[Bioperl-l] Call for code freeze

Jason Stajich jason@chg.mc.duke.edu
Mon, 19 Feb 2001 14:58:54 -0500 (EST)

On Mon, 19 Feb 2001, Hilmar Lapp wrote:

> The Bioperl 0.7 call for code freeze has inofficially taken place
> last Friday night; this is the official call.
> This means that from now on until the release is branched off code
> changes should be restricted to bug fixes, which includes
> documentation updates and additions (missing or wrong
> documentation is a bug).
> I'm afraid at the same time I'll have to issue an exception permit
> for the SeqFeature::Gene stuff to settle down, and for BPlite
> (Jason, any chances?) to adopt the SeqAnalysisParserI interface.
> I'd still like to expire these permits Monday night.

Hmm, in order to do this, either we make Bio::Tools::BPlite::Sbjct a
SeqAnalysisParserI or we need to find a way to make a Sbjct a SeqFeatureI
which doesn't really make sense to me.

How else can I condense this into one next_feature method in
Bio::Tools::BPliite?  I view a Sbjct as a sequence and HSPs as its
SeqFeatures.  In BPlite I can return all the HSPs for every Sbjct but I
can't differentiate when there are > 1 Sbjcts.  I guess SeqAnalysisParserI
expects a single seq to be analyzed, I can just return the data for the
1st Sbjct but that seems incomplete.

> As mentioned in a previous mail, this means we're entering the
> bug-fixing phase. I'll send out a list of bugs and assignments.
> 	Hilmar
> -- 
> -----------------------------------------------------------------
> Hilmar Lapp                              email: hlapp@gmx.net
> GNF, San Diego, Ca. 92122                phone: +1 858 812 1757
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Jason Stajich
Center for Human Genetics
Duke University Medical Center