NAME

Bio::Phylo::Forest::Node - The tree node object.

SYNOPSIS

# some way to get nodes:
use Bio::Phylo::IO;
my $string = '((A,B),C);';
my $forest = Bio::Phylo::IO->parse(
   -format => 'newick',
   -string => $string
);

# prints 'Bio::Phylo::Forest'
print ref $forest;

foreach my $tree ( @{ $forest->get_entities } ) {

   # prints 'Bio::Phylo::Forest::Tree'
   print ref $tree;

   foreach my $node ( @{ $tree->get_entities } ) {

      # prints 'Bio::Phylo::Forest::Node'
      print ref $node;

      # node has a parent, i.e. is not root
      if ( $node->get_parent ) {
         $node->set_branch_length(1);
      }

      # node is root
      else {
         $node->set_branch_length(0);
      }
   }
}

DESCRIPTION

This module defines a node object and its methods. The node is fairly syntactically rich in terms of navigation, and additional getters are provided to further ease navigation from node to node. Typical first daughter -> next sister traversal and recursion is possible, but there are also shrinkwrapped methods that return for example all terminal descendants of the focal node, or all internals, etc.

Node objects are inserted into tree objects, although technically the tree object is only a container holding all the nodes together. Unless there are orphans all nodes can be reached without recourse to the tree object.

METHODS

CONSTRUCTOR

new()

Node constructor.

Type    : Constructor
Title   : new
Usage   : my $node = Bio::Phylo::Forest::Node->new;
Function: Instantiates a Bio::Phylo::Forest::Node object
Returns : Bio::Phylo::Forest::Node
Args    : All optional:
          -parent          => $parent,
          -taxon           => $taxon,
          -branch_length   => 0.423e+2,
          -first_daughter  => $f_daughter,
          -last_daughter   => $l_daughter,
          -next_sister     => $n_sister,
          -previous_sister => $p_sister,
          -name            => 'node_name',
          -desc            => 'this is a node',
          -score           => 0.98,
          -generic         => {
               -posterior => 0.98,
               -bootstrap => 0.80
          }

new_from_bioperl()

Node constructor from bioperl Bio::Tree::NodeI argument.

Type    : Constructor
Title   : new_from_bioperl
Usage   : my $node =
          Bio::Phylo::Forest::Node->new_from_bioperl(
              $bpnode
          );
Function: Instantiates a Bio::Phylo::Forest::Node object
          from a bioperl node object.
Returns : Bio::Phylo::Forest::Node
Args    : An objects that implements Bio::Tree::NodeI

MUTATORS

set_parent()

Sets argument as invocant's parent.

Type    : Mutator
Title   : parent
Usage   : $node->set_parent($parent);
Function: Assigns a node's parent.
Returns : Modified object.
Args    : If no argument is given, the current
          parent is set to undefined. A valid
          argument is Bio::Phylo::Forest::Node
          object.

set_first_daughter()

Sets argument as invocant's first daughter.

Type    : Mutator
Title   : set_first_daughter
Usage   : $node->set_first_daughter($f_daughter);
Function: Assigns a node's leftmost daughter.
Returns : Modified object.
Args    : Undefines the first daughter if no
          argument given. A valid argument is
          a Bio::Phylo::Forest::Node object.

set_last_daughter()

Sets argument as invocant's last daughter.

Type    : Mutator
Title   : set_last_daughter
Usage   : $node->set_last_daughter($l_daughter);
Function: Assigns a node's rightmost daughter.
Returns : Modified object.
Args    : A valid argument consists of a
          Bio::Phylo::Forest::Node object. If
          no argument is given, the value is
          set to undefined.

set_previous_sister()

Sets argument as invocant's previous sister.

Type    : Mutator
Title   : set_previous_sister
Usage   : $node->set_previous_sister($p_sister);
Function: Assigns a node's previous sister (to the left).
Returns : Modified object.
Args    : A valid argument consists of
          a Bio::Phylo::Forest::Node object.
          If no argument is given, the value
          is set to undefined.

set_next_sister()

Sets argument as invocant's next sister.

Type    : Mutator
Title   : set_next_sister
Usage   : $node->set_next_sister($n_sister);
Function: Assigns or retrieves a node's
          next sister (to the right).
Returns : Modified object.
Args    : A valid argument consists of a
          Bio::Phylo::Forest::Node object.
          If no argument is given, the
          value is set to undefined.

set_child()

Sets argument as invocant's child.

Type    : Mutator
Title   : set_child
Usage   : $node->set_child($child);
Function: Assigns a new child to $node
Returns : Modified object.
Args    : A valid argument consists of a
          Bio::Phylo::Forest::Node object.

set_branch_length()

Sets argument as invocant's branch length.

Type    : Mutator
Title   : set_branch_length
Usage   : $node->set_branch_length(0.423e+2);
Function: Assigns a node's branch length.
Returns : Modified object.
Args    : If no argument is given, the
          current branch length is set
          to undefined. A valid argument
          is a number in any of Perl's formats.

set_root_below()

Reroots below invocant.

Type    : Mutator
Title   : set_root_below
Usage   : $node->set_root_below;
Function: Creates a new tree root below $node
Returns : New root if tree was modified, undef otherwise
Args    : NONE
Comments: throws Bio::Phylo::Util::Exceptions::BadArgs if 
          $node isn't part of a tree

ACCESSORS

get_parent()

Gets invocant's parent.

Type    : Accessor
Title   : get_parent
Usage   : my $parent = $node->get_parent;
Function: Retrieves a node's parent.
Returns : Bio::Phylo::Forest::Node
Args    : NONE

get_first_daughter()

Gets invocant's first daughter.

Type    : Accessor
Title   : get_first_daughter
Usage   : my $f_daughter = $node->get_first_daughter;
Function: Retrieves a node's leftmost daughter.
Returns : Bio::Phylo::Forest::Node
Args    : NONE

get_last_daughter()

Gets invocant's last daughter.

Type    : Accessor
Title   : get_last_daughter
Usage   : my $l_daughter = $node->get_last_daughter;
Function: Retrieves a node's rightmost daughter.
Returns : Bio::Phylo::Forest::Node
Args    : NONE

get_previous_sister()

Gets invocant's previous sister.

Type    : Accessor
Title   : get_previous_sister
Usage   : my $p_sister = $node->get_previous_sister;
Function: Retrieves a node's previous sister (to the left).
Returns : Bio::Phylo::Forest::Node
Args    : NONE

get_next_sister()

Gets invocant's next sister.

Type    : Accessor
Title   : get_next_sister
Usage   : my $n_sister = $node->get_next_sister;
Function: Retrieves a node's next sister (to the right).
Returns : Bio::Phylo::Forest::Node
Args    : NONE

get_branch_length()

Gets invocant's branch length.

Type    : Accessor
Title   : get_branch_length
Usage   : my $branch_length = $node->get_branch_length;
Function: Retrieves a node's branch length.
Returns : FLOAT
Args    : NONE
Comments: Test for "defined($node->get_branch_length)"
          for zero-length (but defined) branches. Testing
          "if ( $node->get_branch_length ) { ... }"
          yields false for zero-but-defined branches!

get_ancestors()

Gets invocant's ancestors.

Type    : Query
Title   : get_ancestors
Usage   : my @ancestors = @{ $node->get_ancestors };
Function: Returns an array reference of ancestral nodes,
          ordered from young to old (i.e. $ancestors[-1] is root).
Returns : Array reference of Bio::Phylo::Forest::Node
          objects.
Args    : NONE

get_sisters()

Gets invocant's sisters.

Type    : Query
Title   : get_sisters
Usage   : my @sisters = @{ $node->get_sisters };
Function: Returns an array reference of sisters,
          ordered from left to right.
Returns : Array reference of
          Bio::Phylo::Forest::Node objects.
Args    : NONE

get_children()

Gets invocant's immediate children.

Type    : Query
Title   : get_children
Usage   : my @children = @{ $node->get_children };
Function: Returns an array reference of immediate
          descendants, ordered from left to right.
Returns : Array reference of
          Bio::Phylo::Forest::Node objects.
Args    : NONE

get_descendants()

Gets invocant's descendants.

Type    : Query
Title   : get_descendants
Usage   : my @descendants = @{ $node->get_descendants };
Function: Returns an array reference of
          descendants, recursively ordered
          breadth first.
Returns : Array reference of
          Bio::Phylo::Forest::Node objects.
Args    : none.

get_terminals()

Gets invocant's terminal descendants.

Type    : Query
Title   : get_terminals
Usage   : my @terminals = @{ $node->get_terminals };
Function: Returns an array reference
          of terminal descendants.
Returns : Array reference of
          Bio::Phylo::Forest::Node objects.
Args    : NONE

get_internals()

Gets invocant's internal descendants.

Type    : Query
Title   : get_internals
Usage   : my @internals = @{ $node->get_internals };
Function: Returns an array reference
          of internal descendants.
Returns : Array reference of
          Bio::Phylo::Forest::Node objects.
Args    : NONE

get_mrca()

Gets invocant's most recent common ancestor shared with argument.

Type    : Query
Title   : get_mrca
Usage   : my $mrca = $node->get_mrca($other_node);
Function: Returns the most recent common ancestor
          of $node and $other_node.
Returns : Bio::Phylo::Forest::Node
Args    : A Bio::Phylo::Forest::Node
          object in the same tree.

get_leftmost_terminal()

Gets invocant's leftmost terminal descendant.

