[Biojava-dev] Cleanups for 1.4

[Thomas Down]

Hi...

Some time ago, there was some discussion about making the next
release of BioJava jdk1.4 only.  The response appeared positive.
Since then, a number of files have been committed which only
compile with jdk1.4 (including recent revisions of DNATools
and ProteinTools), without any complaints.

Since it looks like jdk1.4 is the accepted target, I've done
a few bits of tidying up:

    - xerces.jar removed from the biojava-live tree.  This
      was big, and the version we've been shipping now looks
      woefully old (about 2 years old...).  BioJava compiles and
      runs fine with the builtin XML APIs in j2se1.4.  Users
      can still run with xerces (hopefully a more recent version!)
      if they want to, but there's really no reason for BioJava
      to be shipping it any more.

    - jakarta-regexp.jar removed

    - Code which used org.apache.regexp.* APIs has been patched
      to use java.util.regex instead.

    - One source file (SeqAlignReadWrite.java) has been removed,
      since it just contained out-of-date versions of methods
      which have since been added to SeqIOTools.

Any objections?

     Thomas.