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  1. Jalview
  2. JAL-1380

remove gapped columns fails for sequences with ragged trailing gaps

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    Details

    • Type: Bug
    • Status: Resolved
    • Priority: Major
    • Resolution: Fixed
    • Affects Version/s: None
    • Fix Version/s: 2.8.1
    • Component/s: Datamodel
    • Labels:
      None

      Description

      Some alignments can cause the remove gapped columns operation to fail with an unexpected exception, which Jalview does not report to the user.

      To reproduce:
      Import the following as a new alignment

      >a
      acd-d------
      >b
      acd-d--c
      >c
      acd---------

      Apply the 'Remove Gapped Columns' option in the edit menu. An exception from SequenceI.deleteChars(i,j) will be thrown like:
      Exception in thread "AWT-EventQueue-0" java.lang.ArrayIndexOutOfBoundsException: 116
      at jalview.datamodel.Sequence.deleteChars(Sequence.java:720)
      at jalview.commands.EditCommand.deleteGap(EditCommand.java:270)
      at jalview.commands.EditCommand.performEdit(EditCommand.java:188)
      at jalview.commands.RemoveGapColCommand.<init>(RemoveGapColCommand.java:106)
      at jalview.gui.AlignFrame.removeGappedColumnMenuItem_actionPerformed(AlignFrame.java:2339)

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            Assignee:
            jprocter James Procter
            Reporter:
            jprocter James Procter
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              Updated:
              Resolved: