[Bioperl-l] AnnotationCollectionI and SeqFeatureI changes

[Allen Day]

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
Bio::AnnotationCollectionI.

> And I was so hoping to get RC2 packaged up later today ...

Let me know if you want it branched.

-Allen

> -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
> 
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