1 package jalview.datamodel;
4 import java.util.Arrays;
5 import java.util.BitSet;
8 public interface ContactMatrixI
11 ContactListI getContactList(int column);
17 String getAnnotDescr();
19 String getAnnotLabel();
22 * string indicating how the contactMatrix should be rendered - stored in calcId
30 default boolean hasGroups() {
33 default BitSet getGroupsFor(int column) {
34 BitSet colbitset = new BitSet();
35 colbitset.set(column);
39 default List<BitSet> getGroups() {
40 return Arrays.asList();
43 default boolean hasTree() {
48 * Newick representation of clustered matrix
49 * @return null unless hasTree is true
51 default String getNewick() {
55 default String getTreeMethod() {
59 default boolean hasCutHeight() {
63 default double getCutHeight() {
67 void updateGroups(List<BitSet> colGroups);
69 void setColorForGroup(BitSet bs, Color color);
71 default Color getColourForGroup(BitSet bs) { return Color.white;}