JAL-3127: Shade mapped structures or alignment by Sequence's ID colour

Activity

CR-JAL-175 21

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    Participant Role Time Spent Comments Latest Comment
    Author 1h 27m 7 we don't have consistent colourscheme class docs. will ad...
    Reviewer - Complete 43m 14 JAL-2250 now done.
    Total   2h 9m 21  
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    Objectives

    When working with alignments of homologous sequences or sub-sequences, it would be useful to be able to colour associated structures according to their group (as defined by cutting a tree or a 'make subgroups' operation).

    This should work for both whole sequences and subsequences - ie if a subsequence in an alignment view has a particular ID colour, then only the corresponding range of the structure should be coloured in that way.

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    Issues Raised From Comments

    Key Summary State Assignee
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    General Comments

    Mungo Carstairs

    The mechanism to update structure colours on change of group colours seems ov...

    The mechanism to update structure colours on change of group colours seems over-complicated.
    It sets a flag on the viewport which is checked at some future point (chosen to be in AlignmentPanel.adjustAnnotationHeight()) and if set
    ap.paintAlignment(true, true);
    which in turn triggers a call to
    av.getStructureSelectionManager().sequenceColoursChanged(this);

    Why not just make this call at the time of setting the group colours (it works!)?
    Then the new flag wouldn't be needed.

    Jim Procter

    If you call ssm.sequenceColoursChanged(this) when a tree cut occurs, a second...

    If you call ssm.sequenceColoursChanged(this) when a tree cut occurs, a second call will still be need to adjustAnnotationHeight() anyway. Other ways of modifying the alignment view also call adjustAnnotationHeight, with the expectation that updates will be propagated to associated structure and overviews. Either we recode every other caller to also explicitly update structure views (regardless of if there is one or not) before triggering an overview repaint, or we push all the conditional event handling to the end.

    Which way do you vote ?

    Jim Procter

    I'll look at this again, anyway. At the time I thought a 'structure view may ...

    I'll look at this again, anyway. At the time I thought a 'structure view may be dirty' flag was easier to implement than track down every case where AlignPanel.updateAnnotation() is called (this is currently what TreePanel calls to update each associated view), in the spirit of JAL-2773.

    /examples/groovy/colourConserved.groovy Changed
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    /examples/groovy/colourSchemes.groovy Changed
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    /examples/groovy/colourUnconserved.groovy Changed
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    /help/html/calculations/treeviewer.html Changed
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    /help/html/colourSchemes/index.html Changed 3
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    /help/html/menus/alignmentMenu.html Changed
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    /help/html/menus/alwcolour.html Changed
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    /src/jalview/api/AlignViewportI.java Changed
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    /src/jalview/appletgui/AlignViewport.java Changed
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    /src/jalview/appletgui/TreeCanvas.java Changed
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    /src/jalview/bin/Jalview.java Changed
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    /src/.../controller/AlignViewController.java Changed
    /src/jalview/gui/AlignFrame.java Changed
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    /src/jalview/gui/AlignViewport.java Changed
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    /src/jalview/gui/AlignmentPanel.java Changed
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    /src/.../gui/AnnotationColourChooser.java Changed
    /src/jalview/gui/Jalview2XML.java Changed
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    /src/jalview/gui/Jalview2XML_V1.java Changed
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    /src/jalview/gui/PopupMenu.java Changed
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    /src/jalview/gui/StructureViewerBase.java Changed
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    /src/jalview/gui/TreeCanvas.java Changed 6
    /src/jalview/io/AnnotationFile.java Changed
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    /src/.../schemes/AnnotationColourGradient.java Changed
    /src/.../schemes/Blosum62ColourScheme.java Changed
    /src/.../schemes/BuriedColourScheme.java Changed
    /src/.../schemes/ClustalxColourScheme.java Changed
    /src/jalview/schemes/ColourSchemeI.java Changed 2
    /src/.../schemes/ColourSchemeProperty.java Changed
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    /src/jalview/schemes/ColourSchemes.java Changed
    /src/.../schemes/CovariationColourScheme.java Changed
    /src/.../schemes/FollowerColourScheme.java Changed
    /src/.../schemes/HelixColourScheme.java Changed
    /src/.../schemes/HydrophobicColourScheme.java Changed
    /src/jalview/schemes/IdColourScheme.java Added 6
    /src/.../schemes/JalviewColourScheme.java Changed 1
    /src/.../schemes/NucleotideColourScheme.java Changed
    /src/jalview/schemes/PIDColourScheme.java Changed
    /src/.../schemes/PurinePyrimidineColourScheme.java Changed
    /src/jalview/schemes/RNAHelicesColour.java Changed
    /src/.../schemes/RNAInteractionColourScheme.java Changed
    /src/.../schemes/ScoreColourScheme.java Changed
    /src/.../schemes/StrandColourScheme.java Changed
    /src/.../schemes/TCoffeeColourScheme.java Changed
    /src/.../schemes/TaylorColourScheme.java Changed
    /src/jalview/schemes/TurnColourScheme.java Changed
    /src/jalview/schemes/UserColourScheme.java Changed
    /src/.../schemes/ZappoColourScheme.java Changed
    /src/.../viewmodel/AlignmentViewport.java Changed
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    /test/jalview/io/Jalview2xmlTests.java Changed
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    /test/.../schemes/AnnotationColourGradientTest.java Changed
    /test/.../schemes/ColourSchemePropertyTest.java Changed
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    /test/.../schemes/ColourSchemesTest.java Changed

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