int gt_codon_iterator_encseq_unit_test(GtError *err)
{
int had_err = 0,
i, j;
const char *testseq = "gctgatcgactgaacatagctagcacggccgcgcgatcgtacgatg",
*testseq_rc = "catcgtacgatcgcgcggccgtgctagctatgttcagtcgatcagc",
*testseq_rv = "gtagcatgctagcgcgccggcacgatcgatacaagtcagctagtcg",
*testseq_cm = "cgactagctgacttgtatcgatcgtgccggcgcgctagcatgctac";
GtEncseq *encseq;
GtEncseqBuilder *eb;
GtCodonIterator *ci;
GtAlphabet *alpha;
char n1, n2, n3;
unsigned int frame;
gt_error_check(err);
alpha = gt_alphabet_new_dna();
eb = gt_encseq_builder_new(alpha);
gt_encseq_builder_add_cstr(eb, testseq, strlen(testseq), "foo");
encseq = gt_encseq_builder_build(eb, NULL);
/* forward tests */
had_err = gt_codon_iterator_encseq_single_test(encseq, testseq, testseq,
GT_READMODE_FORWARD, err);
/* complement tests */
had_err = gt_codon_iterator_encseq_single_test(encseq, testseq, testseq_cm,
GT_READMODE_COMPL, err);
/* revcompl tests */
had_err = gt_codon_iterator_encseq_single_test(encseq, testseq, testseq_rc,
GT_READMODE_REVCOMPL, err);
/* reverse tests */
had_err = gt_codon_iterator_encseq_single_test(encseq, testseq, testseq_rv,
GT_READMODE_REVERSE, err);
/* lengths < 3 */
for (j = 0; !had_err && j < 3; j++) {
ci = gt_codon_iterator_encseq_new_with_readmode(encseq, 10, j,
GT_READMODE_REVCOMPL, NULL);
i = 10;
while (!(gt_codon_iterator_next(ci, &n1, &n2, &n3, &frame, NULL))) {
gt_ensure(had_err, false);
}
gt_ensure(had_err, i == 10);
gt_codon_iterator_delete(ci);
}
gt_encseq_delete(encseq);
gt_encseq_builder_delete(eb);
gt_alphabet_delete(alpha);
return had_err;
}
static int encseq_builder_lua_new(lua_State *L)
{
GtEncseqBuilder **builder;
GtAlphabet **alpha;
builder = lua_newuserdata(L, sizeof (GtEncseqBuilder*));
alpha = check_alphabet(L, 1);
gt_assert(builder && *alpha);
*builder = gt_encseq_builder_new(*alpha);
gt_assert(*builder);
luaL_getmetatable(L, ENCSEQ_BUILDER_METATABLE);
lua_setmetatable(L, -2);
return 1;
}
int gt_sarrquerysubstringmatch(const GtUchar *dbseq,
GtUword dblen,
const GtUchar *query,
GtUword querylen,
unsigned int minlength,
GtAlphabet *alpha,
GtProcessquerymatch processquerymatch,
void *processquerymatchinfo,
GtLogger *logger,
GtError *err)
{
unsigned int numofchars, recommendedprefixlength;
bool haserr = false;
GtEncseq *dbencseq;
GtEncseqBuilder *eb;
gt_assert(querylen >= (GtUword) minlength && dblen >= (GtUword) minlength);
eb = gt_encseq_builder_new(alpha);
gt_encseq_builder_disable_multiseq_support(eb);
gt_encseq_builder_disable_description_support(eb);
gt_encseq_builder_set_logger(eb, logger);
gt_encseq_builder_add_multiple_encoded(eb,dbseq,dblen);
dbencseq = gt_encseq_builder_build(eb, err);
gt_encseq_builder_delete(eb);
numofchars = gt_alphabet_num_of_chars(alpha);
recommendedprefixlength
= gt_recommendedprefixlength(numofchars,dblen,
GT_RECOMMENDED_MULTIPLIER_DEFAULT,
true);
if (gt_constructsarrandrunmmsearch(dbencseq,
GT_READMODE_FORWARD,
recommendedprefixlength,
1U, /* parts */
0, /* maximumspace */
query,
querylen,
minlength,
processquerymatch,
processquerymatchinfo,
NULL,
false,
logger,
err) != 0)
{
haserr = true;
}
gt_encseq_delete(dbencseq);
dbencseq = NULL;
return haserr ? -1 : 0;
}
static int sarrselfsubstringmatch(const GtUchar *dbseq,
GtUword dblen,
const GtUchar *query,
GtUword querylen,
unsigned int minlength,
GtAlphabet *alpha,
Processmaxpairs processmaxpairs,
void *processmaxpairsinfo,
GtLogger *logger,
GtError *err)
{
Substringmatchinfo ssi;
unsigned int numofchars, recommendedprefixlength;
GtEncseqBuilder *eb;
bool haserr = false;
eb = gt_encseq_builder_new(alpha);
gt_encseq_builder_disable_multiseq_support(eb);
gt_encseq_builder_disable_description_support(eb);
gt_encseq_builder_set_logger(eb, logger);
gt_encseq_builder_add_encoded(eb, dbseq, dblen, NULL);
gt_encseq_builder_add_encoded(eb, query, querylen, NULL);
ssi.encseq = gt_encseq_builder_build(eb, err);
gt_encseq_builder_delete(eb);
ssi.minlength = minlength;
ssi.processmaxpairs = processmaxpairs;
ssi.processmaxpairsinfo = processmaxpairsinfo;
numofchars = gt_alphabet_num_of_chars(alpha);
recommendedprefixlength
= gt_recommendedprefixlength(numofchars,
dblen+querylen+1,
GT_RECOMMENDED_MULTIPLIER_DEFAULT,
true);
if (constructsarrandrunmaxpairs(&ssi,
GT_READMODE_FORWARD,
recommendedprefixlength,
1U, /* parts */
0, /* maximumspace */
NULL,
false,
logger,
err) != 0)
{
haserr = true;
}
gt_encseq_delete(ssi.encseq);
ssi.encseq = NULL;
return haserr ? -1 : 0;
}
int gt_encseq_gc_unit_test(GtError *err)
{
int had_err = 0;
double *results;
GtEncseqBuilder *eb;
GtEncseq *encseq;
const char testseq1[] = "aaaaaa",
testseq2[] = "cccccc",
testseq3[] = "acgtacgt",
testseq4[] = "acgtn";
/* testseq5[] = "xxxxn"; */
GtAlphabet *alpha;
/*GtError *tmp_err;*/
gt_error_check(err);
alpha = gt_alphabet_new_dna();
/* test a-seq */
eb = gt_encseq_builder_new(alpha);
gt_encseq_builder_create_ssp_tab(eb);
gt_encseq_builder_enable_description_support(eb);
gt_encseq_builder_add_cstr(eb, testseq1, 6UL, "only a");
encseq = gt_encseq_builder_build(eb, err);
if ((results = gt_encseq_get_gc(encseq,
false,
true,
err)) != NULL)
{
gt_ensure(had_err, gt_double_equals_double(results[0], 0.0));
}
else
{
had_err = -1;
}
gt_free(results);
gt_encseq_builder_delete(eb);
gt_encseq_delete(encseq);
if (!had_err)
{
/* test c-seq */
eb = gt_encseq_builder_new(alpha);
gt_encseq_builder_create_ssp_tab(eb);
gt_encseq_builder_enable_description_support(eb);
gt_encseq_builder_add_cstr(eb, testseq2, 6UL, "only c");
encseq = gt_encseq_builder_build(eb, err);
if ((results = gt_encseq_get_gc(encseq,
false,
true,
err)) != NULL)
{
gt_ensure(had_err, gt_double_equals_one(results[0]));
}
else
{
had_err = -1;
}
gt_free(results);
gt_encseq_builder_delete(eb);
gt_encseq_delete(encseq);
}
if (!had_err)
{
/* test dna-seq and dna+special-seq*/
eb = gt_encseq_builder_new(alpha);
gt_encseq_builder_create_ssp_tab(eb);
gt_encseq_builder_enable_description_support(eb);
gt_encseq_builder_add_cstr(eb, testseq3, 8UL, "0.5");
gt_encseq_builder_add_cstr(eb, testseq4, 5UL, "0.5+special");
encseq = gt_encseq_builder_build(eb, err);
if ((results = gt_encseq_get_gc(encseq,
false,
true,
err)) != NULL)
{
gt_ensure(had_err, gt_double_equals_double(results[0], 0.5));
gt_ensure(had_err, gt_double_equals_double(results[1], 0.5));
}
else
{
had_err = -1;
}
gt_free(results);
if (!had_err)
{
/* count special chars */
if ((results = gt_encseq_get_gc(encseq,
true,
true,
err)) != NULL)
{
gt_ensure(had_err, gt_double_equals_double(results[0], 0.5));
gt_ensure(had_err, gt_double_equals_double(results[1], (2.0/5.0)));
}
else
{
had_err = -1;
}
gt_free(results);
}
gt_encseq_builder_delete(eb);
gt_encseq_delete(encseq);
}
if (!had_err)
{
/* test dna-seq and dna+special-seq*/
eb = gt_encseq_builder_new(alpha);
gt_encseq_builder_create_ssp_tab(eb);
gt_encseq_builder_enable_description_support(eb);
gt_encseq_builder_add_cstr(eb, testseq3, 8UL, "0.5");
gt_encseq_builder_add_cstr(eb, testseq4, 5UL, "0.5+special");
encseq = gt_encseq_builder_build(eb, err);
/*add mirrored sequence*/
had_err = gt_encseq_mirror(encseq, err);
/* sequence wise */
if ((results = gt_encseq_get_gc(encseq,
false,
true,
err)) != NULL)
{
gt_ensure(had_err, gt_double_equals_double(results[0], 0.5));
gt_ensure(had_err, gt_double_equals_double(results[1], 0.5));
gt_ensure(had_err, gt_double_equals_double(results[2], 0.5));
gt_ensure(had_err, gt_double_equals_double(results[3], 0.5));
}
else
{
had_err = -1;
}
gt_free(results);
if (!had_err)
{
/* count special chars */
if ((results = gt_encseq_get_gc(encseq,
true,
true,
err)) != NULL)
{
gt_ensure(had_err, gt_double_equals_double(results[0], 0.5));
gt_ensure(had_err, gt_double_equals_double(results[1], (2.0/5.0)));
gt_ensure(had_err, gt_double_equals_double(results[2], (2.0/5.0)));
gt_ensure(had_err, gt_double_equals_double(results[3], 0.5));
}
else
{
had_err = -1;
}
gt_free(results);
}
gt_encseq_builder_delete(eb);
gt_encseq_delete(encseq);
}
gt_alphabet_delete(alpha);
return had_err;
}
