/ 
bioperl-1.2.2
/ 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
                                   # you might want to test that it was defined

    my $rootnode = $tree->get_root_node;

    # process just the next generation
    foreach my $node ( $rootnode->each_Descendent() ) {
	print "branch len is ", $node->branch_length, "\n";
    }

    # process all the children
    my $example_leaf_node;
    foreach my $node ( $rootnode->get_Descendents() ) {
	if( $node->is_Leaf ) { 
	    print "node is a leaf ... "; 
            # for example use below
            $example_leaf_node = $node unless defined $example_leaf_node; 
	}
	print "branch len is ", $node->branch_length, "\n";
    }

    # The ancestor() method points to the parent of a node
    # A node can only have one parent

    my $parent = $example_leaf_node->ancestor;

    # parent won't likely have an description because it is an internal node
    # but child will because it is a leaf

    print "Parent id: ", $parent->id," child id: ", 
          $example_leaf_node->id, "\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.

Various implementations of NodeI may extend the basic functions and allow storing of other information (like attatching a species object or full sequences used to build a tree or alternative sequences). If you don't know how to extend a Bioperl object please ask, happy to help, we would also greatly appreciate contributions with improvements or extensions of the objects back to the Bioperl code base so that others don't have to reinvent your ideas.

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 _

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($sortby)
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    : $sortby [optional] "height", "creation" or coderef to be used
          to sort the order of children nodes.

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)

internal_id

Title   : internal_id
Usage   : my $internalid = $node->internal_id
Function: Returns the internal unique id for this Node
Returns : unique id
Args    : none

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