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

[Hilmar Lapp]

I think I like that best too.

	-hilmar

> -----Original Message-----
> From: Lincoln Stein [mailto:lstein@cshl.org]
> Sent: Wednesday, July 17, 2002 1:56 PM
> To: Ewan Birney
> Cc: sac@bioperl.org; Hilmar Lapp; OBDA BioSQL (E-mail); 
> BioPerl (E-mail)
> Subject: Re: [Open-bio-l] Re: [Bioperl-l] seq namespace method
> 
> 
> I liked the compromise you published earlier yesterday:
> 
> 	- Bio::PrimarySeqI inherits/implements IdentifiableI.
> 		This is its "one true" name.
> 	- The cloud of other identifiers is attached to Bio::Seq via
> 	its AnnotationCollectionI.
> 
> I will work on IdentifierCollectionI as a separate interface.
> 
> Lincoln
> 
> On Tuesday 16 July 2002 04:04 am, Ewan Birney wrote:
> > Ok. Both Lincoln and Steve prefer I think the pattern
> >
> >
> >   Bio::IdentifierCollectionI
> >
> >
> > which Bio::PrimarySeqI inheriets from
> >
> >
> > gives out something like ->identifiers() -   # a set of 
> Bio::Identifier
> >                          ->identifier('sp'); # 
> identifier(s?) for this
> > namespace
> >
> >
> > Lincoln is suggesting this handles cardinality/split/merges
> >
> >
> >
> > I am wary of this because of two things:
> >
> >
> >    (a) Most objects come from one authority/namespace - how 
> do we indicate
> > the "main" authority/namespace of this object. There are *very few*
> > objects which honestly have two equally valid Identifiers -
> >
> >
> >     --- my view is that we are giving ourselves too much 
> rope to hang
> > ourselves with and we will endlessly have things about "assummed
> > namespace" or - even worse - assumming that the first 
> identifier in the
> > list of identifiers pulled out of the colleciton is the "main" one.
> >
> >
> >    (b) We are making life harder for non-standard 
> implementations who have
> > to implement this - certainly putting in split/merge 
> capibility as part of
> > the *interface* is a bad idea - split/merge is nasty to implement.
> >
> >
> >
> > Does anyone else want to weigh in. Steve/Lincoln - can you 
> show me that my
> > fears are unfounded?
> >
> >
> >
> >
> >
> >
> > -----------------------------------------------------------------
> > Ewan Birney. Mobile: +44 (0)7970 151230, Work: +44 1223 494420
> > <birney@ebi.ac.uk>.
> > -----------------------------------------------------------------
> 
> -- 
> ==============================================================
> ==========
> Lincoln D. Stein                           Cold Spring Harbor 
> Laboratory
> lstein@cshl.org			                  Cold 
> Spring Harbor, NY
> ==============================================================
> ==========
>