Hierarchy For All Packages

Package Hierarchies:

net.sf.basedb.clients.jobagent, net.sf.basedb.clients.jobagent.executors, net.sf.basedb.clients.jobagent.handlers, net.sf.basedb.clients.jobagent.slotmanager, net.sf.basedb.clients.web, net.sf.basedb.clients.web.extensions, net.sf.basedb.clients.web.extensions.edit, net.sf.basedb.clients.web.extensions.menu, net.sf.basedb.clients.web.extensions.plot, net.sf.basedb.clients.web.extensions.renderer, net.sf.basedb.clients.web.extensions.service, net.sf.basedb.clients.web.extensions.tabcontrol, net.sf.basedb.clients.web.extensions.toolbar, net.sf.basedb.clients.web.fileupload, net.sf.basedb.clients.web.formatter, net.sf.basedb.clients.web.plugins, net.sf.basedb.clients.web.resources, net.sf.basedb.clients.web.servlet, net.sf.basedb.clients.web.taglib, net.sf.basedb.clients.web.taglib.extensions, net.sf.basedb.clients.web.taglib.menu, net.sf.basedb.clients.web.taglib.path, net.sf.basedb.clients.web.taglib.tab, net.sf.basedb.clients.web.taglib.table, net.sf.basedb.clients.web.util, net.sf.basedb.core, net.sf.basedb.core.authentication, net.sf.basedb.core.data, net.sf.basedb.core.data.keyring, net.sf.basedb.core.dbengine, net.sf.basedb.core.filehandler, net.sf.basedb.core.hibernate, net.sf.basedb.core.log, net.sf.basedb.core.log.db, net.sf.basedb.core.plugin, net.sf.basedb.core.query, net.sf.basedb.core.signal, net.sf.basedb.core.snapshot, net.sf.basedb.info, net.sf.basedb.plugins, net.sf.basedb.plugins.batchimport, net.sf.basedb.plugins.executor, net.sf.basedb.plugins.util, net.sf.basedb.util, net.sf.basedb.util.basefile, net.sf.basedb.util.bfs, net.sf.basedb.util.biomaterial, net.sf.basedb.util.collections, net.sf.basedb.util.encode, net.sf.basedb.util.error, net.sf.basedb.util.export, net.sf.basedb.util.export.spotdata, net.sf.basedb.util.extensions, net.sf.basedb.util.extensions.debug, net.sf.basedb.util.extensions.events, net.sf.basedb.util.extensions.xml, net.sf.basedb.util.filter, net.sf.basedb.util.formatter, net.sf.basedb.util.fuzzy, net.sf.basedb.util.importer, net.sf.basedb.util.importer.spotdata, net.sf.basedb.util.jep, net.sf.basedb.util.jep.convert, net.sf.basedb.util.jobagent, net.sf.basedb.util.overview, net.sf.basedb.util.overview.cache, net.sf.basedb.util.overview.filter, net.sf.basedb.util.overview.loader, net.sf.basedb.util.overview.node, net.sf.basedb.util.overview.validator, net.sf.basedb.util.parser, net.sf.basedb.util.plot, net.sf.basedb.util.resources, net.sf.basedb.util.ssl, net.sf.basedb.util.timer, net.sf.basedb.util.units, net.sf.basedb.util.zip, net.sf.basedb.ws.client, net.sf.basedb.ws.server

Class Hierarchy

• java.lang.Object
  • net.sf.basedb.util.extensions.AboutBean (implements net.sf.basedb.core.plugin.About)
  • net.sf.basedb.core.plugin.AboutImpl (implements net.sf.basedb.core.plugin.About)
  • net.sf.basedb.core.query.AbsExpression (implements net.sf.basedb.core.query.Expression)
  • net.sf.basedb.core.AbstractBatcher (implements net.sf.basedb.core.Batcher)
    • net.sf.basedb.core.BasicBatcher<D> (implements net.sf.basedb.core.AccessControlled)
      • net.sf.basedb.core.FeatureBatcher
      • net.sf.basedb.core.RawDataBatcher
      • net.sf.basedb.core.ReporterBatcher
    • net.sf.basedb.core.FilterBatcher
    • net.sf.basedb.core.MappingBatcher
    • net.sf.basedb.core.PositionBatcher
    • net.sf.basedb.core.PositionExtraValueBatcher<I>
    • net.sf.basedb.core.SpotBatcher
    • net.sf.basedb.core.SpotExtraValueBatcher<I>
  • net.sf.basedb.util.export.spotdata.AbstractBioAssaySetExporter
    • net.sf.basedb.util.export.spotdata.BaseFileExporter
      • net.sf.basedb.util.export.spotdata.MatrixBaseFileExporter
      • net.sf.basedb.util.export.spotdata.SerialBaseFileExporter
    • net.sf.basedb.util.export.spotdata.BfsExporter
      • net.sf.basedb.util.export.spotdata.MatrixBfsExporter
      • net.sf.basedb.util.export.spotdata.SerialBfsExporter
  • java.util.AbstractCollection<E> (implements java.util.Collection<E>)
    • java.util.AbstractList<E> (implements java.util.List<E>)
      • java.util.ArrayList<E> (implements java.lang.Cloneable, java.util.List<E>, java.util.RandomAccess, java.io.Serializable)
        • net.sf.basedb.core.UnmodifiableResultList<T> (implements net.sf.basedb.core.query.ResultList<I>)
  • net.sf.basedb.clients.jobagent.handlers.AbstractCustomRequestHandler (implements net.sf.basedb.clients.jobagent.handlers.CustomRequestHandler)
  • net.sf.basedb.core.filehandler.AbstractDataFileHandler (implements net.sf.basedb.core.filehandler.DataFileHandler)
    • net.sf.basedb.core.filehandler.AffymetrixFileHandler
      • net.sf.basedb.core.filehandler.CdfFileHandler (implements net.sf.basedb.core.filehandler.DataFileMetadataReader, net.sf.basedb.core.filehandler.DataFileValidator)
      • net.sf.basedb.core.filehandler.CelFileHandler (implements net.sf.basedb.core.filehandler.DataFileMetadataReader, net.sf.basedb.core.filehandler.DataFileValidator)
  • org.jfree.data.general.AbstractDataset (implements java.lang.Cloneable, org.jfree.data.general.Dataset, java.io.ObjectInputValidation, java.io.Serializable)
    • org.jfree.data.general.AbstractSeriesDataset (implements java.io.Serializable, org.jfree.data.general.SeriesChangeListener, org.jfree.data.general.SeriesDataset)
      • net.sf.basedb.util.plot.HistogramPlot.HistogramDataset (implements org.jfree.data.xy.IntervalXYDataset)
  • net.sf.basedb.util.bfs.AbstractDataWriterFactory<T> (implements net.sf.basedb.util.bfs.DataWriterFactory<T>)
    • net.sf.basedb.util.bfs.GenericBaseDataWriterFactory<T>
    • net.sf.basedb.util.bfs.GenericDiskDataWriterFactory<T>
  • net.sf.basedb.core.dbengine.AbstractDbEngine (implements net.sf.basedb.core.dbengine.DbEngine)
    • net.sf.basedb.core.dbengine.DefaultDbEngine
    • net.sf.basedb.core.dbengine.MySQLEngine (implements net.sf.basedb.core.dbengine.DbEngine)
    • net.sf.basedb.core.dbengine.PostgresDbEngine (implements net.sf.basedb.core.dbengine.DbEngine)
  • net.sf.basedb.util.export.spotdata.AbstractFieldConverter (implements net.sf.basedb.util.export.spotdata.ExportableFieldConverter)
    • net.sf.basedb.util.export.spotdata.StandardFieldConverter
      • net.sf.basedb.util.export.spotdata.AdvancedFieldConverter
      • net.sf.basedb.util.export.spotdata.Base1FieldConverter
  • net.sf.basedb.util.bfs.AbstractFilenameGenerator<T> (implements net.sf.basedb.util.bfs.FilenameGenerator<T>)
    • net.sf.basedb.util.bfs.SuggestedFilenameGenerator
  • net.sf.basedb.util.jep.convert.AbstractJepConversionFunction<T> (implements net.sf.basedb.util.jep.convert.JepConversionFunction<T>)
    • net.sf.basedb.util.jep.convert.AbsConverter
    • net.sf.basedb.util.jep.convert.AddConverter
    • net.sf.basedb.util.jep.convert.AndConverter
    • net.sf.basedb.util.jep.convert.ASTConstantConverter
    • net.sf.basedb.util.jep.convert.ASTFunNodeConverter
    • net.sf.basedb.util.jep.convert.ASTVarNodeConverter
    • net.sf.basedb.util.jep.convert.DivideConverter
    • net.sf.basedb.util.jep.convert.EqualsConverter
    • net.sf.basedb.util.jep.convert.ExpConverter
    • net.sf.basedb.util.jep.convert.FloatConverter
    • net.sf.basedb.util.jep.convert.GreaterConverter
    • net.sf.basedb.util.jep.convert.GreaterEqualsConverter
    • net.sf.basedb.util.jep.convert.IfConverter
    • net.sf.basedb.util.jep.convert.IntegerConverter
    • net.sf.basedb.util.jep.convert.LessConverter
    • net.sf.basedb.util.jep.convert.LessEqualsConverter
    • net.sf.basedb.util.jep.convert.LogarithmConverter
    • net.sf.basedb.util.jep.convert.MultiplyConverter
    • net.sf.basedb.util.jep.convert.NaturalLogarithmConverter
    • net.sf.basedb.util.jep.convert.NotConverter
    • net.sf.basedb.util.jep.convert.NotEqualsConverter
    • net.sf.basedb.util.jep.convert.OrConverter
    • net.sf.basedb.util.jep.convert.SquareRootConverter
    • net.sf.basedb.util.jep.convert.StringConverter
    • net.sf.basedb.util.jep.convert.SubtractConverter
    • net.sf.basedb.util.jep.convert.UMinusConverter
  • net.sf.basedb.clients.web.extensions.AbstractJspFactory
    • net.sf.basedb.clients.web.extensions.AbstractJspActionFactory<A> (implements net.sf.basedb.util.extensions.ActionFactory<A>)
      • net.sf.basedb.clients.web.extensions.edit.DebugOnSaveActionFactory
      • net.sf.basedb.clients.web.extensions.toolbar.FixedButtonFactory (implements net.sf.basedb.clients.web.extensions.toolbar.ButtonAction)
      • net.sf.basedb.clients.web.extensions.menu.FixedMenuItemFactory (implements net.sf.basedb.clients.web.extensions.menu.MenuItemAction)
      • net.sf.basedb.clients.web.extensions.tabcontrol.FixedTabFactory (implements net.sf.basedb.clients.web.extensions.tabcontrol.TabAction)
      • net.sf.basedb.clients.web.extensions.tabcontrol.IncludeContentTabFactory
      • net.sf.basedb.clients.web.extensions.plot.MAPlotFactory
      • net.sf.basedb.clients.web.extensions.toolbar.PermissionButtonFactory
      • net.sf.basedb.clients.web.extensions.menu.PermissionMenuItemFactory
    • net.sf.basedb.clients.web.extensions.AbstractJspRendererFactory<A> (implements net.sf.basedb.util.extensions.RendererFactory<A>)
      • net.sf.basedb.clients.web.extensions.toolbar.CompactButtonRendererFactory
      • net.sf.basedb.clients.web.extensions.toolbar.ToolbarButtonRendererFactory
  • net.sf.basedb.util.overview.loader.AbstractNodeLoader<I> (implements net.sf.basedb.util.overview.loader.NodeLoader<I>)
    • net.sf.basedb.util.overview.loader.BasicItemNodeLoader<I>
      • net.sf.basedb.util.overview.loader.AnnotationLoader
      • net.sf.basedb.util.overview.loader.AnyToAnyLoader
      • net.sf.basedb.util.overview.loader.ArrayBatchLoader
      • net.sf.basedb.util.overview.loader.ArrayDesignLoader
      • net.sf.basedb.util.overview.loader.ArraySlideLoader
      • net.sf.basedb.util.overview.loader.BioSourceLoader
      • net.sf.basedb.util.overview.loader.DataFileLoader
      • net.sf.basedb.util.overview.loader.ExperimentalFactorLoader
      • net.sf.basedb.util.overview.loader.ExperimentLoader
      • net.sf.basedb.util.overview.loader.ExtractLoader
      • net.sf.basedb.util.overview.loader.HardwareLoader
      • net.sf.basedb.util.overview.loader.HybridizationLoader
      • net.sf.basedb.util.overview.loader.ImageLoader
      • net.sf.basedb.util.overview.loader.LabeledExtractLoader
      • net.sf.basedb.util.overview.loader.PlatformLoader
      • net.sf.basedb.util.overview.loader.ProtocolLoader
      • net.sf.basedb.util.overview.loader.ProtocolParameterLoader
      • net.sf.basedb.util.overview.loader.RawBioAssayLoader
      • net.sf.basedb.util.overview.loader.SampleLoader
      • net.sf.basedb.util.overview.loader.ScanLoader
      • net.sf.basedb.util.overview.loader.SoftwareLoader
  • net.sf.basedb.clients.web.extensions.edit.AbstractOnSaveAction (implements net.sf.basedb.clients.web.extensions.edit.OnSaveAction)
    • net.sf.basedb.clients.web.extensions.edit.DebugOnSaveActionFactory.DebugOnSaveAction
  • net.sf.basedb.core.plugin.AbstractPlugin (implements net.sf.basedb.core.plugin.Plugin)
    • net.sf.basedb.core.plugin.AbstractAnalysisPlugin
      • net.sf.basedb.plugins.Base1PluginExecuter (implements net.sf.basedb.core.plugin.InteractivePlugin, net.sf.basedb.core.signal.SignalTarget)
      • net.sf.basedb.plugins.executor.ExternalProgramExecutor (implements net.sf.basedb.core.plugin.InteractivePlugin, net.sf.basedb.core.signal.SignalTarget)
      • net.sf.basedb.plugins.FormulaFilter (implements net.sf.basedb.core.plugin.AnalysisFilterPlugin, net.sf.basedb.core.plugin.InteractivePlugin, net.sf.basedb.core.signal.SignalTarget)
      • net.sf.basedb.plugins.JepExtraValueCalculator (implements net.sf.basedb.core.plugin.InteractivePlugin, net.sf.basedb.core.signal.SignalTarget)
      • net.sf.basedb.plugins.JepIntensityTransformer (implements net.sf.basedb.core.plugin.InteractivePlugin, net.sf.basedb.core.signal.SignalTarget)
      • net.sf.basedb.plugins.LowessNormalization (implements net.sf.basedb.core.plugin.InteractivePlugin, net.sf.basedb.core.signal.SignalTarget)
      • net.sf.basedb.plugins.ManualTransformCreator (implements net.sf.basedb.core.plugin.AnnotationSetterPlugin, net.sf.basedb.core.plugin.InteractivePlugin)
      • net.sf.basedb.plugins.MedianRatioNormalization (implements net.sf.basedb.core.plugin.InteractivePlugin, net.sf.basedb.core.signal.SignalTarget)
    • net.sf.basedb.core.plugin.AbstractExporterPlugin (implements net.sf.basedb.core.plugin.ImmediateDownloadExporter)
      • net.sf.basedb.plugins.BaseFileExporterPlugin (implements net.sf.basedb.core.plugin.InteractivePlugin, net.sf.basedb.core.signal.SignalTarget)
      • net.sf.basedb.plugins.BioAssaySetExporter (implements net.sf.basedb.core.plugin.InteractivePlugin, net.sf.basedb.core.signal.SignalTarget)
      • net.sf.basedb.plugins.GalExporter (implements net.sf.basedb.core.plugin.InteractivePlugin, net.sf.basedb.core.signal.SignalTarget)
      • net.sf.basedb.plugins.HelpExporter (implements net.sf.basedb.core.plugin.InteractivePlugin, net.sf.basedb.core.signal.SignalTarget)
      • net.sf.basedb.plugins.PackedFileExporter (implements net.sf.basedb.core.plugin.InteractivePlugin, net.sf.basedb.core.signal.SignalTarget)
      • net.sf.basedb.plugins.PlateMappingExporter (implements net.sf.basedb.core.plugin.InteractivePlugin, net.sf.basedb.core.signal.SignalTarget)
      • net.sf.basedb.plugins.PluginConfigurationExporter (implements net.sf.basedb.core.plugin.InteractivePlugin, net.sf.basedb.core.signal.SignalTarget)
      • net.sf.basedb.clients.web.plugins.SimpleExport (implements net.sf.basedb.core.plugin.InteractivePlugin, net.sf.basedb.core.plugin.NonRestartable, net.sf.basedb.core.signal.SignalTarget)
    • net.sf.basedb.util.zip.AbstractFileUnpacker (implements net.sf.basedb.util.zip.FileUnpacker, net.sf.basedb.core.plugin.InteractivePlugin, net.sf.basedb.core.signal.SignalTarget)
      • net.sf.basedb.plugins.TarFileUnpacker
      • net.sf.basedb.plugins.ZipFileUnpacker
    • net.sf.basedb.plugins.AbstractFlatFileImporter (implements net.sf.basedb.core.plugin.AutoDetectingImporter, net.sf.basedb.core.signal.SignalTarget)
      • net.sf.basedb.plugins.batchimport.AbstractItemImporter<I> (implements net.sf.basedb.util.parser.ConfigureByExample, net.sf.basedb.core.plugin.InteractivePlugin)
        • net.sf.basedb.plugins.batchimport.ArrayBatchImporter
        • net.sf.basedb.plugins.batchimport.ArrayDesignImporter
        • net.sf.basedb.plugins.batchimport.ArraySlideImporter
        • net.sf.basedb.plugins.batchimport.BioPlateImporter
        • net.sf.basedb.plugins.batchimport.BioSourceImporter
        • net.sf.basedb.plugins.batchimport.ExtractImporter
        • net.sf.basedb.plugins.batchimport.HybridizationImporter
        • net.sf.basedb.plugins.batchimport.LabeledExtractImporter
        • net.sf.basedb.plugins.batchimport.RawBioAssayImporter
        • net.sf.basedb.plugins.batchimport.SampleImporter
        • net.sf.basedb.plugins.batchimport.ScanImporter
      • net.sf.basedb.plugins.AnnotationFlatFileImporter (implements net.sf.basedb.util.parser.ConfigureByExample, net.sf.basedb.core.plugin.InteractivePlugin)
      • net.sf.basedb.plugins.IlluminaRawDataImporter (implements net.sf.basedb.core.plugin.InteractivePlugin)
      • net.sf.basedb.plugins.PlateFlatFileImporter (implements net.sf.basedb.util.parser.ConfigureByExample, net.sf.basedb.core.plugin.InteractivePlugin)
      • net.sf.basedb.plugins.PlateMappingImporter (implements net.sf.basedb.core.plugin.InteractivePlugin)
      • net.sf.basedb.plugins.PrintMapFlatFileImporter (implements net.sf.basedb.core.plugin.InteractivePlugin)
      • net.sf.basedb.plugins.RawDataFlatFileImporter (implements net.sf.basedb.core.plugin.AnnotationSetterPlugin, net.sf.basedb.util.parser.ConfigureByExample, net.sf.basedb.core.plugin.InteractivePlugin)
      • net.sf.basedb.plugins.ReporterFlatFileImporter (implements net.sf.basedb.util.parser.ConfigureByExample, net.sf.basedb.core.plugin.InteractivePlugin)
      • net.sf.basedb.plugins.ReporterMapFlatFileImporter (implements net.sf.basedb.util.parser.ConfigureByExample, net.sf.basedb.core.plugin.InteractivePlugin)
    • net.sf.basedb.plugins.executor.AbstractIOSupport (implements net.sf.basedb.plugins.executor.IOSupport)
      • net.sf.basedb.plugins.executor.BaseFileExporterSupport
      • net.sf.basedb.plugins.executor.BaseFileImporterSupport
      • net.sf.basedb.plugins.executor.BfsExporterSupport
      • net.sf.basedb.plugins.executor.BfsImporterSupport
      • net.sf.basedb.plugins.executor.FileOnlyImporterSupport
    • net.sf.basedb.plugins.BfsExporterPlugin (implements net.sf.basedb.core.plugin.InteractivePlugin, net.sf.basedb.core.signal.SignalTarget)
    • net.sf.basedb.plugins.CdfFileReporterImporter (implements net.sf.basedb.core.plugin.AutoDetectingImporter, net.sf.basedb.core.plugin.InteractivePlugin, net.sf.basedb.core.signal.SignalTarget)
    • net.sf.basedb.plugins.HelpImporter (implements net.sf.basedb.core.plugin.AutoDetectingImporter, net.sf.basedb.core.plugin.InteractivePlugin, net.sf.basedb.core.signal.SignalTarget)
    • net.sf.basedb.plugins.IntensityCalculatorPlugin (implements net.sf.basedb.core.plugin.InteractivePlugin, net.sf.basedb.core.signal.SignalTarget)
    • net.sf.basedb.plugins.PluginConfigurationImporter (implements net.sf.basedb.core.plugin.AutoDetectingImporter, net.sf.basedb.core.plugin.InteractivePlugin, net.sf.basedb.core.signal.SignalTarget)
    • net.sf.basedb.plugins.SpotImageCreator (implements net.sf.basedb.core.plugin.Plugin, net.sf.basedb.core.signal.SignalTarget)
  • net.sf.basedb.core.AbstractQuery (implements net.sf.basedb.core.query.Query)
    • net.sf.basedb.core.AbstractHqlQuery (implements net.sf.basedb.core.query.HqlQuery)
      • net.sf.basedb.core.AbstractEntityQuery (implements net.sf.basedb.core.query.EntityQuery)
        • net.sf.basedb.core.DataQuery<I>
        • net.sf.basedb.core.ItemQuery<I>
        • net.sf.basedb.core.ReporterScoreQuery
    • net.sf.basedb.core.AbstractSqlQuery (implements net.sf.basedb.core.query.SqlQuery)
      • net.sf.basedb.core.DynamicQuery
        • net.sf.basedb.core.DataCube.RawMappingQuery
        • net.sf.basedb.core.DynamicExtraValueQuery
        • net.sf.basedb.core.DynamicPositionQuery
        • net.sf.basedb.core.DynamicSpotQuery
      • net.sf.basedb.core.DynamicRawDataQuery
      • net.sf.basedb.core.DynamicReporterQuery
  • net.sf.basedb.core.hibernate.AbstractQueryCache
    • net.sf.basedb.core.hibernate.SessionWrapper (implements org.hibernate.Session)
    • net.sf.basedb.core.hibernate.StatelessSessionWrapper (implements org.hibernate.StatelessSession)
  • net.sf.basedb.core.AbstractResultList<I> (implements net.sf.basedb.core.query.ResultList<I>)
    • net.sf.basedb.core.ItemResultList<I>
  • net.sf.basedb.ws.client.AbstractRPCClient
    • net.sf.basedb.ws.client.AnnotationTypeClient
    • net.sf.basedb.ws.client.ArrayDesignClient
    • net.sf.basedb.ws.client.BioAssaySetClient
    • net.sf.basedb.ws.client.ExperimentClient
    • net.sf.basedb.ws.client.ProjectClient
    • net.sf.basedb.ws.client.RawBioAssayClient
    • net.sf.basedb.ws.client.ReporterClient
    • net.sf.basedb.ws.client.SessionClient
  • net.sf.basedb.ws.server.AbstractRPCService
    • net.sf.basedb.ws.server.AnnotationTypeService
    • net.sf.basedb.ws.server.ArrayDesignService
    • net.sf.basedb.ws.server.BioAssaySetService
    • net.sf.basedb.ws.server.ExperimentService
    • net.sf.basedb.ws.server.ProjectService
    • net.sf.basedb.ws.server.RawBioAssayService
    • net.sf.basedb.ws.server.ReporterService
    • net.sf.basedb.ws.server.SessionService
  • net.sf.basedb.core.signal.AbstractSignalHandler (implements net.sf.basedb.core.signal.SignalHandler)
    • net.sf.basedb.core.signal.DelegatingSignalHandler
    • net.sf.basedb.core.signal.EnhancedThreadSignalHandler (implements net.sf.basedb.core.signal.InterruptHandler)
    • net.sf.basedb.core.signal.ForwardingSignalHandler
    • net.sf.basedb.core.signal.ProgressReporterSignalHandler (implements net.sf.basedb.core.ProgressReporter)
    • net.sf.basedb.core.signal.ThreadSignalHandler
  • net.sf.basedb.core.signal.AbstractSignalReceiver (implements net.sf.basedb.core.signal.SignalReceiver)
    • net.sf.basedb.core.signal.LocalSignalReceiver
    • net.sf.basedb.core.signal.SocketSignalReceiver
      • net.sf.basedb.clients.jobagent.AgentSignalReceiver
  • net.sf.basedb.core.signal.AbstractSignalTransporter (implements net.sf.basedb.core.signal.SignalTransporter)
    • net.sf.basedb.core.signal.LocalSignalTransporter
    • net.sf.basedb.core.signal.SocketSignalTransporter
  • net.sf.basedb.util.extensions.events.ActionClassEventFilter (implements net.sf.basedb.util.extensions.events.EventFilter)
  • net.sf.basedb.util.extensions.ActionIterator<A> (implements java.util.Iterator<E>)
  • net.sf.basedb.util.collections.AddAllTransformer<I> (implements net.sf.basedb.util.collections.CollectionTransformer<S,D>)
  • net.sf.basedb.core.query.AddExpression (implements net.sf.basedb.core.query.Expression)
  • net.sf.basedb.core.Affymetrix
  • net.sf.basedb.clients.jobagent.Agent
  • net.sf.basedb.clients.jobagent.AgentController
  • net.sf.basedb.core.query.Aggregations
  • net.sf.basedb.util.extensions.events.AllEventsFilter (implements net.sf.basedb.util.extensions.events.EventFilter)
  • net.sf.basedb.util.filter.AllOfFilter<T> (implements net.sf.basedb.util.filter.Filter<T>)
  • net.sf.basedb.util.ssl.AllowAnyHostNameVerifyer (implements org.apache.http.conn.ssl.X509HostnameVerifier)
  • net.sf.basedb.core.query.AndRestriction (implements net.sf.basedb.core.query.Restriction)
  • net.sf.basedb.core.Annotation.QueryRuntimeFilterImpl (implements net.sf.basedb.core.QueryRuntimeFilter)
  • net.sf.basedb.util.export.spotdata.AnnotationAssayField (implements net.sf.basedb.util.export.spotdata.AssayField)
  • net.sf.basedb.core.snapshot.AnnotationFilter (implements net.sf.basedb.util.filter.Filter<T>)
  • net.sf.basedb.plugins.AnnotationFlatFileImporter.AnnotationValue
  • net.sf.basedb.plugins.AnnotationFlatFileImporter.NewAnnotations
  • net.sf.basedb.info.AnnotationInfo (implements java.io.Serializable, net.sf.basedb.info.Transferable)
  • net.sf.basedb.core.log.db.AnnotationLogger (implements net.sf.basedb.core.log.EntityLogger)
  • net.sf.basedb.util.bfs.AnnotationModel (implements net.sf.basedb.util.bfs.EventHandler)
  • net.sf.basedb.util.overview.node.AnnotationNameGenerator (implements net.sf.basedb.util.overview.node.NodeNameGenerator<I>)
  • net.sf.basedb.util.bfs.AnnotationParser (implements net.sf.basedb.util.bfs.BfsParser)
  • net.sf.basedb.core.AnnotationRestriction (implements net.sf.basedb.core.query.Restriction)
    • net.sf.basedb.core.AnnotationBetweenRestriction
    • net.sf.basedb.core.AnnotationInRestriction
    • net.sf.basedb.core.AnnotationSimpleRestriction
    • net.sf.basedb.core.HasAnnotationRestriction
  • net.sf.basedb.core.query.Annotations
  • net.sf.basedb.core.AnnotationSet.QueryRuntimeFilterImpl (implements net.sf.basedb.core.QueryRuntimeFilter)
  • net.sf.basedb.core.log.db.AnnotationSetLogger (implements net.sf.basedb.core.log.EntityLogger)
  • net.sf.basedb.core.snapshot.AnnotationSetSnapshot (implements java.io.Serializable)
  • net.sf.basedb.core.snapshot.AnnotationSnapshot (implements java.io.Serializable)
  • net.sf.basedb.core.snapshot.AnnotationTypeFilter (implements net.sf.basedb.util.filter.Filter<T>)
  • net.sf.basedb.util.AnnotationUtil
  • net.sf.basedb.util.AnnotationUtil.AnnotatableWrapper
  • net.sf.basedb.util.overview.node.AnyToAnyNameGenerator (implements net.sf.basedb.util.overview.node.NodeNameGenerator<I>)
  • net.sf.basedb.core.Application
  • net.sf.basedb.core.Application.Pinger
  • net.sf.basedb.util.ArrayIterator<E> (implements java.util.Iterator<E>)
  • net.sf.basedb.core.query.AscOrder (implements net.sf.basedb.core.query.Order)
  • net.sf.basedb.util.export.spotdata.AssayPropertyField (implements net.sf.basedb.util.export.spotdata.AssayField)
  • net.sf.basedb.core.authentication.AuthenticationInformation
  • net.sf.basedb.util.overview.loader.AutoChildNodeLoader<I> (implements net.sf.basedb.util.overview.loader.NodeLoader<I>)
  • net.sf.basedb.util.AutoDetectFileFormat
  • net.sf.basedb.util.AutoDetectFileFormat.IsImportableFilter (implements net.sf.basedb.util.filter.Filter<T>)
  • net.sf.basedb.clients.web.Base
  • net.sf.basedb.plugins.Base1PluginExecuter.JobParameter
  • net.sf.basedb.ws.server.BaseFileDataSource (implements javax.activation.DataSource)
  • net.sf.basedb.plugins.BaseFileExporterPlugin.ExtendedDynamicField (implements net.sf.basedb.util.export.spotdata.DynamicField)
  • net.sf.basedb.util.importer.spotdata.BaseFileImporter
  • net.sf.basedb.util.importer.spotdata.BaseFileInfo
  • net.sf.basedb.util.importer.spotdata.BaseFileInfo.ChildBioAssay
  • net.sf.basedb.util.importer.spotdata.BaseFileInfo.SpotSectionInfo
  • net.sf.basedb.util.basefile.BaseFileParser
  • net.sf.basedb.util.importer.BaseFileWrapper (implements net.sf.basedb.util.importer.FileWrapper)
  • net.sf.basedb.util.bfs.BaseInputStreamLocator (implements net.sf.basedb.util.bfs.InputStreamLocator)
  • net.sf.basedb.core.data.BasicData (implements net.sf.basedb.core.data.IdentifiableData)
    • net.sf.basedb.core.data.AnnotationData (implements net.sf.basedb.core.data.LoggableData)
    • net.sf.basedb.core.data.AnnotationSetData (implements net.sf.basedb.core.data.LoggableData)
    • net.sf.basedb.core.data.AnyToAnyData (implements net.sf.basedb.core.data.NameableData)
    • net.sf.basedb.core.data.ArrayDesignBlockData
    • net.sf.basedb.core.data.ArrayDesignPlateData
    • net.sf.basedb.core.data.BioAssayData (implements net.sf.basedb.core.data.AnnotatableData, net.sf.basedb.core.data.NameableData)
    • net.sf.basedb.core.data.BioAssaySetData (implements net.sf.basedb.core.data.AnnotatableData, net.sf.basedb.core.data.FileStoreEnabledData, net.sf.basedb.core.data.NameableData, net.sf.basedb.core.data.RemovableData)
    • net.sf.basedb.core.data.BioMaterialEventData (implements net.sf.basedb.core.data.LoggableData, net.sf.basedb.core.data.RegisteredData)
    • net.sf.basedb.core.data.BioPlateEventParticipantData
    • net.sf.basedb.core.data.BioPlateEventTypeData (implements net.sf.basedb.core.data.NameableData, net.sf.basedb.core.data.RemovableData, net.sf.basedb.core.data.SystemData)
    • net.sf.basedb.core.data.BioPlateTypeData (implements net.sf.basedb.core.data.NameableData, net.sf.basedb.core.data.RemovableData)
    • net.sf.basedb.core.data.BioWellData
    • net.sf.basedb.core.data.ChangeHistoryData
    • net.sf.basedb.core.data.ChangeHistoryDetailData
    • net.sf.basedb.core.data.ContextData
    • net.sf.basedb.core.data.DataCubeColumnData
    • net.sf.basedb.core.data.DataCubeData
    • net.sf.basedb.core.data.DataCubeExtraValueData
    • net.sf.basedb.core.data.DataCubeFilterData
    • net.sf.basedb.core.data.DataCubeLayerData
    • net.sf.basedb.core.data.DataFileTypeData (implements net.sf.basedb.core.data.NameableData, net.sf.basedb.core.data.RemovableData)
    • net.sf.basedb.core.data.DiskUsageData
    • net.sf.basedb.core.data.ExtraValueData (implements net.sf.basedb.core.data.FileStoreEnabledData)
    • net.sf.basedb.core.data.ExtraValueTypeData (implements net.sf.basedb.core.data.NameableData, net.sf.basedb.core.data.RegisteredData, net.sf.basedb.core.data.RemovableData)
    • net.sf.basedb.core.data.FeatureData (implements net.sf.basedb.core.data.BatchableData)
    • net.sf.basedb.core.data.FileSetData
    • net.sf.basedb.core.data.FileSetMemberData (implements net.sf.basedb.core.data.LoggableData)
    • net.sf.basedb.core.data.FileTypeData (implements net.sf.basedb.core.data.NameableData, net.sf.basedb.core.data.RegisteredData, net.sf.basedb.core.data.SystemData)
    • net.sf.basedb.core.data.GroupData (implements net.sf.basedb.core.data.NameableData, net.sf.basedb.core.data.RegisteredData, net.sf.basedb.core.data.RemovableData, net.sf.basedb.core.data.SystemData)
    • net.sf.basedb.core.data.HardwareTypeData (implements net.sf.basedb.core.data.NameableData, net.sf.basedb.core.data.RegisteredData, net.sf.basedb.core.data.RemovableData, net.sf.basedb.core.data.SystemData)
    • net.sf.basedb.core.data.HelpData (implements net.sf.basedb.core.data.NameableData)
    • net.sf.basedb.core.data.ImageData (implements net.sf.basedb.core.data.FileAttachableData, net.sf.basedb.core.data.LoggableData, net.sf.basedb.core.data.NameableData, net.sf.basedb.core.data.RemovableData)
    • net.sf.basedb.core.data.JobAgentSettingsData
    • net.sf.basedb.core.data.KeyData
      • net.sf.basedb.core.data.ItemKeyData
      • net.sf.basedb.core.data.ProjectKeyData
      • net.sf.basedb.core.data.RoleKeyData
    • net.sf.basedb.core.data.MessageData (implements net.sf.basedb.core.data.NameableData, net.sf.basedb.core.data.RemovableData)
    • net.sf.basedb.core.data.MimeTypeData (implements net.sf.basedb.core.data.NameableData, net.sf.basedb.core.data.RegisteredData, net.sf.basedb.core.data.RemovableData)
    • net.sf.basedb.core.data.NewsData (implements net.sf.basedb.core.data.NameableData, net.sf.basedb.core.data.RegisteredData, net.sf.basedb.core.data.RemovableData)
    • net.sf.basedb.core.data.OwnedData (implements net.sf.basedb.core.data.OwnableData)
      • net.sf.basedb.core.data.JobData (implements net.sf.basedb.core.data.NameableData, net.sf.basedb.core.data.RemovableData)
      • net.sf.basedb.core.data.ProjectData (implements net.sf.basedb.core.data.NameableData, net.sf.basedb.core.data.RegisteredData, net.sf.basedb.core.data.RemovableData)
      • net.sf.basedb.core.data.SharedData (implements net.sf.basedb.core.data.ShareableData)
        • net.sf.basedb.core.data.CommonData (implements net.sf.basedb.core.data.NameableData, net.sf.basedb.core.data.RemovableData)
          • net.sf.basedb.core.data.AnnotatedData (implements net.sf.basedb.core.data.AnnotatableData, net.sf.basedb.core.data.LoggableData)
            • net.sf.basedb.core.data.ArrayBatchData (implements net.sf.basedb.core.data.RegisteredData)
            • net.sf.basedb.core.data.ArrayDesignData (implements net.sf.basedb.core.data.FileStoreEnabledData, net.sf.basedb.core.data.RegisteredData)
