I ran some benchmarks, which might be of interest. I compared the node object for http://search.cpan.org/~rvosa/Bio-Phylo-0.04/lib/Bio/Phylo/Trees/Node.pm
(actually, for the next version, with a different namespace, but the guts are the same), which uses an anonymous hashref, to the one below:
package Outside::In;
use strict;
use warnings;
use Carp;
use Scalar::Util qw(looks_like_number);
use overload '""' => \&to_string;
{
my @name;
my @parent;
my @first_daughter;
my @last_daughter;
my @next_sister;
my @previous_sister;
my @branch_length;
my @reclaim;
my $obj_counter = 0;
sub new {
my $class = shift;
my $instance_counter = 0;
if ( @reclaim ) {
@reclaim = sort { $a <=> $b } @reclaim;
$instance_counter = shift(@reclaim);
}
else {
$instance_counter = $obj_counter;
$obj_counter++;
}
my $self = \$instance_counter;
bless $self, $class;
return $self;
}
sub set_parent {
$parent[${$_[0]}] = $_[1] if $_[1];
return $_[0];
}
sub get_parent {
return $parent[${$_[0]}];
}
sub to_string {
return 'ObjectID = ' . ${$_[0]};
}
sub DESTROY {
delete $name[${$_[0]}];
delete $parent[${$_[0]}];
delete $first_daughter[${$_[0]}];
delete $last_daughter[${$_[0]}];
delete $next_sister[${$_[0]}];
delete $previous_sister[${$_[0]}];
delete $branch_length[${$_[0]}];
push(@reclaim, ${$_[0]});
}
}
package main;
use strict;
use warnings;
use Benchmark qw(:all);
use Bio::Phylo::Forest::Node;
use Data::Dumper;
my $oldnode1 = Bio::Phylo::Forest::Node->new;
my $oldnode2 = Bio::Phylo::Forest::Node->new;
$oldnode1->set_parent($oldnode2);
my $newnode1 = Outside::In->new;
my $newnode2 = Outside::In->new;
$newnode1->set_parent($newnode2);
cmpthese (1000000, {
'old' => sub { $oldnode1->get_parent },
'new' => sub { $newnode1->get_parent }
});
Result:
Rate old new
old 477555/s -- -34%
new 723066/s 51% --
The salient point is that:
sub get_parent {
return $_[0]->{'PARENT'};
}
seems quite a bit slower than:
sub get_parent {
return $parent[${$_[0]}];
}
I've heard that array look-ups are faster than hash look-ups, but I thought the difference was smaller than it is.