60template <matrix matrix_t,
typename first_sequence_t = std::nullopt_t,
typename second_sequence_t = std::nullopt_t>
74 static constexpr bool is_optional_score = is_type_specialisation_of_v<entry_t, std::optional>;
167 size_t row = coordinate.row;
168 size_t col = coordinate.col;
211 assert(masking_matrix.rows() ==
rows());
212 assert(masking_matrix.cols() ==
cols());
234 assert(new_rows <=
rows());
235 assert(new_cols <=
cols());
273 template <
typename ostream_t>
280 auto char_first_sequence = [&]([[maybe_unused]]
size_t const i) ->
std::string
288 auto char_second_sequence = [&]([[maybe_unused]]
size_t const i) ->
std::string
299 size_t const length_bytes = symbol.size();
301 size_t const offset = length_bytes - length;
306 auto print_first_cell = [&](
std::string const & symbol)
308 cout << symbol << symbols.
col_sep;
312 auto print_first_row = [&]
314 print_first_cell(
" ");
317 for (
size_t col = 0; col <
cols() - 1; ++col)
318 print_cell(char_first_sequence(col));
324 auto print_divider = [&]
327 for (
size_t col = 0; col <
cols(); ++col)
340 if (symbols.
row_sep[0] !=
'\0')
345 print_first_cell(symbols.
epsilon);
347 print_first_cell(char_second_sequence(
row - 1));
349 for (
size_t col = 0; col <
cols(); ++col)
359 size_t col_width = 1;
361 for (
size_t col = 0; col <
cols(); ++col)
383 template <
typename value_type>
388 stream << flags << entry;
389 return strstream.
str();
397 for (
auto it = str.cbegin(); it < str.cend(); ++it, ++length)
400 if ((v & 0b11100000) == 0b11000000)
402 else if ((v & 0b11110000) == 0b11100000)
404 else if ((v & 0b11111000) == 0b11110000)
458template <matrix matrix_t>
463template <matrix matrix_t,
typename first_sequence_t,
typename second_sequence_t>
482template <
typename char_t, detail::matrix alignment_matrix_t>
488 debug.stream_matrix(sstream, s.
flags2());
494template <
typename char_t, std::ranges::input_range alignment_matrix_t>
A "pretty printer" for most SeqAn data structures and related types.
Definition: debug_stream_type.hpp:78
fmtflags2 flags2() const
Retrieve the format flags from the stream.
Definition: debug_stream_type.hpp:201
A debug matrix to wrap alignment matrices and sequences and make them printable together.
Definition: debug_matrix.hpp:62
std::optional< size_t > _cols
The number of columns the debug matrix should have. Must be at most the size of the original matrix.
Definition: debug_matrix.hpp:444
debug_matrix & mask_matrix(row_wise_matrix< bool > masking_matrix) noexcept
Masks entries out of the current matrix. This operations changes the way this.at(i,...
Definition: debug_matrix.hpp:209
first_sequence_t const & first_sequence() const noexcept
The first sequence of the sequence alignment.
Definition: debug_matrix.hpp:147
debug_matrix(matrix_t &&, first_sequence_t &&, second_sequence_t &&) -> debug_matrix< matrix_t, first_sequence_t, second_sequence_t >
The type deduction guide for the constructor seqan3::detail::debug_matrix(matrix_t,...
static constexpr format_type unicode
The format when printing to a unicode stream.
Definition: debug_matrix.hpp:428
static std::string as_string(value_type &&entry, fmtflags2 const flags) noexcept
Convert a value into a std::string.
Definition: debug_matrix.hpp:384
size_t rows() const noexcept
The number of rows in the matrix.
Definition: debug_matrix.hpp:129
size_t cols() const noexcept
The number of columns in the matrix.
Definition: debug_matrix.hpp:138
bool _transpose
Whether the current matrix should be transposed.
Definition: debug_matrix.hpp:448
debug_matrix & operator=(debug_matrix &&)=default
Defaulted.
debug_matrix()=default
Defaulted.
debug_matrix(debug_matrix &&)=default
Defaulted.
bool _transpose_mask
Whether the masking matrix should be transposed.
Definition: debug_matrix.hpp:450
size_t auto_column_width(fmtflags2 const flags) const noexcept
Determines the largest width of all entries in the matrix, e.g. -152 has width 4.
Definition: debug_matrix.hpp:357
debug_matrix(debug_matrix const &)=default
Defaulted.
debug_matrix & sub_matrix(size_t const new_rows, size_t const new_cols) noexcept
Limits the view port of the current matrix.
Definition: debug_matrix.hpp:232
static constexpr bool is_traceback_matrix
Whether the value_type is trace_directions.
Definition: debug_matrix.hpp:71
debug_matrix & mask_matrix(std::vector< bool > masking_vector) noexcept
Creates the masking_matrix out of the given masking_vector and calls mask_matrix(row_wise_matrix<bool...
Definition: debug_matrix.hpp:222
std::conditional_t< is_traceback_matrix||is_optional_score, entry_t, std::optional< entry_t > > value_type
The type of an entry in the matrix.
Definition: debug_matrix.hpp:81
second_sequence_t const & second_sequence() const noexcept
The second sequence of the sequence alignment.
