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  1. Jalview
  2. JAL-712

arrayindexoutofboundsexception thrown when remove empty columns called on alignment with ragged gapped ends

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    Details

    • Type: Bug
    • Status: Open
    • Priority: Major
    • Resolution: Unresolved
    • Affects Version/s: 2.6.1, 2.7, 2.8.1, 2.8.2, 2.8.2b1, 2.9
    • Fix Version/s: None
    • Component/s: Datamodel, editing

      Description


      Importing an alignment such as:
      >f1
      asasas......
      >f2
      asasasa.
      >f3
      asasdad...

      and then selecting 'Edit->remove gapped columns' causes the following exception:

      In applet:
      Exception in thread "AWT-EventQueue-6" java.lang.ArrayIndexOutOfBoundsException: 12
      at jalview.datamodel.r.d(Unknown Source)

      In application:
      Exception in thread "AWT-EventQueue-0" java.lang.ArrayIndexOutOfBoundsException: 158
      at jalview.datamodel.Sequence.deleteChars(Sequence.java:713)
      at jalview.commands.EditCommand.deleteGap(EditCommand.java:246)
      at jalview.commands.EditCommand.performEdit(EditCommand.java:184)
      at jalview.commands.RemoveGapColCommand.<init>(RemoveGapColCommand.java:106)
      at jalview.gui.AlignFrame.removeGappedColumnMenuItem_actionPerformed(AlignFrame.java:2149)

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            Assignee:
            jprocter James Procter
            Reporter:
            jprocter James Procter
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              Dates

              Created:
              Updated: