short_pair*
simpleSuffixSort(const usint* sequence, uint n, uint threads)
{
if(sequence == 0 || n == 0) { return 0; }
skew_pair* pairs = (skew_pair*)new short_pair[n * sizeof(skew_pair) / sizeof(short_pair) + 1];
uint* keys = new uint[n]; // In text order.
std::vector<ss_range> unsorted;
threads = std::max(threads, (uint)1);
#ifdef MULTITHREAD_SUPPORT
omp_set_num_threads(threads);
#endif
// Initialize pairs.
#pragma omp parallel for schedule(static)
for(uint i = 0; i < n; i++) { pairs[i].first = i; pairs[i].second = sequence[i]; }
// Sort according to first character.
parallelSort(pairs, pairs + n, skew_comparator);
unsorted.push_back(ss_range(0, n - 1));
uint total = setRanks(pairs, keys, n, unsorted, threads, 1);
if(sizeof(usint) < 2 * sizeof(uint))
{
return prefixDoubling(packPairs(pairs, n), keys, unsorted, n, threads, total, 1);
}
else
{
return prefixTripling(pairs, keys, unsorted, n, threads, total, 1);
}
}
short_pair*
prefixDoubling(short_pair* pairs, uint* keys, std::vector<ss_range>& unsorted, uint n, uint threads, uint total, uint h)
{
// Double prefix length until sorted.
while(total > 0)
{
uint chunk = std::max((size_t)1, unsorted.size() / (threads * threads));
#pragma omp parallel for schedule(dynamic, chunk)
for(uint i = 0; i < unsorted.size(); i++)
{
// Set sort keys for the current range.
short_pair* limit = pairs + unsorted[i].second;
for(short_pair* curr = pairs + unsorted[i].first; curr <= limit; ++curr)
{
curr->second = keys[curr->first + h];
}
sequentialSort(pairs + unsorted[i].first, pairs + unsorted[i].second + 1, key_comparator);
}
total = setRanks(pairs, keys, n, unsorted, threads, chunk);
h *= 2;
// std::cout << "Sorted with h = " << h << ", unsorted total = " << total << " (" << unsorted.size() << " ranges)" << std::endl;
}
#pragma omp parallel for schedule(static)
for(uint i = 0; i < n; i++) { pairs[i].second = keys[i]; }
delete[] keys; keys = 0;
return pairs;
}
short_pair*
prefixTripling(skew_pair* pairs, uint* keys, std::vector<ss_range>& unsorted, uint n, uint threads, uint total, uint h)
{
const usint PACK_FACTOR = sizeof(usint) * CHAR_BIT / 2;
// Triple prefix length until sorted.
while(total > 0)
{
uint chunk = std::max((size_t)1, unsorted.size() / (threads * threads));
#pragma omp parallel for schedule(dynamic, chunk)
for(uint i = 0; i < unsorted.size(); i++)
{
// Set sort keys for the current range.
skew_pair* limit = pairs + unsorted[i].second;
for(skew_pair* curr = pairs + unsorted[i].first; curr <= limit; ++curr)
{
curr->second = (usint)(keys[curr->first + h]) << PACK_FACTOR;
if(n - h > curr->first + h) { curr->second += keys[curr->first + 2 * h]; }
}
sequentialSort(pairs + unsorted[i].first, pairs + unsorted[i].second + 1, skew_comparator);
}
total = setRanks(pairs, keys, n, unsorted, threads, chunk);
h *= 3;
// std::cout << "Sorted with h = " << h << ", unsorted total = " << total << " (" << unsorted.size() << " ranges)" << std::endl;
}
#pragma omp parallel for schedule(static)
for(uint i = 0; i < n; i++) { pairs[i].second = keys[i]; }
delete[] keys; keys = 0;
return packPairs(pairs, n);
}
uint
initialSort(short_pair* pairs, uint* keys, std::vector<ss_range>& unsorted, uint n, uint threads, uint h)
{
// Sort according to first h characters.
std::cout << "initialSort(short_pair* pairs, uint* keys, std::vector<ss_range>& unsorted, uint n, uint threads, uint h)" << std::endl;
parallelSort(pairs, pairs + n, key_comparator);
unsorted.push_back(ss_range(0, n - 1));
uint total = setRanks(pairs, keys, n, unsorted, threads, 1);
// std::cout << "Sorted with h = " << h << ", unsorted total = " << total << " (" << unsorted.size() << " ranges)" << std::endl;
std::cout << "done initialSort(short_pair* pairs, uint* keys, std::vector<ss_range>& unsorted, uint n, uint threads, uint h) -- Sorted with h = " << h << ", unsorted total = " << total << " (" << unsorted.size() << " ranges)" << std::endl;
return total;
}
/* dot1_rank:
* asp != NULL => g is root
*/
static void dot1_rank(graph_t * g, aspect_t* asp)
{
point p;
#ifdef ALLOW_LEVELS
attrsym_t* N_level;
#endif
edgelabel_ranks(g);
if (asp) {
init_UF_size(g);
initEdgeTypes(g);
}
collapse_sets(g,g);
/*collapse_leaves(g); */
class1(g);
p = minmax_edges(g);
decompose(g, 0);
if (asp && ((GD_comp(g).size > 1)||(GD_n_cluster(g) > 0))) {
asp->badGraph = 1;
asp = NULL;
}
acyclic(g);
if (minmax_edges2(g, p))
decompose(g, 0);
#ifdef ALLOW_LEVELS
if ((N_level = agattr(g,AGNODE,"level",NULL)))
setRanks(g, N_level);
else
#endif
if (asp)
rank3(g, asp);
else
rank1(g);
expand_ranksets(g, asp);
cleanup1(g);
}
