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

[Ewan Birney]

On Mon, 5 Feb 2001, Jason Stajich wrote:

> 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
> end_hmm.

Thanks jason....


> > 
> > <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)). 

seconded..

> 
> > > 	Hilmar
> > -- 
> > -----------------------------------------------------------------
> > Hilmar Lapp                                email: hlapp@gmx.net
> > GNF, San Diego, Ca. 92122                  phone: +1 858 812 1757
> > -----------------------------------------------------------------
> > _______________________________________________
> > Bioperl-l mailing list
> > Bioperl-l@bioperl.org
> > http://bioperl.org/mailman/listinfo/bioperl-l
> > 
> 
> Jason Stajich
> jason@chg.mc.duke.edu
> Center for Human Genetics
> Duke University Medical Center 
> http://www.chg.duke.edu/ 
> 
> 
> _______________________________________________
> Bioperl-l mailing list
> Bioperl-l@bioperl.org
> http://bioperl.org/mailman/listinfo/bioperl-l
> 

-----------------------------------------------------------------
Ewan Birney. Mobile: +44 (0)7970 151230, Work: +44 1223 494420
<birney@ebi.ac.uk>. 
-----------------------------------------------------------------