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

[Sendu Bala]

Chris Fields wrote:
> BTW, what exactly is Bio::Taxonomy::Taxon used for?  Looks like it is used
> more for building taxonomic trees that anything, so shouldn't it be moved to
> Bio::Tree:Taxon (that name isn't used)?  Then you could use
> Bio::Taxonomy::Taxon for your purposes.

It actually seemed more like a possible replacement for 
Bio::Taxonomy::Node. Thanks to its Tree::NodeI implementation it has the 
big advantage over Bio::Taxonomy::Node that you access the lineage 
without a database. From the programmer's point of view it seemed more 
natural, being able to create nodes and add descendants. I decided 
against it because I felt the added complexity wasn't really worth it, 
and Bio::Taxonomy::Node had some of its own advantages.

If this turns out to be the wrong choice, my Bio::Taxon can always be 
reimplemented to also implement Tree::NodeI in the future.


> See, the only concern I have with using the name Bio::Taxon is people
> confusing it with Bio::Taxonomy itself or with Bio::Taxonomy::Taxon.  Though
> I agree that the name makes sense for what you want.

I don't think you'd confuse it directly with Bio::Taxonomy, but you 
could certainly waste some time thinking it was appropriate to stick 
Bio::Taxon objects in Bio::Taxonomy objects - theoretically it might 
work but ultimately you'd just be wasting your time. I'll make sure the 
docs in the Taxonomy modules steer people in the right direction.