Uploaded image for project: 'Jalview'
  1. Jalview
  2. JAL-2262

Drag and drop pdb file onto alignment throws error (and does not seem to work)

    XMLWordPrintable

    Details

    • Type: Bug
    • Status: Closed
    • Priority: Major
    • Resolution: Fixed
    • Affects Version/s: 2.10.0
    • Fix Version/s: 2.10.0b1
    • Component/s: gui, jvdesktop
    • Labels:
      None
    • Environment:
      MacOS El Capitan
      System Version: OS X 10.11.6 (15G31)
        Kernel Version: Darwin 15.6.0

      Description

      Download pdf file http://www.jalview.org/tutorial/DNMT1_MOUSE.pdb. Retrieve PFAM alignment PF01426. Drag and drop pdf file onto alignment. Say yes to dialog box asking if to associate PDB file with sequences in the alignment that have the same name. Nothing happens but console shows following error:

      java.lang.NullPointerException
      at MCview.PDBChain.transferRESNUMFeatures(PDBChain.java:202)
      at jalview.structure.StructureSelectionManager.getNWMappings(StructureSelectionManager.java:677)
      at jalview.structure.StructureSelectionManager.setMapping(StructureSelectionManager.java:573)
      at jalview.gui.AssociatePdbFileWithSeq.associatePdbWithSeq(AssociatePdbFileWithSeq.java:54)
      at jalview.gui.AlignFrame.drop(AlignFrame.java:4923)
      at java.awt.dnd.DropTarget.drop(DropTarget.java:450)
      at sun.awt.dnd.SunDropTargetContextPeer.processDropMessage(SunDropTargetContextPeer.java:537)
      at sun.lwawt.macosx.CDropTargetContextPeer.processDropMessage(CDropTargetContextPeer.java:143)
      at sun.awt.dnd.SunDropTargetContextPeer$EventDispatcher.dispatchDropEvent(SunDropTargetContextPeer.java:851)
      at sun.awt.dnd.SunDropTargetContextPeer$EventDispatcher.dispatchEvent(SunDropTargetContextPeer.java:775)
      at sun.awt.dnd.SunDropTargetEvent.dispatch(SunDropTargetEvent.java:48)
      at java.awt.Component.dispatchEventImpl(Component.java:4727)
      at java.awt.Container.dispatchEventImpl(Container.java:2287)
      at java.awt.Component.dispatchEvent(Component.java:4698)
      at java.awt.LightweightDispatcher.retargetMouseEvent(Container.java:4832)
      at java.awt.LightweightDispatcher.processDropTargetEvent(Container.java:4566)
      at java.awt.LightweightDispatcher.dispatchEvent(Container.java:4417)
      at java.awt.Container.dispatchEventImpl(Container.java:2273)
      at java.awt.Window.dispatchEventImpl(Window.java:2719)
      at java.awt.Component.dispatchEvent(Component.java:4698)
      at java.awt.EventQueue.dispatchEventImpl(EventQueue.java:747)
      at java.awt.EventQueue.access$300(EventQueue.java:103)
      at java.awt.EventQueue$3.run(EventQueue.java:706)
      at java.awt.EventQueue$3.run(EventQueue.java:704)
      at java.security.AccessController.doPrivileged(Native Method)
      at java.security.ProtectionDomain$1.doIntersectionPrivilege(ProtectionDomain.java:76)
      at java.security.ProtectionDomain$1.doIntersectionPrivilege(ProtectionDomain.java:87)
      at java.awt.EventQueue$4.run(EventQueue.java:720)
      at java.awt.EventQueue$4.run(EventQueue.java:718)
      at java.security.AccessController.doPrivileged(Native Method)
      at java.security.ProtectionDomain$1.doIntersectionPrivilege(ProtectionDomain.java:76)
      at java.awt.EventQueue.dispatchEvent(EventQueue.java:717)
      at java.awt.EventDispatchThread.pumpOneEventForFilters(EventDispatchThread.java:242)
      at java.awt.EventDispatchThread.pumpEventsForFilter(EventDispatchThread.java:161)
      at java.awt.EventDispatchThread.pumpEventsForHierarchy(EventDispatchThread.java:150)
      at java.awt.EventDispatchThread.pumpEvents(EventDispatchThread.java:146)
      at java.awt.EventDispatchThread.pumpEvents(EventDispatchThread.java:138)
      at java.awt.EventDispatchThread.run(EventDispatchThread.java:91)

        Attachments

          Issue Links

            Activity

              People

              Assignee:
              tcnofoegbu Tochukwu Charles N Ofoegbu
              Reporter:
              kmourao Kira MourĂ£o
              Votes:
              0 Vote for this issue
              Watchers:
              4 Start watching this issue

                Dates

                Created:
                Updated:
                Resolved: