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  1. Jalview
  2. JAL-619

jalviewLite does not launch if jmol jar is not on classpath

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    Details

    • Type: Bug
    • Status: Closed
    • Priority: Major
    • Resolution: Fixed
    • Affects Version/s: 2.6
    • Fix Version/s: 2.6
    • Component/s: awt-gui, JVL-Ajax
    • Labels:
      None

      Description

      launching the current development build applet test url:
      http://www.compbio.dundee.ac.uk/user/ws-dev1/jalview/latest/applet/embedded.html

      Raises the following exception:
      java.lang.RuntimeException: java.lang.NoClassDefFoundError: org/jmol/api/JmolViewer
      at sun.plugin2.applet.Plugin2Manager.createApplet(Unknown Source)
      at sun.plugin2.applet.Plugin2Manager$AppletExecutionRunnable.run(Unknown Source)
      at java.lang.Thread.run(Unknown Source)

      However, the embbeded.html applet has 'nojmol' enabled, and furthermore, no structure is being imported that might cause this to happen. It looks like the Plugin2Manager is trying to verify all the classes referenced in the jar are available, but this doesn't happen with the 2.5.1 version of jalview (http://www.compbio.dundee.ac.uk/user/ws-dev1/jalview/latest/applet/embedded.html).

      The rest of the trace is below:
      Caused by: java.lang.NoClassDefFoundError: org/jmol/api/JmolViewer
      at java.lang.Class.getDeclaredMethods0(Native Method)
      at java.lang.Class.privateGetDeclaredMethods(Unknown Source)
      at java.lang.Class.getDeclaredMethod(Unknown Source)
      at java.awt.Component.isCoalesceEventsOverriden(Unknown Source)
      at java.awt.Component.access$500(Unknown Source)
      at java.awt.Component$3.run(Unknown Source)
      at java.awt.Component$3.run(Unknown Source)
      at java.security.AccessController.doPrivileged(Native Method)
      at java.awt.Component.checkCoalescing(Unknown Source)
      at java.awt.Component.<init>(Unknown Source)
      at java.awt.Container.<init>(Unknown Source)
      at java.awt.Panel.<init>(Unknown Source)
      at java.awt.Panel.<init>(Unknown Source)
      at java.applet.Applet.<init>(Unknown Source)
      at jalview.bin.JalviewLite.<init>(Unknown Source)
      at sun.reflect.NativeConstructorAccessorImpl.newInstance0(Native Method)
      at sun.reflect.NativeConstructorAccessorImpl.newInstance(Unknown Source)
      at sun.reflect.DelegatingConstructorAccessorImpl.newInstance(Unknown Source)
      at java.lang.reflect.Constructor.newInstance(Unknown Source)
      at java.lang.Class.newInstance0(Unknown Source)
      at java.lang.Class.newInstance(Unknown Source)
      at sun.plugin2.applet.Plugin2Manager$12.run(Unknown Source)
      at java.awt.event.InvocationEvent.dispatch(Unknown Source)
      at java.awt.EventQueue.dispatchEvent(Unknown Source)
      at java.awt.EventDispatchThread.pumpOneEventForFilters(Unknown Source)
      at java.awt.EventDispatchThread.pumpEventsForFilter(Unknown Source)
      at java.awt.EventDispatchThread.pumpEventsForHierarchy(Unknown Source)
      at java.awt.EventDispatchThread.pumpEvents(Unknown Source)
      at java.awt.EventDispatchThread.pumpEvents(Unknown Source)
      at java.awt.EventDispatchThread.run(Unknown Source)
      Caused by: java.lang.ClassNotFoundException: org.jmol.api.JmolViewer
      at sun.plugin2.applet.Applet2ClassLoader.findClass(Unknown Source)
      at java.lang.ClassLoader.loadClass(Unknown Source)
      at java.lang.ClassLoader.loadClass(Unknown Source)
      ... 30 more
      Caused by: java.io.IOException: open HTTP connection failed:http://www.compbio.dundee.ac.uk/user/ws-dev1/jalview/latest/applet/org/jmol/api/JmolViewer.class
      at sun.plugin2.applet.Applet2ClassLoader.getBytes(Unknown Source)
      at sun.plugin2.applet.Applet2ClassLoader.access$000(Unknown Source)
      at sun.plugin2.applet.Applet2ClassLoader$1.run(Unknown Source)
      at java.security.AccessController.doPrivileged(Native Method)
      ... 33 more
      Exception: java.lang.RuntimeException: java.lang.NoClassDefFoundError: org/jmol/api/JmolViewer

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              Assignee:
              jprocter James Procter
              Reporter:
              jprocter James Procter
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                Created:
                Updated:
                Resolved: