[Bioperl-l] AnnotationCollectionI and SeqFeatureI changes

[Jason Stajich]

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/
>>
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--
Jason Stajich
jason.stajich at duke.edu
http://www.duke.edu/~jes12/