.core.Transformation
-
Create a new Transformation
item.
- getNew(DbControl, Quantity, String) - Static method in class net.sf.basedb.core.Unit
-
Create a new Unit
item.
- getNew(DbControl, String, String) - Static method in class net.sf.basedb.core.User
-
Create a new User
item.
- getNew(DbControl, User, Client, String, String) - Static method in class net.sf.basedb.core.UserClientSetting
-
Create a new UserClientSetting
item.
- getNew(DbControl, User, String, String) - Static method in class net.sf.basedb.core.UserDefaultSetting
-
Create a new UserDefaultSetting
item.
- getNew(DbControl) - Static method in class net.sf.basedb.core.VirtualDb
-
Create a new DynamicTables
item.
- getNewBioAssayEvent(DbControl, PhysicalBioAssay, BioPlateEventParticipant) - Static method in class net.sf.basedb.core.BioMaterialEvent
-
- getNewChildren() - Method in class net.sf.basedb.util.overview.Node
-
Get all new children to this node.
- getNewCreationEvent(DbControl, MeasuredBioMaterial, BioPlateEventParticipant) - Static method in class net.sf.basedb.core.BioMaterialEvent
-
- getNewFile(boolean) - Method in class net.sf.basedb.core.File
-
Get a new random file path.
- getNewImageRemapperIfNeeded(ServletContext) - Static method in class net.sf.basedb.clients.web.extensions.skin.ImageRemapperUtil
-
Get a new image remapper if it is needed, otherwise null.
- getNewInherited(DbControl, AnnotationSet, AnnotationData, boolean) - Static method in class net.sf.basedb.core.Annotation
-
Create a new inherited or cloned annotation.
- getNewOrCurrentOverview(DbControl, BasicItem, Project) - Static method in class net.sf.basedb.util.overview.OverviewUtil
-
Get the current overview or create a new overview.
- getNewOrExisting(DbControl, BasicItem, String, BasicItem, boolean) - Static method in class net.sf.basedb.core.AnyToAny
-
Get a new or existing AnyToAny
link.
- getNewOrExisting(DbControl, UserPermissions, GroupPermissions) - Static method in class net.sf.basedb.core.ItemKey
-
Create a new or load an existing ItemKey
when you
have a combination of user/group/permission values.
- getNewOrExisting(DbControl, ProjectPermissions) - Static method in class net.sf.basedb.core.ProjectKey
-
Create a new or load an existing ProjectKey
when you
have a combination of project/permission values.
- getNewOrExistingId(Session, Map<ProjectData, Integer>) - Static method in class net.sf.basedb.core.ProjectKey
-
Find the ID of an existing key with exactly the same
project/permission combination.
- getNewOrExistingKey(Session, Map<UserData, Integer>, Map<GroupData, Integer>) - Static method in class net.sf.basedb.core.ItemKey
-
Find the ID of an existing key with exactly the same
user/group/permission combination.
- getNewOverview(DbControl, BasicItem, Project) - Static method in class net.sf.basedb.util.overview.OverviewUtil
-
Create a new overview for the given item and project.
- getNewParameterVersion() - Method in class net.sf.basedb.core.PluginConfiguration
-
Increase the version number once per transaction.
- getNewPrimary(DbControl, AnnotationSet, AnnotationTypeData) - Static method in class net.sf.basedb.core.Annotation
-
Create a new primary annotation.
- getNewsDate() - Method in class net.sf.basedb.core.data.NewsData
-
Get the news date of this news item.
- getNewsDate() - Method in class net.sf.basedb.core.News
-
Get the date that is shown in listings.
- getNewsFeed(String, boolean) - Method in class net.sf.basedb.clients.web.servlet.RssNewsFeed
-
Generate the XML string for the news feed.
- getNewStream() - Method in class net.sf.basedb.util.StreamCacher
-
Get a new stream that appears to be reading from the start of the
master stream.
- getNewSystemMessage(DbControl, User, String, User, Job) - Static method in class net.sf.basedb.core.Message
-
Create a new Message
from the system.
- getNewValue() - Method in class net.sf.basedb.core.ChangeHistory
-
Get the new value of the property had immediately after this change.
- getNewValue() - Method in class net.sf.basedb.core.data.ChangeHistoryDetailData
-
Get the new value after the change.
- getNewValue() - Method in class net.sf.basedb.core.log.ManualLogEntry
-
New value after the change.
- getNewValues() - Method in class net.sf.basedb.core.AnnotationBatcher.CurrentAnnotationInfo
-
Get the new annotation values.
- getNextColumnId() - Method in class net.sf.basedb.clients.web.taglib.table.ExtensionCells
-
This is called by the Cell taglib when the next extension column
is about to be processed.
- getNextColumnNo() - Method in class net.sf.basedb.core.DataCube
-
Generate the next available column number.
- getNextCommand() - Method in class net.sf.basedb.core.PluginResponse
-
- getNextCubeNo() - Method in class net.sf.basedb.core.VirtualDb
-
Generate the next available cube number.
- getNextEntry(TarInputStream) - Static method in class net.sf.basedb.util.zip.TarUtil
-
Get the next entry from a TAR input stream.
- getNextExtraValueNo() - Method in class net.sf.basedb.core.DataCube
-
Generate the next available extra value number.
- getNextFilename(T, String) - Method in interface net.sf.basedb.util.bfs.FilenameGenerator
-
Get the next file name.
- getNextFilename(Object, String) - Method in class net.sf.basedb.util.bfs.SequenceFilenameGenerator
-
- getNextFilename(Object, String) - Method in class net.sf.basedb.util.bfs.SuggestedFilenameGenerator
-
- getNextFileNumber() - Method in class net.sf.basedb.util.bfs.SequenceFilenameGenerator
-
Get the next file number.
- getNextFilterNo() - Method in class net.sf.basedb.core.DataCube
-
Generate the next available filter number.
- getNextLayerNo() - Method in class net.sf.basedb.core.DataCube
-
Generate the next available layer number.
- getNextLine() - Method in class net.sf.basedb.util.gtf.GtfInputStream
-
Read the next line from the GTF file and split on tab character.
- getNextRequest() - Method in class net.sf.basedb.core.PluginResponse
-
- getNextRowClass() - Method in class net.sf.basedb.clients.web.taglib.table.Table
-
- getNode() - Method in class net.sf.basedb.core.data.JobData
-
The name of the node where the job is executing.
- getNode() - Method in class net.sf.basedb.core.Job
-
Get the name of the node where the job is executing.
- getNode(K) - Method in class net.sf.basedb.util.overview.cache.NodeCache
-
- getNode() - Method in class net.sf.basedb.util.overview.Failure
-
Get the node that failed validation.
- getNode(String) - Method in class net.sf.basedb.util.overview.GenericOverview
-
Get the node with the given ID.
- getNode() - Method in class net.sf.basedb.util.Tree.Entry
-
Get the node element object.
- getNodeCache() - Method in class net.sf.basedb.util.overview.GenericOverview
-
This overview implementation doesn't currently support node caching.
- getNodeCache() - Method in interface net.sf.basedb.util.overview.OverviewContext
-
Get the current node cache.
- getNodeFactory(DbControl, OverviewContext) - Method in class net.sf.basedb.util.overview.loader.BasicItemNodeLoader
-
Get a node factory that can be used to create item nodes.
- getNodeFactory(DbControl, OverviewContext, NodeValidator<? super I>, NodeNameGenerator<? super I>) - Method in class net.sf.basedb.util.overview.loader.BasicItemNodeLoader
-
Get a node factory that can be used to create item nodes using
a non-default name generator and validator.
- getNodeLoader(OverviewContext, Object) - Method in class net.sf.basedb.util.overview.loader.BasicItemNodeLoader
-
Get a node loader for a specific item type using the current context's
node loader factory.
- getNodeLoaderFactory() - Method in class net.sf.basedb.util.overview.GenericOverview
-
Get the current node loader factory.
- getNodeLoaderFactory(OverviewContext) - Method in class net.sf.basedb.util.overview.loader.BasicItemNodeLoader
-
Get the node loader factory used by the current context.
- getNodeLoaderFactory() - Method in interface net.sf.basedb.util.overview.OverviewContext
-
Get the node loader factory that is used to create node loaders.
- getNodeName(Annotation, Node) - Method in class net.sf.basedb.util.overview.node.AnnotationNameGenerator
-
- getNodeName(AnyToAny, Node) - Method in class net.sf.basedb.util.overview.node.AnyToAnyNameGenerator
-
- getNodeName(MeasuredBioMaterial, Node) - Method in class net.sf.basedb.util.overview.node.BioWellNameGenerator
-
- getNodeName(FileSetMember, Node) - Method in class net.sf.basedb.util.overview.node.FileSetMemberNameGenerator
-
- getNodeName(Listable, Node) - Method in class net.sf.basedb.util.overview.node.ItemListMemberNameGenerator
-
- getNodeName(I, Node) - Method in class net.sf.basedb.util.overview.node.NameableNameGenerator
-
- getNodeName(I, Node) - Method in interface net.sf.basedb.util.overview.node.NodeNameGenerator
-
Generate a name for the new node that is about to be
created.
- getNodeNameGenerator() - Method in class net.sf.basedb.util.overview.loader.BasicItemNodeLoader
-
Get the name generator that is used by this loader.
- getNodeTitle(Annotation, Node) - Method in class net.sf.basedb.util.overview.node.AnnotationNameGenerator
-
- getNodeTitle(AnyToAny, Node) - Method in class net.sf.basedb.util.overview.node.AnyToAnyNameGenerator
-
- getNodeTitle(BioPlate, Node) - Method in class net.sf.basedb.util.overview.node.BioPlateNameGenerator
-
The base of the title is generated by the superclass.
- getNodeTitle(MeasuredBioMaterial, Node) - Method in class net.sf.basedb.util.overview.node.BioWellNameGenerator
-
- getNodeTitle(Extract, Node) - Method in class net.sf.basedb.util.overview.node.ExtractNameGenerator
-
The base of the title is generated by the superclass.
- getNodeTitle(FileSetMember, Node) - Method in class net.sf.basedb.util.overview.node.FileSetMemberNameGenerator
-
- getNodeTitle(Listable, Node) - Method in class net.sf.basedb.util.overview.node.ItemListMemberNameGenerator
-
- getNodeTitle(I, Node) - Method in class net.sf.basedb.util.overview.node.NameableNameGenerator
-
- getNodeTitle(I, Node) - Method in interface net.sf.basedb.util.overview.node.NodeNameGenerator
-
Generate a title for the new node that is about to be
created.
- getNodeType() - Method in class net.sf.basedb.util.overview.Node
-
Get the node type of this node.
- getNodeValidator(OverviewContext) - Method in class net.sf.basedb.util.overview.loader.BasicItemNodeLoader
-
Get the default node validator for nodes of this type.
- getNodeValidator() - Method in class net.sf.basedb.util.overview.node.NodeFactory
-
Get the node validator that is used by this factory.
- getNodeValidatorFactory() - Method in class net.sf.basedb.util.overview.GenericOverview
-
Get the current node validator factory.
- getNodeValidatorFactory(OverviewContext) - Method in class net.sf.basedb.util.overview.loader.BasicItemNodeLoader
-
Get the node validator factory used by the current context.
- getNodeValidatorFactory() - Method in interface net.sf.basedb.util.overview.OverviewContext
-
Get the node validator factory that is used to create node validators.
- getNoDuplicates() - Method in class net.sf.basedb.util.annotations.InheritSpecification
-
- getNoSkin() - Method in class net.sf.basedb.clients.web.taglib.Page
-
- getNotNull() - Method in class net.sf.basedb.core.ParameterType
-
Check if the parameter can be null.
- getNulltext() - Method in class net.sf.basedb.clients.web.taglib.PropertyValue
-
- getNullValue() - Method in class net.sf.basedb.util.export.TableWriter
-
The null value string is written to the output instead of
null data values.
- getNumAcceptedWithNullReporterOnFeature() - Method in class net.sf.basedb.core.RawDataBatcher
-
Get the number of accepted inserts because of features with
a NULL reporter.
- getNumAnnotations() - Method in class net.sf.basedb.plugins.AnnotationFlatFileImporter.NewAnnotations
-
The total numer of annotation values that has been added to this
cache.
- getNumArrays() - Method in class net.sf.basedb.core.ArrayDesign
-
Get the number of arrays on a single slide.
- getNumArrays() - Method in class net.sf.basedb.core.data.ArrayDesignData
-
The number of arrays on a single slide.
- getNumberFormat() - Method in class net.sf.basedb.plugins.AbstractFlatFileImporter
-
Get a number formatter that is able to parse numbers with the
specified decimal separator.
- getNumberFormat(char, char) - Static method in class net.sf.basedb.util.NumberFormatUtil
-
- getNumberFormatter(SessionControl) - Static method in class net.sf.basedb.clients.web.formatter.FormatterFactory
-
Get the logged in user's number formatter for float values.
- getNumberOfParameters() - Method in class net.sf.basedb.util.jep.ChannelFunction
-
- getNumberOfParameters() - Method in class net.sf.basedb.util.jep.ExtraValueFunction
-
- getNumberOfParameters() - Method in class net.sf.basedb.util.jep.FunctionSafeJep.UnknownFunction
-
- getNumberOfParameters() - Method in class net.sf.basedb.util.jep.InReporterListFunction
-
- getNumberOfParameters() - Method in class net.sf.basedb.util.jep.LeftFunction
-
- getNumberOfParameters() - Method in class net.sf.basedb.util.jep.Log2Function
-
- getNumberOfParameters() - Method in class net.sf.basedb.util.jep.MeanFunction
-
- getNumberOfParameters() - Method in class net.sf.basedb.util.jep.NotInReporterListFunction
-
- getNumberOfParameters() - Method in class net.sf.basedb.util.jep.PositionFunction
-
- getNumberOfParameters() - Method in class net.sf.basedb.util.jep.RawChannelFunction
-
- getNumberOfParameters() - Method in class net.sf.basedb.util.jep.RawFunction
-
- getNumberOfParameters() - Method in class net.sf.basedb.util.jep.ReporterFunction
-
- getNumberOfParameters() - Method in class net.sf.basedb.util.jep.ScoreFunction
-
- getNumberOfParameters() - Method in class net.sf.basedb.util.jep.SimpleJepFunction
-
- getNumberOfParameters() - Method in class net.sf.basedb.util.parser.ColFunction
-
- getNumberOfParameters() - Method in class net.sf.basedb.util.parser.DataNoFunction
-
- getNumberOfParameters() - Method in class net.sf.basedb.util.parser.DefaultItemFunction
-
- getNumberOfParameters() - Method in class net.sf.basedb.util.parser.LineNoFunction
-
- getNumBioAssays() - Method in class net.sf.basedb.clients.web.ExperimentExplorer
-
Get the number of bioassays in the bioassayset.
- getNumBytes(FlatFileParser) - Method in class net.sf.basedb.plugins.AbstractFlatFileImporter
-
Get the number of bytes read from the file.
- getNumBytes(FlatFileParser) - Method in class net.sf.basedb.plugins.gtf.GtfReporterImporter
-
Get the number of bytes read from the original file.
- getNumBytes(FlatFileParser) - Method in class net.sf.basedb.plugins.gtf.GtfReporterMapImporter
-
Get the number of bytes read from the original file.
- getNumChildren() - Method in class net.sf.basedb.util.Tree.Entry
-
Get the number of children added to this node.
- getNumColumns() - Method in class net.sf.basedb.core.data.DataCubeData
-
The number of columns in this data cube.
- getNumColumns() - Method in class net.sf.basedb.core.DataCube
-
Get the number of columns created in this data cube.
- getNumDbFeatures() - Method in class net.sf.basedb.core.ArrayDesign
-
Get the number of features on this array design that are
stored in the database.
- getNumDbFeatures() - Method in class net.sf.basedb.core.data.ArrayDesignData
-
The number of features on this array design that are stored in
the database.
- getNumDbSpots() - Method in class net.sf.basedb.core.RawBioAssay
-
Get the number of spots on this raw bioassay that are
stored in the database.
- getNumDecimals(SessionControl) - Static method in class net.sf.basedb.clients.web.formatter.FormatterSettings
-
Get the number of decimals a number formatter should display.
- getNumDeleted() - Method in class net.sf.basedb.util.extensions.manager.ExtensionsManager
-
- getNumDeleted() - Method in class net.sf.basedb.util.extensions.manager.processor.DeleteResourcesProcessor
-
Get the total number of resources that was deleted.
- getNumError() - Method in class net.sf.basedb.clients.web.extensions.LoadServletsProcessor
-
Get the number of files that was had an error.
- getNumError() - Method in class net.sf.basedb.plugins.AnnotationFlatFileImporter.NewAnnotations
-
- getNumError() - Method in class net.sf.basedb.util.extensions.manager.processor.DeleteResourcesProcessor
-
Get the number of files that was had an error.
- getNumError() - Method in class net.sf.basedb.util.extensions.manager.processor.DisablePluginsProcessor
-
Get the number of files that was had an error.
- getNumError() - Method in class net.sf.basedb.util.extensions.manager.processor.ExtractResourcesProcessor
-
Get the number of files that was had an error.
- getNumError() - Method in class net.sf.basedb.util.extensions.manager.processor.PluginInstallationProcessor
-
Get the number of files that was had an error.
- getNumError() - Method in class net.sf.basedb.util.extensions.manager.processor.RegisterExtensionsProcessor
-
Get the number of files that was had an error.
- getNumError() - Method in class net.sf.basedb.util.extensions.manager.processor.UnregisterExtensionsProcessor
-
Get the number of files that was had an error.
- getNumErrorFiles() - Method in class net.sf.basedb.util.extensions.manager.ProcessResults
-
The number of extension files that could not be completely loaded
because of an error.
- getNumErrors() - Method in class net.sf.basedb.util.overview.Node
-
Get the number of errors on this node.
- getNumExtensions() - Method in class net.sf.basedb.util.extensions.ExtensionsInvoker
-
Get the number of enabled extensions in this invokation.
- getNumExtracted() - Method in class net.sf.basedb.util.extensions.manager.processor.ExtractResourcesProcessor
-
Get the total number of resources that was extracts.
- getNumExtraValues() - Method in class net.sf.basedb.core.data.DataCubeData
-
The number of extra values in this data cube.
- getNumExtraValues() - Method in class net.sf.basedb.core.DataCube
-
Get the number of extra values created for this data cube.
- getNumFileFeatures() - Method in class net.sf.basedb.core.ArrayDesign
-
Get the number of features on this array design that are
stored inside files.
- getNumFileFeatures() - Method in class net.sf.basedb.core.data.ArrayDesignData
-
The number of features on this array design that are stored inside
files.
- getNumFileReporters() - Method in class net.sf.basedb.core.BioAssaySet
-
Get the number of unique reporters for data that is stored in files.
- getNumFileReporters() - Method in class net.sf.basedb.core.data.BioAssaySetData
-
The number of unique reporters as stored in files in this bioassayset.
- getNumFiles() - Method in class net.sf.basedb.clients.web.extensions.LoadServletsProcessor
-
Get the number of files that was successfully processed.
- getNumFiles() - Method in class net.sf.basedb.clients.web.extensions.UninstalledFileProcessor
-
Get the number of files that was processed.
- getNumFiles() - Method in class net.sf.basedb.util.extensions.manager.processor.DeleteResourcesProcessor
-
Get the number of files that was successfully processed.
- getNumFiles() - Method in class net.sf.basedb.util.extensions.manager.processor.DisablePluginsProcessor
-
Get the number of files that was successfully processed.
- getNumFiles() - Method in class net.sf.basedb.util.extensions.manager.processor.ExtractResourcesProcessor
-
Get the number of files that was successfully processed.
- getNumFiles() - Method in class net.sf.basedb.util.extensions.manager.processor.IgnoreFileProcessor
-
Get the number of files that was processed.
- getNumFiles() - Method in class net.sf.basedb.util.extensions.manager.processor.MarkAsProcessedProcessor
-
Get the number of files that was processed.
- getNumFiles() - Method in class net.sf.basedb.util.extensions.manager.processor.PluginInstallationProcessor
-
Get the number of files that was successfully processed.
- getNumFiles() - Method in class net.sf.basedb.util.extensions.manager.processor.RegisterExtensionsProcessor
-
Get the number of files that was successfully processed.
- getNumFiles() - Method in class net.sf.basedb.util.extensions.manager.processor.ResetErrorFlagProcessor
-
Deprecated.
Get the number of files that was processed.
- getNumFiles() - Method in class net.sf.basedb.util.extensions.manager.processor.ResetProcessor
-
Get the number of files that was processed.
- getNumFiles() - Method in class net.sf.basedb.util.extensions.manager.processor.UnregisterExtensionsProcessor
-
Get the number of files that was successfully processed.
- getNumFileSpots() - Method in class net.sf.basedb.core.BioAssay
-
Get the number of spots that are stored in files.
- getNumFileSpots() - Method in class net.sf.basedb.core.BioAssaySet
-
Get the number of spots that are stored in files.
- getNumFileSpots() - Method in class net.sf.basedb.core.data.BioAssayData
-
The number of unique spots in this bioassayset.
- getNumFileSpots() - Method in class net.sf.basedb.core.data.BioAssaySetData
-
The number of unique spots in this bioassayset.
- getNumFileSpots() - Method in class net.sf.basedb.core.data.RawBioAssayData
-
The number of spots on this raw bioassay that are stored inside
files.
- getNumFileSpots() - Method in class net.sf.basedb.core.RawBioAssay
-
Get the number of spots on this raw bioassay that are
stored inside files.
- getNumFileValues() - Method in class net.sf.basedb.core.data.ExtraValueData
-
The number of extra values that are stored in files.
- getNumFileValues() - Method in class net.sf.basedb.core.ExtraValue
-
Get the number of values that are stored in files.
- getNumFilteredColumns() - Method in class net.sf.basedb.clients.web.taglib.table.Table
-
- getNumFilters() - Method in class net.sf.basedb.core.data.DataCubeData
-
The number of filters in this data cube.
- getNumFilters() - Method in class net.sf.basedb.core.DataCube
-
Get the number of filters created for this data cube.
- getNumFormulas() - Method in class net.sf.basedb.core.Formula
-
Get the number of expression defined by this formula.
- getNumIgnored() - Method in class net.sf.basedb.util.extensions.manager.ExtensionsManager
-
- getNumLayers() - Method in class net.sf.basedb.core.data.DataCubeData
-
The number of layers in this data cube.
- getNumLayers() - Method in class net.sf.basedb.core.DataCube
-
Get the number of layers created in this data cube.
- getNumLines() - Method in class net.sf.basedb.util.gtf.GtfInputStream
-
Get the number of lines parsed so far.
- getNumMembers(DataFileType) - Method in class net.sf.basedb.core.FileSet
-
Get the number of members in the file set of the specified type.
- getNumModified() - Method in class net.sf.basedb.util.extensions.manager.ExtensionsManager
-
- getNumNew() - Method in class net.sf.basedb.util.extensions.manager.ExtensionsManager
-
- getNumPlates() - Method in class net.sf.basedb.core.ArrayDesign
-
The number of plates connected to this array design.
- getNumPlugins() - Method in class net.sf.basedb.util.extensions.manager.processor.DisablePluginsProcessor
-
Get the total number of plug-in installed or updated
by the processor.
- getNumPlugins() - Method in class net.sf.basedb.util.extensions.manager.processor.PluginInstallationProcessor
-
Get the total number of plug-in installed or updated
by the processor.
- getNumPositions(DbControl, int) - Method in class net.sf.basedb.clients.web.ExperimentExplorer
-
Get the number of unique positions the reporter of the specifed
index is present in among all the bioassays in the bioassay set.
- getNumPositions() - Method in class net.sf.basedb.core.data.DataCubeData
-
The number of positions in this data cube.
- getNumPositions() - Method in class net.sf.basedb.core.DataCube
-
Get the number of positions created in this data cube.
- getNumPropertyFilters() - Method in class net.sf.basedb.core.ItemContext
-
Get the total number of property filters stored in this
context.
- getNumPropertyFilters(int) - Method in class net.sf.basedb.core.ItemContext
-
Get the number of property filters stored in this
context for the given filter row.
- getNumRead() - Method in class net.sf.basedb.util.InputStreamSplitter
-
Get the number of bytes that has been read or skipped
from the input stream.
- getNumRead() - Method in class net.sf.basedb.util.InputStreamTracker
-
Get the number of bytes read or skipped from the input stream.
- getNumRecent(Item) - Method in class net.sf.basedb.core.ItemContext
-
Get the number of recently used items in the list.
- getNumRecent(Item, ItemSubtype) - Method in class net.sf.basedb.core.ItemContext
-
Get the number of recently used items in the list.
- getNumRecent(Item, String) - Method in class net.sf.basedb.core.ItemContext
-
Get the number of recently used items in a list with a sublist.
- getNumRecent(String) - Method in class net.sf.basedb.core.ItemContext
-
Get the number of recently used value in the list.
- getNumRegistered() - Method in class net.sf.basedb.util.extensions.manager.processor.RegisterExtensionsProcessor
-
Get the number of extensions + extension points that
was registered.
- getNumRemoved() - Method in class net.sf.basedb.plugins.AnnotationFlatFileImporter.NewAnnotations
-
- getNumReplaced() - Method in class net.sf.basedb.plugins.AnnotationFlatFileImporter.NewAnnotations
-
- getNumReporters() - Method in class net.sf.basedb.clients.web.ExperimentExplorer
-
Get the total number of unique reporters found in the bioassayset.
- getNumReporters() - Method in class net.sf.basedb.core.BioAssaySet
-
Get the number of unique reporters among all bioassays in this bioassayset.
- getNumReporters() - Method in class net.sf.basedb.core.data.BioAssaySetData
-
The number of unique reporters in this bioassayset.
- getNumReportersNotFound() - Method in class net.sf.basedb.core.RawDataBatcher
-
Get the number of reporters that was not found.
- getNumServlets() - Method in class net.sf.basedb.clients.web.extensions.LoadServletsProcessor
-
Get the total number of servlets found during the last processing.
- getNumSet() - Method in class net.sf.basedb.plugins.AnnotationFlatFileImporter.NewAnnotations
-
- getNumSkippedLines() - Method in class net.sf.basedb.util.parser.FlatFileParser
-
- getNumSkippedMissingFeature() - Method in class net.sf.basedb.core.RawDataBatcher
-
Get the number of skipped inserts because of a missing feature.
- getNumSpots() - Method in class net.sf.basedb.clients.web.ExperimentExplorer
-
Get the total number of spots in the bioassayset.
- getNumSpots() - Method in class net.sf.basedb.core.BioAssay
-
Get the number of spots in this bioassay.
- getNumSpots() - Method in class net.sf.basedb.core.BioAssaySet
-
Get the number of spots in all bioassays in this bioassayset.
- getNumSpots() - Method in class net.sf.basedb.core.data.BioAssayData
-
The number of unique spots in this bioassay.
- getNumSpots() - Method in class net.sf.basedb.core.data.BioAssaySetData
-
The number of unique spots in this bioassayset.
- getNumStatements() - Method in class net.sf.basedb.core.hibernate.SchemaGenerator.CollectSqlTarget
-
- getNumUniqueTranscriptIds() - Method in class net.sf.basedb.util.gtf.GtfInputStream
-
Get the number of unique transcript ids found so far.
- getNumUnmodified() - Method in class net.sf.basedb.util.extensions.manager.ExtensionsManager
-
- getNumUnregistered() - Method in class net.sf.basedb.util.extensions.manager.processor.RegisterExtensionsProcessor
-
Get the number of extensions + extension points that
was unregistered.
- getNumUnregistered() - Method in class net.sf.basedb.util.extensions.manager.processor.UnregisterExtensionsProcessor
-
Get the number of extensions + extension points that
was unregistered.
- getNumValues() - Method in class net.sf.basedb.core.data.ExtraValueData
-
The number of extra values that have been inserted.
- getNumValues() - Method in class net.sf.basedb.core.ExtraValue
-
Get the number of extra values inserted.
- getNumValues(String) - Method in class net.sf.basedb.util.QueryParameters
-
Get the number of values for a key.
- getNumWarnings() - Method in class net.sf.basedb.util.overview.Node
-
Get the number of warnings on this node.
- getObject(int) - Method in class net.sf.basedb.clients.web.servlet.PlotServlet.CFSqlResult
-
- getObject(int) - Method in class net.sf.basedb.core.DynamicResultIterator.SqlResultImpl
-
- getObject(String) - Method in class net.sf.basedb.core.ItemContext
-
Get an object.
- getObject(int) - Method in interface net.sf.basedb.core.query.SqlResult
-
Get the value of the specified column as an object.
- getObjectForKey(ObjectKey<O>) - Method in class net.sf.basedb.clients.web.extensions.ExtensionsControl
-
Get the object that was registered for the given key.
- getObjectForKey(ObjectKey<O>) - Method in class net.sf.basedb.util.extensions.manager.ExtensionsFile
-
Get the object that was registered for the given key.
- getObjectsOfClass(Class<T>) - Method in class net.sf.basedb.util.extensions.manager.ExtensionsFile
-
Get a list of all objects defined in this extensions
file that are of the specified class or interface.
- getOldItem(SessionControl, T, int) - Static method in class net.sf.basedb.clients.web.Base
-
Get the old item that is stored in the SessionControl
:s
session setting itemType.item
.
- getOldValue() - Method in class net.sf.basedb.core.ChangeHistory
-
Get the old value of the property had before this change.
- getOldValue() - Method in class net.sf.basedb.core.data.ChangeHistoryDetailData
-
Get the previous value before the change.
- getOldValue() - Method in class net.sf.basedb.core.log.ManualLogEntry
-
Old value before the change.
- getOldValues() - Method in class net.sf.basedb.core.AnnotationBatcher.CurrentAnnotationInfo
-
Get the old annotation values.
- getOldValues() - Method in class net.sf.basedb.core.data.ParameterValueData
-
Get the old values that has been replaced by new values in this session.
- getOpen() - Method in class net.sf.basedb.clients.web.taglib.menu.Menu
-
- getOperator() - Method in class net.sf.basedb.core.data.PropertyFilterData
-
Get the operator used for this filter.
- getOperator() - Method in class net.sf.basedb.core.PropertyFilter
-
Get the operator to use in the filter.
- getOperators() - Static method in class net.sf.basedb.util.jep.Jep
-
- getOptimizeTableSql(String, String, String) - Method in interface net.sf.basedb.core.dbengine.DbEngine
-
Generate SQL to optimize a table.
- getOptimizeTableSql(String, String, String) - Method in class net.sf.basedb.core.dbengine.DefaultDbEngine
-
Return null.
- getOptimizeTableSql(String, String, String) - Method in class net.sf.basedb.core.dbengine.MySQLEngine
-
Generate optimize table <catalog>.
- getOptimizeTableSql(String, String, String) - Method in class net.sf.basedb.core.dbengine.PostgresDbEngine
-
Generate VACUUM FULL <schema>.
- getOption(String) - Method in class net.sf.basedb.clients.jobagent.CmdLine
-
Get the value for the specified option
- getOption(String, String) - Method in class net.sf.basedb.clients.jobagent.CmdLine
-
Get the value for an option.
- getOption(String) - Method in class net.sf.basedb.core.AnnotationType
-
Get an option.
- getOption(String) - Method in class net.sf.basedb.plugins.executor.ParameterDefinition
-
Get the value for an option.
- getOption(Validator, String, String) - Method in class net.sf.basedb.util.overview.ValidationOptions
-
- getOption(ValidationRuleAction, String, String) - Method in class net.sf.basedb.util.overview.ValidationOptions
-
Get the configured option for a validator rule.
- getOptionalFilter(Item) - Static method in class net.sf.basedb.core.QueryRuntimeFilterFactory
-
Get the default optional runtime filter for the speicified item type.
- getOptions() - Method in class net.sf.basedb.core.data.AnnotationTypeData
-
Additional options depending on the value type.
- getOptions() - Method in class net.sf.basedb.plugins.Base1PluginExecuter.JobParameter
-
- getOptions() - Method in class net.sf.basedb.plugins.executor.ParameterDefinition
-
Get the names of other options that are defined for this parmeter.
- getOrdinal() - Method in class net.sf.basedb.core.data.PlateEventTypeData
-
The ordinal of this event type among all event types defined for the plate type.
- getOrdinal() - Method in class net.sf.basedb.core.PlateEventType
-
Get the order of this event among the list of events.
- getOrganisation() - Method in class net.sf.basedb.core.authentication.ExtraUserInformation
-
The organisation of the user.
- getOrganisation() - Method in class net.sf.basedb.core.data.UserData
-
Get the organisation this user works for, or null if unknown.
- getOrganisation() - Method in class net.sf.basedb.core.User
-
Get the organisation this user works for, or null if unknown.
- getOriginalBioMaterial() - Method in class net.sf.basedb.core.BioWell
-
Get the original biomaterial that was placed in this biowell.
- getOriginalBioMaterial() - Method in class net.sf.basedb.core.data.BioWellData
-
- getOriginalPermissions(Group) - Method in class net.sf.basedb.core.GroupPermissions
-
- getOriginalPermissions() - Method in class net.sf.basedb.core.GroupPermissions
-
Get the internal representation of the original permissions.
- getOriginalPermissions(Project) - Method in class net.sf.basedb.core.ProjectPermissions
-
- getOriginalPermissions() - Method in class net.sf.basedb.core.ProjectPermissions
-
Get the internal representation of the original permissions.
- getOriginalPermissions(User) - Method in class net.sf.basedb.core.UserPermissions
-
- getOriginalPermissions() - Method in class net.sf.basedb.core.UserPermissions
-
Get the internal representation of the original permissions.
- getOriginalQuantity() - Method in class net.sf.basedb.core.data.MeasuredBioMaterialData
-
Get the original quantity of the biomaterial.
- getOriginalQuantity() - Method in class net.sf.basedb.core.MeasuredBioMaterial
-
Get the original quantity of the biomaterial.
- getOriginX() - Method in class net.sf.basedb.core.ArrayDesignBlock
-
Get the distance from the left edge of the slide to the top left spot in the block.
- getOriginX() - Method in class net.sf.basedb.core.data.ArrayDesignBlockData
-
Get the distance from the left edge of the slide to the top left spot in the block.
- getOriginX() - Method in class net.sf.basedb.plugins.PrintMapFlatFileImporter.MetaBlock
-
- getOriginY() - Method in class net.sf.basedb.core.ArrayDesignBlock
-
Get the distance from the top edge of the slide to the top left spot in the block.
- getOriginY() - Method in class net.sf.basedb.core.data.ArrayDesignBlockData
-
Get the distance from the top edge of the slide to the top left spot in the block.
- getOriginY() - Method in class net.sf.basedb.plugins.PrintMapFlatFileImporter.MetaBlock
-
- getOut() - Method in class net.sf.basedb.clients.web.extensions.JspContext
-
Get a writer object that can be used to return generated text
to the response that is sent back to the browser.
- getOutputStream(File) - Method in class net.sf.basedb.core.Migration
-
Get a stream for writing to the given file.
- getOutputStream(String) - Method in class net.sf.basedb.util.bfs.AbstractDataWriterFactory
-
Create an output stream for writing to a file with the given
filename.
- getOutputStream(String) - Method in class net.sf.basedb.util.bfs.GenericBaseDataWriterFactory
-
Create a new file in the data directory with the given file
name.
- getOutputStream(String) - Method in class net.sf.basedb.util.bfs.GenericDiskDataWriterFactory
-
Create a new file in the data directory with the given file
name.
- getOutputStream(File) - Static method in class net.sf.basedb.util.FileUtil
-
Get a buffered OutputStream
object writing to
the specified file.
- getOutputStream(String, int) - Method in class net.sf.basedb.util.StaticCache
-
Get a lock-safe output stream.
- getOverrideId() - Method in class net.sf.basedb.core.data.AnnotationData
-
The ID of the default annotation that this project-specific
annotation is overriding. 0 for default annotations.
- getOverrideId() - Method in class net.sf.basedb.core.data.annotations.AnnotationLink
-
- getOverrideId() - Method in class net.sf.basedb.core.snapshot.AnnotationSnapshot
-
Get the id of the default annotation that this project-specific
annotation is overriding.
- getOverwrite() - Method in class net.sf.basedb.core.plugin.AbstractExporterPlugin
-
Get the configured value for the overwrite parameter.
- getOverwrite() - Method in class net.sf.basedb.util.zip.AbstractFileUnpacker
-
If existing file should be overwritten or not.
- getOverwriteAnnotationsParameters(String, String, Boolean) - Method in class net.sf.basedb.core.plugin.AbstractPlugin
-
Parameter definition that asks if copied annotations should overwrite existing
annotations or not.
- getOverwriteParameter(String, String) - Method in class net.sf.basedb.core.plugin.AbstractExporterPlugin
-
Get a plugin parameter that asks if existing files can be overwritten
or not.
- getOverwriteParameter(String, String) - Method in class net.sf.basedb.util.zip.AbstractFileUnpacker
-
Get a plugin parameter that asks if existing files should be overwritten
or not.
- getOwnableItems() - Static method in class net.sf.basedb.core.Metadata
-
Get a set containing all
Ownable
item types.
- getOwner() - Method in interface net.sf.basedb.core.data.OwnableData
-
Get the
UserData
that is the owner of the item.
- getOwner() - Method in class net.sf.basedb.core.data.OwnedData
-
- getOwner() - Method in interface net.sf.basedb.core.Ownable
-
Get the
User
that is the owner of the item.
- getOwner() - Method in class net.sf.basedb.core.OwnedItem
-
- getPacker() - Method in class net.sf.basedb.plugins.PackedFileExporter
-
Get the FilePacker that has been configured in the current configuration.
- getPacker(String) - Method in class net.sf.basedb.plugins.PackedFileExporter
-
Create a FilePacker from the given class.
- getPage() - Method in class net.sf.basedb.clients.web.taglib.table.Navigator
-
- getPage() - Method in class net.sf.basedb.clients.web.taglib.table.Table
-
- getPage() - Method in class net.sf.basedb.core.data.ContextData
-
Get the current page number, starting at 0.
- getPage() - Method in class net.sf.basedb.core.ItemContext
-
Get the current table page.
- getPageContext() - Method in class net.sf.basedb.clients.web.extensions.JspContext
-
Get the JSP Page context object for the current request.
- getPageType() - Method in class net.sf.basedb.clients.web.ModeInfo
-
- getPageType() - Method in exception net.sf.basedb.clients.web.WebException
-
Get the page type to display the error message in.
- getParameter(String) - Method in class net.sf.basedb.clients.web.extensions.AbstractJspFactory
-
Get a generic parameter value.
- getParameter(String) - Method in class net.sf.basedb.clients.web.fileupload.FileUpload
-
Get the value for a form field.
- getParameter(String) - Method in class net.sf.basedb.core.RequestInformation
-
Get the plugin parameter with the specified name.
- getParameter(String) - Method in class net.sf.basedb.util.export.spotdata.BaseFileExporter
-
Get the current value of a 'settings' parameter.
- getParameter(String) - Method in class net.sf.basedb.util.export.spotdata.BfsExporter
-
Get the current value of a parameter.
- getParameterClass() - Method in class net.sf.basedb.core.ParameterType
-
Get the class a value must have to match this parameter type.
- getParameterDefinition() - Method in class net.sf.basedb.plugins.executor.ProgramParameter
-
Get the definition of this parameter.
- getParameterDefinitions(boolean) - Method in class net.sf.basedb.plugins.executor.ExternalProgramExecutor
-
Get the current program parameter definitions.
- getParameterInfo(String) - Method in class net.sf.basedb.core.Job
-
Get extra information about a parameter.
- getParameterInfo(String) - Method in class net.sf.basedb.core.PluginConfiguration
-
Get extra information about a parameter in the latest version.
- getParameterInfo(String, int) - Method in class net.sf.basedb.core.PluginConfiguration
-
Get extra information about a parameter in a specific version.
- getParameterName(String) - Method in class net.sf.basedb.util.extensions.debug.ProxyActionFactory
-
Convert a method name to a parameter name.
- getParameterNames() - Method in class net.sf.basedb.clients.web.fileupload.FileUpload
-
Get the names for all fields used in the form, excluding file input fields.
- getParameterNames() - Method in class net.sf.basedb.core.AbstractQuery
-
- getParameterNames() - Method in class net.sf.basedb.core.Job
-
Get the names of all parameters for the job.
- getParameterNames() - Method in class net.sf.basedb.core.PluginConfiguration
-
Get the names of all configuration values in the latest version.
- getParameterNames(int) - Method in class net.sf.basedb.core.PluginConfiguration
-
Get the names of all configuration values in a specific version.
- getParameterNames() - Method in interface net.sf.basedb.core.query.Query
-
Get a set with the names for all parameters in this
query.
- getParameters() - Method in class net.sf.basedb.core.AbstractQuery
-
Get all query parameters.
- getParameters() - Method in class net.sf.basedb.core.data.JobData
-
The parameters for this job.
- getParameters() - Method in class net.sf.basedb.core.data.ProtocolData
-
This set manages the parameters for this protcol.
- getParameters() - Method in class net.sf.basedb.core.Protocol
-
Get a query that returns all annotation types used as parameters
for this protocol.
- getParameters() - Method in class net.sf.basedb.core.RequestInformation
-
Get a list containing the information about the parameters
needed for the current request.
- getParametersFromBaseFile(File) - Method in class net.sf.basedb.plugins.Base1PluginExecuter
-
Get the data from the configuration file.
- getParameterType(String) - Method in class net.sf.basedb.core.AbstractQuery
-
Get the type of the parameter, or null if not known.
- getParameterType(Class<T>, List<?>) - Method in class net.sf.basedb.core.PluginConfiguration
-
Gets the ParameterType to use with a class.
- getParameterType() - Method in class net.sf.basedb.core.PluginParameter
-
Get the parameter type, which tells the client application the
data type and allowed values for the parameter.
- getParameterValue(String) - Method in class net.sf.basedb.core.AbstractQuery
-
Get the value of the named parameter.
- getParameterValue(String) - Method in class net.sf.basedb.core.Job
-
Get the value of a named parameter.
- getParameterValue(String) - Method in class net.sf.basedb.core.plugin.NamespaceRequestWrapper
-
- getParameterValue(String) - Method in interface net.sf.basedb.core.plugin.Request
-
Get the value for the parameter with the specified name.
- getParameterValue(String) - Method in class net.sf.basedb.core.PluginRequest.RequestImpl
-
- getParameterValue(String) - Method in class net.sf.basedb.plugins.executor.ExternalProgramExecutor.RequestWrapper
-
- getParameterValue(String, Class<?>) - Method in class net.sf.basedb.util.extensions.debug.ProxyActionFactory
-
Get the value of a parameter.
- getParameterValues(String) - Method in class net.sf.basedb.clients.web.fileupload.FileUpload
-
Get an array of values for a form field.
- getParameterValues() - Method in class net.sf.basedb.core.Job
-
- getParameterValues(String) - Method in class net.sf.basedb.core.Job
-
Get the values of a named parameter.
- getParameterValues(String) - Method in class net.sf.basedb.core.plugin.NamespaceRequestWrapper
-
- getParameterValues(String) - Method in interface net.sf.basedb.core.plugin.Request
-
Get the values for the parameter with the specified name.
- getParameterValues(String) - Method in class net.sf.basedb.core.PluginConfiguration
-
Get the values of a configuration parameter in the latest version.
- getParameterValues(String, int) - Method in class net.sf.basedb.core.PluginConfiguration
-
Get the values of a configuration parameter in a specific version.
- getParameterValues(int) - Method in class net.sf.basedb.core.PluginConfiguration
-
- getParameterValues(String) - Method in class net.sf.basedb.core.PluginRequest.RequestImpl
-
- getParameterValues(String) - Method in class net.sf.basedb.plugins.executor.ExternalProgramExecutor.RequestWrapper
-
- getParameterValuesImpl() - Method in class net.sf.basedb.core.Job
-
Get a write-protected ParameterValuesImpl object.
- getParameterValuesImpl(int) - Method in class net.sf.basedb.core.PluginConfiguration
-
Get a write-protected ParameterValuesImpl object so a job can read
the paremeters.
- getParameterVersion() - Method in class net.sf.basedb.core.data.JobData
-
Get the parameter version of the configuration used for this job.
- getParameterVersion() - Method in class net.sf.basedb.core.data.PluginConfigurationData
-
Get the current/latest parameter version.
- getParameterVersion() - Method in class net.sf.basedb.core.Job
-
Get the version number of the configuration parameters used for this job.
- getParameterVersion() - Method in class net.sf.basedb.core.PluginConfiguration
-
Get the latest version number of the parameters.
- getParent() - Method in class net.sf.basedb.clients.web.extensions.renderer.PrefixSuffixRenderer
-
- getParent() - Method in class net.sf.basedb.core.data.DirectoryData
-
Get the parent directory of this directory.
- getParent() - Method in class net.sf.basedb.core.data.MeasuredBioMaterialData
-
Get the parent biomaterial.
- getParent() - Method in class net.sf.basedb.core.data.WellData
-
If the plate was created from a
PlateMappingData
this property points to
the well on the source plate used in the mapping.
- getParent() - Method in class net.sf.basedb.core.DerivedBioAssay
-
- getParent() - Method in class net.sf.basedb.core.Directory
-
Get the parent directory of this directory.
- getParent() - Method in class net.sf.basedb.core.MeasuredBioMaterial
-
Get the parent biomaterial if there is a single parent item only.
- getParent() - Method in class net.sf.basedb.core.Path
-
Get the parent path.
- getParent() - Method in class net.sf.basedb.core.Well
-
Get the parent well.
- getParent() - Method in interface net.sf.basedb.util.extensions.WrappingRenderer
-
Get the current parent renderer.
- getParent() - Method in class net.sf.basedb.util.overview.Node
-
Get the parent of this node.
- getParent() - Method in class net.sf.basedb.util.Tree.Entry
-
Get the entry for the parent node.
- getParentBioAssay() - Method in class net.sf.basedb.core.data.RawBioAssayData
-
Get the derived bioassay that this raw bioassay has been created from.
- getParentBioAssay() - Method in class net.sf.basedb.core.RawBioAssay
-
- getParentExtract() - Method in class net.sf.basedb.core.data.RawBioAssayData
-
Get the derived bioassay that this raw bioassay has been created from.
- getParentExtract() - Method in class net.sf.basedb.core.RawBioAssay
-
Get the
Extract
this raw bioassay is created from.
- getParentFileSets() - Method in class net.sf.basedb.core.ArrayDesign
-
There are no parent file sets.
- getParentFileSets() - Method in class net.sf.basedb.core.BioAssaySet
-
Get the file set from the parent bioassay set if it exists.
- getParentFileSets() - Method in class net.sf.basedb.core.DerivedBioAssay
-
- getParentFileSets() - Method in class net.sf.basedb.core.ExtraValue
-
Get the file set from the parent bioassay set if it exists.
- getParentFileSets() - Method in interface net.sf.basedb.core.FileStoreEnabled
-
Get the file sets of parent item(s) that are related to the current item.
- getParentFileSets() - Method in class net.sf.basedb.core.RawBioAssay
-
Get the file set from the array design, if it exists.
- getParentHasNullReporter() - Method in class net.sf.basedb.util.importer.spotdata.BaseFileInfo
-
A flag that indicates if at least one position in the parent bioassay
set has a null reporter or not.
- getParentHasZeroReporter() - Method in class net.sf.basedb.util.importer.spotdata.BaseFileInfo
-
A flag that indicates if at least one position in the parent bioassay
set has a reporter with ID=0.
- getParentId() - Method in class net.sf.basedb.core.data.keyring.GroupGroups
-
Get the id of the parent group.
- getParentInformation(DbControl, Node) - Method in class net.sf.basedb.util.overview.validator.ProtocolParameterValidator
-
Load parent item information from the current protocol node.
- getParentPlates() - Method in class net.sf.basedb.core.Plate
-
Get a query returning the parent plates of this plate.
- getParentProperties(DbControl, BioAssay, Metadata.PropertyPath<RawBioAssay, ?>) - Static method in class net.sf.basedb.util.BioAssaySetUtil
-
Find the values of parent properties for a given bioassay.
- getParents() - Method in class net.sf.basedb.core.BioAssay
-
Get a query for loading the parents bioassays to this bioassay.
- getParents() - Method in class net.sf.basedb.core.data.BioAssayData
-
Get a set that manages the parent bioassays the data in this bioassay
is based on.
- getParents() - Method in class net.sf.basedb.core.data.DerivedBioAssayData
-
A set that manages the parent bioassays that this derived bioassay
related to.
- getParents() - Method in class net.sf.basedb.core.data.GroupData
-
This is the inverse end.
- getParents() - Method in class net.sf.basedb.core.data.ItemSubtypeData
-
This is the inverse end.
- getParents() - Method in class net.sf.basedb.core.data.PlateData
-
- getParents() - Method in class net.sf.basedb.core.DerivedBioAssay
-
Get all parent derived bioassays.
- getParents() - Method in class net.sf.basedb.util.importer.spotdata.BaseFileInfo.ChildBioAssay
-
Get the parent assays of this child.
- getParentSession() - Method in class net.sf.basedb.core.hibernate.SessionWrapper
-
Get the underlying parent session from Hibernate.
- getParentSession() - Method in class net.sf.basedb.core.hibernate.StatelessSessionWrapper
-
Get the underlying parent session from Hibernate.
- getParentSet() - Method in class net.sf.basedb.core.data.PlateData
-
- getParentSubtypes(DbControl, Subtypable, Item) - Static method in class net.sf.basedb.core.ItemSubtype
-
Utility method for locating all subtypes that have a relationship to the
subtype of the given item.
- getParentSubtypes() - Method in class net.sf.basedb.core.ItemSubtype
-
Get a query returning all subtypes that have a relation to this subtype.
- getParentType() - Method in class net.sf.basedb.core.BasicChildItem
-
Get the type of item that is the parent of this item.
- getParentType() - Method in class net.sf.basedb.core.data.MeasuredBioMaterialData
-
Get the type of the parent item.
- getParentType() - Method in class net.sf.basedb.core.ItemSubtypeFileType
-
- getParentType() - Method in class net.sf.basedb.core.MeasuredBioMaterial
-
Get the item type of the parent biomaterial.
- getParentType() - Method in class net.sf.basedb.core.PlatformFileType
-
- getParentType() - Method in class net.sf.basedb.core.PlatformVariant
-
- getParsedBytes() - Method in class net.sf.basedb.util.bfs.AnnotationParser
-
- getParsedBytes() - Method in interface net.sf.basedb.util.bfs.BfsParser
-
Get the number of parsed bytes so far.
- getParsedBytes() - Method in class net.sf.basedb.util.bfs.DataParser
-
- getParsedBytes() - Method in class net.sf.basedb.util.bfs.MetadataParser
-
- getParsedBytes() - Method in class net.sf.basedb.util.importer.spotdata.SynchronizedSpotDataParser
-
- getParsedBytes() - Method in class net.sf.basedb.util.parser.FlatFileParser
-
Get the number of parsed bytes so far.
- getParsedCharacters() - Method in class net.sf.basedb.util.parser.FlatFileParser
-
Get the number of parsed characters so far.
- getParsedDataLines() - Method in class net.sf.basedb.util.parser.FlatFileParser
-
Get the number of parsed data lines so far in the current section.
- getParsedLines() - Method in class net.sf.basedb.util.parser.FlatFileParser
-
Get the number of parsed lines so far.
- getParser() - Method in class net.sf.basedb.core.data.FormulaData
-
Which parser to use to convert the formula to an expression or restriction.
1 = JEP
- getParser() - Method in class net.sf.basedb.core.Formula
-
Get the parser that converts the formula to an expresion or restriction.
- getParser() - Method in class net.sf.basedb.util.importer.spotdata.SynchronizedSpotDataParser.SynchronizedData
-
The underlying parser.
- getParticipant(BioPlate) - Method in class net.sf.basedb.core.BioPlateEvent
-
Get the participant object representing the given bioplate in this
event.
- getParticipants() - Method in class net.sf.basedb.core.BioPlateEvent
-
Get a query returning all participants in the event.
- getParticipants() - Method in class net.sf.basedb.core.data.BioPlateEventData
-
This is the inverse end.
- getPassword() - Method in class net.sf.basedb.clients.jobagent.Agent
-
Get the agent.password
configuration value.
- getPassword() - Method in class net.sf.basedb.core.authentication.LoginRequest
-
Get the password to use.
- getPassword() - Method in class net.sf.basedb.core.data.FileServerData
-
Get the password that is used to login to the server.
- getPassword() - Method in class net.sf.basedb.core.data.UserData
-
Get the
PasswordData
object which allows you to change the
password for the user.
- getPassword() - Method in class net.sf.basedb.core.FileServer
-
Get the password that is used when authenticating with the file
server.
- getPassword() - Method in class net.sf.basedb.util.uri.ConnectionParameters
-
Get the password that should be used to authenticate the user.
- getPasswordField() - Method in interface net.sf.basedb.clients.web.extensions.login.LoginFormAction
-
Get attributes for the password field on the form.
- getPasswordField() - Method in class net.sf.basedb.clients.web.extensions.login.LoginFormBean
-
- getPath() - Method in class net.sf.basedb.core.Directory
-
Get the complete path to this directory.
- getPath() - Method in class net.sf.basedb.core.File
-
Get the complete path of this file.
- getPath() - Method in class net.sf.basedb.core.Metadata.BasicData2ItemPropertyPath
-
- getPath() - Method in class net.sf.basedb.core.Metadata.BasicItem2DataPropertyPath
-
- getPath() - Method in class net.sf.basedb.core.Metadata.CollectionPropertyPath
-
- getPath() - Method in class net.sf.basedb.core.Metadata.CombinedPropertyPath
-
- getPath() - Method in class net.sf.basedb.core.Metadata.ComponentPropertyPath
-
- getPath() - Method in class net.sf.basedb.core.Metadata.DateCopyPropertyPath
-
- getPath() - Method in class net.sf.basedb.core.Metadata.EntityPropertyPath
-
- getPath() - Method in class net.sf.basedb.core.Metadata.EvictPropertyPath
-
- getPath() - Method in class net.sf.basedb.core.Metadata.IdentifierPropertyPath
-
- getPath() - Method in class net.sf.basedb.core.Metadata.MapPropertyPath
-
- getPath() - Method in class net.sf.basedb.core.Metadata.NoopPropertyPath
-
- getPath() - Method in interface net.sf.basedb.core.Metadata.PropertyPath
-
Get the path that this object represents.
- getPath() - Method in class net.sf.basedb.core.Metadata.ReporterScore2DataPropertyPath
-
- getPathInfo() - Method in class net.sf.basedb.clients.web.extensions.RequestWrapper
-
From the HttpServletRequestInterface
------------------------------------
- getPathType() - Method in class net.sf.basedb.core.PathParameterType
-
Get the type of the path to ask for.
- getPattern(String) - Method in class net.sf.basedb.plugins.AbstractFlatFileImporter
-
- getPattern(ParameterValues, String) - Method in class net.sf.basedb.plugins.AnnotationFlatFileImporter
-
- getPattern(ParameterValues, String) - Method in class net.sf.basedb.plugins.batchimport.AbstractItemImporter
-
- getPattern(String, int, int) - Method in class net.sf.basedb.util.export.spotdata.AdvancedFieldConverter
-
- getPercent() - Method in class net.sf.basedb.core.SimpleProgressReporter
-
Get the last percentage completed of the task.
- getPercentComplete() - Method in class net.sf.basedb.core.data.JobData
-
If the job is running, how many percent has been completed.
- getPercentComplete() - Method in class net.sf.basedb.core.Job
-
An estimate of the percentage of the work currently completed by
an executing job.
- getPercentile(List<? extends Number>, int) - Method in class net.sf.basedb.clients.web.servlet.ExperimentExplorerPlotServlet
-
Calculates the percentile values from a sorted list of values.
- getPermanentSelects() - Method in class net.sf.basedb.core.AbstractQuery
-
Get all permanent selects.
- getPermission() - Method in class net.sf.basedb.core.data.keyring.KeyPermission
-
Get the permission.
- getPermission() - Method in class net.sf.basedb.core.data.keyring.ProjectPermission
-
Get the permission.
- getPermissionCode(Set<Permission>) - Static method in class net.sf.basedb.clients.web.PermissionUtil
-
Translate the given set of permissions to an integer code that
can be used to later recreate the set again.
- getPermissionForUse() - Method in class net.sf.basedb.core.ChildItem
-
Get the permission that is required on the parent item that gives
use permission on the child item.
- getPermissionForWriteDeleteAndCreate() - Method in class net.sf.basedb.core.BasicChildItem
-
Get the permission that is required on the parent item that gives
write, delete and create permission on the child item.
- getPermissionForWriteDeleteAndCreate() - Method in class net.sf.basedb.core.BioAssay
-
USE permission is enough to be able to manage bioassays.
- getPermissionForWriteDeleteAndCreate() - Method in class net.sf.basedb.core.BioAssaySet
-
USE permission is enough to be able to manage bioassay sets.
- getPermissionForWriteDeleteAndCreate() - Method in class net.sf.basedb.core.ChildItem
-
Get the permission that is required on the parent item that gives
write, delete and create permission on the child item.
- getPermissionForWriteDeleteAndCreate() - Method in class net.sf.basedb.core.DataCube
-
USE permission is enough to be able to manage data cubes.
- getPermissionForWriteDeleteAndCreate() - Method in class net.sf.basedb.core.DataCubeColumn
-
USE permission is enough to be able to manage data cubes.
- getPermissionForWriteDeleteAndCreate() - Method in class net.sf.basedb.core.DataCubeExtraValue
-
USE permission is enough to be able to manage data cubes.
- getPermissionForWriteDeleteAndCreate() - Method in class net.sf.basedb.core.DataCubeFilter
-
USE permission is enough to be able to manage data cubes.
- getPermissionForWriteDeleteAndCreate() - Method in class net.sf.basedb.core.DataCubeLayer
-
USE permission is enough to be able to manage data cubes.
- getPermissionForWriteDeleteAndCreate() - Method in class net.sf.basedb.core.ExtraValue
-
USE permission is enough to be able to manage extra values.
- getPermissionForWriteDeleteAndCreate() - Method in class net.sf.basedb.core.RootRawBioAssay
-
WRITE permission is required to be able to manage root raw bioassays.
- getPermissionForWriteDeleteAndCreate() - Method in class net.sf.basedb.core.Transformation
-
USE permission is enough to be able to manage transformations.
- getPermissionForWriteDeleteAndCreate() - Method in class net.sf.basedb.core.VirtualDb
-
USE permission is enough to be able to manage virtual db.
- getPermissionGroups() - Static method in class net.sf.basedb.clients.web.PermissionUtil
-
- getPermissions() - Method in class net.sf.basedb.clients.web.extensions.ExtensionsControl
-
- getPermissions(int) - Static method in class net.sf.basedb.clients.web.PermissionUtil
-
Translate a given integer to a set of permissions.
- getPermissions() - Method in interface net.sf.basedb.core.AccessControlled
-
Get the logged in user's permissions on the item.
- getPermissions() - Method in class net.sf.basedb.core.BasicBatcher
-
- getPermissions() - Method in class net.sf.basedb.core.BasicItem
-
- getPermissions() - Method in class net.sf.basedb.core.BioMaterialEventSource
-
- getPermissions() - Method in class net.sf.basedb.core.Coloring
-
- getPermissions() - Method in class net.sf.basedb.core.data.PluginDefinitionData
-
Get a map containing the rolekey and the permissions for this plugin.
- getPermissions(Group) - Method in class net.sf.basedb.core.GroupPermissions
-
Get the permissions for a group.
- getPermissions(User) - Method in class net.sf.basedb.core.ItemKey
-
Get the permissions for a user.
- getPermissions(Group) - Method in class net.sf.basedb.core.ItemKey
-
Get the permissions for a group.
- getPermissions(User) - Method in class net.sf.basedb.core.MultiPermissions
-
Get the permissions for a user.
- getPermissions(Group) - Method in class net.sf.basedb.core.MultiPermissions
-
Get the permissions for a group.
- getPermissions(Project) - Method in class net.sf.basedb.core.MultiPermissions
-
Get the permissions for a project.
- getPermissions() - Method in class net.sf.basedb.core.plugin.AbstractPlugin
-
Return null, which gives the plugin the same permissions as the logged in user.
- getPermissions() - Method in interface net.sf.basedb.core.plugin.Plugin
-
Get the permissions this plugin requires to function as expected.
- getPermissions(User) - Method in class net.sf.basedb.core.Project
-
Get the permissions for a user in this project.
- getPermissions(Group) - Method in class net.sf.basedb.core.Project
-
Get the permissions for a group in this project.
- getPermissions(Project) - Method in class net.sf.basedb.core.ProjectKey
-
Get the permissions for a project.
- getPermissions(Project) - Method in class net.sf.basedb.core.ProjectPermissions
-
Get the permissions for a project.
- getPermissions(Role) - Method in class net.sf.basedb.core.RoleKey
-
Get the permissions for a role.
- getPermissions(User) - Method in class net.sf.basedb.core.UserPermissions
-
Get the permissions for a user.
- getPermissions() - Method in class net.sf.basedb.plugins.AnnotationFlatFileImporter
-
Request read access to File:s, read access to annotation types
and write access to all annotatable items.
- getPermissions() - Method in class net.sf.basedb.plugins.Base1PluginExecuter
-
- getPermissions() - Method in class net.sf.basedb.plugins.BaseFileExporterPlugin
-
Request create and write access to File:s and Directory:s and read access to
Experiment:s and User:s.
- getPermissions() - Method in class net.sf.basedb.plugins.CdfFileReporterImporter
-
Request create and write access to Reporter:s
and read access to File:s ArrayDesign:s, ReporterType:s,
Platform:s and DataFileType:s
- getPermissions() - Method in class net.sf.basedb.plugins.CloneReportersPlugin
-
Request write permission to Experiment:s and Reporter clone
templates and read permission to reporters.
- getPermissions() - Method in class net.sf.basedb.plugins.FormulaFilter
-
Request use access to Experiment:s and read access to Job:s and ReporterLists.
- getPermissions() - Method in class net.sf.basedb.plugins.GalExporter
-
Request create and write access to File:s, Directory:s and ArrayDesign:s
read access to User:s and forced read access to DataFileType:s.
- getPermissions() - Method in class net.sf.basedb.plugins.HelpExporter
-
Request create and write access to File:s and Directory:s and read access to
Client:s and User:s.
- getPermissions() - Method in class net.sf.basedb.plugins.HelpImporter
-
Request write access to Client:s and read access to
File:s.
- getPermissions() - Method in class net.sf.basedb.plugins.IntensityCalculatorPlugin
-
Request use access to Experiment:s and read access to RawBioAssay:s, ArrayDesign:s,
Formulas:s, Job:s and and Reporter:s.
- getPermissions() - Method in class net.sf.basedb.plugins.JepExtraValueCalculator
-
Request use access to Experiment:s and ExtraValueType:s and read access to Job:s.
- getPermissions() - Method in class net.sf.basedb.plugins.JepIntensityTransformer
-
Request use access to Experiment:s and read access to Job:s.
- getPermissions() - Method in class net.sf.basedb.plugins.LowessNormalization
-
Request use access to Experiment:s and read access to Job:s.
- getPermissions() - Method in class net.sf.basedb.plugins.MedianRatioNormalization
-
Request use access to Experiment:s and read access to Job:s.
- getPermissions() - Method in class net.sf.basedb.plugins.PackedFileExporter
-
Request create and delete access to File:s and Directory:s.
- getPermissions() - Method in class net.sf.basedb.plugins.PlateFlatFileImporter
-
Request create access to Plate:s, use access to PlateType:s and
read access to Reporter:s, PlateGeometry:s and File:s.
- getPermissions() - Method in class net.sf.basedb.plugins.PlateMappingExporter
-
Request create and write access to File:s and Directory:s and read access to
PlateMapping:s and PlateGeometries.
- getPermissions() - Method in class net.sf.basedb.plugins.PlateMappingImporter
-
Request create and write access to PlateMapping:s, create and use
access to PlateGeometries and read access to File:s.
- getPermissions() - Method in class net.sf.basedb.plugins.PluginConfigurationExporter
-
Request create and write access to File:s and Directory:s and read access to
PluginConfigurations:s, PluginDefinition:s and User:s.
- getPermissions() - Method in class net.sf.basedb.plugins.PrintMapFlatFileImporter
-
Request write access to ArrayDesign:s, read access to Plate:s, Reporter:s,
DataFileType:s, Platform:s and File:s.
- getPermissions() - Method in class net.sf.basedb.plugins.RawDataFlatFileImporter
-
Request write access to RawBioAssay:s and read access to ArrayDesign:s, File:s,
Reporter:s, Platform:s and DataFileType:s
- getPermissions() - Method in class net.sf.basedb.plugins.ReporterFlatFileImporter
-
Request create, write and delete access to Reporter:s, write access to ReporterList:s
and read access to File:s and ReporterType:s.
- getPermissions() - Method in class net.sf.basedb.plugins.ReporterMapFlatFileImporter
-
Request write access to ArrayDesign:s, read access to Reporter:s,
DataFileType:s, Platform:s and File:s.
- getPermissions() - Method in class net.sf.basedb.plugins.SpotImageCreator
-
Request write access to RawBioAssay:s, create and write access to File:s,
use access to FileType:s and Directory:s.
- getPermissions() - Method in class net.sf.basedb.util.zip.AbstractFileUnpacker
-
Request create and write access to File:s and Directory:s.
- getPermissionTemplate() - Method in class net.sf.basedb.core.data.ProjectData
-
A permission template can be used to set default permissions
when this project is active.
- getPermissionTemplate() - Method in class net.sf.basedb.core.Project
-
Get the permission template that is used to share new items when this project
is active.
- getPhone() - Method in class net.sf.basedb.core.authentication.ExtraUserInformation
-
The phone number to the user.
- getPhone() - Method in class net.sf.basedb.core.data.UserData
-
Get the phone number to the user, or null if unknown.
- getPhone() - Method in class net.sf.basedb.core.User
-
Get the phone number to the user, or null if unknown.
- getPhysicalBioAssay() - Method in class net.sf.basedb.core.ArraySlide
-
- getPhysicalBioAssay() - Method in class net.sf.basedb.core.BioMaterialEvent
-
- getPhysicalBioAssay() - Method in class net.sf.basedb.core.data.ArraySlideData
-
Get the bioassay.
- getPhysicalBioAssay() - Method in class net.sf.basedb.core.data.BioMaterialEventData
-
Get the physical bioassay that was created by this event.
- getPhysicalBioAssay() - Method in class net.sf.basedb.core.DerivedBioAssay
-
- getPhysicalBioAssays() - Method in class net.sf.basedb.core.data.DerivedBioAssayData
-
A set that manages the parent physical bioassays that this derived bioassay
is related to.
- getPhysicalBioAssays() - Method in class net.sf.basedb.core.DerivedBioAssay
-
Get a query that returns the physical bioassays used to create
this derived bioassay.
- getPhysicalBioAssays() - Method in class net.sf.basedb.core.Extract
-
Get a query that returns all bioassays created from this
extract.
- getPhysicalBioAssays(DbControl, OverviewContext, DerivedBioAssay) - Static method in class net.sf.basedb.util.overview.validator.PhysicalBioAssayValidator
-
Get all physical bioassays that are parents to the given derived bioassay.
- getPlaceHolder() - Method in class net.sf.basedb.clients.web.extensions.login.FieldInfo
-
Get a placeholder text that is displayed in the field when it is empty.
- getPlainConnection() - Static method in class net.sf.basedb.core.HibernateUtil
-
- getPlate(int) - Method in class net.sf.basedb.core.ArrayDesign
-
Get a
Plate
from a given position.
- getPlate() - Method in class net.sf.basedb.core.ArrayDesignPlate
-
Gets the Plate
that belongs to this item.
- getPlate() - Method in class net.sf.basedb.core.BioWell
-
Get the
BioPlate
this biowell belongs to.
- getPlate() - Method in class net.sf.basedb.core.data.ArrayDesignPlateData
-
Get the Plate.
- getPlate() - Method in class net.sf.basedb.core.data.MappingCoordinate
-
Get the plate number.
- getPlate() - Method in class net.sf.basedb.core.data.PlateEventData
-
The plate this event belongs to.
- getPlate() - Method in class net.sf.basedb.core.data.WellData
-
The plate this well belongs to.
- getPlate() - Method in class net.sf.basedb.core.PlateEvent
-
Get the
Plate
this event belongs to.
- getPlate() - Method in class net.sf.basedb.core.Well
-
Get the
Plate
this event belongs to.
- getPlateCoordinate() - Method in class net.sf.basedb.core.BioWell
-
Get the plate coordinate representation of the coordinate for this well.
- getPlateEvents() - Method in class net.sf.basedb.core.data.PlateEventTypeData
-
This is the inverse end.
- getPlateEventType() - Method in class net.sf.basedb.core.data.PlateEventData
-
The event type of this event.
- getPlateEventType() - Method in class net.sf.basedb.core.PlateEvent
-
- getPlateGeometry() - Method in class net.sf.basedb.core.BioPlate
-
- getPlateGeometry() - Method in class net.sf.basedb.core.data.BioPlateData
-
The geometry of this plate type.
- getPlateGeometry() - Method in class net.sf.basedb.core.data.PlateTypeData
-
The geometry of this plate type.
- getPlateGeometry() - Method in class net.sf.basedb.core.PlateType
-
- getPlateMapping() - Method in class net.sf.basedb.core.data.PlateData
-
If this plate was created by a plate mapping, it is linked here.
- getPlateMapping() - Method in class net.sf.basedb.core.Plate
-
- getPlatePosition(Plate) - Method in class net.sf.basedb.core.ArrayDesign
-
Get the position of a
Plate
in this array design.
- getPlates() - Method in class net.sf.basedb.core.ArrayDesign
-
Get a query that returns the plates that are used by this arraydesign.
- getPlates() - Method in class net.sf.basedb.core.data.ArrayDesignData
-
The plates this design is made from.
- getPlates() - Method in class net.sf.basedb.core.data.PlateTypeData
-
The plates of this type.
- getPlates() - Method in class net.sf.basedb.core.PlateType
-
Get a query that returns all plates of this plate type.
- getPlateType() - Method in class net.sf.basedb.core.data.PlateData
-
The plate type of this plate.
- getPlateType() - Method in class net.sf.basedb.core.data.PlateEventTypeData
-
The plate type this event type belongs to.
- getPlateType() - Method in class net.sf.basedb.core.Plate
-
- getPlateType() - Method in class net.sf.basedb.core.PlateEventType
-
Get the
PlateType
this event type belongs to.
- getPlateTypes() - Method in class net.sf.basedb.core.data.PlateGeometryData
-
This is the invers end.
- getPlateTypes() - Method in class net.sf.basedb.core.PlateGeometry
-
Get a query returning all plate types using this geometry.
- getPlatform() - Method in class net.sf.basedb.core.ArrayDesign
-
- getPlatform() - Method in class net.sf.basedb.core.BioAssaySet
-
- getPlatform() - Method in class net.sf.basedb.core.data.ArrayDesignData
-
Get the platform this raw bioassay uses
- getPlatform() - Method in class net.sf.basedb.core.data.PlatformFileTypeData
-
Get the platform.
- getPlatform() - Method in class net.sf.basedb.core.data.PlatformVariantData
-
The parent platform of this variant.
- getPlatform() - Method in class net.sf.basedb.core.data.RawBioAssayData
-
Get the platform this raw bioassay uses.
- getPlatform() - Method in class net.sf.basedb.core.DerivedBioAssay
-
- getPlatform() - Method in class net.sf.basedb.core.ExtraValue
-
- getPlatform() - Method in interface net.sf.basedb.core.FileStoreEnabled
-
Get the platform the item is related to.
- getPlatform() - Method in class net.sf.basedb.core.PlatformFileType
-
Get the platform.
- getPlatform() - Method in class net.sf.basedb.core.PlatformVariant
-
Get that platform this is a variant of.
- getPlatform() - Method in class net.sf.basedb.core.RawBioAssay
-
- getPlatform(DbControl) - Method in class net.sf.basedb.core.RawDataType
-
Get the platform that this raw data type is associated with.
- getPlatformRawDataType(Session, String) - Static method in class net.sf.basedb.core.RawDataTypes
-
- getPlatforms() - Method in class net.sf.basedb.core.data.DataFileTypeData
-
This is the inverse end.
- getPlatforms() - Method in class net.sf.basedb.core.DataFileType
-
Get a query that returns all platforms/variants that are using this
file type.
- getPlotGenerators() - Method in interface net.sf.basedb.clients.web.extensions.plot.OverviewPlotAction
-
The plot generates that contains information for each image that
is generated.
- getPlotGenerators() - Method in class net.sf.basedb.clients.web.extensions.plot.OverviewPlotBean
-
- getPlugin(DbControl, ChangeHistory, boolean, boolean) - Static method in class net.sf.basedb.clients.web.ChangeHistoryUtil
-
Get the plug-in that made the change in HTML format.
- getPlugin(DbControl) - Method in class net.sf.basedb.core.ChangeHistory
-
Load the plug-in that made the change.
- getPlugin() - Method in class net.sf.basedb.core.data.ChangeHistoryData
-
- getPlugin() - Method in class net.sf.basedb.core.PluginRequest
-
Get the plugin object.
- getPluginConfiguration() - Method in class net.sf.basedb.core.data.JobData
-
The plugin configuration for the plugin.
- getPluginConfiguration() - Method in class net.sf.basedb.core.Job
-
- getPluginConfiguration() - Method in class net.sf.basedb.core.ParameterValuesImpl
-
- getPluginConfiguration() - Method in class net.sf.basedb.core.plugin.NamespaceParameterValuesWrapper
-
- getPluginConfiguration() - Method in interface net.sf.basedb.core.plugin.ParameterValues
-
Get the configuration that we are using/configuring.
- getPluginConfiguration() - Method in class net.sf.basedb.core.plugin.ParameterValuesWrapper
-
- getPluginConfiguration() - Method in class net.sf.basedb.plugins.gtf.DefaultConfigurationValues
-
- getPluginConfiguration() - Method in class net.sf.basedb.util.ContextUtil.ContextResult
-
Get the plugin configuration that was checked, or null.
- getPluginConfigurations() - Method in class net.sf.basedb.core.PluginDefinition
-
Get a query that returns the configurations
for this plugin definition.
- getPluginDefinition() - Method in class net.sf.basedb.core.data.JobAgentSettingsData
-
The plugin these settings are used for.
- getPluginDefinition() - Method in class net.sf.basedb.core.data.JobData
-
The plugin that executes the job.
- getPluginDefinition() - Method in class net.sf.basedb.core.data.PluginConfigurationData
-
Get the plugin definition for this configuration.
- getPluginDefinition() - Method in class net.sf.basedb.core.Job
-
- getPluginDefinition() - Method in class net.sf.basedb.core.JobAgentSettings
-
Get the plugin that these settings are used for.
- getPluginDefinition() - Method in class net.sf.basedb.core.ParameterValuesImpl
-
- getPluginDefinition() - Method in class net.sf.basedb.core.plugin.NamespaceParameterValuesWrapper
-
- getPluginDefinition() - Method in interface net.sf.basedb.core.plugin.ParameterValues
-
Get the plugin that we are executing/configuring.
- getPluginDefinition() - Method in class net.sf.basedb.core.plugin.ParameterValuesWrapper
-
Get the PluginDefinition of either the job or the configuration, depending in the
preferJob
parameter that was set when creating this object.
- getPluginDefinition() - Method in class net.sf.basedb.core.PluginConfiguration
-
Get the plugin definition for this configuration.
- getPluginDefinition() - Method in class net.sf.basedb.plugins.gtf.DefaultConfigurationValues
-
- getPluginDefinition() - Method in class net.sf.basedb.util.ContextUtil.ContextResult
-
Get the plugin definition that was checked.
- getPluginDefinitionId() - Method in class net.sf.basedb.core.data.keyring.PluginKeys
-
Gets the id of the plugin
- getPluginDefinitions() - Method in class net.sf.basedb.util.extensions.xml.XmlLoader
-
Get a list with all loaded plug-in definitions.
- getPluginDirectory(DbControl, String) - Method in class net.sf.basedb.plugins.Base1PluginExecuter
-
- getPluginId() - Method in class net.sf.basedb.core.ChangeHistory
-
Get the ID of the plug-in that was making the change.
- getPluginId() - Method in class net.sf.basedb.core.data.ChangeHistoryData
-
The ID of the plug-in that was making the changes.
- getPluginId() - Method in class net.sf.basedb.core.log.TransactionDetails
-
Get the ID of the currently running plug-in or 0 if no plug-in is running.
- getPluginId() - Method in class net.sf.basedb.core.SessionControl
-
Get the id of the plug-in that is currently running with this
session control.
- getPluginName() - Method in class net.sf.basedb.core.log.TransactionDetails
-
Utility method for loading the name of the currently executing plugin.
- getPluginParameter() - Method in class net.sf.basedb.plugins.Base1PluginExecuter.JobParameter
-
- getPluginPermissions() - Method in class net.sf.basedb.core.Annotation
-
- getPluginPermissions() - Method in class net.sf.basedb.core.AnnotationSet
-
- getPluginPermissions() - Method in class net.sf.basedb.core.AnyToAny
-
- getPluginPermissions() - Method in class net.sf.basedb.core.BasicBatcher
-
- getPluginPermissions() - Method in class net.sf.basedb.core.BasicChildItem
-
- getPluginPermissions() - Method in class net.sf.basedb.core.BasicItem
-
- getPluginPermissions() - Method in class net.sf.basedb.core.ChildItem
-
- getPluginPermissions() - Method in class net.sf.basedb.core.FeatureBatcher
-
- getPluginPermissions() - Method in class net.sf.basedb.core.FileSet
-
- getPluginPermissions() - Method in class net.sf.basedb.core.FileSetMember
-
- getPluginPermissions() - Method in class net.sf.basedb.core.ItemKey
-
- getPluginPermissions(Item) - Method in class net.sf.basedb.core.Keyring
-
Get the active plugin's permissions to an unspecified item
of a certain
Item
type.
- getPluginPermissions() - Method in class net.sf.basedb.core.Project
-
Make sure plug-ins always has at least read access to the active project.
- getPluginPermissions() - Method in class net.sf.basedb.core.ProjectKey
-
- getPluginPermissions() - Method in class net.sf.basedb.core.RawDataBatcher
-
- getPluginPermissions() - Method in class net.sf.basedb.core.ReporterCloneTemplate
-
- getPluginPermissions() - Method in class net.sf.basedb.core.RoleKey
-
- getPluginPermissions(Item) - Method in class net.sf.basedb.core.SessionControl
-
Get all plugin-specific permissions for the specified item type.
- getPluginPermissions() - Method in class net.sf.basedb.core.User
-
Make sure plug-ins always has at least read access to the logged in user.
- getPlugins() - Method in class net.sf.basedb.core.data.JobAgentData
-
The plugins that can be executed by this job agent.
- getPlugins() - Method in class net.sf.basedb.core.data.PluginTypeData
-
The plugin implementing this interface.
- getPlugins() - Method in class net.sf.basedb.core.PluginType
-
Get a query that returns the plugin definitions which implements
this type.
- getPluginsDir() - Method in class net.sf.basedb.clients.web.extensions.XJspCompiler
-
Get the path to the plug-in directory from BASE.
- getPluginsDirectory() - Static method in class net.sf.basedb.core.Application
-
Get the directory where plug-ins and extensions must be installed.
- getPluginSessionControl(PluginDefinition, Job) - Method in class net.sf.basedb.core.PluginSessionControl
-
Create a new session control for executing a plugin using the same
parent as this session control has.
- getPluginSessionControl(PluginDefinition, Job) - Method in class net.sf.basedb.core.SessionControl
-
Create a new session control for executing a plugin.
- getPluginTypes() - Method in class net.sf.basedb.core.data.PluginDefinitionData
-
The plugin types of this plugin, ie. all interfaces that it implements.
- getPluginTypes() - Method in class net.sf.basedb.core.PluginDefinition
-
Get a query that returns the plugin types
for this plugin definition.
- getPluginVersion() - Method in class net.sf.basedb.core.data.JobData
-
Get the version of the plugin used to execute this job at the time the
job was executed or registered.
- getPluginVersion() - Method in class net.sf.basedb.core.Job
-
Get the version of the plugin used to execute this job at the time the
job was executed or registered.
- getPort() - Method in class net.sf.basedb.clients.jobagent.Agent
-
Get the agent.port
configuration value.
- getPort() - Method in class net.sf.basedb.core.data.JobAgentData
-
The port the job agent is listening on. null if it doesn't listen.
- getPort() - Method in class net.sf.basedb.core.JobAgent
-
Get the port the job agent is listening on.
- getPosition(DbControl, int, int) - Method in class net.sf.basedb.clients.web.ExperimentExplorer
-
Get the position number of the position specified by the
given reporter and position index.
- getPosition() - Method in class net.sf.basedb.core.ArrayDesignPlate
-
Gets the position of this item.
- getPosition() - Method in class net.sf.basedb.core.BioMaterialEventSource
-
Get the position that the source biomaterial was used on in the event.
- getPosition() - Method in class net.sf.basedb.core.BioPlate
-
Get the position within the "storage location" for this bioplate.
- getPosition() - Method in class net.sf.basedb.core.data.ArrayDesignPlateData
-
Get the index.
- getPosition() - Method in class net.sf.basedb.core.data.BioMaterialEventSourceData
-
Get the position of the parent biomaterial as it was used in the event.
- getPosition() - Method in class net.sf.basedb.core.data.BioPlateData
-
Get the position in the storage location were the bioplate is stored.
- getPosition() - Method in class net.sf.basedb.core.data.FeatureData
-
Get the position number of the feature.
- getPosition() - Method in class net.sf.basedb.core.data.RawData
-
- getPosition() - Method in class net.sf.basedb.core.RawDataBatcher.FeatureInfo
-
- getPosition() - Method in class net.sf.basedb.plugins.Base1PluginExecuter.JobParameter
-
- getPositionBatcher() - Method in class net.sf.basedb.core.BioAssaySet
-
Get a batcher that links position coordinates to reporters
for the data cube this bioassayset uses.
- getPositionBatcher() - Method in class net.sf.basedb.core.DataCube
-
- getPositionData() - Method in class net.sf.basedb.core.BioAssaySet
-
Get a query that returns position data for the data cube where this bioassayset
is located.
- getPositionExtraValueBatcher(Class<I>, ExtraValueType, Job) - Method in class net.sf.basedb.core.BioAssaySet
-
Get a batcher that is used to insert extra values per position of the specified
type.
- getPositionIndex() - Method in class net.sf.basedb.clients.web.ExperimentExplorer
-
Get the index of the current position.
- getPositionIndex() - Method in class net.sf.basedb.util.importer.spotdata.BaseFileInfo.SpotSectionInfo
-
The index of the 'position' data column.
- getPredefinedQuery(Session, String) - Static method in class net.sf.basedb.core.HibernateUtil
-
Get a predefined HQL query.
- getPredefinedQuery(Session, String, String...) - Static method in class net.sf.basedb.core.HibernateUtil
-
Get a predefined HQL query.
- getPredefinedQuery(StatelessSession, String) - Static method in class net.sf.basedb.core.HibernateUtil
-
Get a predefined HQL query using the stateless session.
- getPredefinedSQLQuery(Session, String, String...) - Static method in class net.sf.basedb.core.HibernateUtil
-
Get a predefined SQL query.
- getPredefinedSQLQuery(StatelessSession, String) - Static method in class net.sf.basedb.core.HibernateUtil
-
Get a predefined SQL query using the stateless session.
- getPrefix() - Method in class net.sf.basedb.clients.web.taglib.table.CellValue
-
- getPrefix() - Method in class net.sf.basedb.util.bfs.SequenceFilenameGenerator
-
Get the prefix that is used for file name generation.
- getPreset(String) - Method in class net.sf.basedb.core.Presets
-
Get a named preset.
- getPreviousState() - Method in class net.sf.basedb.core.log.EntityDetails
-
Get an array with the previous state of the entity.
- getPrimaryKey() - Method in class net.sf.basedb.core.dbengine.TableInfo
-
Get information about the primary key of the table
- getPrintRobot() - Method in class net.sf.basedb.core.ArrayBatch
-
- getPrintRobot() - Method in class net.sf.basedb.core.data.ArrayBatchData
-
Get the hardware used for creating this batch.
- getPriority() - Method in class net.sf.basedb.core.data.JobData
-
The jobs priority.
- getPriority() - Method in class net.sf.basedb.core.Job
-
Get the priority of the job.
- getPriorityBoost() - Method in class net.sf.basedb.core.data.JobAgentSettingsData
-
The priority boost for this plugin.
- getPriorityBoost() - Method in class net.sf.basedb.core.JobAgentSettings
-
Get the priority boost given to jobs executed by this plugin.
- getPrivateKey(String) - Method in class net.sf.basedb.util.ssl.StaticKeyManager
-
- getProcessResults() - Method in class net.sf.basedb.util.extensions.manager.processor.DisablePluginsProcessor
-
- getProcessResults() - Method in class net.sf.basedb.util.extensions.manager.processor.PluginInstallationProcessor
-
- getProcessResults() - Method in class net.sf.basedb.util.extensions.manager.processor.RegisterExtensionsProcessor
-
- getProducts() - Method in class net.sf.basedb.core.data.TransformationData
-
This is the inverse end.
- getProducts() - Method in class net.sf.basedb.core.Transformation
-
Get a query that return all bioassaysets created by this
transformation.
- getProgramParameters() - Method in class net.sf.basedb.plugins.executor.ExternalProgramExecutor
-
Get all program parameters and their values.
- getProgress() - Method in class net.sf.basedb.clients.web.fileupload.FileUpload
-
Get progress information about the upload.
- getProgress(FlatFileParser) - Method in class net.sf.basedb.plugins.AbstractFlatFileImporter
-
Get the progress of import as a percentage value.
- getProgress(FlatFileParser) - Method in class net.sf.basedb.plugins.AnnotationFlatFileImporter
-
Overriding default implementation since we want file parsing to
only use 50% and the remaining 50% for storing to the database.
- getProgressReporter(ProgressReporter) - Method in class net.sf.basedb.core.Job
-
Get a progress reporter that reports progress by updating the information
in the database.
- getProgressReporter() - Method in class net.sf.basedb.util.export.spotdata.AbstractBioAssaySetExporter
-
Get the progress reporter
- getProgressReporter() - Method in class net.sf.basedb.util.importer.spotdata.BaseFileImporter
-
Get the progress reporter.
- getProgressReporter() - Method in class net.sf.basedb.util.importer.spotdata.BfsImporter
-
Get the progress reporter.
- getProject(DbControl, ChangeHistory, boolean, boolean) - Static method in class net.sf.basedb.clients.web.ChangeHistoryUtil
-
Get the project that was active when the change was made in HTML format.
- getProject() - Method in class net.sf.basedb.core.Annotation
-
Get the project that this project-specific annotation belongs to.
- getProject(DbControl) - Method in class net.sf.basedb.core.ChangeHistory
-
Load the project that was active when the change was made.
- getProject() - Method in class net.sf.basedb.core.data.ChangeHistoryData
-
- getProject() - Method in class net.sf.basedb.util.overview.GenericOverview
-
Get the project of this overview is using for validating against
project defaults (may be null).
- getProject() - Method in interface net.sf.basedb.util.overview.OverviewContext
-
Get the project the overview is using as the "current" project.
- getProjectAnnotation(AnnotationType, Project) - Method in class net.sf.basedb.core.AnnotationSet
-
Get a value for a project-specific annotation using the specified project instead
of the currently active project.
- getProjectAnnotations(Annotation.Source, Project) - Method in class net.sf.basedb.core.AnnotationSet
-
Get a query returning annotations with the specified source
and belonging to the specified project (or default
values if projectId=0).
- getProjectAnnotations() - Method in class net.sf.basedb.core.AnnotationType
-
If this flag is set, annotation values can be set per project.
- getProjectAnnotations() - Method in class net.sf.basedb.core.data.AnnotationTypeData
-
If this flag is set, annotation values can be set per project.
- getProjectDefaultPlatform(DbControl) - Method in class net.sf.basedb.plugins.batchimport.AbstractItemImporter
-
Get the default platform of the currently active project.
- getProjectDefaultRawDataType(DbControl) - Method in class net.sf.basedb.plugins.batchimport.AbstractItemImporter
-
Get the default raw data type of the currently active project.
- getProjectDefaults() - Method in class net.sf.basedb.core.data.ProjectData
-
Gets the default values
- getProjectDefaultVariant(DbControl) - Method in class net.sf.basedb.plugins.batchimport.AbstractItemImporter
-
Get the default platform variant of the currently active project.
- getProjectId() - Method in class net.sf.basedb.core.Annotation
-
Get the ID of the project that this project-specicif annotation belongs to.
- getProjectId() - Method in class net.sf.basedb.core.ChangeHistory
-
Get the ID of the project that was active when the change
was made.
- getProjectId() - Method in class net.sf.basedb.core.data.AnnotationData
-
The ID of the project that this annotation belongs to. 0
is used for default annotations.
- getProjectId() - Method in class net.sf.basedb.core.data.annotations.AnnotationLink
-
- getProjectId() - Method in class net.sf.basedb.core.data.ChangeHistoryData
-
The ID of the project that was active when the changes were made.
- getProjectId() - Method in class net.sf.basedb.core.data.keyring.ProjectKeys
-
Get the id of the project.
- getProjectId() - Method in class net.sf.basedb.core.data.keyring.ProjectPermission
-
Get the id of the project.
- getProjectId() - Method in class net.sf.basedb.core.log.TransactionDetails
-
Get the ID of the currently active project, or 0 if no project is active.
- getProjectId() - Method in class net.sf.basedb.core.snapshot.AnnotationSnapshot
-
Get the id of the project that this project-specific annotation
belongs to.
- getProjectIds(Permission) - Method in class net.sf.basedb.core.ProjectKey
-
Get the ID:s of all projects that are shared with this project key
having the specified permission.
- getProjectKey() - Method in interface net.sf.basedb.core.data.ShareableData
-
- getProjectKey() - Method in class net.sf.basedb.core.data.SharedData
-
- getProjectKey() - Method in interface net.sf.basedb.core.Shareable
-
Get the
ProjectKey
that is used to share this item to projects.
- getProjectKey() - Method in class net.sf.basedb.core.SharedItem
-
- getProjectKeyId() - Method in class net.sf.basedb.core.SessionControl
-
Get the id of the
ProjectKey
that can be used to share an item to
the active project with full permission, or 0 if no project is active or
the logged in user only has read permission to the active project.
- getProjectKeys() - Method in class net.sf.basedb.core.data.ProjectData
-
This is the inverse end.
- getProjectKeys() - Method in class net.sf.basedb.core.InternalJobQueue.JobQueueKeyring
-
Return empty set.
- getProjectKeys() - Method in class net.sf.basedb.core.InternalStorageController.StorageKeyring
-
Return empty set.
- getProjectKeys() - Method in class net.sf.basedb.core.Job.SignalKeyring
-
Return empty set.
- getProjectKeys(Permission) - Method in class net.sf.basedb.core.Keyring
-
- getProjectKeys() - Method in class net.sf.basedb.core.ServiceSessionControl.ServicesKeyring
-
Return empty set.
- getProjectKeys() - Method in class net.sf.basedb.core.SessionControl
-
Get the id of all project keys where the logged in user has read permission.
- getProjectKeys(Permission) - Method in class net.sf.basedb.core.SessionControl
-
Get the id of all project keys where the logged in user has the
requested permission.
- getProjectName() - Method in class net.sf.basedb.core.log.TransactionDetails
-
Utility method for loading the name of the currently active project.
- getProjectPermission(Project) - Method in class net.sf.basedb.core.SessionControl
-
- getProjectPermissions() - Method in class net.sf.basedb.core.ProjectPermissions
-
Get the internal representation of the permissions.
- getProjects() - Method in class net.sf.basedb.core.data.GroupData
-
This is the inverse end.
- getProjects() - Method in class net.sf.basedb.core.data.PermissionTemplateData
-
This is the inverse end.
- getProjects() - Method in class net.sf.basedb.core.data.ProjectKeyData
-
Get the map that manages which projects that have permissions
for this key.
- getProjects() - Method in class net.sf.basedb.core.data.UserData
-
This is the inverse end.
- getProjects() - Method in class net.sf.basedb.core.Group
-
Get a query that returns the projects that
this group is a member of.
- getProjects() - Method in class net.sf.basedb.core.InternalJobQueue.JobQueueKeyring
-
Return empty map.
- getProjects() - Method in class net.sf.basedb.core.InternalStorageController.StorageKeyring
-
Return empty map.
- getProjects() - Method in class net.sf.basedb.core.Job.SignalKeyring
-
Return empty map.
- getProjects() - Method in class net.sf.basedb.core.Keyring
-
- getProjects() - Method in class net.sf.basedb.core.MultiPermissions
-
Get a query that returns all projects appearing in at least one of
the project keys.
- getProjects() - Method in class net.sf.basedb.core.PermissionTemplate
-
Get a query that returns all projects that use this permission template.
- getProjects() - Method in class net.sf.basedb.core.ServiceSessionControl.ServicesKeyring
-
Return empty map.
- getProjects() - Method in class net.sf.basedb.core.SessionControl
-
Get the id of all projects where the logged in user is a member, directly or indirectly.
- getProjects() - Method in class net.sf.basedb.core.User
-
Get a query that returns the projects where this user is a
member.
- getProjectSpecificAnnotationsManager() - Method in class net.sf.basedb.core.DbControl
-
Get the manager used for handling project specific annotations
in this transaction.
