GO::Node - provides information about a node in the Gene Ontology
The GO::Node package is intended to be used as a container for information about a node in one of the three Gene Ontologies. It allows the storage of the goid, and immediate parents and children, as well as paths to the top of the ontology. This package provides methods to both store and retrieve that information.
It should be strongly noted that clients are not expected to create individual Node objects themselves, but instead should rely in a Node Factory to create nodes and return them. Such a factory would be a concrete subclass of the abstract GO::OntologyProvider package.
The following items needs to be done at some point to make the Node class more flexible, and for it to better model the data.
Add in methods to deal with secondary GOIDs Add in methods to allow definitions to be associated with, and retrieved from Nodes. Add in methods to allow dbxrefs to be included. Not require Factories to add the paths to the root, but instead have this class generate those paths from the inherent structure of the graph in which the Nodes sit. This will also be useful to generate paths to leaves/descendants.
This protected method simply provides a simple way for concrete subclasses to deal with missing arguments from method calls. It will die with an appropriate error message.
Usage:
$self->_handleMissingArgument(argument=>'blah');
This is the constructor for the Node object At a minimum, the constructor expects, as named arguments, a GOID and a GO term, with which to create the node object.
my $node = GO::Node->new(goid => $goid, term => $term);
The public setter method allows a client to indicate that an array of nodes are children of the 'self' node. Only one node per child goid will get stored.
$node->addChildNodes(@childNodes);
The public setter method allows a client to indicate that an array of nodes are parents of the 'self' node. Only one node per parent goid will get stored.
$node->addParentNodes(@parentNodes);
This public setter method expects an array of nodes, that indicates a direct path to the root of the ontology. The array should not contain the self node, but should contain the root node. The last entry in the array is expected to be an immediate parent of the self node, while the first entry is expected to be the root node itself. This method will NOT check to see if the supplied path has not already been added. It is the Node Factory's responsibility to only add a unique path once. Furthermore, it will not check whether there is consistency between addedPaths and addedParents (this can be done using the isValid method though).
$node->addPathToRoot(@nodes);
This public method returns the goid associated with the node.
my $goid = $node->goid;
This public method returns the term associated with the node.
my $goid = $node->term;
This public method returns an array of child nodes for the self node.
my @childNodes = $node->childNodes;
This public method returns an array of parent nodes for the self node.
my @parentNodes = $node->parentNodes;
This public method returns an array of references to arrays, each of which contains the nodes in a path between the self node and the root. The self node is not included in the paths, but the root node is. The first node in each array is the most distant ancestor (the root), the last node is an immediate parent. If there are no paths to the root (i.e. it is the root node) then an empty array will be returned.
my @pathsToRoot = $node->pathsToRoot;
This public method returns an array of references to arrays, each of which contains the nodes in a path between the self node and the specified ancestor. The self node is not included paths, but the specified ancestor node is. The first node in each array is the specified ancestor, the last node is an immediate parent. If there are no paths to the ancestor then an empty array will be returned.
my @pathsToAncestor = $node->pathsToAncestor($ancestorNode);
This public method returns an array of unique GO::Nodes which are the unique ancestors that a node has. These ancestors will be derived from the paths to the root node that have been added to the node.
my @ancestors = $node->ancestors;
This public method returns the length of the longest path to the root of the ontology from the node. If the node is in fact the root, then a value of zero will be returned.
my $length = $node->lengthOfLongestPathToRoot;
This public method returns the length of the shortest path to the root of the ontology from the node. If the node is in fact the root, then a value of zero will be returned.
my $length = $node->lengthOfShortestPathToRoot;
This public method returns the mean length of all paths to the root node. If the node is in fact the root, then a value of zero will be returned.
my $length = $node->meanLengthOfPathsToRoot;
This method can be used to check that a node has been constructed correctly. It checks that it is a child of all its parents, and a parent of all of its children. In addition, it checks that parents exist as the most recent ancestors of the node in its paths to the root node, and vice versa. It returns a boolean.
if ($node->isValid){ # do something }
This public method returns a boolean to indicate whether a node has the supplied node as a child.
Usage :
if ($node->isAParentOf($anotherNode)){ # blah }
This public method returns a boolean to indicate whether a node has the supplied node as a parent.
if ($node->isAChildOf($anotherNode)){ # blah }
This method returns a boolean to indicate whether a node is an ancestor of another.
if ($node->isAnAncestorOf($anotherNode)){ # blah }
This method returns a boolean to indicate whether a node is a descendant of another.
if ($node->isADescendantOf($anotherNode)){ # blah }
This method returns a boolean to indicate whether a node is a leaf in the ontology (i.e. it has no children).
if ($node->isLeaf){ # blah }
This method returns a boolean to indicate whether a node is the root in the ontology (i.e. it has no parents).
if ($node->isRoot){ # blah }
Gavin Sherlock; sherlock@genome.stanford.edu
To install GO::TermFinder, copy and paste the appropriate command in to your terminal.
cpanm
cpanm GO::TermFinder
CPAN shell
perl -MCPAN -e shell install GO::TermFinder
For more information on module installation, please visit the detailed CPAN module installation guide.