Documentation of 'ec.Subpopulation' Java class
Subpopulation
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Class Subpopulation

  • All Implemented Interfaces:
    Group, Setup, java.io.Serializable, java.lang.Cloneable
    Direct Known Subclasses:
    Spatial1DSubpopulation

    public class Subpopulation
extends java.lang.Object
implements Group
    Subpopulation is a group which is basically an array of Individuals. There is always one or more Subpopulations in the Population. Each Subpopulation has a Species, which governs the formation of the Individuals in that Subpopulation. Subpopulations also contain a Fitness prototype which is cloned to form Fitness objects for individuals in the subpopulation.

    An initial subpopulation is populated with new random individuals using the populate(...) method. This method typically populates by filling the array with individuals created using the Subpopulations' species' emptyClone() method, though you might override this to create them with other means, by loading from text files for example.

    In a multithreaded area of a run, Subpopulations should be considered immutable. That is, once they are created, they should not be modified, nor anything they contain. This protocol helps ensure read-safety under multithreading race conditions.

    Parameters

    base.size
    int >= 1    		 (total number of individuals in the subpopulation)
    base.species
    classname, inherits and != ec.Species    		 (the class of the subpopulations' Species)
    base.fitness
    classname, inherits and != ec.Fitness    		 (the class for the prototypical Fitness for individuals in this subpopulation)
    base.file
    String    		 (pathname of file from which the population is to be loaded. If not defined, or empty, then the population will be initialized at random in the standard manner)
    base.duplicate-retries
    int >= 0    		 (during initialization, when we produce an individual which already exists in the subpopulation, the number of times we try to replace it with something unique. Ignored if we're loading from a file.)

    Default Base
    ec.subpop

    Parameter bases

    base.species species (the subpopulations' species)
    See Also:
    Serialized Form

    • Constructor Detail

      • Subpopulation

        public Subpopulation()

    • Method Detail

      • defaultBase

        public Parameter defaultBase()

      • emptyClone

        public Group emptyClone()
        Returns an instance of Subpopulation just like it had been before it was populated with individuals. You may need to override this if you override Subpopulation. IMPORTANT NOTE: if the size of the array in Subpopulation has been changed, then the clone will take on the new array size. This helps some evolution strategies.
        Specified by:
        emptyClone in interface Group
        See Also:
        Group.emptyClone()

      • clear

        public void clear()
        Sets all Individuals in the Subpopulation to null, preparing it to be reused.

      • setup

        public void setup(EvolutionState state,
                  Parameter base)
        Description copied from interface: Setup
        Sets up the object by reading it from the parameters stored in state, built off of the parameter base base. If an ancestor implements this method, be sure to call super.setup(state,base); before you do anything else.
        Specified by:
        setup in interface Setup

      • printSubpopulationForHumans

        public final void printSubpopulationForHumans(EvolutionState state,
                                              int log,
                                              int verbosity)
        Deprecated. Verbosity no longer has meaning
        Prints an entire subpopulation in a form readable by humans.

      • printSubpopulation

        public final void printSubpopulation(EvolutionState state,
                                     int log,
                                     int verbosity)
        Deprecated. Verbosity no longer has meaning
        Prints an entire subpopulation in a form readable by humans but also parseable by the computer using readSubpopulation(EvolutionState, LineNumberReader).

      • printSubpopulationForHumans

        public void printSubpopulationForHumans(EvolutionState state,
                                        int log)
        Prints an entire subpopulation in a form readable by humans, with a verbosity of Output.V_NO_GENERAL.

      • printSubpopulation

        public void printSubpopulation(EvolutionState state,
                               int log)
        Prints an entire subpopulation in a form readable by humans but also parseable by the computer using readSubpopulation(EvolutionState, LineNumberReader) with a verbosity of Output.V_NO_GENERAL.

      • printSubpopulation

        public void printSubpopulation(EvolutionState state,
                               java.io.PrintWriter writer)
        Prints an entire subpopulation in a form readable by humans but also parseable by the computer using readSubpopulation(EvolutionState, LineNumberReader).

      • readSubpopulation

        public void readSubpopulation(EvolutionState state,
                              java.io.LineNumberReader reader)
                       throws java.io.IOException
        Reads a subpopulation from the format generated by printSubpopulation(....). If the number of individuals is not identical, the individuals array will be deleted and replaced with a new array, and a warning will be generated as individuals will have to be created using newIndividual(...) rather than readIndividual(...).
        Throws:
        java.io.IOException

      • writeSubpopulation

        public void writeSubpopulation(EvolutionState state,
                               java.io.DataOutput dataOutput)
                        throws java.io.IOException
        Writes a subpopulation in binary form, in a format readable by readSubpopulation(EvolutionState, DataInput).
        Throws:
        java.io.IOException

      • readSubpopulation

        public void readSubpopulation(EvolutionState state,
                              java.io.DataInput dataInput)
                       throws java.io.IOException
        Reads a subpopulation in binary form, from the format generated by writeSubpopulation(...). If the number of individuals is not identical, the individuals array will be deleted and replaced with a new array, and a warning will be generated as individuals will have to be created using newIndividual(...) rather than readIndividual(...)
        Throws:
        java.io.IOException
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