[Biojava-l] Genbank Problem

[Thomas Down]

This doesn't look like a Genbank parser problem -- the XML
parser is required very early on in the initialization of the
code BioJava code, to load some XML data files.  This is the
point where it seems to be failing.

BioJava now using Sun's JAXP API to obtain XML parsers --
this should make it parser-independant, although we still
recommend Xerces to anyone who's needs a parser.  The
exception below looks like the JAXP infrastructure is getting
confused about which parser to use.  Do you also have a
any of the following files on your CLASSPATH (or in
${JAVA_HOME}/jre/lib/ext):

   jaxp.jar
   parser.jar
   crimson.jar

If so, try removing them and seeing if you get any further.

Are you, by any chance, using JDK1.4?  This includes the latest
version of the Crimson parser, built in.  If so, you might
actually want to try removing xerces.jar from the classpath,
so see if that helps.  BioJava works fine using that
version of crimson.


Let me know if problems persist....

    Thomas.





On Thu, Feb 21, 2002 at 10:29:46AM -0500, cantey.lg@pg.com wrote:
> 
> javax.xml.parsers.FactoryConfigurationError: java.lang.ClassNotFoundException: org.apache.crimson.jaxp.DocumentBuilderFactoryImpl
> 
>      at javax.xml.parsers.DocumentBuilderFactory.newInstance(DocumentBuilderFactory.java:118)
> 
>      at org.biojava.bio.symbol.AlphabetManager.<clinit>(AlphabetManager.java:697)
> 
>      at org.biojava.bio.seq.DNATools.<clinit>(DNATools.java:50)
> 
> rethrown as org.biojava.bio.BioError: Unable to initialize DNATools
> 
>      at org.biojava.bio.seq.DNATools.<clinit>(DNATools.java:83)
> 
>      at org.biojava.bio.seq.io.SeqIOTools.readGenbank(SeqIOTools.java:102)
> 
>      at seq.UpdatedTestGenbank.main(UpdatedTestGenbank.java, Compiled Code)
> 
> 
> The xerces.jar file was in the CLASSPATH....
> 
> Any ideas ???
> 
> Thanks for any help !!!
> 
> Larry Cantey