- sg.setColourScheme(null);
- continue;
- }
- CollectionColourScheme groupColour = new CollectionColourScheme(cs.getInstance(sg,
- getHiddenRepSequences()));
- sg.setGroupColourScheme(groupColour);
- sg.setConsPercGaps(ConsPercGaps);
- if (getAbovePIDThreshold() || cs instanceof PIDColourScheme
- || cs instanceof Blosum62ColourScheme)
- {
- groupColour.setThreshold(viewStyle.getThreshold(),
- isIgnoreGapsConsensus());
- recalc = true;
- }
- else
- {
- groupColour.setThreshold(0, isIgnoreGapsConsensus());
- }
-
- if (getConservationSelected())
- {
- groupColour.setConservationApplied(true);
- recalc = true;
- }
- else
- {
- groupColour.setConservation(null);
- // sg.cs.setThreshold(0, getIgnoreGapsConsensus());
- }
- if (recalc)
- {
- sg.recalcConservation();
- }
- else
- {
- groupColour.alignmentChanged(sg, hiddenRepSequences);
+ sg.getGroupColourScheme()
+ .alignmentChanged(sg, hiddenRepSequences);