From: Jim Procter <jprocter@dundee.ac.uk>
Date: Sun, 27 Apr 2014 15:16:41 +0000 (+0100)
Subject: JAL-952 resolve colour scheme as 'RNA Helices'
X-Git-Tag: Jalview_2_9~193^2~3
X-Git-Url: http://source.jalview.org/gitweb/?a=commitdiff_plain;h=b7e51870168c54685e7cc6f7307400ecf8ddf794;p=jalview.git

JAL-952 resolve colour scheme as 'RNA Helices'
---

diff --git a/src/jalview/schemes/ColourSchemeProperty.java b/src/jalview/schemes/ColourSchemeProperty.java
index c655fe2..bb961d3 100755
--- 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;
 
   /**
    * index of first colourscheme (includes 'None')
@@ -167,6 +169,10 @@ public class ColourSchemeProperty
     {
       ret = PURINEPYRIMIDINE;
     }
+    else if (name.equalsIgnoreCase("RNA Helices"))
+    {
+      ret = RNAHELIX;
+    }
     // else if (name.equalsIgnoreCase("Covariation"))
     // {
     // ret = COVARIATION;
@@ -240,6 +246,10 @@ public class ColourSchemeProperty
     {
       index = TCOFFEE;
     }
+    else if (cs instanceof RNAHelicesColour)
+    {
+      index = RNAHELIX;
+    }
     /*
      * else if (cs instanceof CovariationColourScheme) { index = COVARIATION; }
      */
@@ -334,6 +344,10 @@ public class ColourSchemeProperty
       ret = "T-Coffee Scores";
 
       break;
+    case RNAHELIX:
+      ret = "RNA Helices";
+
+      break;
     /*
      * case COVARIATION: ret = "Covariation";
      * 
@@ -486,6 +500,10 @@ public class ColourSchemeProperty
     case TCOFFEE:
       cs = new TCoffeeColourScheme(coll);
       break;
+    
+    case RNAHELIX:
+      cs = new RNAHelicesColour(coll);
+      break;
       
       // case COVARIATION:
       // cs = new CovariationColourScheme(annotation);