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From l..@apache.org
Subject svn commit: r1085981 - in /commons/proper/math/trunk/src/main/java/org/apache/commons/math: ./ analysis/integration/ distribution/ linear/ optimization/direct/ special/ stat/clustering/ stat/inference/
Date Sun, 27 Mar 2011 16:32:01 GMT
Author: luc
Date: Sun Mar 27 16:32:01 2011
New Revision: 1085981

URL: http://svn.apache.org/viewvc?rev=1085981&view=rev
Log:
fixed checkstyle warnings (no functional changes)

Modified:
    commons/proper/math/trunk/src/main/java/org/apache/commons/math/MathException.java
    commons/proper/math/trunk/src/main/java/org/apache/commons/math/MathRuntimeException.java
    commons/proper/math/trunk/src/main/java/org/apache/commons/math/analysis/integration/UnivariateRealIntegrator.java
    commons/proper/math/trunk/src/main/java/org/apache/commons/math/analysis/integration/UnivariateRealIntegratorImpl.java
    commons/proper/math/trunk/src/main/java/org/apache/commons/math/distribution/AbstractContinuousDistribution.java
    commons/proper/math/trunk/src/main/java/org/apache/commons/math/distribution/KolmogorovSmirnovDistribution.java
    commons/proper/math/trunk/src/main/java/org/apache/commons/math/distribution/KolmogorovSmirnovDistributionImpl.java
    commons/proper/math/trunk/src/main/java/org/apache/commons/math/linear/AbstractFieldMatrix.java
    commons/proper/math/trunk/src/main/java/org/apache/commons/math/linear/AbstractRealMatrix.java
    commons/proper/math/trunk/src/main/java/org/apache/commons/math/linear/FieldMatrix.java
    commons/proper/math/trunk/src/main/java/org/apache/commons/math/linear/RealMatrix.java
    commons/proper/math/trunk/src/main/java/org/apache/commons/math/optimization/direct/CMAESOptimizer.java
    commons/proper/math/trunk/src/main/java/org/apache/commons/math/special/Beta.java
    commons/proper/math/trunk/src/main/java/org/apache/commons/math/special/Gamma.java
    commons/proper/math/trunk/src/main/java/org/apache/commons/math/stat/clustering/KMeansPlusPlusClusterer.java
    commons/proper/math/trunk/src/main/java/org/apache/commons/math/stat/inference/MannWhitneyUTestImpl.java
    commons/proper/math/trunk/src/main/java/org/apache/commons/math/stat/inference/WilcoxonSignedRankTestImpl.java

Modified: commons/proper/math/trunk/src/main/java/org/apache/commons/math/MathException.java
URL: http://svn.apache.org/viewvc/commons/proper/math/trunk/src/main/java/org/apache/commons/math/MathException.java?rev=1085981&r1=1085980&r2=1085981&view=diff
==============================================================================
--- commons/proper/math/trunk/src/main/java/org/apache/commons/math/MathException.java (original)
+++ commons/proper/math/trunk/src/main/java/org/apache/commons/math/MathException.java Sun
Mar 27 16:32:01 2011
@@ -41,6 +41,9 @@ public class MathException extends Excep
     /** Serializable version identifier. */
     private static final long serialVersionUID = 7428019509644517071L;
 
+    /** Deprecation message. */
+    private static final String DEPRECATION_MESSAGE = "This class is deprecated; calling
this method is a bug.";
+
     /**
      * Pattern used to build the message.
      */
@@ -105,22 +108,22 @@ public class MathException extends Excep
     /** {@inheritDoc} */
     public void addMessage(Localizable pat,
                            Object ... args) {
-        throw new UnsupportedOperationException("This class is deprecated; calling this method
is a bug.");
+        throw new UnsupportedOperationException(DEPRECATION_MESSAGE);
     }
 
     /** {@inheritDoc} */
     public void setContext(String key, Object value) {
-        throw new UnsupportedOperationException("This class is deprecated; calling this method
is a bug.");
+        throw new UnsupportedOperationException(DEPRECATION_MESSAGE);
     }
 
     /** {@inheritDoc} */
     public Object getContext(String key) {
-        throw new UnsupportedOperationException("This class is deprecated; calling this method
is a bug.");
+        throw new UnsupportedOperationException(DEPRECATION_MESSAGE);
     }
 
     /** {@inheritDoc} */
     public Set<String> getContextKeys() {
-        throw new UnsupportedOperationException("This class is deprecated; calling this method
is a bug.");
+        throw new UnsupportedOperationException(DEPRECATION_MESSAGE);
     }
 
     /** Gets the message in a specified locale.

Modified: commons/proper/math/trunk/src/main/java/org/apache/commons/math/MathRuntimeException.java
URL: http://svn.apache.org/viewvc/commons/proper/math/trunk/src/main/java/org/apache/commons/math/MathRuntimeException.java?rev=1085981&r1=1085980&r2=1085981&view=diff
==============================================================================
--- commons/proper/math/trunk/src/main/java/org/apache/commons/math/MathRuntimeException.java
(original)
+++ commons/proper/math/trunk/src/main/java/org/apache/commons/math/MathRuntimeException.java
Sun Mar 27 16:32:01 2011
@@ -42,6 +42,9 @@ public class MathRuntimeException extend
     /** Serializable version identifier. */
     private static final long serialVersionUID = 9058794795027570002L;
 
