Running into some issues with running the CGP loop in the background with bindings.

4 files changed, 63 insertions, 86 deletions

diff --git a/src/jcgp/population/Chromosome.java b/src/jcgp/population/Chromosome.java
index 6f50025..297d298 100644
--- a/src/jcgp/population/Chromosome.java
+++ b/src/jcgp/population/Chromosome.java
@@ -55,22 +55,22 @@ public class Chromosome {
 	 *
 	 */
 	private void instantiateElements() {
-		inputs = new Input[((int) resources.get("inputs"))];
-		for (int i = 0; i < ((int) resources.get("inputs")); i++) {
+		inputs = new Input[(resources.getInt("inputs"))];
+		for (int i = 0; i < (resources.getInt("inputs")); i++) {
 			inputs[i] = new Input(i);
 		}
 
-		int arity = (int) resources.get("arity");
+		int arity = resources.getInt("arity");
 		
 		// rows first
-		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 = 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[r][c] = new Node(this, r, c, arity);
 			}
 		}
-		outputs = new Output[((int) resources.get("outputs"))];
-		for (int o = 0; o < ((int) resources.get("outputs")); o++) {
+		outputs = new Output[(resources.getInt("outputs"))];
+		for (int o = 0; o < (resources.getInt("outputs")); o++) {
 			outputs[o] = new Output(this, o);
 		}
 	}
@@ -80,7 +80,7 @@ public class Chromosome {
 	 */
 	private void initialiseConnections() {
 
-		int arity = (int) resources.get("arity");
+		int arity = resources.getInt("arity");
 		
 		// initialise nodes - [rows][columns]
 		for (int r = 0; r < nodes.length; r++) {
@@ -103,7 +103,7 @@ public class Chromosome {
 	 * @param clone
 	 */
 	public void copyConnections(Chromosome clone) {
-		int arity = (int) resources.get("arity");
+		int arity = resources.getInt("arity");
 		
 		// copy nodes - [rows][columns]
 		for (int r = 0; r < nodes.length; r++) {
@@ -186,7 +186,7 @@ public class Chromosome {
 	 */
 	public MutableElement getRandomMutableElement() {
 		// choose output or node
-		int index = resources.getRandomInt(outputs.length + ((int) resources.get("rows")) * ((int) resources.get("columns")));
+		int index = resources.getRandomInt(outputs.length + (resources.getInt("rows")) * (resources.getInt("columns")));
 
 		if (index < outputs.length) {
 			// outputs
@@ -194,7 +194,7 @@ public class Chromosome {
 		} else {
 			// node	
 			index -= outputs.length;
-			return nodes[index / ((int) resources.get("columns"))][index % ((int) resources.get("columns"))];
+			return nodes[index / (resources.getInt("columns"))][index % (resources.getInt("columns"))];
 		}
 	}
 
@@ -208,7 +208,7 @@ public class Chromosome {
 	 */
 	public Connection getRandomConnection(int column) {
 		// work out the allowed range obeying levels back
-		int allowedColumns = ((column >= ((int) resources.get("levelsBack"))) ? ((int) resources.get("levelsBack")) : column);
+		int allowedColumns = ((column >= (resources.getInt("levelsBack"))) ? (resources.getInt("levelsBack")) : column);
 		int offset = ((column - allowedColumns) * nodes.length) - inputs.length;
 
 		// choose input or allowed node
@@ -235,15 +235,14 @@ public class Chromosome {
 	 */
 	public Connection getRandomConnection() {
 		// choose output or node
-		int index = resources.getRandomInt(inputs.length + ((int) resources.get("columns")) * ((int) resources.get("rows")));
-
+		int index = resources.getRandomInt(inputs.length + (resources.getInt("columns")) * (resources.getInt("rows")));
 		if (index < inputs.length) {
 			// outputs
 			return inputs[index];
 		} else {
 			// node	
 			index -= inputs.length;
-			return nodes[index / ((int) resources.get("columns"))][index % ((int) resources.get("columns"))];
+			return nodes[index / (resources.getInt("columns"))][index % (resources.getInt("columns"))];
 		}
 	}
 
@@ -278,15 +277,15 @@ public class Chromosome {
 	}
 
 	public boolean compareTo(Chromosome chromosome) {
-		for (int r = 0; r < ((int) resources.get("rows")); r++) {
-			for (int c = 0; c < ((int) resources.get("columns")); c++) {
+		for (int r = 0; r < (resources.getInt("rows")); r++) {
+			for (int c = 0; c < (resources.getInt("columns")); c++) {
 				if (!(nodes[r][c].copyOf(chromosome.getNode(r, c)))) {
 					return false;
 				}
 			}
 		}
 		
-		for (int o = 0; o < ((int) resources.get("outputs")); o++) {
+		for (int o = 0; o < (resources.getInt("outputs")); o++) {
 			if (!(outputs[o].copyOf(chromosome.getOutput(o)))) {
 				return false;
 			}
@@ -311,11 +310,11 @@ public class Chromosome {
 	}
 	
 	public void printNodes() {
-		int arity = (int) resources.get("arity");
+		int arity = resources.getInt("arity");
 		
-		for (int r = 0; r < ((int) resources.get("rows")); r++) {
+		for (int r = 0; r < (resources.getInt("rows")); r++) {
 			System.out.print("r: " + r + "\t");
-			for (int c = 0; c < ((int) resources.get("columns")); c++) {
+			for (int c = 0; c < (resources.getInt("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).getDescription() + ") ");
@@ -325,7 +324,7 @@ public class Chromosome {
 			System.out.print("\n");
 		}
 		
-		for (int o = 0; o < ((int) resources.get("outputs")); o++) {
+		for (int o = 0; o < (resources.getInt("outputs")); o++) {
 			System.out.print("o: " + o + " (" + outputs[o].getSource().getDescription() + ")\t");
 		}
 	}
diff --git a/src/jcgp/population/Node.java b/src/jcgp/population/Node.java
index d7013d3..141a32a 100644
--- a/src/jcgp/population/Node.java
+++ b/src/jcgp/population/Node.java
@@ -1,58 +1,46 @@
 package jcgp.population;
 
 import java.util.ArrayList;
+import java.util.Arrays;
 
-import javafx.beans.property.SimpleObjectProperty;
 import jcgp.exceptions.InsufficientConnectionsException;
 import jcgp.function.Function;
 
 
 public class Node extends Gene implements MutableElement, Connection {
 
-	private SimpleObjectProperty<Function> function;
-	private ArrayList<SimpleObjectProperty<Connection>> connections;
+	private Function function;
+	private Connection[] connections;
 	private int column, row;
 	private Chromosome chromosome;
 
 	public Node(Chromosome chromosome, int row, int column, int arity) {
-		this.function = new SimpleObjectProperty<Function>();
 		this.chromosome = chromosome;
 		this.column = column;
 		this.row = row;
-		this.connections = new ArrayList<SimpleObjectProperty<Connection>>(arity);
-		for (int c = 0; c < arity; c++) {
-			connections.add(new SimpleObjectProperty<Connection>());
-		}
 	}
 
 	@Override
 	public Object getValue() {
 		//System.out.print("Calculating node: (" + row + ", " + column + ") > ");
-		Connection[] list = new Connection[function.get().getArity()];
-		for (int i = 0; i < list.length; i++) {
-			list[i] = connections.get(i).get();
-		}
-		
-		return function.get().run(list);
+		return function.run(Arrays.copyOfRange(connections, 0, function.getArity()));
 	}
 
 	public void setFunction(Function newFunction) {
-		function.set(newFunction);
+		function = newFunction;
 		chromosome.recomputeActiveNodes();
 	}
 
 	@Override
 	public void setConnection(int index, Connection newConnection) {
-		connections.get(index).set(newConnection);
+		connections[index] = newConnection;
 		chromosome.recomputeActiveNodes();
 	}
 
 	public void initialise(Function newFunction, Connection ... newConnections) throws InsufficientConnectionsException {
-		function.set(newFunction);
-		if (newConnections.length >= connections.size()) {
-			for (int i = 0; i < connections.size(); i++) {
-				connections.get(i).set(newConnections[i]);
-			}
+		function = newFunction;
+		if (newConnections.length == function.getArity()) {
+			connections = newConnections;
 		} else {
 			throw new InsufficientConnectionsException();
 		}
@@ -67,28 +55,20 @@ public class Node extends Gene implements MutableElement, Connection {
 	}
 
 	public Function getFunction() {
-		return function.get();
-	}
-	
-	public SimpleObjectProperty<Function> functionProperty() {
 		return function;
 	}
-
-	public ArrayList<SimpleObjectProperty<Connection>> connections() {
-		return connections;
-	}
 	
 	public Connection getConnection(int index) {
-		return connections.get(index).get();
+		return connections[index];
 	}
 
 	public void getActive(ArrayList<Node> activeNodes) {
 		if (!activeNodes.contains(this)) {
 			activeNodes.add(this);
 		}
-		for (int i = 0; i < function.get().getArity(); i++) {
-			if (connections.get(i).get() instanceof Node) {
-				((Node) connections.get(i).get()).getActive(activeNodes);
+		for (int i = 0; i < function.getArity(); i++) {
+			if (connections[i] instanceof Node) {
+				((Node) connections[i]).getActive(activeNodes);
 			}
 
