[Bioperl-l] Bio::*Taxonomy* changes
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.,
> 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?
> 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'
: Hilmar Lapp -:- Durham, NC -:- hlapp at gmx dot net :
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