[Biojava-l] NoClassDefException

[allanlee]

Hi, Good day!
   I got a "NoClassDefFound" exception when I call:
 
        db = SeqIOTools.readFasta(is,alpha);
 
-----------------------------------------excert from my code--------------------------------------------------
import java.io.*;
import java.util.*;
import org.biojava.bio.*;
import org.biojava.bio.seq.*;
import org.biojava.bio.seq.io.*;
import org.biojava.bio.seq.db.*;
import org.biojava.bio.dist.*;
import org.biojava.bio.dp.*;
import org.biojava.bio.symbol.*;
import org.biojava.bio.seq.Sequence;
 
         .....
        //setup file path + name
        String fileName="..\\input.txt";
        BufferedInputStream is = new BufferedInputStream(new FileInputStream(fileName));
        //get the appropriate alphabet:DNA,RNA, or PROTEIN
        Alphabet alpha = AlphabetManager.alphabetForName("PROTEIN");
        //get a sequenceDB of all sequences in the file
        db = SeqIOTools.readFasta(is,alpha);
        .....
 
-----------------------------------------error message---------------------------------------------------------------

java.lang.NoClassDefFoundError: org/apache/regexp/RESyntaxException
 at BiologicalSequence.PHMM.<init>(PHMM.java:47)
 at BiologicalSequence.PHMM.main(PHMM.java:116)

 
 
   My observation is the missing class is from xerces.jar.  I appreciate your advice pls!
 
thnks & regards,
@llan


---------------------------------
Do you Yahoo!?
The New Yahoo! Shopping - with improved product search