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From er...@apache.org
Subject [38/51] [partial] commons-complex git commit: Removed "site-content" directory.
Date Fri, 06 Jan 2017 17:10:18 GMT
http://git-wip-us.apache.org/repos/asf/commons-complex/blob/b3576eeb/site-content/.svn/pristine/01/01b1c8e58b8edaf62207fec2a0f4e0c3fd53d82b.svn-base
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-<?xml version="1.0" encoding="UTF-8"?><!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Strict//EN" "http://www.w3.org/TR/xhtml1/DTD/xhtml1-strict.dtd"><html xmlns="http://www.w3.org/1999/xhtml" lang="en"><head><meta http-equiv="Content-Type" content="text/html;charset=UTF-8"/><link rel="stylesheet" href="../.resources/report.css" type="text/css"/><link rel="shortcut icon" href="../.resources/report.gif" type="image/gif"/><title>NPointCrossover.java</title><link rel="stylesheet" href="../.resources/prettify.css" type="text/css"/><script type="text/javascript" src="../.resources/prettify.js"></script></head><body onload="window['PR_TAB_WIDTH']=4;prettyPrint()"><div class="breadcrumb" id="breadcrumb"><span class="info"><a href="../.sessions.html" class="el_session">Sessions</a></span><a href="../index.html" class="el_report">Apache Commons Math</a> &gt; <a href="index.source.html" class="el_package">org.apache.commons.math3.genetics</a> &gt; <span class="el_source">NPointCrossover.java</sp
 an></div><h1>NPointCrossover.java</h1><pre class="source lang-java linenums">/*
- * Licensed to the Apache Software Foundation (ASF) under one or more
- * contributor license agreements.  See the NOTICE file distributed with
- * this work for additional information regarding copyright ownership.
- * The ASF licenses this file to You under the Apache License, Version 2.0
- * (the &quot;License&quot;); 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
- *
- * Unless required by applicable law or agreed to in writing, software
- * distributed under the License is distributed on an &quot;AS IS&quot; 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.math3.genetics;
-
-import java.util.ArrayList;
-import java.util.List;
-
-import org.apache.commons.math3.exception.DimensionMismatchException;
-import org.apache.commons.math3.exception.MathIllegalArgumentException;
-import org.apache.commons.math3.exception.NotStrictlyPositiveException;
-import org.apache.commons.math3.exception.NumberIsTooLargeException;
-import org.apache.commons.math3.exception.util.LocalizedFormats;
-import org.apache.commons.math3.random.RandomGenerator;
-
-/**
- * N-point crossover policy. For each iteration a random crossover point is
- * selected and the first part from each parent is copied to the corresponding
- * child, and the second parts are copied crosswise.
- *
- * Example (2-point crossover):
- * &lt;pre&gt;
- * -C- denotes a crossover point
- *           -C-       -C-                         -C-        -C-
- * p1 = (1 0  | 1 0 0 1 | 0 1 1)    X    p2 = (0 1  | 1 0 1 0  | 1 1 1)
- *      \----/ \-------/ \-----/              \----/ \--------/ \-----/
- *        ||      (*)       ||                  ||      (**)       ||
- *        VV      (**)      VV                  VV      (*)        VV
- *      /----\ /--------\ /-----\             /----\ /--------\ /-----\
- * c1 = (1 0  | 1 0 1 0  | 0 1 1)    X   c2 = (0 1  | 1 0 0 1  | 0 1 1)
- * &lt;/pre&gt;
- *
- * This policy works only on {@link AbstractListChromosome}, and therefore it
- * is parameterized by T. Moreover, the chromosomes must have same lengths.
- *
- * @param &lt;T&gt; generic type of the {@link AbstractListChromosome}s for crossover
- * @since 3.1
- */
-public class NPointCrossover&lt;T&gt; implements CrossoverPolicy {
-
-    /** The number of crossover points. */
-    private final int crossoverPoints;
-
-    /**
-     * Creates a new {@link NPointCrossover} policy using the given number of points.
-     * &lt;p&gt;
-     * &lt;b&gt;Note&lt;/b&gt;: the number of crossover points must be &amp;lt; &lt;code&gt;chromosome length - 1&lt;/code&gt;.
-     * This condition can only be checked at runtime, as the chromosome length is not known in advance.
-     *
-     * @param crossoverPoints the number of crossover points
-     * @throws NotStrictlyPositiveException if the number of {@code crossoverPoints} is not strictly positive
-     */
-<span class="fc" id="L66">    public NPointCrossover(final int crossoverPoints) throws NotStrictlyPositiveException {</span>
-<span class="pc bpc" id="L67" title="1 of 2 branches missed.">        if (crossoverPoints &lt;= 0) {</span>
-<span class="nc" id="L68">            throw new NotStrictlyPositiveException(crossoverPoints);</span>
-        }
-<span class="fc" id="L70">        this.crossoverPoints = crossoverPoints;</span>
-<span class="fc" id="L71">    }</span>
-
-    /**
-     * Returns the number of crossover points used by this {@link CrossoverPolicy}.
-     *
-     * @return the number of crossover points
-     */
-    public int getCrossoverPoints() {
-<span class="nc" id="L79">        return crossoverPoints;</span>
-    }
-
-    /**
-     * Performs a N-point crossover. N random crossover points are selected and are used
-     * to divide the parent chromosomes into segments. The segments are copied in alternate
-     * order from the two parents to the corresponding child chromosomes.
-     *
-     * Example (2-point crossover):
-     * &lt;pre&gt;
-     * -C- denotes a crossover point
-     *           -C-       -C-                         -C-        -C-
-     * p1 = (1 0  | 1 0 0 1 | 0 1 1)    X    p2 = (0 1  | 1 0 1 0  | 1 1 1)
-     *      \----/ \-------/ \-----/              \----/ \--------/ \-----/
-     *        ||      (*)       ||                  ||      (**)       ||
-     *        VV      (**)      VV                  VV      (*)        VV
-     *      /----\ /--------\ /-----\             /----\ /--------\ /-----\
-     * c1 = (1 0  | 1 0 1 0  | 0 1 1)    X   c2 = (0 1  | 1 0 0 1  | 0 1 1)
-     * &lt;/pre&gt;
-     *
-     * @param first first parent (p1)
-     * @param second second parent (p2)
-     * @return pair of two children (c1,c2)
-     * @throws MathIllegalArgumentException iff one of the chromosomes is
-     *   not an instance of {@link AbstractListChromosome}
-     * @throws DimensionMismatchException if the length of the two chromosomes is different
-     */
-    @SuppressWarnings(&quot;unchecked&quot;) // OK because of instanceof checks
-    public ChromosomePair crossover(final Chromosome first, final Chromosome second)
-        throws DimensionMismatchException, MathIllegalArgumentException {
-
-<span class="fc bfc" id="L110" title="All 4 branches covered.">        if (!(first instanceof AbstractListChromosome&lt;?&gt; &amp;&amp; second instanceof AbstractListChromosome&lt;?&gt;)) {</span>
-<span class="fc" id="L111">            throw new MathIllegalArgumentException(LocalizedFormats.INVALID_FIXED_LENGTH_CHROMOSOME);</span>
-        }
-<span class="fc" id="L113">        return mate((AbstractListChromosome&lt;T&gt;) first, (AbstractListChromosome&lt;T&gt;) second);</span>
-    }
-
-    /**
-     * Helper for {@link #crossover(Chromosome, Chromosome)}. Performs the actual crossover.
-     *
-     * @param first the first chromosome
-     * @param second the second chromosome
-     * @return the pair of new chromosomes that resulted from the crossover
-     * @throws DimensionMismatchException if the length of the two chromosomes is different
-     * @throws NumberIsTooLargeException if the number of crossoverPoints is too large for the actual chromosomes
-     */
-    private ChromosomePair mate(final AbstractListChromosome&lt;T&gt; first,
-                                final AbstractListChromosome&lt;T&gt; second)
-        throws DimensionMismatchException, NumberIsTooLargeException {
-
-<span class="fc" id="L129">        final int length = first.getLength();</span>
-<span class="fc bfc" id="L130" title="All 2 branches covered.">        if (length != second.getLength()) {</span>
-<span class="fc" id="L131">            throw new DimensionMismatchException(second.getLength(), length);</span>
-        }
-<span class="fc bfc" id="L133" title="All 2 branches covered.">        if (crossoverPoints &gt;= length) {</span>
-<span class="fc" id="L134">            throw new NumberIsTooLargeException(crossoverPoints, length, false);</span>
-        }
-
-        // array representations of the parents
-<span class="fc" id="L138">        final List&lt;T&gt; parent1Rep = first.getRepresentation();</span>
-<span class="fc" id="L139">        final List&lt;T&gt; parent2Rep = second.getRepresentation();</span>
-        // and of the children
-<span class="fc" id="L141">        final List&lt;T&gt; child1Rep = new ArrayList&lt;T&gt;(length);</span>
-<span class="fc" id="L142">        final List&lt;T&gt; child2Rep = new ArrayList&lt;T&gt;(length);</span>
-
-<span class="fc" id="L144">        final RandomGenerator random = GeneticAlgorithm.getRandomGenerator();</span>
-
-<span class="fc" id="L146">        List&lt;T&gt; c1 = child1Rep;</span>
-<span class="fc" id="L147">        List&lt;T&gt; c2 = child2Rep;</span>
-
-<span class="fc" id="L149">        int remainingPoints = crossoverPoints;</span>
-<span class="fc" id="L150">        int lastIndex = 0;</span>
-<span class="fc bfc" id="L151" title="All 2 branches covered.">        for (int i = 0; i &lt; crossoverPoints; i++, remainingPoints--) {</span>
-            // select the next crossover point at random
-<span class="fc" id="L153">            final int crossoverIndex = 1 + lastIndex + random.nextInt(length - lastIndex - remainingPoints);</span>
-
-            // copy the current segment
-<span class="fc bfc" id="L156" title="All 2 branches covered.">            for (int j = lastIndex; j &lt; crossoverIndex; j++) {</span>
-<span class="fc" id="L157">                c1.add(parent1Rep.get(j));</span>
-<span class="fc" id="L158">                c2.add(parent2Rep.get(j));</span>
-            }
-
-            // swap the children for the next segment
-<span class="fc" id="L162">            List&lt;T&gt; tmp = c1;</span>
-<span class="fc" id="L163">            c1 = c2;</span>
-<span class="fc" id="L164">            c2 = tmp;</span>
-
-<span class="fc" id="L166">            lastIndex = crossoverIndex;</span>
-        }
-
-        // copy the last segment
-<span class="fc bfc" id="L170" title="All 2 branches covered.">        for (int j = lastIndex; j &lt; length; j++) {</span>
-<span class="fc" id="L171">            c1.add(parent1Rep.get(j));</span>
-<span class="fc" id="L172">            c2.add(parent2Rep.get(j));</span>
-        }
-
-<span class="fc" id="L175">        return new ChromosomePair(first.newFixedLengthChromosome(child1Rep),</span>
-                                  second.newFixedLengthChromosome(child2Rep));
-    }
-}
-</pre><div class="footer"><span class="right">Created with <a href="http://www.eclemma.org/jacoco">JaCoCo</a> 0.7.5.201505241946</span></div></body></html>
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-
-<!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Transitional//EN" "http://www.w3.org/TR/xhtml1/DTD/xhtml1-transitional.dtd">
-<html xml:lang="en" lang="en">
-	<head>
-		<meta http-equiv="content-type" content="text/html; charset=UTF-8" />
-		<title>Apache Commons Math 3.6.1 Reference Package org.apache.commons.math3.ml.clustering.evaluation</title>
-		<link rel="stylesheet" type="text/css" href="../../../../../../../stylesheet.css" title="style" />
-	</head>
-	<body>
-
-		<h3>
-        	<a href="package-summary.html" target="classFrame">org.apache.commons.math3.ml.clustering.evaluation</a>
-      	</h3>
-
-      	<h3>Classes</h3>
-
-      	<ul>
-      		          	<li>
-            	<a href="SumOfClusterVariancesTest.html" target="classFrame">SumOfClusterVariancesTest</a>
-          	</li>
-          	      	</ul>
-
-	</body>
-</html>
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-<?xml version="1.0" encoding="UTF-8"?><!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Strict//EN" "http://www.w3.org/TR/xhtml1/DTD/xhtml1-strict.dtd"><html xmlns="http://www.w3.org/1999/xhtml" lang="en"><head><meta http-equiv="Content-Type" content="text/html;charset=UTF-8"/><link rel="stylesheet" href="../.resources/report.css" type="text/css"/><link rel="shortcut icon" href="../.resources/report.gif" type="image/gif"/><title>MultivariateFunctionMappingAdapter.java</title><link rel="stylesheet" href="../.resources/prettify.css" type="text/css"/><script type="text/javascript" src="../.resources/prettify.js"></script></head><body onload="window['PR_TAB_WIDTH']=4;prettyPrint()"><div class="breadcrumb" id="breadcrumb"><span class="info"><a href="../.sessions.html" class="el_session">Sessions</a></span><a href="../index.html" class="el_report">Apache Commons Math</a> &gt; <a href="index.source.html" class="el_package">org.apache.commons.math3.optim.nonlinear.scalar</a> &gt; <span class="el
 _source">MultivariateFunctionMappingAdapter.java</span></div><h1>MultivariateFunctionMappingAdapter.java</h1><pre class="source lang-java linenums">/*
- * Licensed to the Apache Software Foundation (ASF) under one or more
- * contributor license agreements.  See the NOTICE file distributed with
- * this work for additional information regarding copyright ownership.
- * The ASF licenses this file to You under the Apache License, Version 2.0
- * (the &quot;License&quot;); 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
- *
- * Unless required by applicable law or agreed to in writing, software
- * distributed under the License is distributed on an &quot;AS IS&quot; 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.math3.optim.nonlinear.scalar;
-
-import org.apache.commons.math3.analysis.MultivariateFunction;
-import org.apache.commons.math3.analysis.UnivariateFunction;
-import org.apache.commons.math3.analysis.function.Logit;
-import org.apache.commons.math3.analysis.function.Sigmoid;
-import org.apache.commons.math3.exception.DimensionMismatchException;
-import org.apache.commons.math3.exception.NumberIsTooSmallException;
-import org.apache.commons.math3.util.FastMath;
-import org.apache.commons.math3.util.MathUtils;
-
-/**
- * &lt;p&gt;Adapter for mapping bounded {@link MultivariateFunction} to unbounded ones.&lt;/p&gt;
- *
- * &lt;p&gt;
- * This adapter can be used to wrap functions subject to simple bounds on
- * parameters so they can be used by optimizers that do &lt;em&gt;not&lt;/em&gt; directly
- * support simple bounds.
- * &lt;/p&gt;
- * &lt;p&gt;
- * The principle is that the user function that will be wrapped will see its
- * parameters bounded as required, i.e when its {@code value} method is called
- * with argument array {@code point}, the elements array will fulfill requirement
- * {@code lower[i] &lt;= point[i] &lt;= upper[i]} for all i. Some of the components
- * may be unbounded or bounded only on one side if the corresponding bound is
- * set to an infinite value. The optimizer will not manage the user function by
- * itself, but it will handle this adapter and it is this adapter that will take
- * care the bounds are fulfilled. The adapter {@link #value(double[])} method will
- * be called by the optimizer with unbound parameters, and the adapter will map
- * the unbounded value to the bounded range using appropriate functions like
- * {@link Sigmoid} for double bounded elements for example.
- * &lt;/p&gt;
- * &lt;p&gt;
- * As the optimizer sees only unbounded parameters, it should be noted that the
- * start point or simplex expected by the optimizer should be unbounded, so the
- * user is responsible for converting his bounded point to unbounded by calling
- * {@link #boundedToUnbounded(double[])} before providing them to the optimizer.
- * For the same reason, the point returned by the {@link
- * org.apache.commons.math3.optimization.BaseMultivariateOptimizer#optimize(int,
- * MultivariateFunction, org.apache.commons.math3.optimization.GoalType, double[])}
- * method is unbounded. So to convert this point to bounded, users must call
- * {@link #unboundedToBounded(double[])} by themselves!&lt;/p&gt;
- * &lt;p&gt;
- * This adapter is only a poor man solution to simple bounds optimization constraints
- * that can be used with simple optimizers like
- * {@link org.apache.commons.math3.optim.nonlinear.scalar.noderiv.SimplexOptimizer
- * SimplexOptimizer}.
- * A better solution is to use an optimizer that directly supports simple bounds like
- * {@link org.apache.commons.math3.optim.nonlinear.scalar.noderiv.CMAESOptimizer
- * CMAESOptimizer} or
- * {@link org.apache.commons.math3.optim.nonlinear.scalar.noderiv.BOBYQAOptimizer
- * BOBYQAOptimizer}.
- * One caveat of this poor-man's solution is that behavior near the bounds may be
- * numerically unstable as bounds are mapped from infinite values.
- * Another caveat is that convergence values are evaluated by the optimizer with
- * respect to unbounded variables, so there will be scales differences when
- * converted to bounded variables.
- * &lt;/p&gt;
- *
- * @see MultivariateFunctionPenaltyAdapter
- *
- * @since 3.0
- */
-public class MultivariateFunctionMappingAdapter
-    implements MultivariateFunction {
-    /** Underlying bounded function. */
-    private final MultivariateFunction bounded;
-    /** Mapping functions. */
-    private final Mapper[] mappers;
-
-    /** Simple constructor.
-     * @param bounded bounded function
-     * @param lower lower bounds for each element of the input parameters array
-     * (some elements may be set to {@code Double.NEGATIVE_INFINITY} for
-     * unbounded values)
-     * @param upper upper bounds for each element of the input parameters array
-     * (some elements may be set to {@code Double.POSITIVE_INFINITY} for
-     * unbounded values)
-     * @exception DimensionMismatchException if lower and upper bounds are not
-     * consistent, either according to dimension or to values
-     */
-    public MultivariateFunctionMappingAdapter(final MultivariateFunction bounded,
-<span class="fc" id="L99">                                              final double[] lower, final double[] upper) {</span>
-        // safety checks
-<span class="fc" id="L101">        MathUtils.checkNotNull(lower);</span>
-<span class="fc" id="L102">        MathUtils.checkNotNull(upper);</span>
-<span class="pc bpc" id="L103" title="1 of 2 branches missed.">        if (lower.length != upper.length) {</span>
-<span class="nc" id="L104">            throw new DimensionMismatchException(lower.length, upper.length);</span>
-        }
-<span class="fc bfc" id="L106" title="All 2 branches covered.">        for (int i = 0; i &lt; lower.length; ++i) {</span>
-            // note the following test is written in such a way it also fails for NaN
-<span class="pc bpc" id="L108" title="1 of 2 branches missed.">            if (!(upper[i] &gt;= lower[i])) {</span>
-<span class="nc" id="L109">                throw new NumberIsTooSmallException(upper[i], lower[i], true);</span>
-            }
-        }
-
-<span class="fc" id="L113">        this.bounded = bounded;</span>
-<span class="fc" id="L114">        this.mappers = new Mapper[lower.length];</span>
-<span class="fc bfc" id="L115" title="All 2 branches covered.">        for (int i = 0; i &lt; mappers.length; ++i) {</span>
-<span class="fc bfc" id="L116" title="All 2 branches covered.">            if (Double.isInfinite(lower[i])) {</span>
-<span class="fc bfc" id="L117" title="All 2 branches covered.">                if (Double.isInfinite(upper[i])) {</span>
-                    // element is unbounded, no transformation is needed
-<span class="fc" id="L119">                    mappers[i] = new NoBoundsMapper();</span>
-                } else {
-                    // element is simple-bounded on the upper side
-<span class="fc" id="L122">                    mappers[i] = new UpperBoundMapper(upper[i]);</span>
-                }
-            } else {
-<span class="fc bfc" id="L125" title="All 2 branches covered.">                if (Double.isInfinite(upper[i])) {</span>
-                    // element is simple-bounded on the lower side
-<span class="fc" id="L127">                    mappers[i] = new LowerBoundMapper(lower[i]);</span>
-                } else {
-                    // element is double-bounded
-<span class="fc" id="L130">                    mappers[i] = new LowerUpperBoundMapper(lower[i], upper[i]);</span>
-                }
-            }
-        }
-<span class="fc" id="L134">    }</span>
-
-    /**
-     * Maps an array from unbounded to bounded.
-     *
-     * @param point Unbounded values.
-     * @return the bounded values.
-     */
-    public double[] unboundedToBounded(double[] point) {
-        // Map unbounded input point to bounded point.
-<span class="fc" id="L144">        final double[] mapped = new double[mappers.length];</span>
-<span class="fc bfc" id="L145" title="All 2 branches covered.">        for (int i = 0; i &lt; mappers.length; ++i) {</span>
-<span class="fc" id="L146">            mapped[i] = mappers[i].unboundedToBounded(point[i]);</span>
-        }
-
-<span class="fc" id="L149">        return mapped;</span>
-    }
-
-    /**
-     * Maps an array from bounded to unbounded.
-     *
-     * @param point Bounded values.
-     * @return the unbounded values.
-     */
-    public double[] boundedToUnbounded(double[] point) {
-        // Map bounded input point to unbounded point.
-<span class="fc" id="L160">        final double[] mapped = new double[mappers.length];</span>
-<span class="fc bfc" id="L161" title="All 2 branches covered.">        for (int i = 0; i &lt; mappers.length; ++i) {</span>
-<span class="fc" id="L162">            mapped[i] = mappers[i].boundedToUnbounded(point[i]);</span>
-        }
-
-<span class="fc" id="L165">        return mapped;</span>
-    }
-
-    /**
-     * Compute the underlying function value from an unbounded point.
-     * &lt;p&gt;
-     * This method simply bounds the unbounded point using the mappings
-     * set up at construction and calls the underlying function using
-     * the bounded point.
-     * &lt;/p&gt;
-     * @param point unbounded value
-     * @return underlying function value
-     * @see #unboundedToBounded(double[])
-     */
-    public double value(double[] point) {
-<span class="fc" id="L180">        return bounded.value(unboundedToBounded(point));</span>
-    }
-
-    /** Mapping interface. */
-    private interface Mapper {
-        /**
-         * Maps a value from unbounded to bounded.
-         *
-         * @param y Unbounded value.
-         * @return the bounded value.
-         */
-        double unboundedToBounded(double y);
-
-        /**
-         * Maps a value from bounded to unbounded.
-         *
-         * @param x Bounded value.
-         * @return the unbounded value.
-         */
-        double boundedToUnbounded(double x);
-    }
-
-    /** Local class for no bounds mapping. */
-<span class="fc" id="L203">    private static class NoBoundsMapper implements Mapper {</span>
-        /** {@inheritDoc} */
-        public double unboundedToBounded(final double y) {
-<span class="fc" id="L206">            return y;</span>
-        }
-
-        /** {@inheritDoc} */
-        public double boundedToUnbounded(final double x) {
-<span class="fc" id="L211">            return x;</span>
-        }
-    }
-
-    /** Local class for lower bounds mapping. */
-    private static class LowerBoundMapper implements Mapper {
-        /** Low bound. */
-        private final double lower;
-
-        /**
-         * Simple constructor.
-         *
-         * @param lower lower bound
-         */
-<span class="fc" id="L225">        LowerBoundMapper(final double lower) {</span>
-<span class="fc" id="L226">            this.lower = lower;</span>
-<span class="fc" id="L227">        }</span>
-
-        /** {@inheritDoc} */
-        public double unboundedToBounded(final double y) {
-<span class="fc" id="L231">            return lower + FastMath.exp(y);</span>
-        }
-
-        /** {@inheritDoc} */
-        public double boundedToUnbounded(final double x) {
-<span class="fc" id="L236">            return FastMath.log(x - lower);</span>
-        }
-
-    }
-
-    /** Local class for upper bounds mapping. */
-    private static class UpperBoundMapper implements Mapper {
-
-        /** Upper bound. */
-        private final double upper;
-
-        /** Simple constructor.
-         * @param upper upper bound
-         */
-<span class="fc" id="L250">        UpperBoundMapper(final double upper) {</span>
-<span class="fc" id="L251">            this.upper = upper;</span>
-<span class="fc" id="L252">        }</span>
-
-        /** {@inheritDoc} */
-        public double unboundedToBounded(final double y) {
-<span class="fc" id="L256">            return upper - FastMath.exp(-y);</span>
-        }
-
-        /** {@inheritDoc} */
-        public double boundedToUnbounded(final double x) {
-<span class="fc" id="L261">            return -FastMath.log(upper - x);</span>
-        }
-
-    }
-
-    /** Local class for lower and bounds mapping. */
-    private static class LowerUpperBoundMapper implements Mapper {
-        /** Function from unbounded to bounded. */
-        private final UnivariateFunction boundingFunction;
-        /** Function from bounded to unbounded. */
-        private final UnivariateFunction unboundingFunction;
-
-        /**
-         * Simple constructor.
-         *
-         * @param lower lower bound
-         * @param upper upper bound
-         */
-<span class="fc" id="L279">        LowerUpperBoundMapper(final double lower, final double upper) {</span>
-<span class="fc" id="L280">            boundingFunction   = new Sigmoid(lower, upper);</span>
-<span class="fc" id="L281">            unboundingFunction = new Logit(lower, upper);</span>
-<span class="fc" id="L282">        }</span>
-
-        /** {@inheritDoc} */
-        public double unboundedToBounded(final double y) {
-<span class="fc" id="L286">            return boundingFunction.value(y);</span>
-        }
-
-        /** {@inheritDoc} */
-        public double boundedToUnbounded(final double x) {
-<span class="fc" id="L291">            return unboundingFunction.value(x);</span>
-        }
-    }
-}
-</pre><div class="footer"><span class="right">Created with <a href="http://www.eclemma.org/jacoco">JaCoCo</a> 0.7.5.201505241946</span></div></body></html>
\ No newline at end of file

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-<?xml version="1.0" encoding="UTF-8"?><!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Strict//EN" "http://www.w3.org/TR/xhtml1/DTD/xhtml1-strict.dtd"><html xmlns="http://www.w3.org/1999/xhtml" lang="en"><head><meta http-equiv="Content-Type" content="text/html;charset=UTF-8"/><link rel="stylesheet" href="../.resources/report.css" type="text/css"/><link rel="shortcut icon" href="../.resources/report.gif" type="image/gif"/><title>ClassicalRungeKuttaFieldStepInterpolator.java</title><link rel="stylesheet" href="../.resources/prettify.css" type="text/css"/><script type="text/javascript" src="../.resources/prettify.js"></script></head><body onload="window['PR_TAB_WIDTH']=4;prettyPrint()"><div class="breadcrumb" id="breadcrumb"><span class="info"><a href="../.sessions.html" class="el_session">Sessions</a></span><a href="../index.html" class="el_report">Apache Commons Math</a> &gt; <a href="index.source.html" class="el_package">org.apache.commons.math3.ode.nonstiff</a> &gt; <span class="el_sou
 rce">ClassicalRungeKuttaFieldStepInterpolator.java</span></div><h1>ClassicalRungeKuttaFieldStepInterpolator.java</h1><pre class="source lang-java linenums">/*
- * Licensed to the Apache Software Foundation (ASF) under one or more
- * contributor license agreements.  See the NOTICE file distributed with
- * this work for additional information regarding copyright ownership.
- * The ASF licenses this file to You under the Apache License, Version 2.0
- * (the &quot;License&quot;); 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
- *
- * Unless required by applicable law or agreed to in writing, software
- * distributed under the License is distributed on an &quot;AS IS&quot; 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.math3.ode.nonstiff;
-
-import org.apache.commons.math3.Field;
-import org.apache.commons.math3.RealFieldElement;
-import org.apache.commons.math3.ode.FieldEquationsMapper;
-import org.apache.commons.math3.ode.FieldODEStateAndDerivative;
-
-/**
- * This class implements a step interpolator for the classical fourth
- * order Runge-Kutta integrator.
- *
- * &lt;p&gt;This interpolator allows to compute dense output inside the last
- * step computed. The interpolation equation is consistent with the
- * integration scheme :
- * &lt;ul&gt;
- *   &lt;li&gt;Using reference point at step start:&lt;br&gt;
- *   y(t&lt;sub&gt;n&lt;/sub&gt; + &amp;theta; h) = y (t&lt;sub&gt;n&lt;/sub&gt;)
- *                    + &amp;theta; (h/6) [  (6 - 9 &amp;theta; + 4 &amp;theta;&lt;sup&gt;2&lt;/sup&gt;) y'&lt;sub&gt;1&lt;/sub&gt;
- *                                     + (    6 &amp;theta; - 4 &amp;theta;&lt;sup&gt;2&lt;/sup&gt;) (y'&lt;sub&gt;2&lt;/sub&gt; + y'&lt;sub&gt;3&lt;/sub&gt;)
- *                                     + (   -3 &amp;theta; + 4 &amp;theta;&lt;sup&gt;2&lt;/sup&gt;) y'&lt;sub&gt;4&lt;/sub&gt;
- *                                    ]
- *   &lt;/li&gt;
- *   &lt;li&gt;Using reference point at step end:&lt;br&gt;
- *   y(t&lt;sub&gt;n&lt;/sub&gt; + &amp;theta; h) = y (t&lt;sub&gt;n&lt;/sub&gt; + h)
- *                    + (1 - &amp;theta;) (h/6) [ (-4 &amp;theta;^2 + 5 &amp;theta; - 1) y'&lt;sub&gt;1&lt;/sub&gt;
- *                                          +(4 &amp;theta;^2 - 2 &amp;theta; - 2) (y'&lt;sub&gt;2&lt;/sub&gt; + y'&lt;sub&gt;3&lt;/sub&gt;)
- *                                          -(4 &amp;theta;^2 +   &amp;theta; + 1) y'&lt;sub&gt;4&lt;/sub&gt;
- *                                        ]
- *   &lt;/li&gt;
- * &lt;/ul&gt;
- * &lt;/p&gt;
- *
- * where &amp;theta; belongs to [0 ; 1] and where y'&lt;sub&gt;1&lt;/sub&gt; to y'&lt;sub&gt;4&lt;/sub&gt; are the four
- * evaluations of the derivatives already computed during the
- * step.&lt;/p&gt;
- *
- * @see ClassicalRungeKuttaFieldIntegrator
- * @param &lt;T&gt; the type of the field elements
- * @since 3.6
- */
-
-class ClassicalRungeKuttaFieldStepInterpolator&lt;T extends RealFieldElement&lt;T&gt;&gt;
-    extends RungeKuttaFieldStepInterpolator&lt;T&gt; {
-
-    /** Simple constructor.
-     * @param field field to which the time and state vector elements belong
-     * @param forward integration direction indicator
-     * @param yDotK slopes at the intermediate points
-     * @param globalPreviousState start of the global step
-     * @param globalCurrentState end of the global step
-     * @param softPreviousState start of the restricted step
-     * @param softCurrentState end of the restricted step
-     * @param mapper equations mapper for the all equations
-     */
-    ClassicalRungeKuttaFieldStepInterpolator(final Field&lt;T&gt; field, final boolean forward,
-                                             final T[][] yDotK,
-                                             final FieldODEStateAndDerivative&lt;T&gt; globalPreviousState,
-                                             final FieldODEStateAndDerivative&lt;T&gt; globalCurrentState,
-                                             final FieldODEStateAndDerivative&lt;T&gt; softPreviousState,
-                                             final FieldODEStateAndDerivative&lt;T&gt; softCurrentState,
-                                             final FieldEquationsMapper&lt;T&gt; mapper) {
-<span class="fc" id="L79">        super(field, forward, yDotK,</span>
-              globalPreviousState, globalCurrentState, softPreviousState, softCurrentState,
-              mapper);
-<span class="fc" id="L82">    }</span>
-
-    /** {@inheritDoc} */
-    @Override
-    protected ClassicalRungeKuttaFieldStepInterpolator&lt;T&gt; create(final Field&lt;T&gt; newField, final boolean newForward, final T[][] newYDotK,
-                                                                 final FieldODEStateAndDerivative&lt;T&gt; newGlobalPreviousState,
-                                                                 final FieldODEStateAndDerivative&lt;T&gt; newGlobalCurrentState,
-                                                                 final FieldODEStateAndDerivative&lt;T&gt; newSoftPreviousState,
-                                                                 final FieldODEStateAndDerivative&lt;T&gt; newSoftCurrentState,
-                                                                 final FieldEquationsMapper&lt;T&gt; newMapper) {
-<span class="fc" id="L92">        return new ClassicalRungeKuttaFieldStepInterpolator&lt;T&gt;(newField, newForward, newYDotK,</span>
-                                                               newGlobalPreviousState, newGlobalCurrentState,
-                                                               newSoftPreviousState, newSoftCurrentState,
-                                                               newMapper);
-    }
-
-    /** {@inheritDoc} */
-    @SuppressWarnings(&quot;unchecked&quot;)
-    @Override
-    protected FieldODEStateAndDerivative&lt;T&gt; computeInterpolatedStateAndDerivatives(final FieldEquationsMapper&lt;T&gt; mapper,
-                                                                                   final T time, final T theta,
-                                                                                   final T thetaH, final T oneMinusThetaH) {
-
-<span class="fc" id="L105">        final T one                       = time.getField().getOne();</span>
-<span class="fc" id="L106">        final T oneMinusTheta             = one.subtract(theta);</span>
-<span class="fc" id="L107">        final T oneMinus2Theta            = one.subtract(theta.multiply(2));</span>
-<span class="fc" id="L108">        final T coeffDot1                 = oneMinusTheta.multiply(oneMinus2Theta);</span>
-<span class="fc" id="L109">        final T coeffDot23                = theta.multiply(oneMinusTheta).multiply(2);</span>
-<span class="fc" id="L110">        final T coeffDot4                 = theta.multiply(oneMinus2Theta).negate();</span>
-        final T[] interpolatedState;
-        final T[] interpolatedDerivatives;
-
-<span class="pc bpc" id="L114" title="1 of 4 branches missed.">        if (getGlobalPreviousState() != null &amp;&amp; theta.getReal() &lt;= 0.5) {</span>
-<span class="fc" id="L115">            final T fourTheta2      = theta.multiply(theta).multiply(4);</span>
-<span class="fc" id="L116">            final T s               = thetaH.divide(6.0);</span>
-<span class="fc" id="L117">            final T coeff1          = s.multiply(fourTheta2.subtract(theta.multiply(9)).add(6));</span>
-<span class="fc" id="L118">            final T coeff23         = s.multiply(theta.multiply(6).subtract(fourTheta2));</span>
-<span class="fc" id="L119">            final T coeff4          = s.multiply(fourTheta2.subtract(theta.multiply(3)));</span>
-<span class="fc" id="L120">            interpolatedState       = previousStateLinearCombination(coeff1, coeff23, coeff23, coeff4);</span>
-<span class="fc" id="L121">            interpolatedDerivatives = derivativeLinearCombination(coeffDot1, coeffDot23, coeffDot23, coeffDot4);</span>
