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
37 default boolean hasGroups() {
40 default BitSet getGroupsFor(int column) {
41 BitSet colbitset = new BitSet();
42 colbitset.set(column);
46 default List<BitSet> getGroups() {
47 return Arrays.asList();
50 default boolean hasTree() {
55 * Newick representation of clustered matrix
56 * @return null unless hasTree is true
58 default String getNewick() {
62 default String getTreeMethod() {
66 default boolean hasCutHeight() {
70 default double getCutHeight() {
74 void updateGroups(List<BitSet> colGroups);
76 void setColorForGroup(BitSet bs, Color color);
78 default Color getColourForGroup(BitSet bs) { return Color.white;};