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

Ewan Birney birney@ebi.ac.uk
Tue, 30 Jan 2001 09:14:42 +0000 (GMT)

On Mon, 29 Jan 2001, 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 the
> flush_sub_SeqFeature should flush the locations, but I'm not sure about
> what the start/end should be reset to...

I guess agree (I am wincing at every one of these decisions you know. It
just pains me to see us have to handle this object complexity in
essentially simple objects. Bugger-it! I know there is no way out here,
but .... it goes against the grain).

> I also had to update FeaturePair to add the method location() which
> delegates to feature1()->location() otherwise things won't work correctly. 
> start/end are defined by feature1 object so location should also reside
> in feature1.

That is the consistent route here...

> Jason
> Jason Stajich
> jason@chg.mc.duke.edu
> Center for Human Genetics
> Duke University Medical Center 
> http://www.chg.duke.edu/ 
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Ewan Birney. Mobile: +44 (0)7970 151230, Work: +44 1223 494420