Final commit, will release later today.

10 files changed, 33 insertions, 18 deletions

diff --git a/src/jcgp/backend/function/Function.java b/src/jcgp/backend/function/Function.java
index f277228..3124e66 100644
--- a/src/jcgp/backend/function/Function.java
+++ b/src/jcgp/backend/function/Function.java
@@ -14,7 +14,7 @@ public abstract class Function {
 	/**
 	 * Executes the function.
 	 * 
-	 * @param args the function arguments.
+	 * @param arguments the function arguments.
 	 * @return the function result.
 	 */
 	public abstract Object run(Object... arguments);
diff --git a/src/jcgp/backend/modules/Module.java b/src/jcgp/backend/modules/Module.java
index a4d36c1..5dea93e 100644
--- a/src/jcgp/backend/modules/Module.java
+++ b/src/jcgp/backend/modules/Module.java
@@ -48,7 +48,7 @@ public abstract class Module {
 	 * 
 	 * @return a list of generic parameters exposed by the module.
 	 */
-	public final ArrayList<Parameter<?>> getLocalParameters() {
+	public ArrayList<Parameter<?>> getLocalParameters() {
 		return localParameters;
 	}
 	
@@ -62,7 +62,7 @@ public abstract class Module {
 	 * 
 	 * @param newParameters the parameter(s) to add to the list.
 	 */
-	protected final void registerParameters(Parameter<?>... newParameters) {
+	protected void registerParameters(Parameter<?>... newParameters) {
 		for (int i = 0; i < newParameters.length; i++) {
 			if (!localParameters.contains(newParameters[i])) {
 				localParameters.add(newParameters[i]);
diff --git a/src/jcgp/backend/modules/mutator/PointMutator.java b/src/jcgp/backend/modules/mutator/PointMutator.java
index 6ba3e10..dd7aa7b 100644
--- a/src/jcgp/backend/modules/mutator/PointMutator.java
+++ b/src/jcgp/backend/modules/mutator/PointMutator.java
@@ -41,7 +41,7 @@ public abstract class PointMutator extends Mutator {
 			// choose a random mutable
 			Mutable mutable = chromosome.getRandomMutable();
 			
-			if (report.get()) getResources().report("[Mutator] Mutation " + i + " selected " + mutable);
+			if (report.get()) getResources().reportln("[Mutator] Mutation " + i + " selected " + mutable);
 			
 			// mutate a random gene
 			mutable.mutate();
diff --git a/src/jcgp/backend/modules/problem/Problem.java b/src/jcgp/backend/modules/problem/Problem.java
index 6785733..453e3a1 100644
--- a/src/jcgp/backend/modules/problem/Problem.java
+++ b/src/jcgp/backend/modules/problem/Problem.java
@@ -48,7 +48,7 @@ public abstract class Problem extends Module {
 	 *
 	 * @param resources a reference to the experiment's resources.
 	 */
-	public Problem(Resources resources) {
+	protected Problem(Resources resources) {
 		super(resources);
 		
 		maxFitness = new DoubleMonitor(0, "Max fitness");
@@ -72,7 +72,6 @@ public abstract class Problem extends Module {
 	 * if a GUI is in use.
 	 * 
 	 * @param population the population to be evaluated.
-	 * @param resources parameters and utilities for optional reference.
 	 */
 	public abstract void evaluate(Population population);
 	
diff --git a/src/jcgp/backend/modules/problem/TestCaseProblem.java b/src/jcgp/backend/modules/problem/TestCaseProblem.java
index 964860c..82eb91a 100644
--- a/src/jcgp/backend/modules/problem/TestCaseProblem.java
+++ b/src/jcgp/backend/modules/problem/TestCaseProblem.java
@@ -71,7 +71,7 @@ public abstract class TestCaseProblem<T> extends Problem {
 	 * 
 	 * @param resources a reference to the experiment's resources.
 	 */
-	public TestCaseProblem(Resources resources) {
+	protected TestCaseProblem(Resources resources) {
 		super(resources);
 		testCases = FXCollections.observableArrayList();
 	}
diff --git a/src/jcgp/backend/resources/ModifiableResources.java b/src/jcgp/backend/resources/ModifiableResources.java
index 2b0c039..0588c05 100644
--- a/src/jcgp/backend/resources/ModifiableResources.java
+++ b/src/jcgp/backend/resources/ModifiableResources.java
@@ -304,7 +304,7 @@ public class ModifiableResources extends Resources {
 				if (newValue.intValue() <= 0) {
 					status = ParameterStatus.INVALID;
 					status.setDetails("Levels back must be at least 1.");
-				} else if (newValue.intValue() > columns.get()) {
+				} else if (newValue.intValue() > columns()) {
 					status = ParameterStatus.INVALID;
 					status.setDetails("Levels back must be less than or equal to the number of columns.");
 				} else {
diff --git a/src/jcgp/gui/console/ConsolePane.java b/src/jcgp/gui/console/ConsolePane.java
index c4cfc21..1e07b7d 100644
--- a/src/jcgp/gui/console/ConsolePane.java
+++ b/src/jcgp/gui/console/ConsolePane.java
@@ -37,7 +37,6 @@ public class ConsolePane extends AnchorPane implements Console {
 	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.
diff --git a/src/jcgp/gui/population/ChromosomePane.java b/src/jcgp/gui/population/ChromosomePane.java
index d9154fc..1e04c37 100644
--- a/src/jcgp/gui/population/ChromosomePane.java
+++ b/src/jcgp/gui/population/ChromosomePane.java
@@ -12,6 +12,15 @@ import jcgp.backend.population.Node;
 import jcgp.backend.resources.Resources;
 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 overlaid over the nodes, inputs and outputs.
+ * 
+ * 
+ * @author Eduardo Pedroni
+ *
+ */
 public class ChromosomePane extends ScrollPane {
 
 	private GUINode[][] guiNodes;
@@ -169,7 +178,7 @@ public class ChromosomePane extends ScrollPane {
 	}
 
 	/**
-	 * @return the evaluating
+	 * @return the evaluating attribute.
 	 */
 	public boolean isEvaluating() {
 		return parent.isEvaluating();
diff --git a/src/jcgp/gui/population/FunctionSelector.java b/src/jcgp/gui/population/FunctionSelector.java
index 69d0d31..0e6c6bb 100644
--- a/src/jcgp/gui/population/FunctionSelector.java
+++ b/src/jcgp/gui/population/FunctionSelector.java
@@ -7,6 +7,14 @@ import javafx.scene.layout.VBox;
 import jcgp.backend.function.FunctionSet;
 import jcgp.gui.GUI;
 
+/**
+ * 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;
diff --git a/src/jcgp/gui/settings/SettingsPane.java b/src/jcgp/gui/settings/SettingsPane.java
index c0939e9..c59244b 100644
--- a/src/jcgp/gui/settings/SettingsPane.java
+++ b/src/jcgp/gui/settings/SettingsPane.java
@@ -157,25 +157,25 @@ public class SettingsPane extends AnchorPane {
 		header.setFont(Font.font("Arial", 14));
 		header.setUnderline(true);
 		
-		final ComboBox<EvolutionaryStrategy> eaCBox = new ComboBox<EvolutionaryStrategy>();
-		eaCBox.getItems().addAll(jcgp.getEvolutionaryStrategies());
-		eaCBox.getSelectionModel().select(jcgp.getEvolutionaryStrategy());
-		eaCBox.prefWidthProperty().bind(mainContainer.widthProperty());
+		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);
 		
-		eaCBox.setOnAction(new EventHandler<ActionEvent>() {
+		esCBox.setOnAction(new EventHandler<ActionEvent>() {
 			@Override
 			public void handle(ActionEvent event) {
-				jcgp.setEvolutionaryStrategy(eaCBox.getSelectionModel().getSelectedIndex());
-				refreshParameters(eaCBox.getSelectionModel().getSelectedItem().getLocalParameters(), eaParameters);
+				jcgp.setEvolutionaryStrategy(esCBox.getSelectionModel().getSelectedIndex());
+				refreshParameters(esCBox.getSelectionModel().getSelectedItem().getLocalParameters(), eaParameters);
 				gui.flushConsole();
 			}
 		});
 		
-		eaPane.getChildren().addAll(header, eaCBox, eaParameters);	
+		eaPane.getChildren().addAll(header, esCBox, eaParameters);	
 		mainContainer.getChildren().add(eaPane);
 	}