org.semanticweb.owlapi.model.OWLPropertyExpression Java Examples

@Test
public void testSagaTypeComplexWithoutChildren() throws Exception {
	OWLObject focusObject = g.getOWLClassByIdentifier("GO:0070461"); // SAGA-type complex
	Set<OWLPropertyExpression> props = new HashSet<OWLPropertyExpression>();
	props.add(g.getOWLObjectProperty(OBOUpperVocabulary.BFO_part_of.getIRI()));
	
	ShuntGraphPair pair = ShuntGraphUtils.createShuntGraphPair(g, focusObject, props, false);
	
	OWLShuntGraph topology = pair.getTopologyGraph();
	
	checkNodesSagaTypeComplexWithoutChildren(g, topology);
	checkTopologyRelationsSagaTypeComplexWithoutChildren(g, topology);
	
	OWLShuntGraph inferred = pair.getInferredGraph();
	
	checkNodesSagaTypeComplexWithoutChildren(g, inferred);
	checkInferredRelationsSagaTypeComplexWithoutChildren(g, inferred);
}
 

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 static  TaxonomyBuilder<OWLPropertyExpression> buildDataPropertyHierarchy(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.getDataPropertiesInSignature());
	} else {
		props = new HashSet<OWLPropertyExpression>( ont.getDataPropertiesInSignature());
	}
	SubPropertyComputation subcomp = new SubPropertyComputation(tbox);
	TaxonomyBuilder<OWLPropertyExpression> taxoBuilder = new TaxonomyBuilder<OWLPropertyExpression>(
			props, 
			fac.getOWLTopDataProperty(),
			fac.getOWLBottomDataProperty(),
			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;
}
 

@Override
public void build() {
	//build taxonomies
	logger.debug("building data property taxonomy ...");
	dataPropTaxo = buildDataPropertyHierarchy(tbox, additionalDataPropertyExpressions);
	logger.debug("building object property taxonomy ...");
	objPropTaxo = buildObjectPropertyHierarchy(tbox, additionalObjectPropertyExpressions);
	
	logger.debug("building class taxonomy ...");
	classTaxo = buildClassHierarchy(tbox, additionalClassExpressions);
	
	logger.debug("All taxonomies built!");
	//
	Graph<TaxonomyBuilder<OWLPropertyExpression>.TaxoNode> lattice = objPropTaxo.getLattice();
	logger.debug("{}", lattice);
	
}
 

protected void filterEdges(Set<OWLGraphEdge> edges, Set<? extends OWLPropertyExpression> overProperties) {
	Set<OWLGraphEdge> rmEdges = new OWLGraphEdgeSet();
	for (OWLGraphEdge e : edges) {
		if (overProperties != null) {
			if (e.getQuantifiedPropertyList().size() > 1) {
				// if a filter set is provided, do not yield any chains
				rmEdges.add(e);
				continue;					
			}
			OWLQuantifiedProperty qp = e.getSingleQuantifiedProperty();
			if (qp.isSomeValuesFrom() && !overProperties.contains(qp.getProperty())) {
				rmEdges.add(e);
				continue;
			}
		}
		if (isExcludeEdge(e)) {
			rmEdges.add(e);
		}
	}

	edges.removeAll(rmEdges);
}
 

/**
 * returns a query triple corresponding to a property expression
 * 	<ul>
 * 	<li> R  --> x R y </li>
 *  <li> inv(R) --> y R x </li>
 * </ul>
 * 
 */
protected static Triple toTriple(OWLPropertyExpression pe, Node x, Node y, NewVariableGenerator varGen) {
	pe = getSimplified(pe);
	if (!pe.isAnonymous()) {
		OWLProperty p = (OWLProperty) pe;
		 return new Triple(
					x,
					NodeFactory.createURI(p.getIRI().toString()),
					y); 
	} else {
		assert pe instanceof OWLObjectInverseOf: pe;
		OWLObjectInverseOf inv = (OWLObjectInverseOf) pe;
		OWLObjectProperty p = (OWLObjectProperty) inv.getInverse();
		 return new Triple(
					y,
					NodeFactory.createURI(p.getIRI().toString()),
					x); 
	}
}
 

@Test
public void testSagaTypeComplexWithChildren() throws Exception {
	OWLObject focusObject = g.getOWLClassByIdentifier("GO:0070461"); // SAGA-type complex
	Set<OWLPropertyExpression> props = new HashSet<OWLPropertyExpression>();
	props.add(g.getOWLObjectProperty(OBOUpperVocabulary.BFO_part_of.getIRI()));
	
	ShuntGraphPair pair = ShuntGraphUtils.createShuntGraphPair(g, focusObject, props, true);
	
	OWLShuntGraph topology = pair.getTopologyGraph();
	
	checkNodesSagaTypeComplexWithChildren(g, topology);
	checkTopologyRelationsSagaTypeComplexWithChildren(g, topology);
	
	OWLShuntGraph inferred = pair.getInferredGraph();
	
	checkNodesSagaTypeComplexWithChildren(g, inferred);
	checkInferredRelationsSagaTypeComplexWithChildren(g, inferred);
}
 

@Test
public void testSagaComplex() throws Exception {
	OWLObject focusObject = g.getOWLClassByIdentifier("GO:0000124"); // SAGA complex
	Set<OWLPropertyExpression> props = new HashSet<OWLPropertyExpression>();
	props.add(g.getOWLObjectProperty(OBOUpperVocabulary.BFO_part_of.getIRI()));
	
	ShuntGraphPair pair = ShuntGraphUtils.createShuntGraphPair(g, focusObject, props, true);
	
	OWLShuntGraph topology = pair.getTopologyGraph();
	
	checkNodesSagaComplex(g, topology);
	checkTopologyRelationsSagaComplex(g, topology);
	
	OWLShuntGraph inferred = pair.getInferredGraph();
	
	checkNodesSagaComplex(g, inferred);
	checkInferredRelationsSagaComplex(g, inferred);
}
 

@Override
public Set<OWLPropertyExpression> getToldSubsumers(
		OWLPropertyExpression sub) {
	if (!sub.isAnonymous()) {
		Set<OWLPropertyExpression> ret = new HashSet<OWLPropertyExpression>();
		Set<? extends OWLSubPropertyAxiom> axioms;// = new HashSet<? extends OWLSubPropertyAxiom>();
		if (sub.isObjectPropertyExpression()) {
			axioms = tbox.getNormalizedOntology().getObjectSubPropertyAxiomsForSubProperty(
					(OWLObjectPropertyExpression) sub);
		} else if (!sub.isAnonymous()) {
			axioms = tbox.getNormalizedOntology().getDataSubPropertyAxiomsForSubProperty(
					((OWLDataPropertyExpression) sub).asOWLDataProperty());
		} else {
			axioms = Collections.EMPTY_SET;
		}
		if (axioms!=null) {
			for (OWLSubPropertyAxiom ax: axioms) {
				assert ax.getSubProperty().equals(sub) : ax+"\n"+sub;
				ret.add(ax.getSuperProperty());
			}
		}
		return ret;
	}
	return Collections.EMPTY_SET;
}
 

/**
 * Test {@link OWLGraphWrapperEdgesExtended#getOntologyRoots(Set)} and 
 * {@link OWLGraphWrapperEdgesExtended#getOntologyRoots()}.
 */
@Test
public void shouldGetOntologyRoots() {
	//the ontology has 2 roots, FOO:0001 and FOO:0100
    //NCBITaxon are due to GCI relations
    Set<OWLClass> expectedRoots = new HashSet<OWLClass>(Arrays.asList(
            wrapper.getOWLClassByIdentifier("FOO:0001"), 
            wrapper.getOWLClassByIdentifier("FOO:0100"), 
            wrapper.getOWLClassByIdentifier("NCBITaxon:1"))); 
	assertEquals("Incorrect roots returned", expectedRoots, wrapper.getOntologyRoots());
	
	expectedRoots = new HashSet<OWLClass>(Arrays.asList(
               wrapper.getOWLClassByIdentifier("FOO:0001"), 
               wrapper.getOWLClassByIdentifier("FOO:0100"), 
               wrapper.getOWLClassByIdentifier("NCBITaxon:1"), 
               wrapper.getOWLClassByIdentifier("FOO:0012"), 
               wrapper.getOWLClassByIdentifier("FOO:0007"), 
               wrapper.getOWLClassByIdentifier("FOO:0008"), 
               wrapper.getOWLClassByIdentifier("FOO:0009")));
       assertEquals("Incorrect roots returned", expectedRoots, 
               wrapper.getOntologyRoots(new HashSet<OWLPropertyExpression>(
                   Arrays.asList(wrapper.getOWLObjectPropertyByIdentifier("BFO:0000050")))));
}
 

@Test
public void testSagaTypeComplexWithoutChildren() throws Exception {
	OWLObject focusObject = g.getOWLClassByIdentifier("GO:0070461"); // SAGA-type complex
	Set<OWLPropertyExpression> props = new HashSet<OWLPropertyExpression>();
	props.add(g.getOWLObjectProperty(OBOUpperVocabulary.BFO_part_of.getIRI()));
	
	ShuntGraphPair pair = ShuntGraphUtils.createShuntGraphPair(g, focusObject, props, false);
	
	OWLShuntGraph topology = pair.getTopologyGraph();
	
	checkNodesSagaTypeComplexWithoutChildren(g, topology);
	checkTopologyRelationsSagaTypeComplexWithoutChildren(g, topology);
	
	OWLShuntGraph inferred = pair.getInferredGraph();
	
	checkNodesSagaTypeComplexWithoutChildren(g, inferred);
	checkInferredRelationsSagaTypeComplexWithoutChildren(g, inferred);
}
 

public Set<OWLPropertyExpression> getUnsatisfiablePropertyExpressions() {
	Set<OWLPropertyExpression> ret = new HashSet<OWLPropertyExpression>();
	ret.addAll(dataPropTaxo.getBottomNode().getEquivalentElements());
	ret.remove(dataPropTaxo.getBottom());
	/*for (OWLPropertyExpression c : objPropTaxo.getBottomNode().getEquivalentElements()) {
		if (!c.isAnonymous()) {
			ret.add(c); 
		} else {
			//OWLObjectProperty op =  ((OWLObjectPropertyExpression) c).getNamedProperty();//fac.getOWLObjectProperty(IRI.create(ATermUtils.makeInv(c).getAFun().getName()));
			//if (oprops.contains(op)) 
			{
				ret.add(c);
			} 
			//else {
				// do nothing: inverse of a create role R, where R is defined as equivalent to the inverse of an existing role
			//}
		}
	}*/
	ret.addAll(objPropTaxo.getBottomNode().getEquivalentElements());
	ret.remove(objPropTaxo.getBottom());
	ret.remove(fac.getOWLObjectInverseOf((OWLObjectPropertyExpression) objPropTaxo.getBottom()).getSimplified());
	return ret;
}
 

public Set<OWLPropertyExpression> getAllSubproperties(
		OWLPropertyExpression roleSup) {
	Set<OWLPropertyExpression> subs = new HashSet<OWLPropertyExpression>();
	for (OWLPropertyExpression sub : 
			roleSup.isDataPropertyExpression()? dataPropTaxo.getSubsumeesOrSelf(roleSup)
			: objPropTaxo.getSubsumeesOrSelf(roleSup)) {
		if (!sub.isAnonymous()) {
			subs.add(sub); 
		} else {
			//OWLObjectProperty op = ((OWLObjectPropertyExpression) c).getNamedProperty(); //fac.getOWLObjectProperty(IRI.create(sub.getInverse().getName().getAFun().getName()));
			//if (oprops.contains(op))
			{
				subs.add(sub);
			} 
			//else {
				// do nothing: inverse of a create role R, where R is defined as equivalent to the inverse of an existing role
			//}
		}
	}
	subs.remove(dataPropTaxo.getBottom());
	subs.remove(objPropTaxo.getBottom());
	subs.remove(fac.getOWLObjectInverseOf((OWLObjectPropertyExpression) objPropTaxo.getBottom()).getSimplified());

	return subs;
}
 

@Test
public void testSagaTypeComplexWithChildren() throws Exception {
	OWLObject focusObject = g.getOWLClassByIdentifier("GO:0070461"); // SAGA-type complex
	Set<OWLPropertyExpression> props = new HashSet<OWLPropertyExpression>();
	props.add(g.getOWLObjectProperty(OBOUpperVocabulary.BFO_part_of.getIRI()));
	
	ShuntGraphPair pair = ShuntGraphUtils.createShuntGraphPair(g, focusObject, props, true);
	
	OWLShuntGraph topology = pair.getTopologyGraph();
	
	checkNodesSagaTypeComplexWithChildren(g, topology);
	checkTopologyRelationsSagaTypeComplexWithChildren(g, topology);
	
	OWLShuntGraph inferred = pair.getInferredGraph();
	
	checkNodesSagaTypeComplexWithChildren(g, inferred);
	checkInferredRelationsSagaTypeComplexWithChildren(g, inferred);
}
 

@Test
public void testSagaComplex() throws Exception {
	OWLObject focusObject = g.getOWLClassByIdentifier("GO:0000124"); // SAGA complex
	Set<OWLPropertyExpression> props = new HashSet<OWLPropertyExpression>();
	props.add(g.getOWLObjectProperty(OBOUpperVocabulary.BFO_part_of.getIRI()));
	
	ShuntGraphPair pair = ShuntGraphUtils.createShuntGraphPair(g, focusObject, props, true);
	
	OWLShuntGraph topology = pair.getTopologyGraph();
	
	checkNodesSagaComplex(g, topology);
	checkTopologyRelationsSagaComplex(g, topology);
	
	OWLShuntGraph inferred = pair.getInferredGraph();
	
	checkNodesSagaComplex(g, inferred);
	checkInferredRelationsSagaComplex(g, inferred);
}
 

/**
 * Test {@link OWLGraphWrapperEdgesExtended#getNamedAncestorsWithGCI(OWLClass, Set)}.
 */
@SuppressWarnings("rawtypes")
@Test
public void shouldGetGCIAncestorsOverProps() throws OWLOntologyCreationException, 
OBOFormatParserException, IOException {
    ParserWrapper parserWrapper = new ParserWrapper();
    OWLOntology ont = parserWrapper.parse(this.getClass().getResource(
            "/graph/gciRelRetrieval.obo").getFile());
    OWLGraphWrapper wrapper = new OWLGraphWrapper(ont);
    
    OWLClass cls8 = wrapper.getOWLClassByIdentifier("ID:8");
    OWLClass cls6 = wrapper.getOWLClassByIdentifier("ID:6");
    OWLClass cls4 = wrapper.getOWLClassByIdentifier("ID:4");
    OWLClass cls5 = wrapper.getOWLClassByIdentifier("ID:5");
    OWLClass cls9 = wrapper.getOWLClassByIdentifier("ID:9");
    OWLClass cls10 = wrapper.getOWLClassByIdentifier("ID:10");
    
    Set<OWLClass> expectedAncestors = new HashSet<OWLClass>();
    Set<OWLPropertyExpression> overProps = new HashSet<OWLPropertyExpression>();
    overProps.add(wrapper.getOWLObjectPropertyByIdentifier("BFO:0000050"));
    //no ancestors through GCI
    expectedAncestors.add(cls4);
    expectedAncestors.add(cls6);
    assertEquals("Incorrect ancestors with GCI over props", expectedAncestors, 
            wrapper.getNamedAncestorsWithGCI(cls8, overProps));
    //ancestors with GCI
    expectedAncestors = new HashSet<OWLClass>();
    overProps = new HashSet<OWLPropertyExpression>();
    overProps.add(wrapper.getOWLObjectPropertyByIdentifier("RO:0002202"));
    expectedAncestors.add(cls10);
    expectedAncestors.add(cls6);
    expectedAncestors.add(cls5);
    assertEquals("Incorrect ancestors through GCI and classical relations", 
            expectedAncestors, wrapper.getNamedAncestorsWithGCI(cls9, overProps));
}
 

public Set<OWLClassExpression> getMostGeneralSubsumees(
		Set<OWLClassExpression> classes,
		Set<OWLPropertyExpression> properties) {
	 Set<OWLClassExpression> existentialRestCandidates = getCommunSubsumees(classes, true);
	 Set<OWLPropertyExpression> roleCandidates = new HashSet<OWLPropertyExpression>();
	 Boolean isDataRole = null;
	 for (OWLClassExpression sub: existentialRestCandidates) {
		 assert sub.getClassExpressionType().equals(ClassExpressionType.DATA_SOME_VALUES_FROM)
		 || sub.getClassExpressionType().equals(ClassExpressionType.OBJECT_SOME_VALUES_FROM): sub;
		 OWLQuantifiedRestriction qSub = (OWLQuantifiedRestriction) sub;
		 OWLPropertyExpression subRole =  qSub.getProperty();
		 assert subRole!=null : "Unkown role : "+ qSub; 
		 roleCandidates.add(subRole);
		 isDataRole = subRole.isDataPropertyExpression();
	 }
	 if (roleCandidates.isEmpty()) {
		 return Collections.EMPTY_SET;
	 }
	 roleCandidates.retainAll(getCommunSubproperty(properties));
	 if (roleCandidates.isEmpty()) {
		 return Collections.EMPTY_SET;
	 }
	
	 // check maximality wrt inverse
	 Set<OWLClassExpression> ret = getMaximum(roleCandidates);
	 //
	return ret;
	

}
 

public boolean isSubProperty(OWLPropertyExpression normalizedSub,
		OWLPropertyExpression normalizedSup) {
	if (normalizedSub.isObjectPropertyExpression() ^ normalizedSup.isDataPropertyExpression()) {
		return false;
	}
	if (normalizedSub.isObjectPropertyExpression()) {
		return objPropTaxo.isSubsumedBy(normalizedSub, normalizedSup);
	} else {
		return dataPropTaxo.isSubsumedBy(normalizedSub, normalizedSup);
	}
}
 

public String getName(OWLPropertyExpression propexp) {
	String name;
	if (!propexp.isAnonymous()) {
		if (propexp.isDataPropertyExpression()) {
			name = ((OWLDataPropertyExpression) propexp).asOWLDataProperty().getIRI().toString();
		} else {
			name = ((OWLObjectPropertyExpression) propexp).asOWLObjectProperty().getIRI().toString();
		}
	} else {
		assert propexp.isObjectPropertyExpression();
		name = ((OWLObjectPropertyExpression) propexp).getNamedProperty().getIRI().toString();
	}
	return name;
}
 

public String getName(OWLPropertyExpression propexp) {
	String name;
	if (!propexp.isAnonymous()) {
		if (propexp.isDataPropertyExpression()) {
			name = ((OWLDataPropertyExpression) propexp).asOWLDataProperty().getIRI().toString();
		} else {
			name = ((OWLObjectPropertyExpression) propexp).asOWLObjectProperty().getIRI().toString();
		}
	} else {
		assert propexp.isObjectPropertyExpression();
		name = ((OWLObjectPropertyExpression) propexp).getNamedProperty().getIRI().toString();
	}
	return name;
}
 

public OWLProperty getNamedProperty(OWLPropertyExpression propexp) {
	OWLProperty ret;
	if (!propexp.isAnonymous()) {
		if (propexp.isDataPropertyExpression()) {
			ret = ((OWLDataPropertyExpression) propexp).asOWLDataProperty();;
		} else {
			ret = ((OWLObjectPropertyExpression) propexp).asOWLObjectProperty();
		}
	} else {
		assert propexp.isObjectPropertyExpression();
		ret = ((OWLObjectPropertyExpression) propexp).getNamedProperty();
	}
	return ret;
}
 

/**
 * returns a map associating a number of wildcards processed (>= minimalNumberOfConceptWildcardsToReport) to the most general subsumees for the corresponding number of wildcards.
 * In other words, for k>= minimalNumberOfConceptWildcardsToReport),  map.get(k) =  getMostGeneralSubsumees(classes, properties, 0,0,k) . 
 * NOTE: for k>= minimalNumberOfConceptWildcardsToReport, map.get(k) may be null if getMostGeneralSubsumees(classes, properties, 0,0,k).isEmpty().
 * @param classes
 * @param properties
 * @param conceptWildcardsToProcess
 * @param minimalNumberOfConceptWildcardsToReport
 * @return
 */
public Map<Integer, Set<OWLClassExpression>> computeMostGeneralSubsumees(
		Set<OWLClassExpression> classes,
		Set<OWLPropertyExpression> properties,
		int conceptWildcardsToProcess, 
		int minimalNumberOfConceptWildcardsToReport) {
	if (minimalNumberOfConceptWildcardsToReport> conceptWildcardsToProcess) {
		throw new IllegalArgumentException("minimalNumberOfConceptWildcardsToReport must be less than or equals to conceptWildcardsToProcess");
	}
	Map<Integer, Set<OWLClassExpression>> ret = new HashMap<Integer, Set<OWLClassExpression>>();
	computeMostGeneralSubsumees(classes, properties, conceptWildcardsToProcess, minimalNumberOfConceptWildcardsToReport, 
			ret, 0);
	return ret;
}
 

protected Set<OWLPropertyExpression> getCommunSubproperty(Set<OWLPropertyExpression> props) {
	Set<OWLPropertyExpression> communSubsumees = null;
	
	for (OWLPropertyExpression propRole: props) {
		Set<OWLPropertyExpression> subs = new HashSet<OWLPropertyExpression>
				(propRole.isDataPropertyExpression()? dataPropTaxo.getSubsumeesOrSelf(propRole)
				: objPropTaxo.getSubsumeesOrSelf(propRole));
		if (propRole.isDataPropertyExpression()) {
			subs.removeAll(dataPropTaxo.getBottomNode().getEquivalentElements());
		} else {
			assert propRole.isObjectPropertyExpression() : propRole;
			subs.removeAll(objPropTaxo.getBottomNode().getEquivalentElements());
		}
		
		if (communSubsumees == null) {
			communSubsumees = new HashSet<OWLPropertyExpression>();
			communSubsumees.addAll(subs);
		} else {
			communSubsumees.retainAll(subs);
		}
		
		if (communSubsumees.isEmpty()) {
			return Collections.EMPTY_SET;
		}
	}
	return communSubsumees == null? new HashSet<OWLPropertyExpression>(): communSubsumees;
}
 

/**
 * returns a map associating a number of wildcards processed (>= minimalNumberOfConceptWildcardsToReport) to the most general subsumees for the corresponding number of wildcards.
 * In other words, for k>= minimalNumberOfConceptWildcardsToReport),  map.get(k) =  getMostGeneralSubsumees(classes, properties, 0,0,k) . 
 * NOTE: for k>= minimalNumberOfConceptWildcardsToReport, map.get(k) may be null if getMostGeneralSubsumees(classes, properties, 0,0,k).isEmpty().
 * @param classes
 * @param properties
 * @param conceptWildcardsToProcess
 * @param minimalNumberOfConceptWildcardsToReport
 * @return
 */
public Map<Integer, Set<OWLClassExpression>> computeMostGeneralSubsumees(
		Set<OWLClassExpression> classes,
		Set<OWLPropertyExpression> properties,
		int conceptWildcardsToProcess, 
		int minimalNumberOfConceptWildcardsToReport) {
	if (minimalNumberOfConceptWildcardsToReport> conceptWildcardsToProcess) {
		throw new IllegalArgumentException("minimalNumberOfConceptWildcardsToReport must be less than or equals to conceptWildcardsToProcess");
	}
	Map<Integer, Set<OWLClassExpression>> ret = new HashMap<Integer, Set<OWLClassExpression>>();
	computeMostGeneralSubsumees(classes, properties, conceptWildcardsToProcess, minimalNumberOfConceptWildcardsToReport, 
			ret, 0);
	return ret;
}
 

/**
 * As {@link getAncestors(OWLObject s, Set<OWLProperty) overProps}, 
 * but if isStrict is true, then only consider paths that include at least one edge
 * with a property in the specified set. i.e. exclude subclass-only paths. 
 * 
 * @param s
 * @param overProperties
 * @return
 */

public Set<OWLObject> getAncestors(OWLObject x, Set<OWLPropertyExpression> overProps, boolean isStrict) {
	Set<OWLObject> ancs = new HashSet<OWLObject>();
	for (OWLGraphEdge e : getOutgoingEdgesClosure(x, overProps)) {
		boolean isAddMe = false;
		if (overProps != null) {
			List<OWLQuantifiedProperty> qps = e.getQuantifiedPropertyList();
			if (qps.size() == 0) {
				// identity
				if (!isStrict)
					isAddMe = true;
			}
			else if (qps.size() == 1) {
				OWLQuantifiedProperty qp = qps.get(0);
				if (qp.isIdentity()) {
					if (!isStrict)
						isAddMe = true;
				}
				else if (qp.isSubClassOf()) {
					if (!isStrict)
						isAddMe = true;
				}
				else if (qp.isSomeValuesFrom() && overProps.contains(qp.getProperty())) {
					isAddMe = true;
				}
			}
			else if (!isStrict) {
			    isAddMe = true;
			}
		}
		else {
			isAddMe = true;
		}
		if (isAddMe)
			ancs.add(e.getTarget());
	}
	return ancs;
}
 

