[Bioperl-l] Auto-method caller proposal

Hilmar Lapp hlapp at gmx.net
Thu Jan 4 11:13:43 EST 2007


I see your point; and for the sake of reducing ambiguity/increasing  
clarity demanding unambiguous parameter names rather than  
disambiguating by the presence or absence of a leading dash is  
preferable I guess.

Just should be clearly documented for module wrapper implementers;  
also, are we going to retrofit existing wrappers?

	-hilmar

On Jan 4, 2007, at 11:00 AM, Sendu Bala wrote:

> Hilmar Lapp wrote:
>> Sounds good to me, except that I'm still not sure that dashed and  
>> dash-less parameters are just variations of the same. What about - 
>> verbose and a verbose parameter for the tool, for example?
>
> That's an open problem. I identified it in a recent thread as one  
> of the few reasons a run-wrapper module might deliberately demand  
> dashless args for program args and only allow dashed args for  
> Bioperl args. The consensus (and I agree) was that it is preferable  
> to allow dashed args for everything regardless of this problem.
>
> For this proposal, Bio::Root::Root's verbose() would be set for  
> both dashed and dashless, and then it would be up to the run- 
> wrapper module author to figure out some extra way to set a verbose  
> option independently for the program being wrapped. I imagine the  
> author might apologise in their POD and tell the user they had to  
> use 'program_verbose' or something, then handle things  
> appropriately when it comes time to create the argument string for  
> passing to the program.
>
> Alternatively (not something I recommend since it will causes  
> confusion and mistakes), you could deliberately request problem  
> cases be dashed or undashed:
>
> package Bio::Tools::Run::Confusing;
> =head2 new
>  ...
>  To set Bioperl verbosity use:
>  -verbose => int
>  To activate program verbosity use:
>  verbose => 1
> =cut
> sub new {
>   my ($class, @args) = @_;
>   my $self = $class->SUPER::new(@args); # Bioperl verbosity set here
>
>   my %args = @args;
>   if (my $program_verbose = $args{verbose}) {
>     delete $args{verbose};
>     $args{program_verbose} = $program_verbose;
>   }
>
>   $self->_set_from_args(\%args,
>                         -methods => [id score program_verbose],
>                         -create => 1);
>
>   return $self;
> }
> 1;
>
> # test code
> my $factory = Bio::Tools::Run::Confusing->new(-verbose => 0,
>                                               verbose => 1);
> is $factory->verbose, 0, 'Bioperl verbosity set correctly';
> is $factory->program_verbose, 1, 'program verbosity set correctly';
>
>
>
> Any other ideas?

-- 
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: Hilmar Lapp  -:-  Durham, NC  -:-  hlapp at gmx dot net :
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