16 files changed, 478 insertions, 375 deletions

diff --git a/src/jcgp/backend/function/BitwiseLogic.java b/src/jcgp/backend/function/BitwiseLogic.java
index 14f4488..a4c2737 100644
--- a/src/jcgp/backend/function/BitwiseLogic.java
+++ b/src/jcgp/backend/function/BitwiseLogic.java
@@ -31,8 +31,8 @@ public class BitwiseLogic extends FunctionSet {
 	
 	public static class ConstantZero extends Function {
 		@Override
-		public Long run(Connection... connections) {
-			return new Long(0);
+		public UnsignedInteger run(Connection... connections) {
+			return new UnsignedInteger(0);
 		}
 
 		@Override
@@ -48,8 +48,8 @@ public class BitwiseLogic extends FunctionSet {
 	
 	public static class ConstantOne extends Function {
 		@Override
-		public Long run(Connection... connections) {
-			return new Long(Long.MAX_VALUE);
+		public UnsignedInteger run(Connection... connections) {
+			return new UnsignedInteger(0xFFFF);
 		}
 
 		@Override
@@ -65,11 +65,11 @@ public class BitwiseLogic extends FunctionSet {
 	
 	public static class WireA extends Function {
 		@Override
-		public Long run(Connection... connections) {
+		public UnsignedInteger run(Connection... connections) {
 			if (connections.length < getArity()) {
 				throw new IllegalArgumentException(getName() + " received " + connections.length + " connections but arity is " + getArity() + ".");
 			} else {
-				return ((Long) connections[0].getValue()).longValue();
+				return ((UnsignedInteger) connections[0].getValue());
 			}
 		}
 
@@ -86,11 +86,11 @@ public class BitwiseLogic extends FunctionSet {
 	
 	public static class WireB extends Function {
 		@Override
-		public Long run(Connection... connections) {
+		public UnsignedInteger run(Connection... connections) {
 			if (connections.length < getArity()) {
 				throw new IllegalArgumentException(getName() + " received " + connections.length + " connections but arity is " + getArity() + ".");
 			} else {
-				return ((Long) connections[1].getValue()).longValue();
+				return ((UnsignedInteger) connections[1].getValue());
 			}
 		}
 
@@ -107,11 +107,11 @@ public class BitwiseLogic extends FunctionSet {
 	
 	public static class NotA extends Function {
 		@Override
-		public Long run(Connection... connections) {
+		public UnsignedInteger run(Connection... connections) {
 			if (connections.length < getArity()) {
 				throw new IllegalArgumentException(getName() + " received " + connections.length + " connections but arity is " + getArity() + ".");
 			} else {
-				return ~((Long) connections[0].getValue()).longValue();
+				return new UnsignedInteger(~((UnsignedInteger) connections[0].getValue()).get());
 			}
 		}
 
@@ -128,11 +128,11 @@ public class BitwiseLogic extends FunctionSet {
 	
 	public static class NotB extends Function {
 		@Override
-		public Long run(Connection... connections) {
+		public UnsignedInteger run(Connection... connections) {
 			if (connections.length < getArity()) {
 				throw new IllegalArgumentException(getName() + " received " + connections.length + " connections but arity is " + getArity() + ".");
 			} else {
-				return ~((Long) connections[1].getValue()).longValue();
+				return new UnsignedInteger(~((UnsignedInteger) connections[1].getValue()).get());
 			}
 		}
 
@@ -149,15 +149,15 @@ public class BitwiseLogic extends FunctionSet {
 	
 	public static class And extends Function {
 		@Override
-		public Long run(Connection... connections) {
+		public UnsignedInteger run(Connection... connections) {
 			if (connections.length < getArity()) {
 				throw new IllegalArgumentException(getName() + " received " + connections.length + " connections but arity is " + getArity() + ".");
 			} else {
-				Long arg1 = ((Long) connections[0].getValue());
-				Long arg2 = ((Long) connections[1].getValue());
-				Long result = arg1 & arg2;
+				UnsignedInteger arg1 = ((UnsignedInteger) connections[0].getValue());
+				UnsignedInteger arg2 = ((UnsignedInteger) connections[1].getValue());
+				Integer result = arg1.get() & arg2.get();
 				
-				return result;
+				return new UnsignedInteger(result);
 			}
 		}
 
@@ -174,15 +174,15 @@ public class BitwiseLogic extends FunctionSet {
 	
 	public static class AndNotA extends Function {
 		@Override
-		public Long run(Connection... connections) {
+		public UnsignedInteger run(Connection... connections) {
 			if (connections.length < getArity()) {
 				throw new IllegalArgumentException(getName() + " received " + connections.length + " connections but arity is " + getArity() + ".");
 			} else {
-				Long arg1 = ((Long) connections[0].getValue());
-				Long arg2 = ((Long) connections[1].getValue());
-				Long result = ~arg1 & arg2;
+				UnsignedInteger arg1 = ((UnsignedInteger) connections[0].getValue());
+				UnsignedInteger arg2 = ((UnsignedInteger) connections[1].getValue());
+				Integer result = ~(arg1.get()) & arg2.get();
 				
