import jalview.structure.StructureImportSettings;
import jalview.structure.StructureMapping;
import jalview.util.Comparison;
import jalview.structure.StructureImportSettings;
import jalview.structure.StructureMapping;
import jalview.util.Comparison;
ana = new AlignmentAnnotation(ana);
ana.liftOver(dsq, sqmpping);
dsq.addAlignmentAnnotation(ana);
ana = new AlignmentAnnotation(ana);
ana.liftOver(dsq, sqmpping);
dsq.addAlignmentAnnotation(ana);
- dsq.addContactListFor(ana, cm);
+ dsq.addContactListFor(ana, ((MappableContactMatrixI) cm)
+ .liftOver(dsq, sqmpping));