Merge pull request #132 from cicirello/code-improvements

cicirello · web-flow · commit ff9062cc0b90 · 2021-05-13T15:47:23.000-04:00
Resolved warnings generated by initial run of MuseDev static analysis
diff --git a/.muse.toml b/.muse.toml
@@ -0,0 +1,21 @@
+# don't run eslint... it is for js and will detect false positives 
+# in javadoc directories.
+
+disableTools = ["eslint"]
+
+# Ignore warnings not relevant to this specific project:
+#
+# 1) FindSecBugs identifies our use of ThreadLocalRandom as predictable.
+# We make extensive use of this class for randomness. Our use of randomness 
+# in this library is NOT at all security related, and rather, we simply need 
+# a fast pseudorandom number generator since we need to generate large 
+# numbers of random numbers. So ignore predictable random warnings. 
+
+ignore = ["PREDICTABLE_RANDOM"]
+
+# Ignore results from these directories
+
+ignoreFiles = """
+docs/api/jquery/
+tests/
+"""
diff --git a/src/org/cicirello/math/MathFunctions.java b/src/org/cicirello/math/MathFunctions.java
@@ -26,7 +26,7 @@
  * MathFunctions is a class of utility methods that implement various mathematical functions.
  *
  * @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 2.12.2021
+ * @version 5.13.2021
  *
  */
 public final class MathFunctions {
@@ -92,7 +92,7 @@ public static double logGamma(double n) {
 			// This check doesn't seem to be necessary given addition of first check in block.
 			// if (z == 0.0) return Double.POSITIVE_INFINITY;
 			// ln(PI)
-			final double LOG_PI = 1.14472988584940017414;
+			final double LOG_PI = 1.1447298858494002;
 			return LOG_PI - Math.log(z) - logGamma(n);
 		} else if (n < 13.0) {
 			double z = 1.0;
@@ -117,13 +117,13 @@ public static double logGamma(double n) {
 				n * evaluatePolynomial(n, POLY_APPROX_2) / evaluatePolynomial(n, POLY_APPROX_3);
 		} else {
 			// ln(sqrt(2pi))
-			final double LOG_SQRT_PI2 = 0.91893853320467274178;
+			final double LOG_SQRT_PI2 = 0.9189385332046727;
 			double q = (n - 0.5) * Math.log(n) - n + LOG_SQRT_PI2; 
 			if (n > 1.0e8) return q;
 			double p = 1.0 / (n * n);
 			if (n >= 1000.0) {
-				q = q + ((7.9365079365079365079365e-4 * p - 2.7777777777777777777778e-3) 
-					* p + 0.0833333333333333333333) / n;
+				q = q + ((7.936507936507937E-4 * p - 0.002777777777777778) 
+					* p + 0.08333333333333333) / n;
 			} else {
 				q += evaluatePolynomial(p, STIRLING_EXPANSION_LN_GAMMA) / n;
 			}
@@ -142,21 +142,22 @@ private static double evaluatePolynomial(double x, double polynomial[]) {
 	}
 	
 	private static final double[] STIRLING_EXPANSION_LN_GAMMA = {
-		8.11614167470508450300E-4, -5.95061904284301438324E-4,
-		7.93650340457716943945E-4, -2.77777777730099687205E-3,
-		8.33333333333331927722E-2
+		8.116141674705085E-4, -5.950619042843014E-4,
+		7.936503404577169E-4, -0.002777777777300997,
+		0.08333333333333319
 	};
 
 	private static final double[] POLY_APPROX_2 = {
-		-1.37825152569120859100E3, -3.88016315134637840924E4,
-		-3.31612992738871184744E5, -1.16237097492762307383E6,
-		-1.72173700820839662146E6, -8.53555664245765465627E5
+		-1378.2515256912086, -38801.631513463784,
+		-331612.9927388712, -1162370.974927623,
+		-1721737.0082083966, -853555.6642457654
 	};
 
 	private static final double[] POLY_APPROX_3 = {
-		1.0, -3.51815701436523470549E2, -1.70642106651881159223E4,
-		-2.20528590553854454839E5, -1.13933444367982507207E6,
-		-2.53252307177582951285E6, -2.01889141433532773231E6
+		1.0, 
+		-351.81570143652345, -17064.210665188115,
+		-220528.59055385445, -1139334.4436798252,
+		-2532523.0717758294, -2018891.4143353277,
 	};
 	
 	// HELPERS FOR logGamma END HERE
diff --git a/src/org/cicirello/math/la/MatrixOps.java b/src/org/cicirello/math/la/MatrixOps.java
@@ -27,7 +27,7 @@
  * represented as 2-D Java arrays.
  *
  * @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 2.13.2021
+ * @version 5.13.2021
  */
 public final class MatrixOps {
 	
@@ -235,7 +235,7 @@ public static double[][] difference(double[][] A, double[][] B) {
 	 * @return A reference to the C matrix.
 	 */
 	public static int[][] product(int[][] A, int[][] B, int[][] C) {
-		if (A.length == 0 && B.length > 0 || A.length > 0 && B.length == 0) {
+		if ((A.length == 0 && B.length > 0) || (A.length > 0 && B.length == 0)) {
 			throw new IllegalArgumentException("If either matrix has 0 rows, both must.");
 		} else if (A.length == 0) {
 			if (C==null) return new int[0][0];
@@ -267,7 +267,7 @@ public static int[][] product(int[][] A, int[][] B, int[][] C) {
 	 * @return A reference to the C matrix.
 	 */
 	public static double[][] product(double[][] A, double[][] B, double[][] C) {
-		if (A.length == 0 && B.length > 0 || A.length > 0 && B.length == 0) {
+		if ((A.length == 0 && B.length > 0) || (A.length > 0 && B.length == 0)) {
 			throw new IllegalArgumentException("If either matrix has 0 rows, both must.");
 		} else if (A.length == 0) {
 			if (C==null) return new double[0][0];
diff --git a/src/org/cicirello/math/rand/RandomIndexer.java b/src/org/cicirello/math/rand/RandomIndexer.java
@@ -33,7 +33,7 @@
  * from the motivating case, the case of efficiently generating random indexes into an array.
  *
  * @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 2.13.2021
+ * @version 5.13.2021
  *
  */
 public final class RandomIndexer {
@@ -152,7 +152,7 @@ public static int nextInt(int bound, Random gen) {
 	 */
 	public static int nextBiasedInt(int bound) {
 		if (bound < 1) throw new IllegalArgumentException("bound must be positive");
-		return (int)((long)(ThreadLocalRandom.current().nextInt() & 0x7fffffff) * (long)bound >> 31);
+		return (int)(((long)(ThreadLocalRandom.current().nextInt() & 0x7fffffff) * (long)bound) >> 31);
 	}
 	
 	/**
@@ -178,7 +178,7 @@ public static int nextBiasedInt(int bound) {
 	 */
 	public static int nextBiasedInt(int bound, SplittableRandom gen) {
 		if (bound < 1) throw new IllegalArgumentException("bound must be positive");
-		return (int)((long)(gen.nextInt() & 0x7fffffff) * (long)bound >> 31);
+		return (int)(((long)(gen.nextInt() & 0x7fffffff) * (long)bound) >> 31);
 	}
 	
 	/**
@@ -211,7 +211,7 @@ public static int nextBiasedInt(int bound, SplittableRandom gen) {
 	 */
 	public static int nextBiasedInt(int bound, Random gen) {
 		if (bound < 1) throw new IllegalArgumentException("bound must be positive");
-		return (int)((long)(gen.nextInt() & 0x7fffffff) * (long)bound >> 31);
+		return (int)(((long)(gen.nextInt() & 0x7fffffff) * (long)bound) >> 31);
 	}
 	
 	
diff --git a/src/org/cicirello/math/stats/Statistics.java b/src/org/cicirello/math/stats/Statistics.java
@@ -1,5 +1,5 @@
 /*
- * Copyright 2018-2020 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/).
  *
@@ -26,7 +26,7 @@
  * Utility class of basic statistics.
  *
  * @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 09-18-2020
+ * @version 5.13.2021
  */
 public final class Statistics {
 	
@@ -39,11 +39,9 @@ private Statistics() {}
 	 * @return the mean of the data.
 	 */
 	public static double mean(int[] data) {
-		double mean = 0;
 		int sum = 0;
 		for (int e : data) sum = sum + e;
-		mean = 1.0 * sum / data.length;
-		return mean;
+		return 1.0 * sum / data.length;
 	}
 	
 	/**
diff --git a/src/org/cicirello/permutations/distance/KendallTauDistance.java b/src/org/cicirello/permutations/distance/KendallTauDistance.java
@@ -48,7 +48,7 @@
  * M. G. Kendall, "A new measure of rank correlation," Biometrika, vol. 30, no. 1/2, pp. 81–93, June 1938.</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 4.2.2021
+ * @version 5.13.2021
  * 
  */
 public final class KendallTauDistance implements NormalizedPermutationDistanceMeasurer {
@@ -83,7 +83,7 @@ public int distance(Permutation p1, Permutation p2) {
 	@Override
 	public int max(int length) {
 		if (length <= 1) return 0;
-		return length*(length - 1)>>1;
+		return (length*(length - 1))>>1;
 	}
 	
 	private int countInversions(int[] array) {
diff --git a/src/org/cicirello/permutations/distance/ReversalDistance.java b/src/org/cicirello/permutations/distance/ReversalDistance.java
@@ -48,7 +48,7 @@
 * <p>We have not used this for N &gt; 10.  Warning: time to construct distance measure increases factorially.</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 4.2.2021
+* @version 5.13.2021
 */
 public final class ReversalDistance implements NormalizedPermutationDistanceMeasurer {
 
