[Bioperl-l] Feature/Annotation rollback finished

Chris Fields cjfields at uiuc.edu
Wed Aug 29 20:13:17 UTC 2007

I'll probably go ahead and start merging this stuff over to CVS HEAD  
then.  There haven't been any objections so far.

The page I posted outlines the more critical fixes, primarily the  
changes to Bio::Ontology::Term methods (along with relevant code) due  
to inconsistencies in the interface.  The Bio::Annotation classes  
also now throw if you attempt to use them in an overloaded context.   
I also split off SeqFeature::Annotated tests into it's own test suite  

Let me know if there are any problems along the way!


On Aug 29, 2007, at 2:45 PM, Scott Cain wrote:

> 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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Christopher Fields
Postdoctoral Researcher
Lab of Dr. Robert Switzer
Dept of Biochemistry
University of Illinois Urbana-Champaign

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