Bioperl-guts: SeqIO/Fasta and ScoringMatrix

[Aaron J Mackey]

I did the superfamily handling in SeqIO/Fasta.pm such that it only gets
turned on if you specify -superfamily => 1 (otherwise the superfamily
information remains a part of the description).  So no one currently using
Fasta.pm will notice a change, and people who need to deal with
superfamily numbers can.

I added the basic PIR.pm SeqIO handler as well (this does superfamily
numbers by default, if they're there at all - all of my PIR-format
databases have them, so if my idea of PIR is different than yours, let
me know).

I also committed in the ScoringMatrix object and its associated matrix
data files.  Please check it out (I even documented it, egads) and let me
know where I can improve things.  Currently I think this object is more of
a learning tool than a production use tool, but I can envision ways that
it may be integrated into SimSearch factories in the future.  And it's a
critical piece of my slow but instructive Smith-Waterman alignment factory
(coming soon, still tweaking a tad).

-Aaron

 -- 
 o ~   ~   ~   ~   ~   ~  o
/ Aaron J Mackey           \
\  Dr. Pearson Laboratory  / 
 \ University of Virginia  \     
 /  (804) 924-2821          \
 \  amackey@virginia.edu    /
  o ~   ~   ~   ~   ~   ~  o


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