[Bioperl-l] est2genome

[Ewan Birney]

>
> >
> > Also, in a final note, Ensembl is starting to standardize their
> > function
> > names from each_XX to get_all_XX
>
> 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

  fetch_all_XXXX_by_YYYYY = ditto except it is a list

  list_all_XXXX = returns a a list of scalar which are not objects (eg,
ids etc)



Is this right guys?



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