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