added a modified version of Iterator.java for use with daikon and added...

added a modified version of Iterator.java for use with daikon and added results for the mutation test on this class

Daikon.hs

@@ -3,11 +3,24 @@ module Daikon where
 import Control.Monad
 import System.FilePath(joinPath)
 import System.Directory
+import Data.List
+
+testNr :: Int
+testNr = 1
 
 source, pathDir, packageDir, methodName :: String
-source = "GradientFunction"
-pathDir = "org/apache/commons/math3/analysis/differentiation"
-methodName = "value"
+source = case testNr of
+            1 -> "Iterator"
+            2 -> "GradientFunction"
+            3 -> "BaseSecantSolver"
+pathDir = case testNr of
+            1 -> "org/apache/commons/math3/util"
+            2 -> "org/apache/commons/math3/analysis/differentiation"
+            3 -> "org/apache/commons/math3/analysis/solvers"
+methodName = case testNr of
+                1 -> "hasNext"
+                2 -> "value"
+                3 -> "doSolve"
 
 packageDir = map (\c -> if c == '/' then '.' else c) pathDir
 
@@ -16,20 +29,28 @@ createDaikonScript :: IO ()
 createDaikonScript = do
     writeFile scriptName ("#!/bin/sh\nHOME=\"T3Daikon\"\nSOURCE=\"" ++ source ++ "\"\nPATHDIR=\"" ++ pathDir ++ "\"\nPACKAGEDIR=\"" ++ packageDir ++ "\"\nMETHODNAME=\"" ++ methodName ++ "\"\n\n")
         
-    mutationFolders <- listDirectory (joinPath ["..", source ++ " mutants"])
+    mutationFolders <- listDirectory (joinPath ["..", "daikon " ++ source ++ " mutants"])
     checkMutants (length mutationFolders)
     
     appendFile scriptName "read -p \"Press enter to continue\""
     
     
 scriptName :: FilePath
-scriptName = joinPath["..", "Daikon check inv " ++ source ++ ".sh"]
+scriptName = joinPath["..", "Daikon check inv " ++ source ++ " " ++ methodName ++ ".sh"]
 
 -- Adds the code to check the mutants
 checkMutants :: Int -> IO ()
 checkMutants 0 = return ()
 checkMutants n = do
-    appendFile scriptName ("echo \"compiling mutation " ++ show n ++ "..\"\njavac -cp \".;wlp/Tests/\" -d \"wlp/Tests\" \"$SOURCE mutants/" ++ show n ++ "/$PATHDIR/$SOURCE.java\"\n\n")
-    appendFile scriptName ("echo \"generating test suite\"\njava -cp \".;$HOME/KWT3daikon.jar;$HOME/libs/T3.jar;$HOME/libs/T3Daikon.jar;wlp/tests\" MyT3Daikon.Generator wlp/tests $PACKAGEDIR.$SOURCE $METHODNAME 50 1000 \"Daikon test suites/$SOURCE\"\n\n")
+    appendFile scriptName ("echo \"compiling mutation " ++ show n ++ "..\"\njavac -cp \".;wlp/Tests/\" -d \"wlp/Tests\" \"daikon $SOURCE mutants/" ++ show n ++ "/$PATHDIR/$SOURCE.java\"\n\n")
     appendFile scriptName ("echo \"checking invariants " ++ show n ++ "..\"\njava -cp \".;$HOME/KWT3daikon.jar;$HOME/libs/T3.jar;$HOME/libs/T3Daikon.jar;wlp/Tests\" MyT3Daikon.Miner -check \"Daikon test suites/$SOURCE.tr\" $METHODNAME \"Daikon invariants/$SOURCE\"\n\n")
-    checkMutants (n-1)
\ No newline at end of file
+    checkMutants (n-1)
+    
+    
+-- Renames mutant directories by subtracting a value from the mutant number
+renameMutants :: Int -> IO ()
+renameMutants n = do
+    let mutantsPath = joinPath ["..", "daikon " ++ source ++ " mutants"]
+    mutationFolders <- listDirectory (mutantsPath)
+    mapM_ (\old -> renameDirectory (joinPath [mutantsPath, show old]) (joinPath [mutantsPath, show (old - n)])) (sort (map read mutationFolders :: [Int]))
+    
\ No newline at end of file

Results/Daikon results.txt

+iterator:
+5 mutations with error found: 2, 3, 4, 5, 32
+4 mutations with error found not detected by wlp: 2, 3, 4, 5
+2 mutations with unterminated calls: 1 and 31
+1 mutation stuck in a loop: 35
\ No newline at end of file

Tests/Iterator.java

@@ -30,7 +30,12 @@ public class Iterator {
     /**
      * Simple constructor.
      */
-    private Iterator() {
+    public Iterator(int[] keys, double[] values, byte[] states, int count) {
+        
+        this.keys = keys;
+        this.values = values;
+        this.states = states;
+        this.count = count;
 
         // preserve the modification this.count of the map to detect concurrent modifications later
         this.referenceCount = this.count;

Tests/original tests/BaseSecantSolver.java

+/*
+ * 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 "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
+ *
+ * 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.math3.analysis.solvers;
+
+import org.apache.commons.math3.util.FastMath;
+import org.apache.commons.math3.analysis.UnivariateFunction;
+import org.apache.commons.math3.exception.ConvergenceException;
+import org.apache.commons.math3.exception.MathInternalError;
+
+import org.apache.commons.math3.exception.NoBracketingException;
+import org.apache.commons.math3.exception.NotStrictlyPositiveException;
+import org.apache.commons.math3.exception.NullArgumentException;
+import org.apache.commons.math3.exception.NumberIsTooLargeException;
+import org.apache.commons.math3.exception.util.LocalizedFormats;
+import org.apache.commons.math3.util.FastMath;
+
+/**
+ * Base class for all bracketing <em>Secant</em>-based methods for root-finding
+ * (approximating a zero of a univariate real function).
+ *
+ * <p>Implementation of the {@link RegulaFalsiSolver <em>Regula Falsi</em>} and
+ * {@link IllinoisSolver <em>Illinois</em>} methods is based on the
+ * following article: M. Dowell and P. Jarratt,
+ * <em>A modified regula falsi method for computing the root of an
+ * equation</em>, BIT Numerical Mathematics, volume 11, number 2,
+ * pages 168-174, Springer, 1971.</p>
+ *
+ * <p>Implementation of the {@link PegasusSolver <em>Pegasus</em>} method is
+ * based on the following article: M. Dowell and P. Jarratt,
+ * <em>The "Pegasus" method for computing the root of an equation</em>,
+ * BIT Numerical Mathematics, volume 12, number 4, pages 503-508, Springer,
+ * 1972.</p>
+ *
+ * <p>The {@link SecantSolver <em>Secant</em>} method is <em>not</em> a
+ * bracketing method, so it is not implemented here. It has a separate
+ * implementation.</p>
+ *
+ * @since 3.0
+ */
+public abstract class BaseSecantSolver
+    extends AbstractUnivariateSolver
+    implements BracketedUnivariateSolver<UnivariateFunction> {
+
+    /** Default absolute accuracy. */
+    protected static final double DEFAULT_ABSOLUTE_ACCURACY = 1e-6;
+
+    /** The kinds of solutions that the algorithm may accept. */
+    private AllowedSolution allowed;
+
+    /** The <em>Secant</em>-based root-finding method to use. */
+    private final Method method;
+
+    /**
+     * Construct a solver.
+     *
+     * @param absoluteAccuracy Absolute accuracy.
+     * @param method <em>Secant</em>-based root-finding method to use.
+     */
+    protected BaseSecantSolver(final double absoluteAccuracy, final Method method1) {
+        super(absoluteAccuracy);
+        this.allowed = AllowedSolution.ANY_SIDE;
+        this.method = method1;
+    }
+
+    /**
+     * Construct a solver.
+     *
+     * @param relativeAccuracy Relative accuracy.
+     * @param absoluteAccuracy Absolute accuracy.
+     * @param method <em>Secant</em>-based root-finding method to use.
+     */
+    protected BaseSecantSolver(final double relativeAccuracy,
+                               final double absoluteAccuracy1,
+                               final Method method2) {
+        super(relativeAccuracy, absoluteAccuracy1);
+        this.allowed = AllowedSolution.ANY_SIDE;
+        this.method = method2;
+    }
+
+    /**
+     * Construct a solver.
+     *
+     * @param relativeAccuracy Maximum relative error.
+     * @param absoluteAccuracy Maximum absolute error.
+     * @param functionValueAccuracy Maximum function value error.
+     * @param method <em>Secant</em>-based root-finding method to use
+     */
+    protected BaseSecantSolver(final double relativeAccuracy2,
+                               final double absoluteAccuracy2,
+                               final double functionValueAccuracy,
+                               final Method method3) {
+        super(relativeAccuracy2, absoluteAccuracy2, functionValueAccuracy);
+        this.allowed = AllowedSolution.ANY_SIDE;
+        this.method = method3;
+    }
+
+    protected final double doSolve()
+        throws ConvergenceException {
+        // Get initial solution
+        double x0 = getMin();
+        double x1 = getMax();
+        double f0 = computeObjectiveValue(x0);
+        double f1 = computeObjectiveValue(x1);
+
+        // If one of the bounds is the exact root, return it. Since these are
+        // not under-approximations or over-approximations, we can return them
+        // regardless of the allowed solutions.
+        if (f0 == 0.0) {
+            return x0;
+        }
+        if (f1 == 0.0) {
+            return x1;
+        }
+
+        // Verify bracketing of initial solution.
+        verifyBracketing(x0, x1);
+
+        // Get accuracies.
+        final double ftol = getFunctionValueAccuracy();
+        final double atol = getAbsoluteAccuracy();
+        final double rtol = getRelativeAccuracy();
+
+        // Keep track of inverted intervals, meaning that the left bound is
+        // larger than the right bound.
+        boolean inverted = false;
+
+        // Keep finding better approximations.
+        while (true) {
+            // Calculate the next approximation.
+            final double x = x1 - ((f1 * (x1 - x0)) / (f1 - f0));
+            final double fx = computeObjectiveValue(x);
+
+            // If the new approximation is the exact root, return it. Since
+            // this is not an under-approximation or an over-approximation,
+            // we can return it regardless of the allowed solutions.
+            if (fx == 0.0) {
+                return x;
+            }
+
+            // Update the bounds with the new approximation.
+            if (f1 * fx < 0) {
+                // The value of x1 has switched to the other bound, thus inverting
+                // the interval.
+                x0 = x1;
+                f0 = f1;
+                inverted = !inverted;
+            } else {
+                switch (this.method) {
+                case ILLINOIS:
+                    f0 *= 0.5;
+                    break;
+                case PEGASUS:
+                    f0 *= f1 / (f1 + fx);
+                    break;
+                case REGULA_FALSI:
+                    // Detect early that algorithm is stuck, instead of waiting
+                    // for the maximum number of iterations to be exceeded.
+                    if (x == x1) {
+                        throw new ConvergenceException();
+                    }
+                    break;
+                default:
+                    // Should never happen.
+                    throw new MathInternalError();
+                }
+            }
+            // Update from [x0, x1] to [x0, x].
+            x1 = x;
+            f1 = fx;
+
+            // If the function value of the last approximation is too small,
+            // given the function value accuracy, then we can't get closer to
+            // the root than we already are.
+            if (FastMath.abs(f1) <= ftol) {
+                switch (this.allowed) {
+                case ANY_SIDE:
+                    return x1;
+                case LEFT_SIDE:
+                    if (inverted) {
+                        return x1;
+                    }
+                    break;
+                case RIGHT_SIDE:
+                    if (!inverted) {
+                        return x1;
+                    }
+                    break;
+                case BELOW_SIDE:
+                    if (f1 <= 0) {
+                        return x1;
+                    }
+                    break;
+                case ABOVE_SIDE:
+                    if (f1 >= 0) {
+                        return x1;
+                    }
+                    break;
+                default:
+                    throw new MathInternalError();
+                }
+            }
+
+            // If the current interval is within the given accuracies, we
+            // are satisfied with the current approximation.
+            if (FastMath.abs(x1 - x0) < FastMath.max(rtol * FastMath.abs(x1),
+                                                     atol)) {
+                switch (this.allowed) {
+                case ANY_SIDE:
+                    return x1;
+                case LEFT_SIDE:
+                    return inverted ? x1 : x0;
+                case RIGHT_SIDE:
+                    return inverted ? x0 : x1;
+                case BELOW_SIDE:
+                    return (f1 <= 0) ? x1 : x0;
+                case ABOVE_SIDE:
+                    return (f1 >= 0) ? x1 : x0;
+                default:
+                    throw new MathInternalError();
+                }
+            }
+        }
+    }
+
+    protected enum Method {
+        REGULA_FALSI,
+        ILLINOIS,
+        PEGASUS;
+    }
+    
+    //
+    // UnivariateSolverUtils
+    //
+    
+    public static double midpoint(double a, double b) {
+        return (a + b) * 0.5;
+    }
+
+    public static boolean isBracketing(UnivariateFunction function1,
+                                       final double lower1,
+                                       final double upper1)
+        throws NullArgumentException {
+        if (function1 == null) {
+            throw new NullArgumentException(LocalizedFormats.FUNCTION);
+        }
+        final double fLo = function1.value(lower1);
+        final double fHi = function1.value(upper1);
+        return (fLo >= 0 && fHi <= 0) || (fLo <= 0 && fHi >= 0);
+    }
+
+    public static boolean isSequence1(final double start,
+                                     final double mid,
+                                     final double end) {
+        return (start < mid) && (mid < end);
+    }
+
+    public static void verifyInterval1(final double lower2,
+                                      final double upper2)
+        throws NumberIsTooLargeException {
+        if (lower2 >= upper2) {
+            throw new NumberIsTooLargeException(LocalizedFormats.ENDPOINTS_NOT_AN_INTERVAL,
+                                                lower2, upper2, false);
+        }
+    }
+
+    public static void verifySequence1(final double lower3,
+                                      final double initial,
+                                      final double upper3)
+        throws NumberIsTooLargeException {
+        verifyInterval1(lower3, initial);
+        verifyInterval1(initial, upper3);
+    }
+
+    public static void verifyBracketing(UnivariateFunction function2,
+                                        final double lower4,
+                                        final double upper4)
+        throws NullArgumentException,
+               NoBracketingException {
+        if (function2 == null) {
+            throw new NullArgumentException(LocalizedFormats.FUNCTION);
+        }
+        verifyInterval1(lower4, upper4);
+        if (!isBracketing(function2, lower4, upper4)) {
+            throw new NoBracketingException(lower4, upper4,
+                                            function2.value(lower4),
+                                            function2.value(upper4));
+        }
+    }
+    
+}

Tests/original tests/GradientFunction.java

+/*
+ * 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 "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
+ *
+ * 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.math3.analysis.differentiation;
+
+import org.apache.commons.math3.analysis.MultivariateVectorFunction;
+
+/** Class representing the gradient of a multivariate function.
+ * <p>
+ * The vectorial components of the function represent the derivatives
+ * with respect to each function parameters.
+ * </p>
+ * @since 3.1
+ */
+public class GradientFunction implements MultivariateVectorFunction {
+
+    /** Underlying real-valued function. */
+    private final MultivariateDifferentiableFunction f;
+
+    /** Simple constructor.
+     * @param f underlying real-valued function
+     */
+    public GradientFunction(final MultivariateDifferentiableFunction f1) {
+        this.f = f1;
+    }
+
+    /** {@inheritDoc} */
+    public double[] value(double[] point) {
+
+        // set up parameters
+        final DerivativeStructure[] dsX = new DerivativeStructure[point.length];
+        for (int i = 0; i < point.length; ++i) {
+            dsX[i] = new DerivativeStructure(point.length, 1, i, point[i]);
+        }
+
+        // compute the derivatives
+        final DerivativeStructure dsY = this.f.value(dsX);
+
+        // extract the gradient
+        final double[] y = new double[point.length];
+        final int[] orders = new int[point.length];
+        for (int j = 0; j < point.length; ++j) {
+            orders[j] = 1;
+            y[j] = dsY.getPartialDerivative(orders);
+            orders[j] = 0;
+        }
+
+        return y;
+
+    }
+
+}

Tests/original tests/Iterator.java

+
+// Copied from OpenIntToDoubleHashMap.java
+
+package org.apache.commons.math3.util;
+
+import java.io.IOException;
+import java.io.ObjectInputStream;
+import java.io.Serializable;
+import java.util.ConcurrentModificationException;
+import java.util.NoSuchElementException;
+
+/** Iterator class for the map. */
+public class Iterator {
+    
+    protected static final byte FULL    = 1;
+    private int[] keys;
+    private double[] values;
+    private byte[] states;
+    private int count;
+    
+    /** Reference modification this.count. */
+    private final int referenceCount;
+
+    /** Index of current element. */
+    private int current;
+
+    /** Index of next element. */
+    private int next;
+
+    /**
+     * Simple constructor.
+     */
+    private Iterator() {
+
+        // preserve the modification this.count of the map to detect concurrent modifications later
+        this.referenceCount = this.count;
+
+        // initialize this.current index
+        this.next = -1;
+        try {
+            this.advance();
+        } catch (NoSuchElementException nsee) { // NOPMD
+            // ignored
+        }
+
+    }
+
+    /**
+     * Check if there is a this.next element in the map.
+     * @return true if there is a this.next element
+     */
+    public boolean hasNext() {
+        return this.next >= 0;
+    }
+
+    /**
+     * Get the key of this.current entry.
+     * @return key of this.current entry
+     * @exception ConcurrentModificationException if the map is modified during iteration
+     * @exception NoSuchElementException if there is no element left in the map
+     */
+    public int key()
+        throws ConcurrentModificationException, NoSuchElementException {
+        if (this.referenceCount != this.count) {
+            throw new ConcurrentModificationException();
+        }
+        if (this.current < 0) {
+            throw new NoSuchElementException();
+        }
+        return this.keys[this.current];
+    }
+
+    /**
+     * Get the value of this.current entry.
+     * @return value of this.current entry
+     * @exception ConcurrentModificationException if the map is modified during iteration
+     * @exception NoSuchElementException if there is no element left in the map
+     */
+    public double value()
+        throws ConcurrentModificationException, NoSuchElementException {
+        if (this.referenceCount != this.count) {
+            throw new ConcurrentModificationException();
+        }
+        if (this.current < 0) {
+            throw new NoSuchElementException();
+        }
+        return this.values[this.current];
+    }
+
+    /**
+     * Advance iterator one step further.
+     * @exception ConcurrentModificationException if the map is modified during iteration
+     * @exception NoSuchElementException if there is no element left in the map
+     */
+    public void advance()
+        throws ConcurrentModificationException, NoSuchElementException {
+
+        if (this.referenceCount != this.count) {
+            throw new ConcurrentModificationException();
+        }
+
+        // advance on step
+        this.current = this.next;
+
+        // prepare this.next step
+        try {
+            while (this.states[++this.next] != this.FULL) { // NOPMD
+                // nothing to do
+            }
+        } catch (ArrayIndexOutOfBoundsException e) {
+            this.next = -2;
+            if (this.current < 0) {
+                throw new NoSuchElementException();
+            }
+        }
+
+    }
+
+}
\ No newline at end of file