6 files changed, 0 insertions, 1253 deletions

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;
-	}
-}