Uploaded image for project: 'Jalview'
  1. Jalview
  2. JAL-3156

Alignment consensus and conservation shading should honour hidden-representative sequences

    XMLWordPrintable

    Details

    • Type: Improvement
    • Status: Open
    • Priority: Minor
    • Resolution: Unresolved
    • Affects Version/s: None
    • Fix Version/s: 2.12.0
    • Component/s: Datamodel, renderer
    • Labels:
      None

      Description

      TIny wrinkle due to jalview.datamodel.Alignment not implementing the getSequences(hidden reps) method correctly: the conservation and consensus rows computed for a view do not include variation due to hidden representatives, whereas the group-wise rows do (but only if the group actually contained the sequences that have been represented by another).

      >a
      AAAAAAAAAAA
      >c1
      CCCCCCCCCC
      >c2
      CCCCCCCCCC
      >c3
      CCCCCCCCCC
      >v
      VVVVVVVVVVV

      Import, show sequence logo for whole view, and enable show group consensus. Create a group containing all sequences. Note C abundance is same as in global consensus. Now press escape to clear selection. Then select c1-c3 and mark as represented by c1. The C abundance is present in the group consensus, but not the alignment consensus.

        Attachments

          Issue Links

            Activity

              People

              Assignee:
              jprocter Jim Procter
              Reporter:
              jprocter Jim Procter
              Votes:
              0 Vote for this issue
              Watchers:
              1 Start watching this issue

                Dates

                Created:
                Updated: