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

Chris Fields cjfields at uiuc.edu
Fri Aug 24 12:23:12 EDT 2007


On Aug 23, 2007, at 10:34 PM, Hilmar Lapp wrote:

> 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.)

Not completely.  You, Jason, Chris M., and several others expressed  
yourselves quite clearly (move the code to a branch and test).  I  
think that everyone was trying to be diplomatic about it and so never  
attempted to do anything except get it working correctly.

>> [...]
>> 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.

Okay, I'll probably go ahead and get a branch started today.  I'll  
have to look at Ewan's interface in more detail; it's possible a new  
SeqFeature implementation will need to be written up to incorporate it.

>> 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 Toronto?)
>
> Seriously, rectifying this problem would lift a huge weight.
>
> 	-hilmar

It would be nice to get regular releases started again.  I think  
this'll help.

chris


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