All Classes

Class	Description
AbstractAnnotation	A utility class to ease the problem of implementing an Annotation to that of providing an apropreate implementation of Map.
AbstractTerm	Abstract implementation of term This provides basic change-forwarding functionality from the annotation and ontology properties.
AlreadyExistsException	Thrown to indicate that a term or triple can't be added to an ontology because it is already present.
Annotatable	Indicates that an object has an associated annotation.
Annotation	Arbitrary annotation associated with one or more objects.
App	Hello world!
AssertionFailure	An unchecked exception representing an Assertion failure.
DefaultOps	Default implementation of OntologyOps.
GOParser	Simple parser for the Gene Ontology (GO) flatfile format.
IntegerOntology
InvalidTermException	Thrown to indicate that an ontology term is not acceptable or appropriate in a given context
KeyedWeakReference	Subclass of WeakReference which includes and extra field (the key) which can be used to help cleanup once this reference has been enqueued.
OboFileEventListener	an interface for events that occur during parsing of .obo files
OboFileHandler	A file handler for .obo files
OboFileParser	A class to parse the content of an OBO file.
OboFileParser.SOPair
OboParser	Parses an OBO file.
Ontology	An ontology.
Ontology.Impl	A basic in-memory implementation of an ontology
OntologyException	Thrown to indicate an error in an Ontology object
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.
OntologyTerm.Impl	Simple in-memory implementation of a remote ontology term.
OntoTools	Tools for manipulating ontologies.
ParseGO
RemoteTerm	A term in another ontology.
RemoteTerm.Impl	Simple in-memory implementation of a remote ontology term.
SmallAnnotation	Annotation that is optimized for memory usage.
SmallMap	Lightweight implementation of Map which uses little memory to store a small number of mappings, at the expense of scalability.
StaticMemberPlaceHolder
Synonym
TabDelimParser	Parse tab-delimited ontology files into Ontology objects.
Term	A term in an ontology.
Term.Impl	Simple in-memory implementation of an ontology term.
Triple	A triple in an ontology.
Triple.Impl	Basic in-memory implementation of a Triple in an ontology This can be used to implement Ontology.createTriple
Variable
Variable.Impl
WeakValueHashMap	Map implementation which keeps weak references to values.