JAL-3416 Use JalviewInternalFrame instead of new JInternalFrame

diff --git a/src/jalview/bin/Jalview.java b/src/jalview/bin/Jalview.java
index 6d2866a..eeac532 100755 (executable)
--- a/src/jalview/bin/Jalview.java
+++ b/src/jalview/bin/Jalview.java
@@ -1403,6 +1403,7 @@ public class Jalview
   private static boolean setFlatLookAndFeel()
   {
     boolean set = false;
+    UIManager.put("InternalFrame.dropShadowPainted", false);
     if (SystemInfo.isMacOS)
     {
       try

diff --git a/src/jalview/fts/core/GFTSPanel.java b/src/jalview/fts/core/GFTSPanel.java
index dd7fd94..ba5f123 100644 (file)
--- a/src/jalview/fts/core/GFTSPanel.java
+++ b/src/jalview/fts/core/GFTSPanel.java
@@ -50,7 +50,7 @@ import javax.swing.JButton;
 import javax.swing.JCheckBox;
 import javax.swing.JComboBox;
 import javax.swing.JFrame;
-import javax.swing.JInternalFrame;
+import jalview.gui.JalviewInternalFrame;
 import javax.swing.JLabel;
 import javax.swing.JPanel;
 import javax.swing.JScrollPane;
@@ -90,7 +90,7 @@ public abstract class GFTSPanel extends JPanel implements GFTSPanelI
 {
   private static final Font VERDANA_12 = new Font("Verdana", 0, 12);
 
-  protected JInternalFrame mainFrame = new JInternalFrame(
+  protected JalviewInternalFrame mainFrame = new JalviewInternalFrame(
           getFTSFrameTitle());
 
   protected JTabbedPane tabs = new JTabbedPane();
@@ -826,7 +826,7 @@ public abstract class GFTSPanel extends JPanel implements GFTSPanelI
     return cmb_searchTarget;
   }
 
-  public JInternalFrame getMainFrame()
+  public JalviewInternalFrame getMainFrame()
   {
     return mainFrame;
   }

diff --git a/src/jalview/gui/AlignFrame.java b/src/jalview/gui/AlignFrame.java
index 5c2f2f6..41777d8 100644 (file)
--- a/src/jalview/gui/AlignFrame.java
+++ b/src/jalview/gui/AlignFrame.java
@@ -3496,7 +3496,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
       pane = editPane;
     }
 
-    JInternalFrame frame = new JInternalFrame();
+    JalviewInternalFrame frame = new JalviewInternalFrame();
     frame.setFrameIcon(null);
     frame.getContentPane().add(new JScrollPane(pane));
 
@@ -3524,7 +3524,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
     {
       return alignPanel.overviewPanel;
     }
-    JInternalFrame frame = new JInternalFrame();
+    JalviewInternalFrame frame = new JalviewInternalFrame();
     frame.setFrameIcon(null);
     final OverviewPanel overview = new OverviewPanel(alignPanel, frame,
             showHidden);
@@ -3803,7 +3803,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener,
     }
     else
     {
-      JInternalFrame frame = new JInternalFrame();
+      JalviewInternalFrame frame = new JalviewInternalFrame();
       frame.setFrameIcon(null);
       frame.setContentPane(new PairwiseAlignPanel(viewport));
       Desktop.addInternalFrame(frame,

diff --git a/src/jalview/gui/AlignViewport.java b/src/jalview/gui/AlignViewport.java
index 5613f16..f45455e 100644 (file)
--- a/src/jalview/gui/AlignViewport.java
+++ b/src/jalview/gui/AlignViewport.java
@@ -30,7 +30,7 @@ import java.util.ArrayList;
 import java.util.Hashtable;
 import java.util.List;
 
-import javax.swing.JInternalFrame;
+import jalview.gui.JalviewInternalFrame;
 
 import jalview.analysis.AlignmentUtils;
 import jalview.analysis.AnnotationSorter.SequenceAnnotationOrder;
@@ -915,7 +915,7 @@ public class AlignViewport extends AlignmentViewport
     /*
      * Open in split pane. DNA sequence above, protein below.
      */
-    JInternalFrame splitFrame = new SplitFrame(cdnaFrame, proteinFrame);
+    JalviewInternalFrame splitFrame = new SplitFrame(cdnaFrame, proteinFrame);
     Desktop.addInternalFrame(splitFrame, linkedTitle, -1, -1);
 
     return proteinFrame.viewport.getAlignment();

diff --git a/src/jalview/gui/AnnotationChooser.java b/src/jalview/gui/AnnotationChooser.java
index d976815..fbfb6e0 100644 (file)
--- a/src/jalview/gui/AnnotationChooser.java
+++ b/src/jalview/gui/AnnotationChooser.java
@@ -36,7 +36,7 @@ import java.util.List;
 import java.util.Map;
 
 import javax.swing.JButton;
-import javax.swing.JInternalFrame;
+import jalview.gui.JalviewInternalFrame;
 import javax.swing.JLayeredPane;
 import javax.swing.JPanel;
 
@@ -63,7 +63,7 @@ public class AnnotationChooser extends JPanel
 
   private static final int MY_FRAME_HEIGHT = 250;
 
-  private JInternalFrame frame;
+  private JalviewInternalFrame frame;
 
   private AlignmentPanel ap;
 
@@ -601,7 +601,7 @@ public class AnnotationChooser extends JPanel
    */
   private void showFrame()
   {
-    frame = new JInternalFrame();
+    frame = new JalviewInternalFrame();
     frame.setFrameIcon(null);
     frame.setContentPane(this);
     frame.setLayer(JLayeredPane.PALETTE_LAYER);

diff --git a/src/jalview/gui/AnnotationColourChooser.java b/src/jalview/gui/AnnotationColourChooser.java
index d898398..7e6a198 100644 (file)
--- a/src/jalview/gui/AnnotationColourChooser.java
+++ b/src/jalview/gui/AnnotationColourChooser.java
@@ -35,7 +35,7 @@ import javax.swing.BorderFactory;
 import javax.swing.JButton;
 import javax.swing.JCheckBox;
 import javax.swing.JComboBox;
-import javax.swing.JInternalFrame;
+import jalview.gui.JalviewInternalFrame;
 import javax.swing.JLayeredPane;
 import javax.swing.JPanel;
 
