/usr/include/sdsl/lcp_support_sada.hpp is in libsdsl-dev 2.0.3-4.
This file is owned by root:root, with mode 0o644.
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1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60 61 62 63 64 65 66 67 68 69 70 71 72 73 74 75 76 77 78 79 80 81 82 83 84 85 86 87 88 89 90 91 92 93 94 95 96 97 98 99 100 101 102 103 104 105 106 107 108 109 110 111 112 113 114 115 116 117 118 119 120 121 122 123 124 125 126 127 128 129 130 131 132 133 134 135 136 137 138 139 140 141 142 143 144 145 146 147 148 149 150 151 152 153 154 155 156 157 158 159 160 161 162 163 164 165 166 167 168 169 170 171 172 173 174 175 176 177 178 179 180 181 182 183 184 185 186 187 188 189 190 191 192 193 194 195 196 197 198 199 200 201 202 203 204 205 206 207 208 209 210 211 212 213 214 215 216 217 218 219 220 221 222 223 224 225 226 227 228 229 230 231 232 233 234 235 236 237 238 | /* sdsl - succinct data structures library
Copyright (C) 2009-2013 Simon Gog
This program is free software: you can redistribute it and/or modify
it under the terms of the GNU General Public License as published by
the Free Software Foundation, either version 3 of the License, or
(at your option) any later version.
This program is distributed in the hope that it will be useful,
but WITHOUT ANY WARRANTY; without even the implied warranty of
MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
GNU General Public License for more details.
You should have received a copy of the GNU General Public License
along with this program. If not, see http://www.gnu.org/licenses/ .
*/
/*! \file lcp_support_sada.hpp
\brief lcp_support_sada.hpp contains a compressed lcp array.
\author Simon Gog
*/
#ifndef INCLUDED_SDSL_LCP_SUPPORT_SADA
#define INCLUDED_SDSL_LCP_SUPPORT_SADA
#include "lcp.hpp"
#include "int_vector.hpp"
#include "iterators.hpp"
#include "csa_sada.hpp" // for default template initialization
#include "select_support.hpp" // for default template initialization
#include <cassert>
namespace sdsl
{
//! A class to represent the LCP array in compressed form.
/*!
* \tparam t_csa Type of the Underlying CSA.
* \tparam t_bitvec Type of the bitvector used to store the unary
* representation of the deltas of the permuted LCP array.
* \tparam t_select Type of the select structure use to select on the
* bitvector of the unary representation of the PLCP array.
*
* \par Space complexity
* \f$ 2n+o(n) \f$ bits, where 2n is the worst case size of the
* unary encoding of the deltas of the PLCP array and o(n) for
* the select support data structure.
* \par Reference
* Kunihiko Sadakane:
* Succinct representations of lcp information and improvements in the
* compressed suffix arrays.
* SODA 2002: 225-232
*/
template<class t_csa = csa_sada<>,
class t_bitvec = bit_vector,
class t_select = typename t_bitvec::select_1_type>
class _lcp_support_sada
{
public:
typedef typename t_csa::value_type value_type;
typedef random_access_const_iterator<
_lcp_support_sada> const_iterator;
typedef const_iterator iterator;
typedef const value_type const_reference;
typedef const_reference reference;
typedef const_reference* pointer;
typedef const pointer const_pointer;
typedef int_vector<>::size_type size_type;
typedef ptrdiff_t difference_type;
typedef t_bitvec bit_vector_type;
typedef t_csa csa_type;
typedef t_select select_type;
typedef lcp_permuted_tag lcp_category;
enum { fast_access = 0,
text_order = 1,
sa_order = 0
};
// inner class which is used in CSTs to parametrize lcp classes
// with information about the CST.
template<class Cst>
struct type {
typedef _lcp_support_sada lcp_type;
};
private:
const csa_type* m_csa;
bit_vector_type m_data;
select_type m_select_support;
void copy(const _lcp_support_sada& lcp_c) {
m_csa = lcp_c.m_csa;
m_data = lcp_c.m_data;
m_select_support = lcp_c.m_select_support;
m_select_support.set_vector(&m_data);
}
public:
const t_csa*& csa = m_csa;
//! Default Constructor
_lcp_support_sada() {}
//! Copy constructor
_lcp_support_sada(const _lcp_support_sada& lcp_c) {
copy(lcp_c);
}
//! Move constructor
_lcp_support_sada(_lcp_support_sada&& lcp_c) {
*this = std::move(lcp_c);
}
//! Constructor
_lcp_support_sada(cache_config& config, const t_csa* f_csa) {
typedef typename t_csa::size_type size_type;
set_csa(f_csa);
if (!cache_file_exists(conf::KEY_ISA, config)) {
construct_isa(config);
}
int_vector<> lcp;
load_from_file(lcp, cache_file_name(conf::KEY_LCP, config));
std::string isa_file = cache_file_name(conf::KEY_ISA, config);
int_vector_buffer<> isa_buf(isa_file);
size_type n = lcp.size();
bit_vector data = bit_vector(2*n, 0);
size_type data_cnt=0;
for (size_type i=0, l=0, old_l=1; i < n; ++i) {
l = lcp[isa_buf[i]];
data_cnt += l + 1 - old_l;
data[data_cnt++] = 1;
old_l = l;
}
data.resize(data_cnt);
m_data = bit_vector_type(data);
util::init_support(m_select_support, &m_data);
}
void set_csa(const t_csa* f_csa) {
m_csa = f_csa;
}
//! Number of elements in the instance.
size_type size()const {
return m_csa->size();
}
//! Returns the largest size that _lcp_support_sada can ever have.
static size_type max_size() {
return t_csa::max_size();
}
//! Returns if the data structure is empty.
bool empty()const {
return m_csa->empty();
}
//! Swap method for _lcp_support_sada
void swap(_lcp_support_sada& lcp_c) {
m_data.swap(lcp_c.m_data);
util::swap_support(m_select_support, lcp_c.m_select_support,
&m_data, &(lcp_c.m_data));
}
//! Returns a const_iterator to the first element.
const_iterator begin()const {
return const_iterator(this, 0);
}
//! Returns a const_iterator to the element after the last element.
const_iterator end()const {
return const_iterator(this, size());
}
//! []-operator
/*! \param i Index of the value. \f$ i \in [0..size()-1]\f$.
* Time complexity: O(suffix array access)
*/
inline value_type operator[](size_type i)const {
size_type j = (*m_csa)[i];
size_type s = m_select_support.select(j+1);
return s-(j<<1);
}
//! Assignment Operator.
_lcp_support_sada& operator=(const _lcp_support_sada& lcp_c) {
if (this != &lcp_c) {
copy(lcp_c);
}
return *this;
}
//! Assignment Move Operator.
_lcp_support_sada& operator=(_lcp_support_sada&& lcp_c) {
if (this != &lcp_c) {
m_csa = std::move(lcp_c.m_csa);
m_data = std::move(lcp_c.m_data);
m_select_support = std::move(lcp_c.m_select_support);
m_select_support.set_vector(&m_data);
}
return *this;
}
//! Serialize to a stream.
size_type
serialize(std::ostream& out, structure_tree_node* v=nullptr,
std::string name="")const {
structure_tree_node* child = structure_tree::add_child(v, name,
util::class_name(*this));
size_type written_bytes = 0;
written_bytes += m_data.serialize(out, child, "data");
written_bytes += m_select_support.serialize(out, child,
"select_support");
structure_tree::add_size(child, written_bytes);
return written_bytes;
}
//! Load from a stream.
void load(std::istream& in, const t_csa* csa) {
m_csa = csa;
m_data.load(in);
m_select_support.load(in, &m_data);
}
};
//! Helper class which provides _lcp_support_sada the context of a CSA.
template<class t_bitvec = bit_vector,
class t_select = typename t_bitvec::select_1_type>
struct lcp_support_sada
{
template<class t_cst>
using type = _lcp_support_sada<typename t_cst::csa_type,
t_bitvec,
t_select>;
};
} // end namespace sdsl
#endif
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