[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
>> analogous and mostly pre-existing Bio::AnnotationCollectionI
>> 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
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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