Package io.jenetics

Class BitChromosome

java.lang.Object

java.lang.Number

io.jenetics.BitChromosome

All Implemented Interfaces:

Chromosome<BitGene>, BaseSeq<BitGene>, Factory<Chromosome<BitGene>>, Verifiable, Serializable, Comparable<BitChromosome>, Iterable<BitGene>, RandomAccess

public class BitChromosome
extends Number
implements Chromosome<BitGene>, Comparable<BitChromosome>, Serializable

Implementation of the classical BitChromosome.

Since:

1.0

Version:

6.1

See Also:

BitGene, Serialized Form

Implementation Requirements:

This class is immutable and thread-safe.

Field Summary

Fields

Modifier and Type	Field	Description
protected byte[]	_genes	The boolean array which holds the BitGenes.
protected int	_length	The length of the chromosomes (number of bits).
protected double	_p	The ones probability of the randomly generated Chromosome.

Constructor Summary

Constructors

Constructor	Description
BitChromosome(byte[] bits)	Create a new BitChromosome from the given byte array.
BitChromosome(byte[] bits, int start, int end)	Create a new bit chromosome from the given bit (byte) array.

Method Summary

Modifier and Type	Method	Description
int	bitCount()	Returns the number of bits set to true in this BitChromosome.
boolean	booleanValue()	Return the value of the first gene of this chromosome.
boolean	booleanValue(int index)	Return the value on the specified index.
int	compareTo(BitChromosome that)
double	doubleValue()	Return the double value this BitChromosome represents.
boolean	equals(Object obj)
float	floatValue()	Return the float value this BitChromosome represents.
BitGene	gene()	Return the first gene of this chromosome.
BitGene	get(int index)	Return the value at the given index.
int	hashCode()
int	intValue()	Return the long value this BitChromosome represents.
BitChromosome	invert()	Invert the ones and zeros of this bit chromosome.
boolean	isValid()	Return always true.
int	length()	Return the length of this sequence.
ListIterator<BitGene>	listIterator()	Return a list iterator over the bit-genes of this chromosome.
long	longValue()	Return the long value this BitChromosome represents.
BitChromosome	map(Function<? super BitSet,? extends BitSet> f)	Maps the gene alleles of this chromosome, given as BitSet, by applying the given mapper function f.
BitChromosome	newInstance()	Create a new instance of type T.
BitChromosome	newInstance(ISeq<BitGene> genes)	A factory method which creates a new Chromosome of specific type and the given genes.
static BitChromosome	of(int length)	Constructing a new BitChromosome with the given _length.
static BitChromosome	of(int length, double p)	Construct a new BitChromosome with the given _length.
static BitChromosome	of(CharSequence value)	Create a new BitChromosome from the given character sequence containing '0' and '1'; as created with the toCanonicalString() method.
static BitChromosome	of(CharSequence value, double p)	Create a new BitChromosome from the given character sequence containing '0' and '1'; as created with the toCanonicalString() method.
static BitChromosome	of(CharSequence value, int length, double p)	Create a new BitChromosome from the given character sequence containing '0' and '1'; as created with the toCanonicalString() method.
static BitChromosome	of(BigInteger value)	Create a new BitChromosome from the given big integer value.
static BitChromosome	of(BigInteger value, double p)	Create a new BitChromosome from the given big integer value and ones probability.
static BitChromosome	of(BitSet bits)	Deprecated, for removal: This API element is subject to removal in a future version. This method doesn't let you control the actual length of the created BitChromosome.
static BitChromosome	of(BitSet bits, int length)	Create a new BitChromosome with the given parameters.
static BitChromosome	of(BitSet bits, int length, double p)	Create a new BitChromosome with the given parameters.
double	oneProbability()	Return the one probability of this chromosome.
IntStream	ones()	Return the indexes of the ones of this bit-chromosome as stream.
BigInteger	toBigInteger()	Return the BigInteger value this BitChromosome represents.
BitSet	toBitSet()	Return the corresponding BitSet of this BitChromosome.
byte[]	toByteArray()
int	toByteArray(byte[] bytes)	Returns the two's-complement binary representation of this large integer.
String	toCanonicalString()	Return the BitChromosome as String.
String	toString()
IntStream	zeros()	Return the indexes of the zeros of this bit-chromosome as stream.

