Bio::NEXUS::Node - Provides functions for manipulating nodes in trees
new Bio::NEXUS::Node;
Provides a few useful functions for nodes.
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).
Weigang Qiu (weigang@genectr.hunter.cuny.edu) Eugene Melamud (melamud@carb.nist.gov) Chengzhi Liang (liangc@umbi.umd.edu) Thomas Hladish (tjhladish at yahoo)
Peter Yang (pyang@rice.edu)
Title : new Usage : $node = new Bio::NEXUS::Node(); Function: Creates a new Bio::NEXUS::Node object Returns : Bio::NEXUS::Node object Args : none
Title : clone Usage : my $newblock = $block->clone(); Function: clone a block object (shallow) Returns : Block object Args : none
Title : get_seq Usage : $sequence = $node->get_seq(); Function: Returns the node's sequence Returns : sequence (string) Args : none
Title : set_seq Usage : $node->set_seq($sequence); Function: Sets sequence of the node Returns : none Args : sequence (string)
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)
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
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)
Title : length Usage : $length=$node->get_length(); Function: Returns the node's length Returns : length (integer) or undef if nonexistent Args : none
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
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)
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
Title : set_name Usage : $node->set_name($name); Function: Sets the node's name Returns : none Args : name (string/integer)
Title : get_name Usage : $name = $node->get_name(); Function: Returns the node's name Returns : name (integer/string) or undef if nonexistent Args : none
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
Title : add_childTU Usage : $node->add_child($node); Function: Adds a child to an existing node Returns : none Args : child (Bio::NEXUS::Node object)
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)
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)
Title : set_children Usage : $node->set_children($children); Function: Sets children Returns : $node Args : arrayref of children
Title : get_children Usage : @children = @{ $node->get_children() }; Function: Retrieves list of children Returns : array of children (Bio::NEXUS::Node objects) Args : none
Title : walk Usage : @descendents = $node->walk(); Function: Walks through tree and compiles a "clade list" (including $self and all inodes and otus descended from $self) Returns : array of nodes Args : generally, none, though walk() calls itself recurseively with 2 arguments: the node list so far, and a counting variable for inode-naming
Title : get_otus Usage : @listOTU = @{$node->get_otu()}; (?) Function: Retrieves list of OTUs Returns : reference to array of OTUs (Bio::NEXUS::Node objects) Args : none
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
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)
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)
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
Name : get_siblings Usage : $node->get_siblings(); Function: get sibling nodes of this node Returns : array ref of sibling nodes Args : none
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
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
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.
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
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
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
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
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
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
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
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 : $tag_name - a string representation of the tag
Title : set_nhx_tag Usage : node_obj->set_nhx_tag($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
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
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
Title : delete_all_nhx_tags Usage : $node_obj->delete_all_nhx_tags(); Function: Removes all tags from $nhx_obj Returns : Nothing Args : None
Title : nhx_command_to_string Usage : $node_obj->nhx_command_to_string(); Function: As NHX command string Returns : NHX command string Args : None
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
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)
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
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
To install Bio::NEXUS, copy and paste the appropriate command in to your terminal.
cpanm
cpanm Bio::NEXUS
CPAN shell
perl -MCPAN -e shell install Bio::NEXUS
For more information on module installation, please visit the detailed CPAN module installation guide.