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

Jason Stajich jason@cgt.mc.duke.edu
Tue, 18 Jun 2002 15:30:48 -0400 (EDT)

On Tue, 18 Jun 2002, Aaron J Mackey wrote:

> 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.

very true.  let's certainly keep with the interfaces for what it is worth.

<<Aaron showing that does like some aspects of the OO in bioperl?>>

> > # 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.

I'm a little confused because I use factory and parser interchangeably at
times even though I shouldn't.  Would we be able to build a single parser
which can process output from all the different PAML programs?  Or should
we be building a SeqIO/SearchIO style where each program has an associated
parser but they end up being part of the same factory system (there I go
again) called something like Bio::Tools::Phylo::PAML  ?  Are the result
objects suitable usable by anything else that they should be moved out of
the Tools directory and into a MolEvo/Phylo namespace (overkill I think)?

Additionally would all the data from the output from the different
programs fit nicely into a single type of Result object or will we need
different objects for different output b/c there are different classes of

Sorry if I muddy the water with my confusion.


> -Aaron

Jason Stajich
Duke University
jason at cgt.mc.duke.edu