All Classes

AboutBox AbstractController AbstractFrame AbstractPainter AbstractPainter AbstractRateMatrix AbstractTreeLayout AbstractTreeLayout ActionPanel AddRemovePanel AdvancedTableUI Align AlignCommand Aligner Alignment AlignmentExporter AlignmentImporter AlignmentTreeBuilderFactory AlignmentTreeBuilderFactory.Result AminoAcidModel AminoAcids AminoAcidScores AminoAcidState Application Arguments Arguments.ArgumentException Arguments.IntegerArrayOption Arguments.IntegerOption Arguments.Option Arguments.RealArrayOption Arguments.RealOption Arguments.StringOption Attributable Attributable.Utils AttributableDecorator AttributableHelper AttributeBranchDecorator AuxilaryFrame BartonSternberg BasicAlignment BasicControlPalette BasicControlPalette BasicControlPalette.DisplayMode BasicControlPalette.DisplayMode BasicDistanceMatrix BasicLabelPainter BasicLabelPainter BasicLabelPainter.PainterIntent BasicLabelPainter.PainterIntent BasicSequence Binomial Blosum45 Blosum50 Blosum55 Blosum60 Blosum62 Blosum65 Blosum70 Blosum75 Blosum80 Blosum85 Blosum90 BootrappedAlignment BranchDecorator BrowserLauncher ByteBuilder CataclysmicDemographic Character CharacterType CladeSystem ClusteringTreeBuilder Coalescent CoalescentIntervalGenerator Codons CodonState ColorEditor ColorRenderer Command CompactRootedTree CompassLayout CompositeProgressListener ConsensusSequence ConsensusTreeBuilder ConsensusTreeBuilder.Method ConsoleApplication ConsoleFrame ConsoleMenuBarFactory ConstantPopulation ConstExponential ConstLogistic ContinuousCharacter ContinuousColorDecorator Controller ControllerListener ControlPalette ControlPalette ControlPaletteListener ControlPaletteListener Controls ControlsProvider ControlsSettings Decorator DefaultEditMenuFactory DefaultFileMenuFactory DefaultHelpMenuFactory DefaultMenuBarFactory DemoApplication DemoFrame DemographicFunction DemographicFunction.Utils DemoMenuBarFactory DemoMenuFactory DemoMenuHandler DisclosureButton DisclosureListener DisclosurePanel DiscreteCharacter DiscreteColorDecorator DistanceMatrix DistanceMatrixImporter DistanceMatrixImporter.Triangle DocumentFrame DocumentFrameFactory Edge Expansion ExponentialGrowth Exportable F84DistanceMatrix FastaExporter FastaImporter FilteredRootedTree FilteredSequence FitchParsimony FixedBitSet GammaFunction GaplessSequence GenericToolbarItem GeneticCode Graph Graph.NoEdgeException Graph.Utils GreedyRootedConsensusTreeBuilder GreedyUnrootedConsensusTreeBuilder Hamming HeaderRenderer HKYDistanceMatrix HTMLViewer IconUtils ImmediateSequenceImporter ImmediateSequenceImporter.Callback ImportException ImportException.BadFormatException ImportException.DuplicateFieldException ImportException.DuplicateTaxaException ImportException.MissingFieldException ImportException.ShortSequenceException ImportException.TooFewTaxaException ImportException.UnknownTaxonException ImportException.UnparsableDataException ImportHelper IntervalGenerator IntervalList IntervalList.IntervalType IntervalList.Utils Intervals JackknifedAlignment JExceptionDialog JukesCantor JukesCantorDistanceMatrix JVerticalLabel LabelPainter LabelPainterController ListItemView LogisticGrowth LongTask LongTaskMonitor MacFileMenuFactory MacHelpMenuFactory MachineAccuracy MacWindowMenuFactory MatrixCalc MatrixCalcException MatrixCalcException.NotSquareMatrixException MatrixCalcException.PositiveDefiniteException MatrixExponential MaximalSegmentPair MEGAExporter MenuBarFactory MenuFactory MinimiserMonitor MinimiserMonitor.Utils MissingTaxonException MLContinuousCharacterReconstructor ModelBasedDistanceMatrix MRCACConsensusTreeBuilder MultiDocApplication MultiDocMenuBarFactory MultipleAligner MultipleTreeViewer MultipleTreeViewer MultipleTreeViewerController MultivariateFunction MultivariateMinimum MultivariateMinimum.Factory MutableRootedTree NeedlemanWunsch NeedlemanWunschAffine NeedlemanWunschLinearSpace NeedlemanWunschLinearSpaceAffine NeighborJoiningTreeBuilder NewickExporter NewickImporter NexusExporter NexusImporter NexusImporter.MissingBlockException NexusImporter.NexusBlock Node NodeBarController NodeBarPainter NodePainter NodeShapeController NodeShapeController.NodePainterType NodeShapePainter NodeShapePainter.NodeShape NonOverlapMultipleLocalAffine Nucleotides NucleotideScores NucleotideState NumberFormatter NumericalDerivative OldNeedlemanWunschAffine OptionsPanel OrderEnumerator OrderEnumerator.OEFactory OrderEnumerator.Utils OrthogonalHints OrthogonalHints.Utils OrthogonalLineFunction OrthogonalSearch OrthogonalSearch.RoundOptimiser OSXAdapter Output OverlapAlign Painter Painter Painter.Justification Painter.Justification Painter.Orientation Painter.Orientation PainterListener PainterListener PairwiseAligner PairwiseAligner.Result Pam100 Pam110 Pam120 Pam130 Pam140 Pam150 Pam160 Pam170 Pam180 Pam190 Pam200 Pam210 Pam220 Pam230 Pam240 Pam250 ParsimonyCriterion Pattern Patterns PHYLIPExporter PhylipSequentialImporter PinnedButton PolarTreeLayout PolarTreeLayout PolarTreeLayout.TaxonLabelPosition PolarTreeLayout.TipLabelPosition PolarTreeLayoutController PreferencesDialog PreferencesSection PrintUtilities ProfileCharacter ProgressListener RadialTreeLayout RadialTreeLayout RadialTreeLayoutController Random RateMatrix RealNumberCellEditor RealNumberField RecentFileList RectilinearTreeLayout RectilinearTreeLayout RectilinearTreeLayoutController ResampledAlignment RootedFromUnrooted RootedTree RootedTreeComponent RootedTreeComponent.Listener RootedTreePainter RootedTreeUtils RuleModel RulesPanel RulesPanel.Rule ScaleBarPainter ScaleBarPainter ScaleBarPainterController ScoreMatrix Scores ScoresFactory SearchPanel SearchPanelListener Sequence SequenceAlignmentsDistanceMatrix SequenceExporter SequenceImporter Sequences SequenceShuffler SequenceStateException SequenceTester SequenceType SequenceType.Utils SimpleLinkListener SimpleListener SimpleListenerManager SimpleLongTask SimpleRootedTree SimpleTree SingleDocApplication SingleDocMenuBarFactory SmithWaterman SmithWatermanLinearSpace SmithWatermanLinearSpaceAffine SortedRootedTree SortedRootedTree.BranchOrdering SplitSystem SplitUtils SquareTreePainter State StateClassification StateClassification.Default StatusBar StatusListener StatusPanel StatusProvider StatusProvider.Helper SubstScoreMatrix SwingWorker TabDelimitedImporter TableRenderer TamuraNeiDistanceMatrix TaskListener Taxon TaxonDecorator TaxonomicLevel Toolbar ToolbarAction ToolbarButton ToolbarItem ToolbarOptions Traceback TracebackPlotter TransformedRootedTree TransformedRootedTree.Transform TranslatedSequence Tree TreeAppearanceController TreeBuilder TreeBuilderFactory TreeBuilderFactory.ConsensusMethod TreeBuilderFactory.DistanceModel TreeBuilderFactory.Method TreeExporter TreeImporter TreeLayout TreeLayout TreeLayout.AxisType TreeLayout.AxisType TreeLayoutListener TreeLayoutListener TreePane TreePane TreePaneController TreePaneListener TreePaneRuler TreePaneRuler TreePaneSelector TreePaneSelector TreePaneSelector.DragMode TreePaneSelector.DragMode TreePaneSelector.SelectionMode TreePaneSelector.SelectionMode TreeSelectionListener TreeSelectionListener TreeSimulator TreeViewer TreeViewer TreeViewer.SearchType TreeViewer.SearchType TreeViewer.TreeLayoutType TreeViewerController TreeViewerController.TreeLayoutType TreeViewerListener TreeViewerPanel UnivariateFunction UnivariateMinimum Utils Utils Utils Utils Utils Utils Utils WAG WholeNumberCellEditor WholeNumberField