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Review fixes.

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This commit is contained in:
Yuri Gorshenin 2017-06-28 13:48:35 +03:00
parent af06dc12ba
commit f08954d648
2 changed files with 60 additions and 56 deletions
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2
base/base_tests/suffix_array_tests.cpp
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@ -60,6 +60,8 @@ UNIT_TEST(Skew_Classic)
{
char const * s = "mississippi";
size_t const n = strlen(s);
TEST_EQUAL(n, 11, ());
vector<size_t> pos(n);
Skew(n, reinterpret_cast<const uint8_t *>(s), pos.data());

114
base/suffix_array.cpp
View file

@ -22,30 +22,36 @@ bool LEQ(size_t a1, size_t a2, size_t a3, size_t b1, size_t b2, size_t b3)
return LEQ(a2, a3, b2, b3);
}
// Actually this is a counting sort, but the name RadixSort is used
// here to keep the correspondence with the article about Skew|DC3.
template <typename Values>
void RadixSort(size_t n, size_t const * keys, size_t maxValue, Values const & values,
void RadixSort(size_t numKeys, size_t const * keys, size_t numValues, Values const & values,
size_t * resultKeys)
{
std::vector<size_t> count(maxValue);
for (size_t i = 0; i < n; ++i)
vector<size_t> count(numValues, 0);
for (size_t i = 0; i < numKeys; ++i)
{
auto const value = values[keys[i]];
ASSERT_LESS(value, count.size(), ());
++count[values[keys[i]]];
for (size_t i = 1; i < maxValue; ++i)
}
for (size_t i = 1; i < numValues; ++i)
count[i] += count[i - 1];
for (size_t i = n - 1; i < n; --i)
for (size_t i = numKeys - 1; i < numKeys; --i)
resultKeys[--count[values[keys[i]]]] = keys[i];
}
bool InLeftHalf(size_t n0, size_t pos) { return pos < n0; }
bool InLeftHalf(size_t middle, size_t pos) { return pos < middle; }
size_t RestoreIndex(size_t n0, size_t pos)
size_t RestoreIndex(size_t middle, size_t pos)
{
return InLeftHalf(n0, pos) ? pos * 3 + 1 : (pos - n0) * 3 + 2;
return InLeftHalf(middle, pos) ? pos * 3 + 1 : (pos - middle) * 3 + 2;
}
struct SkewWrapper
{
SkewWrapper(size_t n, uint8_t const * s) : m_n(n), m_s(s) {}
size_t size() const { return m_n; }
size_t operator[](size_t i) const
{
if (i < m_n)
@ -61,17 +67,18 @@ struct SkewWrapper
template <typename Container>
struct Slice
{
Slice(Container const & c, size_t n, size_t offset) : m_c(c), m_n(n), m_offset(offset) {}
Slice(Container const & c, size_t offset) : m_c(c), m_offset(offset) {}
size_t operator[](size_t i) const { return m_c[i + m_offset]; }
const Container & m_c;
const size_t m_n;
const size_t m_offset;
Container const & m_c;
size_t const m_offset;
};
template <typename Container>
Slice<Container> MakeSlice(Container const & c, size_t offset)
{
return Slice<Container>(c, c.size(), offset);
return Slice<Container>(c, offset);
}
// Builds suffix array over the string s, where for all i < n: 0 < s[i] <= k.
@ -87,7 +94,7 @@ Slice<Container> MakeSlice(Container const & c, size_t offset)
template <typename S>
void RawSkew(size_t n, size_t maxValue, S const & s, size_t * sa)
{
size_t const kInvalidId = std::numeric_limits<size_t>::max();
size_t const kInvalidId = numeric_limits<size_t>::max();
if (n == 0)
return;
@ -98,21 +105,22 @@ void RawSkew(size_t n, size_t maxValue, S const & s, size_t * sa)
return;
}
// The number of =1 (mod 3) suffixes is the same as the number of =0
// (mod 3) suffixes.
const size_t n0 = (n + 2) / 3; // Number of =0 (mod 3) suffixes.
const size_t n1 = (n + 1) / 3; // Number of =1 (mod 3) suffixes.
const size_t n2 = n / 3; // Number of =2 (mod 3) suffixes.
size_t const n0 = (n + 2) / 3; // Number of =0 (mod 3) suffixes.
