4 files changed, 70 insertions, 10 deletions

diff --git a/src/jcgp/backend/parser/ChromosomeParser.java b/src/jcgp/backend/parser/ChromosomeParser.java
index d5af1bd..fd03b7d 100644
--- a/src/jcgp/backend/parser/ChromosomeParser.java
+++ b/src/jcgp/backend/parser/ChromosomeParser.java
@@ -3,10 +3,12 @@ package jcgp.backend.parser;
 import java.io.File;
 import java.io.FileNotFoundException;
 import java.io.FileReader;
+import java.io.PrintWriter;
 import java.util.Scanner;
 
 import jcgp.backend.population.Chromosome;
 import jcgp.backend.population.Connection;
+import jcgp.backend.population.Input;
 import jcgp.backend.population.Node;
 import jcgp.backend.resources.Resources;
 
@@ -73,15 +75,16 @@ public abstract class ChromosomeParser {
 			Connection newConnection;
 			Node changingNode;
 			// for all nodes, columns first
-			for (int c = 0; c < resources.columns(); c ++) {
-				for (int r = 0; r < resources.rows(); r ++) {
+			for (int c = 0; c < resources.columns(); c++) {
+				for (int r = 0; r < resources.rows(); r++) {
 					// store the changing node
 					changingNode = chromosome.getNode(r, c);
 
 					// for every connection
-					for (int i = 0; i < resources.arity(); i ++) {
+					for (int i = 0; i < resources.arity(); i++) {
 						// get connection number from the .chr file
 						gene = in.nextInt();
+						System.out.println("r: " + r + " c: " + c + " i: " + i + " gene: " + gene);
 						if (gene < resources.inputs()) {
 							// connection was an input
 							newConnection = chromosome.getInput(gene);
@@ -113,6 +116,8 @@ public abstract class ChromosomeParser {
 				chromosome.getOutput(o).setConnection(0, newConnection);
 			}
 			in.close();
+		} else {
+			throw new IllegalArgumentException("The topology of the chromosome in " + file.getName() + " does not match that of the experiment.");
 		}
 	}
 	
@@ -120,12 +125,53 @@ public abstract class ChromosomeParser {
 	 * Writes a chromosome into the specified .chr file.
 	 * 
 	 * 
-	 * 
-	 * @param file
-	 * @param chromosome
+	 * @param file the file to write to
+	 * @param chromosome the chromosome to save
 	 */
-	public static void save(File file, Chromosome chromosome) {
+	public static void save(File file, Chromosome chromosome, Resources resources) {
+		PrintWriter writer;
+		try {
+			writer = new PrintWriter(file);
+		} catch (FileNotFoundException e) {
+			// something bad happened
+			return;
+		}
+		
+		// for all nodes, columns first
+		for (int c = 0; c < resources.columns(); c++) {
+			for (int r = 0; r < resources.rows(); r++) {
+				for (int i = 0; i < resources.arity(); i++) {
+					// print the connections, separated by spaces
+					Connection conn = chromosome.getNode(r, c).getConnection(i);
+					if (conn instanceof Input) {
+						writer.print(" " + ((Input) conn).getIndex());
+					} else if (conn instanceof Node) {
+						writer.print(" " + (((((Node) conn).getColumn() + 1) * resources.inputs()) + ((Node) conn).getRow()));
+					} else {
+						throw new ClassCastException("Could not handle " + conn.getClass() + " as a subclass of Connection");
+					}
+				}
+				// print the function numbers
+				writer.print(" " + resources.getFunctionIndex(chromosome.getNode(r, c).getFunction()));
+				// node is done, print tab
+				writer.print("\t");
+			}
+		}
+		// nodes are done, print two tabs to separate from output
+		writer.print("\t\t");
+		for (int o = 0; o < resources.outputs(); o ++) {
+			Connection source = chromosome.getOutput(o).getSource();
+			if (source instanceof Input) {
+				writer.print(" " + ((Input) source).getIndex());
+			} else if (source instanceof Node) {
+				writer.print(" " + (((((Node) source).getColumn() + 1) * resources.inputs()) + ((Node) source).getRow()));
+			} else {
+				throw new ClassCastException("Could not handle " + source.getClass() + " as a subclass of Connection");
+			}
+		}
 		
+		writer.close();
+		System.out.println("writer is closed");
 	}
 	
 }
diff --git a/src/jcgp/backend/population/Node.java b/src/jcgp/backend/population/Node.java
index 6a558a4..b716ff8 100644
--- a/src/jcgp/backend/population/Node.java
+++ b/src/jcgp/backend/population/Node.java
@@ -31,8 +31,12 @@ public class Node extends Gene implements MutableElement, Connection {
 
 	@Override
 	public void setConnection(int index, Connection newConnection) {
-		connections[index] = newConnection;
-		chromosome.recomputeActiveNodes();
+		if (newConnection instanceof Node) {
+			if (((Node) newConnection).getColumn() < column) {
+				connections[index] = newConnection;
+				chromosome.recomputeActiveNodes();
+			}
+		}
 	}
 
 	public void initialise(Function newFunction, Connection ... newConnections) throws InsufficientConnectionsException {
diff --git a/src/jcgp/backend/population/Population.java b/src/jcgp/backend/population/Population.java
index 1bbdc54..b6dd055 100644
--- a/src/jcgp/backend/population/Population.java
+++ b/src/jcgp/backend/population/Population.java
@@ -4,7 +4,7 @@ import jcgp.backend.resources.Resources;
 
 public class Population {
 	
-	private Chromosome[] chromosomes;
+	private final Chromosome[] chromosomes;
 	private final Resources resources;
 	private int fittest = 0;
 	
diff --git a/src/jcgp/backend/resources/Resources.java b/src/jcgp/backend/resources/Resources.java
index 151d536..6eb75cd 100644
--- a/src/jcgp/backend/resources/Resources.java
+++ b/src/jcgp/backend/resources/Resources.java
@@ -320,6 +320,16 @@ public class Resources {
 		return functionSet;
 	}
 	
+	public int getFunctionIndex(Function function) {
+		for (int i = 0; i < functionSet.getTotalFunctionCount(); i++) {
+			if (function == functionSet.getFunction(i)) {
+				return i;
+			}
+		}
+		// not found, default to 0
+		return 0;
+	}
+	
 	/*
 	 * Console functionality
 	 * These are affected by parameter report