JAL-1620 version bump and release notes

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

diff --git a/src/jalview/schemes/RNAHelicesColourChooser.java b/src/jalview/schemes/RNAHelicesColourChooser.java
index 45c374d..d6b514e 100644 (file)
--- a/src/jalview/schemes/RNAHelicesColourChooser.java
+++ b/src/jalview/schemes/RNAHelicesColourChooser.java
@@ -1,19 +1,21 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2b1)
  * Copyright (C) 2014 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;
@@ -97,28 +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);
 
@@ -131,7 +114,7 @@ public class RNAHelicesColourChooser
           continue;
         }
 
-        sg.cs = new RNAHelicesColour(currentAnnotation);
+        sg.cs = new RNAHelicesColour(sg);
 
       }
     }