+    /** Deprecation message. */
+    private static final String DEPRECATION_MESSAGE = "This class is deprecated; calling
this method is a bug.";
+
     /**
      * Pattern used to build the message.
      */
@@ -98,22 +101,22 @@ public class MathRuntimeException extend
     /** {@inheritDoc} */
     public void addMessage(Localizable pat,
                            Object ... args) {
-        throw new UnsupportedOperationException("This class is deprecated; calling this method
is a bug.");
+        throw new UnsupportedOperationException(DEPRECATION_MESSAGE);
     }
 
     /** {@inheritDoc} */
     public void setContext(String key, Object value) {
-        throw new UnsupportedOperationException("This class is deprecated; calling this method
is a bug.");
+        throw new UnsupportedOperationException(DEPRECATION_MESSAGE);
     }
 
     /** {@inheritDoc} */
     public Object getContext(String key) {
-        throw new UnsupportedOperationException("This class is deprecated; calling this method
is a bug.");
+        throw new UnsupportedOperationException(DEPRECATION_MESSAGE);
     }
 
     /** {@inheritDoc} */
     public Set<String> getContextKeys() {
-        throw new UnsupportedOperationException("This class is deprecated; calling this method
is a bug.");
+        throw new UnsupportedOperationException(DEPRECATION_MESSAGE);
     }
 
     /**

Modified: commons/proper/math/trunk/src/main/java/org/apache/commons/math/analysis/integration/UnivariateRealIntegrator.java
URL: http://svn.apache.org/viewvc/commons/proper/math/trunk/src/main/java/org/apache/commons/math/analysis/integration/UnivariateRealIntegrator.java?rev=1085981&r1=1085980&r2=1085981&view=diff
==============================================================================
--- commons/proper/math/trunk/src/main/java/org/apache/commons/math/analysis/integration/UnivariateRealIntegrator.java
(original)
+++ commons/proper/math/trunk/src/main/java/org/apache/commons/math/analysis/integration/UnivariateRealIntegrator.java
Sun Mar 27 16:32:01 2011
@@ -40,14 +40,14 @@ public interface UnivariateRealIntegrato
      *
      * @param count maximum number of iterations
      */
-    public void setMaximalIterationCount(int count);
+    void setMaximalIterationCount(int count);
 
     /**
      * Get the upper limit for the number of iterations.
      *
      * @return the actual upper limit
      */
-    public int getMaximalIterationCount();
+    int getMaximalIterationCount();
 
     /**
      * Set the absolute accuracy.
@@ -64,14 +64,14 @@ public interface UnivariateRealIntegrato
      * @throws IllegalArgumentException if the accuracy can't be achieved by
      * the solver or is otherwise deemed unreasonable.
      */
-    public void setAbsoluteAccuracy(double accuracy);
+    void setAbsoluteAccuracy(double accuracy);
 
     /**
      * Get the actual absolute accuracy.
      *
      * @return the accuracy
      */
-    public double getAbsoluteAccuracy();
+    double getAbsoluteAccuracy();
 
     /**
      * Set the relative accuracy.
@@ -85,13 +85,13 @@ public interface UnivariateRealIntegrato
      *
      * @param accuracy the relative accuracy.
      */
-    public void setRelativeAccuracy(double accuracy);
+    void setRelativeAccuracy(double accuracy);
 
     /**
      * Get the actual relative accuracy.
      * @return the accuracy
      */
-    public double getRelativeAccuracy();
+    double getRelativeAccuracy();
 
     /**
      * Set the lower limit for the number of iterations.

Modified: commons/proper/math/trunk/src/main/java/org/apache/commons/math/analysis/integration/UnivariateRealIntegratorImpl.java
URL: http://svn.apache.org/viewvc/commons/proper/math/trunk/src/main/java/org/apache/commons/math/analysis/integration/UnivariateRealIntegratorImpl.java?rev=1085981&r1=1085980&r2=1085981&view=diff
==============================================================================
--- commons/proper/math/trunk/src/main/java/org/apache/commons/math/analysis/integration/UnivariateRealIntegratorImpl.java
(original)
+++ commons/proper/math/trunk/src/main/java/org/apache/commons/math/analysis/integration/UnivariateRealIntegratorImpl.java
Sun Mar 27 16:32:01 2011
@@ -113,11 +113,11 @@ public abstract class UnivariateRealInte
      * Convenience function for implementations.
      *
      * @param newResult the result to set
-     * @param iterationCount the iteration count to set
+     * @param newCount the iteration count to set
      */
-    protected final void setResult(final double newResult, final int iterationCount) {
+    protected final void setResult(final double newResult, final int newCount) {
         this.result         = newResult;
-        this.iterationCount = iterationCount;
+        this.iterationCount = newCount;
         this.resultComputed = true;
     }
 

Modified: commons/proper/math/trunk/src/main/java/org/apache/commons/math/distribution/AbstractContinuousDistribution.java
URL: http://svn.apache.org/viewvc/commons/proper/math/trunk/src/main/java/org/apache/commons/math/distribution/AbstractContinuousDistribution.java?rev=1085981&r1=1085980&r2=1085981&view=diff
==============================================================================
--- commons/proper/math/trunk/src/main/java/org/apache/commons/math/distribution/AbstractContinuousDistribution.java
(original)
+++ commons/proper/math/trunk/src/main/java/org/apache/commons/math/distribution/AbstractContinuousDistribution.java
Sun Mar 27 16:32:01 2011
@@ -39,10 +39,11 @@ import org.apache.commons.math.util.Fast
 public abstract class AbstractContinuousDistribution
     extends AbstractDistribution
     implements ContinuousDistribution, Serializable {
-    /** Serializable version identifier */
-    private static final long serialVersionUID = -38038050983108802L;
+
     /** Default accuracy. */
     public static final double SOLVER_DEFAULT_ABSOLUTE_ACCURACY = 1e-6;
+    /** Serializable version identifier */
+    private static final long serialVersionUID = -38038050983108802L;
     /**
      * RandomData instance used to generate samples from the distribution
      * @since 2.2

Modified: commons/proper/math/trunk/src/main/java/org/apache/commons/math/distribution/KolmogorovSmirnovDistribution.java
URL: http://svn.apache.org/viewvc/commons/proper/math/trunk/src/main/java/org/apache/commons/math/distribution/KolmogorovSmirnovDistribution.java?rev=1085981&r1=1085980&r2=1085981&view=diff
==============================================================================
--- commons/proper/math/trunk/src/main/java/org/apache/commons/math/distribution/KolmogorovSmirnovDistribution.java
(original)
+++ commons/proper/math/trunk/src/main/java/org/apache/commons/math/distribution/KolmogorovSmirnovDistribution.java
Sun Mar 27 16:32:01 2011
@@ -18,21 +18,21 @@
 package org.apache.commons.math.distribution;
 
 /**
- * Treats the distribution of the two-sided 
+ * Treats the distribution of the two-sided
  * {@code P(D}<sub>{@code n}</sub>{@code < d)}
- * where {@code D}<sub>{@code n}</sub>{@code = sup_x | G(x) - Gn (x) |} for the

+ * where {@code D}<sub>{@code n}</sub>{@code = sup_x | G(x) - Gn (x) |} for the
  * theoretical cdf G and the emperical cdf Gn.
- * 
+ *
  * @version $Revision$ $Date$
  */
 public interface KolmogorovSmirnovDistribution {
-    
+
     /**
      * Calculates {@code P(D}<sub>n</sub> {@code < d)}.
-     * 
+     *
      * @param d statistic
      * @return the two-sided probability of {@code P(D}<sub>n</sub> {@code <
d)}
      */
-    public double cdf(double d);
-    
+    double cdf(double d);
+
 }

Modified: commons/proper/math/trunk/src/main/java/org/apache/commons/math/distribution/KolmogorovSmirnovDistributionImpl.java
URL: http://svn.apache.org/viewvc/commons/proper/math/trunk/src/main/java/org/apache/commons/math/distribution/KolmogorovSmirnovDistributionImpl.java?rev=1085981&r1=1085980&r2=1085981&view=diff
==============================================================================
--- commons/proper/math/trunk/src/main/java/org/apache/commons/math/distribution/KolmogorovSmirnovDistributionImpl.java
(original)
+++ commons/proper/math/trunk/src/main/java/org/apache/commons/math/distribution/KolmogorovSmirnovDistributionImpl.java
Sun Mar 27 16:32:01 2011
@@ -32,26 +32,26 @@ import org.apache.commons.math.linear.Re
 
 /**
  * The default implementation of {@link KolmogorovSmirnovDistribution}.
- * 
- * <p>Treats the distribution of the two-sided 
+ *
+ * <p>Treats the distribution of the two-sided
  * {@code P(D}<sub>{@code n}</sub>{@code < d)}
- * where {@code D}<sub>{@code n}</sub>{@code = sup_x | G(x) - Gn (x) |} for the

+ * where {@code D}<sub>{@code n}</sub>{@code = sup_x | G(x) - Gn (x) |} for the
  * theoretical cdf G and the emperical cdf Gn.</p>
- * 
- * <p>This implementation is based on [1] with certain quick 
+ *
+ * <p>This implementation is based on [1] with certain quick
  * decisions for extreme values given in [2].</p>
- * 
- * <p>In short, when wanting to evaluate {@code P(D}<sub>{@code n}</sub>{@code
< d)}, 
- * the method in [1] is to write {@code d = (k - h) / n} for positive 
- * integer {@code k} and {@code 0 <= h < 1}. Then 
+ *
+ * <p>In short, when wanting to evaluate {@code P(D}<sub>{@code n}</sub>{@code
< d)},
+ * the method in [1] is to write {@code d = (k - h) / n} for positive
+ * integer {@code k} and {@code 0 <= h < 1}. Then
  * {@code P(D}<sub>{@code n}</sub>{@code < d) = (n!/n}<sup>{@code n}</sup>{@code
) * t_kk}
- * where {@code t_kk} is the {@code (k, k)}'th entry in the special 
- * matrix {@code H}<sup>{@code n}</sup>, i.e. {@code H} to the {@code n}'th power.</p>

- * 
+ * where {@code t_kk} is the {@code (k, k)}'th entry in the special
+ * matrix {@code H}<sup>{@code n}</sup>, i.e. {@code H} to the {@code n}'th power.</p>
+ *
  * <p>See also <a href="http://en.wikipedia.org/wiki/Kolmogorov-Smirnov_test">
  * Kolmogorov-Smirnov test on Wikipedia</a> for details.</p>
- * 
- * <p>References: 
+ *
+ * <p>References:
  * <ul>
  * <li>[1] <a href="http://www.jstatsoft.org/v08/i18/">
  * Evaluating Kolmogorov's Distribution</a> by George Marsaglia, Wai
@@ -60,19 +60,20 @@ import org.apache.commons.math.linear.Re
  * Computing the Two-Sided Kolmogorov-Smirnov Distribution</a> by Richard Simard
  * and Pierre L'Ecuyer</li>
  * </ul>
- * Note that [1] contains an error in computing h, refer to 
+ * Note that [1] contains an error in computing h, refer to
  * <a href="https://issues.apache.org/jira/browse/MATH-437">MATH-437</a> for
details.
  * </p>
- * 
+ *
  * @version $Revision$ $Date$
  */
 public class KolmogorovSmirnovDistributionImpl implements KolmogorovSmirnovDistribution,
Serializable {
-    
+
     /** Serializable version identifier. */
     private static final long serialVersionUID = -4670676796862967187L;
 
