Merge branch 'Dbfetch_hotfix-JAL-1238' into develop

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

diff --git a/src/jalview/schemes/ColourSchemeProperty.java b/src/jalview/schemes/ColourSchemeProperty.java
index 608d8ed..4132f32 100755 (executable)
--- a/src/jalview/schemes/ColourSchemeProperty.java
+++ b/src/jalview/schemes/ColourSchemeProperty.java
@@ -1,18 +1,18 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.7)
- * Copyright (C) 2011 J Procter, AM Waterhouse, J Engelhardt, LM Lui, G Barton, M Clamp, S Searle
- *
+ * 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
+ * 
  * 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
+ * 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.
- *
- * 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
+ *  
+ * 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/>.
  */
 package jalview.schemes;
@@ -86,6 +86,8 @@ public class ColourSchemeProperty
 
   public static final int TCOFFEE = 15;
 
+  public static final int RNAINTERACTION = 16;
+
   /**
    * index of first colourscheme (includes 'None')
    */
@@ -166,6 +168,11 @@ public class ColourSchemeProperty
     {
       ret = PURINEPYRIMIDINE;
     }
+    
+    else if (name.equalsIgnoreCase("RNA Interaction type"))
+    {
+      ret = RNAINTERACTION;
+    }
     // else if (name.equalsIgnoreCase("Covariation"))
     // {
     // ret = COVARIATION;
@@ -239,6 +246,12 @@ public class ColourSchemeProperty
     {
       index = TCOFFEE;
     }
+    else if (cs instanceof RNAInteractionColourScheme)
+    {
+      index = RNAINTERACTION;
+    }
+    
+    
     /*
      * else if (cs instanceof CovariationColourScheme) { index = COVARIATION; }
      */
@@ -333,6 +346,11 @@ public class ColourSchemeProperty
       ret = "T-Coffee Scores";
 
       break;
+      
+    case RNAINTERACTION:
+        ret = "RNA Interaction type";
+
+        break;
     /*
      * case COVARIATION: ret = "Covariation";
      * 
@@ -484,8 +502,14 @@ public class ColourSchemeProperty
 
     case TCOFFEE:
       cs = new TCoffeeColourScheme(coll);
-      // case COVARIATION:
-      // cs = new CovariationColourScheme(annotation);
+      break;
+      
+    case RNAINTERACTION:
+        cs = new RNAInteractionColourScheme();
+        break;
+      
+    // case COVARIATION:
+    // cs = new CovariationColourScheme(annotation);
 
       // break;