X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fschemes%2FRNAHelicesColourChooser.java;h=45c374d2f2dab98cd767e6aa0e3cc536f2099447;hb=fe55e5ed429347087cccb692e014f23c01026327;hp=1edca4b2f76198ccd92289ee4242bdb5bc0b9560;hpb=865a855a4ca87eadb3e5ff284ed32ed307d9c34b;p=jalview.git

diff --git a/src/jalview/schemes/RNAHelicesColourChooser.java b/src/jalview/schemes/RNAHelicesColourChooser.java
index 1edca4b..45c374d 100644
--- a/src/jalview/schemes/RNAHelicesColourChooser.java
+++ b/src/jalview/schemes/RNAHelicesColourChooser.java
@@ -98,8 +98,24 @@ 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);