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 = Bio::TreeIO->new(-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_all_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 attaching 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 AT bioperl DOT org - General discussion
http://bioperl.org/wiki/Mailing_lists - About the mailing lists

Support
Please direct usage questions or support issues to the mailing list:

bioperl-l AT bioperl DOT org

rather than to the module maintainer directly. Many experienced and reponsive experts will be able look at the problem and quickly address it. Please include a thorough description of the problem with code and data examples if at all possible.

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:

https://github.com/bioperl/bioperl-live/issues

AUTHOR - Jason Stajich

Email jason AT bioperl DOT org

CONTRIBUTORS

Aaron Mackey amackey AT virginia DOT 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 : $node->add_Descendent($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_all_Descendents
Title : get_all_Descendents($sortby)
Usage : my @nodes = $node->get_all_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", "alpha", "revalpha",
or a 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 to get to the tip.
Returns : The longest length (weighting branches with branch_length) to a leaf
Args : none

depth
Title : depth
Usage : my $len = $node->depth
Function: Returns the depth of the tree starting at this
node. Depth is the distance from this node to the root.
Returns : The branch length to the root.
Args : none

Get/Set methods
branch_length
Title : branch_length
Usage : $obj->branch_length()
Function: Get/Set the branch length
Returns : value of branch_length
Args : newvalue (optional)

id
Title : id
Usage : $obj->id($newval)
Function: The human readable identifier for the node
Returns : value of human readable 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: Get/Set the description string
Returns : value of description
Args : newvalue (optional)

bootstrap
Title : bootstrap
Usage : $obj->bootstrap($newval)
Function: Get/Set the bootstrap value
Returns : value of bootstrap
Args : newvalue (optional)

ancestor
Title : ancestor
Usage : my $node = $node->ancestor;
Function: Get/Set the ancestor node pointer for a 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 height in the tree
Returns : nothing
Args : none

Methods for associating Tag/Values with a Node
These methods associate tag/value pairs with a Node

set_tag_value
Title : set_tag_value
Usage : $node->set_tag_value($tag,$value)
$node->set_tag_value($tag,@values)
Function: Sets a tag value(s) to a node. Replaces old values.
Returns : number of values stored for this tag
Args : $tag - tag name
$value - value to store for the tag

add_tag_value
Title : add_tag_value
Usage : $node->add_tag_value($tag,$value)
Function: Adds a tag value to a node
Returns : number of values stored for this tag
Args : $tag - tag name
$value - value to store for the tag

remove_tag
Title : remove_tag
Usage : $node->remove_tag($tag)
Function: Remove the tag and all values for this tag
Returns : boolean representing success (0 if tag does not exist)
Args : $tag - tagname to remove

remove_all_tags
Title : remove_all_tags
Usage : $node->remove_all_tags()
Function: Removes all tags
Returns : None
Args : None

get_all_tags
Title : get_all_tags
Usage : my @tags = $node->get_all_tags()
Function: Gets all the tag names for this Node
Returns : Array of tagnames
Args : None

get_tag_values
Title : get_tag_values
Usage : my @values = $node->get_tag_values($tag)
Function: Gets the values for given tag ($tag)
Returns : Array of values or empty list if tag does not exist
Args : $tag - tag name

has_tag
Title : has_tag
Usage : $node->has_tag($tag)
Function: Boolean test if tag exists in the Node
Returns : Boolean
Args : $tag - tagname

Helper Functions
id_output
Title : id_output
Usage : my $id = $node->id_output;
Function: Return an id suitable for output in format like newick
so that if it contains spaces or ():; characters it is properly
quoted
Returns : $id string if $node->id has a value
Args : none