6 files changed, 88 insertions, 25 deletions
diff --git a/src/jcgp/population/Chromosome.java b/src/jcgp/population/Chromosome.java
index 2e22cf9..76667e5 100644
--- a/src/jcgp/population/Chromosome.java
+++ b/src/jcgp/population/Chromosome.java
@@ -2,16 +2,19 @@ package jcgp.population;
 
 import java.util.ArrayList;
 
+import jcgp.CGP.Utilities;
+
 public class Chromosome {
 
-	private ArrayList<Input> inputs;
-	private ArrayList<ArrayList<Node>> nodes;
-	private ArrayList<Output> outputs;
+	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 int fitness = 0;
 	
 	/**
 	 * Good citizen.
+	 * 
 	 * @param outputs 
 	 * @param columns 
 	 * @param rows 
@@ -20,13 +23,43 @@ public class Chromosome {
 	 */
 	public Chromosome(int inputCount, int rows, int columns, int outputCount) {
 		
-		inputs = new ArrayList<Input>(inputCount);
+		instantiateElements(inputCount, rows, columns, outputCount);
+		
+		initialiseConnections();
+	
+	}
+
+	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
+	 * @param columns
+	 * @param outputCount
+	 */
+	private void instantiateElements(int inputCount, int rows, int columns,	int outputCount) {
 		for (int i = 0; i < inputCount; i++) {
 			inputs.add(new Input());
 		}
 		
 		// rows first
-		nodes = new ArrayList<ArrayList<Node>>(rows);
 		for (int r = 0; r < rows; r++) {
 			nodes.add(new ArrayList<Node>(columns));
 			for (int c = 0; c < columns; c++) {
@@ -34,11 +67,9 @@ public class Chromosome {
 			}
 		}
 		
-		outputs = new ArrayList<Output>(outputCount);
 		for (int o = 0; o < outputCount; o++) {
 			outputs.add(new Output());
 		}
-	
 	}
 	
 	public int getActiveNodeCount() {
@@ -48,33 +79,33 @@ public class Chromosome {
 	/**
 	 * @return the inputs
 	 */
-	public final ArrayList<Input> getInputs() {
+	public ArrayList<Input> getInputs() {
 		return inputs;
 	}
 
 	/**
 	 * @return the nodes
 	 */
-	public final ArrayList<ArrayList<Node>> getNodes() {
+	public ArrayList<ArrayList<Node>> getNodes() {
 		return nodes;
 	}
 
 	/**
 	 * @return the outputs
 	 */
-	public final ArrayList<Output> getOutputs() {
+	public ArrayList<Output> getOutputs() {
 		return outputs;
 	}
 	
-	public final Node getNode(int row, int column) {
+	public Node getNode(int row, int column) {
 		return nodes.get(row).get(column);
 	}
 	
-	public final Output getOutput(int index) {
+	public Output getOutput(int index) {
 		return outputs.get(index);
 	}
 	
-	public final Input getInputs(int index) {
+	public Input getInput(int index) {
 		return inputs.get(index);
 	}
 	
diff --git a/src/jcgp/population/InsufficientConnectionsException.java b/src/jcgp/population/InsufficientConnectionsException.java
new file mode 100644
index 0000000..807ec53
--- /dev/null
+++ b/src/jcgp/population/InsufficientConnectionsException.java
@@ -0,0 +1,10 @@
+package jcgp.population;
+
+public class InsufficientConnectionsException extends RuntimeException {
+
+	/**
+	 * 
+	 */
+	private static final long serialVersionUID = 660740514800883541L;
+
+}
diff --git a/src/jcgp/population/MutableElement.java b/src/jcgp/population/MutableElement.java
index 4397e46..5eae4ef 100644
--- a/src/jcgp/population/MutableElement.java
+++ b/src/jcgp/population/MutableElement.java
@@ -2,4 +2,6 @@ package jcgp.population;
 
 public interface MutableElement {
 	
+	public void setConnection(Connection newConnection);
+	
 }
diff --git a/src/jcgp/population/Node.java b/src/jcgp/population/Node.java
index cce8dfd..8958475 100644
--- a/src/jcgp/population/Node.java
+++ b/src/jcgp/population/Node.java
@@ -1,5 +1,6 @@
 package jcgp.population;
 
+import jcgp.CGP.Utilities;
 import jcgp.function.Function;
 
 
@@ -8,21 +9,28 @@ public class Node implements MutableElement, Connection {
 	private Function function;
 	private Connection[] connections;
 
-	public Node() {
-		
-	}
-	
 	@Override
 	public int evaluate() {
-		return function.run(connections[0], connections[1]);
+		return function.run(connections);
 	}
 	
 	public void setFunction(Function newFunction) {
 		function = newFunction;
 	}
 	
+	@Override
 	public void setConnection(Connection newConnection) {
+		connections[Utilities.getRandomInt(connections.length)] = newConnection;
+	}
+	
+	public void initialise(Function newFunction, Connection ... newConnections) throws InsufficientConnectionsException {
+		
+		function = newFunction;
 		
+		if (newConnections.length >= Utilities.getMaxArity()) {
+			connections = newConnections;
+		} else {
+			throw new InsufficientConnectionsException();
+		}
 	}
-
 }
diff --git a/src/jcgp/population/Output.java b/src/jcgp/population/Output.java
index 2f2df6e..1640deb 100644
--- a/src/jcgp/population/Output.java
+++ b/src/jcgp/population/Output.java
@@ -2,10 +2,17 @@ package jcgp.population;
 
 
 public class Output implements MutableElement {
+	
+	private Connection source;
 
 	public int calculate() {
-		// TODO Auto-generated method stub
-		return 0;
+		return source.evaluate();
+	}
+
+	@Override
+	public void setConnection(Connection newConnection) {
+		source = newConnection;
+		
 	}
 
 }
diff --git a/src/jcgp/population/Population.java b/src/jcgp/population/Population.java
index e1a9a3c..67b6695 100644
--- a/src/jcgp/population/Population.java
+++ b/src/jcgp/population/Population.java
@@ -3,14 +3,19 @@ package jcgp.population;
 import java.util.ArrayList;
 import java.util.Iterator;
 
+import jcgp.CGP.Parameters;
+
 public final class Population implements Iterable<Chromosome> {
 	
 	private ArrayList<Chromosome> population;
 	
-	public Population(int inputs, int rows, int columns, int outputs, int size) {
-		population = new ArrayList<Chromosome>(size);
-		for (int c = 0; c < size; c++) {
-			population.add(new Chromosome(inputs, rows, columns, outputs));
+	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()));
 		}
 	}