From aebfa57bbc491dfa8c231704a385ed14f6a5e8ae Mon Sep 17 00:00:00 2001
From: jprocter <jprocter@compbio.dundee.ac.uk>
Date: Fri, 7 Dec 2012 14:15:43 +0000
Subject: [PATCH 1/1] remove mentions of non-functional RNAInteraction
 colourscheme

---
 src/jalview/appletgui/AlignFrame.java         |    7 ++-----
 src/jalview/gui/PopupMenu.java                |   24 +++++-------------------
 src/jalview/schemes/ColourSchemeProperty.java |   11 +++--------
 3 files changed, 10 insertions(+), 32 deletions(-)

diff --git a/src/jalview/appletgui/AlignFrame.java b/src/jalview/appletgui/AlignFrame.java
index e5bd3d6..04e86fa 100644
--- a/src/jalview/appletgui/AlignFrame.java
+++ b/src/jalview/appletgui/AlignFrame.java
@@ -1036,10 +1036,7 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener,
     {
       changeColour(new PurinePyrimidineColourScheme());
     }
-    else if (source == RNAInteractionColour)
-    {
-      changeColour(new RNAInteractionColourScheme());
-    }
+
     else if (source == RNAHelixColour)
     {
       new RNAHelicesColourChooser(viewport, alignPanel);
@@ -3271,7 +3268,7 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener,
     colourMenu.add(buriedColour);
     colourMenu.add(nucleotideColour);
     colourMenu.add(purinePyrimidineColour);
-    colourMenu.add(RNAInteractionColour);
+    //    colourMenu.add(RNAInteractionColour);
     colourMenu.add(tcoffeeColour);
     colourMenu.add(userDefinedColour);
     colourMenu.addSeparator();
diff --git a/src/jalview/gui/PopupMenu.java b/src/jalview/gui/PopupMenu.java
index ef19521..aa50dcb 100644
--- a/src/jalview/gui/PopupMenu.java
+++ b/src/jalview/gui/PopupMenu.java
@@ -470,10 +470,7 @@ public class PopupMenu extends JPopupMenu
         purinePyrimidineColour.setSelected(true);
       }
       
-      else if (sg.cs instanceof RNAInteractionColourScheme)
-      {
-        RNAInteractionColour.setSelected(true);
-      }
+   
       /*
        * else if (sg.cs instanceof CovariationColourScheme) {
        * covariationColour.setSelected(true); }
@@ -1165,7 +1162,8 @@ public class PopupMenu extends JPopupMenu
     colourMenu.add(buriedColour);
     colourMenu.add(nucleotideMenuItem);
     if (ap.getAlignment().isNucleotide()) {
-      colourMenu.add(RNAInteractionColour);
+	// JBPNote - commented since the colourscheme isn't functional
+	//  colourMenu.add(RNAInteractionColour);
     	colourMenu.add(purinePyrimidineColour);
     }
     // colourMenu.add(covariationColour);
@@ -1330,15 +1328,7 @@ public class PopupMenu extends JPopupMenu
               }
             });
     
-    RNAInteractionColour.setText("RNA Interaction type");
-    RNAInteractionColour
-            .addActionListener(new java.awt.event.ActionListener()
-            {
-              public void actionPerformed(ActionEvent e)
-              {
-                RNAInteractionColour_actionPerformed();
-              }
-            });
+   
     /*
      * covariationColour.addActionListener(new java.awt.event.ActionListener() {
      * public void actionPerformed(ActionEvent e) {
@@ -1526,11 +1516,7 @@ public class PopupMenu extends JPopupMenu
     refresh();
   }
 
-  protected void RNAInteractionColour_actionPerformed()
-  {
-    getGroup().cs = new RNAInteractionColourScheme();
-    refresh();
-  }
+
   /*
    * protected void covariationColour_actionPerformed() { getGroup().cs = new
    * CovariationColourScheme(sequence.getAnnotation()[0]); refresh(); }
diff --git a/src/jalview/schemes/ColourSchemeProperty.java b/src/jalview/schemes/ColourSchemeProperty.java
index 4132f32..f748c96 100755
--- a/src/jalview/schemes/ColourSchemeProperty.java
+++ b/src/jalview/schemes/ColourSchemeProperty.java
@@ -246,10 +246,7 @@ public class ColourSchemeProperty
     {
       index = TCOFFEE;
     }
-    else if (cs instanceof RNAInteractionColourScheme)
-    {
-      index = RNAINTERACTION;
-    }
+   
     
     
     /*
@@ -504,14 +501,12 @@ public class ColourSchemeProperty
       cs = new TCoffeeColourScheme(coll);
       break;
       
-    case RNAINTERACTION:
-        cs = new RNAInteractionColourScheme();
-        break;
+
       
     // case COVARIATION:
     // cs = new CovariationColourScheme(annotation);
 
-      // break;
+    // break;
 
     case USER_DEFINED:
       Color[] col = new Color[24];
-- 
1.7.10.2