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  1. Jalview
  2. JAL-1068

extend the Alignment Viewport and SequenceGroup model to support shading of sequence ID by T-COFFEE score

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    • Type: Task
    • Status: Open
    • Priority: Major
    • Resolution: Unresolved
    • Affects Version/s: None
    • Fix Version/s: None
    • Component/s: Datamodel, renderer
    • Labels:
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      Description

      The Sequence ID colours are set in the following routine:
      jalview.{applet}gui.IDCanvas.drawIDStrings(..).
      These methods get the sequence ID colour from jalview.{applet}gui.AlignViewport.getSequenceColour(SequenceI) - which is a simple hash lookup to retrieve a colour.
      This is currently used in just one way for sequence group based ID colouring. The jalview.datamodel.SequenceGroup object specifies a single ID colour that is examined and applied for each group member in the AlignViewport.updateSequenceIdColours() method.

      If the T-Coffee colourscheme is selected, it should shade the sequence IDs according to the overall score. The easiest route to achieve this may be to extend the colourscheme interface with a new method: 'getSequenceIdColour(SequenceI)'. This would then get called in the .updateSequenceIdColours() loop to get the colour for each sequence according to the applied colourscheme.

      Note: its important that the existing group idColour is given priority if it is set, because a number of web services used this feature to shade sequence IDs in this manner.

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              Assignee:
              paolodt paolo di tommaso
              Reporter:
              jprocter James Procter
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                Created:
                Updated: