7 files changed, 47 insertions, 19 deletions
diff --git a/src/jcgp/population/Chromosome.java b/src/jcgp/population/Chromosome.java
index f060e14..328a608 100644
--- a/src/jcgp/population/Chromosome.java
+++ b/src/jcgp/population/Chromosome.java
@@ -1,7 +1,8 @@
 package jcgp.population;
 
-import jcgp.CGP.Parameters;
-import jcgp.CGP.Utilities;
+import jcgp.Parameters;
+import jcgp.Utilities;
+import jcgp.fitness.ParameterMismatchException;
 
 public class Chromosome {
 
@@ -41,16 +42,16 @@ public class Chromosome {
 		}
 		
 		// rows first
-		nodes = new Node[Parameters.getRows()][Parameters.getColumns()];
+		nodes = new Node[rows][columns];
 		for (int r = 0; r < rows; r++) {
 			//nodes[r] = new Node[Parameters.getColumns()];
 			for (int c = 0; c < columns; c++) {
-				nodes[r][c] = new Node(c);
+				nodes[r][c] = new Node(r, c);
 			}
 		}
 		outputs = new Output[outputCount];
 		for (int o = 0; o < outputCount; o++) {
-			outputs[o] = new Output();
+			outputs[o] = new Output(o);
 		}
 	}
 	
@@ -97,16 +98,25 @@ public class Chromosome {
 		fitness = newFitness;
 	}
 	
-	public void setInputs(int ... values) {
-		// if the values provided dont match the specified number of inputs, the user should be warned
+	public void setInputs(int ... values) throws ParameterMismatchException {
+		// if the values provided don't match the specified number of inputs, the user should be warned
 		if (values.length == inputs.length) {
 			// set inputs for evaluation
 			for (int i = 0; i < values.length; i++) {
 				inputs[i].setValue(values[i]);
 			}
 		} else {
-			System.out.println("Input mismatch: chromosome has a different number of inputs than the truth table.");
+			throw new ParameterMismatchException();
 		}
 	}
+
+	public MutableElement getMutableElement(int row, int column) {
+		if (column < Parameters.getColumns() && column >= 0) {
+			return nodes[row][column];
+		} else if (column == Parameters.getColumns()) {
+			return outputs[row];
+		}
+		return null;
+	}
 	
 }
diff --git a/src/jcgp/population/Connection.java b/src/jcgp/population/Connection.java
index fa02a22..4e69e99 100644
--- a/src/jcgp/population/Connection.java
+++ b/src/jcgp/population/Connection.java
@@ -2,5 +2,5 @@ package jcgp.population;
 
 public interface Connection {
 
-	public abstract int evaluate();
+	public abstract int getValue();
 }
diff --git a/src/jcgp/population/Input.java b/src/jcgp/population/Input.java
index b9c127f..e00573e 100644
--- a/src/jcgp/population/Input.java
+++ b/src/jcgp/population/Input.java
@@ -9,7 +9,7 @@ public class Input implements Connection {
 	}
 
 	@Override
-	public int evaluate() {
+	public int getValue() {
 		return value;
 	}
 
diff --git a/src/jcgp/population/MutableElement.java b/src/jcgp/population/MutableElement.java
index 8ac3724..c21ee0b 100644
--- a/src/jcgp/population/MutableElement.java
+++ b/src/jcgp/population/MutableElement.java
@@ -5,5 +5,7 @@ public interface MutableElement {
 	public void setConnection(Connection newConnection);
 	
 	public int getColumn();
+
+	public int getRow();
 	
 }
diff --git a/src/jcgp/population/Node.java b/src/jcgp/population/Node.java
index fd0cd47..3dbabb2 100644
--- a/src/jcgp/population/Node.java
+++ b/src/jcgp/population/Node.java
@@ -1,7 +1,7 @@
 package jcgp.population;
 
-import jcgp.CGP.Parameters;
-import jcgp.CGP.Utilities;
+import jcgp.Parameters;
+import jcgp.Utilities;
 import jcgp.function.Function;
 
 
@@ -9,14 +9,15 @@ public class Node implements MutableElement, Connection {
 	
 	private Function function;
 	private Connection[] connections;
-	private int column;
+	private int column, row;
 
-	public Node(int col) {
-		column = col;
+	public Node(int row, int column) {
+		this.column = column;
+		this.row = row;
 	}
 	
 	@Override
-	public int evaluate() {
+	public int getValue() {
 		return function.run(connections);
 	}
 	
@@ -45,4 +46,9 @@ public class Node implements MutableElement, Connection {
 		
 		return column;
 	}
+
+	@Override
+	public int getRow() {
+		return row;
+	}
 }
diff --git a/src/jcgp/population/Output.java b/src/jcgp/population/Output.java
index eeae743..ce4f776 100644
--- a/src/jcgp/population/Output.java
+++ b/src/jcgp/population/Output.java
@@ -1,14 +1,19 @@
 package jcgp.population;
 
-import jcgp.CGP.Parameters;
+import jcgp.Parameters;
 
 
 public class Output implements MutableElement {
 	
 	private Connection source;
+	private int row;
+	
+	public Output(int row) {
+		this.row = row;
+	}
 
 	public int calculate() {
-		return source.evaluate();
+		return source.getValue();
 	}
 
 	@Override
@@ -22,4 +27,9 @@ public class Output implements MutableElement {
 		return Parameters.getColumns();
 	}
 
+	@Override
+	public int getRow() {
+		return row;
+	}
+
 }
diff --git a/src/jcgp/population/Population.java b/src/jcgp/population/Population.java
index c4a0776..b56d992 100644
--- a/src/jcgp/population/Population.java
+++ b/src/jcgp/population/Population.java
@@ -2,7 +2,7 @@ package jcgp.population;
 
 import java.util.Iterator;
 
-import jcgp.CGP.Parameters;
+import jcgp.Parameters;
 
 public class Population implements Iterable<Chromosome> {