/ 
bioperl-1.2.2
/ Bio::Tree::Node

NAME

Bio::Tree::Node - A Simple Tree Node

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.

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/MailList.shtml  - About the mailing lists

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:

http://bugzilla.bioperl.org/

AUTHOR - Jason Stajich

Email jason@bioperl.org

CONTRIBUTORS

Aaron Mackey amackey@virginia.edu

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 = 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)
           -description   => description of node
           -id            => unique id for node

add_Descendent

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
          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" or coderef to be used
           to sort the order of children nodes.

remove_Descendent

Title   : remove_Descendent
Usage   : $node->remove_Descedent($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 be 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 cleanedup - so
          a get_nodes from the Tree object would be a safe thing to do first
Returns : nothing
Args    : none

get_Descendents

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

ancestor

Title   : ancestor
Usage   : $obj->ancestor($newval)
Function: Set the Ancestor
Returns : value of ancestor
Args    : newvalue (optional)

branch_length

Title   : branch_length
Usage   : $obj->branch_length($newval)
Function:
Example :
Returns : value of branch_length
Args    : newvalue (optional)

bootstrap

Title   : bootstrap
Usage   : $obj->bootstrap($newval)
Function:
Example :
Returns : value of bootstrap
Args    : newvalue (optional)

description

Title   : description
Usage   : $obj->description($newval)
Function:
Example :
Returns : value of description
Args    : newvalue (optional)

id

Title   : id
Usage   : $obj->id($newval)
Function:
Example :
Returns : value of id
Args    : newvalue (optional)

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)

is_Leaf

Title   : is_Leaf
Usage   : if( $node->is_Leaf )
Function: Get Leaf status
Returns : boolean
Args    : none

to_string

Title   : to_string
Usage   : my $str = $node->to_string()
Function: For debugging, provide a node as a string
Returns : string
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.
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'e height in the tree
Returns : nothing
Args    : none