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
                                   # you might want to test that it was defined

    my $rootnode = $tree->get_root_node;

    # process just the next generation
    foreach my $node ( $rootnode->each_Descendent() ) {
	print "branch len is ", $node->branch_length, "\n";
    }

    # process all the children
    my $example_leaf_node;
    foreach my $node ( $rootnode->get_Descendents() ) {
	if( $node->is_Leaf ) { 
	    print "node is a leaf ... "; 
            # for example use below
            $example_leaf_node = $node unless defined $example_leaf_node; 
	}
	print "branch len is ", $node->branch_length, "\n";
    }

    # The ancestor() method points to the parent of a node
    # A node can only have one parent

    my $parent = $example_leaf_node->ancestor;

    # parent won't likely have an description because it is an internal node
    # but child will because it is a leaf

    print "Parent id: ", $parent->id," child id: ", 
          $example_leaf_node->id, "\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.
Various implementations of NodeI may extend the basic functions and
allow storing of other information (like attatching a species object
or full sequences used to build a tree or alternative sequences). If
you don't know how to extend a Bioperl object please ask, happy to
help, we would also greatly appreciate contributions with improvements
or extensions of the objects back to the Bioperl code base so that
others don't have to reinvent your ideas.

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($sortby)
 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    : $sortby [optional] "height", "creation" or coderef to be used
           to sort the order of children nodes.

 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   : internal_id
 Usage   : my $internalid = $node->internal_id
 Function: Returns the internal unique id for this Node
 Returns : unique id
 Args    : none

 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

 Title   : invalidate_height
 Usage   : private helper method
 Function: Invalidate our cached value of the node'e height in the tree
 Returns : nothing
 Args    : none

Methods code

sub add_Descendent {

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

   $self->throw_not_implemented();

}

sub each_Descendent {

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

}

sub get_Descendents {

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

}

sub is_Leaf {

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

}

sub descendent_count {

   my ($self) = @_;
   my $count = 0;
   
   foreach my $node ( $self->each_Descendent ) { 
       $count += 1;
       $node->can('descendent_count') ? $count += $node->descendent_count : next;
   }
   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 ) { 
	   $self->debug(sprintf("Trying to calculate height of a node when a Node (%s) has an undefined branch_length",$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 || 1);

}

sub branch_length {

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

}

sub id {

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

}

sub internal_id {

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

}

sub description {

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

}

sub bootstrap {

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

}

sub ancestor {

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

}

sub invalidate_height {

     shift->throw_not_implemented();

}

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
  http://bioperl.org/MailList.shtml  - About the mailing lists

Report bugs to the Bioperl bug tracking system to help us keep track
of the bugs and their resolution. Bug reports can be submitted via
the web:

  http://bugzilla.bioperl.org/

Email jason@bioperl.org

Aaron Mackey amackey@virginia.edu

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