GO::Node(3) User Contributed Perl Documentation GO::Node(3)NAMEGO::Node - provides information about a node in the Gene Ontology
DESCRIPTION
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.
TODO
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.
Protected Methods
_handleMissingArgument
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');
Instance Constructor
new
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.
Usage:
my $node = GO::Node->new(goid => $goid,
term => $term);
Instance Methods
addChildNodes
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.
Usage:
$node->addChildNodes(@childNodes);
addParentNodes
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.
Usage:
$node->addParentNodes(@parentNodes);
addPathToRoot
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).
Usage:
$node->addPathToRoot(@nodes);
goid
This public method returns the goid associated with the node.
Usage:
my $goid = $node->goid;
term
This public method returns the term associated with the node.
Usage:
my $goid = $node->term;
childNodes
This public method returns an array of child nodes for the self node.
Usage:
my @childNodes = $node->childNodes;
parentNodes
This public method returns an array of parent nodes for the self node.
Usage:
my @parentNodes = $node->parentNodes;
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 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.
Usage:
my @pathsToRoot = $node->pathsToRoot;
pathsToAncestor
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.
Usage:
my @pathsToAncestor = $node->pathsToAncestor($ancestorNode);
ancestors
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.
Usage:
my @ancestors = $node->ancestors;
lengthOfLongestPathToRoot
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.
Usage:
my $length = $node->lengthOfLongestPathToRoot;
lengthOfShortestPathToRoot
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.
Usage:
my $length = $node->lengthOfShortestPathToRoot;
meanLengthOfPathsToRoot
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.
Usage:
my $length = $node->meanLengthOfPathsToRoot;
isValid
This method can be used to check that a node has been constructed
correctly. It checks that it is a child of all its parents, and a
parent of all of its children. In addition, it checks that parents
exist as the most recent ancestors of the node in its paths to the root
node, and vice versa. It returns a boolean.
Usage:
if ($node->isValid){
# do something
}
isAParentOf
This public method returns a boolean to indicate whether a node has the
supplied node as a child.
Usage :
if ($node->isAParentOf($anotherNode)){
# blah
}
isAChildOf
This public method returns a boolean to indicate whether a node has the
supplied node as a parent.
Usage :
if ($node->isAChildOf($anotherNode)){
# blah
}
isAnAncestorOf
This method returns a boolean to indicate whether a node is an ancestor
of another.
Usage:
if ($node->isAnAncestorOf($anotherNode)){
# blah
}
isADescendantOf
This method returns a boolean to indicate whether a node is a
descendant of another.
Usage:
if ($node->isADescendantOf($anotherNode)){
# blah
}
isLeaf
This method returns a boolean to indicate whether a node is a leaf in
the ontology (i.e. it has no children).
Usage:
if ($node->isLeaf){
# blah
}
isRoot
This method returns a boolean to indicate whether a node is the root in
the ontology (i.e. it has no parents).
Usage:
if ($node->isRoot){
# blah
}
Authors
Gavin Sherlock; sherlock@genome.stanford.edu
perl v5.14.1 2007-11-15 GO::Node(3)
