Light refactoring, a good amount of testing done, added some new functions.

20 files changed, 593 insertions, 117 deletions

diff --git a/src/jcgp/CGP.java b/src/jcgp/CGP.java
index 0ccd74e..48273e9 100644
--- a/src/jcgp/CGP.java
+++ b/src/jcgp/CGP.java
@@ -9,10 +9,8 @@ import jcgp.ea.StandardMutator;
 import jcgp.fitness.FitnessFunction;
 import jcgp.fitness.TestCase;
 import jcgp.fitness.TruthTableEvaluator;
-import jcgp.function.Addition;
+import jcgp.function.Arithmetic;
 import jcgp.function.FunctionSet;
-import jcgp.function.Multiplication;
-import jcgp.function.Subtraction;
 import jcgp.population.Population;
 
 public final class CGP {
@@ -30,7 +28,10 @@ public final class CGP {
 			Parameters.setCurrentGeneration(i);
 			fitnessFunction.evaluate(population);
 			ea.evolve(population, mutator);
-			if (ea.getBestFitness() >= 3) {
+			if (ea.getFittestChromosome().getFitness() >= 3) {
+				if (Parameters.getDebug()) {
+					ea.getFittestChromosome().printNodes();
+				}
 				break;
 			}
 		}	
@@ -41,7 +42,7 @@ public final class CGP {
 	 */
 	private void initialise() {
 		// initialise function set
-		FunctionSet functionSet = new FunctionSet(new Addition(), new Subtraction(), new Multiplication());
+		FunctionSet functionSet = new FunctionSet(new Arithmetic.Addition(), new Arithmetic.Subtraction(), new Arithmetic.Multiplication());
 		
 		// initialise utilities
 		Utilities.setResources(new Random(1234), functionSet);
@@ -57,6 +58,7 @@ public final class CGP {
 		Parameters.setTotalGenerations(5000);
 		Parameters.setTotalRuns(5);
 		Parameters.setMaxArity(functionSet.getMaxArity());
+		Parameters.setDebug(false);
 		
 		// initialise fitness function and truth table
 		TruthTable.setTestCases(new TestCase(new Object[] {2, 5, 4}, new Object[] {1, 10, 15}));
diff --git a/src/jcgp/Parameters.java b/src/jcgp/Parameters.java
index 0a6abd9..cef1ea4 100644
--- a/src/jcgp/Parameters.java
+++ b/src/jcgp/Parameters.java
@@ -8,6 +8,8 @@ public class Parameters {
 					   currentGeneration = 0, totalRuns = 0, currentRun = 0,
 					   maxArity = 0, maxFitness = 0;
 	
+	private static boolean debug = false;
+	
 	public static int getRows() {
 		return rows;
 	}
@@ -71,6 +73,10 @@ public class Parameters {
 	public static int getMaxFitness() {
 		return maxFitness;
 	}
+	
+	public static boolean getDebug() {
+		return debug;
+	}
 
 	public static void setRows(int rows) {
 		Parameters.rows = rows;
@@ -137,4 +143,8 @@ public class Parameters {
 		Parameters.maxFitness = maxFitness;
 	}
 	
+	public static void setDebug(boolean debug) {
+		Parameters.debug = debug;
+	}
+	
 }
diff --git a/src/jcgp/ea/EvolutionaryAlgorithm.java b/src/jcgp/ea/EvolutionaryAlgorithm.java
index e084da0..ba70671 100644
--- a/src/jcgp/ea/EvolutionaryAlgorithm.java
+++ b/src/jcgp/ea/EvolutionaryAlgorithm.java
@@ -1,11 +1,12 @@
 package jcgp.ea;
 
+import jcgp.population.Chromosome;
 import jcgp.population.Population;
 
 public interface EvolutionaryAlgorithm {
 
 	public abstract void evolve(Population population, Mutator mutator);
 
-	public abstract int getBestFitness();
+	public abstract Chromosome getFittestChromosome();
 
 }
diff --git a/src/jcgp/ea/StandardEA.java b/src/jcgp/ea/StandardEA.java
index 901333b..5f38513 100644
--- a/src/jcgp/ea/StandardEA.java
+++ b/src/jcgp/ea/StandardEA.java
@@ -13,7 +13,7 @@ import jcgp.population.Population;
  */
 public class StandardEA implements EvolutionaryAlgorithm {
 	
-	private int bestFitness = 0;
+	private Chromosome fittestChromosome;
 
 	@Override
 	public void evolve(Population population, Mutator mutator) {
@@ -25,9 +25,11 @@ public class StandardEA implements EvolutionaryAlgorithm {
 				fittest = i;
 			}
 		}
-		bestFitness = population.getChromosome(fittest).getFitness();
+		fittestChromosome = population.getChromosome(fittest);
 		population.setBestIndividual(fittest);
-		System.out.println("Best fitness: " + bestFitness);
+		if (Parameters.getDebug()) {
+			System.out.println("Best fitness: " + fittestChromosome.getFitness());
+		}
 		// create copies of fittest chromosome, mutate them
 		Chromosome fc = population.getChromosome(fittest);
 		for (int i = 0; i < Parameters.getPopulationSize(); i++) {
@@ -37,9 +39,9 @@ public class StandardEA implements EvolutionaryAlgorithm {
 			}
 		}
 	}
-	
+
 	@Override
-	public int getBestFitness() {
-		return bestFitness;
+	public Chromosome getFittestChromosome() {
+		return fittestChromosome;
 	}
 }
diff --git a/src/jcgp/fitness/TruthTableEvaluator.java b/src/jcgp/fitness/TruthTableEvaluator.java
index 2281b3f..4adf435 100644
--- a/src/jcgp/fitness/TruthTableEvaluator.java
+++ b/src/jcgp/fitness/TruthTableEvaluator.java
@@ -22,7 +22,9 @@ public class TruthTableEvaluator implements FitnessFunction {
 				}
 			}
 			population.getChromosome(i).setFitness(fitness);
-			System.out.println("active nodes: " + population.getChromosome(i).getActiveNodes().size());
+			if (Parameters.getDebug()) {
+				System.out.println("active nodes: " + population.getChromosome(i).getActiveNodes().size());
+			}
 		}
 	}
 }
diff --git a/src/jcgp/function/Addition.java b/src/jcgp/function/Addition.java
deleted file mode 100644
index 3a8f123..0000000
--- a/src/jcgp/function/Addition.java
+++ /dev/null
@@ -1,31 +0,0 @@
-package jcgp.function;
-
-import jcgp.exceptions.InvalidArgumentsException;
-import jcgp.population.Connection;
-
-public class Addition extends Function {
-	
-	private int arity = 2;
-
-	@Override
-	public Object run(Connection... connections) {
-		if (connections.length < arity) {
-			throw new InvalidArgumentsException("Not enough connections were given.");
-		} else if (connections[0].getValue() instanceof Integer) {
-			Integer arg1 = ((Integer) connections[0].getValue());
-			Integer arg2 = ((Integer) connections[1].getValue());
-			Integer result = arg1 + arg2;
-			
-			System.out.println(arg1 + " + " + arg2 + " = " + result);
-			return result;
-		} else {
-			throw new InvalidArgumentsException("Wrong data type, this function takes Integer.");
-		}
-	}
-
-	@Override
-	public int getArity() {
-		return arity;
-	}
-
-}
diff --git a/src/jcgp/function/Arithmetic.java b/src/jcgp/function/Arithmetic.java
new file mode 100644
index 0000000..b0bd5ca
--- /dev/null
+++ b/src/jcgp/function/Arithmetic.java
@@ -0,0 +1,123 @@
+package jcgp.function;
+
+import jcgp.Parameters;
+import jcgp.exceptions.InvalidArgumentsException;
+import jcgp.population.Connection;
+
+public class Arithmetic {
+
+	public static class Addition extends Function {
+
+		private int arity = 2;
+
+		@Override
+		public Integer run(Connection... connections) {
+			if (connections.length < arity) {
+				throw new InvalidArgumentsException("Not enough connections were given.");
+			} else {
+				Integer arg1 = ((Integer) connections[0].getValue());
+				Integer arg2 = ((Integer) connections[1].getValue());
+				Integer result = arg1 + arg2;
+
+				if (Parameters.getDebug()) {
+					System.out.println(arg1 + " + " + arg2 + " = " + result);
+				}
+				return result;
+			}
+		}
+
+		@Override
+		public int getArity() {
+			return arity;
+		}
+	}
+
+	public static class Subtraction extends Function {
+
+		private int arity = 2;
+
+		@Override
+		public Integer run(Connection... connections) {
+			if (connections.length < arity) {
+				throw new InvalidArgumentsException("Not enough connections were given.");
+			} else {
+				Integer arg1 = ((Integer) connections[0].getValue());
+				Integer arg2 = ((Integer) connections[1].getValue());
+				Integer result = arg1 - arg2;
+
+				if (Parameters.getDebug()) {
+					System.out.println(arg1 + " - " + arg2 + " = " + result);
+				}
+				return result;
+			}
+		}
+
+		@Override
+		public int getArity() {
+			return arity;
+		}
+	}
+
+	public static class Multiplication extends Function {
+
+		private int arity = 2;
+
+		@Override
+		public Integer run(Connection... connections) {
+			if (connections.length < arity) {
+				throw new InvalidArgumentsException("Not enough connections were given.");
+			} else {
+				Integer arg1 = ((Integer) connections[0].getValue());
+				Integer arg2 = ((Integer) connections[1].getValue());
+				Integer result = arg1 * arg2;
+
+				if (Parameters.getDebug()) {
+					System.out.println(arg1 + " * " + arg2 + " = " + result);
+				}
+				
+
+				return result;
+			} 
+		}
+
+		@Override
+		public int getArity() {
+			return arity;
+		}
+	}
+
+	public static class Division extends Function {
+
+		private int arity = 2;
+
+		@Override
+		public Integer run(Connection... connections) {
+			if (connections.length < arity) {
+				throw new InvalidArgumentsException("Not enough connections were given.");
+			} else {
+				Integer arg1 = ((Integer) connections[0].getValue());
+				Integer arg2 = ((Integer) connections[1].getValue());
+				Integer result;
+				if (arg2 == 0) {
+					result = 0;
+				} else {
+					result = arg1 / arg2;
+				}
+				
+
+				if (Parameters.getDebug()) {
+					System.out.println(arg1 + " / " + arg2 + " = " + result);
+				}
+				
+
+				return result;
+			} 
+		}
+
+		@Override
+		public int getArity() {
+			return arity;
+		}
+	}
+	
+}
diff --git a/src/jcgp/function/BitwiseLogic.java b/src/jcgp/function/BitwiseLogic.java
new file mode 100644
index 0000000..55f5df0
--- /dev/null
+++ b/src/jcgp/function/BitwiseLogic.java
@@ -0,0 +1,178 @@
+package jcgp.function;
+
+import jcgp.Parameters;
+import jcgp.exceptions.InvalidArgumentsException;
+import jcgp.population.Connection;
+
+public class BitwiseLogic {
+
+	public static class And extends Function {	
+		private int arity = 2;
+
+		@Override
+		public Object run(Connection... connections) {
+			if (connections.length < arity) {
+				throw new InvalidArgumentsException("Not enough connections were given.");
+			} else {
+				int arg1 = ((int) connections[0].getValue());
+				int arg2 = ((int) connections[1].getValue());
+				int result = arg1 & arg2;
+				if (Parameters.getDebug()) {
+					System.out.println(arg1 + " AND " + arg2 + " = " + result);
+				}
+				return result;
+			}
+		}
+
+		@Override
+		public int getArity() {
+			return arity;
+		}
+	}
+	
+	public static class Or extends Function {	
+		private int arity = 2;
+
+		@Override
+		public Object run(Connection... connections) {
+			if (connections.length < arity) {
+				throw new InvalidArgumentsException("Not enough connections were given.");
+			} else {
+				int arg1 = ((int) connections[0].getValue());
+				int arg2 = ((int) connections[1].getValue());
+				int result = arg1 | arg2;
+				if (Parameters.getDebug()) {
+					System.out.println(arg1 + " OR " + arg2 + " = " + result);