- getPrompt() - Method in class net.sf.basedb.clients.web.extensions.login.FieldInfo
-
Get the prompt that is associated with the field.
- getProperties() - Method in class net.sf.basedb.core.data.ReporterCloneTemplateData
-
Get the map that manages cloned properties.
- getProperties(String) - Static method in class net.sf.basedb.core.ExtendedProperties
-
Get a list of extended properties for the specified class.
- getProperties() - Method in class net.sf.basedb.core.log.EntityDetails
-
Get an array with the names of all properties.
- getProperties() - Method in class net.sf.basedb.core.RawDataType
-
Get a list of
RawDataProperty
:s with definitions for the
extra properties that has been defined for this raw data type.
- getProperty(String) - Method in class net.sf.basedb.clients.jobagent.Agent
-
Get a configuration property.
- getProperty() - Method in class net.sf.basedb.clients.web.extensions.list.AbstractListColumnBean
-
- getProperty() - Method in interface net.sf.basedb.clients.web.extensions.list.ListColumnAction
-
The property name for referencing data in the column.
- getProperty() - Method in class net.sf.basedb.clients.web.taglib.PropertyValue
-
- getProperty() - Method in class net.sf.basedb.clients.web.taglib.table.ColumnDef
-
- getProperty() - Method in class net.sf.basedb.clients.web.taglib.table.TableColumn
-
- getProperty(String, String) - Static method in class net.sf.basedb.core.ExtendedProperties
-
Find an extended property in a given class.
- getProperty() - Method in class net.sf.basedb.core.PropertyFilter
-
Get the name of the property this filter is used on.
- getProperty(String) - Method in class net.sf.basedb.core.RawDataType
-
- getProperty() - Method in class net.sf.basedb.plugins.batchimport.PropertyIdMethod
-
- getProperty() - Method in class net.sf.basedb.util.export.spotdata.AssayPropertyField
-
Get the configured property.
- getProperty(String) - Method in class net.sf.basedb.util.extensions.xml.PluginInfo
-
- getPropertyAccessStrategy() - Method in class net.sf.basedb.core.ExtendedPropertyAccessor.GetterSetter
-
- getPropertyFilter(String) - Method in class net.sf.basedb.core.ItemContext
-
Get a filter for a property on filter row 0.
- getPropertyFilter(String, int) - Method in class net.sf.basedb.core.ItemContext
-
Get a filter for a property.
- getPropertyFilters() - Method in class net.sf.basedb.core.data.ContextData
-
Get the map that manages property filters in this context.
- getPropertyFilters() - Method in class net.sf.basedb.core.data.ItemListSyncFilterData
-
Get the map that manages property filters in this sync filter.
- getPropertyFilters() - Method in class net.sf.basedb.core.ItemContext
-
Get a collection of all property filters stored in this context.
- getPropertyFilters(int) - Method in class net.sf.basedb.core.ItemContext
-
Get a collection of all property filters stored in this context for
a given filter row.
- getPropertyFilters(int) - Method in class net.sf.basedb.core.SyncFilter
-
Get the filters in the given filter row.
- getPropertyFilterString(PropertyFilter, Formatter<Date>) - Static method in class net.sf.basedb.clients.web.Base
-
Convert a property filter to a displayable string with
operator + value.
- getPropertyName(String) - Method in class net.sf.basedb.core.log.EntityLogOptions
-
Convert a method name into a property name.
- getPropertyObject(String) - Method in class net.sf.basedb.core.ItemContext
-
- getPropertyPath(Object, String) - Method in class net.sf.basedb.clients.web.taglib.PropertyValue
-
- getPropertyPath(String, boolean) - Method in class net.sf.basedb.core.Metadata
-
Get a property path that can be used to retrieve a value
from an item instead of using the regular get
methods.
- getPropertyValue(D, String) - Method in class net.sf.basedb.core.BasicBatcher
-
Get the value of a protected property value on a data object using
Hibernate built-in reflection methods.
- getPropertyValue(String) - Method in class net.sf.basedb.core.ItemContext
-
Get the value of a property filter on row 0.
- getPropertyValue(String, int) - Method in class net.sf.basedb.core.ItemContext
-
Get the value of a property filter on the given filter row.
- getProtocol() - Method in interface net.sf.basedb.core.Annotatable
-
A protcol used in the creation of an item that is used
to attach annotations for the protocol parameters.
- getProtocol() - Method in class net.sf.basedb.core.AnnotatedItem
-
Default implementation returns null.
- getProtocol() - Method in class net.sf.basedb.core.ArrayBatch
-
Get the
Protocol
used for printing the arrays.
- getProtocol() - Method in class net.sf.basedb.core.BioAssay
-
Default implementation returns null.
- getProtocol() - Method in class net.sf.basedb.core.BioAssaySet
-
Default implementation returns null.
- getProtocol() - Method in class net.sf.basedb.core.BioMaterialEvent
-
Get the
Protocol
describing the procedure used in this event.
- getProtocol() - Method in class net.sf.basedb.core.BioPlateEvent
-
Get the
Protocol
describing the procedure used in this event.
- getProtocol() - Method in class net.sf.basedb.core.data.ArrayBatchData
-
Get the protocol used for printing the arrays.
- getProtocol() - Method in class net.sf.basedb.core.data.BioMaterialEventData
-
Get the protocol used in this event.
- getProtocol() - Method in class net.sf.basedb.core.data.BioPlateEventData
-
Get the protocol used in this event.
- getProtocol() - Method in class net.sf.basedb.core.data.DerivedBioAssayData
-
Get the protocol used to create this bioassay set.
- getProtocol() - Method in class net.sf.basedb.core.data.PlateEventData
-
The protocol used for the event.
- getProtocol() - Method in class net.sf.basedb.core.data.RawBioAssayData
-
Get the protocol used for the image analysis.
- getProtocol() - Method in class net.sf.basedb.core.DerivedBioAssay
-
- getProtocol() - Method in class net.sf.basedb.core.MeasuredBioMaterial
-
Get the protocol from the creation event.
- getProtocol() - Method in class net.sf.basedb.core.PhysicalBioAssay
-
Get the protocol from the creation event.
- getProtocol() - Method in class net.sf.basedb.core.PlateEvent
-
Get the
Protocol
that was followed in this event.
- getProtocol() - Method in class net.sf.basedb.core.PluginDefinition
-
- getProtocol() - Method in class net.sf.basedb.core.Project
-
Default implementation returns null.
- getProtocol() - Method in class net.sf.basedb.core.RawBioAssay
-
Get the
Protocol
used while analysing the scanned images.
- getProtocol() - Method in class net.sf.basedb.core.RootRawBioAssay
-
- getProtocol() - Method in class net.sf.basedb.core.Well
-
- getProtocolParametersQuery(Protocol) - Static method in class net.sf.basedb.clients.web.Base
-
Get a query that returns all annotation types assigned as parameters to
a specific protocol.
- getProtocols() - Method in class net.sf.basedb.core.data.AnnotationTypeData
-
This is the inverse end.
- getProtocolType() - Method in class net.sf.basedb.core.data.PlateEventTypeData
-
The protocol type that events of this event type should pick their protocols from.
- getProtocolType() - Method in class net.sf.basedb.core.PlateEventType
-
Get the associated protocol type item.
- getProxy(int) - Static method in class net.sf.basedb.core.Reporter
-
Get a proxy reporter object.
- getPublication() - Method in class net.sf.basedb.core.data.ExperimentData
-
Get the publication for this experiment.
- getPublication() - Method in class net.sf.basedb.core.Experiment
-
Get the publication text.
- getPublicationDate() - Method in class net.sf.basedb.core.data.ExperimentData
-
Get the publication date for this experiment.
- getPublicationDate() - Method in class net.sf.basedb.core.Experiment
-
Get the date this experiment was published.
- getPublicLocalHost() - Static method in class net.sf.basedb.util.SocketUtil
-
Get the external address of the local host.
- getPubMedId() - Method in class net.sf.basedb.core.data.ExperimentData
-
Get the publication for this experiment.
- getPubMedId() - Method in class net.sf.basedb.core.Experiment
-
Get the PubMed ID of the publication.
- getPushAnnotations() - Method in class net.sf.basedb.core.data.ItemSubtypeData
-
If this flag is set, the annotations on items of this subtype should be
enabled for pushing to the parent item.
- getPushAnnotations() - Method in class net.sf.basedb.core.ItemSubtype
-
If this flag is set, the annotations on items of this subtype can be
pushed to the parent item.
- getQualifiedTableName() - Method in class net.sf.basedb.core.RealTable
-
Get the quoted table name of this table in the database.
- getQualifiedTableName(VirtualDb) - Method in enum net.sf.basedb.core.VirtualTable
-
Get the real table name of this table in the database, quoted
and with catalog/schema information prepended to it.
- getQuality() - Method in class net.sf.basedb.core.data.SpotImagesData
-
The quality setting for the spot images.
- getQuality() - Method in class net.sf.basedb.core.SpotImages
-
Get the quality used for the jpeg compression.
- getQuantity() - Method in class net.sf.basedb.core.AnnotationType
-
Get the quantity for this annotation type.
- getQuantity() - Method in class net.sf.basedb.core.data.AnnotationTypeData
-
Get the quantity this annotation type uses.
- getQuantity() - Method in class net.sf.basedb.core.data.UnitData
-
Get the quantity this unit belongs to.
- getQuantity() - Method in class net.sf.basedb.core.data.UnitSymbolData
-
Get the quantity this symbol belongs to.
- getQuantity() - Method in class net.sf.basedb.core.Unit
-
Get the quantity this unit belongs to.
- getQuery() - Static method in class net.sf.basedb.core.Annotation
-
Get a query configured to retrieve annotations.
- getQuery() - Static method in class net.sf.basedb.core.AnnotationSet
-
Get a
ItemQuery
object configured to retrieve
AnnotationSet
items.
- getQuery(Item) - Static method in class net.sf.basedb.core.AnnotationType
-
Get a
ItemQuery
that returns annotation types.
- getQuery() - Static method in class net.sf.basedb.core.AnnotationTypeCategory
-
Get a
ItemQuery
object configured to retrieve
AnnotationTypeCategory
items.
- getQuery() - Static method in class net.sf.basedb.core.ArrayBatch
-
- getQuery() - Static method in class net.sf.basedb.core.ArrayDesign
-
Get a
ItemQuery
object configured
to retrieve array designs.
- getQuery(ArrayDesign) - Static method in class net.sf.basedb.core.ArrayDesignBlock
-
Get a query configured to retrieve array design blocks for
the specified array design.
- getQuery(ArrayDesign) - Static method in class net.sf.basedb.core.ArrayDesignPlate
-
Get a query that returns ArrayDesignPlates connections for the
specified array design.
- getQuery() - Static method in class net.sf.basedb.core.ArraySlide
-
Get a
ItemQuery
object configured
to retrieve array slides.
- getQuery(BioAssaySet) - Static method in class net.sf.basedb.core.BioAssay
-
Get a query configured to retrieve bioassays in
a given bioassayset.
- getQuery(Experiment) - Static method in class net.sf.basedb.core.BioAssaySet
-
Get a query configured to retrieve bioassaysets for
a given experiment.
- getQuery(Transformation) - Static method in class net.sf.basedb.core.BioAssaySet
-
Get a query configured to retrieve bioassaysets
created by a given transformation.
- getQuery(MeasuredBioMaterial) - Static method in class net.sf.basedb.core.BioMaterialEvent
-
Get a query that returns events for a biomaterial.
- getQuery(BioMaterialEvent) - Static method in class net.sf.basedb.core.BioMaterialEventSource
-
Get a query returning source information for a given (creation) event.
- getQuery(BioMaterial) - Static method in class net.sf.basedb.core.BioMaterialEventSource
-
Get a query returning event information where a given biomaterial has been used as
a source.
- getQuery() - Static method in class net.sf.basedb.core.BioPlate
-
Gets query that selects all available bioplates
- getQuery() - Static method in class net.sf.basedb.core.BioPlateEvent
-
Get a query that returns bioplate event items.
- getQuery(BioPlateEvent) - Static method in class net.sf.basedb.core.BioPlateEventParticipant
-
Get a query configured to return all participants for a bioplate event.
- getQuery(BioPlate) - Static method in class net.sf.basedb.core.BioPlateEventParticipant
-
Get a query configured to return all event participants for a bioplate.
- getQuery() - Static method in class net.sf.basedb.core.BioPlateEventType
-
Gets query that returns bioplate event types.
- getQuery() - Static method in class net.sf.basedb.core.BioPlateType
-
Gets query that selects all available bioplates
- getQuery() - Static method in class net.sf.basedb.core.BioSource
-
Get a query that returns biosource items.
- getQuery(BioPlate) - Static method in class net.sf.basedb.core.BioWell
-
Get a query configured to retrieve wells for a plate.
- getQuery() - Static method in class net.sf.basedb.core.Client
-
Get a new query object for this class.
- getQuery(Client) - Static method in class net.sf.basedb.core.ClientDefaultSetting
-
Get a query object configured to retrieve
default settings for the specified client application.
- getQuery() - Static method in class net.sf.basedb.core.DataFileType
-
Get a query configured to retrieve DataFileType
items.
- getQuery(FileStoreEnabled) - Static method in class net.sf.basedb.core.DataFileType
-
Get a query configured to retrieve DataFileType
:s
that can be used on a given item.
- getQuery(Platform, PlatformVariant, Item, ItemSubtype) - Static method in class net.sf.basedb.core.DataFileType
-
Get a query to retrieve DataFileType
:s that can be used
on specific platform/variant for a given item and/or generic file type.
- getQuery() - Static method in class net.sf.basedb.core.DerivedBioAssay
-
Get a query that returns derived bioassay.
- getQuery() - Static method in class net.sf.basedb.core.Directory
-
Get a query configured to retrieve directories.
- getQuery(User, Group) - Static method in class net.sf.basedb.core.DiskUsage
-
Get a query configured to retrieve disk usage for the specified user.
- getQuery(RawBioAssay) - Static method in class net.sf.basedb.core.DynamicRawDataQuery
-
Create a new dynamic query for raw data.
- getQuery(Collection<RawBioAssay>) - Static method in class net.sf.basedb.core.DynamicRawDataQuery
-
Create a new dynamic query for raw data.
- getQuery() - Static method in class net.sf.basedb.core.Experiment
-
Get a query configured to retrieve experiments
- getQuery() - Static method in class net.sf.basedb.core.Extract
-
Get a query that returns extracts.
- getQuery(BioAssaySet) - Static method in class net.sf.basedb.core.ExtraValue
-
Get a query configured to retrieve extra values in a given bioassayset.
- getQuery() - Static method in class net.sf.basedb.core.ExtraValueType
-
Get a query configured to retrieve extra value types.
- getQuery() - Static method in class net.sf.basedb.core.File
-
Get a query configured to retrieve File
items.
- getQuery() - Static method in class net.sf.basedb.core.FileServer
-
Get a new query object for this class.
- getQuery() - Static method in class net.sf.basedb.core.FileSet
-
Get a
ItemQuery
object configured to retrieve
FileSet
items.
- getQuery(FileSet) - Static method in class net.sf.basedb.core.FileSetMember
-
Get a query configured to retrieve FileSetMember
items.
- getQuery() - Static method in class net.sf.basedb.core.Formula
-
Get a new query object for this class.
- getQuery(Formula.Type, RawDataType, IntensityTransform) - Static method in class net.sf.basedb.core.Formula
-
Get a query that return formulas that can be used with the specified
raw data type.
- getQuery() - Static method in class net.sf.basedb.core.GlobalDefaultSetting
-
Get a query configured to retrieve global default settings.
- getQuery() - Static method in class net.sf.basedb.core.Group
-
Get a query configured to retrieve groups.
- getQuery() - Static method in class net.sf.basedb.core.Hardware
-
Get a query configured to retrieve hardware.
- getQuery(Client) - Static method in class net.sf.basedb.core.Help
-
Get a query configured to retrieve
help texts for the specified client application.
- getQuery - Variable in enum net.sf.basedb.core.Item
-
- getQuery() - Method in enum net.sf.basedb.core.Item
-
Get a query returning items of this type.
- getQuery() - Method in class net.sf.basedb.core.ItemContext
-
- getQuery() - Static method in class net.sf.basedb.core.ItemList
-
Get a query that returns item lists.
- getQuery(Item) - Static method in class net.sf.basedb.core.ItemSubtype
-
Get a query configured to retrieve item types.
- getQuery(ItemSubtype) - Static method in class net.sf.basedb.core.ItemSubtypeFileType
-
Get the file types that have been registered for a specific item
subtype.
- getQuery(DataFileType) - Static method in class net.sf.basedb.core.ItemSubtypeFileType
-
Get the item subtype types that have been registered for a specific data
file type.
- getQuery() - Static method in class net.sf.basedb.core.Job
-
Get a query configured to retrieve jobs.
- getQuery() - Static method in class net.sf.basedb.core.JobAgent
-
- getQuery(JobAgent) - Static method in class net.sf.basedb.core.JobAgentSettings
-
Get a query configured to retrieve settings for the specified agent.
- getQuery(PluginDefinition) - Static method in class net.sf.basedb.core.JobAgentSettings
-
Get a query configured to retrieve settings for the specified plugin.
- getQuery() - Static method in class net.sf.basedb.core.Kit
-
Get a query configured to retrieve kits.
- getQuery(User) - Static method in class net.sf.basedb.core.Message
-
Get a query configured to retrieve messages for the specified user.
- getQuery() - Static method in class net.sf.basedb.core.MimeType
-
Get a query configured to retrieve MIME types.
- getQuery() - Static method in class net.sf.basedb.core.News
-
Get a query configured to retrieve news.
- getQuery() - Static method in class net.sf.basedb.core.PermissionTemplate
-
Get a query that returns permission templates.
- getQuery() - Static method in class net.sf.basedb.core.PhysicalBioAssay
-
Get a query that returns physical bioassays.
- getQuery() - Static method in class net.sf.basedb.core.Plate
-
Get a query that returns plates.
- getQuery(Plate) - Static method in class net.sf.basedb.core.PlateEvent
-
Get a query configured to retrieve plate events for the specified plate.
- getQuery(PlateType) - Static method in class net.sf.basedb.core.PlateEventType
-
Get a query configured to retrieve
event types for the specified plate type
- getQuery() - Static method in class net.sf.basedb.core.PlateGeometry
-
Get a query configured to retrieve plate geometries.
- getQuery() - Static method in class net.sf.basedb.core.PlateMapping
-
Get a query that returns plate mappings.
- getQuery() - Static method in class net.sf.basedb.core.PlateType
-
Get a query that returns plate types.
- getQuery() - Static method in class net.sf.basedb.core.Platform
-
Get a query configured to retrieve Platform
items.
- getQuery(Platform, PlatformVariant, boolean) - Static method in class net.sf.basedb.core.PlatformFileType
-
Get the file types that have been registered for a specific platform
and variant.
- getQuery() - Static method in class net.sf.basedb.core.PlatformVariant
-
Get a query configured to retrieve PlatformVariant
items.
- getQuery() - Static method in class net.sf.basedb.core.PluginConfiguration
-
Get a query configured to retrieve plugin configurations.
- getQuery(GuiContext, String) - Static method in class net.sf.basedb.core.PluginConfiguration
-
Get a query that returns all plugins configurations related
to a specified GUI context and implementing a certain interface.
- getQuery() - Static method in class net.sf.basedb.core.PluginDefinition
-
Get a query that returns plugin definitions.
- getQuery(GuiContext, String) - Static method in class net.sf.basedb.core.PluginDefinition
-
Get a query that returns all plugins related
to a specified GUI context and implementing a certain interface.
- getQuery() - Static method in class net.sf.basedb.core.PluginType
-
Get a query configured to retrieve plugin types.
- getQuery() - Static method in class net.sf.basedb.core.Project
-
Get a query configured to retrieve projects.
- getQuery() - Static method in class net.sf.basedb.core.Protocol
-
Get a query configured to retrieve protocols.
- getQuery() - Static method in class net.sf.basedb.core.Quantity
-
Get a query configured to retrieve quantities.
- getQuery() - Static method in class net.sf.basedb.core.Quota
-
Get a query configured to retrieve quota.
- getQuery() - Static method in class net.sf.basedb.core.QuotaType
-
Get a query configured to retrieve QuotaType
.
- getQuery() - Static method in class net.sf.basedb.core.RawBioAssay
-
Get a query configured to retrieve raw bioassays.
- getQuery() - Static method in class net.sf.basedb.core.Reporter
-
Get a query object configured to retrieve reporters.
- getQuery() - Static method in class net.sf.basedb.core.ReporterCloneTemplate
-
Get a query that returns reporter clone templates.
- getQuery() - Static method in class net.sf.basedb.core.ReporterList
-
Get a new query object for this class.
- getQuery(ReporterList) - Static method in class net.sf.basedb.core.ReporterScore
-
Get a query object configured to retrieve reporters.
- getQuery() - Static method in class net.sf.basedb.core.ReporterType
-
Get a query configured to retrieve reporter types.
- getQuery() - Static method in class net.sf.basedb.core.Role
-
Get a
ItemQuery
object configured
to retrieve
Role
items.
- getQuery() - Static method in class net.sf.basedb.core.RoleKey
-
Get a query object configured to retrieve role keys.
- getQuery() - Static method in class net.sf.basedb.core.RootRawBioAssay
-
Get a query configured to retrieve raw bioassays.
- getQuery() - Static method in class net.sf.basedb.core.Sample
-
Get a query that returns samples.
- getQuery(User) - Static method in class net.sf.basedb.core.Session
-
Get a query configured to retrieve sessions for the specified user.
- getQuery() - Static method in class net.sf.basedb.core.Software
-
Get a query configured to retrieve software.
- getQuery(ItemList) - Static method in class net.sf.basedb.core.SyncFilter
-
Get a query configured to retrieve
sync filters for the specified item list.
- getQuery() - Static method in class net.sf.basedb.core.Tag
-
Get a query that returns tags.
- getQuery(Experiment) - Static method in class net.sf.basedb.core.Transformation
-
Get a query configured to retrieve transformations for
a given experiment.
- getQuery(BioAssaySet) - Static method in class net.sf.basedb.core.Transformation
-
Get a query configured to retrieve transformations using the
given bioassayset as source.
- getQuery() - Static method in class net.sf.basedb.core.Unit
-
Get a query configured to retrieve units.
- getQuery() - Static method in class net.sf.basedb.core.User
-
Get a query configured to retrieve users.
- getQuery(User, Client) - Static method in class net.sf.basedb.core.UserClientSetting
-
Get a query configured to retrieve client specific settings for a user.
- getQuery(User) - Static method in class net.sf.basedb.core.UserDefaultSetting
-
Get a query configured to retrieve default settings for a user.
- getQuery(Plate) - Static method in class net.sf.basedb.core.Well
-
Get a query configured to retrieve wells for a plate.
- getQuery(Item) - Static method in class net.sf.basedb.util.biomaterial.ListUtil
-
- getQueryClass() - Method in class net.sf.basedb.core.DynamicPositionQueryJoiners.ExtraValueJoiner
-
- getQueryClass() - Method in class net.sf.basedb.core.DynamicPositionQueryJoiners.ReporterJoiner
-
- getQueryClass() - Method in class net.sf.basedb.core.DynamicPositionQueryJoiners.ReporterListJoiner
-
- getQueryClass() - Method in class net.sf.basedb.core.DynamicRawDataQuery.RawBioAssayJoiner
-
- getQueryClass() - Method in class net.sf.basedb.core.DynamicRawDataQuery.ReporterJoiner
-
- getQueryClass() - Method in class net.sf.basedb.core.DynamicRawDataQuery.ReporterListJoiner
-
- getQueryClass() - Method in class net.sf.basedb.core.DynamicReporterQuery.MasterReporterJoiner
-
- getQueryClass() - Method in class net.sf.basedb.core.DynamicReporterQuery.ReporterListJoiner
-
- getQueryClass() - Method in class net.sf.basedb.core.DynamicSpotQueryJoiners.ExtraValueJoiner
-
- getQueryClass() - Method in class net.sf.basedb.core.DynamicSpotQueryJoiners.RawDataJoiner
-
- getQueryClass() - Method in class net.sf.basedb.core.DynamicSpotQueryJoiners.ReporterJoiner
-
- getQueryClass() - Method in class net.sf.basedb.core.DynamicSpotQueryJoiners.ReporterListJoiner
-
- getQueryClass() - Method in class net.sf.basedb.core.HqlQueryJoiners.AnnotationJoiner
-
- getQueryClass() - Method in class net.sf.basedb.core.HqlQueryJoiners.ReporterListJoiner
-
- getQueryClass() - Method in interface net.sf.basedb.core.query.AutoJoiner
-
The type of the query the implementation works for.
- getQueryFile() - Static method in class net.sf.basedb.core.Application
-
Get the path to the XML file containing predefined
queries for SQL and HQL.
- getQueryParameter(String) - Method in class net.sf.basedb.core.AbstractQuery
-
- getQueryParameter(String) - Method in interface net.sf.basedb.core.query.Query
-
Get parameter information for the parameter with given name.
- getQueryPropertyInspector() - Method in class net.sf.basedb.core.VirtualDb
-
Return a filter that can be used to check that a query is only
using cloned reporter properties for sorting, filtering, etc.
- getQuerySection() - Method in class net.sf.basedb.core.AbstractQuery
-
- getQuerySection() - Method in interface net.sf.basedb.core.query.Query
-
Get the current section of the query that is beeing built.
- getQueryString() - Method in class net.sf.basedb.core.hibernate.QueryWrapper
-
- getQueryString(String, String...) - Static method in class net.sf.basedb.core.PredefinedQuery
-
Get the query string for the predefined query with
the specified name.
- getQueryType() - Method in class net.sf.basedb.core.AbstractEntityQuery
-
- getQueryType() - Method in class net.sf.basedb.core.AbstractHqlQuery
-
- getQueryType() - Method in class net.sf.basedb.core.AbstractSqlQuery
-
- getQueryType() - Method in interface net.sf.basedb.core.query.Query
-
Get the type of query.
- getQuota() - Method in class net.sf.basedb.core.data.GroupData
-
Get the quota object which holds quota information for this group.
- getQuota() - Method in class net.sf.basedb.core.data.UserData
-
Get the quota object which holds quota information for this user.
- getQuota() - Method in class net.sf.basedb.core.Group
-
Get the
Quota
that applies to the group.
- getQuota() - Method in class net.sf.basedb.core.User
-
Get the
Quota
that applies to the user.
- getQuotaGroup() - Method in class net.sf.basedb.core.data.UserData
-
Get the group this user is sharing quota with, or null if this user only
has it's own quota.
- getQuotaGroup() - Method in class net.sf.basedb.core.User
-
Get the
Group
whose
Quota
also applies
to the user.
- getQuotaType() - Method in class net.sf.basedb.core.data.DiskUsageData
-
- getQuotaType() - Method in class net.sf.basedb.core.data.QuotaIndex
-
- getQuotaType() - Method in class net.sf.basedb.core.DiskUsage
-
- getQuotaTypes() - Method in class net.sf.basedb.core.DiskUsageStatistics
-
Get the list of quota types that are registered for
DiskConsumable
items.
- getQuotaTypeSystemId() - Method in interface net.sf.basedb.core.DiskConsumable
-
- getQuotaTypeSystemId() - Method in class net.sf.basedb.core.Experiment
-
- getQuotaTypeSystemId() - Method in class net.sf.basedb.core.File
-
- getQuotaTypeSystemId() - Method in class net.sf.basedb.core.RawBioAssay
-
- getQuotaValue(QuotaType, Location) - Method in class net.sf.basedb.core.Quota
-
Get the quota for the specified type and location.
- getQuotaValues() - Method in class net.sf.basedb.core.data.QuotaData
-
- getQuotedName(String) - Method in class net.sf.basedb.core.dbengine.AbstractDbEngine
-
Put quotes (") around the name.
- getQuotedName(String) - Method in interface net.sf.basedb.core.dbengine.DbEngine
-
Quote the name with the database specific quote character.
- getQuotedName(String) - Method in class net.sf.basedb.core.dbengine.MySQLEngine
-
Put quotes (`) around the name.
- getRawBioAssay() - Method in class net.sf.basedb.core.data.RawData
-
The raw bioassay this raw data spot belongs to.
- getRawBioAssay() - Method in class net.sf.basedb.core.data.RootRawBioAssayData
-
Get the raw bioassay root raw bioassay is derived from.
- getRawBioAssay() - Method in class net.sf.basedb.core.data.SpotImagesData
-
Get the scan that produced this image.
- getRawBioAssay() - Method in class net.sf.basedb.core.DynamicRawDataQuery
-
- getRawBioAssay() - Method in class net.sf.basedb.core.RawDataBatcher
-
Get the raw bioassay this batcher is used for.
- getRawBioAssay(DbControl, RawData) - Static method in class net.sf.basedb.core.RawDataUtil
-
Get the raw bioassay the raw data belongs to.
- getRawBioAssay() - Method in class net.sf.basedb.core.RootRawBioAssay
-
Get the raw bioassay this root raw bioassay is representing.
- getRawBioAssay() - Method in class net.sf.basedb.core.SpotImages
-
Get the raw bioassay the spot images belongs to.
- getRawBioAssayData - Static variable in class net.sf.basedb.core.RawDataUtil
-
- getRawBioAssayQuery(Experiment) - Method in class net.sf.basedb.plugins.RawDataFlatFileImporter
-
Get a query that returns all raw bioassays which it may be possible to
import raw data to for the given experiment.
- getRawBioAssays() - Method in class net.sf.basedb.core.BioAssay
-
- getRawBioAssays() - Method in class net.sf.basedb.core.data.DerivedBioAssayData
-
This is the inverse end.
- getRawBioAssays() - Method in class net.sf.basedb.core.data.ExperimentData
-
- getRawBioAssays() - Method in class net.sf.basedb.core.data.ExtractData
-
This is the inverse end.
- getRawBioAssays() - Method in class net.sf.basedb.core.data.JobData
-
This is the inverse end.
- getRawBioAssays() - Method in class net.sf.basedb.core.DerivedBioAssay
-
- getRawBioAssays() - Method in class net.sf.basedb.core.Experiment
-
Get a query that returns the raw bioassays used in this
experiment.
- getRawData() - Method in class net.sf.basedb.core.RawBioAssay
-
Get a query that returns the raw data of this raw bioassay.
- getRawData() - Method in class net.sf.basedb.util.jep.MeanFunction
-
Get the current raw data object used when evaluating the JEP expression.
- getRawData() - Method in class net.sf.basedb.util.jep.RawFunction
-
Get the current raw data object used when evaluating the JEP expression.
- getRawDataBatcher(FeatureIdentificationMethod, Job) - Method in class net.sf.basedb.core.RawBioAssay
-
Get a raw data batcher object which can be used to add raw data to
the raw bioassay.
- getRawDataById(int) - Method in class net.sf.basedb.core.RawBioAssay
-
Get a raw data spot when you know the id.
- getRawDataById(int, boolean) - Method in class net.sf.basedb.core.RawBioAssay
-
Get a raw data spot when you know the id.
- getRawDataById(DbControl, int) - Method in class net.sf.basedb.core.RawDataType
-
- getRawdataFields(BioAssaySet) - Method in class net.sf.basedb.plugins.BaseFileExporterPlugin
-
- getRawdataFields(BioAssaySet) - Method in class net.sf.basedb.plugins.BfsExporterPlugin
-
- getRawDataJoiner(JoinType) - Static method in class net.sf.basedb.core.DynamicSpotQueryJoiners
-
Get a joiner instance for raw data for the specified join type.
- getRawDataProperty(String, String) - Method in class net.sf.basedb.util.export.spotdata.AbstractFieldConverter
-
Find an extended raw data property with the given name and create
a dynamic field from it using exportTitle as the title.
- getRawDataType() - Method in class net.sf.basedb.core.BioAssay
-
Get the raw data type the experiment uses for the raw data.
- getRawDataType() - Method in class net.sf.basedb.core.BioAssaySet
-
Get the raw data type this experiment uses for the raw data.
- getRawDataType() - Method in class net.sf.basedb.core.data.ExperimentData
-
Get the name of the raw data type used in this experiment.
- getRawDataType() - Method in class net.sf.basedb.core.data.FormulaData
-
The name of raw data type this formula can be used on, or null if it can be used on
any raw data type.
- getRawDataType() - Method in class net.sf.basedb.core.data.ItemListData
-
Get the raw data type of raw bioassays that can be members in this list.
- getRawDataType() - Method in class net.sf.basedb.core.data.PlatformData
-
The raw data type this platform is locked to, or null.
- getRawDataType() - Method in class net.sf.basedb.core.data.PlatformVariantData
-
The raw data type this platform variant is locked to, or null.
- getRawDataType() - Method in class net.sf.basedb.core.data.RawBioAssayData
-
Get the name of the raw data type used by this raw bio assay.
- getRawDataType() - Method in class net.sf.basedb.core.DataCube
-
Get the raw data type this experiment uses for the raw data.
- getRawDataType() - Method in class net.sf.basedb.core.DynamicRawDataQuery
-
- getRawDataType() - Method in class net.sf.basedb.core.Experiment
-
Get the raw data type this experiment uses for the raw data.
- getRawDataType() - Method in class net.sf.basedb.core.ExtraValue
-
Get the raw data type the experiment uses for the raw data.
- getRawDataType() - Method in class net.sf.basedb.core.Formula
-
Get the raw data type this formula can be used on.
- getRawDataType() - Method in class net.sf.basedb.core.ItemList
-
Get the raw data type of raw bioassays that can be members in this list.
- getRawDataType() - Method in class net.sf.basedb.core.Platform
-
Get the raw data type this platform is locked to.
- getRawDataType() - Method in class net.sf.basedb.core.PlatformVariant
-
Get the raw data type this platform variant is locked to.
- getRawDataType() - Method in class net.sf.basedb.core.RawBioAssay
-
Get the raw data type this raw bioassay uses for the raw data.
- getRawDataType(String) - Static method in class net.sf.basedb.core.RawDataTypes
-
Get a information about a raw data type.
- getRawDataType() - Method in class net.sf.basedb.core.VirtualDb
-
Get the raw data type the experiment uses for the raw data.
- getRawDataType() - Method in class net.sf.basedb.util.jep.RawFunction
-
Get the raw data type this function uses.
- getRawDataTypeFiles() - Static method in class net.sf.basedb.core.Application
-
Get the path to the XML file containing raw data type definitions.
- getRawDataTypes() - Static method in class net.sf.basedb.core.RawDataTypes
-
Get a collection with all raw data types that has been defined.
- getRawParents() - Method in class net.sf.basedb.core.data.BioAssayData
-
Get a set that manages the raw parent bioassays the data in this bioassay
is based on.
- getRawSources() - Method in class net.sf.basedb.core.data.TransformationData
-
Get the source raw bioassays for the transformation.
- getRawSources() - Method in class net.sf.basedb.core.Transformation
-
Get a query that returns the raw bioassay sources used by this
transformation.
- getRealTable() - Method in class net.sf.basedb.core.RawDataType
-
- getReceivedSignals() - Method in class net.sf.basedb.core.signal.DelegatingSignalHandler
-
Get the list of received signals.
- getReceivedSignals() - Method in class net.sf.basedb.core.signal.EnhancedThreadSignalHandler
-
Get the list of received signals.
- getReceivedSignals() - Method in class net.sf.basedb.core.signal.ProgressReporterSignalHandler
-
Get the list of received signals.
- getReceiverId() - Method in class net.sf.basedb.core.signal.AbstractSignalReceiver
-
- getReceiverId() - Method in class net.sf.basedb.core.signal.AbstractSignalTransporter
-
Get the receiverId part of the signal URI.
- getRecent() - Method in class net.sf.basedb.clients.web.taglib.Select
-
- getRecent(DbControl, Item) - Method in class net.sf.basedb.core.ItemContext
-
Get all recently used items of the specified type.
- getRecent(DbControl, Item, ItemSubtype) - Method in class net.sf.basedb.core.ItemContext
-
Get all recently used items of the specified type.
- getRecent(DbControl, Item, String) - Method in class net.sf.basedb.core.ItemContext
-
Get all recently used items of the specified type in a given sublist.
- getRecent(DbControl, Item, int) - Method in class net.sf.basedb.core.ItemContext
-
- getRecent(DbControl, Item, String, int) - Method in class net.sf.basedb.core.ItemContext
-
- getRecent(String) - Method in class net.sf.basedb.core.ItemContext
-
Get all recently used values for the specified key.
- getRecent(String, int) - Method in class net.sf.basedb.core.ItemContext
-
- getRecentSettingName(String) - Method in class net.sf.basedb.core.ItemContext
-
- getRedefinedColumnName(String, String) - Method in class net.sf.basedb.util.basefile.BaseFileParser
-
Get the redefined column name for a section.
- getRedImageFile() - Method in class net.sf.basedb.core.data.SpotImagesData
-
The file used for the red component in the spot images.
- getRedImageFile() - Method in class net.sf.basedb.core.SpotImages
-
Get the file which was used for the red channel in the
spot images.
- getRefColumns() - Method in class net.sf.basedb.core.dbengine.TableInfo.ForeignKeyInfo
-
- getReferenceFactor() - Method in class net.sf.basedb.core.data.UnitData
-
Factor that controls how this unit relates to the reference
unit of the quantity.
- getReferenceFactor() - Method in class net.sf.basedb.core.Unit
-
Get the factor that is used for converting values in this
unit into the reference unit of the quantity.
- getReferenceOffset() - Method in class net.sf.basedb.core.data.UnitData
-
An offset that controls how this unit relates to the reference
unit of the quantity.
- getReferenceOffset() - Method in class net.sf.basedb.core.Unit
-
Get the offset that is used for converting values in this
unit into the reference unit of the quantity.
- getReferenceUnit() - Method in class net.sf.basedb.core.data.QuantityData
-
The reference unit that all units of must relate to.
- getReferenceUnit() - Method in class net.sf.basedb.core.Quantity
-
The reference unit describes the unit that all other units must
relate to.
- getRefName() - Method in class net.sf.basedb.core.dbengine.TableInfo.ForeignKeyInfo
-
- getRegistry() - Method in class net.sf.basedb.util.extensions.ExtensionContext
-
- getRegistry() - Method in class net.sf.basedb.util.extensions.ExtensionPointContext
-
- getRegistry() - Method in class net.sf.basedb.util.extensions.InvokationContext
-
Get the registry where this invokation originated from.
- getRegistry() - Method in class net.sf.basedb.util.extensions.manager.ExtensionsManager
-
Get the registry in which all extensions that are managed by this
manager are stored.
- getRegistryBuilder() - Method in class net.sf.basedb.core.ServiceSessionControl.SessionFactoryConfiguration
-
Get the registry for collecting configuration options.
- getRelatedItems(Item) - Static method in class net.sf.basedb.core.ItemSubtype
-
Get a list with (subtypable) items that are related to the given
item (which should also be subtypable).
- getRelatedSubtype(DbControl, Subtypable, Item, int) - Static method in class net.sf.basedb.core.ItemSubtype
-
- getRelatedSubtype(DbControl, Subtypable, Item, int, int) - Static method in class net.sf.basedb.core.ItemSubtype
-
Utility method for loading a subtype that is related to the subtype of the given item.
- getRelatedSubtype(DbControl, Subtypable, Item...) - Static method in class net.sf.basedb.core.ItemSubtype
-
Utility method for locating a subtype that is related to the subtype of
a given item.
- getRelatedSubtype(Item) - Method in class net.sf.basedb.core.ItemSubtype
-
Get a related subtype of another item type.
- getRelatedSubtypes() - Method in class net.sf.basedb.core.data.ItemSubtypeData
-
- getRelatedSubtypes() - Method in class net.sf.basedb.core.ItemSubtype
-
Get a query returning all subtypes that are related to this subtype.
- getRelativePath(File) - Static method in class net.sf.basedb.core.File
-
Get the relative path of the specified file from the base upload
directory and convert directory separator to forward slash.
- getReload() - Method in class net.sf.basedb.core.InternalJobQueue.JobQueueKeyring
-
Never reload since everything is static.
- getReload() - Method in class net.sf.basedb.core.InternalStorageController.StorageKeyring
-
Never reload since everything is static.
- getReload() - Method in class net.sf.basedb.core.Job.SignalKeyring
-
Never reload since everything is static.
- getReload() - Method in class net.sf.basedb.core.Keyring
-
- getReload() - Method in class net.sf.basedb.core.ServiceSessionControl.ServicesKeyring
-
Never reload since everything is static.
- getRemainingQuantity() - Method in class net.sf.basedb.core.data.MeasuredBioMaterialData
-
Get the remaining quantity of the biomaterial.
- getRemainingQuantity() - Method in class net.sf.basedb.core.MeasuredBioMaterial
-
Get the remaining quantity of the biomaterial.
- getRemoteAddresses(String) - Method in class net.sf.basedb.clients.jobagent.Agent
-
Split the string at commas and try to create an
InetAddress
for each part.
- getRemoteId() - Method in class net.sf.basedb.core.data.SessionData
-
Get the login comment.
- getRemoteId() - Method in class net.sf.basedb.core.Session
-
Get the remote ID of the host the user used for this session.
- getRemoteId() - Method in class net.sf.basedb.core.SessionControl
-
- getRemoteSlot(Job.ExecutionTime) - Method in class net.sf.basedb.clients.jobagent.slotmanager.MasterSlotManager
-
Create a slot for a job on a remote job agent with
the specified estimated execution time.
- getRemoteSlot(String) - Method in class net.sf.basedb.clients.jobagent.slotmanager.MasterSlotManager
-
Get the remote slot with the given id.
- getRemovableItems() - Static method in class net.sf.basedb.core.Metadata
-
Get a set containing all
Removable
item types.
- getRemove() - Method in class net.sf.basedb.util.annotations.InheritSpecification
-
- getRemovedBy() - Method in class net.sf.basedb.core.BioAssaySet
-
- getRemovedBy() - Method in class net.sf.basedb.core.BioPlateEventType
-
- getRemovedBy() - Method in class net.sf.basedb.core.BioPlateType
-
- getRemovedBy() - Method in class net.sf.basedb.core.CommonItem
-
- getRemovedBy() - Method in class net.sf.basedb.core.data.BioAssaySetData
-
- getRemovedBy() - Method in class net.sf.basedb.core.data.BioPlateEventTypeData
-
- getRemovedBy() - Method in class net.sf.basedb.core.data.BioPlateTypeData
-
- getRemovedBy() - Method in class net.sf.basedb.core.data.CommonData
-
- getRemovedBy() - Method in class net.sf.basedb.core.data.DataFileTypeData
-
- getRemovedBy() - Method in class net.sf.basedb.core.data.ExtraValueTypeData
-
- getRemovedBy() - Method in class net.sf.basedb.core.data.GroupData
-
- getRemovedBy() - Method in class net.sf.basedb.core.data.ItemSubtypeData
-
- getRemovedBy() - Method in class net.sf.basedb.core.data.MessageData
-
- getRemovedBy() - Method in class net.sf.basedb.core.data.MimeTypeData
-
- getRemovedBy() - Method in class net.sf.basedb.core.data.NewsData
-
- getRemovedBy() - Method in class net.sf.basedb.core.data.PlateEventTypeData
-
- getRemovedBy() - Method in class net.sf.basedb.core.data.PlateGeometryData
-
- getRemovedBy() - Method in class net.sf.basedb.core.data.PlatformData
-
- getRemovedBy() - Method in class net.sf.basedb.core.data.PlatformVariantData
-
- getRemovedBy() - Method in class net.sf.basedb.core.data.PluginDefinitionData
-
- getRemovedBy() - Method in class net.sf.basedb.core.data.PluginTypeData
-
- getRemovedBy() - Method in class net.sf.basedb.core.data.ProjectData
-
- getRemovedBy() - Method in class net.sf.basedb.core.data.QuantityData
-
- getRemovedBy() - Method in class net.sf.basedb.core.data.QuotaData
-
- getRemovedBy() - Method in interface net.sf.basedb.core.data.RemovableData
-
Get the ID of the user that removed this item.
- getRemovedBy() - Method in class net.sf.basedb.core.data.ReporterTypeData
-
- getRemovedBy() - Method in class net.sf.basedb.core.data.RoleData
-
- getRemovedBy() - Method in class net.sf.basedb.core.data.TransformationData
-
- getRemovedBy() - Method in class net.sf.basedb.core.data.UnitData
-
- getRemovedBy() - Method in class net.sf.basedb.core.data.UserData
-
- getRemovedBy() - Method in class net.sf.basedb.core.DataFileType
-
- getRemovedBy() - Method in class net.sf.basedb.core.Directory
-
- getRemovedBy() - Method in class net.sf.basedb.core.ExtraValueType
-
- getRemovedBy() - Method in class net.sf.basedb.core.Group
-
- getRemovedBy() - Method in class net.sf.basedb.core.ItemSubtype
-
- getRemovedBy() - Method in class net.sf.basedb.core.Message
-
- getRemovedBy() - Method in class net.sf.basedb.core.MimeType
-
- getRemovedBy() - Method in class net.sf.basedb.core.News
-
- getRemovedBy() - Method in class net.sf.basedb.core.PlateEventType
-
- getRemovedBy() - Method in class net.sf.basedb.core.PlateGeometry
-
- getRemovedBy() - Method in class net.sf.basedb.core.Platform
-
- getRemovedBy() - Method in class net.sf.basedb.core.PlatformVariant
-
- getRemovedBy() - Method in class net.sf.basedb.core.PluginType
-
- getRemovedBy() - Method in class net.sf.basedb.core.Project
-
- getRemovedBy() - Method in class net.sf.basedb.core.Quantity
-
- getRemovedBy() - Method in class net.sf.basedb.core.Quota
-
- getRemovedBy() - Method in interface net.sf.basedb.core.Removable
-
Get the user that flagged this item for removal.
- getRemovedBy() - Method in class net.sf.basedb.core.ReporterType
-
- getRemovedBy() - Method in class net.sf.basedb.core.Role
-
- getRemovedBy() - Method in class net.sf.basedb.core.Transformation
-
- getRemovedBy() - Method in class net.sf.basedb.core.Unit
-
- getRemovedBy() - Method in class net.sf.basedb.core.User
-
- getRemoveJobWhenFinished() - Method in class net.sf.basedb.core.data.JobData
-
If the core should delete the job when it's finished successfully.
- getRemoveJobWhenFinished() - Method in class net.sf.basedb.core.Job
-
If the job should flagged for deletion after it's done successfully.
- getRenderer(InvokationContext<? extends ButtonAction>) - Method in class net.sf.basedb.clients.web.extensions.toolbar.CompactButtonRendererFactory
-
- getRenderer(InvokationContext<? extends ButtonAction>) - Method in class net.sf.basedb.clients.web.extensions.toolbar.ToolbarButtonRendererFactory
-
- getRenderer() - Method in class net.sf.basedb.util.extensions.ActionIterator
-
Gets the renderer for the current action.
- getRenderer() - Method in class net.sf.basedb.util.extensions.ExtensionContext
-
If the extension point allows it and this extension
specifies a renderer factory, create a new renderer from
it.
- getRenderer() - Method in class net.sf.basedb.util.extensions.ExtensionPointContext
-
If the extension point defines a renderer factory, creates
a new renderer unless one already exists.
- getRenderer() - Method in class net.sf.basedb.util.extensions.InvokationContext
-
Get the renderer, if any.
- getRenderer(InvokationContext<? extends A>) - Method in interface net.sf.basedb.util.extensions.RendererFactory
-
Get a renderer for a given context.
- getRendererFactory() - Method in interface net.sf.basedb.util.extensions.Extension
-
Get an optional factory class for creating renderers for the actions.
- getRendererFactory() - Method in class net.sf.basedb.util.extensions.ExtensionBean
-
- getRendererFactory() - Method in interface net.sf.basedb.util.extensions.ExtensionPoint
-
This is an optional factory for creating
Renderer
instances.
- getRendererFactory() - Method in class net.sf.basedb.util.extensions.ExtensionPointBean
-
- getRendererFactory() - Method in class net.sf.basedb.util.extensions.Registry.RegisteredExtension
-
- getRendererFactory() - Method in class net.sf.basedb.util.extensions.Registry.RegisteredExtensionPoint
-
- getReplaceExisting() - Method in class net.sf.basedb.util.annotations.InheritSpecification
-
- getReporter(DbControl, int) - Method in class net.sf.basedb.clients.web.ExperimentExplorer
-
Get the reporter for the specified index.
- getReporter() - Method in class net.sf.basedb.core.data.FeatureData
-
Get the reporter of the feature.
- getReporter() - Method in class net.sf.basedb.core.data.RawData
-
The reporter this raw data is connected with.
- getReporter() - Method in class net.sf.basedb.core.data.ReporterListScoreData
-
Get the reporter.
- getReporter() - Method in class net.sf.basedb.core.data.WellData
-
The reporter used in this well.
- getReporter(RawDataBatcher.ReporterProxy) - Method in class net.sf.basedb.core.RawDataBatcher.FeatureInfo
-
- getReporter() - Method in class net.sf.basedb.core.ReporterScore
-
Get the reporter.
- getReporter() - Method in class net.sf.basedb.core.Well
-
Get the reporter in this well.
- getReporter(boolean) - Method in class net.sf.basedb.core.Well
-
Get the reporter in this well.
- getReporter() - Method in class net.sf.basedb.util.jep.ReporterFunction
-
Get the current reporter object used when evaluating the JEP expression.
- getReporterAnnotationsWriter() - Method in class net.sf.basedb.util.export.spotdata.BfsExporter
-
Get the writer were reporter annotations should be printed.
- getReporterCloneBatcher(DbControl) - Method in class net.sf.basedb.core.Experiment
-
Get a batcher for managing cloned reporter information for this experiment.
- getReporterCloneTemplate() - Method in class net.sf.basedb.core.data.VirtualDbData
-
Get the template used for creating the cloned reporter table
in this virtual database, or null if there is no cloned
reporter information.
- getReporterCloneTemplate() - Method in class net.sf.basedb.core.VirtualDb
-
Get the reporter clone template that is active in the current virtual database.
- getReporterField(String, boolean) - Method in class net.sf.basedb.util.export.spotdata.AdvancedFieldConverter
-
- getReporterField(String, boolean) - Method in class net.sf.basedb.util.export.spotdata.Base1FieldConverter
-
Convert a reporter field.
- getReporterField(String, boolean) - Method in interface net.sf.basedb.util.export.spotdata.ExportableFieldConverter
-
Create a reporter dynamic field for the given name.
- getReporterField(String, boolean) - Method in class net.sf.basedb.util.export.spotdata.StandardFieldConverter
-
Find a reporter dynamic field.
- getReporterFields() - Method in class net.sf.basedb.plugins.BaseFileExporterPlugin
-
- getReporterFields() - Static method in class net.sf.basedb.plugins.BfsExporterPlugin
-
- getReporterFields() - Method in class net.sf.basedb.util.export.spotdata.AbstractBioAssaySetExporter
-
Get the list of registered reporter fields, in the order they were
registered.
- getReporterFields() - Method in class net.sf.basedb.util.export.spotdata.BaseFileExporter
-
- getReporterFields() - Method in class net.sf.basedb.util.export.spotdata.BfsExporter
-
- getReporterId(int) - Method in class net.sf.basedb.clients.web.ExperimentExplorer
-
Get the reporter id for the specified index.
- getReporterId() - Method in class net.sf.basedb.core.data.ReporterListScoreData
-
The id of the reporter.
- getReporterIndex() - Method in class net.sf.basedb.clients.web.ExperimentExplorer
-
Get the index of the current reporter.
- getReporterJoiner(JoinType) - Static method in class net.sf.basedb.core.DynamicPositionQueryJoiners
-
Get a joiner instance for reporters for the specified join type.
- getReporterJoiner(JoinType) - Static method in class net.sf.basedb.core.DynamicSpotQueryJoiners
-
Get a joiner instance for reporters for the specified join type.
- getReporterList() - Method in class net.sf.basedb.core.data.ReporterListScoreData
-
The reporter list this reporter and score belongs to.
- getReporterList() - Method in class net.sf.basedb.core.query.ReporterListExpression
-
Get the reporter list.
- getReporterListJoiner(JoinType) - Static method in class net.sf.basedb.core.DynamicPositionQueryJoiners
-
Get a joiner instance for reporter lists for the specified join type.
- getReporterListJoiner(JoinType) - Static method in class net.sf.basedb.core.DynamicReporterQuery
-
Get a joiner instance for reporter lists for the specified join type.
- getReporterListJoiner(JoinType) - Static method in class net.sf.basedb.core.DynamicSpotQueryJoiners
-
Get a joiner instance for raw data for the specified join type.
- getReporterListJoiner(JoinType) - Static method in class net.sf.basedb.core.HqlQueryJoiners
-
Get a joiner instance for raw data for the specified join type.
- getReporterLists() - Method in class net.sf.basedb.core.data.ExperimentData
-
This is the inverse end.
- getReporterListScores() - Method in class net.sf.basedb.core.data.ReporterData
-
The lists this reporter is used in.
- getReporterListScores() - Method in class net.sf.basedb.core.data.ReporterListData
-
The list of reporters and their scores.
- getReporterListsEnum(DbControl) - Static method in class net.sf.basedb.clients.web.Base
-
- getReporterProperty(String, String) - Method in class net.sf.basedb.util.export.spotdata.AbstractFieldConverter
-
Get a static or extended reporter property field, such as name, description
or id.
- getReporterQuery(DbControl, List<String>) - Method in class net.sf.basedb.clients.web.ExperimentExplorer
-
Get a query returning the reporter data used by the reporter search page.
- getReporterQuery() - Method in class net.sf.basedb.util.export.spotdata.AbstractBioAssaySetExporter
-
- getReporters() - Method in class net.sf.basedb.core.ArrayDesign
-
Get a query that returns the reporters on this array design.
- getReporters() - Method in class net.sf.basedb.core.data.ReporterTypeData
-
This is the inverse end.
- getReporters() - Method in class net.sf.basedb.core.Plate
-
Get a query that returns the reporters on this plate.
- getReporters() - Method in class net.sf.basedb.core.RawBioAssay
-
Get a query that returns the reporters on this raw bioassay.
- getReporterScores() - Method in class net.sf.basedb.core.ReporterList
-
- getReporterType() - Method in class net.sf.basedb.core.data.ReporterData
-
- getReporterType(DbControl, ReporterData) - Static method in class net.sf.basedb.core.Reporter
-
Get the reporter type item from a reporter data object.
- getReporterType(String) - Method in class net.sf.basedb.plugins.ReporterFlatFileImporter
-
- getRequestInformation(GuiContext, String) - Method in class net.sf.basedb.clients.web.plugins.SimpleExport
-
- getRequestInformation(GuiContext, String) - Method in interface net.sf.basedb.core.plugin.InteractivePlugin
-
- getRequestInformation() - Method in class net.sf.basedb.core.PluginConfigurationRequest
-
Get the request information object containing
information about the parameters needed for the plugin.
- getRequestInformation(GuiContext, String) - Method in class net.sf.basedb.plugins.AnnotationFlatFileImporter
-
- getRequestInformation(GuiContext, String) - Method in class net.sf.basedb.plugins.Base1PluginExecuter
-
- getRequestInformation(GuiContext, String) - Method in class net.sf.basedb.plugins.BaseFileExporterPlugin
-
- getRequestInformation(GuiContext, String) - Method in class net.sf.basedb.plugins.batchimport.AbstractItemImporter
-
- getRequestInformation(GuiContext, String) - Method in class net.sf.basedb.plugins.BfsExporterPlugin
-
- getRequestInformation(GuiContext, String) - Method in class net.sf.basedb.plugins.CdfFileReporterImporter
-
- getRequestInformation(GuiContext, String) - Method in class net.sf.basedb.plugins.executor.BaseFileExporterSupport
-
- getRequestInformation(GuiContext, String) - Method in class net.sf.basedb.plugins.executor.BaseFileImporterSupport
-
- getRequestInformation(GuiContext, String) - Method in class net.sf.basedb.plugins.executor.BfsExporterSupport
-
- getRequestInformation(GuiContext, String) - Method in class net.sf.basedb.plugins.executor.BfsImporterSupport
-
- getRequestInformation(GuiContext, String) - Method in class net.sf.basedb.plugins.executor.ExternalProgramExecutor
-
- getRequestInformation(GuiContext, String) - Method in class net.sf.basedb.plugins.executor.FileOnlyImporterSupport
-
- getRequestInformation(GuiContext, String) - Method in class net.sf.basedb.plugins.FormulaFilter
-
- getRequestInformation(GuiContext, String) - Method in class net.sf.basedb.plugins.GalExporter
-
- getRequestInformation(GuiContext, String) - Method in class net.sf.basedb.plugins.gtf.GtfReporterMapImporter
-
- getRequestInformation(GuiContext, String) - Method in class net.sf.basedb.plugins.HelpExporter
-
- getRequestInformation(GuiContext, String) - Method in class net.sf.basedb.plugins.HelpImporter
-
- getRequestInformation(GuiContext, String) - Method in class net.sf.basedb.plugins.IlluminaRawDataImporter
-
- getRequestInformation(GuiContext, String) - Method in class net.sf.basedb.plugins.IntensityCalculatorPlugin
-
- getRequestInformation(GuiContext, String) - Method in class net.sf.basedb.plugins.JepExtraValueCalculator
-
- getRequestInformation(GuiContext, String) - Method in class net.sf.basedb.plugins.JepIntensityTransformer
-
- getRequestInformation(GuiContext, String) - Method in class net.sf.basedb.plugins.LowessNormalization
-
- getRequestInformation(GuiContext, String) - Method in class net.sf.basedb.plugins.ManualDerivedBioAssayCreator
-
- getRequestInformation(GuiContext, String) - Method in class net.sf.basedb.plugins.ManualTransformCreator
-
- getRequestInformation(GuiContext, String) - Method in class net.sf.basedb.plugins.MedianRatioNormalization
-
- getRequestInformation(GuiContext, String) - Method in class net.sf.basedb.plugins.PackedFileExporter
-
- getRequestInformation(GuiContext, String) - Method in class net.sf.basedb.plugins.PlateFlatFileImporter
-
- getRequestInformation(GuiContext, String) - Method in class net.sf.basedb.plugins.PlateMappingExporter
-
- getRequestInformation(GuiContext, String) - Method in class net.sf.basedb.plugins.PlateMappingImporter
-
- getRequestInformation(GuiContext, String) - Method in class net.sf.basedb.plugins.PluginConfigurationExporter
-
- getRequestInformation(GuiContext, String) - Method in class net.sf.basedb.plugins.PluginConfigurationImporter
-
- getRequestInformation(GuiContext, String) - Method in class net.sf.basedb.plugins.PrintMapFlatFileImporter
-
- getRequestInformation(GuiContext, String) - Method in class net.sf.basedb.plugins.RawDataFlatFileImporter
-
- getRequestInformation(GuiContext, String) - Method in class net.sf.basedb.plugins.ReporterFlatFileImporter
-
- getRequestInformation(GuiContext, String) - Method in class net.sf.basedb.plugins.ReporterMapFlatFileImporter
-
- getRequestInformation(GuiContext, String) - Method in class net.sf.basedb.util.zip.AbstractFileUnpacker
-
- getRequiredFilter(Item) - Static method in class net.sf.basedb.core.QueryRuntimeFilterFactory
-
Get the required runtime filter for the speicified item type.
- getRequiredHeader(FlatFileParser, String, String, String) - Method in class net.sf.basedb.util.basefile.BaseFileParser
-
Get the value of a required header.
- getRequiredHeader(FlatFileParser, String, String, String, String) - Method in class net.sf.basedb.util.basefile.BaseFileParser
-
Get the value of a header as a list of sub-values.
- getRequiredIndex(List<String>, String, String, String, int, String) - Method in class net.sf.basedb.util.basefile.BaseFileParser
-
Get the index of value in a list of values or throw an exception
if the value is not found.
- getRequiredString(String, String) - Static method in class net.sf.basedb.core.Config
-
Get a required configuration setting.
- getRequiresConfiguration() - Method in class net.sf.basedb.core.data.PluginDefinitionData
-
If the plugin requires a configurations or not.
- getResetClassLoader() - Method in class net.sf.basedb.util.extensions.manager.processor.ResetProcessor
-
- getResetrrorFlag() - Method in class net.sf.basedb.util.extensions.manager.processor.ResetProcessor
-
- getResource(String) - Method in class net.sf.basedb.util.JarClassLoader
-
- getResourceBundle(String, SessionControl) - Static method in class net.sf.basedb.util.resources.ResourceBundleFactory
-
Same as getResouceBundle(name, sc, null)
.
- getResourceBundle(String, SessionControl, ClassLoader) - Static method in class net.sf.basedb.util.resources.ResourceBundleFactory
-
Get a resource bundle for the given session control.
- getResourceBundle(String, Locale) - Static method in class net.sf.basedb.util.resources.ResourceBundleFactory
-
Same as getResouceBundle(name, locale, null)
.
- getResourceBundle(String, Locale, ClassLoader) - Static method in class net.sf.basedb.util.resources.ResourceBundleFactory
-
Get a resource bundle for the given locale.
- getResourceBundle() - Method in class net.sf.basedb.util.resources.ResourceBundleWrapper
-
Get access to the underlying resource bundle.
- getResources(String) - Method in class net.sf.basedb.util.JarClassLoader
-
- getResponseImpl() - Method in class net.sf.basedb.core.PluginResponse
-
Get a new reponse object.
- getRestriction(Expression, Expression) - Method in enum net.sf.basedb.core.Operator
-
- getRestriction(Expression, Expression[]) - Method in enum net.sf.basedb.core.Operator
-
- getRestriction(DbControl, EntityQuery) - Method in class net.sf.basedb.core.PropertyFilter
-
Create a restriction from the filter.
- getRestrictionSql(Query, DbControl) - Method in class net.sf.basedb.core.AnnotationBetweenRestriction
-
- getRestrictionSql(Query, DbControl) - Method in class net.sf.basedb.core.AnnotationInRestriction
-
- getRestrictionSql(Query, DbControl) - Method in class net.sf.basedb.core.AnnotationRestriction
-
Get an SQL fragment that includes the actual restriction.
- getRestrictionSql(Query, DbControl) - Method in class net.sf.basedb.core.AnnotationSimpleRestriction
-
- getRestrictionSql(Query, DbControl) - Method in class net.sf.basedb.core.HasAnnotationRestriction
-
- getResult(ResultSet) - Method in class net.sf.basedb.core.AbstractSqlQuery.CountWork
-
- getResult(ResultSet) - Method in class net.sf.basedb.core.hibernate.ResultSetWork
-
This method needs to be overridden by subclasses to extract the
result from the
ResultSet
.
- getResultIntensityTransform() - Method in class net.sf.basedb.core.data.FormulaData
-
A flag indicating what kind of result spot data this formula
generates, or null if it generates the same kind of data that
is used as source.
0 = no transformation; 1 = 2-log; 2 = 10-log
- getResultIntensityTransform() - Method in class net.sf.basedb.core.Formula
-
Get the spot intensity transformation that this formula
generates.
- getResults(ExtensionsFile) - Method in class net.sf.basedb.util.extensions.manager.ProcessResults
-
Get the results for a specific extensions file.
- getResync() - Method in class net.sf.basedb.util.annotations.InheritSpecification
-
- getReturnAliases() - Method in class net.sf.basedb.core.hibernate.QueryWrapper
-
- getReturnType() - Method in class net.sf.basedb.core.ExtendedPropertyAccessor.GetterSetter
-
Always return null.
- getReturnTypes() - Method in class net.sf.basedb.core.hibernate.QueryWrapper
-
- getReverseDirection() - Method in enum net.sf.basedb.core.ItemContext.SortDirection
-
Get the reverse sort direction.
- getRole() - Method in class net.sf.basedb.core.BioPlateEventParticipant
-
Get the role that the plate has in this event.
- getRole() - Method in class net.sf.basedb.core.data.BioPlateEventParticipantData
-
Get the role of the plate in the event.
- getRoleId() - Method in class net.sf.basedb.core.data.keyring.RoleKeys
-
Get the id of the role.
- getRoleId() - Method in class net.sf.basedb.core.data.keyring.UserRoles
-
Get the id of the role.
- getRoleKeyId(Item) - Static method in class net.sf.basedb.core.SystemItems
-
Get the numeric id for a
RoleKey
when you know the
Item
type of the RoleKey.
- getRolePermissions(Item) - Method in class net.sf.basedb.core.InternalJobQueue.JobQueueKeyring
-
- getRolePermissions(Item) - Method in class net.sf.basedb.core.InternalStorageController.StorageKeyring
-
- getRolePermissions(Item) - Method in class net.sf.basedb.core.Job.SignalKeyring
-
- getRolePermissions(Item) - Method in class net.sf.basedb.core.Keyring
-
Get the logged in user's permission to an unspecified item
of a certain
Item
type.
- getRolePermissions(Item) - Method in class net.sf.basedb.core.ServiceSessionControl.ServicesKeyring
-
- getRolePermissions(Item) - Method in class net.sf.basedb.core.SessionControl
-
Get all role-based permissions for the specified type of items.
- getRoles() - Method in class net.sf.basedb.core.data.RoleKeyData
-
Get the map that manages which roles that have permissions
for this key.
- getRoles() - Method in class net.sf.basedb.core.data.UserData
-
This is the inverse end.
- getRoles() - Method in class net.sf.basedb.core.InternalJobQueue.JobQueueKeyring
-
Return empty set.
- getRoles() - Method in class net.sf.basedb.core.InternalStorageController.StorageKeyring
-
Return empty set.
- getRoles() - Method in class net.sf.basedb.core.Job.SignalKeyring
-
Return empty set.
- getRoles() - Method in class net.sf.basedb.core.Keyring
-
- getRoles() - Method in class net.sf.basedb.core.ServiceSessionControl.ServicesKeyring
-
Return empty set.
- getRoles() - Method in class net.sf.basedb.core.SessionControl
-
- getRoles() - Method in class net.sf.basedb.core.User
-
Get a query that returns the roles where this user is a
member.
- getRoot() - Method in class net.sf.basedb.clients.web.extensions.JspContext
-
Get the URL to the web application root as a string.
- getRoot() - Method in class net.sf.basedb.clients.web.taglib.menu.Menu
-
- getRoot() - Method in class net.sf.basedb.clients.web.taglib.Page
-
- getRoot() - Method in class net.sf.basedb.clients.web.taglib.path.Path
-
- getRoot() - Method in class net.sf.basedb.clients.web.taglib.PropertyValue
-
- getRoot() - Method in class net.sf.basedb.util.extensions.xml.PathConverter
-
Get the value of the root path.
- getRootAlias() - Method in class net.sf.basedb.core.AbstractHqlQuery
-
The alias of the item that is the root of this query.
- getRootAlias() - Method in class net.sf.basedb.core.DynamicQuery
-
The alias of the item that is returned by this query.
- getRootAlias() - Method in class net.sf.basedb.core.DynamicRawDataQuery
-
The alias of the item that is returned by this query.
- getRootAlias() - Method in class net.sf.basedb.core.DynamicReporterQuery
-
The alias of the item that is returned by this query.
- getRootAlias() - Method in interface net.sf.basedb.core.query.Query
-
The alias of the root-entity
in the FROM
part.
- getRootDerivedBioAssays() - Method in class net.sf.basedb.core.data.PhysicalBioAssayData
-
This is the inverse end with an extra restriction
- getRootDerivedBioAssays() - Method in class net.sf.basedb.core.PhysicalBioAssay
-
Get a query that returns all root derived bioassay created from this
physical bioassay.
- getRootEntry() - Method in class net.sf.basedb.util.Tree
-
Get the entry for the root node.
- getRootItem() - Method in class net.sf.basedb.util.overview.GenericOverview
-
Get the root item of this overview.
- getRootNode() - Method in class net.sf.basedb.util.overview.GenericOverview
-
Get the root node.
- getRootPath() - Method in class net.sf.basedb.core.data.FileServerData
-
Get the root path that must be added to all URI:s using this file server.
- getRootPath() - Method in class net.sf.basedb.core.FileServer
-
- getRootPath(DbControl) - Method in class net.sf.basedb.plugins.batchimport.FileImporter
-
- getRootPath() - Method in class net.sf.basedb.util.uri.ConnectionParameters
-
Get the root path that must be added to all URI:s used with these
connection parameters.
- getRootRawBioAssay(RawBioAssay) - Method in class net.sf.basedb.core.Experiment
-
Get the root raw bioassay that represents the given raw bioassay
in this experiment.
- getRootRawBioAssays() - Method in class net.sf.basedb.core.BioAssay
-
- getRootRawBioAssays() - Method in class net.sf.basedb.core.data.ExperimentData
-
Manages which raw bioassays are available in the experiment.
- getRootRawBioAssays() - Method in class net.sf.basedb.core.Experiment
-
Get a query that returns the root raw bioassays used in this
experiment.
- getRootTable() - Method in class net.sf.basedb.core.DynamicQuery
-
- getRootTable() - Method in class net.sf.basedb.core.DynamicRawDataQuery
-
- getRootTransformations() - Method in class net.sf.basedb.core.Experiment
-
Get a query that return all root transformations in this
experiment.
- getRootType() - Method in class net.sf.basedb.core.AbstractEntityQuery
-
- getRootType() - Method in interface net.sf.basedb.core.query.EntityQuery
-
The type of items that is the root of the query.
- getRow() - Method in class net.sf.basedb.clients.web.taglib.table.PropertyFilter
-
- getRow() - Method in class net.sf.basedb.core.BioWell
-
Gets the row index where this well is located.
- getRow() - Method in class net.sf.basedb.core.data.BioWellData
-
The row coordinate of this well.
- getRow() - Method in class net.sf.basedb.core.data.FeatureData
-
Get the row coordinate of the feature.
- getRow() - Method in class net.sf.basedb.core.data.MappingCoordinate
-
Get the row number.
- getRow() - Method in class net.sf.basedb.core.data.PlateCoordinate
-
Get the row number.
- getRow() - Method in class net.sf.basedb.core.data.RawData
-
- getRow() - Method in class net.sf.basedb.core.data.WellData
-
The row coordinate of this well.
- getRow() - Method in class net.sf.basedb.core.FeatureCoordinate
-
- getRow() - Method in class net.sf.basedb.core.Well
-
Get the row coordinate of this well on the plate.
- getRowById(int) - Method in class net.sf.basedb.util.bfs.AnnotationModel
-
- getRowByIndex(int) - Method in class net.sf.basedb.util.bfs.AnnotationModel
-
- getRowByIndex(int) - Method in class net.sf.basedb.util.bfs.MatrixModel
-
- getRowCount(DbEngine, Connection, boolean) - Method in class net.sf.basedb.core.dbengine.TableInfo
-
Count the number of rows in the table.
- getRowCount() - Method in class net.sf.basedb.util.bfs.AnnotationModel
-
Get the number of rows.
- getRowCount() - Method in class net.sf.basedb.util.bfs.MatrixModel
-
Get the number of rows.
- getRowId(int) - Method in class net.sf.basedb.util.bfs.AnnotationModel
-
Get the row id for a given row.
- getRowIndex() - Method in class net.sf.basedb.core.PropertyFilter
-
Get the filter row index this filter is part of.
- getRowIndex(int) - Method in class net.sf.basedb.util.bfs.AnnotationModel
-
Get the row index for a given row id.
- getRows() - Method in class net.sf.basedb.core.BioPlate
-
Get the number of rows on this plate.
- getRows() - Method in class net.sf.basedb.core.data.PlateGeometryData
-
The number of rows in this geometry.
- getRows() - Method in class net.sf.basedb.core.PlateGeometry
-
Get the number of rows in this geometry.
- getRowSelectionForLimitHandler() - Method in class net.sf.basedb.core.AbstractSqlQuery
-
Get a RowSelection object to be used with a LimitHandler so
that it can modify and add parameters to the SQL.
- getRowsperpage() - Method in class net.sf.basedb.clients.web.taglib.table.Navigator
-
- getRowsPerPage() - Method in class net.sf.basedb.core.data.ContextData
-
Get the number of rows that are displayed on each table page.
- getRowsPerPage() - Method in class net.sf.basedb.core.ItemContext
-
Get the number of rows the current table page is displaying.
- getRunningJobs() - Method in class net.sf.basedb.clients.jobagent.Agent
-
Get a set containing the ID:s of the jobs that are currently
beeing executed by this job agent.
- getSafeRawDataType(String) - Static method in class net.sf.basedb.core.RawDataTypes
-
Get a information about a raw data type or throw an exception if the
raw data type is not found.
- getSameUnitsParameter() - Method in class net.sf.basedb.clients.web.plugins.SimpleExport
-
- getSamples() - Method in class net.sf.basedb.core.BioSource
-
Get a query that returns all samples created from this biosource.
- getSaveAsParameter(String, String, String, boolean) - Method in class net.sf.basedb.core.plugin.AbstractExporterPlugin
-
Get a plugin parameter that asks for the path to a file where the exported
data should be saved.
- getSaveAsPath(DbControl) - Method in class net.sf.basedb.core.plugin.AbstractExporterPlugin
-
Get the configured path where the exported data should be saved.
- getSaveTo() - Method in class net.sf.basedb.core.plugin.AbstractExporterPlugin
-
Get the file object that the current export is writing to.
- getSc() - Method in class net.sf.basedb.clients.web.taglib.table.Table
-
- getScale(SessionControl) - Static method in class net.sf.basedb.clients.web.Base
-
Get the display scale setting.
- getScheduled() - Method in class net.sf.basedb.core.data.JobData
-
Get the date and time the job was scheduled to the job queue, or null
if it hasn't been scheduled yet.
- getScheduled() - Method in class net.sf.basedb.core.Job
-
Get the date and time the job was scheduled to the job queue.
- getScheduler() - Static method in class net.sf.basedb.core.Application
-
Get a scheduler that can be used for registering
TimerTask
for executions.
- getSchema() - Method in class net.sf.basedb.core.hibernate.SessionFactoryConfiguration
-
Deprecated.
Get the schema.
- getSchema() - Method in class net.sf.basedb.core.ServiceSessionControl.SessionFactoryConfiguration
-
Get the schema.
- getSchemaName(String, String) - Method in class net.sf.basedb.core.dbengine.AbstractDbEngine
-
Return the schema name.
- getSchemaName(String, String) - Method in interface net.sf.basedb.core.dbengine.DbEngine
-
Get the schema name to use for referencing the given catalog/schema
pair.
- getSchemaName(String, String) - Method in class net.sf.basedb.core.dbengine.MySQLEngine
-
Return null.
- getSchemaValidatedXML(URL, String...) - Static method in class net.sf.basedb.util.XmlUtil2
-
Validate an XML file using XML schemas.
- getSchemaValidatedXML(InputStream, String, String...) - Static method in class net.sf.basedb.util.XmlUtil2
-
Validate an XML input stream using XML schemas.
- getSchemaVersion() - Static method in class net.sf.basedb.core.Application
-
Get the current database schema version number.
- getSchemaVersion() - Method in class net.sf.basedb.core.data.SchemaVersionData
-
The current schema version.
- getSchemaVersion() - Method in class net.sf.basedb.core.hibernate.SessionFactoryConfiguration
-
Deprecated.
Get the schema version of the current configuration.
- getSchemaVersion() - Method in class net.sf.basedb.core.ServiceSessionControl.SessionFactoryConfiguration
-
Get the schema version of the current configuration.
- getSchemaVersion(Session, String) - Static method in class net.sf.basedb.core.Update
-
- getSchemaVersionInTransaction(Session, String) - Static method in class net.sf.basedb.core.Update
-
Get the current schema version number as it is stored in the database.
- getScore() - Method in class net.sf.basedb.core.data.ReporterListScoreData
-
Get the score for the reporter, or null if no score has been set.
- getScore(ReporterData) - Method in class net.sf.basedb.core.ReporterList
-
Get the score for the specified reporter.
- getScore() - Method in class net.sf.basedb.core.ReporterScore
-
Get the score for this reporter or null if no score has been set.
- getScore() - Method in class net.sf.basedb.util.fuzzy.StringMatcher.FuzzyMatch
-
Get the similarity score of the key/value strings.
- getScore(String, String) - Method in class net.sf.basedb.util.fuzzy.StringMatcher
-
Get the similarity score of two strings.
- getScripts() - Method in class net.sf.basedb.clients.web.extensions.AbstractJspFactory
-
Get a set with all script references.
- getScripts() - Method in class net.sf.basedb.clients.web.extensions.JspContext
-
Get all scripts that has been added to this context.
- getScripts() - Method in class net.sf.basedb.clients.web.taglib.Head
-
- getSecondaryLocation() - Method in class net.sf.basedb.core.data.QuotaTypeData
-
If this quota type can use disk quota in the secondary location or not.
- getSecondaryStorageController() - Static method in class net.sf.basedb.core.Application
-
Get an object of the class that is used for seconary storage handling.
- getSection() - Method in class net.sf.basedb.core.BioPlate
-
Get the section within the "storage location" for this bioplate.
- getSection() - Method in class net.sf.basedb.core.data.BioPlateData
-
Get the section in the storage location were the bioplate is stored.
- getSection(int) - Method in class net.sf.basedb.util.bfs.MetadataModel
-
Get the section at a given index.
- getSection(String) - Method in class net.sf.basedb.util.bfs.MetadataModel
-
Get the first section with a given name.
- getSectionCount(String) - Method in class net.sf.basedb.util.basefile.BaseFileParser
-
The number of times we have seen a certain section in the
file.
- getSectionCount() - Method in class net.sf.basedb.util.bfs.MetadataModel
-
Get the number of sections.
- getSectionCount() - Method in class net.sf.basedb.util.bfs.MetadataWriter
-
Get the number of sections that has been written to this
file so far.
- getSectionParser(String) - Method in class net.sf.basedb.util.basefile.BaseFileParser
-
Get the parser that is currently registered for a section.
- getSelectdefault() - Method in class net.sf.basedb.clients.web.taglib.Select
-
- getSelected() - Method in class net.sf.basedb.core.ItemContext
-
Get a Set
object to specify the ID:s of all items that are
currently selected.
- getSelectedColumns(ItemContext, List<TableColumn>, boolean) - Static method in class net.sf.basedb.clients.web.DynamicUtil
-
- getSelectrecent() - Method in class net.sf.basedb.clients.web.taglib.Select
-
- getSelects() - Method in class net.sf.basedb.core.AbstractQuery
-
Get all non-permanent selects.
- getSender() - Method in class net.sf.basedb.core.Message
-
Get the user that sent this message.
- getSendMessage() - Method in class net.sf.basedb.core.data.JobData
-
If the core should send a message to the owner when the job is finished
or not.
- getSendMessage() - Method in class net.sf.basedb.core.Job
-
If a message should be sent to the owner once the job has finished
or not.
- getSendMessagesAsEmail() - Method in class net.sf.basedb.core.data.UserData
-
If this flag is set, all messages to this user are sent as an email
also, but only if: the server admin has configured an outgoing smtp
server and the user has supplied a valid email address.
- getSendMessagesAsEmail() - Method in class net.sf.basedb.core.User
-
If this flag has been set, messges to the user is also sent as an
email.
- getSeparator() - Method in class net.sf.basedb.clients.web.taglib.path.Path
-
- getSeparator() - Method in class net.sf.basedb.clients.web.taglib.table.CellValue
-
- getSeriesCount() - Method in class net.sf.basedb.util.plot.HistogramPlot.HistogramDataset
-
- getSeriesKey(int) - Method in class net.sf.basedb.util.plot.HistogramPlot.HistogramDataset
-
- getServer() - Method in class net.sf.basedb.core.data.JobAgentData
-
Get the server name or ip that this jobagent is running on.
- getServer() - Method in class net.sf.basedb.core.data.JobData
-
The name of the server where the job is executing.
- getServer() - Method in class net.sf.basedb.core.Job
-
Get the name of the server where the job is executing.
- getServer() - Method in class net.sf.basedb.core.JobAgent
-
Get the name or IP-adress of the server were the job agent is running.
- getServerAliases(String, Principal[]) - Method in class net.sf.basedb.util.ssl.StaticKeyManager
-
- getServerAndNode() - Method in class net.sf.basedb.core.Job
-
Utility method for getting both the server and node as a single string
(for display purposes).
- getServerCertificate() - Method in class net.sf.basedb.core.data.FileServerData
-
Get the public server certificate indicating that we should trust
https connections to the server.
- getServerCertificate() - Method in class net.sf.basedb.core.FileServer
-
Get the public server certificate that indicates that we should only trust the
server if it can present a certificate that matches this.
- getServerCertificate() - Method in class net.sf.basedb.util.uri.ConnectionParameters
-
Get the public server certificate that indicates that we should only trust the
server if it can present a certificate that matches this.
- getServerInfo() - Method in class net.sf.basedb.core.File
-
- getServerName() - Method in class net.sf.basedb.clients.jobagent.Agent
-
Get the host name of the server where the job agent is running.
- getServerName() - Method in class net.sf.basedb.clients.web.taglib.Page
-
- getServerX509Certificate() - Method in class net.sf.basedb.core.FileServer
-
Get the X.509 certificate for the server.
- getServletContext() - Method in class net.sf.basedb.clients.web.extensions.ServletWrapper
-
- getServletName() - Method in class net.sf.basedb.clients.web.extensions.ServletWrapper
-
- getServletPath() - Method in class net.sf.basedb.clients.web.extensions.RequestWrapper
-
- getServlets() - Method in class net.sf.basedb.clients.web.extensions.ServletLoader
-
Get a list with all loaded servlet definitions.
- getServletUrl(String, String) - Static method in class net.sf.basedb.clients.web.extensions.ExtensionsControl
-
Get the base URL for servlets in the extension with the given ID.
- getSession(DbControl, ChangeHistory, boolean, boolean) - Static method in class net.sf.basedb.clients.web.ChangeHistoryUtil
-
Get the session in which the changes was made in HTML format.
- getSession(DbControl) - Method in class net.sf.basedb.core.ChangeHistory
-
Load the session in which the change was made.
- getSession() - Method in class net.sf.basedb.core.data.ChangeHistoryData
-
- getSession() - Method in class net.sf.basedb.core.LogControl
-
- getSessionControl() - Method in class net.sf.basedb.clients.jobagent.Agent
-
Get a session control with the configured user logged in.
- getSessionControl(PageContext, boolean) - Static method in class net.sf.basedb.clients.web.Base
-
Get a new or existing SessionControl
object
given a PageContext
.
- getSessionControl(ServletRequest, boolean) - Static method in class net.sf.basedb.clients.web.Base
-
Get a session control for the BASE web client "net.sf.basedb.clients.web".
- getSessionControl(ServletRequest, String, boolean) - Static method in class net.sf.basedb.clients.web.Base
-
Get a new or existing SessionControl
object
given a ServletRequest
instance.
- getSessionControl() - Method in class net.sf.basedb.clients.web.taglib.Page
-
- getSessionControl() - Method in class net.sf.basedb.core.AbstractBatcher
-
- getSessionControl(String, String, String, boolean) - Static method in class net.sf.basedb.core.Application
-
Get an existing SessionControl
object if you know
the id.
- getSessionControl(String, String) - Static method in class net.sf.basedb.core.Application
-
- getSessionControl() - Method in class net.sf.basedb.core.BasicItem
-
- getSessionControl() - Method in class net.sf.basedb.core.DbControl
-
- getSessionControl() - Method in class net.sf.basedb.core.PluginRequest
-
- getSessionControl() - Method in class net.sf.basedb.util.extensions.ClientContext
-
Get the current session control.
- getSessionFactory() - Method in class net.sf.basedb.core.hibernate.SessionWrapper
-
- getSessionFactory() - Static method in class net.sf.basedb.core.HibernateUtil
-
Get the configured session factory.
- getSessionId() - Method in class net.sf.basedb.core.ChangeHistory
-
Get the ID of the session in which the change was made.
- getSessionId() - Method in class net.sf.basedb.core.data.ChangeHistoryData
-
The ID of the session in which the changes happened.
- getSessionId() - Method in class net.sf.basedb.core.log.TransactionDetails
-
Get the ID of the session or 0 if no user is logged in.
- getSessions() - Method in class net.sf.basedb.core.data.ClientData
-
This is the invers end.
- getSessions() - Method in class net.sf.basedb.core.data.UserData
-
This is the inverse end.
- getSessionSetting(String) - Method in class net.sf.basedb.core.SessionControl
-
Get the value of a session setting with the specified name.
- getSetParameterMethod(Class<?>) - Method in class net.sf.basedb.util.extensions.xml.XmlLoader
-
Check if the bean class has a setParameter(String, String)
method and return it's reference if it has.
- getSetter() - Method in class net.sf.basedb.core.ExtendedPropertyAccessor.GetterSetter
-
- getSetterMethod(Class<?>, String) - Method in class net.sf.basedb.util.extensions.xml.XmlLoader
-
Get the setter method for a given tag name.
- getSetterMethodNameFromTag(String) - Method in class net.sf.basedb.util.extensions.xml.XmlLoader
-
Convert the tag name to a setter method name.
- getSetting(String, String) - Method in class net.sf.basedb.clients.web.extensions.ExtensionsControl
-
Get a configuration setting for an extension.
- getSetting(String) - Method in class net.sf.basedb.core.ItemContext
-
Get a value.
- getSetting(String) - Method in class net.sf.basedb.core.Presets.Preset
-
Get the value for the setting with the specified name.
- getSetting(String, String) - Method in class net.sf.basedb.util.extensions.manager.Settings
-
Get a configuration setting for an extension.
- getSettings() - Method in class net.sf.basedb.core.data.ContextData
-
Get a map for other settings.
- getSettings(PluginDefinition, boolean) - Method in class net.sf.basedb.core.JobAgent
-
Get the settings for the specified plugin.
- getSettings(Job) - Method in class net.sf.basedb.core.JobAgent
-
Get the settings for the plugin that is used for the specified job.
- getSettings() - Method in class net.sf.basedb.core.JobAgent
-
Get a query that returns all plugin-specific settings for this job agent.
- getSettings() - Method in class net.sf.basedb.util.extensions.manager.ExtensionsManager
-
Get the settings for the extension manager.
- getSettingsForExtension(String) - Method in class net.sf.basedb.util.extensions.manager.Settings
-
Get a preset containing settings for the given extesion.
- getSeverity(Validator) - Method in class net.sf.basedb.util.overview.ValidationOptions
-
- getSeverity(ValidationRuleAction) - Method in class net.sf.basedb.util.overview.ValidationOptions
-
Get the severity level for the specified validator rule.
- getShareableItems() - Static method in class net.sf.basedb.core.Metadata
-
Get a set containing all
Shareable
item types.
- getSharedParent() - Method in class net.sf.basedb.core.ArrayDesignBlock
-
- getSharedParent() - Method in class net.sf.basedb.core.ArrayDesignPlate
-
- getSharedParent() - Method in class net.sf.basedb.core.BioAssay
-
Get the experiment.
- getSharedParent() - Method in class net.sf.basedb.core.BioAssaySet
-
Get the experiment.
- getSharedParent() - Method in class net.sf.basedb.core.BioMaterialEvent
-
- getSharedParent() - Method in class net.sf.basedb.core.BioPlateEventParticipant
-
- getSharedParent() - Method in class net.sf.basedb.core.BioWell
-
- getSharedParent() - Method in class net.sf.basedb.core.ChildItem
-
Get the shareable parent item of this child item.
- getSharedParent() - Method in class net.sf.basedb.core.DataCube
-
Get the experiment.
- getSharedParent() - Method in class net.sf.basedb.core.DataCubeColumn
-
Get the experiment.
- getSharedParent() - Method in class net.sf.basedb.core.DataCubeExtraValue
-
Get the experiment.
- getSharedParent() - Method in class net.sf.basedb.core.DataCubeFilter
-
Get the experiment.
- getSharedParent() - Method in class net.sf.basedb.core.DataCubeLayer
-
Get the experiment.
- getSharedParent() - Method in class net.sf.basedb.core.ExtraValue
-
Get the experiment.
- getSharedParent() - Method in class net.sf.basedb.core.Help
-
- getSharedParent() - Method in class net.sf.basedb.core.JobAgentSettings
-
- getSharedParent() - Method in class net.sf.basedb.core.PlateEvent
-
- getSharedParent() - Method in class net.sf.basedb.core.PlateEventType
-
- getSharedParent() - Method in class net.sf.basedb.core.RootRawBioAssay
-
Get the experiment.
- getSharedParent() - Method in class net.sf.basedb.core.SpotImages
-
- getSharedParent() - Method in class net.sf.basedb.core.SyncFilter
-
- getSharedParent() - Method in class net.sf.basedb.core.Transformation
-
Get the experiment.
- getSharedParent() - Method in class net.sf.basedb.core.VirtualDb
-
Get the experiment.
- getSharedParent() - Method in class net.sf.basedb.core.Well
-
- getSharedPermissions(ShareableData) - Method in class net.sf.basedb.core.InternalJobQueue.JobQueueKeyring
-
Return 0.
- getSharedPermissions(ShareableData) - Method in class net.sf.basedb.core.InternalStorageController.StorageKeyring
-
Return 0.
- getSharedPermissions(ShareableData) - Method in class net.sf.basedb.core.Job.SignalKeyring
-
Return 0.
- getSharedPermissions(ShareableData) - Method in class net.sf.basedb.core.Keyring
-
- getSharedPermissions(ShareableData) - Method in class net.sf.basedb.core.ServiceSessionControl.ServicesKeyring
-
Return 0.
- getSharedPermissions(ShareableData) - Method in class net.sf.basedb.core.SessionControl
-
- getSharedTo(DbControl, SharedItem) - Static method in class net.sf.basedb.util.ShareableUtil
-
Gets a list with the projects, groups and users(in that order) that
an item is shared to.
- getShareToEveryOneKey(DbControl, Permission) - Static method in class net.sf.basedb.core.ItemKey
-
Get a key that can be used to share items to the EVERYONE group with the
given permissions.
- getShort(int) - Method in class net.sf.basedb.clients.web.servlet.PlotServlet.CFSqlResult
-
- getShort(int) - Method in class net.sf.basedb.core.DynamicResultIterator.SqlResultImpl
-
- getShort(int) - Method in interface net.sf.basedb.core.query.SqlResult
-
Get the value of the specified column as a short.
- getShortEntityName(String) - Static method in class net.sf.basedb.core.HibernateUtil
-
Removes the package name part of a class name and any ending 'Data'.
- getShortName() - Method in class net.sf.basedb.plugins.executor.AbstractIOSupport
-
A default implementation to maintain backwards compatibility.
- getShortName() - Method in class net.sf.basedb.plugins.executor.BaseFileExporterSupport
-
- getShortName() - Method in class net.sf.basedb.plugins.executor.BaseFileImporterSupport
-
- getShortName() - Method in class net.sf.basedb.plugins.executor.BfsExporterSupport
-
- getShortName() - Method in class net.sf.basedb.plugins.executor.BfsImporterSupport
-
- getShortName() - Method in class net.sf.basedb.plugins.executor.FileOnlyImporterSupport
-
- getShortName() - Method in interface net.sf.basedb.plugins.executor.IOSupport
-
Get a short name of the plug-in.
- getShortPermissions(Identifiable) - Static method in class net.sf.basedb.clients.web.PermissionUtil
-
- getShow() - Method in class net.sf.basedb.clients.web.taglib.table.ColumnDef
-
- getShow() - Method in class net.sf.basedb.clients.web.taglib.table.TableColumn
-
- getShowClazz() - Method in class net.sf.basedb.clients.web.extensions.section.IncludeContentSectionFactory.Section
-
- getShowClazz() - Method in interface net.sf.basedb.clients.web.extensions.section.SectionAction
-
Additional class attribute of the main section tag that is used
when the section is visible.
- getShowClazz() - Method in class net.sf.basedb.clients.web.extensions.section.SectionBean
-
- getShowclazz() - Method in class net.sf.basedb.clients.web.taglib.HideableSection
-
- getSignal(String) - Static method in class net.sf.basedb.core.signal.Signal
-
Get the signal with a given ID.
- getSignal() - Method in exception net.sf.basedb.core.signal.UnsupportedSignalException
-
Get the signal that is not supported.
- getSignalHandler() - Method in class net.sf.basedb.clients.web.plugins.SimpleExport
-
- getSignalHandler(String) - Method in class net.sf.basedb.core.signal.AbstractSignalReceiver
-
Get the signal handler with a given ID.
- getSignalHandler() - Method in interface net.sf.basedb.core.signal.SignalTarget
-
Get the signal handler that is handling signals on behalf of this
object.
- getSignalHandler() - Method in class net.sf.basedb.plugins.AbstractFlatFileImporter
-
- getSignalHandler() - Method in class net.sf.basedb.plugins.Base1PluginExecuter
-
- getSignalHandler() - Method in class net.sf.basedb.plugins.BaseFileExporterPlugin
-
- getSignalHandler() - Method in class net.sf.basedb.plugins.BfsExporterPlugin
-
- getSignalHandler() - Method in class net.sf.basedb.plugins.CdfFileReporterImporter
-
- getSignalHandler() - Method in class net.sf.basedb.plugins.CloneReportersPlugin
-
- getSignalHandler() - Method in class net.sf.basedb.plugins.executor.ExternalProgramExecutor
-
- getSignalHandler() - Method in class net.sf.basedb.plugins.FormulaFilter
-
- getSignalHandler() - Method in class net.sf.basedb.plugins.GalExporter
-
- getSignalHandler() - Method in class net.sf.basedb.plugins.HelpExporter
-
- getSignalHandler() - Method in class net.sf.basedb.plugins.HelpImporter
-
- getSignalHandler() - Method in class net.sf.basedb.plugins.IntensityCalculatorPlugin
-
- getSignalHandler() - Method in class net.sf.basedb.plugins.JepExtraValueCalculator
-
- getSignalHandler() - Method in class net.sf.basedb.plugins.JepIntensityTransformer
-
- getSignalHandler() - Method in class net.sf.basedb.plugins.LowessNormalization
-
- getSignalHandler() - Method in class net.sf.basedb.plugins.MedianRatioNormalization
-
- getSignalHandler() - Method in class net.sf.basedb.plugins.PackedFileExporter
-
- getSignalHandler() - Method in class net.sf.basedb.plugins.PlateMappingExporter
-
- getSignalHandler() - Method in class net.sf.basedb.plugins.PluginConfigurationExporter
-
- getSignalHandler() - Method in class net.sf.basedb.plugins.PluginConfigurationImporter
-
- getSignalHandler() - Method in class net.sf.basedb.plugins.SpotImageCreator
-
- getSignalHandler() - Method in class net.sf.basedb.util.zip.AbstractFileUnpacker
-
- getSignalReceiver() - Method in class net.sf.basedb.clients.jobagent.Agent
-
Get the signal receiver that is processing signal messages
on behalf of this job agent.
- getSignalReceiver() - Static method in class net.sf.basedb.core.InternalJobQueue
-
Get the signal receiver used by the internal job queue.
- getSignalReceiver(String) - Static method in class net.sf.basedb.core.signal.LocalSignalReceiver
-
Get a signal receiver with a given ID.
- getSignals() - Static method in class net.sf.basedb.core.signal.Signal
-
Get all registered signals.
- getSignals() - Method in exception net.sf.basedb.core.signal.SignalReceivedException
-
Get the signals that has been received.
- getSignalTransporter() - Method in class net.sf.basedb.core.data.JobData
-
Identifies the signal transporter to use.
- getSignalTransporter() - Method in class net.sf.basedb.core.Job
-
Create and initialise a signal transporter object that can be used
to send signal to the plug-in running this job.
- getSignalTransporterClass() - Method in class net.sf.basedb.clients.web.util.SimpleSignalProgressReporter
-
This class does not need any signal transporter.
- getSignalTransporterClass() - Method in class net.sf.basedb.core.signal.LocalSignalReceiver
-
- getSignalTransporterClass() - Method in interface net.sf.basedb.core.signal.SignalReceiver
-
Get the signal transporter class that should be used to
send signals to this receiver.
- getSignalTransporterClass() - Method in class net.sf.basedb.core.signal.SocketSignalReceiver
-
- getSignalURI() - Method in class net.sf.basedb.core.signal.AbstractSignalTransporter
-
Get the URI representation of the global signal ID.
- getSize() - Method in class net.sf.basedb.core.data.FileData
-
Get the size in bytes for this FileData
object.
- getSize() - Method in class net.sf.basedb.core.data.ItemListData
-
The number of biomaterials in the list.
- getSize() - Method in class net.sf.basedb.core.data.PhysicalBioAssayData
-
The number size of the bioassay.
- getSize() - Method in class net.sf.basedb.core.data.ReporterListData
-
The number of reporter in the list.
- getSize() - Method in class net.sf.basedb.core.dbengine.TableInfo.ColumnInfo
-
- getSize() - Method in class net.sf.basedb.core.File
-
Get the (uncompressed) size of this file.
- getSize() - Method in class net.sf.basedb.core.ItemList
-
Get the number of members in this list.
- getSize() - Method in class net.sf.basedb.core.PhysicalBioAssay
-
Get the size of the bioassay.
- getSize() - Method in class net.sf.basedb.core.ReporterList
-
Get the number of reporter in this reporter list.
- getSize() - Method in class net.sf.basedb.core.snapshot.AnnotationSetSnapshot
-
Get the number of annotations.
- getSize() - Method in class net.sf.basedb.core.VirtualColumn
-
Get the maximum size of data in the column if it is a string.
- getSize(String) - Method in class net.sf.basedb.util.bfs.BaseInputStreamLocator
-
- getSize(String) - Method in class net.sf.basedb.util.bfs.DiskInputStreamLocator
-
- getSize(String) - Method in interface net.sf.basedb.util.bfs.InputStreamLocator
-
Get the size in bytes of the given named resource.
- getSize() - Method in class net.sf.basedb.util.importer.BaseFileWrapper
-
- getSize() - Method in class net.sf.basedb.util.importer.DiskFileWrapper
-
- getSize() - Method in interface net.sf.basedb.util.importer.FileWrapper
-
Get the size of the file.
- getSize() - Method in class net.sf.basedb.util.importer.spotdata.BaseFileInfo
-
Get the file size.
- getSkinActions() - Method in class net.sf.basedb.clients.web.taglib.Page
-
Get all skin extension actions.
- getSkinContext() - Method in class net.sf.basedb.clients.web.taglib.Page
-
Get the JSP context used for invoking skin extensions.
- getSkippedLines() - Method in class net.sf.basedb.util.parser.FlatFileParser
-
- getSlot(Job) - Method in class net.sf.basedb.clients.jobagent.Agent
-
Find a free slot for executing a job.
- getSlot(Job) - Method in class net.sf.basedb.clients.jobagent.slotmanager.InternalSlotManager
-
- getSlot(Job.ExecutionTime) - Method in class net.sf.basedb.clients.jobagent.slotmanager.InternalSlotManager
-
Get a slot for a job with the given estimated execution time.
- getSlot() - Method in class net.sf.basedb.clients.jobagent.slotmanager.MasterSlotManager.RemoteSlot
-
- getSlot(Job) - Method in class net.sf.basedb.clients.jobagent.slotmanager.RemoteSlotManager
-
- getSlot(Job) - Method in interface net.sf.basedb.clients.jobagent.slotmanager.SlotManager
-
Get a slot for the specified job.
- getSlot() - Method in class net.sf.basedb.util.jobagent.JobInfo
-
Get the slot the job is using on the job agent.
- getSlotManagerClass(String) - Method in class net.sf.basedb.clients.jobagent.Agent
-
Get the class object for the configured slot manager.
- getSnapshot() - Method in class net.sf.basedb.core.snapshot.AnnotationLoaderUtil
-
- getSnapshot(DbControl, int) - Method in class net.sf.basedb.core.snapshot.SnapshotManager
-
Get the annotation snapshot for the annotation set with the given id.
- getSnapshotDate() - Method in class net.sf.basedb.core.snapshot.AnnotationSetSnapshot
-
Get the date and time this snapshot was created.
- getSnapshotManager() - Method in class net.sf.basedb.clients.web.ExperimentExplorer
-
Get the snapshot manager that is used to load annotation
values.
- getSnapshotManager() - Method in class net.sf.basedb.util.export.spotdata.AbstractBioAssaySetExporter
-
Get the current snapshot manager.
- getSnapshotManager() - Method in class net.sf.basedb.util.export.spotdata.AbstractFieldConverter
-
Get the snapshot manager to use with annotation-based fields.
- getSnapshotManager() - Method in class net.sf.basedb.util.overview.GenericOverview
-
Get the current snapshot manager.
- getSnapshotManager() - Method in interface net.sf.basedb.util.overview.OverviewContext
-
Get the snapshot manager that is used to load annotation
values.
- getSnapshots() - Method in class net.sf.basedb.core.snapshot.AnnotationLoaderUtil
-
- getSoftware() - Method in class net.sf.basedb.core.data.DerivedBioAssayData
-
Get the software used to create this bioassay set.
- getSoftware() - Method in class net.sf.basedb.core.data.RawBioAssayData
-
Get the software used to analyse the scanned image and produce the
raw data.
- getSoftware() - Method in class net.sf.basedb.core.DerivedBioAssay
-
Get the
Software
that was used when
creating this bioassay set.
- getSoftware() - Method in class net.sf.basedb.core.RawBioAssay
-
Get the
Software
used while analysing the scanned images.
- getSortable() - Method in class net.sf.basedb.clients.web.taglib.table.TableColumn
-
- getSortby() - Method in class net.sf.basedb.clients.web.taglib.table.Table
-
- getSortDirection(String) - Method in class net.sf.basedb.clients.web.taglib.table.Table
-
Get the sort direction on the given column.
- getSortDirection() - Method in class net.sf.basedb.core.data.ContextData
-
Get the sort direction, 0 = ascending, 1 = descending
- getSortDirection() - Method in class net.sf.basedb.core.ItemContext
-
If the items are sorted in ascending or descending order.
- getSortedRawDataTypes(Comparator<RawDataType>) - Static method in class net.sf.basedb.core.RawDataTypes
-
Get all raw data types sorted according to the given comparator.
- getSortOrder() - Method in class net.sf.basedb.core.ItemContext
-
Get the current sort property as an Order
instance.
- getSortProperty() - Method in class net.sf.basedb.clients.web.extensions.list.AbstractListColumnBean
-
- getSortProperty() - Method in interface net.sf.basedb.clients.web.extensions.list.ListColumnAction
-
Override the default property when this column is used for sorting.
- getSortproperty() - Method in class net.sf.basedb.clients.web.taglib.table.ColumnDef
-
- getSortProperty() - Method in class net.sf.basedb.core.data.ContextData
-
Get property name to sort on.
- getSortProperty() - Method in class net.sf.basedb.core.ItemContext
-
Get the name of the property the current listing is sorted by.
- getSource() - Method in class net.sf.basedb.core.Annotation
-
Get the annotation source.
- getSource() - Method in class net.sf.basedb.core.data.AnnotationData
-
The annotation source.
0 = primary, 1 = inherited, 2 = cloned
For primary annotations, only one annotation per annotation type is supported.
- getSource() - Method in class net.sf.basedb.core.data.annotations.AnnotationLink
-
- getSource() - Method in class net.sf.basedb.core.data.TransformationData
-
Get the source bioassayset for the transformation.
- getSource() - Method in class net.sf.basedb.core.snapshot.AnnotationSnapshot
-
Get the source of the annotation.
- getSource() - Method in class net.sf.basedb.core.Transformation
-
Get the source bioassayset used by this transformation.
- getSource() - Method in class net.sf.basedb.util.export.spotdata.AbstractBioAssaySetExporter
-
Get the source bioassay set.
- getSource() - Method in class net.sf.basedb.util.export.spotdata.AbstractFieldConverter
-
Get the source bioassay set.
- getSourceBioAssays(DbControl) - Method in class net.sf.basedb.core.plugin.AbstractAnalysisPlugin
-
Gets a list of bioassays that were selected from the current bioassay set, to use for the analysis.
- getSourceBioAssaySet(DbControl) - Method in class net.sf.basedb.core.plugin.AbstractAnalysisPlugin
-
Get the bioassay set that is used as the source for the plugin.
- getSourceBioAssaySetParameter(String, String) - Method in class net.sf.basedb.core.plugin.AbstractAnalysisPlugin
-
Get a plugin parameter that asks for a bioassay set to use as data source for
the plugin.
- getSourceBioAssaysParameter(String, String) - Method in class net.sf.basedb.core.plugin.AbstractAnalysisPlugin
-
Gets a plugin parameter that asks for a subset of bioassays to use as data source
for the plugin.
- getSourceCoordinate(MappingCoordinate) - Method in class net.sf.basedb.core.PlateMapping
-
Get the source coordinate for a given destination coordinate.
- getSourceCount() - Method in class net.sf.basedb.core.data.PlateMappingData
-
The required number of source plates.
- getSourceCount() - Method in class net.sf.basedb.core.PlateMapping
-
Get the number of required source plates.
- getSourceDerivedBioAssay(DbControl) - Method in class net.sf.basedb.core.plugin.AbstractAnalysisPlugin
-
Get the derived bioassay that is used as the source for the plugin.
- getSourceDerivedBioAssayParameter(String, String) - Method in class net.sf.basedb.core.plugin.AbstractAnalysisPlugin
-
Get a plugin parameter that asks for a derived bioassay to use as data source for
the plugin.
- getSourceFileWrapper() - Method in class net.sf.basedb.util.importer.spotdata.BaseFileImporter
-
Get the source file.
- getSourceGeometry() - Method in class net.sf.basedb.core.data.PlateMappingData
-
The required geometry of source plates in this mapping.
- getSourceGeometry() - Method in class net.sf.basedb.core.PlateMapping
-
- getSourceIndex(Plate) - Method in class net.sf.basedb.core.Plate
-
If this plate was created by a
PlateMapping
and the specified plate
is a parent, get the index of the parent plate in the list
of source plates used by the plate mapping.
- getSourceIntensityTransform() - Method in class net.sf.basedb.core.data.FormulaData
-
A flag indicating what kind of spot source data that the formula
can be used with, or null if the formula can be used with
any kind of source data.
0 = no transformation; 1 = 2-log; 2 = 10-log
- getSourceIntensityTransform() - Method in class net.sf.basedb.core.Formula
-
Get the intensity transformation that is required on spot
data if this formula should generate the correct result.
- getSourceItemMustExist() - Method in class net.sf.basedb.core.SyncFilter
-
If set, a source item that matches the filter must exist, otherwise it must
not exist.
- getSourceItemTransform() - Method in class net.sf.basedb.core.data.ItemListSyncFilterData
-
The transform to use for converting filter matches to list members.
0 = none; 1 = parent to child, 2 = child to parent
- getSourceItemTransformation() - Method in class net.sf.basedb.core.SyncFilter
-
Get the transformation to use for converting the items matching
this filter to list members.
- getSourceItemType() - Method in class net.sf.basedb.core.data.ItemListSyncFilterData
-
Get the type of items that this filter is applies to.
- getSourceItemType() - Method in class net.sf.basedb.core.SyncFilter
-
Get the source item type that this synchronization filter applies to.
- getSourceItemType() - Method in class net.sf.basedb.util.listable.AbstractSourceItemTransformer
-
- getSourceItemType() - Method in interface net.sf.basedb.util.listable.SourceItemTransformer
-
Get the item type of the source items.
- getSourceItemType() - Method in class net.sf.basedb.util.listable.SourceItemTransformerChain
-
Get the source item type of the first step in the chain.
- getSourceMustExist() - Method in class net.sf.basedb.core.data.ItemListSyncFilterData
-
If set, the source item must exist, otherwise it must not exist.
- getSources() - Method in class net.sf.basedb.core.BioMaterialEvent
-
Get a query that return all biomaterials used as sources
for this event.
- getSources() - Method in class net.sf.basedb.core.data.BioMaterialEventData
-
Get a map containing information about the source biomaterials used
in the event.
- getSpacingX() - Method in class net.sf.basedb.core.ArrayDesignBlock
-
Get the x spacing between the spots in the slide.
- getSpacingX() - Method in class net.sf.basedb.core.data.ArrayDesignBlockData
-
Get the x spacing.
- getSpacingX() - Method in class net.sf.basedb.plugins.PrintMapFlatFileImporter.MetaBlock
-
- getSpacingY() - Method in class net.sf.basedb.core.ArrayDesignBlock
-
Get the y spacing between the spots in the slide.
- getSpacingY() - Method in class net.sf.basedb.core.data.ArrayDesignBlockData
-
Get the y spacing.
- getSpacingY() - Method in class net.sf.basedb.plugins.PrintMapFlatFileImporter.MetaBlock
-
- getSpotBatcher() - Method in class net.sf.basedb.core.BioAssaySet
-
Get a batcher used to insert spot data for this bioassayset.
- getSpotCount(int) - Method in class net.sf.basedb.core.BioAssaySet
-
Get the number of spots in a single bioassay.
- getSpotData() - Method in class net.sf.basedb.core.BioAssay
-
Get a query that returns spot data for this bioassay.
- getSpotData() - Method in class net.sf.basedb.core.BioAssaySet
-
Get a query that returns spot data for this bioassayset.
- getSpotExtraValueBatcher(Class<I>, ExtraValueType, Job) - Method in class net.sf.basedb.core.BioAssaySet
-
Get a batcher that is used to insert extra values per spot of the specified type.
- getSpotField(String, boolean) - Method in class net.sf.basedb.util.export.spotdata.AdvancedFieldConverter
-
- getSpotField(String, boolean) - Method in class net.sf.basedb.util.export.spotdata.Base1FieldConverter
-
Convert a spot field.
- getSpotField(String, boolean) - Method in interface net.sf.basedb.util.export.spotdata.ExportableFieldConverter
-
Create a spot dynamic field for the given name.
- getSpotField(String, boolean) - Method in class net.sf.basedb.util.export.spotdata.StandardFieldConverter
-
Find a spot dynamic field.
- getSpotFields(BioAssaySet) - Method in class net.sf.basedb.plugins.BaseFileExporterPlugin
-
- getSpotFields(BioAssaySet) - Method in class net.sf.basedb.plugins.BfsExporterPlugin
-
- getSpotFields() - Method in class net.sf.basedb.util.export.spotdata.AbstractBioAssaySetExporter
-
Get the list of registered spot fields, in the order they were
registered.
- getSpotFields() - Method in class net.sf.basedb.util.export.spotdata.BaseFileExporter
-
- getSpotFields() - Method in class net.sf.basedb.util.export.spotdata.BfsExporter
-
- getSpotImage(RawData) - Method in class net.sf.basedb.core.SpotImages
-
Get a spot as a PNG image.
- getSpotImages() - Method in class net.sf.basedb.core.data.RawBioAssayData
-
Get the settings used for generating spot images for this raw bio assay.
- getSpotImages() - Method in class net.sf.basedb.core.RawBioAssay
-
Get the
SpotImages
item used to generate spot images
for this raw bioassay.
- getSpotImages(List<RawData>) - Method in class net.sf.basedb.core.SpotImages
-
Get a list of spot PNG images from a list of RawData
.
- getSpotImagesFile() - Method in class net.sf.basedb.core.data.SpotImagesData
-
The file containing the spot images.
- getSpotImagesFile() - Method in class net.sf.basedb.core.SpotImages
-
Get the file which holds the spot images.
- getSpotIntensityParser() - Method in class net.sf.basedb.util.importer.spotdata.BaseFileInfo.SpotSectionInfo
-
Get the spot intensity parser that should be used for
parsing spot intensities in this section.
- getSpotQuery(DbControl, int, int, List<TableColumn>) - Method in class net.sf.basedb.clients.web.ExperimentExplorer
-
Get a query returning spot data for a given reporter and position.
- getSpotQuery(boolean) - Method in class net.sf.basedb.util.export.spotdata.AbstractBioAssaySetExporter
-
- getSpots() - Method in class net.sf.basedb.core.data.RawBioAssayData
-
The number of data spots in this raw bio assay, that
are stored in the database.
- getSpots() - Method in class net.sf.basedb.core.RawBioAssay
-
Utility method that either returns the number of db spots
or the number of file spots.
- getSpotSectionInfo(int) - Method in class net.sf.basedb.util.importer.spotdata.BaseFileInfo
-
Get information about a spot section.
- getSpotsize() - Method in class net.sf.basedb.core.data.SpotImagesData
-
The size of the spots.
- getSpotsize() - Method in class net.sf.basedb.core.SpotImages
-
Get the size of the spots in pixels.
- getSql() - Method in class net.sf.basedb.core.AnnotationBatcher.InsertBatcher
-
The SQL statement this batcher is executing.
- getSql() - Method in class net.sf.basedb.core.AnnotationBatcher.UpdateBatcher
-
The SQL statement this batcher is executing.
- getSql() - Method in class net.sf.basedb.core.hibernate.ResultSetWork
-
The sql that is executed by this work.
- getSql() - Method in class net.sf.basedb.core.hibernate.SchemaGenerator.CollectSqlTarget
-
- getSqlSymbol() - Method in enum net.sf.basedb.core.Operator
-
Get the SQL symbol for this operator.
- getSqlType() - Method in class net.sf.basedb.core.dbengine.TableInfo.ColumnInfo
-
- getSQLType() - Method in class net.sf.basedb.core.hibernate.TypeWrapper
-
Get the SQL code for database columns that can store this type.
- getSQLType() - Method in enum net.sf.basedb.core.Type
-
Get the type of this parameter as specified by the
java.sql.Types
class.
- getSqlTypeCode() - Method in class net.sf.basedb.core.BatchedPropertyInfo
-
Get the sql type code as defined by
Types
.
- getSqrt() - Method in class net.sf.basedb.core.query.QuadraticMeanExpression
-
- getSshFingerprint() - Method in class net.sf.basedb.core.data.FileServerData
-
Get the fingerprint of the SSH public key for the server
that must be verified when (if) it is accessed via the SSH protocol.
- getSshFingerprint() - Method in class net.sf.basedb.core.FileServer
-
- getSshFingerprint() - Method in class net.sf.basedb.util.uri.ConnectionParameters
-
Get the SSH fingerprint of the server.
- getSSLContext(byte[], byte[], String) - Static method in class net.sf.basedb.util.ssl.SSLUtil2
-
Create a SSL context that optionally uses the given trusted server certificate
and client certificate.
- getSSLSocketFactory() - Static method in class net.sf.basedb.util.ssl.SSLUtil2
-
Get a SSL Socket Factory object that is used to create SSL sockets.
- getSSLSocketFactory(byte[], byte[], String) - Static method in class net.sf.basedb.util.ssl.SSLUtil2
-
Create a SSL socket factory that optionally uses the given trusted server certificate
and client certificate.
- getSSLSocketFactory2() - Method in class net.sf.basedb.core.FileServer
-
Get a socket factory that can be used to create SSL connections to the given
server.
- getStackTrace() - Method in class net.sf.basedb.core.data.JobData
-
Get the stack trace in case of an error
- getStackTrace() - Method in class net.sf.basedb.core.Job
-
Get the stack trace in case the job ended with an error
- getStartDate() - Method in class net.sf.basedb.core.data.NewsData
-
Get the first day this news item should be shown.
- getStartDate() - Method in class net.sf.basedb.core.News
-
Get the start date and time for this news item to be published.
- getStarted() - Method in class net.sf.basedb.core.data.JobData
-
Get the date and time the job was started or null if the job hasn't been started.
- getStarted() - Method in class net.sf.basedb.core.Job
-
Get the date and time the job was started.
- getStartTime() - Method in class net.sf.basedb.util.extensions.manager.ProcessResults
-
Get the start time of the scan as a millisecond value.
- getStartX() - Method in class net.sf.basedb.util.plot.HistogramPlot.HistogramBin
-
- getStartX(int, int) - Method in class net.sf.basedb.util.plot.HistogramPlot.HistogramDataset
-
- getStartXValue(int, int) - Method in class net.sf.basedb.util.plot.HistogramPlot.HistogramDataset
-
- getStartY(int, int) - Method in class net.sf.basedb.util.plot.HistogramPlot.HistogramDataset
-
- getStartYValue(int, int) - Method in class net.sf.basedb.util.plot.HistogramPlot.HistogramDataset
-
- getState() - Method in class net.sf.basedb.core.log.EntityDetails
-
Get an array with the current state of the entity.
- getState() - Method in class net.sf.basedb.core.plugin.NamespaceRequestWrapper
-
- getState() - Method in interface net.sf.basedb.core.plugin.Request
-
- getState() - Method in class net.sf.basedb.core.PluginRequest.RequestImpl
-
- getState() - Method in class net.sf.basedb.core.PluginResponse
-
Get the state information that the plug-in wants to save
until it is restarted again.
- getState() - Method in class net.sf.basedb.plugins.executor.ExternalProgramExecutor.RequestWrapper
-
- getStatelessSession() - Method in class net.sf.basedb.core.DbControl
-
Get a stateless Hibernate session using the same database connection as
the regular session.
- getStaticCache() - Static method in class net.sf.basedb.core.Application
-
Get the static cache mananger.
- getStaticRules() - Static method in class net.sf.basedb.util.overview.OverviewUtil
-
Get all static (built-in) validation rules grouped by relationship.
- getStatistics(String) - Method in class net.sf.basedb.clients.web.ExperimentExplorer.AnnotationGroup
-
- getStatistics(DbControl) - Static method in class net.sf.basedb.core.DiskUsage
-
- getStatistics() - Method in class net.sf.basedb.core.hibernate.SessionWrapper
-
- getStatus() - Method in class net.sf.basedb.clients.jobagent.AgentController
-
Get status info about running job agent by sending an info request to the agents r
emote control service.
- getStatus() - Method in class net.sf.basedb.core.data.JobData
-
Get the status of the job. 1 = waiting, 2 = running, 3 = completed ok, 4 = error
- getStatus() - Method in class net.sf.basedb.core.Job
-
Get the status of the job.
- getStatus() - Method in class net.sf.basedb.core.PluginResponse
-
Get the status of the response.
- getStatus() - Method in class net.sf.basedb.util.extensions.manager.ProcessResults.FileResults
-
A short status message indicating the completed
results on this file.
- getStatusMessage() - Method in class net.sf.basedb.core.data.JobData
-
Get a status message.
- getStatusMessage() - Method in class net.sf.basedb.core.Job
-
Get a message about the current status of the job.
- getStdev() - Method in class net.sf.basedb.util.plot.HistogramPlot.HistogramBin
-
Get the standard deviation of all values in this bin.
- getStorageType() - Method in class net.sf.basedb.core.BioPlateType
-
Get the subtype of storage location where plates of this type are usually stored.
- getStorageType() - Method in class net.sf.basedb.core.data.BioPlateTypeData
-
Get the subtype of storage location where plates of this type are usually stored.
- getStream(String) - Method in class net.sf.basedb.util.extensions.manager.ExtensionsFile
-
Get an input stream for reading the resource specified by the
given path
- getString(int) - Method in class net.sf.basedb.clients.web.servlet.PlotServlet.CFSqlResult
-
- getString(String) - Static method in class net.sf.basedb.core.Config
-
Get the configuration setting specified by key
as a String value.
- getString(String, String) - Static method in class net.sf.basedb.core.Config
-
Get the configuration setting specified by key
as a String value.
- getString(int) - Method in class net.sf.basedb.core.DynamicResultIterator.SqlResultImpl
-
- getString(int) - Method in interface net.sf.basedb.core.query.SqlResult
-
Get the value of the specified column as a string.
- getString(boolean) - Method in enum net.sf.basedb.util.formatter.BooleanFormatter.Type
-
- getString(HttpResponse, String, String) - Static method in class net.sf.basedb.util.HttpUtil
-
- getString(String, boolean, String...) - Method in class net.sf.basedb.util.resources.ResourceBundleWrapper
-
Utility method for returning the value for the key given
by key.0
(variant=false) or key.1
(variant=true) depending on the value of the variant parameter.
- getString(String, int, String...) - Method in class net.sf.basedb.util.resources.ResourceBundleWrapper
-
Utility method for returning the value for the key given by:
key.index
.
- getString(String, String...) - Method in class net.sf.basedb.util.resources.ResourceBundleWrapper
-
Get a string value from the bundle.
- getString(String) - Static method in class net.sf.basedb.util.Values
-
Convert a string to a string, and map NULL to the empty string.
- getString(String, String) - Static method in class net.sf.basedb.util.Values
-
Convert a string to a string.
- getString(Collection<?>, String, boolean) - Static method in class net.sf.basedb.util.Values
-
- getString(Collection<T>, String, boolean, Formatter<? super T>) - Static method in class net.sf.basedb.util.Values
-
- getStringFormatter(SessionControl) - Static method in class net.sf.basedb.clients.web.formatter.FormatterFactory
-
Get the logged in user's formatter for strings.
- getStringOrNull(String) - Static method in class net.sf.basedb.util.Values
-
Convert the empty string ("") to null after removing leading and trailing
whitespace.
- getStringValue() - Method in enum net.sf.basedb.core.Type
-
Get the string value representation of this type.
- getStringValues() - Method in class net.sf.basedb.core.data.annotations.AnnotationLink
-
- getStyle() - Method in class net.sf.basedb.clients.web.extensions.list.AbstractListColumnBean
-
- getStyle() - Method in interface net.sf.basedb.clients.web.extensions.list.ListColumnAction
-
Optional HTML style attribute that is used to style the column
through CSS.
- getStyle() - Method in class net.sf.basedb.clients.web.extensions.login.FieldInfo
-
Get a style attribute that can used to style the input field.
- getStyle() - Method in class net.sf.basedb.clients.web.extensions.menu.FixedMenuItemFactory
-
- getStyle() - Method in interface net.sf.basedb.clients.web.extensions.menu.MenuItemAction
-
Extra CSS style attributes that will be added to the
style
attribute of the menu item div.
- getStyle() - Method in class net.sf.basedb.clients.web.extensions.menu.MenuItemBean
-
- getStyle() - Method in class net.sf.basedb.clients.web.extensions.section.IncludeContentSectionFactory.Section
-
- getStyle() - Method in interface net.sf.basedb.clients.web.extensions.section.SectionAction
-
Extra CSS style attributes that will be added to the
style
attribute of the main section tag.
- getStyle() - Method in class net.sf.basedb.clients.web.extensions.section.SectionBean
-
- getStyle() - Method in class net.sf.basedb.clients.web.extensions.tabcontrol.FixedTabFactory
-
- getStyle() - Method in class net.sf.basedb.clients.web.extensions.tabcontrol.IncludeContentTabFactory.Tab
-
- getStyle() - Method in interface net.sf.basedb.clients.web.extensions.tabcontrol.TabAction
-
Extra CSS style attributes that will be added to the
style
attribute of the main tab tag.
- getStyle() - Method in class net.sf.basedb.clients.web.extensions.tabcontrol.TabBean
-
- getStyle() - Method in interface net.sf.basedb.clients.web.extensions.toolbar.ButtonAction
-
Extra CSS style attributes that will be added to the
style
attribute of the main button tag.
- getStyle() - Method in class net.sf.basedb.clients.web.extensions.toolbar.ButtonBean
-
- getStyle() - Method in class net.sf.basedb.clients.web.extensions.toolbar.FixedButtonFactory
-
- getStyle() - Method in class net.sf.basedb.clients.web.taglib.StylableTag
-
- getStyle() - Method in class net.sf.basedb.clients.web.taglib.tab.Tab
-
- getStyle() - Method in class net.sf.basedb.clients.web.taglib.table.Button.ButtonActionWrapper
-
- getStyle() - Method in class net.sf.basedb.clients.web.taglib.table.Cell
-
- getStyle() - Method in class net.sf.basedb.clients.web.taglib.table.CellValue
-
- getStyles() - Method in class net.sf.basedb.clients.web.taglib.Head
-
- getStylesheets() - Method in class net.sf.basedb.clients.web.extensions.AbstractJspFactory
-
Get a set with all stylesheet references.
- getStylesheets() - Method in class net.sf.basedb.clients.web.extensions.JspContext
-
Get all stylesheets that has been added to this context.
- getSubclass() - Method in class net.sf.basedb.clients.web.taglib.StylableTag
-
- getSubContext() - Method in class net.sf.basedb.clients.web.ExperimentExplorer
-
Get the subcontext name used for the
ItemContext
objects
related to this explorer.
- getSubcontext() - Method in class net.sf.basedb.clients.web.taglib.table.Table
-
- getSubContext() - Method in class net.sf.basedb.core.ContextKey
-
- getSubContext() - Method in class net.sf.basedb.core.data.ContextData
-
Get the subcontext this context belongs to.
- getSubContext() - Method in class net.sf.basedb.core.data.ContextIndex
-
Get the subcontext this Context
belongs to.
- getSubContext() - Method in class net.sf.basedb.core.data.JobData
-
The name of the subcontext that was active whjen configuring
this job.
- getSubContext() - Method in class net.sf.basedb.core.ItemContext
-
Get the sub-context name of this context.
- getSubContext() - Method in class net.sf.basedb.core.plugin.GuiContext
-
- getSubdirectories() - Method in class net.sf.basedb.core.data.DirectoryData
-
This is the inverse end.
- getSubDirectories() - Method in class net.sf.basedb.core.Directory
-
Get a query that return subdirectories of this directory.
- getSubid() - Method in class net.sf.basedb.clients.web.taglib.menu.Submenu
-
- getSubmenuId() - Method in class net.sf.basedb.clients.web.extensions.menu.FixedMenuItemFactory
-
- getSubmenuId() - Method in interface net.sf.basedb.clients.web.extensions.menu.MenuItemAction
-
The ID of a new submenu.
- getSubmenuId() - Method in class net.sf.basedb.clients.web.extensions.menu.MenuItemBean
-
- getSubtypableItems() - Static method in class net.sf.basedb.core.Metadata
-
- getSubtype() - Method in class net.sf.basedb.util.bfs.MetadataModel
-
Get the BFS subtype.
- getSubtype() - Method in class net.sf.basedb.util.bfs.MetadataWriter
-
Get the BFS subtype.
- getSubtypesQuery(Item) - Static method in class net.sf.basedb.clients.web.Base
-
Get a query that returns all subtypes for the given main item type.
- getSuccessMessage() - Method in class net.sf.basedb.clients.web.plugins.SimpleExport
-
- getSuccessMessage() - Method in class net.sf.basedb.core.plugin.AbstractExporterPlugin
-
Called if the export was successful to let the subclass generate a simple
message that is sent back to the core and user interface.
- getSuccessMessage(int) - Method in class net.sf.basedb.plugins.AbstractFlatFileImporter
-
Called if the parsing was successful to let the subclass generate a simple
message that is sent back to the core and user interface.
- getSuccessMessage(int) - Method in class net.sf.basedb.plugins.AnnotationFlatFileImporter
-
- getSuccessMessage() - Method in class net.sf.basedb.plugins.BaseFileExporterPlugin
-
- getSuccessMessage(int) - Method in class net.sf.basedb.plugins.batchimport.AbstractItemImporter
-
- getSuccessMessage() - Method in class net.sf.basedb.plugins.BfsExporterPlugin
-
- getSuccessMessage() - Method in class net.sf.basedb.plugins.GalExporter
-
- getSuccessMessage() - Method in class net.sf.basedb.plugins.HelpExporter
-
- getSuccessMessage() - Method in class net.sf.basedb.plugins.HelpImporter
-
- getSuccessMessage(int) - Method in class net.sf.basedb.plugins.IlluminaRawDataImporter
-
- getSuccessMessage() - Method in class net.sf.basedb.plugins.PackedFileExporter
-
- getSuccessMessage(int) - Method in class net.sf.basedb.plugins.PlateFlatFileImporter
-
Return x plates inserted
.
- getSuccessMessage() - Method in class net.sf.basedb.plugins.PlateMappingExporter
-
- getSuccessMessage(int) - Method in class net.sf.basedb.plugins.PlateMappingImporter
-
Return Platemapping 'name' created.
- getSuccessMessage() - Method in class net.sf.basedb.plugins.PluginConfigurationExporter
-
- getSuccessMessage(int) - Method in class net.sf.basedb.plugins.PrintMapFlatFileImporter
-
- getSuccessMessage(int) - Method in class net.sf.basedb.plugins.RawDataFlatFileImporter
-
Return x spots inserted
.
- getSuccessMessage(int) - Method in class net.sf.basedb.plugins.ReporterFlatFileImporter
-
Return x new reporters; y updated reporters; z reporters added to list
.
- getSuccessMessage(int) - Method in class net.sf.basedb.plugins.ReporterMapFlatFileImporter
-
Return x features inserted; y blocks inserted
.
- getSuffix() - Method in class net.sf.basedb.clients.web.taglib.table.CellValue
-
- getSuffix() - Static method in class net.sf.basedb.core.Version
-
Get the version suffix string (eg "-dev" for development versions)
- getSuffix() - Method in class net.sf.basedb.util.bfs.SequenceFilenameGenerator
-
Get the suffix that is used for file name generation.
- getSuggestedJobName() - Method in class net.sf.basedb.core.PluginResponse
-
Get the job name that was suggested by the job.
- getSum(int) - Method in class net.sf.basedb.clients.web.ExperimentExplorer.AnnotationGroup
-
Get the sum of intensities for the specified channel.
- getSum() - Method in class net.sf.basedb.util.plot.HistogramPlot.HistogramBin
-
Get the sum of all values in this bin.
- getSummary(User) - Method in class net.sf.basedb.core.DiskUsageStatistics
-
Get a summary of the disk usage for the specified user.
- getSummary(Group) - Method in class net.sf.basedb.core.DiskUsageStatistics
-
Get a summary of the disk usage for the specified group.
- getSummary() - Method in class net.sf.basedb.util.extensions.manager.ProcessResults
-
Get a summary of the scan results as a textual description.
- getSupportedSignals() - Method in class net.sf.basedb.core.Job.JobSignalTransporter
-
- getSupportedSignals() - Method in class net.sf.basedb.core.signal.AbstractSignalHandler
-
- getSupportedSignals() - Method in class net.sf.basedb.core.signal.AbstractSignalTransporter
-
- getSupportedSignals() - Method in class net.sf.basedb.core.signal.DelegatingSignalHandler
-
- getSupportedSignals() - Method in interface net.sf.basedb.core.signal.SignalHandler
-
Get all signals that are supported by this handler.
- getSupportedSignals() - Method in interface net.sf.basedb.core.signal.SignalTransporter
-
Get a collection containing the signals supported, by the signal
handler.
- getSupportedSourceItems(SyncFilter.SourceItemTransform) - Method in class net.sf.basedb.util.listable.AbstractSourceItemTransformerFactory
-
- getSupportedSourceItems(SyncFilter.SourceItemTransform) - Method in interface net.sf.basedb.util.listable.SourceItemTransformerFactory
-
Get the supported source item types when transforming in the specified
direction.
- getSupportsConfigurations() - Method in class net.sf.basedb.core.data.PluginDefinitionData
-
If the plugin supports configurations or not.
- getSymbol() - Method in class net.sf.basedb.core.data.ReporterData
-
Get the gene symbol of the reporter.
- getSymbol() - Method in class net.sf.basedb.core.data.UnitSymbolData
-
The symbol, which must be unique for a given quantity.
- getSymbol() - Method in enum net.sf.basedb.core.Operator
-
Get the symbol for this operator, useful for display in client applications.
- getSymbols() - Method in class net.sf.basedb.core.data.QuantityData
-
This is the inverse end.
- getSymbols() - Method in class net.sf.basedb.core.data.UnitData
-
This is the inverse end.
- getSymbols() - Method in class net.sf.basedb.core.Unit
-
Get all symbols that are registered for this unit.
- getSyncDate() - Method in class net.sf.basedb.core.data.ItemListData
-
Get the date and time the list members was last synchronized
by the filter context.
- getSyncDate() - Method in class net.sf.basedb.core.ItemList
-
Get the last sync date+time.
- getSyncFilters() - Method in class net.sf.basedb.core.data.ItemListData
-
This is the inverse end.
- getSyncFilters() - Method in class net.sf.basedb.core.ItemList
-
Get a query returning all synchronization filters
for this list
- getSystemId() - Method in class net.sf.basedb.core.BioPlateEventType
-
- getSystemId() - Method in class net.sf.basedb.core.data.BioPlateEventTypeData
-
- getSystemId() - Method in class net.sf.basedb.core.data.DirectoryData
-
- getSystemId() - Method in class net.sf.basedb.core.data.GroupData
-
- getSystemId() - Method in class net.sf.basedb.core.data.ItemSubtypeData
-
Override the property definition since we may have to update the system id
during installation.
- getSystemId() - Method in class net.sf.basedb.core.data.QuantityData
-
- getSystemId() - Method in class net.sf.basedb.core.data.QuotaData
-
- getSystemId() - Method in class net.sf.basedb.core.data.QuotaTypeData
-
- getSystemId() - Method in class net.sf.basedb.core.data.RoleData
-
- getSystemId() - Method in interface net.sf.basedb.core.data.SystemData
-
Get the system id for the item.
- getSystemId() - Method in class net.sf.basedb.core.data.UserData
-
- getSystemId() - Method in class net.sf.basedb.core.Directory
-
- getSystemId() - Method in class net.sf.basedb.core.Group
-
- getSystemId() - Method in class net.sf.basedb.core.ItemSubtype
-
- getSystemId() - Method in class net.sf.basedb.core.Quantity
-
- getSystemId() - Method in class net.sf.basedb.core.Quota
-
- getSystemId() - Method in class net.sf.basedb.core.QuotaType
-
- getSystemId() - Method in class net.sf.basedb.core.Role
-
- getSystemId() - Method in interface net.sf.basedb.core.SystemItem
-
Get the system id for the item.
- getSystemId() - Method in class net.sf.basedb.core.User
-
- getTabcontrol() - Method in class net.sf.basedb.clients.web.taglib.Help
-
- getTabIndex() - Method in class net.sf.basedb.clients.web.extensions.tabcontrol.FixedTabFactory
-
- getTabIndex() - Method in class net.sf.basedb.clients.web.extensions.tabcontrol.IncludeContentTabFactory.Tab
-
- getTabIndex() - Method in interface net.sf.basedb.clients.web.extensions.tabcontrol.TabAction
-
Get the tab index used to control focus order when tabbing.
- getTabIndex() - Method in class net.sf.basedb.clients.web.extensions.tabcontrol.TabBean
-
- getTabIndex() - Method in interface net.sf.basedb.clients.web.extensions.toolbar.ButtonAction
-
Get the tab index used to control focus order when tabbing.
- getTabIndex() - Method in class net.sf.basedb.clients.web.extensions.toolbar.ButtonBean
-
- getTabIndex() - Method in class net.sf.basedb.clients.web.extensions.toolbar.FixedButtonFactory
-
- getTabindex() - Method in class net.sf.basedb.clients.web.taglib.Button
-
- getTabindex() - Method in class net.sf.basedb.clients.web.taglib.Help
-
- getTabindex() - Method in class net.sf.basedb.clients.web.taglib.Icon
-
- getTabindex() - Method in class net.sf.basedb.clients.web.taglib.Select
-
- getTabindex() - Method in class net.sf.basedb.clients.web.taglib.tab.Tab
-
- getTabIndex() - Method in class net.sf.basedb.clients.web.taglib.tab.Tab
-
- getTabIndex() - Method in class net.sf.basedb.clients.web.taglib.table.Button.ButtonActionWrapper
-
- getTabindex() - Method in class net.sf.basedb.clients.web.taglib.table.Button
-
- getTabindex() - Method in class net.sf.basedb.clients.web.taglib.Zoom
-
- getTable() - Method in class net.sf.basedb.clients.web.taglib.table.ColumnHeaders
-
- getTable() - Method in class net.sf.basedb.clients.web.taglib.table.Data
-
- getTable() - Method in class net.sf.basedb.clients.web.taglib.table.Headers
-
- getTable() - Method in class net.sf.basedb.clients.web.taglib.table.PropertyFilter
-
- getTable() - Method in class net.sf.basedb.clients.web.taglib.table.Row
-
- getTable() - Method in class net.sf.basedb.clients.web.taglib.table.Rows
-
- getTable() - Method in class net.sf.basedb.core.dbengine.TableInfo
-
Get the table this information is representing.
- getTableInfo(Session, String) - Static method in class net.sf.basedb.core.Update
-
- getTableName() - Method in class net.sf.basedb.core.RawDataType
-
Get the name of the database table that is used to store the extra
properties of this raw data type.
- getTableName() - Method in class net.sf.basedb.core.RealTable
-
Get the unquoted table name of this table in the database.
- getTableName() - Method in enum net.sf.basedb.core.Type
-
Get the name of the database table, parameter and annotation
values of this value type are stored in.
- getTableName(VirtualDb) - Method in enum net.sf.basedb.core.VirtualTable
-
Get the real table name of this table in the database.
- getTag() - Method in class net.sf.basedb.core.data.ExtractData
-
The tag used for tagging the extract so that it can be tracked on physical bioassays.
- getTag() - Method in class net.sf.basedb.core.Extract
-
Get the tag that has been applied to this extract in order
to be able to distinguish it from other extracts on a
physical bioassay.
- getTargetItem() - Method in class net.sf.basedb.util.listable.AbstractSourceItemTransformerFactory
-
- getTargetItem() - Method in interface net.sf.basedb.util.listable.SourceItemTransformerFactory
-
Get the target item type of this transformer factory.
- getTargetItemType() - Method in class net.sf.basedb.util.listable.AbstractSourceItemTransformer
-
- getTargetItemType() - Method in interface net.sf.basedb.util.listable.SourceItemTransformer
-
Get the item type of the target items.
- getTargetItemType() - Method in class net.sf.basedb.util.listable.SourceItemTransformerChain
-
Get the target item type of the last step in the chain.
- getTenantIdentifier() - Method in class net.sf.basedb.core.hibernate.SessionWrapper
-
- getTenantIdentifier() - Method in class net.sf.basedb.core.hibernate.StatelessSessionWrapper
-
- GetterSetter(PropertyAccessStrategy, Class<?>, String) - Constructor for class net.sf.basedb.core.ExtendedPropertyAccessor.GetterSetter
-
Create a new getter or setter.
- getTextarea() - Method in class net.sf.basedb.clients.web.taglib.Zoom
-
- getTextValues() - Method in class net.sf.basedb.core.data.annotations.AnnotationLink
-
- getThetaJoin(Query, DbControl) - Method in class net.sf.basedb.core.DynamicJoin
-
- getThetaJoin(Query, DbControl) - Method in class net.sf.basedb.core.ExtraValueJoin
-
- getThetaJoin(Query, DbControl) - Method in class net.sf.basedb.core.query.AnnotationJoin
-
- getThetaJoin(Query, DbControl) - Method in class net.sf.basedb.core.query.HqlInnerJoin
-
- getThetaJoin(Query, DbControl) - Method in class net.sf.basedb.core.query.HqlLeftJoin
-
- getThetaJoin(Query, DbControl) - Method in class net.sf.basedb.core.query.HqlRightJoin
-
- getThetaJoin(Query, DbControl) - Method in interface net.sf.basedb.core.query.Join
-
- getThetaJoin(Query, DbControl) - Method in class net.sf.basedb.core.RealJoin
-
- getThetaJoin(Query, DbControl) - Method in class net.sf.basedb.core.ReporterListJoin
-
- getThetaJoinCondition(Query, DbControl) - Method in class net.sf.basedb.core.DynamicJoin
-
- getThetaJoinCondition(Query, DbControl) - Method in class net.sf.basedb.core.ExtraValueJoin
-
- getThetaJoinCondition(Query, DbControl) - Method in class net.sf.basedb.core.query.AnnotationJoin
-
- getThetaJoinCondition(Query, DbControl) - Method in class net.sf.basedb.core.query.HqlInnerJoin
-
- getThetaJoinCondition(Query, DbControl) - Method in class net.sf.basedb.core.query.HqlLeftJoin
-
- getThetaJoinCondition(Query, DbControl) - Method in class net.sf.basedb.core.query.HqlRightJoin
-
- getThetaJoinCondition(Query, DbControl) - Method in interface net.sf.basedb.core.query.Join
-
- getThetaJoinCondition(Query, DbControl) - Method in class net.sf.basedb.core.RealJoin
-
- getThetaJoinCondition(Query, DbControl) - Method in class net.sf.basedb.core.ReporterListJoin
-
- getThisAnnotation(DbControl) - Method in class net.sf.basedb.core.snapshot.AnnotationSnapshot
-
Get the annotation this is a snapshot of.
- getThisAnnotationId() - Method in class net.sf.basedb.core.snapshot.AnnotationSnapshot
-
Get the id of the annotation this is a snapshot of.
- getThisAnnotationSet(DbControl) - Method in class net.sf.basedb.core.snapshot.AnnotationSnapshot
-
Get the annotation set this annotation belongs to.
- getThisAnnotationSetId() - Method in class net.sf.basedb.core.snapshot.AnnotationSnapshot
-
Get the id of the annotation set this is a snapshot of.
- getThisItem(DbControl) - Method in class net.sf.basedb.core.snapshot.AnnotationSnapshot
-
Get the item that this annotation belongs to.
- getThisItemId() - Method in class net.sf.basedb.core.snapshot.AnnotationSnapshot
-
Get the id of the item this annotation belongs to.
- getThisItemType() - Method in class net.sf.basedb.core.snapshot.AnnotationSnapshot
-
Get the item type of the item this annotation belongs to.
- getThisLastUpdate() - Method in class net.sf.basedb.core.snapshot.AnnotationSnapshot
-
Get the date+time this annotation was last updated.
- getThisUnit(DbControl) - Method in class net.sf.basedb.core.snapshot.AnnotationSnapshot
-
Get the unit the annotatation values should use for display.
- getThisUnitId() - Method in class net.sf.basedb.core.snapshot.AnnotationSnapshot
-
Get the id of the unit that the annotation values should
use when displayed.
- getThisValues() - Method in class net.sf.basedb.core.snapshot.AnnotationSnapshot
-
Get the annotation values for this annotation.
- getThreadPriority(Job.ExecutionTime) - Method in class net.sf.basedb.clients.jobagent.Agent
-
Get the thread priority to use for the specified execution time slot.
- getTime() - Method in class net.sf.basedb.core.ChangeHistory
-
Get the date and time the change was made.
- getTime() - Method in class net.sf.basedb.core.data.ChangeHistoryData
-
Get the time of the change.
- getTime() - Method in class net.sf.basedb.util.extensions.manager.ProcessResults.FileResults
-
Get the time of the results as a millisecond value.
- getTime(int) - Method in class net.sf.basedb.util.timer.PerformanceTimer
-
Get the current time of a timer.
- getTimeout() - Method in class net.sf.basedb.core.hibernate.QueryWrapper
-
- getTimerTask(TimerTask, boolean) - Method in class net.sf.basedb.util.timer.Scheduler
-
- getTimeSent() - Method in class net.sf.basedb.core.data.MessageData
-
Get the date and time this message was sent.
- getTimeSent() - Method in class net.sf.basedb.core.Message
-
Get the date and time the message was sent.
- getTimestampValues() - Method in class net.sf.basedb.core.data.annotations.AnnotationLink
-
- getTitle() - Method in class net.sf.basedb.clients.web.ExperimentExplorer.AnnotationGroup
-
Get the title of this annotation group.
- getTitle() - Method in class net.sf.basedb.clients.web.extensions.list.AbstractListColumnBean
-
- getTitle() - Method in interface net.sf.basedb.clients.web.extensions.list.ListColumnAction
-
The column title.
- getTitle() - Method in class net.sf.basedb.clients.web.extensions.menu.FixedMenuItemFactory
-
- getTitle() - Method in interface net.sf.basedb.clients.web.extensions.menu.MenuItemAction
-
Get the title of the menu.
- getTitle() - Method in class net.sf.basedb.clients.web.extensions.menu.MenuItemBean
-
- getTitle() - Method in interface net.sf.basedb.clients.web.extensions.plot.OverviewPlotAction
-
The title of the overview plots.
- getTitle() - Method in class net.sf.basedb.clients.web.extensions.plot.OverviewPlotBean
-
- getTitle() - Method in interface net.sf.basedb.clients.web.extensions.plot.PlotGenerator
-
Get the title of the generated image.
- getTitle() - Method in class net.sf.basedb.clients.web.extensions.plot.PlotGeneratorBean
-
- getTitle() - Method in class net.sf.basedb.clients.web.extensions.section.IncludeContentSectionFactory.Section
-
- getTitle() - Method in interface net.sf.basedb.clients.web.extensions.section.SectionAction
-
Get the title of the section.
- getTitle() - Method in class net.sf.basedb.clients.web.extensions.section.SectionBean
-
- getTitle() - Method in class net.sf.basedb.clients.web.extensions.tabcontrol.FixedTabFactory
-
- getTitle() - Method in class net.sf.basedb.clients.web.extensions.tabcontrol.IncludeContentTabFactory.Tab
-
- getTitle() - Method in interface net.sf.basedb.clients.web.extensions.tabcontrol.TabAction
-
Get the title of the tab.
- getTitle() - Method in class net.sf.basedb.clients.web.extensions.tabcontrol.TabBean
-
- getTitle() - Method in interface net.sf.basedb.clients.web.extensions.toolbar.ButtonAction
-
Get the title of the button.
- getTitle() - Method in class net.sf.basedb.clients.web.extensions.toolbar.ButtonBean
-
- getTitle() - Method in class net.sf.basedb.clients.web.extensions.toolbar.FixedButtonFactory
-
- getTitle() - Method in class net.sf.basedb.clients.web.taglib.Button
-
- getTitle() - Method in class net.sf.basedb.clients.web.taglib.HideableSection
-
- getTitle() - Method in class net.sf.basedb.clients.web.taglib.menu.Menuitem
-
- getTitle() - Method in class net.sf.basedb.clients.web.taglib.menu.Submenu
-
- getTitle() - Method in class net.sf.basedb.clients.web.taglib.Page
-
- getTitle() - Method in class net.sf.basedb.clients.web.taglib.path.PathElement
-
- getTitle() - Method in class net.sf.basedb.clients.web.taglib.tab.Tab
-
- getTitle() - Method in class net.sf.basedb.clients.web.taglib.table.Button.ButtonActionWrapper
-
- getTitle() - Method in class net.sf.basedb.clients.web.taglib.table.Button
-
- getTitle() - Method in class net.sf.basedb.clients.web.taglib.table.ColumnDef
-
- getTitle() - Method in class net.sf.basedb.clients.web.taglib.table.Label
-
- getTitle() - Method in class net.sf.basedb.clients.web.taglib.table.Table
-
- getTitle() - Method in class net.sf.basedb.clients.web.taglib.table.TableColumn
-
- getTitle() - Method in class net.sf.basedb.clients.web.taglib.Zoom
-
- getTitle() - Method in exception net.sf.basedb.clients.web.WebException
-
Get the title of the error message.
- getTitle() - Method in class net.sf.basedb.core.data.ExperimentData
-
Get the title for this experiment.
- getTitle() - Method in class net.sf.basedb.core.data.ReporterClonePropertyData
-
Get the title of the property.
- getTitle() - Method in class net.sf.basedb.core.Experiment
-
Get the title for the publication for this experiment.
- getTitle() - Method in class net.sf.basedb.core.ExtendedProperty
-
Get the title of the extended property.
- getTitle() - Method in class net.sf.basedb.core.IntensityFormula
-
Get the title of the intensity formula.
- getTitle() - Method in class net.sf.basedb.core.RequestInformation
-
Get the title of the request.
- getTitle() - Method in class net.sf.basedb.plugins.BaseFileExporterPlugin.ExtendedDynamicField
-
- getTitle() - Method in class net.sf.basedb.plugins.batchimport.FallbackIdMethod
-
- getTitle() - Method in class net.sf.basedb.plugins.batchimport.FileImporter.PathIdMethod
-
- getTitle() - Method in interface net.sf.basedb.plugins.batchimport.IdMethod
-
The display title of the method.
- getTitle() - Method in class net.sf.basedb.plugins.batchimport.InternalIdMethod
-
- getTitle() - Method in class net.sf.basedb.plugins.batchimport.MultiPropertyIdMethod
-
- getTitle() - Method in class net.sf.basedb.plugins.batchimport.PropertyIdMethod
-
- getTitle() - Method in class net.sf.basedb.util.export.spotdata.AnnotationAssayField
-
Returns the name of the configured annotation type, or the empty
string if not configured.
- getTitle() - Method in class net.sf.basedb.util.export.spotdata.AssayPropertyField
-
- getTitle() - Method in interface net.sf.basedb.util.export.spotdata.ExportableField
-
Get the column header.
- getTitle() - Method in class net.sf.basedb.util.export.spotdata.JepDynamicField
-
- getTitle() - Method in class net.sf.basedb.util.export.spotdata.SimpleDynamicField
-
- getTitle() - Method in interface net.sf.basedb.util.overview.extensions.ValidationRuleAction
-
Get the title of this validator rule.
- getTitle() - Method in class net.sf.basedb.util.overview.Node
-
Get the display title of this node.
- getTitle() - Method in class net.sf.basedb.util.overview.Validator
-
Get the title of this validator.
- getTo() - Method in class net.sf.basedb.core.AnyToAny
-
Get the item this link is linking to.
- getTo() - Method in class net.sf.basedb.core.data.MessageData
-
The user this message is to.
- getTo() - Method in class net.sf.basedb.core.Message
-
Get the
User
this message was sent to.
- getToId() - Method in class net.sf.basedb.core.AnyToAny
-
Get the ID of the item this link is linking to.
- getToId() - Method in class net.sf.basedb.core.data.AnyToAnyData
-
The ID of the item we are linking to.
- getToolParameters(List<String>) - Method in class net.sf.basedb.plugins.ManualDerivedBioAssayCreator
-
- getToolParameters(List<String>) - Method in class net.sf.basedb.plugins.ManualTransformCreator
-
- getTooltip() - Method in class net.sf.basedb.clients.web.extensions.list.AbstractListColumnBean
-
- getTooltip() - Method in interface net.sf.basedb.clients.web.extensions.list.ListColumnAction
-
An optional tooltip that is displayed when the mouse is over the
column header.
- getTooltip() - Method in class net.sf.basedb.clients.web.extensions.login.FieldInfo
-
Get a tooltip text that is displayed when the user holds the mouse over
the input field.
- getTooltip() - Method in class net.sf.basedb.clients.web.extensions.menu.FixedMenuItemFactory
-
- getTooltip() - Method in interface net.sf.basedb.clients.web.extensions.menu.MenuItemAction
-
A tooltip that is shown as a yellow popup when the
user points the mouse at the menu item.
- getTooltip() - Method in class net.sf.basedb.clients.web.extensions.menu.MenuItemBean
-
- getTooltip() - Method in class net.sf.basedb.clients.web.extensions.tabcontrol.FixedTabFactory
-
- getTooltip() - Method in class net.sf.basedb.clients.web.extensions.tabcontrol.IncludeContentTabFactory.Tab
-
- getTooltip() - Method in interface net.sf.basedb.clients.web.extensions.tabcontrol.TabAction
-
A tooltip that is shown as a yellow popup when the
user points the mouse at the tab.
- getTooltip() - Method in class net.sf.basedb.clients.web.extensions.tabcontrol.TabBean
-
- getTooltip() - Method in interface net.sf.basedb.clients.web.extensions.toolbar.ButtonAction
-
A tooltip that is shown as a yellow popup when the
user points the mouse at the button.
- getTooltip() - Method in class net.sf.basedb.clients.web.extensions.toolbar.ButtonBean
-
- getTooltip() - Method in class net.sf.basedb.clients.web.extensions.toolbar.FixedButtonFactory
-
- getTooltip() - Method in class net.sf.basedb.clients.web.taglib.Button
-
- getTooltip() - Method in class net.sf.basedb.clients.web.taglib.Help
-
- getTooltip() - Method in class net.sf.basedb.clients.web.taglib.Icon
-
- getTooltip() - Method in class net.sf.basedb.clients.web.taglib.menu.Menuitem
-
- getTooltip() - Method in class net.sf.basedb.clients.web.taglib.menu.Submenu
-
- getTooltip() - Method in class net.sf.basedb.clients.web.taglib.path.PathElement
-
- getTooltip() - Method in class net.sf.basedb.clients.web.taglib.PropertyValue
-
- getTooltip() - Method in class net.sf.basedb.clients.web.taglib.tab.Tab
-
- getTooltip() - Method in class net.sf.basedb.clients.web.taglib.table.Button.ButtonActionWrapper
-
- getTooltip() - Method in class net.sf.basedb.clients.web.taglib.table.Button
-
- getTooltip() - Method in class net.sf.basedb.clients.web.taglib.table.ColumnDef
-
- getTooltip() - Method in class net.sf.basedb.clients.web.taglib.table.Label
-
- getTooltip() - Method in class net.sf.basedb.clients.web.taglib.Zoom
-
- getTotal() - Method in class net.sf.basedb.core.DiskUsageStatistics.Summary
-
Get the total disk usage in bytes
- getTotal(Location) - Method in class net.sf.basedb.core.DiskUsageStatistics.Summary
-
Get the total disk usage of the specified location in bytes.
- getTotal(QuotaType) - Method in class net.sf.basedb.core.DiskUsageStatistics.Summary
-
Get the total disk usage for the specified quota type in bytes.
- getTotal(QuotaType, Location) - Method in class net.sf.basedb.core.DiskUsageStatistics.Summary
-
Get the total disk usage of the specified location and
quota type in bytes.
- getTotal() - Method in class net.sf.basedb.core.SimpleAbsoluteProgressReporter
-
Get the end point of the task.
- getTotalBytes() - Method in class net.sf.basedb.clients.web.fileupload.FileUploadProgress
-
Get the total number of bytes expected to upload.
- getTotalCount() - Method in class net.sf.basedb.clients.web.servlet.PlotServlet.CFResultIterator
-
- getTotalCount() - Method in class net.sf.basedb.core.AbstractResultList
-
- getTotalCount() - Method in class net.sf.basedb.core.DataResultIterator
-
From the QueryResult interface
---------------------------------
- getTotalCount() - Method in class net.sf.basedb.core.DynamicResultIterator
-
From the QueryResult interface
---------------------------------
- getTotalCount() - Method in class net.sf.basedb.core.ItemResultIterator
-
From the QueryResult interface
---------------------------------
- getTotalCount() - Method in interface net.sf.basedb.core.query.QueryResult
-
- getTotalCount() - Method in class net.sf.basedb.core.ReporterScoreResultIterator
-
From the QueryResult interface
---------------------------------
- getTotalCount() - Method in class net.sf.basedb.core.UnmodifiableResultList
-
- getTotalFileSize() - Method in class net.sf.basedb.plugins.AbstractFlatFileImporter
-
Get the total file size of all files that are going to be imported.
- getTotalFileSize() - Method in class net.sf.basedb.plugins.RawDataFlatFileImporter
-
- getTotalInsertCount() - Method in class net.sf.basedb.core.BasicBatcher
-
Gets the total number of inserts done by the batcher
- getTotalInsertCount() - Method in class net.sf.basedb.core.MappingBatcher
-
Get the total number of mappings to raw data create by this mapper.
- getTotalMemory() - Method in class net.sf.basedb.core.JobAgent
-
Get the total memory in bytes of the server where the job agent
is running.
- getTotalMemory() - Method in class net.sf.basedb.util.jobagent.JobAgentInfo
-
Get the total memory on the job agent's server in bytes.
- getTotalrows() - Method in class net.sf.basedb.clients.web.taglib.table.Navigator
-
- getTotalSummary() - Method in class net.sf.basedb.core.DiskUsageStatistics
-
Get a summary of the total disk usage.
- getTotalWells() - Method in class net.sf.basedb.core.BioPlate
-
Get the total number of wells on this plate.
- getToType() - Method in class net.sf.basedb.core.AnyToAny
-
Get the type of the item this link is linking to.
- getToType() - Method in class net.sf.basedb.core.data.AnyToAnyData
-
The type code of the item we are linking to.
- getTransaction() - Method in class net.sf.basedb.core.hibernate.SessionWrapper
-
- getTransaction() - Method in class net.sf.basedb.core.hibernate.StatelessSessionWrapper
-
- getTransactionDetails() - Method in class net.sf.basedb.core.LogControl
-
Get information about the current transaction.
- getTransferredBytes() - Method in class net.sf.basedb.clients.web.fileupload.FileUploadProgress
-
Get the number of bytes that have been uploaded so far.
- getTransformation() - Method in class net.sf.basedb.core.BioAssaySet
-
Get the transformation that created this bioassayset.
- getTransformation() - Method in class net.sf.basedb.core.data.BioAssaySetData
-
Get the transformation that created this bioassayset.
- getTransformation() - Method in class net.sf.basedb.util.importer.spotdata.BaseFileImporter
-
Get the destination transformation.
- getTransformation() - Method in class net.sf.basedb.util.importer.spotdata.BfsImporter
-
Get the destination transformation.
- getTransformationName(DbControl) - Method in class net.sf.basedb.core.plugin.AbstractAnalysisPlugin
-
Generate a name for the transformation based on the plugin and it's
configuration.
- getTransformationNameParameter(String, String, String) - Method in class net.sf.basedb.core.plugin.AbstractAnalysisPlugin
-
Create a plugin parameter that asks for the name of the transformation.
- getTransformations() - Method in class net.sf.basedb.core.BioAssaySet
-
Get a query that return all transformations using this bioassayset
as a source.
- getTransformations() - Method in class net.sf.basedb.core.data.BioAssaySetData
-
This is the inverse end.
- getTransformations() - Method in class net.sf.basedb.core.data.ExperimentData
-
This is the inverse end.
- getTransformations() - Method in class net.sf.basedb.core.data.JobData
-
This is the inverse end.
- getTransformations() - Method in class net.sf.basedb.core.data.RawBioAssayData
-
This is the inverse end.
- getTransformations() - Method in class net.sf.basedb.core.Experiment
-
Get a query that return all transformations including root
transformations in this experiment.
- getTransformerFactory(Item) - Static method in class net.sf.basedb.util.listable.ListableUtil
-
Create a source item transformer factory that can transform items to the given
target item type.
- getTray() - Method in class net.sf.basedb.core.BioPlate
-
Get the tray within the "storage location" for this bioplate.
- getTray() - Method in class net.sf.basedb.core.data.BioPlateData
-
Get the tray in the storage location were the bioplate is stored.
- getType() - Method in class net.sf.basedb.clients.web.extensions.menu.FixedMenuItemFactory
-
- getType() - Method in interface net.sf.basedb.clients.web.extensions.menu.MenuItemAction
-
The type of menu item.
- getType() - Method in class net.sf.basedb.clients.web.extensions.menu.MenuItemBean
-
- getType() - Method in class net.sf.basedb.clients.web.taglib.menu.Menu
-
- getType() - Method in class net.sf.basedb.core.Annotation
-
- getType() - Method in class net.sf.basedb.core.AnnotationSet
-
- getType() - Method in class net.sf.basedb.core.AnnotationType
-
- getType() - Method in class net.sf.basedb.core.AnnotationTypeCategory
-
- getType() - Method in class net.sf.basedb.core.AnyToAny
-
- getType() - Method in class net.sf.basedb.core.ArrayBatch
-
- getType() - Method in class net.sf.basedb.core.ArrayDesign
-
- getType() - Method in class net.sf.basedb.core.ArrayDesignBlock
-
- getType() - Method in class net.sf.basedb.core.ArrayDesignPlate
-
- getType() - Method in class net.sf.basedb.core.ArraySlide
-
- getType() - Method in class net.sf.basedb.core.BasicBatcher
-
Get the type of item supported by the batcher.
- getType() - Method in class net.sf.basedb.core.BioAssay
-
- getType() - Method in class net.sf.basedb.core.BioAssaySet
-
- getType() - Method in class net.sf.basedb.core.BioMaterialEvent
-
- getType() - Method in class net.sf.basedb.core.BioPlate
-
- getType() - Method in class net.sf.basedb.core.BioPlateEvent
-
- getType() - Method in class net.sf.basedb.core.BioPlateEventParticipant
-
- getType() - Method in class net.sf.basedb.core.BioPlateEventType
-
- getType() - Method in class net.sf.basedb.core.BioPlateType
-
- getType() - Method in class net.sf.basedb.core.BioSource
-
- getType() - Method in class net.sf.basedb.core.BioWell
-
- getType() - Method in class net.sf.basedb.core.ChangeHistory
-
- getType() - Method in class net.sf.basedb.core.Client
-
- getType() - Method in class net.sf.basedb.core.ClientDefaultSetting
-
- getType() - Method in class net.sf.basedb.core.data.FormulaData
-
The type of formula:
1 = intensity expression; raw data type required, 1 formula for each channel
2 = intensity transformation; raw data type or channels required, 1 formula for each channel
3 = column expression; raw data type or channels required, 1 formula only
4 = column restriction; raw data type or channels required, 1 formula only
- getType() - Method in class net.sf.basedb.core.data.JobData
-
The type of job: 1 = run plugin, 2 = other
- getType() - Method in class net.sf.basedb.core.DataCube
-
- getType() - Method in class net.sf.basedb.core.DataCubeColumn
-
- getType() - Method in class net.sf.basedb.core.DataCubeExtraValue
-
- getType() - Method in class net.sf.basedb.core.DataCubeFilter
-
- getType() - Method in class net.sf.basedb.core.DataCubeLayer
-
- getType() - Method in class net.sf.basedb.core.DataFileType
-
- getType() - Method in class net.sf.basedb.core.dbengine.TableInfo.ColumnInfo
-
- getType() - Method in class net.sf.basedb.core.DerivedBioAssay
-
- getType() - Method in class net.sf.basedb.core.Directory
-
- getType() - Method in class net.sf.basedb.core.DiskUsage
-
- getType() - Method in class net.sf.basedb.core.Experiment
-
- getType() - Method in class net.sf.basedb.core.ExtendedProperty
-
Get the type of the extended property.
- getType() - Method in class net.sf.basedb.core.Extract
-
- getType() - Method in class net.sf.basedb.core.ExtraValue
-
- getType() - Method in class net.sf.basedb.core.ExtraValueType
-
- getType() - Method in class net.sf.basedb.core.FeatureBatcher
-
- getType() - Method in class net.sf.basedb.core.File
-
- getType() - Method in class net.sf.basedb.core.FileServer
-
- getType() - Method in class net.sf.basedb.core.FileSet
-
- getType() - Method in class net.sf.basedb.core.FileSetMember
-
- getType() - Method in class net.sf.basedb.core.Formula
-
- getType() - Method in class net.sf.basedb.core.GlobalDefaultSetting
-
- getType() - Method in class net.sf.basedb.core.Group
-
- getType() - Method in class net.sf.basedb.core.Hardware
-
- getType() - Method in class net.sf.basedb.core.Help
-
- getType() - Method in interface net.sf.basedb.core.Identifiable
-
Get the type of item represented by the object.
- getType() - Method in class net.sf.basedb.core.ItemKey
-
- getType() - Method in class net.sf.basedb.core.ItemList
-
- getType() - Method in class net.sf.basedb.core.ItemProxy
-
- getType() - Method in class net.sf.basedb.core.ItemSubtype
-
- getType() - Method in class net.sf.basedb.core.ItemSubtypeFileType
-
- getType() - Method in class net.sf.basedb.core.Job
-
- getType() - Method in class net.sf.basedb.core.JobAgent
-
- getType() - Method in class net.sf.basedb.core.JobAgentSettings
-
- getType() - Method in class net.sf.basedb.core.Kit
-
- getType() - Method in class net.sf.basedb.core.Message
-
- getType() - Method in class net.sf.basedb.core.MimeType
-
- getType() - Method in class net.sf.basedb.core.News
-
- getType() - Method in class net.sf.basedb.core.Path
-
Get the type of the path.
- getType() - Method in class net.sf.basedb.core.PermissionTemplate
-
- getType() - Method in class net.sf.basedb.core.PhysicalBioAssay
-
- getType() - Method in class net.sf.basedb.core.Plate
-
- getType() - Method in class net.sf.basedb.core.PlateEvent
-
- getType() - Method in class net.sf.basedb.core.PlateEventType
-
- getType() - Method in class net.sf.basedb.core.PlateGeometry
-
- getType() - Method in class net.sf.basedb.core.PlateMapping
-
- getType() - Method in class net.sf.basedb.core.PlateType
-
- getType() - Method in class net.sf.basedb.core.Platform
-
- getType() - Method in class net.sf.basedb.core.PlatformFileType
-
- getType() - Method in class net.sf.basedb.core.PlatformVariant
-
- getType() - Method in class net.sf.basedb.core.plugin.GuiContext
-
- getType() - Method in class net.sf.basedb.core.PluginConfiguration
-
- getType() - Method in class net.sf.basedb.core.PluginDefinition
-
- getType() - Method in class net.sf.basedb.core.PluginType
-
- getType() - Method in class net.sf.basedb.core.Project
-
- getType() - Method in class net.sf.basedb.core.ProjectKey
-
- getType() - Method in class net.sf.basedb.core.Protocol
-
- getType() - Method in class net.sf.basedb.core.Quantity
-
- getType() - Method in class net.sf.basedb.core.query.QueryParameter
-
Get the type of the parameter.
- getType() - Method in class net.sf.basedb.core.Quota
-
- getType() - Method in class net.sf.basedb.core.QuotaType
-
- getType() - Method in class net.sf.basedb.core.RawBioAssay
-
- getType() - Method in class net.sf.basedb.core.RawDataBatcher
-
- getType() - Method in class net.sf.basedb.core.ReporterBatcher
-
- getType() - Method in class net.sf.basedb.core.ReporterCloneTemplate
-
- getType() - Method in class net.sf.basedb.core.ReporterList
-
- getType() - Method in class net.sf.basedb.core.ReporterType
-
Get the type of item represented by the object.
- getType() - Method in class net.sf.basedb.core.Role
-
- getType() - Method in class net.sf.basedb.core.RoleKey
-
- getType() - Method in class net.sf.basedb.core.RootRawBioAssay
-
- getType() - Method in class net.sf.basedb.core.Sample
-
- getType() - Method in class net.sf.basedb.core.Session
-
- getType() - Method in class net.sf.basedb.core.Software
-
- getType() - Method in class net.sf.basedb.core.SpotImages
-
- getType() - Method in class net.sf.basedb.core.SyncFilter
-
- getType() - Method in class net.sf.basedb.core.Tag
-
- getType() - Method in class net.sf.basedb.core.Transformation
-
- getType() - Method in class net.sf.basedb.core.Unit
-
- getType() - Method in class net.sf.basedb.core.User
-
- getType() - Method in class net.sf.basedb.core.UserClientSetting
-
- getType() - Method in class net.sf.basedb.core.UserDefaultSetting
-
- getType() - Method in class net.sf.basedb.core.VirtualDb
-
- getType() - Method in class net.sf.basedb.core.Well
-
- getType() - Method in class net.sf.basedb.plugins.Base1PluginExecuter.JobParameter
-
- getType() - Method in class net.sf.basedb.plugins.BaseFileExporterPlugin.ExtendedDynamicField
-
- getType() - Method in class net.sf.basedb.plugins.executor.ParameterDefinition
-
Get the type of the parameter.
- getType() - Method in class net.sf.basedb.util.export.spotdata.AnnotationAssayField
-
Return the value type of the annotation type, or null if not
configured.
- getType() - Method in class net.sf.basedb.util.export.spotdata.AssayPropertyField
-
- getType() - Method in interface net.sf.basedb.util.export.spotdata.ExportableField
-
Get the data type of the field.
- getType() - Method in class net.sf.basedb.util.export.spotdata.JepDynamicField
-
- getType() - Method in class net.sf.basedb.util.export.spotdata.SimpleDynamicField
-
- getType() - Method in class net.sf.basedb.util.extensions.xml.PluginInfo
-
Get the main type of the plug-in.
- getTypeCode() - Method in class net.sf.basedb.clients.web.taglib.Page
-
- getTypeFormatter(SessionControl, Type) - Static method in class net.sf.basedb.clients.web.formatter.FormatterFactory
-
Get a formatter suitable for displaying values of the given type.
- getTypeHelper() - Method in class net.sf.basedb.core.hibernate.SessionWrapper
-
- getTypes() - Method in class net.sf.basedb.core.log.EntityDetails
-
Get an array representing the data type for each property.
- getTypeWrapper() - Method in enum net.sf.basedb.core.Type
-
Get a wrapper for accessing underlying type information from Hibernate.
- getTypeWrapper() - Method in class net.sf.basedb.core.VirtualColumn
-
Get a wrapper for accessing underlying type information from Hibernate.
- getUniqueKeys() - Method in class net.sf.basedb.util.bfs.MetadataWriter
-
Checks if the current section requires entry names to be unique
or not.
- getUnit() - Method in class net.sf.basedb.clients.web.taglib.table.ColumnDef
-
- getUnit() - Method in class net.sf.basedb.core.Annotation
-
Get the unit used for the values in this annotation.
- getUnit() - Method in class net.sf.basedb.core.data.AnnotationData
-
Get the unit used for the annotation values.
- getUnit() - Method in class net.sf.basedb.core.data.PropertyFilterData
-
- getUnit() - Method in class net.sf.basedb.core.data.UnitSymbolData
-
Get the unit this symbol belongs to.
- getUnit(String) - Method in class net.sf.basedb.core.Quantity
-
Get a a unit by symbol, also checking among the aliases.
- getUnit(Session, String) - Method in class net.sf.basedb.core.Quantity
-
Get the unit with a given symbol, or null if no unit is found.
- getUnit() - Method in class net.sf.basedb.core.snapshot.AnnotationLoaderUtil
-
- getUnit(DbControl) - Method in class net.sf.basedb.core.snapshot.AnnotationSnapshot
-
- getUnit(DbControl, String, String) - Static method in class net.sf.basedb.util.units.UnitUtil
-
Find the unit with a given symbol for a given quantity.
- getUnitConverter(Unit) - Method in class net.sf.basedb.core.Annotation
-
Get a converter for converting the values in this annotation to
a specific unit.
- getUnitConverter(Unit, Unit) - Method in class net.sf.basedb.core.AnnotationBatcher
-
Get/create a unit converter for converting between two units.
- getUnitConverter(Unit) - Method in class net.sf.basedb.core.Unit
-
Create a unit converter for converting from the
reference unit (other) to this unit.
- getUnitFormatter(Formatter<T>, Unit) - Method in class net.sf.basedb.core.Annotation
-
Wrap a parent formatter with a formatter for units.
- getUnitId() - Method in class net.sf.basedb.core.AnnotationBatcher.CurrentAnnotationInfo
-
Get the ID of the unit this annotation is using.
- getUnitId() - Method in class net.sf.basedb.core.snapshot.AnnotationSnapshot
-
- getUnits() - Method in class net.sf.basedb.core.data.QuantityData
-
This is the inverse end.
- getUnits() - Method in class net.sf.basedb.core.Quantity
-
Get a query that returns all units of this quantity.
- getUnitSymbol(Unit) - Method in class net.sf.basedb.core.Annotation
-
Shortcut for Unit.getDisplaySymbol()
, but also
checks the default unit of the annotation type.
- getUnitSymbol() - Method in class net.sf.basedb.core.snapshot.AnnotationLoaderUtil
-
- getUnknownLines() - Method in class net.sf.basedb.util.parser.FlatFileParser
-
- getUnpackDirectory(DbControl) - Method in class net.sf.basedb.util.zip.AbstractFileUnpacker
-
Get the directory where the unpacked files are placed by the plugin.
- getUnselectedtext() - Method in class net.sf.basedb.clients.web.taglib.Select
-
- getUpdatePropertyOrder(Class<? extends BatchableData>) - Static method in class net.sf.basedb.core.BatchUtil
-
Get the order of properties in the update SQL.
- getUpdatePropertyOrder(String) - Static method in class net.sf.basedb.core.BatchUtil
-
Get the order of properties in the update SQL.
- getUpdateSql(Class<? extends BatchableData>) - Static method in class net.sf.basedb.core.BatchUtil
-
Get the SQL that updates a new row of the specified class.
- getUpdateSql(String) - Static method in class net.sf.basedb.core.BatchUtil
-
Get the SQL that updates a new row of the specified class.
- getUploadStream(boolean) - Method in class net.sf.basedb.core.File
-
Get an OutputStream
that can be used
to upload a physical file for this file item.
- getUploadStream(boolean, Boolean) - Method in class net.sf.basedb.core.File
-
Get an OutputStream
that can be used
to upload a physical file for this file item.
- getUpperLimit() - Method in class net.sf.basedb.core.DoubleParameterType
-
Get the highest valid value of the parameter.
- getUpperLimit() - Method in class net.sf.basedb.core.FloatParameterType
-
Get the highest valid value of the parameter.
- getUpperLimit() - Method in class net.sf.basedb.core.IntegerParameterType
-
Get the highest valid value of the parameter.
- getUpperLimit() - Method in class net.sf.basedb.core.LongParameterType
-
Get the highest valid value of the parameter.
- getURI() - Method in class net.sf.basedb.core.File
-
Get the URL of an external file as an URI.
- getURI() - Method in class net.sf.basedb.util.extensions.manager.ExtensionsFile
-
Get an URI that points to the extensions file.
- getURI() - Method in interface net.sf.basedb.util.uri.ConnectionManager
-
Get the URI of the resource we are interested in.
- getURI() - Method in class net.sf.basedb.util.uri.http.HttpConnectionManager
-
- getUrl() - Method in interface net.sf.basedb.clients.web.extensions.plot.PlotGenerator
-
Get the URL to a servlet that is used to generate the image.
- getUrl() - Method in class net.sf.basedb.clients.web.extensions.plot.PlotGeneratorBean
-
- getUrl() - Method in class net.sf.basedb.clients.web.extensions.startpage.FixedStartPageFactory
-
- getUrl() - Method in interface net.sf.basedb.clients.web.extensions.startpage.StartPageAction
-
Get the URL to the start page.
- getUrl() - Method in class net.sf.basedb.clients.web.extensions.startpage.StartPageBean
-
- getUrl() - Method in class net.sf.basedb.core.authentication.ExtraUserInformation
-
An URL to the user homepage (or similar).
- getUrl() - Method in class net.sf.basedb.core.data.FileData
-
Get the URL to the file.
- getUrl() - Method in class net.sf.basedb.core.data.PluginDefinitionData
-
Get a URL with more information about the plugin.
- getUrl() - Method in class net.sf.basedb.core.data.UserData
-
Get the URL to the user's homepage, or null if unknown.
- getUrl(Object) - Method in class net.sf.basedb.core.ExtendedProperty
-
Create a link for this extended property.
- getUrl(Object) - Method in class net.sf.basedb.core.ExtendedPropertyLinker
-
Create a link.
- getUrl() - Method in class net.sf.basedb.core.File
-
Get the URL to the (external) file.
- getUrl() - Method in interface net.sf.basedb.core.plugin.About
-
An URL to get more information about the plugin.
- getUrl() - Method in class net.sf.basedb.core.plugin.AboutImpl
-
- getUrl() - Method in class net.sf.basedb.core.PluginDefinition
-
Get a URL with more information about the plugin.
- getUrl() - Method in class net.sf.basedb.core.User
-
Get the URL to the user's homepage.
- getUrl() - Method in class net.sf.basedb.util.extensions.AboutBean
-
- getUrl() - Method in class net.sf.basedb.util.extensions.Registry.RegisteredAbout
-
- getUsableUnits() - Method in class net.sf.basedb.core.AnnotationType
-
Get a query for returning the units that are considered
"usable" for this annotation type.
- getUsableUnits() - Method in class net.sf.basedb.core.data.AnnotationTypeData
-
The units that it makes sense to use with this annotation type.
- getUsedMemory() - Method in class net.sf.basedb.core.JobAgent
-
Get the current memory usage in bytes of the server where the job agent
is running.
- getUsedMemory() - Method in class net.sf.basedb.util.jobagent.JobAgentInfo
-
Get the used memory on the job agent's server in bytes.
- getUsedQuantity() - Method in class net.sf.basedb.core.BioMaterialEvent
-
Get the quantity that was used from the biomaterial by this event.
- getUsedQuantity(MeasuredBioMaterial) - Method in class net.sf.basedb.core.BioMaterialEvent
-
Get the quantity that was used by this event for the specified biomaterial.
- getUsedQuantity() - Method in class net.sf.basedb.core.BioMaterialEventSource
-
Get the quantity that was used from the source biomaterial by the event.
- getUsedQuantity() - Method in class net.sf.basedb.core.data.BioMaterialEventData
-
Get the used quantity of the biomaterial affected by this event.
- getUsedQuantity() - Method in class net.sf.basedb.core.data.BioMaterialEventSourceData
-
Get the used quantity from the parent biomaterial.
- getUsedSlot() - Method in class net.sf.basedb.core.InternalJobQueue.JobRunner
-
The slot the job is executing in.
- getUsedUnits() - Method in class net.sf.basedb.core.data.UnitData
-
This is the inverse end.
- getUsedWells() - Method in class net.sf.basedb.core.BioPlate
-
Get the number of used wells on this plate.
- getUseInternalJobQueue() - Method in class net.sf.basedb.core.data.PluginDefinitionData
-
If the plug-in can be executed with the internal job queue or
not.
- getUseInternalJobQueue() - Method in class net.sf.basedb.core.PluginDefinition
-
If this plug-in can be executed by the internal job queue or
not.
- getUsePermissions() - Method in class net.sf.basedb.core.data.PluginDefinitionData
-
If the permissions for this plugin should be used or not.
- getUsePermissions() - Method in class net.sf.basedb.core.PluginDefinition
-
Check if this plugin should execute with or without permissions.
- getUser(DbControl, ChangeHistory, boolean, boolean) - Static method in class net.sf.basedb.clients.web.ChangeHistoryUtil
-
Get the user that made the change in HTML format.
- getUser() - Method in class net.sf.basedb.core.BioMaterialEvent
-
Get the
User
that is responsible for this event.
- getUser(DbControl) - Method in class net.sf.basedb.core.ChangeHistory
-
Load the user that made the change.
- getUser() - Method in class net.sf.basedb.core.data.BioMaterialEventData
-
Get the user that is responsible for this event, typically this is the user that
entered the information in the database.
- getUser() - Method in class net.sf.basedb.core.data.ChangeHistoryData
-
- getUser() - Method in class net.sf.basedb.core.data.ContextData
-
Get the user that owns this context.
- getUser() - Method in class net.sf.basedb.core.data.DiskUsageData
-
- getUser() - Method in class net.sf.basedb.core.data.PasswordData
-
Get the user this password is referring to.
- getUser() - Method in class net.sf.basedb.core.data.PlateEventData
-
Get the user that is responsible for this event, typically this is the user that
entered the information in the database.
- getUser() - Method in class net.sf.basedb.core.data.SessionData
-
Get the user that logged in with this session.
- getUser() - Method in class net.sf.basedb.core.data.UserClientSettingData
-
Get the user this setting is valid for.
- getUser() - Method in class net.sf.basedb.core.data.UserDefaultSettingData
-
Get the user this setting is valid for.
- getUser() - Method in class net.sf.basedb.core.DiskUsage
-
- getUser() - Method in class net.sf.basedb.core.PlateEvent
-
Get the
User
that is responsible for this event.
- getUser() - Method in class net.sf.basedb.core.Session
-
Get the user that logged in with this session.
- getUser() - Method in class net.sf.basedb.core.UserClientSetting
-
Get the user this setting is valid for.
- getUser() - Method in class net.sf.basedb.core.UserDefaultSetting
-
Get the user this setting is valid for.
- getUserByExternalId(String) - Method in class net.sf.basedb.core.AuthenticationContext
-
Load a user item from the BASE database given an external id.
- getUserById(int) - Method in class net.sf.basedb.core.AuthenticationContext
-
Load a user item from the BASE database given an internal id.
- getUserByLogin(String) - Method in class net.sf.basedb.core.AuthenticationContext
-
Load a user item from the BASE database given a login name.
- getUserClientSetting(String) - Method in class net.sf.basedb.core.SessionControl
-
- getUserDefaultSetting(String) - Method in class net.sf.basedb.core.SessionControl
-
- getUserFilesDirectory() - Static method in class net.sf.basedb.core.Application
-
Get the path to the directory where uploaded
files are stored.
- getUserId() - Method in class net.sf.basedb.core.authentication.LoginRequest
-
Get the user id to use.
- getUserId() - Method in class net.sf.basedb.core.ChangeHistory
-
Get the ID of the user that made the change.
- getUserId() - Method in class net.sf.basedb.core.data.ChangeHistoryData
-
The ID of the user that made the change.
- getUserId() - Method in class net.sf.basedb.core.data.keyring.UserGroups
-
Get the id of the user.
- getUserId() - Method in class net.sf.basedb.core.data.keyring.UserKeys
-
Get the id of the user.
- getUserId() - Method in class net.sf.basedb.core.data.keyring.UserProjects
-
Get the id of the user.
- getUserId() - Method in class net.sf.basedb.core.data.keyring.UserRoles
-
Get the id of the user.
- getUserId() - Method in class net.sf.basedb.core.log.TransactionDetails
-
Get the ID of the currently logged in user, or 0 if no user is logged in.
- getUserIds(Permission) - Method in class net.sf.basedb.core.ItemKey
-
Get the ID:s of all users that have the specified permission in this item key.
- getUserLogin() - Method in class net.sf.basedb.core.Path
-
Get the userlogin part of the path.
- getUsername() - Method in class net.sf.basedb.core.data.FileServerData
-
Get the username that is used to login to the server.
- getUsername() - Method in class net.sf.basedb.core.FileServer
-
Get the username that is required to authenticate with the file
server.
- getUserName() - Method in class net.sf.basedb.core.log.TransactionDetails
-
Utility method for loading the name of the currently logged in user.
- getUsername() - Method in class net.sf.basedb.util.uri.ConnectionParameters
-
Get the username that should be used to authenticate the user.
- getUserPermissions() - Method in class net.sf.basedb.core.UserPermissions
-
Get the internal representation of the permissions.
- getUsers() - Method in class net.sf.basedb.core.data.GroupData
-
Get the set that manages which users are members of this group.
- getUsers() - Method in class net.sf.basedb.core.data.ItemKeyData
-
Get the map that manages which users that have permissions
for this key.
- getUsers() - Method in class net.sf.basedb.core.data.ProjectData
-
Get the map that manages which users are members of this project
and their permissions.
- getUsers() - Method in class net.sf.basedb.core.data.RoleData
-
Get the set that manages which users are members of this role.
- getUsers() - Method in class net.sf.basedb.core.Group
-
Get a query that returns the users that
are members of this group.
- getUsers() - Method in class net.sf.basedb.core.InternalJobQueue.JobQueueKeyring
-
Return empty set.
- getUsers() - Method in class net.sf.basedb.core.InternalStorageController.StorageKeyring
-
Return empty set.
- getUsers() - Method in class net.sf.basedb.core.Job.SignalKeyring
-
Return empty set.
- getUsers() - Method in class net.sf.basedb.core.Keyring
-
Get all users that share group membership with the logged in user.
- getUsers() - Method in class net.sf.basedb.core.MultiPermissions
-
Get a query that returns all users appearing in at least one of
the item keys.
- getUsers() - Method in class net.sf.basedb.core.Project
-
Get a query that returns the users that
are members of this project.
- getUsers() - Method in class net.sf.basedb.core.Role
-
Get a query that returns the users that
are members of this role.
- getUsers() - Method in class net.sf.basedb.core.ServiceSessionControl.ServicesKeyring
-
Return empty set.
- getUserSettings() - Method in class net.sf.basedb.core.data.ClientData
-
This is the inverse end.
- getUsingItems() - Method in class net.sf.basedb.core.AnnotationSet
-
Get the item this annotation set belongs to.
- getUsingItems() - Method in class net.sf.basedb.core.AnnotationType
-
Get all:
Annotations of this type
Experiments that are using this annotation type as an experimental factor
Protocols that are using this annotation type as a protocol parameter
- getUsingItems() - Method in class net.sf.basedb.core.ArrayBatch
-
- getUsingItems() - Method in class net.sf.basedb.core.ArrayDesign
-
- getUsingItems() - Method in class net.sf.basedb.core.ArrayDesignBlock
-
Get the array design this block is a part of.
- getUsingItems() - Method in class net.sf.basedb.core.ArrayDesignPlate
-
Get the array design this plate is used on.
- getUsingItems() - Method in class net.sf.basedb.core.ArraySlide
-
Get the bioassay that was used on this plate.
- getUsingItems() - Method in class net.sf.basedb.core.BasicItem
-
Get all items that are using this item.
- getUsingItems() - Method in class net.sf.basedb.core.BioPlate
-
Gets all MeasuredBioMaterial
located on this plate
and all child plates created from this plate.
- getUsingItems() - Method in class net.sf.basedb.core.BioPlateEventType
-
Gets all BioPlates
and BioPlateEventDefinitions
using this type
- getUsingItems() - Method in class net.sf.basedb.core.BioPlateType
-
Gets all BioPlates
and BioPlateEventDefinitions
using this type
- getUsingItems() - Method in class net.sf.basedb.core.BioSource
-
Get all:
Sample
:s created from this biosource
- getUsingItems() - Method in class net.sf.basedb.core.BioWell
-
- getUsingItems() - Method in class net.sf.basedb.core.DataFileType
-
- getUsingItems() - Method in class net.sf.basedb.core.DerivedBioAssay
-
Get all:
Child derived bioassays
Child raw bioassays
- getUsingItems() - Method in class net.sf.basedb.core.Directory
-
Get all:
File
:s in this directory
Sub-
Directory
:s in this directory
User
:s having this directory as their home-directory
Experiment
:s having this directory as the plugin directory
- getUsingItems() - Method in class net.sf.basedb.core.DiskUsage
-
Get the item this disk usage information belongs to.
- getUsingItems() - Method in class net.sf.basedb.core.Extract
-
- getUsingItems() - Method in class net.sf.basedb.core.ExtraValueType
-
- getUsingItems() - Method in class net.sf.basedb.core.File
-
- getUsingItems() - Method in class net.sf.basedb.core.FileServer
-
Get all files registered with this server.
- getUsingItems() - Method in class net.sf.basedb.core.FileSet
-
Get the item this file set belongs to.
- getUsingItems() - Method in class net.sf.basedb.core.Group
-
Get all:
User
:s assigned to this group as a quota group
- getUsingItems() - Method in class net.sf.basedb.core.Hardware
-
- getUsingItems() - Method in class net.sf.basedb.core.ItemKey
-
- getUsingItems() - Method in class net.sf.basedb.core.ItemSubtype
-
- getUsingItems() - Method in class net.sf.basedb.core.Job
-
Get the transformation and raw bioassays using this job.
