About to make big changes to the way fitness works, committing just in case

31 files changed, 592 insertions, 283 deletions

diff --git a/src/jcgp/backend/exceptions/ManagedModuleException.java b/src/jcgp/backend/exceptions/ManagedModuleException.java
deleted file mode 100644
index 3452d35..0000000
--- a/src/jcgp/backend/exceptions/ManagedModuleException.java
+++ /dev/null
@@ -1,10 +0,0 @@
-package jcgp.backend.exceptions;
-
-public class ManagedModuleException extends RuntimeException {
-
-	/**
-	 * 
-	 */
-	private static final long serialVersionUID = -3450063156524494967L;
-
-}
diff --git a/src/jcgp/backend/function/BitwiseLogic.java b/src/jcgp/backend/function/BitwiseLogic.java
index bfe361f..5d47ff7 100644
--- a/src/jcgp/backend/function/BitwiseLogic.java
+++ b/src/jcgp/backend/function/BitwiseLogic.java
@@ -1,8 +1,5 @@
 package jcgp.backend.function;
 
-import java.util.ArrayList;
-import java.util.Arrays;
-
 import jcgp.backend.exceptions.InvalidArgumentsException;
 import jcgp.backend.population.Connection;
 
@@ -19,15 +16,13 @@ public class BitwiseLogic extends FunctionSet {
 				new Nor(),
 				new Xnor()};
 		
-		allowedFunctions = new ArrayList<Function>(Arrays.asList(functionList));
+		enableAll();
 	}
 
-	public static class And extends Function {	
-		private int arity = 2;
-
+	public static class And extends Function {
 		@Override
 		public Object run(Connection... connections) {
-			if (connections.length < arity) {
+			if (connections.length < 2) {
 				throw new InvalidArgumentsException("Not enough connections were given.");
 			} else {
 				int arg1 = ((int) connections[0].getValue());
@@ -40,7 +35,7 @@ public class BitwiseLogic extends FunctionSet {
 
 		@Override
 		public int getArity() {
-			return arity;
+			return 2;
 		}
 
 		@Override
@@ -49,12 +44,10 @@ public class BitwiseLogic extends FunctionSet {
 		}
 	}
 	
-	public static class Or extends Function {	
-		private int arity = 2;
-
+	public static class Or extends Function {
 		@Override
 		public Object run(Connection... connections) {
-			if (connections.length < arity) {
+			if (connections.length < 2) {
 				throw new InvalidArgumentsException("Not enough connections were given.");
 			} else {
 				int arg1 = ((int) connections[0].getValue());
@@ -67,7 +60,7 @@ public class BitwiseLogic extends FunctionSet {
 
 		@Override
 		public int getArity() {
-			return arity;
+			return 2;
 		}
 
 		@Override
@@ -76,12 +69,10 @@ public class BitwiseLogic extends FunctionSet {
 		}
 	}
 
-	public static class Not extends Function {	
-		private int arity = 1;
-
+	public static class Not extends Function {
 		@Override
 		public Object run(Connection... connections) {
-			if (connections.length < arity) {
+			if (connections.length < 1) {
 				throw new InvalidArgumentsException("Not enough connections were given.");
 			} else {
 				int arg1 = ((int) connections[0].getValue());
@@ -93,7 +84,7 @@ public class BitwiseLogic extends FunctionSet {
 
 		@Override
 		public int getArity() {
-			return arity;
+			return 1;
 		}
 
 		@Override
@@ -102,12 +93,10 @@ public class BitwiseLogic extends FunctionSet {
 		}
 	}
 
-	public static class Xor extends Function {	
-		private int arity = 2;
-
+	public static class Xor extends Function {
 		@Override
 		public Object run(Connection... connections) {
-			if (connections.length < arity) {
+			if (connections.length < 2) {
 				throw new InvalidArgumentsException("Not enough connections were given.");
 			} else {
 				int arg1 = ((int) connections[0].getValue());
@@ -120,7 +109,7 @@ public class BitwiseLogic extends FunctionSet {
 
 		@Override
 		public int getArity() {
-			return arity;
+			return 2;
 		}
 
 		@Override
@@ -129,12 +118,10 @@ public class BitwiseLogic extends FunctionSet {
 		}
 	}
 
-	public static class Nand extends Function {	
-		private int arity = 2;
-
+	public static class Nand extends Function {
 		@Override
 		public Object run(Connection... connections) {
-			if (connections.length < arity) {
+			if (connections.length < 2) {
 				throw new InvalidArgumentsException("Not enough connections were given.");
 			} else {
 				int arg1 = ((int) connections[0].getValue());
@@ -147,7 +134,7 @@ public class BitwiseLogic extends FunctionSet {
 
 		@Override
 		public int getArity() {
-			return arity;
+			return 2;
 		}
 
 		@Override
@@ -156,12 +143,10 @@ public class BitwiseLogic extends FunctionSet {
 		}
 	}
 
-	public static class Nor extends Function {	
-		private int arity = 2;
-
+	public static class Nor extends Function {
 		@Override
 		public Object run(Connection... connections) {
-			if (connections.length < arity) {
+			if (connections.length < 2) {
 				throw new InvalidArgumentsException("Not enough connections were given.");
 			} else {
 				int arg1 = ((int) connections[0].getValue());
@@ -174,7 +159,7 @@ public class BitwiseLogic extends FunctionSet {
 
 		@Override
 		public int getArity() {
-			return arity;
+			return 2;
 		}
 
 		@Override
@@ -183,12 +168,10 @@ public class BitwiseLogic extends FunctionSet {
 		}
 	}
 
-	public static class Xnor extends Function {	
-		private int arity = 2;
-
+	public static class Xnor extends Function {
 		@Override
 		public Object run(Connection... connections) {
-			if (connections.length < arity) {
+			if (connections.length < 2) {
 				throw new InvalidArgumentsException("Not enough connections were given.");
 			} else {
 				int arg1 = ((int) connections[0].getValue());
@@ -201,7 +184,7 @@ public class BitwiseLogic extends FunctionSet {
 
 		@Override
 		public int getArity() {
-			return arity;
+			return 2;
 		}
 
 		@Override
diff --git a/src/jcgp/backend/function/BooleanLogic.java b/src/jcgp/backend/function/BooleanLogic.java
index e0b5c9c..9e7d1ff 100644
--- a/src/jcgp/backend/function/BooleanLogic.java
+++ b/src/jcgp/backend/function/BooleanLogic.java
@@ -1,7 +1,5 @@
 package jcgp.backend.function;
 
-import java.util.ArrayList;
-import java.util.Arrays;
 
 import jcgp.backend.exceptions.InvalidArgumentsException;
 import jcgp.backend.population.Connection;
@@ -19,15 +17,13 @@ public class BooleanLogic extends FunctionSet {
 				new Nor(),
 				new Xnor()};
 		
-		allowedFunctions = new ArrayList<Function>(Arrays.asList(functionList));
+		enableAll();
 	}
 
-	public static class And extends Function {	
-		private int arity = 2;
-
+	public static class And extends Function {
 		@Override
 		public Boolean run(Connection... connections) {
-			if (connections.length < arity) {
+			if (connections.length < 2) {
 				throw new InvalidArgumentsException("Not enough connections were given.");
 			} else {
 				Boolean arg1 = ((Boolean) connections[0].getValue());
@@ -40,7 +36,7 @@ public class BooleanLogic extends FunctionSet {
 
 		@Override
 		public int getArity() {
-			return arity;
+			return 2;
 		}
 
 		@Override
@@ -49,12 +45,10 @@ public class BooleanLogic extends FunctionSet {
 		}
 	}
 	
-	public static class Or extends Function {	
-		private int arity = 2;
-
+	public static class Or extends Function {
 		@Override
 		public Boolean run(Connection... connections) {
-			if (connections.length < arity) {
+			if (connections.length < 2) {
 				throw new InvalidArgumentsException("Not enough connections were given.");
 			} else {
 				Boolean arg1 = ((Boolean) connections[0].getValue());
@@ -67,7 +61,7 @@ public class BooleanLogic extends FunctionSet {
 
 		@Override
 		public int getArity() {
-			return arity;
+			return 2;
 		}
 
 		@Override
@@ -76,12 +70,10 @@ public class BooleanLogic extends FunctionSet {
 		}
 	}
 
-	public static class Not extends Function {	
-		private int arity = 1;
-
+	public static class Not extends Function {
 		@Override
 		public Boolean run(Connection... connections) {
-			if (connections.length < arity) {
+			if (connections.length < 1) {
 				throw new InvalidArgumentsException("Not enough connections were given.");
 			} else {
 				Boolean arg1 = ((Boolean) connections[0].getValue());
@@ -93,7 +85,7 @@ public class BooleanLogic extends FunctionSet {
 
 		@Override
 		public int getArity() {
-			return arity;
+			return 1;
 		}
 
 		@Override
@@ -102,12 +94,10 @@ public class BooleanLogic extends FunctionSet {
 		}
 	}
 
-	public static class Xor extends Function {	
-		private int arity = 2;
-
+	public static class Xor extends Function {
 		@Override
 		public Boolean run(Connection... connections) {
-			if (connections.length < arity) {
+			if (connections.length < 2) {
 				throw new InvalidArgumentsException("Not enough connections were given.");
 			} else {
 				Boolean arg1 = ((Boolean) connections[0].getValue());
@@ -120,7 +110,7 @@ public class BooleanLogic extends FunctionSet {
 
 		@Override
 		public int getArity() {
-			return arity;
+			return 2;
 		}
 
 		@Override
@@ -129,12 +119,10 @@ public class BooleanLogic extends FunctionSet {
 		}
 	}
 
-	public static class Nand extends Function {	
-		private int arity = 2;
-
+	public static class Nand extends Function {
 		@Override
 		public Boolean run(Connection... connections) {
-			if (connections.length < arity) {
+			if (connections.length < 2) {
 				throw new InvalidArgumentsException("Not enough connections were given.");
 			} else {
 				Boolean arg1 = ((Boolean) connections[0].getValue());
@@ -147,7 +135,7 @@ public class BooleanLogic extends FunctionSet {
 
 		@Override
 		public int getArity() {
-			return arity;
+			return 2;
 		}
 
 		@Override
@@ -156,12 +144,10 @@ public class BooleanLogic extends FunctionSet {
 		}
 	}
 
-	public static class Nor extends Function {	
-		private int arity = 2;
-
+	public static class Nor extends Function {
 		@Override
 		public Boolean run(Connection... connections) {
-			if (connections.length < arity) {
+			if (connections.length < 2) {
 				throw new InvalidArgumentsException("Not enough connections were given.");
 			} else {
 				Boolean arg1 = ((Boolean) connections[0].getValue());
@@ -174,7 +160,7 @@ public class BooleanLogic extends FunctionSet {
 
 		@Override
 		public int getArity() {
-			return arity;
+			return 2;
 		}
 
 		@Override
@@ -183,12 +169,10 @@ public class BooleanLogic extends FunctionSet {
 		}
 	}
 
-	public static class Xnor extends Function {	
-		private int arity = 2;
-
+	public static class Xnor extends Function {
 		@Override
 		public Boolean run(Connection... connections) {
-			if (connections.length < arity) {
+			if (connections.length < 2) {
 				throw new InvalidArgumentsException("Not enough connections were given.");
 			} else {
 				Boolean arg1 = ((Boolean) connections[0].getValue());
@@ -201,7 +185,7 @@ public class BooleanLogic extends FunctionSet {
 
 		@Override
 		public int getArity() {
-			return arity;
+			return 2;
 		}
 
 		@Override
diff --git a/src/jcgp/backend/function/FunctionSet.java b/src/jcgp/backend/function/FunctionSet.java
index 4470ac8..78801fc 100644
--- a/src/jcgp/backend/function/FunctionSet.java
+++ b/src/jcgp/backend/function/FunctionSet.java
@@ -1,6 +1,7 @@
 package jcgp.backend.function;
 
 import java.util.ArrayList;
+import java.util.Collections;
 import java.util.Iterator;
 
 
@@ -11,7 +12,7 @@ import java.util.Iterator;
  */
 public abstract class FunctionSet {
 		protected Function[] functionList;
-		protected ArrayList<Function> allowedFunctions;
+		protected ArrayList<Integer> allowedFunctions;
 		protected String name;
 		
 		public int getAllowedFunctionCount() {
@@ -23,7 +24,7 @@ public abstract class FunctionSet {
 		}
 		
 		public Function getAllowedFunction(int index) {
-			return allowedFunctions.get(index);
+			return functionList[allowedFunctions.get(index)];
 		}
 		
 		public Function getFunction(int index) {
@@ -32,7 +33,7 @@ public abstract class FunctionSet {
 		
 		public int getMaxArity(){
 			int arity = 0;
-			for (Function function : allowedFunctions) {
+			for (Function function : functionList) {
 				if (function.getArity() > arity) {
 					arity = function.getArity();
 				}
@@ -46,9 +47,9 @@ public abstract class FunctionSet {
 		
 		public void disableFunction(int index) {
 			if (index < functionList.length) {
-				for (Iterator<Function> iterator = allowedFunctions.iterator(); iterator.hasNext();) {
-					Function function = (Function) iterator.next();
-					if (function == functionList[index]) {
+				for (Iterator<Integer> iterator = allowedFunctions.iterator(); iterator.hasNext();) {
+					int function = iterator.next();
+					if (function == index) {
 						iterator.remove();
 					}
 				}
@@ -58,8 +59,9 @@ public abstract class FunctionSet {
 		}
 		
 		public void enableFunction(int index) {
-			if (!allowedFunctions.contains(functionList[index])) {
-				allowedFunctions.add(functionList[index]);
+			if (!allowedFunctions.contains(index)) {
+				allowedFunctions.add(index);
+				Collections.sort(allowedFunctions);
 			}
 		}
 		
@@ -69,6 +71,18 @@ public abstract class FunctionSet {
 		}
 		
 		public boolean isEnabled(Function f) {
-			return allowedFunctions.contains(f);
+			for (int i = 0; i < allowedFunctions.size(); i++) {
+				if (functionList[allowedFunctions.get(i)] == f) {
+					return true;
+				}
+			}
+			return false;
+		}
+		
+		protected void enableAll() {
+			allowedFunctions = new ArrayList<Integer>();
+			for (int i = 0; i < functionList.length; i++) {
+				allowedFunctions.add(i);
+			}
 		}
 	}
\ No newline at end of file
diff --git a/src/jcgp/backend/function/Arithmetic.java b/src/jcgp/backend/function/IntegerArithmetic.java
index 6971663..c08a72a 100644
--- a/src/jcgp/backend/function/Arithmetic.java
+++ b/src/jcgp/backend/function/IntegerArithmetic.java
@@ -1,31 +1,25 @@
 package jcgp.backend.function;
 
-import java.util.ArrayList;
-import java.util.Arrays;
-
 import jcgp.backend.exceptions.InvalidArgumentsException;
 import jcgp.backend.population.Connection;
 
-public class Arithmetic extends FunctionSet {
+public class IntegerArithmetic extends FunctionSet {
 	
-	public Arithmetic() {
-		name = "Arithmetic";
+	public IntegerArithmetic() {
+		name = "Integer Arithmetic";
 		functionList = new Function[]{
 				new Addition(),
 				new Subtraction(),
 				new Multiplication(),
 				new Division()};
 		
-		allowedFunctions = new ArrayList<Function>(Arrays.asList(functionList));
+		enableAll();
 	}
 	
 	public static class Addition extends Function {
-
-		private int arity = 2;
-
 		@Override
 		public Integer run(Connection... connections) {
-			if (connections.length < arity) {
+			if (connections.length < 2) {
 				throw new InvalidArgumentsException("Not enough connections were given.");
 			} else {
 				Integer arg1 = ((Integer) connections[0].getValue());
@@ -38,7 +32,7 @@ public class Arithmetic extends FunctionSet {
 
 		@Override
 		public int getArity() {
-			return arity;
+			return 2;
 		}
 
 		@Override
@@ -48,12 +42,9 @@ public class Arithmetic extends FunctionSet {
 	}
 
 	public static class Subtraction extends Function {
-
-		private int arity = 2;
-
 		@Override
 		public Integer run(Connection... connections) {
-			if (connections.length < arity) {
+			if (connections.length < 2) {
 				throw new InvalidArgumentsException("Not enough connections were given.");
 			} else {
 				Integer arg1 = ((Integer) connections[0].getValue());
@@ -66,7 +57,7 @@ public class Arithmetic extends FunctionSet {
 
 		@Override
 		public int getArity() {
-			return arity;
+			return 2;
 		}
 
 		@Override
@@ -76,12 +67,9 @@ public class Arithmetic extends FunctionSet {
 	}
 
 	public static class Multiplication extends Function {
-
-		private int arity = 2;
-
 		@Override
 		public Integer run(Connection... connections) {
-			if (connections.length < arity) {
+			if (connections.length < 2) {
 				throw new InvalidArgumentsException("Not enough connections were given.");
 			} else {
 				Integer arg1 = ((Integer) connections[0].getValue());
@@ -94,7 +82,7 @@ public class Arithmetic extends FunctionSet {
 
 		@Override
 		public int getArity() {
-			return arity;
+			return 2;
 		}
 
 		@Override
@@ -104,12 +92,9 @@ public class Arithmetic extends FunctionSet {
 	}
 
 	public static class Division extends Function {
-
-		private int arity = 2;
-
 		@Override
 		public Integer run(Connection... connections) {
-			if (connections.length < arity) {
+			if (connections.length < 2) {
 				throw new InvalidArgumentsException("Not enough connections were given.");
 			} else {
 				Integer arg1 = ((Integer) connections[0].getValue());
@@ -127,7 +112,7 @@ public class Arithmetic extends FunctionSet {
 
 		@Override
 		public int getArity() {
-			return arity;
+			return 2;
 		}
 
 		@Override
diff --git a/src/jcgp/backend/modules/Module.java b/src/jcgp/backend/modules/Module.java
index 82c3d80..f2b91b0 100644
--- a/src/jcgp/backend/modules/Module.java
+++ b/src/jcgp/backend/modules/Module.java
@@ -1,11 +1,9 @@
 package jcgp.backend.modules;
 
-import jcgp.JCGP.Resources;
-import jcgp.backend.parameters.Parameter;
+import jcgp.backend.resources.parameters.Parameter;
 
 public interface Module {
 	
 	public Parameter[] getLocalParameters();
 	
-	public ModuleStatus getStatus(Resources resources);
 }
diff --git a/src/jcgp/backend/modules/ModuleStatus.java b/src/jcgp/backend/modules/ModuleStatus.java
deleted file mode 100644
index fec8490..0000000
--- a/src/jcgp/backend/modules/ModuleStatus.java
+++ /dev/null
@@ -1,16 +0,0 @@
-package jcgp.backend.modules;
-
-public enum ModuleStatus {
-	ERROR, WARNING, READY;
-	
-	private String details;
-	
-	public void setDetails(String details) {
-		this.details = details;
-	}
-	
-	public String getDetails() {
-		return details;
-	}
-	
-}
diff --git a/src/jcgp/backend/modules/ea/EvolutionaryAlgorithm.java b/src/jcgp/backend/modules/ea/EvolutionaryAlgorithm.java
index 7719111..3aca104 100644
--- a/src/jcgp/backend/modules/ea/EvolutionaryAlgorithm.java
+++ b/src/jcgp/backend/modules/ea/EvolutionaryAlgorithm.java
@@ -1,9 +1,9 @@
 package jcgp.backend.modules.ea;
 