-				return result;
+				return new UnsignedInteger(result);
 			}
 		}
 
@@ -199,15 +199,15 @@ public class BitwiseLogic extends FunctionSet {
 	
 	public static class AndNotB extends Function {
 		@Override
-		public Long run(Connection... connections) {
+		public UnsignedInteger run(Connection... connections) {
 			if (connections.length < getArity()) {
 				throw new IllegalArgumentException(getName() + " received " + connections.length + " connections but arity is " + getArity() + ".");
 			} else {
-				Long arg1 = ((Long) connections[0].getValue());
-				Long arg2 = ((Long) connections[1].getValue());
-				Long result = arg1 & ~arg2;
+				UnsignedInteger arg1 = ((UnsignedInteger) connections[0].getValue());
+				UnsignedInteger arg2 = ((UnsignedInteger) connections[1].getValue());
+				Integer result = arg1.get() & ~(arg2.get());
 				
-				return result;
+				return new UnsignedInteger(result);
 			}
 		}
 
@@ -224,15 +224,15 @@ public class BitwiseLogic extends FunctionSet {
 	
 	public static class Nor extends Function {
 		@Override
-		public Long run(Connection... connections) {
+		public UnsignedInteger run(Connection... connections) {
 			if (connections.length < getArity()) {
 				throw new IllegalArgumentException(getName() + " received " + connections.length + " connections but arity is " + getArity() + ".");
 			} else {
-				Long arg1 = ((Long) connections[0].getValue());
-				Long arg2 = ((Long) connections[1].getValue());
-				Long result = arg1 | arg2;
+				UnsignedInteger arg1 = ((UnsignedInteger) connections[0].getValue());
+				UnsignedInteger arg2 = ((UnsignedInteger) connections[1].getValue());
+				Integer result = arg1.get() | arg2.get();
 
-				return ~result;
+				return new UnsignedInteger(~result);
 			}
 		}
 
@@ -249,15 +249,15 @@ public class BitwiseLogic extends FunctionSet {
 	
 	public static class Xor extends Function {
 		@Override
-		public Long run(Connection... connections) {
+		public UnsignedInteger run(Connection... connections) {
 			if (connections.length < getArity()) {
 				throw new IllegalArgumentException(getName() + " received " + connections.length + " connections but arity is " + getArity() + ".");
 			} else {
-				Long arg1 = ((Long) connections[0].getValue());
-				Long arg2 = ((Long) connections[1].getValue());
-				Long result = arg1 ^ arg2;
+				UnsignedInteger arg1 = ((UnsignedInteger) connections[0].getValue());
+				UnsignedInteger arg2 = ((UnsignedInteger) connections[1].getValue());
+				Integer result = arg1.get() ^ arg2.get();
 
-				return result;
+				return new UnsignedInteger(result);
 			}
 		}
 
@@ -274,15 +274,15 @@ public class BitwiseLogic extends FunctionSet {
 	
 	public static class Xnor extends Function {
 		@Override
-		public Long run(Connection... connections) {
+		public UnsignedInteger run(Connection... connections) {
 			if (connections.length < getArity()) {
 				throw new IllegalArgumentException(getName() + " received " + connections.length + " connections but arity is " + getArity() + ".");
 			} else {
-				Long arg1 = ((Long) connections[0].getValue());
-				Long arg2 = ((Long) connections[1].getValue());
-				Long result = arg1 ^ arg2;
+				UnsignedInteger arg1 = ((UnsignedInteger) connections[0].getValue());
+				UnsignedInteger arg2 = ((UnsignedInteger) connections[1].getValue());
+				Integer result = arg1.get() ^ arg2.get();
 
-				return ~result;
+				return new UnsignedInteger(~result);
 			}
 		}
 
@@ -299,15 +299,15 @@ public class BitwiseLogic extends FunctionSet {
 	
 	public static class Or extends Function {
 		@Override
-		public Long run(Connection... connections) {
+		public UnsignedInteger run(Connection... connections) {
 			if (connections.length < getArity()) {
 				throw new IllegalArgumentException(getName() + " received " + connections.length + " connections but arity is " + getArity() + ".");
 			} else {
-				Long arg1 = ((Long) connections[0].getValue());
-				Long arg2 = ((Long) connections[1].getValue());
-				Long result = arg1 | arg2;
+				UnsignedInteger arg1 = ((UnsignedInteger) connections[0].getValue());
+				UnsignedInteger arg2 = ((UnsignedInteger) connections[1].getValue());
+				Integer result = arg1.get() | arg2.get();
 
-				return result;
+				return new UnsignedInteger(result);
 			}
 		}
 
@@ -324,15 +324,15 @@ public class BitwiseLogic extends FunctionSet {
 	
 	public static class OrNotA extends Function {
 		@Override
-		public Long run(Connection... connections) {
+		public UnsignedInteger run(Connection... connections) {
 			if (connections.length < getArity()) {
 				throw new IllegalArgumentException(getName() + " received " + connections.length + " connections but arity is " + getArity() + ".");
 			} else {
-				Long arg1 = ((Long) connections[0].getValue());
-				Long arg2 = ((Long) connections[1].getValue());
-				Long result = ~arg1 | arg2;
+				UnsignedInteger arg1 = ((UnsignedInteger) connections[0].getValue());
+				UnsignedInteger arg2 = ((UnsignedInteger) connections[1].getValue());
+				Integer result = ~arg1.get() | arg2.get();
 
