1) are you sure you have all the JmolApplet0_xxxx.jar files in place?
2) put JmolApplet.jar in the directory, then try using
jmolInitialize(".","JmolApplet.jar")
This will test whether the Java system can load from multiple Jar files.
On Tue, Nov 18, 2008 at 6:48 AM, Ondrej Certik <[EMAIL PROTECTED]> wrote:
> On Tue, Nov 18, 2008 at 1:19 PM, Ondrej Certik <[EMAIL PROTECTED]> wrote:
> > On Fri, Nov 14, 2008 at 7:17 PM, Ondrej Certik <[EMAIL PROTECTED]> wrote:
> >> On Fri, Nov 14, 2008 at 6:17 PM, Ondrej Certik <[EMAIL PROTECTED]>
> wrote:
> >>> On Fri, Nov 14, 2008 at 5:38 PM, Robert Hanson <[EMAIL PROTECTED]>
> wrote:
> >>>> Ondrej
> >>>>
> >>>> It's a LiveConnect problem. You should be seeing something -- a black
> >>>> window, maybe with the Jmol logo in the bottom right corner. The popup
> menu
> >>>
> >>> I see a gray window.
> >>>
> >>>> might work. You might be able to pull up a console.
> >>>
> >>> Unfortunately, the popup menu doesn't work.
> >>>
> >>>>
> >>>> What won't be working is any JavaScript connectivity. After loading
> >>>> http://www.java.com/en/download/help/testvm.xml, try this on the URL
> line:
> >>>>
> >>>> javascript:alert(document.applets[0].getAppletInfo())
> >>>>
> >>>>
> >>>> If you get an alert with a copyright notice, then we can talk about
> why Jmol
> >>>> might not be working; if you don't, it's not a Jmol problem --
> complain to
> >>>> openjdk-6 folks!
> >>>
> >>> I got:
> >>>
> >>> TypeError: document.applets[0].getAppletInfo is not a function
> >>>
> >>> however, with this:
> >>>
> >>> alert(document.applets[0])
> >>>
> >>> I got:
> >>>
> >>> [object HTMLAppletElement]
> >>>
> >>> So it seems that javascript/java is not working properly in iceweasel.
> >>>
> >>> Thanks for the tip. For reference, here is a test:
> >>>
> >>>
> http://developer.apple.com/internet/safari/samples/ColorBlockApplet.html
> >>>
> >>> and neither way (e.g. js->applet, applet->js) works for me. It seems
> >>> like a known problem though:
> >>>
> >>> https://bugs.launchpad.net/ubuntu/+source/openjdk-6/+bug/282762
> >>
> >> Ok, so one needs to install openjdk packages from Debian experimental:
> >>
> >> $ wajig install -t experimental openjdk-6-jre
> >> $ wajig install icedtea6-plugin
> >>
> >> Then install the plugin to iceweasel by hand:
> >>
> >> http://bugs.debian.org/cgi-bin/bugreport.cgi?bug=505726
> >>
> >> now the js->applet communication works, e.g. clicking the buttons
> >> change the applet color here:
> >>
> >>
> http://developer.apple.com/internet/safari/samples/ColorBlockApplet.html
> >>
> >> unfortunately, the apple->js communication doesn't work (does jmol need
> it?).
> >> Now jmol applets show the loading page and the number of secons
> >> increases in the lower right corner. But it never loads in full. It
> >> seems like an openjdk problem, which still needs to be fixed.
> >
> > Ok, so the maintainer of the openjdk package replied here:
> >
> > http://bugs.debian.org/cgi-bin/bugreport.cgi?bug=505726
> >
> > that:
> >
> > "
> > the applet is lacking a mayscript attribute.
> > "
> >
> > (referencing to the apple ColorBlockApplet demo above) and closed the
> bug.
> >
> >
> > Robert --- do you still think this is a bug in openjdk? As I described
> > above, jmol now loads and runs ---- but it stays in the "load" mode
> > forever. The seconds in the bottom part of the applet are increasing
> > (so the applet itself works and executes), but nothing happens.
