Moved GUI to its own repositoryHEADmaster

25 files changed, 0 insertions, 3579 deletions

diff --git a/src/jcgp/gui/GUI.java b/src/jcgp/gui/GUI.java
deleted file mode 100644
index 689f38c..0000000
--- a/src/jcgp/gui/GUI.java
+++ /dev/null
@@ -1,477 +0,0 @@
-package jcgp.gui;
-
-import javafx.application.Application;
-import javafx.application.Platform;
-import javafx.concurrent.Service;
-import javafx.concurrent.Task;
-import javafx.event.EventHandler;
-import javafx.scene.Scene;
-import javafx.scene.input.MouseEvent;
-import javafx.scene.layout.BorderPane;
-import javafx.scene.layout.Pane;
-import javafx.stage.Stage;
-import javafx.stage.WindowEvent;
-import jcgp.JCGP;
-import jcgp.backend.modules.problem.TestCaseProblem.TestCase;
-import jcgp.backend.resources.Resources;
-import jcgp.gui.console.ConsolePane;
-import jcgp.gui.dragresize.HorizontalDragResize;
-import jcgp.gui.dragresize.VerticalDragResize;
-import jcgp.gui.population.FunctionSelector;
-import jcgp.gui.population.GUINode;
-import jcgp.gui.population.PopulationPane;
-import jcgp.gui.settings.SettingsPane;
-
-/**
- * Main class for the graphical user interface (GUI).
- * <br><br>
- * This class declares the main method used when running the GUI.
- * In addition, all main GUI panes are declared and instantiated here.
- * <br><br>
- * The user interface is divided into 3 main components: the node grid
- * ({@link PopulationPane}), the control pane ({@link SettingsPane}) and
- * the console ({@link ConsolePane}). Click on any of the links in
- * brackets to see more information about each interface component.
- * <br><br>
- * This class also contains the instance of JCGP responsible for
- * running the experiments in GUI mode. JCGP's execution must be delegated
- * to a separate thread so that the GUI remains unblocked. This is done using
- * a JavaFX {@code Service} which calls {@code nextGeneration()} in a loop
- * until it is interrupted by the main JavaFX thread.
- * <br>
- * This service also handles flushing the console in a thread safe way. This
- * is done by synchronizing the {@code nextGeneration()} and {@code flush()}
- * method calls on a lock object.
- * 
- * @author Eduardo Pedroni
- *
- */
-public class GUI extends Application {
-    
-	/*
-	 * Actual GUI elements
-	 */
-	private Stage stage;
-	private PopulationPane populationPane;
-	private ConsolePane console;
-	private SettingsPane settingsPane;
-	private final FunctionSelector functionSelector;
-	
-	/*
-	 * Flow control objects
-	 */
-	private boolean running = false;
-	private final Object printLock = new Object();
-	private Service<Void> jcgpService;
-	private Runnable consoleFlush;
-	
-	/*
-	 * The experiment itself
-	 */
-	private final JCGP jcgp;
-	
-	public static Resources resources;
-	
-	
-	/**
-	 * Start JCGP with the user interface.
-	 * 
-	 * @param args no arguments are used.
-	 */
-	public static void main(String[] args) {
-		// not much to do, simply launch the JavaFX application
-		launch();
-	}
-	
-	/**
-	 * Makes a new instance of GUI. This initialises the JCGP experiment and 
-	 * instantiates the function selector. It also creates the console flush task
-	 * and the service responsible for running the JCGP experiment.
-	 */
-	public GUI() {
-		jcgp = new JCGP();
-		resources = jcgp.getResources();
-		functionSelector = new FunctionSelector(jcgp.getResources().getFunctionSet());
-		
-		/*
-		 * This task flushes the console in a thread-safe way.
-		 * The problem is that this task is executed using Platform.runLater()
-		 * to ensure that the flush itself happens on the JavaFX thread. However,
-		 * runLater() is not guaranteed to run anytime soon. If the time taken for
-		 * jcgp to perform a single generation is shorter than the time taken for
-		 * this task to be executed by the platform, consoleFlush tasks will be 
-		 * scheduled faster than they can be executed and the console will eventually 
-		 * freeze. 
-		 * 
-		 * This is addressed by synchronizing the flushes with each nextGeneration() call.
-		 */
-		consoleFlush = new Runnable() {
-			@Override
-			public void run() {
-				/* 
-				 * Try to acquire printlock - wait here until jcgpService relinquishes it
-				 * by calling wait(). This means that it is finished with the current generation
-				 * and will wait for the console to be flushed to move on.
-				 * It might be the case that the service has already released the lock by waiting
-				 * on it; it makes no difference. In that case this will acquire the lock
-				 * immediately and proceed to flush the console.
-				 */
-				synchronized(printLock) {
-					/*
-					 * The lock is acquired, at this point we are certain that jcgpService
-					 * cannot execute; it is currently waiting to be notified about the lock.
-					 * No additional consoleFlush tasks can be scheduled with runLater() because
-					 * the service is waiting. We can now take our time to flush the console.
-					 */
-					console.flush();
-					/*
-					 * Once the console finishes flushing, we notify jcgpService to perform the
-					 * next generation.
-					 */
-					printLock.notifyAll();
-				}
-			}
-		};
-		
-		/* 
-		 * This service runs on a separate thread and performs
-		 * the experiment, including console prints, in a thread-safe
-		 * way. It is synchronized with consoleFlush.
-		 */
-		jcgpService = new Service<Void> () {
-			@Override
-			protected Task<Void> createTask() {
-				Task<Void> t = new Task<Void>() {
-					@Override
-					protected Void call() throws Exception {
-						/*
-						 * Only execute if the experiment isn't finished
-						 * and the service hasn't been cancelled.
-						 */
-						while (!isCancelled() && !jcgp.isFinished()) {
-							/*
-							 * Attempt to acquire the printlock.
-							 * Successfully doing so means no printing
-							 * is currently taking place and we are free
-							 * to schedule a print task.
-							 * This lock acquisition should never block. It should
-							 * not be possible to execute this statement without
-							 * having been notified by consoleFlush.
-							 */
-							synchronized (printLock) {
-								/*
-								 * Lock has been acquired, schedule a print
-								 * task ahead of time. The actual print messages
-								 * haven't been send to the console yet, that happens
-								 * during nextGeneration(), but since we have the lock
-								 * consoleFlush() will sit and wait for us to release it
-								 * whenever we are finished queueing prints.
-								 */
-								Platform.runLater(consoleFlush);
-								/*
-								 * Perform the actual generation. Here zero or more
-								 * strings might be sent to the console buffer.
-								 */
-								jcgp.nextGeneration();
-								/*
-								 * The generation is complete, relinquish the lock.
-								 * By this point chances are the platform is already trying
-								 * to execute the consoleFlush task that we scheduled. If it
-								 * hasn't already started though, it doesn't matter; we will
-								 * wait for a notification on the lock, which will only come
-								 * when printing is complete.
-								 */
-								printLock.wait();
-								/*
-								 * We have been notified. This means all buffered messages have
-								 * been successfully flushed to the actual console control and
-								 * we are now ready to perform another generation (or break out
-								 * of the loop if the loop conditions are no longer met).
-								 */
-							}
-							/*
-							 * We no longer own the lock, but neither does consoleFlush. 
-							 * The synchrony cycle has returned to its initial state, and we
-							 * are free to acquire the lock again.
-							 */
-						}
-						/*
-						 * Something happened to break the while loop -
-						 * either the experiment finished or the user pressed
-						 * pause.
-						 */
-						if (jcgp.isFinished()) {
-							// the experiment has finished, switch to pause mode
-							Platform.runLater(new Runnable() {
-								@Override
-								public void run() {
-									runningMode(false);
-								}
-							});
-						}
-						return null;
-					}
-				};
-				return t;
-			}
-		};
-	}
-	
-	@Override
-	public void start(Stage primaryStage) throws Exception {
-		/*
-		 * This method gets called when the application launches. Once it
-		 * returns, the application falls into the main loop which handles 
-		 * events, so all elements must be constructed here.
-		 */
-		
-		// make the console and set it so it is used for JCGP prints
-		console = new ConsolePane();
-		jcgp.setConsole(console);
-		
-		// store reference to the stage
-		stage = primaryStage;
-
-		/*
-		 * The experiment layer contains all of the experiment-related panes. 
-		 * The only element that sits higher than this is the function selector.
-		 */
-		BorderPane experimentLayer = new BorderPane();
-		/*
-		 * The left frame encapsulates the population pane and the console.
-		 * It goes into the center position of the experiment layer, next to the settings pane.
-		 */
-		BorderPane leftFrame = new BorderPane();
-		
-		/*
-		 * The population pane is a TabPane containing a tab for each chromosome. 
-		 */
-		populationPane = new PopulationPane(this);
-		
-		/*
-		 * The settings pane is a big class containing the entire control pane
-		 */
-		settingsPane = new SettingsPane(this);
-		
-		// make control pane and console resizable
-		HorizontalDragResize.makeDragResizable(settingsPane);
-		VerticalDragResize.makeDragResizable(console);
-		// prevent resizables from growing larger than the experiment layer
-		settingsPane.maxWidthProperty().bind(experimentLayer.widthProperty());
-		console.maxHeightProperty().bind(experimentLayer.heightProperty());
-
-		// put console and population pane in the main frame
-		leftFrame.setCenter(populationPane);
-		leftFrame.setBottom(console);
-		
-		// set the main frame and the control pane in the experiment layer
-		experimentLayer.setCenter(leftFrame);
-		experimentLayer.setRight(settingsPane);
-		
-		/*
-		 * Now we deal with the stage.
-		 */
-		primaryStage.setTitle("JCGP");
-		
-		// this pane holds the entire scene, that is its sole job.
-		Pane sceneParent = new Pane();
-		// the experiment layer should fill the entire scene parent
-		experimentLayer.prefHeightProperty().bind(sceneParent.heightProperty());
-		experimentLayer.prefWidthProperty().bind(sceneParent.widthProperty());
-		// the function selector goes over the experiment layer so it doesn't get covered by other panes
-		sceneParent.getChildren().addAll(experimentLayer, functionSelector);
-		
-		// set the scene, minimum sizes, show
-		primaryStage.setScene(new Scene(sceneParent));
-		primaryStage.setMinWidth(800);
-		primaryStage.setMinHeight(600);
-		primaryStage.show();
-		
-		// when the main stage closes, close the test case table as well
-		primaryStage.setOnCloseRequest(new EventHandler<WindowEvent>() {
-			@Override
-			public void handle(WindowEvent event) {
-				if (settingsPane.getTestCaseTable() != null) {
-					settingsPane.getTestCaseTable().close();
-				}
-			}
-		});
-	}
-
-	/**
-	 * Run/pause method.
-	 * Run the experiment if it is paused, or pause it if it is running.
-	 * <br>
-	 * This method is the callback used by the run/pause button. It
-	 * controls the jcgp service.
-	 */
-	public void runPause() {
-		// do nothing if experiment is finished or parameters aren't valid
-		if (!jcgp.isFinished() && settingsPane.areParametersValid()) {
-			if (!running) {
-				runningMode(true);
-				jcgpService.restart();
-			} else {
-				jcgpService.cancel();
-				runningMode(false);
-			}
-		}
-	}
-	
-	/**
-	 * Perform a single generation using {@code nextGeneration()}. 
-	 * <br>
-	 * On top of that, this method performs all of the housekeeping 
-	 * that is normally done before and after running, such as 
-	 * refreshing the chromosome panes.
-	 */
-	public void step() {
-		// do nothing if experiment is finished, running or parameters aren't valid
-		if (!running && !jcgp.isFinished() && settingsPane.areParametersValid()) {
-			if (settingsPane.isResetRequired()) {
-				reset();
-			}
-			jcgp.nextGeneration();
-			console.flush();
-			
-			populationPane.updateGenes();
-			settingsPane.revalidateParameters();
-			settingsPane.updateControls(false, jcgp.isFinished());
-		}
-	}
-	
-	/**
-	 * Reset button callback. If the parameters are valid, 
-	 * this resets the entire experiment by calling {@code reset()}
-	 * on jcgp.
-	 */
-	public void reset() {
-		if (!running && settingsPane.areParametersValid()) {
-			setEvaluating(false);
-			jcgp.reset();
-			settingsPane.applyParameters();
-			reDraw();
-		}
-	}
-	
-	/**
-	 * Does a complete GUI refresh. 
-	 * This is potentially lengthy, so use with care.
-	 */
-	public void reDraw() {
-		populationPane.remakeTabs();
-		settingsPane.revalidateParameters();
-		settingsPane.updateControls(false, jcgp.isFinished());
-		console.flush();
-	}
-	
-	/**
-	 * Toggles the entire GUI between run and pause
-	 * mode. 
-	 * <br><br>
-	 * A lot of the GUI must be enabled or disabled
-	 * depending on what the experiment is doing. This
-	 * method provides a one-line way to make
-	 * all required adjustments.
-	 * 
-	 * @param value true if experiment is running, false otherwise.
-	 */
-	private void runningMode(boolean value) {		
-		if (value) {
-			if (settingsPane.isResetRequired()) {
-				reset();
-			}
-		} else {
-			populationPane.updateGenes();
-			settingsPane.revalidateParameters();
-		}
-		populationPane.setDisable(value);
-		settingsPane.updateControls(value, jcgp.isFinished());
-		
-		running = value;
-	}
-	
-	/**
-	 * Refresh the function selector, used when functions are enabled or disabled.
-	 */
-	public void updateFunctionSelector() {
-		functionSelector.remakeFunctions(jcgp.getResources().getFunctionSet());
-	}
-	
-	/**
-	 * @return true if jcgp is evolving.
-	 */
-	public boolean isWorking() {
-		return running;
-	}
-
-	/**
-	 * Relocate the function selector to the right position
-	 * relative to the specified node and set it visible.
-	 * 
-	 * @param event the mouse event containing cursor coordinates.
-	 * @param node the node whose function should be changed.
-	 */
-	public void bringFunctionSelector(MouseEvent event, GUINode node) {
-		functionSelector.relocateAndShow(event, node);
-	}
-
-	/**
-	 * @return a reference to the {@code JCGP} experiment.
-	 */
-	public JCGP getExperiment() {
-		return jcgp;
-	}
-	
-	/**
-	 * Starts the evaluation process with the given test case.
-	 * It does so by calling {@code evaluateTestCase()} on
-	 * the population pane.
-	 * 
-	 * @param testCase the test case to evaluate.
-	 */
-	public void evaluateTestCase(TestCase<Object> testCase) {
-		populationPane.evaluateTestCase(testCase);
-	}
-
-	/**
-	 * Hide all evaluated values. This should be called when
-	 * evaluations are no longer being performed.
-	 */
-	public void hideGeneValues() {
-		populationPane.hideValues();
-	}
-
-	/**
-	 * Set the system into evaluation mode. 
-	 * When in evaluation mode, the population pane
-	 * refreshes the node values whenever connection
-	 * changes happen.
-	 * 
-	 * @param value true if evaluations are happening, false otherwise.
-	 */
-	public void setEvaluating(boolean value) {
-		populationPane.setEvaluating(value);
-	}
-
-	/**
-	 * @return a reference to the GUI stage.
-	 */
-	public Stage getStage() {
-		return stage;
-	}
-	
-	/**
-	 * Writes all buffered content out to the GUI console.
-	 */
-	public void flushConsole() {
-		console.flush();
-	}
-
-	/**
-	 * @return the index of the chromosome currently being looked at.
-	 */
-	public int getChromosomeIndex() {
-		return populationPane.getSelectionModel().getSelectedIndex();
-	}
-}
diff --git a/src/jcgp/gui/console/ConsolePane.java b/src/jcgp/gui/console/ConsolePane.java
deleted file mode 100644
index de193a5..0000000
--- a/src/jcgp/gui/console/ConsolePane.java
+++ /dev/null
@@ -1,122 +0,0 @@
-package jcgp.gui.console;
-
-import javafx.event.ActionEvent;
-import javafx.event.Event;
-import javafx.event.EventDispatchChain;
-import javafx.event.EventDispatcher;
-import javafx.event.EventHandler;
-import javafx.scene.control.ContextMenu;
-import javafx.scene.control.MenuItem;
-import javafx.scene.control.SeparatorMenuItem;
-import javafx.scene.control.TextArea;
-import javafx.scene.input.MouseButton;
-import javafx.scene.input.MouseEvent;
-import javafx.scene.layout.AnchorPane;
-import jcgp.backend.resources.Console;
-import jcgp.gui.constants.Constants;
-
-/**
- * Console pane used by the GUI to display CGP output messages.
- * This class realises {@code Console}. It consists of a JavaFX
- * {@code TextArea} and a {@code StringBuffer}. The buffer is filled
- * as print messages are queued. Calling {@code flush()} writes the
- * contents of the buffer to the {@code TextArea} and empties the buffer.
- * 
- * @see Console
- * @author Eduardo Pedroni
- *
- */
-public class ConsolePane extends AnchorPane implements Console {
-	
-	private TextArea textArea = new TextArea("Welcome to JCGP!\n");
-	private StringBuffer printBuffer = new StringBuffer();
-		
-	/**
-	 * Creates a new instance of this class.
-	 */
-	public ConsolePane() {
-		super();
-		textArea.setEditable(false);
-		/*
-		 * This nasty hack is needed because the default TextArea ContextMenu is not
-		 * in the public API, making it impossible to override it with a custom one.
-		 * This has not been fixed as of 8/4/2014.
-		 * 
-		 * The following code modifies the EventDispatcher to consume the right mouse
-		 * button click, preventing the default menu from appearing. It propagates the mouse
-		 * click further so other elements will respond appropriately.
-		 * 
-		 * TODO this should be refactored once the API is updated.
-		 */
-		final EventDispatcher initial = textArea.getEventDispatcher();
-		textArea.setEventDispatcher(new EventDispatcher() {
-			@Override
-			public Event dispatchEvent(Event event, EventDispatchChain tail) {
-				if (event instanceof MouseEvent) {
-					MouseEvent mouseEvent = (MouseEvent)event;
-					if (mouseEvent.getButton() == MouseButton.SECONDARY || 
-							(mouseEvent.getButton() == MouseButton.PRIMARY && mouseEvent.isControlDown())) {
-						event.consume();
-					}
-				}
-				return initial.dispatchEvent(event, tail);
-			}
-		});
-		
-		// make the new context menu including the clear option		
-		MenuItem copySelected = new MenuItem("Copy");
-		copySelected.setOnAction(new EventHandler<ActionEvent>() {	
-			@Override
-			public void handle(ActionEvent event) {
-				textArea.copy();
-			}
-		});
-		MenuItem selectAll = new MenuItem("Select all");
-		selectAll.setOnAction(new EventHandler<ActionEvent>() {	
-			@Override
-			public void handle(ActionEvent event) {
-				textArea.selectAll();
-			}
-		});
-		MenuItem clearConsole = new MenuItem("Clear");
-		clearConsole.setOnAction(new EventHandler<ActionEvent>() {	
-			@Override
-			public void handle(ActionEvent event) {
-				textArea.setText("");
-			}
-		});
-				
-		textArea.setContextMenu(new ContextMenu(copySelected,
-												selectAll, 
-												new SeparatorMenuItem(),
-												clearConsole));
-		
-		// anchor the text area so it resizes automatically
-		AnchorPane.setTopAnchor(textArea, Constants.RESIZE_MARGIN);
-		AnchorPane.setBottomAnchor(textArea, 0.0);
-		AnchorPane.setRightAnchor(textArea, 0.0);
-		AnchorPane.setLeftAnchor(textArea, 0.0);
-		
-		setMinHeight(Constants.CONSOLE_MIN_HEIGHT);
-		setPrefHeight(Constants.CONSOLE_MIN_HEIGHT);
-		
-		getChildren().add(textArea);
-	}
-
-	@Override
-	public void println(String s) {
-		printBuffer.append(s + "\n");
-	}
-
-	@Override
-	public void print(String s) {
-		printBuffer.append(s);
-	}
-
-	@Override
-	public void flush() {
-		textArea.appendText(printBuffer.toString());
-		printBuffer = new StringBuffer();
-	}
-	
-}
diff --git a/src/jcgp/gui/constants/Constants.java b/src/jcgp/gui/constants/Constants.java
deleted file mode 100644
index 509d982..0000000
--- a/src/jcgp/gui/constants/Constants.java
+++ /dev/null
@@ -1,170 +0,0 @@
-package jcgp.gui.constants;
-
-import javafx.scene.paint.Paint;
-
-/**
- * Holds the constants used in the GUI.
- * 
- * @author Eduardo Pedroni
- *
- */
-public final class Constants {
-
-	/**
-	 * Private constructor to prevent instantiation.
-	 */
-	private Constants(){}
-	
-	/*---------------------------------------------------------------------------------------------------
-	 * Colour Strings 
-	 *-------------------------------------------------------------------------------------------------*/
-	/**
-	 * A {@code String} containing the colour used for representing neutrality.
-	 */
-	public static final String NEUTRAL_COLOUR = "#FFFFFF";
-	/**
-	 * A {@code String} containing the hexadecimal colour used for representing a hard highlight.
-	 * A "hard" select, for instance, happens when an output path is locked on the chromosome pane.
-	 */
-	public static final String HARD_HIGHLIGHT_COLOUR = "#5496FF";
-	/**
-	 * A {@code String} containing the hexadecimal colour used for a medium highlight.
-	 * One example of such a selection is the colour applied to a node when it is hovered over.
-	 */
-	public static final String MEDIUM_HIGHLIGHT_COLOUR = "#75BAFF";
-	/**
-	 * A {@code String} containing the hexadecimal colour used for a soft highlight.
-	 * When hovering over a node, its connections are soft-selected.
-	 */
-	public static final String SOFT_HIGHLIGHT_COLOUR = "#C7DFFF";
-	/**
-	 * A {@code String} containing the hexadecimal colour used for representing a good selection.
-	 * Ideally a shade of green, used for instance when a manual connection is valid.
-	 */
-	public static final String GOOD_SELECTION_COLOUR = "#38C25B";
-	/**
-	 * A {@code String} containing the hexadecimal colour used for representing a neutral selection.
-	 * Ideally a shade of yellow, used for instance when a manual connection is already the current connection.
-	 */
-	public static final String NEUTRAL_SELECTION_COLOUR = "#FFEF73";
-	/**
-	 * A {@code String} containing the hexadecimal colour used for representing a bad selection.
-	 * Ideally a shade of red, use for instance when a manual connection is not valid.
-	 */
-	public static final String BAD_SELECTION_COLOUR = "#FF5C5C";
-	/**
-	 * A {@code String} containing the hexadecimal colour used for the gene sockets.
-	 */
-	public static final String SOCKET_COLOUR = "#FFFFFF";
-	
-	/*---------------------------------------------------------------------------------------------------
-	 * Colour Paints 
-	 *-------------------------------------------------------------------------------------------------*/
-	/**
-	 * A {@code Paint} containing the colour used for representing neutrality.
-	 */
-	public static final Paint NEUTRAL_PAINT = Paint.valueOf(NEUTRAL_COLOUR);
-	/**
-	 * A {@code Paint} containing the colour used for representing a hard highlight.
-	 * A "hard" select, for instance, happens when an output path is locked on the chromosome pane.
-	 */
-	public static final Paint HARD_HIGHLIGHT_PAINT = Paint.valueOf(HARD_HIGHLIGHT_COLOUR);
-	/**
-	 * A {@code Paint} containing the colour used for a medium highlight.
-	 * One example of such a selection is the colour applied to a node when it is hovered over.
-	 */
-	public static final Paint MEDIUM_HIGHLIGHT_PAINT = Paint.valueOf(MEDIUM_HIGHLIGHT_COLOUR);
-	/**
-	 * A {@code Paint} containing the colour used for a soft highlight.
-	 * When hovering over a node, its connections are soft-selected.
-	 */
-	public static final Paint SOFT_HIGHLIGHT_PAINT = Paint.valueOf(SOFT_HIGHLIGHT_COLOUR);
-	/**
-	 * A {@code Paint} containing the colour used for representing a good selection.
-	 * Ideally a shade of green, used for instance when a manual connection is valid.
-	 */
-	public static final Paint GOOD_SELECTION_PAINT = Paint.valueOf(GOOD_SELECTION_COLOUR);
-	/**
-	 * A {@code Paint} containing the colour used for representing a neutral selection.
-	 * Ideally a shade of yellow, used for instance when a manual connection is already the current connection.
-	 */
-	public static final Paint NEUTRAL_SELECTION_PAINT = Paint.valueOf(NEUTRAL_SELECTION_COLOUR);
-	/**
-	 * A {@code Paint} containing the colour used for representing a bad selection.
-	 * Ideally a shade of red, use for instance when a manual connection is not valid.
-	 */
-	public static final Paint BAD_SELECTION_PAINT = Paint.valueOf(BAD_SELECTION_COLOUR);
-	/**
-	 * A {@code Paint} containing the colour used for the gene sockets.
-	 */
-	public static final Paint SOCKET_PAINT = Paint.valueOf(SOCKET_COLOUR);
-	
-	/*---------------------------------------------------------------------------------------------------
-	 * Sizes and distances 
-	 *-------------------------------------------------------------------------------------------------*/
-	/**
-	 * The width or height of the area that can be clicked on
-	 * to drag-resize a pane.
-	 */
-    public static final double RESIZE_MARGIN = 5.0;
-    /**
-	 * The minimum width of the settings pane, to prevent it
-	 * from being resized beyond visibility.
-	 */
-    public static final double SETTINGS_MIN_WIDTH = 200;
-    /**
-	 * The minimum width of the console pane, to prevent it
-	 * from being resized beyond visibility.
-	 */
-    public static final double CONSOLE_MIN_HEIGHT = 100;
-    /**
-     * Radius used for the representation of nodes in the grid.
-     */
-    public static final double NODE_RADIUS = 35;
-	/**
-	 * Spacing between each node.
-	 */
-	public static final double SPACING = 15;
-	/**
-	 * The margin between the genes and the edge of the chromosome pane.
-	 */
-	public static final double CHROMOSOME_PANE_MARGIN = 10;
-	/**
-	 * The angle across which the node's sockets are evenly distributed.
-	 */
-	public static final double THETA = Math.PI / 1.4;
-	/**
-	 * The radius of the connection sockets, calculated as a function of NODE_RADIUS.
-	 */
-	public static final double SOCKET_RADIUS = Math.sqrt(NODE_RADIUS) / 1.8;
-	/**
-	 * Size of the text in each node.
-	 */
-	public static final double NODE_TEXT = NODE_RADIUS / 2.5;
-	
-	/*---------------------------------------------------------------------------------------------------
-	 * CSS Styles
-	 * TODO extract to stylesheet?
-	 *-------------------------------------------------------------------------------------------------*/
-	/**
-	 * The basic style of text boxes used in parameters.
-	 */
-	public static final String BASE_TEXT_STYLE = "-fx-border-color: #C9C9C9; -fx-border-radius: 2; -fx-padding: 0; ";
-	/**
-	 * The basic style of check boxes used in parameters.
-	 */
-	public static final String BASE_CHECKBOX_STYLE = "-fx-padding: 0; ";
-	/**
-	 * The style applied to invalid parameters, using BAD_SELECTION_COLOUR.
-	 */
-	public static final String INVALID_PARAMETER_STYLE = "-fx-background-color: " + BAD_SELECTION_COLOUR;
-	/**
-	 * The style applied to neutral parameters, using NEUTRAL_SELECTION_COLOUR.
-	 */
-	public static final String WARNING_PARAMETER_STYLE = "-fx-background-color: " + NEUTRAL_SELECTION_COLOUR;
-	/**
-	 * The style applied to valid parameters, using NEUTRAL_COLOUR.
-	 */
-	public static final String VALID_PARAMETER_STYLE = "-fx-background-color: " + NEUTRAL_COLOUR;	
-    
-}
diff --git a/src/jcgp/gui/constants/Position.java b/src/jcgp/gui/constants/Position.java
deleted file mode 100644
index 6d4e02b..0000000
--- a/src/jcgp/gui/constants/Position.java
+++ /dev/null
@@ -1,103 +0,0 @@
-package jcgp.gui.constants;
-
-import javafx.scene.shape.Circle;
-import javafx.scene.shape.Line;
-import jcgp.gui.GUI;
-import jcgp.gui.population.GUIGene;
-import jcgp.gui.population.GUIInput;
-import jcgp.gui.population.GUINode;
-import jcgp.gui.population.GUIOutput;
-
-/**
- * Abstracts the task of positioning GUI components.
- * <br>
- * Do not instantiate this class; instead, use the {@code public static} methods provided.
- * 
- * @author Eduardo Pedroni
- *
- */
-public final class Position {
-	
-	/**
-	 * Private constructor to prevent instantiation.
-	 */
-	private Position() {}
-	
-	/**
-	 * Sets the X and Y layouts of the specified input to the appropriate values, according to its index.
-	 * 
-	 * @param input the {@code GUIInput} instance to relocate.
-	 */
-	public static void place(GUIInput input) {
-		// inputs are the first column, so we only worry about the margin and their index
-		input.relocate(Constants.CHROMOSOME_PANE_MARGIN,
-				input.getInput().getIndex() * (2 * Constants.NODE_RADIUS + Constants.SPACING) + Constants.CHROMOSOME_PANE_MARGIN);
-	}
-	
-	/**
-	 * Sets the X and Y layouts of the specified node to the appropriate values, according to its row and column values.
-	 * This also connects the start of every line with its respective socket. Therefore, this method should be called at least
-	 * once when the {@code GUINode} is instantiated.
-	 * 
-	 * @param node the {@code GUINode} instance to relocate.
-	 */
-	public static void place(GUINode node) {
-		// calculate x and y offsets, in relation to the layout origin
-		double xOffset = (node.getNode().getColumn() + 1) * (2 * Constants.NODE_RADIUS + Constants.SPACING) + Constants.CHROMOSOME_PANE_MARGIN;
-		double yOffset = node.getNode().getRow() * (2 * Constants.NODE_RADIUS + Constants.SPACING) + Constants.CHROMOSOME_PANE_MARGIN;
-		
-		// move node
-		node.relocate(xOffset, yOffset);
-		
-		// use the offset and the socket positions to connect the lines
-		for (int i = 0; i < GUI.resources.arity(); i++) {
-			node.getLines()[i].setStartX(node.getSocket(i).getCenterX() + xOffset + Constants.NODE_RADIUS + Constants.SOCKET_RADIUS);
-			node.getLines()[i].setStartY(node.getSocket(i).getCenterY() + yOffset + Constants.NODE_RADIUS);
-		}
-	}
-	
-	/**
-	 * Sets the X and Y layouts of the specified output to the appropriate values, according to its index.
-	 * This also connects the start of the output's single line to its single input socket.Therefore,
-	 * this method should be called at least once when the {@code GUIOutput} is instantiated.
-	 * 
-	 * @param output the {@code GUIOutput} instance to relocate.
-	 */
-	public static void place(GUIOutput output) {
-		// the output's position is a function of the number of columns and its own index
-		output.relocate(((GUI.resources.columns() + 1) * (2 * Constants.NODE_RADIUS + Constants.SPACING)) + Constants.CHROMOSOME_PANE_MARGIN,
-				output.getOutput().getIndex() * (2 * Constants.NODE_RADIUS + Constants.SPACING) + Constants.CHROMOSOME_PANE_MARGIN);
-		output.getLines()[0].setStartX(output.getLayoutX() - Constants.NODE_RADIUS);
-		output.getLines()[0].setStartY(output.getLayoutY());
-	}
-	
-	/**
-	 * Connects the end of a specified line to the specified gene.
-	 * 
-	 * @param line the line to connect.
-	 * @param target the target gene to connect to.
-	 */
-	public static void connect(Line line, GUIGene target) {
-		// set line ends based on the layout position of the target
-		line.setEndX(target.getLayoutX() + Constants.NODE_RADIUS);
-		line.setEndY(target.getLayoutY());
-	}
-
-	/**
-	 * Relocates the given socket to the appropriate position given the 
-	 * socket's index.
-	 * 
-	 * @param index the socket index.
-	 * @param socket the {@code Circle} instance to relocate.
-	 */
-	public static void placeSocket(int index, Circle socket) {
-		// calculate the angle with respect to the x-axis
-		double angle = (((index + 1) / ((double) (GUI.resources.arity() + 1))) * Constants.THETA) - (Constants.THETA / 2);
-		// convert to cartesian form
-		double xPos = -Math.cos(angle) * Constants.NODE_RADIUS;
-		double yPos = Math.sin(angle) * Constants.NODE_RADIUS;
-		// set centre
-		socket.setCenterX(xPos);
-		socket.setCenterY(yPos);
-	}
-}
diff --git a/src/jcgp/gui/dragresize/HorizontalDragResize.java b/src/jcgp/gui/dragresize/HorizontalDragResize.java
deleted file mode 100644
index e88eafd..0000000
--- a/src/jcgp/gui/dragresize/HorizontalDragResize.java
+++ /dev/null
@@ -1,131 +0,0 @@
-package jcgp.gui.dragresize;
-
-import javafx.event.EventHandler;
-import javafx.scene.Cursor;
-import javafx.scene.input.MouseEvent;
-import javafx.scene.layout.Region;
-import jcgp.gui.constants.Constants;
-
-/**
- * This class adds horizontal drag resize functionality to any 
- * arbitrary region provided. This is done by using the static
- * method {@code makeDragResizable()}.
- * <br><br>
- * This is based on a class by Andrew Till found on:
- * http://andrewtill.blogspot.co.uk/2012/12/dragging-to-resize-javafx-region.html
- * 
- */
-public class HorizontalDragResize {
-	
-	private boolean dragging = false;
-	private final Region region;
-	
-	/**
-	 * For internal use only, creates an instance of the actual
-	 * resizer used.
-	 * 
-	 * @param region the region to make resizable.
-	 */
-	private HorizontalDragResize(Region region) {
-		this.region = region;
-	}
-	
-	/**
-	 * Makes the specified region drag resizable.
-	 * This particular implementation only creates a resize 
-	 * click-and-drag area on the left side of the region. 
-	 * The resize area is defined by {@code GUI.RESIZE_MARGIN}.
-	 * 
-	 * @param region the region to make resizable.
-	 */
-	public static void makeDragResizable(final Region region) {
-		// make the instance, this actually performs the resizing
-		final HorizontalDragResize dr = new HorizontalDragResize(region);
-
-		// set mouse listeners
-		region.setOnMousePressed(new EventHandler<MouseEvent>() {
-			@Override
-			public void handle(MouseEvent event) {
-		        dr.mousePressed(event);
-			}
-		});
-		region.setOnMouseDragged(new EventHandler<MouseEvent>() {
-			@Override
-			public void handle(MouseEvent event) {
-				dr.mouseDragged(event);
-			}
-		});
-		region.setOnMouseMoved(new EventHandler<MouseEvent>() {
-			@Override
-			public void handle(MouseEvent event) {
-				dr.mouseMoved(event);
-			}
-		});
-		region.setOnMouseReleased(new EventHandler<MouseEvent>() {
-			@Override
-			public void handle(MouseEvent event) {
-				dr.mouseReleased();
-			}
-		});
-		
-	}
-	
-	/**
-	 * If the press happened in the resize area, raise the drag flag.
-	 * 
-	 * @param event the associated mouse event.
-	 */
-	private void mousePressed(MouseEvent event) {
-		if(isInDraggableZone(event)) {
-	        dragging = true;
-        }
-	}
-
-	/**
-	 * If drag flag is high, resize the region to match the mouse position.
-	 * 
-	 * @param event the associated mouse event.
-	 */
-	private void mouseDragged(MouseEvent event) {
-		if(dragging) {
-			double newWidth = region.getWidth() - event.getX();
-			if (newWidth >= region.getMinWidth()) {
-				region.setPrefWidth(newWidth);
-			} else {
-				region.setPrefWidth(region.getMinWidth());
-			}
-		}
-	}
-	
-	/**
-	 * Change the cursor if the mouse position overlaps with the resize area.
-	 * 
-	 * @param event the associated mouse event.
-	 */
-	private void mouseMoved(MouseEvent event) {
-		if(isInDraggableZone(event) || dragging) {
-			region.setCursor(Cursor.H_RESIZE);
-		} else {
-			region.setCursor(Cursor.DEFAULT);
-		}
-	}
-
-	/**
-	 * Finish resizing.
-	 */
-	private void mouseReleased() {
-		dragging = false;
-		region.setCursor(Cursor.DEFAULT);
-	}
-
-	/**
-	 * Assert whether the mouse cursor is in the draggable area defined by {@code GUI.RESIZE_MARGIN}.
-	 * 
-	 * @param event the associated mouse event.
-	 * @return true if the mouse position is in the draggable area.
-	 */
-	private boolean isInDraggableZone(MouseEvent event) {
-		return event.getX() < (Constants.RESIZE_MARGIN);
-	}
-
-}
diff --git a/src/jcgp/gui/dragresize/VerticalDragResize.java b/src/jcgp/gui/dragresize/VerticalDragResize.java
deleted file mode 100644
index 4f784e5..0000000
--- a/src/jcgp/gui/dragresize/VerticalDragResize.java
+++ /dev/null
@@ -1,132 +0,0 @@
-package jcgp.gui.dragresize;
-
-import javafx.event.EventHandler;
-import javafx.scene.Cursor;
-import javafx.scene.input.MouseEvent;
-import javafx.scene.layout.Region;
-import jcgp.gui.constants.Constants;
-
-/**
- * This class adds vertical drag resize functionality to any 
- * arbitrary region provided. This is done by using the static
- * method {@code makeDragResizable()}.
- * <br><br>
- * This is based on a class by Andrew Till found on:
- * http://andrewtill.blogspot.co.uk/2012/12/dragging-to-resize-javafx-region.html
- * 
- */
-public class VerticalDragResize {
-	
-	private boolean dragging = false;
-	private final Region region;
-	
-	/**
-	 * For internal use only, creates an instance of the actual
-	 * resizer used.
-	 * 
-	 * @param region the region to make resizable.
-	 */
-	private VerticalDragResize(Region region) {
-		this.region = region;
-	}
-	
-	/**
-	 * Makes the specified region drag resizable.
-	 * This particular implementation only creates a resize 
-	 * click-and-drag area on the top side of the region. 
-	 * The resize area is defined by {@code GUI.RESIZE_MARGIN}.
-	 * 
-	 * @param region the region to make resizable.
-	 */
-	public static void makeDragResizable(final Region region) {
-		// make the instance, this actually performs the resizing
-		final VerticalDragResize dr = new VerticalDragResize(region);
-
-		// set mouse listeners
-		region.setOnMousePressed(new EventHandler<MouseEvent>() {
-			@Override
-			public void handle(MouseEvent event) {
-		        dr.mousePressed(event);
-			}
-		});
-		region.setOnMouseDragged(new EventHandler<MouseEvent>() {
-			@Override
-			public void handle(MouseEvent event) {
-				dr.mouseDragged(event);
-			}
-		});
-		region.setOnMouseMoved(new EventHandler<MouseEvent>() {
-			@Override
-			public void handle(MouseEvent event) {
-				dr.mouseMoved(event);
-			}
-		});
-		region.setOnMouseReleased(new EventHandler<MouseEvent>() {
-			@Override
-			public void handle(MouseEvent event) {
-				dr.mouseReleased();
-			}
-		});
-		
-	}
-	
-	/**
-	 * If the press happened in the resize area, raise the drag flag.
-	 * 
-	 * @param event the associated mouse event.
-	 */
-	private void mousePressed(MouseEvent event) {
-		if(isInDraggableZone(event)) {
-	        dragging = true;
-        }
-	}
-
-	/**
-	 * If drag flag is high, resize the region to match the mouse position.
-	 * 
-	 * @param event the associated mouse event.
-	 */
-	private void mouseDragged(MouseEvent event) {
-		if(dragging) {
-			double newHeight = region.getHeight() - event.getY();
-			if (newHeight >= region.getMinHeight()) {
-				region.setPrefHeight(newHeight);
-			} else {
-				region.setPrefHeight(region.getMinHeight());
-			}
-		}
-	}
-	
-	/**
-	 * Change the cursor if the mouse position overlaps with the resize area.
-	 * 
-	 * @param event the associated mouse event.
-	 */
-	private void mouseMoved(MouseEvent event) {
-		if(isInDraggableZone(event) || dragging) {
-			region.setCursor(Cursor.V_RESIZE);
-        }
-        else {
-        	region.setCursor(Cursor.DEFAULT);
-        }
-	}
-
-	/**
-	 * Finish resizing.
-	 */
-	private void mouseReleased() {
-		dragging = false;
-		region.setCursor(Cursor.DEFAULT);
-	}
-
-	/**
-	 * Assert whether the mouse cursor is in the draggable area defined by {@code GUI.RESIZE_MARGIN}.
-	 * 
-	 * @param event the associated mouse event.
-	 * @return true if the mouse position is in the draggable area.
-	 */
-	private boolean isInDraggableZone(MouseEvent event) {
-		return event.getY() < (Constants.RESIZE_MARGIN);
-	}
-
-}
diff --git a/src/jcgp/gui/handlers/InputHandlers.java b/src/jcgp/gui/handlers/InputHandlers.java
deleted file mode 100644
index cc677eb..0000000
--- a/src/jcgp/gui/handlers/InputHandlers.java
+++ /dev/null
@@ -1,56 +0,0 @@
-package jcgp.gui.handlers;
-
-import javafx.event.EventHandler;
-import javafx.scene.input.MouseEvent;
-import jcgp.gui.population.GUIGene.GUIGeneState;
-import jcgp.gui.population.GUIInput;
-
-/**
- * Holds the handlers that define the behaviour of {@code GUIInput}.
- * <br><br>
- * The handlers are instantiated here statically and added to {@code GUIInput}
- * instances using {@code InputHandlers.addHandlers(...)}. This guarantees that
- * all inputs behave the same way without instantiating a new set of handlers for
- * each input instance.
- * 
- * @author Eduardo Pedroni
- *
- */
-public final class InputHandlers {
-	
-	/**
-	 * Private constructor to prevent instantiation.
-	 */
-	private InputHandlers() {}
-
-	/**
-	 * Inputs don't do much; set state to hover when mouse enters.
-	 */
-	private static EventHandler<MouseEvent> mouseEnteredHandler = new EventHandler<MouseEvent>() {
-		@Override
-		public void handle(MouseEvent event) {
-			((GUIInput) event.getSource()).setState(GUIGeneState.HOVER);
-		}
-	};
-	
-	/**
-	 * Inputs don't do much; set state to neutral when mouse exits.
-	 */
-	private static EventHandler<MouseEvent> mouseExitedHandler = new EventHandler<MouseEvent>() {
-		@Override
-		public void handle(MouseEvent event) {
-			((GUIInput) event.getSource()).setState(GUIGeneState.NEUTRAL);
-		}
-	};
-	
-	/**
-	 * Adds all handlers to the specified input.
-	 * 
-	 * @param input the {@code GUIInput} to which the handlers will be added.
-	 */
-	public static void addHandlers(GUIInput input) {
-		input.addEventHandler(MouseEvent.MOUSE_ENTERED, mouseEnteredHandler);
-		input.addEventHandler(MouseEvent.MOUSE_EXITED, mouseExitedHandler);
-	}
-	
-}
diff --git a/src/jcgp/gui/handlers/NodeHandlers.java b/src/jcgp/gui/handlers/NodeHandlers.java
deleted file mode 100644
index b413a62..0000000
--- a/src/jcgp/gui/handlers/NodeHandlers.java
+++ /dev/null
@@ -1,164 +0,0 @@
-package jcgp.gui.handlers;
-
-import javafx.event.EventHandler;
-import javafx.scene.input.MouseDragEvent;
-import javafx.scene.input.MouseEvent;
-import javafx.scene.shape.Circle;
-import javafx.scene.shape.Line;
-import jcgp.backend.population.Gene;
-import jcgp.gui.GUI;
-import jcgp.gui.constants.Position;
-import jcgp.gui.population.ChromosomePane;
-import jcgp.gui.population.GUIConnection;
-import jcgp.gui.population.GUIGene;
-import jcgp.gui.population.GUIGene.GUIGeneState;
-import jcgp.gui.population.GUINode;
-
-/**
- * Holds the handlers that define the behaviour of {@code GUINode}.
- * <br><br>
- * The handlers are instantiated here statically and added to {@code GUINode}
- * instances using {@code NodeHandlers.addHandlers(...)}. This guarantees that
- * all nodes behave the same way without instantiating a new set of handlers for
- * each node instance.
- * 
- * @author Eduardo Pedroni
- *
- */
-public final class NodeHandlers {
-
-	/**
-	 * Private constructor to prevent instantiation.
-	 */
-	private NodeHandlers() {}
-
-	/**
-	 * Set the node to {@code GUIGeneState.HOVER} state, and set its immediate connections to {@code GUIGeneState.EXTENDED_HOVER}.
-	 */
-	private static EventHandler<MouseEvent> mouseEnteredHandler = new EventHandler<MouseEvent>() {
-		@Override
-		public void handle(MouseEvent event) {
-			// acquire the source, we can safely cast it to GUINode
-			GUINode source = (GUINode) event.getSource();
-
-			source.setState(GUIGeneState.HOVER);
-			for (int i = 0; i < GUI.resources.arity(); i++) {
-				((GUIGene) ((Gene) source.getNode().getConnection(i)).getGUIObject()).setState(GUIGeneState.EXTENDED_HOVER);
-			}
-		}
-	};
-
-	/**
-	 * Set the node and its immediate connections to {@code GUIGeneState.NEUTRAL} state.
-	 */
-	private static EventHandler<MouseEvent> mouseExitedHandler = new EventHandler<MouseEvent>() {
-		@Override
-		public void handle(MouseEvent event) {
-			// acquire the source, we can safely cast it to GUINode
-			GUINode source = (GUINode) event.getSource();
-
-			if (Target.getSourceMutable() != source) {
-				source.setState(GUIGeneState.NEUTRAL);
-				for (int i = 0; i < GUI.resources.arity(); i++) {
-					((GUIGene) ((Gene) source.getNode().getConnection(i)).getGUIObject()).setState(GUIGeneState.NEUTRAL);
-				}
-			}
-		}
-	};
-
-	private static EventHandler<MouseEvent> socketDragDetected = new EventHandler<MouseEvent>() {
-		@Override
-		public void handle(MouseEvent event) {
-			// it's safe to assume that the source is the socket
-			((GUINode) ((Circle) event.getSource()).getParent()).startFullDrag();
-		}
-	};
-
-	private static EventHandler<MouseEvent> socketMousePressedHandler = new EventHandler<MouseEvent>() {
-		@Override
-		public void handle(MouseEvent event) {
-			// it's safe to assume that the source is the socket
-			Target.start((Circle) event.getSource());
-		}
-	};
-
-	private static EventHandler<MouseEvent> socketMouseDraggedHandler = new EventHandler<MouseEvent>() {
-		@Override
-		public void handle(MouseEvent event) {
-			// this can only happen after a press, so we know Target is up-to-date
-			if (!Target.isProspecting()) {
-				GUINode node = (GUINode) Target.getSourceMutable();
-				Line line = Target.getConnectionLine();
-				line.setEndX(event.getX() + node.getLayoutX());
-				line.setEndY(event.getY() + node.getLayoutY());
-			}
-
-		}
-	};
-
-	private static EventHandler<MouseEvent> socketMouseReleasedHandler = new EventHandler<MouseEvent>() {
-		@Override
-		public void handle(MouseEvent event) {
-
-			GUINode node = (GUINode) ((Circle) event.getSource()).getParent();
-			int connectionId = Integer.valueOf(((Circle) event.getSource()).getId());
-
-			Position.connect(node.getLines()[connectionId], (GUIGene) ((Gene) node.getNode().getConnection(connectionId)).getGUIObject());
-		}
-	};
-
-	private static EventHandler<MouseDragEvent> dragEnteredHandler = new EventHandler<MouseDragEvent>() {
-		@Override
-		public void handle(MouseDragEvent event) {
-			// acquire the source, we can safely cast it to GUINode
-			GUINode source = (GUINode) event.getSource();
-			if (Target.getCurrentConnection() == source) {
-				source.setState(GUIGeneState.NEUTRAL_TARGET);
-				// we are now prospecting
-				Target.setProspecting(true);
-				Position.connect(Target.getConnectionLine(), source);
-			} else if (ChromosomePane.isAllowed(Target.getSourceMutable(), (GUIConnection) source)) {
-				source.setState(GUIGeneState.GOOD_TARGET);
-				// we are now prospecting
-				Target.setProspecting(true);
-				Position.connect(Target.getConnectionLine(), source);
-			} else {
-				source.setState(GUIGeneState.BAD_TARGET);
-			}
-		}
-	};
-
-	private static EventHandler<MouseDragEvent> dragExitedHandler = new EventHandler<MouseDragEvent>() {
-		@Override
-		public void handle(MouseDragEvent event) {
-			// acquire the source, we can safely cast it to GUINode
-			GUINode source = (GUINode) event.getSource();
-			source.setState(GUIGeneState.NEUTRAL);
-			
-			// no longer prospecting
-			Target.setProspecting(false);
-		}
-	};
-
-	/**
-	 * Adds all handlers to the specified node.
-	 * 
-	 * @param node the {@code GUINode} to which the handlers will be added.
-	 */
-	public static void addHandlers(GUINode node) {
-		node.addEventHandler(MouseEvent.MOUSE_ENTERED, mouseEnteredHandler);
-		node.addEventHandler(MouseEvent.MOUSE_EXITED, mouseExitedHandler);
-
-		node.addEventHandler(MouseDragEvent.MOUSE_DRAG_ENTERED, dragEnteredHandler);
-		node.addEventHandler(MouseDragEvent.MOUSE_DRAG_EXITED, dragExitedHandler);
-
-		Circle[] sockets = node.getSockets();
-		for (int s = 0; s < sockets.length; s++) {
-
-			sockets[s].addEventFilter(MouseEvent.DRAG_DETECTED, socketDragDetected);
-			sockets[s].addEventHandler(MouseEvent.MOUSE_PRESSED, socketMousePressedHandler);
-			sockets[s].addEventHandler(MouseEvent.MOUSE_DRAGGED, socketMouseDraggedHandler);
-			sockets[s].addEventHandler(MouseEvent.MOUSE_RELEASED, socketMouseReleasedHandler);
-		}
-	}
-}
diff --git a/src/jcgp/gui/handlers/OutputHandlers.java b/src/jcgp/gui/handlers/OutputHandlers.java
deleted file mode 100644
index b89d746..0000000
--- a/src/jcgp/gui/handlers/OutputHandlers.java
+++ /dev/null
@@ -1,84 +0,0 @@
-package jcgp.gui.handlers;
-
-import javafx.event.EventHandler;
-import javafx.scene.input.MouseEvent;
-import jcgp.backend.population.Gene;
-import jcgp.gui.population.GUIConnection;
-import jcgp.gui.population.GUIGene.GUIGeneState;
-import jcgp.gui.population.GUIOutput;
-
-/**
- * Holds the handlers that define the behaviour of {@code GUIOutput}.
