jenes.chromosome

Class PermutationChromosome

java.lang.Object

jenes.chromosome.PermutationChromosome

All Implemented Interfaces:

java.lang.Cloneable, Chromosome<PermutationChromosome>

public final class PermutationChromosome
extends java.lang.Object
implements Chromosome<PermutationChromosome>

This class provides a chromosome able to model permutations. An array of integer values is its genoma. Each value is in the range [0,length-1] where length is the chromosome length. The most importatnt property is that each value is never duplicated: each value is contained just once. All the chromosome operations preserve this chromosome property.

Since:

1.0

Version:

2.0

Nested Class Summary

Nested classes/interfaces inherited from interface jenes.chromosome.Chromosome

Chromosome.Util

Field Summary

Fields

Modifier and Type	Field and Description
protected int[]	permutation This data structure keeps the permutation order
protected int[]	position This data structure keeps the position of elements in the permuted order

Constructor Summary

Constructors

Constructor and Description
PermutationChromosome(int length) Creates a new PermutationChromosome with the specified length.
PermutationChromosome(PermutationChromosome chromosome) Creates a new PermutationChromosome using the specified one as model

Method Summary

Methods

Modifier and Type	Method and Description
PermutationChromosome	clone() Performs a chromosome deep-cloning.
void	cross(PermutationChromosome chromosome, int from) Exchanges the genes chromosome starting from a given position
void	cross(PermutationChromosome chromosome, int from, int to) Exchanges the genes chromosome within the range [from,to]
void	difference(PermutationChromosome chromosome, double[] diff) Computes the genetic difference between two chromosomes.
boolean	equals(PermutationChromosome chromosome) Compares the chromosome with another.
int	getElementAt(int index) Returns the element at the specified position
int	getPositionOf(int element) Provides the element position
void	leftShift(int from, int to) Makes a left-shift of the genes between two positions.
int	length() Returns the number of genes contained in the chromosome.
void	randomize() Fills the chromosome with random value.
void	randomize(int pos) Perform a random transformation of gene at the specified positions, by exchanging it with another element randomly chosen.
void	rightShift(int from, int to) Makes a right-shift of the genes between two positions.
void	setAs(PermutationChromosome chromosome) Makes the chromosome a copy of another chromosome.
void	setDefaultValueAt(int pos) Sets the default value at the specified position.
void	swap(int pos1, int pos2) Exchanges two genes at the specified positions
java.lang.Object[]	toArray() Returns an array containing all of the genes in chromosome.
int[]	toNaturalOrdering() Provides the gene offsets to reach the natural order, according to equation p = n + o, where p is the permutation vector, n the natural order (i.e. 0,1,2..) and o the offset vector.
java.lang.String	toString()

Methods inherited from class java.lang.Object

equals, finalize, getClass, hashCode, notify, notifyAll, wait, wait, wait

Field Detail

permutation

protected int[] permutation

This data structure keeps the permutation order

position

protected int[] position

This data structure keeps the position of elements in the permuted order

Constructor Detail

PermutationChromosome

public PermutationChromosome(PermutationChromosome chromosome)

Creates a new PermutationChromosome using the specified one as model

Parameters:

chromosome - the chromosome model

PermutationChromosome

public PermutationChromosome(int length)

Creates a new PermutationChromosome with the specified length.

Parameters:

length - the chromosome length

Method Detail

length

public final int length()

Description copied from interface: Chromosome

Returns the number of genes contained in the chromosome.

Specified by:

length in interface Chromosome<PermutationChromosome>

Returns:

the length of chromosome.

getElementAt

public final int getElementAt(int index)

Returns the element at the specified position

Parameters:

index - of the element to return

Returns:

the desired allele value

getPositionOf

public final int getPositionOf(int element)

Provides the element position

Parameters:

element - a chromosome element

Returns:

the position of the specified element

setDefaultValueAt

public final void setDefaultValueAt(int pos)

Sets the default value at the specified position. For the permutation chromosome it is the original value in that position, that is pos itself.

