2 files changed, 48 insertions, 15 deletions

diff --git a/src/jcgp/backend/population/Chromosome.java b/src/jcgp/backend/population/Chromosome.java
index 18ae9bb..41ba06e 100644
--- a/src/jcgp/backend/population/Chromosome.java
+++ b/src/jcgp/backend/population/Chromosome.java
@@ -43,12 +43,12 @@ public class Chromosome {
 	 */
 	public Chromosome(Chromosome clone) {
 		// store a reference to the parameters
-		this.resources = clone.getParameters();
+		this.resources = clone.getResources();
 		
 		// allocate memory for all elements of the chromosome
 		instantiateElements();
 		// initialise all connections based on argument
-		copyConnections(clone);
+		copyGenes(clone);
 	}
 
 	/**
@@ -102,7 +102,7 @@ public class Chromosome {
 	/**
 	 * @param clone
 	 */
-	public void copyConnections(Chromosome clone) {
+	public void copyGenes(Chromosome clone) {
 		int arity = resources.getInt("arity");
 		
 		// copy nodes - [rows][columns]
@@ -119,7 +119,7 @@ public class Chromosome {
 					} else if (copyConnection instanceof Node) {
 						connections[i] = nodes[((Node) copyConnection).getRow()][((Node) copyConnection).getColumn()];
 					} else {
-						System.out.println("Warning: Connection of subtype " + copyConnection.getClass().toString() + " is not explicitly handled by copy constructor.");
+						System.out.println("Error: Connection of subtype " + copyConnection.getClass().toString() + " is not explicitly handled by copy method.");
 					}
 				}
 				// initialise with copied arguments
@@ -329,7 +329,7 @@ public class Chromosome {
 		}
 	}
 	
-	public Resources getParameters() {
+	public Resources getResources() {
 		return resources;
 	}
 }
diff --git a/src/jcgp/backend/population/Population.java b/src/jcgp/backend/population/Population.java
index 7049d79..7b62d27 100644
--- a/src/jcgp/backend/population/Population.java
+++ b/src/jcgp/backend/population/Population.java
@@ -6,27 +6,41 @@ import jcgp.JCGP.Resources;
 public class Population {
 	
 	private Chromosome[] chromosomes;
-	private int fittest;
+	private Resources resources;
 	
+	/**
+	 * Initialise a random population according to the parameters specified
+	 * in the resources.
+	 * 
+	 * @param resources the CGP resources
+	 */
 	public Population(Resources resources) {
+		this.resources = resources;
+		
 		chromosomes = new Chromosome[(resources.getInt("popSize"))];
 		for (int c = 0; c < chromosomes.length; c++) {
 			chromosomes[c] = new Chromosome(resources);
 		}
 	}
 	
+	/**
+	 * Initialise a population of copies of the given chromosome.
+	 * 
+	 * @param parent
+	 * @param resources
+	 */
 	public Population(Chromosome parent, Resources resources) {
+		this.resources = resources;
+		
 		chromosomes = new Chromosome[(resources.getInt("popSize"))];
-		// make a clone for safety
-		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]);
+		for (int c = 0; c < chromosomes.length; c++) {
+			chromosomes[c] = new Chromosome(parent);
 		}
 	}
 
 	/**
-	 * Returns all chromosomes, parents first, then offspring.
+	 * Returns the indexed chromosome.
 	 * 
 	 * @param index
 	 * @return
@@ -35,11 +49,30 @@ public class Population {
 		return chromosomes[index];
 	}
 	
-	public void setBestIndividual(int index) {
-		fittest = index;
+	/**
+	 * @return a random chromosome from this population.
+	 */
+	public Chromosome getRandomChromosome() {
+		return chromosomes[resources.getRandomInt(chromosomes.length)];
 	}
+
 	
-	public Chromosome getBestIndividual() {
-		return chromosomes[fittest];
+	/**
+	 * Copy a chromosome into a different position.
+	 * After this returns, the target chromosome has
+	 * identical connections and functions to the source
+	 * one, though they are separate instances.
+	 * 
+	 * This method does nothing if source == target.
+	 * 
+	 * @param source 
+	 * @param target
+	 */
+	public void copyChromosome(int source, int target) {
+		if (source != target) {
+			chromosomes[target].copyGenes(chromosomes[source]);
+		}
 	}
+	
+	
 }