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

[Sendu Bala]

Chris Fields wrote:
> A species should not hold more than one node.  A species, by
> definition, is a rank in Taxonomy, and is a node, not a full
> Taxonomy, so Bio::Species should be a Node, not a Taxonomy.  I don't
> see how I can be any clearer...

Right, we have differing viewpoints because you're concerned with what 
Bio::Species /should/ be, based on the name of the file and perhaps its 
original intent, whilst I am treating it as what it actually /is/, which 
is an object that is used to contain information about multiple 
taxonomic nodes.


> The fact that it may work is beyond the point.  That's like putting
> duct tape on a leak to me.  Why not just simplify Bio::Species into a
> Node? Or make it into a Node and get rid of it altogether.

Bio::Species, again ignore the name, is just a thing that lets us store 
and retrieve a certain set of data. If we simplified it into a pure 
Node, it could no longer do that job. If we just get rid of it all 
together it can no longer do its job.

By making it a Bio::Taxonomy it can continue to do its job without 
having to have Node objects with cruft. It would also gain the useful 
methods of Bio::Taxonomy at the same time.


I really don't mean to upset you, and I apologise for having done so. 
I've been presenting what I thought was a logical argument in favour of 
Bio::Species as Bio::Taxonomy, and waiting to see if anyone would come 
up with a logical argument why that would be inappropriate, or why 
something else would be better.

I'm not saying you're wrong and I'm certainly listening and would change 
my choice based on what you have to say. I don't think it's fair to say 
that disregarding what you have to say is 'par for the course' - I 
already /have/ regarded what you had to say in this thread and ended up 
doing scientific_name() as purely what we get from the database.