supergene.java

java实现的遗传算法

/*
 * This file is part of JGAP.
 *
 * JGAP offers a dual license model containing the LGPL as well as the MPL.
 *
 * For licencing information please see the file license.txt included with JGAP
 * or have a look at the top of class org.jgap.Chromosome which representatively
 * includes the JGAP license policy applicable for any file delivered with JGAP.
 */
package org.jgap.supergenes;

import org.jgap.Gene;

/**
 * <p>Supergene represents several genes, which usually control closely
 * related aspects of the phenotype. The Supergene mutates
 * only in such way, that the allele combination remains valid.
 * Mutations, that make allele combination invalid, are rejected
 * inside {@link org.jgap.Gene#applyMutation } method. Supergene components can also be
 * a Supergenes, creating the tree-like structures in this way.
 *</p><p>
 * In biology, the invalid combinations
 * represents completely broken metabolic chains, unbalanced
 * signaling pathways (activator without supressor) and so on.
 *</p><p>
 * At <i>least about 5 % of the randomly
 * generated Supergene suparallele values should be valid.</i> If the valid
 * combinations represents too small part of all possible combinations,
 * it can take too long to find the suitable mutation that does not brake
 * a supergene. If you face this problem, try to split the supergene into
 * several sub-supergenes.
 * </p>
 *
 * @author Audrius Meskauskas
 */

public interface Supergene extends Gene {

    /** String containing the CVS revision. Read out via reflection!*/
    final static String CVS_REVISION = "$Revision: 1.7 $";

    /**
     * Test the allele combination of this supergene for validity.
     * If a validator was previously set be calling setValidator(),
     * the decission is delegated to this validator. The derived
     * classes may have internal default validator for the case
     * when no external validator is set.
     * @see Note in the interface header. *
     * @return true only if the supergene allele combination is valid.
     */
    boolean isValid();

    /**
     * Get the array of genes - components of this supergene.
     * The supergene components may be supergenes itself.
     */
    Gene [] getGenes();

    /**
     * Returns the Gene at the given index (locus) within the Supergene. The
     * first gene is at index zero and the last gene is at the index equal to
     * the size of this Supergene - 1.
     *
     * @param a_desiredLocus: The index of the gene value to be returned.
     * @return The Gene at the given index.
     */
    Gene getGene(int index);

    /**
     * Sets an object, responsible for deciding if the Supergene allele
     * combination is valid. If it is set to null, no validation is performed
     * (all combinations are assumed to be valid). The derived
     * classes may have internal default validator for the case
     * when no external validator is set.
     */
     void setValidator(supergeneValidator a_validator);

     /**
      * Gets an object, responsible for deciding if the Supergene allele
      * combination is valid. If no external validator was set and the
      * class uses its own internal validation method, it still must be
      * able to return a validator, using the same method (typicallly,
      * such classes just return <i>this</i>.
      */
      supergeneValidator getValidator();


}