[Bioperl-l] do not hate individual getter/setters coding?

Jason Stajich jason@cgt.mc.duke.edu
Mon Jan 20 14:08:50 EST 2003

This discussion has been had.

See the following for example and read the whole set of threads.

You are welcome to implement your code with AUTOLOAD (in fact you'll see
the bioperl-run objects often support this), but many of us have our
reasons for not wanting to use it all the time.

Most importantly, get/set methods should be implemented properly
allowing resetting of the value to undef as outlined in one of the posts
and now as provided in the bioperl.lisp emacs template for code

On Wed, 15 Jan 2003, Xiao Juguang wrote:

> Hi guys,
> I may be a very lazy coder, so that I was tired on writing tedious
> getter/setters fragment, as well, as a source code reader, I felt bored
> to read individule getter/setters occupying, sometimes, more than half
> of module. Do you? I thought bioperl follows Perl's neat soul and Perl
> hopes its features to be fully used. Should we just suggest to add 2
> subs in Bio::Root::Root ? _autoload_methods and AUTOLOAD . They look
> like this.
> =head2 _autoload_methods
> This subroutine is usually invoked at the very beginning line of constructor,
> to set subroutine names for getter and setters.
> sub new{
>     my ($class, @args) = @_;
>     my $self = $class->SUPER::new(@args);
>     $self->_autoload_methods([qw(dbhost dbname dbuser dbpass)]); # Don't add if unnecessary.
>     # Then, say
>     my ($dbhost) = $self->_rearrange([qw(DBHOST)], @args);
>     $self->dbhost($dbhost);
>     return $self;
> }
> =cut
> sub _autoload_methods {
>     my ($self, $arg) = @_;
>     if(defined $arg && ref($arg) eq 'ARRAY'){
> #        $self->{_autoload_methods} = $arg;
>         push @{$self->{_autoload_methods}}, @{$arg};
>         # equally explicitly declare the subs !!!
>         use subs @{$self->{_autoload_methods}};
>     }
>     return $self->{_autoload_methods};
> }
>     return if our $AUTOLOAD =~ /::DESTROY$/;
>     my ($self, $arg) = @_;
>     my $field = $AUTOLOAD;
>     $field =~ /::([\w\d]+)$/;
>     if($self->_autoload_methods && grep /$1/, @{$self->_autoload_methods}){
>         $self->{$field} = $arg if defined $arg;
>         return $self->{$field};
>     }else{
>         $self->throw("Can't find the method '$field'");
>     }
> }
> I remembered in this mailing list, there was a discussion on it. However,  I forgot the harm to use it that people mention. In theory, Bio::Root::Root::AUTOLOAD will be almost last visited in the path of method searching. I just quote paragraphs from Programming Perl 3rd Ed. by Larry Wall, for your information.
> When your invoke a method 'methname' on an invocant of type 'classname', Perl tries six different ways to find a subroutine to use:
> 1. First, Perl looks in the invocant's own package for a subroutine named classname::methname. If that fails, inheritance kicks in, and we go to step 2.
> 2. Next, Perl checks for methods inherited from base classes by looking in all the parent packages listed in @classmane::ISA for a parent::methname subroutine. The search is left-to-right, recurive, and depth-first. The recursion assures that grandparent classes, great-grandparent classes, great-great-grandparent classes, and so on, are all searched.
> 3. If that fails, Perl looks for a subroutine named UNIVERSAL::methname.
> 4. At this point, Perl gives up on methname and starts looking for an AUTOLOAD. First, it looks for a subroutine named classname::AUTOLOAD.
> 5. Failing that, Perl searches all parent packages listed in @classname::ISA, for any parent::AUTOLOAD subroutine. The search is again left-to-right, recurive, and depth-first.
> 6. Finally, Perl looks for a subroutine named UNIVERSAL::AUTOLOAD.
> Perl stops after the first successful attempt and invokes that subroutine.
> To make perldoc friendly, developer should write pod for each 'virtual getter/setter' or might write a =head2 item for a group of get/setters. It is also Perl itself friendly. I mean, since we 'use subs @{$self->{_autoload_methods}};', Perl regards them 'virtual' subs as real ones.
> My $0.0000002 worth.
> Please do correct me or my code. Thanks.
> Juguang.
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Jason Stajich
Duke University
jason at cgt.mc.duke.edu

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