+    /** Number of observations. */
     private int n;
-    
+
     /**
      * @param n Number of observations
      * @throws NotStrictlyPositiveException
@@ -82,24 +83,24 @@ public class KolmogorovSmirnovDistributi
         if (n <= 0) {
             throw new NotStrictlyPositiveException(LocalizedFormats.NOT_POSITIVE_NUMBER_OF_SAMPLES,
n);
         }
-        
+
         this.n = n;
     }
 
     /**
      * Calculates {@code P(D}<sub>n</sub> {@code < d)} using method described
in
      * [1] with quick decisions for extreme values given in [2] (see above). The
-     * result is not exact as with 
+     * result is not exact as with
      * {@link KolmogorovSmirnovDistributionImpl#cdfExact(double)} because
-     * calculations are based on double rather than 
+     * calculations are based on double rather than
      * {@link org.apache.commons.math.fraction.BigFraction}.
-     * 
+     *
      * @param d statistic
      * @return the two-sided probability of {@code P(D}<sub>n</sub> {@code <
d)}
      * @throws MathArithmeticException
-     *             if algorithm fails to convert {@code h} to a 
+     *             if algorithm fails to convert {@code h} to a
      *             {@link org.apache.commons.math.fraction.BigFraction} in
-     *             expressing {@code d} as {@code (k - h) / m} for integer 
+     *             expressing {@code d} as {@code (k - h) / m} for integer
      *             {@code k, m} and {@code 0 <= h < 1}.
      */
     public double cdf(double d) throws MathArithmeticException {
@@ -108,19 +109,19 @@ public class KolmogorovSmirnovDistributi
 
     /**
      * Calculates {@code P(D}<sub>n</sub> {@code < d)} using method described
in
-     * [1] with quick decisions for extreme values given in [2] (see above). 
-     * The result is exact in the sense that BigFraction/BigReal is used everywhere 
-     * at the expense of very slow execution time. Almost never choose this in 
+     * [1] with quick decisions for extreme values given in [2] (see above).
+     * The result is exact in the sense that BigFraction/BigReal is used everywhere
+     * at the expense of very slow execution time. Almost never choose this in
      * real applications unless you are very sure; this is almost solely for
-     * verification purposes. Normally, you would choose 
+     * verification purposes. Normally, you would choose
      * {@link KolmogorovSmirnovDistributionImpl#cdf(double)}
-     * 
+     *
      * @param d statistic
      * @return the two-sided probability of {@code P(D}<sub>n</sub> {@code <
d)}
      * @throws MathArithmeticException
-     *             if algorithm fails to convert {@code h} to a 
+     *             if algorithm fails to convert {@code h} to a
      *             {@link org.apache.commons.math.fraction.BigFraction} in
-     *             expressing {@code d} as {@code (k - h) / m} for integer 
+     *             expressing {@code d} as {@code (k - h) / m} for integer
      *             {@code k, m} and {@code 0 <= h < 1}.
      */
     public double cdfExact(double d) throws MathArithmeticException {
@@ -130,26 +131,24 @@ public class KolmogorovSmirnovDistributi
     /**
      * Calculates {@code P(D}<sub>n</sub> {@code < d)} using method described
in
      * [1] with quick decisions for extreme values given in [2] (see above).
-     * 
+     *
      * @param d statistic
      * @param exact
      *            whether the probability should be calculated exact using
      *            BigFraction everywhere at the expense of very
      *            slow execution time, or if double should be used convenient
-     *            places to gain speed. Almost never choose {@code true} in 
-     *            real applications unless you are very sure; {@code true} is 
+     *            places to gain speed. Almost never choose {@code true} in
+     *            real applications unless you are very sure; {@code true} is
      *            almost solely for verification purposes.
      * @return the two-sided probability of {@code P(D}<sub>n</sub> {@code <
d)}
      * @throws MathArithmeticException
-     *             if algorithm fails to convert {@code h} to a 
+     *             if algorithm fails to convert {@code h} to a
      *             {@link org.apache.commons.math.fraction.BigFraction} in
-     *             expressing {@code d} as {@code (k - h) / m} for integer 
+     *             expressing {@code d} as {@code (k - h) / m} for integer
      *             {@code k, m} and {@code 0 <= h < 1}.
      */
     public double cdf(double d, boolean exact)
             throws MathArithmeticException {
-        
-        final int n = this.n;
 
         final double ninv = 1 / ((double) n);
         final double ninvhalf = 0.5 * ninv;
@@ -179,25 +178,24 @@ public class KolmogorovSmirnovDistributi
             return 1;
         }
 
-        return (exact) ? this.exactK(d) : this.roundedK(d);
+        return exact ? exactK(d) : roundedK(d);
     }
 
     /**
      * Calculates {@code P(D}<sub>n</sub> {@code < d)} exact using method
      * described in [1] and BigFraction (see above).
-     * 
+     *
      * @param d statistic
      * @return the two-sided probability of {@code P(D}<sub>n</sub> {@code <
d)}
      * @throws MathArithmeticException
-     *             if algorithm fails to convert {@code h} to a 
+     *             if algorithm fails to convert {@code h} to a
      *             {@link org.apache.commons.math.fraction.BigFraction} in
-     *             expressing {@code d} as {@code (k - h) / m} for integer 
+     *             expressing {@code d} as {@code (k - h) / m} for integer
      *             {@code k, m} and {@code 0 <= h < 1}.
      */
     private double exactK(double d)
             throws MathArithmeticException {
 
-        final int n = this.n;
         final int k = (int) Math.ceil(n * d);
 
         final FieldMatrix<BigFraction> H = this.createH(d);
@@ -214,26 +212,24 @@ public class KolmogorovSmirnovDistributi
          * denominator to double and divides afterwards. That gives NaN quite
          * easy. This does not (scale is the number of digits):
          */
-        return pFrac.bigDecimalValue(20, BigDecimal.ROUND_HALF_UP)
-                .doubleValue();
+        return pFrac.bigDecimalValue(20, BigDecimal.ROUND_HALF_UP).doubleValue();
     }
 
     /**
      * Calculates {@code P(D}<sub>n</sub> {@code < d)} using method described
in
      * [1] and doubles (see above).
-     * 
+     *
      * @param d statistic
      * @return the two-sided probability of {@code P(D}<sub>n</sub> {@code <
d)}
      * @throws MathArithmeticException
-     *             if algorithm fails to convert {@code h} to a 
+     *             if algorithm fails to convert {@code h} to a
      *             {@link org.apache.commons.math.fraction.BigFraction} in
-     *             expressing {@code d} as {@code (k - h) / m} for integer 
+     *             expressing {@code d} as {@code (k - h) / m} for integer
      *             {@code k, m} and {@code 0 <= h < 1}.
      */
     private double roundedK(double d)
             throws MathArithmeticException {
-        
-        final int n = this.n;
+
         final int k = (int) Math.ceil(n * d);
         final FieldMatrix<BigFraction> HBigFraction = this.createH(d);
         final int m = HBigFraction.getRowDimension();
@@ -263,28 +259,27 @@ public class KolmogorovSmirnovDistributi
 
     /***
      * Creates {@code H} of size {@code m x m} as described in [1] (see above).
-     * 
+     *
      * @param d statistic
-     *            
+     * @return H matrix
      * @throws MathArithmeticException
-     *             if algorithm fails to convert {@code h} to a 
+     *             if algorithm fails to convert {@code h} to a
      *             {@link org.apache.commons.math.fraction.BigFraction} in
-     *             expressing {@code d} as {@code (k - h) / m} for integer 
+     *             expressing {@code d} as {@code (k - h) / m} for integer
      *             {@code k, m} and {@code 0 <= h < 1}.
      */
     private FieldMatrix<BigFraction> createH(double d)
             throws MathArithmeticException {
 
-        int n = this.n;
         int k = (int) Math.ceil(n * d);
-        
+
         int m = 2 * k - 1;
         double hDouble = k - n * d;
 
         if (hDouble >= 1) {
             throw new ArithmeticException("Could not ");
         }
-        
+
         BigFraction h = null;
 
         try {
@@ -340,8 +335,7 @@ public class KolmogorovSmirnovDistributi
          * 1/2 is sufficient to check:
          */
         if (h.compareTo(BigFraction.ONE_HALF) == 1) {
-            Hdata[m - 1][0] = Hdata[m - 1][0].add(h.multiply(2).subtract(1)
-                    .pow(m));
+            Hdata[m - 1][0] = Hdata[m - 1][0].add(h.multiply(2).subtract(1).pow(m));
         }
 
         /*
@@ -350,7 +344,7 @@ public class KolmogorovSmirnovDistributi
          * put, so only division with (i - j + 1)! is needed in the elements
          * that have 1's. There is no need to calculate (i - j + 1)! and then
          * divide - small steps avoid overflows.
-         * 
+         *
          * Note that i - j + 1 > 0 <=> i + 1 > j instead of j'ing all the way
to
          * m. Also note that it is started at g = 2 because dividing by 1 isn't
          * really necessary.

Modified: commons/proper/math/trunk/src/main/java/org/apache/commons/math/linear/AbstractFieldMatrix.java
URL: http://svn.apache.org/viewvc/commons/proper/math/trunk/src/main/java/org/apache/commons/math/linear/AbstractFieldMatrix.java?rev=1085981&r1=1085980&r2=1085981&view=diff
==============================================================================
--- commons/proper/math/trunk/src/main/java/org/apache/commons/math/linear/AbstractFieldMatrix.java
(original)
+++ commons/proper/math/trunk/src/main/java/org/apache/commons/math/linear/AbstractFieldMatrix.java
Sun Mar 27 16:32:01 2011
@@ -265,21 +265,21 @@ public abstract class AbstractFieldMatri
     public FieldMatrix<T> preMultiply(final FieldMatrix<T> m) {
         return m.multiply(this);
     }
-    
+
     /** {@inheritDoc} */
     public FieldMatrix<T> power(final int p) {
         if (p < 0) {
             throw new IllegalArgumentException("p must be >= 0");
         }
-        
+
         if (!isSquare()) {
             throw new NonSquareMatrixException(getRowDimension(), getColumnDimension());
         }
-        
+
         if (p == 0) {
             return MatrixUtils.createFieldIdentityMatrix(this.getField(), this.getRowDimension());
         }
-        
+
         if (p == 1) {
             return this.copy();
         }
@@ -289,7 +289,7 @@ public abstract class AbstractFieldMatri
         /*
          * Only log_2(p) operations is used by doing as follows:
          * 5^214 = 5^128 * 5^64 * 5^16 * 5^4 * 5^2
-         * 
+         *
          * In general, the same approach is used for A^p.
          */
 