-				return result;
+				return new UnsignedInteger(result);
 			}
 		}
 
@@ -349,15 +349,15 @@ public class BitwiseLogic extends FunctionSet {
 	
 	public static class OrNotB extends Function {
 		@Override
-		public Long run(Connection... connections) {
+		public UnsignedInteger run(Connection... connections) {
 			if (connections.length < getArity()) {
 				throw new IllegalArgumentException(getName() + " received " + connections.length + " connections but arity is " + getArity() + ".");
 			} else {
-				Long arg1 = ((Long) connections[0].getValue());
-				Long arg2 = ((Long) connections[1].getValue());
-				Long result = arg1 | ~arg2;
+				UnsignedInteger arg1 = ((UnsignedInteger) connections[0].getValue());
+				UnsignedInteger arg2 = ((UnsignedInteger) connections[1].getValue());
+				Integer result = arg1.get() | ~arg2.get();
 
-				return result;
+				return new UnsignedInteger(result);
 			}
 		}
 
@@ -374,15 +374,15 @@ public class BitwiseLogic extends FunctionSet {
 
 	public static class Nand extends Function {
 		@Override
-		public Long run(Connection... connections) {
+		public UnsignedInteger run(Connection... connections) {
 			if (connections.length < getArity()) {
 				throw new IllegalArgumentException(getName() + " received " + connections.length + " connections but arity is " + getArity() + ".");
 			} else {
-				Long arg1 = ((Long) connections[0].getValue());
-				Long arg2 = ((Long) connections[1].getValue());
-				Long result = arg1 & arg2;
+				UnsignedInteger arg1 = ((UnsignedInteger) connections[0].getValue());
+				UnsignedInteger arg2 = ((UnsignedInteger) connections[1].getValue());
+				Integer result = arg1.get() & arg2.get();
 
