Commented lots of packages.

45 files changed, 2487 insertions, 1925 deletions

diff --git a/src/jcgp/JCGP.java b/src/jcgp/JCGP.java
index f980c00..1e6d628 100644
--- a/src/jcgp/JCGP.java
+++ b/src/jcgp/JCGP.java
@@ -5,12 +5,15 @@ import java.io.File;
 import jcgp.backend.modules.es.EvolutionaryStrategy;
 import jcgp.backend.modules.es.MuPlusLambda;
 import jcgp.backend.modules.es.TournamentSelection;
+import jcgp.backend.modules.mutator.FixedPointMutator;
 import jcgp.backend.modules.mutator.Mutator;
-import jcgp.backend.modules.mutator.PointMutator;
+import jcgp.backend.modules.mutator.PercentPointMutator;
+import jcgp.backend.modules.mutator.ProbabilisticMutator;
 import jcgp.backend.modules.problem.DigitalCircuitProblem;
 import jcgp.backend.modules.problem.Problem;
 import jcgp.backend.modules.problem.SymbolicRegressionProblem;
 import jcgp.backend.modules.problem.TestCaseProblem;
+import jcgp.backend.modules.problem.TravellingSalesmanProblem;
 import jcgp.backend.parsers.ChromosomeParser;
 import jcgp.backend.parsers.FunctionParser;
 import jcgp.backend.parsers.ParameterParser;
@@ -49,19 +52,22 @@ public class JCGP {
 	 */
 	// mutators
 	private Mutator[] mutators = new Mutator[] {
-			new PointMutator(resources) };
+			new PercentPointMutator(resources),
+			new FixedPointMutator(resources),
+			new ProbabilisticMutator(resources)};
 	private Mutator mutator = mutators[0];
 	
 	// evolutionary algorithms
 	private EvolutionaryStrategy[] evolutionaryStrategies = new EvolutionaryStrategy[] {
 			new MuPlusLambda(resources),
-			new TournamentSelection(resources) };
+			new TournamentSelection(resources)};
 	private EvolutionaryStrategy evolutionaryStrategy = evolutionaryStrategies[0];
 	
 	// problem types
 	private Problem[] problems = new Problem[] {
 			new SymbolicRegressionProblem(resources),
-			new DigitalCircuitProblem(resources) };
+			new DigitalCircuitProblem(resources),
+			new TravellingSalesmanProblem(resources)};
 	private Problem problem = problems[0];
 
 	/*
@@ -178,7 +184,6 @@ public class JCGP {
 	}
 	
 	public void nextGeneration() {
-		System.out.println("service: doing next gen");
 		if (!finished) {
 			problem.evaluate(population, (Resources) resources);
 			reportGeneration();
@@ -264,12 +269,9 @@ public class JCGP {
 		reset();
 	}
 	
-	public void loadTestCases(File file) {
-		if (problem instanceof TestCaseProblem) {
-			TestCaseParser.parseParameters(file, resources);
-			reset();
-			TestCaseParser.parse(file, (TestCaseProblem<?>) problem, resources);
-		}
+	public void loadProblemData(File file) {
+		problem.parse(file, resources);
+		reset();
 	}
 	
 	public void loadChromosome(File file, int chromosomeIndex) {
diff --git a/src/jcgp/backend/function/BitwiseLogic.java b/src/jcgp/backend/function/BitwiseLogic.java
deleted file mode 100644
index 2466f36..0000000
--- a/src/jcgp/backend/function/BitwiseLogic.java
+++ /dev/null
@@ -1,506 +0,0 @@
-package jcgp.backend.function;
-
-import jcgp.backend.population.Connection;
-
-public class BitwiseLogic extends FunctionSet {
-	
-	public BitwiseLogic() {
-		name = "32-bit Logic";
-		functionList = new Function[]{
-				new ConstantZero(),
-				new ConstantOne(),
-				new WireA(),
-				new WireB(),
-				new NotA(),
-				new NotB(),
-				new And(),
-				new AndNotA(),
-				new AndNotB(),
-				new Nor(),
-				new Xor(),
-				new Xnor(),
-				new Or(),
-				new OrNotA(),
-				new OrNotB(),
-				new Nand()
-//				new Mux1(),
-//				new Mux2(),
-//				new Mux3(),
-//				new Mux4()
-				};
-		
-		enableAll();
-	}
-	
-	public static class ConstantZero extends Function {
-		@Override
-		public UnsignedInteger run(Connection... connections) {
-			return new UnsignedInteger(0);
-		}
-
-		@Override
-		public int getArity() {
-			return 0;
-		}
-
-		@Override
-		public String getName() {
-			return "0";
-		}
-	}
-	
-	public static class ConstantOne extends Function {
-		@Override
-		public UnsignedInteger run(Connection... connections) {
-			return new UnsignedInteger(0xFFFF);
-		}
-
-		@Override
-		public int getArity() {
-			return 0;
-		}
-
-		@Override
-		public String getName() {
-			return "1";
-		}
-	}
-	
-	public static class WireA extends Function {
-		@Override
-		public UnsignedInteger run(Connection... connections) {
-			if (connections.length < getArity()) {
-				throw new IllegalArgumentException(getName() + " received " + connections.length + " connections but arity is " + getArity() + ".");
-			} else {
-				return ((UnsignedInteger) connections[0].getValue());
-			}
-		}
-
-		@Override
-		public int getArity() {
-			return 2;
-		}
-
-		@Override
-		public String getName() {
-			return "Wire A";
-		}
-	}
-	
-	public static class WireB extends Function {
-		@Override
-		public UnsignedInteger run(Connection... connections) {
-			if (connections.length < getArity()) {
-				throw new IllegalArgumentException(getName() + " received " + connections.length + " connections but arity is " + getArity() + ".");
-			} else {
-				return ((UnsignedInteger) connections[1].getValue());
-			}
-		}
-
-		@Override
-		public int getArity() {
-			return 2;
-		}
-
-		@Override
-		public String getName() {
-			return "Wire B";
-		}
-	}
-	
-	public static class NotA extends Function {
-		@Override
-		public UnsignedInteger run(Connection... connections) {
-			if (connections.length < getArity()) {
-				throw new IllegalArgumentException(getName() + " received " + connections.length + " connections but arity is " + getArity() + ".");
-			} else {
-				return new UnsignedInteger(~((UnsignedInteger) connections[0].getValue()).get());
-			}
-		}
-
-		@Override
-		public int getArity() {
-			return 2;
-		}
-
-		@Override
-		public String getName() {
-			return "Not A";
-		}
-	}
-	
-	public static class NotB extends Function {
-		@Override
-		public UnsignedInteger run(Connection... connections) {
-			if (connections.length < getArity()) {
-				throw new IllegalArgumentException(getName() + " received " + connections.length + " connections but arity is " + getArity() + ".");
-			} else {
-				return new UnsignedInteger(~((UnsignedInteger) connections[1].getValue()).get());
-			}
-		}
-
-		@Override
-		public int getArity() {
-			return 2;
-		}
-
-		@Override
-		public String getName() {
-			return "Not B";
-		}
-	}
-	
-	public static class And extends Function {
-		@Override
-		public UnsignedInteger run(Connection... connections) {
-			if (connections.length < getArity()) {
-				throw new IllegalArgumentException(getName() + " received " + connections.length + " connections but arity is " + getArity() + ".");
-			} else {
-				UnsignedInteger in0 = ((UnsignedInteger) connections[0].getValue());
-				UnsignedInteger in1 = ((UnsignedInteger) connections[1].getValue());
-				Integer result = in0.get() & in1.get();
-				
-				return new UnsignedInteger(result);
-			}
-		}
-
-		@Override
-		public int getArity() {
-			return 2;
-		}
-
-		@Override
-		public String getName() {
-			return "And";
-		}
-	}
-	
-	public static class AndNotA extends Function {
-		@Override
-		public UnsignedInteger run(Connection... connections) {
-			if (connections.length < getArity()) {
-				throw new IllegalArgumentException(getName() + " received " + connections.length + " connections but arity is " + getArity() + ".");
-			} else {
-				UnsignedInteger in0 = ((UnsignedInteger) connections[0].getValue());
-				UnsignedInteger in1 = ((UnsignedInteger) connections[1].getValue());
-				Integer result = ~(in0.get()) & in1.get();
-				
-				return new UnsignedInteger(result);
-			}
-		}
-
-		@Override
-		public int getArity() {
-			return 2;
-		}
-
-		@Override
-		public String getName() {
-			return "And !A";
-		}
-	}
-	
-	public static class AndNotB extends Function {
-		@Override
-		public UnsignedInteger run(Connection... connections) {
-			if (connections.length < getArity()) {
-				throw new IllegalArgumentException(getName() + " received " + connections.length + " connections but arity is " + getArity() + ".");
-			} else {
-				UnsignedInteger in0 = ((UnsignedInteger) connections[0].getValue());
-				UnsignedInteger in1 = ((UnsignedInteger) connections[1].getValue());
-				Integer result = in0.get() & ~(in1.get());
-				
-				return new UnsignedInteger(result);
-			}
-		}
-
-		@Override
-		public int getArity() {
-			return 2;
-		}
-
-		@Override
-		public String getName() {
-			return "And !B";
-		}
-	}
-	
-	public static class Nor extends Function {
-		@Override
-		public UnsignedInteger run(Connection... connections) {
-			if (connections.length < getArity()) {
-				throw new IllegalArgumentException(getName() + " received " + connections.length + " connections but arity is " + getArity() + ".");
-			} else {
-				UnsignedInteger in0 = ((UnsignedInteger) connections[0].getValue());
-				UnsignedInteger in1 = ((UnsignedInteger) connections[1].getValue());
-				Integer result = in0.get() | in1.get();
-
-				return new UnsignedInteger(~result);
-			}
-		}
-
-		@Override
-		public int getArity() {
-			return 2;
-		}
-
-		@Override
-		public String getName() {
-			return "Nor";
-		}
-	}
-	
-	public static class Xor extends Function {
-		@Override
-		public UnsignedInteger run(Connection... connections) {
-			if (connections.length < getArity()) {
-				throw new IllegalArgumentException(getName() + " received " + connections.length + " connections but arity is " + getArity() + ".");
-			} else {
-				UnsignedInteger in0 = ((UnsignedInteger) connections[0].getValue());
-				UnsignedInteger in1 = ((UnsignedInteger) connections[1].getValue());
-				Integer result = in0.get() ^ in1.get();
-
-				return new UnsignedInteger(result);
-			}
-		}
-
-		@Override
-		public int getArity() {
-			return 2;
-		}
-
-		@Override
-		public String getName() {
-			return "Xor";
-		}
-	}
-	
-	public static class Xnor extends Function {
-		@Override
-		public UnsignedInteger run(Connection... connections) {
-			if (connections.length < getArity()) {
-				throw new IllegalArgumentException(getName() + " received " + connections.length + " connections but arity is " + getArity() + ".");
-			} else {
-				UnsignedInteger in0 = ((UnsignedInteger) connections[0].getValue());
-				UnsignedInteger in1 = ((UnsignedInteger) connections[1].getValue());
-				Integer result = in0.get() ^ in1.get();
-
-				return new UnsignedInteger(~result);
-			}
-		}
-
-		@Override
-		public int getArity() {
-			return 2;
-		}
-
-		@Override
-		public String getName() {
-			return "Xnor";
-		}
-	}
-	
-	public static class Or extends Function {
-		@Override
-		public UnsignedInteger run(Connection... connections) {
-			if (connections.length < getArity()) {
-				throw new IllegalArgumentException(getName() + " received " + connections.length + " connections but arity is " + getArity() + ".");
-			} else {
-				UnsignedInteger in0 = ((UnsignedInteger) connections[0].getValue());
-				UnsignedInteger in1 = ((UnsignedInteger) connections[1].getValue());
-				Integer result = in0.get() | in1.get();
-
-				return new UnsignedInteger(result);
-			}
-		}
-
-		@Override
-		public int getArity() {
-			return 2;
-		}
-
-		@Override
-		public String getName() {
-			return "Or";
-		}
-	}
-	
-	public static class OrNotA extends Function {
-		@Override
-		public UnsignedInteger run(Connection... connections) {
-			if (connections.length < getArity()) {
-				throw new IllegalArgumentException(getName() + " received " + connections.length + " connections but arity is " + getArity() + ".");
-			} else {
-				UnsignedInteger in0 = ((UnsignedInteger) connections[0].getValue());
-				UnsignedInteger in1 = ((UnsignedInteger) connections[1].getValue());
-				Integer result = ~in0.get() | in1.get();
-
-				return new UnsignedInteger(result);
-			}
-		}
-
-		@Override
-		public int getArity() {
-			return 2;
-		}
-
-		@Override
-		public String getName() {
-			return "Or !A";
-		}
-	}
-	
-	public static class OrNotB extends Function {
-		@Override
-		public UnsignedInteger run(Connection... connections) {
-			if (connections.length < getArity()) {
-				throw new IllegalArgumentException(getName() + " received " + connections.length + " connections but arity is " + getArity() + ".");
-			} else {
-				UnsignedInteger in0 = ((UnsignedInteger) connections[0].getValue());
-				UnsignedInteger in1 = ((UnsignedInteger) connections[1].getValue());
-				Integer result = in0.get() | ~in1.get();
-
-				return new UnsignedInteger(result);
-			}
-		}
-
-		@Override
-		public int getArity() {
-			return 2;
-		}
-
-		@Override
-		public String getName() {
-			return "Or !B";
-		}
-	}
-
-	public static class Nand extends Function {
-		@Override
-		public UnsignedInteger run(Connection... connections) {
-			if (connections.length < getArity()) {
-				throw new IllegalArgumentException(getName() + " received " + connections.length + " connections but arity is " + getArity() + ".");
-			} else {
-				UnsignedInteger in0 = ((UnsignedInteger) connections[0].getValue());
-				UnsignedInteger in1 = ((UnsignedInteger) connections[1].getValue());
-				Integer result = in0.get() & in1.get();
-
-				return new UnsignedInteger(~result);
-			}
-		}
-
-		@Override
-		public int getArity() {
-			return 2;
-		}
-
-		@Override
-		public String getName() {
-			return "Nand";
-		}
-	}
-	
-	public static class Mux1 extends Function {
-		@Override
-		public UnsignedInteger run(Connection... connections) {
-			if (connections.length < getArity()) {
-				throw new IllegalArgumentException(getName() + " received " + connections.length + " connections but arity is " + getArity() + ".");
-			} else {
-				UnsignedInteger in0 = ((UnsignedInteger) connections[0].getValue());
-				UnsignedInteger in1 = ((UnsignedInteger) connections[1].getValue());
-				UnsignedInteger in2 = ((UnsignedInteger) connections[2].getValue());
-				Integer result = ((in0.get() & ~in2.get()) | (in1.get() & in2.get()));
-
-				return new UnsignedInteger(result);
-			}
-		}
-
-		@Override
-		public int getArity() {
-			return 3;
-		}
-
-		@Override
-		public String getName() {
-			return "Mux1";
-		}
-	}
-	
-	public static class Mux2 extends Function {
-		@Override
-		public UnsignedInteger run(Connection... connections) {
-			if (connections.length < getArity()) {
-				throw new IllegalArgumentException(getName() + " received " + connections.length + " connections but arity is " + getArity() + ".");
-			} else {
-				UnsignedInteger in0 = ((UnsignedInteger) connections[0].getValue());
-				UnsignedInteger in1 = ((UnsignedInteger) connections[1].getValue());
-				UnsignedInteger in2 = ((UnsignedInteger) connections[2].getValue());
-				Integer result = ((in0.get() & ~in2.get()) | (~in1.get() & in2.get()));
-
-				return new UnsignedInteger(result);
-			}
-		}
-
-		@Override
-		public int getArity() {
-			return 3;
-		}
-
-		@Override
-		public String getName() {
-			return "Mux2";
-		}
-	}
-	
-	public static class Mux3 extends Function {
-		@Override
-		public UnsignedInteger run(Connection... connections) {
-			if (connections.length < getArity()) {
-				throw new IllegalArgumentException(getName() + " received " + connections.length + " connections but arity is " + getArity() + ".");
-			} else {
-				UnsignedInteger in0 = ((UnsignedInteger) connections[0].getValue());
-				UnsignedInteger in1 = ((UnsignedInteger) connections[1].getValue());
-				UnsignedInteger in2 = ((UnsignedInteger) connections[2].getValue());
-				Integer result = ((~in0.get() & ~in2.get()) | (in1.get() & in2.get()));
-
-				return new UnsignedInteger(result);
-			}
-		}
-
-		@Override
-		public int getArity() {
-			return 3;
-		}
-
-		@Override
-		public String getName() {
-			return "Mux3";
-		}
-	}
-	
-	public static class Mux4 extends Function {
-		@Override
-		public UnsignedInteger run(Connection... connections) {
-			if (connections.length < getArity()) {
-				throw new IllegalArgumentException(getName() + " received " + connections.length + " connections but arity is " + getArity() + ".");
-			} else {
-				UnsignedInteger in0 = ((UnsignedInteger) connections[0].getValue());
-				UnsignedInteger in1 = ((UnsignedInteger) connections[1].getValue());
-				UnsignedInteger in2 = ((UnsignedInteger) connections[2].getValue());
-				Integer result = ((~in0.get() & ~in2.get()) | (~in1.get() & in2.get()));
-
-				return new UnsignedInteger(result);
-			}
-		}
-
-		@Override
-		public int getArity() {
-			return 3;
-		}
-
-		@Override
-		public String getName() {
-			return "Mux4";
-		}
-	}
-}
diff --git a/src/jcgp/backend/function/DigitalCircuitFunctions.java b/src/jcgp/backend/function/DigitalCircuitFunctions.java
new file mode 100644
index 0000000..31cdf17
--- /dev/null
+++ b/src/jcgp/backend/function/DigitalCircuitFunctions.java
@@ -0,0 +1,504 @@
+package jcgp.backend.function;
+
+public class DigitalCircuitFunctions extends FunctionSet {
+	
+	public DigitalCircuitFunctions() {
+		name = "32-bit Logic";
+		functionList = new Function[]{
+				new ConstantZero(),
+				new ConstantOne(),
+				new WireA(),
+				new WireB(),
+				new NotA(),
+				new NotB(),
+				new And(),
+				new AndNotA(),
+				new AndNotB(),
+				new Nor(),
+				new Xor(),
+				new Xnor(),
+				new Or(),
+				new OrNotA(),
+				new OrNotB(),
+				new Nand(),
+				new Mux1(),
+				new Mux2(),
+				new Mux3(),
+				new Mux4()
+				};
+		
+		enableAll();
+	}
+	
+	public static class ConstantZero extends Function {
+		@Override
+		public UnsignedInteger run(Object... args) {
+			return new UnsignedInteger(0);
+		}
+
+		@Override
+		public int getArity() {
+			return 0;
+		}
+
+		@Override
+		public String toString() {
+			return "0";
+		}
+	}
+	
+	public static class ConstantOne extends Function {
+		@Override
+		public UnsignedInteger run(Object... args) {
+			return new UnsignedInteger(0xFFFF);
+		}
+
+		@Override
+		public int getArity() {
+			return 0;
+		}
+
+		@Override
+		public String toString() {
+			return "1";
+		}
+	}
+	
+	public static class WireA extends Function {
+		@Override
+		public UnsignedInteger run(Object... args) {
+			if (args.length < getArity()) {
+				throw new IllegalArgumentException(toString() + " received " + args.length + " in but arity is " + getArity() + ".");
+			} else {
+				return ((UnsignedInteger) args[0]);
+			}
+		}
+
+		@Override
+		public int getArity() {
+			return 2;
+		}
+
+		@Override
+		public String toString() {
+			return "Wire A";
+		}
+	}
+	
+	public static class WireB extends Function {
+		@Override
+		public UnsignedInteger run(Object... args) {
+			if (args.length < getArity()) {
+				throw new IllegalArgumentException(toString() + " received " + args.length + " in but arity is " + getArity() + ".");
+			} else {
+				return ((UnsignedInteger) args[1]);
+			}
+		}
+
+		@Override
+		public int getArity() {
+			return 2;
+		}
+
+		@Override
+		public String toString() {
+			return "Wire B";
+		}
+	}
+	
+	public static class NotA extends Function {
+		@Override
+		public UnsignedInteger run(Object... args) {
+			if (args.length < getArity()) {
+				throw new IllegalArgumentException(toString() + " received " + args.length + " in but arity is " + getArity() + ".");
+			} else {
+				return new UnsignedInteger(~((UnsignedInteger) args[0]).get());
+			}
+		}
+
+		@Override
+		public int getArity() {
+			return 2;
+		}
+
+		@Override
+		public String toString() {
+			return "Not A";
+		}
+	}
+	
+	public static class NotB extends Function {
+		@Override
+		public UnsignedInteger run(Object... args) {
+			if (args.length < getArity()) {
+				throw new IllegalArgumentException(toString() + " received " + args.length + " in but arity is " + getArity() + ".");
+			} else {
+				return new UnsignedInteger(~((UnsignedInteger) args[1]).get());
+			}
+		}
+
+		@Override
+		public int getArity() {
+			return 2;
+		}
+
+		@Override
+		public String toString() {
+			return "Not B";
+		}
+	}
+	
+	public static class And extends Function {
+		@Override
+		public UnsignedInteger run(Object... args) {
+			if (args.length < getArity()) {
+				throw new IllegalArgumentException(toString() + " received " + args.length + " in but arity is " + getArity() + ".");
+			} else {
+				UnsignedInteger in0 = ((UnsignedInteger) args[0]);
+				UnsignedInteger in1 = ((UnsignedInteger) args[1]);
+				Integer result = in0.get() & in1.get();
+				
+				return new UnsignedInteger(result);
+			}
+		}
+
+		@Override
+		public int getArity() {
+			return 2;
+		}
+
+		@Override
+		public String toString() {
+			return "And";
+		}
+	}
+	
+	public static class AndNotA extends Function {
+		@Override
+		public UnsignedInteger run(Object... args) {
+			if (args.length < getArity()) {
+				throw new IllegalArgumentException(toString() + " received " + args.length + " in but arity is " + getArity() + ".");
+			} else {
+				UnsignedInteger in0 = ((UnsignedInteger) args[0]);
+				UnsignedInteger in1 = ((UnsignedInteger) args[1]);
+				Integer result = ~(in0.get()) & in1.get();
+				
+				return new UnsignedInteger(result);
+			}
+		}
+
+		@Override
+		public int getArity() {
+			return 2;
+		}
+
+		@Override
+		public String toString() {
+			return "And !A";
+		}
+	}
+	
+	public static class AndNotB extends Function {
+		@Override
+		public UnsignedInteger run(Object... args) {
+			if (args.length < getArity()) {
+				throw new IllegalArgumentException(toString() + " received " + args.length + " in but arity is " + getArity() + ".");
+			} else {
+				UnsignedInteger in0 = ((UnsignedInteger) args[0]);
+				UnsignedInteger in1 = ((UnsignedInteger) args[1]);
+				Integer result = in0.get() & ~(in1.get());
+				
+				return new UnsignedInteger(result);
+			}
+		}
+
+		@Override
+		public int getArity() {
+			return 2;
+		}
+
+		@Override
+		public String toString() {
+			return "And !B";
+		}
+	}
+	
+	public static class Nor extends Function {
+		@Override
+		public UnsignedInteger run(Object... args) {
+			if (args.length < getArity()) {
+				throw new IllegalArgumentException(toString() + " received " + args.length + " in but arity is " + getArity() + ".");
+			} else {
+				UnsignedInteger in0 = ((UnsignedInteger) args[0]);
+				UnsignedInteger in1 = ((UnsignedInteger) args[1]);
+				Integer result = in0.get() | in1.get();
+
+				return new UnsignedInteger(~result);
+			}
+		}
+
+		@Override
+		public int getArity() {
+			return 2;
+		}
+
+		@Override
+		public String toString() {
+			return "Nor";
+		}
+	}
+	
+	public static class Xor extends Function {
+		@Override
+		public UnsignedInteger run(Object... args) {
+			if (args.length < getArity()) {
+				throw new IllegalArgumentException(toString() + " received " + args.length + " in but arity is " + getArity() + ".");
+			} else {
+				UnsignedInteger in0 = ((UnsignedInteger) args[0]);
+				UnsignedInteger in1 = ((UnsignedInteger) args[1]);
+				Integer result = in0.get() ^ in1.get();
+
+				return new UnsignedInteger(result);
+			}
+		}
+
+		@Override
+		public int getArity() {
+			return 2;
+		}
+
+		@Override
+		public String toString() {
+			return "Xor";
+		}
+	}
+	
+	public static class Xnor extends Function {
+		@Override
+		public UnsignedInteger run(Object... args) {
+			if (args.length < getArity()) {
+				throw new IllegalArgumentException(toString() + " received " + args.length + " in but arity is " + getArity() + ".");
+			} else {
+				UnsignedInteger in0 = ((UnsignedInteger) args[0]);
+				UnsignedInteger in1 = ((UnsignedInteger) args[1]);
+				Integer result = in0.get() ^ in1.get();
+
+				return new UnsignedInteger(~result);
+			}
+		}
+
+		@Override
+		public int getArity() {
+			return 2;
+		}
+
+		@Override
+		public String toString() {
+			return "Xnor";
+		}
+	}
+	
+	public static class Or extends Function {
+		@Override
+		public UnsignedInteger run(Object... args) {
+			if (args.length < getArity()) {
+				throw new IllegalArgumentException(toString() + " received " + args.length + " in but arity is " + getArity() + ".");
+			} else {
+				UnsignedInteger in0 = ((UnsignedInteger) args[0]);
+				UnsignedInteger in1 = ((UnsignedInteger) args[1]);
+				Integer result = in0.get() | in1.get();
+
+				return new UnsignedInteger(result);
+			}
+		}
+
+		@Override
+		public int getArity() {
+			return 2;
+		}
+
+		@Override
+		public String toString() {
+			return "Or";
+		}
+	}
+	
+	public static class OrNotA extends Function {
+		@Override
+		public UnsignedInteger run(Object... args) {
+			if (args.length < getArity()) {
+				throw new IllegalArgumentException(toString() + " received " + args.length + " in but arity is " + getArity() + ".");
+			} else {
+				UnsignedInteger in0 = ((UnsignedInteger) args[0]);
+				UnsignedInteger in1 = ((UnsignedInteger) args[1]);
+				Integer result = ~in0.get() | in1.get();
+
+				return new UnsignedInteger(result);
+			}
+		}
+
+		@Override
+		public int getArity() {
+			return 2;
+		}
+
+		@Override
+		public String toString() {
+			return "Or !A";
+		}
+	}
+	
+	public static class OrNotB extends Function {
+		@Override
+		public UnsignedInteger run(Object... args) {
+			if (args.length < getArity()) {
+				throw new IllegalArgumentException(toString() + " received " + args.length + " in but arity is " + getArity() + ".");
+			} else {
+				UnsignedInteger in0 = ((UnsignedInteger) args[0]);
+				UnsignedInteger in1 = ((UnsignedInteger) args[1]);
+				Integer result = in0.get() | ~in1.get();
+
+				return new UnsignedInteger(result);
+			}
+		}
+
+		@Override
+		public int getArity() {
+			return 2;
+		}
+
+		@Override
+		public String toString() {
+			return "Or !B";
+		}
+	}
+
+	public static class Nand extends Function {
+		@Override
+		public UnsignedInteger run(Object... args) {
+			if (args.length < getArity()) {
+				throw new IllegalArgumentException(toString() + " received " + args.length + " in but arity is " + getArity() + ".");
+			} else {
+				UnsignedInteger in0 = ((UnsignedInteger) args[0]);
+				UnsignedInteger in1 = ((UnsignedInteger) args[1]);
+				Integer result = in0.get() & in1.get();
+
+				return new UnsignedInteger(~result);
+			}
+		}
+
+		@Override
+		public int getArity() {
+			return 2;
+		}
+
+		@Override
+		public String toString() {
+			return "Nand";
+		}
+	}
+	
+	public static class Mux1 extends Function {
+		@Override
+		public UnsignedInteger run(Object... args) {
+			if (args.length < getArity()) {
+				throw new IllegalArgumentException(toString() + " received " + args.length + " in but arity is " + getArity() + ".");
+			} else {
+				UnsignedInteger in0 = ((UnsignedInteger) args[0]);
+				UnsignedInteger in1 = ((UnsignedInteger) args[1]);
+				UnsignedInteger in2 = ((UnsignedInteger) args[2]);
+				Integer result = ((in0.get() & ~in2.get()) | (in1.get() & in2.get()));
+
+				return new UnsignedInteger(result);
+			}
+		}
+
+		@Override
+		public int getArity() {
+			return 3;
+		}
+
+		@Override
+		public String toString() {
+			return "Mux1";
+		}
+	}
+	
+	public static class Mux2 extends Function {
+		@Override
+		public UnsignedInteger run(Object... args) {
+			if (args.length < getArity()) {
+				throw new IllegalArgumentException(toString() + " received " + args.length + " in but arity is " + getArity() + ".");
+			} else {
+				UnsignedInteger in0 = ((UnsignedInteger) args[0]);
+				UnsignedInteger in1 = ((UnsignedInteger) args[1]);
+				UnsignedInteger in2 = ((UnsignedInteger) args[2]);
+				Integer result = ((in0.get() & ~in2.get()) | (~in1.get() & in2.get()));
+
+				return new UnsignedInteger(result);
+			}
+		}
+
+		@Override
+		public int getArity() {
+			return 3;
+		}
+
+		@Override
+		public String toString() {
+			return "Mux2";
+		}
+	}
+	
+	public static class Mux3 extends Function {
+		@Override
+		public UnsignedInteger run(Object... args) {
+			if (args.length < getArity()) {
+				throw new IllegalArgumentException(toString() + " received " + args.length + " in but arity is " + getArity() + ".");
+			} else {
+				UnsignedInteger in0 = ((UnsignedInteger) args[0]);
+				UnsignedInteger in1 = ((UnsignedInteger) args[1]);
+				UnsignedInteger in2 = ((UnsignedInteger) args[2]);
+				Integer result = ((~in0.get() & ~in2.get()) | (in1.get() & in2.get()));
+
+				return new UnsignedInteger(result);
+			}
+		}
+
+		@Override
+		public int getArity() {
+			return 3;
+		}
+
+		@Override
+		public String toString() {
+			return "Mux3";
+		}
+	}
+	
+	public static class Mux4 extends Function {
+		@Override
+		public UnsignedInteger run(Object... args) {
+			if (args.length < getArity()) {
+				throw new IllegalArgumentException(toString() + " received " + args.length + " in but arity is " + getArity() + ".");
+			} else {
+				UnsignedInteger in0 = ((UnsignedInteger) args[0]);
+				UnsignedInteger in1 = ((UnsignedInteger) args[1]);
+				UnsignedInteger in2 = ((UnsignedInteger) args[2]);
+				Integer result = ((~in0.get() & ~in2.get()) | (~in1.get() & in2.get()));
+
+				return new UnsignedInteger(result);
+			}
+		}
+
+		@Override
+		public int getArity() {
+			return 3;
+		}
+
+		@Override
+		public String toString() {
+			return "Mux4";
+		}
+	}
+}
diff --git a/src/jcgp/backend/function/DoubleArithmetic.java b/src/jcgp/backend/function/DoubleArithmetic.java
deleted file mode 100644
index ce4826f..0000000
--- a/src/jcgp/backend/function/DoubleArithmetic.java
+++ /dev/null
@@ -1,589 +0,0 @@
-package jcgp.backend.function;
-
-import jcgp.backend.population.Connection;
-
-public class DoubleArithmetic extends FunctionSet {
-	
-	public final static double DIVISION_LIMIT = 0.0001;
-	
-	public DoubleArithmetic() {
-		name = "Double Arithmetic";
-		functionList = new Function[]{
-				new Absolute(),
-				new SquareRoot(),
-				new Reciprocal(),
-				new Sine(),
-				new Cosine(),
-				new Tangent(),
-				new Exponential(),
-				new HyperbolicSine(),
-				new HyperbolicCosine(),
-				new HyperbolicTangent(),
-				new NaturalLog(),
-				new LogBaseTen(),
-				new SineAB(),
-				new CosineAB(),
-				new Hypotenuse(),
-				new Power(),
-				new Addition(),
-				new Subtraction(),
-				new Multiplication(),
-				new Division()};
-		
-		enableAll();
-	}
-	
-	/**
-	 * Absolute returns the positive value of input 0.
-	 * 
-	 * @see Math.abs()
-	 */
-	public static class Absolute extends Function {
-		@Override
-		public Double run(Connection... connections) {
-			if (connections.length < getArity()) {
-				throw new IllegalArgumentException(getName() + " received " + connections.length + " connections but arity is " + getArity() + ".");
-			} else {
-				Double in0 = ((Double) connections[0].getValue());
-				return Math.abs(in0);
-			}
-		}
-
-		@Override
-		public int getArity() {
-			return 1;
-		}
-
-		@Override
-		public String getName() {
-			return "Absolute";
-		}
-	}
-	
-	/**
-	 * Protected square root function, returns the square root of the absolute
-	 * value of input 0.
-	 * 
-	 * @see Math.abs(), Math.sqrt()
-	 */
-	public static class SquareRoot extends Function {
-		@Override
-		public Double run(Connection... connections) {
-			if (connections.length < getArity()) {
-				throw new IllegalArgumentException(getName() + " received " + connections.length + " connections but arity is " + getArity() + ".");
-			} else {
-				Double in0 = ((Double) connections[0].getValue());
-				return Math.sqrt(Math.abs(in0));
-			}
-		}
-
-		@Override
-		public int getArity() {
-			return 1;
-		}
-
-		@Override
-		public String getName() {
-			return "Square root";
-		}
-	}
-	
-	/**
-	 * Protected reciprocal function, returns (1 / input 0). If input 0 is less than
-	 * {@link DoubleArithmetic.}DIVISION_LIMIT, this returns it unchanged.
-	 *
-	 */
-	public static class Reciprocal extends Function {
-		@Override
-		public Double run(Connection... connections) {
-			if (connections.length < getArity()) {
-				throw new IllegalArgumentException(getName() + " received " + connections.length + " connections but arity is " + getArity() + ".");
-			} else {
-				Double in0 = ((Double) connections[0].getValue());
-				return in0 < DIVISION_LIMIT ? in0 : (1 / in0);
-			}
-		}
-
-		@Override
-		public int getArity() {
-			return 1;
-		}
-
-		@Override
-		public String getName() {
-			return "Reciprocal";
-		}
-	}
-	
-	/**
-	 * Sine function, in radians.
-	 *
-	 * @see Math.sin()
-	 */
-	public static class Sine extends Function {
-		@Override
-		public Double run(Connection... connections) {
-			if (connections.length < getArity()) {
-				throw new IllegalArgumentException(getName() + " received " + connections.length + " connections but arity is " + getArity() + ".");
-			} else {
-				Double in0 = ((Double) connections[0].getValue());
-				return Math.sin(in0);
-			}
-		}
-
-		@Override
-		public int getArity() {
-			return 1;
-		}
-
-		@Override
-		public String getName() {
-			return "Sin";
-		}
-	}
-	
-	/**
-	 * Cosine function, in radians.
-	 *
-	 * @see Math.cos()
-	 */
-	public static class Cosine extends Function {
-		@Override
-		public Double run(Connection... connections) {
-			if (connections.length < getArity()) {
-				throw new IllegalArgumentException(getName() + " received " + connections.length + " connections but arity is " + getArity() + ".");
-			} else {
-				Double in0 = ((Double) connections[0].getValue());
-				return Math.cos(in0);
-			}
-		}
-
-		@Override
-		public int getArity() {
-			return 1;
-		}
-
-		@Override
-		public String getName() {
-			return "Cos";
-		}
-	}
-	
-	/**
-	 * Protected tangent function, in radians. Returns the tangent of input 0.
-	 * If input 0 is less than {@link DoubleArithmetic.}DIVISION_LIMIT, 
-	 * this returns it unchanged.
-	 *
-	 * @see Math.tan()
-	 */
-	public static class Tangent extends Function {
-		@Override
-		public Double run(Connection... connections) {
-			if (connections.length < getArity()) {
-				throw new IllegalArgumentException(getName() + " received " + connections.length + " connections but arity is " + getArity() + ".");
-			} else {
-				Double in0 = ((Double) connections[0].getValue());
-				return in0 < DIVISION_LIMIT ? in0 : Math.tan(in0);
-			}
-		}
-
-		@Override
-		public int getArity() {
-			return 1;
-		}
-
-		@Override
-		public String getName() {
-			return "Tan";
-		}
-	}
-	
-	/**
-	 * Exponential function. Returns the exponential of input 0.
-	 *
-	 * @see Math.exp()
-	 */
-	public static class Exponential extends Function {
-		@Override
-		public Double run(Connection... connections) {
-			if (connections.length < getArity()) {
-				throw new IllegalArgumentException(getName() + " received " + connections.length + " connections but arity is " + getArity() + ".");
-			} else {
-				Double in0 = ((Double) connections[0].getValue());
-				return Math.exp(in0);
-			}
-		}
-
-		@Override
-		public int getArity() {
-			return 1;
-		}
-
-		@Override
-		public String getName() {
-			return "Exp";
-		}
-	}
-	
-	/**
-	 * Returns the hyperbolic sine of input 0.
-	 *
-	 * @see Math.sinh()
-	 */
-	public static class HyperbolicSine extends Function {
-		@Override
-		public Double run(Connection... connections) {
-			if (connections.length < getArity()) {
-				throw new IllegalArgumentException(getName() + " received " + connections.length + " connections but arity is " + getArity() + ".");
-			} else {
-				Double in0 = ((Double) connections[0].getValue());
-				return Math.sinh(in0);
-			}
-		}
-
-		@Override
-		public int getArity() {
-			return 1;
-		}
-
-		@Override
-		public String getName() {
-			return "Sinh";
-		}
-	}
-	
-	/**
-	 * Returns the hyperbolic cosine of input 0.
-	 *
-	 * @see Math.cosh()
-	 */
-	public static class HyperbolicCosine extends Function {
-		@Override
-		public Double run(Connection... connections) {
-			if (connections.length < getArity()) {
-				throw new IllegalArgumentException(getName() + " received " + connections.length + " connections but arity is " + getArity() + ".");
-			} else {
-				Double in0 = ((Double) connections[0].getValue());
-				return Math.cosh(in0);
-			}
-		}
-
-		@Override
-		public int getArity() {
-			return 1;
-		}
-
-		@Override
-		public String getName() {
-			return "Cosh";
-		}
-	}
-	
-	/**
-	 * Returns the hyperbolic tangent of input 0.
-	 *
-	 * @see Math.tanh()
-	 */
-	public static class HyperbolicTangent extends Function {
-		@Override
-		public Double run(Connection... connections) {
-			if (connections.length < getArity()) {
-				throw new IllegalArgumentException(getName() + " received " + connections.length + " connections but arity is " + getArity() + ".");
-			} else {
-				Double in0 = ((Double) connections[0].getValue());
-				return Math.tanh(in0);
-			}
-		}
-
-		@Override
-		public int getArity() {
-			return 1;
-		}
-
-		@Override
-		public String getName() {
-			return "Tanh";
-		}
-	}
-	
-	/**
-	 * Protected natural log function. Returns the natural log of the absolute
-	 * value of input 0. If input 0 is less than {@link DoubleArithmetic.}DIVISION_LIMIT, 
-	 * this returns it unchanged.
-	 *
-	 * @see Math.log(), Math.abs()
-	 */
-	public static class NaturalLog extends Function {
-		@Override
-		public Double run(Connection... connections) {
-			if (connections.length < getArity()) {
-				throw new IllegalArgumentException(getName() + " received " + connections.length + " connections but arity is " + getArity() + ".");
-			} else {
-				Double in0 = ((Double) connections[0].getValue());
-				return in0 < DIVISION_LIMIT ? in0 : Math.log(Math.abs(in0));
-			}
-		}
-
-		@Override
-		public int getArity() {
-			return 1;
-		}
-
-		@Override
-		public String getName() {
-			return "Ln";
-		}
-	}
-	
-	/**
-	 * Protected log base 10 function. Returns the log to base 10 the absolute
-	 * value of input 0. If input 0 is less than {@link DoubleArithmetic.}DIVISION_LIMIT, 
-	 * this returns it unchanged.
-	 *
-	 * @see Math.log10(), Math.abs()
-	 */
-	public static class LogBaseTen extends Function {
-		@Override
-		public Double run(Connection... connections) {
-			if (connections.length < getArity()) {
-				throw new IllegalArgumentException(getName() + " received " + connections.length + " connections but arity is " + getArity() + ".");
-			} else {
-				Double in0 = ((Double) connections[0].getValue());
-				return in0 < DIVISION_LIMIT ? in0 : Math.log10(Math.abs(in0));
-			}
-		}
-
-		@Override
-		public int getArity() {
-			return 1;
-		}
-
-		@Override
-		public String getName() {
-			return "Log";
-		}
-	}
-	
-	/**
-	 * Sine of sum. Returns the sine of the sum of inputs 0 and 1.
-	 *
-	 * @see Math.sin()
-	 */
-	public static class SineAB extends Function {
-		@Override
-		public Double run(Connection... connections) {
-			if (connections.length < getArity()) {
-				throw new IllegalArgumentException(getName() + " received " + connections.length + " connections but arity is " + getArity() + ".");
-			} else {
-				Double in0 = ((Double) connections[0].getValue());
-				Double in1 = ((Double) connections[1].getValue());
-				return Math.sin(in0 + in1);
-			}
-		}
-
-		@Override
-		public int getArity() {
-			return 2;
-		}
-
-		@Override
-		public String getName() {
-			return "Sin(a+b)";
-		}
-	}
-	
-	/**
-	 * Cosine of sum. Returns the cosine of the sum of inputs 0 and 1.
-	 *
-	 * @see Math.cos()
-	 */
-	public static class CosineAB extends Function {
-		@Override
-		public Double run(Connection... connections) {
-			if (connections.length < getArity()) {
-				throw new IllegalArgumentException(getName() + " received " + connections.length + " connections but arity is " + getArity() + ".");
-			} else {
-				Double in0 = ((Double) connections[0].getValue());
-				Double in1 = ((Double) connections[1].getValue());
-				return Math.cos(in0 + in1);
-			}
-		}
-
-		@Override
-		public int getArity() {
-			return 2;
-		}
-
-		@Override
-		public String getName() {
-			return "Cos(a+b)";
-		}
-	}
-	
-	/**
-	 * Hypotenuse function. Returns the square root of input 0 squared
-	 * plus input 1 squared.
-	 *
-	 * @see Math.hypot()
-	 */
-	public static class Hypotenuse extends Function {
-		@Override
-		public Double run(Connection... connections) {
-			if (connections.length < getArity()) {
-				throw new IllegalArgumentException(getName() + " received " + connections.length + " connections but arity is " + getArity() + ".");
-			} else {
-				Double in0 = ((Double) connections[0].getValue());
-				Double in1 = ((Double) connections[1].getValue());
-				return Math.hypot(in0, in1);
-			}
-		}
-
-		@Override
-		public int getArity() {
-			return 2;
-		}
-
-		@Override
-		public String getName() {
-			return "Hypotenuse";
-		}
-	}
-	
-	/**
-	 * Power function. Returns the absolute value of input 0 to the power of input 1.
-	 *
-	 * @see Math.abs(), Math.pow
-	 */
-	public static class Power extends Function {
-		@Override
-		public Double run(Connection... connections) {
-			if (connections.length < getArity()) {
-				throw new IllegalArgumentException(getName() + " received " + connections.length + " connections but arity is " + getArity() + ".");
-			} else {
-				Double in0 = ((Double) connections[0].getValue());
-				Double in1 = ((Double) connections[1].getValue());
-				return Math.pow(Math.abs(in0), in1);
-			}
-		}
-
-		@Override
-		public int getArity() {
-			return 2;
-		}
-
-		@Override
-		public String getName() {
-			return "Power";
-		}
-	}
-	
-	/**
-	 * Addition returns the sum of inputs 0 and 1.
-	 *
-	 */
-	public static class Addition extends Function {
-		@Override
-		public Double run(Connection... connections) {
-			if (connections.length < getArity()) {
-				throw new IllegalArgumentException(getName() + " received " + connections.length + " connections but arity is " + getArity() + ".");
-			} else {
-				Double in0 = ((Double) connections[0].getValue());
-				Double in1 = ((Double) connections[1].getValue());
-				return in0 + in1;
-			}
-		}
-
-		@Override
-		public int getArity() {
-			return 2;
-		}
-
-		@Override
-		public String getName() {
-			return "Addition";
-		}
-	}
-
-	/**
-	 * Subtraction returns the difference between inputs 0 and 1.
-	 *
-	 */
-	public static class Subtraction extends Function {
-		@Override
-		public Double run(Connection... connections) {
-			if (connections.length < getArity()) {
-				throw new IllegalArgumentException(getName() + " received " + connections.length + " connections but arity is " + getArity() + ".");
-			} else {
-				Double in0 = ((Double) connections[0].getValue());
-				Double in1 = ((Double) connections[1].getValue());
-				return in0 - in1;
-			}
-		}
-
-		@Override
-		public int getArity() {
-			return 2;
-		}
-
-		@Override
-		public String getName() {
-			return "Subtraction";
-		}
-	}
-
-	/**
-	 * Multiplication returns the product of inputs 0 and 1.
-	 *
-	 */
-	public static class Multiplication extends Function {
-		@Override
-		public Double run(Connection... connections) {
-			if (connections.length < getArity()) {
-				throw new IllegalArgumentException(getName() + " received " + connections.length + " connections but arity is " + getArity() + ".");
-			} else {
-				Double in0 = ((Double) connections[0].getValue());
-				Double in1 = ((Double) connections[1].getValue());
-				return in0 * in1;
-			} 
-		}
-
-		@Override
-		public int getArity() {
-			return 2;
-		}
-
-		@Override
-		public String getName() {
-			return "Multiplication";
-		}
-	}
-
-	/**
-	 * Protected division, returns the quotient of input 0 (the dividend) and input 1 (the divisor).
-	 * If the divisor is less than {@link DoubleArithmetic.}DIVISION_LIMIT, this returns the it unchanged.
-	 *
-	 */
-	public static class Division extends Function {
-		@Override
-		public Double run(Connection... connections) {
-			if (connections.length < getArity()) {
-				throw new IllegalArgumentException(getName() + " received " + connections.length + " connections but arity is " + getArity() + ".");
-			} else {
-				Double in0 = ((Double) connections[0].getValue());
-				Double in1 = ((Double) connections[1].getValue());
-
-				return in1 < DIVISION_LIMIT ? in0 : (in0 / in1);
-			} 
-		}
-
-		@Override
-		public int getArity() {
-			return 2;
-		}
-
-		@Override
-		public String getName() {
-			return "Division";
-		}
-	}
-}
diff --git a/src/jcgp/backend/function/Function.java b/src/jcgp/backend/function/Function.java
index 30bbcf0..fdacac0 100644
--- a/src/jcgp/backend/function/Function.java
+++ b/src/jcgp/backend/function/Function.java
@@ -1,13 +1,28 @@
 package jcgp.backend.function;
 
-import jcgp.backend.exceptions.InvalidArgumentsException;
-import jcgp.backend.population.Connection;
-
+/**
+ * Function is a callback wrapper. 
+ * <br><br>
+ * A concrete implementation of Function overrides {@code run()} to perform
+ * any arbitrary operation on the arguments specified. It must also override
+ * {@code getArity()} to return the function arity.
+ * 
+ * 
+ * @author Eduardo Pedroni
+ *
+ */
 public abstract class Function {
-			
-	public abstract Object run(Connection ... connections) throws InvalidArgumentsException;
 	
-	public abstract int getArity();
+	/**
+	 * Executes the function.
+	 * 
+	 * @param args the function arguments
+	 * @return the function result
+	 */
+	public abstract Object run(Object... args);
 	
-	public abstract String getName();	
+	/**
+	 * @return the arity of the function.
+	 */
+	public abstract int getArity();
 }
diff --git a/src/jcgp/backend/function/FunctionSet.java b/src/jcgp/backend/function/FunctionSet.java
index 1712b51..926ed68 100644
--- a/src/jcgp/backend/function/FunctionSet.java
+++ b/src/jcgp/backend/function/FunctionSet.java
@@ -6,6 +6,22 @@ import java.util.Iterator;
 
 
 /**
+ * FunctionSet encapsulates a group of functions. This is usually done to
+ * simplify the implementation of problem types.
+ * <br><br>
+ * FunctionSet contains a variety of useful methods for acquiring general
+ * information, such as the maximum arity across all functions and the total
+ * number of functions.
+ * <br><br>
+ * In addition, FunctionSet offers the ability to enable and disable functions.
+ * Accessing the functions through {@code getAllowedFunction()} will return
+ * allowed functions only, providing an easy way to control which functions
+ * can be used in mutations.
+ * <br><br>
+ * An implementation of FunctionSet must simply set the name field and initialise
+ * the functionList array with all of the functions. It is advisable to call
+ * {@code enableAll()} to enable all functions once the array is initialised.
+ * 
  * 
  * @author Eduardo Pedroni
  *
@@ -15,25 +31,55 @@ public abstract class FunctionSet {
 		protected ArrayList<Integer> allowedFunctions;
 		protected String name;
 		
+		/**
+		 * @return the number of currently allowed functions.
+		 */
 		public int getAllowedFunctionCount() {
 			return allowedFunctions.size();
 		}
 		
+		/**
+		 * @return the total number of functions, including disabled ones.
+		 */
 		public int getTotalFunctionCount() {
 			return functionList.length;
 		}
 		
+		/**
+		 * Returns an allowed function. This throws an
+		 * ArrayIndexOutOfBoundsException if the supplied 
+		 * index is beyond the count of allowed functions.
+		 * 
+		 * @param index the allowed function index.
+		 * @return the allowed function object.
+		 */
 		public Function getAllowedFunction(int index) {
 			return functionList[allowedFunctions.get(index)];
 		}
 		
+		/**
+		 * Returns a function from the complete collection,
+		 * enabled or disabled alike. This throws an
+		 * ArrayIndexOutOfBoundsException if the supplied 
+		 * index is beyond the count of allowed functions.
+		 * 
+		 * @param index the function index.
+		 * @return the function object.
+		 */
 		public Function getFunction(int index) {
 			return functionList[index];
 		}
 		
+		/**
+		 * Computes and returns the maximum arity out of
+		 * all the function, enabled or disabled.
+		 * 
+		 * @return
+		 */
 		public int getMaxArity(){
 			int arity = 0;
 			for (Function function : functionList) {
+				// if a higher arity is found, store it
 				if (function.getArity() > arity) {
 					arity = function.getArity();
 				}
@@ -41,25 +87,39 @@ public abstract class FunctionSet {
 			return arity;
 		}
 		
-		public String getName() {
-			return name;
-		}
-		
+		/**
+		 * Disables the indexed function. If the function
+		 * is already disabled, this does nothing.
+		 * 
+		 * @param index the function to disable.
+		 */
 		public void disableFunction(int index) {
+			/*
+			 * allowedFunctions is a list of the indices of all allowed functions, 
+			 * as addressed in functionList. This method iterates through the whole
+			 * list of allowed functions and removes any elements which are equal
+			 * to the specified index.
+			 */
 			if (index < functionList.length) {
 				for (Iterator<Integer> iterator = allowedFunctions.iterator(); iterator.hasNext();) {
 					int function = iterator.next();
 					if (function == index) {
 						iterator.remove();
-						break;
 					}
 				}
 			} else {
-				throw new IndexOutOfBoundsException("Function " + index + " does not exist, the set only has " + functionList.length + " functions.");
+				throw new ArrayIndexOutOfBoundsException("Function " + index + " does not exist, the set only has " + functionList.length + " functions.");
 			}
 		}
 		
+		/**
+		 * Disables the indexed function. If the function is
+		 * already enabled, this does nothing. 
+		 * 
+		 * @param index the function to disable.
+		 */
 		public void enableFunction(int index) {
+			// add the specified index to the list of allowed indices
 			if (!allowedFunctions.contains(index)) {
 				allowedFunctions.add(index);
 				Collections.sort(allowedFunctions);
@@ -71,16 +131,26 @@ public abstract class FunctionSet {
 			return name;
 		}
 		
-		public boolean isEnabled(Function f) {
+		/**
+		 * Checks if a specified function is enabled. If the function
+		 * does not belong in the FunctionSet, this returns false.
+		 * 
+		 * @param function the function to check.
+		 * @return true if the function is enabled.
+		 */
+		public boolean isEnabled(Function function) {
 			for (int i = 0; i < allowedFunctions.size(); i++) {
-				if (functionList[allowedFunctions.get(i)] == f) {
+				if (functionList[allowedFunctions.get(i)] == function) {
 					return true;
 				}
 			}
 			return false;
 		}
 		
-		protected void enableAll() {
+		/**
+		 * Enables all functions. 
+		 */
+		public void enableAll() {
 			allowedFunctions = new ArrayList<Integer>();
 			for (int i = 0; i < functionList.length; i++) {
 				allowedFunctions.add(i);
diff --git a/src/jcgp/backend/function/SymbolicRegressionFunctions.java b/src/jcgp/backend/function/SymbolicRegressionFunctions.java
new file mode 100644
index 0000000..a35f258
--- /dev/null
+++ b/src/jcgp/backend/function/SymbolicRegressionFunctions.java
@@ -0,0 +1,587 @@
+package jcgp.backend.function;
+
+public class SymbolicRegressionFunctions extends FunctionSet {
+	
+	public final static double DIVISION_LIMIT = 0.0001;
+	
+	public SymbolicRegressionFunctions() {
+		name = "Symbolic regression functions";
+		functionList = new Function[] {
+				new Absolute(),
+				new SquareRoot(),
+				new Reciprocal(),
+				new Sine(),
+				new Cosine(),
+				new Tangent(),
+				new Exponential(),
+				new HyperbolicSine(),
+				new HyperbolicCosine(),
+				new HyperbolicTangent(),
+				new NaturalLog(),
+				new LogBaseTen(),
+				new SineAB(),
+				new CosineAB(),
+				new Hypotenuse(),
+				new Power(),
+				new Addition(),
+				new Subtraction(),
+				new Multiplication(),
+				new Division()};
+		
+		enableAll();
+	}
+	
+	/**
+	 * Absolute returns the positive value of input 0.
+	 * 
+	 * @see Math
+	 */
+	public static class Absolute extends Function {
+		@Override
+		public Double run(Object... args) {
+			if (args.length < getArity()) {
+				throw new IllegalArgumentException(toString() + " received " + args.length + " arguments but arity is " + getArity() + ".");
+			} else {
+				Double in0 = ((Double) args[0]);
+				return Math.abs(in0);
+			}
+		}
+
+		@Override
+		public int getArity() {
+			return 1;
+		}
+
+		@Override
+		public String toString() {
+			return "Absolute";
+		}
+	}
+	
+	/**
+	 * Protected square root function, returns the square root of the absolute
+	 * value of input 0.
+	 * 
+	 * @see Math
+	 */
+	public static class SquareRoot extends Function {
+		@Override
+		public Double run(Object... args) {
+			if (args.length < getArity()) {
+				throw new IllegalArgumentException(toString() + " received " + args.length + " arguments but arity is " + getArity() + ".");
+			} else {
+				Double in0 = ((Double) args[0]);
+				return Math.sqrt(Math.abs(in0));
+			}
+		}
+
+		@Override
+		public int getArity() {
+			return 1;
+		}
+
+		@Override
+		public String toString() {
+			return "Square root";
+		}
+	}
+	
+	/**
+	 * Protected reciprocal function, returns (1 / input 0). If input 0 is less than
+	 * {@code DoubleArithmetic.DIVISION_LIMIT}, this returns it unchanged.
+	 *
+	 */
+	public static class Reciprocal extends Function {
+		@Override
+		public Double run(Object... args) {
+			if (args.length < getArity()) {
+				throw new IllegalArgumentException(toString() + " received " + args.length + " arguments but arity is " + getArity() + ".");
+			} else {
+				Double in0 = ((Double) args[0]);
+				return in0 < DIVISION_LIMIT ? in0 : (1 / in0);
+			}
+		}
+
+		@Override
+		public int getArity() {
+			return 1;
+		}
+
+		@Override
+		public String toString() {
+			return "Reciprocal";
+		}
+	}
+	
+	/**
+	 * Sine function, in radians.
+	 *
+	 * @see Math
+	 */
+	public static class Sine extends Function {
+		@Override
+		public Double run(Object... args) {
+			if (args.length < getArity()) {
+				throw new IllegalArgumentException(toString() + " received " + args.length + " arguments but arity is " + getArity() + ".");
+			} else {
+				Double in0 = ((Double) args[0]);
+				return Math.sin(in0);
+			}
+		}
+
+		@Override
+		public int getArity() {
+			return 1;
+		}
+
+		@Override
+		public String toString() {
+			return "Sin";
+		}
+	}
+	
+	/**
+	 * Cosine function, in radians.
+	 *
+	 * @see Math
+	 */
+	public static class Cosine extends Function {
+		@Override
+		public Double run(Object... args) {
+			if (args.length < getArity()) {
+				throw new IllegalArgumentException(toString() + " received " + args.length + " arguments but arity is " + getArity() + ".");
+			} else {
+				Double in0 = ((Double) args[0]);
+				return Math.cos(in0);
+			}
+		}
+
+		@Override
+		public int getArity() {
+			return 1;
+		}
+
+		@Override
+		public String toString() {
+			return "Cos";
+		}
+	}
+	
+	/**
+	 * Protected tangent function, in radians. Returns the tangent of input 0.
+	 * If input 0 is less than {@link DoubleArithmetic.}DIVISION_LIMIT, 
+	 * this returns it unchanged.
+	 *
+	 * @see Math
+	 */
+	public static class Tangent extends Function {
+		@Override
+		public Double run(Object... args) {
+			if (args.length < getArity()) {
+				throw new IllegalArgumentException(toString() + " received " + args.length + " arguments but arity is " + getArity() + ".");
+			} else {
+				Double in0 = ((Double) args[0]);
+				return in0 < DIVISION_LIMIT ? in0 : Math.tan(in0);
+			}
+		}
+
+		@Override
+		public int getArity() {
+			return 1;
+		}
+
+		@Override
+		public String toString() {
+			return "Tan";
+		}
+	}
+	
+	/**
+	 * Exponential function. Returns the exponential of input 0.
+	 *
+	 * @see Math
+	 */
+	public static class Exponential extends Function {
+		@Override
+		public Double run(Object... args) {
+			if (args.length < getArity()) {
+				throw new IllegalArgumentException(toString() + " received " + args.length + " arguments but arity is " + getArity() + ".");
+			} else {
+				Double in0 = ((Double) args[0]);
+				return Math.exp(in0);
+			}
+		}
+
+		@Override
+		public int getArity() {
+			return 1;
+		}
+
+		@Override
+		public String toString() {
+			return "Exp";
+		}
+	}
+	
+	/**
+	 * Returns the hyperbolic sine of input 0.
+	 *
+	 * @see Math
+	 */
+	public static class HyperbolicSine extends Function {
+		@Override
+		public Double run(Object... args) {
+			if (args.length < getArity()) {
+				throw new IllegalArgumentException(toString() + " received " + args.length + " arguments but arity is " + getArity() + ".");
+			} else {
+				Double in0 = ((Double) args[0]);
+				return Math.sinh(in0);
+			}
+		}
+
+		@Override
+		public int getArity() {
+			return 1;
+		}
+
+		@Override
+		public String toString() {
+			return "Sinh";
+		}
+	}
+	
+	/**
+	 * Returns the hyperbolic cosine of input 0.
+	 *
+	 * @see Math
+	 */
+	public static class HyperbolicCosine extends Function {
+		@Override
+		public Double run(Object... args) {
+			if (args.length < getArity()) {
+				throw new IllegalArgumentException(toString() + " received " + args.length + " arguments but arity is " + getArity() + ".");
+			} else {
+				Double in0 = ((Double) args[0]);
+				return Math.cosh(in0);
+			}
+		}
+
+		@Override
+		public int getArity() {
+			return 1;
+		}
+
+		@Override
+		public String toString() {
+			return "Cosh";
+		}
+	}
+	
+	/**
+	 * Returns the hyperbolic tangent of input 0.
+	 *
+	 * @see Math
+	 */
+	public static class HyperbolicTangent extends Function {
+		@Override
+		public Double run(Object... args) {
+			if (args.length < getArity()) {
+				throw new IllegalArgumentException(toString() + " received " + args.length + " arguments but arity is " + getArity() + ".");
+			} else {
+				Double in0 = ((Double) args[0]);
+				return Math.tanh(in0);
+			}
+		}
+
+		@Override
+		public int getArity() {
+			return 1;
+		}
+
+		@Override
+		public String toString() {
+			return "Tanh";
+		}
+	}
+	
+	/**
+	 * Protected natural log function. Returns the natural log of the absolute
+	 * value of input 0. If input 0 is less than {@link DoubleArithmetic.}DIVISION_LIMIT, 
+	 * this returns it unchanged.
+	 *
+	 * @see Math
+	 */
+	public static class NaturalLog extends Function {
+		@Override
+		public Double run(Object... args) {
+			if (args.length < getArity()) {
+				throw new IllegalArgumentException(toString() + " received " + args.length + " arguments but arity is " + getArity() + ".");
+			} else {
+				Double in0 = ((Double) args[0]);
+				return in0 < DIVISION_LIMIT ? in0 : Math.log(Math.abs(in0));
+			}
+		}
+
+		@Override
+		public int getArity() {
+			return 1;
+		}
+
+		@Override
+		public String toString() {
+			return "Ln";
+		}
+	}
+	
+	/**
+	 * Protected log base 10 function. Returns the log to base 10 the absolute
+	 * value of input 0. If input 0 is less than {@link DoubleArithmetic.}DIVISION_LIMIT, 
+	 * this returns it unchanged.
+	 *
+	 * @see Math
+	 */
+	public static class LogBaseTen extends Function {
+		@Override
+		public Double run(Object... args) {
+			if (args.length < getArity()) {
+				throw new IllegalArgumentException(toString() + " received " + args.length + " arguments but arity is " + getArity() + ".");
+			} else {
+				Double in0 = ((Double) args[0]);
+				return in0 < DIVISION_LIMIT ? in0 : Math.log10(Math.abs(in0));
+			}
+		}
+
+		@Override
+		public int getArity() {
+			return 1;
+		}
+
+		@Override
+		public String toString() {
+			return "Log";
+		}
+	}
+	
+	/**
+	 * Sine of sum. Returns the sine of the sum of inputs 0 and 1.
+	 *
+	 * @see Math
+	 */
+	public static class SineAB extends Function {
+		@Override
+		public Double run(Object... args) {
+			if (args.length < getArity()) {
+				throw new IllegalArgumentException(toString() + " received " + args.length + " arguments but arity is " + getArity() + ".");
+			} else {
+				Double in0 = ((Double) args[0]);
+				Double in1 = ((Double) args[1]);
+				return Math.sin(in0 + in1);
+			}
+		}
+
+		@Override
+		public int getArity() {
+			return 2;
+		}
+
+		@Override
+		public String toString() {
+			return "Sin(a+b)";
+		}
+	}
+	
+	/**
+	 * Cosine of sum. Returns the cosine of the sum of inputs 0 and 1.
+	 *
+	 * @see Math
+	 */
+	public static class CosineAB extends Function {
+		@Override
+		public Double run(Object... args) {
+			if (args.length < getArity()) {
+				throw new IllegalArgumentException(toString() + " received " + args.length + " arguments but arity is " + getArity() + ".");
+			} else {
+				Double in0 = ((Double) args[0]);
+				Double in1 = ((Double) args[1]);
+				return Math.cos(in0 + in1);
+			}
+		}
+
+		@Override
+		public int getArity() {
+			return 2;
+		}
+
+		@Override
+		public String toString() {
+			return "Cos(a+b)";
+		}
+	}
+	
+	/**
+	 * Hypotenuse function. Returns the square root of input 0 squared
+	 * plus input 1 squared.
+	 *
+	 * @see Math
+	 */
+	public static class Hypotenuse extends Function {
+		@Override
+		public Double run(Object... args) {
+			if (args.length < getArity()) {
+				throw new IllegalArgumentException(toString() + " received " + args.length + " arguments but arity is " + getArity() + ".");
+			} else {
+				Double in0 = ((Double) args[0]);
+				Double in1 = ((Double) args[1]);
+				return Math.hypot(in0, in1);
+			}
+		}
+
+		@Override
+		public int getArity() {
+			return 2;
+		}
+
+		@Override
+		public String toString() {
+			return "Hypotenuse";
+		}
+	}
+	
+	/**
+	 * Power function. Returns the absolute value of input 0 to the power of input 1.
+	 *
+	 * @see Math
+	 */
+	public static class Power extends Function {
+		@Override
+		public Double run(Object... args) {
+			if (args.length < getArity()) {
+				throw new IllegalArgumentException(toString() + " received " + args.length + " arguments but arity is " + getArity() + ".");
+			} else {
+				Double in0 = ((Double) args[0]);
+				Double in1 = ((Double) args[1]);
+				return Math.pow(Math.abs(in0), in1);
+			}
+		}
+
+		@Override
+		public int getArity() {
+			return 2;
+		}
+
+		@Override
+		public String toString() {
+			return "Power";
+		}
+	}
+	
+	/**
+	 * Addition returns the sum of inputs 0 and 1.
+	 *
+	 */
+	public static class Addition extends Function {
+		@Override
+		public Double run(Object... args) {
+			if (args.length < getArity()) {
+				throw new IllegalArgumentException(toString() + " received " + args.length + " arguments but arity is " + getArity() + ".");
+			} else {
+				Double in0 = ((Double) args[0]);
+				Double in1 = ((Double) args[1]);
+				return in0 + in1;
+			}
+		}
+
+		@Override
+		public int getArity() {
+			return 2;
+		}
+
+		@Override
+		public String toString() {
+			return "Addition";
+		}
+	}
+
+	/**
+	 * Subtraction returns the difference between inputs 0 and 1.
+	 *
+	 */
+	public static class Subtraction extends Function {
+		@Override
+		public Double run(Object... args) {
+			if (args.length < getArity()) {
+				throw new IllegalArgumentException(toString() + " received " + args.length + " arguments but arity is " + getArity() + ".");
+			} else {
+				Double in0 = ((Double) args[0]);
+				Double in1 = ((Double) args[1]);
+				return in0 - in1;
+			}
+		}
+
+		@Override
+		public int getArity() {
+			return 2;
+		}
+
+		@Override
+		public String toString() {
+			return "Subtraction";
+		}
+	}
+
+	/**
+	 * Multiplication returns the product of inputs 0 and 1.
+	 *
+	 */
+	public static class Multiplication extends Function {
+		@Override
+		public Double run(Object... args) {
+			if (args.length < getArity()) {
+				throw new IllegalArgumentException(toString() + " received " + args.length + " arguments but arity is " + getArity() + ".");
+			} else {
+				Double in0 = ((Double) args[0]);
+				Double in1 = ((Double) args[1]);
+				return in0 * in1;
+			} 
+		}
+
+		@Override
+		public int getArity() {
+			return 2;
+		}
+
+		@Override
+		public String toString() {
+			return "Multiplication";
+		}
+	}
+
+	/**
+	 * Protected division, returns the quotient of input 0 (the dividend) and input 1 (the divisor).
+	 * If the divisor is less than {@code DoubleArithmetic.DIVISION_LIMIT}, this returns it unchanged.
+	 *
+	 */
+	public static class Division extends Function {
+		@Override
+		public Double run(Object... args) {
+			if (args.length < getArity()) {
+				throw new IllegalArgumentException(toString() + " received " + args.length + " arguments but arity is " + getArity() + ".");
+			} else {
+				Double in0 = ((Double) args[0]);
+				Double in1 = ((Double) args[1]);
+
+				return in1 < DIVISION_LIMIT ? in0 : (in0 / in1);
+			} 
+		}
+
+		@Override
+		public int getArity() {
+			return 2;
+		}
+
+		@Override
+		public String toString() {
+			return "Division";
+		}
+	}
+}
diff --git a/src/jcgp/backend/function/TravellingSalesmanFunctions.java b/src/jcgp/backend/function/TravellingSalesmanFunctions.java
new file mode 100644
index 0000000..472b7ad
--- /dev/null
+++ b/src/jcgp/backend/function/TravellingSalesmanFunctions.java
@@ -0,0 +1,396 @@
+package jcgp.backend.function;
+
+public class TravellingSalesmanFunctions extends FunctionSet {
+		
+	public TravellingSalesmanFunctions() {
+		name = "Travelling salesman functions";
+		functionList = new Function[]{
+				new SquareRoot(),
+				new Square(),
+				new Cube(),
+				new ScaledExponential(),
+				new AbsoluteSineAB(),
+				new AbsoluteCosineAB(),
+				new AbsoluteHyperbolicTangentAB(),
+				new ScaledHypotenuse(),
+				new ScaledAddition(),
+				new SymmetricSubtraction(),
+				new Multiplication(),
+				new BoundedDivision() };
+		
+		enableAll();
+	}
+	
+	/**
+	 * Protected square root function, returns the square root of the absolute
+	 * value of input 0.
+	 * 
+	 * @see Math
+	 */
+	public static class SquareRoot extends Function {
+		@Override
+		public Double run(Object... args) {
+			if (args.length < getArity()) {
+				throw new IllegalArgumentException(toString() + " received " + args.length + " arguments but arity is " + getArity() + ".");
+			} else {
+				Double in0 = ((Double) args[0]);
+				return Math.sqrt(Math.abs(in0));
+			}
+		}
+
+		@Override
+		public int getArity() {
+			return 1;
+		}
+
+		@Override
+		public String toString() {
+			return "Square root";
+		}
+	}
+	
+	/**
+	 * Square function, returns the square of the
+	 * value of input 0.
+	 * 
+	 */
+	public static class Square extends Function {
+		@Override
+		public Double run(Object... args) {
+			if (args.length < getArity()) {
+				throw new IllegalArgumentException(toString() + " received " + args.length + " arguments but arity is " + getArity() + ".");
+			} else {
+				Double in0 = ((Double) args[0]);
+				return in0 * in0;
+			}
+		}
+
+		@Override
+		public int getArity() {
+			return 1;
+		}
+
+		@Override
+		public String toString() {
+			return "Square";
+		}
+	}
+	
+	/**
+	 * Cube function, returns the value of input 0 cubed.
+	 * 
+	 */
+	public static class Cube extends Function {
+		@Override
+		public Double run(Object... args) {
+			if (args.length < getArity()) {
+				throw new IllegalArgumentException(toString() + " received " + args.length + " arguments but arity is " + getArity() + ".");
+			} else {
+				Double in0 = ((Double) args[0]);
+				return in0 * in0 * in0;
+			}
+		}
+
+		@Override
+		public int getArity() {
+			return 1;
+		}
+
+		@Override
+		public String toString() {
+			return "Cube";
+		}
+	}
+	
+	/**
+	 * Scaled exponential function. Returns the exponential of input 0 
+	 * scaled to the range 0 < x < 1.
+	 *
+	 * @see Math
+	 */
+	public static class ScaledExponential extends Function {
+		@Override
+		public Double run(Object... args) {
+			if (args.length < getArity()) {
+				throw new IllegalArgumentException(toString() + " received " + args.length + " arguments but arity is " + getArity() + ".");
+			} else {
+				Double in0 = ((Double) args[0]);
+				return (Math.exp(in0) - 1) / (Math.exp(-1) - 1);
+			}
+		}
+
+		@Override
+		public int getArity() {
+			return 1;
+		}
+
+		@Override
+		public String toString() {
+			return "Scaled Exp";
+		}
+	}
+	
+	/**
+	 * Sine of sum. Returns the absolute value of the sine 
+	 * of the sum of inputs 0 and 1, in radians.
+	 *
+	 * @see Math
+	 */
+	public static class AbsoluteSineAB extends Function {
+		@Override
+		public Double run(Object... args) {
+			if (args.length < getArity()) {
+				throw new IllegalArgumentException(toString() + " received " + args.length + " arguments but arity is " + getArity() + ".");
+			} else {
+				Double in0 = ((Double) args[0]);
+				Double in1 = ((Double) args[1]);
+				return Math.abs(Math.sin(in0 + in1));
+			}
+		}
+
+		@Override
+		public int getArity() {
+			return 2;
+		}
+
+		@Override
+		public String toString() {
+			return "Abs Sin(a+b)";
+		}
+	}
+	
+	/**
+	 * Cosine of sum. Returns the absolute value of the cosine 
+	 * of the sum of inputs 0 and 1, in radians.
+	 *
+	 * @see Math
+	 */
+	public static class AbsoluteCosineAB extends Function {
+		@Override
+		public Double run(Object... args) {
+			if (args.length < getArity()) {
+				throw new IllegalArgumentException(toString() + " received " + args.length + " arguments but arity is " + getArity() + ".");
+			} else {
+				Double in0 = ((Double) args[0]);
+				Double in1 = ((Double) args[1]);
+				return Math.abs(Math.cos(in0 + in1));
+			}
+		}
+
+		@Override
+		public int getArity() {
+			return 2;
+		}
+
+		@Override
+		public String toString() {
+			return "Abs Cos(a+b)";
+		}
+	}
+	
+	/**
+	 * Hyperbolic tangent of sum. Returns the absolute value of the sine 
+	 * of the sum of inputs 0 and 1, in radians.
+	 *
+	 * @see Math
+	 */
+	public static class AbsoluteHyperbolicTangentAB extends Function {
+		@Override
+		public Double run(Object... args) {
+			if (args.length < getArity()) {
+				throw new IllegalArgumentException(toString() + " received " + args.length + " arguments but arity is " + getArity() + ".");
+			} else {
+				Double in0 = ((Double) args[0]);
+				Double in1 = ((Double) args[1]);
+				return Math.abs(Math.tanh(in0 + in1));
+			}
+		}
+
+		@Override
+		public int getArity() {
+			return 2;
+		}
+
+		@Override
+		public String toString() {
+			return "Abs Tanh(a+b)";
+		}
+	}
+	
+	/**
+	 * Scaled hypotenuse function. Returns the square root of input 0 squared
+	 * plus input 1 squared, scaled to the range 0 < x < 1.
+	 *
+	 * @see Math
+	 */
+	public static class ScaledHypotenuse extends Function {
+		@Override
+		public Double run(Object... args) {
+			if (args.length < getArity()) {
+				throw new IllegalArgumentException(toString() + " received " + args.length + " arguments but arity is " + getArity() + ".");
+			} else {
+				Double in0 = ((Double) args[0]);
+				Double in1 = ((Double) args[1]);
+				return Math.hypot(in0, in1) / Math.sqrt(2);
+			}
+		}
+
+		@Override
+		public int getArity() {
+			return 2;
+		}
+
+		@Override
+		public String toString() {
+			return "Scaled Hypotenuse";
+		}
+	}
+	
+	/**
+	 * Scaled addition returns the sum of inputs 0 and 1 scaled
+	 * to the range 0 < x < 1.
+	 *
+	 */
+	public static class ScaledAddition extends Function {
+		@Override
+		public Double run(Object... args) {
+			if (args.length < getArity()) {
+				throw new IllegalArgumentException(toString() + " received " + args.length + " arguments but arity is " + getArity() + ".");
+			} else {
+				Double in0 = ((Double) args[0]);
+				Double in1 = ((Double) args[1]);
+				return (in0 + in1) / 2.0;
+			}
+		}
+
+		@Override
+		public int getArity() {
+			return 2;
+		}
+
+		@Override
+		public String toString() {
+			return "Scaled Addition";
+		}
+	}
+
+	/**
+	 * Symmetric subtraction returns the absolute difference between inputs 0 and 1,
+	 * scaled to the range 0 < x < 1.
+	 *
+	 */
+	public static class SymmetricSubtraction extends Function {
+		@Override
+		public Double run(Object... args) {
+			if (args.length < getArity()) {
+				throw new IllegalArgumentException(toString() + " received " + args.length + " arguments but arity is " + getArity() + ".");
+			} else {
+				Double in0 = ((Double) args[0]);
+				Double in1 = ((Double) args[1]);
+				return Math.abs(in0 - in1) / 2.0;
+			}
+		}
+
+		@Override
+		public int getArity() {
+			return 2;
+		}
+
+		@Override
+		public String toString() {
+			return "Symmetric Subtraction";
+		}
+	}
+
+	/**
+	 * Multiplication returns the product of inputs 0 and 1.
+	 *
+	 */
+	public static class Multiplication extends Function {
+		@Override
+		public Double run(Object... args) {
+			if (args.length < getArity()) {
+				throw new IllegalArgumentException(toString() + " received " + args.length + " arguments but arity is " + getArity() + ".");
+			} else {
+				Double in0 = ((Double) args[0]);
+				Double in1 = ((Double) args[1]);
+				return in0 * in1;
+			} 
+		}
+
+		@Override
+		public int getArity() {
+			return 2;
+		}
+
+		@Override
+		public String toString() {
+			return "Multiplication";
+		}
+	}
+	
+	/**
+	 * Multiplication returns the product of inputs 0 and 1, squared.
+	 *
+	 */
+	public static class SquaredMultiplication extends Function {
+		@Override
+		public Double run(Object... args) {
+			if (args.length < getArity()) {
+				throw new IllegalArgumentException(toString() + " received " + args.length + " arguments but arity is " + getArity() + ".");
+			} else {
+				Double in0 = ((Double) args[0]);
+				Double in1 = ((Double) args[1]);
+				return in0 * in1 * in0 * in1;
+			} 
+		}
+
+		@Override
+		public int getArity() {
+			return 2;
+		}
+
+		@Override
+		public String toString() {
+			return "Squared Multiplication";
+		}
+	}
+
+	/**
+	 * Bounded division, returns the quotient of the two inputs where the larger
+	 * is the denominator. 
+	 *
+	 */
+	public static class BoundedDivision extends Function {
+		@Override
+		public Double run(Object... args) {
+			if (args.length < getArity()) {
+				throw new IllegalArgumentException(toString() + " received " + args.length + " arguments but arity is " + getArity() + ".");
+			} else {
+				Double in0 = Math.abs((Double) args[0]);
+				Double in1 = Math.abs((Double) args[1]);
+				Double result;
+				
+				if (in1 < 1e-10) {
+					result = 1.0;
+				} else if (in1 > in0) {
+					result = in0 / in1;
+				} else {
+					result = in1 / in0;
+				}
+
+				return result;
+			} 
+		}
+
+		@Override
+		public int getArity() {
+			return 2;
+		}
+
+		@Override
+		public String toString() {
+			return "Bounded Division";
+		}
+	}
+}
diff --git a/src/jcgp/backend/modules/Module.java b/src/jcgp/backend/modules/Module.java
index a6b4d73..7efbf3a 100644
--- a/src/jcgp/backend/modules/Module.java
+++ b/src/jcgp/backend/modules/Module.java
@@ -2,8 +2,22 @@ package jcgp.backend.modules;
 
 import jcgp.backend.resources.parameters.Parameter;
 
+/**
+ * This interface defines the expected behaviour of a module. Specifically, a module
+ * is expected to be able to return a list of local parameters. When a user interface
+ * is used, it is expected to display the parameters of each module and allow user
+ * interaction for parameters which are not monitors.
+ * 
+ * @see Parameter
+ * 
+ * @author Eduardo Pedroni
+ *
+ */
 public interface Module {
 	
+	/**
+	 * @return a list of generic parameters exposed by the module.
+	 */
 	public abstract Parameter<?>[] getLocalParameters();
 	
 }
diff --git a/src/jcgp/backend/modules/es/EvolutionaryStrategy.java b/src/jcgp/backend/modules/es/EvolutionaryStrategy.java
index 8ab287d..70e3cd2 100644
--- a/src/jcgp/backend/modules/es/EvolutionaryStrategy.java
+++ b/src/jcgp/backend/modules/es/EvolutionaryStrategy.java
@@ -5,8 +5,42 @@ import jcgp.backend.modules.mutator.Mutator;
 import jcgp.backend.population.Population;
 import jcgp.backend.resources.Resources;
 
+/**
+ * This interface specifies the required behaviour of an evolutionary strategy. The evolutionary
+ * strategy's job is to generate the next population of solutions. In JCGP this is done by modifying
+ * the provided population object rather than creating a new one. 
+ * <br><br>
+ * A typical implementation of EvolutionaryStratey iterates through the chromosomes
+ * in the population and selects the individual(s) to be promoted. It then uses
+ * {@code mutator.mutate()} to generically mutate the promoted individual(s). Parameter-dependent
+ * strategies can be implemented by accessing the parameters via the resources
+ * argument.
+ * <br><br>
+ * Parameters may be specified to control the implemented strategy. Any parameters
+ * returned by {@code getLocalParameters()} should be displayed by the user interface,
+ * if it is being used. See {@link Parameter} for more information. 
+ * <br><br>
+ * It is advisable to use {@code Resources.reportln()} and {@code Resources.report()}
+ * to print any relevant information. Note that reportln() and report() are affected
+ * by the report interval base parameter. Use {@code Resources.println()} and
+ * {@code Resources.print()} to print information regardless of the current generation.
+ * See {@link Resources} for more information.
+ * 
+ * @see Module
+ * 
+ * @author Eduardo Pedroni
+ *
+ */
 public interface EvolutionaryStrategy extends Module {
 
+	/**
+	 * Performs the selection algorithm and uses the mutator to create
+	 * the next generation of solutions.
+	 * 
+	 * @param population the population to evolve.
+	 * @param mutator the mutator with which to mutate the promoted individuals.
+	 * @param resources parameters and utilities for optional reference.
+	 */
 	public abstract void evolve(Population population, Mutator mutator, Resources resources);
 	
 }
diff --git a/src/jcgp/backend/modules/es/MuPlusLambda.java b/src/jcgp/backend/modules/es/MuPlusLambda.java
index 6a3883b..50bf265 100644
--- a/src/jcgp/backend/modules/es/MuPlusLambda.java
+++ b/src/jcgp/backend/modules/es/MuPlusLambda.java
@@ -9,41 +9,59 @@ import jcgp.backend.resources.parameters.Parameter;
 import jcgp.backend.resources.parameters.ParameterStatus;
 
 /**
- * (μ + λ) EA.
- * 
+ * (μ + λ)-ES
+ * <br><br>
+ * This strategy selects the μ fittest chromosomes from the population.
+ * The promoted individuals are copied into the new population and mutated
+ * λ times, but also carried forward unchanged. The total population size
+ * is μ + λ. 
+ * <br><br>
+ * Two integer parameters are used to control this strategy: parents
+ * and offspring. They are constrained in that they must always add up to
+ * the population size, and must never be smaller than 1.
+ * <br>
+ * One additional parameter, report, controls whether a detailed log of the
+ * algorithm's operation is to be printed or not. Reports respect the report
+ * interval base parameter.
  * 
+ * @see EvolutionaryStrategy
  * @author Eduardo Pedroni
  *
  */
 public class MuPlusLambda implements EvolutionaryStrategy {
 	
-	private IntegerParameter parents, offspring;
+	private IntegerParameter mu, lambda;
 	private BooleanParameter report;
 		
+	/**
+	 * Creates a new instance of MuPlusLambda. 
+	 * 
+	 * @param resources a reference to the experiment's resources.
+	 */
 	public MuPlusLambda(final Resources resources) {
-		parents = new IntegerParameter(1, "Parents") {
+		mu = new IntegerParameter(1, "Parents (μ)") {
 			@Override
 			public void validate(Number newValue) {
-				if (newValue.intValue() + offspring.get() != resources.populationSize()) {
+				if (newValue.intValue() + lambda.get() != resources.populationSize()) {
 					status = ParameterStatus.INVALID;
 					status.setDetails("Parents + offspring must equal population size.");
 				} else if (newValue.intValue() <= 0) {
 					status = ParameterStatus.INVALID;
-					status.setDetails("EA needs at least 1 parent.");
+					status.setDetails("ES needs at least 1 parent.");
 				} else {
 					status = ParameterStatus.VALID;
 				}
 			}
 		};
-		offspring = new IntegerParameter(4, "Offspring") {
+		lambda = new IntegerParameter(4, "Offspring (λ)") {
 			@Override
 			public void validate(Number newValue) {
-				if (newValue.intValue() + parents.get() != resources.populationSize()) {
+				if (newValue.intValue() + mu.get() != resources.populationSize()) {
 					status = ParameterStatus.INVALID;
 					status.setDetails("Parents + offspring must equal population size.");
 				} else if (newValue.intValue() <= 0) {
 					status = ParameterStatus.INVALID;
-					status.setDetails("EA needs at least 1 offspring.");
+					status.setDetails("ES needs at least 1 offspring.");
 				} else {
 					status = ParameterStatus.VALID;
 				}
@@ -58,32 +76,31 @@ public class MuPlusLambda implements EvolutionaryStrategy {
 	}
 	
 	@Override
-	public void evolve(Population population, Mutator mutator, Resources resources) {
-		// select fittest chromosomes
-		if (report.get()) resources.reportln("[ES] Selected chromosome: " + population.getFittestIndex());
-		
-		// create copies of fittest chromosome, mutate them
-		for (int i = 0; i < resources.populationSize(); i++) {
-			if (i != population.getFittestIndex()) {
-				if (report.get()) resources.reportln("[ES] Copying fittest chromosome to population position " + i);
-				population.copyChromosome(population.getFittestIndex(), i);
-				if (report.get()) resources.reportln("[ES] Mutating copied chromosome");
-				mutator.mutate(population.getChromosome(i), resources);
-			}
+	public void evolve(Population population, Mutator mutator, Resources resources) {		
+		/* Population is sorted in ascending order of fitness, so leave the last
+		 * mu chromosomes intact
+		 */
+		for (int i = 0; i < resources.populationSize() - mu.get(); i++) {
+			// select a random parent out of the lambda offspring individuals
+			int randomParent = resources.populationSize() - 1 - resources.getRandomInt(mu.get());
+			if (report.get()) resources.reportln("[ES] Copying Chr " + randomParent + " to population position " + i);
+			population.copyChromosome(randomParent, i);
+			
+			// mutate selected chromosome
+			if (report.get()) resources.reportln("[ES] Mutating copied chromosome");
+			mutator.mutate(population.getChromosome(i), resources);
 		}
 		
-		if (report.get()) resources.reportln("[ES] Generation is complete.");
-		
+		if (report.get()) resources.reportln("[ES] Generation is complete");
 	}
 
 	@Override
 	public Parameter<?>[] getLocalParameters() {
-		return new Parameter[] {parents, offspring, report};
+		return new Parameter[] {mu, lambda, report};
 	}
 
 	@Override
 	public String toString() {
 		return "(μ + λ)";
 	}
-	
 }
diff --git a/src/jcgp/backend/modules/es/TournamentSelection.java b/src/jcgp/backend/modules/es/TournamentSelection.java
index 7cc9706..43fea81 100644
--- a/src/jcgp/backend/modules/es/TournamentSelection.java
+++ b/src/jcgp/backend/modules/es/TournamentSelection.java
@@ -1,35 +1,118 @@
 package jcgp.backend.modules.es;
 
+import java.util.Arrays;
+
 import jcgp.backend.modules.mutator.Mutator;
+import jcgp.backend.population.Chromosome;
 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;
 
+/**
+ * Tournament selection
+ * <br><br>
+ * This strategy generates a new population by selecting a specified number
+ * of chromosomes from the original population and selecting the fittest out
+ * of the isolated subset (the tournament). The selected individual is mutated
+ * using the specified mutator. This process is repeated until the new population
+ * is complete.
+ * <br><br>
+ * One integer parameter is used to control this strategy: tournament
+ * size. This must always be greater than 0 and smaller than or equal to the
+ * population size. Setting it to equal population size results in the same
+ * chromosome being selected for every tournament, and setting it to 1 leads
+ * to an effectively random search.
+ * <br>
+ * One additional parameter, report, controls whether a detailed log of the
+ * algorithm's operation is to be printed or not. Reports respect the report
+ * interval base parameter.
+ * 
+ * @see EvolutionaryStrategy
+ * @author Eduardo Pedroni
+ *
+ */
 public class TournamentSelection implements EvolutionaryStrategy {
 	
 	private IntegerParameter tournamentSize;
+	private BooleanParameter report;
 	
-	public TournamentSelection(Resources resources) {		
+	/**
+	 * Creates a new instance of TournamentSelection. 
+	 * 
+	 * @param resources a reference to the experiment's resources.
+	 */
+	public TournamentSelection(final Resources resources) {		
 		tournamentSize = new IntegerParameter(1, "Tournament size") {
 			@Override
 			public void validate(Number newValue) {
-				// TODO this
+				if (newValue.intValue() <= 0) {
+					status = ParameterStatus.INVALID;
+					status.setDetails("Tournament size must be greater than 0.");
+				} else if (newValue.intValue() > resources.populationSize()) {
+					status = ParameterStatus.INVALID;
+					status.setDetails("Tournament size must not be greater than the population size.");
+				} else if (newValue.intValue() == 1) {
+					status = ParameterStatus.WARNING;
+					status.setDetails("A tournament size of 1 results in a random search.");
+				} else if (newValue.intValue() == resources.populationSize()) {
+					status = ParameterStatus.WARNING;
+					status.setDetails("A tournament size equal to population size results in the same individual being selected every time.");
+				} else {
+					status = ParameterStatus.VALID;
+				}
+			}
+		};
+		report = new BooleanParameter(false, "Report") {
+			@Override
+			public void validate(Boolean newValue) {
+				// blank
 			}
 		};
 	}
 
 	@Override
 	public Parameter<?>[] getLocalParameters() {
-		return new Parameter[] {tournamentSize};
+		return new Parameter[] {tournamentSize, report};
 	}
 
 	@Override
-	public void evolve(Population population, Mutator mutator,
-			Resources parameters) {
-		tournamentSize.set(tournamentSize.get() + 1);
-		// TODO implement this
-
+	public void evolve(Population population, Mutator mutator, Resources resources) {
+		/* Create an entirely new population by isolating random subsets of
+		 * the original population and choosing the fittest individual within
+		 * that subset. Each chosen individual is mutated and copied back into the
+		 * population.
+		 */
+		Chromosome[] newPopulation = new Chromosome[resources.populationSize()];
+		
+		// start by selecting all of the chromosomes that will be promoted
+		for (int i = 0; i < resources.populationSize(); i++) {
+			if (report.get()) resources.reportln("[ES] Starting tournament " + i);
+			
+			/* the population is sorted in ascending order of fitness,
+			 * meaning the higher the index of the contender, the fitter
+			 * it is
+			 */
+			int[] contenders = new int[tournamentSize.get()];
+			for (int t = 0; t < tournamentSize.get() - 1; t++) {
+				contenders[t] = resources.getRandomInt(resources.populationSize());
+			}
+			if (report.get()) resources.reportln("[ES] Selected contenders: " + Arrays.toString(contenders));
+			Arrays.sort(contenders);
+			if (report.get()) resources.reportln("[ES] Chr " + contenders[contenders.length - 1] + " wins the tournament, copying and mutating...");
+			// create a copy of the selected chromosome and mutate it
+			newPopulation[i] = new Chromosome(population.getChromosome(contenders[contenders.length - 1]));
+			mutator.mutate(newPopulation[i], resources);
+		}
+		if (report.get()) resources.reportln("[ES] Tournaments are finished, copying new chromosomes into population");
+		// newPopulation has been generated, copy into the population
+		for (int c = 0; c < resources.populationSize(); c++) {
+			population.getChromosome(c).copyGenes(newPopulation[c]);
+		}
+		
+		if (report.get()) resources.reportln("[ES] Generation is complete");
 	}
 	
 	@Override
diff --git a/src/jcgp/backend/modules/mutator/FixedPointMutator.java b/src/jcgp/backend/modules/mutator/FixedPointMutator.java
new file mode 100644
index 0000000..4088918
--- /dev/null
+++ b/src/jcgp/backend/modules/mutator/FixedPointMutator.java
@@ -0,0 +1,64 @@
+package jcgp.backend.modules.mutator;
+
+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;
+
+/**
+ * Fixed point mutator
+ * <br><br>
+ * This operator uses the point mutator 
+ * algorithm to mutate a user-defined fixed
+ * number of genes.
+ * 
+ * 
+ * @see PointMutator
+ * @author Eduardo Pedroni
+ *
+ */
+public class FixedPointMutator extends PointMutator {
+
+	private IntegerParameter geneMutated;
+	private BooleanParameter report;
+
+	/**
+	 * Creates a new instance of FixedPointMutator. 
+	 * 
+	 * @param resources a reference to the experiment's resources.
+	 */
+	public FixedPointMutator(final Resources resources) {
+		geneMutated = new IntegerParameter(5, "Genes mutated", false, false) {
+			@Override
+			public void validate(Number newValue) {
+				if (newValue.intValue() <= 0) {
+					status = ParameterStatus.INVALID;
+					status.setDetails("At least 1 mutation must take place.");
+				} else if (newValue.intValue() > (resources.nodes() * (resources.arity() + 1)) + resources.outputs()) {
+					status = ParameterStatus.WARNING;
+					status.setDetails("More genes are mutated than there are genes in the genotype.");
+				} else {
+					status = ParameterStatus.VALID;
+				}
+			}
+		};
+		report = new BooleanParameter(false, "Report") {
+			@Override
+			public void validate(Boolean newValue) {
+				// blank
+			}
+		};
+	}
+
+	@Override
+	public Parameter<?>[] getLocalParameters() {
+		return new Parameter[] {geneMutated, report};
+	}
+
+	@Override
+	public String toString() {
+		return "Fixed point mutation";
+	}
+
+}
diff --git a/src/jcgp/backend/modules/mutator/Mutator.java b/src/jcgp/backend/modules/mutator/Mutator.java
index 1d5b99a..7435cc1 100644
--- a/src/jcgp/backend/modules/mutator/Mutator.java
+++ b/src/jcgp/backend/modules/mutator/Mutator.java
@@ -4,8 +4,35 @@ import jcgp.backend.modules.Module;
 import jcgp.backend.population.Chromosome;
 import jcgp.backend.resources.Resources;
 
+/**
+ * This interface specifies the required behaviour of a mutation operator. Its job is 
+ * to modify the connections and functions of the chromosome according to the operator's
+ * parameters.
+ * <br><br>
+ * Parameters may be specified to control the implemented mutation. Any parameters
+ * returned by {@code getLocalParameters()} should be displayed by the user interface,
+ * if it is being used. See {@link Parameter} for more information. 
+ * <br><br>
+ * It is advisable to use {@code Resources.reportln()} and {@code Resources.report()}
+ * to print any relevant information. Note that reportln() and report() are affected
+ * by the report interval base parameter. Use {@code Resources.println()} and
+ * {@code Resources.print()} to print information regardless of the current generation.
+ * See {@link Resources} for more information.
+ * 
+ * @see Module
+ * 
+ * @author Eduardo Pedroni
+ *
+ */
 public interface Mutator extends Module {
 
+	/**
+	 * Applies mutations to the specified chromosome according
+	 * to the parameter values.
+	 * 
+	 * @param chromosome the chromosome to mutate.
+	 * @param resources parameters and utilities for optional reference.
+	 */
 	void mutate(Chromosome chromosome, Resources resources);
 	
 }
diff --git a/src/jcgp/backend/modules/mutator/PercentPointMutator.java b/src/jcgp/backend/modules/mutator/PercentPointMutator.java
new file mode 100644
index 0000000..4057027
--- /dev/null
+++ b/src/jcgp/backend/modules/mutator/PercentPointMutator.java
@@ -0,0 +1,73 @@
+package jcgp.backend.modules.mutator;
+
+import jcgp.backend.resources.Resources;
+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;
+
+/**
+ * Percent point mutator
+ * <br><br>
+ * This operator calculates how many genes to mutate based on the mutation rate
+ * parameter. The total number of genes is computed from the number of nodes, 
+ * the arity and the number of outputs. It then uses the point mutation 
+ * algorithm to perform the required number of mutations.
+ * 
+ * 
+ * @see PointMutator
+ * @author Eduardo Pedroni
+ *
+ */
+public class PercentPointMutator extends PointMutator {
+	
+	private DoubleParameter mutationRate;
+	private IntegerParameter genesMutated;
+	private BooleanParameter report;
+
+	/**
+	 * Creates a new instance of PointMutator. 
+	 * 
+	 * @param resources a reference to the experiment's resources.
+	 */
+	public PercentPointMutator(final Resources resources) {
+		mutationRate = new DoubleParameter(10, "Percent mutation", false, false) {
+			@Override
+			public void validate(Number newValue) {
+				genesMutated.set((int) ((newValue.intValue()) * (((((double) resources.nodes() + resources.outputs()))) / 100)));
+				if (newValue.doubleValue() <= 0 || newValue.doubleValue() > 100) {
+					status = ParameterStatus.INVALID;
+					status.setDetails("Mutation rate must be > 0 and <= 100");
+				} else if (genesMutated.get() <=  0) {
+					status = ParameterStatus.WARNING;
+					status.setDetails("With mutation rate " + mutationRate.get() + ", 0 genes will be mutated.");
+				} else {
+					status = ParameterStatus.VALID;
+				}
+			}
+		};
+		genesMutated = new IntegerParameter(0, "Genes mutated", true, false) {
+			@Override
+			public void validate(Number newValue) {
+				// blank
+			}
+		};
+		report = new BooleanParameter(false, "Report") {
+			@Override
+			public void validate(Boolean newValue) {
+				// blank
+			}
+		};
+	}
+
+	@Override
+	public Parameter<?>[] getLocalParameters() {
+		return new Parameter[] {mutationRate, genesMutated, report};
+	}
+
+	@Override
+	public String toString() {
+		return "Percent point mutation";
+	}
+}
diff --git a/src/jcgp/backend/modules/mutator/PointMutator.java b/src/jcgp/backend/modules/mutator/PointMutator.java
index 44c453a..17c6996 100644
--- a/src/jcgp/backend/modules/mutator/PointMutator.java
+++ b/src/jcgp/backend/modules/mutator/PointMutator.java
@@ -6,88 +6,69 @@ import jcgp.backend.population.Node;
 import jcgp.backend.population.Output;
 import jcgp.backend.resources.Resources;
 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;
 
-public class PointMutator implements Mutator {
-	
-	private DoubleParameter mutationRate;
-	private IntegerParameter nodesMutated;
-	private BooleanParameter report;
+/**
+ * Point mutator
+ * <br><br>
+ * In point mutation, a number of random genes
+ * is picked and mutated until all required
+ * mutations have been performed. The actual number
+ * of genes to be mutated can be defined in any
+ * arbitrary way.
+ * 
+ * @author Eduardo Pedroni
+ *
+ */
+public abstract class PointMutator implements Mutator {
 
-	public PointMutator(final Resources resources) {
-		mutationRate = new DoubleParameter(50, "Percent mutation", false, false) {
-			@Override
-			public void validate(Number newValue) {
-				nodesMutated.set((int) ((newValue.intValue()) * (((((double) resources.nodes() + resources.outputs()))) / 100)));
-				if (newValue.doubleValue() <= 0 || newValue.doubleValue() > 100) {
-					status = ParameterStatus.INVALID;
-					status.setDetails("Mutation rate must be > 0 and <= 100");
-				} else if ((int) ((newValue.doubleValue() / 100) * (double) resources.nodes()) <=  0) {
-					status = ParameterStatus.WARNING;
-					status.setDetails("With mutation rate " + mutationRate.get() + ", 0 genes will be mutated.");
-				} else {
-					status = ParameterStatus.VALID;
-				}
-			}
-		};
-		nodesMutated = new IntegerParameter(0, "Genes mutated", true, false) {
-			@Override
-			public void validate(Number newValue) {
-				// blank
-			}
-		};
-		report = new BooleanParameter(false, "Report") {
-			@Override
-			public void validate(Boolean newValue) {
-				// blank
-			}
-		};
-	}
+	protected IntegerParameter genesMutated;
+	protected BooleanParameter report;
 
 	@Override
 	public void mutate(Chromosome chromosome, Resources resources) {
-		if (report.get()) resources.reportln("[Mutator] Number of mutations to be performed: " + nodesMutated.get());
-		for (int i = 0; i < nodesMutated.get(); i++) {
+		if (report.get()) resources.reportln("[Mutator] Number of mutations to be performed: " + genesMutated.get());
+		
+		// for however many genes must be mutated
+		for (int i = 0; i < genesMutated.get(); i++) {
+			
 			MutableElement m = chromosome.getRandomMutableElement();
-			if (report.get()) resources.report("[Mutator] Mutation " + i + " selected " + m.toString() + ", ");
 			
+			if (report.get()) resources.report("[Mutator] Mutation " + i + " selected " + m + ", ");
+			
+			// outputs and nodes are mutated differently
 			if (m instanceof Output) {
-				if (report.get()) resources.report("changed source from " + ((Output) m).getSource().toString() + " ");
+				if (report.get()) resources.report("changed source from " + ((Output) m).getSource() + " ");
 				
+				// outputs are easy, simply set to a different random connection, any will do
 				m.setConnection(0, chromosome.getRandomConnection());
 				
-				if (report.get()) resources.reportln("to " + ((Output) m).getSource().toString());
+				if (report.get()) resources.reportln("to " + ((Output) m).getSource());
 			} else if (m instanceof Node) {
+				/* nodes are more complicated, first we must decide whether to mutate the function
+				 * or a connection
+				 * we do this by generating a random int between 0 and 1 + arity
+				 */
 				int geneType = resources.getRandomInt(1 + resources.arity());
+				
+				// if the int is less than 1, mutate function, else mutate connections 
 				if (geneType < 1) {
-					if (report.get()) resources.report("changed function from " + ((Node) m).getFunction().getName() + " ");
+					if (report.get()) resources.report("changed function from " + ((Node) m).getFunction() + " ");
 					
 					((Node) m).setFunction(resources.getRandomFunction());
 					
-					if (report.get()) resources.reportln("to " + ((Node) m).getFunction().getName());
+					if (report.get()) resources.reportln("to " + ((Node) m).getFunction());
 				} else {
-					int connection = resources.getRandomInt(resources.arity());
-					if (report.get()) resources.report("changed connection " + connection + " from " + ((Node) m).getConnection(connection) + " ");
+					// if we decided to mutate connection, subtract 1 from geneType so it fits into the arity range
+					geneType -= 1;
+					if (report.get()) resources.report("changed connection " + geneType + " from " + ((Node) m).getConnection(geneType) + " ");
 					
-					m.setConnection(connection, chromosome.getRandomConnection(((Node) m).getColumn()));
+					m.setConnection(geneType, chromosome.getRandomConnection(((Node) m).getColumn()));
 					
-					if (report.get()) resources.reportln("to " + ((Node) m).getConnection(connection));
+					if (report.get()) resources.reportln("to " + ((Node) m).getConnection(geneType));
 				}
 			}
 		}
 	}
 
-	@Override
-	public Parameter<?>[] getLocalParameters() {
-		return new Parameter[] {mutationRate, nodesMutated, report};
-	}
-
-	@Override
-	public String toString() {
-		return "Point mutation";
-	}
-
 }
diff --git a/src/jcgp/backend/modules/mutator/ProbabilisticMutator.java b/src/jcgp/backend/modules/mutator/ProbabilisticMutator.java
new file mode 100644
index 0000000..e3c1d03
--- /dev/null
+++ b/src/jcgp/backend/modules/mutator/ProbabilisticMutator.java
@@ -0,0 +1,131 @@
+package jcgp.backend.modules.mutator;
+
+import jcgp.backend.population.Chromosome;
+import jcgp.backend.population.Node;
+import jcgp.backend.population.Output;
+import jcgp.backend.resources.Resources;
+import jcgp.backend.resources.parameters.BooleanParameter;
+import jcgp.backend.resources.parameters.DoubleParameter;
+import jcgp.backend.resources.parameters.Parameter;
+import jcgp.backend.resources.parameters.ParameterStatus;
+
+/**
+ * Probabilistic mutator
+ * <br><br>
+ * This operator iterates through every mutable gene in the chromosome and 
+ * decides whether to mutate each of them individually. 
+ * The decision is made based on the difference between the mutation probability
+ * and a randomly generated double between 0 and 100.
+ * 
+ * 
+ * @see Mutator
+ * @author Eduardo Pedroni
+ *
+ */
+public class ProbabilisticMutator implements Mutator {
+
+	private DoubleParameter mutationProbability;
+	private BooleanParameter report;
+	
+	private Resources resources;
+	
+	/**
+	 * Creates a new instance of ProbabilisticMutator. 
+	 * 
+	 * @param resources a reference to the experiment's resources.
+	 */
+	public ProbabilisticMutator(Resources resources) {
+		this.resources = resources;
+		
+		mutationProbability = new DoubleParameter(10, "Mutation probability", false, false) {
+			@Override
+			public void validate(Number newValue) {
+				if (newValue.doubleValue() <= 0 || newValue.doubleValue() > 100) {
+					status = ParameterStatus.INVALID;
+					status.setDetails("Mutation rate must be > 0 and <= 100");
+				} else {
+					status = ParameterStatus.VALID;
+				}
+			}
+		};
+		report = new BooleanParameter(false, "Report") {
+			@Override
+			public void validate(Boolean newValue) {
+				// blank
+			}
+		};
+	}
+	
+	@Override
+	public Parameter<?>[] getLocalParameters() {
+		return new Parameter<?>[] {mutationProbability, report};
+	}
+
+	@Override
+	public void mutate(Chromosome chromosome, Resources resources) {
+		if (report.get()) resources.reportln("[Mutator] Starting mutations");
+		
+		// go through nodes - [rows][columns]
+		for (int r = 0; r < resources.rows(); r++) {
+			for (int c = 0; c < resources.columns(); c++) {
+				// go through all connections
+				for (int a = 0; a < resources.arity(); a++) {
+					if (mutate()) {
+						Node n = chromosome.getNode(r, c);
+						
+						if (report.get()) resources.report("[Mutator] Mutating " + n +
+								", changed connection " + a + " from " + n.getConnection(a) + " ");
+						
+						n.setConnection(a, chromosome.getRandomConnection(c));
+						
+						if (report.get()) resources.reportln("to " + n.getConnection(a));
+						
+					}
+				}
+				// deal with node function next
+				if (mutate()) {
+					Node n = chromosome.getNode(r, c);
+					if (report.get()) resources.report("[Mutator] Mutating " + n +
+							", changed function from " + n.getFunction());
+					
+					n.setFunction(resources.getRandomFunction());
+					
+					if (report.get()) resources.reportln(" to " + n.getFunction());
+				}
+			}
+		}
+		// finally, mutate outputs
+		for (int o = 0; o < resources.outputs(); o++) {
+			if (mutate()) {
+				Output out = chromosome.getOutput(o);
+				
+				if (report.get()) resources.report("[Mutator] Mutating " + out +
+						", changed source from " + out.getSource());
+				
+				out.setConnection(0, chromosome.getRandomConnection());
+				
+				if (report.get()) resources.reportln("to " + out.getSource());
+			}
+		}
+		
+		if (report.get()) resources.reportln("[Mutator] Mutation finished ");
+
+	}
+	
+	/**
+	 * This method offers a shorthand to decide whether a mutation should occur or not.
+	 * A random double is generated in the range 0 <= x < 100 and compared with the
+	 * mutation probability parameter. If the generated number is less than the mutation
+	 * probability, this returns true meaning a mutation should occur.
+	 * 
+	 * @return true if a mutation should be performed, false if otherwise.
+	 */
+	private boolean mutate() {
+		return resources.getRandomDouble(100) < mutationProbability.get();
+	}
+
+	@Override
+	public String toString() {
+		return "Probabilistic mutation";
+	}
+}
diff --git a/src/jcgp/backend/modules/problem/DigitalCircuitProblem.java b/src/jcgp/backend/modules/problem/DigitalCircuitProblem.java
index 3c30e4c..099f527 100644
--- a/src/jcgp/backend/modules/problem/DigitalCircuitProblem.java
+++ b/src/jcgp/backend/modules/problem/DigitalCircuitProblem.java
@@ -1,6 +1,6 @@
 package jcgp.backend.modules.problem;
 
-import jcgp.backend.function.BitwiseLogic;
+import jcgp.backend.function.DigitalCircuitFunctions;
 import jcgp.backend.function.UnsignedInteger;
 import jcgp.backend.population.Chromosome;
 import jcgp.backend.population.Population;
@@ -10,14 +10,13 @@ public class DigitalCircuitProblem extends TestCaseProblem<UnsignedInteger> {
 	
 	public DigitalCircuitProblem(Resources resources) {
 		super(resources);
-		functionSet = new BitwiseLogic();
+		functionSet = new DigitalCircuitFunctions();
+		setProblemName("Symbolic regression");
+		setFileExtension(".plu");
 	}
 	
 	@Override
 	public void evaluate(Population population, Resources resources) {
-		// set fittest to 0, change it whenever a fitter one is found
-		population.setFittest(0);
-		
 		// for every chromosome in the population
 		for (int i = 0; i < resources.populationSize(); i++) {
 			// assume an initial fitness of 0
@@ -42,10 +41,10 @@ public class DigitalCircuitProblem extends TestCaseProblem<UnsignedInteger> {
 			
 			// assign the resulting fitness to the respective individual
 			population.getChromosome(i).setFitness(fitness);
-			if (fitness >= population.getFittest().getFitness()) {
-				population.setFittest(i);
-			}
 		}
+		
+		// sort population
+		population.sortAscending();
 	}
 	
 	@Override
@@ -77,9 +76,4 @@ public class DigitalCircuitProblem extends TestCaseProblem<UnsignedInteger> {
 	public boolean isPerfectSolution(Chromosome fittest) {
 		return fittest.getFitness() >= maxFitness.get();
 	}
-
-	@Override
-	public String getFileExtension() {
-		return ".plu";
-	}
 }
diff --git a/src/jcgp/backend/modules/problem/Problem.java b/src/jcgp/backend/modules/problem/Problem.java
index d01f5b0..07183ea 100644
--- a/src/jcgp/backend/modules/problem/Problem.java
+++ b/src/jcgp/backend/modules/problem/Problem.java
@@ -1,14 +1,19 @@
 package jcgp.backend.modules.problem;
 
+import java.io.File;
+
 import jcgp.backend.function.FunctionSet;
 import jcgp.backend.modules.Module;
 import jcgp.backend.population.Chromosome;
 import jcgp.backend.population.Population;
+import jcgp.backend.resources.ModifiableResources;
 import jcgp.backend.resources.Resources;
 
 public abstract class Problem implements Module {
 
 	protected FunctionSet functionSet;
+	private String fileExtension = ".*";
+	private String name = this.getClass().getSimpleName();
 	
 	public abstract void evaluate(Population population, Resources resources);
 	
@@ -17,4 +22,27 @@ public abstract class Problem implements Module {
 	}
 	
 	public abstract boolean isPerfectSolution(Chromosome fittest);
+	
+	public abstract void parse(File file, ModifiableResources resources);
+	
+	public void setFileExtension(String fileExtension) {
+		this.fileExtension = fileExtension;
+	}
+	
+	public String getFileExtension() {
+		return fileExtension;
+	}
+	
+	public void setProblemName(String newName) {
+		this.name = newName;
+	}
+	
+	public String getProblemName() {
+		return name;
+	}
+	
+	@Override
+	public String toString() {
+		return name;
+	}
 }
diff --git a/src/jcgp/backend/modules/problem/SymbolicRegressionProblem.java b/src/jcgp/backend/modules/problem/SymbolicRegressionProblem.java
index 52df0f2..5468157 100644
--- a/src/jcgp/backend/modules/problem/SymbolicRegressionProblem.java
+++ b/src/jcgp/backend/modules/problem/SymbolicRegressionProblem.java
@@ -1,6 +1,6 @@
 package jcgp.backend.modules.problem;
 
-import jcgp.backend.function.DoubleArithmetic;
+import jcgp.backend.function.SymbolicRegressionFunctions;
 import jcgp.backend.population.Chromosome;
 import jcgp.backend.population.Population;
 import jcgp.backend.resources.Resources;
@@ -16,7 +16,9 @@ public class SymbolicRegressionProblem extends TestCaseProblem<Double> {
 	
 	public SymbolicRegressionProblem(Resources resources) {
 		super(resources);
-		functionSet = new DoubleArithmetic();
+		functionSet = new SymbolicRegressionFunctions();
+		setProblemName("Symbolic regression");
+		setFileExtension(".dat");
 		errorThreshold = new DoubleParameter(0.01, "Error threshold") {
 			@Override
 			public void validate(Number newValue) {
@@ -45,7 +47,7 @@ public class SymbolicRegressionProblem extends TestCaseProblem<Double> {
 				}
 			}
 		};
-		hitsBasedFitness = new BooleanParameter(true, "Hits-based fitness") {
+		hitsBasedFitness = new BooleanParameter(true, "HITS-based fitness") {
 			@Override
 			public void validate(Boolean newValue) {
 				// blank
@@ -55,9 +57,6 @@ public class SymbolicRegressionProblem extends TestCaseProblem<Double> {
 	
 	@Override
 	public void evaluate(Population population, Resources resources) {
-		// set fittest to 0, change it whenever a fitter one is found
-		population.setFittest(0);
-		
 		// for every chromosome in the population
 		for (int i = 0; i < resources.populationSize(); i++) {
 			// assume an initial fitness of 0
@@ -81,18 +80,12 @@ public class SymbolicRegressionProblem extends TestCaseProblem<Double> {
 			}
 			// assign the resulting fitness to the respective individual
 			population.getChromosome(i).setFitness(fitness);
-			if (fitness >= population.getFittest().getFitness()) {
-				population.setFittest(i);
-			}
 		}
+		
+		// sort population
+		population.sortAscending();
 	}
 	
-	
-	@Override
-	public String toString() {
-		return "Symbolic regression";
-	}
-
 	@Override
 	public void addTestCase(String[] inputs, String[] outputs) {
 		Double[] inputCases = new Double[inputs.length];
@@ -116,9 +109,4 @@ public class SymbolicRegressionProblem extends TestCaseProblem<Double> {
 	public Parameter<?>[] getLocalParameters() {
 		return new Parameter[]{maxFitness, errorThreshold, perfectionThreshold, hitsBasedFitness};
 	}
-
-	@Override
-	public String getFileExtension() {
-		return ".dat";
-	}
 }
diff --git a/src/jcgp/backend/modules/problem/TestCaseProblem.java b/src/jcgp/backend/modules/problem/TestCaseProblem.java
index d8dd32b..6c4a7dc 100644
--- a/src/jcgp/backend/modules/problem/TestCaseProblem.java
+++ b/src/jcgp/backend/modules/problem/TestCaseProblem.java
@@ -1,9 +1,12 @@
 package jcgp.backend.modules.problem;
 
+import java.io.File;
 import java.util.List;
 
 import javafx.collections.FXCollections;
 import javafx.collections.ObservableList;
+import jcgp.backend.parsers.TestCaseParser;
+import jcgp.backend.resources.ModifiableResources;
 import jcgp.backend.resources.Resources;
 import jcgp.backend.resources.parameters.DoubleParameter;
 import jcgp.backend.resources.parameters.Parameter;
@@ -116,7 +119,10 @@ public abstract class TestCaseProblem<U extends Object> extends Problem {
 		testCases.clear();
 	}
 
-	public abstract String getFileExtension();
+	public void parse(File file, ModifiableResources resources) {
+		TestCaseParser.parseParameters(file, resources);
+		TestCaseParser.parse(file, this, resources);
+	}
 }
 
 
diff --git a/src/jcgp/backend/modules/problem/TravellingSalesmanProblem.java b/src/jcgp/backend/modules/problem/TravellingSalesmanProblem.java
new file mode 100644
index 0000000..6491ec6
--- /dev/null
+++ b/src/jcgp/backend/modules/problem/TravellingSalesmanProblem.java
@@ -0,0 +1,43 @@
+package jcgp.backend.modules.problem;
+
+import java.io.File;
+
+import jcgp.backend.function.TravellingSalesmanFunctions;
+import jcgp.backend.population.Chromosome;
+import jcgp.backend.population.Population;
+import jcgp.backend.resources.ModifiableResources;
+import jcgp.backend.resources.Resources;
+import jcgp.backend.resources.parameters.Parameter;
+
+public class TravellingSalesmanProblem extends Problem {
+	
+	public TravellingSalesmanProblem(Resources resources) {
+		functionSet = new TravellingSalesmanFunctions();
+		setProblemName("Travelling salesman");
+		setFileExtension(".tsp");
+	}
+
+	@Override
+	public Parameter<?>[] getLocalParameters() {
+		// TODO Auto-generated method stub
+		return null;
+	}
+
+	@Override
+	public void evaluate(Population population, Resources resources) {
+		// TODO Auto-generated method stub
+
+	}
+
+	@Override
+	public boolean isPerfectSolution(Chromosome fittest) {
+		// TODO Auto-generated method stub
+		return false;
+	}
+
+	@Override
+	public void parse(File file, ModifiableResources resources) {
+		// TODO Auto-generated method stub
+		
+	}
+}
diff --git a/src/jcgp/backend/parser/ChromosomeParser.java b/src/jcgp/backend/parser/ChromosomeParser.java
deleted file mode 100644
index fd03b7d..0000000
--- a/src/jcgp/backend/parser/ChromosomeParser.java
+++ /dev/null
@@ -1,177 +0,0 @@
-package jcgp.backend.parser;
-
-import java.io.File;
-import java.io.FileNotFoundException;
-import java.io.FileReader;
-import java.io.PrintWriter;
-import java.util.Scanner;
-
-import jcgp.backend.population.Chromosome;
-import jcgp.backend.population.Connection;
-import jcgp.backend.population.Input;
-import jcgp.backend.population.Node;
-import jcgp.backend.resources.Resources;
-
-/**
- * This class includes a method for parsing .chr files and another
- * for writing .chr files from given chromosomes.
- * 
- * @author Eduardo Pedroni
- *
- */
-public abstract class ChromosomeParser {
-
-	/**
-	 * Use this method to parse .chr files into a given chromosome.
-	 * <br><br>
-	 * This is not fully defensive as it doesn't check for number of inputs, 
-	 * doesn't compare rows and columns individually and doesn't account for levels back. It
-	 * is not viable to implement these defensive measures with the chromosome format used 
-	 * by CGP.
-	 * 
-	 * @param file the .chr file to parse from
-	 * @param chromosome the chromosome to configure
-	 * @param resources the experiment resources
-	 */
-	public static void parse(File file, Chromosome chromosome, Resources resources) {
-		/* 
-		 * Count the nodes to make sure the size of the .chr file matches the experiment parameters.
-		 * 
-		 * We do this by using the scanner to get the node and output portions of the file as they
-		 * are separated by 3 tab characters. Every number is replaced by a single known character, 
-		 * and the length of the string with the new characters is compared with that of a string
-		 * where the new known character has been removed, yielding the total number of values.
-		 * 
-		 */
-		FileReader fr;
-		try {
-			fr = new FileReader(file);
-		} catch (FileNotFoundException e) {
-			e.printStackTrace();
-			return;
-		}
-		Scanner in = new Scanner(fr);
-		in.useDelimiter("\\t\\t\\t");
-		String geneString = in.next().replaceAll("[0-9]+", "g");
-		String outString = in.next().replaceAll("[0-9]+", "o");
-		int geneCount = geneString.length() - geneString.replace("g", "").length();
-		int outCount = outString.length() - outString.replace("o", "").length();
-		in.close();
-		
-		
-		// if the acquired values match the current parameters, apply them to the chromosome
-		if ((geneCount == resources.nodes() * (resources.arity() + 1))
-				&& outCount == resources.outputs()) {
-			// prepare a new scanner
-			try {
-				fr = new FileReader(file);
-			} catch (FileNotFoundException e) {
-				e.printStackTrace();
-				return;
-			}
-			in = new Scanner(fr);
-			
-			int gene;
-			Connection newConnection;
-			Node changingNode;
-			// for all nodes, columns first
-			for (int c = 0; c < resources.columns(); c++) {
-				for (int r = 0; r < resources.rows(); r++) {
-					// store the changing node
-					changingNode = chromosome.getNode(r, c);
-
-					// for every connection
-					for (int i = 0; i < resources.arity(); i++) {
-						// get connection number from the .chr file
-						gene = in.nextInt();
-						System.out.println("r: " + r + " c: " + c + " i: " + i + " gene: " + gene);
-						if (gene < resources.inputs()) {
-							// connection was an input
-							newConnection = chromosome.getInput(gene);
-						} else {
-							// connection was another node, calculate which from its number
-							newConnection = chromosome.getNode((gene - resources.inputs()) % resources.rows(), 
-									(gene - resources.inputs()) / resources.rows());
-						}
-						changingNode.setConnection(i, newConnection);
-					}
-
-					// set the function, straight indexing should work - this is not entirely
-					// safe, but it is not viable to check for functionset compatibility
-					changingNode.setFunction(resources.getFunction(in.nextInt()));
-				}
-			}
-
-			// outputs
-			for (int o = 0; o < resources.outputs(); o ++) {
-				gene = in.nextInt();
-				if (gene < resources.inputs()) {
-					// connection was an input
-					newConnection = chromosome.getInput(gene);
-				} else {
-					// connection was another node, calculate which from its number
-					newConnection = chromosome.getNode((gene - resources.inputs()) % resources.rows(), 
-							(gene - resources.inputs()) / resources.rows());
-				}
-				chromosome.getOutput(o).setConnection(0, newConnection);
-			}
-			in.close();
-		} else {
-			throw new IllegalArgumentException("The topology of the chromosome in " + file.getName() + " does not match that of the experiment.");
-		}
-	}
-	
-	/**
-	 * Writes a chromosome into the specified .chr file.
-	 * 
-	 * 
-	 * @param file the file to write to
-	 * @param chromosome the chromosome to save
-	 */
-	public static void save(File file, Chromosome chromosome, Resources resources) {
-		PrintWriter writer;
-		try {
-			writer = new PrintWriter(file);
-		} catch (FileNotFoundException e) {
-			// something bad happened
-			return;
-		}
-		
-		// for all nodes, columns first
-		for (int c = 0; c < resources.columns(); c++) {
-			for (int r = 0; r < resources.rows(); r++) {
-				for (int i = 0; i < resources.arity(); i++) {
-					// print the connections, separated by spaces
-					Connection conn = chromosome.getNode(r, c).getConnection(i);
-					if (conn instanceof Input) {
-						writer.print(" " + ((Input) conn).getIndex());
-					} else if (conn instanceof Node) {
-						writer.print(" " + (((((Node) conn).getColumn() + 1) * resources.inputs()) + ((Node) conn).getRow()));
-					} else {
-						throw new ClassCastException("Could not handle " + conn.getClass() + " as a subclass of Connection");
-					}
-				}
-				// print the function numbers
-				writer.print(" " + resources.getFunctionIndex(chromosome.getNode(r, c).getFunction()));
-				// node is done, print tab
-				writer.print("\t");
-			}
-		}
-		// nodes are done, print two tabs to separate from output
-		writer.print("\t\t");
-		for (int o = 0; o < resources.outputs(); o ++) {
-			Connection source = chromosome.getOutput(o).getSource();
-			if (source instanceof Input) {
-				writer.print(" " + ((Input) source).getIndex());
-			} else if (source instanceof Node) {
-				writer.print(" " + (((((Node) source).getColumn() + 1) * resources.inputs()) + ((Node) source).getRow()));
-			} else {
-				throw new ClassCastException("Could not handle " + source.getClass() + " as a subclass of Connection");
-			}
-		}
-		
-		writer.close();
-		System.out.println("writer is closed");
-	}
-	
-}
diff --git a/src/jcgp/backend/parser/FunctionParser.java b/src/jcgp/backend/parser/FunctionParser.java
deleted file mode 100644
index ab94899..0000000
--- a/src/jcgp/backend/parser/FunctionParser.java
+++ /dev/null
@@ -1,51 +0,0 @@
-package jcgp.backend.parser;
-
-import java.io.File;
-import java.io.FileNotFoundException;
-import java.io.FileReader;
-import java.util.Scanner;
-
-import jcgp.backend.function.FunctionSet;
-import jcgp.backend.modules.problem.Problem;
-
-public class FunctionParser {
-
-private FunctionSet functionSet;
-	
-	private FunctionParser(Problem problem) {
-		this.functionSet = problem.getFunctionSet();
-	}
-
-	public static void parseFunctions(File file, Problem problem) {
-		FunctionParser pp = new FunctionParser(problem);
-		
-		FileReader fr;
-		try {
-			fr = new FileReader(file);
-		} catch (FileNotFoundException e) {
-			e.printStackTrace();
-			return;
-		}
-		
-		Scanner in = new Scanner(fr);
-		
-		while (in.hasNextLine()) {
-			String line = in.nextLine();
-			if (line.substring(line.length() - 1).matches("[0-9]")) {
-				pp.parseAndSet(line.split("[^0-9]+"));
-			}
-		}
-		
-		in.close();
-	}
-	
-	private void parseAndSet(String[] splitString) {
-		int functionIndex = Integer.parseInt(splitString[splitString.length - 1]);
-		if (Integer.parseInt(splitString[0]) != 0) {
-			functionSet.enableFunction(functionIndex);
-		} else {
-			functionSet.disableFunction(functionIndex);
-		}
-		
-	}	
-}
diff --git a/src/jcgp/backend/parser/ParameterParser.java b/src/jcgp/backend/parser/ParameterParser.java
deleted file mode 100644
index f96ebf9..0000000
--- a/src/jcgp/backend/parser/ParameterParser.java
+++ /dev/null
@@ -1,77 +0,0 @@
-package jcgp.backend.parser;
-
-import java.io.File;
-import java.io.FileNotFoundException;
-import java.io.FileReader;
-import java.util.Scanner;
-
-import jcgp.backend.resources.ModifiableResources;
-
-public class ParameterParser {
-	
-	private ModifiableResources resources;
-	
-	private ParameterParser(ModifiableResources resources) {
-		this.resources = resources;
-	}
-
-	public static void parseParameters(File file, ModifiableResources resources) {
-		ParameterParser pp = new ParameterParser(resources);
-		
-		FileReader fr;
-		try {
-			fr = new FileReader(file);
-		} catch (FileNotFoundException e) {
-			e.printStackTrace();
-			return;
-		}
-		
-		Scanner in = new Scanner(fr);
-		
-		while (in.hasNextLine()) {
-			pp.parseAndSet(in.nextLine().split("( |\t)+"));
-		}
-		
-		in.close();
-	}
-	
-	private void parseAndSet(String[] splitString) {
-		switch (splitString[1]) {
-		
-		case "population_size":
-			resources.setPopulationSize(Integer.parseInt(splitString[0]));
-			break;
-			
-		case "num_generations":
-			resources.setGenerations(Integer.parseInt(splitString[0]));
-			break;
-			
-		case "num_runs_total":
-			resources.setRuns(Integer.parseInt(splitString[0]));
-			break;
-			
-		case "num_rows":
-			resources.setRows(Integer.parseInt(splitString[0]));
-			break;
-			
-		case "num_cols":
-			resources.setColumns(Integer.parseInt(splitString[0]));
-			break;
-
-		case "levels_back":
-			resources.setLevelsBack(Integer.parseInt(splitString[0]));
-			break;
-		
-		case "report_interval":
-			resources.setReportInterval(Integer.parseInt(splitString[0]));
-			break;
-		
-		case "global_seed":
-			resources.setSeed(Integer.parseInt(splitString[0]));
-			break;
-
-		default:
-			break;
-		}
-	}
-}
diff --git a/src/jcgp/backend/parser/TestCaseParser.java b/src/jcgp/backend/parser/TestCaseParser.java
deleted file mode 100644
index d47d663..0000000
--- a/src/jcgp/backend/parser/TestCaseParser.java
+++ /dev/null
@@ -1,90 +0,0 @@
-package jcgp.backend.parser;
-
-import java.io.File;
-import java.io.FileNotFoundException;
-import java.io.FileReader;
-import java.util.Scanner;
-
-import jcgp.backend.modules.problem.TestCaseProblem;
-import jcgp.backend.resources.ModifiableResources;
-
-public class TestCaseParser {
-
-	private TestCaseProblem<?> problem;
-	
-	public TestCaseParser(TestCaseProblem<?> problem) {
-		this.problem = problem;
-	}
-	
-	public void parse(File file) {
-		FileReader fr;
-		try {
-			fr = new FileReader(file);
-		} catch (FileNotFoundException e) {
-			e.printStackTrace();
-			return;
-		}
-		
-		Scanner in = new Scanner(fr);
-		boolean readingTestCases = false;
-		int inputs = 0, outputs = 0;
-		
-		problem.clearTestCases();
-		
-		while (in.hasNextLine()) {
-			String nextLine = in.nextLine();
-			
-			if (nextLine.startsWith(".i")) {
-				String[] split = nextLine.split(" +");
-				inputs = Integer.parseInt(split[1]);
-			} else if (nextLine.startsWith(".o")) {
-				String[] split = nextLine.split(" +");
-				outputs = Integer.parseInt(split[1]);
-			} else if (nextLine.startsWith(".p") || nextLine.startsWith(".t")) {
-				readingTestCases = true;
-			} else if (nextLine.startsWith(".e")) {
-				readingTestCases = false;
-				// set test cases? not safe probably
-			} else if (readingTestCases) {
-				String[] split = nextLine.split("( |\t)+");
-				String[] inputCases = new String[inputs];
-				String[] outputCases = new String[outputs];
-				for (int i = 0; i < inputs; i++) {
-					inputCases[i] = split[i];
-				}
-				for (int o = 0; o < outputs; o++) {
-					outputCases[o] = split[o + inputs];
-				}
-				
-				problem.addTestCase(inputCases, outputCases);
-			}
-		}
-		
-		in.close();
-	}
-
-	public static void parseParameters(File file, ModifiableResources resources) {
-		
-		FileReader fr;
-		try {
-			fr = new FileReader(file);
-		} catch (FileNotFoundException e) {
-			e.printStackTrace();
-			return;
-		}
-		
-		Scanner in = new Scanner(fr);
-
-		while (in.hasNextLine()) {
-			String nextLine = in.nextLine();
-			if (nextLine.startsWith(".i")) {
-				String[] split = nextLine.split(" +");
-				resources.setInputs(Integer.parseInt(split[1]));
-			} else if (nextLine.startsWith(".o")) {
-				String[] split = nextLine.split(" +");
-				resources.setOutputs(Integer.parseInt(split[1]));
-			}
-		}
-		in.close();
-	}
-}
diff --git a/src/jcgp/backend/parsers/ChromosomeParser.java b/src/jcgp/backend/parsers/ChromosomeParser.java
index fe58ff8..ed1399a 100644
--- a/src/jcgp/backend/parsers/ChromosomeParser.java
+++ b/src/jcgp/backend/parsers/ChromosomeParser.java
@@ -11,6 +11,7 @@ import jcgp.backend.population.Connection;
 import jcgp.backend.population.Input;
 import jcgp.backend.population.Node;
 import jcgp.backend.resources.ModifiableResources;
+import jcgp.backend.resources.Resources;
 
