From 3a35b4b1a2740fef3fc5f14a784b071a7af15b0a Mon Sep 17 00:00:00 2001
From: jprocter <jprocter@compbio.dundee.ac.uk>
Date: Fri, 28 Oct 2011 17:25:33 +0100
Subject: [PATCH] (JAL-885) RNA helix and purine pyrimidine colouring styles
 in applet

---
 src/jalview/appletgui/AlignFrame.java |   32 +++++++++++++++++++++++++++++++-
 1 file changed, 31 insertions(+), 1 deletion(-)

diff --git a/src/jalview/appletgui/AlignFrame.java b/src/jalview/appletgui/AlignFrame.java
index 3ebc083..ea5ead8 100644
--- a/src/jalview/appletgui/AlignFrame.java
+++ b/src/jalview/appletgui/AlignFrame.java
@@ -131,7 +131,20 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener,
       }
 
     }
-
+    if (viewport.getAlignment().isNucleotide())
+    {
+      viewport.updateStrucConsensus(alignPanel);
+      if (viewport.getAlignment().hasRNAStructure())
+      {
+        RNAHelixColour.setEnabled(true);
+      }
+      else {
+        RNAHelixColour.setEnabled(false);
+      }
+    } else {
+      RNAHelixColour.setEnabled(false);
+      purinePyrimidineColour.setEnabled(false);
+    }
     // Some JVMS send keyevents to Top frame or lowest panel,
     // Havent worked out why yet. So add to both this frame and seqCanvas for
     // now
@@ -919,6 +932,14 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener,
     {
       changeColour(new NucleotideColourScheme());
     }
+    else if (source == purinePyrimidineColour)
+    {
+      changeColour(new PurinePyrimidineColourScheme());
+    }
+    else if (source == RNAHelixColour)
+    {
+      new RNAHelicesColourChooser(viewport, alignPanel);
+    }
     else if (source == modifyPID)
     {
       modifyPID_actionPerformed();
@@ -2774,6 +2795,9 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener,
 
   MenuItem buriedColour = new MenuItem();
 
+  MenuItem purinePyrimidineColour = new MenuItem();
+  MenuItem RNAHelixColour = new MenuItem();
+  
   MenuItem userDefinedColour = new MenuItem();
 
   MenuItem PIDColour = new MenuItem();
@@ -2962,6 +2986,10 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener,
     turnColour.addActionListener(this);
     buriedColour.setLabel("Buried Index");
     buriedColour.addActionListener(this);
+    purinePyrimidineColour.setLabel("Purine/Pyrimidine");
+    purinePyrimidineColour.addActionListener(this);
+    RNAHelixColour.setLabel("by RNA Helices");
+    RNAHelixColour.addActionListener(this);
     userDefinedColour.setLabel("User Defined...");
     userDefinedColour.addActionListener(this);
     PIDColour.setLabel("Percentage Identity");
@@ -3175,6 +3203,7 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener,
     colourMenu.add(turnColour);
     colourMenu.add(buriedColour);
     colourMenu.add(nucleotideColour);
+    colourMenu.add(purinePyrimidineColour);
     colourMenu.add(userDefinedColour);
     colourMenu.addSeparator();
     colourMenu.add(conservationMenuItem);
@@ -3182,6 +3211,7 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener,
     colourMenu.add(abovePIDThreshold);
     colourMenu.add(modifyPID);
     colourMenu.add(annotationColour);
+    colourMenu.add(RNAHelixColour);
     calculateMenu.add(sort);
     calculateMenu.add(calculate);
     calculateMenu.addSeparator();
-- 
1.7.10.2