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  • Read files using an Applet: Please Help :(
    via by 807553,
  • Amila's Blogs: Java Security Model
    via by Unknown author,
  • 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" access denied (java.util.PropertyPermission user.dir read) at Source) at Source) at java.lang.SecurityManager.checkPermission(Unknown Source) at java.lang.SecurityManager.checkPropertyAccess(Unknown Source) at java.lang.System.getProperty(Unknown Source) at Source) at Source) at Source) at org.jmol.viewer.FileManager.classifyName(Unknown Source) at org.jmol.viewer.FileManager.getDefaultDirectory(Unknown Source) at 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<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 Source)
    via by Jim Procter,
  • The FER1_MAIZE and 1gaq.txt example available from the applets examples page does not work properly. Whilst the associated structure is opened, the structure is grey (indicating it is not linked to the alignment window), and the 'View Mapping' menu entry doesn't work. The console is also full of exceptions (produced from applet context: -applet appletDocumentBase= appletCodeBase= (C) 2009 Jmol Development Jmol Version: 12.2.4 2011-10-11 21:29 java.vendor: Apple Inc. java.version: 1.6.0_33 Mac OS X memory: 25.0/85.0 processors available: 4 useCommandThread: false appletId:panel10_jmol_jalview.appletgui.AppletJmolBinding@68de59f0 FileManager.getAtomSetCollectionFromFile( FileManager opening The Resolver thinks Pdb openFile( 131 ms reading 690 atoms ModelSet: haveSymmetry:false haveUnitcells:false haveFractionalCoord:false 1 model in this collection. Use getProperty "modelInfo" or getProperty "auxiliaryInfo" to inspect them. Default Van der Waals type for model set to Jmol 690 atoms created Time to autoBond: 4 ms ModelSet: autobonding; use autobond=false to not generate bonds automatically Jmol 12.2.4 2011-10-11 21:29 DSSP analysis for model 1.1 - 1GAQ W. Kabsch and C. Sander, Biopolymers, vol 22, 1983, pp 2577-2637 We thank Wolfgang Kabsch and Chris Sander for writing the DSSP software, and we thank the CMBI for maintaining it to the extent that it was easy to re-engineer for our purposes. At this point in time, we make no guarantee that this code gives precisely the same analysis as the code available via license from CMBI at All bioshapes have been deleted and must be regenerated. Squashed Jmol callback handler error: access denied (java.util.PropertyPermission user.dir read) at at at java.lang.SecurityManager.checkPermission( at java.lang.SecurityManager.checkPropertyAccess( at java.lang.System.getProperty( at at at jalview.ext.jmol.JalviewJmolBinding.getPdbFile( at jalview.ext.jmol.JalviewJmolBinding.notifyFileLoaded( at jalview.ext.jmol.JalviewJmolBinding.notifyCallback( at org.jmol.viewer.StatusManager.setFileLoadStatus(Unknown Source) at org.jmol.viewer.Viewer.setFileLoadStatus(Unknown Source) at org.jmol.viewer.Viewer.createModelSetAndReturnError(Unknown Source) at org.jmol.viewer.Viewer.loadModelFromFile(Unknown Source) at org.jmol.viewer.Viewer.openFile(Unknown Source) at jalview.appletgui.AppletJmol.<init>( at jalview.appletgui.AlignFrame.newStructureView( at jalview.bin.JalviewLite$LoadingThread.startLoading( at jalview.bin.JalviewLite$ The offending line is: mset[0] = new File(m).getAbsolutePath();
    via by Jim Procter,
  • NT security problems with file I/O
    via by 807556,
  • rgdg
    via by san jan,
  • xmlpserver
    via by nvzhukov,
    • access denied (java.util.PropertyPermission user.dir read) at at at java.lang.SecurityManager.checkPermission( at java.lang.SecurityManager.checkPropertyAccess( at java.lang.System.getProperty( at at at at pacrc.Engine.actionPerformed( at java.awt.Button.processActionEvent( at java.awt.Button.processEvent( at java.awt.Component.dispatchEventImpl( at java.awt.Component.dispatchEvent( at java.awt.EventQueue.dispatchEvent( at java.awt.EventDispatchThread.pumpOneEventForHierarchy( at java.awt.EventDispatchThread.pumpEventsForHierarchy( at java.awt.EventDispatchThread.pumpEvents( at

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