Majorly refactored, node grid is fully implemented. About to attempt active path locking.

1 files changed, 50 insertions, 35 deletions

diff --git a/src/jcgp/population/Chromosome.java b/src/jcgp/population/Chromosome.java
index 1f0b312..a7f2ed3 100644
--- a/src/jcgp/population/Chromosome.java
+++ b/src/jcgp/population/Chromosome.java
@@ -2,11 +2,12 @@ package jcgp.population;
 
 import java.util.ArrayList;
 
-import jcgp.Utilities;
+import jcgp.CGP.Resources;
 import jcgp.exceptions.ParameterMismatchException;
-import jcgp.parameters.Parameters;
 
 public class Chromosome {
+	
+	private Resources resources;
 
 	private Input[] inputs;
 	private Node[][] nodes;
@@ -21,13 +22,12 @@ public class Chromosome {
 	 * Initialise a chromosome with the specified parameters. Random valid connections
 	 * are created.
 	 * 
-	 * @param outputs 
-	 * @param columns 
-	 * @param rows 
-	 * @param inputs 
 	 * 
 	 */
-	public Chromosome() {
+	public Chromosome(Resources resources) {
+		// store a reference to the parameters
+		this.resources = resources;
+		
 		// allocate memory for all elements of the chromosome
 		instantiateElements();
 		// set random connections so that the chromosome can be evaluated
@@ -42,6 +42,9 @@ public class Chromosome {
 	 * @param clone the chromosome to be copied
 	 */
 	public Chromosome(Chromosome clone) {
+		// store a reference to the parameters
+		this.resources = clone.getParameters();
+		
 		// allocate memory for all elements of the chromosome
 		instantiateElements();
 		// initialise all connections based on argument
@@ -52,20 +55,22 @@ public class Chromosome {
 	 *
 	 */
 	private void instantiateElements() {
-		inputs = new Input[((int) Parameters.get("inputs").getValue())];
-		for (int i = 0; i < ((int) Parameters.get("inputs").getValue()); i++) {
+		inputs = new Input[((int) resources.get("inputs"))];
+		for (int i = 0; i < ((int) resources.get("inputs")); i++) {
 			inputs[i] = new Input(i);
 		}
 
+		int arity = (int) resources.get("arity");
+		
 		// rows first
-		nodes = new Node[((int) Parameters.get("rows").getValue())][((int) Parameters.get("columns").getValue())];
-		for (int r = 0; r < ((int) Parameters.get("rows").getValue()); r++) {
-			for (int c = 0; c < ((int) Parameters.get("columns").getValue()); c++) {
-				nodes[r][c] = new Node(this, r, c);
+		nodes = new Node[((int) resources.get("rows"))][((int) resources.get("columns"))];
+		for (int r = 0; r < ((int) resources.get("rows")); r++) {
+			for (int c = 0; c < ((int) resources.get("columns")); c++) {
+				nodes[r][c] = new Node(this, r, c, arity);
 			}
 		}
-		outputs = new Output[((int) Parameters.get("outputs").getValue())];
-		for (int o = 0; o < ((int) Parameters.get("outputs").getValue()); o++) {
+		outputs = new Output[((int) resources.get("outputs"))];
+		for (int o = 0; o < ((int) resources.get("outputs")); o++) {
 			outputs[o] = new Output(this, o);
 		}
 	}
@@ -75,19 +80,21 @@ public class Chromosome {
 	 */
 	private void initialiseConnections() {
 
+		int arity = (int) resources.get("arity");
+		
 		// initialise nodes - [rows][columns]
 		for (int r = 0; r < nodes.length; r++) {
 			for (int c = 0; c < nodes[r].length; c++) {
-				Connection[] connections = new Connection[((int) Parameters.get("maxArity").getValue())];
+				Connection[] connections = new Connection[arity];
 				for (int i = 0; i < connections.length; i++) {
 					connections[i] = getRandomConnection(c);
 				}
-				nodes[r][c].initialise(Utilities.getRandomFunction(), connections);
+				nodes[r][c].initialise(resources.getRandomFunction(), connections);
 			}
 		}
 
 		for (Output output : outputs) {
-			output.setConnection(getRandomConnection());
+			output.setConnection(0, getRandomConnection());
 		}
 
 	}
@@ -96,11 +103,13 @@ public class Chromosome {
 	 * @param clone
 	 */
 	public void copyConnections(Chromosome clone) {
+		int arity = (int) resources.get("arity");
+		
 		// copy nodes - [rows][columns]
 		for (int r = 0; r < nodes.length; r++) {
 			for (int c = 0; c < nodes[r].length; c++) {
 				// make array of connections to initialise with
-				Connection[] connections = new Connection[((int) Parameters.get("maxArity").getValue())];
+				Connection[] connections = new Connection[arity];
 				// populate with connections equivalent to clone
 				Connection copyConnection;
 				for (int i = 0; i < connections.length; i++) {
@@ -123,9 +132,9 @@ public class Chromosome {
 		for (int o = 0; o < outputs.length; o++) {
 			copyOutput = clone.getOutput(o).getSource();
 			if (copyOutput instanceof Input) {
-				outputs[o].setConnection(inputs[((Input) copyOutput).getIndex()]);
+				outputs[o].setConnection(0, inputs[((Input) copyOutput).getIndex()]);
 			} else if (copyOutput instanceof Node) {
-				outputs[o].setConnection(nodes[((Node) copyOutput).getRow()][((Node) copyOutput).getColumn()]);
+				outputs[o].setConnection(0, nodes[((Node) copyOutput).getRow()][((Node) copyOutput).getColumn()]);
 			} else {
 				// something bad happened
 				System.out.println("Warning: Connection of subtype " + copyOutput.getClass().toString() + " is not explicitly handled by copy constructor.");
@@ -177,7 +186,7 @@ public class Chromosome {
 	 */
 	public MutableElement getRandomMutableElement() {
 		// choose output or node
-		int index = Utilities.getRandomInt(outputs.length + ((int) Parameters.get("rows").getValue()) * ((int) Parameters.get("columns").getValue()));
+		int index = resources.getRandomInt(outputs.length + ((int) resources.get("rows")) * ((int) resources.get("columns")));
 
