/usr/include/sdsl/lcp_wt.hpp is in libsdsl-dev 2.0.3-4.
This file is owned by root:root, with mode 0o644.
The actual contents of the file can be viewed below.
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 | /* sdsl - succinct data structures library
Copyright (C) 2010-2013 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_wt.hpp
\brief lcp_wt.hpp contains a (compressed) LCP array based on a WT.
\author Simon Gog
*/
#ifndef INCLUDED_SDSL_LCP_WT
#define INCLUDED_SDSL_LCP_WT
#include "lcp.hpp"
#include "wt_huff.hpp"
#include "int_vector.hpp"
#include "iterators.hpp"
#include "util.hpp"
#include <iostream>
#include <algorithm> // for lower_bound
#include <cassert>
#include <cstring> // for strlen
#include <iomanip>
#include <iterator>
#include <vector>
#include <utility> // for pair
#include <stdexcept>
namespace sdsl
{
//! A class for the compressed version of lcp information of an suffix array
/*! We use \f$H_0\f$ bit for each lcp values < 255 and \f$ log n \f$ bits for
* each LCP value which is greater than 254.
* \tparam t_width Width of int_vector storing the large LCP values.
* \par Time complexity
* - \f$\Order{1}\f$ if the value is less than 255 and
* - \f$\Order{\log n}\f$ (\f$n=size()\f$) otherwise.
*/
template<uint8_t t_width=0>
class lcp_wt
{
public:
typedef typename int_vector<t_width>::value_type value_type;
typedef random_access_const_iterator<lcp_wt> 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 wt_huff<bit_vector, rank_support_v<>,
select_support_scan<1>,
select_support_scan<0>> small_lcp_type;
typedef lcp_plain_tag lcp_category;
enum { fast_access = 0,
text_order = 0,
sa_order = 1
}; // as the lcp_wt is not fast for texts with long repetition
template<class Cst>
using type = lcp_wt;
private:
small_lcp_type m_small_lcp; // vector for lcp values < 255
int_vector<t_width> m_big_lcp; // vector for lcp values > 254
typedef std::pair<size_type, size_type> tPII;
typedef std::vector<tPII> tVPII;
public:
//! Default Constructor
lcp_wt() = default;
//! Copy / Move constructor
lcp_wt(const lcp_wt&) = default;
lcp_wt(lcp_wt&&) = default;
lcp_wt& operator=(const lcp_wt&) = default;
lcp_wt& operator=(lcp_wt&&) = default;
//! 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];
}
}
}
}
//! Number of elements in the instance.
size_type size()const {
return m_small_lcp.size();
}
//! Returns the largest size that lcp_wt can ever have.
static size_type max_size() {
return int_vector<8>::max_size();
}
//! Returns if the data structure is empty.
bool empty()const {
return 0==m_small_lcp.size();
}
//! Swap method for lcp_wt
void swap(lcp_wt& lcp_c) {
m_small_lcp.swap(lcp_c.m_small_lcp);
m_big_lcp.swap(lcp_c.m_big_lcp);
}
//! 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$.
*/
inline value_type operator[](size_type i)const {
if (m_small_lcp[i]!=255) {
return m_small_lcp[i];
} else {
return m_big_lcp[ m_small_lcp.rank(i, 255) ];
}
}
//! 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_small_lcp.serialize(out, child, "small_lcp");
written_bytes += m_big_lcp.serialize(out, child, "large_lcp");
structure_tree::add_size(child, written_bytes);
return written_bytes;
}
//! Load from a stream.
void load(std::istream& in) {
m_small_lcp.load(in);
m_big_lcp.load(in);
}
};
} // end namespace sdsl
#endif
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