 /**
  * This class includes a method for parsing .chr files and another
@@ -33,7 +34,7 @@ public abstract class ChromosomeParser {
 	 * @param chromosome the chromosome to configure
 	 * @param resources the experiment resources
 	 */
-	public static void parse(File file, Chromosome chromosome, ModifiableResources resources) {
+	public static void parse(File file, Chromosome chromosome, Resources resources) {
 		/* 
 		 * Count the nodes to make sure the size of the .chr file matches the experiment parameters.
 		 * 
diff --git a/src/jcgp/backend/parsers/FunctionParser.java b/src/jcgp/backend/parsers/FunctionParser.java
index 6d6c73b..cc52ce9 100644
--- a/src/jcgp/backend/parsers/FunctionParser.java
+++ b/src/jcgp/backend/parsers/FunctionParser.java
@@ -11,7 +11,7 @@ import jcgp.backend.resources.ModifiableResources;
 
 /**
  * Parses the functions from a .par file. 
- * Functions marked with a 1 will be enabled, 
+ * Functions marked with a 1 are enabled, 
  * and those marked with 0 are disabled.
  * 
  * @author Eduardo Pedroni
@@ -25,7 +25,7 @@ public abstract class FunctionParser {
 		try {
 			fr = new FileReader(file);
 		} catch (FileNotFoundException e) {
-			resources.println("[Parser] Error: could not find " + file.getAbsolutePath() + ".");
+			resources.println("[Parser] Error: could not find " + file.getAbsolutePath());
 			return;
 		}
 		
@@ -40,14 +40,14 @@ public abstract class FunctionParser {
 				int functionIndex = Integer.parseInt(splitString[splitString.length - 1]);
 				if (Integer.parseInt(splitString[0]) != 0 && !functionSet.isEnabled(functionSet.getFunction(functionIndex))) {
 					functionSet.enableFunction(functionIndex);
-					resources.println("[Parser] Enabled function: " + functionSet.getFunction(functionIndex).getName() + ".");
+					resources.println("[Parser] Enabled function: " + functionSet.getFunction(functionIndex));
 				} else if (Integer.parseInt(splitString[0]) == 0 && functionSet.isEnabled(functionSet.getFunction(functionIndex))) {
 					functionSet.disableFunction(functionIndex);
-					resources.println("[Parser] Disabled function: " + functionSet.getFunction(functionIndex).getName() + ".");
+					resources.println("[Parser] Disabled function: " + functionSet.getFunction(functionIndex));
 				}
 			}
 		}
 		in.close();
-		resources.println("[Parser] Finished parsing functions.");
+		resources.println("[Parser] Finished parsing functions");
 	}
 }
diff --git a/src/jcgp/backend/population/Chromosome.java b/src/jcgp/backend/population/Chromosome.java
index f8830fa..9e53f85 100644
--- a/src/jcgp/backend/population/Chromosome.java
+++ b/src/jcgp/backend/population/Chromosome.java
@@ -5,7 +5,7 @@ import java.util.ArrayList;
 import jcgp.backend.exceptions.ParameterMismatchException;
 import jcgp.backend.resources.Resources;
 
-public class Chromosome {
+public class Chromosome implements Comparable<Chromosome> {
 	
 	private Resources resources;
 
@@ -276,7 +276,7 @@ public class Chromosome {
 		}
 	}
 
-	public boolean compareTo(Chromosome chromosome) {
+	public boolean compareGenesTo(Chromosome chromosome) {
 		for (int r = 0; r < resources.rows(); r++) {
 			for (int c = 0; c < resources.columns(); c++) {
 				if (!(nodes[r][c].copyOf(chromosome.getNode(r, c)))) {
@@ -294,7 +294,7 @@ public class Chromosome {
 		return true;
 	}
 
-	public boolean compareActiveTo(Chromosome chromosome) {
+	public boolean compareActiveGenesTo(Chromosome chromosome) {
 		// update list if it is out of date
 		computeActiveNodes();
 		
@@ -310,7 +310,6 @@ public class Chromosome {
 	}
 	
 	public void printNodes() {
-		// TODO make this proper
 		int arity = resources.arity();
 		
 		for (int r = 0; r < resources.rows(); r++) {
@@ -320,7 +319,7 @@ public class Chromosome {
 				for (int i = 0; i < arity; i++) {
 					System.out.print("C" + i + ": (" + nodes[r][c].getConnection(i).toString() + ") ");
 				}
-				System.out.print("F: " + nodes[r][c].getFunction().getName() + "\t");
+				System.out.print("F: " + nodes[r][c].getFunction() + "\t");
 			}
 			System.out.print("\n");
 		}
@@ -335,4 +334,15 @@ public class Chromosome {
 	public Resources getResources() {
 		return resources;
 	}
+
+	@Override
+	public int compareTo(Chromosome o) {
+		if (fitness < o.getFitness()) {
+			return -1;
+		} else if (fitness > o.getFitness()) {
+			return 1;
+		} else {
+			return 0;
+		}
+	}
 }
diff --git a/src/jcgp/backend/population/Population.java b/src/jcgp/backend/population/Population.java
index b6dd055..d99c64e 100644
--- a/src/jcgp/backend/population/Population.java
+++ b/src/jcgp/backend/population/Population.java
@@ -1,12 +1,14 @@
 package jcgp.backend.population;
 
+import java.util.Arrays;
+import java.util.Collections;
+
 import jcgp.backend.resources.Resources;
 
 public class Population {
 	
 	private final Chromosome[] chromosomes;
 	private final Resources resources;
-	private int fittest = 0;
 	
 	/**
 	 * Initialise a random population according to the parameters specified
@@ -77,25 +79,26 @@ public class Population {
 			chromosomes[c].reinitialiseConnections();
 		}
 	}
-
-	public void setFittest(int fittest) {
-		this.fittest = fittest;
-	}
-	
-	public void setFittest(Chromosome fittest) {
-		for (int i = 0; i < chromosomes.length; i++) {
-			if (chromosomes[i] == fittest) {
-				this.fittest = i;
-				return;
-			}
-		}
-	}
 	
 	public Chromosome getFittest() {
-		return chromosomes[fittest];
+		return chromosomes[chromosomes.length - 1];
 	}
 	
 	public int getFittestIndex() {
-		return fittest;
+		return chromosomes.length - 1;
+	}
+
+	/**
+	 * Sort the population into ascending order of fitness.
+	 */
+	public void sortAscending() {
+		Arrays.sort(chromosomes);
+	}
+	
+	/**
+	 * Sort the population into descending order of fitness.
+	 */
+	public void sortDescending() {
+		Arrays.sort(chromosomes, Collections.reverseOrder());
 	}
 }
diff --git a/src/jcgp/backend/resources/ModifiableResources.java b/src/jcgp/backend/resources/ModifiableResources.java
index 048e460..53dc815 100644
--- a/src/jcgp/backend/resources/ModifiableResources.java
+++ b/src/jcgp/backend/resources/ModifiableResources.java
@@ -1,7 +1,10 @@
 package jcgp.backend.resources;
 
+import javafx.beans.value.ChangeListener;
+import javafx.beans.value.ObservableValue;
 import jcgp.backend.function.FunctionSet;
 import jcgp.backend.resources.parameters.IntegerParameter;
+import jcgp.backend.resources.parameters.ParameterStatus;
 
 /**
  * 
@@ -10,13 +13,13 @@ import jcgp.backend.resources.parameters.IntegerParameter;
  * and only classes with access to a JCGP instance may modify
  * the resources.
  * 
- * @author eddy
+ * @author Eduardo Pedroni
  *
  */
 public class ModifiableResources extends Resources {
 
 	public ModifiableResources() {
-		super();
+		createBaseParameters();
 	}
 	
 	public void setValues(String filePath) {
@@ -214,21 +217,159 @@ public class ModifiableResources extends Resources {
 		this.console = console;
 	}
 	
-	/*
-	 * Console functionality
-	 * These are not affected by parameter report interval
-	 */
-	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 void createBaseParameters() {
+		rows = new IntegerParameter(5, "Rows", false, true) {
+			@Override
+			public void validate(Number newValue) {
+				if (newValue.intValue() <= 0) {
+					status = ParameterStatus.INVALID;
+					status.setDetails("Chromosome must have at least 1 row.");
+				} else {
+					status = ParameterStatus.VALID;
+				}
+			}
+		};
+		
+		columns = new IntegerParameter(5, "Columns", false, true) {
+			@Override
+			public void validate(Number newValue) {
+				if (newValue.intValue() <= 0) {
+					status = ParameterStatus.INVALID;
+					status.setDetails("Chromosome must have at least 1 column.");
+				} else {
+					status = ParameterStatus.VALID;
+				}
+			}
+		};
+		
+		inputs = new IntegerParameter(3, "Inputs", true, false) {
+			@Override
+			public void validate(Number newValue) {
+				if (newValue.intValue() <= 0) {
+					status = ParameterStatus.INVALID;
+					status.setDetails("Chromosome must have at least 1 input.");
+				} else {
+					status = ParameterStatus.VALID;
+				}
+			}
+		};
+		
+		outputs = new IntegerParameter(3, "Outputs", true, false) {
+			@Override
+			public void validate(Number newValue) {
+				if (newValue.intValue() <= 0) {
+					status = ParameterStatus.INVALID;
+					status.setDetails("Chromosome must have at least 1 output.");
+				} else {
+					status = ParameterStatus.VALID;
+				}
+			}
+		};
+		
+		populationSize = new IntegerParameter(5, "Population", false, true) {
+			@Override
+			public void validate(Number newValue) {
+				if (newValue.intValue() <= 0) {
+					status = ParameterStatus.INVALID;
+					status.setDetails("Population size must be at least 1.");
+				} else {
+					status = ParameterStatus.VALID;
+				}
+			}
+		};
+		
+		levelsBack = new IntegerParameter(2, "Levels back", false, true) {
+			@Override
+			public void validate(Number newValue) {
+				if (newValue.intValue() <= 0) {
+					status = ParameterStatus.INVALID;
+					status.setDetails("Levels back must be at least 1.");
+				} else if (newValue.intValue() > columns.get()) {
+					status = ParameterStatus.INVALID;
+					status.setDetails("Levels back must be less than or equal to the number of columns.");
+				} else {
+					status = ParameterStatus.VALID;
+				}
+			}
+		};
+		
+		generations = new IntegerParameter(1000000, "Generations") {
+			@Override
+			public void validate(Number newValue) {
+				if (newValue.intValue() <= 0) {
+					status = ParameterStatus.INVALID;
+					status.setDetails("Number of generations must be greater than 0.");
+				} else if (newValue.intValue() < currentGeneration.get()) {
+					status = ParameterStatus.WARNING_RESET;
+					status.setDetails("Setting generations to less than the current generation will cause the experiment to restart.");
+				} else {
+					status = ParameterStatus.VALID;
+				}
+			}
+		};
+		
+		currentGeneration = new IntegerParameter(1, "Generation", true, false) {
+			@Override
+			public void validate(Number newValue) {
+				// blank
+			}
+		};
+
+		runs = new IntegerParameter(5, "Runs") {
+			@Override
+			public void validate(Number newValue) {
+				if (newValue.intValue() <= 0) {
+					status = ParameterStatus.INVALID;
+					status.setDetails("Number of runs must be greater than 0.");
+				} else if (newValue.intValue() < currentRun.get()) {
+					status = ParameterStatus.WARNING_RESET;
+					status.setDetails("Setting runs to less than the current run will cause the experiment to restart.");
+				} else {
+					status = ParameterStatus.VALID;
+				}
+			}
+		};
+		
+		currentRun = new IntegerParameter(1, "Run", true, false) {
+			@Override
+			public void validate(Number newValue) {
+				// blank
+			}
+		};
+
+		arity = new IntegerParameter(0, "Max arity", true, false) {
+			@Override
+			public void validate(Number newValue) {
+				// blank
+			}
+		};
+		
+		seed = new IntegerParameter(1234, "Seed", false, true) {
+			@Override
+			public void validate(Number 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());
+		
+		reportInterval = new IntegerParameter(1, "Report interval", false, false) {
+			@Override
+			public void validate(Number newValue) {
+				if (newValue.intValue() > generations.get()) {
+					status = ParameterStatus.WARNING;
+					status.setDetails("No reports will be printed.");
+				} else {
+					status = ParameterStatus.VALID;
+				}
+			}
+		};
 	}
 }
diff --git a/src/jcgp/backend/resources/Resources.java b/src/jcgp/backend/resources/Resources.java
index e83680f..e1438f1 100644
--- a/src/jcgp/backend/resources/Resources.java
+++ b/src/jcgp/backend/resources/Resources.java
@@ -2,12 +2,9 @@ package jcgp.backend.resources;
 
 import java.util.Random;
 
-import javafx.beans.value.ChangeListener;
-import javafx.beans.value.ObservableValue;
 import jcgp.backend.function.Function;
 import jcgp.backend.function.FunctionSet;
 import jcgp.backend.resources.parameters.IntegerParameter;
-import jcgp.backend.resources.parameters.ParameterStatus;
 
 /**
  * 
@@ -28,10 +25,6 @@ public class Resources {
 	// GUI console
 	protected Console console;
 	
-	public Resources() {
-		createBaseParameters();
-	}
-	
 	/**
 	 * @return the rows
 	 */
@@ -129,162 +122,6 @@ public class Resources {
 	public int reportInterval() {
 		return reportInterval.get();
 	}
-
-	private void createBaseParameters() {
-		rows = new IntegerParameter(5, "Rows", false, true) {
-			@Override
-			public void validate(Number newValue) {
-				if (newValue.intValue() <= 0) {
-					status = ParameterStatus.INVALID;
-					status.setDetails("Chromosome must have at least 1 row.");
-				} else {
-					status = ParameterStatus.VALID;
-				}
-			}
-		};
-		
-		columns = new IntegerParameter(5, "Columns", false, true) {
-			@Override
-			public void validate(Number newValue) {
-				if (newValue.intValue() <= 0) {
-					status = ParameterStatus.INVALID;
-					status.setDetails("Chromosome must have at least 1 column.");
-				} else {
-					status = ParameterStatus.VALID;
-				}
-			}
-		};
-		
-		inputs = new IntegerParameter(3, "Inputs", true, false) {
-			@Override
-			public void validate(Number newValue) {
-				if (newValue.intValue() <= 0) {
-					status = ParameterStatus.INVALID;
-					status.setDetails("Chromosome must have at least 1 input.");
-				} else {
-					status = ParameterStatus.VALID;
-				}
-			}
-		};
-		
-		outputs = new IntegerParameter(3, "Outputs", true, false) {
-			@Override
-			public void validate(Number newValue) {
-				if (newValue.intValue() <= 0) {
-					status = ParameterStatus.INVALID;
-					status.setDetails("Chromosome must have at least 1 output.");
-				} else {
-					status = ParameterStatus.VALID;
-				}
-			}
-		};
-		
-		populationSize = new IntegerParameter(5, "Population", false, true) {
-			@Override
-			public void validate(Number newValue) {
-				if (newValue.intValue() <= 0) {
-					status = ParameterStatus.INVALID;
-					status.setDetails("Population size must be at least 1.");
-				} else {
-					status = ParameterStatus.VALID;
-				}
-			}
-		};
-		
-		levelsBack = new IntegerParameter(2, "Levels back", false, true) {
-			@Override
-			public void validate(Number newValue) {
-				if (newValue.intValue() <= 0) {
-					status = ParameterStatus.INVALID;
-					status.setDetails("Levels back must be at least 1.");
-				} else if (newValue.intValue() > columns.get()) {
-					status = ParameterStatus.INVALID;
-					status.setDetails("Levels back must be less than or equal to the number of columns.");
-				} else {
-					status = ParameterStatus.VALID;
-				}
-			}
-		};
-		
-		generations = new IntegerParameter(1000000, "Generations") {
-			@Override
-			public void validate(Number newValue) {
-				if (newValue.intValue() <= 0) {
-					status = ParameterStatus.INVALID;
-					status.setDetails("Number of generations must be greater than 0.");
-				} else if (newValue.intValue() < currentGeneration.get()) {
-					status = ParameterStatus.WARNING_RESET;
-					status.setDetails("Setting generations to less than the current generation will cause the experiment to restart.");
-				} else {
-					status = ParameterStatus.VALID;
-				}
-			}
-		};
-		
-		currentGeneration = new IntegerParameter(1, "Generation", true, false) {
-			@Override
-			public void validate(Number newValue) {
-				// blank
-			}
-		};
-
-		runs = new IntegerParameter(5, "Runs") {
-			@Override
-			public void validate(Number newValue) {
-				if (newValue.intValue() <= 0) {
-					status = ParameterStatus.INVALID;
-					status.setDetails("Number of runs must be greater than 0.");
-				} else if (newValue.intValue() < currentRun.get()) {
-					status = ParameterStatus.WARNING_RESET;
-					status.setDetails("Setting runs to less than the current run will cause the experiment to restart.");
-				} else {
-					status = ParameterStatus.VALID;
-				}
-			}
-		};
-		
-		currentRun = new IntegerParameter(1, "Run", true, false) {
-			@Override
-			public void validate(Number newValue) {
-				// blank
-			}
-		};
-
-		arity = new IntegerParameter(0, "Max arity", true, false) {
-			@Override
-			public void validate(Number newValue) {
-				// blank
-			}
-		};
-		
-		seed = new IntegerParameter(1234, "Seed", false, true) {
-			@Override
-			public void validate(Number 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());
-		
-		reportInterval = new IntegerParameter(1, "Report interval", false, false) {
-			@Override
-			public void validate(Number newValue) {
-				if (newValue.intValue() > generations.get()) {
-					status = ParameterStatus.WARNING;
-					status.setDetails("No reports will be printed.");
-				} else {
-					status = ParameterStatus.VALID;
-				}
-			}
-		};
-	}
 	
 	/*
 	 * Utility functions
@@ -355,4 +192,22 @@ public class Resources {
 			}
 		}
 	}
+	
+	/*
+	 * Console functionality
+	 * These are not affected by parameter report interval
+	 */
+	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/tests/ChromosomeTests.java b/src/jcgp/backend/tests/ChromosomeTests.java
index 36278ba..bc0c57d 100644
--- a/src/jcgp/backend/tests/ChromosomeTests.java
+++ b/src/jcgp/backend/tests/ChromosomeTests.java
@@ -2,7 +2,7 @@ package jcgp.backend.tests;
 
 import static org.junit.Assert.assertTrue;
 import static org.junit.Assert.fail;
-import jcgp.backend.function.DoubleArithmetic;
+import jcgp.backend.function.SymbolicRegressionFunctions;
 import jcgp.backend.population.Chromosome;
 import jcgp.backend.population.Connection;
 import jcgp.backend.population.Input;
@@ -46,7 +46,7 @@ public class ChromosomeTests {
 	@BeforeClass
 	public static void setUpBeforeClass() {
 		resources = new ModifiableResources();
-		resources.setFunctionSet(new DoubleArithmetic());
+		resources.setFunctionSet(new SymbolicRegressionFunctions());
 	}
 
 	@Before
@@ -285,12 +285,12 @@ public class ChromosomeTests {
 	public void compareActiveTest() {
 		// create a clone of the chromosome, compare active nodes - should return true
 		Chromosome c = new Chromosome(chromosome);
-		assertTrue("Active nodes did not match.", chromosome.compareActiveTo(c));
-		assertTrue("Symmetry not obeyed.", c.compareActiveTo(chromosome));
+		assertTrue("Active nodes did not match.", chromosome.compareActiveGenesTo(c));
+		assertTrue("Symmetry not obeyed.", c.compareActiveGenesTo(chromosome));
 
 		// create a new random chromosome, this time they should not match
 		c = new Chromosome(resources);
-		assertTrue("Active nodes did match.", !chromosome.compareActiveTo(c));
+		assertTrue("Active nodes did match.", !chromosome.compareActiveGenesTo(c));
 	}
 
 	/**
@@ -300,12 +300,12 @@ public class ChromosomeTests {
 	public void compareTest() {
 		// create a clone of the chromosome, compare - should return true
 		Chromosome c = new Chromosome(chromosome);
-		assertTrue("Chromosomes did not match.", chromosome.compareTo(c));
-		assertTrue("Symmetry not obeyed.", c.compareTo(chromosome));
+		assertTrue("Chromosomes did not match.", chromosome.compareGenesTo(c));
+		assertTrue("Symmetry not obeyed.", c.compareGenesTo(chromosome));
 
