Java Code Examples for org.semanticweb.owlapi.model.OWLObjectSomeValuesFrom#getFiller()

private static Set<OWLObjectSomeValuesFrom> filterSVFs(final OWLClassFilter clsFilter, Set<OWLObjectSomeValuesFrom> svfs) {
	Predicate<OWLObjectSomeValuesFrom> predicate = new Predicate<OWLObjectSomeValuesFrom>() {

		@Override
		public boolean apply(OWLObjectSomeValuesFrom input) {
			OWLClassExpression filler = input.getFiller();
			Boolean result = filler.accept(new OWLClassExpressionVisitorExAdapter<Boolean>(Boolean.FALSE){
				@Override
				public Boolean visit(OWLClass cls) {
					return clsFilter.use(cls);
				}
			});
			if (result != null) {
				return result.booleanValue();
			}
			return false;
		}
	};
	svfs = Sets.filter(svfs, predicate);
	return svfs;
}
 

private void handleIntersection(List<CheckWarning> warnings, Set<OWLOntology> allOntologies,
		OWLEquivalentClassesAxiom axiom, OWLObjectIntersectionOf intersection, OWLPrettyPrinter pp) 
{
	for(OWLClassExpression operand : intersection.getOperandsAsList()) {
		OWLClass operandCls = null;
		if (!operand.isAnonymous()) {
			operandCls = operand.asOWLClass();
		}
		else if (operand instanceof OWLObjectSomeValuesFrom) {
			OWLObjectSomeValuesFrom ristriction = (OWLObjectSomeValuesFrom) operand;
			OWLClassExpression filler = ristriction.getFiller();
			if (!filler.isAnonymous()) {
				operandCls = filler.asOWLClass();
			}
		}
		else {
			// not translatable to OBO
			handleGeneric(warnings, allOntologies, axiom, operand, pp);
		}
		if (operandCls != null && isDangling(operandCls, allOntologies)) {
			final IRI iri = operandCls.getIRI();
			String message = "Dangling reference "+iri+" in INTERSECTION_OF axiom: "+pp.render(axiom);
			warnings.add(new CheckWarning(getID(), message , isFatal(), iri, OboFormatTag.TAG_INTERSECTION_OF.getTag()));
		}
	}
}
 

private void renderAdditionalNodeExpression(StringBuilder line, OWLClassExpression expression, OWLPrettyPrinter owlpp) {
	if (expression instanceof OWLObjectSomeValuesFrom) {
		OWLObjectSomeValuesFrom object = (OWLObjectSomeValuesFrom) expression;
		OWLObjectPropertyExpression property = object.getProperty();
		OWLClassExpression filler = object.getFiller();
		line.append("<TR><TD>");
		line.append(getLabel(property, owlpp));
		line.append("</TD><TD>");
		line.append(getLabel(filler, owlpp));
		line.append("</TD></TR>");
	}
	else {
		line.append("<TR><TD COLSPAN=\"2\">");
		line.append(getLabel(expression, owlpp));
		line.append("</TD></TR>");
	}
}
 

private void renderAdditionalNodeExpression(StringBuilder line, OWLClassExpression expression, OWLPrettyPrinter owlpp, OWLGraphWrapper graph) {
	if (expression instanceof OWLObjectSomeValuesFrom) {
		OWLObjectSomeValuesFrom object = (OWLObjectSomeValuesFrom) expression;
		OWLObjectPropertyExpression property = object.getProperty();
		OWLClassExpression filler = object.getFiller();
		line.append("<TR><TD>");
		line.append(getLabel(property, owlpp, graph));
		line.append("</TD><TD>");
		line.append(getLabel(filler, owlpp, graph));
		line.append("</TD></TR>");
	}
	else {
		line.append("<TR><TD COLSPAN=\"2\">");
		line.append(getLabel(expression, owlpp, graph));
		line.append("</TD></TR>");
	}
}
 

