[Bioperl-l] AnnotationCollectionI and SeqFeatureI changes
allenday at ucla.edu
Mon Nov 29 17:30:40 EST 2004
On Mon, 29 Nov 2004, Aaron J. Mackey wrote:
> Yep, OK, I hear you. I really thought all this was going to be
> contained to Bio::SeqFeature::Annotated, but I see now that with all
> sorts of implementation happening in the interfaces (ugh!), this can't
> happen. Woe is me.
> Here's what I'm willing to do to keep Allen from pulling his hair out:
> there have been very few changes on the development trunk since RC1
> that aren't Annotated.pm-related; therefore, (if this makes sense to
> everyone) I will branch 1.5.0 off of RC1 and merge only those patches
> that are Annotated.pm-*unrelated* to the 1.5.0 branch. I will then tag
> the branch at RC2 (and similarly tag the HEAD, so that any later
> merging can be done relative to those tags). Make sense?
yeah. i think the easiest way to restore old functionality is going to be
to roll back SeqFeature::Generic to before i removed the current
SeqFeatureI overriding methods (get_tag_values(), add_tag_value(), etc),
or to re-add these methods. this also necessitates rolling back
SeqFeature::AnnotationAdaptor and its unit test, as it assumes the *_tag_*
hash and the attached AC don't overlap.
that's pretty much it. the interface classes can stay the same -- it
won't affect the "heavy" lifter (SeqFeature::Generic), and it will allow
SeqFeature::Annotated to continue to depend on the revised interface.
> Then, the rest of you (Allen, Hilmar, Steffen, etc) need to figure out
> the cleanest path for 1.6.0, in which all things may change (with an
> eye towards at least some backwards compatibility); my vote would be
> that there remain some separation between "heavy" and "light" feature
> types. I don't expect/need my Bio::SeqFeature::Simple to implement
> Thanks again to everyone; let me know if the CVS plan above sounds
> reasonable ...
> On Nov 28, 2004, at 10:08 PM, Hilmar Lapp wrote:
> > I'm not saying this change of direction may be a show-stopper for any
> > dependent package like bioperl-db. All I'm suggesting is let's be
> > clear that this *is* a change of direction for a core interface, and
> > let's give it some time to phase it in and to iron out wrinkles, both
> > on the end of bioperl itself as well as the end of people who write
> > software against bioperl. Let's give it some time to see how it works,
> > and how it works under stress, before letting it lose on the general
> > public who just wanted to get some bugfixes on the 1.4.0 release or
> > some additional parsers.
> 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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