[Biojava-l] NoClassDefException

Schreiber, Mark mark.schreiber at agresearch.co.nz
Mon Oct 6 21:39:09 EDT 2003

Hi -
The missing JAR file is the jakarta regular expression library (required in biojava1.3 not required in biojava-live). You can get it from the biojava download page.
- Mark

	-----Original Message----- 
	From: allanlee [mailto:alkw_1998 at yahoo.com] 
	Sent: Tue 7/10/2003 1:05 p.m. 
	To: biojava-l at biojava.org 
	Subject: [Biojava-l] NoClassDefException

	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,
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