/**
 * Check that the given subClass does not already has a matching subClass axiom.
 * 
 * @param subCls
 * @param p
 * @param superCls
 * @return existing axiom or null
 */
private OWLAxiom hasLinks(OWLClass subCls, OWLObjectProperty p, OWLClass superCls) {
	for(OWLOntology o : allOntologies) {
		Set<OWLSubClassOfAxiom> subClsAxioms = o.getSubClassAxiomsForSubClass(subCls);
		for (OWLSubClassOfAxiom subClsAxiom : subClsAxioms) {
			OWLClassExpression ce = subClsAxiom.getSuperClass();
			if (ce instanceof OWLObjectSomeValuesFrom) {
				OWLObjectSomeValuesFrom someValuesFrom = (OWLObjectSomeValuesFrom) ce;
				OWLObjectPropertyExpression property = someValuesFrom.getProperty();
				if (p.equals(property)) {
					OWLClassExpression filler = someValuesFrom.getFiller();
					if (superCls.equals(filler)) {
						return subClsAxiom;
					}
				}
			}
		}
	}
	return null;
}
 

Set<OWLClass> getSvfClasses(OWLClass c, OWLObjectProperty p) {
	Set<OWLSubClassOfAxiom> axioms = new HashSet<OWLSubClassOfAxiom>();
	for(OWLOntology ont : getAllOntologies()) {
		axioms.addAll(ont.getSubClassAxiomsForSubClass(c));
	}
	Set<OWLClass> superClasses = new HashSet<OWLClass>();
	for (OWLSubClassOfAxiom axiom : axioms) {
		OWLClassExpression expr = axiom.getSuperClass();
		if (expr instanceof OWLObjectSomeValuesFrom) {
			OWLObjectSomeValuesFrom svf = (OWLObjectSomeValuesFrom) expr;
			if (p.equals(svf.getProperty())) {
				OWLClassExpression filler = svf.getFiller();
				if (filler instanceof OWLClass) {
					superClasses.add((OWLClass) filler);
				}
			}
		}
	}
	return superClasses;
}
 

/**
 * Names all inner ObjectSomeValuesFrom expressions
 * 
 * @param srcOntology
 * @param tgtOntology
 * @param qmap
 * @param isAddLabels
 * @return
 */
public static Map<OWLClass, OWLClassExpression> nameObjectSomeValuesFrom(OWLOntology srcOntology,
		OWLOntology tgtOntology,
		Map<OWLClass,OWLClassExpression> qmap,
		boolean isAddLabels) {

	if (qmap == null) 
		qmap = new HashMap<OWLClass, OWLClassExpression>();
	OWLOntologyManager mgr = srcOntology.getOWLOntologyManager();
	OWLDataFactory df = mgr.getOWLDataFactory();
	for (OWLOntology ont : srcOntology.getImportsClosure()) {
		for (OWLAxiom ax : srcOntology.getAxioms()) {
			for (OWLClassExpression x : ax.getNestedClassExpressions()) {
				if (x instanceof OWLObjectSomeValuesFrom) {
					OWLObjectSomeValuesFrom svf = (OWLObjectSomeValuesFrom)x;
					OWLClass filler = (OWLClass) svf.getFiller();
					OWLObjectProperty p = (OWLObjectProperty) svf.getProperty();
					IRI iri = getSkolemIRI(filler, p);
					OWLClass c = df.getOWLClass(iri);
					mgr.addAxiom(tgtOntology, df.getOWLEquivalentClassesAxiom(c, svf));
					qmap.put(c, svf);
					if (isAddLabels) {
						Set<OWLAnnotation> anns = OwlHelper.getAnnotations(filler, df.getRDFSLabel(), ont);
						for (OWLAnnotation ann : anns) {
							mgr.addAxiom(tgtOntology, df.getOWLAnnotationAssertionAxiom(c.getIRI(), ann));
						}
					}
				}
			}
		}
	}
	return qmap;

}
 

/**
 * Retrieve a map of related classes for a particular class.
 * 
 * @param owlClass
 * @return a map of relation type to a list of IRIs for nodes with that
 * relationship.
 */
public Map<String, List<String>> getRestrictions(OWLClass owlClass) {
	RestrictionVisitor visitor = new RestrictionVisitor(Collections.singleton(ontology));
	for (OWLSubClassOfAxiom ax : ontology.getSubClassAxiomsForSubClass(owlClass)) {
		OWLClassExpression superCls = ax.getSuperClass();
		// Ask our superclass to accept a visit from the RestrictionVisitor
		// - if it is an existential restriction then our restriction visitor
		// will answer it - if not our visitor will ignore it
		superCls.accept(visitor);
	}

	Map<String, List<String>> restrictions = new HashMap<>();
	for (OWLObjectSomeValuesFrom val : visitor.getSomeValues()) {
		OWLClassExpression exp = val.getFiller();

		// Get the shortname of the property expression
		String shortForm = null;
		Set<OWLObjectProperty> signatureProps = val.getProperty().getObjectPropertiesInSignature();
		for (OWLObjectProperty sigProp : signatureProps) {
			Collection<String> labels = findLabels(sigProp.getIRI());
			if (labels.size() > 0) {
				shortForm = new ArrayList<String>(labels).get(0);
			}
		}

		if (shortForm != null && !exp.isAnonymous()) {
			IRI iri = exp.asOWLClass().getIRI();

			if (!restrictions.containsKey(shortForm)) {
				restrictions.put(shortForm, new ArrayList<String>());
			}
			restrictions.get(shortForm).add(iri.toString());
		}
	}

	return restrictions;
}
 

/**
 * Classify the an edge and target as a human readable string for further processing.
 * 
 * @param owlGraphEdge edge under consideration
 * @param edgeDirector 
 * @param props properties set
 * @return null, "simplesubclass", "typesubclass", or "identity".
 * @see #addDirectDescendentsToShuntGraph
 * @see #addStepwiseAncestorsToShuntGraph
 */
public String classifyRelationship(OWLGraphEdge owlGraphEdge, OWLObject edgeDirector, Set<? extends OWLPropertyExpression> props){		
	String retval = null;
	
	OWLQuantifiedProperty qp = owlGraphEdge.getSingleQuantifiedProperty();
	if( qp.isSubClassOf() || props.contains(qp.getProperty()) ){
		//OWLObject target = owlGraphEdge.getTarget();
		if( edgeDirector instanceof OWLClass ){
			retval = "simplesubclass";
		}else if( edgeDirector instanceof OWLObjectSomeValuesFrom ){
			OWLObjectSomeValuesFrom some = (OWLObjectSomeValuesFrom)edgeDirector;
			if( props.contains(some.getProperty()) ){
				OWLClassExpression clsexp = some.getFiller();
				if( ! clsexp.isAnonymous()){
					retval = "typesubclass";
				}
			}
		}
	}else if( qp.isIdentity() ){
		retval = "identity";
	}else{
		if (LOG.isDebugEnabled()) {
			LOG.debug("Skipping complex edge: "+owlGraphEdge);
		}
	}
	
	return retval;
}
 

@Override
public OWLObjectSomeValuesFrom visit(OWLObjectSomeValuesFrom ce) {
	if (LOG.isDebugEnabled()) {
		LOG.debug("Unfolding some_values_from: "+ce);
	}
	
	OWLClassExpression filler = ce.getFiller();
	if (filler != null) {
		OWLClassExpression unfold = filler.accept(this);
		if (unfold != null) {
			return factory.getOWLObjectSomeValuesFrom(ce.getProperty(), unfold);
		}
	}
	return null;
}
 

/**
 * Check all classes for potential redundant subClass axioms of type:
 * <pre>
 *   A SubClassOf R some B
 *    and
 *   A SubClassOf B
 * </pre>
 * 
 * @return list of axiom pairs
 */
public List<PotentialRedundant> checkPotentialRedundantSubClassAxioms() {
	List<PotentialRedundant> result = new ArrayList<PotentialRedundant>();
	for(OWLClass cls : graph.getAllOWLClasses()) {
		Set<OWLSubClassOfAxiom> axioms = graph.getAllOWLSubClassOfAxiomsForSubClass(cls);
		if (axioms.size() > 1) {
			// only check sets with more than one axiom
			for (OWLSubClassOfAxiom main : axioms) {
				OWLClassExpression mainSuperClassCE = main.getSuperClass();
				if (mainSuperClassCE.isAnonymous()) {
					continue;
				}
				OWLClass mainSuperClass = mainSuperClassCE.asOWLClass();
				for (OWLSubClassOfAxiom current : axioms) {
					if (main == current) {
						continue;
					}
					OWLClassExpression currentSuperClass = current.getSuperClass();
					if (currentSuperClass.isAnonymous() && currentSuperClass instanceof OWLObjectSomeValuesFrom) {
						OWLObjectSomeValuesFrom someValuesFrom = (OWLObjectSomeValuesFrom) currentSuperClass;
						final OWLClassExpression filler = someValuesFrom.getFiller();
						if (mainSuperClass.equals(someValuesFrom.getFiller())) {
							final OWLObjectPropertyExpression property = someValuesFrom.getProperty();
							final OWLClassExpression subClass = current.getSubClass();
							final PotentialRedundant redundant = new PotentialRedundant(main, current, subClass.asOWLClass(), property.asOWLObjectProperty(), filler.asOWLClass());
							result.add(redundant);
						}
					}
				}
			}
		}
	}
	
