Ewan Birney

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 email or the web:

  bioperl-bugs@bioperl.org
  http://bioperl.org/bioperl-bugs/

AUTHOR - Jason Stajich

Email jason@bioperl.org

Describe contact details here

CONTRIBUTORS

Additional contributors names and emails here

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)
           -desc      => 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

each_Descendent

 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

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)

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