remove mentions of non-functional RNAInteraction colourscheme

diff --git a/src/jalview/appletgui/AlignFrame.java b/src/jalview/appletgui/AlignFrame.java
index e5bd3d6..04e86fa 100644 (file)
--- a/src/jalview/appletgui/AlignFrame.java
+++ b/src/jalview/appletgui/AlignFrame.java
@@ -1036,10 +1036,7 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener,
     {\r
       changeColour(new PurinePyrimidineColourScheme());\r
     }\r
-    else if (source == RNAInteractionColour)\r
-    {\r
-      changeColour(new RNAInteractionColourScheme());\r
-    }\r
+\r
     else if (source == RNAHelixColour)\r
     {\r
       new RNAHelicesColourChooser(viewport, alignPanel);\r
@@ -3271,7 +3268,7 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener,
     colourMenu.add(buriedColour);\r
     colourMenu.add(nucleotideColour);\r
     colourMenu.add(purinePyrimidineColour);\r
-    colourMenu.add(RNAInteractionColour);\r
+    //    colourMenu.add(RNAInteractionColour);\r
     colourMenu.add(tcoffeeColour);\r
     colourMenu.add(userDefinedColour);\r
     colourMenu.addSeparator();\r

diff --git a/src/jalview/gui/PopupMenu.java b/src/jalview/gui/PopupMenu.java
index ef19521..aa50dcb 100644 (file)
--- 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 (executable)
--- 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];