/*
* Java Genetic Algorithm Library (@__identifier__@).
* Copyright (c) @__year__@ Franz Wilhelmstötter
*
* Licensed under the Apache License, Version 2.0 (the "License");
* you may not use this file except in compliance with the License.
* You may obtain a copy of the License at
*
* http://www.apache.org/licenses/LICENSE-2.0
*
* Unless required by applicable law or agreed to in writing, software
* distributed under the License is distributed on an "AS IS" BASIS,
* WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
* See the License for the specific language governing permissions and
* limitations under the License.
*
* Author:
* Franz Wilhelmstötter (franz.wilhelmstoetter@gmx.at)
*/
package org.jenetics;
import static java.lang.Math.min;
import static java.lang.String.format;
import static java.util.Objects.requireNonNull;
import static java.util.stream.Collectors.joining;
import java.io.IOException;
import java.io.ObjectInputStream;
import java.io.ObjectOutputStream;
import java.io.Serializable;
import java.math.BigInteger;
import java.util.BitSet;
import java.util.Iterator;
import java.util.ListIterator;
import java.util.stream.IntStream;
import javax.xml.bind.annotation.XmlAccessType;
import javax.xml.bind.annotation.XmlAccessorType;
import javax.xml.bind.annotation.XmlAttribute;
import javax.xml.bind.annotation.XmlRootElement;
import javax.xml.bind.annotation.XmlType;
import javax.xml.bind.annotation.XmlValue;
import javax.xml.bind.annotation.adapters.XmlAdapter;
import javax.xml.bind.annotation.adapters.XmlJavaTypeAdapter;
import org.jenetics.internal.util.Equality;
import org.jenetics.internal.util.Hash;
import org.jenetics.internal.util.bit;
import org.jenetics.util.ISeq;
/**
* Implementation of the <i>classical</i> BitChromosome.
*
* @author <a href="mailto:franz.wilhelmstoetter@gmx.at">Franz Wilhelmstötter</a>
* @since 1.0
* @version 3.4
*/
@XmlJavaTypeAdapter(BitChromosome.Model.Adapter.class)
public class BitChromosome extends Number
implements
Chromosome<BitGene>,
Comparable<BitChromosome>,
Serializable
{
private static final long serialVersionUID = 2L;
/**
* The ones probability of the randomly generated Chromosome.
*/
protected double _p;
/**
* The length of the chromosomes (number of bits).
*/
protected int _length;
/**
* The boolean array which holds the {@link BitGene}s.
*/
protected byte[] _genes;
// Wraps the genes byte array into a Seq<BitGene>.
private transient BitGeneISeq _seq;
// Private primary constructor.
private BitChromosome(final byte[] bits, final int length, final double p) {
_genes = bits;
_length = length;
_p = p;
_seq = BitGeneMSeq.of(_genes, length).toISeq();
}
/**
* Create a new bit chromosome from the given bit (byte) array.
*
* @param bits the bit values of the new chromosome gene.
* @param start the initial (bit) index of the range to be copied, inclusive
* @param end the final (bit) index of the range to be copied, exclusive.
* (This index may lie outside the array.)
* @throws java.lang.ArrayIndexOutOfBoundsException if {@code start < 0} or
* {@code start > bits.length*8}
* @throws java.lang.IllegalArgumentException if {@code start > end}
* @throws java.lang.NullPointerException if the {@code bits} array is
* {@code null}.
*/
public BitChromosome(final byte[] bits, final int start, final int end) {
this(
bit.copy(bits, start, end),
min(bits.length << 3, end) - start,
0.0
);
_p = (double)bit.count(_genes)/(double)_length;
}
/**
* Create a new {@code BitChromosome} from the given {@code byte} array.
* This is a shortcut for {@code new BitChromosome(bits, 0, bits.length*8)}.
*
* @param bits the {@code byte} array.
