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  1. Jalview
  2. JAL-1859

Jmol / Jalview example not working with Jmol 14.x

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    Details

    • Type: Bug
    • Status: Being tested
    • Priority: Blocker
    • Resolution: Unresolved
    • Affects Version/s: 2.9
    • Fix Version/s: 2.9.0b1
    • Component/s: jvlite, Structures
    • Labels:
      None

      Description

      This looks like something is missing in the applet classpath.

      Currrent build:
      http://www.jalview.org/builds/develop/examples/applets.html

      Click on '1gaq associated with fer1_maize' - see exception:
      Java Plug-in 11.51.2.16
      Using JRE version 1.8.0_51-b16 Java HotSpot(TM) 64-Bit Server VM
      User home directory = /Users/jprocter
      ----------------------------------------------------
      c: clear console window
      f: finalize objects on finalization queue
      g: garbage collect
      h: display this help message
      l: dump classloader list
      m: print memory usage
      o: trigger logging
      q: hide console
      r: reload policy configuration
      s: dump system and deployment properties
      t: dump thread list
      v: dump thread stack
      x: clear classloader cache
      0-5: set trace level to <n>
      ----------------------------------------------------
      Sep 03, 2015 11:59:40 AM jalview.o.k <clinit>
      INFO: Getting messages for lang: en_US
      0
      1822 script command tokens
      applet context: -applet
      appletDocumentBase=http://www.jalview.org/builds/develop/examples/applets.html
      appletCodeBase=http://www.jalview.org/builds/develop/examples/
      (C) 2009 Jmol Development
      Jmol Version: 12.2.4 2011-10-11 21:29
      java.vendor: Oracle Corporation
      java.version: 1.8.0_51
      os.name: Mac OS X
      memory: 30.0/161.0
      processors available: 4
      useCommandThread: false
      appletId:panel0_jmol_jalview.appletgui.I@27bb05f3
      Exception in thread "Thread-40" java.lang.NoSuchMethodError: org.jmol.api.JmolAppConsoleInterface.start(Lorg/jmol/viewer/Viewer;)V
      at jalview.appletgui.I.f(Unknown Source)
      at jalview.f.a.a.a(Unknown Source)
      at jalview.appletgui.F.<init>(Unknown Source)
      at jalview.appletgui.AlignFrame.newStructureView(Unknown Source)
      at jalview.bin.m.a(Unknown Source)
      at jalview.bin.m.run(Unknown Source)

      from debug link:
      http://www.jalview.org/builds/develop/examples/debug/applets.html

      Sep 03, 2015 12:09:57 PM jalview.util.MessageManager <clinit>
      INFO: Getting messages for lang: en_US
      1822 script command tokens
      applet context: -applet
      appletDocumentBase=http://www.jalview.org/builds/develop/examples/debug/applets.html
      appletCodeBase=http://www.jalview.org/builds/develop/examples/debug/
      (C) 2009 Jmol Development
      Jmol Version: 12.2.4 2011-10-11 21:29
      java.vendor: Oracle Corporation
      java.version: 1.8.0_51
      os.name: Mac OS X
      memory: 48.2/152.6
      processors available: 4
      useCommandThread: false
      appletId:panel6_jmol_jalview.appletgui.AppletJmolBinding@1ea57342
      Exception in thread "Thread-84" java.lang.NoSuchMethodError: org.jmol.api.JmolAppConsoleInterface.start(Lorg/jmol/viewer/Viewer;)V
      at jalview.appletgui.AppletJmolBinding.createJmolConsole(AppletJmolBinding.java:169)
      at jalview.ext.jmol.JalviewJmolBinding.allocateViewer(JalviewJmolBinding.java:1380)
      at jalview.appletgui.AppletJmol.<init>(AppletJmol.java:270)
      at jalview.appletgui.AlignFrame.newStructureView(AlignFrame.java:4090)
      at jalview.bin.JalviewLite$LoadingThread.loadPdbFiles(JalviewLite.java:2123)
      at jalview.bin.JalviewLite$LoadingThread.startLoading(JalviewLite.java:1864)
      at jalview.bin.JalviewLite$LoadingThread.run(JalviewLite.java:1835)

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              Assignee:
              gmungoc Mungo Carstairs
              Reporter:
              jprocter Jim Procter
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                Dates

                Created:
                Updated: