Package ec.vector

Class IntegerVectorSpecies

java.lang.Object

ec.Species

ec.vector.VectorSpecies

ec.vector.IntegerVectorSpecies

All Implemented Interfaces:

Prototype, Setup, Serializable, Cloneable

Direct Known Subclasses:

DOVSSpecies, GESpecies, PBILSpecies

public class IntegerVectorSpecies
extends VectorSpecies

IntegerVectorSpecies is a subclass of VectorSpecies with special constraints for integral vectors, namely ByteVectorIndividual, ShortVectorIndividual, IntegerVectorIndividual, and LongVectorIndividual.

IntegerVectorSpecies can specify a number of parameters globally, per-segment, and per-gene. See VectorSpecies for information on how to this works.

IntegerVectorSpecies defines a minimum and maximum gene value. These values are used during initialization and, depending on whether mutation-bounded is true, also during various mutation algorithms to guarantee that the gene value will not exceed these minimum and maximum bounds.

IntegerVectorSpecies provides support for two ways of mutating a gene.

• reset Replacing the gene's value with a value uniformly drawn from the gene's range (the default behavior).
• random-walkReplacing the gene's value by performing a random walk starting at the gene value. The random walk either adds 1 or subtracts 1 (chosen at random), then does a coin-flip to see whether to continue the random walk. When the coin-flip finally comes up false, the gene value is set to the current random walk position.

IntegerVectorSpecies performs gene initialization by resetting the gene.

Parameters

base.min-gene or
base.segment.segment-number.min-gene or
base.min-gene.gene-number long (default=0)	(the minimum gene value)
base.max-gene or
base.segment.segment-number.max-gene or
base.max-gene.gene-number long >= base.min-gene	(the maximum gene value)
base.mutation-type or
base.segment.segment-number.mutation-type or
base.mutation-prob.gene-number reset or random-walk (default=reset)	(the mutation type)
base.random-walk-probability or
base.segment.segment-number.random-walk-probability or
base.random-walk-probability.gene-number 0.0 <= double <= 1.0	(the probability that a random walk will continue. Random walks go up or down by 1.0 until the coin flip comes up false.)
base.mutation-bounded or
base.segment.segment-number.mutation-bounded or
base.mutation-bounded.gene-number boolean (default=true)	(whether mutation is restricted to only being within the min/max gene values. Does not apply to SimulatedBinaryCrossover (which is always bounded))

See Also:

• Serialized Form

Field Summary

Fields

Modifier and Type	Field	Description
static final int	C_RANDOM_WALK_MUTATION
static final int	C_RESET_MUTATION
protected long[]	maxGene	Max-gene value, per gene.
protected long[]	minGene	Min-gene value, per gene.
protected boolean[]	mutationIsBounded	Whether mutation is bounded to the min- and max-gene values, per gene.
protected int[]	mutationType	Mutation type, per gene.
static final String	P_MAXGENE
static final String	P_MINGENE
static final String	P_MUTATION_BOUNDED
static final String	P_MUTATIONTYPE
static final String	P_NUM_SEGMENTS
static final String	P_RANDOM_WALK_PROBABILITY
static final String	P_SEGMENT
static final String	P_SEGMENT_END
static final String	P_SEGMENT_START
static final String	P_SEGMENT_TYPE
protected double[]	randomWalkProbability	The continuation probability for Integer Random Walk Mutation, per gene.
static final String	V_RANDOM_WALK_MUTATION
static final String	V_RESET_MUTATION

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_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	Description
IntegerVectorSpecies()

Method Summary

Modifier and Type	Method	Description
boolean	inNumericalTypeRange(double geneVal)
boolean	inNumericalTypeRange(long geneVal)
protected void	loadParametersForGene(EvolutionState state, int index, Parameter base, Parameter def, String postfix)	Called when VectorSpecies is setting up per-gene and per-segment parameters.
long	maxGene(int gene)
long	minGene(int gene)
boolean	mutationIsBounded(int gene)
int	mutationType(int gene)
double	randomWalkProbability(int gene)
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, mutationProbability, newIndividual, setupGenome

Methods inherited from class ec.Species

buildMisc, clone, newIndividual, newIndividual, updateIndividual, updateSubpopulation

Methods inherited from class java.lang.Object

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

Field Details

P_MINGENE

public static final String P_MINGENE

See Also:

• Constant Field Values

P_MAXGENE

public static final String P_MAXGENE

See Also:

• Constant Field Values

P_NUM_SEGMENTS

public static final String P_NUM_SEGMENTS

See Also:

• Constant Field Values

P_SEGMENT_TYPE

public static final String P_SEGMENT_TYPE

See Also:

• Constant Field Values

P_SEGMENT_START

public static final String P_SEGMENT_START

See Also:

• Constant Field Values

P_SEGMENT_END

public static final String P_SEGMENT_END

See Also:

• Constant Field Values

P_SEGMENT

public static final String P_SEGMENT

See Also:

• Constant Field Values

P_MUTATIONTYPE

public static final String P_MUTATIONTYPE

See Also:

• Constant Field Values

P_RANDOM_WALK_PROBABILITY

public static final String P_RANDOM_WALK_PROBABILITY

See Also:

• Constant Field Values

P_MUTATION_BOUNDED

public static final String P_MUTATION_BOUNDED

See Also:

• Constant Field Values

V_RESET_MUTATION

public static final String V_RESET_MUTATION

See Also:

• Constant Field Values

V_RANDOM_WALK_MUTATION

public static final String V_RANDOM_WALK_MUTATION

See Also:

• Constant Field Values

C_RESET_MUTATION

public static final int C_RESET_MUTATION

See Also:

• Constant Field Values

C_RANDOM_WALK_MUTATION

public static final int C_RANDOM_WALK_MUTATION

See Also:

• Constant Field Values

minGene

protected long[] minGene

Min-gene value, per gene. This array is one longer than the standard genome length. The top element in the array represents the parameters for genes in genomes which have extended beyond the genome length.

maxGene

protected long[] maxGene

Max-gene value, per gene. This array is one longer than the standard genome length. The top element in the array represents the parameters for genes in genomes which have extended beyond the genome length.

mutationType

protected int[] mutationType

Mutation type, per gene. This array is one longer than the standard genome length. The top element in the array represents the parameters for genes in genomes which have extended beyond the genome length.

randomWalkProbability

protected double[] randomWalkProbability

The continuation probability for Integer Random Walk Mutation, per gene. This array is one longer than the standard genome length. The top element in the array represents the parameters for genes in genomes which have extended beyond the genome length.

mutationIsBounded

protected boolean[] mutationIsBounded

Whether mutation is bounded to the min- and max-gene values, per gene. This array is one longer than the standard genome length. The top element in the array represents the parameters for genes in genomes which have extended beyond the genome length.

Constructor Details

IntegerVectorSpecies

public IntegerVectorSpecies()

Method Details

maxGene

public long maxGene(int gene)

minGene

public long minGene(int gene)

mutationType

public int mutationType(int gene)

randomWalkProbability

public double randomWalkProbability(int gene)

mutationIsBounded

public boolean mutationIsBounded(int gene)

inNumericalTypeRange

public boolean inNumericalTypeRange(double geneVal)

inNumericalTypeRange

public boolean inNumericalTypeRange(long geneVal)

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)

loadParametersForGene

protected void loadParametersForGene(EvolutionState state,
 int index,
 Parameter base,
 Parameter def,
 String postfix)

Description copied from class: VectorSpecies

Called when VectorSpecies is setting up per-gene and per-segment parameters. The index is the current gene whose parameter is getting set up. The Parameters in question are the bases for the gene. The postfix should be appended to the end of any parameter looked up (it often contains a number indicating the gene in question), such as state.parameters.exists(base.push(P_PARAM).push(postfix), def.push(P_PARAM).push(postfix)

If you override this method, be sure to call super(...) at some point, ideally first.

Overrides:

loadParametersForGene in class VectorSpecies