[Bioperl-l] t/SimpleAlign: not ok 18

[Allen Smith]

On Sep 16,  8:20pm, Jason Stajich wrote:
> Allen Smith wrote:
> > Well, I've been looking at doing the above - using bioperl-1.1.0 from a
> > mirror site, since CVS was inaccessible (I've now downloaded bioperl-live
> > HEAD). I'm currently looking at consensus et al stuff in SimpleAlign with a
> > view toward enabling a loose consensus mechanism, with that also being used
> > for tiebreaking in ties for strict consensus situations. This would be via
> > matrices, which is leading me into splitting out the matrix code in
> > Bio::Variation::AAChange and SimpleAlign (CONSERVATION_GROUPS) into a
> > seperate Bio::Matrix (and Bio::MatrixI) module. Thoughts?
> 
> We'd like to see this done - but we also have distance matricies that we'd
> like to be able to represent so we have to be careful with the
> Bio::MatrixI interface.

Clonk self on side of head... yes!

> If it can handle both substitution and distance

Depends on how much error-checking one wants. My current design would be
Bio::Matrix::SubstitutionI/Bio::Matrix::Substitution. 

> than I am fine - otherwise we may want to be explicit in the
> names, I'm thinking like Bio::Matix::SubstitutionI Bio::Matrix::DistanceI
> or something more clever.

Sounds good to me.

> I would definitely like to see the CONSERVATION_GROUPS moved into
> something more configurable than the basic groups that I threw in there.

Understand! I have to say that the method of derivation of them from pam250
is not the clearest thing in the world, incidentally...

> Also definitely agree on what your observations for the proper handling of
> consensus generation.  Appreciate your willingness to lend a hand
> and jump in there to fix things.   Need all the hands we can get!

Well, given that my dissertation research area involves alignments,
tree-building, etcetera, and that my main computer language is Perl, it
rather behoves me to assist in such things!

	-Allen

-- 
Allen Smith			http://cesario.rutgers.edu/easmith/
September 11, 2001		A Day That Shall Live In Infamy II
"They that can give up essential liberty to obtain a little temporary
safety deserve neither liberty nor safety." - Benjamin Franklin