// instead we set it manually - recalc called after updateAnnotation
sg.setColourScheme(cs);
sg.getGroupColourScheme().setThreshold(
- av.getViewportColourScheme().getThreshold(),
+ av.getResidueShading().getThreshold(),
av.isIgnoreGapsConsensus());
sg.setName("JTreeGroup:" + sg.hashCode());
sg.setIdColour(col);
if (av.getGlobalColourScheme() != null
- && av.getViewportColourScheme().conservationApplied())
+ && av.getResidueShading().conservationApplied())
{
Conservation c = new Conservation("Group", sg.getSequences(null),
sg.getStartRes(), sg.getEndRes());