Details
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)
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)
Attachments
Issue Links
- blocks
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JAL-582 update Jmol to 2010 series (12.XX)
- Resolved