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

[Lincoln Stein]

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>.
> -----------------------------------------------------------------

-- 
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Lincoln D. Stein                           Cold Spring Harbor Laboratory
lstein@cshl.org			                  Cold Spring Harbor, NY
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