debian man page for bio::phylonetwork::randomfactory

Bio::PhyloNetwork::RandomFactory(3pm)			User Contributed Perl Documentation		     Bio::PhyloNetwork::RandomFactory(3pm)

NAME
       Bio::PhyloNetwork::RandomFactory - Module to generate random Phylogenetic Networks

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()."
";
	}

DESCRIPTION
       Builds a random (binary tree-child) phylogenetic network each time next_network is called.

AUTHOR
       Gabriel Cardona, gabriel(dot)cardona(at)uib(dot)es

SEE ALSO
       Bio::PhyloNetwork

APPENDIX
       The rest of the documentation details each of the object methods.

   new
	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.

   next_network
	Title	: next_network
	Usage	: my $net=$factory->next_network()
	Function: returns a random network
	Returns : Bio::PhyloNetwork
	Args	: none

perl v5.14.2							    2012-03-02				     Bio::PhyloNetwork::RandomFactory(3pm)