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  1. Jalview
  2. JAL-4540

Tree calculation out of memory error not passed to user!

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    Details

    • Type: Bug
    • Status: Open
    • Priority: Major
    • Resolution: Unresolved
    • Affects Version/s: 2.11.4.0, 2.11.4.1
    • Fix Version/s: 2.11.5.0
    • Component/s: gui, trees
    • Labels:
      None
    • Urgency:
      Highest

      Description

      If jalview 2.11.4.1 runs out of memory whilst building the similarity matrix during the tree calculation, it leaves the window showing and doesn't let the user know.

      WARN - Request to http://127.0.0.1:9124 returned java.net.ConnectException: Connection refused (Connection refused)
      Exception in thread "Thread-36" java.lang.OutOfMemoryError: Java heap space
      at jalview.math.Matrix.<init>(Matrix.java:104)
      at jalview.analysis.scoremodels.ScoreMatrix.findSimilarities(ScoreMatrix.java:498)
      at jalview.analysis.scoremodels.ScoreMatrix.findSimilarities(ScoreMatrix.java:471)
      at jalview.analysis.scoremodels.SimilarityScoreModel.findDistances(SimilarityScoreModel.java:40)
      at jalview.analysis.TreeBuilder.computeTree(TreeBuilder.java:124)
      at jalview.analysis.TreeBuilder.<init>(TreeBuilder.java:78)
      at jalview.analysis.AverageDistanceTree.<init>(AverageDistanceTree.java:44)
      at jalview.gui.TreePanel$TreeLoader.run(TreePanel.java:392)

      Simply needs wrapping with an OOMError try/catch and appropriate warning dialog shown as in other places.

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            Assignee:
            jprocter James Procter
            Reporter:
            jprocter James Procter
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              Dates

              Created:
              Updated: