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[FIX] CodeQL reports
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@eseiler
eseiler committed Nov 19, 2024
1 parent 6f38aac commit 18e5ddb
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Showing 4 changed files with 26 additions and 20 deletions.
4 changes: 2 additions & 2 deletions include/seqan3/search/detail/search_scheme_algorithm.hpp
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Original file line number Diff line number Diff line change
Expand Up @@ -244,7 +244,7 @@ inline auto search_scheme_block_info(search_scheme_t const & search_scheme, size
for (uint8_t block_id = 0; block_id < rest; ++block_id)
++blocks_length[block_id];

for (uint8_t search_id = 0; search_id < search_scheme.size(); ++search_id)
for (size_t search_id = 0; search_id < search_scheme.size(); ++search_id)
{
auto const & search = search_scheme[search_id];

Expand Down Expand Up @@ -783,7 +783,7 @@ inline void search_ss(index_t const & index,
// retrieve cumulative block lengths and starting position
auto const block_info = search_scheme_block_info(search_scheme, std::ranges::size(query));

for (uint8_t search_id = 0; search_id < search_scheme.size(); ++search_id)
for (size_t search_id = 0; search_id < search_scheme.size(); ++search_id)
{
auto const & search = search_scheme[search_id];
auto const & [blocks_length, start_pos] = block_info[search_id];
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20 changes: 12 additions & 8 deletions include/seqan3/search/fm_index/bi_fm_index_cursor.hpp
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Original file line number Diff line number Diff line change
Expand Up @@ -335,7 +335,7 @@ class bi_fm_index_cursor

size_type new_parent_lb = fwd_lb, new_parent_rb = fwd_rb;

sdsl_char_type c = 1; // NOTE: start with 0 or 1 depending on implicit_sentintel
sdsl_sigma_type c = 1; // NOTE: start with 0 or 1 depending on implicit_sentintel
while (c < sigma
&& !bidirectional_search(index->fwd_fm.index,
index->fwd_fm.index.comp2char[c],
Expand All @@ -352,7 +352,8 @@ class bi_fm_index_cursor
parent_lb = new_parent_lb;
parent_rb = new_parent_rb;

_last_char = c;
assert(c <= std::numeric_limits<sdsl_char_type>::max());
_last_char = static_cast<sdsl_char_type>(c);
++depth;

return true;
Expand Down Expand Up @@ -387,7 +388,7 @@ class bi_fm_index_cursor

size_type new_parent_lb = rev_lb, new_parent_rb = rev_rb;

sdsl_char_type c = 1; // NOTE: start with 0 or 1 depending on implicit_sentintel
sdsl_sigma_type c = 1; // NOTE: start with 0 or 1 depending on implicit_sentintel
while (c < sigma
&& !bidirectional_search(index->rev_fm.index,
index->rev_fm.index.comp2char[c],
Expand All @@ -404,7 +405,8 @@ class bi_fm_index_cursor
parent_lb = new_parent_lb;
parent_rb = new_parent_rb;

_last_char = c;
assert(c <= std::numeric_limits<sdsl_char_type>::max());
_last_char = static_cast<sdsl_char_type>(c);
++depth;

return true;
Expand Down Expand Up @@ -685,7 +687,7 @@ class bi_fm_index_cursor

assert(index != nullptr && query_length() > 0);

sdsl_char_type c = _last_char + 1;
sdsl_sigma_type c = _last_char + 1;

while (c < sigma
&& !bidirectional_search_cycle(index->fwd_fm.index,
Expand All @@ -702,7 +704,8 @@ class bi_fm_index_cursor

if (c != sigma)
{
_last_char = c;
assert(c <= std::numeric_limits<sdsl_char_type>::max());
_last_char = static_cast<sdsl_char_type>(c);

return true;
}
Expand Down Expand Up @@ -744,7 +747,7 @@ class bi_fm_index_cursor

assert(index != nullptr && query_length() > 0);

sdsl_char_type c = _last_char + 1;
sdsl_sigma_type c = _last_char + 1;
while (c < sigma
&& !bidirectional_search_cycle(index->rev_fm.index,
index->rev_fm.index.comp2char[c],
Expand All @@ -760,7 +763,8 @@ class bi_fm_index_cursor

if (c != sigma)
{
_last_char = c;
assert(c <= std::numeric_limits<sdsl_char_type>::max());
_last_char = static_cast<sdsl_char_type>(c);

return true;
}
Expand Down
10 changes: 6 additions & 4 deletions include/seqan3/search/fm_index/fm_index_cursor.hpp
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Original file line number Diff line number Diff line change
Expand Up @@ -260,7 +260,7 @@ class fm_index_cursor
// store all cursors at once in a private std::array of cursors
assert(index != nullptr);

sdsl_char_type c = 1; // NOTE: start with 0 or 1 depending on implicit_sentintel
sdsl_sigma_type c = 1; // NOTE: start with 0 or 1 depending on implicit_sentintel
size_type _lb = node.lb, _rb = node.rb;
while (c < sigma && !backward_search(index->index, index->index.comp2char[c], _lb, _rb))
{
Expand All @@ -271,7 +271,8 @@ class fm_index_cursor
{
parent_lb = node.lb;
parent_rb = node.rb;
node = {_lb, _rb, node.depth + 1, c};
assert(c <= std::numeric_limits<sdsl_char_type>::max());
node = {_lb, _rb, node.depth + 1, static_cast<sdsl_char_type>(c)};
return true;
}
return false;
Expand Down Expand Up @@ -406,7 +407,7 @@ class fm_index_cursor
// parent_lb > parent_rb --> invalid interval
assert(parent_lb <= parent_rb);

sdsl_char_type c = node.last_char + 1;
sdsl_sigma_type c = node.last_char + 1;
size_type _lb = parent_lb, _rb = parent_rb;

while (c < sigma && !backward_search(index->index, index->index.comp2char[c], _lb, _rb))
Expand All @@ -416,7 +417,8 @@ class fm_index_cursor

if (c != sigma) // Collection has additional sentinel as delimiter
{
node = {_lb, _rb, node.depth, c};
assert(c <= std::numeric_limits<sdsl_char_type>::max());
node = {_lb, _rb, node.depth, static_cast<sdsl_char_type>(c)};
return true;
}
return false;
Expand Down
12 changes: 6 additions & 6 deletions test/unit/utility/math_test.cpp
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Original file line number Diff line number Diff line change
Expand Up @@ -25,7 +25,7 @@ TYPED_TEST(unsigned_operations, floor_log2)
constexpr size_t one2 = seqan3::detail::floor_log2<unsigned_t>(0b0011);
constexpr size_t two1 = seqan3::detail::floor_log2<unsigned_t>(0b0101);
constexpr size_t two2 = seqan3::detail::floor_log2<unsigned_t>(0b0111);
constexpr size_t seven = seqan3::detail::floor_log2<unsigned_t>(0b10010010);
constexpr size_t seven = seqan3::detail::floor_log2<unsigned_t>(0b1001'0010);
EXPECT_EQ(zero, 0u);
EXPECT_EQ(one1, 1u);
EXPECT_EQ(one2, 1u);
Expand All @@ -36,8 +36,8 @@ TYPED_TEST(unsigned_operations, floor_log2)
for (uint8_t log2_value = 0; log2_value < seqan3::detail::bits_of<unsigned_t>; ++log2_value)
{
unsigned_t start = unsigned_t{1u} << log2_value;
unsigned_t end = start << 1u;
for (unsigned_t n = start, k = 0u; n < end && k < max_iterations; ++n, ++k)
unsigned_t end = static_cast<unsigned_t>(std::min<size_t>(start, max_iterations) + start);
for (unsigned_t n = start; n < end; ++n)
{
EXPECT_EQ(seqan3::detail::floor_log2(n), log2_value);
EXPECT_EQ(std::floor(std::log2(n)), log2_value) << "If this fails this might be a floating point rounding "
Expand All @@ -54,7 +54,7 @@ TYPED_TEST(unsigned_operations, ceil_log2)
constexpr size_t two = seqan3::detail::ceil_log2<unsigned_t>(0b0011);
constexpr size_t three1 = seqan3::detail::ceil_log2<unsigned_t>(0b0101);
constexpr size_t three2 = seqan3::detail::ceil_log2<unsigned_t>(0b0111);
constexpr size_t eight = seqan3::detail::ceil_log2<unsigned_t>(0b10010010);
constexpr size_t eight = seqan3::detail::ceil_log2<unsigned_t>(0b1001'0010);
EXPECT_EQ(zero, 0u);
EXPECT_EQ(one, 1u);
EXPECT_EQ(two, 2u);
Expand All @@ -65,13 +65,13 @@ TYPED_TEST(unsigned_operations, ceil_log2)
for (uint8_t log2_value = 0; log2_value < seqan3::detail::bits_of<unsigned_t>; ++log2_value)
{
unsigned_t start = unsigned_t{1u} << log2_value;
unsigned_t end = start << 1u;
unsigned_t end = static_cast<unsigned_t>(std::min<size_t>(start, max_iterations) + start);
EXPECT_EQ(seqan3::detail::ceil_log2(start), log2_value);
EXPECT_EQ(std::ceil(std::log2(start)), log2_value) << "ceil_log2 of " << start << " should be " << log2_value
<< "; If this fails this might be a floating point rounding "
<< "error on your machine.";

for (unsigned_t n = start + 1u, k = 0u; n < end && k < max_iterations; ++n, ++k)
for (unsigned_t n = start + 1u; n < end; ++n)
{
EXPECT_EQ(seqan3::detail::ceil_log2(n), log2_value + 1u);

Expand Down

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