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

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
Notes   : The following BioPerl properties are copied:
          BioPerl output:        Bio::Phylo output:
          ------------------------------------------------
          id                     get_name
          branch_length          get_branch_length
          description            get_desc
          bootstrap              get_generic('bootstrap')
          
          In addition all BioPerl tags and values are copied
          to set_generic( 'tag' => 'value' );

MUTATORS

prune_child()

Sets argument as invocant's parent.

Type    : Mutator
Title   : prune_child
Usage   : $parent->prune_child($child);
Function: Removes $child (and its descendants) from $parent's children
Returns : Modified object.
Args    : A valid argument is Bio::Phylo::Forest::Node object.

collapse()

Collapse node.

Type    : Mutator
Title   : collapse
Usage   : $node->collapse;
Function: Attaches invocant's children to invocant's parent.
Returns : Modified object.
Args    : NONE
Comments: If defined, adds invocant's branch 
          length to that of its children. If
          $node is in a tree, removes itself
          from that tree.

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_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_node_below()

Sets new (unbranched) node below invocant.

Type    : Mutator
Title   : set_node_below
Usage   : my $new_node = $node->set_node_below;
Function: Creates a new node below $node
Returns : New node if tree was modified, undef otherwise
Args    : NONE

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: Implementation incomplete: returns spurious 
          results when $node is grandchild of current root.

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.

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_child()

Gets invocant's i'th child.

Type    : Query
Title   : get_child
Usage   : my $child = $node->get_child($i);
Function: Returns the child at index $i
Returns : A Bio::Phylo::Forest::Node object.
Args    : An index (integer) $i
Comments: if no index is specified, first
          child is returned

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

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

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_first()

Tests if invocant is first sibling in left-to-right order.

Type    : Test
Title   : is_first
Usage   : if ( $node->is_first ) {
             # do something
          }
Function: Returns true if first sibling 
          in left-to-right order.
Returns : BOOLEAN
Args    : NONE

is_last()

Tests if invocant is last sibling in left-to-right order.

Type    : Test
Title   : is_last
Usage   : if ( $node->is_last ) {
             # do something
          }
Function: Returns true if last sibling 
          in left-to-right order.
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_child_of()

Tests if invocant is child of argument.

Type    : Test
Title   : is_child_of
Usage   : if ( $node->is_child_of($parent) ) {
             # do something
          }
Function: Returns true if the node is
          a child of the argument.
Returns : BOOLEAN
Args    : putative parent - 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.

can_contain()

Test if argument(s) can be a child/children of invocant.

Type    : Test
Title   : can_contain
Usage   : if ( $parent->can_contain(@children) ) {
             # do something
          }
Function: Test if arguments can be children of invocant.
Returns : BOOLEAN
Args    : An array of Bio::Phylo::Forest::Node objects;
Comments: This method is an override of 
          Bio::Phylo::Listable::can_contain. Since node
          objects hold a list of their children, they
          inherit from the listable class and so they
          need to be able to validate the contents
          of that list before they are inserted.

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

calc_nodal_distance()

Calculates node distance between invocant and argument.

Type    : Calculation
Title   : calc_nodal_distance
Usage   : my $nodal_distance =
          $node->calc_nodal_distance($other_node);
Function: Returns the number of nodes
          between $node and $other_node.
Returns : INT
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:
           # 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 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 if node has no daughter
           -no_daughter    => sub { print "no_daughter: ",    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 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 if node has no sister
           -no_sister      => sub { print "no_sister: ",      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_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 if node has no sister
            -no_sister      => sub { print "no_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 if node has no daughter
            -no_daughter    => sub { print "no_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:

UTILITY METHODS

clone()

Clones invocant.

Type    : Utility method
Title   : clone
Usage   : my $clone = $object->clone;
Function: Creates a copy of the invocant object.
Returns : A copy of the invocant.
Args    : Optional: a hash of code references to 
          override reflection-based getter/setter copying

          my $clone = $object->clone(  
              'set_forest' => sub {
                  my ( $self, $clone ) = @_;
                  for my $forest ( @{ $self->get_forests } ) {
                      $clone->set_forest( $forest );
                  }
              },
              'set_matrix' => sub {
                  my ( $self, $clone ) = @_;
                  for my $matrix ( @{ $self->get_matrices } ) {
                      $clone->set_matrix( $matrix );
                  }
          );

Comments: Cloning is currently experimental, use with caution.
          It works on the assumption that the output of get_foo
          called on the invocant is to be provided as argument
          to set_foo on the clone - such as 
          $clone->set_name( $self->get_name ). Sometimes this 
          doesn't work, for example where this symmetry doesn't
          exist, or where the return value of get_foo isn't valid
          input for set_foo. If such a copy fails, a warning is 
          emitted. To make sure all relevant attributes are copied
          into the clone, additional code references can be 
          provided, as in the example above. Typically, this is
          done by overrides of this method in child classes.

SERIALIZERS

to_json()

Serializes object to JSON string

Type    : Serializer
Title   : to_json()
Usage   : print $obj->to_json();
Function: Serializes object to JSON string
Returns : String 
Args    : None
Comments:

to_xml()

Serializes invocant to xml.

Type    : Serializer
Title   : to_xml
Usage   : my $xml = $obj->to_xml;
Function: Turns the invocant object (and its descendants )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

INHERITED METHODS

Bio::Phylo::Forest::Node inherits from one or more superclasses. This means that objects of class Bio::Phylo::Forest::Node also "do" the methods from the superclasses in addition to the ones implemented in this class. Below is the documentation for those additional methods, organized by superclass.

SUPERCLASS Bio::Phylo::Taxa::TaxonLinker

Bio::Phylo::Forest::Node inherits from superclass Bio::Phylo::Taxa::TaxonLinker. Below are the public methods (if any) from this superclass.

get_taxon()

Retrieves the Bio::Phylo::Taxa::Taxon object linked to the invocant.

Type    : Accessor
Title   : get_taxon
Usage   : my $taxon = $obj->get_taxon;
Function: Retrieves the Bio::Phylo::Taxa::Taxon
          object linked to the invocant.
Returns : Bio::Phylo::Taxa::Taxon
Args    : NONE
Comments:

set_taxon()

Links the invocant object to a taxon object.

Type    : Mutator
Title   : set_taxon
Usage   : $obj->set_taxon( $taxon );
Function: Links the invocant object
          to a taxon object.
Returns : Modified $obj
Args    : A Bio::Phylo::Taxa::Taxon object.

unset_taxon()

Unlinks the invocant object from any taxon object.

Type    : Mutator
Title   : unset_taxon
Usage   : $obj->unset_taxon();
Function: Unlinks the invocant object
          from any taxon object.
Returns : Modified $obj
Args    : NONE

SUPERCLASS Bio::Phylo::Listable

Bio::Phylo::Forest::Node inherits from superclass Bio::Phylo::Listable. Below are the public methods (if any) from this superclass.

add_set()

Type    : Mutator
Title   : add_set
Usage   : $obj->add_set($set)
Function: Associates a Bio::Phylo::Set object with the invocant
Returns : Invocant
Args    : A Bio::Phylo::Set object

add_to_set()

Type    : Mutator
Title   : add_to_set
Usage   : $listable->add_to_set($obj,$set);
Function: Adds first argument to the second argument
Returns : Invocant
Args    : $obj - an object to add to $set
          $set - the Bio::Phylo::Set object to add to
Notes   : this method assumes that $obj is already 
          part of the invocant. If that assumption is
          violated a warning message is printed.

can_contain()

Tests if argument can be inserted in invocant.

Type    : Test
Title   : can_contain
Usage   : &do_something if $listable->can_contain( $obj );
Function: Tests if $obj can be inserted in $listable
Returns : BOOL
Args    : An $obj to test

clear()

Empties container object.

Type    : Object method
Title   : clear
Usage   : $obj->clear();
Function: Clears the container.
Returns : A Bio::Phylo::Listable object.
Args    : Note.
Note    :

clone()

Clones invocant.

Type    : Utility method
Title   : clone
Usage   : my $clone = $object->clone;
Function: Creates a copy of the invocant object.
Returns : A copy of the invocant.
Args    : None.
Comments: Cloning is currently experimental, use with caution.

contains()

Tests whether the invocant object contains the argument object.

Type    : Test
Title   : contains
Usage   : if ( $obj->contains( $other_obj ) ) {
              # do something
          }
Function: Tests whether the invocant object 
          contains the argument object
Returns : BOOLEAN
Args    : A Bio::Phylo::* object

cross_reference()

The cross_reference method links node and datum objects to the taxa they apply to. After crossreferencing a matrix with a taxa object, every datum object has a reference to a taxon object stored in its $datum->get_taxon field, and every taxon object has a list of references to datum objects stored in its $taxon->get_data field.

Type    : Generic method
Title   : cross_reference
Usage   : $obj->cross_reference($taxa);
Function: Crossreferences the entities 
          in the invocant with names 
          in $taxa
Returns : string
Args    : A Bio::Phylo::Taxa object
Comments:

current()

Returns the current focal element of the listable object.

Type    : Iterator
Title   : current
Usage   : my $current_obj = $obj->current;
Function: Retrieves the current focal 
          entity in the invocant.
Returns : A Bio::Phylo::* object
Args    : none.

current_index()

Returns the current internal index of the invocant.

Type    : Generic query
Title   : current_index
Usage   : my $last_index = $obj->current_index;
Function: Returns the current internal 
          index of the invocant.
Returns : An integer
Args    : none.

delete()

Deletes argument from invocant object.

Type    : Object method
Title   : delete
Usage   : $obj->delete($other_obj);
Function: Deletes an object from its container.
Returns : A Bio::Phylo::Listable object.
Args    : A Bio::Phylo::* object.
Note    : Be careful with this method: deleting 
          a node from a tree like this will 
          result in undefined references in its 
          neighbouring nodes. Its children will 
          have their parent reference become 
          undef (instead of pointing to their 
          grandparent, as collapsing a node would 
          do). The same is true for taxon objects 
          that reference datum objects: if the 
          datum object is deleted from a matrix 
          (say), the taxon will now hold undefined 
          references.

first()

Jumps to the first element contained by the listable object.

Type    : Iterator
Title   : first
Usage   : my $first_obj = $obj->first;
Function: Retrieves the first 
          entity in the invocant.
Returns : A Bio::Phylo::* object
Args    : none.

get_by_index()

Gets element defined by argument index from invocant container.

Type    : Query
Title   : get_by_index
Usage   : my $contained_obj = $obj->get_by_index($i);
Function: Retrieves the i'th entity 
          from a listable object.
Returns : An entity stored by a listable 
          object (or array ref for slices).
Args    : An index or range. This works 
          the way you dereference any perl
          array including through slices, 
          i.e. $obj->get_by_index(0 .. 10)>
          $obj->get_by_index(0, -1) 
          and so on.
Comments: Throws if out-of-bounds

get_by_name()

Gets first element that has argument name

Type    : Visitor predicate
Title   : get_by_name
Usage   : my $found = $obj->get_by_name('foo');
Function: Retrieves the first contained object
          in the current Bio::Phylo::Listable 
          object whose name is 'foo'
Returns : A Bio::Phylo::* object.
Args    : A name (string)

get_by_regular_expression()

Gets elements that match regular expression from invocant container.

Type    : Visitor predicate
Title   : get_by_regular_expression
Usage   : my @objects = @{ 
              $obj->get_by_regular_expression(
                   -value => $method,
                   -match => $re
           ) };
Function: Retrieves the data in the 
          current Bio::Phylo::Listable 
          object whose $method output 
          matches $re
Returns : A list of Bio::Phylo::* objects.
Args    : -value => any of the string 
                    datum props (e.g. 'get_type')
          -match => a compiled regular 
                    expression (e.g. qr/^[D|R]NA$/)

get_by_value()

Gets elements that meet numerical rule from invocant container.

Type    : Visitor predicate
Title   : get_by_value
Usage   : my @objects = @{ $obj->get_by_value(
             -value => $method,
             -ge    => $number
          ) };
Function: Iterates through all objects 
          contained by $obj and returns 
          those for which the output of 
          $method (e.g. get_tree_length) 
          is less than (-lt), less than 
          or equal to (-le), equal to 
          (-eq), greater than or equal to 
          (-ge), or greater than (-gt) $number.
Returns : A reference to an array of objects
Args    : -value => any of the numerical 
                    obj data (e.g. tree length)
          -lt    => less than
          -le    => less than or equals
          -eq    => equals
          -ge    => greater than or equals
          -gt    => greater than

get_entities()

Returns a reference to an array of objects contained by the listable object.

Type    : Generic query
Title   : get_entities
Usage   : my @entities = @{ $obj->get_entities };
Function: Retrieves all entities in the invocant.
Returns : A reference to a list of Bio::Phylo::* 
          objects.
Args    : none.

get_index_of()

Returns the index of the argument in the list, or undef if the list doesn't contain the argument

Type    : Generic query
Title   : get_index_of
Usage   : my $i = $listable->get_index_of($obj)
Function: Returns the index of the argument in the list,
          or undef if the list doesn't contain the argument
Returns : An index or undef
Args    : A contained object

get_logger()

Gets a logger object.

Type    : Accessor
Title   : get_logger
Usage   : my $logger = $obj->get_logger;
Function: Returns a Bio::Phylo::Util::Logger object
Returns : Bio::Phylo::Util::Logger
Args    : None

get_sets()

Type    : Accessor
Title   : get_sets
Usage   : my @sets = @{ $obj->get_sets() };
Function: Retrieves all associated Bio::Phylo::Set objects
Returns : Invocant
Args    : None

insert()

Pushes an object into its container.

Type    : Object method
Title   : insert
Usage   : $obj->insert($other_obj);
Function: Pushes an object into its container.
Returns : A Bio::Phylo::Listable object.
Args    : A Bio::Phylo::* object.

insert_at_index()

Inserts argument object in invocant container at argument index.

Type    : Object method
Title   : insert_at_index
Usage   : $obj->insert_at_index($other_obj, $i);
Function: Inserts $other_obj at index $i in container $obj
Returns : A Bio::Phylo::Listable object.
Args    : A Bio::Phylo::* object.

is_in_set()

Type    : Test
Title   : is_in_set
Usage   : @do_something if $listable->is_in_set($obj,$set);
Function: Returns whether or not the first argument is listed in the second argument
Returns : Boolean
Args    : $obj - an object that may, or may not be in $set
          $set - the Bio::Phylo::Set object to query
Notes   : This method makes two assumptions:
          i) the $set object is associated with the invocant,
             i.e. add_set($set) has been called previously
          ii) the $obj object is part of the invocant
          If either assumption is violated a warning message
          is printed.

last()

Jumps to the last element contained by the listable object.

Type    : Iterator
Title   : last
Usage   : my $last_obj = $obj->last;
Function: Retrieves the last 
          entity in the invocant.
Returns : A Bio::Phylo::* object
Args    : none.

last_index()

Returns the highest valid index of the invocant.

Type    : Generic query
Title   : last_index
Usage   : my $last_index = $obj->last_index;
Function: Returns the highest valid 
          index of the invocant.
Returns : An integer
Args    : none.

next()

Returns the next focal element of the listable object.

Type    : Iterator
Title   : next
Usage   : my $next_obj = $obj->next;
Function: Retrieves the next focal 
          entity in the invocant.
Returns : A Bio::Phylo::* object
Args    : none.

notify_listeners()

Notifies listeners of changed contents.

Type    : Utility method
Title   : notify_listeners
Usage   : $object->notify_listeners;
Function: Notifies listeners of changed contents.
Returns : Invocant.
Args    : NONE.
Comments:

previous()

Returns the previous element of the listable object.

Type    : Iterator
Title   : previous
Usage   : my $previous_obj = $obj->previous;
Function: Retrieves the previous 
          focal entity in the invocant.
Returns : A Bio::Phylo::* object
Args    : none.

remove_from_set()

Type    : Mutator
Title   : remove_from_set
Usage   : $listable->remove_from_set($obj,$set);
Function: Removes first argument from the second argument
Returns : Invocant
Args    : $obj - an object to remove from $set
          $set - the Bio::Phylo::Set object to remove from
Notes   : this method assumes that $obj is already 
          part of the invocant. If that assumption is
          violated a warning message is printed.

remove_set()

Type    : Mutator
Title   : remove_set
Usage   : $obj->remove_set($set)
Function: Removes association between a Bio::Phylo::Set object and the invocant
Returns : Invocant
Args    : A Bio::Phylo::Set object

set_listener()

Attaches a listener (code ref) which is executed when contents change.

Type    : Utility method
Title   : set_listener
Usage   : $object->set_listener( sub { my $object = shift; } );
Function: Attaches a listener (code ref) which is executed when contents change.
Returns : Invocant.
Args    : A code reference.
Comments: When executed, the code reference will receive $object
          (the invocant) as its first argument.

visit()

Iterates over objects contained by invocant, executes argument code reference on each.

Type    : Visitor predicate
Title   : visit
Usage   : $obj->visit( 
              sub{ print $_[0]->get_name, "\n" } 
          );
Function: Implements visitor pattern 
          using code reference.
Returns : The invocant, possibly modified.
Args    : a CODE reference.

SUPERCLASS Bio::Phylo::Util::XMLWritable

Bio::Phylo::Forest::Node inherits from superclass Bio::Phylo::Util::XMLWritable. Below are the public methods (if any) from this superclass.

add_dictionary()

Type    : Mutator
Title   : add_dictionary
Usage   : $obj->add_dictionary($dict);
Function: Adds a dictionary attachment to the object
Returns : $self
Args    : Bio::Phylo::Dictionary

get_attributes()

Retrieves attributes for the element.

Type    : Accessor
Title   : get_attributes
Usage   : my %attrs = %{ $obj->get_attributes };
Function: Gets the xml attributes for the object;
Returns : A hash reference
Args    : None.
Comments: throws ObjectMismatch if no linked taxa object 
          can be found

get_dictionaries()

Retrieves the dictionaries for the element.

Type    : Accessor
Title   : get_dictionaries
Usage   : my @dicts = @{ $obj->get_dictionaries };
Function: Retrieves the dictionaries for the element.
Returns : An array ref of Bio::Phylo::Dictionary objects
Args    : None.

get_namespaces()

Type    : Accessor
Title   : get_namespaces
Usage   : my %ns = %{ $obj->get_namespaces };
Function: Retrieves the known namespaces
Returns : A hash of prefix/namespace key/value pairs, or
          a single namespace if a single, optional
          prefix was provided as argument
Args    : Optional - a namespace prefix

get_tag()

Retrieves tag name for the element.

Type    : Accessor
Title   : get_tag
Usage   : my $tag = $obj->get_tag;
Function: Gets the xml tag name for the object;
Returns : A tag name
Args    : None.

get_xml_id()

Retrieves xml id for the element.

Type    : Accessor
Title   : get_xml_id
Usage   : my $id = $obj->get_xml_id;
Function: Gets the xml id for the object;
Returns : An xml id
Args    : None.

get_xml_tag()

Retrieves tag string

Type    : Accessor
Title   : get_xml_tag
Usage   : my $str = $obj->get_xml_tag;
Function: Gets the xml tag for the object;
Returns : A tag, i.e. pointy brackets
Args    : Optional: a true value, to close an empty tag

is_identifiable()

By default, all XMLWritable objects are identifiable when serialized, i.e. they have a unique id attribute. However, in some cases a serialized object may not have an id attribute (governed by the nexml schema). This method indicates whether that is the case.

Type    : Test
Title   : is_identifiable
Usage   : if ( $obj->is_identifiable ) { ... }
Function: Indicates whether IDs are generated
Returns : BOOLEAN
Args    : NONE

remove_dictionary()

Type    : Mutator
Title   : remove_dictionary
Usage   : $obj->remove_dictionary($dict);
Function: Removes a dictionary attachment from the object
Returns : $self
Args    : Bio::Phylo::Dictionary

set_attributes()

Assigns attributes for the element.

Type    : Mutator
Title   : set_attributes
Usage   : $obj->set_attributes( 'foo' => 'bar' )
Function: Sets the xml attributes for the object;
Returns : $self
Args    : key/value pairs or a hash ref

set_identifiable()

Type    : Mutator
Title   : set_identifiable
Usage   : $obj->set_tag(0);
Function: Enables/disables id generation
Returns : $self
Args    : BOOLEAN

set_namespaces()

Type    : Mutator
Title   : set_namespaces
Usage   : $obj->set_namespaces( 'dwc' => 'http://www.namespaceTBD.org/darwin2' );
Function: Adds one or more prefix/namespace pairs
Returns : $self
Args    : One or more prefix/namespace pairs, as even-sized list, 
          or as a hash reference, i.e.:
          $obj->set_namespaces( 'dwc' => 'http://www.namespaceTBD.org/darwin2' );
          or
          $obj->set_namespaces( { 'dwc' => 'http://www.namespaceTBD.org/darwin2' } );
Notes   : This is a global for the XMLWritable class, so that in a recursive
		   to_xml call the outermost element contains the namespace definitions.
		   This method can also be called as a static class method, i.e.
		   Bio::Phylo::Util::XMLWritable->set_namespaces(
		   'dwc' => 'http://www.namespaceTBD.org/darwin2');

set_tag()

This method is usually only used internally, to define or alter the name of the tag into which the object is serialized. For example, for a Bio::Phylo::Forest::Node object, this method would be called with the 'node' argument, so that the object is serialized into an xml element structure called <node/>

Type    : Mutator
Title   : set_tag
Usage   : $obj->set_tag('node');
Function: Sets the tag name
Returns : $self
Args    : A tag name (must be a valid xml element name)

set_xml_id()

This method is usually only used internally, to store the xml id of an object as it is parsed out of a nexml file - this is for the purpose of round-tripping nexml info sets.

Type    : Mutator
Title   : set_xml_id
Usage   : $obj->set_xml_id('node345');
Function: Sets the xml id
Returns : $self
Args    : An xml id (must be a valid xml NCName)

to_xml()

Serializes invocant to XML.

Type    : XML serializer
Title   : to_xml
Usage   : my $xml = $obj->to_xml;
Function: Serializes $obj to xml
Returns : An xml string
Args    : None

SUPERCLASS Bio::Phylo

Bio::Phylo::Forest::Node inherits from superclass Bio::Phylo. Below are the public methods (if any) from this superclass.

clone()

Clones invocant.

Type    : Utility method
Title   : clone
Usage   : my $clone = $object->clone;
Function: Creates a copy of the invocant object.
Returns : A copy of the invocant.
Args    : None.
Comments: Cloning is currently experimental, use with caution.

get()

Attempts to execute argument string as method on invocant.

Type    : Accessor
Title   : get
Usage   : my $treename = $tree->get('get_name');
Function: Alternative syntax for safely accessing
          any of the object data; useful for
          interpolating runtime $vars.
Returns : (context dependent)
Args    : a SCALAR variable, e.g. $var = 'get_name';

get_desc()

Gets invocant description.

Type    : Accessor
Title   : get_desc
Usage   : my $desc = $obj->get_desc;
Function: Returns the object's description (if any).
Returns : A string
Args    : None

get_generic()

Gets generic hashref or hash value(s).

Type    : Accessor
Title   : get_generic
Usage   : my $value = $obj->get_generic($key);
          or
          my %hash = %{ $obj->get_generic() };
Function: Returns the object's generic data. If an
          argument is used, it is considered a key
          for which the associated value is returned.
          Without arguments, a reference to the whole
          hash is returned.
Returns : A string or hash reference.
Args    : None

get_id()

Gets invocant's UID.

Type    : Accessor
Title   : get_id
Usage   : my $id = $obj->get_id;
Function: Returns the object's unique ID
Returns : INT
Args    : None

get_internal_name()

Gets invocant's 'fallback' name (possibly autogenerated).

Type    : Accessor
Title   : get_internal_name
Usage   : my $name = $obj->get_internal_name;
Function: Returns the object's name (if none was set, the name
          is a combination of the $obj's class and its UID).
Returns : A string
Args    : None

get_logger()

Gets a logger object.

Type    : Accessor
Title   : get_logger
Usage   : my $logger = $obj->get_logger;
Function: Returns a Bio::Phylo::Util::Logger object
Returns : Bio::Phylo::Util::Logger
Args    : None

get_name()

Gets invocant's name.

Type    : Accessor
Title   : get_name
Usage   : my $name = $obj->get_name;
Function: Returns the object's name.
Returns : A string
Args    : None

get_obj_by_id()

Attempts to fetch an in-memory object by its UID

Type    : Accessor
Title   : get_obj_by_id
Usage   : my $obj = Bio::Phylo->get_obj_by_id($uid);
Function: Fetches an object from the IDPool cache
Returns : A Bio::Phylo object 
Args    : A unique id

get_score()

Gets invocant's score.

Type    : Accessor
Title   : get_score
Usage   : my $score = $obj->get_score;
Function: Returns the object's numerical score (if any).
Returns : A number
Args    : None

new()

The Bio::Phylo root constructor, is rarely used directly. Rather, many other objects in Bio::Phylo internally go up the inheritance tree to this constructor. The arguments shown here can therefore also be passed to any of the child classes' constructors, which will pass them on up the inheritance tree. Generally, constructors in Bio::Phylo subclasses can process as arguments all methods that have set_* in their names. The arguments are named for the methods, but "set_" has been replaced with a dash "-", e.g. the method "set_name" becomes the argument "-name" in the constructor.

Type    : Constructor
Title   : new
Usage   : my $phylo = Bio::Phylo->new;
Function: Instantiates Bio::Phylo object
Returns : a Bio::Phylo object 
Args    : Optional, any number of setters. For example,
		   Bio::Phylo->new( -name => $name )
		   will call set_name( $name ) internally

set_desc()

Sets invocant description.

Type    : Mutator
Title   : set_desc
Usage   : $obj->set_desc($desc);
Function: Assigns an object's description.
Returns : Modified object.
Args    : Argument must be a string.

set_generic()

Sets generic key/value pair(s).

Type    : Mutator
Title   : set_generic
Usage   : $obj->set_generic( %generic );
Function: Assigns generic key/value pairs to the invocant.
Returns : Modified object.
Args    : Valid arguments constitute:

          * key/value pairs, for example:
            $obj->set_generic( '-lnl' => 0.87565 );

          * or a hash ref, for example:
            $obj->set_generic( { '-lnl' => 0.87565 } );

          * or nothing, to reset the stored hash, e.g.
               $obj->set_generic( );

set_name()

Sets invocant name.

Type    : Mutator
Title   : set_name
Usage   : $obj->set_name($name);
Function: Assigns an object's name.
Returns : Modified object.
Args    : Argument must be a string, will be single 
          quoted if it contains [;|,|:\(|\)] 
          or spaces. Preceding and trailing spaces
          will be removed.

set_score()

Sets invocant score.

Type    : Mutator
Title   : set_score
Usage   : $obj->set_score($score);
Function: Assigns an object's numerical score.
Returns : Modified object.
Args    : Argument must be any of
          perl's number formats, or undefined
          to reset score.

to_json()

Serializes object to JSON string

Type    : Serializer
Title   : to_json()
Usage   : print $obj->to_json();
Function: Serializes object to JSON string
Returns : String 
Args    : None
Comments:

to_string()

Serializes object to general purpose string

Type    : Serializer
Title   : to_string()
Usage   : print $obj->to_string();
Function: Serializes object to general purpose string
Returns : String 
Args    : None
Comments: This is YAML

REVISION

$Id: Node.pm 844 2009-03-05 00:07:26Z rvos $

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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NAME

SYNOPSIS

DESCRIPTION

METHODS

CONSTRUCTOR

MUTATORS

ACCESSORS

TESTS

CALCULATIONS

VISITOR METHODS

UTILITY METHODS

SERIALIZERS

INHERITED METHODS

SUPERCLASS Bio::Phylo::Taxa::TaxonLinker

SUPERCLASS Bio::Phylo::Listable

SUPERCLASS Bio::Phylo::Util::XMLWritable

SUPERCLASS Bio::Phylo

SEE ALSO

REVISION

Module Install Instructions