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

4 files changed, 79 insertions, 113 deletions

diff --git a/src/jcgp/backend/function/BitwiseLogic.java b/src/jcgp/backend/function/BitwiseLogic.java
index bfe361f..5d47ff7 100644
--- a/src/jcgp/backend/function/BitwiseLogic.java
+++ b/src/jcgp/backend/function/BitwiseLogic.java
@@ -1,8 +1,5 @@
 package jcgp.backend.function;
 
-import java.util.ArrayList;
-import java.util.Arrays;
-
 import jcgp.backend.exceptions.InvalidArgumentsException;
 import jcgp.backend.population.Connection;
 
@@ -19,15 +16,13 @@ public class BitwiseLogic extends FunctionSet {
 				new Nor(),
 				new Xnor()};
 		
-		allowedFunctions = new ArrayList<Function>(Arrays.asList(functionList));
+		enableAll();
 	}
 
-	public static class And extends Function {	
-		private int arity = 2;
-
+	public static class And extends Function {
 		@Override
 		public Object run(Connection... connections) {
-			if (connections.length < arity) {
+			if (connections.length < 2) {
 				throw new InvalidArgumentsException("Not enough connections were given.");
 			} else {
 				int arg1 = ((int) connections[0].getValue());
@@ -40,7 +35,7 @@ public class BitwiseLogic extends FunctionSet {
 
 		@Override
 		public int getArity() {
-			return arity;
+			return 2;
 		}
 
 		@Override
@@ -49,12 +44,10 @@ public class BitwiseLogic extends FunctionSet {
 		}
 	}
 	
-	public static class Or extends Function {	
-		private int arity = 2;
-
+	public static class Or extends Function {
 		@Override
 		public Object run(Connection... connections) {
-			if (connections.length < arity) {
+			if (connections.length < 2) {
 				throw new InvalidArgumentsException("Not enough connections were given.");
 			} else {
 				int arg1 = ((int) connections[0].getValue());
@@ -67,7 +60,7 @@ public class BitwiseLogic extends FunctionSet {
 
 		@Override
 		public int getArity() {
-			return arity;
+			return 2;
 		}
 
 		@Override
@@ -76,12 +69,10 @@ public class BitwiseLogic extends FunctionSet {
 		}
 	}
 
-	public static class Not extends Function {	
-		private int arity = 1;
-
+	public static class Not extends Function {
 		@Override
 		public Object run(Connection... connections) {
-			if (connections.length < arity) {
+			if (connections.length < 1) {
 				throw new InvalidArgumentsException("Not enough connections were given.");
 			} else {
 				int arg1 = ((int) connections[0].getValue());
@@ -93,7 +84,7 @@ public class BitwiseLogic extends FunctionSet {
 
 		@Override
 		public int getArity() {
-			return arity;
+			return 1;
 		}
 
 		@Override
@@ -102,12 +93,10 @@ public class BitwiseLogic extends FunctionSet {
 		}
 	}
 
-	public static class Xor extends Function {	
-		private int arity = 2;
-
+	public static class Xor extends Function {
 		@Override
 		public Object run(Connection... connections) {
-			if (connections.length < arity) {
+			if (connections.length < 2) {
 				throw new InvalidArgumentsException("Not enough connections were given.");
 			} else {
 				int arg1 = ((int) connections[0].getValue());
@@ -120,7 +109,7 @@ public class BitwiseLogic extends FunctionSet {
 
 		@Override
 		public int getArity() {
-			return arity;
+			return 2;
 		}
 
 		@Override
@@ -129,12 +118,10 @@ public class BitwiseLogic extends FunctionSet {
 		}
 	}
 
-	public static class Nand extends Function {	
-		private int arity = 2;
-
+	public static class Nand extends Function {
 		@Override
 		public Object run(Connection... connections) {
-			if (connections.length < arity) {
+			if (connections.length < 2) {
 				throw new InvalidArgumentsException("Not enough connections were given.");
 			} else {
 				int arg1 = ((int) connections[0].getValue());
@@ -147,7 +134,7 @@ public class BitwiseLogic extends FunctionSet {
 
 		@Override
 		public int getArity() {
-			return arity;
+			return 2;
 		}
 
 		@Override
@@ -156,12 +143,10 @@ public class BitwiseLogic extends FunctionSet {
 		}
 	}
 
-	public static class Nor extends Function {	
-		private int arity = 2;
-
+	public static class Nor extends Function {
 		@Override
 		public Object run(Connection... connections) {
-			if (connections.length < arity) {
+			if (connections.length < 2) {
 				throw new InvalidArgumentsException("Not enough connections were given.");
 			} else {
 				int arg1 = ((int) connections[0].getValue());
@@ -174,7 +159,7 @@ public class BitwiseLogic extends FunctionSet {
 
 		@Override
 		public int getArity() {
-			return arity;
+			return 2;
 		}
 
 		@Override
@@ -183,12 +168,10 @@ public class BitwiseLogic extends FunctionSet {
 		}
 	}
 
-	public static class Xnor extends Function {	
-		private int arity = 2;
-
+	public static class Xnor extends Function {
 		@Override
 		public Object run(Connection... connections) {
-			if (connections.length < arity) {
+			if (connections.length < 2) {
 				throw new InvalidArgumentsException("Not enough connections were given.");
 			} else {
 				int arg1 = ((int) connections[0].getValue());
@@ -201,7 +184,7 @@ public class BitwiseLogic extends FunctionSet {
 
 		@Override
 		public int getArity() {
-			return arity;
+			return 2;
 		}
 
 		@Override
diff --git a/src/jcgp/backend/function/BooleanLogic.java b/src/jcgp/backend/function/BooleanLogic.java
index e0b5c9c..9e7d1ff 100644
--- a/src/jcgp/backend/function/BooleanLogic.java
+++ b/src/jcgp/backend/function/BooleanLogic.java
@@ -1,7 +1,5 @@
 package jcgp.backend.function;
 
-import java.util.ArrayList;
-import java.util.Arrays;
 
 import jcgp.backend.exceptions.InvalidArgumentsException;
 import jcgp.backend.population.Connection;
@@ -19,15 +17,13 @@ public class BooleanLogic extends FunctionSet {
 				new Nor(),
 				new Xnor()};
 		
-		allowedFunctions = new ArrayList<Function>(Arrays.asList(functionList));
+		enableAll();
 	}
 
-	public static class And extends Function {	
-		private int arity = 2;
-
+	public static class And extends Function {
 		@Override
 		public Boolean run(Connection... connections) {
-			if (connections.length < arity) {
+			if (connections.length < 2) {
 				throw new InvalidArgumentsException("Not enough connections were given.");
 			} else {
 				Boolean arg1 = ((Boolean) connections[0].getValue());
@@ -40,7 +36,7 @@ public class BooleanLogic extends FunctionSet {
 
 		@Override
 		public int getArity() {
-			return arity;
+			return 2;
 		}
 
 		@Override
@@ -49,12 +45,10 @@ public class BooleanLogic extends FunctionSet {
 		}
 	}
 	
-	public static class Or extends Function {	
-		private int arity = 2;
-
+	public static class Or extends Function {
 		@Override
 		public Boolean run(Connection... connections) {
-			if (connections.length < arity) {
+			if (connections.length < 2) {
 				throw new InvalidArgumentsException("Not enough connections were given.");
 			} else {
 				Boolean arg1 = ((Boolean) connections[0].getValue());
@@ -67,7 +61,7 @@ public class BooleanLogic extends FunctionSet {
 
 		@Override
 		public int getArity() {
-			return arity;
+			return 2;
 		}
 
 		@Override
@@ -76,12 +70,10 @@ public class BooleanLogic extends FunctionSet {
 		}
 	}
 
-	public static class Not extends Function {	
-		private int arity = 1;
-
+	public static class Not extends Function {
 		@Override
 		public Boolean run(Connection... connections) {
-			if (connections.length < arity) {
+			if (connections.length < 1) {
 				throw new InvalidArgumentsException("Not enough connections were given.");
 			} else {
 				Boolean arg1 = ((Boolean) connections[0].getValue());
@@ -93,7 +85,7 @@ public class BooleanLogic extends FunctionSet {
 
 		@Override
 		public int getArity() {
-			return arity;
+			return 1;
 		}
 
 		@Override
@@ -102,12 +94,10 @@ public class BooleanLogic extends FunctionSet {
 		}
 	}
 
-	public static class Xor extends Function {	
-		private int arity = 2;
-
+	public static class Xor extends Function {
 		@Override
 		public Boolean run(Connection... connections) {
-			if (connections.length < arity) {
+			if (connections.length < 2) {
 				throw new InvalidArgumentsException("Not enough connections were given.");
 			} else {
 				Boolean arg1 = ((Boolean) connections[0].getValue());
@@ -120,7 +110,7 @@ public class BooleanLogic extends FunctionSet {
 
 		@Override
 		public int getArity() {
-			return arity;
+			return 2;
 		}
 
 		@Override
@@ -129,12 +119,10 @@ public class BooleanLogic extends FunctionSet {
 		}
 	}
 
-	public static class Nand extends Function {	
-		private int arity = 2;
-
+	public static class Nand extends Function {
 		@Override
 		public Boolean run(Connection... connections) {
-			if (connections.length < arity) {
+			if (connections.length < 2) {
 				throw new InvalidArgumentsException("Not enough connections were given.");
 			} else {
 				Boolean arg1 = ((Boolean) connections[0].getValue());
@@ -147,7 +135,7 @@ public class BooleanLogic extends FunctionSet {
 
 		@Override
 		public int getArity() {
-			return arity;
+			return 2;
 		}
 
 		@Override
@@ -156,12 +144,10 @@ public class BooleanLogic extends FunctionSet {
 		}
 	}
 
-	public static class Nor extends Function {	
-		private int arity = 2;
-
+	public static class Nor extends Function {
 		@Override
 		public Boolean run(Connection... connections) {
-			if (connections.length < arity) {
+			if (connections.length < 2) {
 				throw new InvalidArgumentsException("Not enough connections were given.");
 			} else {
 				Boolean arg1 = ((Boolean) connections[0].getValue());
@@ -174,7 +160,7 @@ public class BooleanLogic extends FunctionSet {
 
 		@Override
 		public int getArity() {
-			return arity;
+			return 2;
 		}
 
 		@Override
@@ -183,12 +169,10 @@ public class BooleanLogic extends FunctionSet {
 		}
 	}
 
-	public static class Xnor extends Function {	
-		private int arity = 2;
-
+	public static class Xnor extends Function {
 		@Override
 		public Boolean run(Connection... connections) {
-			if (connections.length < arity) {
+			if (connections.length < 2) {
 				throw new InvalidArgumentsException("Not enough connections were given.");
 			} else {
 				Boolean arg1 = ((Boolean) connections[0].getValue());
@@ -201,7 +185,7 @@ public class BooleanLogic extends FunctionSet {
 
 		@Override
 		public int getArity() {
-			return arity;
+			return 2;
 		}
 
 		@Override
diff --git a/src/jcgp/backend/function/FunctionSet.java b/src/jcgp/backend/function/FunctionSet.java
index 4470ac8..78801fc 100644
--- a/src/jcgp/backend/function/FunctionSet.java
+++ b/src/jcgp/backend/function/FunctionSet.java
@@ -1,6 +1,7 @@
 package jcgp.backend.function;
 
 import java.util.ArrayList;
+import java.util.Collections;
 import java.util.Iterator;
 
 
@@ -11,7 +12,7 @@ import java.util.Iterator;
  */
 public abstract class FunctionSet {
 		protected Function[] functionList;
-		protected ArrayList<Function> allowedFunctions;
+		protected ArrayList<Integer> allowedFunctions;
 		protected String name;
 		
 		public int getAllowedFunctionCount() {
@@ -23,7 +24,7 @@ public abstract class FunctionSet {
 		}
 		
 		public Function getAllowedFunction(int index) {
-			return allowedFunctions.get(index);
+			return functionList[allowedFunctions.get(index)];
 		}
 		
 		public Function getFunction(int index) {
@@ -32,7 +33,7 @@ public abstract class FunctionSet {
 		
 		public int getMaxArity(){
 			int arity = 0;
-			for (Function function : allowedFunctions) {
+			for (Function function : functionList) {
 				if (function.getArity() > arity) {
 					arity = function.getArity();
 				}
@@ -46,9 +47,9 @@ public abstract class FunctionSet {
 		
 		public void disableFunction(int index) {
 			if (index < functionList.length) {
-				for (Iterator<Function> iterator = allowedFunctions.iterator(); iterator.hasNext();) {
-					Function function = (Function) iterator.next();
-					if (function == functionList[index]) {
+				for (Iterator<Integer> iterator = allowedFunctions.iterator(); iterator.hasNext();) {
+					int function = iterator.next();
+					if (function == index) {
 						iterator.remove();
 					}
 				}
@@ -58,8 +59,9 @@ public abstract class FunctionSet {
 		}
 		
 		public void enableFunction(int index) {
-			if (!allowedFunctions.contains(functionList[index])) {
-				allowedFunctions.add(functionList[index]);
+			if (!allowedFunctions.contains(index)) {
+				allowedFunctions.add(index);
+				Collections.sort(allowedFunctions);
 			}
 		}
 		
@@ -69,6 +71,18 @@ public abstract class FunctionSet {
 		}
 		
 		public boolean isEnabled(Function f) {
-			return allowedFunctions.contains(f);
+			for (int i = 0; i < allowedFunctions.size(); i++) {
+				if (functionList[allowedFunctions.get(i)] == f) {
+					return true;
+				}
+			}
+			return false;
+		}
+		
+		protected void enableAll() {
+			allowedFunctions = new ArrayList<Integer>();
+			for (int i = 0; i < functionList.length; i++) {
+				allowedFunctions.add(i);
+			}
 		}
 	}
\ No newline at end of file
diff --git a/src/jcgp/backend/function/Arithmetic.java b/src/jcgp/backend/function/IntegerArithmetic.java
index 6971663..c08a72a 100644
--- a/src/jcgp/backend/function/Arithmetic.java
+++ b/src/jcgp/backend/function/IntegerArithmetic.java
@@ -1,31 +1,25 @@
 package jcgp.backend.function;
 
-import java.util.ArrayList;
-import java.util.Arrays;
-
 import jcgp.backend.exceptions.InvalidArgumentsException;
 import jcgp.backend.population.Connection;
 
-public class Arithmetic extends FunctionSet {
+public class IntegerArithmetic extends FunctionSet {
 	
-	public Arithmetic() {
-		name = "Arithmetic";
+	public IntegerArithmetic() {
+		name = "Integer Arithmetic";
 		functionList = new Function[]{
 				new Addition(),
 				new Subtraction(),
 				new Multiplication(),
 				new Division()};
 		
-		allowedFunctions = new ArrayList<Function>(Arrays.asList(functionList));
+		enableAll();
 	}
 	
 	public static class Addition extends Function {
-
-		private int arity = 2;
-
 		@Override
 		public Integer run(Connection... connections) {
-			if (connections.length < arity) {
+			if (connections.length < 2) {
 				throw new InvalidArgumentsException("Not enough connections were given.");
 			} else {
 				Integer arg1 = ((Integer) connections[0].getValue());
@@ -38,7 +32,7 @@ public class Arithmetic extends FunctionSet {
 
 		@Override
 		public int getArity() {
-			return arity;
+			return 2;
 		}
 
 		@Override
@@ -48,12 +42,9 @@ public class Arithmetic extends FunctionSet {
 	}
 
 	public static class Subtraction extends Function {
-
-		private int arity = 2;
-
 		@Override
 		public Integer run(Connection... connections) {
-			if (connections.length < arity) {
+			if (connections.length < 2) {
 				throw new InvalidArgumentsException("Not enough connections were given.");
 			} else {
 				Integer arg1 = ((Integer) connections[0].getValue());
@@ -66,7 +57,7 @@ public class Arithmetic extends FunctionSet {
 
 		@Override
 		public int getArity() {
-			return arity;
+			return 2;
 		}
 
 		@Override
@@ -76,12 +67,9 @@ public class Arithmetic extends FunctionSet {
 	}
 
 	public static class Multiplication extends Function {
-
-		private int arity = 2;
-
 		@Override
 		public Integer run(Connection... connections) {
-			if (connections.length < arity) {
+			if (connections.length < 2) {
 				throw new InvalidArgumentsException("Not enough connections were given.");
 			} else {
 				Integer arg1 = ((Integer) connections[0].getValue());
@@ -94,7 +82,7 @@ public class Arithmetic extends FunctionSet {
 
 		@Override
 		public int getArity() {
-			return arity;
+			return 2;
 		}
 
 		@Override
@@ -104,12 +92,9 @@ public class Arithmetic extends FunctionSet {
 	}
 
 	public static class Division extends Function {
-
-		private int arity = 2;
-
 		@Override
 		public Integer run(Connection... connections) {
-			if (connections.length < arity) {
+			if (connections.length < 2) {
 				throw new InvalidArgumentsException("Not enough connections were given.");
 			} else {
 				Integer arg1 = ((Integer) connections[0].getValue());
@@ -127,7 +112,7 @@ public class Arithmetic extends FunctionSet {
 
 		@Override
 		public int getArity() {
-			return arity;
+			return 2;
 		}
 
 		@Override