#
# BioPerl module for Bio::Tree::Node
#
# Please direct questions and support issues to <bioperl-l@bioperl.org>
#
# Cared for by Jason Stajich <jason-at-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::Node - A Simple Tree Node
=head1 SYNOPSIS
use Bio::Tree::Node;
my $nodeA = Bio::Tree::Node->new();
my $nodeL = Bio::Tree::Node->new();
my $nodeR = Bio::Tree::Node->new();
my $node = Bio::Tree::Node->new();
$node->add_Descendent($nodeL);
$node->add_Descendent($nodeR);
print "node is not a leaf \n" if( $node->is_leaf);
=head1 DESCRIPTION
Makes a Tree Node suitable for building a Tree.
=head1 FEEDBACK
=head2 Mailing Lists
User feedback is an integral part of the evolution of this and other
Bioperl modules. Send your comments and suggestions preferably to
the Bioperl mailing list. Your participation is much appreciated.
bioperl-l@bioperl.org - General discussion
http://bioperl.org/wiki/Mailing_lists - About the mailing lists
=head2 Support
Please direct usage questions or support issues to the mailing list:
I<bioperl-l@bioperl.org>
rather than to the module maintainer directly. Many experienced and
reponsive experts will be able look at the problem and quickly
address it. Please include a thorough description of the problem
with code and data examples if at all possible.
=head2 Reporting Bugs
Report bugs to the Bioperl bug tracking system to help us keep track
of the bugs and their resolution. Bug reports can be submitted via
the web:
https://redmine.open-bio.org/projects/bioperl/
=head1 AUTHOR - Jason Stajich
Email jason-at-bioperl-dot-org
=head1 CONTRIBUTORS
Aaron Mackey, amackey-at-virginia-dot-edu
Sendu Bala, bix@sendu.me.uk
=head1 APPENDIX
The rest of the documentation details each of the object methods.
Internal methods are usually preceded with a _
=cut
# Let the code begin...
package Bio::Tree::Node;
use vars qw($CREATIONORDER);
use strict;
use base qw(Bio::Root::Root Bio::Tree::NodeI);
BEGIN {
$CREATIONORDER = 1;
}
=head2 new
Title : new
Usage : my $obj = Bio::Tree::Node->new();
Function: Builds a new Bio::Tree::Node object
Returns : Bio::Tree::Node
Args : -descendents => arrayref of descendents (they will be
updated s.t. their ancestor point is this
node)
-branch_length => branch length [integer] (optional)
-bootstrap => value bootstrap value (string)
-description => description of node
-id => human readable id for node
=cut
sub new {
my($class,@args) = @_;
my $self = $class->SUPER::new(@args);
my ($children, $branchlen,$id,
$bootstrap, $desc,$d) = $self->_rearrange([qw(
DESCENDENTS
BRANCH_LENGTH
ID
BOOTSTRAP
DESC
DESCRIPTION
)],
@args);
$self->_register_for_cleanup(\&node_cleanup);
$self->{'_desc'} = {}; # for descendents
if( defined $d && defined $desc ) {
$self->warn("can only accept -desc or -description, not both, accepting -description");
$desc = $d;
} elsif( defined $d && ! defined $desc ) {
$desc = $d;
}
defined $desc && $self->description($desc);
defined $bootstrap && $self->bootstrap($bootstrap);
defined $id && $self->id($id);
defined $branchlen && $self->branch_length($branchlen);
if( defined $children ) {
if( ref($children) !~ /ARRAY/i ) {
$self->throw("Must specify a valid ARRAY reference to initialize a Node's Descendents");
}
foreach my $c ( @$children ) {
$self->add_Descendent($c);
}
}
$self->_creation_id($CREATIONORDER++);
return $self;
}
=head2 create_node_on_branch
Title : create_node_on_branch
Usage : $node->create_node_on_branch($at_length)
Function: Create a node on the ancestral branch of the calling
object.
Example :
Returns : the created node
Args : -POSITION=>$absolute_branch_length_from_caller (default)
-FRACTION=>$fraction_of_branch_length_from_caller
-ANNOT=>{ -id => "the id", -desc => "the description" }
-FORCE, set to allow nodes with zero branch lengths
=cut
sub create_node_on_branch{
my ($self,@args) = @_;
my ($pos, $frac, $annot, $force) = $self->_rearrange([qw(POSITION FRACTION ANNOT FORCE)], @args);
my ($newpos);
my $blen = $self->branch_length;
# arg checks
$force||=0;
$annot||={};
unless ($self->ancestor) {
$self->throw("Refusing to create nodes above the root--exiting");
}
unless ($blen) {
$self->throw("Calling node's branch length is zero") unless $force;
}
unless ((defined $pos && !defined $frac)||(defined $frac && !defined $pos)) {
$self->throw("Either position or fraction must be specified, but not both");
}
if (defined $frac) {
$self->throw("FRACTION arg must be in the range [0,1]") unless ( (0 <= $frac) && ($frac <= 1) );
$newpos = $frac*$blen;
}
elsif (defined $pos) {
$self->throw("POSITION arg must be in the range [0,$blen]") unless ( (0 <= $pos) && ($pos <= $blen) );
$newpos = $pos;
}
else {
$self->throw("How did I get here?");
}
$self->throw("Calling node's branch length will be zero (set -FORCE to force)--exiting") unless ($newpos > 0) || $force;
$self->throw("Created nodes branch length would be zero (set -FORCE to force)--exiting") unless ($newpos < $blen) || $force;
#guts
$annot->{'-branch_length'} = $blen-$newpos;
my $node = Bio::Tree::Node->new(%$annot);
my $anc = $self->ancestor;
# null anc check is above
$node->add_Descendent($self);
$anc->add_Descendent($node);
$anc->remove_Descendent($self);
$self->branch_length($newpos);
return $node;
}
=head2 add_Descendent
Title : add_Descendent
Usage : $node->add_Descendent($node);
Function: Adds a descendent to a node
Returns : number of current descendents for this node
Args : Bio::Node::NodeI
boolean flag, true if you want to ignore the fact that you are
adding a second node with the same unique id (typically memory
location reference in this implementation). default is false and
will throw an error if you try and overwrite an existing node.
=cut
sub add_Descendent{
my ($self,$node,$ignoreoverwrite) = @_;
return -1 if( ! defined $node );
if( ! ref($node) ||
ref($node) =~ /HASH/ ||
! $node->isa('Bio::Tree::NodeI') ) {
$self->throw("Trying to add a Descendent who is not a Bio::Tree::NodeI");
return -1;
}
$self->{_adding_descendent} = 1;
# avoid infinite recurse
$node->ancestor($self) unless $node->{_setting_ancestor};
$self->{_adding_descendent} = 0;
if( $self->{'_desc'}->{$node->internal_id} && ! $ignoreoverwrite ) {
$self->throw("Going to overwrite a node which is $node that is already stored here, set the ignore overwrite flag (parameter 2) to true to ignore this in the future");
}
$self->{'_desc'}->{$node->internal_id} = $node; # is this safely unique - we've tested before at any rate??
$self->invalidate_height();
return scalar keys %{$self->{'_desc'}};
}
=head2 each_Descendent
Title : each_Descendent($sortby)
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 : $sortby [optional] "height", "creation", "alpha", "revalpha",
or coderef to be used to sort the order of children nodes.
