[Bioperl-l] Bio::SeqFeature::Generic add_sub_SeqFeature

Jason Stajich jason@chg.mc.duke.edu
Mon, 29 Jan 2001 16:26:21 -0500 (EST)

On Mon, 29 Jan 2001, Hilmar Lapp wrote:

> Jason Stajich wrote:
> > 
> > What is the feeling here, we have this old way of doing things which
> > included using the value 'EXPAND' to determine if we should expand the
> > start/end space for a feature when adding a sub_SeqFeature to a feature?
> > 
> > I think this should likely be better modeled through a SplitLocationI
> > which is just a container of LocationObjects.  So I propose to remove all
> > references to 'EXPAND' which means removing the method _expand_region and
> > updating add_sub_Feature to deal with adding the locations.  Similarly 
> Can't we keep a separate method for coping with region extension due
> to a new subfeature, in whatever way the extension is done? As far as
> I can remember I had a good reason to put it into its own method, I
> needed it separately from add_sub_SeqFeature().

I guess it is more sane to let SeqFeature::Generic handle the common case
and the split location case will need to be handled elsewhere.  

In the special case of a feature with multiple locations that feature (or
object creating it) will take care of updating the location object to
point to a splitlocation object.  For example, if we choose to have CDS be
represented as a SplitLocation with the exons being the parts in the
join(...) statement. This will have to be negotiated by the object
creating the Gene/CDS object.

Okay so no changes to check in for Generic.

> 	Hilmar
> -- 
> -------------------------------------------------------------
> Hilmar Lapp                            email: lapp@gnf.org
> GNF, San Diego, Ca. 92121              phone: +1-858-812-1757
> -------------------------------------------------------------
> _______________________________________________
> Bioperl-l mailing list
> Bioperl-l@bioperl.org
> http://bioperl.org/mailman/listinfo/bioperl-l

Jason Stajich
Center for Human Genetics
Duke University Medical Center