Merge branch 'JAL-952_rnahelix' into develop

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

diff --git a/src/jalview/schemes/ColourSchemeProperty.java b/src/jalview/schemes/ColourSchemeProperty.java
index 91a4890..8996691 100755 (executable)
--- a/src/jalview/schemes/ColourSchemeProperty.java
+++ b/src/jalview/schemes/ColourSchemeProperty.java
@@ -86,6 +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;
 
@@ -94,7 +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!
@@ -169,11 +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;
@@ -247,9 +252,16 @@ public class ColourSchemeProperty
     {
       index = TCOFFEE;
     }
+<<<<<<< HEAD
    
     
     
+=======
+    else if (cs instanceof RNAHelicesColour)
+    {
+      index = RNAHELIX;
+    }
+>>>>>>> JAL-952_rnahelix
     /*
      * else if (cs instanceof CovariationColourScheme) { index = COVARIATION; }
      */
@@ -344,11 +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";
      * 
@@ -501,6 +520,10 @@ public class ColourSchemeProperty
     case TCOFFEE:
       cs = new TCoffeeColourScheme(coll);
       break;
+    
+    case RNAHELIX:
+      cs = new RNAHelicesColour(coll);
+      break;
       
       // case COVARIATION:
       // cs = new CovariationColourScheme(annotation);