[Biojava-l] The Java sandbox and BioJava

[Richard Holland]

Not sure exactly, but this might help:

http://java.sun.com/j2se/1.5.0/docs/guide/javaws/developersguide/faq.html#211

cheers,
Richard

On Tue, 2006-06-20 at 10:29 -0400, Andrew Walsh wrote:
> I am working on an application that I want to deliver via Java Web 
> Start.  This application uses BioJava 1.4 to do some basic processing of 
> protein sequence files.  Applications run via Java Web Start have the 
> option of staying in the Java sandbox or requesting to have full 
> access.  I would like to provide both options to the user, but I am 
> having trouble with the in-sandbox version.  When the application tries 
> to open a sequence file, it fails with the following error:
> 
> java.lang.reflect.InvocationTargetException
> <snipped list of Sun classes involved in running an application>
> Caused by: org.biojava.bio.BioError: Couldn't locate 
> AlphabetManager.xml.  This probably means that your biojava.jar file is 
> corrupt or incorrectly built.
>     at 
> org.biojava.bio.symbol.AlphabetManager.<clinit>(AlphabetManager.java:1012)
>     at org.biojava.bio.seq.ProteinTools.<clinit>(ProteinTools.java:75)
>     at 
> org.biojava.bio.seq.io.MSFAlignmentFormat.read(MSFAlignmentFormat.java:187)
>     at org.biojava.bio.seq.io.SeqIOTools.fileToAlign(SeqIOTools.java:1138)
>     at org.biojava.bio.seq.io.SeqIOTools.fileToBiojava(SeqIOTools.java:940)
>     at org.biojava.bio.seq.io.SeqIOTools.fileToBiojava(SeqIOTools.java:908)
>     at org.msaviewer.tools.SequenceFileReader.readAlignmentFile(Unknown 
> Source)
>     at org.msaviewer.MSAViewer.openSafeSession(MSAViewer.java:295)
>     at org.msaviewer.MSAViewer.main(MSAViewer.java:1334)
>     ... 11 more
> 
> It would appear that the way in which the AlphabetManager reads 
> AlphabetManager.xml from the BioJava jar file is not compatible with the 
> Java Web Start sandbox restrictions.  I skimmed the relevant sections of 
> the AlphabetManager code and didn't see an obvious solution.  Does 
> anyone have any experience with getting BioJava to work inside the 
> sandbox that might be able to suggest a fix to this problem?
> 
> Thanks,
> Andy Walsh
> Postdoctoral Fellow
> Language Technologies Institute
> Carnegie Mellon University
> 
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-- 
Richard Holland (BioMart Team)
EMBL-EBI
Wellcome Trust Genome Campus
Hinxton
Cambridge CB10 1SD
UNITED KINGDOM
Tel: +44-(0)1223-494416