Summary

Bio::Tree::NodeI - Interface describing a Tree Node

Package variables

Included modules

Inherit

Bio::Root::RootI

Synopsis

    # get a Tree::NodeI somehow
    # like from a TreeIO
    use Bio::TreeIO;
    # read in a clustalw NJ in phylip/newick format
    my $treeio = new Bio::TreeIO(-format => 'newick', -file => 'file.dnd');
    my $tree = $treeio->next_tree; # we'll assume it worked for demo purposes

    my $rootnode = $tree->get_root_node;

    # process just the next generation
    foreach my $node ( $tree->each_Descendent() ) {
	print "branch len is ", $node->branch_length, "\n";
    }
    # process all the children
    foreach my $node ( $tree->get_Descendents() ) {
	if( $node->is_Leaf ) { 
	    print "node is a leaf ... "; 
	}
	print "branch len is ", $node->branch_length, "\n";
    }

Description

A NodeI is capable of the basic structure of building a tree and
storing the branch length between nodes. The branch length is the
length of the branch between the node and its ancestor, thus a root
node in a Tree will not typically have a valid branch length.

Methods

Methods description

 Title   : add_Descendent
 Usage   : $node->add_Descendant($node);
 Function: Adds a descendent to a node
 Returns : number of current descendents for this node
 Args    : Bio::Node::NodeI

 Title   : each_Descendent
 Usage   : my @nodes = $node->each_Descendent;
 Function: all the descendents for this Node (but not their descendents 
					      i.e. not a recursive fetchall)
 Returns : Array of Bio::Tree::NodeI objects
 Args    : none

 Title   : get_Descendents
 Usage   : my @nodes = $node->get_Descendents;
 Function: Recursively fetch all the nodes and their descendents
           *NOTE* This is different from each_Descendent
 Returns : Array or Bio::Tree::NodeI objects
 Args    : none

 Title   : is_Leaf
 Usage   : if( $node->is_Leaf ) 
 Function: Get Leaf status
 Returns : boolean
 Args    : none

 Title   : descendent_count
 Usage   : my $count = $node->descendent_count;
 Function: Counts the number of descendents a node has 
           (and all of their subnodes)
 Returns : integer
 Args    : none

 Title   : to_string
 Usage   : my $str = $node->to_string()
 Function: For debugging, provide a node as a string
 Returns : string
 Args    : none

 Title   : height
 Usage   : my $len = $node->height
 Function: Returns the height of the tree starting at this
           node.  Height is the maximum branchlength.
 Returns : The longest length (weighting branches with branch_length) to a leaf
 Args    : none

 Title   : branch_length
 Usage   : $obj->branch_length()
 Function: 
 Example : 
 Returns : value of branch_length
 Args    : newvalue (optional)

 Title   : id
 Usage   : $obj->id($newval)
 Function: 
 Example : 
 Returns : value of id
 Args    : newvalue (optional)

 Title   : description
 Usage   : $obj->description($newval)
 Function: 
 Example : 
 Returns : value of description
 Args    : newvalue (optional)

 Title   : bootstrap
 Usage   : $obj->bootstrap($newval)
 Function: 
 Example : 
 Returns : value of bootstrap
 Args    : newvalue (optional)

 Title   : ancestor
 Usage   : my $node = $node->ancestor;
 Function: Get/Set a Node's ancestor node
 Returns : Null if this is top level node
 Args    : none

Methods code

sub add_Descendent {

   my ($self,@args) = @_;

   $self->_abstractDeath('add_Descendent');

}

sub each_Descendent {

   my ($self) = @_;
   $self->_abstractDeath('each_Descendent');

}

sub get_Descendents {

   my ($self) = @_;
   my @nodes;
   foreach my $node ( $self->each_Descendent ) {
       push @nodes, ($node->get_Descendents, $node);
   }
   return @nodes;

}

sub is_Leaf {

    my ($self) = @_;
    $self->_abstractDeath('is_Leaf');

}

sub descendent_count {

   my ($self) = @_;
   my $count = 0;
   
   foreach my $node ( $self->each_Descendent ) { 
       $count += 1 + $node->descendent_count;
   }
   return $count;

}

sub to_string {

   my ($self) = @_;
   return sprintf("%s%s",defined $self->id ? $self->id : '',
		  defined $self->branch_length ? 
		  ":" . $self->branch_length : ' ');

}

sub height {

   my ($self) = @_;
   
   if( $self->is_Leaf ) { 
       if( !defined $self->branch_length ) { 
	   $self->warn(sprintf("Trying to calculate height of a node when a Node (%s) has an undefined branch_length",$self->id || '?' ));
	   return 0;
       }
       return $self->branch_length;
   }
   my $max = 0;
   foreach my $subnode ( $self->each_Descendent ) { 
       my $s = $subnode->height;
       if( $s > $max ) { $max = $s; }
   }
   return $max + $self->branch_length;

}

sub branch_length {

    my ($self)= @_;
    $self->_abstractDeath('branch_length');

}

sub id {

    my ($self)= @_;
    $self->_abstractDeath;

}

sub description {

    my ($self) = @_;
    $self->_abstractDeath;

}

sub bootstrap {

    my ($self) = @_;
    $self->_abstractDeath;

}

sub ancestor {

   my ($self,@args) = @_;
   $self->_abstractDeath;

}

General documentation

User feedback is an integral part of the evolution of this and other
Bioperl modules. Send your comments and suggestions preferably to
the Bioperl mailing list. Your participation is much appreciated.

  bioperl-l@bioperl.org              - General discussion
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of the bugs and their resolution. Bug reports can be submitted via
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  bioperl-bugs@bioperl.org
  http://bioperl.org/bioperl-bugs/

Email jason@bioperl.org
Describe contact details here

Additional contributors names and emails here

The rest of the documentation details each of the object methods.
Internal methods are usually preceded with a _