AAConClient AAFrequency AAStructureBindingModel AAStructureBindingModel.SuperposeData AMSAFile APQHandlers ASequenceFetcher AWSThread AWsJob AlignAnalysisUIText AlignCalcManager AlignCalcWorker AlignExportOptions AlignExportSettingsAdapter AlignFile AlignFrame AlignSeq AlignViewController AlignViewport AlignedCodon AlignedCodonFrame AlignedCodonFrame.SequenceToSequenceMapping Alignment Alignment AlignmentAnnotation AlignmentAnnotation.AnnotCharSequence AlignmentAnnotationPojo AlignmentAnnotationUtils AlignmentDimension AlignmentExportData AlignmentGenerator AlignmentOrder AlignmentPanel AlignmentPojo AlignmentSorter AlignmentUtils AlignmentView AlignmentView.ScGroup AlignmentViewport AllColsCollection AllColsIterator AllRowsCollection AllRowsIterator AlphaFoldAnnotationRowBuilder Annotation Annotation Annotation.ThresholdLine AnnotationChooser AnnotationColourGradient AnnotationColourScheme AnnotationColumnChooser AnnotationColumnChooser.FurtherActionPanel AnnotationColumnChooser.SearchPanel AnnotationColumnChooser.StructureFilterPanel AnnotationDisplaySettingPojo AnnotationElement AnnotationExporter AnnotationFile AnnotationFile AnnotationFile.ViewDef AnnotationFilterParameter AnnotationLabels AnnotationPanel AnnotationPojo AnnotationRenderer AnnotationRendererFactory AnnotationRowBuilder AnnotationRowFilter AnnotationSorter AnnotationSorter.SequenceAnnotationOrder AnnotationWorker Any AppCache AppJmol AppJmol.RenderPanel AppJmolBinding AppVarna AppletFormatAdapter AppletUrlProviderFactory Arg Arg.Opt Arg.Type ArgParser ArgParserUtils ArgValue ArgValues ArgValuesMap ArgsParser ArrayUtils AssociatePdbFileWithSeq Atom AtomSpec AtomSpecModel AverageDistanceEngine BLCFile BackupFilenameFilter BackupFilenameParts BackupFiles BackupFilesPresetEntry BinaryNode BioJSReleasePojo BioJSRepositoryPojo BioJsHTMLOutput BitmapImageSizing BlogReader BlogReader.LaunchJvBrowserOnItem BlossomColourScheme Blosum62ColourScheme Bond BootstrapArgs Boundary Bracket Branch BuildDetails BuriedColourScheme Cache Cache.VersionChecker CalculationChooser CaseInsensitiveString CaseMgr ChannelProperties ChimeraCommands ChimeraXCommands CigarArray CigarBase ClustalFile ClustalxColourScheme ClustalxColourScheme.ClustalColour ClustalxColourScheme.ConsensusColour CodingUtils CodonComparator ColorUtils ColourMenuHelper ColourSchemeMapper ColourSchemeProperty ColourSchemes ColumnSelection ColumnSelection.IntList CommandLineOperations CommandLineOperations.Worker CommandLineOperationsNG CommandLineOperationsNG.Worker Commands Comparison ComplementConsensusThread Condition Consensus ConsensusThread Conservation ConservationThread Console Console Constants ContactGeometry ContactGeometry.contactInterval ContactListImpl ContactMapHolder ContactMapRenderer ContactMapRenderer.Shading ContactMatrix ContactRange ContainerHelpers CrossRef CrossRefAction CustomUrlProvider DBRefEntry DBRefSource DBRefUtils DataSourceType DbReferenceType DbSourceProxyImpl DecimalFormatTableCellRenderer Desktop Desktop.MyDesktopManager Desktop.MyDesktopPane DesktopUrlProviderFactory Discoverer Dna DnaUtils DotMulti DoubleMatrix DoubleVector EBIAlfaFold EBIFetchClient EMBLLikeFlatFile EditCommand EditCommand.Edit EmblCdsSource EmblFlatFile EmblSource EmblXmlSource End EnsemblCdna EnsemblCds EnsemblData EnsemblGene EnsemblGenome EnsemblProtein EnsemblRestClient EnsemblSeqProxy EnsemblSequenceFetcher EnsemblXref EntityType Entry EntryType EntryType.Feature EntryType.Feature.Qualifier EpsDocument EpsGraphics2D ErrorLog EvidencedStringType ExonerateHelper FTSDataColumnPreferences FTSDataColumnPreferences.FTSDataColumnPrefsTableModel FTSRestClient FTSRestRequest FTSRestResponse FastBracket FastChar FastMulti FastaFile Feature Feature.OtherData