[Bioperl-l] Sequence Features... (hello from Singapore...)

[Ewan Birney]

On Mon, 24 Feb 2003, Paul Edlefsen wrote:

> Ewan Birney wrote:
> 
> >  - AnnotationCollection also will have a contains "contains" method,
> >which gives sub Annotations. Therefore a Gene will have Transcripts etc
> >via this method. By placing this method here, and *not* at the feature
> >level (sub_SeqFeatures) we get rid of the ambiguity of "should a
> >sub_SeqFeature be strictly covered by its parent". We officially allow the
> >containment heirarchy to have *nothing* to do with the location system.
> >  
> >
> Where will the SeqFeatureCollectionI stuff go, then?  Will an 
> AnnotationCollectionI *be* a SeqFeatureCollectionI, or *have* one?
> 

This is the problem about the word AnnotationCollection - it is not a
collection of Sequence Features - the word AnnotationSet is better (or
AnnotationBlob).


In short, SeqFeatureCollectionI will be part of SeqI to handle the set of
AnnotationSetI (currently known as AnnotationCollection)


This does get a little tricky. When are you in on the west coast? What
about a quick phone call? I want to make sure we harness your energy in
solving the "fetching sub set of features by range/type
constraints" inside the new system...


> :Paul
> 
> 

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Ewan Birney. Mobile: +44 (0)7970 151230, Work: +44 1223 494420
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