[Biojava-l] Switchover to JAXP1.1

[Thomas Down]

Hi...

I've just updated the BioJava codebase to use the JAXP
(Java API for XML processing) APIs to parse XML documents,
rather than explicitly requiring Xerces.  This means
that we can use alternative parsers if necessary.

This isn't really a particularly big change -- Everything
still works with Xerces (I've been testing with version
1.4.0), and we'll go on recommending Xerces as the standard
parser for BioJava, and including it on the web site.  But
it does mean we now play nicely with various other Java XML
applications, and that anyone who want to change parser can
do so in a reasonably low-stress manner (just add a new .JAR
file to your classpath, and it should Just Work).

Everything compiles again now, and I've tested as extensively
as possible (David: could you test the Ragbag stuff again,
since I'm not sure I checked everything there.  The GAME and
XFF parsers are definitely okay, though).

Let me know if this causes any trouble,

   Thomas.