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[Treebase-guts] SF.net SVN: treebase:[394] trunk/treebase-core/lib/mesquite
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From: <rv...@us...> - 2009-12-16 10:59:06
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Revision: 394
http://treebase.svn.sourceforge.net/treebase/?rev=394&view=rev
Author: rvos
Date: 2009-12-16 10:58:53 +0000 (Wed, 16 Dec 2009)
Log Message:
-----------
Adding mesquite classes
Added Paths:
-----------
trunk/treebase-core/lib/mesquite/ornamental/
trunk/treebase-core/lib/mesquite/ornamental/BranchNotes/
trunk/treebase-core/lib/mesquite/ornamental/BranchNotes/32asteriskTool.gif
trunk/treebase-core/lib/mesquite/ornamental/BranchNotes/64asteriskTool.gif
trunk/treebase-core/lib/mesquite/ornamental/BranchNotes/BranchNotes.class
trunk/treebase-core/lib/mesquite/ornamental/BranchNotes/BranchNotesToolExtra.class
trunk/treebase-core/lib/mesquite/ornamental/BranchNotes/asteriskBIGTool.gif
trunk/treebase-core/lib/mesquite/ornamental/BranchNotes/asteriskTool.gif
trunk/treebase-core/lib/mesquite/ornamental/CircularTree/
trunk/treebase-core/lib/mesquite/ornamental/CircularTree/CircleTreeDrawing.class
trunk/treebase-core/lib/mesquite/ornamental/CircularTree/CircularTree.class
trunk/treebase-core/lib/mesquite/ornamental/CircularTree/PolarCoord.class
trunk/treebase-core/lib/mesquite/ornamental/ColorTreeByPartition/
trunk/treebase-core/lib/mesquite/ornamental/ColorTreeByPartition/ColorByPartitionExtra.class
trunk/treebase-core/lib/mesquite/ornamental/ColorTreeByPartition/ColorTreeByPartition.class
trunk/treebase-core/lib/mesquite/ornamental/Constellation/
trunk/treebase-core/lib/mesquite/ornamental/Constellation/Constellation.class
trunk/treebase-core/lib/mesquite/ornamental/Constellation/ConstellationDrawing.class
trunk/treebase-core/lib/mesquite/ornamental/ManageAttachedNotes/
trunk/treebase-core/lib/mesquite/ornamental/ManageAttachedNotes/ANCT.class
trunk/treebase-core/lib/mesquite/ornamental/ManageAttachedNotes/ManageAttachedNotes.class
trunk/treebase-core/lib/mesquite/ornamental/ManageHyperlinks/
trunk/treebase-core/lib/mesquite/ornamental/ManageHyperlinks/HyperlinkNexusCommandTest.class
trunk/treebase-core/lib/mesquite/ornamental/ManageHyperlinks/ManageHyperlinks.class
trunk/treebase-core/lib/mesquite/ornamental/ManagePictures/
trunk/treebase-core/lib/mesquite/ornamental/ManagePictures/MPCT.class
trunk/treebase-core/lib/mesquite/ornamental/ManagePictures/ManagePictures.class
trunk/treebase-core/lib/mesquite/ornamental/NodeLocsCircular/
trunk/treebase-core/lib/mesquite/ornamental/NodeLocsCircular/NodeLocsCircular.class
trunk/treebase-core/lib/mesquite/ornamental/NodeLocsCircular/NodeLocsCircularExtra.class
trunk/treebase-core/lib/mesquite/ornamental/NodeLocsCircular/PolarCoord.class
trunk/treebase-core/lib/mesquite/ornamental/NodeLocsOval/
trunk/treebase-core/lib/mesquite/ornamental/NodeLocsOval/DoublePt.class
trunk/treebase-core/lib/mesquite/ornamental/NodeLocsOval/NodeLocsOval.class
trunk/treebase-core/lib/mesquite/ornamental/NodeLocsOval/NodeLocsOvalExtra.class
trunk/treebase-core/lib/mesquite/ornamental/NodeNumbers/
trunk/treebase-core/lib/mesquite/ornamental/NodeNumbers/NodeNumbers.class
trunk/treebase-core/lib/mesquite/ornamental/NodeNumbers/SpotsDrawing.class
trunk/treebase-core/lib/mesquite/ornamental/NodePositionAdjust/
trunk/treebase-core/lib/mesquite/ornamental/NodePositionAdjust/32adjustPosition.gif
trunk/treebase-core/lib/mesquite/ornamental/NodePositionAdjust/64adjustPosition.gif
trunk/treebase-core/lib/mesquite/ornamental/NodePositionAdjust/NodePositionAdjust.class
trunk/treebase-core/lib/mesquite/ornamental/NodePositionAdjust/PAdjustToolExtra.class
trunk/treebase-core/lib/mesquite/ornamental/NodePositionAdjust/adjustPosition.gif
trunk/treebase-core/lib/mesquite/ornamental/PictureWindowMaker/
trunk/treebase-core/lib/mesquite/ornamental/PictureWindowMaker/ImagePanel.class
trunk/treebase-core/lib/mesquite/ornamental/PictureWindowMaker/PictureWindow.class
trunk/treebase-core/lib/mesquite/ornamental/PictureWindowMaker/PictureWindowMaker.class
trunk/treebase-core/lib/mesquite/ornamental/Projector/
trunk/treebase-core/lib/mesquite/ornamental/Projector/32projector.gif
trunk/treebase-core/lib/mesquite/ornamental/Projector/64projector.gif
trunk/treebase-core/lib/mesquite/ornamental/Projector/Projector.class
trunk/treebase-core/lib/mesquite/ornamental/Projector/ProjectorPanel.class
trunk/treebase-core/lib/mesquite/ornamental/Projector/ProjectorToolExtra.class
trunk/treebase-core/lib/mesquite/ornamental/Projector/projector.gif
trunk/treebase-core/lib/mesquite/ornamental/TaxonLink/
trunk/treebase-core/lib/mesquite/ornamental/TaxonLink/32link.gif
trunk/treebase-core/lib/mesquite/ornamental/TaxonLink/64link.gif
trunk/treebase-core/lib/mesquite/ornamental/TaxonLink/TaxonLink.class
trunk/treebase-core/lib/mesquite/ornamental/TaxonLink/TaxonLinkToolExtra.class
trunk/treebase-core/lib/mesquite/ornamental/TaxonLink/link.gif
trunk/treebase-core/lib/mesquite/ornamental/explanation.txt
trunk/treebase-core/lib/mesquite/pairwise/
trunk/treebase-core/lib/mesquite/pairwise/PairsNoChars/
trunk/treebase-core/lib/mesquite/pairwise/PairsNoChars/NoCharTaxaPairer.class
trunk/treebase-core/lib/mesquite/pairwise/PairsNoChars/PairsNoChars.class
trunk/treebase-core/lib/mesquite/pairwise/PairsOneChar/
trunk/treebase-core/lib/mesquite/pairwise/PairsOneChar/OneCharTaxaPairer.class
trunk/treebase-core/lib/mesquite/pairwise/PairsOneChar/PairsOneChar.class
trunk/treebase-core/lib/mesquite/pairwise/PairsTwoChars/
trunk/treebase-core/lib/mesquite/pairwise/PairsTwoChars/BestBasisCombos.class
trunk/treebase-core/lib/mesquite/pairwise/PairsTwoChars/BestConditionsAtNode.class
trunk/treebase-core/lib/mesquite/pairwise/PairsTwoChars/PairsTwoChars.class
trunk/treebase-core/lib/mesquite/pairwise/PairsTwoChars/TwoCharTaxaPairer.class
trunk/treebase-core/lib/mesquite/pairwise/PairwiseComparison/
trunk/treebase-core/lib/mesquite/pairwise/PairwiseComparison/PairwiseComparison.class
trunk/treebase-core/lib/mesquite/pairwise/PairwiseComparison/PairwiseDisplayer.class
trunk/treebase-core/lib/mesquite/pairwise/PairwiseComparison/ShowPairsLegend.class
trunk/treebase-core/lib/mesquite/pairwise/aPairwiseIntro/
trunk/treebase-core/lib/mesquite/pairwise/aPairwiseIntro/aPairwiseIntro.class
trunk/treebase-core/lib/mesquite/pairwise/aPairwiseIntro/index.html
trunk/treebase-core/lib/mesquite/pairwise/explanation.txt
trunk/treebase-core/lib/mesquite/pairwise/lib/
trunk/treebase-core/lib/mesquite/pairwise/lib/PairMaker.class
trunk/treebase-core/lib/mesquite/pairwise/lib/PairMakerChars.class
trunk/treebase-core/lib/mesquite/pairwise/lib/TaxaPairer.class
trunk/treebase-core/lib/mesquite/pairwise/lib/TaxaPairerChars.class
trunk/treebase-core/lib/mesquite/pairwise/lib/TaxaPairing.class
trunk/treebase-core/lib/mesquite/pairwise/lib/TaxaPath.class
trunk/treebase-core/lib/mesquite/pal/
trunk/treebase-core/lib/mesquite/pal/aPALIntro/
trunk/treebase-core/lib/mesquite/pal/aPALIntro/aPALIntro.class
trunk/treebase-core/lib/mesquite/pal/aPALIntro/index.html
trunk/treebase-core/lib/mesquite/pal/aPALIntro/splash.gif
trunk/treebase-core/lib/mesquite/pal/explanation.txt
trunk/treebase-core/lib/mesquite/parsimony/
trunk/treebase-core/lib/mesquite/parsimony/CharListParsModels/
trunk/treebase-core/lib/mesquite/parsimony/CharListParsModels/CharListParsModels.class
trunk/treebase-core/lib/mesquite/parsimony/CharStepsDifference/
trunk/treebase-core/lib/mesquite/parsimony/CharStepsDifference/CharStepsDifference.class
trunk/treebase-core/lib/mesquite/parsimony/CurrentParsModels/
trunk/treebase-core/lib/mesquite/parsimony/CurrentParsModels/CurrentParsModels.class
trunk/treebase-core/lib/mesquite/parsimony/InitCategParsimony/
trunk/treebase-core/lib/mesquite/parsimony/InitCategParsimony/InitCategParsimony.class
trunk/treebase-core/lib/mesquite/parsimony/InitContParsimony/
trunk/treebase-core/lib/mesquite/parsimony/InitContParsimony/InitContParsimony.class
trunk/treebase-core/lib/mesquite/parsimony/InitializeParsimony/
trunk/treebase-core/lib/mesquite/parsimony/InitializeParsimony/InitializeParsimony.class
trunk/treebase-core/lib/mesquite/parsimony/ManageTypesets/
trunk/treebase-core/lib/mesquite/parsimony/ManageTypesets/ManageTypesets.class
trunk/treebase-core/lib/mesquite/parsimony/ManageTypesets/TypesetNexusCommandTest.class
trunk/treebase-core/lib/mesquite/parsimony/ParsAncestralStates/
trunk/treebase-core/lib/mesquite/parsimony/ParsAncestralStates/ParsAncestralStates.class
trunk/treebase-core/lib/mesquite/parsimony/ParsCharSteps/
trunk/treebase-core/lib/mesquite/parsimony/ParsCharSteps/ParsCharSteps.class
trunk/treebase-core/lib/mesquite/parsimony/ParsimonyCostMatrix/
trunk/treebase-core/lib/mesquite/parsimony/ParsimonyCostMatrix/ParsimonyCostMatrix.class
trunk/treebase-core/lib/mesquite/parsimony/ParsimonyLinear/
trunk/treebase-core/lib/mesquite/parsimony/ParsimonyLinear/ParsimonyLinear.class
trunk/treebase-core/lib/mesquite/parsimony/ParsimonyOrdered/
trunk/treebase-core/lib/mesquite/parsimony/ParsimonyOrdered/ParsimonyOrdered.class
trunk/treebase-core/lib/mesquite/parsimony/ParsimonySquared/
trunk/treebase-core/lib/mesquite/parsimony/ParsimonySquared/ParsimonySquared.class
trunk/treebase-core/lib/mesquite/parsimony/ParsimonyUnordered/
trunk/treebase-core/lib/mesquite/parsimony/ParsimonyUnordered/ParsimonyUnordered.class
trunk/treebase-core/lib/mesquite/parsimony/StepMatrixCurator/
trunk/treebase-core/lib/mesquite/parsimony/StepMatrixCurator/StepMatrixCurator.class
trunk/treebase-core/lib/mesquite/parsimony/StepMatrixCurator/StepMatrixModel.class
trunk/treebase-core/lib/mesquite/parsimony/StepMatrixCurator/StepmatrixNexusCmdTest.class
trunk/treebase-core/lib/mesquite/parsimony/StepsInCharacter/
trunk/treebase-core/lib/mesquite/parsimony/StepsInCharacter/StepsInCharacter.class
trunk/treebase-core/lib/mesquite/parsimony/StoredParsModel/
trunk/treebase-core/lib/mesquite/parsimony/StoredParsModel/ParsModelCompatInfo.class
trunk/treebase-core/lib/mesquite/parsimony/StoredParsModel/StoredParsModel.class
trunk/treebase-core/lib/mesquite/parsimony/Treelength/
trunk/treebase-core/lib/mesquite/parsimony/Treelength/Treelength.class
trunk/treebase-core/lib/mesquite/parsimony/TreelengthForMatrix/
trunk/treebase-core/lib/mesquite/parsimony/TreelengthForMatrix/TreelengthForMatrix.class
trunk/treebase-core/lib/mesquite/parsimony/TypesetList/
trunk/treebase-core/lib/mesquite/parsimony/TypesetList/TypesetList.class
trunk/treebase-core/lib/mesquite/parsimony/aParsimonyIntro/
trunk/treebase-core/lib/mesquite/parsimony/aParsimonyIntro/aParsimonyIntro.class
trunk/treebase-core/lib/mesquite/parsimony/explanation.txt
trunk/treebase-core/lib/mesquite/parsimony/lib/
trunk/treebase-core/lib/mesquite/parsimony/lib/CategParsimonyModel.class
trunk/treebase-core/lib/mesquite/parsimony/lib/CharacterSteps.class
trunk/treebase-core/lib/mesquite/parsimony/lib/ContParsimonyModel.class
trunk/treebase-core/lib/mesquite/parsimony/lib/CostMatrixModel.class
trunk/treebase-core/lib/mesquite/parsimony/lib/DolloModel.class
trunk/treebase-core/lib/mesquite/parsimony/lib/IrreversibleModel.class
trunk/treebase-core/lib/mesquite/parsimony/lib/LinearModel.class
trunk/treebase-core/lib/mesquite/parsimony/lib/OrderedModel.class
trunk/treebase-core/lib/mesquite/parsimony/lib/ParsAncStatesForModel.class
trunk/treebase-core/lib/mesquite/parsimony/lib/ParsModelSource.class
trunk/treebase-core/lib/mesquite/parsimony/lib/ParsimonyModel.class
trunk/treebase-core/lib/mesquite/parsimony/lib/ParsimonyModelSet.class
trunk/treebase-core/lib/mesquite/parsimony/lib/SquaredModel.class
trunk/treebase-core/lib/mesquite/parsimony/lib/UnorderedModel.class
trunk/treebase-core/lib/mesquite/rhetenor/
trunk/treebase-core/lib/mesquite/rhetenor/CanonicalVariates/
trunk/treebase-core/lib/mesquite/rhetenor/CanonicalVariates/CanonicalVariates.class
trunk/treebase-core/lib/mesquite/rhetenor/CharFromOrdinations/
trunk/treebase-core/lib/mesquite/rhetenor/CharFromOrdinations/CharFromOrdinations.class
trunk/treebase-core/lib/mesquite/rhetenor/CharLoadings/
trunk/treebase-core/lib/mesquite/rhetenor/CharLoadings/CharLoadings.class
trunk/treebase-core/lib/mesquite/rhetenor/CharsFromMatrices/
trunk/treebase-core/lib/mesquite/rhetenor/CharsFromMatrices/CharsFromMatrices.class
trunk/treebase-core/lib/mesquite/rhetenor/EvolutionaryPCA/
trunk/treebase-core/lib/mesquite/rhetenor/EvolutionaryPCA/EvolutionaryPCA.class
trunk/treebase-core/lib/mesquite/rhetenor/LandmarkDrawings/
trunk/treebase-core/lib/mesquite/rhetenor/LandmarkDrawings/32landmark.gif
trunk/treebase-core/lib/mesquite/rhetenor/LandmarkDrawings/64landmark.gif
trunk/treebase-core/lib/mesquite/rhetenor/LandmarkDrawings/DrawingsAtNodes.class
trunk/treebase-core/lib/mesquite/rhetenor/LandmarkDrawings/LandmarkDrawings.class
trunk/treebase-core/lib/mesquite/rhetenor/LandmarkDrawings/LandmarkLegend.class
trunk/treebase-core/lib/mesquite/rhetenor/LandmarkDrawings/NodeDrawing.class
trunk/treebase-core/lib/mesquite/rhetenor/LandmarkDrawings/PlotOperator.class
trunk/treebase-core/lib/mesquite/rhetenor/LandmarkDrawings/landmark.gif
trunk/treebase-core/lib/mesquite/rhetenor/MatricesFromOrdinations/
trunk/treebase-core/lib/mesquite/rhetenor/MatricesFromOrdinations/MatricesFromOrdinations.class
trunk/treebase-core/lib/mesquite/rhetenor/NodeLocs3DPlot/
trunk/treebase-core/lib/mesquite/rhetenor/NodeLocs3DPlot/NodeLocs3DPlot.class
trunk/treebase-core/lib/mesquite/rhetenor/NodeLocs3DPlot/NodeLocs3DPlotExtra.class
trunk/treebase-core/lib/mesquite/rhetenor/NodeLocs3DPlot/NodeLocs3DPlotLegend.class
trunk/treebase-core/lib/mesquite/rhetenor/PlotTree3D/
trunk/treebase-core/lib/mesquite/rhetenor/PlotTree3D/PlotTree3D.class
trunk/treebase-core/lib/mesquite/rhetenor/PlotTree3D/PlotTreeDrawing.class
trunk/treebase-core/lib/mesquite/rhetenor/PrincipalComponents/
trunk/treebase-core/lib/mesquite/rhetenor/PrincipalComponents/PrincipalComponents.class
trunk/treebase-core/lib/mesquite/rhetenor/ShowCharLoadings/
trunk/treebase-core/lib/mesquite/rhetenor/ShowCharLoadings/ShowCharLoadings.class
trunk/treebase-core/lib/mesquite/rhetenor/aPCA/
trunk/treebase-core/lib/mesquite/rhetenor/aPCA/aPCA.class
trunk/treebase-core/lib/mesquite/rhetenor/aRhetenorIntro/
trunk/treebase-core/lib/mesquite/rhetenor/aRhetenorIntro/aRhetenorIntro.class
trunk/treebase-core/lib/mesquite/rhetenor/aRhetenorIntro/index.html
trunk/treebase-core/lib/mesquite/rhetenor/aRhetenorIntro/splash.gif
trunk/treebase-core/lib/mesquite/rhetenor/aRhetenorIntro/splash.gif copy
trunk/treebase-core/lib/mesquite/rhetenor/aRhetenorIntro/splashSmall.gif
trunk/treebase-core/lib/mesquite/rhetenor/explanation.txt
trunk/treebase-core/lib/mesquite/rhetenor/lib/
trunk/treebase-core/lib/mesquite/rhetenor/lib/CVAOrdination.class
trunk/treebase-core/lib/mesquite/rhetenor/lib/CharacterLoadings.class
trunk/treebase-core/lib/mesquite/rhetenor/lib/CharsFromMatrixSource.class
trunk/treebase-core/lib/mesquite/rhetenor/lib/EPCAOrdination.class
trunk/treebase-core/lib/mesquite/rhetenor/lib/MatrixUtil.class
trunk/treebase-core/lib/mesquite/rhetenor/lib/NodeLocsPlot3D.class
trunk/treebase-core/lib/mesquite/rhetenor/lib/Ordination.class
trunk/treebase-core/lib/mesquite/rhetenor/lib/OrdinationAssistant.class
trunk/treebase-core/lib/mesquite/rhetenor/lib/Ordinator.class
trunk/treebase-core/lib/mesquite/rhetenor/lib/PCACorrelOrdination.class
trunk/treebase-core/lib/mesquite/rhetenor/lib/PCAOrdination.class
trunk/treebase-core/lib/mesquite/rhetenor/lib/aPCAOrdination.class
trunk/treebase-core/lib/mesquite/rhetenor/lib/wPCAOrdination.class
trunk/treebase-core/lib/mesquite/rhetenor/wPCA/
