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  1. Jalview
  2. JAL-1399

Allow user to specify 'original colourscheme' or colours provided by annotation row independently

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    Details

    • Type: Improvement
    • Status: Open
    • Priority: Major
    • Resolution: Unresolved
    • Affects Version/s: None
    • Fix Version/s: 2.12.0
    • Component/s: None
    • Labels:
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      Description

      Update for 2.12:
      This requires a rearrangement of the 'use original colours' option logic such that it allows conservation style shading, or even employ a complex graduated scheme, rather than simply re-using the existing shading but *only* when there is no annotation row specific shading provided. The annotation shading mechanism has been recruited for additional purposes (Hmmer posterior bleaching JAL-3623, PAE groups JAL-4158) and will become more sophisticated in the future, so a UX review is now a priority.

      Original story:
      Currently, the AnnotationColourScheme logic supports three modes of per-Sequence or single row based alignment/group shading:

      i. min/max linear gradient
      ii. Reuse of existing 'Background Colour'
      iii. Use of colours defined in alignment annotation row.

      The Annotation Colouring dialog allows the user to switch between i and ii but iii is currently only available for alignment annotation programmatically created (e.g. via a T-COFFEE file import).

      The ability to switch between all three modes, with out data loss, could be useful, but use cases are needed (e.g. toggling between a linear scheme vs the predefined colourscheme provided by T-COFFEE, etc).

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              Assignee:
              jprocter James Procter
              Reporter:
              jprocter James Procter
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                Created:
                Updated: