Merge pull request #14 from felixreimann/feature/#8-citation-annotation

Feature/#8 citation annotation

opt4j-benchmarks/src/main/java/org/opt4j/benchmarks/dtlz/DTLZModule.java

@@ -1,35 +1,32 @@
 /*******************************************************************************
  * 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.benchmarks.dtlz;
 
+import static org.opt4j.core.config.annotations.Citation.PublicationMonth.MAY;
+
 import org.opt4j.benchmarks.BinaryCreator;
 import org.opt4j.benchmarks.BinaryToDoubleDecoder;
 import org.opt4j.benchmarks.Bits;
 import org.opt4j.benchmarks.DoubleCopyDecoder;
 import org.opt4j.benchmarks.DoubleCreator;
 import org.opt4j.benchmarks.M;
 import org.opt4j.benchmarks.N;
+import org.opt4j.core.config.annotations.Citation;
 import org.opt4j.core.config.annotations.Info;
 import org.opt4j.core.config.annotations.Order;
 import org.opt4j.core.config.annotations.Required;
@@ -40,14 +37,13 @@
 import org.opt4j.core.start.Constant;
 
 /**
- * Module for the DTLZ benchmarks as proposed in "Scalable multi-objective
- * optimization test problems, Kalyanmoy Deb,Lothar Thiele, Marco Laumanns,
- * Eckart Zitzler, Proc. Congress Evolutionary Computation Volume 1 (May 2002)".
+ * Module for the DTLZ benchmarks as proposed in Deb et al. 2002.
  * 
  * @author lukasiewycz
  * 
  */
 @Info("DTLZ Problem Suite.  (n = m + k - 1)")
+@Citation(title = "Scalable multi-objective optimization test problems", authors = "Kalyanmoy Deb, Lothar Thiele, Marco Laumanns, and Eckart Zitzler", journal = "Proceedings of the 2002 Congress on Evolutionary Computation", volume = 1, month = MAY, year = 2002, doi = "10.1109/CEC.2002.1007032")
 public class DTLZModule extends ProblemModule {
 
 	@Order(0)

opt4j-benchmarks/src/main/java/org/opt4j/benchmarks/knapsack/KnapsackModule.java

@@ -1,47 +1,42 @@
 /*******************************************************************************
  * 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.benchmarks.knapsack;
 
+import static org.opt4j.core.config.annotations.Citation.PublicationMonth.NOVEMBER;
+
+import org.opt4j.core.config.annotations.Citation;
 import org.opt4j.core.config.annotations.File;
 import org.opt4j.core.config.annotations.Info;
 import org.opt4j.core.config.annotations.Required;
 import org.opt4j.core.problem.ProblemModule;
 import org.opt4j.core.start.Constant;
 
 /**
- * The multiobjective 0/1 ILP knapsack problem as proposed in "E. Zitzler and L.
- * Thiele: Multiobjective evolutionary algorithms: A comparative case study and
- * the strength Pareto approach. IEEE Transactions on Evolutionary Computation,
- * vol. 3, no. 4, pp. 257-271, Nov. 1999.". Either one of the nine benchmark
- * problems from Zitzler and Thiele 1999 can be selected or the number of
- * knapsacks and items can be set manually.
+ * The multiobjective 0/1 ILP knapsack problem as proposed in Zitzler and Thiele 1999. Either one of the nine benchmark
+ * problems from Zitzler and Thiele 1999 can be selected or the number of knapsacks and items can be set manually.
  * 
- * @see <a
- *      href="http://www.tik.ee.ethz.ch/sop/download/supplementary/testProblemSuite/">http://www.tik.ee.ethz.ch/sop/download/supplementary/testProblemSuite/</a>
+ * @see <a href=
+ *      "http://www.tik.ee.ethz.ch/sop/download/supplementary/testProblemSuite/">http://www.tik.ee.ethz.ch/sop/download/supplementary/testProblemSuite/</a>
  * 
  * @author reimann, lukasiewycz
  * 
  */
+@Citation(authors = "Eckart Zitzler and Lothar Thiele", title = "Multiobjective evolutionary algorithms: A comparative case study and the strength Pareto approach", journal = "IEEE Transactions on Evolutionary Computation", volume = 3, number = 4, pageFirst = 257, pageLast = 271, month = NOVEMBER, year = 1999)
 public class KnapsackModule extends ProblemModule {
 
 	protected int knapsacks = 5;
@@ -140,7 +135,8 @@ protected void config() {
 					KnapsackProfitEvaluator.class);
 			break;
 		case SAT:
-			bindProblem(KnapsackSATCreatorDecoder.class, KnapsackSATCreatorDecoder.class, KnapsackProfitEvaluator.class);
+			bindProblem(KnapsackSATCreatorDecoder.class, KnapsackSATCreatorDecoder.class,
+					KnapsackProfitEvaluator.class);
 			break;
 		}
 		addEvaluator(KnapsackOverloadEvaluator.class);

opt4j-benchmarks/src/main/java/org/opt4j/benchmarks/wfg/WFGModule.java

@@ -8,8 +8,8 @@
  * 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,
@@ -19,7 +19,6 @@
  * OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
  * SOFTWARE.
  *******************************************************************************/
-
 
 package org.opt4j.benchmarks.wfg;
 
@@ -31,6 +30,8 @@
 import org.opt4j.benchmarks.K;
 import org.opt4j.benchmarks.M;
 import org.opt4j.benchmarks.N;
+import org.opt4j.core.config.annotations.Citation;
+import org.opt4j.core.config.annotations.Citation.PublicationMonth;
 import org.opt4j.core.config.annotations.Info;
 import org.opt4j.core.config.annotations.Order;
 import org.opt4j.core.config.annotations.Required;
@@ -40,14 +41,13 @@
 import org.opt4j.core.problem.ProblemModule;
 
