Bio::Tree
Node
Summary
Bio::Tree::Node - A Simple Tree Node
Package variables
No package variables defined.
Included modules
Inherit
Synopsis
use Bio::Tree::Node;
my $nodeA = new Bio::Tree::Node();
my $nodeL = new Bio::Tree::Node();
my $nodeR = new Bio::Tree::Node();
my $node = new Bio::Tree::Node();
$node->add_Descendents($nodeL);
$node->add_Descendents($nodeR);
print "node is not a leaf \n" if( $node->is_leaf);
Description
Makes a Tree Node suitable for building a Tree.
Methods
Methods description
Title : new
Usage : my $obj = new Bio::Tree::Node();
Function: Builds a new Bio::Tree::Node object
Returns : Bio::Tree::Node
Args : -left => pointer to Left descendent (optional)
-right => pointer to Right descenent (optional)
-branch_length => branch length [integer] (optional)
-bootstrap => value bootstrap value (string)
-desc => description of node
-id => unique id for node |
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 |
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 |
Title : ancestor
Usage : $obj->ancestor($newval)
Function: Set the Ancestor
Returns : value of ancestor
Args : newvalue (optional) |
Title : branch_length
Usage : $obj->branch_length($newval)
Function:
Example :
Returns : value of branch_length
Args : newvalue (optional) |
Title : bootstrap
Usage : $obj->bootstrap($newval)
Function:
Example :
Returns : value of bootstrap
Args : newvalue (optional) |
Title : description
Usage : $obj->description($newval)
Function:
Example :
Returns : value of description
Args : newvalue (optional) |
Title : id
Usage : $obj->id($newval)
Function:
Example :
Returns : value of id
Args : newvalue (optional) |
Title : is_Leaf
Usage : if( $node->is_Leaf )
Function: Get Leaf status
Returns : boolean
Args : none |
Title : height
Usage : my $len = $node->height
Function: Returns the height of the tree starting at this
node. Height is the maximum branchlength.
Returns : The longest length (weighting branches with branch_length) to a leaf
Args : none |
Title : invalidate_height
Usage : private helper method
Function: Invalidate our cached value of the node'e height in the tree
Returns : nothing
Args : none |
Methods code
sub new
{ my($class,@args) = @_;
my $self = $class->SUPER::new(@args);
my ($children, $branchlen,$id,
$bootstrap, $desc) = $self->_rearrange([qw(DESCENDENTS
BRANCH_LENGTH
ID
BOOTSTRAP
DESC
)],
@args);
$self->{'_desc'} = {};
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->warn("Must specify a valid ARRAY reference to initialize a Node's Descendents");
}
foreach my $c ( @$children ) {
$self->add_Descendent($c);
}
}
return $self;} | sub add_Descendent
{ my ($self,$node) = @_;
return -1 if( ! defined $node ) ;
if( ! $node->isa('Bio::Tree::NodeI') ) {
$self->warn("Trying to add a Descendent who is not a Bio::Tree::NodeI");
return -1;
}
$node->ancestor($self);
$self->{'_desc'}->{$node} = $node;
$self->invalidate_height;
return scalar keys %{$self->{'_desc'}};} | sub each_Descendent
{ my ($self) = @_;
return sort { $a->height <=> $b->height } values %{$self->{'_desc'}}; } | sub ancestor
{ my ($self,$value) = @_;
if( defined $value) {
if(! $value->isa('Bio::Tree::NodeI') ) {
$self->throw("Must specify a valid Bio::Tree::NodeI when setting the ancestor");
}
$self->{'_ancestor'} = $value;
}
return $self->{'_ancestor'};} | sub branch_length
{ my ($self,$value) = @_;
if( defined $value) {
$self->{'branch_length'} = $value;
}
return $self->{'branch_length'};} | sub bootstrap
{ my ($self,$value) = @_;
if( defined $value ) {
$self->{'_bootstrap'} = $value;
}
return $self->{'_bootstrap'};} | sub description
{ my ($self,$value) = @_;
if( defined $value ) {
$self->{'_description'} = $value;
}
return $self->{'_description'};} | sub id
{ my ($self,$value) = @_;
if( defined $value ) {
$self->{'_id'} = $value;
}
return $self->{'_id'};} | sub DESTROY
{ my ($self) = @_;
$self->SUPER::DESTROY();
if( defined $self->{'_desc'} &&
ref($self->{'_desc'}) =~ /ARRAY/i ) {
foreach my $n ( @{$self->{'_desc'}} ) {
$n->DESTROY();
}
$self->{'_desc'} = {};
}} | sub is_Leaf
{ my ($self) = @_;
my $rc = 0;
$rc = 1 if( ! defined $self->{'_desc'} ||
keys %{$self->{'_desc'}} == 0);
return $rc;} | sub height
{ my ($self) = @_;
return $self->{'_height'} if( defined $self->{'_height'} );
if( $self->is_Leaf ) {
if( !defined $self->branch_length ) {
$self->debug(sprintf("Trying to calculate height of a node when a Node (%s) has an undefined branch_length",$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 = $s; }
}
return ($self->{'_height'} = $max + ($self->branch_length || 1));} | sub invalidate_height
{ my ($self) = @_;
$self->{'_height'} = undef;
if( $self->ancestor ) {
$self->ancestor->invalidate_height;
}} | General documentation
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
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
email or the web:
bioperl-bugs@bioperl.org
http://bioperl.org/bioperl-bugs/
| AUTHOR - Jason Stajich | Top |
Additional contributors names and emails here
The rest of the documentation details each of the object methods.
Internal methods are usually preceded with a _
Title : get_Descendents
Usage : my @nodes = $node->get_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 Title : to_string
Usage : my $str = $node->to_string()
Function: For debugging, provide a node as a string
Returns : string
Args : none