bio::phylonetwork::graphviz(3pm) [debian man page]

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

NAME

       Bio::PhyloNetwork::GraphViz - Interface between PhyloNetwork and GraphViz

SYNOPSIS

	 use Bio::PhyloNetwork;
	 use Bio::PhyloNetwork::GraphViz;

	 my $net=Bio::PhyloNetwork->new(
	     -eNewick=>'((H1,(H1,(H2,l))),H2)t0; (some long label)H1; ("quoted label")H2;'
	 );

	 my $gv=Bio::PhyloNetwork::GraphViz->new(-net=>$net,-short_labels=>1);

	 foreach my $u ($net->nodes()) {
	     print "$u:".$gv->nodePN_to_nodeGV->{$u}."
";
	 }

	 print $gv->as_text;

	 open PS, "> net.ps";
	 print PS $gv->as_ps;
	 close PS;

DESCRIPTION

       This is a module to create GraphViz objects representing phylogenetic networks.

AUTHOR

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

SEE ALSO

       Bio::PhyloNetwork, GraphViz

APPENDIX

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

   new
	Title	: new
	Usage	: my $graphv = new Bio::PhyloNetwork::GraphViz();
	Function: Creates a new Bio::PhyloNetwork::GraphViz object
	Returns : Bio::PhyloNetwork::GraphViz
	Args	: -net => Bio::PhyloNetwork object
		  -short_labels => boolean (optional)

       Returns a Bio::PhyloNetwork::GraphViz object, which is an extension of a GraphViz object. The GraphViz object is a representation of the
       phylogenetic network given. The extra information the created object holds is a hash table with keys the nodes of the PhyloNetwork object
       and values the nodes of the GraphViz object. If the optional argument -short_labels=>1 is given, the labels of the nodes in GraphViz are
       shortened to a maximum of 3 letters.

   nodePN_to_nodeGV
	Title	: nodePN_to_nodeGV
	Usage	: my $hashR=$graphv->nodePN_to_nodeGV()
	Function: returns (a reference to) a hash holding the translation between
		  nodes of the Bio::PhyloNetwork object and nodes of the GraphViz
		  object
	Returns : reference to hash
	Args	: none

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

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

NAME

       Bio::PhyloNetwork::FactoryX - 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::FactoryX(3pm)