[Biojava-l] The Java sandbox and BioJava

[Andrew Walsh]

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