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 de1487a..a37746c 100755 (executable)
--- a/src/jalview/jbgui/GAlignFrame.java
+++ b/src/jalview/jbgui/GAlignFrame.java
@@ -139,6 +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();
@@ -182,6 +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();
 
@@ -454,7 +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"));
 
@@ -532,6 +537,11 @@ public class GAlignFrame extends JInternalFrame
         purinePyrimidineColour.setSelected(true);
 
         break;
+        
+      case ColourSchemeProperty.RNAINTERACTION:
+          RNAInteractionColour.setSelected(true);
+
+          break;
       /*
        * case ColourSchemeProperty.COVARIATION:
        * covariationColour.setSelected(true);
@@ -618,7 +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)
@@ -911,14 +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() {
@@ -1200,6 +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()
@@ -1874,6 +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);
@@ -1883,7 +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();
@@ -1947,8 +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();
@@ -2268,6 +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) { }
@@ -2308,6 +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)
   {