static int gt_ltrdigest_pdom_visitor_parse_alignments(GT_UNUSED
GtLTRdigestPdomVisitor
*lv,
GtHMMERParseStatus *status,
char *buf,
FILE *instream,
GtError *err)
{
int had_err = 0, cur_domain = GT_UNDEF_INT, line = -1;
GtHMMERSingleHit *hit = NULL;
gt_assert(lv && instream && status);
gt_error_check(err);
had_err = pdom_parser_get_next_line(buf, instream, err);
gt_assert(buf != NULL);
while (!had_err && strncmp("Internal pipeline statistics",
buf, (size_t) 28) &&
strncmp(">>", buf, (size_t) 2)) {
if ((buf[2] == '=' && buf[3] == '=')) {
buf[17] = '\0';
cur_domain = atoi(buf+12);
gt_assert(cur_domain != GT_UNDEF_INT && cur_domain > 0);
hit = gt_hmmer_parse_status_get_hit(status,
(unsigned long) cur_domain - 1);
gt_assert(hit && !hit->alignment);
hit->alignment = gt_str_new();
hit->aastring = gt_str_new();
line = -2;
} else {
gt_assert(hit && hit->alignment);
gt_str_append_cstr(hit->alignment, buf);
gt_str_append_char(hit->alignment, '\n');
switch (line % 4) {
case 1:
gt_str_append_char(hit->alignment, '\n');
break;
case 0:
{
char *b = buf;
b = strtok(buf, " ");
gt_assert(strspn(b, "012+-") == (size_t) 2);
b = strtok(NULL, " ");
gt_assert(strlen(b) > 0);
b = strtok(NULL, " ");
gt_ltrdigest_pdom_visitor_add_aaseq(b, hit->aastring);
}
break;
}
line++;
}
had_err = pdom_parser_get_next_line(buf, instream, err);
}
return had_err;
}
static int gt_ltrdigest_pdom_visitor_parse_alignments(GT_UNUSED
GtLTRdigestPdomVisitor
*lv,
GtHMMERParseStatus *status,
char *buf,
FILE *instream,
GtError *err)
{
int had_err = 0, cur_domain = GT_UNDEF_INT, line = GT_UNDEF_INT;
bool first_align_line = false;
int mod_val = 4;
GtHMMERSingleHit *hit = NULL;
gt_assert(lv && instream && status);
gt_error_check(err);
had_err = pdom_parser_get_next_line(buf, instream, err);
gt_assert(buf != NULL);
while (!had_err && strncmp("Internal pipeline statistics",
buf, (size_t) 28) &&
strncmp(">>", buf, (size_t) 2)) {
if ((buf[2] == '=' && buf[3] == '=')) {
buf[17] = '\0';
cur_domain = atoi(buf+12);
gt_assert(cur_domain != GT_UNDEF_INT && cur_domain > 0);
hit = gt_hmmer_parse_status_get_hit(status,
(GtUword) cur_domain - 1);
gt_assert(hit && !hit->alignment);
hit->alignment = gt_str_new();
hit->aastring = gt_str_new();
first_align_line = true;
mod_val = 4;
} else {
bool run = true;
char junkbuf[BUFSIZ];
if (first_align_line) {
/* some models contain consensus structure annotation -- in this case
there is an additional line in the output which must be taken
into account */
line = 0;
if (1 == sscanf(buf, "%*s %s", junkbuf)) {
if (0 == strcmp(junkbuf, "CS") || 0 == strcmp(junkbuf, "RF")) {
mod_val = 5;
line = -1;
run = false;
}
}
first_align_line = false;
}
if (run) {
gt_assert(hit && hit->alignment);
gt_str_append_cstr(hit->alignment, buf);
gt_str_append_char(hit->alignment, '\n');
switch (line % mod_val) {
case 1:
gt_str_append_char(hit->alignment, '\n');
break;
case 2:
{
GT_UNUSED char *b = buf;
b = strtok(buf, " ");
gt_assert(strspn(b, "012+-") == (size_t) 2);
b = strtok(NULL, " ");
gt_assert(strlen(b) > 0);
b = strtok(NULL, " ");
gt_ltrdigest_pdom_visitor_add_aaseq(b, hit->aastring);
}
break;
}
}
line++;
}
had_err = pdom_parser_get_next_line(buf, instream, err);
}
return had_err;
}
