Bio::Tree::Node(3pm) User Contributed Perl Documentation Bio::Tree::Node(3pm)
NAME
Bio::Tree::Node - A Simple Tree Node
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
" if( $node->is_leaf);
DESCRIPTION
Makes a Tree Node suitable for building a Tree.
FEEDBACK
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
Support
Please direct usage questions or support issues to the mailing list:
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.
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/
AUTHOR - Jason Stajich
Email jason-at-bioperl-dot-org
CONTRIBUTORS
Aaron Mackey, amackey-at-virginia-dot-edu Sendu Bala, bix@sendu.me.uk
APPENDIX
The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _
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
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
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.
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.
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.
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
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
ancestor
Title : ancestor
Usage : $obj->ancestor($newval)
Function: Set the Ancestor
Returns : ancestral node
Args : newvalue (optional)
branch_length
Title : branch_length
Usage : $obj->branch_length()
Function: Get/Set the branch length
Returns : value of branch_length
Args : newvalue (optional)
bootstrap
Title : bootstrap
Usage : $obj->bootstrap($newval)
Function: Get/Set the bootstrap value
Returns : value of bootstrap
Args : newvalue (optional)
description
Title : description
Usage : $obj->description($newval)
Function: Get/Set the description string
Returns : value of description
Args : newvalue (optional)
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 <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
id_output method does this for you so use the id() method to get the raw string while id_output to get the pre-escaped string.
Helper Functions
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
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
_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)
Bio::Node::NodeI decorated interface implemented
The following methods are implemented by Bio::Node::NodeI decorated interface.
is_Leaf
Title : is_Leaf
Usage : if( $node->is_Leaf )
Function: Get Leaf status
Returns : boolean
Args : none
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
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
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
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
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
remove_all_tags
Title : remove_all_tags
Usage : $node->remove_all_tags()
Function: Removes all tags
Returns : None
Args : None
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
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
has_tag
Title : has_tag
Usage : $node->has_tag($tag)
Function: Boolean test if tag exists in the Node
Returns : Boolean
Args : $tag - tagname
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
perl v5.14.2 2012-03-02 Bio::Tree::Node(3pm)