julianmendez / jcel

 *

 * Copyright (C) 2009-2017 Julian Mendez

 *

 *

 * This file is part of jcel.

 *

 *

 * The contents of this file are subject to the GNU Lesser General Public License

 * version 3

 *

 *

 * This program is free software: you can redistribute it and/or modify

 * it under the terms of the GNU Lesser General Public License as published by

 * the Free Software Foundation, either version 3 of the License, or

 * (at your option) any later version.

 *

 * This program is distributed in the hope that it will be useful,

 * but WITHOUT ANY WARRANTY; without even the implied warranty of

 * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the

 * GNU Lesser General Public License for more details.

 *

 * You should have received a copy of the GNU Lesser General Public License

 * along with this program.  If not, see <http://www.gnu.org/licenses/>.

 *

 *

 * Alternatively, the contents of this file may be used under the terms

 * of the Apache License, Version 2.0, in which case the

 * provisions of the Apache License, Version 2.0 are applicable instead of those

 * above.

 *

 *

 * Licensed under the Apache License, Version 2.0 (the "License");

 * you may not use this file except in compliance with the License.

 * You may obtain a copy of the License at

 *

 *     http://www.apache.org/licenses/LICENSE-2.0

 *

 * Unless required by applicable law or agreed to in writing, software

 * distributed under the License is distributed on an "AS IS" BASIS,

 * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.

 * See the License for the specific language governing permissions and

 * limitations under the License.

 *

 */

package de.tudresden.inf.lat.jcel.core.algorithm.rulebased;

import java.io.IOException;

import java.io.Writer;

import java.util.AbstractMap;

import java.util.ArrayList;

import java.util.Collection;

import java.util.Collections;

import java.util.HashMap;

import java.util.HashSet;

import java.util.List;

import java.util.Map;

import java.util.NoSuchElementException;

import java.util.Objects;

import java.util.Optional;

import java.util.Set;

import java.util.logging.Logger;

import de.tudresden.inf.lat.jcel.core.algorithm.common.Processor;

import de.tudresden.inf.lat.jcel.core.algorithm.common.UnclassifiedOntologyException;

import de.tudresden.inf.lat.jcel.core.completion.common.REntry;

import de.tudresden.inf.lat.jcel.core.completion.common.SEntry;

import de.tudresden.inf.lat.jcel.core.graph.IntegerBinaryRelation;

import de.tudresden.inf.lat.jcel.core.graph.IntegerHierarchicalGraph;

import de.tudresden.inf.lat.jcel.core.graph.IntegerHierarchicalGraphImpl;

import de.tudresden.inf.lat.jcel.core.graph.IntegerSubsumerGraph;

import de.tudresden.inf.lat.jcel.core.graph.IntegerSubsumerGraphImpl;

import de.tudresden.inf.lat.jcel.core.saturation.SubPropertyNormalizer;

import de.tudresden.inf.lat.jcel.coreontology.axiom.ExtendedOntology;

import de.tudresden.inf.lat.jcel.coreontology.axiom.ExtendedOntologyImpl;

import de.tudresden.inf.lat.jcel.coreontology.axiom.NormalizedIntegerAxiom;

import de.tudresden.inf.lat.jcel.coreontology.axiom.NormalizedIntegerAxiomFactory;

import de.tudresden.inf.lat.jcel.coreontology.datatype.IntegerEntityManager;

import de.tudresden.inf.lat.jcel.coreontology.datatype.IntegerEntityType;

import de.tudresden.inf.lat.jcel.coreontology.datatype.OntologyExpressivity;

import de.tudresden.inf.lat.util.map.OptMap;

import de.tudresden.inf.lat.util.map.OptMapImpl;

/**

 * An object of this class is an implementation of a classification algorithm.

 * 

 * @author Julian Mendez

 */

public class RuleBasedProcessor implements Processor {

	private class WorkerThreadR extends Thread {

		@Override

		public void run() {

			while (RuleBasedProcessor.this.status.getNumberOfREntries() > 0) {

				while (RuleBasedProcessor.this.status.getNumberOfREntries() > 0) {

					processREntries();

				}

				try {

					Thread.sleep(threadWaitingTime);

				} catch (InterruptedException e) {

					throw new IllegalStateException(e);

				}

			}

		}

	}

	private class WorkerThreadS extends Thread {

		@Override

		public void run() {

			while (RuleBasedProcessor.this.status.getNumberOfSEntries() > 0) {

				while (RuleBasedProcessor.this.status.getNumberOfSEntries() > 0) {

					processSEntries();

				}

				try {

					Thread.sleep(threadWaitingTime);

				} catch (InterruptedException e) {

					throw new IllegalStateException(e);

				}

			}

		}

	}

	private static final Logger logger = Logger.getLogger(RuleBasedProcessor.class.getName());

	private static final long loggingFrequency = 0x1000000;

	private static final long threadWaitingTime = 0x20;

	private static final Integer topClassId = IntegerEntityManager.topClassId;

	private RChain chainR = null;

	private SChain chainS = null;

	private IntegerHierarchicalGraph classHierarchy = null;

	private IntegerHierarchicalGraph dataPropertyHierarchy = null;

	private OptMap<Integer, Set<Integer>> directTypes = null;

	private final IntegerEntityManager entityManager;

	private final NormalizedIntegerAxiomFactory factory;

	private boolean isReady = false;

	private long iteration = 0;

	private long loggingCount = loggingFrequency;

	private final boolean multiThreadedMode = false;

	private IntegerHierarchicalGraph objectPropertyHierarchy = null;

	private OptMap<Integer, Set<Integer>> sameIndividualMap = null;

	private ClassifierStatusImpl status = null;

	private WorkerThreadR threadR1 = null;

	private WorkerThreadR threadR2 = null;

	private WorkerThreadS threadS1 = null;

	private WorkerThreadS threadS2 = null;

	/**

	 * Constructs a new rule-based processor.

	 * 

	 * @param originalObjectProperties

	 *            set of original object properties

	 * @param originalClasses

	 *            set of original classes

	 * @param normalizedAxiomSet

	 *            set of normalized axioms

	 * @param expressivity

	 *            expressivity

	 * @param factory

	 *            factory of normalized integer axioms

	 * @param entityManager

	 *            entity manager

	 */

	public RuleBasedProcessor(Set<Integer> originalObjectProperties, Set<Integer> originalClasses,

			Set<NormalizedIntegerAxiom> normalizedAxiomSet, OntologyExpressivity expressivity,

			NormalizedIntegerAxiomFactory factory, IntegerEntityManager entityManager) {

		Objects.requireNonNull(originalObjectProperties);

		Objects.requireNonNull(originalClasses);

		Objects.requireNonNull(normalizedAxiomSet);

		Objects.requireNonNull(expressivity);

		Objects.requireNonNull(factory);

		Objects.requireNonNull(entityManager);

		this.factory = factory;

		this.entityManager = entityManager;

		CompletionRuleChainSelector selector = new CompletionRuleChainSelector(expressivity);

		selector.activateProfiler();

		this.chainR = selector.getRChain();

		this.chainS = selector.getSChain();

		preProcess(createExtendedOntology(originalObjectProperties, originalClasses, normalizedAxiomSet));

	}

	public void addAxioms(Set<NormalizedIntegerAxiom> normalizedAxiomSet) {

		Objects.requireNonNull(normalizedAxiomSet);

		logger.fine("adding axioms ...");

		this.status.getExtendedOntology().load(normalizedAxiomSet);

		preProcess(this.status.getExtendedOntology());

		logger.fine("processor reset.");

	}

	/**

	 * @param hierarchicalGraph

	 *            graph containing direct subsumers

	 * @return a map with all the direct types for each individual.

	 */

	private OptMap<Integer, Set<Integer>> computeDirectTypes(IntegerHierarchicalGraph hierarchicalGraph) {

		OptMap<Integer, Set<Integer>> ret = new OptMapImpl<>(new HashMap<>());

		Set<Integer> individuals = getEntityManager().getIndividuals();

		individuals.forEach(indiv -> {

			Set<Integer> subsumers = hierarchicalGraph.getParents(getEntityManager().getAuxiliaryNominal(indiv).get());

			subsumers.forEach(elem -> {

				if (getEntityManager().getAuxiliaryNominals().contains(elem)) {

					throw new IllegalStateException("An individual has another individual as direct subsumer.");

				}

			});

			ret.put(indiv, Collections.unmodifiableSet(subsumers));

		});

		return ret;

	}

	/**

	 * This is a graph reachability algorithm that returns all elements d

	 * reachable from an element c using a path where each segment is from any

	 * of the properties in R.

	 * 

	 * @param c

	 *            first element in the path

	 * @return the set of all nodes reachable from c using any possible segment

	 */

	private Set<Integer> computeReachability(Integer c) {

		Set<Integer> ret = new HashSet<>();

		Set<Integer> toVisit = new HashSet<>();

		toVisit.add(c);

		while (!toVisit.isEmpty()) {

			Integer elem = toVisit.iterator().next();

			toVisit.remove(elem);

			ret.add(elem);

			Set<Integer> newToVisit = new HashSet<>();

			this.status.getObjectPropertiesByFirst(elem).forEach(r -> {

				IntegerBinaryRelation relation = this.status.getRelationSet().get(r);

				newToVisit.addAll(relation.getByFirst(elem));

			});

			newToVisit.removeAll(ret);

			toVisit.addAll(newToVisit);

		}

		return ret;

	}

		OptMap<Integer, Set<Integer>> ret = new OptMapImpl<>(new HashMap<>());

		Set<Integer> individuals = getEntityManager().getIndividuals();

		individuals.forEach(indiv -> {

			Set<Integer> equivalentClasses = hierarchicalGraph

					.getEquivalents(getEntityManager().getAuxiliaryNominal(indiv).get());

			Set<Integer> equivalents = new HashSet<>();

			equivalentClasses.forEach(elem -> {

				if (getEntityManager().getAuxiliaryNominals().contains(elem)) {

					equivalents.add(getEntityManager().getIndividual(elem).get());

				}

			});

			ret.put(indiv, Collections.unmodifiableSet(equivalents));

		});

		return ret;

	}

	/**

	 * Convenience method to create a map entry. This method returns a map

	 * entry.

	 * 

	 * @param key

	 *            key

	 * @param value

	 *            value

	 * @return a map entry created using the parameters

	 */

	private Map.Entry<String, String> createEntry(String key, String value) {

		return new AbstractMap.SimpleEntry<String, String>(key, value);

	}

	private ExtendedOntology createExtendedOntology(Set<Integer> originalObjectPropertySet,

			Set<Integer> originalClassSet, Set<NormalizedIntegerAxiom> axioms) {

		SubPropertyNormalizer subPropNormalizer = new SubPropertyNormalizer(getOntologyObjectFactory(),

				getEntityManager());

		Set<NormalizedIntegerAxiom> saturatedNormalizedAxiomSet = subPropNormalizer.apply(axioms);

		ExtendedOntology extendedOntology = new ExtendedOntologyImpl();

		extendedOntology.load(saturatedNormalizedAxiomSet);

		originalObjectPropertySet.forEach(elem -> extendedOntology.addObjectProperty(elem));

		originalClassSet.forEach(elem -> extendedOntology.addClass(elem));

		return extendedOntology;

	}

	/**

	 * Returns the class graph.

	 * 

	 * @return the class graph.

	 */

	protected IntegerSubsumerGraph getClassGraph() {

		return this.status.getClassGraph();

	}

	@Override

	public IntegerHierarchicalGraph getClassHierarchy() {

		if (!isReady()) {

			throw new UnclassifiedOntologyException();

		}

		return this.classHierarchy;

	}

	/**

	 * Returns information about how the processor configuration.

	 * 

	 * @return information about how the processor configuration

	 */

	public List<Map.Entry<String, String>> getConfigurationInfo() {

		List<Map.Entry<String, String>> ret = new ArrayList<>();

		ret.add(createEntry("processor", getClass().getSimpleName()));

		ret.add(createEntry("iterations per log entry", "" + loggingFrequency));

		ret.add(createEntry("classes read (including TOP and BOTTOM classes)",

				"" + getEntityManager().getEntities(IntegerEntityType.CLASS, false).size()));

		ret.add(createEntry("object properties read (including TOP and BOTTOM object properties)",

				"" + getEntityManager().getEntities(IntegerEntityType.OBJECT_PROPERTY, false).size()));

		ret.add(createEntry("auxiliary classes created (including nominals)",

				"" + getEntityManager().getEntities(IntegerEntityType.CLASS, true).size()));

		ret.add(createEntry("auxiliary classes created for nominals", "" + getEntityManager().getIndividuals().size()));

		ret.add(createEntry("auxiliary object properties created",

				"" + getEntityManager().getEntities(IntegerEntityType.OBJECT_PROPERTY, true).size()));

		ret.add(createEntry("chain S", this.chainS.toString()));

		ret.add(createEntry("chain R", this.chainR.toString()));

		return ret;

	}

	@Override

	public IntegerHierarchicalGraph getDataPropertyHierarchy() throws UnclassifiedOntologyException {

		if (!isReady()) {

			throw new UnclassifiedOntologyException();

		}

		return this.dataPropertyHierarchy;

	}

	/**

	 * Computes the descendants using only a hierarchical graph.

	 * 

	 * @param hierarchicalGraph

	 *            a hierarchical graph containing parents and children

	 * @param vertex

	 *            starting vertex to compute the descendants

	 * @return the descendants according the graph

	 */

		Set<Integer> visited = new HashSet<>();

		Set<Integer> queue = new HashSet<>();

		queue.add(vertex);

		while (!queue.isEmpty()) {

			Integer elem = queue.iterator().next();

			queue.remove(elem);

			visited.add(elem);

			Set<Integer> children = new HashSet<>();

			children.addAll(hierarchicalGraph.getChildren(elem));

			children.removeAll(visited);

			queue.addAll(children);

		}

		return visited;

	}

	@Override

	public Map<Integer, Set<Integer>> getDirectTypes() {

		if (!isReady()) {

			throw new UnclassifiedOntologyException();

		}

		return Collections.unmodifiableMap(this.directTypes.asMap());

	}

	protected IntegerEntityManager getEntityManager() {

		return this.entityManager;

	}

	protected IntegerSubsumerGraph getObjectPropertyGraph() {

		return this.status.getObjectPropertyGraph();

	}

	@Override

	public IntegerHierarchicalGraph getObjectPropertyHierarchy() {

		if (!isReady()) {

			throw new UnclassifiedOntologyException();

		}

		return this.objectPropertyHierarchy;

	}

	/**

	 * Returns the ontology object factory.

	 * 

	 * @return the ontology object factory.

	 */

	public NormalizedIntegerAxiomFactory getOntologyObjectFactory() {

		return this.factory;

	}

	/**

	 * Returns the binary relation for a given id, or and empty relation if the

	 * id is unknown.

	 * 

	 * @param relationId

	 *            relation id

	 * @return the binary relation for the given id, or an empty relation if no

	 *         relation is already defined

	 */

	protected IntegerBinaryRelation getRelation(Integer relationId) {

		Objects.requireNonNull(relationId);

		return this.status.getRelationSet().get(relationId);

	}

	/**

	 * Returns a set containing all relation ids.

	 * 

	 * @return the set of all relation ids

	 */

	protected Set<Integer> getRelationIdSet() {

		return Collections.unmodifiableSet(this.status.getRelationSet().getElements());

	}

	@Override

	public Map<Integer, Set<Integer>> getSameIndividualMap() {

		if (!isReady()) {

			throw new UnclassifiedOntologyException();

		}

		return Collections.unmodifiableMap(this.sameIndividualMap.asMap());

	}

	/**

	 * Returns information about the processor status.

	 * 

	 * @return information about the processor status.

	 */

	public List<Map.Entry<String, String>> getStatusInfo() {

		List<Map.Entry<String, String>> ret = new ArrayList<>();

		ret.add(createEntry("iteration", "" + this.iteration));

		ret.add(createEntry("Q_S", "" + this.status.getNumberOfSEntries()));

		ret.add(createEntry("Q_R", "" + this.status.getNumberOfREntries()));

		ret.add(createEntry("S", "" + this.status.getDeepSizeOfS()));

		ret.add(createEntry("R", "" + this.status.getDeepSizeOfR()));

		ret.add(createEntry("V", "" + this.status.getSizeOfV()));

		ret.add(createEntry("subV", "" + this.status.getDeepSizeOfV()));

		return ret;

	}

	@Override

	public boolean isReady() {

		return this.isReady;

	}

	/**

	 * Post processes the data after the classification phase.

	 */

	protected void postProcess() {

		removeAuxiliaryObjectProperties();

		this.objectPropertyHierarchy = new IntegerHierarchicalGraphImpl(getObjectPropertyGraph());

		removeAuxiliaryClassesExceptNominals();

		IntegerHierarchicalGraph hierarchicalGraph = new IntegerHierarchicalGraphImpl(this.status.getClassGraph());

		processNominals(hierarchicalGraph);

		this.directTypes = computeDirectTypes(hierarchicalGraph);

		this.sameIndividualMap = computeSameIndividualMap(hierarchicalGraph);

		removeAuxiliaryNominals();

		this.classHierarchy = new IntegerHierarchicalGraphImpl(this.status.getClassGraph());

	};

	/**

	 * The configuration follows the following steps:

	 * <ul>

	 * <li>creates the property hierarchy</li>

	 * <li>prepares all the queues to run the algorithm</li>

	 * </ul>

	 * 

	 * @param ontology

	 *            ontology

	 */

	protected void preProcess(ExtendedOntology ontology) {

		logger.fine("configuring processor ...");

		this.isReady = false;

		this.status = new ClassifierStatusImpl(getEntityManager(), ontology);

		this.dataPropertyHierarchy = new IntegerHierarchicalGraphImpl(new IntegerSubsumerGraphImpl(

				IntegerEntityManager.bottomDataPropertyId, IntegerEntityManager.topDataPropertyId));

		Set<Integer> classNameSet = new HashSet<>();

		classNameSet.addAll(this.status.getExtendedOntology().getClassSet());

		classNameSet.forEach(className -> {

			this.status.addNewSEntry(className, className);

			this.status.addNewSEntry(className, topClassId);

		});

		logger.fine("processor configured.");

		logger.fine(showConfigurationInfo());

		int numberOfCores = Runtime.getRuntime().availableProcessors();

		logger.fine("number of cores : " + numberOfCores);

		// uncomment the following two lines to allow multithreaded mode

		// int suggestedNumberOfThreads = (numberOfCores / 2) - 1;

		// this.multiThreadedMode = suggestedNumberOfThreads >= 4;

		if (this.multiThreadedMode) {

			logger.fine("running processor on multiple threads.");

		} else {

			logger.fine("running processor on a single thread.");

		}

	}

	@Override

	public boolean process() {

		boolean ret = false;

		if (this.multiThreadedMode) {

			ret = processMultiThreaded();

		} else {

			ret = processSingleThreaded();

		}

		if (ret) {

			if (this.loggingCount < 1) {

				this.loggingCount = loggingFrequency;

				logger.fine(showStatusInfo());

			}

		}

		return ret;

	};

	private boolean processMultiThreaded() {

		if (!this.isReady) {

			if (Objects.nonNull(this.threadS1) && Objects.nonNull(this.threadS2) && Objects.nonNull(this.threadR1)

					&& Objects.nonNull(this.threadR2) && this.threadS1.getState().equals(Thread.State.TERMINATED)

					&& this.threadS2.getState().equals(Thread.State.TERMINATED)

					&& this.threadR1.getState().equals(Thread.State.TERMINATED)

					&& this.threadR2.getState().equals(Thread.State.TERMINATED)

					&& (this.status.getNumberOfSEntries() == 0) && (this.status.getNumberOfREntries() == 0)) {

				logger.fine(showStatusInfo());

				postProcess();

				logger.fine(showConfigurationInfo());

				this.isReady = true;

			} else {

				if ((Objects.isNull(this.threadS1)) || (Objects.nonNull(this.threadS1)

						&& this.threadS1.getState().equals(Thread.State.TERMINATED))) {

					this.threadS1 = new WorkerThreadS();

					this.threadS1.start();

					logger.finest("starting new thread S-1 ...");

				}

				if ((Objects.isNull(this.threadS2)) || (Objects.nonNull(this.threadS2)

						&& this.threadS2.getState().equals(Thread.State.TERMINATED))) {

					this.threadS2 = new WorkerThreadS();

					this.threadS2.start();

					logger.finest("starting new thread S-2 ...");

				}

				if ((Objects.isNull(this.threadR1)) || (Objects.nonNull(this.threadR1)

						&& this.threadR1.getState().equals(Thread.State.TERMINATED))) {

					this.threadR1 = new WorkerThreadR();

					this.threadR1.start();

					logger.finest("starting new thread R-1 ...");

				}

				if ((Objects.isNull(this.threadR2)) || (Objects.nonNull(this.threadR2)

						&& this.threadR2.getState().equals(Thread.State.TERMINATED))) {

					this.threadR2 = new WorkerThreadR();

					this.threadR2.start();

					logger.finest("starting new thread R-2 ...");

				}

				try {

					if (this.status.getNumberOfREntries() < this.status.getNumberOfSEntries()) {

						if ((this.iteration % 2) == 0) {

							this.threadR1.join();

						} else {

							this.threadR2.join();

						}

					} else {

						if ((this.iteration % 2) == 0) {

							this.threadS1.join();

						} else {

							this.threadS2.join();

						}

					}

				} catch (InterruptedException e) {

					throw new IllegalStateException(e);

				}

			}

		}

		return !this.isReady;

	}

	/**

	 * Processes the nominals after the execution of the classification

	 * algorithm. It requires a hierarchical graph to get the descendants.

	 * 

	 * @param hierarchicalGraph

	 *            the hierarchical graph

	 */

	private void processNominals(IntegerHierarchicalGraph hierarchicalGraph) {

		OptMap<Integer, Set<Integer>> reachabilityCache = new OptMapImpl<>(new HashMap<>());

		Set<Integer> nominals = getEntityManager().getAuxiliaryNominals();

		nominals.forEach(indiv -> {

			Set<Integer> descendants = getDescendants(hierarchicalGraph, indiv);

			descendants.forEach(c -> {

				descendants.forEach(d -> {

					Collection<Integer> sC = getClassGraph().getSubsumers(c);

					Collection<Integer> sD = getClassGraph().getSubsumers(d);

					if (!(sD.containsAll(sC))) {

						if (computeReachability(c, reachabilityCache).contains(d)) {

							sD.forEach(elem -> this.status.getClassGraph().addAncestor(c, elem));

						}

						nominals.forEach(nominal -> {

							if (computeReachability(nominal, reachabilityCache).contains(d)) {

								sD.forEach(elem -> this.status.getClassGraph().addAncestor(c, elem));

