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()
42 default BitSet getGroupsFor(int column)
44 BitSet colbitset = new BitSet();
45 colbitset.set(column);
49 default List<BitSet> getGroups()
51 return Arrays.asList();
54 default boolean hasTree()
60 * Newick representation of clustered matrix
62 * @return null unless hasTree is true
64 default String getNewick()
69 default String getTreeMethod()
74 default boolean hasCutHeight()
79 default double getCutHeight()
84 void updateGroups(List<BitSet> colGroups);
86 void setColorForGroup(BitSet bs, Color color);
88 default Color getColourForGroup(BitSet bs)