Christopher Fields > BioPerl-1.6.920 > Bio::PhyloNetwork::Factory

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Module Version: 1.006920   Source   Latest Release: BioPerl-1.6.924

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()."\n";
 }

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
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