Free node software for linux

XML::DOM::Node is a super class of all nodes in XML::DOM.

XML::DOM::Node is the super class of all nodes in an XML::DOM document. This means that all nodes that subclass XML::DOM::Node also inherit all the methods that XML::DOM::Node implements.

GLOBAL VARIABLES

@NodeNames

The variable @XML::DOM::Node::NodeNames maps the node type constants to strings. It is used by XML::DOM::Node::getNodeTypeName.

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

XML::LibXML::Node is an abstract base class of XML::LibXML nodes.

SYNOPSIS

$name = $node->nodeName;
$node->setNodeName( $newName );
$bool = $node->isSameNode( $other_node );
$bool = $node->isEqual( $other_node );
$content = $node->nodeValue;
$content = $node->textContent;
$type = $node->nodeType;
$node->unbindNode();
$childnode = $node->removeChild( $childnode );
$oldnode = $node->replaceChild( $newNode, $oldNode );
$node->replaceNode($newNode);
$childnode = $node->appendChild( $childnode );
$childnode = $node->addChild( $chilnode );
$node = $parent->addNewChild( $nsURI, $name );
$node->addSibling($newNode);
$newnode =$node->cloneNode( $deep );
$parentnode = $node->parentNode;
$nextnode = $node->nextSibling();
$prevnode = $node->previousSibling();
$boolean = $node->hasChildNodes();
$childnode = $node->firstChild;
$childnode = $node->lastChild;
$documentnode = $node->ownerDocument;
$node = $node->getOwner;
$node->setOwnerDocument( $doc );
$node->insertBefore( $newNode, $refNode );
$node->insertAfter( $newNode, $refNode );
@nodes = $node->findnodes( $xpath_expression );
$result = $node->find( $xpath );
print $node->findvalue( $xpath );
@childnodes = $node->childNodes;
$xmlstring = $node->toString($format,$docencoding);
$c14nstring = $node->toString($with_comments, $xpath_expression);
$str = $doc->serialze($format);
$c14nstr = $doc->serialize_c14n($comment_flag,$xpath);
$localname = $node->localname;
$nameprefix = $node->prefix;
$uri = $node->namespaceURI();
$boolean = $node->hasAttributes();
@attributelist = $node->attributes();
$URI = $node->lookupNamespaceURI( $prefix );
$prefix = $node->lookupNamespacePrefix( $URI );
$iter = $node->iterator;
$node->normalize;
@nslist = $node->getNamespaces;
$node->removeChildNodes();
$node->nodePath();
$lineno = $node->line_number();

XML::LibXML::Node defines functions that are common to all Node Types. A LibXML::Node should never be created standalone, but as an instance of a high level class such as LibXML::Element or LibXML::Text. The class itself should provide only common functionality. In XML::LibXML each node is part either of a document or a document-fragment. Because of this there is no node without a parent. This may causes confusion with "unbound" nodes.

Convert::Wiki::Node::Head is a Perl module that represents a headline node.

SYNOPSIS

use Convert::Wiki::Node::Head;

my $head = Convert::Wiki::Node->new( txt => About Foo, type => head1 );

print $head->as_wiki();

A Convert::Wiki::Node::Head represents a headline node in a text.

Convert::Wiki::Node::Line is a Perl module that represents a horizontal line (aka ruler).

SYNOPSIS

use Convert::Wiki::Node::Line;

my $hr = Convert::Wiki::Node::Line->new( );

print $hr->as_wiki();

A Convert::Wiki::Node::Line represents a horizontal line (aka ruler).

Convert::Wiki::Node::Item is a Perl module that represents an item in a list (aka < li > or *).

SYNOPSIS

use Convert::Wiki::Node::Item;

my $para = Convert::Wiki::Node->new( txt => Foo is a foobar., type => item );

print $para->as_wiki(); # print something like "* Foo is a foorbarn"

A Convert::Wiki::Node::Item represents an item in a list (aka the equivalent of < li > or *.