added built-in check to the Cell data class to ensure initial values cannot be overridden by the user (even accidentally).

src/App.java

@@ -1,4 +1,5 @@
 // GUI imports
+import javax.swing.BoxLayout;
 import javax.swing.JFrame;
 import javax.swing.UIManager;
 import java.awt.BorderLayout;
@@ -18,6 +19,7 @@ public class App extends JFrame {
 
     // Data fields
     private Settings s;
+    private SudokuChecker sc;
 
     /**
      * Create a new App object, initializing the GUI and internal logic.
@@ -27,8 +29,12 @@ public class App extends JFrame {
         s = new Settings();
         initSetup();
         nav = new Nav(s, false);
-        board = new Board(s, nav.getLoadedGrid());
+        sc = new SudokuChecker(nav.getLoadedGrid());
+        board = new Board(s, nav.getLoadedGrid(), sc);
+
         nav.setBoard(board);
+        nav.setChecker(sc);
+
         add(createApp());
     }
 
@@ -69,6 +75,7 @@ public class App extends JFrame {
      */
     private Root createApp() {
         Root root = new Root(s);
+            root.setLayout(new BoxLayout(root, BoxLayout.Y_AXIS));
             root.add(nav);
             root.add(board);
 

src/gui/Board.java

@@ -4,9 +4,12 @@ import java.awt.GridLayout;
 import java.awt.LayoutManager;
 
 import javax.swing.JPanel;
+import javax.swing.border.LineBorder;
 import javax.swing.JLabel;
 
 import gui.backend.Settings;
+import gui.backend.SudokuChecker;
+import gui.backend.Theme;
 
 /**
  * The Board class represents the Sudoku board in the GUI.
@@ -22,6 +25,7 @@ import gui.backend.Settings;
 public class Board extends JPanel {
     private Settings s;
     private Cell[][] grid;
+    private SudokuChecker sc;
     private Cell selected;
 
     /**
@@ -29,10 +33,11 @@ public class Board extends JPanel {
      * 
      * @param s
      */
-    public Board(Settings s, Cell[][] grid) {
+    public Board(Settings s, Cell[][] grid, SudokuChecker sc) {
         super(new GridLayout(9, 9));
         this.s = s;
         this.grid = grid;
+        this.sc = sc;
         style();
         createBoard();
     }
@@ -65,13 +70,19 @@ public class Board extends JPanel {
      * Set up the Board Panel with the appropriate styling.
      */
     private void style() {
-        // TODO: Style the Board Panel.
+        setBackground(s.getTheme().getPrimaryBackground());
+        setForeground(s.getTheme().getPrimaryText());
     }
 
+    /**
+     * Create the Board Panel with the appropriate cells.
+     */
     private void createBoard() {
+        if(s.getAutoFillNotes()) grid = sc.getPossibleValues(grid);
+
         for(int i = 0; i < 9; i++) {
             for(int j = 0; j < 9; j++) {
-                CellGUI cell = new CellGUI(grid[i][j], s.getCellGUIStartMode());
+                CellGUI cell = new CellGUI(grid[i][j], s.getCellGUIStartMode() || s.getAutoFillNotes(), s.getTheme());
                 add(cell);
             }
         }
@@ -81,14 +92,15 @@ public class Board extends JPanel {
      * GUI representation of a single cell in the Sudoku grid.
      */
     private class CellGUI extends JPanel {
-        private static GridLayout noteLayout = new GridLayout(3, 3);
-        private static GridLayout valueLayout = new GridLayout(1, 1);
+        private GridLayout noteLayout = new GridLayout(3, 3);
+        private GridLayout valueLayout = new GridLayout(1, 1);
+        private Theme theme;
 
         private Cell cell;
         private JLabel valueLabel;
-        private JLabel[] notesLabels;
+        private Note[] notesLabels = new Note[9];
         private boolean notes; // true for notes, false for value
-        private boolean startInNotesOrValueMode;
+        private boolean cellGUIStartMode;
 
         /**
          * Create a new CellGUI object with the given single cell.
@@ -98,24 +110,18 @@ public class Board extends JPanel {
          * @param cell
          * @param startInNotesOrValueMode
          */
-        public CellGUI(Cell cell, boolean startInNotesOrValueMode) {
+        public CellGUI(Cell cell, boolean notes, Theme theme) {
             super();
             this.cell = cell;
-            this.startInNotesOrValueMode = startInNotesOrValueMode;
+            this.notes = notes;
+            this.theme = theme;
+            style();
 
             // Populate the cell with the appropriate value or notes.
             if(cell.getValue() == 0) {
-                generateNotes();
-                
-                if(startInNotesOrValueMode) {
-                    setLayout(noteLayout);
-                    notes = true;
-                } else {
-                    setLayout(valueLayout);
-                    notes = false;
+                notes = !notes;
                 valueLabel = new JLabel("");
-                    add(valueLabel);
-                }
+                setNoteMode();
             } else {
                 valueLabel = new JLabel(Integer.toString(cell.getValue()));
                 add(valueLabel);
@@ -131,6 +137,25 @@ public class Board extends JPanel {
             return cell.getValue();
         }
 
+        /**
+         * Set the value of the underlying Cell object.
+         * 
+         * @param value
+         */
+        public void setValue(int value) {
+            cell.setValue(value);
+            valueLabel.setText(Integer.toString(value));
+        }
+
+        /**
+         * Set the possible values of the underlying Cell object.
+         * 
+         * @param value
+         */
+        public void setPossibleValues(int[] values) {
+            cell.setPossibleValues(values);
+        }
+
         /**
          * Add a possible value to the cell.
          * 
@@ -163,44 +188,54 @@ public class Board extends JPanel {
          * layout of the cell.
          */
         public void setNoteMode() {
-            if(notes) {
             removeAll();
+            if(notes) {
                 setLayout(valueLayout);
-                repaint();
-                revalidate();
 
                 add(valueLabel);
             } else {
-                removeAll();
                 setLayout(noteLayout);
-                repaint();
-                revalidate();
 
                 generateNotes();
+                for(int i = 0; i < 9; i++)
+                    add(notesLabels[i]);
             }
             
+            repaint();
+            revalidate();
             notes = !notes;
         }
 
+        /**
+         * Style the cell with the appropriate colors from the theme.
+         */
+        private void style() {
+            setBackground(theme.getPrimaryBackground());
+            setForeground(theme.getPrimaryText());
+            setBorder(new LineBorder(theme.getPrimaryBorder(), 2));
+        }
+
         /**
          * Create the GUI components for the cell.
          */
         private void generateNotes() {
             if(cell.getPossibleValues().length == 0) {
-                notesLabels = new JLabel[9];
+                for(int i = 0; i < 9; i++) {
+                    notesLabels[i] = new Note("", theme);
+                    add(notesLabels[i]);
+                }
                 return;
             }
 
+
             // Add the noted possible values to the cell.
-            int index = 0;
             for(int i = 1; i <= 9; i++) {
-                if(cell.getPossibleValues()[index] == i) {
-                    notesLabels[index] = new JLabel(Integer.toString(i));
-                    index++;
-                } else {
-                    notesLabels[index] = new JLabel("");
-                }
-                add(notesLabels[index]);
+                if(cell.getPossibleValues()[i - 1] == i)
+                    notesLabels[i - 1] = new Note(Integer.toString(i), theme);
+                else
+                    notesLabels[i - 1] = new Note("", theme);
+
+                add(notesLabels[i - 1]);
             }
         }
     }

src/gui/Cell.java

@@ -11,6 +11,8 @@ public class Cell {
     private int col;
     private int box;
     private int value;
+    private boolean initValue;
+
     private List possibleValues;
     
