Bio::Tree::TreeI(3pm)					User Contributed Perl Documentation				     Bio::Tree::TreeI(3pm)

NAME

       Bio::Tree::TreeI - A Tree object suitable for lots of things, designed
	 originally for Phylogenetic Trees.

SYNOPSIS

	 # get a Bio::Tree::TreeI somehow
	 # 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 @leaves = $tree->get_leaf_nodes;
	 my $root   = $tree->get_root_node;

DESCRIPTION

       This object holds a pointer to the Root of a Tree which is a Bio::Tree::NodeI.

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

   Support
       Please direct usage questions or support issues to the mailing list:

       bioperl-l@bioperl.org

       rather than to the module maintainer directly. Many experienced and reponsive experts will be able look at the problem and quickly address
       it. Please include a thorough description of the problem with code and data examples if at all possible.

   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:

	 https://redmine.open-bio.org/projects/bioperl/

AUTHOR - Jason Stajich
       Email jason@bioperl.org

CONTRIBUTORS

       Aaron Mackey, amackey@virginia.edu Elia Stupka,	elia@fugu-sg.org 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 _

   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

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

   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

   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

   id
	Title	: id
	Usage	: my $id = $tree->id();
	Function: An id value for the tree
	Returns : scalar
	Args	:

   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)

   get_leaf_nodes
	Title	: get_leaf_nodes
	Usage	: my @leaves = $tree->get_leaf_nodes()
	Function: Returns the leaves (tips) of the tree
	Returns : Array of Bio::Tree::NodeI objects
	Args	: none

   Methods for associating Tag/Values with a Tree
       These methods associate tag/value pairs with a Tree

   set_tag_value
	Title	: set_tag_value
	Usage	: $tree->set_tag_value($tag,$value)
		  $tree->set_tag_value($tag,@values)
	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

   add_tag_value
	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

   remove_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

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

   get_all_tags
	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

   get_tag_values
	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

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

perl v5.14.2							    2012-03-02						     Bio::Tree::TreeI(3pm)