Java OWLAnnotationProperty.equals方法代码示例

import org.semanticweb.owlapi.model.OWLAnnotationProperty; //导入方法依赖的package包/类
OWLObjectPropertyAssertionAxiom updateAnnotation(ModelContainer model, 
		OWLObjectPropertyAssertionAxiom toModify, OWLAnnotation update,
		METADATA metadata) {
	OWLObjectPropertyAssertionAxiom newAxiom = null;
	if (toModify != null) {
		Set<OWLAnnotation> combindedAnnotations = new HashSet<OWLAnnotation>();
		OWLAnnotationProperty target = update.getProperty();
		for(OWLAnnotation existing : toModify.getAnnotations()) {
			if (target.equals(existing.getProperty()) == false) {
				combindedAnnotations.add(existing);
			}
		}
		combindedAnnotations.add(update);
		newAxiom = modifyAnnotations(toModify, combindedAnnotations, model, metadata);
	}
	return newAxiom;
}
 

import org.semanticweb.owlapi.model.OWLAnnotationProperty; //导入方法依赖的package包/类
/**
 * Find all corresponding {@link OWLObject}s with an OBO-style alternate identifier.
 * <p>
 * WARNING: This methods scans all object annotations in all ontologies. 
 * This is an expensive method.
 * 
 * @return map of altId to OWLObject (never null)
 */
public Map<String, OWLObject> getAllOWLObjectsByAltId() {
	final Map<String, OWLObject> results = new HashMap<String, OWLObject>();
	final OWLAnnotationProperty altIdProperty = getAnnotationProperty(OboFormatTag.TAG_ALT_ID.getTag());
	if (altIdProperty == null) {
		return Collections.emptyMap();
	}
	for (OWLOntology o : getAllOntologies()) {
		Set<OWLAnnotationAssertionAxiom> aas = o.getAxioms(AxiomType.ANNOTATION_ASSERTION);
		for (OWLAnnotationAssertionAxiom aa : aas) {
			OWLAnnotationValue v = aa.getValue();
			OWLAnnotationProperty property = aa.getProperty();
			if (altIdProperty.equals(property) && v instanceof OWLLiteral) {
				String altId = ((OWLLiteral)v).getLiteral();
				OWLAnnotationSubject subject = aa.getSubject();
				if (subject instanceof IRI) {
					OWLObject obj = getOWLObject((IRI) subject);
					if (obj != null) {
						results.put(altId, obj);
					}
				}
			}
		}
	}
	return results;
}
 

import org.semanticweb.owlapi.model.OWLAnnotationProperty; //导入方法依赖的package包/类
static boolean isTagged(Set<OWLAnnotation> annotations, OWLAnnotationProperty p) {
	if (annotations != null && !annotations.isEmpty()) {
		for (OWLAnnotation annotation : annotations) {
			if (p.equals(annotation.getProperty())) {
				String value = annotation.getValue().accept(new OWLAnnotationValueVisitorEx<String>() {

					@Override
					public String visit(IRI iri) {
						return null;
					}

					@Override
					public String visit(OWLAnonymousIndividual individual) {
						return null;
					}

					@Override
					public String visit(OWLLiteral literal) {
						return literal.getLiteral();
					}
				});
				if (value != null && ModelWriterHelper.DERIVED_VALUE.equalsIgnoreCase(value)) {
					return true;
				}
			}
	}
	}
	return false;
}
 

import org.semanticweb.owlapi.model.OWLAnnotationProperty; //导入方法依赖的package包/类
public static Set<OWLObject> findTaggedEntities(OWLAnnotationProperty p, Set<OWLAnnotationValue> values, final OWLGraphWrapper graph) {
	if (p == null || values == null || values.isEmpty()) {
		return Collections.emptySet();
	}
	final Set<OWLObject> entities = new HashSet<OWLObject>();
	Set<OWLOntology> allOntologies = graph.getAllOntologies();
	for (OWLOntology ontology : allOntologies) {
		Set<OWLAnnotationAssertionAxiom> axioms = ontology.getAxioms(AxiomType.ANNOTATION_ASSERTION);
		for (OWLAnnotationAssertionAxiom axiom : axioms) {
			if (p.equals(axiom.getProperty()) && values.contains(axiom.getValue())) {
				axiom.getSubject().accept(new OWLAnnotationSubjectVisitor(){

					@Override
					public void visit(IRI iri) {
						OWLObject owlObject = graph.getOWLObject(iri);
						if (owlObject != null) {
							entities.add(owlObject);
						}
					}

					@Override
					public void visit(OWLAnonymousIndividual individual) {
						// do nothing
					}
				});
			}
		}
	}
	return entities;
}
 

import org.semanticweb.owlapi.model.OWLAnnotationProperty; //导入方法依赖的package包/类
public static Set<OWLAnnotation> getAnnotations(OWLEntity e, OWLAnnotationProperty property, OWLOntology ont) {
	Set<OWLAnnotation> annotations;
	if (e != null && property != null && ont != null) {
		annotations = new HashSet<>();
		for (OWLAnnotationAssertionAxiom ax : ont.getAnnotationAssertionAxioms(e.getIRI())) {
			if (property.equals(ax.getProperty())) {
				annotations.add(ax.getAnnotation());
			}
		}
	}
	else {
		annotations = Collections.emptySet();
	}
	return annotations;
}
 

import org.semanticweb.owlapi.model.OWLAnnotationProperty; //导入方法依赖的package包/类
/**
 * Get the definition xrefs (IAO_0000115)
 * 
 * @param c
 * @return list of definition xrefs
 */
public List<String> getDefXref(OWLObject c){
	OWLAnnotationProperty lap = getDataFactory().getOWLAnnotationProperty(Obo2OWLVocabulary.IRI_IAO_0000115.getIRI()); 
	OWLAnnotationProperty xap = getAnnotationProperty(OboFormatTag.TAG_XREF.getTag());

	if (c instanceof OWLEntity) {
		List<String> list = new ArrayList<String>();
		for (OWLOntology ont : getAllOntologies()) {
			Set<OWLAnnotationAssertionAxiom> axioms = ont.getAnnotationAssertionAxioms(((OWLEntity) c).getIRI());
			for (OWLAnnotationAssertionAxiom axiom :axioms){
				if(lap.equals(axiom.getProperty())){
					for(OWLAnnotation annotation: axiom.getAnnotations(xap)){
						OWLAnnotationValue value = annotation.getValue();
						if(value instanceof OWLLiteral){
							list.add(((OWLLiteral)value).getLiteral());
						}
					}
				}

