[Bioperl-l] Feature/Annotation rollback finished

Hilmar Lapp hlapp at gmx.net
Thu Aug 30 12:20:18 EDT 2007


On Aug 29, 2007, at 11:23 PM, Chris Fields wrote:

>> Once this is merged back to the main trunk, I guess we need to give
>> Bio::SeqFeature::TypedSeqFeatureI a thorough look and make sure it
>> makes real sense.
>
> It describes one method, ontology_term(), which returns a  
> Bio::Ontology::TermI.  This is similar to  
> SeqFeature::Annotated::type(), which returns a  
> Bio::Annotation::OntologyTerm (a Bio::Ontology::TermI).  My thought  
> is to simply deprecate type() in favor of  
> TypedSeqFeatureI::ontology_term().

I think we'll want to think about that. type() gives me some  
indication of what the returned value might represent, whereas  
ontology_term() only tells me about the type of the returned object.

You could make ontology_term() accept a context argument, such as

	my $feature_type = $typedFeat->ontology_term(-context => -type);

Or you could name the method(s) more explicitly, such as

	my $feature_type = $typedFeat->type_term();
	my $feature_source = $typedFeat->source_term();
	my @annTerms = $typedFeat->get_Annotations('Gene Ontology');

Am I making sense?

	-hilmar
-- 
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: Hilmar Lapp  -:-  Durham, NC  -:-  hlapp at gmx dot net :
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