Merge branch 'JAL-952_rnahelix' into develop

Conflicts:
	src/jalview/schemes/ColourSchemeProperty.java

diff --combined src/jalview/schemes/ColourSchemeProperty.java
index 91a4890,76b1ff1..8996691
--- 1/src/jalview/schemes/ColourSchemeProperty.java
--- 2/src/jalview/schemes/ColourSchemeProperty.java
+++ b/src/jalview/schemes/ColourSchemeProperty.java
@@@ -86,15 -86,15 +86,17 @@@ public class ColourSchemePropert
    public static final int COVARIATION = 14;
  
    public static final int TCOFFEE = 15;
+   
+   public static final int RNAHELIX = 16;
  
 +  public static final int RNAINTERACTION = 16;
 +
    /**
     * 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 = RNAHELIX;
  
    /**
     * DOCUMENT ME!
@@@ -169,11 -169,10 +171,14 @@@
      {
        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 -246,10 +252,16 @@@
      {
        index = TCOFFEE;
      }
++<<<<<<< HEAD
 +   
 +    
 +    
++=======
+     else if (cs instanceof RNAHelicesColour)
+     {
+       index = RNAHELIX;
+     }
++>>>>>>> JAL-952_rnahelix
      /*
       * else if (cs instanceof CovariationColourScheme) { index = COVARIATION; }
       */
@@@ -344,11 -344,10 +356,18 @@@
        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";
       * 
@@@ -501,10 -500,15 +520,14 @@@
      case TCOFFEE:
        cs = new TCoffeeColourScheme(coll);
        break;
+     
+     case RNAHELIX:
+       cs = new RNAHelicesColour(coll);
+       break;
        
        // case COVARIATION:
        // cs = new CovariationColourScheme(annotation);
 -
 -      // break;
 +    // break;
  
      case USER_DEFINED:
        Color[] col = new Color[24];