int gt_callenumselfmatches(const char *indexname,
GtReadmode queryreadmode,
unsigned int userdefinedleastlength,
GtProcessquerymatch processquerymatch,
void *processquerymatchinfo,
GtLogger *logger,
GtError *err)
{
Suffixarray suffixarray;
bool haserr = false;
gt_assert(queryreadmode != GT_READMODE_FORWARD);
if (gt_mapsuffixarray(&suffixarray,
SARR_ESQTAB | SARR_SUFTAB | SARR_SSPTAB,
indexname,
logger,
err) != 0)
{
haserr = true;
} else
{
unsigned long seqnum, numofsequences, seqlength, seqstartpos;
GtQuerymatch *querymatchspaceptr = gt_querymatch_new();
GtQueryrep queryrep;
numofsequences = gt_encseq_num_of_sequences(suffixarray.encseq);
queryrep.sequence = NULL;
queryrep.reversecopy = false;
queryrep.encseq = suffixarray.encseq;
queryrep.readmode = queryreadmode;
for (seqnum = 0; seqnum < numofsequences; seqnum++)
{
seqstartpos = gt_encseq_seqstartpos(suffixarray.encseq, seqnum);
seqlength = gt_encseq_seqlength(suffixarray.encseq, seqnum);
if (seqlength >= (unsigned long) userdefinedleastlength)
{
queryrep.startpos = seqstartpos;
queryrep.length = seqlength;
if (gt_querysubstringmatch(true,
&suffixarray,
(uint64_t) seqnum,
&queryrep,
(unsigned long) userdefinedleastlength,
processquerymatch,
processquerymatchinfo,
querymatchspaceptr,
err) != 0)
{
haserr = true;
break;
}
}
}
gt_querymatch_delete(querymatchspaceptr);
}
gt_freesuffixarray(&suffixarray);
return haserr ? -1 : 0;
}
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;
}