*/
public BitChromosome(final byte[] bits) {
this(bits, 0, bits.length << 3);
}
private BitChromosome(final byte[] bits, final int length) {
this(
bits,
length == -1 ? bits.length*8 : length,
(double)bit.count(bits)/
(double)(length == -1 ? bits.length*8 : length)
);
}
private static byte[] toByteArray(final CharSequence value) {
final byte[] bytes = bit.newArray(value.length());
for (int i = value.length(); --i >= 0;) {
final char c = value.charAt(i);
if (c == '1') {
bit.set(bytes, i);
} else if (c != '0') {
throw new IllegalArgumentException(format(
"Illegal character '%s' at position %d", c, i
));
}
}
return bytes;
}
private void rangeCheck(final int index) {
if (index < 0 || index >= _length) {
throw new IndexOutOfBoundsException(
"Index: " + index + ", Length: " + _length
);
}
}
/**
* Return the one probability of this chromosome.
*
* @return the one probability of this chromosome.
*/
double getOneProbability() {
return _p;
}
@Override
public BitGene getGene() {
assert _genes != null;
assert _genes.length > 0;
return BitGene.of(bit.get(_genes, 0));
}
/**
* Return the value of the first gene of this chromosome.
*
* @since 2.0
* @return the first value of this chromosome.
*/
public boolean get() {
return bit.get(_genes, 0);
}
@Override
public BitGene getGene(final int index) {
rangeCheck(index);
assert _genes != null;
return BitGene.of(bit.get(_genes, index));
}
/**
* Return the value on the specified index.
*
* @since 2.0
* @param index the gene index
* @return the wanted gene value
* @throws IndexOutOfBoundsException if the index is out of range
* (index < 1 || index >= length()).
*/
public boolean get(final int index) {
rangeCheck(index);
return bit.get(_genes, index);
}
@Override
public ISeq<BitGene> toSeq() {
return _seq;
}
@Override
public int length() {
return _length;
}
/**
* Returns the number of bits set to true in this {@code BitChromosome}.
*
* @return the number of bits set to true in this {@code BitChromosome}
*/
public int bitCount() {
return bit.count(_genes);
}
@Override
public Iterator<BitGene> iterator() {
return _seq.iterator();
}
public ListIterator<BitGene> listIterator() {
return _seq.listIterator();
}
/**
* Return the long value this BitChromosome represents.
*
* @return long value this BitChromosome represents.
*/
@Override
public int intValue() {
return (int)longValue();
}
/**
* Return the long value this BitChromosome represents.
*
* @return long value this BitChromosome represents.
*/
@Override
public long longValue() {
return toBigInteger().longValue();
}
/**
* Return the float value this BitChromosome represents.
*
* @return float value this BitChromosome represents.
*/
@Override
public float floatValue() {
return (float)longValue();
}
/**
* Return the double value this BitChromosome represents.
*
* @return double value this BitChromosome represents.
*/
@Override
public double doubleValue() {
return longValue();
}
@Override
public boolean isValid() {
return true;
}
/**
* Return the {@code BigInteger} value this {@code BitChromosome} represents.
*
* @return {@code BigInteger} value this {@code BitChromosome} represents.
*/
public BigInteger toBigInteger() {
return new BigInteger(_genes);
}
/**
* Returns the two's-complement binary representation of this
* large integer. The output array is in <i>big-endian</i>
* byte-order: the most significant byte is at the offset position.
*
* <p>Note: This representation is consistent with {@code java.lang.BigInteger
* } byte array representation and can be used for conversion
* between the two classes.</p>
*
* @param bytes the bytes to hold the binary representation
* (two's-complement) of this large integer.
* @return the number of bytes written.
* @throws IndexOutOfBoundsException
* if {@code bytes.length < (int)Math.ceil(length()/8.0)}
* @throws NullPointerException it the give array is {@code null}.
