/usr/include/sdsl/lcp_byte.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 | /* 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_byte.hpp
\brief lcp_byte.hpp contains a (compressed) lcp array.
\author Simon Gog
*/
#ifndef INCLUDED_SDSL_LCP_BYTE
#define INCLUDED_SDSL_LCP_BYTE
#include "lcp.hpp"
#include "int_vector.hpp"
#include "iterators.hpp"
#include <iostream>
#include <algorithm> // for lower_bound
#include <cassert>
#include <iomanip>
#include <iterator>
#include <vector>
#include <utility> // for pair
namespace sdsl
{
//! A class for a simple compressed version of LCP information
/*! Each small LCP value x=LCP[i] (\f$\leq 254\f$) is represented in a byte.
* For x=LCP[i] \f$\geq 255\f$ a pair (i, x) is store an list of word pairs.
* This list is binary search to access LCP[i].
* \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.
* \par Reference
* Mohamed Ibrahim Abouelhoda, Stefan Kurtz, Enno Ohlebusch:
* Replacing suffix trees with enhanced suffix arrays.
* J. Discrete Algorithms 2(1): 53-86 (2004)
*/
template<uint8_t t_width=0>
class lcp_byte
{
public:
typedef typename int_vector<t_width>::value_type value_type;
typedef random_access_const_iterator<lcp_byte> 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 lcp_plain_tag lcp_category;
enum { fast_access = 0,
text_order = 0,
sa_order = 1
}; // as the lcp_byte is not fast for texts with long repetition
template<class Cst>
using type = lcp_byte;
private:
int_vector<8> m_small_lcp; // vector for LCP values < 255
int_vector<t_width> m_big_lcp; // vector for LCP values > 254
int_vector<t_width> m_big_lcp_idx; // index of LCP entries in the LCP array
typedef std::pair<size_type, size_type> tPII;
typedef std::vector<tPII> tVPII;
public:
//! Default Constructor
lcp_byte() = default;
lcp_byte(const lcp_byte&) = default;
lcp_byte(lcp_byte&&) = default;
lcp_byte& operator=(const lcp_byte&) = default;
lcp_byte& operator=(lcp_byte&&) = default;
//! Constructor
lcp_byte(cache_config& config) {
std::string lcp_file = cache_file_name(conf::KEY_LCP, config);
int_vector_buffer<> lcp_buf(lcp_file);
m_small_lcp = int_vector<8>(lcp_buf.size());
size_type l=0, max_l=0, max_big_idx=0, big_sum=0;
for (size_type i=0; i < m_small_lcp.size(); ++i) {
if ((l=lcp_buf[i]) < 255) {
m_small_lcp[i] = l;
} else {
m_small_lcp[i] = 255;
if (l > max_l) max_l = l;
max_big_idx = i;
++big_sum;
}
}
m_big_lcp = int_vector<>(big_sum, 0, bits::hi(max_l)+1);
m_big_lcp_idx = int_vector<>(big_sum, 0, bits::hi(max_big_idx)+1);
for (size_type i=0,ii=0; i<m_small_lcp.size(); ++i) {
if ((l=lcp_buf[i]) >= 255) {
m_big_lcp[ii] = l;
m_big_lcp_idx[ii] = i;
++ii;
}
}
}
//! Number of elements in the instance.
size_type size()const {
return m_small_lcp.size();
}
//! Returns the largest size that lcp_byte can ever have.
static size_type max_size() {
return int_vector<8>::max_size();
}
//! Returns if the data strucutre is empty.
bool empty()const {
return m_small_lcp.empty();
}
//! Swap method for lcp_byte
void swap(lcp_byte& lcp_c) {
m_small_lcp.swap(lcp_c.m_small_lcp);
m_big_lcp.swap(lcp_c.m_big_lcp);
m_big_lcp_idx.swap(lcp_c.m_big_lcp_idx);
}
//! 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(1) for small and O(log n) for large values
*/
inline value_type operator[](size_type i)const {
if (m_small_lcp[i]!=255) {
return m_small_lcp[i];
} else {
size_type idx = lower_bound(m_big_lcp_idx.begin(),
m_big_lcp_idx.end(),i)
- m_big_lcp_idx.begin();
return m_big_lcp[idx];
}
}
//! 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");
written_bytes += m_big_lcp_idx.serialize(out, child, "large_lcp_idx");
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);
m_big_lcp_idx.load(in);
}
};
} // end namespace sdsl
#endif
|