NAME

Bio::Phylo::Forest::Node - Node in a phylogenetic tree

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

set_parent()

Sets argument as invocant's parent.

Type    : Mutator
Title   : set_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_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_tree()

Sets what tree invocant belongs to

Type    : Mutator
Title   : set_tree
Usage   : $node->set_tree($tree);
Function: Sets what tree invocant belongs to
Returns : Invocant
Args    : Bio::Phylo::Forest::Tree
Comments: This method is called automatically 
          when inserting or deleting nodes in
          trees.

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_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_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_tree()

Returns the tree invocant belongs to

Type    : Query
Title   : get_tree
Usage   : my $tree = $node->get_tree;
Function: Returns the tree $node belongs to
Returns : Bio::Phylo::Forest::Tree
Args    : NONE

# podinherit_insert_token

SEE ALSO

There is a mailing list at https://groups.google.com/forum/#!forum/bio-phylo for any user or developer questions and discussions.

Bio::Phylo::Taxa::TaxonLinker

This object inherits from Bio::Phylo::Taxa::TaxonLinker, so methods defined there are also applicable here.

Bio::Phylo::Listable

This object inherits from Bio::Phylo::Listable, so methods defined there are also applicable here.

Bio::Phylo::Manual

Also see the manual: Bio::Phylo::Manual and http://rutgervos.blogspot.com.

CITATION

If you use Bio::Phylo in published research, please cite it:

Rutger A Vos, Jason Caravas, Klaas Hartmann, Mark A Jensen and Chase Miller, 2011. Bio::Phylo - phyloinformatic analysis using Perl. BMC Bioinformatics 12:63. http://dx.doi.org/10.1186/1471-2105-12-63