static void gt_seqorder_get_hdrsorted_seqnums(const GtEncseq *encseq,
GtUword *seqnums,
GtCompareWithData cmpfunc)
{
GtUword i;
gt_assert(encseq != NULL);
for (i = 0UL; i < gt_encseq_num_of_sequences(encseq); i++)
seqnums[i] = i;
(void) gt_qsort_r(seqnums, gt_encseq_num_of_sequences(encseq),
sizeof (GtUword), (void*) encseq, cmpfunc);
}
GtBucketspec2 *gt_bucketspec2_new(const Bcktab *bcktab,
const Encodedsequence *encseq,
Readmode readmode,
Seqpos partwidth,
unsigned int numofchars)
{
GtBucketspec2 *bucketspec2;
unsigned int idx;
gt_assert(numofchars > 0);
bucketspec2 = gt_malloc(sizeof(*bucketspec2));
bucketspec2->partwidth = partwidth;
bucketspec2->prefixlength = bcktab_prefixlength(bcktab);
bucketspec2->numofchars = numofchars;
bucketspec2->numofcharssquared = numofchars * numofchars;
bucketspec2->encseq = encseq;
bucketspec2->readmode = readmode;
bucketspec2->order = gt_malloc(sizeof(*bucketspec2->order) * numofchars);
bucketspec2->superbuckettab
= gt_malloc(sizeof(*bucketspec2->superbuckettab) * numofchars);
gt_array2dim_malloc(bucketspec2->subbuckettab,(unsigned long) numofchars,
(unsigned long) numofchars);
if (bucketspec2->prefixlength == 2U)
{
fill2subbuckets(bucketspec2,bcktab);
} else
{
fillanysubbuckets(bucketspec2,bcktab);
}
for (idx = 0; idx<numofchars; idx++)
{
bucketspec2->order[idx] = idx;
}
gt_qsort_r(bucketspec2->order,(size_t) numofchars,
sizeof (*bucketspec2->order),bucketspec2,
comparesuperbucketsizes);
resetsorted(bucketspec2);
#ifdef SHOWBUCKETSPEC2
showbucketspec2(bucketspec2);
#endif
determinehardwork(bucketspec2);
resetsorted(bucketspec2);
return bucketspec2;
}
unsigned long gt_uint64hashtable_partialsums(GtUint64hashtable *table,
GtTimer *timer)
{
size_t idx, next = 0;
unsigned long psum, maxsize = 0;
table->sortedhspace = gt_malloc((size_t) table->allentries *
sizeof (*table->sortedhspace));
if (timer != NULL)
{
gt_timer_show_progress(timer, "sorting the hashkeys",stdout);
}
for (idx = 0; idx < table->alloc; idx++)
{
if (table->hspace[idx].count > 0)
{
gt_assert(next < (size_t) table->allentries);
table->sortedhspace[next++] = idx;
if (maxsize < table->hspace[idx].count)
{
maxsize = table->hspace[idx].count;
}
}
}
gt_qsort_r(table->sortedhspace,next,sizeof(*table->sortedhspace),
table->hspace,compareGtUint64hashstoredvalue);
gt_assert(next > 0);
if (table->zero_occurs)
{
table->hspace[table->sortedhspace[0]].count += table->zero_count;
}
if (timer != NULL)
{
gt_timer_show_progress(timer, "computing partial sums",stdout);
}
for (idx = (size_t) 1; idx < next; idx++)
{
table->hspace[table->sortedhspace[idx]].count +=
table->hspace[table->sortedhspace[idx-1]].count;
}
psum = table->hspace[table->sortedhspace[next-1]].count;
gt_free(table->sortedhspace);
return psum;
}
