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