+				}
+				return result;
+			}
+		}
+
+		@Override
+		public int getArity() {
+			return arity;
+		}
+	}
+
+	public static class Not extends Function {	
+		private int arity = 1;
+
+		@Override
+		public Object run(Connection... connections) {
+			if (connections.length < arity) {
+				throw new InvalidArgumentsException("Not enough connections were given.");
+			} else {
+				int arg1 = ((int) connections[0].getValue());
+				int result = ~arg1;
+				if (Parameters.getDebug()) {
+					System.out.println("NOT " + arg1 + " = " + result);
+				}
+				return result;
+			}
+		}
+
+		@Override
+		public int getArity() {
+			return arity;
+		}
+	}
+
+	public static class Xor extends Function {	
+		private int arity = 2;
+
+		@Override
+		public Object run(Connection... connections) {
+			if (connections.length < arity) {
+				throw new InvalidArgumentsException("Not enough connections were given.");
+			} else {
+				int arg1 = ((int) connections[0].getValue());
+				int arg2 = ((int) connections[1].getValue());
+				int result = arg1 ^ arg2;
+				if (Parameters.getDebug()) {
+					System.out.println(arg1 + " XOR " + arg2 + " = " + result);
+				}
+				return result;
+			}
+		}
+
+		@Override
+		public int getArity() {
+			return arity;
+		}
+	}
+
+	public static class Nand extends Function {	
+		private int arity = 2;
+
+		@Override
+		public Object run(Connection... connections) {
+			if (connections.length < arity) {
+				throw new InvalidArgumentsException("Not enough connections were given.");
+			} else {
+				int arg1 = ((int) connections[0].getValue());
+				int arg2 = ((int) connections[1].getValue());
+				int result = arg1 & arg2;
+				if (Parameters.getDebug()) {
+					System.out.println(arg1 + " NAND " + arg2 + " = " + ~result);
+				}
+				return ~result;
+			}
+		}
+
+		@Override
+		public int getArity() {
+			return arity;
+		}
+	}
+
+	public static class Nor extends Function {	
+		private int arity = 2;
+
+		@Override
+		public Object run(Connection... connections) {
+			if (connections.length < arity) {
+				throw new InvalidArgumentsException("Not enough connections were given.");
+			} else {
+				int arg1 = ((int) connections[0].getValue());
+				int arg2 = ((int) connections[1].getValue());
+				int result = arg1 | arg2;
+				if (Parameters.getDebug()) {
+					System.out.println(arg1 + " NOR " + arg2 + " = " + ~result);
+				}
+				return ~result;
+			}
+		}
+
+		@Override
+		public int getArity() {
+			return arity;
+		}
+	}
+
+	public static class Xnor extends Function {	
+		private int arity = 2;
+
+		@Override
+		public Object run(Connection... connections) {
+			if (connections.length < arity) {
+				throw new InvalidArgumentsException("Not enough connections were given.");
+			} else {
+				int arg1 = ((int) connections[0].getValue());
+				int arg2 = ((int) connections[1].getValue());
+				int result = arg1 ^ arg2;
+				if (Parameters.getDebug()) {
+					System.out.println(arg1 + " XNOR " + arg2 + " = " + ~result);
+				}
+				return ~result;
+			}
+		}
+
+		@Override
+		public int getArity() {
+			return arity;
+		}
+	}
+
+	
+	
+}
diff --git a/src/jcgp/function/BooleanLogic.java b/src/jcgp/function/BooleanLogic.java
new file mode 100644
index 0000000..713dcf8
--- /dev/null
+++ b/src/jcgp/function/BooleanLogic.java
@@ -0,0 +1,178 @@
+package jcgp.function;
+
+import jcgp.Parameters;
+import jcgp.exceptions.InvalidArgumentsException;
+import jcgp.population.Connection;
+
+public class BooleanLogic {
+
+	public static class And extends Function {	
+		private int arity = 2;
+
+		@Override
+		public Boolean run(Connection... connections) {
+			if (connections.length < arity) {
+				throw new InvalidArgumentsException("Not enough connections were given.");
