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

Hilmar Lapp hlapp at gmx.net
Mon Jul 24 12:31:44 UTC 2006

Sounds good to me, except there is no Bio::TaxonomyI yet, and also  
Bio::Species shouldn't fully depend on an internet connection or flat  
file to do anything meaningful.

I.e., it should take advantage of a lookup database if there is one,  
but in the absence of that one should also be able to statically set  
attribute values to whatever one thinks can be gleaned from a parsed  
text or whatever.


On Jul 24, 2006, at 4:21 AM, Sendu Bala wrote:

>> I think this would be the way to go. I.e.,
>>           |------Node
>> NodeI----|
>>           |-|
>>             |----SpeciesNode
>> Species----|
> Actually, if we're changing the name of the module that Species
> interacts with, any existing code needs to be re-written. So why not
> just do it properly and have Bio::Species interact with Bio::Taxonomy?
>                    |----Bio::Taxonomy
> Bio::TaxonomyI----|
>                    |----Bio::Species
> Or
> Bio::TaxonomyI----|----Bio::Taxonomy----|----Bio::Species
> Leaving Node completely free to be just a node. This way we don't  
> have a
> crufty SpeciesNode there simply for the sake of Bio::Species.
> Bio::Species itself provides all the legacy stuff it needs for itself,
> while interacting with Nodes via TaxonomyI methods in the 'correct'  
> way
> only.

: Hilmar Lapp  -:-  Durham, NC  -:-  hlapp at gmx dot net :

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