X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fappletgui%2FAlignFrame.java;h=16602c8374afc4265cfc513db794218b70dd4dd0;hb=a8f483d04205bb8273ee311c12968b7e86d205fa;hp=40999c6fe223a3200e3a8af43817f6772de3fa07;hpb=279af6f3b1803de7a1e467b83a7205df18e70d48;p=jalview.git

diff --git a/src/jalview/appletgui/AlignFrame.java b/src/jalview/appletgui/AlignFrame.java
index 40999c6..16602c8 100644
--- a/src/jalview/appletgui/AlignFrame.java
+++ b/src/jalview/appletgui/AlignFrame.java
@@ -1,5 +1,5 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2)
  * Copyright (C) 2014 The Jalview Authors
  * 
  * This file is part of Jalview.
@@ -53,6 +53,7 @@ import jalview.schemes.NucleotideColourScheme;
 import jalview.schemes.PIDColourScheme;
 import jalview.schemes.PurinePyrimidineColourScheme;
 import jalview.schemes.RNAHelicesColourChooser;
+import jalview.schemes.RNAInteractionColourScheme;
 import jalview.schemes.ResidueProperties;
 import jalview.schemes.StrandColourScheme;
 import jalview.schemes.TCoffeeColourScheme;
@@ -1045,6 +1046,10 @@ 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);
@@ -2810,6 +2815,8 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener,
 
   MenuItem purinePyrimidineColour = new MenuItem();
 
+  MenuItem RNAInteractionColour = new MenuItem();
+
   MenuItem RNAHelixColour = new MenuItem();
 
   MenuItem userDefinedColour = new MenuItem();
@@ -3017,6 +3024,8 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener,
     buriedColour.addActionListener(this);
     purinePyrimidineColour.setLabel(MessageManager.getString("label.purine_pyrimidine"));
     purinePyrimidineColour.addActionListener(this);
+    RNAInteractionColour.setLabel(MessageManager.getString("label.rna_interaction"));
+    RNAInteractionColour.addActionListener(this);
     RNAHelixColour.setLabel(MessageManager.getString("action.by_rna_helixes"));
     RNAHelixColour.addActionListener(this);
     userDefinedColour.setLabel(MessageManager.getString("action.user_defined"));
@@ -3243,6 +3252,7 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener,
     colourMenu.add(buriedColour);
     colourMenu.add(nucleotideColour);
     colourMenu.add(purinePyrimidineColour);
+    //    colourMenu.add(RNAInteractionColour);
     colourMenu.add(tcoffeeColour);
     colourMenu.add(userDefinedColour);
     colourMenu.addSeparator();
@@ -3362,7 +3372,7 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener,
       fileMenu.remove(closeMenuItem);
       fileMenu.remove(3); // Remove Seperator
       embeddedMenu = makeEmbeddedPopupMenu(alignFrameMenuBar, "Arial",
-              Font.PLAIN, 10, false); // use our own fonts.
+              Font.PLAIN, 11, false); // use our own fonts.
       // and actually add the components to the applet area
       viewport.applet.setLayout(new BorderLayout());
       viewport.applet.add(embeddedMenu, BorderLayout.NORTH);