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  1. Jalview
  2. JAL-2038

Drag-and-drop to associate pdb files with sequences of same name is broken

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    Details

    • Type: Bug
    • Status: Closed
    • Priority: Major
    • Resolution: Fixed
    • Affects Version/s: 2.10.0
    • Fix Version/s: 2.10.0
    • Component/s: Structures
    • Labels:
    • Environment:
      Jalview Version: Development Branch Build
      Jalview Installation: webstart git-commit:123f569 [develop]
      Build Date: 28 March 2016
    • Urgency:
      Highest

      Description

      The current development build doesn't seem to support mass association of PDB files (JAL-732). When I try to drop a PDB file named the same way as a sequence onto an alignment, I get the following exception:


      Exceptions from Jmol when processing data in pdb file
      java.lang.reflect.InvocationTargetException
      at sun.reflect.NativeConstructorAccessorImpl.newInstance0(Native Method)
      at sun.reflect.NativeConstructorAccessorImpl.newInstance(NativeConstructorAccessorImpl.java:62)
      at sun.reflect.DelegatingConstructorAccessorImpl.newInstance(DelegatingConstructorAccessorImpl.java:45)
      at java.lang.reflect.Constructor.newInstance(Constructor.java:423)
      at jalview.io.StructureFile.processWithJmolParser(StructureFile.java:285)
      at jalview.io.StructureFile.addSecondaryStructure(StructureFile.java:251)
      at MCview.PDBfile.parse(PDBfile.java:187)
      at jalview.io.AlignFile.doParse(AlignFile.java:170)
      at MCview.PDBfile.<init>(PDBfile.java:54)
      at jalview.structure.StructureSelectionManager.setMapping(StructureSelectionManager.java:395)
      at jalview.gui.AssociatePdbFileWithSeq.associatePdbWithSeq(AssociatePdbFileWithSeq.java:53)
      at jalview.gui.AlignFrame.drop(AlignFrame.java:5227)
      at java.awt.dnd.DropTarget.drop(DropTarget.java:455)
      at sun.awt.dnd.SunDropTargetContextPeer.processDropMessage(SunDropTargetContextPeer.java:538)
      at sun.lwawt.macosx.CDropTargetContextPeer.processDropMessage(CDropTargetContextPeer.java:143)
      at sun.awt.dnd.SunDropTargetContextPeer$EventDispatcher.dispatchDropEvent(SunDropTargetContextPeer.java:852)
      at sun.awt.dnd.SunDropTargetContextPeer$EventDispatcher.dispatchEvent(SunDropTargetContextPeer.java:776)
      at sun.awt.dnd.SunDropTargetEvent.dispatch(SunDropTargetEvent.java:48)
      at java.awt.Component.dispatchEventImpl(Component.java:4746)
      at java.awt.Container.dispatchEventImpl(Container.java:2294)
      at java.awt.Component.dispatchEvent(Component.java:4713)
      at java.awt.LightweightDispatcher.retargetMouseEvent(Container.java:4888)
      at java.awt.LightweightDispatcher.processDropTargetEvent(Container.java:4599)
      at java.awt.LightweightDispatcher.dispatchEvent(Container.java:4461)
      at java.awt.Container.dispatchEventImpl(Container.java:2280)
      at java.awt.Window.dispatchEventImpl(Window.java:2750)
      at java.awt.Component.dispatchEvent(Component.java:4713)
      at java.awt.EventQueue.dispatchEventImpl(EventQueue.java:758)
      at java.awt.EventQueue.access$500(EventQueue.java:97)
      at java.awt.EventQueue$3.run(EventQueue.java:709)
      at java.awt.EventQueue$3.run(EventQueue.java:703)
      at java.security.AccessController.doPrivileged(Native Method)
      at java.security.ProtectionDomain$JavaSecurityAccessImpl.doIntersectionPrivilege(ProtectionDomain.java:76)
      at java.security.ProtectionDomain$JavaSecurityAccessImpl.doIntersectionPrivilege(ProtectionDomain.java:86)
      at java.awt.EventQueue$4.run(EventQueue.java:731)
      at java.awt.EventQueue$4.run(EventQueue.java:729)
      at java.security.AccessController.doPrivileged(Native Method)
      at java.security.ProtectionDomain$JavaSecurityAccessImpl.doIntersectionPrivilege(ProtectionDomain.java:76)
      at java.awt.EventQueue.dispatchEvent(EventQueue.java:728)
      at java.awt.EventDispatchThread.pumpOneEventForFilters(EventDispatchThread.java:201)
      at java.awt.EventDispatchThread.pumpEventsForFilter(EventDispatchThread.java:116)
