static inline GtContfind find_exact_overlaps(struct Data *d, bool use_kmp,
GtUword min_length, bool find_nonmaximal)
{
GtContfind retval;
if (d->u->seqnum == d->v->seqnum && d->v->direct)
{
if (!(d->mode == GT_OVLFIND_SPM || d->mode == GT_OVLFIND_ALL))
return GT_CONTFIND_EQ;
if (use_kmp)
retval = gt_ovlfind_kmp(d->u->seq, d->u->len, d->u->pi, NULL, 0, NULL,
d->mode, min_length, find_nonmaximal, call_spmproc, d);
else
retval = gt_ovlfind_bf(d->u->seq, d->u->len, NULL, 0, d->mode,
min_length, find_nonmaximal, call_spmproc, d);
}
else
{
if (use_kmp)
retval = gt_ovlfind_kmp(d->u->seq, d->u->len, d->u->pi, d->v->seq,
d->v->len, d->v->pi, d->mode, min_length, find_nonmaximal,
call_spmproc, d);
else
retval = gt_ovlfind_bf(d->u->seq, d->u->len, d->v->seq, d->v->len,
d->mode, min_length, find_nonmaximal, call_spmproc, d);
}
return retval;
}
int gt_ovlfind_kmp_unit_test(GtError *err)
{
int had_err = 0;
GtArray *a;
struct GtOvlfindKmpResult *r;
GtContfind retval;
gt_kmp_t *u_pi, *v_pi;
/*@i1@*/ gt_error_check(err);
had_err = gt_kmp_preproc_unit_test(err);
if (had_err != 0)
return had_err;
a = gt_array_new(sizeof (struct GtOvlfindKmpResult));
/* u suffix == v prefix */
if (!had_err)
{
gt_array_reset(a);
u_pi = gt_kmp_preproc("aacgcacctg", 10UL);
v_pi = gt_kmp_preproc("acctgatttc", 10UL);
retval = gt_ovlfind_kmp("aacgcacctg", 10UL, u_pi, "acctgatttc", 10UL, v_pi,
GT_OVLFIND_PROPER_SPM, 1UL, false, ovlfind_kmp_test_save, a);
gt_ensure(had_err, retval == GT_CONTFIND_NO);
gt_ensure(had_err, gt_array_size(a) == 1UL);
GT_OVLFIND_KMP_EXPECT_RESULT(0UL, true, 5UL);
gt_free(u_pi);
gt_free(v_pi);
}
/* v suffix == u prefix */
if (!had_err)
{
gt_array_reset(a);
u_pi = gt_kmp_preproc("atccgtgacgtg", 12UL);
v_pi = gt_kmp_preproc("aagaagaatccg", 12UL);
retval = gt_ovlfind_kmp("atccgtgacgtg", 12UL, u_pi, "aagaagaatccg", 12UL,
v_pi, GT_OVLFIND_ALL, 1UL, false, ovlfind_kmp_test_save, a);
gt_ensure(had_err, retval == GT_CONTFIND_NO);
gt_ensure(had_err, gt_array_size(a) == 1UL);
GT_OVLFIND_KMP_EXPECT_RESULT(0UL, false, 5UL);
gt_free(u_pi);
gt_free(v_pi);
}
/* no overlap */
if (!had_err)
{
gt_array_reset(a);
u_pi = gt_kmp_preproc("aac", 3UL);
v_pi = gt_kmp_preproc("tgc", 3UL);
retval = gt_ovlfind_kmp("aac", 3UL, u_pi, "tgc", 3UL, v_pi,
GT_OVLFIND_PROPER_SPM, 1UL, false, ovlfind_kmp_test_save, a);
gt_ensure(had_err, retval == GT_CONTFIND_NO);
gt_ensure(had_err, gt_array_size(a) == 0UL);
gt_free(u_pi);
gt_free(v_pi);
}
/* u suffix of v */
if (!had_err)
{
gt_array_reset(a);
u_pi = gt_kmp_preproc("acagc", 5UL);
v_pi = gt_kmp_preproc("gtacagc", 7UL);
