JAL-2499: fix Sequence Features PCA calculation

Activity

CR-JAL-51 4

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    Participant Role Time Spent Comments Latest Comment
    Author 10m 1 sorry to be curmudgeonly - but by getting rid of ViewBase...
    Reviewer - Complete 11m 2 I should clarify that here ugly meant: instanceof + downc...
    Total   20m 4  
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    Objectives

    1. load uniref50.fa and exampleFeatures.txt
    2. Compute a PCA with the Sequence Features Similarity score

    On features/JAL-2393customMatrices (f647b9ceacdc464621491653cfb3382b42ca14a5) this results in a PCA viewer where all the points lie at the origin. File->Output Values shows the input matrix for PCA to be all zeros.

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    /src/jalview/.../scoremodels/PIDModel.java Changed
    /src/jalview/.../scoremodels/ScoreMatrix.java Changed
    /src/jalview/.../scoremodels/ScoreModels.java Changed 4
    /src/jalview/appletgui/TreePanel.java Changed
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    /src/jalview/gui/AlignFrame.java Changed
    /src/jalview/gui/CalculationChooser.java Changed
    /src/jalview/gui/CalculationChooser.java Changed
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    /src/jalview/gui/PCAPanel.java Changed
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    /src/jalview/gui/TreePanel.java Changed
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    /src/jalview/io/ScoreMatrixFile.java Changed
    /src/jalview/jbgui/GAlignFrame.java Changed
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    /src/jalview/viewmodel/PCAModel.java Changed
    /test/.../scoremodels/ScoreMatrixTest.java Changed
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    /test/jalview/io/ScoreMatrixFileTest.java Changed
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