- getUsingItems() - Method in class net.sf.basedb.core.Kit
-
- getUsingItems() - Method in class net.sf.basedb.core.MeasuredBioMaterial
-
Get all:
BioMaterial
:s where this item has been used as a source
- getUsingItems() - Method in class net.sf.basedb.core.PermissionTemplate
-
Get all:
Project
:s using this permission template
- getUsingItems() - Method in class net.sf.basedb.core.PhysicalBioAssay
-
- getUsingItems() - Method in class net.sf.basedb.core.Plate
-
- getUsingItems() - Method in class net.sf.basedb.core.PlateEventType
-
- getUsingItems() - Method in class net.sf.basedb.core.PlateGeometry
-
- getUsingItems() - Method in class net.sf.basedb.core.PlateMapping
-
Get all:
Plate
:s created with this mapping
- getUsingItems() - Method in class net.sf.basedb.core.PlateType
-
Get all:
Plate
:s created from this plate type
- getUsingItems() - Method in class net.sf.basedb.core.Platform
-
- getUsingItems() - Method in class net.sf.basedb.core.PlatformVariant
-
- getUsingItems() - Method in class net.sf.basedb.core.PluginConfiguration
-
Get all:
Job
:s using this configuration
- getUsingItems() - Method in class net.sf.basedb.core.PluginDefinition
-
- getUsingItems() - Method in class net.sf.basedb.core.ProjectKey
-
- getUsingItems() - Method in class net.sf.basedb.core.Protocol
-
- getUsingItems() - Method in class net.sf.basedb.core.Quantity
-
- getUsingItems() - Method in class net.sf.basedb.core.Quota
-
Get all:
User
:s assigned to this quota
Group
:s assigned to this quota
- getUsingItems() - Method in class net.sf.basedb.core.RawBioAssay
-
- getUsingItems() - Method in class net.sf.basedb.core.ReporterCloneTemplate
-
Get all:
Experiment that is using this template
- getUsingItems() - Method in class net.sf.basedb.core.ReporterType
-
- getUsingItems() - Method in class net.sf.basedb.core.Sample
-
Get all:
Extract
:s created from this sample
Pooled samples
- getUsingItems() - Method in class net.sf.basedb.core.Software
-
- getUsingItems() - Method in class net.sf.basedb.core.Tag
-
Get all:
Extract
:s marked with this tag
- getUsingItems() - Method in class net.sf.basedb.core.Unit
-
- getUsingItems() - Method in class net.sf.basedb.core.User
-
Get all:
Ownable
items owned by this user
- getUsingItems() - Method in class net.sf.basedb.core.Well
-
Get all:
Child wells
Features derived from this well
- getValidatedXml(URL, URL) - Static method in class net.sf.basedb.util.XmlUtil2
-
Load and validate an XML file against a DTD, and return it as a
Document
object.
- getValidatedXml(String, URL) - Static method in class net.sf.basedb.util.XmlUtil2
-
- getValidatedXML(InputStream, URL, String) - Static method in class net.sf.basedb.util.XmlUtil2
-
Validate an InputStream
against a DTD file
and return it as a Document
- getValidationError() - Method in class net.sf.basedb.util.extensions.manager.ExtensionsFile
-
Get more information about the error that caused the validation
to fail.
- getValidationOptions() - Method in class net.sf.basedb.util.overview.GenericOverview
-
Get the validation options currently in use.
- getValidationOptions() - Method in interface net.sf.basedb.util.overview.OverviewContext
-
Get the validation options that are currently in effect.
- getValidationPresets(SessionControl) - Static method in class net.sf.basedb.util.overview.OverviewUtil
-
Get the validation options presets for the currently logged in user.
- getValidationRule(InvokationContext<? super ValidationRuleAction>) - Method in class net.sf.basedb.util.overview.extensions.ReflectValidationRuleActionFactory
-
- getValidator() - Method in class net.sf.basedb.util.overview.Failure
-
Get the validation rule that failed.
- getValidators() - Static method in class net.sf.basedb.util.overview.OverviewUtil
-
- getValidators(DbControl) - Method in class net.sf.basedb.util.overview.validator.ExtensionNodeValidator
-
- getValue() - Method in class net.sf.basedb.clients.web.extensions.DynamicActionAttribute
-
Get the value of the dynamic attribute.
- getValue(DbControl, I) - Method in interface net.sf.basedb.clients.web.extensions.list.ListColumnAction
-
Get the value that should be displayed in the column.
- getValue(DbControl, I) - Method in class net.sf.basedb.clients.web.extensions.list.PropertyPathActionFactory.PropertyPathAction
-
- getValue() - Method in class net.sf.basedb.clients.web.taglib.table.Cell
-
- getValue() - Method in class net.sf.basedb.clients.web.taglib.table.CellValue
-
- getValue() - Method in class net.sf.basedb.clients.web.taglib.table.Hidden
-
- getValue() - Method in enum net.sf.basedb.core.BioMaterialEvent.Type
-
Get the integer value that is used when storing a BioMaterialEvent.Type
to the database.
- getValue() - Method in enum net.sf.basedb.core.BioWell.LockMode
-
Get the integer value that is used when storing a lock mode to the database.
- getValue() - Method in class net.sf.basedb.core.data.PropertyFilterData
-
Get the value used in this filter.
- getValue() - Method in class net.sf.basedb.core.data.SettingData
-
Get the value of this setting.
- getValue() - Method in enum net.sf.basedb.core.ExtraValue.CoordinateType
-
Get the integer value that is used when storing a
CoordinateType
in the database.
- getValue() - Method in enum net.sf.basedb.core.FeatureIdentificationMethod
-
Get the integer value that is used when storing the feature identification method
to the database.
- getValue() - Method in enum net.sf.basedb.core.File.Action
-
Get the integer value that is used when storing an File.Action to the database.
- getValue() - Method in enum net.sf.basedb.core.Formula.AverageMethod
-
Get the integer value that is used when storing a
Formula.AverageMethod
in the database.
- getValue() - Method in enum net.sf.basedb.core.Formula.Parser
-
Get the integer value that is used when storing a Formula.Parser
in the database.
- getValue() - Method in enum net.sf.basedb.core.Formula.Type
-
Get the integer value that is used when storing a Formula.Type
in the database.
- getValue() - Method in enum net.sf.basedb.core.Include
-
- getValue() - Method in enum net.sf.basedb.core.IntensityTransform
-
Get the integer value that is used when storing a transform in the database.
- getValue() - Method in enum net.sf.basedb.core.Item
-
Get the integer value that is used when storing an item to the database.
- getValue() - Method in enum net.sf.basedb.core.ItemContext.SortDirection
-
Get the integer value that is used when storing an location to the database.
- getValue() - Method in enum net.sf.basedb.core.Job.ExecutionTime
-
Get the integer value that is used when storing a Job.ExecutionTime
in the database.
- getValue() - Method in enum net.sf.basedb.core.Job.Status
-
Get the integer value that is used when storing a Job.Status
to the database.
- getValue() - Method in enum net.sf.basedb.core.Job.Type
-
Get the integer value that is used when storing a Job.Status
to the database.
- getValue() - Method in enum net.sf.basedb.core.Location
-
Get the integer value that is used when storing an location to the database.
- getValue() - Method in enum net.sf.basedb.core.log.ChangeType
-
Get the numerical value for this change type.
- getValue(DbControl, C) - Method in class net.sf.basedb.core.Metadata.BasicData2ItemPropertyPath
-
- getValue(DbControl, C) - Method in class net.sf.basedb.core.Metadata.BasicItem2DataPropertyPath
-
- getValue(DbControl, Collection<C>) - Method in class net.sf.basedb.core.Metadata.CollectionPropertyPath
-
- getValue(DbControl, C) - Method in class net.sf.basedb.core.Metadata.CombinedPropertyPath
-
- getValue(DbControl, C) - Method in class net.sf.basedb.core.Metadata.ComponentPropertyPath
-
- getValue(DbControl, Date) - Method in class net.sf.basedb.core.Metadata.DateCopyPropertyPath
-
- getValue(DbControl, C) - Method in class net.sf.basedb.core.Metadata.EntityPropertyPath
-
- getValue(DbControl, C) - Method in class net.sf.basedb.core.Metadata.EvictPropertyPath
-
- getValue(DbControl, IdentifiableData) - Method in class net.sf.basedb.core.Metadata.IdentifierPropertyPath
-
- getValue(DbControl, Map) - Method in class net.sf.basedb.core.Metadata.MapPropertyPath
-
- getValue(DbControl, C) - Method in class net.sf.basedb.core.Metadata.NoopPropertyPath
-
- getValue(DbControl, C) - Method in interface net.sf.basedb.core.Metadata.PropertyPath
-
Get the value as defined by the implementation for the given item.
- getValue(DbControl, ReporterScore) - Method in class net.sf.basedb.core.Metadata.ReporterScore2DataPropertyPath
-
- getValue() - Method in enum net.sf.basedb.core.Operator
-
Get the integer value that is used when storing an operator in the database.
- getValue(String) - Method in class net.sf.basedb.core.ParameterValuesImpl
-
- getValue() - Method in enum net.sf.basedb.core.plugin.GuiContext.Type
-
Get the integer value that is used when storing a GuiContext.Type
to the database.
- getValue(String) - Method in class net.sf.basedb.core.plugin.NamespaceParameterValuesWrapper
-
- getValue(String) - Method in interface net.sf.basedb.core.plugin.ParameterValues
-
Get a single value for a specific parameter.
- getValue(String) - Method in class net.sf.basedb.core.plugin.ParameterValuesWrapper
-
Get the value of the parameter with the specified name.
- getValue() - Method in enum net.sf.basedb.core.plugin.Plugin.MainType
-
- getValue() - Method in class net.sf.basedb.core.PropertyFilter
-
Get the value to use in the filter.
- getValue() - Method in class net.sf.basedb.core.query.QueryParameter
-
Get the value of the parameter.
- getValue() - Method in class net.sf.basedb.core.query.WhenStatement
-
Get the value returned by this statement
- getValue() - Method in class net.sf.basedb.core.Setting
-
Get the value of this setting.
- getValue() - Method in enum net.sf.basedb.core.Type
-
Get the integer value that is used when storing a type in the database.
- getValue(String) - Method in class net.sf.basedb.plugins.gtf.DefaultConfigurationValues
-
- getValue(String, String) - Method in class net.sf.basedb.util.bfs.MetadataModel
-
Utility method for getting the value of the first entry
in the first section that matches the given section and
key name.
- getValue(int) - Method in class net.sf.basedb.util.bfs.MetadataModel.Section
-
Get the value of the entry at the given index.
- getValue(String) - Method in class net.sf.basedb.util.bfs.MetadataModel.Section
-
Get the value of the first entry with a given key.
- getValue() - Method in class net.sf.basedb.util.bfs.MetadataModel.SectionEntry
-
Get the value of the entry.
- getValue(T, T, T) - Method in class net.sf.basedb.util.Diff3
-
Get the correct value to set on the newItem
object.
- getValue() - Method in class net.sf.basedb.util.Enumeration.Entry
-
- getValue(int) - Method in class net.sf.basedb.util.Enumeration
-
- getValue() - Method in class net.sf.basedb.util.fuzzy.StringMatcher.FuzzyMatch
-
Get the value string.
- getValue(FlatFileParser.Data, int) - Method in class net.sf.basedb.util.importer.spotdata.ExtraFloatParser
-
Get the extra value from the data.
- getValue(Map<String, List<String>>, String) - Method in class net.sf.basedb.util.jobagent.JobAgentInfo
-
- getValue(Map<String, List<String>>, String) - Method in class net.sf.basedb.util.jobagent.JobInfo
-
- getValue(FlatFileParser.Data) - Method in class net.sf.basedb.util.parser.ColumnMapper
-
Get the value in the data objects column with the index specified
in the constructor.
- getValue(FlatFileParser.Data) - Method in class net.sf.basedb.util.parser.CompoundMapper
-
Get a value by invoking each mapper in the order they appear in
the list and concatenating the result.
- getValue(FlatFileParser.Data) - Method in class net.sf.basedb.util.parser.ConstantMapper
-
- getValue(FlatFileParser.Data) - Method in class net.sf.basedb.util.parser.CropStringMapper
-
Use the parent mapper to get the string value.
- getValue(FlatFileParser.Data) - Method in class net.sf.basedb.util.parser.JepMapper
-
- getValue(FlatFileParser.Data) - Method in interface net.sf.basedb.util.parser.Mapper
-
Get the value for the line of data.
- getValue(FlatFileParser.Data) - Method in class net.sf.basedb.util.parser.NullIfExceptionMapper
-
- getValue(String) - Method in class net.sf.basedb.util.QueryParameters
-
Get the (single) value for a key.
- getValueAsObject() - Method in class net.sf.basedb.core.PropertyFilter
-
Get the value as an object of the correct type.
- getValueAsObject(Unit, boolean) - Method in class net.sf.basedb.core.PropertyFilter
-
Get the value as an object of the proper type converted to the
specified unit.
- getValueAsObject(String, Unit, boolean) - Method in class net.sf.basedb.core.PropertyFilter
-
- getValueAsObject() - Method in class net.sf.basedb.util.jep.FunctionSafeJep
-
Override the superclass method so that exceptions are passed on
instead of swallowed.
- getValueClass() - Method in enum net.sf.basedb.core.Type
-
Get the class of objects that can be used as values for this type.
- getValueCount() - Method in class net.sf.basedb.util.bfs.MetadataModel.SectionEntry
-
Get the number of values in the entry.
- getValueCount() - Method in class net.sf.basedb.util.bfs.MetadataWriter
-
Get the number of values that has been written to the current
section so far.
- getValueId() - Method in class net.sf.basedb.core.data.annotations.AnnotationLink
-
- getValueList2(Element, Class<T>) - Method in class net.sf.basedb.core.PluginConfiguration
-
Gets the list of values for a parameter from the XML-file.
- getValues() - Method in class net.sf.basedb.core.Annotation
-
Get the values this annotation contains.
- getValues(Unit) - Method in class net.sf.basedb.core.Annotation
-
Get the values for this annotation in a specific unit.
- getValues() - Method in class net.sf.basedb.core.AnnotationType
-
Get the list of allowed values if this annotation type is an enumeration.
- getValues() - Method in class net.sf.basedb.core.data.AnnotationData
-
The values of this annotation.
- getValues() - Method in class net.sf.basedb.core.data.BooleanParameterValueData
-
- getValues() - Method in class net.sf.basedb.core.data.DateParameterValueData
-
- getValues() - Method in class net.sf.basedb.core.data.DoubleParameterValueData
-
- getValues() - Method in class net.sf.basedb.core.data.FloatParameterValueData
-
- getValues() - Method in class net.sf.basedb.core.data.IntegerParameterValueData
-
- getValues() - Method in class net.sf.basedb.core.data.ItemParameterValueData
-
- getValues() - Method in class net.sf.basedb.core.data.LongParameterValueData
-
- getValues() - Method in class net.sf.basedb.core.data.ParameterValueData
-
Get values of this parameter.
- getValues() - Method in class net.sf.basedb.core.data.StringParameterValueData
-
- getValues() - Method in class net.sf.basedb.core.data.TextParameterValueData
-
- getValues() - Method in class net.sf.basedb.core.data.TimestampParameterValueData
-
- getValues() - Method in class net.sf.basedb.core.ExtraValue
-
Get a query returning the extra values.
- getValues() - Method in class net.sf.basedb.core.ParameterInfo
-
- getValues(String) - Method in class net.sf.basedb.core.ParameterValuesImpl
-
- getValues(String) - Method in class net.sf.basedb.core.plugin.NamespaceParameterValuesWrapper
-
- getValues(String) - Method in interface net.sf.basedb.core.plugin.ParameterValues
-
Get a List
of values for a specific parameter.
- getValues(String) - Method in class net.sf.basedb.core.plugin.ParameterValuesWrapper
-
Get the values of the parameter with the specified name.
- getValues() - Method in class net.sf.basedb.core.snapshot.AnnotationLoaderUtil
-
- getValues() - Method in class net.sf.basedb.core.snapshot.AnnotationSnapshot
-
- getValues(UnitConverter, Type) - Method in class net.sf.basedb.core.snapshot.AnnotationSnapshot
-
- getValues() - Method in class net.sf.basedb.plugins.executor.ProgramParameter
-
Get the values for this parameter.
- getValues(String) - Method in class net.sf.basedb.plugins.gtf.DefaultConfigurationValues
-
- getValues(String, String) - Method in class net.sf.basedb.util.bfs.MetadataModel
-
Utility method for getting the values of the first entry
in the first section that matches the given section and
key name.
- getValues(int) - Method in class net.sf.basedb.util.bfs.MetadataModel.Section
-
Get the values of the entry at the given index.
- getValues(String) - Method in class net.sf.basedb.util.bfs.MetadataModel.Section
-
Get the values of the first entry with a given key.
- getValues() - Method in class net.sf.basedb.util.bfs.MetadataModel.SectionEntry
-
Get all values.
- getValues(Map<String, List<String>>, String) - Method in class net.sf.basedb.util.jobagent.JobAgentInfo
-
- getValues() - Method in class net.sf.basedb.util.plot.PlotAnnotation
-
The values that falls into this annotation.
- getValues(String) - Method in class net.sf.basedb.util.QueryParameters
-
Get all values for a key.
- getValuesAsObjects() - Method in class net.sf.basedb.core.PropertyFilter
-
Splits the value string at each "|" and creates
a list with objects from the substrings that were found.
- getValuesAsObjects(Unit, boolean) - Method in class net.sf.basedb.core.PropertyFilter
-
- getValuesAsObjects(String, Unit, boolean) - Method in class net.sf.basedb.core.PropertyFilter
-
- getValueSeparator() - Method in class net.sf.basedb.core.PropertyFilter
-
- getValuesOrMask() - Method in class net.sf.basedb.core.ParameterInfo
-
- getValuesOrMask(String) - Method in class net.sf.basedb.core.ParameterInfo
-
- getValuesVersion() - Method in class net.sf.basedb.core.Annotation
-
Get the version number of the item keeping the values.
- getValueType() - Method in class net.sf.basedb.clients.web.extensions.list.AbstractListColumnBean
-
- getValueType() - Method in interface net.sf.basedb.clients.web.extensions.list.ListColumnAction
-
The data type of the values that are referenced by the property.
- getValueType() - Method in class net.sf.basedb.clients.web.taglib.table.ColumnDef
-
- getValueType() - Method in class net.sf.basedb.core.Annotation
-
Get the value type for this annotation type.
- getValueType() - Method in class net.sf.basedb.core.AnnotationBatcher.CurrentAnnotationInfo
-
- getValueType() - Method in class net.sf.basedb.core.AnnotationType
-
Get the value type for this annotation type.
- getValueType() - Method in class net.sf.basedb.core.data.AnnotationTypeData
-
The code for the value type.
- getValueType() - Method in class net.sf.basedb.core.data.BooleanParameterValueData
-
- getValueType() - Method in class net.sf.basedb.core.data.DataCubeExtraValueData
-
The type of value, ie. int, float or string.
- getValueType() - Method in class net.sf.basedb.core.data.DateParameterValueData
-
- getValueType() - Method in class net.sf.basedb.core.data.DoubleParameterValueData
-
- getValueType() - Method in class net.sf.basedb.core.data.ExtraValueTypeData
-
The code for the value type.
- getValueType() - Method in class net.sf.basedb.core.data.FloatParameterValueData
-
- getValueType() - Method in class net.sf.basedb.core.data.FormulaData
-
The code for the value type. null = not known or doesn't care.
- getValueType() - Method in class net.sf.basedb.core.data.IntegerParameterValueData
-
- getValueType() - Method in class net.sf.basedb.core.data.ItemParameterValueData
-
- getValueType() - Method in class net.sf.basedb.core.data.LongParameterValueData
-
- getValueType() - Method in class net.sf.basedb.core.data.ParameterValueData
-
Get the type of parameter values that are store in this parameter.
- getValueType() - Method in class net.sf.basedb.core.data.PropertyFilterData
-
Get the type of value user for this filter.
- getValueType() - Method in class net.sf.basedb.core.data.ReporterClonePropertyData
-
The code for the value type.
- getValueType() - Method in class net.sf.basedb.core.data.StringParameterValueData
-
- getValueType() - Method in class net.sf.basedb.core.data.TextParameterValueData
-
- getValueType() - Method in class net.sf.basedb.core.data.TimestampParameterValueData
-
- getValueType() - Method in class net.sf.basedb.core.DataCubeExtraValue
-
Get the value type of the extra values.
- getValueType() - Method in class net.sf.basedb.core.ExtraValue
-
Get the type of values.
- getValueType() - Method in class net.sf.basedb.core.ExtraValueType
-
Get the value type for this extra value type.
- getValueType() - Method in class net.sf.basedb.core.Formula
-
Get the type of values that this formula produces.
- getValueType() - Method in enum net.sf.basedb.core.Formula.Type
-
Get the type of values that formulas of this type must produce or
null if it can be any type of values.
- getValueType() - Method in class net.sf.basedb.core.ParameterInfo
-
Get the matching
Type
for the values stored in
this parameter.
- getValueType() - Method in class net.sf.basedb.core.ParameterType
-
Get the date type of values that can be stored in this parameter.
- getValueType() - Method in class net.sf.basedb.core.PropertyFilter
-
Get the type of the property.
- getValueType() - Method in class net.sf.basedb.core.query.ParameterExpression
-
Get the type of value.
- getValueType() - Method in class net.sf.basedb.plugins.batchimport.MultiPropertyIdMethod
-
- getValueType() - Method in class net.sf.basedb.plugins.batchimport.PropertyIdMethod
-
- getVariable(String) - Method in class net.sf.basedb.util.extensions.xml.VariableConverter
-
Get the value of a variable.
- getVariant() - Method in class net.sf.basedb.core.ArrayDesign
-
- getVariant() - Method in class net.sf.basedb.core.BioAssaySet
-
- getVariant() - Method in class net.sf.basedb.core.data.ArrayDesignData
-
Get the platform variant this raw bioassay uses, or null.
- getVariant() - Method in class net.sf.basedb.core.data.FileTypeIndex
-
- getVariant() - Method in class net.sf.basedb.core.data.PlatformFileTypeData
-
Get the platform variant or null.
- getVariant() - Method in class net.sf.basedb.core.data.RawBioAssayData
-
Get the platform variant this raw bioassay uses, or null.
- getVariant() - Method in class net.sf.basedb.core.DerivedBioAssay
-
- getVariant() - Method in class net.sf.basedb.core.ExtraValue
-
- getVariant() - Method in interface net.sf.basedb.core.FileStoreEnabled
-
Get the platform variant the item is related to.
- getVariant() - Method in class net.sf.basedb.core.PlatformFileType
-
Get the platform variant.
- getVariant() - Method in class net.sf.basedb.core.RawBioAssay
-
- getVariant(DbControl) - Method in class net.sf.basedb.core.RawDataType
-
Get the platform variant that this raw data type is associated with.
- getVariantRawDataType(Session, String) - Static method in class net.sf.basedb.core.RawDataTypes
-
- getVariants() - Method in class net.sf.basedb.core.data.PlatformData
-
The variants of this platform.
- getVariants() - Method in class net.sf.basedb.core.Platform
-
Get a query that returns variants of this platform.
- getVersion() - Method in class net.sf.basedb.core.BasicItem
-
- getVersion() - Method in class net.sf.basedb.core.data.BasicData
-
Get the version of the item.
- getVersion() - Method in interface net.sf.basedb.core.data.IdentifiableData
-
Get the version of this item.
- getVersion() - Method in class net.sf.basedb.core.data.VersionedParameter
-
Get the parameter version.
- getVersion() - Method in interface net.sf.basedb.core.Identifiable
-
Get the version number of the item.
- getVersion() - Method in interface net.sf.basedb.core.plugin.About
-
The version of the plugin software.
- getVersion() - Method in class net.sf.basedb.core.plugin.AboutImpl
-
- getVersion() - Static method in class net.sf.basedb.core.Version
-
- getVersion() - Method in class net.sf.basedb.util.extensions.AboutBean
-
- getVersion() - Method in class net.sf.basedb.util.extensions.Registry.RegisteredAbout
-
- getVersionParameter(String) - Static method in class net.sf.basedb.clients.web.taglib.Head
-
Get query parameter to the given absolute path (including root directory).
- getVersionString() - Static method in class net.sf.basedb.core.Application
-
Get the BASE version string.
- getVersionString() - Method in class net.sf.basedb.core.data.HardwareData
-
- getVersionString() - Method in class net.sf.basedb.core.data.PluginDefinitionData
-
Get the version of the plugin.
- getVersionString() - Method in class net.sf.basedb.core.data.SoftwareData
-
- getVersionString() - Method in class net.sf.basedb.core.Hardware
-
Get the versionstring of this Hardware
item.
- getVersionString() - Method in class net.sf.basedb.core.PluginDefinition
-
Get the version of the plugin.
- getVersionString() - Method in class net.sf.basedb.core.Software
-
Get the versionstring of this Software
item.
- getVersionSuffix() - Method in class net.sf.basedb.core.Application
-
Get the version suffix (eg.
- getVirtualColumn() - Method in class net.sf.basedb.core.ExtraValue
-
Get the virtual column object that represents the column where the
extra values are stored.
- getVirtualDb() - Method in class net.sf.basedb.core.BioAssaySet
-
Get the virtual database this bioassayset stores it's data in.
- getVirtualDb() - Method in interface net.sf.basedb.core.ClonableReporterQuery
-
Get the virtual database that the query is using.
- getVirtualDb() - Method in class net.sf.basedb.core.data.DataCubeData
-
Get the virtual database this cube belongs to.
- getVirtualDb() - Method in class net.sf.basedb.core.data.ExperimentData
-
Get the virtual database this experiment stores the analyzed data in.
- getVirtualDb() - Method in class net.sf.basedb.core.DataCube
-
Get the virtual database this cube is a part of.
- getVirtualDb() - Method in class net.sf.basedb.core.DataCubeColumn
-
Get the virtual database this column belongs to.
- getVirtualDb() - Method in class net.sf.basedb.core.DataCubeExtraValue
-
Get the virtual database this extra value belongs to.
- getVirtualDb() - Method in class net.sf.basedb.core.DataCubeFilter
-
Get the virtual database this filter belongs to.
- getVirtualDb() - Method in class net.sf.basedb.core.DataCubeLayer
-
Get the virtual database this layer belongs to.
- getVirtualDb() - Method in class net.sf.basedb.core.DynamicQuery
-
Get the virtual database that this query is using.
- getVirtualDb() - Method in class net.sf.basedb.core.DynamicReporterQuery
-
Get the virtual database that this query is using.
- getVirtualDb() - Method in class net.sf.basedb.core.Experiment
-
Get the virtual database ite that is used to manage experiment-specific
tables in the dynamic database for this experiment.
- getVirtualDb() - Method in class net.sf.basedb.core.ExtraValue
-
- getVirtualTable() - Method in class net.sf.basedb.core.DataCubeExtraValue
-
Get the virtual table this extra value stores it's data in.
- getVirtualTable(Type) - Method in enum net.sf.basedb.core.ExtraValue.CoordinateType
-
Get the VirtualTable
used to store extra values of
this coordinate type given the value type.
- getVirtualTable() - Method in class net.sf.basedb.core.ExtraValue
-
- getVisibleColumns() - Method in class net.sf.basedb.clients.web.taglib.table.Table
-
- getWaitingJobs() - Method in class net.sf.basedb.core.JobAgent
-
Get a query that returns all jobs that are waiting to be executed sorted
by their priority taking the priority boost into account.
- getWebAppClassLoader() - Method in class net.sf.basedb.clients.web.extensions.XJspCompiler
-
Get the class loader for the web application this JSP is
located in.
- getWell() - Method in class net.sf.basedb.core.data.FeatureData
-
Get the well of the feature.
- getWell(DbControl, FeatureData) - Static method in class net.sf.basedb.core.Feature
-
Get the well from a feature.
- getWell(int, int) - Method in class net.sf.basedb.core.Plate
-
Get the well on the specified plate coordinate.
- getWells() - Method in class net.sf.basedb.core.data.PlateData
-
The wells on this plate.
- getWells() - Method in class net.sf.basedb.core.Plate
-
Get a query returning all wells for this plate.
- getWhichItemsParameter() - Method in class net.sf.basedb.clients.web.plugins.SimpleExport
-
- getWhichPropertiesParameter() - Method in class net.sf.basedb.clients.web.plugins.SimpleExport
-
- getWidth() - Method in interface net.sf.basedb.clients.web.extensions.plot.PlotGenerator
-
Get the width of the generated image.
- getWidth() - Method in class net.sf.basedb.clients.web.extensions.plot.PlotGeneratorBean
-
- getWidth() - Method in class net.sf.basedb.core.AnnotationType
-
Get the recommended width in characters a client application should use
to render an input field for annotations of this annotation type.
- getWidth() - Method in class net.sf.basedb.core.data.AnnotationTypeData
-
The recommended width (characters) to display input fields for this
annotation in client applications.
- getWidth() - Method in class net.sf.basedb.core.ParameterType
-
Get the width of the input field in the GUI.
- getWorkingDirectory() - Method in class net.sf.basedb.plugins.executor.ExternalProgramExecutor
-
Get the current working directory were data files for the
external program are stored.
- getWriteableFile() - Method in class net.sf.basedb.util.extensions.manager.ExtensionsFile
-
Get a writeable view for the current file.
- getX() - Method in class net.sf.basedb.core.data.RawData
-
- getX(int, int) - Method in class net.sf.basedb.util.plot.HistogramPlot.HistogramDataset
-
- getX() - Method in class net.sf.basedb.util.plot.HistogramPlot.TempSeries
-
- getXml(String, URL, boolean) - Static method in class net.sf.basedb.util.XmlUtil2
-
Parse a string containing XML, optionally validating it against a DTD,
and return it as a Document
object.
- getXmlLoader() - Method in class net.sf.basedb.util.extensions.manager.processor.PluginInstallationProcessor
-
Get the loader the processor is using for parsing xml files with
plug-in definitions.
- getXmlLoader() - Method in class net.sf.basedb.util.extensions.manager.processor.RegisterExtensionsProcessor
-
Get the loader the processor is using for parsing xml files with
extension definitions.
- getXmlStream() - Method in class net.sf.basedb.util.extensions.manager.ExtensionsFile
-
Get an input stream for reading the XML file containing the extension
definitions.
- getXOffset() - Method in class net.sf.basedb.core.data.SpotImagesData
-
Get the x-axis offset.
- getXOffset() - Method in class net.sf.basedb.core.SpotImages
-
Get the X-axis offset used to convert data coordinates to image
pixel values: xPixel = (xData - xOffset) / xScale
.
- getXScale() - Method in class net.sf.basedb.core.data.SpotImagesData
-
Get the x-axis scale.
- getXScale() - Method in class net.sf.basedb.core.SpotImages
-
Get the X-axis scale factor used to convert data coordinates to image
pixel values: xPixel = (xData - xOffset) / xScale
.
- getXValue(int, int) - Method in class net.sf.basedb.util.plot.HistogramPlot.HistogramDataset
-
- getY() - Method in class net.sf.basedb.core.data.RawData
-
- getY(int, int) - Method in class net.sf.basedb.util.plot.HistogramPlot.HistogramDataset
-
- getY() - Method in class net.sf.basedb.util.plot.HistogramPlot.TempSeries
-
- getYOffset() - Method in class net.sf.basedb.core.data.SpotImagesData
-
The y-axis offset.
- getYOffset() - Method in class net.sf.basedb.core.SpotImages
-
Get the Y-axis offset used to convert data coordinates to image
pixel values: yPixel = (yData - yOffset) / yScale
.
- getYScale() - Method in class net.sf.basedb.core.data.SpotImagesData
-
Get the y-axis scale.
- getYScale() - Method in class net.sf.basedb.core.SpotImages
-
Get the Y-axis scale factor used to convert data coordinates to image
pixel values: yPixel = (yData - yOffset) / yScale
.
- getYValue(int, int) - Method in class net.sf.basedb.util.plot.HistogramPlot.HistogramDataset
-
- getZipFile(DbControl) - Method in class net.sf.basedb.util.zip.AbstractFileUnpacker
-
Get the file that is going to be unpacked by the plugin.
- getZipFileParameter(String, String) - Method in class net.sf.basedb.util.zip.AbstractFileUnpacker
-
Get a plugin parameter that asks for the file that is going to
be unpacked.
- GlobalDefaultSetting - Class in net.sf.basedb.core
-
This class is used to represent a global default setting.
- GlobalDefaultSetting(GlobalDefaultSettingData) - Constructor for class net.sf.basedb.core.GlobalDefaultSetting
-
- GlobalDefaultSettingData - Class in net.sf.basedb.core.data
-
- GlobalDefaultSettingData() - Constructor for class net.sf.basedb.core.data.GlobalDefaultSettingData
-
- globalSignalId - Variable in class net.sf.basedb.core.signal.AbstractSignalTransporter
-
- globalVersion - Static variable in class net.sf.basedb.clients.web.taglib.Head
-
- grant(Permission) - Static method in enum net.sf.basedb.core.Permission
-
Convert the given permission to the integer grant value.
- grant(Permission...) - Static method in enum net.sf.basedb.core.Permission
-
Combine the given permissions and convert to the integer grant value.
- grant(Set<Permission>) - Static method in enum net.sf.basedb.core.Permission
-
Combine the given permission and convert to the integer grant value.
- granted - Variable in class net.sf.basedb.core.data.keyring.PluginKeys
-
- granted - Variable in class net.sf.basedb.core.data.PluginPermission
-
- granted - Variable in class net.sf.basedb.core.PluginPermission
-
- grantValue - Variable in enum net.sf.basedb.core.Permission
-
- grantValue() - Method in enum net.sf.basedb.core.Permission
-
- GreaterConverter - Class in net.sf.basedb.util.jep.convert
-
- GreaterConverter() - Constructor for class net.sf.basedb.util.jep.convert.GreaterConverter
-
- GreaterEqualsConverter - Class in net.sf.basedb.util.jep.convert
-
- GreaterEqualsConverter() - Constructor for class net.sf.basedb.util.jep.convert.GreaterEqualsConverter
-
- greenImageFile - Variable in class net.sf.basedb.core.data.SpotImagesData
-
- group(Expression) - Method in class net.sf.basedb.core.AbstractEntityQuery
-
Not supported.
- group(Expression) - Method in class net.sf.basedb.core.AbstractQuery
-
- group - Variable in class net.sf.basedb.core.data.DiskUsageData
-
- Group - Class in net.sf.basedb.core
-
This class is used to represent groups.
- Group(GroupData) - Constructor for class net.sf.basedb.core.Group
-
- group(Expression) - Method in interface net.sf.basedb.core.query.Query
-
Add an expression query element to the group list.
- Group.QueryRuntimeFilterImpl - Class in net.sf.basedb.core
-
A runtime filter implementation that limits a query to only
return groups where the logged in user is a member unless the logged in user
has generic read permission.
- GroupData - Class in net.sf.basedb.core.data
-
This class holds information about a group.
- GroupData() - Constructor for class net.sf.basedb.core.data.GroupData
-
- GroupGroups - Class in net.sf.basedb.core.data.keyring
-
Class for mapping the GroupGroups
table.
- GroupGroups() - Constructor for class net.sf.basedb.core.data.keyring.GroupGroups
-
Create a new GroupGroups
object.
- groupId - Variable in class net.sf.basedb.core.data.keyring.GroupKeys
-
- groupId - Variable in class net.sf.basedb.core.data.keyring.GroupProjects
-
- groupId - Variable in class net.sf.basedb.core.data.keyring.UserGroups
-
- GroupKeys - Class in net.sf.basedb.core.data.keyring
-
Class for mapping the GroupKeys
table.
- GroupKeys() - Constructor for class net.sf.basedb.core.data.keyring.GroupKeys
-
Create a new GroupKeys
object.
- groupPermanent(Expression) - Method in class net.sf.basedb.core.AbstractEntityQuery
-
Not supported.
- groupPermanent(Expression) - Method in class net.sf.basedb.core.AbstractQuery
-
- groupPermanent(Expression) - Method in interface net.sf.basedb.core.query.Query
-
Permanently add an expression query element to the group list.
- GroupPermissions - Class in net.sf.basedb.core
-
This class is used to specify permissions to share an item to
groups.
- GroupPermissions() - Constructor for class net.sf.basedb.core.GroupPermissions
-
Create a new empty object.
- GroupPermissions(ItemKey) - Constructor for class net.sf.basedb.core.GroupPermissions
-
Create a new object, and initialise it with the permissions from a
ItemKey
.
- groupPermissions - Variable in class net.sf.basedb.core.GroupPermissions
-
- groupPermissions - Variable in class net.sf.basedb.core.MultiPermissions
-
- GroupProjects - Class in net.sf.basedb.core.data.keyring
-
Class for mapping the GroupProjects
table.
- GroupProjects() - Constructor for class net.sf.basedb.core.data.keyring.GroupProjects
-
Create a new GroupProjects
object.
- groups - Variable in class net.sf.basedb.clients.web.ExperimentExplorer.AnnotationSummary
-
- groups - Variable in class net.sf.basedb.core.AbstractQuery
-
List of group expressions added to the query.
- groups - Variable in class net.sf.basedb.core.data.ItemKeyData
-
- groups - Variable in class net.sf.basedb.core.data.ProjectData
-
- groups - Variable in class net.sf.basedb.core.data.UserData
-
- groups - Variable in class net.sf.basedb.core.Keyring
-
Holds the ID of all groups that the user is a
member of, directly or indirectly.
- groups - Variable in class net.sf.basedb.core.query.SharedToRestriction
-
- groupsWithNonHiddenMembers - Variable in class net.sf.basedb.core.Keyring
-
A subset of the 'groups' set that holds the id of the groups
that has hiddenMembers = false
- GT - Static variable in class net.sf.basedb.clients.web.util.HTML
-
- gt(String, AnnotationType, Object, boolean) - Static method in class net.sf.basedb.core.query.Annotations
-
- gt(Expression, Expression) - Static method in class net.sf.basedb.core.query.Restrictions
-
Compare if one expression is greater than another: new restriction = e1 > e2.
- gteq(String, AnnotationType, Object, boolean) - Static method in class net.sf.basedb.core.query.Annotations
-
- gteq(Expression, Expression) - Static method in class net.sf.basedb.core.query.Restrictions
-
Compare if one expression is greater than or equal
to another: new restriction = e1 >= e2.
- GteqRestriction - Class in net.sf.basedb.core.query
-
Compare if one expression is greater than or equal to
another: e1 > e2.
- GteqRestriction(Expression, Expression) - Constructor for class net.sf.basedb.core.query.GteqRestriction
-
- GtfInputStream - Class in net.sf.basedb.util.gtf
-
Input stream implementation that reads from a GTF file and converts it to
a simple tab-separated file with a single line of column headers.
- GtfInputStream(InputStream, String, boolean) - Constructor for class net.sf.basedb.util.gtf.GtfInputStream
-
Create a new input stream reading from the master.
- GtfInputStream.Attribute - Class in net.sf.basedb.util.gtf
-
- GtfReporterImporter - Class in net.sf.basedb.plugins.gtf
-
Reporter importer implementation that create reporters from information
in GTF files.
- GtfReporterImporter() - Constructor for class net.sf.basedb.plugins.gtf.GtfReporterImporter
-
- GtfReporterMapImporter - Class in net.sf.basedb.plugins.gtf
-
Import features to an array design from a GTF file.
- GtfReporterMapImporter() - Constructor for class net.sf.basedb.plugins.gtf.GtfReporterMapImporter
-
- GtfValidationAction - Class in net.sf.basedb.util.gtf
-
Action for validation of GTF files in a file set.
- GtfValidationAction(DbControl, ArrayDesign, int) - Constructor for class net.sf.basedb.util.gtf.GtfValidationAction
-
Create a new action.
- GtfValidationFactory - Class in net.sf.basedb.util.gtf
-
Action factory for creating GTF file validators.
- GtfValidationFactory() - Constructor for class net.sf.basedb.util.gtf.GtfValidationFactory
-
- GtRestriction - Class in net.sf.basedb.core.query
-
Compare if one expression is greater than another: e1 > e2.
- GtRestriction(Expression, Expression) - Constructor for class net.sf.basedb.core.query.GtRestriction
-
- GUEST - Static variable in class net.sf.basedb.core.Role
-
The id for the Role
item representing guests.
- guiContext - Variable in class net.sf.basedb.clients.web.extensions.JspContext
-
- GuiContext - Class in net.sf.basedb.core.plugin
-
- GuiContext(Item, GuiContext.Type) - Constructor for class net.sf.basedb.core.plugin.GuiContext
-
- GuiContext(Item, GuiContext.Type, String) - Constructor for class net.sf.basedb.core.plugin.GuiContext
-
- GuiContext.Type - Enum in net.sf.basedb.core.plugin
-
- GuiContextData - Class in net.sf.basedb.core.data
-
This is a helper component for the
PluginDefinitionData
item to
store the contexts where a plugin can be used in a client application.
- GuiContextData() - Constructor for class net.sf.basedb.core.data.GuiContextData
-
- GuiContextData(int, int) - Constructor for class net.sf.basedb.core.data.GuiContextData
-
- guiContexts - Static variable in class net.sf.basedb.clients.web.plugins.SimpleExport
-
- guiContexts - Variable in class net.sf.basedb.core.data.PluginDefinitionData
-
- guiContexts - Static variable in class net.sf.basedb.plugins.AnnotationFlatFileImporter
-
- guiContexts - Static variable in class net.sf.basedb.plugins.BaseFileExporterPlugin
-
- guiContexts - Static variable in class net.sf.basedb.plugins.batchimport.AnnotationTypeImporter
-
- guiContexts - Static variable in class net.sf.basedb.plugins.batchimport.ArrayBatchImporter
-
- guiContexts - Static variable in class net.sf.basedb.plugins.batchimport.ArrayDesignImporter
-
- guiContexts - Static variable in class net.sf.basedb.plugins.batchimport.ArraySlideImporter
-
- guiContexts - Static variable in class net.sf.basedb.plugins.batchimport.BioPlateImporter
-
- guiContexts - Static variable in class net.sf.basedb.plugins.batchimport.BioSourceImporter
-
- guiContexts - Static variable in class net.sf.basedb.plugins.batchimport.DerivedBioAssayImporter
-
- guiContexts - Static variable in class net.sf.basedb.plugins.batchimport.ExtractImporter
-
- guiContexts - Static variable in class net.sf.basedb.plugins.batchimport.FileImporter
-
- guiContexts - Static variable in class net.sf.basedb.plugins.batchimport.HybridizationImporter
-
Deprecated.
- guiContexts - Static variable in class net.sf.basedb.plugins.batchimport.KitImporter
-
- guiContexts - Static variable in class net.sf.basedb.plugins.batchimport.LabeledExtractImporter
-
Deprecated.
- guiContexts - Static variable in class net.sf.basedb.plugins.batchimport.PhysicalBioAssayImporter
-
- guiContexts - Static variable in class net.sf.basedb.plugins.batchimport.RawBioAssayImporter
-
- guiContexts - Static variable in class net.sf.basedb.plugins.batchimport.SampleImporter
-
- guiContexts - Static variable in class net.sf.basedb.plugins.batchimport.ScanImporter
-
Deprecated.
- guiContexts - Static variable in class net.sf.basedb.plugins.BfsExporterPlugin
-
- guiContexts - Static variable in class net.sf.basedb.plugins.CdfFileReporterImporter
-
- guiContexts - Static variable in class net.sf.basedb.plugins.FormulaFilter
-
- guiContexts - Static variable in class net.sf.basedb.plugins.GalExporter
-
- guiContexts - Static variable in class net.sf.basedb.plugins.HelpExporter
-
- guiContexts - Static variable in class net.sf.basedb.plugins.HelpImporter
-
- guiContexts - Static variable in class net.sf.basedb.plugins.IlluminaRawDataImporter
-
- guiContexts - Static variable in class net.sf.basedb.plugins.IntensityCalculatorPlugin
-
- guiContexts - Static variable in class net.sf.basedb.plugins.JepExtraValueCalculator
-
- guiContexts - Static variable in class net.sf.basedb.plugins.JepIntensityTransformer
-
- guiContexts - Static variable in class net.sf.basedb.plugins.PackedFileExporter
-
- guiContexts - Static variable in class net.sf.basedb.plugins.PlateFlatFileImporter
-
- guiContexts - Static variable in class net.sf.basedb.plugins.PlateMappingExporter
-
- guiContexts - Static variable in class net.sf.basedb.plugins.PlateMappingImporter
-
- guiContexts - Static variable in class net.sf.basedb.plugins.PluginConfigurationExporter
-
- guiContexts - Static variable in class net.sf.basedb.plugins.PluginConfigurationImporter
-
- guiContexts - Static variable in class net.sf.basedb.plugins.PrintMapFlatFileImporter
-
- guiContexts - Static variable in class net.sf.basedb.plugins.RawDataFlatFileImporter
-
- guiContexts - Static variable in class net.sf.basedb.plugins.ReporterFlatFileImporter
-
- guiContexts - Static variable in class net.sf.basedb.plugins.ReporterMapFlatFileImporter
-
- guiContexts - Static variable in class net.sf.basedb.util.zip.AbstractFileUnpacker
-
The context is always [ FILE, ITEM].
- guiTitle - Variable in class net.sf.basedb.plugins.BaseFileExporterPlugin.ExtendedDynamicField
-
- guiTitle - Variable in class net.sf.basedb.plugins.BfsExporterPlugin.ExtendedExportableField
-
- gzip - Variable in class net.sf.basedb.util.zip.GzipFilePacker
-
- GzipFilePacker - Class in net.sf.basedb.util.zip
-
This class wraps the
TarFilePacker
in a GZIP stream, creating
a tar.gz file.
- GzipFilePacker() - Constructor for class net.sf.basedb.util.zip.GzipFilePacker
-
Create a new packer that compresses files with the gzip format.
- GzipFileUnpacker - Class in net.sf.basedb.plugins
-
A plugin for unpacking a gzipped file to
the BASE file system.
- GzipFileUnpacker() - Constructor for class net.sf.basedb.plugins.GzipFileUnpacker
-
- s - Variable in class net.sf.basedb.core.QueryExecutor.CancelableStatement
-
- S - Variable in class net.sf.basedb.util.bcrypt.BCrypt
-
- S_orig - Static variable in class net.sf.basedb.util.bcrypt.BCrypt
-
- SAFE_TAGS - Static variable in class net.sf.basedb.clients.web.util.HTML
-
This pattern is a list of HTML tags considered "safe".
- safeEquals(Date, Date, boolean) - Static method in class net.sf.basedb.core.DateUtil
-
Compare two date instances for equality while protecting from
strange implementations in the java.util.Date and java.sql.Timestamp
classes.
- SafeFunctionTable(FunctionSafeJep) - Constructor for class net.sf.basedb.util.jep.FunctionSafeJep.SafeFunctionTable
-
- safeIdList(DbControl, ItemQuery<?>, String, Set<Integer>) - Method in class net.sf.basedb.util.listable.AbstractSourceItemTransformer
-
- safeInvariantEquals(List<Date>, List<Date>, boolean) - Static method in class net.sf.basedb.core.DateUtil
-
Checks if two lists contains equal elements disregarding
their positions in the array.
- safeToDrop(TableInfo.IndexInfo) - Method in class net.sf.basedb.core.dbengine.TableInfo
-
It is safe to drop an index if it is not the primary key.
- SAM - Static variable in class net.sf.basedb.core.DataFileType
-
The external ID for the file type representing
a SAM (Sequence Alignment/Map) file.
- SAME_UNITS - Static variable in class net.sf.basedb.clients.web.plugins.SimpleExport
-
- sameVersion - Variable in class net.sf.basedb.util.Diff3
-
- Sample - Class in net.sf.basedb.core
-
This class is used to represent sample items.
- Sample(SampleData) - Constructor for class net.sf.basedb.core.Sample
-
- SampleData - Class in net.sf.basedb.core.data
-
This represents a sample.
- SampleData() - Constructor for class net.sf.basedb.core.data.SampleData
-
- SampleImporter - Class in net.sf.basedb.plugins.batchimport
-
Plug-in for importing sample items in a batch.
- SampleImporter() - Constructor for class net.sf.basedb.plugins.batchimport.SampleImporter
-
- SampleLoader - Class in net.sf.basedb.util.overview.loader
-
Node loader implementation for samples.
- SampleLoader() - Constructor for class net.sf.basedb.util.overview.loader.SampleLoader
-
- sampleQuery - Variable in class net.sf.basedb.plugins.batchimport.AbstractItemImporter
-
- SampleToBioSourceTransformer - Class in net.sf.basedb.util.biomaterial
-
- SampleToBioSourceTransformer(DbControl) - Constructor for class net.sf.basedb.util.biomaterial.SampleToBioSourceTransformer
-
Deprecated.
- SampleToBioSourceTransformer - Class in net.sf.basedb.util.listable
-
Source item transformer that transform sample items to their parent
biosources.
- SampleToBioSourceTransformer() - Constructor for class net.sf.basedb.util.listable.SampleToBioSourceTransformer
-
- SampleToChildSampleTransformer - Class in net.sf.basedb.util.listable
-
Source item transformer implementation that transform sample items to their
child sample items.
- SampleToChildSampleTransformer(boolean) - Constructor for class net.sf.basedb.util.listable.SampleToChildSampleTransformer
-
Create a new sample to child sample transformer.
- SampleToExtractTransformer - Class in net.sf.basedb.util.biomaterial
-
- SampleToExtractTransformer(DbControl) - Constructor for class net.sf.basedb.util.biomaterial.SampleToExtractTransformer
-
Deprecated.
Create a new Sample-to-extract transformer.
- SampleToExtractTransformer - Class in net.sf.basedb.util.listable
-
Source item transformer that transform sample items to their child
extract.
- SampleToExtractTransformer() - Constructor for class net.sf.basedb.util.listable.SampleToExtractTransformer
-
- SampleToParentSampleTransformer - Class in net.sf.basedb.util.listable
-
Source item transformer implementation that transform sample items to their
parent sample items.
- SampleToParentSampleTransformer(boolean) - Constructor for class net.sf.basedb.util.listable.SampleToParentSampleTransformer
-
Create a new sample to parent sample transformer.
- SampleValidator - Class in net.sf.basedb.util.overview.validator
-
Validator implementation for sample.
- SampleValidator() - Constructor for class net.sf.basedb.util.overview.validator.SampleValidator
-
- SAMPLING - Static variable in class net.sf.basedb.core.Kit
-
The ID for the sampling kit type, for example a kit
used when creating a
Sample
from a
BioSource
.
- SAMPLING - Static variable in class net.sf.basedb.core.Protocol
-
The ID for the sampling protocol type, for example a protocol
used when creating a
Sample
from a
BioSource
.
- save(Object) - Method in class net.sf.basedb.core.hibernate.SessionWrapper
-
- save(String, Object) - Method in class net.sf.basedb.core.hibernate.SessionWrapper
-
- save() - Method in class net.sf.basedb.util.extensions.manager.Settings
-
Save the settings to disk.
- SAVE_AS - Static variable in class net.sf.basedb.core.plugin.AbstractExporterPlugin
-
- saveAllCurrentContexts(Session, UserData, ClientData) - Method in class net.sf.basedb.core.SessionControl
-
- saveAllUserSettings(Session) - Method in class net.sf.basedb.core.SessionControl
-
Saves all user settings.
- saveCurrentContextAs(Item, String, boolean, boolean) - Method in class net.sf.basedb.core.SessionControl
-
Same as: saveCurrentContextAs(item, "", name, overwrite, isPublic)
.
- saveCurrentContextAs(Item, String, String, boolean, boolean) - Method in class net.sf.basedb.core.SessionControl
-
Save the current context as a named context.
- saveData(Session, BasicData) - Static method in class net.sf.basedb.core.HibernateUtil
-
Save a new data object to the database.
- saveData(StatelessSession, BasicData) - Static method in class net.sf.basedb.core.HibernateUtil
-
Save a new data object to the database.
- SaveIf(BasicItem, boolean) - Constructor for class net.sf.basedb.core.DbControl.SaveIf
-
- saveIfQueue - Variable in class net.sf.basedb.core.DbControl
-
Lists items that are saved only if the parent item is also saved.
- saveImage(ZipOutputStream, String, RenderedImage, float) - Method in class net.sf.basedb.core.SpotImages
-
Saving an image as jpeg and putting it in a zip file
- saveImageToFile(DbControl, BufferedImage, String, String, boolean) - Method in class net.sf.basedb.clients.web.servlet.ExperimentExplorerPlotServlet
-
- saveItem(BasicItem) - Method in class net.sf.basedb.core.DbControl
-
Schedule a new item to be saved in the database.
- saveItemIf(BasicItem, BasicItem, boolean) - Method in class net.sf.basedb.core.DbControl
-
Schedule a new item to be saved in the database if another item is also saved.
- saveOrUpdate(Object) - Method in class net.sf.basedb.core.hibernate.SessionWrapper
-
- saveOrUpdate(String, Object) - Method in class net.sf.basedb.core.hibernate.SessionWrapper
-
- saveParameters(Job, Map<String, PluginParameter<?>>) - Method in class net.sf.basedb.core.ParameterValuesImpl
-
- saveParameters(PluginConfiguration, Map<String, PluginParameter<?>>) - Method in class net.sf.basedb.core.ParameterValuesImpl
-
- saveParameters(DbControl, GuiContext) - Method in class net.sf.basedb.core.PluginRequest
-
Save all parameters that have got values in this request/response session.
- saveParameters(DbControl) - Method in class net.sf.basedb.core.PluginResponse
-
Save all parameters that has been configured during the configuration sequence to
the database.
- SavePointWork<R> - Class in net.sf.basedb.core.hibernate
-
A wrapper work that protects a parent work with a savepoint.
- SavePointWork(ReturningWork<R>) - Constructor for class net.sf.basedb.core.hibernate.SavePointWork
-
Create a new work item.
- saveSettings() - Method in class net.sf.basedb.clients.web.extensions.ExtensionsControl
-
Save the settings.
- saveSettings(Session, Query, Map<String, SessionControl.SettingInfo>, Class<I>, UserData, ClientData) - Method in class net.sf.basedb.core.SessionControl
-
Save settings when a user logs out.
- saveState(Serializable) - Method in class net.sf.basedb.core.Job
-
Save the job state to the static cache.
- saveTo - Variable in class net.sf.basedb.core.plugin.AbstractExporterPlugin
-
- saveToPreset(Presets.Preset) - Method in class net.sf.basedb.util.overview.ValidationOptions
-
Save the current settings to a preset.
- saveValidationPresets(SessionControl) - Static method in class net.sf.basedb.util.overview.OverviewUtil
-
Save the validation option presets for the logged in user.
- sc - Variable in class net.sf.basedb.clients.jobagent.Agent
-
- sc - Variable in class net.sf.basedb.clients.web.servlet.RssNewsFeed
-
- sc - Variable in class net.sf.basedb.clients.web.taglib.Page
-
The SessionControl object in use for this request.
- sc - Variable in class net.sf.basedb.clients.web.taglib.table.Table
-
- sc - Variable in class net.sf.basedb.core.AbstractBatcher
-
- sc - Variable in class net.sf.basedb.core.Application.Pinger
-
- sc - Variable in class net.sf.basedb.core.DataResultIterator
-
The SessionControl
- sc - Variable in class net.sf.basedb.core.DbControl
-
- sc - Variable in class net.sf.basedb.core.hibernate.ExecuteUpdateWork
-
- sc - Variable in class net.sf.basedb.core.hibernate.ResultSetWork
-
- sc - Variable in class net.sf.basedb.core.InternalJobQueue
-
The job queues session controller.
- sc - Variable in class net.sf.basedb.core.InternalStorageController
-
The session controller.
- sc - Variable in class net.sf.basedb.core.Job.ProgressReporterImpl
-
- sc - Variable in class net.sf.basedb.core.plugin.AbstractPlugin
-
- sc - Variable in class net.sf.basedb.core.PluginRequest
-
- sc - Variable in class net.sf.basedb.util.annotations.RunnableInheritAnnotationsManager
-
- sc - Variable in class net.sf.basedb.util.extensions.ClientContext
-
- scale - Variable in class net.sf.basedb.util.ChainedProgressReporter
-
- scan(DbControl, HttpServletRequest) - Static method in class net.sf.basedb.clients.web.extensions.ExtensionsControl
-
- SCAN - Static variable in class net.sf.basedb.core.DerivedBioAssay
-
The id for the DerivedBioAssayType
item representing a
scanned hybridization.
- scanForChanges() - Method in class net.sf.basedb.clients.web.extensions.ExtensionsControl
-
Scan the managed directories for new/updated/deleted extensions.
- scanForChanges() - Method in class net.sf.basedb.util.extensions.manager.ExtensionsManager
-
Scan the managed directories for new, updated and deleted files.
- scanForInstalledFiles(File, Settings) - Method in class net.sf.basedb.util.extensions.manager.ExtensionsManager
-
Scan the given directory and add files that are installed
according to the settings.
- scanForLinks(String) - Static method in class net.sf.basedb.clients.web.util.HTML
-
Scans a string for email addresses and URL:s and replaces them
with <a href="---">
tags.
- scanForLinks(String, int) - Static method in class net.sf.basedb.clients.web.util.HTML
-
Scans a string for email addresses and URL:s and replaces them
with <a href="---">
tags.
- scanForLinks(String, String) - Static method in class net.sf.basedb.clients.web.util.HTML
-
Scans a string for email addresses and URL:s and replaces them
with <a href="---">
tags.
- scanForLinks(String, int, String) - Static method in class net.sf.basedb.clients.web.util.HTML
-
Scans a string for email addresses and URL:s and replaces them
with <a href="---">
tags.
- scanForNewFiles(File) - Method in class net.sf.basedb.util.extensions.manager.ExtensionsManager
-
Scan the given directory and add files that are new.
- ScanImporter - Class in net.sf.basedb.plugins.batchimport
-
- ScanImporter() - Constructor for class net.sf.basedb.plugins.batchimport.ScanImporter
-
Deprecated.
- SCANNER - Static variable in class net.sf.basedb.core.Hardware
-
The id for the HardwareType
object representing a
scanner.
- SCANNING - Static variable in class net.sf.basedb.core.Protocol
-
The ID for the scanning protocol type, for example a protocol
used for scanning the microarray slide after an experiment.
- ScatterPlot - Class in net.sf.basedb.util.plot
-
A simple plot utility for generating scatter plots without
the need to delve deep into the JFreePlot package.
- ScatterPlot(String, String) - Constructor for class net.sf.basedb.util.plot.ScatterPlot
-
Create a new ScatterPlot.
- scHasBeenSet - Variable in class net.sf.basedb.clients.web.taglib.Page
-
- schedule(TimerTask, Date, boolean) - Method in class net.sf.basedb.util.timer.Scheduler
-
- schedule(TimerTask, Date, long, boolean) - Method in class net.sf.basedb.util.timer.Scheduler
-
- schedule(TimerTask, long, boolean) - Method in class net.sf.basedb.util.timer.Scheduler
-
- schedule(TimerTask, long, long, boolean) - Method in class net.sf.basedb.util.timer.Scheduler
-
- scheduleAtFixedRate(TimerTask, Date, long, boolean) - Method in class net.sf.basedb.util.timer.Scheduler
-
- scheduleAtFixedRate(TimerTask, long, long, boolean) - Method in class net.sf.basedb.util.timer.Scheduler
-
- scheduled - Variable in class net.sf.basedb.core.data.JobData
-
- scheduler - Static variable in class net.sf.basedb.core.Application
-
An interface for adding timed task to the core timer.
- Scheduler - Class in net.sf.basedb.util.timer
-
This class is a cousin to the standard
Timer
class
but only allows scheduling of tasks.
- Scheduler(Timer, boolean) - Constructor for class net.sf.basedb.util.timer.Scheduler
-
Create a new scheduler object.
- schema - Variable in class net.sf.basedb.core.hibernate.SchemaExistsWork
-
- schema - Variable in class net.sf.basedb.core.hibernate.TableExistsWork
-
- schema - Variable in class net.sf.basedb.core.ServiceSessionControl.SessionFactoryConfiguration
-
- SCHEMA_FILE_URL - Static variable in class net.sf.basedb.util.extensions.xml.XmlLoader
-
The URL pointing to the extensions.xsd schema.
- SchemaChange() - Constructor for class net.sf.basedb.core.Update.SchemaChange
-
- schemaExists(String, String) - Method in class net.sf.basedb.core.ServiceSessionControl
-
- SchemaExistsWork - Class in net.sf.basedb.core.hibernate
-
A work implementation that checks if a given catalog+schema exists
in the database or not.
- SchemaExistsWork(String, String) - Constructor for class net.sf.basedb.core.hibernate.SchemaExistsWork
-
Create a new work item.
- schemaFileURL - Static variable in class net.sf.basedb.clients.web.extensions.ServletLoader
-
The URL pointing to the servlets.xsd schema.
- SchemaGenerator - Class in net.sf.basedb.core.hibernate
-
Replaces the Hibernate SchemaExport and SchemaUpdate tools.
- SchemaGenerator(Metadata, Dialect, DbEngine, SchemaGenerator.Mode, ProgressReporter) - Constructor for class net.sf.basedb.core.hibernate.SchemaGenerator
-
Create a new schema generator.
- SchemaGenerator.CollectSqlTarget - Class in net.sf.basedb.core.hibernate
-
Helper class used for collecting SQL statements generated by Hibernate
schema creation/update tools.
- SchemaGenerator.Mode - Enum in net.sf.basedb.core.hibernate
-
The installation mode.
- SchemaGenerator.SqlStatement - Class in net.sf.basedb.core.hibernate
-
- schemaVersion - Static variable in class net.sf.basedb.core.Application
-
- schemaVersion - Variable in class net.sf.basedb.core.data.SchemaVersionData
-
- schemaVersion - Static variable in class net.sf.basedb.core.Install
-
- schemaVersion - Variable in class net.sf.basedb.core.ServiceSessionControl.SessionFactoryConfiguration
-
- SchemaVersionData - Class in net.sf.basedb.core.data
-
This class holds information about the current schema version of the database.
- SchemaVersionData() - Constructor for class net.sf.basedb.core.data.SchemaVersionData
-
- score - Variable in class net.sf.basedb.core.data.ReporterListScoreData
-
- score(ReporterList) - Static method in class net.sf.basedb.core.query.Dynamic
-
- score - Variable in class net.sf.basedb.util.fuzzy.StringMatcher.FuzzyMatch
-
- score() - Method in class net.sf.basedb.util.jep.ScoreFunction
-
Get the score value from the current sql result.
- scoreColumnMapping - Static variable in class net.sf.basedb.plugins.ReporterFlatFileImporter
-
- ScoreFunction - Class in net.sf.basedb.util.jep
-
A JEP function class that adds a score(reporterListId)
function to a
JEP expression parser.
- ScoreFunction(DbControl) - Constructor for class net.sf.basedb.util.jep.ScoreFunction
-
Create a new instance of this function.
- ScoreFunction(DbControl, int) - Constructor for class net.sf.basedb.util.jep.ScoreFunction
-
Create a new instance of this function which can be used
to dynamically evaluate expressions.
- scoreIndex - Variable in class net.sf.basedb.util.jep.ScoreFunction
-
- scoreMapper - Variable in class net.sf.basedb.plugins.ReporterFlatFileImporter
-
- scripts - Variable in class net.sf.basedb.clients.web.extensions.AbstractJspFactory
-
- scripts - Variable in class net.sf.basedb.clients.web.extensions.JspContext
-
- Scripts - Class in net.sf.basedb.clients.web.taglib.extensions
-
- Scripts() - Constructor for class net.sf.basedb.clients.web.taglib.extensions.Scripts
-
- scripts - Variable in class net.sf.basedb.clients.web.taglib.Head
-
A comma-separated list of JavaScript filenames.
- scroll() - Method in class net.sf.basedb.core.hibernate.QueryWrapper
-
- scroll(ScrollMode) - Method in class net.sf.basedb.core.hibernate.QueryWrapper
-
- ScrollIterator<E> - Class in net.sf.basedb.core
-
This is an iterator view of the result from a query
using the Hibernate ScrollableResults
object.
- ScrollIterator(Class<E>, ScrollableResults) - Constructor for class net.sf.basedb.core.ScrollIterator
-
- searchInherited - Variable in class net.sf.basedb.core.snapshot.AnnotationLoaderUtil
-
- searchMapping - Variable in class net.sf.basedb.plugins.AnnotationFlatFileImporter
-
- searchParameterType - Variable in class net.sf.basedb.plugins.AnnotationFlatFileImporter
-
- searchPrimary - Variable in class net.sf.basedb.core.snapshot.AnnotationLoaderUtil
-
- searchProperty - Variable in class net.sf.basedb.plugins.AnnotationFlatFileImporter
-
- secondaryLocation - Variable in class net.sf.basedb.core.data.QuotaTypeData
-
- SecondaryStorageController - Interface in net.sf.basedb.core
-
This interface defines the methods that needs to be implemented
by a class to be able to use it as a controller for seconday storage.
- SecondaryStorageControllerTask(SecondaryStorageController) - Constructor for class net.sf.basedb.core.Application.SecondaryStorageControllerTask
-
- secondaryStorageDriver - Static variable in class net.sf.basedb.core.Application
-
The name of the secondary storage controller class, if any.
- secondLevelCache - Variable in class net.sf.basedb.core.AnnotationBatcher
-
- SecondPassSectionSpotsParser - Class in net.sf.basedb.util.importer.spotdata
-
The second pass of the 'spots' section extracts spot and extra value
data.
- SecondPassSectionSpotsParser(DbControl, BaseFileInfo, BioAssaySet, int) - Constructor for class net.sf.basedb.util.importer.spotdata.SecondPassSectionSpotsParser
-
Creates a new 'section spot' parser for the first pass.
- Section(JspContext) - Constructor for class net.sf.basedb.clients.web.extensions.section.IncludeContentSectionFactory.Section
-
- section - Variable in class net.sf.basedb.core.data.BioPlateData
-
- section - Variable in class net.sf.basedb.plugins.PrintMapFlatFileImporter
-
- Section(String) - Constructor for enum net.sf.basedb.plugins.PrintMapFlatFileImporter.Section
-
- Section(String) - Constructor for class net.sf.basedb.util.bfs.MetadataModel.Section
-
Create a new section.
- SECTION - Static variable in class net.sf.basedb.util.importer.spotdata.FirstPassSectionSpotsParser
-
The section of the BASEfile this parser can parse, eg.
- section - Variable in class net.sf.basedb.util.parser.FlatFileParser
-
The regular expression for matching the fist line of a section.
- SECTION_END_EVENT - Static variable in class net.sf.basedb.util.bfs.MetadataParser
-
Event type that is issued at the end of each section in the file.
- SECTION_EVENT - Static variable in class net.sf.basedb.util.bfs.MetadataParser
-
Event type that is issued for each new section that is found in the file.
- SectionAction - Interface in net.sf.basedb.clients.web.extensions.section
-
Action that inserts a new section in a jsp page.
- SectionAssaysParser - Class in net.sf.basedb.util.importer.spotdata
-
Parses the 'assays' section of a BASEfile with bioassay set spot
data.
- SectionAssaysParser(DbControl, BaseFileInfo) - Constructor for class net.sf.basedb.util.importer.spotdata.SectionAssaysParser
-
Creates a new 'section assays' parser.
- SectionBean - Class in net.sf.basedb.clients.web.extensions.section
-
A simple bean-like implementation of the SectionAction
interface.
- SectionBean() - Constructor for class net.sf.basedb.clients.web.extensions.section.SectionBean
-
- sectionColumnMapping - Static variable in class net.sf.basedb.plugins.batchimport.BioPlateImporter
-
- sectionCount - Variable in class net.sf.basedb.util.basefile.BaseFileParser
-
- sectionCount - Variable in class net.sf.basedb.util.bfs.MetadataWriter
-
- sectionCount - Variable in class net.sf.basedb.util.importer.spotdata.FirstPassSectionSpotsParser
-
- sectionCount - Variable in class net.sf.basedb.util.importer.spotdata.SecondPassSectionSpotsParser
-
- sectionCount - Variable in class net.sf.basedb.util.importer.spotdata.SectionReporterListParser
-
- sectionEntries - Variable in class net.sf.basedb.util.bfs.MetadataParser
-
- SectionEntry(String, String) - Constructor for class net.sf.basedb.util.bfs.MetadataModel.SectionEntry
-
Create a new single-valued section entry.
- SectionEntry(String, String...) - Constructor for class net.sf.basedb.util.bfs.MetadataModel.SectionEntry
-
Create a new section entry with an array of values.
- SectionHeaders(String, String, String) - Constructor for class net.sf.basedb.clients.web.fileupload.FileUpload.SectionHeaders
-
- sectionMapper - Variable in class net.sf.basedb.plugins.batchimport.BioPlateImporter
-
- sectionRegexpParameter - Static variable in class net.sf.basedb.plugins.AbstractFlatFileImporter
-
Parameter definition that asks for the regular expression that
matches a section line and extracts the section name.
- SectionReporterListParser - Class in net.sf.basedb.util.importer.spotdata
-
Parses the 'reporterlist' section of a BASEfile.
- SectionReporterListParser(DbControl, BaseFileInfo, Transformation) - Constructor for class net.sf.basedb.util.importer.spotdata.SectionReporterListParser
-
- sections - Variable in class net.sf.basedb.util.bfs.MetadataModel
-
- Select - Class in net.sf.basedb.clients.web.taglib
-
This tag is used to display a selection list of items.
- Select() - Constructor for class net.sf.basedb.clients.web.taglib.Select
-
- select(Select) - Method in class net.sf.basedb.core.AbstractEntityQuery
-
Not supported.
- select(Select) - Method in class net.sf.basedb.core.AbstractQuery
-
- select(VirtualColumn) - Static method in class net.sf.basedb.core.query.Dynamic
-
Select a column in the root table.
- select(VirtualTable, VirtualColumn) - Static method in class net.sf.basedb.core.query.Dynamic
-
Select a column in a joined or the root table.
- select(ExtraValue, String) - Static method in class net.sf.basedb.core.query.Dynamic
-
Select an extra value.
- select(Select) - Method in interface net.sf.basedb.core.query.Query
-
Add a selection query element to the selection list.
- Select - Interface in net.sf.basedb.core.query
-
A selection query element.
- select - Variable in class net.sf.basedb.core.query.SelectedExpression
-
- SELECT_FILTER - Static variable in class net.sf.basedb.clients.web.ModeInfo
-
- selectdefault - Variable in class net.sf.basedb.clients.web.taglib.Select
-
If the default item should be selected for new items with
no current or recently used items.
- selected - Variable in class net.sf.basedb.core.ItemContext
-
- selected(Select) - Static method in class net.sf.basedb.core.query.Expressions
-
Create an expression for an already selected query element.
- selectedColumns - Variable in class net.sf.basedb.clients.web.DynamicUtil.SelectedInfo
-
- selectedDirs - Variable in class net.sf.basedb.plugins.PackedFileExporter
-
- SelectedExpression - Class in net.sf.basedb.core.query
-
An expression representing an already selected expression.
- SelectedExpression(Select) - Constructor for class net.sf.basedb.core.query.SelectedExpression
-
- selectedFiles - Variable in class net.sf.basedb.plugins.PackedFileExporter
-
- selectedFilesAndDirs - Variable in class net.sf.basedb.plugins.PackedFileExporter
-
- selectedIds - Variable in class net.sf.basedb.clients.web.DynamicUtil.SelectedInfo
-
- SelectedInfo(List<String>, List<String>, List<TableColumn>) - Constructor for class net.sf.basedb.clients.web.DynamicUtil.SelectedInfo
-
- selectedProperties - Variable in class net.sf.basedb.clients.web.DynamicUtil.SelectedInfo
-
- selectedSubtype - Variable in class net.sf.basedb.plugins.batchimport.AbstractItemImporter
-
- SELECTION_MODE - Static variable in class net.sf.basedb.clients.web.ModeInfo
-
- selectionMode - Variable in class net.sf.basedb.clients.web.ModeInfo
-
- SELECTMULTIPLE - Static variable in class net.sf.basedb.clients.web.ModeInfo
-
- SELECTMULTIPLE_NOBUTTONS - Static variable in class net.sf.basedb.clients.web.ModeInfo
-
- SELECTONE - Static variable in class net.sf.basedb.clients.web.ModeInfo
-
- selectOrderByColumnsIfDistinct() - Method in class net.sf.basedb.core.dbengine.AbstractDbEngine
-
Returns FALSE.
- selectOrderByColumnsIfDistinct() - Method in interface net.sf.basedb.core.dbengine.DbEngine
-
If the database requires that columns appearing in the
ORDER BY part of the query must also be part of the SELECT
list when using the DISTINCT keyword.
- selectOrderByColumnsIfDistinct() - Method in class net.sf.basedb.core.dbengine.PostgresDbEngine
-
Returns TRUE.
- selectPermanent(Select) - Method in class net.sf.basedb.core.AbstractEntityQuery
-
Not supported.
- selectPermanent(Select) - Method in class net.sf.basedb.core.AbstractQuery
-
- selectPermanent(Select) - Method in interface net.sf.basedb.core.query.Query
-
Permanently add a selection query element to the selection list.
- selectRawBioAssay(String) - Static method in class net.sf.basedb.core.query.Dynamic
-
Select a column in the rawbioassay table.
- selectRawData(String) - Static method in class net.sf.basedb.core.query.Dynamic
-
Select a column in the raw data table.
- selectRecent - Variable in class net.sf.basedb.clients.web.taglib.Select
-
If we can select the most recently used item for new items
with nu current item.
- selectReporter(String) - Static method in class net.sf.basedb.core.query.Dynamic
-
Select a column in the reporters table.
- selectReporter(String, Boolean) - Static method in class net.sf.basedb.core.query.Dynamic
-
Select a column in the reporters table.
- selects - Variable in class net.sf.basedb.core.AbstractQuery
-
List of selections added to the query.
- Selects - Class in net.sf.basedb.core.query
-
A factory class to create select expressions.
- Selects() - Constructor for class net.sf.basedb.core.query.Selects
-
- send(String, BufferedWriter, BufferedReader) - Method in class net.sf.basedb.core.authentication.POP3Authenticator
-
Deprecated.
Send cmd
to the out
buffer.
- send(Signal) - Method in class net.sf.basedb.core.Job.JobSignalTransporter
-
- send(Signal) - Method in class net.sf.basedb.core.signal.ExtensionSignalTransporter
-
- send(String, Signal) - Method in class net.sf.basedb.core.signal.LocalSignalReceiver
-
Send the signal to a registered handler.
- send(Signal) - Method in class net.sf.basedb.core.signal.LocalSignalTransporter
-
Send the signal to a local signal receiver.
- send(Signal) - Method in interface net.sf.basedb.core.signal.SignalTransporter
-
Send a signal.
- send(Signal) - Method in class net.sf.basedb.core.signal.SocketSignalTransporter
-
Connect to the remote host and send the signal.
- send(String) - Method in class net.sf.basedb.util.jobagent.JobAgentConnection
-
Send a remote control command to the job agent.
- send(Socket, String, boolean) - Static method in class net.sf.basedb.util.SocketUtil
-
Send output to a socket.
- sendAsEmail - Variable in class net.sf.basedb.core.Message
-
- sendAsEmail() - Method in class net.sf.basedb.core.Message
-
Send this message as an email.
- sendCmd(Socket, String) - Method in class net.sf.basedb.util.jobagent.JobAgentConnection
-
Send a command to the job agent and return the answer.
- senderEmail - Static variable in class net.sf.basedb.util.EmailUtil
-
- senderName - Static variable in class net.sf.basedb.util.EmailUtil
-
- sendErrorMessage(SessionControl, int, Throwable) - Method in class net.sf.basedb.core.InternalJobQueue
-
- sendMessage - Variable in class net.sf.basedb.core.data.JobData
-
- sendMessage() - Method in class net.sf.basedb.core.Job
-
Send a message to the owner of the job when the job has finished
- sendMessagesAsEmail - Variable in class net.sf.basedb.core.data.UserData
-
- sendPause() - Method in class net.sf.basedb.util.jobagent.JobAgentConnection
-
- sendPing() - Method in class net.sf.basedb.util.jobagent.JobAgentConnection
-
Send the ping
command to the job agent.
- SendSignalRenderer(Signal) - Constructor for class net.sf.basedb.core.signal.ExtensionSignalTransporter.SendSignalRenderer
-
- sendStart() - Method in class net.sf.basedb.util.jobagent.JobAgentConnection
-
Send a start
request to the job agent.
- sendStop() - Method in class net.sf.basedb.util.jobagent.JobAgentConnection
-
- sendTo(SignalHandler) - Method in class net.sf.basedb.core.signal.ShutdownSignalSender
-
- sendTo(SignalHandler) - Method in interface net.sf.basedb.core.signal.SignalSender
-
Send a signal to the specific signal handler.
- sendTo(SignalHandler) - Method in class net.sf.basedb.core.signal.SimpleSignalSender
-
- sendToAll(SignalSender) - Method in class net.sf.basedb.clients.web.util.SimpleSignalProgressReporter
-
- sendToAll(SignalSender) - Method in class net.sf.basedb.core.signal.AbstractSignalReceiver
-
- sendToAll(SignalSender) - Method in interface net.sf.basedb.core.signal.SignalReceiver
-
Let the signal sender send one or more signals to all registered
signal handlers on this reciever.
- separator - Variable in class net.sf.basedb.clients.web.taglib.path.Path
-
- separator - Variable in class net.sf.basedb.clients.web.taglib.table.CellValue
-
- separator - Static variable in class net.sf.basedb.core.File
-
- SequenceFilenameGenerator - Class in net.sf.basedb.util.bfs
-
File name generator implementation that generates file names using
a simple numerical counter.
- SequenceFilenameGenerator() - Constructor for class net.sf.basedb.util.bfs.SequenceFilenameGenerator
-
Create a new sequence file name generator.
- SequenceFilenameGenerator(String, String, int) - Constructor for class net.sf.basedb.util.bfs.SequenceFilenameGenerator
-
Create a new sequence file name generator.
- SEQUENCER - Static variable in class net.sf.basedb.core.Hardware
-
The id for the HardwareType
object representing a
sequencer.
- SEQUENCES - Static variable in class net.sf.basedb.core.DerivedBioAssay
-
The id for the DerivedBioAssayType
item representing
original sequenced data.
- SEQUENCING - Static variable in class net.sf.basedb.core.Kit
-
- SEQUENCING - Static variable in class net.sf.basedb.core.Platform
-
The external id for the generic Sequencing
platform.
- SEQUENCING - Static variable in class net.sf.basedb.core.Protocol
-
- SEQUENCING_EXPRESSION - Static variable in class net.sf.basedb.core.PlatformVariant
-
The external id for the expression-like sequencing data.
- SerialBaseFileExporter - Class in net.sf.basedb.util.export.spotdata
-
Exporter implementation that exports bioassay set data as a serial
BASEfile.
- SerialBaseFileExporter() - Constructor for class net.sf.basedb.util.export.spotdata.SerialBaseFileExporter
-
Create a new serial BASEfile exporter.
- SerialBfsExporter - Class in net.sf.basedb.util.export.spotdata
-
BFS exporter implementation that exports spot data in serial format.
- SerialBfsExporter() - Constructor for class net.sf.basedb.util.export.spotdata.SerialBfsExporter
-
Create a new serial BFS exporter.
- serialFormatParameter - Variable in class net.sf.basedb.plugins.Base1PluginExecuter
-
This parameter describes if the data should be exported in serial format or
in matrix.
- serializeObject(ObjectOutputStream) - Method in class net.sf.basedb.core.snapshot.AnnotationSnapshot
-
- SerialSpotIntensityEventHandler - Class in net.sf.basedb.util.importer.spotdata
-
Event handler that extracts spot intensity information from serial BFS
data files and inserts the values to a spot batcher.
- SerialSpotIntensityEventHandler(SpotBatcher, PositionEventHandler, BioAssay[], int[]) - Constructor for class net.sf.basedb.util.importer.spotdata.SerialSpotIntensityEventHandler
-
Create a new spot instensity event handler.
- serialVersionUID - Static variable in exception net.sf.basedb.clients.web.DuplicateWizardException
-
- serialVersionUID - Static variable in exception net.sf.basedb.clients.web.fileupload.UploadAbortedException
-
- serialVersionUID - Static variable in class net.sf.basedb.clients.web.servlet.CompileAll
-
- serialVersionUID - Static variable in class net.sf.basedb.clients.web.servlet.ContentSecurityPolicyReportServlet
-
- serialVersionUID - Static variable in class net.sf.basedb.clients.web.servlet.Download
-
- serialVersionUID - Static variable in class net.sf.basedb.clients.web.servlet.ExperimentExplorerPlotServlet
-
- serialVersionUID - Static variable in class net.sf.basedb.clients.web.servlet.ExtensionsServlet
-
- serialVersionUID - Static variable in class net.sf.basedb.clients.web.servlet.PlotServlet
-
- serialVersionUID - Static variable in class net.sf.basedb.clients.web.servlet.RssNewsFeed
-
- serialVersionUID - Static variable in class net.sf.basedb.clients.web.servlet.StartStopServlet
-
- serialVersionUID - Static variable in class net.sf.basedb.clients.web.servlet.Upload
-
- serialVersionUID - Static variable in class net.sf.basedb.clients.web.servlet.ViewSpotImage
-
- serialVersionUID - Static variable in class net.sf.basedb.clients.web.taglib.Body
-
- serialVersionUID - Static variable in class net.sf.basedb.clients.web.taglib.Button
-
- serialVersionUID - Static variable in class net.sf.basedb.clients.web.taglib.ButtonGroup
-
- serialVersionUID - Static variable in class net.sf.basedb.clients.web.taglib.CalendarButton
-
- serialVersionUID - Static variable in class net.sf.basedb.clients.web.taglib.ExceptionCatcher
-
- serialVersionUID - Static variable in class net.sf.basedb.clients.web.taglib.extensions.Render
-
- serialVersionUID - Static variable in class net.sf.basedb.clients.web.taglib.extensions.Scripts
-
- serialVersionUID - Static variable in class net.sf.basedb.clients.web.taglib.extensions.Stylesheets
-
- serialVersionUID - Static variable in class net.sf.basedb.clients.web.taglib.Head
-
- serialVersionUID - Static variable in class net.sf.basedb.clients.web.taglib.Help
-
- serialVersionUID - Static variable in class net.sf.basedb.clients.web.taglib.HideableSection
-
- serialVersionUID - Static variable in class net.sf.basedb.clients.web.taglib.Icon
-
- serialVersionUID - Static variable in class net.sf.basedb.clients.web.taglib.menu.Menuitem
-
- serialVersionUID - Static variable in class net.sf.basedb.clients.web.taglib.menu.Menuseparator
-
- serialVersionUID - Static variable in class net.sf.basedb.clients.web.taglib.menu.Submenu
-
- serialVersionUID - Static variable in class net.sf.basedb.clients.web.taglib.Page
-
- serialVersionUID - Static variable in class net.sf.basedb.clients.web.taglib.path.Path
-
- serialVersionUID - Static variable in class net.sf.basedb.clients.web.taglib.path.PathElement
-
- serialVersionUID - Static variable in class net.sf.basedb.clients.web.taglib.PropertyValue
-
- serialVersionUID - Static variable in class net.sf.basedb.clients.web.taglib.Select
-
- serialVersionUID - Static variable in class net.sf.basedb.clients.web.taglib.StylableTag
-
- serialVersionUID - Static variable in class net.sf.basedb.clients.web.taglib.tab.Tab
-
- serialVersionUID - Static variable in class net.sf.basedb.clients.web.taglib.tab.TabControl
-
- serialVersionUID - Static variable in class net.sf.basedb.clients.web.taglib.table.Button
-
- serialVersionUID - Static variable in class net.sf.basedb.clients.web.taglib.table.Cell
-
- serialVersionUID - Static variable in class net.sf.basedb.clients.web.taglib.table.CellValue
-
- serialVersionUID - Static variable in class net.sf.basedb.clients.web.taglib.table.ColumnDef
-
- serialVersionUID - Static variable in class net.sf.basedb.clients.web.taglib.table.ColumnHeaders
-
- serialVersionUID - Static variable in class net.sf.basedb.clients.web.taglib.table.Data
-
- serialVersionUID - Static variable in class net.sf.basedb.clients.web.taglib.table.ExtensionCells
-
- serialVersionUID - Static variable in class net.sf.basedb.clients.web.taglib.table.Form
-
- serialVersionUID - Static variable in class net.sf.basedb.clients.web.taglib.table.Header
-
- serialVersionUID - Static variable in class net.sf.basedb.clients.web.taglib.table.HeaderRow
-
- serialVersionUID - Static variable in class net.sf.basedb.clients.web.taglib.table.Headers
-
- serialVersionUID - Static variable in class net.sf.basedb.clients.web.taglib.table.Hidden
-
- serialVersionUID - Static variable in class net.sf.basedb.clients.web.taglib.table.Label
-
- serialVersionUID - Static variable in class net.sf.basedb.clients.web.taglib.table.Navigator
-
- serialVersionUID - Static variable in class net.sf.basedb.clients.web.taglib.table.Panel
-
- serialVersionUID - Static variable in class net.sf.basedb.clients.web.taglib.table.PresetSelector
-
- serialVersionUID - Static variable in class net.sf.basedb.clients.web.taglib.table.PropertyFilter
-
- serialVersionUID - Static variable in class net.sf.basedb.clients.web.taglib.table.Row
-
- serialVersionUID - Static variable in class net.sf.basedb.clients.web.taglib.table.Rows
-
- serialVersionUID - Static variable in class net.sf.basedb.clients.web.taglib.table.Table
-
- serialVersionUID - Static variable in class net.sf.basedb.clients.web.taglib.table.Toolbar
-
- serialVersionUID - Static variable in class net.sf.basedb.clients.web.taglib.Zoom
-
- serialVersionUID - Static variable in exception net.sf.basedb.clients.web.WebException
-
- serialVersionUID - Static variable in exception net.sf.basedb.core.AccountExpiredException
-
- serialVersionUID - Static variable in exception net.sf.basedb.core.AlreadyLoggedInException
-
- serialVersionUID - Static variable in exception net.sf.basedb.core.authentication.AuthenticationException
-
- serialVersionUID - Static variable in exception net.sf.basedb.core.authentication.InvalidPasswordException
-
- serialVersionUID - Static variable in exception net.sf.basedb.core.authentication.LoginException
-
- serialVersionUID - Static variable in exception net.sf.basedb.core.authentication.UnknownLoginException
-
- serialVersionUID - Static variable in exception net.sf.basedb.core.BaseException
-
- serialVersionUID - Static variable in exception net.sf.basedb.core.ConfigurationException
-
- serialVersionUID - Static variable in exception net.sf.basedb.core.ConnectionClosedException
-
- serialVersionUID - Static variable in class net.sf.basedb.core.data.AnnotationSetData
-
- serialVersionUID - Static variable in class net.sf.basedb.core.data.ContextIndex
-
- serialVersionUID - Static variable in class net.sf.basedb.core.data.FileTypeIndex
-
- serialVersionUID - Static variable in class net.sf.basedb.core.data.GuiContextData
-
- serialVersionUID - Static variable in class net.sf.basedb.core.data.keyring.GroupGroups
-
- serialVersionUID - Static variable in class net.sf.basedb.core.data.keyring.GroupKeys
-
- serialVersionUID - Static variable in class net.sf.basedb.core.data.keyring.GroupProjects
-
- serialVersionUID - Static variable in class net.sf.basedb.core.data.keyring.PluginKeys
-
- serialVersionUID - Static variable in class net.sf.basedb.core.data.keyring.ProjectKeys
-
- serialVersionUID - Static variable in class net.sf.basedb.core.data.keyring.RoleKeys
-
- serialVersionUID - Static variable in class net.sf.basedb.core.data.keyring.UserGroups
-
- serialVersionUID - Static variable in class net.sf.basedb.core.data.keyring.UserKeys
-
- serialVersionUID - Static variable in class net.sf.basedb.core.data.keyring.UserProjects
-
- serialVersionUID - Static variable in class net.sf.basedb.core.data.keyring.UserRoles
-
- serialVersionUID - Static variable in class net.sf.basedb.core.data.MappingCoordinate
-
- serialVersionUID - Static variable in class net.sf.basedb.core.data.PlateCoordinate
-
- serialVersionUID - Static variable in class net.sf.basedb.core.data.QuotaIndex
-
- serialVersionUID - Static variable in class net.sf.basedb.core.data.ReporterListScoreData
-
- serialVersionUID - Static variable in class net.sf.basedb.core.data.VersionedParameter
-
- serialVersionUID - Static variable in exception net.sf.basedb.core.DatabaseException
-
- serialVersionUID - Static variable in exception net.sf.basedb.core.DateFormatException
-
- serialVersionUID - Static variable in exception net.sf.basedb.core.DetachedItemException
-
- serialVersionUID - Static variable in exception net.sf.basedb.core.DisallowedValueException
-
- serialVersionUID - Static variable in class net.sf.basedb.core.ExtendedPropertyAccessor.GetterSetter
-
- serialVersionUID - Static variable in class net.sf.basedb.core.hibernate.SessionWrapper
-
- serialVersionUID - Static variable in class net.sf.basedb.core.hibernate.StatelessSessionWrapper
-
- serialVersionUID - Static variable in exception net.sf.basedb.core.InvalidAnnotationException
-
- serialVersionUID - Static variable in exception net.sf.basedb.core.InvalidDataException
-
- serialVersionUID - Static variable in exception net.sf.basedb.core.InvalidPasswordException
-
- serialVersionUID - Static variable in exception net.sf.basedb.core.InvalidPathException
-
- serialVersionUID - Static variable in exception net.sf.basedb.core.InvalidRelationException
-
- serialVersionUID - Static variable in exception net.sf.basedb.core.InvalidUseOfNullException
-
- serialVersionUID - Static variable in exception net.sf.basedb.core.ItemAlreadyExistsException
-
- serialVersionUID - Static variable in exception net.sf.basedb.core.ItemInUseException
-
- serialVersionUID - Static variable in exception net.sf.basedb.core.ItemModifiedException
-
- serialVersionUID - Static variable in exception net.sf.basedb.core.ItemNotFoundException
-
- serialVersionUID - Static variable in class net.sf.basedb.core.log.LoggingInterceptor
-
- serialVersionUID - Static variable in exception net.sf.basedb.core.LoginException
-
- serialVersionUID - Static variable in exception net.sf.basedb.core.NotLoggedInException
-
- serialVersionUID - Static variable in exception net.sf.basedb.core.NumberOutOfRangeException
-
- serialVersionUID - Static variable in exception net.sf.basedb.core.ParameterException
-
- serialVersionUID - Static variable in exception net.sf.basedb.core.PermissionDeniedException
-
- serialVersionUID - Static variable in exception net.sf.basedb.core.QuotaException
-
- serialVersionUID - Static variable in exception net.sf.basedb.core.signal.SignalException
-
- serialVersionUID - Static variable in exception net.sf.basedb.core.signal.SignalReceivedException
-
- serialVersionUID - Static variable in exception net.sf.basedb.core.signal.UnsupportedSignalException
-
- serialVersionUID - Static variable in class net.sf.basedb.core.snapshot.AnnotationSetSnapshot
-
- serialVersionUID - Static variable in class net.sf.basedb.core.snapshot.AnnotationSnapshot
-
- serialVersionUID - Static variable in exception net.sf.basedb.core.StringTooLongException
-
- serialVersionUID - Static variable in class net.sf.basedb.core.UnmodifiableResultList
-
- serialVersionUID - Static variable in exception net.sf.basedb.core.UnsavedItemException
-
- serialVersionUID - Static variable in exception net.sf.basedb.core.UnsupportedFileFormatException
-
- serialVersionUID - Static variable in class net.sf.basedb.util.Enumeration
-
- serialVersionUID - Static variable in class net.sf.basedb.util.jep.FunctionSafeJep.SafeFunctionTable
-
- serialVersionUID - Static variable in class net.sf.basedb.util.jep.FunctionSafeJep.UnknownFunction
-
- serialVersionUID - Static variable in class net.sf.basedb.util.NameableComparator
-
- serialVersionUID - Static variable in class net.sf.basedb.util.plot.HistogramPlot.HistogramBin
-
- serialVersionUID - Static variable in class net.sf.basedb.util.plot.HistogramPlot.HistogramDataset
-
- serialVersionUID - Static variable in class net.sf.basedb.util.plot.HistogramPlot.HistogramSeries
-
- serialVersionUID - Static variable in class net.sf.basedb.util.ToStringComparator
-
- server - Variable in class net.sf.basedb.clients.jobagent.Agent
-
- server - Variable in class net.sf.basedb.core.data.JobAgentData
-
- server - Variable in class net.sf.basedb.core.data.JobData
-
- server - Variable in class net.sf.basedb.core.Job.ProgressReporterImpl
-
- server - Variable in class net.sf.basedb.util.jobagent.JobAgentConnection
-
- SERVER_NAME - Static variable in class net.sf.basedb.clients.web.taglib.Page
-
The name of this webserver.
- serverAddress - Variable in class net.sf.basedb.clients.jobagent.Agent
-
- serverCertificate - Variable in class net.sf.basedb.core.data.FileServerData
-
- serverCertificate - Variable in class net.sf.basedb.util.uri.ConnectionParameters
-
- service(RequestHandler) - Method in class net.sf.basedb.clients.jobagent.Agent
-
Start the listener service that listens for control commands such
as start
, stop
, pause
and
info
.
- service(HttpServletRequest, HttpServletResponse) - Method in class net.sf.basedb.clients.web.extensions.ServletWrapper
-
Service a request to the wrapped servlet.
- service - Static variable in class net.sf.basedb.core.QueryExecutor
-
- SERVICE_STARTED - Static variable in class net.sf.basedb.clients.web.extensions.service.Services
-
Events of this type are sent to the extensions registry whenever a
service extension is started.
- SERVICE_STOPPED - Static variable in class net.sf.basedb.clients.web.extensions.service.Services
-
Events of this type are sent to the extensions registry whenever a
service extension is stopped.
- ServiceControllerAction - Interface in net.sf.basedb.clients.web.extensions.service
-
Action for controlling services installed under the extensions system.
- Services - Class in net.sf.basedb.clients.web.extensions.service
-
Utility class for starting and stopping services.
