[Bioperl-l] Bio::Seq::SeqWithQuality and Bio::SeqIO::phd
Fri, 10 Aug 2001 17:31:45 -0600 (CST)
I have completed Bio::Seq::QualI, Bio::Seq::PrimaryQual, and
Bio::Seq::SeqWithQuality ISA qw(Bio::Seq::QualI Bio::PrimarySeqI) and can
be constructed a number of ways all of which result in a SeqWithQuality
object containing a PrimarySeq object, a PrimaryQual object, and bundles
of methods for attempting to set descriptors like id, desc, etc for
the SeqWithQuality object where they are common between PrimarySeq
Complete POD and tests are in place.
Methods to set things like quality and sequence for the subobjects are set
up and work as I have forseen them.
I haven't CVS commit'ed them yet because I haven't received the permission
(should come RSN) but I would really like somebody who cares to take a
look at them. I put the modules I created in a little devel directory and
the t/ things use my modules from devel/blib and the rest of the Bioperl
modules from @INC. Any volunteers?
At them moment I am working on Bio::SeqIO::phd and I was going to design
such that it returns a SeqWithQuality object. Any opinions?
My thought for Bio::SeqIO::qual is that it should return a Bio::Seq::Qual
object and the user can create their own SeqWithQuality object if/when
they get the sequence. Any opinions on that?