Subpopulation (ECJ 22 API)

java.lang.Object
- ec.Subpopulation

All Implemented Interfaces:: Group, Setup, Serializable, Cloneable

Direct Known Subclasses:: Spatial1DSubpopulation

public class Subpopulation
extends 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)

Version:: 1.0
Author:: Sean Luke
See Also:: Serialized Form

Field Summary

Fields
Modifier and Type	Field and Description
`int`	`extraBehavior` What is our fill behavior beyond files?
`Parameter`	`file`
`static int`	`FILL`
`static String`	`INDIVIDUAL_INDEX_PREAMBLE`
`Individual[]`	`individuals` The subpopulation's individuals.
`boolean`	`loadInds`
`static String`	`NUM_INDIVIDUALS_PREAMBLE`
`int`	`numDuplicateRetries` Do we allow duplicates?
`static String`	`P_EXTRA_BEHAVIOR`
`static String`	`P_FILE`
`static String`	`P_RETRIES`
`static String`	`P_SPECIES`
`static String`	`P_SUBPOPSIZE`
`static String`	`P_SUBPOPULATION`
`private static long`	`serialVersionUID`
`Species`	`species` The species for individuals in this subpopulation.
`static int`	`TRUNCATE`
`static String`	`V_FILL`
`static String`	`V_TRUNCATE`
`static String`	`V_WRAP`
`static int`	`WRAP`

Constructor Summary

Constructors
Constructor and Description

Subpopulation()

Constructors
Constructor and Description
`Subpopulation()`

Method Summary

Methods
Modifier and Type	Method and Description
`void`	`clear()` Sets all Individuals in the Subpopulation to null, preparing it to be reused.
`Parameter`	`defaultBase()`
`Group`	`emptyClone()` Returns an instance of Subpopulation just like it had been before it was populated with individuals.
`void`	`populate(EvolutionState state, int thread)`
`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.
`void`	`printSubpopulation(EvolutionState state, int log, int verbosity)` Deprecated. Verbosity no longer has meaning
`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).
`void`	`printSubpopulationForHumans(EvolutionState state, int log)` Prints an entire subpopulation in a form readable by humans, with a verbosity of Output.V_NO_GENERAL.
`void`	`printSubpopulationForHumans(EvolutionState state, int log, int verbosity)` Deprecated. Verbosity no longer has meaning
`void`	`readSubpopulation(EvolutionState state, DataInput dataInput)` Reads a subpopulation in binary form, from the format generated by writeSubpopulation(...).
`void`	`readSubpopulation(EvolutionState state, LineNumberReader reader)` Reads a subpopulation from the format generated by printSubpopulation(....).
`void`	`setup(EvolutionState state, Parameter base)` Sets up the object by reading it from the parameters stored in state, built off of the parameter base base.
`void`	`writeSubpopulation(EvolutionState state, DataOutput dataOutput)` Writes a subpopulation in binary form, in a format readable by readSubpopulation(EvolutionState, DataInput).

Methods inherited from class java.lang.Object
clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

- Field Detail
  - serialVersionUID
```
private static final long serialVersionUID
```
    See Also:
    Constant Field Values
  - loadInds
```
public boolean loadInds
```
  - file
```
public Parameter file
```
  - species
```
public Species species
```
    The species for individuals in this subpopulation.
  - individuals
```
public Individual[] individuals
```
    The subpopulation's individuals.
  - numDuplicateRetries
```
public int numDuplicateRetries
```
    Do we allow duplicates?
  - extraBehavior
```
public int extraBehavior
```
    What is our fill behavior beyond files?
  - P_SUBPOPULATION
```
public static final String P_SUBPOPULATION
```
    See Also:
    Constant Field Values
  - P_FILE
```
public static final String P_FILE
```
    See Also:
    Constant Field Values
  - P_SUBPOPSIZE
```
public static final String P_SUBPOPSIZE
```
    See Also:
    Constant Field Values
  - P_SPECIES
```
public static final String P_SPECIES
```
    See Also:
    Constant Field Values
  - P_RETRIES
```
public static final String P_RETRIES
```
    See Also:
    Constant Field Values
  - P_EXTRA_BEHAVIOR
```
public static final String P_EXTRA_BEHAVIOR
```
    See Also:
    Constant Field Values
  - V_TRUNCATE
```
public static final String V_TRUNCATE
```
    See Also:
    Constant Field Values
  - V_WRAP
```
public static final String V_WRAP
```
    See Also:
    Constant Field Values
  - V_FILL
```
public static final String V_FILL
```
    See Also:
    Constant Field Values
  - NUM_INDIVIDUALS_PREAMBLE
```
public static final String NUM_INDIVIDUALS_PREAMBLE
```
    See Also:
    Constant Field Values
  - INDIVIDUAL_INDEX_PREAMBLE
```
public static final String INDIVIDUAL_INDEX_PREAMBLE
```
    See Also:
    Constant Field Values
  - TRUNCATE
```
public static final int TRUNCATE
```
    See Also:
    Constant Field Values
  - WRAP
```
public static final int WRAP
```
    See Also:
    Constant Field Values
  - FILL
```
public static final int FILL
```
    See Also:
    Constant Field Values
- 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
  - populate
```
public void populate(EvolutionState state,
            int thread)
```
  - 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,
                      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

Class Subpopulation

Field Summary

Constructor Summary

Method Summary

Methods inherited from class java.lang.Object

Field Detail

serialVersionUID

loadInds

file

species

individuals

numDuplicateRetries

extraBehavior

P_SUBPOPULATION

P_FILE

P_SUBPOPSIZE

P_SPECIES

P_RETRIES

P_EXTRA_BEHAVIOR

V_TRUNCATE

V_WRAP

V_FILL

NUM_INDIVIDUALS_PREAMBLE

INDIVIDUAL_INDEX_PREAMBLE

TRUNCATE

WRAP

FILL

Constructor Detail

Subpopulation

Method Detail

defaultBase

emptyClone

clear

setup

populate

printSubpopulationForHumans

printSubpopulation

printSubpopulationForHumans

printSubpopulation

printSubpopulation

readSubpopulation

writeSubpopulation

readSubpopulation