[Bioperl-l] naming conventions

[Hilmar Lapp]

(changed the subject to be proper)

On Saturday, October 12, 2002, at 09:26 AM, Ewan Birney wrote:
> >
> > Excellent - that's very similar to how we're moving, right? The
> > difference is that we have get_XXXXs which returns an array, and
> > get_all_XXXXs, which returns a possibly flattened array (e.g., for
> > SeqI this would be get_SeqFeatures() instead of top_SeqFeatures(),
> > and get_all_SeqFeatures() instead of all_SeqFeatures().
> >
> > Ewan what's the plan for this distinction in Ensembl?
>
> I am not the person with the definitive answer - I have cc'd in 
> Arne and
> Graham who do have the definitive answer - my reading of it is that we
> have the following conventions:
>
>
>   get_all_XXXXX = returns a list of XXXX
>
>   get_XXXXX = returns a single scalar of XXXX
>
>   fetch_XXXX_by_YYYYY = is a database adaptor specific convention,
> returning one XXXX by criteria YYYY

Hm. When I rewrote the bioperl-db adaptors I decided to closely 
follow the already existing J2EE conventions, which makes life 
easier for people having to deal with both. So, there's now

	find_by_primary_key
	find_by_unique_key
	find_by_query
	find_by_association

in every adaptor. An adaptor adapts only a specific interface, hence 
it is clear which type of object it returns. With this naming you 
wouldn't know though whether to expect a list or a  single object 
(but you could treat them all as returning a list in perl).

Just my $0.02.

	-hilmar

--
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Hilmar Lapp                            email: lapp at gnf.org
GNF, San Diego, Ca. 92121              phone: +1-858-812-1757
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