            • net.sf.basedb.core.data.ArraySlideData (implements net.sf.basedb.core.data.RegisteredData)
            • net.sf.basedb.core.data.BioMaterialData
              • net.sf.basedb.core.data.BioSourceData (implements net.sf.basedb.core.data.RegisteredData)
              • net.sf.basedb.core.data.MeasuredBioMaterialData
                • net.sf.basedb.core.data.ExtractData
                • net.sf.basedb.core.data.LabeledExtractData
                • net.sf.basedb.core.data.SampleData
            • net.sf.basedb.core.data.BioPlateData
            • net.sf.basedb.core.data.HybridizationData
            • net.sf.basedb.core.data.PlateData (implements net.sf.basedb.core.data.RegisteredData)
            • net.sf.basedb.core.data.PluginConfigurationData (implements net.sf.basedb.core.data.RegisteredData)
            • net.sf.basedb.core.data.ProtocolData (implements net.sf.basedb.core.data.FileAttachableData, net.sf.basedb.core.data.RegisteredData)
            • net.sf.basedb.core.data.RawBioAssayData (implements net.sf.basedb.core.data.DiskConsumableData, net.sf.basedb.core.data.FileStoreEnabledData, net.sf.basedb.core.data.RegisteredData)
            • net.sf.basedb.core.data.ScanData (implements net.sf.basedb.core.data.RegisteredData)
          • net.sf.basedb.core.data.AnnotationTypeCategoryData (implements net.sf.basedb.core.data.RegisteredData)
          • net.sf.basedb.core.data.AnnotationTypeData (implements net.sf.basedb.core.data.LoggableData, net.sf.basedb.core.data.RegisteredData)
          • net.sf.basedb.core.data.BioMaterialListData
          • net.sf.basedb.core.data.BioPlateEventData (implements net.sf.basedb.core.data.LoggableData, net.sf.basedb.core.data.RegisteredData)
          • net.sf.basedb.core.data.ClientData (implements net.sf.basedb.core.data.RegisteredData)
          • net.sf.basedb.core.data.DirectoryData (implements net.sf.basedb.core.data.SystemData)
          • net.sf.basedb.core.data.ExperimentData (implements net.sf.basedb.core.data.DiskConsumableData, net.sf.basedb.core.data.LoggableData, net.sf.basedb.core.data.RegisteredData)
          • net.sf.basedb.core.data.FileData (implements net.sf.basedb.core.data.DiskConsumableData, net.sf.basedb.core.data.LoggableData)
          • net.sf.basedb.core.data.FileServerData
          • net.sf.basedb.core.data.FormulaData (implements net.sf.basedb.core.data.LoggableData, net.sf.basedb.core.data.RegisteredData)
          • net.sf.basedb.core.data.HardwareData (implements net.sf.basedb.core.data.RegisteredData)
          • net.sf.basedb.core.data.JobAgentData
          • net.sf.basedb.core.data.LabelData (implements net.sf.basedb.core.data.RegisteredData)
          • net.sf.basedb.core.data.PermissionTemplateData
          • net.sf.basedb.core.data.PlateMappingData (implements net.sf.basedb.core.data.RegisteredData)
          • net.sf.basedb.core.data.PlateTypeData (implements net.sf.basedb.core.data.RegisteredData)
          • net.sf.basedb.core.data.ReporterListData (implements net.sf.basedb.core.data.RegisteredData)
          • net.sf.basedb.core.data.SoftwareData (implements net.sf.basedb.core.data.RegisteredData)
        • net.sf.basedb.core.data.PluginDefinitionData (implements net.sf.basedb.core.data.AnnotatableData, net.sf.basedb.core.data.RegisteredData, net.sf.basedb.core.data.RemovableData)
    • net.sf.basedb.core.data.ParameterValueData<T>
      • net.sf.basedb.core.data.BooleanParameterValueData
      • net.sf.basedb.core.data.DateParameterValueData
      • net.sf.basedb.core.data.DoubleParameterValueData
      • net.sf.basedb.core.data.FloatParameterValueData
      • net.sf.basedb.core.data.IntegerParameterValueData
      • net.sf.basedb.core.data.ItemParameterValueData
      • net.sf.basedb.core.data.LongParameterValueData
      • net.sf.basedb.core.data.StringParameterValueData
      • net.sf.basedb.core.data.TextParameterValueData
      • net.sf.basedb.core.data.TimestampParameterValueData
    • net.sf.basedb.core.data.PasswordData
    • net.sf.basedb.core.data.PlateEventData (implements net.sf.basedb.core.data.LoggableData)
    • net.sf.basedb.core.data.PlateEventTypeData (implements net.sf.basedb.core.data.NameableData, net.sf.basedb.core.data.RemovableData)
    • net.sf.basedb.core.data.PlateGeometryData (implements net.sf.basedb.core.data.NameableData, net.sf.basedb.core.data.RegisteredData, net.sf.basedb.core.data.RemovableData)
    • net.sf.basedb.core.data.PlatformData (implements net.sf.basedb.core.data.NameableData, net.sf.basedb.core.data.RemovableData)
    • net.sf.basedb.core.data.PlatformFileTypeData
    • net.sf.basedb.core.data.PlatformVariantData (implements net.sf.basedb.core.data.NameableData, net.sf.basedb.core.data.RemovableData)
    • net.sf.basedb.core.data.PluginTypeData (implements net.sf.basedb.core.data.NameableData, net.sf.basedb.core.data.RegisteredData, net.sf.basedb.core.data.RemovableData)
    • net.sf.basedb.core.data.ProtocolTypeData (implements net.sf.basedb.core.data.NameableData, net.sf.basedb.core.data.RegisteredData, net.sf.basedb.core.data.RemovableData, net.sf.basedb.core.data.SystemData)
    • net.sf.basedb.core.data.QuantityData (implements net.sf.basedb.core.data.NameableData, net.sf.basedb.core.data.RemovableData, net.sf.basedb.core.data.SystemData)
    • net.sf.basedb.core.data.QuotaData (implements net.sf.basedb.core.data.NameableData, net.sf.basedb.core.data.RemovableData, net.sf.basedb.core.data.SystemData)
    • net.sf.basedb.core.data.QuotaTypeData (implements net.sf.basedb.core.data.NameableData, net.sf.basedb.core.data.RegisteredData, net.sf.basedb.core.data.SystemData)
    • net.sf.basedb.core.data.RawData (implements net.sf.basedb.core.data.BatchableData, net.sf.basedb.core.data.ExtendableData)
      • net.sf.basedb.util.importer.spotdata.BaseFileImporter.RawDataProxy
    • net.sf.basedb.core.data.ReporterData (implements net.sf.basedb.core.data.BatchableData, net.sf.basedb.core.data.ExtendableData, net.sf.basedb.core.data.NameableData, net.sf.basedb.core.data.RegisteredData)
      • net.sf.basedb.util.importer.spotdata.BaseFileImporter.ReporterProxy
    • net.sf.basedb.core.data.ReporterTypeData (implements net.sf.basedb.core.data.NameableData, net.sf.basedb.core.data.RegisteredData, net.sf.basedb.core.data.RemovableData)
    • net.sf.basedb.core.data.RoleData (implements net.sf.basedb.core.data.NameableData, net.sf.basedb.core.data.RegisteredData, net.sf.basedb.core.data.RemovableData, net.sf.basedb.core.data.SystemData)
    • net.sf.basedb.core.data.SchemaVersionData
    • net.sf.basedb.core.data.SessionData
    • net.sf.basedb.core.data.SettingData
      • net.sf.basedb.core.data.ClientDefaultSettingData
      • net.sf.basedb.core.data.GlobalDefaultSettingData
      • net.sf.basedb.core.data.UserClientSettingData
      • net.sf.basedb.core.data.UserDefaultSettingData
    • net.sf.basedb.core.data.SoftwareTypeData (implements net.sf.basedb.core.data.NameableData, net.sf.basedb.core.data.RegisteredData, net.sf.basedb.core.data.SystemData)
    • net.sf.basedb.core.data.SpotImagesData
    • net.sf.basedb.core.data.TransformationData (implements net.sf.basedb.core.data.NameableData, net.sf.basedb.core.data.RemovableData)
    • net.sf.basedb.core.data.UnitData (implements net.sf.basedb.core.data.NameableData, net.sf.basedb.core.data.RemovableData)
    • net.sf.basedb.core.data.UnitSymbolData
    • net.sf.basedb.core.data.UserData (implements net.sf.basedb.core.data.ExtendableData, net.sf.basedb.core.data.NameableData, net.sf.basedb.core.data.RegisteredData, net.sf.basedb.core.data.RemovableData, net.sf.basedb.core.data.SystemData)
    • net.sf.basedb.core.data.VirtualDbData
    • net.sf.basedb.core.data.WellData (implements net.sf.basedb.core.data.AnnotatableData)
  • net.sf.basedb.core.BasicItem<D> (implements net.sf.basedb.core.Identifiable)
    • net.sf.basedb.core.Annotation
    • net.sf.basedb.core.AnnotationSet (implements net.sf.basedb.core.Transactional)
    • net.sf.basedb.core.AnyToAny (implements net.sf.basedb.core.Nameable)
    • net.sf.basedb.core.BasicChildItem<D>
      • net.sf.basedb.core.PlatformFileType
      • net.sf.basedb.core.PlatformVariant (implements net.sf.basedb.core.Nameable, net.sf.basedb.core.Removable)
    • net.sf.basedb.core.BioPlateEventType (implements net.sf.basedb.core.Nameable, net.sf.basedb.core.Removable, net.sf.basedb.core.SystemItem)
    • net.sf.basedb.core.BioPlateType (implements net.sf.basedb.core.Nameable, net.sf.basedb.core.Removable)
    • net.sf.basedb.core.ChangeHistory
    • net.sf.basedb.core.ChildItem<D>
      • net.sf.basedb.core.ArrayDesignBlock
      • net.sf.basedb.core.ArrayDesignPlate
      • net.sf.basedb.core.BioAssay (implements net.sf.basedb.core.Annotatable, net.sf.basedb.core.Nameable)
      • net.sf.basedb.core.BioAssaySet (implements net.sf.basedb.core.Annotatable, net.sf.basedb.core.FileStoreEnabled, net.sf.basedb.core.Nameable, net.sf.basedb.core.Removable, net.sf.basedb.info.ToTransferable<T>)
      • net.sf.basedb.core.BioMaterialEvent (implements net.sf.basedb.core.Registered)
      • net.sf.basedb.core.BioPlateEventParticipant
      • net.sf.basedb.core.BioWell
      • net.sf.basedb.core.DataCube
      • net.sf.basedb.core.DataCubeColumn
      • net.sf.basedb.core.DataCubeExtraValue
      • net.sf.basedb.core.DataCubeFilter
      • net.sf.basedb.core.DataCubeLayer
      • net.sf.basedb.core.ExtraValue (implements net.sf.basedb.core.FileStoreEnabled)
      • net.sf.basedb.core.Help (implements net.sf.basedb.core.Nameable)
      • net.sf.basedb.core.Image (implements net.sf.basedb.core.FileAttachable, net.sf.basedb.core.Nameable, net.sf.basedb.core.Removable)
      • net.sf.basedb.core.JobAgentSettings
      • net.sf.basedb.core.PlateEvent (implements net.sf.basedb.core.Registered)
      • net.sf.basedb.core.PlateEventType (implements net.sf.basedb.core.Nameable, net.sf.basedb.core.Removable)
      • net.sf.basedb.core.SpotImages
      • net.sf.basedb.core.Transformation (implements net.sf.basedb.core.Nameable, net.sf.basedb.core.Removable)
      • net.sf.basedb.core.VirtualDb
      • net.sf.basedb.core.Well (implements net.sf.basedb.core.Annotatable)
    • net.sf.basedb.core.DataFileType (implements net.sf.basedb.core.Nameable, net.sf.basedb.core.Removable, net.sf.basedb.info.ToTransferable<T>, net.sf.basedb.core.Validatable)
    • net.sf.basedb.core.DiskUsage
    • net.sf.basedb.core.ExtraValueType (implements net.sf.basedb.core.Nameable, net.sf.basedb.core.Registered, net.sf.basedb.core.Removable)
    • net.sf.basedb.core.FileSet
    • net.sf.basedb.core.FileSetMember
    • net.sf.basedb.core.FileType (implements net.sf.basedb.core.Nameable, net.sf.basedb.core.Registered, net.sf.basedb.core.SystemItem)
    • net.sf.basedb.core.Group (implements net.sf.basedb.core.Nameable, net.sf.basedb.core.Registered, net.sf.basedb.core.Removable, net.sf.basedb.core.SystemItem)
    • net.sf.basedb.core.HardwareType (implements net.sf.basedb.core.Nameable, net.sf.basedb.core.Registered, net.sf.basedb.core.Removable, net.sf.basedb.core.SystemItem)
    • net.sf.basedb.core.Key<D>
      • net.sf.basedb.core.ItemKey
      • net.sf.basedb.core.ProjectKey
      • net.sf.basedb.core.RoleKey (implements net.sf.basedb.core.Nameable)
    • net.sf.basedb.core.Message (implements net.sf.basedb.core.Nameable, net.sf.basedb.core.Removable)
    • net.sf.basedb.core.MimeType (implements net.sf.basedb.core.Nameable, net.sf.basedb.core.Registered, net.sf.basedb.core.Removable)
    • net.sf.basedb.core.News (implements net.sf.basedb.core.Nameable, net.sf.basedb.core.Registered, net.sf.basedb.core.Removable, net.sf.basedb.core.Validatable)
    • net.sf.basedb.core.OwnedItem<D> (implements net.sf.basedb.core.Ownable)
      • net.sf.basedb.core.Job (implements net.sf.basedb.core.Nameable, net.sf.basedb.core.Removable, net.sf.basedb.core.Transactional)
      • net.sf.basedb.core.Project (implements net.sf.basedb.core.Nameable, net.sf.basedb.core.Registered, net.sf.basedb.core.Removable, net.sf.basedb.info.ToTransferable<T>)
      • net.sf.basedb.core.SharedItem<D> (implements net.sf.basedb.core.Shareable)
        • net.sf.basedb.core.CommonItem<D> (implements net.sf.basedb.core.Nameable, net.sf.basedb.core.Removable)
          • net.sf.basedb.core.AnnotatedItem<D> (implements net.sf.basedb.core.Annotatable)
            • net.sf.basedb.core.ArrayBatch (implements net.sf.basedb.core.Registered)
            • net.sf.basedb.core.ArrayDesign (implements net.sf.basedb.core.FileStoreEnabled, net.sf.basedb.core.Registered, net.sf.basedb.info.ToTransferable<T>)
            • net.sf.basedb.core.ArraySlide (implements net.sf.basedb.core.Registered)
            • net.sf.basedb.core.BioMaterial<D>
              • net.sf.basedb.core.BioSource (implements net.sf.basedb.core.Registered)
              • net.sf.basedb.core.MeasuredBioMaterial<D> (implements net.sf.basedb.core.Registered)
                • net.sf.basedb.core.Extract
                • net.sf.basedb.core.LabeledExtract
                • net.sf.basedb.core.Sample
            • net.sf.basedb.core.BioPlate
            • net.sf.basedb.core.Hybridization (implements net.sf.basedb.core.Registered)
            • net.sf.basedb.core.Plate (implements net.sf.basedb.core.Registered)
            • net.sf.basedb.core.PluginConfiguration (implements net.sf.basedb.core.AnnotatableProxy, net.sf.basedb.core.Registered, net.sf.basedb.core.Transactional)
            • net.sf.basedb.core.Protocol (implements net.sf.basedb.core.FileAttachable, net.sf.basedb.core.Registered)
            • net.sf.basedb.core.RawBioAssay (implements net.sf.basedb.core.DiskConsumable, net.sf.basedb.core.FileStoreEnabled, net.sf.basedb.core.Registered, net.sf.basedb.info.ToTransferable<T>)
            • net.sf.basedb.core.Scan (implements net.sf.basedb.core.Registered)
          • net.sf.basedb.core.AnnotationType (implements net.sf.basedb.core.Registered, net.sf.basedb.info.ToTransferable<T>)
          • net.sf.basedb.core.AnnotationTypeCategory (implements net.sf.basedb.core.Registered)
          • net.sf.basedb.core.BioMaterialList
          • net.sf.basedb.core.BioPlateEvent (implements net.sf.basedb.core.Registered, net.sf.basedb.core.Transactional)
          • net.sf.basedb.core.Client (implements net.sf.basedb.core.Registered)
          • net.sf.basedb.core.Experiment (implements net.sf.basedb.core.DiskConsumable, net.sf.basedb.core.Registered, net.sf.basedb.info.ToTransferable<T>, net.sf.basedb.core.Transactional)
          • net.sf.basedb.core.File (implements net.sf.basedb.core.DiskConsumable, net.sf.basedb.core.Transactional)
          • net.sf.basedb.core.FileServer
          • net.sf.basedb.core.Formula (implements net.sf.basedb.core.Registered, net.sf.basedb.core.Validatable)
          • net.sf.basedb.core.Hardware (implements net.sf.basedb.core.Registered)
          • net.sf.basedb.core.JobAgent
          • net.sf.basedb.core.Label (implements net.sf.basedb.core.Registered)
          • net.sf.basedb.core.PermissionTemplate
          • net.sf.basedb.core.PlateMapping (implements net.sf.basedb.core.Registered)
          • net.sf.basedb.core.PlateType (implements net.sf.basedb.core.Registered)
          • net.sf.basedb.core.ReporterList (implements net.sf.basedb.core.Registered, net.sf.basedb.info.ToTransferable<T>)
          • net.sf.basedb.core.Software (implements net.sf.basedb.core.Registered)
        • net.sf.basedb.core.Directory (implements net.sf.basedb.core.Nameable, net.sf.basedb.core.Removable, net.sf.basedb.core.SystemItem)
        • net.sf.basedb.core.PluginDefinition (implements net.sf.basedb.core.AnnotatableProxy, net.sf.basedb.core.Nameable, net.sf.basedb.core.Registered, net.sf.basedb.core.Removable)
    • net.sf.basedb.core.PlateGeometry (implements net.sf.basedb.core.Nameable, net.sf.basedb.core.Registered, net.sf.basedb.core.Removable)
    • net.sf.basedb.core.Platform (implements net.sf.basedb.core.Nameable, net.sf.basedb.core.Removable)
    • net.sf.basedb.core.PluginType (implements net.sf.basedb.core.Nameable, net.sf.basedb.core.Registered, net.sf.basedb.core.Removable)
    • net.sf.basedb.core.ProtocolType (implements net.sf.basedb.core.Nameable, net.sf.basedb.core.Registered, net.sf.basedb.core.Removable, net.sf.basedb.core.SystemItem)
    • net.sf.basedb.core.Quantity (implements net.sf.basedb.core.Nameable, net.sf.basedb.core.Removable, net.sf.basedb.core.SystemItem)
    • net.sf.basedb.core.Quota (implements net.sf.basedb.core.Nameable, net.sf.basedb.core.Removable, net.sf.basedb.core.SystemItem)
    • net.sf.basedb.core.QuotaType (implements net.sf.basedb.core.Nameable, net.sf.basedb.core.Registered, net.sf.basedb.core.SystemItem)
    • net.sf.basedb.core.ReporterType (implements net.sf.basedb.core.Nameable, net.sf.basedb.core.Registered, net.sf.basedb.core.Removable)
    • net.sf.basedb.core.Role (implements net.sf.basedb.core.Nameable, net.sf.basedb.core.Registered, net.sf.basedb.core.Removable, net.sf.basedb.core.SystemItem)
    • net.sf.basedb.core.Session
    • net.sf.basedb.core.Setting<D>
      • net.sf.basedb.core.ClientDefaultSetting
      • net.sf.basedb.core.GlobalDefaultSetting
      • net.sf.basedb.core.UserClientSetting
      • net.sf.basedb.core.UserDefaultSetting
    • net.sf.basedb.core.SoftwareType (implements net.sf.basedb.core.Nameable, net.sf.basedb.core.Registered, net.sf.basedb.core.SystemItem)
    • net.sf.basedb.core.Unit (implements net.sf.basedb.core.Nameable, net.sf.basedb.core.Removable)
    • net.sf.basedb.core.User (implements net.sf.basedb.core.Nameable, net.sf.basedb.core.Registered, net.sf.basedb.core.Removable, net.sf.basedb.core.SystemItem)
  • net.sf.basedb.util.overview.filter.BasicItemFilter (implements net.sf.basedb.util.filter.Filter<T>)
  • net.sf.basedb.info.BasicItemInfo (implements net.sf.basedb.info.Transferable)
    • net.sf.basedb.info.BioAssaySetInfo (implements net.sf.basedb.info.NameableInfo, java.io.Serializable)
    • net.sf.basedb.info.DataFileTypeInfo (implements net.sf.basedb.info.NameableInfo, java.io.Serializable)
    • net.sf.basedb.info.OwnedItemInfo
      • net.sf.basedb.info.ProjectInfo (implements net.sf.basedb.info.NameableInfo, java.io.Serializable)
      • net.sf.basedb.info.SharedItemInfo
        • net.sf.basedb.info.CommonItemInfo (implements net.sf.basedb.info.NameableInfo)
          • net.sf.basedb.info.AnnotatedItemInfo
            • net.sf.basedb.info.ArrayDesignInfo (implements java.io.Serializable)
            • net.sf.basedb.info.RawBioAssayInfo (implements java.io.Serializable)
          • net.sf.basedb.info.AnnotationTypeInfo (implements java.io.Serializable)
          • net.sf.basedb.info.ExperimentInfo (implements java.io.Serializable)
          • net.sf.basedb.info.ReporterListInfo (implements java.io.Serializable)
  • net.sf.basedb.util.overview.loader.BasicItemNodeLoaderFactory (implements net.sf.basedb.util.overview.loader.NodeLoaderFactory<L,K>)
  • net.sf.basedb.util.overview.validator.BasicItemNodeValidatorFactory (implements net.sf.basedb.util.overview.validator.NodeValidatorFactory<L,K>)
  • net.sf.basedb.util.collections.BasicItemToIdTransformer (implements net.sf.basedb.util.collections.CollectionTransformer<S,D>)
  • net.sf.basedb.util.overview.validator.BasicNodeValidator<I> (implements net.sf.basedb.util.overview.validator.NodeValidator<I>)
    • net.sf.basedb.util.overview.validator.AnnotationValidator
    • net.sf.basedb.util.overview.validator.AnyToAnyValidator
    • net.sf.basedb.util.overview.validator.DataFileValidator
    • net.sf.basedb.util.overview.validator.NameableNodeValidator<I>
      • net.sf.basedb.util.overview.validator.ArrayBatchValidator
      • net.sf.basedb.util.overview.validator.ArrayDesignValidator
      • net.sf.basedb.util.overview.validator.ArraySlideValidator
      • net.sf.basedb.util.overview.validator.BioSourceValidator
      • net.sf.basedb.util.overview.validator.ExperimentalFactorValidator
      • net.sf.basedb.util.overview.validator.ExperimentValidator
      • net.sf.basedb.util.overview.validator.ExtractValidator
      • net.sf.basedb.util.overview.validator.HardwareValidator
      • net.sf.basedb.util.overview.validator.HybridizationValidator
      • net.sf.basedb.util.overview.validator.LabeledExtractValidator
      • net.sf.basedb.util.overview.validator.PlatformValidator
      • net.sf.basedb.util.overview.validator.ProtocolParameterValidator
      • net.sf.basedb.util.overview.validator.ProtocolValidator
      • net.sf.basedb.util.overview.validator.RawBioAssayValidator
      • net.sf.basedb.util.overview.validator.SampleValidator
      • net.sf.basedb.util.overview.validator.ScanValidator
      • net.sf.basedb.util.overview.validator.SoftwareValidator
  • net.sf.basedb.core.BatchedPropertyInfo
  • net.sf.basedb.core.BatchUtil
  • net.sf.basedb.util.extensions.debug.BeanActionFactory (implements net.sf.basedb.util.extensions.ActionFactory<A>)
  • net.sf.basedb.core.query.BetweenRestriction (implements net.sf.basedb.core.query.Restriction)
  • net.sf.basedb.plugins.BfsExporterPlugin.ExtendedExportableField
  • net.sf.basedb.util.importer.spotdata.BfsImporter
  • net.sf.basedb.util.importer.spotdata.BfsImporter.ProgressEventHandler (implements net.sf.basedb.util.bfs.EventHandler)
  • net.sf.basedb.clients.web.plugins.BioAssayExperimentalFactorLoader (implements net.sf.basedb.clients.web.plugins.DataLoader<T>)
  • net.sf.basedb.plugins.BioAssaySetExporter.QueryItem
  • net.sf.basedb.plugins.BioAssaySetExporter.QueryItemTitleComparator (implements java.util.Comparator<T>, java.io.Serializable)
  • net.sf.basedb.util.BioAssaySetFilterUtil
  • net.sf.basedb.util.BioAssaySetUtil
  • net.sf.basedb.core.log.db.BioMaterialEventLogger (implements net.sf.basedb.core.log.EntityLogger)
  • net.sf.basedb.core.data.BioMaterialSourceEventData
  • net.sf.basedb.util.biomaterial.BioSourceToSampleTransformer (implements net.sf.basedb.util.collections.CollectionTransformer<S,D>)
  • net.sf.basedb.core.BlockInfo
  • net.sf.basedb.util.formatter.BooleanFormatter (implements net.sf.basedb.util.formatter.Formatter<T>)
  • net.sf.basedb.clients.web.resources.Bundle
  • net.sf.basedb.clients.web.extensions.toolbar.ButtonBean (implements net.sf.basedb.clients.web.extensions.toolbar.ButtonAction)
  • net.sf.basedb.core.query.CaseExpression (implements net.sf.basedb.core.query.Expression)
  • net.sf.basedb.util.ChainedProgressReporter (implements net.sf.basedb.core.ProgressReporter)
  • net.sf.basedb.clients.web.ChangeHistoryUtil
  • net.sf.basedb.util.jep.ChannelFunction (implements net.sf.basedb.util.jep.JepExpressionFunction)
  • net.sf.basedb.clients.web.servlet.CharacterEncodingFilter (implements javax.servlet.Filter)
  • java.lang.ClassLoader
    • net.sf.basedb.util.JarClassLoader
  • net.sf.basedb.util.ClassLocal<E>
  • net.sf.basedb.util.error.ClassMapErrorHandler (implements net.sf.basedb.util.error.ErrorHandler)
  • net.sf.basedb.util.ClassUtil
  • net.sf.basedb.util.extensions.ClientContext
    • net.sf.basedb.clients.web.extensions.JspContext
  • net.sf.basedb.clients.jobagent.CmdLine
  • net.sf.basedb.util.parser.ColFunction (implements net.sf.basedb.util.jep.JepFunction)
  • net.sf.basedb.clients.web.formatter.ColorFormatter (implements net.sf.basedb.util.formatter.Formatter<T>)
  • net.sf.basedb.util.ColorGenerator
  • net.sf.basedb.core.Coloring (implements net.sf.basedb.core.AccessControlled)
  • net.sf.basedb.core.data.ColoringData (implements net.sf.basedb.core.data.ComponentData)
  • net.sf.basedb.util.parser.ColumnMapper (implements net.sf.basedb.util.parser.Mapper)
  • net.sf.basedb.util.extensions.events.CombiningEventFilter (implements net.sf.basedb.util.extensions.events.EventFilter)
  • net.sf.basedb.clients.web.extensions.toolbar.CompactButtonRenderer (implements net.sf.basedb.util.extensions.Renderer<A>)
  • net.sf.basedb.util.ComparableComparator<T> (implements java.util.Comparator<T>)
  • org.apache.jasper.compiler.Compiler
    • org.apache.jasper.compiler.JDTCompiler
      • net.sf.basedb.clients.web.extensions.XJspCompiler
  • net.sf.basedb.util.parser.CompoundMapper (implements net.sf.basedb.util.parser.Mapper)
  • net.sf.basedb.core.Config
  • net.sf.basedb.ws.client.ConfigurableServiceFactory (implements net.sf.basedb.ws.client.ServiceFactory)
  • net.sf.basedb.util.ConsoleProgressReporter (implements net.sf.basedb.core.ProgressReporter)
  • net.sf.basedb.util.parser.ConstantMapper (implements net.sf.basedb.util.parser.Mapper)
  • net.sf.basedb.core.data.ContextIndex (implements java.io.Serializable)
  • net.sf.basedb.core.ContextKey
  • net.sf.basedb.util.ContextUtil
  • net.sf.basedb.util.ContextUtil.ContextResult
  • net.sf.basedb.util.ContextUtil.IsInContextFilter (implements net.sf.basedb.util.filter.Filter<T>)
  • net.sf.basedb.util.jep.convert.ConverterFactory
  • net.sf.basedb.util.Coordinate
  • net.sf.basedb.core.query.CountExpression (implements net.sf.basedb.core.query.Expression)
  • net.sf.basedb.util.parser.CropStringMapper (implements net.sf.basedb.util.parser.Mapper)
  • net.sf.basedb.util.parser.DataNoFunction (implements net.sf.basedb.util.jep.JepFunction)
  • net.sf.basedb.util.bfs.DataParser (implements net.sf.basedb.util.bfs.BfsParser)
  • net.sf.basedb.clients.web.plugins.DataQueryWrapper (implements net.sf.basedb.clients.web.plugins.QueryWrapper<T>)
  • net.sf.basedb.core.DataResultIterator<I> (implements net.sf.basedb.core.query.ResultIterator<I>)
  • net.sf.basedb.util.formatter.DateFormatter (implements net.sf.basedb.util.formatter.Formatter<T>)
  • net.sf.basedb.core.DateUtil
  • net.sf.basedb.core.DbControl
  • net.sf.basedb.core.DbControl.SaveIf
  • net.sf.basedb.core.log.db.DbLogManager (implements net.sf.basedb.core.log.LogManager)
  • net.sf.basedb.core.log.db.DbLogManagerFactory (implements net.sf.basedb.core.log.LogManagerFactory)
  • net.sf.basedb.core.log.db.DefaultEntityLogger (implements net.sf.basedb.core.log.EntityLogger)
  • net.sf.basedb.util.extensions.DefaultFilter (implements net.sf.basedb.util.extensions.ExtensionsFilter)
    • net.sf.basedb.clients.web.extensions.Settings (implements net.sf.basedb.util.extensions.ExtensionsFilter)
  • net.sf.basedb.clients.jobagent.handlers.DefaultRequestHandler (implements net.sf.basedb.util.jobagent.RequestHandler)
  • net.sf.basedb.core.query.DescOrder (implements net.sf.basedb.core.query.Order)
  • java.util.Dictionary<K,V>
    • java.util.Hashtable<K,V> (implements java.lang.Cloneable, java.util.Map<K,V>, java.io.Serializable)
      • org.nfunk.jep.FunctionTable
        • net.sf.basedb.util.jep.FunctionSafeJep.SafeFunctionTable
  • net.sf.basedb.util.Diff3
  • net.sf.basedb.util.overview.cache.DirectionalCacheKey
  • net.sf.basedb.util.importer.DiskFileWrapper (implements net.sf.basedb.util.importer.FileWrapper)
  • net.sf.basedb.util.bfs.DiskInputStreamLocator (implements net.sf.basedb.util.bfs.InputStreamLocator)
  • net.sf.basedb.core.DiskUsageStatistics
  • net.sf.basedb.core.DiskUsageStatistics.Summary
  • net.sf.basedb.core.query.DivideExpression (implements net.sf.basedb.core.query.Expression)
  • net.sf.basedb.clients.jobagent.executors.DummyJobExecutor (implements net.sf.basedb.clients.jobagent.JobExecutor)
  • net.sf.basedb.clients.web.extensions.service.DummyService (implements net.sf.basedb.util.extensions.ActionFactory<A>, net.sf.basedb.clients.web.extensions.service.ServiceControllerAction)
  • net.sf.basedb.core.query.Dynamic
  • net.sf.basedb.core.DynamicJoin (implements net.sf.basedb.core.query.Join)
  • net.sf.basedb.core.DynamicPositionQueryJoiners
  • net.sf.basedb.core.DynamicPositionQueryJoiners.ExtraValueJoiner (implements net.sf.basedb.core.query.AutoJoiner<Q,E>)
  • net.sf.basedb.core.DynamicPositionQueryJoiners.ReporterJoiner (implements net.sf.basedb.core.query.AutoJoiner<Q,E>)
  • net.sf.basedb.clients.web.plugins.DynamicQueryWrapper (implements net.sf.basedb.clients.web.plugins.QueryWrapper<T>)
  • net.sf.basedb.core.DynamicRestriction (implements net.sf.basedb.core.query.Restriction)
  • net.sf.basedb.core.DynamicResultIterator (implements net.sf.basedb.core.query.SqlResultIterator)
  • net.sf.basedb.core.DynamicResultIterator.SqlResultImpl (implements net.sf.basedb.core.query.SqlResult)
  • net.sf.basedb.core.DynamicSpotQueryJoiners
  • net.sf.basedb.core.DynamicSpotQueryJoiners.ExtraValueJoiner (implements net.sf.basedb.core.query.AutoJoiner<Q,E>)
  • net.sf.basedb.core.DynamicSpotQueryJoiners.RawDataJoiner (implements net.sf.basedb.core.query.AutoJoiner<Q,E>)
  • net.sf.basedb.core.DynamicSpotQueryJoiners.ReporterJoiner (implements net.sf.basedb.core.query.AutoJoiner<Q,E>)
  • net.sf.basedb.core.DynamicSpotQueryJoiners.ReporterListJoiner (implements net.sf.basedb.core.query.AutoJoiner<Q,E>)
  • net.sf.basedb.clients.web.DynamicUtil
  • net.sf.basedb.clients.web.DynamicUtil.SelectedInfo
  • net.sf.basedb.clients.web.extensions.edit.EditUtil
  • net.sf.basedb.util.EmailUtil
  • org.hibernate.EmptyInterceptor (implements org.hibernate.Interceptor, java.io.Serializable)
    • net.sf.basedb.core.log.LoggingInterceptor
  • net.sf.basedb.util.encode.EncodeUtil
  • net.sf.basedb.core.dbengine.EngineFactory
  • net.sf.basedb.core.log.EntityDetails
  • net.sf.basedb.util.Enumeration<K,V> (implements java.io.Serializable)
  • net.sf.basedb.util.Enumeration.Entry<K,V>
  • net.sf.basedb.core.query.EqRestriction (implements net.sf.basedb.core.query.Restriction)
  • net.sf.basedb.util.filter.EqualsFilter<T> (implements net.sf.basedb.util.filter.Filter<T>)
  • net.sf.basedb.util.EqualsHelper
  • net.sf.basedb.util.bfs.EventType<T>
  • net.sf.basedb.util.extensions.events.EventType
  • net.sf.basedb.util.extensions.events.EventTypeFilter (implements net.sf.basedb.util.extensions.events.EventFilter)
  • net.sf.basedb.core.signal.ExceptionInterruptHandler (implements net.sf.basedb.core.signal.InterruptHandler)
  • net.sf.basedb.core.hibernate.ExecuteUpdateWork (implements net.sf.basedb.core.hibernate.JdbcWork<R>)
  • net.sf.basedb.clients.web.ExperimentExplorer
  • net.sf.basedb.clients.web.ExperimentExplorer.AnnotationGroup (implements java.lang.Comparable<T>)
  • net.sf.basedb.clients.web.ExperimentExplorer.AnnotationSummary
  • net.sf.basedb.clients.web.ExperimentExplorer.ReporterPositions
  • net.sf.basedb.clients.web.servlet.ExperimentExplorerPlotServlet.ColumnKey (implements java.lang.Comparable<T>)
  • net.sf.basedb.util.overview.ExperimentOverview
  • net.sf.basedb.core.query.ExpExpression (implements net.sf.basedb.core.query.Expression)
  • net.sf.basedb.util.export.spotdata.ExportableFieldFactory
  • net.sf.basedb.util.export.spotdata.ExportableFieldFormatter (implements net.sf.basedb.util.formatter.Formatter<T>)
  • net.sf.basedb.clients.web.plugins.ExportedProperty
  • net.sf.basedb.core.query.Expressions
  • net.sf.basedb.core.query.ExpressionSelect (implements net.sf.basedb.core.query.Select)
  • net.sf.basedb.core.ExtendedProperties
  • net.sf.basedb.core.ExtendedProperty (implements net.sf.basedb.info.ToTransferable<T>)
    • net.sf.basedb.core.RawDataProperty
  • net.sf.basedb.core.ExtendedPropertyAccessor (implements org.hibernate.property.PropertyAccessor)
  • net.sf.basedb.core.ExtendedPropertyAccessor.GetterSetter (implements org.hibernate.property.Getter, org.hibernate.property.Setter)
  • net.sf.basedb.clients.web.formatter.ExtendedPropertyFormatter<T> (implements net.sf.basedb.util.formatter.Formatter<T>)
  • net.sf.basedb.info.ExtendedPropertyInfo (implements java.io.Serializable, net.sf.basedb.info.Transferable)
  • net.sf.basedb.core.ExtendedPropertyLinker
  • net.sf.basedb.util.extensions.ExtensionBean<A> (implements net.sf.basedb.util.extensions.Extension<A>)
  • net.sf.basedb.util.extensions.ExtensionPointBean<A> (implements net.sf.basedb.util.extensions.ExtensionPoint<A>)
  • net.sf.basedb.util.extensions.events.ExtensionPointEventFilter (implements net.sf.basedb.util.extensions.events.EventFilter)
  • net.sf.basedb.clients.web.extensions.ExtensionsControl (implements net.sf.basedb.core.AccessControlled)
  • net.sf.basedb.clients.web.extensions.ExtensionsDirectory
  • net.sf.basedb.clients.web.extensions.ExtensionsFile (implements java.lang.Comparable<T>)
  • net.sf.basedb.util.extensions.ExtensionsInvoker<A>
  • net.sf.basedb.plugins.executor.ExternalProgramExecutor.RequestWrapper (implements net.sf.basedb.core.plugin.Request)
  • net.sf.basedb.plugins.executor.ExternalProgramExecutor.ResponseWrapper (implements net.sf.basedb.core.plugin.Response)
  • net.sf.basedb.util.biomaterial.ExtractToLabeledExtractTransformer (implements net.sf.basedb.util.collections.CollectionTransformer<S,D>)
  • net.sf.basedb.util.biomaterial.ExtractToSampleTransformer (implements net.sf.basedb.util.collections.CollectionTransformer<S,D>)
  • net.sf.basedb.util.importer.spotdata.ExtraFloatParser
  • net.sf.basedb.core.ExtraValueExpression (implements net.sf.basedb.core.query.Expression)
  • net.sf.basedb.util.jep.ExtraValueFunction (implements net.sf.basedb.util.jep.JepExpressionFunction)
  • net.sf.basedb.core.ExtraValueJoin (implements net.sf.basedb.core.query.Join)
  • net.sf.basedb.ws.client.Factories
  • net.sf.basedb.util.overview.Failure
  • net.sf.basedb.plugins.batchimport.FallbackIdMethod (implements net.sf.basedb.plugins.batchimport.IdMethod)
  • net.sf.basedb.core.Feature
  • net.sf.basedb.core.FeatureCoordinate
  • net.sf.basedb.util.export.spotdata.FieldConverter
  • net.sf.basedb.util.FileCopyRunnable (implements java.lang.Runnable)
  • javax.activation.FileDataSource (implements javax.activation.DataSource)
    • net.sf.basedb.ws.server.TempFileDataSource
  • net.sf.basedb.util.formatter.FilePathFormatter (implements net.sf.basedb.util.formatter.Formatter<T>)
  • net.sf.basedb.core.FileSet.DataFileHandlerWrapper
  • net.sf.basedb.core.FileSet.QueryRuntimeFilterImpl (implements net.sf.basedb.core.QueryRuntimeFilter)
  • net.sf.basedb.core.FileSetMember.QueryRuntimeFilterImpl (implements net.sf.basedb.core.QueryRuntimeFilter)
  • net.sf.basedb.clients.web.plugins.FileSetMemberLoader (implements net.sf.basedb.clients.web.plugins.DataLoader<T>)
  • net.sf.basedb.core.log.db.FileSetMemberLogger (implements net.sf.basedb.core.log.EntityLogger)
  • net.sf.basedb.util.overview.node.FileSetMemberNameGenerator (implements net.sf.basedb.util.overview.node.NodeNameGenerator<I>)
  • net.sf.basedb.core.FileStoreUtil
  • net.sf.basedb.core.data.FileTypeIndex (implements java.io.Serializable)
  • net.sf.basedb.clients.web.fileupload.FileUpload
  • net.sf.basedb.clients.web.fileupload.FileUpload.SectionHeaders
  • net.sf.basedb.clients.web.fileupload.FileUpload.UploadStatus
  • net.sf.basedb.clients.web.fileupload.FileUploadProgress
  • net.sf.basedb.util.FileUtil
  • net.sf.basedb.util.filter.FilterUtil
  • net.sf.basedb.util.importer.spotdata.FirstPassSectionSpotsParser (implements net.sf.basedb.util.basefile.BaseFileSectionParser)
  • net.sf.basedb.util.overview.Fix
  • net.sf.basedb.util.parser.FlatFileParser
  • net.sf.basedb.util.parser.FlatFileParser.Data
  • net.sf.basedb.util.parser.FlatFileParser.Line
  • net.sf.basedb.core.query.FloatExpression (implements net.sf.basedb.core.query.Expression)
  • net.sf.basedb.clients.web.formatter.FormatterFactory
  • net.sf.basedb.clients.web.formatter.FormatterSettings
  • net.sf.basedb.util.jep.FunctionSafeJep.UnknownFunction (implements org.nfunk.jep.function.PostfixMathCommandI, java.io.Serializable)
  • net.sf.basedb.util.bfs.GenericExtraFileImporter (implements net.sf.basedb.util.bfs.ExtraFileImporter)
  • net.sf.basedb.util.importer.spotdata.GenericIntensityParser (implements net.sf.basedb.util.importer.spotdata.SpotIntensityParser)
  • net.sf.basedb.util.overview.GenericOverview (implements net.sf.basedb.util.overview.OverviewContext)
  • javax.servlet.GenericServlet (implements java.io.Serializable, javax.servlet.Servlet, javax.servlet.ServletConfig)
    • javax.servlet.http.HttpServlet (implements java.io.Serializable)
      • net.sf.basedb.clients.web.servlet.CompileAll
      • net.sf.basedb.clients.web.servlet.Download
      • net.sf.basedb.clients.web.servlet.ExperimentExplorerPlotServlet
      • net.sf.basedb.clients.web.servlet.ExtensionsServlet
      • net.sf.basedb.clients.web.servlet.PlotServlet
      • net.sf.basedb.clients.web.servlet.RssNewsFeed
      • net.sf.basedb.clients.web.servlet.StartStopServlet
      • net.sf.basedb.clients.web.servlet.Upload
      • net.sf.basedb.clients.web.servlet.ViewSpotImage
  • net.sf.basedb.core.query.GeometricMeanExpression (implements net.sf.basedb.core.query.Expression)
  • net.sf.basedb.core.Group.QueryRuntimeFilterImpl (implements net.sf.basedb.core.QueryRuntimeFilter)
  • net.sf.basedb.core.data.keyring.GroupGroups (implements java.io.Serializable)
  • net.sf.basedb.core.GroupPermissions
  • net.sf.basedb.core.query.GteqRestriction (implements net.sf.basedb.core.query.Restriction)
  • net.sf.basedb.core.query.GtRestriction (implements net.sf.basedb.core.query.Restriction)
  • net.sf.basedb.core.plugin.GuiContext
  • net.sf.basedb.core.data.GuiContextData (implements java.io.Serializable)
  • net.sf.basedb.core.HibernateUtil
  • net.sf.basedb.util.plot.HistogramPlot
  • net.sf.basedb.util.plot.HistogramPlot.HistogramBin (implements java.io.Serializable)
  • net.sf.basedb.util.plot.HistogramPlot.HistogramSeries (implements java.io.Serializable)
  • net.sf.basedb.util.plot.HistogramPlot.TempSeries
  • net.sf.basedb.core.query.Hql
  • net.sf.basedb.core.query.HqlElementsExpression (implements net.sf.basedb.core.query.Expression)
  • net.sf.basedb.core.query.HqlEntityExpression (implements net.sf.basedb.core.query.Expression)
  • net.sf.basedb.core.query.HqlEntityParameterExpression (implements net.sf.basedb.core.query.Expression)
  • net.sf.basedb.core.query.HqlExpression (implements net.sf.basedb.core.query.Expression, net.sf.basedb.core.query.Restriction)
  • net.sf.basedb.core.query.HqlIndexExpression (implements net.sf.basedb.core.query.Expression)
  • net.sf.basedb.core.query.HqlInnerJoin (implements net.sf.basedb.core.query.Join)
  • net.sf.basedb.core.query.HqlLeftJoin (implements net.sf.basedb.core.query.Join)
  • net.sf.basedb.core.query.HqlPropertyExpression (implements net.sf.basedb.core.query.Expression)
  • net.sf.basedb.core.HqlQueryJoiners
  • net.sf.basedb.core.HqlQueryJoiners.ReporterListJoiner (implements net.sf.basedb.core.query.AutoJoiner<Q,E>)
  • net.sf.basedb.core.query.HqlRightJoin (implements net.sf.basedb.core.query.Join)
  • net.sf.basedb.core.query.HqlSizeExpression (implements net.sf.basedb.core.query.Expression)
  • net.sf.basedb.clients.web.util.HTML
  • net.sf.basedb.util.HttpUtil
  • net.sf.basedb.util.formatter.IdentifiableFormatter (implements net.sf.basedb.util.formatter.Formatter<T>)
  • net.sf.basedb.util.encode.IdentityEncoderDecoder (implements net.sf.basedb.util.encode.EncoderDecoder)
  • net.sf.basedb.util.filter.IdentityFilter<T> (implements net.sf.basedb.util.filter.Filter<T>)
  • net.sf.basedb.util.units.IdentityUnitConverter (implements net.sf.basedb.util.units.UnitConverter)
  • net.sf.basedb.plugins.IlluminaRawDataImporter.BatchAndMapHolder
  • net.sf.basedb.core.log.db.ImageLogger (implements net.sf.basedb.core.log.EntityLogger)
  • net.sf.basedb.clients.web.extensions.tabcontrol.IncludeContentTabFactory.Tab (implements net.sf.basedb.clients.web.extensions.tabcontrol.TabAction)
  • net.sf.basedb.util.IncludeExcludeFilter (implements net.sf.basedb.util.DynamicFilter)
  • net.sf.basedb.util.overview.cache.IndexedCacheKey
  • net.sf.basedb.clients.jobagent.handlers.InfoRequestHandler (implements net.sf.basedb.util.jobagent.RequestHandler)
  • java.io.InputStream (implements java.io.Closeable)
    • net.sf.basedb.clients.web.fileupload.FileUpload.UploadStream
    • java.io.FilterInputStream
      • net.sf.basedb.core.plugin.ImportInputStream
        • net.sf.basedb.util.FileImportInputStream
      • net.sf.basedb.util.StaticCache.LockSafeInputStream
      • net.sf.basedb.ws.server.TempFileDataSource.TempInputStream
    • net.sf.basedb.util.InputStreamCombiner
    • net.sf.basedb.util.InputStreamSplitter
    • net.sf.basedb.util.InputStreamTracker
  • net.sf.basedb.util.jep.InReporterListFunction (implements net.sf.basedb.util.jep.JepRestrictionFunction)
  • net.sf.basedb.core.query.InRestriction (implements net.sf.basedb.core.query.Restriction)
  • net.sf.basedb.core.Install
  • net.sf.basedb.core.Install.PlatformFT
  • net.sf.basedb.util.filter.InstanceOfFilter<T> (implements net.sf.basedb.util.filter.Filter<T>)
  • net.sf.basedb.core.query.IntegerExpression (implements net.sf.basedb.core.query.Expression)
  • net.sf.basedb.util.formatter.IntegerFormatter (implements net.sf.basedb.util.formatter.Formatter<T>)
  • net.sf.basedb.core.IntegerUtil
  • net.sf.basedb.util.IntensityCalculatorUtil
  • net.sf.basedb.util.IntensityCalculatorUtil.JepIntensityCalculatorImpl (implements net.sf.basedb.util.IntensityCalculator)
  • net.sf.basedb.core.IntensityFormula
  • net.sf.basedb.plugins.batchimport.InternalIdMethod (implements net.sf.basedb.plugins.batchimport.IdMethod)
  • net.sf.basedb.core.InternalJobQueue.JobRunner (implements java.lang.Runnable)
  • net.sf.basedb.clients.jobagent.slotmanager.InternalSlotManager (implements net.sf.basedb.clients.jobagent.slotmanager.SlotManager)
    • net.sf.basedb.clients.jobagent.slotmanager.MasterSlotManager
  • net.sf.basedb.core.InternalStorageController (implements net.sf.basedb.core.SecondaryStorageController)
  • net.sf.basedb.util.filter.InverseFilter<T> (implements net.sf.basedb.util.filter.Filter<T>)
  • net.sf.basedb.util.extensions.InvokationContext<A>
    • net.sf.basedb.util.extensions.ExtensionContext<A>
    • net.sf.basedb.util.extensions.ExtensionPointContext<A>
  • net.sf.basedb.core.Item.DefinedPermissions
  • net.sf.basedb.core.ItemContext
  • net.sf.basedb.core.ItemContext.PropertyFilterPair
  • net.sf.basedb.core.ItemProxy (implements java.lang.Comparable<T>)
  • net.sf.basedb.clients.web.plugins.ItemQueryLoader (implements net.sf.basedb.clients.web.plugins.DataLoader<T>)
  • net.sf.basedb.clients.web.plugins.ItemQueryWrapper (implements net.sf.basedb.clients.web.plugins.QueryWrapper<T>)
  • net.sf.basedb.core.ItemResultIterator<I> (implements net.sf.basedb.core.query.ResultIterator<I>)
  • net.sf.basedb.core.ItemResultList.ResultListIterator<T> (implements java.util.Iterator<E>)
  • net.sf.basedb.core.ItemResultList.ResultListListIterator<T> (implements java.util.ListIterator<E>)
  • net.sf.basedb.util.overview.filter.ItemTypeFilter (implements net.sf.basedb.util.filter.Filter<T>)
  • net.sf.basedb.util.JarClassLoader.JarInfo
  • net.sf.basedb.util.jep.Jep
  • org.nfunk.jep.JEP
    • net.sf.basedb.util.jep.FunctionSafeJep
  • net.sf.basedb.util.export.spotdata.JepDynamicField (implements net.sf.basedb.util.export.spotdata.DynamicField)
  • net.sf.basedb.util.parser.JepMapper (implements net.sf.basedb.util.parser.Mapper)
  • net.sf.basedb.core.Job.JobSignalTransporter (implements net.sf.basedb.core.signal.SignalTransporter)
  • net.sf.basedb.core.Job.ProgressReporterImpl (implements net.sf.basedb.core.ProgressReporter)
  • net.sf.basedb.util.jobagent.JobAgentConnection
  • net.sf.basedb.util.jobagent.JobAgentInfo
  • net.sf.basedb.util.jobagent.JobAgentServerConnection
  • net.sf.basedb.util.jobagent.JobAgentServerConnection.ListenerThread (implements java.lang.Runnable)
  • net.sf.basedb.util.jobagent.JobAgentServerConnection.RequestHandlerThread (implements java.lang.Runnable)
  • net.sf.basedb.util.jobagent.JobInfo
  • net.sf.basedb.clients.jobagent.JobRunner (implements java.lang.Runnable)
  • net.sf.basedb.core.data.keyring.KeyPermission (implements java.lang.Comparable<T>)
    • net.sf.basedb.core.data.keyring.GroupKeys (implements java.io.Serializable)
    • net.sf.basedb.core.data.keyring.ProjectKeys (implements java.io.Serializable)
    • net.sf.basedb.core.data.keyring.RoleKeys (implements java.io.Serializable)
    • net.sf.basedb.core.data.keyring.UserKeys (implements java.io.Serializable)
  • net.sf.basedb.core.Keyring
    • net.sf.basedb.core.InternalJobQueue.JobQueueKeyring
    • net.sf.basedb.core.InternalStorageController.StorageKeyring
  • net.sf.basedb.util.biomaterial.LabeledExtractToExtractTransformer (implements net.sf.basedb.util.collections.CollectionTransformer<S,D>)
  • net.sf.basedb.core.query.LikeRestriction (implements net.sf.basedb.core.query.Restriction)
  • net.sf.basedb.util.units.LinearUnitConverter (implements net.sf.basedb.util.units.UnitConverter)
  • net.sf.basedb.util.parser.LineNoFunction (implements net.sf.basedb.util.jep.JepFunction)
  • net.sf.basedb.util.biomaterial.ListUtil
  • net.sf.basedb.util.jep.Log2Function (implements net.sf.basedb.util.jep.JepExpressionFunction)
  • net.sf.basedb.core.LogControl
  • net.sf.basedb.core.query.LogExpression (implements net.sf.basedb.core.query.Expression)
  • net.sf.basedb.util.extensions.LoggingErrorHandlerFactory (implements net.sf.basedb.util.extensions.ErrorHandler<A>, net.sf.basedb.util.extensions.ErrorHandlerFactory<A>)
    • net.sf.basedb.util.extensions.RethrowErrorHandlerFactory
  • net.sf.basedb.core.LogUtil
  • net.sf.basedb.util.formatter.LookupFormatter<T> (implements net.sf.basedb.util.formatter.Formatter<T>)
  • net.sf.basedb.plugins.LowessNormalization.CallableWorker (implements java.util.concurrent.Callable<V>)
  • net.sf.basedb.plugins.LowessNormalization.SpotData (implements java.lang.Comparable<T>)
  • net.sf.basedb.core.query.LteqRestriction (implements net.sf.basedb.core.query.Restriction)
  • net.sf.basedb.core.query.LtRestriction (implements net.sf.basedb.core.query.Restriction)
  • net.sf.basedb.util.importer.spotdata.MAParser (implements net.sf.basedb.util.importer.spotdata.SpotIntensityParser)
  • net.sf.basedb.core.data.MappingCoordinate (implements java.io.Serializable)
  • net.sf.basedb.clients.jobagent.slotmanager.MasterSlotManager.RemoteSlot
  • net.sf.basedb.clients.jobagent.slotmanager.MasterSlotManager.RemoteSlotRequestHandler (implements net.sf.basedb.util.jobagent.RequestHandler)
  • net.sf.basedb.util.bfs.MatrixModel (implements net.sf.basedb.util.bfs.EventHandler)
  • net.sf.basedb.util.importer.spotdata.MatrixSpotIntensityEventHandler (implements net.sf.basedb.util.bfs.EventHandler)
  • net.sf.basedb.core.query.MaxExpression (implements net.sf.basedb.core.query.Expression)
  • net.sf.basedb.util.MD5
  • net.sf.basedb.core.query.MeanExpression (implements net.sf.basedb.core.query.Expression)
  • net.sf.basedb.util.jep.MeanFunction (implements net.sf.basedb.util.jep.JepExpressionFunction)
  • net.sf.basedb.core.MeanRawDataPropertyExpression (implements net.sf.basedb.core.query.Expression)
  • net.sf.basedb.plugins.MedianRatioNormalization.SpotData (implements java.lang.Comparable<T>)
  • net.sf.basedb.clients.web.extensions.menu.MenuItemBean (implements net.sf.basedb.clients.web.extensions.menu.MenuItemAction)
  • net.sf.basedb.core.Metadata<C>
  • net.sf.basedb.core.Metadata.BasicData2ItemPropertyPath<C,V> (implements net.sf.basedb.core.Metadata.PropertyPath<C,V>)
  • net.sf.basedb.core.Metadata.BasicItem2DataPropertyPath<C,V> (implements net.sf.basedb.core.Metadata.PropertyPath<C,V>)
  • net.sf.basedb.core.Metadata.CollectionPropertyPath<C> (implements net.sf.basedb.core.Metadata.PropertyPath<C,V>)
  • net.sf.basedb.core.Metadata.CombinedPropertyPath<C,V> (implements net.sf.basedb.core.Metadata.PropertyPath<C,V>)
  • net.sf.basedb.core.Metadata.ComponentPropertyPath<C,V> (implements net.sf.basedb.core.Metadata.PropertyPath<C,V>)
  • net.sf.basedb.core.Metadata.DateCopyPropertyPath (implements net.sf.basedb.core.Metadata.PropertyPath<C,V>)
  • net.sf.basedb.core.Metadata.EntityPropertyPath<C,V> (implements net.sf.basedb.core.Metadata.PropertyPath<C,V>)
  • net.sf.basedb.core.Metadata.EvictPropertyPath<C> (implements net.sf.basedb.core.Metadata.PropertyPath<C,V>)
  • net.sf.basedb.core.Metadata.IdentifierPropertyPath (implements net.sf.basedb.core.Metadata.PropertyPath<C,V>)
  • net.sf.basedb.core.Metadata.MapPropertyPath (implements net.sf.basedb.core.Metadata.PropertyPath<C,V>)
  • net.sf.basedb.core.Metadata.NoopPropertyPath<C> (implements net.sf.basedb.core.Metadata.PropertyPath<C,V>)
  • net.sf.basedb.core.Metadata.ReporterScore2DataPropertyPath (implements net.sf.basedb.core.Metadata.PropertyPath<C,V>)
  • net.sf.basedb.util.bfs.MetadataModel (implements net.sf.basedb.util.bfs.EventHandler)
  • net.sf.basedb.util.bfs.MetadataModel.Section
  • net.sf.basedb.util.bfs.MetadataModel.SectionEntry
  • net.sf.basedb.util.bfs.MetadataParser (implements net.sf.basedb.util.bfs.BfsParser)
  • net.sf.basedb.core.query.MinExpression (implements net.sf.basedb.core.query.Expression)
  • net.sf.basedb.clients.web.ModeInfo
  • net.sf.basedb.util.bfs.MultiEventHandler (implements net.sf.basedb.util.bfs.EventHandler)
  • net.sf.basedb.util.formatter.MultiFormatter (implements net.sf.basedb.util.formatter.Formatter<T>)
  • net.sf.basedb.core.MultiPermissions
  • net.sf.basedb.core.query.MultiplyExpression (implements net.sf.basedb.core.query.Expression)
  • net.sf.basedb.plugins.batchimport.MultiPropertyIdMethod (implements net.sf.basedb.plugins.batchimport.IdMethod)
  • net.sf.basedb.clients.jobagent.handlers.MultiProtocolRequestHandler (implements net.sf.basedb.util.jobagent.RequestHandler)
  • net.sf.basedb.util.collections.MultiStepCollectionTransformer<S,D> (implements net.sf.basedb.util.collections.CollectionTransformer<S,D>)
  • net.sf.basedb.core.hibernate.MultiUpdateWork (implements net.sf.basedb.core.hibernate.JdbcWork<R>)
  • net.sf.basedb.util.NameableComparator<T> (implements java.util.Comparator<T>, java.io.Serializable)
  • net.sf.basedb.util.formatter.NameableFormatter (implements net.sf.basedb.util.formatter.Formatter<T>)
  • net.sf.basedb.util.overview.node.NameableNameGenerator<I> (implements net.sf.basedb.util.overview.node.NodeNameGenerator<I>)
    • net.sf.basedb.util.overview.node.LabeledExtractNameGenerator
  • net.sf.basedb.clients.web.util.NameablePluginAdaptor (implements net.sf.basedb.core.Nameable)
  • net.sf.basedb.core.NameableUtil
  • net.sf.basedb.core.plugin.NamespaceParameterValuesWrapper (implements net.sf.basedb.core.plugin.ParameterValues)
  • net.sf.basedb.core.plugin.NamespaceRequestWrapper (implements net.sf.basedb.core.plugin.Request)
  • net.sf.basedb.core.query.NegateExpression (implements net.sf.basedb.core.query.Expression)
  • net.sf.basedb.core.query.NeqRestriction (implements net.sf.basedb.core.query.Restriction)
  • net.sf.basedb.util.NestedIterator<E> (implements java.util.Iterator<E>)
  • net.sf.basedb.core.News.QueryRuntimeFilterImpl (implements net.sf.basedb.core.QueryRuntimeFilter)
  • net.sf.basedb.util.overview.Node (implements java.lang.Comparable<T>)
  • net.sf.basedb.util.overview.cache.NodeCache<K>
  • net.sf.basedb.util.overview.node.NodeFactory<I>
  • net.sf.basedb.util.filter.NoneOfFilter<T> (implements net.sf.basedb.util.filter.Filter<T>)
  • net.sf.basedb.util.jep.NotInReporterListFunction (implements net.sf.basedb.util.jep.JepRestrictionFunction)
  • net.sf.basedb.util.filter.NotNullFilter<T> (implements net.sf.basedb.util.filter.Filter<T>)
  • net.sf.basedb.core.query.NotRestriction (implements net.sf.basedb.core.query.Restriction)
  • net.sf.basedb.util.parser.NullIfExceptionMapper (implements net.sf.basedb.util.parser.Mapper)
  • net.sf.basedb.util.overview.loader.NullNodeLoader<I> (implements net.sf.basedb.util.overview.loader.NodeLoader<I>)
  • net.sf.basedb.util.overview.validator.NullNodeValidator<I> (implements net.sf.basedb.util.overview.validator.NodeValidator<I>)
  • net.sf.basedb.util.formatter.NumberFormatter (implements net.sf.basedb.util.formatter.Formatter<T>)
  • net.sf.basedb.util.NumberFormatUtil
  • net.sf.basedb.util.OlderThanFileFilter (implements java.io.FileFilter)
  • net.sf.basedb.util.filter.OneOfFilter<T> (implements net.sf.basedb.util.filter.Filter<T>)
  • net.sf.basedb.clients.web.extensions.edit.OnSaveRenderer (implements net.sf.basedb.util.extensions.Renderer<A>)
  • net.sf.basedb.core.query.Orders
  • net.sf.basedb.core.query.OrRestriction (implements net.sf.basedb.core.query.Restriction)
  • java.io.OutputStream (implements java.io.Closeable, java.io.Flushable)
    • net.sf.basedb.core.plugin.ExportOutputStream
      • net.sf.basedb.util.FileExportOutputStream
      • net.sf.basedb.clients.web.util.ServletExportOutputStream
    • java.io.FilterOutputStream
      • java.io.BufferedOutputStream
        • net.sf.basedb.core.File.UploadStream
      • net.sf.basedb.util.StaticCache.LockSafeOutputStream
  • net.sf.basedb.clients.web.extensions.plot.OverviewPlotBean (implements net.sf.basedb.clients.web.extensions.plot.OverviewPlotAction)
  • net.sf.basedb.util.overview.OverviewUtil
  • net.sf.basedb.core.OwnableUtil
  • net.sf.basedb.util.OwnableUtil
  • net.sf.basedb.plugins.executor.ParameterDefinition
  • net.sf.basedb.core.query.ParameterExpression (implements net.sf.basedb.core.query.Expression)
  • net.sf.basedb.core.ParameterInfo
  • net.sf.basedb.plugins.util.Parameters
  • net.sf.basedb.core.ParameterType<T>
    • net.sf.basedb.core.BooleanParameterType
    • net.sf.basedb.core.DateParameterType
    • net.sf.basedb.core.DoubleParameterType
    • net.sf.basedb.core.FileParameterType
    • net.sf.basedb.core.FloatParameterType
    • net.sf.basedb.core.IntegerParameterType
    • net.sf.basedb.core.ItemParameterType<T>
    • net.sf.basedb.core.LongParameterType
    • net.sf.basedb.core.PathParameterType
    • net.sf.basedb.core.StringParameterType
    • net.sf.basedb.core.TimestampParameterType
  • net.sf.basedb.core.ParameterValuesImpl (implements net.sf.basedb.core.plugin.ParameterValues)
  • net.sf.basedb.core.plugin.ParameterValuesWrapper (implements net.sf.basedb.core.plugin.ParameterValues)
  • net.sf.basedb.clients.web.plugins.ParentBioMaterialLoader (implements net.sf.basedb.clients.web.plugins.DataLoader<T>)
  • net.sf.basedb.core.Path
  • net.sf.basedb.util.extensions.xml.PathConverter (implements net.sf.basedb.util.extensions.xml.ValueConverter)
  • net.sf.basedb.clients.jobagent.handlers.PauseRequestHandler (implements net.sf.basedb.util.jobagent.RequestHandler)
  • net.sf.basedb.util.timer.PerformanceTimer
  • net.sf.basedb.core.plugin.Permissions
  • net.sf.basedb.clients.web.PermissionUtil
  • net.sf.basedb.clients.jobagent.handlers.PingRequestHandler (implements net.sf.basedb.util.jobagent.RequestHandler)
  • net.sf.basedb.clients.web.plugins.PlainTextTemplate (implements net.sf.basedb.clients.web.plugins.ExportTemplate)
  • net.sf.basedb.core.data.PlateCoordinate (implements java.io.Serializable)
  • net.sf.basedb.core.log.db.PlateEventLogger (implements net.sf.basedb.core.log.EntityLogger)
  • net.sf.basedb.util.plot.PlotAnnotation (implements java.lang.Comparable<T>)
  • net.sf.basedb.clients.web.extensions.plot.PlotGeneratorBean (implements net.sf.basedb.clients.web.extensions.plot.PlotGenerator)
  • net.sf.basedb.clients.web.servlet.PlotServlet.CFResultIterator (implements net.sf.basedb.core.query.SqlResultIterator)
  • net.sf.basedb.clients.web.servlet.PlotServlet.CFSqlResult (implements net.sf.basedb.core.query.SqlResult)
  • net.sf.basedb.util.PluginConfigInfo
  • net.sf.basedb.util.PluginInfo
  • net.sf.basedb.core.data.keyring.PluginKeys (implements java.lang.Comparable<T>, java.io.Serializable)
  • net.sf.basedb.core.PluginParameter<T>
    • net.sf.basedb.core.plugin.NamespacePluginParameter<T>
  • net.sf.basedb.core.PluginPermission
  • net.sf.basedb.core.data.PluginPermission
  • net.sf.basedb.core.PluginRequest<P>
    • net.sf.basedb.core.PluginConfigurationRequest
    • net.sf.basedb.core.PluginExecutionRequest (implements java.lang.Runnable)
  • net.sf.basedb.core.PluginRequest.RequestImpl (implements net.sf.basedb.core.plugin.Request)
  • net.sf.basedb.core.PluginResponse
  • net.sf.basedb.core.PluginResponse.ResponseImpl (implements net.sf.basedb.core.plugin.Response)
  • net.sf.basedb.util.biomaterial.PooledChildrenTransformer<I> (implements net.sf.basedb.util.collections.CollectionTransformer<S,D>)
  • net.sf.basedb.util.biomaterial.PooledParentsTransformer<I> (implements net.sf.basedb.util.collections.CollectionTransformer<S,D>)
  • net.sf.basedb.core.authentication.POP3Authenticator (implements net.sf.basedb.core.authentication.Authenticator)
  • net.sf.basedb.util.importer.spotdata.PositionEventHandler (implements net.sf.basedb.util.bfs.EventHandler)
  • net.sf.basedb.util.jep.PositionFunction (implements net.sf.basedb.util.jep.JepExpressionFunction)
  • net.sf.basedb.core.query.PowerExpression (implements net.sf.basedb.core.query.Expression)
  • net.sf.basedb.core.PredefinedQuery
  • net.sf.basedb.util.formatter.PrefixSuffixFormatter<T> (implements net.sf.basedb.util.formatter.Formatter<T>)
  • net.sf.basedb.clients.web.extensions.renderer.PrefixSuffixRenderer<A> (implements net.sf.basedb.util.extensions.WrappingRenderer<A>)
  • net.sf.basedb.core.Presets (implements java.lang.Iterable<T>)
  • net.sf.basedb.core.Presets.Preset (implements java.lang.Iterable<T>)
  • net.sf.basedb.plugins.PrintMapFlatFileImporter.MetaBlock
  • net.sf.basedb.util.PriorityComparator<T> (implements java.util.Comparator<T>)
  • net.sf.basedb.clients.jobagent.executors.ProcessJobExecutor (implements net.sf.basedb.clients.jobagent.JobExecutor)
  • net.sf.basedb.clients.jobagent.executors.ProcessJobExecutor.StreamRedirector (implements java.lang.Runnable)
  • net.sf.basedb.plugins.executor.ProgramParameter
  • net.sf.basedb.core.Project.QueryRuntimeFilterImpl (implements net.sf.basedb.core.QueryRuntimeFilter)
  • net.sf.basedb.core.data.keyring.ProjectPermission (implements java.lang.Comparable<T>)
    • net.sf.basedb.core.data.keyring.GroupProjects (implements java.io.Serializable)
    • net.sf.basedb.core.data.keyring.UserProjects (implements java.io.Serializable)
  • net.sf.basedb.core.ProjectPermissions
  • net.sf.basedb.core.PropertyFilter
  • net.sf.basedb.core.data.PropertyFilterData
  • net.sf.basedb.plugins.batchimport.PropertyIdMethod (implements net.sf.basedb.plugins.batchimport.IdMethod)
  • net.sf.basedb.util.extensions.debug.ProxyActionFactory (implements net.sf.basedb.util.extensions.ActionFactory<A>, java.lang.reflect.InvocationHandler)
  • net.sf.basedb.core.query.QuadraticMeanExpression (implements net.sf.basedb.core.query.Expression)
  • net.sf.basedb.core.QueryExecutor
  • net.sf.basedb.core.QueryExecutor.CancelableSession (implements net.sf.basedb.core.QueryExecutor.Cancelable)
  • net.sf.basedb.core.QueryExecutor.CancelableStatelessSession (implements net.sf.basedb.core.QueryExecutor.Cancelable)
  • net.sf.basedb.core.QueryExecutor.CancelableStatement (implements net.sf.basedb.core.QueryExecutor.Cancelable)
  • net.sf.basedb.core.QueryExecutor.FutureItem<T> (implements java.util.concurrent.Callable<V>)
  • net.sf.basedb.core.QueryExecutor.FutureResultSet (implements java.util.concurrent.Callable<V>)
  • net.sf.basedb.core.QueryExecutor.FutureScrollIterator<T> (implements java.util.concurrent.Callable<V>)
  • net.sf.basedb.core.QueryExecutor.FutureUpdate (implements java.util.concurrent.Callable<V>)
  • net.sf.basedb.info.QueryOptions (implements net.sf.basedb.info.Transferable)
  • net.sf.basedb.info.QueryParameter
  • net.sf.basedb.core.query.QueryParameter
  • net.sf.basedb.util.QueryParameters
  • net.sf.basedb.core.QueryRuntimeFilterFactory
  • net.sf.basedb.core.QueryRuntimeFilterFactory.AnnotatableFilter (implements net.sf.basedb.core.QueryRuntimeFilter)
  • net.sf.basedb.core.QueryRuntimeFilterFactory.BasicFilter (implements net.sf.basedb.core.QueryRuntimeFilter)
  • net.sf.basedb.core.QueryRuntimeFilterFactory.ChainedFilter (implements net.sf.basedb.core.QueryRuntimeFilter)
  • net.sf.basedb.core.QueryRuntimeFilterFactory.ChildFilter (implements net.sf.basedb.core.QueryRuntimeFilter)
  • net.sf.basedb.core.QueryRuntimeFilterFactory.DenyAllFilter (implements net.sf.basedb.core.QueryRuntimeFilter)
  • net.sf.basedb.core.QueryRuntimeFilterFactory.OwnableFilter (implements net.sf.basedb.core.QueryRuntimeFilter)
  • net.sf.basedb.core.QueryRuntimeFilterFactory.RemovableFilter (implements net.sf.basedb.core.QueryRuntimeFilter)
  • net.sf.basedb.core.QueryRuntimeFilterFactory.ShareableFilter (implements net.sf.basedb.core.QueryRuntimeFilter)
