package jalview.datamodel;
+import java.awt.Color;
+import java.util.Arrays;
+import java.util.BitSet;
+import java.util.List;
+
public interface ContactMatrixI
{
float getMax();
+ String getAnnotDescr();
+
+ String getAnnotLabel();
+
+ /**
+ * string indicating how the contactMatrix should be rendered - stored in
+ * calcId
+ *
+ * @return
+ */
+ String getType();
+
+ int getWidth();
+
+ int getHeight();
+
+ public GroupSetI getGroupSet();
+
+ /// proxy methods to simplify use of the interface
+ /// Mappable contact matrices can override these to perform mapping
+
+ default public boolean hasGroupSet()
+ {
+ return getGroupSet() != null;
+ }
+
+ default boolean hasGroups()
+ {
+ return hasGroupSet() && getGroupSet().hasGroups();
+ }
+
+ default BitSet getGroupsFor(int column)
+ {
+ if (!hasGroupSet())
+ {
+ BitSet colbitset = new BitSet();
+ colbitset.set(column);
+ return colbitset;
+ }
+ return getGroupSet().getGroupsFor(column);
+ }
+
+ default List<BitSet> getGroups()
+ {
+ if (!hasGroupSet())
+ {
+ return Arrays.asList();
+ }
+ return getGroupSet().getGroups();
+ }
+
+ default boolean hasTree()
+ {
+ return hasGroupSet() ? getGroupSet().hasTree() : false;
+ }
+
+ /**
+ * Newick representation of clustered matrix
+ *
+ * @return null unless hasTree is true
+ */
+ default String getNewick()
+ {
+ return hasGroupSet() ? getGroupSet().getNewick() : null;
+ }
+
+ default String getTreeMethod()
+ {
+ return hasGroupSet() ? getGroupSet().getTreeMethod() : null;
+ }
+
+ default boolean hasCutHeight()
+ {
+ return hasGroupSet() ? getGroupSet().hasCutHeight() : false;
+ }
+
+ default double getCutHeight()
+ {
+ return hasGroupSet() ? getGroupSet().getCutHeight() : 0;
+ }
+
+ default void updateGroups(List<BitSet> colGroups)
+ {
+ if (hasGroupSet())
+ {
+ getGroupSet().updateGroups(colGroups);
+ }
+ }
+
+ default void setColorForGroup(BitSet bs, Color color)
+ {
+ if (hasGroupSet())
+ {
+ getGroupSet().setColorForGroup(bs, color);
+ }
+ }
+
+ default Color getColourForGroup(BitSet bs)
+ {
+ if (hasGroupSet())
+ {
+ return getGroupSet().getColourForGroup(bs);
+ }
+ else
+ {
+ return Color.white;
+ }
+ }
+
+ void setGroupSet(GroupSet makeGroups);
+
}