[Bioperl-l] Bio::Species, Bio::Taxonomy::Node overhaul

Chris Fields cjfields at uiuc.edu
Mon Aug 7 08:41:22 EDT 2006

Sendu's been documenting this under Bugzilla (Bug 2061), but the wiki  
may be a better place.  The changes are extensive.

The only part I don't agree with is the use of species() to return a  
binomial name, which I already responded to (and don't plan dragging  
out).  I don't use Bio::Tools::Phylo::PAML or the Tree modules so I  
can't give much input there, but I would suggest that changes there  
need to be listed in a separate post.  Lots of people use  
Bio::Tools::Phylo::PAML so there may be some who might not agree.


On Aug 6, 2006, at 2:38 PM, Hilmar Lapp wrote:

> I have three comments.
> 1) It sounds a bit that you changed the behavior of get_lca() such
> that users may have to adjust their code? If this is true, then this
> needs to be made clear in the 1.6 release as that part will not be
> backward compatible. If this is not true, then why did you have to
> change the implementation of Bio::Tools::Phylo::PAML to make tests
> pass? I.e., to what extent can what broke Bio::Tools::Phylo::PAML
> also break someone's script?
> 2) I can't find object_id() on Tree::Node or Taxonomy::Taxon. Where
> is/was it? The reason I am asking is that this method is part of the
> Bio::IdentifiableI API and therefore if you want to deprecate it you
> are suggesting to deprecate implementing Bio::IdentifiableI, and the
> rest of those methods need to be deprecated along.
> 3) Your whole email should probably go on the wiki, linked somewhere
> under documentation or release notes. Or somebody has a better idea?
> 	-hilmar

Christopher Fields
Postdoctoral Researcher
Lab of Dr. Robert Switzer
Dept of Biochemistry
University of Illinois Urbana-Champaign

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