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

Chris Fields cjfields at uiuc.edu
Fri Aug 24 17:12:25 EDT 2007


Okay, I have started a new branch in cvs (tagged featann_rollback).   
I'll start looking through everything within the next few days to get  
a general idea of what needs to be done.  All I know is the changes  
were extensive and included modifications to tests.

If anyone has comments I have added a wiki page here:

http://www.bioperl.org/wiki/Feature_Annotation_rollback

chris

On Aug 24, 2007, at 11:23 AM, Chris Fields wrote:

> 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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Christopher Fields
Postdoctoral Researcher
Lab of Dr. Robert Switzer
Dept of Biochemistry
University of Illinois Urbana-Champaign





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