+			} else {
+				Boolean arg1 = ((Boolean) connections[0].getValue());
+				Boolean arg2 = ((Boolean) connections[1].getValue());
+				Boolean result = arg1 && arg2;
+				if (Parameters.getDebug()) {
+					System.out.println(arg1 + " AND " + arg2 + " = " + result);
+				}
+				return result;
+			}
+		}
+
+		@Override
+		public int getArity() {
+			return arity;
+		}
+	}
+	
+	public static class Or extends Function {	
+		private int arity = 2;
+
+		@Override
+		public Boolean run(Connection... connections) {
+			if (connections.length < arity) {
+				throw new InvalidArgumentsException("Not enough connections were given.");
+			} else {
+				Boolean arg1 = ((Boolean) connections[0].getValue());
+				Boolean arg2 = ((Boolean) connections[1].getValue());
+				Boolean result = arg1 || arg2;
+				if (Parameters.getDebug()) {
+					System.out.println(arg1 + " OR " + arg2 + " = " + result);
+				}
+				return result;
+			}
+		}
+
+		@Override
+		public int getArity() {
+			return arity;
+		}
+	}
+
+	public static class Not extends Function {	
+		private int arity = 1;
+
+		@Override
+		public Boolean run(Connection... connections) {
+			if (connections.length < arity) {
+				throw new InvalidArgumentsException("Not enough connections were given.");
+			} else {
+				Boolean arg1 = ((Boolean) connections[0].getValue());
+				Boolean result = !arg1;
+				if (Parameters.getDebug()) {
+					System.out.println("NOT " + arg1 + " = " + result);
+				}
+				return result;
+			}
+		}
+
+		@Override
+		public int getArity() {
+			return arity;
+		}
+	}
+
+	public static class Xor extends Function {	
+		private int arity = 2;
+
+		@Override
+		public Boolean run(Connection... connections) {
+			if (connections.length < arity) {
+				throw new InvalidArgumentsException("Not enough connections were given.");
+			} else {
+				Boolean arg1 = ((Boolean) connections[0].getValue());
+				Boolean arg2 = ((Boolean) connections[1].getValue());
+				Boolean result = arg1 ^ arg2;
+				if (Parameters.getDebug()) {
+					System.out.println(arg1 + " XOR " + arg2 + " = " + result);
+				}
+				return result;
+			}
+		}
+
+		@Override
+		public int getArity() {
+			return arity;
+		}
+	}
+
+	public static class Nand extends Function {	
+		private int arity = 2;
+
+		@Override
+		public Boolean run(Connection... connections) {
+			if (connections.length < arity) {
+				throw new InvalidArgumentsException("Not enough connections were given.");
+			} else {
+				Boolean arg1 = ((Boolean) connections[0].getValue());
+				Boolean arg2 = ((Boolean) connections[1].getValue());
+				Boolean result = arg1 && arg2;
+				if (Parameters.getDebug()) {
+					System.out.println(arg1 + " NAND " + arg2 + " = " + !result);
+				}
+				return !result;
+			}
+		}
+
+		@Override
+		public int getArity() {
+			return arity;
+		}
+	}
+
+	public static class Nor extends Function {	
+		private int arity = 2;
+
+		@Override
+		public Boolean run(Connection... connections) {
+			if (connections.length < arity) {
+				throw new InvalidArgumentsException("Not enough connections were given.");
+			} else {
+				Boolean arg1 = ((Boolean) connections[0].getValue());
+				Boolean arg2 = ((Boolean) connections[1].getValue());
+				Boolean result = arg1 || arg2;
+				if (Parameters.getDebug()) {
+					System.out.println(arg1 + " NOR " + arg2 + " = " + !result);
+				}
+				return !result;
+			}
+		}
+
+		@Override
+		public int getArity() {
+			return arity;
+		}
+	}
+
+	public static class Xnor extends Function {	
+		private int arity = 2;
+
+		@Override
+		public Boolean run(Connection... connections) {
+			if (connections.length < arity) {
+				throw new InvalidArgumentsException("Not enough connections were given.");
+			} else {
+				Boolean arg1 = ((Boolean) connections[0].getValue());
+				Boolean arg2 = ((Boolean) connections[1].getValue());
+				Boolean result = arg1 ^ arg2;
+				if (Parameters.getDebug()) {
+					System.out.println(arg1 + " XNOR " + arg2 + " = " + !result);
+				}
+				return !result;
+			}
+		}
+
+		@Override
+		public int getArity() {
+			return arity;
+		}
+	}
+
+	
+	
+}
diff --git a/src/jcgp/function/Multiplication.java b/src/jcgp/function/Multiplication.java
deleted file mode 100644
index 986faa8..0000000
--- a/src/jcgp/function/Multiplication.java
+++ /dev/null
@@ -1,31 +0,0 @@
-package jcgp.function;
-
-import jcgp.exceptions.InvalidArgumentsException;
-import jcgp.population.Connection;
-
-public class Multiplication extends Function {
-
-	private int arity = 2;
-
-	@Override
-	public Object run(Connection... connections) {
-		if (connections.length < arity) {
-			throw new InvalidArgumentsException("Not enough connections were given.");
-		} else if (connections[0].getValue() instanceof Integer) {
-			Integer arg1 = ((Integer) connections[0].getValue());
-			Integer arg2 = ((Integer) connections[1].getValue());
-			Integer result = arg1 * arg2;
-			
-			System.out.println(arg1 + " * " + arg2 + " = " + result);
-			return result;
-		} else {
-			throw new InvalidArgumentsException("Wrong data type, this function takes Integer.");
-		}
-	}
-
-	@Override
-	public int getArity() {
-		return arity;
-	}
-
-}
diff --git a/src/jcgp/function/Subtraction.java b/src/jcgp/function/Subtraction.java
deleted file mode 100644
index cfbb907..0000000
--- a/src/jcgp/function/Subtraction.java
+++ /dev/null
@@ -1,31 +0,0 @@
-package jcgp.function;
-
-import jcgp.exceptions.InvalidArgumentsException;
-import jcgp.population.Connection;
-
-public class Subtraction extends Function {
-
-	private int arity = 2;
-
-	@Override
-	public Object run(Connection... connections) {
-		if (connections.length < arity) {
-			throw new InvalidArgumentsException("Not enough connections were given.");
-		} else if (connections[0].getValue() instanceof Integer) {
-			Integer arg1 = ((Integer) connections[0].getValue());
-			Integer arg2 = ((Integer) connections[1].getValue());
-			Integer result = arg1 - arg2;
-			
-			System.out.println(arg1 + " - " + arg2 + " = " + result);
-			return result;
-		} else {
-			throw new InvalidArgumentsException("Wrong data type, this function takes Integer.");
-		}
-	}
-
-	@Override
-	public int getArity() {
-		return arity;
-	}
-
-}
diff --git a/src/jcgp/population/Chromosome.java b/src/jcgp/population/Chromosome.java
index 3e61a10..996e765 100644
--- a/src/jcgp/population/Chromosome.java
+++ b/src/jcgp/population/Chromosome.java
@@ -300,4 +300,22 @@ public class Chromosome {
 		}
 		return false;
 	}
+	
+	public void printNodes() {
+		for (int r = 0; r < Parameters.getRows(); r++) {
+			System.out.print("r: " + r + "\t");
+			for (int c = 0; c < Parameters.getColumns(); c++) {
+				System.out.print("N: (" + r + ", " + c + ") ");
+				for (int i = 0; i < Parameters.getMaxArity(); i++) {
+					System.out.print("C" + i + ": (" + nodes[r][c].getConnection(i).getDescription() + ") ");
+				}
+				System.out.print("F: " + nodes[r][c].getFunction().toString() + "\t");
+			}
+			System.out.print("\n");
+		}
+		
+		for (int o = 0; o < Parameters.getOutputs(); o++) {
+			System.out.print("o: " + o + " (" + outputs[o].getSource().getDescription() + ")\t");
+		}
+	}
 }
diff --git a/src/jcgp/population/Connection.java b/src/jcgp/population/Connection.java
index 751fe10..63a171e 100644
--- a/src/jcgp/population/Connection.java
+++ b/src/jcgp/population/Connection.java
@@ -4,5 +4,6 @@ public interface Connection {
 
 	public Object getValue();
 	
+	public String getDescription();
 
 }
diff --git a/src/jcgp/population/Input.java b/src/jcgp/population/Input.java
index e793bf6..5c545d6 100644
--- a/src/jcgp/population/Input.java
+++ b/src/jcgp/population/Input.java
@@ -21,4 +21,9 @@ public class Input implements Connection {
 	public int getIndex() {
 		return index;
 	}
+
+	@Override
+	public String getDescription() {
+		return "i: " + index;
+	}
 }
diff --git a/src/jcgp/population/Node.java b/src/jcgp/population/Node.java
index 35d33cb..1741235 100644
--- a/src/jcgp/population/Node.java
+++ b/src/jcgp/population/Node.java
@@ -25,6 +25,7 @@ public class Node implements MutableElement, Connection {
 
 	@Override
 	public Object getValue() {
+		//System.out.print("Calculating node: (" + row + ", " + column + ") > ");
 		return function.run(Arrays.copyOfRange(connections, 0, function.getArity()));
 	}
 
@@ -110,4 +111,9 @@ public class Node implements MutableElement, Connection {
 		}
 		return false;
 	}
+
+	@Override
+	public String getDescription() {
+		return "n: " + row + ", " + column;
+	}
 }
diff --git a/src/jcgp/population/Output.java b/src/jcgp/population/Output.java
index b3ce74f..0df51e9 100644
--- a/src/jcgp/population/Output.java
+++ b/src/jcgp/population/Output.java
@@ -2,6 +2,8 @@ package jcgp.population;
 
 import java.util.ArrayList;
 
+import jcgp.Parameters;
+
 public class Output implements MutableElement {
 	
 	private Connection source;
@@ -15,7 +17,9 @@ public class Output implements MutableElement {
 
 	public Object calculate() {
 		Object result = source.getValue();
-		System.out.println("Output " + index + ": " + result);
+		if (Parameters.getDebug()) {
+			System.out.println("Output " + index + ": " + result);
+		}
 		return result;
 	}
 
diff --git a/src/jcgp/tests/ChromosomeTests.java b/src/jcgp/tests/ChromosomeTests.java
index c943da8..46463c5 100644
--- a/src/jcgp/tests/ChromosomeTests.java
+++ b/src/jcgp/tests/ChromosomeTests.java
@@ -6,9 +6,8 @@ import java.util.Random;
 
 import jcgp.Parameters;
 import jcgp.Utilities;
-import jcgp.function.Addition;
+import jcgp.function.Arithmetic;
 import jcgp.function.FunctionSet;
-import jcgp.function.Subtraction;
 import jcgp.population.Chromosome;
 import jcgp.population.Connection;
 import jcgp.population.Input;
@@ -50,7 +49,7 @@ public class ChromosomeTests {
 	@BeforeClass
 	public static void setUpBeforeClass() {
 		// initialise function set
-		FunctionSet functionSet = new FunctionSet(new Addition(), new Subtraction());
+		FunctionSet functionSet = new FunctionSet(new Arithmetic.Addition(), new Arithmetic.Subtraction());
 
 		// initialise utilities
 		Utilities.setResources(new Random(1234), functionSet);
diff --git a/src/jcgp/tests/NodeTests.java b/src/jcgp/tests/NodeTests.java
index 9ea6769..ee26d38 100644
--- a/src/jcgp/tests/NodeTests.java
+++ b/src/jcgp/tests/NodeTests.java
@@ -6,9 +6,8 @@ import java.util.Random;
 
 import jcgp.Parameters;
 import jcgp.Utilities;
-import jcgp.function.Addition;
+import jcgp.function.Arithmetic;
 import jcgp.function.Function;
-import jcgp.function.Subtraction;
 import jcgp.population.Chromosome;
 import jcgp.population.Connection;
 import jcgp.population.Node;
@@ -63,7 +62,7 @@ public class NodeTests {
 	public void setUp() throws Exception {
 		node = new Node(chromosome, 0, 0);
 		// make node with anonymous addition function and hard-coded value connections
-		node.initialise(new Addition(),
+		node.initialise(new Arithmetic.Addition(),
 				new Connection[]{new Connection() {
 
