001 /*
002 * Java Genetic Algorithm Library (jenetics-4.2.0).
003 * Copyright (c) 2007-2018 Franz Wilhelmstötter
004 *
005 * Licensed under the Apache License, Version 2.0 (the "License");
006 * you may not use this file except in compliance with the License.
007 * You may obtain a copy of the License at
008 *
009 * http://www.apache.org/licenses/LICENSE-2.0
010 *
011 * Unless required by applicable law or agreed to in writing, software
012 * distributed under the License is distributed on an "AS IS" BASIS,
013 * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
014 * See the License for the specific language governing permissions and
015 * limitations under the License.
016 *
017 * Author:
018 * Franz Wilhelmstötter (franz.wilhelmstoetter@gmail.com)
019 */
020 package io.jenetics;
021
022 import static java.lang.Math.min;
023 import static java.lang.String.format;
024 import static java.util.Objects.requireNonNull;
025 import static java.util.stream.Collectors.joining;
026
027 import java.io.IOException;
028 import java.io.ObjectInputStream;
029 import java.io.ObjectOutputStream;
030 import java.io.Serializable;
031 import java.math.BigInteger;
032 import java.util.BitSet;
033 import java.util.Iterator;
034 import java.util.ListIterator;
035 import java.util.stream.IntStream;
036
037 import io.jenetics.internal.util.Equality;
038 import io.jenetics.internal.util.Hash;
039 import io.jenetics.internal.util.bit;
040 import io.jenetics.internal.util.require;
041 import io.jenetics.util.ISeq;
042
043 /**
044 * Implementation of the <i>classical</i> BitChromosome.
045 *
046 * @see BitGene
047 *
048 * @implSpec
049 * This class is immutable and thread-safe.
050 *
051 * @author <a href="mailto:franz.wilhelmstoetter@gmail.com">Franz Wilhelmstötter</a>
052 * @since 1.0
053 * @version 4.0
054 */
055 public class BitChromosome extends Number
056 implements
057 Chromosome<BitGene>,
058 Comparable<BitChromosome>,
059 Serializable
060 {
061 private static final long serialVersionUID = 2L;
062
063
064 /**
065 * The ones probability of the randomly generated Chromosome.
066 */
067 protected double _p;
068
069 /**
070 * The length of the chromosomes (number of bits).
071 */
072 protected int _length;
073
074 /**
075 * The boolean array which holds the {@link BitGene}s.
076 */
077 protected byte[] _genes;
078
079 // Wraps the genes byte array into a Seq<BitGene>.
080 private transient BitGeneISeq _seq;
081
082 // Private primary constructor.
083 private BitChromosome(final byte[] bits, final int length, final double p) {
084 _genes = bits;
085 _length = length;
086 _p = p;
087 _seq = BitGeneMSeq.of(_genes, length).toISeq();
088 }
089
090 /**
091 * Create a new bit chromosome from the given bit (byte) array.
092 *
093 * @param bits the bit values of the new chromosome gene.
094 * @param start the initial (bit) index of the range to be copied, inclusive
095 * @param end the final (bit) index of the range to be copied, exclusive.
096 * (This index may lie outside the array.)
097 * @throws java.lang.ArrayIndexOutOfBoundsException if {@code start < 0} or
098 * {@code start > bits.length*8}
099 * @throws java.lang.IllegalArgumentException if {@code start > end}
100 * @throws java.lang.NullPointerException if the {@code bits} array is
101 * {@code null}.
102 */
103 public BitChromosome(final byte[] bits, final int start, final int end) {
104 this(
105 bit.copy(bits, start, end),
106 min(bits.length << 3, end) - start,
107 0.0
108 );
109 _p = (double)bit.count(_genes)/(double)_length;
110 }
111
112 /**
113 * Create a new {@code BitChromosome} from the given {@code byte} array.
114 * This is a shortcut for {@code new BitChromosome(bits, 0, bits.length*8)}.
115 *
116 * @param bits the {@code byte} array.
117 */
118 public BitChromosome(final byte[] bits) {
119 this(bits, 0, bits.length << 3);
120 }
121
122 private BitChromosome(final byte[] bits, final int length) {
123 this(
124 bits,
125 length == -1 ? bits.length*8 : length,
126 (double)bit.count(bits)/
127 (double)(length == -1 ? bits.length*8 : length)
128 );
129 }
130
131 private static byte[] toByteArray(final CharSequence value) {
132 final byte[] bytes = bit.newArray(value.length());
133 for (int i = value.length(); --i >= 0;) {
134 final char c = value.charAt(i);
135 if (c == '1') {
136 bit.set(bytes, i);
137 } else if (c != '0') {
138 throw new IllegalArgumentException(format(
139 "Illegal character '%s' at position %d", c, i
140 ));
141 }
142 }
143
144 return bytes;
145 }
146
147 private void rangeCheck(final int index) {
148 if (index < 0 || index >= _length) {
149 throw new IndexOutOfBoundsException(
150 "Index: " + index + ", Length: " + _length
151 );
152 }
153 }
154
155 /**
156 * Return the one probability of this chromosome.
157 *
158 * @since 3.9
159 *
160 * @return the one probability of this chromosome.
161 */
162 public double getOneProbability() {
163 return _p;
164 }
165
166 @Override
167 public BitGene getGene() {
168 assert _genes != null;
169 assert _genes.length > 0;
170 return BitGene.of(bit.get(_genes, 0));
171 }
172
173 /**
174 * Return the value of the first gene of this chromosome.
175 *
176 * @since 2.0
177 * @return the first value of this chromosome.
178 * @deprecated Use {@link #booleanValue()} instead
179 */
180 @Deprecated
181 public boolean get() {
182 return bit.get(_genes, 0);
183 }
184
185 /**
186 * Return the value of the first gene of this chromosome.
187 *
188 * @since 4.2
189 *
190 * @return the first value of this chromosome.
191 */
192 public boolean booleanValue() {
193 return bit.get(_genes, 0);
194 }
195
196 @Override
197 public BitGene getGene(final int index) {
198 rangeCheck(index);
199 assert _genes != null;
200 return BitGene.of(bit.get(_genes, index));
201 }
202
203 /**
204 * Return the value on the specified index.
205 *
206 * @since 2.0
207 * @param index the gene index
208 * @return the wanted gene value
209 * @throws IndexOutOfBoundsException if the index is out of range
210 * (index < 1 || index >= length()).
211 * @deprecated Use {@link #booleanValue(int)} instead
212 */
213 @Deprecated
214 public boolean get(final int index) {
215 rangeCheck(index);
216 return bit.get(_genes, index);
217 }
218
219 /**
220 * Return the value on the specified index.
221 *
222 * @since 4.2
223 *
224 * @param index the gene index
225 * @return the wanted gene value
226 * @throws IndexOutOfBoundsException if the index is out of range
227 * (index < 1 || index >= length()).
228 */
229 public boolean booleanValue(final int index) {
230 rangeCheck(index);
231 return bit.get(_genes, index);
232 }
233
234 @Override
235 public ISeq<BitGene> toSeq() {
236 return _seq;
237 }
238
239 @Override
240 public int length() {
241 return _length;
242 }
243
244 /**
245 * Returns the number of bits set to true in this {@code BitChromosome}.
246 *
247 * @return the number of bits set to true in this {@code BitChromosome}
248 */
249 public int bitCount() {
250 return bit.count(_genes);
251 }
252
253 @Override
254 public Iterator<BitGene> iterator() {
255 return _seq.iterator();
256 }
257
258 public ListIterator<BitGene> listIterator() {
259 return _seq.listIterator();
260 }
261
262 /**
263 * Return the long value this BitChromosome represents.
264 *
265 * @return long value this BitChromosome represents.
266 */
267 @Override
268 public int intValue() {
269 return (int)longValue();
270 }
271
272 /**
273 * Return the long value this BitChromosome represents.
274 *
275 * @return long value this BitChromosome represents.
276 */
277 @Override
278 public long longValue() {
279 return toBigInteger().longValue();
280 }
281
282 /**
283 * Return the float value this BitChromosome represents.
284 *
285 * @return float value this BitChromosome represents.
286 */
287 @Override
288 public float floatValue() {
289 return (float)longValue();
290 }
291
292 /**
293 * Return the double value this BitChromosome represents.
294 *
295 * @return double value this BitChromosome represents.
296 */
297 @Override
298 public double doubleValue() {
299 return longValue();
300 }
301
302 @Override
303 public boolean isValid() {
304 return true;
305 }
306
307 /**
308 * Return the {@code BigInteger} value this {@code BitChromosome} represents.
