// ******************************************************************************
   //
   // 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;
  
  /**
   * Immutable-like holder describing a pair of clusters and the linkage distance
   * between them; used as entries within the DistanceMap during agglomeration.
   *
   * @author Lars Behnke, 2013
   * @author Michael J. Schnieders
   * @since 1.0
   */
  public class ClusterPair implements Comparable<ClusterPair> {
  
    private Cluster lCluster;
    private Cluster rCluster;
    private Double linkageDistance;
  
    /**
     * Creates an empty ClusterPair.
     */
    public ClusterPair() {
    }
  
    /**
     * Creates a ClusterPair linking two clusters at a given distance.
     *
     * @param left     the left cluster
     * @param right    the right cluster
     * @param distance the linkage distance between clusters
     */
    public ClusterPair(Cluster left, Cluster right, Double distance) {
      lCluster = left;
      rCluster = right;
      linkageDistance = distance;
    }
  
    /**
     * Returns the opposite cluster of the provided one in this pair.
     *
     * @param c one cluster in this pair
     * @return the other cluster in the pair
     */
    public Cluster getOtherCluster(Cluster c) {
      return lCluster == c ? rCluster : lCluster;
    }
  
    /**
     * Gets the left cluster.
     *
     * @return the left cluster
     */
    public Cluster getlCluster() {
      return lCluster;
    }
  
    /**
     * Sets the left cluster.
     *
     * @param lCluster the left cluster
     */
    public void setlCluster(Cluster lCluster) {
      this.lCluster = lCluster;
    }
 
   /**
    * Gets the right cluster.
    *
    * @return the right cluster
    */
   public Cluster getrCluster() {
     return rCluster;
   }
 
   /**
    * Sets the right cluster.
    *
    * @param rCluster the right cluster
    */
   public void setrCluster(Cluster rCluster) {
     this.rCluster = rCluster;
   }
 
   /**
    * Gets the linkage distance.
    *
    * @return the linkage distance
    */
   public Double getLinkageDistance() {
     return linkageDistance;
   }
 
   /**
    * Sets the linkage distance.
    *
    * @param distance the linkage distance to set
    */
   public void setLinkageDistance(Double distance) {
     this.linkageDistance = distance;
   }
 
   /**
    * Creates a new ClusterPair with left and right clusters swapped.
    *
    * @return a new ClusterPair with the two left/right inverted
    */
   public ClusterPair reverse() {
     return new ClusterPair(getrCluster(), getlCluster(), getLinkageDistance());
   }
 
 
   /**
    * {@inheritDoc}
    */
   @Override
   public int compareTo(ClusterPair o) {
     int result;
     if (o == null || o.getLinkageDistance() == null) {
       result = -1;
     } else if (getLinkageDistance() == null) {
       result = 1;
     } else {
       result = getLinkageDistance().compareTo(o.getLinkageDistance());
     }
 
     return result;
   }
 
   /**
    * Agglomerates left and right clusters under an auto-generated name.
    *
    * @param clusterIdx index appended to the generated cluster name
    * @return the new parent Cluster
    */
   public Cluster agglomerate(int clusterIdx) {
     return agglomerate("clstr#" + clusterIdx);
   }
 
   /**
    * Agglomerates left and right clusters into a new parent with the given name.
    *
    * @param name name of the new parent cluster
    * @return the new parent Cluster
    */
   public Cluster agglomerate(String name) {
     Cluster cluster = new Cluster(name);
     cluster.setDistance(new Distance(getLinkageDistance()));
     //New clusters will track their children's leaf names; i.e. each cluster knows what part of the original data it contains
     cluster.appendLeafNames(lCluster.getLeafNames());
     cluster.appendLeafNames(rCluster.getLeafNames());
     cluster.addChild(lCluster);
     cluster.addChild(rCluster);
     lCluster.setParent(cluster);
     rCluster.setParent(cluster);
 
     Double lWeight = lCluster.getWeightValue();
     Double rWeight = rCluster.getWeightValue();
     double weight = lWeight + rWeight;
     cluster.getDistance().setWeight(weight);
 
     return cluster;
   }
 
   /**
    * {@inheritDoc}
    */
   @Override
   public String toString() {
     StringBuilder sb = new StringBuilder();
     if (lCluster != null) {
       sb.append(lCluster.getName());
     }
     if (rCluster != null) {
       if (!sb.isEmpty()) {
         sb.append(" + ");
       }
       sb.append(rCluster.getName());
     }
     sb.append(" : ").append(linkageDistance);
     return sb.toString();
   }
 
 }