-				return ~result;
+				return new UnsignedInteger(~result);
 			}
 		}
 
diff --git a/src/jcgp/backend/function/BooleanLogic.java b/src/jcgp/backend/function/BooleanLogic.java
deleted file mode 100644
index 9e7d1ff..0000000
--- a/src/jcgp/backend/function/BooleanLogic.java
+++ /dev/null
@@ -1,199 +0,0 @@
-package jcgp.backend.function;
-
-
-import jcgp.backend.exceptions.InvalidArgumentsException;
-import jcgp.backend.population.Connection;
-
-public class BooleanLogic extends FunctionSet {
-	
-	public BooleanLogic() {
-		name = "1-bit Logic";
-		functionList = new Function[]{
-				new And(),
-				new Or(),
-				new Not(),
-				new Xor(),
-				new Nand(),
-				new Nor(),
-				new Xnor()};
-		
-		enableAll();
-	}
-
-	public static class And extends Function {
-		@Override
-		public Boolean run(Connection... connections) {
-			if (connections.length < 2) {
-				throw new InvalidArgumentsException("Not enough connections were given.");
-			} else {
-				Boolean arg1 = ((Boolean) connections[0].getValue());
-				Boolean arg2 = ((Boolean) connections[1].getValue());
-				Boolean result = arg1 && arg2;
-
-				return result;
-			}
-		}
-
-		@Override
-		public int getArity() {
-			return 2;
-		}
-
-		@Override
-		public String getName() {
-			return "AND";
-		}
-	}
-	
-	public static class Or extends Function {
-		@Override
-		public Boolean run(Connection... connections) {
-			if (connections.length < 2) {
-				throw new InvalidArgumentsException("Not enough connections were given.");
-			} else {
-				Boolean arg1 = ((Boolean) connections[0].getValue());
-				Boolean arg2 = ((Boolean) connections[1].getValue());
-				Boolean result = arg1 || arg2;
-
-				return result;
-			}
-		}
-
-		@Override
-		public int getArity() {
-			return 2;
-		}
-
-		@Override
-		public String getName() {
-			return "OR";
-		}
-	}
-
-	public static class Not extends Function {
-		@Override
-		public Boolean run(Connection... connections) {
-			if (connections.length < 1) {
-				throw new InvalidArgumentsException("Not enough connections were given.");
-			} else {
-				Boolean arg1 = ((Boolean) connections[0].getValue());
-				Boolean result = !arg1;
-
-				return result;
-			}
-		}
-
-		@Override
-		public int getArity() {
-			return 1;
-		}
-
-		@Override
-		public String getName() {
-			return "NOT";
-		}
-	}
-
-	public static class Xor extends Function {
-		@Override
-		public Boolean run(Connection... connections) {
-			if (connections.length < 2) {
-				throw new InvalidArgumentsException("Not enough connections were given.");
-			} else {
-				Boolean arg1 = ((Boolean) connections[0].getValue());
-				Boolean arg2 = ((Boolean) connections[1].getValue());
-				Boolean result = arg1 ^ arg2;
-
-				return result;
-			}
-		}
-
-		@Override
-		public int getArity() {
-			return 2;
-		}
-
-		@Override
-		public String getName() {
-			return "XOR";
-		}
-	}
-
-	public static class Nand extends Function {
-		@Override
-		public Boolean run(Connection... connections) {
-			if (connections.length < 2) {
-				throw new InvalidArgumentsException("Not enough connections were given.");
-			} else {
-				Boolean arg1 = ((Boolean) connections[0].getValue());
-				Boolean arg2 = ((Boolean) connections[1].getValue());
-				Boolean result = arg1 && arg2;
-
-				return !result;
-			}
-		}
-
-		@Override
-		public int getArity() {
-			return 2;
-		}
-
-		@Override
-		public String getName() {
-			return "NAND";
-		}
-	}
-
-	public static class Nor extends Function {
-		@Override
-		public Boolean run(Connection... connections) {
-			if (connections.length < 2) {
-				throw new InvalidArgumentsException("Not enough connections were given.");
-			} else {
-				Boolean arg1 = ((Boolean) connections[0].getValue());
-				Boolean arg2 = ((Boolean) connections[1].getValue());
-				Boolean result = arg1 || arg2;
-
-				return !result;
-			}
-		}
-
-		@Override
-		public int getArity() {
-			return 2;
-		}
-
-		@Override
-		public String getName() {
-			return "NOR";
-		}
-	}
-
-	public static class Xnor extends Function {
-		@Override
-		public Boolean run(Connection... connections) {
-			if (connections.length < 2) {
-				throw new InvalidArgumentsException("Not enough connections were given.");
-			} else {
-				Boolean arg1 = ((Boolean) connections[0].getValue());
-				Boolean arg2 = ((Boolean) connections[1].getValue());
-				Boolean result = arg1 ^ arg2;
-
-				return !result;
-			}
-		}
-
-		@Override
-		public int getArity() {
-			return 2;
-		}
-
-		@Override
-		public String getName() {
-			return "XNOR";
-		}
-	}
-
-	
-	
-}
diff --git a/src/jcgp/backend/function/UnsignedInteger.java b/src/jcgp/backend/function/UnsignedInteger.java
new file mode 100644
index 0000000..7feb33f
--- /dev/null
+++ b/src/jcgp/backend/function/UnsignedInteger.java
@@ -0,0 +1,66 @@
+package jcgp.backend.function;
+
+/**
+ * Integer wrapper type for unsigned integer values. 
+ * <br><br>
+ * Java offers no support for unsigned types save from 
+ * unsigned conversion methods. This class uses those methods
+ * to simulate the unsigned int data type, useful for circuit 
+ * truth table encodings.
+ * <br><br>
+ * When a string representation of an unsigned integer is parsed
+ * using Integer.parseUnsignedInt(), an Integer is created using
+ * all 32 bits for unsigned magnitude. The integer however is still
+ * signed and will behave as such for all arithmetic operations.
+ * Bitwise operations can still be performed as they work at the bit
+ * level, making this data type particularly suitable for circuit design. 
+ * 
+ * 
+ * @author Eduardo Pedroni
+ * @see Integer
+ *
+ */
+public class UnsignedInteger {
+	
+	private Integer value;
+	
+	/**
+	 * Makes a new instance of UnsignedInteger with a specified value.
+	 * 
+	 * @param i the value with which to initialise
+	 */
+	public UnsignedInteger(int i) {
+		value = new Integer(i);
+	}
+	
+	/**
+	 * Makes a new instance of UnsignedInteger with a specified value.
+	 * 
+	 * @param i the value with which to initialise
+	 */
+	public UnsignedInteger(Integer i) {
+		value = i;
+	}
+	
+	/**
+	 * Makes a new instance of UnsignedInteger from the string representation
+	 * of an unsigned integer.
+	 * 
+	 * @param i the string with which to initialise
+	 */
+	public UnsignedInteger(String i) {
+		value = Integer.parseUnsignedInt(i);
+	}
+	
+	/**
+	 * @return the wrapped Integer object
+	 */
+	public Integer get() {
+		return value;
+	}
+	
+	@Override
+	public String toString() {
+		return Integer.toUnsignedString(value);
+	}
+}
diff --git a/src/jcgp/backend/modules/mutator/PointMutator.java b/src/jcgp/backend/modules/mutator/PointMutator.java
index ab8efad..44c453a 100644
--- a/src/jcgp/backend/modules/mutator/PointMutator.java
+++ b/src/jcgp/backend/modules/mutator/PointMutator.java
@@ -7,18 +7,21 @@ 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;
 
 	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");
@@ -30,7 +33,12 @@ public class PointMutator implements Mutator {
 				}
 			}
 		};
-		
+		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) {
@@ -41,9 +49,8 @@ public class PointMutator implements Mutator {
 
 	@Override
 	public void mutate(Chromosome chromosome, Resources resources) {
-		int mutations = (int) ((mutationRate.get()) * (((((double) resources.nodes() + resources.outputs()))) / 100));
-		if (report.get()) resources.reportln("[Mutator] Number of mutations to be performed: " + mutations);
-		for (int i = 0; i < mutations; i++) {
+		if (report.get()) resources.reportln("[Mutator] Number of mutations to be performed: " + nodesMutated.get());
+		for (int i = 0; i < nodesMutated.get(); i++) {
 			MutableElement m = chromosome.getRandomMutableElement();
 			if (report.get()) resources.report("[Mutator] Mutation " + i + " selected " + m.toString() + ", ");
 			
