NAME

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

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_raw_parent()

Sets argument as invocant's parent. This method does NO sanity checks on the rest of the topology. Use with caution.

 Type    : Mutator
 Title   : set_raw_parent
 Usage   : $node->set_raw_parent($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_raw_child()

Sets argument as invocant's child. This method does NO sanity checks on the rest of the topology. Use with caution.

 Type    : Mutator
 Title   : set_raw_child
 Usage   : $node->set_raw_child($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.
    

set_rank()

Sets the taxonomic rank of the node

 Type    : Mutator
 Title   : set_rank
 Usage   : $node->set_rank('genus');
 Function: Sets the taxonomic rank of the node
 Returns : Invocant
 Args    : String
 Comments: Free-form, but highly recommended to use same rank names as in Bio::Taxon
    

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
    

get_rank()

Gets the taxonomic rank of the node

 Type    : Mutator
 Title   : get_rank
 Usage   : my $rank = $node->get_rank;
 Function: Gets the taxonomic rank of the node
 Returns : String
 Args    : NONE
 Comments:
    

    # podinherit_insert_token

SEE ALSO

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

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>