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