static int extracttarget_from_seqfiles(const char *target,
GtStrArray *seqfiles,
GtError *err)
{
GtStr *unescaped_target;
char *escaped_target;
GtSplitter *splitter;
unsigned long i;
int had_err = 0;
gt_error_check(err);
gt_assert(target && seqfiles);
splitter = gt_splitter_new();
unescaped_target = gt_str_new();
escaped_target = gt_cstr_dup(target);
gt_splitter_split(splitter, escaped_target, strlen(escaped_target), ',');
for (i = 0; !had_err && i < gt_splitter_size(splitter); i++) {
GtSplitter *blank_splitter;
char *token = gt_splitter_get_token(splitter, i);
blank_splitter = gt_splitter_new();
gt_splitter_split(blank_splitter, token, strlen(token), ' ');
had_err = gt_gff3_unescape(unescaped_target,
gt_splitter_get_token(blank_splitter, 0),
strlen(gt_splitter_get_token(blank_splitter, 0)),
err);
if (!had_err) {
unsigned long j;
for (j = 0; j < gt_str_array_size(seqfiles); j++) {
unsigned long k;
GtBioseq *bioseq;
if (!(bioseq = gt_bioseq_new(gt_str_array_get(seqfiles, j), err))) {
had_err = -1;
break;
}
for (k = 0; k < gt_bioseq_number_of_sequences(bioseq); k++) {
TargetInfo target_info;
const char *desc = gt_bioseq_get_description(bioseq, k);
target_info.bioseq = bioseq;
target_info.seqnum = k;
gt_string_matching_bmh(desc, strlen(desc),
gt_str_get(unescaped_target),
gt_str_length(unescaped_target), show_target,
&target_info);
}
gt_bioseq_delete(bioseq);
}
}
gt_splitter_delete(blank_splitter);
}
gt_free(escaped_target);
gt_str_delete(unescaped_target);
gt_splitter_delete(splitter);
return had_err;
}
int gt_string_matching_unit_test(GtError *err)
{
char s[STRING_MATCHING_MAX_STRING_LENGTH+1],
p[STRING_MATCHING_MAX_PATTERN_LENGTH+1], *text = "foo";
GtArray *brute_force_matches,
*bmh_matches,
*kmp_matches,
*shift_and_matches;
unsigned long i, brute_force_match, bmh_match, kmp_match, shift_and_match;
int had_err = 0;
gt_error_check(err);
brute_force_matches = gt_array_new(sizeof (unsigned long));
bmh_matches = gt_array_new(sizeof (unsigned long));
kmp_matches = gt_array_new(sizeof (unsigned long));
shift_and_matches = gt_array_new(sizeof (unsigned long));
/* match the empty pattern */
gt_string_matching_brute_force(text, strlen(text), "", 0, store_match,
brute_force_matches);
gt_string_matching_bmh(text, strlen(text), "", 0, store_match, bmh_matches);
gt_string_matching_kmp(text, strlen(text), "", 0, store_match, kmp_matches);
gt_string_matching_shift_and(text, strlen(text), "", 0, store_match,
shift_and_matches);
ensure(had_err, !gt_array_size(brute_force_matches));
ensure(had_err, !gt_array_size(bmh_matches));
ensure(had_err, !gt_array_size(kmp_matches));
ensure(had_err, !gt_array_size(shift_and_matches));
for (i = 0; !had_err && i < STRING_MATCHING_NUM_OF_TESTS; i++) {
unsigned long j, n, m;
/* generate random string and pattern */
n = gt_rand_max(STRING_MATCHING_MAX_STRING_LENGTH);
m = gt_rand_max(STRING_MATCHING_MAX_PATTERN_LENGTH);
for (j = 0; j < n; j++)
s[j] = gt_rand_char();
s[n] = '\0';
for (j = 0; j < m; j++)
p[j] = gt_rand_char();
p[m] = '\0';
/* matching (first match) */
brute_force_match = GT_UNDEF_ULONG;
bmh_match = GT_UNDEF_ULONG;
kmp_match = GT_UNDEF_ULONG;
shift_and_match = GT_UNDEF_ULONG;
gt_string_matching_brute_force(s, n, p, m, store_first_match,
&brute_force_match);
gt_string_matching_bmh(s, n, p, m, store_first_match, &bmh_match);
gt_string_matching_kmp(s, n, p, m, store_first_match, &kmp_match);
gt_string_matching_shift_and(s, n, p, m, store_first_match,
&shift_and_match);
/* comparing (first match) */
ensure(had_err, brute_force_match == bmh_match);
ensure(had_err, brute_force_match == kmp_match);
ensure(had_err, brute_force_match == shift_and_match);
/* matching (all matches) */
gt_string_matching_brute_force(s, n, p, m, store_match,
brute_force_matches);
gt_string_matching_bmh(s, n, p, m, store_match, bmh_matches);
gt_string_matching_kmp(s, n, p, m, store_match, kmp_matches);
gt_string_matching_shift_and(s, n, p, m, store_match, shift_and_matches);
/* comparing (all matches) */
ensure(had_err, gt_array_size(brute_force_matches) ==
gt_array_size(bmh_matches));
ensure(had_err, gt_array_size(brute_force_matches) ==
gt_array_size(kmp_matches));
ensure(had_err, gt_array_size(brute_force_matches) ==
gt_array_size(shift_and_matches));
ensure(had_err, !gt_array_cmp(brute_force_matches, bmh_matches));
ensure(had_err, !gt_array_cmp(brute_force_matches, kmp_matches));
ensure(had_err, !gt_array_cmp(brute_force_matches, shift_and_matches));
/* reset */
gt_array_reset(brute_force_matches);
gt_array_reset(bmh_matches);
gt_array_reset(kmp_matches);
gt_array_reset(shift_and_matches);
}
gt_array_delete(shift_and_matches);
gt_array_delete(bmh_matches);
gt_array_delete(kmp_matches);
gt_array_delete(brute_force_matches);
return had_err;
}
