ec
Class Individual

java.lang.Object
  extended by ec.Individual
All Implemented Interfaces:
Prototype, Setup, java.io.Serializable, java.lang.Cloneable
Direct Known Subclasses:
GPIndividual, RuleIndividual, VectorIndividual

public abstract class Individual
extends java.lang.Object
implements Prototype

An Individual is an item in the EC population stew which is evaluated and assigned a fitness which determines its likelihood of selection. Individuals are created most commonly by the newIndividual(...) method of the ec.Species class.

In general Individuals are immutable. That is, once they are created their genetic material should not be modified. This protocol helps insure that they are safe to read under multithreaded conditions. You can violate this protocol, but try to do so when you know you have only have a single thread.

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

Since individuals should be largely immutable, why is there a readIndividual method? after all this method doesn't create a new individual -- it just erases the existing one. This is largely historical; but the method is used underneath by the various newIndividual methods in Species, which do create new individuals read from files. If you're trying to create a brand new individual read from a file, look in Species.

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

Field Summary
 boolean evaluated
          Has the individual been evaluated and its fitness determined yet?
static java.lang.String EVALUATED_PREAMBLE
          A string appropriate to put in front of whether or not the individual has been printed.
 Fitness fitness
          The fitness of the Individual.
static java.lang.String P_INDIVIDUAL
          A reasonable parameter base element for individuals
 Species species
          The species of the Individual.
 
Constructor Summary
Individual()
           
 
Method Summary
 java.lang.Object clone()
          Creates a new individual cloned from a prototype, and suitable to begin use in its own evolutionary context.
abstract  boolean equals(java.lang.Object ind)
          Returns true if I am genetically "equal" to ind.
 java.lang.String genotypeToString()
          Print to a string the genotype of the Individual in a fashion intended to be parsed in again via parseGenotype(...).
 java.lang.String genotypeToStringForHumans()
          Print to a string the genotype of the Individual in a fashion readable by humans, and not intended to be parsed in again.
abstract  int hashCode()
          Returns a hashcode for the individual, such that individuals which are equals(...) each other always return the same hash code.
protected  void parseGenotype(EvolutionState state, java.io.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, int verbosity)
          Should print the individual in a way that can be read by computer, including its fitness, using state.output.println(...,verbosity,log) You can get fitness to print itself at the appropriate time by calling fitness.printFitness(state,log,verbosity);
 void printIndividual(EvolutionState state, java.io.PrintWriter writer)
          Should print the individual in a way that can be read by computer, including its fitness.
 void printIndividualForHumans(EvolutionState state, int log, int verbosity)
          Should print the individual out in a pleasing way for humans, including its fitness, using state.output.println(...,verbosity,log) You can get fitness to print itself at the appropriate time by calling fitness.printFitnessForHumans(state,log,verbosity);
 void readGenotype(EvolutionState state, java.io.DataInput dataInput)
          Reads in the genotypic information from a DataInput, erasing the previous genotype of this Individual.
 void readIndividual(EvolutionState state, java.io.DataInput dataInput)
          Reads the binary form of an individual from a DataInput, erasing the previous information stored in this Individual.
 void readIndividual(EvolutionState state, java.io.LineNumberReader reader)
          Reads in the individual from a form printed by printIndividual(), erasing the previous information stored in this Individual.
 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.
 long size()
          Returns the "size" of the individual.
 java.lang.String toString()
          Overridden here because hashCode() is not expected to return the pointer to the object.
 void writeGenotype(EvolutionState state, java.io.DataOutput dataOutput)
          Writes the genotypic information to a DataOutput.
 void writeIndividual(EvolutionState state, java.io.DataOutput dataOutput)
          Writes the binary form of an individual out to a DataOutput.
 
Methods inherited from class java.lang.Object
finalize, getClass, notify, notifyAll, wait, wait, wait
 
Methods inherited from interface ec.Prototype
defaultBase
 

Field Detail

P_INDIVIDUAL

public static final java.lang.String P_INDIVIDUAL
A reasonable parameter base element for individuals

See Also:
Constant Field Values

EVALUATED_PREAMBLE

public static final java.lang.String EVALUATED_PREAMBLE
A string appropriate to put in front of whether or not the individual has been printed.

