All Classes

AAProperty Abortable AdjustableDistribution AdjustableTree AlertDialog AlignMatch AlignmentHelper AlignmentHelperLinearSpace AlignmentHelperQuadraticSpace AlignScoreForTaxonGen AlignTool AlignUtil Annotatable AnnotationsPanel AnnotPanelOwner aPCAOrdination Arguments Associable AssociableWithSpecs AssociationHistory AssociationsManager AssociationSource AsymmModel Attachable AttachedNote AttachedNotesVector Author BasicStatPak Binomial Bits BitsSpecsSet BlockFromTreeSource BlockMover BooleanForCharacter BooleanForItem BooleanForTaxon BooleanForTree BooleanForTreeIncr BooleanForTreeM BranchLengthsAlterer BranchLengthsAltererMult BrownianMotionModel BrowseHierarchy CardPanel CategColorTable CategDataAlterer CategDataEditorInit CategDataMatcher CategDataSearcher CategDataUtility CategInternodeEvent CategMatrixManager CategoricalAdjustable CategoricalData CategoricalDistribution CategoricalEmbedded CategoricalHistory CategoricalState CategoricalStates CategParsimonyModel CategProbModelCurator CategStateForCharacter CategTModel CategTModelEditWindow CellBlock CellColorer CentralModelListener ChangeAuthority ChangeEvent ChangeHistory CharacterData CharacterDistribution CharacterHistory CharacterLikelihood CharacterLoadings CharacterModel CharacterModelSource CharacterObedSource CharacterOneSource CharacterPartition CharactersBlock CharacterSelector CharactersGroup CharactersGroupVector CharacterSimulator CharactersManager CharacterSource CharacterState CharacterStates CharacterStatesHolder CharacterStateTest CharacterSteps CharacterSubmodel CharBitsSet CharHistoryContainer CharHistorySource CharInclSetListAsst CharInclusionSet CharListAssistant CharListAssistantI CharListModel CharListPartitionUtil CharMapper CharMatrixFiller CharMatrixManager CharMatrixObedSource CharMatrixOneSource CharMatrixSource CharModelCurator CharNumSet CharObjectSpecsSet CharRateMatrixModelSet CharRatesCodePos CharRatesCurator CharRatesEqual CharRatesGamma CharRatesGammaInvar CharRatesInvar CharRatesModel CharRatesModelInfo CharRatesModelSet CharSelectCoordinator CharSelectionSet CharSetListAsst CharsFromMatrixSource CharSort CharSourceCoord CharSourceCoordObed CharSpecsSet CharSpecsSetManager CharsStatesForNodes CharStatesForNodes CharSubmodelCurator CharTableAssistantI ChartAssistant ChartBkgdExtra Charter ChartExtra ChartField ChartListener ChartTool ChartWindow CharWeightSet ChecklistDialog CircleSymbol Clade Clades ClassVector CLikelihoodCalculator ClockPanel CLogger CModelEstimator CMTable CoalescedNode Coalescer CoalescerObed CodonPositionsSet Colorable ColorDialog ColorDistribution ColorEvent ColorEventVector ColorPickerPanel ColorRecord ColumnNamesPanel Commandable CommandableOwner CommandChecker CommandCommunicator CommandRecord CommandRecordHolder CommandThread CompatibilityChecker CompatibilityTest ComplexMatrix CompositProbCategModel Consenser ConsoleThread ConsoleWindow ContainedTreeSim ContColorTable ContDataAlterer ContDataSearcher ContDataUtility ContentArea Context ContinuousAdjustable ContinuousData ContinuousDistribution ContinuousEmbedded ContinuousHistory ContinuousState ContinuousStates ContinuousStateTest ContParsimonyModel CornerPanel CostMatrixModel CuratorWithSettings CVAOrdination DataAlterer DataAltererCon DataColumnNamesAssistant DataMatcher DataSearcher DataSetsListAssistant DatasetsListUtility DataSpecsListWindow DataSpecssetList DataUtility DataWindow DataWindowAssistant DataWindowAssistantA DataWindowAssistantI DataWindowMaker DataWSelectionAssistant Debugg DefaultReference