[Biojava-l] ChromatogramFactory fails on Windows and Mac

[hkaya]

You are right. When I do the following replacements
"his" -> "HIS" and
"ile" -> "ILE" 
in the  org/biojava/bio/seq/TranslationTables.xml 
my code and a TraceViewer demo in biojava package perfectly worked on 
Windows and Linux. I think the problem is related with lower/upper case
conversions. In turkish uppercase of 'i' is not 'I' but 'I' with a dot.
Also lower case of 'I' is not 'i' but lower case dotless i (ı).  
Current locale settings affects the behaivour of toLower(), toUpper().

http://java.sun.com/j2se/1.4.2/docs/api/java/lang/String.html#toUpperCase(java.util.Locale)

I made the code run by modifying XML file in biojava.jar 
but i know it is not a nice solution.  

Thank you
Huseyin Kaya


On Mon, 24 Sep 2007 08:59:20 +0100, Richard Holland wrote
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> 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 <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
> > 
> > _______________________________________________
> > Biojava-l mailing list  -  Biojava-l at lists.open-bio.org
> > http://lists.open-bio.org/mailman/listinfo/biojava-l
> > 
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Huseyin