Package ec

Class Subpopulation

java.lang.Object
ec.Subpopulation
All Implemented Interfaces:
Setup, Serializable, Cloneable
Direct Known Subclasses:
Spatial1DSubpopulation
public class Subpopulation extends Object implements Cloneable, Setup
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:

  • Field Details

  • Constructor Details

    • Subpopulation

      public Subpopulation()

  • Method Details

    • defaultBase

      public Parameter defaultBase()

    • emptyClone

      public Subpopulation 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.

    • truncate

      public void truncate(int toThis)
      Truncates the Subpopulation to a new size. The Subpopulation is truncated such that the higher indexed individuals may be deleted.

    • 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

    • populate

      public void populate(EvolutionState state, int thread)

    • printSubpopulationForHumans

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

    • printSubpopulation

      public final void printSubpopulation(EvolutionState state, int log, int verbosity)
      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)

    • 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, 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, LineNumberReader reader) throws 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:
      IOException

    • writeSubpopulation

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

    • readSubpopulation

      public void readSubpopulation(EvolutionState state, DataInput dataInput) throws 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:
      IOException