[Bioperl-l] GFF and LocatableSeq refactoring

[Chris Fields]

As we have pretty much everything in place for another point release  
(which I will start merging over this weekend into the 1.6 branch), I  
have gone ahead and made two branches for refactoring some of the more  
important pieces of bioperl code.  Both refactors may require API  
changes; if so these will be part of a 1.7 release.

1) GFF - entail refactoring bioperl code to better handle GFF2/3.

This is a large section of code, so small incremental changes may be  
merged to trunk over time (and thus may involve several branches).   
Included is refactoring of feature typing to be more consistent and  
lightweight, and will initially involve Bio::FeatureIO and  
Bio::SeqFeature::Annotated (which may be deprecated in the process).   
See the following for additional details:

http://www.bioperl.org/wiki/GFF_Refactor

2) Align/LocatableSeq - dealing with inconsistencies in Bio::AlignI  
(SimpleAlign) and LocatableSeq.  This is primarily to address  
significant bugs but will also entail cleaning up SimpleAlign methods  
(factoring out more utility-like methods into Bio::Align::AlignUtils  
or similar).  This also may involve several branches.  See the  
following for additional details:

http://www.bioperl.org/wiki/Align_Refactor

Any help/suggestions for the above two would be greatly appreciated!   
Robert Buels may be heading up the initial FeatureIO work; I will  
likely start on LocatableSeq/Align (Mark, wanna help?).

chris