JAL-2428: NJTree refactoring

Activity

CR-JAL-36 4

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    Details

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    Participant Role Time Spent Comments Latest Comment
    Author 2m 2 done
    Reviewer - Complete 19m 2 Missing/to be removed documentation on methods
    Total   20m 4  
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    Objectives

    Just a tidy up, not functional change:

    Separate loading tree from file, from computing a tree.
    Make 3 NJ-specific methods overloads in a subclass instead of an if-else choice.
    Use BitSet instead of int[] for Cluster and 'done' field.
    Add Javadoc, tests, as time permits.

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    Issues Raised From Comments

    Key Summary State Assignee
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    General Comments

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    /src/jalview/analysis/AlignmentSorter.java Changed
    /src/.../analysis/AverageDistanceTree.java Added 2
    /src/jalview/analysis/NJTree.java Changed 2
    /src/jalview/analysis/TreeBuilder.java Changed
    /src/jalview/analysis/TreeModel.java Changed
    /src/jalview/api/analysis/ScoreModelI.java Changed
    /src/jalview/appletgui/AlignFrame.java Changed
    /src/jalview/appletgui/AlignViewport.java Changed
    /src/jalview/appletgui/TreeCanvas.java Changed
    /src/jalview/appletgui/TreePanel.java Changed
    /src/jalview/gui/AlignViewport.java Changed
    /src/jalview/gui/Jalview2XML.java Changed
    /src/jalview/gui/TreeCanvas.java Changed
    /src/jalview/gui/TreeChooser.java Deleted
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    /src/jalview/gui/TreePanel.java Changed
    /src/jalview/io/packed/JalviewDataset.java Changed
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    /src/jalview/io/vamsas/Tree.java Changed
    /test/jalview/io/NewickFileTests.java Changed
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