debian man page for bio::phylonetwork::factory

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

NAME
       Bio::PhyloNetwork::Factory - Module to sequentially generate Phylogenetic Networks

SYNOPSIS
	use strict;
	use warnings;

	use Bio::PhyloNetwork;
	use Bio::PhyloNetwork::Factory;

	# Will generate sequentially all the 4059 binary tree-child phylogenetic
	# networks with 4 leaves

	my $factory=Bio::PhyloNetwork::Factory->new(-numleaves=>4);

	my @nets;

	while (my $net=$factory->next_network()) {
	  push @nets,$net;
	  print "".(scalar @nets).": ".$net->eNewick()."
";
	}

DESCRIPTION
       Sequentially builds a (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::Factory();
	Function: Creates a new Bio::PhyloNetwork::Factory
	Returns : Bio::PhyloNetwork::RandomFactory
	Args	: -numleaves => integer
		   OR
		  -leaves => reference to an array (of leaves names)
		  -numhybrids => integer [default = numleaves -1]
		  -recurse => boolean [optional]

       Returns a Bio::PhyloNetwork::Factory object. Such an object will sequentially create 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 at most $numhybrids hybrid nodes. Note that,
       necessarily, $numhybrids < $numleaves.

       If the parameter -recurse=>1 is given, then all networks with number of hybrid nodes less or equal to $numhybrids will be given; otherwise
       only those with exactly $numhybrids hybrid nodes.

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

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