[Bioperl-l] SeqFeature/AnnotatableI and rel. 1.6

Hilmar Lapp hlapp at gmx.net
Fri Aug 24 03:34:12 UTC 2007

On Aug 23, 2007, at 12:53 AM, Chris Fields wrote:

> There has been little work done over the last 2 1/2 years to undo or
> rectify problems associated with those additions; I feel like those
> of us still routinely contributing have been left holding the bag.

Not by intention, but unfortunately that's probably a fair  
assessment. (And I'm one of those guilty of inaction.)

> [...]
> I would like to suggest the radical idea of rolling back AnnotatableI/
> SeqFeatureI changes to a much simpler rel. 1.4-like behavior (tags
> are simple scalars) and possibly work in implementing Ewan's
> SeqFeature::TypedSeqFeatureI for those who want strong data types
> (i.e. Bio::FeatureIO/Bio::SeqFeature::Annotated).

I fully support this; to me that sounds exactly like the way to go.

> The various AnnotatableI changes, odd inheritance, and operator  
> overloading have
> really obfuscated the code to the point where no one wants to touch
> it in case it breaks something important.  However, I believe it is
> the one serious impediment to a new stable release.

Yes, I think you're hitting the nail on the head.

Chris, if you take the lead on this and carry it through we will all  
owe you hugely. I'm not sure how many beers that would compare to,  
but I'll throw in some. (Who else do I owe beer? I'm losing track.  
Strangely nobody tried to redeem beer from me in Vienna. Maybe in  

Seriously, rectifying this problem would lift a huge weight.

: Hilmar Lapp  -:-  Durham, NC  -:-  hlapp at gmx dot net :

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