 		}
@@ -99,17 +79,17 @@ public class Node extends Gene implements MutableElement, Connection {
 		if (this != m) {
 			if (m instanceof Node) {
 				Node n = (Node) m;
-				if (function.get() == n.getFunction()) {
+				if (function == n.getFunction()) {
 					if (column == n.getColumn() && row == n.getRow()) {
-						for (int i = 0; i < connections.size(); i++) {
-							if (connections.get(i).get() != n.getConnection(i)) {
-								if (connections.get(i).get() instanceof Input && n.getConnection(i) instanceof Input) {
-									if (((Input) connections.get(i).get()).getIndex() != ((Input) n.getConnection(i)).getIndex()) {
+						for (int i = 0; i < connections.length; i++) {
+							if (connections[i] != n.getConnection(i)) {
+								if (connections[i] instanceof Input && n.getConnection(i) instanceof Input) {
+									if (((Input) connections[i]).getIndex() != ((Input) n.getConnection(i)).getIndex()) {
 										return false;
 									}
-								} else if (connections.get(i).get() instanceof Node && n.getConnection(i) instanceof Node) {
-									if (((Node) connections.get(i).get()).getRow() != ((Node) n.getConnection(i)).getRow() &&
-											((Node) connections.get(i).get()).getColumn() != ((Node) n.getConnection(i)).getColumn()) {
+								} else if (connections[i] instanceof Node && n.getConnection(i) instanceof Node) {
+									if (((Node) connections[i]).getRow() != ((Node) n.getConnection(i)).getRow() &&
+											((Node) connections[i]).getColumn() != ((Node) n.getConnection(i)).getColumn()) {
 										return false;
 									}
 								} else {
diff --git a/src/jcgp/population/Output.java b/src/jcgp/population/Output.java
index b7c6128..5cc6dcf 100644
--- a/src/jcgp/population/Output.java
+++ b/src/jcgp/population/Output.java
@@ -2,18 +2,16 @@ package jcgp.population;
 
 import java.util.ArrayList;
 
-import javafx.beans.property.SimpleObjectProperty;
-
 public class Output extends Gene implements MutableElement {
 	
-	private SimpleObjectProperty<Connection> source;
+	private Connection source;
 	private Chromosome chromosome;
 	private int index;
 	
 	public Output(Chromosome chromosome, int index) {
 		this.chromosome = chromosome;
 		this.index = index;
-		this.source = new SimpleObjectProperty<Connection>();
+		//this.source = new SimpleObjectProperty<Connection>();
 	}
 
 	public Object calculate() {
@@ -23,7 +21,7 @@ public class Output extends Gene implements MutableElement {
 
 	@Override
 	public void setConnection(int index, Connection newConnection) {
-		source.set(newConnection);
+		source = newConnection;
 		chromosome.recomputeActiveNodes();
 	}
 
@@ -32,16 +30,16 @@ public class Output extends Gene implements MutableElement {
 	}
 
 	public Connection getSource() {
-		return source.get();
-	}
-	
-	public SimpleObjectProperty<Connection> sourceProperty() {
 		return source;
 	}
+	
+//	public SimpleObjectProperty<Connection> sourceProperty() {
+//		return source;
+//	}
 
 	public void getActiveNodes(ArrayList<Node> activeNodes) {
-		if (source.get() instanceof Node) {
-			((Node) source.get()).getActive(activeNodes);
+		if (source instanceof Node) {
+			((Node) source).getActive(activeNodes);
 		}
 	}
 	
@@ -51,14 +49,14 @@ public class Output extends Gene implements MutableElement {
 			if (m instanceof Output) {
 				Output o = (Output) m;
 				if (index == o.getIndex()) {
-					if (source.get() != o.getSource()) {
-						if (source.get() instanceof Input && o.getSource() instanceof Input) {
-							if (((Input) source.get()).getIndex() == ((Input) o.getSource()).getIndex()) {
+					if (source != o.getSource()) {
+						if (source instanceof Input && o.getSource() instanceof Input) {
+							if (((Input) source).getIndex() == ((Input) o.getSource()).getIndex()) {
 								return true;
 							}
-						} else if (source.get() instanceof Node && o.getSource() instanceof Node) {
-							if (((Node) source.get()).getRow() == ((Node) o.getSource()).getRow() &&
-									((Node) source.get()).getColumn() == ((Node) o.getSource()).getColumn()) {
+						} else if (source instanceof Node && o.getSource() instanceof Node) {
+							if (((Node) source).getRow() == ((Node) o.getSource()).getRow() &&
+									((Node) source).getColumn() == ((Node) o.getSource()).getColumn()) {
 								return true;
 							}
 						} 
diff --git a/src/jcgp/population/Population.java b/src/jcgp/population/Population.java
index 586f556..f5e0517 100644
--- a/src/jcgp/population/Population.java
+++ b/src/jcgp/population/Population.java
@@ -8,15 +8,15 @@ public class Population {
 	private Chromosome[] chromosomes;
 	private int fittest;
 	
-	public Population(Resources parameters) {
-		chromosomes = new Chromosome[((int) parameters.get("popSize"))];
+	public Population(Resources resources) {
+		chromosomes = new Chromosome[(resources.getInt("popSize"))];
 		for (int c = 0; c < chromosomes.length; c++) {
-			chromosomes[c] = new Chromosome(parameters);
+			chromosomes[c] = new Chromosome(resources);
 		}
 	}
 	
-	public Population(Chromosome parent, Resources parameters) {
-		chromosomes = new Chromosome[((int) parameters.get("popSize"))];
+	public Population(Chromosome parent, Resources resources) {
+		chromosomes = new Chromosome[(resources.getInt("popSize"))];
 		// make a clone for safety
 		this.chromosomes[0] = new Chromosome(parent);
 		// generate the rest of the individuals