Merge branch 'fix_JAL-1423' into Release_2_8_1_Branch

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

diff --git a/src/jalview/schemes/RNAHelicesColourChooser.java b/src/jalview/schemes/RNAHelicesColourChooser.java
index 5b97a12..cef7eb6 100644 (file)
--- a/src/jalview/schemes/RNAHelicesColourChooser.java
+++ b/src/jalview/schemes/RNAHelicesColourChooser.java
@@ -1,13 +1,13 @@
 /*
- * 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 
  * 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 
@@ -97,8 +97,24 @@ public class RNAHelicesColourChooser
       return;
     }
 
-    currentAnnotation = av.getAlignment().getAlignmentAnnotation()[0];// annotations.getSelectedIndex()];
-
+    // 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);