Bio::PhyloNetwork
RandomFactory
Toolbar
Summary
Bio::PhyloNetwork::RandomFactory - Module to generate random
Phylogenetic Networks
Package variables
No package variables defined.
Included modules
Inherit
Synopsis
use strict;
use warnings;
use Bio::PhyloNetwork;
use Bio::PhyloNetwork::RandomFactory;
# Will generate at random all the 66 binary tree-child phylogenetic
# networks with 3 leaves
my $factory=Bio::PhyloNetwork::RandomFactory->new(-numleaves=>3,-norepeat=>1);
my @nets;
for (my $i=0; $i<66; $i++) {
my $net=$factory->next_network();
push @nets,$net;
print "".(scalar @nets).": ".$net->eNewick()."\n";
}
Description
Builds a random (binary tree-child) phylogenetic network each time
next_network is called.
Methods
Methods description
Title : new
Usage : my $factory = new Bio::PhyloNetwork::RandomFactory();
Function: Creates a new Bio::PhyloNetwork::RandomFactory
Returns : Bio::PhyloNetwork::RandomFactory
Args : -numleaves => integer
OR
-leaves => reference to an array (of leaves names)
-numhybrids => integer [optional]
-norepeat => boolean [optional]
Returns a Bio::PhyloNetwork::RandomFactory object. Such an object will create
random binary tree-child phylogenetic networks each time next_network
is called.
If the parameter -leaves=>\@leaves is given, then the set of leaves of
these networks will be @leaves. If it is given the parameter
-numleaves=>$numleaves, then the set of leaves will be "l1"..."l$numleaves".
If the parameter -numhybrids=>$numhybrids is given, then the generated
networks will have exactly $numhybrids hybrid nodes. Note that, necessarily,
$numhybrids < $numleaves. Otherwise, the number of hybrid nodes will be chosen
at random for each call of next_network.
If the parameter -norepeat=>1 is given, then successive calls of next_network
will give non-isomorphic networks. |
Title : next_network
Usage : my $net=$factory->next_network()
Function: returns a random network
Returns : Bio::PhyloNetwork
Args : none |
Methods code
sub new
{ my ($pkg,@args)=@_;
my $self=$pkg->SUPER::new(@args);
my ($leavesR,$numleaves,$numhybrids,$norepeat)=
$self->_rearrange([qw(LEAVES
NUMLEAVES
NUMHYBRIDS
NOREPEAT)],@args);
my @leaves;
if ((! defined $leavesR) && (defined $numleaves)) {
@leaves=map {"l$_"} (1..$numleaves);
$leavesR=\@leaves;
}
if (! defined $leavesR) {
$self->throw("No leaves set neither numleaves given");
}
$norepeat ||= 0;
$self->{leaves}=\@leaves;
$self->{numleaves}=$numleaves;
$self->{numhybrids}=$numhybrids if defined $numhybrids;
$self->{norepeat}=$norepeat;
$self->{found}=[];
$self->{tree_factory}=Bio::Tree::RandomFactory->new(-taxa =>\@ leaves);
bless($self,$pkg);} | sub next_network
{ my ($self)=@_;
my $numleaves=$self->{numleaves};
my @found=@{$self->{found}};
my $numhybrids;
START:
if (! defined $self->{numhybrids}) {
$numhybrids=int(rand($numleaves));
}
else {
$numhybrids=$self->{numhybrids};
}
my $tf=$self->{tree_factory};
my $tree=$tf->next_tree;
my $net=Bio::PhyloNetwork->new(-tree=>$tree);
for (my $i=1; $i<=$numhybrids; $i++) {
$net=random_attack($net,$i);
}
if ($self->{norepeat}) {
foreach my $ant (@found) {
goto START if $net->is_mu_isomorphic($ant);
}
push @found,$net;
$self->{found}=\@found;
}
return $net;} | | random_attack | description | prev | next | Top |
sub random_attack
{ my ($net,$lbl)=@_;
my $graph=$net->{graph};
my ($u1,$v1,$u2,$v2);
do {
my $e1=$graph->random_edge;
my $e2=$graph->random_edge;
$u1=$e1->[0];
$v1=$e1->[1];
$u2=$e2->[0];
$v2=$e2->[1];
} while (! $net->is_attackable($u1,$v1,$u2,$v2,$lbl));
$net->do_attack($u1,$v1,$u2,$v2,$lbl);
return $net;
}
1;} | General documentation
Gabriel Cardona, gabriel(dot)cardona(at)uib(dot)es
The rest of the documentation details each of the object methods.