-import jcgp.JCGP.Resources;
 import jcgp.backend.modules.Module;
 import jcgp.backend.modules.mutator.Mutator;
 import jcgp.backend.population.Population;
+import jcgp.backend.resources.Resources;
 
 public interface EvolutionaryAlgorithm extends Module {
 
diff --git a/src/jcgp/backend/modules/ea/MuPlusLambda.java b/src/jcgp/backend/modules/ea/MuPlusLambda.java
index ad8c5d8..0d16111 100644
--- a/src/jcgp/backend/modules/ea/MuPlusLambda.java
+++ b/src/jcgp/backend/modules/ea/MuPlusLambda.java
@@ -1,13 +1,12 @@
 package jcgp.backend.modules.ea;
 
-import jcgp.JCGP.Resources;
-import jcgp.backend.modules.ModuleStatus;
 import jcgp.backend.modules.mutator.Mutator;
-import jcgp.backend.parameters.BooleanParameter;
-import jcgp.backend.parameters.IntegerParameter;
-import jcgp.backend.parameters.Parameter;
-import jcgp.backend.parameters.ParameterStatus;
 import jcgp.backend.population.Population;
+import jcgp.backend.resources.Resources;
+import jcgp.backend.resources.parameters.BooleanParameter;
+import jcgp.backend.resources.parameters.IntegerParameter;
+import jcgp.backend.resources.parameters.Parameter;
+import jcgp.backend.resources.parameters.ParameterStatus;
 
 /**
  * (μ + λ) EA.
@@ -62,8 +61,7 @@ public class MuPlusLambda implements EvolutionaryAlgorithm {
 
 	@Override
 	public void evolve(Population population, Mutator mutator, Resources resources) {
-		// TODO actually use parents and offspring
-		// select fittest chromosome
+		// select fittest chromosomes
 		fittestChromosome = 0;
 		
 		for (int i = 1; i < resources.getInt("popSize"); i++) {
@@ -79,6 +77,7 @@ public class MuPlusLambda implements EvolutionaryAlgorithm {
 				mutator.mutate(population.getChromosome(i), resources);
 			}
 		}
+		
 	}
 
 	@Override
@@ -95,10 +94,5 @@ public class MuPlusLambda implements EvolutionaryAlgorithm {
 	public String toString() {
 		return "(μ + λ)";
 	}
-
-	@Override
-	public ModuleStatus getStatus(Resources resources) {
-		return ModuleStatus.READY;
-	}
 	
 }
diff --git a/src/jcgp/backend/modules/ea/TournamentSelection.java b/src/jcgp/backend/modules/ea/TournamentSelection.java
index 32ac54d..baf6704 100644
--- a/src/jcgp/backend/modules/ea/TournamentSelection.java
+++ b/src/jcgp/backend/modules/ea/TournamentSelection.java
@@ -2,12 +2,11 @@ package jcgp.backend.modules.ea;
 
 import java.util.HashMap;
 
-import jcgp.JCGP.Resources;
-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.Population;
+import jcgp.backend.resources.Resources;
+import jcgp.backend.resources.parameters.IntegerParameter;
+import jcgp.backend.resources.parameters.Parameter;
 
 public class TournamentSelection implements EvolutionaryAlgorithm {
 	
@@ -51,9 +50,4 @@ public class TournamentSelection implements EvolutionaryAlgorithm {
 	public String toString() {
 		return "Tournament";
 	}
-
-	@Override
-	public ModuleStatus getStatus(Resources resources) {
-		return null;
-	}
 }
diff --git a/src/jcgp/backend/modules/fitness/FitnessFunction.java b/src/jcgp/backend/modules/fitness/FitnessFunction.java
index ffce9b7..d3b76cb 100644
--- a/src/jcgp/backend/modules/fitness/FitnessFunction.java
+++ b/src/jcgp/backend/modules/fitness/FitnessFunction.java
@@ -1,8 +1,8 @@
 package jcgp.backend.modules.fitness;
 
-import jcgp.JCGP.Resources;
 import jcgp.backend.modules.Module;
 import jcgp.backend.population.Population;
+import jcgp.backend.resources.Resources;
 
 public interface FitnessFunction extends Module {
 
diff --git a/src/jcgp/backend/modules/fitness/TestCase.java b/src/jcgp/backend/modules/fitness/TestCase.java
deleted file mode 100644
index 23f7ecf..0000000
--- a/src/jcgp/backend/modules/fitness/TestCase.java
+++ /dev/null
@@ -1,29 +0,0 @@
-package jcgp.backend.modules.fitness;
-
-public class TestCase {
-
-	private Object[] inputs;
-	private Object[] outputs;
-	
-	public TestCase(Object[] inputs, Object[] outputs) {
-		this.inputs = inputs;
-		this.outputs = outputs;
-	}
-	
-	public Object getInput(int index) {
-		return inputs[index];
-	}
-	
-	public Object getOutput(int index) {
-		return outputs[index];
-	}
-	
-	public Object[] getInputs() {
-		return inputs;
-	}
-	
-	public Object[] getOutputs() {
-		return outputs;
-	}
-	
-}
diff --git a/src/jcgp/backend/modules/fitness/TestCaseEvaluator.java b/src/jcgp/backend/modules/fitness/TestCaseEvaluator.java
deleted file mode 100644
index 5ff6973..0000000
--- a/src/jcgp/backend/modules/fitness/TestCaseEvaluator.java
+++ /dev/null
@@ -1,43 +0,0 @@
-package jcgp.backend.modules.fitness;
-
-import jcgp.JCGP.Resources;
-import jcgp.backend.modules.ModuleStatus;
-import jcgp.backend.parameters.Parameter;
-import jcgp.backend.population.Population;
-
-public class TestCaseEvaluator implements FitnessFunction {
-	
-	@Override
-	public void evaluate(Population population, Resources resources) {		
-		// for every chromosome in the population
-		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 < resources.getInt("outputs"); o++) {
-					if (population.getChromosome(i).getOutput(o).calculate() == resources.getTestCase(t).getOutput(o)) {
-						fitness++;
-					}
-				}
-			}
-			population.getChromosome(i).setFitness(fitness);
-		}
-	}
-
-	@Override
-	public Parameter[] getLocalParameters() {
-		return null;
-	}
-
-	@Override
-	public String toString() {
-		return "Test case";
-	}
-
-	@Override
-	public ModuleStatus getStatus(Resources resources) {
-		return null;
-	}
-}
diff --git a/src/jcgp/backend/modules/fitness/testcase/TestCaseEvaluator.java b/src/jcgp/backend/modules/fitness/testcase/TestCaseEvaluator.java
new file mode 100644
index 0000000..51676e3
--- /dev/null
+++ b/src/jcgp/backend/modules/fitness/testcase/TestCaseEvaluator.java
@@ -0,0 +1,75 @@
+package jcgp.backend.modules.fitness.testcase;
+
+import java.util.ArrayList;
+
+import jcgp.backend.modules.fitness.FitnessFunction;
+import jcgp.backend.population.Population;
+import jcgp.backend.resources.Resources;
+
+/**
+ * 
+ * This fitness function module implements a simple test case evaluator.
+ * 
+ * A TestCase object is a 
+ * 
+ * 
+ * @author Eduardo Pedroni
+ *
+ */
+public abstract class TestCaseEvaluator implements FitnessFunction {
+	
+	public static class TestCase<T> {
+
+		private T[] inputs;
+		private T[] outputs;
+		
+		public TestCase(T[] inputs, T[] outputs) {
+			this.inputs = inputs;
+			this.outputs = outputs;
+		}
+		
+		public T getInput(int index) {
+			return inputs[index];
+		}
+		
+		public T getOutput(int index) {
+			return outputs[index];
+		}
+		
+		public T[] getInputs() {
+			return inputs;
+		}
+		
+		public T[] getOutputs() {
+			return outputs;
+		}
+	}
+	
+	protected ArrayList<TestCase> testCases;
+	
+	@Override
+	public void evaluate(Population population, Resources resources) {
+		// for every chromosome in the population
+		for (int i = 0; i < resources.getInt("popSize"); i++) {
+			// assume an initial fitness of 0
+			int fitness = 0;
+			// for each test case
+			for (int t = 0; t < testCases.size(); t++) {
+				population.getChromosome(i).setInputs(testCases.get(t).getInputs());
+				// check each output
+				for (int o = 0; o < resources.getInt("outputs"); o++) {
+					if (population.getChromosome(i).getOutput(o).calculate() == testCases.get(t).getOutput(o)) {
+						fitness++;
+					}
+				}
+			}
+			// assign the resulting fitness to the respective individual
+			population.getChromosome(i).setFitness(fitness);
+		}
+	}
+	
+	public int getMaxFitness() {
+		return 0;
+	}
+}
+
diff --git a/src/jcgp/backend/modules/mutator/Mutator.java b/src/jcgp/backend/modules/mutator/Mutator.java
index fd7cd27..ffdd35c 100644
--- a/src/jcgp/backend/modules/mutator/Mutator.java
+++ b/src/jcgp/backend/modules/mutator/Mutator.java
@@ -1,8 +1,8 @@
 package jcgp.backend.modules.mutator;
 
-import jcgp.JCGP.Resources;
 import jcgp.backend.modules.Module;
 import jcgp.backend.population.Chromosome;
+import jcgp.backend.resources.Resources;
 
 public interface Mutator extends Module {
 
diff --git a/src/jcgp/backend/modules/mutator/PointMutator.java b/src/jcgp/backend/modules/mutator/PointMutator.java
index cdac8bb..54d5f3d 100644
--- a/src/jcgp/backend/modules/mutator/PointMutator.java
+++ b/src/jcgp/backend/modules/mutator/PointMutator.java
@@ -1,33 +1,39 @@
 package jcgp.backend.modules.mutator;
 
 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.backend.resources.Resources;
+import jcgp.backend.resources.parameters.DoubleParameter;
+import jcgp.backend.resources.parameters.Parameter;
+import jcgp.backend.resources.parameters.ParameterStatus;
 
 public class PointMutator implements Mutator {
 	
 	private DoubleParameter mutationRate;
 
-	private ModuleStatus status = ModuleStatus.READY;
-	
-	public PointMutator() {
-		mutationRate = new DoubleParameter(0.5, "Percent mutation", false, false) {
+	public PointMutator(final Resources resources) {
+		mutationRate = new DoubleParameter(50, "Percent mutation", false, false) {
 			@Override
 			public void validate(double newValue) {
-				// TODO this
+				if (newValue <= 0 || newValue > 100) {
+					status = ParameterStatus.INVALID;
+					status.setDetails("Mutation rate must be > 0 and <= 100");
+				} else if ((int) ((newValue / 100) * resources.getDouble("nodes")) <=  0) {
+					status = ParameterStatus.WARNING;
+					status.setDetails("With mutation rate " + mutationRate.get() + ", 0 genes will be mutated.");
+				} else {
+					status = ParameterStatus.VALID;
+				}
 			}
 		};
 	}
 
 	@Override
 	public void mutate(Chromosome chromosome, Resources resources) {
-		int mutations = (int) Math.ceil(((mutationRate.get()) * ((((resources.getDouble("nodes")) + (resources.getDouble("outputs")))) / (double) 100)));
+		int mutations = (int) ((mutationRate.get()) * ((((resources.getDouble("nodes")) + (resources.getDouble("outputs")))) / 100));
 		for (int i = 0; i < mutations; i++) {
 			MutableElement m = chromosome.getRandomMutableElement();
 			
@@ -55,18 +61,4 @@ 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/backend/population/Chromosome.java b/src/jcgp/backend/population/Chromosome.java
index c7493b9..d438375 100644
--- a/src/jcgp/backend/population/Chromosome.java
+++ b/src/jcgp/backend/population/Chromosome.java
@@ -2,8 +2,8 @@ package jcgp.backend.population;
 
 import java.util.ArrayList;
 
-import jcgp.JCGP.Resources;
 import jcgp.backend.exceptions.ParameterMismatchException;
+import jcgp.backend.resources.Resources;
 
 public class Chromosome {
 	
diff --git a/src/jcgp/backend/population/Node.java b/src/jcgp/backend/population/Node.java
index f1d37a1..6960ded 100644
--- a/src/jcgp/backend/population/Node.java
+++ b/src/jcgp/backend/population/Node.java
@@ -37,7 +37,7 @@ public class Node extends Gene implements MutableElement, Connection {
 
 	public void initialise(Function newFunction, Connection ... newConnections) throws InsufficientConnectionsException {
 		function = newFunction;
-		if (newConnections.length == function.getArity()) {
+		if (newConnections.length == chromosome.getResources().getInt("arity")) {
 			connections = newConnections;
 		} else {
 			throw new InsufficientConnectionsException();
diff --git a/src/jcgp/backend/population/Population.java b/src/jcgp/backend/population/Population.java
index 7b62d27..d2e6058 100644
--- a/src/jcgp/backend/population/Population.java
+++ b/src/jcgp/backend/population/Population.java
@@ -1,7 +1,6 @@
 package jcgp.backend.population;
 
-import jcgp.JCGP.Resources;
-
+import jcgp.backend.resources.Resources;
 
 public class Population {
 	
@@ -56,7 +55,6 @@ public class Population {
 		return chromosomes[resources.getRandomInt(chromosomes.length)];
 	}
 
-	
 	/**
 	 * Copy a chromosome into a different position.
 	 * After this returns, the target chromosome has
@@ -75,4 +73,6 @@ public class Population {
 	}
 	