size_t const n1 = (n + 1) / 3; // Number of =1 (mod 3) suffixes.
size_t const n2 = n / 3; // Number of =2 (mod 3) suffixes.
const size_t n02 = n0 + n2;
size_t const n02 = n0 + n2;
const bool fake1 = n0 != n1;
size_t const fake1 = n0 != n1 ? 1 : 0;
// The total number of =1 (mod 3) suffixes (including the fake one)
// is the same as the number of =0 (mod 3) suffixes.
ASSERT_EQUAL(n1 + fake1, n0, ());
ASSERT_EQUAL(fake1, (n % 3 == 1), ());
ASSERT_EQUAL(fake1, static_cast<uint32_t>(n % 3 == 1), ());
// Generate positions of =(1|2) (mod 3) suffixes.
std::vector<size_t> s12(n02 + 3);
std::vector<size_t> sa12(n02 + 3);
vector<size_t> s12(n02 + 3);
vector<size_t> sa12(n02 + 3);
// (n0 - n1) is needed in case when n == 0 (mod 3). We need a fake
// =1 (mod 3) suffix for proper sorting of =0 (mod 3) suffixes.
@ -125,6 +133,10 @@ void RawSkew(size_t n, size_t maxValue, S const & s, size_t * sa)
s12[j++] = i;
}
// Following three lines perform a stable sorting of all triples
// <s[i], s[i + 1], s[i + 2]> where i =(1|2) (mod 3), including
// possible fake1 suffix. Final order of these triples is written to
// |sa12|.
RadixSort(n02, s12.data(), maxValue + 1, MakeSlice(s, 2), sa12.data());
RadixSort(n02, sa12.data(), maxValue + 1, MakeSlice(s, 1), s12.data());
RadixSort(n02, s12.data(), maxValue + 1, s, sa12.data());
@ -157,7 +169,7 @@ void RawSkew(size_t n, size_t maxValue, S const & s, size_t * sa)
{
// When not all triples unique, we need to build a suffix array
// for them.
RawSkew(n02, name, s12, sa12.data());
RawSkew(n02 /* n */, name /* maxValue */, s12, sa12.data());
for (size_t i = 0; i < n02; ++i)
s12[sa12[i]] = i + 1;
}
@ -172,8 +184,8 @@ void RawSkew(size_t n, size_t maxValue, S const & s, size_t * sa)
// in s12 are unique.
// Need to do a stable sort for all =0 (mod 3) suffixes.
std::vector<size_t> s0(n0);
std::vector<size_t> sa0(n0);
vector<size_t> s0(n0);
vector<size_t> sa0(n0);
for (size_t i = 0, j = 0; i < n02; ++i)
{
if (sa12[i] < n0)
@ -195,39 +207,28 @@ void RawSkew(size_t n, size_t maxValue, S const & s, size_t * sa)
size_t k = 0;
while (i12 != n02 && i0 != n0)
{
const size_t p0 = sa0[i0];
const size_t p12 = RestoreIndex(n0, sa12[i12]);
size_t const p0 = sa0[i0];
size_t const p12 = RestoreIndex(n0, sa12[i12]);
ASSERT_LESS(p12 / 3, n0, ());
if (InLeftHalf(n0, sa12[i12]))
bool const isLEQ =
InLeftHalf(n0, sa12[i12])
? LEQ(s[p12], s12[sa12[i12] + n0], s[p0], s12[p0 / 3])
: LEQ(s[p12], s[p12 + 1], s12[sa12[i12] - n0 + 1], s[p0], s[p0 + 1], s12[p0 / 3 + n0]);
if (isLEQ)
{
if (LEQ(s[p12], s12[sa12[i12] + n0], s[p0], s12[p0 / 3]))
{
// Suffix =(1|2) (mod 3) is smaller.
sa[k++] = p12;
++i12;
}
else
{
sa[k++] = p0;
++i0;
}
// Suffix =(1|2) (mod 3) is smaller.
sa[k++] = p12;
++i12;
}
else
{
if (LEQ(s[p12], s[p12 + 1], s12[sa12[i12] - n0 + 1], s[p0], s[p0 + 1], s12[p0 / 3 + n0]))
{
// Suffix =(1|2) (mod 3) is smaller.
sa[k++] = p12;
++i12;
}
else
{
sa[k++] = p0;
++i0;
}
sa[k++] = p0;
++i0;
}
}
for (; i12 != n02; ++k, ++i12)
sa[k] = RestoreIndex(n0, sa12[i12]);
for (; i0 != n0; ++k, ++i0)
@ -240,13 +241,14 @@ namespace base
{
void Skew(size_t n, uint8_t const * s, size_t * sa)
{
RawSkew(n, 0xFF /* maxValue */, SkewWrapper(n, s), sa);
auto const maxValue = static_cast<size_t>(numeric_limits<uint8_t>::max());
RawSkew(n, maxValue, SkewWrapper(n, s), sa);
}
void Skew(std::string const & s, std::vector<size_t> & sa)
void Skew(string const & s, vector<size_t> & sa)
{
auto const n = s.size();
sa.assign(n, 0);
Skew(n, reinterpret_cast<const uint8_t *>(s.data()), sa.data());
Skew(n, reinterpret_cast<uint8_t const *>(s.data()), sa.data());
}
} // namespace base