X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fjbgui%2FGStructureViewer.java;h=b1b5200a249c4f19838ef482af31f4a6b3868515;hb=d904a499f1863e96cd699e0c5f7f0f81710e8ad9;hp=f7fa6db1b1c52e3cc5b7a071248ca71a5b21fa92;hpb=0061941739d032ad91aed23bda07e2ad543c2ccb;p=jalview.git

diff --git a/src/jalview/jbgui/GStructureViewer.java b/src/jalview/jbgui/GStructureViewer.java
index f7fa6db..b1b5200 100644
--- a/src/jalview/jbgui/GStructureViewer.java
+++ b/src/jalview/jbgui/GStructureViewer.java
@@ -1,6 +1,6 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.5)
- * 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 +181,17 @@ 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()
@@ -181,9 +201,20 @@ public class GStructureViewer extends JInternalFrame
         jmolHelp_actionPerformed(actionEvent);
       }
     });
+    alignStructs.setText("Align structures");
+    alignStructs.addActionListener(new ActionListener()
+    {
+      public void actionPerformed(ActionEvent actionEvent)
+      {
+        alignStructs_actionPerformed(actionEvent);
+      }
+    });
+    jmolActionMenu.setText("Jmol");
     menuBar.add(fileMenu);
     menuBar.add(viewMenu);
     menuBar.add(colourMenu);
+    menuBar.add(jmolActionMenu);
+    jmolActionMenu.setVisible(false);
     menuBar.add(helpMenu);
     fileMenu.add(savemenu);
     fileMenu.add(viewMapping);
@@ -202,7 +233,9 @@ 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);
@@ -216,8 +249,18 @@ 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)
+  {
   }
 
   JMenuBar menuBar = new JMenuBar();
@@ -234,13 +277,17 @@ 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();
+
+  protected JMenuItem alignStructs = new JMenuItem();
 
   JMenuItem backGround = new JMenuItem();
 
@@ -263,9 +310,14 @@ public class GStructureViewer extends JInternalFrame
   protected JRadioButtonMenuItem turnColour = new JRadioButtonMenuItem();
 
   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();
@@ -341,6 +393,11 @@ public class GStructureViewer extends JInternalFrame
   {
 
   }
+  
+  public void purinePyrimidineColour_actionPerformed(ActionEvent actionEvent)
+  {
+
+  }
 
   public void userColour_actionPerformed(ActionEvent actionEvent)
   {