Population and Chromosome classes refactored so that EAs are easier to implement.

24 files changed, 251 insertions, 196 deletions

diff --git a/README b/README
index 1095912..5152bc8 100644
--- a/README
+++ b/README
@@ -139,5 +139,10 @@ Tests have been refactored to deal with the new data system. The system uses Obj
 any class to be used (and also primitive types).
 
 
+15/2
 
+The Population class will be refactored to contain two collections of chromosomes, one for parents and one for offpsring. This allows
+for (1+λ) and (1,λ) EAs, for example. It no longer makes sense for Population to implement Iterable, so the tests will be changed to reflect
+the specification change. Population can still return an addressed chromosome in general, which it does by returning parents followed by offspring.
 
+The chromosome copyConnections method has been made public to facilitate the EA implementation.
diff --git a/src/jcgp/CGP.java b/src/jcgp/CGP.java
index d2be161..0ccd74e 100644
--- a/src/jcgp/CGP.java
+++ b/src/jcgp/CGP.java
@@ -1,6 +1,7 @@
 package jcgp;
 
 import java.util.Random;
+
 import jcgp.ea.EvolutionaryAlgorithm;
 import jcgp.ea.Mutator;
 import jcgp.ea.StandardEA;
@@ -10,6 +11,7 @@ import jcgp.fitness.TestCase;
 import jcgp.fitness.TruthTableEvaluator;
 import jcgp.function.Addition;
 import jcgp.function.FunctionSet;
+import jcgp.function.Multiplication;
 import jcgp.function.Subtraction;
 import jcgp.population.Population;
 
@@ -28,9 +30,10 @@ public final class CGP {
 			Parameters.setCurrentGeneration(i);
 			fitnessFunction.evaluate(population);
 			ea.evolve(population, mutator);
-		}
-		
-		
+			if (ea.getBestFitness() >= 3) {
+				break;
+			}
+		}	
 	}
 
 	/**
@@ -38,19 +41,20 @@ public final class CGP {
 	 */
 	private void initialise() {
 		// initialise function set
-		FunctionSet functionSet = new FunctionSet(new Addition(), new Subtraction());
+		FunctionSet functionSet = new FunctionSet(new Addition(), new Subtraction(), new Multiplication());
 		
 		// initialise utilities
 		Utilities.setResources(new Random(1234), functionSet);
 		
 		// initialise parameters
 		Parameters.setColumns(3);
-		Parameters.setRows(3);
+		Parameters.setRows(6);
 		Parameters.setInputs(3);
 		Parameters.setOutputs(3);
-		Parameters.setLevelsBack(1);
+		Parameters.setLevelsBack(3);
+		Parameters.setPopulationSize(1, 4);
 		Parameters.setMutationRate(10);
-		Parameters.setTotalGenerations(100);
+		Parameters.setTotalGenerations(5000);
 		Parameters.setTotalRuns(5);
 		Parameters.setMaxArity(functionSet.getMaxArity());
 		
diff --git a/src/jcgp/Main.java b/src/jcgp/Main.java
index 598c720..97b5c4a 100644
--- a/src/jcgp/Main.java
+++ b/src/jcgp/Main.java
@@ -1,10 +1,10 @@
 package jcgp;
 
 public class Main {
-
+	
 	public static void main(String[] args) {
 		CGP cgp = new CGP();
 		cgp.getClass();
+			
 	}
-
 }
diff --git a/src/jcgp/Parameters.java b/src/jcgp/Parameters.java
index 26eb61c..0a6abd9 100644
--- a/src/jcgp/Parameters.java
+++ b/src/jcgp/Parameters.java
@@ -2,11 +2,12 @@ package jcgp;
 
 public class Parameters {
 	
-	private static int rows, columns, inputs, outputs, levelsBack, 
-					   mutationRate, populationSize, totalGenerations,
-					   currentGeneration = 0, totalRuns, currentRun = 0,
-					   maxArity, maxFitness;
 
