001 /*
002 * Java Genetic Algorithm Library (jenetics-6.0.0).
003 * Copyright (c) 2007-2020 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 io.jenetics.CharacterGene.DEFAULT_CHARACTERS;
023 import static io.jenetics.internal.util.Hashes.hash;
024 import static io.jenetics.internal.util.SerialIO.readInt;
025 import static io.jenetics.internal.util.SerialIO.readString;
026 import static io.jenetics.internal.util.SerialIO.writeInt;
027 import static io.jenetics.internal.util.SerialIO.writeString;
028
029 import java.io.DataInput;
030 import java.io.DataOutput;
031 import java.io.IOException;
032 import java.io.InvalidObjectException;
033 import java.io.ObjectInputStream;
034 import java.io.Serializable;
035 import java.util.Objects;
036
037 import io.jenetics.util.CharSeq;
038 import io.jenetics.util.ISeq;
039 import io.jenetics.util.IntRange;
040 import io.jenetics.util.MSeq;
041
042 /**
043 * CharacterChromosome which represents character sequences.
044 *
045 * @see CharacterGene
046 *
047 * @implNote
048 * This class is immutable and thread-safe.
049 *
050 * @author <a href="mailto:franz.wilhelmstoetter@gmail.com">Franz Wilhelmstötter</a>
051 * @since 1.0
052 * @version 5.2
053 */
054 public class CharacterChromosome
055 extends VariableChromosome<CharacterGene>
056 implements
057 CharSequence,
058 Serializable
059 {
060 private static final long serialVersionUID = 3L;
061
062 private transient final CharSeq _validCharacters;
063
064 /**
065 * Create a new chromosome from the given {@code genes} array. The genes
066 * array is copied, so changes to the given genes array doesn't effect the
067 * genes of this chromosome.
068 *
069 * @since 4.0
070 *
071 * @param genes the genes that form the chromosome.
072 * @param lengthRange the allowed length range of the chromosome.
073 * @throws NullPointerException if the given gene array is {@code null}.
074 * @throws IllegalArgumentException if the length of the gene array is
075 * smaller than one.
076 */
077 protected CharacterChromosome(
078 final ISeq<CharacterGene> genes,
079 final IntRange lengthRange
080 ) {
081 super(genes, lengthRange);
082 _validCharacters = genes.get(0).validChars();
083 }
084
085 @Override
086 public char charAt(final int index) {
087 return get(index).charValue();
088 }
089
090 @Override
091 public CharacterChromosome subSequence(final int start, final int end) {
092 return new CharacterChromosome(_genes.subSeq(start, end), lengthRange());
093 }
094
095 /**
096 * @throws NullPointerException if the given gene array is {@code null}.
097 */
098 @Override
099 public CharacterChromosome newInstance(final ISeq<CharacterGene> genes) {
100 return new CharacterChromosome(genes, lengthRange());
101 }
102
103 /**
104 * Create a new, <em>random</em> chromosome.
105 */
106 @Override
107 public CharacterChromosome newInstance() {
108 return of(_validCharacters, lengthRange());
109 }
110
111 @Override
112 public int hashCode() {
113 return hash(super.hashCode(), hash(_validCharacters));
114 }
115
116 @Override
117 public boolean equals(final Object obj) {
118 return obj == this ||
119 obj != null &&
120 getClass() == obj.getClass() &&
121 Objects.equals(_validCharacters, ((CharacterChromosome)obj)._validCharacters) &&
122 super.equals(obj);
123 }
124
125 @Override
126 public String toString() {
127 return new String(toArray());
128 }
129
130 /**
131 * Returns an char array containing all of the elements in this chromosome
132 * in proper sequence. If the chromosome fits in the specified array, it is
133 * returned therein. Otherwise, a new array is allocated with the length of
134 * this chromosome.
135 *
136 * @since 3.0
137 *
138 * @param array the array into which the elements of this chromosomes are to
139 * be stored, if it is big enough; otherwise, a new array is
140 * allocated for this purpose.
141 * @return an array containing the elements of this chromosome
142 * @throws NullPointerException if the given {@code array} is {@code null}
143 */
144 public char[] toArray(final char[] array) {
145 final char[] a = array.length >= length()
146 ? array
147 : new char[length()];
148
149 for (int i = length(); --i >= 0;) {
150 a[i] = charAt(i);
151 }
152
153 return a;
154 }
155
156 /**
157 * Returns an char array containing all of the elements in this chromosome
158 * in proper sequence.
159 *
160 * @since 3.0
161 *
162 * @return an array containing the elements of this chromosome
163 */
164 public char[] toArray() {
165 return toArray(new char[length()]);
166 }
167
168
169 /* *************************************************************************
170 * Static factory methods.
171 * ************************************************************************/
172
173 /**
174 * Create a new chromosome with the {@code validCharacters} char set as
175 * valid characters.
176 *
177 * @since 4.3
178 *
179 * @param validCharacters the valid characters for this chromosome.
