Package ec.vector

Class BitVectorSpecies

java.lang.Object

ec.Species

ec.vector.VectorSpecies

ec.vector.BitVectorSpecies

All Implemented Interfaces:

Prototype, Setup, Serializable, Cloneable

public class BitVectorSpecies
extends VectorSpecies

BitVectorSpecies is a subclass of VectorSpecies with special constraints for boolean vectors, namely BitVectorIndividual.

BitVectorSpecies can specify some parameters globally, per-segment, and per-gene. See VectorSpecies for information on how to this works.

BitVectorSpecies 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 [true, false].
• flipFlipping the bit of the gene value. This is the default.

BitVectorSpecies provides support for two ways of initializing a gene. The initialization procedure is determined by the choice of mutation procedure as described above. If the mutation is floating-point (reset, gauss, polynomial), then initialization will be done by resetting the gene to uniformly chosen double floating-point value between the minimum and maximum legal gene values, inclusive. If the mutation is integer (integer-reset, integer-random-walk), then initialization will be done by performing the same kind of reset, but restricting values to integers only.

Parameters

base.mutation-type or
base.segment.segment-number.mutation-type or
base.mutation-prob.gene-number reset, flip, (default=flip)	(the mutation type)

See Also:

• Serialized Form

Field Summary

Fields

Modifier and Type	Field	Description
static final int	C_FLIP_MUTATION
static final int	C_RESET_MUTATION
protected int[]	mutationType	Mutation type, per gene.
static final String	P_MUTATIONTYPE
static final String	V_FLIP_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_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	Description
BitVectorSpecies()

Method Summary

Modifier and Type	Method	Description
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.
int	mutationType(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_MUTATIONTYPE

public static final String P_MUTATIONTYPE

See Also:

• Constant Field Values

V_RESET_MUTATION

public static final String V_RESET_MUTATION

See Also:

• Constant Field Values

V_FLIP_MUTATION

public static final String V_FLIP_MUTATION

See Also:

• Constant Field Values

C_RESET_MUTATION

public static final int C_RESET_MUTATION

See Also:

• Constant Field Values

C_FLIP_MUTATION

public static final int C_FLIP_MUTATION

See Also:

• Constant Field Values

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.

Constructor Details

BitVectorSpecies

public BitVectorSpecies()

Method Details

mutationType

public int mutationType(int gene)

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)

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