@@ -90,7 +90,7 @@ public class AnnotationColourChooser extends AnnotationRowFilter
         }
       }
     }
-    frame = new JInternalFrame();
+    frame = new JalviewInternalFrame();
     frame.setFrameIcon(null);
     frame.setContentPane(this);
     frame.setLayer(JLayeredPane.PALETTE_LAYER);

diff --git a/src/jalview/gui/AnnotationColumnChooser.java b/src/jalview/gui/AnnotationColumnChooser.java
index 0483aa6..a7b9149 100644 (file)
--- a/src/jalview/gui/AnnotationColumnChooser.java
+++ b/src/jalview/gui/AnnotationColumnChooser.java
@@ -36,7 +36,7 @@ import java.awt.event.KeyEvent;
 import javax.swing.ButtonGroup;
 import javax.swing.JCheckBox;
 import javax.swing.JComboBox;
-import javax.swing.JInternalFrame;
+import jalview.gui.JalviewInternalFrame;
 import javax.swing.JLayeredPane;
 import javax.swing.JPanel;
 import javax.swing.JRadioButton;
@@ -101,7 +101,7 @@ public class AnnotationColumnChooser extends AnnotationRowFilter
   public AnnotationColumnChooser(AlignViewport av, final AlignmentPanel ap, AlignmentAnnotation selectedAnnotation)
   {
     super(av, ap);
-    frame = new JInternalFrame();
+    frame = new JalviewInternalFrame();
     frame.setFrameIcon(null);
     frame.setContentPane(this);
     frame.setLayer(JLayeredPane.PALETTE_LAYER);

diff --git a/src/jalview/gui/AnnotationExporter.java b/src/jalview/gui/AnnotationExporter.java
index 894db79..4881176 100644 (file)
--- a/src/jalview/gui/AnnotationExporter.java
+++ b/src/jalview/gui/AnnotationExporter.java
@@ -32,7 +32,7 @@ import javax.swing.BoxLayout;
 import javax.swing.ButtonGroup;
 import javax.swing.JButton;
 import javax.swing.JCheckBox;
-import javax.swing.JInternalFrame;
+import jalview.gui.JalviewInternalFrame;
 import javax.swing.JLabel;
 import javax.swing.JLayeredPane;
 import javax.swing.JPanel;
@@ -59,7 +59,7 @@ import jalview.util.MessageManager;
  */
 public class AnnotationExporter extends JPanel
 {
-  private JInternalFrame frame;
+  private JalviewInternalFrame frame;
 
   private AlignmentPanel ap;
 
@@ -106,7 +106,7 @@ public class AnnotationExporter extends JPanel
       ex.printStackTrace();
     }
 
-    frame = new JInternalFrame();
+    frame = new JalviewInternalFrame();
     frame.setFrameIcon(null);
     frame.setContentPane(this);
     frame.setLayer(JLayeredPane.PALETTE_LAYER);

diff --git a/src/jalview/gui/AnnotationRowFilter.java b/src/jalview/gui/AnnotationRowFilter.java
index 44a1668..a9806fe 100644 (file)
--- a/src/jalview/gui/AnnotationRowFilter.java
+++ b/src/jalview/gui/AnnotationRowFilter.java
@@ -44,7 +44,7 @@ import java.util.Vector;
 import javax.swing.JButton;
 import javax.swing.JCheckBox;
 import javax.swing.JComboBox;
-import javax.swing.JInternalFrame;
+import jalview.gui.JalviewInternalFrame;
 import javax.swing.JPanel;
 import javax.swing.JTextField;
 import javax.swing.event.ChangeEvent;
@@ -73,7 +73,7 @@ public abstract class AnnotationRowFilter extends JPanel
 
   protected JTextField thresholdValue = new JTextField(20);
 
-  protected JInternalFrame frame;
+  protected JalviewInternalFrame frame;
 
   protected JButton ok = new JButton();
 

diff --git a/src/jalview/gui/AppVarna.java b/src/jalview/gui/AppVarna.java
index 6fac8fc..02fdd7b 100644 (file)
--- a/src/jalview/gui/AppVarna.java
+++ b/src/jalview/gui/AppVarna.java
@@ -28,7 +28,7 @@ import java.util.LinkedHashMap;
 import java.util.List;
 import java.util.Map;
 
-import javax.swing.JInternalFrame;
+import jalview.gui.JalviewInternalFrame;
 import javax.swing.JSplitPane;
 import javax.swing.event.InternalFrameAdapter;
 import javax.swing.event.InternalFrameEvent;
@@ -60,7 +60,7 @@ import jalview.util.Comparison;
 import jalview.util.MessageManager;
 import jalview.util.ShiftList;
 
-public class AppVarna extends JInternalFrame
+public class AppVarna extends JalviewInternalFrame
         implements SelectionListener, SecondaryStructureListener,
         InterfaceVARNASelectionListener, VamsasSource
 {

diff --git a/src/jalview/gui/CalculationChooser.java b/src/jalview/gui/CalculationChooser.java
index af41e58..e3af388 100644 (file)
--- a/src/jalview/gui/CalculationChooser.java
+++ b/src/jalview/gui/CalculationChooser.java
@@ -44,7 +44,7 @@ import javax.swing.DefaultComboBoxModel;
 import javax.swing.JButton;
 import javax.swing.JCheckBox;
 import javax.swing.JComboBox;
-import javax.swing.JInternalFrame;
+import jalview.gui.JalviewInternalFrame;
 import javax.swing.JLabel;
 import javax.swing.JLayeredPane;
 import javax.swing.JPanel;
@@ -92,7 +92,7 @@ public class CalculationChooser extends JPanel
 
   JButton calculate;
 
-  private JInternalFrame frame;
+  private JalviewInternalFrame frame;
 
   private JCheckBox includeGaps;
 
@@ -129,7 +129,7 @@ public class CalculationChooser extends JPanel
   void init()
   {
     setLayout(new BorderLayout());
-    frame = new JInternalFrame();
+    frame = new JalviewInternalFrame();
     frame.setFrameIcon(null);
     frame.setContentPane(this);
     this.setBackground(Color.white);

diff --git a/src/jalview/gui/ChimeraViewFrame.java b/src/jalview/gui/ChimeraViewFrame.java
index cc6a785..3f926e3 100644 (file)
--- a/src/jalview/gui/ChimeraViewFrame.java
+++ b/src/jalview/gui/ChimeraViewFrame.java
@@ -30,7 +30,7 @@ import java.util.Collections;
 import java.util.List;
 import java.util.Map;
 
-import javax.swing.JInternalFrame;
+import jalview.gui.JalviewInternalFrame;
 import javax.swing.JMenu;
 import javax.swing.JMenuItem;
 import javax.swing.event.InternalFrameAdapter;
@@ -312,7 +312,7 @@ public class ChimeraViewFrame extends StructureViewerBase
      * closeViewer will decide whether or not to close this frame
      * depending on whether user chooses to Cancel or not
      */
-    setDefaultCloseOperation(JInternalFrame.DO_NOTHING_ON_CLOSE);
+    setDefaultCloseOperation(JalviewInternalFrame.DO_NOTHING_ON_CLOSE);
   }
 
   /**

diff --git a/src/jalview/gui/Desktop.java b/src/jalview/gui/Desktop.java
index 6fd70a9..d308f62 100644 (file)
--- a/src/jalview/gui/Desktop.java
+++ b/src/jalview/gui/Desktop.java
@@ -890,7 +890,7 @@ public class Desktop extends jalview.jbgui.GDesktop
    *          height
    */
   public static synchronized void addInternalFrame(
-          final JInternalFrame frame, String title, int w, int h)
+          final JalviewInternalFrame frame, String title, int w, int h)
   {
     addInternalFrame(frame, title, true, w, h, true, false);
   }
@@ -911,8 +911,8 @@ public class Desktop extends jalview.jbgui.GDesktop
    *          height
    */
   public static synchronized void addInternalFrame(
-          final JInternalFrame frame, String title, boolean makeVisible,
-          int w, int h)
+          final JalviewInternalFrame frame, String title,
+          boolean makeVisible, int w, int h)
   {
     addInternalFrame(frame, title, makeVisible, w, h, true, false);
   }
@@ -932,7 +932,7 @@ public class Desktop extends jalview.jbgui.GDesktop
    *          Allow resize
    */
   public static synchronized void addInternalFrame(
-          final JInternalFrame frame, String title, int w, int h,
+          final JalviewInternalFrame frame, String title, int w, int h,
           boolean resizable)
   {
     addInternalFrame(frame, title, true, w, h, resizable, false);
@@ -958,8 +958,9 @@ public class Desktop extends jalview.jbgui.GDesktop
    *          Do not set the default minimum size for frame
    */
   public static synchronized void addInternalFrame(
-          final JInternalFrame frame, String title, boolean makeVisible,
-          int w, int h, boolean resizable, boolean ignoreMinSize)
+          final JalviewInternalFrame frame, String title,
+          boolean makeVisible, int w, int h, boolean resizable,
+          boolean ignoreMinSize)
   {
 
     // TODO: allow callers to determine X and Y position of frame (eg. via
@@ -1096,12 +1097,12 @@ public class Desktop extends jalview.jbgui.GDesktop
   }
 
   /**
-   * Add key bindings to a JInternalFrame so that Ctrl-W and Cmd-W will close
-   * the window
+   * Add key bindings to a JalviewInternalFrame so that Ctrl-W and Cmd-W will
+   * close the window
    * 
    * @param frame
    */
-  private static void setKeyBindings(JInternalFrame frame)
+  private static void setKeyBindings(JalviewInternalFrame frame)
   {
     @SuppressWarnings("serial")
     final Action closeAction = new AbstractAction()
@@ -3213,7 +3214,7 @@ public class Desktop extends jalview.jbgui.GDesktop
 
       topPanel.av.setGatherViewsHere(false);
       bottomPanel.av.setGatherViewsHere(false);
-      JInternalFrame splitFrame = new SplitFrame(newTopFrame,
+      JalviewInternalFrame splitFrame = new SplitFrame(newTopFrame,
               newBottomFrame);
       if (geometry != null)
       {

diff --git a/src/jalview/gui/FeatureSettings.java b/src/jalview/gui/FeatureSettings.java
index 2e9731d..a90ce59 100644 (file)
--- a/src/jalview/gui/FeatureSettings.java
+++ b/src/jalview/gui/FeatureSettings.java
@@ -62,7 +62,7 @@ import javax.swing.BorderFactory;
 import javax.swing.Icon;
 import javax.swing.JButton;
 import javax.swing.JCheckBox;
-import javax.swing.JInternalFrame;
+import jalview.gui.JalviewInternalFrame;
 import javax.swing.JLabel;
 import javax.swing.JLayeredPane;
 import javax.swing.JMenuItem;
@@ -156,7 +156,7 @@ public class FeatureSettings extends JPanel
 
   private Map<String, FeatureMatcherSetI> originalFilters;
 
-  final JInternalFrame frame;
+  final JalviewInternalFrame frame;
 
   JScrollPane scrollPane = new JScrollPane();
 
@@ -409,7 +409,7 @@ public class FeatureSettings extends JPanel
     }
     else
     {
-      frame = new JInternalFrame();
+      frame = new JalviewInternalFrame();
       frame.setContentPane(this);
       frame.setFrameIcon(null);
       Rectangle bounds = af.getFeatureSettingsGeometry();

diff --git a/src/jalview/gui/Finder.java b/src/jalview/gui/Finder.java
index 2756b14..f641f4b 100755 (executable)
--- a/src/jalview/gui/Finder.java
+++ b/src/jalview/gui/Finder.java
@@ -75,7 +75,7 @@ public class Finder extends GFinder
 
   private AlignmentPanel ap;
 
-  private JInternalFrame frame;
+  private JalviewInternalFrame frame;
 
   /*
    * Finder agent per viewport searched
@@ -107,7 +107,7 @@ public class Finder extends GFinder
     ap = alignPanel;
     focusFixed = fixedFocus;
     finders = new HashMap<>();
-    frame = new JInternalFrame();
+    frame = new JalviewInternalFrame();
     frame.setFrameIcon(null);
     frame.setContentPane(this);
     frame.setLayer(JLayeredPane.PALETTE_LAYER);

diff --git a/src/jalview/gui/FontChooser.java b/src/jalview/gui/FontChooser.java
index f532706..6e5d7de 100755 (executable)
--- a/src/jalview/gui/FontChooser.java
+++ b/src/jalview/gui/FontChooser.java
@@ -24,7 +24,7 @@ import java.awt.Font;
 import java.awt.FontMetrics;
 import java.awt.geom.Rectangle2D;
 
-import javax.swing.JInternalFrame;
+import jalview.gui.JalviewInternalFrame;
 import javax.swing.JLayeredPane;
 
 import jalview.bin.Cache;
@@ -66,7 +66,7 @@ public class FontChooser extends GFontChooser
 
   boolean init = true;
 
-  JInternalFrame frame;
+  JalviewInternalFrame frame;
 
   /*
    * The last font settings selected in the dialog
@@ -111,7 +111,7 @@ public class FontChooser extends GFontChooser
 
   void init()
   {
-    frame = new JInternalFrame();
+    frame = new JalviewInternalFrame();
     frame.setFrameIcon(null);
     frame.setContentPane(this);
 

diff --git a/src/jalview/gui/JalviewInternalFrame.java b/src/jalview/gui/JalviewInternalFrame.java
new file mode 100644 (file)
index 0000000..c019629
--- /dev/null
+++ b/src/jalview/gui/JalviewInternalFrame.java
@@ -0,0 +1,25 @@
+package jalview.gui;
+
+import javax.swing.JInternalFrame;
+
+public class JalviewInternalFrame extends JInternalFrame
+{
+  public JalviewInternalFrame()
+  {
+    super();
+    init();
+  }
+
+  public JalviewInternalFrame(String title)
+  {
+    super(title);
+    init();
+  }
+
+  private void init()
+  {
+    this.setFrameIcon(null);
+    this.setOpaque(true);
+  }
+
+}

diff --git a/src/jalview/gui/JvOptionPane.java b/src/jalview/gui/JvOptionPane.java
index c0efd4a..703958b 100644 (file)
--- a/src/jalview/gui/JvOptionPane.java
+++ b/src/jalview/gui/JvOptionPane.java
@@ -901,9 +901,9 @@ public class JvOptionPane extends JOptionPane
               if (raiseParent)
               {
                 parentComponent.requestFocus();
-                if (parentComponent instanceof JInternalFrame)
+                if (parentComponent instanceof JalviewInternalFrame)
                 {
-                  JInternalFrame jif = (JInternalFrame) parentComponent;
+                  JalviewInternalFrame jif = (JalviewInternalFrame) parentComponent;
                   jif.show();
                   jif.moveToFront();
                   jif.grabFocus();
@@ -1009,9 +1009,9 @@ public class JvOptionPane extends JOptionPane
               if (raiseParent)
               {
                 parentComponent.requestFocus();
-                if (parentComponent instanceof JInternalFrame)
+                if (parentComponent instanceof JalviewInternalFrame)
                 {
-                  JInternalFrame jif = (JInternalFrame) parentComponent;
+                  JalviewInternalFrame jif = (JalviewInternalFrame) parentComponent;
                   jif.show();
                   jif.moveToFront();
                   jif.grabFocus();
@@ -1421,9 +1421,9 @@ public class JvOptionPane extends JOptionPane
             if (raiseParent)
             {
               parentComponent.requestFocus();
-              if (parentComponent instanceof JInternalFrame)
+              if (parentComponent instanceof JalviewInternalFrame)
               {
-                JInternalFrame jif = (JInternalFrame) parentComponent;
+                JalviewInternalFrame jif = (JalviewInternalFrame) parentComponent;
                 jif.show();
                 jif.moveToFront();
                 jif.grabFocus();
@@ -1472,13 +1472,13 @@ public class JvOptionPane extends JOptionPane
   }
 
