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  1. Jalview
  2. JAL-4539

find causes stack overflow

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    Details

    • Type: Bug
    • Status: Open
    • Priority: Blocker
    • Resolution: Unresolved
    • Affects Version/s: 2.11.5.0
    • Fix Version/s: 2.11.5.1
    • Component/s: find
    • Labels:

      Description

      I managed to have this happen when drag/dropping a structure onto an alignment during the '3 pfam alignments, one structure' conservation visualisation on structure exercise.

      Exception in thread "AWT-EventQueue-0" java.lang.StackOverflowError
      at jalview.datamodel.Alignment.getHeight(Alignment.java:707)
      at jalview.analysis.Finder.getSequence(Finder.java:230)
      at jalview.analysis.Finder.nextSequence(Finder.java:358)
      at jalview.analysis.Finder.getSequence(Finder.java:239)
      at jalview.analysis.Finder.nextSequence(Finder.java:358)
      at jalview.analysis.Finder.getSequence(Finder.java:239)
      at jalview.analysis.Finder.nextSequence(Finder.java:358)

      Steps to reproduce:
      1. Import uniref50.fa
      2. Copy and paste the first four sequences to a new alignment window.
      3. Open 'Find' and search for FER1_SPIOL in the new alignment. click away the 'Finished searching' dialog, but keep the Find dialog open.
      4. Select FER1_SPIOL in the first alignment.
      5. Click 'Find' in the find dialog, FER1_SPIOL will be found.
      6. Click 'Find' again - jalview will wait a bit - and eventually return control without any other dialog appearing, and without FER1_SPIOL being highlighted as found. If the console is open, the stackoverflow error will be shown - otherwise check the log file.

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            Assignee:
            reniacorreya Renia Correya
            Reporter:
            jprocter James Procter
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              Created:
              Updated: