Minor bug fixes and improved test coverage

CHANGELOG.md

@@ -4,21 +4,40 @@ All notable changes to this project will be documented in this file.
 The format is based on [Keep a Changelog](https://keepachangelog.com/en/1.0.0/),
 and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0.html).
 
-## [Unreleased] - 2021-01-27
+## [Unreleased] - 2021-01-30
 
 ### Added
 
 ### Changed
-* Modified API documentation website (https://jpt.cicirello.org/) to improve browsing on mobile devices.
 
 ### Deprecated
 
+### Removed
+
+### Fixed
+
+### CI/CD
+
+
+## [2.3.0] - 2021-01-30
+
+### Added
+* Test cases added to improve test coverage.
+
+### Changed
+* Modified API documentation website (https://jpt.cicirello.org/) to improve browsing on mobile devices.
+* Minor optimizations in Permutation class.
+
 ### Removed
 * Moved the example programs to a new repository. They were previously found in directories examples and replication, both of which have been removed. All of the examples are now located in the repository: https://github.com/cicirello/jpt-examples.
 * Removed jars of the library from the repo. These have been available from Maven Central, GitHub Packages, and GitHub Releases, for quite some time. No need to store in repo, and it is inefficient to do so.
 * Removed the zip files generated by javadoc of the indexes for the api website. These are not needed for search functionality, as javadoc also stores and uses the js files contained in these zips. Later versions of javadoc no longer generate these. Also gitignored these to prevent future storage.
 
 ### Fixed
+* Bug in Permutation.toString which was inserting an extra space at end.
+* Added validation checking for all permutation distance measures validating same length permutations (except for EditDistance which can handle that case).
+* Bug in ReversalDistance.max in case when permutation length is 2, and also added missing parameter validation.
+* Minor bug fix in KendallTauSequenceDistance in the case of distance between arrays of floats.
 
 ### CI/CD
 * Migrated build process from Ant to Maven, including GitHub workflows.

src/org/cicirello/permutations/Permutation.java

@@ -1,5 +1,5 @@
 /*
- * Copyright 2005, 2010, 2014-2019 Vincent A. Cicirello, <https://www.cicirello.org/>.
+ * Copyright 2005, 2010, 2014-2021 Vincent A. Cicirello, <https://www.cicirello.org/>.
  *
  * This file is part of JavaPermutationTools (https://jpt.cicirello.org/).
  *
@@ -38,8 +38,7 @@
  * manipulate permutations in a variety of ways.
  * 
  * @author <a href=https://www.cicirello.org/ target=_top>Vincent A. Cicirello</a>, <a href=https://www.cicirello.org/ target=_top>https://www.cicirello.org/</a> 
- * @version 9.23.2019
- * @since 1.0
+ * @version 1.28.2021
  */
 public final class Permutation implements Serializable, Iterable<Permutation>, Copyable<Permutation> {
 
@@ -777,7 +776,7 @@ public void removeAndInsert(int i, int size, int j) {
 			System.arraycopy(permutation, j, temp, 0, i-j);
 			System.arraycopy(permutation, i, permutation, j, size);
 			System.arraycopy(temp, 0, permutation, j+size, i-j);
-		} else if (i < j) {
+		} else { // Condition is implied by above: if (i < j)
 			int[] temp = new int[size];
 			System.arraycopy(permutation, i, temp, 0, size);
 			System.arraycopy(permutation, i+size, permutation, i, j-i);
@@ -828,8 +827,11 @@ public Iterator<Permutation> iterator() {
 	@Override
 	public String toString() {
 		String permS = "";
-		for (int i : permutation) {
-			permS += (i + " ");   
+		if (permutation.length > 0) {
+			permS += permutation[0];
+			for (int i = 1; i < permutation.length; i++) {
+				permS += " " + permutation[i];
+			}
 		}
 		return permS;
 	}

src/org/cicirello/permutations/distance/AbstractPermutationDistanceMeasurer.java

@@ -1,5 +1,5 @@
 /*
- * Copyright 2010, 2015, 2017-2019 Vincent A. Cicirello, <https://www.cicirello.org/>.
+ * Copyright 2010, 2015, 2017-2021 Vincent A. Cicirello, <https://www.cicirello.org/>.
  *
  * This file is part of JavaPermutationTools (https://jpt.cicirello.org/).
  *
@@ -27,30 +27,30 @@
  * where distance is an integer value.
  * 
  * @author <a href=https://www.cicirello.org/ target=_top>Vincent A. Cicirello</a>, <a href=https://www.cicirello.org/ target=_top>https://www.cicirello.org/</a>
- * @version 1.19.6.12
- * @since 1.0
+ * @version 1.28.2021
  *
  */
 abstract class AbstractPermutationDistanceMeasurer implements PermutationDistanceMeasurer, NormalizedPermutationDistanceMeasurer {
 
