52 files changed, 602 insertions, 393 deletions

diff --git a/src/jcgp/JCGP.java b/src/jcgp/JCGP.java
index 807739f..7451d4f 100644
--- a/src/jcgp/JCGP.java
+++ b/src/jcgp/JCGP.java
@@ -6,24 +6,27 @@ import java.util.Map.Entry;
 import java.util.Random;
 
 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.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;
+import javafx.beans.value.ChangeListener;
+import javafx.beans.value.ObservableValue;
+import jcgp.backend.function.Arithmetic;
+import jcgp.backend.function.BitwiseLogic;
+import jcgp.backend.function.BooleanLogic;
+import jcgp.backend.function.Function;
+import jcgp.backend.function.FunctionSet;
+import jcgp.backend.modules.ea.EvolutionaryAlgorithm;
+import jcgp.backend.modules.ea.MuPlusLambda;
+import jcgp.backend.modules.ea.TournamentSelection;
+import jcgp.backend.modules.fitness.FitnessFunction;
+import jcgp.backend.modules.fitness.TestCase;
+import jcgp.backend.modules.fitness.TestCaseEvaluator;
+import jcgp.backend.modules.mutator.Mutator;
+import jcgp.backend.modules.mutator.PointMutator;
+import jcgp.backend.parameters.BooleanParameter;
+import jcgp.backend.parameters.DoubleParameter;
+import jcgp.backend.parameters.IntegerParameter;
+import jcgp.backend.parameters.Parameter;
+import jcgp.backend.population.Population;
+import jcgp.gui.console.Console;
 
 /**
  * @author Eduardo Pedroni
@@ -33,6 +36,9 @@ public class JCGP {
 
 	/**
 	 * 
+	 * The resources class encapsulates all of the resources based on which the program operates.
+	 * Each instance of JCGP contains a single instance of Resources, which gets passed to the selected
+	 * modules as the program executes.
 	 * 
 	 * @author Eduardo Pedroni
 	 *
@@ -51,8 +57,11 @@ public class JCGP {
 				new BooleanLogic() };
 		private FunctionSet functionSet = functionSets[0];
 		
+		// GUI console
+		private Console console;
+		
 		public Resources() {
-			createCoreParameters();
+			createBaseParameters();
 			
 			numberGenerator = new Random(getInt("seed"));
 			set("arity", functionSet.getMaxArity());
@@ -104,7 +113,7 @@ public class JCGP {
 			return parameters.containsKey(key);
 		}
 		
-		private void createCoreParameters() {
+		private void createBaseParameters() {
 			parameters.put("rows", new IntegerParameter(8, "Rows"));
 			parameters.put("columns", new IntegerParameter(9, "Columns"));
 			parameters.put("inputs", new IntegerParameter(3, "Inputs"));
@@ -112,21 +121,73 @@ public class JCGP {
 			parameters.put("popSize", new IntegerParameter(5, "Population"));
 			parameters.put("levelsBack", new IntegerParameter(2, "Levels back"));
 			
-			IntegerParameter nodes = new IntegerParameter(1, "Nodes", false, true);
+			IntegerParameter nodes = new IntegerParameter(1, "Nodes", true, true, false);
 			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(1, "Generation", false, false));
+			parameters.put("currentGen", new IntegerParameter(1, "Generation", true, false, false));
 			
 			parameters.put("runs", new IntegerParameter(5, "Runs"));
-			parameters.put("currentRun", new IntegerParameter(1, "Run", false, false));
+			parameters.put("currentRun", new IntegerParameter(1, "Run", true, false, false));
 
-			parameters.put("arity", new IntegerParameter(0, "Max arity", true, true));
-			parameters.put("seed", new IntegerParameter(123, "Seed"));
+			parameters.put("arity", new IntegerParameter(0, "Max arity", false, true, false));
+			
+			IntegerParameter seed = new IntegerParameter(123, "Seed");
+			seed.valueProperty().addListener(new ChangeListener<Number>() {
+				@Override
+				public void changed(
+						ObservableValue<? extends Number> observable,
+						Number oldValue, Number newValue) {
+					numberGenerator.setSeed(newValue.longValue());
+				}
+			});
+			parameters.put("seed", seed);
 			
-			parameters.put("verbose", new BooleanParameter(false, "Verbose"));
-			parameters.put("report", new IntegerParameter(1, "Report"));
+			parameters.put("report", new IntegerParameter(1, "Report", false, false, false));
+		}
+		
+		private boolean validateBaseParameters() {
+			boolean valid = true;
+			
+			if (getInt("rows") <= 0) {
+				valid = false;
+				println("Error: number of rows must be greater than 0.");
+			}
+			if (getInt("columns") <= 0) {
+				valid = false;
+				println("Error: number of columns must be greater than 0.");
+			}
+			if (getInt("inputs") <= 0) {
+				valid = false;
+				println("Error: number of inputs must be greater than 0.");
+			}
+			if (getInt("outputs") <= 0) {
+				println("Error: number of outputs must be greater than 0.");
+				valid = false;
+			}
+			if (getInt("popSize") <= 0) {
+				println("Error: population size must be greater than 0.");
+				valid = false;
+			}
+			if (getInt("levelsBack") <= 0 || getInt("levelsBack") > getInt("columns")) {
+				println("Error: levels back must be greater than 0 and no greater than the number of columns.");
+				valid = false;
+			}
+			if (getInt("generations") <= 0) {
+				println("Error: number of generations must be greater than 0.");
+				valid = false;
+			}
+			if (getInt("runs") <= 0) {
+				println("Error: number of runs must be greater than 0.");
+				valid = false;
+			}
+			if (getInt("report") < 0) {
+				println("Error: report frequency must not be smaller than 0.");
+				valid = false;
+			}
+			
+			return valid;
 		}
 		
 		/**
@@ -157,7 +218,8 @@ public class JCGP {
 		 * FunctionSet functions
 		 */
 		public Function getRandomFunction() {
-			return functionSet.getAllowedFunction(numberGenerator.nextInt(functionSet.getAllowedFunctionCount()));
+			Function f = functionSet.getAllowedFunction(numberGenerator.nextInt(functionSet.getAllowedFunctionCount()));
+			return f;
 		}
 
 		public Function getFunction(int index) {
@@ -196,7 +258,27 @@ public class JCGP {
 		public int getTestCaseCount() {
 			return testCases.length;
 		}
-
+	
+		/*
+		 * Console functionality
+		 */
+		public void setConsole(Console console) {
+			this.console = console;
+		}
+		
+		public void println(String s) {
+			System.out.println(s);
+			if (console != null) {
+				console.println(s);
+			}
+		}
+		
+		public void print(String s) {
+			System.out.print(s);
+			if (console != null) {
+				console.print(s);
+			}
+		}
 	}
 	
 	private Resources resources = new Resources();
@@ -242,21 +324,12 @@ public class JCGP {
 		
 		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);
-//			
-//			fitnessFunction.evaluate(population, resources);
-//			evolutionaryAlgorithm.evolve(population, mutator, resources);
-//			
-//			System.out.println("fitness: " + evolutionaryAlgorithm.getFittestChromosome().getFitness());
-//			
-//			if (evolutionaryAlgorithm.getFittestChromosome().getFitness() >= 6) {
-//				System.out.println("solution found");
-//				evolutionaryAlgorithm.getFittestChromosome().printNodes();
-//				break;
-//			}
-//		}	
+
+	}
+
+
+	public void remakePopulation() {
+		population = new Population(resources);
 	}
 
 
@@ -342,23 +415,22 @@ public class JCGP {
 	}
 	
 	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");
+			resources.println("solution found");
 			evolutionaryAlgorithm.getFittestChromosome().printNodes();
 		} else {
-			System.out.println("Generation: " + resources.getInt("currentGen") + ", fitness: " + evolutionaryAlgorithm.getFittestChromosome().getFitness());
+			resources.println("Generation: " + resources.getInt("currentGen") + ", fitness: " + evolutionaryAlgorithm.getFittestChromosome().getFitness());
 		}
+		resources.set("currentGen", resources.getInt("currentGen") + 1);
 	}
 	
 	public void start() {		
 		while (resources.getInt("currentGen") <= resources.getInt("generations")) {
 			nextGeneration();
 		}
-		// TODO print something?
-	}	
+	}
 }
diff --git a/src/jcgp/exceptions/InsufficientConnectionsException.java b/src/jcgp/backend/exceptions/InsufficientConnectionsException.java
index 2ffc10f..15ac845 100644
--- a/src/jcgp/exceptions/InsufficientConnectionsException.java
+++ b/src/jcgp/backend/exceptions/InsufficientConnectionsException.java
@@ -1,4 +1,4 @@
-package jcgp.exceptions;
+package jcgp.backend.exceptions;
 
 public class InsufficientConnectionsException extends RuntimeException {
 
diff --git a/src/jcgp/exceptions/InvalidArgumentsException.java b/src/jcgp/backend/exceptions/InvalidArgumentsException.java
index 537018d..bbae976 100644
--- a/src/jcgp/exceptions/InvalidArgumentsException.java
+++ b/src/jcgp/backend/exceptions/InvalidArgumentsException.java
@@ -1,4 +1,4 @@
-package jcgp.exceptions;
+package jcgp.backend.exceptions;
 
 public class InvalidArgumentsException extends RuntimeException {
 
diff --git a/src/jcgp/exceptions/ManagedModuleException.java b/src/jcgp/backend/exceptions/ManagedModuleException.java
index a327dfb..3452d35 100644
--- a/src/jcgp/exceptions/ManagedModuleException.java
+++ b/src/jcgp/backend/exceptions/ManagedModuleException.java
@@ -1,4 +1,4 @@
-package jcgp.exceptions;
+package jcgp.backend.exceptions;
 
 public class ManagedModuleException extends RuntimeException {
 
diff --git a/src/jcgp/exceptions/ParameterMismatchException.java b/src/jcgp/backend/exceptions/ParameterMismatchException.java
index 93a8f10..3ab9fa1 100644
--- a/src/jcgp/exceptions/ParameterMismatchException.java
+++ b/src/jcgp/backend/exceptions/ParameterMismatchException.java
@@ -1,4 +1,4 @@
-package jcgp.exceptions;
+package jcgp.backend.exceptions;
 
 public class ParameterMismatchException extends RuntimeException {
 
diff --git a/src/jcgp/function/Arithmetic.java b/src/jcgp/backend/function/Arithmetic.java
index b61ee65..6971663 100644
--- a/src/jcgp/function/Arithmetic.java
+++ b/src/jcgp/backend/function/Arithmetic.java
@@ -1,10 +1,10 @@
-package jcgp.function;
+package jcgp.backend.function;
 
 import java.util.ArrayList;
 import java.util.Arrays;
 
-import jcgp.exceptions.InvalidArgumentsException;
-import jcgp.population.Connection;
+import jcgp.backend.exceptions.InvalidArgumentsException;
+import jcgp.backend.population.Connection;
 
 public class Arithmetic extends FunctionSet {
 	
diff --git a/src/jcgp/function/BitwiseLogic.java b/src/jcgp/backend/function/BitwiseLogic.java
index 7ced8e8..bfe361f 100644
--- a/src/jcgp/function/BitwiseLogic.java
+++ b/src/jcgp/backend/function/BitwiseLogic.java
@@ -1,10 +1,10 @@
-package jcgp.function;
+package jcgp.backend.function;
 
 import java.util.ArrayList;
 import java.util.Arrays;
 
-import jcgp.exceptions.InvalidArgumentsException;
-import jcgp.population.Connection;
+import jcgp.backend.exceptions.InvalidArgumentsException;
+import jcgp.backend.population.Connection;
 
 public class BitwiseLogic extends FunctionSet {
 	
diff --git a/src/jcgp/function/BooleanLogic.java b/src/jcgp/backend/function/BooleanLogic.java
index 7e441f2..e0b5c9c 100644
--- a/src/jcgp/function/BooleanLogic.java
+++ b/src/jcgp/backend/function/BooleanLogic.java
@@ -1,10 +1,10 @@
-package jcgp.function;
+package jcgp.backend.function;
 
 import java.util.ArrayList;
 import java.util.Arrays;
 
-import jcgp.exceptions.InvalidArgumentsException;
-import jcgp.population.Connection;
+import jcgp.backend.exceptions.InvalidArgumentsException;
+import jcgp.backend.population.Connection;
 
 public class BooleanLogic extends FunctionSet {
 	
diff --git a/src/jcgp/function/Function.java b/src/jcgp/backend/function/Function.java
index 64dd206..30bbcf0 100644
--- a/src/jcgp/function/Function.java
+++ b/src/jcgp/backend/function/Function.java
@@ -1,7 +1,7 @@
-package jcgp.function;
+package jcgp.backend.function;
 
-import jcgp.exceptions.InvalidArgumentsException;
-import jcgp.population.Connection;
+import jcgp.backend.exceptions.InvalidArgumentsException;
+import jcgp.backend.population.Connection;
 
 public abstract class Function {
 			
diff --git a/src/jcgp/function/FunctionSet.java b/src/jcgp/backend/function/FunctionSet.java
index fef8f88..4470ac8 100644
--- a/src/jcgp/function/FunctionSet.java
+++ b/src/jcgp/backend/function/FunctionSet.java
@@ -1,4 +1,4 @@
-package jcgp.function;
+package jcgp.backend.function;
 
 import java.util.ArrayList;
 import java.util.Iterator;
diff --git a/src/jcgp/modules/Module.java b/src/jcgp/backend/modules/Module.java
index 9e0b267..f9114de 100644
--- a/src/jcgp/modules/Module.java
+++ b/src/jcgp/backend/modules/Module.java
@@ -1,9 +1,9 @@
-package jcgp.modules;
+package jcgp.backend.modules;
 
 import java.util.HashMap;
 
 import jcgp.JCGP.Resources;
-import jcgp.parameters.Parameter;
+import jcgp.backend.parameters.Parameter;
 
 public interface Module {
 	public HashMap<String, Parameter> getLocalParameters();
diff --git a/src/jcgp/modules/ModuleStatus.java b/src/jcgp/backend/modules/ModuleStatus.java
index 02e2c01..fec8490 100644
--- a/src/jcgp/modules/ModuleStatus.java
+++ b/src/jcgp/backend/modules/ModuleStatus.java
@@ -1,4 +1,4 @@
-package jcgp.modules;
+package jcgp.backend.modules;
 
 public enum ModuleStatus {
 	ERROR, WARNING, READY;
diff --git a/src/jcgp/modules/ea/EvolutionaryAlgorithm.java b/src/jcgp/backend/modules/ea/EvolutionaryAlgorithm.java
index 3bc7fcf..ce457ef 100644
--- a/src/jcgp/modules/ea/EvolutionaryAlgorithm.java
+++ b/src/jcgp/backend/modules/ea/EvolutionaryAlgorithm.java
@@ -1,10 +1,10 @@
-package jcgp.modules.ea;
+package jcgp.backend.modules.ea;
 
 import jcgp.JCGP.Resources;
-import jcgp.modules.Module;
-import jcgp.modules.mutator.Mutator;
-import jcgp.population.Chromosome;
-import jcgp.population.Population;
+import jcgp.backend.modules.Module;
+import jcgp.backend.modules.mutator.Mutator;
+import jcgp.backend.population.Chromosome;
+import jcgp.backend.population.Population;
 
 public interface EvolutionaryAlgorithm extends Module {
 
diff --git a/src/jcgp/modules/ea/MuPlusLambda.java b/src/jcgp/backend/modules/ea/MuPlusLambda.java
index 94900ca..fcfba05 100644
--- a/src/jcgp/modules/ea/MuPlusLambda.java
+++ b/src/jcgp/backend/modules/ea/MuPlusLambda.java
@@ -1,14 +1,14 @@
-package jcgp.modules.ea;
+package jcgp.backend.modules.ea;
 
 import java.util.HashMap;
 
 import jcgp.JCGP.Resources;
-import jcgp.modules.ModuleStatus;
-import jcgp.modules.mutator.Mutator;
-import jcgp.parameters.IntegerParameter;
-import jcgp.parameters.Parameter;
-import jcgp.population.Chromosome;
-import jcgp.population.Population;
+import jcgp.backend.modules.ModuleStatus;
+import jcgp.backend.modules.mutator.Mutator;
+import jcgp.backend.parameters.IntegerParameter;
+import jcgp.backend.parameters.Parameter;
+import jcgp.backend.population.Chromosome;
+import jcgp.backend.population.Population;
 
 /**
  * (μ + λ) EA.
diff --git a/src/jcgp/modules/ea/TournamentSelection.java b/src/jcgp/backend/modules/ea/TournamentSelection.java
index c2915a5..6cbaa45 100644
--- a/src/jcgp/modules/ea/TournamentSelection.java
+++ b/src/jcgp/backend/modules/ea/TournamentSelection.java
@@ -1,14 +1,14 @@
-package jcgp.modules.ea;
+package jcgp.backend.modules.ea;
 
 import java.util.HashMap;
 
 import jcgp.JCGP.Resources;
-import jcgp.modules.ModuleStatus;
-import jcgp.modules.mutator.Mutator;
-import jcgp.parameters.IntegerParameter;
-import jcgp.parameters.Parameter;
-import jcgp.population.Chromosome;
-import jcgp.population.Population;
+import jcgp.backend.modules.ModuleStatus;
+import jcgp.backend.modules.mutator.Mutator;
+import jcgp.backend.parameters.IntegerParameter;
+import jcgp.backend.parameters.Parameter;
+import jcgp.backend.population.Chromosome;
+import jcgp.backend.population.Population;
 
 public class TournamentSelection implements EvolutionaryAlgorithm {
 	
@@ -18,7 +18,7 @@ public class TournamentSelection implements EvolutionaryAlgorithm {
 	private HashMap<String, Parameter> localParameters;
 	
 	public TournamentSelection() {		
-		tournament = new IntegerParameter(1, "Tournament size");	
+		tournament = new IntegerParameter(1, "Tournament size");
 		
 		localParameters = new HashMap<String, Parameter>();
 		localParameters.put("tournament", tournament);
@@ -32,7 +32,8 @@ public class TournamentSelection implements EvolutionaryAlgorithm {
 	@Override
 	public void evolve(Population population, Mutator mutator,
 			Resources parameters) {
-		
+		tournament.set(tournament.get() + 1);
+		fittestChromosome = population.getChromosome(0);
 		// TODO implement this
 
 	}
diff --git a/src/jcgp/modules/fitness/FitnessFunction.java b/src/jcgp/backend/modules/fitness/FitnessFunction.java
index f0800b0..ffce9b7 100644
--- a/src/jcgp/modules/fitness/FitnessFunction.java
+++ b/src/jcgp/backend/modules/fitness/FitnessFunction.java
@@ -1,8 +1,8 @@
-package jcgp.modules.fitness;
+package jcgp.backend.modules.fitness;
 
 import jcgp.JCGP.Resources;
-import jcgp.modules.Module;
-import jcgp.population.Population;
+import jcgp.backend.modules.Module;
+import jcgp.backend.population.Population;
 
 public interface FitnessFunction extends Module {
 
diff --git a/src/jcgp/modules/fitness/TestCase.java b/src/jcgp/backend/modules/fitness/TestCase.java
index 081a257..23f7ecf 100644
--- a/src/jcgp/modules/fitness/TestCase.java
+++ b/src/jcgp/backend/modules/fitness/TestCase.java
@@ -1,4 +1,4 @@
-package jcgp.modules.fitness;
+package jcgp.backend.modules.fitness;
 
 public class TestCase {
 
diff --git a/src/jcgp/modules/fitness/TestCaseEvaluator.java b/src/jcgp/backend/modules/fitness/TestCaseEvaluator.java
index d8c1255..3b67f28 100644
--- a/src/jcgp/modules/fitness/TestCaseEvaluator.java
+++ b/src/jcgp/backend/modules/fitness/TestCaseEvaluator.java
@@ -1,11 +1,11 @@
-package jcgp.modules.fitness;
+package jcgp.backend.modules.fitness;
 
 import java.util.HashMap;
 
 import jcgp.JCGP.Resources;
-import jcgp.modules.ModuleStatus;
-import jcgp.parameters.Parameter;
-import jcgp.population.Population;
+import jcgp.backend.modules.ModuleStatus;
+import jcgp.backend.parameters.Parameter;
+import jcgp.backend.population.Population;
 
 public class TestCaseEvaluator implements FitnessFunction {
 	
diff --git a/src/jcgp/modules/mutator/Mutator.java b/src/jcgp/backend/modules/mutator/Mutator.java
index 8dfa0f9..fd7cd27 100644
--- a/src/jcgp/modules/mutator/Mutator.java
+++ b/src/jcgp/backend/modules/mutator/Mutator.java
@@ -1,8 +1,8 @@
-package jcgp.modules.mutator;
+package jcgp.backend.modules.mutator;
 
 import jcgp.JCGP.Resources;
-import jcgp.modules.Module;
-import jcgp.population.Chromosome;
+import jcgp.backend.modules.Module;
+import jcgp.backend.population.Chromosome;
 
 public interface Mutator extends Module {
 
diff --git a/src/jcgp/modules/mutator/PointMutator.java b/src/jcgp/backend/modules/mutator/PointMutator.java
index 2298368..62d827d 100644
--- a/src/jcgp/modules/mutator/PointMutator.java
+++ b/src/jcgp/backend/modules/mutator/PointMutator.java
@@ -1,15 +1,16 @@
-package jcgp.modules.mutator;
+package jcgp.backend.modules.mutator;
 
 import java.util.HashMap;
 
-import jcgp.modules.ModuleStatus;
-import jcgp.parameters.DoubleParameter;
-import jcgp.parameters.Parameter;
+import jcgp.backend.function.Function;
+import jcgp.backend.modules.ModuleStatus;
+import jcgp.backend.parameters.DoubleParameter;
+import jcgp.backend.parameters.Parameter;
+import jcgp.backend.population.Chromosome;
+import jcgp.backend.population.MutableElement;
+import jcgp.backend.population.Node;
+import jcgp.backend.population.Output;
 import jcgp.JCGP.Resources;
-import jcgp.population.Chromosome;
-import jcgp.population.MutableElement;
-import jcgp.population.Node;
-import jcgp.population.Output;
 
 public class PointMutator implements Mutator {
 	
@@ -19,7 +20,7 @@ public class PointMutator implements Mutator {
 	private ModuleStatus status = ModuleStatus.READY;
 	
 	public PointMutator() {
-		mutationRate = new DoubleParameter(0.5, "Percent mutation");
+		mutationRate = new DoubleParameter(0.5, "Percent mutation", false, false, false);
 		
 		localParameters = new HashMap<String, Parameter>();
 		localParameters.put("mutRate", mutationRate);
@@ -36,7 +37,8 @@ public class PointMutator implements Mutator {
 			} else if (m instanceof Node) {
 				int geneType = resources.getRandomInt(1 + resources.getInt("arity"));
 				if (geneType < 1) {
-					((Node) m).setFunction(resources.getRandomFunction());
+					Function f = resources.getRandomFunction();
+					((Node) m).setFunction(f);
 				} else {
 					m.setConnection(resources.getRandomInt(resources.getInt("arity")), chromosome.getRandomConnection(((Node) m).getColumn()));
 				}
diff --git a/src/jcgp/parameters/BooleanParameter.java b/src/jcgp/backend/parameters/BooleanParameter.java
index 63e9c73..d5904cd 100644
--- a/src/jcgp/parameters/BooleanParameter.java
+++ b/src/jcgp/backend/parameters/BooleanParameter.java
@@ -1,4 +1,4 @@
-package jcgp.parameters;
+package jcgp.backend.parameters;
 
 import javafx.beans.property.SimpleBooleanProperty;
 
@@ -6,13 +6,13 @@ public class BooleanParameter extends Parameter {
 	
 	private SimpleBooleanProperty value;
 	
-	public BooleanParameter(boolean value, String name, boolean editable, boolean hidden) {
-		super(name, editable, hidden);
+	public BooleanParameter(boolean value, String name, boolean monitor, boolean hidden, boolean critical) {
+		super(name, monitor, hidden, critical);
 		this.value = new SimpleBooleanProperty(value);
 	}
 	
 	public BooleanParameter(boolean value, String name) {
-		super(name, true, false);
+		super(name, false, false, true);
 		this.value = new SimpleBooleanProperty(value);
 	}
 	
diff --git a/src/jcgp/parameters/DoubleParameter.java b/src/jcgp/backend/parameters/DoubleParameter.java
index d555452..26031be 100644
--- a/src/jcgp/parameters/DoubleParameter.java
+++ b/src/jcgp/backend/parameters/DoubleParameter.java
@@ -1,4 +1,4 @@
-package jcgp.parameters;
+package jcgp.backend.parameters;
 
 import javafx.beans.property.SimpleDoubleProperty;
 
@@ -6,13 +6,13 @@ public class DoubleParameter extends Parameter {
 	
 	protected SimpleDoubleProperty value;
 		
-	public DoubleParameter(double value, String name, boolean editable, boolean hidden) {
-		super(name, editable, hidden);
+	public DoubleParameter(double value, String name, boolean monitor, boolean hidden, boolean critical) {
+		super(name, monitor, hidden, critical);
 		this.value = new SimpleDoubleProperty(value);
 	}
 	
 	public DoubleParameter(double value, String name) {
-		super(name, true, false);
+		super(name, false, false, true);
 		this.value = new SimpleDoubleProperty(value);
 	}
 
diff --git a/src/jcgp/parameters/IntegerParameter.java b/src/jcgp/backend/parameters/IntegerParameter.java
index c743e97..dbfa5c5 100644
--- a/src/jcgp/parameters/IntegerParameter.java
+++ b/src/jcgp/backend/parameters/IntegerParameter.java
@@ -1,4 +1,4 @@
-package jcgp.parameters;
+package jcgp.backend.parameters;
 
 import javafx.beans.property.SimpleIntegerProperty;
 
@@ -6,13 +6,13 @@ public class IntegerParameter extends Parameter {
 	
 	protected SimpleIntegerProperty value;
 	
-	public IntegerParameter(int value, String name, boolean editable, boolean hidden) {
-		super(name, editable, hidden);
+	public IntegerParameter(int value, String name, boolean monitor, boolean hidden, boolean critical) {
+		super(name, monitor, hidden, critical);
 		this.value = new SimpleIntegerProperty(value);
 	}
 	
 	public IntegerParameter(int value, String name) {
-		super(name, true, false);
+		super(name, false, false, true);
 		this.value = new SimpleIntegerProperty(value);
 	}
 
diff --git a/src/jcgp/backend/parameters/Parameter.java b/src/jcgp/backend/parameters/Parameter.java
new file mode 100644
index 0000000..2f584a4
--- /dev/null
+++ b/src/jcgp/backend/parameters/Parameter.java
@@ -0,0 +1,35 @@
+package jcgp.backend.parameters;
+
+import javafx.beans.property.Property;
+
+public abstract class Parameter {
+	
+	protected boolean hidden, monitor, critical;
+	
+	protected String name;
+	
+	public Parameter(String name, boolean monitor, boolean hidden, boolean critical) {
+		this.name = name;
+		this.hidden = hidden;
+		this.monitor = monitor;
+		this.critical = critical;
+	}
+	
+	public boolean isHidden() {
+		return hidden;
+	}
+	
+	public boolean isMonitor() {
+		return monitor;
+	}
+	
+	public boolean isCritical() {
+		return critical;
+	}
+	
+	public String getName() {
+		return name;
+	}
+	
+	public abstract Property<?> valueProperty();
+}
diff --git a/src/jcgp/population/Chromosome.java b/src/jcgp/backend/population/Chromosome.java
index 297d298..18ae9bb 100644
--- a/src/jcgp/population/Chromosome.java
+++ b/src/jcgp/backend/population/Chromosome.java
@@ -1,9 +1,9 @@
-package jcgp.population;
+package jcgp.backend.population;
 
 import java.util.ArrayList;
 
 import jcgp.JCGP.Resources;
-import jcgp.exceptions.ParameterMismatchException;
+import jcgp.backend.exceptions.ParameterMismatchException;
 
 public class Chromosome {
 	
diff --git a/src/jcgp/population/Connection.java b/src/jcgp/backend/population/Connection.java
index 63a171e..ea4f10f 100644
--- a/src/jcgp/population/Connection.java
+++ b/src/jcgp/backend/population/Connection.java
@@ -1,4 +1,4 @@
-package jcgp.population;
+package jcgp.backend.population;
 
 public interface Connection {
 
diff --git a/src/jcgp/population/Gene.java b/src/jcgp/backend/population/Gene.java
index 8865a01..6b90949 100644
--- a/src/jcgp/population/Gene.java
+++ b/src/jcgp/backend/population/Gene.java
@@ -1,4 +1,4 @@
-package jcgp.population;
+package jcgp.backend.population;
 
 public abstract class Gene {
 
diff --git a/src/jcgp/population/Input.java b/src/jcgp/backend/population/Input.java
index cfcb3ce..83fba07 100644
--- a/src/jcgp/population/Input.java
+++ b/src/jcgp/backend/population/Input.java
@@ -1,4 +1,4 @@
-package jcgp.population;
+package jcgp.backend.population;
 
 public class Input extends Gene implements Connection {
 	
diff --git a/src/jcgp/population/MutableElement.java b/src/jcgp/backend/population/MutableElement.java
index 12f6bd1..8548e63 100644
--- a/src/jcgp/population/MutableElement.java
+++ b/src/jcgp/backend/population/MutableElement.java
@@ -1,4 +1,4 @@
-package jcgp.population;
+package jcgp.backend.population;
 
 public interface MutableElement {
 	
diff --git a/src/jcgp/population/Node.java b/src/jcgp/backend/population/Node.java
index 141a32a..f1d37a1 100644
--- a/src/jcgp/population/Node.java
+++ b/src/jcgp/backend/population/Node.java
@@ -1,10 +1,10 @@
-package jcgp.population;
+package jcgp.backend.population;
 
 import java.util.ArrayList;
 import java.util.Arrays;
 
-import jcgp.exceptions.InsufficientConnectionsException;
-import jcgp.function.Function;
+import jcgp.backend.exceptions.InsufficientConnectionsException;
+import jcgp.backend.function.Function;
 
 
 public class Node extends Gene implements MutableElement, Connection {
@@ -22,13 +22,11 @@ public class Node extends Gene implements MutableElement, Connection {
 
 	@Override
 	public Object getValue() {
-		//System.out.print("Calculating node: (" + row + ", " + column + ") > ");
 		return function.run(Arrays.copyOfRange(connections, 0, function.getArity()));
 	}
 
 	public void setFunction(Function newFunction) {
 		function = newFunction;
-		chromosome.recomputeActiveNodes();
 	}
 
 	@Override
diff --git a/src/jcgp/population/Output.java b/src/jcgp/backend/population/Output.java
index 5cc6dcf..aa94ab6 100644
--- a/src/jcgp/population/Output.java
+++ b/src/jcgp/backend/population/Output.java
@@ -1,4 +1,4 @@
-package jcgp.population;
+package jcgp.backend.population;
 
 import java.util.ArrayList;
 
diff --git a/src/jcgp/population/Population.java b/src/jcgp/backend/population/Population.java
index f5e0517..7049d79 100644
--- a/src/jcgp/population/Population.java
+++ b/src/jcgp/backend/population/Population.java
@@ -1,4 +1,4 @@
-package jcgp.population;
+package jcgp.backend.population;
 
 import jcgp.JCGP.Resources;
 
diff --git a/src/jcgp/tests/ChromosomeTests.java b/src/jcgp/backend/tests/ChromosomeTests.java
index eb4b5d1..1cd067e 100644
--- a/src/jcgp/tests/ChromosomeTests.java
+++ b/src/jcgp/backend/tests/ChromosomeTests.java
@@ -1,14 +1,14 @@
-package jcgp.tests;
+package jcgp.backend.tests;
 
 import static org.junit.Assert.assertTrue;
 import static org.junit.Assert.fail;
 import jcgp.JCGP.Resources;
-import jcgp.population.Chromosome;
-import jcgp.population.Connection;
-import jcgp.population.Input;
-import jcgp.population.MutableElement;
-import jcgp.population.Node;
-import jcgp.population.Output;
+import jcgp.backend.population.Chromosome;
+import jcgp.backend.population.Connection;
+import jcgp.backend.population.Input;
+import jcgp.backend.population.MutableElement;
+import jcgp.backend.population.Node;
+import jcgp.backend.population.Output;
 
 import org.junit.Before;
 import org.junit.BeforeClass;
diff --git a/src/jcgp/tests/InputTests.java b/src/jcgp/backend/tests/InputTests.java
index 012a734..4d15667 100644
--- a/src/jcgp/tests/InputTests.java
+++ b/src/jcgp/backend/tests/InputTests.java
@@ -1,7 +1,7 @@
-package jcgp.tests;
+package jcgp.backend.tests;
 
 import static org.junit.Assert.assertTrue;
-import jcgp.population.Input;
+import jcgp.backend.population.Input;
 
 import org.junit.Before;
 import org.junit.Test;
diff --git a/src/jcgp/tests/NodeTests.java b/src/jcgp/backend/tests/NodeTests.java
index d8aa742..7121e81 100644
--- a/src/jcgp/tests/NodeTests.java
+++ b/src/jcgp/backend/tests/NodeTests.java
@@ -1,12 +1,12 @@
-package jcgp.tests;
+package jcgp.backend.tests;
 
 import static org.junit.Assert.assertTrue;
 import jcgp.JCGP.Resources;
-import jcgp.function.Arithmetic;
-import jcgp.function.Function;
-import jcgp.population.Chromosome;
-import jcgp.population.Connection;
-import jcgp.population.Node;
+import jcgp.backend.function.Arithmetic;
+import jcgp.backend.function.Function;
+import jcgp.backend.population.Chromosome;
+import jcgp.backend.population.Connection;
+import jcgp.backend.population.Node;
 
 import org.junit.Before;
 import org.junit.BeforeClass;
diff --git a/src/jcgp/tests/OutputTests.java b/src/jcgp/backend/tests/OutputTests.java
index 8658fa4..7ff8a4a 100644
--- a/src/jcgp/tests/OutputTests.java
+++ b/src/jcgp/backend/tests/OutputTests.java
@@ -1,11 +1,10 @@
-package jcgp.tests;
+package jcgp.backend.tests;
 
 import static org.junit.Assert.assertTrue;
-
 import jcgp.JCGP.Resources;
-import jcgp.population.Chromosome;
-import jcgp.population.Connection;
-import jcgp.population.Output;
+import jcgp.backend.population.Chromosome;
+import jcgp.backend.population.Connection;
+import jcgp.backend.population.Output;
 
 import org.junit.Before;
 import org.junit.BeforeClass;
diff --git a/src/jcgp/tests/PopulationTests.java b/src/jcgp/backend/tests/PopulationTests.java
index a11becf..51b5168 100644
--- a/src/jcgp/tests/PopulationTests.java
+++ b/src/jcgp/backend/tests/PopulationTests.java
@@ -1,9 +1,9 @@
-package jcgp.tests;
+package jcgp.backend.tests;
 
 import static org.junit.Assert.assertTrue;
 import jcgp.JCGP.Resources;
-import jcgp.population.Chromosome;
-import jcgp.population.Population;
+import jcgp.backend.population.Chromosome;
+import jcgp.backend.population.Population;
 
 import org.junit.Before;
 import org.junit.BeforeClass;
diff --git a/src/jcgp/gui/ChromosomePane.java b/src/jcgp/gui/ChromosomePane.java
index b4a628f..b1f4bf0 100644
--- a/src/jcgp/gui/ChromosomePane.java
+++ b/src/jcgp/gui/ChromosomePane.java
@@ -6,14 +6,14 @@ import javafx.scene.control.ScrollPane;
 import javafx.scene.layout.Pane;
 import javafx.scene.shape.Line;
 import jcgp.JCGP.Resources;
+import jcgp.backend.population.Chromosome;
+import jcgp.backend.population.Connection;
+import jcgp.backend.population.Input;
+import jcgp.backend.population.Node;
 import jcgp.gui.population.GUIGene;
 import jcgp.gui.population.GUIInput;
 import jcgp.gui.population.GUINode;
 import jcgp.gui.population.GUIOutput;
-import jcgp.population.Chromosome;
-import jcgp.population.Connection;
-import jcgp.population.Input;
-import jcgp.population.Node;
 
 
 public class ChromosomePane extends ScrollPane {
@@ -26,14 +26,14 @@ public class ChromosomePane extends ScrollPane {
 	
 	private ArrayList<Line> connectionLines;
 	
+	private ArrayList<GUIOutput> relock = new ArrayList<GUIOutput>();
+	
 	private boolean target = false;
 	
 	public ChromosomePane(Chromosome chromosome, Resources resources) {
 		super();		
 		connectionLines = new ArrayList<Line>();
 		
-		//setMouseTransparent(true);
-		
 		content = new Pane();
 		content.setId("content pane for genes");
 		
@@ -119,4 +119,20 @@ public class ChromosomePane extends ScrollPane {
 			guiOutputs[i].updateLines();
 		}
 	}
+
+	public void unlockOutputs() {
+		relock.clear();
+		for (int i = 0; i < guiOutputs.length; i++) {
+			if (guiOutputs[i].isLocked()) {
+				guiOutputs[i].unlock();
+				relock.add(guiOutputs[i]);
+			}	
+		}
+	}
+	
+	public void relockOutputs() {
+		for (int i = 0; i < relock.size(); i++) {
+			relock.get(i).lock();
+		}
+	}
 }
diff --git a/src/jcgp/GUI.java b/src/jcgp/gui/GUI.java
index d81e760..7e7f385 100644
--- a/src/jcgp/GUI.java
+++ b/src/jcgp/gui/GUI.java
@@ -1,6 +1,4 @@
-package jcgp;
-
-import java.util.concurrent.ExecutionException;
+package jcgp.gui;
 
 import javafx.application.Application;
 import javafx.application.Platform;
@@ -12,8 +10,8 @@ import javafx.scene.control.TabPane;
 import javafx.scene.control.TabPane.TabClosingPolicy;
 import javafx.scene.layout.BorderPane;
 import javafx.stage.Stage;
+import jcgp.JCGP;
 import jcgp.JCGP.Resources;
-import jcgp.gui.ChromosomePane;
 import jcgp.gui.console.GUIConsole;
 import jcgp.gui.settings.SettingsPane;
 
@@ -40,7 +38,7 @@ public class GUI extends Application {
     
     public static final double SETTINGS_WIDTH = 200;
     public static final double CONSOLE_HEIGHT = 100;
-        
+    
     public static final double WRAP_WIDTH = 90;
     
 	private static JCGP cgp;
@@ -50,40 +48,55 @@ public class GUI extends Application {
 	private BorderPane window;
 	
 	private ChromosomePane[] chromosomes;
-	private TabPane mainPane;
+	private TabPane chromosomeTabs;
 	
 	private GUIConsole console = new GUIConsole();
 	private SettingsPane settings;
 	
-	private Service<Integer> cgpService;
+	private Service<Void> cgpService;
+	
+	private boolean evolving = false;
 	
-	private static boolean evolving = false;
+	private Object printLock = new Object();
+	
+	private Runnable consoleFlush = new Runnable() {
+		@Override
+		public void run() {
+			synchronized(printLock) {
+				console.flush();
+				printLock.notifyAll();
+			}
+		}
+	};
 	
 	public static void main(String[] args) {
 		cgp = new JCGP();
-		resources = cgp.getResources();
+		resources = cgp.getResources();		
 		
 		launch();
 	}
 	
 	@Override
 	public void start(Stage primaryStage) throws Exception {
-				
-		cgpService = new Service<Integer> () {
-			
+		resources.setConsole(console);
+		
+		cgpService = new Service<Void> () {
 			@Override
-			protected Task<Integer> createTask() {
+			protected Task<Void> createTask() {
 				
-				Task<Integer> t = new Task<Integer>() {
+				Task<Void> t = new Task<Void>() {
 					@Override
-					protected Integer call() throws Exception {
+					protected Void call() throws Exception {
 						while (!isCancelled()) {
-							cgp.nextGeneration();
+							Platform.runLater(consoleFlush);
+							synchronized (printLock) {
+								cgp.nextGeneration();
+								printLock.wait();
+							}
 						}
 						return null;
 					}
 				};
-				
 				return t;
 			}
 		};
@@ -94,23 +107,15 @@ public class GUI extends Application {
 		 * 
 		 */
 		
-		mainPane = new TabPane();
-		mainPane.setTabClosingPolicy(TabClosingPolicy.UNAVAILABLE);
-		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), resources);
-			tab = new Tab("Chr " + i);
-			tab.setContent(chromosomes[i]);
-			mainPane.getTabs().add(tab);
-		}
+		leftPane = new BorderPane();
+		
+		chromosomeTabs = new TabPane();
+		chromosomeTabs.setTabClosingPolicy(TabClosingPolicy.UNAVAILABLE);
+		makeChromosomeTabPane();
 		
 		settings = new SettingsPane(cgp, this);
 		
-		//mainPane.setPrefHeight(500);
-				
-		leftPane = new BorderPane();
-		leftPane.setCenter(mainPane);
+		leftPane.setCenter(chromosomeTabs);
 		leftPane.setBottom(console);
 		
 		window = new BorderPane();
@@ -118,52 +123,89 @@ public class GUI extends Application {
 		window.setCenter(leftPane);
 		window.setRight(settings);
 		
-		//primaryStage.setMinHeight(600);
-		//primaryStage.setMinWidth(800);
-		
 		primaryStage.setTitle("JCGP");
 		
 		primaryStage.setScene(new Scene(window));
 		primaryStage.show();
 	}
+
+	/**
+	 * 
+	 */
+	private void makeChromosomeTabPane() {
+		chromosomeTabs.getTabs().clear();
+		
+		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), resources);
+			tab = new Tab("Chr " + i);
+			tab.setContent(chromosomes[i]);
+			chromosomeTabs.getTabs().add(tab);
+		}
+	}
 	
-	public void updateNodeGrids() {
+	private void updateNodeGrids() {
 		for (int i = 0; i < chromosomes.length; i++) {
 			chromosomes[i].update();
 		}
 	}
+	
+	private void unlockOutputs() {
+		for (int i = 0; i < chromosomes.length; i++) {
+			chromosomes[i].unlockOutputs();
+		}
+	}
+	
+	private void relockOutputs() {
+		for (int i = 0; i < chromosomes.length; i++) {
+			chromosomes[i].relockOutputs();
+		}
+	}
+	
+	public void disableChromosomePanes(boolean value) {
+		chromosomeTabs.setDisable(value);
+	}
 
-	public void playPause() {		
+	public void playPause() {
 		if (!evolving) {
+			settings.disableSettings(true);
+			disableChromosomePanes(true);
+			unlockOutputs();
 			evolving = true;
 			cgpService.restart();
 		} else {
-			cgpService.cancel();
+			settings.disableSettings(false);
+			disableChromosomePanes(false);
+			updateNodeGrids();
 			evolving = false;
+			cgpService.cancel();
+			relockOutputs();
 		}
 	}
 	
 	public void step() {
 		if (!evolving) {
-			Thread t = new Thread(new Task<Object>() {
+			Thread t = new Thread(new Task<Void>() {
 				@Override
-				protected Object call() throws Exception {
+				protected Void call() throws Exception {
+					unlockOutputs();
 					cgp.nextGeneration();
-					evolving = false;
+					console.flush();
+					updateNodeGrids();
+					relockOutputs();
 					return null;
 				}
 			});
-			evolving = true;
 			t.start();
 		}
 	}
 	
-	public boolean isEvolving() {
-		return evolving;
-	}
-	
-	public Service<Integer> getCGPService() {
-		return cgpService;
+	public void resetCGP() {
+		cgp.remakePopulation();
+		makeChromosomeTabPane();
+		
+		resources.set("currentGen", 1);
+		resources.set("currentRun", 1);
 	}
-
 }
diff --git a/src/jcgp/gui/Messenger.java b/src/jcgp/gui/Messenger.java
deleted file mode 100644
index becf47c..0000000
--- a/src/jcgp/gui/Messenger.java
+++ /dev/null
@@ -1,7 +0,0 @@
-package jcgp.gui;
-
-public class Messenger {
-
-	
-	
-}
diff --git a/src/jcgp/gui/console/Console.java b/src/jcgp/gui/console/Console.java
new file mode 100644
index 0000000..63c7f5b
--- /dev/null
+++ b/src/jcgp/gui/console/Console.java
@@ -0,0 +1,11 @@
+package jcgp.gui.console;
+
+public interface Console {
+	
+	public void println(String s);
+	
+	public void print(String s);
+	
+	public void flush();
+
+}
diff --git a/src/jcgp/gui/console/GUIConsole.java b/src/jcgp/gui/console/GUIConsole.java
index 0ef2be3..8fdb1a5 100644
--- a/src/jcgp/gui/console/GUIConsole.java
+++ b/src/jcgp/gui/console/GUIConsole.java
@@ -5,13 +5,15 @@ import javafx.scene.Cursor;
 import javafx.scene.control.TextArea;
 import javafx.scene.input.MouseEvent;
 import javafx.scene.layout.AnchorPane;
-import jcgp.GUI;
+import jcgp.gui.GUI;
 
-public class GUIConsole extends AnchorPane {
+public class GUIConsole extends AnchorPane implements Console {
 	
 	private boolean dragging;
 	private TextArea textArea = new TextArea("Welcome to JCGP!\n");
 	
+	private StringBuffer printBuffer = new StringBuffer();
+		
 	public GUIConsole() {
 		super();
 		textArea.setEditable(false);
@@ -87,8 +89,20 @@ public class GUIConsole extends AnchorPane {
         return event.getY() < (GUI.RESIZE_MARGIN);
     }
 	
-	public TextArea getTextArea() {
-		return textArea;
+	@Override
+	public void println(String s) {
+		printBuffer.append(s + "\n");
+	}
+
+	@Override
+	public void print(String s) {
+		printBuffer.append(s);
+	}
+
+	@Override
+	public void flush() {
+		textArea.appendText(printBuffer.toString());
+		printBuffer = new StringBuffer();
 	}
 	
 }
diff --git a/src/jcgp/gui/population/GUIGene.java b/src/jcgp/gui/population/GUIGene.java
index a37eb19..26be2a5 100644
--- a/src/jcgp/gui/population/GUIGene.java
+++ b/src/jcgp/gui/population/GUIGene.java
@@ -4,9 +4,9 @@ import javafx.beans.property.SimpleObjectProperty;
 import javafx.scene.Group;
 import javafx.scene.shape.Circle;
 import javafx.scene.text.Text;
+import jcgp.backend.population.Connection;
+import jcgp.backend.population.Gene;
 import jcgp.gui.ChromosomePane;
-import jcgp.population.Connection;
-import jcgp.population.Gene;
 
 enum GUIGeneState {
 	NEUTRAL,
@@ -59,7 +59,7 @@ public abstract class GUIGene extends Group {
 		return locked;
 	}
 	
-	public abstract void setLocked(boolean value);
+	abstract void setLocked(boolean value);
 	
 	public abstract void addLocks(int value);
 	
diff --git a/src/jcgp/gui/population/GUIInput.java b/src/jcgp/gui/population/GUIInput.java
index 30ce4ac..f47186c 100644
--- a/src/jcgp/gui/population/GUIInput.java
+++ b/src/jcgp/gui/population/GUIInput.java
@@ -11,11 +11,11 @@ import javafx.scene.shape.Circle;
 import javafx.scene.text.Font;
 import javafx.scene.text.Text;
 import javafx.scene.text.TextAlignment;
-import jcgp.GUI;
+import jcgp.backend.population.Connection;
+import jcgp.backend.population.Input;
+import jcgp.backend.population.Output;
 import jcgp.gui.ChromosomePane;
-import jcgp.population.Connection;
-import jcgp.population.Input;
-import jcgp.population.Output;
+import jcgp.gui.GUI;
 
 public class GUIInput extends GUIGene {
 
@@ -212,7 +212,7 @@ public class GUIInput extends GUIGene {
 	}
 
 	@Override
-	public void setLocked(boolean value) {
+	void setLocked(boolean value) {
 		locked += value ? 1 : -1;
 		stateProperty.set(locked > 0 ? GUIGeneState.HOVER : GUIGeneState.ACTIVE_HOVER);
 	}
diff --git a/src/jcgp/gui/population/GUINode.java b/src/jcgp/gui/population/GUINode.java
index 6fc84da..450647f 100644
--- a/src/jcgp/gui/population/GUINode.java
+++ b/src/jcgp/gui/population/GUINode.java
@@ -13,11 +13,11 @@ import javafx.scene.shape.Line;
 import javafx.scene.text.Font;
 import javafx.scene.text.Text;
 import javafx.scene.text.TextAlignment;
-import jcgp.GUI;
+import jcgp.backend.population.Connection;
+import jcgp.backend.population.Input;
+import jcgp.backend.population.Node;
 import jcgp.gui.ChromosomePane;
-import jcgp.population.Connection;
-import jcgp.population.Input;
-import jcgp.population.Node;
+import jcgp.gui.GUI;
 
 public class GUINode extends GUIGene {
 
@@ -429,7 +429,7 @@ public class GUINode extends GUIGene {
 	}
 
 	@Override
-	public void setLocked(boolean value) {
+	void setLocked(boolean value) {
 		locked += value ? 1 : -1;
 		stateProperty.set(locked > 0 ? GUIGeneState.HOVER : GUIGeneState.ACTIVE_HOVER);
 
diff --git a/src/jcgp/gui/population/GUIOutput.java b/src/jcgp/gui/population/GUIOutput.java
index 16d95f0..9c5dfa5 100644
--- a/src/jcgp/gui/population/GUIOutput.java
+++ b/src/jcgp/gui/population/GUIOutput.java
@@ -13,12 +13,12 @@ import javafx.scene.shape.Line;
 import javafx.scene.text.Font;
 import javafx.scene.text.Text;
 import javafx.scene.text.TextAlignment;
-import jcgp.GUI;
+import jcgp.backend.population.Connection;
+import jcgp.backend.population.Input;
+import jcgp.backend.population.Node;
+import jcgp.backend.population.Output;
 import jcgp.gui.ChromosomePane;
-import jcgp.population.Connection;
-import jcgp.population.Input;
-import jcgp.population.Node;
-import jcgp.population.Output;
+import jcgp.gui.GUI;
 
 public class GUIOutput extends GUIGene {
 
@@ -281,7 +281,7 @@ public class GUIOutput extends GUIGene {
 	}
 
 	@Override
-	public void setLocked(boolean value) {
+	void setLocked(boolean value) {
 		locked += value ? 1 : -1;
 		setConnections(value ? GUIGeneState.HOVER : GUIGeneState.ACTIVE_HOVER);
 
@@ -314,5 +314,20 @@ public class GUIOutput extends GUIGene {
 		sourceLine.setEndX(gene.getLayoutX() + NODE_RADIUS);
 		sourceLine.setEndY(gene.getLayoutY());	
 	}
+	
+	public void unlock() {
+		if (isLocked()) {
+			setLocked(false);
+			stateProperty.set(GUIGeneState.NEUTRAL);
+			setConnections(GUIGeneState.NEUTRAL);
+		}
+	}
+
+	public void lock() {
+		if (!isLocked()) {
+			stateProperty.set(GUIGeneState.HOVER);
+			setLocked(true);
+		}
+	}
 
 }
diff --git a/src/jcgp/gui/settings/SettingsPane.java b/src/jcgp/gui/settings/SettingsPane.java
index 9edcbdb..61011aa 100644
--- a/src/jcgp/gui/settings/SettingsPane.java
+++ b/src/jcgp/gui/settings/SettingsPane.java
@@ -5,7 +5,6 @@ import java.util.Iterator;
 import java.util.Map;
 import java.util.Map.Entry;
 
-import javafx.beans.property.SimpleIntegerProperty;
 import javafx.event.ActionEvent;
 import javafx.event.EventHandler;
 import javafx.geometry.Insets;
@@ -22,14 +21,15 @@ import javafx.scene.layout.VBox;
 import javafx.scene.text.Font;
 import javafx.scene.text.FontSmoothingType;
 import javafx.scene.text.Text;
-import jcgp.GUI;
 import jcgp.JCGP;
-import jcgp.function.FunctionSet;
+import jcgp.backend.function.FunctionSet;
+import jcgp.backend.modules.ea.EvolutionaryAlgorithm;
+import jcgp.backend.modules.fitness.FitnessFunction;
+import jcgp.backend.modules.mutator.Mutator;
+import jcgp.backend.parameters.IntegerParameter;
+import jcgp.backend.parameters.Parameter;
+import jcgp.gui.GUI;
 import jcgp.gui.settings.parameters.*;
-import jcgp.modules.ea.EvolutionaryAlgorithm;
-import jcgp.modules.fitness.FitnessFunction;
-import jcgp.modules.mutator.Mutator;
-import jcgp.parameters.*;
 
 public class SettingsPane extends AnchorPane {
 	
@@ -84,31 +84,28 @@ public class SettingsPane extends AnchorPane {
 		
 		bpPane.getChildren().add(header);
 		
-		final GUIIntegerParameter generation = new GUIIntegerParameter((IntegerParameter) cgp.getResources().getParameter("currentGen"));
-		final GUIIntegerParameter run = new GUIIntegerParameter((IntegerParameter) cgp.getResources().getParameter("currentRun"));
+		GUIParameter rows = GUIParameter.create((IntegerParameter) cgp.getResources().getParameter("rows"));
+		parameters.add(rows);
+		parameters.add(GUIParameter.create((IntegerParameter) cgp.getResources().getParameter("columns")));
+		parameters.add(GUIParameter.create((IntegerParameter) cgp.getResources().getParameter("inputs")));
+		parameters.add(GUIParameter.create((IntegerParameter) cgp.getResources().getParameter("outputs")));
+		parameters.add(GUIParameter.create((IntegerParameter) cgp.getResources().getParameter("levelsBack")));
 		
-		parameters.add(new GUIIntegerParameter((IntegerParameter) cgp.getResources().getParameter("rows")));
-		parameters.add(new GUIIntegerParameter((IntegerParameter) cgp.getResources().getParameter("columns")));
-		parameters.add(new GUIIntegerParameter((IntegerParameter) cgp.getResources().getParameter("inputs")));
-		parameters.add(new GUIIntegerParameter((IntegerParameter) cgp.getResources().getParameter("outputs")));
-		parameters.add(new GUIIntegerParameter((IntegerParameter) cgp.getResources().getParameter("levelsBack")));
+		parameters.add(GUIParameter.create((IntegerParameter) cgp.getResources().getParameter("popSize")));
+		parameters.add(GUIParameter.create((IntegerParameter) cgp.getResources().getParameter("generations")));
+		parameters.add(GUIParameter.create((IntegerParameter) cgp.getResources().getParameter("runs")));
 		
-		parameters.add(new GUIIntegerParameter((IntegerParameter) cgp.getResources().getParameter("popSize")));
-		parameters.add(new GUIIntegerParameter((IntegerParameter) cgp.getResources().getParameter("generations")));
-		parameters.add(new GUIIntegerParameter((IntegerParameter) cgp.getResources().getParameter("runs")));
+		parameters.add(GUIParameter.create((IntegerParameter) cgp.getResources().getParameter("currentGen")));
+		parameters.add(GUIParameter.create((IntegerParameter) cgp.getResources().getParameter("currentRun")));				
 		
-		parameters.add(generation);
-		parameters.add(run);
-		
-		parameters.add(new GUIIntegerParameter((IntegerParameter) cgp.getResources().getParameter("seed")));
-		parameters.add(new GUIIntegerParameter((IntegerParameter) cgp.getResources().getParameter("report")));
-		parameters.add(new GUIBooleanParameter((BooleanParameter) cgp.getResources().getParameter("verbose")));
+		parameters.add(GUIParameter.create((IntegerParameter) cgp.getResources().getParameter("seed")));
+		parameters.add(GUIParameter.create((IntegerParameter) cgp.getResources().getParameter("report")));
 		
 		bpPane.getChildren().addAll(parameters);
 		
 		mainContainer.getChildren().add(bpPane);
 		
-		generation.getTextField().textProperty().bind(((SimpleIntegerProperty) cgp.getResources().getParameter("currentGen").valueProperty()).asString());
+		
 	}
 
 	private void initialiseEAParameters(final JCGP cgp) {
@@ -245,13 +242,16 @@ public class SettingsPane extends AnchorPane {
 		
 		play.setOnAction(new EventHandler<ActionEvent>() {
 			@Override
-			public void handle(ActionEvent event) {
-				gui.playPause();
-				if (gui.isEvolving()) {
+			public void handle(ActionEvent event) {				
+				if (play.getText() == "Run") {
+					if (applyChanges()) {
+						gui.resetCGP();
+					}
 					play.setText("Pause");
 				} else {
 					play.setText("Run");
 				}
+				gui.playPause();
 			}
 		});
 		
@@ -260,6 +260,9 @@ public class SettingsPane extends AnchorPane {
 		step.setOnAction(new EventHandler<ActionEvent>() {
 			@Override
 			public void handle(ActionEvent event) {
+				if (applyChanges()) {
+					gui.resetCGP();
+				}
 				gui.step();
 			}
 		});
@@ -274,8 +277,7 @@ public class SettingsPane extends AnchorPane {
 		
 		controls.getChildren().add(flowButtons);
 		
-		mainContainer.getChildren().add(controls);
-		
+		mainContainer.getChildren().add(controls);	
 	}
 	
 	/**
@@ -287,19 +289,10 @@ public class SettingsPane extends AnchorPane {
 		vb.getChildren().clear();
 	    while (it.hasNext()) {
 	        Parameter parameter = ((Map.Entry<String, Parameter>) it.next()).getValue();
-	        if (parameter instanceof IntegerParameter) {
-	        	GUIIntegerParameter gip = new GUIIntegerParameter((IntegerParameter) parameter);
-	        	parameters.add(gip);
-	        	vb.getChildren().add(gip);
-	        } else if (parameter instanceof DoubleParameter) {
-	        	GUIDoubleParameter gdp = new GUIDoubleParameter((DoubleParameter) parameter);
-	        	parameters.add(gdp);
-	        	vb.getChildren().add(gdp);
-	        } else if (parameter instanceof BooleanParameter) {
-	        	GUIBooleanParameter gbp = new GUIBooleanParameter((BooleanParameter) parameter);
-	        	parameters.add(gbp);
-	        	vb.getChildren().add(gbp);
-	        }
+	        GUIParameter gp = GUIParameter.create(parameter);
+	        
+	        parameters.add(gp);
+        	vb.getChildren().add(gp);
 	    }
 	}
 	
@@ -371,30 +364,29 @@ public class SettingsPane extends AnchorPane {
         return event.getX() < (GUI.RESIZE_MARGIN);
     }
 	
-	public void refreshValues() {
-		for (GUIParameter parameter : parameters) {
-			parameter.refreshValue();
-		}
-		//parent.updateNodeGrids();
-	}
-	
-//	public void bindParameters() {
-//		for (GUIParameter parameter : parameters) {
-//			parameter.doBindings();
-//		}
-//	}
-//	
-//	public void unbindParameters() {
-//		for (GUIParameter parameter : parameters) {
-//			parameter.undoBindings();
-//		}
-//	}
-	
-	public void toggleSettings(boolean value) {
+	public void disableSettings(boolean value) {
 		bpPane.setDisable(value);
 		eaPane.setDisable(value);
 		mutatorPane.setDisable(value);
 		ffPane.setDisable(value);
 		nfPane.setDisable(value);
 	}
+	
+	/**
+	 * Writes the GUI parameter value back to the resources parameter,
+	 * if any changes were made.
+	 * 
+	 * @return true if the experiment needs to be reset, false otherwise.
+	 */
+	private boolean applyChanges() {
+		boolean reset = false;
+		
+		for (GUIParameter parameter : parameters) {
+			reset |= parameter.applyChange();
+		}
+		
+		return reset;
+	}
+	
+	
 }
diff --git a/src/jcgp/gui/settings/parameters/GUIBooleanParameter.java b/src/jcgp/gui/settings/parameters/GUIBooleanParameter.java
index a9f6753..8acd6dd 100644
--- a/src/jcgp/gui/settings/parameters/GUIBooleanParameter.java
+++ b/src/jcgp/gui/settings/parameters/GUIBooleanParameter.java
@@ -1,11 +1,11 @@
 package jcgp.gui.settings.parameters;
 
 import javafx.scene.control.CheckBox;
-import jcgp.parameters.BooleanParameter;
+import jcgp.backend.parameters.BooleanParameter;
 
 public class GUIBooleanParameter extends GUIParameter {
 	
-	public GUIBooleanParameter(BooleanParameter parameter) {
+	GUIBooleanParameter(BooleanParameter parameter) {
 		super();
 		
 		this.parameter = parameter;
@@ -13,22 +13,16 @@ public class GUIBooleanParameter extends GUIParameter {
 		value = new CheckBox(parameter.getName());
 		((CheckBox) value).setSelected(parameter.get());
 		
-		value.setDisable(!parameter.isEditable());
+		value.setDisable(parameter.isMonitor());
 		
-		getChildren().add(value);
+		if (parameter.isMonitor()) {
+			makeLightBinding();
+			System.out.println("light binding made for " + name);
+		}
 		
