static void handle_align(char *s)
{
taddr a = parse_constexpr(&s);
if (a > 63)
syntax_error(21); /* bad alignment */
do_alignment(1LL<<a,number_expr(0));
eol(s);
}
static void handle_even(char *s)
{
do_alignment(2,number_expr(0));
eol(s);
}
static void handle_qphrase(char *s)
{
do_alignment(32,number_expr(0),1,NULL);
eol(s);
}
static void handle_long(char *s)
{
do_alignment(4,number_expr(0),1,NULL);
eol(s);
}
int main (int argc, const char * argv[]) {
// get start time
double t = gettime();
// Display each command-line argument.
// show_args(argc, argv);
if (argc <= 1) {
fprintf(stderr, "sw <seqfile> [threads]\n");
exit(1);
}
// get number of threads (default is 1)
// and set that number for OpenMP
int num_threads = 1;
if (argc == 3) {
num_threads = atoi(argv[2]);
}
omp_set_num_threads(num_threads);
fprintf(stderr, "running with %d threads\n", omp_get_max_threads() );
// open file and initialize vars
FILE *file;
char lineAs[num_threads][MAXLINELEN];
char lineBs[num_threads][MAXLINELEN];
file = fopen(argv[1], "r");
if (file == NULL) {
perror ("Error reading file");
exit(1);
}
int c = 0;
while (!feof(file)) {
// grab two lines and store them in our line arrays A & B
char lineA [MAXLINELEN];
char lineB [MAXLINELEN];
fgets(lineA, MAXLINELEN, file);
fgets(lineB, MAXLINELEN, file);
chomp(lineA);
chomp(lineB);
strcpy(lineAs[c], lineA);
strcpy(lineBs[c], lineB);
// fprintf(stderr, "c = %d\n", c);
// fire off a batch
if (c != 0 && c % (num_threads-1) == 0) {
int job_num;
// each loop is one alignment (2 lines)
#pragma omp parallel for
for (job_num = 0; job_num < num_threads; job_num++) {
char line1 [MAXLINELEN];
char line2 [MAXLINELEN];
strcpy(line1, lineAs[job_num]);
strcpy(line2, lineBs[job_num]);
// fprintf(stderr, "thread %d got job %d\n", omp_get_thread_num(), job_num);
// fprintf(stderr, "thread %d got job %d and seq %s\n", omp_get_thread_num(), job_num, line1);
do_alignment(line1, line2);
}
c=0;
}
else {
c++;
}
}
fclose(file);
// get and print elapsed time
t = gettime() - t;
printf("elapsed time: %f secs\n", t);
return 0;
}
int
main(int argc, char **argv) {
char line[MAX_STR];
char pgm_desc[MAX_STR];
char s_name0[MAX_STR], s_name1[MAX_STR];
char s_desc0[MAX_STR], s_desc1[MAX_STR];
int p0_beg, p1_beg, p0_end, p1_end;
int open_plt = 0;
int copt;
/* check options */
while ((copt = getopt(argc, argv, "BZ:")) != -1) {
switch (copt) {
case 'B':
have_bits = 1;
break;
case 'Z':
sscanf(optarg, "%ld", &zdb_size);
have_zdb = 1;
break;
case '?':
default:
fprintf(stderr," usage - ps_lav -B -Z db_size\n");
}
}
while (fgets(line,sizeof(line), stdin)!=NULL) {
if (line[0] == '#' || line[0] == '\n') continue;
else {
switch(line[0]) {
case 'd':
get_str(stdin, pgm_desc, sizeof(pgm_desc));
break;
case 'h':
get_str2(stdin,
s_desc0, sizeof(s_desc0),
s_desc1, sizeof(s_desc1));
break;
case 's':
get_seq_info(stdin,
s_name0, sizeof(s_name0), &p0_beg, &p0_end,
s_name1, sizeof(s_name1), &p1_beg, &p1_end);
g_n0 = p0_end - p0_beg + 1;
g_n1 = p1_end - p1_beg + 1;
break;
case 'a':
if (!open_plt) {
openplt(g_n0, g_n1, p0_beg, p1_beg, s_desc0, s_desc1);
if ((g_n0 == g_n1) && (p0_beg == p1_beg) && (p0_end == p0_end) &&
strcmp(s_name0, s_name1) == 0) {
drawdiag(p0_end-p0_beg + 1, p1_end - p1_beg + 1);
}
open_plt = 1;
}
do_alignment(stdin, p0_beg, p1_beg);
break;
}
}
}
if (!open_plt) {
openplt(g_n0, g_n1, p0_beg, p1_beg, s_desc0, s_desc1);
if ((g_n0 == g_n1) && (p0_beg == p1_beg) && (p0_end == p0_end) &&
strcmp(s_name0, s_name1) == 0) {
drawdiag(p0_end-p0_beg + 1, p1_end - p1_beg + 1);
}
open_plt = 1;
}
closeplt();
exit(0);
}
