[Jalview-discuss] Re: installation problems

[James Procter]

Daniel Rigden wrote:
> Hi James
> 
> I appear to have a solution that works, although some errors still pop
> up.  I removed the openjdk and instead installed sun's 1.6 jre.  Then I
> set JAVA_HOME and did your 
>  java -Djava.ext.dirs=. jalview.bin.Jalview
> 
> The first time I did this, although Jalview window opened everything was
> a mess and non-functional.  There were huge numbers of errors.  The
> *second* time I get something that appears to work perfectly.  
ok - odd - normally errors like this are reproducible - maybe something
got set up after the first run.


However,
> I do get this upon starting up
> 
> daniel at adenine:~/progs/jalview_cl$ java -Djava.ext.dirs=.
> jalview.bin.Jalview
> Java version: 1.6.0_06
> amd64 Linux 2.6.24-19-generic
> Jalview Version: Automated Build
> Exception in thread "Thread-0" java.lang.NullPointerException
> 	at java.util.Hashtable.put(Hashtable.java:394)
> 	at java.util.Properties.setProperty(Properties.java:143)
> 	at java.lang.System.setProperty(System.java:731)
> 	at jalview.bin.Cache$1VersionChecker.run(Cache.java:269)
this exception isn't serious. its a minor bug in the jalview version
check code that is just about to be fixed.

> Later, I get this
> 
> Exception in thread "AWT-EventQueue-0"
> java.lang.ArrayIndexOutOfBoundsException: No such child: 7
> 	at java.awt.Container.getComponent(Container.java:281)
> 	at javax.swing.JComponent.rectangleIsObscured(JComponent.java:4337)
> 	at javax.swing.JComponent.paint(JComponent.java:1025)
> 	at javax.swing.JLayeredPane.paint(JLayeredPane.java:564)
> 	at javax.swing.JComponent.paintToOffscreen(JComponent.java:5122)
> 	at
> javax.swing.BufferStrategyPaintManager.paint(BufferStrategyPaintManager.java:285)
> 	at javax.swing.RepaintManager.paint(RepaintManager.java:1128)
> 	at javax.swing.JComponent._paintImmediately(JComponent.java:5070)
> 	at javax.swing.JComponent.paintImmediately(JComponent.java:4880)
> 	at
> javax.swing.RepaintManager.paintDirtyRegions(RepaintManager.java:723)
> 	at
> javax.swing.RepaintManager.paintDirtyRegions(RepaintManager.java:679)
> 	at
> javax.swing.RepaintManager.seqPaintDirtyRegions(RepaintManager.java:659)
> 	at javax.swing.SystemEventQueueUtilities
> $ComponentWorkRequest.run(SystemEventQueueUtilities.java:128)
> 	at java.awt.event.InvocationEvent.dispatch(InvocationEvent.java:209)
> 	at java.awt.EventQueue.dispatchEvent(EventQueue.java:597)
> 	at
> java.awt.EventDispatchThread.pumpOneEventForFilters(EventDispatchThread.java:273)
> 	at
> java.awt.EventDispatchThread.pumpEventsForFilter(EventDispatchThread.java:183)
> 	at
> java.awt.EventDispatchThread.pumpEventsForHierarchy(EventDispatchThread.java:173)
> 	at
> java.awt.EventDispatchThread.pumpEventsForHierarchy(EventDispatchThread.java:164)
> 	at java.awt.Container$2.run(Container.java:2701)
> 	at java.awt.event.InvocationEvent.dispatch(InvocationEvent.java:209)
> 	at java.awt.EventQueue.dispatchEvent(EventQueue.java:597)
> 	at
> java.awt.EventDispatchThread.pumpOneEventForFilters(EventDispatchThread.java:273)
> 	at
> java.awt.EventDispatchThread.pumpEventsForFilter(EventDispatchThread.java:183)
> 	at
> java.awt.EventDispatchThread.pumpEventsForHierarchy(EventDispatchThread.java:173)
> 	at
> java.awt.EventDispatchThread.pumpEvents(EventDispatchThread.java:168)
> 	at
> java.awt.EventDispatchThread.pumpEvents(EventDispatchThread.java:160)
> 	at java.awt.EventDispatchThread.run(EventDispatchThread.java:121)
again - a non-serious exception raised by the windowing system .. one
day, it may be fixed (if we can work out how :).
> but things seem to carry on working.  Are these errors likely to a
> problem later?
nope.

> Hopefully a much simpler question... What alias would I use to set up a
> jalview command to run from anywhere in the file hierarchy, not just
> where jalview was installed?
basically, a shell script like this would do it :

#!/bin/bash
JALVIEW_HOME=/path to jalview lib dir
JAVA_HOME=/path to java jre dir
$JAVA_HOME/bin/java -Djava.ext.dirs=$JALVIEW_HOME jalview.bin.Jalview $@

save it somewhere on your $PATH and make sure its executable, and all
should work.

I really think that you should be able to get the webstart version
working now you have the sun jvm installed. You'll need to make sure
that the javaws executable from the sun JRE is being used to start
jalview - you should be able to find it under the bin directory of the
JRE (<path to sun JRE>/bin/javaws), but it seems to wander around
between different JVM installations. if you could find a javaws
executable under that path then you should be able to do something like:
<path to sun JRE>/bin/javaws
http://www.compbio.dundee.ac.uk/~ws-dev1/jalview/latest/webstart/jalview.jnlp

to start up Jalview via webstart. Obviously, you'd also need to fix your
web browser to launch the correct javaws executable, as well.

good to hear things are working for you now!
Jim