309 *
310 * @return {@code BigInteger} value this {@code BitChromosome} represents.
311 */
312 public BigInteger toBigInteger() {
313 return new BigInteger(_genes);
314 }
315
316 /**
317 * Returns the two's-complement binary representation of this
318 * large integer. The output array is in <i>big-endian</i>
319 * byte-order: the most significant byte is at the offset position.
320 *
321 * <p>Note: This representation is consistent with {@code java.lang.BigInteger
322 * } byte array representation and can be used for conversion
323 * between the two classes.</p>
324 *
325 * @param bytes the bytes to hold the binary representation
326 * (two's-complement) of this large integer.
327 * @return the number of bytes written.
328 * @throws IndexOutOfBoundsException
329 * if {@code bytes.length < (int)Math.ceil(length()/8.0)}
330 * @throws NullPointerException it the give array is {@code null}.
331 */
332 public int toByteArray(final byte[] bytes) {
333 if (bytes.length < _genes.length) {
334 throw new IndexOutOfBoundsException();
335 }
336
337 System.arraycopy(_genes, 0, bytes, 0, _genes.length);
338 return _genes.length;
339 }
340
341 /**
342 * @return a byte array which represents this {@code BitChromosome}. The
343 * length of the array is {@code (int)Math.ceil(length()/8.0)}.
344 *
345 * @see #toByteArray(byte[])
346 */
347 public byte[] toByteArray() {
348 final byte[] data = new byte[_genes.length];
349 toByteArray(data);
350 return data;
351 }
352
353 /**
354 * Return the corresponding BitSet of this BitChromosome.
355 *
356 * @return The corresponding BitSet of this BitChromosome.
357 */
358 public BitSet toBitSet() {
359 final BitSet set = new BitSet(length());
360 for (int i = 0, n = length(); i < n; ++i) {
361 set.set(i, getGene(i).getBit());
362 }
363 return set;
364 }
365
366 /**
367 * Return the indexes of the <i>ones</i> of this bit-chromosome as stream.
368 *
369 * @since 3.0
370 *
371 * @return the indexes of the <i>ones</i> of this bit-chromosome
372 */
373 public IntStream ones() {
374 return IntStream.range(0, length())
375 .filter(index -> bit.get(_genes, index));
376 }
377
378 /**
379 * Return the indexes of the <i>zeros</i> of this bit-chromosome as stream.
380 *
381 * @since 3.0
382 *
383 * @return the indexes of the <i>zeros</i> of this bit-chromosome
384 */
385 public IntStream zeros() {
386 return IntStream.range(0, length())
387 .filter(index -> !bit.get(_genes, index));
388 }
389
390 @Override
391 public BitChromosome newInstance(final ISeq<BitGene> genes) {
392 requireNonNull(genes, "Genes");
393 if (genes.isEmpty()) {
394 throw new IllegalArgumentException(
395 "The genes sequence must contain at least one gene."
396 );
397 }
398
399 final BitChromosome chromosome = new BitChromosome(
400 bit.newArray(genes.length()), genes.length()
401 );
402 int ones = 0;
403
404 if (genes instanceof BitGeneISeq) {
405 final BitGeneISeq iseq = (BitGeneISeq)genes;
406 iseq.copyTo(chromosome._genes);
407 ones = bit.count(chromosome._genes);
408 } else {
409 for (int i = genes.length(); --i >= 0;) {
410 if (genes.get(i).booleanValue()) {
411 bit.set(chromosome._genes, i);
412 ++ones;
413 }
414 }
415 }
416
417 chromosome._p = (double)ones/(double)genes.length();
418 return chromosome;
419 }
420
421 @Override
422 public BitChromosome newInstance() {
423 return of(_length, _p);
424 }
425
426 /**
427 * Return the BitChromosome as String. A TRUE is represented by a 1 and
428 * a FALSE by a 0. The returned string can be used to create a new
429 * chromosome with the {@link #of(CharSequence)} constructor.
430 *
431 * @return String representation (containing only '1' and '0') of the
432 * BitChromosome.
433 */
434 public String toCanonicalString() {
435 return toSeq().stream()
436 .map(g -> g.booleanValue() ? "1" : "0")
437 .collect(joining());
438 }
439
440 @Override
441 public int compareTo(final BitChromosome that) {
442 return toBigInteger().compareTo(that.toBigInteger());
443 }
444
445 /**
446 * Invert the ones and zeros of this bit chromosome.
