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