[Bioperl-l] split seq feature and fuzzy feature proposal

[Ewan Birney]

On Thu, 18 Jan 2001, Jason Stajich wrote:

> On Thu, 18 Jan 2001, Hilmar Lapp wrote:
> 
> > Jason Stajich wrote:
> > > 
> > > http://www.bioperl.org/wiki/html/BioPerl/AdvancedSeqFeatureLocations.html
> > > 
> > > Please look it over, I didn't describe the detail of the fuzzy feature
> > > methods because I'm not sure there will be extra methods, just overriding
> > > things like start,end to be remapped.  The different feature types need to
> > > be differentiated so that Bio::SeqIO::FTHelper can handle then differently
> > > when parsing/writing.
> > > 
> > > Ewan, Let me know what I've left off.  Hilmar does this sound reasonable,
> > > straightforward enough to you?
> > > 
> > 
> > You didn't include actual interface definitions, did you? Just
> > wondering whether I missed the link.
> 
> No - didn't describe actual interfaces since we are still struggling
> through this.  Will do that when we agree enough.
> 
> > 
> > As mentioned before, what bothers me is that in this layout
> > location-specific issues impact the class (type) of a SeqFeature.
> > Why should any SeqFeature change it's type only because its
> > location becomes uncertain or compound, and vice-versa?
> 
> 
> Ewan and I had decoupled the LocationI from SeqFeature but there was no
> seen advantage, just interface mish-mash, perhaps we were too hasty?


Just to chime in, my original proposal had locations separate from
SeqFeatures, but at the end of the day we seemed to be making two parallel
interface heirarchies with no real gain in abstraction or understanding,
and the potential for generating alot of confusion

So - I guess to flip around the question - what do we gain from hanging
location "off" seqfeature rather than merging the interfaces?


(remember interface definitions can be implemented with any number of
objects or object collections if so desired...)


e.