 		// create a new random chromosome, this time they should not match
 		c = new Chromosome(resources);
-		assertTrue("Chromosomes did match.", !chromosome.compareTo(c));
+		assertTrue("Chromosomes did match.", !chromosome.compareGenesTo(c));
 	}
 	/**
 	 * Utility for creating a chromosome of known configuration.
diff --git a/src/jcgp/backend/tests/NodeTests.java b/src/jcgp/backend/tests/NodeTests.java
index 4054661..c63b41e 100644
--- a/src/jcgp/backend/tests/NodeTests.java
+++ b/src/jcgp/backend/tests/NodeTests.java
@@ -2,7 +2,7 @@ package jcgp.backend.tests;
 
 import static org.junit.Assert.assertTrue;
 import jcgp.backend.exceptions.InvalidArgumentsException;
-import jcgp.backend.function.DoubleArithmetic;
+import jcgp.backend.function.SymbolicRegressionFunctions;
 import jcgp.backend.function.Function;
 import jcgp.backend.population.Chromosome;
 import jcgp.backend.population.Connection;
@@ -41,7 +41,7 @@ public class NodeTests {
 	public static void setUpBeforeClass() {
 		
 		resources = new ModifiableResources();
-		resources.setFunctionSet(new DoubleArithmetic());
+		resources.setFunctionSet(new SymbolicRegressionFunctions());
 		chromosome = new Chromosome(resources);
 	}
 
@@ -49,7 +49,7 @@ public class NodeTests {
 	public void setUp() throws Exception {
 		node = new Node(chromosome, 0, 0, resources.arity());
 		// make node with anonymous addition function and hard-coded value connections
-		node.initialise(new DoubleArithmetic.Addition(),
+		node.initialise(new SymbolicRegressionFunctions.Addition(),
 				new Connection[]{new Connection() {
 
 					@Override
@@ -80,7 +80,7 @@ public class NodeTests {
 		Function f = new Function() {
 
 			@Override
-			public Object run(Connection... connections) {
+			public Object run(Object... connections) {
 				// blank
 				return 0;
 			}
@@ -90,12 +90,6 @@ public class NodeTests {
 				// blank
 				return 0;
 			}
-
-			@Override
-			public String getName() {
-				// blank
-				return null;
-			}
 		};
 
 		node.setFunction(f);
@@ -113,7 +107,7 @@ public class NodeTests {
 				((int) node.getValue()) == arg1 + arg2);
 
 		// put in a different function, check the output has changed appropriately
-		node.setFunction(new DoubleArithmetic.Subtraction());
+		node.setFunction(new SymbolicRegressionFunctions.Subtraction());
 
 		assertTrue("Node did not return expected value (difference of arguments).", ((Integer) node.getValue()) == arg1 - arg2);
 
@@ -142,7 +136,7 @@ public class NodeTests {
 		
 		Function function = new Function() {
 			@Override
-			public Object run(Connection... connections)
+			public Object run(Object... connections)
 					throws InvalidArgumentsException {
 				// blank
 				return null;
@@ -152,12 +146,6 @@ public class NodeTests {
 			public int getArity() {
 				return 2;
 			}
-
-			@Override
-			public String getName() {
-				// blank
-				return null;
-			}
 		};
 		
 		node.initialise(function, conn0, conn1);
diff --git a/src/jcgp/backend/tests/OutputTests.java b/src/jcgp/backend/tests/OutputTests.java
index 95b7fc7..8cc10a8 100644
--- a/src/jcgp/backend/tests/OutputTests.java
+++ b/src/jcgp/backend/tests/OutputTests.java
@@ -1,7 +1,7 @@
 package jcgp.backend.tests;
 
 import static org.junit.Assert.assertTrue;
-import jcgp.backend.function.DoubleArithmetic;
+import jcgp.backend.function.SymbolicRegressionFunctions;
 import jcgp.backend.population.Chromosome;
 import jcgp.backend.population.Connection;
 import jcgp.backend.population.Output;
@@ -35,7 +35,7 @@ public class OutputTests {
 	@BeforeClass
 	public static void setUpBeforeClass() {
 		resources = new ModifiableResources();
-		resources.setFunctionSet(new DoubleArithmetic());
+		resources.setFunctionSet(new SymbolicRegressionFunctions());
 		chromosome = new Chromosome(resources);
 	}
 
diff --git a/src/jcgp/backend/tests/PopulationTests.java b/src/jcgp/backend/tests/PopulationTests.java
index fca9c4f..2f36ce1 100644
--- a/src/jcgp/backend/tests/PopulationTests.java
+++ b/src/jcgp/backend/tests/PopulationTests.java
@@ -1,7 +1,7 @@
 package jcgp.backend.tests;
 
 import static org.junit.Assert.assertTrue;
-import jcgp.backend.function.DoubleArithmetic;
+import jcgp.backend.function.SymbolicRegressionFunctions;
 import jcgp.backend.population.Chromosome;
 import jcgp.backend.population.Population;
 import jcgp.backend.resources.ModifiableResources;
@@ -32,7 +32,7 @@ public class PopulationTests {
 	@BeforeClass
 	public static void setUpBeforeClass() throws Exception {
 		resources = new ModifiableResources();
-		resources.setFunctionSet(new DoubleArithmetic());
+		resources.setFunctionSet(new SymbolicRegressionFunctions());
 	}
 
 	@Before
@@ -64,6 +64,6 @@ public class PopulationTests {
 		// initialise a population with a copy of it
 		population = new Population(oc, resources);
 		// check that the first parent chromosome is identical to, but not the same instance as, the one given
-		assertTrue("Incorrect chromosome in population.", population.getChromosome(0).compareTo(oc) && population.getChromosome(0) != oc);
+		assertTrue("Incorrect chromosome in population.", population.getChromosome(0).compareGenesTo(oc) && population.getChromosome(0) != oc);
 	}
 }
diff --git a/src/jcgp/gui/console/GUIConsole.java b/src/jcgp/gui/console/GUIConsole.java
index e77e222..de4b378 100644
--- a/src/jcgp/gui/console/GUIConsole.java
+++ b/src/jcgp/gui/console/GUIConsole.java
@@ -38,7 +38,6 @@ public class GUIConsole extends AnchorPane implements Console {
 			@Override
 			public Event dispatchEvent(Event event, EventDispatchChain tail) {
 				if (event instanceof MouseEvent) {
-					//shot in the dark guess for OSX, might not work
 					MouseEvent mouseEvent = (MouseEvent)event;
 					if (mouseEvent.getButton() == MouseButton.SECONDARY || 
 							(mouseEvent.getButton() == MouseButton.PRIMARY && mouseEvent.isControlDown())) {
diff --git a/src/jcgp/gui/population/FunctionSelector.java b/src/jcgp/gui/population/FunctionSelector.java
index 28eb54d..69d0d31 100644
--- a/src/jcgp/gui/population/FunctionSelector.java
+++ b/src/jcgp/gui/population/FunctionSelector.java
@@ -31,7 +31,7 @@ public class FunctionSelector extends VBox {
 		
 		for (int i = 0; i < fs.getAllowedFunctionCount(); i++) {
 			final int index = i;
-			Label l = new Label(fs.getAllowedFunction(i).getName());
+			Label l = new Label(fs.getAllowedFunction(i).toString());
 			l.setMaxWidth(Double.MAX_VALUE);
 			l.setStyle("-fx-background-color: #FFFFFF; -fx-border-color: #A0A0A0; -fx-border-width: 0 0 1 0; -fx-padding: 2");
 			
diff --git a/src/jcgp/gui/population/GUINode.java b/src/jcgp/gui/population/GUINode.java
index f50edd3..731db8f 100644
--- a/src/jcgp/gui/population/GUINode.java
+++ b/src/jcgp/gui/population/GUINode.java
@@ -454,9 +454,9 @@ public class GUINode extends GUIGene {
 
 	public void updateText() {
 		if (parent.isEvaluating()) {
-			text.setText(node.getFunction().getName() + "\n" + value.toString());
+			text.setText(node.getFunction() + "\n" + value.toString());
 		} else {
-			text.setText(node.getFunction().getName());
+			text.setText(node.getFunction().toString());
 		}
 	}
 
diff --git a/src/jcgp/gui/settings/SettingsPane.java b/src/jcgp/gui/settings/SettingsPane.java
index 302e96d..7fc5621 100644
--- a/src/jcgp/gui/settings/SettingsPane.java
+++ b/src/jcgp/gui/settings/SettingsPane.java
@@ -126,17 +126,13 @@ public class SettingsPane extends AnchorPane {
 		
 		final VBox eaParameters = new VBox(2);
 		
-		if (jcgp.getEvolutionaryStrategy().getLocalParameters() != null) {
-			refreshParameters(jcgp.getEvolutionaryStrategy().getLocalParameters(), eaParameters);
-		}
+		refreshParameters(jcgp.getEvolutionaryStrategy().getLocalParameters(), eaParameters);
 		
 		eaCBox.setOnAction(new EventHandler<ActionEvent>() {
 			@Override
 			public void handle(ActionEvent event) {
 				jcgp.setEvolutionaryStrategy(eaCBox.getSelectionModel().getSelectedIndex());
-				if (eaCBox.getSelectionModel().getSelectedItem().getLocalParameters() != null) {
-					refreshParameters(eaCBox.getSelectionModel().getSelectedItem().getLocalParameters(), eaParameters);
-				}
+				refreshParameters(eaCBox.getSelectionModel().getSelectedItem().getLocalParameters(), eaParameters);
 			}
 		});
 		
@@ -157,17 +153,13 @@ public class SettingsPane extends AnchorPane {
 		mutatorCBox.prefWidthProperty().bind(mainContainer.widthProperty());
 		
 		final VBox mutatorParameters = new VBox(2);
-		if (jcgp.getEvolutionaryStrategy().getLocalParameters() != null) {
-			refreshParameters(jcgp.getMutator().getLocalParameters(), mutatorParameters);
-		}
+		refreshParameters(jcgp.getMutator().getLocalParameters(), mutatorParameters);
 		
 		mutatorCBox.setOnAction(new EventHandler<ActionEvent>() {
 			@Override
 			public void handle(ActionEvent event) {
 				jcgp.setMutator(mutatorCBox.getSelectionModel().getSelectedIndex());
-				if (mutatorCBox.getSelectionModel().getSelectedItem().getLocalParameters() != null) {
-					refreshParameters(mutatorCBox.getSelectionModel().getSelectedItem().getLocalParameters(), mutatorParameters);
-				}			
+				refreshParameters(mutatorCBox.getSelectionModel().getSelectedItem().getLocalParameters(), mutatorParameters);
 			}
 		});
 		
@@ -189,22 +181,22 @@ public class SettingsPane extends AnchorPane {
 		
 		final VBox problemParameters = new VBox(2);
 		problemParameters.setPadding(new Insets(0, 0, 4, 0));
-		if (jcgp.getProblem().getLocalParameters() != null) {
-			refreshParameters(jcgp.getProblem().getLocalParameters(), problemParameters);
-		}
+		refreshParameters(jcgp.getProblem().getLocalParameters(), problemParameters);
 		
 		final HBox testCaseControlContainer = new HBox(2);
 		
 		final Button showTestCaseButton = makeTestCaseButton();
-		final Button loadTestCaseButton = makeLoadTestCaseButton();
+		final Button loadProblemDataButton = makeLoadTestCaseButton();
 		HBox.setHgrow(showTestCaseButton, Priority.ALWAYS);
 		showTestCaseButton.setMaxWidth(Double.MAX_VALUE);
-		HBox.setHgrow(loadTestCaseButton, Priority.ALWAYS);
-		loadTestCaseButton.setMaxWidth(Double.MAX_VALUE);
+		HBox.setHgrow(loadProblemDataButton, Priority.ALWAYS);
+		loadProblemDataButton.setMaxWidth(Double.MAX_VALUE);
 		
 		if (jcgp.getProblem() instanceof TestCaseProblem<?>) {
-			testCaseControlContainer.getChildren().addAll(showTestCaseButton, loadTestCaseButton);
+			testCaseControlContainer.getChildren().addAll(showTestCaseButton, loadProblemDataButton);
 			remakeTestCaseTable();
+		} else {
+			testCaseControlContainer.getChildren().add(loadProblemDataButton);
 		}
 		
 		nodeFunctions = new VBox(2);
@@ -215,16 +207,16 @@ public class SettingsPane extends AnchorPane {
 			@Override
 			public void handle(ActionEvent event) {
 				jcgp.setProblem(problemCBox.getSelectionModel().getSelectedIndex());
-				if (jcgp.getProblem().getLocalParameters() != null) {
-					refreshParameters(jcgp.getProblem().getLocalParameters(), problemParameters);
-				}
+				refreshParameters(jcgp.getProblem().getLocalParameters(), problemParameters);
 				testCaseTable.close();
 				gui.setEvaluating(false);
 				refreshFunctions();
 				testCaseControlContainer.getChildren().clear();
 				if (jcgp.getProblem() instanceof TestCaseProblem) {
-					testCaseControlContainer.getChildren().addAll(showTestCaseButton, loadTestCaseButton);
+					testCaseControlContainer.getChildren().addAll(showTestCaseButton, loadProblemDataButton);
 					remakeTestCaseTable();
+				} else {
+					testCaseControlContainer.getChildren().add(loadProblemDataButton);
 				}
 				gui.reset();
 			}
@@ -236,17 +228,17 @@ public class SettingsPane extends AnchorPane {
 	}
 	
 	private Button makeLoadTestCaseButton() {
-		Button b = new Button("Load test cases");
+		Button b = new Button("Load problem data");
 		b.setOnAction(new EventHandler<ActionEvent>() {
 			@Override
 			public void handle(ActionEvent event) {
 				FileChooser fc = new FileChooser();
-				fc.setTitle("Open test case file...");
+				fc.setTitle("Open problem file...");
 				fc.getExtensionFilters().add(new ExtensionFilter("CGP " + gui.getExperiment().getProblem() + " files", "*" + ((TestCaseProblem<?>) gui.getExperiment().getProblem()).getFileExtension()));
 				fc.getExtensionFilters().add(new ExtensionFilter("All files", "*.*"));
 				File chrFile = fc.showOpenDialog(gui.getStage());
 				if (chrFile != null) {
-					gui.getExperiment().loadTestCases(chrFile);
+					gui.getExperiment().loadProblemData(chrFile);
 					remakeTestCaseTable();
 					gui.reDraw();
 				}
@@ -369,10 +361,12 @@ public class SettingsPane extends AnchorPane {
 	private void refreshParameters(Parameter<?>[] newParameters, VBox vb) {
 		parameters.removeAll(vb.getChildren());
 		vb.getChildren().clear();
-		for (int i = 0; i < newParameters.length; i++) {
-	        GUIParameter<?> gp = GUIParameter.create(newParameters[i], this);
-	        parameters.add(gp);
-        	vb.getChildren().add(gp);
+		if (newParameters != null) {
+			for (int i = 0; i < newParameters.length; i++) {
+				GUIParameter<?> gp = GUIParameter.create(newParameters[i], this);
+				parameters.add(gp);
+				vb.getChildren().add(gp);
+			}
 		}
 		revalidateParameters();
 	}
@@ -386,7 +380,7 @@ public class SettingsPane extends AnchorPane {
 		CheckBox cb;
 		final FunctionSet fs = gui.getExperiment().getResources().getFunctionSet();
 		for (int i = 0; i < fs.getTotalFunctionCount(); i++) {
-			cb = new CheckBox(fs.getFunction(i).getName());
+			cb = new CheckBox(fs.getFunction(i).toString());
 			cb.setId(String.valueOf(i));
 			cb.setSelected(fs.isEnabled(fs.getFunction(i)));
 			final int index = i;
diff --git a/src/jcgp/gui/settings/parameters/GUIBooleanParameter.java b/src/jcgp/gui/settings/parameters/GUIBooleanParameter.java
index e708c53..cc7113d 100644
--- a/src/jcgp/gui/settings/parameters/GUIBooleanParameter.java
+++ b/src/jcgp/gui/settings/parameters/GUIBooleanParameter.java
@@ -62,7 +62,8 @@ public class GUIBooleanParameter extends GUIParameter<Boolean> {
 			checkBox.setStyle(BASE_CHECKBOX_STYLE + INVALID_PARAMETER_STYLE);
 			checkBox.setTooltip(tooltip);
 			tooltip.setText(parameter.getStatus().getDetails());
-		} else if (parameter.getStatus() == ParameterStatus.WARNING || parameter.getStatus() ==  ParameterStatus.WARNING_RESET) {
+		} else if (parameter.getStatus() == ParameterStatus.WARNING 
+				|| parameter.getStatus() == ParameterStatus.WARNING_RESET) {
 			checkBox.setStyle(BASE_CHECKBOX_STYLE + WARNING_PARAMETER_STYLE);
 			checkBox.setTooltip(tooltip);
 			tooltip.setText(parameter.getStatus().getDetails());
diff --git a/src/jcgp/gui/settings/parameters/GUIDoubleParameter.java b/src/jcgp/gui/settings/parameters/GUIDoubleParameter.java
index f177ffa..777e739 100644
--- a/src/jcgp/gui/settings/parameters/GUIDoubleParameter.java
+++ b/src/jcgp/gui/settings/parameters/GUIDoubleParameter.java
@@ -36,6 +36,7 @@ public class GUIDoubleParameter extends GUIParameter<Number> {
 	
 	@Override
 	protected Control makeControl() {
+		// we use a text field, and a formatting class to enforce decimals
 		decimalFormat = new DecimalFormat();
 		decimalFormat.setMaximumFractionDigits(10);
 		textField = new TextField(decimalFormat.format(parameter.get().doubleValue()));
@@ -48,14 +49,16 @@ public class GUIDoubleParameter extends GUIParameter<Number> {
 	@Override
 	protected void setControlListeners() {
 		/* pass the TextField value back to the parameter whenever it gets
-		 * modified, provided it is not empty and the experiment isn't running */
+		 * modified, provided it is not empty, the experiment isn't running
+		 * and it matches the double-precision regex filter */
 		textField.textProperty().addListener(new ChangeListener<String>() {
 			@Override
 			public void changed(
 					ObservableValue<? extends String> observable,
 					String oldValue, String newValue) {
 				if (!settingsPane.isExperimentRunning()) {
-					if (newValue.matches("([0-9]*[.]*[0-9]*)")) {
+					//if (newValue.matches("([0-9]*[.]?[0-9]*)")) {
+					if (newValue.matches("^[-+]?[0-9]*\\.?[0-9]+$")) {
 						if (!newValue.isEmpty()) {
 							double value = Double.parseDouble(newValue);
 							parameter.set(value);
diff --git a/src/jcgp/gui/settings/parameters/GUIIntegerParameter.java b/src/jcgp/gui/settings/parameters/GUIIntegerParameter.java
index e1b0b75..6e8b3f1 100644
--- a/src/jcgp/gui/settings/parameters/GUIIntegerParameter.java
+++ b/src/jcgp/gui/settings/parameters/GUIIntegerParameter.java
@@ -33,6 +33,7 @@ public class GUIIntegerParameter extends GUIParameter<Number> {
 
 	@Override
 	protected Control makeControl() {
+		// this uses a text field
 		textField = new TextField(String.valueOf(parameter.get()));
 		textField.setStyle(VALID_PARAMETER_STYLE);
 		textField.setAlignment(Pos.CENTER_RIGHT);
@@ -44,7 +45,8 @@ public class GUIIntegerParameter extends GUIParameter<Number> {
 	@Override
 	protected void setControlListeners() {
 		/* pass the TextField value back to the parameter whenever it gets
-		 * modified, provided it is not empty and the experiment isn't running */
+		 * modified, provided it is not empty, the experiment isn't running
+		 * and it matches the integer regex pattern */
 		textField.textProperty().addListener(new ChangeListener<String>() {
 			@Override
 			public void changed(
@@ -98,7 +100,7 @@ public class GUIIntegerParameter extends GUIParameter<Number> {
 	@Override
 	public void refreshValue() {
 		if (!textField.isFocused()) {
-			textField.setText(String.valueOf(parameter.get()));
+			textField.setText(parameter.get().toString());
 		}
 	}
 }
diff --git a/src/jcgp/gui/settings/parameters/GUIParameter.java b/src/jcgp/gui/settings/parameters/GUIParameter.java
index 79762ff..b675fb5 100644
--- a/src/jcgp/gui/settings/parameters/GUIParameter.java
+++ b/src/jcgp/gui/settings/parameters/GUIParameter.java
@@ -30,9 +30,8 @@ import jcgp.gui.settings.SettingsPane;
  * Monitor parameters have their Control disabled so that no changed can be made via the GUI.
  * Non-monitor parameters are updated automatically as well, but may be changed by the user
  * if the program is not evolving.
- * <br><br>
- * For more information on how parameters work in JCGP, see {@link Parameter}.
  * 
+ * @see Parameter
  * @author Eduardo Pedroni
  * @param <T> the parameter data type
  */
@@ -174,7 +173,6 @@ public abstract class GUIParameter<T> extends HBox {
 	 */
 	public void validate() {
 		parameter.validate(parameter.get());
-		//refreshValue();
 		setValidityStyle();
 	}
 	
diff --git a/test.chr b/test.chr
index d015918..34664df 100644
--- a/test.chr
+++ b/test.chr
@@ -1 +1 @@
- 1 0 7	 0 0 6	 1 2 7	 3 5 7	 1 3 7	 3 5 7	 4 7 7	 7 4 10	 6 3 7	 10 11 7	 2 11 7	 6 11 6	 13 0 7	 13 12 10	 14 10 7			 16
\ No newline at end of file
+ 0 0 7	 0 0 6	 0 0 15	 0 0 6	 0 0 18	 2 0 6	 2 0 8	 1 3 14	 5 0 13	 2 4 11	 4 2 14	 4 2 0	 3 6 2	 2 5 1	 3 1 6	 6 5 3	 5 5 9	 3 3 13	 4 2 19	 3 4 18	 5 5 11	 7 6 5	 4 7 12	 0 5 4	 3 5 7			 3
\ No newline at end of file