7 files changed, 64 insertions, 53 deletions
diff --git a/src/jcgp/population/Chromosome.java b/src/jcgp/population/Chromosome.java
index 12a8978..3e61a10 100644
--- a/src/jcgp/population/Chromosome.java
+++ b/src/jcgp/population/Chromosome.java
@@ -4,7 +4,7 @@ import java.util.ArrayList;
 
 import jcgp.Parameters;
 import jcgp.Utilities;
-import jcgp.fitness.ParameterMismatchException;
+import jcgp.exceptions.ParameterMismatchException;
 
 public class Chromosome {
 
@@ -95,7 +95,7 @@ public class Chromosome {
 	/**
 	 * @param clone
 	 */
-	private void copyConnections(Chromosome clone) {
+	public void copyConnections(Chromosome clone) {
 		// copy nodes - [rows][columns]
 		for (int r = 0; r < nodes.length; r++) {
 			for (int c = 0; c < nodes[r].length; c++) {
diff --git a/src/jcgp/population/Connection.java b/src/jcgp/population/Connection.java
index ff11d7c..751fe10 100644
--- a/src/jcgp/population/Connection.java
+++ b/src/jcgp/population/Connection.java
@@ -3,5 +3,6 @@ package jcgp.population;
 public interface Connection {
 
 	public Object getValue();
+	
 
 }
diff --git a/src/jcgp/population/Input.java b/src/jcgp/population/Input.java
index 2154dd9..e793bf6 100644
--- a/src/jcgp/population/Input.java
+++ b/src/jcgp/population/Input.java
@@ -21,5 +21,4 @@ public class Input implements Connection {
 	public int getIndex() {
 		return index;
 	}
-
 }
diff --git a/src/jcgp/population/InsufficientConnectionsException.java b/src/jcgp/population/InsufficientConnectionsException.java
deleted file mode 100644
index 807ec53..0000000
--- a/src/jcgp/population/InsufficientConnectionsException.java
+++ /dev/null
@@ -1,10 +0,0 @@
-package jcgp.population;
-
-public class InsufficientConnectionsException extends RuntimeException {
-
-	/**
-	 * 
-	 */
-	private static final long serialVersionUID = 660740514800883541L;
-
-}
diff --git a/src/jcgp/population/Node.java b/src/jcgp/population/Node.java
index e58c1a4..35d33cb 100644
--- a/src/jcgp/population/Node.java
+++ b/src/jcgp/population/Node.java
@@ -5,6 +5,7 @@ import java.util.Arrays;
 
 import jcgp.Parameters;
 import jcgp.Utilities;
+import jcgp.exceptions.InsufficientConnectionsException;
 import jcgp.function.Function;
 
 
diff --git a/src/jcgp/population/Output.java b/src/jcgp/population/Output.java
index dae7278..b3ce74f 100644
--- a/src/jcgp/population/Output.java
+++ b/src/jcgp/population/Output.java
@@ -14,7 +14,9 @@ public class Output implements MutableElement {
 	}
 
 	public Object calculate() {
-		return source.getValue();
+		Object result = source.getValue();
+		System.out.println("Output " + index + ": " + result);
+		return result;
 	}
 
 	@Override
diff --git a/src/jcgp/population/Population.java b/src/jcgp/population/Population.java
index 4153e0f..9cd7430 100644
--- a/src/jcgp/population/Population.java
+++ b/src/jcgp/population/Population.java
@@ -1,54 +1,72 @@
 package jcgp.population;
 
-import java.util.Iterator;
-
 import jcgp.Parameters;
 
-public class Population implements Iterable<Chromosome> {
+public class Population {
 	
-	private Chromosome[] population;
+	private Chromosome[] parents;
+	private Chromosome[] offspring;
+	private Chromosome bestIndividual;
 	
-	public Population(Chromosome chromosome) {
-		population = new Chromosome[Parameters.getPopulationSize()];
-		for (int c = 0; c < population.length; c++) {
-			population[c] = new Chromosome(chromosome);
+	public Population(Chromosome parent) {
+		parents = new Chromosome[Parameters.getParentCount()];
+		// 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();
 		}
 	}
 	
 	public Population() {
-		population = new Chromosome[Parameters.getPopulationSize()];
-		for (int c = 0; c < population.length; c++) {
-			population[c] = new Chromosome();
+		parents = new Chromosome[Parameters.getParentCount()];
+		for (int c = 0; c < parents.length; c++) {
+			parents[c] = new Chromosome();
 		}
-	}
-
-	@Override
-	public Iterator<Chromosome> iterator() {
-		return new Iterator<Chromosome>() {
-			
-			private int index = 0;
-
-			@Override
-			public boolean hasNext() {
-				if (index < population.length) {
-					return true;
-				} else {
-					return false;
-				}
-			}
 
-			@Override
-			public Chromosome next() {
-				Chromosome next = population[index];
-				index++;
-				return next;
-			}
+		offspring = new Chromosome[Parameters.getOffspringCount()];
+		for (int c = 0; c < offspring.length; c++) {
+			offspring[c] = new Chromosome();
+		}
+	}
 
-			@Override
-			public void remove() {
-				// not allowed
-				throw new UnsupportedOperationException("Removing chromosomes from the population is not allowed. Instead, re-instantiate the chromosome.");
-			}
-		};
+	public Chromosome getOffspring(int index) {
+		return offspring[index];
+	}
+	
+	public Chromosome getParent(int index) {
+		return parents[index];
+	}
+	
+	/**
+	 * Returns all chromosomes, parents first, then offspring.
+	 * 
+	 * @param index
+	 * @return
+	 */
+	public Chromosome getChromosome(int index) {
+		if (index < parents.length) {
+			return parents[index];
+		} else {
+			return offspring[index - parents.length];
+		}
+	}
+	
+	public void setBestIndividual(int index) {
+		if (index < parents.length) {
+			bestIndividual = parents[index];
+		} else {
+			bestIndividual = offspring[index - parents.length];
+		}
+	}
+	
+	public Chromosome getBestIndividual() {
+		return bestIndividual;
 	}
 }