protegeproject · vChavezB · Oct 3, 2025
diff --git a/protege-editor-core/src/main/java/org/protege/editor/core/ProtegeApplication.java b/protege-editor-core/src/main/java/org/protege/editor/core/ProtegeApplication.java
@@ -320,13 +320,8 @@ private void initializeLookAndFeel() {
                 // Force the Look & Feel to be instantiated.
                 UIDefaults defaults = UIManager.getDefaults();
                 if (lafClsName.equals(PlasticLookAndFeel.class.getName())) {
-                    // Truly strange.  If we don't do this then the LAF cannot be found.
-                    PlasticLookAndFeel.setCurrentTheme(new ProtegePlasticTheme());
-                    UIManager.put("ClassLoader", PlasticLookAndFeel.class.getClassLoader());
-                    // For plastic this needs to be instantiated here - otherwise SwingUtilities uses the wrong class
-                    // loaded.
-                    LookAndFeel lookAndFeel = (LookAndFeel) Class.forName(lafClsName).newInstance();
-                    UIManager.setLookAndFeel(lookAndFeel);
+                    // Use ThemeManager to apply the correct theme (light or dark)
+                    org.protege.editor.core.ui.util.ThemeManager.loadTheme();
                 }
                 else {
                     // Now set the class loader for Component UI loading to this one.  Works for non Plastic LAFs.

diff --git a/...ege-editor-core/src/main/java/org/protege/editor/core/log/TextForegroundPreviewPanel.java b/...ege-editor-core/src/main/java/org/protege/editor/core/log/TextForegroundPreviewPanel.java
@@ -29,7 +29,11 @@ public class TextForegroundPreviewPanel extends JPanel
 	public TextForegroundPreviewPanel(JColorChooser chooser) {
 		chooser.getSelectionModel().addChangeListener(this);
 		setForeground(color);
-		setBackground(Color.WHITE);
+		Color panelBg = javax.swing.UIManager.getColor("Panel.background");
+		if (panelBg == null) {
+			panelBg = Color.WHITE;
+		}
+		setBackground(panelBg);
 		setOpaque(true);
 		setFont(new Font("monospaced", Font.PLAIN, 12));
 		text.setBorder(BorderFactory.createEmptyBorder(10, 10, 10, 10));

diff --git a/protege-editor-core/src/main/java/org/protege/editor/core/ui/list/MList.java b/protege-editor-core/src/main/java/org/protege/editor/core/ui/list/MList.java
@@ -33,8 +33,39 @@ public class MList extends JList {
 
     private Font sectionHeaderFont = new Font("Lucida Grande", Font.PLAIN, 10);
 
-    private static final Color itemBackgroundColor = Color.WHITE;
+    private static final Color DEFAULT_LIST_DIVIDER_COLOR = new Color(240, 240, 240);
 
+    private Color getListBackgroundColor() {
+        Color bg = getBackground();
+        if (bg == null) {
+            bg = UIManager.getColor("MList.background");
+        }
+        if (bg == null) {
+            bg = UIManager.getColor("List.background");
+        }
+        if (bg == null) {
+            bg = UIManager.getColor("Panel.background");
+        }
+        if (bg == null) {
+            bg = UIManager.getColor("control");
+        }
+        return bg != null ? bg : Color.WHITE;
+    }
+
+    private Color resolveBackground(Color candidate) {
+        return candidate != null ? candidate : getListBackgroundColor();
+    }
+
+    private Color getListDividerColor() {
+        Color divider = UIManager.getColor("Separator.foreground");
+        if (divider == null) {
+            divider = UIManager.getColor("controlShadow");
+        }
+        if (divider == null) {
+            divider = DEFAULT_LIST_DIVIDER_COLOR;
+        }
+        return divider;
+    }
 
     ////////////////////////////////////////////////////////////////////////////////////////////////////////////////////
 
@@ -266,7 +297,7 @@ protected List<MListButton> getListItemButtons(MListItem item) {
     }
 
     protected Color getItemBackgroundColor(MListItem item) {
-        return itemBackgroundColor;
+        return getListBackgroundColor();
     }
 
     public class MListCellRenderer implements ListCellRenderer {
@@ -336,7 +367,7 @@ protected Border createPaddingBorder(JList list, Object value, int index, boolea
                 bottomMargin = getRowHeightPadding(index);
             }
         }
-        return BorderFactory.createMatteBorder(0, 0, bottomMargin, 0, Color.WHITE);
+        return BorderFactory.createMatteBorder(0, 0, bottomMargin, 0, resolveBackground(list.getBackground()));
     }
 
     private int getRowHeightPadding(int index) {
@@ -349,8 +380,8 @@ private int getRowHeightPadding(int index) {
 
     protected Border createListItemBorder(JList list, Object value, int index, boolean isSelected, boolean cellHasFocus) {
         Border internalPadding = BorderFactory.createEmptyBorder(1, 1, 1, 1);
-        Border line = BorderFactory.createMatteBorder(0, 0, 1, 0, new Color(240, 240, 240));
-        Border externalBorder = BorderFactory.createMatteBorder(0, 20, 0, 0, list.getBackground());
+        Border line = BorderFactory.createMatteBorder(0, 0, 1, 0, getListDividerColor());
+        Border externalBorder = BorderFactory.createMatteBorder(0, 20, 0, 0, resolveBackground(list.getBackground()));
         return BorderFactory.createCompoundBorder(
                 externalBorder,
                 BorderFactory.createCompoundBorder(line, internalPadding)

diff --git a/...tor-core/src/main/java/org/protege/editor/core/ui/preferences/PreferencesDialogPanel.java b/...tor-core/src/main/java/org/protege/editor/core/ui/preferences/PreferencesDialogPanel.java
@@ -47,6 +47,8 @@ public class PreferencesDialogPanel extends JPanel implements Disposable {
     public PreferencesDialogPanel(EditorKit editorKit) {
     	this.editorKit = editorKit;
         setLayout(new BorderLayout());
+        setBackground(UIManager.getColor("Panel.background"));
+        setOpaque(true);
         add(tabbedPane);
         Dimension screenSize = Toolkit.getDefaultToolkit().getScreenSize();
         int margin = 300;
@@ -59,6 +61,8 @@ public PreferencesDialogPanel(EditorKit editorKit) {
     private void reload() {
     	dispose();
     	tabbedPane.removeAll();
+    	tabbedPane.setBackground(UIManager.getColor("Panel.background"));
+    	tabbedPane.setOpaque(true);
     	PreferencesPanelPluginLoader loader = new PreferencesPanelPluginLoader(editorKit);
         Set<PreferencesPanelPlugin> plugins = new TreeSet<>((o1, o2) -> {
                 String s1 = o1.getLabel();
@@ -73,6 +77,10 @@ private void reload() {
                 final String label = plugin.getLabel();
                 final JScrollPane sp = new JScrollPane(panel);
                 sp.setBorder(new EmptyBorder(0, 0, 0, 0));
+                sp.setBackground(UIManager.getColor("Panel.background"));
+                sp.setOpaque(true);
+                sp.getViewport().setBackground(UIManager.getColor("Panel.background"));
+                sp.getViewport().setOpaque(true);
                 map.put(label, panel);
                 componentMap.put(label, sp);
                 tabbedPane.addTab(label, sp);
@@ -130,6 +138,8 @@ public static void showPreferencesDialog(String selectedPanel, EditorKit editorK
         final PreferencesDialogPanel preferencesPanel = new PreferencesDialogPanel(editorKit);
 
         JPanel holder = new JPanel(new BorderLayout(4, 4));
+        holder.setBackground(UIManager.getColor("Panel.background"));
+        holder.setOpaque(true);
         holder.add(preferencesPanel);
 
         if (selectedPanel == null){
@@ -139,6 +149,8 @@ public static void showPreferencesDialog(String selectedPanel, EditorKit editorK
         preferencesPanel.setSelectedPanel(selectedPanel);
 
         JPanel resetPanel = new JPanel(new FlowLayout(FlowLayout.LEFT));
+        resetPanel.setBackground(UIManager.getColor("Panel.background"));
+        resetPanel.setOpaque(true);
         JButton resetPreferencesButton = new JButton(new AbstractAction("Reset preferences...") {
             public void actionPerformed(ActionEvent e) {
                 handleResetPreferences(preferencesPanel);
@@ -148,7 +160,14 @@ public void actionPerformed(ActionEvent e) {
         holder.add(resetPanel, BorderLayout.SOUTH);
 