Methods inherited from class java.lang.Number

byteValue, shortValue

Methods inherited from class java.lang.Object

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

Methods inherited from interface io.jenetics.util.BaseSeq

isEmpty, iterator, nonEmpty, spliterator, stream

Methods inherited from interface io.jenetics.Chromosome

as

Methods inherited from interface io.jenetics.util.Factory

instances

Methods inherited from interface java.lang.Iterable

forEach

Field Detail

_p

protected double _p

The ones probability of the randomly generated Chromosome.

_length

protected final int _length

The length of the chromosomes (number of bits).

_genes

protected final byte[] _genes

The boolean array which holds the BitGenes.

Constructor Detail

BitChromosome

public BitChromosome(byte[] bits,
                     int start,
                     int end)

Create a new bit chromosome from the given bit (byte) array.

Parameters:

bits - the bit values of the new chromosome gene.

start - the initial (bit) index of the range to be copied, inclusive

end - the final (bit) index of the range to be copied, exclusive. (This index may lie outside the array.)

Throws:

ArrayIndexOutOfBoundsException - if start < 0 or start > bits.length*8

IllegalArgumentException - if start > end

NullPointerException - if the bits array is null.

BitChromosome

public BitChromosome(byte[] bits)

Create a new BitChromosome from the given byte array. This is a shortcut for new BitChromosome(bits, 0, bits.length*8).

Parameters:

bits - the byte array.

Method Detail

oneProbability

public double oneProbability()

Return the one probability of this chromosome.

Returns:

the one probability of this chromosome.

Since:

5.2

gene

public BitGene gene()

Description copied from interface: Chromosome

Return the first gene of this chromosome. Each chromosome must contain at least one gene.

Specified by:

gene in interface Chromosome<BitGene>

Returns:

the first gene of this chromosome.

booleanValue

public boolean booleanValue()

Return the value of the first gene of this chromosome.

Returns:

the first value of this chromosome.

Since:

4.2

get

public BitGene get(int index)

Description copied from interface: BaseSeq

Return the value at the given index.

Specified by:

get in interface BaseSeq<BitGene>

Parameters:

index - index of the element to return.

Returns:

the value at the given index.

length

public int length()

Description copied from interface: BaseSeq

Return the length of this sequence. Once the sequence is created, the length can't be changed.

Specified by:

length in interface BaseSeq<BitGene>

Returns:

the length of this sequence.

booleanValue

public boolean booleanValue(int index)

Return the value on the specified index.

Parameters:

index - the gene index

Returns:

the wanted gene value

Throws:

IndexOutOfBoundsException - if the index is out of range (index < 1 || index >= length()).

Since:

4.2

bitCount

public int bitCount()

Returns the number of bits set to true in this BitChromosome.

Returns:

the number of bits set to true in this BitChromosome

listIterator

public ListIterator<BitGene> listIterator()

Return a list iterator over the bit-genes of this chromosome.

Specified by:

listIterator in interface BaseSeq<BitGene>

Returns:

a list iterator over the bit-genes of this chromosome

intValue

public int intValue()

Return the long value this BitChromosome represents.

Specified by:

intValue in class Number

Returns:

long value this BitChromosome represents.

longValue

public long longValue()

Return the long value this BitChromosome represents.

Specified by:

longValue in class Number

Returns:

long value this BitChromosome represents.

floatValue

public float floatValue()

Return the float value this BitChromosome represents.

