orbital.algorithm.evolutionary
Class Genome

java.lang.Object
  orbital.util.DelegateCollection
      orbital.util.DelegateList
          orbital.algorithm.evolutionary.Gene.List
              orbital.algorithm.evolutionary.Genome

All Implemented Interfaces:

java.io.Serializable, java.lang.Iterable, java.util.Collection, java.util.List, Gene

public class Genome
extends Gene.List

The Genome data in a population represents a state. For bio informatics, genomes and chromosomes are treated as synonyms.

A Genome provides the following operators and functions:

• mutate that defines how its mutation is done, depending on a probability.
• recombine for recombining genetic information of the parents to generate genomes of the children (reproduction).
• an evaluation function.
• and a difference measure.

Genomes provide fitness caching and clearing.

Author:

André Platzer

See Also:

Serialized Form

Nested Class Summary

Nested classes/interfaces inherited from interface orbital.algorithm.evolutionary.Gene

Gene.BitSet, Gene.BoundedFloat, Gene.BoundedInteger, Gene.Fixed, Gene.Float, Gene.Integer, Gene.List, Gene.Number

Field Summary

static java.util.Comparator

comparator Compare two Genomes according to their fitness, descending.

Constructor Summary

Genome()

Genome(Gene content)
Construct a genome with a single gene.

Method Summary

void	add(int index, java.lang.Object o) Insert one gene.
boolean	add(java.lang.Object o) Add one gene.
void	clearFitness() Clears the fitness.
java.lang.Object	clone() Returns a deep copy of this exact type of gene.
boolean	equals(java.lang.Object o) Compares the specified object with this collection for equality.
void	evaluate(Population population, boolean redo) Evaluates the fitness of the Genomes, if necessary.
java.lang.Object	get() Use with care!! Will not clear fitness if the return-value is modified.
java.lang.Object	get(int i) Use with care! Will not clear fitness if the return-value is modified.
double	getFitness() Get the fitness calculated the least recently.
boolean	hasFitness() Whether genome has a fitness != Double.NaN.
int	hashCode() Returns the hash code value for this collection.
Gene	inverse() Get an inverted version of this Genome.
Gene	mutate(double probability) Get a mutated version of this Gene.
Gene[]	recombine(Gene[] parents, int childrenCount, double recombinationProbability) Genetically recombine gene data of parents to their children via reproduction..
java.lang.Object	set(int i, java.lang.Object g) Set one gene.
void	set(java.lang.Object list) Set the Genome data.
void	setFitness(double fitness) Set the fitness calculated.
void	setFitness(java.lang.Number fitness)

Methods inherited from class orbital.algorithm.evolutionary.Gene.List

distanceMeasure, elementwiseRecombine, toString, uniformRecombine

Methods inherited from class orbital.util.DelegateList

addAll, indexOf, lastIndexOf, listIterator, listIterator, remove, setDelegatee, setDelegatee, subList

Methods inherited from class orbital.util.DelegateCollection

addAll, clear, contains, containsAll, getDelegatee, isEmpty, iterator, remove, removeAll, retainAll, size, toArray, toArray

Methods inherited from class java.lang.Object

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

Methods inherited from interface java.util.List

addAll, clear, contains, containsAll, isEmpty, iterator, remove, removeAll, retainAll, size, toArray, toArray

Field Detail

comparator

public static final java.util.Comparator comparator

Compare two Genomes according to their fitness, descending.

Constructor Detail

Genome

public Genome()

Genome

public Genome(Gene content)

Construct a genome with a single gene.

Parameters:

content - the initial member gene.

See Also:

add(Object)

Method Detail

clone

public java.lang.Object clone()

Description copied from class: Gene.List

Returns a deep copy of this exact type of gene.

Specified by:

clone in interface Gene

Overrides:

clone in class Gene.List

equals

public boolean equals(java.lang.Object o)

Description copied from class: DelegateCollection

Compares the specified object with this collection for equality.

While the Collection interface adds no stipulations to the general contract for the Object.equals, programmers who implement the Collection interface "directly" (in other words, create a class that is a Collection but is not a Set or a List) must exercise care if they choose to override the Object.equals. It is not necessary to do so, and the simplest course of action is to rely on Object's implementation, but the implementer may wish to implement a "value comparison" in place of the default "reference comparison." (The List and Set interfaces mandate such value comparisons.)

The general contract for the Object.equals method states that equals must be symmetric (in other words, a.equals(b) if and only if b.equals(a)). The contracts for List.equals and Set.equals state that lists are only equal to other lists, and sets to other sets. Thus, a custom equals method for a collection class that implements neither the List nor Set interface must return false when this collection is compared to any list or set. (By the same logic, it is not possible to write a class that correctly implements both the Set and List interfaces.)

Specified by:

equals in interface java.util.Collection

Specified by:

equals in interface java.util.List

Specified by:

equals in interface Gene

Overrides:

equals in class Gene.List

Parameters:

o - Object to be compared for equality with this collection.

