[Bioperl-l] GenericHSP and SimpleAlign

[Jason Stajich]

I added a method
get_aln to Bio::Search::HSP::HSPI and implemented it in
Bio::Search::HSP::GenericHSP.   It returns a Bio::SimpleAlign for an HSP
so that one can evaluate an HSP output the alignmet in one of the AlignIO
supported format.  Once bl2seq parsing is possible in blast.pm and/or
blastxml.pm we can reimplement Bio::AlignIO::bl2seq with the SearchIO
system.   This can further help us focus on SearchIO as the single system
to focus our energy.

There are a couple of other places that BPlite and Blast parsing
modules are used - in Bio::SeqFeature::SimilarityPair - I would like to
possibly like to remove this method in favor of the SearchIO system.
Hilmar are you okay with this?

Also thanks to James D for the bug submission on GenericHSP - checked in
the suggested fix.

-jason

-- 
Jason Stajich
Duke University
jason@cgt.mc.duke.edu