[Bioperl-l] Feature/Annotation rollback finished

Thu Aug 30 17:45:44 UTC 2007

Sounds good but I have yet to commit some of the Ontology changes  
Hilmar and I discussed (whereupon our brace heroes deprecate dblinks  
methods in favor of dbxrefs).  These should be committed fairly soon  
(hour or two).

My guess is the change will be fairly transparent so shouldn't affect  
anything unless you have scripts using those methods directly.

chris

On Aug 30, 2007, at 10:46 AM, Scott Cain wrote:

> Hi Chris,
>
> Good news!  I only had to add a few defineds and a few  
> display_texts and
> I was able to successfully create a database and load the yeast GFF3
> file.  While I want to do more testing with GFF from other sources,
> clearly, I am 95% of the way there with relatively little work.
>
> Nice job and Thanks!
> Scott
>
>
> On Wed, 2007-08-29 at 23:17 -0500, Chris Fields wrote:
>> 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
>>
>>
>>
>> _______________________________________________
>> 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.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