      at java.awt.EventDispatchThread.pumpEventsForHierarchy(EventDispatchThread.java:105)
      at java.awt.EventDispatchThread.pumpEvents(EventDispatchThread.java:101)
      at java.awt.EventDispatchThread.pumpEvents(EventDispatchThread.java:93)
      at java.awt.EventDispatchThread.run(EventDispatchThread.java:82)
      Caused by: java.lang.NullPointerException
      at MCview.PDBChain.<init>(PDBChain.java:85)
      at jalview.ext.jmol.JmolParser.transformJmolModelToJalview(JmolParser.java:162)
      at jalview.ext.jmol.JmolParser.parse(JmolParser.java:109)
      at jalview.io.AlignFile.doParse(AlignFile.java:170)
      at jalview.io.AlignFile.<init>(AlignFile.java:152)
      at jalview.io.AlignFile.<init>(AlignFile.java:134)
      at jalview.io.StructureFile.<init>(StructureFile.java:56)
      at jalview.ext.jmol.JmolParser.<init>(JmolParser.java:72)
      ... 45 more
      java.lang.NullPointerException
      at jalview.structure.StructureSelectionManager.setProgressBar(StructureSelectionManager.java:1293)
      at jalview.structure.StructureSelectionManager.setMapping(StructureSelectionManager.java:525)
      at jalview.gui.AssociatePdbFileWithSeq.associatePdbWithSeq(AssociatePdbFileWithSeq.java:53)
      at jalview.gui.AlignFrame.drop(AlignFrame.java:5227)
      at java.awt.dnd.DropTarget.drop(DropTarget.java:455)
      at sun.awt.dnd.SunDropTargetContextPeer.processDropMessage(SunDropTargetContextPeer.java:538)
      at sun.lwawt.macosx.CDropTargetContextPeer.processDropMessage(CDropTargetContextPeer.java:143)
      at sun.awt.dnd.SunDropTargetContextPeer$EventDispatcher.dispatchDropEvent(SunDropTargetContextPeer.java:852)
      at sun.awt.dnd.SunDropTargetContextPeer$EventDispatcher.dispatchEvent(SunDropTargetContextPeer.java:776)
      at sun.awt.dnd.SunDropTargetEvent.dispatch(SunDropTargetEvent.java:48)
      at java.awt.Component.dispatchEventImpl(Component.java:4746)
      at java.awt.Container.dispatchEventImpl(Container.java:2294)
      at java.awt.Component.dispatchEvent(Component.java:4713)
      at java.awt.LightweightDispatcher.retargetMouseEvent(Container.java:4888)
      at java.awt.LightweightDispatcher.processDropTargetEvent(Container.java:4599)
      at java.awt.LightweightDispatcher.dispatchEvent(Container.java:4461)
      at java.awt.Container.dispatchEventImpl(Container.java:2280)
      at java.awt.Window.dispatchEventImpl(Window.java:2750)
      at java.awt.Component.dispatchEvent(Component.java:4713)
      at java.awt.EventQueue.dispatchEventImpl(EventQueue.java:758)
      at java.awt.EventQueue.access$500(EventQueue.java:97)
      at java.awt.EventQueue$3.run(EventQueue.java:709)
      at java.awt.EventQueue$3.run(EventQueue.java:703)
      at java.security.AccessController.doPrivileged(Native Method)
      at java.security.ProtectionDomain$JavaSecurityAccessImpl.doIntersectionPrivilege(ProtectionDomain.java:76)
      at java.security.ProtectionDomain$JavaSecurityAccessImpl.doIntersectionPrivilege(ProtectionDomain.java:86)
      at java.awt.EventQueue$4.run(EventQueue.java:731)
      at java.awt.EventQueue$4.run(EventQueue.java:729)
      at java.security.AccessController.doPrivileged(Native Method)
      at java.security.ProtectionDomain$JavaSecurityAccessImpl.doIntersectionPrivilege(ProtectionDomain.java:76)
      at java.awt.EventQueue.dispatchEvent(EventQueue.java:728)
      at java.awt.EventDispatchThread.pumpOneEventForFilters(EventDispatchThread.java:201)
      at java.awt.EventDispatchThread.pumpEventsForFilter(EventDispatchThread.java:116)
      at java.awt.EventDispatchThread.pumpEventsForHierarchy(EventDispatchThread.java:105)
      at java.awt.EventDispatchThread.pumpEvents(EventDispatchThread.java:101)
      at java.awt.EventDispatchThread.pumpEvents(EventDispatchThread.java:93)
      at java.awt.EventDispatchThread.run(EventDispatchThread.java:82)

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              Assignee:
              tcnofoegbu Tochukwu Charles N Ofoegbu
              Reporter:
              jprocter Jim Procter
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                Created:
                Updated:
                Resolved: