1GO::OntologyProvider(3)User Contributed Perl DocumentatioGnO::OntologyProvider(3)
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NAME

6       GO::OntologyProvider - abstract base class providing API for the
7       provision on Gene Ontology information
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DESCRIPTION

10       GO::OntologyProvider is an abstract class that defines an interface
11       that should be implemented by specific subclasses, which may read
12       ontology information from databases, flatfiles, XML files etc.
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14       All of the methods return either one or many GO::Node(s), and any
15       concrete subclass is expected to fully flesh out the such Node objects
16       with all the parents, children and paths to the root, such that any
17       node should return a true value when the isValid method is invoked on
18       it.
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Constructor

21       Because this is an abstract class, there is no constructor.  A
22       constructor must be implemented by concrete subclasses.
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Public instance methods

25       All of these public instance methods must be implemented by concrete
26       subclasses.
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28   allNodes
29       This method returns an array of all the GO::Nodes that have been
30       created.
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32       Usage:
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34           my @nodes = $ontologyProvider->allNodes;
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36   rootNode
37       This method returns the root node in the ontology.
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39       Usage:
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41               my $rootNode = $ontologyProvider->rootNode;
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43   nodeFromId
44       This method returns a GO::Node corresponding to the provided GOID,
45       should one exist.  Otherwise it returns undef.
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47       Usage:
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49               my $node = $ontologyProvider->nodeFromId("GO:0003673");
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51   numNodes
52       This method returns the number of nodes that exist within the ontology.
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54       Usage:
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56               my $numNodes = $ontologyProvider->numNodes;
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AUTHOR

59       Gavin Sherlock,  sherlock@genome.stanford.edu
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63perl v5.28.0                      2004-05-05           GO::OntologyProvider(3)