See Also:
Constant Field Values

fitness

public Fitness fitness
The fitness of the Individual.


species

public Species species
The species of the Individual.


evaluated

public boolean evaluated
Has the individual been evaluated and its fitness determined yet?

Constructor Detail

Individual

public Individual()
Method Detail

clone

public java.lang.Object clone()
Description copied from interface: Prototype
Creates a new individual cloned from a prototype, and suitable to begin use in its own evolutionary context.

Typically this should be a full "deep" clone. However, you may share certain elements with other objects rather than clone hem, depending on the situation:

  • If you hold objects which are shared with other instances, don't clone them.
  • If you hold objects which must be unique, clone them.
  • If you hold objects which were given to you as a gesture of kindness, and aren't owned by you, you probably shouldn't clone them.
  • DON'T attempt to clone: Singletons, Cliques, or Groups.
  • Arrays are not cloned automatically; you may need to clone an array if you're not sharing it with other instances. Arrays have the nice feature of being copyable by calling clone() on them.

Implementations.

  • If no ancestor of yours implements clone(), and you have no need to do clone deeply, and you are abstract, then you should not declare clone().
  • If no ancestor of yours implements clone(), and you have no need to do clone deeply, and you are not abstract, then you should implement it as follows:

     public Object clone() 
         {
         try
             { 
             return super.clone();
             }
         catch ((CloneNotSupportedException e)
             { throw new InternalError(); } // never happens
         }
            
  • If no ancestor of yours implements clone(), but you need to deep-clone some things, then you should implement it as follows:

     public Object clone() 
         {
         try
             { 
             MyObject myobj = (MyObject) (super.clone());
    
             // put your deep-cloning code here...
             }
         catch ((CloneNotSupportedException e)
             { throw new InternalError(); } // never happens
         return myobj;
         } 
            
  • If an ancestor has implemented clone(), and you also need to deep clone some things, then you should implement it as follows:

     public Object clone() 
         { 
         MyObject myobj = (MyObject) (super.clone());
    
         // put your deep-cloning code here...
    
         return myobj;
         } 
            

Specified by:
clone in interface Prototype
Overrides:
clone in class java.lang.Object

size

public long size()
Returns the "size" of the individual. This is used for things like parsimony pressure. The default form of this method returns 0 -- if you care about parsimony pressure, you'll need to override the default to provide a more descriptive measure of size.


equals

public abstract boolean equals(java.lang.Object ind)
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.

Overrides:
equals in class java.lang.Object

hashCode

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

Overrides:
hashCode in class java.lang.Object

toString

public java.lang.String toString()
Overridden here because hashCode() is not expected to return the pointer to the object. toString() normally uses hashCode() to print a unique identifier, and that's no longer the case. You're welcome to override this anyway you like to make the individual print out in a more lucid fashion.

Overrides:
toString in class java.lang.Object

genotypeToStringForHumans

public java.lang.String genotypeToStringForHumans()
Print to a string the genotype of the Individual in a fashion readable by humans, and not intended to be parsed in again. The fitness and evaluated flag should not be included. The default form simply calls toString(), but you'll probably want to override this to something else.


genotypeToString

public java.lang.String genotypeToString()
Print to a string the genotype of the Individual in a fashion intended to be parsed in again via parseGenotype(...). The fitness and evaluated flag should not be included. The default form simply calls toString(), which is almost certainly wrong, and you'll probably want to override this to something else.


setup

public void setup(EvolutionState state,
                  Parameter base)
Description copied from interface: Prototype
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.

For prototypes, setup(...) is typically called once for the prototype instance; cloned instances do not receive the setup(...) call. setup(...) may be called more than once; the only guarantee is that it will get called at least once on an instance or some "parent" object from which it was ultimately cloned.

