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

[Sendu Bala]

Hilmar Lapp wrote:
> The only reservation I have is that you'd have methods on Node that  
> don't really operate on the node instance but rather operate on the  
> taxonomy (database) behind the scenes. That's what I would have used  
> Bio::Taxonomy for, not so much as a container than as a class with  
> (conceptually) 'static' methods corresponding to those that are now  
> in Node, like get_Lineage_Nodes().

Yes, I had the same reservation. But it somehow seemed reasonable for me 
to ask a node for its lineage, though I draw the line at having a method 
like get_node('rank_name'). That's the only thing Bio::Taxonomy would 
have been good for, so it's a trade off between some nice methods and 
the problems inherent in a node-container class.

Though, perhaps we almost have the best of both worlds, since the 
database is effectively a container without the problems:
$node->db_handle->get_Taxonomy_Node(-rank 'rank_name',
                                     -lineage_of => $node); ?


> So overall I think you should just go ahead.

Great, will do.