/* Never fails. */
static int cmdline_get_module_path_via_argv(const char *argv, int overwrite)
{
char buffer[PATH_MAX];
int ret;
if (overwrite) {
/* Arbitrary order. */
cmdline_free(g_module_basename);
cmdline_free(g_module_dirname);
cmdline_free(g_module_basename);
g_module_basename = NULL;
g_module_dirname = NULL;
}
if (!g_module_dirname) {
ret = snprintf(buffer, sizeof(buffer), "%s", argv);
if (ret >= 0 && (size_t)ret < sizeof(buffer)) {
g_module_dirname = cmdline_strdup(dirname(buffer));
}
}
if (!g_module_basename) {
ret = snprintf(buffer, sizeof(buffer), "%s", argv);
if (ret >= 0 && (size_t)ret < sizeof(buffer)) {
g_module_basename = cmdline_strdup(basename(buffer));
}
}
return 0;
}
/* Only dirname is retrieved. */
static int cmdline_get_module_path_via_fd(const char *argv)
{
char buffer[PATH_MAX];
char path[128];
char *ptr;
int ret;
int fd;
if (g_module_dirname) {
return 0;
}
ptr = cmdline_strdup(argv);
fd = open(dirname(ptr), O_RDONLY | O_NOCTTY);
cmdline_free(ptr);
if (fd < 0) {
return -1;
}
ret = snprintf(path, sizeof(path), "/proc/%d/fd/%d", getpid(), fd);
if (ret < 0 || (size_t)ret >= sizeof(path)) {
return -1;
}
ret = readlink(path, buffer, sizeof(buffer));
close(fd);
if (ret <= 0) {
return -1;
}
buffer[ret] = '\0';
g_module_dirname = cmdline_strdup(buffer);
return 0;
}
void cmdline_unset_process_name(void)
{
size_t len;
if (!g_saved_program_name) {
return;
}
len = strlen(g_saved_program_name);
memcpy(g_arg_name, g_saved_program_name, len);
memset(g_arg_name + len, 0, g_max_length - len);
cmdline_free(g_saved_program_name);
g_saved_program_name = NULL;
}
int main(int argc, char* argv[])
{
#ifdef SEQ_ALIGN_VERBOSE
printf("VERBOSE: on\n");
#endif
sw_set_default_scoring();
cmd = cmdline_new(argc, argv, &scoring, SEQ_ALIGN_SW_CMD);
// Align!
sw = smith_waterman_new();
result = alignment_create(256);
if(cmd->seq1 != NULL)
{
// Align seq1 and seq2
align(cmd->seq1, cmd->seq2, NULL, NULL);
}
// Align from files
size_t i, num_of_file_pairs = cmdline_get_num_of_file_pairs(cmd);
for(i = 0; i < num_of_file_pairs; i++)
{
const char *file1 = cmdline_get_file1(cmd, i);
const char *file2 = cmdline_get_file2(cmd, i);
if(file1 != NULL && *file1 == '\0' && file2 == NULL) {
wait_on_keystroke = 1;
file1 = "-";
}
align_from_file(file1, file2, &align_pair_from_file, !cmd->interactive);
}
// Free memory for storing alignment results
smith_waterman_free(sw);
alignment_free(result);
cmdline_free(cmd);
return EXIT_SUCCESS;
}
/* Only dirname is retrieved. */
static int cmdline_get_module_path_via_cwd(const char *argv)
{
char buffer[PATH_MAX];
char cwd[PATH_MAX];
char *ptr;
char *pwd;
int ret;
if (g_module_dirname) {
return 0;
}
if (!getcwd(cwd, sizeof(cwd))) {
return -1;
}
pwd = NULL;
if (*argv != '/') {
ptr = cmdline_strdup(argv);
ret = snprintf(buffer, sizeof(buffer), "%s/%s", cwd, dirname(ptr));
cmdline_free(ptr);
if (ret < 0 || (size_t)ret >= sizeof(buffer)) {
return -1;
}
pwd = make_clean_path(buffer, 0);
}
if (!pwd) {
return -1;
}
g_module_dirname = cmdline_strdup(pwd);
free(pwd);
return 0;
}
void cmdline_shutdown(void)
{
cmdline_free();
lib_free(options);
}
int cmdline_set_process_name(const char *fmt, ...)
{
int with_prefix;
int eraser;
va_list ap;
size_t max;
size_t off;
if (!g_max_length || !g_arg_name) {
errno = EINVAL;
return -1;
}
if (!fmt) {
fmt = g_module_arg;
with_prefix = 0;
} else if (*fmt == '-') {
with_prefix = 0;
++fmt;
} else {
with_prefix = g_prefix_length ? 1 : 0;
}
if (with_prefix) {
if (g_prefix_length <= g_max_length) {
off = g_prefix_length;
} else {
off = g_max_length;
}
memcpy(g_arg_name, g_prefix, off);
max = g_max_length - off;
} else {
max = g_max_length;
off = 0;
}
cmdline_free(g_saved_program_name);
g_saved_program_name = cmdline_strdup(g_arg_name);
/* g_max_length doesn't include the trailing zero, so add 1 to it. */
va_start(ap, fmt);
eraser = vsnprintf(g_arg_name + off, max + 1, fmt, ap);
va_end(ap);
if (eraser < 0) {
return -1;
}
/* And we erase all remaining buffer to 0, since some OS might remember the old length. */
if (max > (size_t)eraser) {
off += eraser;
} else {
off += max;
}
memset(g_arg_name + off, 0, g_max_length - off);
return 0;
}
