Uses of Interface
org.biojava.ontology.Ontology

Packages that use Ontology

Package	Description
org.biojava.bio.program.gff3	Support for reading and writing GFF3.
org.biojava.bio.seq.db.biosql	General purpose Sequence storage in a relational database.
org.biojava.ontology	A general-purpose API for ontologies.
org.biojava.ontology.io	Tools for loading and saving ontologies.
org.biojava.ontology.obo
org.biojavax.ontology	Extensions to the biojava ontology model that represent BioSQL ontology.

Uses of Ontology in org.biojava.bio.program.gff3

Methods in org.biojava.bio.program.gff3 with parameters of type Ontology

Modifier and Type	Method and Description
protected GFF3Record	GFF3Parser.createRecord(GFF3DocumentHandler handler, List aList, String rest, String comment, Ontology ontology, Ontology fallBack) Actually turns a list of tokens, some value string and a comment into a GFF3Record and informs handler.
void	GFF3Parser.parse(BufferedReader bReader, GFF3DocumentHandler handler, Ontology ontology) Informs handler of each line of gff read from bReader.
void	GFF3Parser.parse(BufferedReader bReader, GFF3DocumentHandler handler, Ontology ontology, String locator) Informs handler of each line of GFF read from bReader
protected void	GFF3Parser.parseAttribute(String attValList, Annotation anno, Ontology onto, Ontology fallBack) Parse attValList into a Map of attributes and value lists.

Uses of Ontology in org.biojava.bio.seq.db.biosql

Methods in org.biojava.bio.seq.db.biosql that return Ontology

Modifier and Type	Method and Description
Ontology	BioSQLSequenceDB.addOntology(Ontology onto) Deprecated.
Ontology	BioSQLSequenceDB.createOntology(String name, String description) Deprecated.
Ontology	BioSQLSequenceDB.getOntology(String name) Deprecated.

Methods in org.biojava.bio.seq.db.biosql with parameters of type Ontology

Modifier and Type	Method and Description
Ontology	BioSQLSequenceDB.addOntology(Ontology onto) Deprecated.

Uses of Ontology in org.biojava.ontology

Classes in org.biojava.ontology that implement Ontology

Modifier and Type	Class and Description
class	IntegerOntology
static class	Ontology.Impl A basic in-memory implementation of an ontology

Methods in org.biojava.ontology that return Ontology

Modifier and Type	Method and Description
Ontology	OntologyFactory.createOntology(String name, String description) Creates a new Ontology
static Ontology	OntoTools.getCoreOntology() Get the Ontology that defines our core "central dogma".
Ontology	Triple.Impl.getOntology()
Ontology	Term.getOntology() Return the ontology in which this term exists.
Ontology	Term.Impl.getOntology()
Ontology	RemoteTerm.Impl.getOntology()
Ontology	OntologyTerm.getOntology() Get the remote ontology referenced by this term
Ontology	OntologyTerm.Impl.getOntology()
Ontology	IntegerOntology.IntTerm.getOntology()
Ontology	OntologyTerm.Impl.getTargetOntology()

Methods in org.biojava.ontology with parameters of type Ontology

Modifier and Type	Method and Description
OntologyTerm	Ontology.Impl.createOntologyTerm(Ontology o)

Constructors in org.biojava.ontology with parameters of type Ontology

Constructor and Description
OntologyTerm.Impl(Ontology ontology, Ontology target)
OntologyTerm.Impl(Ontology ontology, Ontology target, Object[] synonyms)
RemoteTerm.Impl(Ontology ontology, Term remoteTerm, String name)
RemoteTerm.Impl(Ontology ontology, Term remoteTerm, String name, Object[] synonyms)
Term.Impl(Ontology ontology, String name)
Term.Impl(Ontology ontology, String name, String description)
Term.Impl(Ontology ontology, String name, String description, Object[] synonyms)
Variable.Impl(Ontology ontology, String name, String description)
Variable.Impl(Ontology ontology, String name, String description, Object[] synonyms)

Uses of Ontology in org.biojava.ontology.io

Methods in org.biojava.ontology.io that return Ontology

Modifier and Type	Method and Description
Ontology	TabDelimParser.parse(BufferedReader in, OntologyFactory of) Parse an ontology from a reader.
Ontology	GOParser.parseGO(BufferedReader goFile, String ontoName, String ontoDescription, OntologyFactory factory)
Ontology	OboParser.parseOBO(BufferedReader oboFile, String ontoName, String ontoDescription) Parse a OBO file and return its content as a BioJava Ontology object

Uses of Ontology in org.biojava.ontology.obo

Constructors in org.biojava.ontology.obo with parameters of type Ontology

Constructor and Description
OboFileHandler(Ontology ontology)

Uses of Ontology in org.biojavax.ontology

Subinterfaces of Ontology in org.biojavax.ontology

Modifier and Type	Interface and Description
interface	ComparableOntology An Ontology that can be compared to another.

Classes in org.biojavax.ontology that implement Ontology

Modifier and Type	Class and Description
class	SimpleComparableOntology Represents an ontology that can be compared to other ontologies.

Methods in org.biojavax.ontology that return Ontology

Modifier and Type	Method and Description
Ontology	SimpleComparableTriple.getOntology() Return the ontology in which this term exists.
Ontology	SimpleComparableTerm.getOntology() Return the ontology in which this term exists.