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

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)

Bio::Seq::SeqFastaSpeedFactory(3pm)			User Contributed Perl Documentation		       Bio::Seq::SeqFastaSpeedFactory(3pm)

NAME

       Bio::Seq::SeqFastaSpeedFactory - Instantiates a new Bio::PrimarySeqI (or derived class) through a factory

SYNOPSIS

	   use Bio::Seq::SeqFastaSpeedFactory;
	   my $factory = Bio::Seq::SeqFastaSpeedFactory->new();
	   my $seq = $factory->create(-seq => 'WYRAVLC',
				      -id  => 'name');

	   # If you want the factory to create Bio::Seq objects instead
	   # of the default Bio::PrimarySeq objects, use the -type parameter:

	   my $factory = Bio::Seq::SeqFastaSpeedFactory->new(-type => 'Bio::Seq');

DESCRIPTION

       This object will build Bio::Seq objects generically.

FEEDBACK

   Mailing Lists
       User feedback is an integral part of the evolution of this and other Bioperl modules. Send your comments and suggestions preferably to the
       Bioperl mailing list.  Your participation is much appreciated.

	 bioperl-l@bioperl.org			- General discussion
	 http://bioperl.org/wiki/Mailing_lists	- About the mailing lists

   Support
       Please direct usage questions or support issues to the mailing list:

       bioperl-l@bioperl.org

       rather than to the module maintainer directly. Many experienced and reponsive experts will be able look at the problem and quickly address
       it. Please include a thorough description of the problem with code and data examples if at all possible.

   Reporting Bugs
       Report bugs to the Bioperl bug tracking system to help us keep track of the bugs and their resolution. Bug reports can be submitted via the
       web:

	 https://redmine.open-bio.org/projects/bioperl/

AUTHOR - Jason Stajich
       Email jason@bioperl.org

APPENDIX

       The rest of the documentation details each of the object methods.  Internal methods are usually preceded with a _

   new
	Title	: new
	Usage	: my $obj = Bio::Seq::SeqFastaSpeedFactory->new();
	Function: Builds a new Bio::Seq::SeqFastaSpeedFactory object
	Returns : Bio::Seq::SeqFastaSpeedFactory
	Args	: -type => string, name of a PrimarySeqI derived class
			   This is optional. Default=Bio::PrimarySeq.

   create
	Title	: create
	Usage	: my $seq = $seqbuilder->create(-seq => 'CAGT', -id => 'name');
	Function: Instantiates a new Bio::Seq object, correctly built but very
		  fast, knowing stuff about Bio::PrimarySeq and Bio::Seq
	Returns : Bio::Seq

	Args	: initialization parameters specific to the type of sequence
		  object we want.  Typically
		  -seq	      => $str,
		  -id	      => $name

perl v5.14.2							    2012-03-02				       Bio::Seq::SeqFastaSpeedFactory(3pm)