csa_wt<t_wt, t_dens, t_inv_dens, t_sa_sample_strat, t_isa, t_alphabet_strat>::csa_wt(cache_config& config)
{
if (!cache_file_exists(key_trait<alphabet_type::int_width>::KEY_BWT, config)) {
return;
}
{
auto event = memory_monitor::event("construct csa-alpbabet");
int_vector_buffer<alphabet_type::int_width> bwt_buf(cache_file_name(key_trait<alphabet_type::int_width>::KEY_BWT,config));
size_type n = bwt_buf.size();
alphabet_type tmp_alphabet(bwt_buf, n);
m_alphabet.swap(tmp_alphabet);
}
{
auto event = memory_monitor::event("construct wavelet tree");
int_vector_buffer<alphabet_type::int_width> bwt_buf(cache_file_name(key_trait<alphabet_type::int_width>::KEY_BWT,config));
size_type n = bwt_buf.size();
wavelet_tree_type tmp_wt(bwt_buf, n);
m_wavelet_tree.swap(tmp_wt);
}
{
auto event = memory_monitor::event("sample SA");
sa_sample_type tmp_sa_sample(config);
m_sa_sample.swap(tmp_sa_sample);
}
{
auto event = memory_monitor::event("sample ISA");
isa_sample_type isa_s(config, &m_sa_sample);
util::swap_support(m_isa_sample, isa_s, &m_sa_sample, &m_sa_sample);
}
}
csa_sada<t_enc_vec, t_dens, t_inv_dens, t_sa_sample_strat, t_isa, t_alphabet_strat>::csa_sada(cache_config& config)
{
create_buffer();
if (!cache_file_exists(key_trait<alphabet_type::int_width>::KEY_BWT, config)) {
return;
}
int_vector_buffer<alphabet_type::int_width> bwt_buf(cache_file_name(key_trait<alphabet_type::int_width>::KEY_BWT,config));
size_type n = bwt_buf.size();
{
auto event = memory_monitor::event("construct csa-alpbabet");
alphabet_type tmp_alphabet(bwt_buf, n);
m_alphabet.swap(tmp_alphabet);
}
int_vector<> cnt_chr(sigma, 0, bits::hi(n)+1);
for (typename alphabet_type::sigma_type i=0; i < sigma; ++i) {
cnt_chr[i] = C[i];
}
// calculate psi
{
auto event = memory_monitor::event("construct PSI");
// TODO: move PSI construct into construct_PSI.hpp
int_vector<> psi(n, 0, bits::hi(n)+1);
for (size_type i=0; i < n; ++i) {
psi[ cnt_chr[ char2comp[bwt_buf[i]] ]++ ] = i;
}
std::string psi_file = cache_file_name(conf::KEY_PSI, config);
if (!store_to_cache(psi, conf::KEY_PSI, config)) {
return;
}
}
{
auto event = memory_monitor::event("encode PSI");
int_vector_buffer<> psi_buf(cache_file_name(conf::KEY_PSI, config));
t_enc_vec tmp_psi(psi_buf);
m_psi.swap(tmp_psi);
}
{
auto event = memory_monitor::event("sample SA");
sa_sample_type tmp_sa_sample(config);
m_sa_sample.swap(tmp_sa_sample);
}
{
auto event = memory_monitor::event("sample ISA");
isa_sample_type isa_s(config, &m_sa_sample);
util::swap_support(m_isa_sample, isa_s, &m_sa_sample, (const sa_sample_type*)nullptr);
}
}
//! Constructor
lcp_byte(cache_config& config) {
std::string lcp_file = cache_file_name(conf::KEY_LCP, config);
int_vector_buffer<> lcp_buf(lcp_file);
m_small_lcp = int_vector<8>(lcp_buf.size());
size_type l=0, max_l=0, max_big_idx=0, big_sum=0;
for (size_type i=0; i < m_small_lcp.size(); ++i) {
if ((l=lcp_buf[i]) < 255) {
m_small_lcp[i] = l;
} else {
m_small_lcp[i] = 255;
if (l > max_l) max_l = l;
max_big_idx = i;
++big_sum;
}
}
m_big_lcp = int_vector<>(big_sum, 0, bits::hi(max_l)+1);
m_big_lcp_idx = int_vector<>(big_sum, 0, bits::hi(max_big_idx)+1);
for (size_type i=0,ii=0; i<m_small_lcp.size(); ++i) {
if ((l=lcp_buf[i]) >= 255) {
m_big_lcp[ii] = l;
m_big_lcp_idx[ii] = i;
++ii;
}
}
}
void register_cache_file(const char* key, cache_config &config){
std::string file_name = cache_file_name(key, config);
std::ifstream in(file_name.c_str());
if ( in ){ // if file exists, register it.
config.file_map[std::string(key)] = file_name;
}
}
void construct(matching_index<t_wt, t_bv>& idx, const std::string& file, sdsl::cache_config& config, uint8_t num_bytes)
{
sdsl::int_vector<0> text;
{
//auto event = memory_monitor::event("text");
load_vector_from_file(text, file, num_bytes);
}
sdsl::csa_wt<sdsl::wt_int<>> csa;
{
//auto event = memory_monitor::event("csa");
construct(csa, file, config, num_bytes);
}
t_wt wts;
{
//auto event = memory_monitor::event("wt");
construct(wts, cache_file_name(sdsl::conf::KEY_SA, config));
}
sdsl::util::delete_all_files(config.file_map);
{
//auto event = memory_monitor::event("compose"); // contains rank support initialization
idx = std::move(matching_index<t_wt, t_bv>(text, wts));
}
}
//! Constructor taking a cache_config
lcp_bitcompressed(cache_config& config) {
std::string lcp_file = cache_file_name(conf::KEY_LCP, config);
int_vector_buffer<> lcp_buf(lcp_file);
m_lcp = int_vector<t_width>(lcp_buf.size(), 0, lcp_buf.width());
for (size_type i=0; i < m_lcp.size(); ++i) {
m_lcp[i] = lcp_buf[i];
}
}
void construct_lcp_PHI(cache_config& config)
{
static_assert(t_width == 0 or t_width == 8 , "construct_lcp_PHI: width must be `0` for integer alphabet and `8` for byte alphabet");
typedef int_vector<>::size_type size_type;
typedef int_vector<t_width> text_type;
const char* KEY_TEXT = key_text_trait<t_width>::KEY_TEXT;
int_vector_buffer<> sa_buf(config.file_map[conf::KEY_SA]);
size_type n = sa_buf.size();
assert(n > 0);
if (1 == n) { // Handle special case: Input only the sentinel character.
int_vector<> lcp(1, 0);
store_to_cache(lcp, conf::KEY_LCP, config);
return;
}
// (1) Calculate PHI (stored in array plcp)
int_vector<> plcp(n, 0, sa_buf.width());
for (size_type i=0, sai_1 = 0; i < n; ++i) {
size_type sai = sa_buf[i];
plcp[ sai ] = sai_1;
sai_1 = sai;
}
// (2) Load text from disk
text_type text;
load_from_cache(text, KEY_TEXT, config);
// (3) Calculate permuted LCP array (text order), called PLCP
size_type max_l = 0;
for (size_type i=0, l=0; i < n-1; ++i) {
size_type phii = plcp[i];
while (text[i+l] == text[phii+l]) {
++l;
}
plcp[i] = l;
if (l) {
max_l = std::max(max_l, l);
--l;
}
}
util::clear(text);
uint8_t lcp_width = bits::hi(max_l)+1;
// (4) Transform PLCP into LCP
std::string lcp_file = cache_file_name(conf::KEY_LCP, config);
size_type buffer_size = 1000000; // buffer_size is a multiple of 8!
int_vector_buffer<> lcp_buf(lcp_file, std::ios::out, buffer_size, lcp_width); // open buffer for lcp
lcp_buf[0] = 0;
sa_buf.buffersize(buffer_size);
for (size_type i=1; i < n; ++i) {
size_type sai = sa_buf[i];
lcp_buf[i] = plcp[sai];
}
lcp_buf.close();
register_cache_file(conf::KEY_LCP, config);
}
//! Construct
lcp_vlc(cache_config& config, std::string other_key="")
{
std::string lcp_key = conf::KEY_LCP;
if ("" != other_key) {
lcp_key = other_key;
}
int_vector_buffer<> lcp_buf(cache_file_name(lcp_key, config));
vlc_vec_type tmp_vec(lcp_buf);
m_vec.swap(tmp_vec);
}
//! Constructor
csa_bitcompressed(cache_config& config) {
std::string text_file = cache_file_name(key_trait<alphabet_type::int_width>::KEY_TEXT,config);
int_vector_buffer<alphabet_type::int_width> text_buf(text_file);
int_vector_buffer<> sa_buf(cache_file_name(conf::KEY_SA,config));
size_type n = text_buf.size();
{
alphabet_type tmp_alphabet(text_buf, n);
m_alphabet.swap(tmp_alphabet);
}
{
sa_sample_type tmp_sample(config);
m_sa.swap(tmp_sample);
}
set_isa_samples<csa_bitcompressed>(sa_buf, m_isa);
if (!store_to_file(m_isa, cache_file_name(conf::KEY_ISA,config), true)) {
throw std::ios_base::failure("#csa_bitcompressed: Cannot store ISA to file system!");
} else {
register_cache_file(conf::KEY_ISA, config);
}
}
doc_list_index_greedy(std::string file_name, sdsl::cache_config& cconfig, uint8_t num_bytes) {
construct(m_csa_full, file_name, cconfig, num_bytes);
const char* KEY_TEXT = key_text_trait<WIDTH>::KEY_TEXT;
std::string text_file = cache_file_name(KEY_TEXT, cconfig);
bit_vector doc_border;
construct_doc_border(text_file,doc_border);
bit_vector::rank_1_type doc_border_rank(&doc_border);
m_doc_cnt = doc_border_rank(doc_border.size());
int_vector_buffer<0> sa_buf(cache_file_name(conf::KEY_SA, cconfig));
{
int_vector<> D;
construct_D_array(sa_buf, doc_border_rank, m_doc_cnt, D);
std::string d_file = cache_file_name("DARRAY", cconfig);
store_to_file(D, d_file);
util::clear(D);
construct(m_wtd, d_file);
sdsl::remove(d_file);
}
}
void construct(t_index& idx, const std::string& file, cache_config& config, uint8_t num_bytes, wt_tag)
{
auto event = memory_monitor::event("construct wavelet tree");
int_vector<t_index::alphabet_category::WIDTH> text;
load_vector_from_file(text, file, num_bytes);
std::string tmp_key = util::to_string(util::pid())+"_"+util::to_string(util::id());
std::string tmp_file_name = cache_file_name(tmp_key, config);
store_to_file(text, tmp_file_name);
util::clear(text);
{
int_vector_buffer<t_index::alphabet_category::WIDTH> text_buf(tmp_file_name);
t_index tmp(text_buf, text_buf.size());
idx.swap(tmp);
}
sdsl::remove(tmp_file_name);
}
void lcp_info(cache_config& config)
{
typedef int_vector<>::size_type size_type;
int_vector_buffer<> lcp_buf(cache_file_name(conf::KEY_LCP, config));
size_type n = lcp_buf.size();
size_type max_lcp = 0;
size_type sum_lcp = 0;
for (size_type i=0; i < n; ++i) {
