Details
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Type:
Bug
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Status: Resolved
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Priority:
Minor
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Resolution: Cannot Reproduce
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Affects Version/s: 2.8
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Fix Version/s: 2.8
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Component/s: jvdesktop, Structures
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Labels:
Description
Selecting all sequences in an the feredoxin example alignment, discover all PDB ids, then view all structures for selection yields a Jmol window containing all structures but no superposition takes place.
An exception is raised like the one below:
INFO - Couldn't align structures with the '/Users/jimp/git/jalview_clean/examples/uniref50.fa' associated alignment panels.
java.lang.ArrayIndexOutOfBoundsException: -1
at jalview.ext.jmol.JalviewJmolBinding.superposeStructures(JalviewJmolBinding.java:508)
at jalview.gui.AppJmol.alignStructs_withAllAlignPanels(AppJmol.java:1266)
at jalview.gui.AppJmol.access$6(AppJmol.java:1241)
at jalview.gui.AppJmol$9.run(AppJmol.java:854)
at java.awt.event.InvocationEvent.dispatch(InvocationEvent.java:209)
at java.awt.EventQueue.dispatchEventImpl(EventQueue.java:677)
at java.awt.EventQueue.access$000(EventQueue.java:85)
at java.awt.EventQueue$1.run(EventQueue.java:638)
at java.awt.EventQueue$1.run(EventQueue.java:636)
at java.security.AccessController.doPrivileged(Native Method)
at java.security.AccessControlContext$1.doIntersectionPrivilege(AccessControlContext.java:87)
at java.awt.EventQueue.dispatchEvent(EventQueue.java:647)
at java.awt.EventDispatchThread.pumpOneEventForFilters(EventDispatchThread.java:296)
at java.awt.EventDispatchThread.pumpEventsForFilter(EventDispatchThread.java:211)
at java.awt.EventDispatchThread.pumpEventsForHierarchy(EventDispatchThread.java:201)
at java.awt.EventDispatchThread.pumpEvents(EventDispatchThread.java:196)
at java.awt.EventDispatchThread.pumpEvents(EventDispatchThread.java:188)
at java.awt.EventDispatchThread.run(EventDispatchThread.java:122)
Its still possible to superpose, but a '-1' is given as the reference structure in the 'alignStructs_withAllAlignPanels()' private method that opens all structures and attempts to align them.
An exception is raised like the one below:
INFO - Couldn't align structures with the '/Users/jimp/git/jalview_clean/examples/uniref50.fa' associated alignment panels.
java.lang.ArrayIndexOutOfBoundsException: -1
at jalview.ext.jmol.JalviewJmolBinding.superposeStructures(JalviewJmolBinding.java:508)
at jalview.gui.AppJmol.alignStructs_withAllAlignPanels(AppJmol.java:1266)
at jalview.gui.AppJmol.access$6(AppJmol.java:1241)
at jalview.gui.AppJmol$9.run(AppJmol.java:854)
at java.awt.event.InvocationEvent.dispatch(InvocationEvent.java:209)
at java.awt.EventQueue.dispatchEventImpl(EventQueue.java:677)
at java.awt.EventQueue.access$000(EventQueue.java:85)
at java.awt.EventQueue$1.run(EventQueue.java:638)
at java.awt.EventQueue$1.run(EventQueue.java:636)
at java.security.AccessController.doPrivileged(Native Method)
at java.security.AccessControlContext$1.doIntersectionPrivilege(AccessControlContext.java:87)
at java.awt.EventQueue.dispatchEvent(EventQueue.java:647)
at java.awt.EventDispatchThread.pumpOneEventForFilters(EventDispatchThread.java:296)
at java.awt.EventDispatchThread.pumpEventsForFilter(EventDispatchThread.java:211)
at java.awt.EventDispatchThread.pumpEventsForHierarchy(EventDispatchThread.java:201)
at java.awt.EventDispatchThread.pumpEvents(EventDispatchThread.java:196)
at java.awt.EventDispatchThread.pumpEvents(EventDispatchThread.java:188)
at java.awt.EventDispatchThread.run(EventDispatchThread.java:122)
Its still possible to superpose, but a '-1' is given as the reference structure in the 'alignStructs_withAllAlignPanels()' private method that opens all structures and attempts to align them.
