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

Ewan Birney birney@ebi.ac.uk
Fri, 7 Jul 2000 17:24:52 +0100 (GMT)

On Fri, 7 Jul 2000, Thomas Down wrote:

> 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...

Oooooh. I think that is a great idea Thomas. The Annotator interface was
one of the sore thumbs (in my view) in biojava, (to be honest, along with
the sequence not as strings, but I doubt I am going to win that one...)

Good move.

Ewan Birney. Mobile: +44 (0)7970 151230, Work: +44 1223 494420