[Biocorba-l] SeqFeature -> get_Primary_Seq

[Thomas Down]

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...)

     Thomas.