import jalview.datamodel.AlignmentAnnotation;
import jalview.datamodel.AlignmentI;
import jalview.datamodel.AlignmentView;
+import jalview.datamodel.SeqDistanceContactMatrix;
import jalview.datamodel.PDBEntry.Type;
import jalview.datamodel.SequenceI;
import jalview.ext.jmol.JmolParser;
alignFile.addGroups(al);
+ al.addContactList(new SeqDistanceContactMatrix(al.getWidth()));
+
return al;
}