			}
		}
		return list;
	}
	else {
		return null;
	}
}
 

import org.semanticweb.owlapi.model.OWLAnnotationProperty; //导入方法依赖的package包/类
/**
 * Find the corresponding {@link OWLObject}s for a given set of OBO-style alternate identifiers.
 * <p>
 * WARNING: This methods scans all object annotations in all ontologies. 
 * This is an expensive method.
 * <p>
 * Consider loading all altId-mappings using {@link #getAllOWLObjectsByAltId()}.
 * 
 * @param altIds
 * @return map of altId to OWLObject (never null)
 * @see #getAllOWLObjectsByAltId()
 */
public Map<String, OWLObject> getOWLObjectsByAltId(Set<String> altIds) {
	final Map<String, OWLObject> results = new HashMap<String, OWLObject>();
	final OWLAnnotationProperty altIdProperty = getAnnotationProperty(OboFormatTag.TAG_ALT_ID.getTag());
	if (altIdProperty == null) {
		return Collections.emptyMap();
	}
	for (OWLOntology o : getAllOntologies()) {
		Set<OWLAnnotationAssertionAxiom> aas = o.getAxioms(AxiomType.ANNOTATION_ASSERTION);
		for (OWLAnnotationAssertionAxiom aa : aas) {
			OWLAnnotationValue v = aa.getValue();
			OWLAnnotationProperty property = aa.getProperty();
			if (altIdProperty.equals(property) && v instanceof OWLLiteral) {
				String altId = ((OWLLiteral)v).getLiteral();
				if (altIds.contains(altId)) {
					OWLAnnotationSubject subject = aa.getSubject();
					if (subject instanceof IRI) {
						OWLObject obj = getOWLObject((IRI) subject);
						if (obj != null) {
							results.put(altId, obj);
						}
					}
				}
			}
		}
	}
	return results;
}
 

import org.semanticweb.owlapi.model.OWLAnnotationProperty; //导入方法依赖的package包/类
/**
 * Convenience method to get the first string literal of an
 * annotation property.
 *
 * @param ontology the current ontology
 * @param taxon the subject
 * @param property the property
 * @return null or the label content
 */
protected static String getFirstLiteral(OWLOntology ontology,
		OWLEntity taxon, OWLAnnotationProperty property) {
	Set<OWLAnnotationAssertionAxiom> axioms = ontology.getAnnotationAssertionAxioms(taxon.getIRI());
	for (OWLAnnotationAssertionAxiom axiom : axioms) {
		if (property.equals(axiom.getProperty())) {
			OWLAnnotationValue value = axiom.getValue();
			if (value instanceof OWLLiteral) {
				OWLLiteral literal = (OWLLiteral)value;
				return literal.getLiteral();
			}
		}
	}
	return null;
}
 

import org.semanticweb.owlapi.model.OWLAnnotationProperty; //导入方法依赖的package包/类
public IRI getIRIByIdentifier(String id, boolean isAutoResolve) {
	if (isAutoResolve) {
		OWLObject obj = this.getObjectByAltId(id);
		if (obj != null) {
			return ((OWLNamedObject) obj).getIRI();
		}
	}

	// special magic for finding IRIs from a non-standard identifier
	// This is the case for relations (OWLObject properties) with a short hand
	// or for relations with a non identifiers with-out a colon, e.g. negative_regulation
	if (!id.contains(":")) {
		final OWLAnnotationProperty shortHand = getDataFactory().getOWLAnnotationProperty(Obo2OWLVocabulary.IRI_OIO_shorthand.getIRI());
		final OWLAnnotationProperty oboIdInOwl = getDataFactory().getOWLAnnotationProperty(Obo2Owl.trTagToIRI(OboFormatTag.TAG_ID.getTag()));
		for (OWLOntology o : getAllOntologies()) {
			for(OWLObjectProperty p : o.getObjectPropertiesInSignature()) {
				// check for short hand or obo ID in owl
				Set<OWLAnnotation> annotations = OwlHelper.getAnnotations(p, o);
				if (annotations != null) {
					for (OWLAnnotation owlAnnotation : annotations) {
						OWLAnnotationProperty property = owlAnnotation.getProperty();
						if ((shortHand != null && shortHand.equals(property)) 
								|| (oboIdInOwl != null && oboIdInOwl.equals(property)))
						{
							OWLAnnotationValue value = owlAnnotation.getValue();
							if (value != null && value instanceof OWLLiteral) {
								OWLLiteral literal = (OWLLiteral) value;
								String shortHandLabel = literal.getLiteral();
								if (id.equals(shortHandLabel)) {
									return p.getIRI();
								}
							}
						}
					}
				}
			}
		}
	}


	// otherwise use the obo2owl method
	Obo2Owl b = new Obo2Owl(getManager()); // re-use manager, creating a new one can be expensive as this is a highly used code path
	b.setObodoc(new OBODoc());
	return b.oboIdToIRI(id);
}