1 package jalview.datamodel;
3 import java.util.Arrays;
4 import java.util.BitSet;
7 public interface ContactMatrixI
10 ContactListI getContactList(int column);
16 boolean hasReferenceSeq();
18 SequenceI getReferenceSeq();
20 String getAnnotDescr();
22 String getAnnotLabel();
25 * string indicating how the contactMatrix should be rendered - stored in calcId
33 default boolean hasGroups() {
36 default BitSet getGroupsFor(int column) {
37 BitSet colbitset = new BitSet();
38 colbitset.set(column);
42 default List<BitSet> getGroups() {
43 return Arrays.asList();
46 default boolean hasTree() {
51 * Newick representation of clustered matrix
52 * @return null unless hasTree is true
54 default String getNewick() {
58 default String getTreeMethod() {
62 default boolean hasCutHeight() {
66 default double getCutHeight() {