Merge branch 'JAL-1139_proguard' into develop

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

diff --git a/src/jalview/jbgui/GAlignFrame.java b/src/jalview/jbgui/GAlignFrame.java
index c64568a..a37746c 100755 (executable)
--- a/src/jalview/jbgui/GAlignFrame.java
+++ b/src/jalview/jbgui/GAlignFrame.java
@@ -1,13 +1,13 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.7)
- * Copyright (C) 2011 J Procter, AM Waterhouse, J Engelhardt, LM Lui, G Barton, M Clamp, S Searle
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8)
+ * Copyright (C) 2012 J Procter, AM Waterhouse, LM Lui, J Engelhardt, G Barton, M Clamp, S Searle
  * 
  * This file is part of Jalview.
  * 
  * Jalview is free software: you can redistribute it and/or
  * modify it under the terms of the GNU General Public License 
  * as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
- * 
+ *  
  * Jalview is distributed in the hope that it will be useful, but 
  * WITHOUT ANY WARRANTY; without even the implied warranty 
  * of MERCHANTABILITY or FITNESS FOR A PARTICULAR 
@@ -18,6 +18,7 @@
 package jalview.jbgui;
 
 import jalview.schemes.ColourSchemeProperty;
+import jalview.util.MessageManager;
 
 import java.awt.BorderLayout;
 import java.awt.Color;
@@ -138,6 +139,8 @@ public class GAlignFrame extends JInternalFrame
   protected JRadioButtonMenuItem nucleotideColour = new JRadioButtonMenuItem();
 
   protected JRadioButtonMenuItem purinePyrimidineColour = new JRadioButtonMenuItem();
+  
+  protected JRadioButtonMenuItem RNAInteractionColour = new JRadioButtonMenuItem();
 
   // protected JRadioButtonMenuItem covariationColour = new
   // JRadioButtonMenuItem();
@@ -181,6 +184,9 @@ public class GAlignFrame extends JInternalFrame
   public JCheckBoxMenuItem showSeqFeaturesHeight = new JCheckBoxMenuItem();
 
   JMenuItem deleteGroups = new JMenuItem();
+  
+  JMenuItem createGroup = new JMenuItem();
+  JMenuItem unGroup = new JMenuItem();
 
   JMenuItem delete = new JMenuItem();
 
@@ -404,8 +410,8 @@ public class GAlignFrame extends JInternalFrame
 
               int option = JOptionPane.showInternalConfirmDialog(
                       jalview.gui.Desktop.desktop,
-                      "Remove from default list?",
-                      "Remove user defined colour",
+                      MessageManager.getString("label.remove_from_default_list"),
+                      MessageManager.getString("label.remove_user_defined_colour"),
                       JOptionPane.YES_NO_OPTION);
               if (option == JOptionPane.YES_OPTION)
               {
@@ -453,7 +459,7 @@ public class GAlignFrame extends JInternalFrame
     colours.add(purinePyrimidineColour);
     // colours.add(covariationColour);
     colours.add(tcoffeeColour);
-
+    colours.add(RNAInteractionColour);
     setColourSelected(jalview.bin.Cache
             .getDefault("DEFAULT_COLOUR", "None"));
 
@@ -531,6 +537,11 @@ public class GAlignFrame extends JInternalFrame
         purinePyrimidineColour.setSelected(true);
 
         break;
+        
+      case ColourSchemeProperty.RNAINTERACTION:
+          RNAInteractionColour.setSelected(true);
+
+          break;
       /*
        * case ColourSchemeProperty.COVARIATION:
        * covariationColour.setSelected(true);
@@ -617,7 +628,7 @@ public class GAlignFrame extends JInternalFrame
                 invertSequenceMenuItem_actionPerformed(e);
               }
             });
-    grpsFromSelection.setText("Make Groups for selection");
+    grpsFromSelection.setText("Make Groups For Selection");
     grpsFromSelection.addActionListener(new java.awt.event.ActionListener()
     {
       public void actionPerformed(ActionEvent e)
@@ -910,14 +921,22 @@ public class GAlignFrame extends JInternalFrame
     });
 
     purinePyrimidineColour.setText("Purine/Pyrimidine");
-    purinePyrimidineColour
-            .addActionListener(new java.awt.event.ActionListener()
+    purinePyrimidineColour.addActionListener(new java.awt.event.ActionListener()
             {
               public void actionPerformed(ActionEvent e)
               {
                 purinePyrimidineColour_actionPerformed(e);
               }
             });
+    
+    RNAInteractionColour.setText("RNA Interaction type");
+    RNAInteractionColour.addActionListener(new java.awt.event.ActionListener()
+            {
+              public void actionPerformed(ActionEvent e)
+              {
+                 RNAInteractionColour_actionPerformed(e);
+              }
+            });
     /*
      * covariationColour.setText("Covariation");
      * covariationColour.addActionListener(new java.awt.event.ActionListener() {
@@ -1199,6 +1218,28 @@ public class GAlignFrame extends JInternalFrame
         deleteGroups_actionPerformed(e);
       }
     });
+    createGroup.setText("Create group");
+    createGroup.setAccelerator(javax.swing.KeyStroke.getKeyStroke(
+            java.awt.event.KeyEvent.VK_G, Toolkit.getDefaultToolkit()
+                    .getMenuShortcutKeyMask(), false));
+    createGroup.addActionListener(new java.awt.event.ActionListener()
+    {
+      public void actionPerformed(ActionEvent e)
+      {
+        createGroup_actionPerformed(e);
+      }
+    });
+    unGroup.setText("Remove Group");
+    unGroup.setAccelerator(javax.swing.KeyStroke.getKeyStroke(
+            java.awt.event.KeyEvent.VK_G,Toolkit.getDefaultToolkit()
+                    .getMenuShortcutKeyMask() | java.awt.event.KeyEvent.SHIFT_MASK, false));
+    unGroup.addActionListener(new java.awt.event.ActionListener()
+    {
+      public void actionPerformed(ActionEvent e)
+      {
+        unGroup_actionPerformed(e);
+      }
+    });
     copy.setText("Copy");
     copy.setAccelerator(javax.swing.KeyStroke.getKeyStroke(
             java.awt.event.KeyEvent.VK_C, Toolkit.getDefaultToolkit()
@@ -1873,6 +1914,7 @@ public class GAlignFrame extends JInternalFrame
     colourMenu.add(buriedColour);
     colourMenu.add(nucleotideColour);
     colourMenu.add(purinePyrimidineColour);
+    colourMenu.add(RNAInteractionColour);
     // colourMenu.add(covariationColour);
     colourMenu.add(tcoffeeColour);
     colourMenu.add(userDefinedColour);
@@ -1882,7 +1924,7 @@ public class GAlignFrame extends JInternalFrame
     colourMenu.add(abovePIDThreshold);
     colourMenu.add(modifyPID);
     colourMenu.add(annotationColour);
-    colourMenu.add(rnahelicesColour);
+    colourMenu.add(rnahelicesColour);  
     calculateMenu.add(sort);
     calculateMenu.add(calculateTree);
     calculateMenu.addSeparator();
@@ -1946,8 +1988,10 @@ public class GAlignFrame extends JInternalFrame
     selectMenu.add(deselectAllSequenceMenuItem);
     selectMenu.add(invertSequenceMenuItem);
     selectMenu.add(invertColSel);
-    selectMenu.add(deleteGroups);
+    selectMenu.add(createGroup);
+    selectMenu.add(unGroup);
     selectMenu.add(grpsFromSelection);
+    selectMenu.add(deleteGroups);
     // TODO - determine if the listenToViewSelections button is needed : see bug
     // JAL-574
     // selectMenu.addSeparator();
@@ -2267,6 +2311,11 @@ public class GAlignFrame extends JInternalFrame
   protected void purinePyrimidineColour_actionPerformed(ActionEvent e)
   {
   }
+  
+  protected void RNAInteractionColour_actionPerformed(ActionEvent e)
+  {
+  }
+  
 
   /*
    * protected void covariationColour_actionPerformed(ActionEvent e) { }
@@ -2307,6 +2356,14 @@ public class GAlignFrame extends JInternalFrame
   protected void deleteGroups_actionPerformed(ActionEvent e)
   {
   }
+  
+  protected void createGroup_actionPerformed(ActionEvent e)
+  {
+  }
+  
+  protected void unGroup_actionPerformed(ActionEvent e)
+  {
+  }
 
   protected void copy_actionPerformed(ActionEvent e)
   {