 	
+	
+	
 }
diff --git a/src/jcgp/backend/resources/Console.java b/src/jcgp/backend/resources/Console.java
new file mode 100644
index 0000000..6bbd5ba
--- /dev/null
+++ b/src/jcgp/backend/resources/Console.java
@@ -0,0 +1,11 @@
+package jcgp.backend.resources;
+
+public interface Console {
+	
+	public void println(String s);
+	
+	public void print(String s);
+	
+	public void flush();
+
+}
diff --git a/src/jcgp/backend/resources/ModifiableResources.java b/src/jcgp/backend/resources/ModifiableResources.java
new file mode 100644
index 0000000..3e6b55e
--- /dev/null
+++ b/src/jcgp/backend/resources/ModifiableResources.java
@@ -0,0 +1,42 @@
+package jcgp.backend.resources;
+
+import jcgp.backend.resources.parameters.BooleanParameter;
+import jcgp.backend.resources.parameters.DoubleParameter;
+import jcgp.backend.resources.parameters.IntegerParameter;
+
+/**
+ * 
+ * This subclass of Resources allows modifications to be made.
+ * A read-only cast of this class is passed to modules for safety, 
+ * and only classes with access to a JCGP instance may modify
+ * the resources.
+ * 
+ * @author eddy
+ *
+ */
+public class ModifiableResources extends Resources {
+
+	public ModifiableResources() {
+		super();
+	}
+	
+	public void set(String key, Object value) {
+		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 void setFunctionSet(int index) {
+		functionSet = functionSets[index];
+		set("arity", functionSet.getMaxArity());
+	}
+	
+	public void setConsole(Console console) {
+		this.console = console;
+	}
+	
+}
diff --git a/src/jcgp/backend/resources/Resources.java b/src/jcgp/backend/resources/Resources.java
new file mode 100644
index 0000000..c1c3e4c
--- /dev/null
+++ b/src/jcgp/backend/resources/Resources.java
@@ -0,0 +1,310 @@
+package jcgp.backend.resources;
+
+import java.util.HashMap;
+import java.util.Random;
+
+import javafx.beans.value.ChangeListener;
+import javafx.beans.value.ObservableValue;
+import jcgp.backend.function.BitwiseLogic;
+import jcgp.backend.function.BooleanLogic;
+import jcgp.backend.function.Function;
+import jcgp.backend.function.FunctionSet;
+import jcgp.backend.function.IntegerArithmetic;
+import jcgp.backend.resources.parameters.BooleanParameter;
+import jcgp.backend.resources.parameters.DoubleParameter;
+import jcgp.backend.resources.parameters.IntegerParameter;
+import jcgp.backend.resources.parameters.Parameter;
+import jcgp.backend.resources.parameters.ParameterStatus;
+
+/**
+ * 
+ * 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
+ *
+ */
+public class Resources {
+	protected HashMap<String, Parameter> parameters = new HashMap<String, Parameter>();
+
+	protected Random numberGenerator = new Random();
+		
+	// function sets
+	protected FunctionSet[] functionSets =  new FunctionSet[] {
+			new IntegerArithmetic(),
+			new BitwiseLogic(),
+			new BooleanLogic() };
+	protected FunctionSet functionSet = functionSets[0];
+	
+	// GUI console
+	protected Console console;
+	
+	public Resources() {
+		createBaseParameters();
+	}
+	
+	public int getInt(String key) {
+		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) {
+		if (parameters.get(key) instanceof IntegerParameter) {
+			return ((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) {
+		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 Parameter getParameter(String key) {
+		return parameters.get(key);
+	}
+	
+	public boolean contains(String key) {
+		return parameters.containsKey(key);
+	}
+	
+	private void createBaseParameters() {
+		parameters.put("rows", new IntegerParameter(8, "Rows", false, true) {
+			@Override
+			public void validate(int newValue) {
+				if (newValue <= 0) {
+					status = ParameterStatus.INVALID;
+					status.setDetails("Chromosome must have at least 1 row.");
+				} else {
+					status = ParameterStatus.VALID;
+				}
+			}
+		});
+		parameters.put("columns", new IntegerParameter(9, "Columns", false, true) {
+			@Override
+			public void validate(int newValue) {
+				if (newValue <= 0) {
+					status = ParameterStatus.INVALID;
+					status.setDetails("Chromosome must have at least 1 column.");
+				} else {
+					status = ParameterStatus.VALID;
+				}
+			}
+		});
+		parameters.put("inputs", new IntegerParameter(3, "Inputs", false, true) {
+			@Override
+			public void validate(int newValue) {
+				if (newValue <= 0) {
+					status = ParameterStatus.INVALID;
+					status.setDetails("Chromosome must have at least 1 input.");
+				} else {
+					status = ParameterStatus.VALID;
+				}
+			}
+		});
+		parameters.put("outputs", new IntegerParameter(3, "Outputs", false, true) {
+			@Override
+			public void validate(int newValue) {
+				if (newValue <= 0) {
+					status = ParameterStatus.INVALID;
+					status.setDetails("Chromosome must have at least 1 output.");
+				} else {
+					status = ParameterStatus.VALID;
+				}
+			}
+		});
+		parameters.put("popSize", new IntegerParameter(5, "Population", false, true) {
+			@Override
+			public void validate(int newValue) {
+				if (newValue <= 0) {
+					status = ParameterStatus.INVALID;
+					status.setDetails("Population size must be at least 1.");
+				} else {
+					status = ParameterStatus.VALID;
+				}
+			}
+		});
+		parameters.put("levelsBack", new IntegerParameter(2, "Levels back", false, true) {
+			@Override
+			public void validate(int newValue) {
+				if (newValue <= 0) {
+					status = ParameterStatus.INVALID;
+					status.setDetails("Levels back must be at least 1.");
+				} else if (newValue > getInt("columns")) {
+					status = ParameterStatus.INVALID;
+					status.setDetails("Levels back must be less than or equal to the number of columns.");
+				} else {
+					status = ParameterStatus.VALID;
+				}
+			}
+		});
+		
+		IntegerParameter nodes = new IntegerParameter(1, "Nodes", true, false) {
+			@Override
+			public void validate(int newValue) {
+				// blank
+			}
+		};
+		nodes.valueProperty().bind(((IntegerParameter) parameters.get("rows")).valueProperty().multiply(((IntegerParameter) parameters.get("columns")).valueProperty()));
+		parameters.put("nodes", nodes);
+					
+		parameters.put("generations", new IntegerParameter(1000000, "Generations") {
+			@Override
+			public void validate(int newValue) {
+				if (newValue <= 0) {
+					status = ParameterStatus.INVALID;
+					status.setDetails("Number of generations must be greater than 0.");
+				} else if (newValue < getInt("currentGen")) {
+					status = ParameterStatus.WARNING_RESET;
+					status.setDetails("Setting generations to less than the current generation will cause the experiment to restart.");
+				} else {
+					status = ParameterStatus.VALID;
+				}
+			}
+		});
+		parameters.put("currentGen", new IntegerParameter(1, "Generation", true, false) {
+			@Override
+			public void validate(int newValue) {
+				// blank
+			}
+		});
+
+		parameters.put("runs", new IntegerParameter(5, "Runs") {
+			@Override
+			public void validate(int newValue) {
+				if (newValue <= 0) {
+					status = ParameterStatus.INVALID;
+					status.setDetails("Number of runs must be greater than 0.");
+				} else if (newValue < getInt("currentRun")) {
+					status = ParameterStatus.WARNING_RESET;
+					status.setDetails("Setting runs to less than the current run will cause the experiment to restart.");
+				} else {
+					status = ParameterStatus.VALID;
+				}
+			}
+		});
+		parameters.put("currentRun", new IntegerParameter(1, "Run", true, false) {
+			@Override
+			public void validate(int newValue) {
+				// blank
+			}
+		});
+
+		parameters.put("arity", new IntegerParameter(functionSet.getMaxArity(), "Max arity", true, false) {
+			@Override
+			public void validate(int newValue) {
+				// blank
+			}
+		});
+		
+		IntegerParameter seed = new IntegerParameter(1234, "Seed", false, true) {
+			@Override
+			public void validate(int newValue) {
+				status = ParameterStatus.VALID;
+			}
+		};
+		seed.valueProperty().addListener(new ChangeListener<Number>() {
+			@Override
+			public void changed(
+					ObservableValue<? extends Number> observable,
+					Number oldValue, Number newValue) {
+				numberGenerator.setSeed(newValue.longValue());
+			}
+		});
+		numberGenerator.setSeed(seed.get());
+		parameters.put("seed", seed);
+		
+		parameters.put("report", new IntegerParameter(1, "Report", false, false) {
+			@Override
+			public void validate(int newValue) {
+				if (newValue > getInt("generations")) {
+					status = ParameterStatus.WARNING;
+					status.setDetails("No reports will be printed.");
+				} else {
+					status = ParameterStatus.VALID;
+				}
+			}
+		});
+	}
+	
+	/*
+	 * Utility functions
+	 */
+	public int getRandomInt(int limit) {
+		return numberGenerator.nextInt(limit);
+	}
+	
+	public double getRandomDouble(int limit) {
+		return numberGenerator.nextDouble() * limit;
+	}
+	
+	public double getRandomDouble() {
+		return numberGenerator.nextDouble();
+	}
+	
+	/*
+	 * FunctionSet functions
+	 */
+	public Function getRandomFunction() {
+		Function f = functionSet.getAllowedFunction(numberGenerator.nextInt(functionSet.getAllowedFunctionCount()));
+		return f;
+	}
+
+	public Function getFunction(int index) {
+		return functionSet.getAllowedFunction(index);
+	}
+	
+	/**
+	 * @return the functionSets
+	 */
+	public FunctionSet[] getFunctionSets() {
+		return functionSets;
+	}
+
+	/**
+	 * @return the functionSet
+	 */
+	public FunctionSet getFunctionSet() {
+		return functionSet;
+	}
+	
+//	/*
+//	 * Test cases
+//	 */
+//	public TestCase getTestCase(int index) {
+//		return testCases[index];
+//	}
+//
+//	public int getTestCaseCount() {
+//		return testCases.length;
+//	}
+
+	/*
+	 * Console functionality
+	 */
+	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);
+		}
+	}
+}
\ No newline at end of file
diff --git a/src/jcgp/backend/parameters/BooleanParameter.java b/src/jcgp/backend/resources/parameters/BooleanParameter.java
index 43825be..cd17649 100644
--- a/src/jcgp/backend/parameters/BooleanParameter.java
+++ b/src/jcgp/backend/resources/parameters/BooleanParameter.java
@@ -1,4 +1,4 @@
-package jcgp.backend.parameters;
+package jcgp.backend.resources.parameters;
 
 import javafx.beans.property.SimpleBooleanProperty;
 
@@ -35,6 +35,7 @@ public abstract class BooleanParameter extends Parameter {
 	
 	public abstract void validate(boolean newValue);
 	
+	@Override
 	public SimpleBooleanProperty valueProperty() {
 		return value;
 	}
diff --git a/src/jcgp/backend/parameters/DoubleParameter.java b/src/jcgp/backend/resources/parameters/DoubleParameter.java
index 53551f5..8464c83 100644
--- a/src/jcgp/backend/parameters/DoubleParameter.java
+++ b/src/jcgp/backend/resources/parameters/DoubleParameter.java
@@ -1,4 +1,4 @@
-package jcgp.backend.parameters;
+package jcgp.backend.resources.parameters;
 
 import javafx.beans.property.SimpleDoubleProperty;
 
@@ -26,6 +26,7 @@ public abstract class DoubleParameter extends Parameter {
 		}
 	}
 	