Modified: commons/proper/math/trunk/src/main/java/org/apache/commons/math/linear/AbstractRealMatrix.java
URL: http://svn.apache.org/viewvc/commons/proper/math/trunk/src/main/java/org/apache/commons/math/linear/AbstractRealMatrix.java?rev=1085981&r1=1085980&r2=1085981&view=diff
==============================================================================
--- commons/proper/math/trunk/src/main/java/org/apache/commons/math/linear/AbstractRealMatrix.java
(original)
+++ commons/proper/math/trunk/src/main/java/org/apache/commons/math/linear/AbstractRealMatrix.java
Sun Mar 27 16:32:01 2011
@@ -149,64 +149,64 @@ public abstract class AbstractRealMatrix
     /** {@inheritDoc} */
     public RealMatrix preMultiply(final RealMatrix m) {
         return m.multiply(this);
-    }    
+    }
 
     /** {@inheritDoc} */
     public RealMatrix power(final int p) {
         if (p < 0) {
             throw new IllegalArgumentException("p must be >= 0");
         }
-        
+
         if (!isSquare()) {
             throw new NonSquareMatrixException(getRowDimension(), getColumnDimension());
         }
-        
+
         if (p == 0) {
             return MatrixUtils.createRealIdentityMatrix(this.getRowDimension());
         }
-        
+
         if (p == 1) {
             return this.copy();
         }
 
         final int power = p - 1;
-        
+
         /*
          * Only log_2(p) operations is used by doing as follows:
          * 5^214 = 5^128 * 5^64 * 5^16 * 5^4 * 5^2
-         * 
+         *
          * In general, the same approach is used for A^p.
-         */        
-        
-        final char[] binaryRepresentation = Integer.toBinaryString(power).toCharArray();
      
+         */
+
+        final char[] binaryRepresentation = Integer.toBinaryString(power).toCharArray();
         final ArrayList<Integer> nonZeroPositions = new ArrayList<Integer>();
         int maxI = -1;
-        
-        for (int i = 0; i < binaryRepresentation.length; ++i) {            
+
+        for (int i = 0; i < binaryRepresentation.length; ++i) {
             if (binaryRepresentation[i] == '1') {
                 final int pos = binaryRepresentation.length - i - 1;
                 nonZeroPositions.add(pos);
-                
+
                 // The positions are taken in turn, so maxI is only changed once
                 if (maxI == -1) {
                     maxI = pos;
                 }
             }
         }
-        
+
         RealMatrix[] results = new RealMatrix[maxI + 1];
         results[0] = this.copy();
-        
+
         for (int i = 1; i <= maxI; ++i) {
             results[i] = results[i-1].multiply(results[i-1]);
         }
-        
+
         RealMatrix result = this.copy();
-        
+
         for (Integer i : nonZeroPositions) {
             result = result.multiply(results[i]);
-        }        
-        
+        }
+
         return result;
     }
 

Modified: commons/proper/math/trunk/src/main/java/org/apache/commons/math/linear/FieldMatrix.java
URL: http://svn.apache.org/viewvc/commons/proper/math/trunk/src/main/java/org/apache/commons/math/linear/FieldMatrix.java?rev=1085981&r1=1085980&r2=1085981&view=diff
==============================================================================
--- commons/proper/math/trunk/src/main/java/org/apache/commons/math/linear/FieldMatrix.java
(original)
+++ commons/proper/math/trunk/src/main/java/org/apache/commons/math/linear/FieldMatrix.java
Sun Mar 27 16:32:01 2011
@@ -116,16 +116,16 @@ public interface FieldMatrix<T extends F
     FieldMatrix<T> preMultiply(FieldMatrix<T> m);
 
     /**
-     * Returns the result multiplying this with itself <code>p</code> times.

-     * Depending on the type of the field elements, T, 
-     * instability for high powers might occur. 
+     * Returns the result multiplying this with itself <code>p</code> times.
+     * Depending on the type of the field elements, T,
+     * instability for high powers might occur.
      * @param      p raise this to power p
      * @return     this^p
      * @throws     IllegalArgumentException if p < 0
      *             NonSquareMatrixException if the matrix is not square
      */
     FieldMatrix<T> power(final int p);
-    
+
     /**
      * Returns matrix entries as a two-dimensional array.
      *

Modified: commons/proper/math/trunk/src/main/java/org/apache/commons/math/linear/RealMatrix.java
URL: http://svn.apache.org/viewvc/commons/proper/math/trunk/src/main/java/org/apache/commons/math/linear/RealMatrix.java?rev=1085981&r1=1085980&r2=1085981&view=diff
==============================================================================
--- commons/proper/math/trunk/src/main/java/org/apache/commons/math/linear/RealMatrix.java
(original)
+++ commons/proper/math/trunk/src/main/java/org/apache/commons/math/linear/RealMatrix.java
Sun Mar 27 16:32:01 2011
@@ -98,10 +98,10 @@ public interface RealMatrix extends AnyM
      *             if rowDimension(this) != columnDimension(m)
      */
     RealMatrix preMultiply(RealMatrix m);
-    
+
     /**
-     * Returns the result multiplying this with itself <code>p</code> times.

-     * Depending on the underlying storage, instability for high powers might occur. 
+     * Returns the result multiplying this with itself <code>p</code> times.
+     * Depending on the underlying storage, instability for high powers might occur.
      * @param      p raise this to power p
      * @return     this^p
      * @throws     IllegalArgumentException if p < 0

Modified: commons/proper/math/trunk/src/main/java/org/apache/commons/math/optimization/direct/CMAESOptimizer.java
URL: http://svn.apache.org/viewvc/commons/proper/math/trunk/src/main/java/org/apache/commons/math/optimization/direct/CMAESOptimizer.java?rev=1085981&r1=1085980&r2=1085981&view=diff
==============================================================================
--- commons/proper/math/trunk/src/main/java/org/apache/commons/math/optimization/direct/CMAESOptimizer.java
(original)
+++ commons/proper/math/trunk/src/main/java/org/apache/commons/math/optimization/direct/CMAESOptimizer.java
Sun Mar 27 16:32:01 2011
@@ -826,19 +826,26 @@ public class CMAESOptimizer extends
     private class FitnessFunction {
 
         /** Determines the penalty for boundary violations */
-        private double valueRange = 1.0;
+        private double valueRange;
         /**
          * Flag indicating whether the objective variables are forced into their
          * bounds if defined
          */
-        private boolean isRepairMode = true;
+        private boolean isRepairMode;
+
+        /** Simple constructor.
+         */
+        public FitnessFunction() {
+            valueRange = 1.0;
+            isRepairMode = true;
+        }
 
         /**
          * @param x
          *            Original objective variables.
          * @return Normalized objective variables.
          */
-        private double[] encode(final double[] x) {
+        public double[] encode(final double[] x) {
             if (boundaries == null)
                 return x;
             double[] res = new double[x.length];
@@ -854,7 +861,7 @@ public class CMAESOptimizer extends
          *            Normalized objective variables.
          * @return Original objective variables.
          */
-        private double[] decode(final double[] x) {
+        public double[] decode(final double[] x) {
             if (boundaries == null)
                 return x;
             double[] res = new double[x.length];
@@ -870,7 +877,7 @@ public class CMAESOptimizer extends
          *            Normalized objective variables.
          * @return Objective value + penalty for violated bounds.
          */
-        private double value(final double[] point) {
+        public double value(final double[] point) {
             double value;
             if (boundaries != null && isRepairMode) {
                 double[] repaired = repair(point);
@@ -888,7 +895,7 @@ public class CMAESOptimizer extends
          *            Normalized objective variables.
          * @return True if in bounds
          */
-        private boolean isFeasible(final double[] x) {
+        public boolean isFeasible(final double[] x) {
             if (boundaries == null)
                 return true;
             for (int i = 0; i < x.length; i++) {
@@ -904,7 +911,7 @@ public class CMAESOptimizer extends
          * @param valueRange
          *            Adjusts the penalty computation.
          */
-        private void setValueRange(double valueRange) {
+        public void setValueRange(double valueRange) {
             this.valueRange = valueRange;
         }
 

Modified: commons/proper/math/trunk/src/main/java/org/apache/commons/math/special/Beta.java
URL: http://svn.apache.org/viewvc/commons/proper/math/trunk/src/main/java/org/apache/commons/math/special/Beta.java?rev=1085981&r1=1085980&r2=1085981&view=diff
==============================================================================
--- commons/proper/math/trunk/src/main/java/org/apache/commons/math/special/Beta.java (original)
+++ commons/proper/math/trunk/src/main/java/org/apache/commons/math/special/Beta.java Sun
Mar 27 16:32:01 2011
@@ -45,7 +45,6 @@ public class Beta {
      * @return the regularized beta function I(x, a, b).
      * @throws org.apache.commons.math.exception.MaxCountExceededException
      * if the algorithm fails to converge.
-     * @throws MathException if the algorithm fails to converge.
      */
     public static double regularizedBeta(double x, double a, double b) {
         return regularizedBeta(x, a, b, DEFAULT_EPSILON, Integer.MAX_VALUE);

Modified: commons/proper/math/trunk/src/main/java/org/apache/commons/math/special/Gamma.java
URL: http://svn.apache.org/viewvc/commons/proper/math/trunk/src/main/java/org/apache/commons/math/special/Gamma.java?rev=1085981&r1=1085980&r2=1085981&view=diff
==============================================================================
--- commons/proper/math/trunk/src/main/java/org/apache/commons/math/special/Gamma.java (original)
+++ commons/proper/math/trunk/src/main/java/org/apache/commons/math/special/Gamma.java Sun
Mar 27 16:32:01 2011
@@ -191,7 +191,7 @@ public class Gamma {
      * @param a the a parameter.
      * @param x the value.
      * @return the regularized gamma function Q(a, x)
-     * @throws MathException if the algorithm fails to converge.
+     * @throws MaxCountExceededException if the algorithm fails to converge.
      */
     public static double regularizedGammaQ(double a, double x) {
         return regularizedGammaQ(a, x, DEFAULT_EPSILON, Integer.MAX_VALUE);

