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  1. Jalview
  2. JAL-1694

JalviewLite can't import sequences with ID descriptions containing angle brackets

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    Details

    • Type: Bug
    • Status: Closed
    • Priority: Major
    • Resolution: Fixed
    • Affects Version/s: 2.8.2, 2.8.2b1
    • Fix Version/s: 2.8.2b1, 2.9
    • Component/s: file format issue
    • Labels:
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      Description

      Reported by Kazutaka Katoh - sequence ID lines with angle brackets cause VARNA exceptions to be thrown. Most likely cause is angle-brackets match the jalview.io.Identify pattern for an RNAML file, so Jalview attempts to call the VARNA rnaml parser.

      Importing this:

      >aseq 5 soso <>[some reference]
      MSTFMSTF

      Results in the following stacktrace:
      Exception in thread "AWT-EventQueue-2" java.lang.NoClassDefFoundError: fr/orsay/lri/varna/exceptions/ExceptionFileFormatOrSyntax
      at jalview.g.e.a(Unknown Source)
      at jalview.appletgui.A.a(Unknown Source)
      at jalview.appletgui.A.actionPerformed(Unknown Source)

      Unobfuscated:
      Exception in thread "AWT-EventQueue-3" java.lang.NoClassDefFoundError: fr/orsay/lri/varna/exceptions/ExceptionFileFormatOrSyntax
      at jalview.io.AppletFormatAdapter.readFile(AppletFormatAdapter.java:273)
      at jalview.appletgui.CutAndPasteTransfer.ok(CutAndPasteTransfer.java:237)
      at jalview.appletgui.CutAndPasteTransfer.actionPerformed(CutAndPasteTransfer.java:98)

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              Assignee:
              tcnofoegbu Tochukwu Charles N Ofoegbu
              Reporter:
              jprocter James Procter
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                Created:
                Updated:
                Resolved: