[Bioperl-l] Re: Bio::SeqFeature::FeaturePair, HMMER

Ewan Birney birney@ebi.ac.uk
Thu, 14 Sep 2000 11:53:55 +0100 (GMT)

On Thu, 14 Sep 2000, Hilmar Lapp wrote:

> Ewan Birney wrote:
> > 
> > For better or worse we should try to keep changes on the branch to being
> > *just bug fixes*. I don't think this qualifies as a bug fix.
> > 
> I agree very much with you with regard to the stability. However, this
> _is_ a bug fix. The problem arose when I fixed the has_tag/each_tag_value
> bug in SeqFeatureI. This broke HMMER::Domain because it called
> each_tag_value and inherited from FeaturePair first, and
> SeqFeature::Generic as second. FeaturePair in turn only implemented part
> of the SeqFeatureI tag methods, and those without functionality, thereby
> turning them into silent bugs in HMMER::Domain (bad!). Now, prior to the
> change each_tag_value was not found in FeaturePair, and therefore the
> implementation in Generic.pm was used (different from all_tags()! so you
> could get tags by each_tag_value, but all_tags() would have told you that
> there are no tags). Now guess what happened after the change.

;) Hmmm. Sounds like you have cleared things up nicely...

> In general, those two modules should now be much less fragile than
> before.
> I agree that the 0.6 branch contains some code from the middle of a
> 'mutating' stage, so there is unfortunately an inherent instability with
> this release.

Ok. I have just been paranoid and popped in a tag before these changes so
if ensembl throws a wobbly we can roll back to before here. 

It is good we are on the same wavelength. I'll be running the ensembl
tests against this new branch today/tomorrow so that will give us extra
confidence that this is not breaking things...

> 	Hilmar
> -- 
> -----------------------------------------------------------------
> Hilmar Lapp                                email: hlapp@gmx.net
> NFI Vienna, IFD/Bioinformatics             phone: +43 1 86634 631
> A-1235 Vienna                                fax: +43 1 86634 727
> -----------------------------------------------------------------

Ewan Birney. Mobile: +44 (0)7970 151230, Work: +44 1223 494420