A3mFile AAConClient AAFrequency AAStructureBindingModel AAStructureBindingModel.SuperposeData AMSAFile APQHandlers ASequenceFetcher AWSThread AWsJob AbstractWebServiceDiscoverer AlignAnalysisUIText AlignCalcManager2 AlignCalcManager2.SimpleWorkerManager AlignCalcManager2.WorkerManager AlignCalcWorker AlignExportOptions AlignExportSettingsAdapter AlignFile AlignFrame AlignSeq AlignViewController AlignViewport AlignedCodon AlignedCodonFrame AlignedCodonFrame.SequenceToSequenceMapping Alignment Alignment AlignmentAction AlignmentAction.Builder AlignmentAnnotation AlignmentAnnotation.AnnotCharSequence AlignmentAnnotationPojo AlignmentAnnotationUtils AlignmentDimension AlignmentExportData AlignmentGenerator AlignmentJob AlignmentOrder AlignmentPanel AlignmentPojo AlignmentResult AlignmentSorter AlignmentTask AlignmentUtils AlignmentView AlignmentView.ScGroup AlignmentViewport AllColsCollection AllColsIterator AllRowsCollection AllRowsIterator AlphaFoldAnnotationRowBuilder Annotation Annotation AnnotationAction AnnotationAction.Builder AnnotationChooser AnnotationColourGradient AnnotationColourScheme AnnotationColumnChooser AnnotationColumnChooser.FurtherActionPanel AnnotationColumnChooser.SearchPanel AnnotationColumnChooser.StructureFilterPanel AnnotationDisplaySettingPojo AnnotationElement AnnotationExporter AnnotationFile AnnotationFile AnnotationFile.ViewDef AnnotationFilterParameter AnnotationJob AnnotationLabels AnnotationPanel AnnotationPojo AnnotationRenderer AnnotationRendererFactory AnnotationRowBuilder AnnotationRowFilter AnnotationSorter AnnotationSorter.SequenceAnnotationOrder AnnotationWorker AnnotationsMatcher Any AppCache AppJmol AppJmol.RenderPanel AppJmolBinding AppVarna AppletFormatAdapter AppletUrlProviderFactory ApplicationSingletonProvider Arg Arg.Opt Arg.Type ArgParser ArgParserUtils ArgValue ArgValues ArgValuesMap ArgsParser ArrayUtils AssociatePdbFileWithSeq Atom AtomSpec AtomSpecModel AverageDistanceEngine BLCFile BSMLFile BackupFilenameFilter BackupFilenameParts BackupFiles BackupFilesPresetEntry BaseAction BaseAction.Builder BaseJob BaseTask BinaryNode BioJSReleasePojo BioJSRepositoryPojo BioJsHTMLOutput BitmapImageSizing BlogReader BlogReader.LaunchJvBrowserOnItem BlossomColourScheme Blosum62ColourScheme Bond BooleanOption BooleanOption.Builder 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 ComboBoxTooltipRenderer 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 Credentials CrossRef CrossRefAction CustomUrlProvider DBRefEntry DBRefSource DBRefUtils DataSourceType DbReferenceType DbSourceProxyImpl DelegateJobEventListener Desktop Desktop.MyDesktopManager Desktop.MyDesktopPane DesktopUrlProviderFactory DigestUtils Discoverer Dna DnaUtils DotMulti DoubleMatrix DoubleParameter DoubleParameter.Builder 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 GPreferences GPreferences.RadioButtonEditor GPreferences.RadioButtonRenderer GSliderPanel GSplitFrame GStructureChooser GStructureChooser.AssociateSeqOptions GStructureChooser.AssociateSeqPanel GStructureChooser.CustomComboSeparatorsRenderer GStructureViewer GTreePanel GWsPreferences GenBankFile GeneLocus GeneticCodes GetMemory Gff2Helper Gff3Helper GffHelperBase GffHelperFactory GraphLine GroupSet GroupSetHolder Grouping HMMFile HMMMatchScoreColourScheme HMMMatchScoreColourScheme.MatchProbReader HMMNode HTMLOutput HelixColourScheme Help.HelpId HiDPISetting HiddenColumns HiddenColumnsCursor HiddenCursorPosition HiddenMarkovModel HiddenSequences HmmerColourScheme HmmerCommand HmmerGlobalBackground HmmerJSONProcessor HmmerLocalBackground HtmlSvgOutput HtsContigDb HttpUtils HydrophobicColourScheme IdCanvas IdColourScheme IdOrgSettings IdPanel IdentifiersUrlProvider IdentifyFile IdwidthAdjuster ImageExporter ImageMaker ImageMaker.TYPE InformationThread InputType IntKeyStringValueEntry IntRangeComparator IntegerParameter IntegerParameter.Builder InterProScanHelper ItemsRenderer JLogger JLoggerLog4j JPred4WSClient JPred4WSDiscoverer JPredClient JPredFile JSONArray JSONArray JSONFile JSONObject JSONObject JSONObject.Null JSONParser JSONTokener JSONUtils JSONValue JabaParamStore JabaPreset JabaWsServerQuery Jalview Jalview2XML Jalview2XML.JvAnnotRow Jalview2XML.forwardRef Jalview2xmlBase JalviewAppender JalviewBooleanRadioButtons 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.Tree.TreeColorMap JalviewModel.Tree.TreeColorMap.ColorEntry