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

Scott Cain cain.cshl at gmail.com
Thu Aug 23 19:53:37 UTC 2007

Hi Chris,

GBrowse would be unaffected by this as it doesn't use
Bio::SeqFeature::Annotated.  The GMOD GFF3 Chado loader on the other
hand will almost certainly break horribly, as it depends on the strong
typing of Bio::FeatureIO/Bio::SeqFeature::Annotated.  If you could try
your ideas out in a branch that I could checkout and test on, that would
be good.


On Wed, 2007-08-22 at 23:53 -0500, Chris Fields wrote:
> As many of the devs know, there are a number of Feature/Annotation  
> issues that need to be resolved prior to a 1.6 release:
> http://www.bioperl.org/wiki/Release_Schedule#SeqFeature. 
> 2FAnnotation_changes:_Keep_or_roll_back.3F
> 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.   
> There has also been very little attempt to document any of this  
> adequately enough; as an example see POD for  
> Bio::SeqFeature::Annotated (what little there is).
> 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).  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.
> My thought is we simplify all the relevant interfaces, essentially  
> reverting back to rel 1.4.  For instance, we move the various  
> Bio::AnnotatableI tag methods back into Bio::SeqFeatureI.   
> Bio::SeqFeature::Annotated would implement Bio::AnnotatableI  
> directly, and (if needed) also implement  
> Bio::SeqFeature::TypedSeqFeatureI, so the impetus is on  
> Bio::SeqFeature::Annotated to overload the relevant SeqFeatureI  
> methods correctly, just as any other class would when implementing an  
> abstract interface.  I have played around with this a bit and managed  
> to get most tests working again for Bio::SeqFeature::Generic and  
> FeatureIO but a number of others break.
> If needed I can try this out on a branch (a bit ironic, since the  
> changes instigating this mess should have been tested on a branch!).   
> Maybe this will get the ball rolling towards a 1.6 release.  Any  
> thoughts?
> chris
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Scott Cain, Ph. D.                                         cain at cshl.edu
GMOD Coordinator (http://www.gmod.org/)                     216-392-3087
Cold Spring Harbor Laboratory
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