[Bioperl-l] Sequence Features... (hello from Singapore...)

[Paul Edlefsen]

I am happy to hear that some changes will come to the SeqFeatureI
interface, because I agree that it is presently confusing.  Our
discussions about resolving some of these issues have been tangled and
difficult.  I only wish that I could be there in Singapore to
participate!  Reading about the proposed changes, I wonder what
immediate impact this will have on some of the work that I am doing.

In particular I have these questions:
  * Will the new SeqFeature be a LocationI?  Or something new?
  * Will the new SeqFeature *not* be a SeqFeature::Collection?
  * What will the relationship between [Primary]SeqI and a coordinate
system (and its resolver) be?  Will a sequence *be* a coordinate system
(and/or its resolver)?

I have been working these past couple of days on the modifications to
Bio::DB::* for the collection consolodation (and the more general
gbrowse data access refactoring), and this involves making a
Bio::DB::FeatureProviderI, a Bio::DB::SequenceProviderI, and a
Bio::DB::SegmentProviderI (this last is a simple combination of the
first two, and it provides an object called Bio::SeqFeature::SegmentI,
which is a SeqFeature::CollectionI defined over a range of a sequence).
 The SequenceProviderI folds together the present interfaces
Bio::DB::RandomAccessI and Bio::DB::SeqI and Bio::DB::UpdateableSeqI.
 In the proposed SeqFeatureI update, will the database interface (one
of these ProviderI objects) be responsible for maintaining the
coordinate system, or will that be up to the sequence, or something
else?

Thanks,

:Paul

Paul T. Edlefsen  Software Engineer
<<<<<<<<<<<<<<<<  >>>>>>>>>>>>>>>>>
The Institute for Systems Biology
1441 North 34th Street
Seattle, Washington 98103-8904
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Email: paul at systemsbiology.org
Phone: (206)732-1336
Fax:   (206)732-1260