- Services() - Constructor for class net.sf.basedb.clients.web.extensions.service.Services
-
- ServiceSessionControl - Class in net.sf.basedb.core
-
A special session control implementation used for services.
- ServiceSessionControl() - Constructor for class net.sf.basedb.core.ServiceSessionControl
-
- ServiceSessionControl.FlushSessionAction - Class in net.sf.basedb.core
-
Flushes the given session before the transaction is committed.
- ServiceSessionControl.ServicesKeyring - Class in net.sf.basedb.core
-
- ServiceSessionControl.SessionFactoryConfiguration - Class in net.sf.basedb.core
-
Used for creating a configuration that is the basis for building a
session factory.
- ServicesEventHandler - Class in net.sf.basedb.clients.web.extensions.service
-
Event handler for managing services when new extension are added
or existing extension are updated or deleted.
- ServicesEventHandler() - Constructor for class net.sf.basedb.clients.web.extensions.service.ServicesEventHandler
-
- ServicesKeyring() - Constructor for class net.sf.basedb.core.ServiceSessionControl.ServicesKeyring
-
- ServicesUtil - Class in net.sf.basedb.core
-
Utility class for the "services" extension point.
- ServicesUtil() - Constructor for class net.sf.basedb.core.ServicesUtil
-
- SERVLET_URL - Static variable in class net.sf.basedb.clients.web.extensions.ExtensionsControl
-
The location where extension servlets are registered.
- servletClass - Variable in class net.sf.basedb.clients.web.extensions.ServletWrapper
-
- servletContext - Static variable in class net.sf.basedb.clients.web.extensions.ExtensionsControl
-
- servletContext - Static variable in class net.sf.basedb.clients.web.extensions.skin.ImageRemapperUtil
-
- ServletExportOutputStream - Class in net.sf.basedb.clients.web.util
-
- ServletExportOutputStream(HttpServletResponse) - Constructor for class net.sf.basedb.clients.web.util.ServletExportOutputStream
-
Create a new servlet export stream.
- ServletLoader - Class in net.sf.basedb.clients.web.extensions
-
Loads servlet definitions from an XML file.
- ServletLoader() - Constructor for class net.sf.basedb.clients.web.extensions.ServletLoader
-
Create a new XML loader instance.
- servletName - Variable in class net.sf.basedb.clients.web.extensions.ServletWrapperKey
-
- servletPath - Variable in class net.sf.basedb.clients.web.extensions.plot.MAPlotFactory
-
- servletPath - Variable in class net.sf.basedb.clients.web.extensions.RequestWrapper
-
- servlets - Variable in class net.sf.basedb.clients.web.extensions.ServletLoader
-
- servletsPath - Variable in class net.sf.basedb.clients.web.extensions.WebClientRegisterExtensionsProcessor
-
- ServletWrapper - Class in net.sf.basedb.clients.web.extensions
-
A wrapper class for servlets defined by extensions.
- ServletWrapper(Class<? extends Servlet>, String) - Constructor for class net.sf.basedb.clients.web.extensions.ServletWrapper
-
- ServletWrapperKey - Class in net.sf.basedb.clients.web.extensions
-
Key implementation used to identify servlets.
- ServletWrapperKey(String, String) - Constructor for class net.sf.basedb.clients.web.extensions.ServletWrapperKey
-
Create a new key for a servlet defined in a file with the
given name.
- session - Variable in class net.sf.basedb.core.AuthenticationContext
-
- session - Variable in class net.sf.basedb.core.data.ChangeHistoryData
-
- session - Variable in class net.sf.basedb.core.DataResultIterator
-
The Hibernate Session that was used in the query, null if a stateless
session is used.
- session - Variable in class net.sf.basedb.core.hibernate.SessionWrapper
-
- session - Variable in class net.sf.basedb.core.hibernate.StatelessSessionWrapper
-
- session - Static variable in class net.sf.basedb.core.Install
-
- session - Variable in class net.sf.basedb.core.LogControl
-
- session - Variable in class net.sf.basedb.core.Migration
-
- session - Variable in class net.sf.basedb.core.ProjectSpecificAnnotationsManager
-
- session - Variable in class net.sf.basedb.core.QueryExecutor.CancelableSession
-
- session - Variable in class net.sf.basedb.core.QueryExecutor.CancelableStatelessSession
-
- session - Variable in class net.sf.basedb.core.QueryRuntimeFilterManager
-
The Hibernate session where the filters should be enabled.
- session - Variable in class net.sf.basedb.core.ServiceSessionControl.FlushSessionAction
-
- Session - Class in net.sf.basedb.core
-
A session represents the time between login and logout for a single
user.
- Session(SessionData) - Constructor for class net.sf.basedb.core.Session
-
- sessionCache - Static variable in class net.sf.basedb.core.Application
-
A cache of SessionControl objects.
- sessionCacheTimeout - Static variable in class net.sf.basedb.core.Application
-
Number of minutes a SessionControl object can be unused before
it is removed from the cache.
- sessionCacheTimeout() - Static method in class net.sf.basedb.core.Application
-
Gets the maximum number of minutes before an active session
is logged out.
- sessionControl - Static variable in class net.sf.basedb.core.Install
-
- SessionControl - Class in net.sf.basedb.core
-
This class handles user sessions.
- SessionControl(String, SessionControl, PluginDefinition, Job) - Constructor for class net.sf.basedb.core.SessionControl
-
Create a new session control object using another one as the template.
- SessionControl(String, String, boolean, String) - Constructor for class net.sf.basedb.core.SessionControl
-
Creates a new SessionControl
object.
- SessionControl.LoginInfo - Class in net.sf.basedb.core
-
Internal class to hold information about the logged in user.
- SessionControl.SettingInfo - Class in net.sf.basedb.core
-
Internal class to hold information about a setting
- SessionControlCacheCleaner() - Constructor for class net.sf.basedb.core.Application.SessionControlCacheCleaner
-
- SessionData - Class in net.sf.basedb.core.data
-
This class holds information about a session.
- SessionData() - Constructor for class net.sf.basedb.core.data.SessionData
-
- SessionFactoryConfiguration - Class in net.sf.basedb.core.hibernate
-
- SessionFactoryConfiguration(String, ClassLoader) - Constructor for class net.sf.basedb.core.hibernate.SessionFactoryConfiguration
-
Deprecated.
Create a configuration instance.
- SessionFactoryConfiguration(String, String, int, ClassLoader) - Constructor for class net.sf.basedb.core.ServiceSessionControl.SessionFactoryConfiguration
-
- sessionId - Variable in class net.sf.basedb.core.data.ChangeHistoryData
-
- sessionId - Variable in class net.sf.basedb.core.log.TransactionDetails
-
- sessionId - Variable in class net.sf.basedb.core.SessionControl.LoginInfo
-
- sessions - Variable in class net.sf.basedb.core.data.ClientData
-
- sessions - Variable in class net.sf.basedb.core.data.UserData
-
- sessionSettings - Variable in class net.sf.basedb.core.SessionControl.LoginInfo
-
Stores name and value of session settings.
- sessionWithOptions() - Method in class net.sf.basedb.core.hibernate.SessionWrapper
-
- SessionWrapper - Class in net.sf.basedb.core.hibernate
-
Wrapper around Hibernate sessions that includes a query cache.
- SessionWrapper(Session) - Constructor for class net.sf.basedb.core.hibernate.SessionWrapper
-
Creates a new session wrapper
- set(int, I) - Method in class net.sf.basedb.core.AbstractResultList
-
Not supported.
- set(Object, Object, SessionFactoryImplementor) - Method in class net.sf.basedb.core.ExtendedPropertyAccessor.GetterSetter
-
Set the value of the extended property.
- set(T) - Method in class net.sf.basedb.core.ItemResultList.ResultListListIterator
-
This operation is not supported.
- set(int, T) - Method in class net.sf.basedb.core.UnmodifiableResultList
-
Not supported.
- set(Object, E) - Method in class net.sf.basedb.util.ClassLocal
-
Store an object and associate it with the class
of the specified instance.
- setAbort() - Method in class net.sf.basedb.clients.web.fileupload.FileUploadProgress
-
Request that the upload should be aborted.
- setAbout(About, boolean) - Method in class net.sf.basedb.core.PluginDefinition
-
Update the plug-in information with the information in the
about object.
- setAbout(About) - Method in class net.sf.basedb.util.extensions.ExtensionBean
-
- setAbout(About) - Method in class net.sf.basedb.util.extensions.xml.PluginInfo
-
- setAbsolute(long, String) - Method in class net.sf.basedb.core.SimpleAbsoluteProgressReporter
-
Set a basic progress level.
- setAbstract(String) - Method in class net.sf.basedb.core.data.ExperimentData
-
- setAbstract(String) - Method in class net.sf.basedb.core.Experiment
-
Set the abstract text for the publication of this experiment.
- setAction(String) - Method in class net.sf.basedb.clients.web.taglib.table.Table
-
- setAction(int) - Method in class net.sf.basedb.core.data.FileData
-
- setAction(File.Action) - Method in class net.sf.basedb.core.File
-
Set the action of this File
item.
- setActionClass(Class<A>) - Method in class net.sf.basedb.util.extensions.ExtensionPointBean
-
- setActionFactory(ActionFactory<? extends A>) - Method in class net.sf.basedb.util.extensions.ExtensionBean
-
- setActive(String) - Method in class net.sf.basedb.clients.web.taglib.tab.TabControl
-
- setActiveProject(ProjectData) - Method in class net.sf.basedb.core.Keyring
-
Set the active project.
- setActiveProject(Project) - Method in class net.sf.basedb.core.SessionControl
-
Set the active project.
- setActiveProjectId(int) - Method in class net.sf.basedb.core.data.JobData
-
- setAddress(String) - Method in class net.sf.basedb.core.authentication.ExtraUserInformation
-
- setAddress(String) - Method in class net.sf.basedb.core.data.UserData
-
- setAddress(String) - Method in class net.sf.basedb.core.User
-
Set the address for the user, or null if unknown.
- setAffiliations(String) - Method in class net.sf.basedb.core.data.ExperimentData
-
- setAffiliations(String) - Method in class net.sf.basedb.core.Experiment
-
Set the affiliations for this experiment.
- setAllowImmediateExecution(boolean) - Method in class net.sf.basedb.core.data.PluginDefinitionData
-
- setAllowImmediateExecution(boolean) - Method in class net.sf.basedb.core.PluginDefinition
-
- setAllowMultiple(boolean) - Method in class net.sf.basedb.core.data.ItemSubtypeFileTypeData
-
- setAllowMultiple(boolean) - Method in class net.sf.basedb.core.data.PlatformFileTypeData
-
- setAllowMultiple(boolean) - Method in class net.sf.basedb.core.ItemSubtypeFileType
-
Allow or disallow multiple files of this file type in a file set.
- setAllowMultiple(boolean) - Method in class net.sf.basedb.core.PlatformFileType
-
Allow or disallow multiple files of this file type in a file set.
- setAllowRendererOverrider(boolean) - Method in class net.sf.basedb.util.extensions.ExtensionPointBean
-
- setAnalyzeAfterImport(boolean) - Method in class net.sf.basedb.core.Migration
-
Should we execute an analyis command after the import has
been completed.
- setAnnotation(boolean) - Method in class net.sf.basedb.clients.web.taglib.table.ColumnDef
-
- setAnnotation(Annotation) - Method in class net.sf.basedb.core.snapshot.AnnotationFilter
-
Set the annotation this filter should match.
- setAnnotationId(int) - Method in class net.sf.basedb.core.snapshot.AnnotationFilter
-
Set the annotation this filter should match.
- setAnnotations(Set<AnnotationLink>) - Method in class net.sf.basedb.core.data.AnnotatedData
-
- setAnnotations(Set<AnnotationData>) - Method in class net.sf.basedb.core.data.AnnotationSetData
-
- setAnnotations(Set<AnnotationData>) - Method in class net.sf.basedb.core.data.AnnotationTypeData
-
- setAnnotations(Set<AnnotationLink>) - Method in class net.sf.basedb.core.data.BioAssayData
-
- setAnnotations(Set<AnnotationLink>) - Method in class net.sf.basedb.core.data.BioAssaySetData
-
- setAnnotations(Set<AnnotationLink>) - Method in class net.sf.basedb.core.data.PluginDefinitionData
-
- setAnnotations(Set<AnnotationLink>) - Method in class net.sf.basedb.core.data.ProjectData
-
- setAnnotations(Set<AnnotationLink>) - Method in class net.sf.basedb.core.data.RootRawBioAssayData
-
- setAnnotations(Set<AnnotationLink>) - Method in class net.sf.basedb.core.data.WellData
-
- setAnnotationSet(AnnotationSetData) - Method in interface net.sf.basedb.core.data.AnnotatableData
-
Change the annotation set.
- setAnnotationSet(AnnotationSetData) - Method in class net.sf.basedb.core.data.AnnotatedData
-
- setAnnotationSet(AnnotationSetData) - Method in class net.sf.basedb.core.data.AnnotationData
-
- setAnnotationSet(AnnotationSetData) - Method in class net.sf.basedb.core.data.BioAssayData
-
- setAnnotationSet(AnnotationSetData) - Method in class net.sf.basedb.core.data.BioAssaySetData
-
- setAnnotationSet(AnnotationSetData) - Method in class net.sf.basedb.core.data.PluginDefinitionData
-
- setAnnotationSet(AnnotationSetData) - Method in class net.sf.basedb.core.data.ProjectData
-
- setAnnotationSet(AnnotationSetData) - Method in class net.sf.basedb.core.data.RootRawBioAssayData
-
- setAnnotationSet(AnnotationSetData) - Method in class net.sf.basedb.core.data.WellData
-
- setAnnotationSetId(int) - Method in class net.sf.basedb.core.data.annotations.AnnotationLink
-
- setAnnotationType(AnnotationTypeData) - Method in class net.sf.basedb.core.data.AnnotationData
-
- setAnnotationType(AnnotationType) - Method in class net.sf.basedb.core.snapshot.AnnotationTypeFilter
-
Set the annotation type this filter should match.
- setAnnotationType(AnnotationType) - Method in class net.sf.basedb.util.export.spotdata.AnnotationAssayField
-
Set the annotation type of the annotations that should be
exported in this field.
- setAnnotationTypeId(int) - Method in class net.sf.basedb.core.data.annotations.AnnotationLink
-
- setAnnotationTypeIds(Collection<Integer>) - Method in class net.sf.basedb.clients.web.ExperimentExplorer
-
Update the selected annotation types.
- setAnnotationTypes(Set<AnnotationTypeData>) - Method in class net.sf.basedb.core.data.AnnotationTypeCategoryData
-
- setAppId(String) - Method in class net.sf.basedb.core.data.SchemaVersionData
-
- setArrayBatch(ArrayBatch) - Method in class net.sf.basedb.core.ArraySlide
-
- setArrayBatch(ArrayBatchData) - Method in class net.sf.basedb.core.data.ArraySlideData
-
- setArrayBatches(Set<ArrayBatchData>) - Method in class net.sf.basedb.core.data.ArrayDesignData
-
- setArrayDesign(ArrayDesign) - Method in class net.sf.basedb.core.ArrayBatch
-
- setArrayDesign(ArrayDesign) - Method in class net.sf.basedb.core.ArrayDesignBlock
-
Set the ArrayDesign
for this block.
- setArrayDesign(ArrayDesignData) - Method in class net.sf.basedb.core.data.ArrayBatchData
-
- setArrayDesign(ArrayDesignData) - Method in class net.sf.basedb.core.data.ArrayDesignBlockData
-
- setArrayDesign(ArrayDesignData) - Method in class net.sf.basedb.core.data.ArrayDesignPlateData
-
- setArrayDesign(ArrayDesignData) - Method in class net.sf.basedb.core.data.RawBioAssayData
-
- setArrayDesign(ArrayDesign) - Method in class net.sf.basedb.core.RawBioAssay
-
- setArrayDesignBlock(ArrayDesignBlockData) - Method in class net.sf.basedb.core.data.FeatureData
-
- setArrayDesignBlocks(Set<ArrayDesignBlockData>) - Method in class net.sf.basedb.core.data.ArrayDesignData
-
- setArrayDesigns(Set<ArrayDesignData>) - Method in class net.sf.basedb.core.data.JobData
-
- setArrayDesigns(Set<ArrayDesignPlateData>) - Method in class net.sf.basedb.core.data.PlateData
-
- setArraySlide(ArraySlideData) - Method in class net.sf.basedb.core.data.PhysicalBioAssayData
-
- setArraySlide(ArraySlide) - Method in class net.sf.basedb.core.PhysicalBioAssay
-
- setArraySlides(Set<ArraySlideData>) - Method in class net.sf.basedb.core.data.ArrayBatchData
-
- setAssayAnnotationsWriter(AnnotationWriter) - Method in class net.sf.basedb.util.export.spotdata.BfsExporter
-
Set the stream were assay annotations should be written.
- setAssayFields(List<String>) - Method in class net.sf.basedb.util.importer.spotdata.BaseFileInfo.SpotSectionInfo
-
Set the list of all assay data fields, in the order
the appear in the file.
- setAssays(List<Integer>) - Method in class net.sf.basedb.util.importer.spotdata.BaseFileInfo.SpotSectionInfo
-
Set a list with the ID:s of all assays, in the
order the appearu in the data columns.
- setAssaysHaveParentAssaysMapping(boolean) - Method in class net.sf.basedb.util.importer.spotdata.BaseFileInfo
-
Set a flag that indicates if the BASEfile includes a mapping
from child to parent assays.
- setAttribute(String, String) - Method in class net.sf.basedb.core.authentication.LoginRequest
-
Set an extra attribute to use for the login request.
- setAttribute(String, String) - Method in class net.sf.basedb.util.extensions.AboutBean
-
Set an attribute for the given name.
- setAttribute(String, Object) - Method in class net.sf.basedb.util.extensions.ClientContext
-
Set an attribute of the context.
- setAttribute(String, String, Object) - Method in class net.sf.basedb.util.extensions.Registry
-
Set an extra attribute on a registered extension or extension point.
- setAttribute(NodeAttribute<T>, T) - Method in class net.sf.basedb.util.overview.Node
-
Set a node attribute.
- setAuthenticationMethod(String) - Method in class net.sf.basedb.core.data.SessionData
-
- setAuthors(String) - Method in class net.sf.basedb.core.data.ExperimentData
-
- setAuthors(String) - Method in class net.sf.basedb.core.Experiment
-
Set the authors of the publication for this experiment.
- setAutoCloseParsers(boolean) - Method in class net.sf.basedb.util.importer.spotdata.BfsImporter
-
If this option is set then all parsers are automatically closed
when all data has been read to them.
- setAutoCloseWriters(boolean) - Method in class net.sf.basedb.util.export.spotdata.BaseFileExporter
-
If this option is set then all writers are automatically closed
when all data has been writted to them.
- setAutoCloseWriters(boolean) - Method in class net.sf.basedb.util.export.spotdata.BfsExporter
-
If this option is set then all writers are automatically closed
when all data has been writted to them.
- setAutoCompress(boolean) - Method in class net.sf.basedb.core.data.DirectoryData
-
- setAutoCompress(boolean) - Method in class net.sf.basedb.core.data.MimeTypeData
-
- setAutoCompress(boolean) - Method in class net.sf.basedb.core.Directory
-
Set if files of should automatically
be compressed when they are uploaded to this directory.
- setAutoCompress(boolean) - Method in class net.sf.basedb.core.MimeType
-
Set if files of this MIME type should automatically
be compressed when they are uploaded to BASE.
- setAutoJoinType(JoinType) - Method in class net.sf.basedb.core.AbstractEntityQuery
-
Specify the join type of automatic joins.
- setAutoJoinType(JoinType) - Method in class net.sf.basedb.core.DynamicPositionQuery
-
Specify the join type of automatic joins.
- setAutoJoinType(JoinType) - Method in class net.sf.basedb.core.DynamicRawDataQuery
-
Specify the join type of automatic joins.
- setAutoJoinType(JoinType) - Method in class net.sf.basedb.core.DynamicReporterQuery
-
Specify the join type of automatic joins.
- setAutoJoinType(JoinType) - Method in class net.sf.basedb.core.DynamicSpotQuery
-
Specify the join type of automatic joins.
- setAutoLoadChildren(boolean) - Method in class net.sf.basedb.util.overview.loader.BasicItemNodeLoaderFactory
-
Set a flag that determines if the factory should create
node loaders that automatically loads child nodes or not.
- setAutoPermission(int) - Method in class net.sf.basedb.core.data.ProjectData
-
- setAutoPermission(Set<Permission>) - Method in class net.sf.basedb.core.Project
-
Set the default permissions to use when automatically sharing
new item the project when it is the active project.
- setAutoReload(boolean) - Method in class net.sf.basedb.util.units.UnitCache
-
Specifies if a cached unit that may have been loaded
by a closed DbControl should be reloaded with the
current DbControl or not.
- setAutoShare(boolean) - Method in class net.sf.basedb.core.data.DirectoryData
-
- setAutoShare(boolean) - Method in class net.sf.basedb.core.Directory
-
Set if new files and subdirectories of should automatically
be shared with the same permissions as this directory.
- setAutoshow(boolean) - Method in class net.sf.basedb.clients.web.taglib.table.Cell
-
- setAverageMethod(int) - Method in class net.sf.basedb.core.data.ExtraValueTypeData
-
- setAverageMethod(int) - Method in class net.sf.basedb.core.data.FormulaData
-
- setAverageMethod(int) - Method in class net.sf.basedb.core.data.ReporterClonePropertyData
-
- setAverageMethod(Formula.AverageMethod) - Method in class net.sf.basedb.core.ExtraValueType
-
Set the average method of the extra value type..
- setAverageMethod(Formula.AverageMethod) - Method in class net.sf.basedb.core.Formula
-
Set the average method of the formula.
- setAverageMethod(Formula.AverageMethod) - Method in class net.sf.basedb.util.export.spotdata.JepDynamicField
-
Set the average method to use when exporting averaged data.
- setAverageMethod(Formula.AverageMethod) - Method in class net.sf.basedb.util.export.spotdata.SimpleDynamicField
-
Set the average method to use when exporting averaged data.
- setAverageOnReporter(boolean) - Method in class net.sf.basedb.util.export.spotdata.AbstractBioAssaySetExporter
-
Specify if the exported data should be averaged on reporter
or not.
- setAverageOnReporter(boolean) - Method in class net.sf.basedb.util.export.spotdata.BaseFileExporter
-
- setBarcode(String) - Method in class net.sf.basedb.core.ArraySlide
-
Set the barcode for the slide.
- setBarcode(String) - Method in class net.sf.basedb.core.BioPlate
-
Sets the bio plates barcode
- setBarcode(String) - Method in class net.sf.basedb.core.data.ArraySlideData
-
- setBarcode(String) - Method in class net.sf.basedb.core.data.BioPlateData
-
- setBarcode(String) - Method in class net.sf.basedb.core.data.PlateData
-
- setBarcode(String) - Method in class net.sf.basedb.core.Plate
-
Set the barcode for the plate.
- setBatchIndex(int) - Method in class net.sf.basedb.core.ArraySlide
-
Set the index of this slide in the batch.
- setBatchIndex(int) - Method in class net.sf.basedb.core.data.ArraySlideData
-
- setBatchSize(int) - Method in class net.sf.basedb.core.AbstractBatcher
-
- setBatchSize(int) - Method in interface net.sf.basedb.core.Batcher
-
Sets the batch size.
- setBeanClass(String) - Method in class net.sf.basedb.util.extensions.debug.BeanActionFactory
-
Set the name of the class to use as a bean.
- setBigDecimal(int, BigDecimal) - Method in class net.sf.basedb.core.hibernate.QueryWrapper
-
- setBigDecimal(String, BigDecimal) - Method in class net.sf.basedb.core.hibernate.QueryWrapper
-
- setBigInteger(int, BigInteger) - Method in class net.sf.basedb.core.hibernate.QueryWrapper
-
- setBigInteger(String, BigInteger) - Method in class net.sf.basedb.core.hibernate.QueryWrapper
-
- setBinary(int, byte[]) - Method in class net.sf.basedb.core.hibernate.QueryWrapper
-
- setBinary(String, byte[]) - Method in class net.sf.basedb.core.hibernate.QueryWrapper
-
- setBioAssays(Set<BioAssayData>) - Method in class net.sf.basedb.core.data.BioAssaySetData
-
- setBioAssays(Set<BioAssayData>) - Method in class net.sf.basedb.core.data.RawBioAssayData
-
- setBioAssaySet(BioAssaySet) - Method in class net.sf.basedb.core.BioAssay
-
Set the experiment.
- setBioAssaySet(BioAssaySetData) - Method in class net.sf.basedb.core.data.BioAssayData
-
- setBioAssaySet(BioAssaySetData) - Method in class net.sf.basedb.core.data.ExtraValueData
-
- setBioAssaySet(BioAssaySet) - Method in class net.sf.basedb.core.ExtraValue
-
Set the bioassayset.
- setBioAssaySets(Set<BioAssaySetData>) - Method in class net.sf.basedb.core.data.ExperimentData
-
- setBioMaterial(MeasuredBioMaterial) - Method in class net.sf.basedb.core.BioMaterialEvent
-
Set the biomaterial that was affected or created by this event.
- setBioMaterial(MeasuredBioMaterialData) - Method in class net.sf.basedb.core.data.BioMaterialEventData
-
- setBioMaterial(BioMaterialData) - Method in class net.sf.basedb.core.data.BioMaterialEventSourceData
-
- setBioMaterial(MeasuredBioMaterialData) - Method in class net.sf.basedb.core.data.BioWellData
-
- setBioMaterialEvents(Set<BioMaterialEventData>) - Method in class net.sf.basedb.core.data.BioPlateEventParticipantData
-
- setBioMaterialType(Item) - Method in class net.sf.basedb.core.BioPlateType
-
Set the type of biomaterial that can be stored on plates with
this type.
- setBioMaterialType(Integer) - Method in class net.sf.basedb.core.data.BioPlateTypeData
-
- setBioPlate(BioPlateData) - Method in class net.sf.basedb.core.data.BioPlateEventParticipantData
-
- setBioPlate(BioPlateData) - Method in class net.sf.basedb.core.data.BioWellData
-
- setBioPlateEventParticipant(BioPlateEventParticipantData) - Method in class net.sf.basedb.core.data.BioMaterialEventData
-
- setBioPlateEventParticipant(BioPlateEventParticipant) - Method in class net.sf.basedb.core.MeasuredBioMaterial
-
- setBioPlateEventParticipant(BioPlateEventParticipant) - Method in class net.sf.basedb.core.PhysicalBioAssay
-
- setBioPlates(Set<BioPlateData>) - Method in class net.sf.basedb.core.data.BioPlateTypeData
-
- setBioPlateType(BioPlateType) - Method in class net.sf.basedb.core.BioPlate
-
- setBioPlateType(BioPlateTypeData) - Method in class net.sf.basedb.core.data.BioPlateData
-
- setBioWell(BioWellData) - Method in class net.sf.basedb.core.data.MeasuredBioMaterialData
-
- setBioWell(BioWell) - Method in class net.sf.basedb.core.MeasuredBioMaterial
-
Sets the BioWell
where this biomaterial is located.
- setBioWells(Map<PlateCoordinate, BioWellData>) - Method in class net.sf.basedb.core.data.BioPlateData
-
- setBlock(Integer) - Method in class net.sf.basedb.core.data.RawData
-
- setBlockNumber(int) - Method in class net.sf.basedb.core.ArrayDesignBlock
-
Set the block number of this block.
- setBlockNumber(int) - Method in class net.sf.basedb.core.data.ArrayDesignBlockData
-
- setBlockNumber(int) - Method in enum net.sf.basedb.plugins.PrintMapFlatFileImporter.Section
-
- setBlockSizeX(int) - Method in class net.sf.basedb.core.ArrayDesignBlock
-
Set the number of columns in this block.
- setBlockSizeX(int) - Method in class net.sf.basedb.core.data.ArrayDesignBlockData
-
- setBlockSizeX(Integer) - Method in class net.sf.basedb.plugins.PrintMapFlatFileImporter.MetaBlock
-
- setBlockSizeY(int) - Method in class net.sf.basedb.core.ArrayDesignBlock
-
Set the number of rows in this block.
- setBlockSizeY(int) - Method in class net.sf.basedb.core.data.ArrayDesignBlockData
-
- setBlockSizeY(Integer) - Method in class net.sf.basedb.plugins.PrintMapFlatFileImporter.MetaBlock
-
- setBlockValue(PrintMapFlatFileImporter.MetaBlock, FlatFileParser.Line) - Method in class net.sf.basedb.plugins.PrintMapFlatFileImporter
-
- setBlueImageFile(FileData) - Method in class net.sf.basedb.core.data.SpotImagesData
-
- setBlueImageFile(File) - Method in class net.sf.basedb.core.SpotImages
-
- setBofMarkerRegexp(Pattern) - Method in class net.sf.basedb.util.parser.FlatFileParser
-
Set a regular expression that maches a beginning-of-file
marker.
- setBoolean(int, boolean) - Method in class net.sf.basedb.core.hibernate.QueryWrapper
-
- setBoolean(String, boolean) - Method in class net.sf.basedb.core.hibernate.QueryWrapper
-
- setBooleanValues(List<Boolean>) - Method in class net.sf.basedb.core.data.annotations.AnnotationLink
-
- setBuild(int) - Method in class net.sf.basedb.core.data.SchemaVersionData
-
- setButtonclass(String) - Method in class net.sf.basedb.clients.web.taglib.Select
-
- setButtonicon(String) - Method in class net.sf.basedb.clients.web.taglib.Select
-
- setButtonstyle(String) - Method in class net.sf.basedb.clients.web.taglib.Select
-
- setButtontitle(String) - Method in class net.sf.basedb.clients.web.taglib.Select
-
- setByte(int, byte) - Method in class net.sf.basedb.core.hibernate.QueryWrapper
-
- setByte(String, byte) - Method in class net.sf.basedb.core.hibernate.QueryWrapper
-
- setBytes(long) - Method in class net.sf.basedb.core.data.DataCubeData
-
- setBytes(long) - Method in class net.sf.basedb.core.data.DataCubeExtraValueData
-
- setBytes(long) - Method in class net.sf.basedb.core.data.DataCubeFilterData
-
- setBytes(long) - Method in class net.sf.basedb.core.data.DataCubeLayerData
-
- setBytes(long) - Method in class net.sf.basedb.core.data.DiskUsageData
-
- setBytes(long) - Method in class net.sf.basedb.core.data.ExperimentData
-
- setBytes(long) - Method in class net.sf.basedb.core.data.RawBioAssayData
-
- setBytes(long) - Method in class net.sf.basedb.core.data.ReporterCloneTemplateData
-
- setCacheable(boolean) - Method in class net.sf.basedb.core.hibernate.QueryWrapper
-
- setCachedObject(Object, Object) - Method in class net.sf.basedb.util.overview.GenericOverview
-
Store an auxilliary object in the overview cache.
- setCachedObject(Object, Object) - Method in interface net.sf.basedb.util.overview.OverviewContext
-
Store an auxilliary object in the overview cache.
- setCacheMode(CacheMode) - Method in class net.sf.basedb.core.hibernate.QueryWrapper
-
- setCacheMode(CacheMode) - Method in class net.sf.basedb.core.hibernate.SessionWrapper
-
- setCacheRegion(String) - Method in class net.sf.basedb.core.hibernate.QueryWrapper
-
- setCacheResult(boolean) - Method in class net.sf.basedb.core.AbstractHqlQuery
-
- setCacheResult(boolean) - Method in interface net.sf.basedb.core.query.HqlQuery
-
Specify if the query results should be cached or not.
- setCalendar(int, Calendar) - Method in class net.sf.basedb.core.hibernate.QueryWrapper
-
- setCalendar(String, Calendar) - Method in class net.sf.basedb.core.hibernate.QueryWrapper
-
- setCalendarDate(int, Calendar) - Method in class net.sf.basedb.core.hibernate.QueryWrapper
-
- setCalendarDate(String, Calendar) - Method in class net.sf.basedb.core.hibernate.QueryWrapper
-
- setCategories(Set<AnnotationTypeCategoryData>) - Method in class net.sf.basedb.core.data.AnnotationTypeData
-
- setChangeHistory(ChangeHistoryData) - Method in class net.sf.basedb.core.data.ChangeHistoryDetailData
-
- setChangeInfo(String) - Method in class net.sf.basedb.core.data.ChangeHistoryDetailData
-
- setChangeType(int) - Method in class net.sf.basedb.core.data.ChangeHistoryDetailData
-
- setChannels(int) - Method in class net.sf.basedb.core.data.FormulaData
-
- setChannels(int) - Method in class net.sf.basedb.core.data.PlatformData
-
- setChannels(int) - Method in class net.sf.basedb.core.data.PlatformVariantData
-
- setChannels(int) - Method in class net.sf.basedb.core.Formula
-
Set the number of channels that are required to use this formula.
- setChannels(int) - Method in class net.sf.basedb.core.Platform
-
Set the number of channels for a file-only platform.
- setChannels(int) - Method in class net.sf.basedb.core.PlatformVariant
-
Set the number of channels for a file-only platform variant.
- setCharacter(int, char) - Method in class net.sf.basedb.core.hibernate.QueryWrapper
-
- setCharacter(String, char) - Method in class net.sf.basedb.core.hibernate.QueryWrapper
-
- setCharacterSet(String) - Method in class net.sf.basedb.clients.web.util.ServletExportOutputStream
-
- setCharacterSet(String) - Method in class net.sf.basedb.core.data.FileData
-
- setCharacterSet(String) - Method in class net.sf.basedb.core.File
-
Set the character set used in this file (for text-files only).
- setCharacterSet(String) - Method in class net.sf.basedb.core.plugin.ExportOutputStream
-
Do nothing should be overridden by subclasses.
- setCharacterSet(String) - Method in class net.sf.basedb.util.FileExportOutputStream
-
- setCharacterSet(String) - Method in class net.sf.basedb.util.uri.UriMetadata
-
- setChild(BioAssay) - Method in class net.sf.basedb.util.importer.spotdata.BaseFileInfo.ChildBioAssay
-
Set the real child bioassay object.
- setChildCreationEvents(Set<BioMaterialEventSourceData>) - Method in class net.sf.basedb.core.data.BioMaterialData
-
- setChildHasDifferentReporterPositionMapping(boolean) - Method in class net.sf.basedb.util.importer.spotdata.BaseFileInfo
-
Set a flag that indicates if the child data has a different position/reporter
mapping than the parent bioassay set.
- setChildId(int) - Method in class net.sf.basedb.core.data.keyring.GroupGroups
-
Set the id of the child group.
- setChildren(Set<BioAssayData>) - Method in class net.sf.basedb.core.data.BioAssayData
-
- setChildren(Set<MeasuredBioMaterialData>) - Method in class net.sf.basedb.core.data.BioMaterialData
-
- setChildren(Set<DerivedBioAssayData>) - Method in class net.sf.basedb.core.data.DerivedBioAssayData
-
- setChildren(Set<GroupData>) - Method in class net.sf.basedb.core.data.GroupData
-
- setChildren(Set<PlateData>) - Method in class net.sf.basedb.core.data.PlateData
-
- setChildrenLoaded() - Method in class net.sf.basedb.util.overview.Node
-
Sets a flag to indicate that all children has been loaded.
- setClassName(String) - Method in class net.sf.basedb.core.data.PluginDefinitionData
-
- setClassName(String) - Method in class net.sf.basedb.core.PluginDefinition
-
The class name cannot be changed.
- setClassName(String) - Method in class net.sf.basedb.util.extensions.xml.PluginInfo
-
- setClazz(String) - Method in class net.sf.basedb.clients.web.extensions.list.AbstractListColumnBean
-
- setClazz(String) - Method in class net.sf.basedb.clients.web.extensions.list.PropertyPathActionFactory
-
- setClazz(String) - Method in class net.sf.basedb.clients.web.extensions.login.FieldInfo
-
- setClazz(String) - Method in class net.sf.basedb.clients.web.extensions.menu.FixedMenuItemFactory
-
- setClazz(String) - Method in class net.sf.basedb.clients.web.extensions.menu.MenuItemBean
-
- setClazz(String) - Method in class net.sf.basedb.clients.web.extensions.tabcontrol.FixedTabFactory
-
- setClazz(String) - Method in class net.sf.basedb.clients.web.extensions.tabcontrol.IncludeContentTabFactory
-
- setClazz(String) - Method in class net.sf.basedb.clients.web.extensions.tabcontrol.TabBean
-
- setClazz(String) - Method in class net.sf.basedb.clients.web.extensions.toolbar.ButtonBean
-
- setClazz(String) - Method in class net.sf.basedb.clients.web.extensions.toolbar.FixedButtonFactory
-
- setClazz(String) - Method in class net.sf.basedb.clients.web.extensions.toolbar.PermissionButtonFactory
-
Set the class to use in all cases.
- setClazz(String) - Method in class net.sf.basedb.clients.web.taglib.ExceptionCatcher
-
- setClazz(String) - Method in class net.sf.basedb.clients.web.taglib.StylableTag
-
- setClazz(String) - Method in class net.sf.basedb.clients.web.taglib.tab.Tab
-
- setClazz(String) - Method in class net.sf.basedb.clients.web.taglib.table.Cell
-
- setClazz(String) - Method in class net.sf.basedb.clients.web.taglib.table.CellValue
-
- setClearErrors(boolean) - Method in class net.sf.basedb.util.extensions.ExtensionsInvoker
-
Set a flag to indicate if existing errors should be cleared
before an action is rendered.
- setClearState() - Method in interface net.sf.basedb.core.plugin.Response
-
This can be used in the configuration phase of a plug-in
to clear the stored state and nextCommand information.
- setClearState() - Method in class net.sf.basedb.core.PluginResponse.ResponseImpl
-
- setClearState() - Method in class net.sf.basedb.plugins.executor.ExternalProgramExecutor.ResponseWrapper
-
- setClient(Client) - Method in class net.sf.basedb.core.ClientDefaultSetting
-
Set the client application this setting is valid for.
- setClient(ClientData) - Method in class net.sf.basedb.core.data.ChangeHistoryData
-
- setClient(ClientData) - Method in class net.sf.basedb.core.data.ClientDefaultSettingData
-
- setClient(ClientData) - Method in class net.sf.basedb.core.data.ContextData
-
- setClient(ClientData) - Method in class net.sf.basedb.core.data.ContextIndex
-
- setClient(ClientData) - Method in class net.sf.basedb.core.data.HelpData
-
- setClient(ClientData) - Method in class net.sf.basedb.core.data.SessionData
-
- setClient(ClientData) - Method in class net.sf.basedb.core.data.UserClientSettingData
-
- setClient(Client) - Method in class net.sf.basedb.core.Help
-
Set the client application this setting is valid for.
- setClient(Client) - Method in class net.sf.basedb.core.UserClientSetting
-
Set the client application this setting is valid for.
- setClientCertificate(byte[]) - Method in class net.sf.basedb.core.data.FileServerData
-
- setClientCertificate(byte[]) - Method in class net.sf.basedb.core.FileServer
-
Set the client certificate that BASE should use to authenticate with the server
when connecting with https.
- setClientCertificate(byte[]) - Method in class net.sf.basedb.util.uri.ConnectionParameters
-
- setClientCertificatePassword(String) - Method in class net.sf.basedb.core.data.FileServerData
-
- setClientCertificatePassword(String) - Method in class net.sf.basedb.core.FileServer
-
Set the password that is needed to unlock the client
certificate.
- setClientCertificatePassword(String) - Method in class net.sf.basedb.util.uri.ConnectionParameters
-
- setClientId(Integer) - Method in class net.sf.basedb.core.data.ChangeHistoryData
-
- setClientSettings(Set<UserClientSettingData>) - Method in class net.sf.basedb.core.data.UserData
-
- setClone(boolean) - Method in class net.sf.basedb.util.annotations.InheritSpecification
-
Set a flag to inherit annotations by cloning the original values.
- setColor(String) - Method in class net.sf.basedb.clients.web.ExperimentExplorer.AnnotationGroup
-
Sets the color for this annotation group.
- setColor(String, Color) - Method in class net.sf.basedb.clients.web.servlet.ExperimentExplorerPlotServlet.ColumnKey
-
- setColoring(ColoringData) - Method in class net.sf.basedb.core.data.ExtraValueTypeData
-
- setColoring(ColoringData) - Method in class net.sf.basedb.core.data.FormulaData
-
- setColorsAuto() - Method in class net.sf.basedb.clients.web.ExperimentExplorer.AnnotationSummary
-
- setColspan(int) - Method in class net.sf.basedb.clients.web.taglib.table.Header
-
- setColumn(String) - Method in class net.sf.basedb.clients.web.taglib.table.Cell
-
- setColumn(int) - Method in class net.sf.basedb.core.data.BioWellData
-
- setColumn(int) - Method in class net.sf.basedb.core.data.FeatureData
-
- setColumn(int) - Method in class net.sf.basedb.core.data.MappingCoordinate
-
Set the location.
- setColumn(int) - Method in class net.sf.basedb.core.data.PlateCoordinate
-
Set the location.
- setColumn(Integer) - Method in class net.sf.basedb.core.data.RawData
-
- setColumn(String) - Method in class net.sf.basedb.core.data.ReporterClonePropertyData
-
- setColumn(int) - Method in class net.sf.basedb.core.data.WellData
-
- setColumnContent(String, String) - Method in class net.sf.basedb.clients.web.taglib.table.Table
-
- setColumnCount(int) - Method in class net.sf.basedb.util.bfs.DataWriter
-
Set the number of data columns.
- setColumnFilter(String, int, String) - Method in class net.sf.basedb.clients.web.taglib.table.Table
-
- setColumnNo(short) - Method in class net.sf.basedb.core.data.DataCubeColumnData
-
- setColumnNo(short) - Method in class net.sf.basedb.core.DataCubeColumn
-
- setColumns(String) - Method in class net.sf.basedb.clients.web.taglib.table.Table
-
- setColumns(Set<DataCubeColumnData>) - Method in class net.sf.basedb.core.data.DataCubeData
-
- setColumns(int) - Method in class net.sf.basedb.core.data.PlateGeometryData
-
- setColumns(int) - Method in class net.sf.basedb.core.PlateGeometry
-
The number of columns cannot be changed, used at object creation only.
- setComment(String) - Method in class net.sf.basedb.core.authentication.LoginRequest
-
Set the comment to use.
- setComment(String) - Method in class net.sf.basedb.core.BioMaterialEvent
-
Set the comment about this event.
- setComment(String) - Method in class net.sf.basedb.core.data.BioMaterialEventData
-
- setComment(String) - Method in class net.sf.basedb.core.data.PlateEventData
-
- setComment(String) - Method in class net.sf.basedb.core.hibernate.QueryWrapper
-
- setComment(String) - Method in class net.sf.basedb.core.PlateEvent
-
Set the comment about this event.
- setCompressed(boolean) - Method in class net.sf.basedb.core.data.FileData
-
- setCompressedSize(long) - Method in class net.sf.basedb.core.data.FileData
-
- setCondition(String) - Method in class net.sf.basedb.core.dbengine.TableInfo.IndexInfo
-
- setConfigurations(Set<PluginConfigurationData>) - Method in class net.sf.basedb.core.data.PluginDefinitionData
-
- setConfigurationValues(Map<VersionedParameter, ParameterValueData<?>>) - Method in class net.sf.basedb.core.data.PluginConfigurationData
-
- setConfigured(PluginResponse) - Method in class net.sf.basedb.core.Job.ProgressReporterImpl
-
- setConnectionManagerFactory(String) - Method in class net.sf.basedb.core.data.FileServerData
-
- setConnectionManagerFactoryId(String) - Method in class net.sf.basedb.core.FileServer
-
Set the ID of the connection manager factory.
- setConnectionManagerFactoryId(String) - Method in class net.sf.basedb.util.uri.ConnectionParameters
-
- setContact(String) - Method in class net.sf.basedb.core.data.PluginDefinitionData
-
- setContact(String) - Method in class net.sf.basedb.core.PluginDefinition
-
Set contact information for this plug-in.
- setContact(String) - Method in class net.sf.basedb.util.extensions.AboutBean
-
- setContent(String) - Method in class net.sf.basedb.clients.web.extensions.section.SectionBean
-
- setContent(String) - Method in class net.sf.basedb.clients.web.extensions.tabcontrol.FixedTabFactory
-
- setContent(String) - Method in class net.sf.basedb.clients.web.extensions.tabcontrol.TabBean
-
- setContentLength(long) - Method in class net.sf.basedb.clients.web.util.ServletExportOutputStream
-
- setContentLength(long) - Method in class net.sf.basedb.core.plugin.ExportOutputStream
-
Do nothing.
- setContentLength(long) - Method in class net.sf.basedb.util.FileExportOutputStream
-
Ignored.
- setContentStyle(String) - Method in class net.sf.basedb.clients.web.extensions.section.IncludeContentSectionFactory
-
- setContentStyle(String) - Method in class net.sf.basedb.clients.web.extensions.section.SectionBean
-
- setContentstyle(String) - Method in class net.sf.basedb.clients.web.taglib.HideableSection
-
- setContentstyle(String) - Method in class net.sf.basedb.clients.web.taglib.tab.TabControl
-
- setContext(JspContext) - Method in class net.sf.basedb.clients.web.taglib.extensions.Render
-
- setContext(JspContext) - Method in class net.sf.basedb.clients.web.taglib.extensions.Scripts
-
- setContext(JspContext) - Method in class net.sf.basedb.clients.web.taglib.extensions.Stylesheets
-
- setContext(ItemContext) - Method in class net.sf.basedb.clients.web.taglib.HideableSection
-
- setContext(ClientContext) - Method in class net.sf.basedb.core.signal.ExtensionSignalTransporter
-
- setContextClassLoader() - Method in class net.sf.basedb.clients.web.extensions.XJspCompiler
-
Sets the context class loader if this JSP page is an
extension JSP page and if the extensions JAR file has been
modified since the last time the class loader was set.
- setContextItem(Integer) - Method in class net.sf.basedb.core.data.JobData
-
- setContexts(Set<ContextData>) - Method in class net.sf.basedb.core.data.ClientData
-
- setContexts(Map<ContextIndex, ContextData>) - Method in class net.sf.basedb.core.data.UserData
-
- setContextType(int) - Method in class net.sf.basedb.core.data.GuiContextData
-
- setContextType(Integer) - Method in class net.sf.basedb.core.data.JobData
-
- setContinue(String) - Method in interface net.sf.basedb.core.plugin.Response
-
This method will continue the configuration or execution of the
job with a new command to the plugin.
- setContinue(String, Serializable) - Method in interface net.sf.basedb.core.plugin.Response
-
Can be used by an executing job to also store state information
that will be restored when the job is starting up again.
- setContinue(String) - Method in class net.sf.basedb.core.PluginResponse.ResponseImpl
-
- setContinue(String, Serializable) - Method in class net.sf.basedb.core.PluginResponse.ResponseImpl
-
- setContinue(String) - Method in class net.sf.basedb.plugins.executor.ExternalProgramExecutor.ResponseWrapper
-
- setContinue(String, Serializable) - Method in class net.sf.basedb.plugins.executor.ExternalProgramExecutor.ResponseWrapper
-
- setCoordinateType(int) - Method in class net.sf.basedb.core.data.DataCubeExtraValueData
-
- setCoordinateType(ExtraValue.CoordinateType) - Method in class net.sf.basedb.core.DataCubeExtraValue
-
Set the coordinate type.
- setCopyright(String) - Method in class net.sf.basedb.core.data.PluginDefinitionData
-
- setCopyright(String) - Method in class net.sf.basedb.core.PluginDefinition
-
Update copyright information about this plug-in.
- setCopyright(String) - Method in class net.sf.basedb.util.extensions.AboutBean
-
- setCounting(boolean) - Method in class net.sf.basedb.core.AbstractQuery
-
Set the counting status of the query.
- setCreated(Date) - Method in class net.sf.basedb.core.data.JobData
-
- setCreationEvent(BioMaterialEventData) - Method in class net.sf.basedb.core.data.MeasuredBioMaterialData
-
- setCreationEvent(BioMaterialEventData) - Method in class net.sf.basedb.core.data.PhysicalBioAssayData
-
- setCryptedPassword(String) - Method in class net.sf.basedb.core.data.PasswordData
-
Set the encrypted password.
- setCubeNo(short) - Method in class net.sf.basedb.core.data.DataCubeData
-
- setCubeNo(short) - Method in class net.sf.basedb.core.DataCube
-
- setCubes(short) - Method in class net.sf.basedb.core.data.VirtualDbData
-
- setCurNumberOfParameters(int) - Method in class net.sf.basedb.util.jep.ChannelFunction
-
- setCurNumberOfParameters(int) - Method in class net.sf.basedb.util.jep.ExtraValueFunction
-
- setCurNumberOfParameters(int) - Method in class net.sf.basedb.util.jep.FunctionSafeJep.UnknownFunction
-
- setCurNumberOfParameters(int) - Method in class net.sf.basedb.util.jep.InReporterListFunction
-
- setCurNumberOfParameters(int) - Method in class net.sf.basedb.util.jep.LeftFunction
-
- setCurNumberOfParameters(int) - Method in class net.sf.basedb.util.jep.Log2Function
-
- setCurNumberOfParameters(int) - Method in class net.sf.basedb.util.jep.MeanFunction
-
- setCurNumberOfParameters(int) - Method in class net.sf.basedb.util.jep.NotInReporterListFunction
-
- setCurNumberOfParameters(int) - Method in class net.sf.basedb.util.jep.PositionFunction
-
Can't be changed.
- setCurNumberOfParameters(int) - Method in class net.sf.basedb.util.jep.RawChannelFunction
-
- setCurNumberOfParameters(int) - Method in class net.sf.basedb.util.jep.RawFunction
-
- setCurNumberOfParameters(int) - Method in class net.sf.basedb.util.jep.ReporterFunction
-
- setCurNumberOfParameters(int) - Method in class net.sf.basedb.util.jep.ScoreFunction
-
- setCurNumberOfParameters(int) - Method in class net.sf.basedb.util.jep.SimpleJepFunction
-
- setCurNumberOfParameters(int) - Method in class net.sf.basedb.util.parser.ColFunction
-
- setCurNumberOfParameters(int) - Method in class net.sf.basedb.util.parser.DataNoFunction
-
- setCurNumberOfParameters(int) - Method in class net.sf.basedb.util.parser.DefaultItemFunction
-
- setCurNumberOfParameters(int) - Method in class net.sf.basedb.util.parser.LineNoFunction
-
- setCurrent(BasicItem) - Method in class net.sf.basedb.clients.web.taglib.Select
-
- setCurrentBioWell(BioWell) - Method in class net.sf.basedb.util.overview.node.BioPlateNameGenerator
-
Set the current biowell object that should be used when
generating names for bioplates that are reached by navigating via a biomaterial.
- setCurrentEventParticipant(BioPlateEventParticipant) - Method in class net.sf.basedb.util.overview.node.BioPlateNameGenerator
-
Set the current bioplate event participant object that should be used when
generating names for bioplates that are part of a bioplate event.
- setCurrentFilename(String) - Method in class net.sf.basedb.clients.web.fileupload.FileUploadProgress
-
Sets the name of the file that is currently uploading
- setCurrentItem(Annotatable) - Method in class net.sf.basedb.core.AnnotationBatcher
-
Set the current item to work with from now on.
- setCurrentItem(Object) - Method in class net.sf.basedb.util.extensions.ClientContext
-
Set the currently active item.
- setCurrentMapper(ImageRemapper) - Static method in class net.sf.basedb.clients.web.extensions.skin.ImageRemapperUtil
-
Changes the current image remapper.
- setCurrentSubtype(ItemSubtype) - Method in class net.sf.basedb.util.parser.DefaultItemFunction
-
Set the current subtype to use when looking for default items.
- setCurrentWell(BioWell) - Method in class net.sf.basedb.util.overview.node.BioWellNameGenerator
-
Set the well we are currently working with.
- setData(String[]) - Method in class net.sf.basedb.util.importer.spotdata.SynchronizedSpotDataParser.SynchronizedData
-
- setData(FlatFileParser.Data) - Method in class net.sf.basedb.util.parser.ColFunction
-
- setData(FlatFileParser.Data) - Method in class net.sf.basedb.util.parser.DataNoFunction
-
- setData(FlatFileParser.Data) - Method in class net.sf.basedb.util.parser.JepMapper
-
- setData(FlatFileParser.Data) - Method in class net.sf.basedb.util.parser.LineNoFunction
-
- setDataCube(DataCubeData) - Method in class net.sf.basedb.core.data.DataCubeColumnData
-
- setDataCube(DataCubeData) - Method in class net.sf.basedb.core.data.DataCubeExtraValueData
-
- setDataCube(DataCubeData) - Method in class net.sf.basedb.core.data.DataCubeFilterData
-
- setDataCube(DataCubeData) - Method in class net.sf.basedb.core.data.DataCubeLayerData
-
- setDataCube(DataCube) - Method in class net.sf.basedb.core.DataCubeColumn
-
Set the experiment.
- setDataCube(DataCube) - Method in class net.sf.basedb.core.DataCubeExtraValue
-
Set the data cube.
- setDataCube(DataCube) - Method in class net.sf.basedb.core.DataCubeFilter
-
Set the data cube.
- setDataCube(DataCube) - Method in class net.sf.basedb.core.DataCubeLayer
-
Set the data cube.
- setDataCubeColumn(DataCubeColumn) - Method in class net.sf.basedb.core.BioAssay
-
- setDataCubeColumn(DataCubeColumnData) - Method in class net.sf.basedb.core.data.BioAssayData
-
- setDataCubeExtraValue(DataCubeExtraValueData) - Method in class net.sf.basedb.core.data.ExtraValueData
-
- setDataCubeExtraValue(DataCubeExtraValue) - Method in class net.sf.basedb.core.ExtraValue
-
- setDataCubeFilter(DataCubeFilter) - Method in class net.sf.basedb.core.BioAssaySet
-
- setDataCubeFilter(DataCubeFilterData) - Method in class net.sf.basedb.core.data.BioAssaySetData
-
- setDataCubeLayer(DataCubeLayer) - Method in class net.sf.basedb.core.BioAssaySet
-
- setDataCubeLayer(DataCubeLayerData) - Method in class net.sf.basedb.core.data.BioAssaySetData
-
- setDataCubes(Set<DataCubeData>) - Method in class net.sf.basedb.core.data.VirtualDbData
-
- setDataFile(DbControl, FileStoreEnabled, String, File) - Static method in class net.sf.basedb.core.FileStoreUtil
-
- setDataFileType(DataFileTypeData) - Method in class net.sf.basedb.core.data.FileSetMemberData
-
- setDataFileType(DataFileTypeData) - Method in class net.sf.basedb.core.data.FileTypeIndex
-
- setDataFileType(DataFileTypeData) - Method in class net.sf.basedb.core.data.ItemSubtypeFileTypeData
-
- setDataFileType(DataFileTypeData) - Method in class net.sf.basedb.core.data.PlatformFileTypeData
-
- setDataFooterRegexp(Pattern) - Method in class net.sf.basedb.util.parser.FlatFileParser
-
Set a regular expression that can be matched against a
data footer.
- setDataHeaderRegexp(Pattern) - Method in class net.sf.basedb.util.parser.FlatFileParser
-
Set a regular expression that can be matched against the data
header.
- setDataSeparator(String) - Method in class net.sf.basedb.util.export.TableWriter
-
Change the data separator string.
- setDataSplitterRegexp(Pattern) - Method in class net.sf.basedb.util.parser.FlatFileParser
-
Set a regular expression that is used to split a data line into
columns.
- setDatatype(String) - Method in class net.sf.basedb.clients.web.taglib.table.ColumnDef
-
- setDataWriterFactory(DataWriterFactory<?>) - Method in class net.sf.basedb.util.export.spotdata.BfsExporter
-
Set the data writer factory to use for generating spot data files.
- setDate(int, Date) - Method in class net.sf.basedb.core.hibernate.QueryWrapper
-
- setDate(String, Date) - Method in class net.sf.basedb.core.hibernate.QueryWrapper
-
- setDateFormat(SessionControl, String) - Static method in class net.sf.basedb.clients.web.formatter.FormatterSettings
-
Set the format string for a date formatter.
- setDateOrToday(Date) - Static method in class net.sf.basedb.core.DateUtil
-
Make a copy of the date.
- setDateTimeFormat(SessionControl, String) - Static method in class net.sf.basedb.clients.web.formatter.FormatterSettings
-
Set the format string for a datetime formatter.
- setDateValues(List<Date>) - Method in class net.sf.basedb.core.data.annotations.AnnotationLink
-
- setDbcontrol(DbControl) - Method in class net.sf.basedb.clients.web.taglib.PropertyValue
-
- setDbControl(DbControl) - Method in class net.sf.basedb.core.AbstractBatcher
-
Set the DbControl that is controlling this batcher.
- setDbControl(DbControl) - Method in class net.sf.basedb.core.BasicItem
-
Set the
DbControl
object that should manage this item.
- setDbControl(DbControl) - Method in class net.sf.basedb.core.DiskUsageStatistics
-
Set the DbControl which will be used to get statisics if it is not
cached.
- setDbControl(DbControl) - Method in class net.sf.basedb.util.export.spotdata.AbstractBioAssaySetExporter
-
Set's the DbControl that should be used to get data from the database.
- setDbControl(DbControl) - Method in class net.sf.basedb.util.importer.spotdata.BaseFileImporter
-
Set's the DbControl that should be used to get data from the database.
- setDbControl(DbControl) - Method in class net.sf.basedb.util.importer.spotdata.BfsImporter
-
Set's the DbControl that should be used to get data from the database.
- setDbControl(DbControl) - Method in class net.sf.basedb.util.units.UnitCache
-
Set the DbControl to use for database access
- setDc(DbControl) - Method in class net.sf.basedb.clients.web.taglib.table.ExtensionCells
-
- setDefault(boolean) - Method in class net.sf.basedb.core.data.GroupData
-
- setDefault(boolean) - Method in class net.sf.basedb.core.data.RoleData
-
- setDefault(boolean) - Method in class net.sf.basedb.core.Group
-
If this group should be assigned to new users by default or not.
- setDefault(boolean) - Method in class net.sf.basedb.core.Role
-
If this role should be assigned to new users by default or not.
- setDefaultErrorHandlerFactory(ErrorHandlerFactory<Action>) - Method in class net.sf.basedb.util.extensions.Registry
-
Set the default error handler factory.
- setDefaultitem(BasicItem) - Method in class net.sf.basedb.clients.web.taglib.Select
-
- setDefaultitems(List<? extends BasicItem>) - Method in class net.sf.basedb.clients.web.taglib.Select
-
- setDefaultItems(ItemParameterValueData) - Method in class net.sf.basedb.core.data.ProjectData
-
- setDefaultNumberFormat(NumberFormat) - Method in class net.sf.basedb.util.parser.FlatFileParser
-
Set the default number format to use when creating mappers.
- setDefaultRawDataType(RawDataType) - Method in class net.sf.basedb.core.Project
-
Sets a raw data type to be used as default for a project.
- setDefaultReadOnly(boolean) - Method in class net.sf.basedb.core.hibernate.SessionWrapper
-
- setDefaultSettings(Set<ClientDefaultSettingData>) - Method in class net.sf.basedb.core.data.ClientData
-
- setDefaultSettings(Set<UserDefaultSettingData>) - Method in class net.sf.basedb.core.data.UserData
-
- setDefaultUnit(Unit) - Method in class net.sf.basedb.core.AnnotationType
-
Set the default unit to use for this annotation type.
- setDefaultUnit(UnitData) - Method in class net.sf.basedb.core.data.AnnotationTypeData
-
- setDefaultValue(String) - Method in class net.sf.basedb.core.AnnotationType
-
Set the recommended default value for new annotation of this annotation type.
- setDefaultValue(String) - Method in class net.sf.basedb.core.data.AnnotationTypeData
-
- setDefaultValue(String) - Method in class net.sf.basedb.plugins.executor.ParameterDefinition
-
Set the default value for this parameter.
- setDefaultValue(String) - Method in class net.sf.basedb.util.formatter.LookupFormatter
-
- setDelayRegistration(boolean) - Method in class net.sf.basedb.util.extensions.manager.processor.IgnoreFileProcessor
-
Set a flag to indicate if the actual registration of the found
extensions and extension points should be delayed or not.
- setDelayRegistration(boolean) - Method in class net.sf.basedb.util.extensions.manager.processor.RegisterExtensionsProcessor
-
Set a flag to indicate if the actual registration of the found
extensions and extension points should be delayed or not.
- setDelegateFirst(boolean) - Method in class net.sf.basedb.util.JarClassLoader
-
If the class loader should delegate to the parent class loader
before trying to find the class by it's own.
- setDenied(boolean) - Method in class net.sf.basedb.clients.web.taglib.Select
-
- setDenied(int) - Method in class net.sf.basedb.core.data.keyring.PluginKeys
-
Set the denied permissions.
- setDenied(int) - Method in class net.sf.basedb.core.data.PluginPermission
-
- setDerivedBioAssays(Set<DerivedBioAssayData>) - Method in class net.sf.basedb.core.data.ExtractData
-
- setDerivedBioAssays(Set<DerivedBioAssayData>) - Method in class net.sf.basedb.core.data.JobData
-
- setDerivedBioAssays(Set<DerivedBioAssayData>) - Method in class net.sf.basedb.core.data.PhysicalBioAssayData
-
- setDescription(String) - Method in class net.sf.basedb.clients.web.extensions.plot.OverviewPlotBean
-
- setDescription(String) - Method in class net.sf.basedb.clients.web.extensions.startpage.FixedStartPageFactory
-
- setDescription(String) - Method in class net.sf.basedb.clients.web.extensions.startpage.StartPageBean
-
- setDescription(String) - Method in class net.sf.basedb.core.AnyToAny
-
- setDescription(String) - Method in class net.sf.basedb.core.authentication.ExtraUserInformation
-
- setDescription(String) - Method in class net.sf.basedb.core.BioAssay
-
- setDescription(String) - Method in class net.sf.basedb.core.BioAssaySet
-
- setDescription(String) - Method in class net.sf.basedb.core.BioPlateEvent
-
Set the description.
- setDescription(String) - Method in class net.sf.basedb.core.BioPlateEventType
-
- setDescription(String) - Method in class net.sf.basedb.core.BioPlateType
-
- setDescription(String) - Method in class net.sf.basedb.core.CommonItem
-
- setDescription(String) - Method in class net.sf.basedb.core.data.AnyToAnyData
-
- setDescription(String) - Method in class net.sf.basedb.core.data.BioAssayData
-
- setDescription(String) - Method in class net.sf.basedb.core.data.BioAssaySetData
-
- setDescription(String) - Method in class net.sf.basedb.core.data.BioPlateEventTypeData
-
- setDescription(String) - Method in class net.sf.basedb.core.data.BioPlateTypeData
-
- setDescription(String) - Method in class net.sf.basedb.core.data.CommonData
-
- setDescription(String) - Method in class net.sf.basedb.core.data.DataFileTypeData
-
- setDescription(String) - Method in class net.sf.basedb.core.data.ExtraValueTypeData
-
- setDescription(String) - Method in class net.sf.basedb.core.data.GroupData
-
- setDescription(String) - Method in class net.sf.basedb.core.data.HelpData
-
- setDescription(String) - Method in class net.sf.basedb.core.data.ItemListSyncFilterData
-
- setDescription(String) - Method in class net.sf.basedb.core.data.ItemSubtypeData
-
- setDescription(String) - Method in class net.sf.basedb.core.data.MessageData
-
- setDescription(String) - Method in class net.sf.basedb.core.data.MimeTypeData
-
- setDescription(String) - Method in interface net.sf.basedb.core.data.NameableData
-
Set the description for the item.
- setDescription(String) - Method in class net.sf.basedb.core.data.NewsData
-
- setDescription(String) - Method in class net.sf.basedb.core.data.ParameterValueData
-
- setDescription(String) - Method in class net.sf.basedb.core.data.PlateEventTypeData
-
- setDescription(String) - Method in class net.sf.basedb.core.data.PlateGeometryData
-
- setDescription(String) - Method in class net.sf.basedb.core.data.PlatformData
-
- setDescription(String) - Method in class net.sf.basedb.core.data.PlatformVariantData
-
- setDescription(String) - Method in class net.sf.basedb.core.data.PluginDefinitionData
-
- setDescription(String) - Method in class net.sf.basedb.core.data.PluginTypeData
-
- setDescription(String) - Method in class net.sf.basedb.core.data.ProjectData
-
- setDescription(String) - Method in class net.sf.basedb.core.data.QuantityData
-
- setDescription(String) - Method in class net.sf.basedb.core.data.QuotaData
-
- setDescription(String) - Method in class net.sf.basedb.core.data.QuotaTypeData
-
- setDescription(String) - Method in class net.sf.basedb.core.data.ReporterClonePropertyData
-
- setDescription(String) - Method in class net.sf.basedb.core.data.ReporterData
-
- setDescription(String) - Method in class net.sf.basedb.core.data.ReporterTypeData
-
- setDescription(String) - Method in class net.sf.basedb.core.data.RoleData
-
- setDescription(String) - Method in class net.sf.basedb.core.data.RoleKeyData
-
- setDescription(String) - Method in class net.sf.basedb.core.data.RootRawBioAssayData
-
- setDescription(String) - Method in class net.sf.basedb.core.data.TransformationData
-
- setDescription(String) - Method in class net.sf.basedb.core.data.UnitData
-
- setDescription(String) - Method in class net.sf.basedb.core.data.UserData
-
- setDescription(String) - Method in class net.sf.basedb.core.DataFileType
-
- setDescription(String) - Method in class net.sf.basedb.core.Directory
-
- setDescription(String) - Method in class net.sf.basedb.core.ExtraValueType
-
- setDescription(String) - Method in class net.sf.basedb.core.Group
-
- setDescription(String) - Method in class net.sf.basedb.core.Help
-
- setDescription(String) - Method in class net.sf.basedb.core.ItemSubtype
-
- setDescription(String) - Method in class net.sf.basedb.core.Message
-
- setDescription(String) - Method in class net.sf.basedb.core.MimeType
-
- setDescription(String) - Method in interface net.sf.basedb.core.Nameable
-
Set the description for the item.
- setDescription(NameableData, String) - Static method in class net.sf.basedb.core.NameableUtil
-
- setDescription(String) - Method in class net.sf.basedb.core.News
-
- setDescription(String) - Method in class net.sf.basedb.core.PlateEventType
-
- setDescription(String) - Method in class net.sf.basedb.core.PlateGeometry
-
- setDescription(String) - Method in class net.sf.basedb.core.Platform
-
- setDescription(String) - Method in class net.sf.basedb.core.PlatformVariant
-
- setDescription(String) - Method in class net.sf.basedb.core.PluginType
-
- setDescription(String) - Method in class net.sf.basedb.core.Project
-
- setDescription(String) - Method in class net.sf.basedb.core.Quantity
-
- setDescription(String) - Method in class net.sf.basedb.core.Quota
-
- setDescription(String) - Method in class net.sf.basedb.core.QuotaType
-
- setDescription(String) - Method in class net.sf.basedb.core.ReporterCloneTemplate
-
Allow the description to be changed with RESTRICTED_WRITE
permission.
- setDescription(String) - Method in class net.sf.basedb.core.ReporterType
-
- setDescription(String) - Method in class net.sf.basedb.core.Role
-
- setDescription(String) - Method in class net.sf.basedb.core.RoleKey
-
- setDescription(String) - Method in class net.sf.basedb.core.RootRawBioAssay
-
- setDescription(String) - Method in class net.sf.basedb.core.SyncFilter
-
- setDescription(String) - Method in class net.sf.basedb.core.Transformation
-
- setDescription(String) - Method in class net.sf.basedb.core.Unit
-
- setDescription(String) - Method in class net.sf.basedb.core.User
-
- setDescription(String) - Method in class net.sf.basedb.plugins.executor.ParameterDefinition
-
Set a description/help text for this parmeter.
- setDescription(String) - Method in class net.sf.basedb.util.extensions.AboutBean
-
- setDescription(String) - Method in class net.sf.basedb.util.extensions.ExtensionPointBean
-
- setDescriptor(Object) - Method in class net.sf.basedb.util.overview.Failure
-
Set a descriptor on this failure.
- setDestinationCount(int) - Method in class net.sf.basedb.core.data.PlateMappingData
-
- setDestinationCount(int) - Method in class net.sf.basedb.core.PlateMapping
-
Set the number of produced destination plates.
- setDestinationGeometry(PlateGeometryData) - Method in class net.sf.basedb.core.data.PlateMappingData
-
- setDestinationGeometry(PlateGeometry) - Method in class net.sf.basedb.core.PlateMapping
-
Set the destination geometry.
- setDestinationIndex(int) - Method in class net.sf.basedb.core.data.PlateData
-
- setDestroyed(boolean) - Method in class net.sf.basedb.core.ArraySlide
-
Set if the slide should be flagged as destroyed.
- setDestroyed(boolean) - Method in class net.sf.basedb.core.BioPlate
-
Set the destroyed flag.
- setDestroyed(boolean) - Method in class net.sf.basedb.core.data.ArraySlideData
-
- setDestroyed(boolean) - Method in class net.sf.basedb.core.data.BioPlateData
-
- setDestroyed(boolean) - Method in class net.sf.basedb.core.data.PlateData
-
- setDestroyed(boolean) - Method in class net.sf.basedb.core.Plate
-
Set the destroyed flag.
- setDetails(Set<ChangeHistoryDetailData>) - Method in class net.sf.basedb.core.data.ChangeHistoryData
-
- setDetails(Map<MappingCoordinate, MappingCoordinate>) - Method in class net.sf.basedb.core.data.PlateMappingData
-
- setDirection(String) - Method in class net.sf.basedb.clients.web.taglib.table.Table
-
- setDirection(ItemContext.SortDirection) - Method in class net.sf.basedb.clients.web.taglib.table.Table
-
- setDirectory(DirectoryData) - Method in class net.sf.basedb.core.data.ExperimentData
-
- setDirectory(DirectoryData) - Method in class net.sf.basedb.core.data.FileData
-
- setDirectory(Directory) - Method in class net.sf.basedb.core.Experiment
-
Set the directory where it is recommended that plugins
store files that are related to this experiment.
- setDirectory(Directory) - Method in class net.sf.basedb.core.File
-
Set the directory of this File
item.
- setDirty(int, int) - Method in class net.sf.basedb.core.log.EntityDetails
-
Set the dirtyness for the property with the given index.
- setDisabled(boolean) - Method in class net.sf.basedb.clients.web.taglib.Button
-
- setDisabled(boolean) - Method in class net.sf.basedb.clients.web.taglib.Select
-
- setDisabled(boolean) - Method in class net.sf.basedb.clients.web.taglib.table.Button
-
- setDisabled(boolean) - Method in class net.sf.basedb.core.data.ItemListSyncFilterData
-
- setDisabled(boolean) - Method in class net.sf.basedb.core.data.PluginDefinitionData
-
- setDisabled(boolean) - Method in class net.sf.basedb.core.data.UserData
-
- setDisabled(boolean) - Method in class net.sf.basedb.core.PluginDefinition
-
Disabled or enable this plugin.
- setDisabled(boolean) - Method in class net.sf.basedb.core.SyncFilter
-
Disabled/enable this filter.
- setDisabled(boolean) - Method in class net.sf.basedb.core.User
-
Disables or enables the account.
- setDisabled(String) - Method in class net.sf.basedb.util.extensions.debug.BeanActionFactory
-
Sets the disabled/enabled status of this factory.
- setDisabled(String) - Method in class net.sf.basedb.util.extensions.debug.ProxyActionFactory
-
Sets the disabled/enabled status of this factory.
- setDisabled(boolean) - Method in class net.sf.basedb.util.extensions.xml.PluginInfo
-
- setDisabled(boolean) - Method in class net.sf.basedb.util.overview.validator.BasicItemNodeValidatorFactory
-
- setDisabled(boolean) - Method in interface net.sf.basedb.util.overview.validator.NodeValidatorFactory
-
Disable/enabled node validation programmatically.
- setDisabled(boolean) - Method in class net.sf.basedb.util.StaticCache
-
Disable or enable the cache.
- setDisabledClazz(String) - Method in class net.sf.basedb.clients.web.extensions.menu.PermissionMenuItemFactory
-
Set the class to use when the menu is disabled.
- setDisabledClazz(String) - Method in class net.sf.basedb.clients.web.extensions.toolbar.PermissionButtonFactory
-
Set the class to use when the button is disabled.
- setDisabledIcon(String) - Method in class net.sf.basedb.clients.web.extensions.menu.PermissionMenuItemFactory
-
Set the icon to use when the menu is disabled.
- setDisabledIcon(String) - Method in class net.sf.basedb.clients.web.extensions.toolbar.PermissionButtonFactory
-
Set the icon to use when the button is disabled.
- setDisabledStyle(String) - Method in class net.sf.basedb.clients.web.extensions.menu.PermissionMenuItemFactory
-
Set the style to use when the menu is disabled.
- setDisabledStyle(String) - Method in class net.sf.basedb.clients.web.extensions.toolbar.PermissionButtonFactory
-
Set the style to use when the button is disabled.
- setDisabledTitle(String) - Method in class net.sf.basedb.clients.web.extensions.menu.PermissionMenuItemFactory
-
Set the title of the menu item when it is disabled.
- setDisabledTitle(String) - Method in class net.sf.basedb.clients.web.extensions.toolbar.PermissionButtonFactory
-
Set the title of the button when it is disabled.
- setDisabledTooltip(String) - Method in class net.sf.basedb.clients.web.extensions.menu.PermissionMenuItemFactory
-
Set the tooltip of the menu item when it is disabled.
- setDisabledTooltip(String) - Method in class net.sf.basedb.clients.web.extensions.toolbar.PermissionButtonFactory
-
Set the tooltip of the button when it is disabled.
- setDisableInheritance(boolean) - Method in class net.sf.basedb.core.AnnotationType
-
If this flag is set, annotations of this type can't be inherited
to child items.
- setDisableInheritance(boolean) - Method in class net.sf.basedb.core.data.AnnotationTypeData
-
- setDisableinproject(boolean) - Method in class net.sf.basedb.clients.web.taglib.table.PresetSelector
-
- setDisableLogOfValues(boolean) - Method in class net.sf.basedb.core.AnnotationType
-
If this flag is set, the change history logging will not include
actual annotation values.
- setDisableLogOfValues(boolean) - Method in class net.sf.basedb.core.data.AnnotationTypeData
-
- setDisableManualMembers(boolean) - Method in class net.sf.basedb.core.data.ItemListData
-
- setDisableManualMembers(boolean) - Method in class net.sf.basedb.core.ItemList
-
Disable or enable manual modification of members.
- setDisableothers(boolean) - Method in class net.sf.basedb.clients.web.taglib.table.PresetSelector
-
- setDisableownedby(boolean) - Method in class net.sf.basedb.clients.web.taglib.table.PresetSelector
-
- setDisableRawJoinOnMergedData(boolean) - Method in class net.sf.basedb.core.DynamicSpotQuery
-
Disable automatic and manual joining of raw data if the bioassay set
contains merged data.
- setDisableremoved(boolean) - Method in class net.sf.basedb.clients.web.taglib.table.PresetSelector
-
- setDisablesharedto(boolean) - Method in class net.sf.basedb.clients.web.taglib.table.PresetSelector
-
- setDisableSyncFilters(boolean) - Method in class net.sf.basedb.core.data.ItemListData
-
- setDisableSyncFilters(boolean) - Method in class net.sf.basedb.core.ItemList
-
Disable or enable synchronization of members with sync filters.
- setDiskUsage(DiskUsageData) - Method in class net.sf.basedb.core.data.ExperimentData
-
- setDiskUsage(DiskUsageData) - Method in class net.sf.basedb.core.data.FileData
-
- setDiskUsage(DiskUsageData) - Method in class net.sf.basedb.core.data.RawBioAssayData
-
- setDisplayAsList(boolean) - Method in class net.sf.basedb.core.AnnotationType
-
Set if the enumeration values should be displayed as a selection list
or as radio buttons/checkboxes by the client application.
- setDisplaySymbol(String) - Method in class net.sf.basedb.core.data.UnitData
-
- setDisplaySymbol(String) - Method in class net.sf.basedb.core.Unit
-
Set the display symbol for this unit.
- setDistinct(boolean) - Method in class net.sf.basedb.core.AbstractQuery
-
- setDistinct(boolean) - Method in interface net.sf.basedb.core.query.Query
-
Specify if the query should only return distinct rows.
- setDoctype(String) - Method in class net.sf.basedb.clients.web.taglib.Page
-
- setDone(String, Job.ExecutionTime) - Method in interface net.sf.basedb.core.plugin.Response
-
This will end the configuration of a job and set the estimated
execution time for it.
- setDone(String) - Method in interface net.sf.basedb.core.plugin.Response
-
This will end the job execution and report it as a success.
- setDone(String, Job.ExecutionTime) - Method in class net.sf.basedb.core.PluginResponse.ResponseImpl
-
- setDone(String) - Method in class net.sf.basedb.core.PluginResponse.ResponseImpl
-
- setDone(String, Job.ExecutionTime) - Method in class net.sf.basedb.plugins.executor.ExternalProgramExecutor.ResponseWrapper
-
- setDone(String) - Method in class net.sf.basedb.plugins.executor.ExternalProgramExecutor.ResponseWrapper
-
- setDouble(int, double) - Method in class net.sf.basedb.core.hibernate.QueryWrapper
-
- setDouble(String, double) - Method in class net.sf.basedb.core.hibernate.QueryWrapper
-
- setDoubleValues(List<Double>) - Method in class net.sf.basedb.core.data.annotations.AnnotationLink
-
- setDownloadImmediately(String, Job.ExecutionTime, boolean) - Method in interface net.sf.basedb.core.plugin.Response
-
This will end the configuration of a export job, and start to execute it
for immediate download.
- setDownloadImmediately(String, Job.ExecutionTime, boolean) - Method in class net.sf.basedb.core.PluginResponse.ResponseImpl
-
- setDownloadImmediately(String, Job.ExecutionTime, boolean) - Method in class net.sf.basedb.plugins.executor.ExternalProgramExecutor.ResponseWrapper
-
- setDragcolumns(Boolean) - Method in class net.sf.basedb.clients.web.taglib.table.Table
-
- setDropConstraintsBeforeImport(boolean) - Method in class net.sf.basedb.core.Migration
-
Should we drop the unique constraints and indexes before importing
data?
- setDropPrimaryKeyBeforeImport(boolean) - Method in class net.sf.basedb.core.Migration
-
Should we drop the primary key before importing data?
- setDryRun(boolean) - Method in class net.sf.basedb.core.data.JobData
-
- setDryRun(boolean) - Method in interface net.sf.basedb.core.plugin.Response
-
A plug-in may call this method in it's configuration phase or
after it has been executed to indicate that the job should be
or was executed as a dry-run job.
- setDryRun(boolean) - Method in class net.sf.basedb.core.PluginResponse.ResponseImpl
-
- setDryRun(boolean) - Method in class net.sf.basedb.plugins.executor.ExternalProgramExecutor.ResponseWrapper
-
- setDynamic(Iterator<DynamicActionAttribute>) - Method in class net.sf.basedb.clients.web.taglib.menu.Menuitem
-
- setDynamic(Iterator<DynamicActionAttribute>) - Method in class net.sf.basedb.clients.web.taglib.menu.Menuseparator
-
- setDynamic(Iterator<DynamicActionAttribute>) - Method in class net.sf.basedb.clients.web.taglib.menu.Submenu
-
- setDynamicActionAttributesSource(DynamicActionAttributes) - Method in class net.sf.basedb.clients.web.extensions.DynamicActionAttributeSupport
-
Set the source of dynamic action attributes.
- setDynamicAttribute(String, String, Object) - Method in class net.sf.basedb.clients.web.taglib.StylableTag
-
- setDynamicAttribute(String, String, Object) - Method in class net.sf.basedb.clients.web.taglib.tab.Tab
-
- setEmail(String) - Method in class net.sf.basedb.core.authentication.ExtraUserInformation
-
The email address to the user.
- setEmail(String) - Method in class net.sf.basedb.core.data.PluginDefinitionData
-
- setEmail(String) - Method in class net.sf.basedb.core.data.UserData
-
- setEmail(String) - Method in class net.sf.basedb.core.PluginDefinition
-
Set the email address that can be used to contact the
developer of the plug-in.
- setEmail(String) - Method in class net.sf.basedb.core.User
-
Set the email address to the user, or null if unknown.
- setEmail(String) - Method in class net.sf.basedb.util.extensions.AboutBean
-
- setEnabled(boolean) - Method in class net.sf.basedb.clients.web.extensions.menu.FixedMenuItemFactory
-
- setEnabled(String) - Method in class net.sf.basedb.clients.web.extensions.menu.FixedMenuItemFactory
-
- setEnabled(boolean) - Method in class net.sf.basedb.clients.web.extensions.menu.MenuItemBean
-
- setEnabled(boolean) - Method in class net.sf.basedb.clients.web.extensions.toolbar.ButtonBean
-
- setEnabled(boolean) - Method in class net.sf.basedb.clients.web.extensions.toolbar.FixedButtonFactory
-
- setEnabled(String) - Method in class net.sf.basedb.clients.web.extensions.toolbar.FixedButtonFactory
-
- setEnabled(boolean) - Method in class net.sf.basedb.clients.web.taglib.Icon
-
- setEnabled(boolean) - Method in class net.sf.basedb.clients.web.taglib.menu.Menuitem
-
- setEnabled(boolean) - Method in class net.sf.basedb.clients.web.taglib.menu.Submenu
-
- setEnabled(boolean) - Method in class net.sf.basedb.clients.web.taglib.path.PathElement
-
- setEnabledClazz(String) - Method in class net.sf.basedb.clients.web.extensions.menu.PermissionMenuItemFactory
-
Set the class to use when the menu is enabled.
- setEnabledClazz(String) - Method in class net.sf.basedb.clients.web.extensions.toolbar.PermissionButtonFactory
-
Set the class to use when the button is enabled.
- setEnabledIcon(String) - Method in class net.sf.basedb.clients.web.extensions.menu.PermissionMenuItemFactory
-
Set the icon to use when the menu is enabled.
- setEnabledIcon(String) - Method in class net.sf.basedb.clients.web.extensions.toolbar.PermissionButtonFactory
-
Set the icon to use when the button is enabled.
- setEnableDownloadLink(boolean) - Method in class net.sf.basedb.clients.web.taglib.PropertyValue
-
- setEnabledPermission(String) - Method in class net.sf.basedb.clients.web.extensions.menu.PermissionMenuItemFactory
-
Set the minimum permission that is required to make the
menu item enabled.
- setEnabledPermission(String) - Method in class net.sf.basedb.clients.web.extensions.toolbar.PermissionButtonFactory
-
Set the minimum permission that is required to make the
button enabled.
- setEnabledStyle(String) - Method in class net.sf.basedb.clients.web.extensions.menu.PermissionMenuItemFactory
-
Set the style to use when the menu is enabled.
- setEnabledStyle(String) - Method in class net.sf.basedb.clients.web.extensions.toolbar.PermissionButtonFactory
-
Set the style to use when the button is enabled.
- setEnabledTitle(String) - Method in class net.sf.basedb.clients.web.extensions.menu.PermissionMenuItemFactory
-
Set the title of the menu item when it is enabled.
- setEnabledTitle(String) - Method in class net.sf.basedb.clients.web.extensions.toolbar.PermissionButtonFactory
-
Set the title of the button when it is enabled.
- setEnabledTooltip(String) - Method in class net.sf.basedb.clients.web.extensions.menu.PermissionMenuItemFactory
-
Set the tooltip of the menu item when it is enabled.
- setEnabledTooltip(String) - Method in class net.sf.basedb.clients.web.extensions.toolbar.PermissionButtonFactory
-
Set the tooltip of the button when it is enabled.
- setEnableEditLink(boolean) - Method in class net.sf.basedb.clients.web.taglib.PropertyValue
-
- setEnablePropertyLink(boolean) - Method in class net.sf.basedb.clients.web.taglib.PropertyValue
-
- setEncoder(EncoderDecoder) - Method in class net.sf.basedb.util.export.TableWriter
-
Change the encoder.
- setEndDate(Date) - Method in class net.sf.basedb.core.data.NewsData
-
- setEndDate(Date) - Method in class net.sf.basedb.core.News
-
Set the end date and time for this item to be published.
- setEnded(Date) - Method in class net.sf.basedb.core.data.JobData
-
- setEnded(PluginResponse, boolean) - Method in class net.sf.basedb.core.Job.ProgressReporterImpl
-
- setEnded() - Method in class net.sf.basedb.util.extensions.manager.ProcessResults
-
Set the end time of the scan.
- setEntity(int, Object) - Method in class net.sf.basedb.core.hibernate.EntityQueryWrapper
-
- setEntity(String, Object) - Method in class net.sf.basedb.core.hibernate.EntityQueryWrapper
-
- setEntity(int, Object) - Method in class net.sf.basedb.core.hibernate.QueryWrapper
-
- setEntity(String, Object) - Method in class net.sf.basedb.core.hibernate.QueryWrapper
-
- setEntityParameter(String, BasicItem) - Method in class net.sf.basedb.core.AbstractHqlQuery
-
- setEntityParameter(String, BasicItem) - Method in interface net.sf.basedb.core.query.HqlQuery
-
Set the value of an entity parameter.
- setEntryDate(Date) - Method in class net.sf.basedb.core.AnnotationType
-
- setEntryDate(Date) - Method in class net.sf.basedb.core.AnnotationTypeCategory
-
- setEntryDate(Date) - Method in class net.sf.basedb.core.ArrayBatch
-
- setEntryDate(Date) - Method in class net.sf.basedb.core.ArrayDesign
-
- setEntryDate(Date) - Method in class net.sf.basedb.core.ArraySlide
-
- setEntryDate(Date) - Method in class net.sf.basedb.core.BioMaterialEvent
-
- setEntryDate(Date) - Method in class net.sf.basedb.core.BioPlate
-
- setEntryDate(Date) - Method in class net.sf.basedb.core.BioPlateEvent
-
- setEntryDate(Date) - Method in class net.sf.basedb.core.BioSource
-
- setEntryDate(Date) - Method in class net.sf.basedb.core.Client
-
- setEntryDate(Date) - Method in class net.sf.basedb.core.data.AnnotationTypeCategoryData
-
- setEntryDate(Date) - Method in class net.sf.basedb.core.data.AnnotationTypeData
-
- setEntryDate(Date) - Method in class net.sf.basedb.core.data.ArrayBatchData
-
- setEntryDate(Date) - Method in class net.sf.basedb.core.data.ArrayDesignData
-
- setEntryDate(Date) - Method in class net.sf.basedb.core.data.ArraySlideData
-
- setEntryDate(Date) - Method in class net.sf.basedb.core.data.BioMaterialEventData
-
- setEntryDate(Date) - Method in class net.sf.basedb.core.data.BioPlateData
-
- setEntryDate(Date) - Method in class net.sf.basedb.core.data.BioPlateEventData
-
- setEntryDate(Date) - Method in class net.sf.basedb.core.data.BioSourceData
-
- setEntryDate(Date) - Method in class net.sf.basedb.core.data.ClientData
-
- setEntryDate(Date) - Method in class net.sf.basedb.core.data.DerivedBioAssayData
-
- setEntryDate(Date) - Method in class net.sf.basedb.core.data.ExperimentData
-
- setEntryDate(Date) - Method in class net.sf.basedb.core.data.ExtraValueTypeData
-
- setEntryDate(Date) - Method in class net.sf.basedb.core.data.FormulaData
-
- setEntryDate(Date) - Method in class net.sf.basedb.core.data.GroupData
-
- setEntryDate(Date) - Method in class net.sf.basedb.core.data.HardwareData
-
- setEntryDate(Date) - Method in class net.sf.basedb.core.data.ItemSubtypeData
-
- setEntryDate(Date) - Method in class net.sf.basedb.core.data.KitData
-
- setEntryDate(Date) - Method in class net.sf.basedb.core.data.MimeTypeData
-
- setEntryDate(Date) - Method in class net.sf.basedb.core.data.NewsData
-
- setEntryDate(Date) - Method in class net.sf.basedb.core.data.PlateData
-
- setEntryDate(Date) - Method in class net.sf.basedb.core.data.PlateEventData
-
- setEntryDate(Date) - Method in class net.sf.basedb.core.data.PlateGeometryData
-
- setEntryDate(Date) - Method in class net.sf.basedb.core.data.PlateMappingData
-
- setEntryDate(Date) - Method in class net.sf.basedb.core.data.PlateTypeData
-
- setEntryDate(Date) - Method in class net.sf.basedb.core.data.PluginConfigurationData
-
- setEntryDate(Date) - Method in class net.sf.basedb.core.data.PluginDefinitionData
-
- setEntryDate(Date) - Method in class net.sf.basedb.core.data.PluginTypeData
-
- setEntryDate(Date) - Method in class net.sf.basedb.core.data.ProjectData
-
- setEntryDate(Date) - Method in class net.sf.basedb.core.data.ProtocolData
-
- setEntryDate(Date) - Method in class net.sf.basedb.core.data.QuotaTypeData
-
- setEntryDate(Date) - Method in class net.sf.basedb.core.data.RawBioAssayData
-
- setEntryDate(Date) - Method in class net.sf.basedb.core.data.ReporterCloneTemplateData
-
- setEntryDate(Date) - Method in class net.sf.basedb.core.data.ReporterData
-
- setEntryDate(Date) - Method in class net.sf.basedb.core.data.ReporterListData
-
- setEntryDate(Date) - Method in class net.sf.basedb.core.data.ReporterTypeData
-
- setEntryDate(Date) - Method in class net.sf.basedb.core.data.RoleData
-
- setEntryDate(Date) - Method in class net.sf.basedb.core.data.SoftwareData
-
- setEntryDate(Date) - Method in class net.sf.basedb.core.data.TagData
-
- setEntryDate(Date) - Method in class net.sf.basedb.core.data.UserData
-
- setEntryDate(Date) - Method in class net.sf.basedb.core.DerivedBioAssay
-
- setEntryDate(Date) - Method in class net.sf.basedb.core.Experiment
-
- setEntryDate(Date) - Method in class net.sf.basedb.core.ExtraValueType
-
- setEntryDate(Date) - Method in class net.sf.basedb.core.Formula
-
- setEntryDate(Date) - Method in class net.sf.basedb.core.Group
-
- setEntryDate(Date) - Method in class net.sf.basedb.core.Hardware
-
- setEntryDate(Date) - Method in class net.sf.basedb.core.ItemSubtype
-
- setEntryDate(Date) - Method in class net.sf.basedb.core.Kit
-
- setEntryDate(Date) - Method in class net.sf.basedb.core.MeasuredBioMaterial
-
- setEntryDate(Date) - Method in class net.sf.basedb.core.MimeType
-
- setEntryDate(Date) - Method in class net.sf.basedb.core.News
-
- setEntryDate(Date) - Method in class net.sf.basedb.core.PhysicalBioAssay
-
- setEntryDate(Date) - Method in class net.sf.basedb.core.Plate
-
- setEntryDate(Date) - Method in class net.sf.basedb.core.PlateEvent
-
- setEntryDate(Date) - Method in class net.sf.basedb.core.PlateGeometry
-
- setEntryDate(Date) - Method in class net.sf.basedb.core.PlateMapping
-
- setEntryDate(Date) - Method in class net.sf.basedb.core.PlateType
-
- setEntryDate(Date) - Method in class net.sf.basedb.core.PluginConfiguration
-
- setEntryDate(Date) - Method in class net.sf.basedb.core.PluginDefinition
-
- setEntryDate(Date) - Method in class net.sf.basedb.core.PluginType
-
- setEntryDate(Date) - Method in class net.sf.basedb.core.Project
-
- setEntryDate(Date) - Method in class net.sf.basedb.core.Protocol
-
- setEntryDate(Date) - Method in class net.sf.basedb.core.QuotaType
-
- setEntryDate(Date) - Method in class net.sf.basedb.core.RawBioAssay
-
- setEntryDate(Date) - Method in interface net.sf.basedb.core.Registered
-
Set the date the entry was registered in the database.
- setEntryDate(Date) - Method in class net.sf.basedb.core.ReporterCloneTemplate
-
- setEntryDate(Date) - Method in class net.sf.basedb.core.ReporterList
-
- setEntryDate(Date) - Method in class net.sf.basedb.core.ReporterType
-
- setEntryDate(Date) - Method in class net.sf.basedb.core.Role
-
- setEntryDate(Date) - Method in class net.sf.basedb.core.Software
-
- setEntryDate(Date) - Method in class net.sf.basedb.core.Tag
-
- setEntryDate(Date) - Method in class net.sf.basedb.core.User
-
- setEnumeration(Enumeration<String, String>) - Method in class net.sf.basedb.clients.web.extensions.list.AbstractListColumnBean
-
- setEnumeration(Enumeration<String, String>) - Method in class net.sf.basedb.clients.web.taglib.table.ColumnDef
-
- setEnumeration(boolean) - Method in class net.sf.basedb.core.AnnotationType
-
Set if this annotation type should provide a list of predefined allowed values.
- setEnumeration(boolean) - Method in class net.sf.basedb.core.data.AnnotationTypeData
-
- setEnumerationValues(ParameterValueData<?>) - Method in class net.sf.basedb.core.data.AnnotationTypeData
-
- setError(String, List<? extends Throwable>) - Method in interface net.sf.basedb.core.plugin.Response
-
This will end the job execution or configuration and report it as a
failure.
