static int callenummaxpairs(const char *indexname,
unsigned int userdefinedleastlength,
bool scanfile,
Processmaxpairs processmaxpairs,
void *processmaxpairsinfo,
GtLogger *logger,
GtError *err)
{
bool haserr = false;
Sequentialsuffixarrayreader *ssar;
gt_error_check(err);
ssar = gt_newSequentialsuffixarrayreaderfromfile(indexname,
SARR_LCPTAB |
SARR_SUFTAB |
SARR_ESQTAB |
SARR_SSPTAB,
scanfile ? SEQ_scan
: SEQ_mappedboth,
logger,
err);
if (ssar == NULL)
{
haserr = true;
}
if (!haserr &&
gt_enumeratemaxpairs(ssar,
gt_encseqSequentialsuffixarrayreader(ssar),
gt_readmodeSequentialsuffixarrayreader(ssar),
userdefinedleastlength,
processmaxpairs,
processmaxpairsinfo,
err) != 0)
{
haserr = true;
}
if (ssar != NULL)
{
gt_freeSequentialsuffixarrayreader(&ssar);
}
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;
}
