JAL-2379: Improve PCA memory management

Activity

CR-JAL-11 5

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    Participant Role Time Spent Comments Latest Comment
    Author 11m 1 The original changes (to encode sequences as SparseMatrix...
    Reviewer - Complete 32m 4 I"ve only found some very minor tidies
    Total   44m 5  
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    Objectives

    Investigate possible improvements to the memory footprint of the PCA calculation.

    Branches in review

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    Issues Raised From Comments

    Key Summary State Assignee
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    General Comments

    Kira Mourão

    I"ve only found some very minor tidies

    I"ve only found some very minor tidies

    Mungo Carstairs

    The original changes (to encode sequences as SparseMatrix using SparseDoubleA...

    The original changes (to encode sequences as SparseMatrix using SparseDoubleArray) got superseded by a further refactoring.
    This skips encoding and instead does the Blosum (or other) score matrix lookup while computing an NxN (N = number of seqs) pairwise similarity score matrix.

    Reviews of these changes under CR-JAL-13.

    /src/jalview/analysis/PCA.java Changed
    /src/jalview/datamodel/BinarySequence.java Changed
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    /src/jalview/.../android/ContainerHelpers.java Changed
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    /src/.../android/SparseDoubleArray.java Added
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    /src/jalview/gui/PCAPanel.java Changed
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    /src/jalview/math/Matrix.java Changed 2
    /src/jalview/math/MatrixI.java Added
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    /src/jalview/math/SparseMatrix.java Added
    /src/jalview/viewmodel/PCAModel.java Changed 1
    /test/.../android/SparseDoubleArrayTest.java Added
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    /test/jalview/math/MatrixTest.java Changed
    /test/jalview/math/SparseMatrixTest.java Added
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