[Bioperl-l] porting from BlastXXX to GenericXXX

[Jason Stajich]

Steve - I'm slowly getting this going again - I've ported seq_inds to the
GenericHSP object.  This will work with FASTA HSPs too as the objects
seems to be sufficiently generic (a couple of places where I do
if($hsp->algorithm =~ /FAST/ ) for fasta specific things).

I've also added the convenience methods
GenericHit-> hsps()

GenericResult-> hits()

to allow retrieval of the contained objects in a list manner in addition
to the next_XX() / rewind() iterator methods.

My priorities in this are to get Bio::SearchIO::Writer::XXTableWriters
to work for the blast objects and see about adding parser for a couple of
other pairwise alignment outputs.  If all is well I'd like to see about
moving the psiblast code into the blast.pm if possible.   This would mean
adding and iteration method to the Hit objects and what else?  Should it
be peeled off into a separate 'psiblast' parsing module after all?

At any rate we'll have to agree some on common methods that need to be
established in the interfaces first.  There is some variation in what
we've each been using: evalue/expect, signif/significance, etc.

I think I'll go ahead and port/write the SearchIO::emboss parser which
will produce Search objects from EMBOSS water/needle alignments - we
already parse these in AlignIO but they produce Align::AlignI objects and
someone may want to have Search::HSP objects.  I'm still undecided as to
how we should merge pairwise and MSA objects into a common framework -
right now we can convert from HSP to Align::AlignI but not in the reverse
for obvious reasons.  Perhaps this is good enough?


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