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From l..@apache.org
Subject svn commit: r1178235 - in /commons/proper/math/trunk/src: main/java/org/apache/commons/math/ main/java/org/apache/commons/math/analysis/integration/ main/java/org/apache/commons/math/analysis/polynomials/ main/java/org/apache/commons/math/distribution/...
Date Sun, 02 Oct 2011 19:43:18 GMT
Author: luc
Date: Sun Oct  2 19:43:17 2011
New Revision: 1178235

URL: http://svn.apache.org/viewvc?rev=1178235&view=rev
Log:
Fixed about 90 checkstyle errors.

The errors were mainly trailing blanks, missing javadoc, wrong javadoc
parameters, hidden variables ...

Modified:
    commons/proper/math/trunk/src/main/java/org/apache/commons/math/Field.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/analysis/polynomials/PolynomialsUtils.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/fraction/BigFraction.java
    commons/proper/math/trunk/src/main/java/org/apache/commons/math/geometry/partitioning/BSPTree.java
    commons/proper/math/trunk/src/main/java/org/apache/commons/math/ode/AbstractIntegrator.java
    commons/proper/math/trunk/src/main/java/org/apache/commons/math/ode/EquationsMapper.java
    commons/proper/math/trunk/src/main/java/org/apache/commons/math/ode/ExpandableStatefulODE.java
    commons/proper/math/trunk/src/main/java/org/apache/commons/math/ode/JacobianMatrices.java
    commons/proper/math/trunk/src/main/java/org/apache/commons/math/ode/MainStateJacobianProvider.java
    commons/proper/math/trunk/src/main/java/org/apache/commons/math/ode/MultistepIntegrator.java
    commons/proper/math/trunk/src/main/java/org/apache/commons/math/ode/ParameterConfiguration.java
    commons/proper/math/trunk/src/main/java/org/apache/commons/math/ode/ParameterJacobianProvider.java
    commons/proper/math/trunk/src/main/java/org/apache/commons/math/ode/ParameterJacobianWrapper.java
    commons/proper/math/trunk/src/main/java/org/apache/commons/math/ode/ParameterizedODE.java
    commons/proper/math/trunk/src/main/java/org/apache/commons/math/ode/ParameterizedWrapper.java
    commons/proper/math/trunk/src/main/java/org/apache/commons/math/ode/nonstiff/AdaptiveStepsizeIntegrator.java
    commons/proper/math/trunk/src/main/java/org/apache/commons/math/ode/nonstiff/DormandPrince853StepInterpolator.java
    commons/proper/math/trunk/src/main/java/org/apache/commons/math/ode/sampling/AbstractStepInterpolator.java
    commons/proper/math/trunk/src/main/java/org/apache/commons/math/stat/correlation/StorelessBivariateCovariance.java
    commons/proper/math/trunk/src/main/java/org/apache/commons/math/stat/correlation/StorelessCovariance.java
    commons/proper/math/trunk/src/main/java/org/apache/commons/math/stat/descriptive/package-info.java
    commons/proper/math/trunk/src/main/java/org/apache/commons/math/util/FastMath.java
    commons/proper/math/trunk/src/main/java/org/apache/commons/math/util/FastMathCalc.java
    commons/proper/math/trunk/src/test/java/org/apache/commons/math/ode/sampling/DummyStepInterpolatorTest.java

Modified: commons/proper/math/trunk/src/main/java/org/apache/commons/math/Field.java
URL: http://svn.apache.org/viewvc/commons/proper/math/trunk/src/main/java/org/apache/commons/math/Field.java?rev=1178235&r1=1178234&r2=1178235&view=diff
==============================================================================
--- commons/proper/math/trunk/src/main/java/org/apache/commons/math/Field.java (original)
+++ commons/proper/math/trunk/src/main/java/org/apache/commons/math/Field.java Sun Oct  2 19:43:17 2011
@@ -49,8 +49,8 @@ public interface Field<T> {
     T getOne();
 
     /**
-     * Returns the runtime class of the FieldElement. 
-     * 
+     * Returns the runtime class of the FieldElement.
+     *
      * @return The {@code Class} object that represents the runtime
      *         class of this object.
      */

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=1178235&r1=1178234&r2=1178235&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 Oct  2 19:43:17 2011
@@ -214,23 +214,23 @@ public abstract class UnivariateRealInte
      *
      * @param maxEval Maximum number of evaluations.
      * @param f the integrand function
-     * @param min the min bound for the interval
-     * @param max the upper bound for the interval
+     * @param lower the min bound for the interval
+     * @param upper the upper bound for the interval
      * @throws NullArgumentException if {@code f} is {@code null}.
      * @throws MathIllegalArgumentException if {@code min >= max}.
      */
     protected void setup(final int maxEval,
                          final UnivariateRealFunction f,
-                         final double min, final double max)
+                         final double lower, final double upper)
         throws NullArgumentException, MathIllegalArgumentException {
 
         // Checks.
         MathUtils.checkNotNull(f);
-        UnivariateRealSolverUtils.verifyInterval(min, max);
+        UnivariateRealSolverUtils.verifyInterval(lower, upper);
 
         // Reset.
-        this.min = min;
-        this.max = max;
+        this.min = lower;
+        this.max = upper;
         function = f;
         evaluations.setMaximalCount(maxEval);
         evaluations.resetCount();
@@ -240,12 +240,12 @@ public abstract class UnivariateRealInte
 
     /** {@inheritDoc} */
     public double integrate(final int maxEval, final UnivariateRealFunction f,
-                            final double min, final double max)
+                            final double lower, final double upper)
         throws TooManyEvaluationsException, MaxCountExceededException,
                MathIllegalArgumentException, NullArgumentException {
 
         // Initialization.
-        setup(maxEval, f, min, max);
+        setup(maxEval, f, lower, upper);
 
         // Perform computation.
         return doIntegrate();

Modified: commons/proper/math/trunk/src/main/java/org/apache/commons/math/analysis/polynomials/PolynomialsUtils.java
URL: http://svn.apache.org/viewvc/commons/proper/math/trunk/src/main/java/org/apache/commons/math/analysis/polynomials/PolynomialsUtils.java?rev=1178235&r1=1178234&r2=1178235&view=diff
==============================================================================
--- commons/proper/math/trunk/src/main/java/org/apache/commons/math/analysis/polynomials/PolynomialsUtils.java (original)
+++ commons/proper/math/trunk/src/main/java/org/apache/commons/math/analysis/polynomials/PolynomialsUtils.java Sun Oct  2 19:43:17 2011
@@ -268,7 +268,7 @@ public class PolynomialsUtils {
     }
 
     /** Interface for recurrence coefficients generation. */
-    private static interface RecurrenceCoefficientsGenerator {
+    private interface RecurrenceCoefficientsGenerator {
         /**
          * Generate recurrence coefficients.
          * @param k highest degree of the polynomials used in the recurrence

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=1178235&r1=1178234&r2=1178235&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 Oct  2 19:43:17 2011
@@ -272,7 +272,7 @@ public class KolmogorovSmirnovDistributi
      *             {@code k, m} and {@code 0 <= h < 1}.
      */
     private FieldMatrix<BigFraction> createH(double d)
-            throws MathArithmeticException {
+            throws NumberIsTooLargeException, FractionConversionException {
 
         int k = (int) Math.ceil(n * d);
 

