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[Treebase-guts] SF.net SVN: treebase:[392] trunk/treebase-core/lib/mesquite
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From: <rv...@us...> - 2009-12-16 10:14:42
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Revision: 392
http://treebase.svn.sourceforge.net/treebase/?rev=392&view=rev
Author: rvos
Date: 2009-12-16 10:14:30 +0000 (Wed, 16 Dec 2009)
Log Message:
-----------
Adding mesquite classes
Added Paths:
-----------
trunk/treebase-core/lib/mesquite/charts/
trunk/treebase-core/lib/mesquite/charts/CharacterValuesChart/
trunk/treebase-core/lib/mesquite/charts/CharacterValuesChart/CharacterValuesChart.class
trunk/treebase-core/lib/mesquite/charts/CharsScattergram/
trunk/treebase-core/lib/mesquite/charts/CharsScattergram/CharsScattergram.class
trunk/treebase-core/lib/mesquite/charts/Histogram/
trunk/treebase-core/lib/mesquite/charts/Histogram/Histogram.class
trunk/treebase-core/lib/mesquite/charts/Histogram/HistogramCharter.class
trunk/treebase-core/lib/mesquite/charts/Histogram/LittlePanel.class
trunk/treebase-core/lib/mesquite/charts/ItemValuesChart/
trunk/treebase-core/lib/mesquite/charts/ItemValuesChart/ChartMessages.class
trunk/treebase-core/lib/mesquite/charts/ItemValuesChart/ItemValuesChart.class
trunk/treebase-core/lib/mesquite/charts/ItemValuesChart/ItemsChartWindow.class
trunk/treebase-core/lib/mesquite/charts/ItemsBiplot/
trunk/treebase-core/lib/mesquite/charts/ItemsBiplot/ItemsBiplot.class
trunk/treebase-core/lib/mesquite/charts/ItemsBiplot/ItemsBiplotWindow.class
trunk/treebase-core/lib/mesquite/charts/ItemsBiplot/TChartMessages.class
trunk/treebase-core/lib/mesquite/charts/MatrixValuesChart/
trunk/treebase-core/lib/mesquite/charts/MatrixValuesChart/MatrixValuesChart.class
trunk/treebase-core/lib/mesquite/charts/NodesScattergram/
trunk/treebase-core/lib/mesquite/charts/NodesScattergram/NodeLabeller.class
trunk/treebase-core/lib/mesquite/charts/NodesScattergram/NodeScattergramWindow.class
trunk/treebase-core/lib/mesquite/charts/NodesScattergram/NodesScattergram.class
trunk/treebase-core/lib/mesquite/charts/Notes/
trunk/treebase-core/lib/mesquite/charts/Notes/Chart Notes.txt
trunk/treebase-core/lib/mesquite/charts/Scattergram/
trunk/treebase-core/lib/mesquite/charts/Scattergram/Scattergram.class
trunk/treebase-core/lib/mesquite/charts/Scattergram/ScattergramCharter.class
trunk/treebase-core/lib/mesquite/charts/Scattergram/ScattergramColorLegend.class
trunk/treebase-core/lib/mesquite/charts/ShowMean/
trunk/treebase-core/lib/mesquite/charts/ShowMean/ShowMean.class
trunk/treebase-core/lib/mesquite/charts/ShowMean/ShowMeanExtra.class
trunk/treebase-core/lib/mesquite/charts/ShowPercentile/
trunk/treebase-core/lib/mesquite/charts/ShowPercentile/001.gif
trunk/treebase-core/lib/mesquite/charts/ShowPercentile/01.gif
trunk/treebase-core/lib/mesquite/charts/ShowPercentile/05.gif
trunk/treebase-core/lib/mesquite/charts/ShowPercentile/ShowPercentile.class
trunk/treebase-core/lib/mesquite/charts/ShowPercentile/ShowPercentileExtra.class
trunk/treebase-core/lib/mesquite/charts/ShowPercentile/manual.html
trunk/treebase-core/lib/mesquite/charts/ShowYEqualsX/
trunk/treebase-core/lib/mesquite/charts/ShowYEqualsX/ShowYEqualsX.class
trunk/treebase-core/lib/mesquite/charts/ShowYEqualsX/ShowYEqualsXExtra.class
trunk/treebase-core/lib/mesquite/charts/TaxaScattergram/
trunk/treebase-core/lib/mesquite/charts/TaxaScattergram/TaxaScattergram.class
trunk/treebase-core/lib/mesquite/charts/TaxonPairValuesChart/
trunk/treebase-core/lib/mesquite/charts/TaxonPairValuesChart/TaxonPairValuesChart.class
trunk/treebase-core/lib/mesquite/charts/TaxonPairsScattergram/
trunk/treebase-core/lib/mesquite/charts/TaxonPairsScattergram/TaxonPairsScattergram.class
trunk/treebase-core/lib/mesquite/charts/TaxonValuesChart/
trunk/treebase-core/lib/mesquite/charts/TaxonValuesChart/TaxonValuesChart.class
trunk/treebase-core/lib/mesquite/charts/TreeBlockValues/
trunk/treebase-core/lib/mesquite/charts/TreeBlockValues/TreeBlockValues.class
trunk/treebase-core/lib/mesquite/charts/TreeValuesChart/
trunk/treebase-core/lib/mesquite/charts/TreeValuesChart/TreeValuesChart.class
trunk/treebase-core/lib/mesquite/charts/TreesScattergram/
trunk/treebase-core/lib/mesquite/charts/TreesScattergram/TreesScattergram.class
trunk/treebase-core/lib/mesquite/charts/explanation.txt
trunk/treebase-core/lib/mesquite/coalesce/
trunk/treebase-core/lib/mesquite/coalesce/CoalescenceWMigration/
trunk/treebase-core/lib/mesquite/coalesce/CoalescenceWMigration/CoalescenceWMigration.class
trunk/treebase-core/lib/mesquite/coalesce/CoalescentTrees/
trunk/treebase-core/lib/mesquite/coalesce/CoalescentTrees/CoalescentTrees.class
trunk/treebase-core/lib/mesquite/coalesce/ContainedCoalescSim/
trunk/treebase-core/lib/mesquite/coalesce/ContainedCoalescSim/ContainedCoalescSim.class
trunk/treebase-core/lib/mesquite/coalesce/ContainedCoalescence/
trunk/treebase-core/lib/mesquite/coalesce/ContainedCoalescence/ContainedCoalescence.class
trunk/treebase-core/lib/mesquite/coalesce/DeepCoalMultLoci/
trunk/treebase-core/lib/mesquite/coalesce/DeepCoalMultLoci/DeepCoalMultLoci.class
trunk/treebase-core/lib/mesquite/coalesce/DeepCoalescencesG/
trunk/treebase-core/lib/mesquite/coalesce/DeepCoalescencesG/DeepCoalescencesG.class
trunk/treebase-core/lib/mesquite/coalesce/DeepCoalescencesSp/
trunk/treebase-core/lib/mesquite/coalesce/DeepCoalescencesSp/DeepCoalescencesSp.class
trunk/treebase-core/lib/mesquite/coalesce/DuplicationsExtinctionsG/
trunk/treebase-core/lib/mesquite/coalesce/DuplicationsExtinctionsG/DuplicationsExtinctionsG.class
trunk/treebase-core/lib/mesquite/coalesce/DuplicationsExtinctionsSp/
trunk/treebase-core/lib/mesquite/coalesce/DuplicationsExtinctionsSp/DuplicationsExtinctionsSp.class
trunk/treebase-core/lib/mesquite/coalesce/InsertNode/
trunk/treebase-core/lib/mesquite/coalesce/InsertNode/32insertNode.gif
trunk/treebase-core/lib/mesquite/coalesce/InsertNode/64insertNode.gif
trunk/treebase-core/lib/mesquite/coalesce/InsertNode/InsertNode.class
trunk/treebase-core/lib/mesquite/coalesce/InsertNode/InsertToolExtra.class
trunk/treebase-core/lib/mesquite/coalesce/InsertNode/insertNode.gif
trunk/treebase-core/lib/mesquite/coalesce/LineageWidth/
trunk/treebase-core/lib/mesquite/coalesce/LineageWidth/32adjustWidths.gif
trunk/treebase-core/lib/mesquite/coalesce/LineageWidth/64adjustWidths.gif
trunk/treebase-core/lib/mesquite/coalesce/LineageWidth/LineageWidth.class
trunk/treebase-core/lib/mesquite/coalesce/LineageWidth/WidthsToolExtra.class
trunk/treebase-core/lib/mesquite/coalesce/LineageWidth/adjustWidths.gif
trunk/treebase-core/lib/mesquite/coalesce/NeutralCoalescence/
trunk/treebase-core/lib/mesquite/coalesce/NeutralCoalescence/NeutralCoalescence.class
trunk/treebase-core/lib/mesquite/coalesce/RecCoalescenceHistory/
trunk/treebase-core/lib/mesquite/coalesce/RecCoalescenceHistory/RecCoalescenceHistory.class
trunk/treebase-core/lib/mesquite/coalesce/RecCoalescenceHistory/RerootStore.class
trunk/treebase-core/lib/mesquite/coalesce/SlatkinMaddisonS/
trunk/treebase-core/lib/mesquite/coalesce/SlatkinMaddisonS/SlatkinMaddisonS.class
trunk/treebase-core/lib/mesquite/coalesce/TreeDepth/
trunk/treebase-core/lib/mesquite/coalesce/TreeDepth/TreeDepth.class
trunk/treebase-core/lib/mesquite/coalesce/aCoalescencePkgIntro/
trunk/treebase-core/lib/mesquite/coalesce/aCoalescencePkgIntro/aCoalescencePkgIntro.class
trunk/treebase-core/lib/mesquite/coalesce/aCoalescencePkgIntro/index.html
trunk/treebase-core/lib/mesquite/coalesce/aCoalescencePkgIntro/splash.gif
trunk/treebase-core/lib/mesquite/coalesce/aCoalescencePkgIntro/splash.gif copy
trunk/treebase-core/lib/mesquite/coalesce/aCoalescencePkgIntro/splashSmall.gif
trunk/treebase-core/lib/mesquite/coalesce/explanation.txt
trunk/treebase-core/lib/mesquite/coalesce/lib/
trunk/treebase-core/lib/mesquite/coalesce/lib/CoalescedNode.class
trunk/treebase-core/lib/mesquite/coalesce/lib/Coalescer.class
trunk/treebase-core/lib/mesquite/coalesce/lib/CoalescerObed.class
trunk/treebase-core/lib/mesquite/coalesce/lib/ContainedTreeSim.class
trunk/treebase-core/lib/mesquite/coalesce/lib/GeneTreeFit.class
trunk/treebase-core/lib/mesquite/coalesce/lib/SpeciesTreeFit.class
trunk/treebase-core/lib/mesquite/coalesce/macros/
trunk/treebase-core/lib/mesquite/coalesce/macros/s_by_depth
trunk/treebase-core/lib/mesquite/cont/
trunk/treebase-core/lib/mesquite/cont/AddItem/
trunk/treebase-core/lib/mesquite/cont/AddItem/AddItem.class
trunk/treebase-core/lib/mesquite/cont/AddNoise/
trunk/treebase-core/lib/mesquite/cont/AddNoise/AddNoise.class
trunk/treebase-core/lib/mesquite/cont/AddToStates/
trunk/treebase-core/lib/mesquite/cont/AddToStates/AddToStates.class
trunk/treebase-core/lib/mesquite/cont/ContCharFrTaxonValue/
trunk/treebase-core/lib/mesquite/cont/ContCharFrTaxonValue/ContCharFrTaxonValue.class
trunk/treebase-core/lib/mesquite/cont/ContinuousStatesT/
trunk/treebase-core/lib/mesquite/cont/ContinuousStatesT/ContinuousStatesT.class
trunk/treebase-core/lib/mesquite/cont/LogTransform/
trunk/treebase-core/lib/mesquite/cont/LogTransform/LogTransform.class
trunk/treebase-core/lib/mesquite/cont/ManageContChars/
trunk/treebase-core/lib/mesquite/cont/ManageContChars/ManageContChars.class
trunk/treebase-core/lib/mesquite/cont/ManageGeogChars/
trunk/treebase-core/lib/mesquite/cont/ManageGeogChars/ManageGeogChars.class
trunk/treebase-core/lib/mesquite/cont/MapContinuous/
trunk/treebase-core/lib/mesquite/cont/MapContinuous/MapContinuous.class
trunk/treebase-core/lib/mesquite/cont/MeanValue/
trunk/treebase-core/lib/mesquite/cont/MeanValue/MeanValue.class
trunk/treebase-core/lib/mesquite/cont/MultiplyStates/
trunk/treebase-core/lib/mesquite/cont/MultiplyStates/MultiplyStates.class
trunk/treebase-core/lib/mesquite/cont/NodeLocs2DPlot/
trunk/treebase-core/lib/mesquite/cont/NodeLocs2DPlot/NodeLocs2DPlot.class
trunk/treebase-core/lib/mesquite/cont/NodeLocs2DPlot/NodeLocs2DPlotExtra.class
trunk/treebase-core/lib/mesquite/cont/NodeLocs2DPlot/NodeLocs2DPlotLegend.class
trunk/treebase-core/lib/mesquite/cont/PlotTree/
trunk/treebase-core/lib/mesquite/cont/PlotTree/PlotTree.class
trunk/treebase-core/lib/mesquite/cont/PlotTree/PlotTreeDrawing.class
trunk/treebase-core/lib/mesquite/cont/RandomFillCont/
trunk/treebase-core/lib/mesquite/cont/RandomFillCont/RandomFillCont.class
trunk/treebase-core/lib/mesquite/cont/RandomFillUniform/
trunk/treebase-core/lib/mesquite/cont/RandomFillUniform/RandomFillUniform.class
trunk/treebase-core/lib/mesquite/cont/RemoveItem/
trunk/treebase-core/lib/mesquite/cont/RemoveItem/RemoveItem.class
trunk/treebase-core/lib/mesquite/cont/RenameItem/
trunk/treebase-core/lib/mesquite/cont/RenameItem/RenameItem.class
trunk/treebase-core/lib/mesquite/cont/Standardize/
trunk/treebase-core/lib/mesquite/cont/Standardize/Standardize.class
trunk/treebase-core/lib/mesquite/cont/explanation.txt
trunk/treebase-core/lib/mesquite/cont/lib/
trunk/treebase-core/lib/mesquite/cont/lib/BasicStatPak.class
trunk/treebase-core/lib/mesquite/cont/lib/ContColorTable.class
trunk/treebase-core/lib/mesquite/cont/lib/ContDataAlterer.class
trunk/treebase-core/lib/mesquite/cont/lib/ContDataSearcher.class
trunk/treebase-core/lib/mesquite/cont/lib/ContDataUtility.class
trunk/treebase-core/lib/mesquite/cont/lib/ContinuousAdjustable.class
trunk/treebase-core/lib/mesquite/cont/lib/ContinuousData.class
trunk/treebase-core/lib/mesquite/cont/lib/ContinuousDistribution.class
trunk/treebase-core/lib/mesquite/cont/lib/ContinuousEmbedded.class
trunk/treebase-core/lib/mesquite/cont/lib/ContinuousHistory.class
trunk/treebase-core/lib/mesquite/cont/lib/ContinuousState.class
trunk/treebase-core/lib/mesquite/cont/lib/ContinuousStateTest.class
trunk/treebase-core/lib/mesquite/cont/lib/ContinuousStates.class
trunk/treebase-core/lib/mesquite/cont/lib/EigenAnalysis.class
trunk/treebase-core/lib/mesquite/cont/lib/GeogDataSearcher.class
trunk/treebase-core/lib/mesquite/cont/lib/GeogDataUtility.class
trunk/treebase-core/lib/mesquite/cont/lib/GeographicAdjustable.class
trunk/treebase-core/lib/mesquite/cont/lib/GeographicData.class
trunk/treebase-core/lib/mesquite/cont/lib/GeographicState.class
trunk/treebase-core/lib/mesquite/cont/lib/GeographicStateTest.class
trunk/treebase-core/lib/mesquite/cont/lib/GeographicStates.class
trunk/treebase-core/lib/mesquite/cont/lib/ItemContainer.class
trunk/treebase-core/lib/mesquite/cont/lib/MContinuousAdjustable.class
trunk/treebase-core/lib/mesquite/cont/lib/MContinuousDistribution.class
trunk/treebase-core/lib/mesquite/cont/lib/MContinuousEmbedded.class
trunk/treebase-core/lib/mesquite/cont/lib/MContinuousHistory.class
trunk/treebase-core/lib/mesquite/cont/lib/MContinuousStates.class
trunk/treebase-core/lib/mesquite/cont/lib/MGeographicStates.class
trunk/treebase-core/lib/mesquite/cont/lib/ManageContCharsA.class
trunk/treebase-core/lib/mesquite/cont/lib/SquaredReconstructor.class
trunk/treebase-core/lib/mesquite/correl/
trunk/treebase-core/lib/mesquite/correl/CorrelationViewer/
trunk/treebase-core/lib/mesquite/correl/CorrelationViewer/CorrelPanel.class
trunk/treebase-core/lib/mesquite/correl/CorrelationViewer/CorrelationViewer.class
trunk/treebase-core/lib/mesquite/correl/Pagel94/
trunk/treebase-core/lib/mesquite/correl/Pagel94/Pagel94.class
trunk/treebase-core/lib/mesquite/correl/aCorrelPackageIntro/
trunk/treebase-core/lib/mesquite/correl/aCorrelPackageIntro/aCorrelPackageIntro.class
trunk/treebase-core/lib/mesquite/correl/aCorrelPackageIntro/splash.gif
trunk/treebase-core/lib/mesquite/correl/aCorrelPackageIntro/splash.psd
trunk/treebase-core/lib/mesquite/correl/lib/
trunk/treebase-core/lib/mesquite/correl/lib/CLogger.class
trunk/treebase-core/lib/mesquite/correl/lib/ComplexMatrix.class
trunk/treebase-core/lib/mesquite/correl/lib/MultipleProbCategCharModel.class
trunk/treebase-core/lib/mesquite/correl/lib/MultipleProbabilityModel.class
trunk/treebase-core/lib/mesquite/correl/lib/Pagel94Calculator.class
trunk/treebase-core/lib/mesquite/correl/lib/PagelMatrixModel$StuckSearchException.class
trunk/treebase-core/lib/mesquite/correl/lib/PagelMatrixModel.class
trunk/treebase-core/lib/mesquite/correl/notes/
trunk/treebase-core/lib/mesquite/correl/notes/PEM Notes
trunk/treebase-core/lib/mesquite/correl/notes/Pagel94Hominids.nex
trunk/treebase-core/lib/mesquite/correl/notes/Pagel94test.nex
trunk/treebase-core/lib/mesquite/correl/notes/Pagel94test.ppy
trunk/treebase-core/lib/mesquite/correl/notes/Putzer method
trunk/treebase-core/lib/mesquite/correl/notes/disc2.nex
trunk/treebase-core/lib/mesquite/correl/notes/disc2.ppy
trunk/treebase-core/lib/mesquite/correl/notes/omphalina.nex
trunk/treebase-core/lib/mesquite/correl/notes/omphalina.ppy
trunk/treebase-core/lib/mesquite/distance/
trunk/treebase-core/lib/mesquite/distance/AverageOfDistances/
trunk/treebase-core/lib/mesquite/distance/AverageOfDistances/AverageOfDistances.class
trunk/treebase-core/lib/mesquite/distance/AverageOfDistances/AvgDistances.class
trunk/treebase-core/lib/mesquite/distance/ClusterAnalysis/
trunk/treebase-core/lib/mesquite/distance/ClusterAnalysis/ClusterAnalysis.class
trunk/treebase-core/lib/mesquite/distance/DistanceContainedTaxa/
trunk/treebase-core/lib/mesquite/distance/DistanceContainedTaxa/ContainedDistances.class
trunk/treebase-core/lib/mesquite/distance/DistanceContainedTaxa/DistanceContainedTaxa.class
trunk/treebase-core/lib/mesquite/distance/F81Distance/
trunk/treebase-core/lib/mesquite/distance/F81Distance/F81Distance.class
trunk/treebase-core/lib/mesquite/distance/F81Distance/F81TD.class
trunk/treebase-core/lib/mesquite/distance/F84Distance/
trunk/treebase-core/lib/mesquite/distance/F84Distance/F84Distance.class
trunk/treebase-core/lib/mesquite/distance/F84Distance/F84TD.class
trunk/treebase-core/lib/mesquite/distance/JukesCantorDistance/
trunk/treebase-core/lib/mesquite/distance/JukesCantorDistance/JukesCantorDistance.class
trunk/treebase-core/lib/mesquite/distance/JukesCantorDistance/JukesCantorTD.class
trunk/treebase-core/lib/mesquite/distance/K2PDistance/
trunk/treebase-core/lib/mesquite/distance/K2PDistance/K2PDistance.class
trunk/treebase-core/lib/mesquite/distance/K2PDistance/K2PTD.class
trunk/treebase-core/lib/mesquite/distance/NodeCountDist/
trunk/treebase-core/lib/mesquite/distance/NodeCountDist/NodeCountDist$NodeCountTD.class
trunk/treebase-core/lib/mesquite/distance/NodeCountDist/NodeCountDist.class
trunk/treebase-core/lib/mesquite/distance/Notes/
trunk/treebase-core/lib/mesquite/distance/Notes/Distance Notes
trunk/treebase-core/lib/mesquite/distance/PDistance/
trunk/treebase-core/lib/mesquite/distance/PDistance/PDistance.class
trunk/treebase-core/lib/mesquite/distance/PDistance/PTD.class
trunk/treebase-core/lib/mesquite/distance/PatristicDistance/
trunk/treebase-core/lib/mesquite/distance/PatristicDistance/PatristicDistance.class
trunk/treebase-core/lib/mesquite/distance/PatristicDistance/PatristicTD.class
trunk/treebase-core/lib/mesquite/distance/SharedHistoryDistance/
trunk/treebase-core/lib/mesquite/distance/SharedHistoryDistance/SharedHistoryDistance$SharedHistoryTD.class
trunk/treebase-core/lib/mesquite/distance/SharedHistoryDistance/SharedHistoryDistance.class
trunk/treebase-core/lib/mesquite/distance/SharedProportionalDistance/
trunk/treebase-core/lib/mesquite/distance/SharedProportionalDistance/SharedProportionalDistance$SharedProportionTD.class
trunk/treebase-core/lib/mesquite/distance/SharedProportionalDistance/SharedProportionalDistance.class
trunk/treebase-core/lib/mesquite/distance/SingleLinkage/
trunk/treebase-core/lib/mesquite/distance/SingleLinkage/SingleLinkage.class
trunk/treebase-core/lib/mesquite/distance/TaxaDistFromMatrixSrc/
trunk/treebase-core/lib/mesquite/distance/TaxaDistFromMatrixSrc/TaxaDistFromMatrixSrc.class
trunk/treebase-core/lib/mesquite/distance/TaxonDistance/
trunk/treebase-core/lib/mesquite/distance/TaxonDistance/TaxonDistance.class
trunk/treebase-core/lib/mesquite/distance/UPGMA/
trunk/treebase-core/lib/mesquite/distance/UPGMA/UPGMA.class
trunk/treebase-core/lib/mesquite/distance/UncorrectedDistance/
trunk/treebase-core/lib/mesquite/distance/UncorrectedDistance/SimpleTD.class
trunk/treebase-core/lib/mesquite/distance/UncorrectedDistance/UncorrectedDistance.class
trunk/treebase-core/lib/mesquite/distance/explanation.txt
trunk/treebase-core/lib/mesquite/distance/lib/
trunk/treebase-core/lib/mesquite/distance/lib/DNATaxaDistFromMatrix.class
trunk/treebase-core/lib/mesquite/distance/lib/DNATaxaDistFromMatrixFreq.class
trunk/treebase-core/lib/mesquite/distance/lib/DNATaxaDistance.class
trunk/treebase-core/lib/mesquite/distance/lib/GeoTaxaDistFromMatrix.class
trunk/treebase-core/lib/mesquite/distance/lib/GeoTaxaDistance.class
trunk/treebase-core/lib/mesquite/distance/lib/IncTaxaDistanceSource.class
trunk/treebase-core/lib/mesquite/distance/lib/MolecularTaxaDistance.class
trunk/treebase-core/lib/mesquite/distance/lib/PairsChartMessages.class
trunk/treebase-core/lib/mesquite/distance/lib/PairsWindow.class
trunk/treebase-core/lib/mesquite/distance/lib/TaxaDistFromMatrix.class
trunk/treebase-core/lib/mesquite/distance/lib/TaxaDistance.class
trunk/treebase-core/lib/mesquite/distance/lib/TaxaDistanceSource.class
trunk/treebase-core/lib/mesquite/distance/lib/TreeClusterer.class
trunk/treebase-core/lib/mesquite/diverse/
trunk/treebase-core/lib/mesquite/diverse/BiSSELikelihood/
trunk/treebase-core/lib/mesquite/diverse/BiSSELikelihood/BiSSELikelihood.class
trunk/treebase-core/lib/mesquite/diverse/BiSSELikelihoodCalculator/
trunk/treebase-core/lib/mesquite/diverse/BiSSELikelihoodCalculator/BiSSELikelihoodCalculator.class
trunk/treebase-core/lib/mesquite/diverse/BiSSELikelihoodCalculator/SpecExtincCategModel.class
trunk/treebase-core/lib/mesquite/diverse/BiSSELikelihoodRatio/
trunk/treebase-core/lib/mesquite/diverse/BiSSELikelihoodRatio/BiSSELikelihoodRatio.class
trunk/treebase-core/lib/mesquite/diverse/BiSSETreeCharSim/
trunk/treebase-core/lib/mesquite/diverse/BiSSETreeCharSim/BiSSETreeCharSim.class
trunk/treebase-core/lib/mesquite/diverse/BirthDeathTrees/
trunk/treebase-core/lib/mesquite/diverse/BirthDeathTrees/BirthDeathTrees.class
trunk/treebase-core/lib/mesquite/diverse/CharAssocDivViewer/
trunk/treebase-core/lib/mesquite/diverse/CharAssocDivViewer/CADPanel.class
trunk/treebase-core/lib/mesquite/diverse/CharAssocDivViewer/CharAssocDivViewer.class
trunk/treebase-core/lib/mesquite/diverse/CharIndepDivViewer/
trunk/treebase-core/lib/mesquite/diverse/CharIndepDivViewer/CADPanel.class
trunk/treebase-core/lib/mesquite/diverse/CharIndepDivViewer/CharIndepDivViewer.class
trunk/treebase-core/lib/mesquite/diverse/ContCharSpeciation/
trunk/treebase-core/lib/mesquite/diverse/ContCharSpeciation/ContCharSpeciation.class
trunk/treebase-core/lib/mesquite/diverse/DivCategCharMLCalculator/
trunk/treebase-core/lib/mesquite/diverse/DivCategCharMLCalculator/DivCategCharMLCalculator.class
trunk/treebase-core/lib/mesquite/diverse/DivCategCharMLCalculator/DiversificationCategModel.class
trunk/treebase-core/lib/mesquite/diverse/DiversCategCharLikelihood/
trunk/treebase-core/lib/mesquite/diverse/DiversCategCharLikelihood/DiversCategCharLikelihood.class
trunk/treebase-core/lib/mesquite/diverse/EvolveTreesDiversChars/
trunk/treebase-core/lib/mesquite/diverse/EvolveTreesDiversChars/EvolveTreesDiversChars.class
trunk/treebase-core/lib/mesquite/diverse/LineagesThroughTime/
trunk/treebase-core/lib/mesquite/diverse/LineagesThroughTime/LinPanel.class
trunk/treebase-core/lib/mesquite/diverse/LineagesThroughTime/LineagesThroughTime.class
trunk/treebase-core/lib/mesquite/diverse/LineagesThroughTime/LineagesWindow.class
trunk/treebase-core/lib/mesquite/diverse/SisterDiversification/
trunk/treebase-core/lib/mesquite/diverse/SisterDiversification/SisterDiversification.class
trunk/treebase-core/lib/mesquite/diverse/SpecExtincLikelihood/
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+++ trunk/treebase-core/lib/mesquite/charts/Notes/Chart Notes.txt 2009-12-16 10:14:30 UTC (rev 392)
@@ -0,0 +1,8 @@
+Notes for mesquite.charts
+----------------------------------
+
+- rewrite entire charting undercode into separate components:
+ - generation and storage of data (one, two, three... values per item)
+ - modules for display of charts that would allow much more flexibility in presentation
+
+-color by codon positions
\ No newline at end of file
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--- trunk/treebase-core/lib/mesquite/charts/ShowPercentile/manual.html (rev 0)
+++ trunk/treebase-core/lib/mesquite/charts/ShowPercentile/manual.html 2009-12-16 10:14:30 UTC (rev 392)
@@ -0,0 +1,47 @@
+<HTML>
+<!--This file created 14/3/01 8:53 AM by Claris Home Page version 3.0-->
+<HEAD>
+ <TITLE>Show Percentile</TITLE>
+ <META NAME=GENERATOR CONTENT="Claris Home Page 3.0">
+ <X-CLARIS-WINDOW TOP=42 BOTTOM=757 LEFT=4 RIGHT=534>
+ <X-CLARIS-TAGVIEW MODE=minimal>
+<meta http-equiv="content-type" content="text/html;charset=iso-8859-1">
+</HEAD>
+<BODY>
+<H2><TABLE BORDER=4 CELLPADDING=0>
+ <TR>
+ <TD>
+ <H2>Mesquite: Show Percentile</H2>
+ </TD>
+ </TR>
+</TABLE>
+</H2>
+
+<H4>David Maddison & Wayne Maddison</H4>
+
+<P>August 2005</P>
+
+<P>Show Percentile calculates and displays percentile values in histograms.</P>
+<P>For example, the lower (left) tail of the following distribution has the 0.01
+ percentile marked, as exactly 1 of the 100 values is less than or equal to the
+ marked value. </P>
+<P><img src="01.gif" width="468" height="250"></P>
+<P>Show Percentile shows that value that corresponds to the specified percentile.
+ However, if there is no value that exactly corresponds to a percentile, then
+ it shows the value that corresponds most closely to the requested percentile,
+ but that is less than the requested percentile. For example, the nearest two
+ percentiles in this distribution to 0.001 would be either 0.0 (including 0 values)
+ or 0.01 (including 1 value); Show Percentile chooses 0.0, as that is the nearest
+ value that does not exceed the requested percentile:</P>
+<P><img src="001.gif" width="468" height="250"></P>
+<P>The 0.05 lower percentile for this distribution is shown below:</P>
+<P><img src="05.gif" width="468" height="250"></P>
+<P>This might also be the distribution shown if you requested 0.06, as the nearest
+ percentiles for that value are 0.05 or 0.07, and so Show Percentile would choose
+ 0.05. <br>
+</P>
+<P>Full details of the percentiles displayed can be seen by touching the Text
+ tab of the histogram window.</P>
+<P>© David Maddison & Wayne Maddison, 2005</P>
+</BODY>
+</HTML>
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--- trunk/treebase-core/lib/mesquite/charts/explanation.txt (rev 0)
+++ trunk/treebase-core/lib/mesquite/charts/explanation.txt 2009-12-16 10:14:30 UTC (rev 392)
@@ -0,0 +1,2 @@
+Charting Package
+One of the core Mesquite packages. Provides basic charting facilities (histograms, scatter plots) and some particular charts (histograms and scattergrams for trees, characters, taxa and other objects).
\ No newline at end of file
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