AAConClient AAFrequency AAStructureBindingModel AAStructureBindingModel.SuperposeData AMSAFile ASequenceFetcher AWSThread AWsJob AlignAnalysisUIText AlignCalcManager AlignCalcWorker AlignExportSettingsAdapter AlignFile AlignFrame AlignSeq AlignViewController AlignViewport AlignedCodon AlignedCodonFrame AlignedCodonFrame.SequenceToSequenceMapping Alignment Alignment AlignmentAnnotation AlignmentAnnotation.AnnotCharSequence AlignmentAnnotationPojo AlignmentAnnotationUtils AlignmentGenerator AlignmentOrder AlignmentPanel AlignmentPojo AlignmentSorter AlignmentUtils AlignmentUtils.DnaVariant AlignmentView AlignmentView.ScGroup AlignmentViewport AllColsIterator AllRowsIterator Annotation Annotation AnnotationChooser AnnotationColourGradient AnnotationColourScheme AnnotationColourSchemeDescriptor AnnotationColours AnnotationColoursDescriptor AnnotationColumnChooser AnnotationColumnChooser.FurtherActionPanel AnnotationColumnChooser.SearchPanel AnnotationColumnChooser.StructureFilterPanel AnnotationDescriptor AnnotationDisplaySettingPojo AnnotationElement AnnotationElementDescriptor AnnotationFile AnnotationFile AnnotationFile.ViewDef AnnotationFilterParameter AnnotationLabels AnnotationPanel AnnotationPojo AnnotationRenderer AnnotationRowFilter AnnotationSorter AnnotationSorter.SequenceAnnotationOrder AnnotationWorker AppCache AppJmol AppJmol.RenderPanel AppJmolBinding AppVarna AppletFormatAdapter AppletUrlProviderFactory ArgsParser ArrayUtils Atom AtomSpec AtomSpecModel BLCFile BinaryNode BioJSReleasePojo BioJSRepositoryPojo BioJsHTMLOutput BlogReader BlogReader.LaunchJvBrowserOnItem Blosum62ColourScheme Bond BuildDetails BuriedColourScheme Cache CaseInsensitiveString ChimeraCommands ChimeraConnect ChimeraManager CigarArray CigarBase ClustalFile ClustalxColourScheme ClustalxColourScheme.ClustalColour ClustalxColourScheme.ConsensusColour CodingUtils CodonComparator ColorUtils Colour ColourDescriptor ColourMenuHelper ColourSchemeMapper ColourSchemeProperty ColourSchemes ColourThreshTypeType ColumnSelection ColumnSelection.IntList CommandLineOperations CommandLineOperations.Worker Comparison ComplementConsensusThread CompoundMatcher CompoundMatcherDescriptor Condition Consensus ConsensusThread Conservation ConservationThread Console ContainerHelpers CrossRef CustomUrlProvider DBRef DBRefDescriptor DBRefEntry DBRefSource DBRefUtils DbSourceProxyImpl Desktop Desktop.MyDesktopManager Desktop.MyDesktopPane DesktopUrlProviderFactory DialogRunner Discoverer Dna DnaUtils EBIFetchClient EditCommand EditCommand.Edit EmblCdsSource EmblEntry EmblFeature EmblFile EmblSequence EmblSource EmblTestHelper EmblXmlSource EnsemblCdna EnsemblCds EnsemblData EnsemblGene EnsemblGenome EnsemblGenomes EnsemblProtein EnsemblRestClient EnsemblSeqProxy EnsemblSequenceFetcher EnsemblXref EntityType Entry Entry.Entity Entry.Entity.Segment Entry.Entity.Segment.ListResidue Entry.Entity.Segment.ListResidue.Residue Entry.Entity.Segment.ListResidue.Residue.CrossRefDb ExonerateHelper FTSDataColumnPreferences FTSDataColumnPreferences.FTSDataColumnPrefsTableModel FTSRestClient FTSRestRequest FastaFile Feature FeatureAttributes FeatureAttributes.AttributeData FeatureColour FeatureColourFinder FeatureDescriptor FeatureDistanceModel FeatureMatcher FeatureMatcher FeatureMatcherByType FeatureMatcherDescriptor FeatureMatcherSet FeatureMatcherSet FeatureMatcherSetDescriptor FeatureRenderer FeatureRenderer FeatureRendererModel FeatureRendererModel.FeatureSettingsBean FeatureRendererSettings FeatureSettings FeatureSettings FeatureSettings.ColorEditor FeatureSettings.ColorRenderer FeatureSettings.FeatureTableModel FeatureSettings.FilterEditor FeatureSettings.FilterRenderer FeatureSettingsAdapter FeatureSettingsDescriptor FeatureSource FeatureSources FeatureStore FeatureStore.SearchCriterion Features FeaturesDescriptor FeaturesDisplayed FeaturesFile FileFormat FileFormatException FileFormats FileLoader FileParse Filter FilterDescriptor Finder FollowerColourScheme Format FormatAdapter GAlignFrame GAlignmentPanel GDesktop GFTSPanel GFTSPanel.DeferredTextInputListener GPairwiseAlignPanel GSliderPanel GStructureChooser GStructureChooser.AssociateSeqPanel GStructureChooser.CustomComboSeparatorsRenderer GStructureChooser.FilterOption GStructureViewer GTreePanel Gff2Helper Gff3Helper GffHelperBase GffHelperFactory GraphLine Group GroupDescriptor Grouping HTMLOutput HelixColourScheme Help.HelpId HiddenColumns HiddenColumns HiddenColumnsCursor HiddenColumnsDescriptor HiddenCursorPosition HiddenSequences HtsContigDb HydrophobicColourScheme IdCanvas IdOrgSettings IdPanel IdentifiersUrlProvider IdentifyFile IdwidthAdjuster InputType IntRangeComparator InterProScanHelper ItemsRenderer JGroup JGroupDescriptor JPredClient JSONFile JSeq JSeqDescriptor JabaParamStore JabaPreset JabaWsServerQuery Jalview Jalview2XML Jalview2XML.JvAnnotRow Jalview2xmlBase JalviewAppender JalviewChangeSupport JalviewColourScheme JalviewDialog JalviewFileChooser JalviewFileChooser.RecentlyOpened JalviewFileFilter JalviewFileView JalviewJmolBinding JalviewLite JalviewModel JalviewModelDescriptor JalviewModelSequence JalviewModelSequenceDescriptor JalviewUserColours JalviewUserColoursDescriptor JmolCommands JmolParser JobStateSummary JvCacheableInputBox JvOptionPane JvSwingUtils Jws2Client Jws2Discoverer Jws2Instance Jws2InstanceFactory Jws2ParamView LinkedIdentityHashSet LinkedIdentityHashSet.IdentityWrapper MSFfile MapList Mapping Mapping Mapping.AlignedCodonIterator MappingType MappingUtils MatchCondition MatchConditionDescriptor Matcher MatcherSet MatcherSetDescriptor MathUtils Matrix MessageManager ModellerDescription MsaWSClient MsaWSClient NCList NCNode NewickFile NoValueColour NucleotideColourScheme OtherData OtherDataDescriptor OverviewDimensions OverviewDimensionsHideHidden OverviewDimensionsShowHidden OverviewResColourFinder PA PDBChain PDBEntry PDBEntry.Type PDBFTSPanel PDBFTSRestClient PDBFeatureSettings PDBfile PIDColourScheme PIDModel PIRFile PaintRefresher PairwiseAlignPanel ParseHtmlBodyAndLinks ParseProperties Pdb Pdbentry PdbentryDescriptor PdbentryItem PdbentryItemDescriptor Pdbids PdbidsDescriptor Pfam PfamFile PfamFull PfamSeed PhylipFile PileUpfile Platform PopupMenu Preferences PrivilegedAccessor Profile Profiles ProgressBar PromptUserConfig Property PropertyDescriptor PurinePyrimidineColourScheme Qualifier QuickSort QuickSort.DoubleComparator QuickSort.ExternalComparator QuickSort.FloatComparator QuickSort.IntComparator RNAHelicesColour RNAInteractionColourScheme RNAalifoldClient Range RangeComparator RangeElementsIterator RangeIterator Residue ResidueColourFinder ResidueColourScheme ResidueCount ResidueCount.SymbolCounts ResidueProperties ResidueShader Response RestClient RestJob RestJobThread RestServiceDescription ReverseListIterator Rfam RfamFull RfamSeed Rna RnamlFile RunResponse ScalePanel ScaleRenderer ScaleRenderer.ScaleMark ScoreColourScheme ScoreMatrix ScoreMatrixFile ScoreModels SearchResults SearchResults.Match SecStrConsensus.SimpleBP SeqCanvas SeqCigar SeqGroupIndexVector SeqPanel SeqSearchWSClient SeqsetUtils Sequence Sequence SequenceAnnotationReport SequenceAnnotationWSClient SequenceCursor SequenceDescriptor SequenceDummy SequenceFeature SequenceFeatures SequenceFeaturesPojo SequenceFetcher SequenceFetcher SequenceGroup SequenceGrpPojo SequenceIdMatcher SequenceIdMatcher.SeqIdName SequenceNode SequenceOntology SequenceOntologyFactory SequenceOntologyLite SequencePojo SequenceRenderer SequenceSet SequenceSetDescriptor SequenceSetProperties SequenceSetPropertiesDescriptor SequenceStructureBindingModel SequenceType SequenceTypeDescriptor ServiceHandle SetUtils Setting SettingDescriptor ShiftList ShmmrRSBSService SiftsClient SiftsClient.CoordinateSys SiftsClient.SiftsEntitySortPojo SiftsException SiftsSettings SimilarityParams SliderPanel SparseCount SparseDoubleArray SparseIntArray SparseMatrix SparseShortArray SplashScreen SplashScreen.SplashImage StartRegionIterator StockholmFile StrandColourScheme StringUtils StrucConsensusThread StructureChooser StructureChooser.PDBEntryTableModel StructureFile StructureFrequency StructureImportSettings StructureManager StructureMapping StructureMappingcommandSet StructureSelectionManager StructureState StructureStateDescriptor StructureViewer StructureViewerBase StructureViewerModel StructureViewerModel.StructureData TCoffeeColourScheme TCoffeeScoreFile TCoffeeScoreFile.Block TCoffeeScoreFile.Header TaylorColourScheme ThresholdLine ThresholdLineDescriptor Tree TreeCanvas TreeDescriptor TreeModel TreePanel TreePanel.TreeLoader TrimRegionCommand TurnColourScheme Uniprot UniprotEntry UniprotFeature UniprotFile UniprotProteinName UniprotSequence UrlConstants UrlDownloadClient UrlLink UrlLinkDisplay UrlLinkTableModel UrlProvider UrlProviderImpl UserColourScheme UserQuestionnaireCheck VAMSAS VAMSASDescriptor VCFLoader VCFLoader.VCFMap VCFReader VamsasModel VamsasModelDescriptor ViewSelectionMenu ViewStyle Viewport ViewportDescriptor ViewportProperties ViewportRanges VisibleContigsIterator VisibleRowsIterator WS1Client WSClient WUSSParseException WsParamSetManager Xfam ZappoColourScheme