Bio::Tree
NodeI
Summary
Bio::Tree::NodeI - Interface describing a Tree Node
Package variables
No package variables defined.
Included modules
Inherit
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
my $rootnode = $tree->get_root_node;
# process just the next generation
foreach my $node ( $tree->each_Descendent() ) {
print "branch len is ", $node->branch_length, "\n";
}
# process all the children
foreach my $node ( $tree->get_Descendents() ) {
if( $node->is_Leaf ) {
print "node is a leaf ... ";
}
print "branch len is ", $node->branch_length, "\n";
}
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.
Methods
Methods description
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 : 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 : is_Leaf
Usage : if( $node->is_Leaf )
Function: Get Leaf status
Returns : boolean
Args : none |
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 |
Title : to_string
Usage : my $str = $node->to_string()
Function: For debugging, provide a node as a string
Returns : string
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 : branch_length
Usage : $obj->branch_length()
Function:
Example :
Returns : value of branch_length
Args : newvalue (optional) |
Title : id
Usage : $obj->id($newval)
Function:
Example :
Returns : value of id
Args : newvalue (optional) |
Title : description
Usage : $obj->description($newval)
Function:
Example :
Returns : value of description
Args : newvalue (optional) |
Title : bootstrap
Usage : $obj->bootstrap($newval)
Function:
Example :
Returns : value of bootstrap
Args : newvalue (optional) |
Title : ancestor
Usage : my $node = $node->ancestor;
Function: Get/Set a Node's ancestor node
Returns : Null if this is top level node
Args : none |
Title : invalidate_height
Usage : private helper method
Function: Invalidate our cached value of the node'e height in the tree
Returns : nothing
Args : none |
Methods code
sub add_Descendent
{ my ($self,@args) = @_;
$self->throw_not_implemented(); } | sub each_Descendent
{ my ($self) = @_;
$self->throw_not_implemented(); } | sub get_Descendents
{ my ($self) = @_;
my @nodes;
foreach my $node ( $self->each_Descendent ) {
push @nodes, ($node->get_Descendents, $node);
}
return @nodes;} | sub is_Leaf
{ my ($self) = @_;
$self->throw_not_implemented();} | sub descendent_count
{ my ($self) = @_;
my $count = 0;
foreach my $node ( $self->each_Descendent ) {
$count += 1 + $node->descendent_count;
}
return $count;} | sub to_string
{ my ($self) = @_;
return sprintf("%s%s",defined $self->id ? $self->id : '',
defined $self->branch_length ?
":" . $self->branch_length : ' ');} | sub height
{ my ($self) = @_;
if( $self->is_Leaf ) {
if( !defined $self->branch_length ) {
$self->debug(sprintf("Trying to calculate height of a node when a Node (%s) has an undefined branch_length",$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 || 0);} | sub branch_length
{ my ($self)= @_;
$self->throw_not_implemented();} | sub id
{ my ($self)= @_;
$self->throw_not_implemented();} | sub description
{ my ($self) = @_;
$self->throw_not_implemented();} | sub bootstrap
{ my ($self) = @_;
$self->throw_not_implemented();} | sub ancestor
{ my ($self,@args) = @_;
$self->throw_not_implemented();} | sub invalidate_height
{ shift->throw_not_implemented(); } | 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 _
| Decorated Interface methods | Top |