Type    : Query
Title   : get_leftmost_terminal
Usage   : my $leftmost_terminal =
          $node->get_leftmost_terminal;
Function: Returns the leftmost
          terminal descendant of $node.
Returns : Bio::Phylo::Forest::Node
Args    : NONE

get_rightmost_terminal()

Gets invocant's rightmost terminal descendant

Type    : Query
Title   : get_rightmost_terminal
Usage   : my $rightmost_terminal =
          $node->get_rightmost_terminal;
Function: Returns the rightmost
          terminal descendant of $node.
Returns : Bio::Phylo::Forest::Node
Args    : NONE

TESTS

is_terminal()

Tests if invocant is a terminal node.

Type    : Test
Title   : is_terminal
Usage   : if ( $node->is_terminal ) {
             # do something
          }
Function: Returns true if node has
          no children (i.e. is terminal).
Returns : BOOLEAN
Args    : NONE

is_internal()

Tests if invocant is an internal node.

Type    : Test
Title   : is_internal
Usage   : if ( $node->is_internal ) {
             # do something
          }
Function: Returns true if node
          has children (i.e. is internal).
Returns : BOOLEAN
Args    : NONE

is_root()

Tests if invocant is a root.

Type    : Test
Title   : is_root
Usage   : if ( $node->is_root ) {
             # do something
          }
Function: Returns true if node is a root       
Returns : BOOLEAN
Args    : NONE

is_descendant_of()

Tests if invocant is descendant of argument.

Type    : Test
Title   : is_descendant_of
Usage   : if ( $node->is_descendant_of($grandparent) ) {
             # do something
          }
Function: Returns true if the node is
          a descendant of the argument.
Returns : BOOLEAN
Args    : putative ancestor - a
          Bio::Phylo::Forest::Node object.

is_ancestor_of()

Tests if invocant is ancestor of argument.

Type    : Test
Title   : is_ancestor_of
Usage   : if ( $node->is_ancestor_of($grandchild) ) {
             # do something
          }
Function: Returns true if the node
          is an ancestor of the argument.
Returns : BOOLEAN
Args    : putative descendant - a
          Bio::Phylo::Forest::Node object.

is_sister_of()

Tests if invocant is sister of argument.

Type    : Test
Title   : is_sister_of
Usage   : if ( $node->is_sister_of($sister) ) {
             # do something
          }
Function: Returns true if the node is
          a sister of the argument.
Returns : BOOLEAN
Args    : putative sister - a
          Bio::Phylo::Forest::Node object.

is_outgroup_of()

Test if invocant is outgroup of argument nodes.

Type    : Test
Title   : is_outgroup_of
Usage   : if ( $node->is_outgroup_of(\@ingroup) ) {
             # do something
          }
Function: Tests whether the set of
          \@ingroup is monophyletic
          with respect to the $node.
Returns : BOOLEAN
Args    : A reference to an array of
          Bio::Phylo::Forest::Node objects;
Comments: This method is essentially the same as
          &Bio::Phylo::Forest::Tree::is_monophyletic.

CALCULATIONS

calc_path_to_root()

Calculates path to root.

Type    : Calculation
Title   : calc_path_to_root
Usage   : my $path_to_root =
          $node->calc_path_to_root;
Function: Returns the sum of branch
          lengths from $node to the root.
Returns : FLOAT
Args    : NONE

calc_nodes_to_root()

Calculates number of nodes to root.

Type    : Calculation
Title   : calc_nodes_to_root
Usage   : my $nodes_to_root =
          $node->calc_nodes_to_root;
Function: Returns the number of nodes
          from $node to the root.
Returns : INT
Args    : NONE

calc_max_nodes_to_tips()

Calculates maximum number of nodes to tips.

Type    : Calculation
Title   : calc_max_nodes_to_tips
Usage   : my $max_nodes_to_tips =
          $node->calc_max_nodes_to_tips;
Function: Returns the maximum number
          of nodes from $node to tips.
Returns : INT
Args    : NONE

calc_min_nodes_to_tips()

Calculates minimum number of nodes to tips.

Type    : Calculation
Title   : calc_min_nodes_to_tips
Usage   : my $min_nodes_to_tips =
          $node->calc_min_nodes_to_tips;
Function: Returns the minimum number of
          nodes from $node to tips.
Returns : INT
Args    : NONE

calc_max_path_to_tips()

Calculates longest path to tips.

Type    : Calculation
Title   : calc_max_path_to_tips
Usage   : my $max_path_to_tips =
          $node->calc_max_path_to_tips;
Function: Returns the path length from
          $node to the tallest tip.
Returns : FLOAT
Args    : NONE

calc_min_path_to_tips()

Calculates shortest path to tips.

Type    : Calculation
Title   : calc_min_path_to_tips
Usage   : my $min_path_to_tips =
          $node->calc_min_path_to_tips;
Function: Returns the path length from
          $node to the shortest tip.
Returns : FLOAT
Args    : NONE

calc_patristic_distance()

Calculates patristic distance between invocant and argument.

Type    : Calculation
Title   : calc_patristic_distance
Usage   : my $patristic_distance =
          $node->calc_patristic_distance($other_node);
Function: Returns the patristic distance
          between $node and $other_node.
Returns : FLOAT
Args    : Bio::Phylo::Forest::Node

VISITOR METHODS

The methods below are similar in spirit to those by the same name in Bio::Phylo::Forest::Tree, except those in the tree class operate from the tree root, and those in this node class operate on an invocant node, and so these process a subtree.

visit_depth_first()

Visits nodes depth first

 Type    : Visitor method
 Title   : visit_depth_first
 Usage   : $tree->visit_depth_first( -pre => sub{ ... }, -post => sub { ... } );
 Function: Visits nodes in a depth first traversal, executes subs
 Returns : $tree
 Args    : Optional:
			-pre            => sub { print "pre: ",            shift->get_name, "\n" },
			-pre_daughter   => sub { print "pre_daughter: ",   shift->get_name, "\n" },	
			-post_daughter  => sub { print "post_daughter: ",  shift->get_name, "\n" },		
			-in             => sub { print "in: ",             shift->get_name, "\n" },
			-pre_sister     => sub { print "pre_sister: ",     shift->get_name, "\n" },	
			-post_sister    => sub { print "post_sister: ",    shift->get_name, "\n" },			
			-post           => sub { print "post: ",           shift->get_name, "\n" },
			-order          => 'ltr', # ltr = left-to-right, 'rtl' = right-to-left
 Comments:

visit_breadth_first()

Visits nodes breadth first

 Type    : Visitor method
 Title   : visit_breadth_first
 Usage   : $tree->visit_breadth_first( -pre => sub{ ... }, -post => sub { ... } );
 Function: Visits nodes in a breadth first traversal, executes handlers
 Returns : $tree
 Args    : Optional handlers in the order in which they would be executed on an internal node:
			
			# first event handler, is executed when node is reached in recursion
			-pre            => sub { print "pre: ",            shift->get_name, "\n" },
			
			# is executed if node has a sister, before sister is processed
			-pre_sister     => sub { print "pre_sister: ",     shift->get_name, "\n" },	
			
			# is executed if node has a sister, after sister is processed
			-post_sister    => sub { print "post_sister: ",    shift->get_name, "\n" },			
			
			# is executed whether or not node has sisters, if it does have sisters
			# they're processed first	
			-in             => sub { print "in: ",             shift->get_name, "\n" },			
			
			# is executed if node has a daughter, but before that daughter is processed
			-pre_daughter   => sub { print "pre_daughter: ",   shift->get_name, "\n" },
			
			# is executed if node has a daughter, after daughter has been processed	
			-post_daughter  => sub { print "post_daughter: ",  shift->get_name, "\n" },				
			
			# is executed last			
			-post           => sub { print "post: ",           shift->get_name, "\n" },
			
			# specifies traversal order, default 'ltr' means first_daugher -> next_sister
			# traversal, alternate value 'rtl' means last_daughter -> previous_sister traversal
			-order          => 'ltr', # ltr = left-to-right, 'rtl' = right-to-left
 Comments:

visit_level_order()

Visits nodes in a level order traversal.

Type    : Visitor method
Title   : visit_level_order
Usage   : $tree->visit_level_order( sub{...} );
Function: Visits nodes in a level order traversal, executes sub
Returns : $tree
Args    : A subroutine reference that operates on visited nodes.
Comments:

SERIALIZERS

to_xml()

Serializes invocant to xml.

Type    : Serializer
Title   : to_xml
Usage   : my $xml = $obj->to_xml;
Function: Turns the invocant object into an XML string.
Returns : SCALAR
Args    : NONE

to_newick()

Serializes subtree subtended by invocant to newick string.

Type    : Serializer
Title   : to_newick
Usage   : my $newick = $obj->to_newick;
Function: Turns the invocant object into a newick string.
Returns : SCALAR
Args    : takes same arguments as Bio::Phylo::Unparsers::Newick
Comments: takes same arguments as Bio::Phylo::Unparsers::Newick

REVISION

$Id: Node.pm 4252 2007-07-19 14:39:42Z rvosa $

To install Bio::Phylo, copy and paste the appropriate command in to your terminal.

cpanm

cpanm Bio::Phylo

CPAN shell

perl -MCPAN -e shell
install Bio::Phylo

For more information on module installation, please visit the detailed CPAN module installation guide.

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