int allkeysdefined(const GtStr *indexname,const char *suffix,
const GtArray *riktab,Verboseinfo *verboseinfo,
GtError *err)
{
unsigned long i;
Readintkeys *rikptr;
gt_error_check(err);
for (i=0; i<gt_array_size(riktab); i++)
{
rikptr = (Readintkeys *) gt_array_get(riktab,i);
if (rikptr->found)
{
if (rikptr->ptrdefined)
{
if (rikptr->smallvalueptr != NULL)
{
showverbose(verboseinfo,"%s=%u",
rikptr->keystring,
(unsigned int) *(rikptr->smallvalueptr));
} else
{
if (rikptr->bigvalueptr != NULL)
{
showverbose(verboseinfo,"%s=" Formatuint64_t,
rikptr->keystring,
PRINTuint64_tcast(*(rikptr->bigvalueptr)));
} else
{
gt_assert(false);
}
}
} else
{
showverbose(verboseinfo,"%s=0",rikptr->keystring);
}
if (rikptr->readflag != NULL)
{
*(rikptr->readflag) = true;
}
} else
{
if (rikptr->readflag == NULL)
{
gt_error_set(err,"file %s%s: missing line beginning with \"%s=\"",
gt_str_get(indexname),
suffix,
rikptr->keystring);
return -1;
}
*(rikptr->readflag) = false;
}
}
return 0;
}
void gt_copysortsuffixes(const GtBucketspec2 *bucketspec2,
Seqpos *suftab,
Verboseinfo *verboseinfo)
{
Seqpos hardwork = 0, **targetptr;
unsigned int idx, idxsource, source, second;
#ifdef WITHSUFFIXES
{
const Seqpos *ptr;
for (ptr = suftab; ptr < suftab + bucketspec2->partwidth; ptr++)
{
showsequenceatstartpos(stdout,
ISDIRREVERSE(readmode) ? false : true,
ISDIRCOMPLEMENT(readmode) ? true : false,
encseq,
*ptr);
}
}
#endif
targetptr = gt_malloc(sizeof(*targetptr) * bucketspec2->numofchars);
for (idxsource = 0; idxsource<bucketspec2->numofchars; idxsource++)
{
source = bucketspec2->order[idxsource];
for (second = 0; second < bucketspec2->numofchars; second++)
{
if (!bucketspec2->subbuckettab[source][second].sorted && source != second)
{
gt_assert(bucketspec2->subbuckettab[source][second].hardworktodo);
showverbose(verboseinfo,"hard work for %u %u",source,second);
hardwork += getendidx(bucketspec2,source,second) -
getstartidx(bucketspec2,source,second);
bucketspec2->subbuckettab[source][second].sorted = true;
} else
{
gt_assert(!bucketspec2->subbuckettab[source][second].hardworktodo);
}
}
if (getstartidx(bucketspec2,source,0) <
getstartidx(bucketspec2,source,source))
{
for (idx = 0; idx < bucketspec2->numofchars; idx++)
{
targetptr[idx] = suftab + getstartidx(bucketspec2,idx,source);
}
forwardderive(bucketspec2,
targetptr,
source,
suftab + getstartidx(bucketspec2,source,0));
}
if (getendidx(bucketspec2,source,source) <
getendidx(bucketspec2,source,bucketspec2->numofchars))
{
for (idx = 0; idx < bucketspec2->numofchars; idx++)
{
targetptr[idx] = suftab + getendidx(bucketspec2,idx,source) - 1;
}
backwardderive(bucketspec2,
targetptr,
source,
suftab +
getendidx(bucketspec2,source,bucketspec2->numofchars) - 1);
}
for (idx = 0; idx < bucketspec2->numofchars; idx++)
{
bucketspec2->subbuckettab[idx][source].sorted = true;
}
bucketspec2->superbuckettab[source].sorted = true;
}
gt_free(targetptr);
showverbose(verboseinfo,"hardwork = " FormatSeqpos " (%.2f)",
PRINTSeqposcast(hardwork),
(double) hardwork/getencseqtotallength(bucketspec2->encseq));
}
