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

33 files changed, 408 insertions, 860 deletions

diff --git a/README b/README
index 950ae46..b73e257 100644
--- a/README
+++ b/README
@@ -170,8 +170,9 @@ Adding GUI package, refactoring CGP class to interact appropriately with GUI.
 
 15/3
 
-Currently refactoring Parameters. It is now a part of CGP.class as stated in the phase report. The rest of the program will now be refactored to accommodate these changes. Inversion of
-will be employed to avoid static accesses to CGP, and the tests will be modified accordingly. This will allow multiple instances of CGP to co-exist.
+Currently refactoring Parameters. It is now a part of CGP.class as stated in the phase report. The rest of the program will now be refactored to accommodate
+these changes. Inversion of control will be employed to avoid static accesses to CGP, and the tests will be modified accordingly. 
+This will allow multiple instances of CGP to co-exist.
 
 18/3
 
@@ -205,4 +206,9 @@ grid node grows to fill the void.
 
 26/3
 
-Sorted out the console, resizing is mint, settings are nearing completion and the node grid has been refactored multiple times.
\ No newline at end of file
+Sorted out the console, resizing is mint, settings are nearing completion and the node grid has been refactored multiple times.
+
+
+28/3
+
+Refactoring parameters to overhaul the mechanism that allows modules to manage parameters.
\ No newline at end of file
diff --git a/src/jcgp/GUI.java b/src/jcgp/GUI.java
index a893494..98545db 100644
--- a/src/jcgp/GUI.java
+++ b/src/jcgp/GUI.java
@@ -1,10 +1,8 @@
 package jcgp;
 
-import java.io.IOException;
-import java.io.OutputStream;
-import java.io.PrintStream;
-
 import javafx.application.Application;
+import javafx.concurrent.Service;
+import javafx.concurrent.Task;
 import javafx.scene.Scene;
 import javafx.scene.control.Tab;
 import javafx.scene.control.TabPane;
@@ -12,9 +10,9 @@ import javafx.scene.control.TabPane.TabClosingPolicy;
 import javafx.scene.layout.BorderPane;
 import javafx.stage.Stage;
 import jcgp.JCGP.Resources;
+import jcgp.gui.ChromosomePane;
 import jcgp.gui.GUIConsole;
-import jcgp.gui.SettingsPane;
-import jcgp.gui.population.ChromosomePane;
+import jcgp.gui.settings.SettingsPane;
 
 public class GUI extends Application {
 	
@@ -35,10 +33,9 @@ public class GUI extends Application {
 	
 	
 	/* Sizes and distances */
-	
     public static final double RESIZE_MARGIN = 5.0;
     
-    public static final double SETTINGS_WIDTH = 190;
+    public static final double SETTINGS_WIDTH = 200;
     public static final double CONSOLE_HEIGHT = 100;
         
     public static final double WRAP_WIDTH = 90;
@@ -52,18 +49,14 @@ public class GUI extends Application {
 	private ChromosomePane[] chromosomes;
 	private TabPane mainPane;
 	
-	private static GUIConsole console = new GUIConsole();
+	private GUIConsole console = new GUIConsole();
 	private SettingsPane settings;
 	
-	public static final PrintStream out = new PrintStream(new OutputStream() {
-		@Override
-		public void write(int b) throws IOException {
-			console.getTextArea().appendText(String.valueOf((char) b));
-		}
-	});
-
+	private Service<Object> cgpService;
+	
+	private static boolean evolving = false;
+	
 	public static void main(String[] args) {
-		
 		cgp = new JCGP();
 		resources = cgp.getResources();
 		
@@ -73,6 +66,28 @@ public class GUI extends Application {
 	@Override
 	public void start(Stage primaryStage) throws Exception {
 		
+		
+		cgpService = new Service<Object> () {
+
+			@Override
+			protected Task<Object> createTask() {
+				Task<Object> t = new Task<Object>() {
+					@Override
+					protected Object call() throws Exception {
+						while (true) {
+							if (isCancelled()) {
+								return null;
+							} else {
+								cgp.nextGeneration();
+							}
+						}
+					}
+				};
+				
+				return t;
+			}
+		};
+		
 		/*
 		 * Instantiate the various GUI elements here. 
 		 * 
@@ -81,16 +96,16 @@ public class GUI extends Application {
 		
 		mainPane = new TabPane();
 		mainPane.setTabClosingPolicy(TabClosingPolicy.UNAVAILABLE);
-		chromosomes = new ChromosomePane[(int) cgp.getResources().get("popSize")];
+		chromosomes = new ChromosomePane[cgp.getResources().getInt("popSize")];
 		Tab tab;
 		for (int i = 0; i < chromosomes.length; i++) {
-			chromosomes[i] = new ChromosomePane(cgp.getPopulation().getChromosome(i));
+			chromosomes[i] = new ChromosomePane(cgp.getPopulation().getChromosome(i), resources);
 			tab = new Tab("Chr " + i);
 			tab.setContent(chromosomes[i]);
 			mainPane.getTabs().add(tab);
 		}
 		
-		settings = new SettingsPane(cgp);
+		settings = new SettingsPane(cgp, this);
 		
 		//mainPane.setPrefHeight(500);
 				
@@ -102,7 +117,7 @@ public class GUI extends Application {
 		
 		window.setCenter(leftPane);
 		window.setRight(settings);
-				
+		
 		//primaryStage.setMinHeight(600);
 		//primaryStage.setMinWidth(800);
 		
@@ -111,5 +126,51 @@ public class GUI extends Application {
 		primaryStage.setScene(new Scene(window));
 		primaryStage.show();
 	}
+	
+	public void updateNodeGrids() {
+		for (int i = 0; i < chromosomes.length; i++) {
+			chromosomes[i].update();
+		}
+	}
+
+	public void playPause() {		
+		if (!evolving) {
+			setEvolving(true);
+			cgpService.restart();
+		} else {
+			cgpService.cancel();
+			setEvolving(false);
+		}
+	}
+	
+	public void step() {
+		if (!evolving) {
+			Thread t = new Thread(new Task<Object>() {
+				@Override
+				protected Object call() throws Exception {
+					cgp.nextGeneration();
+					setEvolving(false);
+					return null;
+				}
+			});
+			setEvolving(true);
+			t.start();
+		}
+	}
+	
+	private void setEvolving(boolean value) {
+		evolving = value;
+		settings.toggleSettings(value);
+		if (value) {
+			settings.bindParameters();
+		} else {
+			updateNodeGrids();
+			settings.unbindParameters();
+		}
+	}
+	
+	public boolean isEvolving() {
+		return evolving;
+	}
 
 }
diff --git a/src/jcgp/JCGP.java b/src/jcgp/JCGP.java
index dc121c9..1742b6a 100644
--- a/src/jcgp/JCGP.java
+++ b/src/jcgp/JCGP.java
@@ -2,28 +2,33 @@ package jcgp;
 
 import java.util.HashMap;
 import java.util.Iterator;
-import java.util.Map;
 import java.util.Map.Entry;
 import java.util.Random;
 
-import javafx.beans.property.Property;
+import javafx.beans.property.SimpleIntegerProperty;
 import jcgp.function.Arithmetic;
 import jcgp.function.BitwiseLogic;
 import jcgp.function.BooleanLogic;
 import jcgp.function.Function;
 import jcgp.function.FunctionSet;
 import jcgp.modules.ea.EvolutionaryAlgorithm;
-import jcgp.modules.ea.StandardEA;
+import jcgp.modules.ea.MuPlusLambda;
+import jcgp.modules.ea.TournamentSelection;
 import jcgp.modules.fitness.FitnessFunction;
 import jcgp.modules.fitness.TestCase;
 import jcgp.modules.fitness.TestCaseEvaluator;
 import jcgp.modules.mutator.Mutator;
 import jcgp.modules.mutator.PointMutator;
 import jcgp.parameters.BooleanParameter;
+import jcgp.parameters.DoubleParameter;
 import jcgp.parameters.IntegerParameter;
 import jcgp.parameters.Parameter;
 import jcgp.population.Population;
 
+/**
+ * @author Eduardo Pedroni
+ *
+ */
 public class JCGP {
 
 	/**
@@ -49,52 +54,57 @@ public class JCGP {
 		public Resources() {
 			createCoreParameters();
 			
-			numberGenerator = new Random((int) get("seed"));
-			
+			numberGenerator = new Random(getInt("seed"));
 			set("arity", functionSet.getMaxArity());
 		}
 		
-		public Object get(String key) {
-			return parameters.get(key).getValue();
-		}
-		
 		public int getInt(String key) {
-			return (int) parameters.get(key).getValue();
+			if (parameters.get(key) instanceof IntegerParameter) {
+				return ((IntegerParameter) parameters.get(key)).get();
+			} else if (parameters.get(key) instanceof DoubleParameter) {
+				return (int) ((DoubleParameter) parameters.get(key)).get();
+			} else {
+				throw new ClassCastException("Could not cast " + parameters.get(key).getClass() + " to int.");
+			}
 		}
 		
 		public double getDouble(String key) {
-			return (double) parameters.get(key).getValue();
+			if (parameters.get(key) instanceof IntegerParameter) {
+				return (double) ((IntegerParameter) parameters.get(key)).get();
+			} else if (parameters.get(key) instanceof DoubleParameter) {
+				return ((DoubleParameter) parameters.get(key)).get();
+			} else {
+				throw new ClassCastException("Could not cast " + parameters.get(key).getClass() + " to double.");
+			}
 		}
 		
 		public boolean getBoolean(String key) {
-			return (boolean) parameters.get(key).getValue();
+			if (parameters.get(key) instanceof BooleanParameter) {
+				return ((BooleanParameter) parameters.get(key)).get();
+			} else {
+				throw new ClassCastException("Could not cast " + parameters.get(key).getClass() + " to int.");
+			}
 		}
 		
 		public void set(String key, Object value) {
-			parameters.get(key).setValue(value);
-		}
-		
-		public Property<?> getProperty(String key) {
-			return parameters.get(key).valueProperty();
+			if (parameters.get(key) instanceof IntegerParameter) {
+				((IntegerParameter) parameters.get(key)).set(((Integer) value).intValue());
+			} else if (parameters.get(key) instanceof DoubleParameter) {
+				((DoubleParameter) parameters.get(key)).set(((Double) value).doubleValue());
+			} else if (parameters.get(key) instanceof BooleanParameter) {
+				((BooleanParameter) parameters.get(key)).set(((Boolean) value).booleanValue());
+			}
 		}
 		
 		public Parameter getParameter(String key) {
 			return parameters.get(key);
 		}
 		
-		public void setManagedParameter(String key, boolean value) {
-			parameters.get(key).setManaged(value);
-		}
-		
-		public void setHiddenParameter(String key, boolean value) {
-			parameters.get(key).setHidden(value);
-		}
-		
 		public boolean contains(String key) {
 			return parameters.containsKey(key);
 		}
 		
-		private void createCoreParameters() {		
+		private void createCoreParameters() {
 			parameters.put("rows", new IntegerParameter(8, "Rows"));
 			parameters.put("columns", new IntegerParameter(9, "Columns"));
 			parameters.put("inputs", new IntegerParameter(3, "Inputs"));
@@ -102,28 +112,23 @@ public class JCGP {
 			parameters.put("popSize", new IntegerParameter(5, "Population"));
 			parameters.put("levelsBack", new IntegerParameter(2, "Levels back"));
 			
-			parameters.put("nodes", new IntegerParameter(72, "Nodes", true, true));
-			
+			IntegerParameter nodes = new IntegerParameter(1, "Nodes", false, true);
+			nodes.valueProperty().bind(((SimpleIntegerProperty) ((IntegerParameter) parameters.get("rows")).valueProperty()).multiply((SimpleIntegerProperty) ((IntegerParameter) parameters.get("columns")).valueProperty()));
+			parameters.put("nodes", nodes);
+						
 			parameters.put("generations", new IntegerParameter(1000000, "Generations"));
-			parameters.put("currentGen", new IntegerParameter(0, "Generation", true, false));
+			parameters.put("currentGen", new IntegerParameter(1, "Generation", false, false));
+			
 			parameters.put("runs", new IntegerParameter(5, "Runs"));
+			parameters.put("currentRun", new IntegerParameter(1, "Run", false, false));
 
 			parameters.put("arity", new IntegerParameter(0, "Max arity", true, true));
-
 			parameters.put("seed", new IntegerParameter(123, "Seed"));
 			
-			parameters.put("debug", new BooleanParameter(false, "Debug"));
+			parameters.put("verbose", new BooleanParameter(false, "Verbose"));
 			parameters.put("report", new IntegerParameter(1, "Report"));
 		}
 		
-		// TODO fix this up
-		private void resetParameters(EvolutionaryAlgorithm ea, Mutator mu, FitnessFunction ff) {
-			Iterator<Entry<String, Parameter>> it = parameters.entrySet().iterator();
-		    while (it.hasNext()) {
-		    	((Parameter) ((Map.Entry<String, Parameter>) it.next()).getValue()).reset();
-		    }
-		}
-
 		/**
 		 * 
 		 * 
@@ -152,11 +157,11 @@ public class JCGP {
 		 * FunctionSet functions
 		 */
 		public Function getRandomFunction() {
-			return functionSet.getFunction(numberGenerator.nextInt(functionSet.getAllowedFunctionCount()));
+			return functionSet.getAllowedFunction(numberGenerator.nextInt(functionSet.getAllowedFunctionCount()));
 		}
 
 		public Function getFunction(int index) {
-			return functionSet.getFunction(index);
+			return functionSet.getAllowedFunction(index);
 		}
 		
 		public void setFunctionSet(int index) {
@@ -205,27 +210,36 @@ public class JCGP {
 	// mutators
 	private Mutator[] mutators = new Mutator[] {
 			new PointMutator() };
-	private Mutator mutator = mutators[0];
+	private Mutator mutator;
 	
 	// evolutionary algorithms
 	private EvolutionaryAlgorithm[] evolutionaryAlgorithms = new EvolutionaryAlgorithm[] {
-			new StandardEA() };
-	private EvolutionaryAlgorithm evolutionaryAlgorithm = evolutionaryAlgorithms[0];
+			new MuPlusLambda(),
+			new TournamentSelection()};
+	private EvolutionaryAlgorithm evolutionaryAlgorithm;
 	
 	// fitness evaluators
 	private FitnessFunction[] fitnessFunctions = new FitnessFunction[] {
 			new TestCaseEvaluator() };
-	private FitnessFunction fitnessFunction = fitnessFunctions[0];
-
-	// the population of chromosomes	
-	private Population population = new Population(resources);
-
+	private FitnessFunction fitnessFunction;
 
+	/*
+	 * the population of chromosomes
+	 */
+	private Population population;
+	
 	public JCGP() {
 		
+		population = new Population(resources);
+
+		evolutionaryAlgorithm = evolutionaryAlgorithms[0];
+		
+		mutator = mutators[0];
+		
+		fitnessFunction = fitnessFunctions[0];
+		
 		resources.setTestCases(new TestCase(new Integer[]{1, 2, 3}, new Integer[]{4, 5, 6}),
 							   new TestCase(new Integer[]{1, 12, 4}, new Integer[]{6, 21, 2}));
-		
 //		for (int i = 0; i < (int) resources.get("generations"); i++) {
 //			
 //			resources.set("currentGen", ((int) resources.get("currentGen")) + 1);
@@ -301,4 +315,48 @@ public class JCGP {
 		return fitnessFunction;
 	}
 	
+	
+	/**
+	 * @param mutator the mutator to set
+	 */
+	public void setMutator(int index) {
+		this.mutator = mutators[index];
+	}
+
+
+	/**
+	 * @param evolutionaryAlgorithm the evolutionaryAlgorithm to set
+	 */
+	public void setEvolutionaryAlgorithm(int index) {		
+		this.evolutionaryAlgorithm = evolutionaryAlgorithms[index];
+	}
+
+
+	/**
+	 * @param fitnessFunction the fitnessFunction to set
+	 */
+	public void setFitnessFunction(int index) {
+		this.fitnessFunction = fitnessFunctions[index];
+	}
+	
+	public void nextGeneration() {
+		resources.set("currentGen", resources.getInt("currentGen") + 1);
+		
+		fitnessFunction.evaluate(population, resources);
+		evolutionaryAlgorithm.evolve(population, mutator, resources);
+		
+		if (evolutionaryAlgorithm.getFittestChromosome().getFitness() >= 6) {
+			System.out.println("solution found");
+			evolutionaryAlgorithm.getFittestChromosome().printNodes();
+		} else {
+			System.out.println("Generation: " + resources.getInt("currentGen") + ", fitness: " + evolutionaryAlgorithm.getFittestChromosome().getFitness());
+		}
+	}
+	
+	public void start() {		
+		while (resources.getInt("currentGen") <= resources.getInt("generations")) {
+			nextGeneration();
+		}
+		// TODO print something?
+	}
 }
diff --git a/src/jcgp/function/Arithmetic.java b/src/jcgp/function/Arithmetic.java
index 7ec1366..b61ee65 100644
--- a/src/jcgp/function/Arithmetic.java
+++ b/src/jcgp/function/Arithmetic.java
@@ -9,7 +9,6 @@ import jcgp.population.Connection;
 public class Arithmetic extends FunctionSet {
 	
 	public Arithmetic() {
-		maxArity = 2;
 		name = "Arithmetic";
 		functionList = new Function[]{
 				new Addition(),
diff --git a/src/jcgp/function/BitwiseLogic.java b/src/jcgp/function/BitwiseLogic.java
index 033534d..7ced8e8 100644
--- a/src/jcgp/function/BitwiseLogic.java
+++ b/src/jcgp/function/BitwiseLogic.java
@@ -9,7 +9,6 @@ import jcgp.population.Connection;
 public class BitwiseLogic extends FunctionSet {
 	
 	public BitwiseLogic() {
-		maxArity = 2;
 		name = "32-bit Logic";
 		functionList = new Function[]{
 				new And(),
diff --git a/src/jcgp/function/BooleanLogic.java b/src/jcgp/function/BooleanLogic.java
index d31b798..7e441f2 100644
--- a/src/jcgp/function/BooleanLogic.java
+++ b/src/jcgp/function/BooleanLogic.java
@@ -9,7 +9,6 @@ import jcgp.population.Connection;
 public class BooleanLogic extends FunctionSet {
 	
 	public BooleanLogic() {
-		maxArity = 2;
 		name = "1-bit Logic";
 		functionList = new Function[]{
 				new And(),
diff --git a/src/jcgp/function/FunctionSet.java b/src/jcgp/function/FunctionSet.java
index 49ff7e7..fef8f88 100644
--- a/src/jcgp/function/FunctionSet.java
+++ b/src/jcgp/function/FunctionSet.java
@@ -12,7 +12,6 @@ import java.util.Iterator;
 public abstract class FunctionSet {
 		protected Function[] functionList;
 		protected ArrayList<Function> allowedFunctions;
-		protected int maxArity;
 		protected String name;
 		
 		public int getAllowedFunctionCount() {
@@ -23,12 +22,22 @@ public abstract class FunctionSet {
 			return functionList.length;
 		}
 		
-		public Function getFunction(int index) {
+		public Function getAllowedFunction(int index) {
 			return allowedFunctions.get(index);
 		}
 		
+		public Function getFunction(int index) {
+			return functionList[index];
+		}
+		
 		public int getMaxArity(){
-			return maxArity;
+			int arity = 0;
+			for (Function function : allowedFunctions) {
+				if (function.getArity() > arity) {
+					arity = function.getArity();
+				}
+			}
+			return arity;
 		}
 		
 		public String getName() {
@@ -58,4 +67,8 @@ public abstract class FunctionSet {
 		public String toString() {
 			return name;
 		}
+		
+		public boolean isEnabled(Function f) {
+			return allowedFunctions.contains(f);
+		}
 	}
\ No newline at end of file
diff --git a/src/jcgp/gui/GUIConsole.java b/src/jcgp/gui/GUIConsole.java
index a14a23b..15ef2f6 100644
--- a/src/jcgp/gui/GUIConsole.java
+++ b/src/jcgp/gui/GUIConsole.java
@@ -1,5 +1,10 @@
 package jcgp.gui;
 
+import java.io.IOException;
+import java.io.OutputStream;
+import java.io.PrintStream;
+
+import javafx.application.Platform;
 import javafx.event.EventHandler;
 import javafx.scene.Cursor;
 import javafx.scene.control.TextArea;
@@ -17,7 +22,12 @@ public class GUIConsole extends AnchorPane {
 		textArea.setEditable(false);
 		textArea.setWrapText(true);
 		
-		//setStyle("-fx-border-width: 5 0 0 0; -fx-border-color: #D1D1D1");
+//		System.setOut(new PrintStream(new OutputStream() {
+//			@Override
+//			public void write(final int b) throws IOException {
+//				textArea.appendText(String.valueOf((char) b));
+//			}
+//		}));
 		
 		setResizeListeners();
 		
