1 files changed, 0 insertions, 335 deletions
diff --git a/src/jcgp/population/Chromosome.java b/src/jcgp/population/Chromosome.java
deleted file mode 100644
index 297d298..0000000
--- a/src/jcgp/population/Chromosome.java
+++ /dev/null
@@ -1,335 +0,0 @@
-package jcgp.population;
-
-import java.util.ArrayList;
-
-import jcgp.JCGP.Resources;
-import jcgp.exceptions.ParameterMismatchException;
-
-public class Chromosome {
-	
-	private Resources resources;
-
-	private Input[] inputs;
-	private Node[][] nodes;
-	private Output[] outputs;
-
-	private ArrayList<Node> activeNodes;
-
-	private int fitness = 0;
-	private boolean recomputeActiveNodes = true;
-
-	/**
-	 * Initialise a chromosome with the specified parameters. Random valid connections
-	 * are created.
-	 * 
-	 * 
-	 */
-	public Chromosome(Resources resources) {
-		// store a reference to the parameters
-		this.resources = resources;
-		
-		// allocate memory for all elements of the chromosome
-		instantiateElements();
-		// set random connections so that the chromosome can be evaluated
-		initialiseConnections();
-	}
-
-	/**
-	 * Copy constructor.
-	 * 
-	 * Initialise a new chromosome with the exact same connections as a given instance of Chromosome.
-	 * 
-	 * @param clone the chromosome to be copied
-	 */
-	public Chromosome(Chromosome clone) {
-		// store a reference to the parameters
-		this.resources = clone.getParameters();
-		
-		// allocate memory for all elements of the chromosome
-		instantiateElements();
-		// initialise all connections based on argument
-		copyConnections(clone);
-	}
-
-	/**
-	 *
-	 */
-	private void instantiateElements() {
-		inputs = new Input[(resources.getInt("inputs"))];
-		for (int i = 0; i < (resources.getInt("inputs")); i++) {
-			inputs[i] = new Input(i);
-		}
-
-		int arity = resources.getInt("arity");
-		
-		// rows first
-		nodes = new Node[(resources.getInt("rows"))][(resources.getInt("columns"))];
-		for (int r = 0; r < (resources.getInt("rows")); r++) {
-			for (int c = 0; c < (resources.getInt("columns")); c++) {
-				nodes[r][c] = new Node(this, r, c, arity);
-			}
-		}
-		outputs = new Output[(resources.getInt("outputs"))];
-		for (int o = 0; o < (resources.getInt("outputs")); o++) {
-			outputs[o] = new Output(this, o);
-		}
-	}
-
-	/**
-	 * 
-	 */
-	private void initialiseConnections() {
-
-		int arity = resources.getInt("arity");
-		
-		// initialise nodes - [rows][columns]
-		for (int r = 0; r < nodes.length; r++) {
-			for (int c = 0; c < nodes[r].length; c++) {
-				Connection[] connections = new Connection[arity];
-				for (int i = 0; i < connections.length; i++) {
-					connections[i] = getRandomConnection(c);
-				}
-				nodes[r][c].initialise(resources.getRandomFunction(), connections);
-			}
-		}
-
-		for (Output output : outputs) {
-			output.setConnection(0, getRandomConnection());
-		}
-
-	}
-
-	/**
-	 * @param clone
-	 */
-	public void copyConnections(Chromosome clone) {
-		int arity = resources.getInt("arity");
-		
-		// copy nodes - [rows][columns]
-		for (int r = 0; r < nodes.length; r++) {
-			for (int c = 0; c < nodes[r].length; c++) {
-				// make array of connections to initialise with
-				Connection[] connections = new Connection[arity];
-				// populate with connections equivalent to clone
-				Connection copyConnection;
-				for (int i = 0; i < connections.length; i++) {
-					copyConnection = clone.getNode(r, c).getConnection(i);
-					if (copyConnection instanceof Input) {
-						connections[i] = inputs[((Input) copyConnection).getIndex()];
-					} 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.");
-					}
-				}
-				// initialise with copied arguments
-				nodes[r][c].initialise(clone.getNode(r, c).getFunction(), connections);
-			}
-		}
-
-		// do the same to outputs
-		Connection copyOutput;
-		for (int o = 0; o < outputs.length; o++) {
-			copyOutput = clone.getOutput(o).getSource();
-			if (copyOutput instanceof Input) {
-				outputs[o].setConnection(0, inputs[((Input) copyOutput).getIndex()]);
-			} else if (copyOutput instanceof Node) {
-				outputs[o].setConnection(0, nodes[((Node) copyOutput).getRow()][((Node) copyOutput).getColumn()]);
-			} else {
-				// something bad happened
-				System.out.println("Warning: Connection of subtype " + copyOutput.getClass().toString() + " is not explicitly handled by copy constructor.");
-			}
-		}
-	}
-
-	public Node getNode(int row, int column) {
-		return nodes[row][column];
-	}
-
-	public Output getOutput(int index) {
-		return outputs[index];
-	}
-
-	public Input getInput(int index) {
-		return inputs[index];
-	}
-
-	public int getFitness() {
-		return fitness;
-	}
-
-	public void setFitness(int newFitness) {
-		fitness = newFitness;
-	}
-
-	/**
-	 * 
-	 * @param values
-	 * @throws ParameterMismatchException
-	 */
-	public void setInputs(Object ... 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 {
-			throw new ParameterMismatchException();
-		}
-	}
-
-	/**
-	 * This method is useful for mutating chromosomes.
-	 * 
-	 * @return a random element that can be mutated - Node or Output
-	 */
-	public MutableElement getRandomMutableElement() {
-		// choose output or node
-		int index = resources.getRandomInt(outputs.length + (resources.getInt("rows")) * (resources.getInt("columns")));
-
-		if (index < outputs.length) {
-			// outputs
-			return outputs[index];
-		} else {
-			// node	
-			index -= outputs.length;
-			return nodes[index / (resources.getInt("columns"))][index % (resources.getInt("columns"))];
-		}
-	}
-
-	/**
-	 * Returns a random allowed connection respecting levels back.</br>
-	 * This method may always pick inputs, as they can be picked
-	 * regardless of the column.
-	 * 
-	 * @param column the column to use as reference
-	 * @return a random connection
-	 */
-	public Connection getRandomConnection(int column) {
-		// work out the allowed range obeying levels back
-		int allowedColumns = ((column >= (resources.getInt("levelsBack"))) ? (resources.getInt("levelsBack")) : column);
-		int offset = ((column - allowedColumns) * nodes.length) - inputs.length;
-
-		// choose input or allowed node
-		int index = resources.getRandomInt(inputs.length + (nodes.length * allowedColumns));
-		if (index < inputs.length) {
-			// input
-			return inputs[index];
-		} else {
-			// node	
-			// offset it to address the right columns
-			index += offset;
-			return nodes[index % nodes.length][index / nodes.length];
-		}
-	}
-
-	/**
-	 * This method will pick a completely random connection, independently
-	 * of levels back, including inputs.
-	 * 
-	 * Useful for setting outputs.
-	 * 
-	 * 
-	 * @return a random connection
-	 */
-	public Connection getRandomConnection() {
-		// choose output or node
-		int index = resources.getRandomInt(inputs.length + (resources.getInt("columns")) * (resources.getInt("rows")));
-		if (index < inputs.length) {
-			// outputs
-			return inputs[index];
-		} else {
-			// node	
-			index -= inputs.length;
-			return nodes[index / (resources.getInt("columns"))][index % (resources.getInt("columns"))];
-		}
-	}
-
-	/**
-	 * This causes the list of active nodes to be recomputed lazily (once it is actually requested).
-	 */
-	public void recomputeActiveNodes() {
-		recomputeActiveNodes = true;
-	}
-
-	/**
-	 * This method computes a list of active connections (if necessary) and returns it.
-	 *
-	 * @return
-	 */
-	public ArrayList<Node> getActiveNodes() {
-		computeActiveNodes();
-		return activeNodes;
-	}
-
-	private void computeActiveNodes() {
-		// lazy recomputation has been triggered, do it
-		if (recomputeActiveNodes) {
-			recomputeActiveNodes = false;
-			activeNodes = new ArrayList<Node>();
-
-			for (Output output : outputs) {
-				output.getActiveNodes(activeNodes);
-			}
-		}
-
-	}
-
-	public boolean compareTo(Chromosome chromosome) {
-		for (int r = 0; r < (resources.getInt("rows")); r++) {
-			for (int c = 0; c < (resources.getInt("columns")); c++) {
-				if (!(nodes[r][c].copyOf(chromosome.getNode(r, c)))) {
-					return false;
-				}
-			}
-		}
-		
-		for (int o = 0; o < (resources.getInt("outputs")); o++) {
-			if (!(outputs[o].copyOf(chromosome.getOutput(o)))) {
-				return false;
-			}
-		}
-		
-		return true;
-	}
-
-	public boolean compareActiveTo(Chromosome chromosome) {
-		// update list if it is out of date
-		computeActiveNodes();
-		
-		if (activeNodes.size() == chromosome.getActiveNodes().size()) {
-			for (int i = 0; i < activeNodes.size(); i++) {
-				if (!(activeNodes.get(i).copyOf(chromosome.getActiveNodes().get(i)))){
-					return false;
-				}
-			}
-			return true;
-		}
-		return false;
-	}
-	
-	public void printNodes() {
-		int arity = resources.getInt("arity");
-		
-		for (int r = 0; r < (resources.getInt("rows")); r++) {
-			System.out.print("r: " + r + "\t");
-			for (int c = 0; c < (resources.getInt("columns")); c++) {
-				System.out.print("N: (" + r + ", " + c + ") ");
-				for (int i = 0; i < arity; i++) {
-					System.out.print("C" + i + ": (" + nodes[r][c].getConnection(i).getDescription() + ") ");
-				}
-				System.out.print("F: " + nodes[r][c].getFunction().getName() + "\t");
-			}
-			System.out.print("\n");
-		}
-		
-		for (int o = 0; o < (resources.getInt("outputs")); o++) {
-			System.out.print("o: " + o + " (" + outputs[o].getSource().getDescription() + ")\t");
-		}
-	}
-	
-	public Resources getParameters() {
-		return resources;
-	}
-}