[Biocorba-l] SeqFeature -> get_Primary_Seq

[Ewan Birney]

On Thu, 8 Feb 2001, Matthew Pocock wrote:

> > The SeqFeature interface includes a method 'seq_primary_id()' that returns
> > the primary identifier for the Seq that this SeqFeature belongs to.
> > 
> > For a little while longer, I'm going to continue my crusade for SeqFeature
> > to be naive about the actual sequence from whence it came outside the
> > range of the feature (other than via a primary identifier!)  :)
> > 
> > 
> > cheers,
> > alan
> 
> An understandable view - solves issues with circular references & object 
> ownership for naive implementations. Do bioperl features hold references 
> to their 'containing' sequences?

Nope. This difference between Bio::Seq and Bio::PrimarySeq (PrimarySeq's
don't have features, features have a link to PrimarySeq's).

I find this a good model.


> 
> Just to give my ID crusade - they are of no meaning without knowing 
> which database to look them up in - the tuple {ID, SeqDB} is what is 
> realy required if you use ID at all. Also, there is the issue of wether 
> resolving the ID gives you back a CORBA object that is equivalent or 
> identical.
> 
> Matthew
> 
> _______________________________________________
> Biocorba-l mailing list
> Biocorba-l@biocorba.org
> http://www.biocorba.org/mailman/listinfo/biocorba-l
> 

-----------------------------------------------------------------
Ewan Birney. Mobile: +44 (0)7970 151230, Work: +44 1223 494420
<birney@ebi.ac.uk>. 
-----------------------------------------------------------------