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

[Hilmar Lapp]

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.

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?

I'd rather favor uncoupling a feature and its location, with
features having a reference to a location object which will give
further detailsif the application worries. An application that
doesn't do anything with the coordinates wouldn't notice a change,
but an application that e.g. draws features on sequences will have
to decide what to do if the location object says that the
coordinates are not well determined. Retrieving the sequence part
the feature refers to on its attached seq will also be affected:
doing so for a feature with an uncertain location will result in
an exception being thrown. Separating SeqFeatureI and LocationI
allows also for the following: assume a feature with uncertain
start and end. If you're satisfied with an average start and end,
you can substitute the location object by a Range with certain
start and end, and voila - drawing, sequence excision etc will
just work fine on the very same feature object.

Maybe I'm missing something.

	Hilmar

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Hilmar Lapp                                email: hlapp@gmx.net
GNF, San Diego, Ca. 92122                  phone: +1 858 812 1757
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