Specified by:

floatValue in class Number

Returns:

float value this BitChromosome represents.

doubleValue

public double doubleValue()

Return the double value this BitChromosome represents.

Specified by:

doubleValue in class Number

Returns:

double value this BitChromosome represents.

isValid

public boolean isValid()

Return always true.

Specified by:

isValid in interface Chromosome<BitGene>

Specified by:

isValid in interface Verifiable

Returns:

true, always

toBigInteger

public BigInteger toBigInteger()

Return the BigInteger value this BitChromosome represents.

Returns:

BigInteger value this BitChromosome represents.

toByteArray

public int toByteArray(byte[] bytes)

Returns the two's-complement binary representation of this large integer. The output array is in big-endian byte-order: the most significant byte is at the offset position.

Note: This representation is consistent with java.lang.BigInteger byte array representation and can be used for conversion between the two classes.

Parameters:

bytes - the bytes to hold the binary representation (two's-complement) of this large integer.

Returns:

the number of bytes written.

Throws:

IndexOutOfBoundsException - if bytes.length < (int)Math.ceil(length()/8.0)

NullPointerException - it the give array is null.

toByteArray

public byte[] toByteArray()

Returns:

a byte array which represents this BitChromosome. The length of the array is (int)Math.ceil(length()/8.0).

See Also:

toByteArray(byte[])

toBitSet

public BitSet toBitSet()

Return the corresponding BitSet of this BitChromosome.

Returns:

The corresponding BitSet of this BitChromosome.

ones

public IntStream ones()

Return the indexes of the ones of this bit-chromosome as stream.

Returns:

the indexes of the ones of this bit-chromosome

Since:

3.0

zeros

public IntStream zeros()

Return the indexes of the zeros of this bit-chromosome as stream.

Returns:

the indexes of the zeros of this bit-chromosome

Since:

3.0

newInstance

public BitChromosome newInstance(ISeq<BitGene> genes)

Description copied from interface: Chromosome

A factory method which creates a new Chromosome of specific type and the given genes.

Specified by:

newInstance in interface Chromosome<BitGene>

Parameters:

genes - the genes of the new chromosome. The given genes array is not copied.

Returns:

A new Chromosome of the same type with the given genes.

newInstance

public BitChromosome newInstance()

Description copied from interface: Factory

Create a new instance of type T.

Specified by:

newInstance in interface Factory<Chromosome<BitGene>>

Returns:

a new instance of type T

map

public BitChromosome map(Function<? super BitSet,? extends BitSet> f)

Maps the gene alleles of this chromosome, given as BitSet, by applying the given mapper function f. The mapped gene values are then wrapped into a newly created chromosome.

Parameters:

f - the mapper function

Returns:

a newly created chromosome with the mapped gene values

Throws:

NullPointerException - if the mapper function is null.

Since:

6.1

toCanonicalString

public String toCanonicalString()

Return the BitChromosome as String. A TRUE is represented by a 1 and a FALSE by a 0. The returned string can be used to create a new chromosome with the of(CharSequence) constructor.

Returns:

String representation (containing only '1' and '0') of the BitChromosome.

compareTo

public int compareTo(BitChromosome that)

Specified by:

compareTo in interface Comparable<BitChromosome>

invert

public BitChromosome invert()

Invert the ones and zeros of this bit chromosome.

Returns:

a new BitChromosome with inverted ones and zeros.

of

public static BitChromosome of(int length,
                               double p)

Construct a new BitChromosome with the given _length.

Parameters:

length - Length of the BitChromosome, number of bits.

p - Probability of the TRUEs in the BitChromosome.

Returns:

a new BitChromosome with the given parameter

Throws:

NegativeArraySizeException - if the length is smaller than one.

IllegalArgumentException - if p is not a valid probability.

of

public static BitChromosome of(int length)

Constructing a new BitChromosome with the given _length. The TRUEs and FALSE in the Chromosome are equally distributed.

Parameters:

length - Length of the BitChromosome.

