SpliceNoRepeat.java

/*
 * Encog(tm) Core v3.4 - Java Version
 * http://www.heatonresearch.com/encog/
 * https://github.com/encog/encog-java-core
 
 * Copyright 2008-2016 Heaton Research, Inc.
 *
 * 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.
 *   
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 * and trademarks visit:
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 */
package org.encog.ml.genetic.crossover;

import java.util.HashSet;
import java.util.Random;
import java.util.Set;

import org.encog.ml.ea.genome.Genome;
import org.encog.ml.ea.opp.EvolutionaryOperator;
import org.encog.ml.ea.train.EvolutionaryAlgorithm;
import org.encog.ml.genetic.GeneticError;
import org.encog.ml.genetic.genome.IntegerArrayGenome;

/**
 * A simple cross over where genes are simply "spliced". Genes are not allowed
 * to repeat.  This method only works with IntegerArrayGenome.
 */
public class SpliceNoRepeat implements EvolutionaryOperator {
	
	/**
	 * The owner.
	 */
	private EvolutionaryAlgorithm owner;

	/**
	 * Get a list of the genes that have not been taken before. This is useful
	 * if you do not wish the same gene to appear more than once in a
	 * genome.
	 * 
	 * @param source
	 *            The pool of genes to select from.
	 * @param taken
	 *            An array of the taken genes.
	 * @return Those genes in source that are not taken.
	 */
	private static int getNotTaken(final IntegerArrayGenome source,
			final Set<Integer> taken) {

		for (final int trial : source.getData()) {
			if (!taken.contains(trial)) {
				taken.add(trial);
				return trial;
			}
		}

		throw new GeneticError("Ran out of integers to select.");
	}

	/**
	 * The cut length.
	 */
	private int cutLength;

	/**
	 * Construct a splice crossover.
	 * 
	 * @param theCutLength
	 *            The cut length.
	 */
	public SpliceNoRepeat(final int theCutLength) {
		this.cutLength = theCutLength;
	}

	/**
	 * {@inheritDoc}
	 */
	@Override
	public void performOperation(Random rnd, Genome[] parents, int parentIndex,
			Genome[] offspring, int offspringIndex) {
		
		IntegerArrayGenome mother = (IntegerArrayGenome)parents[parentIndex];
		IntegerArrayGenome father = (IntegerArrayGenome)parents[parentIndex+1];
		IntegerArrayGenome offspring1 = (IntegerArrayGenome)this.owner.getPopulation().getGenomeFactory().factor();
		IntegerArrayGenome offspring2 = (IntegerArrayGenome)this.owner.getPopulation().getGenomeFactory().factor();
		
		offspring[offspringIndex] = offspring1;
		offspring[offspringIndex+1] = offspring2;
		
		final int geneLength = mother.size();

		// the chromosome must be cut at two positions, determine them
		final int cutpoint1 = (int) (rnd.nextInt(geneLength - this.cutLength));
		final int cutpoint2 = cutpoint1 + this.cutLength;

		// keep track of which genes have been taken in each of the two
		// offspring, defaults to false.
		final Set<Integer> taken1 = new HashSet<Integer>();
		final Set<Integer> taken2 = new HashSet<Integer>();

		// handle cut section
		for (int i = 0; i < geneLength; i++) {
			if (!((i < cutpoint1) || (i > cutpoint2))) {
				offspring1.copy(father,i,i);
				offspring2.copy(mother,i,i);
				taken1.add(father.getData()[i]);
				taken2.add(mother.getData()[i]);
			}
		}

		// handle outer sections
		for (int i = 0; i < geneLength; i++) {
			if ((i < cutpoint1) || (i > cutpoint2)) {

				offspring1.getData()[i] = SpliceNoRepeat.getNotTaken(mother, taken1);
				offspring2.getData()[i] = SpliceNoRepeat.getNotTaken(father, taken2);

			}
		}
	}
	
	/**
	 * @return The number of offspring produced, which is 2 for splice crossover.
	 */
	@Override
	public int offspringProduced() {
		return 2;
	}

	/**
	 * {@inheritDoc}
	 */
	@Override
	public int parentsNeeded() {
		return 2;
	}

	/**
	 * {@inheritDoc}
	 */
	@Override
	public void init(EvolutionaryAlgorithm theOwner) {
		this.owner = theOwner;	
	}
}