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#include "base/bwt.hpp"
#include "base/assert.hpp"
#include "base/suffix_array.hpp"
#include <algorithm>
#include <array>
#include <limits>
#include <vector>
using namespace std;
namespace
{
size_t const kNumBytes = 256;
// Fake trailing '$' for the BWT, used for original string
// reconstruction.
uint32_t const kEOS = 256;
// FirstColumn represents the first column in the BWT matrix. As
// during reverse BWT we need to reconstruct canonical first column,
// with '$' as the first element, this wrapper is used. Also note that
// other characters in the first column are sorted, so we actually
// don't need to store them explicitly, it's enough to store start
// positions of the corresponding groups of consecutive characters.
class FirstColumn
{
public:
FirstColumn(size_t n, uint8_t const * s) : m_n(n), m_starts({})
{
m_starts.fill(0);
for (size_t i = 0; i < n; ++i)
++m_starts[s[i]];
size_t offset = 0;
for (size_t i = 0; i < m_starts.size(); ++i)
{
auto const count = m_starts[i];
m_starts[i] = offset;
offset += count;
}
}
size_t Size() const { return m_n + 1; }
uint32_t operator[](size_t i) const
{
ASSERT_LESS(i, Size(), ());
if (i == 0)
return kEOS;
--i;
auto it = upper_bound(m_starts.begin(), m_starts.end(), i);
ASSERT(it != m_starts.begin(), ());
--it;
return static_cast<uint32_t>(distance(m_starts.begin(), it));
}
// Returns the rank of the i-th symbol among symbols with the same
// value.
size_t Rank(size_t i) const
{
ASSERT_LESS(i, Size(), ());
if (i == 0)
return 0;
--i;
auto it = upper_bound(m_starts.begin(), m_starts.end(), i);
if (it == m_starts.begin())
return i;
--it;
return i - *it;
}
private:
size_t const m_n;
array<size_t, kNumBytes> m_starts;
};
// LastColumn represents the last column in the BWT matrix. As during
// reverse BWT we need to reconstruct canonical last column, |s| is
// replaced by s[start] + s[0, start) + '$' + s[start, n).
class LastColumn
{
public:
LastColumn(size_t n, size_t start, uint8_t const * s) : m_n(n), m_start(start), m_s(s)
{
for (size_t i = 0; i < Size(); ++i)
{
auto const b = (*this)[i];
if (b == kEOS)
continue;
ASSERT_LESS(b, kNumBytes, ());
m_table[b].push_back(i);
}
}
size_t Size() const { return m_n + 1; }
uint32_t operator[](size_t i) const
{
if (i == 0)
{
ASSERT_LESS(m_start, m_n, ());
return m_s[m_start];
}
if (i == m_start + 1)
return kEOS;
ASSERT_LESS_OR_EQUAL(i, m_n, ());
return m_s[i - 1];
}
// Returns the index of the |rank|-th |byte| in the canonical BWT
// last column.
size_t Select(uint32_t byte, size_t rank)
{
if (byte == kEOS)
{
ASSERT_EQUAL(rank, 0, ());
return 0;
}
ASSERT_LESS(rank, m_table[byte].size(), (byte, rank));
return m_table[byte][rank];
}
private:
size_t const m_n;
size_t const m_start;
uint8_t const * const m_s;
array<vector<size_t>, kNumBytes> m_table;
};
} // namespace
namespace base
{
size_t BWT(size_t n, uint8_t const * s, uint8_t * r)
{
vector<size_t> sa(n);
Skew(n, s, sa.data());
size_t result = 0;
for (size_t i = 0; i < n; ++i)
{
if (sa[i] != 0)
{
r[i] = s[sa[i] - 1];
}
else
{
result = i;
r[i] = s[n - 1];
}
}
return result;
}
size_t BWT(string const & s, string & r)
{
auto const n = s.size();
r.assign(n, '\0');
return BWT(n, reinterpret_cast<uint8_t const *>(s.data()), reinterpret_cast<uint8_t *>(&r[0]));
}
void RevBWT(size_t n, size_t start, uint8_t const * s, uint8_t * r)
{
if (n == 0)
return;
FirstColumn first(n, s);
LastColumn last(n, start, s);
auto curr = start + 1;
for (size_t i = 0; i < n; ++i)
{
ASSERT_LESS(curr, first.Size(), ());
ASSERT(first[curr] != kEOS, ());
r[i] = first[curr];
curr = last.Select(r[i], first.Rank(curr));
}
ASSERT_EQUAL(first[curr], kEOS, ());
}
void RevBWT(size_t start, string const & s, string & r)
{
auto const n = s.size();
r.assign(n, '\0');
RevBWT(n, start, reinterpret_cast<uint8_t const *>(s.data()), reinterpret_cast<uint8_t *>(&r[0]));
}
} // namespace base
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