[Biojava-l] Sample compilation requirement

[John Ling]

Perhaps I'm not understanding the packages very well.

There are two versions of the GCContent demo.  One is supplied in the
/biojava-live/demo/seq directory.  The other is the one in the tutorial:
http://www.biojava.org/tutorials/chap1.html.

In my jar classpath I have put three jars:
biojava.jar, bytecode.jar, and xerces.jar

With the /biojava-live/demo/seq/GCContent.java I have no problem running
it.

With the tutorial version, I get the following at runtime:
 Exception in thread "main"
java.lang.NoClassDefFoundError: org/apache/regexp/RESyntaxException

I was able to run the tutorial version properly only after I additionally
added the jakarta-regexp.jar to the classpath.

The only real difference I can see between the demo versions is that the
tutorial version uses SeqIOTools.readFastaDNA(br).

What is jakarta-regexp.jar used for and why does SeqIOTools.readFastaDNA
rely on it?  I thought jakarta-regexp.jar was only used for ANT during the
package building process.

If it is required to include jakarta-regexp.jar in the classpath, then
perhaps this requirement could be documented in "Getting started" section
of the documentation.

Thanks,
John Ling