[Bioperl-l] GFF and LocatableSeq refactoring

[Mark A. Jensen]

Hey Chris et al, 
I'm there on LocatableSeq, definitely. I do have one project to finish 
this weekend before I move to that: I'm planning to move Chase Miller's
excellent NeXML read/write implementation into the trunk, complete 
with tests. If we can get it to pass the test suite, is there room in the 
point release for it?
MAJ
----- Original Message ----- 
From: "Chris Fields" <cjfields at illinois.edu>
To: "BioPerl List" <bioperl-l at lists.open-bio.org>
Sent: Friday, August 14, 2009 7:29 PM
Subject: [Bioperl-l] GFF and LocatableSeq refactoring


> 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
> 
> _______________________________________________
> Bioperl-l mailing list
> Bioperl-l at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/bioperl-l
> 
>