[Bioperl-l] clustalw output format updated

[Jason Eric Stajich]

Made changes so that weak/strong conservation of aa bases is reflected in
match line (updated Bio::SimpleAlign function match_line).  So one can
technically take MSA output from any format supported by bioperl and make
it look pretty much like clustalw 1.8X format.

Do we want to support a clustal format w/o these lines (old way), not sure
where one would parametrize that - probably in the AlignIO initialization?

Also made the clustalw output 60 lines (as this is current default output
format for 1.8x) instead of 50 and added a global variable LINELENGTH that
this is based on - perhaps it should be a class variable/state at some point.

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