*/
public int toByteArray(final byte[] bytes) {
if (bytes.length < _genes.length) {
throw new IndexOutOfBoundsException();
}
System.arraycopy(_genes, 0, bytes, 0, _genes.length);
return _genes.length;
}
/**
* @return a byte array which represents this {@code BitChromosome}. The
* length of the array is {@code (int)Math.ceil(length()/8.0)}.
*
* @see #toByteArray(byte[])
*/
public byte[] toByteArray() {
final byte[] data = new byte[_genes.length];
toByteArray(data);
return data;
}
/**
* Return the corresponding BitSet of this BitChromosome.
*
* @return The corresponding BitSet of this BitChromosome.
*/
public BitSet toBitSet() {
final BitSet set = new BitSet(length());
for (int i = 0, n = length(); i < n; ++i) {
set.set(i, getGene(i).getBit());
}
return set;
}
/**
* Return the indexes of the <i>ones</i> of this bit-chromosome as stream.
*
* @since 3.0
*
* @return the indexes of the <i>ones</i> of this bit-chromosome
*/
public IntStream ones() {
return IntStream.range(0, length())
.filter(index -> bit.get(_genes, index));
}
/**
* Return the indexes of the <i>zeros</i> of this bit-chromosome as stream.
*
* @since 3.0
*
* @return the indexes of the <i>zeros</i> of this bit-chromosome
*/
public IntStream zeros() {
return IntStream.range(0, length())
.filter(index -> !bit.get(_genes, index));
}
@Override
public BitChromosome newInstance(final ISeq<BitGene> genes) {
requireNonNull(genes, "Genes");
if (genes.isEmpty()) {
throw new IllegalArgumentException(
"The genes sequence must contain at least one gene."
);
}
final BitChromosome chromosome = new BitChromosome(
bit.newArray(genes.length()), genes.length()
);
int ones = 0;
if (genes instanceof BitGeneISeq) {
final BitGeneISeq iseq = (BitGeneISeq)genes;
iseq.copyTo(chromosome._genes);
ones = bit.count(chromosome._genes);
} else {
for (int i = genes.length(); --i >= 0;) {
if (genes.get(i).booleanValue()) {
bit.set(chromosome._genes, i);
++ones;
}
}
}
chromosome._p = (double)ones/(double)genes.length();
return chromosome;
}
@Override
public BitChromosome newInstance() {
return of(_length, _p);
}
/**
* 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 {@link #of(CharSequence)} constructor.
*
* @return String representation (containing only '1' and '0') of the
* BitChromosome.
*/
public String toCanonicalString() {
return toSeq().stream()
.map(g -> g.booleanValue() ? "1" : "0")
.collect(joining());
}
@Override
public int compareTo(final BitChromosome that) {
return toBigInteger().compareTo(that.toBigInteger());
}
/**
* Invert the ones and zeros of this bit chromosome.
*
* @return a new BitChromosome with inverted ones and zeros.
*/
public BitChromosome invert() {
final byte[] data = _genes.clone();
bit.invert(data);
return new BitChromosome(data, _length, 1.0 - _p);
}
/**
* Construct a new BitChromosome with the given _length.
*
* @param length Length of the BitChromosome, number of bits.
* @param p Probability of the TRUEs in the BitChromosome.
* @return a new {@code BitChromosome} with the given parameter
* @throws NegativeArraySizeException if the {@code length} is smaller
* than one.
* @throws IllegalArgumentException if {@code p} is not a valid probability.
*/
public static BitChromosome of(final int length, final double p) {
return new BitChromosome(bit.newArray(length, p), length, p);
}
/**
* Constructing a new BitChromosome with the given _length. The TRUEs and
* FALSE in the {@code Chromosome} are equally distributed.
*
* @param length Length of the BitChromosome.
* @return a new {@code BitChromosome} with the given parameter
* @throws NegativeArraySizeException if the {@code _length} is smaller
* than one.
*/
public static BitChromosome of(final int length) {
return new BitChromosome(bit.newArray(length, 0.5), length, 0.5);
}
/**
* @param length length of the BitChromosome.
* @param bits the bit-set which initializes the chromosome
* @return a new {@code BitChromosome} with the given parameter
* @throws NegativeArraySizeException if the {@code length} is smaller
* than one.
* @throws NullPointerException if the {@code bitSet} is
* {@code null}.
*/
public static BitChromosome of(final BitSet bits, final int length) {
final byte[] bytes = bit.newArray(length);
for (int i = 0; i < length; ++i) {
if (bits.get(i)) {
bit.set(bytes, i);
}
}
final double p = (double)bit.count(bytes)/(double)length;
return new BitChromosome(bytes, length, p);
}
/**
* Constructing a new BitChromosome from a given BitSet.
* The BitSet is copied while construction. The length of the constructed
* BitChromosome will be {@code bitSet.length()} ({@link BitSet#length}).
*
* @param bits the bit-set which initializes the chromosome
* @return a new {@code BitChromosome} with the given parameter
* @throws NullPointerException if the {@code bitSet} is
* {@code null}.
*/
public static BitChromosome of(final BitSet bits) {
return new BitChromosome(bits.toByteArray(), -1);
}
/**
* Create a new {@code BitChromosome} from the given big integer value.
*
* @param value the value of the created {@code BitChromosome}
* @return a new {@code BitChromosome} with the given parameter
* @throws NullPointerException if the given {@code value} is {@code null}.
*/
public static BitChromosome of(final BigInteger value) {
return new BitChromosome(value.toByteArray(), -1);
}
/**
* Create a new {@code BitChromosome} from the given character sequence
* containing '0' and '1'; as created with the {@link #toCanonicalString()}
* method.
*
* @param value the input string.
* @return a new {@code BitChromosome} with the given parameter
* @throws NullPointerException if the {@code value} is {@code null}.
* @throws IllegalArgumentException if the length of the character sequence
* is zero or contains other characters than '0' or '1'.
*/
public static BitChromosome of(final CharSequence value) {
return new BitChromosome(toByteArray(requireNonNull(value, "Input")), -1);
}
@Override
public int hashCode() {
return Hash.of(getClass()).and(_genes).value();
}
@Override
public boolean equals(final Object obj) {
return Equality.of(this, obj).test(c -> {
boolean equals = length() == c.length();
for (int i = 0, n = length(); equals && i < n; ++i) {
equals = getGene(i) == c.getGene(i);
}
return equals;
});
}
@Override
public String toString() {
return bit.toByteString(_genes);
}
/* *************************************************************************
* Java object serialization
* ************************************************************************/
private void writeObject(final ObjectOutputStream out)
throws IOException
{
out.defaultWriteObject();
out.writeInt(_length);
out.writeDouble(_p);
out.writeInt(_genes.length);
out.write(_genes);
}
private void readObject(final ObjectInputStream in)
throws IOException, ClassNotFoundException
{
in.defaultReadObject();
_length = in.readInt();
_p = in.readDouble();
final int bytes = in.readInt();
_genes = new byte[bytes];
in.readFully(_genes);
_seq = BitGeneISeq.of(_genes, _length);
}
/* *************************************************************************
* JAXB object serialization
* ************************************************************************/
@XmlRootElement(name = "bit-chromosome")
@XmlType(name = "org.jenetics.BitChromosome")
@XmlAccessorType(XmlAccessType.FIELD)
final static class Model {
@XmlAttribute(name = "length", required = true)
public int length;
@XmlAttribute(name = "ones-probability", required = true)
public double probability;
@XmlValue
public String value;
public final static class Adapter
extends XmlAdapter<Model, BitChromosome>
{
@Override
public Model marshal(final BitChromosome chromosome) {
final Model model = new Model();
model.length = chromosome._length;
model.probability = chromosome._p;
model.value = chromosome.toCanonicalString();
return model;
}
@Override
public BitChromosome unmarshal(final Model model) {
return new BitChromosome(
toByteArray(model.value),
model.length,
model.probability
);
}
}
}
}