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[MISC] automatic linting
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@seqan-actions
seqan-actions committed Jan 25, 2024
1 parent 5c7ed74 commit e0406f3
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Showing 11 changed files with 219 additions and 167 deletions.
11 changes: 6 additions & 5 deletions include/seqan3/alignment/aligned_sequence/debug_stream_alignment.hpp
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Expand Up @@ -112,16 +112,17 @@ inline debug_stream_type<char_t> & operator<<(debug_stream_type<char_t> & stream
{
#else
template <typename alignment_t>
requires (tuple_like<std::remove_cvref_t<alignment_t>> && detail::all_model_aligned_seq<detail::tuple_type_list_t<std::remove_cvref_t<alignment_t>>>)
requires (tuple_like<std::remove_cvref_t<alignment_t>>
&& detail::all_model_aligned_seq<detail::tuple_type_list_t<std::remove_cvref_t<alignment_t>>>)
struct alignment_printer<alignment_t>
{
constexpr static auto print = [](auto & stream, auto && alignment)
static constexpr auto print = [](auto & stream, auto && alignment)
{
constexpr size_t sequence_count = std::tuple_size_v<std::remove_cvref_t<alignment_t>>;
constexpr size_t sequence_count = std::tuple_size_v<std::remove_cvref_t<alignment_t>>;

static_assert(sequence_count >= 2, "An alignment requires at least two sequences.");
static_assert(sequence_count >= 2, "An alignment requires at least two sequences.");

detail::stream_alignment(stream, alignment, std::make_index_sequence<sequence_count - 1>{});
detail::stream_alignment(stream, alignment, std::make_index_sequence<sequence_count - 1>{});
};
};
#endif
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4 changes: 2 additions & 2 deletions include/seqan3/alignment/matrix/detail/advanceable_alignment_coordinate.hpp
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Expand Up @@ -319,9 +319,9 @@ template <typename coordinate_type>
detail::advanceable_alignment_coordinate>
struct advanceable_alignment_coordinate_printer<coordinate_type>
{
constexpr static auto print = [](auto & s, coordinate_type const & c)
static constexpr auto print = [](auto & s, coordinate_type const & c)
{
s << std::tie(c.first, c.second);
s << std::tie(c.first, c.second);
};
};
#endif
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10 changes: 5 additions & 5 deletions include/seqan3/alignment/matrix/detail/debug_matrix.hpp
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Expand Up @@ -488,13 +488,13 @@ template <typename alignment_matrix_t>
requires detail::matrix<std::remove_cvref_t<alignment_matrix_t>>
struct alignment_matrix_printer<alignment_matrix_t>
{
constexpr static auto print = [](auto & s, auto && matrix)
static constexpr auto print = [](auto & s, auto && matrix)
{
detail::debug_matrix debug{std::forward<alignment_matrix_t>(matrix)};
detail::debug_matrix debug{std::forward<alignment_matrix_t>(matrix)};

std::stringstream sstream{};
debug.stream_matrix(sstream, s.flags2());
s << sstream.str();
std::stringstream sstream{};
debug.stream_matrix(sstream, s.flags2());
s << sstream.str();
};
};
#endif
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21 changes: 11 additions & 10 deletions include/seqan3/alignment/matrix/detail/trace_directions.hpp
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Expand Up @@ -84,20 +84,21 @@ template <typename trace_directions_t>
requires std::is_same_v<std::remove_cvref_t<trace_directions_t>, detail::trace_directions>
struct trace_directions_printer<trace_directions_t>
{
constexpr static auto print = [](auto & s, detail::trace_directions const trace)
static constexpr auto print = [](auto & s, detail::trace_directions const trace)
{
static char const * unicode[32]{"↺", "↖", "↑", "↖↑", "⇡", "↖⇡", "↑⇡", "↖↑⇡", "←", "↖←", "↑←",
"↖↑←", "⇡←", "↖⇡←", "↑⇡←", "↖↑⇡←", "⇠", "↖⇠", "↑⇠", "↖↑⇠", "⇡⇠", "↖⇡⇠",
"↑⇡⇠", "↖↑⇡⇠", "←⇠", "↖←⇠", "↑←⇠", "↖↑←⇠", "⇡←⇠", "↖⇡←⇠", "↑⇡←⇠", "↖↑⇡←⇠"};
static char const * unicode[32]{"↺", "↖", "↑", "↖↑", "⇡", "↖⇡", "↑⇡", "↖↑⇡",
"←", "↖←", "↑←", "↖↑←", "⇡←", "↖⇡←", "↑⇡←", "↖↑⇡←",
"⇠", "↖⇠", "↑⇠", "↖↑⇠", "⇡⇠", "↖⇡⇠", "↑⇡⇠", "↖↑⇡⇠",
"←⇠", "↖←⇠", "↑←⇠", "↖↑←⇠", "⇡←⇠", "↖⇡←⇠", "↑⇡←⇠", "↖↑⇡←⇠"};

static char const * csv[32]{"N", "D", "U", "DU", "u", "Du", "Uu", "DUu", "L", "DL", "UL",
"DUL", "uL", "DuL", "UuL", "DUuL", "l", "Dl", "Ul", "DUl", "ul", "Dul",
"Uul", "DUul", "Ll", "DLl", "ULl", "DULl", "uLl", "DuLl", "UuLl", "DUuLl"};
static char const * csv[32]{"N", "D", "U", "DU", "u", "Du", "Uu", "DUu", "L", "DL", "UL",
"DUL", "uL", "DuL", "UuL", "DUuL", "l", "Dl", "Ul", "DUl", "ul", "Dul",
"Uul", "DUul", "Ll", "DLl", "ULl", "DULl", "uLl", "DuLl", "UuLl", "DUuLl"};

bool is_unicode = (s.flags2() & fmtflags2::utf8) == fmtflags2::utf8;
auto const & trace_dir = is_unicode ? unicode : csv;
bool is_unicode = (s.flags2() & fmtflags2::utf8) == fmtflags2::utf8;
auto const & trace_dir = is_unicode ? unicode : csv;

s << trace_dir[static_cast<size_t>(trace)];
s << trace_dir[static_cast<size_t>(trace)];
};
};
#endif
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83 changes: 44 additions & 39 deletions include/seqan3/alignment/pairwise/alignment_result.hpp
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Original file line number Diff line number Diff line change
Expand Up @@ -421,50 +421,55 @@ inline debug_stream_type<char_t> & operator<<(debug_stream_type<char_t> & stream
template <typename T>
requires (!std::is_same_v<T, std::remove_cvref_t<T>>)
struct alignment_result_printer<T> : public alignment_result_printer<std::remove_cvref_t<T>>
{
};
{};

template <typename result_value_t>
struct alignment_result_printer<alignment_result<result_value_t>>
{
constexpr static auto print = [](auto & stream, alignment_result<result_value_t> const & result)
{
using alignment_result_t = alignment_result<result_value_t>;
using disabled_t = std::nullopt_t *;
using result_data_t =
typename detail::alignment_result_value_type_accessor<std::remove_cvref_t<alignment_result_t>>::type;

constexpr bool has_sequence1_id = !std::is_same_v<decltype(std::declval<result_data_t>().sequence1_id), disabled_t>;
constexpr bool has_sequence2_id = !std::is_same_v<decltype(std::declval<result_data_t>().sequence2_id), disabled_t>;
constexpr bool has_score = !std::is_same_v<decltype(std::declval<result_data_t>().score), disabled_t>;
constexpr bool has_end_positions =
!std::is_same_v<decltype(std::declval<result_data_t>().end_positions), disabled_t>;
constexpr bool has_begin_positions =
!std::is_same_v<decltype(std::declval<result_data_t>().begin_positions), disabled_t>;
constexpr bool has_alignment = !std::is_same_v<decltype(std::declval<result_data_t>().alignment), disabled_t>;

bool prepend_comma = false;
auto append_to_stream = [&](auto &&... args)
static constexpr auto print = [](auto & stream, alignment_result<result_value_t> const & result)
{
((stream << (prepend_comma ? std::string{", "} : std::string{})) << ... << std::forward<decltype(args)>(args));
prepend_comma = true;
};

stream << '{';
if constexpr (has_sequence1_id)
append_to_stream("sequence1 id: ", result.sequence1_id());
if constexpr (has_sequence2_id)
append_to_stream("sequence2 id: ", result.sequence2_id());
if constexpr (has_score)
append_to_stream("score: ", result.score());
if constexpr (has_begin_positions)
append_to_stream("begin: (", result.sequence1_begin_position(), ",", result.sequence2_begin_position(), ")");
if constexpr (has_end_positions)
append_to_stream("end: (", result.sequence1_end_position(), ",", result.sequence2_end_position(), ")");
if constexpr (has_alignment)
append_to_stream("\nalignment:\n", result.alignment());
stream << '}';

using alignment_result_t = alignment_result<result_value_t>;
using disabled_t = std::nullopt_t *;
using result_data_t =
typename detail::alignment_result_value_type_accessor<std::remove_cvref_t<alignment_result_t>>::type;

constexpr bool has_sequence1_id =
!std::is_same_v<decltype(std::declval<result_data_t>().sequence1_id), disabled_t>;
constexpr bool has_sequence2_id =
!std::is_same_v<decltype(std::declval<result_data_t>().sequence2_id), disabled_t>;
constexpr bool has_score = !std::is_same_v<decltype(std::declval<result_data_t>().score), disabled_t>;
constexpr bool has_end_positions =
!std::is_same_v<decltype(std::declval<result_data_t>().end_positions), disabled_t>;
constexpr bool has_begin_positions =
!std::is_same_v<decltype(std::declval<result_data_t>().begin_positions), disabled_t>;
constexpr bool has_alignment = !std::is_same_v<decltype(std::declval<result_data_t>().alignment), disabled_t>;

bool prepend_comma = false;
auto append_to_stream = [&](auto &&... args)
{
((stream << (prepend_comma ? std::string{", "} : std::string{}))
<< ... << std::forward<decltype(args)>(args));
prepend_comma = true;
};

stream << '{';
if constexpr (has_sequence1_id)
append_to_stream("sequence1 id: ", result.sequence1_id());
if constexpr (has_sequence2_id)
append_to_stream("sequence2 id: ", result.sequence2_id());
if constexpr (has_score)
append_to_stream("score: ", result.score());
if constexpr (has_begin_positions)
append_to_stream("begin: (",
result.sequence1_begin_position(),
",",
result.sequence2_begin_position(),
")");
if constexpr (has_end_positions)
append_to_stream("end: (", result.sequence1_end_position(), ",", result.sequence2_end_position(), ")");
if constexpr (has_alignment)
append_to_stream("\nalignment:\n", result.alignment());
stream << '}';
};
};
#endif
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4 changes: 2 additions & 2 deletions include/seqan3/alphabet/detail/debug_stream_alphabet.hpp
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Original file line number Diff line number Diff line change
Expand Up @@ -39,7 +39,7 @@ template <typename alphabet_t>
requires alphabet<alphabet_t>
struct alphabet_printer<alphabet_t>
{
constexpr static auto print = [](auto & s, alphabet_t l)
static constexpr auto print = [](auto & s, alphabet_t l)
{
s << to_char(l);
};
Expand Down Expand Up @@ -69,7 +69,7 @@ template <typename alphabet_t>
requires std::same_as<std::remove_cvref_t<alphabet_t>, mask>
struct mask_printer<alphabet_t>
{
constexpr static auto print = [](auto & s, alphabet_t const l)
static constexpr auto print = [](auto & s, alphabet_t const l)
{
s << (l == std::remove_cvref_t<alphabet_t>{} ? "UNMASKED" : "MASKED");
};
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19 changes: 12 additions & 7 deletions include/seqan3/core/debug_stream/debug_stream_type.hpp
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Original file line number Diff line number Diff line change
Expand Up @@ -133,9 +133,12 @@ class debug_stream_type
{
using t_ = std::remove_cvref_t<t>;

if constexpr(default_printer::is_printable<t_>) {
if constexpr (default_printer::is_printable<t_>)
{
default_printer::print(s, v);
} else {
}
else
{
std::string const msg = std::string{"debug_stream has no print overload for type: "} + typeid(v).name();
throw std::runtime_error{msg};
}
Expand Down Expand Up @@ -171,10 +174,10 @@ class debug_stream_type
}
#else

template<typename T>
template <typename T>
friend struct debug_stream_printer;

template<typename T>
template <typename T>
friend struct std_printer;

#endif
Expand Down Expand Up @@ -216,14 +219,14 @@ class debug_stream_type
#ifdef _LIBCPP_VERSION
static_assert(std::same_as<fmtflags, unsigned>);
#else
#if 0
# if 0
//!\copybrief setf()
debug_stream_type & operator<<(fmtflags const flag)
{
setf(flag);
return *this;
}
#endif
# endif
//!\}
#endif

Expand Down Expand Up @@ -275,7 +278,9 @@ class debug_stream_type
};

template <typename value_t>
requires (std::is_same_v<std::remove_cvref_t<value_t>, int8_t> || std::is_same_v<std::remove_cvref_t<value_t>, uint8_t> || std::is_same_v<std::remove_cvref_t<value_t>, fmtflags2>)
requires (std::is_same_v<std::remove_cvref_t<value_t>, int8_t>
|| std::is_same_v<std::remove_cvref_t<value_t>, uint8_t>
|| std::is_same_v<std::remove_cvref_t<value_t>, fmtflags2>)
struct debug_stream_printer<value_t>
{
struct print_fn
Expand Down
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