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Bio::Phylo::Forest::NoUser)Contributed Perl DocumenBio::Phylo::Forest::Node(3)

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 has the getters and setters that alter the state of a node
       object. Useful behaviours (which	are also available) are	defined	in the
       Bio::Phylo::Forest::NodeRole package.

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::Forest::NodeRole
	   This	object inherits	from Bio::Phylo::Forest::NodeRole, 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>

perl v5.24.1			  2014-03-27	   Bio::Phylo::Forest::Node(3)

NAME | SYNOPSIS | DESCRIPTION | METHODS | SEE ALSO | CITATION

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