TreeSpeciation.java

/*
 * Artificial Intelligence for Humans
 * Volume 2: Nature Inspired Algorithms
 * Java Version
 * http://www.aifh.org
 * http://www.jeffheaton.com
 *
 * Code repository:
 * https://github.com/jeffheaton/aifh
 *
 * Copyright 2014 by Jeff Heaton
 *
 * 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.
 *
 * For more information on Heaton Research copyrights, licenses
 * and trademarks visit:
 * http://www.heatonresearch.com/copyright
 */
package com.heatonresearch.aifh.genetic.species;

import com.heatonresearch.aifh.evolutionary.genome.Genome;
import com.heatonresearch.aifh.evolutionary.species.ThresholdSpeciation;
import com.heatonresearch.aifh.genetic.trees.TreeGenome;
import com.heatonresearch.aifh.genetic.trees.TreeGenomeNode;

/**
 * Created with IntelliJ IDEA.
 * User: jheaton
 * Date: 5/7/14
 * Time: 8:07 PM
 * To change this template use File | Settings | File Templates.
 */
public class TreeSpeciation extends ThresholdSpeciation {

    /**
     * Compare two nodes.
     *
     * @param result The result of previous comparisons.
     * @param node1  The first node to compare.
     * @param node2  The second node to compare.
     * @return The result.
     */
    private double compareNode(final double result, final TreeGenomeNode node1,
                               final TreeGenomeNode node2) {
        double newResult = result;

        final int node1Size = node1.getChildren().size();
        final int node2Size = node2.getChildren().size();
        final int childNodeCount = Math.max(node1Size, node2Size);

        for (int i = 0; i < childNodeCount; i++) {
            if (i < node1Size && i < node2Size) {
                final TreeGenomeNode childNode1 = node1.getChildren().get(i);
                final TreeGenomeNode childNode2 = node2.getChildren().get(i);
                newResult = compareNode(newResult, childNode1, childNode2);
            } else {
                newResult++;
            }
        }

        return newResult;
    }

    @Override
    public double getCompatibilityScore(final Genome genome1, final Genome genome2) {
        return compareNode(0, ((TreeGenome) genome1).getRoot(),
                ((TreeGenome) genome2).getRoot());
    }
}