JAL-1632: Dialog to create/edit tree calculation settings

Activity

CR-JAL-39 0

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    Objectives

    The number of score models make the existing tree calculation submenu unwieldly since it is at least 2*(PAM, Blosum, PID, etc) long. It would be better to be able to open a parameter settings dialog to configure a particular tree building calculation which provides the option to create favourite settings combinations.

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    Issues Raised From Comments

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    General Comments

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    /resources/lang/Messages.properties Changed
    /resources/lang/Messages_es.properties Changed
    /resources/scoreModel/blosum62.scm Added
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    /resources/scoreModel/dna.scm Added
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    /resources/scoreModel/pam250.scm Added
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    /src/MCview/AppletPDBCanvas.java Changed
    /src/MCview/PDBCanvas.java Changed
    /src/.../scoremodels/FeatureDistanceModel.java Changed
    /src/jalview/.../scoremodels/PIDModel.java Changed
    /src/.../scoremodels/PairwiseSeqScoreModel.java Changed
    /src/jalview/.../scoremodels/ScoreMatrix.java Added
    /src/jalview/.../scoremodels/ScoreModels.java Added
    /src/.../scoremodels/SimilarityParams.java Changed
    /src/jalview/analysis/AlignSeq.java Changed
    /src/jalview/analysis/Conservation.java Changed
    /src/jalview/analysis/NJTree.java Changed
    /src/jalview/analysis/PCA.java Changed
    /src/jalview/api/analysis/ScoreModelI.java Changed
    /src/.../analysis/SimilarityParamsI.java Changed
    /src/jalview/appletgui/AlignFrame.java Changed
    /src/jalview/appletgui/PCAPanel.java Changed
    /src/jalview/appletgui/TreePanel.java Changed
    /src/jalview/bin/Jalview.java Changed
    /src/jalview/datamodel/BinarySequence.java Changed
    /src/jalview/gui/AlignFrame.java Changed
    /src/jalview/gui/AlignmentPanel.java Changed
    /src/jalview/gui/CalculationChooser.java Added
    /src/jalview/gui/Jalview2XML.java Changed
    /src/jalview/gui/Jalview2XML_V1.java Changed
    /src/jalview/gui/PCAPanel.java Changed
    /src/jalview/gui/SeqPanel.java Changed
    /src/jalview/gui/TreeChooser.java Deleted
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    /src/jalview/gui/TreePanel.java Changed
    /src/jalview/io/vamsas/Tree.java Changed
    /src/jalview/io/VamsasAppDatastore.java Changed
    /src/jalview/jbgui/GAlignFrame.java Changed
    /src/.../schemes/Blosum62ColourScheme.java Changed
    /src/.../schemes/ResidueProperties.java Changed
    /src/jalview/schemes/ScoreMatrix.java Deleted
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    /src/.../structure/StructureSelectionManager.java Changed
    /src/jalview/viewmodel/PCAModel.java Changed
    /src/jalview/.../jws1/SeqSearchWSThread.java Changed
    /test/.../scoremodels/FeatureDistanceModelTest.java Changed
    /test/.../scoremodels/ScoreMatrixTest.java Added
    /test/jalview/analysis/TestAlignSeq.java Changed
    /test/.../schemes/ScoreMatrixPrinter.java Changed

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