Raw content of Bio::Tree::Tree
<![CDATA[# $Id: Tree.pm,v 1.13.2.2 2003/09/14 20:22:31 jason Exp $
#
# BioPerl module for Bio::Tree::Tree
#
# Cared for by Jason Stajich <jason@bioperl.org>
#
# Copyright Jason Stajich
#
# You may distribute this module under the same terms as perl itself
# POD documentation - main docs before the code
=head1 NAME
Bio::Tree::Tree - An Implementation of TreeI interface.
=head1 SYNOPSIS
# like from a TreeIO
my $treeio = new Bio::TreeIO(-format => 'newick', -file => 'treefile.dnd');
my $tree = $treeio->next_tree;
my @nodes = $tree->get_nodes;
my $root = $tree->get_root_node;
=head1 DESCRIPTION
This object holds handles to Nodes which make up a tree.
=head1 FEEDBACK
=head2 Mailing Lists
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
=head2 Reporting Bugs
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/
=head1 AUTHOR - Jason Stajich
Email jason@bioperl.org
=head1 CONTRIBUTORS
Aaron Mackey amackey@virginia.edu
=head1 APPENDIX
The rest of the documentation details each of the object methods.
Internal methods are usually preceded with a _
=cut
# Let the code begin...
package Bio::Tree::Tree;
use vars qw(@ISA);
use strict;
# Object preamble - inherits from Bio::Root::Root
use Bio::Root::Root;
use Bio::Tree::TreeFunctionsI;
use Bio::Tree::TreeI;
@ISA = qw(Bio::Root::Root Bio::Tree::TreeI Bio::Tree::TreeFunctionsI );
=head2 new
Title : new
Usage : my $obj = new Bio::Tree::Tree();
Function: Builds a new Bio::Tree::Tree object
Returns : Bio::Tree::Tree
Args : -root => L<Bio::Tree::NodeI> object which is the root
-nodelete => boolean, whether or not to try and cleanup all
the nodes when this this tree goes out
of scope.
=cut
sub new {
my($class,@args) = @_;
my $self = $class->SUPER::new(@args);
$self->{'_rootnode'} = undef;
$self->{'_maxbranchlen'} = 0;
$self->_register_for_cleanup(\&cleanup_tree);
my ($root,$nodel)= $self->_rearrange([qw(ROOT NODELETE)], @args);
if( $root ) { $self->set_root_node($root); }
$self->nodelete($nodel || 0);
return $self;
}
=head2 nodelete
Title : nodelete
Usage : $obj->nodelete($newval)
Function: Get/Set Boolean whether or not to delete the underlying
nodes when it goes out of scope. By default this is false
meaning trees are cleaned up.
Returns : boolean
Args : on set, new boolean value
=cut
sub nodelete{
my $self = shift;
return $self->{'nodelete'} = shift if @_;
return $self->{'nodelete'};
}
=head2 get_nodes
Title : get_nodes
Usage : my @nodes = $tree->get_nodes()
Function: Return list of Tree::NodeI objects
Returns : array of Tree::NodeI objects
Args : (named values) hash with one value
order => 'b|breadth' first order or 'd|depth' first order
=cut
sub get_nodes{
my ($self, @args) = @_;
my ($order, $sortby) = $self->_rearrange([qw(ORDER SORTBY)],@args);
$order ||= 'depth';
$sortby ||= 'height';
return () unless defined $self->get_root_node;
if ($order =~ m/^b|(breadth)$/oi) {
my $node = $self->get_root_node;
my @children = ($node);
for (@children) {
push @children, $_->each_Descendent($sortby);
}
return @children;
}
if ($order =~ m/^d|(depth)$/oi) {
# this is depth-first search I believe
my $node = $self->get_root_node;
my @children = ($node,$node->get_Descendents($sortby));
return @children;
}
}
=head2 get_root_node
Title : get_root_node
Usage : my $node = $tree->get_root_node();
Function: Get the Top Node in the tree, in this implementation
Trees only have one top node.
Returns : Bio::Tree::NodeI object
Args : none
=cut
sub get_root_node{
my ($self) = @_;
return $self->{'_rootnode'};
}
=head2 set_root_node
Title : set_root_node
Usage : $tree->set_root_node($node)
Function: Set the Root Node for the Tree
Returns : Bio::Tree::NodeI
Args : Bio::Tree::NodeI
=cut
sub set_root_node{
my $self = shift;
if( @_ ) {
my $value = shift;
if( defined $value &&
! $value->isa('Bio::Tree::NodeI') ) {
$self->warn("Trying to set the root node to $value which is not a Bio::Tree::NodeI");
return $self->get_root_node;
}
$self->{'_rootnode'} = $value;
}
return $self->get_root_node;
}
=head2 total_branch_length
Title : total_branch_length
Usage : my $size = $tree->total_branch_length
Function: Returns the sum of the length of all branches
Returns : integer
Args : none
=cut
sub total_branch_length {
my ($self) = @_;
my $sum = 0;
if( defined $self->get_root_node ) {
for ( $self->get_root_node->get_Descendents() ) {
$sum += $_->branch_length || 0;
}
}
return $sum;
}
=head2 id
Title : id
Usage : my $id = $tree->id();
Function: An id value for the tree
Returns : scalar
Args : [optional] new value to set
=cut
sub id{
my ($self,$val) = @_;
if( defined $val ) {
$self->{'_treeid'} = $val;
}
return $self->{'_treeid'};
}
=head2 score
Title : score
Usage : $obj->score($newval)
Function: Sets the associated score with this tree
This is a generic slot which is probably best used
for log likelihood or other overall tree score
Returns : value of score
Args : newvalue (optional)
=cut
sub score{
my ($self,$val) = @_;
if( defined $val ) {
$self->{'_score'} = $val;
}
return $self->{'_score'};
}
# decorated interface TreeI Implements this
=head2 height
Title : height
Usage : my $height = $tree->height
Function: Gets the height of tree - this LOG_2($number_nodes)
WARNING: this is only true for strict binary trees. The TreeIO
system is capable of building non-binary trees, for which this
method will currently return an incorrect value!!
Returns : integer
Args : none
=head2 number_nodes
Title : number_nodes
Usage : my $size = $tree->number_nodes
Function: Returns the number of nodes
Example :
Returns :
Args :
=cut
# -- private internal methods --
sub cleanup_tree {
my $self = shift;
unless( $self->nodelete ) {
foreach my $node ( $self->get_nodes ) {
$node->ancestor(undef);
$node = undef;
}
}
$self->{'_rootnode'} = undef;
}
1;
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