 	/**
 	 * {@inheritDoc}
+	 *
+	 * @throws IllegalArgumentException if p1.length() is not equal to p2.length().
 	 */
 	@Override
 	public final double distancef(Permutation p1, Permutation p2) {
 		return distance(p1,p2);
 	}
 
-	/**
-	 * {@inheritDoc}
-	 */
 	@Override
 	public final double maxf(int length) {
 		return max(length);
 	}
 
 	/**
 	 * {@inheritDoc}
+	 *
+	 * @throws IllegalArgumentException if p1.length() is not equal to p2.length().
 	 */
 	@Override
 	public final double normalizedDistance(Permutation p1, Permutation p2) {

src/org/cicirello/permutations/distance/AcyclicEdgeDistance.java

@@ -1,5 +1,5 @@
 /*
- * Copyright 2014-2019 Vincent A. Cicirello, <https://www.cicirello.org/>.
+ * Copyright 2014-2021 Vincent A. Cicirello, <https://www.cicirello.org/>.
  *
  * This file is part of JavaPermutationTools (https://jpt.cicirello.org/).
  *
@@ -42,8 +42,7 @@
  * S. Ronald, "Distance functions for order-based encodings," in Proc. IEEE CEC. IEEE Press, 1997, pp. 49–54.</p>
  *
  * @author <a href=https://www.cicirello.org/ target=_top>Vincent A. Cicirello</a>, <a href=https://www.cicirello.org/ target=_top>https://www.cicirello.org/</a>
- * @version 1.19.6.12 
- * @since 1.0
+ * @version 1.28.2021
  */
 public final class AcyclicEdgeDistance extends AbstractPermutationDistanceMeasurer {
 
@@ -54,28 +53,28 @@ public AcyclicEdgeDistance() {}
 
 	/**
 	 * {@inheritDoc}
+	 *
+	 * @throws IllegalArgumentException if p1.length() is not equal to p2.length().
 	 */
 	@Override
 	public int distance(Permutation p1, Permutation p2) {
+		if (p1.length() != p2.length()) {
+			throw new IllegalArgumentException("Permutations must be the same length");
+		}
 		int countNonSharedEdges = 0;
-		int L1 = p1.length();
-		int L2 = p2.length();
-		if (L1==L2 && L1==0) return 0;
-		int[] successors2 = new int[L2];
-		for (int i = 0; i < L2 - 1; i++) {
+		if (p1.length()==0) return 0;
+		int[] successors2 = new int[p2.length()];
+		for (int i = 0; i < p2.length() - 1; i++) {
 			successors2[p2.get(i)] = p2.get(i+1);
 		}
-		successors2[p2.get(L2-1)] = -1;
+		successors2[p2.get(p2.length()-1)] = -1;
 
-		for (int i = 0; i < L1 - 1; i++) {
+		for (int i = 0; i < p1.length() - 1; i++) {
 			if (p1.get(i+1) != successors2[p1.get(i)] && p1.get(i) != successors2[p1.get(i+1)]) countNonSharedEdges++;
 		}
 		return countNonSharedEdges;
 	}
 
-	/**
-	 * {@inheritDoc}
-	 */
 	@Override
 	public int max(int length) {
 		if (length <= 2) return 0;

src/org/cicirello/permutations/distance/BlockInterchangeDistance.java

@@ -1,5 +1,5 @@
 /*
- * Copyright 2019 Vincent A. Cicirello, <https://www.cicirello.org/>.
+ * Copyright 2019, 2021 Vincent A. Cicirello, <https://www.cicirello.org/>.
  *
  * This file is part of JavaPermutationTools (https://jpt.cicirello.org/).
  *
@@ -40,8 +40,7 @@
  * <p>Runtime: O(n), where n is the permutation length.</p>
  *
  * @author <a href=https://www.cicirello.org/ target=_top>Vincent A. Cicirello</a>, <a href=https://www.cicirello.org/ target=_top>https://www.cicirello.org/</a>
- * @version 7.26.19
- * @since 2.0
+ * @version 1.28.2021
  */
 public class BlockInterchangeDistance extends AbstractPermutationDistanceMeasurer {
 