   /**
-   * This helper method makes the JInternalFrame wait until it is notified by an
-   * InternalFrameClosing event. This method also adds the given JOptionPane to
-   * the JInternalFrame and sizes it according to the JInternalFrame's preferred
-   * size.
+   * This helper method makes the JalviewInternalFrame wait until it is notified
+   * by an InternalFrameClosing event. This method also adds the given
+   * JOptionPane to the JalviewInternalFrame and sizes it according to the
+   * JalviewInternalFrame's preferred size.
    *
    * @param f
-   *          The JInternalFrame to make modal.
+   *          The JalviewInternalFrame to make modal.
    */
   private static void startModal(JInternalFrame f)
   {

diff --git a/src/jalview/gui/OverviewPanel.java b/src/jalview/gui/OverviewPanel.java
index 872d142..cde4ea9 100755 (executable)
--- a/src/jalview/gui/OverviewPanel.java
+++ b/src/jalview/gui/OverviewPanel.java
@@ -35,7 +35,7 @@ import java.beans.PropertyChangeEvent;
 import java.beans.PropertyVetoException;
 
 import javax.swing.JCheckBoxMenuItem;
-import javax.swing.JInternalFrame;
+import jalview.gui.JalviewInternalFrame;
 import javax.swing.JPanel;
 import javax.swing.JPopupMenu;
 import javax.swing.SwingUtilities;
@@ -67,7 +67,7 @@ public class OverviewPanel extends JPanel
 
   private AlignmentPanel ap;
 
-  private JInternalFrame internalFrame;
+  private JalviewInternalFrame internalFrame;
 
   protected JCheckBoxMenuItem displayToggle;
 
@@ -86,7 +86,7 @@ public class OverviewPanel extends JPanel
    * @param isShowHidden
    *          TODO
    */
-  public OverviewPanel(AlignmentPanel alPanel, JInternalFrame frame,
+  public OverviewPanel(AlignmentPanel alPanel, JalviewInternalFrame frame,
           boolean isShowHidden)
   {
     this.av = alPanel.av;
@@ -413,8 +413,8 @@ public class OverviewPanel extends JPanel
        * close the parent frame (which also removes it from the
        * Desktop Windows menu)
        */
-      ((JInternalFrame) SwingUtilities
-              .getAncestorOfClass(JInternalFrame.class, (this)))
+      ((JalviewInternalFrame) SwingUtilities
+              .getAncestorOfClass(JalviewInternalFrame.class, (this)))
                       .setClosed(true);
     } catch (PropertyVetoException e)
     {

diff --git a/src/jalview/gui/PopupMenu.java b/src/jalview/gui/PopupMenu.java
index 57a2fa0..c8708bf 100644 (file)
--- a/src/jalview/gui/PopupMenu.java
+++ b/src/jalview/gui/PopupMenu.java
@@ -41,7 +41,7 @@ import java.util.Vector;
 
 import javax.swing.ButtonGroup;
 import javax.swing.JCheckBoxMenuItem;
-import javax.swing.JInternalFrame;
+import jalview.gui.JalviewInternalFrame;
 import javax.swing.JLabel;
 import javax.swing.JMenu;
 import javax.swing.JMenuItem;
@@ -902,10 +902,10 @@ public class PopupMenu extends JPopupMenu implements ColourChangeListener
   protected void showFeatureDetails(SequenceFeature sf, String seqName,
           MappedFeatures mf)
   {
-    JInternalFrame details;
+    JalviewInternalFrame details;
     if (Platform.isJS())
     {
-      details = new JInternalFrame();
+      details = new JalviewInternalFrame();
       details.setFrameIcon(null);
       JPanel panel = new JPanel(new BorderLayout());
       panel.setOpaque(true);
@@ -1825,7 +1825,7 @@ public class PopupMenu extends JPopupMenu implements ColourChangeListener
     contents.append("</body></html>");
     String report = contents.toString();
 
-    JInternalFrame frame;
+    JalviewInternalFrame frame;
     if (Platform.isJS())
     {
       JLabel textLabel = new JLabel();
@@ -1835,7 +1835,7 @@ public class PopupMenu extends JPopupMenu implements ColourChangeListener
       pane.setOpaque(true);
       pane.setBackground(Color.WHITE);
       pane.add(textLabel, BorderLayout.NORTH);
-      frame = new JInternalFrame();
+      frame = new JalviewInternalFrame();
       frame.setFrameIcon(null);
       frame.getContentPane().add(new JScrollPane(pane));
     }

diff --git a/src/jalview/gui/Preferences.java b/src/jalview/gui/Preferences.java
index c4f32c3..5769bb7 100755 (executable)
--- a/src/jalview/gui/Preferences.java
+++ b/src/jalview/gui/Preferences.java
@@ -34,7 +34,7 @@ import java.util.concurrent.CompletableFuture;
 
 import javax.help.HelpSetException;
 import javax.swing.JComboBox;
-import javax.swing.JInternalFrame;
+import jalview.gui.JalviewInternalFrame;
 import javax.swing.JPanel;
 import javax.swing.ListSelectionModel;
 import javax.swing.RowFilter;
@@ -188,7 +188,7 @@ public class Preferences extends GPreferences
     Cache.enableSessionProperties();
   }
 
-  JInternalFrame frame;
+  JalviewInternalFrame frame;
 
   private WsPreferences wsPrefs;
 
@@ -257,7 +257,7 @@ public class Preferences extends GPreferences
     // don't populate with session properties
     Cache.disableSessionProperties();
 
-    frame = new JInternalFrame();
+    frame = new JalviewInternalFrame();
     frame.setFrameIcon(null);
     frame.setContentPane(this);
     if (!Platform.isJS())

diff --git a/src/jalview/gui/PymolViewer.java b/src/jalview/gui/PymolViewer.java
index 52c253d..f68e503 100644 (file)
--- a/src/jalview/gui/PymolViewer.java
+++ b/src/jalview/gui/PymolViewer.java
@@ -27,7 +27,7 @@ import java.util.ArrayList;
 import java.util.List;
 import java.util.Map;
 
-import javax.swing.JInternalFrame;
+import jalview.gui.JalviewInternalFrame;
 import javax.swing.JMenuItem;
 import javax.swing.event.InternalFrameAdapter;
 import javax.swing.event.InternalFrameEvent;
@@ -63,7 +63,7 @@ public class PymolViewer extends StructureViewerBase
      * closeViewer will decide whether or not to close this frame
      * depending on whether user chooses to Cancel or not
      */
-    setDefaultCloseOperation(JInternalFrame.DO_NOTHING_ON_CLOSE);
+    setDefaultCloseOperation(JalviewInternalFrame.DO_NOTHING_ON_CLOSE);
   }
 
   public PymolViewer(PDBEntry pdb, SequenceI[] seqs, Object object,

diff --git a/src/jalview/gui/RedundancyPanel.java b/src/jalview/gui/RedundancyPanel.java
index 8d66a44..0bf7477 100755 (executable)
--- a/src/jalview/gui/RedundancyPanel.java
+++ b/src/jalview/gui/RedundancyPanel.java
@@ -26,7 +26,7 @@ import java.util.List;
 import java.util.Stack;
 import java.util.Vector;
 
-import javax.swing.JInternalFrame;
+import jalview.gui.JalviewInternalFrame;
 import javax.swing.JProgressBar;
 import javax.swing.event.ChangeEvent;
 import javax.swing.event.ChangeListener;
@@ -62,7 +62,7 @@ public class RedundancyPanel extends GSliderPanel implements Runnable
 
   SequenceI[] originalSequences;
 
-  JInternalFrame frame;
+  JalviewInternalFrame frame;
 
   Vector redundantSeqs;
 
@@ -99,7 +99,7 @@ public class RedundancyPanel extends GSliderPanel implements Runnable
     Thread worker = new Thread(this);
     worker.start();
 
-    frame = new JInternalFrame();
+    frame = new JalviewInternalFrame();
     frame.setFrameIcon(null);
     frame.setContentPane(this);
     Desktop.addInternalFrame(frame,

diff --git a/src/jalview/gui/SequenceFetcher.java b/src/jalview/gui/SequenceFetcher.java
index 6b4c74a..cae7c02 100755 (executable)
--- a/src/jalview/gui/SequenceFetcher.java
+++ b/src/jalview/gui/SequenceFetcher.java
@@ -35,7 +35,7 @@ import java.util.List;
 import javax.swing.JButton;
 import javax.swing.JCheckBox;
 import javax.swing.JComboBox;
-import javax.swing.JInternalFrame;
+import jalview.gui.JalviewInternalFrame;
 import javax.swing.JLabel;
 import javax.swing.JPanel;
 import javax.swing.JScrollPane;
@@ -125,7 +125,7 @@ public class SequenceFetcher extends JPanel implements Runnable
 
   JTextArea textArea;
 
-  JInternalFrame frame;
+  JalviewInternalFrame frame;
 
   IProgressIndicator guiWindow;
 
@@ -184,7 +184,7 @@ public class SequenceFetcher extends JPanel implements Runnable
     jbInit(selectedDb);
     textArea.setText(queryString);
 
-    frame = new JInternalFrame();
+    frame = new JalviewInternalFrame();
     frame.setContentPane(this);
     frame.setFrameIcon(null);
     Desktop.addInternalFrame(frame, getFrameTitle(), true, 400,

diff --git a/src/jalview/gui/SliderPanel.java b/src/jalview/gui/SliderPanel.java
index 1d59853..2a198d9 100755 (executable)
--- a/src/jalview/gui/SliderPanel.java
+++ b/src/jalview/gui/SliderPanel.java
@@ -25,7 +25,7 @@ import java.awt.event.MouseEvent;
 import java.beans.PropertyVetoException;
 import java.util.List;
 
-import javax.swing.JInternalFrame;
+import jalview.gui.JalviewInternalFrame;
 import javax.swing.JLayeredPane;
 import javax.swing.event.ChangeEvent;
 import javax.swing.event.ChangeListener;
@@ -48,9 +48,9 @@ public class SliderPanel extends GSliderPanel
 {
   private static final String BACKGROUND = "Background";
 
-  static JInternalFrame conservationSlider;
+  static JalviewInternalFrame conservationSlider;
 
-  static JInternalFrame PIDSlider;
+  static JalviewInternalFrame PIDSlider;
 
   AlignmentPanel ap;
 
@@ -155,7 +155,7 @@ public class SliderPanel extends GSliderPanel
     if (conservationSlider == null)
     {
       sliderPanel = new SliderPanel(ap, rs.getConservationInc(), true, rs);
-      conservationSlider = new JInternalFrame();
+      conservationSlider = new JalviewInternalFrame();
       conservationSlider.setFrameIcon(null);
       conservationSlider.setContentPane(sliderPanel);
       conservationSlider.setLayer(JLayeredPane.PALETTE_LAYER);
@@ -269,7 +269,7 @@ public class SliderPanel extends GSliderPanel
     if (PIDSlider == null)
     {
       sliderPanel = new SliderPanel(ap, threshold, false, rs);
-      PIDSlider = new JInternalFrame();
+      PIDSlider = new JalviewInternalFrame();
       PIDSlider.setFrameIcon(null);
       PIDSlider.setContentPane(sliderPanel);
       PIDSlider.setLayer(JLayeredPane.PALETTE_LAYER);
@@ -304,7 +304,7 @@ public class SliderPanel extends GSliderPanel
    * 
    * @return
    */
-  public static JInternalFrame showPIDSlider()
+  public static JalviewInternalFrame showPIDSlider()
   {
     hideConservationSlider();
 
@@ -457,7 +457,7 @@ public class SliderPanel extends GSliderPanel
     return getValue(conservationSlider);
   }
 
-  static int getValue(JInternalFrame slider)
+  static int getValue(JalviewInternalFrame slider)
   {
     return slider == null ? 0
             : ((SliderPanel) slider.getContentPane()).getValue();

diff --git a/src/jalview/gui/SplashScreen.java b/src/jalview/gui/SplashScreen.java
index 61273c7..83cd0dc 100755 (executable)
--- a/src/jalview/gui/SplashScreen.java
+++ b/src/jalview/gui/SplashScreen.java
@@ -31,7 +31,7 @@ import java.awt.MediaTracker;
 import java.awt.event.MouseAdapter;
 import java.awt.event.MouseEvent;
 
-import javax.swing.JInternalFrame;
+import jalview.gui.JalviewInternalFrame;
 import javax.swing.JLabel;
 import javax.swing.JLayeredPane;
 import javax.swing.JPanel;
@@ -72,7 +72,7 @@ public class SplashScreen extends JPanel
    */
   private Component splashText;
 
-  private JInternalFrame iframe;
+  private JalviewInternalFrame iframe;
 
   private Image image;
 
@@ -184,7 +184,7 @@ public class SplashScreen extends JPanel
     this.setForeground(fg);
     this.setFont(font);
 
