[BioSQL-l] Re: [Bioperl-l] Bio::BioEntry

[Lincoln Stein]

When a piece of code is handed a random Bio::BioEntry, what is the approved 
mechanism for determining what it is?  Will the approved method be to ask if 
it supports Bio::Seql vs Bio::BiblioI interfaces?  (h'mmm, I don't see a 
Bio::BiblioI....)

Lincoln

On Monday 09 September 2002 03:35 am, Hilmar Lapp wrote:
> On Sunday, September 8, 2002, at 06:38  AM, Ewan Birney wrote:
> > On Fri, 6 Sep 2002, Hilmar Lapp wrote:
> >> BioEntry would be different from PrimarySeq in not having a
> >> sequence associated with it.
> >>
> >> 	Bio::BioEntry is-a Bio::IdentifiableI
> >> 	Bio::BioEntry is-a Bio::DescribableI
> >>
> >> and that's about it.
> >
> > [...]
> > Is there any better solution. What do you have as BioEntries and not as
> > Bio::Seq's?
>
> All objects that are to end up as Bioentries in biosql, but aren't
> sequences. E.g. OMIM entries, or clusters (Unigene). Of course,
> those would have additional annotation that needed to be stored too.
>
> The advantage could rather be that you can inherit off a base class
> that gives you IdentifiableI and DescribableI implemented via @ISA.
> Not a big deal OTOH.
>
> I needed it already in one place in bioperl-db to store a namespace
> in some object, so I did implement it. Right now it's in
> Bio::BioEntry in bioperl-db. It can stay there as it may indeed only
> be relevant in bioperl-db, or I can move it over to the bioperl-live
> trunk. Whatever people vote (also, I'm open to renaming
> suggestions) ... :-)
>
> 	-hilmar

-- 
Lincoln Stein
lstein@cshl.org