All Classes

AAMultiSequenceAlignerPanel AbstractApolloAdapter AbstractLazySequence AbstractParser AbstractScrollablePanel AbstractSequence AbstractTierPanel ActionEventRouter AdapterModel AddFilterAction AddFilterPanel AddFilterPanel.TYPES AddResultFilterAction AddTransaction AlignBlockChooser AlignmentParser AllTests AllTests AlternateEnsJSequence AlternateEnsJSequence AminoAcidBaseRenderer AminoAcidRenderer AminoAcidRenderer AminoAcidRendererOLD AminoAcidRendererSpaced AnalysisAdapter AnalysisAdapterGUI AnalysisAdaptor AnalysisDataAdapterI AnalysisFilter AnalysisFilterI AnalysisGUI AnalysisInput AnalysisMenu AnalysisPanel AnalysisParserI AnnotatedFeature AnnotatedFeatureI AnnotationAddEvent AnnotationChangeEvent AnnotationChangeListener AnnotationChangeLog AnnotationCompoundEvent AnnotationDeleteEvent AnnotationEditor AnnotationEditorMouseListener AnnotationEnsJAdapter AnnotationEnsJAdapterGUI AnnotationFeatureComparator AnnotationHeaderMouseListener AnnotationMenu AnnotationRenderer AnnotationReplaceEvent AnnotationRighClickMenu AnnotationsModel AnnotationSourceChooser AnnotationsPanel AnnotationUpdateEvent AnnotationView AnnotSessionDoneEvent Apollo ApolloAdapterException ApolloControlServer ApolloControlServlet ApolloDataAdapterGUI ApolloDataAdapterI ApolloDataI ApolloFrame ApolloJalviewEventBridge ApolloLaundry ApolloLayoutManager ApolloLoaderI ApolloMetalScrollBarUI ApolloNameAdapterI ApolloPanel ApolloPanelHolderI ApolloPanelI ApolloRunner ApolloScrollBar ApolloTest ArrayListTransferHandler AssemblyFeature AssemblyFeatureI AutoSaveThread BaseAdaptor BaseEditorPanel BaseEditorPanel BaseFilter BaseFineEditor BaseFineEditor BaseFineEditorHorizontalColHeader BaseFineEditorRowHeader BaseFineEditorRowHeader BaseFocusEvent BaseFocusListener BaseGFFAdapter BaseRenderer BaseRenderer BaseRendererFactory BaseRendererI BaseScrollable BasicWindowListener BlastFilterPanel BlastHandler BlastParser BlastXMLParser BlastXMLParserTest BlatParser BlixemRunner BookmarkMenu bop BopException BuilderAdapter BuilderAdapterGUI CacheSeqIdLoader CacheSequenceLoader CaseInsensitiveStringHash CGI ChadoAdapter ChadoAdapterGUI ChadoAdHocFlatFileWriter ChadoDatabase ChadoInstance ChadoJdbcNameAdapter ChadoProgram ChadoTransaction ChadoTransaction.Operation ChadoTransactionTransformer ChadoTransactionXMLTemplate ChadoTransactionXMLWriter ChadoUpdateTransaction ChadoXmlAdapter ChadoXmlAdapterGUI ChadoXmlUtils ChadoXmlWrite ChainedRepaintEvent ChainedRepaintListener ChangeDatabaseHandler ChangeList CheckMemoryThread Chromosome ChromosomeAdapter ChromosomeBand ChromosomeDrawer ChromosomeField ChromosomePanel CigarUtil ClearSeqRegionsHandler ClipboardUtil CodingPropertiesI CollectionUtil ColumnApolloLayout ColumnProperty CommandLine Comment CompactFeaturePlaceFinder Comparable Comparator ComparatorBase ComparatorFactory ComparatorFactory.TYPE ComparatorReverse ComparatorSeqFeatureDisplayType ComparatorSeqFeatureFrame ComparatorSeqFeatureLength ComparatorSeqFeatureName ComparatorSeqFeatureScore CompositeApolloFrame CompositeApolloFrame.MacApplicationSupport CompositeDataHolder CompositeDataSourceConfigurationPanel CompoundTransaction Compress Config ContainerView ContainerViewI ControlledObjectI ControlledPanel Controller Controller Controller ControllerDebugListener Coverage CreateExonAction CreateIntronAction CurationManager CurationSet CurationState CutSite DAS2Adapter DAS2AdapterGUI DAS2FeatureSaxParser DAS2Request DAS2Writer DASDsn DASDsnContentHandler DASEntryPointContentHandler DASFeature DASFeatureContentHandler DASLazySequence DASSegment DASSequence DASSequenceContentHandler DASServerI Database DatabaseModel DatabasePanel DataFetcher DataInput DataInputType DataInputType.UnknownTypeException DataListener DataLoader DataLoadEvent DataLoadListener DataModelConversionUtil DataSourceConfigurationPanel DataUtil DateUtil DBAdaptor DbXref DebugLazySequence DefaultBaseRenderer DefaultBaseRenderer DefaultDisplayPrefs DefaultNameAdapter DeleteExonAction DeleteTransaction DetailInfo Directions Directions DisabledEditor DiscreteGraphView DisplayPrefsI DisplaySequenceAction DisplayTool DNAMultiSequenceAlignerPanel DNAResultRenderer DoubleHeadedArrow DragView DragViewI Drawable DrawableAnnotationConstants DrawableDisplayTool DrawableEnsemblFeatureSet DrawableFeatureSet DrawableGeneFeatureSet DrawableGeneSeqFeature DrawableHalfArrow DrawablePhaseHighlightGeneFeatureSet DrawablePhaseHighlightGeneSeqFeature DrawablePhaseHighlightNoHatGeneFeatureSet DrawablePrimerSet DrawableResultFeatureSet DrawableResultSeqFeature DrawableSeqFeature DrawableSetI DrawableTierManager DrawableTierManagerI DrawableUtil DriverDialog DropTargetViewI DummySequenceAdapter EditMenu EditWindowI EditWindowListener EfetchSequenceAdapter EnsCGIAdapter EnsCGIAdapterGUI EnsCGISequence EnsJAdapter EnsJAdapter EnsJAdapterGUI EnsJAdapterGUI EnsJAdapterUtil EnsJConnectionUtil EnsjDisplayPrefs EnsJFeatureSetBuilder EnsJSequence EventHandler EventRouter Evidence EvidenceConstants EvidenceFinder EvidenceNameTagHandler EvidencePanel EvidencePanelContainer EvidencePanelOrientationManager EvidenceSet EvidenceTagHandler EvidenceTypeTagHandler ExampleFileFilter Exon ExonEndTagHandler ExonFrameTagHandler ExonI ExonStableIdTagHandler ExonStartTagHandler ExonStrandTagHandler ExonTagHandler FastaFile FastaHeader FastClippingGraphics FatalException FeatureAdaptor FeatureAlphabeticalComparator FeatureChangeEvent FeatureChangeListener FeatureComparator FeatureEditorDialog FeatureEditPanel FeatureIterator FeatureList FeatureNavigationI FeaturePair FeaturePairI FeaturePlaceFinder FeaturePlaceFinder.Type FeatureProperty FeaturePropertyPanel FeatureSelectionEvent FeatureSelectionListener FeatureSet FeatureSetBuilder FeatureSetI FeatureTier FeatureTierManager FeatureTierManagerI FeatureTreeFrame FeatureTreePanel FeatureValidatorI FeatureView FgeneshGFFParser FgeneshParser FileMenu FileParse FileTabPanel FileUtil FileUtilTest Filter FilterDisplayType FilterFactory FilterInverse FilterName FilterPanel FilterPanelI FilterReadingFrame FilterSequenceType FilterStrand FindCoordSystemsHandler FindDialog FindEnsemblDatabaseNamesHandler FindPanel FindSeqRegionsHandler FlybaseChadoInstance FlybaseWrite FlyChadoXmlAdapter FlyChadoXmlAdapterGUI FlyDisplayPrefs FlyGAMEAdapter FlyGAMEAdapterGUI FlyIdValidator FlyNameAdapter Format FrameShiftAction FrameShiftAction.FrameShiftType FullEnsJDBCSyntenyPanel FullSyntenyPanel GAMEAdapter GAMEAdapterGUI GAMEPanel GAMESave GAMESequence GbrowseAdapter GbrowseAdapterGUI GCScoreCalculator GenbankAdapter GenbankAdapterGUI GenbankFormatter GenbankRead GenbankReport GenbankSequence GenbankValidator GeneEditPanel GeneFinderParser GenericFileAdapterGUI GenericFileFilter GenericFileFilterTest GenericProgramHandler GenericTagHandler GenieParser GenomicRange GenscanFilterPanel GenscanParser GFF3Adapter GFF3AdapterGUI GFF3AdapterTest GFF3Entry GFF3EntryTest GFFAdapter GFFAdapterGUI GFFFile GFFSyntenyAdapter GlyphChooser GmodNameAdapter GoToDialog GraphAdapter GraphAdapterGUI GraphMenu GraphView GuiCurationState GuideLine GuiTabPanel GuiUtil HashDB HashMatch HelpMenu HideShowAnnotationsHandler HideShowDatabasesHandler HideShowLocationsHandler HideShowOptionsHandler HideShowTypesHandler HomogeneousPanel HorizontalScrollBarAdjustmentListener HTMLUtil HuffNode Identifier IgbBridge InsertionDialog Interval IntervalComponent IntervalComponent.Valignment IntervalTree IOUtil JdbcChadoAdapter JdbcChadoWriter JDBCPipelineAdapter JDBCTransactionLoader JDBCTransactionWriter JobOutput Karyotype KaryotypeAdapter KaryotypeAdapterI KaryotypeUtil KeyEventRouter KeyViewI LaidoutViewContainer LazyLoadEvent LazyLoadListener LazySequenceI LinearView Link LinkerI LinkSet LinksMenu LinkType LoaderPanel LoadSeqRegionByHistoryHandler LoadUtil LocationChadoPanel LocationGAMEPanel LocationModel LocationPanel LocusAuthorEmailTagHandler LocusAuthorTagHandler LocusKnownTagHandler LocusNameTagHandler LocusRemarkTagHandler LocusStableIdTagHandler LocusSynonymTagHandler LocusTagHandler LocusTypeTagHandler ManagedView ManagedViewI MenuManager MergeExonAction MethodRunnerActionListener Model Model MouseButtonEvent MSPFile MultiComparator MultiComparatorArrayList MultiController MultiFilter MultiFilterAnd MultiFilterOr MultiSequenceAlignerFrame MultiSequenceAlignerPanel MultiTierPanel MultiTierPanelHeaderTable MySQLDatabase MySQLInstance NamedFeatureSelectionEvent NamedFeatureSelectionListener NavigationBar NoFilterPanel NonFatalDataAdapterException NonFatalException NonWindowControlledObject NoOutputException NoOverlap NotImplementedException NumericKeyFilter OBOParser OBOParserTest OptionsModel OptionsPanel ORF_Overlap Orientation OrientationEvent OrientationListener Orientations OtterAdapter OtterAdapterGUI OtterAnnotationSourceChooser OtterContentHandler OtterTagHandler OtterXMLAdapter OtterXMLAdapterGUI OtterXMLRenderingVisitor OverlapI Overview Pair PairTest PanelFactory ParameciumDBChadoInstance ParameciumDisplayPrefs ParameciumNameAdapter PeptideMenu PeptideNote PeptideStatus PeptideValidator PFetchSequence PickViewI PixelMask PixelMaskI PlotUtil PopupPropertyListener PopupRouter PopupViewI PostgresChadoAdapter PreferencesDialog PreferenceWindow PrefsPanel PrimerBlastHtmlParser PrimerBlastHtmlParserTest ProgramHandlerFactory ProgramHandlerI ProgressFrame PromoterGlyph PropertyDisplay PropertyMenu PropertyPanel PropertyScheme PropSchemeChangeEvent PropSchemeChangeListener Protein ProxyDialog PublicDbFeature PureJDBCTransactionWriter QuickSort Range RangeI RbNode RbTree ReadHandler ReadingFrame ReferenceFactory ReferenceFactoryI ReferencePanel ReferencePanel ReferenceTierPanelHeader Region RegionSelectableI RemoteBlastNCBI RemoteBlastNCBI.BlastOptions RemoteBlastNCBI.BlastType RemoteBlastNCBITest RemotePrimerBlastNCBI RemotePrimerBlastNCBI.PrimerBlastOptions RemotePrimerBlastNCBI.PrimerBlastOptions.Database RemotePrimerBlastNCBITest ResidueProperties ResponseTagHandler RestrictionEnzyme ResultChangeEvent ResultChangeListener ResultFeatureComparator ResultHeaderMouseListener ResultMouseListener ResultRenderer ResultRendererFactory ResultRightClickMenu ResultView RevCompListener ReverseComplementEvent ReverseComplementListener RiceChadoInstance RiceNameAdapter Robby RpMaskerParser Rubberband RubberbandEvent RubberbandListener RubberbandRectangle SampleAdapter SampleAdapterGUI ScaleMenu ScaleView SchemaVersion Score ScoreCalculator ScrollAdjustedView ScrollEvent ScrollListener SegmentParser SelectableDNARenderer SelectableDNARenderer SelectableI Selection SelectionItem SelectionManager SelectionType SelectNewEnsemblDatabaseHandler SelectSeqRegionHandler SelectViewI SemiCompactFeaturePlaceFinder SeqAlignPanel SeqAlignPanel SeqAnalysisBase SeqAnalysisBDGP SeqAnalysisFactory SeqAnalysisGUI SeqAnalysisI SeqAnalysisLocal SeqAnalysisNCBI SeqAnalysisRemote SeqAnalysisTest SeqExport SeqFeature SeqFeatureI SeqFeatureTableModel SeqFeatureTableModel.ColumnTypes SeqFeatureUtil SeqMatchPanel SeqSelectorTable SeqType Sequence SequenceEdit SequenceEditAction