X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fschemes%2FColourSchemeProperty.java;h=cc303d65e21308178bd79cd596701250d85897e8;hb=5002a0f587ac8f1c18117e29bb4be2754743afc2;hp=f748c967b0188602d9bf18db6fffed4854f374ce;hpb=aebfa57bbc491dfa8c231704a385ed14f6a5e8ae;p=jalview.git

diff --git a/src/jalview/schemes/ColourSchemeProperty.java b/src/jalview/schemes/ColourSchemeProperty.java
index f748c96..cc303d6 100755
--- a/src/jalview/schemes/ColourSchemeProperty.java
+++ b/src/jalview/schemes/ColourSchemeProperty.java
@@ -1,19 +1,22 @@
 /*
- * 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 2.8.2)
+ * Copyright (C) 2014 The Jalview Authors
  * 
  * This file is part of Jalview.
  * 
  * Jalview is free software: you can redistribute it and/or
  * modify it under the terms of the GNU General Public License 
- * as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
+ * as published by the Free Software Foundation, either version 3
+ * of the License, or (at your option) any later version.
  *  
  * Jalview is distributed in the hope that it will be useful, but 
  * WITHOUT ANY WARRANTY; without even the implied warranty 
  * of MERCHANTABILITY or FITNESS FOR A PARTICULAR 
  * 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/>.
+ * 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;
 
@@ -86,14 +89,16 @@ public class ColourSchemeProperty
 
   public static final int TCOFFEE = 15;
 
-  public static final int RNAINTERACTION = 16;
+  public static final int RNAHELIX = 16;
+
+  public static final int RNAINTERACTION = 17;
 
   /**
    * index of first colourscheme (includes 'None')
    */
   public static final int FIRST_COLOUR = NONE;
 
-  public static final int LAST_COLOUR = NUCLEOTIDE;
+  public static final int LAST_COLOUR = RNAINTERACTION;
 
   /**
    * DOCUMENT ME!
@@ -168,11 +173,14 @@ 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;
@@ -246,9 +254,10 @@ public class ColourSchemeProperty
     {
       index = TCOFFEE;
     }
-   
-    
-    
+    else if (cs instanceof RNAHelicesColour)
+    {
+      index = RNAHELIX;
+    }
     /*
      * else if (cs instanceof CovariationColourScheme) { index = COVARIATION; }
      */
@@ -343,11 +352,15 @@ public class ColourSchemeProperty
       ret = "T-Coffee Scores";
 
       break;
-      
+
     case RNAINTERACTION:
-        ret = "RNA Interaction type";
+      ret = "RNA Interaction type";
 
-        break;
+      break;
+    case RNAHELIX:
+      ret = "RNA Helices";
+
+      break;
     /*
      * case COVARIATION: ret = "Covariation";
      * 
@@ -500,12 +513,13 @@ public class ColourSchemeProperty
     case TCOFFEE:
       cs = new TCoffeeColourScheme(coll);
       break;
-      
 
-      
+    case RNAHELIX:
+      cs = new RNAHelicesColour(coll);
+      break;
+
     // case COVARIATION:
     // cs = new CovariationColourScheme(annotation);
-
     // break;
 
     case USER_DEFINED: