1 files changed, 31 insertions, 140 deletions

diff --git a/src/jcgp/JCGP.java b/src/jcgp/JCGP.java
index 898f229..f60fc22 100644
--- a/src/jcgp/JCGP.java
+++ b/src/jcgp/JCGP.java
@@ -1,13 +1,17 @@
 package jcgp;
 
 import java.io.File;
-import java.lang.reflect.Constructor;
-import java.util.ArrayList;
-import java.util.Set;
 
 import jcgp.backend.modules.es.EvolutionaryStrategy;
+import jcgp.backend.modules.es.MuPlusLambda;
+import jcgp.backend.modules.es.TournamentSelection;
+import jcgp.backend.modules.mutator.FixedPointMutator;
 import jcgp.backend.modules.mutator.Mutator;
+import jcgp.backend.modules.mutator.PercentPointMutator;
+import jcgp.backend.modules.mutator.ProbabilisticMutator;
+import jcgp.backend.modules.problem.DigitalCircuitProblem;
 import jcgp.backend.modules.problem.Problem;
+import jcgp.backend.modules.problem.SymbolicRegressionProblem;
 import jcgp.backend.modules.problem.TestCaseProblem;
 import jcgp.backend.parsers.ChromosomeParser;
 import jcgp.backend.parsers.FunctionParser;
@@ -19,8 +23,6 @@ import jcgp.backend.resources.ModifiableResources;
 import jcgp.backend.resources.Resources;
 import jcgp.backend.statistics.StatisticsLogger;
 
-import org.reflections.Reflections;
-
 /**
  * 
  * Top-level JCGP class. This class is the entry point for a CGP experiment. 
@@ -51,21 +53,30 @@ public class JCGP {
 	 * module, 0 by default.
 	 */
 	// mutators
-	private ArrayList<Mutator> mutators;
+	private Mutator[] mutators = new Mutator[] {
+			new PercentPointMutator(resources),
+			new FixedPointMutator(resources),
+			new ProbabilisticMutator(resources)
+	};
 	private Mutator mutator;
 	
 	// evolutionary algorithms
-	private ArrayList<EvolutionaryStrategy> evolutionaryStrategies;
+	private EvolutionaryStrategy[] evolutionaryStrategies = new EvolutionaryStrategy[] {
+			new MuPlusLambda(resources),
+			new TournamentSelection(resources)
+	};
 	private EvolutionaryStrategy evolutionaryStrategy;
 	
 	// problem types
-	private ArrayList<Problem> problems;
+	private Problem[] problems = new Problem[] {
+			new DigitalCircuitProblem(resources),
+			new SymbolicRegressionProblem(resources)
+	};
 	private Problem problem;
 
 	private Population population;
 
 	private StatisticsLogger statistics = new StatisticsLogger();
-	private Reflections reflections;
 	
 	// these record the best results found in the run, in case the runs ends before a perfect solution is found
 	private int lastImprovementGeneration = 0, activeNodes = 0;
@@ -104,135 +115,15 @@ public class JCGP {
 	 * Creates a new instance of JCGP.
 	 */
 	public JCGP() {
-		// prepare reflections instance
-		reflections = new Reflections("jcgp");
-		
-		// generate module lists from all encountered valid modules
-		createEvolutionaryStrategyList();
-		createMutatorList();
-		createProblemList();
+		// initialise modules
+		setEvolutionaryStrategy(0);
+		setMutator(0);
+		setProblem(0);
 
 		// create a new population
 		population = new Population(resources);
 	}
-
-	/**
-	 * Iterates through all classes in the classpath and builds a list
-	 * of instances of all valid evolutionary strategies found. In order
-	 * to be included in this list, a class must implement {@code EvolutionaryStrategy}
-	 * and must contain a constructor with a {@code Resources} object as its only argument.
-	 */
-	private void createEvolutionaryStrategyList() {
-		Set<Class<? extends EvolutionaryStrategy>> esList = reflections.getSubTypesOf(EvolutionaryStrategy.class);
-		evolutionaryStrategies = new ArrayList<EvolutionaryStrategy>();
-		
-		// go through all subclasses of EvolutionaryStrategy
-		for (Class<? extends EvolutionaryStrategy> esType : esList) {
-			Constructor<? extends EvolutionaryStrategy> constructor;
-			try {
-				constructor = esType.getConstructor(Resources.class);
-			} catch (NoSuchMethodException | SecurityException e) {
-				// constructor most likely doesnt exist, try next class
-				System.out.println("Warning: could not find valid constructor for " + esType.getName() + ", skipping...");
-				continue;
-			}
-			
-			if (constructor != null) {
-				EvolutionaryStrategy es;
-				try {
-					es = (EvolutionaryStrategy) constructor.newInstance(resources);
-				} catch (Exception e) {
-					// could not instantiate for some reason, keep going
-					System.out.println("Warning: could not instantiate " + esType.getName() + ", skipping...");
-					continue;
-				}
-				// add it to the list if it was instantiated properly
-				evolutionaryStrategies.add(es);
-			}
-		}
-		// choose the initial module
-		evolutionaryStrategy = evolutionaryStrategies.get(0);
-	}
 	
-	/**
-	 * Iterates through all classes in the classpath and builds a list
-	 * of instances of all valid mutators found. In order to be included 
-	 * in this list, a class must implement {@code Mutator}
-	 * and must contain a constructor with a {@code Resources} object as its only argument.
-	 */
-	private void createMutatorList() {
-		Set<Class<? extends Mutator>> mutatorList = reflections.getSubTypesOf(Mutator.class);
-		mutators = new ArrayList<Mutator>();
-		
-		// go through all subclasses of Mutator
-		for (Class<? extends Mutator> mutatorType : mutatorList) {
-			Constructor<? extends Mutator> constructor;
-			try {
-				constructor = mutatorType.getConstructor(Resources.class);
-			} catch (NoSuchMethodException | SecurityException e) {
-				// constructor most likely doesnt exist, try next class
-				System.out.println("Warning: could not find valid constructor for " 
-				+ mutatorType.getName() + ", skipping...");
-				continue;
-			}
-			
-			if (constructor != null) {
-				Mutator mutator;
-				try {
-					mutator = (Mutator) constructor.newInstance(resources);
-				} catch (Exception e) {
-					// could not instantiate for some reason, keep going
-					System.out.println("Warning: could not instantiate " + mutatorType.getName() + ", skipping...");
-					continue;
-				}
-				// add it to the list if it was instantiated properly
-				mutators.add(mutator);
-			}
-		}
-		// choose the initial module
-		mutator = mutators.get(0);
-	}
-	
-	/**
-	 * Iterates through all classes in the classpath and builds a list
-	 * of instances of all valid problem types found. In order to be included 
-	 * in this list, a class must implement {@code Problem}
-	 * and must contain a constructor with a {@code Resources} object as its only argument.
-	 */
-	private void createProblemList() {
-		Set<Class<? extends Problem>> problemTypes = reflections.getSubTypesOf(Problem.class);
-		problems = new ArrayList<Problem>();
-		
-		// go through all subclasses of Problem
-		for (Class<? extends Problem> problemType : problemTypes) {
-			
-			Constructor<? extends Problem> constructor;
-			try {
-				constructor = problemType.getConstructor(Resources.class);
-			} catch (NoSuchMethodException | SecurityException e) {
-				// constructor most likely doesnt exist, try next class
-				System.out.println("Warning: could not find valid constructor for " 
-				+ problemType.getName() + ", skipping...");
-				continue;
-			}
-			
-			if (constructor != null) {
-				Problem problem;
-				try {
-					problem = (Problem) constructor.newInstance(resources);
-				} catch (Exception e) {
-					// could not instantiate for some reason, keep going
-					System.out.println("Warning: could not instantiate " + problemType.getName() + ", skipping...");
-					continue;
-				}
-				// add it to the list if it was instantiated properly
-				problems.add(problem);
-			}
-		}
-		// choose the initial module
-		problem = problems.get(0);
-		resources.setFunctionSet(problem.getFunctionSet());
-	}
 
 	/**
 	 * Returns a reference to the {@code ModifiableResources} used by the
@@ -256,7 +147,7 @@ public class JCGP {
 	/**
 	 * @return a complete list of the experiment's mutators.
 	 */
-	public ArrayList<Mutator> getMutators() {
+	public Mutator[] getMutators() {
 		return mutators;
 	}
 
@@ -272,7 +163,7 @@ public class JCGP {
 	/**
 	 * @return a complete list of the experiment's evolutionary strategies.
 	 */
-	public ArrayList<EvolutionaryStrategy> getEvolutionaryStrategies() {
+	public EvolutionaryStrategy[] getEvolutionaryStrategies() {
 		return evolutionaryStrategies;
 	}
 
@@ -288,7 +179,7 @@ public class JCGP {
 	/**
 	 * @return a complete list of the experiment's problem types.
 	 */
-	public ArrayList<Problem> getProblems() {
+	public Problem[] getProblems() {
 		return problems;
 	}
 
@@ -305,7 +196,7 @@ public class JCGP {
 	 * @param index the index of the desired mutator.
 	 */
 	public void setMutator(int index) {
-		this.mutator = mutators.get(index);
+		this.mutator = mutators[index];
 		resources.println("[CGP] Mutator selected: " + mutator.toString());
 	}
 
@@ -314,7 +205,7 @@ public class JCGP {
 	 * @param index the index of the desired evolutionary strategy.
 	 */
 	public void setEvolutionaryStrategy(int index) {	
-		this.evolutionaryStrategy = evolutionaryStrategies.get(index);
+		this.evolutionaryStrategy = evolutionaryStrategies[index];
 		resources.println("[CGP] Evolutionary strategy selected: " + evolutionaryStrategy.toString());
 	}
 
@@ -323,7 +214,7 @@ public class JCGP {
 	 * @param index the index of the desired problem type.
 	 */
 	public void setProblem(int index) {
-		this.problem = problems.get(index);
+		this.problem = problems[index];
 		resources.setFunctionSet(problem.getFunctionSet());
 		resources.setFitnessOrientation(problem.getFitnessOrientation());
 	}
@@ -348,7 +239,7 @@ public class JCGP {
 			if (resources.currentGeneration() < resources.generations()) {
 				
 				// we still have generations left to go
-				int perfect = problem.perfectSolutionFound(population);
+				int perfect = problem.hasPerfectSolution(population);
 				if (perfect >= 0) {
 					// log results
 					statistics.logRun(resources.currentGeneration(), population.get(perfect).getFitness(), population.get(perfect).getActiveNodes().size(), true);