From d1123894d33922e7c8ca838f9dac9bdceefa3f7a Mon Sep 17 00:00:00 2001 From: Gilles Date: Tue, 29 Dec 2015 01:49:36 +0100 Subject: [PATCH 1/6] Minor change. Make method parameter names consistent (cf. MATH-1307). --- .../commons/math4/random/BaseRandomGenerator.java | 14 +++++++------- 1 file changed, 7 insertions(+), 7 deletions(-) diff --git a/src/main/java/org/apache/commons/math4/random/BaseRandomGenerator.java b/src/main/java/org/apache/commons/math4/random/BaseRandomGenerator.java index da801b03b..bc6442e41 100644 --- a/src/main/java/org/apache/commons/math4/random/BaseRandomGenerator.java +++ b/src/main/java/org/apache/commons/math4/random/BaseRandomGenerator.java @@ -228,17 +228,17 @@ public abstract class BaseRandomGenerator *

* * @param bytes Array in which to put the generated bytes. Cannot be {@code null}. - * @param position Index at which to start inserting the generated bytes. - * @param length Number of bytes to insert. + * @param start Index at which to start inserting the generated bytes. + * @param len Number of bytes to insert. */ private void nextBytesFill(byte[] bytes, - int position, - int length) { - int index = position; // Index of first insertion. + int start, + int len) { + int index = start; // Index of first insertion. // Index of first insertion plus multiple 4 part of length (i.e. length // with two least significant bits unset). - final int indexLoopLimit = index + (length & 0x7ffffffc); + final int indexLoopLimit = index + (len & 0x7ffffffc); // Start filling in the byte array, 4 bytes at a time. while (index < indexLoopLimit) { @@ -249,7 +249,7 @@ public abstract class BaseRandomGenerator bytes[index++] = (byte) (random >>> 24); } - final int indexLimit = position + length; // Index of last insertion + 1. + final int indexLimit = start + len; // Index of last insertion + 1. // Fill in the remaining bytes. if (index < indexLimit) { From fb83ba3fdb46537a36832a900f124d4c400f7ed9 Mon Sep 17 00:00:00 2001 From: Dave Brosius Date: Tue, 29 Dec 2015 13:52:48 -0500 Subject: [PATCH 2/6] push down allocations/calculations to where they are needed --- .../optim/nonlinear/scalar/noderiv/CMAESOptimizer.java | 10 ++++++---- .../math4/stat/interval/ClopperPearsonInterval.java | 4 ++-- 2 files changed, 8 insertions(+), 6 deletions(-) diff --git a/src/main/java/org/apache/commons/math4/optim/nonlinear/scalar/noderiv/CMAESOptimizer.java b/src/main/java/org/apache/commons/math4/optim/nonlinear/scalar/noderiv/CMAESOptimizer.java index f76958563..727fd1848 100644 --- a/src/main/java/org/apache/commons/math4/optim/nonlinear/scalar/noderiv/CMAESOptimizer.java +++ b/src/main/java/org/apache/commons/math4/optim/nonlinear/scalar/noderiv/CMAESOptimizer.java @@ -556,14 +556,16 @@ public class CMAESOptimizer * Checks dimensions and values of boundaries and inputSigma if defined. */ private void checkParameters() { - final double[] init = getStartPoint(); - final double[] lB = getLowerBound(); - final double[] uB = getUpperBound(); - if (inputSigma != null) { + final double[] init = getStartPoint(); + if (inputSigma.length != init.length) { throw new DimensionMismatchException(inputSigma.length, init.length); } + + final double[] lB = getLowerBound(); + final double[] uB = getUpperBound(); + for (int i = 0; i < init.length; i++) { if (inputSigma[i] > uB[i] - lB[i]) { throw new OutOfRangeException(inputSigma[i], 0, uB[i] - lB[i]); diff --git a/src/main/java/org/apache/commons/math4/stat/interval/ClopperPearsonInterval.java b/src/main/java/org/apache/commons/math4/stat/interval/ClopperPearsonInterval.java index 17dc9f55d..bf5d6ad6a 100644 --- a/src/main/java/org/apache/commons/math4/stat/interval/ClopperPearsonInterval.java +++ b/src/main/java/org/apache/commons/math4/stat/interval/ClopperPearsonInterval.java @@ -39,16 +39,16 @@ public class ClopperPearsonInterval implements BinomialConfidenceInterval { final FDistribution distributionLowerBound = new FDistribution(2 * (numberOfTrials - numberOfSuccesses + 1), 2 * numberOfSuccesses); - final double fValueLowerBound = distributionLowerBound.inverseCumulativeProbability(1 - alpha); if (numberOfSuccesses > 0) { + final double fValueLowerBound = distributionLowerBound.inverseCumulativeProbability(1 - alpha); lowerBound = numberOfSuccesses / (numberOfSuccesses + (numberOfTrials - numberOfSuccesses + 1) * fValueLowerBound); } final FDistribution distributionUpperBound = new FDistribution(2 * (numberOfSuccesses + 1), 2 * (numberOfTrials - numberOfSuccesses)); - final double fValueUpperBound = distributionUpperBound.inverseCumulativeProbability(1 - alpha); if (numberOfSuccesses > 0) { + final double fValueUpperBound = distributionUpperBound.inverseCumulativeProbability(1 - alpha); upperBound = (numberOfSuccesses + 1) * fValueUpperBound / (numberOfTrials - numberOfSuccesses + (numberOfSuccesses + 1) * fValueUpperBound); } From e779883b29a67d411493f985de984ffb8088ca05 Mon Sep 17 00:00:00 2001 From: Dave Brosius Date: Tue, 29 Dec 2015 14:21:42 -0500 Subject: [PATCH 3/6] simplify: instanceof checks for nulls --- .../math4/stat/descriptive/rank/PSquarePercentile.java | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/src/main/java/org/apache/commons/math4/stat/descriptive/rank/PSquarePercentile.java b/src/main/java/org/apache/commons/math4/stat/descriptive/rank/PSquarePercentile.java index 79bdc5ead..7ba2d16ae 100644 --- a/src/main/java/org/apache/commons/math4/stat/descriptive/rank/PSquarePercentile.java +++ b/src/main/java/org/apache/commons/math4/stat/descriptive/rank/PSquarePercentile.java @@ -159,7 +159,7 @@ public class PSquarePercentile extends AbstractStorelessUnivariateStatistic boolean result = false; if (this == o) { result = true; - } else if (o != null && o instanceof PSquarePercentile) { + } else if (o instanceof PSquarePercentile) { PSquarePercentile that = (PSquarePercentile) o; boolean isNotNull = markers != null && that.markers != null; boolean isNull = markers == null && that.markers == null; @@ -410,7 +410,7 @@ public class PSquarePercentile extends AbstractStorelessUnivariateStatistic boolean result = false; if (this == o) { result = true; - } else if (o != null && o instanceof Markers) { + } else if (o instanceof Markers) { Markers that = (Markers) o; result = Arrays.deepEquals(markerArray, that.markerArray); } @@ -802,7 +802,7 @@ public class PSquarePercentile extends AbstractStorelessUnivariateStatistic boolean result = false; if (this == o) { result = true; - } else if (o != null && o instanceof Marker) { + } else if (o instanceof Marker) { Marker that = (Marker) o; result = Double.compare(markerHeight, that.markerHeight) == 0; From a71c820baeb91025eaa7f07b172a39500c6f5692 Mon Sep 17 00:00:00 2001 From: Dave Brosius Date: Tue, 29 Dec 2015 14:26:06 -0500 Subject: [PATCH 4/6] use short-circuiting ops --- .../java/org/apache/commons/math4/util/ArithmeticUtils.java | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/src/main/java/org/apache/commons/math4/util/ArithmeticUtils.java b/src/main/java/org/apache/commons/math4/util/ArithmeticUtils.java index 4b5487536..bab02d371 100644 --- a/src/main/java/org/apache/commons/math4/util/ArithmeticUtils.java +++ b/src/main/java/org/apache/commons/math4/util/ArithmeticUtils.java @@ -650,7 +650,7 @@ public final class ArithmeticUtils { */ private static long addAndCheck(long a, long b, Localizable pattern) throws MathArithmeticException { final long result = a + b; - if (!((a ^ b) < 0 | (a ^ result) >= 0)) { + if (!