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.internal.util.Equality.eq;
023 import static org.jenetics.util.ISeq.toISeq;
024
025 import java.io.Serializable;
026 import java.util.Iterator;
027 import java.util.List;
028
029 import javax.xml.bind.annotation.XmlAccessType;
030 import javax.xml.bind.annotation.XmlAccessorType;
031 import javax.xml.bind.annotation.XmlAttribute;
032 import javax.xml.bind.annotation.XmlElement;
033 import javax.xml.bind.annotation.XmlRootElement;
034 import javax.xml.bind.annotation.XmlType;
035 import javax.xml.bind.annotation.adapters.XmlAdapter;
036 import javax.xml.bind.annotation.adapters.XmlJavaTypeAdapter;
037
038 import org.jenetics.internal.util.Equality;
039 import org.jenetics.internal.util.Hash;
040 import org.jenetics.internal.util.jaxb;
041 import org.jenetics.internal.util.reflect;
042
043 import org.jenetics.util.Factory;
044 import org.jenetics.util.ISeq;
045 import org.jenetics.util.MSeq;
046 import org.jenetics.util.Seq;
047 import org.jenetics.util.Verifiable;
048
049 /**
050 * The central class the GA is working with, is the {@code Genotype}. It is the
051 * structural representative of an individual. This class is the encoded problem
052 * solution with one to many {@link Chromosome}.
053 * <p>
054 * <img alt="Genotype" src="doc-files/Genotype.svg" width="400" height="252" >
055 * </p>
056 * The chromosomes of a genotype doesn't have to have necessarily the same size.
057 * It is only required that all genes are from the same type and the genes within
058 * a chromosome have the same constraints; e. g. the same min- and max values
059 * for number genes.
060 *
061 * [code]
062 * final Genotype<DoubleGene> genotype = Genotype.of(
063 * DoubleChromosome.of(0.0, 1.0, 8),
064 * DoubleChromosome.of(1.0, 2.0, 10),
065 * DoubleChromosome.of(0.0, 10.0, 9),
066 * DoubleChromosome.of(0.1, 0.9, 5)
067 * );
068 * [/code]
069 * The code snippet above creates a genotype with the same structure as shown in
070 * the figure above. In this example the {@link DoubleGene} has been chosen as
071 * gene type.
072 *
073 * @author <a href="mailto:franz.wilhelmstoetter@gmx.at">Franz Wilhelmstötter</a>
074 * @since 1.0
075 * @version 3.0 — <em>$Date: 2014-12-28 $</em>
076 */
077 @XmlJavaTypeAdapter(Genotype.Model.Adapter.class)
078 public final class Genotype<G extends Gene<?, G>>
079 implements
080 Factory<Genotype<G>>,
081 Iterable<Chromosome<G>>,
082 Verifiable,
083 Serializable
084 {
085 private static final long serialVersionUID = 3L;
086
087 private final ISeq<Chromosome<G>> _chromosomes;
088 private final int _ngenes;
089
090 //Caching isValid value.
091 private volatile Boolean _valid = null;
092
093 private Genotype(
094 final ISeq<? extends Chromosome<G>> chromosomes,
095 final int ngenes
096 ) {
097 if (chromosomes.length() == 0) {
098 throw new IllegalArgumentException("No chromosomes given.");
099 }
100
101 _chromosomes = reflect.cast(chromosomes);
102 _ngenes = ngenes;
103 }
104
105 /**
106 * Create a new Genotype from a given sequence of {@code Chromosomes}.
107 *
108 * @param chromosomes The {@code Chromosome} array the {@code Genotype}
109 * consists of.
110 * @throws NullPointerException if {@code chromosomes} is null or one of its
111 * element.
112 * @throws IllegalArgumentException if {@code chromosome.length == 0}.
113 */
114 Genotype(final ISeq<? extends Chromosome<G>> chromosomes) {
115 this(chromosomes, ngenes(chromosomes));
116 }
117
118 private static int ngenes(final Seq<? extends Chromosome<?>> chromosomes) {
119 return chromosomes.stream()
120 .mapToInt(c -> c.length())
121 .sum();
122 }
123
124 /**
125 * Return the chromosome at the given index. It is guaranteed, that the
126 * returned chromosome is not null.