Returns:

a new BitChromosome with the given parameter

Throws:

NegativeArraySizeException - if the _length is smaller than one.

of

public static BitChromosome of(BitSet bits,
                               int length)

Create a new BitChromosome with the given parameters.

Parameters:

length - length of the BitChromosome.

bits - the bit-set which initializes the chromosome

Returns:

a new BitChromosome with the given parameter

Throws:

NegativeArraySizeException - if the length is smaller than one.

NullPointerException - if the bitSet is null.

of

public static BitChromosome of(BitSet bits,
                               int length,
                               double p)

Create a new BitChromosome with the given parameters.

Parameters:

length - length of the BitChromosome.

bits - the bit-set which initializes the chromosome

p - Probability of the TRUEs in the BitChromosome.

Returns:

a new BitChromosome with the given parameter

Throws:

NegativeArraySizeException - if the length is smaller than one.

NullPointerException - if the bitSet is null.

IllegalArgumentException - if p is not a valid probability.

of

@Deprecated(since="6.1",
            forRemoval=true)
public static BitChromosome of(BitSet bits)

Deprecated, for removal: This API element is subject to removal in a future version.

This method doesn't let you control the actual length of the created BitChromosome. Use of(BitSet, int, double) or of(BitSet, int) instead.

Constructing a new BitChromosome from a given BitSet. The BitSet is copied while construction. The length of the constructed BitChromosome will be bitSet.length() (BitSet.length()).

Parameters:

bits - the bit-set which initializes the chromosome

Returns:

a new BitChromosome with the given parameter

Throws:

NullPointerException - if the bitSet is null.

of

public static BitChromosome of(BigInteger value)

Create a new BitChromosome from the given big integer value.

Parameters:

value - the value of the created BitChromosome

Returns:

a new BitChromosome with the given parameter

Throws:

NullPointerException - if the given value is null.

of

public static BitChromosome of(BigInteger value,
                               double p)

Create a new BitChromosome from the given big integer value and ones probability.

Parameters:

value - the value of the created BitChromosome

p - Probability of the TRUEs in the BitChromosome.

Returns:

a new BitChromosome with the given parameter

Throws:

NullPointerException - if the given value is null.

IllegalArgumentException - if p is not a valid probability.

of

public static BitChromosome of(CharSequence value)

Create a new BitChromosome from the given character sequence containing '0' and '1'; as created with the toCanonicalString() method.

Parameters:

value - the input string.

Returns:

a new BitChromosome with the given parameter

Throws:

NullPointerException - if the value is null.

IllegalArgumentException - if the length of the character sequence is zero or contains other characters than '0' or '1'.

of

public static BitChromosome of(CharSequence value,
                               double p)

Create a new BitChromosome from the given character sequence containing '0' and '1'; as created with the toCanonicalString() method.

Parameters:

value - the input string.

p - Probability of the TRUEs in the BitChromosome.

Returns:

a new BitChromosome with the given parameter

Throws:

NullPointerException - if the value is null.

IllegalArgumentException - if the length of the character sequence is zero or contains other characters than '0' or '1'.

IllegalArgumentException - if p is not a valid probability.

of

public static BitChromosome of(CharSequence value,
                               int length,
                               double p)

Create a new BitChromosome from the given character sequence containing '0' and '1'; as created with the toCanonicalString() method.

Parameters:

value - the input string.

length - length of the BitChromosome

p - Probability of the TRUEs in the BitChromosome.

Returns:

a new BitChromosome with the given parameter

Throws:

NullPointerException - if the value is null.

IllegalArgumentException - if the length of the character sequence is zero or contains other characters than '0' or '1'.

IllegalArgumentException - if p is not a valid probability.

hashCode

public int hashCode()

Overrides:

hashCode in class Object

equals

public boolean equals(Object obj)

Overrides:

equals in class Object

toString

public String toString()

Overrides:

toString in class Object