	if (!result.isEmpty()) {
		return result;
	}
	return null;
}
 

/**
	 * Add a set of edges, as ancestors to x in OWLShuntGraph g.
	 * This is reflexive.
	 *
	 * @param x
	 * @param g
	 * @param rel_ids
	 * @return the modified OWLShuntGraph
	 */
	public OWLShuntGraph addStepwiseAncestorsToShuntGraph(OWLObject x, OWLShuntGraph g, List<String> rel_ids) {

		// Add this node, our seed.
		String topicID = getIdentifier(x);
		String topicLabel = getLabel(x);
		OWLShuntNode tn = new OWLShuntNode(topicID, topicLabel);
		g.addNode(tn);

		// NEW VERSION
		Set<OWLObjectProperty> props = relationshipIDsToPropertySet(rel_ids);
		for (OWLGraphEdge e : getOutgoingEdges(x, props)) {
			OWLObject target = e.getTarget();
			String rel = classifyRelationship(e, target, props);

			if( rel != null ){

				// Placeholders.
				String objectID = null;
				String objectLabel = null;
				String elabel = null;
				
				if( rel == "simplesubclass" ){
					objectID = getIdentifier(target);
					objectLabel = getLabelOrDisplayId(target);
					elabel = getEdgeLabel(e);
				}else if( rel == "typesubclass" ){
					OWLObjectSomeValuesFrom some = (OWLObjectSomeValuesFrom)target;
					OWLClassExpression clsexp = some.getFiller();
					OWLClass cls = clsexp.asOWLClass();
					objectID = getIdentifier(cls);
					objectLabel = getLabelOrDisplayId(cls);
					elabel = getEdgeLabel(e);
				}
				
				// Only add when subject, object, and relation are properly defined.
				if(	elabel != null &&
					topicID != null && ! topicID.equals("") &&
					objectID != null &&	! objectID.equals("") ){
	
					// Add node.
					OWLShuntNode sn = new OWLShuntNode(objectID, objectLabel);
					boolean wuzAdded = g.addNode(sn);

					// Recur on node if it already wasn't there.
					if( wuzAdded ){
						addStepwiseAncestorsToShuntGraph(target, g, rel_ids);
					}
				
					//Add edge 
					OWLShuntEdge se = new OWLShuntEdge(topicID, objectID, elabel);
					g.addEdge(se);
				}
			}
		}

// ORIGINAL VERSION
//		// Next, get all of the named ancestors and add them to our shunt graph.
//		// We need some traversal code going up!
//		for (OWLGraphEdge e : getOutgoingEdges(x)) {
//			OWLObject t = e.getTarget();
//			if (t instanceof OWLNamedObject){				
//
//				// Figure out object.
//				String objectID = getIdentifier(t);
//				String objectLabel = getLabel(t);
//
//				// Edge.
//				String elabel = getEdgeLabel(e);
//				
//				// Only add when subject, object, and relation are properly defined.
//				if( elabel != null &&
//					topicID != null && ! topicID.equals("") &&
//					objectID != null &&	! objectID.equals("") ){
//				
//					// Add node.
//					OWLShuntNode sn = new OWLShuntNode(objectID, objectLabel);
//					boolean wuzAdded = g.addNode(sn);
//
//					// Recur on node if it already wasn't there.
//					if( wuzAdded ){
//						addStepwiseAncestorsToShuntGraph(t, g);
//					}
//				
//					//Add edge 
//					OWLShuntEdge se = new OWLShuntEdge(topicID, objectID, elabel);
//					g.addEdge(se);
//				}
//			}
//		}
		
		return g;
	}
 

/**
 * Generates trivial SVF axioms from existing GCIs
 * 
 * <pre>
 * For each GCI of the form CX SubClassOf R some DX
 *  for each C that is an inferred direct subclass of or equivalent to CX
 *     for each D that is an inferred direct superclass of or equivalent to DX
 *       add an axiom C SubClassOf R some D
 * </pre>
 * @param ontology
 * @param reasoner
 * @return axioms
 */
public static Set<OWLSubClassOfAxiom> getSubClassOfSomeValuesFromAxioms(OWLOntology ontology,
		OWLReasoner reasoner) {

	Set<OWLSubClassOfAxiom> axioms = new HashSet<OWLSubClassOfAxiom>();
	OWLDataFactory df = ontology.getOWLOntologyManager().getOWLDataFactory();
	for (OWLSubClassOfAxiom ax : ontology.getAxioms(AxiomType.SUBCLASS_OF)) {
		OWLClassExpression c = ax.getSubClass();
		if (ax.getSuperClass() instanceof OWLObjectSomeValuesFrom) {
			OWLObjectSomeValuesFrom svf = (OWLObjectSomeValuesFrom)ax.getSuperClass();
			OWLObjectPropertyExpression p = svf.getProperty();
			OWLClassExpression filler = svf.getFiller();
			if (filler.isAnonymous() || c.isAnonymous()) {
				if (c.isBottomEntity())
					continue;
				if (filler.isTopEntity())
					continue;
				
				Set<OWLClass> childSet = reasoner.getEquivalentClasses(c).getEntities();
				if (childSet.size() == 0) {
					childSet = reasoner.getSubClasses(c, true).getFlattened();
				}
				for (OWLClass childClass : childSet) {
					if (childClass.isBottomEntity())
						continue;
					Set<OWLClass> childClassSuperClasses = 
							reasoner.getSuperClasses(childClass, false).getFlattened();
					childClassSuperClasses.addAll(reasoner.getEquivalentClasses(childClass).getEntities());
					Set<OWLClass> parentSet = reasoner.getEquivalentClasses(filler).getEntities();
					if (parentSet.size() == 0) {
						parentSet = reasoner.getSuperClasses(filler, true).getFlattened();
					}
					// TODO: remove additional redundancy (R some X) SubClassOf (R some Y)
					// Elk cannot test arbitrary entailments
						for (OWLClass parentClass : parentSet) {
						if (parentClass.isTopEntity())
							continue;
						
						// do not assert C SubClassOf part-of some D, if C SubClassOf D is entailed
						if (childClassSuperClasses.contains(parentClass))
							continue;
						axioms.add(df.getOWLSubClassOfAxiom(childClass, 
								df.getOWLObjectSomeValuesFrom(p, parentClass)));
					}
				}
			}

		}
	}
	LOG.info("Inferred SVFs: "+axioms.size());
	return axioms;
}
 

/**
 * Relaxes all {@code OWLObjectIntersectionOf}s. This method will relax 
 * {@code OWLSubClassOfAxiom}s, whose superclass is an {@code OWLObjectIntersectionOf}, 
 * into multiple {@code OWLSubClassOfAxiom}s, using a <a 
 * href='http://owlapi.sourceforge.net/javadoc/org/semanticweb/owlapi/SplitSubClassAxioms.html'>
 * SplitSubClassAxioms</a>. It will also relax {@code OWLSubClassOfAxiom}s, whose 
 * superclass is an {@code OWLObjectSomeValuesFrom} with a filler being an 
 * {@code OWLObjectIntersectionOf}, into multiple {@code OWLSubClassOfAxiom}s with 
 * an {@code OWLObjectSomeValuesFrom} as superclass, with the same 
 * {@code OWLPropertyExpression}, and individual operands as filler. 
 * <p>
 * Note that it is likely that the {@code OWLObjectIntersectionOf}s where used in
 * {@code OWLEquivalentClassesAxiom}s, rather than in {@code OWLSubClassOfAxiom}s. 
 * But the method {@link #convertEquivalentClassesToSuperClasses()} would have transformed 
 * them into {@code OWLSubClassOfAxiom}s. It must be called before this method.
 * 
 * @see #performDefaultModifications()
 * @see #convertEquivalentClassesToSuperClasses()
 */
private void splitSubClassAxioms() {
    log.info("Relaxing OWLSubClassOfAxioms whose superclass is an OWLObjectIntersectionOf");
    
    //first, split subClassOf axioms whose superclass is an OWLObjectIntersectionOf
    SplitSubClassAxioms split = new SplitSubClassAxioms(
            this.getOwlGraphWrapper().getAllOntologies(), 
            this.getOwlGraphWrapper().getDataFactory());
    this.getOwlGraphWrapper().getManager().applyChanges(split.getChanges());
    this.triggerWrapperUpdate();
    
    //some ontologies use an OWLObjectIntersectionOf as the filler of 
    //an OWLObjectSomeValuesFrom class expression. We go only one level down 
    //(i.e., we would not translate another OWLObjectSomeValuesFrom part of the 
    //OWLObjectIntersectionOf)
    OWLDataFactory dataFactory = this.getOwlGraphWrapper().getDataFactory();
    List<OWLOntologyChange> changes = new ArrayList<OWLOntologyChange>();
    for (OWLOntology ont : this.getOwlGraphWrapper().getAllOntologies()) {
        for (OWLSubClassOfAxiom ax : ont.getAxioms(AxiomType.SUBCLASS_OF)) {
            OWLClassExpression superClsExpr = ax.getSuperClass();
            if (superClsExpr instanceof OWLObjectSomeValuesFrom) {
                OWLObjectSomeValuesFrom someValuesFrom = 
                        (OWLObjectSomeValuesFrom) superClsExpr;
                if (someValuesFrom.getFiller() instanceof OWLObjectIntersectionOf) {
                    //remove original axiom
                    changes.add(new RemoveAxiom(ont, ax));
                    
                    OWLObjectIntersectionOf filler = 
                            (OWLObjectIntersectionOf) someValuesFrom.getFiller();
                    for (OWLClassExpression op : filler.getOperands()) {
                        //we accept only OWLClasses, otherwise we would need to compose 
                        //OWLObjectPropertyExpressions
                        if (op instanceof OWLClass) {
                            OWLAxiom replAx = dataFactory.
                                    getOWLSubClassOfAxiom(ax.getSubClass(), 
                                    dataFactory.getOWLObjectSomeValuesFrom(
                                                someValuesFrom.getProperty(), op));
                            changes.add(new AddAxiom(ont, replAx));
                        }
                    }
                }
                
            }
        }
    }
    this.getOwlGraphWrapper().getManager().applyChanges(changes);
    this.triggerWrapperUpdate();
    
    log.info("OWLObjectIntersectionOf relaxation done.");
}
 

/**
 * Search for the first class with a matching equivalent class definition. 
 * 
 * @param c
 * @param genus
 * @param relation
 * @return match or null
 */
private OWLClass hasMatchingIntersection(OWLClass c, OWLClass genus, OWLObjectProperty relation) {
	for(OWLOntology o : allOntologies) {
		Set<OWLEquivalentClassesAxiom> eqAxioms = o.getEquivalentClassesAxioms(c);
		for (OWLEquivalentClassesAxiom eqAxiom : eqAxioms) {
			Set<OWLClassExpression> expressions = eqAxiom.getClassExpressionsMinus(c);
			for (OWLClassExpression expression : expressions) {
				if (expression instanceof OWLObjectIntersectionOf) {
					OWLObjectIntersectionOf intersection = (OWLObjectIntersectionOf) expression;
					OWLClass differentiaCls = null;
					boolean matchesGenus = false;
					boolean matchesRelation = false;
					Set<OWLClassExpression> operands = intersection.getOperands();
					if (operands.size() == 2) {
						for (OWLClassExpression operand : operands) {
							if (operand.isAnonymous() == false) {
								OWLClass currentGenus = operand.asOWLClass();
								if (genus.equals(currentGenus)) {
									matchesGenus = true;
								}
							}
							else if (operand instanceof OWLObjectSomeValuesFrom) {
								OWLObjectSomeValuesFrom differentia = (OWLObjectSomeValuesFrom) operand;
								if (relation.equals(differentia.getProperty())) {
									matchesRelation = true;
									OWLClassExpression filler = differentia.getFiller();
									if (!filler.isAnonymous() && !filler.isOWLNothing() && !filler.isOWLThing()) {
										differentiaCls = filler.asOWLClass();
									}
								}
							}
						}
						if (matchesGenus && matchesRelation ) {
							 return differentiaCls;
						}
					}
				}
			}
		}
	}
	return null;
}
 

