diff --git a/.muse.toml b/.muse.toml
new file mode 100644
index 00000000..72d0f660
--- /dev/null
+++ 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/
+"""
\ No newline at end of file
diff --git a/src/org/cicirello/math/MathFunctions.java b/src/org/cicirello/math/MathFunctions.java
index 29c6c685..f3e9b030 100644
--- 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 Vincent A. Cicirello, https://www.cicirello.org/
- * @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
index 7d79f692..25af34b3 100644
--- 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 Vincent A. Cicirello, https://www.cicirello.org/
- * @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
index d20627a4..11d69060 100644
--- 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 Vincent A. Cicirello, https://www.cicirello.org/
- * @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
index 7076ea61..7e81ab05 100644
--- 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, .
+ * Copyright 2018-2021 Vincent A. Cicirello, .
*
* This file is part of JavaPermutationTools (https://jpt.cicirello.org/).
*
@@ -26,7 +26,7 @@
* Utility class of basic statistics.
*
* @author Vincent A. Cicirello, https://www.cicirello.org/
- * @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
index 49ed5899..1233801c 100644
--- 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.
*
* @author Vincent A. Cicirello, https://www.cicirello.org/
- * @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
index 8c8b5610..93676ce5 100644
--- a/src/org/cicirello/permutations/distance/ReversalDistance.java
+++ b/src/org/cicirello/permutations/distance/ReversalDistance.java
@@ -48,7 +48,7 @@
* We have not used this for N > 10. Warning: time to construct distance measure increases factorially.
*
* @author Vincent A. Cicirello, https://www.cicirello.org/
-* @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
index ab79aa45..cc65b70f 100644
--- 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.
*
* @author Vincent A. Cicirello, https://www.cicirello.org/
- * @version 4.2.2021
+ * @version 5.13.2021
*/
public final class KendallTauSequenceDistance implements SequenceDistanceMeasurer {