+ // 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()];
+ }
+