[Bioperl-l] AnnotationCollectionI and SeqFeatureI changes
allenday at ucla.edu
Tue Nov 23 15:10:42 EST 2004
On Tue, 23 Nov 2004, 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?
all tests pass here.
> 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.
there hasn't really been any functionality change. just reorganization of
interfaces. i put the deprecation warnings in where interface methods
moved or mapped from one interface class to another.
the changes are directly related to getting FeatureIO working, because
Bio::SeqFeature::Annotated needs to fully implement Bio::SeqFeatureI. I
didn't want to write the *_tag_* methods into Bio::SeqFeature::Annotated,
which precipitated their deprecation and mapping to
> And I was so hoping to get RC2 packaged up later today ...
Let me know if you want it branched.
> 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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