package jalview.datamodel;
+import java.awt.Color;
+import java.util.Arrays;
+import java.util.BitSet;
+import java.util.List;
+
public interface ContactMatrixI
{
ContactListI getContactList(int column);
+ float getMin();
+
+ float getMax();
+
+ boolean hasReferenceSeq();
+
+ SequenceI getReferenceSeq();
+
+ String getAnnotDescr();
+
+ String getAnnotLabel();
+
+ /**
+ * string indicating how the contactMatrix should be rendered - stored in
+ * calcId
+ *
+ * @return
+ */
+ String getType();
+
+ int getWidth();
+
+ int getHeight();
+
+ default boolean hasGroups()
+ {
+ return false;
+ }
+
+ default BitSet getGroupsFor(int column)
+ {
+ BitSet colbitset = new BitSet();
+ colbitset.set(column);
+ return colbitset;
+ }
+
+ default List<BitSet> getGroups()
+ {
+ return Arrays.asList();
+ }
+
+ default boolean hasTree()
+ {
+ return false;
+ }
+
+ /**
+ * Newick representation of clustered matrix
+ *
+ * @return null unless hasTree is true
+ */
+ default String getNewick()
+ {
+ return null;
+ }
+
+ default String getTreeMethod()
+ {
+ return null;
+ }
+
+ default boolean hasCutHeight()
+ {
+ return false;
+ }
+
+ default double getCutHeight()
+ {
+ return 0;
+ }
+
+ void updateGroups(List<BitSet> colGroups);
+
+ void setColorForGroup(BitSet bs, Color color);
+
+ default Color getColourForGroup(BitSet bs)
+ {
+ return Color.white;
+ };
}