[Bioperl-l] global verbosity

Mark A. Jensen maj at fortinbras.us
Wed Dec 3 10:23:32 EST 2008

I was looking for a way to set verbosity globally (but not for
debugging), so that all subsequently created objects would be
absolutely quiet. I found $Bio::Root::Root:VERBOSITY, but saw that it
didn't matter to downstream objects when it was changed. Digging in to
the issue, found that global verbosity can't really be set, though one
can access the value of $VERBOSITY with
Bio::Root::Root::verbose(). http://bugzilla.open-bio.org/show_bug.cgi?id=2696
has a patch + .t to Root.pm that I
think solves the issue, allowing getting and setting of global
verbosity, so that the global value now propagates to new objects.

There is a stickier issue (example using Bio::Seq and
Bio::Seq->primary_seq() in the .t file), in which
setting an object's verbosity post-construction does not propagate to
sub-objects contained in the object, so that one might not get what
one expects. 
cheers MAJ

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