Documentation of 'org.jgap.Chromosome' Java class
Chromosome
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org.jgap

Class Chromosome

  • All Implemented Interfaces:
    java.io.Serializable, java.lang.Cloneable, java.lang.Comparable, IBusinessKey, IChromosome, IHandler, IInitializer, IPersistentRepresentation, IUniqueKey, ICloneable

    public class Chromosome
extends BaseChromosome
    Chromosomes represent potential solutions and consist of a fixed-length collection of genes. Each gene represents a discrete part of the solution. Each gene in the Chromosome may be backed by a different concrete implementation of the Gene interface, but all genes in a respective position (locus) must share the same concrete implementation across Chromosomes within a single population (genotype). In other words, gene 1 in a chromosome must share the same concrete implementation as gene 1 in all other chromosomes in the population.
    Since:
    1.0
    See Also:
    Serialized Form

    • Constructor Detail

      • Chromosome

        public Chromosome(Configuration a_configuration,
                  Gene a_sampleGene,
                  int a_desiredSize)
           throws InvalidConfigurationException
        Constructs a Chromosome of the given size separate from any specific Configuration. This constructor will use the given sample Gene to construct a new Chromosome instance containing genes all of the same type as the sample Gene. This can be useful for constructing sample chromosomes that use the same Gene type for all of their genes and that are to be used to setup a Configuration object.
        Parameters:
        a_configuration - the configuration to use
        a_sampleGene - a concrete sampleGene instance that will be used as a template for all of the genes in this Chromosome
        a_desiredSize - the desired size (number of genes) of this Chromosome
        Throws:
        InvalidConfigurationException
        Since:
        1.0

      • Chromosome

        public Chromosome(Configuration a_configuration,
                  Gene[] a_initialGenes)
           throws InvalidConfigurationException
        Constructs a Chromosome separate from any specific Configuration. This can be useful for constructing sample chromosomes that are to be used to setup a Configuration object.
        Parameters:
        a_configuration - the configuration to use
        a_initialGenes - the initial genes of this Chromosome
        Throws:
        InvalidConfigurationException
        Since:
        1.0

      • Chromosome

        public Chromosome(Configuration a_configuration,
                  Gene[] a_initialGenes,
                  IGeneConstraintChecker a_constraintChecker)
           throws InvalidConfigurationException
        Constructs a Chromosome separate from any specific Configuration. This can be useful for constructing sample chromosomes that are to be used to setup a Configuration object. Additionally, a constraint checker can be specified. It is used right here to verify the validity of the gene types supplied.
        Parameters:
        a_configuration - the configuration to use
        a_initialGenes - the initial genes of this Chromosome
        a_constraintChecker - constraint checker to use
        Throws:
        InvalidConfigurationException - in case the constraint checker reports a configuration error
        Since:
        2.5

    • Method Detail

      • clone

        public java.lang.Object clone()
        Returns a copy of this Chromosome. The returned instance can evolve independently of this instance. Note that, if possible, this method will first attempt to acquire a Chromosome instance from the active ChromosomePool (if any) and set its value appropriately before returning it. If that is not possible, then a new Chromosome instance will be constructed and its value set appropriately before returning.
        Specified by:
        clone in interface ICloneable
        Specified by:
        clone in class BaseChromosome
        Returns:
        copy of this Chromosome
        Throws:
        java.lang.IllegalStateException - instead of CloneNotSupportedException
        Since:
        1.0

      • cloneObject

        public static java.lang.Object cloneObject(Configuration a_config,
                                           java.lang.Object a_object,
                                           java.lang.Object a_master)
                                    throws java.lang.Exception
        Static convenience method. Clones an object by using clone handlers. If no deep cloning possible, then return the reference.
        Parameters:
        a_config - a valid configuration to obtain the JGAPFactory from
        a_object - the object to clone
        a_master - the super object of a_object, e.g. a chromosome in case of application to be cloned
        Returns:
        the cloned object, or the object itself if no coning supported
        Throws:
        java.lang.Exception
        Since:
        3.5

      • getFitnessValue

        public double getFitnessValue()
        Retrieves the fitness value of this Chromosome, as determined by the active fitness function. If a bulk fitness function is in use and has not yet assigned a fitness value to this Chromosome, then -1 is returned.

        Attention: should not be called from toString() as the fitness value would be computed if it was initial!

        Returns:
        a positive double value representing the fitness of this Chromosome, or -1 if a bulk fitness function is in use and has not yet assigned a fitness value to this Chromosome
        Since:
        2.0

      • getFitnessValueDirectly

        public double getFitnessValueDirectly()
        Returns:
        the lastly computed fitness value, or FitnessFunction.NO_FITNESS_VALUE in case no value has been computed yet.

      • setFitnessValue

        public void setFitnessValue(double a_newFitnessValue)
        Sets the fitness value of this Chromosome. This method is for use by bulk fitness functions and should not be invokved from anything else (except test cases).
        Parameters:
        a_newFitnessValue - a positive integer representing the fitness of this Chromosome
        Since:
        1.0

      • setFitnessValueDirectly

        public void setFitnessValueDirectly(double a_newFitnessValue)
        Sets the fitness value of this Chromosome directly without any constraint checks, conversions or checks. Only use if you know what you do.
        Parameters:
        a_newFitnessValue - a positive integer representing the fitness of this Chromosome

      • toString

        public java.lang.String toString()
        Overrides:
        toString in class java.lang.Object
        Returns:
        a string representation of this Chromosome, useful for display purposes
        Since:
        1.0

      • randomInitialChromosome

        public static IChromosome randomInitialChromosome(Configuration a_configuration)
                                           throws InvalidConfigurationException
        Convenience method that returns a new Chromosome instance with its genes values (alleles) randomized. Note that, if possible, this method will acquire a Chromosome instance from the active ChromosomePool (if any) and then randomize its gene values before returning it. If a Chromosome cannot be acquired from the pool, then a new instance will be constructed and its gene values randomized before returning it.
        Parameters:
        a_configuration - the configuration to use
        Returns:
        randomly initialized Chromosome
        Throws:
        InvalidConfigurationException - if the given Configuration instance is invalid
        java.lang.IllegalArgumentException - if the given Configuration instance is null
        Since:
        1.0

      • equals

        public boolean equals(java.lang.Object other)
        Compares this Chromosome against the specified object. The result is true if and the argument is an instance of the Chromosome class and has a set of genes equal to this one.
        Overrides:
        equals in class java.lang.Object
        Parameters:
        other - the object to compare against
        Returns:
        true: if the objects are the same, false otherwise
        Since:
        1.0

      • hashCode

        public int hashCode()
        Retrieve a hash code for this Chromosome. Does not considers the order of the Genes for all cases (especially when gene is empty).
        Overrides:
        hashCode in class java.lang.Object
        Returns:
        the hash code of this Chromosome
        Since:
        1.0

      • compareTo

        public int compareTo(java.lang.Object other)
        Compares the given Chromosome to this Chromosome. This chromosome is considered to be "less than" the given chromosome if it has a fewer number of genes or if any of its gene values (alleles) are less than their corresponding gene values in the other chromosome.
        Parameters:
        other - the Chromosome against which to compare this chromosome
        Returns:
        a negative number if this chromosome is "less than" the given chromosome, zero if they are equal to each other, and a positive number if this chromosome is "greater than" the given chromosome
        Since:
        1.0

      • setIsSelectedForNextGeneration

        public void setIsSelectedForNextGeneration(boolean a_isSelected)
        Sets whether this Chromosome has been selected by the natural selector to continue to the next generation or manually (e.g. via an add-method).
        Parameters:
        a_isSelected - true if this Chromosome has been selected, false otherwise
        Since:
        1.0

      • isSelectedForNextGeneration

        public boolean isSelectedForNextGeneration()
        Retrieves whether this Chromosome has been selected by the natural selector to continue to the next generation.
        Returns:
        true if this Chromosome has been selected, false otherwise
        Since:
        1.0

      • cleanup

        public void cleanup()
        Invoked when this Chromosome is no longer needed and should perform any necessary cleanup. Note that this method will attempt to release this Chromosome instance to the active ChromosomePool, if any.
        Since:
        1.0

      • setApplicationData

        public void setApplicationData(java.lang.Object a_newData)
        This sets the application-specific data that is attached to this Chromosome. Attaching application-specific data may be useful for some applications when it comes time to evaluate this Chromosome in the fitness function. JGAP ignores this data, except for cloning and comparison (latter only if opted in via setCompareApplicationData(..))
        Parameters:
        a_newData - the new application-specific data to attach to this Chromosome. Should be an instance of IApplicationData
        Since:
        1.1

      • getApplicationData

        public java.lang.Object getApplicationData()
        Retrieves the application-specific data that is attached to this Chromosome. Attaching application-specific data may be useful for some applications when it comes time to evaluate this Chromosome in the fitness function. JGAP ignores this data functionally.
        Returns:
        the application-specific data previously attached to this Chromosome, or null if there is no data attached
        Since:
        1.1

      • setCompareApplicationData

        public void setCompareApplicationData(boolean a_doCompare)
        Should we also consider the application data when comparing? Default is "false" as "true" means a Chromosome is losing its identity when application data is set differently!
        Parameters:
        a_doCompare - true: consider application data in method compareTo
        Since:
        2.2

      • isCompareApplicationData

        public boolean isCompareApplicationData()

      • getConstraintChecker

        public IGeneConstraintChecker getConstraintChecker()
        Returns:
        IGeneConstraintChecker the constraint checker to be used whenever method setGenes(Gene[]) is called.
        Since:
        2.5

      • isHandlerFor

        public boolean isHandlerFor(java.lang.Object a_obj,
                            java.lang.Class a_class)
        Determines whether the handler is suitable for the given object instance or class.
        Parameters:
        a_obj - the object instance to check
        a_class - the class to check, alternatively if no object instance is available (some handlers could need to get an object and would always return false if only a class is provided)
        Returns:
        true: handler suitable for given object or class

      • perform

        public java.lang.Object perform(java.lang.Object a_obj,
                                java.lang.Class a_class,
                                java.lang.Object a_params)
                         throws java.lang.Exception
        Performs a task for the given object or class. For some handlers, additional parameters are necessary, which could be provided.
        Parameters:
        a_obj - the object instance to perform the handler task for
        a_class - the class to perform the handler task for, in case no object instance is available (some handlers could need to get an object and would always throw an exception if only a class is provided)
        a_params - optional parameters needed for the handler to perform its task
        Returns:
        Object
        Throws:
        java.lang.Exception - in case of any error

      • setMultiObjectives

        public void setMultiObjectives(java.util.List a_values)

      • getMultiObjectives

        public java.util.List getMultiObjectives()
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