[Bioperl-l] Philosophy, BioPerl Object Creation

[Hilmar Lapp]

On Thursday, March 27, 2003, at 04:15  AM, Heikki Lehvaslaiho wrote:

> In related note: I wanted to inherit directly from a non-bioperl class
> and merge it with the rest of bioperl and came up with this:
>
> package Bio::WebAgent;
> use vars qw(@ISA);
> use strict;
> use LWP::UserAgent;
> use Bio::Root::Root;
>
> @ISA = qw(LWP::UserAgent Bio::Root::Root);
>
> sub new {
>     my $class = shift;
>
>     my $self = $class->SUPER::new();
>     while( @_ ) {
> 	my $key = shift;
>         $key =~ s/^-//;
>         $self->$key(shift);
>     }
>
>     return $self; # success - we hope!
>
> }
>
> This actually faster than using _rearrange. In some of my tests old_new
> versus new_new was 19:14 seconds, sometimes less.
>
> Can anyone point out why this would be bad and perhaps show me a better
> way of doing the same thing.

Well, you don't pass on any parameters, so you rely on every class down 
the tree having a method named identically to the parameter.

Would be nice if that were the case, but in bioperl it's definitely 
not...

	-hilmar


>
> 	-Heikki
>
>
>
>
> On Thu, 2003-03-27 at 11:32, Matthew Pocock wrote:
>>> argument list intact. Also, parameters may be used
>>> in more than one
>>> level in the hierarchy.
>>>
>>> 	-hilmar
>>
>> That seems a little rude. Can we get around this a bit
>> by accessing the parameter via an accessor? e.g.
>>
>> my $self = my_super->new(@_);
>> // pigColor was an argument but I need to know it to
>> // set myself up - use an accessor
>> my $pigColor = $self->pigColor();
>>
>> Matthew
>>
>>> -- 
>>>
>> -------------------------------------------------------------
>>> Hilmar Lapp                            email: lapp
>>> at gnf.org
>>> GNF, San Diego, Ca. 92121              phone:
>>> +1-858-812-1757
>>>
>> -------------------------------------------------------------
>>>
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> -- 
> ______ _/      _/_____________________________________________________
>       _/      _/                      http://www.ebi.ac.uk/mutations/
>      _/  _/  _/  Heikki Lehvaslaiho          heikki at ebi.ac.uk
>     _/_/_/_/_/  EMBL Outstation, European Bioinformatics Institute
>    _/  _/  _/  Wellcome Trust Genome Campus, Hinxton
>   _/  _/  _/  Cambs. CB10 1SD, United Kingdom
>      _/      Phone: +44 (0)1223 494 644   FAX: +44 (0)1223 494 468
> ___ _/_/_/_/_/________________________________________________________
>
>
-- 
-------------------------------------------------------------
Hilmar Lapp                            email: lapp at gnf.org
GNF, San Diego, Ca. 92121              phone: +1-858-812-1757
-------------------------------------------------------------