+	private static int rows = 0, columns = 0, inputs = 0, outputs = 0, levelsBack = 0, 
+					   mutationRate = 0, totalGenerations = 0, parents = 0, offspring = 0,
+					   currentGeneration = 0, totalRuns = 0, currentRun = 0,
+					   maxArity = 0, maxFitness = 0;
+	
 	public static int getRows() {
 		return rows;
 	}
@@ -36,9 +37,17 @@ public class Parameters {
 	}
 
 	public static int getPopulationSize() {
-		return populationSize;
+		return offspring + parents;
 	}
-
+	
+	public static int getOffspringCount() {
+		return offspring;
+	}
+	
+	public static int getParentCount() {
+		return parents;
+	}
+	
 	public static int getTotalGenerations() {
 		return totalGenerations;
 	}
@@ -87,8 +96,17 @@ public class Parameters {
 		Parameters.mutationRate = mutationRate;
 	}
 
-	public static void setPopulationSize(int populationSize) {
-		Parameters.populationSize = populationSize;
+	public static void setPopulationSize(int parents, int offspring) {
+		Parameters.parents = parents;
+		Parameters.offspring = offspring;
+	}
+	
+	public static void setOffspringCount(int offspring) {
+		Parameters.offspring = offspring;
+	}
+	
+	public static void setParentCount(int parents) {
+		Parameters.parents = parents;
 	}
 
 	public static void setTotalGenerations(int totalGenerations) {
diff --git a/src/jcgp/ea/EvolutionaryAlgorithm.java b/src/jcgp/ea/EvolutionaryAlgorithm.java
index 9e72a1b..e084da0 100644
--- a/src/jcgp/ea/EvolutionaryAlgorithm.java
+++ b/src/jcgp/ea/EvolutionaryAlgorithm.java
@@ -4,12 +4,8 @@ import jcgp.population.Population;
 
 public interface EvolutionaryAlgorithm {
 
-//	protected Mutator mutator;
-//	
-//	public EvolutionaryAlgorithm(Mutator mutator) {
-//		this.mutator = mutator;
-//	}
-	
 	public abstract void evolve(Population population, Mutator mutator);
 
+	public abstract int getBestFitness();
+
 }
diff --git a/src/jcgp/ea/StandardEA.java b/src/jcgp/ea/StandardEA.java
index b34c421..901333b 100644
--- a/src/jcgp/ea/StandardEA.java
+++ b/src/jcgp/ea/StandardEA.java
@@ -1,18 +1,45 @@
 package jcgp.ea;
 
+import jcgp.Parameters;
 import jcgp.population.Chromosome;
 import jcgp.population.Population;
 
+/**
+ * (1 + λ) EA.
+ * 
+ * 
+ * @author Eduardo Pedroni
+ *
+ */
 public class StandardEA implements EvolutionaryAlgorithm {
+	
+	private int bestFitness = 0;
 
 	@Override
-	public void evolve(Population population, Mutator mutator) {	
-		Chromosome select;
-		for (Chromosome chromosome : population) {
-			
-			
-			mutator.mutate(chromosome);
+	public void evolve(Population population, Mutator mutator) {
+		// select fittest chromosome
+		int fittest = 0;
+		
+		for (int i = 1; i < Parameters.getPopulationSize(); i++) {
+			if (population.getChromosome(i).getFitness() >= population.getChromosome(fittest).getFitness()) {
+				fittest = i;
+			}
+		}
+		bestFitness = population.getChromosome(fittest).getFitness();
+		population.setBestIndividual(fittest);
+		System.out.println("Best fitness: " + bestFitness);
+		// create copies of fittest chromosome, mutate them
+		Chromosome fc = population.getChromosome(fittest);
+		for (int i = 0; i < Parameters.getPopulationSize(); i++) {
+			if (i != fittest) {
+				population.getChromosome(i).copyConnections(fc);
+				mutator.mutate(population.getChromosome(i));
+			}
 		}
 	}
-
+	
+	@Override
+	public int getBestFitness() {
+		return bestFitness;
+	}
 }
diff --git a/src/jcgp/ea/StandardMutator.java b/src/jcgp/ea/StandardMutator.java
index 447338a..b9c0a4e 100644
--- a/src/jcgp/ea/StandardMutator.java
+++ b/src/jcgp/ea/StandardMutator.java
@@ -11,7 +11,7 @@ public class StandardMutator implements Mutator {
 
 	@Override
 	public void mutate(Chromosome chromosome) {
-		int mutations = (int) (Parameters.getMutationRate() * ((double) Parameters.getNodeCount() / 100));
+		int mutations = (int) (Parameters.getMutationRate() * (((double) Parameters.getNodeCount() + Parameters.getOutputs()) / 100));
 		
 		for (int i = 0; i < mutations; i++) {
 			MutableElement m = chromosome.getRandomMutableElement();
diff --git a/src/jcgp/population/InsufficientConnectionsException.java b/src/jcgp/exceptions/InsufficientConnectionsException.java
index 807ec53..2ffc10f 100644
--- a/src/jcgp/population/InsufficientConnectionsException.java
+++ b/src/jcgp/exceptions/InsufficientConnectionsException.java
@@ -1,4 +1,4 @@
-package jcgp.population;
+package jcgp.exceptions;
 
 public class InsufficientConnectionsException extends RuntimeException {
 
diff --git a/src/jcgp/function/InvalidArgumentsException.java b/src/jcgp/exceptions/InvalidArgumentsException.java
index cf55937..537018d 100644
--- a/src/jcgp/function/InvalidArgumentsException.java
+++ b/src/jcgp/exceptions/InvalidArgumentsException.java
@@ -1,4 +1,4 @@
-package jcgp.function;
+package jcgp.exceptions;
 
 public class InvalidArgumentsException extends RuntimeException {
 
diff --git a/src/jcgp/fitness/ParameterMismatchException.java b/src/jcgp/exceptions/ParameterMismatchException.java
index 0ca69a7..93a8f10 100644
--- a/src/jcgp/fitness/ParameterMismatchException.java
+++ b/src/jcgp/exceptions/ParameterMismatchException.java
@@ -1,4 +1,4 @@
-package jcgp.fitness;
+package jcgp.exceptions;
 
 public class ParameterMismatchException extends RuntimeException {
 
diff --git a/src/jcgp/fitness/TestCase.java b/src/jcgp/fitness/TestCase.java
index 4c10de7..e506d38 100644
--- a/src/jcgp/fitness/TestCase.java
+++ b/src/jcgp/fitness/TestCase.java
@@ -1,6 +1,7 @@
 package jcgp.fitness;
 
 import jcgp.Parameters;
+import jcgp.exceptions.ParameterMismatchException;
 
 public class TestCase {
 
diff --git a/src/jcgp/fitness/TruthTableEvaluator.java b/src/jcgp/fitness/TruthTableEvaluator.java
index 4c26d60..2281b3f 100644
--- a/src/jcgp/fitness/TruthTableEvaluator.java
+++ b/src/jcgp/fitness/TruthTableEvaluator.java
@@ -2,26 +2,27 @@ package jcgp.fitness;
 
 import jcgp.Parameters;
 import jcgp.TruthTable;
-import jcgp.population.Chromosome;
 import jcgp.population.Population;
 