 /**
- * Module for the WFG (Walking Fish Group) benchmarks, see "A Scalable
- * Multi-objective Test Problem Toolkit, Simon Huband, Luigi Barone, R. Lyndon
- * While, and Philip Hingston (EMO 2005)".
+ * Module for the WFG (Walking Fish Group) benchmarks, see Huband et al. 2005.
  * 
  * @author lukasiewycz
  * 
  */
 @Info("WFG Problem Suite. The number of search variables is n=k+l.")
+@Citation(title = "A Scalable Multi-objective Test Problem Toolkit", authors = "Simon Huband, Luigi Barone, Lyndon While, and Philip Hingston", journal = "Evolutionary Multi-Criterion Optimization", pageFirst = 280, pageLast = 295, year = 2005, month = PublicationMonth.UNKNOWN, doi = "10.1007/978-3-540-31880-4_20")
 public class WFGModule extends ProblemModule {
 
 	@Order(0)

opt4j-benchmarks/src/main/java/org/opt4j/benchmarks/zdt/ZDTModule.java

@@ -8,8 +8,8 @@
  * 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,
@@ -19,7 +19,6 @@
  * OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
  * SOFTWARE.
  *******************************************************************************/
-
 
 package org.opt4j.benchmarks.zdt;
 
@@ -30,6 +29,8 @@
 import org.opt4j.benchmarks.DoubleCopyDecoder;
 import org.opt4j.benchmarks.DoubleCreator;
 import org.opt4j.benchmarks.N;
+import org.opt4j.core.config.annotations.Citation;
+import org.opt4j.core.config.annotations.Citation.PublicationMonth;
 import org.opt4j.core.config.annotations.Info;
 import org.opt4j.core.config.annotations.Order;
 import org.opt4j.core.config.annotations.Required;
@@ -39,15 +40,13 @@
 import org.opt4j.core.problem.ProblemModule;
 
 /**
- * The {@link ZDTModule} configures the ZDT benchmarks, see "Comparison of
- * Multiobjective Evolutionary Algorithms: Empirical Results, Eckart Zitzler,
- * Kalyanmoy Deb, Lothar Thiele, Evolutionary Computation Volume 8 , Issue 2
- * (June 2000)".
+ * The {@link ZDTModule} configures the ZDT benchmarks, see Zitzler et al. 2000.
  * 
  * @author lukasiewycz
  * 
  */
 @Info("ZDT Problem Suite.")
+@Citation(title = "Comparison of Multiobjective Evolutionary Algorithms: Empirical Results", authors = "Eckart Zitzler, Kalyanmoy Deb, and Lothar Thiele", journal = "Evolutionary Computation Volume", volume = 8, number = 2, month = PublicationMonth.JUNE, year = 2000)
 public class ZDTModule extends ProblemModule {
 
 	@Order(0)

opt4j-core/src/main/java/org/opt4j/core/common/archive/AdaptiveGridArchive.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;
@@ -38,10 +33,9 @@
 import com.google.inject.Inject;
 
 /**
- * The {@link AdaptiveGridArchive} uses an adaptive grid in order to bound the
- * size of the {@link Archive}, see "Properties of an Adaptive Archiving
- * Algorithm for Storing Nondominated Vectors, J. Knowles, D. Corne,
- * Transactions of Evolutionary Computation, Vol. 7, No. 2, April 2003".
+ * The {@link AdaptiveGridArchive} uses an adaptive grid in order to bound the size of the {@link Archive}, see
+ * "Properties of an Adaptive Archiving Algorithm for Storing Nondominated Vectors, J. Knowles, D. Corne, Transactions
+ * of Evolutionary Computation, Vol. 7, No. 2, April 2003".
  * 
  * @author lukasiewycz, helwig
  * 
@@ -119,9 +113,7 @@ public AdaptiveGridArchive(@Constant(value = "capacity", namespace = BoundedArch
 	/*
 	 * (non-Javadoc)
 	 * 
-	 * @see
-	 * org.opt4j.common.archive.AbstractArchive#updateWithNondominated(java.
-	 * util.Collection)
+	 * @see org.opt4j.common.archive.AbstractArchive#updateWithNondominated(java. util.Collection)
 	 */
 	@Override
 	protected boolean updateWithNondominated(Collection<Individual> candidates) {
@@ -277,8 +269,7 @@ public boolean remove(Object o) {
 	}
 
 	/**
-	 * Adds all {@link Individual}s to theirs {@link Cell}s and the {@link Cell}
-	 * s to the {@link Archive}.
+	 * Adds all {@link Individual}s to theirs {@link Cell}s and the {@link Cell} s to the {@link Archive}.
 	 * 
 	 * @param individuals
 	 *            the individuals to be added
@@ -292,9 +283,8 @@ protected void addToCell(Iterable<Individual> individuals) {
 	}
 
 	/**
-	 * Removes this {@link Individual} from its {@link Cell} and removes the
-	 * {@link Cell} from the {@link org.opt4j.core.optimizer.Archive} if it is
-	 * empty.
+	 * Removes this {@link Individual} from its {@link Cell} and removes the {@link Cell} from the
+	 * {@link org.opt4j.core.optimizer.Archive} if it is empty.
 	 * 
 	 * @param individual
 	 *            the individual to be removed
@@ -308,8 +298,7 @@ protected void removeFromCell(Individual individual) {
 	}
 
 	/**
-	 * Determines the new bounds for the individuals and returns {@code true} if
-	 * the bounds have changed.
+	 * Determines the new bounds for the individuals and returns {@code true} if the bounds have changed.
 	 * 
 	 * @param individuals
 	 *            the individuals