Definition: debug_matrix.hpp:156
static constexpr bool is_optional_score
Whether a score matrix already returns std::optional scores. (Where std::nullopt means unset/invalid/...
Definition: debug_matrix.hpp:74
~debug_matrix()=default
Defaulted.
static constexpr format_type csv
The format when printing to a ascii stream.
Definition: debug_matrix.hpp:426
std::optional< row_wise_matrix< bool > > _masking_matrix
The masking matrix.
Definition: debug_matrix.hpp:446
value_type reference
The type of a reference to an entry in the matrix.
Definition: debug_matrix.hpp:83
static constexpr bool has_second_sequence
Whether the current debug_matrix was given a second_sequence.
Definition: debug_matrix.hpp:67
std::optional< size_t > _rows
The number of rows the debug matrix should have. Must be at most the size of the original matrix.
Definition: debug_matrix.hpp:442
matrix_t _matrix
The matrix.
Definition: debug_matrix.hpp:436
first_sequence_t _first_sequence
The first sequence of the sequence alignment.
Definition: debug_matrix.hpp:438
debug_matrix & transpose_matrix() noexcept
Transposes the current matrix.
Definition: debug_matrix.hpp:252
debug_matrix(matrix_t matrix)
Construct the matrix out of an existing matrix.
Definition: debug_matrix.hpp:103
second_sequence_t _second_sequence
The second sequence of the sequence alignment.
Definition: debug_matrix.hpp:440
typename std::remove_reference_t< matrix_t >::value_type entry_t
The entry type.
Definition: debug_matrix.hpp:69
void stream_matrix(ostream_t &cout, fmtflags2 const flags) const noexcept
Prints this matrix into the given stream.
Definition: debug_matrix.hpp:274
debug_matrix & operator=(debug_matrix const &)=default
Defaulted.
debug_matrix(matrix_t &&) -> debug_matrix< matrix_t >
The type deduction guide for the constructor seqan3::detail::debug_matrix(matrix_t)
const_reference at(matrix_coordinate const &coordinate) const noexcept
A reference to the entry of the matrix at the given coordinate.
Definition: debug_matrix.hpp:165
typename std::remove_reference_t< matrix_t >::size_type size_type
The size type.
Definition: debug_matrix.hpp:87
std::string entry_at(matrix_coordinate const coordinate, fmtflags2 flags) const noexcept
Same as at(coordinate), but as string.
Definition: debug_matrix.hpp:371
debug_matrix(matrix_t matrix, first_sequence_t first_sequence, second_sequence_t second_sequence)
Construct the matrix out of an existing matrix and two sequences.
Definition: debug_matrix.hpp:111
static size_t unicode_str_length(std::string const &str) noexcept
The length of the str (traceback symbols are unicode aware).
Definition: debug_matrix.hpp:394
std::optional< size_t > column_width
What is the width (number of chars) of an entry. Defaults to auto_column_width.
Definition: debug_matrix.hpp:432
static constexpr bool has_first_sequence
Whether the current debug_matrix was given a first_sequence.
Definition: debug_matrix.hpp:65
Defines the requirements of a matrix (e.g. score matrices, trace matrices).
Definition: matrix_concept.hpp:61
A two dimensional matrix used inside of alignment algorithms.
Definition: two_dimensional_matrix.hpp:65
A helper concept definition for ranges that can be streamed to the seqan3::debug_stream.
Definition: range.hpp:39
Provides seqan3::debug_stream and related types.
Provides seqan3::debug_stream and related types.
debug_stream_type< char_t > & operator<<(debug_stream_type< char_t > &stream, alignment_t &&alignment)
Stream operator for alignments, which are represented as tuples of aligned sequences.
Definition: debug_stream_alignment.hpp:110
trace_directions
The possible directions a trace can have. The values can be combined by the logical |-operator.
Definition: trace_directions.hpp:29
@ row
The corresponding alignment coordinate will be incrementable/decrementable in the row index.
@ up
Trace comes from the above entry.
@ left
Trace comes from the left entry.
@ diagonal
Trace comes from the diagonal entry.
fmtflags2
Flags that change the behaviour of the seqan3::debug_stream.
Definition: debug_stream_type.hpp:31
@ utf8
Enables use of non-ASCII UTF8 characters in formatted output.
Definition: debug_stream_type.hpp:33
@ offset
Sequence (seqan3::field::seq) relative start position (0-based), unsigned value.
Provides seqan3::detail::matrix.
The internal SeqAn3 namespace.
Definition: aligned_sequence_concept.hpp:29
The main SeqAn3 namespace.
Definition: aligned_sequence_concept.hpp:29
SeqAn specific customisations in the standard namespace.
Provides seqan3::debug_stream and related types.
Provides seqan3::debug_stream and related types.
Provides seqan3::detail::row_wise_matrix.
A strong type for designated initialisation of the column index of a matrix.
Definition: matrix_coordinate.hpp:32
Strong type for setting the column dimension of a matrix.
Definition: two_dimensional_matrix.hpp:32
Strong type for setting the row dimension of a matrix.
Definition: two_dimensional_matrix.hpp:40
A strong type for designated initialisation of the row index of a matrix.
Definition: matrix_coordinate.hpp:61
Provides type traits for working with templates.
Provides the declaration of seqan3::detail::trace_directions.