@@ -75,7 +82,7 @@ public class PointMutator implements Mutator {
 
 	@Override
 	public Parameter<?>[] getLocalParameters() {
-		return new Parameter[] {mutationRate, report};
+		return new Parameter[] {mutationRate, nodesMutated, report};
 	}
 
 	@Override
diff --git a/src/jcgp/backend/modules/problem/DigitalCircuit.java b/src/jcgp/backend/modules/problem/DigitalCircuit.java
deleted file mode 100644
index d94197d..0000000
--- a/src/jcgp/backend/modules/problem/DigitalCircuit.java
+++ /dev/null
@@ -1,25 +0,0 @@
-package jcgp.backend.modules.problem;
-
-import java.util.ArrayList;
-
-import jcgp.backend.function.BitwiseLogic;
-import jcgp.backend.resources.Resources;
-
-public class DigitalCircuit extends TestCaseProblem<Integer> {
-
-	public DigitalCircuit(Resources resources) {
-		super(resources);
-		functionSet = new BitwiseLogic();
-		
-		ArrayList<TestCase<Integer>> tc = new ArrayList<TestCase<Integer>>();
-		tc.add(new TestCase<Integer>(new Integer[]{1, 2, 3}, new Integer[]{-4, 5, 6}));
-		
-		setTestCases(tc);
-	}
-	
-	@Override
-	public String toString() {
-		return "Digital circuit";
-	}
-	
-}
diff --git a/src/jcgp/backend/modules/problem/DigitalCircuitProblem.java b/src/jcgp/backend/modules/problem/DigitalCircuitProblem.java
new file mode 100644
index 0000000..e92989e
--- /dev/null
+++ b/src/jcgp/backend/modules/problem/DigitalCircuitProblem.java
@@ -0,0 +1,85 @@
+package jcgp.backend.modules.problem;
+
+import jcgp.backend.function.BitwiseLogic;
+import jcgp.backend.function.UnsignedInteger;
+import jcgp.backend.population.Chromosome;
+import jcgp.backend.population.Population;
+import jcgp.backend.resources.Resources;
+
+public class DigitalCircuitProblem extends TestCaseProblem<UnsignedInteger> {
+	
+	public DigitalCircuitProblem(Resources resources) {
+		super(resources);
+		functionSet = new BitwiseLogic();
+	}
+	
+	@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
+			int fitness = 0;
+			
+			// iterate over every test case
+			for (int t = 0; t < testCases.size(); t++) {
+				population.getChromosome(i).setInputs((Object[]) testCases.get(t).getInputs());
+				// check each output
+				for (int o = 0; o < resources.outputs(); o++) {
+					Integer output = ((UnsignedInteger) population.getChromosome(i).getOutput(o).calculate()).get();
+					Integer matches = ~(output ^ testCases.get(t).getOutput(o).get());
+					// check only the relevant bits
+					int bits = (int) Math.pow(2.0, (double) resources.inputs());
+					for (int b = 0; b < bits; b++) {
+						if (((matches >>> b) & 1) == 1) {
+							fitness++;
+						}
+					}
+				}
+			}
+			
+			// assign the resulting fitness to the respective individual
+			population.getChromosome(i).setFitness(fitness);
+			if (fitness >= population.getFittest().getFitness()) {
+				population.setFittest(i);
+			}
+		}
+	}
+	
+	@Override
+	protected int getMaxFitness() {
+		int maxFitness = (int) Math.pow(2.0, (double) resources.inputs()) * resources.outputs();
+		return maxFitness;
+	}
+	
+	@Override
+	public String toString() {
+		return "Digital circuit";
+	}
+
+	@Override
+	public void addTestCase(String[] inputs, String[] outputs) {
+		UnsignedInteger[] inputCases = new UnsignedInteger[inputs.length];
+		UnsignedInteger[] outputCases = new UnsignedInteger[outputs.length];
+		for (int i = 0; i < inputCases.length; i++) {
+			inputCases[i] = new UnsignedInteger(inputs[i]);
+		}
+		for (int o = 0; o < outputCases.length; o++) {
+			outputCases[o] = new UnsignedInteger(outputs[o]);
+		}
+		
+		addTestCase(new TestCase<UnsignedInteger>(inputCases, outputCases));
+	}
+	
+	@Override
+	public boolean isPerfectSolution(Chromosome fittest) {
+		return fittest.getFitness() >= maxFitness.get();
+	}
+
+	@Override
+	public String getFileExtension() {
+		return ".plu";
+	}
+}
diff --git a/src/jcgp/backend/modules/problem/SymbolicRegression.java b/src/jcgp/backend/modules/problem/SymbolicRegression.java
deleted file mode 100644
index 46b8e09..0000000
--- a/src/jcgp/backend/modules/problem/SymbolicRegression.java
+++ /dev/null
@@ -1,26 +0,0 @@
-package jcgp.backend.modules.problem;
-
-import java.util.ArrayList;
-
-import jcgp.backend.function.DoubleArithmetic;
-import jcgp.backend.resources.Resources;
-
-public class SymbolicRegression extends TestCaseProblem<Double> {	
-	
-	public SymbolicRegression(Resources resources) {
-		super(resources);
-		functionSet = new DoubleArithmetic();
-		
-		ArrayList<TestCase<Double>> tc = new ArrayList<TestCase<Double>>();
-		tc.add(new TestCase<Double>(new Double[]{1.0, 2.0, 3.0}, new Double[]{-4.0, 5.0, 6.0}));
-		tc.add(new TestCase<Double>(new Double[]{3.0, 2.0, 5.0}, new Double[]{2.0, 5.0, 9.0}));
-		
-		setTestCases(tc);
-	}
-	
-	@Override
-	public String toString() {
-		return "Symbolic regression";
-	}
-
-}
diff --git a/src/jcgp/backend/modules/problem/SymbolicRegressionProblem.java b/src/jcgp/backend/modules/problem/SymbolicRegressionProblem.java
new file mode 100644
index 0000000..52df0f2
--- /dev/null
+++ b/src/jcgp/backend/modules/problem/SymbolicRegressionProblem.java
@@ -0,0 +1,124 @@
+package jcgp.backend.modules.problem;
+
+import jcgp.backend.function.DoubleArithmetic;
+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.DoubleParameter;
+import jcgp.backend.resources.parameters.Parameter;
+import jcgp.backend.resources.parameters.ParameterStatus;
+
+public class SymbolicRegressionProblem extends TestCaseProblem<Double> {
+	
+	private DoubleParameter errorThreshold, perfectionThreshold;
+	private BooleanParameter hitsBasedFitness;
+	
+	public SymbolicRegressionProblem(Resources resources) {
+		super(resources);
+		functionSet = new DoubleArithmetic();
+		errorThreshold = new DoubleParameter(0.01, "Error threshold") {
+			@Override
+			public void validate(Number newValue) {
+				if (newValue.doubleValue() < 0) {
+					status = ParameterStatus.INVALID;
+					status.setDetails("Error threshold must be a positive value.");
+				} else if (newValue.doubleValue() == 0) {
+					status = ParameterStatus.WARNING;
+					status.setDetails("An error threshold of 0 is very rigorous and difficult to achieve.");
+				} else {
+					status = ParameterStatus.VALID;
+				}
+			}
+		};
+		perfectionThreshold = new DoubleParameter(0.000001, "Perfection threshold") {
+			@Override
+			public void validate(Number newValue) {
+				if (newValue.doubleValue() < 0) {
+					status = ParameterStatus.INVALID;
+					status.setDetails("Perfection threshold must be a positive value.");
+				} else if (newValue.doubleValue() == 0) {
+					status = ParameterStatus.WARNING;
+					status.setDetails("A perfection threshold of 0 is very rigorous and difficult to achieve.");
+				} else {
+					status = ParameterStatus.VALID;
+				}
+			}
+		};
+		hitsBasedFitness = new BooleanParameter(true, "Hits-based fitness") {
+			@Override
+			public void validate(Boolean newValue) {
+				// blank
+			}
+		};
+	}
+	
+	@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
+			double fitness = 0;
+			// for each test case
+			for (int t = 0; t < testCases.size(); t++) {
+				population.getChromosome(i).setInputs((Object[]) testCases.get(t).getInputs());
+				// check each output
+				for (int o = 0; o < resources.outputs(); o++) {
+					Double cgpValue = (Double) population.getChromosome(i).getOutput(o).calculate();
+					Double dataValue = testCases.get(t).getOutput(o);
+					if (hitsBasedFitness.get()) {
+						if (Math.abs(cgpValue - dataValue) <= errorThreshold.get()) {
+							fitness++;
+						}
+					} else {
+						fitness += 1 - Math.abs(cgpValue - dataValue);
+					}
+					
+				}
+			}
+			// assign the resulting fitness to the respective individual
+			population.getChromosome(i).setFitness(fitness);
+			if (fitness >= population.getFittest().getFitness()) {
+				population.setFittest(i);
+			}
+		}
+	}
+	
+	
+	@Override
+	public String toString() {
+		return "Symbolic regression";
+	}
+
+	@Override
+	public void addTestCase(String[] inputs, String[] outputs) {
+		Double[] inputCases = new Double[inputs.length];
+		Double[] outputCases = new Double[outputs.length];
+		for (int i = 0; i < inputCases.length; i++) {
+			inputCases[i] = Double.parseDouble(inputs[i]);
+		}
+		for (int o = 0; o < outputCases.length; o++) {
+			outputCases[o] = Double.parseDouble(outputs[o]);
+		}
+		
+		addTestCase(new TestCase<Double>(inputCases, outputCases));
+	}
+
+	@Override
+	public boolean isPerfectSolution(Chromosome fittest) {
+		return fittest.getFitness() >= maxFitness.get() - perfectionThreshold.get();
+	}
+	
+	@Override
+	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 ee72860..ff13c2e 100644
--- a/src/jcgp/backend/modules/problem/TestCaseProblem.java
+++ b/src/jcgp/backend/modules/problem/TestCaseProblem.java
@@ -1,11 +1,11 @@
 package jcgp.backend.modules.problem;
 
+import java.io.File;
 import java.util.List;
 
 import javafx.collections.FXCollections;
 import javafx.collections.ObservableList;
-import jcgp.backend.population.Chromosome;
-import jcgp.backend.population.Population;
+import jcgp.backend.parser.TestCaseParser;
 import jcgp.backend.resources.Resources;
 import jcgp.backend.resources.parameters.IntegerParameter;
 import jcgp.backend.resources.parameters.Parameter;
@@ -48,15 +48,16 @@ public abstract class TestCaseProblem<U extends Object> extends Problem {
 		}
 	}
 	
-	private ObservableList<TestCase<U>> testCases;
-	private IntegerParameter maxFitness;
-	private final int inputCount, outputCount;
+	protected ObservableList<TestCase<U>> testCases;
+	protected IntegerParameter maxFitness;
+	protected Resources resources;
+	
+	protected TestCaseParser parser;
 	
 	public TestCaseProblem(Resources resources) {
 		super();
 		
-		inputCount = resources.inputs();
-		outputCount = resources.outputs();
+		this.resources = resources;
 		
 		maxFitness = new IntegerParameter(0, "Max fitness", true, false) {
 			@Override
@@ -65,34 +66,26 @@ public abstract class TestCaseProblem<U extends Object> extends Problem {
 			}
 		};
 		testCases = FXCollections.observableArrayList();
+		
+		parser = new TestCaseParser(this);
 	}
 	
-	
-	@Override
-	public void evaluate(Population population, Resources resources) {
-		// set fittest to 0, change it whenever a fitter one is found
-		population.setFittest(0);
+	public TestCaseProblem(Resources resources, File testCase) {
+		super();
 		
-		// for every chromosome in the population
-		for (int i = 0; i < resources.populationSize(); i++) {
-			// assume an initial fitness of 0
-			int fitness = 0;
-			// for each test case
-			for (int t = 0; t < testCases.size(); t++) {
-				population.getChromosome(i).setInputs(testCases.get(t).getInputs());
-				// check each output
-				for (int o = 0; o < resources.outputs(); o++) {
-					if (population.getChromosome(i).getOutput(o).calculate() == testCases.get(t).getOutput(o)) {
-						fitness++;
-					}
-				}
-			}
-			// assign the resulting fitness to the respective individual
-			population.getChromosome(i).setFitness(fitness);
-			if (fitness >= population.getFittest().getFitness()) {
-				population.setFittest(i);
+		this.resources = resources;
+		
+		maxFitness = new IntegerParameter(0, "Max fitness", true, false) {
+			@Override
+			public void validate(Number newValue) {
+				// blank
 			}
-		}
+		};
+		testCases = FXCollections.observableArrayList();
+		
+		parser = new TestCaseParser(this);
+		
+		parser.parse(testCase);
 	}
 	
 	@Override
@@ -100,12 +93,7 @@ public abstract class TestCaseProblem<U extends Object> extends Problem {
 		return new Parameter[]{maxFitness};
 	}
 	
-	@Override
-	public boolean isPerfectSolution(Chromosome fittest) {
-		return fittest.getFitness() >= maxFitness.get();
-	}
-	
-	private int getMaxFitness() {
+	protected int getMaxFitness() {
 		int fitness = 0;
 		
 		for (TestCase<U> tc : testCases) {
@@ -125,13 +113,15 @@ public abstract class TestCaseProblem<U extends Object> extends Problem {
 		return testCases;
 	}
 	
+	public abstract void addTestCase(String[] inputs, String[] outputs);
+	
 	public void addTestCase(TestCase<U> testCase) {
-		if (testCase.getInputs().length != inputCount) {
+		if (testCase.getInputs().length != resources.inputs()) {
 			throw new IllegalArgumentException("Received test case with " + testCase.getInputs().length + 
-					"inputs but need exactly " + inputCount);
-		} else if (testCase.getOutputs().length != outputCount) {
+					" inputs but need exactly " + resources.inputs());
+		} else if (testCase.getOutputs().length != resources.outputs()) {
 			throw new IllegalArgumentException("Received test case with " + testCase.getOutputs().length + 
-					"outputs but need exactly " + outputCount);
+					" outputs but need exactly " + resources.outputs());
 		} else {
 			this.testCases.add(testCase);
 			maxFitness.set(getMaxFitness());
@@ -144,12 +134,22 @@ public abstract class TestCaseProblem<U extends Object> extends Problem {
 	}
 	
 	public int getInputCount() {
-		return inputCount;
+		return resources.inputs();
 	}
 	
 	public int getOutputCount() {
-		return outputCount;
+		return resources.outputs();
+	}
+
+	public void parse(File file) {
+		parser.parse(file);
 	}
+
+	public void clearTestCases() {
+		testCases.clear();
+	}
+
+	public abstract String getFileExtension();
 }
 
 
diff --git a/src/jcgp/backend/parser/ChromosomeParser.java b/src/jcgp/backend/parser/ChromosomeParser.java
index 74f638c..d5af1bd 100644
--- a/src/jcgp/backend/parser/ChromosomeParser.java
+++ b/src/jcgp/backend/parser/ChromosomeParser.java
@@ -17,7 +17,7 @@ import jcgp.backend.resources.Resources;
  * @author Eduardo Pedroni
  *
  */
-public class ChromosomeParser {
+public abstract class ChromosomeParser {
 
