org.jgap
Class Genotype

java.lang.Object
  org.jgap.Genotype

All Implemented Interfaces:

java.io.Serializable, java.lang.Runnable

Direct Known Subclasses:

DistributedGenotype

public class Genotype
extends java.lang.Object
implements java.io.Serializable, java.lang.Runnable

Genotypes are fixed-length populations of chromosomes. As an instance of a Genotype is evolved, all of its Chromosomes are also evolved. A Genotype may be constructed normally via constructor, or the static randomInitialGenotype() method can be used to generate a Genotype with a randomized Chromosome population.

Please note that among all created Genotype instances there may only be one configuration, used by all Genotype instances.

Since:

1.0

See Also:

Serialized Form

Constructor Summary

Genotype(Configuration a_configuration)
Don't use this constructor, it's only for internal use.

Genotype(Configuration a_configuration, IChromosome[] a_initialChromosomes)
Deprecated. use Genotype(Configuration, Population) instead

Genotype(Configuration a_configuration, Population a_population)
Constructs a new Genotype instance with the given array of Chromosomes and the given active Configuration instance.

Method Summary

protected void	applyGeneticOperator(GeneticOperator a_operator, Population a_population, java.util.List a_chromosomes) Overwritable method that calls a GeneticOperator to operate on a given population and asks him to store the result in the list of chromosomes.
void	applyGeneticOperators() Applies all GeneticOperators registered with the Configuration.
protected void	applyNaturalSelectors(boolean a_processBeforeGeneticOperators) Applies all NaturalSelectors registered with the Configuration.
boolean	equals(java.lang.Object a_other) Compares this Genotype against the specified object.
void	evolve() Evolves the population of Chromosomes within this Genotype.
java.util.List<java.lang.String>	evolve(IEvolutionMonitor a_monitor) Evolves this genotype until the given monitor asks to quit the evolution cycle.
void	evolve(int a_numberOfEvolutions) Evolves this Genotype the specified number of times.
void	fillPopulation(int a_num) Fills up the population with random chromosomes if necessary.
IChromosome[]	getChromosomes() Deprecated. uses getPopulation() instead
Configuration	getConfiguration()
java.util.List<IEvolveJob>	getEvolves(IPopulationSplitter a_splitter) Splits a population into pieces that can be evolved independently.
IChromosome	getFittestChromosome() Retrieves the Chromosome in the Population with the highest fitness value.
IChromosome	getFittestChromosome(int a_startIndex, int a_endIndex) Retrieves the Chromosome in the Population with the highest fitness value within the given indices.
java.util.List	getFittestChromosomes(int a_numberOfChromosomes) Retrieves the top n Chromsomes in the population (the ones with the best fitness values).
Population	getPopulation()
static Configuration	getStaticConfiguration()
int	hashCode() Hashcode function for the genotype, tries to create a unique hashcode for the chromosomes within the population.
protected void	keepPopSizeConstant(Population a_pop, int a_maxSize) Cares that the population size does not exceed the given maximum size.
void	mergeResults(IPopulationMerger a_merger, EvolveResult[] a_results)
static Genotype	randomInitialGenotype(Configuration a_configuration) Convenience method that returns a newly constructed Genotype instance configured according to the given Configuration instance.
void	run() If used in a Thread: runs the evolution forever.
protected void	setPopulation(Population a_pop)
static void	setStaticConfiguration(Configuration a_configuration) Sets the configuration to use with the Genetic Algorithm.
java.lang.String	toString()

Methods inherited from class java.lang.Object

clone, finalize, getClass, notify, notifyAll, wait, wait, wait

Constructor Detail

Genotype

public Genotype(Configuration a_configuration,
                IChromosome[] a_initialChromosomes)
         throws InvalidConfigurationException

Deprecated. use Genotype(Configuration, Population) instead

Constructs a new Genotype instance with the given array of Chromosomes and the given active Configuration instance. Note that the Configuration object must be in a valid state when this method is invoked, or a InvalidConfigurationException will be thrown.

Parameters:

a_configuration - the Configuration object to use

a_initialChromosomes - the Chromosome population to be managed by this Genotype instance

Throws:

InvalidConfigurationException - if the given Configuration object is in an invalid state

Since:

1.0

Genotype

public Genotype(Configuration a_configuration,
                Population a_population)
         throws InvalidConfigurationException

Constructs a new Genotype instance with the given array of Chromosomes and the given active Configuration instance. Note that the Configuration object must be in a valid state when this method is invoked, or a InvalidconfigurationException will be thrown.

Parameters:

a_configuration - the Configuration object to use

a_population - the Chromosome population to be managed by this Genotype instance

Throws:

InvalidConfigurationException

Since:

2.0

Genotype

public Genotype(Configuration a_configuration)
         throws InvalidConfigurationException

Don't use this constructor, it's only for internal use.

Parameters:

a_configuration - not used here!

Throws:

InvalidConfigurationException

Since:

3.0

Method Detail

getChromosomes

public IChromosome[] getChromosomes()

Deprecated. uses getPopulation() instead

Retrieves the array of Chromosomes that make up the population of this Genotype instance.

Returns:

the Population of Chromosomes

Since:

1.0

getPopulation

public Population getPopulation()

Returns:

the current population of chromosomes

Since:

2.1

getFittestChromosome

public IChromosome getFittestChromosome()

Retrieves the Chromosome in the Population with the highest fitness value.

Returns:

the Chromosome with the highest fitness value, or null if there are no chromosomes in this Genotype

Since:

1.0

getFittestChromosome

public IChromosome getFittestChromosome(int a_startIndex,
                                        int a_endIndex)

Retrieves the Chromosome in the Population with the highest fitness value within the given indices.

Parameters:

a_startIndex - the index to start the determination with

a_endIndex - the index to end the determination with

Returns:

the Chromosome with the highest fitness value within the given indices, or null if there are no chromosomes in this Genotype

Since:

3.0

getFittestChromosomes

public java.util.List getFittestChromosomes(int a_numberOfChromosomes)

Retrieves the top n Chromsomes in the population (the ones with the best fitness values).

Parameters:

a_numberOfChromosomes - the number of chromosomes desired

Returns:

the list of Chromosomes with the highest fitness values, or null if there are no chromosomes in this Genotype

Since:

2.4

evolve

public void evolve()

Evolves the population of Chromosomes within this Genotype. This will execute all of the genetic operators added to the present active configuration and then invoke the natural selector to choose which chromosomes will be included in the next generation population. Note that the population size not always remains constant (dependent on the NaturalSelectors used!). To consecutively call this method, use evolve(int)!!!

Since:

1.0

evolve

public void evolve(int a_numberOfEvolutions)

Evolves this Genotype the specified number of times. This is equivalent to invoking the standard evolve() method the given number of times in a row.

Parameters:

a_numberOfEvolutions - the number of times to evolve this Genotype before returning

Since:

1.1

evolve

public java.util.List<java.lang.String> evolve(IEvolutionMonitor a_monitor)

Evolves this genotype until the given monitor asks to quit the evolution cycle.

Parameters:

a_monitor - the monitor used to decide when to stop evolution

Returns:

messages of the registered evolution monitor. May indicate why the evolution was asked to be stopped. May be empty, depending on the implementation of the used monitor

Since:

3.4.4

toString

public java.lang.String toString()

Overrides:

toString in class java.lang.Object

Returns:

string representation of this Genotype instance, useful for display or debug purposes

Since:

1.0

randomInitialGenotype

public static Genotype randomInitialGenotype(Configuration a_configuration)
                                      throws InvalidConfigurationException

Convenience method that returns a newly constructed Genotype instance configured according to the given Configuration instance. The population of Chromosomes will be created according to the setup of the sample Chromosome in the Configuration object, but the gene values (alleles) will be set to random legal values.

Parameters:

a_configuration - the current active Configuration object

Returns:

a newly constructed Genotype instance

Throws:

java.lang.IllegalArgumentException - if the given Configuration object is null

InvalidConfigurationException - if the given Configuration instance is not in a valid state

Since:

2.3

fillPopulation

public void fillPopulation(int a_num)
                    throws InvalidConfigurationException

Fills up the population with random chromosomes if necessary.

Parameters:

a_num - the number of chromosomes to add

Throws:

InvalidConfigurationException

Since:

3.2

equals

public boolean equals(java.lang.Object a_other)

Compares this Genotype against the specified object. The result is true if the argument is an instance of the Genotype class, has exactly the same number of chromosomes as the given Genotype, and, for each Chromosome in this Genotype, there is an equal chromosome in the given Genotype. The chromosomes do not need to appear in the same order within the population.

Overrides:

equals in class java.lang.Object

Parameters:

a_other - the object to compare against

Returns:

true if the objects are the same, false otherwise

Since:

1.0

applyNaturalSelectors

protected void applyNaturalSelectors(boolean a_processBeforeGeneticOperators)

Applies all NaturalSelectors registered with the Configuration.

Parameters:

a_processBeforeGeneticOperators - true apply NaturalSelectors applicable before GeneticOperators, false: apply the ones applicable after GeneticOperators

Since:

2.0

applyGeneticOperators

public void applyGeneticOperators()

Applies all GeneticOperators registered with the Configuration.

Since:

3.0

getStaticConfiguration

public static Configuration getStaticConfiguration()

Returns:

the configuration to use with the Genetic Algorithm

Since:

2.0

setStaticConfiguration

public static void setStaticConfiguration(Configuration a_configuration)

Sets the configuration to use with the Genetic Algorithm.

Parameters:

a_configuration - the configuration to use

Since:

2.0

getConfiguration

public Configuration getConfiguration()

hashCode

public int hashCode()

Hashcode function for the genotype, tries to create a unique hashcode for the chromosomes within the population. The logic for the hashcode is Step Result ---- ------ 1 31*0 + hashcode_0 = y(1) 2 31*y(1) + hashcode_1 = y(2) 3 31*y(2) + hashcode_2 = y(3) n 31*y(n-1) + hashcode_n-1 = y(n) Each hashcode is a number and the binary equivalent is computed and returned.

Overrides:

hashCode in class java.lang.Object

Returns:

the computed hashcode

Since:

2.1

setPopulation

protected void setPopulation(Population a_pop)

applyGeneticOperator

protected void applyGeneticOperator(GeneticOperator a_operator,
                                    Population a_population,
                                    java.util.List a_chromosomes)

Overwritable method that calls a GeneticOperator to operate on a given population and asks him to store the result in the list of chromosomes. Override this method if you want to ensure that a_chromosomes is not part of a_population resp. if you want to use a different list.

Parameters:

a_operator - the GeneticOperator to call

a_population - the population to use

a_chromosomes - the list of Chromosome objects to return

Since:

2.4

keepPopSizeConstant

protected void keepPopSizeConstant(Population a_pop,
                                   int a_maxSize)

Cares that the population size does not exceed the given maximum size.

Parameters:

a_pop - the population to keep constant in size

a_maxSize - the maximum size allowed for the population

Since:

2.5

run

public void run()

If used in a Thread: runs the evolution forever. You have to implement a listener to stop computation sometime. See examples.simpleBooleanThreaded for a possible implementation of such a listener.

Specified by:

run in interface java.lang.Runnable

Since:

3.01

getEvolves

public java.util.List<IEvolveJob> getEvolves(IPopulationSplitter a_splitter)
                                      throws java.lang.Exception

Splits a population into pieces that can be evolved independently.

Parameters:

a_splitter - splits the population

Returns:

list of IEvolveJob objects

Throws:

java.lang.Exception

mergeResults

public void mergeResults(IPopulationMerger a_merger,
                         EvolveResult[] a_results)
                  throws java.lang.Exception

Throws:

java.lang.Exception