[Biojava-l] Sample compilation requirement

Thomas Down td2@sanger.ac.uk
Sun, 29 Sep 2002 17:22:51 +0100

On Sun, Sep 29, 2002 at 10:16:15AM -0400, John Ling wrote:
> 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.

Are you using a CVS version or snapshot of BioJava?  Recent versions
include some `format guessing' code in SeqIOTools, which relies on
the regexp library.  This dependancy wasn't there in 1.2 (unless some
1.3-only code managed to creep onto the 1.2 branch).

> 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.

Added this now.