// ******************************************************************************
   //
   // Title:       Force Field X.
   // Description: Force Field X - Software for Molecular Biophysics.
   // Copyright:   Copyright (c) Michael J. Schnieders 2001-2025.
   //
   // This file is part of Force Field X.
   //
   // Force Field X is free software; you can redistribute it and/or modify it
  // under the terms of the GNU General Public License version 3 as published by
  // the Free Software Foundation.
  //
  // Force Field X is distributed in the hope that it will be useful, but WITHOUT
  // ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS
  // FOR A PARTICULAR PURPOSE. See the GNU General Public License for more
  // details.
  //
  // You should have received a copy of the GNU General Public License along with
  // Force Field X; if not, write to the Free Software Foundation, Inc., 59 Temple
  // Place, Suite 330, Boston, MA 02111-1307 USA
  //
  // Linking this library statically or dynamically with other modules is making a
  // combined work based on this library. Thus, the terms and conditions of the
  // GNU General Public License cover the whole combination.
  //
  // As a special exception, the copyright holders of this library give you
  // permission to link this library with independent modules to produce an
  // executable, regardless of the license terms of these independent modules, and
  // to copy and distribute the resulting executable under terms of your choice,
  // provided that you also meet, for each linked independent module, the terms
  // and conditions of the license of that module. An independent module is a
  // module which is not derived from or based on this library. If you modify this
  // library, you may extend this exception to your version of the library, but
  // you are not obligated to do so. If you do not wish to do so, delete this
  // exception statement from your version.
  //
  // ******************************************************************************
  package ffx.numerics.clustering;
  
  import java.util.ArrayList;
  import java.util.HashMap;
  import java.util.List;
  import java.util.Map;
  import java.util.PriorityQueue;
  import java.util.logging.Logger;
  
  /**
   * Container for linkages
   * with the minimal methods needed in the package
   * Created by Alexandre Masselot on 7/18/14.
   *
   * @author Lars Behnke, 2013
   * @author Michael J. Schnieders
   * @since 1.0
   */
  public class DistanceMap {
  
    public static final Logger logger = Logger.getLogger(DistanceMap.class.getName());
  
    private final Map<String, Item> pairHash;
    private final PriorityQueue<Item> data;
  
    private class Item implements Comparable<Item> {
      final ClusterPair pair;
      final String hash;
      boolean removed = false;
  
      Item(ClusterPair p) {
        pair = p;
        hash = hashCodePair(p);
      }
  
      @Override
      public int compareTo(Item o) {
        return pair.compareTo(o.pair);
      }
  
      @Override
      public String toString() {
        return hash;
      }
    }
  
    public DistanceMap() {
      data = new PriorityQueue<>();
      pairHash = new HashMap<>();
    }
  
    /**
     * Returns a snapshot list of all cluster pairs currently stored.
     *
     * @return list of ClusterPair entries in this map
     */
    public List<ClusterPair> list() {
      List<ClusterPair> l = new ArrayList<>(data.size());
      for (Item clusterPair : data) {
        l.add(clusterPair.pair);
      }
      return l;
   }
 
   /**
    * Finds the ClusterPair for the two provided clusters.
    *
    * @param c1 the first cluster
    * @param c2 the second cluster
    * @return the matching ClusterPair, or null if absent
    */
   public ClusterPair findByCodePair(Cluster c1, Cluster c2) {
     String inCode = hashCodePair(c1, c2);
     Item item = pairHash.get(inCode);
     return item == null ? null : item.pair;
   }
 
   /**
    * Removes and returns the minimal-distance pair (according to priority queue ordering).
    *
    * @return the next ClusterPair, or null if none
    */
   public ClusterPair removeFirst() {
     Item poll = data.poll();
     while (poll != null && poll.removed) {
       poll = data.poll();
     }
     if (poll == null) {
       return null;
     }
     ClusterPair link = poll.pair;
     pairHash.remove(poll.hash);
     return link;
   }
 
   /**
    * Marks the given ClusterPair as removed (lazy removal) and drops it from the hash index.
    *
    * @param link the ClusterPair to remove
    * @return true if the pair was present and marked removed; false otherwise
    */
   public boolean remove(ClusterPair link) {
     Item remove = pairHash.remove(hashCodePair(link));
     if (remove == null) {
       return false;
     }
     remove.removed = true;
     // data.remove(remove);  // bottleneck
     return true;
   }
 
   /**
    * Adds a new ClusterPair if no equivalent pair already exists.
    *
    * @param link the pair to add
    * @return true if added; false if a duplicate existed
    */
   public boolean add(ClusterPair link) {
     Item e = new Item(link);
     Item existingItem = pairHash.get(e.hash);
     if (existingItem != null) {
       logger.info("hashCode = " + existingItem.hash +
           " adding redundant link:" + link + " (exist:" + existingItem + ")");
       return false;
     } else {
       pairHash.put(e.hash, e);
       data.add(e);
       return true;
     }
   }
 
   /**
    * Peek at the minimal linkage distance currently in the map.
    *
    * @return the smallest linkage distance, or null if empty
    */
   public Double minDist() {
     Item peek = data.peek();
     if (peek != null)
       return peek.pair.getLinkageDistance();
     else
       return null;
   }
 
   /**
    * Compute some kind of unique ID for a given cluster pair.
    *
    * @return The ID
    */
   private String hashCodePair(ClusterPair link) {
     return hashCodePair(link.getlCluster(), link.getrCluster());
   }
 
   private String hashCodePair(Cluster lCluster, Cluster rCluster) {
     return hashCodePairNames(lCluster.getName(), rCluster.getName());
   }
 
   private String hashCodePairNames(String lName, String rName) {
     if (lName.compareTo(rName) < 0) {
       return lName + "~~~" + rName;//getlCluster().hashCode() + 31 * (getrCluster().hashCode());
     } else {
       return rName + "~~~" + lName;//return getrCluster().hashCode() + 31 * (getlCluster().hashCode());
     }
   }
 
   @Override
   public String toString() {
     return data.toString();
   }
 }