 	/**
 	 * Use this method to parse .chr files into a given chromosome.
diff --git a/src/jcgp/backend/parser/FunctionParser.java b/src/jcgp/backend/parser/FunctionParser.java
index 64a095c..ab94899 100644
--- a/src/jcgp/backend/parser/FunctionParser.java
+++ b/src/jcgp/backend/parser/FunctionParser.java
@@ -40,17 +40,10 @@ private FunctionSet functionSet;
 	}
 	
 	private void parseAndSet(String[] splitString) {
-//		System.out.println("new line");
-//		for (int i= 0; i < splitString.length; i++) {
-//			System.out.println(i + ": " + splitString[i]);
-//		}
 		int functionIndex = Integer.parseInt(splitString[splitString.length - 1]);
-		System.out.println("index: " + functionIndex);
 		if (Integer.parseInt(splitString[0]) != 0) {
-			System.out.println("enabling: " + functionSet.getFunction(functionIndex).getName());
 			functionSet.enableFunction(functionIndex);
 		} else {
-			System.out.println("disabling: " + functionSet.getFunction(functionIndex).getName());
 			functionSet.disableFunction(functionIndex);
 		}
 		
diff --git a/src/jcgp/backend/parser/ParameterParser.java b/src/jcgp/backend/parser/ParameterParser.java
index 473b632..f96ebf9 100644
--- a/src/jcgp/backend/parser/ParameterParser.java
+++ b/src/jcgp/backend/parser/ParameterParser.java
@@ -4,6 +4,7 @@ import java.io.File;
 import java.io.FileNotFoundException;
 import java.io.FileReader;
 import java.util.Scanner;
+
 import jcgp.backend.resources.ModifiableResources;
 
 public class ParameterParser {
diff --git a/src/jcgp/backend/parser/TestCaseParser.java b/src/jcgp/backend/parser/TestCaseParser.java
index c997177..d47d663 100644
--- a/src/jcgp/backend/parser/TestCaseParser.java
+++ b/src/jcgp/backend/parser/TestCaseParser.java
@@ -1,13 +1,90 @@
 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 {
 
-	public static void parse(File file, TestCaseProblem<?> problem) {
+	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/population/Chromosome.java b/src/jcgp/backend/population/Chromosome.java
index 71e19ec..f8830fa 100644
--- a/src/jcgp/backend/population/Chromosome.java
+++ b/src/jcgp/backend/population/Chromosome.java
@@ -15,7 +15,7 @@ public class Chromosome {
 
 	private ArrayList<Node> activeNodes;
 
-	private int fitness = 0;
+	private double fitness = 0;
 	private boolean recomputeActiveNodes = true;
 
 	/**
@@ -154,11 +154,11 @@ public class Chromosome {
 		return inputs[index];
 	}
 
-	public int getFitness() {
+	public double getFitness() {
 		return fitness;
 	}
 
-	public void setFitness(int newFitness) {
+	public void setFitness(double newFitness) {
 		fitness = newFitness;
 	}
 
diff --git a/src/jcgp/backend/resources/Resources.java b/src/jcgp/backend/resources/Resources.java
index 0bf1ee1..151d536 100644
--- a/src/jcgp/backend/resources/Resources.java
+++ b/src/jcgp/backend/resources/Resources.java
@@ -155,7 +155,7 @@ public class Resources {
 			}
 		};
 		
-		inputs = new IntegerParameter(3, "Inputs", false, true) {
+		inputs = new IntegerParameter(3, "Inputs", true, false) {
 			@Override
 			public void validate(Number newValue) {
 				if (newValue.intValue() <= 0) {
@@ -167,7 +167,7 @@ public class Resources {
 			}
 		};
 		
-		outputs = new IntegerParameter(3, "Outputs", false, true) {
+		outputs = new IntegerParameter(3, "Outputs", true, false) {
 			@Override
 			public void validate(Number newValue) {
 				if (newValue.intValue() <= 0) {
diff --git a/src/jcgp/backend/tests/NodeTests.java b/src/jcgp/backend/tests/NodeTests.java
index c9f247a..4054661 100644
--- a/src/jcgp/backend/tests/NodeTests.java
+++ b/src/jcgp/backend/tests/NodeTests.java
@@ -2,8 +2,8 @@ package jcgp.backend.tests;
 
 import static org.junit.Assert.assertTrue;
 import jcgp.backend.exceptions.InvalidArgumentsException;
-import jcgp.backend.function.Function;
 import jcgp.backend.function.DoubleArithmetic;
+import jcgp.backend.function.Function;
 import jcgp.backend.population.Chromosome;
 import jcgp.backend.population.Connection;
 import jcgp.backend.population.Node;