-
- // 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);