Uses of Interface
org.biojava.ontology.Term
Packages that use Term
Package
Description
Support for reading and writing GFF3.
Classes and interfaces for defining biological sequences and informatics
objects.
Standard in-memory implementations of
Sequence
and
Feature
.
A general-purpose API for ontologies.
Rich implementations of Sequences, Locations and Features.
Extensions to the biojava ontology model that represent BioSQL ontology.
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Uses of Term in org.biojava.bio.program.gff3
Methods in org.biojava.bio.program.gff3 that return TermModifier and TypeMethodDescriptionGFF3Record.getSource()
GFF3Record.Impl.getSource()
GFF3Record.getType()
GFF3Record.Impl.getType()
Methods in org.biojava.bio.program.gff3 with parameters of type Term -
Uses of Term in org.biojava.bio.seq
Fields in org.biojava.bio.seq declared as TermMethods in org.biojava.bio.seq that return TermModifier and TypeMethodDescriptionFeature.getSourceTerm()
An ontology term defining the source of this feature.Feature.getTypeTerm()
An ontology term defining the type of feature.Methods in org.biojava.bio.seq with parameters of type TermModifier and TypeMethodDescriptionvoid
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 TermMethods in org.biojava.bio.seq.impl with parameters of type TermModifier and TypeMethodDescriptionvoid
SimpleFeature.setSourceTerm
(Term t) void
SimpleFeature.setTypeTerm
(Term t) -
Uses of Term in org.biojava.ontology
Subinterfaces of Term in org.biojava.ontologyModifier and TypeInterfaceDescriptioninterface
A term in an ontology which identifies another ontology.interface
A term in another ontology.interface
A triple in an ontology.interface
Classes in org.biojava.ontology that implement TermModifier and TypeClassDescriptionclass
Abstract implementation of term This provides basic change-forwarding functionality from the annotation and ontology properties.final class
static final class
Simple in-memory implementation of a remote ontology term.static final class
Simple in-memory implementation of a remote ontology term.static class
Simple in-memory implementation of an ontology term.static final class
Basic in-memory implementation of a Triple in an ontology This can be used to implement Ontology.createTriplestatic class
Fields in org.biojava.ontology declared as TermModifier and TypeFieldDescriptionstatic final Term
OntoTools.ANY
static final Term
OntoTools.EQUIVALENCE
static final Term
OntoTools.IS_A
static final Term
OntoTools.NONE
static final Term
OntoTools.PART_OF
static final Term
OntoTools.PARTIAL_ORDER
static final Term
OntoTools.REFLEXIVE
static final Term
OntoTools.RELATION
static final Term
OntoTools.SYMMETRIC
static final Term
OntoTools.TRANSITIVE
Methods in org.biojava.ontology that return TermModifier and TypeMethodDescriptionIntegerOntology.createTerm
(String name) IntegerOntology.createTerm
(String name, String description) IntegerOntology.createTerm
(String name, String description, Object[] synonyms) Ontology.createTerm
(String name) Create a new term in this ontology.Ontology.createTerm
(String name, String description) Create a new term in this ontology.Ontology.createTerm
(String name, String description, Object[] synonyms) Create a new term in this ontology.Ontology.Impl.createTerm
(String name) Ontology.Impl.createTerm
(String name, String description) Ontology.Impl.createTerm
(String name, String description, Object[] synonyms) Triple.getObject()
Return the object term of this triple.Triple.Impl.getObject()
Triple.getPredicate()
Return a Term which defines the type of relationship between the subject and object terms.Triple.Impl.getPredicate()
RemoteTerm.getRemoteTerm()
Return the imported termRemoteTerm.Impl.getRemoteTerm()
Triple.getSubject()
Return the subject term of this tripleTriple.Impl.getSubject()
Fetch the term with the specified name.IntegerOntology.importTerm
(Term t, String name) Ontology.Impl.importTerm
(Term t, String name) 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 TermModifier and TypeMethodDescriptionOntology.getTerms()
Return all the terms in this ontologyOntology.Impl.getTerms()
Methods in org.biojava.ontology with parameters of type TermModifier and TypeMethodDescriptionboolean
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) IntegerOntology.createTriple
(Term subject, Term object, Term predicate, String name, String description) Creates a new 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) IntegerOntology.getTriples
(Term subject, Term object, Term predicate) Ontology.getTriples
(Term subject, Term object, Term predicate) Return all triples from this ontology which match the supplied pattern.Ontology.Impl.getTriples
(Term subject, Term object, Term predicate) IntegerOntology.importTerm
(Term t, String name) Ontology.Impl.importTerm
(Term t, String name) Ontology.importTerm
(Term t, String localName) Create a view of a term from another ontology.Constructors in org.biojava.ontology with parameters of type TermModifierConstructorDescription -
Uses of Term in org.biojavax.bio.seq
Methods in org.biojavax.bio.seq that return TermModifier and TypeMethodDescriptionSimpleRichFeature.getSourceTerm()
An ontology term defining the source of this feature.SimpleRichFeature.getTypeTerm()
An ontology term defining the type of feature.Methods in org.biojavax.bio.seq with parameters of type TermModifier and TypeMethodDescriptionvoid
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.ontologyModifier and TypeInterfaceDescriptioninterface
Makes Term objects comparable properly and adds some extra features to them.interface
Comparable triples, obviously.Classes in org.biojavax.ontology that implement TermModifier and TypeClassDescriptionclass
A Term object that can be compared and thus sorted.class
Basic comparable triple, BioSQL style.Methods in org.biojavax.ontology that return TermModifier and TypeMethodDescriptionSimpleComparableOntology.createTerm
(String name) Create a new term in this ontology.SimpleComparableOntology.createTerm
(String name, String description) Create a new term in this ontology.SimpleComparableOntology.createTerm
(String name, String description, Object[] synonyms) Create a new term in this ontology.SimpleComparableTriple.getObject()
Return the object term of this triple.SimpleComparableTriple.getPredicate()
Return a Term which defines the type of relationship between the subject and object terms.SimpleComparableTriple.getSubject()
Return the subject term of this tripleFetch the term with the specified name.SimpleComparableOntology.importTerm
(Term t, String localName) Create a view of a term from another ontology.Methods in org.biojavax.ontology with parameters of type TermModifier and TypeMethodDescriptionboolean
SimpleComparableOntology.containsTriple
(Term subject, Term object, Term predicate) See if a triple exists in this ontologySimpleComparableOntology.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.ComparableOntology.getOrCreateTriple
(Term subject, Term object, Term predicate) Looks for a triple with the given subject object and predicate and returns it.SimpleComparableOntology.getOrCreateTriple
(Term subject, Term object, Term predicate) Looks for a triple with the given subject object and predicate and returns it.ComparableOntology.getOrImportTerm
(Term term) Looks for a term with the same name as the given term and returns it.SimpleComparableOntology.getOrImportTerm
(Term term) Looks for a term with the same name as the given term and returns it.SimpleComparableOntology.getTriples
(Term subject, Term object, Term predicate) Return all triples from this ontology which match the supplied pattern.SimpleComparableOntology.importTerm
(Term t, String localName) Create a view of a term from another ontology.