[Biojava-l] ChromatogramFactory fails on Windows and Mac

[Mark Schreiber]

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
>
>
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