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