[Bioperl-l] OntologyTermI

[Lincoln Stein]

Hi,

This is what I was saying.  That is, Term is something separable from the 
graph.

Lincoln

On Monday 02 September 2002 12:34 am, Chris Mungall wrote:
> what about cyclical references? do we really want to go mucking around
> with the WeakRef module?
>
> in the current GO object model, Terms are dumb, all the smarts are in the
> graph object
>
> so you say
>
> $graph->get_children($term)
>
> rather than
>
> $term->children()
>
> which i prefer anyway
>
> On Fri, 30 Aug 2002, Kris Boulez wrote:
> > Quoting Lincoln Stein (lstein@cshl.org):
> > > In a classic "have your cake and eat it too" compromise, we could have
> > > a NodeI interface that Bio::Ontology::Term can choose to implement. 
> > > Methods are:
> > >
> > > 	children()		# return NodeI children
> > > 	parents()		# return NodeI parents
> > > 	all_children()	# return all NodeI children
> > > 	all_parents()	# return all NodeI parents
> >
> > I would be very much intrested in such methods. Bio::Structure now
> > has a set of self-grown methods like these.
> >
> > Some time ago Jason mentioned to me Tree-DAG_Node. That version (1.04)
> > seemed to do most of what is needed, but it wasn't -w clean.
> >
> > Kris,

-- 
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Lincoln D. Stein                           Cold Spring Harbor Laboratory
lstein@cshl.org			                  Cold Spring Harbor, NY
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