[Bioperl-l] Feature/Annotation rollback (update #2)

Chris Fields cjfields at uiuc.edu
Tue Aug 28 04:18:19 UTC 2007

Okay, the planned rollback on is pretty much complete with a few  
exceptions.  I'll probably merge back to bioperl-live within the next  
few days once the following issues are addressed:

1)  Bio::Ontology::Term - several classes are using  
Bio::Ontology::Term in ways inconsistent with one another; some are  
passing Bio::Annotation::DBLink instances and other are passing  
simple strings.  This was somewhat transparent with various operator  
overloads but now they have really come to the surface.  I'll  
probably work on Hilmar's suggestion on adding extra class methods to  
give it a more consistent interface and deprecate the older ones.  As  
one might guess this affects much of Bio::Ontology but also  
Bio::Seqfeature::Annotated; strangely enough FeatureIO tests pass  
(which may simply mean there isn't enough test coverage for FeatureIO).

2)  Bio::SeqFeature::Annotated - no word back on maintenance for this  
module.  It needs to implement Bio::SeqFeature::TypedSeqFeatureI  
(pretty easy) and needs documentation (not so easy).  It's apparently  
essential for FeatureIO.  I'll basically get it up-and-running and  
clean up the API.

There are a few odds and ends that need to be addressed with  
roundtripping, but these are already problems on the MAIN trunk so  
they will be addressed once code is merged back in.


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