[Bioperl-l] Annotation of features

[Hilmar Lapp]

Currently the only annotation you can stick on SeqFeatureIs is 
tag/value pairs. This is orthogonal to SeqIs.

I just realized that SeqFeature::Generic does have annotation(). I 
vote for propagating this method to the interface level.

SeqFeatureI's tag/value annotation should be transparently the same 
as for SeqI. This means tag/value pairs should be annotated as 
Bio::Annotation::SimpleValue instances added to the
AnnotationCollection.

This may, however, create significant overhead when SeqFeatureIs are 
instantiated (every tag/value pair amounts to an object). 
Thoughts/comments?

The problem could possibly be alleviated by writing an adaptor that 
adapts SeqFeatureI to AnnotationCollectionI, and annotation() would 
return an instance of that adaptor. In that case the implementation 
could make sure that you only incur the overhead once you actually 
request those values.

I'd be glad to hear anyone's thoughts on this.

	-hilmar

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Hilmar Lapp                            email: lapp at gnf.org
GNF, San Diego, Ca. 92121              phone: +1-858-812-1757
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