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  1. Jalview
  2. JAL-1185

NPE with v2.7 example when clicking on Tree associated with all views

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    Details

    • Type: Bug
    • Status: Resolved
    • Priority: Major
    • Resolution: Fixed
    • Affects Version/s: 2.7
    • Fix Version/s: 2.8
    • Component/s: analysis, gui, jvdesktop
    • Labels:
      None

      Description

      Steps to reproduce:
      1. Open http://www.jalview.org/examples/exampleFile_2_7.jar
      2. Select 'All' for View->Associated leaves with ->
      3. Click on tree to partition.

      Symptoms: when Jalview java console is open, redraw is slow, as NPE exception is generated in console.

      Output is here:
      Null annotation row: ignoring.
      Null annotation row: ignoring.
      Exception in thread "AWT-EventQueue-0" java.lang.NullPointerException
      at jalview.datamodel.Alignment.removeAnnotationForGroup(Alignment.java:364)
      at jalview.datamodel.Alignment.deleteAllGroups(Alignment.java:409)
      at jalview.gui.TreeCanvas.mousePressed(TreeCanvas.java:854)
      at java.awt.AWTEventMulticaster.mousePressed(AWTEventMulticaster.java:262)
      at java.awt.Component.processMouseEvent(Component.java:6370)
      at javax.swing.JComponent.processMouseEvent(JComponent.java:3267)
      at java.awt.Component.processEvent(Component.java:6138)
      at java.awt.Container.processEvent(Container.java:2085)
      at java.awt.Component.dispatchEventImpl(Component.java:4735)
      at java.awt.Container.dispatchEventImpl(Container.java:2143)
      at java.awt.Component.dispatchEvent(Component.java:4565)
      at java.awt.LightweightDispatcher.retargetMouseEvent(Container.java:4621)
      at java.awt.LightweightDispatcher.processMouseEvent(Container.java:4279)
      at java.awt.LightweightDispatcher.dispatchEvent(Container.java:4212)
      at java.awt.Container.dispatchEventImpl(Container.java:2129)
      at java.awt.Window.dispatchEventImpl(Window.java:2478)
      at java.awt.Component.dispatchEvent(Component.java:4565)
      at java.awt.EventQueue.dispatchEventImpl(EventQueue.java:679)
      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.security.AccessControlContext$1.doIntersectionPrivilege(AccessControlContext.java:98)
      at java.awt.EventQueue$2.run(EventQueue.java:652)
      at java.awt.EventQueue$2.run(EventQueue.java:650)
      at java.security.AccessController.doPrivileged(Native Method)
      at java.security.AccessControlContext$1.doIntersectionPrivilege(AccessControlContext.java:87)
      at java.awt.EventQueue.dispatchEvent(EventQueue.java:649)
      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)
      Exception in thread "AWT-EventQueue-0" java.lang.NullPointerException
      at jalview.datamodel.Alignment.removeAnnotationForGroup(Alignment.java:364)
      at jalview.datamodel.Alignment.deleteAllGroups(Alignment.java:409)
      at jalview.gui.TreeCanvas.mousePressed(TreeCanvas.java:854)
      at java.awt.AWTEventMulticaster.mousePressed(AWTEventMulticaster.java:262)
      at java.awt.Component.processMouseEvent(Component.java:6370)
      at javax.swing.JComponent.processMouseEvent(JComponent.java:3267)
      at java.awt.Component.processEvent(Component.java:6138)
      at java.awt.Container.processEvent(Container.java:2085)
      at java.awt.Component.dispatchEventImpl(Component.java:4735)
      at java.awt.Container.dispatchEventImpl(Container.java:2143)
      at java.awt.Component.dispatchEvent(Component.java:4565)
      at java.awt.LightweightDispatcher.retargetMouseEvent(Container.java:4621)
      at java.awt.LightweightDispatcher.processMouseEvent(Container.java:4279)
      at java.awt.LightweightDispatcher.dispatchEvent(Container.java:4212)
      at java.awt.Container.dispatchEventImpl(Container.java:2129)
      at java.awt.Window.dispatchEventImpl(Window.java:2478)
      at java.awt.Component.dispatchEvent(Component.java:4565)
      at java.awt.EventQueue.dispatchEventImpl(EventQueue.java:679)
      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.security.AccessControlContext$1.doIntersectionPrivilege(AccessControlContext.java:98)
      at java.awt.EventQueue$2.run(EventQueue.java:652)
      at java.awt.EventQueue$2.run(EventQueue.java:650)
      at java.security.AccessController.doPrivileged(Native Method)
      at java.security.AccessControlContext$1.doIntersectionPrivilege(AccessControlContext.java:87)
      at java.awt.EventQueue.dispatchEvent(EventQueue.java:649)
      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)

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            Assignee:
            jprocter James Procter
            Reporter:
            jprocter James Procter
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              Dates

              Created:
              Updated:
              Resolved: