JAL-2397: Correct PCA (Jalview/SeqSpace) and substitution matrix based tree...

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CR-JAL-35 7

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    Participant Role Time Spent Comments Latest Comment
    Author 8m 4 now done
    Reviewer - Complete 21m 3 I've outlined how this could be done in CR-JAL-33.
    Total   29m 7  
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    Objectives

    Tree distances calculation uses column 23 of the Blosum62 matrix to score char-gap (as -4) or gap-gap (as +1).
    PCA calculation uses column 22 (residue 'X') which scores 0 for A/S/T and -1 or -2 for other residues (-1 for X-X).
    a) should these be consistent?
    b) should they both use zero for gap scores?

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    Issues Raised From Comments

    Key Summary State Assignee
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    General Comments

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    /examples/groovy/pcaMode.groovy Deleted
    Open in IDE #permalink
    /src/jalview/analysis/PCA.java Changed 7
    /src/jalview/appletgui/PCAPanel.java Changed
    /src/jalview/math/Matrix.java Changed
    /src/jalview/math/MatrixI.java Changed
    /src/jalview/schemes/ScoreMatrix.java Changed
    Open in IDE #permalink
    /src/jalview/viewmodel/PCAModel.java Changed
    Open in IDE #permalink
    /test/jalview/math/MatrixTest.java Changed
    /test/jalview/schemes/ScoreMatrixTest.java Changed

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