Settings pane now actually controls the parameters, not much left to do.

8 files changed, 0 insertions, 640 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;
-	}
-}
diff --git a/src/jcgp/population/Connection.java b/src/jcgp/population/Connection.java
deleted file mode 100644
index 63a171e..0000000
--- a/src/jcgp/population/Connection.java
+++ /dev/null
@@ -1,9 +0,0 @@
-package jcgp.population;
-
-public interface Connection {
-
-	public Object getValue();
-	
-	public String getDescription();
-
-}
diff --git a/src/jcgp/population/Gene.java b/src/jcgp/population/Gene.java
deleted file mode 100644
index 8865a01..0000000
--- a/src/jcgp/population/Gene.java
+++ /dev/null
@@ -1,5 +0,0 @@
-package jcgp.population;
-
-public abstract class Gene {
-
-}
diff --git a/src/jcgp/population/Input.java b/src/jcgp/population/Input.java
deleted file mode 100644
index cfcb3ce..0000000
--- a/src/jcgp/population/Input.java
+++ /dev/null
@@ -1,29 +0,0 @@
-package jcgp.population;
-
-public class Input extends Gene implements Connection {
-	
-	private Object value = 0;
-	private int index;
-	
-	public Input(int index) {
-		this.index = index;
-	}
-	
-	public void setValue(Object newValue) {
-		value = newValue;
-	}
-
-	@Override
-	public Object getValue() {
-		return value;
-	}
-
-	public int getIndex() {
-		return index;
-	}
-
-	@Override
-	public String getDescription() {
-		return "i: " + index;
-	}
-}
diff --git a/src/jcgp/population/MutableElement.java b/src/jcgp/population/MutableElement.java
deleted file mode 100644
index 12f6bd1..0000000
--- a/src/jcgp/population/MutableElement.java
+++ /dev/null
@@ -1,34 +0,0 @@
-package jcgp.population;
-
-public interface MutableElement {
-	
-	/**
-	 * This method sets the indexed connection to the specified new connection.
-	 * Implementing classes may choose to ignore the given index (such as in the
-	 * case of outputs, which only have one connection).
-	 * 
-	 * @param index
-	 * @param newConnection
-	 */
-	public void setConnection(int index, Connection newConnection);
-	
-	/**
-	 * This method returns true if and only if:</br>
-	 * 	- the elements being compared are not the same instance;</br>
-	 *  - the connections of the compared elements are not the same instance;</br>
-	 *  - the elements have the same function (in the case of Node);</br>
-	 *  - the grid position of the elements themselves are the same;</br>
-	 *  - the grid position of all equivalent connections are the same;</br></br>
-	 * 
-	 * The relationship computed by this method is:</br>
-	 *  - symmetric: a.copyOf(b) == b.copyOf(a);</br>
-	 *  - not reflexive: a.copyOf(a) returns false;</br>
-	 *  - not transitive: if a.copyOf(b) is true and b.copyOf(c) is true, a.copyOf(c) is
-	 *    not necessarily true since it is possible that a == c.</br>
-	 * 
-	 * @param m
-	 * @return
-	 */
-	boolean copyOf(MutableElement m);
-	
-}
diff --git a/src/jcgp/population/Node.java b/src/jcgp/population/Node.java
deleted file mode 100644
index 141a32a..0000000
--- a/src/jcgp/population/Node.java
+++ /dev/null
@@ -1,114 +0,0 @@
-package jcgp.population;
-
-import java.util.ArrayList;
-import java.util.Arrays;
-
-import jcgp.exceptions.InsufficientConnectionsException;
-import jcgp.function.Function;
-
-
-public class Node extends Gene implements MutableElement, Connection {
-
-	private Function function;
-	private Connection[] connections;
-	private int column, row;
-	private Chromosome chromosome;
-
-	public Node(Chromosome chromosome, int row, int column, int arity) {
-		this.chromosome = chromosome;
-		this.column = column;
-		this.row = row;
-	}
-
-	@Override
-	public Object getValue() {
-		//System.out.print("Calculating node: (" + row + ", " + column + ") > ");
-		return function.run(Arrays.copyOfRange(connections, 0, function.getArity()));
-	}
-
-	public void setFunction(Function newFunction) {
-		function = newFunction;
-		chromosome.recomputeActiveNodes();
-	}
-
-	@Override
-	public void setConnection(int index, Connection newConnection) {
-		connections[index] = newConnection;
-		chromosome.recomputeActiveNodes();
-	}
-
-	public void initialise(Function newFunction, Connection ... newConnections) throws InsufficientConnectionsException {
-		function = newFunction;
-		if (newConnections.length == function.getArity()) {
-			connections = newConnections;
-		} else {
-			throw new InsufficientConnectionsException();
-		}
-	}
-
-	public int getColumn() {
-		return column;
-	}
-
-	public int getRow() {
-		return row;
-	}
-
-	public Function getFunction() {
-		return function;
-	}
-	
-	public Connection getConnection(int index) {
-		return connections[index];
-	}
-
-	public void getActive(ArrayList<Node> activeNodes) {
-		if (!activeNodes.contains(this)) {
-			activeNodes.add(this);
-		}
-		for (int i = 0; i < function.getArity(); i++) {
-			if (connections[i] instanceof Node) {
-				((Node) connections[i]).getActive(activeNodes);
-			}
-
-		}
-	}
-
-	@Override
-	public boolean copyOf(MutableElement m) {
-		if (this != m) {
-			if (m instanceof Node) {
-				Node n = (Node) m;
-				if (function == n.getFunction()) {
-					if (column == n.getColumn() && row == n.getRow()) {
-						for (int i = 0; i < connections.length; i++) {
-							if (connections[i] != n.getConnection(i)) {
-								if (connections[i] instanceof Input && n.getConnection(i) instanceof Input) {
-									if (((Input) connections[i]).getIndex() != ((Input) n.getConnection(i)).getIndex()) {
-										return false;
-									}
-								} else if (connections[i] instanceof Node && n.getConnection(i) instanceof Node) {
-									if (((Node) connections[i]).getRow() != ((Node) n.getConnection(i)).getRow() &&
-											((Node) connections[i]).getColumn() != ((Node) n.getConnection(i)).getColumn()) {
-										return false;
-									}
-								} else {
-									return false;
-								}
-							} else {
-								return false;
-							}
-						}
-						return true;
-					}
-				}
-			}
-		}
-		return false;
-	}
-
-	@Override
-	public String getDescription() {
-		return "n: " + row + ", " + column;
-	}
-}
diff --git a/src/jcgp/population/Output.java b/src/jcgp/population/Output.java
deleted file mode 100644
index 5cc6dcf..0000000
--- a/src/jcgp/population/Output.java
+++ /dev/null
@@ -1,69 +0,0 @@
-package jcgp.population;
-
-import java.util.ArrayList;
-
-public class Output extends Gene implements MutableElement {
-	
-	private Connection source;
-	private Chromosome chromosome;
-	private int index;
-	
-	public Output(Chromosome chromosome, int index) {
-		this.chromosome = chromosome;
-		this.index = index;
-		//this.source = new SimpleObjectProperty<Connection>();
-	}
-
-	public Object calculate() {
-		Object result = source.getValue();
-		return result;
-	}
-
-	@Override
-	public void setConnection(int index, Connection newConnection) {
-		source = newConnection;
-		chromosome.recomputeActiveNodes();
-	}
-
-	public int getIndex() {
-		return index;
-	}
-
-	public Connection getSource() {
-		return source;
-	}
-	
-//	public SimpleObjectProperty<Connection> sourceProperty() {
-//		return source;
-//	}
-
-	public void getActiveNodes(ArrayList<Node> activeNodes) {
-		if (source instanceof Node) {
-			((Node) source).getActive(activeNodes);
-		}
-	}
-	
-	@Override
-	public boolean copyOf(MutableElement m) {
-		if (this != m) {
-			if (m instanceof Output) {
-				Output o = (Output) m;
-				if (index == o.getIndex()) {
-					if (source != o.getSource()) {
-						if (source instanceof Input && o.getSource() instanceof Input) {
-							if (((Input) source).getIndex() == ((Input) o.getSource()).getIndex()) {
-								return true;
-							}
-						} else if (source instanceof Node && o.getSource() instanceof Node) {
-							if (((Node) source).getRow() == ((Node) o.getSource()).getRow() &&
-									((Node) source).getColumn() == ((Node) o.getSource()).getColumn()) {
-								return true;
-							}
-						} 
-					}
-				}
-			}
-		}
-		return false;
-	}
-}
diff --git a/src/jcgp/population/Population.java b/src/jcgp/population/Population.java
deleted file mode 100644
index f5e0517..0000000
--- a/src/jcgp/population/Population.java
+++ /dev/null
@@ -1,45 +0,0 @@
-package jcgp.population;
-
-import jcgp.JCGP.Resources;
-
-
-public class Population {
-	
-	private Chromosome[] chromosomes;
-	private int fittest;
-	
-	public Population(Resources resources) {
-		chromosomes = new Chromosome[(resources.getInt("popSize"))];
-		for (int c = 0; c < chromosomes.length; c++) {
-			chromosomes[c] = new Chromosome(resources);
-		}
-	}
-	
-	public Population(Chromosome parent, 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]);
-		}
-	}
-
-	/**
-	 * Returns all chromosomes, parents first, then offspring.
-	 * 
-	 * @param index
-	 * @return
-	 */
-	public Chromosome getChromosome(int index) {
-		return chromosomes[index];
-	}
-	
-	public void setBestIndividual(int index) {
-		fittest = index;
-	}
-	
-	public Chromosome getBestIndividual() {
-		return chromosomes[fittest];
-	}
-}