org.evosuite.ga.Chromosome Maven / Gradle / Ivy
/**
* Copyright (C) 2010-2018 Gordon Fraser, Andrea Arcuri and EvoSuite
* contributors
*
* This file is part of EvoSuite.
*
* EvoSuite is free software: you can redistribute it and/or modify it
* under the terms of the GNU Lesser General Public License as published
* by the Free Software Foundation, either version 3.0 of the License, or
* (at your option) any later version.
*
* EvoSuite is distributed in the hope that it will be useful, but
* WITHOUT ANY WARRANTY; without even the implied warranty of
* MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
* Lesser Public License for more details.
*
* You should have received a copy of the GNU Lesser General Public
* License along with EvoSuite. If not, see , Serializable,
PublicCloneable {
private static final long serialVersionUID = -6921897301005213358L;
/** Constant logger */
private static final Logger logger = LoggerFactory.getLogger(Chromosome.class);
/**
* only used for testing/debugging
*/
protected Chromosome() {
// empty
}
/** Last recorded fitness value */
private LinkedHashMap, Double> fitnessValues = new LinkedHashMap, Double>();
/** Previous fitness, to see if there was an improvement */
private LinkedHashMap, Double> previousFitnessValues = new LinkedHashMap, Double>();
/** Has this chromosome changed since its fitness was last evaluated? */
private boolean changed = true;
/** Has local search been applied to this individual since it was last changed? */
private boolean localSearchApplied = false;
private LinkedHashMap, Double> coverageValues = new LinkedHashMap, Double>();
private LinkedHashMap, Integer> numsNotCoveredGoals = new LinkedHashMap, Integer>();
private LinkedHashMap, Integer> numsCoveredGoals = new LinkedHashMap, Integer>();
// protected double coverage = 0.0;
// protected int numOfCoveredGoals = 0;
/** Generation in which this chromosome was created */
protected int age = 0;
/** */
protected int rank = -1;
/** */
protected double distance = 0.0;
/** Keep track of how many times this Chromosome has been mutated */
private int numberOfMutations = 0;
/** Keep track of how many times this Chromosome has been evaluated */
private int numberOfEvaluations = 0;
// It is a non-negative number and it quantifies the tolerance of the system accepting a worse
// solution than the existing one. (field used by Chemical Reaction Optimization algorithms)
protected double kineticEnergy = Properties.INITIAL_KINETIC_ENERGY;
// When a molecule undergoes a collision, one of the elementary reactions will be triggered and it
// may experience a change in its molecular structure. It is a record of the total number of collisions
// a molecule has taken. (field used by Chemical Reaction Optimization algorithms)
protected int numCollisions = 0;
/**
* Return current fitness value
*
* @return a double.
*/
public double getFitness() {
if (fitnessValues.size() > 1) {
double sumFitnesses = 0.0;
for (FitnessFunction fitnessFunction : fitnessValues.keySet()) {
sumFitnesses += fitnessValues.get(fitnessFunction);
}
return sumFitnesses;
} else
return fitnessValues.isEmpty() ? 0.0 : fitnessValues.get(fitnessValues.keySet().iterator().next());
}
public double getFitness(FitnessFunction ff) {
return fitnessValues.containsKey(ff) ? fitnessValues.get(ff) : ff.getFitness((T)this); // Calculate new value if non is cached
}
public Map, Double> getFitnessValues() {
return this.fitnessValues;
}
public Map, Double> getPreviousFitnessValues() {
return this.previousFitnessValues;
}
public boolean hasExecutedFitness(FitnessFunction ff) {
return this.previousFitnessValues.containsKey(ff);
}
public void setFitnessValues(Map, Double> fits) {
//TODO mainfitness?
this.fitnessValues.clear();
this.fitnessValues.putAll(fits);
}
public void setPreviousFitnessValues(Map, Double> lastFits) {
this.previousFitnessValues.clear();
this.previousFitnessValues.putAll(lastFits);
}
/**
* Adds a fitness function and sets fitness, coverage, and numCoveredGoal
* default.
*
* @param ff
* a fitness function
*/
public void addFitness(FitnessFunction ff) {
if (ff.isMaximizationFunction())
this.addFitness(ff, 0.0, 0.0, 0);
else
this.addFitness(ff, Double.MAX_VALUE, 0.0, 0);
}
/**
* Adds a fitness function with an associated fitness value
*
* @param ff
* a fitness function
* @param fitnessValue
* the fitness value for {@code ff}
*/
public void addFitness(FitnessFunction ff, double fitnessValue) {
this.addFitness(ff, fitnessValue, 0.0, 0);
}
/**
* Adds a fitness function with an associated fitness value and coverage
* value
*
* @param ff
* a fitness function
* @param fitnessValue
* the fitness value for {@code ff}
* @param coverage
* the coverage value for {@code ff}
*/
public void addFitness(FitnessFunction ff, double fitnessValue, double coverage) {
this.addFitness(ff, fitnessValue, coverage, 0);
}
/**
* Adds a fitness function with an associated fitness value, coverage value,
* and number of covered goals.
*
* @param ff
* a fitness function
* @param fitnessValue
* the fitness value for {@code ff}
* @param coverage
* the coverage value for {@code ff}
* @param numCoveredGoals
* the number of covered goals for {@code ff}
*/
public void addFitness(FitnessFunction ff, double fitnessValue, double coverage,
int numCoveredGoals) {
this.fitnessValues.put(ff, fitnessValue);
this.previousFitnessValues.put(ff, fitnessValue);
this.coverageValues.put(ff, coverage);
this.numsCoveredGoals.put(ff, numCoveredGoals);
this.numsNotCoveredGoals.put(ff, -1);
}
/**
* Set new fitness value
*
* @param value
* a double.
*/
public void setFitness(FitnessFunction ff, double value) throws IllegalArgumentException {
if ((Double.compare(value, Double.NaN) == 0) || (Double.isInfinite(value))) {
// || ( value < 0 ) || ( ff == null ))
throw new IllegalArgumentException("Invalid value of Fitness: " + value + ", Fitness: "
+ ff.getClass().getName());
}
if (!fitnessValues.containsKey(ff)) {
previousFitnessValues.put(ff, value);
fitnessValues.put(ff, value);
} else {
previousFitnessValues.put(ff, fitnessValues.get(ff));
fitnessValues.put(ff, value);
}
}
public boolean hasFitnessChanged() {
for (FitnessFunction ff : fitnessValues.keySet()) {
if (!fitnessValues.get(ff).equals(previousFitnessValues.get(ff))) {
return true;
}
}
return false;
}
/**
* {@inheritDoc}
*
* Create a deep copy of the chromosome
*/
@Override
public abstract Chromosome clone();
/** {@inheritDoc} */
@Override
public abstract boolean equals(Object obj);
/** {@inheritDoc} */
@Override
public abstract int hashCode();
/**
* {@inheritDoc}
*
* Determine relative ordering of this chromosome to another chromosome. If
* the fitness values are equal, go through all secondary objectives and try
* to find one where the two are not equal.
*/
@Override
public int compareTo(Chromosome c) {
int i = (int) Math.signum(this.getFitness() - c.getFitness());
if (i == 0){
return compareSecondaryObjective(c);
}else
return i;
}
/**
* Secondary Objectives are specific to chromosome types
*
* @param o
* a {@link org.evosuite.ga.Chromosome} object.
* @return a int.
*/
public abstract int compareSecondaryObjective(T o);
/**
* Apply mutation
*/
public abstract void mutate();
/**
* Fixed single point cross over
*
* @param other
* a {@link org.evosuite.ga.Chromosome} object.
* @param position
* a int.
* @throws org.evosuite.ga.ConstructionFailedException
* if any.
*/
public void crossOver(Chromosome other, int position) throws ConstructionFailedException {
crossOver(other, position, position);
}
/**
* Single point cross over
*
* @param other
* a {@link org.evosuite.ga.Chromosome} object.
* @param position1
* a int.
* @param position2
* a int.
* @throws org.evosuite.ga.ConstructionFailedException
* if any.
*/
public abstract void crossOver(Chromosome other, int position1, int position2)
throws ConstructionFailedException;
/**
* Apply the local search
*
* @param objective
* a {@link org.evosuite.ga.localsearch.LocalSearchObjective}
* object.
*/
public abstract boolean localSearch(LocalSearchObjective objective);
/**
* Apply the local search
*
* @param objective
* a {@link org.evosuite.ga.LocalSearchObjective} object.
*/
// public void applyAdaptiveLocalSearch(LocalSearchObjective objective) {
// // No-op
// }
/**
* Apply DSE
*
* @param algorithm
* a {@link org.evosuite.ga.GeneticAlgorithm} object.
*/
// public abstract boolean applyDSE(GeneticAlgorithm algorithm);
/**
* Return length of individual
*
* @return a int.
*/
public abstract int size();
/**
* Return whether the chromosome has changed since the fitness value was
* computed last
*
* @return a boolean.
*/
public boolean isChanged() {
return changed;
}
/**
* Set changed status to @param changed
*
* @param changed
* a boolean.
*/
public void setChanged(boolean changed) {
this.changed = changed;
// If it's changed, then that also implies LS is possible again
localSearchApplied = false;
}
public boolean hasLocalSearchBeenApplied() {
return localSearchApplied;
}
public void setLocalSearchApplied(boolean localSearchApplied) {
this.localSearchApplied = localSearchApplied;
}
/**
*
* Getter for the field coverage.
*
*
* Returns a single coverage value calculated as the average of
* coverage values for all fitness functions.
*
* @return a double.
*/
public double getCoverage() {
double sum = 0;
for (FitnessFunction fitnessFunction : coverageValues.keySet()) {
sum += coverageValues.get(fitnessFunction);
}
double cov = coverageValues.isEmpty() ? 0.0 : sum / coverageValues.size();
assert (cov >= 0.0 && cov <= 1.0) : "Incorrect coverage value " + cov + ". Expected value between 0 and 1";
return cov;
}
public int getNumOfCoveredGoals() {
int sum = 0;
for (FitnessFunction fitnessFunction : numsCoveredGoals.keySet()) {
sum += numsCoveredGoals.get(fitnessFunction);
}
return sum;
}
public int getNumOfNotCoveredGoals() {
int sum = 0;
for (FitnessFunction fitnessFunction : numsNotCoveredGoals.keySet()) {
sum += numsNotCoveredGoals.get(fitnessFunction);
}
return sum;
}
public void setNumsOfCoveredGoals(Map, Integer> fits) {
this.numsCoveredGoals.clear();
this.numsCoveredGoals.putAll(fits);
}
public void setNumsOfNotCoveredGoals(Map, Integer> fits) {
this.numsNotCoveredGoals.clear();
this.numsNotCoveredGoals.putAll(fits);
}
public void setNumOfNotCoveredGoals(FitnessFunction ff, int numCoveredGoals) {
this.numsNotCoveredGoals.put(ff, numCoveredGoals);
}
public Map, Integer> getNumsOfCoveredGoals() {
return this.numsCoveredGoals;
}
public LinkedHashMap, Integer> getNumsNotCoveredGoals() {
return numsNotCoveredGoals;
}
public Map, Double> getCoverageValues() {
return this.coverageValues;
}
public void setCoverageValues(Map, Double> coverages) {
this.coverageValues.clear();
this.coverageValues.putAll(coverages);
}
// public void setNumOfCoveredGoals(int numOfCoveredGoals) {
// this.numOfCoveredGoals = numOfCoveredGoals;
// }
/**
* Gets the coverage value for a given fitness function
*
* @param ff
* a fitness function
* @return the number of covered goals for {@code ff}
*/
public double getCoverage(FitnessFunction ff) {
return coverageValues.containsKey(ff) ? coverageValues.get(ff) : 0.0;
}
/**
* Sets the coverage value for a given fitness function
*
* @param ff
* a fitness function
* @param coverage
* the coverage value
*/
public void setCoverage(FitnessFunction ff, double coverage) {
this.coverageValues.put(ff, coverage);
}
/**
* Gets the number of covered goals for a given fitness function
*
* @param ff
* a fitness function
* @return the number of covered goals for {@code ff}
*/
public int getNumOfCoveredGoals(FitnessFunction ff) {
return numsCoveredGoals.containsKey(ff) ? numsCoveredGoals.get(ff) : 0;
}
/**
* Gets the number of not covered goals for a given fitness function
*
* @param ff
* a fitness function
* @return the number of covered goals for {@code ff}
*/
public int getNumOfNotCoveredGoals(FitnessFunction ff) {
return numsNotCoveredGoals.containsKey(ff) ? numsNotCoveredGoals.get(ff) : 0;
}
/**
* Sets the number of covered goals for a given fitness function
*
* @param ff
* a fitness function
* @param numCoveredGoals
* the number of covered goals
*/
public void setNumOfCoveredGoals(FitnessFunction ff, int numCoveredGoals) {
this.numsCoveredGoals.put(ff, numCoveredGoals);
}
public void updateAge(int generation) {
this.age = generation;
}
public int getAge() {
return age;
}
public int getRank() {
return this.rank;
}
public void setRank(int r) {
this.rank = r;
}
public double getDistance() {
return this.distance;
}
public void setDistance(double d) {
this.distance = d;
}
public double getFitnessInstanceOf(Class clazz) {
for (FitnessFunction fitnessFunction : fitnessValues.keySet()) {
if (clazz.isInstance(fitnessFunction))
return fitnessValues.get(fitnessFunction);
}
return 0.0;
}
public double getCoverageInstanceOf(Class clazz) {
for (FitnessFunction fitnessFunction : coverageValues.keySet()) {
if (clazz.isInstance(fitnessFunction))
return coverageValues.get(fitnessFunction);
}
return 0.0;
}
/**
* Increases by one the number of times this chromosome has been mutated
*/
public void increaseNumberOfMutations() {
this.numberOfMutations++;
}
/**
* Return number of times this chromosome has been mutated
*/
public int getNumberOfMutations() {
return this.numberOfMutations;
}
/**
* Set number of times this chromosome has been mutated
*/
public void setNumberOfMutations(int numberOfMutations) {
this.numberOfMutations = numberOfMutations;
}
/**
* Increases by one the number of times this chromosome has been evaluated
*/
public void increaseNumberOfEvaluations() {
this.numberOfEvaluations++;
}
/**
* Return number of times this chromosome has been evaluated
*/
public int getNumberOfEvaluations() {
return this.numberOfEvaluations;
}
/**
* Set number of times this chromosome has been evaluated
*/
public void setNumberOfEvaluations(int numberOfEvaluations) {
this.numberOfEvaluations = numberOfEvaluations;
}
/**
* Returns the tolerance of the system accepting a worse solution than the existing one. (Note:
* method used by Chemical Reaction Optimization algorithms)
*
* @return a double value
*/
public double getKineticEnergy() {
return this.kineticEnergy;
}
/**
* Sets the tolerance of the system accepting a worse solution than the existing one. (Note:
* method used by Chemical Reaction Optimization algorithms)
*
* @param kineticEnergy a double value
*/
public void setKineticEnergy(double kineticEnergy) {
this.kineticEnergy = kineticEnergy;
}
/**
* Returns the total number of collisions a chromosome (i.e., a molecule in a CRO scenario) has
* taken. (Note: method used by Chemical Reaction Optimization algorithms)
*
* @return a integer value
*/
public int getNumCollisions() {
return this.numCollisions;
}
/**
* Sets the total number of collisions of a chromosome (i.e., a molecule in a CRO scenario).
* (Note: method used by Chemical Reaction Optimization algorithms)
*
* @param numCollisions a integer value
*/
public void setNumCollisions(int numCollisions) {
this.numCollisions = numCollisions;
}
/**
* Sets the total number of collisions of a chromosome (i.e., a molecule in a CRO scenario) to
* zero. (Note: method used by Chemical Reaction Optimization algorithms)
*/
public void resetNumCollisions() {
this.numCollisions = 0;
}
/**
* Increases the total number of collisions of a chromosome (i.e., a molecule in a CRO scenario)
* by one. (Note: method used by Chemical Reaction Optimization algorithms)
*/
public void increaseNumCollisionsByOne() {
this.numCollisions++;
}
}