[Bioperl-l] WARNING INCOMING: collection consolidation

[Lincoln Stein]

Uh oh.  I thought we had agreed to name it Bio::SeqFeature::CollectionI, 
following Hilmar's conventions.  What Ewan has proposed and what Paul is 
working on are very much the same thing.

Lincoln

On Thursday 27 February 2003 02:31 pm, Paul Edlefsen wrote:
> Ewan Birney wrote:
> >At singapore I proposed a reordering of the
> >classes to deal with the "multiple coordinate system" (one feature being
> >on - say - 3 coordinate systems, being genomic, contig and cDNA) whilst
> >neatly maintaining backward compatibility of SeqFeatures and - very
> >attractively in my view - unifying the objects to store annotation about a
> >feature with the objects to store annotation about a sequence.
> >
> >
> >Did my proposal make sense? I think your Bio::DB::FeatureProviderI is very
> >close to my proposed Bio::Seq::CoordinateManagerI and/or
> >Bio::Seq::FeatureCollectionI.
>
> Yeah I'm not very clear on either your proposal or its relation to what
> I'm proposing.  I do think that it'd be worth fleshing out.
>
> First of all, what is your Bio::Seq::FeatureCollectionI?!  I'm concerned
> because I've been working on a Bio::SeqFeature::CollectionI.  Eegads.
>
> >Aaron is planning to do some commentary about this. Realistically we do
> >need to all get into the same room. Don't suppose you can fly
> >Seattle-->NY in the next couple of days?
>
> I agree that it would be ideal, but alas!  I won't be on that coast
> until March 19->?, and I'll be in Boston (though if necessary I could do
> the Chinatown->Chinatown thing for $15).  What about a phone conference?
>
> :Paul
>
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-- 
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Lincoln D. Stein                           Cold Spring Harbor Laboratory
lstein at cshl.org			                  Cold Spring Harbor, NY
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