diff --git a/src/jcgp/gui/SettingsPane.java b/src/jcgp/gui/SettingsPane.java
deleted file mode 100644
index 594147f..0000000
--- a/src/jcgp/gui/SettingsPane.java
+++ /dev/null
@@ -1,266 +0,0 @@
-package jcgp.gui;
-
-import java.util.ArrayList;
-import java.util.Iterator;
-import java.util.Map;
-import java.util.Map.Entry;
-
-import javafx.event.ActionEvent;
-import javafx.event.EventHandler;
-import javafx.geometry.Insets;
-import javafx.scene.Cursor;
-import javafx.scene.control.CheckBox;
-import javafx.scene.control.ComboBox;
-import javafx.scene.input.MouseEvent;
-import javafx.scene.layout.AnchorPane;
-import javafx.scene.layout.VBox;
-import javafx.scene.text.Font;
-import javafx.scene.text.Text;
-import jcgp.GUI;
-import jcgp.JCGP;
-import jcgp.function.FunctionSet;
-import jcgp.gui.settings.GUIBooleanParameter;
-import jcgp.gui.settings.GUIDoubleParameter;
-import jcgp.gui.settings.GUIIntegerParameter;
-import jcgp.gui.settings.GUIParameter;
-import jcgp.modules.ea.EvolutionaryAlgorithm;
-import jcgp.modules.fitness.FitnessFunction;
-import jcgp.modules.mutator.Mutator;
-import jcgp.parameters.BooleanParameter;
-import jcgp.parameters.DoubleParameter;
-import jcgp.parameters.IntegerParameter;
-import jcgp.parameters.Parameter;
-
-public class SettingsPane extends AnchorPane {
-	
-	private VBox mainContainer, eas, mutators, ffs;
-	private boolean dragging = false;
-		
-	public SettingsPane(JCGP cgp) {
-		super();
-		setResizeListeners();
-		
-		//setStyle("-fx-border-width: 0 0 0 5; -fx-border-color: #D1D1D1");
-		
-		mainContainer = new VBox();
-		
-		AnchorPane.setTopAnchor(mainContainer, 0.0);
-		AnchorPane.setBottomAnchor(mainContainer, 0.0);
-		AnchorPane.setRightAnchor(mainContainer, 0.0);
-		AnchorPane.setLeftAnchor(mainContainer, GUI.RESIZE_MARGIN);
-		mainContainer.setPadding(new Insets(5, 0, 0, 0));
-		mainContainer.setSpacing(6);
-		
-		setMinWidth(GUI.SETTINGS_WIDTH);
-		setPrefWidth(GUI.SETTINGS_WIDTH);
-		
-		makeBaseParameters(cgp);
-		makeEAParameters(cgp);
-		mainContainer.getChildren().add(eas); 
-		
-		makeMutatorParameters(cgp);
-		mainContainer.getChildren().add(mutators);
-		
-		makeFitnessFunctionParameters(cgp);
-		mainContainer.getChildren().add(ffs);
-		
-		makeNodeFunctionParameters(cgp);
-				
-		getChildren().add(mainContainer);
-	}
-
-	private void makeBaseParameters(JCGP cgp) {
-		VBox vb = new VBox();
-		vb.setSpacing(2);
-		
-		Text header = new Text("Base Parameters");
-		header.setFont(Font.font("Arial", 14));
-		header.setUnderline(true);	
-		
-		vb.getChildren().add(header);
-		
-		ArrayList<GUIParameter> gp = new ArrayList<GUIParameter>();
-		
-		gp.add(new GUIIntegerParameter((IntegerParameter) cgp.getResources().getParameter("rows")));
-		gp.add(new GUIIntegerParameter((IntegerParameter) cgp.getResources().getParameter("columns")));
-		gp.add(new GUIIntegerParameter((IntegerParameter) cgp.getResources().getParameter("inputs")));
-		gp.add(new GUIIntegerParameter((IntegerParameter) cgp.getResources().getParameter("outputs")));
-		gp.add(new GUIIntegerParameter((IntegerParameter) cgp.getResources().getParameter("levelsBack")));
-		
-		gp.add(new GUIIntegerParameter((IntegerParameter) cgp.getResources().getParameter("popSize")));
-		gp.add(new GUIIntegerParameter((IntegerParameter) cgp.getResources().getParameter("generations")));
-		gp.add(new GUIIntegerParameter((IntegerParameter) cgp.getResources().getParameter("runs")));
-		
-		gp.add(new GUIIntegerParameter((IntegerParameter) cgp.getResources().getParameter("seed")));
-		gp.add(new GUIIntegerParameter((IntegerParameter) cgp.getResources().getParameter("report")));
-		gp.add(new GUIBooleanParameter((BooleanParameter) cgp.getResources().getParameter("debug")));
-		
-		vb.getChildren().addAll(gp);
-		
-		mainContainer.getChildren().add(vb);
-	}
-
-	private void makeEAParameters(JCGP cgp) {
-		eas = new VBox();
-		eas.setSpacing(2);
-		
-		Text header = new Text("EA");
-		header.setFont(Font.font("Arial", 14));
-		header.setUnderline(true);
-		
-		eas.getChildren().add(header);
-		
-		ComboBox<EvolutionaryAlgorithm> eab = new ComboBox<EvolutionaryAlgorithm>();
-		eab.getItems().addAll(cgp.getEvolutionaryAlgorithms());
-		eab.getSelectionModel().select(cgp.getEvolutionaryAlgorithm());
-		eab.prefWidthProperty().bind(mainContainer.widthProperty());
-		eas.getChildren().add(eab);
-		
-		addParameters(cgp.getEvolutionaryAlgorithm().getLocalParameters().entrySet().iterator(), eas);
-	}
-
-	private void makeMutatorParameters(JCGP cgp) {
-		mutators = new VBox();
-		mutators.setSpacing(2);
-		
-		Text header = new Text("Mutator");
-		header.setFont(Font.font("Arial", 14));
-		header.setUnderline(true);
-		
-		mutators.getChildren().add(header);
-		
-		ComboBox<Mutator> mb = new ComboBox<Mutator>();
-		mb.getItems().addAll(cgp.getMutators());
-		mb.getSelectionModel().select(cgp.getMutator());
-		mb.prefWidthProperty().bind(mainContainer.widthProperty());
-		mutators.getChildren().add(mb);
-		
-		addParameters(cgp.getMutator().getLocalParameters().entrySet().iterator(), mutators);
-	}
-	
-	private void makeFitnessFunctionParameters(JCGP cgp) {
-		ffs = new VBox();
-		ffs.setSpacing(2);
-		
-		Text header = new Text("Fitness Function");
-		header.setFont(Font.font("Arial", 14));
-		header.setUnderline(true);
-		
-		ffs.getChildren().add(header);
-		
-		ComboBox<FitnessFunction> ff = new ComboBox<FitnessFunction>();
-		ff.getItems().addAll(cgp.getFitnessFunctions());
-		ff.getSelectionModel().select(cgp.getFitnessFunction());
-		ff.prefWidthProperty().bind(mainContainer.widthProperty());
-		ffs.getChildren().add(ff); 
-		
-		addParameters(cgp.getFitnessFunction().getLocalParameters().entrySet().iterator(), ffs);
-	}
-	
-	private void makeNodeFunctionParameters(JCGP cgp) {
-		VBox vb = new VBox();
-		vb.setSpacing(2);
-		
-		Text header = new Text("Node Functions");
-		header.setFont(Font.font("Arial", 14));
-		header.setUnderline(true);
-		
-		vb.getChildren().add(header);
-		
-		ComboBox<FunctionSet> nf = new ComboBox<FunctionSet>();
-		nf.getItems().addAll(cgp.getResources().getFunctionSets());
-		nf.getSelectionModel().select(cgp.getResources().getFunctionSet());
-		nf.prefWidthProperty().bind(mainContainer.widthProperty());
-		vb.getChildren().add(nf);
-		
-		// TODO make this function re-usable
-		addFunctions(cgp.getResources().getFunctionSet(), vb);
-		
-		mainContainer.getChildren().add(vb); 
-	}
-	
-	/**
-	 * @param cgp
-	 * @param vb
-	 */
-	private void addParameters(Iterator<Entry<String, Parameter>> it, VBox vb) {
-	    while (it.hasNext()) {
-	        Parameter parameter = ((Map.Entry<String, Parameter>) it.next()).getValue();
-	        if (parameter instanceof IntegerParameter) {
-	        	vb.getChildren().add(new GUIIntegerParameter((IntegerParameter) parameter));
-	        } else if (parameter instanceof DoubleParameter) {
-	        	vb.getChildren().add(new GUIDoubleParameter((DoubleParameter) parameter));
-	        } else if (parameter instanceof BooleanParameter) {
-	        	vb.getChildren().add(new GUIBooleanParameter((BooleanParameter) parameter));
-	        }
-	    }
-	}
-	
-	private void addFunctions(final FunctionSet fs, VBox vb) {
-		CheckBox cb;
-		for (int i = 0; i < fs.getTotalFunctionCount(); i++) {
-			cb = new CheckBox(fs.getFunction(i).getName());
-			cb.setId(String.valueOf(i));
-			cb.setSelected(true);
-			final int index = i;
-			cb.setOnAction(new EventHandler<ActionEvent>() {
-				@Override
-				public void handle(ActionEvent event) {
-					if (((CheckBox) event.getSource()).isSelected()) {
-						fs.enableFunction(index);
-					} else {
-						fs.disableFunction(index);
-					}
-				}
-			});
-			vb.getChildren().add(cb);
-		}
-	}
-	
-	private void setResizeListeners() {
-		setOnMousePressed(new EventHandler<MouseEvent>() {
-			@Override
-			public void handle(MouseEvent event) {
-		        if(isInDraggableZone(event)) {
-			        dragging = true;
-		        }
-			}
-		});
-		setOnMouseDragged(new EventHandler<MouseEvent>() {
-			@Override
-			public void handle(MouseEvent event) {
-				if(dragging) {
-					double newWidth = getWidth() - event.getX();
-					if (newWidth >= getMinWidth()) {
-						setPrefWidth(newWidth);
-					} else {
-						setPrefWidth(getMinWidth());
-					}
-				}
-			}
-		});
-		setOnMouseMoved(new EventHandler<MouseEvent>() {
-			@Override
-			public void handle(MouseEvent event) {
-				if(isInDraggableZone(event) || dragging) {
-		            setCursor(Cursor.H_RESIZE);
-		        }
-		        else {
-		            setCursor(Cursor.DEFAULT);
-		        }
-			}
-		});
-		setOnMouseReleased(new EventHandler<MouseEvent>() {
-			@Override
-			public void handle(MouseEvent event) {
-				dragging = false;
-		        setCursor(Cursor.DEFAULT);
-			}
-		});
-	}
-	
-	private boolean isInDraggableZone(MouseEvent event) {
-        return event.getX() < (GUI.RESIZE_MARGIN);
-    }
-		
-}
diff --git a/src/jcgp/gui/population/ChromosomePane.java b/src/jcgp/gui/population/ChromosomePane.java
deleted file mode 100644
index 7fa8a54..0000000
--- a/src/jcgp/gui/population/ChromosomePane.java
+++ /dev/null
@@ -1,106 +0,0 @@
-package jcgp.gui.population;
-
-import java.util.ArrayList;
-
-import javafx.scene.control.ScrollPane;
-import javafx.scene.layout.Pane;
-import javafx.scene.shape.Line;
-import jcgp.GUI;
-import jcgp.population.Chromosome;
-import jcgp.population.Connection;
-import jcgp.population.Input;
-import jcgp.population.Node;
-
-
-public class ChromosomePane extends ScrollPane {
-
-	private GUINode[][] guiNodes;
-	private GUIInput[] guiInputs;
-	private GUIOutput[] guiOutputs;
-	
-	private Pane content;
-	
-	private ArrayList<Line> connectionLines;
-	
-	private boolean target = false;
-	
-	public ChromosomePane(Chromosome chromosome) {
-		super();		
-		connectionLines = new ArrayList<Line>();
-		
-		//setMouseTransparent(true);
-		
-		content = new Pane();
-		content.setId("content pane for genes");
-		
-		// generate the GUIGenes
-		// inputs
-		guiInputs = new GUIInput[(int) GUI.resources.get("inputs")];
-		for (int i = 0; i < guiInputs.length; i++) {
-			// make the GUI elements
-			guiInputs[i] = new GUIInput(this, chromosome.getInput(i));
-			content.getChildren().addAll(guiInputs[i]);
-		}
-		// nodes
-		guiNodes = new GUINode[(int) GUI.resources.get("rows")][(int) GUI.resources.get("columns")];
-		double angle, xPos, yPos;
-		for (int r = 0; r < guiNodes.length; r++) {
-			for (int c = 0; c < guiNodes[r].length; c++) {
-				// make the connection lines
-				Line lines[] = new Line[(int) GUI.resources.get("arity")];
-				for (int l = 0; l < lines.length; l++) {
-					angle = ((((double) (l + 1)) / ((double) (lines.length + 1))) * GUIGene.THETA) - (GUIGene.THETA / 2);
-					xPos = (-Math.cos(angle) * GUIGene.NODE_RADIUS) + (((c + 1) * (2 * GUIGene.NODE_RADIUS + GUIGene.SPACING)) + GUIGene.NODE_RADIUS);
-					yPos = (Math.sin(angle) * GUIGene.NODE_RADIUS) + ((r * (2 * GUIGene.NODE_RADIUS + GUIGene.SPACING)) + GUIGene.NODE_RADIUS);
-					
-					lines[l] = new Line(xPos, yPos, xPos, yPos);
-					lines[l].setMouseTransparent(true);
-					lines[l].setVisible(false);
-					connectionLines.add(lines[l]);
-				}
-				// make the GUI elements
-				guiNodes[r][c] = new GUINode(this, chromosome.getNode(r, c), lines);
-			}
-			content.getChildren().addAll(guiNodes[r]);
-		}
-		
-		// outputs
-		guiOutputs = new GUIOutput[(int) GUI.resources.get("outputs")];
-		for (int i = 0; i < guiOutputs.length; i++) {
-			xPos = (((int) GUI.resources.get("columns") + 1) * (2 * GUIGene.NODE_RADIUS + GUIGene.SPACING));
-			yPos = (chromosome.getOutput(i).getIndex() * (2 * GUIGene.NODE_RADIUS + GUIGene.SPACING)) + GUIGene.NODE_RADIUS;
-			// make the line
-			Line line = new Line(xPos, yPos, xPos, yPos);
-			line.setMouseTransparent(true);
-			line.setVisible(false);
-			connectionLines.add(line);
-			// make the GUI elements
-			guiOutputs[i] = new GUIOutput(this, chromosome.getOutput(i), line);
-			content.getChildren().addAll(guiOutputs[i]);
-		}
-
-		content.getChildren().addAll(connectionLines);
-		setPrefWidth(620);	
-		setContent(content);
-	}
-	
-	public GUIGene getGuiGene(Connection gene) {
-		if (gene instanceof Input) {
-			return guiInputs[((Input) gene).getIndex()];
-		} else if (gene instanceof Node) {
-			return guiNodes[((Node) gene).getRow()][((Node) gene).getColumn()];
-		} else {
-			// something bad happened!
-			throw new ClassCastException();
-		}
-		
-	}
-	
-	public boolean isTarget() {
-		return target;
-	}
-	
-	public void setTarget(boolean newValue) {
-		target = newValue;
-	}
-}
diff --git a/src/jcgp/gui/population/GUIGene.java b/src/jcgp/gui/population/GUIGene.java
index 3addca7..a37eb19 100644
--- a/src/jcgp/gui/population/GUIGene.java
+++ b/src/jcgp/gui/population/GUIGene.java
@@ -4,6 +4,7 @@ import javafx.beans.property.SimpleObjectProperty;
 import javafx.scene.Group;
 import javafx.scene.shape.Circle;
 import javafx.scene.text.Text;
+import jcgp.gui.ChromosomePane;
 import jcgp.population.Connection;
 import jcgp.population.Gene;
 
