Ewan Birney

NAME

Bio::Tree::NodeI - Interface describing a Tree Node

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

    my $rootnode = $tree->get_root_node;

    # process just the next generation
    foreach my $node ( $tree->each_Descendent() ) {
        print "branch len is ", $node->branch_length, "\n";
    }
    # process all the children
    foreach my $node ( $tree->get_Descendents() ) {
        if( $node->is_Leaf ) { 
            print "node is a leaf ... "; 
        }
        print "branch len is ", $node->branch_length, "\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.

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 _

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

Decorated Interface methods

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

is_Leaf

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

descendent_count

 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

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

Get/Set methods

branch_length

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

id

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

description

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

bootstrap

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

ancestor

 Title   : ancestor
 Usage   : my $node = $node->ancestor;
 Function: Get/Set a Node's ancestor node
 Returns : Null if this is top level node
 Args    : none