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  1. Jalview
  2. JAL-1866

review and decide on rna helix colouring w.r.t groups

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    Details

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

      RNA Helix colouring is provided as an option in the colour menu, and behaves like an overlay colourscheme (like the sequence feature renderer), but it has a number of issues:

      * no simple way to pick the RNA secondary structure used to colour the alignment
      * Reflects only one rna structure
      * doesn't support conservation shading although the UI allows these functions to be enabled.

      It's functionality is also superseded by the Colour by annotation functon, which for an RNA secondary structure line, creates either a per-sequence or whole alignment colouring.

      There's also a problem with groups and RNA Helix colouring - 'Apply to all groups' sets groups to have the same colouring as the alignment, using the same annotation row as picked for the alignment. However, groups might have their own RNA consensus structure, which could be employed to create subgroup shading in the same way as the current sequence consensus/conservation shading operates.

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              Assignee:
              jprocter Jim Procter
              Reporter:
              jprocter Jim Procter
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