[Bioperl-l] Re: [SO-devel] GFF3 - Bioperl - SO

Allen Day allenday at ucla.edu
Wed Oct 20 00:08:45 EDT 2004

this sounds like reusable code for tag->annotationcollection mapping for 
annotated seqfeatures.  may help to ease the seqfeature api transition.


On Mon, 18 Oct 2004, Hilmar Lapp wrote:

> On Oct 18, 2004, at 1:03 AM, Allen Day wrote:
> > I haven't looked at the AnnotationAdaptor you mention
> > below, but it sounds like a reasonable approach.
> I wrote that module to integrate the tag system of SeqFeatureI's with 
> the annotation bundle, which SeqFeatureI's also happen to have. 
> SeqFeature::AnnotationAdaptor allows one to look at a feature's tags 
> and annotation collection together as if there were no tag system but 
> only an annotation bundle instead. It works bi-directional, i.e., if 
> you modify an annotation object that in reality is a tag it will modify 
> the tag.
> The motivation (use case) was that for bioperl-db I had already written 
> modules for serializing and de-serializing an annotation bundle (along 
> with seq objects), and didn't want to write ugly special case code for 
> a feature's tag system.
> 	-hilmar

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