private String getLabel(OWLClassExpression expression, OWLPrettyPrinter owlpp, OWLGraphWrapper graph) {
	if (expression instanceof OWLClass) {
		return graph.getLabelOrDisplayId(expression);
	}
	else if (expression instanceof OWLObjectIntersectionOf) {
		StringBuilder sb = new StringBuilder();
		OWLObjectIntersectionOf intersectionOf = (OWLObjectIntersectionOf) expression;
		sb.append("<TABLE>");
		for (OWLClassExpression ce : intersectionOf.getOperands()) {
			sb.append("<TR><TD>");
			if (ce instanceof OWLClass) {
				sb.append(graph.getLabelOrDisplayId((OWLClass)ce));
			}
			else if (ce instanceof OWLObjectSomeValuesFrom){
				OWLObjectSomeValuesFrom some = (OWLObjectSomeValuesFrom) ce;
				OWLObjectPropertyExpression property = some.getProperty();
				if (property.isAnonymous()) {
					sb.append(owlpp.render(property));
				}
				else {
					sb.append(graph.getLabelOrDisplayId(property.asOWLObjectProperty()));
				}
				sb.append(" <B>some</B> ");
				OWLClassExpression filler = some.getFiller();
				if (filler instanceof OWLClass) {
					sb.append(graph.getLabelOrDisplayId((OWLClass)filler));
				}
				else {
					sb.append(owlpp.render(filler));
				}
			}
			else {
				sb.append(ce.toString());
			}
			sb.append("</TD></TR>");
		}
		sb.append("</TABLE>");
		return sb.toString();
	}
	return owlpp.render(expression);
}
 

private CharSequence getLabel(OWLClassExpression expression, OWLPrettyPrinter owlpp) {
	if (expression instanceof OWLClass) {
		return insertLineBrakes(graph.getLabelOrDisplayId(expression));
	}
	else if (expression instanceof OWLObjectIntersectionOf) {
		StringBuilder sb = new StringBuilder();
		OWLObjectIntersectionOf intersectionOf = (OWLObjectIntersectionOf) expression;
		sb.append("<TABLE>");
		for (OWLClassExpression ce : intersectionOf.getOperands()) {
			sb.append("<TR><TD>");
			if (ce instanceof OWLClass) {
				sb.append(insertLineBrakes(graph.getLabelOrDisplayId((OWLClass)ce)));
			}
			else if (ce instanceof OWLObjectSomeValuesFrom){
				OWLObjectSomeValuesFrom some = (OWLObjectSomeValuesFrom) ce;
				OWLObjectPropertyExpression property = some.getProperty();
				if (property.isAnonymous()) {
					sb.append(owlpp.render(property));
				}
				else {
					sb.append(insertLineBrakes(graph.getLabelOrDisplayId(property.asOWLObjectProperty())));
				}
				sb.append(" <B>some</B> ");
				OWLClassExpression filler = some.getFiller();
				if (filler instanceof OWLClass) {
					sb.append(insertLineBrakes(graph.getLabelOrDisplayId((OWLClass)filler)));
				}
				else {
					sb.append(insertLineBrakes(escape(owlpp.render(filler))));
				}
			}
			else {
				sb.append(insertLineBrakes(escape(ce.toString())));
			}
			sb.append("</TD></TR>");
		}
		sb.append("</TABLE>");
		return sb.toString();
	}
	return insertLineBrakes(escape(owlpp.render(expression)));
}
 

