Uploaded image for project: 'Jalview'
  1. Jalview
  2. JAL-2940

Deleting sequence from alignment doesn't delete it from sequence group

    XMLWordPrintable

    Details

    • Type: Bug
    • Status: Open
    • Priority: Minor
    • Resolution: Unresolved
    • Affects Version/s: 2.10.3
    • Fix Version/s: None
    • Component/s: Datamodel
    • Labels:
      None

      Description

      Load uniref50.fa and make a group of 3 sequences.
      Select any sequence in the group and Edit | Cut (or Delete).
      Right-click in the group and Output to Textbox as Fasta.
      No output produced, ArrayIndexOutOfBoundsException in the console.
      Cause: the list of sequences in SequenceGroup still includes the deleted sequences. SequenceGroup.size() returns 3 but getSequencesInOrder(alignment) (intersection) returns 2 sequences.
      This is one symptom, there may be others.
      Note the group consensus calculation does calculate correctly: AAFrequency.calculate() receives the deleted sequence, but it has zero length, so is ignored in the calculation.
      Is this a bug or by design?
      If sequence were to be deleted from any sequence groups as well, would want to ensure that Undo restored it...

        Attachments

          Activity

            People

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

              Dates

              Created:
              Updated: