/ 
BioPerl-1.6.0
River stage two • 61 direct dependents • 66 total dependents
/ Bio::Tree::Tree

NAME

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

SYNOPSIS

# 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.

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

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:

http://bugzilla.open-bio.org/

AUTHOR - Jason Stajich

Email jason@bioperl.org

CONTRIBUTORS

Aaron Mackey amackey@virginia.edu 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 _

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

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

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