- * <br><br>
- * The handlers are instantiated here statically and added to {@code GUIOutput}
- * instances using {@code OutputHandlers.addHandlers(...)}. This guarantees that
- * all outputs behave the same way without instantiating a new set of handlers for
- * each output instance.
- * 
- * @author Eduardo Pedroni
- *
- */
-public final class OutputHandlers {
-	
-	/**
-	 * Private constructor to prevent instantiation.
-	 */
-	private OutputHandlers() {}
-
-	/**
-	 * Set the output to {@code GUIGeneState.HOVER} state, and recursively set its active genes
-	 * to {@code GUIGeneState.ACTIVE_HOVER}.
-	 */
-	private static EventHandler<MouseEvent> mouseEnteredHandler = new EventHandler<MouseEvent>() {
-		@Override
-		public void handle(MouseEvent event) {
-			// acquire the source, we can safely cast it to GUIOutput
-			GUIOutput source = (GUIOutput) event.getSource();
-
-			source.setState(GUIGeneState.HOVER);
-			((GUIConnection) ((Gene) source.getOutput().getSource()).getGUIObject()).setStateRecursively(GUIGeneState.ACTIVE_HOVER);
-		}
-	};
-
-	/**
-	 * Set the output and all of its active genes to {@code GUIGeneState.NEUTRAL} state.
-	 */
-	private static EventHandler<MouseEvent> mouseExitedHandler = new EventHandler<MouseEvent>() {
-		@Override
-		public void handle(MouseEvent event) {
-			// acquire the source, we can safely cast it to GUIOutput
-			GUIOutput source = (GUIOutput) event.getSource();
-			
-			source.setState(GUIGeneState.NEUTRAL);
-			((GUIConnection) ((Gene) source.getOutput().getSource()).getGUIObject()).setStateRecursively(GUIGeneState.NEUTRAL);
-		}
-	};
-
-	/**
-	 * If the output is locked, unlock it and all of its associated genes recursively.
-	 * If it is unlocked, lock it and its active genes.
-	 */
-	private static EventHandler<MouseEvent> mouseClickHandler = new EventHandler<MouseEvent>() {
-		@Override
-		public void handle(MouseEvent event) {
-			// acquire the source, we can safely cast it to GUIOutput
-			GUIOutput source = (GUIOutput) event.getSource();
-
-			boolean lock = !source.isLocked();
-			source.setLock(lock);
-			((GUIConnection) ((Gene) source.getOutput().getSource()).getGUIObject()).setLockRecursively(lock);
-		}
-	};
-
-	/**
-	 * Adds all handlers to the specified output.
-	 * 
-	 * @param output the {@code GUIOutput} to which the handlers will be added.
-	 */
-	public static void addHandlers(GUIOutput output) {
-		output.addEventHandler(MouseEvent.MOUSE_ENTERED, mouseEnteredHandler);
-		output.addEventHandler(MouseEvent.MOUSE_EXITED, mouseExitedHandler);
-		output.addEventHandler(MouseEvent.MOUSE_CLICKED, mouseClickHandler);
-	}
-
-}
diff --git a/src/jcgp/gui/handlers/Target.java b/src/jcgp/gui/handlers/Target.java
deleted file mode 100644
index b050663..0000000
--- a/src/jcgp/gui/handlers/Target.java
+++ /dev/null
@@ -1,70 +0,0 @@
-package jcgp.gui.handlers;
-
-import javafx.scene.shape.Circle;
-import javafx.scene.shape.Line;
-import jcgp.gui.population.GUIConnection;
-import jcgp.gui.population.GUIMutable;
-
-/**
- * @author Eduardo Pedroni
- *
- */
-public final class Target {
-
-	/**
-	 * Private constructor to prevent instantiation.
-	 */
-	private Target() {}
-	
-	private static GUIConnection targetConnection;
-	private static GUIMutable sourceMutable;
-	private static int connectionIndex;
-	private static Line connectionLine;
-	private static Circle sourceSocket;
-	private static boolean prospecting = false;
-	
-	public static void start(Circle newSocket) {
-		// store new socket
-		sourceSocket = newSocket;
-		// derive the rest of the information from it
-		connectionIndex = Integer.valueOf(newSocket.getId());
-		sourceMutable = (GUIMutable) newSocket.getParent();
-		connectionLine = sourceMutable.getLines()[connectionIndex];
-	}
-	
-	public static GUIMutable getSourceMutable() {
-		return sourceMutable;
-	}
-	
-	public static int getConnectionIndex() {
-		return connectionIndex;
-	}
-	
-	public static Line getConnectionLine() {
-		return connectionLine;
-	}
-	
-	public static Circle getSourceSocket() {
-		return sourceSocket;
-	}
-	
-	public static GUIConnection getTarget() {
-		return targetConnection;
-	}
-	
-	public static GUIConnection getCurrentConnection() {
-		return sourceMutable.getConnections()[connectionIndex];
-	}
-	
-	public static void setProspecting(boolean value) {
-		prospecting = value;
-	}
-	
-	public static boolean isProspecting() {
-		return prospecting;
-	}
-	
-	public static void setTarget(GUIConnection newTarget) {
-		targetConnection = newTarget;
-	}
-}
diff --git a/src/jcgp/gui/population/ChromosomePane.java b/src/jcgp/gui/population/ChromosomePane.java
deleted file mode 100644
index a87a054..0000000
--- a/src/jcgp/gui/population/ChromosomePane.java
+++ /dev/null
@@ -1,140 +0,0 @@
-package jcgp.gui.population;
-
-import java.util.ArrayList;
-
-import javafx.scene.control.ScrollPane;
-import javafx.scene.layout.Pane;
-import javafx.scene.shape.Line;
-import jcgp.backend.population.Chromosome;
-import jcgp.backend.population.Node;
-import jcgp.gui.GUI;
-
-/**
- * This extension of {@code ScrollPane} contains a series of
- * nodes, inputs and outputs spread across a grid. It also contains
- * all of the connection lines laid over the nodes, inputs and outputs.
- * 
- * 
- * @author Eduardo Pedroni
- *
- */
-public class ChromosomePane extends ScrollPane {
-
-	private GUIInput[] guiInputs;
-	private GUINode[][] guiNodes;
-	private GUIOutput[] guiOutputs;
-
-	private Pane content;
-
-	private boolean target = false;
-
-	public ChromosomePane(Chromosome chromosome) {
-		super();
-
-		ArrayList<Line> connectionLines = new ArrayList<Line>();
-
-		int rows = GUI.resources.rows();
-		int columns = GUI.resources.columns();
-
-		content = new Pane();
-		content.setId("content pane for genes");
-
-		/* 
-		 * inputs
-		 */
-		guiInputs = new GUIInput[GUI.resources.inputs()];
-		for (int i = 0; i < guiInputs.length; i++) {
-			guiInputs[i] = new GUIInput(chromosome.getInput(i));
-		}
-		// add inputs to content pane
-		content.getChildren().addAll(guiInputs);
-
-		/*
-		 * nodes
-		 */
-		guiNodes = new GUINode[rows][columns];
-		for (int c = 0; c < columns; c++) {
-			for (int r = 0; r < rows; r++) {
-				// make the connection lines
-				Line lines[] = new Line[GUI.resources.arity()];
-				for (int l = 0; l < lines.length; l++) {
-					lines[l] = new Line();
-					lines[l].setMouseTransparent(true);
-					lines[l].setVisible(false);
-					connectionLines.add(lines[l]);
-				}
-				// make the GUI element
-				guiNodes[r][c] = new GUINode(chromosome.getNode(r, c), lines);
-				// add node to content pane
-				content.getChildren().add(guiNodes[r][c]);
-			}
-		}
-
-		/* 
-		 * outputs
-		 */
-		guiOutputs = new GUIOutput[GUI.resources.outputs()];
-		for (int i = 0; i < guiOutputs.length; i++) {
-			// make the connection line
-			Line line = new Line();
-			line.setVisible(false);
-			line.setMouseTransparent(true);
-			connectionLines.add(line);
-			// make the GUI element
-			guiOutputs[i] = new GUIOutput(chromosome.getOutput(i), line);
-		}
-		// add outputs to content pane
-		content.getChildren().addAll(guiOutputs);
-
-		// add lines to the pane on top of genes
-		content.getChildren().addAll(connectionLines);
-
-		setPrefWidth(620);
-		setContent(content);
-	}
-
-	protected boolean isTarget() {
-		return target;
-	}
-
-	protected void setTarget(boolean newValue) {
-		target = newValue;
-	}
-
-	public void updateGenes(Chromosome chr) {
-		for (int r = 0; r < GUI.resources.rows(); r++) {
-			for (int c = 0; c < GUI.resources.columns(); c++) {
-				guiNodes[r][c].setNode(chr.getNode(r, c));
-			}
-		}
-		for (int i = 0; i < guiOutputs.length; i++) {
-			guiOutputs[i].setOutput(chr.getOutput(i));
-		}
-	}
-
-	public static boolean isAllowed(GUIMutable source, GUIConnection target) {
-		if (source instanceof GUINode) {
-			// if the source is a node, all inputs and some nodes are valid
-			if (target instanceof GUIInput) {
-				return true;
-			} else if (target instanceof GUINode) {
-				// target and source are nodes, let's look at levels back
-				Node t = ((GUINode) target).getNode(), s = ((GUINode) source).getNode();
-				if (s.getColumn() - t.getColumn() > 0 && s.getColumn() - t.getColumn() <= GUI.resources.levelsBack()) {
-					return true;
-				}
-			}
-			return false;
-		} else if (source instanceof GUIOutput) {
-			// if the source is an output, any node or input is valid
-			if (target instanceof GUINode || target instanceof GUIInput) {
-				return true;
-			} else {
-				// this should never happen...
-				return false;
-			}
-		}
-		// if the source was neither node nor output, something bad is happening
-		throw new ClassCastException("Source was neither GUINode nor GUIOutput.");
-	}
-}
diff --git a/src/jcgp/gui/population/FunctionSelector.java b/src/jcgp/gui/population/FunctionSelector.java
deleted file mode 100644
index 14614e5..0000000
--- a/src/jcgp/gui/population/FunctionSelector.java
+++ /dev/null
@@ -1,80 +0,0 @@
-package jcgp.gui.population;
-
-import javafx.event.EventHandler;
-import javafx.scene.control.Label;
-import javafx.scene.input.MouseEvent;
-import javafx.scene.layout.VBox;
-import jcgp.backend.function.FunctionSet;
-import jcgp.gui.constants.Constants;
-
-/**
- * A menu class, exposes all of the allowed functions
- * when called by a node, so that the node function can be changed.
- * 
- * 
- * @author Eduardo Pedroni
- *
- */
-public class FunctionSelector extends VBox {
-	
-	private GUINode target;
-		
-	public FunctionSelector(FunctionSet functionSet) {
-		setFillWidth(true);
-		setVisible(false);
-		setStyle("-fx-border-color: #A0A0A0; -fx-border-width: 1 1 0 1");
-		
-		remakeFunctions(functionSet);
-		
-		addEventFilter(MouseEvent.MOUSE_EXITED, new EventHandler<MouseEvent>() {
-			@Override
-			public void handle(MouseEvent event) {
-				dismiss();
-			}
-		});
-	}
-	
-	public void remakeFunctions(final FunctionSet fs) {
-		getChildren().clear();
-		
-		for (int i = 0; i < fs.getAllowedFunctionCount(); i++) {
-			final int index = i;
-			Label l = new Label(fs.getAllowedFunction(i).toString());
-			l.setMaxWidth(Double.MAX_VALUE);
-			l.setStyle("-fx-background-color: #FFFFFF; -fx-border-color: #A0A0A0; -fx-border-width: 0 0 1 0; -fx-padding: 2");
-			
-			l.addEventFilter(MouseEvent.MOUSE_ENTERED, new EventHandler<MouseEvent>() {
-				@Override
-				public void handle(MouseEvent event) {
-					((Label) event.getSource()).setStyle("-fx-background-color: " + Constants.SOFT_HIGHLIGHT_PAINT + "; -fx-border-color: #B0B0B0; -fx-border-width: 0 0 1 0; -fx-padding: 2");
-				}
-			});
-			l.addEventFilter(MouseEvent.MOUSE_EXITED, new EventHandler<MouseEvent>() {
-				@Override
-				public void handle(MouseEvent event) {
-					((Label) event.getSource()).setStyle("-fx-background-color: #FFFFFF; -fx-border-color: #A0A0A0; -fx-border-width: 0 0 1 0; -fx-padding: 2");
-				}
-			});
-			l.addEventFilter(MouseEvent.MOUSE_CLICKED, new EventHandler<MouseEvent>() {
-				@Override
-				public void handle(MouseEvent event) {
-					//target.setFunction(fs.getAllowedFunction(index));
-					dismiss();
-				}
-			});
-			
-			getChildren().add(l);
-		}
-	}
-	
-	public void relocateAndShow(MouseEvent event, GUINode node) {
-		relocate(event.getSceneX() - 5, event.getSceneY() - 5);
-		target = node;
-		setVisible(true);
-	}
-	
-	private void dismiss() {
-		setVisible(false);
-	}
-	
-}
diff --git a/src/jcgp/gui/population/GUIConnection.java b/src/jcgp/gui/population/GUIConnection.java
deleted file mode 100644
index dc7fcc8..0000000
--- a/src/jcgp/gui/population/GUIConnection.java
+++ /dev/null
@@ -1,32 +0,0 @@
-package jcgp.gui.population;
-
-import jcgp.gui.population.GUIGene.GUIGeneState;
-
-/**
- * A loose equivalent to {@link jcgp.backend.population.Connection}.
- * <br>
- * This defines behaviour that all GUI representations of connections
- * should be capable of.
- * 
- * @author Eduardo Pedroni
- *
- */
-public interface GUIConnection {
-
-	/**
-	 * Set the connection's state, but also recursively propagate that state
-	 * all the way back to the inputs.
-	 * 
-	 * @param state the state to set.
-	 */
-	public void setStateRecursively(GUIGeneState state);
-	
-	/**
-	 * Add or remove a lock, but also recursively propagate that change
-	 * all the way back to the inputs.
-	 * 
-	 * @param value true to lock, false to unlock.
-	 */
-	public void setLockRecursively(boolean value);
-	
-}
diff --git a/src/jcgp/gui/population/GUIGene.java b/src/jcgp/gui/population/GUIGene.java
deleted file mode 100644
index 5e6107f..0000000
--- a/src/jcgp/gui/population/GUIGene.java
+++ /dev/null
@@ -1,187 +0,0 @@
-package jcgp.gui.population;
-
-import javafx.geometry.VPos;
-import javafx.scene.Group;
-import javafx.scene.paint.Paint;
-import javafx.scene.shape.Circle;
-import javafx.scene.text.Font;
-import javafx.scene.text.Text;
-import javafx.scene.text.TextAlignment;
-import jcgp.gui.constants.Constants;
-
-/**
- * Defines the general behaviour of the visual representation of each chromosome gene.
- * <br><br>
- * In practice, this is subclass of {@code javafx.scene.Group} containing a {@code Circle}
- * object and a {@code Text} object. Subclasses may add further elements to the group, for
- * instance to display connection input and output sockets.
- * <br><br>
- * Genes also contain a locked property. When locked, some gene states behave slightly
- * differently. This is used so genes remain highlighted even in the neutral state. The
- * gene lock is in fact recursive; a gene can be locked multiple times and only unlocking
- * it as many times will actually revert it back to its unlocked state. This allows multiple
- * pathways to lock the same gene independently without affecting each other; the gene remains
- * locked until no pathways are locking it.
- * 
- * @author Eduardo Pedroni
- *
- */
-public abstract class GUIGene extends Group {
-
-	/**
-	 * This {@code enum} type defines a finite list of all states
-	 * a gene can take. Each state represents a particular steady
-	 * situation, and has its own GUI appearance associated with it:
-	 * a combination of connection line visibility, gene background colour
-	 * and other visual characteristics.
-	 * 
-	 * @author Eduardo Pedroni
-	 *
-	 */
-	public enum GUIGeneState {
-		/**
-		 * No user interaction at all.
-		 */
-		NEUTRAL,
-		/**
-		 * User is simply hovering over the node.
-		 */
-		HOVER,
-		/**
-		 * User is hovering over a node connected to this one.
-		 */
-		EXTENDED_HOVER,
-		/**
-		 * User is hovering over an output connected to this gene.
-		 */
-		ACTIVE_HOVER,
-		
-		GOOD_TARGET,
-		
-		NEUTRAL_TARGET,
-		
-		BAD_TARGET
-	}
-
-	private GUIGeneState currentState = GUIGeneState.NEUTRAL;
-
-	private Text text;
-	private Circle mainCircle;
-	
-	/**
-	 * Recursive lock; lock == 0 means unlocked, lock > 0 means locked.
-	 * Accessing using {@code setLock(...)}.
-	 */
-	private int lock = 0;
-
-	/**
-	 * Initialises the {@code Text} and {@code Circle} objects so that all genes are standardised.
-	 */
-	protected GUIGene() {
-		text = new Text();
-		text.setFont(Font.font("Arial", 12));
-		text.setTextOrigin(VPos.CENTER);
-		text.setTextAlignment(TextAlignment.CENTER);
-		text.setWrappingWidth(Constants.NODE_RADIUS * 2);
-		text.setX(-Constants.NODE_RADIUS);
-
-		mainCircle = new Circle(Constants.NODE_RADIUS, Constants.NEUTRAL_PAINT);
-		mainCircle.setStroke(Paint.valueOf("black"));
-		
-		getChildren().addAll(mainCircle, text);
-	}
-
-	/**
-	 * Sets the gene's text field.
-	 * 
-	 * @param newText the text string to be displayed.
-	 */
-	public void setText(String newText) {
-		text.setText(newText);
-	}
-
-	/**
-	 * @return the gene's current state.
-	 */
-	public GUIGeneState getState() {
-		return currentState;
-	}
-
-	/**
-	 * Gene states are standardised: all gene subclasses behave the same way in each state.
-	 * <br>
-	 * This design choice was made for the sake of consistency. Rather than controlling the 
-	 * appearance of the genes with logic in the state transition method AND the mouse handlers, 
-	 * the states are now consistent across all types of gene. The mouse handlers implement
-	 * whatever logic is necessary to determine the gene's new state given a certain user input,
-	 * but the states themselves are the same for all genes.
-	 * <br>
-	 * The transition logic for each type of gene is defined in its respective handler class:
-	 * {@code InputHandlers}, {@code NodeHandlers} and {@code OutputHandlers}.   
-	 * 
-	 * @param newState the gene's new state.
-	 */
-	public final void setState(GUIGeneState newState) {
-		switch (newState) {
-		case NEUTRAL:
-			mainCircle.setFill(isLocked() ? Constants.HARD_HIGHLIGHT_PAINT : Constants.NEUTRAL_PAINT);
-			setLinesVisible(isLocked());
-			break;
-		case HOVER:
-			mainCircle.setFill(Constants.MEDIUM_HIGHLIGHT_PAINT);
-			setLinesVisible(true);
-			break;
-		case EXTENDED_HOVER:
-			mainCircle.setFill(Constants.SOFT_HIGHLIGHT_PAINT);
-			setLinesVisible(isLocked());
-			break;
-		case ACTIVE_HOVER:
-			mainCircle.setFill(Constants.SOFT_HIGHLIGHT_PAINT);
-			setLinesVisible(true);
-			break;
-		case GOOD_TARGET:
-			mainCircle.setFill(Constants.GOOD_SELECTION_PAINT);
-			break;
-		case NEUTRAL_TARGET:
-			mainCircle.setFill(Constants.NEUTRAL_SELECTION_PAINT);
-			break;
-		case BAD_TARGET:
-			mainCircle.setFill(Constants.BAD_SELECTION_PAINT);
-			break;
-		}
-		currentState = newState;
-	}
-	
-	/**
-	 * For the sake of practicality, all {@code GUIGene} instances must implement this
-	 * method. It sets the visibility of all of the gene's lines, if it has any.
-	 * 
-	 * @param value the visibility value.
-	 */
-	protected abstract void setLinesVisible(boolean value);
-	
-	/**
-	 * @return true if the gene is locked, false otherwise.
-	 */
-	public boolean isLocked() {
-		return lock > 0;
-	}
-	
-	/**
-	 * Locks or unlocks the gene once. Locked genes
-	 * behave slightly differently in some states. 
-	 * <br>
-	 * Unlocking an already unlocked gene does nothing.
-	 * 
-	 * @param value true to lock, false to unlock;
-	 */
-	public void setLock(boolean value) {
-		if (value) {
-			lock++;
-		} else if (lock > 0) {
-			lock--;
-		} else {
-			lock = 0;
-		}
-	}
-}
diff --git a/src/jcgp/gui/population/GUIInput.java b/src/jcgp/gui/population/GUIInput.java
deleted file mode 100644
index 3db7416..0000000
--- a/src/jcgp/gui/population/GUIInput.java
+++ /dev/null
@@ -1,70 +0,0 @@
-package jcgp.gui.population;
-
-import javafx.scene.paint.Paint;
-import javafx.scene.shape.Circle;
-import jcgp.backend.population.Input;
-import jcgp.gui.constants.Constants;
-import jcgp.gui.constants.Position;
-import jcgp.gui.handlers.InputHandlers;
-
-/**
- * The GUI counterpart of {@link jcgp.backend.population.Input}. This is a 
- * subclass of {@code GUIGene} which represents a chromosome input.
- * 
- * @author Eduardo Pedroni
- */
-public class GUIInput extends GUIGene implements GUIConnection {
-
-	private Input input;
-	
-	/**
-	 * Instantiate {@code GUIInput} given an {@code Input}.
-	 * 
-	 * @param input the associated backend input.
-	 */
-	public GUIInput(final Input input) {
-		super();
-		// store the input, associate itself with it
-		this.input = input;
-		input.setGUIObject(this);
-		
-		// inputs only have a single output socket
-		Circle outputSocket = new Circle(Constants.NODE_RADIUS, 0, Constants.SOCKET_RADIUS, Paint.valueOf("white"));
-		outputSocket.setStroke(Paint.valueOf("black"));
-		outputSocket.setId(String.valueOf(0));
-		getChildren().add(outputSocket);
-		
-		// relocate to the right position, add mouse handlers
-		Position.place(this);
-		InputHandlers.addHandlers(this);
-	}
-
-	/**
-	 * @return the {@code Input} instance associated with this object.
-	 */
-	public Input getInput() {
-		return input;
-	}
-	
-	/**
-	 * Associates this instance with a new input.
-	 * 
-	 * @param input the new input.
-	 */
-	void setInput(Input input) {
-		this.input = input;
-	}
-
-	@Override
-	public void setStateRecursively(GUIGeneState state) {
-		setState(state);
-	}
-
-	@Override
-	protected void setLinesVisible(boolean value) {}
-
-	@Override
-	public void setLockRecursively(boolean value) {
-		setLock(value);
-	}
-}
diff --git a/src/jcgp/gui/population/GUIMutable.java b/src/jcgp/gui/population/GUIMutable.java
deleted file mode 100644
index fa996e2..0000000
--- a/src/jcgp/gui/population/GUIMutable.java
+++ /dev/null
@@ -1,20 +0,0 @@
-package jcgp.gui.population;
-
-import javafx.scene.shape.Line;
-
-/**
- * A loose equivalent to {@link jcgp.backend.population.Mutable}.
- * <br>
- * This defines behaviour that all GUI representations of mutables
- * should be capable of.
- * 
- * @author Eduardo Pedroni
- *
- */
-public interface GUIMutable {
-	
-	public Line[] getLines();
-	
-	public GUIConnection[] getConnections();
-	
-}
diff --git a/src/jcgp/gui/population/GUINode.java b/src/jcgp/gui/population/GUINode.java
deleted file mode 100644
index 1a32426..0000000
--- a/src/jcgp/gui/population/GUINode.java
+++ /dev/null
@@ -1,134 +0,0 @@
-package jcgp.gui.population;
-
-import javafx.scene.paint.Paint;
-import javafx.scene.shape.Circle;
-import javafx.scene.shape.Line;
-import jcgp.backend.population.Gene;
-import jcgp.backend.population.Node;
-import jcgp.gui.GUI;
-import jcgp.gui.constants.Constants;
-import jcgp.gui.constants.Position;
-import jcgp.gui.handlers.NodeHandlers;
-
-/**
- * The GUI counterpart of {@link jcgp.backend.population.Node}. This is a 
- * subclass of {@code GUIGene} which represents a chromosome node.
- * 
- * @author Eduardo Pedroni
- */
-public class GUINode extends GUIGene implements GUIMutable, GUIConnection {
-
-	private Node node;
-	private Line[] lines;
-	private Circle[] sockets;
-	
-	/**
-	 * Instantiate {@code GUINode} given a {@code Node} and the lines needed
-	 * to show its connections.
-	 * 
-	 * @param node the associated backend node.
-	 * @param lines the lines used to display connections.
-	 */
-	public GUINode(Node node, Line[] lines) {
-		super();
-		// store references, associate with node
-		this.node = node;
-		this.lines = lines;
-		node.setGUIObject(this);
-
-		// create the output socket
-		Circle output = new Circle(Constants.NODE_RADIUS, 0, Constants.SOCKET_RADIUS, Constants.SOCKET_PAINT);
-		output.setStroke(Paint.valueOf("black"));
-		
-		// create input sockets
-		sockets = new Circle[GUI.resources.arity()];
-		for (int l = 0; l < sockets.length; l++) {
-			sockets[l] = new Circle(Constants.SOCKET_RADIUS, Constants.SOCKET_PAINT);
-			sockets[l].setStroke(Paint.valueOf("black"));
-			sockets[l].setId(String.valueOf(l));
-			// relocate them
-			Position.placeSocket(l, sockets[l]);
-			Position.connect(lines[l], (GUIGene) ((Gene) node.getConnection(l)).getGUIObject());
-		}
-		
-		// add elements
-		getChildren().addAll(sockets);
-		getChildren().add(output);
-		
-		// relocate node, add handlers
-		Position.place(this);
-		NodeHandlers.addHandlers(this);
-	}
-	
-	/**
-	 * @return the {@code Node} instance associated with this object.
-	 */
-	public Node getNode() {
-		return node;
-	}
-
-	/**
-	 * Associates this instance with a new node.
-	 * 
-	 * @param node the new node.
-	 */
-	void setNode(Node node) {
-		this.node = node;
-	}
-	
-	@Override
-	public Line[] getLines() {
-		return lines;
-	}
-	
-	/**
-	 * Returns one of this object's connection sockets. They are 
-	 * indexed in the same order as lines and the connections
-	 * they represent.
-	 * 
-	 * @param index the socket to return.
-	 * @return the indexed socket object.
-	 */
-	public Circle getSocket(int index) {
-		return sockets[index];
-	}
-	
-	/**
-	 * @return the entire {@code Socket} array.
-	 */
-	public Circle[] getSockets() {
-		return sockets;
-	}
-
-	@Override
-	public void setStateRecursively(GUIGeneState state) {
-		setState(state);
-		for (int i = 0; i < GUI.resources.arity(); i++) {
-			((GUIConnection) ((Gene) node.getConnection(i)).getGUIObject()).setStateRecursively(state);
-		}
-	}
-
-	@Override
-	protected void setLinesVisible(boolean value) {
-		for (int i = 0; i < lines.length; i++) {
-			lines[i].setVisible(value);
-		}
-	}
-
-	@Override
-	public void setLockRecursively(boolean value) {
-		setLock(value);
-		for (int i = 0; i < GUI.resources.arity(); i++) {
-			((GUIConnection) ((Gene) node.getConnection(i)).getGUIObject()).setLockRecursively(value);
-		}
-	}
-
-	@Override
-	public GUIConnection[] getConnections() {
-		GUIConnection[] connections = new GUIConnection[GUI.resources.arity()];
-		for (int c = 0; c < connections.length; c++) {
-			connections[c] = (GUIConnection) ((Gene) node.getConnection(c)).getGUIObject();
-		}
-		return connections;
-	}
-}
diff --git a/src/jcgp/gui/population/GUIOutput.java b/src/jcgp/gui/population/GUIOutput.java
deleted file mode 100644
index f023d00..0000000
--- a/src/jcgp/gui/population/GUIOutput.java
+++ /dev/null
@@ -1,79 +0,0 @@
-package jcgp.gui.population;
-
-import javafx.scene.paint.Paint;
-import javafx.scene.shape.Circle;
-import javafx.scene.shape.Line;
-import jcgp.backend.population.Gene;
-import jcgp.backend.population.Output;
-import jcgp.gui.constants.Constants;
-import jcgp.gui.constants.Position;
-import jcgp.gui.handlers.OutputHandlers;
-
-/**
- * The GUI counterpart of {@link jcgp.backend.population.Output}. This is a 
- * subclass of {@code GUIGene} which represents a chromosome output.
- * 
- * @author Eduardo Pedroni
- */
-public class GUIOutput extends GUIGene implements GUIMutable {
-
-	private Output output;
-	private Line line;
-
-	/**
-	 * Instantiate {@code GUIOutput} given an {@code Output} and the line needed
-	 * to show its connection.
-	 * 
-	 * @param output the associated backend output.
-	 * @param line the line used to display connection.
-	 */
-	public GUIOutput(final Output output, Line line) {
-		super();
-		// store references, associate with backend object
-		this.output = output;
-		this.line = line;
-		output.setGUIObject(this);
-
-		// create input socket
-		Circle socket = new Circle(-Constants.NODE_RADIUS, 0, Constants.SOCKET_RADIUS, Constants.SOCKET_PAINT);
-		socket.setStroke(Paint.valueOf("black"));
-		socket.setId(String.valueOf(0));
-		Position.connect(line, (GUIGene) ((Gene) output.getSource()).getGUIObject());
-		getChildren().add(socket);
-
-		// relocate output, add handlers
-		Position.place(this);
-		OutputHandlers.addHandlers(this);
-	}
-
-	/**
-	 * @return the {@code Output} instance associated with this object.
-	 */
-	public Output getOutput() {
-		return output;
-	}
-	
-	/**
-	 * Associates this instance with a new output.
-	 * 
-	 * @param output the new output.
-	 */
-	void setOutput(Output output) {
-		this.output = output;
-	}
-
-	@Override
-	public Line[] getLines() {
-		return new Line[] {line};
-	}
-
-	@Override
-	protected void setLinesVisible(boolean value) {
-		line.setVisible(value);
-	}
-
-	@Override
-	public GUIConnection[] getConnections() {
-		return new GUIConnection[] {(GUIConnection) output.getGUIObject()};
-	}
-}
diff --git a/src/jcgp/gui/population/PopulationPane.java b/src/jcgp/gui/population/PopulationPane.java
deleted file mode 100644
index 51b5ba4..0000000
--- a/src/jcgp/gui/population/PopulationPane.java
+++ /dev/null
@@ -1,75 +0,0 @@
-package jcgp.gui.population;
-
-import javafx.scene.control.Tab;
-import javafx.scene.control.TabPane;
-import jcgp.JCGP;
-import jcgp.backend.modules.problem.TestCaseProblem;
-import jcgp.backend.modules.problem.TestCaseProblem.TestCase;
-import jcgp.gui.GUI;
-
-public class PopulationPane extends TabPane {
-	
-	private GUI gui;
-	private TestCase<Object> currentTestCase;
-	private boolean evaluating = false;
-	
-	public PopulationPane(GUI gui) {
-		super();
-		this.gui = gui;
-		setTabClosingPolicy(TabClosingPolicy.UNAVAILABLE);
-		remakeTabs();
-	}
-	
-	public void remakeTabs() {
-		getTabs().clear();
-		JCGP jcgp = gui.getExperiment();
-		
-		Tab tab;
-		ChromosomePane cp;
-		for (int i = 0; i < jcgp.getResources().populationSize(); i++) {
-			cp = new ChromosomePane(jcgp.getPopulation().get(i));
-			tab = new Tab("Chr " + i);
-			tab.setContent(cp);
-			getTabs().add(tab);
-		}
-	}
-		
-	public void updateGenes() {
-		if (evaluating) {
-			evaluateTestCase(currentTestCase);
-		}
-		for (int i = 0; i < getTabs().size(); i++) {
-			((ChromosomePane) getTabs().get(i).getContent()).updateGenes(gui.getExperiment().getPopulation().get(i));
-		}
-	}
-	
-	public void evaluateTestCase(TestCase<Object> testCase) {
-		if (gui.getExperiment().getProblem() instanceof TestCaseProblem && testCase != null) {
-			currentTestCase = testCase;
-			if (testCase.getInputs().length == gui.getExperiment().getResources().inputs()) {
-				evaluating = true;
-				for (int i = 0; i < getTabs().size(); i++) {
-					//((ChromosomePane) getTabs().get(i).getContent()).setInputs(testCase.getInputs());
-				}
-			} else {
-				throw new IllegalArgumentException("Test case has " + testCase.getInputs().length
-						+ " inputs and chromosome has " + gui.getExperiment().getResources().inputs());
-			}
-		}
-	}
-	
-	public void hideValues() {
-		evaluating = false;
-		for (int i = 0; i < getTabs().size(); i++) {
-			//((ChromosomePane) getTabs().get(i).getContent()).updateValues();
-		}
-	}
-
-	public boolean isEvaluating() {
-		return evaluating;
-	}
-
-	public void setEvaluating(boolean value) {
-		evaluating = value;
-	}
-}
diff --git a/src/jcgp/gui/settings/SettingsPane.java b/src/jcgp/gui/settings/SettingsPane.java
deleted file mode 100644
index bad42cd..0000000
--- a/src/jcgp/gui/settings/SettingsPane.java
+++ /dev/null
@@ -1,595 +0,0 @@
-package jcgp.gui.settings;
-
-import java.io.File;
-import java.util.ArrayList;
-
-import javafx.event.ActionEvent;
-import javafx.event.EventHandler;
-import javafx.geometry.Insets;
-import javafx.scene.control.Button;
-import javafx.scene.control.CheckBox;
-import javafx.scene.control.ComboBox;
-import javafx.scene.control.ScrollPane;
-import javafx.scene.layout.AnchorPane;
-import javafx.scene.layout.HBox;
-import javafx.scene.layout.Priority;
-import javafx.scene.layout.VBox;
-import javafx.scene.text.Font;
-import javafx.scene.text.Text;
-import javafx.stage.FileChooser;
-import javafx.stage.FileChooser.ExtensionFilter;
-import jcgp.JCGP;
-import jcgp.backend.function.FunctionSet;
-import jcgp.backend.modules.es.EvolutionaryStrategy;
-import jcgp.backend.modules.mutator.Mutator;
-import jcgp.backend.modules.problem.Problem;
-import jcgp.backend.modules.problem.TestCaseProblem;
-import jcgp.backend.parameters.Parameter;
-import jcgp.gui.GUI;
-import jcgp.gui.constants.Constants;
-import jcgp.gui.settings.parameters.GUIParameter;
-import jcgp.gui.settings.testcase.TestCaseTable;
-
-/**
- * This is a fairly hefty class which encapsulates the entire right-hand
- * control pane. It contains base parameters, module selectors and their
- * associated parameters, flow controls and file loading/saving buttons.
- * <br><br>
- * A single instance of this class is used in {@code GUI}.
- * 
- * 
- * @author Eduardo Pedroni
- *
- */
-public class SettingsPane extends AnchorPane {
-	
-	/*
-	 * The primary containers, these make up each section of the settings pane.
-	 */
-	private VBox mainContainer;
-	private VBox baseParameterPane, eaPane, mutatorPane, problemPane;
-	private VBox nodeFunctions;
-	
-	// all buttons
-	private Button runPause = new Button("Run"), step = new Button("Step"), reset = new Button("Reset");
-	private Button loadParameters = new Button("Load parameters"), loadChromosome = new Button("Load chromosome"), saveChromosome = new Button("Save chromosome");
-	
-	// this is a list of parameters used for parameter validity checks
-	private ArrayList<GUIParameter<?>> parameters = new ArrayList<GUIParameter<?>>();
-	
-	// the test case table stage
-	private TestCaseTable testCaseTable;
-	
-	// a reference to the parent GUI
-	private GUI gui;
-	
-	private int currentArity;
-		
-	/**
-	 * Create a new instance of {@code SettingsPane} associated
-	 * with the specified {@code GUI} object.
-	 * 
-	 * @param gui a reference to this object's parent.
-	 */
-	public SettingsPane(GUI gui) {
-		super();
-		this.gui = gui;
-		
-		// acquire a reference to jcgp, for convenience
-		final JCGP jcgp = gui.getExperiment();
-		
-		// make the overarching container
-		mainContainer = new VBox(8);
-		mainContainer.setPadding(new Insets(5, Constants.RESIZE_MARGIN, 0, 2));
-		
-		setMinWidth(Constants.SETTINGS_MIN_WIDTH);
-		setPrefWidth(Constants.SETTINGS_MIN_WIDTH);
-		
-		// initialise all sub-divisions
-		initialiseBaseParameters(jcgp);
-		
-		initialiseEAParameters(jcgp);
-		
-		initialiseMutatorParameters(jcgp);
-		
-		initialiseProblemTypeParameters(jcgp, gui);
-		
-		createControls(gui);
-		
-		// prepare the scroll pane
-		ScrollPane scroll = new ScrollPane();
-		scroll.setFitToWidth(true);
-		scroll.setContent(mainContainer);
-		scroll.setStyle("-fx-background-color: #FFFFFF");
-		
-		// anchor the scroll pane to itself, bearing in mind the resize margin
-		AnchorPane.setTopAnchor(scroll, 0.0);
-		AnchorPane.setBottomAnchor(scroll, 0.0);
-		AnchorPane.setRightAnchor(scroll, 0.0);
-		AnchorPane.setLeftAnchor(scroll, Constants.RESIZE_MARGIN);
-		
-		// add the scroll pane, all done!
-		getChildren().add(scroll);
-	}
-
-	/**
-	 * Creates the base parameters pane
-	 * 
-	 * @param jcgp
-	 */
-	private void initialiseBaseParameters(JCGP jcgp) {
-		baseParameterPane = new VBox(2);
-		
-		Text header = new Text("Base Parameters");
-		header.setFont(Font.font("Arial", 14));
-		header.setUnderline(true);
-		
-		baseParameterPane.getChildren().add(header);
-
-		parameters.add(GUIParameter.create(jcgp.getResources().getRowsParameter(), this));
-		parameters.add(GUIParameter.create(jcgp.getResources().getColumnsParameter(), this));
-		parameters.add(GUIParameter.create(jcgp.getResources().getInputsParameter(), this));
-		parameters.add(GUIParameter.create(jcgp.getResources().getOutputsParameter(), this));
-		parameters.add(GUIParameter.create(jcgp.getResources().getLevelsBackParameter(), this));
-		
-		GUIParameter<?> gp = GUIParameter.create(jcgp.getResources().getPopulationSizeParameter(), this);
-		gp.setPadding(new Insets(0, 0, 10, 0));
-		parameters.add(gp);
-		
-		parameters.add(GUIParameter.create(jcgp.getResources().getCurrentGenerationParameter(), this));
-		parameters.add(GUIParameter.create(jcgp.getResources().getGenerationsParameter(), this));
-		parameters.add(GUIParameter.create(jcgp.getResources().getCurrentRunParameter(), this));
-		
-		gp = GUIParameter.create(jcgp.getResources().getRunsParameter(), this);
-		gp.setPadding(new Insets(0, 0, 10, 0));
-		parameters.add(gp);
-		
-		parameters.add(GUIParameter.create(jcgp.getResources().getSeedParameter(), this));
-		parameters.add(GUIParameter.create(jcgp.getResources().getReportIntervalParameter(), this));
-		
-		baseParameterPane.getChildren().addAll(parameters);
-		mainContainer.getChildren().add(baseParameterPane);
-	}
-
-	private void initialiseEAParameters(final JCGP jcgp) {
-		eaPane = new VBox(2);
-		
-		Text header = new Text("Evolutionary Strategy");
-		header.setFont(Font.font("Arial", 14));
-		header.setUnderline(true);
-		
-		final ComboBox<EvolutionaryStrategy> esCBox = new ComboBox<EvolutionaryStrategy>();
-		esCBox.getItems().addAll(jcgp.getEvolutionaryStrategies());
-		esCBox.getSelectionModel().select(jcgp.getEvolutionaryStrategy());
-		esCBox.prefWidthProperty().bind(mainContainer.widthProperty());
-		
-		final VBox eaParameters = new VBox(2);
-		
-		refreshParameters(jcgp.getEvolutionaryStrategy().getLocalParameters(), eaParameters);
-		
-		esCBox.setOnAction(new EventHandler<ActionEvent>() {
-			@Override
-			public void handle(ActionEvent event) {
-				jcgp.setEvolutionaryStrategy(esCBox.getSelectionModel().getSelectedIndex());
-				refreshParameters(esCBox.getSelectionModel().getSelectedItem().getLocalParameters(), eaParameters);
-				gui.flushConsole();
-			}
-		});
-		
-		eaPane.getChildren().addAll(header, esCBox, eaParameters);	
-		mainContainer.getChildren().add(eaPane);
-	}
-
-	private void initialiseMutatorParameters(final JCGP jcgp) {
-		mutatorPane = new VBox(2);
-		
-		Text header = new Text("Mutator");
-		header.setFont(Font.font("Arial", 14));
-		header.setUnderline(true);
-		
-		final ComboBox<Mutator> mutatorCBox = new ComboBox<Mutator>();
-		mutatorCBox.getItems().addAll(jcgp.getMutators());
-		mutatorCBox.getSelectionModel().select(jcgp.getMutator());
-		mutatorCBox.prefWidthProperty().bind(mainContainer.widthProperty());
-		
-		final VBox mutatorParameters = new VBox(2);
-		refreshParameters(jcgp.getMutator().getLocalParameters(), mutatorParameters);
-		
-		mutatorCBox.setOnAction(new EventHandler<ActionEvent>() {
-			@Override
-			public void handle(ActionEvent event) {
-				jcgp.setMutator(mutatorCBox.getSelectionModel().getSelectedIndex());
-				refreshParameters(mutatorCBox.getSelectionModel().getSelectedItem().getLocalParameters(), mutatorParameters);
-				gui.flushConsole();
-			}
-		});
-		
-		mutatorPane.getChildren().addAll(header, mutatorCBox, mutatorParameters);
-		mainContainer.getChildren().add(mutatorPane); 
-	}
-	
-	private void initialiseProblemTypeParameters(final JCGP jcgp, final GUI gui) {
-		updateArity();
-		
-		problemPane= new VBox(2);
-		
-		Text header = new Text("Problem Type");
-		header.setFont(Font.font("Arial", 14));
-		header.setUnderline(true);
-		
-		final ComboBox<Problem> problemCBox = new ComboBox<Problem>();
-		problemCBox.getItems().addAll(jcgp.getProblems());
-		problemCBox.getSelectionModel().select(jcgp.getProblem());
-		problemCBox.prefWidthProperty().bind(mainContainer.widthProperty());
-		
-		final VBox problemParameters = new VBox(2);
-		problemParameters.setPadding(new Insets(0, 0, 4, 0));
-		refreshParameters(jcgp.getProblem().getLocalParameters(), problemParameters);
-		
-		final HBox testCaseControlContainer = new HBox(2);
-		
-		final Button showTestCaseButton = makeTestCaseButton();
-		final Button loadProblemDataButton = makeLoadTestCaseButton();
-		HBox.setHgrow(showTestCaseButton, Priority.ALWAYS);
-		showTestCaseButton.setMaxWidth(Double.MAX_VALUE);
-		HBox.setHgrow(loadProblemDataButton, Priority.ALWAYS);
-		loadProblemDataButton.setMaxWidth(Double.MAX_VALUE);
-		
-		if (jcgp.getProblem() instanceof TestCaseProblem<?>) {
-			testCaseControlContainer.getChildren().addAll(showTestCaseButton, loadProblemDataButton);
-			remakeTestCaseTable();
-		} else {
-			testCaseControlContainer.getChildren().add(loadProblemDataButton);
-		}
-		
-		nodeFunctions = new VBox(2);
-		nodeFunctions.setPadding(new Insets(0, 0, 4, 0));
-		refreshFunctions();
-		
-		problemCBox.setOnAction(new EventHandler<ActionEvent>() {
-			@Override
-			public void handle(ActionEvent event) {
-				jcgp.setProblem(problemCBox.getSelectionModel().getSelectedIndex());
-				updateArity();
-				refreshParameters(jcgp.getProblem().getLocalParameters(), problemParameters);
-				if (testCaseTable != null) {
-					testCaseTable.close();
-				}
-				gui.setEvaluating(false);
-				refreshFunctions();
-				testCaseControlContainer.getChildren().clear();
-				if (jcgp.getProblem() instanceof TestCaseProblem) {
-					testCaseControlContainer.getChildren().addAll(showTestCaseButton, loadProblemDataButton);
-					remakeTestCaseTable();
-				} else {
-					testCaseControlContainer.getChildren().add(loadProblemDataButton);
-				}
-				gui.reset();
-			}
-		});
-		
-		problemPane.getChildren().addAll(header, problemCBox, problemParameters, nodeFunctions, testCaseControlContainer); 
-		mainContainer.getChildren().add(problemPane);
-		
-	}
-	
-	private Button makeLoadTestCaseButton() {
-		Button b = new Button("Load data");
-		b.setOnAction(new EventHandler<ActionEvent>() {
-			@Override
-			public void handle(ActionEvent event) {
-				FileChooser fc = new FileChooser();
-				fc.setTitle("Open problem file...");
-				fc.getExtensionFilters().add(new ExtensionFilter("CGP " + gui.getExperiment().getProblem() + " files", "*" + ((TestCaseProblem<?>) gui.getExperiment().getProblem()).getFileExtension()));
-				fc.getExtensionFilters().add(new ExtensionFilter("All files", "*.*"));
-				File chrFile = fc.showOpenDialog(gui.getStage());
-				if (chrFile != null) {
-					gui.getExperiment().loadProblemData(chrFile);
-					remakeTestCaseTable();
-					gui.reDraw();
-				}
-			}
-		});
-		return b;
-	}
-
-	private Button makeTestCaseButton() {
-		Button b = new Button("Show data");
-		b.setOnAction(new EventHandler<ActionEvent>() {
-			@Override
-			public void handle(ActionEvent event) {
-				testCaseTable.show(); 
-			}
-		});
-		return b;
-	}
-
-	private void createControls(final GUI gui) {
-		Text header = new Text("Experiment controls");
-		header.setFont(Font.font("Arial", 14));
-		header.setUnderline(true);
-		
-		final VBox controls = new VBox(2);
-		controls.setFillWidth(true);
-		
-		final HBox flowButtons = new HBox(2);
-		runPause.setOnAction(new EventHandler<ActionEvent>() {
-			@Override
-			public void handle(ActionEvent event) {				
-				gui.runPause();
-			}
-		});
-		
-		step.setOnAction(new EventHandler<ActionEvent>() {
-			@Override
-			public void handle(ActionEvent event) {
-				gui.step();
-			}
-		});
-		
-		reset.setOnAction(new EventHandler<ActionEvent>() {
-			@Override
-			public void handle(ActionEvent event) {
-				gui.reset();
-			}
-		});
-		
-		HBox.setHgrow(runPause, Priority.ALWAYS);
-		runPause.setMaxWidth(Double.MAX_VALUE);
-		HBox.setHgrow(step, Priority.ALWAYS);
-		step.setMaxWidth(Double.MAX_VALUE);
-		HBox.setHgrow(reset, Priority.ALWAYS);
-		reset.setMaxWidth(Double.MAX_VALUE);
-		
-		flowButtons.getChildren().addAll(runPause, step, reset);
-		flowButtons.setPadding(new Insets(0, 0, 10, 0));
-		
-		loadParameters.setOnAction(new EventHandler<ActionEvent>() {
-			@Override
-			public void handle(ActionEvent event) {				
-				FileChooser fc = new FileChooser();
-				fc.setTitle("Open .par file...");
-				fc.getExtensionFilters().add(new ExtensionFilter("CGP parameter files", "*.par"));
-				fc.getExtensionFilters().add(new ExtensionFilter("All files", "*.*"));
-				File parFile = fc.showOpenDialog(gui.getStage());
-				if (parFile != null) {
-					gui.getExperiment().loadParameters(parFile);
-					gui.reDraw();
-					refreshFunctions();
-				}
-				gui.flushConsole();
-			}
-		});
-		
-		loadChromosome.setOnAction(new EventHandler<ActionEvent>() {
-			@Override
-			public void handle(ActionEvent event) {
-				FileChooser fc = new FileChooser();
-				fc.setTitle("Load .chr file...");
-				fc.getExtensionFilters().add(new ExtensionFilter("CGP chromosome files", "*.chr"));
-				fc.getExtensionFilters().add(new ExtensionFilter("All files", "*.*"));
-				File chrFile = fc.showOpenDialog(gui.getStage());
-				if (chrFile != null) {
-					gui.getExperiment().loadChromosome(chrFile, gui.getChromosomeIndex());
-					gui.reDraw();
-				}
-				gui.flushConsole();
-			}
-		});
-		saveChromosome.setOnAction(new EventHandler<ActionEvent>() {
-			@Override
-			public void handle(ActionEvent event) {
-				FileChooser fc = new FileChooser();
-				fc.setTitle("Save .chr file...");
-				fc.getExtensionFilters().add(new ExtensionFilter("CGP chromosome files", "*.chr"));
-				fc.getExtensionFilters().add(new ExtensionFilter("All files", "*.*"));
-				File chrFile = fc.showSaveDialog(gui.getStage());
-				if (chrFile != null) {
-					gui.getExperiment().saveChromosome(chrFile, gui.getChromosomeIndex());
-				}
-				gui.flushConsole();
-			}
-		});
-		
-		HBox.setHgrow(loadParameters, Priority.ALWAYS);
-		loadParameters.setMaxWidth(Double.MAX_VALUE);
-		HBox.setHgrow(loadChromosome, Priority.ALWAYS);
-		loadChromosome.setMaxWidth(Double.MAX_VALUE);
-		HBox.setHgrow(saveChromosome, Priority.ALWAYS);
-		saveChromosome.setMaxWidth(Double.MAX_VALUE);
-		
-		controls.getChildren().addAll(header, flowButtons, loadParameters, loadChromosome, saveChromosome);
-		
-		mainContainer.getChildren().add(controls);	
-	}
-	
-	/**
-	 * Builds {@code GUIParameter}s and adds them to the provided {@code VBox}. 
-	 * The parameters built are taken from the specified list.
-	 *
-	 * @param newParameters the list of parameters to add.
-	 * @param container the container to add the parameters to.
-	 */
-	private void refreshParameters(ArrayList<Parameter<?>> newParameters, VBox container) {
-		// remove what is currently in the container from the parameter list
-		parameters.removeAll(container.getChildren());
-		// remove everything in the container
-		container.getChildren().clear();
-		// if there are parameters to add, add them all
-		if (newParameters != null) {
-			for (int i = 0; i < newParameters.size(); i++) {
-				// factory method returns the right subtype of GUIParameter
-				GUIParameter<?> guiParameter = GUIParameter.create(newParameters.get(i), this);
-				// make sure to add it to the parameter list as well
-				parameters.add(guiParameter);
-				container.getChildren().add(guiParameter);
-			}
-		}
-		// do a quick refresh just in case something is invalid
-		revalidateParameters();
-	}
-	
-	/**
-	 * This method handles a problem type change by updating the list of allowed
-	 * node functions.
-	 * <br><br>
-	 * It does so by creating new checkboxes for each function in the function set.
-	 */
-	private void refreshFunctions() {
-		// remove all current functions
-		nodeFunctions.getChildren().clear();
-		CheckBox checkBox;
-		// get a reference to the function set
-		final FunctionSet functionSet = gui.getExperiment().getResources().getFunctionSet();
-		for (int i = 0; i < functionSet.getTotalFunctionCount(); i++) {
-			// add a checkbox for each function
-			checkBox = new CheckBox(functionSet.getFunction(i).toString());
-			checkBox.setId(String.valueOf(i));
-			// make sure the selection matches the function set
-			checkBox.setSelected(functionSet.isEnabled(functionSet.getFunction(i)));
-			final int index = i;
-			// set listener so function set gets updated if the checkboxes change
-			checkBox.setOnAction(new EventHandler<ActionEvent>() {
-				@Override
-				public void handle(ActionEvent event) {
-					if (((CheckBox) event.getSource()).isSelected()) {
-						functionSet.enableFunction(index);
-					} else {
-						functionSet.disableFunction(index);
-					}
-					gui.updateFunctionSelector();
-					revalidateParameters();
-				}
-			});
-			// add the new checkbox
-			nodeFunctions.getChildren().add(checkBox);
-		}
-		// make sure function selector has all functions
-		gui.updateFunctionSelector();
-	}
-	
-	/**
-	 * @return true if the experiment is currently evolving something, false otherwise.
-	 */
-	public boolean isExperimentRunning() {
-		return gui.isWorking();
-	}
-	
-	/**
-	 * 
-	 * @return true if the experiment needs to be reset, false if otherwise.
-	 */
-	public boolean isResetRequired() {
-		for (GUIParameter<?> parameter : parameters) {
-			if (parameter.requiresReset()) {
-				return true;
-			}
-		}
-		if (arityChanged()) {
-			return true;
-		}
-		return false;
-	}
-	
-	/**
-	 * @return true if no parameters have their status set to ParameterStatus.INVALID.
-	 */
-	public boolean areParametersValid() {
-		for (GUIParameter<?> parameter : parameters) {
-			if (!parameter.isValid()) {
-				return false;
-			}
-		}
-		return true;
-	}
-	
-	/**
-	 * Calls validate() on every parameter. This is called whenever a parameter changes,
-	 * so that other parameters update their status in case they were dependent on the
-	 * changed parameter.
-	 * <br><br>
-	 * This also disables the controls if a reset is necessary, preventing the experiment
-	 * from running until it has happened.
-	 */
-	public void revalidateParameters() {
-		boolean disableControls = false;
-		for (GUIParameter<?> parameter : parameters) {
-			parameter.validate();
-			if (parameter.requiresReset()) {
-				disableControls = true;
-			}
-		}
-		if (arityChanged()) {
-			disableControls = true;
-		}
-		
-		runPause.setDisable(disableControls);
-		step.setDisable(disableControls);
-	}
-	
-	/**
-	 * Calls applyValue() on every parameter. This is called when a reset occurs, so that
-	 * the new value will be used as a reference instead of the old reference value.
-	 * <br><br>
-	 * It also closes the test case table, just in case.
-	 */
-	public void applyParameters() {
-		for (GUIParameter<?> parameter : parameters) {
-			parameter.applyValue();
-		}
-		updateArity();
-		if (testCaseTable != null) {
-			testCaseTable.close();
-		}
-	}
-
-	/**
-	 * Updates all of the controls to their appropriate state based on the status of the
-	 * experiment, in order to prevent inappropriate operations if the experiment is
-	 * running or finished.
-	 * 
-	 * @param running true if the experiment is running.
-	 * @param finished true if the experiment is finished.
-	 */
-	public void updateControls(boolean running, boolean finished) {
-		baseParameterPane.setDisable(running);
-		eaPane.setDisable(running);
-		mutatorPane.setDisable(running);
-		problemPane.setDisable(running);
-		
-		runPause.setText(running ? "Pause" : "Run");
-		runPause.setDisable(finished);
-		step.setDisable(running || finished);
-		reset.setDisable(running);
-		
-		loadParameters.setDisable(running);
-		loadChromosome.setDisable(running);
-		saveChromosome.setDisable(running);
-		
-		testCaseTable.getTable().setDisable(running);
-	}
-	
-	private void remakeTestCaseTable() {
-		boolean wasShowing = false;
-		if (testCaseTable != null) {
-			wasShowing = testCaseTable.isShowing();
-			testCaseTable.close();
-		}
-		testCaseTable = new TestCaseTable((TestCaseProblem<Object>) gui.getExperiment().getProblem(), gui);
-		if (wasShowing) {
-			testCaseTable.show();
-		}
-	}
-	
-	public TestCaseTable getTestCaseTable() {
-		return testCaseTable;
-	}
-	
-	private void updateArity() {
-		currentArity = gui.getExperiment().getProblem().getFunctionSet().getMaxArity();
-	}
-	
-	private boolean arityChanged() {
-		return currentArity != gui.getExperiment().getProblem().getFunctionSet().getMaxArity();
-	}
-}
diff --git a/src/jcgp/gui/settings/parameters/GUIBooleanParameter.java b/src/jcgp/gui/settings/parameters/GUIBooleanParameter.java
deleted file mode 100644
index a1f03fe..0000000
--- a/src/jcgp/gui/settings/parameters/GUIBooleanParameter.java
+++ /dev/null
@@ -1,82 +0,0 @@
-package jcgp.gui.settings.parameters;
-
-import javafx.beans.value.ChangeListener;
-import javafx.beans.value.ObservableValue;
-import javafx.scene.control.CheckBox;
-import javafx.scene.control.Control;
-import jcgp.backend.parameters.BooleanParameter;
-import jcgp.backend.parameters.ParameterStatus;
-import jcgp.gui.constants.Constants;
-import jcgp.gui.settings.SettingsPane;
-
-/**
- * This extension of @code{GUIParameter} uses a @code{CheckBox} to display
- * the value of a @code{BooleanParameter}. It cannot be constructed
- * directly - instead, use @code{GUIParameter.create()}.
- * <br><br>
- * See {@link GUIParameter} for more information.
- * 
- * @author Eduardo Pedroni
- */
-public class GUIBooleanParameter extends GUIParameter<Boolean> {
-
-	private CheckBox checkBox;
-	
-	/**
-	 * This protected constructor is intended for use
-	 * by the factory method only.
-	 * 
-	 */
-	protected GUIBooleanParameter(BooleanParameter parameter, SettingsPane sp) {
-		super(parameter, sp);
-	}
-	
-	@Override
-	protected Control makeControl() {
-		checkBox = new CheckBox();
-		checkBox.setSelected(parameter.get());
-		
-		return checkBox;
-	}
-	
-	@Override
-	protected void setControlListeners() {
-		/* pass the CheckBox value back to the parameter whenever it gets
-		 * modified, provided the experiment isn't running */
-		checkBox.selectedProperty().addListener(new ChangeListener<Boolean>() {
-			@Override
-			public void changed(
-					ObservableValue<? extends Boolean> observable,
-					Boolean oldValue, Boolean newValue) {
-				if (!settingsPane.isExperimentRunning()) {
-					parameter.set(newValue);
-					settingsPane.revalidateParameters();
-				}
-			}
-		});
-	}
-	
-	@Override
-	protected void setValidityStyle() {
-		// update the Control's style and tooltip based on the status of the parameter
-		if (parameter.getStatus() == ParameterStatus.INVALID) {
-			checkBox.setStyle(Constants.BASE_CHECKBOX_STYLE + Constants.INVALID_PARAMETER_STYLE);
-			checkBox.setTooltip(tooltip);
-			tooltip.setText(parameter.getStatus().getDetails());
-		} else if (parameter.getStatus() == ParameterStatus.WARNING 
-				|| parameter.getStatus() == ParameterStatus.WARNING_RESET) {
-			checkBox.setStyle(Constants.BASE_CHECKBOX_STYLE + Constants.WARNING_PARAMETER_STYLE);
-			checkBox.setTooltip(tooltip);
-			tooltip.setText(parameter.getStatus().getDetails());
-		} else {
-			checkBox.setStyle(Constants.BASE_CHECKBOX_STYLE + Constants.VALID_PARAMETER_STYLE);
-			checkBox.setTooltip(null);
-		}
-	}
-
-	@Override
-	public void refreshValue() {
-		checkBox.setSelected(parameter.get());
-	}
-	
-}
diff --git a/src/jcgp/gui/settings/parameters/GUIDoubleParameter.java b/src/jcgp/gui/settings/parameters/GUIDoubleParameter.java
deleted file mode 100644
index feee34c..0000000
--- a/src/jcgp/gui/settings/parameters/GUIDoubleParameter.java
+++ /dev/null
@@ -1,110 +0,0 @@
-package jcgp.gui.settings.parameters;
-
-import java.text.DecimalFormat;
-
-import javafx.beans.value.ChangeListener;
-import javafx.beans.value.ObservableValue;
-import javafx.geometry.Pos;
-import javafx.scene.control.Control;
-import javafx.scene.control.TextField;
-import jcgp.backend.parameters.DoubleParameter;
-import jcgp.backend.parameters.ParameterStatus;
-import jcgp.gui.constants.Constants;
-import jcgp.gui.settings.SettingsPane;
-
-/**
- * This extension of @code{GUIParameter} uses a @code{TextField} to display
- * the value of a @code{DoubleParameter}. It cannot be constructed
- * directly - instead, use @code{GUIParameter.create()}.
- * <br><br>
- * See {@link GUIParameter} for more information.
- * 
- * @author Eduardo Pedroni
- */
-public class GUIDoubleParameter extends GUIParameter<Number> {
-
-	private TextField textField;
-	private DecimalFormat decimalFormat;
-	
-	/**
-	 * This protected constructor is intended for use
-	 * by the factory method only.
-	 * 
-	 */
-	protected GUIDoubleParameter(DoubleParameter parameter, SettingsPane sp) {
-		super(parameter, sp);
-	}
-	
-	@Override
-	protected Control makeControl() {
-		// we use a text field, and a formatting class to enforce decimals
-		decimalFormat = new DecimalFormat();
-		decimalFormat.setMaximumFractionDigits(10);
-		textField = new TextField(decimalFormat.format(parameter.get().doubleValue()));
-		textField.setStyle(Constants.VALID_PARAMETER_STYLE);
-		textField.setAlignment(Pos.CENTER_RIGHT);
-		textField.prefWidthProperty().bind(widthProperty().divide(2));
-		return textField;
-	}
-
-	@Override
-	protected void setControlListeners() {
-		/* pass the TextField value back to the parameter whenever it gets
-		 * modified, provided it is not empty, the experiment isn't running
-		 * and it matches the double-precision regex filter */
-		textField.textProperty().addListener(new ChangeListener<String>() {
-			@Override
-			public void changed(
-					ObservableValue<? extends String> observable,
-					String oldValue, String newValue) {
-				if (!settingsPane.isExperimentRunning()) {
-					if (newValue.matches("^[-+]?[0-9]*\\.?[0-9]+$")) {
-						if (!newValue.isEmpty()) {
-							double value = Double.parseDouble(newValue);
-							parameter.set(value);
-							settingsPane.revalidateParameters();
-						}
-					} else {
-						refreshValue();
-					}
-				}
-			}
-		});
-		/* if the TextField loses focus and is empty, set it to the current
-		 * value of the parameter */
-		textField.focusedProperty().addListener(new ChangeListener<Boolean>() {
-			@Override
-			public void changed(
-					ObservableValue<? extends Boolean> observable,
-					Boolean oldValue, Boolean newValue) {
-				if (!newValue) {
-					refreshValue();
-				}
-			}
-		});
-	}
-
-	@Override
-	protected void setValidityStyle() {
-		// update the Control's style and tooltip based on the status of the parameter
-		if (parameter.getStatus() == ParameterStatus.INVALID) {
-			textField.setStyle(Constants.BASE_TEXT_STYLE + Constants.INVALID_PARAMETER_STYLE);
-			textField.setTooltip(tooltip);
-			tooltip.setText(parameter.getStatus().getDetails());
-		} else if (parameter.getStatus() == ParameterStatus.WARNING || parameter.getStatus() ==  ParameterStatus.WARNING_RESET) {
-			textField.setStyle(Constants.BASE_TEXT_STYLE + Constants.WARNING_PARAMETER_STYLE);
-			textField.setTooltip(tooltip);
-			tooltip.setText(parameter.getStatus().getDetails());
-		} else {
-			textField.setStyle(Constants.BASE_TEXT_STYLE + Constants.VALID_PARAMETER_STYLE);
-			textField.setTooltip(null);
-		}
-	}
-	
-	@Override
-	public void refreshValue() {
-		if (!textField.isFocused()) {
-			textField.setText(decimalFormat.format(parameter.get().doubleValue()));
-		}
-	}
-}
diff --git a/src/jcgp/gui/settings/parameters/GUIIntegerParameter.java b/src/jcgp/gui/settings/parameters/GUIIntegerParameter.java
deleted file mode 100644
index bcfbe50..0000000
--- a/src/jcgp/gui/settings/parameters/GUIIntegerParameter.java
+++ /dev/null
@@ -1,107 +0,0 @@
-package jcgp.gui.settings.parameters;
-
-import javafx.beans.value.ChangeListener;
-import javafx.beans.value.ObservableValue;
-import javafx.geometry.Pos;
-import javafx.scene.control.Control;
-import javafx.scene.control.TextField;
-import jcgp.backend.parameters.IntegerParameter;
-import jcgp.backend.parameters.ParameterStatus;
-import jcgp.gui.constants.Constants;
-import jcgp.gui.settings.SettingsPane;
-
-/**
- * This extension of @code{GUIParameter} uses a @code{TextField} to display
- * the value of a @code{IntegerParameter}. It cannot be constructed
- * directly - instead, use @code{GUIParameter.create()}.
- * <br><br>
- * See {@link GUIParameter} for more information.
- * 
- * @author Eduardo Pedroni
- */
-public class GUIIntegerParameter extends GUIParameter<Number> {
-	
-	private TextField textField;
-	
-	/**
-	 * This protected constructor is intended for use
-	 * by the factory method only.
-	 * 
-	 */
-	protected GUIIntegerParameter(IntegerParameter parameter, SettingsPane sp) {
-		super(parameter, sp);
-	}
-
-	@Override
-	protected Control makeControl() {
-		// this uses a text field
-		textField = new TextField(String.valueOf(parameter.get()));
-		textField.setStyle(Constants.VALID_PARAMETER_STYLE);
-		textField.setAlignment(Pos.CENTER_RIGHT);
-		textField.prefWidthProperty().bind(widthProperty().divide(2));
-		
-		return textField;
-	}
-
-	@Override
-	protected void setControlListeners() {
-		/* pass the TextField value back to the parameter whenever it gets
-		 * modified, provided it is not empty, the experiment isn't running
-		 * and it matches the integer regex pattern */
-		textField.textProperty().addListener(new ChangeListener<String>() {
-			@Override
-			public void changed(
-					ObservableValue<? extends String> observable,
-					String oldValue, String newValue) {
-				if (!settingsPane.isExperimentRunning()) {
-					if (newValue.matches("[0-9]*")) {
-						if (!newValue.isEmpty()) {
-							int value = Integer.parseInt(newValue);
-							parameter.set(value);
-							settingsPane.revalidateParameters();
-						}
-					} else {
-						refreshValue();
-					}
-				}
-			}
-		});
-		/* if the TextField loses focus and is empty, set it to the current
-		 * value of the parameter */
-		textField.focusedProperty().addListener(new ChangeListener<Boolean>() {
-			@Override
-			public void changed(
-					ObservableValue<? extends Boolean> observable,
-					Boolean oldValue, Boolean newValue) {
-				if (!newValue) {
-					refreshValue();
-				}
-			}
-		});
-	}
-	
-	@Override
-	protected void setValidityStyle() {
-		// update the Control's style and tooltip based on the status of the parameter
-		if (parameter.getStatus() == ParameterStatus.INVALID) {
-			textField.setStyle(Constants.BASE_TEXT_STYLE + Constants.INVALID_PARAMETER_STYLE);
-			textField.setTooltip(tooltip);
-			tooltip.setText(parameter.getStatus().getDetails());
-		} else if (parameter.getStatus() == ParameterStatus.WARNING 
-				|| parameter.getStatus() ==  ParameterStatus.WARNING_RESET) {
-			textField.setStyle(Constants.BASE_TEXT_STYLE + Constants.WARNING_PARAMETER_STYLE);
-			textField.setTooltip(tooltip);
-			tooltip.setText(parameter.getStatus().getDetails());
-		} else {
-			textField.setStyle(Constants.BASE_TEXT_STYLE + Constants.VALID_PARAMETER_STYLE);
-			textField.setTooltip(null);
-		}
-	}
-
-	@Override
-	public void refreshValue() {
-		if (!textField.isFocused()) {
-			textField.setText(parameter.get().toString());
-		}
-	}
-}
diff --git a/src/jcgp/gui/settings/parameters/GUIParameter.java b/src/jcgp/gui/settings/parameters/GUIParameter.java
deleted file mode 100644
index 59aecf6..0000000
--- a/src/jcgp/gui/settings/parameters/GUIParameter.java
+++ /dev/null
@@ -1,235 +0,0 @@
-package jcgp.gui.settings.parameters;
-
-import java.util.concurrent.atomic.AtomicBoolean;
-
-import javafx.application.Platform;
-import javafx.beans.value.ChangeListener;
-import javafx.beans.value.ObservableValue;
-import javafx.geometry.Pos;
-import javafx.scene.control.Control;
-import javafx.scene.control.Label;
-import javafx.scene.control.Tooltip;
-import javafx.scene.layout.HBox;
-import jcgp.backend.parameters.BooleanParameter;
-import jcgp.backend.parameters.DoubleParameter;
-import jcgp.backend.parameters.IntegerParameter;
-import jcgp.backend.parameters.Parameter;
-import jcgp.backend.parameters.ParameterStatus;
-import jcgp.gui.settings.SettingsPane;
-
-/**
- * 
- * This is the base class for all @code{GUIParameter}s. Using the factory method @code{GUIParameter.create()}
- * generates an appropriate instance of this class for the specified parameter.
- * <br><br>
- * A @code{GUIParameter} is an @code{HBox} containing a @code{Text} for the parameter name 
- * and a @code{Control} for interaction.
- * It stores an instance of its associated @code{Parameter} object and also contains a @code{Tooltip} for 
- * displaying status information.
- * <br><br>
- * Monitor parameters are updated automatically and have their @code{Control} disabled so
- * that no changes can be made via the GUI.
- * Non-monitor parameters are updated automatically as well, but may be changed by the user
- * if the program is not evolving.
- * 
- * @see Parameter
- * @author Eduardo Pedroni
- * @param <T> the parameter data type
- */
-public abstract class GUIParameter<T> extends HBox {
-	
-	private Label name;
-	private Control valueControl;
-	
-	protected SettingsPane settingsPane;
-	protected Tooltip tooltip;
-	protected Parameter<T> parameter;
-	
-	/** This is the lock used to prevent more than one update task to be scheduled
-	 *  at the same time on the same GUIParameter. */
-	private AtomicBoolean updateLock = new AtomicBoolean(false);
-	
-	/**
-	 * This value is used to assert whether the control has changed values since 
-	 * the program last ran. Therefore, it is updated whenever a generation occurs
-	 * or the experiment is reset.
-	 */
-	private T referenceValue;
-	
-	/**
-	 * This protected template constructor contains the common elements to all
-	 * @code{GUIParameter}s and should be invoked by any subclasses using @code{super()}. It
-	 * defers the creation of the parameter {@code Control} object to the subclass
-	 * currently being built (which in turn is defined by the factory method).
-	 * 
-	 * @param parameter a @code{Parameter} for which to generate a @code{GUIParameter}.
-	 * @param sp a reference to the @code{SettingsPane}.
-	 */
-	protected GUIParameter(Parameter<T> parameter, final SettingsPane settingsPane) {
-		this.parameter = parameter;
-		this.referenceValue = parameter.get();
-		
-		this.settingsPane = settingsPane;
-		
-		setAlignment(Pos.CENTER_LEFT);
-		setSpacing(5);
-		
-		name = new Label(parameter.toString());
-		// set text width to half of the total width of the GUIParameter
-		name.prefWidthProperty().bind(widthProperty().divide(2));
-		
-		// the tooltip is the hover-over label containing status information, when appropriate
-		tooltip = new Tooltip();
-		tooltip.setSkin(null);
-		
-		valueControl = makeControl();
-		
-		// if the parameter is a monitor, it should be permanently disabled
-		valueControl.setDisable(parameter.isMonitor());
-		
-		// bind to parameter value property in a thread-safe way
-		makeThreadSafeBinding();
-		
-		// if parameter is not a monitor, make sure the control is constrained appropriately
-		if (!parameter.isMonitor()) {
-			setControlListeners();
-		}
-		
-		getChildren().addAll(name, valueControl);
-	}
-	
-	/**
-	 * Factory method to create @code{GUIParameter}s from @code{Parameter}s. 
-	 * Use this to create an appropriate @code{GUIParameter} from any instance of @code{Parameter},
-	 * rather than manually downcasting the @code{Parameter} object every time.
-	 * 
-	 * @param parameter a parameter for which to generate a @code{GUIParameter}.
-	 * @param sp a reference to the @code{SettingsPane}.
-	 * @return an appropriate instance of @code{GUIParameter}.
-	 */
-	public static GUIParameter<?> create(Parameter<?> parameter, SettingsPane sp) {
-		if (parameter instanceof IntegerParameter) {
-			return new GUIIntegerParameter((IntegerParameter) parameter, sp);
-		} else if (parameter instanceof DoubleParameter) {
-			return new GUIDoubleParameter((DoubleParameter) parameter, sp);
-		} else if (parameter instanceof BooleanParameter) {
-			return new GUIBooleanParameter((BooleanParameter) parameter, sp);
-		} else {
-			throw new ClassCastException("No GUIParameter subclass exists for argument of type " + parameter.getClass());
-		}
-	}
-
-	/**
-	 * Parameters are intended to communicate information from the experiment
-	 * to the GUI. Since the experiment runs on a separate threads and it is illegal
-	 * to modify JavaFX objects from outside the JavaFX Application thread, this
-	 * special ChangeListener updates the GUIParameter in a safe way.
-	 * <br><br>
-	 * Note that this is applied to all parameters regardless of whether they are 
-	 * monitors or not; the only difference between monitor and non-monitor parameters
-	 * is that monitor parameters cannot be modified from the GUI.
-	 */
-	private void makeThreadSafeBinding() {
-		parameter.valueProperty().addListener(new ChangeListener<Object>() {
-			@Override
-			public void changed(
-					ObservableValue<? extends Object> observable,
-					Object oldValue, Object newValue) {
-				// only do this if the experiment is running
-				if (settingsPane.isExperimentRunning() || !isFocused()) {
-					/* here's the catch - atomically get the lock state and set it to true
-					 * the lock will only be false again when the runnable is finished executing, 
-					 * preventing multiple runnables to concurrently update the same GUIParameter
-					 */
-					if (!updateLock.getAndSet(true)) {
-						Platform.runLater(new Runnable() {
-							@Override
-							public void run() {
-								refreshValue();
-								updateLock.set(false);
-							}
-						});
-					}
-				}
-			}
-		});
-	}
-	
-	/**
-	 * @return true if the current value of the parameter does not prevent the 
-	 * experiment from running.
-	 */
-	public boolean isValid() {
-		return parameter.getStatus() != ParameterStatus.INVALID;
-	}
-	
-	/**
-	 * Force the parameter to validate its current value, and apply the associated
-	 * style to the @code{GUIParameter}.
-	 */
-	public void validate() {
-		parameter.validate(parameter.get());
-		setValidityStyle();
-	}
-	
-	/**
-	 * Certain parameter changes might require the experiment to be reset, either
-	 * because the parameter is critical or because its status requires a reset.
-	 * 
-	 * @return true if an experiment reset is required due to this parameter changing.
-	 */
-	public boolean requiresReset() {
-		return (parameter.isCritical() && !parameter.get().equals(referenceValue))
-				|| parameter.getStatus() == ParameterStatus.WARNING_RESET;
-	}
-	
-	/**
-	 * Set the current parameter value as the reference value of the @code{GUIParameter}.
-	 * The new reference value will be used to determine the validity of the parameter, 
-	 * should its value change.
-	 */
-	public void applyValue() {
-		referenceValue = parameter.get();
-	}
-	
-	/* 
-	 * The following prototypes are instance-dependent and are called from
-	 * GUIParameter() as necessary.
-	 */
-	/**
-	 * This method returns the @code{Control} object used to control the parameter.
-	 * <br><br>
-	 * Implementations of @code{GUIParameter} must override this method and return 
-	 * a @code{Control} appropriate to the type of parameter. This will typically be
-	 * done by referencing the protected field @code{GUIParameter.parameter}.
-	 * 
-	 * @return the Control object to be added to the GUIParameter.
-	 */
-	protected abstract Control makeControl();
-	
-	/**
-	 * Adds the necessary handlers to the @code{Control} object in order to modify
-	 * the underlying parameter. This will typically consist of filtering key
-	 * presses to ensure no invalid characters are inserted, applying the new 
-	 * value to the underlying parameter and revalidating the parameters to
-	 * reflect the changes made.
-	 */
-	protected abstract void setControlListeners();
-	
-	/**
-	 * This method is called to style the @code{GUIParameter} according to the status of
-	 * the parameter, which can be obtained with @code{parameter.getStatus()}. While the
-	 * subclass is free to style itself in any way, the CSS strings defined here 
-	 * (INVALID_PARAMETER_STYLE, WARNING_PARAMETER_STYLE, VALID_PARAMETER_STYLE)
-	 * provide a way to keep the GUI consistent.
-	 * 
-	 * @see ParameterStatus
-	 */
-	protected abstract void setValidityStyle();
-	
-	/**
-	 * Update the control so it shows the correct value of the parameter. This method
-	 * is used exclusively by the thread-safe binding created if the module is a monitor.
-	 */
-	protected abstract void refreshValue();
-}
diff --git a/src/jcgp/gui/settings/testcase/TestCaseTable.java b/src/jcgp/gui/settings/testcase/TestCaseTable.java
deleted file mode 100644
index 605b75e..0000000
--- a/src/jcgp/gui/settings/testcase/TestCaseTable.java
+++ /dev/null
@@ -1,124 +0,0 @@
-package jcgp.gui.settings.testcase;
-
-import java.util.ArrayList;
-
-import javafx.beans.property.SimpleStringProperty;
-import javafx.beans.value.ChangeListener;
-import javafx.beans.value.ObservableValue;
-import javafx.collections.ObservableList;
-import javafx.event.EventHandler;
-import javafx.scene.Scene;
-import javafx.scene.control.TableColumn;
-import javafx.scene.control.TableColumn.CellDataFeatures;
-import javafx.scene.control.TableView;
-import javafx.stage.Stage;
-import javafx.stage.WindowEvent;
-import javafx.util.Callback;
-import jcgp.backend.modules.problem.TestCaseProblem;
-import jcgp.backend.modules.problem.TestCaseProblem.TestCase;
-import jcgp.backend.resources.Resources;
-import jcgp.gui.GUI;
-
-/**
- * This is a test case table. For problems that have test cases, 
- * this table shows the test case inputs and outputs. Clicking on 
- * a test case (one is shown per row) applies the values to all 
- * chromosome inputs shows the calculated values throughout the chromosome.
- * 
- * @author Eduardo Pedroni
- *
- */
-public class TestCaseTable extends Stage {
-
-	private TableView<TestCase<Object>> table;
-
-	/**
-	 * Make a new instance of {@code TestCaseTable}.
-	 * 
-	 * @param testCaseProblem the {@code TestCaseProblem} whose data must be displayed.
-	 * @param gui a reference to the GUI.
-	 */
-	public TestCaseTable(final TestCaseProblem<Object> testCaseProblem, final GUI gui) {
-		super();
-		
-		Resources resources = gui.getExperiment().getResources();
-		
-		// create the actual table view
-		table = new TableView<TestCase<Object>>();
-		// get test cases from problem
-		ObservableList<TestCase<Object>> testCaseList = testCaseProblem.getTestCases();
-		
-		// prepare input and output columns
-		ArrayList<TableColumn<TestCase<Object>, String>> inputs = new ArrayList<TableColumn<TestCase<Object>, String>>(resources.inputs());
-		ArrayList<TableColumn<TestCase<Object>, String>> outputs = new ArrayList<TableColumn<TestCase<Object>, String>>(resources.outputs());
-
-		// create input columns
-		TableColumn<TestCase<Object>, String> tc;
-		for (int i = 0; i < resources.inputs(); i++) {
-			tc = new TableColumn<TestCase<Object>, String>("I: " + i);
-			inputs.add(tc);
-			final int index = i;
-			tc.setCellValueFactory(new Callback<TableColumn.CellDataFeatures<TestCase<Object>,String>, ObservableValue<String>>() {
-				@Override
-				public ObservableValue<String> call(CellDataFeatures<TestCase<Object>, String> param) {
-					// create a new string property and give it the test case value, no need for dynamic binding - this wont change often
-					return new SimpleStringProperty(param.getValue().getInputs()[index].toString());
-				}
-			});
-			tc.setSortable(false);
-			// set column width so all columns are distributed across the width of the stage
-			tc.prefWidthProperty().bind(table.widthProperty().divide(resources.inputs() + resources.outputs()));
-		}
-		
-		// create output columns
-		for (int o = 0; o < resources.outputs(); o++) {
-			tc = new TableColumn<TestCase<Object>, String>("O: " + o);
-			outputs.add(tc);
-			final int index = o;
-			tc.setCellValueFactory(new Callback<TableColumn.CellDataFeatures<TestCase<Object>,String>, ObservableValue<String>>() {
-				@Override
-				public ObservableValue<String> call(CellDataFeatures<TestCase<Object>, String> param) {
-					// create a new string property and give it the test case value, no need for dynamic binding - this wont change often
-					return new SimpleStringProperty(param.getValue().getOutputs()[index].toString());
-				}
-			});
-			tc.setSortable(false);
-			// set column width so all columns are distributed across the width of the stage
-			tc.prefWidthProperty().bind(table.widthProperty().divide(resources.inputs() + resources.outputs()));
-		}
-		
-		// add created columns
-		table.getColumns().addAll(inputs);
-		table.getColumns().addAll(outputs);
-		
-		// populate table with actual data
-		table.setItems(testCaseList);
-		
-		// apply test case values when a new test case is selected
-		table.getSelectionModel().selectedItemProperty().addListener(new ChangeListener<TestCase<Object>>() {
-			@Override
-			public void changed(ObservableValue<? extends TestCase<Object>> observable,	TestCase<Object> oldValue, TestCase<Object> newValue) {
-				gui.evaluateTestCase(newValue);
-			}
-		});
-		
-		// when the stage is closed, clear the selection
-		// this doesn't work if the stage is closed by the program for some reason...
-		setOnCloseRequest(new EventHandler<WindowEvent>() {
-			@Override
-			public void handle(WindowEvent event) {
-				gui.hideGeneValues();
-				table.getSelectionModel().clearSelection();
-			}
-		});
-		
-		setScene(new Scene(table));
-	}
-
-	/**
-	 * @return a reference to the actual table of test cases.
-	 */
-	public TableView<TestCase<Object>> getTable() {
-		return table;
-	}
-}