- setError(String, List<? extends Throwable>) - Method in class net.sf.basedb.core.PluginResponse.ResponseImpl
-
- setError(String, Throwable) - Method in class net.sf.basedb.core.PluginResponse
-
Set a singe error message.
- setError(Throwable) - Method in class net.sf.basedb.core.SimpleProgressReporter
-
Set an error that happened while processing some action that
was reported via this progress reporter.
- setError(String, List<? extends Throwable>) - Method in class net.sf.basedb.plugins.executor.ExternalProgramExecutor.ResponseWrapper
-
- setError(Throwable) - Method in class net.sf.basedb.util.extensions.ActionIterator
-
Register an error for the current action.
- setError(String, Throwable) - Method in class net.sf.basedb.util.extensions.ActionIterator
-
Register an error with a message for the current action.
- setError(A, Throwable) - Method in class net.sf.basedb.util.extensions.ExtensionContext
-
- setError(A, Throwable) - Method in class net.sf.basedb.util.extensions.ExtensionPointContext
-
- setError(A, Throwable) - Method in class net.sf.basedb.util.extensions.InvokationContext
-
Register an error for the current extension or extension point.
- setError(boolean) - Method in class net.sf.basedb.util.extensions.manager.ExtensionsFile.WriteableExtensionsFile
-
Sets the error status.
- setError(A, Throwable) - Method in class net.sf.basedb.util.extensions.Registry.RegisteredExtension
-
- setError(A, Throwable) - Method in class net.sf.basedb.util.extensions.Registry.RegisteredExtensionPoint
-
- setErrorclazz(String) - Method in class net.sf.basedb.clients.web.taglib.table.Cell
-
- setErrorHandlerFactory(ErrorHandlerFactory<? super A>) - Method in class net.sf.basedb.util.extensions.ExtensionPointBean
-
- setErrorMessage(String) - Method in class net.sf.basedb.core.data.FileSetMemberData
-
- setErrors(int) - Method in class net.sf.basedb.util.overview.Node
-
Set the number of errors that was found while validating this
node.
- setEstimatedExecutionTime(int) - Method in class net.sf.basedb.core.data.JobData
-
- setEvent(BioMaterialEventData) - Method in class net.sf.basedb.core.data.BioMaterialEventSourceData
-
- setEvent(BioPlateEventData) - Method in class net.sf.basedb.core.data.BioPlateEventParticipantData
-
- setEventDate(Date) - Method in class net.sf.basedb.core.BioMaterialEvent
-
Set the date this event was done in the lab.
- setEventDate(Date) - Method in class net.sf.basedb.core.BioPlate
-
Set the date this plate was created.
- setEventDate(Date) - Method in class net.sf.basedb.core.BioPlateEvent
-
Set the date this event was done in the lab.
- setEventDate(Date) - Method in class net.sf.basedb.core.data.BioMaterialEventData
-
- setEventDate(Date) - Method in class net.sf.basedb.core.data.BioPlateData
-
- setEventDate(Date) - Method in class net.sf.basedb.core.data.BioPlateEventData
-
- setEventDate(Date) - Method in class net.sf.basedb.core.data.PlateEventData
-
- setEventDate(Date) - Method in class net.sf.basedb.core.PlateEvent
-
Set the date this event was done in the lab.
- setEventParticipants(Set<BioPlateEventParticipantData>) - Method in class net.sf.basedb.core.data.BioPlateData
-
- setEvents(Set<BioPlateEventData>) - Method in class net.sf.basedb.core.data.BioPlateEventTypeData
-
- setEvents(Set<BioMaterialEventData>) - Method in class net.sf.basedb.core.data.MeasuredBioMaterialData
-
- setEvents(Map<PlateEventTypeData, PlateEventData>) - Method in class net.sf.basedb.core.data.PlateData
-
- setEventType(BioPlateEventType) - Method in class net.sf.basedb.core.BioPlateEvent
-
- setEventType(int) - Method in class net.sf.basedb.core.data.BioMaterialEventData
-
- setEventType(BioPlateEventTypeData) - Method in class net.sf.basedb.core.data.BioPlateEventData
-
- setEventTypes(Set<PlateEventTypeData>) - Method in class net.sf.basedb.core.data.PlateTypeData
-
- setException(Throwable) - Method in class net.sf.basedb.clients.web.fileupload.FileUpload
-
- setException(Throwable) - Method in class net.sf.basedb.clients.web.fileupload.FileUploadProgress
-
Set the exception that caused the upload to fail.
- setExcludeDefaultValues(boolean) - Method in class net.sf.basedb.core.AnnotationRestriction.Options
-
- setExecuteCommand(String) - Method in class net.sf.basedb.core.data.JobData
-
- setExecuteImmediately(String, Job.ExecutionTime, boolean) - Method in interface net.sf.basedb.core.plugin.Response
-
This will end the configuration of a job, and start to execute it
immediately if the plugin is permitted to do so.
- setExecuteImmediately(String, Job.ExecutionTime, boolean) - Method in class net.sf.basedb.core.PluginResponse.ResponseImpl
-
- setExecuteImmediately(String, Job.ExecutionTime, boolean) - Method in class net.sf.basedb.plugins.executor.ExternalProgramExecutor.ResponseWrapper
-
- setExperiment(Experiment) - Method in class net.sf.basedb.core.BioAssaySet
-
Set the experiment.
- setExperiment(ExperimentData) - Method in class net.sf.basedb.core.data.BioAssaySetData
-
- setExperiment(ExperimentData) - Method in class net.sf.basedb.core.data.JobData
-
- setExperiment(ExperimentData) - Method in class net.sf.basedb.core.data.ReporterListData
-
- setExperiment(ExperimentData) - Method in class net.sf.basedb.core.data.RootRawBioAssayData
-
- setExperiment(ExperimentData) - Method in class net.sf.basedb.core.data.TransformationData
-
- setExperiment(ExperimentData) - Method in class net.sf.basedb.core.data.VirtualDbData
-
- setExperiment(Experiment) - Method in class net.sf.basedb.core.Job
-
Set the experiment this job is part of.
- setExperiment(Experiment) - Method in class net.sf.basedb.core.ReporterList
-
Set the experiment.
- setExperiment(Experiment) - Method in class net.sf.basedb.core.Transformation
-
Set the experiment.
- setExperimentalFactors(Set<AnnotationTypeData>) - Method in class net.sf.basedb.core.data.ExperimentData
-
- setExperimentDesign(String) - Method in class net.sf.basedb.core.data.ExperimentData
-
- setExperimentDesign(String) - Method in class net.sf.basedb.core.Experiment
-
Set a text describing the experimental design.
- setExperiments(Set<ExperimentData>) - Method in class net.sf.basedb.core.data.AnnotationTypeData
-
- setExperiments(Set<ExperimentData>) - Method in class net.sf.basedb.core.data.RawBioAssayData
-
- setExperimentType(String) - Method in class net.sf.basedb.core.data.ExperimentData
-
- setExperimentType(String) - Method in class net.sf.basedb.core.Experiment
-
Set a text describing the experiment type.
- setExpirationDate(Date) - Method in class net.sf.basedb.core.data.KitData
-
- setExpirationDate(Date) - Method in class net.sf.basedb.core.data.UserData
-
- setExpirationDate(Date) - Method in class net.sf.basedb.core.Kit
-
Set the expiration date.
- setExpirationDate(Date) - Method in class net.sf.basedb.core.User
-
Sets the expiration date of the account.
- setExportable(boolean) - Method in class net.sf.basedb.clients.web.extensions.list.AbstractListColumnBean
-
- setExportable(String) - Method in class net.sf.basedb.clients.web.extensions.list.PropertyPathActionFactory
-
- setExportable(boolean) - Method in class net.sf.basedb.clients.web.taglib.table.ColumnDef
-
- setExportCompressed(boolean) - Method in class net.sf.basedb.core.Migration
-
Should the exporter compress the data files or leave them
as is?
- setExportFormatter(Formatter<?>) - Method in class net.sf.basedb.clients.web.extensions.list.AbstractListColumnBean
-
- setExportFormatterClass(String) - Method in class net.sf.basedb.clients.web.extensions.list.PropertyPathActionFactory
-
- setExportProperty(String) - Method in class net.sf.basedb.clients.web.extensions.list.AbstractListColumnBean
-
- setExportProperty(String) - Method in class net.sf.basedb.clients.web.extensions.list.PropertyPathActionFactory
-
- setExportproperty(String) - Method in class net.sf.basedb.clients.web.taglib.table.ColumnDef
-
- setExpression(Expression) - Method in class net.sf.basedb.util.export.spotdata.SimpleDynamicField
-
Set the expression used to select data in the query.
- setExtended(String, Object) - Method in class net.sf.basedb.core.authentication.ExtraUserInformation
-
Set the value of an extended property.
- setExtended(String, Object) - Method in interface net.sf.basedb.core.data.ExtendableData
-
Set the value of an extended property.
- setExtended(String, Object) - Method in class net.sf.basedb.core.data.RawData
-
- setExtended(String, Object) - Method in class net.sf.basedb.core.data.ReporterData
-
- setExtended(String, Object) - Method in class net.sf.basedb.core.data.UserData
-
- setExtended(String, Object) - Method in class net.sf.basedb.core.User
-
Sets an extended property
- setExtendedProperty(boolean) - Method in class net.sf.basedb.core.data.ReporterClonePropertyData
-
- setExtends(String) - Method in class net.sf.basedb.util.extensions.ExtensionBean
-
- setExtension(String) - Method in class net.sf.basedb.core.data.DataFileTypeData
-
- setExtension(String) - Method in class net.sf.basedb.core.data.MimeTypeData
-
- setExtension(String) - Method in class net.sf.basedb.core.DataFileType
-
Set the most common gile extension for data file of this
type.
- setExtension(String) - Method in class net.sf.basedb.core.MimeType
-
Set the extension variable for this MimeType
item.
- setExtensionPointId(String) - Method in class net.sf.basedb.core.signal.ExtensionSignalTransporter
-
- setExtensions(ExtensionsInvoker<?>) - Method in class net.sf.basedb.clients.web.taglib.extensions.Render
-
- setExtensions(ExtensionsInvoker<TabAction>) - Method in class net.sf.basedb.clients.web.taglib.tab.TabControl
-
- setExtensions(ExtensionsInvoker<ListColumnAction>) - Method in class net.sf.basedb.clients.web.taglib.table.ColumnDef
-
- setExtensionVersion(String, String) - Static method in class net.sf.basedb.clients.web.taglib.Head
-
Register the version for an exteniosn JAR file.
- setExternalId(String) - Method in class net.sf.basedb.core.AnnotationType
-
Set the external id of the annotation type.
- setExternalId(String) - Method in class net.sf.basedb.core.BioMaterial
-
Set the external id of the biomaterial.
- setExternalId(String) - Method in class net.sf.basedb.core.BioPlate
-
Sets the external id of this bio plate
- setExternalId(String) - Method in class net.sf.basedb.core.Client
-
Set the external id for this Client
item.
- setExternalId(String) - Method in class net.sf.basedb.core.data.AnnotationTypeData
-
- setExternalId(String) - Method in class net.sf.basedb.core.data.BioMaterialData
-
- setExternalId(String) - Method in class net.sf.basedb.core.data.BioPlateData
-
- setExternalId(String) - Method in class net.sf.basedb.core.data.ClientData
-
- setExternalId(String) - Method in class net.sf.basedb.core.data.DataFileTypeData
-
- setExternalId(String) - Method in class net.sf.basedb.core.data.ExtraValueTypeData
-
- setExternalId(String) - Method in class net.sf.basedb.core.data.FeatureData
-
- setExternalId(String) - Method in class net.sf.basedb.core.data.HelpData
-
- setExternalId(String) - Method in class net.sf.basedb.core.data.ItemListData
-
- setExternalId(String) - Method in class net.sf.basedb.core.data.JobAgentData
-
- setExternalId(String) - Method in class net.sf.basedb.core.data.JobData
-
- setExternalId(String) - Method in class net.sf.basedb.core.data.PlatformData
-
- setExternalId(String) - Method in class net.sf.basedb.core.data.PlatformVariantData
-
- setExternalId(String) - Method in class net.sf.basedb.core.data.ProtocolData
-
- setExternalId(String) - Method in class net.sf.basedb.core.data.ReporterData
-
- setExternalId(String) - Method in class net.sf.basedb.core.data.ReporterListData
-
- setExternalId(String) - Method in class net.sf.basedb.core.data.UserData
-
- setExternalId(String) - Method in class net.sf.basedb.core.DataFileType
-
- setExternalId(String) - Method in class net.sf.basedb.core.ExtraValueType
-
Set the external id for this Client
item.
- setExternalId(String) - Method in class net.sf.basedb.core.Help
-
Set the external id for this Help
item.
- setExternalId(String) - Method in class net.sf.basedb.core.ItemList
-
Set the external id for this list.
- setExternalId(String) - Method in class net.sf.basedb.core.Job
-
Set the external ID.
- setExternalId(String) - Method in class net.sf.basedb.core.JobAgent
-
Set the external id for the job agent.
- setExternalId(String) - Method in class net.sf.basedb.core.Platform
-
- setExternalId(String) - Method in class net.sf.basedb.core.PlatformVariant
-
- setExternalId(String) - Method in class net.sf.basedb.core.Protocol
-
Set the external id of the protocol.
- setExternalId(String) - Method in class net.sf.basedb.core.ReporterList
-
Set the external id for this ReporterList
item.
- setExternalId(String) - Method in class net.sf.basedb.core.User
-
Set the external id for the user account.
- setExtract(ExtractData) - Method in class net.sf.basedb.core.data.DerivedBioAssayData
-
- setExtract(Extract) - Method in class net.sf.basedb.core.DerivedBioAssay
-
Set the extract that is the parent of data in this bioassay.
- setExtraFileImporter(ExtraFileImporter) - Method in class net.sf.basedb.util.importer.spotdata.BfsImporter
-
- setExtraInformation(ExtraUserInformation) - Method in class net.sf.basedb.core.authentication.AuthenticatedUser
-
Set extra information about the user.
- setExtraNo(short) - Method in class net.sf.basedb.core.data.DataCubeExtraValueData
-
- setExtraNo(short) - Method in class net.sf.basedb.core.DataCubeExtraValue
-
- setExtraValues(Map<ExtraValueTypeData, ExtraValueData>) - Method in class net.sf.basedb.core.data.BioAssaySetData
-
- setExtraValues(Set<DataCubeExtraValueData>) - Method in class net.sf.basedb.core.data.DataCubeData
-
- setExtraValues(Set<ExtraValueData>) - Method in class net.sf.basedb.core.data.ExtraValueTypeData
-
- setExtraValueType(ExtraValueTypeData) - Method in class net.sf.basedb.core.data.ExtraValueData
-
- setExtraValueType(ExtraValueType) - Method in class net.sf.basedb.core.ExtraValue
-
Set the extra value type.
- setFailSafe(boolean) - Method in class net.sf.basedb.core.AbstractQuery
-
- setFailSafe(boolean) - Method in interface net.sf.basedb.core.query.Query
-
Set this flag to ensure that the transaction used to execute the query
is allowed to continue even after a failure at the SQL level of this query.
- setFavicon(String) - Method in class net.sf.basedb.clients.web.extensions.skin.FixedSkinActionFactory
-
- setFavicon(String) - Method in class net.sf.basedb.clients.web.taglib.Page
-
- setFax(String) - Method in class net.sf.basedb.core.authentication.ExtraUserInformation
-
- setFax(String) - Method in class net.sf.basedb.core.data.UserData
-
- setFax(String) - Method in class net.sf.basedb.core.User
-
Set the fax number to the user, or null if unknown.
- setFeature(FeatureData) - Method in class net.sf.basedb.core.data.RawData
-
- setFeatureDiameter(int) - Method in class net.sf.basedb.core.ArrayDesignBlock
-
Set the expected diameter of spots on the slide.
- setFeatureDiameter(int) - Method in class net.sf.basedb.core.data.ArrayDesignBlockData
-
- setFeatureIdentificationMethod(int) - Method in class net.sf.basedb.core.data.ArrayDesignData
-
- setFeatures(Set<FeatureData>) - Method in class net.sf.basedb.core.data.ArrayDesignBlockData
-
- setFetchSize(int) - Method in class net.sf.basedb.core.hibernate.QueryWrapper
-
- setFetchSize(int) - Method in class net.sf.basedb.core.Migration
-
Set the JDBC fetch size to use when fetching rows from the database.
- setField(String) - Method in class net.sf.basedb.util.overview.extensions.ReflectValidationRuleActionFactory
-
- setFile(FileData) - Method in interface net.sf.basedb.core.data.FileAttachableData
-
Attach a file to the item.
- setFile(FileData) - Method in class net.sf.basedb.core.data.FileSetMemberData
-
- setFile(FileData) - Method in class net.sf.basedb.core.data.ProtocolData
-
- setFile(File) - Method in interface net.sf.basedb.core.FileAttachable
-
Attach a file to the item.
- setFile(File) - Method in class net.sf.basedb.core.Protocol
-
- setFileId(int) - Method in class net.sf.basedb.util.importer.spotdata.BaseFileInfo.ChildBioAssay
-
Set the id of the child bioassay as it appears in the BASEfile.
- setFilename(String) - Method in class net.sf.basedb.clients.web.util.ServletExportOutputStream
-
- setFilename(String) - Method in class net.sf.basedb.core.plugin.ExportOutputStream
-
Do nothing.
- setFilename(String) - Method in class net.sf.basedb.util.bfs.AnnotationParser
-
Set the file name that this parser is reading from.
- setFilename(String) - Method in class net.sf.basedb.util.bfs.AnnotationWriter
-
Set the file name that this writer is printing to.
- setFilename(String) - Method in class net.sf.basedb.util.bfs.DataParser
-
Set the file name that this parser is reading from.
- setFilename(String) - Method in class net.sf.basedb.util.bfs.DataWriter
-
Set the file name that this writer is printing to.
- setFilename(String) - Method in class net.sf.basedb.util.bfs.MetadataParser
-
Set the file name that this writer is printing to.
- setFilename(String) - Method in class net.sf.basedb.util.bfs.MetadataWriter
-
Set the file name that this writer is printing to.
- setFilename(String) - Method in class net.sf.basedb.util.FileExportOutputStream
-
- setFileOnly(boolean) - Method in class net.sf.basedb.core.data.PlatformData
-
- setFileOnly(boolean) - Method in class net.sf.basedb.core.data.PlatformVariantData
-
- setFileProperties(File) - Method in class net.sf.basedb.util.bfs.GenericBaseDataWriterFactory
-
Set file properties on the newly created file object.
- setFiles(Set<FileData>) - Method in class net.sf.basedb.core.data.DirectoryData
-
- setFiles(Set<FileData>) - Method in class net.sf.basedb.core.data.FileServerData
-
- setFileServer(FileServerData) - Method in class net.sf.basedb.core.data.FileData
-
- setFileServer(FileServer) - Method in class net.sf.basedb.core.File
-
Set the file server on which this external file is located.
- setFileSet(FileSetData) - Method in class net.sf.basedb.core.data.ArrayDesignData
-
- setFileSet(FileSetData) - Method in class net.sf.basedb.core.data.BioAssaySetData
-
- setFileSet(FileSetData) - Method in class net.sf.basedb.core.data.DerivedBioAssayData
-
- setFileSet(FileSetData) - Method in class net.sf.basedb.core.data.ExtraValueData
-
- setFileSet(FileSetData) - Method in class net.sf.basedb.core.data.FileSetMemberData
-
- setFileSet(FileSetData) - Method in interface net.sf.basedb.core.data.FileStoreEnabledData
-
Attach a file set to the item.
- setFileSet(FileSetData) - Method in class net.sf.basedb.core.data.RawBioAssayData
-
- setFileSetMembers(Set<FileSetMemberData>) - Method in class net.sf.basedb.core.data.DataFileTypeData
-
- setFileSize(long) - Method in class net.sf.basedb.util.bfs.AnnotationParser
-
Set the size of the file or -1 if not known.
- setFileSize(long) - Method in class net.sf.basedb.util.bfs.DataParser
-
Set the size of the file or -1 if not known.
- setFileSize(long) - Method in class net.sf.basedb.util.bfs.MetadataParser
-
Set the size of the file or -1 if not known.
- setFileType(ItemSubtypeData) - Method in class net.sf.basedb.core.data.MimeTypeData
-
- setFileType(ItemSubtype) - Method in class net.sf.basedb.core.MimeType
-
Set the filetype of this item.
- setFileTypes(Map<DataFileTypeData, ItemSubtypeFileTypeData>) - Method in class net.sf.basedb.core.data.ItemSubtypeData
-
- setFileTypes(Map<FileTypeIndex, PlatformFileTypeData>) - Method in class net.sf.basedb.core.data.PlatformData
-
- setFileTypes(Set<PlatformFileTypeData>) - Method in class net.sf.basedb.core.data.PlatformVariantData
-
- setFilltext(String) - Method in class net.sf.basedb.clients.web.taglib.menu.Menu
-
- setFilter(Filter<Element>) - Method in class net.sf.basedb.util.extensions.xml.XmlLoader
-
Set a filter that all <extension-point>, <extension>,
<ref> and <plugin-definition> tags must pass to be loaded
and registered.
- setFilterable(boolean) - Method in class net.sf.basedb.clients.web.extensions.list.AbstractListColumnBean
-
- setFilterable(String) - Method in class net.sf.basedb.clients.web.extensions.list.PropertyPathActionFactory
-
- setFilterable(boolean) - Method in class net.sf.basedb.clients.web.taglib.table.ColumnDef
-
- setFilterNo(short) - Method in class net.sf.basedb.core.data.DataCubeFilterData
-
- setFilterNo(short) - Method in class net.sf.basedb.core.DataCubeFilter
-
- setFilterProperty(String) - Method in class net.sf.basedb.clients.web.extensions.list.AbstractListColumnBean
-
- setFilterProperty(String) - Method in class net.sf.basedb.clients.web.extensions.list.PropertyPathActionFactory
-
- setFilterproperty(String) - Method in class net.sf.basedb.clients.web.taglib.table.ColumnDef
-
- setFilterrows(int) - Method in class net.sf.basedb.clients.web.taglib.table.Table
-
- setFilters(Set<DataCubeFilterData>) - Method in class net.sf.basedb.core.data.DataCubeData
-
- setFingerprintType(String) - Method in class net.sf.basedb.core.data.FileServerData
-
- setFirstAssayFieldIndex(int) - Method in class net.sf.basedb.util.importer.spotdata.BaseFileInfo.SpotSectionInfo
-
Set the index of the first data column that contains assay data.
- setFirstResult(int) - Method in class net.sf.basedb.core.AbstractQuery
-
- setFirstResult(int) - Method in class net.sf.basedb.core.hibernate.QueryWrapper
-
- setFirstResult(int) - Method in interface net.sf.basedb.core.query.Query
-
Specify that the query should start returning rows from the
specified row number. 0 = start returning from the first row.
- setFloat(int, float) - Method in class net.sf.basedb.core.hibernate.QueryWrapper
-
- setFloat(String, float) - Method in class net.sf.basedb.core.hibernate.QueryWrapper
-
- setFloatValues(List<Float>) - Method in class net.sf.basedb.core.data.annotations.AnnotationLink
-
- setFlushMode(FlushMode) - Method in class net.sf.basedb.core.hibernate.QueryWrapper
-
- setFlushMode(FlushMode) - Method in class net.sf.basedb.core.hibernate.SessionWrapper
-
- setForceOverwrite(boolean) - Method in class net.sf.basedb.util.extensions.manager.processor.ExtractResourcesProcessor
-
- setForceStop(boolean) - Method in class net.sf.basedb.core.signal.ThreadSignalHandler
-
- setForceUpdate(boolean) - Method in class net.sf.basedb.util.extensions.manager.processor.RegisterExtensionsProcessor
-
Set a flag to indicate if already registered extensions should
be re-registered or not.
- setFormatter(Formatter<? super V>) - Method in class net.sf.basedb.clients.web.extensions.list.AbstractListColumnBean
-
- setFormatter(Formatter<?>) - Method in class net.sf.basedb.clients.web.taglib.table.ColumnDef
-
- setFormatter(Formatter<?>) - Method in class net.sf.basedb.clients.web.taglib.table.TableColumn
-
- setFormatter(Formatter<?>) - Method in class net.sf.basedb.util.export.spotdata.AnnotationAssayField
-
Set a formatter to use for formatting the exported values.
- setFormatter(Formatter<?>) - Method in class net.sf.basedb.util.export.spotdata.AssayPropertyField
-
Set a formatter to use for formatting the exported values.
- setFormatter(Formatter<?>) - Method in class net.sf.basedb.util.export.spotdata.JepDynamicField
-
Set a formatter to use for formatting the exported values.
- setFormatter(Formatter<?>) - Method in class net.sf.basedb.util.export.spotdata.SimpleDynamicField
-
Set a formatter to use for formatting the exported values.
- setFormatterClass(String) - Method in class net.sf.basedb.clients.web.extensions.list.PropertyPathActionFactory
-
- setFormulas(List<String>) - Method in class net.sf.basedb.core.data.FormulaData
-
- setFormulas(List<String>) - Method in class net.sf.basedb.core.Formula
-
Set the expressions used by this formula.
- setFormulaType(Formula.Type) - Method in class net.sf.basedb.core.Formula
-
Set the type of the formula.
- setFreeWells(int) - Method in class net.sf.basedb.core.data.BioPlateData
-
- setFreezer(Hardware) - Method in class net.sf.basedb.core.BioPlate
-
Sets the freezer where this bio plate is stored
- setFreezer(HardwareData) - Method in class net.sf.basedb.core.data.BioPlateData
-
- setFrom(BasicItem) - Method in class net.sf.basedb.core.AnyToAny
-
- setFrom(String) - Method in class net.sf.basedb.core.data.MessageData
-
- setFrom(String) - Method in class net.sf.basedb.core.Message
-
Set the name of the sender of the message.
- setFromId(int) - Method in class net.sf.basedb.core.data.AnyToAnyData
-
- setFromId(int) - Method in class net.sf.basedb.core.data.MessageData
-
- setFromType(int) - Method in class net.sf.basedb.core.data.AnyToAnyData
-
- setGamma(float) - Method in class net.sf.basedb.core.data.SpotImagesData
-
- setGamma(float) - Method in class net.sf.basedb.core.SpotImages
-
- setGenericDataFile(DbControl, FileStoreEnabled, String, String, File) - Static method in class net.sf.basedb.core.FileStoreUtil
-
- setGenericType(ItemSubtypeData) - Method in class net.sf.basedb.core.data.DataFileTypeData
-
- setGenericType(ItemSubtype) - Method in class net.sf.basedb.core.DataFileType
-
Set the generic file type of this item.
- setGranted(int) - Method in class net.sf.basedb.core.data.keyring.PluginKeys
-
Set the granted permissions.
- setGranted(int) - Method in class net.sf.basedb.core.data.PluginPermission
-
- setGreenImageFile(FileData) - Method in class net.sf.basedb.core.data.SpotImagesData
-
- setGreenImageFile(File) - Method in class net.sf.basedb.core.SpotImages
-
- setGroup(GroupData) - Method in class net.sf.basedb.core.data.DiskUsageData
-
- setGroupId(int) - Method in class net.sf.basedb.core.data.keyring.GroupKeys
-
Set the id of the group.
- setGroupId(int) - Method in class net.sf.basedb.core.data.keyring.GroupProjects
-
Set the id of the group.
- setGroupId(int) - Method in class net.sf.basedb.core.data.keyring.UserGroups
-
Set the id of the group.
- setGroups(Map<GroupData, Integer>) - Method in class net.sf.basedb.core.data.ItemKeyData
-
- setGroups(Map<GroupData, Integer>) - Method in class net.sf.basedb.core.data.ProjectData
-
- setGroups(Set<GroupData>) - Method in class net.sf.basedb.core.data.UserData
-
- setGuiContexts(Set<GuiContextData>) - Method in class net.sf.basedb.core.data.PluginDefinitionData
-
- setGuiContexts(Set<GuiContext>) - Method in class net.sf.basedb.core.PluginDefinition
-
Set the contexts where this plugin can be used.
- setHardware(Hardware) - Method in class net.sf.basedb.core.BioMaterialEvent
-
Get the
Hardware
that was used in this event.
- setHardware(Hardware) - Method in class net.sf.basedb.core.BioPlateEvent
-
Set the
Hardware
that was used in this event.
- setHardware(HardwareData) - Method in class net.sf.basedb.core.data.BioMaterialEventData
-
- setHardware(HardwareData) - Method in class net.sf.basedb.core.data.BioPlateEventData
-
- setHardware(HardwareData) - Method in class net.sf.basedb.core.data.DerivedBioAssayData
-
- setHardware(HardwareData) - Method in class net.sf.basedb.core.data.PlateEventData
-
- setHardware(Hardware) - Method in class net.sf.basedb.core.DerivedBioAssay
-
Set the
Hardware
that was used when
creating this bioassay set.
- setHardware(Hardware) - Method in class net.sf.basedb.core.PlateEvent
-
Set the
Hardware
that was used in this event.
- setHasData(boolean) - Method in class net.sf.basedb.core.data.RawBioAssayData
-
- setHasFeatures(boolean) - Method in class net.sf.basedb.core.data.ArrayDesignData
-
- setHasHiddenCharacters(boolean) - Method in class net.sf.basedb.clients.web.extensions.login.FieldInfo
-
- setHeader(String, String) - Method in class net.sf.basedb.core.RawBioAssay
-
Set the value for a raw data header.
- setHeader(RawBioAssay, String, String) - Method in class net.sf.basedb.util.affymetrix.CelValidator
-
- setHeaderRegexp(Pattern) - Method in class net.sf.basedb.util.parser.FlatFileParser
-
Set a regular expression that can be matched against a header.
- setHeaders(Map<String, String>) - Method in class net.sf.basedb.core.data.RawBioAssayData
-
- setHeaders(String...) - Method in class net.sf.basedb.util.bfs.AnnotationModel
-
Set the column headers.
- setHeight(String) - Method in class net.sf.basedb.clients.web.extensions.plot.MAPlotFactory
-
- setHeight(int) - Method in class net.sf.basedb.clients.web.extensions.plot.PlotGeneratorBean
-
- setHeight(int) - Method in class net.sf.basedb.core.AnnotationType
-
Set the recommended height in characters a client application should use
to render an input field for annotations of this annotation type.
- setHeight(int) - Method in class net.sf.basedb.core.data.AnnotationTypeData
-
- setHelp(String) - Method in class net.sf.basedb.clients.web.extensions.login.LoginFormBean
-
- setHelpId(String) - Method in class net.sf.basedb.clients.web.extensions.tabcontrol.FixedTabFactory
-
- setHelpId(String) - Method in class net.sf.basedb.clients.web.extensions.tabcontrol.IncludeContentTabFactory
-
- setHelpId(String) - Method in class net.sf.basedb.clients.web.extensions.tabcontrol.TabBean
-
- setHelpid(String) - Method in class net.sf.basedb.clients.web.taglib.Help
-
- setHelpid(String) - Method in class net.sf.basedb.clients.web.taglib.tab.Tab
-
- setHelpTexts(Set<HelpData>) - Method in class net.sf.basedb.core.data.ClientData
-
- setHiddenMembers(boolean) - Method in class net.sf.basedb.core.data.GroupData
-
- setHiddenMembers(boolean) - Method in class net.sf.basedb.core.Group
-
Set the hidden members flag for this group.
- setHideClazz(String) - Method in class net.sf.basedb.clients.web.extensions.section.IncludeContentSectionFactory
-
- setHideClazz(String) - Method in class net.sf.basedb.clients.web.extensions.section.SectionBean
-
- setHideclazz(String) - Method in class net.sf.basedb.clients.web.taglib.HideableSection
-
- setHightligh(String) - Method in class net.sf.basedb.clients.web.taglib.table.Row
-
- setHome(String) - Method in class net.sf.basedb.util.extensions.xml.PathConverter
-
Set the value of the home path.
- setHomeDirectory(DirectoryData) - Method in class net.sf.basedb.core.data.UserData
-
- setHomeDirectory(Directory) - Method in class net.sf.basedb.core.User
-
Set the home directory for the user.
- setHost(String) - Method in class net.sf.basedb.core.data.FileServerData
-
- setHost(String) - Method in class net.sf.basedb.core.FileServer
-
Set the host:port that should overrride the host:port
specified in file urls.
- setHost(String) - Method in class net.sf.basedb.util.uri.ConnectionParameters
-
- setHref(String) - Method in class net.sf.basedb.clients.web.taglib.path.PathElement
-
- setIcon(String) - Method in class net.sf.basedb.clients.web.extensions.menu.FixedMenuItemFactory
-
- setIcon(String) - Method in class net.sf.basedb.clients.web.extensions.menu.MenuItemBean
-
- setIcon(String) - Method in class net.sf.basedb.clients.web.extensions.menu.PermissionMenuItemFactory
-
Set the icon to use in all cases.
- setIcon(String) - Method in class net.sf.basedb.clients.web.extensions.toolbar.ButtonBean
-
- setIcon(String) - Method in class net.sf.basedb.clients.web.extensions.toolbar.FixedButtonFactory
-
- setIcon(String) - Method in class net.sf.basedb.clients.web.extensions.toolbar.PermissionButtonFactory
-
Set the icon to use in all cases.
- setIcon(String) - Method in class net.sf.basedb.clients.web.taglib.menu.Menuitem
-
- setIcon(String) - Method in class net.sf.basedb.clients.web.taglib.menu.Submenu
-
- setId(String) - Method in class net.sf.basedb.clients.web.extensions.list.AbstractListColumnBean
-
- setId(String) - Method in class net.sf.basedb.clients.web.extensions.list.PropertyPathActionFactory
-
- setId(String) - Method in class net.sf.basedb.clients.web.extensions.menu.FixedMenuItemFactory
-
- setId(String) - Method in class net.sf.basedb.clients.web.extensions.menu.MenuItemBean
-
- setId(String) - Method in class net.sf.basedb.clients.web.extensions.menu.PermissionMenuItemFactory
-
- setId(String) - Method in class net.sf.basedb.clients.web.extensions.plot.OverviewPlotBean
-
- setId(String) - Method in class net.sf.basedb.clients.web.extensions.plot.PlotGeneratorBean
-
- setId(String) - Method in class net.sf.basedb.clients.web.extensions.section.IncludeContentSectionFactory
-
- setId(String) - Method in class net.sf.basedb.clients.web.extensions.section.SectionBean
-
- setId(String) - Method in class net.sf.basedb.clients.web.extensions.skin.FixedSkinActionFactory
-
- setId(String) - Method in class net.sf.basedb.clients.web.extensions.startpage.StartPageBean
-
- setId(String) - Method in class net.sf.basedb.clients.web.extensions.tabcontrol.FixedTabFactory
-
- setId(String) - Method in class net.sf.basedb.clients.web.extensions.tabcontrol.IncludeContentTabFactory
-
- setId(String) - Method in class net.sf.basedb.clients.web.extensions.tabcontrol.TabBean
-
- setId(String) - Method in class net.sf.basedb.clients.web.extensions.toolbar.ButtonBean
-
- setId(String) - Method in class net.sf.basedb.clients.web.extensions.toolbar.FixedButtonFactory
-
- setId(String) - Method in class net.sf.basedb.clients.web.extensions.toolbar.PermissionButtonFactory
-
Set the ID of the button.
- setId(int) - Method in class net.sf.basedb.core.data.annotations.AnnotationLink
-
- setId(int) - Method in class net.sf.basedb.core.data.BasicData
-
Set the id of the item.
- setId(int) - Method in class net.sf.basedb.core.ItemContext
-
Set the ID of the current item in this context.
- setId(String) - Method in class net.sf.basedb.util.extensions.ExtensionBean
-
- setId(String) - Method in class net.sf.basedb.util.extensions.ExtensionPointBean
-
- setIgnoredFile(File, boolean) - Method in class net.sf.basedb.util.extensions.manager.Settings
-
Mark the given file as ignored/not ignored by the extension system.
- setIgnoreNonExistingColumns(boolean) - Method in class net.sf.basedb.util.parser.ColFunction
-
Set to TRUE to ignore non-existing columns.
- setIgnoreNonExistingColumns(boolean) - Method in class net.sf.basedb.util.parser.FlatFileParser
-
Specify if trying to create a mapper with one of the
FlatFileParser.getMapper(String)
methods for an expression which references a non-existing column should
result in an exception or be ignored.
- setIgnoreRegexp(Pattern) - Method in class net.sf.basedb.util.parser.FlatFileParser
-
Set a regular expression that is used to match a line that should
be ignored.
- setImage(String) - Method in class net.sf.basedb.clients.web.taglib.Button
-
- setImage(String) - Method in class net.sf.basedb.clients.web.taglib.Help
-
- setImage(String) - Method in class net.sf.basedb.clients.web.taglib.Icon
-
- setImage(String) - Method in class net.sf.basedb.clients.web.taglib.table.Button
-
- setImage(String) - Method in class net.sf.basedb.clients.web.taglib.table.Label
-
- setImage(String) - Method in class net.sf.basedb.clients.web.taglib.Zoom
-
- setImage(String) - Method in class net.sf.basedb.core.data.PlateMappingData
-
- setImage(String) - Method in class net.sf.basedb.core.PlateMapping
-
Set the name of a small image that is a graphical representation of the mapping.
- setImageRemapDir(String) - Method in class net.sf.basedb.clients.web.extensions.skin.FixedSkinActionFactory
-
- setImgClass(String) - Method in class net.sf.basedb.clients.web.formatter.SpotImageFormatter
-
Sets the class attribute for the generated <img> tag
that displays the spot image.
- setImpersonated(boolean) - Method in class net.sf.basedb.core.data.SessionData
-
- setInactive(boolean) - Method in class net.sf.basedb.core.data.KitData
-
- setInactive(boolean) - Method in class net.sf.basedb.core.Kit
-
Set the inactive flag.
- setInclude(Set<Include>, String, Include) - Static method in class net.sf.basedb.clients.web.Base
-
Set include option if option parameter isn't null.
- setInclude(String) - Method in class net.sf.basedb.clients.web.extensions.section.IncludeContentSectionFactory
-
- setInclude(String) - Method in class net.sf.basedb.clients.web.extensions.tabcontrol.IncludeContentTabFactory
-
- setInclude(int) - Method in class net.sf.basedb.core.data.ContextData
-
- setInclude(int) - Method in class net.sf.basedb.core.data.ItemListSyncFilterData
-
- setInclude(Collection<Include>) - Method in class net.sf.basedb.util.listable.TransformContext
-
- setIncludeInherited(boolean) - Method in class net.sf.basedb.core.AnnotationRestriction.Options
-
- setIncludePrimary(boolean) - Method in class net.sf.basedb.core.AnnotationRestriction.Options
-
- setIncludes(Collection<Include>) - Method in class net.sf.basedb.core.AbstractEntityQuery
-
- setIncludes(Collection<Include>) - Method in interface net.sf.basedb.core.query.EntityQuery
-
Clears the lists of includes and adds a new collection.
- setIndex(int) - Method in class net.sf.basedb.core.BioPlateEventParticipant
-
Set the index of the plate in this event.
- setIndex(int) - Method in class net.sf.basedb.core.data.BioPlateEventParticipantData
-
- setIndex(float) - Method in class net.sf.basedb.util.extensions.ExtensionBean
-
- setInheritedFrom(AnnotationData) - Method in class net.sf.basedb.core.data.AnnotationData
-
- setInheritedFrom(AnnotationSnapshot) - Method in class net.sf.basedb.core.snapshot.AnnotationSnapshot
-
Set the primary annotation for an inherited annotation.
- setInheritingAnnotations(Set<AnnotationData>) - Method in class net.sf.basedb.core.data.AnnotationData
-
- setInitial(String) - Method in class net.sf.basedb.clients.web.taglib.HideableSection
-
- setInputStream(InputStream) - Method in class net.sf.basedb.util.bfs.AnnotationParser
-
Set the input stream that should be parsed.
- setInputStream(InputStream) - Method in class net.sf.basedb.util.bfs.DataParser
-
Set the input stream that should be parsed.
- setInputStream(InputStream) - Method in class net.sf.basedb.util.bfs.MetadataParser
-
Set the input stream that should be parsed.
- setInputStream(InputStream, String) - Method in class net.sf.basedb.util.parser.FlatFileParser
-
Set the input stream that will be parsed.
- setInputStreamLocator(InputStreamLocator) - Method in class net.sf.basedb.util.importer.spotdata.BfsImporter
-
Set the input stream locator that is responsible for opening files
that are referenced from the metadata file.
- setInstalled() - Method in class net.sf.basedb.util.extensions.manager.ExtensionsFile.WriteableExtensionsFile
-
Mark the file as installed.
- setInstalledFile(File) - Method in class net.sf.basedb.util.extensions.manager.Settings
-
Mark the given file as installed by the extension system.
- setInstalledSchemaVersion(int) - Method in class net.sf.basedb.core.hibernate.SessionFactoryConfiguration
-
Deprecated.
Callback intended for BASE core to set the installed schema version.
- setInteger(int, int) - Method in class net.sf.basedb.core.hibernate.QueryWrapper
-
- setInteger(String, int) - Method in class net.sf.basedb.core.hibernate.QueryWrapper
-
- setIntegerValues(List<Integer>) - Method in class net.sf.basedb.core.data.annotations.AnnotationLink
-
- setIntensities(FlatFileParser.Data, float[], int) - Method in class net.sf.basedb.util.importer.spotdata.GenericIntensityParser
-
- setIntensities(FlatFileParser.Data, float[], int) - Method in class net.sf.basedb.util.importer.spotdata.MAParser
-
- setIntensities(FlatFileParser.Data, float[], int) - Method in interface net.sf.basedb.util.importer.spotdata.SpotIntensityParser
-
Extract the intensity values from the current data line for a single
bioassay.
- setIntensityTransform(IntensityTransform) - Method in class net.sf.basedb.core.BioAssaySet
-
Sets the transform used on the spot intensities before they were stored
in the database.
- setIntensityTransform(int) - Method in class net.sf.basedb.core.data.BioAssaySetData
-
- setIntensityTransform(IntensityTransform) - Method in class net.sf.basedb.util.importer.spotdata.BaseFileImporter
-
Set the intensity transform that have been applied to the spot
data in the file.
- setInteractive(boolean) - Method in class net.sf.basedb.core.data.PluginDefinitionData
-
- setInteractive(boolean) - Method in class net.sf.basedb.core.PluginDefinition
-
- setInterfaceName(String) - Method in class net.sf.basedb.core.data.PluginTypeData
-
- setInterfaceName(String) - Method in class net.sf.basedb.core.PluginType
-
The class name cannot be changed.
- setInternalId(int) - Method in class net.sf.basedb.util.extensions.xml.PluginInfo
-
- setInternalName(String) - Method in class net.sf.basedb.core.data.FileData
-
- setInternalName(String) - Method in class net.sf.basedb.core.File
-
Set the internal name of this file.
- setInterruptHandler(InterruptHandler) - Static method in class net.sf.basedb.core.signal.ThreadSignalHandler
-
Register an interrupt handler with the current thread.
- setInterval(String) - Method in class net.sf.basedb.clients.web.extensions.service.DummyService
-
Set the interval between writes to stdout.
- setItem(String) - Method in class net.sf.basedb.clients.web.extensions.menu.PermissionMenuItemFactory
-
Set the item type to check the permission for.
- setItem(String) - Method in class net.sf.basedb.clients.web.extensions.toolbar.PermissionButtonFactory
-
Set the item type to check the permission for.
- setItem(Object) - Method in class net.sf.basedb.clients.web.taglib.extensions.Render
-
- setItem(Object) - Method in class net.sf.basedb.clients.web.taglib.PropertyValue
-
- setItem(Object) - Method in class net.sf.basedb.clients.web.taglib.table.ExtensionCells
-
- setItem(Item) - Method in class net.sf.basedb.clients.web.taglib.table.Table
-
- setItem(Annotatable) - Method in class net.sf.basedb.core.AnnotationSet
-
Set the item this annotation set belongs to.
- setItem(FileStoreEnabled) - Method in class net.sf.basedb.core.FileSet
-
Set the item this file set belongs to.
- setItem(int, Item) - Method in class net.sf.basedb.core.snapshot.AnnotationSnapshot
-
- setItemId(Integer) - Method in class net.sf.basedb.core.data.AnnotationSetData
-
- setItemId(int) - Method in class net.sf.basedb.core.data.ChangeHistoryDetailData
-
- setItemId(int) - Method in class net.sf.basedb.core.data.ContextData
-
- setItemKey(ItemKeyData) - Method in interface net.sf.basedb.core.data.ShareableData
-
- setItemKey(ItemKeyData) - Method in class net.sf.basedb.core.data.SharedData
-
- setItemKey(ItemKey) - Method in interface net.sf.basedb.core.Shareable
-
- setItemKey(DbControl, ShareableData, ItemKey) - Static method in class net.sf.basedb.core.ShareableUtil
-
- setItemKey(ItemKey) - Method in class net.sf.basedb.core.SharedItem
-
- setItemKeys(Set<ItemKeyData>) - Method in class net.sf.basedb.core.data.GroupData
-
- setItemKeys(Set<ItemKeyData>) - Method in class net.sf.basedb.core.data.UserData
-
- setItemList(ItemListData) - Method in class net.sf.basedb.core.data.ItemListSyncFilterData
-
- setItemPermission(Permission) - Method in class net.sf.basedb.core.AbstractEntityQuery
-
- setItemPermission(Permission) - Method in class net.sf.basedb.core.ItemContext
-
Specify the permission the logged in user must have for items returned
by a query.
- setItemPermission(Permission) - Method in interface net.sf.basedb.core.query.EntityQuery
-
Only return items which the logged in user has the specified
permission for.
- setItemSubtype(ItemSubtype) - Method in class net.sf.basedb.core.BioMaterial
-
- setItemSubtype(ItemSubtype) - Method in class net.sf.basedb.core.BioPlateType
-
Set the subtype that biomaterial items should have when placed on a
plate with the bioplate type.
- setItemSubtype(ItemSubtypeData) - Method in class net.sf.basedb.core.data.BioMaterialData
-
- setItemSubtype(ItemSubtypeData) - Method in class net.sf.basedb.core.data.BioPlateTypeData
-
- setItemSubtype(ItemSubtypeData) - Method in class net.sf.basedb.core.data.DerivedBioAssayData
-
- setItemSubtype(ItemSubtypeData) - Method in class net.sf.basedb.core.data.FileData
-
- setItemSubtype(ItemSubtypeData) - Method in class net.sf.basedb.core.data.HardwareData
-
- setItemSubtype(ItemSubtypeData) - Method in class net.sf.basedb.core.data.ItemListData
-
- setItemSubtype(ItemSubtypeData) - Method in class net.sf.basedb.core.data.ItemSubtypeFileTypeData
-
- setItemSubtype(ItemSubtypeData) - Method in class net.sf.basedb.core.data.JobData
-
- setItemSubtype(ItemSubtypeData) - Method in class net.sf.basedb.core.data.KitData
-
- setItemSubtype(ItemSubtypeData) - Method in class net.sf.basedb.core.data.PhysicalBioAssayData
-
- setItemSubtype(ItemSubtypeData) - Method in class net.sf.basedb.core.data.ProtocolData
-
- setItemSubtype(ItemSubtypeData) - Method in class net.sf.basedb.core.data.SoftwareData
-
- setItemSubtype(ItemSubtypeData) - Method in interface net.sf.basedb.core.data.SubtypableData
-
Set the subtype of the item.
- setItemSubtype(ItemSubtypeData) - Method in class net.sf.basedb.core.data.TagData
-
- setItemSubtype(ItemSubtype) - Method in class net.sf.basedb.core.DerivedBioAssay
-
- setItemSubtype(ItemSubtype) - Method in class net.sf.basedb.core.File
-
- setItemSubtype(ItemSubtype) - Method in class net.sf.basedb.core.Hardware
-
- setItemSubtype(ItemSubtype) - Method in class net.sf.basedb.core.ItemList
-
Set the subtype of items that can be members in this list.
- setItemSubtype(ItemSubtype) - Method in class net.sf.basedb.core.ItemSubtype
-
Do nothing.
- setItemSubtype(ItemSubtype) - Method in class net.sf.basedb.core.Job
-
- setItemSubtype(ItemSubtype) - Method in class net.sf.basedb.core.Kit
-
- setItemSubtype(ItemSubtype) - Method in class net.sf.basedb.core.PhysicalBioAssay
-
- setItemSubtype(ItemSubtype) - Method in class net.sf.basedb.core.Protocol
-
- setItemSubtype(ItemSubtype) - Method in class net.sf.basedb.core.Software
-
- setItemSubtype(ItemSubtype) - Method in interface net.sf.basedb.core.Subtypable
-
Set the subtype on the item.
- setItemSubtype(ItemSubtype) - Method in class net.sf.basedb.core.Tag
-
- setItemSubtype(ItemSubtype) - Method in class net.sf.basedb.util.annotations.InheritSpecification
-
Set the subtype a parent item must have if annotations should be
inherited from it.
- setItemSubtypes(Set<ItemSubtypeFileTypeData>) - Method in class net.sf.basedb.core.data.DataFileTypeData
-
- setItemType(int) - Method in class net.sf.basedb.core.data.AnnotationSetData
-
- setItemType(int) - Method in class net.sf.basedb.core.data.ChangeHistoryDetailData
-
- setItemType(int) - Method in class net.sf.basedb.core.data.ContextData
-
- setItemType(int) - Method in class net.sf.basedb.core.data.ContextIndex
-
- setItemType(int) - Method in class net.sf.basedb.core.data.DataFileTypeData
-
- setItemType(int) - Method in class net.sf.basedb.core.data.DiskUsageData
-
- setItemType(int) - Method in class net.sf.basedb.core.data.FileSetData
-
- setItemType(int) - Method in class net.sf.basedb.core.data.GuiContextData
-
- setItemType(int) - Method in class net.sf.basedb.core.data.ItemSubtypeData
-
- setItemType(int) - Method in class net.sf.basedb.core.data.RoleKeyData
-
- setItemType(Item) - Method in class net.sf.basedb.core.DataFileType
-
- setItemType(Item) - Method in class net.sf.basedb.core.query.QueryParameter
-
Changes the type of the parameter.
- setItemTypes(Collection<Item>) - Method in class net.sf.basedb.core.AnnotationType
-
Enable the annotation type for all of the specified item
and disable it for all other.
- setItemTypes(Set<Integer>) - Method in class net.sf.basedb.core.data.AnnotationTypeData
-
- setJarFile(String) - Method in class net.sf.basedb.core.data.PluginDefinitionData
-
- setJarFile(String) - Method in class net.sf.basedb.core.data.PluginTypeData
-
- setJarFile(String) - Method in class net.sf.basedb.core.PluginDefinition
-
The jar path cannot be changed.
- setJarFile(String) - Method in class net.sf.basedb.core.PluginType
-
The jar path cannot be changed.
- setJep(String) - Method in class net.sf.basedb.util.export.spotdata.JepDynamicField
-
Set the expression used to select data in the query.
- setJob(JobData) - Method in class net.sf.basedb.core.data.ArrayDesignData
-
- setJob(JobData) - Method in class net.sf.basedb.core.data.ChangeHistoryData
-
- setJob(JobData) - Method in class net.sf.basedb.core.data.DerivedBioAssayData
-
- setJob(JobData) - Method in class net.sf.basedb.core.data.ExtraValueData
-
- setJob(JobData) - Method in class net.sf.basedb.core.data.MessageData
-
- setJob(JobData) - Method in class net.sf.basedb.core.data.RawBioAssayData
-
- setJob(JobData) - Method in class net.sf.basedb.core.data.TransformationData
-
- setJob(Job) - Method in class net.sf.basedb.core.ExtraValue
-
Set the job that created the extra values.
- setJob(Job) - Method in class net.sf.basedb.core.Message
-
- setJob(Job) - Method in class net.sf.basedb.core.Transformation
-
Set the job that executed this transformation.
- setJobAgent(JobAgentData) - Method in class net.sf.basedb.core.data.JobAgentSettingsData
-
- setJobAgent(JobAgent) - Method in class net.sf.basedb.core.Job
-
Set the job agent this job should run on.
- setJobAgent(JobAgent) - Method in class net.sf.basedb.core.JobAgentSettings
-
- setJobAgentId(Integer) - Method in class net.sf.basedb.core.data.JobData
-
- setJobAgentSettings(Set<JobAgentSettingsData>) - Method in class net.sf.basedb.core.data.PluginDefinitionData
-
- setJobId(Integer) - Method in class net.sf.basedb.core.data.ChangeHistoryData
-
- setJobs(Set<JobData>) - Method in class net.sf.basedb.core.data.ExperimentData
-
- setJspContext(JspContext) - Method in class net.sf.basedb.clients.web.extensions.edit.AbstractOnSaveAction
-
Get the JSP context of the current invokation.
- setJspcontext(JspContext) - Method in class net.sf.basedb.clients.web.taglib.table.ColumnDef
-
- setKeepSkippedLines(boolean) - Method in class net.sf.basedb.util.parser.FlatFileParser
-
- setKeyId(int) - Method in class net.sf.basedb.core.data.keyring.KeyPermission
-
Set the id of the key.
- setKeyId(int) - Method in class net.sf.basedb.core.data.keyring.PluginKeys
-
Sets the id of the RoleKey
- setKeys(Set<RoleKeyData>) - Method in class net.sf.basedb.core.data.RoleData
-
- setKit(Kit) - Method in class net.sf.basedb.core.BioMaterialEvent
-
Set the
Kit
that was used in this event.
- setKit(Kit) - Method in class net.sf.basedb.core.BioPlateEvent
-
Set the
Kit
that was used in this event.
- setKit(KitData) - Method in class net.sf.basedb.core.data.BioMaterialEventData
-
- setKit(KitData) - Method in class net.sf.basedb.core.data.BioPlateEventData
-
- setKit(KitData) - Method in class net.sf.basedb.core.data.DerivedBioAssayData
-
- setKit(Kit) - Method in class net.sf.basedb.core.DerivedBioAssay
-
Set the
Kit
that was used when creating this bioassay.
- setLabel(String) - Method in class net.sf.basedb.core.data.ParameterValueData
-
- setLastModified(Date) - Method in class net.sf.basedb.util.uri.UriMetadata
-
- setLastProcessResults(ProcessResults) - Method in class net.sf.basedb.util.extensions.manager.ExtensionsManager
-
Save the last process results so that they can be used
later on.
- setLastSource(String) - Method in class net.sf.basedb.core.data.ReporterData
-
- setLastUpdate(Date) - Method in class net.sf.basedb.core.data.AnnotationData
-
- setLastUpdate(Date) - Method in class net.sf.basedb.core.data.FileData
-
- setLastUpdate(Date) - Method in class net.sf.basedb.core.data.ReporterData
-
- setLastUpdated() - Method in class net.sf.basedb.clients.jobagent.slotmanager.MasterSlotManager.RemoteSlot
-
- setLayerNo(short) - Method in class net.sf.basedb.core.data.DataCubeLayerData
-
- setLayerNo(short) - Method in class net.sf.basedb.core.DataCubeLayer
-
- setLayers(Set<DataCubeLayerData>) - Method in class net.sf.basedb.core.data.DataCubeData
-
- setLength(int) - Method in class net.sf.basedb.core.data.ReporterClonePropertyData
-
- setLength(Long) - Method in class net.sf.basedb.util.uri.UriMetadata
-
- setLevel(String) - Method in class net.sf.basedb.util.extensions.LoggingErrorHandlerFactory
-
Set the level of the error handler.
- setLimit(int) - Method in class net.sf.basedb.core.signal.ProgressReporterSignalHandler
-
Set the percentage limit.
- setList(Iterable<?>) - Method in class net.sf.basedb.clients.web.taglib.table.CellValue
-
- setLocale(int, Locale) - Method in class net.sf.basedb.core.hibernate.QueryWrapper
-
- setLocale(String, Locale) - Method in class net.sf.basedb.core.hibernate.QueryWrapper
-
- setLocation(int) - Method in class net.sf.basedb.core.data.DiskUsageData
-
- setLocation(int) - Method in class net.sf.basedb.core.data.FileData
-
- setLocation(int) - Method in class net.sf.basedb.core.data.QuotaIndex
-
- setLocation(Location) - Method in class net.sf.basedb.core.File
-
Set the location of this File
item.
- setLocked(boolean) - Method in class net.sf.basedb.clients.web.taglib.table.Navigator
-
- setLocked(boolean) - Method in class net.sf.basedb.core.data.ReporterCloneTemplateData
-
- setLockMode(BioWell.LockMode) - Method in class net.sf.basedb.core.BioPlateType
-
Set the lock mode for wells on plates of this plate type.
- setLockMode(int) - Method in class net.sf.basedb.core.data.BioPlateTypeData
-
- setLockMode(String, LockMode) - Method in class net.sf.basedb.core.hibernate.QueryWrapper
-
- setLockOptions(LockOptions) - Method in class net.sf.basedb.core.hibernate.QueryWrapper
-
- setLogarithmic(boolean) - Method in class net.sf.basedb.core.Coloring
-
Specify if we should take the logarithm of values before the color is
generated or not.
- setLogarithmic(boolean) - Method in class net.sf.basedb.core.data.ColoringData
-
- setLogin(String) - Method in class net.sf.basedb.core.authentication.LoginRequest
-
Set the login name to use.
- setLogin(String) - Method in class net.sf.basedb.core.data.UserData
-
- setLogin(String) - Method in class net.sf.basedb.core.User
-
Set the login for the user account.
- setLoginComment(String) - Method in class net.sf.basedb.core.data.SessionData
-
- setLoginField(FieldInfo) - Method in class net.sf.basedb.clients.web.extensions.login.LoginFormBean
-
- setLoginTime(Date) - Method in class net.sf.basedb.core.data.SessionData
-
- setLogoutTime(Date) - Method in class net.sf.basedb.core.data.SessionData
-
- setLong(int, long) - Method in class net.sf.basedb.core.hibernate.QueryWrapper
-
- setLong(String, long) - Method in class net.sf.basedb.core.hibernate.QueryWrapper
-
- setLongValues(List<Long>) - Method in class net.sf.basedb.core.data.annotations.AnnotationLink
-
- setMainItemType(Item) - Method in class net.sf.basedb.core.ItemSubtype
-
- setMainType(int) - Method in class net.sf.basedb.core.data.PluginDefinitionData
-
- setMainType(Plugin.MainType) - Method in class net.sf.basedb.core.PluginDefinition
-
The type cannot be changed.
- setMandatory(boolean) - Method in class net.sf.basedb.core.data.ReporterClonePropertyData
-
- setMappings(short) - Method in class net.sf.basedb.core.data.VirtualDbData
-
- setMasked(boolean) - Method in class net.sf.basedb.core.data.ParameterValueData
-
- setMasterParser(AnnotationParser) - Method in class net.sf.basedb.util.importer.spotdata.SynchronizedSpotDataParser
-
Sets the master parser.
- setMatchingSource(int) - Method in class net.sf.basedb.core.data.ItemListSyncFilterData
-
- setMatchingTransformed(int) - Method in class net.sf.basedb.core.data.ItemListSyncFilterData
-
- setMaxAge(int) - Method in class net.sf.basedb.core.DiskUsageStatistics
-
Set the max age in seconds for a disk usage summary
object before it is reloaded from the database again.
- setMaxBaseVersion(String) - Method in class net.sf.basedb.util.extensions.AboutBean
-
- setMaxBytes(long) - Method in class net.sf.basedb.core.data.QuotaIndex
-
- setMaxcharacters(int) - Method in class net.sf.basedb.clients.web.taglib.table.Cell
-
- setMaxDataColumns(int) - Method in class net.sf.basedb.util.parser.FlatFileParser
-
Set the maximum number of columns a data line can contain in
order for it to be counted as a data line.
- setMaxheight(String) - Method in class net.sf.basedb.clients.web.taglib.table.Cell
-
- setMaxLength(Integer) - Method in class net.sf.basedb.core.AnnotationType
-
Set the maximum allowed string length for a
Type.STRING
annotation.
- setMaxMemory(Long) - Method in class net.sf.basedb.core.data.JobAgentSettingsData
-
- setMaxMemory(Long) - Method in class net.sf.basedb.core.data.PluginDefinitionData
-
- setMaxMemory(Long) - Method in class net.sf.basedb.core.JobAgentSettings
-
Set maximim amount of memory the plugin is allowed to use.
- setMaxMemory(Long) - Method in class net.sf.basedb.core.PluginDefinition
-
Set the maximum amount of memory the plugin is allowed to use.
- setMaxRawMappingsForSpot(int) - Method in class net.sf.basedb.core.data.DataCubeData
-
- setMaxResults(int) - Method in class net.sf.basedb.core.AbstractQuery
-
- setMaxResults(int) - Method in class net.sf.basedb.core.hibernate.QueryWrapper
-
- setMaxResults(int) - Method in interface net.sf.basedb.core.query.Query
-
Specify that the query should at most return the specified number of
rows.
- setMaxUnknownLines(int) - Method in class net.sf.basedb.util.parser.FlatFileParser
-
The number of unknown lines in a row that can be parsed by
the
parseHeaders
method before it gives
up.
- setMaxValue(Float) - Method in class net.sf.basedb.core.Coloring
-
Set the value that represents the maximum value.
- setMaxValue(Float) - Method in class net.sf.basedb.core.data.ColoringData
-
- setMaxValueDouble(Double) - Method in class net.sf.basedb.core.AnnotationType
-
- setMaxValueLong(Long) - Method in class net.sf.basedb.core.AnnotationType
-
- setMaxwidth(String) - Method in class net.sf.basedb.clients.web.taglib.table.Cell
-
- setMd5(String) - Method in class net.sf.basedb.core.data.FileData
-
- setMd5(String) - Method in class net.sf.basedb.core.data.ItemListSyncFilterData
-
- setMd5(String) - Method in class net.sf.basedb.util.uri.UriMetadata
-
- setMember(File, DataFileType) - Method in class net.sf.basedb.core.FileSet
-
Set a file of a given type as a member of this file set.
- setMembers(Set<FileSetMemberData>) - Method in class net.sf.basedb.core.data.FileSetData
-
- setMembers(Set<Integer>) - Method in class net.sf.basedb.core.data.ItemListData
-
- setMemberType(int) - Method in class net.sf.basedb.core.data.ItemListData
-
- setMemberType(Item) - Method in class net.sf.basedb.core.ItemList
-
- setMenu(String) - Method in class net.sf.basedb.clients.web.taglib.Page
-
- setMenuId(String) - Method in class net.sf.basedb.clients.web.extensions.menu.FixedMenuItemFactory
-
- setMenuId(String) - Method in class net.sf.basedb.clients.web.extensions.menu.MenuItemBean
-
- setMenuId(String) - Method in class net.sf.basedb.clients.web.extensions.menu.PermissionMenuItemFactory
-
- setMessage(String) - Method in class net.sf.basedb.core.ItemContext
-
Set a message to be displayed by a client application as soon as
it is appropriate to do so.
- setMessagePrefix(String) - Method in class net.sf.basedb.util.ChainedProgressReporter
-
Set a message prefix that is pre-pended to message before it is sent to the
master progress reporter.
- setMessages(Set<MessageData>) - Method in class net.sf.basedb.core.data.JobData
-
- setMessages(Set<MessageData>) - Method in class net.sf.basedb.core.data.UserData
-
- setMetadataFromURI(UriMetadata) - Method in class net.sf.basedb.core.File
-
- setMetadataParser(MetadataParser) - Method in class net.sf.basedb.util.importer.spotdata.BfsImporter
-
Set the metadata file parser.
- setMetadataPrefix(String) - Method in class net.sf.basedb.util.basefile.BaseFileWriter
-
Change the metadata prefix string.
- setMetadataWriter(MetadataWriter) - Method in class net.sf.basedb.util.export.spotdata.BfsExporter
-
Set the stream were the metadata should be written.
- setMetaGrid(int, int) - Method in class net.sf.basedb.core.ArrayDesignBlock
-
Set the metagrid coordinates.
- setMetaGridX(int) - Method in class net.sf.basedb.core.data.ArrayDesignBlockData
-
- setMetaGridX(Integer) - Method in class net.sf.basedb.core.data.RawData
-
- setMetaGridX(Integer) - Method in class net.sf.basedb.plugins.PrintMapFlatFileImporter.MetaBlock
-
- setMetaGridY(int) - Method in class net.sf.basedb.core.data.ArrayDesignBlockData
-
- setMetaGridY(Integer) - Method in class net.sf.basedb.core.data.RawData
-
- setMetaGridY(Integer) - Method in class net.sf.basedb.plugins.PrintMapFlatFileImporter.MetaBlock
-
- setMidValue(Float) - Method in class net.sf.basedb.core.Coloring
-
Set the value that represents the midpoint value.
- setMidValue(Float) - Method in class net.sf.basedb.core.data.ColoringData
-
- setMimeType(String) - Method in class net.sf.basedb.clients.web.util.ServletExportOutputStream
-
- setMimeType(String) - Method in class net.sf.basedb.core.data.FileData
-
- setMimeType(String) - Method in class net.sf.basedb.core.File
-
Set the mime type for this File
item.
- setMimeType(String) - Method in class net.sf.basedb.core.plugin.ExportOutputStream
-
Do nothing.
- setMimeType(String) - Method in class net.sf.basedb.util.FileExportOutputStream
-
- setMimeType(String) - Method in class net.sf.basedb.util.uri.UriMetadata
-
- setMimeTypeAuto(String, ItemSubtype) - Method in class net.sf.basedb.core.File
-
Set the mime type automatically by checking the extension of the
name.
- setMinBaseVersion(String) - Method in class net.sf.basedb.util.extensions.AboutBean
-
- setMinDataColumns(int) - Method in class net.sf.basedb.util.parser.FlatFileParser
-
Set the minimum number of columns a data line must contain in
order for it to be counted as a data line.
- setMinValue(Float) - Method in class net.sf.basedb.core.Coloring
-
Set the value that represents the minimum value.
- setMinValue(Float) - Method in class net.sf.basedb.core.data.ColoringData
-
- setMinValueDouble(Double) - Method in class net.sf.basedb.core.AnnotationType
-
- setMinValueLong(Long) - Method in class net.sf.basedb.core.AnnotationType
-
- setMode(boolean, boolean) - Method in class net.sf.basedb.util.basefile.BaseFileWriter
-
- setMore(JSONObject, T) - Method in class net.sf.basedb.util.json.NameableConverter
-
Can be used by subclasses to set more properties on the
JSON object.
- setMoreDynamicAttributes(Iterator<DynamicActionAttribute>) - Method in class net.sf.basedb.clients.web.taglib.StylableTag
-
- setMultiple(boolean) - Method in class net.sf.basedb.clients.web.taglib.table.ColumnDef
-
- setMultiple(boolean) - Method in class net.sf.basedb.plugins.executor.ParameterDefinition
-
Set if this parameter can have multiple values or only one.
- setMultiplicity(int) - Method in class net.sf.basedb.core.AnnotationType
-
Set the multiplicity.
- setMultiplicity(int) - Method in class net.sf.basedb.core.data.AnnotationTypeData
-
- setMultiuserAccount(boolean) - Method in class net.sf.basedb.core.data.UserData
-
- setMultiuserAccount(boolean) - Method in class net.sf.basedb.core.User
-
Sets if the user account is multiuser account.
- setName(String) - Method in class net.sf.basedb.clients.web.extensions.startpage.FixedStartPageFactory
-
- setName(String) - Method in class net.sf.basedb.clients.web.extensions.startpage.StartPageBean
-
- setName(String) - Method in class net.sf.basedb.clients.web.taglib.table.Hidden
-
- setName(String) - Method in class net.sf.basedb.core.AnyToAny
-
- setName(String) - Method in class net.sf.basedb.core.authentication.ExtraUserInformation
-
- setName(String) - Method in class net.sf.basedb.core.BioAssay
-
- setName(String) - Method in class net.sf.basedb.core.BioAssaySet
-
- setName(String) - Method in class net.sf.basedb.core.BioPlateEventType
-
- setName(String) - Method in class net.sf.basedb.core.BioPlateType
-
- setName(String) - Method in class net.sf.basedb.core.CommonItem
-
- setName(String) - Method in class net.sf.basedb.core.data.AnyToAnyData
-
- setName(String) - Method in class net.sf.basedb.core.data.BioAssayData
-
- setName(String) - Method in class net.sf.basedb.core.data.BioAssaySetData
-
- setName(String) - Method in class net.sf.basedb.core.data.BioPlateEventTypeData
-
- setName(String) - Method in class net.sf.basedb.core.data.BioPlateTypeData
-
- setName(String) - Method in class net.sf.basedb.core.data.CommonData
-
- setName(String) - Method in class net.sf.basedb.core.data.ContextData
-
- setName(String) - Method in class net.sf.basedb.core.data.ContextIndex
-
- setName(String) - Method in class net.sf.basedb.core.data.DataFileTypeData
-
- setName(String) - Method in class net.sf.basedb.core.data.ExtraValueTypeData
-
- setName(String) - Method in class net.sf.basedb.core.data.GroupData
-
- setName(String) - Method in class net.sf.basedb.core.data.HelpData
-
- setName(String) - Method in class net.sf.basedb.core.data.ItemListSyncFilterData
-
- setName(String) - Method in class net.sf.basedb.core.data.ItemSubtypeData
-
- setName(String) - Method in class net.sf.basedb.core.data.MessageData
-
- setName(String) - Method in class net.sf.basedb.core.data.MimeTypeData
-
- setName(String) - Method in interface net.sf.basedb.core.data.NameableData
-
Set the name of the item.
- setName(String) - Method in class net.sf.basedb.core.data.NewsData
-
- setName(String) - Method in class net.sf.basedb.core.data.PlateEventTypeData
-
- setName(String) - Method in class net.sf.basedb.core.data.PlateGeometryData
-
- setName(String) - Method in class net.sf.basedb.core.data.PlatformData
-
- setName(String) - Method in class net.sf.basedb.core.data.PlatformVariantData
-
- setName(String) - Method in class net.sf.basedb.core.data.PluginDefinitionData
-
- setName(String) - Method in class net.sf.basedb.core.data.PluginTypeData
-
- setName(String) - Method in class net.sf.basedb.core.data.ProjectData
-
- setName(String) - Method in class net.sf.basedb.core.data.QuantityData
-
- setName(String) - Method in class net.sf.basedb.core.data.QuotaData
-
- setName(String) - Method in class net.sf.basedb.core.data.QuotaTypeData
-
- setName(String) - Method in class net.sf.basedb.core.data.ReporterData
-
- setName(String) - Method in class net.sf.basedb.core.data.ReporterTypeData
-
- setName(String) - Method in class net.sf.basedb.core.data.RoleData
-
- setName(String) - Method in class net.sf.basedb.core.data.RoleKeyData
-
- setName(String) - Method in class net.sf.basedb.core.data.RootRawBioAssayData
-
- setName(String) - Method in class net.sf.basedb.core.data.SettingData
-
- setName(String) - Method in class net.sf.basedb.core.data.TransformationData
-
- setName(String) - Method in class net.sf.basedb.core.data.UnitData
-
- setName(String) - Method in class net.sf.basedb.core.data.UserData
-
- setName(String) - Method in class net.sf.basedb.core.data.VersionedParameter
-
- setName(String) - Method in class net.sf.basedb.core.DataFileType
-
- setName(String) - Method in class net.sf.basedb.core.Directory
-
- setName(String) - Method in class net.sf.basedb.core.ExtraValueType
-
- setName(String) - Method in class net.sf.basedb.core.File
-
- setName(String) - Method in class net.sf.basedb.core.Group
-
- setName(String) - Method in class net.sf.basedb.core.Help
-
- setName(String) - Method in class net.sf.basedb.core.ItemSubtype
-
- setName(String) - Method in class net.sf.basedb.core.Message
-
- setName(String) - Method in class net.sf.basedb.core.MimeType
-
- setName(String) - Method in interface net.sf.basedb.core.Nameable
-
Set the name of the item.
- setName(NameableData, String) - Static method in class net.sf.basedb.core.NameableUtil
-
- setName(String) - Method in class net.sf.basedb.core.News
-
- setName(String) - Method in class net.sf.basedb.core.PlateEventType
-
- setName(String) - Method in class net.sf.basedb.core.PlateGeometry
-
- setName(String) - Method in class net.sf.basedb.core.Platform
-
- setName(String) - Method in class net.sf.basedb.core.PlatformVariant
-
- setName(String) - Method in class net.sf.basedb.core.PluginType
-
- setName(String) - Method in class net.sf.basedb.core.Project
-
- setName(String) - Method in class net.sf.basedb.core.Quantity
-
- setName(String) - Method in class net.sf.basedb.core.Quota
-
- setName(String) - Method in class net.sf.basedb.core.QuotaType
-
- setName(String) - Method in class net.sf.basedb.core.RawDataType
-
Update the name.
- setName(String) - Method in class net.sf.basedb.core.ReporterType
-
- setName(String) - Method in class net.sf.basedb.core.Role
-
- setName(String) - Method in class net.sf.basedb.core.RoleKey
-
- setName(String) - Method in class net.sf.basedb.core.RootRawBioAssay
-
- setName(String) - Method in class net.sf.basedb.core.Setting
-
Set the name for this setting.
- setName(String) - Method in class net.sf.basedb.core.SyncFilter
-
- setName(String) - Method in class net.sf.basedb.core.Transformation
-
- setName(String) - Method in class net.sf.basedb.core.Unit
-
- setName(String) - Method in class net.sf.basedb.core.User
-
- setName(String) - Method in class net.sf.basedb.plugins.executor.ParameterDefinition
-
Set the name of the parameter.
- setName(String) - Method in class net.sf.basedb.util.extensions.AboutBean
-
- setName(String) - Method in class net.sf.basedb.util.extensions.ExtensionPointBean
-
- setName(String) - Method in class net.sf.basedb.util.importer.spotdata.BaseFileInfo.ChildBioAssay
-
Set the name of the child bioassay.
- setNewAnnotations(AnnotationBatcher, boolean, boolean, boolean, boolean) - Method in class net.sf.basedb.plugins.AnnotationFlatFileImporter.NewAnnotations
-
Annotate the item with the annotation values from the file.
- setNewitem(boolean) - Method in class net.sf.basedb.clients.web.taglib.Select
-
- setNewsDate(Date) - Method in class net.sf.basedb.core.data.NewsData
-
- setNewsDate(Date) - Method in class net.sf.basedb.core.News
-
Set the date that is shown in listings.
- setNewValue(String) - Method in class net.sf.basedb.core.data.ChangeHistoryDetailData
-
- setNextCommand(String) - Method in class net.sf.basedb.core.PluginRequest
-
Sets the next command in a configuration sequence.
- setNode(String) - Method in class net.sf.basedb.core.data.JobData
-
- setNoDuplicates(boolean) - Method in class net.sf.basedb.util.annotations.InheritSpecification
-
If this flag is set (default=true), only one annotation of the specified
annotation type can be inherited.
- setNoProject() - Method in class net.sf.basedb.core.snapshot.SnapshotManager
-
Revert to the default bahavior for loading project-specific annotations.
- setNoskin(boolean) - Method in class net.sf.basedb.clients.web.taglib.Page
-
Set to TRUE to disable skins.
- setNotabs(boolean) - Method in class net.sf.basedb.clients.web.taglib.tab.TabControl
-
- setNotFound(boolean) - Method in class net.sf.basedb.util.extensions.xml.PluginInfo
-
- setNotNullDate(Date, String) - Static method in class net.sf.basedb.core.DateUtil
-
Make a copy of a Date
object.
- setNotNullString(String, String, int) - Static method in class net.sf.basedb.core.StringUtil
-
Trim and check the length of a string.
- setNullable(boolean) - Method in class net.sf.basedb.core.data.ReporterClonePropertyData
-
- setNullableDate(Date, String) - Static method in class net.sf.basedb.core.DateUtil
-
Make a copy of a Date
object.
- setNullableString(String, String, int) - Static method in class net.sf.basedb.core.StringUtil
-
Trim and check the length of a string.
- setNulltext(String) - Method in class net.sf.basedb.clients.web.taglib.PropertyValue
-
- setNullValue(String) - Method in class net.sf.basedb.util.export.TableWriter
-
Change the null value string.
- setNumArrays(int) - Method in class net.sf.basedb.core.ArrayDesign
-
Set the number of arrays on a single slide.
- setNumArrays(int) - Method in class net.sf.basedb.core.data.ArrayDesignData
-
- setNumColumns(int) - Method in class net.sf.basedb.clients.web.taglib.table.Table
-
- setNumColumns(short) - Method in class net.sf.basedb.core.data.DataCubeData
-
- setNumColumns(int) - Method in class net.sf.basedb.util.bfs.DataParser
-
Set the number of data columns that are expected to be found in this
file.
- setNumDbFeatures(int) - Method in class net.sf.basedb.core.data.ArrayDesignData
-
- setNumDecimals(SessionControl, int) - Static method in class net.sf.basedb.clients.web.formatter.FormatterSettings
-
Set the number of decimals a number formatter should display.
- setNumExtraValues(short) - Method in class net.sf.basedb.core.data.DataCubeData
-
- setNumFileFeatures(int) - Method in class net.sf.basedb.core.ArrayDesign
-
Set the number of features that are stored in files.
- setNumFileFeatures(int) - Method in class net.sf.basedb.core.data.ArrayDesignData
-
- setNumFileReporters(int) - Method in class net.sf.basedb.core.BioAssaySet
-
Set the number of unique reporters for data that is stored in files.
- setNumFileReporters(int) - Method in class net.sf.basedb.core.data.BioAssaySetData
-
- setNumFileSpots(int) - Method in class net.sf.basedb.core.BioAssay
-
Set the number of spots that are stored in files.
- setNumFileSpots(int) - Method in class net.sf.basedb.core.BioAssaySet
-
Set the number of spots that are stored in files.
- setNumFileSpots(int) - Method in class net.sf.basedb.core.data.BioAssayData
-
- setNumFileSpots(int) - Method in class net.sf.basedb.core.data.BioAssaySetData
-
- setNumFileSpots(int) - Method in class net.sf.basedb.core.data.RawBioAssayData
-
- setNumFileSpots(int) - Method in class net.sf.basedb.core.RawBioAssay
-
Set the number of spots that are stored in files.
- setNumFileValues(int) - Method in class net.sf.basedb.core.data.ExtraValueData
-
- setNumFileValues(int) - Method in class net.sf.basedb.core.ExtraValue
-
Set the number of extra values that are stored in files.
- setNumFilters(short) - Method in class net.sf.basedb.core.data.DataCubeData
-
- setNumLayers(short) - Method in class net.sf.basedb.core.data.DataCubeData
-
- setNumPositions(int) - Method in class net.sf.basedb.core.data.DataCubeData
-
- setNumPositions(int) - Method in class net.sf.basedb.core.DataCube
-
- setNumReporters(int) - Method in class net.sf.basedb.core.data.BioAssaySetData
-
- setNumSpots(int) - Method in class net.sf.basedb.core.data.BioAssayData
-
- setNumSpots(int) - Method in class net.sf.basedb.core.data.BioAssaySetData
-
- setNumValues(int) - Method in class net.sf.basedb.core.data.ExtraValueData
-
- setNumValues(int) - Method in class net.sf.basedb.core.ExtraValue
-
Called from batcher when it is closed.
- setObject(String, Object) - Method in class net.sf.basedb.core.ItemContext
-
Set a value.
- setOldValue(String) - Method in class net.sf.basedb.core.data.ChangeHistoryDetailData
-
- setOnClick(String) - Method in class net.sf.basedb.clients.web.extensions.toolbar.PermissionButtonFactory
-
- setOnItem(Subtypable) - Method in class net.sf.basedb.core.ItemSubtype
-
- setOpen(String) - Method in class net.sf.basedb.clients.web.taglib.menu.Menu
-
- setOperator(int) - Method in class net.sf.basedb.core.data.PropertyFilterData
-
- setOperator(Operator) - Method in class net.sf.basedb.core.PropertyFilter
-
Set the operator to use in the filter.
- setOption(String, String) - Method in class net.sf.basedb.core.AnnotationType
-
Set an option.
- setOption(String, String) - Method in class net.sf.basedb.plugins.executor.ParameterDefinition
-
Set the value for an option.
- setOption(Validator, String, String) - Method in class net.sf.basedb.util.overview.ValidationOptions
-
- setOption(ValidationRuleAction, String, String) - Method in class net.sf.basedb.util.overview.ValidationOptions
-
Set an option for a validator rule.
- setOptions(Map<String, String>) - Method in class net.sf.basedb.core.data.AnnotationTypeData
-
- setOrAddFile(FileStoreEnabled, DataFileType, File) - Method in class net.sf.basedb.plugins.batchimport.AbstractItemImporter
-
Set or add a file to a file set.
- setOrdinal(int) - Method in class net.sf.basedb.core.data.PlateEventTypeData
-
- setOrdinal(int) - Method in class net.sf.basedb.core.PlateEventType
-
Set the order of this event in relation to the list
of all events.
- setOrganisation(String) - Method in class net.sf.basedb.core.authentication.ExtraUserInformation
-
- setOrganisation(String) - Method in class net.sf.basedb.core.data.UserData
-
- setOrganisation(String) - Method in class net.sf.basedb.core.User
-
Set the organisation this user works for, or null if unknown.
- setOriginalBioMaterial(MeasuredBioMaterialData) - Method in class net.sf.basedb.core.data.BioWellData
-
- setOriginalQuantity(Float) - Method in class net.sf.basedb.core.data.MeasuredBioMaterialData
-
- setOriginalQuantity(Float) - Method in class net.sf.basedb.core.MeasuredBioMaterial
-
Set the original quantity of the biomaterial.
- setOriginX(int) - Method in class net.sf.basedb.core.ArrayDesignBlock
-
Set the distance from the left edge of the slide to the top left spot in this block.
- setOriginX(int) - Method in class net.sf.basedb.core.data.ArrayDesignBlockData
-
- setOriginX(Integer) - Method in class net.sf.basedb.plugins.PrintMapFlatFileImporter.MetaBlock
-
- setOriginY(int) - Method in class net.sf.basedb.core.ArrayDesignBlock
-
Set the distance from the top edge of the slide to the top left spot in this block.
- setOriginY(int) - Method in class net.sf.basedb.core.data.ArrayDesignBlockData
-
- setOriginY(Integer) - Method in class net.sf.basedb.plugins.PrintMapFlatFileImporter.MetaBlock
-
- setOutputStream(OutputStream) - Method in class net.sf.basedb.util.zip.Bzip2FilePacker
-
- setOutputStream(OutputStream) - Method in interface net.sf.basedb.util.zip.FilePacker
-
The output stream that the compressed files should be written to.
- setOutputStream(OutputStream) - Method in class net.sf.basedb.util.zip.GzipFilePacker
-
- setOutputStream(OutputStream) - Method in class net.sf.basedb.util.zip.TarFilePacker
-
Wrap the output stream in a TarOutputStream
.
- setOutputStream(OutputStream) - Method in class net.sf.basedb.util.zip.ZipFilePacker
-
- setOverrideId(int) - Method in class net.sf.basedb.core.data.AnnotationData
-
- setOverrideId(int) - Method in class net.sf.basedb.core.data.annotations.AnnotationLink
-
- setOwner(UserData) - Method in interface net.sf.basedb.core.data.OwnableData
-
Change the owner of the item.
- setOwner(UserData) - Method in class net.sf.basedb.core.data.OwnedData
-
- setOwner(User) - Method in interface net.sf.basedb.core.Ownable
-
Change the owner of the item.
- setOwner(OwnableData, User) - Static method in class net.sf.basedb.core.OwnableUtil
-
- setOwner(User) - Method in class net.sf.basedb.core.OwnedItem
-
- setOwner(DbControl, Item, Set<Integer>, User) - Static method in class net.sf.basedb.util.OwnableUtil
-
Change the owner of all specified items.
- setOwner(DbControl, Set<OwnedItem>, User) - Static method in class net.sf.basedb.util.OwnableUtil
-
Change the owner of all specified items.
- setPage(String) - Method in class net.sf.basedb.clients.web.taglib.table.Navigator
-
- setPage(int) - Method in class net.sf.basedb.clients.web.taglib.table.Navigator
-
- setPage(int) - Method in class net.sf.basedb.core.data.ContextData
-
- setPage(int) - Method in class net.sf.basedb.core.ItemContext
-
Set the current table page.
- setPageContext(PageContext) - Method in class net.sf.basedb.clients.web.taglib.Head
-
- setPageContext(PageContext) - Method in class net.sf.basedb.clients.web.taglib.Page
-
- setPageContext(PageContext) - Method in class net.sf.basedb.clients.web.taglib.StylableTag
-
Reset the dynamic attributes to make sure old ones are not
included in case the tag object is reused.
- setPageContext(PageContext) - Method in class net.sf.basedb.clients.web.taglib.tab.Tab
-
Reset the dynamic attributes to make sure old ones are not
included in case the tag object is reused.
- setParameter(String, String) - Method in class net.sf.basedb.clients.web.extensions.AbstractJspFactory
-
Generic parameter setter metod.
- setParameter(String, String) - Method in class net.sf.basedb.clients.web.extensions.ServletWrapper
-
Set the value of a servlet parameter.
- setParameter(String, boolean, Object, Type) - Method in class net.sf.basedb.core.AbstractQuery
-
- setParameter(String, Object, Type) - Method in class net.sf.basedb.core.AbstractQuery
-
- setParameter(int, Object) - Method in class net.sf.basedb.core.hibernate.EntityQueryWrapper
-
- setParameter(String, Object) - Method in class net.sf.basedb.core.hibernate.EntityQueryWrapper
-
- setParameter(int, Object, Type) - Method in class net.sf.basedb.core.hibernate.EntityQueryWrapper
-
- setParameter(String, Object, Type) - Method in class net.sf.basedb.core.hibernate.EntityQueryWrapper
-
- setParameter(int, Object) - Method in class net.sf.basedb.core.hibernate.QueryWrapper
-
- setParameter(String, Object) - Method in class net.sf.basedb.core.hibernate.QueryWrapper
-
- setParameter(int, Object, Type) - Method in class net.sf.basedb.core.hibernate.QueryWrapper
-
- setParameter(String, Object, Type) - Method in class net.sf.basedb.core.hibernate.QueryWrapper
-
- setParameter(String, Object, Type) - Method in interface net.sf.basedb.core.query.Query
-
Set the value of a query parameter.
- setParameter(String, Object) - Method in class net.sf.basedb.plugins.executor.ExternalProgramExecutor.RequestWrapper
-
- setParameter(String, String) - Method in class net.sf.basedb.util.export.spotdata.BaseFileExporter
-
Add a parameter that is exported in the 'settings' section, which
is the first section in the BASEfile.
- setParameter(String, String...) - Method in class net.sf.basedb.util.export.spotdata.BfsExporter
-
Add a parameter that is exported in the [parameters] section.
- setParameter(String, String) - Method in class net.sf.basedb.util.extensions.debug.BeanActionFactory
-
Set generic parameters.
- setParameter(String, String) - Method in class net.sf.basedb.util.extensions.debug.ProxyActionFactory
-
Set generic parameters.
- setParameterDefinition(ParameterDefinition) - Method in class net.sf.basedb.plugins.executor.ProgramParameter
-
- setParameterList(String, Collection) - Method in class net.sf.basedb.core.hibernate.EntityQueryWrapper
-
- setParameterList(String, Object[]) - Method in class net.sf.basedb.core.hibernate.EntityQueryWrapper
-
- setParameterList(String, Collection, Type) - Method in class net.sf.basedb.core.hibernate.EntityQueryWrapper
-
- setParameterList(String, Object[], Type) - Method in class net.sf.basedb.core.hibernate.EntityQueryWrapper
-
- setParameterList(String, Collection) - Method in class net.sf.basedb.core.hibernate.QueryWrapper
-
- setParameterList(String, Object[]) - Method in class net.sf.basedb.core.hibernate.QueryWrapper
-
- setParameterList(String, Collection, Type) - Method in class net.sf.basedb.core.hibernate.QueryWrapper
-
- setParameterList(String, Object[], Type) - Method in class net.sf.basedb.core.hibernate.QueryWrapper
-
- setParameters(Query, Map<String, QueryParameter>) - Method in class net.sf.basedb.core.AbstractHqlQuery
-
Set parameter values on a query.
- setParameters(PreparedStatement) - Method in class net.sf.basedb.core.AbstractSqlQuery.CountWork
-
- setParameters(PreparedStatement, List<String>, int) - Method in class net.sf.basedb.core.AbstractSqlQuery
-
Set parameter values on a prepared statement.
- setParameters(Map<String, ParameterValueData<?>>) - Method in class net.sf.basedb.core.data.JobData
-
- setParameters(Set<AnnotationTypeData>) - Method in class net.sf.basedb.core.data.ProtocolData
-
- setParameters(PreparedStatement) - Method in class net.sf.basedb.core.hibernate.ExecuteUpdateWork
-
This method should be overridden by subclasses that needs to
set parameters on the statement that is going to be executed.
- setParameters(Object[], Type[]) - Method in class net.sf.basedb.core.hibernate.QueryWrapper
-
- setParameters(PreparedStatement) - Method in class net.sf.basedb.core.hibernate.ResultSetWork
-
This method should be overridden by subclasses that needs to
set parameters on the statement that is going to be executed.
- setParameterValue(PreparedStatement, int, Object, Type) - Method in class net.sf.basedb.core.AbstractSqlQuery
-
Set a parameter value on a prepared statement.
- setParameterValue(String, ParameterType<?>, Object) - Method in class net.sf.basedb.core.Job
-
Set the value of a configuration parameter.
- setParameterValue(String, String, String, ParameterType<?>, Object) - Method in class net.sf.basedb.core.Job
-
Set the value of a configuration parameter.
- setParameterValue(String, Object) - Method in class net.sf.basedb.core.PluginRequest
-
Set the value of a request parameter to a single value.
- setParameterValues(String, ParameterType<?>, List<?>) - Method in class net.sf.basedb.core.Job
-
Set the value of a configuration parameter.
- setParameterValues(String, String, String, ParameterType<?>, List<?>) - Method in class net.sf.basedb.core.Job
-
Set the value of a configuration parameter.
- setParameterValues(String, ParameterType<?>, List<?>) - Method in class net.sf.basedb.core.PluginConfiguration
-
Set a configuration parameter.
- setParameterValues(String, String, String, ParameterType<?>, List<?>) - Method in class net.sf.basedb.core.PluginConfiguration
-
Set a configuration parameter.
- setParameterValues(String, List<?>) - Method in class net.sf.basedb.core.PluginRequest
-
Set the value of a request parameter to a list of values.
- setParameterValues2(List<Element>) - Method in class net.sf.basedb.core.PluginConfiguration
-
Sets parameters for a PluginConfiguration from the elements in a xml
configurations file.
- setParameterValuesInternal(String, String, String, ParameterType<?>, List<?>, boolean) - Method in class net.sf.basedb.core.Job
-
Set the values of a configuration parameter.
- setParameterValuesInternal(String, String, String, ParameterType<?>, List<?>, boolean) - Method in class net.sf.basedb.core.PluginConfiguration
-
Set the values of a configuration parameter.
- setParameterVersion(int) - Method in class net.sf.basedb.core.data.JobData
-
- setParameterVersion(int) - Method in class net.sf.basedb.core.data.PluginConfigurationData
-
- setParent(Renderer<? super A>) - Method in class net.sf.basedb.clients.web.extensions.renderer.PrefixSuffixRenderer
-
- setParent(DirectoryData) - Method in class net.sf.basedb.core.data.DirectoryData
-
- setParent(BioMaterialData) - Method in class net.sf.basedb.core.data.MeasuredBioMaterialData
-
- setParent(WellData) - Method in class net.sf.basedb.core.data.WellData
-
- setParent(Directory) - Method in class net.sf.basedb.core.Directory
-
Set the parent directory of this directory.
- setParent(Well) - Method in class net.sf.basedb.core.Well
-
Set the parent well.
- setParent(Renderer<? super A>) - Method in interface net.sf.basedb.util.extensions.WrappingRenderer
-
Set a parent renderer.
- setParentBioAssay(DerivedBioAssayData) - Method in class net.sf.basedb.core.data.RawBioAssayData
-
- setParentBioAssay(DerivedBioAssay) - Method in class net.sf.basedb.core.RawBioAssay
-
- setParentExtract(ExtractData) - Method in class net.sf.basedb.core.data.RawBioAssayData
-
- setParentExtract(Extract) - Method in class net.sf.basedb.core.RawBioAssay
-
Set the
Extract
this raw bioassay is created from.
- setParentFilter(Filter<? super AnnotationSnapshot>) - Method in class net.sf.basedb.core.snapshot.DisabledInheritanceFilter
-
Set a parent filter that must also be passed in order for the
this filter to pass an annotation.
- setParentHasNullReporter(boolean) - Method in class net.sf.basedb.util.importer.spotdata.BaseFileInfo
-
Set a flag indicating that at least one position in the parent bioassay
set has a null reporter.
- setParentHasZeroReporter(boolean) - Method in class net.sf.basedb.util.importer.spotdata.BaseFileInfo
-
Set a flag indicating that at least one position in the parent bioassay
set has a reporter with ID=0.
- setParentId(int) - Method in class net.sf.basedb.core.data.keyring.GroupGroups
-
Set the id of the parent group.