 					@Override
@@ -72,6 +71,12 @@ public class NodeTests {
 						return arg1;
 					}
 
+					@Override
+					public String getDescription() {
+						// blank
+						return null;
+					}
+
 				},
 				new Connection() {
 
@@ -81,6 +86,12 @@ public class NodeTests {
 						return arg2;
 					}
 
+					@Override
+					public String getDescription() {
+						// blank
+						return null;
+					}
+
 				}});
 	}
 
@@ -123,7 +134,7 @@ public class NodeTests {
 				((int) node.getValue()) == arg1 + arg2);
 
 		// put in a different function, check the output has changed appropriately
-		node.setFunction(new Subtraction());
+		node.setFunction(new Arithmetic.Subtraction());
 
 		assertTrue("Node did not return expected value (difference of arguments).", ((Integer) node.getValue()) == arg1 - arg2);
 
@@ -141,6 +152,12 @@ public class NodeTests {
 				return 0;
 			}
 
+			@Override
+			public String getDescription() {
+				// blank
+				return null;
+			}
+
 		};
 		conn1 = new Connection() {
 
@@ -150,6 +167,12 @@ public class NodeTests {
 				return 0;
 			}
 
+			@Override
+			public String getDescription() {
+				// blank
+				return null;
+			}
+
 		};
 		node.initialise(null, conn0, conn1);
 
@@ -164,6 +187,12 @@ public class NodeTests {
 				// blank
 				return 0;
 			}
+
+			@Override
+			public String getDescription() {
+				// blank
+				return null;
+			}
 		};
 		node.setConnection(conn2);
 
diff --git a/src/jcgp/tests/OutputTests.java b/src/jcgp/tests/OutputTests.java
index c877c03..20e1c7f 100644
--- a/src/jcgp/tests/OutputTests.java
+++ b/src/jcgp/tests/OutputTests.java
@@ -68,6 +68,12 @@ public class OutputTests {
 				// test value
 				return outputValue;
 			}
+
+			@Override
+			public String getDescription() {
+				// blank
+				return null;
+			}
 		});
 
 		assertTrue("Incorrect evaluation.", ((Integer) output.calculate()) == outputValue);
@@ -83,6 +89,12 @@ public class OutputTests {
 				// blank
 				return 0;
 			}
+
+			@Override
+			public String getDescription() {
+				// blank
+				return null;
+			}
 		};
 		output.setConnection(newConn);
 
diff --git a/src/jcgp/tests/PopulationTests.java b/src/jcgp/tests/PopulationTests.java
index b8639bf..a6ab141 100644
--- a/src/jcgp/tests/PopulationTests.java
+++ b/src/jcgp/tests/PopulationTests.java
@@ -6,9 +6,8 @@ import java.util.Random;
 
 import jcgp.Parameters;
 import jcgp.Utilities;
-import jcgp.function.Addition;
+import jcgp.function.Arithmetic;
 import jcgp.function.FunctionSet;
-import jcgp.function.Subtraction;
 import jcgp.population.Chromosome;
 import jcgp.population.Population;
 
@@ -39,7 +38,7 @@ public class PopulationTests {
 	@BeforeClass
 	public static void setUpBeforeClass() throws Exception {
 		// initialise function set
-		FunctionSet functionSet = new FunctionSet(new Addition(), new Subtraction());
+		FunctionSet functionSet = new FunctionSet(new Arithmetic.Addition(), new Arithmetic.Subtraction());
 
 		// initialise utilities
 		Utilities.setResources(new Random(1234), functionSet);