[Bioperl-l] Re: questions and freeze

[Dan Kortschak]

On Fri, 4 Oct 2002, Jason Stajich wrote:

> I'm wary of changing the object - I understand your reasons, but I'd
> rather we build a separate set of objects like Bio::Taxonomy::Species to
> handle what you are trying to accomplish and then we can show that it
> should swap in for Bio::Species and eventually deprecate Bio::Species.
> This is because you have to remember there is a lot of history in the
> current API so big changes to core objects need to be thought about some.

That's what I was thinking too, I wasn't sure what to do about it. I think
that probably a Bio::Taxonomy::Taxon that takes on the function would be
the way to go - since that doesn't then assume that you are talking about
a species.

> Are you sure your recent_common_ancestor isn't a duplication of our
> get_lca() that is part of Bio::Tree::TreeFunctionI interface

No, recent_common_ancestor can find the phylogenetic common ancestor
(which may not yet be included in the same tree structure )while
lca finds the common ancestor already in a tree, being based on the
internal id rather than an externally defined taxonomic level and taxon
name. Though they look pretty similar other than that.

> > When you have time, comments and answers would be appreciated.
> >
>
> Okay, other people are interested in this as well so it makes sense for
> you to post a lot of this to the list.  Aaron Mackey and some folks in
> Bill Pearson's lab are using these objects for their own work as well.
> I'll try and look over things, but busy busy these week so getting
> feedback from the whole community is often better.
>
> In general, I'd rather like to see the Taxonomic objects extend the
> existing Node interface which was intended to be generic and not
> necessarily represent species or sequences.  Because, taxonomies !=
> phylogenetic trees I don't want people to think we are generalizing the
> two.  So I'd like to see your changes be extensions (in the OO sense) of
> Bio::Tree::Node that live in Bio::Taxonomy.  More to think about here.

Where it's been non-redundant, I think that's what I've done - if there
was a useful method in Bio::Tree::Node I used that hence inheritance from
that class rather than Bio::Tree::NodeI (while I was writing, I wasn't
comfortable with it, but...). Though looking back, there's some weird
stuff in what I wrote :) -> I'll go over what I've done and sort that out
over the next few days.

cheers
Dan

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