impl()
{
m_nr_to_bin.resize(1<<n);
m_bin_to_nr.resize(1<<n);
for (int i=0, cnt=0, class_cnt=0; i<=n; ++i) {
m_C[i] = cnt;
class_cnt = 0;
std::vector<bool> b(n,0);
for (int j=0; j<i; ++j) b[n-j-1] = 1;
do {
uint32_t x=0;
for (int k=0; k<n; ++k)
x |= ((uint32_t)b[n-k-1])<<(n-1-k);
m_nr_to_bin[cnt] = x;
m_bin_to_nr[x] = class_cnt;
++cnt;
++class_cnt;
} while (next_permutation(b.begin(), b.end()));
if (class_cnt == 1)
m_space_for_bt[i] = 0;
else
m_space_for_bt[i] = bits::hi(class_cnt)+1;
}
if (n == 15) {
for (int x=0; x<256; ++x) {
m_space_for_bt_pair[x] = m_space_for_bt[x>>4] + m_space_for_bt[x&0x0F];
}
}
}
void calculate_sa(const unsigned char* c, typename int_vector<fixedIntWidth>::size_type len, int_vector<fixedIntWidth>& sa)
{
typedef typename int_vector<fixedIntWidth>::size_type size_type;
if (len <= 1) { // handle special case
sa = int_vector<fixedIntWidth>(len,0);
return;
}
bool small_file = (sizeof(len) <= 4 or len < 0x7FFFFFFFULL);
if (small_file) {
uint8_t oldIntWidth = sa.width();
if (32 == fixedIntWidth or (0==fixedIntWidth and 32 >= oldIntWidth)) {
sa.width(32);
sa.resize(len);
divsufsort(c, (int32_t*)sa.m_data, len);
// copy integers back to the right positions
if (oldIntWidth!=32) {
for (size_type i=0; i<len; ++i) {
sa.set_int(i*oldIntWidth, sa.get_int(i<<5, 32), oldIntWidth);
}
sa.width(oldIntWidth);
sa.resize(len);
}
} else {
if (sa.width() < bits::hi(len)+1) {
throw std::logic_error("width of int_vector is to small for the text!!!");
}
int_vector<> sufarray(len,0,32);
divsufsort(c, (int32_t*)sufarray.m_data, len);
for (size_type i=0; i<len; ++i) {
sa[i] = sufarray[i];
}
}
} else {
uint8_t oldIntWidth = sa.width();
sa.width(64);
sa.resize(len);
divsufsort64(c, (int64_t*)sa.m_data, len);
// copy integers back to the right positions
if (oldIntWidth!=64) {
for (size_type i=0; i<len; ++i) {
sa.set_int(i*oldIntWidth, sa.get_int(i<<6, 64), oldIntWidth);
}
sa.width(oldIntWidth);
sa.resize(len);
}
}
}
void index_bidirectional_waveletindex<WaveletTree, SampleDens>::extract_sa(size_t occ_begin, size_t occ_end, int_vector<> &occ) {
occ.resize(occ_end-occ_begin);
for (size_t k=0; k<occ_end-occ_begin; k++) {
size_t i = occ_begin+k;
size_t off = 0;
while( (size()-1-i) % SampleDens != 0 ){// while SA[i] is not sampled
// go to the position where SA[i]-1 is located
// i := LF(i)
uint64_t bwt_result = backward_index.extract(i);
i = m_C[bwt_result] + backward_index.occ(bwt_result, i);
// add 1 to the offset
++off;
}
occ[k] = (m_sa_sample[i / SampleDens]+off) % size();
}
}
/*!