diff --git a/src/jcgp/gui/population/GUIInput.java b/src/jcgp/gui/population/GUIInput.java
index 84e8a2a..30ce4ac 100644
--- a/src/jcgp/gui/population/GUIInput.java
+++ b/src/jcgp/gui/population/GUIInput.java
@@ -12,6 +12,7 @@ import javafx.scene.text.Font;
 import javafx.scene.text.Text;
 import javafx.scene.text.TextAlignment;
 import jcgp.GUI;
+import jcgp.gui.ChromosomePane;
 import jcgp.population.Connection;
 import jcgp.population.Input;
 import jcgp.population.Output;
diff --git a/src/jcgp/gui/population/GUINode.java b/src/jcgp/gui/population/GUINode.java
index eeacb9e..6fc84da 100644
--- a/src/jcgp/gui/population/GUINode.java
+++ b/src/jcgp/gui/population/GUINode.java
@@ -14,6 +14,7 @@ import javafx.scene.text.Font;
 import javafx.scene.text.Text;
 import javafx.scene.text.TextAlignment;
 import jcgp.GUI;
+import jcgp.gui.ChromosomePane;
 import jcgp.population.Connection;
 import jcgp.population.Input;
 import jcgp.population.Node;
@@ -56,10 +57,10 @@ public class GUINode extends GUIGene {
 		text.setX(-NODE_RADIUS);
 		text.setVisible(true);
 
-		Circle[] sockets = new Circle[(int) GUI.resources.get("arity")];
+		Circle[] sockets = new Circle[GUI.resources.getInt("arity")];
 		double angle, xPos, yPos;
 		for (int l = 0; l < sockets.length; l++) {
-			angle = ((((double) (l + 1)) / ((double) ((int) GUI.resources.get("arity") + 1))) * THETA) - (THETA / 2);
+			angle = ((((double) (l + 1)) / ((GUI.resources.getDouble("arity") + 1))) * THETA) - (THETA / 2);
 			xPos = -Math.cos(angle) * NODE_RADIUS;
 			yPos = Math.sin(angle) * NODE_RADIUS;
 
@@ -335,7 +336,7 @@ public class GUINode extends GUIGene {
 			} else if (target instanceof GUINode) {
 				// target and source are nodes, let's look at levels back
 				Node t = ((GUINode) target).getGene(), s = ((GUINode) source).getGene();
-				if (s.getColumn() - t.getColumn() > 0 && s.getColumn() - t.getColumn() <= (int) GUI.resources.get("levelsBack")) {
+				if (s.getColumn() - t.getColumn() > 0 && s.getColumn() - t.getColumn() <= GUI.resources.getInt("levelsBack")) {
 					return true;
 				}
 				return false;
@@ -462,4 +463,8 @@ public class GUINode extends GUIGene {
 		lines[connectionIndex].setEndX(gene.getLayoutX() + NODE_RADIUS);
 		lines[connectionIndex].setEndY(gene.getLayoutY());
 	}
+
+	public void updateFunction() {
+		text.setText(node.getFunction().getName());
+	}
 }
diff --git a/src/jcgp/gui/population/GUIOutput.java b/src/jcgp/gui/population/GUIOutput.java
index 57042eb..16d95f0 100644
--- a/src/jcgp/gui/population/GUIOutput.java
+++ b/src/jcgp/gui/population/GUIOutput.java
@@ -14,6 +14,7 @@ import javafx.scene.text.Font;
 import javafx.scene.text.Text;
 import javafx.scene.text.TextAlignment;
 import jcgp.GUI;
+import jcgp.gui.ChromosomePane;
 import jcgp.population.Connection;
 import jcgp.population.Input;
 import jcgp.population.Node;
@@ -31,7 +32,7 @@ public class GUIOutput extends GUIGene {
 		this.output = output;
 		this.sourceLine = line;
 
-		relocate((((int) GUI.resources.get("columns") + 1) * (2 * NODE_RADIUS + SPACING)) + NODE_RADIUS,
+		relocate(((GUI.resources.getInt("columns") + 1) * (2 * NODE_RADIUS + SPACING)) + NODE_RADIUS,
 				(output.getIndex() * (2 * NODE_RADIUS + SPACING)) + NODE_RADIUS);
 
 		// set the line ends correctly
@@ -242,14 +243,6 @@ public class GUIOutput extends GUIGene {
 			}
 		});
 
-		output.sourceProperty().addListener(new ChangeListener<Connection>() {
-			@Override
-			public void changed(ObservableValue<? extends Connection> observable,
-					Connection oldValue, Connection newValue) {
-				updateLines();
-			}
-		});
-
 	}
 
 	@Override
diff --git a/src/jcgp/gui/settings/GUIBooleanParameter.java b/src/jcgp/gui/settings/GUIBooleanParameter.java
deleted file mode 100644
index 7b20c3b..0000000
--- a/src/jcgp/gui/settings/GUIBooleanParameter.java
+++ /dev/null
@@ -1,24 +0,0 @@
-package jcgp.gui.settings;
-
-import javafx.geometry.Pos;
-import javafx.scene.control.CheckBox;
-import jcgp.parameters.BooleanParameter;
-
-public class GUIBooleanParameter extends GUIParameter {
-	
-	public GUIBooleanParameter(BooleanParameter parameter) {
-		setAlignment(Pos.CENTER_LEFT);
-		setSpacing(5);
-		
-		this.parameter = parameter;
-		
-		value = new CheckBox(parameter.getName());
-		((CheckBox) value).setSelected(parameter.getValue());
-		
-		value.setDisable(parameter.isManaged());
-		
-		getChildren().add(value);
-		
-	}
-	
-}
diff --git a/src/jcgp/gui/settings/GUIDoubleParameter.java b/src/jcgp/gui/settings/GUIDoubleParameter.java
deleted file mode 100644
index d61899b..0000000
--- a/src/jcgp/gui/settings/GUIDoubleParameter.java
+++ /dev/null
@@ -1,33 +0,0 @@
-package jcgp.gui.settings;
-
-import javafx.geometry.Pos;
-import javafx.scene.control.TextField;
-import javafx.scene.layout.Priority;
-import javafx.scene.text.Text;
-import jcgp.GUI;
-import jcgp.parameters.DoubleParameter;
-
-public class GUIDoubleParameter extends GUIParameter {
-	
-	public GUIDoubleParameter(DoubleParameter parameter) {
-		setAlignment(Pos.CENTER_LEFT);
-		setSpacing(5);
-		
-		this.parameter = parameter;
-		
-		name = new Text(parameter.getName());
-		value = new TextField(String.valueOf(parameter.getValue()));
-		
-		((TextField) value).setAlignment(Pos.CENTER_RIGHT);
-		
-		setHgrow(value, Priority.ALWAYS);
-		
-		name.setWrappingWidth(GUI.WRAP_WIDTH);
-		
-		value.setDisable(parameter.isManaged());
-		
-		getChildren().addAll(name, value);
-		
-	}
-	
-}
diff --git a/src/jcgp/gui/settings/GUIIntegerParameter.java b/src/jcgp/gui/settings/GUIIntegerParameter.java
deleted file mode 100644
index b7a23a4..0000000
--- a/src/jcgp/gui/settings/GUIIntegerParameter.java
+++ /dev/null
@@ -1,31 +0,0 @@
-package jcgp.gui.settings;
-
-import javafx.geometry.Pos;
-import javafx.scene.control.TextField;
-import javafx.scene.layout.Priority;
-import javafx.scene.text.Text;
-import jcgp.GUI;
-import jcgp.parameters.IntegerParameter;
-
-public class GUIIntegerParameter extends GUIParameter {
-
-	public GUIIntegerParameter(IntegerParameter parameter) {
-		setAlignment(Pos.CENTER_LEFT);
-		setSpacing(5);
-		
-		this.parameter = parameter;
-		
-		name = new Text(parameter.getName());
-		value = new TextField(String.valueOf(parameter.getValue()));
-		
-		((TextField) value).setAlignment(Pos.CENTER_RIGHT);
-				
-		setHgrow(value, Priority.ALWAYS);
-		
-		name.setWrappingWidth(GUI.WRAP_WIDTH);
-		
-		value.setDisable(parameter.isManaged());
-		
-		getChildren().addAll(name, value);
-	}
-}
diff --git a/src/jcgp/gui/settings/GUIParameter.java b/src/jcgp/gui/settings/GUIParameter.java
deleted file mode 100644
index 0547758..0000000
--- a/src/jcgp/gui/settings/GUIParameter.java
+++ /dev/null
@@ -1,14 +0,0 @@
-package jcgp.gui.settings;
-
-import javafx.scene.control.Control;
-import javafx.scene.layout.HBox;
-import javafx.scene.text.Text;
-import jcgp.parameters.Parameter;
-
-public abstract class GUIParameter extends HBox {
-		
-	protected Parameter parameter;
-	protected Text name;
-	protected Control value;
-	
-}
diff --git a/src/jcgp/modules/Module.java b/src/jcgp/modules/Module.java
index 7cf0b8d..9e0b267 100644
--- a/src/jcgp/modules/Module.java
+++ b/src/jcgp/modules/Module.java
@@ -6,9 +6,6 @@ import jcgp.JCGP.Resources;
 import jcgp.parameters.Parameter;
 
 public interface Module {
-
-	public void activate(Resources parameters);
-	
 	public HashMap<String, Parameter> getLocalParameters();
-
+	public ModuleStatus getStatus(Resources resources);
 }
diff --git a/src/jcgp/modules/ea/StandardEA.java b/src/jcgp/modules/ea/StandardEA.java
deleted file mode 100644
index 1d27004..0000000
--- a/src/jcgp/modules/ea/StandardEA.java
+++ /dev/null
@@ -1,79 +0,0 @@
-package jcgp.modules.ea;
-
-import java.util.HashMap;
-
-import jcgp.JCGP.Resources;
-import jcgp.modules.mutator.Mutator;
-import jcgp.parameters.IntegerParameter;
-import jcgp.parameters.Parameter;
-import jcgp.population.Chromosome;
-import jcgp.population.Population;
-
-/**
- * (μ + λ) EA.
- * 
- * 
- * @author Eduardo Pedroni
- *
- */
-public class StandardEA implements EvolutionaryAlgorithm {
-	
-	private Chromosome fittestChromosome;
-	
-	private IntegerParameter parents, offspring;
-	private HashMap<String, Parameter> localParameters;
-	
-	public StandardEA() {		
-		parents = new IntegerParameter(1, "Parents");
-		offspring = new IntegerParameter(4, "Offspring");		
-		
-		localParameters = new HashMap<String, Parameter>();
-		
-		localParameters.put("mu", parents);
-		localParameters.put("lambda", offspring);
-	}
-
-	@Override
-	public void evolve(Population population, Mutator mutator, Resources parameters) {
-		// select fittest chromosome
-		int fittest = 0;
-		
-		for (int i = 1; i < (int) parameters.get("popSize"); i++) {
-			if (population.getChromosome(i).getFitness() >= population.getChromosome(fittest).getFitness()) {
-				fittest = i;
-			}
-		}
-		fittestChromosome = population.getChromosome(fittest);
-		population.setBestIndividual(fittest);
-		// create copies of fittest chromosome, mutate them
-		Chromosome fc = population.getChromosome(fittest);
-		for (int i = 0; i < (int) parameters.get("popSize"); i++) {
-			if (i != fittest) {
-				population.getChromosome(i).copyConnections(fc);
-				mutator.mutate(population.getChromosome(i), parameters);
-			}
-		}
-	}
-
-	@Override
-	public Chromosome getFittestChromosome() {
-		return fittestChromosome;
-	}
-
-	@Override
-	public void activate(Resources parameters) {
-		parameters.getParameter("popSize").setManaged(true);
-	}
-
-	@Override
-	public HashMap<String, Parameter> getLocalParameters() {
-		return localParameters;
-	}
-
-	@Override
-	public String toString() {
-		return "(μ + λ)";
-	}
-	
-	
-}
diff --git a/src/jcgp/modules/fitness/TestCaseEvaluator.java b/src/jcgp/modules/fitness/TestCaseEvaluator.java
index 77b282c..d8c1255 100644
--- a/src/jcgp/modules/fitness/TestCaseEvaluator.java
+++ b/src/jcgp/modules/fitness/TestCaseEvaluator.java
@@ -3,6 +3,7 @@ package jcgp.modules.fitness;
 import java.util.HashMap;
 
 import jcgp.JCGP.Resources;
+import jcgp.modules.ModuleStatus;
 import jcgp.parameters.Parameter;
 import jcgp.population.Population;
 
@@ -11,13 +12,13 @@ public class TestCaseEvaluator implements FitnessFunction {
 	@Override
 	public void evaluate(Population population, Resources resources) {
 		// for every chromosome in the population
-		for (int i = 0; i < (int) resources.get("popSize"); i++) {
+		for (int i = 0; i < resources.getInt("popSize"); i++) {
 			int fitness = 0;
 			// for every test case
 			for (int t = 0; t < resources.getTestCaseCount(); t++) {
 				population.getChromosome(i).setInputs(resources.getTestCase(t).getInputs());
 				// check every output
-				for (int o = 0; o < (int) resources.get("outputs"); o++) {
+				for (int o = 0; o < resources.getInt("outputs"); o++) {
 					if (population.getChromosome(i).getOutput(o).calculate() == resources.getTestCase(t).getOutput(o)) {
 						fitness++;
 					}
@@ -28,17 +29,17 @@ public class TestCaseEvaluator implements FitnessFunction {
 	}
 
 	@Override
-	public void activate(Resources parameters) {
-		// nothing
-	}
-
-	@Override
 	public HashMap<String, Parameter> getLocalParameters() {
-		return new HashMap<String, Parameter>();
+		return null;
 	}
 
 	@Override
 	public String toString() {
 		return "Test case";
 	}
+
+	@Override
+	public ModuleStatus getStatus(Resources resources) {
+		return null;
+	}
 }
diff --git a/src/jcgp/modules/mutator/PointMutator.java b/src/jcgp/modules/mutator/PointMutator.java
index e9be153..2298368 100644
--- a/src/jcgp/modules/mutator/PointMutator.java
+++ b/src/jcgp/modules/mutator/PointMutator.java
@@ -2,6 +2,7 @@ package jcgp.modules.mutator;
 
 import java.util.HashMap;
 
+import jcgp.modules.ModuleStatus;
 import jcgp.parameters.DoubleParameter;
 import jcgp.parameters.Parameter;
 import jcgp.JCGP.Resources;
@@ -12,9 +13,11 @@ import jcgp.population.Output;
 
 public class PointMutator implements Mutator {
 	
-	private Parameter mutationRate;
+	private DoubleParameter mutationRate;
 	private HashMap<String, Parameter> localParameters;
 	
+	private ModuleStatus status = ModuleStatus.READY;
+	
 	public PointMutator() {
 		mutationRate = new DoubleParameter(0.5, "Percent mutation");
 		
