[Bioperl-l] Bio::Root::Object cleanup

Jason Stajich jason@chg.mc.duke.edu
Tue, 30 Jan 2001 15:40:38 -0500 (EST)

On Tue, 30 Jan 2001, Hilmar Lapp wrote:

> In an attempt to tidy up our transition to Bio::Root::RootI I
> added a note about deprecation to Root/Object.pm and a warning to
> _initialize(). The warning will be suppressed for modules of which
> we know that they're in love with Root::Object.
> These revealed some to me unexpected modules. In total, the
> following modules contain a 'use Bio::Root::Object'statement:

I skipped most of SteveC's modules initially because he likes to utilize
the functionality he built into Bio::Root::Object and Bio::Root::Global
(understandably).  below is log of what I just checked in.

> Bio/Root/Global.pm (*)
> Bio/Root/Err.pm (*)
> Bio/Root/IOManager.pm (*)
> Bio/Root/Utilities.pm (*)
> Bio/Root/Vector.pm (*)
> Bio/Root/Xref.pm (*)
> Bio/Search/Hit/HitI.pm (?)
I believe the entire Search dir is to be removed per Aaron Mackey saying
that it is not in a usuable state and probably never will....
> Bio/SeqIO/bioxml.pm (?)
I can fix it if we are definitely keeping it, I am under the impression it
is to be trashed...  not sure though.
> Bio/Tools/Blast/Sbjct.pm (*)
> Bio/Tools/Blast/HSP.pm (*)
> Bio/Tools/Blast/Run/LocalBlast.pm (*)
> Bio/Tools/AlignFactory.pm
> Bio/Tools/IUPAC.pm
> Bio/Tools/SeqAnal.pm (*)
> Bio/Tools/SeqPattern.pm
> Bio/Tools/WWW.pm
dependance on Bio::Root::Global and the $AUTHORITY variable 
which steve had this coded to his old stanford email address,  
I removed this dependance and hardcoded the $AUTHORITY var to be local to
WWW.pm and have the value 'nobody@localhost' if anyone is using it they
probably should speak up.... 

> Bio/Tools/PPSEARCH/Parse.pm
depends on old Bio::SeqFeatureSet which no longer exists, I'm not sure
what to do here
> Bio/Tools/PRFSCAN/Parse.pm
> Bio/Tools/PRINTS/Parse.pm
> Those marked with (*) are obvious. Those marked with (?) are
> likely to be absent from the release. I presently have no overview
> of the others. Jason, did you leave them out on purpose?
> In addition, the Variation code contains the line
> Bio/Variation/IO.pm:       return Bio::Root::Object::new($class,
> %param);
> Heikki, I don't know about the context, just wanted to make sure
> this is indispensable.
> 	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