Added fitness evaluation mechanism, though it might not be a very good design. Tests will be done to verify that.

16 files changed, 205 insertions, 72 deletions

diff --git a/README b/README
index 0b886c9..3241aae 100644
--- a/README
+++ b/README
@@ -66,3 +66,16 @@ sets the chromosome inputs and compares outputs for all TestCase objects given,
 accordingly.
 
 
+4/2
+
+TestCase has been implemented with a fair degree of defensiveness. A TruthTable class contains the test cases and provides
+a way to evaluate fitness.
+
+TruthTable is a system-wide resource, which may or may not be used by FitnessFunction to assign fitness values to the
+population; that is up to the user. 
+
+A standard fitness function which uses TruthTable is defined in TruthTableEvaluator.
+
+StandardMutator has been implemented, though it looks like it may need refactoring in the future.
+
+
diff --git a/src/jcgp/CGP.java b/src/jcgp/CGP.java
index 44c76b2..26d1d2b 100644
--- a/src/jcgp/CGP.java
+++ b/src/jcgp/CGP.java
@@ -3,20 +3,27 @@ package jcgp;
 import java.util.Random;
 
 import jcgp.ea.EvolutionaryAlgorithm;
+import jcgp.ea.Mutator;
 import jcgp.ea.StandardEA;
 import jcgp.ea.StandardMutator;
 import jcgp.fitness.FitnessFunction;
-import jcgp.fitness.TestFitFunction;
+import jcgp.fitness.TestCase;
+import jcgp.fitness.TruthTableEvaluator;
 import jcgp.function.Addition;
 import jcgp.function.Function;
 import jcgp.function.FunctionSet;
 import jcgp.function.Subtraction;
-import jcgp.population.*;
+import jcgp.population.Chromosome;
+import jcgp.population.Connection;
+import jcgp.population.Input;
+import jcgp.population.MutableElement;
+import jcgp.population.Node;
+import jcgp.population.Population;
 
 public final class CGP {
 
 	public static class Parameters {
-		private static int rows, columns, inputs, outputs, mutationRate, generations, runs, populationSize, levelsBack;
+		private static int rows, columns, inputs, outputs, mutationRate, generations, runs, populationSize, levelsBack, maxArity;
 
 		/**
 		 * @return the number of nodes
@@ -151,9 +158,25 @@ public final class CGP {
 			Parameters.runs = runs;
 		}
 
+		/**
+		 * @return the maxArity
+		 */
+		public static int getMaxArity() {
+			return maxArity;
+		}
+
+		/**
+		 * @param maxArity the maxArity to set
+		 */
+		private static void setMaxArity(int maxArity) {
+			Parameters.maxArity = maxArity;
+		}
+
+		
+		
 	}
 
-	public static class Utilities {
+	public abstract static class Utilities {
 
 		public static int getRandomInt(int limit){
 			return numberGenerator.nextInt(limit);
@@ -304,28 +327,42 @@ public final class CGP {
 		public static Function getFunction(int index) {
 			return functionSet.getFunction(index);
 		}
+	}
 
-		public static int getMaxArity() {
-			return maxArity;
+	public static class TruthTable {
+		
+		private static TestCase[] testCases;
+		
+		private static void setTestCases(TestCase ... testCases) {
+			TruthTable.testCases = testCases;
 		}
+		
+		public static TestCase getTestCase(int index) {
+			return testCases[index];
+		}
+		
+		public static int getTestCaseCount() {
+			return testCases.length;
+		}
+	
 	}
-
+	
 	// system-wide resources
 	private static FunctionSet functionSet;
 	private static Random numberGenerator;
-	private static int maxArity = 0;
 
-	// 
-	private FitnessFunction fitnessFunction;
+	// CGP components
 	private EvolutionaryAlgorithm ea;
+	private Mutator mutator;
 	private Population population;
+	private FitnessFunction fitnessFunction;
 
 	public CGP() {
 		initialise();
 
-		fitnessFunction.evaluatePopulation(population);
+		fitnessFunction.evaluate(population);
 
-		ea.evolve(population);
+		ea.evolve(population, mutator);
 	}
 
 	/**
@@ -350,14 +387,16 @@ public final class CGP {
 		functionSet = new FunctionSet(new Addition(), new Subtraction());
 
