/**
* Marshall a Genotype instance into an XML Element representation, including its population of
* Chromosome instances as sub-elements. This may be useful in scenarios where representation as
* an entire Document is undesirable, such as when the representation of this Genotype is to be
* combined with other elements in a single Document.
*
* @param a_subject the genotype to represent as an XML element
* @param a_xmlDocument a Document instance that will be used to create the Element instance. Note
* that the element will NOT be added to the document by this method
* @return an Element object representing the given Genotype
* @author Neil Rotstan
* @since 1.0
* @deprecated use XMLDocumentBuilder instead
*/
public static Element representGenotypeAsElement(
final Genotype a_subject, final Document a_xmlDocument) {
Population population = a_subject.getPopulation();
// Start by creating the genotype element and its size attribute,
// which represents the number of chromosomes present in the
// genotype.
// --------------------------------------------------------------
Element genotypeTag = a_xmlDocument.createElement(GENOTYPE_TAG);
genotypeTag.setAttribute(SIZE_ATTRIBUTE, Integer.toString(population.size()));
// Next, add nested elements for each of the chromosomes in the
// genotype.
// ------------------------------------------------------------
for (int i = 0; i < population.size(); i++) {
Element chromosomeElement =
representChromosomeAsElement(population.getChromosome(i), a_xmlDocument);
genotypeTag.appendChild(chromosomeElement);
}
return genotypeTag;
}
/**
* Executes the genetic algorithm to determine the minimum number of items necessary to make up
* the given target volume. The solution will then be written to the console.
*
* @param a_knapsackVolume the target volume for which this method is attempting to produce the
* optimal list of items
* @throws Exception
* @author Klaus Meffert
* @since 2.3
*/
public static void findItemsForVolume(double a_knapsackVolume) throws Exception {
// Start with a DefaultConfiguration, which comes setup with the
// most common settings.
// -------------------------------------------------------------
Configuration conf = new DefaultConfiguration();
conf.setPreservFittestIndividual(true);
// Set the fitness function we want to use. We construct it with
// the target volume passed in to this method.
// ---------------------------------------------------------
FitnessFunction myFunc = new KnapsackFitnessFunction(a_knapsackVolume);
conf.setFitnessFunction(myFunc);
// Now we need to tell the Configuration object how we want our
// Chromosomes to be setup. We do that by actually creating a
// sample Chromosome and then setting it on the Configuration
// object. As mentioned earlier, we want our Chromosomes to each
// have as many genes as there are different items available. We want the
// values (alleles) of those genes to be integers, which represent
// how many items of that type we have. We therefore use the
// IntegerGene class to represent each of the genes. That class
// also lets us specify a lower and upper bound, which we set
// to senseful values (i.e. maximum possible) for each item type.
// --------------------------------------------------------------
Gene[] sampleGenes = new Gene[itemVolumes.length];
for (int i = 0; i < itemVolumes.length; i++) {
sampleGenes[i] = new IntegerGene(conf, 0, (int) Math.ceil(a_knapsackVolume / itemVolumes[i]));
}
IChromosome sampleChromosome = new Chromosome(conf, sampleGenes);
conf.setSampleChromosome(sampleChromosome);
// Finally, we need to tell the Configuration object how many
// Chromosomes we want in our population. The more Chromosomes,
// the larger number of potential solutions (which is good for
// finding the answer), but the longer it will take to evolve
// the population (which could be seen as bad).
// ------------------------------------------------------------
conf.setPopulationSize(50);
// Create random initial population of Chromosomes.
// Here we try to read in a previous run via XMLManager.readFile(..)
// for demonstration purpose!
// -----------------------------------------------------------------
Genotype population;
try {
Document doc = XMLManager.readFile(new File("knapsackJGAP.xml"));
population = XMLManager.getGenotypeFromDocument(conf, doc);
} catch (FileNotFoundException fex) {
population = Genotype.randomInitialGenotype(conf);
}
population = Genotype.randomInitialGenotype(conf);
// Evolve the population. Since we don't know what the best answer
// is going to be, we just evolve the max number of times.
// ---------------------------------------------------------------
for (int i = 0; i < MAX_ALLOWED_EVOLUTIONS; i++) {
population.evolve();
}
// Save progress to file. A new run of this example will then be able to
// resume where it stopped before!
// ---------------------------------------------------------------------
// represent Genotype as tree with elements Chromomes and Genes
// ------------------------------------------------------------
DataTreeBuilder builder = DataTreeBuilder.getInstance();
IDataCreators doc2 = builder.representGenotypeAsDocument(population);
// create XML document from generated tree
// ---------------------------------------
XMLDocumentBuilder docbuilder = new XMLDocumentBuilder();
Document xmlDoc = (Document) docbuilder.buildDocument(doc2);
XMLManager.writeFile(xmlDoc, new File("knapsackJGAP.xml"));
// Display the best solution we found.
// -----------------------------------
IChromosome bestSolutionSoFar = population.getFittestChromosome();
System.out.println(
"The best solution has a fitness value of " + bestSolutionSoFar.getFitnessValue());
System.out.println("It contained the following: ");
int count;
double totalVolume = 0.0d;
for (int i = 0; i < bestSolutionSoFar.size(); i++) {
count = ((Integer) bestSolutionSoFar.getGene(i).getAllele()).intValue();
if (count > 0) {
System.out.println("\t " + count + " x " + itemNames[i]);
totalVolume += itemVolumes[i] * count;
}
}
System.out.println("\nFor a total volume of " + totalVolume + " ccm");
System.out.println("Expected volume was " + a_knapsackVolume + " ccm");
System.out.println("Volume difference is " + Math.abs(totalVolume - a_knapsackVolume) + " ccm");
}
public static void main(String[] args) throws InvalidConfigurationException {
// Reading data from xml
try {
new InputData().readFromFile(XML_TEST_FILENAME);
} catch (SAXException e) {
System.out.println(e.getMessage());
} catch (IOException e) {
System.out.println(e.getMessage());
} catch (ParserConfigurationException e) {
System.out.println(e.getMessage());
}
// Configuration conf = new DefaultConfiguration();
Configuration conf = new Configuration("myconf");
TimetableFitnessFunction fitnessFunction = new TimetableFitnessFunction();
InitialConstraintChecker timetableConstraintChecker = new InitialConstraintChecker();
// Creating genes
Gene[] testGenes = new Gene[CHROMOSOME_SIZE];
for (int i = 0; i < CHROMOSOME_SIZE; i++) {
testGenes[i] =
new GroupClassTeacherLessonTimeSG(
conf,
new Gene[] {
new GroupGene(conf, 1),
new ClassGene(conf, 1),
new TeacherGene(conf, 1),
new LessonGene(conf, 1),
new TimeGene(conf, 1)
});
}
System.out.println("==================================");
// Creating chromosome
Chromosome testChromosome;
testChromosome = new Chromosome(conf, testGenes);
testChromosome.setConstraintChecker(timetableConstraintChecker);
// Setup configuration
conf.setSampleChromosome(testChromosome);
conf.setPopulationSize(POPULATION_SIZE);
conf.setFitnessFunction(fitnessFunction); // add fitness function
BestChromosomesSelector myBestChromosomesSelector = new BestChromosomesSelector(conf);
conf.addNaturalSelector(myBestChromosomesSelector, false);
conf.setRandomGenerator(new StockRandomGenerator());
conf.setEventManager(new EventManager());
conf.setFitnessEvaluator(new DefaultFitnessEvaluator());
CrossoverOperator myCrossoverOperator = new CrossoverOperator(conf);
conf.addGeneticOperator(myCrossoverOperator);
TimetableMutationOperator myMutationOperator = new TimetableMutationOperator(conf);
conf.addGeneticOperator(myMutationOperator);
conf.setKeepPopulationSizeConstant(false);
// Creating genotype
// Population pop = new Population(conf, testChromosome);
// Genotype population = new Genotype(conf, pop);
Genotype population = Genotype.randomInitialGenotype(conf);
System.out.println("Our Chromosome: \n " + testChromosome.getConfiguration().toString());
System.out.println("------------evolution-----------------------------");
// Begin evolution
Calendar cal = Calendar.getInstance();
start_t = cal.getTimeInMillis();
for (int i = 0; i < MAX_EVOLUTIONS; i++) {
System.out.println(
"generation#: " + i + " population size:" + (Integer) population.getPopulation().size());
if (population.getFittestChromosome().getFitnessValue() >= THRESHOLD) break;
population.evolve();
}
cal = Calendar.getInstance();
finish_t = cal.getTimeInMillis();
System.out.println("--------------end of evolution--------------------");
Chromosome fittestChromosome = (Chromosome) population.getFittestChromosome();
System.out.println(
"-------------The best chromosome---fitness="
+ fittestChromosome.getFitnessValue()
+ "---");
System.out.println(" Group Class Time");
for (int i = 0; i < CHROMOSOME_SIZE; i++) {
GroupClassTeacherLessonTimeSG s =
(GroupClassTeacherLessonTimeSG) fittestChromosome.getGene(i);
System.out.println(
"Gene "
+ i
+ " contains: "
+ (Integer) s.geneAt(GROUP).getAllele()
+ " "
+ (Integer) s.geneAt(CLASS).getAllele()
+ " "
+ (Integer) s.geneAt(TEACHER).getAllele()
+ " "
+ (Integer) s.geneAt(LESSON).getAllele()
+ " "
+ (Integer) s.geneAt(TIME).getAllele());
// GroupGene gg = (GroupGene)s.geneAt(GROUP);
// System.out.println("gg's idGroup"+gg.getAllele()+" gg.getGroupSize()"+ gg.getGroupSize() );
}
System.out.println("Elapsed time:" + (double) (finish_t - start_t) / 1000 + "s");
// Display the best solution
OutputData od = new OutputData();
od.printToConsole(fittestChromosome);
// Write population to the disk
try {
od.printToFile(population, GENOTYPE_FILENAME, BEST_CHROMOSOME_FILENAME);
} catch (IOException e) {
System.out.println("IOException raised! " + e.getMessage());
}
}