Genome.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.evolutionary.genome;

import com.heatonresearch.aifh.evolutionary.population.Population;
import com.heatonresearch.aifh.evolutionary.species.Species;
import com.heatonresearch.aifh.learning.MLMethod;

/**
 * A genome is the basic blueprint for creating an phenome (organism) in Encog.
 * Some genomes also function as phenomes.
 */
public interface Genome extends MLMethod {

    /**
     * Copy from the specified genome into this one.
     *
     * @param source The source genome.
     */
    void copy(Genome source);

    /**
     * Get the adjusted score, this considers old-age penalties and youth
     * bonuses. If there are no such bonuses or penalties, this is the same as
     * the score.
     *
     * @return The adjusted score.
     */
    double getAdjustedScore();

    /**
     * @return The birth generation (or iteration).
     */
    int getBirthGeneration();

    /**
     * @return The population that this genome belongs to.
     */
    Population getPopulation();

    /**
     * @return The score for this genome.
     */
    double getScore();

    /**
     * Set the adjusted score.
     *
     * @param adjustedScore The adjusted score.
     */
    void setAdjustedScore(double adjustedScore);

    /**
     * Set the birth genertion (or iteration).
     *
     * @param birthGeneration The birth generation.
     */
    void setBirthGeneration(int birthGeneration);

    /**
     * Set the population that this genome belongs to.
     *
     * @param population The population that this genome belongs to.
     */
    void setPopulation(Population population);

    /**
     * Set the score.
     *
     * @param score The new score.
     */
    void setScore(double score);

    /**
     * @return Return the size of this genome. This size is a relative number
     *         that indicates the complexity of the genome.
     */
    int size();


    /**
     * @return The species for this genome.
     */
    Species getSpecies();

    /**
     * Set the species for this genome.
     *
     * @param s The species.
     */
    void setSpecies(Species s);
}