- setParents(Set<BioAssayData>) - Method in class net.sf.basedb.core.data.BioAssayData
-
- setParents(Set<DerivedBioAssayData>) - Method in class net.sf.basedb.core.data.DerivedBioAssayData
-
- setParents(Set<GroupData>) - Method in class net.sf.basedb.core.data.GroupData
-
- setParents(Set<ItemSubtypeData>) - Method in class net.sf.basedb.core.data.ItemSubtypeData
-
- setParents(Map<PlateData, Integer>) - Method in class net.sf.basedb.core.data.PlateData
-
- setParents(Set<Integer>) - Method in class net.sf.basedb.util.importer.spotdata.BaseFileInfo.ChildBioAssay
-
Set the parents for this child.
- setParentSet(Set<PlateData>) - Method in class net.sf.basedb.core.data.PlateData
-
- setParentType(Integer) - Method in class net.sf.basedb.core.data.MeasuredBioMaterialData
-
- setParser(int) - Method in class net.sf.basedb.core.data.FormulaData
-
- setParser(Formula.Parser) - Method in class net.sf.basedb.core.Formula
-
Set the parser used to convert the formula to an expression or restriction.
- setParticipants(Set<BioPlateEventParticipantData>) - Method in class net.sf.basedb.core.data.BioPlateEventData
-
- setPassword(String) - Method in class net.sf.basedb.core.authentication.LoginRequest
-
Set the password to use.
- setPassword(String) - Method in class net.sf.basedb.core.data.FileServerData
-
- setPassword(PasswordData) - Method in class net.sf.basedb.core.data.UserData
-
- setPassword(String) - Method in class net.sf.basedb.core.FileServer
-
Set the password to use when authenticating with the file server.
- setPassword(String) - Method in class net.sf.basedb.core.User
-
Set the password.
- setPassword(String) - Method in class net.sf.basedb.util.uri.ConnectionParameters
-
- setPasswordField(FieldInfo) - Method in class net.sf.basedb.clients.web.extensions.login.LoginFormBean
-
- setPause(String, String, Serializable) - Method in interface net.sf.basedb.core.plugin.Response
-
A plug-in can call this method to notify the core that it has been
paused.
- setPause(String, String, Serializable) - Method in class net.sf.basedb.core.PluginResponse.ResponseImpl
-
- setPause(String, String, Serializable) - Method in class net.sf.basedb.plugins.executor.ExternalProgramExecutor.ResponseWrapper
-
- setPercentComplete(int) - Method in class net.sf.basedb.core.data.JobData
-
- setPermanentEntityParameter(String, BasicItem) - Method in class net.sf.basedb.core.AbstractHqlQuery
-
- setPermanentEntityParameter(String, BasicItem) - Method in interface net.sf.basedb.core.query.HqlQuery
-
Permanently set the value of an entity parameter.
- setPermanentParameter(String, Object, Type) - Method in class net.sf.basedb.core.AbstractQuery
-
- setPermanentParameter(String, Object, Type) - Method in interface net.sf.basedb.core.query.Query
-
Permanently set the value of a query parameter.
- setPermission(int) - Method in class net.sf.basedb.core.data.keyring.KeyPermission
-
Set the permission.
- setPermission(int) - Method in class net.sf.basedb.core.data.keyring.ProjectPermission
-
Set the permission.
- setPermissions(Map<RoleKeyData, PluginPermission>) - Method in class net.sf.basedb.core.data.PluginDefinitionData
-
- setPermissions(Group, Set<Permission>) - Method in class net.sf.basedb.core.GroupPermissions
-
Grant permissions to a group.
- setPermissions(Item, int, ItemKeyData, ProjectKeyData) - Static method in class net.sf.basedb.core.Install
-
- setPermissions(User, Set<Permission>) - Method in class net.sf.basedb.core.MultiPermissions
-
Grant permissions to a user.
- setPermissions(Group, Set<Permission>) - Method in class net.sf.basedb.core.MultiPermissions
-
Grant permissions to a group.
- setPermissions(Project, Set<Permission>) - Method in class net.sf.basedb.core.MultiPermissions
-
Grant permissions to a project.
- setPermissions(RoleKey, Set<Permission>, Set<Permission>) - Method in class net.sf.basedb.core.PluginDefinition
-
Sets the permissions for this plugin.
- setPermissions(User, Set<Permission>) - Method in class net.sf.basedb.core.Project
-
Grant a user permissions to this project.
- setPermissions(Group, Set<Permission>) - Method in class net.sf.basedb.core.Project
-
Grant a group permissions to this project.
- setPermissions(Project, Set<Permission>) - Method in class net.sf.basedb.core.ProjectPermissions
-
Grant permissions to a project.
- setPermissions(Role, Set<Permission>) - Method in class net.sf.basedb.core.RoleKey
-
Grant permissions to a role.
- setPermissions(User, Set<Permission>) - Method in class net.sf.basedb.core.UserPermissions
-
Grant permissions to a user.
- setPermissions - Variable in class net.sf.basedb.plugins.PluginConfigurationImporter
-
- setPermissionsParameter - Static variable in class net.sf.basedb.plugins.PluginConfigurationImporter
-
- setPermissionTemplate(PermissionTemplateData) - Method in class net.sf.basedb.core.data.ProjectData
-
- setPermissionTemplate(PermissionTemplate) - Method in class net.sf.basedb.core.Project
-
Set the permission template that should be used to share new items when
this project is active.
- setPhone(String) - Method in class net.sf.basedb.core.authentication.ExtraUserInformation
-
- setPhone(String) - Method in class net.sf.basedb.core.data.UserData
-
- setPhone(String) - Method in class net.sf.basedb.core.User
-
Set the phone number to the user, or null if unknown.
- setPhysicalBioAssay(PhysicalBioAssay) - Method in class net.sf.basedb.core.BioMaterialEvent
-
Set the hybidization that was created by this event.
- setPhysicalBioAssay(PhysicalBioAssayData) - Method in class net.sf.basedb.core.data.ArraySlideData
-
- setPhysicalBioAssay(PhysicalBioAssayData) - Method in class net.sf.basedb.core.data.BioMaterialEventData
-
- setPhysicalBioAssays(Set<PhysicalBioAssayData>) - Method in class net.sf.basedb.core.data.DerivedBioAssayData
-
- setPlaceHolder(String) - Method in class net.sf.basedb.clients.web.extensions.login.FieldInfo
-
- setPlate(PlateData) - Method in class net.sf.basedb.core.data.ArrayDesignPlateData
-
- setPlate(int) - Method in class net.sf.basedb.core.data.MappingCoordinate
-
Set the plate number.
- setPlate(PlateData) - Method in class net.sf.basedb.core.data.PlateEventData
-
- setPlate(PlateData) - Method in class net.sf.basedb.core.data.WellData
-
- setPlate(Plate) - Method in class net.sf.basedb.core.PlateEvent
-
Set the plate owning this event.
- setPlateEvents(Set<PlateEventData>) - Method in class net.sf.basedb.core.data.PlateEventTypeData
-
- setPlateEventType(PlateEventTypeData) - Method in class net.sf.basedb.core.data.PlateEventData
-
- setPlateEventType(PlateEventType) - Method in class net.sf.basedb.core.PlateEvent
-
Set the plate event type of this event.
- setPlateGeometry(PlateGeometry) - Method in class net.sf.basedb.core.BioPlate
-
- setPlateGeometry(PlateGeometryData) - Method in class net.sf.basedb.core.data.BioPlateData
-
- setPlateGeometry(PlateGeometryData) - Method in class net.sf.basedb.core.data.PlateTypeData
-
- setPlateGeometry(PlateGeometry) - Method in class net.sf.basedb.core.PlateType
-
Set the plate geometry of this plate type.
- setPlateList(List<Plate>) - Method in class net.sf.basedb.core.ArrayDesign
-
Set the list of plates to be used by this array design.
- setPlateMapping(PlateMappingData) - Method in class net.sf.basedb.core.data.PlateData
-
- setPlates(Set<ArrayDesignPlateData>) - Method in class net.sf.basedb.core.data.ArrayDesignData
-
- setPlates(Set<PlateData>) - Method in class net.sf.basedb.core.data.PlateTypeData
-
- setPlateType(PlateTypeData) - Method in class net.sf.basedb.core.data.PlateData
-
- setPlateType(PlateTypeData) - Method in class net.sf.basedb.core.data.PlateEventTypeData
-
- setPlateType(PlateType) - Method in class net.sf.basedb.core.Plate
-
Set the plate type of this plate.
- setPlateType(PlateType) - Method in class net.sf.basedb.core.PlateEventType
-
Set the plate type owning this event type.
- setPlateTypes(Set<PlateTypeData>) - Method in class net.sf.basedb.core.data.PlateGeometryData
-
- setPlatform(Platform) - Method in class net.sf.basedb.core.ArrayDesign
-
Set the platform of the array design.
- setPlatform(PlatformData) - Method in class net.sf.basedb.core.data.ArrayDesignData
-
- setPlatform(PlatformData) - Method in class net.sf.basedb.core.data.PlatformFileTypeData
-
- setPlatform(PlatformData) - Method in class net.sf.basedb.core.data.PlatformVariantData
-
- setPlatform(PlatformData) - Method in class net.sf.basedb.core.data.RawBioAssayData
-
- setPlatform(Platform) - Method in class net.sf.basedb.core.PlatformVariant
-
- setPlatform(Platform, RawDataType) - Method in class net.sf.basedb.core.RawBioAssay
-
Set the platform and raw data type of the raw bioassay.
- setPlatforms(Set<PlatformFileTypeData>) - Method in class net.sf.basedb.core.data.DataFileTypeData
-
- setPlotGenerators(PlotGenerator[]) - Method in class net.sf.basedb.clients.web.extensions.plot.OverviewPlotBean
-
- setPlotServler(String) - Method in class net.sf.basedb.clients.web.extensions.plot.MAPlotFactory
-
- setPlugin(PluginDefinitionData) - Method in class net.sf.basedb.core.data.ChangeHistoryData
-
- setPluginConfiguration(PluginConfigurationData) - Method in class net.sf.basedb.core.data.JobData
-
- setPluginConfiguration(PluginConfiguration) - Method in class net.sf.basedb.core.Job
-
Set the plugin configuration of this job.
- setPluginDefinition(PluginDefinitionData) - Method in class net.sf.basedb.core.data.JobAgentSettingsData
-
- setPluginDefinition(PluginDefinitionData) - Method in class net.sf.basedb.core.data.JobData
-
- setPluginDefinition(PluginDefinitionData) - Method in class net.sf.basedb.core.data.PluginConfigurationData
-
- setPluginDefinition(PluginDefinition) - Method in class net.sf.basedb.core.Job
-
Set the plugin configuration of this job.
- setPluginDefinition(PluginDefinition) - Method in class net.sf.basedb.core.JobAgentSettings
-
- setPluginDefinition(PluginDefinition) - Method in class net.sf.basedb.core.PluginConfiguration
-
The definition cannot be changed.
- setPluginDefinitionId(int) - Method in class net.sf.basedb.core.data.keyring.PluginKeys
-
Sets the PluginDefinition
:s ID
- setPluginId(Integer) - Method in class net.sf.basedb.core.data.ChangeHistoryData
-
- setPlugins(Map<PluginDefinitionData, JobAgentSettingsData>) - Method in class net.sf.basedb.core.data.JobAgentData
-
- setPlugins(Set<PluginDefinitionData>) - Method in class net.sf.basedb.core.data.PluginTypeData
-
- setPluginTypes(Set<PluginTypeData>) - Method in class net.sf.basedb.core.data.PluginDefinitionData
-
- setPluginVersion(String) - Method in class net.sf.basedb.core.data.JobData
-
- setPluginVersion(String) - Method in class net.sf.basedb.core.Job
-
Set the version of the plugin that executes the job.
- setPort(Integer) - Method in class net.sf.basedb.core.data.JobAgentData
-
- setPort(Integer) - Method in class net.sf.basedb.core.JobAgent
-
Set the port the job agent is listening on.
- setPosition(String) - Method in class net.sf.basedb.clients.web.taglib.tab.TabControl
-
- setPosition(int) - Method in class net.sf.basedb.core.BioMaterialEventSource
-
- setPosition(String) - Method in class net.sf.basedb.core.BioPlate
-
Set the position within the "storage location" for this bioplate.
- setPosition(int) - Method in class net.sf.basedb.core.data.ArrayDesignPlateData
-
- setPosition(int) - Method in class net.sf.basedb.core.data.BioMaterialEventSourceData
-
- setPosition(String) - Method in class net.sf.basedb.core.data.BioPlateData
-
- setPosition(int) - Method in class net.sf.basedb.core.data.FeatureData
-
This method was private until 2.6.
- setPosition(int) - Method in class net.sf.basedb.core.data.RawData
-
This method was private before 2.6.
- setPositionIndex(int) - Method in class net.sf.basedb.clients.web.ExperimentExplorer
-
Set the index of the curren position.
- setPositionIndex(int) - Method in class net.sf.basedb.util.importer.spotdata.BaseFileInfo.SpotSectionInfo
-
Set the column index of the 'position' data column.
- setPrefix(String) - Method in class net.sf.basedb.clients.web.taglib.table.CellValue
-
- setPrefix(String) - Method in class net.sf.basedb.util.bfs.SequenceFilenameGenerator
-
Set the prefix that is used for file name generation.
- setPrepared(String, JobAgent) - Method in class net.sf.basedb.core.Job
-
- setPrintRobot(Hardware) - Method in class net.sf.basedb.core.ArrayBatch
-
- setPrintRobot(HardwareData) - Method in class net.sf.basedb.core.data.ArrayBatchData
-
- setPriority(int) - Method in class net.sf.basedb.core.data.JobData
-
- setPriority(int) - Method in class net.sf.basedb.core.Job
-
Set the priority of the job.
- setPriorityBoost(int) - Method in class net.sf.basedb.core.data.JobAgentSettingsData
-
- setPriorityBoost(int) - Method in class net.sf.basedb.core.JobAgentSettings
-
Set the priority boost given to jobs executed by this plugin.
- setProducts(Set<BioAssaySetData>) - Method in class net.sf.basedb.core.data.TransformationData
-
- setProgress(int, String) - Method in class net.sf.basedb.core.Job
-
Set the progress of the job.
- setProgress(long, String) - Method in class net.sf.basedb.util.basefile.BaseFileParser
-
Update the progress of the parsing.
- setProgress(int, String) - Method in class net.sf.basedb.util.export.spotdata.AbstractBioAssaySetExporter
-
Update the progress of the export.
- setProgress(int, String) - Method in class net.sf.basedb.util.importer.spotdata.BaseFileImporter
-
Update the progress of the export.
- setProgress(int, String) - Method in class net.sf.basedb.util.importer.spotdata.BfsImporter
-
Update the progress of the export.
- setProgressReporter(Job.ProgressReporterImpl) - Method in class net.sf.basedb.core.PluginConfigurationRequest
-
- setProgressReporter(Job.ProgressReporterImpl) - Method in class net.sf.basedb.core.PluginExecutionRequest
-
Initialise a progress reporter that the plugin can use to store
progress information in the database.
- setProgressReporter(ProgressReporter) - Method in class net.sf.basedb.util.annotations.RunnableInheritAnnotationsManager
-
Set the progress reporter to use for reporting progress.
- setProgressReporter(AbsoluteProgressReporter) - Method in class net.sf.basedb.util.basefile.BaseFileParser
-
Set a progress reporter that will be used to report
how the parsing is progressing.
- setProgressReporter(ProgressReporter) - Method in class net.sf.basedb.util.export.spotdata.AbstractBioAssaySetExporter
-
Set the progress reporter that is used to report progress.
- setProgressReporter(ProgressReporter) - Method in class net.sf.basedb.util.importer.spotdata.BaseFileImporter
-
Set the progress reporter that is used to report progress.
- setProgressReporter(ProgressReporter) - Method in class net.sf.basedb.util.importer.spotdata.BfsImporter
-
Set the progress reporter that is used to report progress.
- setProject(ProjectData) - Method in class net.sf.basedb.core.data.ChangeHistoryData
-
- setProject(Project) - Method in class net.sf.basedb.core.snapshot.SnapshotManager
-
When a project is set, the snapshot manager will only
search for project-specific annotations explicitely belonging
to that project (or default values if project == null).
- setProjectAnnotations(boolean) - Method in class net.sf.basedb.core.AnnotationType
-
If this flag is set, annotation values can be set per project.
- setProjectAnnotations(boolean) - Method in class net.sf.basedb.core.data.AnnotationTypeData
-
- setProjectDefaults(Project) - Method in class net.sf.basedb.core.ArrayBatch
-
Set print robot and protocol from project default settings.
- setProjectDefaults(Project) - Method in class net.sf.basedb.core.BasicItem
-
This method is called before inserting new items into the database
to allow items to propagate default values from the active project.
- setProjectDefaults(Project) - Method in class net.sf.basedb.core.BioMaterialEvent
-
Set protocol and hardware from project default settings.
- setProjectDefaults(Map<String, String>) - Method in class net.sf.basedb.core.data.ProjectData
-
- setProjectDefaults(Project) - Method in class net.sf.basedb.core.DerivedBioAssay
-
Set protocol, hardware and software from project default settings.
- setProjectDefaults(Project) - Method in class net.sf.basedb.core.RawBioAssay
-
Set software, protocol and array design from project default settings.
- setProjectId(int) - Method in class net.sf.basedb.core.Annotation
-
Set the project that this annotation value should
belong to.
- setProjectId(int) - Method in class net.sf.basedb.core.data.AnnotationData
-
- setProjectId(int) - Method in class net.sf.basedb.core.data.annotations.AnnotationLink
-
- setProjectId(Integer) - Method in class net.sf.basedb.core.data.ChangeHistoryData
-
- setProjectId(int) - Method in class net.sf.basedb.core.data.keyring.ProjectKeys
-
Set the id of the project.
- setProjectId(int) - Method in class net.sf.basedb.core.data.keyring.ProjectPermission
-
Set the id of the project.
- setProjectKey(ProjectKeyData) - Method in interface net.sf.basedb.core.data.ShareableData
-
- setProjectKey(ProjectKeyData) - Method in class net.sf.basedb.core.data.SharedData
-
- setProjectKey(ProjectKey) - Method in interface net.sf.basedb.core.Shareable
-
- setProjectKey(ShareableData, ProjectKey) - Static method in class net.sf.basedb.core.ShareableUtil
-
- setProjectKey(ProjectKey) - Method in class net.sf.basedb.core.SharedItem
-
- setProjectKeys(Set<ProjectKeyData>) - Method in class net.sf.basedb.core.data.ProjectData
-
- setProjects(Set<ProjectData>) - Method in class net.sf.basedb.core.data.GroupData
-
- setProjects(Set<ProjectData>) - Method in class net.sf.basedb.core.data.PermissionTemplateData
-
- setProjects(Map<ProjectData, Integer>) - Method in class net.sf.basedb.core.data.ProjectKeyData
-
- setProjects(Set<ProjectData>) - Method in class net.sf.basedb.core.data.UserData
-
- setPrompt(String) - Method in class net.sf.basedb.clients.web.extensions.login.FieldInfo
-
- setProperties(Map<String, ReporterClonePropertyData>) - Method in class net.sf.basedb.core.data.ReporterCloneTemplateData
-
- setProperties(Object) - Method in class net.sf.basedb.core.hibernate.QueryWrapper
-
- setProperties(Map) - Method in class net.sf.basedb.core.hibernate.QueryWrapper
-
- setProperty(String) - Method in class net.sf.basedb.clients.web.extensions.list.AbstractListColumnBean
-
- setProperty(String) - Method in class net.sf.basedb.clients.web.extensions.list.PropertyPathActionFactory
-
- setProperty(String) - Method in class net.sf.basedb.clients.web.taglib.PropertyValue
-
- setProperty(String) - Method in class net.sf.basedb.clients.web.taglib.table.ColumnDef
-
- setProperty(String, String) - Static method in class net.sf.basedb.core.Config
-
Programatically set a configuration property that overrides a configuration
setting in the base.config file.
- setProperty(String) - Method in class net.sf.basedb.util.export.spotdata.AssayPropertyField
-
Set the property that should be exported.
- setProperty(String, String) - Method in class net.sf.basedb.util.extensions.xml.PluginInfo
-
- setPropertyFilter(PropertyFilter) - Method in class net.sf.basedb.core.ItemContext
-
Set a property filter.
- setPropertyFilters(Map<String, PropertyFilterData>) - Method in class net.sf.basedb.core.data.ContextData
-
- setPropertyFilters(Map<String, PropertyFilterData>) - Method in class net.sf.basedb.core.data.ItemListSyncFilterData
-
- setPropertyInspector(Filter<String>) - Method in class net.sf.basedb.core.ItemContext
-
Set a filter for this context that is used to inspect which properties
that are allowed to be used in queries.
- setPropertyValue(D, String, Object) - Method in class net.sf.basedb.core.BasicBatcher
-
Set a protected property value on a data object using Hibernate
built-in reflection methods.
- setProtocol(Protocol) - Method in class net.sf.basedb.core.ArrayBatch
-
Set the
Protocol
used for printing the arrays.
- setProtocol(Protocol) - Method in class net.sf.basedb.core.BioMaterialEvent
-
Set the
Protocol
that describes the procedure used in this event.
- setProtocol(Protocol) - Method in class net.sf.basedb.core.BioPlateEvent
-
Set the
Protocol
that describes the procedure used in this event.
- setProtocol(ProtocolData) - Method in class net.sf.basedb.core.data.ArrayBatchData
-
- setProtocol(ProtocolData) - Method in class net.sf.basedb.core.data.BioMaterialEventData
-
- setProtocol(ProtocolData) - Method in class net.sf.basedb.core.data.BioPlateEventData
-
- setProtocol(ProtocolData) - Method in class net.sf.basedb.core.data.DerivedBioAssayData
-
- setProtocol(ProtocolData) - Method in class net.sf.basedb.core.data.PlateEventData
-
- setProtocol(ProtocolData) - Method in class net.sf.basedb.core.data.RawBioAssayData
-
- setProtocol(Protocol) - Method in class net.sf.basedb.core.DerivedBioAssay
-
Set the
Protocol
that describes the procedure used when
creating this bioassay set.
- setProtocol(Protocol) - Method in class net.sf.basedb.core.PlateEvent
-
Set the protocol that was followed in this event.
- setProtocol(Protocol) - Method in class net.sf.basedb.core.RawBioAssay
-
Set the
Protocol
used while analysing the scanned images.
- setProtocolParameter(boolean) - Method in class net.sf.basedb.core.AnnotationType
-
Specify if this annotation type should be used as a protocol parameter
or as a regular annotation type
- setProtocolParameter(boolean) - Method in class net.sf.basedb.core.data.AnnotationTypeData
-
- setProtocols(Set<ProtocolData>) - Method in class net.sf.basedb.core.data.AnnotationTypeData
-
- setProtocolType(ItemSubtypeData) - Method in class net.sf.basedb.core.data.PlateEventTypeData
-
- setProtocolType(ItemSubtype) - Method in class net.sf.basedb.core.PlateEventType
-
Set the protocol type of this PlateTypeEvent
item.
- setPublic(boolean) - Method in class net.sf.basedb.core.data.ContextData
-
- setPublication(String) - Method in class net.sf.basedb.core.data.ExperimentData
-
- setPublication(String) - Method in class net.sf.basedb.core.Experiment
-
Set publication text.
- setPublicationDate(Date) - Method in class net.sf.basedb.core.data.ExperimentData
-
- setPublicationDate(Date) - Method in class net.sf.basedb.core.Experiment
-
Set the date this experiment was published.
- setPubMedId(String) - Method in class net.sf.basedb.core.data.ExperimentData
-
- setPubMedId(String) - Method in class net.sf.basedb.core.Experiment
-
Set the PubMed ID of the publication.
- setPushAnnotations(boolean) - Method in class net.sf.basedb.core.data.ItemSubtypeData
-
- setPushAnnotations(boolean) - Method in class net.sf.basedb.core.ItemSubtype
-
- setQuality(float) - Method in class net.sf.basedb.core.data.SpotImagesData
-
- setQuality(float) - Method in class net.sf.basedb.core.SpotImages
-
- setQuantity(QuantityData) - Method in class net.sf.basedb.core.data.AnnotationTypeData
-
- setQuantity(QuantityData) - Method in class net.sf.basedb.core.data.UnitData
-
- setQuantity(QuantityData) - Method in class net.sf.basedb.core.data.UnitSymbolData
-
- setQuantity(Quantity) - Method in class net.sf.basedb.core.Unit
-
- setQuery(Query) - Method in class net.sf.basedb.core.ItemContext
-
- setQuota(QuotaData) - Method in class net.sf.basedb.core.data.GroupData
-
- setQuota(QuotaData) - Method in class net.sf.basedb.core.data.UserData
-
- setQuota(Quota) - Method in class net.sf.basedb.core.Group
-
Set the quota for the group.
- setQuota(Quota) - Method in class net.sf.basedb.core.User
-
Set the quota for the user.
- setQuotaGroup(GroupData) - Method in class net.sf.basedb.core.data.UserData
-
- setQuotaGroup(Group) - Method in class net.sf.basedb.core.User
-
Set the group whose quota should be checked for disk consuming
items.
- setQuotaType(QuotaTypeData) - Method in class net.sf.basedb.core.data.DiskUsageData
-
- setQuotaType(QuotaTypeData) - Method in class net.sf.basedb.core.data.QuotaIndex
-
- setQuotaValue(QuotaType, Location, long) - Method in class net.sf.basedb.core.Quota
-
Set the quota for the specified type, location and size.
- setQuotaValues(Set<QuotaIndex>) - Method in class net.sf.basedb.core.data.QuotaData
-
- setRange(int, int) - Method in class net.sf.basedb.util.ChainedProgressReporter
-
Set the range to use for the percentage values.
- setRawBioAssay(RawBioAssayData) - Method in class net.sf.basedb.core.data.RawData
-
- setRawBioAssay(RawBioAssayData) - Method in class net.sf.basedb.core.data.RootRawBioAssayData
-
- setRawBioAssay(RawBioAssayData) - Method in class net.sf.basedb.core.data.SpotImagesData
-
- setRawBioAssay(RawBioAssay) - Method in class net.sf.basedb.core.SpotImages
-
Set the raw bioassay the spot images belongs to.
- setRawBioAssays(Set<RawBioAssayData>) - Method in class net.sf.basedb.core.data.DerivedBioAssayData
-
- setRawBioAssays(Set<RawBioAssayData>) - Method in class net.sf.basedb.core.data.ExperimentData
-
- setRawBioAssays(Set<RawBioAssayData>) - Method in class net.sf.basedb.core.data.ExtractData
-
- setRawBioAssays(Set<RawBioAssayData>) - Method in class net.sf.basedb.core.data.JobData
-
- setRawData(RawData) - Method in class net.sf.basedb.util.jep.MeanFunction
-
Set a new raw data object that will be used the next time the
JEP expression is evaluated.
- setRawData(RawData) - Method in class net.sf.basedb.util.jep.RawFunction
-
Set a new raw data object that will be used the next time the
JEP expression is evaluated.
- setRawDataType(String) - Method in class net.sf.basedb.core.data.ExperimentData
-
- setRawDataType(String) - Method in class net.sf.basedb.core.data.FormulaData
-
- setRawDataType(String) - Method in class net.sf.basedb.core.data.ItemListData
-
- setRawDataType(String) - Method in class net.sf.basedb.core.data.PlatformData
-
- setRawDataType(String) - Method in class net.sf.basedb.core.data.PlatformVariantData
-
- setRawDataType(String) - Method in class net.sf.basedb.core.data.RawBioAssayData
-
- setRawDataType(RawDataType) - Method in class net.sf.basedb.core.Experiment
-
Set the raw data type.
- setRawDataType(RawDataType) - Method in class net.sf.basedb.core.Formula
-
Set the raw data type this formula can be used on.
- setRawDataType(RawDataType) - Method in class net.sf.basedb.core.ItemList
-
Set the raw data type of raw bioassays that can be members in this list.
- setRawDataType(RawDataType) - Method in class net.sf.basedb.core.Platform
-
Set the raw data type.
- setRawDataType(RawDataType) - Method in class net.sf.basedb.core.PlatformVariant
-
Set the raw data type.
- setRawParents(Set<RawBioAssayData>) - Method in class net.sf.basedb.core.data.BioAssayData
-
- setRawSources(Set<RawBioAssayData>) - Method in class net.sf.basedb.core.data.TransformationData
-
- setRawSources(Collection<RawBioAssay>) - Method in class net.sf.basedb.core.Transformation
-
Set the raw bioassay sources used in this transformation.
- setRead(boolean) - Method in class net.sf.basedb.core.data.MessageData
-
- setRead(boolean) - Method in class net.sf.basedb.core.Message
-
Set read status of the message.
- setReadOnly(boolean) - Method in class net.sf.basedb.core.hibernate.QueryWrapper
-
- setReadOnly(Object, boolean) - Method in class net.sf.basedb.core.hibernate.SessionWrapper
-
- setRecent(List<? extends BasicItem>) - Method in class net.sf.basedb.clients.web.taglib.Select
-
- setRecent(BasicItem, int) - Method in class net.sf.basedb.core.ItemContext
-
Add an item to the "recently used items" list.
- setRecent(BasicItem, ItemSubtype, int) - Method in class net.sf.basedb.core.ItemContext
-
Add an item to the "recently used items" list when used for a specific
item subtype.
- setRecent(BasicItem, String, int) - Method in class net.sf.basedb.core.ItemContext
-
Add an item to the "recently used items" list.
- setRecent(String, String, int) - Method in class net.sf.basedb.core.ItemContext
-
Add a value to the list of recently used values for the specified key.
- setRecent(String, List<String>) - Method in class net.sf.basedb.core.ItemContext
-
- setRedefinedColumnName(String, String, String) - Method in class net.sf.basedb.util.basefile.BaseFileParser
-
Redefined a column name for a specified section.
- setRedImageFile(FileData) - Method in class net.sf.basedb.core.data.SpotImagesData
-
- setRedImageFile(File) - Method in class net.sf.basedb.core.SpotImages
-
- setReferenceFactor(double) - Method in class net.sf.basedb.core.data.UnitData
-
- setReferenceOffset(double) - Method in class net.sf.basedb.core.data.UnitData
-
- setReferenceUnit(String) - Method in class net.sf.basedb.core.data.QuantityData
-
- setReferenceUnit(String) - Method in class net.sf.basedb.core.Quantity
-
Sets the reference unit.
- setRelatedSubtype(ItemSubtype) - Method in class net.sf.basedb.core.ItemSubtype
-
Set a subtype that is related to this subtype.
- setRelatedSubtypes(Map<Integer, ItemSubtypeData>) - Method in class net.sf.basedb.core.data.ItemSubtypeData
-
- setReload(boolean) - Method in class net.sf.basedb.core.Keyring
-
- setRemainingQuantity(Float) - Method in class net.sf.basedb.core.data.MeasuredBioMaterialData
-
- setRemember(boolean) - Method in class net.sf.basedb.clients.web.taglib.tab.TabControl
-
- setRememberLast(String) - Method in class net.sf.basedb.util.extensions.LoggingErrorHandlerFactory
-
Set a flag indicating if errors should be remembered
by the registry.
- setRememberLastLogin(boolean) - Method in class net.sf.basedb.clients.web.extensions.login.LoginFormBean
-
- setRemoteId(String) - Method in class net.sf.basedb.core.data.SessionData
-
- setRemove(boolean) - Method in class net.sf.basedb.util.annotations.InheritSpecification
-
Set a flag to remove all inherited annotations of the specified annotation type.
- setRemoved(boolean) - Method in class net.sf.basedb.core.BioAssaySet
-
- setRemoved(boolean) - Method in class net.sf.basedb.core.BioPlateEventType
-
- setRemoved(boolean) - Method in class net.sf.basedb.core.BioPlateType
-
- setRemoved(boolean) - Method in class net.sf.basedb.core.CommonItem
-
- setRemoved(boolean) - Method in class net.sf.basedb.core.DataFileType
-
- setRemoved(boolean) - Method in class net.sf.basedb.core.Directory
-
- setRemoved(boolean) - Method in class net.sf.basedb.core.ExtraValueType
-
- setRemoved(boolean) - Method in class net.sf.basedb.core.Group
-
- setRemoved(boolean) - Method in class net.sf.basedb.core.ItemSubtype
-
- setRemoved(boolean) - Method in class net.sf.basedb.core.Message
-
- setRemoved(boolean) - Method in class net.sf.basedb.core.MimeType
-
- setRemoved(boolean) - Method in class net.sf.basedb.core.News
-
- setRemoved(boolean) - Method in class net.sf.basedb.core.PlateEventType
-
- setRemoved(boolean) - Method in class net.sf.basedb.core.PlateGeometry
-
- setRemoved(boolean) - Method in class net.sf.basedb.core.Platform
-
- setRemoved(boolean) - Method in class net.sf.basedb.core.PlatformVariant
-
- setRemoved(boolean) - Method in class net.sf.basedb.core.PluginDefinition
-
- setRemoved(boolean) - Method in class net.sf.basedb.core.PluginType
-
- setRemoved(boolean) - Method in class net.sf.basedb.core.Project
-
- setRemoved(boolean) - Method in class net.sf.basedb.core.Quantity
-
- setRemoved(boolean) - Method in class net.sf.basedb.core.Quota
-
- setRemoved(boolean) - Method in interface net.sf.basedb.core.Removable
-
Set the removed flag for this item.
- setRemoved(boolean) - Method in class net.sf.basedb.core.ReporterType
-
- setRemoved(boolean) - Method in class net.sf.basedb.core.Role
-
- setRemoved(boolean) - Method in class net.sf.basedb.core.Transformation
-
- setRemoved(boolean) - Method in class net.sf.basedb.core.Unit
-
- setRemoved(boolean) - Method in class net.sf.basedb.core.User
-
- setRemoved(DbControl, Item, Set<Integer>, boolean) - Static method in class net.sf.basedb.util.RemovableUtil
-
- setRemovedBy(Integer) - Method in class net.sf.basedb.core.data.BioAssaySetData
-
- setRemovedBy(Integer) - Method in class net.sf.basedb.core.data.BioPlateEventTypeData
-
- setRemovedBy(Integer) - Method in class net.sf.basedb.core.data.BioPlateTypeData
-
- setRemovedBy(Integer) - Method in class net.sf.basedb.core.data.CommonData
-
- setRemovedBy(Integer) - Method in class net.sf.basedb.core.data.DataFileTypeData
-
- setRemovedBy(Integer) - Method in class net.sf.basedb.core.data.ExtraValueTypeData
-
- setRemovedBy(Integer) - Method in class net.sf.basedb.core.data.GroupData
-
- setRemovedBy(Integer) - Method in class net.sf.basedb.core.data.ItemSubtypeData
-
- setRemovedBy(Integer) - Method in class net.sf.basedb.core.data.MessageData
-
- setRemovedBy(Integer) - Method in class net.sf.basedb.core.data.MimeTypeData
-
- setRemovedBy(Integer) - Method in class net.sf.basedb.core.data.NewsData
-
- setRemovedBy(Integer) - Method in class net.sf.basedb.core.data.PlateEventTypeData
-
- setRemovedBy(Integer) - Method in class net.sf.basedb.core.data.PlateGeometryData
-
- setRemovedBy(Integer) - Method in class net.sf.basedb.core.data.PlatformData
-
- setRemovedBy(Integer) - Method in class net.sf.basedb.core.data.PlatformVariantData
-
- setRemovedBy(Integer) - Method in class net.sf.basedb.core.data.PluginDefinitionData
-
- setRemovedBy(Integer) - Method in class net.sf.basedb.core.data.PluginTypeData
-
- setRemovedBy(Integer) - Method in class net.sf.basedb.core.data.ProjectData
-
- setRemovedBy(Integer) - Method in class net.sf.basedb.core.data.QuantityData
-
- setRemovedBy(Integer) - Method in class net.sf.basedb.core.data.QuotaData
-
- setRemovedBy(Integer) - Method in interface net.sf.basedb.core.data.RemovableData
-
Set the ID of the user that removed this item or null
to restore the item.
- setRemovedBy(Integer) - Method in class net.sf.basedb.core.data.ReporterTypeData
-
- setRemovedBy(Integer) - Method in class net.sf.basedb.core.data.RoleData
-
- setRemovedBy(Integer) - Method in class net.sf.basedb.core.data.TransformationData
-
- setRemovedBy(Integer) - Method in class net.sf.basedb.core.data.UnitData
-
- setRemovedBy(Integer) - Method in class net.sf.basedb.core.data.UserData
-
- setRemovedFlag(Removable, boolean) - Static method in class net.sf.basedb.util.RemovableUtil
-
- setRemoveJobWhenFinished(boolean) - Method in class net.sf.basedb.core.data.JobData
-
- setRemoveJobWhenFinished(boolean) - Method in class net.sf.basedb.core.Job
-
Set if the job should be deleted after it has finished successfully.
- setRenderer(Renderer<?>) - Method in class net.sf.basedb.clients.web.taglib.extensions.Render
-
- setRendererFactory(RendererFactory<? super A>) - Method in class net.sf.basedb.util.extensions.ExtensionBean
-
- setRendererFactory(RendererFactory<? super A>) - Method in class net.sf.basedb.util.extensions.ExtensionPointBean
-
- setReplaceExisting(boolean) - Method in class net.sf.basedb.util.annotations.InheritSpecification
-
If this flag is set (default=false), existing inherited annotations
of the specified annotation type are removed before inheriting new
ones.
- setReporter(ReporterData) - Method in class net.sf.basedb.core.data.FeatureData
-
- setReporter(ReporterData) - Method in class net.sf.basedb.core.data.RawData
-
- setReporter(ReporterData) - Method in class net.sf.basedb.core.data.ReporterListScoreData
-
- setReporter(ReporterData) - Method in class net.sf.basedb.core.data.WellData
-
- setReporter(ReporterData) - Method in class net.sf.basedb.core.Well
-
Set the reporter of this well.
- setReporter(ReporterData) - Method in class net.sf.basedb.util.jep.ReporterFunction
-
Set a new reporter object that will be used the next time the
JEP expression is evaluated.
- setReporterAnnotationsWriter(AnnotationWriter) - Method in class net.sf.basedb.util.export.spotdata.BfsExporter
-
Set the stream were reporter annotations should be written.
- setReporterCloneTemplate(ReporterCloneTemplateData) - Method in class net.sf.basedb.core.data.VirtualDbData
-
- setReporterId(int) - Method in class net.sf.basedb.core.data.ReporterListScoreData
-
- setReporterIndex(int) - Method in class net.sf.basedb.clients.web.ExperimentExplorer
-
Set the index of the currently viewed reporter.
- setReporterList(ReporterListData) - Method in class net.sf.basedb.core.data.ReporterListScoreData
-
- setReporterLists(Set<ReporterListData>) - Method in class net.sf.basedb.core.data.ExperimentData
-
- setReporterListScores(Set<ReporterListScoreData>) - Method in class net.sf.basedb.core.data.ReporterData
-
- setReporterListScores(Map<Integer, ReporterListScoreData>) - Method in class net.sf.basedb.core.data.ReporterListData
-
- setReporters(Set<ReporterData>) - Method in class net.sf.basedb.core.data.ReporterTypeData
-
This is the inverse end.
- setReporterType(ReporterTypeData) - Method in class net.sf.basedb.core.data.ReporterData
-
- setReporterType(ReporterData, ReporterType) - Static method in class net.sf.basedb.core.Reporter
-
Set the reporter type on a reporter data object.
- setRequired(boolean) - Method in class net.sf.basedb.clients.web.taglib.Select
-
- setRequired(boolean) - Method in class net.sf.basedb.core.data.ItemSubtypeFileTypeData
-
- setRequired(boolean) - Method in class net.sf.basedb.core.data.PlatformFileTypeData
-
- setRequired(boolean) - Method in class net.sf.basedb.core.ItemSubtypeFileType
-
Set the required flag for this file type.
- setRequired(boolean) - Method in class net.sf.basedb.core.PlatformFileType
-
Set the required flag for this file type.
- setRequired(boolean) - Method in class net.sf.basedb.plugins.executor.ParameterDefinition
-
Set if this parameter should be a required or optional parameter.
- setRequiredForMiame(boolean) - Method in class net.sf.basedb.core.AnnotationType
-
Set if an annotation of this annotation type is required for an item to
be compliant with the MIAME recommendation.
- setRequiredForMiame(boolean) - Method in class net.sf.basedb.core.data.AnnotationTypeData
-
- setRequiresConfiguration(boolean) - Method in class net.sf.basedb.core.data.PluginDefinitionData
-
- setRequiresConfiguration(boolean) - Method in class net.sf.basedb.core.PluginDefinition
-
- setResetClassLoader(boolean) - Method in class net.sf.basedb.util.extensions.manager.processor.ResetProcessor
-
This flag controls if the class loader should be
reset or not.
- setResetErrorFlag(boolean) - Method in class net.sf.basedb.util.extensions.manager.processor.ResetProcessor
-
This flag controls if the error flag should be
reset or not.
- setRestrictionParameters(SQLQuery) - Method in class net.sf.basedb.core.AnnotationBetweenRestriction
-
- setRestrictionParameters(SQLQuery) - Method in class net.sf.basedb.core.AnnotationInRestriction
-
- setRestrictionParameters(SQLQuery) - Method in class net.sf.basedb.core.AnnotationRestriction
-
- setRestrictionParameters(SQLQuery) - Method in class net.sf.basedb.core.AnnotationSimpleRestriction
-
- setRestrictionParameters(SQLQuery) - Method in class net.sf.basedb.core.HasAnnotationRestriction
-
- setResult(SqlResult, SqlResult) - Method in class net.sf.basedb.clients.web.servlet.PlotServlet.CFSqlResult
-
- setResult(boolean, String) - Method in class net.sf.basedb.util.fileset.ValidatingFileSetMember
-
Set the result of the validation for this file.
- setResultIntensityTransform(Integer) - Method in class net.sf.basedb.core.data.FormulaData
-
- setResultIntensityTransform(IntensityTransform) - Method in class net.sf.basedb.core.Formula
-
Sets the transform that this formula generates.
- setResultTransformer(ResultTransformer) - Method in class net.sf.basedb.core.hibernate.QueryWrapper
-
- setResyncCloned(boolean) - Method in class net.sf.basedb.util.annotations.InheritSpecification
-
- setReturnKeys(boolean) - Method in class net.sf.basedb.util.resources.ResourceBundleWrapper
-
Set a flag indicating that the various getString()
methods
should always return the key instead of trying to find a value for it.
- setReturnTotalCount(boolean) - Method in class net.sf.basedb.core.AbstractQuery
-
- setReturnTotalCount(boolean) - Method in interface net.sf.basedb.core.query.Query
-
Specify if the query should return a count for the total number
of items that would have been returned if the
Query.setFirstResult(int)
and
Query.setMaxResults(int)
had been disabled, or if the results are
loaded by an iterator where the number of rows not are known beforehand.
- setRole(String) - Method in class net.sf.basedb.core.BioPlateEventParticipant
-
Set the role that the plate has in this event.
- setRole(String) - Method in class net.sf.basedb.core.data.BioPlateEventParticipantData
-
- setRoleId(int) - Method in class net.sf.basedb.core.data.keyring.RoleKeys
-
Set the id of the role.
- setRoleId(int) - Method in class net.sf.basedb.core.data.keyring.UserRoles
-
Set the id of the role.
- setRoleInactive(int, boolean) - Method in class net.sf.basedb.core.Keyring
-
Set a roles as inactive (or active).
- setRoleInactive(int, boolean) - Method in class net.sf.basedb.core.SessionControl
-
Set a role as active or inactive.
- setRoles(Map<RoleData, Integer>) - Method in class net.sf.basedb.core.data.RoleKeyData
-
- setRoles(Set<RoleData>) - Method in class net.sf.basedb.core.data.UserData
-
- setRoot(boolean) - Method in class net.sf.basedb.core.data.DerivedBioAssayData
-
- setRoot(String) - Method in class net.sf.basedb.util.extensions.xml.PathConverter
-
Set the value of the root path.
- setRootDerivedBioAssays(Set<DerivedBioAssayData>) - Method in class net.sf.basedb.core.data.PhysicalBioAssayData
-
- setRootPath(String) - Method in class net.sf.basedb.core.data.FileServerData
-
- setRootPath(String) - Method in class net.sf.basedb.core.FileServer
-
Set the root path that should be added to all URI:s when used with this file
server.
- setRootPath(String) - Method in class net.sf.basedb.util.uri.ConnectionParameters
-
- setRootRawBioAssays(Map<RawBioAssayData, RootRawBioAssayData>) - Method in class net.sf.basedb.core.data.ExperimentData
-
- setRow(int) - Method in class net.sf.basedb.clients.web.taglib.table.PropertyFilter
-
- setRow(int) - Method in class net.sf.basedb.core.data.BioWellData
-
- setRow(int) - Method in class net.sf.basedb.core.data.FeatureData
-
- setRow(int) - Method in class net.sf.basedb.core.data.MappingCoordinate
-
Set the row number.
- setRow(int) - Method in class net.sf.basedb.core.data.PlateCoordinate
-
Set the row number.
- setRow(Integer) - Method in class net.sf.basedb.core.data.RawData
-
- setRow(int) - Method in class net.sf.basedb.core.data.WellData
-
- setRowIndex(int) - Method in class net.sf.basedb.core.PropertyFilter
-
Only used internally when removing filter rows
- setRows(int) - Method in class net.sf.basedb.core.data.PlateGeometryData
-
- setRows(int) - Method in class net.sf.basedb.core.PlateGeometry
-
The number of rows cannot be changed, used at object creation only.
- setRowsperpage(String) - Method in class net.sf.basedb.clients.web.taglib.table.Navigator
-
- setRowsperpage(int) - Method in class net.sf.basedb.clients.web.taglib.table.Navigator
-
- setRowsPerPage(int) - Method in class net.sf.basedb.core.data.ContextData
-
- setRowsPerPage(int) - Method in class net.sf.basedb.core.ItemContext
-
Set the number of rows the current table page should show.
- setSafeResources(String, boolean) - Static method in class net.sf.basedb.clients.web.servlet.ContentSecurityPolicyFilter
-
Set a flag indicating if resources from the given extension JAR file are
should use the regular policy or the 'unsafe-resources' policy.
- setSc(SessionControl) - Method in class net.sf.basedb.clients.web.taglib.Page
-
Set the session control to use in this request.
- setSc(SessionControl) - Method in class net.sf.basedb.clients.web.taglib.table.Table
-
- setScheduled(Date) - Method in class net.sf.basedb.core.data.JobData
-
- setScheduled(String, JobAgent) - Method in class net.sf.basedb.core.Job
-
- setSchemaVersion(int) - Method in class net.sf.basedb.core.data.SchemaVersionData
-
- setSchemaVersion(String, int) - Method in class net.sf.basedb.core.hibernate.SessionFactoryConfiguration
-
Deprecated.
Set the schema version of the current configuration.
- setSchemaVersion(Session, String, int, int) - Static method in class net.sf.basedb.core.Update
-
Update the database with a new schema version number.
- setSchemaVersion(Session, int) - Static method in class net.sf.basedb.core.Update
-
- setSchemaVersionInTransaction(Session, int) - Static method in class net.sf.basedb.core.Update
-
Update the schema version version number using a new transaction.
- setScore(Float) - Method in class net.sf.basedb.core.data.ReporterListScoreData
-
- setScript(String) - Method in class net.sf.basedb.clients.web.extensions.AbstractJspFactory
-
Add a reference to a javascript file to the factory.
- setScripts(String) - Method in class net.sf.basedb.clients.web.taglib.Head
-
- setSecondaryLocation(boolean) - Method in class net.sf.basedb.core.data.QuotaTypeData
-
- setSection(String) - Method in class net.sf.basedb.core.BioPlate
-
Set the section within the "storage location" for this bioplate.
- setSection(String) - Method in class net.sf.basedb.core.data.BioPlateData
-
- setSectionParser(String, BaseFileSectionParser) - Method in class net.sf.basedb.util.basefile.BaseFileParser
-
Adds a section parser.
- setSectionRegexp(Pattern) - Method in class net.sf.basedb.util.parser.FlatFileParser
-
Set a regular expression that can be matched against the section
line.
- setSelectdefault(boolean) - Method in class net.sf.basedb.clients.web.taglib.Select
-
- setSelectrecent(boolean) - Method in class net.sf.basedb.clients.web.taglib.Select
-
- setSender(User) - Method in class net.sf.basedb.core.Message
-
- setSendMessage(boolean) - Method in class net.sf.basedb.core.data.JobData
-
- setSendMessage(boolean) - Method in class net.sf.basedb.core.Job
-
Set if a message should be sent to owner when the job finishes.
- setSendMessagesAsEmail(boolean) - Method in class net.sf.basedb.core.data.UserData
-
- setSendMessagesAsEmail(boolean) - Method in class net.sf.basedb.core.User
-
Set a flag indicating that all messages should also be sent as
email.
- setSeparator(String) - Method in class net.sf.basedb.clients.web.taglib.table.CellValue
-
- setSerializable(int, Serializable) - Method in class net.sf.basedb.core.hibernate.QueryWrapper
-
- setSerializable(String, Serializable) - Method in class net.sf.basedb.core.hibernate.QueryWrapper
-
- setServer(String) - Method in class net.sf.basedb.core.data.JobAgentData
-
- setServer(String) - Method in class net.sf.basedb.core.data.JobData
-
- setServer(String) - Method in class net.sf.basedb.core.JobAgent
-
Set the name/IP of the server where the job agent is running.
- setServerCertificate(byte[]) - Method in class net.sf.basedb.core.data.FileServerData
-
- setServerCertificate(byte[]) - Method in class net.sf.basedb.core.FileServer
-
Set the public server certificate so that BASE can trust https connections to
the server.
- setServerCertificate(byte[]) - Method in class net.sf.basedb.util.uri.ConnectionParameters
-
- setServletContext(ServletContext) - Method in class net.sf.basedb.clients.web.extensions.ServletWrapper
-
Set the servlet context from the web application.
- setSession(SessionData) - Method in class net.sf.basedb.core.data.ChangeHistoryData
-
- setSessionId(int) - Method in class net.sf.basedb.core.data.ChangeHistoryData
-
- setSessions(Set<SessionData>) - Method in class net.sf.basedb.core.data.ClientData
-
- setSessions(Set<SessionData>) - Method in class net.sf.basedb.core.data.UserData
-
- setSessionSetting(String, Object) - Method in class net.sf.basedb.core.SessionControl
-
Set the value of a session setting.
- setSetting(String, String, String) - Method in class net.sf.basedb.clients.web.extensions.ExtensionsControl
-
Set a configuration setting for an extension.
- setSetting(String, String) - Method in class net.sf.basedb.core.ItemContext
-
Set a value.
- setSetting(String, String) - Method in class net.sf.basedb.core.Presets.Preset
-
Set a value for the specified setting.
- setSetting(String, String, String) - Method in class net.sf.basedb.util.extensions.manager.Settings
-
Set a configuration setting for an extension.
- setSettings(Map<String, String>) - Method in class net.sf.basedb.core.data.ContextData
-
- setSeverity(Validator, Severity) - Method in class net.sf.basedb.util.overview.ValidationOptions
-
- setSeverity(ValidationRuleAction, Severity) - Method in class net.sf.basedb.util.overview.ValidationOptions
-
Set a severity level for the specified validation rule.
- setShort(int, short) - Method in class net.sf.basedb.core.hibernate.QueryWrapper
-
- setShort(String, short) - Method in class net.sf.basedb.core.hibernate.QueryWrapper
-
- setShow(String) - Method in class net.sf.basedb.clients.web.taglib.table.ColumnDef
-
- setShowClazz(String) - Method in class net.sf.basedb.clients.web.extensions.section.IncludeContentSectionFactory
-
- setShowClazz(String) - Method in class net.sf.basedb.clients.web.extensions.section.SectionBean
-
- setShowclazz(String) - Method in class net.sf.basedb.clients.web.taglib.HideableSection
-
- setSignalReceiver(SignalReceiver) - Method in class net.sf.basedb.clients.jobagent.executors.ThreadJobExecutor
-
- setSignalTransporter(String) - Method in class net.sf.basedb.core.data.JobData
-
- setSignalTransporter(Class<? extends SignalTransporter>, String) - Method in class net.sf.basedb.core.Job
-
Set information needed to create a signal transporter object that can be used
to send signals to the plug-in that is currently executing this job.
- setSize(long) - Method in class net.sf.basedb.core.data.FileData
-
- setSize(int) - Method in class net.sf.basedb.core.data.ItemListData
-
- setSize(int) - Method in class net.sf.basedb.core.data.PhysicalBioAssayData
-
- setSize(int) - Method in class net.sf.basedb.core.data.ReporterListData
-
- setSize(int) - Method in class net.sf.basedb.core.PhysicalBioAssay
-
Set the size of the bioassay.
- setSkip(boolean) - Method in class net.sf.basedb.clients.web.taglib.table.Hidden
-
- setSmartenum(boolean) - Method in class net.sf.basedb.clients.web.taglib.table.ColumnDef
-
- setSnapshotInvalid() - Method in class net.sf.basedb.core.AnnotationSet
-
Mark the snapshot (if it exists) of this annotation set as
invalid.
- setSnapshotManager(SnapshotManager) - Method in class net.sf.basedb.util.export.spotdata.AbstractBioAssaySetExporter
-
Set's the snapshot manager that should be used to load annotation values.
- setSnapshotManager(SnapshotManager) - Method in class net.sf.basedb.util.export.spotdata.AbstractFieldConverter
-
Set a snapshot manager that should be used with annotation-based
fields.
- setSnapshotManager(SnapshotManager) - Method in class net.sf.basedb.util.export.spotdata.AnnotationAssayField
-
Set the snapshot manager that should be used to load annotation values.
- setSoftware(SoftwareData) - Method in class net.sf.basedb.core.data.DerivedBioAssayData
-
- setSoftware(SoftwareData) - Method in class net.sf.basedb.core.data.RawBioAssayData
-
- setSoftware(Software) - Method in class net.sf.basedb.core.DerivedBioAssay
-
Set the
Software
that was used when
creating this bioassay set.
- setSoftware(Software) - Method in class net.sf.basedb.core.RawBioAssay
-
Set the
Software
used while analysing the scanned images.
- setSortable(boolean) - Method in class net.sf.basedb.clients.web.extensions.list.AbstractListColumnBean
-
- setSortable(String) - Method in class net.sf.basedb.clients.web.extensions.list.PropertyPathActionFactory
-
- setSortable(boolean) - Method in class net.sf.basedb.clients.web.taglib.table.ColumnDef
-
- setSortby(String) - Method in class net.sf.basedb.clients.web.taglib.table.Table
-
- setSortDirection(int) - Method in class net.sf.basedb.core.data.ContextData
-
- setSortDirection(ItemContext.SortDirection) - Method in class net.sf.basedb.core.ItemContext
-
Set the sort direction (ascending or descending) of the current listing.
- setSortProperty(String) - Method in class net.sf.basedb.clients.web.extensions.list.AbstractListColumnBean
-
- setSortProperty(String) - Method in class net.sf.basedb.clients.web.extensions.list.PropertyPathActionFactory
-
- setSortproperty(String) - Method in class net.sf.basedb.clients.web.taglib.table.ColumnDef
-
- setSortProperty(String) - Method in class net.sf.basedb.core.data.ContextData
-
- setSortProperty(String) - Method in class net.sf.basedb.core.ItemContext
-
Set the name of the property that the current listing is sorted by.
- setSource(BioMaterial) - Method in class net.sf.basedb.core.BioMaterialEvent
-
Set a single parent item for this event.
- setSource(int) - Method in class net.sf.basedb.core.data.AnnotationData
-
- setSource(int) - Method in class net.sf.basedb.core.data.annotations.AnnotationLink
-
- setSource(BioAssaySetData) - Method in class net.sf.basedb.core.data.TransformationData
-
- setSource(BioAssaySet) - Method in class net.sf.basedb.core.Transformation
-
Set the source bioassayset.
- setSource(BioAssaySet) - Method in class net.sf.basedb.util.export.spotdata.AbstractBioAssaySetExporter
-
Set the bioassay set that is used as a source for the spot data.
- setSourceCoordinate(MappingCoordinate, MappingCoordinate) - Method in class net.sf.basedb.core.PlateMapping
-
Set the source coordinate for a given destination coordinate.
- setSourceCount(int) - Method in class net.sf.basedb.core.data.PlateMappingData
-
- setSourceCount(int) - Method in class net.sf.basedb.core.PlateMapping
-
Set the number of source plates.
- setSourceFileWrapper(FileWrapper) - Method in class net.sf.basedb.util.importer.spotdata.BaseFileImporter
-
Set the source BASEfile to import data from.
- setSourceGeometry(PlateGeometryData) - Method in class net.sf.basedb.core.data.PlateMappingData
-
- setSourceGeometry(PlateGeometry) - Method in class net.sf.basedb.core.PlateMapping
-
Set the source geometry.
- setSourceIntensityTransform(Integer) - Method in class net.sf.basedb.core.data.FormulaData
-
- setSourceIntensityTransform(IntensityTransform) - Method in class net.sf.basedb.core.Formula
-
Sets the transform that is required on spot data if this
formula should generate the correct result.
- setSourceItemMustExist(boolean) - Method in class net.sf.basedb.core.SyncFilter
-
- setSourceItemTransform(int) - Method in class net.sf.basedb.core.data.ItemListSyncFilterData
-
- setSourceItemType(int) - Method in class net.sf.basedb.core.data.ItemListSyncFilterData
-
- setSourceMustExist(boolean) - Method in class net.sf.basedb.core.data.ItemListSyncFilterData
-
- setSources(Map<BioMaterialData, BioMaterialEventSourceData>) - Method in class net.sf.basedb.core.data.BioMaterialEventData
-
- setSpacingX(int) - Method in class net.sf.basedb.core.ArrayDesignBlock
-
Set the x spacing between the spots in the slide.
- setSpacingX(int) - Method in class net.sf.basedb.core.data.ArrayDesignBlockData
-
- setSpacingX(Integer) - Method in class net.sf.basedb.plugins.PrintMapFlatFileImporter.MetaBlock
-
- setSpacingY(int) - Method in class net.sf.basedb.core.ArrayDesignBlock
-
Set the y spacing between the spots in the slide.
- setSpacingY(int) - Method in class net.sf.basedb.core.data.ArrayDesignBlockData
-
- setSpacingY(Integer) - Method in class net.sf.basedb.plugins.PrintMapFlatFileImporter.MetaBlock
-
- setSpecialLogger(Class<? extends LoggableData>, EntityLogger) - Method in class net.sf.basedb.core.log.db.DbLogManagerFactory
-
Register a special logger for entities of the given class.
- setSpotImages(SpotImagesData) - Method in class net.sf.basedb.core.data.RawBioAssayData
-
- setSpotImagesFile(FileData) - Method in class net.sf.basedb.core.data.SpotImagesData
-
- setSpotIntensityParser(SpotIntensityParser) - Method in class net.sf.basedb.util.importer.spotdata.BaseFileInfo.SpotSectionInfo
-
Set the spot intensity parser for the section.
- setSpots(int) - Method in class net.sf.basedb.core.data.RawBioAssayData
-
- setSpotsize(int) - Method in class net.sf.basedb.core.data.SpotImagesData
-
- setSpotsize(int) - Method in class net.sf.basedb.core.SpotImages
-
- setSqlResult(SqlResult) - Method in class net.sf.basedb.util.jep.ChannelFunction
-
Set a new
SqlResult
object that will be used the next time the
JEP expression is evaluated.
- setSqlResult(SqlResult) - Method in class net.sf.basedb.util.jep.ExtraValueFunction
-
Set a new
SqlResult
object that will be used the next time the
JEP expression is evaluated.
- setSqlResult(SqlResult) - Method in class net.sf.basedb.util.jep.RawChannelFunction
-
Set a new
SqlResult
object that will be used the next time the
JEP expression is evaluated.
- setSqlResult(SqlResult) - Method in class net.sf.basedb.util.jep.ScoreFunction
-
Set a new
SqlResult
object that will be used the next time the
JEP expression is evaluated.
- setSshFingerprint(String) - Method in class net.sf.basedb.core.data.FileServerData
-
- setSshFingerprint(String) - Method in class net.sf.basedb.core.FileServer
-
Set the SSH fingerprint for the server.
- setSshFingerprint(String) - Method in class net.sf.basedb.util.uri.ConnectionParameters
-
- setStackTrace(String) - Method in class net.sf.basedb.core.data.JobData
-
- setStartDate(Date) - Method in class net.sf.basedb.core.data.NewsData
-
- setStartDate(Date) - Method in class net.sf.basedb.core.News
-
Set the start date and time for this item to be published.
- setStarted(Date) - Method in class net.sf.basedb.core.data.JobData
-
- setStarted(Class<? extends SignalTransporter>, String) - Method in class net.sf.basedb.core.Job.ProgressReporterImpl
-
- setStatus(int) - Method in class net.sf.basedb.core.data.JobData
-
- setStatus(ExtensionsFile, String) - Method in class net.sf.basedb.util.extensions.manager.ProcessResults
-
Sets a short overall status message for an entire file.
- setStatusMessage(String) - Method in class net.sf.basedb.core.data.JobData
-
- setStorageType(ItemSubtype) - Method in class net.sf.basedb.core.BioPlateType
-
Set the subtype of storage location where plates of this type are usually stored.
- setStorageType(ItemSubtypeData) - Method in class net.sf.basedb.core.data.BioPlateTypeData
-
- setString(int, String) - Method in class net.sf.basedb.core.hibernate.QueryWrapper
-
- setString(String, String) - Method in class net.sf.basedb.core.hibernate.QueryWrapper
-
- setStringValues(List<String>) - Method in class net.sf.basedb.core.data.annotations.AnnotationLink
-
- setStyle(String) - Method in class net.sf.basedb.clients.web.extensions.list.AbstractListColumnBean
-
- setStyle(String) - Method in class net.sf.basedb.clients.web.extensions.list.PropertyPathActionFactory
-
- setStyle(String) - Method in class net.sf.basedb.clients.web.extensions.login.FieldInfo
-
- setStyle(String) - Method in class net.sf.basedb.clients.web.extensions.menu.FixedMenuItemFactory
-
- setStyle(String) - Method in class net.sf.basedb.clients.web.extensions.menu.MenuItemBean
-
- setStyle(String) - Method in class net.sf.basedb.clients.web.extensions.menu.PermissionMenuItemFactory
-
Set the style to use in all cases.
- setStyle(String) - Method in class net.sf.basedb.clients.web.extensions.section.IncludeContentSectionFactory
-
- setStyle(String) - Method in class net.sf.basedb.clients.web.extensions.section.SectionBean
-
- setStyle(String) - Method in class net.sf.basedb.clients.web.extensions.tabcontrol.FixedTabFactory
-
- setStyle(String) - Method in class net.sf.basedb.clients.web.extensions.tabcontrol.IncludeContentTabFactory
-
- setStyle(String) - Method in class net.sf.basedb.clients.web.extensions.tabcontrol.TabBean
-
- setStyle(String) - Method in class net.sf.basedb.clients.web.extensions.toolbar.ButtonBean
-
- setStyle(String) - Method in class net.sf.basedb.clients.web.extensions.toolbar.FixedButtonFactory
-
- setStyle(String) - Method in class net.sf.basedb.clients.web.extensions.toolbar.PermissionButtonFactory
-
Set the style to use in all cases.
- setStyle(String) - Method in class net.sf.basedb.clients.web.taglib.StylableTag
-
- setStyle(String) - Method in class net.sf.basedb.clients.web.taglib.tab.Tab
-
- setStyle(String) - Method in class net.sf.basedb.clients.web.taglib.table.Cell
-
- setStyle(String) - Method in class net.sf.basedb.clients.web.taglib.table.CellValue
-
- setStyles(String) - Method in class net.sf.basedb.clients.web.taglib.Head
-
- setStylesheet(String) - Method in class net.sf.basedb.clients.web.extensions.AbstractJspFactory
-
Add a reference to a CSS stylesheet file to the factory.
- setSubclass(String) - Method in class net.sf.basedb.clients.web.taglib.StylableTag
-
- setSubcontext(String) - Method in class net.sf.basedb.clients.web.taglib.table.Table
-
- setSubContext(String) - Method in class net.sf.basedb.core.data.ContextData
-
- setSubContext(String) - Method in class net.sf.basedb.core.data.ContextIndex
-
- setSubContext(String) - Method in class net.sf.basedb.core.data.JobData
-
- setSubdirectories(Set<DirectoryData>) - Method in class net.sf.basedb.core.data.DirectoryData
-
- setSubid(String) - Method in class net.sf.basedb.clients.web.taglib.menu.Submenu
-
- setSubmenuId(String) - Method in class net.sf.basedb.clients.web.extensions.menu.FixedMenuItemFactory
-
- setSubmenuId(String) - Method in class net.sf.basedb.clients.web.extensions.menu.MenuItemBean
-
- setSubmenuId(String) - Method in class net.sf.basedb.clients.web.extensions.menu.PermissionMenuItemFactory
-
- setSubtype(String) - Method in class net.sf.basedb.util.bfs.MetadataModel
-
Set the subtype of the BFS.
- setSubtype(String) - Method in class net.sf.basedb.util.bfs.MetadataWriter
-
Set the BFS subtype for this writer.
- setSuffix(String) - Method in class net.sf.basedb.clients.web.taglib.table.CellValue
-
- setSuffix(String) - Method in class net.sf.basedb.util.bfs.SequenceFilenameGenerator
-
Set the suffix that is used for file name generation.
- setSuggestedJobName(String) - Method in interface net.sf.basedb.core.plugin.Response
-
A plug-in may call this method on it's job configuration phase
to suggest a name for the job.
- setSuggestedJobName(String) - Method in class net.sf.basedb.core.PluginResponse.ResponseImpl
-
- setSuggestedJobName(String) - Method in class net.sf.basedb.plugins.executor.ExternalProgramExecutor.ResponseWrapper
-
- setSummary(String) - Method in class net.sf.basedb.util.extensions.manager.ProcessResults
-
Set a summary of the results.
- setSupportsConfigurations(boolean) - Method in class net.sf.basedb.core.data.PluginDefinitionData
-
- setSupportsConfigurations(boolean) - Method in class net.sf.basedb.core.PluginDefinition
-
- setSymbol(String) - Method in class net.sf.basedb.core.data.ReporterData
-
- setSymbol(String) - Method in class net.sf.basedb.core.data.UnitSymbolData
-
- setSymbols(Set<UnitSymbolData>) - Method in class net.sf.basedb.core.data.QuantityData
-
- setSymbols(Set<UnitSymbolData>) - Method in class net.sf.basedb.core.data.UnitData
-
- setSymbols(Set<String>) - Method in class net.sf.basedb.core.Unit
-
Set the symbols that should be registered for this unit.
- setSyncContext(ItemContext, SyncFilter.SourceItemTransform) - Method in class net.sf.basedb.core.SyncFilter
-
Copy filters and other settings from the given context
to this synchronization filter.
- setSyncDate(Date) - Method in class net.sf.basedb.core.data.ItemListData
-
- setSyncFilters(Set<ItemListSyncFilterData>) - Method in class net.sf.basedb.core.data.ItemListData
-
- setSystemId(String) - Method in class net.sf.basedb.core.BioPlateEventType
-
- setSystemId(String) - Method in class net.sf.basedb.core.data.BioPlateEventTypeData
-
- setSystemId(String) - Method in class net.sf.basedb.core.data.DirectoryData
-
- setSystemId(String) - Method in class net.sf.basedb.core.data.GroupData
-
- setSystemId(String) - Method in class net.sf.basedb.core.data.ItemSubtypeData
-
- setSystemId(String) - Method in class net.sf.basedb.core.data.QuantityData
-
- setSystemId(String) - Method in class net.sf.basedb.core.data.QuotaData
-
- setSystemId(String) - Method in class net.sf.basedb.core.data.QuotaTypeData
-
- setSystemId(String) - Method in class net.sf.basedb.core.data.RoleData
-
- setSystemId(String) - Method in class net.sf.basedb.core.data.UserData
-
- setTabcontrol(String) - Method in class net.sf.basedb.clients.web.taglib.Help
-
- setTabIndex(String) - Method in class net.sf.basedb.clients.web.extensions.tabcontrol.FixedTabFactory
-
- setTabIndex(String) - Method in class net.sf.basedb.clients.web.extensions.tabcontrol.IncludeContentTabFactory
-
- setTabIndex(int) - Method in class net.sf.basedb.clients.web.extensions.tabcontrol.TabBean
-
- setTabIndex(int) - Method in class net.sf.basedb.clients.web.extensions.toolbar.ButtonBean
-
- setTabIndex(int) - Method in class net.sf.basedb.clients.web.extensions.toolbar.FixedButtonFactory
-
- setTabindex(int) - Method in class net.sf.basedb.clients.web.taglib.Button
-
- setTabindex(int) - Method in class net.sf.basedb.clients.web.taglib.Help
-
- setTabindex(int) - Method in class net.sf.basedb.clients.web.taglib.Icon
-
- setTabindex(int) - Method in class net.sf.basedb.clients.web.taglib.Select
-
- setTabindex(int) - Method in class net.sf.basedb.clients.web.taglib.tab.Tab
-
- setTabindex(int) - Method in class net.sf.basedb.clients.web.taglib.table.Button
-
- setTabindex(int) - Method in class net.sf.basedb.clients.web.taglib.Zoom
-
- setTag(TagData) - Method in class net.sf.basedb.core.data.ExtractData
-
- setTag(Tag) - Method in class net.sf.basedb.core.Extract
-
Set the tag that was applied to this extract in order
to be able to distinguish it from other extracts on a
physical bioassay.
- setTarget(Target) - Method in class net.sf.basedb.core.hibernate.DbIndexWork
-
Set a target for receiving information about SQL
statements that are needed to create missing foreign keys
and indexes.
- setTemporary(boolean) - Method in class net.sf.basedb.core.PropertyFilter
-
Set or clear a flag indicating that this filter is temporary filter.
- setText(int, String) - Method in class net.sf.basedb.core.hibernate.QueryWrapper
-
- setText(String, String) - Method in class net.sf.basedb.core.hibernate.QueryWrapper
-
- setTextarea(String) - Method in class net.sf.basedb.clients.web.taglib.CalendarButton
-
- setTextarea(String) - Method in class net.sf.basedb.clients.web.taglib.Zoom
-
- setTextValues(List<String>) - Method in class net.sf.basedb.core.data.annotations.AnnotationLink
-
- setTheId(int) - Method in class net.sf.basedb.core.RawDataBatcher.FeatureProxy
-
- setTheId(int, String) - Method in class net.sf.basedb.core.RawDataBatcher.ReporterProxy
-
- setTheId(int) - Method in class net.sf.basedb.util.importer.spotdata.BaseFileImporter.RawDataProxy
-
- setTheId(int) - Method in class net.sf.basedb.util.importer.spotdata.BaseFileImporter.ReporterProxy
-
- setTime(Date) - Method in class net.sf.basedb.core.data.ChangeHistoryData
-
- setTime(int, Date) - Method in class net.sf.basedb.core.hibernate.QueryWrapper
-
- setTime(String, Date) - Method in class net.sf.basedb.core.hibernate.QueryWrapper
-
- setTimeout(int) - Method in class net.sf.basedb.core.hibernate.QueryWrapper
-
- setTimeSent(Date) - Method in class net.sf.basedb.core.data.MessageData
-
- setTimestamp(int, Date) - Method in class net.sf.basedb.core.hibernate.QueryWrapper
-
- setTimestamp(String, Date) - Method in class net.sf.basedb.core.hibernate.QueryWrapper
-
- setTimestampValues(List<Date>) - Method in class net.sf.basedb.core.data.annotations.AnnotationLink
-
- Setting - Class in net.sf.basedb.core
-
This is the base class for all setting items.
- Setting(SettingData) - Constructor for class net.sf.basedb.core.Setting
-
- SettingData - Class in net.sf.basedb.core.data
-
- SettingData() - Constructor for class net.sf.basedb.core.data.SettingData
-
- SettingInfo(String, boolean) - Constructor for class net.sf.basedb.core.SessionControl.SettingInfo
-
- settings - Variable in class net.sf.basedb.clients.jobagent.JobRunner
-
- settings - Static variable in class net.sf.basedb.clients.web.extensions.ExtensionsControl
-
- settings - Variable in class net.sf.basedb.clients.web.extensions.service.ServicesEventHandler
-
- settings - Variable in class net.sf.basedb.core.data.ContextData
-
- settings - Variable in class net.sf.basedb.core.ItemContext
-
- settings - Variable in class net.sf.basedb.core.Presets.Preset
-
The key-value pairs in this preset.
- settings - Variable in class net.sf.basedb.util.extensions.manager.ExtensionsManager
-
- settings - Variable in class net.sf.basedb.util.extensions.manager.filter.InstalledFilter
-
- Settings - Class in net.sf.basedb.util.extensions.manager
-
Class for keeping settings for the extensions system.
- Settings(ExtensionsManager, File) - Constructor for class net.sf.basedb.util.extensions.manager.Settings
-
Create a new Settings object.
- settings - Variable in class net.sf.basedb.util.extensions.manager.Settings
-
- setTitle(String) - Method in class net.sf.basedb.clients.web.extensions.list.AbstractListColumnBean
-
- setTitle(String) - Method in class net.sf.basedb.clients.web.extensions.list.PropertyPathActionFactory
-
- setTitle(String) - Method in class net.sf.basedb.clients.web.extensions.menu.FixedMenuItemFactory
-
- setTitle(String) - Method in class net.sf.basedb.clients.web.extensions.menu.MenuItemBean
-
- setTitle(String) - Method in class net.sf.basedb.clients.web.extensions.menu.PermissionMenuItemFactory
-
Set the title of the menu item in all cases.
- setTitle(String) - Method in class net.sf.basedb.clients.web.extensions.plot.OverviewPlotBean
-
- setTitle(String) - Method in class net.sf.basedb.clients.web.extensions.plot.PlotGeneratorBean
-
- setTitle(String) - Method in class net.sf.basedb.clients.web.extensions.section.IncludeContentSectionFactory
-
- setTitle(String) - Method in class net.sf.basedb.clients.web.extensions.section.SectionBean
-
- setTitle(String) - Method in class net.sf.basedb.clients.web.extensions.tabcontrol.FixedTabFactory
-
- setTitle(String) - Method in class net.sf.basedb.clients.web.extensions.tabcontrol.IncludeContentTabFactory
-
- setTitle(String) - Method in class net.sf.basedb.clients.web.extensions.tabcontrol.TabBean
-
- setTitle(String) - Method in class net.sf.basedb.clients.web.extensions.toolbar.ButtonBean
-
- setTitle(String) - Method in class net.sf.basedb.clients.web.extensions.toolbar.FixedButtonFactory
-
- setTitle(String) - Method in class net.sf.basedb.clients.web.extensions.toolbar.PermissionButtonFactory
-
Set the title of the button in all cases.
- setTitle(String) - Method in class net.sf.basedb.clients.web.taglib.Button
-
- setTitle(String) - Method in class net.sf.basedb.clients.web.taglib.CalendarButton
-
The title attribute now goes into the calendar
popup dialog instead.
- setTitle(String) - Method in class net.sf.basedb.clients.web.taglib.HideableSection
-
- setTitle(String) - Method in class net.sf.basedb.clients.web.taglib.menu.Menuitem
-
- setTitle(String) - Method in class net.sf.basedb.clients.web.taglib.menu.Submenu
-
- setTitle(String) - Method in class net.sf.basedb.clients.web.taglib.Page
-
- setTitle(String) - Method in class net.sf.basedb.clients.web.taglib.path.PathElement
-
- setTitle(String) - Method in class net.sf.basedb.clients.web.taglib.tab.Tab
-
- setTitle(String) - Method in class net.sf.basedb.clients.web.taglib.table.Button
-
- setTitle(String) - Method in class net.sf.basedb.clients.web.taglib.table.ColumnDef
-
- setTitle(String) - Method in class net.sf.basedb.clients.web.taglib.table.Label
-
- setTitle(String) - Method in class net.sf.basedb.clients.web.taglib.table.Table
-
- setTitle(String) - Method in class net.sf.basedb.clients.web.taglib.Zoom
-
- setTitle(String) - Method in class net.sf.basedb.core.data.ExperimentData
-
- setTitle(String) - Method in class net.sf.basedb.core.data.ReporterClonePropertyData
-
- setTitle(String) - Method in class net.sf.basedb.core.Experiment
-
Set the title for the publication of this experiment.
- setTitle(String) - Method in class net.sf.basedb.util.export.spotdata.AnnotationAssayField
-
Set a custom title for the assay field.
- setTitle(String) - Method in class net.sf.basedb.util.export.spotdata.AssayPropertyField
-
Set the title of the exported property.
- setTitle(String) - Method in class net.sf.basedb.util.export.spotdata.JepDynamicField
-
Set the column header title.
- setTitle(String) - Method in class net.sf.basedb.util.export.spotdata.SimpleDynamicField
-
Set the column header title.
- setTo(BasicItem) - Method in class net.sf.basedb.core.AnyToAny
-
Set the destination item of the link.
- setTo(UserData) - Method in class net.sf.basedb.core.data.MessageData
-
- setTo(User) - Method in class net.sf.basedb.core.Message
-
Set the user this message should be sent to.
- setToId(int) - Method in class net.sf.basedb.core.data.AnyToAnyData
-
- setTooltip(String) - Method in class net.sf.basedb.clients.web.extensions.list.AbstractListColumnBean
-
- setTooltip(String) - Method in class net.sf.basedb.clients.web.extensions.list.PropertyPathActionFactory
-
- setTooltip(String) - Method in class net.sf.basedb.clients.web.extensions.login.FieldInfo
-
- setTooltip(String) - Method in class net.sf.basedb.clients.web.extensions.menu.FixedMenuItemFactory
-
- setTooltip(String) - Method in class net.sf.basedb.clients.web.extensions.menu.MenuItemBean
-
- setTooltip(String) - Method in class net.sf.basedb.clients.web.extensions.menu.PermissionMenuItemFactory
-
Set the tooltip of the menu item in all cases.
- setTooltip(String) - Method in class net.sf.basedb.clients.web.extensions.tabcontrol.FixedTabFactory
-
- setTooltip(String) - Method in class net.sf.basedb.clients.web.extensions.tabcontrol.IncludeContentTabFactory
-
- setTooltip(String) - Method in class net.sf.basedb.clients.web.extensions.tabcontrol.TabBean
-
- setTooltip(String) - Method in class net.sf.basedb.clients.web.extensions.toolbar.ButtonBean
-
- setTooltip(String) - Method in class net.sf.basedb.clients.web.extensions.toolbar.FixedButtonFactory
-
- setTooltip(String) - Method in class net.sf.basedb.clients.web.extensions.toolbar.PermissionButtonFactory
-
Set the tooltip of the button in all cases.
- setTooltip(String) - Method in class net.sf.basedb.clients.web.taglib.Button
-
- setTooltip(String) - Method in class net.sf.basedb.clients.web.taglib.Help
-
- setTooltip(String) - Method in class net.sf.basedb.clients.web.taglib.Icon
-
- setTooltip(String) - Method in class net.sf.basedb.clients.web.taglib.menu.Menuitem
-
- setTooltip(String) - Method in class net.sf.basedb.clients.web.taglib.menu.Submenu
-
- setTooltip(String) - Method in class net.sf.basedb.clients.web.taglib.path.PathElement
-
- setTooltip(String) - Method in class net.sf.basedb.clients.web.taglib.PropertyValue
-
- setTooltip(String) - Method in class net.sf.basedb.clients.web.taglib.tab.Tab
-
- setTooltip(String) - Method in class net.sf.basedb.clients.web.taglib.table.Button
-
- setTooltip(String) - Method in class net.sf.basedb.clients.web.taglib.table.ColumnDef
-
- setTooltip(String) - Method in class net.sf.basedb.clients.web.taglib.table.Label
-
- setTooltip(String) - Method in class net.sf.basedb.clients.web.taglib.Zoom
-
- setTotalrows(String) - Method in class net.sf.basedb.clients.web.taglib.table.Navigator
-
- setTotalrows(int) - Method in class net.sf.basedb.clients.web.taglib.table.Navigator
-
- setTotalrows(long) - Method in class net.sf.basedb.clients.web.taglib.table.Navigator
-
- setToType(int) - Method in class net.sf.basedb.core.data.AnyToAnyData
-
- setTransferredBytes(long) - Method in class net.sf.basedb.clients.web.fileupload.FileUploadProgress
-
Sets the number of transferred bytes.
- setTransformation(Transformation) - Method in class net.sf.basedb.core.BioAssaySet
-
Set the transformation that created this bioassayset.
- setTransformation(TransformationData) - Method in class net.sf.basedb.core.data.BioAssaySetData
-
- setTransformation(Transformation) - Method in class net.sf.basedb.util.importer.spotdata.BaseFileImporter
-
Set the destination transformation.
- setTransformation(Transformation) - Method in class net.sf.basedb.util.importer.spotdata.BfsImporter
-
Set the destination transformation.
- setTransformations(Set<TransformationData>) - Method in class net.sf.basedb.core.data.BioAssaySetData
-
- setTransformations(Set<TransformationData>) - Method in class net.sf.basedb.core.data.ExperimentData
-
- setTransformations(Set<TransformationData>) - Method in class net.sf.basedb.core.data.JobData
-
- setTransformations(Set<TransformationData>) - Method in class net.sf.basedb.core.data.RawBioAssayData
-
- setTray(String) - Method in class net.sf.basedb.core.BioPlate
-
Set the tray within the "storage location" for this bioplate.
- setTray(String) - Method in class net.sf.basedb.core.data.BioPlateData
-
- setTrimQuotes(boolean) - Method in class net.sf.basedb.util.parser.FlatFileParser
-
Set if quotes around each data value should be removed or not.
- setTrusted(Boolean) - Method in class net.sf.basedb.core.data.JobAgentSettingsData
-
- setTrusted(boolean) - Method in class net.sf.basedb.core.data.PluginDefinitionData
-
- setTrusted(Boolean) - Method in class net.sf.basedb.core.JobAgentSettings
-
Set the trusted flag for this plugin.
- setTrusted(boolean) - Method in class net.sf.basedb.core.PluginDefinition
-
Set if this plugin should be trusted or not.
- setType(MenuItemAction.MenuType) - Method in class net.sf.basedb.clients.web.extensions.menu.FixedMenuItemFactory
-
- setType(String) - Method in class net.sf.basedb.clients.web.extensions.menu.FixedMenuItemFactory
-
- setType(MenuItemAction.MenuType) - Method in class net.sf.basedb.clients.web.extensions.menu.MenuItemBean
-
- setType(MenuItemAction.MenuType) - Method in class net.sf.basedb.clients.web.extensions.menu.PermissionMenuItemFactory
-
Set the type of the menu.
- setType(String) - Method in class net.sf.basedb.clients.web.extensions.menu.PermissionMenuItemFactory
-
Set the type of menu.
- setType(String) - Method in class net.sf.basedb.clients.web.taglib.menu.Menu
-
- setType(String) - Method in class net.sf.basedb.clients.web.taglib.Page
-
- setType(int) - Method in class net.sf.basedb.core.data.FormulaData
-
- setType(int) - Method in class net.sf.basedb.core.data.JobData
-
- setType(Type) - Method in class net.sf.basedb.core.query.QueryParameter
-
Changes the type of the parameter.
- setType(String) - Method in class net.sf.basedb.plugins.executor.ParameterDefinition
-
Set the type of the parameter.
- setType(Type) - Method in class net.sf.basedb.util.export.spotdata.AssayPropertyField
-
Set the data type of the exported property.
- setType(Type) - Method in class net.sf.basedb.util.export.spotdata.JepDynamicField
-
Set the data type of the exported field.
- setType(Type) - Method in class net.sf.basedb.util.export.spotdata.SimpleDynamicField
-
Set the data type of the exported field.
- setType(Plugin.MainType) - Method in class net.sf.basedb.util.extensions.xml.PluginInfo
-
- setUninstalled() - Method in class net.sf.basedb.util.extensions.manager.ExtensionsFile.WriteableExtensionsFile
-
Mark the file as uninstalled.
- setUninstalledFile(File) - Method in class net.sf.basedb.util.extensions.manager.Settings
-
Mark the given file as uninstalled.
- setUnit(Unit) - Method in class net.sf.basedb.clients.web.taglib.table.ColumnDef
-
- setUnit(UnitData) - Method in class net.sf.basedb.core.data.AnnotationData
-
- setUnit(UnitData) - Method in class net.sf.basedb.core.data.PropertyFilterData
-
- setUnit(UnitData) - Method in class net.sf.basedb.core.data.UnitSymbolData
-
- setUnit(Unit) - Method in class net.sf.basedb.core.PropertyFilter
-
Sets the unit the values for the property are stored in the
database.
- setUnits(Set<UnitData>) - Method in class net.sf.basedb.core.data.QuantityData
-
- setUnselectedtext(String) - Method in class net.sf.basedb.clients.web.taglib.Select
-
- setUpdateSource(String) - Method in class net.sf.basedb.core.ReporterBatcher
-
Set the source that was used when updating the reporters.
- setUpErrorHandling() - Method in class net.sf.basedb.plugins.AbstractFlatFileImporter
-
Initialise the error handling system.
- setUpErrorHandling() - Method in class net.sf.basedb.plugins.AnnotationFlatFileImporter
-
Don't use AbstractFlatFileImporter to handle errors.
- setUpErrorHandling() - Method in class net.sf.basedb.plugins.batchimport.AbstractItemImporter
-
Don't use AbstractFlatFileImporter to handle errors.
- setUrl(String) - Method in class net.sf.basedb.clients.web.extensions.plot.PlotGeneratorBean
-
- setUrl(String) - Method in class net.sf.basedb.clients.web.extensions.startpage.FixedStartPageFactory
-
- setUrl(String) - Method in class net.sf.basedb.clients.web.extensions.startpage.StartPageBean
-
- setUrl(String) - Method in class net.sf.basedb.clients.web.taglib.menu.Menuitem
-
- setUrl(String) - Method in class net.sf.basedb.core.authentication.ExtraUserInformation
-
- setUrl(String) - Method in class net.sf.basedb.core.data.FileData
-
- setUrl(String) - Method in class net.sf.basedb.core.data.PluginDefinitionData
-
- setUrl(String) - Method in class net.sf.basedb.core.data.UserData
-
- setUrl(String, boolean) - Method in class net.sf.basedb.core.File
-
Set the URL to an external file that should represent this file
object.
- setUrl(String, UriMetadata) - Method in class net.sf.basedb.core.File
-
Set the URL to an external file that should represent this file
object and update the metadata without going to the remote server.
- setUrl(String) - Method in class net.sf.basedb.core.PluginDefinition
-
Set the URL to a web page with more information about the plug-in.
- setUrl(String) - Method in class net.sf.basedb.core.User
-
Set the URL to the user's homepage, or null if unknown.
- setUrl(String) - Method in class net.sf.basedb.util.extensions.AboutBean
-
- setUsableUnits(Set<UnitData>) - Method in class net.sf.basedb.core.data.AnnotationTypeData
-
- setUseClonedReporters(boolean) - Method in interface net.sf.basedb.core.ClonableReporterQuery
-
Set if cloned reporters should be used by default or not.
- setUseClonedReporters(boolean) - Method in class net.sf.basedb.core.DynamicQuery
-
Set if cloned reporters should be used by default or not.
- setUseClonedReporters(boolean) - Method in class net.sf.basedb.core.DynamicReporterQuery
-
Set if cloned reporters should be used by default or not.
- setUsedQuantity(Float) - Method in class net.sf.basedb.core.BioMaterialEvent
-
Set the used quantity.
- setUsedQuantity(Float) - Method in class net.sf.basedb.core.BioMaterialEventSource
-
Set the quantity that was used from the source biomaterial by the event.
- setUsedQuantity(Float) - Method in class net.sf.basedb.core.data.BioMaterialEventData
-
- setUsedQuantity(Float) - Method in class net.sf.basedb.core.data.BioMaterialEventSourceData
-
- setUsedUnits(Set<AnnotationTypeData>) - Method in class net.sf.basedb.core.data.UnitData
-
- setUseInternalJobQueue(boolean) - Method in class net.sf.basedb.core.data.PluginDefinitionData
-
- setUseInternalJobQueue(boolean) - Method in class net.sf.basedb.core.PluginDefinition
-
Set if the plug-in can use the internal job queue or not.
- setUseNullIfEmpty(boolean) - Method in class net.sf.basedb.util.parser.FlatFileParser
-
Specify if null
values should be returned instead of empty strings
for columns that doesn't contain any value.
- setUseNullIfException(boolean) - Method in class net.sf.basedb.util.parser.FlatFileParser
-
Specify if null
should be returned if a (numeric)
value can't be parsed.
- setUseNullIfNull(boolean) - Method in class net.sf.basedb.util.parser.FlatFileParser
-
Specify if null
values should be returned for strings
having the value "NULL" (ignoring case).
- setUseNullLoaderIfNotFound(boolean) - Method in class net.sf.basedb.util.overview.loader.BasicItemNodeLoaderFactory
-
- setUsePermissions(boolean) - Method in class net.sf.basedb.core.data.PluginDefinitionData
-
- setUsePermissions(boolean) - Method in class net.sf.basedb.core.PluginDefinition
-
- setUser(UserData) - Method in class net.sf.basedb.core.data.BioMaterialEventData
-
- setUser(UserData) - Method in class net.sf.basedb.core.data.ChangeHistoryData
-
- setUser(UserData) - Method in class net.sf.basedb.core.data.ContextData
-
- setUser(UserData) - Method in class net.sf.basedb.core.data.DiskUsageData
-
- setUser(UserData) - Method in class net.sf.basedb.core.data.PasswordData
-
- setUser(UserData) - Method in class net.sf.basedb.core.data.PlateEventData
-
- setUser(UserData) - Method in class net.sf.basedb.core.data.SessionData
-
- setUser(UserData) - Method in class net.sf.basedb.core.data.UserClientSettingData
-
- setUser(UserData) - Method in class net.sf.basedb.core.data.UserDefaultSettingData
-
- setUser(User) - Method in class net.sf.basedb.core.UserClientSetting
-
Set the user this setting is valid for.
- setUser(User) - Method in class net.sf.basedb.core.UserDefaultSetting
-
Set the user this setting is valid for.
- setUserClientSetting(String, String) - Method in class net.sf.basedb.core.SessionControl
-
- setUserDefaultSetting(String, String) - Method in class net.sf.basedb.core.SessionControl
-
- setUserId(int) - Method in class net.sf.basedb.core.authentication.LoginRequest
-
Set the user id to use.
- setUserId(int) - Method in class net.sf.basedb.core.data.ChangeHistoryData
-
- setUserId(int) - Method in class net.sf.basedb.core.data.keyring.UserGroups
-
Set the id of the user.
- setUserId(int) - Method in class net.sf.basedb.core.data.keyring.UserKeys
-
Set the id of the user.
- setUserId(int) - Method in class net.sf.basedb.core.data.keyring.UserProjects
-
Set the id of the user.
- setUserId(int) - Method in class net.sf.basedb.core.data.keyring.UserRoles
-
Set the id of the user.
- setUsername(String) - Method in class net.sf.basedb.core.data.FileServerData
-
- setUsername(String) - Method in class net.sf.basedb.core.FileServer
-
Set the username that is required to authenticate with the file
server.
- setUsername(String) - Method in class net.sf.basedb.util.uri.ConnectionParameters
-
- setUsers(Set<UserData>) - Method in class net.sf.basedb.core.data.GroupData
-
- setUsers(Map<UserData, Integer>) - Method in class net.sf.basedb.core.data.ItemKeyData
-
- setUsers(Map<UserData, Integer>) - Method in class net.sf.basedb.core.data.ProjectData
-
- setUsers(Set<UserData>) - Method in class net.sf.basedb.core.data.RoleData
-
- setUserSettings(Set<UserClientSettingData>) - Method in class net.sf.basedb.core.data.ClientData
-
- setUseSeparateConnections(boolean) - Method in class net.sf.basedb.core.hibernate.SessionFactoryConfiguration
-
Deprecated.
Set to TRUE to use connections separate from BASE connections.
- setUseSeparateConnections(boolean) - Method in class net.sf.basedb.core.ServiceSessionControl.SessionFactoryConfiguration
-
Set to TRUE to use connections separate from BASE connections.
- setUsingColors(boolean) - Method in class net.sf.basedb.core.Coloring
-
Specifiy if colors should be used when displaying values for this
item or not.
- setUsingColors(boolean) - Method in class net.sf.basedb.core.data.ColoringData
-
- setUsingTo(boolean) - Method in class net.sf.basedb.core.AnyToAny
-
If this link counts as using the destination item.
- setUsingTo(boolean) - Method in class net.sf.basedb.core.data.AnyToAnyData
-
- setUsNullValidatorIfNotFound(boolean) - Method in class net.sf.basedb.util.overview.validator.BasicItemNodeValidatorFactory
-
- setValid(Boolean) - Method in class net.sf.basedb.core.data.FileSetMemberData
-
- setValid(Boolean, String) - Method in class net.sf.basedb.core.FileSetMember
-
Set the validation status of this member.
- setValue(Object) - Method in class net.sf.basedb.clients.web.taglib.table.Cell
-
- setValue(Object) - Method in class net.sf.basedb.clients.web.taglib.table.CellValue
-
- setValue(String) - Method in class net.sf.basedb.clients.web.taglib.table.Hidden
-
- setValue(Object) - Method in class net.sf.basedb.core.Annotation
-
Deprecated.
