diff --git a/build.xml b/build.xml
index 4984b6d78..09177b03e 100644
--- a/build.xml
+++ b/build.xml
@@ -245,7 +245,7 @@
doctitle="<h1>${component.title} ${component.version}</h1>"
windowtitle="${component.title} ${component.version}"
bottom="Copyright (c) 2003-${current.year} Apache Software Foundation"
- additionalparam="-header '<script type="text/javascript" src="http://cdn.mathjax.org/mathjax/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML"></script>'"
+ additionalparam="-header '<script type="text/javascript" src="http://cdn.mathjax.org/mathjax/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML"></script>'"
classpathref="compile.classpath">
diff --git a/src/test/java/org/apache/commons/math3/distribution/AbstractIntegerDistributionTest.java b/src/test/java/org/apache/commons/math3/distribution/AbstractIntegerDistributionTest.java
index d6f668bb2..6e140eb56 100644
--- a/src/test/java/org/apache/commons/math3/distribution/AbstractIntegerDistributionTest.java
+++ b/src/test/java/org/apache/commons/math3/distribution/AbstractIntegerDistributionTest.java
@@ -30,20 +30,20 @@ public class AbstractIntegerDistributionTest {
@Test
public void testInverseCumulativeProbabilityMethod()
{
- double precision = 0.000000000000001;
- Assert.assertEquals(1, diceDistribution.inverseCumulativeProbability(0));
- Assert.assertEquals(1, diceDistribution.inverseCumulativeProbability((1d-Double.MIN_VALUE)/6d));
- Assert.assertEquals(2, diceDistribution.inverseCumulativeProbability((1d+precision)/6d));
- Assert.assertEquals(2, diceDistribution.inverseCumulativeProbability((2d-Double.MIN_VALUE)/6d));
- Assert.assertEquals(3, diceDistribution.inverseCumulativeProbability((2d+precision)/6d));
- Assert.assertEquals(3, diceDistribution.inverseCumulativeProbability((3d-Double.MIN_VALUE)/6d));
- Assert.assertEquals(4, diceDistribution.inverseCumulativeProbability((3d+precision)/6d));
- Assert.assertEquals(4, diceDistribution.inverseCumulativeProbability((4d-Double.MIN_VALUE)/6d));
- Assert.assertEquals(5, diceDistribution.inverseCumulativeProbability((4d+precision)/6d));
- Assert.assertEquals(5, diceDistribution.inverseCumulativeProbability((5d-precision)/6d));//Can't use Double.MIN
- Assert.assertEquals(6, diceDistribution.inverseCumulativeProbability((5d+precision)/6d));
- Assert.assertEquals(6, diceDistribution.inverseCumulativeProbability((6d-precision)/6d));//Can't use Double.MIN
- Assert.assertEquals(6, diceDistribution.inverseCumulativeProbability((6d)/6d));
+ double precision = 0.000000000000001;
+ Assert.assertEquals(1, diceDistribution.inverseCumulativeProbability(0));
+ Assert.assertEquals(1, diceDistribution.inverseCumulativeProbability((1d-Double.MIN_VALUE)/6d));
+ Assert.assertEquals(2, diceDistribution.inverseCumulativeProbability((1d+precision)/6d));
+ Assert.assertEquals(2, diceDistribution.inverseCumulativeProbability((2d-Double.MIN_VALUE)/6d));
+ Assert.assertEquals(3, diceDistribution.inverseCumulativeProbability((2d+precision)/6d));
+ Assert.assertEquals(3, diceDistribution.inverseCumulativeProbability((3d-Double.MIN_VALUE)/6d));
+ Assert.assertEquals(4, diceDistribution.inverseCumulativeProbability((3d+precision)/6d));
+ Assert.assertEquals(4, diceDistribution.inverseCumulativeProbability((4d-Double.MIN_VALUE)/6d));
+ Assert.assertEquals(5, diceDistribution.inverseCumulativeProbability((4d+precision)/6d));
+ Assert.assertEquals(5, diceDistribution.inverseCumulativeProbability((5d-precision)/6d));//Can't use Double.MIN
+ Assert.assertEquals(6, diceDistribution.inverseCumulativeProbability((5d+precision)/6d));
+ Assert.assertEquals(6, diceDistribution.inverseCumulativeProbability((6d-precision)/6d));//Can't use Double.MIN
+ Assert.assertEquals(6, diceDistribution.inverseCumulativeProbability((6d)/6d));
}
@Test
diff --git a/src/test/java/org/apache/commons/math3/ml/distance/EarthMoversDistanceTest.java b/src/test/java/org/apache/commons/math3/ml/distance/EarthMoversDistanceTest.java
index 01d1e7977..43d3b6f52 100644
--- a/src/test/java/org/apache/commons/math3/ml/distance/EarthMoversDistanceTest.java
+++ b/src/test/java/org/apache/commons/math3/ml/distance/EarthMoversDistanceTest.java
@@ -26,25 +26,25 @@ import org.junit.Test;
*/
public class EarthMoversDistanceTest {
- final DistanceMeasure distance = new EarthMoversDistance();
- final double[] a = { 0.1, 0.3, 0.2, 0.0, 0.25, 0.15 };
- final double[] b = { 0.3, 0.0, 0.4, 0.1, 0.0, 0.2 };
-
- @Test
- public void testZero() {
- Assert.assertEquals(0, distance.compute(a, a), 0d);
- }
-
- @Test
- public void testZero2() {
- final double[] zero = new double[] { 0, 0 };
- Assert.assertEquals(0, distance.compute(zero, zero), 0d);
- }
+ final DistanceMeasure distance = new EarthMoversDistance();
+ final double[] a = { 0.1, 0.3, 0.2, 0.0, 0.25, 0.15 };
+ final double[] b = { 0.3, 0.0, 0.4, 0.1, 0.0, 0.2 };
- @Test
- public void test() {
- double expected = 0.65; //0.2 + 0.1 + 0.1 + 0.2 + 0.05 + 0.0;
- Assert.assertEquals(expected, distance.compute(a, b), 1e-10);
- Assert.assertEquals(expected, distance.compute(b, a), 1e-10);
- }
+ @Test
+ public void testZero() {
+ Assert.assertEquals(0, distance.compute(a, a), 0d);
+ }
+
+ @Test
+ public void testZero2() {
+ final double[] zero = new double[] { 0, 0 };
+ Assert.assertEquals(0, distance.compute(zero, zero), 0d);
+ }
+
+ @Test
+ public void test() {
+ double expected = 0.65; //0.2 + 0.1 + 0.1 + 0.2 + 0.05 + 0.0;
+ Assert.assertEquals(expected, distance.compute(a, b), 1e-10);
+ Assert.assertEquals(expected, distance.compute(b, a), 1e-10);
+ }
}
diff --git a/src/test/java/org/apache/commons/math3/stat/descriptive/SummaryStatisticsTest.java b/src/test/java/org/apache/commons/math3/stat/descriptive/SummaryStatisticsTest.java
index ba77d8709..f104d6542 100644
--- a/src/test/java/org/apache/commons/math3/stat/descriptive/SummaryStatisticsTest.java
+++ b/src/test/java/org/apache/commons/math3/stat/descriptive/SummaryStatisticsTest.java
@@ -338,20 +338,20 @@ public class SummaryStatisticsTest {
@Test
public void testToString() {
- SummaryStatistics u = createSummaryStatistics();
- for (int i = 0; i < 5; i++) {
- u.addValue(i);
- }
- final String[] labels = {"min", "max", "sum", "geometric mean", "variance",
- "population variance", "second moment", "sum of squares", "standard deviation",
- "sum of logs"};
- final double[] values = {u.getMin(), u.getMax(), u.getSum(), u.getGeometricMean(),
- u.getVariance(), u.getPopulationVariance(), u.getSecondMoment(), u.getSumsq(),
- u.getStandardDeviation(), u.getSumOfLogs()};
