Uses of Interface
org.biojava.ontology.Term

Packages that use Term

Package	Description
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.impl	Standard in-memory implementations of Sequence and Feature.
org.biojava.ontology	A general-purpose API for 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.

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

Methods in org.biojava.bio.program.gff3 that return Term

Modifier and Type	Method	Description
Term	GFF3Record.getSource()
Term	GFF3Record.Impl.getSource()
Term	GFF3Record.getType()
Term	GFF3Record.Impl.getType()

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

Modifier and Type	Method	Description
void	GFF3Record.Impl.setSource(Term source)
void	GFF3Record.Impl.setType(Term type)

Uses of Term in org.biojava.bio.seq

Fields in org.biojava.bio.seq declared as Term

Modifier and Type	Field	Description
Term	Feature.Template.sourceTerm
Term	Feature.Template.typeTerm

Methods in org.biojava.bio.seq that return Term

Modifier and Type	Method	Description
Term	Feature.getSourceTerm()	An ontology term defining the source of this feature.
Term	Feature.getTypeTerm()	An ontology term defining the type of feature.

Methods in org.biojava.bio.seq with parameters of type Term

Modifier and Type	Method	Description
void	Feature.setSourceTerm(Term t)	Set the source ontology-term for this feature.
void	Feature.setTypeTerm(Term t)	Set the type ontology-term for this feature.

Uses of Term in org.biojava.bio.seq.impl

Methods in org.biojava.bio.seq.impl that return Term

Modifier and Type	Method	Description
Term	SimpleFeature.getSourceTerm()
Term	SimpleFeature.getTypeTerm()

Methods in org.biojava.bio.seq.impl with parameters of type Term

Modifier and Type	Method	Description
void	SimpleFeature.setSourceTerm(Term t)
void	SimpleFeature.setTypeTerm(Term t)

Uses of Term in org.biojava.ontology

Subinterfaces of Term in org.biojava.ontology

Modifier and Type	Interface	Description
interface	OntologyTerm	A term in an ontology which identifies another ontology.
interface	RemoteTerm	A term in another ontology.
interface	Triple	A triple in an ontology.
interface	Variable

Classes in org.biojava.ontology that implement Term

Modifier and Type	Class	Description
class	AbstractTerm	Abstract implementation of term This provides basic change-forwarding functionality from the annotation and ontology properties.
class	IntegerOntology.IntTerm
static class	OntologyTerm.Impl	Simple in-memory implementation of a remote ontology term.
static class	RemoteTerm.Impl	Simple in-memory implementation of a remote ontology term.
static class	Term.Impl	Simple in-memory implementation of an ontology term.
static class	Triple.Impl	Basic in-memory implementation of a Triple in an ontology This can be used to implement Ontology.createTriple
static class	Variable.Impl

Fields in org.biojava.ontology declared as Term

Modifier and Type	Field	Description
static Term	OntoTools.ANY
static Term	OntoTools.EQUIVALENCE
static Term	OntoTools.IS_A
static Term	OntoTools.NONE
static Term	OntoTools.PART_OF
static Term	OntoTools.PARTIAL_ORDER
static Term	OntoTools.REFLEXIVE
static Term	OntoTools.RELATION
static Term	OntoTools.SYMMETRIC
static Term	OntoTools.TRANSITIVE

Methods in org.biojava.ontology that return Term

Modifier and Type	Method	Description
Term	IntegerOntology.createTerm(String name)
Term	IntegerOntology.createTerm(String name, String description)
Term	IntegerOntology.createTerm(String name, String description, Object[] synonyms)
Term	Ontology.createTerm(String name)	Create a new term in this ontology.
Term	Ontology.createTerm(String name, String description)	Create a new term in this ontology.
Term	Ontology.createTerm(String name, String description, Object[] synonyms)	Create a new term in this ontology.
Term	Ontology.Impl.createTerm(String name)
Term	Ontology.Impl.createTerm(String name, String description)
Term	Ontology.Impl.createTerm(String name, String description, Object[] synonyms)
Term	Triple.getObject()	Return the object term of this triple.
Term	Triple.Impl.getObject()
Term	Triple.getPredicate()	Return a Term which defines the type of relationship between the subject and object terms.
Term	Triple.Impl.getPredicate()
Term	RemoteTerm.getRemoteTerm()	Return the imported term
Term	RemoteTerm.Impl.getRemoteTerm()
Term	Triple.getSubject()	Return the subject term of this triple
Term	Triple.Impl.getSubject()
Term	IntegerOntology.getTerm(String s)
Term	Ontology.getTerm(String name)	Fetch the term with the specified name.
Term	Ontology.Impl.getTerm(String name)
Term	IntegerOntology.importTerm(Term t, String name)
Term	Ontology.Impl.importTerm(Term t, String name)
Term	Ontology.importTerm(Term t, String localName)	Create a view of a term from another ontology.

