Merge pull request #15 from felixreimann/feature/archives-test

abstract archive tests added
SDARG · Mar 21, 2018 · 6f469a4 · 6f469a4
2 parents e472c45 + d8d4dbe
commit 6f469a4
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diff --git a/opt4j-core/src/main/java/org/opt4j/core/common/archive/AbstractArchive.java b/opt4j-core/src/main/java/org/opt4j/core/common/archive/AbstractArchive.java
@@ -1,23 +1,18 @@
 /*******************************************************************************
  * Copyright (c) 2014 Opt4J
  *
- * Permission is hereby granted, free of charge, to any person obtaining a copy
- * of this software and associated documentation files (the "Software"), to deal
- * in the Software without restriction, including without limitation the rights
- * to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
- * copies of the Software, and to permit persons to whom the Software is
- * furnished to do so, subject to the following conditions:
+ * Permission is hereby granted, free of charge, to any person obtaining a copy of this software and associated
+ * documentation files (the "Software"), to deal in the Software without restriction, including without limitation the
+ * rights to use, copy, modify, merge, publish, distribute, sublicense, and/or sell copies of the Software, and to
+ * permit persons to whom the Software is furnished to do so, subject to the following conditions:
  *
- * The above copyright notice and this permission notice shall be included in all
- * copies or substantial portions of the Software.
+ * The above copyright notice and this permission notice shall be included in all copies or substantial portions of the
+ * Software.
  *
- * THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
- * IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
- * FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
- * AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
- * LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
- * OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
- * SOFTWARE.
+ * THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE
+ * WARRANTIES OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR
+ * COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR
+ * OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE SOFTWARE.
  *******************************************************************************/
 
 package org.opt4j.core.common.archive;
@@ -54,17 +49,31 @@ public abstract class AbstractArchive extends Archive {
 	@Override
 	public boolean update(Set<? extends Individual> individuals) {
 		List<Individual> candidates = new ArrayList<Individual>(individuals);
-		Objectives o1, o2;
-
 		/*
-		 * Remove all individuals that are already in the archive and those that
-		 * are dominated among the candidates
+		 * Remove all individuals that are already in the archive.
 		 */
 		candidates.removeAll(this);
+		removeDominatedCandidates(candidates);
+
+		removeArchiveDominated(candidates);
+
+		return updateWithNondominated(candidates);
+	}
+
+	/**
+	 * Remove candidates, which are weakly dominated by another candidate.
+	 * 
+	 * Thus, the list of candidates which need to be tested against the whole
+	 * archive is reduced.
+	 * 
+	 * @param candidates
+	 *            the list of candidates to sanitize
+	 */
+	void removeDominatedCandidates(List<Individual> candidates) {
 		for (int i = 0; i < candidates.size() - 1; i++) {
-			o1 = candidates.get(i).getObjectives();
+			Objectives o1 = candidates.get(i).getObjectives();
 			for (int j = i + 1; j < candidates.size(); j++) {
-				o2 = candidates.get(j).getObjectives();
+				Objectives o2 = candidates.get(j).getObjectives();
 				if (o2.weaklyDominates(o1)) {
 					candidates.remove(i);
 					i--;
@@ -75,19 +84,23 @@ public boolean update(Set<? extends Individual> individuals) {
 				}
 			}
 		}
+	}
 