@@ -52,9 +51,14 @@ public BlockInterchangeDistance() {}
 
 	/**
 	 * {@inheritDoc}
+	 *
+	 * @throws IllegalArgumentException if p1.length() is not equal to p2.length().
 	 */
 	@Override
 	public int distance(Permutation p1, Permutation p2) {
+		if (p1.length() != p2.length()) {
+			throw new IllegalArgumentException("Permutations must be the same length");
+		}
 		int[] inv2 = p2.getInverse();
 		int[] p = new int[inv2.length+2];
 		int[] inv = new int[p.length];
@@ -81,9 +85,6 @@ public int distance(Permutation p1, Permutation p2) {
 		return (p1.length()+1-cycles)/2;
 	}
 
-	/**
-	 * {@inheritDoc}
-	 */
 	@Override
 	public int max(int length) {
 		return length >> 1;

src/org/cicirello/permutations/distance/CyclicEdgeDistance.java

@@ -1,5 +1,5 @@
 /*
- * Copyright 2014-2019 Vincent A. Cicirello, <https://www.cicirello.org/>.
+ * Copyright 2014-2021 Vincent A. Cicirello, <https://www.cicirello.org/>.
  *
  * This file is part of JavaPermutationTools (https://jpt.cicirello.org/).
  *
@@ -42,8 +42,7 @@
  * S. Ronald, "Distance functions for order-based encodings," in Proc. IEEE CEC. IEEE Press, 1997, pp. 49–54.</p>
  *
  * @author <a href=https://www.cicirello.org/ target=_top>Vincent A. Cicirello</a>, <a href=https://www.cicirello.org/ target=_top>https://www.cicirello.org/</a>
- * @version 1.19.6.12 
- * @since 1.0
+ * @version 1.28.2021
  */
 public final class CyclicEdgeDistance extends AbstractPermutationDistanceMeasurer {
 
@@ -54,28 +53,27 @@ public CyclicEdgeDistance() {}
 
 	/**
 	 * {@inheritDoc}
+	 *
+	 * @throws IllegalArgumentException if p1.length() is not equal to p2.length().
 	 */
 	@Override
 	public int distance(Permutation p1, Permutation p2) {
+		if (p1.length() != p2.length()) {
+			throw new IllegalArgumentException("Permutations must be the same length");
+		}
 		int countNonSharedEdges = 0;
-		int L1 = p1.length();
-		int L2 = p2.length();
-
-		int[] successors2 = new int[L2];
-		for (int i = 0; i < L2; i++) {
-			successors2[p2.get(i)] = p2.get((i+1) % L2);
+		int[] successors2 = new int[p2.length()];
+		for (int i = 0; i < successors2.length; i++) {
+			successors2[p2.get(i)] = p2.get((i+1) % successors2.length);
 		}
 
-		for (int i = 0; i < L1; i++) {
-			if (p1.get((i+1) % L1) != successors2[p1.get(i)] && p1.get(i) != successors2[p1.get((i+1) % L1)]) countNonSharedEdges++;
+		for (int i = 0; i < successors2.length; i++) {
+			if (p1.get((i+1) % successors2.length) != successors2[p1.get(i)] && p1.get(i) != successors2[p1.get((i+1) % successors2.length)]) countNonSharedEdges++;
 		}
 
 		return countNonSharedEdges;
 	}
 
-	/**
-	 * {@inheritDoc}
-	 */
 	@Override
 	public int max(int length) {
 		if (length <= 3) return 0;

src/org/cicirello/permutations/distance/CyclicIndependentDistance.java

@@ -1,5 +1,5 @@
 /*
- * Copyright 2018-2019 Vincent A. Cicirello, <https://www.cicirello.org/>.
+ * Copyright 2018-2021 Vincent A. Cicirello, <https://www.cicirello.org/>.
  *
  * This file is part of JavaPermutationTools (https://jpt.cicirello.org/).
  *
@@ -32,8 +32,7 @@
  * the constructor.</p>
  *
  * @author <a href=https://www.cicirello.org/ target=_top>Vincent A. Cicirello</a>, <a href=https://www.cicirello.org/ target=_top>https://www.cicirello.org/</a>
- * @version 1.19.6.12
- * @since 1.0
+ * @version 1.28.2021
  *  
  */
 public final class CyclicIndependentDistance implements PermutationDistanceMeasurer {
@@ -56,6 +55,7 @@ public CyclicIndependentDistance(PermutationDistanceMeasurer d) {
 	 * @param p1 first permutation
 	 * @param p2 second permutation 
 	 * @return distance between p1 and p2 
+	 * @throws IllegalArgumentException if p1.length() is not equal to p2.length().
 	 */
 	@Override
 	public int distance(Permutation p1, Permutation p2) {
@@ -70,7 +70,13 @@ public int distance(Permutation p1, Permutation p2) {
 	}
 
 	/**
-	 * {@inheritDoc}
+	 * Measures the distance between two permutations, with cyclic independence:
+	 * distance = min_{i in [0,N)} distance(p1,rotate(p2,i))
+	 * 
+	 * @param p1 first permutation
+	 * @param p2 second permutation 
+	 * @return distance between p1 and p2 
+	 * @throws IllegalArgumentException if p1.length() is not equal to p2.length().
 	 */
 	@Override
 	public final double distancef(Permutation p1, Permutation p2) {

src/org/cicirello/permutations/distance/CyclicIndependentDistanceDouble.java

@@ -1,5 +1,5 @@
 /*
- * Copyright 2018-2019 Vincent A. Cicirello, <https://www.cicirello.org/>.
+ * Copyright 2018-2021 Vincent A. Cicirello, <https://www.cicirello.org/>.
  *
  * This file is part of JavaPermutationTools (https://jpt.cicirello.org/).
  *
@@ -32,8 +32,7 @@
  * the constructor.</p>
  *
  * @author <a href=https://www.cicirello.org/ target=_top>Vincent A. Cicirello</a>, <a href=https://www.cicirello.org/ target=_top>https://www.cicirello.org/</a>
- * @version 1.19.5.10
- * @since 1.0
+ * @version 1.28.2021
  *  
  */
 public final class CyclicIndependentDistanceDouble implements PermutationDistanceMeasurerDouble {
@@ -56,6 +55,7 @@ public CyclicIndependentDistanceDouble(PermutationDistanceMeasurerDouble d) {
 	 * @param p1 first permutation
 	 * @param p2 second permutation 
 	 * @return distance between p1 and p2 
+	 * @throws IllegalArgumentException if p1.length() is not equal to p2.length().
 	 */
 	@Override
 	public double distancef(Permutation p1, Permutation p2) {

src/org/cicirello/permutations/distance/CyclicRTypeDistance.java

@@ -1,5 +1,5 @@
 /*
- * Copyright 2010, 2014-2015, 2017-2019 Vincent A. Cicirello, <https://www.cicirello.org/>.
+ * Copyright 2010, 2014-2015, 2017-2021 Vincent A. Cicirello, <https://www.cicirello.org/>.
  *
  * This file is part of JavaPermutationTools (https://jpt.cicirello.org/).
  *
@@ -44,8 +44,7 @@
  * IEEE Transactions on Evolutionary Computation, 20(3):434-446, June 2016.</p>
  *
  * @author <a href=https://www.cicirello.org/ target=_top>Vincent A. Cicirello</a>, <a href=https://www.cicirello.org/ target=_top>https://www.cicirello.org/</a>
- * @version 1.19.6.12 
- * @since 1.0
+ * @version 1.28.2021
  */
 public final class CyclicRTypeDistance extends AbstractPermutationDistanceMeasurer {
 
@@ -56,27 +55,26 @@ public CyclicRTypeDistance() {}
 
 	/**
 	 * {@inheritDoc}
+	 *
+	 * @throws IllegalArgumentException if p1.length() is not equal to p2.length().
 	 */
 	@Override
 	public int distance(Permutation p1, Permutation p2) {
+		if (p1.length() != p2.length()) {
+			throw new IllegalArgumentException("Permutations must be the same length");
+		}
 		int countNonSharedEdges = 0;
-		int L1 = p1.length();
-		int L2 = p2.length();
-
-		int[] successors2 = new int[L2];
-		for (int i = 0; i < L2; i++) {
-			successors2[p2.get(i)] = p2.get((i+1) % L2);
+		int[] successors2 = new int[p2.length()];
+		for (int i = 0; i < successors2.length; i++) {
+			successors2[p2.get(i)] = p2.get((i+1) % successors2.length);
 		}
 
-		for (int i = 0; i < L1; i++) {
-			if (p1.get((i+1) % L1) != successors2[p1.get(i)]) countNonSharedEdges++;
+		for (int i = 0; i < successors2.length; i++) {
+			if (p1.get((i+1) % successors2.length) != successors2[p1.get(i)]) countNonSharedEdges++;
 		}
 		return countNonSharedEdges;
 	}
 
-	/**
-	 * {@inheritDoc}
-	 */
 	@Override
 	public int max(int length) {
 		if (length <= 2) return 0;