formatting

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

diff --git a/src/jalview/jbgui/GStructureViewer.java b/src/jalview/jbgui/GStructureViewer.java
index 0fb2c4c..2b99d2b 100644 (file)
--- a/src/jalview/jbgui/GStructureViewer.java
+++ b/src/jalview/jbgui/GStructureViewer.java
@@ -1,6 +1,6 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.6)
- * Copyright (C) 2010 J Procter, AM Waterhouse, G Barton, M Clamp, S Searle
+ * 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
  * 
  * This file is part of Jalview.
  * 
@@ -83,7 +83,7 @@ public class GStructureViewer extends JInternalFrame
         backGround_actionPerformed(actionEvent);
       }
     });
-    seqColour.setSelected(true);
+    seqColour.setSelected(false);
     seqColour.setText("By Sequence");
     seqColour.addActionListener(new ActionListener()
     {
@@ -164,6 +164,15 @@ public class GStructureViewer extends JInternalFrame
         buriedColour_actionPerformed(actionEvent);
       }
     });
+    purinePyrimidineColour.setText("Purine/Pyrimidine");
+    purinePyrimidineColour.addActionListener(new ActionListener()
+    {
+      public void actionPerformed(ActionEvent actionEvent)
+      {
+        purinePyrimidineColour_actionPerformed(actionEvent);
+      }
+    });
+
     userColour.setText("User Defined ...");
     userColour.addActionListener(new ActionListener()
     {
@@ -172,6 +181,16 @@ public class GStructureViewer extends JInternalFrame
         userColour_actionPerformed(actionEvent);
       }
     });
+    jmolColour.setSelected(false);
+    jmolColour.setText("Colour with Jmol");
+    jmolColour.setToolTipText("Let Jmol manage structure colours.");
+    jmolColour.addActionListener(new ActionListener()
+    {
+      public void actionPerformed(ActionEvent actionEvent)
+      {
+        jmolColour_actionPerformed(actionEvent);
+      }
+    });
     helpMenu.setText("Help");
     jmolHelp.setText("Jmol Help");
     jmolHelp.addActionListener(new ActionListener()
@@ -213,7 +232,9 @@ public class GStructureViewer extends JInternalFrame
     colourMenu.add(strandColour);
     colourMenu.add(turnColour);
     colourMenu.add(buriedColour);
+    colourMenu.add(purinePyrimidineColour);
     colourMenu.add(userColour);
+    colourMenu.add(jmolColour);
     colourMenu.add(backGround);
 
     colourButtons.add(seqColour);
@@ -227,11 +248,16 @@ public class GStructureViewer extends JInternalFrame
     colourButtons.add(turnColour);
     colourButtons.add(buriedColour);
     colourButtons.add(userColour);
-    
+    colourButtons.add(jmolColour);
+
     helpMenu.add(jmolHelp);
     jmolActionMenu.add(alignStructs);
   }
 
+  protected void jmolColour_actionPerformed(ActionEvent actionEvent)
+  {
+  }
+
   protected void alignStructs_actionPerformed(ActionEvent actionEvent)
   {
   }
@@ -250,17 +276,17 @@ public class GStructureViewer extends JInternalFrame
 
   JMenuItem viewMapping = new JMenuItem();
 
-  JMenu viewMenu = new JMenu();
+  protected JMenu viewMenu = new JMenu();
 
   protected JMenu chainMenu = new JMenu();
 
   JMenu jMenu1 = new JMenu();
 
-  JMenu colourMenu = new JMenu();
+  protected JMenu colourMenu = new JMenu();
 
   protected JMenu jmolActionMenu = new JMenu();
 
-  JMenuItem alignStructs = new JMenuItem();
+  protected JMenuItem alignStructs = new JMenuItem();
 
   JMenuItem backGround = new JMenuItem();
 
@@ -284,8 +310,12 @@ public class GStructureViewer extends JInternalFrame
 
   protected JRadioButtonMenuItem buriedColour = new JRadioButtonMenuItem();
 
+  protected JRadioButtonMenuItem purinePyrimidineColour = new JRadioButtonMenuItem();
+
   protected JRadioButtonMenuItem userColour = new JRadioButtonMenuItem();
 
+  protected JRadioButtonMenuItem jmolColour = new JRadioButtonMenuItem();
+
   protected ButtonGroup colourButtons = new ButtonGroup();
 
   JMenu helpMenu = new JMenu();
@@ -362,6 +392,11 @@ public class GStructureViewer extends JInternalFrame
 
   }
 
+  public void purinePyrimidineColour_actionPerformed(ActionEvent actionEvent)
+  {
+
+  }
+
   public void userColour_actionPerformed(ActionEvent actionEvent)
   {