// Find the maximum value of an array.
float array_max(const float* array, int length)
{
int i;
float max = find_array_max(array, length, &i);
(void)i;
return max;
}
float sift_extract_one_orientation(float* hist, int nbins)
{
float ori; // return value
int i,i_prev,i_next; // bin indices
float offset; // for normalization and interpolation
// Smooth histogram : 6 iterated box filters
smooth_circular_histogram(6, hist, nbins);
// Find the histogram global extrema
float t = find_array_max(hist, nbins, &i);
(void)t;
i_prev=(i-1+nbins)%nbins;
i_next=(i+1)%nbins;
// Quadratic interpolation of the position of each local maximum
offset = interpolate_peak(hist[i_prev], hist[i], hist[i_next]);
ori = bin_to_ori((float)i + offset, nbins);
return ori;
}
int main(int argc, char** argv)
{
if(argc!=5){
printf("Please provide correct number of input arguments: \n");
printf("1:gap 2:filename sequence_A 3:filename sequence_B 4:chunk_size\n");
exit(0);
}
gap = atof(argv[1]); // loading gap
int i,ii,j,a,b,c,d;
double t1,t2,total;
int chunk;
chunk = atoi(argv[4]);
//load sequences
FILE *fpa;
fpa = fopen(argv[2], "r");
if (fpa == NULL) {
printf("Error: could not open seqA file!\n");
exit(0);
}
unsigned int N_a, num_a;
fscanf(fpa, "%d %d\n", &num_a, &N_a);
char **seq_a = malloc(num_a * sizeof(char*));
for(a=0; a < num_a; a++) {
seq_a[a] = malloc((N_a+1) * sizeof(char));
fscanf(fpa, "%s\n", seq_a[a]);
}
fclose(fpa);
FILE *fpb;
fpb = fopen(argv[3], "r");
if (fpb == NULL) {
printf("Error: could not open seqB file!\n");
exit(0);
}
unsigned int N_b, num_b;
fscanf(fpb, "%d %d\n", &num_b, &N_b);
char **seq_b = malloc(num_b * sizeof(char*));
for(a=0; a < num_b; a++) {
seq_b[a] = malloc((N_b+1) * sizeof(char));
fscanf(fpb, "%s\n", seq_b[a]);
}
//strcpy(seq_b,"");
fclose(fpb);
/* if( N_a != N_b) {
printf("not a square matrix \n");
exit(0);
}*/
/* printf("N_a:%d num_a:%d\n", N_a, num_a);
printf("printing seq_a: \n");
for(a=0; a < num_a; a++) {
for(i = 0;i < N_a; i++) {
printf("%c", seq_a[a][i]);
}
printf("\n");
}
printf("N_b:%d num_b:%d\n", N_b, num_b);
printf("printing seq_b: \n");
for(a=0; a < num_b; a++) {
for(i = 0;i < N_b; i++) {
printf("%c", seq_b[a][i]);
}
printf("\n");
} */
//initialize H
// int H[N_a+1][N_b+1];
int **H;
H = malloc((N_a + 1) * sizeof(int *));
//#pragma omp parallel for
for(i=0; i< N_a + 1; i++)
H[i] = malloc((N_b + 1) * sizeof(int));
for(i=0;i<=N_a;i++){
for(j=0;j<=N_b;j++){
H[i][j]=0;
}
}
int temp[4];
//int I_i[N_a+1][N_b+1],I_j[N_a+1][N_b+1]; // Index matrices to remember the 'path' for backtracking
int H_max = 0.;
int i_max=0,j_max=0;
int current_i,current_j;
int next_i;
int next_j;
int tick=0;
//char consensus_a[N_a+N_b+2],consensus_b[N_a+N_b+2];
//strcpy(consensus_a,"");
//strcpy(consensus_b,"");
int waves = N_a + N_b +1;
int wave, elements, np, mp;
int min = 0;
//t1 = GetTickCount();
for(a=0; a < num_a; a++) {
//for(a=0; a < 1; a++) {
for(c=0;c<=N_a;c++){
for(d=0;d<=N_b;d++){
