Fixed checkstyle, javadoc, findbugs and eclipse warnings.

git-svn-id: https://svn.apache.org/repos/asf/commons/proper/math/trunk@1139915 13f79535-47bb-0310-9956-ffa450edef68

src/main/java/org/apache/commons/math/filter/KalmanFilter.java

@@ -81,8 +81,6 @@ import org.apache.commons.math.util.MathUtils;
  * @version $Id$
  */
 public class KalmanFilter {
-    /** Serializable version identifier. */
-    private static final long serialVersionUID = 4878026651422612760L;
     /** The process model used by this filter instance. */
     private final ProcessModel processModel;
     /** The measurement model used by this filter instance. */
@@ -343,8 +341,8 @@ public class KalmanFilter {
      */
     public void correct(final RealVector z) {
         // sanity checks
-        if (z != null &&
-            z.getDimension() != measurementMatrix.getRowDimension()) {
+        MathUtils.checkNotNull(z);
+        if (z.getDimension() != measurementMatrix.getRowDimension()) {
             throw new DimensionMismatchException(z.getDimension(),
                                                  measurementMatrix.getRowDimension());
         }

src/main/java/org/apache/commons/math/geometry/euclidean/twod/PolygonsSet.java

@@ -345,6 +345,7 @@ public class PolygonsSet extends AbstractRegion<Euclidean2D, Euclidean1D> {
 
     }
 
+    /** Private extension of Segment allowing comparison. */
     private static class ComparableSegment extends Segment implements Comparable<ComparableSegment> {
 
         /** Sorting key. */

src/main/java/org/apache/commons/math/geometry/partitioning/AbstractRegion.java

@@ -133,9 +133,6 @@ public abstract class AbstractRegion<S extends Space, T extends Space> implement
 
     }
 
-    /** {@inheritDoc} */
-    public abstract AbstractRegion<S, T> buildNew(BSPTree<S> newTree);
-
     /** Build a convex region from an array of bounding hyperplanes.
      * @param hyperplanes array of bounding hyperplanes (if null, an
      * empty region will be built)
@@ -164,6 +161,9 @@ public abstract class AbstractRegion<S extends Space, T extends Space> implement
 
     }
 
+    /** {@inheritDoc} */
+    public abstract AbstractRegion<S, T> buildNew(BSPTree<S> newTree);
+
     /** Recursively build a tree by inserting cut sub-hyperplanes.
      * @param node current tree node (it is a leaf node at the beginning
      * of the call)

src/main/java/org/apache/commons/math/optimization/direct/CMAESOptimizer.java

@@ -855,6 +855,30 @@ public class CMAESOptimizer extends
         public int compareTo(DoubleIndex o) {
             return Double.compare(value, o.value);
         }
+
+        /** {@inheritDoc} */
+        @Override
+        public boolean equals(Object other) {
+
+            if (this == other) {
+                return true;
+            }
+
+            if (other instanceof DoubleIndex) {
+                return Double.compare(value, ((DoubleIndex) other).value) == 0;
+            }
+
+            return false;
+
+        }
+
+        /** {@inheritDoc} */
+        @Override
+        public int hashCode() {
+            long bits = Double.doubleToLongBits(value);
+            return (int) ((1438542 ^ (bits >>> 32) ^ bits) & 0xffffffff);
+        }
+
     }
 
     /**

src/main/java/org/apache/commons/math/stat/clustering/KMeansPlusPlusClusterer.java

@@ -89,8 +89,9 @@ public class KMeansPlusPlusClusterer<T extends Clusterable<T>> {
      *
      * @param points the points to cluster
      * @param k the number of clusters to split the data into
-     * @param maxIterations the maximum number of iterations to run the algorithm
-     *     for.  If negative, no maximum will be used
+     * @param numTrials number of trial runs
+     * @param maxIterationsPerTrial the maximum number of iterations to run the algorithm
+     *     for at each trial run.  If negative, no maximum will be used
      * @return a list of clusters containing the points
      * @throws MathIllegalArgumentException if the data points are null or the number
      *     of clusters is larger than the number of data points

src/main/java/org/apache/commons/math/stat/inference/ChiSquareTestImpl.java

@@ -356,7 +356,7 @@ public class ChiSquareTestImpl implements UnknownDistributionChiSquareTest {
      * Check all entries of the input array are strictly positive.
      *
      * @param in Array to be tested.
-     * @exception NotStrictlyPositiveException if one entry is not positive.
+     * @exception MathIllegalArgumentException if one entry is not positive.
      */
     private void checkPositive(double[] in) {
         for (int i = 0; i < in.length; i++) {
@@ -372,7 +372,7 @@ public class ChiSquareTestImpl implements UnknownDistributionChiSquareTest {
      * Check all entries of the input array are >= 0.
      *
      * @param in Array to be tested.
-     * @exception NotPositiveException if one entry is negative.
+     * @exception MathIllegalArgumentException if one entry is negative.
      */
     private void checkNonNegative(long[] in) {
         for (int i = 0; i < in.length; i++) {
@@ -388,7 +388,7 @@ public class ChiSquareTestImpl implements UnknownDistributionChiSquareTest {
      * Check all entries of the input array are >= 0.
      *
      * @param in Array to be tested.
-     * @exception NotPositiveException if one entry is negative.
+     * @exception MathIllegalArgumentException if one entry is negative.
      */
     private void checkNonNegative(long[][] in) {
         for (int i = 0; i < in.length; i ++) {