FeatureAttributes FeatureAttributes.AttributeData FeatureColour FeatureColourFinder FeatureDistanceModel FeatureMatcher FeatureMatcher FeatureMatcherSet FeatureMatcherSet FeatureMatcherSet.CompoundMatcher FeatureProperties FeatureRenderer FeatureRenderer FeatureRendererModel FeatureRendererModel.FeatureSettingsBean FeatureRendererSettings FeatureSettings FeatureSettings.ColorEditor FeatureSettings.ColorRenderer FeatureSettings.FeatureTableModel FeatureSettings.FilterEditor FeatureSettings.FilterRenderer FeatureSettingsAdapter FeatureSource FeatureSources FeatureStore FeatureType FeaturesDisplayed FeaturesFile FileFormat FileFormatException FileFormats FileLoader FileParse FileUtils FilterBy FilterOption Finder FloatContactMatrix FlowerColourScheme FollowerColourScheme Format FormatAdapter GAlignFrame GAlignmentPanel GDesktop GFTSPanel GFTSPanel.DeferredTextInputListener GPCAPanel GPairwiseAlignPanel GSliderPanel GSplitFrame GStructureChooser GStructureChooser.AssociateSeqOptions GStructureChooser.AssociateSeqPanel GStructureChooser.CustomComboSeparatorsRenderer GStructureViewer GTreePanel GenBankFile GeneLocus GeneticCodes GetMemory Gff2Helper Gff3Helper GffHelperBase GffHelperFactory GraphLine GroupSet GroupSetHolder Grouping HTMLOutput HelixColourScheme Help.HelpId HiDPISetting HiddenColumns HiddenColumnsCursor HiddenCursorPosition HiddenSequences HtmlSvgOutput HtsContigDb HttpUtils HydrophobicColourScheme IdCanvas IdColourScheme IdOrgSettings IdPanel IdentifiersUrlProvider IdentifyFile IdwidthAdjuster ImageExporter ImageMaker ImageMaker.TYPE InputType IntKeyStringValueEntry IntRangeComparator InterProScanHelper ItemsRenderer JLogger JLoggerLog4j JPredClient JSONArray JSONArray JSONFile JSONObject JSONObject JSONObject.Null JSONParser JSONUtils JSONValue JabaParamStore JabaPreset JabaWsServerQuery Jalview Jalview2XML Jalview2XML.JvAnnotRow Jalview2XML.forwardRef Jalview2xmlBase JalviewAppender JalviewChangeSupport JalviewColourScheme JalviewDialog JalviewFileChooser JalviewFileChooser.RecentlyOpened JalviewFileChooser.recentlyOpenedCellRenderer JalviewFileFilter JalviewFileView JalviewJmolBinding JalviewLite JalviewModel JalviewModel.FeatureSettings JalviewModel.FeatureSettings.Group JalviewModel.FeatureSettings.Setting JalviewModel.JGroup JalviewModel.JSeq JalviewModel.JSeq.Pdbids JalviewModel.JSeq.Pdbids.StructureState JalviewModel.PcaViewer JalviewModel.PcaViewer.Axis JalviewModel.PcaViewer.SeqPointMax JalviewModel.PcaViewer.SeqPointMin JalviewModel.PcaViewer.SequencePoint JalviewModel.Tree JalviewModel.Viewport JalviewModel.Viewport.HiddenColumns JalviewModel.Viewport.Overview JalviewTaskbar JalviewUserColours JalviewUserColours.Colour JalviewUserColours.Filter JmolCommands JmolParser JobStateSummary JustifyLeftOrRightCommand JvCacheableInputBox JvOptionPane JvSwingUtils Jws2Client Jws2Discoverer Jws2Instance Jws2InstanceFactory Jws2ParamView LaunchUtils LinkedIdentityHashSet LinkedIdentityHashSet.IdentityWrapper LocationType Log4j MSFfile MapList MapListType MapListType.MapListFrom MapListType.MapListTo MapOnAMatrixType MapUtils MappableContactMatrix MappedFeatures Mapping Mapping Mapping Mapping.AlignedCodonIterator MappingType MappingUtils Matcher MathUtils Matrix MatrixType MemorySetting MessageManager MiscMath ModellerDescription MsaWSClient MsaWSClient Multi Multi_stage2 NewickFile NoValueColour NucleotideAmbiguityColourScheme NucleotideColourScheme NullPattern ObjectFactory OceanColourScheme Or OrMark OrderCommand OverviewCanvas OverviewDimensions OverviewDimensionsHideHidden OverviewDimensionsShowHidden OverviewPanel OverviewRenderer OverviewResColourFinder PA PAEContactMatrix PCA PCAModel PCAPanel PDBChain PDBEntry PDBEntry.Type PDBFTSPanel