[Bioperl-l] Re: [Open-bio-l] seq namespace method

[Jason Stajich]

On Mon, 8 Jul 2002, Hilmar Lapp wrote:

> According to BioSQL, sequences (bioentries) live in a namespace, e.g.,
> the name of the databank that maintains and/or serves them.
>
> None of the Bio:: seq objects/interfaces have a method for that.
>
> I propose to add one, specifically to the lowest level
> Bio::PrimarySeqI (bioentries are pretty general, and a namespace is
> needed for /any and all/ bioentries). To me, the namespace doesn't
> have to do much with whether this seq is going to be stored in BioSQL
> or not. A sequence with an accession number has (implicitly or
> explicitly) a namespace in which this accession number is valid.
> PrimarySeqI has an accession.

Will is be a required method or should we have it default to returning
''/undef unless it is overridden outside of the interface.  I just worry
about adding a method to a top level interface which is implemented by a
variety of toolkits - we will need to programtically depend on the method
existing, but there may be a lot of PrimarySeqI (Ensembl, GMOD, TFBS,
others?) implementers which will have to update their code for the changes
to the interface.  Perhaps we do want them to be updated?

-jason
>
> Anyone has other suggestions, objections?
>
> 	-hilmar
>

-- 
Jason Stajich
Duke University
jason at cgt.mc.duke.edu