- sg.cs.setThreshold(viewStyle.getThreshold(),
- isIgnoreGapsConsensus());
- recalc = true;
- }
- else
- {
- sg.cs.setThreshold(0, isIgnoreGapsConsensus());
- }
-
- if (getConservationSelected())
- {
- sg.cs.setConservationApplied(true);
- recalc = true;
- }
- else
- {
- sg.cs.setConservation(null);
- // sg.cs.setThreshold(0, getIgnoreGapsConsensus());
- }
- if (recalc)
- {
- sg.recalcConservation();
- }
- else
- {
- sg.cs.alignmentChanged(sg, hiddenRepSequences);
+ sg.getGroupColourScheme()
+ .alignmentChanged(sg, hiddenRepSequences);