[Bioperl-l] AnnotationCollectionI and SeqFeatureI changes

Hilmar Lapp hlapp at gmx.net
Sat Nov 20 01:39:19 EST 2004

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.

This is a fairly substantial if not huge change, and this is happening 
on the main trunk.

Basically, with this change the 1.5 release has moved far far away from 
a drop-in replacement (it's not tagged yet or is it?). Bioperl-db for 
instance is incompatible with this, and anybody using bioperl-db will 
then need a solid 1.4 support for some time to come. It'd interesting 
to which degree GBrowse is fine with these changes.

I think the deprecation warnings are a really *bad* idea. The effect 
will be that anyone who has written code against a version that is 
older than today the screen will be cluttered over and over with 

My suggestion is to either do this on a branch first, or if on the main 
trunk then in a way that is completely transparent to the API 
programmer for some time to come. You can think about cluttering 
people's screen after 1.6.

Hilmar Lapp                            email: lapp at gnf.org
GNF, San Diego, Ca. 92121              phone: +1-858-812-1757

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