[Biojava-l] ChromatogramFactory fails on Windows and Mac

[Richard Holland]

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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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