Details
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Type: Bug
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Status: Closed
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Priority: Critical
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Resolution: Fixed
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Affects Version/s: 2.8.2, 2.8.2b1, 2.9
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Fix Version/s: 2.10.0
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Component/s: None
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Labels:
Description
While testing JAL-1829, I discovered that the StructureSelectionManager class throws an ArrayIndexOutOfBoundsException while attempting to load some PDB structures concurrently, this happens on both JMol and Chimera
To reproduce:
- fetch the following sequences from PDB: 3nh6; 4rvc; 4q4h.
- select all of the sequence and attempt to view all structures for them together.
Stack trace for JMol:
Squashed Jmol callback handler error:
java.lang.ArrayIndexOutOfBoundsException: -2
at jalview.structure.StructureSelectionManager.setMapping(StructureSelectionManager.java:521)
at jalview.structure.StructureSelectionManager.setMapping(StructureSelectionManager.java:323)
at jalview.ext.jmol.JalviewJmolBinding.notifyFileLoaded(JalviewJmolBinding.java:1185)
at jalview.ext.jmol.JalviewJmolBinding.notifyCallback(JalviewJmolBinding.java:995)
at org.jmol.viewer.StatusManager.setFileLoadStatus(Unknown Source)
at org.jmol.viewer.Viewer.setFileLoadStatus(Unknown Source)
at org.jmol.viewer.Viewer.createModelSetAndReturnError(Unknown Source)
at org.jmol.viewer.Viewer.loadModelFromFile(Unknown Source)
at org.jmol.script.ScriptEval.cmdLoad(Unknown Source)
at org.jmol.script.ScriptEval.processCommand(Unknown Source)
at org.jmol.script.ScriptEval.commandLoop(Unknown Source)
at org.jmol.script.ScriptEval.dispatchCommands(Unknown Source)
at org.jmol.script.ScriptEval.executeCommands(Unknown Source)
at org.jmol.script.ScriptEval.evaluateCompiledScript(Unknown Source)
at org.jmol.script.ScriptManager.evalStringWaitStatusQueued(Unknown Source)
at org.jmol.viewer.Viewer.evalStringWaitStatusQueued(Unknown Source)
at org.jmol.script.ScriptQueueThread.runNextScript(Unknown Source)
at org.jmol.script.ScriptQueueThread.run1(Unknown Source)
at org.jmol.thread.JmolThread.run(Unknown Source)
Stack trace for Chimera:
ERROR: jalview.bin.Jalview - Couldn't open /var/folders/yk/7sbd4m7x5gbf5_lx4kz8rd99t8z5dm/T/jalview2451205814476899932.xml in Chimera viewer!
java.lang.ArrayIndexOutOfBoundsException: -2
at jalview.structure.StructureSelectionManager.setMapping(StructureSelectionManager.java:521)
at jalview.structure.StructureSelectionManager.setMapping(StructureSelectionManager.java:323)
at jalview.gui.ChimeraViewFrame.run(ChimeraViewFrame.java:861)
at java.lang.Thread.run(Thread.java:745)
ERROR - Couldn't open /var/folders/yk/7sbd4m7x5gbf5_lx4kz8rd99t8z5dm/T/jalview2451205814476899932.xml in Chimera viewer!
java.lang.ArrayIndexOutOfBoundsException: -2
at jalview.structure.StructureSelectionManager.setMapping(StructureSelectionManager.java:521)
at jalview.structure.StructureSelectionManager.setMapping(StructureSelectionManager.java:323)
at jalview.gui.ChimeraViewFrame.run(ChimeraViewFrame.java:861)
at java.lang.Thread.run(Thread.java:745)
To reproduce:
- fetch the following sequences from PDB: 3nh6; 4rvc; 4q4h.
- select all of the sequence and attempt to view all structures for them together.
Stack trace for JMol:
Squashed Jmol callback handler error:
java.lang.ArrayIndexOutOfBoundsException: -2
at jalview.structure.StructureSelectionManager.setMapping(StructureSelectionManager.java:521)
at jalview.structure.StructureSelectionManager.setMapping(StructureSelectionManager.java:323)
at jalview.ext.jmol.JalviewJmolBinding.notifyFileLoaded(JalviewJmolBinding.java:1185)
at jalview.ext.jmol.JalviewJmolBinding.notifyCallback(JalviewJmolBinding.java:995)
at org.jmol.viewer.StatusManager.setFileLoadStatus(Unknown Source)
at org.jmol.viewer.Viewer.setFileLoadStatus(Unknown Source)
at org.jmol.viewer.Viewer.createModelSetAndReturnError(Unknown Source)
at org.jmol.viewer.Viewer.loadModelFromFile(Unknown Source)
at org.jmol.script.ScriptEval.cmdLoad(Unknown Source)
at org.jmol.script.ScriptEval.processCommand(Unknown Source)
at org.jmol.script.ScriptEval.commandLoop(Unknown Source)
at org.jmol.script.ScriptEval.dispatchCommands(Unknown Source)
at org.jmol.script.ScriptEval.executeCommands(Unknown Source)
at org.jmol.script.ScriptEval.evaluateCompiledScript(Unknown Source)
at org.jmol.script.ScriptManager.evalStringWaitStatusQueued(Unknown Source)
at org.jmol.viewer.Viewer.evalStringWaitStatusQueued(Unknown Source)
at org.jmol.script.ScriptQueueThread.runNextScript(Unknown Source)
at org.jmol.script.ScriptQueueThread.run1(Unknown Source)
at org.jmol.thread.JmolThread.run(Unknown Source)
Stack trace for Chimera:
ERROR: jalview.bin.Jalview - Couldn't open /var/folders/yk/7sbd4m7x5gbf5_lx4kz8rd99t8z5dm/T/jalview2451205814476899932.xml in Chimera viewer!
java.lang.ArrayIndexOutOfBoundsException: -2
at jalview.structure.StructureSelectionManager.setMapping(StructureSelectionManager.java:521)
at jalview.structure.StructureSelectionManager.setMapping(StructureSelectionManager.java:323)
at jalview.gui.ChimeraViewFrame.run(ChimeraViewFrame.java:861)
at java.lang.Thread.run(Thread.java:745)
ERROR - Couldn't open /var/folders/yk/7sbd4m7x5gbf5_lx4kz8rd99t8z5dm/T/jalview2451205814476899932.xml in Chimera viewer!
java.lang.ArrayIndexOutOfBoundsException: -2
at jalview.structure.StructureSelectionManager.setMapping(StructureSelectionManager.java:521)
at jalview.structure.StructureSelectionManager.setMapping(StructureSelectionManager.java:323)
at jalview.gui.ChimeraViewFrame.run(ChimeraViewFrame.java:861)
at java.lang.Thread.run(Thread.java:745)