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

[Chris Fields]

Sounds good to me; agree with Hilmar's suggestion of 'in_memory' as well,
but it's your choice.

Chris

> -----Original Message-----
> From: bioperl-l-bounces at lists.open-bio.org [mailto:bioperl-l-
> bounces at lists.open-bio.org] On Behalf Of Sendu Bala
> Sent: Thursday, July 27, 2006 2:07 AM
> To: bioperl-l at bioperl.org
> Subject: Re: [Bioperl-l] Bio::*Taxonomy* changes
> 
> 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.
> 
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