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

[Chris Fields]

I would say go ahead, why not?  This would likely lead to the eventual
deprecation of Bio::Species, which was in the cards anyway.  

The only problem I can foresee is which class to use with
Bio::DB::Taxonomy*?  I guess one could settle on one class by default and
have the option to use another Bio::Taxonomy::NodeI-implementing class if
you wanted more data/methods available...

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 20, 2006 12:56 PM
> To: bioperl-l at bioperl.org
> Subject: Re: [Bioperl-l] Bio::*Taxonomy* changes
> 
> Chris Fields wrote:
> > Just thought of something...
> >
> > You had mentioned using a stripped-down version of Bio::Taxonomy::Node
> > previously, which led to a bit of contention.  One way to make everybody
> > happy would be to create an interface class that contains the basic
> shared
> > methods (Bio::Taxonomy::NodeI), then have the currently-named
> > Bio::Taxonomy::Node (which could be renamed to Bio::Taxonomy::Species or
> > something similar) implement those methods along with the current
> methods.
> > Another class (your stripped down version, which could then be
> > Bio::Taxonomy::Node) would also implement whatever base class methods
> were
> > needed.  They would both be Bio::Taxonomy::NodeI-implementing, so you
> could
> > use either object type where required.
> >
> >          |------Node
> > NodeI----|
> >          |------Species
> [...]
> > I favor the interface version as it
> > sticks with the interface-implementation design that Bioperl has been
> > migrating towards:
> >
> > http://www.bioperl.org/wiki/Advanced_BioPerl#Bioperl_Interface_design
> >
> > This would also help out with the whole Bio::Species issue; just have
> > Bio::Taxonomy::Species replace it.
> 
> Yes, this sounds good to me. Should I still wait until Jason/elders are
> able to comment before I start exploring this avenue?
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