- setValue(Object, Unit) - Method in class net.sf.basedb.core.Annotation
-
- setValue(AnnotationType, Object, Unit, boolean) - Method in class net.sf.basedb.core.AnnotationBatcher
-
Add, update or delete a single-valued annotation.
- setValue(String) - Method in class net.sf.basedb.core.data.PropertyFilterData
-
- setValue(String) - Method in class net.sf.basedb.core.data.SettingData
-
- setValue(String, ParameterType<T>, T) - Method in class net.sf.basedb.core.ParameterValuesImpl
-
- setValue(String, ParameterType<T>, T) - Method in class net.sf.basedb.core.plugin.NamespaceParameterValuesWrapper
-
- setValue(String, ParameterType<T>, T) - Method in interface net.sf.basedb.core.plugin.ParameterValues
-
Set a single value for a parameter.
- setValue(String, ParameterType<T>, T) - Method in class net.sf.basedb.core.plugin.ParameterValuesWrapper
-
Set the value on either the job or configuration, depending in the
preferJob
parameter that was set when creating this object.
- setValue(String) - Method in class net.sf.basedb.core.PropertyFilter
-
Set the value to use in the filter.
- setValue(Object) - Method in class net.sf.basedb.core.query.QueryParameter
-
Change the value of the parameter.
- setValue(String) - Method in class net.sf.basedb.core.Setting
-
Set the value for this setting.
- setValue(String, ParameterType<T>, T) - Method in class net.sf.basedb.plugins.gtf.DefaultConfigurationValues
-
- setValueId(int) - Method in class net.sf.basedb.core.data.annotations.AnnotationLink
-
- setValueIfDifferent(Object, Unit) - Method in class net.sf.basedb.core.Annotation
-
Set the value of the annotation, replacing any previous values if they
are different.
- setValues(List<?>) - Method in class net.sf.basedb.core.Annotation
-
Deprecated.
- setValues(List<?>, Unit) - Method in class net.sf.basedb.core.Annotation
-
- setValues(AnnotationType, List<?>, Unit, boolean) - Method in class net.sf.basedb.core.AnnotationBatcher
-
Add, update or delete annotation values for the current item.
- setValues(List<?>) - Method in class net.sf.basedb.core.AnnotationType
-
Set the list of allowed values for an enumerated annotation type.
- setValues(ParameterValueData<?>) - Method in class net.sf.basedb.core.data.AnnotationData
-
- setValues(List<Boolean>) - Method in class net.sf.basedb.core.data.BooleanParameterValueData
-
- setValues(List<Date>) - Method in class net.sf.basedb.core.data.DateParameterValueData
-
- setValues(List<Double>) - Method in class net.sf.basedb.core.data.DoubleParameterValueData
-
- setValues(List<Float>) - Method in class net.sf.basedb.core.data.FloatParameterValueData
-
- setValues(List<Integer>) - Method in class net.sf.basedb.core.data.IntegerParameterValueData
-
- setValues(List<BasicData>) - Method in class net.sf.basedb.core.data.ItemParameterValueData
-
- setValues(List<Long>) - Method in class net.sf.basedb.core.data.LongParameterValueData
-
- setValues(List<T>) - Method in class net.sf.basedb.core.data.ParameterValueData
-
Set values of this parameter.
- setValues(List<String>) - Method in class net.sf.basedb.core.data.StringParameterValueData
-
- setValues(List<String>) - Method in class net.sf.basedb.core.data.TextParameterValueData
-
- setValues(List<Date>) - Method in class net.sf.basedb.core.data.TimestampParameterValueData
-
- setValues(String, ParameterType<T>, List<T>) - Method in class net.sf.basedb.core.ParameterValuesImpl
-
- setValues(String, ParameterType<T>, List<T>) - Method in class net.sf.basedb.core.plugin.NamespaceParameterValuesWrapper
-
- setValues(String, ParameterType<T>, List<T>) - Method in interface net.sf.basedb.core.plugin.ParameterValues
-
Set a list of values for a parameter.
- setValues(String, ParameterType<T>, List<T>) - Method in class net.sf.basedb.core.plugin.ParameterValuesWrapper
-
Set the value on either the job or configuration, depending in the
preferJob
parameter that was set when creating this object.
- setValues(List<?>) - Method in class net.sf.basedb.plugins.executor.ProgramParameter
-
- setValues(String, ParameterType<T>, List<T>) - Method in class net.sf.basedb.plugins.gtf.DefaultConfigurationValues
-
- setValuesIfDifferent(List<?>, Unit) - Method in class net.sf.basedb.core.Annotation
-
Set the values of the annotation, replacing any previous values if they
are different.
- setValueType(Type) - Method in class net.sf.basedb.clients.web.extensions.list.AbstractListColumnBean
-
- setValueType(String) - Method in class net.sf.basedb.clients.web.extensions.list.PropertyPathActionFactory
-
- setValueType(Type) - Method in class net.sf.basedb.clients.web.taglib.table.ColumnDef
-
- setValueType(int) - Method in class net.sf.basedb.core.data.AnnotationTypeData
-
- setValueType(int) - Method in class net.sf.basedb.core.data.DataCubeExtraValueData
-
- setValueType(int) - Method in class net.sf.basedb.core.data.ExtraValueTypeData
-
- setValueType(Integer) - Method in class net.sf.basedb.core.data.FormulaData
-
- setValueType(int) - Method in class net.sf.basedb.core.data.PropertyFilterData
-
- setValueType(int) - Method in class net.sf.basedb.core.data.ReporterClonePropertyData
-
- setValueType(Type) - Method in class net.sf.basedb.core.DataCubeExtraValue
-
Set the value type.
- setValueType(Type) - Method in class net.sf.basedb.core.ExtraValueType
-
Set the value type for this extra value type.
- setValueType(Type) - Method in class net.sf.basedb.core.Formula
-
Set the type of the values that this formula produces.
- setValueType(Type) - Method in class net.sf.basedb.core.PropertyFilter
-
Set the type of the property.
- setVariable(String, String) - Method in class net.sf.basedb.util.extensions.xml.VariableConverter
-
Set the value of a variable.
- setVariant(PlatformVariant) - Method in class net.sf.basedb.core.ArrayDesign
-
Set the platform and variant of the array design.
- setVariant(PlatformVariantData) - Method in class net.sf.basedb.core.data.ArrayDesignData
-
- setVariant(PlatformVariantData) - Method in class net.sf.basedb.core.data.FileTypeIndex
-
- setVariant(PlatformVariantData) - Method in class net.sf.basedb.core.data.PlatformFileTypeData
-
- setVariant(PlatformVariantData) - Method in class net.sf.basedb.core.data.RawBioAssayData
-
- setVariant(PlatformVariant, RawDataType) - Method in class net.sf.basedb.core.RawBioAssay
-
Set the platform and variant of the raw bioassay.
- setVariants(Set<PlatformVariantData>) - Method in class net.sf.basedb.core.data.PlatformData
-
- setVersion(int) - Method in class net.sf.basedb.core.data.BasicData
-
Set the version of the item.
- setVersion(int) - Method in class net.sf.basedb.core.data.VersionedParameter
-
- setVersion(String) - Method in class net.sf.basedb.util.extensions.AboutBean
-
- setVersionString(String) - Method in class net.sf.basedb.core.data.HardwareData
-
- setVersionString(String) - Method in class net.sf.basedb.core.data.PluginDefinitionData
-
- setVersionString(String) - Method in class net.sf.basedb.core.data.SoftwareData
-
- setVersionString(String) - Method in class net.sf.basedb.core.Hardware
-
Set the versionstring for this Hardware
item.
- setVersionString(String) - Method in class net.sf.basedb.core.PluginDefinition
-
Update version information for this plug-in.
- setVersionString(String) - Method in class net.sf.basedb.core.Software
-
Set the versionstring for this Software
item.
- setVertical(boolean) - Method in class net.sf.basedb.clients.web.taglib.ButtonGroup
-
- setVirtualDb(VirtualDbData) - Method in class net.sf.basedb.core.data.DataCubeData
-
- setVirtualDb(VirtualDbData) - Method in class net.sf.basedb.core.data.ExperimentData
-
- setVirtualDb(VirtualDb) - Method in class net.sf.basedb.core.DataCube
-
Set the experiment.
- setVisible(boolean) - Method in class net.sf.basedb.clients.web.extensions.menu.FixedMenuItemFactory
-
- setVisible(String) - Method in class net.sf.basedb.clients.web.extensions.menu.FixedMenuItemFactory
-
- setVisible(boolean) - Method in class net.sf.basedb.clients.web.extensions.menu.MenuItemBean
-
- setVisible(boolean) - Method in class net.sf.basedb.clients.web.extensions.tabcontrol.FixedTabFactory
-
- setVisible(String) - Method in class net.sf.basedb.clients.web.extensions.tabcontrol.FixedTabFactory
-
- setVisible(boolean) - Method in class net.sf.basedb.clients.web.extensions.tabcontrol.IncludeContentTabFactory
-
- setVisible(String) - Method in class net.sf.basedb.clients.web.extensions.tabcontrol.IncludeContentTabFactory
-
- setVisible(boolean) - Method in class net.sf.basedb.clients.web.extensions.tabcontrol.TabBean
-
- setVisible(boolean) - Method in class net.sf.basedb.clients.web.extensions.toolbar.ButtonBean
-
- setVisible(boolean) - Method in class net.sf.basedb.clients.web.extensions.toolbar.FixedButtonFactory
-
- setVisible(String) - Method in class net.sf.basedb.clients.web.extensions.toolbar.FixedButtonFactory
-
- setVisible(boolean) - Method in class net.sf.basedb.clients.web.taglib.Button
-
- setVisible(boolean) - Method in class net.sf.basedb.clients.web.taglib.Help
-
- setVisible(boolean) - Method in class net.sf.basedb.clients.web.taglib.HideableSection
-
- setVisible(boolean) - Method in class net.sf.basedb.clients.web.taglib.Icon
-
- setVisible(boolean) - Method in class net.sf.basedb.clients.web.taglib.menu.Menuitem
-
- setVisible(boolean) - Method in class net.sf.basedb.clients.web.taglib.menu.Menuseparator
-
- setVisible(boolean) - Method in class net.sf.basedb.clients.web.taglib.menu.Submenu
-
- setVisible(boolean) - Method in class net.sf.basedb.clients.web.taglib.path.PathElement
-
- setVisible(boolean) - Method in class net.sf.basedb.clients.web.taglib.Select
-
- setVisible(boolean) - Method in class net.sf.basedb.clients.web.taglib.tab.Tab
-
- setVisible(boolean) - Method in class net.sf.basedb.clients.web.taglib.table.Button
-
- setVisible(boolean) - Method in class net.sf.basedb.clients.web.taglib.table.Cell
-
- setVisible(boolean) - Method in class net.sf.basedb.clients.web.taglib.table.Header
-
- setVisible(boolean) - Method in class net.sf.basedb.clients.web.taglib.table.Label
-
- setVisible(boolean) - Method in class net.sf.basedb.clients.web.taglib.table.Navigator
-
- setVisible(boolean) - Method in class net.sf.basedb.clients.web.taglib.table.Panel
-
- setVisible(boolean) - Method in class net.sf.basedb.clients.web.taglib.table.PresetSelector
-
- setVisible(boolean) - Method in class net.sf.basedb.clients.web.taglib.table.Row
-
- setVisible(boolean) - Method in class net.sf.basedb.clients.web.taglib.table.Toolbar
-
- setVisible(boolean) - Method in class net.sf.basedb.clients.web.taglib.Zoom
-
- setVisiblePermission(String) - Method in class net.sf.basedb.clients.web.extensions.menu.PermissionMenuItemFactory
-
Set the minimum permission that is required to make the
menu item visible.
- setVisiblePermission(String) - Method in class net.sf.basedb.clients.web.extensions.toolbar.PermissionButtonFactory
-
Set the minimum permission that is required to make the
button visible.
- setWarnings(int) - Method in class net.sf.basedb.util.overview.Node
-
Set the number of warnings that was found while validating this
node.
- setWell(WellData) - Method in class net.sf.basedb.core.data.FeatureData
-
- setWells(Map<PlateCoordinate, WellData>) - Method in class net.sf.basedb.core.data.PlateData
-
- setWidth(String) - Method in class net.sf.basedb.clients.web.extensions.plot.MAPlotFactory
-
- setWidth(int) - Method in class net.sf.basedb.clients.web.extensions.plot.PlotGeneratorBean
-
- setWidth(int) - Method in class net.sf.basedb.clients.web.taglib.table.Form
-
- setWidth(int) - Method in class net.sf.basedb.core.AnnotationType
-
Set the recommended width in characters a client application should use
to render an input field for annotations of this annotation type.
- setWidth(int) - Method in class net.sf.basedb.core.data.AnnotationTypeData
-
- setWorkerThread() - Method in class net.sf.basedb.core.signal.EnhancedThreadSignalHandler
-
Set the worker thread to the current thread.
- setWorkerThread(Thread) - Method in class net.sf.basedb.core.signal.ThreadSignalHandler
-
Set the worker thread that should be interrupted when a signal is
receiver.
- setWrapper(WrappingRenderer<?>) - Method in class net.sf.basedb.clients.web.taglib.extensions.Render
-
- setWriteProtected(boolean) - Method in class net.sf.basedb.core.data.FileData
-
- setWriteProtected(boolean) - Method in class net.sf.basedb.core.File
-
Set the write protected flag for this file.
- setWriter(BaseFileWriter) - Method in class net.sf.basedb.util.export.spotdata.BaseFileExporter
-
Set the stream were the exported data should be written.
- setX(Float) - Method in class net.sf.basedb.core.data.RawData
-
- setXOffset(int) - Method in class net.sf.basedb.core.data.SpotImagesData
-
- setXOffset(int) - Method in class net.sf.basedb.core.SpotImages
-
- setXScale(int) - Method in class net.sf.basedb.core.data.SpotImagesData
-
- setXScale(int) - Method in class net.sf.basedb.core.SpotImages
-
- setY(Float) - Method in class net.sf.basedb.core.data.RawData
-
- setYOffset(int) - Method in class net.sf.basedb.core.data.SpotImagesData
-
- setYOffset(int) - Method in class net.sf.basedb.core.SpotImages
-
- setYScale(int) - Method in class net.sf.basedb.core.data.SpotImagesData
-
- setYScale(int) - Method in class net.sf.basedb.core.SpotImages
-
- severities - Variable in class net.sf.basedb.util.overview.ValidationOptions
-
Maps Validator ID to severity.
- Severity - Enum in net.sf.basedb.util.overview
-
Severity levels for a validation rule.
- Severity(String) - Constructor for enum net.sf.basedb.util.overview.Severity
-
- sf - Static variable in class net.sf.basedb.core.HibernateUtil
-
The single SessionFactory.
- SHA256_FINGERPRINT_PATTERN - Static variable in class net.sf.basedb.core.FileServer
-
Pattern that matches a SSH SHa256 fingerprint in BASE64 encoding (padding is optional).
- shareable - Static variable in class net.sf.basedb.core.Item.DefinedPermissions
-
- Shareable - Interface in net.sf.basedb.core
-
An
Shareable
item is an item which can be shared to
other
User
:s,
Group
:s and
Project
:s.
- shareable_annotatable - Static variable in class net.sf.basedb.core.Item.DefinedPermissions
-
- SHAREABLE_FILTER - Static variable in class net.sf.basedb.core.QueryRuntimeFilterFactory
-
- ShareableData - Interface in net.sf.basedb.core.data
-
A shareable item is an item which can be shared to other users,
groups or projects.
- ShareableFilter() - Constructor for class net.sf.basedb.core.QueryRuntimeFilterFactory.ShareableFilter
-
- shareableItems - Static variable in class net.sf.basedb.core.Metadata
-
- ShareableUtil - Class in net.sf.basedb.core
-
Utility methods that will make it easier to implement
the
Shareable
interface, including data validation.
- ShareableUtil() - Constructor for class net.sf.basedb.core.ShareableUtil
-
- ShareableUtil - Class in net.sf.basedb.util
-
- ShareableUtil() - Constructor for class net.sf.basedb.util.ShareableUtil
-
- SharedData - Class in net.sf.basedb.core.data
-
- SharedData() - Constructor for class net.sf.basedb.core.data.SharedData
-
- SharedItem - Class in net.sf.basedb.core
-
- SharedItem(SharedData) - Constructor for class net.sf.basedb.core.SharedItem
-
- sharedTo(boolean, Restriction, Restriction, Restriction) - Static method in class net.sf.basedb.core.query.Hql
-
A special restriction that works on
Shareable
items.
- sharedTo - Variable in class net.sf.basedb.core.query.SharedToRestriction
-
- SharedToRestriction - Class in net.sf.basedb.core.query
-
A special restriction that works on
Shareable
items.
- SharedToRestriction(boolean, Restriction, Restriction, Restriction) - Constructor for class net.sf.basedb.core.query.SharedToRestriction
-
- shareRecursively(DbControl, Directory) - Static method in class net.sf.basedb.core.ShareableUtil
-
Share all files and sub-directories in the given directory with the
same permissions.
- SHORT - Static variable in class net.sf.basedb.core.hibernate.TypeWrapper
-
- ShortWriter - Class in net.sf.basedb.core.migrate
-
Database-independent writer implementation that writes short
values from a result set.
- ShortWriter(ResultSet, int, Writer, char[]) - Constructor for class net.sf.basedb.core.migrate.ShortWriter
-
- shouldSend(EventType, ExtensionPoint<?>, Extension<?>) - Method in class net.sf.basedb.util.extensions.events.ActionClassEventFilter
-
- shouldSend(EventType, ExtensionPoint<?>, Extension<?>) - Method in class net.sf.basedb.util.extensions.events.AllEventsFilter
-
- shouldSend(EventType, ExtensionPoint<?>, Extension<?>) - Method in class net.sf.basedb.util.extensions.events.CombiningEventFilter
-
- shouldSend(EventType, ExtensionPoint<?>, Extension<?>) - Method in interface net.sf.basedb.util.extensions.events.EventFilter
-
Determine if the event should be sent to the event handler or not.
- shouldSend(EventType, ExtensionPoint<?>, Extension<?>) - Method in class net.sf.basedb.util.extensions.events.EventTypeFilter
-
- shouldSend(EventType, ExtensionPoint<?>, Extension<?>) - Method in class net.sf.basedb.util.extensions.events.ExtensionEventFilter
-
- shouldSend(EventType, ExtensionPoint<?>, Extension<?>) - Method in class net.sf.basedb.util.extensions.events.ExtensionPointEventFilter
-
- show - Variable in class net.sf.basedb.clients.web.taglib.table.ColumnDef
-
If the column should be visible or not.
- show - Variable in class net.sf.basedb.clients.web.taglib.table.TableColumn
-
- showChangeHistoryTab(SessionControl) - Static method in class net.sf.basedb.clients.web.ChangeHistoryUtil
-
Check if the "Change history" tab should be visible for
the current user or not.
- showClass - Variable in class net.sf.basedb.clients.web.taglib.HideableSection
-
- showClazz - Variable in class net.sf.basedb.clients.web.extensions.section.IncludeContentSectionFactory
-
- showClazz - Variable in class net.sf.basedb.clients.web.extensions.section.SectionBean
-
- showInitially - Variable in class net.sf.basedb.clients.web.taglib.HideableSection
-
If the section should be shown or hidden to start with.
- SHUTDOWN - Static variable in class net.sf.basedb.core.signal.Signal
-
The SHUTDOWN signal, that requests that the receiver should
clean up and die.
- shutdown(CloseableHttpClient) - Static method in class net.sf.basedb.util.HttpUtil
-
Safely shuts down a http client and it's connection manager
without trowing an exception.
- ShutdownHook(SignalReceiver) - Constructor for class net.sf.basedb.clients.jobagent.executors.ThreadJobExecutor.ShutdownHook
-
- ShutdownSignalSender - Class in net.sf.basedb.core.signal
-
A signal sender implementation that is used by the system when
shutting down.
- ShutdownSignalSender() - Constructor for class net.sf.basedb.core.signal.ShutdownSignalSender
-
- signal - Variable in class net.sf.basedb.core.signal.ExtensionSignalTransporter.SendSignalRenderer
-
- Signal - Class in net.sf.basedb.core.signal
-
Represents a signal that can be sent to a class implementing the
SignalTarget
interface.
- Signal(String, String, String) - Constructor for class net.sf.basedb.core.signal.Signal
-
- signal - Variable in class net.sf.basedb.core.signal.SimpleSignalSender
-
- signal - Variable in exception net.sf.basedb.core.signal.UnsupportedSignalException
-
- SignalException - Exception in net.sf.basedb.core.signal
-
Base class for all signal exceptions.
- SignalException() - Constructor for exception net.sf.basedb.core.signal.SignalException
-
- SignalException(String) - Constructor for exception net.sf.basedb.core.signal.SignalException
-
- SignalException(Throwable) - Constructor for exception net.sf.basedb.core.signal.SignalException
-
- SignalException(String, Throwable) - Constructor for exception net.sf.basedb.core.signal.SignalException
-
- signalHandler - Variable in class net.sf.basedb.clients.jobagent.executors.ProcessJobExecutor
-
- signalHandler - Variable in class net.sf.basedb.clients.web.plugins.SimpleExport
-
- SignalHandler - Interface in net.sf.basedb.core.signal
-
A signal handler is an object that is able to receive and act on signals.
- signalHandler - Variable in class net.sf.basedb.plugins.AbstractFlatFileImporter
-
- signalHandler - Variable in class net.sf.basedb.plugins.Base1PluginExecuter
-
- signalHandler - Variable in class net.sf.basedb.plugins.BaseFileExporterPlugin
-
- signalHandler - Variable in class net.sf.basedb.plugins.BfsExporterPlugin
-
- signalHandler - Variable in class net.sf.basedb.plugins.CdfFileReporterImporter
-
- signalHandler - Variable in class net.sf.basedb.plugins.CloneReportersPlugin
-
- signalHandler - Variable in class net.sf.basedb.plugins.executor.ExternalProgramExecutor
-
- signalHandler - Variable in class net.sf.basedb.plugins.FormulaFilter
-
- signalHandler - Variable in class net.sf.basedb.plugins.GalExporter
-
- signalHandler - Variable in class net.sf.basedb.plugins.HelpExporter
-
- signalHandler - Variable in class net.sf.basedb.plugins.HelpImporter
-
- signalHandler - Variable in class net.sf.basedb.plugins.IntensityCalculatorPlugin
-
- signalHandler - Variable in class net.sf.basedb.plugins.JepExtraValueCalculator
-
- signalHandler - Variable in class net.sf.basedb.plugins.JepIntensityTransformer
-
- signalHandler - Variable in class net.sf.basedb.plugins.LowessNormalization
-
- signalHandler - Variable in class net.sf.basedb.plugins.MedianRatioNormalization
-
- signalHandler - Variable in class net.sf.basedb.plugins.PackedFileExporter
-
- signalHandler - Variable in class net.sf.basedb.plugins.PlateMappingExporter
-
- signalHandler - Variable in class net.sf.basedb.plugins.PluginConfigurationExporter
-
- signalHandler - Variable in class net.sf.basedb.plugins.PluginConfigurationImporter
-
- signalHandler - Variable in class net.sf.basedb.plugins.SpotImageCreator
-
- signalHandler - Variable in class net.sf.basedb.util.zip.AbstractFileUnpacker
-
- signalHandlerURI - Variable in class net.sf.basedb.core.signal.AbstractSignalTransporter
-
- SignalKeyring() - Constructor for class net.sf.basedb.core.Job.SignalKeyring
-
- SignalReceivedException - Exception in net.sf.basedb.core.signal
-
This exception can be thrown by signal handlers when one or more
signal has been received.
- SignalReceivedException(Signal) - Constructor for exception net.sf.basedb.core.signal.SignalReceivedException
-
Create a new UnsupportedSignalException.
- SignalReceivedException(Signal...) - Constructor for exception net.sf.basedb.core.signal.SignalReceivedException
-
Create a new SignalReceivedException when multiple signals has
been received.
- SignalReceivedException(List<Signal>) - Constructor for exception net.sf.basedb.core.signal.SignalReceivedException
-
Create a new SignalReceivedException when multiple signals has
been received.
- signalReceiver - Variable in class net.sf.basedb.clients.jobagent.Agent
-
- signalReceiver - Variable in class net.sf.basedb.clients.jobagent.executors.ProcessJobExecutor
-
- signalReceiver - Variable in class net.sf.basedb.clients.jobagent.executors.ThreadJobExecutor.ShutdownHook
-
- signalReceiver - Variable in class net.sf.basedb.clients.jobagent.executors.ThreadJobExecutor
-
- signalReceiver - Variable in class net.sf.basedb.clients.jobagent.handlers.SignalRequestHandler
-
- signalReceiver - Static variable in class net.sf.basedb.core.InternalJobQueue
-
Use the local signal receiver only.
- signalReceiver - Variable in class net.sf.basedb.core.PluginExecutionRequest
-
- SignalReceiver - Interface in net.sf.basedb.core.signal
-
- SignalRequestHandler - Class in net.sf.basedb.clients.jobagent.handlers
-
This is a request handler for the signal
commands.
- SignalRequestHandler(Agent) - Constructor for class net.sf.basedb.clients.jobagent.handlers.SignalRequestHandler
-
- signals - Variable in class net.sf.basedb.core.signal.AbstractSignalTransporter
-
- signals - Static variable in class net.sf.basedb.core.signal.Signal
-
Holds all registered signals.
- signals - Variable in exception net.sf.basedb.core.signal.SignalReceivedException
-
- SignalSender - Interface in net.sf.basedb.core.signal
-
A signal sender is responsible for sending a signal to
a signal handler.
- SignalTarget - Interface in net.sf.basedb.core.signal
-
This interface should be implemented by classes that are able
to receive
Signal
:s.
- signalTransporter - Variable in class net.sf.basedb.core.data.JobData
-
- signalTransporter - Variable in class net.sf.basedb.core.Job
-
- SignalTransporter - Interface in net.sf.basedb.core.signal
-
A signal transporter is a class that knows how to send a signal to a
specific
SignalReceiver
implementation.
- silent - Variable in class net.sf.basedb.core.hibernate.DbIndexWork
-
- simple(Expression, String, Type, Formula.AverageMethod, Formatter<?>) - Static method in class net.sf.basedb.util.export.spotdata.ExportableFieldFactory
-
Create a simple dynamic field.
- SimpleAbsoluteProgressReporter - Class in net.sf.basedb.core
-
- SimpleAbsoluteProgressReporter(ProgressReporter, long) - Constructor for class net.sf.basedb.core.SimpleAbsoluteProgressReporter
-
Create a new absolute progress reporter.
- SimpleAuthenticator - Class in net.sf.basedb.core.authentication
-
- SimpleAuthenticator() - Constructor for class net.sf.basedb.core.authentication.SimpleAuthenticator
-
Deprecated.
Create a new SimpleAuthenticator
object.
- SimpleDynamicField - Class in net.sf.basedb.util.export.spotdata
-
Represents an exported data field.
- SimpleDynamicField() - Constructor for class net.sf.basedb.util.export.spotdata.SimpleDynamicField
-
Create a new object.
- SimpleErrorHandler - Class in net.sf.basedb.util.error
-
A simple error handler that either ignores all errors or
re-throws them.
- SimpleErrorHandler(boolean) - Constructor for class net.sf.basedb.util.error.SimpleErrorHandler
-
Create a new simple error handler.
- SimpleExport - Class in net.sf.basedb.clients.web.plugins
-
Export plugin for exporting data from table listings in the web client.
- SimpleExport() - Constructor for class net.sf.basedb.clients.web.plugins.SimpleExport
-
- SimpleJepFunction - Class in net.sf.basedb.util.jep
-
A simple base class for registering a JEP function by name and number
of parameters.
- SimpleJepFunction(String, int) - Constructor for class net.sf.basedb.util.jep.SimpleJepFunction
-
- SimpleProgressReporter - Class in net.sf.basedb.core
-
This is a simple implementation of the
ProgressReporter
interface,
which simply remembers that last values.
- SimpleProgressReporter(ProgressReporter) - Constructor for class net.sf.basedb.core.SimpleProgressReporter
-
Create a new simple progress reporter.
- SimpleSignalProgressReporter - Class in net.sf.basedb.clients.web.util
-
This class can be used to report progress and hold signal receiver
for those export plugins that download immediately.
- SimpleSignalProgressReporter(ProgressReporter) - Constructor for class net.sf.basedb.clients.web.util.SimpleSignalProgressReporter
-
- SimpleSignalSender - Class in net.sf.basedb.core.signal
-
A signal sender implementation that sends a specific signal
to all handlers that supports it.
- SimpleSignalSender(Signal) - Constructor for class net.sf.basedb.core.signal.SimpleSignalSender
-
Create a new signal sender.
- SINGLE_QUOTE - Static variable in class net.sf.basedb.clients.web.util.HTML
-
- SingleExtensionFilter - Class in net.sf.basedb.util.extensions
-
A filter implementation that enables a single extension and
disables all other.
- SingleExtensionFilter(Extension<?>) - Constructor for class net.sf.basedb.util.extensions.SingleExtensionFilter
-
Create a filter that enables the given extension
and disables all other.
- SingleExtensionFilter(String) - Constructor for class net.sf.basedb.util.extensions.SingleExtensionFilter
-
Create a filter that enables the extension with the
given ID and disables all others.
- SingleFileValidationAction - Class in net.sf.basedb.util.fileset
-
Base class for validators that works on single files
of a known data file type.
- SingleFileValidationAction(String) - Constructor for class net.sf.basedb.util.fileset.SingleFileValidationAction
-
Create a new instance.
- size() - Method in class net.sf.basedb.clients.web.extensions.skin.ImageRemapper
-
Get the number of remapped images.
- size - Variable in class net.sf.basedb.core.data.FileData
-
- size - Variable in class net.sf.basedb.core.data.ItemListData
-
- size - Variable in class net.sf.basedb.core.data.PhysicalBioAssayData
-
- size - Variable in class net.sf.basedb.core.data.ReporterListData
-
- size - Variable in class net.sf.basedb.core.dbengine.TableInfo.ColumnInfo
-
- size() - Method in class net.sf.basedb.core.GroupPermissions
-
Get the number of entries.
- size - Variable in class net.sf.basedb.core.hibernate.TypeWrapper
-
- size() - Method in class net.sf.basedb.core.ItemResultList
-
- size - Variable in class net.sf.basedb.core.log.EntityLogOptions
-
- size() - Method in class net.sf.basedb.core.Presets.Preset
-
Get the number of settings in the preset.
- size() - Method in class net.sf.basedb.core.ProjectPermissions
-
Get the number of entries.
- size(String, String) - Static method in class net.sf.basedb.core.query.Hql
-
Create a size expression for a property that is a collection
of values.
- size() - Method in class net.sf.basedb.core.UserPermissions
-
Get the number of entries.
- size - Variable in class net.sf.basedb.core.VirtualColumn
-
The size of the column if it is a string.
- size() - Method in class net.sf.basedb.util.Enumeration
-
- size() - Method in class net.sf.basedb.util.formatter.LookupFormatter
-
Get the number of registered lookup entries.
- size - Variable in class net.sf.basedb.util.JarClassLoader.JarInfo
-
- size(String) - Method in class net.sf.basedb.util.StaticCache
-
Checks the size (in bytes) of a cache entry.
- size() - Method in class net.sf.basedb.util.Tree
-
- sizeColumnMapping - Static variable in class net.sf.basedb.plugins.batchimport.PhysicalBioAssayImporter
-
- sizeMapper - Variable in class net.sf.basedb.plugins.batchimport.PhysicalBioAssayImporter
-
- sizeOf(Object) - Method in enum net.sf.basedb.core.Type
-
Get the size in bytes an object of this type requires when
stored in the database.
- SkinAction - Interface in net.sf.basedb.clients.web.extensions.skin
-
Action for adding skins to BASE.
- skinActions - Variable in class net.sf.basedb.clients.web.taglib.Page
-
- skinContext - Variable in class net.sf.basedb.clients.web.taglib.Page
-
- skip - Variable in class net.sf.basedb.clients.web.taglib.table.Hidden
-
If the hidden element should be included or not.
- skip(long) - Method in class net.sf.basedb.util.InputStreamCombiner
-
- skip(long) - Method in class net.sf.basedb.util.InputStreamSplitter
-
- skip(long) - Method in class net.sf.basedb.util.InputStreamTracker
-
- skipInsertIfMissingFeature - Variable in class net.sf.basedb.core.RawDataBatcher
-
If inserts that can't find a matching feature should be skipped
or generate an error.
- skipInsertIfMissingFeature(boolean) - Method in class net.sf.basedb.core.RawDataBatcher
-
Specify if the insert method should skip the insert if a feature for
the spot can't be found.
- skippedLast - Variable in class net.sf.basedb.plugins.batchimport.AbstractItemImporter
-
- skippedLines - Variable in class net.sf.basedb.plugins.AbstractFlatFileImporter
-
- skippedLines - Variable in class net.sf.basedb.util.parser.FlatFileParser
-
- skipRepeatedTranscriptIds - Variable in class net.sf.basedb.util.gtf.GtfInputStream
-
- slot - Variable in class net.sf.basedb.clients.jobagent.slotmanager.MasterSlotManager.RemoteSlot
-
- Slot - Class in net.sf.basedb.clients.jobagent.slotmanager
-
Represents a slot that has been assigned to a job.
- Slot(Job.ExecutionTime) - Constructor for class net.sf.basedb.clients.jobagent.slotmanager.Slot
-
Create a new slot and automatically assign an id to
it.
- Slot(String, Job.ExecutionTime) - Constructor for class net.sf.basedb.clients.jobagent.slotmanager.Slot
-
Create a new slot.
- slot - Variable in class net.sf.basedb.core.InternalJobQueue.JobRunner
-
- slot - Variable in class net.sf.basedb.util.jobagent.JobInfo
-
- slotManager - Variable in class net.sf.basedb.clients.jobagent.Agent
-
- SlotManager - Interface in net.sf.basedb.clients.jobagent.slotmanager
-
A slot manager is responsible for slot assigment to jobs.
- slotManagerClass - Variable in class net.sf.basedb.clients.jobagent.Agent
-
- SMART_IMAGES - Static variable in class net.sf.basedb.clients.web.util.HTML
-
- smartEnum - Variable in class net.sf.basedb.clients.web.taglib.table.ColumnDef
-
- snapshotIsInvalid - Variable in class net.sf.basedb.core.AnnotationSet
-
Flag to indicate if this annotation set has been modified
and the snapshot must be removed.
- snapshotManager - Variable in class net.sf.basedb.clients.web.ExperimentExplorer
-
The snapshot manager that loads annotation values.
- snapshotManager - Variable in class net.sf.basedb.clients.web.plugins.BioAssayExperimentalFactorLoader
-
- SnapshotManager - Class in net.sf.basedb.core.snapshot
-
Manager for annotation snapshots.
- SnapshotManager() - Constructor for class net.sf.basedb.core.snapshot.SnapshotManager
-
Create a new snapshot manager.
- snapshotManager - Variable in class net.sf.basedb.util.annotations.InheritAnnotationsManager
-
- snapshotManager - Variable in class net.sf.basedb.util.export.spotdata.AbstractBioAssaySetExporter
-
- snapshotManager - Variable in class net.sf.basedb.util.export.spotdata.AbstractFieldConverter
-
- snapshotManager - Variable in class net.sf.basedb.util.export.spotdata.AnnotationAssayField
-
- snapshotManager - Variable in class net.sf.basedb.util.overview.GenericOverview
-
- snapshots - Variable in class net.sf.basedb.core.snapshot.AnnotationLoaderUtil
-
- snapshots - Variable in class net.sf.basedb.core.snapshot.SnapshotManager
-
- snapshotsToDelete - Variable in class net.sf.basedb.core.AnnotationBatcher
-
- socket - Variable in class net.sf.basedb.core.signal.SocketSignalReceiver.ListenerThread
-
- socket - Variable in class net.sf.basedb.util.jobagent.JobAgentServerConnection.ListenerThread
-
- SocketSignalReceiver - Class in net.sf.basedb.core.signal
-
A signal receiver implementation that listens on a socket for incoming signals.
- SocketSignalReceiver() - Constructor for class net.sf.basedb.core.signal.SocketSignalReceiver
-
Create a new socket signal receiver.
- SocketSignalReceiver.ListenerThread - Class in net.sf.basedb.core.signal
-
This class is used for listening to the specified socket for
incoming connections.
- SocketSignalTransporter - Class in net.sf.basedb.core.signal
-
- SocketSignalTransporter() - Constructor for class net.sf.basedb.core.signal.SocketSignalTransporter
-
Create a new socket signal transporter.
- SocketUtil - Class in net.sf.basedb.util
-
This class contains some useful methods when working with sockets.
- SocketUtil() - Constructor for class net.sf.basedb.util.SocketUtil
-
- software - Variable in class net.sf.basedb.core.data.DerivedBioAssayData
-
- software - Variable in class net.sf.basedb.core.data.RawBioAssayData
-
- Software - Class in net.sf.basedb.core
-
This class is used to represent individual software items
and information about them.
- Software(SoftwareData) - Constructor for class net.sf.basedb.core.Software
-
Creates a new software item.
- software - Variable in class net.sf.basedb.plugins.IlluminaRawDataImporter
-
- softwareColumnMapping - Static variable in class net.sf.basedb.plugins.batchimport.DerivedBioAssayImporter
-
- softwareColumnMapping - Static variable in class net.sf.basedb.plugins.batchimport.RawBioAssayImporter
-
- SoftwareData - Class in net.sf.basedb.core.data
-
This class holds information about a software.
- SoftwareData() - Constructor for class net.sf.basedb.core.data.SoftwareData
-
- softwareHasBeenSet - Variable in class net.sf.basedb.core.DerivedBioAssay
-
- softwareHasBeenSet - Variable in class net.sf.basedb.core.RawBioAssay
-
- SoftwareLoader - Class in net.sf.basedb.util.overview.loader
-
Node loader implementation for software.
- SoftwareLoader() - Constructor for class net.sf.basedb.util.overview.loader.SoftwareLoader
-
- softwareMapper - Variable in class net.sf.basedb.plugins.batchimport.DerivedBioAssayImporter
-
- softwareMapper - Variable in class net.sf.basedb.plugins.batchimport.RawBioAssayImporter
-
- softwareQuery - Variable in class net.sf.basedb.plugins.batchimport.AbstractItemImporter
-
- SoftwareValidator - Class in net.sf.basedb.util.overview.validator
-
Validator implementation for software.
- SoftwareValidator() - Constructor for class net.sf.basedb.util.overview.validator.SoftwareValidator
-
- sort(List<? extends InvokationContext<?>>) - Method in class net.sf.basedb.util.extensions.DefaultFilter
-
- sort(List<? extends InvokationContext<?>>) - Method in interface net.sf.basedb.util.extensions.ExtensionsFilter
-
Sort a list of invoked extensions according to some property.
- sort(List<? extends InvokationContext<?>>) - Method in class net.sf.basedb.util.extensions.SingleExtensionFilter
-
Do nothing since the list should contain only a single extension.
- sortable - Variable in class net.sf.basedb.clients.web.extensions.list.AbstractListColumnBean
-
- sortable - Variable in class net.sf.basedb.clients.web.extensions.list.PropertyPathActionFactory
-
- sortable - Variable in class net.sf.basedb.clients.web.taglib.table.ColumnDef
-
If the column is sortable or not
- sortable - Variable in class net.sf.basedb.clients.web.taglib.table.TableColumn
-
- sortby - Variable in class net.sf.basedb.clients.web.taglib.table.Table
-
The column to sort by.
- sortBy(Expression) - Method in enum net.sf.basedb.core.ItemContext.SortDirection
-
- sortByAnnotationType(DbControl) - Static method in class net.sf.basedb.core.snapshot.AnnotationSnapshot
-
Create a comparator for sorting annotation snapshots by the name
of the annotation type.
- SortByProjectComparator() - Constructor for class net.sf.basedb.core.snapshot.AnnotationSetSnapshot.SortByProjectComparator
-
- sortChildren(Comparator<? super Node>) - Method in class net.sf.basedb.util.overview.Node
-
Sorts the list of child nodes.
- sortColumns - Variable in class net.sf.basedb.clients.web.taglib.table.Table
-
- sortDirection - Variable in class net.sf.basedb.clients.web.taglib.table.Table
-
ASC or DESC
- sortDirection - Variable in class net.sf.basedb.core.data.ContextData
-
- sortDirection - Variable in class net.sf.basedb.core.ItemContext
-
- SortDirection(int, String) - Constructor for enum net.sf.basedb.core.ItemContext.SortDirection
-
Creates a new direction.
- sortKeys() - Method in class net.sf.basedb.util.Enumeration
-
- sortProperty - Variable in class net.sf.basedb.clients.web.extensions.list.AbstractListColumnBean
-
- sortProperty - Variable in class net.sf.basedb.clients.web.extensions.list.PropertyPathActionFactory
-
- sortProperty - Variable in class net.sf.basedb.clients.web.taglib.table.ColumnDef
-
Optional property used for sorting.
- sortProperty - Variable in class net.sf.basedb.core.data.ContextData
-
- sortProperty - Variable in class net.sf.basedb.core.ItemContext
-
- sortValues() - Method in class net.sf.basedb.util.Enumeration
-
- source - Variable in class net.sf.basedb.clients.web.extensions.DynamicActionAttributeSupport
-
- Source() - Constructor for enum net.sf.basedb.core.Annotation.Source
-
- source - Variable in class net.sf.basedb.core.data.AnnotationData
-
- source - Variable in class net.sf.basedb.core.data.annotations.AnnotationLink
-
- source - Variable in class net.sf.basedb.core.data.TransformationData
-
- source - Variable in class net.sf.basedb.core.snapshot.AnnotationSnapshot
-
- source - Variable in class net.sf.basedb.util.annotations.InheritAnnotationsManager.AnnotationTypeFilter
-
- source - Variable in class net.sf.basedb.util.export.spotdata.AbstractBioAssaySetExporter
-
- source - Variable in class net.sf.basedb.util.export.spotdata.AbstractFieldConverter
-
- source - Variable in class net.sf.basedb.util.listable.AbstractSourceItemTransformer
-
- source - Variable in class net.sf.basedb.util.listable.SourceItemTransformerChain
-
- SOURCE_BIOASSAYS - Static variable in class net.sf.basedb.core.plugin.AbstractAnalysisPlugin
-
- SOURCE_BIOASSAYSET - Static variable in class net.sf.basedb.core.plugin.AbstractAnalysisPlugin
-
- SOURCE_DERIVEDBIOASSAY - Static variable in class net.sf.basedb.core.plugin.AbstractAnalysisPlugin
-
- sourceBioAssaySetParameter - Variable in class net.sf.basedb.core.plugin.AbstractAnalysisPlugin
-
The source parameter for bioassay set.
- sourceBioAssaySetType - Static variable in class net.sf.basedb.core.plugin.AbstractAnalysisPlugin
-
The parameter type for the source bioassay set.
- sourceColumnMapper - Variable in class net.sf.basedb.plugins.PlateMappingImporter
-
- sourceCount - Variable in class net.sf.basedb.core.data.PlateMappingData
-
- sourceDerivedBioAssayParameter - Variable in class net.sf.basedb.core.plugin.AbstractAnalysisPlugin
-
The source parameter for derived bioassay.
- sourceDerivedBioAssayType - Static variable in class net.sf.basedb.core.plugin.AbstractAnalysisPlugin
-
The parameter type for the source derived bioassay.
- sourceFile - Variable in class net.sf.basedb.util.importer.spotdata.BaseFileImporter
-
- sourceGeometry - Variable in class net.sf.basedb.core.data.PlateMappingData
-
- sourceIntensityTransform - Variable in class net.sf.basedb.core.data.FormulaData
-
- sourceItemTransform - Variable in class net.sf.basedb.core.data.ItemListSyncFilterData
-
- SourceItemTransform() - Constructor for enum net.sf.basedb.core.SyncFilter.SourceItemTransform
-
- SourceItemTransformer - Interface in net.sf.basedb.util.listable
-
Implementations are responsible for transforming a set of source item
ID:s into a set of related target item ID:s.
- SourceItemTransformerChain - Class in net.sf.basedb.util.listable
-
Chains together one or more source item transformers.
- SourceItemTransformerChain(List<SourceItemTransformer>) - Constructor for class net.sf.basedb.util.listable.SourceItemTransformerChain
-
Create a new source item transformer chain.
- SourceItemTransformerFactory - Interface in net.sf.basedb.util.listable
-
- sourceItemType - Variable in class net.sf.basedb.core.data.ItemListSyncFilterData
-
- sourceMustExist - Variable in class net.sf.basedb.core.data.ItemListSyncFilterData
-
- sourcePlateMapper - Variable in class net.sf.basedb.plugins.PlateMappingImporter
-
- sourceRowMapper - Variable in class net.sf.basedb.plugins.PlateMappingImporter
-
- sources - Variable in class net.sf.basedb.core.data.BioMaterialEventData
-
- sourceSubSetParameter - Variable in class net.sf.basedb.core.plugin.AbstractAnalysisPlugin
-
The bioAssays subset parameter.
- SPACE - Static variable in class net.sf.basedb.clients.web.util.HTML
-
- spacingX - Variable in class net.sf.basedb.core.data.ArrayDesignBlockData
-
- spacingX - Variable in class net.sf.basedb.plugins.PrintMapFlatFileImporter.MetaBlock
-
- spacingY - Variable in class net.sf.basedb.core.data.ArrayDesignBlockData
-
- spacingY - Variable in class net.sf.basedb.plugins.PrintMapFlatFileImporter.MetaBlock
-
- specialLoggers - Variable in class net.sf.basedb.core.log.db.DbLogManagerFactory
-
- SpecialQuery<C> - Class in net.sf.basedb.core
-
A special HQL query implementation that can return almost any kind of object.
- SpecialQuery(String, String, String, Transformer<C, ?>) - Constructor for class net.sf.basedb.core.SpecialQuery
-
- specifications - Variable in class net.sf.basedb.util.annotations.InheritAnnotationsManager
-
- specifications - Variable in class net.sf.basedb.util.annotations.RunnableInheritAnnotationsManager
-
- spiParser - Variable in class net.sf.basedb.util.importer.spotdata.BaseFileInfo.SpotSectionInfo
-
- splitHeader - Static variable in class net.sf.basedb.plugins.IlluminaRawDataImporter
-
A column header must be like: extendedpropertyname-arrayname
- splitter - Variable in class net.sf.basedb.util.StreamCacher
-
- splitValueWithUnit(String) - Static method in class net.sf.basedb.util.units.UnitUtil
-
Splits a value with an optional unit.
- SPOT_ALL - Static variable in class net.sf.basedb.clients.web.ExperimentExplorer
-
- SPOT_AVG - Static variable in class net.sf.basedb.clients.web.ExperimentExplorer
-
- SPOT_DATA - Static variable in class net.sf.basedb.core.File
-
The id for the FileType
item representing a
file containing analysed spot data.
- SPOT_IMAGES - Static variable in class net.sf.basedb.core.File
-
The id for the FileType
item representing a
spot images file.
- spotBatcher - Variable in class net.sf.basedb.core.BioAssaySet
-
The one and only spot batcher for this bioassayset.
- SpotBatcher - Class in net.sf.basedb.core
-
Batcher class for per-spot intensity values for bioassaysets.
- SpotBatcher(DbControl, BioAssaySet) - Constructor for class net.sf.basedb.core.SpotBatcher
-
Create a new spot batcher for a bioassayset.
- spotBatcher - Variable in class net.sf.basedb.util.importer.spotdata.MatrixSpotIntensityEventHandler
-
- spotBatcher - Variable in class net.sf.basedb.util.importer.spotdata.SerialSpotIntensityEventHandler
-
- spotCount - Variable in class net.sf.basedb.util.export.spotdata.BfsExporter
-
- spotCount - Variable in class net.sf.basedb.util.export.spotdata.MatrixBaseFileExporter
-
- spotCount - Variable in class net.sf.basedb.util.export.spotdata.SerialBaseFileExporter
-
- SpotData(short, int, float, float, int, boolean, MACalculator) - Constructor for class net.sf.basedb.plugins.LowessNormalization.SpotData
-
- SpotData(int, float, float, int, MACalculator) - Constructor for class net.sf.basedb.plugins.MedianRatioNormalization.SpotData
-
- SpotExtraValueBatcher<I> - Class in net.sf.basedb.core
-
Batcher class for per-spot extra values.
- SpotExtraValueBatcher(DbControl, ExtraValue) - Constructor for class net.sf.basedb.core.SpotExtraValueBatcher
-
Create a new spot batcher for a bioassayset.
- spotExtraValueBatchers - Variable in class net.sf.basedb.core.BioAssaySet
-
Cache of already created spot extra value batchers.
- spotFields - Variable in class net.sf.basedb.util.export.spotdata.AbstractBioAssaySetExporter
-
- SpotImage - Class in net.sf.basedb.core
-
Holds the image information about a single spot image
in PNG format.
- SpotImage(byte[]) - Constructor for class net.sf.basedb.core.SpotImage
-
Constructor that takes the image as a byte array.
- SpotImageCreator - Class in net.sf.basedb.plugins
-
- SpotImageCreator() - Constructor for class net.sf.basedb.plugins.SpotImageCreator
-
- SpotImageFormatter - Class in net.sf.basedb.clients.web.formatter
-
- SpotImageFormatter(DbControl, RawDataType, String) - Constructor for class net.sf.basedb.clients.web.formatter.SpotImageFormatter
-
- spotImages - Variable in class net.sf.basedb.core.data.RawBioAssayData
-
- SpotImages - Class in net.sf.basedb.core
-
Holds settings for creating small spot iamges from 1-3
image files and the raw data information for a single raw bioassay.
- SpotImages(SpotImagesData) - Constructor for class net.sf.basedb.core.SpotImages
-
- SpotImagesData - Class in net.sf.basedb.core.data
-
This class holds information about the settiings used to generate spot images
for a raw bio assay.
- SpotImagesData() - Constructor for class net.sf.basedb.core.data.SpotImagesData
-
- spotImagesFile - Variable in class net.sf.basedb.core.data.SpotImagesData
-
- SpotIntensityParser - Interface in net.sf.basedb.util.importer.spotdata
-
A spot intensity parser is responsible for parsing and extracting
spot intensity data on a row-by-row basis from a BASEfile.
- spotIntensityParsers - Variable in class net.sf.basedb.util.importer.spotdata.FirstPassSectionSpotsParser
-
- spotQuery - Variable in class net.sf.basedb.util.export.spotdata.MatrixBaseFileExporter
-
- spotQuery - Variable in class net.sf.basedb.util.export.spotdata.SerialBaseFileExporter
-
- spots - Variable in class net.sf.basedb.core.data.RawBioAssayData
-
- spotSectionInfo - Variable in class net.sf.basedb.util.importer.spotdata.BaseFileInfo
-
- SpotSectionInfo() - Constructor for class net.sf.basedb.util.importer.spotdata.BaseFileInfo.SpotSectionInfo
-
Creates a new object.
- spotsize - Variable in class net.sf.basedb.core.data.SpotImagesData
-
- spotSize - Variable in class net.sf.basedb.plugins.PrintMapFlatFileImporter
-
- spotSql - Variable in class net.sf.basedb.core.SpotBatcher
-
The statement that inserts spot data.
- spotSqlStatement - Variable in class net.sf.basedb.core.SpotBatcher
-
- sql - Variable in class net.sf.basedb.core.AnnotationBatcher.InsertBatcher
-
- sql - Variable in class net.sf.basedb.core.AnnotationBatcher.UpdateBatcher
-
- sql - Variable in class net.sf.basedb.core.hibernate.ExecuteUpdateWork
-
- sql - Variable in class net.sf.basedb.core.hibernate.ResultSetWork
-
- SqlColumnExpression - Class in net.sf.basedb.core.query
-
An expression representing the column in a
database tabe: alias.column.
- SqlColumnExpression(String, String) - Constructor for class net.sf.basedb.core.query.SqlColumnExpression
-
- sqlDeletes - Static variable in class net.sf.basedb.core.BatchUtil
-
Mapping classes/entity names to SQL deletes.
- sqlInserts - Static variable in class net.sf.basedb.core.BatchUtil
-
Mapping classes/entity names to SQL inserts.
- SqlQuery - Interface in net.sf.basedb.core.query
-
This is a query that is using SQL as the query language.
- sqlResult - Variable in class net.sf.basedb.core.DynamicResultIterator
-
- SqlResult - Interface in net.sf.basedb.core.query
-
This interface represents a single row in the results of
a
SqlQuery
.
- SqlResultImpl() - Constructor for class net.sf.basedb.core.DynamicResultIterator.SqlResultImpl
-
- SqlResultIterator - Interface in net.sf.basedb.core.query
-
Return the result of a
SqlQuery
as an iterator.
- SqlResultList<I> - Interface in net.sf.basedb.core.query
-
- SqlStatement(String) - Constructor for class net.sf.basedb.core.hibernate.SchemaGenerator.SqlStatement
-
- SqlStatement(String, String) - Constructor for class net.sf.basedb.core.hibernate.SchemaGenerator.SqlStatement
-
- sqlSymbol - Variable in enum net.sf.basedb.core.Operator
-
- sqlType - Variable in class net.sf.basedb.core.dbengine.TableInfo.ColumnInfo
-
- sqlType - Variable in class net.sf.basedb.core.hibernate.TypeWrapper
-
- sqlType - Variable in class net.sf.basedb.core.PositionExtraValueBatcher
-
The sql type code of the value to insert.
- sqlType - Variable in class net.sf.basedb.core.SpotExtraValueBatcher
-
The sql type code of the value to insert.
- sqlTypeCode - Variable in class net.sf.basedb.core.BatchedPropertyInfo
-
- sqlUpdates - Static variable in class net.sf.basedb.core.BatchUtil
-
Mapping classes/entity names to SQL updates.
- sqrt(Expression) - Static method in class net.sf.basedb.core.query.Expressions
-
Calculate the square root of an expression: new expression = sqrt(e).
- sqrt - Variable in class net.sf.basedb.core.query.QuadraticMeanExpression
-
- SqrtExpression - Class in net.sf.basedb.core.query
-
- SqrtExpression(Expression) - Constructor for class net.sf.basedb.core.query.SqrtExpression
-
- squaredSum - Variable in class net.sf.basedb.util.plot.HistogramPlot.HistogramBin
-
- SquareRootConverter - Class in net.sf.basedb.util.jep.convert
-
- SquareRootConverter() - Constructor for class net.sf.basedb.util.jep.convert.SquareRootConverter
-
- ssc - Variable in class net.sf.basedb.core.Application.SecondaryStorageControllerTask
-
- sshFingerprint - Variable in class net.sf.basedb.core.data.FileServerData
-
- sshFingerprint - Variable in class net.sf.basedb.util.uri.ConnectionParameters
-
- ssl - Static variable in class net.sf.basedb.util.EmailUtil
-
- SSLUtil2 - Class in net.sf.basedb.util.ssl
-
Utility class for working with SSL connections.
- SSLUtil2() - Constructor for class net.sf.basedb.util.ssl.SSLUtil2
-
- stackTrace - Variable in class net.sf.basedb.core.data.JobData
-
- stackTraceToImage(Throwable, int, int) - Static method in class net.sf.basedb.util.error.ThrowableUtil
-
Prints as much of a stacktrace as possible to an image.
- stackTraceToString(Throwable) - Static method in class net.sf.basedb.util.error.ThrowableUtil
-
- StandardFieldConverter - Class in net.sf.basedb.util.export.spotdata
-
Default field converter implementation that works mainly by
checking names and/or external id values of formulas, extra
values, experimental factors etc.
- StandardFieldConverter(DbControl, BioAssaySet) - Constructor for class net.sf.basedb.util.export.spotdata.StandardFieldConverter
-
Create a new standard field converter.
- start() - Method in class net.sf.basedb.clients.jobagent.Agent
-
Start the job agent.
- start() - Method in class net.sf.basedb.clients.web.extensions.service.DummyService
-
- start() - Method in interface net.sf.basedb.clients.web.extensions.service.ServiceControllerAction
-
Start the service if it is not already running.
- start(Extension<ServiceControllerAction>) - Static method in class net.sf.basedb.clients.web.extensions.service.Services
-
Start services as a result of an administrator has installed a new extension
or updated/enabled an existing on.
- start - Variable in class net.sf.basedb.clients.web.fileupload.FileUpload.UploadStream
-
- start() - Static method in class net.sf.basedb.core.Application
-
Starts the BASE application.
- start(boolean) - Static method in class net.sf.basedb.core.Application
-
Starts the BASE application.
- start(boolean, boolean, Boolean) - Static method in class net.sf.basedb.core.Application
-
Starts the BASE application.
- start(String, String, JobAgent) - Method in class net.sf.basedb.core.Job
-
Register the job as started.
- start(String, String, JobAgent, Date) - Method in class net.sf.basedb.core.Job
-
- start(String, String, String, JobAgent, Date) - Method in class net.sf.basedb.core.Job
-
Register the job as started.
- start() - Method in class net.sf.basedb.plugins.AbstractFlatFileImporter
-
Called once before starting the import.
- start() - Method in class net.sf.basedb.plugins.RawDataFlatFileImporter
-
Prepare for the import.
- start - Variable in class net.sf.basedb.util.ChainedProgressReporter
-
- start(int) - Method in class net.sf.basedb.util.timer.PerformanceTimer
-
Start the timer with the given index.
- startAgent() - Method in class net.sf.basedb.clients.jobagent.AgentController
-
Start the agent this controller is controlling.
- startDate - Variable in class net.sf.basedb.core.data.NewsData
-
- started - Variable in class net.sf.basedb.core.data.JobData
-
- startJob(Job, JobAgentSettings) - Method in class net.sf.basedb.clients.jobagent.Agent
-
Start a job.
- StartPageAction - Interface in net.sf.basedb.clients.web.extensions.startpage
-
Action for selecting the start page that should be displayed after
logging in to BASE.
- StartPageBean - Class in net.sf.basedb.clients.web.extensions.startpage
-
- StartPageBean() - Constructor for class net.sf.basedb.clients.web.extensions.startpage.StartPageBean
-
- StartRequestHandler - Class in net.sf.basedb.clients.jobagent.handlers
-
This is a request handler for the start
command.
- StartRequestHandler(Agent) - Constructor for class net.sf.basedb.clients.jobagent.handlers.StartRequestHandler
-
- StartServiceRenderer - Class in net.sf.basedb.clients.web.extensions.service
-
- StartServiceRenderer() - Constructor for class net.sf.basedb.clients.web.extensions.service.StartServiceRenderer
-
- StartStopServlet - Class in net.sf.basedb.clients.web.servlet
-
Servlet listener for starting BASE when the web server is started and
stopping BASE when the web server is stopped.
- StartStopServlet() - Constructor for class net.sf.basedb.clients.web.servlet.StartStopServlet
-
- startTime - Variable in class net.sf.basedb.clients.web.fileupload.FileUploadProgress
-
- startTime - Variable in class net.sf.basedb.util.extensions.manager.ProcessResults
-
- startTime - Variable in class net.sf.basedb.util.TransferRateProgressReporter
-
- startX - Variable in class net.sf.basedb.util.plot.HistogramPlot.HistogramBin
-
- state - Variable in class net.sf.basedb.core.log.EntityDetails
-
- state - Variable in class net.sf.basedb.core.PluginRequest
-
- state - Variable in class net.sf.basedb.core.PluginResponse
-
- stateless - Variable in class net.sf.basedb.core.AbstractHqlQuery
-
If the query should be executed in a stateless session or not.
- statelessSession - Variable in class net.sf.basedb.core.AnnotationBatcher
-
- StatelessSessionWrapper - Class in net.sf.basedb.core.hibernate
-
Wrapper around stateless Hibernate sessions that includes a query cache.
- StatelessSessionWrapper(StatelessSession) - Constructor for class net.sf.basedb.core.hibernate.StatelessSessionWrapper
-
Creates a new session wrapper
- statement - Variable in class net.sf.basedb.core.AnnotationBatcher.InsertBatcher
-
- statement - Variable in class net.sf.basedb.core.AnnotationBatcher.UpdateBatcher
-
- statements - Variable in class net.sf.basedb.core.hibernate.MultiUpdateWork
-
- staticCache - Static variable in class net.sf.basedb.core.Application
-
Cache for static data.
- StaticCache - Class in net.sf.basedb.util
-
A cache for storing data to files on the file system.
- StaticCache(File) - Constructor for class net.sf.basedb.util.StaticCache
-
Creates a new static cache.
- StaticCache.CleanupTask - Class in net.sf.basedb.util
-
A timer task that clean up the cache when it is executed.
- StaticCache.LockEntry - Class in net.sf.basedb.util
-
Keeps track of a locked cached entry.
- StaticCache.LockSafeInputStream - Class in net.sf.basedb.util
-
A lock-safe input stream that releases the associated
read lock when the stream is closed.
- StaticCache.LockSafeOutputStream - Class in net.sf.basedb.util
-
A lock-safe output stream that releases the associated
write lock when the stream is closed.
- StaticFilter<T> - Class in net.sf.basedb.util.filter
-
A filter implementation that either rejects or accepts all
object (including null).
- StaticFilter(boolean) - Constructor for class net.sf.basedb.util.filter.StaticFilter
-
Create a new filter.
- StaticKeyManager - Class in net.sf.basedb.util.ssl
-
A key manager implementation that always selects a specified keystore entry.
- StaticKeyManager(KeyStore, String, String) - Constructor for class net.sf.basedb.util.ssl.StaticKeyManager
-
Create a new key manager
- staticRules - Static variable in class net.sf.basedb.util.overview.OverviewUtil
-
- statistics - Variable in class net.sf.basedb.clients.web.ExperimentExplorer.AnnotationGroup
-
- status - Variable in class net.sf.basedb.clients.web.fileupload.FileUpload
-
The status of the upload.
- status - Variable in class net.sf.basedb.core.data.JobData
-
- Status(int, String, boolean) - Constructor for enum net.sf.basedb.core.Job.Status
-
- Status(boolean) - Constructor for enum net.sf.basedb.core.plugin.Response.Status
-
- status - Variable in class net.sf.basedb.core.PluginResponse
-
- STATUS - Static variable in class net.sf.basedb.core.signal.Signal
-
The STATUS signal, that requests that the receiver should
update the status on the system.
- status - Variable in class net.sf.basedb.util.extensions.manager.ProcessResults.FileResults
-
- statusMessage - Variable in class net.sf.basedb.core.data.JobData
-
- steps - Variable in class net.sf.basedb.util.collections.MultiStepCollectionTransformer
-
- stop() - Method in class net.sf.basedb.clients.jobagent.Agent
-
Stop the job agent.
- stop() - Method in class net.sf.basedb.clients.web.extensions.service.DummyService
-
- stop() - Method in interface net.sf.basedb.clients.web.extensions.service.ServiceControllerAction
-
Stop the service if it is running.
- stop(Extension<ServiceControllerAction>) - Static method in class net.sf.basedb.clients.web.extensions.service.Services
-
Start services as a result of an administrator has uninstalled an extension
or is updating/disabling an existing on.
- stop() - Method in class net.sf.basedb.core.Application.Pinger
-
Stop this pinger.
- stop() - Static method in class net.sf.basedb.core.Application
-
Stops the BASE application.
- stop(int) - Method in class net.sf.basedb.util.timer.PerformanceTimer
-
Stop a running timer.
- stopAgent() - Method in class net.sf.basedb.clients.jobagent.AgentController
-
Stop a running job agent by sending a stop request to the agents remote control
service.
- stopAll() - Method in class net.sf.basedb.util.timer.PerformanceTimer
-
Stop all running timers
- stopPinger(Application.Pinger) - Static method in class net.sf.basedb.core.Application
-
- StopRequestHandler - Class in net.sf.basedb.clients.jobagent.handlers
-
This is a request handler for the stop
command.
- StopRequestHandler(Agent) - Constructor for class net.sf.basedb.clients.jobagent.handlers.StopRequestHandler
-
Create a new stop request handler.
- StopServiceRenderer - Class in net.sf.basedb.clients.web.extensions.service
-
- StopServiceRenderer() - Constructor for class net.sf.basedb.clients.web.extensions.service.StopServiceRenderer
-
- stopStart(int, int) - Method in class net.sf.basedb.util.timer.PerformanceTimer
-
Start one timer and stop another.
- STORAGE_SIZE - Static variable in class net.sf.basedb.core.Quantity
-
The id for the Quantity
object representing storage sizes.
- StorageKeyring() - Constructor for class net.sf.basedb.core.InternalStorageController.StorageKeyring
-
- storageType - Variable in class net.sf.basedb.core.data.BioPlateTypeData
-
- store(String, Object, int) - Method in class net.sf.basedb.util.StaticCache
-
Store a serializable object in the cache.
- storeCurrentValuesAsOld(List<T>) - Method in class net.sf.basedb.core.data.ParameterValueData
-
Store the current values as old values, except
if there are no current values or if old values
have already been stored.
- storePropertyFilters(Map<String, PropertyFilterData>) - Method in class net.sf.basedb.core.ItemContext
-
Store the current property filters and save them in the give filterData
map.
- storeValue(ParameterValues, Request, PluginParameter<T>) - Method in class net.sf.basedb.core.plugin.AbstractPlugin
-
- storeValue(ParameterValues, PluginParameter<T>, T) - Method in class net.sf.basedb.core.plugin.AbstractPlugin
-
- storeValues(ParameterValues, Request, PluginParameter<T>) - Method in class net.sf.basedb.core.plugin.AbstractPlugin
-
- strategy - Variable in class net.sf.basedb.core.ExtendedPropertyAccessor.GetterSetter
-
- StreamCacher - Class in net.sf.basedb.util
-
Caches the contents of a stream to a local temporary file.
- StreamCacher(InputStream) - Constructor for class net.sf.basedb.util.StreamCacher
-
Create a new stream cacher for reading from the given master stream.
- StreamCacher(InputStream, File) - Constructor for class net.sf.basedb.util.StreamCacher
-
Create a new stream cacher for reading from the given master stream.
- StreamRedirector(Reader, Writer) - Constructor for class net.sf.basedb.clients.jobagent.executors.ProcessJobExecutor.StreamRedirector
-
- streamtoword(byte[], int[]) - Static method in class net.sf.basedb.util.bcrypt.BCrypt
-
Cycically extract a word of key material
- STRING - Static variable in class net.sf.basedb.core.hibernate.TypeWrapper
-
- string(String) - Static method in class net.sf.basedb.core.query.Expressions
-
Create a constant expression from a string.
- STRING_TOO_LONG_ERROR - Static variable in class net.sf.basedb.plugins.util.Parameters
-
- STRING_TYPE - Static variable in class net.sf.basedb.core.dbengine.TableInfo
-
- StringConverter - Class in net.sf.basedb.util.extensions.debug
-
Convert strings to other data types.
- StringConverter(Type, Object) - Constructor for class net.sf.basedb.util.extensions.debug.StringConverter
-
- StringConverter - Class in net.sf.basedb.util.jep.convert
-
- StringConverter() - Constructor for class net.sf.basedb.util.jep.convert.StringConverter
-
- StringFormatter - Class in net.sf.basedb.clients.web.formatter
-
Format a string for output on a web page.
- StringFormatter() - Constructor for class net.sf.basedb.clients.web.formatter.StringFormatter
-
Create a new string formatter.
- StringLengthComparator - Class in net.sf.basedb.util
-
A comparator implementation for strings that sorts them according
to their length.
- StringLengthComparator() - Constructor for class net.sf.basedb.util.StringLengthComparator
-
Create a new string length comparator instance.
- stringMapping - Static variable in enum net.sf.basedb.core.Type
-
- stringMapping - Static variable in enum net.sf.basedb.plugins.PrintMapFlatFileImporter.Section
-
- StringMatcher - Class in net.sf.basedb.util.fuzzy
-
A wrapper class for fuzzy string matching using the SecondString package.
- StringMatcher() - Constructor for class net.sf.basedb.util.fuzzy.StringMatcher
-
Create a new matcher using the default fuzzy matching algorithm:
Level2JaroWinkler
.
- StringMatcher(StringDistance) - Constructor for class net.sf.basedb.util.fuzzy.StringMatcher
-
Create a new matcher using a specific fuzzy matching algorithm.
- StringMatcher.FuzzyMatch - Class in net.sf.basedb.util.fuzzy
-
Wrapper that holds information about a fuzzy match.
- StringParameterType - Class in net.sf.basedb.core
-
This class represent a parameter type that is a string.
- StringParameterType() - Constructor for class net.sf.basedb.core.StringParameterType
-
Create a new string parameter type, setting the max length to 255 and
nulls are allowed.
- StringParameterType(Integer, String, boolean) - Constructor for class net.sf.basedb.core.StringParameterType
-
Create a new string parameter type.
- StringParameterType(Integer, String, boolean, int, int, int) - Constructor for class net.sf.basedb.core.StringParameterType
-
- StringParameterType(Integer, String, boolean, int, int, int, List<String>) - Constructor for class net.sf.basedb.core.StringParameterType
-
- StringParameterType(Integer, String, boolean, int, int, int, Enumeration<String, String>) - Constructor for class net.sf.basedb.core.StringParameterType
-
- StringParameterType(Integer, String, boolean, int, int, int, Enumeration<String, String>, boolean) - Constructor for class net.sf.basedb.core.StringParameterType
-
- StringParameterValueData - Class in net.sf.basedb.core.data
-
String parameter value.
- StringParameterValueData() - Constructor for class net.sf.basedb.core.data.StringParameterValueData
-
- StringParameterValueData(String...) - Constructor for class net.sf.basedb.core.data.StringParameterValueData
-
- stringTooLongError(String, String, String, String...) - Static method in class net.sf.basedb.plugins.util.Parameters
-
Create the parameter for handling too long strings.
- stringTooLongErrorParameter - Static variable in class net.sf.basedb.plugins.AbstractFlatFileImporter
-
- stringTooLongErrorParameter - Static variable in class net.sf.basedb.plugins.AnnotationFlatFileImporter
-
- StringTooLongException - Exception in net.sf.basedb.core
-
This exception is thrown when an item's field or a parameter
which must be shorter than a specified length exceeds that length.
- StringTooLongException() - Constructor for exception net.sf.basedb.core.StringTooLongException
-
Create a new StringTooLongException
object.
- StringTooLongException(String, String, int) - Constructor for exception net.sf.basedb.core.StringTooLongException
-
Create a new StringTooLongException
object.
- StringUtil - Class in net.sf.basedb.core
-
Utility methods that will make it easier to implement
data validation for string attributes.
- StringUtil() - Constructor for class net.sf.basedb.core.StringUtil
-
- stringValue - Variable in enum net.sf.basedb.core.Type
-
- stripMarkup(CharSequence) - Static method in class net.sf.basedb.clients.web.util.HTML
-
Remove all HTML markup in a string and return what is left.
- StylableTag - Class in net.sf.basedb.clients.web.taglib
-
Generic tag class for tags that want to support
id, class and style of the main html object they
use.
- StylableTag(String) - Constructor for class net.sf.basedb.clients.web.taglib.StylableTag
-
Create a new stylable tag.
- style - Variable in class net.sf.basedb.clients.web.extensions.list.AbstractListColumnBean
-
- style - Variable in class net.sf.basedb.clients.web.extensions.list.PropertyPathActionFactory
-
- style - Variable in class net.sf.basedb.clients.web.extensions.login.FieldInfo
-
- style - Variable in class net.sf.basedb.clients.web.extensions.menu.FixedMenuItemFactory
-
- style - Variable in class net.sf.basedb.clients.web.extensions.menu.MenuItemBean
-
- style - Variable in class net.sf.basedb.clients.web.extensions.section.IncludeContentSectionFactory
-
- style - Variable in class net.sf.basedb.clients.web.extensions.section.SectionBean
-
- style - Variable in class net.sf.basedb.clients.web.extensions.tabcontrol.FixedTabFactory
-
- style - Variable in class net.sf.basedb.clients.web.extensions.tabcontrol.IncludeContentTabFactory
-
- style - Variable in class net.sf.basedb.clients.web.extensions.tabcontrol.TabBean
-
- style - Variable in class net.sf.basedb.clients.web.extensions.toolbar.ButtonBean
-
- style - Variable in class net.sf.basedb.clients.web.extensions.toolbar.FixedButtonFactory
-
- style - Variable in class net.sf.basedb.clients.web.taglib.menu.Menuseparator
-
Optional style
attribute
- style - Variable in class net.sf.basedb.clients.web.taglib.StylableTag
-
- style - Variable in class net.sf.basedb.clients.web.taglib.tab.Tab
-
Optional style
attribute
- style - Variable in class net.sf.basedb.clients.web.taglib.table.Cell
-
Optional style
attribute
- style - Variable in class net.sf.basedb.clients.web.taglib.table.CellValue
-
- styles - Variable in class net.sf.basedb.clients.web.taglib.Head
-
A comma-separated list of stylesheets filenames.
- stylesheets - Variable in class net.sf.basedb.clients.web.extensions.AbstractJspFactory
-
- stylesheets - Variable in class net.sf.basedb.clients.web.extensions.JspContext
-
- Stylesheets - Class in net.sf.basedb.clients.web.taglib.extensions
-
Tag for creating <link> tags to stylesheets
from a
JspContext
.
- Stylesheets() - Constructor for class net.sf.basedb.clients.web.taglib.extensions.Stylesheets
-
- subclass - Variable in class net.sf.basedb.clients.web.taglib.StylableTag
-
- subcontext - Variable in class net.sf.basedb.clients.web.taglib.table.Table
-
- subContext - Variable in class net.sf.basedb.core.ContextKey
-
- subContext - Variable in class net.sf.basedb.core.data.ContextData
-
- subContext - Variable in class net.sf.basedb.core.data.ContextIndex
-
- subContext - Variable in class net.sf.basedb.core.data.JobData
-
- subContext - Variable in class net.sf.basedb.core.ItemContext
-
- subContext - Variable in class net.sf.basedb.core.plugin.GuiContext
-
- SUBDIR_FORMAT - Static variable in class net.sf.basedb.core.File
-
- subdirectories - Variable in class net.sf.basedb.core.data.DirectoryData
-
- subId - Variable in class net.sf.basedb.clients.web.taglib.menu.Submenu
-
The ID of the submenu.
- subList(int, int) - Method in class net.sf.basedb.core.ItemResultList
-
- Submenu - Class in net.sf.basedb.clients.web.taglib.menu
-
This tag defines a menu item inside a drop-down menu.
- Submenu() - Constructor for class net.sf.basedb.clients.web.taglib.menu.Submenu
-
- submenuId - Variable in class net.sf.basedb.clients.web.extensions.menu.FixedMenuItemFactory
-
- submenuId - Variable in class net.sf.basedb.clients.web.extensions.menu.MenuItemBean
-
- submenuId - Variable in class net.sf.basedb.clients.web.extensions.menu.PermissionMenuItemFactory
-
- subquery - Variable in class net.sf.basedb.core.query.SubqueryExpression
-
- SubqueryExpression - Class in net.sf.basedb.core.query
-
Expression that returns the result of a query as it's value.
- SubqueryExpression(String, Query) - Constructor for class net.sf.basedb.core.query.SubqueryExpression
-
- SUBSTANCE - Static variable in class net.sf.basedb.core.Quantity
-
The id for the Quantity
object representing "amount
of substance".
- subtract(Expression, Expression) - Static method in class net.sf.basedb.core.query.Expressions
-
Subtract one expression from another: new expression = e1 - e2.
- SubtractConverter - Class in net.sf.basedb.util.jep.convert
-
- SubtractConverter() - Constructor for class net.sf.basedb.util.jep.convert.SubtractConverter
-
- SubtractExpression - Class in net.sf.basedb.core.query
-
Subtract one expression from another: e1 - e2.
- SubtractExpression(Expression, Expression) - Constructor for class net.sf.basedb.core.query.SubtractExpression
-
- subTreeIterator - Variable in class net.sf.basedb.util.Tree.EntryIterator
-
An iterator over the subtree for each child of the root entry.
- Subtypable - Interface in net.sf.basedb.core
-
A subtypable item is an item that can have a subtype.
- SubtypableData - Interface in net.sf.basedb.core.data
-
A subtypable item is an item that can have a subtype.
- subtypableItems - Static variable in class net.sf.basedb.core.Metadata
-
- SubtypableRelatedItems - Annotation Type in net.sf.basedb.core
-
Annotation that can be used by
Subtypable
items to tell
about related items.
- subtype - Variable in class net.sf.basedb.core.data.BioMaterialData
-
- subtype - Variable in class net.sf.basedb.core.data.BioPlateTypeData
-
- subtype - Variable in class net.sf.basedb.core.data.DerivedBioAssayData
-
- subtype - Variable in class net.sf.basedb.core.data.FileData
-
- subtype - Variable in class net.sf.basedb.core.data.HardwareData
-
- subtype - Variable in class net.sf.basedb.core.data.ItemListData
-
- subtype - Variable in class net.sf.basedb.core.data.ItemSubtypeFileTypeData
-
- subtype - Variable in class net.sf.basedb.core.data.JobData
-
- subtype - Variable in class net.sf.basedb.core.data.KitData
-
- subtype - Variable in class net.sf.basedb.core.data.PhysicalBioAssayData
-
- subtype - Variable in class net.sf.basedb.core.data.ProtocolData
-
- subtype - Variable in class net.sf.basedb.core.data.SoftwareData
-
- subtype - Variable in class net.sf.basedb.core.data.TagData
-
- subtype - Variable in class net.sf.basedb.core.Install.ItemSubtypeFT
-
- subtype - Variable in class net.sf.basedb.util.annotations.InheritSpecification
-
- subtype - Variable in class net.sf.basedb.util.bfs.MetadataModel
-
- subtype - Variable in class net.sf.basedb.util.bfs.MetadataWriter
-
- SUBTYPE - Static variable in class net.sf.basedb.util.export.spotdata.MatrixBaseFileExporter
-
- SUBTYPE - Static variable in class net.sf.basedb.util.export.spotdata.MatrixBfsExporter
-
- SUBTYPE - Static variable in class net.sf.basedb.util.export.spotdata.SerialBaseFileExporter
-
- SUBTYPE - Static variable in class net.sf.basedb.util.export.spotdata.SerialBfsExporter
-
- subtype - Variable in class net.sf.basedb.util.parser.DefaultItemFunction
-
- subtypeColumnMapping - Static variable in class net.sf.basedb.plugins.batchimport.AbstractItemImporter
-
- subtypeMapper - Variable in class net.sf.basedb.plugins.batchimport.AbstractItemImporter
-
- subtypeQuery - Variable in class net.sf.basedb.plugins.batchimport.AbstractItemImporter
-
- successMessage - Variable in class net.sf.basedb.clients.web.plugins.SimpleExport
-
- suffix - Variable in class net.sf.basedb.clients.web.extensions.renderer.PrefixSuffixRenderer
-
- suffix - Variable in class net.sf.basedb.clients.web.taglib.table.CellValue
-
- suffix - Static variable in class net.sf.basedb.core.Version
-
- suffix - Variable in class net.sf.basedb.util.bfs.SequenceFilenameGenerator
-
- suffix - Variable in class net.sf.basedb.util.formatter.PrefixSuffixFormatter
-
- SuggestedFilenameGenerator - Class in net.sf.basedb.util.bfs
-
File name generator implementation that uses the suggested file name.
- SuggestedFilenameGenerator() - Constructor for class net.sf.basedb.util.bfs.SuggestedFilenameGenerator
-
- suggestedJobName - Variable in class net.sf.basedb.core.PluginResponse
-
- sum - Variable in class net.sf.basedb.clients.web.ExperimentExplorer.AnnotationGroup
-
- sum(Expression) - Static method in class net.sf.basedb.core.query.Aggregations
-
Calculates the sum of all values of an expression: new expression = SUM(e)
- sum - Variable in class net.sf.basedb.util.plot.HistogramPlot.HistogramBin
-
- sumArrays(int[], int[]) - Static method in class net.sf.basedb.util.RemovableUtil
-
- SumExpression - Class in net.sf.basedb.core.query
-
Calculates the sum of an expression: SUM(e)
- SumExpression(Expression) - Constructor for class net.sf.basedb.core.query.SumExpression
-
- summaries - Variable in class net.sf.basedb.core.DiskUsageStatistics
-
- Summary() - Constructor for class net.sf.basedb.core.DiskUsageStatistics.Summary
-
- Summary(User) - Constructor for class net.sf.basedb.core.DiskUsageStatistics.Summary
-
- Summary(Group) - Constructor for class net.sf.basedb.core.DiskUsageStatistics.Summary
-
- summary - Variable in class net.sf.basedb.util.extensions.manager.ProcessResults
-
- summaryCache - Variable in class net.sf.basedb.clients.web.ExperimentExplorer
-
Caches annotation summaries.
- SUPERVISOR - Static variable in class net.sf.basedb.core.Role
-
The id for the Role
item representing supervisors.
- supportColumnAliasInGroupBy() - Method in class net.sf.basedb.core.dbengine.AbstractDbEngine
-
Returns FALSE.
- supportColumnAliasInGroupBy() - Method in interface net.sf.basedb.core.dbengine.DbEngine
-
If the current database supports column aliases in the group by part of
a query or not.
- supportColumnAliasInGroupBy() - Method in class net.sf.basedb.core.dbengine.MySQLEngine
-
Returns TRUE.
- supportColumnAliasInGroupBy() - Method in class net.sf.basedb.core.dbengine.PostgresDbEngine
-
Returns TRUE.
- supportColumnAliasInHaving() - Method in class net.sf.basedb.core.dbengine.AbstractDbEngine
-
Returns FALSE.
- supportColumnAliasInHaving() - Method in interface net.sf.basedb.core.dbengine.DbEngine
-
If the current database supports column aliases in the order by part of
a query or not.
- supportColumnAliasInHaving() - Method in class net.sf.basedb.core.dbengine.MySQLEngine
-
Returns TRUE.
- supportColumnAliasInHaving() - Method in class net.sf.basedb.core.dbengine.PostgresDbEngine
-
Returns FALSE.
- supportColumnAliasInOrderBy() - Method in class net.sf.basedb.core.dbengine.AbstractDbEngine
-
Returns FALSE.
- supportColumnAliasInOrderBy() - Method in interface net.sf.basedb.core.dbengine.DbEngine
-
If the current database supports column aliases in the order by part of
a query or not.
- supportColumnAliasInOrderBy() - Method in class net.sf.basedb.core.dbengine.MySQLEngine
-
Returns TRUE.
- supportColumnAliasInOrderBy() - Method in class net.sf.basedb.core.dbengine.PostgresDbEngine
-
Returns TRUE.
- supported - Variable in class net.sf.basedb.core.signal.AbstractSignalHandler
-
Holds the supported signals.
- supported - Static variable in class net.sf.basedb.core.signal.ThreadSignalHandler
-
- supports(PluginType) - Method in class net.sf.basedb.core.PluginDefinition
-
Check if a plugin implements the interface specified by the plugin
type.
- supports(String) - Method in class net.sf.basedb.core.PluginDefinition
-
Check if a plugin implements the interface specified by the plugin
type.
- supports(Signal) - Method in class net.sf.basedb.core.signal.AbstractSignalHandler
-
- supports(Signal) - Method in class net.sf.basedb.core.signal.DelegatingSignalHandler
-
Check if at least one handler has been registered for the given signal.
- supports(Signal) - Method in interface net.sf.basedb.core.signal.SignalHandler
-
Check if a given signal is supported.
- supports(URI) - Method in interface net.sf.basedb.util.uri.ConnectionManagerFactory
-
Check if the given factory knows how to create a handler
for the given URI.
- supports(URI) - Method in class net.sf.basedb.util.uri.http.HttpConnectionManagerFactory
-
- supportsAverage - Variable in enum net.sf.basedb.core.Formula.Type
-
- supportsAverage() - Method in enum net.sf.basedb.core.Formula.Type
-
If a formula of this type can be used in an average expression or not.
- supportsColumnAlias(DbEngine) - Method in enum net.sf.basedb.core.query.QuerySection
-
If the current database supports column aliases in that part of the query.
- supportsColumnAliasInWhere() - Method in class net.sf.basedb.core.dbengine.AbstractDbEngine
-
Returns FALSE.
- supportsColumnAliasInWhere() - Method in interface net.sf.basedb.core.dbengine.DbEngine
-
If the current database supports column aliases in the where part of
a query or not.
- supportsColumnAliasInWhere() - Method in class net.sf.basedb.core.dbengine.MySQLEngine
-
Returns FALSE.
- supportsColumnAliasInWhere() - Method in class net.sf.basedb.core.dbengine.PostgresDbEngine
-
Returns FALSE.
- supportsConfigurations() - Method in class net.sf.basedb.clients.web.plugins.SimpleExport
-
- supportsConfigurations - Variable in class net.sf.basedb.core.data.PluginDefinitionData
-
- supportsConfigurations() - Method in class net.sf.basedb.core.plugin.AbstractPlugin
-
Returns TRUE, since that is how the plugins used to work before this method
was introduced.
- supportsConfigurations() - Method in interface net.sf.basedb.core.plugin.Plugin
-
Return TRUE if the plugin supports different configurations when
executing a job.
- supportsConfigurations() - Method in class net.sf.basedb.core.PluginDefinition
-
Check if the plugin supports configurations or not when executing a job.
- supportsConfigurations() - Method in class net.sf.basedb.plugins.AnnotationFlatFileImporter
-
- supportsConfigurations() - Method in class net.sf.basedb.plugins.Base1PluginExecuter
-
- supportsConfigurations() - Method in class net.sf.basedb.plugins.BaseFileExporterPlugin
-
- supportsConfigurations() - Method in class net.sf.basedb.plugins.batchimport.AbstractItemImporter
-
- supportsConfigurations() - Method in class net.sf.basedb.plugins.BfsExporterPlugin
-
- supportsConfigurations() - Method in class net.sf.basedb.plugins.CdfFileReporterImporter
-
- supportsConfigurations() - Method in class net.sf.basedb.plugins.CloneReportersPlugin
-
- supportsConfigurations() - Method in class net.sf.basedb.plugins.executor.AbstractIOSupport
-
- supportsConfigurations() - Method in class net.sf.basedb.plugins.executor.ExternalProgramExecutor
-
- supportsConfigurations() - Method in class net.sf.basedb.plugins.FormulaFilter
-
- supportsConfigurations() - Method in class net.sf.basedb.plugins.GalExporter
-
- supportsConfigurations() - Method in class net.sf.basedb.plugins.HelpExporter
-
- supportsConfigurations() - Method in class net.sf.basedb.plugins.HelpImporter
-
- supportsConfigurations() - Method in class net.sf.basedb.plugins.IlluminaRawDataImporter
-
- supportsConfigurations() - Method in class net.sf.basedb.plugins.IntensityCalculatorPlugin
-
- supportsConfigurations() - Method in class net.sf.basedb.plugins.JepExtraValueCalculator
-
- supportsConfigurations() - Method in class net.sf.basedb.plugins.JepIntensityTransformer
-
- supportsConfigurations() - Method in class net.sf.basedb.plugins.LowessNormalization
-
- supportsConfigurations() - Method in class net.sf.basedb.plugins.ManualDerivedBioAssayCreator
-
- supportsConfigurations() - Method in class net.sf.basedb.plugins.ManualTransformCreator
-
- supportsConfigurations() - Method in class net.sf.basedb.plugins.MedianRatioNormalization
-
- supportsConfigurations() - Method in class net.sf.basedb.plugins.PackedFileExporter
-
- supportsConfigurations() - Method in class net.sf.basedb.plugins.PlateFlatFileImporter
-
- supportsConfigurations() - Method in class net.sf.basedb.plugins.PlateMappingExporter
-
- supportsConfigurations() - Method in class net.sf.basedb.plugins.PlateMappingImporter
-
- supportsConfigurations() - Method in class net.sf.basedb.plugins.PluginConfigurationExporter
-
Always false
- supportsConfigurations() - Method in class net.sf.basedb.plugins.PluginConfigurationImporter
-
- supportsConfigurations() - Method in class net.sf.basedb.plugins.PrintMapFlatFileImporter
-
- supportsConfigurations() - Method in class net.sf.basedb.plugins.RawDataFlatFileImporter
-
- supportsConfigurations() - Method in class net.sf.basedb.plugins.ReporterFlatFileImporter
-
- supportsConfigurations() - Method in class net.sf.basedb.plugins.ReporterMapFlatFileImporter
-
- supportsConfigurations() - Method in class net.sf.basedb.plugins.SpotImageCreator
-
- supportsConfigurations() - Method in class net.sf.basedb.util.zip.AbstractFileUnpacker
-
Returns FALSE.
- supportsExtraInformation() - Method in interface net.sf.basedb.core.authentication.Authenticator
-
Deprecated.
Should return TRUE or FALSE depending on if the authentication
server returns additional information about the user.
- supportsExtraInformation() - Method in class net.sf.basedb.core.authentication.POP3Authenticator
-
Deprecated.
Always return FALSE.
- supportsExtraInformation() - Method in class net.sf.basedb.core.authentication.SimpleAuthenticator
-
Deprecated.
Always return FALSE.
- supportsGetQuery() - Method in enum net.sf.basedb.core.Item
-
- supportsPushAnnotations(Item) - Static method in class net.sf.basedb.core.ItemSubtype
-
Check if the given item type has support for pushing annotations to
the parent item or not.
- SupportsPushAnnotations - Annotation Type in net.sf.basedb.core
-
Annotation (java) that can be used by
Subtypable
items to
enable/disable support for pushing annotations (BASE) to parent
items.
- supportUnits() - Method in class net.sf.basedb.core.AnnotationType
-
Checks if this annotation types support units.
- SYMBOL - Static variable in class net.sf.basedb.core.ClonableProperty
-
- symbol - Variable in class net.sf.basedb.core.data.ReporterData
-
- symbol - Variable in class net.sf.basedb.core.data.UnitSymbolData
-
- symbol - Variable in enum net.sf.basedb.core.Operator
-
- symbol - Variable in class net.sf.basedb.util.units.UnitCache.CacheKey
-
- symbolColumnMapping - Static variable in class net.sf.basedb.plugins.ReporterFlatFileImporter
-
- symbolMapper - Variable in class net.sf.basedb.plugins.ReporterFlatFileImporter
-
- symbols - Variable in class net.sf.basedb.core.data.QuantityData
-
- symbols - Variable in class net.sf.basedb.core.data.UnitData
-
- syncDate - Variable in class net.sf.basedb.core.data.ItemListData
-
- SyncFilter - Class in net.sf.basedb.core
-
Holds information about a synchronization filter used
by an item list.
- SyncFilter(ItemListSyncFilterData) - Constructor for class net.sf.basedb.core.SyncFilter
-
- SyncFilter.SourceItemTransform - Enum in net.sf.basedb.core
-
- syncFilters - Variable in class net.sf.basedb.core.data.ItemListData
-
- synchronize(Set<Integer>, Set<Integer>) - Method in enum net.sf.basedb.core.ItemList.SynchronizeOption
-
Synchronize the existing members with the items matching the
current filter context.
- synchronizeAllBioMaterialEvents() - Method in class net.sf.basedb.core.BioPlateEvent
-
Synchronize all properties on the child biomaterial
events that are related to this event.
- SynchronizedData(BfsParser) - Constructor for class net.sf.basedb.util.importer.spotdata.SynchronizedSpotDataParser.SynchronizedData
-
- SynchronizedSpotDataParser - Class in net.sf.basedb.util.importer.spotdata
-
A parser that synchronizes the parsing of multiple underlying
data parsers and a master reporter annotations parser.
- SynchronizedSpotDataParser() - Constructor for class net.sf.basedb.util.importer.spotdata.SynchronizedSpotDataParser
-
Create a new synchronized data parser.
- SynchronizedSpotDataParser.SynchronizedData - Class in net.sf.basedb.util.importer.spotdata
-
- SynchronizeOption() - Constructor for enum net.sf.basedb.core.ItemList.SynchronizeOption
-
- synchronizeProperties(BioMaterialEventData, BioPlateEventParticipantData) - Method in class net.sf.basedb.core.BioPlateEvent
-
Synchronize all related properties between this event and the
biomaterial event.
- systemCreated - Variable in class net.sf.basedb.core.Message
-
- SystemData - Interface in net.sf.basedb.core.data
-
A system item is an item which has an
additional id in the form of string.
- systemId - Variable in class net.sf.basedb.core.data.BioPlateEventTypeData
-
- systemId - Variable in class net.sf.basedb.core.data.DirectoryData
-
- systemId - Variable in class net.sf.basedb.core.data.GroupData
-
- systemId - Variable in class net.sf.basedb.core.data.ItemSubtypeData
-
- systemId - Variable in class net.sf.basedb.core.data.QuantityData
-
- systemId - Variable in class net.sf.basedb.core.data.QuotaData
-
- systemId - Variable in class net.sf.basedb.core.data.QuotaTypeData
-
- systemId - Variable in class net.sf.basedb.core.data.RoleData
-
- systemId - Variable in class net.sf.basedb.core.data.UserData
-
- systemIds - Static variable in class net.sf.basedb.core.SystemItems
-
A map from system id --> numeric id
- SystemItem - Interface in net.sf.basedb.core
-
A SystemItem
is an item which has an
additional systemwide unique id in the form of string.
- SystemItems - Class in net.sf.basedb.core
-
This class is used to map the system id of all
SystemData
items to the numerical internal
id in the current installation.
- SystemItems() - Constructor for class net.sf.basedb.core.SystemItems
-
- systemPermissions - Variable in class net.sf.basedb.core.InternalJobQueue.JobQueueKeyring
-
- systemPermissions - Variable in class net.sf.basedb.core.ServiceSessionControl.ServicesKeyring
-