 		if (index < outputs.length) {
 			// outputs
@@ -185,7 +194,7 @@ public class Chromosome {
 		} else {
 			// node	
 			index -= outputs.length;
-			return nodes[index / ((int) Parameters.get("columns").getValue())][index % ((int) Parameters.get("columns").getValue())];
+			return nodes[index / ((int) resources.get("columns"))][index % ((int) resources.get("columns"))];
 		}
 	}
 
@@ -199,11 +208,11 @@ public class Chromosome {
 	 */
 	public Connection getRandomConnection(int column) {
 		// work out the allowed range obeying levels back
-		int allowedColumns = ((column >= ((int) Parameters.get("levelsBack").getValue())) ? ((int) Parameters.get("levelsBack").getValue()) : column);
+		int allowedColumns = ((column >= ((int) resources.get("levelsBack"))) ? ((int) resources.get("levelsBack")) : column);
 		int offset = ((column - allowedColumns) * nodes.length) - inputs.length;
 
 		// choose input or allowed node
-		int index = Utilities.getRandomInt(inputs.length + (nodes.length * allowedColumns));
+		int index = resources.getRandomInt(inputs.length + (nodes.length * allowedColumns));
 		if (index < inputs.length) {
 			// input
 			return inputs[index];
@@ -226,7 +235,7 @@ public class Chromosome {
 	 */
 	public Connection getRandomConnection() {
 		// choose output or node
-		int index = Utilities.getRandomInt(inputs.length + ((int) Parameters.get("columns").getValue()) * ((int) Parameters.get("rows").getValue()));
+		int index = resources.getRandomInt(inputs.length + ((int) resources.get("columns")) * ((int) resources.get("rows")));
 
 		if (index < inputs.length) {
 			// outputs
@@ -234,7 +243,7 @@ public class Chromosome {
 		} else {
 			// node	
 			index -= inputs.length;
-			return nodes[index / ((int) Parameters.get("columns").getValue())][index % ((int) Parameters.get("columns").getValue())];
+			return nodes[index / ((int) resources.get("columns"))][index % ((int) resources.get("columns"))];
 		}
 	}
 
@@ -269,15 +278,15 @@ public class Chromosome {
 	}
 
 	public boolean compareTo(Chromosome chromosome) {
-		for (int r = 0; r < ((int) Parameters.get("rows").getValue()); r++) {
-			for (int c = 0; c < ((int) Parameters.get("columns").getValue()); c++) {
+		for (int r = 0; r < ((int) resources.get("rows")); r++) {
+			for (int c = 0; c < ((int) resources.get("columns")); c++) {
 				if (!(nodes[r][c].copyOf(chromosome.getNode(r, c)))) {
 					return false;
 				}
 			}
 		}
 		
-		for (int o = 0; o < ((int) Parameters.get("outputs").getValue()); o++) {
+		for (int o = 0; o < ((int) resources.get("outputs")); o++) {
 			if (!(outputs[o].copyOf(chromosome.getOutput(o)))) {
 				return false;
 			}
@@ -302,20 +311,26 @@ public class Chromosome {
 	}
 	
 	public void printNodes() {
-		for (int r = 0; r < ((int) Parameters.get("rows").getValue()); r++) {
+		int arity = (int) resources.get("arity");
+		
+		for (int r = 0; r < ((int) resources.get("rows")); r++) {
 			System.out.print("r: " + r + "\t");
-			for (int c = 0; c < ((int) Parameters.get("columns").getValue()); c++) {
+			for (int c = 0; c < ((int) resources.get("columns")); c++) {
 				System.out.print("N: (" + r + ", " + c + ") ");
-				for (int i = 0; i < ((int) Parameters.get("maxArity").getValue()); i++) {
+				for (int i = 0; i < arity; i++) {
 					System.out.print("C" + i + ": (" + nodes[r][c].getConnection(i).getDescription() + ") ");
 				}
-				System.out.print("F: " + nodes[r][c].getFunction().toString() + "\t");
+				System.out.print("F: " + nodes[r][c].getFunction().getName() + "\t");
 			}
 			System.out.print("\n");
 		}
 		
-		for (int o = 0; o < ((int) Parameters.get("outputs").getValue()); o++) {
+		for (int o = 0; o < ((int) resources.get("outputs")); o++) {
 			System.out.print("o: " + o + " (" + outputs[o].getSource().getDescription() + ")\t");
 		}
 	}
+	
+	public Resources getParameters() {
+		return resources;
+	}
 }