Java OWLAnnotation.getProperty方法代码示例

import org.semanticweb.owlapi.model.OWLAnnotation; //导入方法依赖的package包/类
@Override
public Set<String> getPrefLabels(OWLEntity cpt) {
	Set<String> finalLabels = new HashSet<String>();
	Set<OWLAnnotation> annotations = cpt.getAnnotations(ontology);
	for(OWLAnnotation annot : annotations) {
		if(annot.getValue() instanceof OWLLiteral) {
			OWLAnnotationProperty prop = annot.getProperty();
			// The DOE prefLabel, if they exist
			if(prop.getIRI().equals(prefLabelIRI) ||
				prop.getIRI().equals(SKOSVocabulary.PREFLABEL.getIRI()) ||
				prop.getIRI().equals(OWLRDFVocabulary.RDFS_LABEL.getIRI())) {

				OWLLiteral literal = (OWLLiteral)annot.getValue();
				finalLabels.add(literal.getLiteral());
			}
		}
	}
	return finalLabels;
}
 

import org.semanticweb.owlapi.model.OWLAnnotation; //导入方法依赖的package包/类
@Override
public Set<String> getAltLabels(OWLEntity cpt) {
	Set<String> finalLabels = new HashSet<String>();
	Set<OWLAnnotation> annotations = cpt.getAnnotations(ontology);
	for(OWLAnnotation annot : annotations) {
		if(annot.getValue() instanceof OWLLiteral) {
			OWLAnnotationProperty prop = annot.getProperty();
			// The DOE prefLabel, if they exist
			if(prop.getIRI().equals(altLabelIRI) ||
				prop.getIRI().equals(hiddenLabelIRI) ||
				prop.getIRI().equals(SKOSVocabulary.ALTLABEL.getIRI()) ||
				prop.getIRI().equals(SKOSVocabulary.HIDDENLABEL.getIRI())) {

				OWLLiteral literal = (OWLLiteral)annot.getValue();
				finalLabels.add(literal.getLiteral());
			}
		}
	}
	return finalLabels;
}
 

import org.semanticweb.owlapi.model.OWLAnnotation; //导入方法依赖的package包/类
private static void extractEvidenceIRIValues(OWLAnnotation annotation, final Set<IRI> iriSet) {
	if (annotation != null) {
		OWLAnnotationProperty property = annotation.getProperty();
		if (HAS_EVIDENCE_IRI.equals(property.getIRI()) || HAS_EVIDENCE_IRI_OLD.equals(property.getIRI())){
			annotation.getValue().accept(new OWLAnnotationValueVisitor() {

				@Override
				public void visit(OWLLiteral literal) {
					// ignore
				}

				@Override
				public void visit(OWLAnonymousIndividual individual) {
					// ignore
				}

				@Override
				public void visit(IRI iri) {
					iriSet.add(iri);
				}
			});
		}
	}
}
 

import org.semanticweb.owlapi.model.OWLAnnotation; //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.OWLAnnotation; //导入方法依赖的package包/类
private Map<String,String> renderAnnotations(Set<OWLAnnotation> annotations) {
	Map<String,String> result = null;
	if (annotations != null && !annotations.isEmpty()) {
		for (OWLAnnotation annotation : annotations) {
			OWLAnnotationProperty prop = annotation.getProperty();
			String literal = getLiteralValue(annotation.getValue());
			if (literal != null) {
				if (result == null) {
					result = new HashMap<String, String>();
				}
				result.put(prop.toStringID(), literal);
			}
		}
	}
	return result;
}
 

import org.semanticweb.owlapi.model.OWLAnnotation; //导入方法依赖的package包/类
private void removeDirectives() {
	// TODO decide: move the set of directives into a constant/static collection?
	
	Set<IRI> directivesIRIs = new HashSet<IRI>();
	directivesIRIs.add(Obo2OWLVocabulary.IRI_OIO_LogicalDefinitionViewRelation.getIRI());
	directivesIRIs.add(Obo2OWLVocabulary.IRI_OIO_treatXrefsAsEquivalent.getIRI());
	directivesIRIs.add(Obo2OWLVocabulary.IRI_OIO_treatXrefsAsGenusDifferentia.getIRI());
	directivesIRIs.add(Obo2OWLVocabulary.IRI_OIO_treatXrefsAsHasSubClass.getIRI());
	directivesIRIs.add(Obo2OWLVocabulary.IRI_OIO_treatXrefsAsIsA.getIRI());
	directivesIRIs.add(Obo2OWLVocabulary.IRI_OIO_treatXrefsAsRelationship.getIRI());
	directivesIRIs.add(Obo2OWLVocabulary.IRI_OIO_treatXrefsAsReverseGenusDifferentia.getIRI());
	
	OWLOntology o = graph.getSourceOntology();
	for(OWLAnnotation ann : o.getAnnotations()) {
		final OWLAnnotationProperty property = ann.getProperty();
		if (directivesIRIs.contains(property.getIRI())) {
			manager.applyChange(new RemoveOntologyAnnotation(o, ann));
		}
	}
}
 

import org.semanticweb.owlapi.model.OWLAnnotation; //导入方法依赖的package包/类
/**
 * Retrieve the literal values for the axiom annotations with the given
 * annotation property IRI.
 * 
 * @param iri
 * @param axiom
 * @return literal values or null
 */
public static List<String> getAxiomAnnotationValues(IRI iri, OWLAxiom axiom) {
	List<String> result = null;
	for(OWLAnnotation annotation : axiom.getAnnotations()) {
		OWLAnnotationProperty property = annotation.getProperty();
		if (property.getIRI().equals(iri)) {
			OWLAnnotationValue value = annotation.getValue();
			if (value instanceof OWLLiteral) {
				String literal = ((OWLLiteral) value).getLiteral();
				if (result == null) {
					result = Collections.singletonList(literal);
				}
				else if (result.size() == 1) {
					result = new ArrayList<String>(result);
					result.add(literal);
				}
				else {
					result.add(literal);
				}
			}
		}
	}
	return result;
}
 

import org.semanticweb.owlapi.model.OWLAnnotation; //导入方法依赖的package包/类
private String getOntologyAnnotationValue(OWLOntology o, OboFormatTag tag) {
	IRI dateTagIRI = Obo2Owl.trTagToIRI(tag.getTag());
	Set<OWLAnnotation> annotations = o.getAnnotations();
	for (OWLAnnotation annotation : annotations) {
		OWLAnnotationProperty property = annotation.getProperty();
		if(dateTagIRI.equals(property.getIRI())) {
			OWLAnnotationValue value = annotation.getValue();
			if (value != null) {
				if (value instanceof IRI) {
					return ((IRI) value).toString();
				}
				else if (value instanceof OWLLiteral) {
					return ((OWLLiteral) value).getLiteral();
				}
			}
		}
	}
	return null;
}
 

import org.semanticweb.owlapi.model.OWLAnnotation; //导入方法依赖的package包/类
private Metadata extractMetadata(Collection<OWLAnnotation> annotations, OWLGraphWrapper modelGraph, String modelId) {
	Metadata metadata = new Metadata();
	metadata.modelId = modelId;
	if (annotations != null && !annotations.isEmpty()) {
		for (OWLAnnotation owlAnnotation : annotations) {
			OWLAnnotationProperty currentProperty = owlAnnotation.getProperty();
			OWLAnnotationValue value = owlAnnotation.getValue();
			extractMetadata(currentProperty, value, metadata);
		}
	}
	return metadata;
}
 