PDBFTSRestClient PDBFeatureSettings PDBStructureChooserQuerySource PDBfile PIDColourScheme PIDModel PIRFile PaintRefresher PairwiseAlignPanel ParseHtmlBodyAndLinks ParseProperties Pattern PcaDataType Pdb Pdbentry Pdbentry.Property Pfam PfamFile PfamFull PfamSeed PhylipFile PileUpfile Platform Plausible Point PopupMenu PositionType Preferences PrivilegedAccessor Profile Profiles ProgressBar ProgressPanel PromptUserConfig PropertyType ProteinType ProteinType.RecommendedName PurinePyrimidineColourScheme PymolCommands PymolManager QuickSort QuickSort.DoubleComparator QuickSort.ExternalComparator QuickSort.FloatComparator QuickSort.IntComparator QuitHandler RNAHelicesColour RNAInteractionColourScheme RNAalifoldClient ROOT Range Range RangeElementsIterator RangeIterator RegOpt RegRes RegSyntax Regex RemoveGapColCommand ReplaceRule Replacer Residue ResidueColourFinder ResidueColourScheme ResidueCount ResidueCount.SymbolCounts ResidueProperties ResidueShader RestClient RestJob RestJobThread RestServiceDescription ReverseListIterator Rfam RfamFull RfamSeed Rna RnamlFile RotatableCanvas RotatableMatrix Rthings SFSortByEnd ScalePanel ScaleRenderer ScaleRenderer.ScaleMark ScoreColourScheme ScoreMatrix ScoreMatrixFile ScoreModels SearchResults SearchResults.Match SecStrConsensus.SimpleBP SecondaryStructureCount SecondaryStructureDistanceModel SeqCanvas SeqCigar SeqDistanceContactMatrix SeqGroupIndexVector SeqPanel SeqPanel.MousePos SeqSearchWSClient SeqsetUtils Sequence Sequence Sequence.DBModList Sequence.DBRef SequenceAnnotationReport SequenceAnnotationWSClient SequenceCursor SequenceDummy SequenceFeature SequenceFeatures SequenceFeaturesPojo SequenceFetcher SequenceFetcher SequenceFetcherFactory SequenceGroup SequenceGrpPojo SequenceIdMatcher SequenceIdMatcher.SeqIdName SequenceNode SequenceOntology SequenceOntologyFactory SequenceOntologyLite SequencePoint SequencePojo SequenceRenderer SequenceSet SequenceSet.SequenceSetProperties SequenceStructureBindingModel SequenceType SequenceType ServiceHandle SetUtils ShiftList ShmmrRSBSService ShortcutKeyMaskExWrapper ShortcutKeyMaskExWrapper11 SiftsClient SiftsClient.CoordinateSys SiftsSettings SimilarityParams SimilarityScoreModel Skip Skip2 Slider SliderPanel SparseCount SparseDoubleArray SparseIntArray SparseMatrix SparseShortArray SpatialModel SpatialPanel SplashScreen SplashScreen.SplashImage SplitFrame Start StartRegionIterator StockholmFile StrPos StrandColourScheme StringBufferLike StringBufferWrap StringRule StringUtils StringWrap StrucConsensusThread StructureChooser StructureChooser.PDBEntryTableModel StructureChooserQuerySource StructureCommand StructureCommandsBase StructureFile StructureFrequency StructureImportSettings StructureImportSettings.TFType StructureMapping StructureSelectionManager StructureViewer StructureViewer.ViewerType StructureViewerBase StructureViewerModel StructureViewerModel.StructureData SubMark SubVals SunsetColourScheme TCoffeeColourScheme TCoffeeScoreFile TCoffeeScoreFile.Block TCoffeeScoreFile.Header TDBResultAnalyser TDB_FTSData TDBeaconsFTSPanel TDBeaconsFTSRestClient TaylorColourScheme ThreeDBStructureChooserQuerySource TreeCanvas TreeEngine TreeModel TreePanel TreePanel.TreeLoader TrimRegionCommand TurnColourScheme Uniprot Uniprot UrlConstants UrlDownloadClient UrlLink UrlLinkDisplay UrlLinkTableModel UrlProvider UrlProviderImpl UserAgent UserColourScheme UserQuestionnaireCheck VAMSAS VCFLoader VCFLoader.VCFMap VCFReader ViewSelectionMenu ViewStyle ViewportProperties ViewportRanges VisibleColsCollection VisibleContigsIterator VisibleRowsCollection VisibleRowsIterator WS1Client WSClient WUSSParseException WsParamSetManager Xfam XrefType Yylex Yytoken ZappoColourScheme oneChar parsePerl patInf patInt