/**
  * Returns a list of du pairs of the specific type.
  *
  * @param type the type of pairs. See DefUseCoverageTestFitness.DefUsePairType
  * @return
  */
 private static ArrayList<DefUseCoverageTestFitness> getPairsOfType(DefUsePairType type) {
   ArrayList<DefUseCoverageTestFitness> pairs = new ArrayList<DefUseCoverageTestFitness>();
   for (DefUseCoverageTestFitness pair : DefUseCoverageFactory.getDUGoals()) {
     if (pair.getType() == type) pairs.add(pair);
   }
   return pairs;
 }
  public DefUseCoverageSuiteFitness() {
    branchFitness = new BranchCoverageSuiteFitness();

    for (DefUseCoverageTestFitness defUse : goals) {
      if (defUse.isParameterGoal()) {
        String methodName = defUse.getGoalUse().getMethodName();
        if (!maxMethodCount.containsKey(methodName)) {
          maxMethodCount.put(methodName, 0);
        }

        maxMethodCount.put(methodName, maxMethodCount.get(methodName) + 1);
      } else {

        Definition def = defUse.getGoalDefinition();
        if (def == null) {
          // TODO: For this def we need to count method invocations
          logger.warn("Def is null for " + defUse);
        }
        if (!maxDefinitionCount.containsKey(def)) {
          maxDefinitionCount.put(def, 0);
        }
        maxDefinitionCount.put(def, maxDefinitionCount.get(def) + 1);
      }
    }
    // Why should this be a warning??
    //		for (Definition def : maxDefinitionCount.keySet()) {
    //			logger.warn("Known definition: " + def + ", " + maxDefinitionCount.get(def));
    //		}
  }
  /** printCoverage */
  public static void printCoverage() {

    LoggingUtils.getEvoLogger()
        .info(
            "* Time spent optimizing covered goals analysis: "
                + DefUseExecutionTraceAnalyzer.timeGetCoveredGoals
                + "ms");
    Map<DefUsePairType, Integer> totalGoals = initTotalGoals();
    for (DefUsePairType type : DefUseCoverageTestFitness.DefUsePairType.values()) {
      LoggingUtils.getEvoLogger()
          .info(
              "* Covered goals of type "
                  + type
                  + ": "
                  + mostCoveredGoals.get(type)
                  + " / "
                  + totalGoals.get(type));
      for (DefUseCoverageTestFitness pair : getPairsOfType(type)) {
        if (pair.isCovered()) {
          LoggingUtils.getEvoLogger().info("*(X) " + pair.toString());
        } else {
          LoggingUtils.getEvoLogger().info("*( ) " + pair.toString());
        }
      }
    }

    LoggingUtils.getEvoLogger()
        .info("* Covered " + countMostCoveredGoals() + "/" + countGoalsIn(totalGoals) + " goals");
  }
  // @Override
  public double getFitnessOld(Chromosome individual) {
    logger.trace("Calculating defuse fitness");

    TestSuiteChromosome suite = (TestSuiteChromosome) individual;
    List<ExecutionResult> results = runTestSuite(suite);
    double fitness = 0.0;

    if (DefUseCoverageFactory.detectAliasingGoals(results)) {
      goals = DefUseCoverageFactory.getDUGoals();
      logger.debug("New total number of goals: " + goals.size());
      totalGoals = initTotalGoals();
      for (DefUsePairType type : totalGoals.keySet()) {
        logger.info(type + ":" + totalGoals.get(type));
      }
    }

    Set<DefUseCoverageTestFitness> coveredGoalsSet =
        DefUseExecutionTraceAnalyzer.getCoveredGoals(results);

    initCoverageMaps();

    for (DefUseCoverageTestFitness goal : goals) {
      if (coveredGoalsSet.contains(goal)) {
        goal.setCovered(true);
        continue;
      }

      double goalFitness = 2.0;
      for (ExecutionResult result : results) {
        TestChromosome tc = new TestChromosome();
        tc.setTestCase(result.test);
        double resultFitness = goal.getFitness(tc, result);
        if (resultFitness < goalFitness) goalFitness = resultFitness;
        if (goalFitness == 0.0) {
          result.test.addCoveredGoal(goal);
          coveredGoalsSet.add(goal);
          goal.setCovered(true);
          break;
        }
      }
      fitness += goalFitness;
    }

