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 / 
bioperl-1.2
++
/ 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)