180 * @param lengthRange the allowed length range of the chromosome.
181 * @return a new {@code CharacterChromosome} with the given parameter
182 * @throws NullPointerException if the {@code validCharacters} is
183 * {@code null}.
184 * @throws IllegalArgumentException if the length of the gene sequence is
185 * empty, doesn't match with the allowed length range, the minimum
186 * or maximum of the range is smaller or equal zero or the given
187 * range size is zero.
188 */
189 public static CharacterChromosome of(
190 final CharSeq validCharacters,
191 final IntRange lengthRange
192 ) {
193 return new CharacterChromosome(
194 CharacterGene.seq(validCharacters, lengthRange),
195 lengthRange
196 );
197 }
198
199 /**
200 * Create a new chromosome with the {@link CharacterGene#DEFAULT_CHARACTERS}
201 * char set as valid characters.
202 *
203 * @param lengthRange the allowed length range of the chromosome.
204 * @return a new {@code CharacterChromosome} with the given parameter
205 * @throws IllegalArgumentException if the {@code length} is smaller than
206 * one.
207 */
208 public static CharacterChromosome of(final IntRange lengthRange) {
209 return of(DEFAULT_CHARACTERS, lengthRange);
210 }
211
212 /**
213 * Create a new chromosome with the {@code validCharacters} char set as
214 * valid characters.
215 *
216 * @since 4.3
217 *
218 * @param validCharacters the valid characters for this chromosome.
219 * @param length the {@code length} of the new chromosome.
220 * @return a new {@code CharacterChromosome} with the given parameter
221 * @throws NullPointerException if the {@code validCharacters} is
222 * {@code null}.
223 * @throws IllegalArgumentException if the length of the gene sequence is
224 * empty, doesn't match with the allowed length range, the minimum
225 * or maximum of the range is smaller or equal zero or the given
226 * range size is zero.
227 */
228 public static CharacterChromosome of(
229 final CharSeq validCharacters,
230 final int length
231 ) {
232 return of(validCharacters, IntRange.of(length));
233 }
234
235 /**
236 * Create a new chromosome with the {@link CharacterGene#DEFAULT_CHARACTERS}
237 * char set as valid characters.
238 *
239 * @param length the {@code length} of the new chromosome.
240 * @return a new {@code CharacterChromosome} with the given parameter
241 * @throws IllegalArgumentException if the {@code length} is smaller than
242 * one.
243 */
244 public static CharacterChromosome of(final int length) {
245 return of(DEFAULT_CHARACTERS, length);
246 }
247
248 /**
249 * Create a new chromosome from the given genes (given as string).
250 *
251 * @param alleles the character genes.
252 * @param validChars the valid characters.
253 * @return a new {@code CharacterChromosome} with the given parameter
254 * @throws IllegalArgumentException if the genes string is empty.
255 */
256 public static CharacterChromosome of(
257 final String alleles,
258 final CharSeq validChars
259 ) {
260 final MSeq<CharacterGene> genes = MSeq.ofLength(alleles.length());
261 for (int i = 0; i < alleles.length(); ++i) {
262 genes.set(i, CharacterGene.of(alleles.charAt(i), validChars));
263 }
264
265 return new CharacterChromosome(genes.toISeq(), IntRange.of(alleles.length()));
266 }
267
268 /**
269 * Create a new chromosome from the given genes (given as string).
270 *
271 * @param alleles the character genes.
272 * @return a new {@code CharacterChromosome} with the given parameter
273 * @throws IllegalArgumentException if the genes string is empty.
274 */
275 public static CharacterChromosome of(final String alleles) {
276 return of(alleles, DEFAULT_CHARACTERS);
277 }
278
279
280 /* *************************************************************************
281 * Java object serialization
282 * ************************************************************************/
283
284 private Object writeReplace() {
285 return new Serial(Serial.CHARACTER_CHROMOSOME, this);
286 }
287
288 private void readObject(final ObjectInputStream stream)
289 throws InvalidObjectException
290 {
291 throw new InvalidObjectException("Serialization proxy required.");
292 }
293
294 void write(final DataOutput out) throws IOException {
295 writeInt(lengthRange().min(), out);
296 writeInt(lengthRange().max(), out);
297 writeString(_validCharacters.toString(), out);
298 writeString(toString(), out);
299 }
300
301 static CharacterChromosome read(final DataInput in) throws IOException {
302 final var lengthRange = IntRange.of(readInt(in), readInt(in));
303 final var validCharacters = new CharSeq(readString(in));
304 final var chars = readString(in);
305
306 final MSeq<CharacterGene> values = MSeq.ofLength(chars.length());
307 for (int i = 0, n = chars.length(); i < n; ++i) {
308 values.set(i, CharacterGene.of(chars.charAt(i), validCharacters));
309 }
310
311 return new CharacterChromosome(values.toISeq(), lengthRange);
312 }
313
314 }
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