[Bioperl-l] AnnotationCollectionI and SeqFeatureI changes

Steffen Grossmann grossman at molgen.mpg.de
Mon Nov 29 10:32:50 EST 2004

I definitely support this solution!

I have some gff3 related code which got broken by the Annotated.pm 
related changes made after 1.5.0RC1. E.g. Chris Mungall's functioning 
Bio::Tools::GFF and Bio::SeqFeature::Tools::IDHandler stuff is not in 
1.4. and doesn't seem to work with the changes.

But still, I think we can do much better with the annotation business as 
proposed up to now, so let's go for this when heading towards 1.6.0.


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?
> 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 
> AnnotationCollection!
> Thanks again to everyone; let me know if the CVS plan above sounds 
> reasonable ...
> -Aaron
> 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
> _______________________________________________
> Bioperl-l mailing list
> Bioperl-l at portal.open-bio.org
> http://portal.open-bio.org/mailman/listinfo/bioperl-l

%            Steffen Grossmann                %
%                                             %
% Max Planck Institute for Molecular Genetics %
%      Computational Molecular Biology        %
%              Ihnestrasse 73                 %
%               14195 Berlin                  %
%                 Germany                     %
%         Tel: (++49 +30) 8413-1167           %
%         Fax: (++49 +30) 8413-1152           %

More information about the Bioperl-l mailing list