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  1. Jalview
  2. JAL-620

Jmol 12.0.6 property permission exception when opening a pdb file

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    Details

    • Type: Bug
    • Status: Resolved
    • Priority: Major
    • Resolution: Fixed
    • Affects Version/s: 2.6
    • Fix Version/s: 2.6
    • Component/s: awt-gui, JVL-Ajax
    • Labels:
      None
    • Environment:
      Windows XP SP3
      Using JRE version 1.6.0_20-b02 Java HotSpot(TM) Client VM
      Observed on Mozilla 3.6.8 and Chrome.

      Description

      When the allocateViewer method is called to open an embedded Jmol with a particular pdb file (pasted as text or supplied as URL), the operation fails with the folllowing stack trace:

      AppletJmol: PDB ID is 'PASTED PDB_'
      GT could not find the class org.jmol.translation.Jmol.en_GB.Messages_en_GB
      1694 script command tokens
      Exception in thread "AWT-EventQueue-4" java.security.AccessControlException: access denied (java.util.PropertyPermission user.dir read)
      at java.security.AccessControlContext.checkPermission(Unknown Source)
      at java.security.AccessController.checkPermission(Unknown Source)
      at java.lang.SecurityManager.checkPermission(Unknown Source)
      at java.lang.SecurityManager.checkPropertyAccess(Unknown Source)
      at java.lang.System.getProperty(Unknown Source)
      at java.io.Win32FileSystem.getUserPath(Unknown Source)
      at java.io.Win32FileSystem.resolve(Unknown Source)
      at java.io.File.getAbsolutePath(Unknown Source)
      at org.jmol.viewer.FileManager.classifyName(Unknown Source)
      at org.jmol.viewer.FileManager.getDefaultDirectory(Unknown Source)
      at org.jmol.viewer.Viewer.cd(Unknown Source)
      at org.jmol.viewer.Viewer.setAppletContext(Unknown Source)
      at org.jmol.viewer.Viewer.allocateViewer(Unknown Source)
      at org.jmol.api.JmolViewer.allocateViewer(Unknown Source)
      at jalview.ext.jmol.a.a(Unknown Source)
      at jalview.appletgui.am.<init>(Unknown Source)
      at jalview.appletgui.Z.a(Unknown Source)
      at jalview.appletgui.Z.actionPerformed(Unknown Source)
      at java.awt.Button.processActionEvent(Unknown Source)
      at java.awt.Button.processEvent(Unknown Source)
      at java.awt.Component.dispatchEventImpl(Unknown Source)
      at java.awt.Component.dispatchEvent(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)

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              Assignee:
              jprocter James Procter
              Reporter:
              jprocter James Procter
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                Dates

                Created:
                Updated:
                Resolved: