Started refactoring backend in preparation for integration with the GUI

16 files changed, 218 insertions, 221 deletions

diff --git a/src/jcgp/CGP.java b/src/jcgp/CGP.java
index 6ac8ff8..1004001 100644
--- a/src/jcgp/CGP.java
+++ b/src/jcgp/CGP.java
@@ -1,79 +1,140 @@
 package jcgp;
 
+import java.util.HashMap;
 import java.util.Random;
 
+import javafx.beans.property.SimpleIntegerProperty;
 import jcgp.modules.ea.EvolutionaryAlgorithm;
 import jcgp.modules.ea.StandardEA;
 import jcgp.modules.fitness.FitnessFunction;
 import jcgp.modules.fitness.TestCase;
 import jcgp.modules.fitness.TruthTableEvaluator;
 import jcgp.modules.function.Arithmetic;
+import jcgp.modules.function.BitwiseLogic;
+import jcgp.modules.function.BooleanLogic;
 import jcgp.modules.function.FunctionSet;
 import jcgp.modules.mutator.Mutator;
-import jcgp.modules.mutator.StandardMutator;
+import jcgp.modules.mutator.PointMutator;
 import jcgp.parameters.BooleanParameter;
+import jcgp.parameters.DoubleParameter;
 import jcgp.parameters.IntegerParameter;
+import jcgp.parameters.Parameter;
 import jcgp.parameters.Parameters;
 import jcgp.population.Population;
 
 public class CGP {
 
 	// CGP components
-	private EvolutionaryAlgorithm evolutionaryAlgorithm;
-	private Mutator mutator;
-	private Population population;
-	private FitnessFunction fitnessFunction;
+	private Mutator[] mutators = new Mutator[] {
+			new PointMutator()};
+	private Mutator mutator = mutators[0];
+	
+	private EvolutionaryAlgorithm[] evolutionaryAlgorithms = new EvolutionaryAlgorithm[] {
+			new StandardEA()};
+	private EvolutionaryAlgorithm evolutionaryAlgorithm = evolutionaryAlgorithms[0];
+	
+	private FitnessFunction[] fitnessFunctions = new FitnessFunction[] {
+			new TruthTableEvaluator()};
+	private FitnessFunction fitnessFunction = fitnessFunctions[0];
+
+	private FunctionSet[] functionSets =  new FunctionSet[] {
+			new FunctionSet("Arithmetic",
+					new Arithmetic.Addition(),
+					new Arithmetic.Subtraction(),
+					new Arithmetic.Multiplication(),
+					new Arithmetic.Division()),
+
+			new FunctionSet("32-bit logic",
+					new BitwiseLogic.And(), 
+					new BitwiseLogic.Or(), 
+					new BitwiseLogic.Nand(), 
+					new BitwiseLogic.Nor(), 
+					new BitwiseLogic.Xor(),
+					new BitwiseLogic.Xnor(),
+					new BitwiseLogic.Not()),
+
+			new FunctionSet("1-bit logic",
+					new BooleanLogic.And(), 
+					new BooleanLogic.Or(), 
+					new BooleanLogic.Nand(), 
+					new BooleanLogic.Nor(), 
+					new BooleanLogic.Xor(),
+					new BooleanLogic.Xnor(),
+					new BooleanLogic.Not())};
 
 	
 	
+	private Population population;
+
+	private static HashMap<String, Parameter> parameters = new HashMap<String, Parameter>();
+
 	public CGP() {
-		initialise();
+		createBaseParameters();
 
 		for (int i = 0; i < Parameters.getTotalGenerations(); i++) {
-			Parameters.setCurrentGeneration(i);
+			
+			((SimpleIntegerProperty) get("currentGen").getValue()).set(i);
 			fitnessFunction.evaluate(population);
 			evolutionaryAlgorithm.evolve(population, mutator);
+			
 			if (evolutionaryAlgorithm.getFittestChromosome().getFitness() >= 3) {
-				if (Parameters.getDebug()) {
-					evolutionaryAlgorithm.getFittestChromosome().printNodes();
-				}
 				break;
 			}
 		}	
 	}
 
-	/**
-	 * 
-	 */
-	private void initialise() {
+	private void createBaseParameters() {
 		// make fundamental parameters
-		Parameters.add("Rows", new IntegerParameter(3));
-		Parameters.add("Columns", new IntegerParameter(3));
-		Parameters.add("Inputs", new IntegerParameter(3));
-		Parameters.add("Outputs", new IntegerParameter(3));
-		Parameters.add("population", new IntegerParameter(5));
-		
-		Parameters.add("generations", new IntegerParameter(100));
-		Parameters.add("runs", new IntegerParameter(5));
-		
-		Parameters.add("debug", new BooleanParameter(false));
+		parameters.put("rows", new IntegerParameter(3, "Rows"));
+		parameters.put("columns", new IntegerParameter(3, "Columns"));
+		parameters.put("inputs", new IntegerParameter(3, "Inputs"));
+		parameters.put("outputs", new IntegerParameter(3, "Outputs"));
+		parameters.put("popSize", new IntegerParameter(5, "Population"));
 		
-		// initialise function set
-		FunctionSet functionSet = new FunctionSet(new Arithmetic.Addition(), new Arithmetic.Subtraction(), new Arithmetic.Multiplication());
+		parameters.put("nodes", new IntegerParameter(9, "", true, true));
 		
-		// initialise utilities
-		Utilities.setResources(new Random(1234), functionSet);
+		parameters.put("gens", new IntegerParameter(100, "Generations"));
+		parameters.put("currentGen", new IntegerParameter(0, "Generation"));
+		parameters.put("runs", new IntegerParameter(5, "Runs"));
 		
-		// initialise fitness function and truth table
-		TruthTable.setTestCases(new TestCase(new Object[] {2, 5, 4}, new Object[] {1, 10, 15}));
-		fitnessFunction = new TruthTableEvaluator();
-
-		// initialise EA
-		evolutionaryAlgorithm = new StandardEA();
-		mutator = new StandardMutator();
-		
-		// initialise population
-		population = new Population();
+		parameters.put("debug", new BooleanParameter(false, "Debug"));
+	}
 
+//	/**
+//	 * 
+//	 */
+//	private void loadModules() {
+//		// initialise function set
+//		FunctionSet functionSet = new FunctionSet(new Arithmetic.Addition(), new Arithmetic.Subtraction(), new Arithmetic.Multiplication());
+//		
+//		// initialise utilities
+//		Utilities.setResources(new Random(1234), functionSet);
+//		
+//		// initialise fitness function and truth table
+//		TruthTable.setTestCases(new TestCase(new Object[] {2, 5, 4}, new Object[] {1, 10, 15}));
+//		fitnessFunction = new TruthTableEvaluator();
+//
+//		// initialise EA
+//		evolutionaryAlgorithm = new StandardEA();
+//		mutator = new StandardMutator();
+//		
+//		// initialise population
+//		population = new Population();
+//	}
+	
+	// Parameter methods
+	public static void registerParameter(String key, Parameter value) {
+		parameters.put(key, value);
+	}
+	
+	public static Parameter get(String key) {
+		return parameters.get(key);
+	}
+	
+	public static boolean contains(String key) {
+		return parameters.containsKey(key);
 	}
+	
+	// Utility methods
+	
 }
diff --git a/src/jcgp/modules/Module.java b/src/jcgp/modules/Module.java
index a0da50a..b8d44d2 100644
--- a/src/jcgp/modules/Module.java
+++ b/src/jcgp/modules/Module.java
@@ -11,5 +11,4 @@ public abstract class Module {
 	protected final void registerParameter(String key, Parameter value) {
 		Parameters.add(key, value);
 	};
-	
 }
diff --git a/src/jcgp/modules/function/Arithmetic.java b/src/jcgp/modules/function/Arithmetic.java
index 73debd2..aa5e9bf 100644
--- a/src/jcgp/modules/function/Arithmetic.java
+++ b/src/jcgp/modules/function/Arithmetic.java
@@ -1,7 +1,6 @@
 package jcgp.modules.function;
 
 import jcgp.exceptions.InvalidArgumentsException;
-import jcgp.parameters.Parameters;
 import jcgp.population.Connection;
 
 public class Arithmetic {
@@ -19,9 +18,6 @@ public class Arithmetic {
 				Integer arg2 = ((Integer) connections[1].getValue());
 				Integer result = arg1 + arg2;
 
-				if (Parameters.getDebug()) {
-					System.out.println(arg1 + " + " + arg2 + " = " + result);
-				}
 				return result;
 			}
 		}
@@ -45,9 +41,6 @@ public class Arithmetic {
 				Integer arg2 = ((Integer) connections[1].getValue());
 				Integer result = arg1 - arg2;
 
-				if (Parameters.getDebug()) {
-					System.out.println(arg1 + " - " + arg2 + " = " + result);
-				}
 				return result;
 			}
 		}
@@ -71,11 +64,6 @@ public class Arithmetic {
 				Integer arg2 = ((Integer) connections[1].getValue());
 				Integer result = arg1 * arg2;
 
-				if (Parameters.getDebug()) {
-					System.out.println(arg1 + " * " + arg2 + " = " + result);
-				}
-				
-
 				return result;
 			} 
 		}
@@ -103,12 +91,6 @@ public class Arithmetic {
 				} else {
 					result = arg1 / arg2;
 				}
-				
-
-				if (Parameters.getDebug()) {
-					System.out.println(arg1 + " / " + arg2 + " = " + result);
-				}
-				
 
 				return result;
 			} 
diff --git a/src/jcgp/modules/function/BitwiseLogic.java b/src/jcgp/modules/function/BitwiseLogic.java
index a260715..c8452e6 100644
--- a/src/jcgp/modules/function/BitwiseLogic.java
+++ b/src/jcgp/modules/function/BitwiseLogic.java
@@ -1,7 +1,6 @@
 package jcgp.modules.function;
 
 import jcgp.exceptions.InvalidArgumentsException;
-import jcgp.parameters.Parameters;
 import jcgp.population.Connection;
 
 public class BitwiseLogic {
@@ -17,9 +16,7 @@ public class BitwiseLogic {
 				int arg1 = ((int) connections[0].getValue());
 				int arg2 = ((int) connections[1].getValue());
 				int result = arg1 & arg2;
-				if (Parameters.getDebug()) {
-					System.out.println(arg1 + " AND " + arg2 + " = " + result);
-				}
+				
 				return result;
 			}
 		}
@@ -41,9 +38,7 @@ public class BitwiseLogic {
 				int arg1 = ((int) connections[0].getValue());
 				int arg2 = ((int) connections[1].getValue());
 				int result = arg1 | arg2;
-				if (Parameters.getDebug()) {
-					System.out.println(arg1 + " OR " + arg2 + " = " + result);
-				}
+
 				return result;
 			}
 		}
@@ -64,9 +59,7 @@ public class BitwiseLogic {
 			} else {
 				int arg1 = ((int) connections[0].getValue());
 				int result = ~arg1;
-				if (Parameters.getDebug()) {
-					System.out.println("NOT " + arg1 + " = " + result);
-				}
+
 				return result;
 			}
 		}
@@ -88,9 +81,7 @@ public class BitwiseLogic {
 				int arg1 = ((int) connections[0].getValue());
 				int arg2 = ((int) connections[1].getValue());
 				int result = arg1 ^ arg2;
-				if (Parameters.getDebug()) {
-					System.out.println(arg1 + " XOR " + arg2 + " = " + result);
-				}
+
 				return result;
 			}
 		}
@@ -112,9 +103,7 @@ public class BitwiseLogic {
 				int arg1 = ((int) connections[0].getValue());
 				int arg2 = ((int) connections[1].getValue());
 				int result = arg1 & arg2;
-				if (Parameters.getDebug()) {
-					System.out.println(arg1 + " NAND " + arg2 + " = " + ~result);
-				}
+
 				return ~result;
 			}
 		}
@@ -136,9 +125,7 @@ public class BitwiseLogic {
 				int arg1 = ((int) connections[0].getValue());
 				int arg2 = ((int) connections[1].getValue());
 				int result = arg1 | arg2;
-				if (Parameters.getDebug()) {
-					System.out.println(arg1 + " NOR " + arg2 + " = " + ~result);
-				}
+
 				return ~result;
 			}
 		}
@@ -160,9 +147,7 @@ public class BitwiseLogic {
 				int arg1 = ((int) connections[0].getValue());
 				int arg2 = ((int) connections[1].getValue());
 				int result = arg1 ^ arg2;
-				if (Parameters.getDebug()) {
-					System.out.println(arg1 + " XNOR " + arg2 + " = " + ~result);
-				}
+
 				return ~result;
 			}
 		}
diff --git a/src/jcgp/modules/function/BooleanLogic.java b/src/jcgp/modules/function/BooleanLogic.java
index 887e0e6..f98d1db 100644
--- a/src/jcgp/modules/function/BooleanLogic.java
+++ b/src/jcgp/modules/function/BooleanLogic.java
@@ -1,7 +1,6 @@
 package jcgp.modules.function;
 
 import jcgp.exceptions.InvalidArgumentsException;
-import jcgp.parameters.Parameters;
 import jcgp.population.Connection;
 
 public class BooleanLogic {
@@ -17,9 +16,7 @@ public class BooleanLogic {
 				Boolean arg1 = ((Boolean) connections[0].getValue());
 				Boolean arg2 = ((Boolean) connections[1].getValue());
 				Boolean result = arg1 && arg2;
-				if (Parameters.getDebug()) {
-					System.out.println(arg1 + " AND " + arg2 + " = " + result);
-				}
+
 				return result;
 			}
 		}
@@ -41,9 +38,7 @@ public class BooleanLogic {
 				Boolean arg1 = ((Boolean) connections[0].getValue());
 				Boolean arg2 = ((Boolean) connections[1].getValue());
 				Boolean result = arg1 || arg2;
-				if (Parameters.getDebug()) {
-					System.out.println(arg1 + " OR " + arg2 + " = " + result);
-				}
+
 				return result;
 			}
 		}
@@ -64,9 +59,7 @@ public class BooleanLogic {
 			} else {
 				Boolean arg1 = ((Boolean) connections[0].getValue());
 				Boolean result = !arg1;
-				if (Parameters.getDebug()) {
-					System.out.println("NOT " + arg1 + " = " + result);
-				}
+
 				return result;
 			}
 		}
@@ -88,9 +81,7 @@ public class BooleanLogic {
 				Boolean arg1 = ((Boolean) connections[0].getValue());
 				Boolean arg2 = ((Boolean) connections[1].getValue());
 				Boolean result = arg1 ^ arg2;
-				if (Parameters.getDebug()) {
-					System.out.println(arg1 + " XOR " + arg2 + " = " + result);
-				}
+
 				return result;
 			}
 		}
@@ -112,9 +103,7 @@ public class BooleanLogic {
 				Boolean arg1 = ((Boolean) connections[0].getValue());
 				Boolean arg2 = ((Boolean) connections[1].getValue());
 				Boolean result = arg1 && arg2;
-				if (Parameters.getDebug()) {
-					System.out.println(arg1 + " NAND " + arg2 + " = " + !result);
-				}
+
 				return !result;
 			}
 		}
@@ -136,9 +125,7 @@ public class BooleanLogic {
 				Boolean arg1 = ((Boolean) connections[0].getValue());
 				Boolean arg2 = ((Boolean) connections[1].getValue());
 				Boolean result = arg1 || arg2;
-				if (Parameters.getDebug()) {
-					System.out.println(arg1 + " NOR " + arg2 + " = " + !result);
-				}
+
 				return !result;
 			}
 		}
@@ -160,9 +147,7 @@ public class BooleanLogic {
 				Boolean arg1 = ((Boolean) connections[0].getValue());
 				Boolean arg2 = ((Boolean) connections[1].getValue());
 				Boolean result = arg1 ^ arg2;
-				if (Parameters.getDebug()) {
-					System.out.println(arg1 + " XNOR " + arg2 + " = " + !result);
-				}
+
 				return !result;
 			}
 		}
diff --git a/src/jcgp/modules/function/FunctionSet.java b/src/jcgp/modules/function/FunctionSet.java
index 8a2190a..fb3724f 100644
--- a/src/jcgp/modules/function/FunctionSet.java
+++ b/src/jcgp/modules/function/FunctionSet.java
@@ -13,16 +13,18 @@ package jcgp.modules.function;
 public class FunctionSet {
 		private Function[] functionList;
 		private int maxArity = 0;
+		private String name;
 		
-		public FunctionSet(Function ... functions) {
+		public FunctionSet(String name, Function ... functions) {
 			functionList = functions;
-			
 			for (Function function : functionList) {
 				if (function.getArity() > maxArity) {
 					maxArity = function.getArity();
 				}
 			}
 			
+			this.name = name;
+			
 		}
 		
 		public int getFunctionCount() {
@@ -36,4 +38,8 @@ public class FunctionSet {
 		public int getMaxArity(){
 			return maxArity;
 		}
+		
+		public String getName() {
+			return name;
+		}
 	}
\ No newline at end of file
diff --git a/src/jcgp/modules/mutator/StandardMutator.java b/src/jcgp/modules/mutator/PointMutator.java
index 17bd0be..b06d678 100644
--- a/src/jcgp/modules/mutator/StandardMutator.java
+++ b/src/jcgp/modules/mutator/PointMutator.java
@@ -1,17 +1,22 @@
 package jcgp.modules.mutator;
 
 import jcgp.Utilities;
+import jcgp.parameters.IntegerParameter;
 import jcgp.parameters.Parameters;
 import jcgp.population.Chromosome;
 import jcgp.population.MutableElement;
 import jcgp.population.Node;
 import jcgp.population.Output;
 
-public class StandardMutator implements Mutator {
+public class PointMutator implements Mutator {
 
+	public PointMutator() {
+		Parameters.add("mutRate", new IntegerParameter(10, "Mutation rate"));
+	}
+	
 	@Override
 	public void mutate(Chromosome chromosome) {
-		int mutations = (int) (Parameters.getMutationRate() * (((double) Parameters.getNodeCount() + Parameters.getOutputs()) / 100));
+		int mutations = (int) (((int) Parameters.get("mutRate").getValue()) * ((((double) Parameters.get("nodes").getValue()) + ((double) Parameters.get("outputs").getValue())) / 100));
 		
 		for (int i = 0; i < mutations; i++) {
 			MutableElement m = chromosome.getRandomMutableElement();
@@ -19,7 +24,7 @@ public class StandardMutator implements Mutator {
 			if (m instanceof Output) {
 				m.setConnection(chromosome.getRandomConnection());
 			} else if (m instanceof Node) {
-				int geneType = Utilities.getRandomInt(1 + Parameters.getMaxArity());
+				int geneType = Utilities.getRandomInt(1 + ((int) Parameters.get("Max arity").getValue()));
 				if (geneType < 1) {
 					((Node) m).setFunction(Utilities.getRandomFunction());
 				} else {
diff --git a/src/jcgp/parameters/BooleanParameter.java b/src/jcgp/parameters/BooleanParameter.java
index 738b733..9402620 100644
--- a/src/jcgp/parameters/BooleanParameter.java
+++ b/src/jcgp/parameters/BooleanParameter.java
@@ -3,30 +3,31 @@ package jcgp.parameters;
 import javafx.beans.property.SimpleBooleanProperty;
 
 public class BooleanParameter extends Parameter {
-	
-	private SimpleBooleanProperty value;
-	
-	public BooleanParameter(boolean value) {
-		
-		this.value.set(value);
 		
+	public BooleanParameter(boolean value, String name) {
+		this.value = new SimpleBooleanProperty(value);
+		this.name = name;
 	}
 	
-	public BooleanParameter(boolean value, boolean managed) {
-		this.value.set(value);
+	public BooleanParameter(boolean value, String name, boolean managed, boolean hidden) {
+		this.value = new SimpleBooleanProperty(value);
+		this.name = name;
 		this.managed = managed;
+		this.hidden = hidden;
 	}
 	
 	public void setValue(boolean value) {
-		this.value.set(value);
+		((SimpleBooleanProperty) this.value).set(value);
 	}
 	
-	public boolean getValue() {
-		return this.value.get();
+	@Override
+	public Object getValue() {
+		return ((SimpleBooleanProperty) this.value).get();
 	}
 	
+	@Override
 	public SimpleBooleanProperty valueProperty() {
-		return value;
+		return (SimpleBooleanProperty) value;
 	}
 	
 }
diff --git a/src/jcgp/parameters/DoubleParameter.java b/src/jcgp/parameters/DoubleParameter.java
index 9349502..2c2ec34 100644
--- a/src/jcgp/parameters/DoubleParameter.java
+++ b/src/jcgp/parameters/DoubleParameter.java
@@ -3,30 +3,30 @@ package jcgp.parameters;
 import javafx.beans.property.SimpleDoubleProperty;
 
 public class DoubleParameter extends Parameter {
-	
-	private SimpleDoubleProperty value;
-	
-	public DoubleParameter(double value) {
-		
-		this.value.set(value);
 		
+	public DoubleParameter(double value, String name) {
+		this.value = new SimpleDoubleProperty(value);
+		this.name = name;
 	}
 	
-	public DoubleParameter(double value, boolean managed) {
-		this.value.set(value);
+	public DoubleParameter(double value, String name, boolean managed, boolean hidden) {
+		this.value = new SimpleDoubleProperty(value);
+		this.name = name;
 		this.managed = managed;
+		this.hidden = hidden;
 	}
 	
 	public void setValue(double value) {
-		this.value.set(value);
+		((SimpleDoubleProperty) this.value).set(value);
 	}
 	
-	public double getValue() {
-		return this.value.get();
+	@Override
+	public Object getValue() {
+		return ((SimpleDoubleProperty) this.value).get();
 	}
 	
 	public SimpleDoubleProperty valueProperty() {
-		return value;
+		return (SimpleDoubleProperty) value;
 	}
 	
 }
diff --git a/src/jcgp/parameters/IntegerParameter.java b/src/jcgp/parameters/IntegerParameter.java
index 2aac3e1..6b4c20f 100644
--- a/src/jcgp/parameters/IntegerParameter.java
+++ b/src/jcgp/parameters/IntegerParameter.java
@@ -3,30 +3,31 @@ package jcgp.parameters;
 import javafx.beans.property.SimpleIntegerProperty;
 
 public class IntegerParameter extends Parameter {
-	
-	private SimpleIntegerProperty value;
-	
-	public IntegerParameter(int value) {
-		
-		this.value.set(value);
 		
+	public IntegerParameter(int value, String name) {
+		this.value = new SimpleIntegerProperty(value);
+		this.name = name;
 	}
 	
-	public IntegerParameter(int value, boolean managed) {
-		this.value.set(value);
+	public IntegerParameter(int value, String name, boolean managed, boolean hidden) {
+		this.value = new SimpleIntegerProperty(value);
+		this.name = name;
 		this.managed = managed;
+		this.hidden = hidden;
 	}
 	
 	public void setValue(int value) {
-		this.value.set(value);
+		((SimpleIntegerProperty) this.value).set(value);
 	}
 	
-	public int getValue() {
-		return this.value.get();
+	@Override
+	public Object getValue() {
+		return ((SimpleIntegerProperty) this.value).get();
 	}
 	
+	@Override
 	public SimpleIntegerProperty valueProperty() {
-		return value;
+		return (SimpleIntegerProperty) value;
 	}
 	
 }
diff --git a/src/jcgp/parameters/Parameter.java b/src/jcgp/parameters/Parameter.java
index 8b63868..ffcf3b4 100644
--- a/src/jcgp/parameters/Parameter.java
+++ b/src/jcgp/parameters/Parameter.java
@@ -1,8 +1,14 @@
 package jcgp.parameters;
 
+import javafx.beans.property.Property;
+
 public abstract class Parameter {
+	
 	protected boolean managed = false;
 	protected boolean hidden = false;
+	protected String name;
+	@SuppressWarnings("rawtypes")
+	protected Property value;
 	
 	public void setManaged(boolean value) {
 		managed = value;
@@ -19,4 +25,13 @@ public abstract class Parameter {
 	public boolean isHidden() {
 		return hidden;
 	}
+	
+	public String getName() {
+		return name;
+	}
+	
+	public abstract Object getValue();
+	
+	@SuppressWarnings("rawtypes")
+	public abstract Property valueProperty();
 }
diff --git a/src/jcgp/parameters/Parameters.java b/src/jcgp/parameters/Parameters.java
index 54b54e3..723c5dc 100644
--- a/src/jcgp/parameters/Parameters.java
+++ b/src/jcgp/parameters/Parameters.java
@@ -4,19 +4,7 @@ import java.util.HashMap;
 
 public class Parameters {
 	
-	private static HashMap<String, Parameter> parameters;
 
-	public static void add(String key, Parameter value) {
-		parameters.put(key, value);
-	}
-	
-	public static Parameter get(String key) {
-		return parameters.get(key);
-	}
-	
-	public static boolean contains(String key) {
-		return parameters.containsKey(key);
-	}
 	
 //	private static int rows = 0, columns = 0, inputs = 0, outputs = 0, levelsBack = 0, 
 //					   mutationRate = 0, totalGenerations = 0, parents = 0, offspring = 0,
@@ -25,6 +13,8 @@ public class Parameters {
 	
 //	private static boolean debug = false;
 	
+	
+	
 
 	
 	
diff --git a/src/jcgp/population/Chromosome.java b/src/jcgp/population/Chromosome.java
index df2a9d4..1f0b312 100644
--- a/src/jcgp/population/Chromosome.java
+++ b/src/jcgp/population/Chromosome.java
@@ -52,20 +52,20 @@ public class Chromosome {
 	 *
 	 */
 	private void instantiateElements() {
-		inputs = new Input[Parameters.getInputs()];
-		for (int i = 0; i < Parameters.getInputs(); i++) {
+		inputs = new Input[((int) Parameters.get("inputs").getValue())];
+		for (int i = 0; i < ((int) Parameters.get("inputs").getValue()); i++) {
 			inputs[i] = new Input(i);
 		}
 
 		// rows first
-		nodes = new Node[Parameters.getRows()][Parameters.getColumns()];
-		for (int r = 0; r < Parameters.getRows(); r++) {
-			for (int c = 0; c < Parameters.getColumns(); c++) {
+		nodes = new Node[((int) Parameters.get("rows").getValue())][((int) Parameters.get("columns").getValue())];
+		for (int r = 0; r < ((int) Parameters.get("rows").getValue()); r++) {
+			for (int c = 0; c < ((int) Parameters.get("columns").getValue()); c++) {
 				nodes[r][c] = new Node(this, r, c);
 			}
 		}
-		outputs = new Output[Parameters.getOutputs()];
-		for (int o = 0; o < Parameters.getOutputs(); o++) {
+		outputs = new Output[((int) Parameters.get("outputs").getValue())];
+		for (int o = 0; o < ((int) Parameters.get("outputs").getValue()); o++) {
 			outputs[o] = new Output(this, o);
 		}
 	}
@@ -78,7 +78,7 @@ public class Chromosome {
 		// initialise nodes - [rows][columns]
 		for (int r = 0; r < nodes.length; r++) {
 			for (int c = 0; c < nodes[r].length; c++) {
-				Connection[] connections = new Connection[Parameters.getMaxArity()];
+				Connection[] connections = new Connection[((int) Parameters.get("maxArity").getValue())];
 				for (int i = 0; i < connections.length; i++) {
 					connections[i] = getRandomConnection(c);
 				}
@@ -100,7 +100,7 @@ public class Chromosome {
 		for (int r = 0; r < nodes.length; r++) {
 			for (int c = 0; c < nodes[r].length; c++) {
 				// make array of connections to initialise with
-				Connection[] connections = new Connection[Parameters.getMaxArity()];
+				Connection[] connections = new Connection[((int) Parameters.get("maxArity").getValue())];
 				// populate with connections equivalent to clone
 				Connection copyConnection;
 				for (int i = 0; i < connections.length; i++) {
@@ -177,7 +177,7 @@ public class Chromosome {
 	 */
 	public MutableElement getRandomMutableElement() {
 		// choose output or node
-		int index = Utilities.getRandomInt(outputs.length + Parameters.getNodeCount());
+		int index = Utilities.getRandomInt(outputs.length + ((int) Parameters.get("rows").getValue()) * ((int) Parameters.get("columns").getValue()));
 
 		if (index < outputs.length) {
 			// outputs
@@ -185,7 +185,7 @@ public class Chromosome {
 		} else {
 			// node	
 			index -= outputs.length;
-			return nodes[index / Parameters.getColumns()][index % Parameters.getColumns()];
+			return nodes[index / ((int) Parameters.get("columns").getValue())][index % ((int) Parameters.get("columns").getValue())];
 		}
 	}
 
@@ -199,7 +199,7 @@ public class Chromosome {
 	 */
 	public Connection getRandomConnection(int column) {
 		// work out the allowed range obeying levels back
-		int allowedColumns = ((column >= Parameters.getLevelsBack()) ? Parameters.getLevelsBack() : column);
+		int allowedColumns = ((column >= ((int) Parameters.get("levelsBack").getValue())) ? ((int) Parameters.get("levelsBack").getValue()) : column);
 		int offset = ((column - allowedColumns) * nodes.length) - inputs.length;
 
 		// choose input or allowed node
@@ -226,7 +226,7 @@ public class Chromosome {
 	 */
 	public Connection getRandomConnection() {
 		// choose output or node
-		int index = Utilities.getRandomInt(inputs.length + Parameters.getNodeCount());
+		int index = Utilities.getRandomInt(inputs.length + ((int) Parameters.get("columns").getValue()) * ((int) Parameters.get("rows").getValue()));
 
 		if (index < inputs.length) {
 			// outputs
@@ -234,7 +234,7 @@ public class Chromosome {
 		} else {
 			// node	
 			index -= inputs.length;
-			return nodes[index / Parameters.getColumns()][index % Parameters.getColumns()];
+			return nodes[index / ((int) Parameters.get("columns").getValue())][index % ((int) Parameters.get("columns").getValue())];
 		}
 	}
 
@@ -269,15 +269,15 @@ public class Chromosome {
 	}
 
 	public boolean compareTo(Chromosome chromosome) {
-		for (int r = 0; r < Parameters.getRows(); r++) {
-			for (int c = 0; c < Parameters.getColumns(); c++) {
+		for (int r = 0; r < ((int) Parameters.get("rows").getValue()); r++) {
+			for (int c = 0; c < ((int) Parameters.get("columns").getValue()); c++) {
 				if (!(nodes[r][c].copyOf(chromosome.getNode(r, c)))) {
 					return false;
 				}
 			}
 		}
 		
-		for (int o = 0; o < Parameters.getOutputs(); o++) {
+		for (int o = 0; o < ((int) Parameters.get("outputs").getValue()); o++) {
 			if (!(outputs[o].copyOf(chromosome.getOutput(o)))) {
 				return false;
 			}
@@ -302,11 +302,11 @@ public class Chromosome {
 	}
 	
 	public void printNodes() {
-		for (int r = 0; r < Parameters.getRows(); r++) {
+		for (int r = 0; r < ((int) Parameters.get("rows").getValue()); r++) {
 			System.out.print("r: " + r + "\t");
-			for (int c = 0; c < Parameters.getColumns(); c++) {
+			for (int c = 0; c < ((int) Parameters.get("columns").getValue()); c++) {
 				System.out.print("N: (" + r + ", " + c + ") ");
-				for (int i = 0; i < Parameters.getMaxArity(); i++) {
+				for (int i = 0; i < ((int) Parameters.get("maxArity").getValue()); i++) {
 					System.out.print("C" + i + ": (" + nodes[r][c].getConnection(i).getDescription() + ") ");
 				}
 				System.out.print("F: " + nodes[r][c].getFunction().toString() + "\t");
@@ -314,7 +314,7 @@ public class Chromosome {
 			System.out.print("\n");
 		}
 		
-		for (int o = 0; o < Parameters.getOutputs(); o++) {
+		for (int o = 0; o < ((int) Parameters.get("outputs").getValue()); o++) {
 			System.out.print("o: " + o + " (" + outputs[o].getSource().getDescription() + ")\t");
 		}
 	}
diff --git a/src/jcgp/population/Node.java b/src/jcgp/population/Node.java
index 4203f25..9fafe32 100644
--- a/src/jcgp/population/Node.java
+++ b/src/jcgp/population/Node.java
@@ -20,7 +20,7 @@ public class Node implements MutableElement, Connection {
 		this.chromosome = chromosome;
 		this.column = column;
 		this.row = row;
-		this.connections = new Connection[Parameters.getMaxArity()];
+		this.connections = new Connection[((int) Parameters.get("maxArity").getValue())];
 	}
 
 	@Override
@@ -44,7 +44,7 @@ public class Node implements MutableElement, Connection {
 
 		function = newFunction;
 
-		if (newConnections.length >= Parameters.getMaxArity()) {
+		if (newConnections.length >= ((int) Parameters.get("maxArity").getValue())) {
 			connections = newConnections;
 		} else {
 			throw new InsufficientConnectionsException();
diff --git a/src/jcgp/population/Output.java b/src/jcgp/population/Output.java
index 89ca13c..ccecae0 100644
--- a/src/jcgp/population/Output.java
+++ b/src/jcgp/population/Output.java
@@ -2,8 +2,6 @@ package jcgp.population;
 
 import java.util.ArrayList;
 
-import jcgp.parameters.Parameters;
-
 public class Output implements MutableElement {
 	
 	private Connection source;
@@ -17,9 +15,6 @@ public class Output implements MutableElement {
 
 	public Object calculate() {
 		Object result = source.getValue();
-		if (Parameters.getDebug()) {
-			System.out.println("Output " + index + ": " + result);
-		}
 		return result;
 	}
 
diff --git a/src/jcgp/population/Population.java b/src/jcgp/population/Population.java
index 3e7b590..5718515 100644
--- a/src/jcgp/population/Population.java
+++ b/src/jcgp/population/Population.java
@@ -4,46 +4,26 @@ import jcgp.parameters.Parameters;
 
 public class Population {
 	
-	private Chromosome[] parents;
-	private Chromosome[] offspring;
+	private Chromosome[] chromosomes;
 	private Chromosome bestIndividual;
 	
 	public Population(Chromosome parent) {
-		parents = new Chromosome[Parameters.getParentCount()];
+		chromosomes = new Chromosome[((int) Parameters.get("population").getValue())];
 		// make a clone for safety
-		this.parents[0] = new Chromosome(parent);
-		// generate the rest of parents
-		for (int c = 1; c < parents.length; c++) {
-			parents[c] = new Chromosome();
-		}
-		
-		offspring = new Chromosome[Parameters.getOffspringCount()];
-		for (int c = 0; c < offspring.length; c++) {
-			// completely random offspring? depending on EA, this means the given parent won't be selected
-			offspring[c] = new Chromosome();
+		this.chromosomes[0] = new Chromosome(parent);
+		// generate the rest of the individuals
+		for (int c = 1; c < chromosomes.length; c++) {
+			chromosomes[c] = new Chromosome(chromosomes[0]);
 		}
 	}
 	
 	public Population() {
-		parents = new Chromosome[Parameters.getParentCount()];
-		for (int c = 0; c < parents.length; c++) {
-			parents[c] = new Chromosome();
-		}
-
-		offspring = new Chromosome[Parameters.getOffspringCount()];
-		for (int c = 0; c < offspring.length; c++) {
-			offspring[c] = new Chromosome();
+		chromosomes = new Chromosome[((int) Parameters.get("population").getValue())];
+		for (int c = 0; c < chromosomes.length; c++) {
+			chromosomes[c] = new Chromosome();
 		}
 	}
 
-	public Chromosome getOffspring(int index) {
-		return offspring[index];
-	}
-	
-	public Chromosome getParent(int index) {
-		return parents[index];
-	}
-	
 	/**
 	 * Returns all chromosomes, parents first, then offspring.
 	 * 
@@ -51,19 +31,11 @@ public class Population {
 	 * @return
 	 */
 	public Chromosome getChromosome(int index) {
-		if (index < parents.length) {
-			return parents[index];
-		} else {
-			return offspring[index - parents.length];
-		}
+		return chromosomes[index];
 	}
 	
 	public void setBestIndividual(int index) {
-		if (index < parents.length) {
-			bestIndividual = parents[index];
-		} else {
-			bestIndividual = offspring[index - parents.length];
-		}
+		bestIndividual = chromosomes[index];
 	}
 	
 	public Chromosome getBestIndividual() {