+		getChildren().add(value);
 	}
 
-//	@Override
-//	public void doBindings() {
-//		((CheckBox) value).selectedProperty().bind(((BooleanParameter) parameter).valueProperty());
-//	}
-//
-//	@Override
-//	public void undoBindings() {
-//		((CheckBox) value).selectedProperty().unbind();
-//	}
-
 	@Override
 	public void refreshValue() {
 		if (!((CheckBox) value).selectedProperty().isBound()) {
@@ -36,5 +30,17 @@ public class GUIBooleanParameter extends GUIParameter {
 		}
 		
 	}
+
+	@Override
+	public boolean applyChange() {
+		if (((CheckBox) value).isSelected() != ((BooleanParameter) parameter).get() && (!parameter.isMonitor())) {
+			// apply value
+			((BooleanParameter) parameter).set(((CheckBox) value).isSelected());
+			if (parameter.isCritical()) {
+				return true;
+			}
+		}
+		return false;
+	}
 	
 }
diff --git a/src/jcgp/gui/settings/parameters/GUIDoubleParameter.java b/src/jcgp/gui/settings/parameters/GUIDoubleParameter.java
index 25d5b9f..4b74c6e 100644
--- a/src/jcgp/gui/settings/parameters/GUIDoubleParameter.java
+++ b/src/jcgp/gui/settings/parameters/GUIDoubleParameter.java
@@ -4,12 +4,12 @@ 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;
+import jcgp.backend.parameters.DoubleParameter;
+import jcgp.gui.GUI;
 
 public class GUIDoubleParameter extends GUIParameter {
 	
-	public GUIDoubleParameter(DoubleParameter parameter) {
+	GUIDoubleParameter(DoubleParameter parameter) {
 		super();
 		
 		this.parameter = parameter;
@@ -23,26 +23,29 @@ public class GUIDoubleParameter extends GUIParameter {
 		
 		name.setWrappingWidth(GUI.WRAP_WIDTH);
 		
-		((TextField) value).setEditable(parameter.isEditable());
+		((TextField) value).setEditable(!parameter.isMonitor());
+		
+		if (parameter.isMonitor()) {
+			makeLightBinding();
+		}
 		
 		getChildren().addAll(name, value);
 	}
 
-//	@Override
-//	public void doBindings() {
-//		((TextField) value).textProperty().bind(((DoubleParameter) parameter).valueProperty().asString());
-//	}
-//
-//	@Override
-//	public void undoBindings() {
-//		((TextField) value).textProperty().unbind();
-//	}
-
 	@Override
 	public void refreshValue() {
-		if (!((TextField) value).textProperty().isBound()) {
-			((TextField) value).setText(String.valueOf(((DoubleParameter) parameter).get()));
-		}
+		((TextField) value).setText(String.valueOf(((DoubleParameter) parameter).get()));
 	}
-	
+
+	@Override
+	public boolean applyChange() {
+		if (Double.valueOf(((TextField) value).getText()) != ((DoubleParameter) parameter).get() && (!parameter.isMonitor())) {
+			// apply value
+			((DoubleParameter) parameter).set(Double.valueOf(((TextField) value).getText()));
+			if (parameter.isCritical()) {
+				return true;
+			}
+		}
+		return false;
+	}	
 }
diff --git a/src/jcgp/gui/settings/parameters/GUIIntegerParameter.java b/src/jcgp/gui/settings/parameters/GUIIntegerParameter.java
index 6bcfd55..70b78a6 100644
--- a/src/jcgp/gui/settings/parameters/GUIIntegerParameter.java
+++ b/src/jcgp/gui/settings/parameters/GUIIntegerParameter.java
@@ -4,12 +4,12 @@ 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;
+import jcgp.backend.parameters.IntegerParameter;
+import jcgp.gui.GUI;
 
 public class GUIIntegerParameter extends GUIParameter {
 
-	public GUIIntegerParameter(IntegerParameter parameter) {	
+	GUIIntegerParameter(IntegerParameter parameter) {	
 		super();
 		
 		this.parameter = parameter;
@@ -23,27 +23,27 @@ public class GUIIntegerParameter extends GUIParameter {
 		
 		name.setWrappingWidth(GUI.WRAP_WIDTH);
 		
-		((TextField) value).setEditable(parameter.isEditable());
+		((TextField) value).setEditable(!parameter.isMonitor());
+
+		if (parameter.isMonitor()) {
+			makeLightBinding();
+		}
 				
 		getChildren().addAll(name, value);
 	}
 
-//	@Override
-//	public void doBindings() {
-//		((TextField) value).textProperty().bind(((IntegerParameter) parameter).valueProperty().asString());
-//	}
-//
-//	@Override
-//	public void undoBindings() {
-//		((TextField) value).textProperty().unbind();
-//	}
-	
-	public TextField getTextField() {
-		return (TextField) value;
-	}
-
 	@Override
 	public void refreshValue() {
 		((TextField) value).setText(String.valueOf(((IntegerParameter) parameter).get()));
 	}
+
+	@Override
+	public boolean applyChange() {
+		if (Integer.valueOf(((TextField) value).getText()) != ((IntegerParameter) parameter).get() && (!parameter.isMonitor())) {
+			// apply value
+			((IntegerParameter) parameter).set(Integer.valueOf(((TextField) value).getText()));
+			return parameter.isCritical();
+		}
+		return false;
+	}
 }
diff --git a/src/jcgp/gui/settings/parameters/GUIParameter.java b/src/jcgp/gui/settings/parameters/GUIParameter.java
index a2f2f9c..a783d71 100644
--- a/src/jcgp/gui/settings/parameters/GUIParameter.java
+++ b/src/jcgp/gui/settings/parameters/GUIParameter.java
@@ -1,10 +1,18 @@
 package jcgp.gui.settings.parameters;
 
+import java.util.concurrent.atomic.AtomicBoolean;
+
+import javafx.application.Platform;
+import javafx.beans.value.ChangeListener;
+import javafx.beans.value.ObservableValue;
 import javafx.geometry.Pos;
 import javafx.scene.control.Control;
 import javafx.scene.layout.HBox;
 import javafx.scene.text.Text;
-import jcgp.parameters.Parameter;
+import jcgp.backend.parameters.BooleanParameter;
+import jcgp.backend.parameters.DoubleParameter;
+import jcgp.backend.parameters.IntegerParameter;
+import jcgp.backend.parameters.Parameter;
 
 public abstract class GUIParameter extends HBox {
 		
@@ -12,19 +20,51 @@ public abstract class GUIParameter extends HBox {
 	protected Text name;
 	protected Control value;
 	
-	public GUIParameter() {
+	protected AtomicBoolean updateCheck = new AtomicBoolean(true);
+	
+	protected GUIParameter() {
 		setAlignment(Pos.CENTER_LEFT);
 		setSpacing(5);
 	}
 	
-	public Parameter getParameter() {
-		return parameter;
+	protected final void makeLightBinding() {
+		parameter.valueProperty().addListener(new ChangeListener<Object>() {
+			@Override
+			public void changed(
+					ObservableValue<? extends Object> observable,
+					Object oldValue, Object newValue) {
+				if (updateCheck.getAndSet(false)) {
+					Platform.runLater(new Runnable() {
+						@Override
+						public void run() {
+							updateCheck.set(true);
+							refreshValue();
+						}
+					});
+				}
+			}
+		});
 	}
 	
-//	public abstract void doBindings();
-//	
-//	public abstract void undoBindings();
-	
 	public abstract void refreshValue();
 	
+	public static GUIParameter create(Parameter parameter) {
+		if (parameter instanceof IntegerParameter) {
+			return new GUIIntegerParameter((IntegerParameter) parameter);
+		} else if (parameter instanceof DoubleParameter) {
+			return new GUIDoubleParameter((DoubleParameter) parameter);
+		} else if (parameter instanceof BooleanParameter) {
+			return new GUIBooleanParameter((BooleanParameter) parameter);
+		} else {
+			throw new ClassCastException("No GUIParameter subclass exists for argument of type " + parameter.getClass());
+		}
+	}
+	
+	/**
+	 * Writes the GUI parameter value back to the resources parameter,
+	 * if any changes were made.
+	 * 
+	 * @return true if the experiment needs to be reset, false otherwise.
+	 */
+	public abstract boolean applyChange();
 }
diff --git a/src/jcgp/parameters/Parameter.java b/src/jcgp/parameters/Parameter.java
deleted file mode 100644
index a5ecf9e..0000000
--- a/src/jcgp/parameters/Parameter.java
+++ /dev/null
@@ -1,30 +0,0 @@
-package jcgp.parameters;
-
-import javafx.beans.property.Property;
-
-public abstract class Parameter {
-	
-	protected boolean hidden = false, editable = true;
-	
-	protected String name;
-	
-	public Parameter(String name, boolean editable, boolean hidden) {
-		this.name = name;
-		this.hidden = hidden;
-		this.editable = editable;
-	}
-	
-	public boolean isHidden() {
-		return hidden;
-	}
-	
-	public boolean isEditable() {
-		return editable;
-	}
-	
-	public String getName() {
-		return name;
-	}
-	
-	public abstract Property<?> valueProperty();
-}