[Bioperl-l] deprecated modules

[Hilmar Lapp]

I haven't followed too closely the SearchIO::Blast implementation, hence my question: Does that re-implement HSP tiling? (The Tools::Blast code does, and I found it to be an essential feature for certain purposes)

	-hilmar

> -----Original Message-----
> From: Jason Stajich [mailto:jason@cgt.mc.duke.edu]
> Sent: Wednesday, August 14, 2002 11:22 AM
> To: Bioperl
> Subject: [Bioperl-l] deprecated modules
> 
> 
> Bio::Tools::Blast has been deprecated for a while - I'd like 
> to remove it
> from the trunk.  Additionally I'd like to remove Bio::UnivAln 
> as it too
> has been deprecated.  Steve and I have agreed that
> Bio::SearchIO::psiblast, Bio::Search::HSP::BlastHSP
> Bio::Search::Hit::BlastHit, and 
> Bio::Search::Result::BlastResult will be
> deprecated in 1.2 assuming we get all the functionality moved 
> over to the
> SearchIO::blast and XX::GenericXX objects.
> 
> I can create a DEPRECATED file to list module history like this:
> 
> # These are modules which are deprecated and later removed from the
> toolkit
> 
> Deprecated Modules     Version Deprecated   Version Removed
> --------------------------------------------------------------
> Bio::Tools::Blast            1.0	          1.1
> Bio::Tools::Blast::HSP       1.0		  1.1
> Bio::Tools::Blast::HTML      1.0		  1.1
> Bio::Tools::Blast::Sbjct     1.0		  1.1
> 
> Bio::Tools::WWW		     1.1
> 
> Bio::UnivAln		     1.0		  1.1
> 
> 
> My feeling is that BPlite currently still serves a purpose 
> and should stay
> on the trunk, but it might need some maintence/testing at some point.
> 
> Shout if you don't want to see this happen.
> 
> -jason
> -- 
> Jason Stajich
> Duke University
> jason at cgt.mc.duke.edu
> 
> 
> _______________________________________________
> Bioperl-l mailing list
> Bioperl-l@bioperl.org
> http://bioperl.org/mailman/listinfo/bioperl-l
>