Modified: commons/proper/math/trunk/src/main/java/org/apache/commons/math/fraction/BigFraction.java
URL: http://svn.apache.org/viewvc/commons/proper/math/trunk/src/main/java/org/apache/commons/math/fraction/BigFraction.java?rev=1178235&r1=1178234&r2=1178235&view=diff
==============================================================================
--- commons/proper/math/trunk/src/main/java/org/apache/commons/math/fraction/BigFraction.java (original)
+++ commons/proper/math/trunk/src/main/java/org/apache/commons/math/fraction/BigFraction.java Sun Oct  2 19:43:17 2011
@@ -167,7 +167,7 @@ public class BigFraction
      * @param value the double value to convert to a fraction.
      * @exception MathIllegalArgumentException if value is NaN or infinite
      */
-    public BigFraction(final double value) throws IllegalArgumentException {
+    public BigFraction(final double value) throws MathIllegalArgumentException {
         if (Double.isNaN(value)) {
             throw new MathIllegalArgumentException(LocalizedFormats.NAN_VALUE_CONVERSION);
         }

Modified: commons/proper/math/trunk/src/main/java/org/apache/commons/math/geometry/partitioning/BSPTree.java
URL: http://svn.apache.org/viewvc/commons/proper/math/trunk/src/main/java/org/apache/commons/math/geometry/partitioning/BSPTree.java?rev=1178235&r1=1178234&r2=1178235&view=diff
==============================================================================
--- commons/proper/math/trunk/src/main/java/org/apache/commons/math/geometry/partitioning/BSPTree.java (original)
+++ commons/proper/math/trunk/src/main/java/org/apache/commons/math/geometry/partitioning/BSPTree.java Sun Oct  2 19:43:17 2011
@@ -429,7 +429,7 @@ public class BSPTree<S extends Space> {
      * difference and symmetric difference (exclusive or).</p>
      * @param <S> Type of the space.
      */
-    public static interface LeafMerger<S extends Space> {
+    public interface LeafMerger<S extends Space> {
 
         /** Merge a leaf node and a tree node.
          * <p>This method is called at the end of a recursive merging

Modified: commons/proper/math/trunk/src/main/java/org/apache/commons/math/ode/AbstractIntegrator.java
URL: http://svn.apache.org/viewvc/commons/proper/math/trunk/src/main/java/org/apache/commons/math/ode/AbstractIntegrator.java?rev=1178235&r1=1178234&r2=1178235&view=diff
==============================================================================
--- commons/proper/math/trunk/src/main/java/org/apache/commons/math/ode/AbstractIntegrator.java (original)
+++ commons/proper/math/trunk/src/main/java/org/apache/commons/math/ode/AbstractIntegrator.java Sun Oct  2 19:43:17 2011
@@ -76,8 +76,8 @@ public abstract class AbstractIntegrator
     /** Counter for number of evaluations. */
     private Incrementor evaluations;
 
-    /** Differential equations to integrate. */
-    private transient ExpandableStatefulODE equations;
+    /** Differential expandable to integrate. */
+    private transient ExpandableStatefulODE expandable;
 
     /** Build an instance.
      * @param name name of the method
@@ -189,7 +189,7 @@ public abstract class AbstractIntegrator
      * @param equations equations to set
      */
     protected void setEquations(final ExpandableStatefulODE equations) {
-        this.equations = equations;
+        this.expandable = equations;
     }
 
     /** {@inheritDoc} */
@@ -204,31 +204,31 @@ public abstract class AbstractIntegrator
             throw new DimensionMismatchException(y.length, equations.getDimension());
         }
 
-        // prepare expandable stateful equations
-        final ExpandableStatefulODE expandable = new ExpandableStatefulODE(equations);
-        expandable.setTime(t0);
-        expandable.setPrimaryState(y0);
+        // prepare expandable stateful expandable
+        final ExpandableStatefulODE expandableODE = new ExpandableStatefulODE(equations);
+        expandableODE.setTime(t0);
+        expandableODE.setPrimaryState(y0);
 
         // perform integration
-        integrate(expandable, t);
+        integrate(expandableODE, t);
 
-        // extract results back from the stateful equations
-        System.arraycopy(expandable.getPrimaryState(), 0, y, 0, y.length);
-        return expandable.getTime();
+        // extract results back from the stateful expandable
+        System.arraycopy(expandableODE.getPrimaryState(), 0, y, 0, y.length);
+        return expandableODE.getTime();
 
     }
 
-    /** Integrate a set of differential equations up to the given time.
+    /** Integrate a set of differential expandable up to the given time.
      * <p>This method solves an Initial Value Problem (IVP).</p>
-     * <p>The set of differential equations is composed of a main set, which
-     * can be extended by some sets of secondary equations. The set of
-     * equations must be already set up with initial time and partial states.
+     * <p>The set of differential expandable is composed of a main set, which
+     * can be extended by some sets of secondary expandable. The set of
+     * expandable must be already set up with initial time and partial states.
      * At integration completion, the final time and partial states will be
      * available in the same object.</p>
      * <p>Since this method stores some internal state variables made
      * available in its public interface during integration ({@link
      * #getCurrentSignedStepsize()}), it is <em>not</em> thread-safe.</p>
-     * @param equations complete set of differential equations to integrate
+     * @param equations complete set of differential expandable to integrate
      * @param t target time for the integration
      * (can be set to a value smaller than <code>t0</code> for backward integration)
      * @throws MathIllegalStateException if the integrator cannot perform integration
@@ -247,7 +247,7 @@ public abstract class AbstractIntegrator
     public void computeDerivatives(final double t, final double[] y, final double[] yDot)
         throws MaxCountExceededException {
         evaluations.incrementCount();
-        equations.computeDerivatives(t, y, yDot);
+        expandable.computeDerivatives(t, y, yDot);
     }
 
     /** Set the stateInitialized flag.
@@ -374,6 +374,7 @@ public abstract class AbstractIntegrator
     }
 
     /** Check the integration span.
+     * @param equations set of differential equations
      * @param t target time for the integration
      * @exception NumberIsTooSmallException if integration span is too small
      */

Modified: commons/proper/math/trunk/src/main/java/org/apache/commons/math/ode/EquationsMapper.java
URL: http://svn.apache.org/viewvc/commons/proper/math/trunk/src/main/java/org/apache/commons/math/ode/EquationsMapper.java?rev=1178235&r1=1178234&r2=1178235&view=diff
==============================================================================
--- commons/proper/math/trunk/src/main/java/org/apache/commons/math/ode/EquationsMapper.java (original)
+++ commons/proper/math/trunk/src/main/java/org/apache/commons/math/ode/EquationsMapper.java Sun Oct  2 19:43:17 2011
@@ -37,10 +37,10 @@ public class EquationsMapper implements 
     private static final long serialVersionUID = 20110925L;
 
     /** Index of the first equation element in complete state arrays. */
-    final int firstIndex;
+    private final int firstIndex;
 
     /** Dimension of the secondary state parameters. */
-    final int dimension;
+    private final int dimension;
 
     /** simple constructor.
      * @param firstIndex index of the first equation element in complete state arrays

Modified: commons/proper/math/trunk/src/main/java/org/apache/commons/math/ode/ExpandableStatefulODE.java
URL: http://svn.apache.org/viewvc/commons/proper/math/trunk/src/main/java/org/apache/commons/math/ode/ExpandableStatefulODE.java?rev=1178235&r1=1178234&r2=1178235&view=diff
==============================================================================
--- commons/proper/math/trunk/src/main/java/org/apache/commons/math/ode/ExpandableStatefulODE.java (original)
+++ commons/proper/math/trunk/src/main/java/org/apache/commons/math/ode/ExpandableStatefulODE.java Sun Oct  2 19:43:17 2011
@@ -297,7 +297,6 @@ public class ExpandableStatefulODE {
     /** Components of the compound stateful ODE. */
     private static class SecondaryComponent {
 
-        
         /** Secondary differential equation. */
         private final SecondaryEquations equation;
 
@@ -312,7 +311,7 @@ public class ExpandableStatefulODE {
 
         /** Simple constructor.
          * @param equation secondary differential equation
-         * @param first index index to use for the first element in the complete arrays
+         * @param firstIndex index to use for the first element in the complete arrays
          */
         public SecondaryComponent(final SecondaryEquations equation, final int firstIndex) {
             final int n   = equation.getDimension();

Modified: commons/proper/math/trunk/src/main/java/org/apache/commons/math/ode/JacobianMatrices.java
URL: http://svn.apache.org/viewvc/commons/proper/math/trunk/src/main/java/org/apache/commons/math/ode/JacobianMatrices.java?rev=1178235&r1=1178234&r2=1178235&view=diff
==============================================================================
--- commons/proper/math/trunk/src/main/java/org/apache/commons/math/ode/JacobianMatrices.java (original)
+++ commons/proper/math/trunk/src/main/java/org/apache/commons/math/ode/JacobianMatrices.java Sun Oct  2 19:43:17 2011
@@ -154,6 +154,7 @@ public class JacobianMatrices {
     }
 
     /** Register the variational equations for the Jacobians matrices to the expandable set.
+     * @param expandable expandable set into which variational equations should be registered
      * @exception MathIllegalArgumentException if the primary set of the expandable set does
      * not match the one used to build the instance
      * @see ExpandableStatefulODE#addSecondaryEquations(SecondaryEquations)
@@ -183,10 +184,10 @@ public class JacobianMatrices {
     }
 
     /** Add a parameter Jacobian provider.
-     * @param pode the parameterized ODE to compute the parameter Jacobian matrix using finite differences 
+     * @param parameterizedOde the parameterized ODE to compute the parameter Jacobian matrix using finite differences
      */
-    public void setParameterizedODE(final ParameterizedODE pode) {
-        this.pode = pode;
+    public void setParameterizedODE(final ParameterizedODE parameterizedOde) {
+        this.pode = parameterizedOde;
         dirtyParameter = true;
     }
 
@@ -227,10 +228,10 @@ public class JacobianMatrices {
      * matrix with respect to state is set to identity.
      * </p>
      * @param dYdY0 initial Jacobian matrix w.r.t. state
-     * @exception IllegalArgumentException if matrix dimensions are incorrect
+     * @exception DimensionMismatchException if matrix dimensions are incorrect
      */
     public void setInitialMainStateJacobian(final double[][] dYdY0)
-        throws MathIllegalArgumentException {
+        throws DimensionMismatchException {
 
         // Check dimensions
         checkDimension(stateDim, dYdY0);
@@ -289,16 +290,16 @@ public class JacobianMatrices {
         // get current state for this set of equations from the expandable fode
         double[] p = efode.getSecondaryState(index);
 
-        int index = 0;
+        int j = 0;
         for (int i = 0; i < stateDim; i++) {
-            System.arraycopy(p, index, dYdY0[i], 0, stateDim);
-            index += stateDim;
+            System.arraycopy(p, j, dYdY0[i], 0, stateDim);
+            j += stateDim;
         }
 
     }
 
     /** Get the current value of the Jacobian matrix with respect to one parameter.
-     * @param pName name of the parameter for the computed Jacobian matrix 
+     * @param pName name of the parameter for the computed Jacobian matrix
      * @param dYdP current Jacobian matrix with respect to the named parameter
      */
     public void getCurrentParameterJacobian(String pName, final double[] dYdP) {
@@ -306,13 +307,13 @@ public class JacobianMatrices {
         // get current state for this set of equations from the expandable fode
         double[] p = efode.getSecondaryState(index);
 
-        int index = stateDim * stateDim;
+        int i = stateDim * stateDim;
         for (ParameterConfiguration param: selectedParameters) {
             if (param.getParameterName().equals(pName)) {
-                System.arraycopy(p, index, dYdP, 0, stateDim);
-                break;
+                System.arraycopy(p, i, dYdP, 0, stateDim);
+                return;
             }
-            index += stateDim;
+            i += stateDim;
         }
 
     }

Modified: commons/proper/math/trunk/src/main/java/org/apache/commons/math/ode/MainStateJacobianProvider.java
URL: http://svn.apache.org/viewvc/commons/proper/math/trunk/src/main/java/org/apache/commons/math/ode/MainStateJacobianProvider.java?rev=1178235&r1=1178234&r2=1178235&view=diff
==============================================================================
--- commons/proper/math/trunk/src/main/java/org/apache/commons/math/ode/MainStateJacobianProvider.java (original)
+++ commons/proper/math/trunk/src/main/java/org/apache/commons/math/ode/MainStateJacobianProvider.java Sun Oct  2 19:43:17 2011
@@ -19,7 +19,7 @@ package org.apache.commons.math.ode;
 /** Interface expanding {@link FirstOrderDifferentialEquations first order
  *  differential equations} in order to compute exactly the main state jacobian
  *  matrix for {@link JacobianMatrices partial derivatives equations}.
- * 
+ *
  * @version $Id$
  * @since 3.0
  */

Modified: commons/proper/math/trunk/src/main/java/org/apache/commons/math/ode/MultistepIntegrator.java
URL: http://svn.apache.org/viewvc/commons/proper/math/trunk/src/main/java/org/apache/commons/math/ode/MultistepIntegrator.java?rev=1178235&r1=1178234&r2=1178235&view=diff
==============================================================================
--- commons/proper/math/trunk/src/main/java/org/apache/commons/math/ode/MultistepIntegrator.java (original)
+++ commons/proper/math/trunk/src/main/java/org/apache/commons/math/ode/MultistepIntegrator.java Sun Oct  2 19:43:17 2011
@@ -294,7 +294,7 @@ public abstract class MultistepIntegrato
     }
 
     /** Transformer used to convert the first step to Nordsieck representation. */
-    public static interface NordsieckTransformer {
+    public interface NordsieckTransformer {
         /** Initialize the high order scaled derivatives at step start.
          * @param h step size to use for scaling
          * @param t first steps times

Modified: commons/proper/math/trunk/src/main/java/org/apache/commons/math/ode/ParameterConfiguration.java
URL: http://svn.apache.org/viewvc/commons/proper/math/trunk/src/main/java/org/apache/commons/math/ode/ParameterConfiguration.java?rev=1178235&r1=1178234&r2=1178235&view=diff
==============================================================================
--- commons/proper/math/trunk/src/main/java/org/apache/commons/math/ode/ParameterConfiguration.java (original)
+++ commons/proper/math/trunk/src/main/java/org/apache/commons/math/ode/ParameterConfiguration.java Sun Oct  2 19:43:17 2011
@@ -19,8 +19,8 @@ package org.apache.commons.math.ode;
 import java.io.Serializable;
 
