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);
}
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);
}
