-----BEGIN PGP SIGNED MESSAGE----- Hash: SHA1 Could this be an encoding problem with the XML file in the JAR? i.e. Linux and Windows generally use different text encodings and so may misinterpret some of the characters in the XML file, generating the errors you see. I suppose this could be an issue if the Windows environment is running internationalisation under a non-Western-European character set, whereas the Linux box is running with an English character set.
Unfortunately I do not have access to a Windows machine to test this on. Do any other BJ developers out there have access to a Windows machine that they can investigate this with? cheers, Richard hkaya wrote: > On windows machine, I downloaded > http://www.biojava.org/download/bj15/bin/BioJava1.5-bin.tar.gz with Internet > Explorer and extract jar files. I also tried downloading the same file on > linux and > copy the jar files to windows with samba. On both case the same error occurs. > After your message I delete and downloaded the same file again, but > the situation is same. > > Huseyin > > On Sun, 23 Sep 2007 20:19:09 +0800, Mark Schreiber wrote >> The stack trace indicates that the resources in you biojava.jar file >> are missing or corrupt. Where did you get it from? >> >> If you copy the jar from you linux machine to windows do you still >> get the same error? >> >> - Mark >> >> On 9/23/07, hkaya <[EMAIL PROTECTED]> wrote: >>> Hello >>> >>> The following small code perfectly runs on Linux but >>> it fails on Windows and Mac. I'm using biojava 1.5. >>> Could anybody tell me where i am doing something wrong? >>> >>> Thanks >>> Huseyin Kaya >>> >>> >>> 1. TraceTest.java >>> >>> import java.io.File; >>> import org.biojava.bio.chromatogram.Chromatogram; >>> import org.biojava.bio.chromatogram.ChromatogramFactory; >>> >>> public class TraceTest { >>> public static void main(String[] args) { >>> try { >>> Chromatogram trace = > ChromatogramFactory.create(new File("test.scf")); >>> System.out.println("Success!"); >>> } catch (Exception e){ >>> System.out.println("Failed!"); >>> e.printStackTrace(); >>> } >>> } >>> } >>> >>> 2. Test chromatogram file : http://istanbul.be.itu.edu.tr/~huseyin/test.scf >>> >>> 3. Exception thrown in Windows XP/Vista: >>> >>> Desktop> java -classpath biojava-1.5.jar;. TraceTest >>> Exception in thread "main" org.biojava.bio.BioError: Unable to initialize >>> DNATools >>> at org.biojava.bio.seq.DNATools.<clinit>(DNATools.java:117) >>> at >>> org.biojava.bio.program.scf.SCF$V3Parser.parseSamples(SCF.java:560) >>> at org.biojava.bio.program.scf.SCF$Parser.parse(SCF.java:350) >>> at org.biojava.bio.program.scf.SCF$ParserFactory.parse(SCF.java:206) >>> at org.biojava.bio.program.scf.SCF.load(SCF.java:149) >>> at org.biojava.bio.program.scf.SCF.load(SCF.java:141) >>> at org.biojava.bio.program.scf.SCF.create(SCF.java:126) >>> at >>> > org.biojava.bio.chromatogram.ChromatogramFactory.create(ChromatogramFactory.java:75) >>> at TraceTest.main(TraceTest.java:8) >>> Caused by: org.biojava.bio.BioError: Unable to initialize RNATools >>> at org.biojava.bio.seq.RNATools.<clinit>(RNATools.java:126) >>> at org.biojava.bio.seq.DNATools.<clinit>(DNATools.java:110) >>> ... 8 more >>> Caused by: org.biojava.bio.BioError: Couldn't parse TranslationTables.xml >>> at org.biojava.bio.seq.RNATools.loadGeneticCodes(RNATools.java:529) >>> at org.biojava.bio.seq.RNATools.<clinit>(RNATools.java:124) >>> ... 9 more >>> Caused by: org.biojava.bio.symbol.IllegalSymbolException: >>> Token `his' does not appear as a named symbol in alphabet > `PROTEIN-TERM' >>> at >>> org.biojava.bio.seq.io.NameTokenization.parseToken(NameTokenization.java:110) >>> at org.biojava.bio.seq.RNATools.loadGeneticCodes(RNATools.java:520) >>> ... 10 more >>> >>> >>> _______________________________________________ >>> Biojava-l mailing list - [email protected] >>> http://lists.open-bio.org/mailman/listinfo/biojava-l >>> > > > Huseyin > > _______________________________________________ > Biojava-l mailing list - [email protected] > http://lists.open-bio.org/mailman/listinfo/biojava-l > -----BEGIN PGP SIGNATURE----- Version: GnuPG v1.4.2.2 (GNU/Linux) Comment: Using GnuPG with Mozilla - http://enigmail.mozdev.org iD8DBQFG925X4C5LeMEKA/QRAhP0AKCM42VcwZmwPFBRvwK3NtNdmZJwJQCdF3EO GNJ0p5xNdQeQ1oNYwrdSmMg= =Hu8w -----END PGP SIGNATURE----- _______________________________________________ Biojava-l mailing list - [email protected] http://lists.open-bio.org/mailman/listinfo/biojava-l
