source: branches/ali/GDE/PROBCONS/probcons/EvolutionaryTree.h

/////////////////////////////////////////////////////////////////
// EvolutionaryTree.h
//
// Utilities for reading/writing multiple sequence data.
/////////////////////////////////////////////////////////////////

#ifndef EVOLUTIONARYTREE_H
#define EVOLUTIONARYTREE_H

#include <string>
#include <list>
#include <stdio.h>
#include "SafeVector.h"
#include "MultiSequence.h"
#include "Sequence.h"

using namespace std;

/////////////////////////////////////////////////////////////////
// TreeNode
//
// The fundamental unit for representing an alignment tree.  The
// guide tree is represented as a binary tree.
/////////////////////////////////////////////////////////////////

class TreeNode {
  int sequenceLabel;                  // sequence label
  TreeNode *left, *right, *parent;    // pointers to left, right children

  /////////////////////////////////////////////////////////////////
  // TreeNode::PrintNode()
  //
  // Internal routine used to print out the sequence comments
  // associated with the evolutionary tree, using a hierarchical
  // parenthesized format.
  /////////////////////////////////////////////////////////////////

  void PrintNode (ostream &outfile, const MultiSequence *sequences) const {

    // if this is a leaf node, print out the associated sequence comment
    if (sequenceLabel >= 0)
      outfile << sequences->GetSequence (sequenceLabel)->GetHeader();

    // otherwise, it must have two children; print out their subtrees recursively
    else {
      assert (left);
      assert (right);

      outfile << "(";
      left->PrintNode (outfile, sequences);
      outfile << " ";
      right->PrintNode (outfile, sequences);
      outfile << ")";
    }
  }

 public:

  /////////////////////////////////////////////////////////////////
  // TreeNode::TreeNode()
  //
  // Constructor for a tree node.  Note that sequenceLabel = -1
  // implies that the current node is not a leaf in the tree.
  /////////////////////////////////////////////////////////////////

  TreeNode (int sequenceLabel) : sequenceLabel (sequenceLabel),
    left (NULL), right (NULL), parent (NULL) {
    assert (sequenceLabel >= -1);
  }

  /////////////////////////////////////////////////////////////////
  // TreeNode::~TreeNode()
  //
  // Destructor for a tree node.  Recursively deletes all children.
  /////////////////////////////////////////////////////////////////

  ~TreeNode (){
    if (left){ delete left; left = NULL; }
    if (right){ delete right; right = NULL; }
    parent = NULL;
  }


  // getters
  int GetSequenceLabel () const { return sequenceLabel; }
  TreeNode *GetLeftChild () const { return left; }
  TreeNode *GetRightChild () const { return right; }
  TreeNode *GetParent () const { return parent; }

  // setters
  void SetSequenceLabel (int sequenceLabel){ this->sequenceLabel = sequenceLabel; assert (sequenceLabel >= -1); }
  void SetLeftChild (TreeNode *left){ this->left = left; }
  void SetRightChild (TreeNode *right){ this->right = right; }
  void SetParent (TreeNode *parent){ this->parent = parent; }

  /////////////////////////////////////////////////////////////////
  // TreeNode::ComputeTree()
  //
  // Routine used to compute an evolutionary tree based on the
  // given distance matrix.  We assume the distance matrix has the
  // form, distMatrix[i][j] = expected accuracy of aligning i with j.
  /////////////////////////////////////////////////////////////////

  static TreeNode *ComputeTree (const VVF &distMatrix){

    int numSeqs = distMatrix.size();                 // number of sequences in distance matrix
    VVF distances (numSeqs, VF (numSeqs));           // a copy of the distance matrix
    SafeVector<TreeNode *> nodes (numSeqs, NULL);    // list of nodes for each sequence
    SafeVector<int> valid (numSeqs, 1);              // valid[i] tells whether or not the ith
                                                     // nodes in the distances and nodes array
                                                     // are valid

    // initialization: make a copy of the distance matrix
    for (int i = 0; i < numSeqs; i++)
      for (int j = 0; j < numSeqs; j++)
        distances[i][j] = distMatrix[i][j];

    // initialization: create all the leaf nodes
    for (int i = 0; i < numSeqs; i++){
      nodes[i] = new TreeNode (i);
      assert (nodes[i]);
    }

    // repeat until only a single node left
    for (int numNodesLeft = numSeqs; numNodesLeft > 1; numNodesLeft--){
      float bestProb = -1;
      pair<int,int> bestPair;

      // find the closest pair
      for (int i = 0; i < numSeqs; i++) if (valid[i]){
        for (int j = i+1; j < numSeqs; j++) if (valid[j]){
          if (distances[i][j] > bestProb){
            bestProb = distances[i][j];
            bestPair = make_pair(i, j);
          }
        }
      }

      // merge the closest pair
      TreeNode *newParent = new TreeNode (-1);
      newParent->SetLeftChild (nodes[bestPair.first]);
      newParent->SetRightChild (nodes[bestPair.second]);
      nodes[bestPair.first]->SetParent (newParent);
      nodes[bestPair.second]->SetParent (newParent);
      nodes[bestPair.first] = newParent;
      nodes[bestPair.second] = NULL;

      // now update the distance matrix
      for (int i = 0; i < numSeqs; i++) if (valid[i]){
        distances[bestPair.first][i] = distances[i][bestPair.first]
          = (distances[i][bestPair.first] + distances[i][bestPair.second]) * bestProb / 2;
      }

      // finally, mark the second node entry as no longer valid
      valid[bestPair.second] = 0;
    }

    assert (nodes[0]);
    return nodes[0];
  }

  /////////////////////////////////////////////////////////////////
  // TreeNode::Print()
  //
  // Print out the subtree associated with this node in a
  // parenthesized representation.
  /////////////////////////////////////////////////////////////////

  void Print (ostream &outfile, const MultiSequence *sequences) const {
    outfile << "Alignment tree: ";
    PrintNode (outfile, sequences);
    outfile << endl;
  }
};

#endif