=cut
sub each_Descendent{
my ($self, $sortby) = @_;
# order can be based on branch length (and sub branchlength)
$sortby ||= 'none';
if (ref $sortby eq 'CODE') {
my @values = sort { $sortby->($a,$b) } values %{$self->{'_desc'}};
return @values;
} elsif ($sortby eq 'height') {
return map { $_->[0] }
sort { $a->[1] <=> $b->[1] ||
$a->[2] <=> $b->[2] }
map { [$_, $_->height, $_->internal_id ] }
values %{$self->{'_desc'}};
} elsif( $sortby eq 'alpha' ) {
my @set;
for my $v ( values %{$self->{'_desc'}} ) {
unless( $v->is_Leaf ) {
my @lst = ( sort { $a cmp $b } map { $_->id }
grep { $_->is_Leaf }
$v->get_all_Descendents($sortby));
push @set, [$v, $lst[0], $v->internal_id];
} else {
push @set, [$v, $v->id, $v->internal_id];
}
}
return map { $_->[0] }
sort {$a->[1] cmp $b->[1] || $a->[2] <=> $b->[2] } @set;
} elsif( $sortby eq 'revalpha' ) {
my @set;
for my $v ( values %{$self->{'_desc'}} ) {
if( ! defined $v->id &&
! $v->is_Leaf ) {
my ($l) = ( sort { $b cmp $a } map { $_->id }
grep { $_->is_Leaf }
$v->get_all_Descendents($sortby));
push @set, [$v, $l, $v->internal_id];
} else {
push @set, [$v, $v->id, $v->internal_id];
}
}
return map { $_->[0] }
sort {$b->[1] cmp $a->[1] || $b->[2] <=> $a->[2] } @set;
} else { # creation
return map { $_->[0] }
sort { $a->[1] <=> $b->[1] }
map { [$_, $_->internal_id ] }
grep {defined $_}
values %{$self->{'_desc'}};
}
}
=head2 remove_Descendent
Title : remove_Descendent
Usage : $node->remove_Descendent($node_foo);
Function: Removes a specific node from being a Descendent of this node
Returns : nothing
Args : An array of Bio::Node::NodeI objects which have been previously
passed to the add_Descendent call of this object.
=cut
sub remove_Descendent{
my ($self,@nodes) = @_;
my $c= 0;
foreach my $n ( @nodes ) {
if( $self->{'_desc'}->{$n->internal_id} ) {
$self->{_removing_descendent} = 1;
$n->ancestor(undef);
$self->{_removing_descendent} = 0;
# should be redundant
$self->{'_desc'}->{$n->internal_id}->ancestor(undef);
delete $self->{'_desc'}->{$n->internal_id};
$c++;
} else {
if( $self->verbose ) {
$self->debug(sprintf("no node %s (%s) listed as a descendent in this node %s (%s)\n",$n->id, $n,$self->id,$self));
$self->debug("Descendents are " . join(',', keys %{$self->{'_desc'}})."\n");
}
}
}
$c;
}
=head2 remove_all_Descendents
Title : remove_all_Descendents
Usage : $node->remove_All_Descendents()
Function: Cleanup the node's reference to descendents and reset
their ancestor pointers to undef, if you don't have a reference
to these objects after this call they will be cleaned up - so
a get_nodes from the Tree object would be a safe thing to do first
Returns : nothing
Args : none
=cut
sub remove_all_Descendents{
my ($self) = @_;