 /** Simple container pairing a parameter name with a step in order to compute
- *  the associated jacobian matrix by finite difference.
- * 
+ *  the associated Jacobian matrix by finite difference.
+ *
  * @version $Id$
  * @since 3.0
  */

Modified: commons/proper/math/trunk/src/main/java/org/apache/commons/math/ode/ParameterJacobianProvider.java
URL: http://svn.apache.org/viewvc/commons/proper/math/trunk/src/main/java/org/apache/commons/math/ode/ParameterJacobianProvider.java?rev=1178235&r1=1178234&r2=1178235&view=diff
==============================================================================
--- commons/proper/math/trunk/src/main/java/org/apache/commons/math/ode/ParameterJacobianProvider.java (original)
+++ commons/proper/math/trunk/src/main/java/org/apache/commons/math/ode/ParameterJacobianProvider.java Sun Oct  2 19:43:17 2011
@@ -20,7 +20,7 @@ import org.apache.commons.math.exception
 
 /** Interface to compute exactly Jacobian matrix for some parameter
  *  when computing {@link JacobianMatrices partial derivatives equations}.
- * 
+ *
  * @version $Id$
  * @since 3.0
  */

Modified: commons/proper/math/trunk/src/main/java/org/apache/commons/math/ode/ParameterJacobianWrapper.java
URL: http://svn.apache.org/viewvc/commons/proper/math/trunk/src/main/java/org/apache/commons/math/ode/ParameterJacobianWrapper.java?rev=1178235&r1=1178234&r2=1178235&view=diff
==============================================================================
--- commons/proper/math/trunk/src/main/java/org/apache/commons/math/ode/ParameterJacobianWrapper.java (original)
+++ commons/proper/math/trunk/src/main/java/org/apache/commons/math/ode/ParameterJacobianWrapper.java Sun Oct  2 19:43:17 2011
@@ -22,7 +22,7 @@ import java.util.Map;
 
 /** Wrapper class to compute Jacobian matrices by finite differences for ODE
  *  which do not compute them by themselves.
- *  
+ *
  * @version $Id$
  * @since 3.0
  */
@@ -85,7 +85,7 @@ class ParameterJacobianWrapper implement
             dFdP[i] = (tmpDot[i] - yDot[i]) / hP;
         }
         pode.setParameter(paramName, p);
-       
+
     }
 
 }

Modified: commons/proper/math/trunk/src/main/java/org/apache/commons/math/ode/ParameterizedODE.java
URL: http://svn.apache.org/viewvc/commons/proper/math/trunk/src/main/java/org/apache/commons/math/ode/ParameterizedODE.java?rev=1178235&r1=1178234&r2=1178235&view=diff
==============================================================================
--- commons/proper/math/trunk/src/main/java/org/apache/commons/math/ode/ParameterizedODE.java (original)
+++ commons/proper/math/trunk/src/main/java/org/apache/commons/math/ode/ParameterizedODE.java Sun Oct  2 19:43:17 2011
@@ -18,7 +18,7 @@ package org.apache.commons.math.ode;
 
 /** Interface to compute by finite difference Jacobian matrix for some parameter
  *  when computing {@link JacobianMatrices partial derivatives equations}.
- * 
+ *
  * @version $Id$
  * @since 3.0
  */

Modified: commons/proper/math/trunk/src/main/java/org/apache/commons/math/ode/ParameterizedWrapper.java
URL: http://svn.apache.org/viewvc/commons/proper/math/trunk/src/main/java/org/apache/commons/math/ode/ParameterizedWrapper.java?rev=1178235&r1=1178234&r2=1178235&view=diff
==============================================================================
--- commons/proper/math/trunk/src/main/java/org/apache/commons/math/ode/ParameterizedWrapper.java (original)
+++ commons/proper/math/trunk/src/main/java/org/apache/commons/math/ode/ParameterizedWrapper.java Sun Oct  2 19:43:17 2011
@@ -22,10 +22,9 @@ import java.util.Collection;
 import org.apache.commons.math.exception.MathIllegalArgumentException;
 import org.apache.commons.math.exception.util.LocalizedFormats;
 
-
 /** Wrapper class enabling {@link FirstOrderDifferentialEquations basic simple}
  *  ODE instances to be used when processing {@link JacobianMatrices}.
- *  
+ *
  * @version $Id$
  * @since 3.0
  */

Modified: commons/proper/math/trunk/src/main/java/org/apache/commons/math/ode/nonstiff/AdaptiveStepsizeIntegrator.java
URL: http://svn.apache.org/viewvc/commons/proper/math/trunk/src/main/java/org/apache/commons/math/ode/nonstiff/AdaptiveStepsizeIntegrator.java?rev=1178235&r1=1178234&r2=1178235&view=diff
==============================================================================
--- commons/proper/math/trunk/src/main/java/org/apache/commons/math/ode/nonstiff/AdaptiveStepsizeIntegrator.java (original)
+++ commons/proper/math/trunk/src/main/java/org/apache/commons/math/ode/nonstiff/AdaptiveStepsizeIntegrator.java Sun Oct  2 19:43:17 2011
@@ -24,7 +24,6 @@ import org.apache.commons.math.exception
 import org.apache.commons.math.exception.util.LocalizedFormats;
 import org.apache.commons.math.ode.AbstractIntegrator;
 import org.apache.commons.math.ode.ExpandableStatefulODE;
-import org.apache.commons.math.ode.FirstOrderDifferentialEquations;
 import org.apache.commons.math.util.FastMath;
 
 /**
@@ -44,7 +43,8 @@ import org.apache.commons.math.util.Fast
  * </p>
  * <p>
  * If the Ordinary Differential Equations is an {@link ExpandableStatefulODE
- * extended ODE} rather than a {@link FirstOrderDifferentialEquations basic ODE}, then
+ * extended ODE} rather than a {@link
+ * org.apache.commons.math.ode.FirstOrderDifferentialEquations basic ODE}, then
  * <em>only</em> the {@link ExpandableStatefulODE#getPrimaryState() primary part}
  * of the state vector is used for stepsize control, not the complete state vector.
  * </p>
@@ -316,7 +316,7 @@ public abstract class AdaptiveStepsizeIn
    * @exception NumberIsTooSmallException if the step is too small and acceptSmall is false
    */
   protected double filterStep(final double h, final boolean forward, final boolean acceptSmall)
-    throws MathIllegalArgumentException {
+    throws NumberIsTooSmallException {
 
       double filteredH = h;
       if (FastMath.abs(h) < minStep) {

Modified: commons/proper/math/trunk/src/main/java/org/apache/commons/math/ode/nonstiff/DormandPrince853StepInterpolator.java
URL: http://svn.apache.org/viewvc/commons/proper/math/trunk/src/main/java/org/apache/commons/math/ode/nonstiff/DormandPrince853StepInterpolator.java?rev=1178235&r1=1178234&r2=1178235&view=diff
==============================================================================
--- commons/proper/math/trunk/src/main/java/org/apache/commons/math/ode/nonstiff/DormandPrince853StepInterpolator.java (original)
+++ commons/proper/math/trunk/src/main/java/org/apache/commons/math/ode/nonstiff/DormandPrince853StepInterpolator.java Sun Oct  2 19:43:17 2011
@@ -433,14 +433,9 @@ class DormandPrince853StepInterpolator
   public void writeExternal(final ObjectOutput out)
     throws IOException {
 
-    try {
-      // save the local attributes
-      finalizeStep();
-    } catch (Exception e) {
-        IOException ioe = new IOException(e.getLocalizedMessage());
-        ioe.initCause(e);
-        throw ioe;
-    }
+    // save the local attributes
+    finalizeStep();
+
     final int dimension = (currentState == null) ? -1 : currentState.length;
     out.writeInt(dimension);
     for (int i = 0; i < dimension; ++i) {

Modified: commons/proper/math/trunk/src/main/java/org/apache/commons/math/ode/sampling/AbstractStepInterpolator.java
URL: http://svn.apache.org/viewvc/commons/proper/math/trunk/src/main/java/org/apache/commons/math/ode/sampling/AbstractStepInterpolator.java?rev=1178235&r1=1178234&r2=1178235&view=diff
==============================================================================
--- commons/proper/math/trunk/src/main/java/org/apache/commons/math/ode/sampling/AbstractStepInterpolator.java (original)
+++ commons/proper/math/trunk/src/main/java/org/apache/commons/math/ode/sampling/AbstractStepInterpolator.java Sun Oct  2 19:43:17 2011
@@ -121,7 +121,7 @@ public abstract class AbstractStepInterp
     this.dirtyState    = true;
     primaryMapper      = null;
     secondaryMappers   = null;
-    allocateInterpolatedArrays(-1, null, null);
+    allocateInterpolatedArrays(-1);
   }
 
   /** Simple constructor.
@@ -147,7 +147,7 @@ public abstract class AbstractStepInterp
     this.dirtyState       = true;
     this.primaryMapper    = primaryMapper;
     this.secondaryMappers = (secondaryMappers == null) ? null : secondaryMappers.clone();
-    allocateInterpolatedArrays(y.length, primaryMapper, secondaryMappers);
+    allocateInterpolatedArrays(y.length);
 
   }
 
@@ -178,8 +178,10 @@ public abstract class AbstractStepInterp
     interpolatedTime   = interpolator.interpolatedTime;
 
     if (interpolator.currentState == null) {
-        currentState = null;
-        allocateInterpolatedArrays(-1, null, null);
+        currentState     = null;
+        primaryMapper    = null;
+        secondaryMappers = null;
+        allocateInterpolatedArrays(-1);
     } else {
       currentState                     = interpolator.currentState.clone();
       interpolatedState                = interpolator.interpolatedState.clone();
@@ -205,12 +207,8 @@ public abstract class AbstractStepInterp
 
   /** Allocate the various interpolated states arrays.
    * @param dimension total dimension (negative if arrays should be set to null)
-   * @param primaryMapper equations mapper for the primary equations set
-   * @param secondaryMappers equations mappers for the secondary equations sets
    */
-  private void allocateInterpolatedArrays(final int dimension,
-                                          final EquationsMapper primaryMapper,
-                                          final EquationsMapper[] secondaryMappers) {
+  private void allocateInterpolatedArrays(final int dimension) {
       if (dimension < 0) {
           interpolatedState                = null;
           interpolatedDerivatives          = null;
@@ -240,12 +238,12 @@ public abstract class AbstractStepInterp
   /** Reinitialize the instance
    * @param y reference to the integrator array holding the state at the end of the step
    * @param isForward integration direction indicator
-   * @param primaryMapper equations mapper for the primary equations set
-   * @param secondaryMappers equations mappers for the secondary equations sets
+   * @param primary equations mapper for the primary equations set
+   * @param secondary equations mappers for the secondary equations sets
    */
   protected void reinitialize(final double[] y, final boolean isForward,
-                              final EquationsMapper primaryMapper,
-                              final EquationsMapper[] secondaryMappers) {
+                              final EquationsMapper primary,
+                              final EquationsMapper[] secondary) {
 
     globalPreviousTime    = Double.NaN;
     globalCurrentTime     = Double.NaN;
@@ -257,9 +255,9 @@ public abstract class AbstractStepInterp
     finalized             = false;
     this.forward          = isForward;
     this.dirtyState       = true;
-    this.primaryMapper    = primaryMapper;
-    this.secondaryMappers = secondaryMappers.clone();
-    allocateInterpolatedArrays(y.length, primaryMapper, secondaryMappers);
+    this.primaryMapper    = primary;
+    this.secondaryMappers = secondary.clone();
+    allocateInterpolatedArrays(y.length);
 
   }
 
@@ -540,13 +538,7 @@ public abstract class AbstractStepInterp
     // it will be recomputed as needed after reading
 
     // finalize the step (and don't bother saving the now true flag)
-    try {
-      finalizeStep();
-    } catch (Exception e) {
-        IOException ioe = new IOException(e.getLocalizedMessage());
-        ioe.initCause(e);
-        throw ioe;
-    }
+    finalizeStep();
 
   }
 
@@ -558,6 +550,8 @@ public abstract class AbstractStepInterp
    * @param in stream where to read the state from
    * @return interpolated time to be set later by the caller
    * @exception IOException in case of read error
+   * @exception ClassNotFoundException if an equation mapper class
+   * cannot be found
    */
   protected double readBaseExternal(final ObjectInput in)
     throws IOException, ClassNotFoundException {
@@ -587,7 +581,7 @@ public abstract class AbstractStepInterp
 
     // we do NOT handle the interpolated time and state here
     interpolatedTime = Double.NaN;
-    allocateInterpolatedArrays(dimension, primaryMapper, secondaryMappers);
+    allocateInterpolatedArrays(dimension);
 
     finalized = true;
 

Modified: commons/proper/math/trunk/src/main/java/org/apache/commons/math/stat/correlation/StorelessBivariateCovariance.java
URL: http://svn.apache.org/viewvc/commons/proper/math/trunk/src/main/java/org/apache/commons/math/stat/correlation/StorelessBivariateCovariance.java?rev=1178235&r1=1178234&r2=1178235&view=diff
==============================================================================
--- commons/proper/math/trunk/src/main/java/org/apache/commons/math/stat/correlation/StorelessBivariateCovariance.java (original)
+++ commons/proper/math/trunk/src/main/java/org/apache/commons/math/stat/correlation/StorelessBivariateCovariance.java Sun Oct  2 19:43:17 2011
@@ -42,32 +42,34 @@ public class StorelessBivariateCovarianc
 
     private boolean biasCorrected = true;
 
-    public StorelessBivariateCovariance(){ 
+    public StorelessBivariateCovariance() {
     }
 
-    public StorelessBivariateCovariance(boolean biasCorrected){
+    public StorelessBivariateCovariance(boolean biasCorrected) {
         this.biasCorrected = biasCorrected;
     }
 
-    public void increment(double x, double y){
+    public void increment(double x, double y) {
         n++;
         deltaX = x - meanX;
         deltaY = y - meanY;
         meanX += deltaX / n;
         meanY += deltaY / n;
-        covarianceNumerator += ((n-1.0) / n) * deltaX * deltaY;
+        covarianceNumerator += ((n - 1.0) / n) * deltaX * deltaY;
     }
 
-    public double getN(){
+    public double getN() {
         return n;
     }
 
-    public double getResult()throws IllegalArgumentException{
-        if (n < 2) throw new MathIllegalArgumentException(
-                  LocalizedFormats.INSUFFICIENT_DIMENSION, n, 2);
-        if(biasCorrected){
+    public double getResult() throws IllegalArgumentException {
+        if (n < 2) {
+            throw new MathIllegalArgumentException(LocalizedFormats.INSUFFICIENT_DIMENSION,
+                                                   n, 2);
+        }
+        if (biasCorrected) {
             return covarianceNumerator / (n - 1d);
-        }else{
+        } else {
             return covarianceNumerator / n;
         }
     }

Modified: commons/proper/math/trunk/src/main/java/org/apache/commons/math/stat/correlation/StorelessCovariance.java
URL: http://svn.apache.org/viewvc/commons/proper/math/trunk/src/main/java/org/apache/commons/math/stat/correlation/StorelessCovariance.java?rev=1178235&r1=1178234&r2=1178235&view=diff
==============================================================================
--- commons/proper/math/trunk/src/main/java/org/apache/commons/math/stat/correlation/StorelessCovariance.java (original)
+++ commons/proper/math/trunk/src/main/java/org/apache/commons/math/stat/correlation/StorelessCovariance.java Sun Oct  2 19:43:17 2011
@@ -109,9 +109,12 @@ public class StorelessCovariance extends
      * This {@link Covariance} method is not supported by StorelessCovariance, since
      * the number of bivariate observations does not have to be the same for different
      * pairs of covariates - i.e., N as defined in {@link Covariance#getN()} is undefined.
+     * @return nothing as this implementation always throws a {@link MathUnsupportedOperationException}
+     * @throws MathUnsupportedOperationException in all cases
      */
     @Override
-    public int getN() {
+    public int getN()
+        throws MathUnsupportedOperationException {
         throw new MathUnsupportedOperationException();
     }
 

Modified: commons/proper/math/trunk/src/main/java/org/apache/commons/math/stat/descriptive/package-info.java
URL: http://svn.apache.org/viewvc/commons/proper/math/trunk/src/main/java/org/apache/commons/math/stat/descriptive/package-info.java?rev=1178235&r1=1178234&r2=1178235&view=diff
==============================================================================
--- commons/proper/math/trunk/src/main/java/org/apache/commons/math/stat/descriptive/package-info.java (original)
+++ commons/proper/math/trunk/src/main/java/org/apache/commons/math/stat/descriptive/package-info.java Sun Oct  2 19:43:17 2011
@@ -24,20 +24,20 @@
  *        <code>/&lowast; evaluation approach &lowast;/<br/>
  *          double[] values = new double[] { 1, 2, 3, 4, 5 };<br/>
  *          <span style="font-weight: bold;">UnivariateStatistic stat = new Mean();</span><br/>
- *          System.out.println("mean = " + <span style="font-weight: bold;">stat.evaluate(values)</span>);<br/>
+ *          out.println("mean = " + <span style="font-weight: bold;">stat.evaluate(values)</span>);<br/>
  *        </code>
  *
  *        <h4>StorelessUnivariateStatistic:</h4>
  *        <code>/&lowast; incremental approach &lowast;/<br/>
  *          double[] values = new double[] { 1, 2, 3, 4, 5 };<br/>
  *          <span style="font-weight: bold;">StorelessUnivariateStatistic stat = new Mean();</span><br/>
- *          System.out.println("mean before adding a value is NaN = " + <span style="font-weight: bold;">stat.getResult()</span>);<br/>
+ *          out.println("mean before adding a value is NaN = " + <span style="font-weight: bold;">stat.getResult()</span>);<br/>
  *          for (int i = 0; i &lt; values.length; i++) {<br/>
  *            &nbsp;&nbsp;&nbsp; <span style="font-weight: bold;">stat.increment(values[i]);</span><br/>
- *            &nbsp;&nbsp;&nbsp; System.out.println("current mean = " + <span style="font-weight: bold;">stat2.getResult()</span>);<br/>
+ *            &nbsp;&nbsp;&nbsp; out.println("current mean = " + <span style="font-weight: bold;">stat2.getResult()</span>);<br/>
  *          }<br/>
  *          <span style="font-weight: bold;"> stat.clear();</span><br/>
- *          System.out.println("mean after clear is NaN = " + <span style="font-weight: bold;">stat.getResult()</span>);
+ *          out.println("mean after clear is NaN = " + <span style="font-weight: bold;">stat.getResult()</span>);
  *        </code>
  *
  */

Modified: commons/proper/math/trunk/src/main/java/org/apache/commons/math/util/FastMath.java
URL: http://svn.apache.org/viewvc/commons/proper/math/trunk/src/main/java/org/apache/commons/math/util/FastMath.java?rev=1178235&r1=1178234&r2=1178235&view=diff
==============================================================================
--- commons/proper/math/trunk/src/main/java/org/apache/commons/math/util/FastMath.java (original)
+++ commons/proper/math/trunk/src/main/java/org/apache/commons/math/util/FastMath.java Sun Oct  2 19:43:17 2011
@@ -16,6 +16,8 @@
  */
 package org.apache.commons.math.util;
 
+import java.io.PrintStream;
+
 /**
  * Faster, more accurate, portable alternative to {@link Math} and
  * {@link StrictMath} for large scale computation.
@@ -30,7 +32,7 @@ package org.apache.commons.math.util;
  * FastMath speed is achieved by relying heavily on optimizing compilers
  * to native code present in many JVMs today and use of large tables.
  * The larger tables are lazily initialised on first use, so that the setup
- * time does not penalise methods that don't need them. 
+ * time does not penalise methods that don't need them.
  * </p>
  * <p>
  * Note that FastMath is
@@ -83,6 +85,7 @@ public class FastMath {
     /** Napier's constant e, base of the natural logarithm. */
     public static final double E = 2850325.0 / 1048576.0 + 8.254840070411028747e-8;
 
+    /** Constant 2<sup>10</sup>. */
     private static final int TWO_POWER_10 = 1024;
 
     /** Indicator for tables initialization.
@@ -127,7 +130,7 @@ public class FastMath {
 
     /** Sine, Cosine, Tangent tables are for 0, 1/8, 2/8, ... 13/8 = PI/2 approx. */
     private static final int SINE_TABLE_LEN = 14;
-    
+
     /** Sine table (high bits). */
     private static final double SINE_TABLE_A[] =
         {
@@ -300,7 +303,7 @@ public class FastMath {
 
     /** 2^52 - double numbers this large must be integral (no fraction) or NaN or Infinite */
     private static final double TWO_POWER_52 = 4503599627370496.0;
-    
+
     /**
      * Private Constructor
      */
@@ -345,7 +348,7 @@ public class FastMath {
 
       // cosh[z] = (exp(z) + exp(-z))/2
 
-      // for numbers with magnitude 20 or so, 
+      // for numbers with magnitude 20 or so,
       // exp(-z) can be ignored in comparison with exp(z)
 
       if (x > 20.0) {
@@ -404,10 +407,10 @@ public class FastMath {
       }
 
       // sinh[z] = (exp(z) - exp(-z) / 2
-      
-      // for values of z larger than about 20, 
+
+      // for values of z larger than about 20,
       // exp(-z) can be ignored in comparison with exp(z)
-      
+
       if (x > 20.0) {
           return exp(x)/2.0;
       }
@@ -519,10 +522,10 @@ public class FastMath {
           return x;
       }
 
-      // tanh[z] = sinh[z] / cosh[z] 
+      // tanh[z] = sinh[z] / cosh[z]
       // = (exp(z) - exp(-z)) / (exp(z) + exp(-z))
       // = (exp(2x) - 1) / (exp(2x) + 1)
-      
+
       // for magnitude > 20, sinh[z] == cosh[z] in double precision
 
       if (x > 20.0) {
@@ -3630,20 +3633,24 @@ public class FastMath {
         return ((Float.floatToIntBits(f) >>> 23) & 0xff) - 127;
     }
 
-    // print out contents of arrays, and check the length
-    // used to generate the preset arrays originally
-    public static void main(String[] a){
-        FastMathCalc.printarray("EXP_INT_TABLE_A", EXP_INT_TABLE_LEN, ExpIntTable.EXP_INT_TABLE_A);
-        FastMathCalc.printarray("EXP_INT_TABLE_B", EXP_INT_TABLE_LEN, ExpIntTable.EXP_INT_TABLE_B);
-        FastMathCalc.printarray("EXP_FRAC_TABLE_A", EXP_FRAC_TABLE_LEN, ExpFracTable.EXP_FRAC_TABLE_A);
-        FastMathCalc.printarray("EXP_FRAC_TABLE_B", EXP_FRAC_TABLE_LEN, ExpFracTable.EXP_FRAC_TABLE_B);
-        FastMathCalc.printarray("LN_MANT",LN_MANT_LEN, lnMant.LN_MANT);
-        FastMathCalc.printarray("SINE_TABLE_A", SINE_TABLE_LEN, SINE_TABLE_A);
-        FastMathCalc.printarray("SINE_TABLE_B", SINE_TABLE_LEN, SINE_TABLE_B);
-        FastMathCalc.printarray("COSINE_TABLE_A", SINE_TABLE_LEN, COSINE_TABLE_A);
-        FastMathCalc.printarray("COSINE_TABLE_B", SINE_TABLE_LEN, COSINE_TABLE_B);
-        FastMathCalc.printarray("TANGENT_TABLE_A", SINE_TABLE_LEN, TANGENT_TABLE_A);
-        FastMathCalc.printarray("TANGENT_TABLE_B", SINE_TABLE_LEN, TANGENT_TABLE_B);
+    /**
+     * Print out contents of arrays, and check the length.
+     * <p>used to generate the preset arrays originally.</p>
+     * @param a unused
+     */
+    public static void main(String[] a) {
+        PrintStream out = System.out;
+        FastMathCalc.printarray(out, "EXP_INT_TABLE_A", EXP_INT_TABLE_LEN, ExpIntTable.EXP_INT_TABLE_A);
+        FastMathCalc.printarray(out, "EXP_INT_TABLE_B", EXP_INT_TABLE_LEN, ExpIntTable.EXP_INT_TABLE_B);
+        FastMathCalc.printarray(out, "EXP_FRAC_TABLE_A", EXP_FRAC_TABLE_LEN, ExpFracTable.EXP_FRAC_TABLE_A);
+        FastMathCalc.printarray(out, "EXP_FRAC_TABLE_B", EXP_FRAC_TABLE_LEN, ExpFracTable.EXP_FRAC_TABLE_B);
+        FastMathCalc.printarray(out, "LN_MANT",LN_MANT_LEN, lnMant.LN_MANT);
+        FastMathCalc.printarray(out, "SINE_TABLE_A", SINE_TABLE_LEN, SINE_TABLE_A);
+        FastMathCalc.printarray(out, "SINE_TABLE_B", SINE_TABLE_LEN, SINE_TABLE_B);
+        FastMathCalc.printarray(out, "COSINE_TABLE_A", SINE_TABLE_LEN, COSINE_TABLE_A);
+        FastMathCalc.printarray(out, "COSINE_TABLE_B", SINE_TABLE_LEN, COSINE_TABLE_B);
+        FastMathCalc.printarray(out, "TANGENT_TABLE_A", SINE_TABLE_LEN, TANGENT_TABLE_A);
+        FastMathCalc.printarray(out, "TANGENT_TABLE_B", SINE_TABLE_LEN, TANGENT_TABLE_B);
     }
 
 
@@ -3656,7 +3663,7 @@ public class FastMath {
     /** Length of the array of integer exponentials. */
     static final int EXP_INT_TABLE_LEN = EXP_INT_TABLE_MAX_INDEX * 2;
 
-    // Enclose large data table in nested static class so it's only loaded on first access
+    /** Enclose large data table in nested static class so it's only loaded on first access. */
     private static class ExpIntTable {
         /** Exponential evaluated at integer values,
          * exp(x) =  expIntTableA[x + EXP_INT_TABLE_MAX_INDEX] + expIntTableB[x+EXP_INT_TABLE_MAX_INDEX].
@@ -6702,9 +6709,10 @@ public class FastMath {
         }
     }
 
+    /** Exponential fractions table length. */
     static final int EXP_FRAC_TABLE_LEN = TWO_POWER_10 + 1; // 0, 1/1024, ... 1024/1024
 
-    // Enclose large data table in nested static class so it's only loaded on first access
+    /** Enclose large data table in nested static class so it's only loaded on first access. */
     private static class ExpFracTable {
         /** Exponential over the range of 0 - 1 in increments of 2^-10
          * exp(x/1024) =  expFracTableA[x] + expFracTableB[x].
@@ -8793,9 +8801,10 @@ public class FastMath {
         }
     }
 
+    /** Logarithm table length. */
     static final int LN_MANT_LEN = TWO_POWER_10; // (see LN_MANT comment below)
 
-    // Enclose large data table in nested static class so it's only loaded on first access
+    /** Enclose large data table in nested static class so it's only loaded on first access. */
     private static class lnMant {
         /** Extended precision logarithm table over the range 1 - 2 in increments of 2^-10. */
         private static final double[][] LN_MANT;
@@ -8812,7 +8821,7 @@ public class FastMath {
             } else if (LOAD_RESOURCES) {
                 LN_MANT = FastMathResources.loadLnMant();
             } else {
-                LN_MANT = new double[][] { 
+                LN_MANT = new double[][] {
       {+0.0d,                   +0.0d,                   }, // 0
       {+9.760860120877624E-4d,  -3.903230345984362E-11d, }, // 1
       {+0.0019512202125042677d, -8.124251825289188E-11d, }, // 2

Modified: commons/proper/math/trunk/src/main/java/org/apache/commons/math/util/FastMathCalc.java
URL: http://svn.apache.org/viewvc/commons/proper/math/trunk/src/main/java/org/apache/commons/math/util/FastMathCalc.java?rev=1178235&r1=1178234&r2=1178235&view=diff
==============================================================================
--- commons/proper/math/trunk/src/main/java/org/apache/commons/math/util/FastMathCalc.java (original)
+++ commons/proper/math/trunk/src/main/java/org/apache/commons/math/util/FastMathCalc.java Sun Oct  2 19:43:17 2011
@@ -6,20 +6,24 @@
  * (the "License"); you may not use this file except in compliance with
  * the License.  You may obtain a copy of the License at
  *
- *   http://www.apache.org/licenses/LICENSE-2.0
+ *      http://www.apache.org/licenses/LICENSE-2.0
  *
  * Unless required by applicable law or agreed to in writing, software
  * distributed under the License is distributed on an "AS IS" BASIS,
  * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
  * See the License for the specific language governing permissions and
  * limitations under the License.
- * 
  */
-
 package org.apache.commons.math.util;
 
