File: suffix_tree_helper.hpp

package info (click to toggle)
libsdsl 2.0.3-4
  • links: PTS, VCS
  • area: main
  • in suites: stretch
  • size: 7,204 kB
  • ctags: 12,713
  • sloc: cpp: 64,225; python: 3,856; ansic: 3,651; makefile: 1,537; sh: 449
file content (288 lines) | stat: -rw-r--r-- 11,661 bytes parent folder | download | duplicates (2)
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
239
240
241
242
243
244
245
246
247
248
249
250
251
252
253
254
255
256
257
258
259
260
261
262
263
264
265
266
267
268
269
270
271
272
273
274
275
276
277
278
279
280
281
282
283
284
285
286
287
288
#ifndef INCLUDED_SDSL_SUFFIX_TREE_HELPER
#define INCLUDED_SDSL_SUFFIX_TREE_HELPER

#include <stdint.h>
#include <cstdlib>
#include <cassert>
#include <stack>
#include "sorted_multi_stack_support.hpp"
#include "sorted_stack_support.hpp"
#include "iterators.hpp"

namespace sdsl
{


template <class t_cst>
class cst_node_child_proxy_iterator : public std::iterator<std::forward_iterator_tag, typename t_cst::node_type>
{
    public:
        using node_type = typename t_cst::node_type;
        using value_type = node_type;
        using const_reference = const node_type;
        using iterator_type =  cst_node_child_proxy_iterator<t_cst>;
    private:
        const t_cst* m_cst;
        node_type m_cur_node;
    public:
        cst_node_child_proxy_iterator() : m_cst(nullptr) {};
        cst_node_child_proxy_iterator(const t_cst* cst,const node_type& v) : m_cst(cst) , m_cur_node(v) {}
        cst_node_child_proxy_iterator(const iterator_type& it): m_cst(it.m_cst), m_cur_node(it.m_cur_node) {}
    public:
        const_reference operator*() const {
            return m_cur_node;
        }
        iterator_type& operator++() {
            m_cur_node = m_cst->sibling(m_cur_node);
            return *this;
        }
        iterator_type& operator++(int) {
            iterator_type it = *this;
            ++(*this);
            return it;
        }
        bool operator==(const iterator_type& it)const {
            return it.m_cur_node == m_cur_node;
        }
        bool operator!=(const iterator_type& it)const {
            return !(*this==it);
        }
};

template <class t_cst>
class cst_node_child_proxy
{
    public: // types
        using iterator_type = cst_node_child_proxy_iterator<t_cst>;
        using node_type = typename t_cst::node_type;
        using size_type = typename t_cst::size_type;
    private: // data
        const node_type& m_parent;
        const t_cst* m_cst;
    public: // constructors
        cst_node_child_proxy() = delete;
        explicit cst_node_child_proxy(const t_cst* cst,const node_type& v) : m_parent(v) , m_cst(cst) {};
        cst_node_child_proxy(const cst_node_child_proxy& p) : m_parent(p.m_parent) , m_cst(p.m_cst) {};
    public: // methods
        node_type operator[](size_type i) const { return m_cst->select_child(m_parent,i+1); } // enumeration starts with 1 not 0
        size_type size() { return m_cst->degree(m_parent); }
        iterator_type begin() const { return iterator_type(m_cst,m_cst->select_child(m_parent,1)); }
        iterator_type end() const { return iterator_type(m_cst,m_cst->root()); }
};

//! Calculate the balanced parentheses of the Super-Cartesian tree, described in Ohlebusch and Gog (SPIRE 2009).
/*! \param vec Random access container for which the Super-Cartesian tree representation should be calculated.
 *             The value_type of vec should be an unsigned integer type.
 *  \param bp Reference to the balanced parentheses sequence which represents the Super-Cartesian tree.
 *  \param minimum Specifies if the higher levels contains minima or maxima. Default is maxima.
 *  \par Time complexity
 *       \f$ \Order{2n} \f$, where \f$ n=\f$vec.size()
 *  \par Space complexity
 *       \f$ \Order{n \cdot \log n } \f$ bits.
 */
template<class t_rac>
void construct_supercartesian_tree_bp(const t_rac& vec, bit_vector& bp, const bool minimum=true)
{
    typedef typename t_rac::size_type size_type;
    bp.resize(2*vec.size());      // resize bit vector for balanaced parantheses to 2 n bits
    util::set_to_value(bp, 0);
    std::stack<typename t_rac::value_type> vec_stack;

    size_type k=0;
    for (size_type i=0; i < vec.size(); ++i) {
        typename t_rac::value_type l = vec[i];
        if (minimum) {
            while (vec_stack.size() > 0 and l < vec_stack.top()) {
                vec_stack.pop(); ++k; /*bp[k++] = 0; bp is already initialized to zero*/ // writing a closing parenthesis
            }

        } else {
            while (vec_stack.size() > 0 and l > vec_stack.top()) {
                vec_stack.pop(); ++k; /*bp[k++] = 0; bp is already initialized to zero*/ // writing a closing parenthesis
            }
        }
        vec_stack.push(l);
        bp[k++] = 1; // writing an opening  parenthesis
    }
    while (vec_stack.size() > 0) {
        vec_stack.pop();
        bp[k++] = 0; // writing a closing parenthesis
    }
    assert(k == 2*vec.size());
}

//! Calculate the balanced parentheses of the Super-Cartesian tree, described in Ohlebusch and Gog (SPIRE 2009).
/*! \param vec Random access container for which the Super-Cartesian tree representation should be calculated.
 *             The value_type of vec should be an unsigned integer type.
 *  \param minimum Specifies if the higher levels contains minima or maxima. Default is maxima.
 *  \return The balanced parentheses sequence representing the Super-Cartesian tree.
 *  \par Time complexity
 *       \f$ \Order{2n} \f$, where \f$ n=\f$vec.size()
 *  \par Space complexity
 *       \f$\Order{n}\f$ bits
 */
template<class t_rac>
bit_vector
construct_supercartesian_tree_bp_succinct(const t_rac& vec, const bool minimum=true)
{
    typedef typename t_rac::size_type size_type;
    bit_vector bp(2*vec.size(), 0); // initialize result
    if (vec.size() > 0) {
        sorted_stack_support vec_stack(vec.size());

        size_type k=0;
        if (minimum) {
            bp[k++] = 1;
            for (size_type i=1; i < vec.size(); ++i) {
                if (vec[i] < vec[i-1]) {
                    ++k;
                    while (vec_stack.size() > 0 and vec[i] < vec[vec_stack.top()]) {
                        vec_stack.pop(); ++k; // writing a closing parenthesis, bp is already initialized to zero
                    }
                } else {
                    vec_stack.push(i-1); // "lazy stack" trick: speed-up approx. 25%
                }
                bp[k++] = 1; // writing an opening  parenthesis
            }
        } else {
            // no "lazy stack" trick used here
            for (size_type i=0; i < vec.size(); ++i) {
                while (vec_stack.size() > 0 and vec[i] > vec[vec_stack.top()]) {
                    vec_stack.pop(); ++k; /*bp[k++] = 0; bp is already initialized to zero*/ // writing a closing parenthesis
                }
                vec_stack.push(i);
                bp[k++] = 1; // writing an opening  parenthesis
            }
        }
    }
    return bp;
}

//! Calculate the balanced parentheses of the Super-Cartesian tree, described in Ohlebusch and Gog (SPIRE 2009).
/*! \param lcp_buf int_vector_buffer of the LCP Array for which the Super-Cartesian tree representation should be calculated.
 *             The value_type of vec should be an unsigned integer type.
 *  \param minimum Specifies if the higher levels contains minima or maxima. Default is maxima.
 *  \return The balanced parentheses sequence representing the Super-Cartesian tree.
 *  \par Time complexity
 *       \f$ \Order{2n} \f$, where \f$ n=\f$vec.size()
 *  \par Space complexity
 *       \f$\Order{2n}\f$ bits, by the multi_stack_support
 *  \pre
 *  The largest value in lcp_buf has to be smaller than lcp_buf.size().
 */
template<uint8_t t_width>
bit_vector
construct_supercartesian_tree_bp_succinct(int_vector_buffer<t_width>& lcp_buf, const bool minimum=true)
{
    typedef bit_vector::size_type size_type;
    bit_vector bp(2*lcp_buf.size(), 0); // initialize result
    if (lcp_buf.size() > 0)	{
        sorted_multi_stack_support vec_stack(lcp_buf.size());

