[Bioperl-l] BPlite as SeqAnalyisParserI

Hilmar Lapp hilmarl@yahoo.com
Mon, 19 Feb 2001 12:19:07 -0800

Jason Stajich wrote:
> >
> > I'm afraid at the same time I'll have to issue an exception permit
> > for the SeqFeature::Gene stuff to settle down, and for BPlite
> > (Jason, any chances?) to adopt the SeqAnalysisParserI interface.
> > I'd still like to expire these permits Monday night.
> Hmm, in order to do this, either we make Bio::Tools::BPlite::Sbjct a
> SeqAnalysisParserI or we need to find a way to make a Sbjct a SeqFeatureI
> which doesn't really make sense to me.

The SeqAnalyisParserI is supposed to convert input into a stream
of seqFeatures, so Sbjct cannot take that role. It should be
possible to make Sbjct a SimilarityPair-derived object, which will
make it a SeqFeatureI automatically. Check out
Bio::SeqFeature::SimilarityPair::_fromBlastObj(), where I create a
SimilarityPair object from a Blast::Sbjct object (or a Blast::HSP

So, provided BPlite::Sbjct can be made to inherit off
SimilarityPair, next_feature() in BPlite.pm would simply return
one subject after another, until there are no more. If changing
BPlite::Sbjct to inherit off SimilarityPair is too cumbersome,
next_feature() could also grab the next BPlite::Sbjct object and
create a SimilarityPair instance from its properties, much like
SimilarityPair::_fromBlastObj() does it from a Blast::Sbjct.

Sounds okay? Am I missing something?

Hilmar Lapp                              email: hlapp@gmx.net
GNF, San Diego, Ca. 92122                phone: +1 858 812 1757