DefaultsAssistant DEQNumSolver DESystem DetTreeModifier DialogGraphicsPanel DisplayCharsStsAtNodes DisplayNumbersAtNodes DisplayStatesAtNodes DistanceBetween2Trees DistanceMatrixExporterDialog DNACharacterAdjustable DNACharacterHistory DNAColorTable DNAData DNADataAlterer DNADataAltererCon DNADataSearcher DNADataUtility DNAEmbedded DNAState DNATaxaDistance DNATaxaDistFromMatrix DNATaxaDistFromMatrixFreq DolloModel Doomable Double2DArray DoubleArray DoubleClickList DoubleClickListener DoubleField DoubleMiniScroll DoubleSliderWindow DoubleSqMatrixFields DragRectangle DrawChart DrawNamesTaxaDisplay DrawNamesTreeDisplay DrawTaxa DrawTaxaCoordinator DrawTree DrawTreeCoordinator DrawTreeUtil EditingCurator EditorPanel EditorTextField EditRawNexusBlock EigenAnalysis ElementManager EmployeeNeed EmployeeTree EmployeeVector EmployerEmployee EnterButton EPCAOrdination Evaluator Explainable ExplanationArea ExponentialDistribution ExporterDialog ExtensibleDialog ExtensibleExplDialog ExtensibleListDialog FileAssistant FileAssistantC FileAssistantCH FileAssistantCP FileAssistantCS FileAssistantN FileAssistantT FileBlock FileCoordinator FileDirtier FileElement FileElementManager FileInit FileInitEarlyLoad FileInterpreter FileInterpreterI FileInterpreterITree FillableMesquiteSymbol FindSequenceCriterion FindSequenceCriterionG Fittable FunctionExplainable FunctionExplanation GenCodeBacteria GenCodeCiliate GenCodeEchino GenCodeEuplotid GenCodeInvertMito GenCodeModel GenCodeModelBacteria GenCodeModelCiliate GenCodeModelEchino GenCodeModelEuplotid GenCodeModelInvertMito GenCodeModelMoldProtMito GenCodeModelSet GenCodeModelSource GenCodeModelStandard GenCodeModelVertMito GenCodeModelYeastMito GenCodeMoldProtMito GenCodeStandard GenCodeVertMito GenCodeYeastMito GeneralFileMaker GeneticCode GeneTreeFit GeogDataSearcher GeogDataUtility GeographicAdjustable GeographicData GeographicState GeographicStates GeographicStateTest GeoTaxaDistance GeoTaxaDistFromMatrix GraphicsUtil GroupDialog GroupLabel HelpSearchManager HelpSearchStrip HistogramAssistantA HNode HorizontalLine HPanel HTMLDescribable HTMLSidePanel Hyperlink Identifiable Illustratable ImageLabel ImageOwner ImagePanel ImagePanelListener Incrementable IncTaxaDistanceSource InfoBar Integer2DArray IntegerArray IntegerField IntegerSqMatrixFields InterpretClustal InterpretFasta InterpretNBRF InterpretPhylip InterpretSimple IrreversibleModel ItemContainer ItemsBiplotter ItemsCharter ItemsSource JointLikeAncStForModel Journal LabelsAtNodes LeakFinder Legend LegendHolder LightLabel LightLabelsAtNodes LinearModel LinearValueToPixel Listable ListableVector ListableVectorWindow ListAssistant ListDialog Listenable Listened ListLVModule ListModule ListTable ListWindow LiveTreeBlocks Logger LogValueToPixel LogWindow Long2DArray LongArray LongField MAdjustableDistribution MaintainSequenceMatch MainThread ManageContCharsA ManageModelSet ManagerAssistant ManyTreesFromFileLib MargLikeAncStCLForModel MargLikeAncStForModel MargLikelihoodForModel MatrixCharter MatrixPanel MatrixSourceCoord MatrixSourceCoordObed MatrixUtil MCategoricalAdjustable MCategoricalDistribution MCategoricalEmbedded MCategoricalHistory MCategoricalStates MCharactersDistribution MCharactersHistory MCharactersStates MCharactersStatesHolder MContinuousAdjustable MContinuousDistribution MContinuousEmbedded MContinuousHistory MContinuousStates MDNAAdjustable MDNAEmbedded MDNAHistory MenuItemsSpecsVector MenuOwner Mesquite3DIntPoint MesquiteBoolean MesquiteButton MesquiteChart MesquiteCheckMenuItem MesquiteCMenuItemSpec MesquiteColorTable MesquiteCommand MesquiteCursor MesquiteDialog MesquiteDialogParent MesquiteDouble MesquiteDroppedFileHandler MesquiteEvent MesquiteException MesquiteFile MesquiteFileDialog MesquiteFrame MesquiteHTMLWindow MesquiteImage MesquiteInit MesquiteInteger MesquiteLabel MesquiteListener MesquiteListTable MesquiteListWindow MesquiteLong MesquiteMacro MesquiteMenu MesquiteMenuBar MesquiteMenuItem MesquiteMenuItemSpec MesquiteMenuSpec MesquiteMessage MesquiteModule MesquiteModuleInfo MesquiteNumber MesquitePackageRecord MesquitePanel MesquiteParameter MesquitePDFFile MesquitePopup MesquitePrintJob MesquiteProject MesquiteScrollbar MesquiteSequence MesquiteSet MesquiteString MesquiteSubmenu MesquiteSubmenuSpec MesquiteSymbol MesquiteTable MesquiteTextWindow MesquiteThread MesquiteTimer MesquiteTool MesquiteTree MesquiteTrunk MesquiteWindow MesquiteXMLPreferencesModule MesquiteXMLUtilities MessagePanel MGeographicStates MiniControl MiniNumberEditor MiniScroll MiniScrollButton MiniSlider MiniSliderWithText MiniStringEditor MkModel ModelCompatibilityInfo ModelSet ModelSetListAsst ModelsListAssistant ModelVector ModuleInfoWindow ModulesInfoVector MolecDataEditorInit MolecularData MolecularDataAlterer MolecularState MolecularTaxaDistance MousePanel MProteinAdjustable MProteinEmbedded MProteinHistory MRPopup MultipleProbabilityModel MultipleProbCategCharModel MultipleSequenceAligner NameReference NCBIUtil NexusBlock NexusBlockEditableRaw NexusBlockTest NexusCommandTest NexusFileInterpreter NexusWritable NForTaxonWithTree NForTaxonWithTrees NodeChooser NodeLocs NodeLocsCircle NodeLocsFree NodeLocsPlot NodeLocsPlot3D NodeLocsVH Notification Number2DArray NumberArray NumberFor2Characters NumberFor2CharAndTree NumberFor2Taxa NumberFor2TaxaIncr NumberFor2Trees NumberForCharacter NumberForCharacterIncr NumberForCharAndTaxon NumberForCharAndTree NumberForCharAndTreeM NumberForItem NumberForMatrix NumberForMatrixAndTree NumberForNode NumberForTaxon NumberForTaxonIncr NumberForTree NumberForTreeBlock NumberForTreeDivers NumberForTreeIncr NumberForTreeM NumberForTreeWContext NumbersForNodes NumbersForNodesAndChar NumbersForNodesAndHistory NumbersForNodesAndMatrix NumbersForNodesIncr NumbersForNodesWith2Char NumFor2CharHistAndTree NumForCharAndTreeDivers NumForCharHistAndTree NumForCharTreeDep NumForCharTreeIndep NumSpecsSet Object2DArray ObjectArray ObjectContainer ObjectSpecsSet OffersCategoricalData OffersDNAData OffersProteinData OneTreeSource Optimizer OrderedModel Ordination OrdinationAssistant Ordinator OwnedByModule PackageIntro PackageIntroInterface Pagel94Calculator PagelFormatI PagelMatrixModel PagNodeRecord PairMaker PairMakerChars PairsWindow PairwiseAligner PanelOfCards PanelsAtNodes ParametersDialog ParametersExplorable ParametersExplorer ParsAncStatesForModel Parser ParseUtil ParsimonyModel ParsimonyModelSet ParsModelSource PathHolder PatristicDistances PCACorrelOrdination PCAOrdination PendingCommand PhylipExporterDialog PopUpPanelOfCards Prioritizable Priority ProbabilityCategCharModel ProbabilityContCharModel ProbabilityDNAModel ProbabilityModel ProbabilityModelSet ProbModelSource ProbModelSourceLike ProbModelSourceSim ProbPhenCategCharModel ProbSubModel ProbSubModelCurator ProgressIndicator ProgressPanel ProgressWindow ProjectRead ProjectReadThread Projects PropertyNamesProvider ProteinAdjustable ProteinCharacterHistory ProteinColorTable ProteinData ProteinEmbedded ProteinState Puppeteer PuppetThread QueryDialogs RadioButtons RandomBetween RandomMatrixModifier RateMatrixCatModel RateMatrixCatModelInfo RateMatrixCurator RateMatrixDNAModel RateMatrixEqualDNAModel RateMatrixGTRModel RateMatrixTiTvModel ReadFileFromString ReconstructAssociation Renamable RequiresAnyCategoricalData RequiresAnyDNAData RequiresAnyMolecularData RequiresExactlyCategoricalData RequiresProteinData ResizableLegend RK4Solver RKF45Solver RNACharacterAdjustable RNACharacterHistory RNAData RNAState RndTreeModifier RotatedRectangle RowNamesPanel ScattergramAssistantA ScriptingManager ScrollTextField Selectionable SeqLedge ShellScriptUtil Short2DArray ShortArray Showable SimModelCompatInfo SimpleTaxaList SimulationDNAModel SingleLineTextArea SingleLineTextField SlicedCharacterHistory SliderWindow Snapshot SourceFromTreeSource SourceModifiedMatrix SourceModifiedTree SourceModRespectiveMatrix SpecialListName SpeciesTreeFit SpecsSet SpecsSetManager SpecsSetVector SquaredModel SquaredReconstructor StateFreqCurator StateFreqDNAEmpir StateFreqDNAEqual StateFreqDNAModel StateFreqDNASpecif StateFreqModel StateFreqModelSet StateFreqUserCurator StateFreqUserDNAModel StateFreqUserModel StoredCharacterHistory StringArray StringInABox StringIntegerDialog StringIntegerListDlog StringLister StringUtil SubmodelInfo SymbolGraphicsPanel SymbolsVector SystemUtil SystemWindow TableTool TableWindow Taxa TaxaAssociation TaxaBitsSet TaxaBlock TaxaBlocksListAssistant TaxaBlocksListUtility TaxaDisplay TaxaDisplayActive TaxaDisplayAssistant TaxaDisplayAssistantA TaxaDisplayAssistantAD TaxaDisplayAssistantD TaxaDisplayAssistantDI TaxaDisplayAssistantI TaxaDisplayAssistantMA TaxaDisplayBkgdExtra TaxaDisplayDrawnExtra TaxaDisplayExtra TaxaDistance TaxaDistanceSource TaxaDistFromMatrix TaxaDrawing TaxaGroup TaxaGroupVector TaxaInclusionSet TaxaListAssistantI TaxaManager TaxaPairer TaxaPairerChars TaxaPairing TaxaPartition TaxaPartitionSource TaxaPartListAssistant TaxaPath TaxaSelectCoordinator TaxaSelectionSet TaxaSetListAssistant TaxaSource TaxaSpecsListWindow TaxaSpecsSet TaxaSpecssetList TaxaStringsSet TaxaTableAssistantI TaxaTool TaxaTreeDisplay TaxaWindowAssistant TaxaWindowAssistantC TaxaWindowAssistantI TaxaWindowAssistantN TaxaWindowMaker Taxon TaxonListAssistant TaxonNameAlterer TaxonPair TaxonPairSource TaxonSelector TaxonSource TaxonUtility TDLegendWithColors TemplateManager TemplateRecord TextDisplayer TextRotator TextTree ThermoPanel ToolKeyListener ToolPalette TraceCharacterInit TranslationTable Tree TreeAlterer TreeAltererMult TreeBlockFiller TreeBlockListUtility TreeblocksListAssistant TreeBlockSource TreeCharSimulate TreeClusterer TreeContext TreeContextListener TreeDataModelBundle TreeDecorator TreeDisplay TreeDisplayActive TreeDisplayAssistant TreeDisplayAssistantA TreeDisplayAssistantAD TreeDisplayAssistantAO TreeDisplayAssistantD TreeDisplayAssistantDI TreeDisplayAssistantI TreeDisplayAssistantMA TreeDisplayBkgdExtra TreeDisplayDrawnExtra TreeDisplayExtra TreeDisplayLegend TreeDrawing TreeListAssistant TreeListUtility TreeReference Trees TreeSearcher TreeSimulate TreesManager TreeSource TreeSourceDefinite TreeSwapper TreeTool TreeTransformer TreeTransformerMult TreeUtility TreeVector TreeWindowAssistant TreeWindowAssistantA TreeWindowAssistantC TreeWindowAssistantI TreeWindowAssistantN TreeWindowMaker TWindowMaker TwoIntegersDialog TwoSequenceAligner TwoSequenceAlignerGaps TwoStringsDialog Undoer UndoInstructions UndoReference UnorderedModel UtilitiesAssistant ValueToPixel WholeCharacterModel WholeCharModelCurator WindowButton WindowHolder WithStringDetails wPCAOrdination ZipUtil