 public class TruthTableEvaluator implements FitnessFunction {
 
 	@Override
 	public void evaluate(Population population) {
-		for (Chromosome chromosome : population) {
+		// for every chromosome in the population
+		for (int i = 0; i < Parameters.getPopulationSize(); i++) {
+			int fitness = 0;
+			// for every test case
 			for (int t = 0; t < TruthTable.getTestCaseCount(); t++) {
-				chromosome.setInputs(TruthTable.getTestCase(t).getInputs());
-				int fitness = 0;
+				population.getChromosome(i).setInputs(TruthTable.getTestCase(t).getInputs());
+				// check every output
 				for (int o = 0; o < Parameters.getOutputs(); o++) {
-					if (chromosome.getOutput(o).calculate() == TruthTable.getTestCase(t).getOutput(o)) {
+					if (population.getChromosome(i).getOutput(o).calculate() == TruthTable.getTestCase(t).getOutput(o)) {
 						fitness++;
 					}
 				}
-				chromosome.setFitness(fitness);
-				System.out.println("Fitness: " + fitness);
 			}
+			population.getChromosome(i).setFitness(fitness);
+			System.out.println("active nodes: " + population.getChromosome(i).getActiveNodes().size());
 		}
 	}
-
 }
diff --git a/src/jcgp/function/Addition.java b/src/jcgp/function/Addition.java
index f40bc24..3a8f123 100644
--- a/src/jcgp/function/Addition.java
+++ b/src/jcgp/function/Addition.java
@@ -1,5 +1,6 @@
 package jcgp.function;
 
+import jcgp.exceptions.InvalidArgumentsException;
 import jcgp.population.Connection;
 
 public class Addition extends Function {
@@ -11,7 +12,12 @@ public class Addition extends Function {
 		if (connections.length < arity) {
 			throw new InvalidArgumentsException("Not enough connections were given.");
 		} else if (connections[0].getValue() instanceof Integer) {
-			return ((Integer) connections[0].getValue()) + ((Integer) connections[1].getValue());
+			Integer arg1 = ((Integer) connections[0].getValue());
+			Integer arg2 = ((Integer) connections[1].getValue());
+			Integer result = arg1 + arg2;
+			
+			System.out.println(arg1 + " + " + arg2 + " = " + result);
+			return result;
 		} else {
 			throw new InvalidArgumentsException("Wrong data type, this function takes Integer.");
 		}
diff --git a/src/jcgp/function/Function.java b/src/jcgp/function/Function.java
index 118131a..584421a 100644
--- a/src/jcgp/function/Function.java
+++ b/src/jcgp/function/Function.java
@@ -1,11 +1,11 @@
 package jcgp.function;
 
+import jcgp.exceptions.InvalidArgumentsException;
 import jcgp.population.Connection;
-import jcgp.population.InsufficientConnectionsException;
 
 public abstract class Function {
 		
-	public abstract Object run(Connection ... connections) throws InsufficientConnectionsException;
+	public abstract Object run(Connection ... connections) throws InvalidArgumentsException;
 	
 	public abstract int getArity();
 	
diff --git a/src/jcgp/function/Multiplication.java b/src/jcgp/function/Multiplication.java
new file mode 100644
index 0000000..986faa8
--- /dev/null
+++ b/src/jcgp/function/Multiplication.java
@@ -0,0 +1,31 @@
+package jcgp.function;
+
+import jcgp.exceptions.InvalidArgumentsException;
+import jcgp.population.Connection;
+
+public class Multiplication extends Function {
+
+	private int arity = 2;
+
+	@Override
+	public Object run(Connection... connections) {
+		if (connections.length < arity) {
+			throw new InvalidArgumentsException("Not enough connections were given.");
+		} else if (connections[0].getValue() instanceof Integer) {
+			Integer arg1 = ((Integer) connections[0].getValue());
+			Integer arg2 = ((Integer) connections[1].getValue());
+			Integer result = arg1 * arg2;
+			
+			System.out.println(arg1 + " * " + arg2 + " = " + result);
+			return result;
+		} else {
+			throw new InvalidArgumentsException("Wrong data type, this function takes Integer.");
+		}
+	}
+
+	@Override
+	public int getArity() {
+		return arity;
+	}
+
+}
diff --git a/src/jcgp/function/Subtraction.java b/src/jcgp/function/Subtraction.java
index d785614..cfbb907 100644
--- a/src/jcgp/function/Subtraction.java
+++ b/src/jcgp/function/Subtraction.java
@@ -1,5 +1,6 @@
 package jcgp.function;
 
+import jcgp.exceptions.InvalidArgumentsException;
 import jcgp.population.Connection;
 
 public class Subtraction extends Function {
@@ -11,7 +12,12 @@ public class Subtraction extends Function {
 		if (connections.length < arity) {
 			throw new InvalidArgumentsException("Not enough connections were given.");
 		} else if (connections[0].getValue() instanceof Integer) {
-			return ((Integer) connections[0].getValue()) - ((Integer) connections[1].getValue());
+			Integer arg1 = ((Integer) connections[0].getValue());
+			Integer arg2 = ((Integer) connections[1].getValue());
+			Integer result = arg1 - arg2;
+			
+			System.out.println(arg1 + " - " + arg2 + " = " + result);
+			return result;
 		} else {
 			throw new InvalidArgumentsException("Wrong data type, this function takes Integer.");
 		}
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/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;
 	}
 }
diff --git a/src/jcgp/tests/ChromosomeTests.java b/src/jcgp/tests/ChromosomeTests.java
index 8092d60..c943da8 100644
--- a/src/jcgp/tests/ChromosomeTests.java
+++ b/src/jcgp/tests/ChromosomeTests.java
@@ -31,8 +31,7 @@ import org.junit.Test;
  *  - It should contain a freely modifiable fitness value.
  *  - For truth table evaluations, it should be able to have its inputs set.
  *  - For truth table evaluations, the output should return a value according to the inputs.
- *  - It should feature a clone constructor, which creates a deep copy of a 
- *    specified Chromosome object.
+ *  - It should feature a copy method, which creates a deep copy of a specified Chromosome object.
  *  - It should be able to return a list of active nodes.
  *  - It should contain a method to evaluate whether a given chromosome is identical
  *    to it.
@@ -65,11 +64,11 @@ public class ChromosomeTests {
 
 	@Before
 	public void setUp() throws Exception {
-		Parameters.setColumns(10);
+		Parameters.setColumns(5);
 		Parameters.setRows(2);
 		Parameters.setInputs(2);
 		Parameters.setOutputs(4);
-		Parameters.setLevelsBack(10);
+		Parameters.setLevelsBack(5);
 		chromosome = new Chromosome();
 	}
 
@@ -183,10 +182,9 @@ public class ChromosomeTests {
 			assertTrue("Connection is not an input.", connectionReturn);
 		}
 
-		// get random connections with column 1
-		// they should all be nodes, and their columns should be within range
+		// get random connections with the last column as reference, check that they're all within range
 		int connectionNodes = 0, connectionOutOfRange = 0, connectionInputs = 0, connectionPicks = 100000;
-		int chosenColumn = 1;
+		int chosenColumn = Parameters.getColumns() - 1;
 		for (int i = 0; i < connectionPicks; i++) {
 			Connection c = chromosome.getRandomConnection(chosenColumn);
 			if (c instanceof Node) {
diff --git a/src/jcgp/tests/PopulationTests.java b/src/jcgp/tests/PopulationTests.java
index bb8fece..b8639bf 100644
--- a/src/jcgp/tests/PopulationTests.java
+++ b/src/jcgp/tests/PopulationTests.java
@@ -2,7 +2,6 @@ package jcgp.tests;
 
 import static org.junit.Assert.*;
 
-import java.util.Iterator;
 import java.util.Random;
 
 import jcgp.Parameters;
@@ -11,8 +10,6 @@ import jcgp.function.Addition;
 import jcgp.function.FunctionSet;
 import jcgp.function.Subtraction;
 import jcgp.population.Chromosome;
-import jcgp.population.Input;
-import jcgp.population.Node;
 import jcgp.population.Population;
 
 import org.junit.Before;
@@ -23,14 +20,13 @@ import org.junit.Test;
  * 
  * Tests which cover the behaviour specified for a population.
  * 
- *  - A population is a collection of chromosomes. It should be Iterable
- *    so the chromosomes can be accessed. 
- *  - Iterator.remove() should generate an UnsupportedOperationException
- *    since chromosomes may not be removed.
+ *  - A population should be able to return parents and offspring separately. 
+ *  - It should be possible to iterate through all the chromosomes in a population
+ *    with one indexing system - parents then offspring.
  *  - When constructed with no arguments, it should generate populationSize
- *    random chromosomes.
- *  - If a chromosome is passed as an argument to the constructor, it should
- *    create a population of copies of that chromosome.
+ *    random chromosomes, distributed according to the EA parameters.
+ *  - If one or more chromosomes are passed into the constructor, it should use them
+ *    as parents to create the rest of the population.
  *  
  * 
  * @author Eduardo Pedroni
@@ -57,7 +53,7 @@ public class PopulationTests {
 		Parameters.setMutationRate(10);
 		Parameters.setTotalGenerations(100);
 		Parameters.setTotalRuns(5);
-		Parameters.setPopulationSize(5);
+		Parameters.setPopulationSize(1, 4);
 		Parameters.setMaxArity(functionSet.getMaxArity());
 	}
 
@@ -67,42 +63,43 @@ public class PopulationTests {
 	}
 
 	@Test
-	public void iterableTest() {
-		// check that Population is really Iterable
-		assertTrue("Population must implement Iterable.", population instanceof Iterable);
-
-		// iterate through, check that different chromosomes are returned and no chromosome can be removed
-		Chromosome comparison = null;
-		int iterationCount = 0;
-		boolean exceptionThrown = false;
-
-		for (Chromosome chromosome : population) {
-			iterationCount++;
-			assertTrue("Same chromosome returned twice.", comparison != chromosome);
-			comparison = chromosome;
-
+	public void defaultPopulationTest() {
+		// check that the constructor really generates populationSize chromosomes when none is given
+		int offspring = 0, parent = 0;
+		while (true) {
 			try {
-				population.iterator().remove();
-			} catch (UnsupportedOperationException e) {
-				exceptionThrown = true;
+				population.getOffspring(offspring);
+			} catch (IndexOutOfBoundsException e) {
+				break;
 			}
-			assertTrue("Chromosome removed.", exceptionThrown);	
-			exceptionThrown = false;
+			offspring++;
 		}
-		// check that all chromosomes were iterated through
-		assertTrue("Number of elements in population does not match specified parameter size.",
-				iterationCount == Parameters.getPopulationSize());
+		while (true) {
+			try {
+				population.getParent(parent);
+			} catch (IndexOutOfBoundsException e) {
+				break;
+			}
+			parent++;
+		}
+		assertTrue("Incorrect number of chromosomes generated.", offspring + parent == Parameters.getPopulationSize());
 	}
-
+	
 	@Test
-	public void defaultPopulationTest() {
-		// check that the constructor really generates populationSize chromosomes when none is given
-		int populationCount = 0;
-		for (Iterator<Chromosome> iterator = population.iterator(); iterator.hasNext();) {
-			populationCount++;
-			iterator.next();
+	public void offspringParentTest() {
+		// the first parent should not be the same as the first offspring
+		assertTrue("Same chromosome returned as parent and offspring", population.getOffspring(0) != population.getParent(0));
+	}
+	
+	@Test
+	public void singleIndexTest() {
+		// assuming 1+4
+		// the first chromosome should be the first (and only) parent
+		assertTrue("Incorrect chromosome returned.", population.getChromosome(0) == population.getParent(0));
+		// the next 4 chromosomes should be the offspring, in order
+		for (int i = 0; i < Parameters.getOffspringCount(); i++) {
+			assertTrue("Incorrect chromosome returned.", population.getChromosome(i + 1) == population.getOffspring(i));
 		}
-		assertTrue("Incorrect number of chromosomes generated.", populationCount == Parameters.getPopulationSize());
 	}
 
