From edb7307f4dc2c0c67a2d172b01644891d87f96a8 Mon Sep 17 00:00:00 2001
From: Koen Wermer <koenwermer@gmail.com>
Date: Tue, 28 Feb 2017 22:48:59 +0100
Subject: [PATCH] added a modified version of Iterator.java for use with daikon
and added results for the mutation test on this class
---
Daikon.hs | 37 ++-
Results/Daikon results.txt | 5 +
Tests/Iterator.java | 7 +-
Tests/original tests/BaseSecantSolver.java | 305 +++++++++++++++++++++
Tests/original tests/GradientFunction.java | 65 +++++
Tests/original tests/Iterator.java | 119 ++++++++
6 files changed, 529 insertions(+), 9 deletions(-)
create mode 100644 Results/Daikon results.txt
create mode 100644 Tests/original tests/BaseSecantSolver.java
create mode 100644 Tests/original tests/GradientFunction.java
create mode 100644 Tests/original tests/Iterator.java
diff --git a/Daikon.hs b/Daikon.hs
index 1061d0e..2d363cc 100644
--- a/Daikon.hs
+++ b/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
diff --git a/Results/Daikon results.txt b/Results/Daikon results.txt
new file mode 100644
index 0000000..855df37
--- /dev/null
+++ b/Results/Daikon results.txt
@@ -0,0 +1,5 @@
+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
diff --git a/Tests/Iterator.java b/Tests/Iterator.java
index eda7b85..26bd75a 100644
--- a/Tests/Iterator.java
+++ b/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;
diff --git a/Tests/original tests/BaseSecantSolver.java b/Tests/original tests/BaseSecantSolver.java
new file mode 100644
index 0000000..48d835c
--- /dev/null
+++ b/Tests/original tests/BaseSecantSolver.java
@@ -0,0 +1,305 @@
+/*
+ * 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));
+ }
+ }
+
+}
diff --git a/Tests/original tests/GradientFunction.java b/Tests/original tests/GradientFunction.java
new file mode 100644
index 0000000..c85f6cf
--- /dev/null
+++ b/Tests/original tests/GradientFunction.java
@@ -0,0 +1,65 @@
+/*
+ * 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;
+
+ }
+
+}
diff --git a/Tests/original tests/Iterator.java b/Tests/original tests/Iterator.java
new file mode 100644
index 0000000..eda7b85
--- /dev/null
+++ b/Tests/original tests/Iterator.java
@@ -0,0 +1,119 @@
+
+// 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
--
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