-<span class="fc" id="L122">        } else {</span>
-<span class="fc" id="L123">            final T fourTheta       = theta.multiply(4);</span>
-<span class="fc" id="L124">            final T s               = oneMinusThetaH.divide(6);</span>
-<span class="fc" id="L125">            final T coeff1          = s.multiply(theta.multiply(fourTheta.negate().add(5)).subtract(1));</span>
-<span class="fc" id="L126">            final T coeff23         = s.multiply(theta.multiply(fourTheta.subtract(2)).subtract(2));</span>
-<span class="fc" id="L127">            final T coeff4          = s.multiply(theta.multiply(fourTheta.negate().subtract(1)).subtract(1));</span>
-<span class="fc" id="L128">            interpolatedState       = currentStateLinearCombination(coeff1, coeff23, coeff23, coeff4);</span>
-<span class="fc" id="L129">            interpolatedDerivatives = derivativeLinearCombination(coeffDot1, coeffDot23, coeffDot23, coeffDot4);</span>
-        }
-
-<span class="fc" id="L132">        return new FieldODEStateAndDerivative&lt;T&gt;(time, interpolatedState, interpolatedDerivatives);</span>
-
-    }
-
-}
-</pre><div class="footer"><span class="right">Created with <a href="http://www.eclemma.org/jacoco">JaCoCo</a> 0.7.5.201505241946</span></div></body></html>
\ No newline at end of file

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-<!-- NewPage -->
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-<h2 title="Class TestProblem4" class="title">Class TestProblem4</h2>
-</div>
-<div class="contentContainer">
-<ul class="inheritance">
-<li><a href="http://docs.oracle.com/javase/6/docs/api/java/lang/Object.html?is-external=true" title="class or interface in java.lang">java.lang.Object</a></li>
-<li>
-<ul class="inheritance">
-<li><a href="../../../../../org/apache/commons/math3/ode/TestProblemAbstract.html" title="class in org.apache.commons.math3.ode">org.apache.commons.math3.ode.TestProblemAbstract</a></li>
-<li>
-<ul class="inheritance">
-<li>org.apache.commons.math3.ode.TestProblem4</li>
-</ul>
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-</ul>
-</li>
-</ul>
-<div class="description">
-<ul class="blockList">
-<li class="blockList">
-<dl>
-<dt>All Implemented Interfaces:</dt>
-<dd><a href="../../../../../../apidocs/org/apache/commons/math3/ode/FirstOrderDifferentialEquations.html?is-external=true" title="class or interface in org.apache.commons.math3.ode">FirstOrderDifferentialEquations</a></dd>
-</dl>
-<hr>
-<br>
-<pre>public class <a href="../../../../../src-html/org/apache/commons/math3/ode/TestProblem4.html#line.38">TestProblem4</a>
-extends <a href="../../../../../org/apache/commons/math3/ode/TestProblemAbstract.html" title="class in org.apache.commons.math3.ode">TestProblemAbstract</a></pre>
-<div class="block">This class is used in the junit tests for the ODE integrators.
-
- <p>This specific problem is the following differential equation :
- <pre>
-    x'' = -x
- </pre>
- And when x decreases down to 0, the state should be changed as follows :
- <pre>
-   x' -> -x'
- </pre>
- The theoretical solution of this problem is x = |sin(t+a)|
- </p></div>
-</li>
-</ul>
-</div>
-<div class="summary">
-<ul class="blockList">
-<li class="blockList">
-<!-- =========== FIELD SUMMARY =========== -->
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-<code><a href="../../../../../org/apache/commons/math3/ode/TestProblemAbstract.html#calls">calls</a>, <a href="../../../../../org/apache/commons/math3/ode/TestProblemAbstract.html#errorScale">errorScale</a>, <a href="../../../../../org/apache/commons/math3/ode/TestProblemAbstract.html#n">n</a>, <a href="../../../../../org/apache/commons/math3/ode/TestProblemAbstract.html#t0">t0</a>, <a href="../../../../../org/apache/commons/math3/ode/TestProblemAbstract.html#t1">t1</a>, <a href="../../../../../org/apache/commons/math3/ode/TestProblemAbstract.html#y0">y0</a></code></li>
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-<caption><span>Constructors</span><span class="tabEnd">&nbsp;</span></caption>
-<tr>
-<th class="colOne" scope="col">Constructor and Description</th>
-</tr>
-<tr class="altColor">
-<td class="colOne"><code><strong><a href="../../../../../org/apache/commons/math3/ode/TestProblem4.html#TestProblem4()">TestProblem4</a></strong>()</code>
-<div class="block">Simple constructor.</div>
-</td>
-</tr>
-<tr class="rowColor">
-<td class="colOne"><code><strong><a href="../../../../../org/apache/commons/math3/ode/TestProblem4.html#TestProblem4(org.apache.commons.math3.ode.TestProblem4)">TestProblem4</a></strong>(<a href="../../../../../org/apache/commons/math3/ode/TestProblem4.html" title="class in org.apache.commons.math3.ode">TestProblem4</a>&nbsp;problem)</code>
-<div class="block">Copy constructor.</div>
-</td>
-</tr>
-</table>
-</li>
-</ul>
-<!-- ========== METHOD SUMMARY =========== -->
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