groups[i].setIgnoreGapsinConsensus(sg.getIgnoreGapsConsensus());
groups[i].setShowConsensusHistogram(sg.isShowConsensusHistogram());
groups[i].setShowSequenceLogo(sg.isShowSequenceLogo());
groups[i].setIgnoreGapsinConsensus(sg.getIgnoreGapsConsensus());
groups[i].setShowConsensusHistogram(sg.isShowConsensusHistogram());
groups[i].setShowSequenceLogo(sg.isShowSequenceLogo());
for (int s = 0; s < sg.getSize(); s++)
{
jalview.datamodel.Sequence seq = (jalview.datamodel.Sequence) sg
for (int s = 0; s < sg.getSize(); s++)
{
jalview.datamodel.Sequence seq = (jalview.datamodel.Sequence) sg
view.setTextColThreshold(av.thresholdTextColour);
view.setShowConsensusHistogram(av.isShowConsensusHistogram());
view.setShowSequenceLogo(av.isShowSequenceLogo());
view.setTextColThreshold(av.thresholdTextColour);
view.setShowConsensusHistogram(av.isShowConsensusHistogram());
view.setShowSequenceLogo(av.isShowSequenceLogo());
view.setShowGroupConsensus(av.isShowGroupConsensus());
view.setShowGroupConservation(av.isShowGroupConservation());
view.setShowNPfeatureTooltip(av.isShowNpFeats());
view.setShowGroupConsensus(av.isShowGroupConsensus());
view.setShowGroupConservation(av.isShowGroupConservation());
view.setShowNPfeatureTooltip(av.isShowNpFeats());
if (groups[i].hasIgnoreGapsinConsensus())
{
sg.setIgnoreGapsConsensus(groups[i].getIgnoreGapsinConsensus());
if (groups[i].hasIgnoreGapsinConsensus())
{
sg.setIgnoreGapsConsensus(groups[i].getIgnoreGapsinConsensus());