ec.gp

Class GPIndividual

java.lang.Object

ec.Individual

ec.gp.GPIndividual

All Implemented Interfaces:

Prototype, Setup, Serializable, Cloneable, Comparable

public class GPIndividual
extends Individual

GPIndividual is an Individual used for GP evolution runs. GPIndividuals contain, at the very least, a nonempty array of GPTrees. You can use GPIndividual directly, or subclass it to extend it as you see fit.

GPIndividuals have two clone methods: clone() and lightClone(). clone() is a deep clone method as usual. lightClone() is a light clone which does not copy the trees.

In addition to serialization for checkpointing, Individuals may read and write themselves to streams in three ways.

• writeIndividual(...,DataOutput)/readIndividual(...,DataInput) This method transmits or receives an individual in binary. It is the most efficient approach to sending individuals over networks, etc. These methods write the evaluated flag and the fitness, then call readGenotype/writeGenotype, which you must implement to write those parts of your Individual special to your functions-- the default versions of readGenotype/writeGenotype throw errors. You don't need to implement them if you don't plan on using read/writeIndividual.
• printIndividual(...,PrintWriter)/readIndividual(...,LineNumberReader) This approach transmits or receives an indivdual in text encoded such that the individual is largely readable by humans but can be read back in 100% by ECJ as well. Because GPIndividuals are often very large, GPIndividual has overridden these methods -- they work differently than in Individual (the superclass). In specific: readIndividual by default reads in the fitness and the evaluation flag, then calls parseGenotype to read in the trees (via GPTree.readTree(...)). However printIndividual by default prints the fitness and evaluation flag, and prints all the trees by calling GPTree.printTree(...). It does not call genotypeToString at all. This is because it's very wasteful to build up a large string holding the printed form of the GPIndividual just to pump it out a stream once.
• printIndividualForHumans(...,PrintWriter) This approach prints an individual in a fashion intended for human consumption only. Because GPIndividuals are often very large, GPIndividual has overridden this methods -- it works differently than in Individual (the superclass). In specific: printIndividual by default prints the fitness and evaluation flag, and prints all the trees by calling GPTree.printTreeForHumans(...). It does not call genotypeToStringForHumans at all. This is because it's very wasteful to build up a large string holding the printed form of the GPIndividual just to pump it out a stream once.

  In general, the various readers and writers do three things: they tell the Fitness to read/write itself, they read/write the evaluated flag, and they read/write the GPTree array (by having each GPTree read/write itself). If you add instance variables to GPIndividual, you'll need to read/write those variables as well.

  Parameters
  

  base.numtrees int >= 1	(number of trees in the GPIndividual)
  base.tree.n classname, inherits or = ec.gp.GPTree	(class of tree n in the individual)

  Default Base
  gp.individual

  Parameter bases
  

  base.tree.n

  tree n in the individual

Version:

1.0

Author:

Sean Luke

See Also:

Serialized Form

Field Summary

Fields

Modifier and Type	Field and Description
static String	P_NUMTREES
static String	P_TREE
private static long	serialVersionUID
GPTree[]	trees

Fields inherited from class ec.Individual

evaluated, EVALUATED_PREAMBLE, fitness, P_INDIVIDUAL, species

Constructor Summary

Constructors

Constructor and Description
GPIndividual()

Method Summary

Methods

Modifier and Type	Method and Description
Object	clone() Deep-clones the GPIndividual.
Parameter	defaultBase() Returns the default base for this prototype.
boolean	equals(Object ind) Returns true if I am genetically "equal" to ind.
int	hashCode() Returns a hashcode for the individual, such that individuals which are equals(...) each other always return the same hash code.
GPIndividual	lightClone() Like clone(), but doesn't force the GPTrees to deep-clone themselves.
void	parseGenotype(EvolutionState state, LineNumberReader reader) This method is used only by the default version of readIndividual(state,reader), and it is intended to be overridden to parse in that part of the individual that was outputted in the genotypeToString() method.
void	printIndividual(EvolutionState state, int log) Should print the individual in a way that can be read by computer, including its fitness, with a verbosity of Output.V_NO_GENERAL.
void	printIndividual(EvolutionState state, PrintWriter writer) Should print the individual in a way that can be read by computer, including its fitness.
void	printIndividualForHumans(EvolutionState state, int log) Should print the individual out in a pleasing way for humans, with a verbosity of Output.V_NO_GENERAL.
void	printTrees(EvolutionState state, int log) Prints just the trees of the GPIndividual.
void	readGenotype(EvolutionState state, DataInput dataInput) Overridden for the GPIndividual genotype.
void	setup(EvolutionState state, Parameter base) Sets up a prototypical GPIndividual with those features which it shares with other GPIndividuals in its species, and nothing more.
long	size() Returns the "size" of the individual, namely, the number of nodes in all of its subtrees.
void	verify(EvolutionState state) Verification of validity of the GPIndividual -- strictly for debugging purposes only
void	writeGenotype(EvolutionState state, DataOutput dataOutput) Overridden for the GPIndividual genotype.

