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.\"
.IX Title "Bio::PhyloNetwork::RandomFactory 3pm"
.TH Bio::PhyloNetwork::RandomFactory 3pm "2018-10-27" "perl v5.26.2" "User Contributed Perl Documentation"
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.SH "NAME"
Bio::PhyloNetwork::RandomFactory \- Module to generate random
Phylogenetic Networks
.SH "SYNOPSIS"
.IX Header "SYNOPSIS"
.Vb 2
\& 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()."\en";
\& }
.Ve
.SH "DESCRIPTION"
.IX Header "DESCRIPTION"
Builds a random (binary tree-child) phylogenetic network each time
next_network is called.
.SH "AUTHOR"
.IX Header "AUTHOR"
Gabriel Cardona, gabriel(dot)cardona(at)uib(dot)es
.SH "SEE ALSO"
.IX Header "SEE ALSO"
Bio::PhyloNetwork
.SH "APPENDIX"
.IX Header "APPENDIX"
The rest of the documentation details each of the object methods.
.SS "new"
.IX Subsection "new"
.Vb 9
\& Title   : new
\& Usage   : my $factory = new Bio::PhyloNetwork::RandomFactory();
\& Function: Creates a new Bio::PhyloNetwork::RandomFactory
\& Returns : Bio::PhyloNetwork::RandomFactory
\& Args    : \-numleaves => integer
\&            OR
\&           \-leaves => reference to an array (of leaves names)
\&           \-numhybrids => integer [optional]
\&           \-norepeat => boolean [optional]
.Ve
.PP
Returns a Bio::PhyloNetwork::RandomFactory object. Such an object will create
random binary tree-child phylogenetic networks each time next_network
is called.
.PP
If the parameter \-leaves=>\e@leaves is given, then the set of leaves of
these networks will be \f(CW@leaves\fR. If it is given the parameter
\&\-numleaves=>$numleaves, then the set of leaves will be \*(L"l1\*(R"...\*(L"l$numleaves\*(R".
.PP
If the parameter \-numhybrids=>$numhybrids is given, then the generated
networks will have exactly \f(CW$numhybrids\fR hybrid nodes. Note that, necessarily,
\&\f(CW$numhybrids\fR < \f(CW$numleaves\fR. Otherwise, the number of hybrid nodes will be chosen
at random for each call of next_network.
.PP
If the parameter \-norepeat=>1 is given, then successive calls of next_network
will give non-isomorphic networks.
.SS "next_network"
.IX Subsection "next_network"
.Vb 5
\& Title   : next_network
\& Usage   : my $net=$factory\->next_network()
\& Function: returns a random network
\& Returns : Bio::PhyloNetwork
\& Args    : none
.Ve