Bio::Tree::Tree(3)

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/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
Aaron Mackey amackey@virginia.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 $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
           -nodelete => boolean, whether or not to try and cleanup all
                                 the nodes when this this tree goes out
                                 of scope.

  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
 Example :
 Returns :
 Args    :