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;
  };
}