[Bioperl-l] Feature/Annotation rollback finished

Scott Cain cain.cshl at gmail.com
Wed Aug 29 15:45:48 EDT 2007


Hi Chris,

I just wanted to let you know that I was out of town for a few days, but
now I'm back and I'm doing testing of GMOD software based on the branch
you are working on.  I'll let you know how it goes, but don't let me
stop you if you confident of your changes.  I'm sure whatever goes
wrong, it will just point out holes in the FeatureIO tests (I'm sure
there are plenty) and will require hopefully minimal changes on my end.

Thanks for your considerable efforts on this!  (Regardless of how much
work it makes for me :-)
Scott


On Tue, 2007-08-28 at 16:05 -0500, Chris Fields wrote:
> I'm now wrapping up the Feature/Annotation rollback.  I will probably  
> start merging back to the main branch in the next day or two., as  
> soon as interested parties (*cough*devs*cough*) look over the last  
> batch of changes.
> 
> http://www.bioperl.org/wiki/Feature_Annotation_rollback#Fourth_Round
> 
> I have also added a small benchmark test which indicates a decrease  
> in parsing time in SeqIO::genbank with all tests passing.  I expect  
> this will translate over to any Bio::SeqFeature::Generic-using class  
> (open mouth, prepare to insert foot....).
> 
> It is also possible there are still some instances where overloading  
> is expected lurking about in the ~1000 or so modules, so I'll leave  
> the exceptions I added to all Bio::AnnotationI; we can remove them  
> down the line, maybe prior to rel1.6, after more tests are added or  
> if they get particularly annoying.  My guess is I caught 99.99% of  
> them (prepare to insert other foot....).
> 
> The key change in this last round is the addition of several class  
> *dbxref* methods to Bio::Ontology::Term and  
> Bio::Annotation::OntologyTerm, all of which are capable of working  
> with either DBLink instances or simple scalars.  This was primarily  
> done in order to clear up inconsistencies in the older *dblink*  
> methods, which were ambiguous (some indicates simple scalar  
> arguments, others DBLink objects); operator overloading was used  
> extensively in these cases, which led to several issues.  I have  
> added deprecation warnings to the older methods which now map to  
> using the newer methods.  All tests pass with the exception of a few  
> already failing on the MAIN branch; the single test which needs to be  
> fixed is a round-tripping error in swiss.t (now a TODO), which can be  
> fixed after merging back.
> 
> Please respond to this if there are any questions or if I need to  
> clarify the changes I made a bit more.
> 
> chris
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-- 
------------------------------------------------------------------------
Scott Cain, Ph. D.                                         cain at cshl.edu
GMOD Coordinator (http://www.gmod.org/)                     216-392-3087
Cold Spring Harbor Laboratory
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