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densityfold.cpp
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densityfold.cpp
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#include <iostream>
#include <string>
#include <vector>
using namespace std;
#define infinity 9999999
#define INF 100
#define a -3.0
#define c -3.0 // contribution for each base pair ???
#define b -3.0 // unpaired base penalty ???
#define sigma 2 // ???
////////////////
// GLOBALS
///////////////
string str = "-GCCGCGACAAGCGGUCCGGGCGCCCUAGGGGCCCGGCGGAGACGGGCGCCGGAGGUGUCCGACGCCUGCUCGUACCCAUCUUGCUCCUUGGAGGAUUUGGCUAUGAGGA";
int n = str.length();
vector<std::pair<int, int> > result;
// DP tables to be computed.
vector<float> ED (n, 0);
vector<vector<float> > EDs ( n, std::vector<float> ( n, 0 ) );
vector<vector<float> > Es ( n, std::vector<float> ( n, 0 ) );
vector<vector<float> > EDm ( n, std::vector<float> ( n, 0 ) );
vector<vector<float> > Em ( n, std::vector<float> ( n, 0 ) );
// std::vector< std::vector< float > > item ( 2, std::vector<float> ( 2, 0 ) );
vector<float> tracebackED (n, 0);
vector<vector<float> > tracebackEDs ( n, std::vector<float> ( n, 0 ) );
vector<vector<float> > tracebackEs ( n, std::vector<float> ( n, 0 ) );
vector<vector<float> > tracebackEDm ( n, std::vector<float> ( n, 0 ) );
vector<vector<float> > tracebackEm ( n, std::vector<float> ( n, 0 ) );
// Method declarations.
float eS(char x, char y);
float eBI(char i, char j, char x, char y);
float eH(char x, char y);
// TODO
float eDA(char x, char y);
void findSecondaryStructure();
void computeED();
float computeEDs();
float computeEs();
float computeEm();
float computeEDm(); // ------- This is actually ECM on the paper.
void print_matrix(const vector<vector<float> > &A);
void printStructure(const std::vector<std::pair<int, int> >& result);
void tbEs(int i, int j, std::vector<std::pair<int, int> >* result);
void tbEDs(int i, int j, std::vector<std::pair<int, int> >* result);
void tbED(int j, std::vector<std::pair<int, int> >* result);
void tbEm(int i, int j, std::vector<std::pair<int, int> >* result);
void tbEDm(int i, int j, std::vector<std::pair<int, int> >* result);
/*
* Initial implementation of density fold
* algorithm for RNA structure prediction.
*/
int main(int argc, char **argv){
cout << "" << n << endl;
findSecondaryStructure();
return 0;
}
void findSecondaryStructure(){
std::vector<std::pair<int, int> > result;
computeEm();
computeEDm();
computeEs();
computeEDs();
computeED();
tbED(n-1, &result);
printStructure(result);
}
void computeED(){
float min = infinity;
for( int j = 1; j <= n; j++){
// case 1
if( ED[j-1] < min){
min = ED[j-1];
tracebackED[j] = -1;
}
// case 2
for( int i = 1; i <= j-1; i++){
float case2_min = ED[i-1] + EDs[i][j];
if( case2_min < min){
tracebackED[j] = i;
}
}
ED[j] = min;
}
}
void tbED(int j, std::vector<std::pair<int, int> >* result){
if(tracebackED[j] == -1){
tbED(j-1, result);
}else{
int i = tracebackED[j];
if(i > 1 && i <= j-1){
tbED(i-1, result);
tbEDs(i, j, result);
}
}
}
float computeEDs(){
for (int l = 2; l < n; l++){
for( int i = 1; i < n-l+1; i++){
int j = i+l-1;
// case 1
float min = infinity;
tracebackEDs[i][j] = -1;
// case 2
if (eH(str[i], str[j]) < min){
min = eH(str[i], str[j]);
tracebackEDs[i][j] = -2;
}
// case 3
float density = (2* ((eS(str[i], str[j]) + Es[i+1][j-1] )/(j-i+1)) ) + EDs[i+1][j-1];
if( density < min){
min = density;
tracebackEDs[i][j] = -3;
}
// case 4
// EDbi case: have ommited creating a separate table
for( int i_prime = i+1; i_prime <= j-2; i_prime++){
for( int j_prime = i_prime +1; j_prime <= j-1; j_prime++){
float temp = (((eBI(str[i], str[j], str[i_prime], str[j_prime])
+ Es[i_prime][j_prime])/ j-i+1 ) * ((i_prime-i) + (j - j_prime))) + EDs[i_prime][j_prime];
if( temp < min){
min = temp;
tracebackEDs[i][j] = -4;
}
}
}
// case 5
if( EDm[i][j] < min){
min = EDm[i][j];
tracebackEDs[i][j] = -5;
}
EDs[i][j] = min;
}
}
}
void tbEDs(int i, int j, std::vector<std::pair<int, int> >* result){
if(tracebackEDs[i][j] == -1){
cout << "Whaat?" << endl;
}else if( tracebackEDs[i][j] == -2){
result->push_back(std::make_pair(i, j));
}else if( tracebackEDs[i][j] == -3){
result->push_back(std::make_pair(i, j));
tbEs(i+1, j-1, result);
tbEDs(i+1, j-1, result);
}else if( tracebackEDs[i][j] == -4){
result->push_back(std::make_pair(i, j));
tbEs(i+1, j-1, result);
tbEDs(i+1, j-1, result);
}else if( tracebackEDs[i][j] == -5){
tbEDm(i, j, result);
}
}
float computeEs(){
for (int l = 2; l < n; l++){
for( int i = 1; i < n-l+1; i++){
int j = i+l-1;
// case 1
float min = infinity;
tracebackEs[i][j] = -1;
// case 2
if(eH(str[i], str[j]) < min){
min = eH(str[i], str[j]);
tracebackEs[i][j] = -2;
}
// case 3
if (i < j)
if( (Es[i+1][j-1] + eS(str[i], str[j])) < min){
min = Es[i+1][j-1] + eS(str[i], str[j]);
tracebackEs[i][j] = -3;
}
// case 4
// Ebi case: have ommited creating a separate table
for( int i_prime = i+1; i_prime <= j-2 && i_prime < n; i_prime++){
for( int j_prime = i_prime +1; j_prime <= j-1 && j_prime < n; j_prime++){
float temp = eBI(str[i], str[j], str[i_prime], str[j_prime]) + Es[i_prime][j_prime];
if( temp < min){
min = temp;
tracebackEs[i][j] = -4;
}
}
}
// case 5
if( Em[i][j] < min){
min = Em[i][j];
tracebackEs[i][j] = -5;
}
Es[i][j] = min;
}
}
}
void tbEs(int i, int j, std::vector<std::pair<int, int> >* result){
if(tracebackEs[i][j] == -1){
cout << "woot" << endl;
}else if( tracebackEs[i][j] == -2){
result->push_back(std::make_pair(i, j));
}else if( tracebackEs[i][j] == -3){
result->push_back(std::make_pair(i, j));
tbEs(i+1, j-1, result);
}else if( tracebackEs[i][j] == -4){
result->push_back(std::make_pair(i, j));
tbEs(i+1, j-1, result);
}else if( tracebackEs[i][j] == -5){
tbEm(i, j, result);
}
}
float computeEDm(){
// Initialization code
for(int i = 1; i < n-2; i++){
for( int j = i+2; j < n;j++){
float min = infinity;
float b_dash = (Em[i][j]) / (j-i+1);
for(int k = i+1; k < j; k++){
float temp = EDm[i][k] + EDm[k+1][j];
if(temp < min){
min = temp;
}
EDm[k][k] = b_dash + sigma * b;
}
EDm[i][j] = sigma * a + min;
}
}
// Implementation
for (int d = 2; d < n; d++){
for( int k = 1; k < n-d+1; k++){
int l = k+d-1;
float min = infinity;
// case 1
float temp = EDs[k][l] + sigma * (c + eDA(str[k-1], str[k]) + eDA(str[l], str[l+1]) );
if(temp < min){
min = temp;
tracebackEDm[k][l] = -1;
}
// case 2
for( int h = k; h < l; h++){
if(Em[k][h] + Em[h+1][l] < min){
min = EDm[k][h] + EDm[h+1][l];
tracebackEDm[k][l] = k;
}
}
EDm[k][l] = min;
}
}
}
void tbEm(int i, int j, std::vector<std::pair<int, int> >* result){
}
float computeEm(){
// Initialization code
for(int i = 1; i < n-2; i++){
for( int j = i+2; j < n;j++){
float min = infinity;
for(int k = i+1; k < j; k++){
float temp = Em[i][k] + Em[k+1][j];
if(temp < min){
min = temp;
}
Em[k][k] = b; // ???
}
Em[i][j] = a + min;
}
}
// Implementation
for (int d = 2; d < n; d++){
for( int k = 1; k < n-d+1; k++){
int l = k+d-1;
float min = infinity;
// case 1
float temp = EDs[k][l] + c + eDA(str[k-1], str[k]) + eDA(str[l], str[l+1]);
if(temp < min){
min = temp;
tracebackEm[k][l] = -1;
}
// case 2
for( int h = k; h < l; h++){
if(Em[k][h] + Em[h+1][l] < min){
min = Em[k][h] + Em[h+1][l];
tracebackEm[k][l] = k;
}
}
Em[k][l] = min;
}
}
}
void tbEDm(int i, int j, std::vector<std::pair<int, int> >* result){
if(tracebackEDm[i][j] == -1){
result->push_back(std::make_pair(i, j));
result->push_back(std::make_pair(i, j));
// tbEDs[][] /// ?????
}else{
}
}
void printStructure(const std::vector<std::pair<int, int> >& result){
for (size_t i = 0; i < result.size(); i++){
// we actually keep the index values in result.
cout << "("<< result[i].first + 1 << ", " << result[i].second + 1 << ") ";
}
cout << endl;
char res[n];
for( int index = 0; index < n; index++){
res[index] = '.';
}
for(size_t in = 0; in < result.size(); in++){
int wee = result[in].first;
int s = result[in].second;
res[wee] = '(';
res[s] = ')';
}
string r = res;
cout << r.substr(0, n) << endl;
}
void print_matrix(const vector<vector<float> > &A){
for (int i = 0; i < A.size(); i++){
for (int j = 0; j < A[i].size()-1; j++){
if (i <= j){
cout << A[i][j] << "\t";
}else{
cout << '-' << "\t";
}
}
cout << endl;
}
}
// ----------------------------------------------------
// TODO ????
// Method for calculating the energies of ???.
float eDA(char x, char y){
return - 3.0;
}
// Method for calculating the energies of Hairpin loop.
float eH(char x, char y)
{
if ((x == 'G' && y == 'C') || (x == 'C' && y == 'G'))
return -20.4;
else if ((x == 'A' && y == 'U') || (x == 'U' && y == 'A'))
return -20.7;
else if ((x == 'G' && y == 'U') || (x == 'U' && y == 'G'))
return -20.5;
else
return INF;
}
// Method for calculating the energies of bulge or interior loop.
float eBI(char i, char j, char x, char y)
{
if ((i == 'A' && j == 'U' && x == 'G' && y == 'C') ||
(i == 'U' && j == 'A' && x == 'C' && y == 'G') ||
(i == 'A' && j == 'U' && x == 'C' && y == 'G') ||
(i == 'U' && j == 'A' && x == 'G' && y == 'C'))
return -8.1;
else if ((i == 'A' && j == 'U' && x == 'U' && y == 'G') ||
(i == 'A' && j == 'U' && x == 'G' && y == 'U') ||
(i == 'U' && j == 'A' && x == 'U' && y == 'G') ||
(i == 'U' && j == 'A' && x == 'G' && y == 'U'))
return -8.2;
else if (( i == 'A' && j == 'U' && x == 'A' && y == 'U') ||
(i == 'A' && j == 'U' && x == 'U' && y == 'A') ||
(i == 'U' && j == 'A' && x == 'A' && y == 'U') ||
(i == 'U' && j == 'A' && x == 'U' && y == 'A'))
return -8.3;
else if ((i == 'C' && j == 'G' && x == 'C' && y == 'G') ||
(i == 'C' && j == 'G' && x == 'G' && y == 'C') ||
(i == 'G' && j == 'C' && x == 'C' && y == 'G') ||
(i == 'G' && j == 'C' && x == 'G' && y == 'C'))
return -8.15;
else if ((i == 'C' && j == 'G' && x == 'A' && y == 'U') ||
(i == 'C' && j == 'G' && x == 'U' && y == 'A') ||
(i == 'G' && j == 'C' && x == 'A' && y == 'U') ||
(i == 'G' && j == 'C' && x == 'U' && y == 'A'))
return -8.25;
else if ((i == 'C' && j == 'G' && x == 'G' && y == 'U') ||
(i == 'C' && j == 'G' && x == 'U' && y == 'G') ||
(i == 'G' && j == 'C' && x == 'U' && y == 'G') ||
(i == 'G' && j == 'C' && x == 'G' && y == 'U'))
return -8.35;
else if ((i == 'G' && j == 'U' && x == 'C' && y == 'G') ||
(i == 'G' && j == 'U' && x == 'G' && y == 'C') ||
(i == 'U' && j == 'G' && x == 'C' && y == 'G') ||
(i == 'U' && j == 'G' && x == 'G' && y == 'C'))
return -8.05;
else if ((i == 'G' && j == 'U' && x == 'A' && y == 'U') ||
(i == 'G' && j == 'U' && x == 'U' && y == 'A') ||
(i == 'U' && j == 'G' && x == 'A' && y == 'U') ||
(i == 'U' && j == 'G' && x == 'U' && y == 'A'))
return -8.06;
else if ((i == 'G' && j == 'U' && x == 'G' && y == 'U') ||
(i == 'G' && j == 'U' && x == 'U' && y == 'G') ||
(i == 'U' && j == 'G' && x == 'U' && y == 'G') ||
(i == 'U' && j == 'G' && x == 'G' && y == 'U'))
return -8.07;
else
return INF;
}
// Method for calculating the energies of Stacking loop.
float eS(char x, char y)
{
if ((x == 'G' && y == 'C') || (x == 'C' && y == 'G'))
return -12.0;
else if ((x == 'A' && y == 'U') || (x == 'U' && y == 'A'))
return -12.1;
else if ((x == 'G' && y == 'U') || (x == 'U' && y == 'G'))
return -11.8;
else
return INF;
}