/**
 * returns the key associated with a property expression
 * @param pe
 * @return
 */
public static String getKey(OWLPropertyExpression pe) {
	if (pe.isObjectPropertyExpression()) {
		pe = ((OWLObjectPropertyExpression) pe).getSimplified();
	}
	if (!pe.isAnonymous()) {
		return ((OWLNamedObject) pe).getIRI().toString();
	} else {
		OWLObjectInverseOf ope = (OWLObjectInverseOf) pe;
		OWLObjectProperty op = (OWLObjectProperty) ope.getInverse();
		return op.getIRI().toString();
		
	}
}
 

/**
 * retrieves direct edges from a source
 * to the direct **named** target for a given set of properties
 * <ul>
 * <li>e.g. if (A SubClassOf B) then outgoing(A) = { &lt;A,sub,B&gt;}</li>
 * <li>e.g. if (A SubClassOf R some B) then outgoing(A) = { &lt;A, R-some, B&gt; }</li>
 * <li>e.g. if (A SubClassOf R some (R2 some B)) then outgoing(A) = { &lt;A, [R-some,R2-same], B&gt; }</li>
 * </ul>
 * @param cls source
 * @param props
 * @return all edges that originate from source to nearest named object target
 */
public Set<OWLGraphEdge> getOutgoingEdges(OWLObject cls, Set<? extends OWLPropertyExpression> props) {
	Set<OWLGraphEdge> pEdges = getPrimitiveOutgoingEdges(cls);
	LOG.debug("primitive edges:"+cls+" --> "+pEdges);

	Set<OWLGraphEdge> edges = new OWLGraphEdgeSet();
	for (OWLGraphEdge e : pEdges) {
	    edges.addAll(primitiveEdgeToFullEdges(e));
	}
       if (props != null) {
           filterEdges(edges, props);
       }
	LOG.debug("  all:"+cls+" --> "+edges);
	return edges;
}
 

/**
 * Find lest common ancestors to {@code x} and {@code y} that can be reached 
 * over the specified set of relations. 
 * @param g
 * @param x
 * @param y
 * @param overProps
 * @return
 */
public static Set<OWLObject> findLeastCommonAncestors(OWLGraphWrapper g,
        OWLObject x, OWLObject y, Set<OWLPropertyExpression> overProps) {
    Set<OWLObject> cas = findCommonAncestors(g,x,y, overProps);
    Set<OWLObject> lcas = new HashSet<OWLObject>();
    lcas.addAll(cas);
    for (OWLObject z : cas) {
        lcas.removeAll(g.getAncestors(z, overProps));
    }
    return lcas;
}
 

/**
 * side-effects: removes redundant predictions over a set of relationships.
 * If overProps set is empty, only the subClassOf hierarchy is used, if it's
 * null all relationships are used.
 * 
 * @param predictions
 * @param aClasses
 * @param overProps
 */
protected void setAndFilterRedundantPredictions(Set<Prediction> predictions, Set<OWLClass> aClasses, Set<OWLPropertyExpression> overProps) {
	Set<Prediction> newPredictions = new HashSet<Prediction>();

	for (Prediction p : predictions) {
		boolean isRedundant = false;
		GeneAnnotation a = p.getGeneAnnotation();
		OWLClass cls = (OWLClass) graph.getOWLObjectByIdentifier(a.getCls());
		for (OWLClass aClass : aClasses) {
			if (graph.getAncestorsReflexive(aClass, overProps).contains(cls)) {
				isRedundant = true;
				break;
			}
		}
		if (isRedundant && this.removeAllRedundant) {
			continue;
		}
		p.setRedundantWithExistingAnnotations(isRedundant);
		
		isRedundant = false;
		for (Prediction p2 : predictions) {
			GeneAnnotation a2 = p2.getGeneAnnotation();
			OWLClass cls2 = (OWLClass) graph.getOWLObjectByIdentifier(a2.getCls());
			if (graph.getAncestors(cls2).contains(cls)) {
				isRedundant = true;
				break;
			}
		}
		if (isRedundant && this.removeAllRedundant) {
			continue;
		}
		p.setRedundantWithOtherPredictions(isRedundant);
		newPredictions.add(p);
	}
	predictions.clear();
	predictions.addAll(newPredictions);

}
 

/**
 * 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;
}