  • net.sf.basedb.core.QueryRuntimeFilterManager
  • net.sf.basedb.core.hibernate.QueryWrapper (implements org.hibernate.Query)
    • net.sf.basedb.core.hibernate.EntityQueryWrapper
  • net.sf.basedb.core.Quota.QueryRuntimeFilterImpl (implements net.sf.basedb.core.QueryRuntimeFilter)
  • net.sf.basedb.core.data.QuotaIndex (implements java.io.Serializable)
  • net.sf.basedb.util.jep.RawChannelFunction (implements net.sf.basedb.util.jep.JepExpressionFunction)
  • net.sf.basedb.plugins.RawDataFlatFileImporter.FileIterator (implements java.util.Iterator<E>)
  • net.sf.basedb.core.RawDataPropertyExpression (implements net.sf.basedb.core.query.Expression)
  • net.sf.basedb.core.RawDataType (implements java.lang.Comparable<T>)
  • net.sf.basedb.core.RawDataTypes
  • net.sf.basedb.core.RawDataTypes.NameComparator (implements java.util.Comparator<T>)
  • net.sf.basedb.core.RawDataUtil
  • net.sf.basedb.util.jep.RawFunction (implements net.sf.basedb.util.jep.JepExpressionFunction)
  • net.sf.basedb.core.RealJoin (implements net.sf.basedb.core.query.Join)
  • net.sf.basedb.core.RealTable
  • net.sf.basedb.util.RegexpFileFilter (implements java.io.FileFilter)
  • net.sf.basedb.util.extensions.Registry
  • net.sf.basedb.util.extensions.Registry.AttributeKey
  • net.sf.basedb.util.extensions.Registry.RegisteredAbout (implements net.sf.basedb.core.plugin.About)
  • net.sf.basedb.util.extensions.Registry.RegisteredExtension<A> (implements net.sf.basedb.util.extensions.Extension<A>)
  • net.sf.basedb.util.extensions.Registry.RegisteredExtensionPoint<A> (implements net.sf.basedb.util.extensions.ExtensionPoint<A>)
  • net.sf.basedb.clients.jobagent.slotmanager.RemoteSlotManager (implements net.sf.basedb.clients.jobagent.slotmanager.SlotManager)
  • net.sf.basedb.util.RemovableUtil
  • net.sf.basedb.util.collections.RemoveAllTransformer<I> (implements net.sf.basedb.util.collections.CollectionTransformer<S,D>)
  • net.sf.basedb.core.Reporter
  • net.sf.basedb.util.jep.ReporterFunction (implements net.sf.basedb.util.jep.JepExpressionFunction)
  • net.sf.basedb.core.query.ReporterListExpression (implements net.sf.basedb.core.query.Expression)
  • net.sf.basedb.core.ReporterListJoin (implements net.sf.basedb.core.query.Join)
  • net.sf.basedb.core.data.ReporterListScoreData (implements java.io.Serializable)
  • net.sf.basedb.core.ReporterPropertyExpression (implements net.sf.basedb.core.query.Expression)
  • net.sf.basedb.core.ReporterScore
  • net.sf.basedb.clients.web.plugins.ReporterScoreQueryWrapper (implements net.sf.basedb.clients.web.plugins.QueryWrapper<T>)
  • net.sf.basedb.core.ReporterScoreResultIterator (implements net.sf.basedb.core.query.ResultIterator<I>)
  • net.sf.basedb.core.RequestInformation
  • java.util.ResourceBundle.Control
    • net.sf.basedb.util.resources.Utf8PropertiesResourceBundleControl
  • net.sf.basedb.util.resources.ResourceBundleFactory
  • net.sf.basedb.util.resources.ResourceBundleWrapper
  • net.sf.basedb.core.query.Restrictions
  • net.sf.basedb.core.hibernate.ResultSetWork<R> (implements net.sf.basedb.core.hibernate.JdbcWork<R>)
  • net.sf.basedb.core.query.RlikeRestriction (implements net.sf.basedb.core.query.Restriction)
  • net.sf.basedb.core.Role.QueryRuntimeFilterImpl (implements net.sf.basedb.core.QueryRuntimeFilter)
  • net.sf.basedb.util.biomaterial.SampleToBioSourceTransformer (implements net.sf.basedb.util.collections.CollectionTransformer<S,D>)
  • net.sf.basedb.util.biomaterial.SampleToExtractTransformer (implements net.sf.basedb.util.collections.CollectionTransformer<S,D>)
  • net.sf.basedb.clients.web.extensions.ScanResults
  • net.sf.basedb.clients.web.extensions.ScanResults.FileResults
  • net.sf.basedb.util.plot.ScatterPlot
  • net.sf.basedb.util.timer.Scheduler
  • net.sf.basedb.core.hibernate.SchemaGenerator (implements org.hibernate.jdbc.Work)
  • net.sf.basedb.util.jep.ScoreFunction (implements net.sf.basedb.util.jep.JepExpressionFunction)
  • net.sf.basedb.core.ScrollIterator<E> (implements java.util.Iterator<E>)
  • net.sf.basedb.util.importer.spotdata.SecondPassSectionSpotsParser (implements net.sf.basedb.util.basefile.BaseFileSectionParser)
  • net.sf.basedb.util.importer.spotdata.SectionAssaysParser (implements net.sf.basedb.util.basefile.BaseFileSectionParser)
  • net.sf.basedb.util.importer.spotdata.SectionReporterListParser (implements net.sf.basedb.util.basefile.BaseFileSectionParser)
  • net.sf.basedb.core.query.SelectedExpression (implements net.sf.basedb.core.query.Expression)
  • net.sf.basedb.core.query.Selects
  • net.sf.basedb.util.bfs.SequenceFilenameGenerator (implements net.sf.basedb.util.bfs.FilenameGenerator<T>)
  • net.sf.basedb.util.importer.spotdata.SerialSpotIntensityEventHandler (implements net.sf.basedb.util.bfs.EventHandler)
  • net.sf.basedb.clients.web.extensions.service.Services
  • net.sf.basedb.clients.web.extensions.service.ServicesEventHandler (implements net.sf.basedb.util.extensions.events.EventHandler)
  • net.sf.basedb.ws.server.ServicesUtil
  • net.sf.basedb.clients.web.extensions.ServletLoader
  • javax.servlet.ServletRequestWrapper (implements javax.servlet.ServletRequest)
    • javax.servlet.http.HttpServletRequestWrapper (implements javax.servlet.http.HttpServletRequest)
      • net.sf.basedb.clients.web.extensions.RequestWrapper
  • net.sf.basedb.clients.web.extensions.ServletWrapper (implements javax.servlet.ServletConfig)
  • net.sf.basedb.core.SessionControl
    • net.sf.basedb.core.PluginSessionControl
  • net.sf.basedb.core.SessionControl.LoginInfo
  • net.sf.basedb.core.SessionControl.SettingInfo
  • net.sf.basedb.core.ShareableUtil
  • net.sf.basedb.util.ShareableUtil
  • net.sf.basedb.core.query.SharedToRestriction (implements net.sf.basedb.core.query.Restriction)
  • net.sf.basedb.core.signal.ShutdownSignalSender (implements net.sf.basedb.core.signal.SignalSender)
  • net.sf.basedb.core.signal.Signal
  • net.sf.basedb.clients.jobagent.handlers.SignalRequestHandler (implements net.sf.basedb.util.jobagent.RequestHandler)
  • net.sf.basedb.core.authentication.SimpleAuthenticator (implements net.sf.basedb.core.authentication.Authenticator)
  • net.sf.basedb.util.export.spotdata.SimpleDynamicField (implements net.sf.basedb.util.export.spotdata.DynamicField)
  • net.sf.basedb.util.error.SimpleErrorHandler (implements net.sf.basedb.util.error.ErrorHandler)
  • net.sf.basedb.core.SimpleProgressReporter (implements net.sf.basedb.core.ProgressReporter)
    • net.sf.basedb.core.SimpleAbsoluteProgressReporter (implements net.sf.basedb.core.AbsoluteProgressReporter)
    • net.sf.basedb.clients.web.util.SimpleSignalProgressReporter (implements net.sf.basedb.core.signal.SignalReceiver)
  • net.sf.basedb.core.signal.SimpleSignalSender (implements net.sf.basedb.core.signal.SignalSender)
  • net.sf.basedb.util.extensions.SingleExtensionFilter (implements net.sf.basedb.util.extensions.ExtensionsFilter)
  • net.sf.basedb.clients.jobagent.slotmanager.Slot
  • net.sf.basedb.core.snapshot.SnapshotManager
  • net.sf.basedb.core.signal.SocketSignalReceiver.ListenerThread (implements java.lang.Runnable)
  • net.sf.basedb.util.SocketUtil
  • net.sf.basedb.core.SpotImage
  • net.sf.basedb.clients.web.formatter.SpotImageFormatter (implements net.sf.basedb.util.formatter.Formatter<T>)
  • net.sf.basedb.core.query.SqlColumnExpression (implements net.sf.basedb.core.query.Expression)
  • net.sf.basedb.core.query.SqrtExpression (implements net.sf.basedb.core.query.Expression)
  • net.sf.basedb.util.ssl.SSLUtil
  • net.sf.basedb.clients.jobagent.handlers.StartRequestHandler (implements net.sf.basedb.util.jobagent.RequestHandler)
  • net.sf.basedb.clients.web.extensions.service.StartServiceRenderer (implements net.sf.basedb.util.extensions.Renderer<A>)
  • net.sf.basedb.util.StaticCache
  • net.sf.basedb.util.StaticCache.LockEntry (implements java.util.concurrent.locks.ReadWriteLock)
  • net.sf.basedb.util.filter.StaticFilter<T> (implements net.sf.basedb.util.filter.Filter<T>)
  • net.sf.basedb.util.ssl.StaticKeyManager (implements javax.net.ssl.X509KeyManager)
  • net.sf.basedb.clients.jobagent.handlers.StopRequestHandler (implements net.sf.basedb.util.jobagent.RequestHandler)
  • net.sf.basedb.clients.web.extensions.service.StopServiceRenderer (implements net.sf.basedb.util.extensions.Renderer<A>)
  • net.sf.basedb.util.StreamCacher
  • net.sf.basedb.util.extensions.debug.StringConverter
  • net.sf.basedb.clients.web.formatter.StringFormatter (implements net.sf.basedb.util.formatter.Formatter<T>)
  • net.sf.basedb.util.StringLengthComparator (implements java.util.Comparator<T>)
  • net.sf.basedb.util.fuzzy.StringMatcher
  • net.sf.basedb.util.fuzzy.StringMatcher.FuzzyMatch
  • net.sf.basedb.core.StringUtil
  • net.sf.basedb.core.query.SubqueryExpression (implements net.sf.basedb.core.query.Expression)
  • net.sf.basedb.core.query.SubtractExpression (implements net.sf.basedb.core.query.Expression)
  • net.sf.basedb.core.query.SumExpression (implements net.sf.basedb.core.query.Expression)
  • net.sf.basedb.util.importer.spotdata.SynchronizedSpotDataParser (implements net.sf.basedb.util.bfs.BfsParser)
  • net.sf.basedb.util.importer.spotdata.SynchronizedSpotDataParser.SynchronizedData
  • net.sf.basedb.core.SystemItems
  • net.sf.basedb.clients.web.extensions.tabcontrol.TabBean (implements net.sf.basedb.clients.web.extensions.tabcontrol.TabAction)
  • net.sf.basedb.util.encode.TabCrLfEncoderDecoder (implements net.sf.basedb.util.encode.EncoderDecoder)
  • net.sf.basedb.clients.web.taglib.table.TableColumn
  • net.sf.basedb.core.hibernate.TableExistsWork (implements net.sf.basedb.core.hibernate.JdbcWork<R>)
  • net.sf.basedb.core.dbengine.TableInfo
  • net.sf.basedb.core.dbengine.TableInfo.ColumnInfo
  • net.sf.basedb.core.dbengine.TableInfo.ForeignKeyInfo
  • net.sf.basedb.core.dbengine.TableInfo.IndexInfo
  • net.sf.basedb.core.dbengine.TableInfo.PrimaryKeyInfo
  • net.sf.basedb.core.hibernate.TableInfoWork (implements net.sf.basedb.core.hibernate.JdbcWork<R>)
  • javax.servlet.jsp.tagext.TagSupport (implements javax.servlet.jsp.tagext.IterationTag, java.io.Serializable)
    • net.sf.basedb.clients.web.taglib.Body
    • javax.servlet.jsp.tagext.BodyTagSupport (implements javax.servlet.jsp.tagext.BodyTag)
      • net.sf.basedb.clients.web.taglib.table.Cell (implements javax.servlet.jsp.tagext.TryCatchFinally)
      • net.sf.basedb.clients.web.taglib.ExceptionCatcher (implements javax.servlet.jsp.tagext.TryCatchFinally)
      • net.sf.basedb.clients.web.taglib.tab.Tab (implements net.sf.basedb.clients.web.extensions.tabcontrol.TabAction)
    • net.sf.basedb.clients.web.taglib.Button
    • net.sf.basedb.clients.web.taglib.table.Button (implements net.sf.basedb.clients.web.extensions.toolbar.ButtonAction)
    • net.sf.basedb.clients.web.taglib.ButtonGroup
    • net.sf.basedb.clients.web.taglib.table.CellValue
    • net.sf.basedb.clients.web.taglib.table.ColumnDef
    • net.sf.basedb.clients.web.taglib.table.Columns
    • net.sf.basedb.clients.web.taglib.table.Data
    • net.sf.basedb.clients.web.taglib.table.Form
    • net.sf.basedb.clients.web.taglib.Head
    • net.sf.basedb.clients.web.taglib.table.Header
    • net.sf.basedb.clients.web.taglib.Help
    • net.sf.basedb.clients.web.taglib.table.Hidden
    • net.sf.basedb.clients.web.taglib.HideableSection
    • net.sf.basedb.clients.web.taglib.Icon
    • net.sf.basedb.clients.web.taglib.table.Label
    • net.sf.basedb.clients.web.taglib.menu.Menu
    • net.sf.basedb.clients.web.taglib.menu.Menuitem
    • net.sf.basedb.clients.web.taglib.menu.Menuseparator
    • net.sf.basedb.clients.web.taglib.table.Navigator
    • net.sf.basedb.clients.web.taglib.Note
    • net.sf.basedb.clients.web.taglib.Page
    • net.sf.basedb.clients.web.taglib.table.Panel
    • net.sf.basedb.clients.web.taglib.path.Path
    • net.sf.basedb.clients.web.taglib.path.PathElement
    • net.sf.basedb.clients.web.taglib.table.PresetSelector
    • net.sf.basedb.clients.web.taglib.table.PropertyFilter
    • net.sf.basedb.clients.web.taglib.PropertyValue
    • net.sf.basedb.clients.web.taglib.extensions.Render
    • net.sf.basedb.clients.web.taglib.table.Row
    • net.sf.basedb.clients.web.taglib.table.Rows
    • net.sf.basedb.clients.web.taglib.extensions.Scripts
    • net.sf.basedb.clients.web.taglib.Select
    • net.sf.basedb.clients.web.taglib.extensions.Stylesheets
    • net.sf.basedb.clients.web.taglib.menu.Submenu
    • net.sf.basedb.clients.web.taglib.tab.TabControl (implements net.sf.basedb.util.extensions.Renderer<A>)
    • net.sf.basedb.clients.web.taglib.table.Table
    • net.sf.basedb.clients.web.taglib.table.Toolbar
  • net.sf.basedb.util.zip.TarFilePacker (implements net.sf.basedb.util.zip.FilePacker)
    • net.sf.basedb.util.zip.Bzip2FilePacker
    • net.sf.basedb.util.zip.GzipFilePacker
  • net.sf.basedb.util.zip.TarUtil
  • net.sf.basedb.clients.jobagent.executors.ThreadJobExecutor (implements net.sf.basedb.clients.jobagent.JobExecutor)
  • net.sf.basedb.clients.jobagent.executors.ThreadJobExecutor.ShutdownHook (implements java.lang.Runnable)
  • java.lang.Throwable (implements java.io.Serializable)
    • java.lang.Exception
      • net.sf.basedb.core.authentication.AuthenticationException
        • net.sf.basedb.core.authentication.InvalidPasswordException
        • net.sf.basedb.core.authentication.UnknownLoginException
      • java.io.IOException
        • net.sf.basedb.clients.web.fileupload.UploadAbortedException
      • java.lang.RuntimeException
        • net.sf.basedb.core.BaseException
          • net.sf.basedb.core.ConfigurationException
          • net.sf.basedb.core.ConnectionClosedException
          • net.sf.basedb.core.DatabaseException
          • net.sf.basedb.core.DetachedItemException
          • net.sf.basedb.core.InvalidDataException
            • net.sf.basedb.core.DateFormatException
            • net.sf.basedb.core.DisallowedValueException
            • net.sf.basedb.core.InvalidAnnotationException
            • net.sf.basedb.core.InvalidPathException
            • net.sf.basedb.core.InvalidUseOfNullException
            • net.sf.basedb.core.ItemAlreadyExistsException
            • net.sf.basedb.core.ItemNotFoundException
            • net.sf.basedb.core.NumberOutOfRangeException
            • net.sf.basedb.core.ParameterException
            • net.sf.basedb.core.QuotaException
            • net.sf.basedb.core.StringTooLongException
            • net.sf.basedb.core.UnsavedItemException
            • net.sf.basedb.core.UnsupportedFileFormatException
          • net.sf.basedb.core.InvalidPasswordException
          • net.sf.basedb.core.InvalidRelationException
          • net.sf.basedb.core.PermissionDeniedException
            • net.sf.basedb.core.AccountExpiredException
            • net.sf.basedb.core.AlreadyLoggedInException
            • net.sf.basedb.core.ItemInUseException
            • net.sf.basedb.core.ItemModifiedException
            • net.sf.basedb.core.NotLoggedInException
          • net.sf.basedb.core.signal.SignalException
            • net.sf.basedb.core.signal.SignalReceivedException