Modified: commons/proper/math/trunk/src/main/java/org/apache/commons/math/stat/clustering/KMeansPlusPlusClusterer.java
URL: http://svn.apache.org/viewvc/commons/proper/math/trunk/src/main/java/org/apache/commons/math/stat/clustering/KMeansPlusPlusClusterer.java?rev=1085981&r1=1085980&r2=1085981&view=diff
==============================================================================
--- commons/proper/math/trunk/src/main/java/org/apache/commons/math/stat/clustering/KMeansPlusPlusClusterer.java
(original)
+++ commons/proper/math/trunk/src/main/java/org/apache/commons/math/stat/clustering/KMeansPlusPlusClusterer.java
Sun Mar 27 16:32:01 2011
@@ -100,12 +100,12 @@ public class KMeansPlusPlusClusterer<T e
 
         // sanity checks
         MathUtils.checkNotNull(points);
-        
+
         // number of clusters has to be smaller or equal the number of data points
         if (points.size() < k) {
             throw new NumberIsTooSmallException(points.size(), k, false);
         }
-        
+
         // create the initial clusters
         List<Cluster<T>> clusters = chooseInitialCenters(points, k, random);
         assignPointsToClusters(clusters, points);

Modified: commons/proper/math/trunk/src/main/java/org/apache/commons/math/stat/inference/MannWhitneyUTestImpl.java
URL: http://svn.apache.org/viewvc/commons/proper/math/trunk/src/main/java/org/apache/commons/math/stat/inference/MannWhitneyUTestImpl.java?rev=1085981&r1=1085980&r2=1085981&view=diff
==============================================================================
--- commons/proper/math/trunk/src/main/java/org/apache/commons/math/stat/inference/MannWhitneyUTestImpl.java
(original)
+++ commons/proper/math/trunk/src/main/java/org/apache/commons/math/stat/inference/MannWhitneyUTestImpl.java
Sun Mar 27 16:32:01 2011
@@ -30,6 +30,8 @@ import org.apache.commons.math.util.Fast
  * @version $Revision$ $Date$
  */
 public class MannWhitneyUTestImpl implements MannWhitneyUTest {
+
+    /** Ranking algorithm. */
     private NaturalRanking naturalRanking;
 
     /**
@@ -59,8 +61,8 @@ public class MannWhitneyUTestImpl implem
     /**
      * Ensures that the provided arrays fulfills the assumptions.
      *
-     * @param x
-     * @param y
+     * @param x first sample
+     * @param y second sample
      * @throws IllegalArgumentException
      *             if assumptions are not met
      */
@@ -85,7 +87,12 @@ public class MannWhitneyUTestImpl implem
         }
     }
 
-    private double[] concatinateSamples(final double[] x, final double[] y) {
+    /** Concatenate the samples into one array.
+     * @param x first sample
+     * @param y second sample
+     * @return concatenated array
+     */
+    private double[] concatenateSamples(final double[] x, final double[] y) {
         final double[] z = new double[x.length + y.length];
 
         System.arraycopy(x, 0, z, 0, x.length);
@@ -110,7 +117,7 @@ public class MannWhitneyUTestImpl implem
 
         ensureDataConformance(x, y);
 
-        final double[] z = concatinateSamples(x, y);
+        final double[] z = concatenateSamples(x, y);
         final double[] ranks = naturalRanking.rank(z);
 
         double sumRankX = 0;

Modified: commons/proper/math/trunk/src/main/java/org/apache/commons/math/stat/inference/WilcoxonSignedRankTestImpl.java
URL: http://svn.apache.org/viewvc/commons/proper/math/trunk/src/main/java/org/apache/commons/math/stat/inference/WilcoxonSignedRankTestImpl.java?rev=1085981&r1=1085980&r2=1085981&view=diff
==============================================================================
--- commons/proper/math/trunk/src/main/java/org/apache/commons/math/stat/inference/WilcoxonSignedRankTestImpl.java
(original)
+++ commons/proper/math/trunk/src/main/java/org/apache/commons/math/stat/inference/WilcoxonSignedRankTestImpl.java
Sun Mar 27 16:32:01 2011
@@ -29,6 +29,8 @@ import org.apache.commons.math.util.Fast
  * @version $Revision$ $Date$
  */
 public class WilcoxonSignedRankTestImpl implements WilcoxonSignedRankTest {
+
+    /** Ranking algorithm. */
     private NaturalRanking naturalRanking;
 
     /**
@@ -58,8 +60,8 @@ public class WilcoxonSignedRankTestImpl 
     /**
      * Ensures that the provided arrays fulfills the assumptions.
      *
-     * @param x
-     * @param y
+     * @param x first sample
+     * @param y second sample
      * @throws IllegalArgumentException
      *             if assumptions are not met
      */
@@ -87,13 +89,11 @@ public class WilcoxonSignedRankTestImpl 
     /**
      * Calculates y[i] - x[i] for all i
      *
-     * @param x
-     * @param y
-     * @throws IllegalArgumentException
-     *             if assumptions are not met
+     * @param x first sample
+     * @param y second sample
+     * @return z = y - x
      */
-    private double[] calculateDifferences(final double[] x, final double[] y)
-            throws IllegalArgumentException {
+    private double[] calculateDifferences(final double[] x, final double[] y) {
 
         final double[] z = new double[x.length];
 
@@ -107,7 +107,8 @@ public class WilcoxonSignedRankTestImpl 
     /**
      * Calculates |z[i]| for all i
      *
-     * @param z
+     * @param z sample
+     * @return |z|
      * @throws IllegalArgumentException
      *             if assumptions are not met
      */



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