@@ -24,29 +27,24 @@ public class PointMutator implements Mutator {
 
 	@Override
 	public void mutate(Chromosome chromosome, Resources resources) {
-		int mutations = (int) Math.ceil((((double) mutationRate.getValue()) * (((((Integer) resources.get("nodes")).doubleValue() + ((Integer) resources.get("outputs")).doubleValue())) / (double) 100)));
+		int mutations = (int) Math.ceil(((mutationRate.get()) * ((((resources.getDouble("nodes")) + (resources.getDouble("outputs")))) / (double) 100)));
 		for (int i = 0; i < mutations; i++) {
 			MutableElement m = chromosome.getRandomMutableElement();
 			
 			if (m instanceof Output) {
 				m.setConnection(0, chromosome.getRandomConnection());
 			} else if (m instanceof Node) {
-				int geneType = resources.getRandomInt(1 + ((int) resources.get("arity")));
+				int geneType = resources.getRandomInt(1 + resources.getInt("arity"));
 				if (geneType < 1) {
 					((Node) m).setFunction(resources.getRandomFunction());
 				} else {
-					m.setConnection(resources.getRandomInt((int) resources.get("arity")), chromosome.getRandomConnection(((Node) m).getColumn()));
+					m.setConnection(resources.getRandomInt(resources.getInt("arity")), chromosome.getRandomConnection(((Node) m).getColumn()));
 				}
 			}
 		}
 	}
 
 	@Override
-	public void activate(Resources parameters) {
-		// nothing
-	}
-
-	@Override
 	public HashMap<String, Parameter> getLocalParameters() {
 		return localParameters;
 	}
@@ -56,4 +54,18 @@ public class PointMutator implements Mutator {
 		return "Point mutation";
 	}
 
+	@Override
+	public ModuleStatus getStatus(Resources resources) {
+		if (mutationRate.get() <= 0 || mutationRate.get() > 100) {
+			status = ModuleStatus.ERROR;
+			status.setDetails("Mutation rate must be > 0 and <= 100");
+		} else if ((int) ((mutationRate.get() / 100) * resources.getDouble("nodes")) >  0) {
+			status = ModuleStatus.WARNING;
+			status.setDetails("With mutation rate " + mutationRate.get() + ", no mutations will occur.");
+		} else {
+			status = ModuleStatus.READY;
+			status.setDetails("");
+		}
+		return status;
+	}
 }
diff --git a/src/jcgp/parameters/BooleanParameter.java b/src/jcgp/parameters/BooleanParameter.java
index 0f339a1..63e9c73 100644
--- a/src/jcgp/parameters/BooleanParameter.java
+++ b/src/jcgp/parameters/BooleanParameter.java
@@ -3,30 +3,30 @@ package jcgp.parameters;
 import javafx.beans.property.SimpleBooleanProperty;
 
 public class BooleanParameter extends Parameter {
-			
-	public BooleanParameter(boolean value, String name) {
-		super(name);
+	
+	private SimpleBooleanProperty value;
+	
+	public BooleanParameter(boolean value, String name, boolean editable, boolean hidden) {
+		super(name, editable, hidden);
 		this.value = new SimpleBooleanProperty(value);
 	}
 	
-	public BooleanParameter(boolean value, String name, boolean managed, boolean hidden) {
-		super(name, managed, hidden);
+	public BooleanParameter(boolean value, String name) {
+		super(name, true, false);
 		this.value = new SimpleBooleanProperty(value);
 	}
 	
-	@Override
-	public Boolean getValue() {
-		return ((SimpleBooleanProperty) this.value).get();
+	public boolean get() {
+		return value.get();
 	}
 	
-	@Override
-	public SimpleBooleanProperty valueProperty() {
-		return (SimpleBooleanProperty) value;
-	}
-
-	@Override
-	public void setValue(Object value) {
-		((SimpleBooleanProperty) this.value).set((boolean) value);
+	public void set(boolean newValue) {
+		if (!value.isBound()) {
+			value.set(newValue);
+		}
 	}
 	
+	public SimpleBooleanProperty valueProperty() {
+		return value;
+	}
 }
diff --git a/src/jcgp/parameters/DoubleParameter.java b/src/jcgp/parameters/DoubleParameter.java
index ade99cc..d555452 100644
--- a/src/jcgp/parameters/DoubleParameter.java
+++ b/src/jcgp/parameters/DoubleParameter.java
@@ -3,31 +3,31 @@ package jcgp.parameters;
 import javafx.beans.property.SimpleDoubleProperty;
 
 public class DoubleParameter extends Parameter {
-			
-	public DoubleParameter(double value, String name) {
-		super(name);
+	
+	protected SimpleDoubleProperty value;
+		
+	public DoubleParameter(double value, String name, boolean editable, boolean hidden) {
+		super(name, editable, hidden);
 		this.value = new SimpleDoubleProperty(value);
 	}
 	
-	public DoubleParameter(double value, String name, boolean managed, boolean hidden) {
-		super(name, managed, hidden);
+	public DoubleParameter(double value, String name) {
+		super(name, true, false);
 		this.value = new SimpleDoubleProperty(value);
 	}
+
+	public double get() {
+		return value.get();
+	}
 	
-	@Override
-	public Double getValue() {
-		return ((SimpleDoubleProperty) value).get();
+	public void set(double newValue) {
+		if (!value.isBound()) {
+			value.set(newValue);
+		}
 	}
 	
-	@Override
 	public SimpleDoubleProperty valueProperty() {
-		return (SimpleDoubleProperty) value;
-	}
-
-	@Override
-	public void setValue(Object value) {
-		((SimpleDoubleProperty) this.value).set((double) value);
-		
+		return value;
 	}
 	
 }
diff --git a/src/jcgp/parameters/IntegerParameter.java b/src/jcgp/parameters/IntegerParameter.java
index cc60179..c743e97 100644
--- a/src/jcgp/parameters/IntegerParameter.java
+++ b/src/jcgp/parameters/IntegerParameter.java
@@ -4,29 +4,30 @@ import javafx.beans.property.SimpleIntegerProperty;
 
 public class IntegerParameter extends Parameter {
 	
-	public IntegerParameter(int value, String name) {
-		super(name);
+	protected SimpleIntegerProperty value;
+	
+	public IntegerParameter(int value, String name, boolean editable, boolean hidden) {
+		super(name, editable, hidden);
 		this.value = new SimpleIntegerProperty(value);
 	}
 	
-	public IntegerParameter(int value, String name, boolean managed, boolean hidden) {
-		super(name, managed, hidden);
+	public IntegerParameter(int value, String name) {
+		super(name, true, false);
 		this.value = new SimpleIntegerProperty(value);
 	}
+
+	public int get() {
+		return value.get();
+	}
 	
-	@Override
-	public Integer getValue() {
-		return ((SimpleIntegerProperty) this.value).get();
+	public void set(int newValue) {
+		if (!value.isBound()) {
+			value.set(newValue);
+		}
 	}
 	
-	@Override
 	public SimpleIntegerProperty valueProperty() {
-		return (SimpleIntegerProperty) value;
-	}
-
-	@Override
-	public void setValue(Object value) {
-		((SimpleIntegerProperty) this.value).set((int) value);
+		return value;
 	}
 	
 }
diff --git a/src/jcgp/parameters/Parameter.java b/src/jcgp/parameters/Parameter.java
index fcff9fd..42c70e4 100644
--- a/src/jcgp/parameters/Parameter.java
+++ b/src/jcgp/parameters/Parameter.java
@@ -1,58 +1,26 @@
 package jcgp.parameters;
 
-import javafx.beans.property.Property;
 public abstract class Parameter {
 	
-	protected boolean managed = false;
-	protected boolean hidden = false;
-	
-	protected boolean originalManaged = false;
-	protected boolean originalHidden = false;
-	
-	protected Property<?> value;
+	protected boolean hidden = false, editable = true;
 	
 	protected String name;
 	
-	public Parameter(String name, boolean managed, boolean hidden) {
-		this.name = name;
-		this.managed = originalManaged = managed;
-		this.hidden = originalHidden = hidden;
-	}
-	
-	public Parameter(String name) {
+	public Parameter(String name, boolean editable, boolean hidden) {
 		this.name = name;
-	}
-	
-	public void setManaged(boolean value) {
-		managed = value;
-	}
-	
-	public boolean isManaged() {
-		return managed;
-	}
-	
-	public void setHidden(boolean value) {
-		hidden = value;
+		this.hidden = hidden;
+		this.editable = editable;
 	}
 	
 	public boolean isHidden() {
 		return hidden;
 	}
 	
-	public String getName() {
-		return name;
+	public boolean isEditable() {
+		return editable;
 	}
 	
-	public abstract Object getValue();
-	
-	public abstract void setValue(Object value);
-	
-	public Property<?> valueProperty() {
-		return value;
-	}
-
-	public void reset() {
-		hidden = originalHidden;
-		managed = originalManaged;
+	public String getName() {
+		return name;
 	}
 }
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
diff --git a/src/jcgp/tests/ChromosomeTests.java b/src/jcgp/tests/ChromosomeTests.java
index f4ed79c..eb4b5d1 100644
--- a/src/jcgp/tests/ChromosomeTests.java
+++ b/src/jcgp/tests/ChromosomeTests.java
@@ -62,7 +62,7 @@ public class ChromosomeTests {
 
