Bio::Tree::Tree(3)

NAME
Bio::Tree::Tree - An implementation of the TreeI interface.

SYNOPSIS
    use Bio::TreeIO;

    # 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;

DESCRIPTION
This object holds handles to Nodes which make up a tree.

IMPLEMENTATION NOTE
This implementation of Bio::Tree::Tree contains Bio::Tree:::NodeI; mainly linked via the root node. As NodeI can potentially contain circular references (as nodes will need to refer to both parent and child nodes), Bio::Tree::Tree will remove those circular references when the object is garbage-collected. This has some side effects; primarily, one must keep the Tree in scope or have at least one reference to it if working with nodes. The fix is to count the references to the nodes and if it is greater than expected retain all of them, but it requires an additional prereq and thus may not be worth the effort. This only shows up in minor edge cases, though (see Bug #2869).

Example of issue:

  # tree is not assigned to a variable, so passes from memory after
  # root node is passed
  my $root = Bio::TreeIO->new(-format => 'newick', -file => 'foo.txt')->next_tree
                 ->get_root_node;

  # gets nothing, as all Node links are broken when Tree is garbage-collected above
  my @descendents = $root->get_all_Descendents;

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 Sendu Bala bix@sendu.me.uk Mark A. Jensen maj@fortinbras.us

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 = 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
              OR
           -node     => L<Bio::Tree::NodeI> object from which the root will be
                        determined

           -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

  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 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
           sortby => [optional] "height", "creation", "alpha", "revalpha",
           or coderef to be used to sort the order of children nodes. See L<Bio::Tree::Node> for details

  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 : real
 Args    : none

  subtree_length
 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

  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 in the tree
 Returns : integer
 Args    : none

  as_text
 Title   : as_text
 Usage   : my $tree_as_string = $tree->as_text($format)
 Function: Returns the tree as a string representation in the
           desired format, e.g.: 'newick', 'nhx' or 'tabtree' (the default)
 Returns : scalar string
 Args    : format type as specified by Bio::TreeIO
 Note    : This method loads the Bio::TreeIO::$format module
           on the fly, and commandeers the _write_tree_Helper
           routine therein to create the tree string.

  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

  clone
 Title   : clone
 Alias   : _clone
 Usage   : $tree_copy = $tree->clone();
           $subtree_copy = $tree->clone($internal_node);
 Function: Safe tree clone that doesn't segfault
 Returns : Bio::Tree::Tree object
 Args    : [optional] $start_node, Bio::Tree::Node object