Uses of Interface
org.biojava.ontology.Term

Packages that use Term

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.

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

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

Term	GFF3Record.getSource()
Term	GFF3Record.getType()
Term	GFF3Record.Impl.getSource()
Term	GFF3Record.Impl.getType()

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

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

Term	Feature.Template.typeTerm
Term	Feature.Template.sourceTerm

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

Term	Feature.getTypeTerm() An ontology term defining the type of feature.
Term	Feature.getSourceTerm() An ontology term defining the source of this feature.

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

void	Feature.setTypeTerm(Term t) Set the type ontology-term for this feature.
void	Feature.setSourceTerm(Term t) Set the source ontology-term for this feature.

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

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

Term	SimpleFeature.getTypeTerm()
Term	SimpleFeature.getSourceTerm()

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

void	SimpleFeature.setTypeTerm(Term t)
void	SimpleFeature.setSourceTerm(Term t)

Uses of Term in org.biojava.ontology

Subinterfaces of Term in org.biojava.ontology

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

class	AbstractTerm Abstract implementation of term
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
static class	Variable.Impl

Fields in org.biojava.ontology declared as Term

static Term	OntoTools.RELATION
static Term	OntoTools.ANY
static Term	OntoTools.NONE
static Term	OntoTools.IS_A
static Term	OntoTools.REFLEXIVE
static Term	OntoTools.SYMMETRIC
static Term	OntoTools.TRANSITIVE
static Term	OntoTools.EQUIVALENCE
static Term	OntoTools.PARTIAL_ORDER

Methods in org.biojava.ontology that return Term

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

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

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

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

Triple.Impl(Term subject, Term object, Term predicate)

Triple.Impl(Term subject, Term object, Term predicate, String name, String description)

RemoteTerm.Impl(Ontology ontology, Term remoteTerm, String name)