[Bioperl-l] named parameters

[Ewan Birney]

On Wed, 3 Jan 2001, Jason Stajich wrote:

> 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.


I think we should stick to named parameters throughout and have it as a
programming convention...




> 
> -Jason
> 
> 
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> 

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Ewan Birney. Mobile: +44 (0)7970 151230, Work: +44 1223 494420
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