From: Diane Trout <diane@caltech.edu>
Date: Sat, 24 Mar 2007 01:00:49 +0000 (+0000)
Subject: move strand into seqspan
X-Git-Url: http://woldlab.caltech.edu/gitweb/?p=mussa.git;a=commitdiff_plain;h=75496e2c562d728af983c347527270eba360c6ee;hp=75496e2c562d728af983c347527270eba360c6ee

move strand into seqspan
this patch moves strand storage from Sequence into SeqSpan,
also when accessing sequence data from a SeqSpan that is currently
on the minus side it correctly returns reverse complemented data.

Unfortunately getting iterators that point to data thats a
transformation of currently existing data is a giant pain and
was making SeqSpan way to complicated.

So I took the easy way out. SeqSpan will now cache a reverse complement
of the region its pointing to and return iterators based on that.

Also Alphabet can reverse complement a string,

Drat, just realized that if one changes the region of SeqSpan,
the rc_seq will need to be invalidated.
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