CR-JAL-175 JAL-3127: Shade mapped structures or alignment by Sequence's ID colour

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

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General Comments 3
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Resolved
Number of files included: 52

jalview 0
- Folder examples/groovy 0
  - File colourConserved.groovy 0 Remove
  - File colourSchemes.groovy 0 Remove
  - File colourUnconserved.groovy 0 Remove
- Folder help/html 0
  - Folder calculations 0
    - File treeviewer.html 0 Remove
  - Folder colourSchemes 0
    - File index.html 3 Remove
  - Folder menus 0
    - File alignmentMenu.html 0 Remove
    - File alwcolour.html 0 Remove
- Folder src/jalview 0
  - Folder api 0
    - File AlignViewportI.java 0 Remove
  - Folder appletgui 0
    - File AlignViewport.java 0 Remove
    - File TreeCanvas.java 0 Remove
  - Folder bin 0
    - File Jalview.java 0 Remove
  - Folder controller 0
    - File AlignViewController.java 0 Remove
  - Folder gui 0
    - File AlignFrame.java 0 Remove
    - File AlignViewport.java 0 Remove
    - File AlignmentPanel.java 0 Remove
    - File AnnotationColourChooser.java 0 Remove
    - File Jalview2XML.java 0 Remove
    - File Jalview2XML_V1.java 0 Remove
    - File PopupMenu.java 0 Remove
    - File StructureViewerBase.java 0 Remove
    - File TreeCanvas.java 6 Remove
  - Folder io 0
    - File AnnotationFile.java 0 Remove
  - Folder schemes 0
    - File AnnotationColourGradient.java 0 Remove
    - File Blosum62ColourScheme.java 0 Remove
    - File BuriedColourScheme.java 0 Remove
    - File ClustalxColourScheme.java 0 Remove
    - File ColourSchemeI.java 2 Remove
    - File ColourSchemeProperty.java 0 Remove
    - File ColourSchemes.java 0 Remove
    - File CovariationColourScheme.java 0 Remove
    - File FollowerColourScheme.java 0 Remove
    - File HelixColourScheme.java 0 Remove
    - File HydrophobicColourScheme.java 0 Remove
    - File IdColourScheme.java 6 Remove
    - File JalviewColourScheme.java 1 Remove
    - File NucleotideColourScheme.java 0 Remove
    - File PIDColourScheme.java 0 Remove
    - File PurinePyrimidineColourScheme.java 0 Remove
    - File RNAHelicesColour.java 0 Remove
    - File RNAInteractionColourScheme.java 0 Remove
    - File ScoreColourScheme.java 0 Remove
    - File StrandColourScheme.java 0 Remove
    - File TCoffeeColourScheme.java 0 Remove
    - File TaylorColourScheme.java 0 Remove
    - File TurnColourScheme.java 0 Remove
    - File UserColourScheme.java 0 Remove
    - File ZappoColourScheme.java 0 Remove
  - Folder viewmodel 0
    - File AlignmentViewport.java 0 Remove
- Folder test/jalview 0
  - Folder io 0
    - File Jalview2xmlTests.java 0 Remove
  - Folder schemes 0
    - File AnnotationColourGradientTest.java 0 Remove
    - File ColourSchemePropertyTest.java 0 Remove
    - File ColourSchemesTest.java 0 Remove

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

Linked Issue:
JAL-3127

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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.

Branches in review

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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.

09 Nov 18

Mungo Carstairs

Unresolved

09 Nov 18

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 ?

09 Nov 18

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.

09 Nov 18

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CR-JAL-175

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

CR-JAL-175 21

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Issues Raised From Comments

General Comments

Mungo Carstairs

Jim Procter

Jim Procter

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

CR-JAL-175 21

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Details

Objectives

Branches in review

Issues Raised From Comments

General Comments

Mungo Carstairs

Jim Procter

Jim Procter

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