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

Chris Fields cjfields at uiuc.edu
Sat Oct 27 10:53:59 EDT 2007

On Oct 27, 2007, at 2:03 AM, Sendu Bala wrote:

> Chris Fields wrote:
>> On Oct 26, 2007, at 6:47 PM, Sendu Bala wrote:
>>> I've left source() as a SimpleValue, at least until issues with
>>> DB::Store are resolved wrt ontologies (it stores the entire
>>> ontology for each feature in the database, increasing storage
>>> requirments > 800x).
>> Do you mean SeqFeature::Store or OntologyStore (I'm guessing the
>> latter)?
> Sorry, I meant Bio::DB::SeqFeature::Store. This problem exists if you
> set the type() as well of course; the only reason I don't suffer from
> that is that I deliberately avoid setting the type on my features.

Makes sense if you're using $store->add_SeqFeatures (it stores a  
serializized SF along with the data via Storable, so the  
OntologyStore probably goes along for the ride).  If we make type  
checking optional and lazily create the OntologyStore singleton it  
would probably reduce the space, as you wouldn't create it unless  
needed.  Or you could map it over to a DB::SeqFeature after  
validating the type.

Just noticed something: DB::SeqFeature uses type() and source() as  
synonyms of primary_tag() and source_tag(); both use strings instead  
of SimpleValues.


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