/ 
Bio-NEXUS-0.76
River stage one • 1 direct dependent • 1 total dependent
/ Bio::NEXUS::Node

NAME

Bio::NEXUS::Node - Provides functions for manipulating nodes in trees

SYNOPSIS

new Bio::NEXUS::Node;

DESCRIPTION

Provides a few useful functions for nodes.

FEEDBACK

All feedback (bugs, feature enhancements, etc.) are all greatly appreciated. There are no mailing lists at this time for the Bio::NEXUS::Node module, so send all relevant contributions to Dr. Weigang Qiu (weigang@genectr.hunter.cuny.edu).

AUTHORS

Weigang Qiu (weigang@genectr.hunter.cuny.edu)
Eugene Melamud (melamud@carb.nist.gov)
Chengzhi Liang (liangc@umbi.umd.edu)
Thomas Hladish (tjhladish at yahoo)

CONTRIBUTORS

Peter Yang (pyang@rice.edu)

METHODS

new

Title   : new
Usage   : $node = new Bio::NEXUS::Node();
Function: Creates a new Bio::NEXUS::Node object
Returns : Bio::NEXUS::Node object
Args    : none

clone

Title   : clone
Usage   : my $newblock = $block->clone();
Function: clone a block object (shallow)
Returns : Block object
Args    : none

get_seq

Title   : get_seq
Usage   : $sequence = $node->get_seq();
Function: Returns the node's sequence
Returns : sequence (string)
Args    : none

set_seq

Title   : set_seq
Usage   : $node->set_seq($sequence);
Function: Sets sequence of the node
Returns : none
Args    : sequence (string)

set_parent_node

Title   : set_parent_node
Usage   : $node->set_parent_node($parent);
Function: Sets the parent node of the node
Returns : none
Args    : parent node (Bio::NEXUS::Node object)

get_parent

Title   : get_parent
Usage   : $parent=$node->get_parent();
Function: Returns the parent node of the node
Returns : parent node (Bio::NEXUS::Node object) or undef if nonexistent
Args    : none

set_length

Title   : set_length
Usage   : $node->set_length($length);
Function: Sets the node's length (meaning the length of the branch leading to the node)
Returns : none
Args    : length (number)

get_length

Title   : length
Usage   : $length=$node->get_length();
Function: Returns the node's length
Returns : length (integer) or undef if nonexistent
Args    : none

get_total_length

Title   : get_total_length
Usage   : $total_length = $node->get_total_length();
Function: Gets the total branch length of the node and that of all the children (???)
Returns : total branch length
Args    : none

set_support_value

Title   : set_support_value
Usage   : $node->set_support_value($bootstrap);
Function: Sets the branch support value associated with this node
Returns : none
Args    : bootstrap value (integer)

get_support_value

Title   : get_support_value
Usage   : $bootstrap = $node->get_support_value();
Function: Returns the branch support value associated with this node
Returns : bootstrap value (integer) or undef if nonexistent
Args    : none

set_name

Title   : set_name
Usage   : $node->set_name($name);
Function: Sets the node's name
Returns : none
Args    : name (string/integer)

get_name

Title   : get_name
Usage   : $name = $node->get_name();
Function: Returns the node's name
Returns : name (integer/string) or undef if nonexistent
Args    : none

is_otu

Title   : is_otu
Usage   : $node->is_otu();
Function: Returns 1 if the node is an OTU or 0 if it is not (internal node)
Returns : 1 or 0
Args    : none

add_child

Title   : add_childTU
Usage   : $node->add_child($node);
Function: Adds a child to an existing node
Returns : none
Args    : child (Bio::NEXUS::Node object)

get_distance

Title   : get_distance
Usage   : $distance = $node1->get_distance($node2);
Function: Calculates tree distance from one node to another (?)
Returns : distance (floating-point number)
Args    : target node (Bio::NEXUS::Node objects)

to_string

Title   : to_string
Usage   : my $string; $root->tree_string(\$string, 0, $format)
Function: recursively builds Newick tree string from root to tips 
Returns : none
Args    : reference to string, boolean $remove_inode_names flag, string - $format (NHX or STD)

set_children

Title   : set_children
Usage   : $node->set_children($children);
Function: Sets children
Returns : $node
Args    : arrayref of children

get_children

Title   : get_children
Usage   : @children = @{ $node->get_children() };
Function: Retrieves list of children
Returns : array of children (Bio::NEXUS::Node objects)
Args    : none

walk

Title   : walk
Usage   : @descendents = $node->walk();
Function: Walks through tree and compiles a "clade list" 
    (including $self and all inodes and otus descended from $self)
Returns : array of nodes
Args    : generally, none, though walk() calls itself recurseively with 
    2 arguments: the node list so far, and a counting variable for inode-naming

get_otus

Title   : get_otus
Usage   : @listOTU = @{$node->get_otu()}; (?)
Function: Retrieves list of OTUs
Returns : reference to array of OTUs (Bio::NEXUS::Node objects)
Args    : none

printall

Title   : printall
Usage   : $tree_as_string = $self->printall(); 
Function: Gets the node properties as a tabbed string for printing nicely 
          formatted trees (developed by Tom)
Returns : Formatted string
Args    : Bio::NEXUS::Node object

find

Title   : find
Usage   : $node = $node->find($name);
Function: Finds the first occurrence of a node called 'name' in the tree
Returns : Bio::NEXUS::Node object
Args    : name (string)

