static int encseq_builder_lua_disable_description_support(lua_State *L)
{
GtEncseqBuilder **builder;
builder = check_encseq_builder(L, 1);
gt_assert(*builder);
gt_encseq_builder_disable_description_support(*builder);
return 0;
}
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;
}
