[Bioperl-l] WARNING INCOMING: collection consolidation

[Paul Edlefsen]

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