@@ -128,7 +128,7 @@ public int distance(Permutation p1, Permutation p2) {
 		for (int i = 0; i < inv1.length; i++) {
 			r2[i] = inv1[p2.get(i)];
 		}
-		return dist[(new Permutation(r2)).toInteger()];
+		return dist[new Permutation(r2).toInteger()];
 	}	
 	
 	/**
diff --git a/src/org/cicirello/sequences/distance/KendallTauSequenceDistance.java b/src/org/cicirello/sequences/distance/KendallTauSequenceDistance.java
@@ -20,7 +20,6 @@
  */
 package org.cicirello.sequences.distance;
 
-
 import java.util.Arrays;
 import java.util.HashMap;
 import java.util.List;
@@ -77,7 +76,7 @@
  * Industrial Networks and Intelligent Systems, 7(23), Article e1, April 2020.</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 4.2.2021
+ * @version 5.13.2021
  */
 public final class KendallTauSequenceDistance implements SequenceDistanceMeasurer {
 	

Original file line number	Diff line number	Diff line change
`@@ -33,7 +33,7 @@`
`33`	`33`	`* from the motivating case, the case of efficiently generating random indexes into an array.`
`34`	`34`	`*`
`35`	`35`	`* @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>`
`36`		`- * @version 2.13.2021`
	`36`	`+ * @version 5.13.2021`
`37`	`37`	`*`
`38`	`38`	`*/`
`39`	`39`	`public final class RandomIndexer {`
`@@ -152,7 +152,7 @@ public static int nextInt(int bound, Random gen) {`
`152`	`152`	`*/`
`153`	`153`	`public static int nextBiasedInt(int bound) {`
`154`	`154`	`if (bound < 1) throw new IllegalArgumentException("bound must be positive");`
`155`		`- return (int)((long)(ThreadLocalRandom.current().nextInt() & 0x7fffffff) * (long)bound >> 31);`
	`155`	`+ return (int)(((long)(ThreadLocalRandom.current().nextInt() & 0x7fffffff) * (long)bound) >> 31);`
`156`	`156`	`}`
`157`	`157`
`158`	`158`	`/**`
`@@ -178,7 +178,7 @@ public static int nextBiasedInt(int bound) {`
`178`	`178`	`*/`
`179`	`179`	`public static int nextBiasedInt(int bound, SplittableRandom gen) {`
`180`	`180`	`if (bound < 1) throw new IllegalArgumentException("bound must be positive");`
`181`		`- return (int)((long)(gen.nextInt() & 0x7fffffff) * (long)bound >> 31);`
	`181`	`+ return (int)(((long)(gen.nextInt() & 0x7fffffff) * (long)bound) >> 31);`
`182`	`182`	`}`
`183`	`183`
`184`	`184`	`/**`
`@@ -211,7 +211,7 @@ public static int nextBiasedInt(int bound, SplittableRandom gen) {`
`211`	`211`	`*/`
`212`	`212`	`public static int nextBiasedInt(int bound, Random gen) {`
`213`	`213`	`if (bound < 1) throw new IllegalArgumentException("bound must be positive");`
`214`		`- return (int)((long)(gen.nextInt() & 0x7fffffff) * (long)bound >> 31);`
	`214`	`+ return (int)(((long)(gen.nextInt() & 0x7fffffff) * (long)bound) >> 31);`
`215`	`215`	`}`
`216`	`216`
`217`	`217`
Original file line number	Diff line number	Diff line change
`@@ -48,7 +48,7 @@`
`48`	`48`	`* M. G. Kendall, "A new measure of rank correlation," Biometrika, vol. 30, no. 1/2, pp. 81–93, June 1938.</p>`
`49`	`49`	`*`
`50`	`50`	`* @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>`
`51`		`- * @version 4.2.2021`
	`51`	`+ * @version 5.13.2021`
`52`	`52`	`*`
`53`	`53`	`*/`
`54`	`54`	`public final class KendallTauDistance implements NormalizedPermutationDistanceMeasurer {`
`@@ -83,7 +83,7 @@ public int distance(Permutation p1, Permutation p2) {`
`83`	`83`	`@Override`
`84`	`84`	`public int max(int length) {`
`85`	`85`	`if (length <= 1) return 0;`
`86`		`- return length*(length - 1)>>1;`
	`86`	`+ return (length*(length - 1))>>1;`
`87`	`87`	`}`
`88`	`88`
`89`	`89`	`private int countInversions(int[] array) {`