 		// compare all elements, one by one
 		// check outputs
-		for (int o = 0; o < (int) resources.get("outputs"); o++) {
+		for (int o = 0; o < resources.getInt("outputs"); o++) {
 			// check that no cross-references exist between chromosomes
 			assertTrue("Cloned chromosome contains a reference to a member of the original chromosome.",
 					clone.getOutput(o) != chromosome.getOutput(o) && 
@@ -80,8 +80,8 @@ public class ChromosomeTests {
 			}
 		}
 		// check nodes, rows first
-		for (int row = 0; row < (int) resources.get("rows"); row++) {
-			for (int column = 0; column < (int) resources.get("columns"); column++) {
+		for (int row = 0; row < resources.getInt("rows"); row++) {
+			for (int column = 0; column < resources.getInt("columns"); column++) {
 				// check that nodes are not pointers to the same instance
 				assertTrue("Both chromosomes contain a reference to the same node.", clone.getNode(row, column) != chromosome.getNode(row, column));
 				// check that both nodes reference their own position in the grid correctly
@@ -91,7 +91,7 @@ public class ChromosomeTests {
 				assertTrue("Equivalent nodes have different functions.", clone.getNode(row, column).getFunction() == chromosome.getNode(row, column).getFunction());
 
 				// compare each connection
-				for (int connection = 0; connection < (int) resources.get("arity"); connection++) {
+				for (int connection = 0; connection < resources.getInt("arity"); connection++) {
 					// first look at whether they are actually the same instance
 					assertTrue("Nodes are connected to the same connection instance.", 
 							clone.getNode(row, column).getConnection(connection) !=	chromosome.getNode(row, column).getConnection(connection));
@@ -130,12 +130,12 @@ public class ChromosomeTests {
 		clone.setInputs((Object[]) testInputs);
 
 		// check that both chromosomes have the same outputs
-		for (int i = 0; i < (int) resources.get("outputs"); i++) {
+		for (int i = 0; i < resources.getInt("outputs"); i++) {
 			assertTrue("Incorrect output returned", ((Integer) chromosome.getOutput(i).calculate()) == ((Integer) clone.getOutput(i).calculate()));
 		}
 
 		// mutate an output in clone, check that the same node in chromosome produces a different output
-		clone.getOutput(1).setConnection(resources.getRandomInt((int) resources.get("arity")), clone.getInput(2));
+		clone.getOutput(1).setConnection(resources.getRandomInt(resources.getInt("arity")), clone.getInput(2));
 
 		assertTrue("Mutation affected nodes in both chromosomes.",
 				clone.getOutput(1).calculate() != chromosome.getOutput(1).calculate());
@@ -164,7 +164,7 @@ public class ChromosomeTests {
 
 		// get random connections with the last column as reference, check that they're all within range
 		int connectionNodes = 0, connectionOutOfRange = 0, connectionInputs = 0, connectionPicks = 100000;
-		int chosenColumn = (int) resources.get("columns") - 1;
+		int chosenColumn = resources.getInt("columns") - 1;
 		for (int i = 0; i < connectionPicks; i++) {
 			Connection c = chromosome.getRandomConnection(chosenColumn);
 			if (c instanceof Node) {
@@ -180,10 +180,10 @@ public class ChromosomeTests {
 
 			}	
 		}
-		System.out.println("Out of " + connectionPicks + " connections picked from " + ((chosenColumn >= (int) resources.get("levelsBack")) ? (int) resources.get("levelsBack") : chosenColumn) * (int) resources.get("rows") +
-				" allowed nodes and " + (int) resources.get("inputs") + " inputs, " + connectionNodes + " were nodes and " + connectionInputs + " were inputs.");
+		System.out.println("Out of " + connectionPicks + " connections picked from " + ((chosenColumn >= resources.getInt("levelsBack")) ? resources.getInt("levelsBack") : chosenColumn) * resources.getInt("rows") +
+				" allowed nodes and " + resources.getInt("inputs") + " inputs, " + connectionNodes + " were nodes and " + connectionInputs + " were inputs.");
 
-		System.out.println("Node/input ratio: " + ((Integer) (((chosenColumn >= (int) resources.get("levelsBack")) ? (int) resources.get("levelsBack") : chosenColumn) * (Integer) resources.get("rows"))).doubleValue() / ((Integer) resources.get("inputs")).doubleValue() +
+		System.out.println("Node/input ratio: " + (chosenColumn >= resources.getInt("levelsBack") ? resources.getInt("levelsBack") : chosenColumn) * resources.getDouble("rows") / resources.getDouble("inputs") +
 				", picked ratio: " + (double) connectionNodes / (double) connectionInputs);
 
 		System.out.println(connectionOutOfRange + " nodes that disrespected levels back were picked.");
@@ -207,10 +207,10 @@ public class ChromosomeTests {
 				fail("Return is neither Node nor Output.");
 			}
 		}
-		System.out.println("Out of " + mutablePicks + " mutable elements picked from " + (int) resources.get("nodes") +
-				" nodes and " + (int) resources.get("outputs") + " outputs, " + mutableNodes + " were nodes and " +
+		System.out.println("Out of " + mutablePicks + " mutable elements picked from " + resources.getInt("nodes") +
+				" nodes and " + resources.getInt("outputs") + " outputs, " + mutableNodes + " were nodes and " +
 				mutableOutputs + " were outputs.");
-		System.out.println("Node/output ratio: " + ((Integer) resources.get("nodes")).doubleValue() / ((Integer) resources.get("outputs")).doubleValue() +
+		System.out.println("Node/output ratio: " + resources.getDouble("nodes") / resources.getDouble("outputs") +
 				", picked ratio: " + (double) mutableNodes / (double) mutableOutputs + "\n");
 	}
 
@@ -234,12 +234,12 @@ public class ChromosomeTests {
 	@Test
 	public void setInputTest() {
 		// set input values, check that acquired values are correct
-		Integer[] testInputs = new Integer[(int) resources.get("inputs")];
-		for (int i = 0; i < (int) resources.get("inputs"); i++) {
+		Integer[] testInputs = new Integer[resources.getInt("inputs")];
+		for (int i = 0; i < resources.getInt("inputs"); i++) {
 			testInputs[i] = i * 2 - 3;
 		}
 		chromosome.setInputs((Object[]) testInputs);
-		for (int i = 0; i < (int) resources.get("inputs"); i++) {
+		for (int i = 0; i < resources.getInt("inputs"); i++) {
 			assertTrue("Incorrect input returned.", ((Integer) chromosome.getInput(i).getValue()) == i * 2 - 3);
 		}
 	}
@@ -250,8 +250,8 @@ public class ChromosomeTests {
 	@Test
 	public void getNodeTest() {
 		// get all nodes one by one, check that they are all correct
-		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++) {
 				assertTrue("Incorrect node returned.", chromosome.getNode(r, c).getColumn() == c &&
 						chromosome.getNode(r, c).getRow() == r);
 			}
diff --git a/src/jcgp/tests/NodeTests.java b/src/jcgp/tests/NodeTests.java
index 7ce5701..d8aa742 100644
--- a/src/jcgp/tests/NodeTests.java
+++ b/src/jcgp/tests/NodeTests.java
@@ -46,7 +46,7 @@ public class NodeTests {
 
 	@Before
 	public void setUp() throws Exception {
-		node = new Node(chromosome, 0, 0, (int) resources.get("arity"));
+		node = new Node(chromosome, 0, 0, resources.getInt("arity"));
 		// make node with anonymous addition function and hard-coded value connections
 		node.initialise(new Arithmetic.Addition(),
 				new Connection[]{new Connection() {
@@ -186,7 +186,7 @@ public class NodeTests {
 				return null;
 			}
 		};
-		node.setConnection(resources.getRandomInt((int) resources.get("arity")), conn2);
+		node.setConnection(resources.getRandomInt(resources.getInt("arity")), conn2);
 
 		assertTrue("Connection was not found in node.", node.getConnection(0) == conn2 || node.getConnection(1) == conn2);
 
diff --git a/src/jcgp/tests/PopulationTests.java b/src/jcgp/tests/PopulationTests.java
index ca737d6..a11becf 100644
--- a/src/jcgp/tests/PopulationTests.java
+++ b/src/jcgp/tests/PopulationTests.java
@@ -70,7 +70,7 @@ public class PopulationTests {
 			chromosomes++;
 		}
 
-		assertTrue("Incorrect number of chromosomes generated.", chromosomes == (int) resources.get("popSize"));
+		assertTrue("Incorrect number of chromosomes generated.", chromosomes == resources.getInt("popSize"));
 	}
 	
 	@Test