447 *
448 * @return a new BitChromosome with inverted ones and zeros.
449 */
450 public BitChromosome invert() {
451 final byte[] data = _genes.clone();
452 bit.invert(data);
453 return new BitChromosome(data, _length, 1.0 - _p);
454 }
455
456 /**
457 * Construct a new BitChromosome with the given _length.
458 *
459 * @param length Length of the BitChromosome, number of bits.
460 * @param p Probability of the TRUEs in the BitChromosome.
461 * @return a new {@code BitChromosome} with the given parameter
462 * @throws NegativeArraySizeException if the {@code length} is smaller
463 * than one.
464 * @throws IllegalArgumentException if {@code p} is not a valid probability.
465 */
466 public static BitChromosome of(final int length, final double p) {
467 return new BitChromosome(bit.newArray(length, p), length, p);
468 }
469
470 /**
471 * Constructing a new BitChromosome with the given _length. The TRUEs and
472 * FALSE in the {@code Chromosome} are equally distributed.
473 *
474 * @param length Length of the BitChromosome.
475 * @return a new {@code BitChromosome} with the given parameter
476 * @throws NegativeArraySizeException if the {@code _length} is smaller
477 * than one.
478 */
479 public static BitChromosome of(final int length) {
480 return new BitChromosome(bit.newArray(length, 0.5), length, 0.5);
481 }
482
483 /**
484 * Create a new {@code BitChromosome} with the given parameters.
485 *
486 * @param length length of the BitChromosome.
487 * @param bits the bit-set which initializes the chromosome
488 * @return a new {@code BitChromosome} with the given parameter
489 * @throws NegativeArraySizeException if the {@code length} is smaller
490 * than one.
491 * @throws NullPointerException if the {@code bitSet} is
492 * {@code null}.
493 */
494 public static BitChromosome of(final BitSet bits, final int length) {
495 final byte[] bytes = bit.newArray(length);
496 for (int i = 0; i < length; ++i) {
497 if (bits.get(i)) {
498 bit.set(bytes, i);
499 }
500 }
501 final double p = (double)bit.count(bytes)/(double)length;
502
503 return new BitChromosome(bytes, length, p);
504 }
505
506 /**
507 * Create a new {@code BitChromosome} with the given parameters.
508 *
509 * @param length length of the BitChromosome.
510 * @param bits the bit-set which initializes the chromosome
511 * @param p Probability of the TRUEs in the BitChromosome.
512 * @return a new {@code BitChromosome} with the given parameter
513 * @throws NegativeArraySizeException if the {@code length} is smaller than
514 * one.
515 * @throws NullPointerException if the {@code bitSet} is {@code null}.
516 * @throws IllegalArgumentException if {@code p} is not a valid probability.
517 */
518 public static BitChromosome of(
519 final BitSet bits,
520 final int length,
521 final double p
522 ) {
523 final byte[] bytes = bit.newArray(length);
524 for (int i = 0; i < length; ++i) {
525 if (bits.get(i)) {
526 bit.set(bytes, i);
527 }
528 }
529
530 return new BitChromosome(bytes, length, require.probability(p));
531 }
532
533 /**
534 * Constructing a new BitChromosome from a given BitSet.
535 * The BitSet is copied while construction. The length of the constructed
536 * BitChromosome will be {@code bitSet.length()} ({@link BitSet#length}).
537 *
538 * @param bits the bit-set which initializes the chromosome
539 * @return a new {@code BitChromosome} with the given parameter
540 * @throws NullPointerException if the {@code bitSet} is
541 * {@code null}.
542 */
543 public static BitChromosome of(final BitSet bits) {
544 return new BitChromosome(bits.toByteArray(), -1);
545 }
546
547 /**
548 * Create a new {@code BitChromosome} from the given big integer value.
549 *
550 * @param value the value of the created {@code BitChromosome}
551 * @return a new {@code BitChromosome} with the given parameter
552 * @throws NullPointerException if the given {@code value} is {@code null}.
553 */
554 public static BitChromosome of(final BigInteger value) {
555 return new BitChromosome(value.toByteArray(), -1);
556 }
557
558 /**
559 * Create a new {@code BitChromosome} from the given big integer value and
560 * ones probability.
