[Bioperl-l] Bio::SeqFeature::Annotated API change

Hilmar Lapp hlapp at gmx.net
Fri Oct 12 10:46:19 EDT 2007

On Oct 12, 2007, at 9:04 AM, Sendu Bala wrote:

> Or, heck, since it's such a mess, do we just want to drop Annotated
> entirely and recommend using AnnotationAdaptor with Generic? What does
> Annotated bring to the table?

My recollection may be wrong since it's been quite a while, but I  
believe one of the main motivations was to reflect the ontology- 
typing of feature type and other annotation that GFF3 requires.

The motivation of AnnotationAdaptor was primarily to provide a view  
onto a SeqFeatureI that makes tag/value annotation transparently  
appear as B:AnnotatableI and B:AnnotationCollectionI compliant, mixed  
in with the annotation collection that B:S:Generic may hold already.

Although sometimes confused, these are not the same motivations.  
AnnotationAdaptor provides a view - you use it when that's the view  
you need on a SeqFeatureI object you have in hand. For example,  
bioperl-db uses it so it doesn't have to bother about how to de/ 
serialize tag/value pairs, when it knows how to de/serialize  
annotation collections already from sequence objects.  
AnnotationAdaptor doesn't care whether the primary_tag, or any other  
tag, is from an ontology.

> (Since its one of the modules added in 1.5 I think it's fair to  
> drop it
>> from the 1.6 release: stuff that doesn't work can and should be moved
> out of the path of stable branches.)

I agree with that unless someone steps up and makes it work.

: Hilmar Lapp  -:-  Durham, NC  -:-  hlapp at gmx dot net :

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