[Bioperl-l] AnnotationCollectionI and SeqFeatureI changes

Aaron J. Mackey amackey at pcbi.upenn.edu
Tue Nov 23 14:28:49 EST 2004

> 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 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

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