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  1. Jalview
  2. JAL-4179

Common nucleotide symbols turns sequence into 'protein', cannot set colour to 'nucleotide'

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    Details

    • Type: Bug
    • Status: Open
    • Priority: Major
    • Resolution: Unresolved
    • Affects Version/s: 2.11.2.6
    • Fix Version/s: 2.11.3
    • Component/s: gui design issue
    • Labels:
    • Environment:
      linux/java

      Description

      After saving an alignment of RNAs/DNAs with (very common) symbols like 'R' (i.e. A or G), and 'Y' (i.e. C or T) in a sequence alignment turns this alignment into one of 'proteins'.

      In Jalview, on reopening this alignment such a sequence alignment cannot be coloured as 'nucleotide' under 'Colour' in the GUI, 'nucleotide' is greyed out.

      This is hugely interfering with work flow; needs to keep separate versions for jalview-use.

      Please take that needless restriction out of the GUI.

      Cheers

      Rob.

        Attachments

          Issue Links

          related with

          New Feature - A new feature of the product, which has yet to be developed. JAL-3963 colour ambiguous nucleotides and report residue statistics in alignment properties

          • Trivial - Cosmetic problem like misspelt words or misaligned text.
          • Open

          New Feature - A new feature of the product, which has yet to be developed. JAL-4019 Ambiguous Base Colourscheme

          • Minor - Minor loss of function, or other problem where easy workaround is present.
          • Closed

          Bug - A problem which impairs or prevents the functions of the product. JAL-4184 After exporting Fasta (.fa) to Stockholm (.sto) sequence descriptions are lost

          • Major - Major loss of function.
          • Closed

          New Feature - A new feature of the product, which has yet to be developed. JAL-3963 colour ambiguous nucleotides and report residue statistics in alignment properties

          • Trivial - Cosmetic problem like misspelt words or misaligned text.
          • Open

            Activity

              People

              Assignee:
              jprocter James Procter
              Reporter:
              brobr Rob v N
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                Dates

                Created:
                Updated: