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/////////////////////////////////////////////////////////////////
// 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
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