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  1. Jalview
  2. JAL-579

very large sequences cause buffer overflow when passing instructions to Jmol

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    Details

    • Type: Bug
    • Status: Open
    • Priority: Major
    • Resolution: Unresolved
    • Affects Version/s: 2.5.1
    • Fix Version/s: None
    • Component/s: Structures
    • Labels:
      None

      Description

      Reproduce by:
      Import structure 3i8f, and try to view the first, and then the second RNA chain.
      The following exception is raised:

      Exception in thread "Thread-43" java.lang.StringIndexOutOfBoundsException: String index out of range: -65517
      at java.lang.String.substring(String.java:1937)
      at org.jmol.viewer.Eval.getCommand(Eval.java:861)
      at org.jmol.viewer.Eval.instructionDispatchLoop(Eval.java:491)
      at org.jmol.viewer.Eval.runEval(Eval.java:110)
      at org.jmol.viewer.Viewer.evalStringWaitStatus(Viewer.java:2573)
      at org.jmol.viewer.ScriptManager.runScript(ScriptManager.java:130)
      at org.jmol.viewer.ScriptManager.runNextScript(ScriptManager.java:119)
      at org.jmol.viewer.ScriptManager$ScriptQueueRunnable.run(ScriptManager.java:147)
      at java.lang.Thread.run(Thread.java:619)


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              Assignee:
              jprocter James Procter
              Reporter:
              jprocter James Procter
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                Dates

                Created:
                Updated: