Merge branch 'develop' into bug/JAL-1608createGroups

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

diff --git a/src/jalview/jbgui/GAlignFrame.java b/src/jalview/jbgui/GAlignFrame.java
index c8aa94f..b759d64 100755 (executable)
--- a/src/jalview/jbgui/GAlignFrame.java
+++ b/src/jalview/jbgui/GAlignFrame.java
@@ -113,7 +113,7 @@ public class GAlignFrame extends JInternalFrame
 
   protected JMenu colourMenu = new JMenu();
 
-  protected JRadioButtonMenuItem textColour;
+  protected JMenuItem textColour;
 
   protected JCheckBoxMenuItem conservationMenuItem;
 
@@ -752,17 +752,6 @@ public class GAlignFrame extends JInternalFrame
     };
     addMenuActionAndAccelerator(keyStroke, redoMenuItem, al);
 
-    conservationMenuItem.setText(MessageManager
-            .getString("action.by_conservation"));
-    conservationMenuItem.addActionListener(new ActionListener()
-    {
-      @Override
-      public void actionPerformed(ActionEvent e)
-      {
-        conservationMenuItem_actionPerformed();
-      }
-    });
-
     wrapMenuItem.setText(MessageManager.getString("label.wrap"));
     wrapMenuItem.addActionListener(new ActionListener()
     {
@@ -815,17 +804,6 @@ public class GAlignFrame extends JInternalFrame
     };
     addMenuActionAndAccelerator(keyStroke, findMenuItem, al);
 
-    abovePIDThreshold.setText(MessageManager
-            .getString("label.above_identity_threshold"));
-    abovePIDThreshold.addActionListener(new ActionListener()
-    {
-      @Override
-      public void actionPerformed(ActionEvent e)
-      {
-        abovePIDThreshold_actionPerformed();
-      }
-    });
-
     showSeqFeatures.setText(MessageManager
             .getString("label.show_sequence_features"));
     showSeqFeatures.addActionListener(new ActionListener()
@@ -997,7 +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()
@@ -1217,27 +1195,6 @@ public class GAlignFrame extends JInternalFrame
 
     });
 
-    modifyPID = new JMenuItem(
-            MessageManager.getString("label.modify_identity_threshold"));
-    modifyPID.addActionListener(new ActionListener()
-    {
-      @Override
-      public void actionPerformed(ActionEvent e)
-      {
-        modifyPID_actionPerformed();
-      }
-    });
-    modifyConservation.setText(MessageManager
-            .getString("label.modify_conservation_threshold"));
-    modifyConservation.addActionListener(new ActionListener()
-    {
-      @Override
-      public void actionPerformed(ActionEvent e)
-      {
-        modifyConservation_actionPerformed();
-      }
-    });
-
     sortByTreeMenu
             .setText(MessageManager.getString("action.by_tree_order"));
     sort.setText(MessageManager.getString("action.sort"));
@@ -1696,6 +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()
@@ -1947,6 +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).
@@ -1960,12 +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
@@ -1982,7 +1946,8 @@ public class GAlignFrame extends JInternalFrame
       @Override
       public void actionPerformed(ActionEvent e)
       {
-        conservationMenuItem_actionPerformed();
+        conservationMenuItem_actionPerformed(conservationMenuItem
+                .isSelected());
       }
     });
 
@@ -1993,7 +1958,7 @@ public class GAlignFrame extends JInternalFrame
       @Override
       public void actionPerformed(ActionEvent e)
       {
-        abovePIDThreshold_actionPerformed();
+        abovePIDThreshold_actionPerformed(abovePIDThreshold.isSelected());
       }
     });
     modifyPID = new JMenuItem(
@@ -2385,7 +2350,7 @@ public class GAlignFrame extends JInternalFrame
   {
   }
 
-  protected void conservationMenuItem_actionPerformed()
+  protected void conservationMenuItem_actionPerformed(boolean selected)
   {
   }
 
@@ -2401,7 +2366,7 @@ public class GAlignFrame extends JInternalFrame
   {
   }
 
-  protected void abovePIDThreshold_actionPerformed()
+  protected void abovePIDThreshold_actionPerformed(boolean selected)
   {
   }
 
@@ -2441,7 +2406,7 @@ public class GAlignFrame extends JInternalFrame
   {
   }
 
-  protected void applyToAllGroups_actionPerformed()
+  protected void applyToAllGroups_actionPerformed(boolean selected)
   {
   }