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#include "config.h"
/* getopt needs _POSIX_C_SOURCE 2 */
#define _POSIX_C_SOURCE 2
#include <ctype.h>
#include <limits.h>
#include <math.h>
#include <stddef.h>
#include <stdint.h>
#include <stdio.h>
#include <stdlib.h>
#include <string.h>
#include <errno.h>
#include <unistd.h>
#if defined(_OPENMP)
#include <omp.h>
#endif
#include "parasail.h"
#include "parasail/io.h"
#include "parasail/stats.h"
/*#include "timer.h"*/
#include "timer_real.h"
int main(int argc, char **argv)
{
unsigned long i = 0;
unsigned long j = 0;
char *filename_database = NULL;
parasail_sequences_t *sequences_database = NULL;
size_t seq_count_database = 0;
char *filename_queries = NULL;
parasail_sequences_t *sequences_queries = NULL;
size_t seq_count_queries = 0;
char *endptr = NULL;
char *funcname = NULL;
parasail_function_t *function = NULL;
int c = 0;
const char *matrixname = "blosum62";
const parasail_matrix_t *matrix = NULL;
int gap_open = 10;
int gap_extend = 1;
int truncate = 0;
int exact_length = 0;
stats_t stats_time;
size_t biggest = 0;
char *seen = NULL;
stats_clear(&stats_time);
while ((c = getopt(argc, argv, "a:b:f:q:o:e:t:x:")) != -1) {
switch (c) {
case 'a':
funcname = optarg;
break;
case 'b':
matrixname = optarg;
break;
case 'f':
filename_database = optarg;
break;
case 'q':
filename_queries = optarg;
break;
case 'o':
errno = 0;
gap_open = strtol(optarg, &endptr, 10);
if (errno) {
perror("strtol");
exit(1);
}
break;
case 'e':
errno = 0;
gap_extend = strtol(optarg, &endptr, 10);
if (errno) {
perror("strtol");
exit(1);
}
break;
case 't':
errno = 0;
truncate = strtol(optarg, &endptr, 10);
if (errno) {
perror("strtol");
exit(1);
}
break;
case 'x':
errno = 0;
exact_length = strtol(optarg, &endptr, 10);
if (errno) {
perror("strtol");
exit(1);
}
break;
case '?':
if (optopt == 'a'
|| optopt == 'b'
|| optopt == 'f'
|| optopt == 'q'
|| optopt == 'o'
|| optopt == 'e'
|| optopt == 't'
|| optopt == 'x')
{
fprintf(stderr,
"Option -%c requires an argument.\n",
optopt);
}
else if (isprint(optopt)) {
fprintf(stderr, "Unknown option `-%c'.\n",
optopt);
}
else {
fprintf(stderr,
"Unknown option character `\\x%x'.\n",
optopt);
}
exit(1);
default:
fprintf(stderr, "default case in getopt\n");
exit(1);
}
}
/* select the function */
if (funcname) {
function = parasail_lookup_function(funcname);
if (NULL == function) {
fprintf(stderr, "Specified function not found.\n");
exit(1);
}
}
else {
fprintf(stderr, "No alignment function specified.\n");
exit(1);
}
/* select the substitution matrix */
if (matrixname) {
matrix = parasail_matrix_lookup(matrixname);
if (NULL == matrix) {
fprintf(stderr, "Specified substitution matrix not found.\n");
exit(1);
}
}
if (filename_database) {
sequences_database = parasail_sequences_from_file(filename_database);
seq_count_database = sequences_database->l;
}
else {
fprintf(stderr, "missing database filename\n");
exit(1);
}
if (filename_queries) {
sequences_queries = parasail_sequences_from_file(filename_queries);
seq_count_queries = sequences_queries->l;
biggest = 0;
for (i=0; i<seq_count_queries; ++i) {
if (sequences_queries->seqs[i].seq.l > biggest) {
biggest = sequences_queries->seqs[i].seq.l;
}
}
}
else {
fprintf(stderr, "missing query filename\n");
exit(1);
}
seen = malloc(sizeof(char)*biggest);
for (i=0; i<biggest; ++i) {
seen[i] = 0;
}
for (i=0; i<seq_count_queries; ++i) {
int saturated_query = 0;
double local_timer = timer_real();
if (truncate > 0 && sequences_queries->seqs[i].seq.l > (unsigned long)truncate) {
continue;
}
if (exact_length > 0 && sequences_queries->seqs[i].seq.l != (unsigned long)exact_length) {
continue;
}
if (seen[sequences_queries->seqs[i].seq.l]) {
/*printf("skipping %d\n", i);*/
continue;
}
else {
seen[sequences_queries->seqs[i].seq.l] = 1;
}
for (j=0; j<seq_count_database; ++j) {
parasail_result_t *result = function(
sequences_queries->seqs[i].seq.s,
sequences_queries->seqs[i].seq.l,
sequences_database->seqs[j].seq.s,
sequences_database->seqs[j].seq.l,
gap_open, gap_extend, matrix);
saturated_query += parasail_result_is_saturated(result);
parasail_result_free(result);
}
local_timer = timer_real() - local_timer;
printf("%lu\t %lu\t %d\t %f\n",
i, (unsigned long)sequences_queries->seqs[i].seq.l,
saturated_query,
local_timer);
if (exact_length != 0) {
/* if we got this far, we found our query, so break */
break;
}
}
return 0;
}
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