SYNOPSIS
use Bio::Tree::Node;
my $nodeA = Bio::Tree::Node->new();
my $nodeL = Bio::Tree::Node->new();
my $nodeR = Bio::Tree::Node->new();
my $node = Bio::Tree::Node->new();
$node->add_Descendent($nodeL);
$node->add_Descendent($nodeR);
print "node is not a leaf \n" if( $node->is_leaf);
DESCRIPTION
Makes a Tree Node suitable for building a Tree.FEEDBACK
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Reporting Bugs
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AUTHOR - Jason Stajich
Email jason-at-bioperl-dot-orgCONTRIBUTORS
Aaron Mackey, amackey-at-virginia-dot-edu Sendu Bala, [email protected]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 = Bio::Tree::Node->new(); Function: Builds a new Bio::Tree::Node object Returns : Bio::Tree::Node Args : -descendents => arrayref of descendents (they will be updated s.t. their ancestor point is this node) -branch_length => branch length [integer] (optional) -bootstrap => value bootstrap value (string) -description => description of node -id => human readable id for node
create_node_on_branch
Title : create_node_on_branch Usage : $node->create_node_on_branch($at_length) Function: Create a node on the ancestral branch of the calling object. Example : Returns : the created node Args : -POSITION=>$absolute_branch_length_from_caller (default) -FRACTION=>$fraction_of_branch_length_from_caller -ANNOT=>{ -id => "the id", -desc => "the description" } -FORCE, set to allow nodes with zero branch lengths
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 boolean flag, true if you want to ignore the fact that you are adding a second node with the same unique id (typically memory location reference in this implementation). default is false and will throw an error if you try and overwrite an existing node.
each_Descendent
Title : each_Descendent($sortby) 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 : $sortby [optional] "height", "creation", "alpha", "revalpha", or coderef to be used to sort the order of children nodes.
remove_Descendent
Title : remove_Descendent Usage : $node->remove_Descendent($node_foo); Function: Removes a specific node from being a Descendent of this node Returns : nothing Args : An array of Bio::Node::NodeI objects which have been previously passed to the add_Descendent call of this object.
remove_all_Descendents
Title : remove_all_Descendents Usage : $node->remove_All_Descendents() Function: Cleanup the node's reference to descendents and reset their ancestor pointers to undef, if you don't have a reference to these objects after this call they will be cleaned up - so a get_nodes from the Tree object would be a safe thing to do first Returns : nothing Args : none
get_all_Descendents
Title : get_all_Descendents 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 : none
ancestor
Title : ancestor Usage : $obj->ancestor($newval) Function: Set the Ancestor Returns : ancestral node Args : newvalue (optional)
branch_length
Title : branch_length Usage : $obj->branch_length() Function: Get/Set the branch length Returns : value of branch_length Args : newvalue (optional)
bootstrap
Title : bootstrap Usage : $obj->bootstrap($newval) Function: Get/Set the bootstrap value Returns : value of bootstrap Args : newvalue (optional)
description
Title : description Usage : $obj->description($newval) Function: Get/Set the description string Returns : value of description 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)
``A name can be any string of printable characters except blanks, colons, semicolons, parentheses, and square brackets. Because you may want to include a blank in a name, it is assumed that an underscore character (''_``) stands for a blank; any of these in a name will be converted to a blank when it is read in.''
from <http://evolution.genetics.washington.edu/phylip/newicktree.html>
Also note that these objects now support spaces, ();: because we can automatically quote the strings if they contain these characters. The id_output method does this for you so use the id() method to get the raw string while id_output to get the pre-escaped string.
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
internal_id
Title : internal_id Usage : my $internalid = $node->internal_id Function: Returns the internal unique id for this Node (a monotonically increasing number for this in-memory implementation but could be a database determined unique id in other implementations) Returns : unique id Args : none
_creation_id
Title : _creation_id Usage : $obj->_creation_id($newval) Function: a private method signifying the internal creation order Returns : value of _creation_id Args : newvalue (optional)
Bio::Node::NodeI decorated interface implemented
The following methods are implemented by Bio::Node::NodeI decorated interface.is_Leaf
Title : is_Leaf Usage : if( $node->is_Leaf ) Function: Get Leaf status Returns : boolean 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
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
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 : In array context returns an array of values or an empty list if tag does not exist. In scalar context returns the first value or undef. 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
reverse_edge
Title : reverse_edge Usage : $node->reverse_edge(child); Function: makes child be a parent of node Requires: child must be a direct descendent of node Returns : 1 on success, 0 on failure Args : Bio::Tree::NodeI that is in the tree