The London Perl and Raku Workshop takes place on 26th Oct 2024. If your company depends on Perl, please consider sponsoring and/or attending.
 / 
BioPerl-1.007002
River stage two • 60 direct dependents • 65 total dependents
/ Bio::Tree::Node

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 \n" 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://github.com/bioperl/bioperl-live/issues

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