[Bioperl-l] named parameters

[Jason Stajich]

This is a bit on inconsistency when we specify parameters to new in some
of the bioperl modules.  Whenever we don't use named parameters (ie
-file=> 'filename'), we are inconsistent with the fact that all modules
inherit from  Bio::Root::RootI.  This is because Bio::Root::RootI will
parse a couple of special parameters - specifically 
-verbose, -strict, -name, -obj, -record_err

now we really don't use these that much, however, in the case of
Bio::Species

one would call 
my @classification = qw( sapiens Homo Hominidae
                                   Catarrhini Primates Eutheria
                                   Mammalia Vertebrata Chordata
                                   Metazoa Eukaryota )

my $sp = new Bio::Species(@classification);

but if one also wanted debugging turned on, one might call this
my $sp = new Bio::Species(-verbose=>1, @classification);

This won't bother RootI, but Bio::Species expects all the parameters to be
part of the classification array.

A solution is to change Bio::Species to expect named parameters so an
array ref is 

$sp = new Bio::Species(-verbose=>1, -classification => \@classification );

What are people's reactions to this?  If we can agree that this is
expected then we can add this to our programming conventions wiki page.

-Jason