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/* Copyright 2016 Google Inc. All Rights Reserved.
Author: zip753@gmail.com (Ivan Nikulin)
Distributed under MIT license.
See file LICENSE for detail or copy at https://opensource.org/licenses/MIT
*/
/* Tool for generating optimal backward references for the input file. Uses
sais-lite library for building suffix array. */
#include <algorithm>
#include <cassert>
#include <cstdio>
#include <cstring>
#include <functional>
#include <utility>
#include <vector>
#include <gflags/gflags.h>
using gflags::ParseCommandLineFlags;
#include "third_party/absl/flags/flag.h"
#include "third_party/esaxx/sais.hxx"
DEFINE_bool(advanced, false, "Advanced searching mode: finds all longest "
"matches at positions that are not covered by matches of length at least "
"max_length. WARNING: uses much more memory than simple mode, especially "
"for small values of min_length.");
DEFINE_int32(min_length, 1, "Minimal length of found backward references.");
/* For advanced mode. */
DEFINE_int32(long_length, 32,
"Maximal length of found backward references for advanced mode.");
DEFINE_int32(skip, 1, "Number of bytes to skip.");
const size_t kFileBufferSize = (1 << 16); // 64KB
typedef int sarray_type; // Can't make it unsigned because of templates :(
typedef uint8_t input_type;
typedef uint32_t lcp_type;
typedef std::pair<int, std::vector<int> > entry_type;
typedef std::function<void(sarray_type*, lcp_type*, size_t, int, int, int, int,
int)> Fn;
void ReadInput(FILE* fin, input_type* storage, size_t input_size) {
size_t last_pos = 0;
size_t available_in;
fseek(fin, 0, SEEK_SET);
do {
available_in = fread(storage + last_pos, 1, kFileBufferSize, fin);
last_pos += available_in;
} while (available_in != 0);
assert(last_pos == input_size);
}
void BuildLCP(input_type* storage, sarray_type* sarray, lcp_type* lcp,
size_t size, uint32_t* pos) {
for (int i = 0; i < size; ++i) {
pos[sarray[i]] = i;
}
uint32_t k = 0;
lcp[size - 1] = 0;
for (int i = 0; i < size; ++i) {
if (pos[i] == size - 1) {
k = 0;
continue;
}
uint32_t j = sarray[pos[i] + 1]; // Suffix which follow i-th suffix in SA.
while (i + k < size && j + k < size && storage[i + k] == storage[j + k]) {
++k;
}
lcp[pos[i]] = k;
if (k > 0) --k;
}
}
inline void PrintReference(sarray_type* sarray, lcp_type* lcp, size_t size,
int idx, int left_ix, int right_ix, int left_lcp,
int right_lcp, FILE* fout) {
int max_lcp_ix;
if (right_ix == size - 1 || (left_ix >= 0 && left_lcp >= right_lcp)) {
max_lcp_ix = left_ix;
} else {
max_lcp_ix = right_ix;
}
int dist = idx - sarray[max_lcp_ix];
assert(dist > 0);
fputc(1, fout);
fwrite(&idx, sizeof(int), 1, fout); // Position in input.
fwrite(&dist, sizeof(int), 1, fout); // Backward distance.
}
inline void GoLeft(sarray_type* sarray, lcp_type* lcp, int idx, int left_ix,
int left_lcp, entry_type* entry) {
entry->first = left_lcp;
if (left_lcp > absl::GetFlag(FLAGS_long_length)) return;
for (; left_ix >= 0; --left_ix) {
if (lcp[left_ix] < left_lcp) break;
if (sarray[left_ix] < idx) {
entry->second.push_back(idx - sarray[left_ix]);
}
}
}
inline void GoRight(sarray_type* sarray, lcp_type* lcp, int idx, size_t size,
int right_ix, int right_lcp, entry_type* entry) {
entry->first = right_lcp;
if (right_lcp > absl::GetFlag(FLAGS_long_length)) return;
for (; right_ix < size - 1; ++right_ix) {
if (lcp[right_ix] < right_lcp) break;
if (sarray[right_ix] < idx) {
entry->second.push_back(idx - sarray[right_ix]);
}
}
}
inline void StoreReference(sarray_type* sarray, lcp_type* lcp, size_t size,
int idx, int left_ix, int right_ix, int left_lcp,
int right_lcp, entry_type* entries) {
if (right_ix == size - 1 || (left_ix >= 0 && left_lcp > right_lcp)) {
// right is invalid or left is better
GoLeft(sarray, lcp, idx, left_ix, left_lcp, &entries[idx]);
} else if (left_ix < 0 || (right_ix < size - 1 && right_lcp > left_lcp)) {
// left is invalid or right is better
GoRight(sarray, lcp, idx, size, right_ix, right_lcp, &entries[idx]);
} else { // both are valid and of equal length
GoLeft(sarray, lcp, idx, left_ix, left_lcp, &entries[idx]);
GoRight(sarray, lcp, idx, size, right_ix, right_lcp, &entries[idx]);
}
}
void ProcessReferences(sarray_type* sarray, lcp_type* lcp, size_t size,
uint32_t* pos, const Fn& process_output) {
int min_length = absl::GetFlag(FLAGS_min_length);
for (int idx = absl::GetFlag(FLAGS_skip); idx < size; ++idx) {
int left_lcp = -1;
int left_ix;
for (left_ix = pos[idx] - 1; left_ix >= 0; --left_ix) {
if (left_lcp == -1 || left_lcp > lcp[left_ix]) {
left_lcp = lcp[left_ix];
}
if (left_lcp == 0) break;
if (sarray[left_ix] < idx) break;
}
int right_lcp = -1;
int right_ix;
for (right_ix = pos[idx]; right_ix < size - 1; ++right_ix) {
if (right_lcp == -1 || right_lcp > lcp[right_ix]) {
right_lcp = lcp[right_ix];
}
// Stop if we have better result from the left side already.
if (right_lcp < left_lcp && left_ix >= 0) break;
if (right_lcp == 0) break;
if (sarray[right_ix] < idx) break;
}
if ((left_ix >= 0 && left_lcp >= min_length) ||
(right_ix < size - 1 && right_lcp >= min_length)) {
process_output(sarray, lcp, size, idx, left_ix, right_ix, left_lcp,
right_lcp);
}
}
}
void ProcessEntries(entry_type* entries, size_t size, FILE* fout) {
int long_length = absl::GetFlag(FLAGS_long_length);
std::vector<std::pair<int, int> > segments;
size_t idx;
for (idx = 0; idx < size;) {
entry_type& entry = entries[idx];
if (entry.first > long_length) {
// Add segment.
if (segments.empty() || segments.back().second < idx) {
segments.push_back({idx, idx + entry.first});
} else {
segments.back().second = idx + entry.first;
}
}
++idx;
}
printf("Segments generated.\n");
size_t segments_ix = 0;
for (idx = 0; idx < size;) {
if (idx == segments[segments_ix].first) {
// Skip segment.
idx = segments[segments_ix].second;
} else {
for (auto& dist : entries[idx].second) {
fputc(1, fout);
fwrite(&idx, sizeof(int), 1, fout); // Position in input.
fwrite(&dist, sizeof(int), 1, fout); // Backward distance.
}
++idx;
}
}
}
int main(int argc, char* argv[]) {
base::ParseCommandLine(&argc, &argv);
if (argc != 3) {
printf("usage: %s input_file output_file\n", argv[0]);
return 1;
}
FILE* fin = fopen(argv[1], "rb");
FILE* fout = fopen(argv[2], "w");
fseek(fin, 0, SEEK_END);
int input_size = ftell(fin);
fseek(fin, 0, SEEK_SET);
printf("The file size is %u bytes\n", input_size);
input_type* storage = new input_type[input_size];
ReadInput(fin, storage, input_size);
fclose(fin);
sarray_type* sarray = new sarray_type[input_size];
saisxx(storage, sarray, input_size);
printf("Suffix array calculated.\n");
// Inverse suffix array.
uint32_t* pos = new uint32_t[input_size];
lcp_type* lcp = new lcp_type[input_size];
BuildLCP(storage, sarray, lcp, input_size, pos);
printf("LCP array constructed.\n");
delete[] storage;
using std::placeholders::_1;
using std::placeholders::_2;
using std::placeholders::_3;
using std::placeholders::_4;
using std::placeholders::_5;
using std::placeholders::_6;
using std::placeholders::_7;
using std::placeholders::_8;
entry_type* entries;
if (absl::GetFlag(FLAGS_advanced)) {
entries = new entry_type[input_size];
for (size_t i = 0; i < input_size; ++i) entries[i].first = -1;
}
Fn print = std::bind(PrintReference, _1, _2, _3, _4, _5, _6, _7, _8, fout);
Fn store = std::bind(StoreReference, _1, _2, _3, _4, _5, _6, _7, _8, entries);
ProcessReferences(sarray, lcp, input_size, pos,
absl::GetFlag(FLAGS_advanced) ? store : print);
printf("References processed.\n");
if (absl::GetFlag(FLAGS_advanced)) {
int good_cnt = 0;
uint64_t avg_cnt = 0;
for (size_t i = 0; i < input_size; ++i) {
if (entries[i].first != -1) {
++good_cnt;
avg_cnt += entries[i].second.size();
}
}
printf("Number of covered positions = %d\n", good_cnt);
printf("Average number of references per covered position = %.4lf\n",
static_cast<double>(avg_cnt) / good_cnt);
ProcessEntries(entries, input_size, fout);
printf("Entries processed.\n");
}
fclose(fout);
return 0;
}