Refactored Mutable, commented a little bit of the GUI package

5 files changed, 223 insertions, 37 deletions

diff --git a/src/jcgp/gui/GUI.java b/src/jcgp/gui/GUI.java
index 437a739..2f09dea 100644
--- a/src/jcgp/gui/GUI.java
+++ b/src/jcgp/gui/GUI.java
@@ -13,7 +13,7 @@ import javafx.stage.Stage;
 import javafx.stage.WindowEvent;
 import jcgp.JCGP;
 import jcgp.backend.modules.problem.TestCaseProblem.TestCase;
-import jcgp.gui.console.GUIConsole;
+import jcgp.gui.console.ConsolePane;
 import jcgp.gui.dragresize.HorizontalDragResize;
 import jcgp.gui.dragresize.VerticalDragResize;
 import jcgp.gui.population.FunctionSelector;
@@ -22,8 +22,25 @@ import jcgp.gui.population.PopulationPane;
 import jcgp.gui.settings.SettingsPane;
 
 /**
- * Main class for the graphical user interface (GUI)
- * 
+ * 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
  *
@@ -31,72 +48,213 @@ import jcgp.gui.settings.SettingsPane;
 public class GUI extends Application {
 	
 	/* Colours */
+	/**
+	 * A string containing the hexadecimal colour used for representing neutrality.
+	 */
 	public static final String NEUTRAL_COLOUR = "#FFFFFF";
+	/**
+	 * A 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 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 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 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 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 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";
 	
 	/* 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;
     
-	private final JCGP jcgp;
-	
+	/*
+	 * Actual GUI elements
+	 */
 	private Stage stage;
-	
-	private final FunctionSelector functionSelector;
-	
 	private PopulationPane populationPane;
-	
-	private GUIConsole console;
-	
+	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;
 	
-	private Service<Void> cgpService;
+	/*
+	 * The experiment itself
+	 */
+	private final JCGP jcgp;
 	
-	private Runnable consoleFlush;
 	
+	/**
+	 * 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();
 		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();
 				}
 			}
 		};
 		
-		cgpService = new Service<Void> () {
+		/* 
+		 * 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() {
@@ -114,60 +272,95 @@ public class GUI extends Application {
 	
 	@Override
 	public void start(Stage primaryStage) throws Exception {
-		console = new GUIConsole();
+		/*
+		 * 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;
+
 		/*
-		 * Instantiate the various GUI elements here. 
-		 * 
-		 * 
+		 * The experiment layer contains all of the experiment-related panes. 
+		 * The only element that sits higher than this is the function selector.
 		 */
-		BorderPane leftFrame = new BorderPane();
 		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);
-		settingsPane.maxWidthProperty().bind(experimentLayer.widthProperty());
-		
-		console.maxHeightProperty().bind(experimentLayer.heightProperty());
 		
+		// 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) {
-				settingsPane.getTestCaseTable().close();
+				if (settingsPane.getTestCaseTable() != null) {
+					settingsPane.getTestCaseTable().close();
+				}
 			}
 		});
 	}
 
+	/**
+	 * 
+	 */
 	public void runPause() {
 		if (!jcgp.isFinished() && settingsPane.areParametersValid()) {
 			if (!running) {
 				runningMode(true);
-				cgpService.restart();
+				jcgpService.restart();
 			} else {
-				cgpService.cancel();
+				jcgpService.cancel();
 				runningMode(false);
 			}
 		}
diff --git a/src/jcgp/gui/console/GUIConsole.java b/src/jcgp/gui/console/ConsolePane.java
index b3d037c..c4cfc21 100644
--- a/src/jcgp/gui/console/GUIConsole.java
+++ b/src/jcgp/gui/console/ConsolePane.java
@@ -26,7 +26,7 @@ import jcgp.gui.GUI;
  * @author Eduardo Pedroni
  *
  */
-public class GUIConsole extends AnchorPane implements Console {
+public class ConsolePane extends AnchorPane implements Console {
 	
 	private TextArea textArea = new TextArea("Welcome to JCGP!\n");
 	private StringBuffer printBuffer = new StringBuffer();
@@ -34,7 +34,7 @@ public class GUIConsole extends AnchorPane implements Console {
 	/**
 	 * Creates a new instance of this class.
 	 */
-	public GUIConsole() {
+	public ConsolePane() {
 		super();
 		textArea.setEditable(false);
 		
diff --git a/src/jcgp/gui/population/GUIGene.java b/src/jcgp/gui/population/GUIGene.java
index 0eea045..3d9cffb 100644
--- a/src/jcgp/gui/population/GUIGene.java
+++ b/src/jcgp/gui/population/GUIGene.java
@@ -71,11 +71,6 @@ public abstract class GUIGene extends Group {
 	
 	public abstract void addLocks(int value);
 	
-	/**
-	 * 
-	 * 
-	 * @param value
-	 */
 	public abstract void removeLocks(int value);
 	
 	public abstract void updateLines();
diff --git a/src/jcgp/gui/population/GUIOutput.java b/src/jcgp/gui/population/GUIOutput.java
index 5a76298..364458b 100644
--- a/src/jcgp/gui/population/GUIOutput.java
+++ b/src/jcgp/gui/population/GUIOutput.java
@@ -266,7 +266,7 @@ public class GUIOutput extends GUIGene {
 
 	@Override
 	public void setChangingConnection(Connection newConnection) {
-		output.setConnection(0, newConnection);	
+		output.setSource(newConnection);	
 		updateText();
 	}
 
diff --git a/src/jcgp/gui/settings/parameters/GUIParameter.java b/src/jcgp/gui/settings/parameters/GUIParameter.java
index f896fa3..9188aec 100644
--- a/src/jcgp/gui/settings/parameters/GUIParameter.java
+++ b/src/jcgp/gui/settings/parameters/GUIParameter.java
@@ -231,8 +231,6 @@ public abstract class GUIParameter<T> extends HBox {
 	 * (INVALID_PARAMETER_STYLE, WARNING_PARAMETER_STYLE, VALID_PARAMETER_STYLE)
 	 * provide a way to keep the GUI consistent.
 	 * 
-	 * TODO update this if the strings are externalised
-	 * 
 	 * @see ParameterStatus
 	 */
 	protected abstract void setValidityStyle();