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:[EMAIL PROTECTED]
Sent: Tue 7/10/2003 1:05 p.m.
To: [EMAIL PROTECTED]
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
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