}
af.viewport.setGlobalColourScheme(cs);
- af.viewport.getResidueShading().setThreshold(
- view.getPidThreshold(), true);
+ af.viewport.getResidueShading().setThreshold(view.getPidThreshold(),
+ view.getIgnoreGapsinConsensus());
af.viewport.getResidueShading().setConsensus(
af.viewport.getSequenceConsensusHash());
af.viewport.setColourAppliesToAllGroups(false);