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);
}
}
