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SmithWaterman_parallel.cpp
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SmithWaterman_parallel.cpp
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#include <iostream>
#include <iomanip>
#include <fstream>
#include <cstdlib>
#include <string>
#include <cmath>
#include <sys/time.h>
#include <omp.h>
using namespace std;
float similarity_score(char a, char b);
float find_array_max(float array[], int length,int &ind);
void checkfile(int open, char filename[]);
string read_sequence(ifstream& f);
//int ind;
unsigned short **I_i, **I_j;
float mu, delta,**H;
struct timeval StartTime, EndTime;
int main(int argc, char** argv) {
float temp[4];
unsigned int i,j;
int ind;
// read info from arguments
if(argc!=6) {
cout<<"Give me the propen number of input arguments:"<<endl<<"1 : mu"<<endl;
cout<<"2 : delta"<<endl<<"3 : filename sequence A"<<endl<<"4 : filename sequence B"<<endl;
cout<<"5 : maximal length N of sequences"<<endl;
exit(1);
}
mu = atof(argv[1]);
delta = atof(argv[2]);
char *nameof_seq_a = argv[3];
char *nameof_seq_b = argv[4];
int N_max = atoi(argv[5]);
string seq_a,seq_b;
// read the sequences into two vectors:
ifstream stream_seq_a;
stream_seq_a.open(nameof_seq_a);
checkfile(! stream_seq_a,nameof_seq_a);
cout << "Reading file \"" << nameof_seq_a << "\"\n";
seq_a = read_sequence(stream_seq_a);
cout << "File \"" << nameof_seq_a << "\" read\n\n";
ifstream stream_seq_b;
stream_seq_b.open(nameof_seq_b);
checkfile(! stream_seq_b,nameof_seq_b);
cout << "Reading file \"" << nameof_seq_b << "\"\n";
seq_b = read_sequence(stream_seq_b);
cout << "File \"" << nameof_seq_b << "\" read\n\n";
int N_a = seq_a.length();
int N_b = seq_b.length();
cout << "First sequence has length : " << setw(6) << N_a <<endl;
cout << "Second sequence has length : " << setw(6) << N_b << endl << endl;
#pragma omp parallel
{
#pragma omp sections
{
#pragma omp section
{
cout << "Allocating memory for matrix H\n";
H = (float **)malloc((N_a + 1) * sizeof(float *));
if (H == NULL)
{
cout << "Could not allocate memory for matrix H\n";
exit(1);
}
#pragma omp parallel for
for (int i = 0; i < (N_a + 1); i++) {
H[i] = (float *)malloc((N_b + 1) * sizeof(float));
if (H[i] == NULL)
{
cout << "Could not allocate memory for matrix H[" << setw(6) << i << "]\n";
exit(1);
}
}
cout << "Memory for matrix H allocated\n\n";
cout << "Initializing matrix H\n";
#pragma omp parallel for
for(int i=0; i<=N_a; i++) {
for(int j=0; j<=N_b; j++) {
H[i][j]=0.;
}
}
cout << "Matrix H initialized\n\n";
}
#pragma omp section
{
cout << "Allocating memory for matrix I_i\n";
I_i = (unsigned short **)malloc((N_a + 1) * sizeof(unsigned short *));
if (I_i == NULL)
{
cout << "Could not allocate memory for matrix I_i\n";
exit(1);
}
#pragma omp parallel for
for (int i = 0; i < (N_a + 1); i++) {
I_i[i] = (unsigned short *)malloc((N_b + 1) * sizeof(unsigned short));
if (I_i[i] == NULL)
{
cout << "Could not allocate memory for matrix I_i[" << setw(6) << i << "]\n";
exit(1);
}
}
cout << "Memory for matrix I_i allocated\n\n";
}
#pragma omp section
{
cout << "Allocating memory for matrix I_j\n";
I_j = (unsigned short **)malloc((N_a + 1) * sizeof(unsigned short *));
if (I_j == NULL) {
cout << "Could not allocate memory for matrix I_j\n";
exit(1);
}
#pragma omp parallel for
for (int i = 0; i < (N_a + 1); i++) {
I_j[i] = (unsigned short *)malloc((N_b + 1) * sizeof(unsigned short));
if (I_j[i] == NULL) {
cout << "Could not allocate memory for matrix I_j[" << setw(6) << i << "]\n";
exit(1);
}
}
cout << "Memory for matrix I_j allocated\n\n";
}
}
}
// here comes the actual algorithm
gettimeofday(&StartTime, NULL);
int z1,z2;
int m = N_a,my_i,my_j;
int n = N_b;
for (my_i = 0; my_i < m + n - 1; ++my_i)
{
if( my_i < n )
z1 = 0;
else
z1 = my_i - n + 1;
if( my_i < m )
z2 = 0;
else
z2 = my_i - m + 1;
#pragma omp parallel for private(ind,temp,i,j)
for (my_j = my_i - z2; my_j >= z1; --my_j)
{
i = my_j + 1;
j = my_i - my_j + 1;
temp[0] = H[i-1][j-1] + similarity_score(seq_a[i-1],seq_b[j-1]);
temp[1] = H[i-1][j]-delta;
temp[2] = H[i][j-1]-delta;
temp[3] = 0.;
H[i][j] = find_array_max(temp, 4,ind);
switch(ind)
{
case 0: // score in (i,j) stems from a match/mismatch
I_i[i][j] = i-1;
I_j[i][j] = j-1;
break;
case 1: // score in (i,j) stems from a deletion in sequence A
