[Bioperl-l] Bio::SeqFeature::Annotated migration branch

[Chris Fields]

After removal and some changes for API consistency, all tests pass on the branch, so it's ready to merge.

chris

On Jun 5, 2010, at 9:38 PM, Chris Fields wrote:

> As Bio::SeqFeature::Annotated is a bit heavy, has some problems, and seems mainly centralized around Bio::FeatureIO, I'm planning on eventually moving it completely over to the Bio-FeatureIO refactoring (in a separate dist).  It may eventually be removed altogether in the long term.
> 
> However, there are a few modules outside of Bio::FeatureIO in core that seem to be using this class for unknown reasons:
> 
> Bio::Tools::Match
> Bio::Tools::Phylo::Gerp
> Bio::Tools::Phylo::Gumby
> 
> As it's long been considered too heavy and will be deprecated in favor of something more lightweight, I'll try moving these over to either SF::Generic or to a factory for flexibility.  I've created a branch on bioperl-live to do this:
> 
> http://github.com/bioperl/bioperl-live/tree/topic/switch_sf_annotated
> 
> If anyone knows why the above modules might absolutely require this please let me know.  I'll not merge anything over until we do a final review on list.
> 
> chris
> 
> 
> 
> 
> _______________________________________________
> Bioperl-l mailing list
> Bioperl-l at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/bioperl-l