Merge branch 'features/JAL-1933_occupancy' into develop

[jalview.git] / src / jalview / jbgui / GAlignFrame.java

diff --git a/src/jalview/jbgui/GAlignFrame.java b/src/jalview/jbgui/GAlignFrame.java
index dff20d3..b759d64 100755 (executable)
--- a/src/jalview/jbgui/GAlignFrame.java
+++ b/src/jalview/jbgui/GAlignFrame.java
@@ -25,7 +25,7 @@ import jalview.api.SplitContainerI;
 import jalview.bin.Cache;
 import jalview.gui.JvSwingUtils;
 import jalview.gui.Preferences;
-import jalview.io.FileFormat;
+import jalview.io.FileFormats;
 import jalview.util.MessageManager;
 import jalview.util.Platform;
 
@@ -65,8 +65,6 @@ public class GAlignFrame extends JInternalFrame
 
   protected JMenuItem closeMenuItem = new JMenuItem();
 
-  protected JMenu colourMenu = new JMenu();
-
   protected JMenu webService = new JMenu();
 
   protected JMenuItem webServiceNoServices;
@@ -81,8 +79,6 @@ public class GAlignFrame extends JInternalFrame
 
   protected JMenu outputTextboxMenu = new JMenu();
 
-  protected JRadioButtonMenuItem textColour;
-
   protected JCheckBoxMenuItem annotationPanelMenuItem = new JCheckBoxMenuItem();
 
   protected JCheckBoxMenuItem colourTextMenuItem = new JCheckBoxMenuItem();
@@ -93,14 +89,10 @@ public class GAlignFrame extends JInternalFrame
 
   protected JMenuItem redoMenuItem = new JMenuItem();
 
-  protected JCheckBoxMenuItem conservationMenuItem;
-
   protected JCheckBoxMenuItem wrapMenuItem = new JCheckBoxMenuItem();
 
   protected JCheckBoxMenuItem renderGapsMenuItem = new JCheckBoxMenuItem();
 
-  protected JCheckBoxMenuItem abovePIDThreshold;
-
   public JCheckBoxMenuItem showSeqFeatures = new JCheckBoxMenuItem();
 
   JMenuItem copy = new JMenuItem();
@@ -109,8 +101,6 @@ public class GAlignFrame extends JInternalFrame
 
   JMenu pasteMenu = new JMenu();
 
-  protected JCheckBoxMenuItem applyToAllGroups;
-
   protected JCheckBoxMenuItem seqLimits = new JCheckBoxMenuItem();
 
   protected JCheckBoxMenuItem scaleAbove = new JCheckBoxMenuItem();
@@ -119,10 +109,20 @@ public class GAlignFrame extends JInternalFrame
 
   protected JCheckBoxMenuItem scaleRight = new JCheckBoxMenuItem();
 
-  protected JMenuItem modifyPID;
+  protected JCheckBoxMenuItem applyToAllGroups;
+
+  protected JMenu colourMenu = new JMenu();
+
+  protected JMenuItem textColour;
+
+  protected JCheckBoxMenuItem conservationMenuItem;
 
   protected JMenuItem modifyConservation;
 
+  protected JCheckBoxMenuItem abovePIDThreshold;
+
+  protected JMenuItem modifyPID;
+
   protected JMenuItem annotationColour;
 
   protected JMenu sortByTreeMenu = new JMenu();
@@ -211,7 +211,7 @@ public class GAlignFrame extends JInternalFrame
       setJMenuBar(alignFrameMenuBar);
 
       // dynamically fill save as menu with available formats
-      for (String ff : FileFormat.getWritableFormats(true))
+      for (String ff : FileFormats.getInstance().getWritableFormats(true))
       {
         JMenuItem item = new JMenuItem(ff);
 
@@ -975,7 +975,7 @@ public class GAlignFrame extends JInternalFrame
     });
 
     JMenuItem createGroup = new JMenuItem(
-            MessageManager.getString("action.create_groups"));
+            MessageManager.getString("action.create_group"));
     keyStroke = KeyStroke.getKeyStroke(KeyEvent.VK_G, Toolkit
             .getDefaultToolkit().getMenuShortcutKeyMask(), false);
     al = new ActionListener()
@@ -1653,6 +1653,7 @@ public class GAlignFrame extends JInternalFrame
 
     formatMenu.setText(MessageManager.getString("action.format"));
     JMenu selectMenu = new JMenu(MessageManager.getString("action.select"));
+
     idRightAlign.setText(MessageManager
             .getString("label.right_align_sequence_id"));
     idRightAlign.addActionListener(new ActionListener()
@@ -1904,6 +1905,12 @@ public class GAlignFrame extends JInternalFrame
     // selectMenu.add(listenToViewSelections);
   }
 
+  protected void configureSelectMenu()
+  {
+    // TODO Auto-generated method stub
+
+  }
+
   /**
    * Constructs the entries on the Colour menu (but does not add them to the
    * menu).
@@ -1917,12 +1924,12 @@ public class GAlignFrame extends JInternalFrame
       @Override
       public void actionPerformed(ActionEvent e)
       {
-        applyToAllGroups_actionPerformed();
+        applyToAllGroups_actionPerformed(applyToAllGroups.isSelected());
       }
     });
 
-    textColour = new JRadioButtonMenuItem(
-            MessageManager.getString("action.set_text_colour"));
+    textColour = new JMenuItem(
+            MessageManager.getString("label.text_colour"));
     textColour.addActionListener(new ActionListener()
     {
       @Override
@@ -1939,7 +1946,8 @@ public class GAlignFrame extends JInternalFrame
       @Override
       public void actionPerformed(ActionEvent e)
       {
-        conservationMenuItem_actionPerformed();
+        conservationMenuItem_actionPerformed(conservationMenuItem
+                .isSelected());
       }
     });
 
@@ -1950,7 +1958,7 @@ public class GAlignFrame extends JInternalFrame
       @Override
       public void actionPerformed(ActionEvent e)
       {
-        abovePIDThreshold_actionPerformed();
+        abovePIDThreshold_actionPerformed(abovePIDThreshold.isSelected());
       }
     });
     modifyPID = new JMenuItem(
@@ -2342,7 +2350,7 @@ public class GAlignFrame extends JInternalFrame
   {
   }
 
-  protected void conservationMenuItem_actionPerformed()
+  protected void conservationMenuItem_actionPerformed(boolean selected)
   {
   }
 
@@ -2358,7 +2366,7 @@ public class GAlignFrame extends JInternalFrame
   {
   }
 
-  protected void abovePIDThreshold_actionPerformed()
+  protected void abovePIDThreshold_actionPerformed(boolean selected)
   {
   }
 
@@ -2398,7 +2406,7 @@ public class GAlignFrame extends JInternalFrame
   {
   }
 
-  protected void applyToAllGroups_actionPerformed()
+  protected void applyToAllGroups_actionPerformed(boolean selected)
   {
   }