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. 
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
 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
 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.sourceTerm
           
 Term Feature.Template.typeTerm
           
 

Methods in org.biojava.bio.seq that return Term
 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
 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
 Term SimpleFeature.getSourceTerm()
           
 Term SimpleFeature.getTypeTerm()
           
 

Methods in org.biojava.bio.seq.impl with parameters of type Term
 void SimpleFeature.setSourceTerm(Term t)
           
 void SimpleFeature.setTypeTerm(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.ANY
           
static Term OntoTools.EQUIVALENCE
           
static Term OntoTools.IS_A
           
static Term OntoTools.NONE
           
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
 Term Ontology.createTerm(String name, String description)
          Create a new term in this ontology.
 Term Ontology.Impl.createTerm(String name, String description)
           
 Term IntegerOntology.createTerm(String name, String description)
           
 Term Ontology.createTerm(String name, String description, Object[] synonyms)
          Create a new term in this ontology.
 Term Ontology.Impl.createTerm(String name, String description, Object[] synonyms)
           
 Term IntegerOntology.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 Ontology.getTerm(String s)
          Fetch the term with the specified name.
 Term Ontology.Impl.getTerm(String name)
           
 Term IntegerOntology.getTerm(String s)
           
 Term Ontology.importTerm(Term t, String localName)
          Create a view of a term from another ontology.
 Term Ontology.Impl.importTerm(Term t, String name)
           
 Term IntegerOntology.importTerm(Term t, String name)
           
 

Methods in org.biojava.ontology with parameters of type Term
 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)
           
 boolean IntegerOntology.containsTriple(Term subject, Term object, Term predicate)
           
 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)
           
 Triple IntegerOntology.createTriple(Term subject, Term object, Term predicate, String name, String description)
           
 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)
           
 void IntegerOntology.deleteTerm(Term t)
           
 Set Ontology.getTriples(Term subject, Term object, Term predicate)
          Return all triples from this ontology which match the supplied pattern.
 Set Ontology.Impl.getTriples(Term subject, Term object, Term predicate)
           
 Set IntegerOntology.getTriples(Term subject, Term object, Term predicate)
           
 Term Ontology.importTerm(Term t, String localName)
          Create a view of a term from another ontology.
 Term Ontology.Impl.importTerm(Term t, String name)
           
 Term IntegerOntology.importTerm(Term t, String name)
           
 

Constructors in org.biojava.ontology with parameters of type Term
RemoteTerm.Impl(Ontology ontology, Term remoteTerm, String name)
           
RemoteTerm.Impl(Ontology ontology, Term remoteTerm, String name, Object[] synonyms)
           
Triple.Impl(Term subject, Term object, Term predicate)
           
Triple.Impl(Term subject, Term object, Term predicate, Object[] synonyms)
           
Triple.Impl(Term subject, Term object, Term predicate, String name, String description)
           
Triple.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
 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
 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
 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
 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
 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. This particular implementation merely copies the term into this ontology, and returns a pointer to the copied term.
 

Methods in org.biojavax.ontology with parameters of type Term
 boolean SimpleComparableOntology.containsTriple(Term subject, Term object, Term predicate)
          See if a triple exists in this ontology If you call this method with plain Terms instead of ComparableTerms, it may not match any of the triples in the ontology as they are all stored as ComparableTerms.
 Triple SimpleComparableOntology.createTriple(Term subject, Term object, Term predicate, String name, String description)
          Creates a new Triple. If you call this method with plain Terms instead of ComparableTerms, it will import them into the local ontology first.
 void SimpleComparableOntology.deleteTerm(Term t)
          Remove a term from an ontology, together with all triples which refer to it. If you call this method with a plain Term instead of a ComparableTerm, it may not match any of the terms in the ontology as they are all stored as ComparableTerms.
 ComparableTriple SimpleComparableOntology.getOrCreateTriple(Term subject, Term object, Term predicate)
          Looks for a triple with the given subject object and predicate and returns it.
 ComparableTriple ComparableOntology.getOrCreateTriple(Term subject, Term object, Term predicate)
          Looks for a triple with the given subject object and predicate and returns it.
 ComparableTerm SimpleComparableOntology.getOrImportTerm(Term term)
          Looks for a term with the same name as the given term and returns it.
 ComparableTerm ComparableOntology.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. If you call this method with plain Terms instead of ComparableTerms, it may not match any of the triples in the ontology as they are all stored as ComparableTerms.
 Term SimpleComparableOntology.importTerm(Term t, String localName)
          Create a view of a term from another ontology. This particular implementation merely copies the term into this ontology, and returns a pointer to the copied term.