[Bioperl-l] Bio::*Taxonomy* changes

[Chris Fields]

Sounds good to me.  I'm fine with any way that it's worked out, either
Taxonomy or Node-based, as long as there no Bio::Species-based confusion re:
Taxonomy, and that this eventually leads to getting rid of Bio::Species
altogether.

Have fun, guys!

(hey, probably the shortest response I have written)...

Chris

> -----Original Message-----
> From: Hilmar Lapp [mailto:hlapp at gmx.net]
> Sent: Tuesday, July 25, 2006 2:18 PM
> To: Chris Fields
> Cc: 'Sendu Bala'; bioperl-l at lists.open-bio.org
> Subject: Re: [Bioperl-l] Bio::*Taxonomy* changes
> 
> 
> On Jul 25, 2006, at 2:24 PM, Chris Fields wrote:
> 
> > Once this is all done, will we really have a need for Bio::Species?
> 
> No, except for backwards compatibility. Phasing it out will go over a
> couple of releases. E.g., v1.6.x could have deprecation warning in
> the documentation. v1.7+ would have deprecation warnings in the code
> written to stderr.
> 
> Just as an aside, we can't just drastically change the return type of
> a method. Instead, if at all possible, there should be a new method
> so that the old can be phased out over time but otherwise not
> changed. I.e., don't change $seq->species() to now all of a sudden
> return a node or taxonomic lineage, even if initially Bio::Species is
> returned with some magic under the hood. Instead, create something like
> 
> 	# return a Bio::Taxonomy::Node:
> 	my $taxon = $seq->taxon();
> 
> 	# alternative approach: return a lineage (taxonomy)
> 	# this would be Bio::TaxonomyI compliant
> 	my $lineage = $seq->lineage();
> 
> The former would require the lineage (and organelle for completeness)
> information to be either easily (though not necessarily directly)
> accessible through the node, or added as annotation.
> 
> 	-hilmar
> --
> ===========================================================
> : Hilmar Lapp  -:-  Durham, NC  -:-  hlapp at gmx dot net :
> ===========================================================
> 
> 
>