Added javadocs, made minor changes to the comments

13 files changed, 190 insertions, 65 deletions

diff --git a/src/jcgp/gui/GUI.java b/src/jcgp/gui/GUI.java
index cd4778f..437a739 100644
--- a/src/jcgp/gui/GUI.java
+++ b/src/jcgp/gui/GUI.java
@@ -257,4 +257,8 @@ public class GUI extends Application {
 	public void flushConsole() {
 		console.flush();
 	}
+
+	public int getChromosomeIndex() {
+		return populationPane.getSelectionModel().getSelectedIndex();
+	}
 }
diff --git a/src/jcgp/gui/console/GUIConsole.java b/src/jcgp/gui/console/GUIConsole.java
index de4b378..b3d037c 100644
--- a/src/jcgp/gui/console/GUIConsole.java
+++ b/src/jcgp/gui/console/GUIConsole.java
@@ -15,12 +15,25 @@ import javafx.scene.layout.AnchorPane;
 import jcgp.backend.resources.Console;
 import jcgp.gui.GUI;
 
+/**
+ * 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 GUIConsole 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 GUIConsole() {
 		super();
 		textArea.setEditable(false);
@@ -31,7 +44,10 @@ public class GUIConsole extends AnchorPane implements Console {
 		 * 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.
+		 * 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() {
@@ -76,6 +92,7 @@ public class GUIConsole extends AnchorPane implements Console {
 												new SeparatorMenuItem(),
 												clearConsole));
 		
+		// anchor the text area so it resizes automatically
 		AnchorPane.setTopAnchor(textArea, GUI.RESIZE_MARGIN);
 		AnchorPane.setBottomAnchor(textArea, 0.0);
 		AnchorPane.setRightAnchor(textArea, 0.0);
diff --git a/src/jcgp/gui/dragresize/HorizontalDragResize.java b/src/jcgp/gui/dragresize/HorizontalDragResize.java
index 84c322f..b618b74 100644
--- a/src/jcgp/gui/dragresize/HorizontalDragResize.java
+++ b/src/jcgp/gui/dragresize/HorizontalDragResize.java
@@ -7,9 +7,11 @@ import javafx.scene.layout.Region;
 import jcgp.gui.GUI;
 
 /**
- * 
- * Decorator pattern.
- * 
+ * 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
  * 
  */
@@ -18,13 +20,29 @@ 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) {
@@ -52,12 +70,22 @@ public class HorizontalDragResize {
 		
 	}
 	
+	/**
+	 * 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();
@@ -69,20 +97,33 @@ public class HorizontalDragResize {
 		}
 	}
 	
+	/**
+	 * 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 {
+		} 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() < (GUI.RESIZE_MARGIN);
 	}
diff --git a/src/jcgp/gui/dragresize/VerticalDragResize.java b/src/jcgp/gui/dragresize/VerticalDragResize.java
index 9397e5d..06186c6 100644
--- a/src/jcgp/gui/dragresize/VerticalDragResize.java
+++ b/src/jcgp/gui/dragresize/VerticalDragResize.java
@@ -7,7 +7,11 @@ import javafx.scene.layout.Region;
 import jcgp.gui.GUI;
 
 /**
- * 
+ * 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
  * 
  */
@@ -16,13 +20,29 @@ 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) {
@@ -50,12 +70,22 @@ public class VerticalDragResize {
 		
 	}
 	
+	/**
+	 * 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();
@@ -67,6 +97,11 @@ public class VerticalDragResize {
 		}
 	}
 	
+	/**
+	 * 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);
@@ -76,11 +111,20 @@ public class VerticalDragResize {
         }
 	}
 
+	/**
+	 * 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() < (GUI.RESIZE_MARGIN);
 	}
diff --git a/src/jcgp/gui/population/ChromosomePane.java b/src/jcgp/gui/population/ChromosomePane.java
index 4a47f34..d40de2e 100644
--- a/src/jcgp/gui/population/ChromosomePane.java
+++ b/src/jcgp/gui/population/ChromosomePane.java
@@ -25,6 +25,8 @@ public class ChromosomePane extends ScrollPane {
 	
 	private int rows, columns;
 	
+	private Object[] testInputs;
+	
 	private boolean target = false;
 	private PopulationPane parent;
 	
@@ -111,20 +113,21 @@ public class ChromosomePane extends ScrollPane {
 		target = newValue;
 	}
 	
-	public void updateGenes() {
+	public void updateGenes(Chromosome chr) {
 		for (int r = 0; r < rows; r++) {
 			for (int c = 0; c < columns; c++) {
+				guiNodes[r][c].setNode(chr.getNode(r, c));
 				guiNodes[r][c].updateLines();
 				guiNodes[r][c].updateText();
 			}
 		}
 		for (int i = 0; i < guiOutputs.length; i++) {
+			guiOutputs[i].setOutput(chr.getOutput(i));
 			guiOutputs[i].updateLines();
 		}
 		if (isEvaluating()) {
-			evaluate(0);
+			setInputs(testInputs);
 		}
-		
 	}
 	
 	public void unlockOutputs() {
@@ -144,29 +147,27 @@ public class ChromosomePane extends ScrollPane {
 	}
 	
 	public void setInputs(Object[] values) {
+		testInputs = values;
 		for (int i = 0; i < guiInputs.length; i++) {
 			guiInputs[i].setValue(values[i]);
-			guiInputs[i].updateText();
 		}
-		evaluate(0);
+		updateValues();
 	}
 
-	public void evaluate(int start) {
-		if (start >= 0 || start < columns) {
-			for (int c = start; c < columns; c++) {
-				for (int r = 0; r < rows; r++) {
-					guiNodes[r][c].calculate();
-					guiNodes[r][c].updateText();
-				}
-			}
-			for (int o = 0; o < guiOutputs.length; o++) {
-				guiOutputs[o].calculate();
-				guiOutputs[o].updateText();
-			}
-		}
-	}
+//	public void evaluate(int start) {
+//		if (start >= 0 || start < columns) {
+//			for (int c = 0; c < columns; c++) {
+//				for (int r = 0; r < rows; r++) {
+//					guiNodes[r][c].updateText();
+//				}
+//			}
+//			for (int o = 0; o < guiOutputs.length; o++) {
+//				guiOutputs[o].updateText();
+//			}
+//		}
+//	}
 	
-	public void hideValues() {
+	public void updateValues() {
 		for (int i = 0; i < guiInputs.length; i++) {
 			guiInputs[i].updateText();
 		}
diff --git a/src/jcgp/gui/population/GUIGene.java b/src/jcgp/gui/population/GUIGene.java
index 3ace150..0eea045 100644
--- a/src/jcgp/gui/population/GUIGene.java
+++ b/src/jcgp/gui/population/GUIGene.java
@@ -39,8 +39,6 @@ public abstract class GUIGene extends Group {
 	protected ChromosomePane parent;
 	
 	protected int locked = 0;
-	
-	protected Object value;
 
 	public GUIGene() {
 		text.setFont(Font.font("Arial", 12));
@@ -92,9 +90,5 @@ public abstract class GUIGene extends Group {
 	
 	public abstract void setConnectionLine(GUIGene gene);
 	
-	public Object getValue() {
-		return value;
-	}
-	
 	public abstract void updateText();
 }
diff --git a/src/jcgp/gui/population/GUIInput.java b/src/jcgp/gui/population/GUIInput.java
index 05372c4..fd66ab4 100644
--- a/src/jcgp/gui/population/GUIInput.java
+++ b/src/jcgp/gui/population/GUIInput.java
@@ -219,14 +219,13 @@ public class GUIInput extends GUIGene {
 	}
 
 	public void setValue(Object newValue) {
-		value = newValue;
 		input.setValue(newValue);
 	}
 
 	@Override
 	public void updateText() {
 		if (parent.isEvaluating()) {
-			text.setText("I: " + input.getIndex() + "\n" + value.toString());
+			text.setText("I: " + input.getIndex() + "\n" + input.getValue().toString());
 		} else {
 			text.setText("I: " + input.getIndex());
 		}
diff --git a/src/jcgp/gui/population/GUINode.java b/src/jcgp/gui/population/GUINode.java
index 6dfeaa4..d3ae27f 100644
--- a/src/jcgp/gui/population/GUINode.java
+++ b/src/jcgp/gui/population/GUINode.java
@@ -398,7 +398,8 @@ public class GUINode extends GUIGene {
 	public void setChangingConnection(Connection newConnection) {
 		node.setConnection(connectionIndex, newConnection);
 		if (parent.isEvaluating()) {
-			parent.evaluate(node.getColumn());
+			parent.updateValues();
+//			parent.evaluate(node.getColumn());
 		}
 	}
 
@@ -452,24 +453,23 @@ public class GUINode extends GUIGene {
 
 	public void updateText() {
 		if (parent.isEvaluating()) {
-			text.setText(node.getFunction() + "\n" + value.toString());
+			text.setText(node.getFunction() + "\n" + node.getValue().toString());
 		} else {
 			text.setText(node.getFunction().toString());
 		}
 	}
-
-	public void calculate() {
-		value = node.getValue();
-	}
 	
 	public void setFunction(Function function) {
 		node.setFunction(function);
 		if (parent.isEvaluating()) {
-			calculate();
-			parent.evaluate(node.getColumn());
+//			parent.evaluate(node.getColumn());
+			parent.updateValues();
 		} else {
 			updateText();
 		}
-		
+	}
+
+	public void setNode(Node newNode) {
+		node = newNode;
 	}
 }
diff --git a/src/jcgp/gui/population/GUIOutput.java b/src/jcgp/gui/population/GUIOutput.java
index 29752cd..5a76298 100644
--- a/src/jcgp/gui/population/GUIOutput.java
+++ b/src/jcgp/gui/population/GUIOutput.java
@@ -267,10 +267,7 @@ public class GUIOutput extends GUIGene {
 	@Override
 	public void setChangingConnection(Connection newConnection) {
 		output.setConnection(0, newConnection);	
-		if (parent.isEvaluating()) {
-			calculate();
-			updateText();
-		}
+		updateText();
 	}
 
 	@Override
@@ -308,19 +305,19 @@ public class GUIOutput extends GUIGene {
 			setLocked(true);
 		}
 	}
-	
-	public void calculate() {
-		value = output.getSource().getValue();
-	}
 
 	@Override
 	public void updateText() {
 		if (parent.isEvaluating()) {
-			text.setText("O: " + output.getIndex() + "\n" + value.toString());
+			text.setText("O: " + output.getIndex() + "\n" + output.getSource().getValue().toString());
 		} else {
 			text.setText("O: " + output.getIndex());
 		}
 		
 	}
 
+	public void setOutput(Output newOutput) {
+		output = newOutput;
+	}
+
 }
diff --git a/src/jcgp/gui/population/PopulationPane.java b/src/jcgp/gui/population/PopulationPane.java
index 5fa6067..4b1b7f8 100644
--- a/src/jcgp/gui/population/PopulationPane.java
+++ b/src/jcgp/gui/population/PopulationPane.java
@@ -27,7 +27,7 @@ public class PopulationPane extends TabPane {
 		Tab tab;
 		ChromosomePane cp;
 		for (int i = 0; i < jcgp.getResources().populationSize(); i++) {
-			cp = new ChromosomePane(jcgp.getPopulation().getChromosome(i), gui, this);
+			cp = new ChromosomePane(jcgp.getPopulation().get(i), gui, this);
 			tab = new Tab("Chr " + i);
 			tab.setContent(cp);
 			getTabs().add(tab);
@@ -39,7 +39,7 @@ public class PopulationPane extends TabPane {
 			evaluateTestCase(currentTestCase);
 		}
 		for (int i = 0; i < getTabs().size(); i++) {
-			((ChromosomePane) getTabs().get(i).getContent()).updateGenes();
+			((ChromosomePane) getTabs().get(i).getContent()).updateGenes(gui.getExperiment().getPopulation().get(i));
 		}
 	}
 	
