static void resetsorted(GtBucketspec2 *bucketspec2)
{
unsigned int idx, idx2;
for (idx = 0; idx<bucketspec2->numofchars; idx++)
{
bucketspec2->superbuckettab[idx].sorted = false;
for (idx2 = 0; idx2<bucketspec2->numofchars; idx2++)
{
Seqpos startidx = getstartidx(bucketspec2,idx,idx2),
endidx = getendidx(bucketspec2,idx,idx2);
bucketspec2->subbuckettab[idx][idx2].sorted =
(startidx < endidx) ? false : true;
}
}
}
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));
}
void gt_copysort_derivesorting(const GtBucketspec2 *bucketspec2,
GtSuffixsortspace *suffixsortspace,
GtLogger *logger)
{
GtUword hardwork = 0,
*targetoffset;
unsigned int idx, idxsource, source, second;
#ifdef WITHSUFFIXES
{
GtUword idx;
for (idx = 0; idx < bucketspec2->partwidth; idx++)
{
gt_encseq_showatstartpos(
stdout,
GT_ISDIRREVERSE(readmode) ? false : true,
GT_ISDIRCOMPLEMENT(readmode) ? true : false,
encseq,
gt_suffixsortspace_getdirect(suffixsortspace,idx));
}
}
#endif
targetoffset = gt_malloc(sizeof (*targetoffset) * 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);
gt_logger_log(logger,"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++)
{
targetoffset[idx] = getstartidx(bucketspec2,idx,source);
}
forwardderive(bucketspec2,
suffixsortspace,
targetoffset,
source,
getstartidx(bucketspec2,source,0));
}
if (getendidx(bucketspec2,source,source) <
getendidx(bucketspec2,source,bucketspec2->numofchars))
{
for (idx = 0; idx < bucketspec2->numofchars; idx++)
{
/* do not need to assert that getendidx(idx,source) > 0, as later the
value stored in targetoffset is incremented */
targetoffset[idx] = getendidx(bucketspec2,idx,source) - 1;
}
gt_assert(getendidx(bucketspec2,source,bucketspec2->numofchars) > 0);
backwardderive(bucketspec2,
suffixsortspace,
targetoffset,
source,
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(targetoffset);
gt_logger_log(logger,"hardwork = "GT_WU" (%.2f)",
hardwork,
(double) hardwork/gt_encseq_total_length(bucketspec2->encseq));
}