 		// compute and set maximum arity
-		maxArity = functionSet.getMaxArity();
+		Parameters.setMaxArity(functionSet.getMaxArity());
 
 		// initialise EA
-		ea = new StandardEA(new StandardMutator());
-
-		// initialise fitness function
-		fitnessFunction = new TestFitFunction();
+		ea = new StandardEA();
+		mutator = new StandardMutator();
 
+		// initialise fitness function and truth table
+		TruthTable.setTestCases(new TestCase(new int[] {2, 5, 4}, new int[] {1, 10, 15}));
+		fitnessFunction = new TruthTableEvaluator();
+		
 		// initialise population
 		population = new Population();
 
diff --git a/src/jcgp/ea/EvolutionaryAlgorithm.java b/src/jcgp/ea/EvolutionaryAlgorithm.java
index 6e264aa..9e72a1b 100644
--- a/src/jcgp/ea/EvolutionaryAlgorithm.java
+++ b/src/jcgp/ea/EvolutionaryAlgorithm.java
@@ -2,14 +2,14 @@ package jcgp.ea;
 
 import jcgp.population.Population;
 
-public abstract class EvolutionaryAlgorithm {
+public interface EvolutionaryAlgorithm {
 
-	protected Mutator mutator;
+//	protected Mutator mutator;
+//	
+//	public EvolutionaryAlgorithm(Mutator mutator) {
+//		this.mutator = mutator;
+//	}
 	
-	public EvolutionaryAlgorithm(Mutator mutator) {
-		this.mutator = mutator;
-	}
-	
-	public abstract void evolve(Population population);
+	public abstract void evolve(Population population, Mutator mutator);
 
 }
diff --git a/src/jcgp/ea/StandardEA.java b/src/jcgp/ea/StandardEA.java
index fe0b3f9..b98fe9e 100644
--- a/src/jcgp/ea/StandardEA.java
+++ b/src/jcgp/ea/StandardEA.java
@@ -3,15 +3,12 @@ package jcgp.ea;
 import jcgp.population.Chromosome;
 import jcgp.population.Population;
 
-public class StandardEA extends EvolutionaryAlgorithm {
-
-	public StandardEA(Mutator mutator) {
-		super(mutator);
-		
-	}
+public class StandardEA implements EvolutionaryAlgorithm {
 
 	@Override
-	public void evolve(Population population) {
+	public void evolve(Population population, Mutator mutator) {
+		
+		
 		for (Chromosome chromosome : population) {
 			mutator.mutate(chromosome);
 		}
diff --git a/src/jcgp/ea/StandardMutator.java b/src/jcgp/ea/StandardMutator.java
index 731215d..cab5c76 100644
--- a/src/jcgp/ea/StandardMutator.java
+++ b/src/jcgp/ea/StandardMutator.java
@@ -1,13 +1,31 @@
 package jcgp.ea;
 
+import jcgp.CGP.Parameters;
+import jcgp.CGP.Utilities;
 import jcgp.population.Chromosome;
+import jcgp.population.MutableElement;
+import jcgp.population.Node;
+import jcgp.population.Output;
 
 public class StandardMutator implements Mutator {
 
 	@Override
 	public void mutate(Chromosome chromosome) {
+		int mutations = (int) (Parameters.getMutationRate() * ((double) Parameters.getNodeNumber() / 100));
 		
-		
+		for (int i = 0; i < mutations; i++) {
+			MutableElement m = Utilities.getRandomMutable(chromosome);
+			
+			if (m instanceof Output) {
+				m.setConnection(Utilities.getRandomConnection(chromosome, m.getColumn()));
+			} else if (m instanceof Node) {
+				int geneType = Utilities.getRandomInt(1 + Parameters.getMaxArity());
+				if (geneType < 1) {
+					((Node) m).setFunction(Utilities.getRandomFunction());
+				} else {
+					m.setConnection(Utilities.getRandomConnection(chromosome, m.getColumn()));
+				}
+			}
+		}
 	}
-
 }
diff --git a/src/jcgp/fitness/FitnessEvaluator.java b/src/jcgp/fitness/FitnessEvaluator.java
deleted file mode 100644
index 5ecf679..0000000
--- a/src/jcgp/fitness/FitnessEvaluator.java
+++ /dev/null
@@ -1,17 +0,0 @@
-package jcgp.fitness;
-
-import jcgp.population.Population;
-
-public class FitnessEvaluator {
-
-	private FitnessFunction fitnessFunction;
-	
-	public FitnessEvaluator(FitnessFunction fitnessFunction) {
-		this.fitnessFunction = fitnessFunction;
-	}
-	
-	public void evaluateFitness(Population population) {
-		
-	}
-	
-}
diff --git a/src/jcgp/fitness/FitnessFunction.java b/src/jcgp/fitness/FitnessFunction.java
index 2155542..6fa63ef 100644
--- a/src/jcgp/fitness/FitnessFunction.java
+++ b/src/jcgp/fitness/FitnessFunction.java
@@ -3,7 +3,7 @@ package jcgp.fitness;
 import jcgp.population.Population;
 
 public interface FitnessFunction {
-	
-	public void evaluatePopulation(Population population);
+
+	public void evaluate(Population population);
 	
 }
diff --git a/src/jcgp/fitness/ParameterMismatchException.java b/src/jcgp/fitness/ParameterMismatchException.java
new file mode 100644
index 0000000..0ca69a7
--- /dev/null
+++ b/src/jcgp/fitness/ParameterMismatchException.java
@@ -0,0 +1,10 @@
+package jcgp.fitness;
+
+public class ParameterMismatchException extends RuntimeException {
+
+	/**
+	 * 
+	 */
+	private static final long serialVersionUID = -3161318886125868134L;
+
+}
diff --git a/src/jcgp/fitness/TestCase.java b/src/jcgp/fitness/TestCase.java
new file mode 100644
index 0000000..e2bd5ed
--- /dev/null
+++ b/src/jcgp/fitness/TestCase.java
@@ -0,0 +1,41 @@
+package jcgp.fitness;
+
+import jcgp.CGP.Parameters;
+
+public class TestCase {
+
+	private int[] inputs;
+	private int[] outputs;
+	
+	public TestCase(int[] inputs, int[] outputs) throws ParameterMismatchException {
+		if (inputs.length == Parameters.getInputs()) {
+			this.inputs = inputs;
+		} else {
+			throw new ParameterMismatchException();
+		}
+		
+		if (outputs.length == Parameters.getOutputs()) {
+			this.outputs = outputs;
+		} else {
+			throw new ParameterMismatchException();
+		}
+		
+	}
+	
+	public int getInput(int index) {
+		return inputs[index];
+	}
+	
+	public int getOutput(int index) {
+		return outputs[index];
+	}
+	
+	public int[] getInputs() {
+		return inputs;
+	}
+	
+	public int[] getOutputs() {
+		return outputs;
+	}
+	
+}
diff --git a/src/jcgp/fitness/TestFitFunction.java b/src/jcgp/fitness/TestFitFunction.java
deleted file mode 100644
index 00ee833..0000000
--- a/src/jcgp/fitness/TestFitFunction.java
+++ /dev/null
@@ -1,17 +0,0 @@
-package jcgp.fitness;
-
-import jcgp.population.Chromosome;
-import jcgp.population.Population;
-
-public class TestFitFunction implements FitnessFunction {
-
-	@Override
-	public void evaluatePopulation(Population population) {
-		
-		for (Chromosome c : population) {
-			int i = c.getOutput(0).calculate();
-			System.out.println(i);
-			c.setFitness(1);
-		}
-	}
-}
diff --git a/src/jcgp/fitness/TruthTableEvaluator.java b/src/jcgp/fitness/TruthTableEvaluator.java
new file mode 100644
index 0000000..64ca209
--- /dev/null
+++ b/src/jcgp/fitness/TruthTableEvaluator.java
@@ -0,0 +1,26 @@
+package jcgp.fitness;
+
+import jcgp.CGP.Parameters;
+import jcgp.CGP.TruthTable;
+import jcgp.population.Chromosome;
+import jcgp.population.Population;
+
+public class TruthTableEvaluator implements FitnessFunction {
+
+	@Override
+	public void evaluate(Population population) {
+		for (Chromosome chromosome : population) {
+			for (int t = 0; t < TruthTable.getTestCaseCount(); t++) {
+				chromosome.setInputs(TruthTable.getTestCase(t).getInputs());
+				int fitness = 0;
+				for (int o = 0; o < Parameters.getOutputs(); o++) {
+					if (chromosome.getOutput(o).calculate() == TruthTable.getTestCase(t).getOutput(o)) {
+						fitness++;
+					}
+				}
+				chromosome.setFitness(fitness);
+			}
+		}
+	}
+
+}
diff --git a/src/jcgp/population/Chromosome.java b/src/jcgp/population/Chromosome.java
index 70e8836..f060e14 100644
--- a/src/jcgp/population/Chromosome.java
+++ b/src/jcgp/population/Chromosome.java
@@ -45,7 +45,7 @@ public class Chromosome {
 		for (int r = 0; r < rows; r++) {
 			//nodes[r] = new Node[Parameters.getColumns()];
 			for (int c = 0; c < columns; c++) {
-				nodes[r][c] = new Node();
+				nodes[r][c] = new Node(c);
 			}
 		}
 		outputs = new Output[outputCount];
@@ -59,7 +59,7 @@ public class Chromosome {
 		// initialise nodes - [rows][columns]
 		for (int r = 0; r < nodes.length; r++) {
 			for (int c = 0; c < nodes.length; c++) {
-				Connection[] connections = new Connection[Utilities.getMaxArity()];
+				Connection[] connections = new Connection[Parameters.getMaxArity()];
 				for (int i = 0; i < connections.length; i++) {
 					connections[i] = Utilities.getRandomConnection(this, c);
 				}
diff --git a/src/jcgp/population/MutableElement.java b/src/jcgp/population/MutableElement.java
index 5eae4ef..8ac3724 100644
--- a/src/jcgp/population/MutableElement.java
+++ b/src/jcgp/population/MutableElement.java
@@ -4,4 +4,6 @@ public interface MutableElement {
 	
 	public void setConnection(Connection newConnection);
 	
+	public int getColumn();
+	
 }
diff --git a/src/jcgp/population/Node.java b/src/jcgp/population/Node.java
index 8958475..fd0cd47 100644
--- a/src/jcgp/population/Node.java
+++ b/src/jcgp/population/Node.java
@@ -1,5 +1,6 @@
 package jcgp.population;
 
+import jcgp.CGP.Parameters;
 import jcgp.CGP.Utilities;
 import jcgp.function.Function;
 
@@ -8,7 +9,12 @@ public class Node implements MutableElement, Connection {
 	
 	private Function function;
 	private Connection[] connections;
+	private int column;
 
+	public Node(int col) {
+		column = col;
+	}
+	
 	@Override
 	public int evaluate() {
 		return function.run(connections);
@@ -27,10 +33,16 @@ public class Node implements MutableElement, Connection {
 		
 		function = newFunction;
 		
-		if (newConnections.length >= Utilities.getMaxArity()) {
+		if (newConnections.length >= Parameters.getMaxArity()) {
 			connections = newConnections;
 		} else {
 			throw new InsufficientConnectionsException();
 		}
 	}
+
+	@Override
+	public int getColumn() {
+		
+		return column;
+	}
 }
diff --git a/src/jcgp/population/Output.java b/src/jcgp/population/Output.java
index 1640deb..eeae743 100644
--- a/src/jcgp/population/Output.java
+++ b/src/jcgp/population/Output.java
@@ -1,5 +1,7 @@
 package jcgp.population;
 
+import jcgp.CGP.Parameters;
+
 
 public class Output implements MutableElement {
 	
@@ -15,4 +17,9 @@ public class Output implements MutableElement {
 		
 	}
 
+	@Override
+	public int getColumn() {
+		return Parameters.getColumns();
+	}
+
 }
diff --git a/src/jcgp/population/Population.java b/src/jcgp/population/Population.java
index 55f756a..e171a2f 100644
--- a/src/jcgp/population/Population.java
+++ b/src/jcgp/population/Population.java
@@ -43,6 +43,8 @@ public class Population implements Iterable<Chromosome> {
 			@Override
 			public void remove() {
 				// not allowed
+				// since this would shift everything back one position, increment index
+				index++;
 			}
 			
 		};