[Biojava-l] ChromatogramFactory fails on Windows and Mac

[hkaya]

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 <hkaya at iontek.com.tr> 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  -  Biojava-l at lists.open-bio.org
> > http://lists.open-bio.org/mailman/listinfo/biojava-l
> >


Huseyin