     /**
@@ -41,6 +43,8 @@ public class Cell {
         this.row = row;
         this.col = col;
         this.value = value;
+        initValue = value != 0;
+
         setBox();
         possibleValues = new List();
     }
@@ -69,6 +73,8 @@ public class Cell {
      * @param value
      */
     public void setValue(int value) {
+        if(initValue) return;
+
         possibleValues.clear();
         this.value = value;
     }
@@ -99,6 +105,8 @@ public class Cell {
      * @param value
      */
     public void addPossibleValue(int value) {
+        if(initValue) return;
+
         if(possibleValues.contains(value)) {
             return;
         } else if(value < 1 || value > 9) {
@@ -114,6 +122,8 @@ public class Cell {
      * @param possibleValues
      */
     public void setPossibleValues(int[] possibleValues) {
+        if(initValue) return;
+
         this.possibleValues = new List(possibleValues);
     }
 

src/gui/Nav.java

@@ -6,6 +6,7 @@ import java.io.FileNotFoundException;
 import javax.swing.JPanel;
 
 import gui.backend.Settings;
+import gui.backend.SudokuChecker;
 
 import javax.swing.JLabel;
 import javax.swing.JButton;
@@ -26,6 +27,7 @@ import javax.swing.JButton;
  */
 public class Nav extends JPanel {
     private Settings s;
+    private SudokuChecker sc;
     private File f;
     private Board b;
     private Cell[][] grid;
@@ -111,6 +113,22 @@ public class Nav extends JPanel {
         this.b = b;
     }
 
+    /**
+     * Set the SudokuChecker object for the Nav bar.
+     * 
+     * This is necessary for the Nav bar to be able to interact with the
+     * SudokuChecker object for the solve button. This shouldn't be necessary
+     * to change once the program is running.
+     */
+    public void setChecker(SudokuChecker sc) {
+        this.sc = sc;
+    }
+
+    private void style() {
+        setBackground(s.getTheme().getPrimaryBackground());
+        setForeground(s.getTheme().getPrimaryText());
+    }
+
     /**
      * Create the GUI for the Nav bar.
      * 
@@ -119,6 +137,7 @@ public class Nav extends JPanel {
      * debugging purposes.
      */
     private void createGUI() {
+        style();
         JLabel elapsedTime = new JLabel("Elapsed Time: 00:00:00");
             elapsedTime.setFont(s.getFont()); // TODO: Make custom Label class.
         JButton solve = new JButton("Solve");

src/gui/Note.java

@@ -0,0 +1,35 @@
+package gui;
+
+import javax.swing.JLabel;
+
+import gui.backend.Theme;
+
+/**
+ * The Note class represents a single note of a cell in the Sudoku board.
+ * 
+ * This is the GUI abstraction for the underlying Cell object, and is used to
+ * display and manage the note for a cell.
+ */
+public class Note extends JLabel {
+    private Theme t;
+    
+    /**
+     * Create a new Note object with the given text and theme.
+     * 
+     * @param text
+     * @param t
+     */
+    public Note(String text, Theme t) {
+        super(text);
+        this.t = t;
+        style();
+    }
+
+    /**
+     * Style the Note component with the current theme.
+     */
+    private void style() {
+        setBackground(t.getPrimaryBackground());
+        setForeground(t.getPrimaryText());
+    }
+}

src/gui/Root.java

@@ -1,5 +1,6 @@
 package gui;
 
+import java.awt.LayoutManager;
 import javax.swing.JPanel;
 
 import gui.backend.Settings;

src/gui/backend/Settings.java

@@ -50,6 +50,12 @@ public class Settings {
     // Default open state for the application.
     private int defaultOpenState;
 
+    // Theme object storing the colors for the GUI components.
+    private Theme theme;
+
+    // Auto-fill notes
+    private boolean autoFillNotes;
+
     /**
      * Create a new Settings object, initializing the default settings
      * or reading in the settings from settings file if it exists.
@@ -244,6 +250,65 @@ public class Settings {
         updateSettingsFile();
     }
 