-    iframe = new JInternalFrame();
+    iframe = new JalviewInternalFrame();
     iframe.setFrameIcon(null);
     iframe.setClosable(true);
     this.setLayout(new BorderLayout());

diff --git a/src/jalview/gui/SplitFrame.java b/src/jalview/gui/SplitFrame.java
index 73744b3..b2de97b 100644 (file)
--- a/src/jalview/gui/SplitFrame.java
+++ b/src/jalview/gui/SplitFrame.java
@@ -861,7 +861,7 @@ public class SplitFrame extends GSplitFrame implements SplitContainerI
    * holds the frame for feature settings, so Protein and DNA tabs can be
    * managed
    */
-  JInternalFrame featureSettingsUI;
+  JalviewInternalFrame featureSettingsUI;
 
   JTabbedPane featureSettingsPanels;
 
@@ -898,7 +898,7 @@ public class SplitFrame extends GSplitFrame implements SplitContainerI
           getAlignFrames().get(tab).showFeatureSettingsUI();
         }
       });
-      featureSettingsUI = new JInternalFrame(MessageManager.getString(
+      featureSettingsUI = new JalviewInternalFrame(MessageManager.getString(
               "label.sequence_feature_settings_for_CDS_and_Protein"));
       featureSettingsUI.setFrameIcon(null);
       featureSettingsPanels.setOpaque(true);

diff --git a/src/jalview/gui/UserDefinedColours.java b/src/jalview/gui/UserDefinedColours.java
index 14f9adf..9569918 100755 (executable)
--- a/src/jalview/gui/UserDefinedColours.java
+++ b/src/jalview/gui/UserDefinedColours.java
@@ -34,7 +34,7 @@ import java.util.List;
 import java.util.Locale;
 
 import javax.swing.JButton;
-import javax.swing.JInternalFrame;
+import jalview.gui.JalviewInternalFrame;
 import javax.swing.event.ChangeEvent;
 import javax.swing.event.ChangeListener;
 import javax.xml.bind.JAXBContext;
@@ -94,7 +94,7 @@ public class UserDefinedColours extends GUserDefinedColours
    */
   boolean changedButNotSaved;
 
-  JInternalFrame frame;
+  JalviewInternalFrame frame;
 
   List<JButton> upperCaseButtons;
 
@@ -147,7 +147,7 @@ public class UserDefinedColours extends GUserDefinedColours
   void showFrame()
   {
     colorChooser.getSelectionModel().addChangeListener(this);
-    frame = new JInternalFrame();
+    frame = new JalviewInternalFrame();
     frame.setFrameIcon(null);
     frame.setContentPane(this);
     Desktop.addInternalFrame(frame,

diff --git a/src/jalview/gui/VamsasApplication.java b/src/jalview/gui/VamsasApplication.java
index 8a8ba8d..e49fcaa 100644 (file)
--- a/src/jalview/gui/VamsasApplication.java
+++ b/src/jalview/gui/VamsasApplication.java
@@ -20,6 +20,16 @@
  */
 package jalview.gui;
 
+import java.beans.PropertyChangeEvent;
+import java.beans.PropertyChangeListener;
+import java.io.File;
+import java.io.IOException;
+import java.util.Hashtable;
+import java.util.IdentityHashMap;
+import java.util.Iterator;
+
+import javax.swing.JInternalFrame;
+
 import jalview.bin.Cache;
 import jalview.bin.Console;
 import jalview.datamodel.AlignmentI;
@@ -35,17 +45,6 @@ import jalview.structure.VamsasListener;
 import jalview.structure.VamsasSource;
 import jalview.util.MessageManager;
 import jalview.viewmodel.AlignmentViewport;
-
-import java.beans.PropertyChangeEvent;
-import java.beans.PropertyChangeListener;
-import java.io.File;
-import java.io.IOException;
-import java.util.Hashtable;
-import java.util.IdentityHashMap;
-import java.util.Iterator;
-
-import javax.swing.JInternalFrame;
-
 import uk.ac.vamsas.client.ClientHandle;
 import uk.ac.vamsas.client.IClient;
 import uk.ac.vamsas.client.IClientDocument;
@@ -932,8 +931,8 @@ public class VamsasApplication implements SelectionSource, VamsasSource
                         jselection.setEndRes(prange[p + u] - 1);
                       }
                       // mark all the columns in the range.
-                      for (int sr = prange[p], er = prange[p + 1], de = er
-                              + d; sr != de; sr += d)
+                      for (int sr = prange[p], er = prange[p + 1],
+                              de = er + d; sr != de; sr += d)
                       {
                         colsel.addElement(sr - 1);
                       }

diff --git a/src/jalview/gui/WebserviceInfo.java b/src/jalview/gui/WebserviceInfo.java
index 7eeee9a..20d5c34 100644 (file)
--- a/src/jalview/gui/WebserviceInfo.java
+++ b/src/jalview/gui/WebserviceInfo.java
@@ -36,7 +36,7 @@ import java.util.Vector;
 
 import javax.swing.JComponent;
 import javax.swing.JEditorPane;
-import javax.swing.JInternalFrame;
+import jalview.gui.JalviewInternalFrame;
 import javax.swing.JPanel;
 import javax.swing.JScrollPane;
 import javax.swing.JTabbedPane;
@@ -94,7 +94,7 @@ public class WebserviceInfo extends GWebserviceInfo
 
   boolean serviceIsCancellable;
 
-  JInternalFrame frame;
+  JalviewInternalFrame frame;
 
   private IProgressIndicator progressBar;
 
@@ -322,7 +322,7 @@ public class WebserviceInfo extends GWebserviceInfo
   void init(String title, String info, int width, int height,
           boolean makeVisible)
   {
-    frame = new JInternalFrame();
+    frame = new JalviewInternalFrame();
     frame.setFrameIcon(null);
     frame.setContentPane(this);
     Desktop.addInternalFrame(frame, title, makeVisible, width, height);

diff --git a/src/jalview/io/VamsasAppDatastore.java b/src/jalview/io/VamsasAppDatastore.java
index dd4b72c..6119db2 100644 (file)
--- a/src/jalview/io/VamsasAppDatastore.java
+++ b/src/jalview/io/VamsasAppDatastore.java
@@ -20,6 +20,17 @@
  */
 package jalview.io;
 
+import java.io.IOException;
+import java.util.Enumeration;
+import java.util.HashMap;
+import java.util.Hashtable;
+import java.util.IdentityHashMap;
+import java.util.Iterator;
+import java.util.List;
+import java.util.Vector;
+import java.util.jar.JarInputStream;
+import java.util.jar.JarOutputStream;
+
 import jalview.bin.Console;
 import jalview.datamodel.AlignedCodonFrame;
 import jalview.datamodel.AlignmentAnnotation;
@@ -36,18 +47,6 @@ import jalview.io.vamsas.Rangetype;
 import jalview.project.Jalview2XML;
 import jalview.util.MessageManager;
 import jalview.viewmodel.AlignmentViewport;
-
-import java.io.IOException;
-import java.util.Enumeration;
-import java.util.HashMap;
-import java.util.Hashtable;
-import java.util.IdentityHashMap;
-import java.util.Iterator;
-import java.util.List;
-import java.util.Vector;
-import java.util.jar.JarInputStream;
-import java.util.jar.JarOutputStream;
-
 import uk.ac.vamsas.client.IClientAppdata;
 import uk.ac.vamsas.client.IClientDocument;
 import uk.ac.vamsas.client.Vobject;
@@ -506,8 +505,8 @@ public class VamsasAppDatastore
       }
       // ////////////////////////////////////////////
       // SAVE Alignment Sequence Features
-      for (int i = 0, iSize = alignment
-              .getAlignmentSequenceCount(); i < iSize; i++)
+      for (int i = 0,
+              iSize = alignment.getAlignmentSequenceCount(); i < iSize; i++)
       {
         AlignmentSequence valseq;
         SequenceI alseq = (SequenceI) getvObj2jv(
@@ -1687,7 +1686,7 @@ public class VamsasAppDatastore
                                 + ((Vobject) dataset
                                         .getDataSetAnnotations(dsa)
                                         .getSeqRef(0)).getVorbaId()
-                                                .getId());
+                                        .getId());
               }
               else
               {
@@ -1719,8 +1718,8 @@ public class VamsasAppDatastore
         {
           // LOAD ALIGNMENTS from DATASET
 
-          for (int al = 0, nal = dataset
-                  .getAlignmentCount(); al < nal; al++)
+          for (int al = 0,
+                  nal = dataset.getAlignmentCount(); al < nal; al++)
           {
             uk.ac.vamsas.objects.core.Alignment alignment = dataset
                     .getAlignment(al);
@@ -1837,8 +1836,8 @@ public class VamsasAppDatastore
             if (newasAnnots != null && newasAnnots.size() > 0)
             {
               // Add the new sequence annotations in to the alignment.
-              for (int an = 0, anSize = newasAnnots
-                      .size(); an < anSize; an++)
+              for (int an = 0,
+                      anSize = newasAnnots.size(); an < anSize; an++)
               {
                 jal.addAnnotation(
                         (AlignmentAnnotation) newasAnnots.elementAt(an));
@@ -1912,8 +1911,8 @@ public class VamsasAppDatastore
                       .getAction();
               if (alignment.getPropertyCount() > 0)
               {
-                for (int p = 0, pe = alignment
-                        .getPropertyCount(); p < pe; p++)
+                for (int p = 0,
+                        pe = alignment.getPropertyCount(); p < pe; p++)
                 {
                   if (alignment.getProperty(p).getName().equals("title"))
                   {

diff --git a/src/jalview/jbgui/GAlignFrame.java b/src/jalview/jbgui/GAlignFrame.java
index 2d151bc..b43d17f 100755 (executable)
--- a/src/jalview/jbgui/GAlignFrame.java
+++ b/src/jalview/jbgui/GAlignFrame.java
@@ -36,7 +36,7 @@ import java.util.Map;
 import javax.swing.BorderFactory;
 import javax.swing.ButtonGroup;
 import javax.swing.JCheckBoxMenuItem;
-import javax.swing.JInternalFrame;
+import jalview.gui.JalviewInternalFrame;
 import javax.swing.JLabel;
 import javax.swing.JMenu;
 import javax.swing.JMenuBar;
@@ -62,7 +62,7 @@ import jalview.util.MessageManager;
 import jalview.util.Platform;
 
 @SuppressWarnings("serial")
-public class GAlignFrame extends JInternalFrame
+public class GAlignFrame extends JalviewInternalFrame
 {
   protected JMenuBar alignFrameMenuBar = new JMenuBar();
 

diff --git a/src/jalview/jbgui/GCutAndPasteHtmlTransfer.java b/src/jalview/jbgui/GCutAndPasteHtmlTransfer.java
index ef09b6a..3c76977 100644 (file)
--- a/src/jalview/jbgui/GCutAndPasteHtmlTransfer.java
+++ b/src/jalview/jbgui/GCutAndPasteHtmlTransfer.java
@@ -29,7 +29,7 @@ import java.awt.event.MouseEvent;
 import javax.swing.JButton;
 import javax.swing.JCheckBoxMenuItem;
 import javax.swing.JEditorPane;
-import javax.swing.JInternalFrame;
+import jalview.gui.JalviewInternalFrame;
 import javax.swing.JMenu;
 import javax.swing.JMenuBar;
 import javax.swing.JMenuItem;
@@ -47,7 +47,7 @@ import jalview.util.MessageManager;
  * @author $author$
  * @version $Revision$
  */
-public class GCutAndPasteHtmlTransfer extends JInternalFrame
+public class GCutAndPasteHtmlTransfer extends JalviewInternalFrame
 {
   protected JEditorPane textarea = new JEditorPane("text/html", "");
 

diff --git a/src/jalview/jbgui/GCutAndPasteTransfer.java b/src/jalview/jbgui/GCutAndPasteTransfer.java
index 3cd52ae..100ca95 100755 (executable)
--- a/src/jalview/jbgui/GCutAndPasteTransfer.java
+++ b/src/jalview/jbgui/GCutAndPasteTransfer.java
@@ -27,7 +27,7 @@ import java.awt.event.ActionListener;
 import java.awt.event.MouseEvent;
 
 import javax.swing.JButton;
-import javax.swing.JInternalFrame;
+import jalview.gui.JalviewInternalFrame;
 import javax.swing.JMenu;
 import javax.swing.JMenuBar;
 import javax.swing.JMenuItem;
@@ -44,7 +44,7 @@ import jalview.util.MessageManager;
  * @author $author$
  * @version $Revision$
  */
-public class GCutAndPasteTransfer extends JInternalFrame
+public class GCutAndPasteTransfer extends JalviewInternalFrame
 {
   protected JTextArea textarea = new JTextArea();
 

diff --git a/src/jalview/jbgui/GPCAPanel.java b/src/jalview/jbgui/GPCAPanel.java
index cf7bc4e..1f1c728 100755 (executable)
--- a/src/jalview/jbgui/GPCAPanel.java
+++ b/src/jalview/jbgui/GPCAPanel.java
@@ -31,7 +31,7 @@ import java.awt.event.ActionListener;
 import javax.swing.JButton;
 import javax.swing.JCheckBoxMenuItem;
 import javax.swing.JComboBox;
-import javax.swing.JInternalFrame;
+import jalview.gui.JalviewInternalFrame;
 import javax.swing.JLabel;
 import javax.swing.JMenu;
 import javax.swing.JMenuBar;
@@ -43,7 +43,7 @@ import javax.swing.event.MenuListener;
 import jalview.util.ImageMaker.TYPE;
 import jalview.util.MessageManager;
 
-public class GPCAPanel extends JInternalFrame
+public class GPCAPanel extends JalviewInternalFrame
 {
   private static final Font VERDANA_12 = new Font("Verdana", 0, 12);
 

diff --git a/src/jalview/jbgui/GRnaStructureViewer.java b/src/jalview/jbgui/GRnaStructureViewer.java
index 663245f..df0786c 100644 (file)
--- a/src/jalview/jbgui/GRnaStructureViewer.java
+++ b/src/jalview/jbgui/GRnaStructureViewer.java
@@ -20,10 +20,10 @@
  */
 package jalview.jbgui;
 
-import javax.swing.JInternalFrame;
+import jalview.gui.JalviewInternalFrame;
 
