[Bioperl-l] Feature/Annotation rollback finished

Scott Cain cain.cshl at gmail.com
Thu Aug 30 00:05:06 EDT 2007


Hi Chris,

Is there a reason that the value method of the
Bio::Annotation::SimpleValue (and possibly some of its siblings)
returning "Value: $value"?  It didn't used to have the "Value: " before,
did it?

Thanks,
Scott


On Wed, 2007-08-29 at 15:13 -0500, Chris Fields wrote:
> 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  
> (SeqFeatAnnotated.t).
> 
> Let me know if there are any problems along the way!
> 
> chris
> 
> 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
> >> _______________________________________________
> >> Bioperl-l mailing list
> >> Bioperl-l at lists.open-bio.org
> >> http://lists.open-bio.org/mailman/listinfo/bioperl-l
> > -- 
> > ---------------------------------------------------------------------- 
> > --
> > Scott Cain, Ph. D.                                          
> > cain at cshl.edu
> > GMOD Coordinator (http://www.gmod.org/)                      
> > 216-392-3087
> > Cold Spring Harbor Laboratory
> > _______________________________________________
> > Bioperl-l mailing list
> > Bioperl-l at lists.open-bio.org
> > http://lists.open-bio.org/mailman/listinfo/bioperl-l
> 
> Christopher Fields
> Postdoctoral Researcher
> Lab of Dr. Robert Switzer
> Dept of Biochemistry
> University of Illinois Urbana-Champaign
> 
> 
> 
-- 
------------------------------------------------------------------------
Scott Cain, Ph. D.                                   cain.cshl at gmail.com
GMOD Coordinator (http://www.gmod.org/)                     216-392-3087
Cold Spring Harbor Laboratory

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