1 files changed, 27 insertions, 25 deletions

diff --git a/src/jcgp/backend/population/Chromosome.java b/src/jcgp/backend/population/Chromosome.java
index bbada14..71e19ec 100644
--- a/src/jcgp/backend/population/Chromosome.java
+++ b/src/jcgp/backend/population/Chromosome.java
@@ -31,7 +31,7 @@ public class Chromosome {
 		// allocate memory for all elements of the chromosome
 		instantiateElements();
 		// set random connections so that the chromosome can be evaluated
-		initialiseConnections();
+		reinitialiseConnections();
 	}
 
 	/**
@@ -55,22 +55,22 @@ public class Chromosome {
 	 *
 	 */
 	private void instantiateElements() {
-		inputs = new Input[(resources.getInt("inputs"))];
-		for (int i = 0; i < (resources.getInt("inputs")); i++) {
+		inputs = new Input[(resources.inputs())];
+		for (int i = 0; i < inputs.length; i++) {
 			inputs[i] = new Input(i);
 		}
 
-		int arity = resources.getInt("arity");
+		int arity = resources.arity();
 		
 		// rows first
-		nodes = new Node[(resources.getInt("rows"))][(resources.getInt("columns"))];
-		for (int r = 0; r < (resources.getInt("rows")); r++) {
-			for (int c = 0; c < (resources.getInt("columns")); c++) {
+		nodes = new Node[(resources.rows())][(resources.columns())];
+		for (int r = 0; r < nodes.length; r++) {
+			for (int c = 0; c < nodes[r].length; c++) {
 				nodes[r][c] = new Node(this, r, c, arity);
 			}
 		}
-		outputs = new Output[(resources.getInt("outputs"))];
-		for (int o = 0; o < (resources.getInt("outputs")); o++) {
+		outputs = new Output[resources.outputs()];
+		for (int o = 0; o < outputs.length; o++) {
 			outputs[o] = new Output(this, o);
 		}
 	}
@@ -78,9 +78,9 @@ public class Chromosome {
 	/**
 	 * 
 	 */
-	private void initialiseConnections() {
+	public void reinitialiseConnections() {
 
-		int arity = resources.getInt("arity");
+		int arity = resources.arity();
 		
 		// initialise nodes - [rows][columns]
 		for (int r = 0; r < nodes.length; r++) {
@@ -103,7 +103,7 @@ public class Chromosome {
 	 * @param clone
 	 */
 	public void copyGenes(Chromosome clone) {
-		int arity = resources.getInt("arity");
+		int arity = resources.arity();
 		
 		// copy nodes - [rows][columns]
 		for (int r = 0; r < nodes.length; r++) {
@@ -164,6 +164,7 @@ public class Chromosome {
 
 	/**
 	 * 
+	 * 
 	 * @param values
 	 * @throws ParameterMismatchException
 	 */
@@ -186,7 +187,7 @@ public class Chromosome {
 	 */
 	public MutableElement getRandomMutableElement() {
 		// choose output or node
-		int index = resources.getRandomInt(outputs.length + (resources.getInt("rows")) * (resources.getInt("columns")));
+		int index = resources.getRandomInt(outputs.length + (resources.rows() * resources.columns()));
 
 		if (index < outputs.length) {
 			// outputs
@@ -194,7 +195,7 @@ public class Chromosome {
 		} else {
 			// node	
 			index -= outputs.length;
-			return nodes[index / (resources.getInt("columns"))][index % (resources.getInt("columns"))];
+			return nodes[index / resources.columns()][index % resources.columns()];
 		}
 	}
 
@@ -208,7 +209,7 @@ public class Chromosome {
 	 */
 	public Connection getRandomConnection(int column) {
 		// work out the allowed range obeying levels back
-		int allowedColumns = ((column >= (resources.getInt("levelsBack"))) ? (resources.getInt("levelsBack")) : column);
+		int allowedColumns = column >= resources.levelsBack() ? resources.levelsBack() : column;
 		int offset = ((column - allowedColumns) * nodes.length) - inputs.length;
 
 		// choose input or allowed node
@@ -235,14 +236,14 @@ public class Chromosome {
 	 */
 	public Connection getRandomConnection() {
 		// choose output or node
-		int index = resources.getRandomInt(inputs.length + (resources.getInt("columns")) * (resources.getInt("rows")));
+		int index = resources.getRandomInt(inputs.length + (resources.columns() * resources.rows()));
 		if (index < inputs.length) {
 			// outputs
 			return inputs[index];
 		} else {
 			// node	
 			index -= inputs.length;
-			return nodes[index / (resources.getInt("columns"))][index % (resources.getInt("columns"))];
+			return nodes[index / resources.columns()][index % resources.columns()];
 		}
 	}
 
@@ -273,19 +274,18 @@ public class Chromosome {
 				output.getActiveNodes(activeNodes);
 			}
 		}
-
 	}
 
 	public boolean compareTo(Chromosome chromosome) {
-		for (int r = 0; r < (resources.getInt("rows")); r++) {
-			for (int c = 0; c < (resources.getInt("columns")); c++) {
+		for (int r = 0; r < resources.rows(); r++) {
+			for (int c = 0; c < resources.columns(); c++) {
 				if (!(nodes[r][c].copyOf(chromosome.getNode(r, c)))) {
 					return false;
 				}
 			}
 		}
 		
-		for (int o = 0; o < (resources.getInt("outputs")); o++) {
+		for (int o = 0; o < resources.outputs(); o++) {
 			if (!(outputs[o].copyOf(chromosome.getOutput(o)))) {
 				return false;
 			}
@@ -311,11 +311,11 @@ public class Chromosome {
 	
 	public void printNodes() {
 		// TODO make this proper
-		int arity = resources.getInt("arity");
+		int arity = resources.arity();
 		
-		for (int r = 0; r < (resources.getInt("rows")); r++) {
+		for (int r = 0; r < resources.rows(); r++) {
 			System.out.print("r: " + r + "\t");
-			for (int c = 0; c < (resources.getInt("columns")); c++) {
+			for (int c = 0; c < resources.columns(); c++) {
 				System.out.print("N: (" + r + ", " + c + ") ");
 				for (int i = 0; i < arity; i++) {
 					System.out.print("C" + i + ": (" + nodes[r][c].getConnection(i).toString() + ") ");
@@ -325,9 +325,11 @@ public class Chromosome {
 			System.out.print("\n");
 		}
 		
-		for (int o = 0; o < (resources.getInt("outputs")); o++) {
+		for (int o = 0; o < resources.outputs(); o++) {
 			System.out.print("o: " + o + " (" + outputs[o].getSource().toString() + ")\t");
 		}
+		
+		System.out.println();
 	}
 	
 	public Resources getResources() {