[Bioperl-l] AnnotationCollectionI and SeqFeatureI changes

[Aaron J. Mackey]

Allen, thanks a ton for going the extra mile.  Hilmar, does this 
solution satisfy your worries a bit?

Thanks again to everyone,

-Aaron

On Nov 23, 2004, at 9:16 PM, Allen Day wrote:

> Fixed.  Here is a summary of what I did to make this happen.  I went 
> ahead
> and did the work necessary to make Bio::SeqFeatureI AnnotatableI 
> instead
> of being itself an AnnotationCollectionI.
>
> . Bio::SeqFeatureI inherits Bio::AnnotatableI NOT
>   Bio::AnnotationCollectionI
> . *_tag_* methods are in Bio::AnnotatableI, and internally defer to
>   Bio::AnnotatableI->annotation->some_analagous_mapped_function()
>   . method behavior is now more similar to original *_tag_* method
>     behavior ; tag "values" are now instantiated as
>     Bio::Annotation::SimpleValue objects by default, unless their name
>     indicates they should be otherwise (e.g. tag name "comment" or
>     "dblink")
> . deprecation warnings commented until 1.6
> . Bio::AnnotatableI now keeps a tag->annotation_type registry to allow
>   new tags to be created (see Bio::SeqFeature::AnnotationAdaptor).
>   . Bio::SeqFeature::AnnotationAdaptor is now not very useful, as 
> *_tag_*
>     methods map directly onto Bio::AnnotationI's
>     Bio::AnnotationCollectionI instance.
> . Unflattener and Unflattener2 tests pass with no changes.
> . All tests pass.
>
> -Allen
>
>
> On Tue, 23 Nov 2004, Chris Mungall wrote:
>
>>
>> Unflattener.t is failing because someone has messed up 
>> get_tagset_values()
>> - this is a convenience method I originally added to SeqFeatureI. I'm 
>> not
>> familiar enough with the new changes and AnnotationCollections to fix
>> this.
>>
>> Surely the onus has always been on the person making changes to make 
>> sure
>> the test suite passes before committing their changes? In which case, 
>> how
>> did these changes make it in in the first place?
>>
>> On Tue, 23 Nov 2004, Jason Stajich wrote:
>>
>>>
>>> On Nov 23, 2004, at 4:47 PM, Allen Day wrote:
>>>
>>>> On Tue, 23 Nov 2004, Jason Stajich wrote:
>>>>
>>>>> I think if we just don't issue deprecation warnings it will be 
>>>>> fine by
>>>>> me -- even if we are just calling the new subroutine under the 
>>>>> hood.
>>>>> Tests seem to pass although Unflattner.t is falling over today not
>>>>> sure
>>>>> what is problem.
>>>>
>>>> that fails for me too, in addition to spewing out lots of
>>>> diagnotistics.
>>>> however, if you run 'make test_Unflattener2', it passes.  strange.
>>>>
>>> no it is Unflattner not Unflattner2
>>>
>>> % make test_Unflattener
>>> [SNIP OUT SOME STUFF]
>>>
>>> -------------------- WARNING ---------------------
>>> MSG: get_tagset_values() is deprecated.  use get_Annotations()
>>> ---------------------------------------------------
>>>
>>> ------------- EXCEPTION: Bio::Root::Exception -------------
>>> MSG: Abstract method "Bio::AnnotationCollectionI::get_Annotations" is
>>> not implemented by package Bio::SeqFeature::Generic.
>>>
>>>
>>>> -allen
>>>>
>>>>>
>>>>> -jason
>>>>> On Nov 23, 2004, at 2:28 PM, Aaron J. Mackey wrote:
>>>>>
>>>>>>
>>>>>>> On Friday, November 19, 2004, at 02:50  PM, Allen Day wrote:
>>>>>>>
>>>>>>>> * Bio::SeqFeatureI now ISA Bio::AnnotationCollectionI
>>>>>>>> * All Bio::SeqFeatureI *_tag_* methods have been moved to
>>>>>>>>   Bio::AnnotationCollectionI, marked as deprecated, and mapped 
>>>>>>>> to
>>>>>>>> their
>>>>>>>>   analogous and mostly pre-existing Bio::AnnotationCollectionI
>>>>>>>> methods.
>>>>>>>>
>>>>>>>>   Methods which were not in Bio::AnnotationCollectionI, but 
>>>>>>>> were i
>>>>>>>>   Bio::Annotation::Collection and were necessary for *_tag_* 
>>>>>>>> method
>>>>>>>>   remapping were created in Bio::AnnotationCollecitonI.
>>>>>>
>>>>>> I've been paying some attention to this, but thought that the 
>>>>>> changes
>>>>>> were only those required to get Bio::FeatureIO working (i.e.
>>>>>> recapitulate GFF3 logic) without hampering object usage; do our 
>>>>>> tests
>>>>>> pass with these changes in place?
>>>>>>
>>>>>> On Nov 23, 2004, at 2:12 PM, Jason Stajich wrote:
>>>>>>
>>>>>>> it has not been tagged yet.  I think Aaron is just really busy on
>>>>>>> this front.
>>>>>>
>>>>>> I did tag the HEAD at RC1, so we could branch from there if we 
>>>>>> needed
>>>>>> to; if this is really the big bug-bear that Hilmar and Jason are
>>>>>> claiming, then I'd ask Allen to retract his patches that alter
>>>>>> interface definitions, and branch.
>>>>>>
>>>>>> And I was so hoping to get RC2 packaged up later today ...
>>>>>>
>>>>>> -Aaron
>>>>>>
>>>>>> --
>>>>>> Aaron J. Mackey, Ph.D.
>>>>>> Dept. of Biology, Goddard 212
>>>>>> University of Pennsylvania       email:  amackey at pcbi.upenn.edu
>>>>>> 415 S. University Avenue         office: 215-898-1205
>>>>>> Philadelphia, PA  19104-6017     fax:    215-746-6697
>>>>>>
>>>>>>
>>>>> --
>>>>> Jason Stajich
>>>>> jason.stajich at duke.edu
>>>>> http://www.duke.edu/~jes12/
>>>>>
>>>>> _______________________________________________
>>>>> Bioperl-l mailing list
>>>>> Bioperl-l at portal.open-bio.org
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>>>>>
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>>>>
>>> --
>>> Jason Stajich
>>> jason.stajich at duke.edu
>>> http://www.duke.edu/~jes12/
>>>
>>> _______________________________________________
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>>>
>>
>
>
--
Aaron J. Mackey, Ph.D.
Dept. of Biology, Goddard 212
University of Pennsylvania       email:  amackey at pcbi.upenn.edu
415 S. University Avenue         office: 215-898-1205
Philadelphia, PA  19104-6017     fax:    215-746-6697