-		/*
-		 * Remove those individuals from the candidates which are weakly
-		 * dominated by the archive. Remove those individuals from the archive
-		 * which are dominated by the candidates. In case of equal objectives,
-		 * this gives priority to the individuals in the archive and avoids
-		 * unnecessary archive updates.
-		 */
+	/**
+   * Remove those individuals from the candidates which are weakly
+   * dominated by the archive. Remove those individuals from the archive
+   * which are dominated by the candidates. In case of equal objectives,
+   * this gives priority to the individuals in the archive and avoids
+   * unnecessary archive updates.
+	 * @param candidates
+	 *            the list of candidates to sanitize
+	 */
+	void removeArchiveDominated(List<Individual> candidates) {
 		Iterator<Individual> i1, i2;
 		for (i1 = candidates.iterator(); i1.hasNext();) {
-			o1 = i1.next().getObjectives();
+			Objectives o1 = i1.next().getObjectives();
 			for (i2 = this.iterator(); i2.hasNext();) {
-				o2 = i2.next().getObjectives();
+				Objectives o2 = i2.next().getObjectives();
 				if (o2.weaklyDominates(o1)) {
 					i1.remove();
 					break;
@@ -96,8 +109,6 @@ public boolean update(Set<? extends Individual> individuals) {
 				}
 			}
 		}
-
-		return updateWithNondominated(candidates);
 	}
 
 	/**

diff --git a/opt4j-core/src/main/java/org/opt4j/core/genotype/DoubleGenotype.java b/opt4j-core/src/main/java/org/opt4j/core/genotype/DoubleGenotype.java
@@ -1,26 +1,20 @@
 /*******************************************************************************
  * Copyright (c) 2014 Opt4J
  *
- * Permission is hereby granted, free of charge, to any person obtaining a copy
- * of this software and associated documentation files (the "Software"), to deal
- * in the Software without restriction, including without limitation the rights
- * to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
- * copies of the Software, and to permit persons to whom the Software is
- * furnished to do so, subject to the following conditions:
+ * Permission is hereby granted, free of charge, to any person obtaining a copy of this software and associated
+ * documentation files (the "Software"), to deal in the Software without restriction, including without limitation the
+ * rights to use, copy, modify, merge, publish, distribute, sublicense, and/or sell copies of the Software, and to
+ * permit persons to whom the Software is furnished to do so, subject to the following conditions:
  *
- * The above copyright notice and this permission notice shall be included in all
- * copies or substantial portions of the Software.
+ * The above copyright notice and this permission notice shall be included in all copies or substantial portions of the
+ * Software.
  *
- * THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
- * IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
- * FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
- * AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
- * LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
- * OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
- * SOFTWARE.
+ * THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE
+ * WARRANTIES OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR
+ * COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR
+ * OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE SOFTWARE.
  *******************************************************************************/
 
-
 package org.opt4j.core.genotype;
 
 import java.lang.reflect.Constructor;
@@ -31,8 +25,7 @@
 
 /**
  * <p>
- * The {@link DoubleGenotype} consists of double values that can be used as a
- * {@link Genotype}.
+ * The {@link DoubleGenotype} consists of double values that can be used as a {@link Genotype}.
  * </p>
  * <p>
  * Example problem: Select filling level of five bottles<br/>
@@ -43,8 +36,8 @@
  * genotype.init(new Random(), 5);
  * </pre>
  * 
- * </blockquote> Example instance: [0.5035947840006195, 0.9693492473483428,
- * 0.12786372316728167, 0.5299369900029843, 0.8055193291478467]<br/>
+ * </blockquote> Example instance: [0.5035947840006195, 0.9693492473483428, 0.12786372316728167, 0.5299369900029843,
+ * 0.8055193291478467]<br/>
  * Example search space size: [0;1]<sup>5</sup>
  * </p>
  * 
@@ -57,16 +50,14 @@ public class DoubleGenotype extends ArrayList<Double> implements ListGenotype<Do
 	protected final Bounds<Double> bounds;
 
 	/**
-	 * Constructs a {@link DoubleGenotype} with lower bounds {@code 0.0} and
-	 * upper bounds {@code 1.0}.
+	 * Constructs a {@link DoubleGenotype} with lower bounds {@code 0.0} and upper bounds {@code 1.0}.
 	 */
 	public DoubleGenotype() {
 		this(0, 1);
 	}
 
 	/**
-	 * Constructs a {@link DoubleGenotype} with a specified lower and upper
-	 * bound for all values.
+	 * Constructs a {@link DoubleGenotype} with a specified lower and upper bound for all values.
 	 * 
 	 * @param lowerBound
 	 *            the lower bound
@@ -138,9 +129,9 @@ public void init(Random random, int n) {
 			getLowerBound(n - 1);
 			getUpperBound(n - 1);
 		} catch (IndexOutOfBoundsException outOfBoundException) {
-			String message = outOfBoundException.getMessage() == null ? "" : outOfBoundException.getMessage() + "\n";
-			message += "Can not initialize a genotype with " + n + " entries with the specified bounds";
-			throw new IndexOutOfBoundsException(message);
+			throw new IllegalArgumentException(
+					"Cannot initialize a genotype with " + n + " entries with the specified bounds",
+					outOfBoundException);
 		}
 		for (int i = 0; i < n; i++) {
 			double lo = getLowerBound(i);

diff --git a/opt4j-core/src/main/java/org/opt4j/core/genotype/IntegerGenotype.java b/opt4j-core/src/main/java/org/opt4j/core/genotype/IntegerGenotype.java
@@ -1,23 +1,18 @@
 /*******************************************************************************
  * Copyright (c) 2014 Opt4J
  *
- * Permission is hereby granted, free of charge, to any person obtaining a copy
- * of this software and associated documentation files (the "Software"), to deal
- * in the Software without restriction, including without limitation the rights
- * to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
- * copies of the Software, and to permit persons to whom the Software is
- * furnished to do so, subject to the following conditions:
+ * Permission is hereby granted, free of charge, to any person obtaining a copy of this software and associated
+ * documentation files (the "Software"), to deal in the Software without restriction, including without limitation the
+ * rights to use, copy, modify, merge, publish, distribute, sublicense, and/or sell copies of the Software, and to
+ * permit persons to whom the Software is furnished to do so, subject to the following conditions:
  *
- * The above copyright notice and this permission notice shall be included in all
- * copies or substantial portions of the Software.
+ * The above copyright notice and this permission notice shall be included in all copies or substantial portions of the
+ * Software.
  *
- * THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
- * IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
- * FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
- * AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
- * LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
- * OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
- * SOFTWARE.
+ * THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE
+ * WARRANTIES OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR
+ * COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR
+ * OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE SOFTWARE.
  *******************************************************************************/
 
 package org.opt4j.core.genotype;
@@ -30,8 +25,7 @@
 
 /**
  * <p>
- * The {@link IntegerGenotype} is a {@link Genotype} that consists of
- * {@link Integer} values.
+ * The {@link IntegerGenotype} is a {@link Genotype} that consists of {@link Integer} values.
  * </p>
  * <p>
  * Example problem: Select the outcome of throwing five dice<br/>
@@ -54,8 +48,7 @@ public class IntegerGenotype extends ArrayList<Integer> implements ListGenotype<
 	protected final Bounds<Integer> bounds;
 
 	/**
-	 * Constructs a {@link IntegerGenotype} with a specified lower and upper
-	 * bound for all values.
+	 * Constructs a {@link IntegerGenotype} with a specified lower and upper bound for all values.
 	 * 
 	 * @param lowerBound
 	 *            the lower bound
@@ -127,9 +120,9 @@ public void init(Random random, int n) {
 			getLowerBound(n - 1);
 			getUpperBound(n - 1);
 		} catch (IndexOutOfBoundsException outOfBoundException) {
-			String message = outOfBoundException.getMessage() == null ? "" : outOfBoundException.getMessage() + "\n";
-			message += "Can not initialize a genotype with " + n + " entries with the specified bounds";
-			throw new IndexOutOfBoundsException(message);
+			throw new IllegalArgumentException(
+					"Cannot initialize a genotype with " + n + " entries with the specified bounds",
+					outOfBoundException);
 		}
 
 		for (int i = 0; i < n; i++) {