[Bioperl-l] Bio::Species, Bio::Taxonomy::Node overhaul

Sendu Bala bix at sendu.me.uk
Sat Aug 12 08:06:32 EDT 2006


Sendu Bala wrote:
> After the initial round of changes to Taxonomy described at
> http://bugzilla.open-bio.org/show_bug.cgi?id=2047 (now committed),
> further changes will allow for the transition of Bio::Species to
> Bio::Taxonomy::Node (renamed to Bio::Taxon), and for Taxon to be fully
> usable without external database access.
> 
> In brief: rename Bio::Taxonomy::Node to Bio::Taxon, make Bio::Taxon
> implement Bio::Tree::NodeI, make Bio::Species a Bio::Taxon, remove all
> Bio::Species-related-backward-compatible methods from Bio::Taxon, create
> Bio::DB::Taxonomy::list, update Bio::SeqIO::genbank et al.

These changes have now been committed.


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