JAL-2438: Make findFeatureColour thread-safe and smarter

Activity

CR-JAL-18 11

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    Participant Role Time Spent Comments Latest Comment
    Author 20m 5 I agree. I had swerved these fields as not sure what they...
    Reviewer - Complete 57m 4 I realise this code is unchanged, but I think it actually...
    Total   1h 17m 11  
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    Objectives

    FeatureRenderer.findFeatureColour is called when determining feature colours for structures or the overview window. Because it is not currently thread-safe, 'clones' of FeatureRenderer are used for this. This is fragile (see JAL-2436 for a bug resulting).

    Proposed to explore how to make the method thread-safe so that no clones are needed, only a 'read-only' view of the FeatureRenderer.

    Performance is critical here so must be preserved - and improved where possible.

    Branches in review

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    Issues Raised From Comments

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    General Comments

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    /src/MCview/AppletPDBCanvas.java Changed
    /src/MCview/PDBCanvas.java Changed
    /src/jalview/api/FeatureRenderer.java Changed
    /src/jalview/api/SequenceRenderer.java Changed
    /src/.../appletgui/AppletJmolBinding.java Changed
    /src/jalview/appletgui/ExtJmol.java Changed
    /src/jalview/appletgui/OverviewPanel.java Changed
    /src/jalview/appletgui/SeqCanvas.java Changed
    /src/.../appletgui/SequenceRenderer.java Changed
    /src/jalview/.../jmol/JalviewJmolBinding.java Changed 3
    /src/jalview/ext/jmol/JmolCommands.java Changed
    /src/jalview/.../chimera/ChimeraCommands.java Changed
    /src/.../chimera/JalviewChimeraBinding.java Changed 2
    /src/jalview/ext/varna/VarnaCommands.java Changed
    /src/jalview/gui/AppJmolBinding.java Changed
    /src/jalview/gui/FeatureRenderer.java Changed
    /src/.../gui/JalviewChimeraBindingModel.java Changed 3
    /src/jalview/gui/OverviewPanel.java Changed
    /src/jalview/gui/SeqCanvas.java Changed
    /src/jalview/gui/SequenceRenderer.java Changed
    /src/jalview/io/JSONFile.java Changed
    /src/.../javascript/MouseOverStructureListener.java Changed
    /src/.../seqfeatures/FeatureColourFinder.java Added
    /src/.../seqfeatures/FeatureRenderer.java Changed 3
    /src/.../models/AAStructureBindingModel.java Changed
    /src/.../seqfeatures/FeatureRendererModel.java Changed
    /test/jalview/.../jmol/JmolCommandsTest.java Changed
    /test/.../chimera/ChimeraCommandsTest.java Changed
    /test/.../seqfeatures/FeatureColourFinderTest.java Changed
    /test/.../models/AAStructureBindingModelTest.java Changed

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