[Bioperl-l] Bio::Tools::HMMER

Jason Stajich jason@chg.mc.duke.edu
Mon, 5 Feb 2001 09:14:20 -0500 (EST)

On Sun, 4 Feb 2001, Hilmar Lapp wrote:

> I've added some deprecation warnings where the documentation says
> that the methods *are* deprecated. This is now triggering lots of
> warnings in the HMMER test. Anyone willing to fix it?
Renamed start_hmm to hstart wherever start_hmm was used, likewise for
> <Warning: the following is purely technical and may mean nothing
> to those who don't know the module's code> In addition, I've
> changed the way the 2 features are initialized in Domain.pm. The
> potential problem here is that if you set freshly initialized
> SeqFeature objects after initializing $self you may lose all
> -start etc initialization parameters. 
I think this goes with the FeaturePair territority, I'm not sure how to
better protect against this. 

> BTW is creating the two feature objects still necessary, as
> FeaturePair creates them itself if requested and not yet
> set.</warning>
Probably not unless there is something in the @args we want (verbosity?
-- actually verbosity is not consistenly passed down to subobjects very
well in much of the code, but since it is really for debugging purposes
I put that on the low priority)). 

> > 	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