[Biocorba-l] SeqFeature -> get_Primary_Seq

[Alan Robinson]

Ewan wrote:

> > On Tue, Feb 06, 2001 at 10:39:52AM -0500, Jason Stajich wrote:
> > > In the IDL for the object SeqFeature, the method get_Primary_seq I have
> > > the follow question.
> > > 
> > > Is the intention to return the PrimarySeq that is bounded by the
> > > start/end of the SeqFeature (as we do in bioperl) or the entire PrimarySeq
> > > that the Feature lies on?
> > 
> 
> if we have to go one way on this, I would go for the entire sequence
> coming back.
> 
> As it is a PrimarySeq, it does not have seqfeatures. This does mean that
> we don't have to haul around the entire seqfeatures set of a sequence as a
> consequence of one seqfeature being asked for. Which is good.
> 
> 
> BTW - I would like the
> 
>    interface SeqFeature {
> 	AnonymousSeq just_the_region_seq;
> 	PrimarySeq   the_entire_seq;
> 	};
> 
> type route. This is a good use of an "identifier-less" sequence...


Hmmmm... Initially, I'm not keen on this suggestion for the PrimarySeq
behaviour.

If I'm getting a sequence from a 'SeqFeature' object, I expect it to
relate to the SeqFeature in question, not the original sequence (I'll use
the methods of the 'Seq' interface for that).

However, I agree there may be a case for adding a 'get_AnonymousSeq()'
method to the 'SeqFeature' interface.


Alan.