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


    # like from a TreeIO
    my $treeio = Bio::TreeIO->new(-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.


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AUTHOR - Jason Stajich

Email jason@bioperl.org


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


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


 Title   : new
 Usage   : my $obj = Bio::Tree::Tree->new();
 Function: Builds a new Bio::Tree::Tree object 
 Returns : Bio::Tree::Tree
 Args    : -root     => L<Bio::Tree::NodeI> object which is the root
           -node     => L<Bio::Tree::NodeI> object from which the root will be

           -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


 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


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


 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


 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


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


 Title   : subtree_length
 Usage   : my $subtree_size = $tree->subtree_length($internal_node)
 Function: Returns the sum of the length of all branches in a subtree
           under the node. Calculates the size of the whole tree
           without an argument (but only if root node is defined)
 Returns : real or undef
 Args    : Bio::Tree::NodeI object, defaults to the root node


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


 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)


 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


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

Methods for associating Tag/Values with a Tree

These methods associate tag/value pairs with a Tree


 Title   : set_tag_value
 Usage   : $tree->set_tag_value($tag,$value)
 Function: Sets a tag value(s) to a tree. Replaces old values.
 Returns : number of values stored for this tag
 Args    : $tag   - tag name
           $value - value to store for the tag


 Title   : add_tag_value
 Usage   : $tree->add_tag_value($tag,$value)
 Function: Adds a tag value to a tree 
 Returns : number of values stored for this tag
 Args    : $tag   - tag name
           $value - value to store for the tag


 Title   : remove_tag
 Usage   : $tree->remove_tag($tag)
 Function: Remove the tag and all values for this tag
 Returns : boolean representing success (0 if tag does not exist)
 Args    : $tag - tagname to remove


 Title   : remove_all_tags
 Usage   : $tree->remove_all_tags()
 Function: Removes all tags 
 Returns : None
 Args    : None


 Title   : get_all_tags
 Usage   : my @tags = $tree->get_all_tags()
 Function: Gets all the tag names for this Tree
 Returns : Array of tagnames
 Args    : None


 Title   : get_tag_values
 Usage   : my @values = $tree->get_tag_values($tag)
 Function: Gets the values for given tag ($tag)
 Returns : Array of values or empty list if tag does not exist
 Args    : $tag - tag name


 Title   : has_tag
 Usage   : $tree->has_tag($tag)
 Function: Boolean test if tag exists in the Tree
 Returns : Boolean
 Args    : $tag - tagname