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

[Hilmar Lapp]

On Jul 25, 2006, at 2:24 PM, Chris Fields wrote:

> Once this is all done, will we really have a need for Bio::Species?

No, except for backwards compatibility. Phasing it out will go over a  
couple of releases. E.g., v1.6.x could have deprecation warning in  
the documentation. v1.7+ would have deprecation warnings in the code  
written to stderr.

Just as an aside, we can't just drastically change the return type of  
a method. Instead, if at all possible, there should be a new method  
so that the old can be phased out over time but otherwise not  
changed. I.e., don't change $seq->species() to now all of a sudden  
return a node or taxonomic lineage, even if initially Bio::Species is  
returned with some magic under the hood. Instead, create something like

	# return a Bio::Taxonomy::Node:
	my $taxon = $seq->taxon();

	# alternative approach: return a lineage (taxonomy)
	# this would be Bio::TaxonomyI compliant
	my $lineage = $seq->lineage();

The former would require the lineage (and organelle for completeness)  
information to be either easily (though not necessarily directly)  
accessible through the node, or added as annotation.

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