prune

Name    : prune
Usage   : $node->prune($OTUlist);
Function: Removes everything from the tree except for OTUs specified in $OTUlist
Returns : none
Args    : list of OTUs (string)

equals

Name    : equals
Usage   : $node->equals($another_node);
Function: compare if two nodes (and their subtrees) are equivalent
Returns : 1 if equal or 0 if not
Args    : another Node object

get_siblings

Name    : get_siblings
Usage   : $node->get_siblings();
Function: get sibling nodes of this node
Returns : array ref of sibling nodes
Args    : none

is_sibling

Name    : is_sibling
Usage   : $node1->is_sibling($node2);
Function: tests whether node1 and node2 are siblings
Returns : 1 if true, 0 if false
Args    : second node

adopt

Title   : adopt
Usage   : $parent->adopt($child, $overwrite_children);
Function: make a parent-child relationship between two nodes
Returns : none
Args    : the child node, boolean clobber flag

combine

 Title   : combine
 Usage   : my $newblock = $node->combine($child);
 Function: removes a node from the tree, effectively by sliding its only child up the branch to its former position
 Returns : none
 Args    : the child node
 Methods : Combines the child node and the current node by assigning the
           name, bootstrap value, children and other properties of the child.  The branch length
	   of the current node is added to the child node's branch length.

set_depth

Title   : set_depth
Usage   : $root->set_depth();
Function: Determines depth in tree of every node below this one
Returns : none
Args    : This node's depth

get_depth

Title   : get_depth
Usage   : $depth = $node->get_depth();
Function: Returns the node's depth (number of 'generations' removed from the root) in tree
Returns : integer representing node's depth
Args    : none

find_lengths

Title   : find_lengths
Usage   : $cladogram = 1 unless $root->find_lengths();
Function: Tries to determine if branch lengths are present in the tree
Returns : 1 if lengths are found, 0 if not
Args    : none

mrca

Title     : mrca
Usage     : $mrca = $otu1-> mrca($otu2, $treename);
Function  : Finds most recent common ancestor of otu1 and otu2
Returns   : Node object of most recent common ancestor
Args      : Nexus object, two otu objects, name of tree to look in

get_mrca_of_otus

Title     : get_mrca_of_otus
Usage     : $mrca = $root->get_mrca_of_otus(\@otus);
Function  : Finds most recent common ancestor of set of OTUs
Returns   : Node object of most recent common ancestor
Args      : Nexus object, two otu objects, name of tree to look in

contains_nhx_tag

Title : contains_nhx_tag Usage : $node_obj->_contains_nhx_tag($tag_name) Function: Checks if a given tag exists Returns : 1 if the tax exists, 0 if it doesn't Args : $tag_name - a string representation of a tag

get_nhx_tags

Title : get_nhx_tags Usage : $node_obj->get_nhx_tags(); Function: Reads and returns an array of tags Returns : An array of tags Args : None

get_nhx_values

Title : get_nhx_values Usage : $node_obj->get_nhx_values($tag_name); Function: Returns the list of values associated with a given tag ($tag_name) Returns : Array of values Args : $tag_name - a string representation of the tag

set_nhx_tag

Title : set_nhx_tag Usage : node_obj->set_nhx_tag($tag_name, $tag_reference); Function: Updates the list of values associated with a given tag Returns : Nothing Args : $tag_name - a string, $tag_reference - an array-reference

add_nhx_tag_value

Title : add_nhx_tag_value Usage : $node_obj->add_nhx_tag_value($tag_name, $tag_value); Function: Adds a new tag/value set to the $nhx_obj; Returns : Nothing Args : $tag_name - a string, $tag_reference - an array-reference

delete_nhx_tag

Title : delete_nhx_tag Usage : $node_obj->delete_nhx_tag($tag_name); Function: Removes a given tag (and the associated valus) from the $nhx_obj Returns : Nothing Args : $tag_name - a string representation of the tag

delete_all_nhx_tags

Title : delete_all_nhx_tags Usage : $node_obj->delete_all_nhx_tags(); Function: Removes all tags from $nhx_obj Returns : Nothing Args : None

nhx_command_to_string

Title : nhx_command_to_string Usage : $node_obj->nhx_command_to_string(); Function: As NHX command string Returns : NHX command string Args : None

clone_nhx_command

Title : clone_nhx_command Usage : $some_node_obj->clone_nhx_command($original_node); Function: Copies the data of the NHX command of the $original_node object into the NHX command of the $some_node_obj Returns : Nothing Args : $original_node - Bio::NEXUS::NHXCmd object whose NHX command data will be cloned

check_nhx_tag_value_present

Title : check_nhx_tag_value Usage : $boolean = nhx_obj->check_nhx_tag_value($tag_name, $value); Function: check whether a particular value is present in a tag Returns : 0 or 1 [ true or false] Args : $tag_name - a string, $value - scalar (string or number)

set_nhx_obj

Title : set_nhx_obj Usage : $node->set_nhx_obj($nhx_obj); Function: Sets Bio::NEXUS::NHXCmd object associated with this node Returns : Nothing Args : Reference of the NHXCmd object othing

get_nhx_obj

Title : get_nhx_obj Usage : $nhx_obj = get_nhx_obj(); Function: Returns Bio::NEXUS::NHXCmd object associated with this node Returns : Reference of the NHXCmd object Args : Nothing