[Open-bio-l] RE: seqfeature

[Hilmar Lapp]

I guess I should have said seqfeature (and there is a StrandedFeature or something in BioJava isn't there?). Also, I cared much more about the frame, which is absent too. Wouldn't you want to know the frame for a translation feature?

	-hilmar

> -----Original Message-----
> From: Thomas Down [mailto:td2@sanger.ac.uk]
> Sent: Wednesday, May 01, 2002 12:55 AM
> To: Hilmar Lapp
> Cc: Chris Mungall; OBDA BioSQL (E-mail);
> gmod-devel@lists.sourceforge.net
> Subject: Re: [Open-bio-l] RE: seqfeature
> 
> 
> On Tue, Apr 30, 2002 at 05:49:08PM -0700, Hilmar Lapp wrote:
> > Seqfeature_location does not have a frame attribute (nor a 
> phase). On purpose?
> 
> Phase (at least in the way it's normally used) is quite specific
> to coding exons.
> 
> I'd actually argue that no `biological' meaning should ever
> be attached to locations (let alone /parts/ of a location).
> If it's important to you, create individual `exon' features
> and put the phase as a qualifier_value on that.  (Note: this
> is coming from the BioJava `location-is-a-set-of-integers'
> point of view.  BioJava locations don't even have strand
> information, so they're already a little different from the
> BioSQL model).
> 
> If you really, really, want phase on individual location spans,
> why not put it in the location_qualifier table.  That at least
> makes it clear that phase isn't a property that every location
> is expected to have.
> 
> 
>      Thomas.
>