/ 
bioperl-1.2.2
/ Bio::Tree::RandomFactory

NAME

Bio::Tree::RandomFactory - TreeFactory for generating Random Trees

SYNOPSIS

  use Bio::Tree::RandomFactory
  my $factory = new Bio::Tree::RandomFactory( -samples => \@taxonnames,
  					      -maxcount => 10);

  # or for anonymous samples

  my $factory = new Bio::Tree::RandomFactory( -sample_size => 6, 
					      -maxcount = 50);

DESCRIPTION

Builds a random tree every time next_tree is called or up to -maxcount times.

This algorithm is based on the make_tree algorithm from Richard Hudson 1990.

Hudson, R. R. 1990. Gene genealogies and the coalescent process. Pp. 1-44 in D. Futuyma and J. Antonovics, eds. Oxford surveys in evolutionary biology. Vol. 7. Oxford University Press, New York

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/MailList.shtml  - About the mailing lists

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:

http://bugzilla.bioperl.org/

AUTHOR - Jason Stajich

Email jason@bioperl.org

CONTRIBUTORS

Matthew Hahn, <matthew.hahn@duke.edu>

APPENDIX

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

new

 Title   : new
 Usage   : my $factory = new Bio::Tree::RandomFactory(-samples => \@samples,
						      -maxcount=> $N);
 Function: Initializes a Bio::Tree::RandomFactory object
 Returns : Bio::Tree::RandomFactory
 Args    :

next_tree

Title   : next_tree
Usage   : my $tree = $factory->next_tree
Function: Returns a random tree based on the initialized number of nodes
          NOTE: if maxcount is not specified on initialization or
                set to a valid integer, subsequent calls to next_tree will 
                continue to return random trees and never return undef

Returns : Bio::Tree::TreeI object
Args    : none

add_Mutations

 Title   : add_Mutations
 Usage   : $factory->add_Mutations($tree, $mutcount);
 Function: Adds mutations to a tree via a random process weighted by 
           branch length (it is a poisson distribution 
			  as part of a coalescent process) 
 Returns : none
 Args    : $tree - Bio::Tree::TreeI 
           $nummut - number of mutations

maxcount

Title   : maxcount
Usage   : $obj->maxcount($newval)
Function: 
Example : 
Returns : value of maxcount
Args    : newvalue (optional)

samples

Title   : samples
Usage   : $obj->samples($newval)
Function: 
Example : 
Returns : value of samples
Args    : newvalue (optional)

sample_size

Title   : sample_size
Usage   : $obj->sample_size($newval)
Function: 
Example : 
Returns : value of sample_size
Args    : newvalue (optional)

attach_EventHandler

Title   : attach_EventHandler
Usage   : $parser->attatch_EventHandler($handler)
Function: Adds an event handler to listen for events
Returns : none
Args    : Bio::Event::EventHandlerI

_eventHandler

Title   : _eventHandler
Usage   : private
Function: Get the EventHandler
Returns : Bio::Event::EventHandlerI
Args    : none

random

Title   : random
Usage   : my $rfloat = $node->random($size)
Function: Generates a random number between 0 and $size
          This is abstracted so that someone can override and provide their
          own special RNG.  This is expected to be a uniform RNG.
Returns : Floating point random
Args    : $maximum size for random number (defaults to 1)