001 /*
002 * Java Genetic Algorithm Library (jenetics-3.0.0).
003 * Copyright (c) 2007-2014 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@gmx.at)
019 */
020 package org.jenetics;
021
022 import static org.jenetics.CharacterGene.DEFAULT_CHARACTERS;
023 import static org.jenetics.internal.util.Equality.eq;
024
025 import java.io.IOException;
026 import java.io.ObjectInputStream;
027 import java.io.ObjectOutputStream;
028 import java.io.Serializable;
029 import java.util.function.Supplier;
030 import java.util.stream.Collectors;
031
032 import javax.xml.bind.annotation.XmlAccessType;
033 import javax.xml.bind.annotation.XmlAccessorType;
034 import javax.xml.bind.annotation.XmlAttribute;
035 import javax.xml.bind.annotation.XmlElement;
036 import javax.xml.bind.annotation.XmlRootElement;
037 import javax.xml.bind.annotation.XmlType;
038 import javax.xml.bind.annotation.adapters.XmlAdapter;
039 import javax.xml.bind.annotation.adapters.XmlJavaTypeAdapter;
040
041 import org.jenetics.internal.util.Equality;
042 import org.jenetics.internal.util.Hash;
043 import org.jenetics.internal.util.IntRef;
044
045 import org.jenetics.util.CharSeq;
046 import org.jenetics.util.ISeq;
047 import org.jenetics.util.MSeq;
048
049 /**
050 * CharacterChromosome which represents character sequences.
051 *
052 * @author <a href="mailto:franz.wilhelmstoetter@gmx.at">Franz Wilhelmstötter</a>
053 * @since 1.0
054 * @version 3.0 — <em>$Date: 2014-12-28 $</em>
055 */
056 @XmlJavaTypeAdapter(CharacterChromosome.Model.Adapter.class)
057 public class CharacterChromosome
058 extends
059 AbstractChromosome<CharacterGene>
060 implements
061 CharSequence,
062 Serializable
063 {
064 private static final long serialVersionUID = 2L;
065
066 private transient CharSeq _validCharacters;
067
068 /**
069 * Create a new chromosome from the given {@code genes} array. The genes
070 * array is copied, so changes to the given genes array doesn't effect the
071 * genes of this chromosome.
072 *
073 * @param genes the genes that form the chromosome.
074 * @throws NullPointerException if the given gene array is {@code null}.
075 * @throws IllegalArgumentException if the length of the gene array is
076 * smaller than one.
077 */
078 protected CharacterChromosome(final ISeq<CharacterGene> genes) {
079 super(genes);
080 _validCharacters = genes.get(0).getValidCharacters();
081 }
082
083 /**
084 * Create a new chromosome with the {@code validCharacters} char set as
085 * valid characters.
086 *
087 * @param validCharacters the valid characters for this chromosome.
088 * @param length the length of the new chromosome.
089 * @throws NullPointerException if the {@code validCharacters} is
090 * {@code null}.
091 * @throws IllegalArgumentException if the {@code length} is smaller than
092 * one.
093 */
094 public CharacterChromosome(final CharSeq validCharacters, final int length) {
095 this(CharacterGene.seq(validCharacters, length));
096 _valid = true;
097 }
098
099 @Override
100 public char charAt(final int index) {
101 return getGene(index).charValue();
102 }
103
104 @Override
105 public CharacterChromosome subSequence(final int start, final int end) {
106 return new CharacterChromosome(_genes.subSeq(start, end));
107 }
108
109 /**
110 * @throws NullPointerException if the given gene array is {@code null}.
111 */
112 @Override
113 public CharacterChromosome newInstance(final ISeq<CharacterGene> genes) {
114 return new CharacterChromosome(genes);
115 }
116
117 /**
118 * Create a new, <em>random</em> chromosome.
119 */
120 @Override
121 public CharacterChromosome newInstance() {
122 return new CharacterChromosome(_validCharacters, length());
123 }
124
125 @Override
126 public int hashCode() {
127 return Hash.of(getClass())
128 .and(super.hashCode())
129 .and(_validCharacters).value();
130 }
131
132 @Override
133 public boolean equals(final Object obj) {
134 return Equality.of(this, obj).test(cc ->
135 super.equals(obj) &&
136 eq(_validCharacters, cc._validCharacters)
137 );
138 }
139
140 @Override
141 public String toString() {
142 return toSeq().stream()
143 .map(Object::toString)
144 .collect(Collectors.joining());
145 }
146
147 /**
148 * Returns an char array containing all of the elements in this chromosome
149 * in proper sequence. If the chromosome fits in the specified array, it is
150 * returned therein. Otherwise, a new array is allocated with the length of
151 * this chromosome.
152 *
153 * @since 3.0
154 *
155 * @param array the array into which the elements of this chromosomes are to
156 * be stored, if it is big enough; otherwise, a new array is
157 * allocated for this purpose.
158 * @return an array containing the elements of this chromosome
159 * @throws NullPointerException if the given {@code array} is {@code null}
160 */
161 public char[] toArray(final char[] array) {
162 final char[] a = array.length >= length() ?
163 array : new char[length()];
164
165 for (int i = length(); --i >= 0;) {
166 a[i] = charAt(i);
167 }
168
169 return a;
170 }
171
172 /**
173 * Returns an char array containing all of the elements in this chromosome
174 * in proper sequence.
175 *
176 * @since 3.0
177 *
178 * @return an array containing the elements of this chromosome
179 */
180 public char[] toArray() {
181 return toArray(new char[length()]);
182 }
183
184
185 /**
186 * Create a new chromosome with the {@link CharacterGene#DEFAULT_CHARACTERS}
187 * char set as valid characters.
188 *
189 * @param length the {@code length} of the new chromosome.
190 * @return a new {@code CharacterChromosome} with the given parameter
191 * @throws IllegalArgumentException if the {@code length} is smaller than
192 * one.
193 */
194 public static CharacterChromosome of(final int length) {
195 return new CharacterChromosome(
196 CharacterGene.seq(DEFAULT_CHARACTERS, length)
197 );
198 }
199
200 /**
201 * Create a new chromosome from the given genes (given as string).
202 *
203 * @param alleles the character genes.
204 * @param validChars the valid characters.
205 * @return a new {@code CharacterChromosome} with the given parameter
206 * @throws IllegalArgumentException if the genes string is empty.
207 */
208 public static CharacterChromosome of(
209 final String alleles,
210 final CharSeq validChars
211 ) {
212 final IntRef index = new IntRef();
213 final Supplier<CharacterGene> geneFactory = () -> CharacterGene.of(
214 alleles.charAt(index.value++), validChars
215 );
216
217 final ISeq<CharacterGene> genes =
218 MSeq.<CharacterGene>ofLength(alleles.length())
219 .fill(geneFactory)
220 .toISeq();
221
222 return new CharacterChromosome(genes);
223 }
224
225 /**
226 * Create a new chromosome from the given genes (given as string).
227 *
228 * @param alleles the character genes.
229 * @return a new {@code CharacterChromosome} with the given parameter
230 * @throws IllegalArgumentException if the genes string is empty.
231 */
232 public static CharacterChromosome of(final String alleles) {
233 return of(alleles, DEFAULT_CHARACTERS);
234 }
235
236
237 /* *************************************************************************
238 * Java object serialization
239 * ************************************************************************/
240
241 private void writeObject(final ObjectOutputStream out)
242 throws IOException
243 {
244 out.defaultWriteObject();
245
246 out.writeInt(length());
247 out.writeObject(_validCharacters);
248
249 for (CharacterGene gene : _genes) {
250 out.writeChar(gene.getAllele().charValue());
251 }
252 }
253
254 private void readObject(final ObjectInputStream in)
255 throws IOException, ClassNotFoundException
256 {
257 in.defaultReadObject();
258
259 final int length = in.readInt();
260 _validCharacters = (CharSeq)in.readObject();
261
262 final MSeq<CharacterGene> genes = MSeq.ofLength(length);
263 for (int i = 0; i < length; ++i) {
264 final CharacterGene gene = CharacterGene.of(
265 in.readChar(),
266 _validCharacters
267 );
268 genes.set(i, gene);
269 }
270
271 _genes = genes.toISeq();
272 }
273
274 /* *************************************************************************
275 * JAXB object serialization
276 * ************************************************************************/
277
278 @XmlRootElement(name = "character-chromosome")
279 @XmlType(name = "org.jenetics.CharacterChromosome")
280 @XmlAccessorType(XmlAccessType.FIELD)
281 final static class Model {
282
283 @XmlAttribute(name = "length", required = true)
284 public int length;
285
286 @XmlElement(name = "valid-alleles", required = true, nillable = false)
287 public String validCharacters;
288
289 @XmlElement(name = "alleles", required = true, nillable = false)
290 public String genes;
291
292 public final static class Adapter
293 extends XmlAdapter<Model, CharacterChromosome>
294 {
295 @Override
296 public Model marshal(final CharacterChromosome value) {
297 final Model m = new Model();
298 m.length = value.length();
299 m.validCharacters = value._validCharacters.toString();
300 m.genes = value.toString();
301 return m;
302 }
303
304 @Override
305 public CharacterChromosome unmarshal(final Model m) {
306 return CharacterChromosome.of(
307 m.genes,
308 new CharSeq(m.validCharacters)
309 );
310 }
311 }
312 }
313 }
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