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  1. Jalview
  2. JAL-2360

Make available colour schemes dependent on sequence collection

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    Details

    • Type: Improvement
    • Status: Closed
    • Priority: Minor
    • Resolution: Fixed
    • Affects Version/s: 2.10.1
    • Fix Version/s: 2.10.2
    • Component/s: None
    • Labels:
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      Description

      Currently hard-coded:
      - nucleotide colour schemes are enabled in the Colour menu if alignment is nucleotide, else disabled (except for 'Nucleotide'!!)
      - this logic is missing in the pop-up menu for a selection group
      - peptide colour schemes are always enabled (although not applicable to nucleotide data)

      Three possible improvements:
      1) enable/disable nucleotide colour schemes also in the pop-up menu
      2) enable/disable peptide colour schemes in AlignFrame and pop-up menus
      3) drive this by a property of the SequenceCollectionI rather than hard-code lists of colour schemes

      1) and 2) are straightforward. Adding methods isNucleotide(), isPeptide() to ColourSchemeI would help.
      3) needs some thought:
      - SequenceGroup doesn't have a method isNucleotide(), preventing adding this to SequenceCollectionI
      - could perhaps abstract a bit further e.g.
          ColourSchemeI.isApplicableTo(SequenceCollectionI)
          - with current implementation limited to the nucleotide / peptide check

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              Assignee:
              gmungoc Mungo Carstairs
              Reporter:
              gmungoc Mungo Carstairs
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                Updated:
                Resolved: