1 files changed, 52 insertions, 11 deletions

diff --git a/src/jcgp/population/Chromosome.java b/src/jcgp/population/Chromosome.java
index 08ff9b9..f61b780 100644
--- a/src/jcgp/population/Chromosome.java
+++ b/src/jcgp/population/Chromosome.java
@@ -11,8 +11,8 @@ public class Chromosome {
 	private Input[] inputs;
 	private Node[][] nodes;
 	private Output[] outputs;
-	
-	private ArrayList<Connection> activeNodes;
+
+	private ArrayList<Node> activeNodes;
 
 	private int fitness = 0;
 	private boolean recomputeActiveNodes = true;
@@ -117,7 +117,7 @@ public class Chromosome {
 				nodes[r][c].initialise(clone.getNode(r, c).getFunction(), connections);
 			}
 		}
-		
+
 		// do the same to outputs
 		Connection copyOutput;
 		for (int o = 0; o < outputs.length; o++) {
@@ -153,6 +153,11 @@ public class Chromosome {
 		fitness = newFitness;
 	}
 
+	/**
+	 * 
+	 * @param values
+	 * @throws ParameterMismatchException
+	 */
 	public void setInputs(int ... values) throws ParameterMismatchException {
 		// if the values provided don't match the specified number of inputs, the user should be warned
 		if (values.length == inputs.length) {
@@ -232,31 +237,67 @@ public class Chromosome {
 			return nodes[index / Parameters.getColumns()][index % Parameters.getColumns()];
 		}
 	}
-	
+
 	/**
 	 * This causes the list of active nodes to be recomputed lazily (once it is actually requested).
 	 */
 	public void recomputeActiveNodes() {
 		recomputeActiveNodes = true;
 	}
-	
+
 	/**
-	 * This method computes a list of active nodes (if necessary) and returns it.
+	 * This method computes a list of active connections (if necessary) and returns it.
 	 *
 	 * @return
 	 */
-	public ArrayList<Connection> getActiveNodes() {
+	public ArrayList<Node> getActiveNodes() {
+		computeActiveNodes();
+		return activeNodes;
+	}
+
+	private void computeActiveNodes() {
 		// lazy recomputation has been triggered, do it
 		if (recomputeActiveNodes) {
 			recomputeActiveNodes = false;
-			activeNodes = new ArrayList<Connection>();
-			
+			activeNodes = new ArrayList<Node>();
+
 			for (Output output : outputs) {
 				output.getActiveNodes(activeNodes);
 			}
-			
 		}
-		return activeNodes;
+
 	}
 
+	public boolean compareTo(Chromosome chromosome) {
+		for (int r = 0; r < Parameters.getRows(); r++) {
+			for (int c = 0; c < Parameters.getColumns(); c++) {
+				if (!(nodes[r][c].copyOf(chromosome.getNode(r, c)))) {
+					return false;
+				}
+			}
+		}
+		
+		for (int o = 0; o < Parameters.getOutputs(); o++) {
+			if (!(outputs[o].copyOf(chromosome.getOutput(o)))) {
+				return false;
+			}
+		}
+		
+		return true;
+	}
+
+	public boolean compareActiveTo(Chromosome chromosome) {
+		// update list if it is out of date
+		computeActiveNodes();
+		
+		if (activeNodes.size() == chromosome.getActiveNodes().size()) {
+			for (int i = 0; i < activeNodes.size(); i++) {
+				if (!(activeNodes.get(i).copyOf(chromosome.getActiveNodes().get(i)))){
+					return false;
+				}
+			}
+			return true;
+		}
+		return false;
+	}
 }