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

[Lincoln Stein]

I agree with Steve.

Lincoln

On Monday 15 July 2002 03:42 pm, Steve Chervitz wrote:
> Glad we're all thinking alike here. However, why not use containment
> instead of inheritance, to allow a Bio::IdentifiableI to contain one or
> more
> Bio::Identifiers?
>
> If an IdentifiableI also has a preferred identifier slot, then it could
> have methods such as namespace(), id(), version() that would delegate to
> their preferred identifier. This would allow us to maintain the current
> interface yet still be I3C-compliant.
>
> For those that don't know about it, the I3C thingy that Ewan mentions is
> called the LSID (Life Science Identifier), a draft specification of which
> can be found at
> http://www.i3c.org/workgroups/technical_architecture/index.html. It's
> generated a bunch of interesting discussion.
>
> The LSID concept is still evolving, but current thinking is to have at
> least these fields: authority, namespace, id. A version field will probably
> be added and security info may be dropped.
>
> Steve
>
> --- Lincoln Stein <lstein@cshl.org> wrote:
> > Yes.
> >
> > Lincoln
> >
> > On Monday 15 July 2002 04:48 am, Ewan Birney wrote:
> > > I would claim the right pattern here is to have
> > >
> > >
> > >   Bio::IdentifiableI
> > >
> > > which Bio::PrimarySeqI inheriets from and Bio::PrimarySeq implements.
> > >
> > >
> > >   Bio::IdentifiableI would have slots for namespace, version, id (NB
> > > **no** type) and would be compatiable with the 13C naming convention
> > > thingy to produce I3C style names (so it might also have "authority" as
> > > a slot).
> > >
> > >
> > >
> > >
> > >
> > >
> > > -----------------------------------------------------------------
> > > 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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> > Bioperl-l@bioperl.org
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>
> =====
> Steve Chervitz
> sac@bioperl.org
>
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-- 
========================================================================
Lincoln D. Stein                           Cold Spring Harbor Laboratory
lstein@cshl.org			                  Cold Spring Harbor, NY
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