[Bioperl-l] Annotation of features

[David Block]

On Wednesday, September 25, 2002, at 12:36  PM, Hilmar Lapp wrote:

> 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.

So the tag-value hash would be replaced by an annotation object, which 
would have an internal tag-value hash, and would allow you to act as if 
those hash key-value pairs were full-fledged AnnotationI objects?

Sounds good to me.  The key-value pairs are completely optional as far 
as creating SeqFeatures, right?  So even the object creation for 
Annotations will be only for the objects that currently require creating 
a hash - some inevitable overhead, but the benefit of being able to 
create an annotation and hang it off of virtually anything in the 
Bio::Seq and Bio::SeqFeature hierarchy.

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

There - you've got mine.

Dave
> --
> -------------------------------------------------------------
> Hilmar Lapp                            email: lapp at gnf.org
> GNF, San Diego, Ca. 92121              phone: +1-858-812-1757
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--
David Block                                  dblock@gnf.org
GNF - San Diego, CA             http://www.gnf.org
Genome Informatics / Enterprise Programming
Weblog:      http://radio.weblogs.com/0104507/