All Classes

ADatum ADatumController ADatumView AParamsDialog APhyloTool AResultsDialog BatchDatum BatchDatumController BatchDatumView BfsSearch BinaryMaxHeap BinaryMinHeap Bipartitions BitVector BitVectorTestCase BniNetNode BniNetwork Bootstrap BootstrapCmdLineTool BrowseButton CharnetClusterResultsDialog CharnetCmdLineTool CharnetParamsDialog CharnetResultsDialog CharnetTool CharnetTreeResultsDialog CharnetTripartitionResultsDialog Clustering ClusteringInference ClustersReader CmdLineTool CmpnetsCmdLineTool CmpnetsParamsDialog CmpnetsResultsDialog CmpnetsTool CoalescentCounter CoalescentCounterTestCase Collapse Collapse.CollapseDescriptor CollapseTestCase CommandLineApp CommandLineAppTestCase CompatCmdLineTool ConsensusTestCase Consolidate Consolidate.ConsolidateDescriptor CountCoalCmdLineTool CountCoalParamsDialog CountCoalResultsDialog CountCoalTool DataCriterion DatumThumbnailView DeepCoalCountCmdLineTool DeepCoalescencesCounter DemocraticVoteInference DfsSearch Dialogs DialogsTestCase Dijkstra DijkstraTestCase Edge EdgeListReader EventBootstrap ExMultipleMasts ExMultipleMastsTestCase ExNewickException ExNewickReader ExNewickReaderTestCase ExNewickWriter ExRiataMultipleHgtTestCase ExtendableComboBoxList ExtendableNodeSetsList FastaReader FastaReader.FastaRecord GaneshkumarWarnowMCT GaneshkumarWarnowMCTTestCase GenCplexCmdLineTool GeneTreeRefinement GenstCmdLineTool GLASSInference GlassMatrixSubpanel GlassTreeSubpanel Graph GraphComponent GraphListener GTDistributionInNetwork GTDistrInNetworkCmdLineTool GTRefineAndRootCmdLineTool HershbergerMaxelSuriKSSP HershbergerMaxelSuriKSSPTestCase HGTDatum HGTDatumController HGTDatumView HgtEvent HgtReader HgtScenario HungarianBipartiteMatcher HungarianTestCase IlpGenerator IlpGeneratorTestCase ImmutableCollection ImmutableCollectionWrapper ImmutableSet ImmutableSetWrapper InferenceMethod InferenceMethodParametersSubpanel InferStCmdLineTool InferSTParamsDialog InferStResultsDialog InferSTTool InvalidParameterException Iterating LcaCmdLineTool LCAParamsDialog LCAResultsDialog LCATool LIDAMath LineReader MajorityConsensusInference MajoritySubpanel MastCmdLineTool MASTParamsDialog MASTResultsDialog MastTool MastWrapper MastWrapperTestCase MaxClique MaxCliqueNonParameterizedTestCase MaxCliqueParameterizedTestCase MaxDoubleHeap MaxHeap MaxIntHeap MdcDpRootedTimeSubpanel MdcDpSubpanel MdcIlpSubpanel MdcIlpTimeSubpanel MDCInference_DP MDCInference_ILP MDCURInference MDCURInference_DP MDCURInference_ILP MDCWithTime MinFibonacciHeap MinFibonacciHeapTestCase MinHeap MutableEdge MutableGraph MutableNode MutableTree NeighborJoining NetNode NetNodes NetparsCmdLineTool NetparsParamsDialog NetparsResultsDialog NetparsTool Network NetworkCharacterizationMeasure NetworkCluster NetworkDatum NetworkDatumController NetworkDatumView NetworkEdge Networks NetworkTree NetworkTreeEnumerator NetworkTripartition NewickReader NewickReaderTestCase NewickViewer NewickWriter NJTestCase Node NodeListReader NoParametersSubpanel ParseException ParsimonyCalculator ParsimonyCalculatorTestCase Path PathImpl PAUPAvgMaxComparator PAUPAvgMinComparator PAUPIntersectionComparator PAUPParsDiffComparator PAUPWindowComparator PAUPWindowComparator.DistanceMeasure PhyloComboBox PhyloLogger PhyloNetApp PhyloNetAppController PhyloNetAppModel PhyloNetAppView PhyloTestCase PhyloTextArea PhyloTextField PlainXReader PlainXReader.PlainXRecord PostTraversal Printable RECOMP RecompCmdLineTool RECOMPParamsDialog RECOMPParamsDialog.ComparisonFunction RECOMPResultsDialog RecompTool Resolve RfCmdLineTool RFParamsDialog RFResultsDialog RFTool RiataHgt RiataHgtCmdLineTool RiataHGTParamsDialog RiataHGTResultsDialog RiataHGTTestCase RIATAHGTTool RiataViewerFrame RiataViewerFrameTestCase SchieberVishkinLCA SchieberVishkinLCATestCase SequenceAlignment SequenceAlignmentDatum SequenceAlignmentDatumController SequenceAlignmentDatumView SequenceAlignmentTestCase SequenceException SGIEdge SGIGraph SGINode SimGTInNetwork SimGTInNetworkCmdLineTool SmithWaterman SmithWaterman.Match Solution SteelWarnowMAST SteelWarnowMASTTestCase STINode STITree STITreeBipartition STITreeCluster STITreeClusterWD SymmetricDifference SymmetricDifferenceTestCase TaxaDistanceMatrix TMutableNode TNode ToolException ToolInitializationException Tree TreeCanvas TreeCompatibility TreeConsensusCalculator TreeDatum TreeDatumController TreeDatumView Trees TreesReader TreesTestCase TreeView TreeView.TreeStyle TreeWithBranchLengthsDatum TripartitionsReader WindowComparator