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

[Chris Fields]

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