         JOptionPane op = new JOptionPane(holder, JOptionPane.PLAIN_MESSAGE, JOptionPane.OK_CANCEL_OPTION);
+        op.setBackground(UIManager.getColor("Panel.background"));
+        op.setOpaque(true);
         JDialog dlg = op.createDialog(editorKit.getWorkspace(), "Preferences");
+        dlg.getContentPane().setBackground(UIManager.getColor("Panel.background"));
+
+        // Recursively set background colors on all components in the dialog
+        setBackgroundRecursive(dlg, UIManager.getColor("Panel.background"));
+
         dlg.setResizable(true);
         dlg.setVisible(true);
         Object o = op.getValue();
@@ -175,4 +194,30 @@ private static void handleResetPreferences(PreferencesDialogPanel panel) {
         panel.reload();
         panel.setSelectedPanel(selectedPanel);
     }
+
+    /**
+     * Recursively sets the background color on all components in a container.
+     * This ensures that all nested components use the correct theme background.
+     */
+    private static void setBackgroundRecursive(Container container, Color background) {
+        if (container == null || background == null) return;
+
+        // Set background on the container itself
+        container.setBackground(background);
+        if (container instanceof JComponent) {
+            ((JComponent) container).setOpaque(true);
+        }
+
+        // Recursively set background on all child components
+        for (Component component : container.getComponents()) {
+            if (component instanceof Container) {
+                setBackgroundRecursive((Container) component, background);
+            } else {
+                component.setBackground(background);
+                if (component instanceof JComponent) {
+                    ((JComponent) component).setOpaque(true);
+                }
+            }
+        }
+    }
 }
diff --git a/...tor-core/src/main/java/org/protege/editor/core/ui/preferences/PreferencesLayoutPanel.java b/...tor-core/src/main/java/org/protege/editor/core/ui/preferences/PreferencesLayoutPanel.java
@@ -25,7 +25,14 @@ public class PreferencesLayoutPanel extends JComponent {
     public PreferencesLayoutPanel() {
         setLayout(new BorderLayout());
         setBorder(BorderFactory.createEmptyBorder(12, 12, 12, 12));
+        Color panelBg = UIManager.getColor("Panel.background");
+        if (panelBg == null) {
+            panelBg = Color.WHITE;
+        }
+        setBackground(panelBg);
         backingPanel = new JPanel(new GridBagLayout());
+        backingPanel.setBackground(panelBg);
+        backingPanel.setOpaque(true);
         add(backingPanel, BorderLayout.NORTH);
     }
 
@@ -165,7 +172,11 @@ private void handleComponentAdded(JComponent component) {
     public void addHelpText(String helpText) {
         JLabel label = new JLabel(helpText);
         label.setFont(label.getFont().deriveFont(Font.PLAIN, 10f));
-        label.setForeground(Color.GRAY);
+        Color helpFg = UIManager.getColor("Label.disabledForeground");
+        if (helpFg == null) {
+            helpFg = Color.GRAY;
+        }
+        label.setForeground(helpFg);
         label.setBorder(BorderFactory.createEmptyBorder(3, 20, 7, 0));
         addGroupComponent(label);
 

diff --git a/...ge-editor-core/src/main/java/org/protege/editor/core/ui/preferences/PreferencesPanel.java b/...ge-editor-core/src/main/java/org/protege/editor/core/ui/preferences/PreferencesPanel.java
@@ -29,6 +29,12 @@ public void setup(String label, EditorKit editorKit) {
         this.editorKit = editorKit;
         setBorder(BorderFactory.createEmptyBorder(30, 20, 20, 20));
         setLayout(new PreferencesPanelLayoutManager(this));
+        Color panelBg = UIManager.getColor("Panel.background");
+        if (panelBg == null) {
+            panelBg = Color.WHITE;
+        }
+        setBackground(panelBg);
+        setOpaque(true);
     }
 
 

diff --git a/protege-editor-core/src/main/java/org/protege/editor/core/ui/util/ComponentFactory.java b/protege-editor-core/src/main/java/org/protege/editor/core/ui/util/ComponentFactory.java
@@ -34,7 +34,17 @@ public static JComponent createExceptionComponent(String message, Throwable exce
 
     public static JScrollPane createScrollPane(JComponent content) {
         JScrollPane sp = new JScrollPane(content);
-        sp.getViewport().setBackground(Color.WHITE);
+        Color background = content != null ? content.getBackground() : null;
+        if (background == null) {
+            background = UIManager.getColor("ScrollPane.background");
+        }
+        if (background == null) {
+            background = UIManager.getColor("Panel.background");
+        }
+        if (background == null) {
+            background = UIManager.getColor("control");
+        }
+        sp.getViewport().setBackground(background != null ? background : Color.WHITE);
         return sp;
     }
 

diff --git a/protege-editor-core/src/main/java/org/protege/editor/core/ui/util/LinkLabel.java b/protege-editor-core/src/main/java/org/protege/editor/core/ui/util/LinkLabel.java
@@ -22,44 +22,40 @@
 public class LinkLabel extends JLabel {
 
     private Color linkColor;
-
     private Color hoverColor;
-
     private Cursor oldCursor;
-
     private ActionListener linkListener;
+    private boolean hoverMode;
+    private boolean isClickable;
 
 
     public LinkLabel(String text, ActionListener linkListener) {
         super(text);
         this.linkListener = linkListener;
-        linkColor = Color.BLACK;
-        hoverColor = Color.BLUE;
-
-        setForeground(linkColor);
-
-        addMouseListener(new MouseAdapter() {
-            public void mouseEntered(MouseEvent e) {
-                setHoverMode(true);
-            }
-
-
-            public void mouseExited(MouseEvent e) {
-                setHoverMode(false);
-            }
-
-
-            public void mouseReleased(MouseEvent e) {
-                activateLink();
-            }
-        });
-
+        this.isClickable = linkListener != null;
+        updateColorsFromUI();
+        if (isClickable) {
+            addMouseListener(new MouseAdapter() {
+                public void mouseEntered(MouseEvent e) {
+                    setHoverMode(true);
+                }
+                public void mouseExited(MouseEvent e) {
+                    setHoverMode(false);
+                }
+                public void mouseReleased(MouseEvent e) {
+                    activateLink();
+                }
+            });
+        }
         setFont(Fonts.getMediumDialogFont().deriveFont(Font.BOLD, 14f));
     }
 
 
     public void setLinkColor(Color color) {
         linkColor = color;
+        if (!hoverMode) {
+            setForeground(linkColor);
+        }
     }
 
 
@@ -70,11 +66,13 @@ public void setHoverColor(Color color) {
 
     private void setHoverMode(boolean b) {
         if (b && isEnabled()) {
+            hoverMode = true;
             setForeground(hoverColor);
             oldCursor = getCursor();
             setCursor(Cursor.getPredefinedCursor(Cursor.HAND_CURSOR));
         }
         else {
+            hoverMode = false;
             setForeground(linkColor);
             if (oldCursor != null) {
                 setCursor(oldCursor);
@@ -89,4 +87,38 @@ private void activateLink() {
             linkListener.actionPerformed(new ActionEvent(this, 0, getText()));
         }
     }
+
+    @Override
+    public void updateUI() {
+        super.updateUI();
+        updateColorsFromUI();
+    }
+
+    private void updateColorsFromUI() {
+        if (isClickable) {
+            Color uiLink = UIManager.getColor("Link.foreground");
+            Color uiHover = UIManager.getColor("Link.hoverForeground");
+            // Theme-aware fallback colors
+            if (uiLink == null) {
+                uiLink = ThemeManager.isDarkTheme() ? 
+                    new Color(0x80, 0x70, 0xFF) : new Color(0x00, 0x64, 0xC8);  // Dark blue for light theme
+            }
+            if (uiHover == null) {
+                uiHover = ThemeManager.isDarkTheme() ? 
+                    uiLink.brighter() : uiLink.darker();
+            }
+            linkColor = uiLink;
+            hoverColor = uiHover;
+            if (!hoverMode) {
+                setForeground(linkColor);
+            }
+        } else {
+            // Use label foreground for non-clickable labels
+            Color labelColor = UIManager.getColor("Label.foreground");
+            if (labelColor == null) {
+                labelColor = ThemeManager.isDarkTheme() ? Color.WHITE : Color.BLACK;
+            }
+            setForeground(labelColor);
+        }
+    }
 }