    countCoveredGoals(coveredGoalsSet);
    trackCoverageStatistics(suite);
    updateIndividual(this, suite, fitness);

    int coveredGoalCount = countCoveredGoals();
    int totalGoalCount = countTotalGoals();
    if (fitness == 0.0 && coveredGoalCount < totalGoalCount)
      throw new IllegalStateException(
          "Fitness 0 implies 100% coverage "
              + coveredGoalCount
              + " / "
              + totalGoals
              + " (covered / total)");

    return fitness;
  }
  public static Map<DefUsePairType, Integer> initTotalGoals() {
    Map<DefUsePairType, Integer> r = new HashMap<DefUsePairType, Integer>();

    // init map
    for (DefUsePairType type : DefUseCoverageTestFitness.DefUsePairType.values()) r.put(type, 0);

    int num = 0;
    // count total goals according to type
    for (DefUseCoverageTestFitness goal : DefUseCoverageFactory.getDUGoals()) {
      logger.info("Goal " + num);
      num++;
      r.put(goal.getType(), r.get(goal.getType()) + 1);
    }

    return r;
  }
 private void countCoveredGoals(Set<DefUseCoverageTestFitness> coveredGoalsSet) {
   for (DefUseCoverageTestFitness goal : coveredGoalsSet) {
     coveredGoals.put(goal.getType(), coveredGoals.get(goal.getType()) + 1);
   }
 }
  // Not working yet
  // @Override
  public double getFitnessAlternative(
      AbstractTestSuiteChromosome<? extends ExecutableChromosome> individual) {
    TestSuiteChromosome suite = (TestSuiteChromosome) individual;
    List<ExecutionResult> results = runTestSuite(suite);
    if (DefUseCoverageFactory.detectAliasingGoals(results)) {
      logger.debug("New total number of goals: " + goals.size());
      totalGoals = initTotalGoals();
      for (DefUsePairType type : totalGoals.keySet()) {
        logger.info(type + ":" + totalGoals.get(type));
      }
    }

    Map<Definition, Set<TestChromosome>> passedDefinitions =
        new HashMap<Definition, Set<TestChromosome>>();
    Map<Definition, Integer> passedDefinitionCount = new HashMap<Definition, Integer>();
    Map<String, Set<TestChromosome>> executedMethods = new HashMap<String, Set<TestChromosome>>();
    Map<String, Integer> executedMethodsCount = new HashMap<String, Integer>();

    for (Definition def : maxDefinitionCount.keySet()) {
      passedDefinitionCount.put(def, 0);
    }
    for (String methodName : maxMethodCount.keySet()) {
      executedMethodsCount.put(methodName, 0);
    }

    for (TestChromosome test : suite.getTestChromosomes()) {
      ExecutionResult result = test.getLastExecutionResult();

      if (result.hasTimeout()) {
        logger.debug("Skipping test with timeout");
        double fitness = goals.size() * 100;
        updateIndividual(this, individual, fitness);
        suite.setCoverage(this, 0.0);
        logger.debug("Test case has timed out, setting fitness to max value " + fitness);
        return fitness;
      }

      for (Entry<Integer, Integer> entry :
          result.getTrace().getDefinitionExecutionCount().entrySet()) {
        Definition def = DefUsePool.getDefinitionByDefId(entry.getKey());
        if (def == null) {
          logger.warn("Could not find def " + entry.getKey());
          continue;
        }
        if (!passedDefinitions.containsKey(def))
          passedDefinitions.put(def, new HashSet<TestChromosome>());

        if (!passedDefinitionCount.containsKey(def)) {
          // logger.warn("Weird, definition is not known: " + def);
          passedDefinitionCount.put(def, 0);
        }
        passedDefinitions.get(def).add(test);
        passedDefinitionCount.put(def, passedDefinitionCount.get(def) + entry.getValue());
      }

      for (Entry<String, Integer> entry : result.getTrace().getMethodExecutionCount().entrySet()) {
        if (executedMethodsCount.containsKey(entry.getKey()))
          executedMethodsCount.put(
              entry.getKey(), executedMethodsCount.get(entry.getKey()) + entry.getValue());
        if (!executedMethods.containsKey(entry.getKey())) {
          executedMethods.put(entry.getKey(), new HashSet<TestChromosome>());
        }
        executedMethods.get(entry.getKey()).add(test);
      }
      /*
      for (Integer id : result.getTrace().getPassedDefIDs()) {
      	Definition def = DefUsePool.getDefinitionByDefId(id);
      	if (!passedDefinitions.containsKey(def))
      		passedDefinitions.put(def, new HashSet<TestChromosome>());

      	passedDefinitions.get(def).add(test);
      	passedDefinitionCount.put(def, passedDefinitionCount.get(def) + 1);
      }
      */
    }

    // 1. Need to reach each definition
    double fitness = branchFitness.getFitness(individual);
    // logger.info("Branch fitness: " + fitness);

    // 3. For all covered defs, calculate minimal use distance
    // Set<DefUseCoverageTestFitness> coveredGoalsSet =
    // DefUseExecutionTraceAnalyzer.getCoveredGoals(results);
    Set<DefUseCoverageTestFitness> coveredGoalsSet =
        new HashSet<
            DefUseCoverageTestFitness>(); // DefUseExecutionTraceAnalyzer.getCoveredGoals(results);

    initCoverageMaps();
    Set<Definition> notFullyCoveredDefs = new HashSet<Definition>();
    boolean methodIsNotFullyCovered = false;

    for (DefUseCoverageTestFitness goal : goals) {
      if (coveredGoalsSet.contains(goal)) {
        continue;
      }

      double goalFitness = 2.0;
      Set<TestChromosome> coveringTests = new HashSet<TestChromosome>();

      if (goal.isParameterGoal()) {
        String methodKey =
            goal.getGoalUse().getClassName() + "." + goal.getGoalUse().getMethodName();
        if (executedMethods.containsKey(methodKey)) {
          coveringTests.addAll(executedMethods.get(methodKey));
        }
      } else {
        if (passedDefinitions.containsKey(goal.getGoalDefinition())) {
          coveringTests.addAll(passedDefinitions.get(goal.getGoalDefinition()));
        }
      }
      if (coveringTests.isEmpty()) {
        logger.debug("No tests cover " + goal);
      } else {
        logger.debug("Checking " + coveringTests.size() + " tests covering " + goal);
      }
      //			for (TestChromosome test : passedDefinitions.get(goal.getGoalDefinition())) {
      for (TestChromosome test : coveringTests) {
        // for (TestChromosome test : suite.getTestChromosomes()) {

        ExecutionResult result = test.getLastExecutionResult();
        DefUseFitnessCalculator calculator = new DefUseFitnessCalculator(goal, test, result);
        // double resultFitness = goal.getFitness(test, result);
        double resultFitness = calculator.calculateDUFitness();

        if (resultFitness < goalFitness) goalFitness = resultFitness;
        if (goalFitness == 0.0) {
          result.test.addCoveredGoal(goal);
          coveredGoalsSet.add(goal);
          break;
        }
      }
      if (goalFitness > 0.0) {
        if (goal.isParameterGoal()) notFullyCoveredDefs.add(goal.getGoalDefinition());
        else methodIsNotFullyCovered = true;
      }

      fitness += goalFitness;
    }

    // 2. Need to execute each definition X times
    // TODO ...unless all defuse pairs are covered?
    for (Entry<Definition, Integer> defCount : maxDefinitionCount.entrySet()) {
      if (notFullyCoveredDefs.contains(defCount.getKey())) {
        int executionCount = passedDefinitionCount.get(defCount.getKey());
        int max = defCount.getValue();
        if (executionCount < max) {
          fitness += normalize(max - executionCount);
        }
      }
    }
    if (methodIsNotFullyCovered) {
      for (Entry<String, Integer> methodCount : maxMethodCount.entrySet()) {
        int executionCount = executedMethodsCount.get(methodCount.getKey());
        int max = methodCount.getValue();
        if (executionCount < max) {
          fitness += normalize(max - executionCount);
        }
      }
    }

    countCoveredGoals(coveredGoalsSet);
    trackCoverageStatistics(suite);
    updateIndividual(this, individual, fitness);

    int coveredGoalCount = countCoveredGoals();
    int totalGoalCount = countTotalGoals();
    if (fitness == 0.0 && coveredGoalCount < totalGoalCount)
      throw new IllegalStateException(
          "Fitness 0 implies 100% coverage "
              + coveredGoalCount
              + " / "
              + totalGoals
              + " (covered / total)");

    return fitness;
  }