Methods in org.biojava.ontology that return types with arguments of type Term

Modifier and Type	Method	Description
Set<Term>	Ontology.getTerms()	Return all the terms in this ontology
Set<Term>	Ontology.Impl.getTerms()

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

Modifier and Type	Method	Description
boolean	IntegerOntology.containsTriple(Term subject, Term object, Term predicate)
boolean	Ontology.containsTriple(Term subject, Term object, Term predicate)	See if a triple exists in this ontology
boolean	Ontology.Impl.containsTriple(Term subject, Term object, Term predicate)
Triple	IntegerOntology.createTriple(Term subject, Term object, Term predicate, String name, String description)
Triple	Ontology.createTriple(Term subject, Term object, Term predicate, String name, String description)	Creates a new Triple.
Triple	Ontology.Impl.createTriple(Term subject, Term object, Term predicate, String name, String description)
void	IntegerOntology.deleteTerm(Term t)
void	Ontology.deleteTerm(Term t)	Remove a term from an ontology, together with all triples which refer to it.
void	Ontology.Impl.deleteTerm(Term t)
Set	IntegerOntology.getTriples(Term subject, Term object, Term predicate)
Set<Triple>	Ontology.getTriples(Term subject, Term object, Term predicate)	Return all triples from this ontology which match the supplied pattern.
Set<Triple>	Ontology.Impl.getTriples(Term subject, Term object, Term predicate)
Term	IntegerOntology.importTerm(Term t, String name)
Term	Ontology.Impl.importTerm(Term t, String name)
Term	Ontology.importTerm(Term t, String localName)	Create a view of a term from another ontology.

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

Constructor	Description
Impl(Ontology ontology, Term remoteTerm, String name)
Impl(Ontology ontology, Term remoteTerm, String name, Object[] synonyms)
Impl(Term subject, Term object, Term predicate)
Impl(Term subject, Term object, Term predicate, Object[] synonyms)
Impl(Term subject, Term object, Term predicate, String name, String description)
Impl(Term subject, Term object, Term predicate, String name, String description, Object[] synonyms)

Uses of Term in org.biojavax.bio.seq

Methods in org.biojavax.bio.seq that return Term

Modifier and Type	Method	Description
Term	SimpleRichFeature.getSourceTerm()	An ontology term defining the source of this feature.
Term	SimpleRichFeature.getTypeTerm()	An ontology term defining the type of feature.

Methods in org.biojavax.bio.seq with parameters of type Term

Modifier and Type	Method	Description
void	SimpleRichFeature.setSourceTerm(Term t)	Set the source ontology-term for this feature.
void	SimpleRichFeature.setTypeTerm(Term t)	Set the type ontology-term for this feature.

Uses of Term in org.biojavax.ontology

Subinterfaces of Term in org.biojavax.ontology

Modifier and Type	Interface	Description
interface	ComparableTerm	Makes Term objects comparable properly and adds some extra features to them.
interface	ComparableTriple	Comparable triples, obviously.

Classes in org.biojavax.ontology that implement Term

Modifier and Type	Class	Description
class	SimpleComparableTerm	A Term object that can be compared and thus sorted.
class	SimpleComparableTriple	Basic comparable triple, BioSQL style.

Methods in org.biojavax.ontology that return Term

Modifier and Type	Method	Description
Term	SimpleComparableOntology.createTerm(String name)	Create a new term in this ontology.
Term	SimpleComparableOntology.createTerm(String name, String description)	Create a new term in this ontology.
Term	SimpleComparableOntology.createTerm(String name, String description, Object[] synonyms)	Create a new term in this ontology.
Term	SimpleComparableTriple.getObject()	Return the object term of this triple.
Term	SimpleComparableTriple.getPredicate()	Return a Term which defines the type of relationship between the subject and object terms.
Term	SimpleComparableTriple.getSubject()	Return the subject term of this triple
Term	SimpleComparableOntology.getTerm(String s)	Fetch the term with the specified name.
Term	SimpleComparableOntology.importTerm(Term t, String localName)	Create a view of a term from another ontology.

Methods in org.biojavax.ontology with parameters of type Term

Modifier and Type	Method	Description
boolean	SimpleComparableOntology.containsTriple(Term subject, Term object, Term predicate)	See if a triple exists in this ontology
Triple	SimpleComparableOntology.createTriple(Term subject, Term object, Term predicate, String name, String description)	Creates a new Triple.
void	SimpleComparableOntology.deleteTerm(Term t)	Remove a term from an ontology, together with all triples which refer to it.
ComparableTriple	ComparableOntology.getOrCreateTriple(Term subject, Term object, Term predicate)	Looks for a triple with the given subject object and predicate and returns it.
ComparableTriple	SimpleComparableOntology.getOrCreateTriple(Term subject, Term object, Term predicate)	Looks for a triple with the given subject object and predicate and returns it.
ComparableTerm	ComparableOntology.getOrImportTerm(Term term)	Looks for a term with the same name as the given term and returns it.
ComparableTerm	SimpleComparableOntology.getOrImportTerm(Term term)	Looks for a term with the same name as the given term and returns it.
Set	SimpleComparableOntology.getTriples(Term subject, Term object, Term predicate)	Return all triples from this ontology which match the supplied pattern.
Term	SimpleComparableOntology.importTerm(Term t, String localName)	Create a view of a term from another ontology.