[Biojava-dev] [Bug 2371] New: ChromatogramFactory.create fails on Windows

[bugzilla-daemon at portal.open-bio.org]

http://bugzilla.open-bio.org/show_bug.cgi?id=2371

           Summary: ChromatogramFactory.create fails on Windows
           Product: BioJava
           Version: 1.5
          Platform: PC
        OS/Version: Windows
            Status: NEW
          Severity: normal
          Priority: P2
         Component: bio
        AssignedTo: biojava-dev at biojava.org
        ReportedBy: hkaya at be.itu.edu.tr


The following small code perfectly runs on Linux but
it fails on Windows.  I'm using biojava 1.5.


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


-- 
Configure bugmail: http://bugzilla.open-bio.org/userprefs.cgi?tab=email
------- You are receiving this mail because: -------
You are the assignee for the bug, or are watching the assignee.