ec.vector

Class GeneVectorSpecies

java.lang.Object

ec.Species

ec.vector.VectorSpecies

ec.vector.GeneVectorSpecies

All Implemented Interfaces:

Prototype, Setup, Serializable, Cloneable

public class GeneVectorSpecies
extends VectorSpecies

GeneVectorSpecies is a subclass of VectorSpecies with special constraints for GeneVectorIndividuals.

At present there is exactly one item stored in GeneVectorSpecies: the prototypical Gene that populates the genome array stored in a GeneVectorIndividual.

Version:

1.0

Parameters

gene classname, inherits and != ec.Gene

(the prototypical gene for this kind of individual)

Parameter bases

base.gene

The prototypical gene for this kind of individual

Author:

Sean Luke

See Also:

Serialized Form

Field Summary

Fields

Modifier and Type	Field and Description
Gene	genePrototype
static String	P_GENE
private static long	serialVersionUID

Fields inherited from class ec.vector.VectorSpecies

C_ANY_POINT, C_GEOMETRIC, C_INTERMED_RECOMB, C_LINE_RECOMB, C_NONE, C_ONE_POINT, C_ONE_POINT_NO_NOP, C_SIMULATED_BINARY, C_TWO_POINT, C_TWO_POINT_NO_NOP, C_UNIFORM, chunksize, crossoverDistributionIndex, crossoverProbability, crossoverType, duplicateRetries, dynamicInitialSize, genomeIncreaseProbability, genomeResizeAlgorithm, genomeSize, lineDistance, maxInitialSize, minInitialSize, mutationProbability, P_CHUNKSIZE, P_CROSSOVER_DISTRIBUTION_INDEX, P_CROSSOVERPROB, P_CROSSOVERTYPE, P_DUPLICATE_RETRIES, P_GENOMESIZE, P_GEOMETRIC_PROBABILITY, P_LINEDISTANCE, P_MUTATIONPROB, P_NUM_SEGMENTS, P_SEGMENT, P_SEGMENT_END, P_SEGMENT_START, P_SEGMENT_TYPE, P_UNIFORM_MAX, P_UNIFORM_MIN, P_VECTORSPECIES, V_ANY_POINT, V_GEOMETRIC, V_INTERMED_RECOMB, V_LINE_RECOMB, V_ONE_POINT, V_ONE_POINT_NO_NOP, V_SIMULATED_BINARY, V_TWO_POINT, V_TWO_POINT_NO_NOP, V_UNIFORM

Fields inherited from class ec.Species

f_prototype, i_prototype, P_FITNESS, P_INDIVIDUAL, P_PIPE, pipe_prototype

Constructor Summary

Constructors

Constructor and Description
GeneVectorSpecies()

Method Summary

Methods

Modifier and Type	Method and Description
void	setup(EvolutionState state, Parameter base) The default version of setup(...) loads requested pipelines and calls setup(...) on them and normalizes their probabilities.

Methods inherited from class ec.vector.VectorSpecies

contains, contains, contains, contains, defaultBase, duplicateRetries, fill, fill, fill, fill, initializeGenomeSegmentsByEndIndices, initializeGenomeSegmentsByStartIndices, loadParametersForGene, mutationProbability, newIndividual, setupGenome

Methods inherited from class ec.Species

clone, newIndividual, newIndividual

Methods inherited from class java.lang.Object

equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

Field Detail

serialVersionUID

private static final long serialVersionUID

See Also:

Constant Field Values

P_GENE

public static final String P_GENE

See Also:

Constant Field Values

genePrototype

public Gene genePrototype

Constructor Detail

GeneVectorSpecies

public GeneVectorSpecies()

Method Detail

setup

public void setup(EvolutionState state,
         Parameter base)

Description copied from class: Species

The default version of setup(...) loads requested pipelines and calls setup(...) on them and normalizes their probabilities. If your individual prototype might need to know special things about the species (like parameters stored in it), then when you override this setup method, you'll need to set those parameters BEFORE you call super.setup(...), because the setup(...) code in Species sets up the prototype.

Specified by:

setup in interface Prototype

Specified by:

setup in interface Setup

Overrides:

setup in class VectorSpecies

See Also:

Prototype.setup(EvolutionState,Parameter)