 @SuppressWarnings("serial")
-public class GRnaStructureViewer extends JInternalFrame
+public class GRnaStructureViewer extends JalviewInternalFrame
 {
   public GRnaStructureViewer()
   {

diff --git a/src/jalview/jbgui/GSplitFrame.java b/src/jalview/jbgui/GSplitFrame.java
index 4d531be..4faab0a 100644 (file)
--- a/src/jalview/jbgui/GSplitFrame.java
+++ b/src/jalview/jbgui/GSplitFrame.java
@@ -25,13 +25,13 @@ import java.awt.MouseInfo;
 import java.awt.Point;
 import java.awt.Rectangle;
 
-import javax.swing.JInternalFrame;
+import jalview.gui.JalviewInternalFrame;
 import javax.swing.JSplitPane;
 import javax.swing.plaf.basic.BasicInternalFrameUI;
 
 import jalview.util.Platform;
 
-public class GSplitFrame extends JInternalFrame
+public class GSplitFrame extends JalviewInternalFrame
 {
   protected static final int DIVIDER_SIZE = 5;
 
@@ -107,9 +107,9 @@ public class GSplitFrame extends JInternalFrame
     if (Platform.isAMacAndNotJS())
     {
       // this saves some space - but doesn't hide the title bar
-      topFrame.putClientProperty("JInternalFrame.isPalette", true);
+      topFrame.putClientProperty("JalviewInternalFrame.isPalette", true);
       // topFrame.getRootPane().putClientProperty("Window.style", "small");
-      bottomFrame.putClientProperty("JInternalFrame.isPalette", true);
+      bottomFrame.putClientProperty("JalviewInternalFrame.isPalette", true);
     }
     else
     {

diff --git a/src/jalview/jbgui/GStructureChooser.java b/src/jalview/jbgui/GStructureChooser.java
index 8cb5b3c..e9e12a5 100644 (file)
--- a/src/jalview/jbgui/GStructureChooser.java
+++ b/src/jalview/jbgui/GStructureChooser.java
@@ -49,7 +49,7 @@ import javax.swing.JButton;
 import javax.swing.JCheckBox;
 import javax.swing.JComboBox;
 import javax.swing.JFrame;
-import javax.swing.JInternalFrame;
+import jalview.gui.JalviewInternalFrame;
 import javax.swing.JLabel;
 import javax.swing.JList;
 import javax.swing.JPanel;
@@ -115,7 +115,7 @@ public abstract class GStructureChooser extends JPanel
   protected String frameTitle = MessageManager
           .getString("label.structure_chooser");
 
-  protected JInternalFrame mainFrame = new JInternalFrame(frameTitle);
+  protected JalviewInternalFrame mainFrame = new JalviewInternalFrame(frameTitle);
 
   protected JComboBox<FilterOption> cmb_filterOption = new JComboBox<>();
 
@@ -1067,7 +1067,7 @@ public abstract class GStructureChooser extends JPanel
 
   protected abstract void validateSelections();
 
-  public JInternalFrame getFrame()
+  public JalviewInternalFrame getFrame()
   {
     return mainFrame;
   }

diff --git a/src/jalview/jbgui/GStructureViewer.java b/src/jalview/jbgui/GStructureViewer.java
index 18e4c9f..19196f8 100644 (file)
--- a/src/jalview/jbgui/GStructureViewer.java
+++ b/src/jalview/jbgui/GStructureViewer.java
@@ -25,7 +25,7 @@ import java.awt.GridLayout;
 import java.awt.event.ActionEvent;
 import java.awt.event.ActionListener;
 
-import javax.swing.JInternalFrame;
+import jalview.gui.JalviewInternalFrame;
 import javax.swing.JLabel;
 import javax.swing.JMenu;
 import javax.swing.JMenuBar;
@@ -39,7 +39,7 @@ import jalview.util.ImageMaker.TYPE;
 import jalview.util.MessageManager;
 
 @SuppressWarnings("serial")
-public abstract class GStructureViewer extends JInternalFrame
+public abstract class GStructureViewer extends JalviewInternalFrame
         implements JalviewStructureDisplayI, ColourChangeListener
 {
   // private AAStructureBindingModel bindingModel;

diff --git a/src/jalview/jbgui/GTreePanel.java b/src/jalview/jbgui/GTreePanel.java
index 2a1b11f..a90771b 100755 (executable)
--- a/src/jalview/jbgui/GTreePanel.java
+++ b/src/jalview/jbgui/GTreePanel.java
@@ -26,7 +26,7 @@ import java.awt.event.ActionEvent;
 import java.awt.event.ActionListener;
 
 import javax.swing.JCheckBoxMenuItem;
-import javax.swing.JInternalFrame;
+import jalview.gui.JalviewInternalFrame;
 import javax.swing.JMenu;
 import javax.swing.JMenuBar;
 import javax.swing.JMenuItem;
@@ -38,7 +38,7 @@ import jalview.util.ImageMaker.TYPE;
 import jalview.util.MessageManager;
 
 @SuppressWarnings("serial")
-public class GTreePanel extends JInternalFrame
+public class GTreePanel extends JalviewInternalFrame
 {
   BorderLayout borderLayout1 = new BorderLayout();
 

diff --git a/src/jalview/project/Jalview2XML.java b/src/jalview/project/Jalview2XML.java
index 6f26036..52d818c 100644 (file)
--- a/src/jalview/project/Jalview2XML.java
+++ b/src/jalview/project/Jalview2XML.java
@@ -26,7 +26,6 @@ import static jalview.math.RotatableMatrix.Axis.Z;
 
 import java.awt.Color;
 import java.awt.Font;
-import java.awt.FontMetrics;
 import java.awt.Rectangle;
 import java.io.BufferedReader;
 import java.io.ByteArrayInputStream;
@@ -2516,6 +2515,7 @@ public class Jalview2XML
     return BitSet.valueOf(newlongvals);
 
   }
+
   private CalcIdParam createCalcIdParam(String calcId, AlignViewport av)
   {
     AutoCalcSetting settings = av.getCalcIdSettingsFor(calcId);

diff --git a/src/jalview/ws/jws2/MsaWSThread.java b/src/jalview/ws/jws2/MsaWSThread.java
index ee0fbc5..6ab0c4f 100644 (file)
--- a/src/jalview/ws/jws2/MsaWSThread.java
+++ b/src/jalview/ws/jws2/MsaWSThread.java
@@ -46,7 +46,7 @@ import java.util.List;
 import java.util.Map;
 import java.util.Vector;
 
-import javax.swing.JInternalFrame;
+import jalview.gui.JalviewInternalFrame;
 
 import compbio.data.msa.MsaWS;
 import compbio.metadata.Argument;
@@ -1045,7 +1045,7 @@ class MsaWSThread extends AWS2Thread implements WSClientI
         af2.setTitle(complementTitle);
         String linkedTitle = MessageManager
                 .getString("label.linked_view_title");
-        JInternalFrame splitFrame = new SplitFrame(
+        JalviewInternalFrame splitFrame = new SplitFrame(
                 al.isNucleotide() ? af : af2, al.isNucleotide() ? af2 : af);
         Desktop.addInternalFrame(splitFrame, linkedTitle, -1, -1);
         return;