Uses of Interface
org.biojava.nbio.ontology.Term
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Packages that use Term Package Description org.biojava.nbio.ontology -
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Uses of Term in org.biojava.nbio.ontology
Subinterfaces of Term in org.biojava.nbio.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.nbio.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.createTriplestatic class
Variable.Impl
Fields in org.biojava.nbio.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.nbio.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 termTerm
RemoteTerm.Impl. getRemoteTerm()
Term
Triple. getSubject()
Return the subject term of this tripleTerm
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.nbio.ontology that return types with arguments of type Term Modifier and Type Method Description Set<Term>
Ontology. getTerms()
Return all the terms in this ontologySet<Term>
Ontology.Impl. getTerms()
Methods in org.biojava.nbio.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 ontologyboolean
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.nbio.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)
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