I_i[i][j] = i-1;
I_j[i][j] = j;
break;
case 2: // score in (i,j) stems from a deletion in sequence B
I_i[i][j] = i;
I_j[i][j] = j-1;
break;
case 3: // (i,j) is the beginning of a subsequence
I_i[i][j] = i;
I_j[i][j] = j;
break;
}
}
}
#if 0
// Print the matrix H to the console
cout<<"**********************************************"<<endl;
cout<<"The scoring matrix is given by "<<endl<<endl;
for(int i=1; i<=N_a; i++) {
for(int j=1; j<=N_b; j++) {
cout<<H[i][j]<<" ";
}
cout<<endl;
}
#endif
#if 0
// Print the matrix I_ito the console
cout<<"**********************************************"<<endl;
cout<<"The matrix I_i is given by "<<endl<<endl;
for(int i=0; i<N_a; i++) {
for(int j=0; j<N_b; j++) {
cout<<I_i[i][j]<<" ";
}
cout<<endl;
}
#endif
#if 0
// Print the matrix I_j to the console
cout<<"**********************************************"<<endl;
cout<<"The smatrix I_j is given by "<<endl<<endl;
for(int i=0; i<N_a; i++) {
for(int j=0; j<N_b; j++) {
cout<<I_j[i][j]<<" ";
}
cout<<endl;
}
#endif
// search H for the maximal score
float H_max = 0.;
int i_max=0,j_max=0;
#pragma omp parallel
{
for(int i=1; i<=N_a; i++) {
#pragma omp for schedule(static)
for(int j=1; j<=N_b; j++) {
if(H[i][j]>H_max) {
H_max = H[i][j];
i_max = i;
j_max = j;
}
}
}
}
// Backtracking from H_max
int current_i = i_max, current_j = j_max;
int next_i = I_i[current_i][current_j];
int next_j = I_j[current_i][current_j];
int tick = 0;
char consensus_a[N_a+N_b+2], consensus_b[N_a+N_b+2];
while(((current_i!=next_i) || (current_j!=next_j)) && (next_j!=0) && (next_i!=0)) {
if(next_i==current_i) consensus_a[tick] = '-'; // deletion in A
else consensus_a[tick] = seq_a[current_i-1]; // match/mismatch in A
if(next_j==current_j) consensus_b[tick] = '-'; // deletion in B
else consensus_b[tick] = seq_b[current_j-1]; // match/mismatch in B
current_i = next_i;
current_j = next_j;
next_i = I_i[current_i][current_j];
next_j = I_j[current_i][current_j];
tick++;
}
gettimeofday(&EndTime, NULL);
#if 1
cout<<endl<<"***********************************************"<<endl;
cout<<"The alignment of the sequences"<<endl<<endl;
for(int i=0; i<N_a; i++) {
cout<<seq_a[i];
};
cout<<" and"<<endl;
for(int i=0; i<N_b; i++) {
cout<<seq_b[i];
};
cout<<endl<<endl;
cout<<"is for the parameters mu = "<<mu<<" and delta = "<<delta<<" given by"<<endl<<endl;
for(int i=tick-1; i>=0; i--) cout<<consensus_a[i];
cout<<endl;
for(int j=tick-1; j>=0; j--) cout<<consensus_b[j];
cout<<endl;
#endif
if (EndTime.tv_usec < StartTime.tv_usec) {
int nsec = (StartTime.tv_usec - EndTime.tv_usec) / 1000000 + 1;
StartTime.tv_usec -= 1000000 * nsec;
StartTime.tv_sec += nsec;
}
if (EndTime.tv_usec - StartTime.tv_usec > 1000000) {
int nsec = (EndTime.tv_usec - StartTime.tv_usec) / 1000000;
StartTime.tv_usec += 1000000 * nsec;
StartTime.tv_sec -= nsec;
}
printf("\n\nParallel calculation time: %ld.%.6ld seconds\n", EndTime.tv_sec - StartTime.tv_sec, EndTime.tv_usec - StartTime.tv_usec);
}
/******************************************************************************/
/* auxiliary functions used by main */
/******************************************************************************/
void checkfile(int open, char filename[]) {
if (open) {
cout << "Error: Can't open the file "<<filename<<endl;
exit(1);
}
else cout<<"Opened file \"" << filename << "\"\n";
}
/******************************************************************************/
float similarity_score(char a,char b) {
float result;
if(a==b) {
result=1.;
}
else {
result=-mu;
}
return result;
}
/******************************************************************************/
float find_array_max(float array[],int length,int &ind) {
float max = array[0]; // start with max = first element
ind = 0;
for(int i = 1; i<length; i++) {
if(array[i] > max) {
max = array[i];
ind = i;
}
}
return max; // return highest value in array
}
/******************************************************************************/
string read_sequence(ifstream& f)
{
string seq;
char line[20000];
while( f.good() )
{
f.getline(line,20000);
if( line[0] == 0 || line[0]=='#' )
continue;
for(int i = 0; line[i] != 0; ++i)
{
int c = toupper(line[i]);
if( c != 'A' && c != 'G' && c != 'C' && c != 'T' )
continue;
seq.push_back(char(c));
}
}
return seq;
}
/******************************************************************************/