All Classes and Interfaces
Class
Description
A utility class to ease the problem of implementing an Annotation to that of
providing an apropreate implementation of Map.
Abstract implementation of term
This provides basic change-forwarding functionality from
the annotation and ontology properties.
Thrown to indicate that a term or triple can't be added to an ontology
because it is already present.
Indicates that an object has an associated annotation.
Arbitrary annotation associated with one or more objects.
Hello world!
An unchecked exception representing an Assertion failure.
Default implementation of OntologyOps.
Simple parser for the Gene Ontology (GO) flatfile format.
Thrown to indicate that an ontology term is not acceptable or
appropriate in a given context
Subclass of WeakReference which includes and extra field (the key)
which can be used to help cleanup once this reference has been
enqueued.
an interface for events that occur during parsing of .obo files
A file handler for .obo files
A class to parse the content of an OBO file.
Parses an OBO file.
An ontology.
A basic in-memory implementation of an ontology
Thrown to indicate an error in an Ontology object
A factory for Ontology instances.
This is an interface for optimizing ontology operators.
A term in an ontology which identifies another ontology.
Simple in-memory implementation of a remote ontology term.
Tools for manipulating ontologies.
A term in another ontology.
Simple in-memory implementation of a remote ontology term.
Annotation that is optimized for memory usage.
Lightweight implementation of Map which uses little memory to store a
small number of mappings, at the expense of scalability.
Parse tab-delimited ontology files into Ontology objects.
A term in an ontology.
Simple in-memory implementation of an ontology term.
A triple in an ontology.
Basic in-memory implementation of a Triple in an ontology
This can be used to implement Ontology.createTriple
Map implementation which keeps weak references to values.