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 > > _______________________________________________ > Biojava-l mailing list - [email protected] > http://lists.open-bio.org/mailman/listinfo/biojava-l -- Richard Holland (BioMart Team) EMBL-EBI Wellcome Trust Genome Campus Hinxton Cambridge CB10 1SD UNITED KINGDOM Tel: +44-(0)1223-494416 _______________________________________________ Biojava-l mailing list - [email protected] http://lists.open-bio.org/mailman/listinfo/biojava-l