@@ -73,7 +73,7 @@ public class PopulationPane extends TabPane {
 	public void hideValues() {
 		evaluating = false;
 		for (int i = 0; i < getTabs().size(); i++) {
-			((ChromosomePane) getTabs().get(i).getContent()).hideValues();
+			((ChromosomePane) getTabs().get(i).getContent()).updateValues();
 		}
 	}
 
diff --git a/src/jcgp/gui/settings/SettingsPane.java b/src/jcgp/gui/settings/SettingsPane.java
index 802c1f1..2898dc3 100644
--- a/src/jcgp/gui/settings/SettingsPane.java
+++ b/src/jcgp/gui/settings/SettingsPane.java
@@ -255,7 +255,7 @@ public class SettingsPane extends AnchorPane {
 	}
 
 	private Button makeTestCaseButton() {
-		Button b = new Button("Show data1");
+		Button b = new Button("Show data");
 		b.setOnAction(new EventHandler<ActionEvent>() {
 			@Override
 			public void handle(ActionEvent event) {
@@ -331,7 +331,7 @@ public class SettingsPane extends AnchorPane {
 				fc.getExtensionFilters().add(new ExtensionFilter("All files", "*.*"));
 				File chrFile = fc.showOpenDialog(gui.getStage());
 				if (chrFile != null) {
-					gui.getExperiment().loadChromosome(chrFile, 0);
+					gui.getExperiment().loadChromosome(chrFile, gui.getChromosomeIndex());
 					gui.reDraw();
 				}
 				gui.flushConsole();
@@ -346,7 +346,7 @@ public class SettingsPane extends AnchorPane {
 				fc.getExtensionFilters().add(new ExtensionFilter("All files", "*.*"));
 				File chrFile = fc.showSaveDialog(gui.getStage());
 				if (chrFile != null) {
-					gui.getExperiment().saveChromosome(chrFile, 0);
+					gui.getExperiment().saveChromosome(chrFile, gui.getChromosomeIndex());
 				}
 				gui.flushConsole();
 			}
@@ -474,6 +474,9 @@ public class SettingsPane extends AnchorPane {
 			parameter.applyValue();
 		}
 		updateArity();
+		if (testCaseTable != null) {
+			testCaseTable.close();
+		}
 	}
 
 	/**
diff --git a/src/jcgp/gui/settings/parameters/GUIParameter.java b/src/jcgp/gui/settings/parameters/GUIParameter.java
index 3009340..f896fa3 100644
--- a/src/jcgp/gui/settings/parameters/GUIParameter.java
+++ b/src/jcgp/gui/settings/parameters/GUIParameter.java
@@ -23,7 +23,7 @@ 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>
- * @code{GUIParameter} is an @code{HBox} containing a @code{Text} for the parameter name 
+ * 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.
diff --git a/src/jcgp/gui/settings/testcase/TestCaseTable.java b/src/jcgp/gui/settings/testcase/TestCaseTable.java
index d4c1ff9..d4f789c 100644
--- a/src/jcgp/gui/settings/testcase/TestCaseTable.java
+++ b/src/jcgp/gui/settings/testcase/TestCaseTable.java
@@ -20,7 +20,10 @@ 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
  *
@@ -29,17 +32,27 @@ 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);
@@ -48,13 +61,16 @@ public class TestCaseTable extends Stage {
 			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().getInput(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);
@@ -62,37 +78,46 @@ public class TestCaseTable extends Stage {
 			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().getOutput(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) {
+			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().select(null);
+				table.getSelectionModel().clearSelection();
 			}
 		});
 		
 		setScene(new Scene(table));
 	}
 
+	/**
+	 * @return a reference to the actual table of test cases.
+	 */
 	public TableView<TestCase<Object>> getTable() {
 		return table;
 	}