trunk/treebase-core/lib/mesquite/rhetenor/wPCA/wPCA.class
trunk/treebase-core/lib/mesquite/search/
trunk/treebase-core/lib/mesquite/search/AddAndRearrange/
trunk/treebase-core/lib/mesquite/search/AddAndRearrange/AddAndRearrange.class
trunk/treebase-core/lib/mesquite/search/NNIRearranger/
trunk/treebase-core/lib/mesquite/search/NNIRearranger/NNIRearranger.class
trunk/treebase-core/lib/mesquite/search/SPRRearranger/
trunk/treebase-core/lib/mesquite/search/SPRRearranger/SPRRearranger.class
trunk/treebase-core/lib/mesquite/search/TreeSearch/
trunk/treebase-core/lib/mesquite/search/TreeSearch/TreeSearch.class
trunk/treebase-core/lib/mesquite/search/aSearchIntro/
trunk/treebase-core/lib/mesquite/search/aSearchIntro/aSearchIntro.class
trunk/treebase-core/lib/mesquite/search/explanation.txt
trunk/treebase-core/lib/mesquite/stochchar/
trunk/treebase-core/lib/mesquite/stochchar/AsymmMkExplorer/
trunk/treebase-core/lib/mesquite/stochchar/AsymmMkExplorer/AMEOperator.class
trunk/treebase-core/lib/mesquite/stochchar/AsymmMkExplorer/AsymmMkExplorer.class
trunk/treebase-core/lib/mesquite/stochchar/AsymmModelCurator/
trunk/treebase-core/lib/mesquite/stochchar/AsymmModelCurator/AsymmModelCurator.class
trunk/treebase-core/lib/mesquite/stochchar/AsymmModelCurator/AsymmModelEditor.class
trunk/treebase-core/lib/mesquite/stochchar/AsymmetryLR/
trunk/treebase-core/lib/mesquite/stochchar/AsymmetryLR/AsymmetryLR.class
trunk/treebase-core/lib/mesquite/stochchar/Brownian/
trunk/treebase-core/lib/mesquite/stochchar/Brownian/Brownian.class
trunk/treebase-core/lib/mesquite/stochchar/CharLikelihood/
trunk/treebase-core/lib/mesquite/stochchar/CharLikelihood/CharLikelihood.class
trunk/treebase-core/lib/mesquite/stochchar/CharListProbModels/
trunk/treebase-core/lib/mesquite/stochchar/CharListProbModels/CharListProbModels.class
trunk/treebase-core/lib/mesquite/stochchar/CurrentProbModels/
trunk/treebase-core/lib/mesquite/stochchar/CurrentProbModels/CurrentProbModels.class
trunk/treebase-core/lib/mesquite/stochchar/EvolveCategChars/
trunk/treebase-core/lib/mesquite/stochchar/EvolveCategChars/ECCCategoricalStateTest.class
trunk/treebase-core/lib/mesquite/stochchar/EvolveCategChars/EvolveCategChars.class
trunk/treebase-core/lib/mesquite/stochchar/EvolveContinuous/
trunk/treebase-core/lib/mesquite/stochchar/EvolveContinuous/ECoCCategoricalStateTest.class
trunk/treebase-core/lib/mesquite/stochchar/EvolveContinuous/EvolveContinuous.class
trunk/treebase-core/lib/mesquite/stochchar/GainLossRates/
trunk/treebase-core/lib/mesquite/stochchar/GainLossRates/GainLossRates.class
trunk/treebase-core/lib/mesquite/stochchar/InterpretPagelFormat/
trunk/treebase-core/lib/mesquite/stochchar/InterpretPagelFormat/InterpretPagelFormat.class
trunk/treebase-core/lib/mesquite/stochchar/InterpretPagelFormatM/
trunk/treebase-core/lib/mesquite/stochchar/InterpretPagelFormatM/InterpretPagelFormatM.class
trunk/treebase-core/lib/mesquite/stochchar/LikelihoodInCharacter/
trunk/treebase-core/lib/mesquite/stochchar/LikelihoodInCharacter/LikelihoodInCharacter.class
trunk/treebase-core/lib/mesquite/stochchar/ManageCharModelsBlock/
trunk/treebase-core/lib/mesquite/stochchar/ManageCharModelsBlock/ManageCharModelsBlock.class
trunk/treebase-core/lib/mesquite/stochchar/ManageCharModelsBlock/ProbCharModelsBlock.class
trunk/treebase-core/lib/mesquite/stochchar/ManageCharModelsBlock/ProbCharModelsBlockTest.class
trunk/treebase-core/lib/mesquite/stochchar/ManageProbModelSets/
trunk/treebase-core/lib/mesquite/stochchar/ManageProbModelSets/ManageProbModelSets.class
trunk/treebase-core/lib/mesquite/stochchar/ManageProbModelSets/ModelsetNexusCommandTest.class
trunk/treebase-core/lib/mesquite/stochchar/MargProbAncStates/
trunk/treebase-core/lib/mesquite/stochchar/MargProbAncStates/MargProbAncStates.class
trunk/treebase-core/lib/mesquite/stochchar/Mk1Rate/
trunk/treebase-core/lib/mesquite/stochchar/Mk1Rate/Mk1Rate.class
trunk/treebase-core/lib/mesquite/stochchar/MkModelCurator/
trunk/treebase-core/lib/mesquite/stochchar/MkModelCurator/MkModelCurator.class
trunk/treebase-core/lib/mesquite/stochchar/ProbModelSetList/
trunk/treebase-core/lib/mesquite/stochchar/ProbModelSetList/ProbModelSetList.class
trunk/treebase-core/lib/mesquite/stochchar/SimAncestralStates/
trunk/treebase-core/lib/mesquite/stochchar/SimAncestralStates/SimAncestralStates.class
trunk/treebase-core/lib/mesquite/stochchar/SimCharsOnTrees/
trunk/treebase-core/lib/mesquite/stochchar/SimCharsOnTrees/SCCompatibilityTest.class
trunk/treebase-core/lib/mesquite/stochchar/SimCharsOnTrees/SimCharsOnTrees.class
trunk/treebase-core/lib/mesquite/stochchar/SimMatricesOnTrees/
trunk/treebase-core/lib/mesquite/stochchar/SimMatricesOnTrees/SMoSTCompatibilityTest.class
trunk/treebase-core/lib/mesquite/stochchar/SimMatricesOnTrees/SimMatricesOnTrees.class
trunk/treebase-core/lib/mesquite/stochchar/SimulatedCharacters/
trunk/treebase-core/lib/mesquite/stochchar/SimulatedCharacters/SCCompatibilityTest.class
trunk/treebase-core/lib/mesquite/stochchar/SimulatedCharacters/SimulatedCharacters.class
trunk/treebase-core/lib/mesquite/stochchar/SimulatedMatrix/
trunk/treebase-core/lib/mesquite/stochchar/SimulatedMatrix/SMCompatibilityTest.class
trunk/treebase-core/lib/mesquite/stochchar/SimulatedMatrix/SimulatedMatrix.class
trunk/treebase-core/lib/mesquite/stochchar/StochCharMapper/
trunk/treebase-core/lib/mesquite/stochchar/StochCharMapper/StochCharMapper.class
trunk/treebase-core/lib/mesquite/stochchar/StoredProbModel/
trunk/treebase-core/lib/mesquite/stochchar/StoredProbModel/LikeModelCompatInfo.class
trunk/treebase-core/lib/mesquite/stochchar/StoredProbModel/StoredProbModel.class
trunk/treebase-core/lib/mesquite/stochchar/StoredProbModelSim/
trunk/treebase-core/lib/mesquite/stochchar/StoredProbModelSim/StoredProbModelSim.class
trunk/treebase-core/lib/mesquite/stochchar/aStochCharIntro/
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+++ trunk/treebase-core/lib/mesquite/ornamental/explanation.txt 2009-12-16 10:58:53 UTC (rev 394)
@@ -0,0 +1,2 @@
+Ornaments for Tree Window
+Provides several special ways to draw trees (circular, constellation), facilities to attach extra information to trees (pictures, notes at branches, hyperlinks), and extra tree tools.
\ No newline at end of file
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===================================================================
--- trunk/treebase-core/lib/mesquite/pairwise/aPairwiseIntro/index.html (rev 0)
+++ trunk/treebase-core/lib/mesquite/pairwise/aPairwiseIntro/index.html 2009-12-16 10:58:53 UTC (rev 394)
@@ -0,0 +1,57 @@
+<html>
+
+ <head>
+ <meta http-equiv="content-type" content="text/html;charset=iso-8859-1">
+ <meta name="generator" content="Adobe GoLive 4">
+ <title>Pairwise</title>
+ </head>
+
+ <body bgcolor="#ffeaab">
+ <h2>
+ <table border="4" cellpadding="0" cellspacing="2">
+ <tr>
+ <td></td>
+ <td>
+ <h2>Pairwise comparisons package for Mesquite</h2>
+ </td>
+ </tr>
+ </table>
+ </h2>
+ <h4>Wayne Maddison</h4>
+
+<p>August 2005, version 1.06.</p>
+ <ul>
+ <li><a href="#overview">Overview</a>
+ <li><a href="#modules">Modules</a>
+ <li><a href="#installation">Installation</a>
+ <li><a href="#examples">Examples</a>
+ </ul>
+ <h3><a name="overview"></a>Overview</h3>
+ <p>This package performs the pairwise comparisons calculations of W. Maddison 2000 (Testing character correlation using pairwise comparisons on a phylogeny. Journal of Theoretical Biology. 202: 195-204).</p>
+
+<p>This package and its source are free and modifiable under the terms of the
+ GNU Lesser General Public License (see bottom of this page). The source is included
+ with the Mesquite source, available from <a href="http://mesquiteproject.org">mesquiteproject.org</a>.</p>
+ <h3><a name="modules"></a>Modules</h3>
+ <p>The modules currently included are:</p>
+ <ul>
+ <li><b>PairwiseComparison</b> -- Supervises the calculation of pairwise comparisons, and displays results in a tree window.
+ <li><b>PairsTwoChars</b> -- Finds pairs of taxa contrasting the state of two binary characters.
+ <li><b>PairsOneChar</b> -- Finds pairs of taxa contrasting the state of one binary character.
+ <li><b>PairsNoChars</b> -- Finds pairs of taxa regardless of whether they contrast the states of two characters.
+ </ul>
+ <h3><a name="installation"></a>Installation</h3>
+ <p>To install the Pairwise comparisons package, the "pairwise" directory must be installed in the "mesquite" directory within "Mesquite Folder".</p>
+ <h3><a name="examples"></a>Examples</h3>
+
+<p>A directory "Pairwise_Comparison" is included in the Mesquite examples
+ folder in Mesquite_Folder/examples/.</p>
+ <p>
+ <hr>
+ </p>
+
+<p>© Wayne Maddison, 2001-2005</p>
+ <p>
+ <p> </body>
+
+</html>
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+++ trunk/treebase-core/lib/mesquite/pairwise/explanation.txt 2009-12-16 10:58:53 UTC (rev 394)
@@ -0,0 +1,2 @@
+Pairwise Comparisons for Character Correlation
+Finds phylogenetically independent pairs of taxa and compares traits in two characters to explore character correlation (see W. Maddison 2000, Journal of Theoretical Biology, 202: 195-204)
\ No newline at end of file
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+ <meta http-equiv="content-type" content="text/html;charset=iso-8859-1">
+ <meta name="generator" content="Adobe GoLive 4">
+ <title>PAL</title>
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+ <h2>
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+ <td width="165"><img src="splash.gif" width="164" height="64" x-claris-useimagewidth x-claris-useimageheight align="bottom"></td>
+ <td>
+ <h2>Phylogenetic Analysis Library</h2>
+ <h2>Version 1.3</h2>
+ </td>
+ </tr>
+ </table>
+ </h2>
+ <h4>Alexei Drummond and Korbinian Strimmer</h4>
+ <ul>
+ <li><a href="#overview">Overview</a>
+ <li><a href="#installation">Installation</a>
+ </ul>
+ <h3><a name="overview"></a>Overview</h3>
+ <p>This page represents the Phylogenetic Analysis Library (PAL) by Drummond and Strimmer, as installed for use in Mesquite. When installed, various modules in Mesquite have the option of using PAL methods for calculations. To find out what modules might be using PAL, look through their documentation.</p>
+
+<p>PAL is distributed under the terms of the GNU <a href="http://www.gnu.org/copyleft/lesser.html">Lesser
+ General Public License</a>. Source code and documentation of PAL are at the
+ <a href="http://mesquiteproject.org/mesquite/pal/">Mesquite web site</a>. For
+ the latest version of PAL, please go to <a href="http://www.cebl.auckland.ac.nz/pal-project/">http://www.cebl.auckland.ac.nz/pal-project/</a></p>
+ <h3><a name="installation"></a>Installation</h3>
+ <p>To install PAL, the "pal" directory must be installed within "Mesquite_Folder" directory.</p>
+ <p>
+ <hr>
+ </body>
+
+</html>
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+Introduction to PAL
+This package contains no substantive modules. It has a single module that serves to introduce to the user the PAL package (Drummond & Strimmer) of molecular phylogenetic & population genetic routines. If this package is deactivated, the PAL package is NOT deactivated.
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