[Bioperl-l] Feature/Annotation rollback finished
hlapp at gmx.net
Thu Aug 30 16:20:18 UTC 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
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 Lapp -:- Durham, NC -:- hlapp at gmx dot net :
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