import jalview.api.AlignViewportI;
import jalview.io.FileFormatI;
import jalview.util.MessageManager;
import jalview.api.AlignViewportI;
import jalview.io.FileFormatI;
import jalview.util.MessageManager;
this.settings = defaults;
this.isComplexAlignFile = format.isComplexAlignFile();
init(viewport.hasHiddenRows(), viewport.hasHiddenColumns());
this.settings = defaults;
this.isComplexAlignFile = format.isComplexAlignFile();
init(viewport.hasHiddenRows(), viewport.hasHiddenColumns());