            • net.sf.basedb.core.signal.UnsupportedSignalException
        • net.sf.basedb.clients.web.DuplicateWizardException
      • net.sf.basedb.clients.web.WebException
  • net.sf.basedb.util.error.ThrowableUtil
  • java.util.TimerTask (implements java.lang.Runnable)
    • net.sf.basedb.core.Application.DbCleaner
    • net.sf.basedb.core.Application.SecondaryStorageControllerTask
    • net.sf.basedb.core.Application.SessionControlCacheCleaner
    • net.sf.basedb.clients.web.extensions.ExtensionsControl.AutoInstallTask
    • net.sf.basedb.core.InternalJobQueue
    • net.sf.basedb.clients.jobagent.JobQueueChecker
    • net.sf.basedb.core.Keyring.ReloadTask
    • net.sf.basedb.clients.jobagent.slotmanager.MasterSlotManager.RemoteSlotTimeoutChecker
    • net.sf.basedb.clients.jobagent.slotmanager.RemoteSlotManager.RemoteSlotPinger
    • net.sf.basedb.util.StaticCache.CleanupTask
    • net.sf.basedb.util.timer.ThreadTimerTask
  • net.sf.basedb.core.query.ToDateExpression (implements net.sf.basedb.core.query.Expression)
  • net.sf.basedb.clients.web.extensions.toolbar.ToolbarButtonRenderer (implements net.sf.basedb.util.extensions.Renderer<A>)
  • net.sf.basedb.clients.web.extensions.toolbar.ToolbarUtil
  • net.sf.basedb.util.encode.ToSpaceEncoderDecoder (implements net.sf.basedb.util.encode.EncoderDecoder)
  • net.sf.basedb.util.ToStringComparator<T> (implements java.util.Comparator<T>, java.io.Serializable)
  • net.sf.basedb.util.formatter.ToStringFormatter<T> (implements net.sf.basedb.util.formatter.Formatter<T>)
  • net.sf.basedb.core.log.TransactionDetails
  • net.sf.basedb.core.Trashcan
  • net.sf.basedb.util.Tree<E> (implements java.util.Collection<E>)
  • net.sf.basedb.util.Tree.ElementIterator (implements java.util.Iterator<E>)
  • net.sf.basedb.util.Tree.Entry<E>
  • net.sf.basedb.util.Tree.EntryIterator (implements java.util.Iterator<E>)
  • net.sf.basedb.core.hibernate.TypeWrapper<T>
  • net.sf.basedb.util.units.UnitCache
  • net.sf.basedb.util.units.UnitCache.CacheKey (implements java.lang.Comparable<T>)
  • net.sf.basedb.util.units.UnitUtil
  • net.sf.basedb.core.Update
  • net.sf.basedb.clients.web.fileupload.UploadedFile
  • net.sf.basedb.core.data.UsedQuantity (implements java.io.Serializable)
  • net.sf.basedb.core.User.QueryRuntimeFilterImpl (implements net.sf.basedb.core.QueryRuntimeFilter)
  • net.sf.basedb.core.data.keyring.UserGroups (implements java.io.Serializable)
  • net.sf.basedb.core.UserPermissions
  • net.sf.basedb.core.data.keyring.UserRoles (implements java.io.Serializable)
  • net.sf.basedb.util.overview.ValidationOptions
  • net.sf.basedb.util.overview.Validator
  • net.sf.basedb.core.Values
  • net.sf.basedb.util.Values
  • net.sf.basedb.util.extensions.xml.VariableConverter (implements net.sf.basedb.util.extensions.xml.ValueConverter)
  • net.sf.basedb.core.Version
  • net.sf.basedb.core.data.VersionedParameter (implements java.io.Serializable)
  • net.sf.basedb.info.VersionInfo (implements java.io.Serializable, net.sf.basedb.info.Transferable)
  • net.sf.basedb.core.VirtualColumn
  • net.sf.basedb.core.query.VirtualColumnExpression (implements net.sf.basedb.core.query.Expression)
  • net.sf.basedb.core.query.VirtualColumnExpression.WrappedExpression (implements net.sf.basedb.core.query.Expression)
  • net.sf.basedb.util.formatter.WellCoordinateFormatter (implements net.sf.basedb.util.formatter.Formatter<T>)
  • net.sf.basedb.core.query.WhenStatement
  • java.io.Writer (implements java.lang.Appendable, java.io.Closeable, java.io.Flushable)
    • java.io.PrintWriter
      • net.sf.basedb.clients.web.util.AjaxWriter
      • net.sf.basedb.util.bfs.MetadataWriter
      • net.sf.basedb.util.export.TableWriter
        • net.sf.basedb.util.bfs.AnnotationWriter
        • net.sf.basedb.util.basefile.BaseFileWriter
        • net.sf.basedb.util.bfs.DataWriter
  • net.sf.basedb.util.extensions.xml.XmlLoader
  • net.sf.basedb.clients.web.plugins.XMLTemplate (implements net.sf.basedb.clients.web.plugins.ExportTemplate)
  • net.sf.basedb.util.XMLUtil
  • net.sf.basedb.util.XMLUtil.Validator (implements org.xml.sax.EntityResolver, org.xml.sax.ErrorHandler)
  • net.sf.basedb.util.zip.ZipFilePacker (implements net.sf.basedb.util.zip.FilePacker)
  • net.sf.basedb.util.zip.ZipUnpacker

Interface Hierarchy

• net.sf.basedb.core.plugin.About
• net.sf.basedb.core.AccessControlled
  • net.sf.basedb.core.Annotatable
    • net.sf.basedb.core.AnnotatableProxy
  • net.sf.basedb.core.AnnotatableProxy
  • net.sf.basedb.core.DiskConsumable (also extends net.sf.basedb.core.Controlled, net.sf.basedb.core.Ownable)
  • net.sf.basedb.core.FileAttachable
  • net.sf.basedb.core.FileStoreEnabled
  • net.sf.basedb.core.Identifiable
    • net.sf.basedb.core.Annotatable
      • net.sf.basedb.core.AnnotatableProxy
    • net.sf.basedb.core.AnnotatableProxy
    • net.sf.basedb.core.DiskConsumable (also extends net.sf.basedb.core.Controlled, net.sf.basedb.core.Ownable)
    • net.sf.basedb.core.FileAttachable
    • net.sf.basedb.core.FileStoreEnabled
    • net.sf.basedb.core.Nameable
    • net.sf.basedb.core.Ownable
      • net.sf.basedb.core.DiskConsumable (also extends net.sf.basedb.core.Controlled)
      • net.sf.basedb.core.Shareable
    • net.sf.basedb.core.Registered
    • net.sf.basedb.core.Removable
    • net.sf.basedb.core.Shareable
    • net.sf.basedb.core.SystemItem
  • net.sf.basedb.core.Nameable
  • net.sf.basedb.core.Ownable
    • net.sf.basedb.core.DiskConsumable (also extends net.sf.basedb.core.Controlled)
    • net.sf.basedb.core.Shareable
  • net.sf.basedb.core.Registered
  • net.sf.basedb.core.Removable
  • net.sf.basedb.core.Shareable
  • net.sf.basedb.core.SystemItem
• net.sf.basedb.util.extensions.Action
  • net.sf.basedb.clients.web.extensions.toolbar.ButtonAction
  • net.sf.basedb.clients.web.extensions.menu.MenuItemAction
  • net.sf.basedb.clients.web.extensions.edit.OnSaveAction
  • net.sf.basedb.clients.web.extensions.plot.OverviewPlotAction
  • net.sf.basedb.clients.web.extensions.service.ServiceControllerAction
  • net.sf.basedb.clients.web.extensions.tabcontrol.TabAction
• net.sf.basedb.util.extensions.ActionFactory<A>
• net.sf.basedb.core.authentication.Authenticator
• net.sf.basedb.core.query.AutoJoiner<Q,E>
• net.sf.basedb.util.basefile.BaseFileSectionParser
• net.sf.basedb.core.Batcher
• net.sf.basedb.util.bfs.BfsParser
• net.sf.basedb.util.collections.CollectionTransformer<S,D>
• net.sf.basedb.core.data.ComponentData
• net.sf.basedb.core.Controlled
  • net.sf.basedb.core.DiskConsumable (also extends net.sf.basedb.core.Ownable)
  • net.sf.basedb.core.Transactional
  • net.sf.basedb.core.Validatable
• net.sf.basedb.core.filehandler.DataFileHandler
  • net.sf.basedb.core.filehandler.DataFileMetadataReader
  • net.sf.basedb.core.filehandler.DataFileValidator
• net.sf.basedb.clients.web.plugins.DataLoader<T>
  • net.sf.basedb.clients.web.plugins.QueryWrapper<T>
• net.sf.basedb.util.bfs.DataWriterFactory<T>
• net.sf.basedb.core.dbengine.DbEngine
• net.sf.basedb.util.DynamicFilter
• net.sf.basedb.util.encode.EncoderDecoder
• net.sf.basedb.core.log.EntityLogger
• net.sf.basedb.util.error.ErrorHandler
• net.sf.basedb.util.extensions.ErrorHandler<A>
• net.sf.basedb.util.extensions.ErrorHandlerFactory<A>
• net.sf.basedb.util.extensions.events.EventFilter
• net.sf.basedb.util.bfs.EventHandler
• java.util.EventListener
  • net.sf.basedb.util.extensions.events.EventHandler
• net.sf.basedb.util.export.spotdata.ExportableField
  • net.sf.basedb.util.export.spotdata.AssayField
  • net.sf.basedb.util.export.spotdata.DynamicField
• net.sf.basedb.util.export.spotdata.ExportableFieldConverter
• net.sf.basedb.clients.web.plugins.ExportTemplate
• net.sf.basedb.util.extensions.Extension<A>
• net.sf.basedb.util.extensions.ExtensionPoint<A>
• net.sf.basedb.util.extensions.ExtensionsFilter
• net.sf.basedb.util.bfs.ExtraFileImporter
• net.sf.basedb.util.bfs.FilenameGenerator<T>
• net.sf.basedb.util.zip.FilePacker
• net.sf.basedb.util.importer.FileWrapper
• net.sf.basedb.util.filter.Filter<T>
• net.sf.basedb.util.formatter.Formatter<T>
• net.sf.basedb.core.data.IdentifiableData
  • net.sf.basedb.core.data.AnnotatableData
  • net.sf.basedb.core.data.BatchableData
  • net.sf.basedb.core.data.DiskConsumableData
  • net.sf.basedb.core.data.ExtendableData
  • net.sf.basedb.core.data.FileAttachableData
  • net.sf.basedb.core.data.FileStoreEnabledData
  • net.sf.basedb.core.data.NameableData
  • net.sf.basedb.core.data.OwnableData
    • net.sf.basedb.core.data.DiskConsumableData
    • net.sf.basedb.core.data.ShareableData
  • net.sf.basedb.core.data.RegisteredData
  • net.sf.basedb.core.data.RemovableData
  • net.sf.basedb.core.data.ShareableData
  • net.sf.basedb.core.data.SystemData
• net.sf.basedb.plugins.batchimport.IdMethod
• net.sf.basedb.util.bfs.InputStreamLocator
• net.sf.basedb.util.IntensityCalculator
• net.sf.basedb.core.signal.InterruptHandler
• java.lang.Iterable<T>
  • java.util.Collection<E>
    • java.util.List<E>
      • net.sf.basedb.core.query.ResultList<I> (also extends net.sf.basedb.core.query.QueryResult)
        • net.sf.basedb.core.query.SqlResultList<I>
• java.util.Iterator<E>
  • net.sf.basedb.core.query.ResultIterator<I> (also extends net.sf.basedb.core.query.QueryResult)
    • net.sf.basedb.core.query.SqlResultIterator
• net.sf.basedb.util.jep.convert.JepConversionFunction<T>
• net.sf.basedb.clients.jobagent.JobExecutor
• net.sf.basedb.core.data.LoggableData
• net.sf.basedb.core.log.LogManager
• net.sf.basedb.core.log.LogManagerFactory
• net.sf.basedb.util.parser.Mapper
• net.sf.basedb.core.Metadata.PropertyPath<C,V>
• net.sf.basedb.info.NameableInfo
• net.sf.basedb.util.overview.loader.NodeLoader<I>
• net.sf.basedb.util.overview.loader.NodeLoaderFactory<L,K>
• net.sf.basedb.util.overview.node.NodeNameGenerator<I>
• net.sf.basedb.util.overview.validator.NodeValidator<I>
• net.sf.basedb.util.overview.validator.NodeValidatorFactory<L,K>
• net.sf.basedb.core.plugin.NonRestartable
• net.sf.basedb.util.overview.OverviewContext
• net.sf.basedb.core.plugin.ParameterValues
• net.sf.basedb.clients.web.extensions.plot.PlotGenerator
• net.sf.basedb.core.plugin.Plugin
  • net.sf.basedb.core.plugin.AnalysisFilterPlugin
  • net.sf.basedb.core.plugin.AnnotationSetterPlugin
  • net.sf.basedb.core.plugin.AutoDetectingImporter
  • net.sf.basedb.util.parser.ConfigureByExample
  • net.sf.basedb.util.zip.FileUnpacker
  • net.sf.basedb.core.plugin.ImmediateDownloadExporter
  • net.sf.basedb.core.plugin.InteractivePlugin
    • net.sf.basedb.plugins.executor.IOSupport
  • net.sf.basedb.plugins.executor.IOSupport
  • net.sf.basedb.util.parser.WrappedConfigureByExample
• org.nfunk.jep.function.PostfixMathCommandI
  • net.sf.basedb.util.jep.JepFunction
    • net.sf.basedb.util.jep.JepExpressionFunction
    • net.sf.basedb.util.jep.JepRestrictionFunction
• net.sf.basedb.core.ProgressReporter
  • net.sf.basedb.core.AbsoluteProgressReporter
• net.sf.basedb.core.query.Query
  • net.sf.basedb.core.query.EntityQuery
  • net.sf.basedb.core.query.HqlQuery
    • net.sf.basedb.core.query.EntityQuery
  • net.sf.basedb.core.query.SqlQuery
• net.sf.basedb.core.query.QueryElement
  • net.sf.basedb.core.query.Expression
  • net.sf.basedb.core.query.Join
  • net.sf.basedb.core.query.Order
  • net.sf.basedb.core.query.Restriction
  • net.sf.basedb.core.query.Select
• net.sf.basedb.core.QueryExecutor.Cancelable
• net.sf.basedb.core.query.QueryResult
  • net.sf.basedb.core.query.ResultIterator<I> (also extends java.util.Iterator<E>)
    • net.sf.basedb.core.query.SqlResultIterator
  • net.sf.basedb.core.query.ResultList<I> (also extends java.util.List<E>)
    • net.sf.basedb.core.query.SqlResultList<I>
  • net.sf.basedb.core.query.SqlResultIterator
  • net.sf.basedb.core.query.SqlResultList<I>
• net.sf.basedb.core.QueryRuntimeFilter
• net.sf.basedb.util.extensions.Renderer<A>
  • net.sf.basedb.util.extensions.WrappingRenderer<A>
• net.sf.basedb.util.extensions.RendererFactory<A>
• net.sf.basedb.core.plugin.Request
• net.sf.basedb.util.jobagent.RequestHandler
  • net.sf.basedb.clients.jobagent.handlers.CustomRequestHandler
• net.sf.basedb.core.plugin.Response
• net.sf.basedb.core.SecondaryStorageController
• net.sf.basedb.ws.client.ServiceFactory
• net.sf.basedb.core.signal.SignalHandler
• net.sf.basedb.core.signal.SignalReceiver
• net.sf.basedb.core.signal.SignalSender
• net.sf.basedb.core.signal.SignalTarget
• net.sf.basedb.core.signal.SignalTransporter
• net.sf.basedb.clients.jobagent.slotmanager.SlotManager
• net.sf.basedb.util.importer.spotdata.SpotIntensityParser
• net.sf.basedb.core.query.SqlResult
• net.sf.basedb.info.ToTransferable<T>
• net.sf.basedb.info.Transferable
• net.sf.basedb.util.units.UnitConverter
• net.sf.basedb.util.extensions.xml.ValueConverter
• org.hibernate.jdbc.Work
  • net.sf.basedb.core.hibernate.JdbcWork<R>

Annotation Type Hierarchy

• net.sf.basedb.util.extensions.xml.VariableSetter (implements java.lang.annotation.Annotation)
• net.sf.basedb.util.extensions.xml.PathSetter (implements java.lang.annotation.Annotation)

Enum Hierarchy

• java.lang.Object
  • java.lang.Enum<E> (implements java.lang.Comparable<T>, java.io.Serializable)
    • net.sf.basedb.core.Permission
    • net.sf.basedb.core.ExtraValue.CoordinateType
    • net.sf.basedb.core.ItemContext.SortDirection
    • net.sf.basedb.core.File.Action
    • net.sf.basedb.core.Image.Format
    • net.sf.basedb.core.BioMaterialEvent.Type
    • net.sf.basedb.core.IntensityTransform
    • net.sf.basedb.core.Location
    • net.sf.basedb.core.Type
    • net.sf.basedb.core.Formula.AverageMethod
    • net.sf.basedb.core.Formula.Type
    • net.sf.basedb.core.Formula.Parser
    • net.sf.basedb.core.VirtualTable
    • net.sf.basedb.core.Project.Default
    • net.sf.basedb.core.BioWell.LockMode
    • net.sf.basedb.core.Include
    • net.sf.basedb.core.Operator
    • net.sf.basedb.core.Path.Type
    • net.sf.basedb.core.Item
    • net.sf.basedb.core.Job.Type
    • net.sf.basedb.core.Job.Status
    • net.sf.basedb.core.Job.ExecutionTime
    • net.sf.basedb.core.Transactional.Action
    • net.sf.basedb.core.FeatureIdentificationMethod
    • net.sf.basedb.core.log.ChangeType
    • net.sf.basedb.core.plugin.Plugin.MainType
    • net.sf.basedb.core.plugin.GuiContext.Type
    • net.sf.basedb.core.plugin.Response.Status
    • net.sf.basedb.core.query.QueryType
    • net.sf.basedb.core.query.QuerySection
    • net.sf.basedb.core.query.JoinType
    • net.sf.basedb.util.extensions.xml.PathType
    • net.sf.basedb.util.formatter.BooleanFormatter.Type
    • net.sf.basedb.util.overview.Severity
    • net.sf.basedb.util.overview.Node.Type
    • net.sf.basedb.util.overview.node.ChildNodeDirection
    • net.sf.basedb.util.parser.FlatFileParser.LineType
    • net.sf.basedb.util.plot.HistogramPlot.YAggregate
    • net.sf.basedb.plugins.Base1PluginExecuter.Base1JobParameterType
    • net.sf.basedb.plugins.PrintMapFlatFileImporter.Section
    • net.sf.basedb.plugins.PrintMapFlatFileImporter.FormatType
    • net.sf.basedb.clients.web.extensions.menu.MenuItemAction.MenuType