GO::OntologyProvider(3User Contributed Perl DocumentatiGO::OntologyProvider(3)NAMEGO::OntologyProvider - abstract base class providing API for the
provision on Gene Ontology information
DESCRIPTIONGO::OntologyProvider is an abstract class that defines an interface
that should be implemented by specific subclasses, which may read
ontology information from databases, flatfiles, XML files etc.
All of the methods return either one or many GO::Node(s), and any
concrete subclass is expected to fully flesh out the such Node objects
with all the parents, children and paths to the root, such that any
node should return a true value when the isValid method is invoked on
it.
Constructor
Because this is an abstract class, there is no constructor. A
constructor must be implemented by concrete subclasses.
Public instance methods
All of these public instance methods must be implemented by concrete
subclasses.
allNodes
This method returns an array of all the GO::Nodes that have been
created.
Usage:
my @nodes = $ontologyProvider->allNodes;
rootNode
This method returns the root node in the ontology.
Usage:
my $rootNode = $ontologyProvider->rootNode;
nodeFromId
This method returns a GO::Node corresponding to the provided GOID,
should one exist. Otherwise it returns undef.
Usage:
my $node = $ontologyProvider->nodeFromId("GO:0003673");
numNodes
This method returns the number of nodes that exist within the ontology.
Usage:
my $numNodes = $ontologyProvider->numNodes;
AUTHOR
Gavin Sherlock, sherlock@genome.stanford.edu
perl v5.14.1 2004-05-05 GO::OntologyProvider(3)