- final String toString = u.toString();
- Assert.assertTrue(toString.indexOf("n: " + u.getN()) > 0); // getN() returns a long
- for (int i = 0; i < values.length; i++) {
- Assert.assertTrue(toString.indexOf(labels[i] + ": " + String.valueOf(values[i])) > 0);
- }
+ SummaryStatistics u = createSummaryStatistics();
+ for (int i = 0; i < 5; i++) {
+ u.addValue(i);
+ }
+ final String[] labels = {"min", "max", "sum", "geometric mean", "variance",
+ "population variance", "second moment", "sum of squares", "standard deviation",
+ "sum of logs"};
+ final double[] values = {u.getMin(), u.getMax(), u.getSum(), u.getGeometricMean(),
+ u.getVariance(), u.getPopulationVariance(), u.getSecondMoment(), u.getSumsq(),
+ u.getStandardDeviation(), u.getSumOfLogs()};
+ final String toString = u.toString();
+ Assert.assertTrue(toString.indexOf("n: " + u.getN()) > 0); // getN() returns a long
+ for (int i = 0; i < values.length; i++) {
+ Assert.assertTrue(toString.indexOf(labels[i] + ": " + String.valueOf(values[i])) > 0);
+ }
}
}
diff --git a/src/userguide/java/org/apache/commons/math3/userguide/genetics/HelloWorldExample.java b/src/userguide/java/org/apache/commons/math3/userguide/genetics/HelloWorldExample.java
index 00c40e819..b4db00fcd 100644
--- a/src/userguide/java/org/apache/commons/math3/userguide/genetics/HelloWorldExample.java
+++ b/src/userguide/java/org/apache/commons/math3/userguide/genetics/HelloWorldExample.java
@@ -38,16 +38,16 @@ import org.apache.commons.math3.util.FastMath;
import org.apache.commons.math3.util.Precision;
public class HelloWorldExample {
- public static final int POPULATION_SIZE = 1000;
- public static final double CROSSOVER_RATE = 0.9;
- public static final double MUTATION_RATE = 0.03;
- public static final double ELITISM_RATE = 0.1;
- public static final int TOURNAMENT_ARITY = 2;
+ public static final int POPULATION_SIZE = 1000;
+ public static final double CROSSOVER_RATE = 0.9;
+ public static final double MUTATION_RATE = 0.03;
+ public static final double ELITISM_RATE = 0.1;
+ public static final int TOURNAMENT_ARITY = 2;
- public static final String TARGET_STRING = "Hello World!";
- public static final int DIMENSION = TARGET_STRING.length();
+ public static final String TARGET_STRING = "Hello World!";
+ public static final int DIMENSION = TARGET_STRING.length();
- public static void main(String[] args) {
+ public static void main(String[] args) {
long startTime = System.currentTimeMillis();
// initialize a new genetic algorithm
@@ -93,8 +93,8 @@ public class HelloWorldExample {
Chromosome best = finalPopulation.getFittestChromosome();
System.out.println("Generation " + ga.getGenerationsEvolved() + ": " + best.toString());
System.out.println("Total execution time: " + (endTime - startTime) + "ms");
- }
-
+ }
+
private static List randomRepresentation(int length) {
return asList(RandomStringUtils.randomAscii(length));
}
@@ -112,20 +112,20 @@ public class HelloWorldExample {
return new ElitisticListPopulation(popList, 2 * popList.size(), ELITISM_RATE);
}
- /**
- * String Chromosome represented by a list of characters.
- */
- public static class StringChromosome extends AbstractListChromosome {
+ /**
+ * String Chromosome represented by a list of characters.
+ */
+ public static class StringChromosome extends AbstractListChromosome {
- public StringChromosome(List repr) {
- super(repr);
- }
+ public StringChromosome(List repr) {
+ super(repr);
+ }
- public StringChromosome(String str) {
- this(asList(str));
- }
+ public StringChromosome(String str) {
+ this(asList(str));
+ }
- public double fitness() {
+ public double fitness() {
String target = TARGET_STRING;
int f = 0; // start at 0; the best fitness
List chromosome = getRepresentation();
@@ -137,51 +137,51 @@ public class HelloWorldExample {
return f;
}
- @Override
- protected void checkValidity(List repr) throws InvalidRepresentationException {
- for (char c : repr) {
- if (c < 32 || c > 126) {
- throw new InvalidRepresentationException(LocalizedFormats.INVALID_FIXED_LENGTH_CHROMOSOME);
- }
- }
- }
+ @Override
+ protected void checkValidity(List repr) throws InvalidRepresentationException {
+ for (char c : repr) {
+ if (c < 32 || c > 126) {
+ throw new InvalidRepresentationException(LocalizedFormats.INVALID_FIXED_LENGTH_CHROMOSOME);
+ }
+ }
+ }
- public List getStringRepresentation() {
- return getRepresentation();
- }
+ public List getStringRepresentation() {
+ return getRepresentation();
+ }
- @Override
- public StringChromosome newFixedLengthChromosome(List repr) {
- return new StringChromosome(repr);
- }
+ @Override
+ public StringChromosome newFixedLengthChromosome(List repr) {
+ return new StringChromosome(repr);
+ }
- @Override
- public String toString() {
- StringBuffer sb = new StringBuffer();
- for (Character i : getRepresentation()) {
- sb.append(i.charValue());
- }
- return String.format("(f=%s '%s')", getFitness(), sb.toString());
- }
+ @Override
+ public String toString() {
+ StringBuffer sb = new StringBuffer();
+ for (Character i : getRepresentation()) {
+ sb.append(i.charValue());
+ }
+ return String.format("(f=%s '%s')", getFitness(), sb.toString());
+ }
- }
+ }
- private static class RandomCharacterMutation implements MutationPolicy {
- public Chromosome mutate(Chromosome original) {
- if (!(original instanceof StringChromosome)) {
- throw new IllegalArgumentException();
- }
+ private static class RandomCharacterMutation implements MutationPolicy {
+ public Chromosome mutate(Chromosome original) {
+ if (!(original instanceof StringChromosome)) {
+ throw new IllegalArgumentException();
+ }
- StringChromosome strChromosome = (StringChromosome) original;
- List characters = strChromosome.getStringRepresentation();
-
- int mutationIndex = GeneticAlgorithm.getRandomGenerator().nextInt(characters.size());
+ StringChromosome strChromosome = (StringChromosome) original;
+ List characters = strChromosome.getStringRepresentation();
+
+ int mutationIndex = GeneticAlgorithm.getRandomGenerator().nextInt(characters.size());
- List mutatedChromosome = new ArrayList(characters);
- char newValue = (char) (32 + GeneticAlgorithm.getRandomGenerator().nextInt(127 - 32));
- mutatedChromosome.set(mutationIndex, newValue);
+ List mutatedChromosome = new ArrayList(characters);
+ char newValue = (char) (32 + GeneticAlgorithm.getRandomGenerator().nextInt(127 - 32));
+ mutatedChromosome.set(mutationIndex, newValue);
- return strChromosome.newFixedLengthChromosome(mutatedChromosome);
- }
- }
+ return strChromosome.newFixedLengthChromosome(mutatedChromosome);
+ }
+ }
}
diff --git a/src/userguide/java/org/apache/commons/math3/userguide/sofm/ChineseRingsClassifier.java b/src/userguide/java/org/apache/commons/math3/userguide/sofm/ChineseRingsClassifier.java
index d27d0d9c4..871d9d6ae 100644
--- a/src/userguide/java/org/apache/commons/math3/userguide/sofm/ChineseRingsClassifier.java
+++ b/src/userguide/java/org/apache/commons/math3/userguide/sofm/ChineseRingsClassifier.java
@@ -58,7 +58,7 @@ public class ChineseRingsClassifier {
/** Distance function. */
private final DistanceMeasure distance = new EuclideanDistance();
- public static void main(String[] args) {
+ public static void main(String[] args) {
final ChineseRings rings = new ChineseRings(new Vector3D(1, 2, 3),
25, 2,
20, 1,