org.jgap.supergenes.Supergene Maven / Gradle / Ivy
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/*
* This file is part of JGAP.
*
* JGAP offers a dual license model containing the LGPL as well as the MPL.
*
* For licensing 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.*;
/**
* 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 Supergene, creating the tree-like
* structures in this way.
*
* In biology, the invalid combinations represent completely broken metabolic
* chains, unbalanced signaling pathways (activator without supressor) and so
* on.
*
* At least about 5 % of the randomly generated Supergene suparallele values
* should be valid. 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.
*
* @author Audrius Meskauskas
*/
public interface Supergene
extends Gene, ICompositeGene {
/** String containing the CVS revision. Read out via reflection!*/
final static String CVS_REVISION = "$Revision: 1.14 $";
/**
* 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_index the index of the gene value to be returned
* @return the Gene at the given index
*/
Gene geneAt(int a_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 this.
*/
SupergeneValidator getValidator();
}