X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;ds=sidebyside;f=src%2Fjalview%2Fschemes%2FRNAHelicesColourChooser.java;h=ee9792a36efd356180025a13fcef7cd1357ff224;hb=061a05484ccda133e2e77b19454238fb0ba8f11d;hp=cef7eb6627ae4f573492672d1bbd5e6861981c9d;hpb=2efd78f2ea2ca9cb61b259fbb22d6d125db7fd4c;p=jalview.git

diff --git a/src/jalview/schemes/RNAHelicesColourChooser.java b/src/jalview/schemes/RNAHelicesColourChooser.java
index cef7eb6..ee9792a 100644
--- a/src/jalview/schemes/RNAHelicesColourChooser.java
+++ b/src/jalview/schemes/RNAHelicesColourChooser.java
@@ -1,19 +1,22 @@
 /*
- * 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
+ * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
+ * Copyright (C) $$Year-Rel$$ The Jalview Authors
  * 
  * 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 
- * as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
+ * 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 
  * 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/>.
+ * You should have received a copy of the GNU General Public License
+ * along with Jalview.  If not, see <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
  */
 package jalview.schemes;
 
@@ -96,28 +99,9 @@ public class RNAHelicesColourChooser
     {
       return;
     }
-
-    // This loop will find the first rna structure annotation by which to colour
-    //  the sequences.
-    AlignmentAnnotation[] annotations = av.getAlignment().getAlignmentAnnotation();
-    for (int i = 0; i < annotations.length; i++) {
-    	
-    	// is this a sensible way of determining type of annotation?
-    	if (annotations[i].getRNAStruc() != null) { 
-    		currentAnnotation = annotations[i];
-    		break;
-    	}
-    }
-    if (currentAnnotation == null)   
-    {
-    	System.err.println("Jalview is about to try and colour by RNAHelices even"
-    			+ " though there are no RNA secondary structure annotations present!");
-    	currentAnnotation = av.getAlignment().getAlignmentAnnotation()[0];// annotations.getSelectedIndex()];
-    }
-    
     RNAHelicesColour rhc = null;
 
-    rhc = new RNAHelicesColour(currentAnnotation);
+    rhc = new RNAHelicesColour(av.getAlignment());
 
     av.setGlobalColourScheme(rhc);
 
@@ -130,7 +114,7 @@ public class RNAHelicesColourChooser
           continue;
         }
 
-        sg.cs = new RNAHelicesColour(currentAnnotation);
+        sg.cs = new RNAHelicesColour(sg);
 
       }
     }