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

Sendu Bala bix at sendu.me.uk
Fri Oct 26 10:48:27 EDT 2007

Hilmar Lapp wrote:
> On Oct 11, 2007, at 6:40 AM, Sendu Bala wrote:
>> seq_id()
>>   Usage   : $obj->seq_id($newval)
>>   Function: holds a string corresponding to the unique
>>             seq_id of the sequence underlying the feature
>>             (e.g. database accession or primary key).
>>   Returns : a Bio::Annotation::SimpleValue object representing the
>>             seq_id.
> type() and source() should be ontology-typed in a TypedSeqFeatureI (and 
> therefore be instances of Bio::Annotation::OntologyTerm, not 
> Bio::Annotation::SimpleValue) to be more GFF3-compliant, but I don't 
> understand what the benefit of typing seq_id() any stronger than a 
> string would be.

Would there be any problem with having source() return a string, but 
still allow access to the OntologyTerm object via 
get_Annotations('source')? (Ditto with type?)

I think that's the way I'm going to go for now.

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