Uses of Interface org.biojava.ontology.Term (BioJava-1.5-beta API)

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## 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.

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