Package org.biojava.nbio.ontology
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Interface Summary Interface Description Ontology An ontology.OntologyFactory A factory for Ontology instances.OntologyOps This is an interface for optimizing ontology operators.OntologyTerm A term in an ontology which identifies another ontology.RemoteTerm A term in another ontology.Term A term in an ontology.Triple A triple in an ontology.Variable -
Class Summary Class Description AbstractTerm Abstract implementation of term This provides basic change-forwarding functionality from the annotation and ontology properties.App Hello world!DefaultOps Default implementation of OntologyOps.IntegerOntology Ontology.Impl A basic in-memory implementation of an ontologyOntologyTerm.Impl Simple in-memory implementation of a remote ontology term.OntoTools Tools for manipulating ontologies.RemoteTerm.Impl Simple in-memory implementation of a remote ontology term.Synonym Term.Impl Simple in-memory implementation of an ontology term.Triple.Impl Basic in-memory implementation of a Triple in an ontology This can be used to implement Ontology.createTripleVariable.Impl -
Exception Summary Exception Description AlreadyExistsException Thrown to indicate that a term or triple can't be added to an ontology because it is already present.InvalidTermException Thrown to indicate that an ontology term is not acceptable or appropriate in a given contextOntologyException Thrown to indicate an error in an Ontology object