#
# BioPerl module for Bio::Tree::TreeI
#
# Please direct questions and support issues to <bioperl-l@bioperl.org>
#
# 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 = Bio::TreeIO->new(-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/wiki/Mailing_lists - About the mailing lists
=head2 Support
Please direct usage questions or support issues to the mailing list:
I<bioperl-l@bioperl.org>
rather than to the module maintainer directly. Many experienced and
reponsive experts will be able look at the problem and quickly
address it. Please include a thorough description of the problem
with code and data examples if at all possible.
=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:
https://redmine.open-bio.org/projects/bioperl/
=head1 AUTHOR - Jason Stajich
Email jason@bioperl.org
=head1 CONTRIBUTORS
Aaron Mackey, amackey@virginia.edu
Elia Stupka, elia@fugu-sg.org
Sendu Bala, bix@sendu.me.uk
=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 strict;
use base qw(Bio::Root::RootI);
=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 = $tree->number_nodes
Function: Find the number of nodes in the tree.
Returns : int
Args : none
=cut
sub number_nodes{
my ($self) = @_;
my $root = $self->get_root_node;
if( defined $root && $root->isa('Bio::Tree::NodeI')) {
return ($root->descendent_count + 1);
}
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 => 'none');
}
=head2 Methods for associating Tag/Values with a Tree
These methods associate tag/value pairs with a Tree
=head2 set_tag_value
Title : set_tag_value
Usage : $tree->set_tag_value($tag,$value)
$tree->set_tag_value($tag,@values)
Function: Sets a tag value(s) to a tree. Replaces old values.
Returns : number of values stored for this tag
Args : $tag - tag name
$value - value to store for the tag
=cut
sub set_tag_value{
shift->throw_not_implemented();
}
=head2 add_tag_value
Title : add_tag_value
Usage : $tree->add_tag_value($tag,$value)
Function: Adds a tag value to a tree
Returns : number of values stored for this tag
Args : $tag - tag name
$value - value to store for the tag
=cut
sub add_tag_value{
shift->throw_not_implemented();
}
=head2 remove_tag
Title : remove_tag
Usage : $tree->remove_tag($tag)
Function: Remove the tag and all values for this tag
Returns : boolean representing success (0 if tag does not exist)
Args : $tag - tagname to remove
=cut
sub remove_tag {
shift->throw_not_implemented();
}
=head2 remove_all_tags
Title : remove_all_tags
Usage : $tree->remove_all_tags()
Function: Removes all tags
Returns : None
Args : None
=cut
sub remove_all_tags{
shift->throw_not_implemented();
}
=head2 get_all_tags
Title : get_all_tags
Usage : my @tags = $tree->get_all_tags()
Function: Gets all the tag names for this Tree
Returns : Array of tagnames
Args : None
=cut
sub get_all_tags {
shift->throw_not_implemented();
}
=head2 get_tag_values
Title : get_tag_values
Usage : my @values = $tree->get_tag_values($tag)
Function: Gets the values for given tag ($tag)
Returns : Array of values or empty list if tag does not exist
Args : $tag - tag name
=cut
sub get_tag_values{
shift->throw_not_implemented();
}
=head2 has_tag
Title : has_tag
Usage : $tree->has_tag($tag)
Function: Boolean test if tag exists in the Tree
Returns : Boolean
Args : $tag - tagname
=cut
sub has_tag{
shift->throw_not_implemented();
}
1;