if (lcp_buf[i] > max_lcp)
max_lcp = lcp_buf[i];
sum_lcp += lcp_buf[i];
}
std::cout<<"# max lcp = " << max_lcp << std::endl;
std::cout<<"# sum lcp = " << sum_lcp << std::endl;
std::cout<<"# avg lcp = " << sum_lcp/(double)n << std::endl;
}
//! Constructor
lcp_wt(cache_config& config, std::string other_key="") {
std::string temp_file = tmp_file(config, "_lcp_sml");
std::string lcp_key = conf::KEY_LCP;
if ("" != other_key) {
lcp_key = other_key;
}
int_vector_buffer<> lcp_buf(cache_file_name(lcp_key, config));
size_type l=0, max_l=0, big_sum=0, n = lcp_buf.size();
{
int_vector<8> small_lcp = int_vector<8>(n);
for (size_type i=0; i < n; ++i) {
if ((l=lcp_buf[i]) < 255) {
small_lcp[i] = l;
} else {
small_lcp[i] = 255;
if (l > max_l) max_l = l;
++big_sum;
}
}
store_to_file(small_lcp, temp_file);
}
{
int_vector_buffer<8> lcp_sml_buf(temp_file);
small_lcp_type tmp(lcp_sml_buf, lcp_sml_buf.size());
m_small_lcp.swap(tmp);
}
sdsl::remove(temp_file);
m_big_lcp = int_vector<>(big_sum, 0, bits::hi(max_l)+1);
{
for (size_type i=0, ii=0; i < n; ++i) {
if (lcp_buf[i] >= 255) {
m_big_lcp[ ii++ ] = lcp_buf[i];
}
}
}
}
lcp_dac<t_b, t_rank>::lcp_dac(cache_config& config)
{
// (1) Count for each level, how many blocks are needed for the representation
// Running time: \f$ O(n \times \frac{\log n}{b} \f$
// Result is sorted in m_level_pointer_and_rank
std::string lcp_file = cache_file_name(conf::KEY_LCP, config);
int_vector_buffer<> lcp_buf(lcp_file);
size_type n = lcp_buf.size(), val=0;
if (n == 0)
return;
// initialize counter
auto _size = std::max(4*bits::hi(2), 2*(((bits::hi(n)+1)+t_b-1) / t_b));
m_level_pointer_and_rank.resize(_size);
for (size_type i=0; i < m_level_pointer_and_rank.size(); ++i)
m_level_pointer_and_rank[i] = 0;
m_level_pointer_and_rank[0] = n; // level 0 has n entries
uint8_t level_x_2 = 0;
for (size_type i=0; i < n; ++i) {
val=lcp_buf[i];
val >>= t_b; // shift value b bits to the right
level_x_2 = 2;
while (val) {
// increase counter for current level by 1
++m_level_pointer_and_rank[level_x_2];
val >>= t_b; // shift value b bits to the right
level_x_2 += 2; // increase level by 1
}
}
// (2) Determine maximum level and prefix sums of level counters
m_max_level = 0;
size_type sum_blocks = 0, last_block_size=0;
for (size_type i=0, t=0; i < m_level_pointer_and_rank.size(); i+=2) {
t = sum_blocks;
sum_blocks += m_level_pointer_and_rank[i];
m_level_pointer_and_rank[i] = t;
if (sum_blocks > t) {
++m_max_level;
last_block_size = sum_blocks - t;
}
}
m_overflow = bit_vector(sum_blocks - last_block_size, 0);
m_data.resize(sum_blocks);
assert(last_block_size > 0);
// (3) Enter block and overflow data
int_vector<64> cnt = m_level_pointer_and_rank;
const uint64_t mask = bits::lo_set[t_b];
for (size_type i=0, j=0; i < n; ++i) {
val=lcp_buf[i];
j = cnt[0]++;
m_data[ j ] = val & mask;
val >>= t_b; // shift value b bits to the right
level_x_2 = 2;
while (val) {