((a ^ b) < 0 || (a ^ result) >= 0)) { throw new MathArithmeticException(pattern, a, b); } return result; From a4eff51bedd73a0ea56afc23b1021187dd03561b Mon Sep 17 00:00:00 2001 From: Dave Brosius Date: Tue, 29 Dec 2015 14:31:35 -0500 Subject: [PATCH 5/6] simplify: remove dead params --- .../commons/math4/analysis/solvers/LaguerreSolver.java | 9 +++------ 1 file changed, 3 insertions(+), 6 deletions(-) diff --git a/src/main/java/org/apache/commons/math4/analysis/solvers/LaguerreSolver.java b/src/main/java/org/apache/commons/math4/analysis/solvers/LaguerreSolver.java index f233d42a0..b038abb96 100644 --- a/src/main/java/org/apache/commons/math4/analysis/solvers/LaguerreSolver.java +++ b/src/main/java/org/apache/commons/math4/analysis/solvers/LaguerreSolver.java @@ -113,7 +113,7 @@ public class LaguerreSolver extends AbstractPolynomialSolver { // Reduce interval if min and initial bracket the root. if (yInitial * yMin < 0) { - return laguerre(min, initial, yMin, yInitial); + return laguerre(min, initial); } // Return the second endpoint if it is good enough. @@ -124,7 +124,7 @@ public class LaguerreSolver extends AbstractPolynomialSolver { // Reduce interval if initial and max bracket the root. if (yInitial * yMax < 0) { - return laguerre(initial, max, yInitial, yMax); + return laguerre(initial, max); } throw new NoBracketingException(min, max, yMin, yMax); @@ -144,12 +144,9 @@ public class LaguerreSolver extends AbstractPolynomialSolver { * * @param lo Lower bound of the search interval. * @param hi Higher bound of the search interval. - * @param fLo Function value at the lower bound of the search interval. - * @param fHi Function value at the higher bound of the search interval. * @return the point at which the function value is zero. */ - private double laguerre(double lo, double hi, - double fLo, double fHi) { + private double laguerre(double lo, double hi) { final Complex c[] = ComplexUtils.convertToComplex(getCoefficients()); final Complex initial = new Complex(0.5 * (lo + hi), 0); From 8f6bedeb724fa78583c26423aaece05cfddc04c9 Mon Sep 17 00:00:00 2001 From: Gilles Date: Thu, 31 Dec 2015 01:31:24 +0100 Subject: [PATCH 6/6] MATH-1309 Constructors should not call overridable methods, even indirectly. --- .../java/org/apache/commons/math4/random/AbstractWell.java | 2 +- .../java/org/apache/commons/math4/random/ISAACRandom.java | 6 +++--- 2 files changed, 4 insertions(+), 4 deletions(-) diff --git a/src/main/java/org/apache/commons/math4/random/AbstractWell.java b/src/main/java/org/apache/commons/math4/random/AbstractWell.java index 88cb2bbee..461e54747 100644 --- a/src/main/java/org/apache/commons/math4/random/AbstractWell.java +++ b/src/main/java/org/apache/commons/math4/random/AbstractWell.java @@ -134,7 +134,7 @@ public abstract class AbstractWell */ private void setSeedInternal(final int[] seed) { if (seed == null) { - setSeed(System.currentTimeMillis() + System.identityHashCode(this)); + setSeedInternal(System.currentTimeMillis() + System.identityHashCode(this)); return; } diff --git a/src/main/java/org/apache/commons/math4/random/ISAACRandom.java b/src/main/java/org/apache/commons/math4/random/ISAACRandom.java index 185710f70..47597495f 100644 --- a/src/main/java/org/apache/commons/math4/random/ISAACRandom.java +++ b/src/main/java/org/apache/commons/math4/random/ISAACRandom.java @@ -131,7 +131,7 @@ public class ISAACRandom * @param seed Seed. */ private void setSeedInternal(int seed) { - setSeed(new int[]{seed}); + setSeedInternal(new int[] { seed }); } /** @@ -140,7 +140,7 @@ public class ISAACRandom * @param seed Seed. */ private void setSeedInternal(long seed) { - setSeed(new int[]{(int) (seed >>> 32), (int) (seed & 0xffffffffL)}); + setSeedInternal(new int[] { (int) (seed >>> 32), (int) (seed & 0xffffffffL) }); } /** @@ -150,7 +150,7 @@ public class ISAACRandom */ private void setSeedInternal(int[] seed) { if (seed == null) { - setSeed(System.currentTimeMillis() + System.identityHashCode(this)); + setSeedInternal(System.currentTimeMillis() + System.identityHashCode(this)); return; } final int seedLen = seed.length;