Methods inherited from class ec.Individual

compareTo, distanceTo, genotypeToString, genotypeToStringForHumans, merge, printIndividual, printIndividualForHumans, readIndividual, readIndividual, toString, writeIndividual

Methods inherited from class java.lang.Object

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

Field Detail

serialVersionUID

private static final long serialVersionUID

See Also:

Constant Field Values

P_NUMTREES

public static final String P_NUMTREES

See Also:

Constant Field Values

P_TREE

public static final String P_TREE

See Also:

Constant Field Values

trees

public GPTree[] trees

Constructor Detail

GPIndividual

public GPIndividual()

Method Detail

defaultBase

public Parameter defaultBase()

Description copied from interface: Prototype

Returns the default base for this prototype. This should generally be implemented by building off of the static base() method on the DefaultsForm object for the prototype's package. This should be callable during setup(...).

equals

public boolean equals(Object ind)

Description copied from class: Individual

Returns true if I am genetically "equal" to ind. This should mostly be interpreted as saying that we are of the same class and that we hold the same data. It should NOT be a pointer comparison.

Specified by:

equals in class Individual

hashCode

public int hashCode()

Description copied from class: Individual

Returns a hashcode for the individual, such that individuals which are equals(...) each other always return the same hash code.

Specified by:

hashCode in class Individual

setup

public void setup(EvolutionState state,
         Parameter base)

Sets up a prototypical GPIndividual with those features which it shares with other GPIndividuals in its species, and nothing more.

Specified by:

setup in interface Prototype

Specified by:

setup in interface Setup

Overrides:

setup in class Individual

See Also:

Prototype.setup(EvolutionState,Parameter)

verify

public void verify(EvolutionState state)

Verification of validity of the GPIndividual -- strictly for debugging purposes only

printTrees

public void printTrees(EvolutionState state,
              int log)

Prints just the trees of the GPIndividual. Broken out like this to be used by GEIndividual to avoid re-printing the fitness and evaluated premables.

printIndividualForHumans

public void printIndividualForHumans(EvolutionState state,
                            int log)

Description copied from class: Individual

Should print the individual out in a pleasing way for humans, with a verbosity of Output.V_NO_GENERAL.

Overrides:

printIndividualForHumans in class Individual

printIndividual

public void printIndividual(EvolutionState state,
                   int log)

Description copied from class: Individual

Should print the individual in a way that can be read by computer, including its fitness, with a verbosity of Output.V_NO_GENERAL.

Overrides:

printIndividual in class Individual

printIndividual

public void printIndividual(EvolutionState state,
                   PrintWriter writer)

Description copied from class: Individual

Should print the individual in a way that can be read by computer, including its fitness. You can get fitness to print itself at the appropriate time by calling fitness.printFitness(state,log,writer); Usually you should try to use printIndividual(state,log,verbosity) instead -- use this method only if you can't print through the Output facility for some reason.

The default form of this method simply prints out whether or not the individual has been evaluated, its fitness, and then calls Individual.genotypeToString(). Feel free to override this to produce more sophisticated behavior, though it is rare to need to -- instead you could just override genotypeToString().

Overrides:

printIndividual in class Individual

writeGenotype

public void writeGenotype(EvolutionState state,
                 DataOutput dataOutput)
                   throws IOException

Overridden for the GPIndividual genotype.

Overrides:

writeGenotype in class Individual

Throws:

IOException

readGenotype

public void readGenotype(EvolutionState state,
                DataInput dataInput)
                  throws IOException

Overridden for the GPIndividual genotype.

Overrides:

readGenotype in class Individual

Throws:

IOException

parseGenotype

public void parseGenotype(EvolutionState state,
                 LineNumberReader reader)
                   throws IOException

Description copied from class: Individual

This method is used only by the default version of readIndividual(state,reader), and it is intended to be overridden to parse in that part of the individual that was outputted in the genotypeToString() method. The default version of this method exits the program with an "unimplemented" error. You'll want to override this method, or to override readIndividual(...) to not use this method.

Overrides:

parseGenotype in class Individual

Throws:

IOException

clone

public Object clone()

Deep-clones the GPIndividual. Note that you should not deep-clone the prototypical GPIndividual stored in GPSpecies: they contain blank GPTrees with null roots, and this method, which calls GPTree.clone(), will produce a NullPointerException as a result. Instead, you probably want to use GPSpecies.newIndividual(...) if you're thinking of playing with the prototypical GPIndividual.

Specified by:

clone in interface Prototype

Overrides:

clone in class Individual

lightClone

public GPIndividual lightClone()

Like clone(), but doesn't force the GPTrees to deep-clone themselves.

size

public long size()

Returns the "size" of the individual, namely, the number of nodes in all of its subtrees.

Overrides:

size in class Individual