H[c][d]=0;
}
}
//for(i=0;i< N_a;i++){
// for(j=0;j< N_b;j++){
t1 = omp_get_wtime();
#pragma omp parallel firstprivate(a, gap, waves) private(temp, wave, ii, i) shared(np, mp, elements)
{
#pragma omp master
{
for(wave = 0; wave < waves; ++wave) {
// 0 <= wave < n-1
if(wave < N_a-1) {
elements = wave+1;
np = wave+1;
mp = 0+1;
}
// n-1 <= wave < m
else if(wave < N_b) {
elements = N_a;
np = N_a-1+1;
mp = wave-(N_a-1)+1;
}
// m <= wave < m+n-1
else {
elements = N_a-1-(wave-N_b);
np = N_a-1+1;
mp = wave-(N_a-1)+1;
}
for(ii = 0; ii < elements; ii+=chunk) {
min = MIN(elements,ii + chunk);
#pragma omp task firstprivate(ii, np, mp, chunk, elements)
{
for (i = ii; i < min; i++)
//for (i = ii; i < MIN(elements,ii + chunk); i++)
{
//printf("breakpoint 3- %d \n",i);
//printf("{%d,(%d,%d)\n",omp_get_thread_num(), (np-i), (mp+i));
//printf("elements=%d\n", elements);
//printf("similarity=%d\n",similarity(seq_a[a][(np-i)-1],seq_b[a][(mp+i)-1]));
//printf("H= %d\n", H[(np-i)-1][(mp+i)-1]);
temp[0] = H[(np-i)-1][(mp+i)-1] + similarity(seq_a[a][(np-i)-1],seq_b[a][(mp+i)-1]);
temp[1] = H[(np-i)-1][(mp+i)]-gap;
temp[2] = H[(np-i)][(mp+i)-1]-gap;
temp[3] = 0;
//printf("%d,%d,%d\n", temp[0],temp[1],temp[2]);
H[(np-i)][(mp+i)] = find_array_max(temp,4);
}
} // task
} //for loop
#pragma omp taskwait
}
}
}
t2 = omp_get_wtime();
total += t2 - t1;
/* printf("The scoring matrix is given by:\n");
for(i=1;i<=N_a;i++){
for(j=1;j<=N_b;j++){
printf("%d ",H[i][j]);
}
printf("\n");
}
*/
/*
//search H for maximal score
H_max = 0.;
i_max=0,j_max=0;
for(i=1;i<=N_a;i++){
for(j=1;j<=N_b;j++){
if(H[i][j]>H_max){
H_max = H[i][j];
i_max = i;
j_max = j;
}
}
}
//printing maximum score cell
printf("H_max:%f (%d,%d) \n",H_max,i_max,j_max);
//Backtracking from H_max
current_i=i_max,current_j=j_max;
next_i=I_i[current_i][current_j];
next_j=I_j[current_i][current_j];
tick=0;
//char consensus_a[N_a+N_b+2],consensus_b[N_a+N_b+2];
strcpy(consensus_a,"");
strcpy(consensus_b,"");
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[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[a][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++;
}
//output of consensus
printf("***********************************************\n");
printf("tick:%d\n",tick);
printf("The alignment of the sequences \n");
for(i=0;i<N_a;i++){printf("%c",seq_a[a][i]);} printf(" and\n");
for(i=0;i<N_b;i++){printf("%c",seq_b[a][i]);} printf("\n\n");
printf("is for the parameter gap = %f \n", gap);
for(i=tick-1;i>=0;i--) printf("%c",consensus_a[i]);
printf("\n");
for(j=tick-1;j>=0;j--) printf("%c",consensus_b[j]);
printf("\n");
printf("-----------------------------------------------------------------------\n");
printf("-----------------------------------------------------------------------\n");
*/
}
//t2 = GetTickCount();
//printf("Time for Smith-Watterman in secs: %f \n", (t2-t1)/1000000);
printf("Time for Smith-Watterman in secs: %f \n", total);
} // END of main