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

[Hilmar Lapp]

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.

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.

	Hilmar

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