127 *
128 * @param index Chromosome index.
129 * @return The Chromosome.
130 * @throws IndexOutOfBoundsException if
131 * {@code (index < 0 || index >= _length)}.
132 */
133 public Chromosome<G> getChromosome(final int index) {
134 assert(_chromosomes != null);
135 assert(_chromosomes.get(index) != null);
136
137 return _chromosomes.get(index);
138 }
139
140 /**
141 * Return the first chromosome. This is a shortcut for
142 * [code]
143 * final Genotype<DoubleGene> gt = ...
144 * final Chromosome<DoubleGene> chromosome = gt.getChromosome(0);
145 * [/code]
146 *
147 * @return The first chromosome.
148 */
149 public Chromosome<G> getChromosome() {
150 assert(_chromosomes != null);
151 assert(_chromosomes.get(0) != null);
152
153 return _chromosomes.get(0);
154 }
155
156 /**
157 * Return the first {@link Gene} of the first {@link Chromosome} of this
158 * {@code Genotype}. This is a shortcut for
159 * [code]
160 * final Genotype<DoubleGene> gt = ...
161 * final DoubleGene gene = gt.getChromosome(0).getGene(0);
162 * [/code]
163 *
164 * @return the first {@link Gene} of the first {@link Chromosome} of this
165 * {@code Genotype}.
166 */
167 public G getGene() {
168 assert(_chromosomes != null);
169 assert(_chromosomes.get(0) != null);
170
171 return _chromosomes.get(0).getGene();
172 }
173
174 /**
175 * Return the gene from the given chromosome- and gene index. This is a
176 * shortcut for {@code gt.getChromosome(chromosomeIndex).getGene(geneIndex)}.
177 *
178 * @since 3.0
179 *
180 * @param chromosomeIndex the chromosome index
181 * @param geneIndex the gene index within the chromosome
182 * @return the gene with the given indexes
183 * @throws IndexOutOfBoundsException if the given indexes are not within the
184 * allowed range
185 */
186 public G get(final int chromosomeIndex, final int geneIndex) {
187 return getChromosome(chromosomeIndex).getGene(geneIndex);
188 }
189
190 public ISeq<Chromosome<G>> toSeq() {
191 return _chromosomes;
192 }
193
194 @Override
195 public Iterator<Chromosome<G>> iterator() {
196 return _chromosomes.iterator();
197 }
198
199 /**
200 * Getting the number of chromosomes of this genotype.
201 *
202 * @return number of chromosomes.
203 */
204 public int length() {
205 return _chromosomes.length();
206 }
207
208 /**
209 * Return the number of genes this genotype consists of. This is the sum of
210 * the number of genes of the genotype chromosomes.
211 *
212 * @return Return the number of genes this genotype consists of.
213 */
214 public int getNumberOfGenes() {
215 return _ngenes;
216 }
217
218 /**
219 * Test if this genotype is valid. A genotype is valid if all its
220 * {@link Chromosome}s are valid.
221 *
222 * @return true if this genotype is valid, false otherwise.
223 */
224 @Override
225 public boolean isValid() {
226 if (_valid == null) {
227 _valid = _chromosomes.forAll(Verifiable::isValid);
228 }
229 return _valid;
230 }
231
232 /**
233 * Return a new, random genotype by creating new, random chromosomes (calling
234 * the {@link Chromosome#newInstance()} method) from the chromosomes of this
235 * genotype.
236 */
237 @Override
238 public Genotype<G> newInstance() {
239 return new Genotype<>(_chromosomes.map(Factory::newInstance), _ngenes);
240 }
241
242 Genotype<G> newInstance(final ISeq<Chromosome<G>> chromosomes) {
243 return new Genotype<>(chromosomes, _ngenes);
244 }
245
246 @Override
247 public int hashCode() {
248 return Hash.of(getClass()).and(_chromosomes).value();
249 }
250
251 @Override
252 public boolean equals(final Object obj) {
253 return Equality.of(this, obj).test(gt ->
254 eq(_chromosomes, gt._chromosomes)
255 );
256 }
257
258 @Override
259 public String toString() {
260 return _chromosomes.toString();
261 }
262
263 /**
264 * Create a new {@code Genotype} from a given array of {@code Chromosomes}.
265 *
266 * @since 3.0
267 *
268 * @param <G> the gene type
269 * @param first the first {@code Chromosome} of the {@code Genotype}
270 * @param rest the rest of the genotypes chromosomes.
271 * @return a new {@code Genotype} from the given chromosomes
272 * @throws NullPointerException if {@code chromosomes} is {@code null} or
273 * one of its element.
274 */
275 @SafeVarargs
276 public static <G extends Gene<?, G>> Genotype<G> of(
277 final Chromosome<G> first,
278 final Chromosome<G>... rest
279 ) {
280 final MSeq<Chromosome<G>> seq = MSeq.ofLength(1 + rest.length);
281 seq.set(0, first);
282 for (int i = 0; i < rest.length; ++i) {
283 seq.set(i + 1, rest[i]);
284 }
285 return new Genotype<>(seq.toISeq());
286 }
287
288 /**
289 * Create a new {@code Genotype} which consists of {@code n} chromosomes,
290 * which are created by the given {@code factory}. This method can be used
291 * for easily creating a <i>gene matrix</i>. The following example will
292 * create a 10x5 {@code DoubleGene} <i>matrix</i>.
293 *
294 * [code]
295 * final Genotype<DoubleGene> gt = Genotype
296 * .of(DoubleChromosome.of(0.0, 1.0, 10), 5);
297 * [/code]
298 *
299 * @since 3.0
300 *
301 * @param <G> the gene type
302 * @param factory the factory which creates the chromosomes this genotype
303 * consists of
304 * @param n the number of chromosomes this genotype consists of
305 * @return new {@code Genotype} containing {@code n} chromosomes
306 * @throws IllegalArgumentException if {@code n < 1}.
307 * @throws NullPointerException if the {@code factory} is {@code null}.
308 */
309 public static <G extends Gene<?, G>> Genotype<G>
310 of(final Factory<? extends Chromosome<G>> factory, final int n) {
311 final ISeq<Chromosome<G>> ch = ISeq.of(factory::newInstance, n);
312 return new Genotype<>(ch);
313 }
314
315 /**
316 * Create a new {@code Genotype} from a given array of {@code chromosomes}.
317 *
318 * @since 3.0
319 *
320 * @param <G> the gene type
321 * @param chromosomes the {@code Chromosome}s the returned genotype consists
322 * of
323 * @return a new {@code Genotype} from the given chromosomes
324 * @throws NullPointerException if {@code chromosomes} is {@code null} or
325 * one of its element.
326 * @throws IllegalArgumentException if {@code chromosome.length() < 1}.
327 */
328 public static <G extends Gene<?, G>> Genotype<G>
329 of(final Iterable<? extends Chromosome<G>> chromosomes) {
330 return new Genotype<>(ISeq.of(chromosomes));
331 }
332
333 /* *************************************************************************
334 * JAXB object serialization
335 * ************************************************************************/
336
337 @XmlRootElement(name = "genotype")
338 @XmlType(name = "org.jenetics.Genotype")
339 @XmlAccessorType(XmlAccessType.FIELD)
340 @SuppressWarnings({"unchecked", "rawtypes"})
341 static final class Model {
342
343 @XmlAttribute(name = "length", required = true)
344 public int length;
345
346 @XmlAttribute(name = "ngenes", required = true)
347 public int ngenes;
348
349 @XmlElement(name = "chromosome", required = true, nillable = false)
350 public List chromosomes;
351
352 public static final class Adapter
353 extends XmlAdapter<Model, Genotype>
354 {
355 @Override
356 public Model marshal(final Genotype gt) throws Exception {
357 final Model model = new Model();
358 model.length = gt.length();
359 model.ngenes = gt.getNumberOfGenes();
360 model.chromosomes = gt.toSeq()
361 .map(jaxb.Marshaller(gt.getChromosome()))
362 .asList();
363
364 return model;
365 }
366
367 @Override
368 public Genotype unmarshal(final Model model) throws Exception {
369 final ISeq chs = (ISeq)model.chromosomes.stream()
370 .map(jaxb.Unmarshaller(model.chromosomes.get(0)))
371 .collect(toISeq());
372
373 return new Genotype(chs, model.ngenes);
374 }
375 }
376
377 public static final Adapter ADAPTER = new Adapter();
378 }
379 }
|