Uses of Package
org.biojava.ontology

Packages that use org.biojava.ontology

org.biojava.bio.program.gff3	Support for reading and writing GFF3.
org.biojava.bio.seq	Classes and interfaces for defining biological sequences and informatics objects.
org.biojava.bio.seq.db.biosql	General purpose Sequence storage in a relational database.
org.biojava.bio.seq.impl	Standard in-memory implementations of Sequence and Feature.
org.biojava.ontology	A general-purpose API for ontologies.
org.biojava.ontology.io	Tools for loading and saving ontologies.
org.biojavax.bio.seq	Rich implementations of Sequences, Locations and Features.
org.biojavax.ontology	Extensions to the biojava ontology model that represent BioSQL ontology.

Classes in org.biojava.ontology used by org.biojava.bio.program.gff3

Ontology
An ontology.

Term
A term in an ontology.

Classes in org.biojava.ontology used by org.biojava.bio.seq

InvalidTermException
Thrown to indicate that an ontology term is not acceptable or appropriate in a given context

Term
A term in an ontology.

Classes in org.biojava.ontology used by org.biojava.bio.seq.db.biosql

Ontology
An ontology.

Classes in org.biojava.ontology used by org.biojava.bio.seq.impl

Term
A term in an ontology.

Classes in org.biojava.ontology used by org.biojava.ontology

AbstractTerm
Abstract implementation of term

AlreadyExistsException
Thrown to indicate that a term or triple can't be added to an ontology because it is already present.

IntegerOntology

IntegerOntology.IntTerm

Ontology
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.

RemoteTerm
A term in another ontology.

Term
A term in an ontology.

Term.Impl
Simple in-memory implementation of an ontology term.

Triple
A triple in an ontology.

Variable

Classes in org.biojava.ontology used by org.biojava.ontology.io

Ontology
An ontology.

OntologyException
Thrown to indicate an error in an Ontology object

OntologyFactory
A factory for Ontology instances.

Classes in org.biojava.ontology used by org.biojavax.bio.seq

InvalidTermException
Thrown to indicate that an ontology term is not acceptable or appropriate in a given context

Term
A term in an ontology.

Classes in org.biojava.ontology used by org.biojavax.ontology

AlreadyExistsException
Thrown to indicate that a term or triple can't be added to an ontology because it is already present.

Ontology
An ontology.

OntologyOps
This is an interface for optimizing ontology operators.

Term
A term in an ontology.

Triple
A triple in an ontology.

Variable