> >
> > How would you suggest me to investigate further?
>
> I realized that if I start iceweasel from the command line, I get some
> useful reports. As you can see below, jmol is raising some exception:
>
> $ iceweasel
> ** Message: GetValue variable 1 (1)
> ** Message: GetValue variable 2 (2)
> ** Message: GetValue variable 1 (1)
> ** Message: GetValue variable 2 (2)
> ** Message: GetValue variable 1 (1)
> ** Message: GetValue variable 2 (2)
> ** Message: GetValue variable 1 (1)
> ** Message: GetValue variable 2 (2)
> ** Message: GetValue variable 1 (1)
> ** Message: GetValue variable 2 (2)
> ICEDTEAPLUGIN_DEBUG = (null)
> Initializing JVM...
> NOT IMPLEMENTED: virtual nsresult IcedTeaPluginInstance::Start()
> Jar string: JmolApplet0.jar
> jars length: 1
> JNLPRuntime already initialized
> urlImage=jar:file:/tmp/cache/http/
> jmol.sourceforge.net/jmol/JmolApplet0.jar!/jmol75x29x8.gif<http://jmol.sourceforge.net/jmol/JmolApplet0.jar%21/jmol75x29x8.gif>
> Jmol applet jmolApplet0__0245810961582291__ initializing
> language=en_US
> AppletRegistry.checkIn(jmolApplet0__0245810961582291__)
> error preloading org.jmol.popup.JmolPopup: org.jmol.popup.JmolPopup
> net.sourceforge.jnlp.runtime.JNLPClassLoader - 700 - loadClassExt
> net.sourceforge.jnlp.runtime.JNLPClassLoader - 657 - loadClass
> java.lang.ClassLoader - 336 - loadClassInternal
> java.lang.Class - -2 - forName0
> java.lang.Class - 186 - forName
> org.jmol.appletwrapper.ClassPreloader - -1 - run
> applet context: -applet
> appletDocumentBase=http://jmol.sourceforge.net/demo/alphahelix/
> appletCodeBase=http://jmol.sourceforge.net/jmol/<http://jmol.sourceforge.net/demo/alphahelix/appletCodeBase=http://jmol.sourceforge.net/jmol/>
> (C) 2008 Jmol Development
> Jmol Version 11.6 2008-09-20 22:06
> java.vendor:Sun Microsystems Inc.
> java.version:1.6.0_0
> os.name:Linux
> memory:3.1/5.2
> useCommandThread: false
> appletId:jmolApplet0__0245810961582291__
> popup menu not available
> Exception in thread "Thread-9" java.lang.NoClassDefFoundError:
> org/jmol/popup/JmolPopup
> at org.jmol.applet.Jmol.getPopupMenu(Unknown Source)
> at org.jmol.applet.Jmol.initApplication(Unknown Source)
> at org.jmol.applet.Jmol.init(Unknown Source)
> at org.jmol.appletwrapper.WrappedAppletLoader.run(Unknown Source)
> Caused by: java.lang.ClassNotFoundException: org.jmol.popup.JmolPopup
> at
> net.sourceforge.jnlp.runtime.JNLPClassLoader.loadClassExt(JNLPClassLoader.java:700)
> at
> net.sourceforge.jnlp.runtime.JNLPClassLoader.loadClass(JNLPClassLoader.java:657)
> at java.lang.ClassLoader.loadClassInternal(ClassLoader.java:336)
> ... 4 more
>
>
>
> Why is this exception being raised?
>
> Ondrej
>
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--
Robert M. Hanson
Professor of Chemistry
St. Olaf College
1520 St. Olaf Ave.
Northfield, MN 55057
http://www.stolaf.edu/people/hansonr
phone: 507-786-3107
If nature does not answer first what we want,
it is better to take what answer we get.
-- Josiah Willard Gibbs, Lecture XXX, Monday, February 5, 1900
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