        size_type k=0;
        if (minimum) {
            bp[k++] = 1;
            size_type last = lcp_buf[0];
            for (size_type i=1, x; i < lcp_buf.size(); ++i) {
                x = lcp_buf[i];
                if (x < last) {
                    ++k; // writing a closing parenthesis for last
                    while (!vec_stack.empty() and x < vec_stack.top()) {
                        vec_stack.pop(); ++k; // writing a closing parenthesis, bp is already initialized to zeros
                    }
                } else {
                    vec_stack.push(last); // "lazy stack" trick: speed-up about 25 %
                }
                bp[k++] = 1; // writing an opening parenthesis
                last = x;
            }
        } else {
            // no "lazy stack" trick use here
            for (size_type i=0, x; i < lcp_buf.size(); ++i) {
                x = lcp_buf[i];
                while (!vec_stack.empty() and x > vec_stack.top()) {
                    vec_stack.pop(); ++k; // writing a closing parenthesis, bp is already initialized to zeros
                }
                vec_stack.push(x);
                bp[k++] = 1; // writing an opening parenthesis
            }
        }
    }
    return bp;
}

//! Calculate the balanced parentheses of the Super-Cartesian tree, described in Ohlebusch and Gog (SPIRE 2009) and the first_child bit_vector
/*! \param lcp_buf int_vector_buffer for the lcp array for which the Super-Cartesian tree representation should be calculated.
 *             The value_type of vec should be an unsigned integer type.
 *  \param bp Reference to the balanced parentheses sequence which represents the Super-Cartesian tree.
 *  \param bp_fc Reference to the first child bit_vector of bp.
 *  \param minimum Specifies if the higher levels contains minima or maxima. Default is maxima.
 *  \par Time complexity
 *       \f$ \Order{2n} \f$, where \f$ n=\f$vec.size()
 *  \par Space complexity
 *       \f$\Order{2n}\f$ bits, by the multi_stack_support
 */
template<uint8_t t_width>
bit_vector::size_type
construct_supercartesian_tree_bp_succinct_and_first_child(int_vector_buffer<t_width>& lcp_buf, bit_vector& bp, bit_vector& bp_fc, const bool minimum=true)
{
    typedef bit_vector::size_type size_type;
    size_type n = lcp_buf.size();
    bp.resize(2*n);      // resize bit vector for balanced parentheses to 2 n bits
    bp_fc.resize(n);
    if (n == 0)	// if n == 0 we are done
        return 0;
    size_type fc_cnt=0; // first child counter
    util::set_to_value(bp, 0);
    util::set_to_value(bp_fc, 0);
    sorted_multi_stack_support vec_stack(n);

    size_type k=0;
    size_type k_fc=0; // first child index
    if (minimum) {
        // no "lazy stack" trick used here
        for (size_type i=0, x; i < n; ++i) {
            x = lcp_buf[i];
            while (!vec_stack.empty() and x < vec_stack.top()) {
                if (vec_stack.pop()) {
                    bp_fc[k_fc] = 1;
                    ++fc_cnt;
                }
                ++k; // writing a closing parenthesis, bp is already initialized to zeros
                ++k_fc; // write a bit in first_child
            }
            vec_stack.push(x);
            bp[k++] = 1; // writing an opening parenthesis
        }

    } else {
        // no "lazy stack" trick used here
        for (size_type i=0, x; i < n; ++i) {
            x = lcp_buf[i];
            while (!vec_stack.empty() and x > vec_stack.top()) {
                if (vec_stack.pop()) {
                    bp_fc[k_fc] = 1;
                    ++fc_cnt;
                }
                ++k; // writing a closing parenthesis, bp is already initialized to zeros
                ++k_fc; // write a bit in first_child
            }
            vec_stack.push(x);
            bp[k++] = 1; // writing an opening parenthesis
        }
    }
    while (!vec_stack.empty()) {
        if (vec_stack.pop()) {
            bp_fc[k_fc] = 1;
            ++fc_cnt;
        }
        // writing a closing parenthesis in bp, not necessary as bp is initialized with zeros
        ++k;
        ++k_fc;
    }
    return fc_cnt;
}

}

#endif