[Bioperl-l] Bio::AnnotatableI vs Bio::FeatureHolderI

Chris Fields cjfields at uiuc.edu
Fri Feb 23 13:49:44 EST 2007


To add to that, there's a HOWTO describing the differences:

http://www.bioperl.org/wiki/HOWTO:Feature-Annotation

I agree w/ Aaron; if it has a location it's a feature,  otherwise  
it's an annotation.

chris

On Feb 23, 2007, at 8:36 AM, aaron.j.mackey at gsk.com wrote:

> The fundamental difference (in my mind) between a feature and an
> annotation, is that a feature has a location/range, and thus the
> information represented in the feature is applicable only to that
> location/range.  An annotation, on the other hand, is "global", or at
> least non-localizable (note: a feature with a "fuzzy" location of
> "somewhere along this sequence, but I'm not sure where" is still not
> global - if you did/could know the location, you'd describe it as a
> feature, so it shouldn't be represented with an annotation).
>
> -Aaron
>
> bioperl-l-bounces at lists.open-bio.org wrote on 02/22/2007 03:36:33 PM:
>
>> Are Bio::AnnotatableI and Bio::FeatureHolderI competing interfaces?
>>
>> I get the impression they are designed to do similar things.  If  
>> so is
>> one deprecated and the other preferred?
>>
>> If their responsibilities are orthogonal to each other, what sorts of
>> tasks are suited to each?
>>
>> Thanks,
>> Michael
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>
>
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Christopher Fields
Postdoctoral Researcher
Lab of Dr. Robert Switzer
Dept of Biochemistry
University of Illinois Urbana-Champaign





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