From: Jim Procter <jprocter@dundee.ac.uk>
Date: Sun, 27 Apr 2014 20:41:06 +0000 (+0100)
Subject: Merge branch 'JAL-952_rnahelix' into develop
X-Git-Tag: Jalview_2_9~193
X-Git-Url: http://source.jalview.org/gitweb/?a=commitdiff_plain;h=f806dc4df78ef916ec8c41abeda1e836821ac18d;p=jalview.git

Merge branch 'JAL-952_rnahelix' into develop

Conflicts:
	src/jalview/schemes/ColourSchemeProperty.java
---

f806dc4df78ef916ec8c41abeda1e836821ac18d
diff --cc src/jalview/schemes/ColourSchemeProperty.java
index 91a4890,76b1ff1..8996691
--- a/src/jalview/schemes/ColourSchemeProperty.java
+++ b/src/jalview/schemes/ColourSchemeProperty.java
@@@ -86,9 -86,9 +86,11 @@@ 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')
     */
@@@ -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";
       *