- if (av.getAlignment().getGroups() != null)
- {
- Vector allGroups = ap.getAlignment().getGroups();
- SequenceGroup sg;
- for (int g = 0; g < allGroups.size(); g++)
- {
- sg = (SequenceGroup) allGroups.get(g);
-
- if (sg.cs == null)
- {
- continue;
- }
-
- sg.cs = new RNAHelicesColour(currentAnnotation);
-
- }
- }