com.hfg.bio.phylogeny.UPGMA Maven / Gradle / Ivy

Show more of this group Show more artifacts with this name
Show all versions of com_hfg Show documentation
com.hfg xml, html, svg, and bioinformatics utility library
There is a newer version: 20240423
package com.hfg.bio.phylogeny;

import java.util.HashMap;
import java.util.Map;

import com.hfg.network.Edge;

//------------------------------------------------------------------------------
/**
 * UPGMA (unweighted pair-group method using arithmetic averages) method of
 * phylogenetic tree construction.
 * 
 * See wikipedia.
 * Note that distances in the resulting tree will not exactly match those from
 * the input distance matrix.
 * 
 * @author J. Alex Taylor, hairyfatguy.com
 */
//------------------------------------------------------------------------------
// com.hfg Library
//
// This library is free software; you can redistribute it and/or
// modify it under the terms of the GNU Lesser General Public
// License as published by the Free Software Foundation; either
// version 2.1 of the License, or (at your option) any later version.
//
// This library 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
// Lesser General Public License for more details.
//
// You should have received a copy of the GNU Lesser General Public
// License along with this library; if not, write to the Free Software
// Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA  02111-1307  USA
//
// J. Alex Taylor, President, Founder, CEO, COO, CFO, OOPS hairyfatguy.com
// [email protected]
//------------------------------------------------------------------------------

public class UPGMA implements TreeMethod
{

   //**************************************************************************
   // CONSTRUCTORS
   //**************************************************************************

   //---------------------------------------------------------------------------
   public UPGMA()
   {
   }

   //**************************************************************************
   // PUBLIC METHODS
   //**************************************************************************

   //--------------------------------------------------------------------------
   @Override
   public String toString()
   {
      return getClass().getSimpleName();
   }

   //--------------------------------------------------------------------------
   @Override
   public boolean equals(Object inObj2)
   {
      return (inObj2 != null
              && inObj2.getClass().equals(getClass()));
   }

   //--------------------------------------------------------------------------
   public PhylogeneticTree constructTree(DistanceMatrix inDistanceMatrix)
   {
      int nodeIndex = 1;
      Map nodeMap = new HashMap<>();

      DistanceMatrix matrix = inDistanceMatrix;
      if (! matrix.isConsumable())
      {
         matrix = matrix.clone();
      }

      while (matrix.size() > 1)
      {
         Edge shortestEdge = matrix.getShortestEdge();
         String minKey1 = shortestEdge.getFrom();
         String minKey2 = shortestEdge.getTo();
         float  minDistance = shortestEdge.getDistance();

         String newNodeName = "_" + (nodeIndex++);
         PhyloNode newNode = new PhyloNode();
         nodeMap.put(newNodeName, newNode);

         if (! nodeMap.containsKey(minKey1))
         {
            PhyloNode childNode = new PhyloNode().setLabel(minKey1);
            newNode.addEdge(childNode, minDistance / 2);
         }
         else
         {
            float distance = (minDistance / 2) - nodeMap.get(minKey1).getMaxDistanceToLeaf();
            newNode.addEdge(nodeMap.get(minKey1), distance);
            nodeMap.remove(minKey1);
         }

         if (! nodeMap.containsKey(minKey2))
         {
            PhyloNode childNode = new PhyloNode().setLabel(minKey2);
            newNode.addEdge(childNode, minDistance / 2);
         }
         else
         {
            float distance = (minDistance / 2) - nodeMap.get(minKey2).getMaxDistanceToLeaf();
            newNode.addEdge(nodeMap.get(minKey2), distance);
            nodeMap.remove(minKey2);
         }

         // Reduce the matrix
         matrix.addKey(newNodeName);
         for (String key : matrix.keySet())
         {
            if (key.equals(minKey1) || key.equals(minKey2) || key.equals(newNodeName)) continue;

            float avgDistance = (matrix.getDistance(minKey1, key) + matrix.getDistance(minKey2, key)) / 2;
            matrix.setDistance(newNodeName, key, avgDistance);
         }

         // It is (slightly) faster to remove both keys at once
 //        Set keys = new HashSet<>(2);
 //        keys.add(minKey1);
 //        keys.add(minKey2);
 //        matrix.removeKeys(keys);
         matrix.removeKey(minKey1);
         matrix.removeKey(minKey2);
      }

      PhylogeneticTree tree = new PhylogeneticTree();
      tree.setRootNode(nodeMap.get(matrix.keySet().iterator().next()));
      tree.orderByNodeCount();

      matrix.setIsConsumed();

      return tree;
   }
}