[Bioperl-l] SeqFeature/AnnotatableI and rel. 1.6
cain.cshl at gmail.com
Thu Aug 23 15:53:37 EDT 2007
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
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:
> 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
> Bioperl-l mailing list
> Bioperl-l at lists.open-bio.org
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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