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

[Hilmar Lapp]

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:

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 (?)
Bio/SeqIO/bioxml.pm (?)
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
Bio/Tools/PPSEARCH/Parse.pm
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
-- 
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Hilmar Lapp                                email: hlapp@gmx.net
GNF, San Diego, Ca. 92122                  phone: +1 858 812 1757
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