561 *
562 * @param value the value of the created {@code BitChromosome}
563 * @param p Probability of the TRUEs in the BitChromosome.
564 * @return a new {@code BitChromosome} with the given parameter
565 * @throws NullPointerException if the given {@code value} is {@code null}.
566 * @throws IllegalArgumentException if {@code p} is not a valid probability.
567 */
568 public static BitChromosome of(final BigInteger value, final double p) {
569 final byte[] bits = value.toByteArray();
570 return new BitChromosome(bits, bits.length*8, require.probability(p));
571 }
572
573 /**
574 * Create a new {@code BitChromosome} from the given character sequence
575 * containing '0' and '1'; as created with the {@link #toCanonicalString()}
576 * method.
577 *
578 * @param value the input string.
579 * @return a new {@code BitChromosome} with the given parameter
580 * @throws NullPointerException if the {@code value} is {@code null}.
581 * @throws IllegalArgumentException if the length of the character sequence
582 * is zero or contains other characters than '0' or '1'.
583 */
584 public static BitChromosome of(final CharSequence value) {
585 return new BitChromosome(toByteArray(requireNonNull(value, "Input")), -1);
586 }
587
588 /**
589 * Create a new {@code BitChromosome} from the given character sequence
590 * containing '0' and '1'; as created with the {@link #toCanonicalString()}
591 * method.
592 *
593 * @param value the input string.
594 * @param p Probability of the TRUEs in the BitChromosome.
595 * @return a new {@code BitChromosome} with the given parameter
596 * @throws NullPointerException if the {@code value} is {@code null}.
597 * @throws IllegalArgumentException if the length of the character sequence
598 * is zero or contains other characters than '0' or '1'.
599 * @throws IllegalArgumentException if {@code p} is not a valid probability.
600 */
601 public static BitChromosome of(final CharSequence value, final double p) {
602 final byte[] bits = toByteArray(requireNonNull(value, "Input"));
603 return new BitChromosome(bits, bits.length*8, require.probability(p));
604 }
605
606 /**
607 * Create a new {@code BitChromosome} from the given character sequence
608 * containing '0' and '1'; as created with the {@link #toCanonicalString()}
609 * method.
610 *
611 * @param value the input string.
612 * @param length length of the BitChromosome
613 * @param p Probability of the TRUEs in the BitChromosome.
614 * @return a new {@code BitChromosome} with the given parameter
615 * @throws NullPointerException if the {@code value} is {@code null}.
616 * @throws IllegalArgumentException if the length of the character sequence
617 * is zero or contains other characters than '0' or '1'.
618 * @throws IllegalArgumentException if {@code p} is not a valid probability.
619 */
620 public static BitChromosome of(
621 final CharSequence value,
622 final int length,
623 final double p
624 ) {
625 final byte[] bits = toByteArray(requireNonNull(value, "Input"));
626 return new BitChromosome(bits, length, require.probability(p));
627 }
628
629 @Override
630 public int hashCode() {
631 return Hash.of(getClass()).and(_genes).value();
632 }
633
634 @Override
635 public boolean equals(final Object obj) {
636 return Equality.of(this, obj).test(c -> {
637 boolean equals = length() == c.length();
638 for (int i = 0, n = length(); equals && i < n; ++i) {
639 equals = getGene(i) == c.getGene(i);
640 }
641 return equals;
642 });
643 }
644
645 @Override
646 public String toString() {
647 return bit.toByteString(_genes);
648 }
649
650 /* *************************************************************************
651 * Java object serialization
652 * ************************************************************************/
653
654 private void writeObject(final ObjectOutputStream out)
655 throws IOException
656 {
657 out.defaultWriteObject();
658
659 out.writeInt(_length);
660 out.writeDouble(_p);
661 out.writeInt(_genes.length);
662 out.write(_genes);
663 }
664
665 private void readObject(final ObjectInputStream in)
666 throws IOException, ClassNotFoundException
667 {
668 in.defaultReadObject();
669
670 _length = in.readInt();
671 _p = in.readDouble();
672
673 final int bytes = in.readInt();
674 _genes = new byte[bytes];
675 in.readFully(_genes);
676
677 _seq = BitGeneISeq.of(_genes, _length);
678 }
679
680 }
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