Merge branch 'JAL-1397' into develop

[jalview.git] / src / jalview / schemes / ColourSchemeProperty.java

diff --git a/src/jalview/schemes/ColourSchemeProperty.java b/src/jalview/schemes/ColourSchemeProperty.java
index 4132f32..8996691 100755 (executable)
--- a/src/jalview/schemes/ColourSchemeProperty.java
+++ b/src/jalview/schemes/ColourSchemeProperty.java
@@ -1,6 +1,6 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8)
- * Copyright (C) 2012 J Procter, AM Waterhouse, LM Lui, J Engelhardt, G Barton, M Clamp, S Searle
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Copyright (C) 2014 The Jalview Authors
  * 
  * This file is part of Jalview.
  * 
@@ -14,6 +14,7 @@
  * PURPOSE.  See the GNU General Public License for more details.
  * 
  * You should have received a copy of the GNU General Public License along with Jalview.  If not, see <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
  */
 package jalview.schemes;
 
@@ -85,6 +86,8 @@ public class ColourSchemeProperty
   public static final int COVARIATION = 14;
 
   public static final int TCOFFEE = 15;
+  
+  public static final int RNAHELIX = 16;
 
   public static final int RNAINTERACTION = 16;
 
@@ -93,7 +96,7 @@ public class ColourSchemeProperty
    */
   public static final int FIRST_COLOUR = NONE;
 
-  public static final int LAST_COLOUR = NUCLEOTIDE;
+  public static final int LAST_COLOUR = RNAHELIX;
 
   /**
    * DOCUMENT ME!
@@ -168,11 +171,14 @@ public class ColourSchemeProperty
     {
       ret = PURINEPYRIMIDINE;
     }
-    
     else if (name.equalsIgnoreCase("RNA Interaction type"))
     {
       ret = RNAINTERACTION;
     }
+    else if (name.equalsIgnoreCase("RNA Helices"))
+    {
+      ret = RNAHELIX;
+    }
     // else if (name.equalsIgnoreCase("Covariation"))
     // {
     // ret = COVARIATION;
@@ -246,12 +252,16 @@ public class ColourSchemeProperty
     {
       index = TCOFFEE;
     }
-    else if (cs instanceof RNAInteractionColourScheme)
-    {
-      index = RNAINTERACTION;
-    }
+<<<<<<< HEAD
+   
     
     
+=======
+    else if (cs instanceof RNAHelicesColour)
+    {
+      index = RNAHELIX;
+    }
+>>>>>>> JAL-952_rnahelix
     /*
      * else if (cs instanceof CovariationColourScheme) { index = COVARIATION; }
      */
@@ -346,11 +356,18 @@ public class ColourSchemeProperty
       ret = "T-Coffee Scores";
 
       break;
+<<<<<<< HEAD
       
     case RNAINTERACTION:
         ret = "RNA Interaction type";
 
         break;
+=======
+    case RNAHELIX:
+      ret = "RNA Helices";
+
+      break;
+>>>>>>> JAL-952_rnahelix
     /*
      * case COVARIATION: ret = "Covariation";
      * 
@@ -503,15 +520,14 @@ public class ColourSchemeProperty
     case TCOFFEE:
       cs = new TCoffeeColourScheme(coll);
       break;
+    
+    case RNAHELIX:
+      cs = new RNAHelicesColour(coll);
+      break;
       
-    case RNAINTERACTION:
-        cs = new RNAInteractionColourScheme();
-        break;
-      
-    // case COVARIATION:
-    // cs = new CovariationColourScheme(annotation);
-
-      // break;
+      // case COVARIATION:
+      // cs = new CovariationColourScheme(annotation);
+    // break;
 
     case USER_DEFINED:
       Color[] col = new Color[24];