# This won't cleanup the nodes themselves if you also have
# a copy/pointer of them (I think)...
# That's true. But that's not a bug; if we retain a reference to them it's
# very possible we want to keep them. The only way to truly destroy them is
# to call DESTROY on the instance.
while( my ($node,$val) = each %{ $self->{'_desc'} } ) {
delete $self->{'_desc'}->{$node}
}
$self->{'_desc'} = {};
1;
}
=head2 get_all_Descendents
Title : get_all_Descendents
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 : none
=cut
# get_all_Descendents implemented in the interface
=head2 ancestor
Title : ancestor
Usage : $obj->ancestor($newval)
Function: Set the Ancestor
Returns : ancestral node
Args : newvalue (optional)
=cut
sub ancestor {
my $self = shift;
if (@_) {
my $new_ancestor = shift;
# we can set ancestor to undef
if ($new_ancestor) {
$self->throw("This is [$new_ancestor], not a Bio::Tree::NodeI")
unless $new_ancestor->isa('Bio::Tree::NodeI');
}
my $old_ancestor = $self->{'_ancestor'} || '';
if (!$old_ancestor ||
($old_ancestor && ( !$new_ancestor ||
$new_ancestor ne $old_ancestor)) ) {
if( $old_ancestor && ! $old_ancestor->{_removing_descendent}) {
$old_ancestor->remove_Descendent($self);
}
if ($new_ancestor &&
! $new_ancestor->{_adding_descendent} ) { # avoid infinite recurse
$self->{_setting_ancestor} = 1;
$new_ancestor->add_Descendent($self, 1);
$self->{_setting_ancestor} = 0;
}
}
$self->{'_ancestor'} = $new_ancestor;
}
return $self->{'_ancestor'};
}
=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 = shift;
if( @_ ) {
my $bl = shift;
if( defined $bl &&
$bl =~ s/\[(\d+)\]// ) {
$self->bootstrap($1);
}
$self->{'_branch_length'} = $bl;
$self->invalidate_height();
}
return $self->{'_branch_length'};
}
=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 = shift;
if( @_ ) {
if( $self->has_tag('B') ) {
$self->remove_tag('B');
}
$self->add_tag_value('B',shift);
}
return ($self->get_tag_values('B'))[0];
}
=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 = shift;
$self->{'_description'} = shift @_ if @_;
return $self->{'_description'};
}
=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)
"A name can be any string of printable characters except blanks,
colons, semicolons, parentheses, and square brackets. Because you may
want to include a blank in a name, it is assumed that an underscore
character ("_") stands for a blank; any of these in a name will be
converted to a blank when it is read in."
from L<http://evolution.genetics.washington.edu/phylip/newicktree.html>
Also note that these objects now support spaces, ();: because we can
automatically quote the strings if they contain these characters. The
L<id_output> method does this for you so use the id() method to get
the raw string while L<id_output> to get the pre-escaped string.
=cut
sub id {
my ($self, $value) = @_;
if (defined $value) {
#$self->warn("Illegal characters ();: and space in the id [$value], converting to _ ")
# if $value =~ /\(\);:/ and $self->verbose >= 0;
#$value =~ s/[\(\);:\s]/_/g;
$self->{'_id'} = $value;
}
return $self->{'_id'};
}
=head2 Helper Functions
=cut
=head2 id_output
Title : id_output
Usage : my $id = $node->id_output;
Function: Return an id suitable for output in format like newick
so that if it contains spaces or ():; characters it is properly
quoted
Returns : $id string if $node->id has a value
Args : none
=cut
# implemented in NodeI interface
=head2 internal_id
Title : internal_id
Usage : my $internalid = $node->internal_id
Function: Returns the internal unique id for this Node
(a monotonically increasing number for this in-memory implementation
but could be a database determined unique id in other
implementations)
Returns : unique id
Args : none
=cut
sub internal_id {
return $_[0]->_creation_id;
}
=head2 _creation_id
Title : _creation_id
Usage : $obj->_creation_id($newval)
Function: a private method signifying the internal creation order
Returns : value of _creation_id
Args : newvalue (optional)
=cut
sub _creation_id {
my $self = shift @_;
$self->{'_creation_id'} = shift @_ if( @_);
return $self->{'_creation_id'} || 0;
}
=head2 Bio::Node::NodeI decorated interface implemented
The following methods are implemented by L<Bio::Node::NodeI> decorated
interface.
=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) = @_;
my $isleaf = ! (defined $self->{'_desc'} &&
(keys %{$self->{'_desc'}} > 0) );
return $isleaf;
}
=head2 height
Title : height
Usage : my $len = $node->height
Function: Returns the height of the tree starting at this
node. Height is the maximum branchlength to get to the tip.
Returns : The longest length (weighting branches with branch_length) to a leaf
Args : none
=cut
sub height {
my ($self) = @_;
return $self->{'_height'} if( defined $self->{'_height'} );
return 0 if( $self->is_Leaf );
my $max = 0;
foreach my $subnode ( $self->each_Descendent ) {
my $bl = $subnode->branch_length;
$bl = 1 unless (defined $bl && $bl =~ /^\-?\d+(\.\d+)?$/);
my $s = $subnode->height + $bl;
if( $s > $max ) { $max = $s; }
}
return ($self->{'_height'} = $max);
}
=head2 invalidate_height
Title : invalidate_height
Usage : private helper method
Function: Invalidate our cached value of the node height in the tree
Returns : nothing
Args : none
=cut
sub invalidate_height {
my ($self) = @_;
$self->{'_height'} = undef;
if( defined $self->ancestor ) {
$self->ancestor->invalidate_height;
}
}
=head2 set_tag_value
Title : set_tag_value
Usage : $node->set_tag_value($tag,$value)
$node->set_tag_value($tag,@values)
Function: Sets a tag value(s) to a node. Replaces old values.
Returns : number of values stored for this tag
Args : $tag - tag name
$value - value to store for the tag
=cut
sub set_tag_value{
my ($self,$tag,@values) = @_;
if( ! defined $tag || ! scalar @values ) {
$self->warn("cannot call set_tag_value with an undefined value");
}
$self->remove_tag ($tag);
map { push @{$self->{'_tags'}->{$tag}}, $_ } @values;
return scalar @{$self->{'_tags'}->{$tag}};
}
=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
$value - value to store for the tag
=cut
sub add_tag_value{
my ($self,$tag,$value) = @_;
if( ! defined $tag || ! defined $value ) {
$self->warn("cannot call add_tag_value with an undefined value".($tag ? " ($tag)" : ''));
$self->warn($self->stack_trace_dump,"\n");
}
push @{$self->{'_tags'}->{$tag}}, $value;
return scalar @{$self->{'_tags'}->{$tag}};
}
=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 : $tag - tagname to remove
=cut
sub remove_tag {
my ($self,$tag) = @_;
if( exists $self->{'_tags'}->{$tag} ) {
$self->{'_tags'}->{$tag} = undef;
delete $self->{'_tags'}->{$tag};
return 1;
}
return 0;
}
=head2 remove_all_tags
Title : remove_all_tags
Usage : $node->remove_all_tags()
Function: Removes all tags
Returns : None
Args : None
=cut
sub remove_all_tags{
my ($self) = @_;
$self->{'_tags'} = {};
return;
}
=head2 get_all_tags
Title : get_all_tags
Usage : my @tags = $node->get_all_tags()
Function: Gets all the tag names for this Node
Returns : Array of tagnames
Args : None
=cut
sub get_all_tags{
my ($self) = @_;
my @tags = sort keys %{$self->{'_tags'} || {}};
return @tags;
}
=head2 get_tag_values
Title : get_tag_values
Usage : my @values = $node->get_tag_values($tag)
Function: Gets the values for given tag ($tag)
Returns : In array context returns an array of values
or an empty list if tag does not exist.
In scalar context returns the first value or undef.
Args : $tag - tag name
=cut
sub get_tag_values{
my ($self,$tag) = @_;
return wantarray ? @{$self->{'_tags'}->{$tag} || []} :
(@{$self->{'_tags'}->{$tag} || []})[0];
}
=head2 has_tag
Title : has_tag
Usage : $node->has_tag($tag)
Function: Boolean test if tag exists in the Node
Returns : Boolean
Args : $tag - tagname
=cut
sub has_tag {
my ($self,$tag) = @_;
return exists $self->{'_tags'}->{$tag};
}
sub node_cleanup {
my $self = shift;
return unless defined $self;
#*** below is wrong, cleanup doesn't actually occur. Will replace with:
# $self->remove_all_Descendents; once further fixes in place..
#if( defined $self->{'_desc'} &&
# ref($self->{'_desc'}) =~ /HASH/i ) {
# while( my ($nodeid,$node) = each %{ $self->{'_desc'} } ) {
# $node->ancestor(undef); # insure no circular references
# $node = undef;
# }
#}
$self->remove_all_Descendents;
#$self->{'_desc'} = {};
1;
}
=head2 reverse_edge
Title : reverse_edge
Usage : $node->reverse_edge(child);
Function: makes child be a parent of node
Requires: child must be a direct descendent of node
Returns : 1 on success, 0 on failure
Args : Bio::Tree::NodeI that is in the tree
=cut
sub reverse_edge {
my ($self,$node) = @_;
if( $self->delete_edge($node) ) {
$node->add_Descendent($self);
return 1;
}
return 0;
}
1;