							}

						});

					}

				});

			});

		});

	}

	private boolean processREntries() {

		boolean ret = false;

		REntry entry = null;

		try {

			entry = this.status.removeNextREntry();

		} catch (NoSuchElementException e) {

		}

		if (Objects.nonNull(entry)) {

			ret = true;

			int property = entry.getProperty();

			int leftClass = entry.getLeftClass();

			int rightClass = entry.getRightClass();

			boolean applied = this.status.addToR(property, leftClass, rightClass);

			if (applied) {

				this.chainR.apply(this.status, property, leftClass, rightClass);

				this.loggingCount--;

				this.iteration++;

			}

		}

		return ret;

	}

	private boolean processSEntries() {

		boolean ret = false;

		SEntry entry = null;

		try {

			entry = this.status.removeNextSEntry();

		} catch (NoSuchElementException e) {

		}

		if (Objects.nonNull(entry)) {

			ret = true;

			int subClass = entry.getSubClass();

			int superClass = entry.getSuperClass();

			boolean applied = this.status.addToS(subClass, superClass);

			if (applied) {

				this.chainS.apply(this.status, subClass, superClass);

				this.loggingCount--;

				this.iteration++;

			}

		}

		return ret;

	}

	private boolean processSingleThreaded() {

		if (!this.isReady) {

			if ((this.status.getNumberOfSEntries() == 0) && (this.status.getNumberOfREntries() == 0)) {

				logger.fine(showStatusInfo());

				postProcess();

				logger.fine(showConfigurationInfo());

				this.isReady = true;

			} else {

				if (this.status.getNumberOfSEntries() > this.status.getNumberOfREntries()) {

					processSEntries();

				} else {

					processREntries();

				}

			}

		}

		return !this.isReady;

	}

	private void removeAuxiliaryClassesExceptNominals() {

		Set<Integer> reqClasses = new HashSet<>();

		getClassGraph().getElements().forEach(elem -> {

			if (!getEntityManager().isAuxiliary(elem)) {

				reqClasses.add(elem);

			}

		});

		reqClasses.addAll(getEntityManager().getAuxiliaryNominals());

		this.status.getClassGraph().retainAll(reqClasses);

	}

	private void removeAuxiliaryNominals() {

		Set<Integer> reqClasses = new HashSet<>();

		reqClasses.addAll(getClassGraph().getElements());

		reqClasses.removeAll(getEntityManager().getAuxiliaryNominals());

		this.status.getClassGraph().retainAll(reqClasses);

	}

	/**

	 * This method removes the auxiliary object properties that were not

	 * generated as inverse of another one.

	 */

	private void removeAuxiliaryObjectProperties() {

		Set<Integer> reqObjectProperties = new HashSet<>();

		getObjectPropertyGraph().getElements().forEach(elem -> {

			if (!getEntityManager().isAuxiliary(elem)) {

				reqObjectProperties.add(elem);

			}

		});

		this.status.getObjectPropertyGraph().retainAll(reqObjectProperties);

	}

	public String showConfigurationInfo() {

		StringBuffer sbuf = new StringBuffer();

		getConfigurationInfo().forEach(entry -> {

			sbuf.append(entry.getKey());

			sbuf.append(" = ");

			sbuf.append(entry.getValue());

			sbuf.append("\n");

		});

		return sbuf.toString();

	}

	public String showStatusInfo() {

		StringBuffer sbuf = new StringBuffer();

		getStatusInfo().forEach(entry -> {

			sbuf.append(entry.getKey());

			sbuf.append("=");

			sbuf.append(entry.getValue());

			sbuf.append(" ");

		});

		return sbuf.toString();

	}

	public void outputSetS(Writer writer) throws IOException {

		this.status.outputSetS(writer);

	}

	public void outputSetR(Writer writer) throws IOException {

		this.status.outputSetR(writer);

	}

}