4 files changed, 93 insertions, 83 deletions

diff --git a/src/jcgp/fitness/FitnessEvaluator.java b/src/jcgp/fitness/FitnessEvaluator.java
new file mode 100644
index 0000000..5ecf679
--- /dev/null
+++ b/src/jcgp/fitness/FitnessEvaluator.java
@@ -0,0 +1,17 @@
+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/function/FunctionSet.java b/src/jcgp/function/FunctionSet.java
index 30e1067..cbe2f05 100644
--- a/src/jcgp/function/FunctionSet.java
+++ b/src/jcgp/function/FunctionSet.java
@@ -1,37 +1,39 @@
 package jcgp.function;
 
-import java.util.ArrayList;
-
-
+/**
+ * 
+ * TODO: if function set flexibility is desired (i.e. add more functions as the program runs)
+ * an add function method should be created
+ * this would lead to concurrency problems, so tread lightly!
+ * 
+ * 
+ * @author Eduardo Pedroni
+ *
+ */
 public class FunctionSet {
-		private ArrayList<Function> functionList;
+		private Function[] functionList;
+		private int maxArity = 0;
 		
 		public FunctionSet(Function ... functions) {
-			functionList = new ArrayList<Function>(functions.length);
+			functionList = functions;
 			
-			for (int i = 0; i < functions.length; i++) {
-				functionList.add(functions[i]);
+			for (Function function : functionList) {
+				if (function.getArity() > maxArity) {
+					maxArity = function.getArity();
+				}
 			}
+			
 		}
 		
 		public int getFunctionCount() {
-			return functionList.size();
+			return functionList.length;
 		}
 		
 		public Function getFunction(int index) {
-			return functionList.get(index);
+			return functionList[index];
 		}
 		
 		public int getMaxArity(){
-			
-			int maxArity = 0;
-			
-			for (Function function : functionList) {
-				if (function.getArity() > maxArity) {
-					maxArity = function.getArity();
-				}
-			}
-			
 			return maxArity;
 		}
 	}
\ No newline at end of file
diff --git a/src/jcgp/population/Chromosome.java b/src/jcgp/population/Chromosome.java
index 76667e5..70e8836 100644
--- a/src/jcgp/population/Chromosome.java
+++ b/src/jcgp/population/Chromosome.java
@@ -1,14 +1,13 @@
 package jcgp.population;
 
-import java.util.ArrayList;
-
+import jcgp.CGP.Parameters;
 import jcgp.CGP.Utilities;
 
 public class Chromosome {
 
-	private final ArrayList<Input> inputs = new ArrayList<Input>();
-	private final ArrayList<ArrayList<Node>> nodes = new ArrayList<ArrayList<Node>>();;
-	private final ArrayList<Output> outputs = new ArrayList<Output>();
+	private Input[] inputs;
+	private Node[][] nodes;
+	private Output[] outputs;
 	
 	private int fitness = 0;
 	
@@ -29,25 +28,6 @@ public class Chromosome {
 	
 	}
 
-	private void initialiseConnections() {
-		
-		// initialise nodes
-		for (int r = 0; r < nodes.size(); r++) {
-			for (int c = 0; c < nodes.size(); c++) {
-				Connection[] connections = new Connection[Utilities.getMaxArity()];
-				for (int i = 0; i < connections.length; i++) {
-					connections[i] = Utilities.getRandomConnection(this, c);
-				}
-				nodes.get(r).get(c).initialise(Utilities.getRandomFunction(), connections);
-			}
-		}
-		
-		for (Output output : outputs) {
-			output.setConnection(Utilities.getRandomNode(this));
-		}
-		
-	}
-
 	/**
 	 * @param inputCount
 	 * @param rows
@@ -55,58 +35,58 @@ public class Chromosome {
 	 * @param outputCount
 	 */
 	private void instantiateElements(int inputCount, int rows, int columns,	int outputCount) {
+		inputs = new Input[inputCount];
 		for (int i = 0; i < inputCount; i++) {
-			inputs.add(new Input());
+			inputs[i] = new Input();
 		}
 		
 		// rows first
+		nodes = new Node[Parameters.getRows()][Parameters.getColumns()];
 		for (int r = 0; r < rows; r++) {
-			nodes.add(new ArrayList<Node>(columns));
+			//nodes[r] = new Node[Parameters.getColumns()];
 			for (int c = 0; c < columns; c++) {
-				nodes.get(r).add(new Node());
+				nodes[r][c] = new Node();
 			}
 		}
-		
+		outputs = new Output[outputCount];
 		for (int o = 0; o < outputCount; o++) {
-			outputs.add(new Output());
+			outputs[o] = new Output();
+		}
+	}
+	
+	private void initialiseConnections() {
+		
+		// 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()];
+				for (int i = 0; i < connections.length; i++) {
+					connections[i] = Utilities.getRandomConnection(this, c);
+				}
+				nodes[r][c].initialise(Utilities.getRandomFunction(), connections);
+			}
+		}
+		
+		for (Output output : outputs) {
+			output.setConnection(Utilities.getRandomNode(this));
 		}
+		
 	}
 	
 	public int getActiveNodeCount() {
 		return 0;
 	}
 
-	/**
-	 * @return the inputs
-	 */
-	public ArrayList<Input> getInputs() {
-		return inputs;
-	}
-
-	/**
-	 * @return the nodes
-	 */
-	public ArrayList<ArrayList<Node>> getNodes() {
-		return nodes;
-	}
-
-	/**
-	 * @return the outputs
-	 */
-	public ArrayList<Output> getOutputs() {
-		return outputs;
-	}
-	
 	public Node getNode(int row, int column) {
-		return nodes.get(row).get(column);
+		return nodes[row][column];
 	}
 	
 	public Output getOutput(int index) {
-		return outputs.get(index);
+		return outputs[index];
 	}
 	
 	public Input getInput(int index) {
-		return inputs.get(index);
+		return inputs[index];
 	}
 	
 	public int getFitness() {
@@ -117,4 +97,16 @@ public class Chromosome {
 		fitness = newFitness;
 	}
 	
+	public void setInputs(int ... values) {
+		// if the values provided dont match the specified number of inputs, the user should be warned
+		if (values.length == inputs.length) {
+			// set inputs for evaluation
+			for (int i = 0; i < values.length; i++) {
+				inputs[i].setValue(values[i]);
+			}
+		} else {
+			System.out.println("Input mismatch: chromosome has a different number of inputs than the truth table.");
+		}
+	}
+	
 }
diff --git a/src/jcgp/population/Population.java b/src/jcgp/population/Population.java
index 67b6695..55f756a 100644
--- a/src/jcgp/population/Population.java
+++ b/src/jcgp/population/Population.java
@@ -1,21 +1,20 @@
 package jcgp.population;
 
-import java.util.ArrayList;
 import java.util.Iterator;
 
 import jcgp.CGP.Parameters;
 
-public final class Population implements Iterable<Chromosome> {
+public class Population implements Iterable<Chromosome> {
 	
-	private ArrayList<Chromosome> population;
+	private Chromosome[] population;
 	
 	public Population() {
-		population = new ArrayList<Chromosome>(Parameters.getPopulationSize());
-		for (int c = 0; c < Parameters.getPopulationSize(); c++) {
-			population.add(new Chromosome(Parameters.getInputs(),
-										  Parameters.getRows(),
-										  Parameters.getColumns(),
-										  Parameters.getOutputs()));
+		population = new Chromosome[Parameters.getPopulationSize()];
+		for (int c = 0; c < population.length; c++) {
+			population[c] = new Chromosome(Parameters.getInputs(),
+										   Parameters.getRows(),
+										   Parameters.getColumns(),
+										   Parameters.getOutputs());
 		}
 	}
 
@@ -27,7 +26,7 @@ public final class Population implements Iterable<Chromosome> {
 
 			@Override
 			public boolean hasNext() {
-				if (index < population.size()) {
+				if (index < population.length) {
 					return true;
 				} else {
 					return false;
@@ -36,14 +35,14 @@ public final class Population implements Iterable<Chromosome> {
 
 			@Override
 			public Chromosome next() {
-				Chromosome next = population.get(index);
+				Chromosome next = population[index];
 				index++;
 				return next;
 			}
 
 			@Override
 			public void remove() {
-				// not allowed				
+				// not allowed
 			}
 			
 		};