/ 
BioPerl-1.007001
River stage two • 60 direct dependents • 65 total dependents
/ Bio::Tree::Tree

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