m_overflow[j] = 1;
// increase counter for current level by 1
j = cnt[level_x_2]++;
m_data[ j ] = val & mask;
val >>= t_b; // shift value b bits to the right
level_x_2 += 2; // increase level by 1
}
}
// (4) Initialize rank data structure for m_overflow and precalc rank for
// pointers
util::init_support(m_overflow_rank, &m_overflow);
for (size_type i=0; 2*i < m_level_pointer_and_rank.size() and
m_level_pointer_and_rank[2*i] < m_overflow.size(); ++i) {
m_level_pointer_and_rank[2*i+1] = m_overflow_rank(
m_level_pointer_and_rank[2*i]);
}
}
std::string CDDB::cddb_cache_file() {
return cache_dir() + Dir::DIR_SEP + cache_file_name();
}
void construct_lcp_PHI(cache_config& config)
{
typedef int_vector<>::size_type size_type;
typedef int_vector<t_width> text_type;
const char* KEY_TEXT = key_text_trait<t_width>::KEY_TEXT;
int_vector_file_buffer<> sa_buf(config.file_map[constants::KEY_SA]);
size_type n = sa_buf.int_vector_size;
assert(n > 0);
if (1 == n) { // Handle special case: Input only the sentinel character.
int_vector<> lcp(1, 0);
store_to_cache(lcp, constants::KEY_LCP, config);
return;
}
// (1) Calculate PHI (stored in array plcp)
int_vector<> plcp(n, 0, sa_buf.width);
for (size_type i=0, r_sum=0, r=sa_buf.load_next_block(), sai_1 = 0; r_sum < n;) {
for (; i < r_sum+r; ++i) {
size_type sai = sa_buf[i-r_sum];
plcp[ sai ] = sai_1;
sai_1 = sai;
}
r_sum += r; r = sa_buf.load_next_block();
}
// (2) Load text from disk
text_type text;
load_from_cache(text, KEY_TEXT, config);
// (3) Calculate permuted LCP array (text order), called PLCP
size_type max_l = 0;
for (size_type i=0, l=0; i < n-1; ++i) {
size_type phii = plcp[i];
while (text[i+l] == text[phii+l]) {
++l;
}
plcp[i] = l;
if (l) {
max_l = std::max(max_l, l);
--l;
}
}
util::clear(text);
uint8_t lcp_width = bits::hi(max_l)+1;
// (4) Transform PLCP into LCP
std::string lcp_file = cache_file_name(constants::KEY_LCP, config);
osfstream lcp_out_buf(lcp_file, std::ios::binary | std::ios::app | std::ios::out); // open buffer for lcp
size_type bit_size = n*lcp_width;
lcp_out_buf.write((char*) &(bit_size), sizeof(bit_size)); // write size of vector
lcp_out_buf.write((char*) &(lcp_width),sizeof(lcp_width)); // write int_width of vector
size_type wb = 0; // bytes written into lcp int_vector
size_type buffer_size = 1000000; // buffer_size is a multiple of 8!
int_vector<> lcp_buf(buffer_size, 0, lcp_width);
lcp_buf[0] = 0;
sa_buf.reset(buffer_size);
size_type r = 0;// sa_buf.load_next_block();
for (size_type i=1, r_sum=0; r_sum < n;) {
for (; i < r_sum+r; ++i) {
size_type sai = sa_buf[i-r_sum];
lcp_buf[ i-r_sum ] = plcp[sai];
}
if (r > 0) {
size_type cur_wb = (r*lcp_buf.width()+7)/8;
lcp_out_buf.write((const char*)lcp_buf.data(), cur_wb);
wb += cur_wb;
}
r_sum += r; r = sa_buf.load_next_block();
}
if (wb%8) {
lcp_out_buf.write("\0\0\0\0\0\0\0\0", 8-wb%8);
}
lcp_out_buf.close();
register_cache_file(constants::KEY_LCP, config);
}
