[Bioperl-l] some checkins

[Jason Stajich]

- There was a little bug in SeqIO::swiss - were redeclaring $acc again.

  Please run make test before committing to be sure you are not breaking
  the build if at all possible.  The really sane thing here is to check
  out a new versino of the code in a second dir and make sure it still
  makes with no errors. 

- There were some typos in the Docs of SeqFeatureI and DB::RandomAccessI

[cvs update -d  to get the new directory ]

- added Bio::SeqFeatureProducerI, and one implementing class
Bio::SeqFeatureProducer::GFF which just uses the SeqFeature::Generic GFF
parsing to add features to a sequence.  The design might need some more
discussion, only two functions add_features, and _parse_rpt, but at least
is a start.

- added a test for it in t/SeqFeatureProducer.t and a .fasta and .gff
  file for this.

Comments are always welcome.  Himlar if we can make a BLAST
FeatureProducer the same way we'd have a nice way of adding features to
sequences.  More feature producing report parsing can be added in this way
hopefully.

-Jason

Jason Stajich
jason@chg.mc.duke.edu
http://galton.mc.duke.edu/~jason/
(919)684-1806 (office) 
(919)684-2275 (fax) 
Center for Human Genetics - Duke University Medical Center
http://wwwchg.mc.duke.edu/