JAL-3127: Shade mapped structures or alignment by Sequence's ID colour
CR-JAL-175 21
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- Objectives
- General Comments 3
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- Resolved
- Number of files included: 52
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jalview
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examples/groovy
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- File colourConserved.groovy 0 Remove
- File colourSchemes.groovy 0 Remove
- File colourUnconserved.groovy 0 Remove
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help/html
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calculations
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- File treeviewer.html 0 Remove
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colourSchemes
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- File index.html 3 Remove
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menus
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- File alignmentMenu.html 0 Remove
- File alwcolour.html 0 Remove
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calculations
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src/jalview
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api
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- File AlignViewportI.java 0 Remove
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appletgui
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- File AlignViewport.java 0 Remove
- File TreeCanvas.java 0 Remove
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bin
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- File Jalview.java 0 Remove
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controller
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- File AlignViewController.java 0 Remove
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gui
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- 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
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io
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- File AnnotationFile.java 0 Remove
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schemes
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- 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
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viewmodel
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- File AlignmentViewport.java 0 Remove
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api
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test/jalview
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io
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- File Jalview2xmlTests.java 0 Remove
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schemes
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- File AnnotationColourGradientTest.java 0 Remove
- File ColourSchemePropertyTest.java 0 Remove
- File ColourSchemesTest.java 0 Remove
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io
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examples/groovy
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Details
Participant | Role | Time Spent | Comments | Latest Comment |
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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 |
- Linked Issue:
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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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General Comments
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 ?
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.
Mungo Carstairs marked as Unresolved 09 Nov 18