[Biojava-l] New package for SequenceDBs, and GFF parsing changes

[Thomas Down]

Hi...

Since I haven't seen any objections, I've moved SequenceDB
into its own package.  Hopefully this now leaves us in a
position where all the core APIs are in sensible places, and
we won't have to move anything again in future (touch wood...).
CVS users should do a "cvs update -d" to make sure they get
the new package.  I hope any changes needed to user code
because of this move will be minimal.

This package is now the logical place for all new SequenceDB
related code that's being proposed at the moment.

One consequence of this is that we're now in a position
where Annotator (currently in org.biojava.bio.seq) is a bit
uncertain of its home.  Since it acts on SequenceDBs, it
probably actually belongs in the seq.db package.  However,
I'm rather dubious about the value of this interface: it seems
a bit over the top to have an interface which acts on whole
SequenceDBs (which could be anything up to and including
EMBL).  My preferred replacement is to have a new SequenceAnnotator
interface (which does the same kind of job as Annotator, but
on a smaller scale), plus an implementation of SequenceDB which
lazily applies a SequenceAnnotator to sequences as they are
retrieved from an underlying database.  This solution seems
more flexible and more general to me...

As a stopgap measure, I've deprecated Annotator (and Abstract
Annotator), but left them in their old location.  If there's
anyone out there who is actively using these and wants them
to stay, please speak out now.  Otherwise they can hopefully
be removed in time for 1.0.



And in other news...

I've made some modifications to the org.biojava.bio.program.gff
package -- mainly behind the scenes.  Some bugs are fixed, and
I've split the old GFFDocumentHandler interface into two:
GFFDocumentHandler, and GFFErrorHandler.  If you just use
the parser to create GFFEntrySets, you may not notice these changes
at all (but do look at the revised API).  If you have written
your own GFFDocumentHandler, you'll need to make a few changes,
but these should not be substantial.


Happy hacking!
   Thomas.
-- 
He looked up with big brown eyes.  ``They're really only
tiny little A-bombs, honest.''
                                     -- David Brin.