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  1. Jalview
  2. JAL-2946

SIFTs mapping error for pdb ID 1eg3 [when DbRefs -> Trim Sequences enabled]

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    Details

    • Type: Bug
    • Status: In Progress
    • Priority: Major
    • Resolution: Unresolved
    • Affects Version/s: 2.10.3, 2.10.4, 2.10.5, 2.11.0, 2.11.1_js
    • Fix Version/s: None
    • Component/s: Structures
    • Labels:

      Description

      Encountered this error when trying to import structures for all transcripts for Ensembl human gene DMD:

      >>> SIFTS File already downloaded for 1EG3
      Getting SIFTS mapping for 1EG3|A: seq ENSP00000367997
      Squashed Jmol callback handler error:
      java.lang.StringIndexOutOfBoundsException: begin 3046, end 635, length 635
      at java.base/java.lang.String.checkBoundsBeginEnd(Unknown Source)
      at java.base/java.lang.String.substring(Unknown Source)
      at jalview.ws.sifts.SiftsClient.getGreedyMapping(SiftsClient.java:583)
      at jalview.ws.sifts.SiftsClient.getSiftsStructureMapping(SiftsClient.java:450)
      at jalview.structure.StructureSelectionManager.getStructureMapping(StructureSelectionManager.java:685)
      at jalview.structure.StructureSelectionManager.computeMapping(StructureSelectionManager.java:531)
      at jalview.structure.StructureSelectionManager.setMapping(StructureSelectionManager.java:324)
      at jalview.ext.jmol.JalviewJmolBinding.notifyFileLoaded(JalviewJmolBinding.java:1163)
      at jalview.ext.jmol.JalviewJmolBinding.notifyCallback(JalviewJmolBinding.java:970)
      at org.jmol.viewer.StatusManager.setFileLoadStatus(StatusManager.java:407)
      at org.jmol.viewer.Viewer.setFileLoadStatus(Viewer.java:4694)
      at org.jmol.viewer.Viewer.createModelSetAndReturnError(Viewer.java:2249)
      at org.jmol.viewer.Viewer.loadModelFromFile(Viewer.java:1737)
      at org.jmol.script.ScriptEval.cmdLoad(ScriptEval.java:4671)
      at org.jmol.script.ScriptEval.processCommand(ScriptEval.java:2380)
      at org.jmol.script.ScriptEval.commandLoop(ScriptEval.java:2248)
      at org.jmol.script.ScriptEval.dispatchCommands(ScriptEval.java:2111)
      at org.jmol.script.ScriptEval.executeCommands(ScriptEval.java:417)
      at org.jmol.script.ScriptEval.evaluateCompiledScript(ScriptEval.java:403)
      at org.jmol.script.ScriptManager.evalStringWaitStatusQueued(ScriptManager.java:356)
      at org.jmol.viewer.Viewer.evalStringWaitStatusQueued(Viewer.java:3835)
      at org.jmol.script.ScriptQueueThread.runNextScript(ScriptQueueThread.java:111)
      at org.jmol.script.ScriptQueueThread.run1(ScriptQueueThread.java:78)
      at org.jmol.thread.JmolThread.run(JmolThread.java:105)
      Time for creating model: 266 ms
      4 models

      Need to test if it can be reproduced with just one transcript and structure.

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            Assignee:
            jprocter Jim Procter
            Reporter:
            jprocter Jim Procter
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              Dates

              Created:
              Updated: