/ 
bioperl-1.0.2
/ Bio::Tree::NodeI

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

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