[Bioperl-l] AnnotationCollectionI and SeqFeatureI changes

Aaron J. Mackey amackey at pcbi.upenn.edu
Mon Nov 29 09:07:31 EST 2004

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?

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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