[Bioperl-l] Feature/Annotation rollback finished

Chris Fields cjfields at uiuc.edu
Thu Aug 30 00:17:18 EDT 2007


It shouldn't, that sounds like the output for add_text().  value()  
should just return the scalar value.

As a note, I added a new method, display_text(), for all  
Bio::AnnotationI classes which by default replicates the same output  
that stringification overloads produced.  So you should be able to  
explicitly call $ann->display_text for any Bio::AnnotationI where you  
once used an implicit call:

# old
print "$ann\n";

# new
print $ann->display_text,"\n";

chris

On Aug 29, 2007, at 11:05 PM, Scott Cain wrote:

> 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
>

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





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