Bio::Tree::Tree - An Implementation of TreeI interface. # 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; This object holds handles to Nodes which make up a tree.

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/ Email jason@bioperl.org Aaron Mackey amackey@virginia.edu 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 :