Hi all. I'm currently updating the version of Jmol used by Jalview to the 12.x branch, and have run into an unexpected permissions problem when launching Jmol from the Jalview applet. Try the two versions of JalviewLite on this page:
http://www.compbio.dundee.ac.uk/user/ws-dev1/jalview/latest/applet/testJmol12.html One starts JalviewLite with its build in PDB viewer - just to show that the data is present and accessible.The other starts JalviewLite with Jmol 12.0.6 - and for machines I have access to, it generates the following exception: 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) <platform dep lines here> 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.JalviewJmolBinding.allocateViewer(JalviewJmolBinding.java:1068) at jalview.appletgui.AppletJmol.<init>(AppletJmol.java:183) at jalview.appletgui.AlignFrame.newStructureView(AlignFrame.java:3307) at jalview.bin.JalviewLite$LoadingThread.startLoading(JalviewLite.java:985) at jalview.bin.JalviewLite$LoadingThread.run(JalviewLite.java:728) The text prior to the exception is generated by JalviewLite when it receives the exception: Couldn't create a jmol viewer. Args to allocate viewer were: DocumentBase=http://www.compbio.dundee.ac.uk/user/ws-dev1/jalview/latest/applet/testJmol12.html Codebase=http://www.compbio.dundee.ac.uk/user/ws-dev1/jalview/latest/applet/ Unfortunately, this has me stumped for the moment. Any ideas what I might be doing wrong, or is this actually a bug ? The JalviewLite/Jmol combination works fine under the appletviewer (which doesn't have the same sandbox constraints), and the Jalview desktop application is now also playing nice with version 12, so whilst I think I'm initing Jmol correctly, it still wants to try to access the client machine's file system - even when it isn't allowed to. cheers. Jim. -- ------------------------------------------------------------------- J. B. Procter (JALVIEW/ENFIN) Barton Bioinformatics Research Group Phone/Fax:+44(0)1382 388734/345764 http://www.compbio.dundee.ac.uk The University of Dundee is a Scottish Registered Charity, No. SC015096. ------------------------------------------------------------------------------ This SF.net email is sponsored by Make an app they can't live without Enter the BlackBerry Developer Challenge http://p.sf.net/sfu/RIM-dev2dev _______________________________________________ Jmol-developers mailing list Jmol-developers@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-developers