/**
 * Check the list of axioms for potential redundant subClass axioms of type:
 * <pre>
 *   A SubClassOf R some B
 *    and
 *   A SubClassOf B
 * </pre>
 * 
 * @param inferredAxioms
 * @return list of axiom pairs
 */
public List<PotentialRedundant> checkPotentialRedundantSubClassAxioms(Collection<? extends OWLAxiom> inferredAxioms) {
	List<PotentialRedundant> result = new ArrayList<PotentialRedundant>();
	for(OWLAxiom axiom : inferredAxioms) {
		if (axiom instanceof OWLSubClassOfAxiom) {
			OWLSubClassOfAxiom main = (OWLSubClassOfAxiom) axiom;
			OWLClassExpression mainSuperClassCE = main.getSuperClass();
			if (mainSuperClassCE.isAnonymous()) {
				continue;
			}
			OWLClassExpression mainSubClassCE = main.getSubClass();
			if (mainSubClassCE.isAnonymous()) {
				continue;
			}
			OWLClass mainSuperClass = mainSuperClassCE.asOWLClass();
			OWLClass mainSubClass = mainSubClassCE.asOWLClass();
			Set<OWLSubClassOfAxiom> subClassAxioms = graph.getAllOWLSubClassOfAxiomsForSubClass(mainSubClass);
			if (subClassAxioms != null && subClassAxioms.size() > 1) {
				for (OWLSubClassOfAxiom current : subClassAxioms) {
					if (main == current) {
						continue;
					}
					OWLClassExpression currentSuperClass = current.getSuperClass();
					if (currentSuperClass.isAnonymous() && currentSuperClass instanceof OWLObjectSomeValuesFrom) {
						OWLObjectSomeValuesFrom someValuesFrom = (OWLObjectSomeValuesFrom) currentSuperClass;
						final OWLClassExpression filler = someValuesFrom.getFiller();
						if (mainSuperClass.equals(filler)) {
							final OWLObjectPropertyExpression property = someValuesFrom.getProperty();
							final OWLClassExpression subClass = current.getSubClass();
							result.add(new PotentialRedundant(main, current, subClass.asOWLClass(), property.asOWLObjectProperty(), filler.asOWLClass()));
						}
					}
				}
			}
		}
	}
	if (!result.isEmpty()) {
		return result;
	}
	return null;
}
 

/**
 * Create the GCIs for BioChEBI. Add the axioms into the given ontology.
 * 
 * @param ontology
 * @param ignoredClasses
 */
public void expand(OWLOntology ontology, Set<OWLClass> ignoredClasses) {
	final OWLOntologyManager manager = ontology.getOWLOntologyManager();
	final OWLDataFactory factory = manager.getOWLDataFactory();
	
	// scan axioms
	Set<OWLSubClassOfAxiom> axioms = ontology.getAxioms(AxiomType.SUBCLASS_OF, Imports.INCLUDED);
	for (OWLSubClassOfAxiom axiom : axioms) {
		OWLClassExpression superCE = axiom.getSuperClass();
		OWLClassExpression subCE = axiom.getSubClass();
		if (subCE.isAnonymous()) {
			// sub class needs to be an named OWLClass
			continue;
		}

		if (superCE instanceof OWLObjectSomeValuesFrom == false) {
			continue;
		}
		OWLObjectSomeValuesFrom some = (OWLObjectSomeValuesFrom) superCE;

		OWLObjectPropertyExpression expression = some.getProperty();
		if (expression.isAnonymous()) {
			// object property expression needs to be a named OWLObjectProperty 
			continue;
		}

		OWLObjectProperty p = (OWLObjectProperty) expression;
		
		Set<OWLObjectProperty> expansions = expansionMap.get(p);
		if (expansions == null) {
			continue;
		}

		// get content for GCI
		OWLClassExpression y = some.getFiller();
		OWLClass x = subCE.asOWLClass();
		if (ignoredClasses.contains(x)) {
			continue;
		}
		for (OWLObjectProperty createProperty : expansions) {
			OWLClassExpression ce1 = factory.getOWLObjectSomeValuesFrom(createProperty, x);
			OWLClassExpression ce2 = factory.getOWLObjectSomeValuesFrom(createProperty, y);
			OWLEquivalentClassesAxiom eq = factory.getOWLEquivalentClassesAxiom(ce1, ce2);
			manager.addAxiom(ontology, eq);
		}
	}
	
	Set<OWLOntology> imports = ontology.getImports();
	StringBuilder sb = new StringBuilder();
	DateFormat dateFormat = new SimpleDateFormat("yyyy-MM-dd");
	sb.append("Generated on ").append(dateFormat.format(new Date())).append(" using the following import chain:");
	for (OWLOntology owlOntology : imports) {
		OWLOntologyID ontologyID = owlOntology.getOntologyID();
		sb.append(" ");
		appendOntologyId(ontologyID, sb);
	}
	addComment(sb.toString(), ontology);
}