/ 
bioperl-1.5.2_004-RCb
/ Bio::Tree::Tree

NAME

Bio::Tree::Tree - An Implementation of TreeI interface.

SYNOPSIS

# like from a TreeIO
my $treeio = new Bio::TreeIO(-format => 'newick', -file => 'treefile.dnd');
my $tree = $treeio->next_tree;
my @nodes = $tree->get_nodes;
my $root = $tree->get_root_node;

DESCRIPTION

This object holds handles to Nodes which make up a tree.

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

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.open-bio.org/

AUTHOR - Jason Stajich

Email jason@bioperl.org

CONTRIBUTORS

Aaron Mackey amackey@virginia.edu Sendu Bala bix@sendu.me.uk

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 = new Bio::Tree::Tree();
Function: Builds a new Bio::Tree::Tree object 
Returns : Bio::Tree::Tree
Args    : -root     => L<Bio::Tree::NodeI> object which is the root
            OR
          -node     => L<Bio::Tree::NodeI> object from which the root will be
                       determined

          -nodelete => boolean, whether or not to try and cleanup all
                                the nodes when this this tree goes out
                                of scope.
          -id       => optional tree ID
          -score    => optional tree score value

nodelete

Title   : nodelete
Usage   : $obj->nodelete($newval)
Function: Get/Set Boolean whether or not to delete the underlying
          nodes when it goes out of scope.  By default this is false
          meaning trees are cleaned up.
Returns : boolean
Args    : on set, new boolean value

get_nodes

Title   : get_nodes
Usage   : my @nodes = $tree->get_nodes()
Function: Return list of Tree::NodeI objects
Returns : array of Tree::NodeI objects
Args    : (named values) hash with one value 
          order => 'b|breadth' first order or 'd|depth' first order

get_root_node

Title   : get_root_node
Usage   : my $node = $tree->get_root_node();
Function: Get the Top Node in the tree, in this implementation
          Trees only have one top node.
Returns : Bio::Tree::NodeI object
Args    : none

set_root_node

Title   : set_root_node
Usage   : $tree->set_root_node($node)
Function: Set the Root Node for the Tree
Returns : Bio::Tree::NodeI
Args    : Bio::Tree::NodeI

total_branch_length

Title   : total_branch_length
Usage   : my $size = $tree->total_branch_length
Function: Returns the sum of the length of all branches
Returns : integer
Args    : none

id

Title   : id
Usage   : my $id = $tree->id();
Function: An id value for the tree
Returns : scalar
Args    : [optional] new value to set

score

Title   : score
Usage   : $obj->score($newval)
Function: Sets the associated score with this tree
          This is a generic slot which is probably best used 
          for log likelihood or other overall tree score
Returns : value of score
Args    : newvalue (optional)

height

Title   : height
Usage   : my $height = $tree->height
Function: Gets the height of tree - this LOG_2($number_nodes)
          WARNING: this is only true for strict binary trees.  The TreeIO
          system is capable of building non-binary trees, for which this
          method will currently return an incorrect value!!
Returns : integer
Args    : none

number_nodes

Title   : number_nodes
Usage   : my $size = $tree->number_nodes
Function: Returns the number of nodes in the tree
Returns : integer
Args    : none