SequenceFragmentAccessionTagHandler SequenceFragmentAssemblyEndTagHandler SequenceFragmentAssemblyStartTagHandler SequenceFragmentAuthorEmailTagHandler SequenceFragmentAuthorTagHandler SequenceFragmentChromosomeTagHandler SequenceFragmentFragmentOffsetTagHandler SequenceFragmentFragmentOrientationTagHandler SequenceFragmentIdTagHandler SequenceFragmentKeywordTagHandler SequenceFragmentRemarkTagHandler SequenceFragmentTagHandler SequenceFragmentVersionTagHandler SequenceI SequenceSelector SequenceSetAssemblyTypeTagHandler SequenceSetAuthorTagHandler SequenceSetTagHandler SequenceType SequenceUtil SerialAdapterGUI SerialDiskAdapter SetActiveCurStateEvent SetActiveCurStateListener SetDetailPanel SetEndAction SetTranslationStartAction SgrScoreCalculator ShowAbInitioCountsByTypeHandler ShowDitagFeatureCountsByTypeHandler ShowDnaDnaAlignCountsByTypeHandler ShowDnaProteinAlignCountsByTypeHandler ShowGeneCountsByTypeHandler ShowMenu ShowSimpleFeatureCountsByTypeHandler Sim4FilterPanel Sim4Parser SimpleDASAdapter SimpleDASAdapterGUI SimpleDASDsn SimpleDASFeature SimpleDASSegment SimpleDASSequence SimpleDASServer SimpleNameAdapter SimpleOverlap SiteCodon Sites SiteTier SiteTierManager SiteView SliderWindow SourceChooserWithHistory SourceParser SpeciesComparison SplitterView SRSSequence StateInformation StatisticUpdate StatusBar StatusPane StoredScoreCalculator Strand StrandedFeatureSet StrandedFeatureSetI StrandedZoomableApolloPanel StrandVisibilityListener StreamMatch Style StyleWizard SwingMissingUtil SwingWorker SybaseChadoAdapter Synonym SyntenyAdapter SyntenyAdapter SyntenyAdapterGUI SyntenyAdapterI SyntenyChoiceMenu SyntenyComparaAdapter SyntenyComparaAdapterGUI SyntenyGFFAdapter SyntenyLayout SyntenyLinkMenu SyntenyLinkPanel SyntenyMenu SyntenyMenuManager SyntenyPanel SyntenyRegion SyntenyViewMenu Table TableColumn TableColumnChooser TablePanel TagHandler TestApollo TestBaseRenderer TestJDBCTransactions TestTransactions ThinRectangle ThresholdMenu Tier Tier TierFactory TierFactoryI TierI TierI.Level TierManager TierManagerEvent TierManagerI TierManagerListener TierPanel TierPanelAddressHeader TierPanelI TierPopupMenu TierProperty TiersIO TiersMenu TierView TierViewI TigrAnnotDisplayPrefs TigrAnnotNameAdapter TigrChadoInstance TigrSybilChadoInstance TigrSybilNameAdapter Transaction TransactionClass TransactionManager TransactionOperation TransactionOutputAdapter TransactionSubpart TransactionTransformer TransactionTransformException TransactionUtil TransactionXMLAdapter Transcript TranscriptAuthorEmailTagHandler TranscriptAuthorTagHandler TranscriptCdsEndNotFoundTagHandler TranscriptCdsStartNotFoundTagHandler TranscriptClassTagHandler TranscriptMenu TranscriptMRNAEndNotFoundTagHandler TranscriptMRNAStartNotFoundTagHandler TranscriptNameTagHandler TranscriptOverview TranscriptRemarkTagHandler TranscriptStableIdTagHandler TranscriptTagHandler TranscriptTranslationEndTagHandler TranscriptTranslationStableIdTagHandler TranscriptTranslationStartTagHandler Transformer TranslationI TranslationView TreeMenu Triangle tRNA_Parser tRNAValidator Tweeker TwilightFilter TypePanel TypesMenu TypesModel TypesPanel TypesWizard UnBorderedSplitPane UpdateDetailsI UpdateHandler UpdateParentTransaction UpdateTransaction UpdateWorkRoundComboBox URLDiagnosticTool URLQueryGenerator UserName UseSeqRegionLocationHandler UseStableIDLocationHandler Utils Version VerticalScrollBarAdjustmentListener View View ViewEvent ViewI ViewListener ViewMenu ViewportChangeListener VisibilityEvent VisibilityListener Visitor WashingLine WiggleScoreCalculator WiggleScoreCalculator.WiggleType WindowMenu WindowScoreCalculator XMLParser XrefUtil Zigzag ZoomEvent ZoomListener