static void gt_seqorder_sort(GtSuffixsortspace *suffixsortspace,
const GtEncseq *encseq)
{
Sfxstrategy sfxstrategy;
defaultsfxstrategy(&sfxstrategy, false);
gt_suffixsortspace_init_seqstartpos(suffixsortspace,encseq);
gt_sortallsuffixesfromstart(suffixsortspace,
gt_encseq_num_of_sequences(encseq), encseq, GT_READMODE_FORWARD, NULL, 0,
&sfxstrategy, NULL, NULL, NULL);
}
static void gt_seqorder_sort(GtSuffixsortspace *suffixsortspace,
GtEncseq *encseq)
{
unsigned long i;
Sfxstrategy sfxstrategy;
defaultsfxstrategy(&sfxstrategy, false);
for (i = 0; i < gt_encseq_num_of_sequences(encseq); i++)
gt_suffixsortspace_setdirect(suffixsortspace, i,
gt_encseq_seqstartpos(encseq, i));
gt_sortallsuffixesfromstart(suffixsortspace,
gt_encseq_num_of_sequences(encseq), encseq, GT_READMODE_FORWARD, NULL, 0,
&sfxstrategy, NULL, NULL, NULL);
}
static int gt_constructsarrandrunmmsearch(
const GtEncseq *dbencseq,
GtReadmode readmode,
unsigned int prefixlength,
unsigned int numofparts,
GtUword maximumspace,
const GtUchar *query,
GtUword querylen,
unsigned int minlength,
GtProcessquerymatch processquerymatch,
void *processquerymatchinfo,
GtTimer *sfxprogress,
bool withprogressbar,
GtLogger *logger,
GtError *err)
{
bool haserr = false;
Sfxiterator *sfi;
Sfxstrategy sfxstrategy;
defaultsfxstrategy(&sfxstrategy,
gt_encseq_bitwise_cmp_ok(dbencseq) ? false : true);
sfxstrategy.outsuftabonfile = false;
sfi = gt_Sfxiterator_new(dbencseq,
readmode,
prefixlength,
numofparts,
maximumspace,
&sfxstrategy, /* sfxstrategy */
sfxprogress,
withprogressbar,
logger, /* logger */
err);
if (sfi == NULL)
{
haserr = true;
} else
{
const GtSuffixsortspace *suffixsortspace;
GtUword numberofsuffixes;
GtQuerymatch *querymatchspaceptr = gt_querymatch_new();
GtQueryrepresentation queryrep;
queryrep.sequence = query;
queryrep.encseq = NULL;
queryrep.readmode = GT_READMODE_FORWARD;
queryrep.startpos = 0;
queryrep.seqlen = querylen;
while (true)
{
suffixsortspace = gt_Sfxiterator_next(&numberofsuffixes,NULL,sfi);
if (suffixsortspace == NULL)
{
break;
}
gt_querysubstringmatch(false,
dbencseq,
(const ESASuffixptr *)
gt_suffixsortspace_ulong_get(suffixsortspace),
readmode,
numberofsuffixes,
0,
&queryrep,
(GtUword) minlength,
processquerymatch,
processquerymatchinfo,
querymatchspaceptr);
}
gt_querymatch_delete(querymatchspaceptr);
}
if (gt_Sfxiterator_delete(sfi,err) != 0)
{
haserr = true;
}
return haserr ? -1 : 0;
}
static int constructsarrandrunmaxpairs(
Substringmatchinfo *ssi,
GtReadmode readmode,
unsigned int prefixlength,
unsigned int numofparts,
GtUword maximumspace,
GtTimer *sfxprogress,
bool withprogressbar,
GT_UNUSED GtLogger *logger,
GtError *err)
{
const GtSuffixsortspace *suffixsortspace;
GtUword numberofsuffixes;
bool haserr = false;
Sfxiterator *sfi;
bool specialsuffixes = false;
Sfxstrategy sfxstrategy;
defaultsfxstrategy(&sfxstrategy,
gt_encseq_bitwise_cmp_ok(ssi->encseq) ? false : true);
sfi = gt_Sfxiterator_new(ssi->encseq,
readmode,
prefixlength,
numofparts,
maximumspace,
&sfxstrategy,
sfxprogress,
withprogressbar,
NULL, /* logger */
err);
if (sfi == NULL)
{
haserr = true;
} else
{
Sequentialsuffixarrayreader *ssar = NULL;
bool firstpage = true;
ssar = gt_newSequentialsuffixarrayreaderfromRAM(ssi->encseq,
readmode);
while (true)
{
suffixsortspace = gt_Sfxiterator_next(&numberofsuffixes,&specialsuffixes,
sfi);
if (suffixsortspace == NULL || specialsuffixes)
{
break;
}
gt_updateSequentialsuffixarrayreaderfromRAM(
ssar,
(const ESASuffixptr *)
gt_suffixsortspace_ulong_get(suffixsortspace),
firstpage,
numberofsuffixes);
firstpage = false;
if (gt_enumeratemaxpairs(ssar,
ssi->encseq,
readmode,
ssi->minlength,
ssi->processmaxpairs,
ssi->processmaxpairsinfo,
err) != 0)
{
haserr = true;
}
}
if (ssar != NULL)
{
gt_freeSequentialsuffixarrayreader(&ssar);
}
}
if (gt_Sfxiterator_delete(sfi,err) != 0)
{
haserr = true;
}
return haserr ? -1 : 0;
}
