[Bioperl-l] Genquire id's

[Ewan Birney]

On Mon, 4 Mar 2002, Mark Wilkinson wrote:

[moving to the bioperl mailing list]

> w.r.t. the Genquire OBDA layer:  we never came to a decision about how to "link"
> database features with their corresponding BioPerl Feature object in order to allow
> write-back.  Would people prefer that I create a new feature type OBDAFeatureGeneric,
> for example, that the OBDA features inherit from and has a single "ODBAid" method
> which returns the ID of the feature row in the database?  Or should I leave things as
> they are, and simply use the Feature tag/value system hold the ODBAid of the entry?
> Or...???  If we could reach a consensus on this before I plunged into the coding it
> would be great!
> 


What I would go for is (this would all be in bioperl-db)


  Bio::DB::IdentifiableI

which defines the method

  $obj->dbID 

or perhaps

  $obj->database_id


and then have a 

  Bio::DB::SeqFeature::Generic

or perhaps

  Bio::SeqFeature::GenericDB


which inheriets its implementation from Bio::SeqFeature::Generic and
inheriets Bio::DB::IdentifiableI and has an additional method


  $obj->database_id()



We then can extend the idea of "identifiable in a database" into other
objects...



sane/not sane? Chris --- views?







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