Specified by:

setDefaultValueAt in interface Chromosome<PermutationChromosome>

Parameters:

pos - the position where to set the default value

cross

public final void cross(PermutationChromosome chromosome,
         int from)

Description copied from interface: Chromosome

Exchanges the genes chromosome starting from a given position

Specified by:

cross in interface Chromosome<PermutationChromosome>

Parameters:

chromosome - the chromosome to cross with

from - the start position of the genes to exchange

cross

public final void cross(PermutationChromosome chromosome,
         int from,
         int to)

Description copied from interface: Chromosome

Exchanges the genes chromosome within the range [from,to]

Specified by:

cross in interface Chromosome<PermutationChromosome>

Parameters:

chromosome - the chromosome to cross with

from - the start position of the genes to exchange

to - the final position of the genes to exchange

leftShift

public final void leftShift(int from,
             int to)

Description copied from interface: Chromosome

Makes a left-shift of the genes between two positions. The shift is circular, so the most left-side gene becomes the last gene on right.

Specified by:

leftShift in interface Chromosome<PermutationChromosome>

Parameters:

from - the start position to be shifted

to - the final position to be shifted

rightShift

public final void rightShift(int from,
              int to)

Description copied from interface: Chromosome

Makes a right-shift of the genes between two positions. The shift is circular, so the most right-side gene becomes the first gene on left.

Specified by:

rightShift in interface Chromosome<PermutationChromosome>

Parameters:

from - the start position to be shifted

to - the final position to be shifted

randomize

public final void randomize(int pos)

Perform a random transformation of gene at the specified positions, by exchanging it with another element randomly chosen.

Specified by:

randomize in interface Chromosome<PermutationChromosome>

Parameters:

pos - the position to randomize

randomize

public final void randomize()

Description copied from interface: Chromosome

Fills the chromosome with random value.

Specified by:

randomize in interface Chromosome<PermutationChromosome>

setAs

public final void setAs(PermutationChromosome chromosome)

Description copied from interface: Chromosome

Makes the chromosome a copy of another chromosome.

Specified by:

setAs in interface Chromosome<PermutationChromosome>

Parameters:

chromosome - the chromosome to be copied

swap

public final void swap(int pos1,
        int pos2)

Description copied from interface: Chromosome

Exchanges two genes at the specified positions

Specified by:

swap in interface Chromosome<PermutationChromosome>

Parameters:

pos1 - the position of first gene

pos2 - the position of second gene

equals

public final boolean equals(PermutationChromosome chromosome)

Description copied from interface: Chromosome

Compares the chromosome with another.

Specified by:

equals in interface Chromosome<PermutationChromosome>

Parameters:

chromosome - the cromosome to compare to.

Returns:

true if the two chromosome are equal, false otherwise.

clone

public final PermutationChromosome clone()

Description copied from interface: Chromosome

Performs a chromosome deep-cloning.

Specified by:

clone in interface Chromosome<PermutationChromosome>

Overrides:

clone in class java.lang.Object

Returns:

a chromosome clone.

toString

public final java.lang.String toString()

Overrides:

toString in class java.lang.Object

toNaturalOrdering

public final int[] toNaturalOrdering()

Provides the gene offsets to reach the natural order, according to equation p = n + o, where p is the permutation vector, n the natural order (i.e. 0,1,2..) and o the offset vector. In other words, if we sum to permutation the offsets, we get the natural ordering, or if we subtract the offsets to the natural order we get the permutation.

Returns:

- gene offsets;

difference

public void difference(PermutationChromosome chromosome,
              double[] diff)

Description copied from interface: Chromosome

Computes the genetic difference between two chromosomes. NOTICE: This should not be invoked directly. Please, use #getDifference instead.

Specified by:

difference in interface Chromosome<PermutationChromosome>

Parameters:

chromosome - - the chromosome to quantify the minus from

diff - - the variable to be filled by the minus values

toArray

public java.lang.Object[] toArray()

Description copied from interface: Chromosome

Returns an array containing all of the genes in chromosome.

Specified by:

toArray in interface Chromosome<PermutationChromosome>

Returns:

an array containing all of the genes in chromosome.