import org.semanticweb.owlapi.model.OWLAnnotation; //导入方法依赖的package包/类
public void getRdfsLabels() {
	rdfsLabels = new HashMap<String, String>();
	prefAltLabels = new HashMap<String, String>();
	Set<OWLClass> classes = getAllConcepts();
	String prefLabelIri = "<http://www.w3.org/2004/02/skos/core#prefLabel>";
	String altLabelIri = "<http://www.w3.org/2004/02/skos/core#altLabel>";
	for (OWLClass cls : classes) {
		for (OWLAnnotation a : EntitySearcher.getAnnotations(cls, ontology)) {
			// properties are of several types: rdfs-label, altLabel or prefLabel
			OWLAnnotationProperty prop = a.getProperty();
			OWLAnnotationValue val = a.getValue();
			if (val instanceof OWLLiteral) {
				// RDFS-labels
				if (prop.isLabel()) {
					// System.out.println(cls + " labelled " + ((OWLLiteral) val).getLiteral());
					// classes can have several rdfs labels
					rdfsLabels.put(((OWLLiteral)val).getLiteral(), cls.toString());
				}
				// preferred or alternative labels
				else if (prop.toString().equals(prefLabelIri) || prop.toString().equals(altLabelIri)) {
					// System.out.println(cls + " labelled (pref or alt) " + ((OWLLiteral)
					// val).getLiteral());
					// classes can have several labels
					prefAltLabels.put(((OWLLiteral)val).getLiteral(), cls.toString());
				}
			}
		}
	}
}
 

import org.semanticweb.owlapi.model.OWLAnnotation; //导入方法依赖的package包/类
/**
 * Remove axiom annotations, which do not comply with the OBO-Basic level,
 * i.e. trailing qualifier values in OBO.<br>
 * <b>Side effect</b>: This removes the old axiom and adds the new axiom to
 * the given ontology. The method also returns the new axiom to enable
 * chaining.
 * 
 * @param axiom
 * @param ontology
 * @return axiom
 */
public static OWLAxiom reduceAxiomAnnotationsToOboBasic(OWLAxiom axiom, OWLOntology ontology) {
	Set<OWLAnnotation> annotations = axiom.getAnnotations();
	if (annotations != null && !annotations.isEmpty()) {
		boolean changed = false;
		Set<OWLAnnotation> newAnnotations = new HashSet<OWLAnnotation>();
		for (OWLAnnotation owlAnnotation : annotations) {
			OWLAnnotationProperty p = owlAnnotation.getProperty();
			IRI iri = p.getIRI();
			/*
			 * if the property IRI is not in a predefined annotation property in 
			 * Obo2Owl assume that it's not OBO-Basic
			 */
			if (Obo2Owl.ANNOTATIONPROPERTYMAP.containsValue(iri) == false) {
				// remove axiom annotation
				changed = true;
			}
			else {
				newAnnotations.add(owlAnnotation);
			}
		}
		if (changed) {
			// only update the axiom if the annotations have been changed
			OWLAxiom newAxiom = AxiomAnnotationTools.changeAxiomAnnotations(axiom, newAnnotations, ontology);
			return newAxiom;
		}
	}
	return axiom;
}
 

import org.semanticweb.owlapi.model.OWLAnnotation; //导入方法依赖的package包/类
public List<String> validateBeforeSave(ModelContainer model) throws OWLOntologyCreationException {
	// get model
	List<String> errors = new ArrayList<String>(3);
	// check that model has required meta data
	OWLOntology aboxOntology = model.getAboxOntology();
	boolean hasTitle = false;
	boolean hasContributor = false;
	
	// get ontology annotations
	Set<OWLAnnotation> annotations = aboxOntology.getAnnotations();
	for (OWLAnnotation annotation : annotations) {
		OWLAnnotationProperty p = annotation.getProperty();
		AnnotationShorthand legoType = AnnotationShorthand.getShorthand(p.getIRI());
		if (legoType != null) {
			// check for title
			if (AnnotationShorthand.title.equals(legoType)) {
				hasTitle = true;
			}
			// check for contributor
			else if (AnnotationShorthand.contributor.equals(legoType)) {
				hasContributor = true;
			}
		}
	}

	if (hasTitle == false) {
		errors.add("The model has no title. All models must have a human readable title.");
	}
	if (hasContributor == false) {
		errors.add("The model has no contributors. All models must have an association with their contributors.");
	}
	
	// require at least one declared instance
	Set<OWLNamedIndividual> individuals = aboxOntology.getIndividualsInSignature();
	if (individuals.isEmpty()) {
		errors.add("The model has no individuals. Empty models should not be saved.");
	}
	
	// avoid returning empty list
	if (errors.isEmpty()) {
		errors = null;
	}
	return errors;
}
 

import org.semanticweb.owlapi.model.OWLAnnotation; //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);
}