* Constructor for building the Index
* \param[in] str C-string of the text
*/
index_bidirectional_waveletindex(const unsigned char* str) : index() {
size_t n = strlen((const char*)str);
int_vector<> sa(n+1, 0, bit_magic::l1BP(n+1)+1);
setText(str, n+1);
unsigned char *bwt = new unsigned char[n+1];
algorithm::calculate_sa(str, n+1, sa); // calculate the suffix array sa of str
{ /* Calculate Burrows-Wheeler-Transform */
size_t i = 0;
for(int_vector<>::const_iterator it = sa.begin(), end = sa.end(); it != end; ++it, ++i){
bwt[i] = m_char2comp[str[(*it+n)%(n+1)]];
}
}
backward_index = WaveletTree(bwt, n+1, m_sigma);
/* Construct the SA-Samples */
m_sa_sample.setIntWidth( bit_magic::l1BP(sa.size())+1 );
m_sa_sample.resize( (sa.size()+SampleDens-1)/SampleDens );
size_t idx=0;
size_t i=(sa.size()-1-SampleDens*(m_sa_sample.size()-1));
for(int_vector<>::const_iterator it = sa.begin()+(ptrdiff_t)i; i < sa.size(); it += (ptrdiff_t)SampleDens, i += SampleDens, ++idx){
m_sa_sample[idx] = *it;
}
unsigned char* reverse = new unsigned char[n+1];
for (size_t i=0; i<n; i++) reverse[i] = str[n-1-i];
reverse[n] = '\0';
algorithm::calculate_sa(reverse, n+1, sa); // calculate the suffix array sa of reverse string str
{ /* Calculate Burrows-Wheeler-Transform */
size_t i = 0;
for(int_vector<>::const_iterator it = sa.begin(), end = sa.end(); it != end; ++it, ++i){
bwt[i] = m_char2comp[reverse[(*it+n)%(n+1)]];
}
}
forward_index = WaveletTree(bwt, n+1, m_sigma);
delete [] bwt;
delete [] reverse;
}
/*!
* Constructor for building the Index
* \param[in] str C-string of the text
*/
index_csa_psi_text(const unsigned char *str) : index() {
size_t n = strlen((const char*)str);
int_vector<> sa(n+1, 0, bit_magic::l1BP(n+1)+1);
algorithm::calculate_sa(str, n+1, sa); // calculate the suffix array sa of str
int_vector<> m_psi;
sdsl::algorithm::sa2psi(sa, m_psi);
psi = EncVector(m_psi);
setText(str, n+1);
text = int_vector<>(sa.size(), 0, bit_magic::l1BP(sigma)+1);
for (size_t i=0; i<sa.size(); i++) text[i] = char2comp[str[i]];
/* Construct the SA-Samples */
m_sa_sample.setIntWidth( bit_magic::l1BP(sa.size())+1 );
m_sa_sample.resize( (sa.size()+SampleDens-1)/SampleDens );
size_t i=0, idx=0;
for(int_vector<>::const_iterator it = sa.begin(); i < sa.size(); it += (ptrdiff_t)SampleDens, i += SampleDens, ++idx) {
m_sa_sample[idx] = *it;
}
}
void index_sa_text_occ<Occ>::extract_sa(size_t occ_begin, size_t occ_end, int_vector<> &occs) {
occs.resize(occ_end-occ_begin);
for (size_t k=0; k<occ_end-occ_begin; k++) occs[k] = sa[occ_begin+k];
}
void append_zero_symbol(int_vector& text)
{
text.resize(text.size()+1);
text[text.size()-1] = 0;
}
void index_csa_psi_text<EncVector, SampleDens>::extract_sa(size_t occ_begin, size_t occ_end, int_vector<> &occ) {
occ.resize(occ_end-occ_begin);
for (size_t k=0; k<occ_end-occ_begin; k++) occ[k] = getSAValue(occ_begin+k);
}
void index_sa_text_psi::extract_sa(size_t occ_begin, size_t occ_end, int_vector<> &occ) {
occ.resize(occ_end-occ_begin);
for (size_t k=0; k<occ_end-occ_begin; k++) occ[k] = sa[occ_begin+k];
}