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
# 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";
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.
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 = $node->each_Descendent;
Function: all the descendents for this Node (but not their descendents
i.e. not a recursive fetchall)
Returns : Array of Bio::Tree::NodeI objects
Args : none |
Title : get_all_Descendents($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. |
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: Get/Set the branch length
Returns : value of branch_length
Args : newvalue (optional) |
Title : id
Usage : $obj->id($newval)
Function: The human readable identifier for the node
Returns : value of human readable id
Args : newvalue (optional) |
Title : internal_id
Usage : my $internalid = $node->internal_id
Function: Returns the internal unique id for this Node
Returns : unique id
Args : none |
Title : description
Usage : $obj->description($newval)
Function: Get/Set the description string
Returns : value of description
Args : newvalue (optional) |
Title : bootstrap
Usage : $obj->bootstrap($newval)
Function: Get/Set the bootstrap value
Returns : value of bootstrap
Args : newvalue (optional) |
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 |
Title : invalidate_height
Usage : private helper method
Function: Invalidate our cached value of the node height in the tree
Returns : nothing
Args : none |
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 |
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 |
Title : remove_all_tags
Usage : $node->remove_all_tags()
Function: Removes all tags
Returns : None
Args : None |
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 |
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 |
Title : has_tag
Usage : $node->has_tag($tag)
Function: Boolean test if tag exists in the Node
Returns : Boolean
Args : $tag - tagname |
Methods code
sub add_Descendent
{ my ($self,@args) = @_;
$self->throw_not_implemented(); } | sub each_Descendent
{ my ($self) = @_;
$self->throw_not_implemented(); } | sub get_all_Descendents
{ my ($self, $sortby) = @_;
$sortby ||= 'height';
my @nodes;
foreach my $node ( $self->each_Descendent($sortby) ) {
push @nodes, ($node->get_all_Descendents($sortby), $node);
}
return @nodes;} | sub is_Leaf
{ my ($self) = @_;
$self->throw_not_implemented();} | sub descendent_count
{ my ($self) = @_;
my $count = 0;
foreach my $node ( $self->each_Descendent ) {
$count += 1;
$node->can('descendent_count') ? $count += $node->descendent_count : next;
}
return $count;} | sub to_string
{ my ($self) = @_;
return join('',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 ) {
$self->debug(sprintf("Trying to calculate height of a node when a Node (%s) has an undefined branch_length\n",$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);} | sub branch_length
{ my ($self)= @_;
$self->throw_not_implemented();} | sub id
{ my ($self)= @_;
$self->throw_not_implemented();} | sub internal_id
{ my ($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(); } | sub add_tag_value
{ shift->throw_not_implemented(); } | sub remove_tag
{ shift->throw_not_implemented(); } | sub remove_all_tags
{ shift->throw_not_implemented(); } | sub get_all_tags
{ shift->throw_not_implemented(); } | sub get_tag_values
{ shift->throw_not_implemented(); } | sub has_tag
{ 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
the web:
http://bugzilla.bioperl.org/
| AUTHOR - Jason Stajich | Top |
The rest of the documentation details each of the object methods.
Internal methods are usually preceded with a _
| Decorated Interface methods | Top |
| Methods for associating Tag/Values with a Node | Top |
These methods associate tag/value pairs with a Node