Java Code Examples for org.semanticweb.owlapi.model.OWLOntology#getObjectPropertiesInSignature()

public static  TaxonomyBuilder<OWLPropertyExpression> buildObjectPropertyHierarchy(NormalizedOWLQLTbox tbox, Collection<? extends OWLPropertyExpression> additionalPropertyExpressions) {
	OWLOntology ont = tbox.getNormalizedOntology();
	OWLDataFactory fac = ont.getOWLOntologyManager().getOWLDataFactory();
	Set< OWLPropertyExpression> props;
	if (additionalPropertyExpressions!=null) {
		props = new HashSet<OWLPropertyExpression>(additionalPropertyExpressions);
		props.addAll(ont.getObjectPropertiesInSignature());
	} else {
		props = new HashSet<OWLPropertyExpression>( ont.getObjectPropertiesInSignature());
	}
	SubPropertyComputation subcomp = new SubPropertyComputation(tbox);
	TaxonomyBuilder<OWLPropertyExpression> taxoBuilder = new TaxonomyBuilder<OWLPropertyExpression>(
			props, 
			fac.getOWLTopObjectProperty(),
			fac.getOWLBottomObjectProperty(),
			subcomp);
	taxoBuilder.build();
	logger.debug("Number of direct subsumption tests performed: {}", subcomp.numOfDirectSubsumptionTests);
	long size = props.size(); 
	logger.debug("Worst Case number of direct subsumption tests performed: {}^2 = {}",size, size*size);
	return taxoBuilder;
}
 

public void excludeAllWith(OWLAnnotationProperty ap, OWLOntology o) {
	for (OWLObjectProperty p : o.getObjectPropertiesInSignature(Imports.INCLUDED)) {
		Set<OWLAnnotation> anns = OwlHelper.getAnnotations(p, ap, o);
		for (OWLAnnotation ann : anns) {
			if (ann.getValue() instanceof OWLLiteral) {
				OWLLiteral v = (OWLLiteral) ann.getValue();
				if (v.parseBoolean()) {
					excludeProperty(p);
				}
			}

		}
	}
}
 

public void includeAllWith(OWLAnnotationProperty ap, OWLOntology o) {
	for (OWLObjectProperty p : o.getObjectPropertiesInSignature(Imports.INCLUDED)) {
		Set<OWLAnnotation> anns = OwlHelper.getAnnotations(p, ap, o);
		for (OWLAnnotation ann : anns) {
			if (ann.getValue() instanceof OWLLiteral) {
				OWLLiteral v = (OWLLiteral) ann.getValue();
				if (v.parseBoolean()) {
					includeProperty(p);
				}
			}

		}
	}
}
 

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
	// we first collect all candidate matching properties in candIRISet.
	Set<IRI> candIRISet = Sets.newHashSet();
	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)) {
									candIRISet.add(p.getIRI());
								}
							}
						}
					}
				}
			}
		}
	}

	// In the case where we find multiple candidate IRIs, we give priorities for IRIs from BFO or RO ontologies.
	IRI returnIRI = null;
	for (IRI iri: candIRISet) {
		String iriStr = iri.toString();
		if (iriStr.contains("BFO") || iriStr.contains("RO")) {
			returnIRI = iri;
		}
	}

	// If we were not able to find RO/BFO candidate IRIs for id
	if (returnIRI == null) {
		// We return it only if we have only one candidate. 
		if (candIRISet.size() == 1)
			return new ArrayList<IRI>(candIRISet).get(0);
		// This is the unexpected case. Multiple non-RO/BPO properties are mapped to given id and it's not clear what to return.
		else if (candIRISet.size() > 1)
			throw new RuntimeException("Multiple candidate IRIs are found for id: " +  id + ". None of them are from BFO or RO.");
	}
	// If we were able to find the property from RO/BFO, just return it. 
	else {
		return returnIRI;
	}

	// 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);
}