Raw content of Bio::Tree::TreeI
<![CDATA[# $Id: TreeI.pm,v 1.11.2.1 2003/09/14 20:21:10 jason Exp $
#
# BioPerl module for Bio::Tree::TreeI
#
# 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::TreeI - A Tree object suitable for lots of things, designed
originally for Phylogenetic Trees.
=head1 SYNOPSIS
# get a Bio::Tree::TreeI somehow
# 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 @leaves = $tree->get_leaf_nodes;
my $root = $tree->get_root_node;
=head1 DESCRIPTION
This object holds a pointer to the Root of a Tree which is a
Bio::Tree::NodeI.
=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
Elia Stupka, elia@fugu-sg.org
=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::TreeI;
use Bio::Tree::NodeI;
use vars qw(@ISA);
use strict;
@ISA = qw(Bio::Tree::NodeI);
=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) = @_;
$self->throw_not_implemented();
}
=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) = @_;
$self->throw_not_implemented();
}
=head2 number_nodes
Title : number_nodes
Usage : my $size = $tree->number_nodes
Function: Returns the number of nodes
Example :
Returns :
Args :
=cut
sub number_nodes{
my ($self) = @_;
my $root = $self->get_root_node;
if( defined $root && $root->isa('Bio::Tree::NodeI')) {
return $root->descendent_count;
}
return 0;
}
=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) = @_;
$self->throw_not_implemented();
}
=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
=cut
sub height{
my ($self) = @_;
my $nodect = $self->number_nodes;
return 0 if( ! $nodect );
return log($nodect) / log(2);
}
=head2 id
Title : id
Usage : my $id = $tree->id();
Function: An id value for the tree
Returns : scalar
Args :
=cut
sub id{
my ($self,@args) = @_;
$self->throw_not_implemented();
}
=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 ($self,$value) = @_;
$self->throw_not_implemented();
}
=head2 get_leaf_nodes
Title : get_leaf_nodes
Usage : my @leaves = $tree->get_leaf_nodes()
Function: Returns the leaves (tips) of the tree
Returns : Array of Bio::Tree::NodeI objects
Args : none
=cut
sub get_leaf_nodes{
my ($self) = @_;
return grep { $_->is_Leaf() } $self->get_nodes(-sortby => 'creation');
}
1;
]]>