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

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)

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

NAME

       Bio::Factory::LocationFactoryI - A factory interface for generating locations from a string

SYNOPSIS

	# Do not use directly, see Bio::Factory::LocationFactory for example
	use Bio::Factory::FTLocationFactory;
	my $locfact = Bio::Factory::FTLocationFactory->new();
	my $location = $locfact->from_string("1..200");
	print $location->start(), " ", $location->end(), " ", $location->strand,"
";

DESCRIPTION

       An interface for Location Factories which generate Bio::LocationI objects from a string.

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 - Hilmar Lapp
       Email hlapp at gmx.net

APPENDIX

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

   from_string
	Title	: from_string
	Usage	: $loc = $locfactory->from_string("100..200");
	Function: Parses the given string and returns a Bio::LocationI implementing
		  object representing the location encoded by the string.

		  Different implementations may support different encodings. An
		  example of a commonly used encoding is the Genbank feature table
		  encoding of locations.
	Example :
	Returns : A Bio::LocationI implementing object.
	Args	: A string.

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