+import java.io.PrintStream;
+
 import org.apache.commons.math.exception.DimensionMismatchException;
 
+/** Class used to compute the classical functions tables.
+ * @version $Id$
+ * @since 3.0
+ */
 class FastMathCalc {
 
     /**
@@ -29,9 +33,9 @@ class FastMathCalc {
     private static final long HEX_40000000 = 0x40000000L; // 1073741824L
 
     /** Factorial table, for Taylor series expansions. 0!, 1!, 2!, ... 19! */
-    private static final double FACT[] = new double[] 
+    private static final double FACT[] = new double[]
         {
-        +1.0d,                        // 0               
+        +1.0d,                        // 0
         +1.0d,                        // 1
         +2.0d,                        // 2
         +6.0d,                        // 3
@@ -73,17 +77,31 @@ class FastMathCalc {
         {0.14982303977012634, 1.225743062930824E-8},
     };
 
+    /** Table start declaration. */
+    private static final String TABLE_START_DECL = "    {";
+
+    /** Table end declaration. */
+    private static final String TABLE_END_DECL   = "    };";
+
+    /**
+     * Private Constructor.
+     */
+    private FastMathCalc() {
+    }
+
     /** Build the sine and cosine tables.
-     * @param SINE_TABLE_A 
-     * @param SINE_TABLE_B 
-     * @param COSINE_TABLE_A 
-     * @param COSINE_TABLE_B 
-     * @param SINE_TABLE_LEN 
-     * @param TANGENT_TABLE_A 
-     * @param TANGENT_TABLE_B 
+     * @param SINE_TABLE_A table of the most significant part of the sines
+     * @param SINE_TABLE_B table of the least significant part of the sines
+     * @param COSINE_TABLE_A table of the most significant part of the cosines
+     * @param COSINE_TABLE_B table of the most significant part of the cosines
+     * @param SINE_TABLE_LEN length of the tables
+     * @param TANGENT_TABLE_A table of the most significant part of the tangents
+     * @param TANGENT_TABLE_B table of the most significant part of the tangents
      */
     @SuppressWarnings("unused")
-    private static void buildSinCosTables(double[] SINE_TABLE_A, double[] SINE_TABLE_B, double[] COSINE_TABLE_A, double[] COSINE_TABLE_B, int SINE_TABLE_LEN, double[] TANGENT_TABLE_A, double[] TANGENT_TABLE_B) {
+    private static void buildSinCosTables(double[] SINE_TABLE_A, double[] SINE_TABLE_B,
+                                          double[] COSINE_TABLE_A, double[] COSINE_TABLE_B,
+                                          int SINE_TABLE_LEN, double[] TANGENT_TABLE_A, double[] TANGENT_TABLE_B) {
         final double result[] = new double[2];
 
         /* Use taylor series for 0 <= x <= 6/8 */
@@ -574,34 +592,65 @@ class FastMathCalc {
     }
 
 
-    static void printarray(String string, int expectedLen, double[][] array2d) {
-        System.out.println(string);
+    /**
+     * Print an array.
+     * @param out text output stream where output should be printed
+     * @param name array name
+     * @param expectedLen expected length of the array
+     * @param array2d array data
+     */
+    static void printarray(PrintStream out, String name, int expectedLen, double[][] array2d) {
+        out.println(name);
         checkLen(expectedLen, array2d.length);
-        System.out.println("    { ");
+        out.println(TABLE_START_DECL + " ");
         int i = 0;
         for(double array[] : array2d) {
-            System.out.print("        {");
+            out.print("        {");
             for(double d : array) { // assume inner array has very few entries
-                String ds = d >= 0 ? "+"+Double.toString(d)+"d," : Double.toString(d)+"d,";
-                System.out.printf("%-25.25s",ds); // multiple entries per line
+                out.printf("%-25.25s", format(d)); // multiple entries per line
             }
-            System.out.println("}, // "+i++);
+            out.println("}, // " + i++);
         }
-        System.out.println("    };");
+        out.println(TABLE_END_DECL);
     }
 
-    static void printarray(String string, int expectedLen, double[] array) {
-        System.out.println(string+"=");
+    /**
+     * Print an array.
+     * @param out text output stream where output should be printed
+     * @param name array name
+     * @param expectedLen expected length of the array
+     * @param array array data
+     */
+    static void printarray(PrintStream out, String name, int expectedLen, double[] array) {
+        out.println(name + "=");
         checkLen(expectedLen, array.length);
-        System.out.println("    {");
+        out.println(TABLE_START_DECL);
         for(double d : array){
-            String ds = d!=d ? "Double.NaN," : d >= 0 ? "+"+Double.toString(d)+"d," : Double.toString(d)+"d,";
-            System.out.printf("        %s%n",ds); // one entry per line
+            out.printf("        %s%n", format(d)); // one entry per line
+        }
+        out.println(TABLE_END_DECL);
+    }
+
+    /** Format a double.
+     * @param d double number to format
+     * @return formatted number
+     */
+    static String format(double d) {
+        if (d != d) {
+            return "Double.NaN,";
+        } else {
+            return ((d >= 0) ? "+" : "") + Double.toString(d) + "d,";
         }
-        System.out.println("    };");
     }
 
-    private static void checkLen(int expectedLen, int actual) {
+    /**
+     * Check two lengths are equal.
+     * @param expectedLen expected length
+     * @param actual actual length
+     * @exception DimensionMismatchException if the two lengths are not equal
+     */
+    private static void checkLen(int expectedLen, int actual)
+        throws DimensionMismatchException {
         if (expectedLen != actual) {
             throw new DimensionMismatchException(actual, expectedLen);
         }

Modified: commons/proper/math/trunk/src/test/java/org/apache/commons/math/ode/sampling/DummyStepInterpolatorTest.java
URL: http://svn.apache.org/viewvc/commons/proper/math/trunk/src/test/java/org/apache/commons/math/ode/sampling/DummyStepInterpolatorTest.java?rev=1178235&r1=1178234&r2=1178235&view=diff
==============================================================================
--- commons/proper/math/trunk/src/test/java/org/apache/commons/math/ode/sampling/DummyStepInterpolatorTest.java (original)
+++ commons/proper/math/trunk/src/test/java/org/apache/commons/math/ode/sampling/DummyStepInterpolatorTest.java Sun Oct  2 19:43:17 2011
@@ -115,9 +115,9 @@ public class DummyStepInterpolatorTest {
     try {
         oos.writeObject(interpolator);
         Assert.fail("an exception should have been thrown");
-    } catch (IOException ioe) {
+    } catch (MathIllegalStateException mise) {
         // expected behavior
-        Assert.assertEquals(0, ioe.getMessage().length());
+        Assert.assertEquals(0, mise.getMessage().length());
     }
   }
 



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