+	@Override
 	public SimpleDoubleProperty valueProperty() {
 		return value;
 	}
diff --git a/src/jcgp/backend/parameters/IntegerParameter.java b/src/jcgp/backend/resources/parameters/IntegerParameter.java
index 68095d9..2a7b2a7 100644
--- a/src/jcgp/backend/parameters/IntegerParameter.java
+++ b/src/jcgp/backend/resources/parameters/IntegerParameter.java
@@ -1,4 +1,4 @@
-package jcgp.backend.parameters;
+package jcgp.backend.resources.parameters;
 
 import javafx.beans.property.SimpleIntegerProperty;
 
@@ -27,6 +27,7 @@ public abstract class IntegerParameter extends Parameter {
 		}
 	}
 	
+	@Override
 	public SimpleIntegerProperty valueProperty() {
 		return value;
 	}
diff --git a/src/jcgp/backend/parameters/Parameter.java b/src/jcgp/backend/resources/parameters/Parameter.java
index ddd5d5b..7e12ff8 100644
--- a/src/jcgp/backend/parameters/Parameter.java
+++ b/src/jcgp/backend/resources/parameters/Parameter.java
@@ -1,4 +1,4 @@
-package jcgp.backend.parameters;
+package jcgp.backend.resources.parameters;
 
 import javafx.beans.property.Property;
 
diff --git a/src/jcgp/backend/parameters/ParameterStatus.java b/src/jcgp/backend/resources/parameters/ParameterStatus.java
index 86abe33..11da4c2 100644
--- a/src/jcgp/backend/parameters/ParameterStatus.java
+++ b/src/jcgp/backend/resources/parameters/ParameterStatus.java
@@ -1,4 +1,4 @@
-package jcgp.backend.parameters;
+package jcgp.backend.resources.parameters;
 
 public enum ParameterStatus {
 	INVALID, WARNING, WARNING_RESET, VALID;
diff --git a/src/jcgp/backend/tests/ChromosomeTests.java b/src/jcgp/backend/tests/ChromosomeTests.java
index 1cd067e..a16ba75 100644
--- a/src/jcgp/backend/tests/ChromosomeTests.java
+++ b/src/jcgp/backend/tests/ChromosomeTests.java
@@ -2,13 +2,13 @@ package jcgp.backend.tests;
 
 import static org.junit.Assert.assertTrue;
 import static org.junit.Assert.fail;
-import jcgp.JCGP.Resources;
 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 jcgp.backend.resources.ModifiableResources;
 
 import org.junit.Before;
 import org.junit.BeforeClass;
@@ -40,11 +40,11 @@ import org.junit.Test;
 public class ChromosomeTests {
 
 	private Chromosome chromosome;
-	private static Resources resources;
+	private static ModifiableResources resources;
 
 	@BeforeClass
 	public static void setUpBeforeClass() {
-		resources = new Resources();
+		resources = new ModifiableResources();
 	}
 
 	@Before
diff --git a/src/jcgp/backend/tests/NodeTests.java b/src/jcgp/backend/tests/NodeTests.java
index 7121e81..2294816 100644
--- a/src/jcgp/backend/tests/NodeTests.java
+++ b/src/jcgp/backend/tests/NodeTests.java
@@ -1,12 +1,13 @@
 package jcgp.backend.tests;
 
 import static org.junit.Assert.assertTrue;
-import jcgp.JCGP.Resources;
-import jcgp.backend.function.Arithmetic;
+import jcgp.backend.exceptions.InvalidArgumentsException;
 import jcgp.backend.function.Function;
+import jcgp.backend.function.IntegerArithmetic;
 import jcgp.backend.population.Chromosome;
 import jcgp.backend.population.Connection;
 import jcgp.backend.population.Node;
+import jcgp.backend.resources.Resources;
 
 import org.junit.Before;
 import org.junit.BeforeClass;
@@ -48,7 +49,7 @@ public class NodeTests {
 	public void setUp() throws Exception {
 		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(),
+		node.initialise(new IntegerArithmetic.Addition(),
 				new Connection[]{new Connection() {
 
 					@Override
@@ -126,7 +127,7 @@ public class NodeTests {
 				((int) node.getValue()) == arg1 + arg2);
 
 		// put in a different function, check the output has changed appropriately
-		node.setFunction(new Arithmetic.Subtraction());
+		node.setFunction(new IntegerArithmetic.Subtraction());
 
 		assertTrue("Node did not return expected value (difference of arguments).", ((Integer) node.getValue()) == arg1 - arg2);
 
@@ -166,7 +167,28 @@ public class NodeTests {
 			}
 
 		};
-		node.initialise(null, conn0, conn1);
+		
+		Function function = new Function() {
+			@Override
+			public Object run(Connection... connections)
+					throws InvalidArgumentsException {
+				// blank
+				return null;
+			}
+
+			@Override
+			public int getArity() {
+				return 2;
+			}
+
+			@Override
+			public String getName() {
+				// blank
+				return null;
+			}
+		};
+		
+		node.initialise(function, conn0, conn1);
 
 		assertTrue("Connection 0 is incorrect.", node.getConnection(0) == conn0);
 		assertTrue("Connection 1 is incorrect.", node.getConnection(1) == conn1);
diff --git a/src/jcgp/backend/tests/OutputTests.java b/src/jcgp/backend/tests/OutputTests.java
index 7ff8a4a..b2bc7ec 100644
--- a/src/jcgp/backend/tests/OutputTests.java
+++ b/src/jcgp/backend/tests/OutputTests.java
@@ -1,10 +1,10 @@
 package jcgp.backend.tests;
 
 import static org.junit.Assert.assertTrue;
-import jcgp.JCGP.Resources;
 import jcgp.backend.population.Chromosome;
 import jcgp.backend.population.Connection;
 import jcgp.backend.population.Output;
+import jcgp.backend.resources.Resources;
 
 import org.junit.Before;
 import org.junit.BeforeClass;
diff --git a/src/jcgp/backend/tests/PopulationTests.java b/src/jcgp/backend/tests/PopulationTests.java
index 51b5168..31df8b9 100644
--- a/src/jcgp/backend/tests/PopulationTests.java
+++ b/src/jcgp/backend/tests/PopulationTests.java
@@ -1,9 +1,9 @@
 package jcgp.backend.tests;
 
 import static org.junit.Assert.assertTrue;
-import jcgp.JCGP.Resources;
 import jcgp.backend.population.Chromosome;
 import jcgp.backend.population.Population;
+import jcgp.backend.resources.Resources;
 
 import org.junit.Before;
 import org.junit.BeforeClass;