1 package jalview.ws.datamodel;
3 import jalview.datamodel.ContactListI;
4 import jalview.datamodel.ContactMatrixI;
5 import jalview.datamodel.Mapping;
6 import jalview.datamodel.SequenceI;
8 public interface MappableContactMatrixI extends ContactMatrixI
11 boolean hasReferenceSeq();
13 SequenceI getReferenceSeq();
15 * remaps the matrix to a new reference sequence
17 * @param sqmpping - mapping from current reference to new reference - 1:1 only
18 * @return new ContactMatrixI instance with updated mapping
20 MappableContactMatrixI liftOver(SequenceI dsq, Mapping sqmpping);
23 * like ContactMatrixI.getContactList(int column) but
24 * @param localFrame - sequence or other object that this contact matrix is associated with
25 * @param column - position in localFrame
26 * @return ContactListI that returns contacts w.r.t. localFrame
29 ContactListI getMappableContactList(SequenceI localFrame, int column);