[Biocorba-l] SeqFeature -> get_Primary_Seq

[Ewan Birney]

On Tue, 6 Feb 2001, Thomas Down 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?
> 
> Just as a datum...
> 
> The org.biojava.bio.seq.Feature interface has a getSequence()
> method which returns the complete sequence on which the feature
> was defined.  I'm quite keen on this, since it means that every
> feature knows its coordinate system (and of course, the `location'
> part of the feature is only meaningful in the context of that
> system).  
> 
> The fact that the method is returning a PrimarySeq and not
> an AnonymousSeq also tends to back this up.  Arbitrary fragments
> of sequences covered by a particular feature don't (generally)
> have their own ID and accession.
> 
> Currently, the BioJava implementation of the CORBA SeqFeature
> does return the whole parent sequence.  (which may or may not
> be right...)
> 

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...




>      Thomas.
> 
>    
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