[Bioperl-l] TermI::get_dblinks inconsistent?

[Ewan Birney]

On Sat, 24 May 2003, Hilmar Lapp wrote:

> Ontology::TermI::get_dblinks() returns an array of scalars. I.e., if
> you ask an ontology term for its dblinks, you get an array of strings.
>
> Are people happy with this? Or is the fact that it does not return an
> array of Bio::Annotation::DBLink objects rather confusing and an
> example of inconsistency?

I think it should return a set of DbLinks Objects...

>
> The reason I'm asking is that I ran into this myself in bioperl-db. Not
> having read the POD carefully, I wrote TermAdaptor such that it assumes
> the return values are objects, not scalars. I can fix this in
> TermAdaptor (create DBLink objects on the fly), or I can change the
> interface definition and accordingly the implementations. The third
> option is to introduce another method that would return the dblinks as
> objects.
>
> Any opinions on what sounds most attractive? Personally, I'm leaning
> towards being drastic and change the interface definition as it's
> really inconsistent. Unfortunately I don't know how one would be able
> to provide backwards compatibility. I can also go for any of the other
> options.
>
> 	-hilmar
> --
> -------------------------------------------------------------
> Hilmar Lapp                            email: lapp at gnf.org
> GNF, San Diego, Ca. 92121              phone: +1-858-812-1757
> -------------------------------------------------------------
>
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