Specified by:
setup in interface Prototype
Specified by:
setup in interface Setup

printIndividualForHumans

public void printIndividualForHumans(EvolutionState state,
                                     int log,
                                     int verbosity)
Should print the individual out in a pleasing way for humans, including its fitness, using state.output.println(...,verbosity,log) You can get fitness to print itself at the appropriate time by calling fitness.printFitnessForHumans(state,log,verbosity);

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


printIndividual

public void printIndividual(EvolutionState state,
                            int log,
                            int verbosity)
Should print the individual in a way that can be read by computer, including its fitness, using state.output.println(...,verbosity,log) You can get fitness to print itself at the appropriate time by calling fitness.printFitness(state,log,verbosity);

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().


printIndividual

public void printIndividual(EvolutionState state,
                            java.io.PrintWriter writer)
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().


readIndividual

public void readIndividual(EvolutionState state,
                           java.io.LineNumberReader reader)
                    throws java.io.IOException
Reads in the individual from a form printed by printIndividual(), erasing the previous information stored in this Individual. If you are trying to create an Individual from information read in from a stream or DataInput, see the various newIndividual() methods in Species. The default form of this method simply reads in evaluation information, then fitness information, and then calls parseGenotype() (which you should implement). The Species is not changed or attached, so you may need to do that elsewhere. Feel free to override this method to produce more sophisticated behavior, though it is rare to need to -- instead you could just override parseGenotype().

Throws:
java.io.IOException

parseGenotype

protected void parseGenotype(EvolutionState state,
                             java.io.LineNumberReader reader)
                      throws java.io.IOException
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.

Throws:
java.io.IOException

writeIndividual

public void writeIndividual(EvolutionState state,
                            java.io.DataOutput dataOutput)
                     throws java.io.IOException
Writes the binary form of an individual out to a DataOutput. This is not for serialization: the object should only write out the data relevant to the object sufficient to rebuild it from a DataInput. The Species will be reattached later, and you should not write it. The default version of this method writes the evaluated and fitness information, then calls writeGenotype() to write the genotype information. Feel free to override this method to produce more sophisticated behavior, though it is rare to need to -- instead you could just override writeGenotype().

Throws:
java.io.IOException

writeGenotype

public void writeGenotype(EvolutionState state,
                          java.io.DataOutput dataOutput)
                   throws java.io.IOException
Writes the genotypic information to a DataOutput. Largely called by writeIndividual(), and nothing else. The default simply throws an error. Various subclasses of Individual override this as appropriate. For example, if your custom individual's genotype consists of an array of integers, you might do this:

 dataOutput.writeInt(integers.length);
 for(int x=0;x

Throws:
java.io.IOException

readGenotype

public void readGenotype(EvolutionState state,
                         java.io.DataInput dataInput)
                  throws java.io.IOException
Reads in the genotypic information from a DataInput, erasing the previous genotype of this Individual. Largely called by readIndividual(), and nothing else. If you are trying to create an Individual from information read in from a stream or DataInput, see the various newIndividual() methods in Species. The default simply throws an error. Various subclasses of Individual override this as appropriate. For example, if your custom individual's genotype consists of an array of integers, you might do this:

 integers = new int[dataInput.readInt()];
 for(int x=0;x

Throws:
java.io.IOException

readIndividual

public void readIndividual(EvolutionState state,
                           java.io.DataInput dataInput)
                    throws java.io.IOException
Reads the binary form of an individual from a DataInput, erasing the previous information stored in this Individual. This is not for serialization: the object should only read in the data written out via printIndividual(state,dataInput). If you are trying to create an Individual from information read in from a stream or DataInput, see the various newIndividual() methods in Species. The default form of this method simply reads in evaluation information, then fitness information, and then calls readGenotype() (which you will need to override -- its default form simply throws an error). The Species is not changed or attached, so you may need to do that elsewhere. Feel free to override this method to produce more sophisticated behavior, though it is rare to need to -- instead you could just override readGenotype().

Throws:
java.io.IOException