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  1. Jalview
  2. JAL-1145

exceptions when copy/paste sequences with grouped annotation rows to new window

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    Details

    • Type: Bug
    • Status: Resolved
    • Priority: Major
    • Resolution: Fixed
    • Affects Version/s: 2.8
    • Fix Version/s: 2.8
    • Component/s: Datamodel
    • Labels:
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      Description

      Grouping of annotation rows on an alignment view is defined by the jalview.datamodel.AlignmentAnnotation.graphGroup field, an integer, that when above -1, indicates a group index where annotation rows can be grouped to overlay line graphs.

      Copy and pasting sequence associated annotation with line_graph groups results in exceptions in the following example:
      >a
      asdasd
      >b
      asdasd
      >c
      asdasd


      SEQUENCE_REF a
      annotation group 1 (annotation row 1 and 2)
      SEQUENCE_REF b
      annotation group 2 (annotation row 3 and 4)
      SEQUENCE_REF c
      annotation group 3 (annotation row 5 and 6)

      The problem occurs when b is copied into a new window. The rendering code in v2.7 uses a preallocated boolean array to decide if a graphGroup has been laid out already, which is set to be the length of the alignment's annotation row vector. Since alignmentAnnotation rows are copied across - they inherit the same graphGroup in the new window, which for sequence C will be 3. This will cause an ArrayIndexOutOfBounds exception..

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            Assignee:
            jprocter Jim Procter
            Reporter:
            jprocter Jim Procter
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              Created:
              Updated:
              Resolved: