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 AllColsIterator AllRowsIterator Annotation Annotation Annotation.ThresholdLine AnnotationChooser AnnotationColourGradient AnnotationColourScheme AnnotationColumnChooser AnnotationColumnChooser.FurtherActionPanel AnnotationColumnChooser.SearchPanel AnnotationColumnChooser.StructureFilterPanel AnnotationDisplaySettingPojo AnnotationElement AnnotationFile AnnotationFile AnnotationFile.ViewDef AnnotationFilterParameter AnnotationLabels AnnotationPanel AnnotationPojo AnnotationRenderer AnnotationRowFilter AnnotationSorter AnnotationSorter.SequenceAnnotationOrder AnnotationWorker Any AppCache AppJmol AppJmol.RenderPanel AppJmolBinding AppVarna AppletFormatAdapter AppletUrlProviderFactory ArgsParser ArrayUtils Atom AtomSpec AtomSpecModel BLCFile BackupFilenameFilter BackupFilenameParts BackupFiles BackupFilesPresetEntry BinaryNode BioJSReleasePojo BioJSRepositoryPojo BioJsHTMLOutput BlogReader BlogReader.LaunchJvBrowserOnItem Blosum62ColourScheme Bond Boundary Bracket Branch BuildDetails BuriedColourScheme Cache CalculationChooser CaseInsensitiveString ChimeraCommands ChimeraXCommands CigarArray CigarBase ClustalFile ClustalxColourScheme ClustalxColourScheme.ClustalColour ClustalxColourScheme.ConsensusColour CodingUtils CodonComparator ColorUtils ColourMenuHelper ColourSchemeMapper ColourSchemeProperty ColourSchemes ColumnSelection ColumnSelection.IntList CommandLineOperations CommandLineOperations.Worker Comparison ComplementConsensusThread Condition Consensus ConsensusThread Conservation ConservationThread Console ContainerHelpers CrossRef CrossRefAction CustomUrlProvider DBRefEntry DBRefSource DBRefUtils DbReferenceType DbSourceProxyImpl Desktop Desktop.MyDesktopManager Desktop.MyDesktopPane DesktopUrlProviderFactory Discoverer Dna DnaUtils DotMulti DoubleMatrix DoubleVector EBIFetchClient EditCommand EditCommand.Edit EmblCdsSource EmblSource EmblXmlSource End EnsemblCdna EnsemblCds EnsemblData EnsemblGene EnsemblGenome EnsemblProtein EnsemblRestClient EnsemblSeqProxy EnsemblSequenceFetcher EnsemblXref EntityType Entry EntryType EntryType.Feature EntryType.Feature.Qualifier EpsDocument EpsGraphics2D EvidencedStringType ExonerateHelper FTSDataColumnPreferences FTSDataColumnPreferences.FTSDataColumnPrefsTableModel FTSRestClient FTSRestRequest FastBracket FastChar FastMulti FastaFile Feature Feature.OtherData FeatureAttributes FeatureAttributes.AttributeData FeatureColour FeatureColourFinder FeatureDistanceModel FeatureIcon 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 FilterBy Finder FollowerColourScheme Format FormatAdapter GAlignFrame GAlignmentPanel GDesktop GFTSPanel GFTSPanel.DeferredTextInputListener GPCAPanel GPairwiseAlignPanel GSliderPanel GSplitFrame GStructureChooser GStructureChooser.AssociateSeqOptions GStructureChooser.AssociateSeqPanel GStructureChooser.CustomComboSeparatorsRenderer GStructureChooser.FilterOption GStructureViewer GTreePanel GeneLocus GeneticCodes GetMemory Gff2Helper Gff3Helper GffHelperBase GffHelperFactory GraphLine Grouping HTMLOutput HelixColourScheme Help.HelpId HiddenColumns HiddenColumnsCursor HiddenCursorPosition HiddenSequences HtmlSvgOutput HtsContigDb HydrophobicColourScheme IdCanvas IdColourScheme IdOrgSettings IdPanel IdentifiersUrlProvider IdentifyFile IdwidthAdjuster ImageExporter ImageMaker ImageMaker.TYPE InputType IntKeyStringValueEntry IntRangeComparator InterProScanHelper ItemsRenderer JPredClient JSONArray JSONFile JSONObject JSONObject JSONObject.Null JSONParser JSONUtils JabaParamStore JabaPreset JabaWsServerQuery Jalview Jalview2XML Jalview2XML.JvAnnotRow Jalview2xmlBase JalviewAppender JalviewChangeSupport JalviewColourScheme JalviewDialog JalviewFileChooser JalviewFileChooser.RecentlyOpened 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 JalviewTaskbar JalviewUserColours JalviewUserColours.Colour JalviewUserColours.Filter JmolCommands JmolParser JobStateSummary JvCacheableInputBox JvOptionPane JvSwingUtils Jws2Client Jws2Discoverer Jws2Instance Jws2InstanceFactory Jws2ParamView LinkedIdentityHashSet LinkedIdentityHashSet.IdentityWrapper LocationType MSFfile MapList MapListType MapListType.MapListFrom MapListType.MapListTo MappedFeatures Mapping Mapping Mapping Mapping.AlignedCodonIterator MappingType MappingUtils Matcher MathUtils Matrix MemorySetting MessageManager ModellerDescription MsaWSClient MsaWSClient Multi Multi_stage2 NewickFile NoValueColour NucleotideColourScheme NullPattern ObjectFactory Or OrMark OverviewDimensions OverviewDimensionsHideHidden OverviewDimensionsShowHidden OverviewResColourFinder PA PCA PCAModel PCAPanel PDBChain PDBEntry PDBEntry.Type PDBFTSPanel PDBFTSRestClient PDBFeatureSettings PDBfile PIDColourScheme PIDModel PIRFile PaintRefresher PairwiseAlignPanel ParseHtmlBodyAndLinks ParseProperties Pattern PcaDataType Pdb Pdbentry Pdbentry.Property Pfam PfamFile PfamFull PfamSeed PhylipFile PileUpfile Platform Point PopupMenu PositionType Preferences PrivilegedAccessor Profile Profiles ProgressBar PromptUserConfig PropertyType ProteinType ProteinType.RecommendedName PurinePyrimidineColourScheme PymolCommands PymolManager QuickSort QuickSort.DoubleComparator QuickSort.ExternalComparator QuickSort.FloatComparator QuickSort.IntComparator 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 SeqCanvas SeqCigar 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 Skip Skip2 Slider SliderPanel SparseCount SparseDoubleArray SparseIntArray SparseMatrix SparseShortArray SplashScreen SplashScreen.SplashImage SplitFrame Start StartRegionIterator StockholmFile StrPos StrandColourScheme StringBufferLike StringBufferWrap StringRule StringUtils StringWrap StrucConsensusThread StructureChooser StructureChooser.PDBEntryTableModel StructureCommand StructureCommandsBase StructureFile StructureFrequency StructureImportSettings StructureMapping StructureSelectionManager StructureViewer StructureViewerBase StructureViewerModel StructureViewerModel.StructureData SubMark TCoffeeColourScheme TCoffeeScoreFile TCoffeeScoreFile.Block TCoffeeScoreFile.Header TaylorColourScheme TreeCanvas TreeModel TreePanel TreePanel.TreeLoader TrimRegionCommand TurnColourScheme Uniprot Uniprot UrlConstants UrlDownloadClient UrlLink UrlLinkDisplay UrlLinkTableModel UrlProvider UrlProviderImpl UserColourScheme VAMSAS VCFLoader VCFLoader.VCFMap VCFReader ViewSelectionMenu ViewStyle ViewportProperties ViewportRanges VisibleContigsIterator VisibleRowsIterator WS1Client WSClient WUSSParseException WsParamSetManager Xfam XrefType Yylex Yytoken ZappoColourScheme oneChar parsePerl patInf patInt