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Bio::NEXUS::Node 0.67

  Date Added: November 27, 2010  |  Visits: 900

Bio::NEXUS::Node

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Bio::NEXUS::Node is a Perl module that provides functions for manipulating nodes in trees. SYNOPSIS new Bio::NEXUS::Node; 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 nodes 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 nodes 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 nodes 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 nodes name Returns : none Args : name (string/integer) get_name Title : get_name Usage : $name = $node->get_name(); Function: Returns the nodes 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) distance Title : distance Usage : $distance = $node1->distance($node2); Function: Calculates tree distance from one node to another (?) Returns : distance (floating-point number) Args : node1, node2 (Bio::NEXUS::Node objects) to_string Title : to_string Usage : my $string; $root->tree_string($string, 0) Function: recursively builds Newick tree string from root to tips Returns : none Args : reference to string, boolean $remove_inode_names flag 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 nodes 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 nodes depth get_depth Title : get_depth Usage : $depth = $node->get_depth(); Function: Returns the nodes depth (number of generations removed from the root) in tree Returns : integer representing nodes 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.

Requirements: No special requirements
Platforms: Linux
Keyword: Args Bionexusnode Libraries Name Nexus Node Otus Parent Node Perl Module Programming Returns Title Usage
Users rating: 0/10

License: Freeware Size: 153.6 KB
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