[Bioperl-l] Re: Bio::Tools::Phylo::PAML::Codeml

[Aaron J Mackey]

On Tue, 18 Jun 2002, Jason Stajich wrote:

> [...] there aren't any other interfaces other than the AnalysisResultI
> which I am not sure has shown much utillity at this point.  We can
> sort that out later I think.

Well, it's worth trying to use it, if only to find out that it's not
useful.

> # parser will be a Bio::Tools::Phylo::PAML::IO::codeml object.
> # ala Bio::SeqIO::genbank -- I'll code this up.

Uhh, why not stick with the Bio::Factory::ResultI model ... ?  I think we
can subsume all of the PAML (codeml, baseml, codonsites, yn00) output
(like blast, blastx, tblastx, etc - variations on the same theme) under
one factory ... that returns various PAML::Result::* objects (which
themselves are AnalysisResultI's).  Just my random musings, you know this
part better than I.

-Aaron

-- 
 Aaron J Mackey
 Pearson Laboratory
 University of Virginia
 (434) 924-2821
 amackey@virginia.edu