+    /**
+     * The Theme object stores the colors for the GUI components.
+     * 
+     * The available colors for customization are:
+     *      - primaryBackground
+     *      - secondaryBackground
+     *      - primaryText
+     *      - secondaryText
+     *      - primaryHighlight
+     *      - secondaryHighlight
+     *      - primaryBorder
+     *      - secondaryBorder
+     *      - primaryButton
+     *      - secondaryButton
+     *      - primaryButtonHighlight
+     *      - secondaryButtonHighlight
+     *      - primaryButtonBorder
+     *      - secondaryButtonBorder
+     *
+     * @see Theme
+     * @return
+     */
+    public Theme getTheme() {
+        return theme;
+    }
+
+    /**
+     * Set the theme and write it to the settings file.
+     * 
+     * @param theme
+     */
+    public void setTheme(Theme theme) {
+        this.theme = theme;
+        updateSettingsFile();
+    }
+
+    /**
+     * The Auto-fill notes setting is a configurable setting, where the user
+     * can specify whether notes should be automatically filled in when a
+     * value is placed in a cell.
+     * 
+     * By default, the auto-fill notes setting is set to false.
+     * 
+     * @return boolean
+     */
+    public boolean getAutoFillNotes() {
+        return autoFillNotes;
+    }
+
+    /**
+     * Set the auto-fill notes setting and write it to the settings file.
+     * 
+     * @param autoFillNotes
+     */
+    public void setAutoFillNotes(boolean autoFillNotes) {
+        this.autoFillNotes = autoFillNotes;
+        updateSettingsFile();
+    }
+
     /**
      * Open and write the settings to the settings file.
      * 
@@ -279,6 +344,8 @@ public class Settings {
         resizable = false;
         cellGUIStartMode = false;
         defaultOpenState = 0;
+        theme = new Theme(new File(appDirectory + "default.theme"));
+        autoFillNotes = true;
 
         updateSettingsFile();
     }

src/gui/backend/SudokuChecker.java

@@ -28,7 +28,44 @@ public class SudokuChecker {
      */
     public SudokuChecker(Cell[][] grid) {
         this.grid = grid;
-        solve();
+    }
+
+    /**
+     * Get the possible values for each cell in the Sudoku puzzle.
+     * 
+     * Intended to be used for auto-filling in possible values in the GUI.
+     * 
+     * @return
+     */
+    public Cell[][] getPossibleValues(Cell[][] grid) {
+        for(int row = 0; row < grid.length; row++) {
+            for(int col = 0; col < grid[row].length; col++) {
+                if(grid[row][col].getValue() == 0)
+                    continue;
+
+                ArrayList<Integer> intersection = intersection(
+                    getRowRemainingNumbers(row),
+                    getColRemainingNumbers(col)
+                );
+
+                intersection = intersection(
+                    intersection,
+                    getBoxRemainingNumbers(row, col)
+                );
+
+                // Join the arrays and find the intersection of the three arrays
+                ArrayList<Integer> availableNumbers = new ArrayList<Integer>();
+                for(int i = 0; i < intersection.size(); i++) {
+                    availableNumbers.add(intersection.get(i));
+                }
+
+                grid[row][col].setPossibleValues(
+                    arrayListToArray(availableNumbers)
+                );
+            }
+        }
+
+        return grid;
     }
 
     /**
@@ -37,6 +74,7 @@ public class SudokuChecker {
      * @return Cell[][]
      */
     public Cell[][] getSolution() {
+        solve();
         return grid;
     }
 

src/gui/backend/Theme.java

@@ -71,10 +71,11 @@ public class Theme {
      * Sets the theme for the GUI components.
      */
     private void setTheme() {
-        primaryBackground = Color.WHITE;
+        primaryBackground = Color.LIGHT_GRAY;
         secondaryBackground = Color.LIGHT_GRAY;
-        primaryText = Color.BLACK;
+        primaryText = Color.DARK_GRAY;
         secondaryText = Color.DARK_GRAY;
+        primaryBorder = Color.BLACK;
     }
 
     /**