Bio::Tree::TreeI(3)

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://github.com/bioperl/bioperl-live/issues

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