Raw content of Bio::Tree::NodeI
<![CDATA[# $Id: NodeI.pm,v 1.19.2.2 2003/09/14 19:00:35 jason Exp $
#
# BioPerl module for Bio::Tree::NodeI
#
# 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::NodeI - Interface describing a Tree Node
=head1 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_all_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";
=head1 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.
=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::NodeI;
use vars qw(@ISA);
use strict;
use Bio::Root::RootI;
@ISA = qw(Bio::Root::RootI);
=head2 add_Descendent
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
=cut
sub add_Descendent{
my ($self,@args) = @_;
$self->throw_not_implemented();
}
=head2 each_Descendent
Title : each_Descendent
Usage : my @nodes = $node->each_Descendent;
Function: all the descendents for this Node (but not their descendents
i.e. not a recursive fetchall)
Returns : Array of Bio::Tree::NodeI objects
Args : none
=cut
sub each_Descendent{
my ($self) = @_;
$self->throw_not_implemented();
}
=head2 Decorated Interface methods
=cut
=head2 get_all_Descendents
Title : get_all_Descendents($sortby)
Usage : my @nodes = $node->get_all_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 : $sortby [optional] "height", "creation" or coderef to be used
to sort the order of children nodes.
=cut
sub get_all_Descendents{
my ($self, $sortby) = @_;
$sortby ||= 'height';
my @nodes;
foreach my $node ( $self->each_Descendent($sortby) ) {
push @nodes, ($node->get_all_Descendents($sortby), $node);
}
return @nodes;
}
*get_Descendents = \&get_all_Descendents;
=head2 is_Leaf
Title : is_Leaf
Usage : if( $node->is_Leaf )
Function: Get Leaf status
Returns : boolean
Args : none
=cut
sub is_Leaf{
my ($self) = @_;
$self->throw_not_implemented();
}
=head2 descendent_count
Title : descendent_count
Usage : my $count = $node->descendent_count;
Function: Counts the number of descendents a node has
(and all of their subnodes)
Returns : integer
Args : none
=cut
sub descendent_count{
my ($self) = @_;
my $count = 0;
foreach my $node ( $self->each_Descendent ) {
$count += 1;
$node->can('descendent_count') ? $count += $node->descendent_count : next;
}
return $count;
}
=head2 to_string
Title : to_string
Usage : my $str = $node->to_string()
Function: For debugging, provide a node as a string
Returns : string
Args : none
=cut
sub to_string{
my ($self) = @_;
return sprintf("%s%s%s",
defined $self->id ? $self->id : '',
defined $self->branch_length ? ':' . $self->branch_length : ' ',
$self->is_Leaf() ? '(leaf)' : ''
);
}
=head2 height
Title : height
Usage : my $len = $node->height
Function: Returns the height of the tree starting at this
node. Height is the maximum branchlength.
Returns : The longest length (weighting branches with branch_length) to a leaf
Args : none
=cut
sub height{
my ($self) = @_;
if( $self->is_Leaf ) {
if( !defined $self->branch_length ) {
$self->debug(sprintf("Trying to calculate height of a node when a Node (%s) has an undefined branch_length\n",$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);
}
=head2 Get/Set methods
=cut
=head2 branch_length
Title : branch_length
Usage : $obj->branch_length()
Function: Get/Set the branch length
Returns : value of branch_length
Args : newvalue (optional)
=cut
sub branch_length{
my ($self)= @_;
$self->throw_not_implemented();
}
=head2 id
Title : id
Usage : $obj->id($newval)
Function: The human readable identifier for the node
Returns : value of human readable id
Args : newvalue (optional)
=cut
sub id{
my ($self)= @_;
$self->throw_not_implemented();
}
=head2 internal_id
Title : internal_id
Usage : my $internalid = $node->internal_id
Function: Returns the internal unique id for this Node
Returns : unique id
Args : none
=cut
sub internal_id{
my ($self) = @_;
$self->throw_not_implemented();
}
=head2 description
Title : description
Usage : $obj->description($newval)
Function: Get/Set the description string
Returns : value of description
Args : newvalue (optional)
=cut
sub description{
my ($self) = @_;
$self->throw_not_implemented();
}
=head2 bootstrap
Title : bootstrap
Usage : $obj->bootstrap($newval)
Function: Get/Set the bootstrap value
Returns : value of bootstrap
Args : newvalue (optional)
=cut
sub bootstrap{
my ($self) = @_;
$self->throw_not_implemented();
}
=head2 ancestor
Title : ancestor
Usage : my $node = $node->ancestor;
Function: Get/Set the ancestor node pointer for a Node
Returns : Null if this is top level node
Args : none
=cut
sub ancestor{
my ($self,@args) = @_;
$self->throw_not_implemented();
}
=head2 invalidate_height
Title : invalidate_height
Usage : private helper method
Function: Invalidate our cached value of the node height in the tree
Returns : nothing
Args : none
=cut
sub invalidate_height {
shift->throw_not_implemented();
}
=head2 Methods for associating Tag/Values with a Node
These methods associate tag/value pairs with a Node
=head2 add_tag_value
Title : add_tag_value
Usage : $node->add_tag_value($tag,$value)
Function: Adds a tag value to a node
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 : $node->remove_tag($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 : $node->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 = $node->get_all_tags()
Function: Gets all the tag names for this Node
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 = $node->get_tag_value($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 : $node->has_tag($tag)
Function: Boolean test if tag exists in the Node
Returns : Boolean
Args : $tag - tagname
=cut
sub has_tag{
shift->throw_not_implemented();
}
1;
]]>