[Bioperl-l] Bio::SeqFeature::Annotated and mandatory type checking

Sendu Bala bix at sendu.me.uk
Thu Dec 14 17:15:07 EST 2006


Matthew Vaughn wrote:
> Dear all,
> 
> I'm trying to bring some of my code into compliance with the BioPerl 
> 1.5.2 and am running into some design decisions that I am unclear on. 
> Can I ask why Bio::SeqFeature::Annotated enforces mandatory checking of 
> the 'type' against SOFA? It seems to me that this should be optional 
> behavior as is the case with the Bio::FeatureIO family. I'd be happy to 
> write the patch if there is any agreement with me on this case.

Lots of people seem to have worked on it over the years, but perhaps 
Scott Cain is the person to talk to?

revision 1.4
date: 2004/09/25 11:41:29;  author: scain;  state: Exp;  lines: +1 -1
two things:
   * adding SOFA as an available ontology to DocumentRegistry.pm
   * modifying FeatureIO::gff to use SOFA to validate, and to parse 
Ontology_term


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