JalviewModel.Viewport JalviewModel.Viewport.HiddenColumns JalviewModel.Viewport.Overview JalviewTaskbar JalviewUserColours JalviewUserColours.Colour JalviewUserColours.Filter JmolCommands JmolParser JnetAnnotationMaker JobDispatcherWSDiscoverer JobStateSummary JobStatus JustifyLeftOrRightCommand JvCacheableInputBox JvOptionPane JvSwingUtils Jws2Client Jws2ClientFactory 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 Matchers MathUtils Matrix MatrixType MemorySetting MessageManager MiscMath ModellerDescription MsaWSClient MsaWSClient Multi Multi_stage2 NJTree NewickFile NoValueColour NucleotideAmbiguityColourScheme NucleotideColourScheme NullPattern OOMWarning ObjectFactory OceanColourScheme Option Option.Builder 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 ParamStores ParseHtmlBodyAndLinks ParseProperties Pattern PcaDataType Pdb Pdbentry Pdbentry.Property Pfam PfamFile PfamFull PfamSeed PhmmerAction PhmmerAction.Builder PhmmerWSClient PhylipFile PileUpfile Platform Platform.PlatformDependentValue Plausible Point PollingTaskExecutor PollingTaskExecutor.TaskRunnable PopupMenu PositionType Preferences Preferences.OptionsParam PreferredServiceRegistry PrivilegedAccessor Profile Profiles ProgressBar ProgressPanel PromptUserConfig Property 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 RemoveGapsCommand 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 ScopeFunctions ScoreColourScheme ScoreMatrix ScoreMatrixFile ScoreModels SearchResults SearchResults.Match SecStrConsensus.SimpleBP SecStructPredAction SecStructPredAction.Builder SecStructPredMsaTask SecStructPredMsaTask.SecStructPredJob SecStructPredPDBSearchTask SecStructPredPDBSearchTask.SecStructPredJob SecondaryStructureConsensusThread SecondaryStructureCount SecondaryStructureCount.SymbolCounts SecondaryStructureDistanceModel SeqCanvas SeqCigar SeqDistanceContactMatrix SeqGroupIndexVector SeqPanel SeqPanel.MousePos SeqSearchWSClient SeqsetUtils SeqsetUtils.SequenceInfo Sequence Sequence Sequence.DBModList Sequence.DBRef SequenceAnnotationReport SequenceAnnotationWSClient SequenceCursor SequenceDummy SequenceFeature SequenceFeatures SequenceFeaturesPojo SequenceFetcher SequenceFetcher SequenceGroup SequenceGrpPojo SequenceIdMatcher SequenceIdMatcher.SeqIdName SequenceNode SequenceOntology SequenceOntologyFactory SequenceOntologyLite SequencePoint SequencePojo SequenceRenderer SequenceSet SequenceSet.SequenceSetProperties SequenceStringMatcher SequenceStructureBindingModel SequenceType SequenceType ServiceHandle ServiceInputInvalidException ServiceWithParameters SetUtils Sha256 ShiftList ShmmrRSBSService ShmrRestClient SiftsClient SiftsClient.CoordinateSys SiftsSettings SimilarityParams SimilarityScoreModel SimpleParamDatastore Skip Skip2 Slider SliderPanel SlivkaAlignmentWSClient SlivkaAnnotationWSClient SlivkaParamStoreFactory SlivkaPreferences SlivkaWSClient SlivkaWSDiscoverer SparseCount SparseDoubleArray SparseIntArray SparseMatrix SparseShortArray SplashScreen SplashScreen.SplashImage SplitFrame Start StartRegionIterator StockholmFile StrPos StrandColourScheme StringBufferLike StringBufferWrap StringParameter StringParameter.Builder StringRule StringUtils StringWrap StrucConsensusThread StructureChooser StructureChooser.PDBEntryTableModel StructureChooserQuerySource StructureCommand StructureCommandsBase StructureFile StructureFrequency StructureImportSettings StructureImportSettings.TFType StructureLine StructureMapping StructureSelectionManager StructureViewer StructureViewer.ViewerType StructureViewerBase StructureViewerModel StructureViewerModel.StructureData StructuresFile SubMark SubVals SunsetColourScheme SwingJSUtils.StateHelper TCoffeeColourScheme TCoffeeScoreFile TCoffeeScoreFile.Block TCoffeeScoreFile.Header TDBResultAnalyser TDB_FTSData TDBeaconsFTSPanel TDBeaconsFTSRestClient TaskEventSupport TaylorColourScheme ThreeDBStructureChooserQuerySource TreeBuilder TreeCanvas TreeEngine TreeModel TreePanel TreePanel.TreeLoader TrimRegionCommand TurnColourScheme UIinfo 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 WebService WebService.Builder WebServiceJobHandle WebServicesMenuManager WebServicesMenuManager.InteractiveServiceEntryGroup WsParamSetManager WsPreferences WsPreferences.JabaWSStatusRenderer WsPreferences.WsUrlTableModel Xfam XrefType Yylex Yytoken ZappoColourScheme oneChar parsePerl patInf patInt