retval = gt_ovlfind_kmp("acagc", 5UL, u_pi, "gtacagc", 7UL, v_pi,
GT_OVLFIND_SPM, 1UL, false, ovlfind_kmp_test_save, a);
gt_ensure(had_err, gt_array_size(a) == 1UL);
gt_ensure(had_err, retval == GT_CONTFIND_OFF);
GT_OVLFIND_KMP_EXPECT_RESULT(0UL, false, 5UL);
gt_array_reset(a);
retval = gt_ovlfind_kmp("acagc", 5UL, u_pi, "gtacagc", 7UL, v_pi,
GT_OVLFIND_PROPER_SPM, 1UL, false, ovlfind_kmp_test_save, a);
gt_ensure(had_err, retval == GT_CONTFIND_U);
gt_ensure(had_err, gt_array_size(a) == 0UL);
gt_array_reset(a);
retval = gt_ovlfind_kmp("acagc", 5UL, u_pi, "gtacagc", 7UL, v_pi,
GT_OVLFIND_CNT, 1UL, false, ovlfind_kmp_test_save, a);
gt_ensure(had_err, gt_array_size(a) == 0UL);
gt_ensure(had_err, retval == GT_CONTFIND_U);
gt_array_reset(a);
retval = gt_ovlfind_kmp("acagc", 5UL, u_pi, "gtacagc", 7UL, v_pi,
GT_OVLFIND_ALL, 1UL, false, ovlfind_kmp_test_save, a);
gt_ensure(had_err, gt_array_size(a) == 1UL);
gt_ensure(had_err, retval == GT_CONTFIND_U);
GT_OVLFIND_KMP_EXPECT_RESULT(0UL, false, 5UL);
gt_free(u_pi);
gt_free(v_pi);
}
/* v suffix of u */
if (!had_err)
{
gt_array_reset(a);
u_pi = gt_kmp_preproc("gtacagc", 7UL);
v_pi = gt_kmp_preproc("acagc", 5UL);
retval = gt_ovlfind_kmp("gtacagc", 7UL, u_pi, "acagc", 5UL, v_pi,
GT_OVLFIND_SPM, 1UL, false, ovlfind_kmp_test_save, a);
gt_ensure(had_err, retval == GT_CONTFIND_OFF);
gt_ensure(had_err, gt_array_size(a) == 1UL);
GT_OVLFIND_KMP_EXPECT_RESULT(0UL, true, 5UL);
gt_array_reset(a);
retval = gt_ovlfind_kmp("gtacagc", 7UL, u_pi, "acagc", 5UL, v_pi,
GT_OVLFIND_PROPER_SPM, 1UL, false, ovlfind_kmp_test_save, a);
gt_ensure(had_err, retval == GT_CONTFIND_V);
gt_ensure(had_err, gt_array_size(a) == 0UL);
gt_free(u_pi);
gt_free(v_pi);
}
/* u prefix of v */
if (!had_err)
{
gt_array_reset(a);
u_pi = gt_kmp_preproc("ctat", 4UL);
v_pi = gt_kmp_preproc("ctatacagg", 9UL);
retval = gt_ovlfind_kmp("ctat", 4UL, u_pi, "ctatacagg", 9UL, v_pi,
GT_OVLFIND_SPM, 1UL, false, ovlfind_kmp_test_save, a);
gt_ensure(had_err, retval == GT_CONTFIND_OFF);
gt_ensure(had_err, gt_array_size(a) == 1UL);
GT_OVLFIND_KMP_EXPECT_RESULT(0UL, true, 4UL);
gt_array_reset(a);
retval = gt_ovlfind_kmp("ctat", 4UL, u_pi, "ctatacagg", 9UL, v_pi,
GT_OVLFIND_PROPER_SPM, 1UL, false, ovlfind_kmp_test_save, a);
gt_ensure(had_err, retval == GT_CONTFIND_U);
gt_ensure(had_err, gt_array_size(a) == 0UL);
gt_free(u_pi);
gt_free(v_pi);
}
/* v prefix of u */
if (!had_err)
{
gt_array_reset(a);
u_pi = gt_kmp_preproc("ctatacagg", 9UL);
v_pi = gt_kmp_preproc("ctat", 4UL);
retval = gt_ovlfind_kmp("ctatacagg", 9UL, u_pi, "ctat", 4UL, v_pi,
GT_OVLFIND_SPM, 1UL, false, ovlfind_kmp_test_save, a);
gt_ensure(had_err, retval == GT_CONTFIND_OFF);
gt_ensure(had_err, gt_array_size(a) == 1UL);
GT_OVLFIND_KMP_EXPECT_RESULT(0UL, false, 4UL);
gt_array_reset(a);
retval = gt_ovlfind_kmp("ctatacagg", 9UL, u_pi, "ctat", 4UL, v_pi,
GT_OVLFIND_PROPER_SPM, 1UL, false, ovlfind_kmp_test_save, a);
gt_ensure(had_err, retval == GT_CONTFIND_V);
gt_ensure(had_err, gt_array_size(a) == 0UL);
gt_free(u_pi);
gt_free(v_pi);
}
/* identical sequences */
if (!had_err)
{
gt_array_reset(a);
u_pi = gt_kmp_preproc("acagc", 5UL);
retval = gt_ovlfind_kmp("acagc", 5UL, u_pi, "acagc", 5UL, u_pi,
GT_OVLFIND_SPM, 1UL, false, ovlfind_kmp_test_save, a);
gt_ensure(had_err, retval == GT_CONTFIND_OFF);
gt_ensure(had_err, gt_array_size(a) == 2UL);
GT_OVLFIND_KMP_EXPECT_RESULT(0UL, true, 5UL);
GT_OVLFIND_KMP_EXPECT_RESULT(1UL, false, 5UL);
gt_array_reset(a);
retval = gt_ovlfind_kmp("acagc", 5UL, u_pi, "acagc", 5UL, u_pi,
GT_OVLFIND_PROPER_SPM, 1UL, false, ovlfind_kmp_test_save, a);
gt_ensure(had_err, retval == GT_CONTFIND_EQ);
gt_ensure(had_err, gt_array_size(a) == 0UL);
gt_free(u_pi);
}
/* find_nonmaximal */
if (!had_err)
{
gt_array_reset(a);
u_pi = gt_kmp_preproc("aacagtagtagt", 12UL);
v_pi = gt_kmp_preproc("agtagtagttaa", 12UL);
retval = gt_ovlfind_kmp("aacagtagtagt", 12UL, u_pi, "agtagtagttaa", 12UL,
v_pi, GT_OVLFIND_SPM, 1UL, false, ovlfind_kmp_test_save, a);
gt_ensure(had_err, retval == GT_CONTFIND_OFF);
gt_ensure(had_err, gt_array_size(a) == 2UL);
GT_OVLFIND_KMP_EXPECT_RESULT(0UL, true, 9UL);
GT_OVLFIND_KMP_EXPECT_RESULT(1UL, false, 2UL);
gt_array_reset(a);
retval = gt_ovlfind_kmp("aacagtagtagt", 12UL, u_pi, "agtagtagttaa", 12UL,
v_pi, GT_OVLFIND_SPM, 1UL, true, ovlfind_kmp_test_save, a);
gt_ensure(had_err, gt_array_size(a) == 5UL);
gt_ensure(had_err, retval == GT_CONTFIND_OFF);
gt_free(u_pi);
gt_free(v_pi);
}
/* min_length */
if (!had_err)
{
gt_array_reset(a);
u_pi = gt_kmp_preproc("aggaccagtagt", 12UL);
v_pi = gt_kmp_preproc("agtagttactac", 12UL);
retval = gt_ovlfind_kmp("aggaccagtagt", 12UL, u_pi, "agtagttactac", 12UL,
v_pi, GT_OVLFIND_SPM, 1UL, true, ovlfind_kmp_test_save, a);
gt_ensure(had_err, retval == GT_CONTFIND_OFF);
gt_ensure(had_err, gt_array_size(a) == 2UL);
gt_array_reset(a);
retval = gt_ovlfind_kmp("aggaccagtagt", 12UL, u_pi, "agtagttactac", 12UL,
v_pi, GT_OVLFIND_SPM, 4UL, true, ovlfind_kmp_test_save, a);
gt_ensure(had_err, gt_array_size(a) == 1UL);
gt_ensure(had_err, retval == GT_CONTFIND_OFF);
gt_free(u_pi);
gt_free(v_pi);
}
gt_array_delete(a);
return had_err;
}