 	@Test
@@ -110,65 +107,9 @@ public class PopulationTests {
 		// the original chromosome that will be cloned
 		Chromosome oc = new Chromosome();
 
-		// initialise a population with copies of it
+		// initialise a population with a copy of it
 		population = new Population(oc);
-		// check that the chromosomes returned are identical to the one given
-		int index = 0;
-		for (Chromosome c : population) {
-			assertTrue("Incorrect chromosome in population.", c != oc);
-			index++;
-		}
-		// check that the right number of copies was made
-		assertTrue("Wrong number of chromosomes in population.", index == Parameters.getPopulationSize());
-
-		// check that the copies are exact copies
-		for (Chromosome c : population) {
-			// check outputs
-			for (int o = 0; o < Parameters.getOutputs(); o++) {
-				// check that no cross-references exist between chromosomes
-				assertTrue("Cloned chromosome contained a reference to a member of the original chromosome.",
-						c.getOutput(o) != oc.getOutput(o) && 
-						c.getOutput(o).getSource() != oc.getOutput(o).getSource());
-				// check that the connections are equivalent
-				if (c.getOutput(o).getSource() instanceof Input && oc.getOutput(o).getSource() instanceof Input) {
-					assertTrue("Outputs did not connect to equivalent inputs.", 
-							((Input) c.getOutput(o).getSource()).getIndex() == ((Input) oc.getOutput(o).getSource()).getIndex());
-				} else if (c.getOutput(o).getSource() instanceof Node && oc.getOutput(o).getSource() instanceof Node) {
-					assertTrue("Outputs did not connect to equivalent nodes.", 
-							((Node) c.getOutput(o).getSource()).getRow() == ((Node) oc.getOutput(o).getSource()).getRow() && 
-							((Node) c.getOutput(o).getSource()).getColumn() == ((Node) oc.getOutput(o).getSource()).getColumn());
-				} else {
-					fail("Output source types did not match.");
-				}
-			}
-			// check nodes, rows first
-			for (int row = 0; row < Parameters.getRows(); row++) {
-				for (int column = 0; column < Parameters.getColumns(); column++) {
-					// look at each connection
-					for (int connection = 0; connection < Parameters.getMaxArity(); connection++) {
-						if (c.getNode(row, column).getConnection(connection) instanceof Input && 
-								oc.getNode(row, column).getConnection(connection) instanceof Input) {
-							
-							assertTrue("Nodes did not connect to equivalent inputs.", 
-									((Input) c.getNode(row, column).getConnection(connection)).getIndex() ==
-									((Input) oc.getNode(row, column).getConnection(connection)).getIndex());
-							
-						} else if (c.getNode(row, column).getConnection(connection) instanceof Node && 
-								oc.getNode(row, column).getConnection(connection) instanceof Node) {
-							
-							assertTrue("Nodes did not connect to equivalent nodes.", 
-									((Node) c.getNode(row, column).getConnection(connection)).getRow() ==
-									((Node) oc.getNode(row, column).getConnection(connection)).getRow() &&
-									
-									((Node) c.getNode(row, column).getConnection(connection)).getColumn() ==
-									((Node) oc.getNode(row, column).getConnection(connection)).getColumn());
-							
-						} else {
-							fail("Connection types did not match.");
-						}
-					}
-				}
-			}
-		}
+		// check that the first parent chromosome is identical to, but not the same instance as, the one given
+		assertTrue("Incorrect chromosome in population.", population.getParent(0).compareTo(oc) && population.getParent(0) != oc);
 	}
 }