Returns:

true if the specified object is equal to this collection

See Also:

Object.equals(Object), Set.equals(Object), List.equals(Object)

hashCode

public int hashCode()

Description copied from class: DelegateCollection

Returns the hash code value for this collection. While the Collection interface adds no stipulations to the general contract for the Object.hashCode method, programmers should take note that any class that overrides the Object.equals method must also override the Object.hashCode method in order to satisfy the general contract for the Object.hashCodemethod. In particular, c1.equals(c2) implies that c1.hashCode()==c2.hashCode().

Specified by:

hashCode in interface java.util.Collection

Specified by:

hashCode in interface java.util.List

Specified by:

hashCode in interface Gene

Overrides:

hashCode in class Gene.List

Returns:

the hash code value for this collection

See Also:

Object.hashCode(), Object.equals(Object)

getFitness

public double getFitness()

Get the fitness calculated the least recently.

See Also:

evaluate(Population, boolean), setFitness(double)

hasFitness

public boolean hasFitness()

Whether genome has a fitness != Double.NaN.

Returns:

!Double.isNaN(getFitness()).

See Also:

getFitness()

setFitness

public void setFitness(double fitness)

Set the fitness calculated.

setFitness

public void setFitness(java.lang.Number fitness)

clearFitness

public void clearFitness()

Clears the fitness. Called to say that the fitness has changed and must be re-evaluated. Sets the fitness to Double.NaN.

See Also:

setFitness(double)

get

public java.lang.Object get(int i)

Use with care! Will not clear fitness if the return-value is modified. This constraint does apply to all parts of the gene returned, as well, if they are modified, the fitness must be cleared and re-evaluated.

Specified by:

get in interface java.util.List

Overrides:

get in class DelegateList

set

public java.lang.Object set(int i,
                            java.lang.Object g)

Set one gene. Will clear fitness.

Specified by:

set in interface java.util.List

Overrides:

set in class DelegateList

add

public boolean add(java.lang.Object o)

Add one gene. Will clear fitness.

Specified by:

add in interface java.util.Collection

Specified by:

add in interface java.util.List

Overrides:

add in class DelegateCollection

Parameters:

o - element whose presence in this collection is to be ensured.

Returns:

true if this collection changed as a result of the call

add

public void add(int index,
                java.lang.Object o)

Insert one gene. Will clear fitness.

Specified by:

add in interface java.util.List

Overrides:

add in class DelegateList

get

public java.lang.Object get()

Use with care!! Will not clear fitness if the return-value is modified.

Specified by:

get in interface Gene

Overrides:

get in class Gene.List

Returns:

the Object represented by this gene. Interprets gene by decoding its data.

See Also:

get(int)

set

public void set(java.lang.Object list)

Set the Genome data. Will clear fitness.

Specified by:

set in interface Gene

Overrides:

set in class Gene.List

Parameters:

list - the Object this gene should represent. Encodes the value such that this gene represents the given object.

mutate

public Gene mutate(double probability)

Description copied from class: Gene.List

Get a mutated version of this Gene.

Implemented as Element-wise mutation.

Specified by:

mutate in interface Gene

Overrides:

mutate in class Gene.List

Parameters:

probability - the probability rating of mutation level. f.ex. probability with that each bit of the Gene mutates.

Returns:

a new gene that is a mutation of this one.

recombine

public Gene[] recombine(Gene[] parents,
                        int childrenCount,
                        double recombinationProbability)

Description copied from class: Gene.List

Genetically recombine gene data of parents to their children via reproduction.

 a       a  = direct ancestors to be used
 n * --- ;    n  = number of children to be produced
 p       p  = probability for each part of parent's Gene to be inherited
 a/p = elongation of Gene length
 n/a = growth of population size
 if n/a < 1 the population is contracting.
 if n/a = 1 the population size is fixed.
 if n/a > 1 the population is growing.
 

Usually it is p=n/a..

Specified by:

recombine in interface Gene

Overrides:

recombine in class Gene.List

Parameters:

parents - the Genes to be used as parents for the children. a is the number of parents (direct ancestors). parents are readonly.

childrenCount - the number of Gene children to produce and return. n is the number of children to be produced.

recombinationProbability - the probability with that parts of the inherited gene data is recombined. This does not necessarily imply an exchange of data, Genes might as well realign or repair at random. But it makes a data recombination possible.

Returns:

the new childrenCount children produced.

See Also:

Gene.List.elementwiseRecombine(Gene[],int,double)

inverse

public Gene inverse()

Get an inverted version of this Genome.

Specified by:

inverse in interface Gene

Overrides:

inverse in class Gene.List

Returns:

inverted Genome where all data booleans are negated.

evaluate

public void evaluate(Population population,
                     boolean redo)

Evaluates the fitness of the Genomes, if necessary.

Default implementation will consider GeneticAlgorithm.getEvaluation().

Parameters:

redo - force whole evaluation again, even for cached fitness values. Should usually be false for efficiency reasons.

population - the population containing this genome. (Redundant information but required for better performance).

See Also:

getFitness()