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 AnnotationChooser AnnotationColourGradient AnnotationColumnChooser AnnotationColumnChooser.FurtherActionPanel AnnotationColumnChooser.SearchPanel AnnotationColumnChooser.StructureFilterPanel AnnotationDisplaySettingPojo AnnotationElement AnnotationFile AnnotationFile AnnotationFilterParameter AnnotationLabels AnnotationPanel AnnotationPojo AnnotationRenderer AnnotationRendererFactory AnnotationRowBuilder AnnotationRowFilter AnnotationSorter AnnotationSorter.SequenceAnnotationOrder 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 ChannelProperties ChimeraCommands ChimeraXCommands CigarArray CigarBase ClustalFile ClustalxColourScheme ClustalxColourScheme.ClustalColour ClustalxColourScheme.ConsensusColour CodingUtils CodonComparator ColorUtils ColourMenuHelper ColourSchemeMapper ColourSchemeProperty ColourSchemes ColumnSelection ColumnSelection.IntList Commands Comparison ComplementConsensusThread Condition Consensus ConsensusThread Conservation ConservationThread Console Console Constants ContactListImpl ContactMapHolder ContainerHelpers CrossRef CustomUrlProvider DBRefEntry DBRefSource DBRefUtils DataSourceType DbReferenceType DbSourceProxyImpl Desktop Desktop.MyDesktopManager Desktop.MyDesktopPane DesktopUrlProviderFactory Discoverer Dna DnaUtils DotMulti EBIAlfaFold EBIFetchClient EMBLLikeFlatFile 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 ErrorLog EvidencedStringType FTSDataColumnPreferences FTSDataColumnPreferences.FTSDataColumnPrefsTableModel FTSRestClient FTSRestRequest FTSRestResponse FastBracket FastChar FastMulti FastaFile Feature 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 FeatureStore FeatureType FeaturesDisplayed FileFormat FileFormatException FileFormats FileLoader FileParse FileUtils FilterBy FilterOption Finder FloatContactMatrix FlowerColourScheme FollowerColourScheme Format FormatAdapter GAlignFrame GAlignmentPanel GDesktop GFTSPanel GFTSPanel.DeferredTextInputListener GPairwiseAlignPanel GSliderPanel GSplitFrame GStructureChooser GStructureChooser.AssociateSeqOptions GStructureChooser.AssociateSeqPanel GStructureChooser.CustomComboSeparatorsRenderer GStructureViewer GenBankFile GeneLocus GeneticCodes GetMemory GraphLine GroupSet GroupSetHolder Grouping HelixColourScheme Help.HelpId HiDPISetting HiddenColumns HiddenColumnsCursor HiddenCursorPosition HiddenSequences HtsContigDb HttpUtils HydrophobicColourScheme IdCanvas IdColourScheme IdOrgSettings IdPanel IdentifiersUrlProvider IdentifyFile IdwidthAdjuster ImageExporter ImageMaker ImageMaker.TYPE InputType IntKeyStringValueEntry IntRangeComparator ItemsRenderer JLogger JLoggerLog4j JPredClient JSONArray JSONArray JSONFile JSONObject JSONObject JSONObject.Null JSONParser JSONUtils JSONValue JabaParamStore JabaPreset JabaWsServerQuery Jalview Jalview2XML Jalview2XML.JvAnnotRow 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.Viewport 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 MapUtils MappableContactMatrix MappedFeatures Mapping Mapping Mapping.AlignedCodonIterator MappingType MappingUtils Matcher MathUtils Matrix MemorySetting MessageManager MiscMath ModellerDescription MsaWSClient MsaWSClient Multi Multi_stage2 NewickFile NoValueColour NucleotideAmbiguityColourScheme NucleotideColourScheme NullPattern ObjectFactory OceanColourScheme Or OrMark OverviewCanvas OverviewDimensions OverviewDimensionsHideHidden OverviewDimensionsShowHidden OverviewPanel OverviewRenderer OverviewResColourFinder PA PAEContactMatrix PDBChain PDBEntry PDBEntry.Type PDBEntryUtils PDBFTSPanel PDBFTSRestClient PDBFeatureSettings PDBStructureChooserQuerySource PDBfile PIDColourScheme PIDModel PIRFile PaintRefresher PairwiseAlignPanel ParseHtmlBodyAndLinks Pattern Pdb Pdbentry Pdbentry.Property Pfam PfamFile PfamFull PfamSeed PhylipFile PileUpfile Platform 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 Regex RemoveGapColCommand ReplaceRule Replacer Residue ResidueColourFinder ResidueColourScheme ResidueCount ResidueCount.SymbolCounts ResidueProperties ResidueShader RestClient RestJob RestJobThread RestServiceDescription ReverseListIterator Rfam RfamFull RfamSeed Rna RnamlFile Rthings SFSortByEnd ScalePanel ScaleRenderer ScaleRenderer.ScaleMark ScoreColourScheme ScoreMatrix ScoreMatrixFile ScoreModels SearchResults SearchResults.Match SecStrConsensus.SimpleBP SecondaryStructureConsensusThread SecondaryStructureCount SecondaryStructureCount.SymbolCounts 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 SequencePojo SequenceRenderer SequenceSet SequenceStructureBindingModel SequenceType SequenceType ServiceHandle SetUtils ShiftList ShmmrRSBSService ShortcutKeyMaskExWrapper ShortcutKeyMaskExWrapper11 SiftsClient SiftsClient.CoordinateSys SiftsSettings Skip Skip2 Slider SliderPanel SparseCount SparseIntArray SparseShortArray SplashScreen SplashScreen.SplashImage SplitFrame Start StartRegionIterator StockholmFile StrPos StrandColourScheme StringBufferLike StringBufferWrap StringRule StringUtils StringWrap StructureChooser StructureChooser.PDBEntryTableModel StructureChooserQuerySource StructureCommand StructureCommandsBase StructureFile StructureImportSettings StructureImportSettings.TFType StructureMapping StructureSelectionManager StructureViewer StructureViewerBase SubMark SubVals SunsetColourScheme TCoffeeColourScheme TCoffeeScoreFile TCoffeeScoreFile.Block TCoffeeScoreFile.Header TDBResultAnalyser TDB_FTSData TDBeaconsFTSPanel TDBeaconsFTSRestClient TaylorColourScheme ThreeDBStructureChooserQuerySource TreeEngine TreeModel TrimRegionCommand TurnColourScheme Uniprot Uniprot UrlConstants UrlDownloadClient UrlLink UrlLinkDisplay UrlLinkTableModel UrlProvider UrlProviderImpl UserAgent UserColourScheme UserQuestionnaireCheck VAMSAS VCFReader ViewSelectionMenu ViewStyle ViewportProperties ViewportRanges VisibleColsCollection VisibleContigsIterator VisibleRowsCollection VisibleRowsIterator WS1Client WSClient WUSSParseException WsParamSetManager Xfam XrefType Yylex Yytoken ZappoColourScheme oneChar parsePerl patInf patInt