[Biojava-l] NoClassDefException

[Schreiber, Mark]

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 
	Cc: 
	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,
	@llan
	
	
	---------------------------------
	Do you Yahoo!?
	The New Yahoo! Shopping - with improved product search 


=======================================================================
Attention: The information contained in this message and/or attachments
from AgResearch Limited is intended only for the persons or entities
to which it is addressed and may contain confidential and/or privileged
material. Any review, retransmission, dissemination or other use of, or
taking of any action in reliance upon, this information by persons or
entities other than the intended recipients is prohibited by AgResearch
Limited. If you have received this message in error, please notify the
sender immediately.
=======================================================================