107 template <
typename stream_type,
108 typename legal_alph_type,
109 typename stream_pos_type,
115 stream_pos_type & position_buffer,
118 qual_type & SEQAN3_DOXYGEN_ONLY(qualities))
123 position_buffer = stream.tellg();
126 read_id(stream_view, options,
id);
133 template <
typename stream_type,
141 qual_type && SEQAN3_DOXYGEN_ONLY(qualities))
146 if constexpr (detail::decays_to_ignore_v<id_type>)
148 throw std::logic_error{
"The ID field may not be set to ignore when writing FASTA files."};
152 if (std::ranges::empty(
id))
159 if constexpr (detail::decays_to_ignore_v<seq_type>)
162 "The SEQ and SEQ_QUAL fields may not both be set to ignore when writing FASTA files."};
176 template <
typename stream_view_t,
typename seq_legal_alph_type,
typename id_type>
182 if (!is_id(*begin(stream_view)))
186 if constexpr (detail::decays_to_ignore_v<id_type>)
194#if SEQAN3_WORKAROUND_VIEW_PERFORMANCE
195 auto it = stream_view.begin();
196 auto e = stream_view.end();
201 for (; (it != e) && (
is_blank)(*it); ++it)
205 bool at_delimiter =
false;
206 for (; it != e; ++it)
213 id.push_back(
assign_char_to(*it, std::ranges::range_value_t<id_type>{}));
219 for (; (it != e) && ((!
is_char<
'\n'>)(*it)); ++it)
226 stream_view | std::views::drop(1)
235 stream_view | std::views::drop(1)
247#if SEQAN3_WORKAROUND_VIEW_PERFORMANCE
248 auto it = stream_view.begin();
249 auto e = stream_view.end();
254 for (; (it != e) && (
is_blank)(*it); ++it)
258 bool at_delimiter =
false;
259 for (; it != e; ++it)
266 id.push_back(
assign_char_to(*it, std::ranges::range_value_t<id_type>{}));
276 | std::views::drop(1)
284 | std::views::drop(1)
294 template <
typename stream_view_t,
typename seq_legal_alph_type,
typename seq_type>
299 if constexpr (!detail::decays_to_ignore_v<seq_type>)
301 constexpr auto is_legal_alph = char_is_valid_for<seq_legal_alph_type>;
303#if SEQAN3_WORKAROUND_VIEW_PERFORMANCE
304 auto it = stream_view.begin();
305 auto e = stream_view.end();
310 for (; (it != e) && ((!is_id)(*it)); ++it)
316 else if (is_legal_alph(*it))
324 + detail::type_name_as_string<seq_legal_alph_type>
337 | std::views::transform(
338 [is_legal_alph](
char const c)
340 if (!is_legal_alph(c))
343 +
"char_is_valid_for<"
344 + detail::type_name_as_string<seq_legal_alph_type>
360 template <
typename stream_it_t,
typename id_type>
371 stream_it.write_range(
id);
376 template <
typename stream_it_t,
typename seq_type>
385 auto end = std::ranges::end(char_sequence);
390 auto current_end = it;
392 using subrange_t = std::ranges::subrange<
decltype(it),
decltype(it), std::ranges::subrange_kind::sized>;
399 stream_it.write_range(char_sequence);
Provides aliases for qualified.
Core alphabet concept and free function/type trait wrappers.
T back_inserter(T... args)
Provides alphabet adaptations for standard char types.
Provides seqan3::views::char_to.
Functionally the same as std::ostreambuf_iterator, but offers writing a range more efficiently.
Definition: fast_ostreambuf_iterator.hpp:40
Provides various utility functions.
Provides various transformation traits used by the range module.
Provides seqan3::dna5, container aliases and string literals.
Provides seqan3::detail::fast_ostreambuf_iterator.
auto const to_char
A view that calls seqan3::to_char() on each element in the input range.
Definition: to_char.hpp:63
auto const char_to
A view over an alphabet, given a range of characters.
Definition: char_to.hpp:67
constexpr auto assign_char_to
Assign a character to an alphabet object.
Definition: alphabet/concept.hpp:524
constexpr void consume(rng_t &&rng)
Iterate over a range (consumes single-pass input ranges).
Definition: core/range/detail/misc.hpp:28
constexpr auto take_until
A view adaptor that returns elements from the underlying range until the functor evaluates to true (o...
Definition: take_until_view.hpp:560
constexpr auto take_until_or_throw
A view adaptor that returns elements from the underlying range until the functor evaluates to true (t...
Definition: take_until_view.hpp:574
constexpr auto istreambuf
A view factory that returns a view over the stream buffer of an input stream.
Definition: istreambuf_view.hpp:107
constexpr auto take_line_or_throw
A view adaptor that returns a single line from the underlying range (throws if there is no end-of-lin...
Definition: take_line_view.hpp:85
@ seq
The "sequence", usually a range of nucleotides or amino acids.
constexpr auto is_blank
Checks whether c is a blank character.
Definition: predicate.hpp:142
constexpr auto is_digit
Checks whether c is a digital character.
Definition: predicate.hpp:262
std::string make_printable(char const c)
Returns a printable value for the given character c.
Definition: pretty_print.hpp:48
constexpr auto is_char
Checks whether a given letter is the same as the template non-type argument.
Definition: predicate.hpp:63
constexpr auto is_space
Checks whether c is a space character.
Definition: predicate.hpp:125
constexpr auto is_cntrl
Checks whether c is a control character.
Definition: predicate.hpp:90
Provides seqan3::detail::ignore_output_iterator for writing to null stream.
The generic concept for a (biological) sequence.
Provides various utility functions.
Provides seqan3::detail::istreambuf.
The main SeqAn3 namespace.
Definition: aligned_sequence_concept.hpp:29
SeqAn specific customisations in the standard namespace.
Provides character predicates for tokenisation.
Provides seqan3::sequence_file_output_options.
Thrown if there is a parse error, such as reading an unexpected character from an input stream.
Definition: io/exception.hpp:48
The options type defines various option members that influence the behaviour of all or some formats.
Definition: sequence_file/output_options.hpp:26
uint32_t fasta_letters_per_line
Inserts linebreaks after every n-th letter in the sequence; 0 means no linebreaks.
Definition: sequence_file/output_options.hpp:32
bool fasta_legacy_id_marker
Begin the ID line with ";" instead of ">" (not recommended).
Definition: sequence_file/output_options.hpp:28
bool add_carriage_return
The default plain text line-ending is "\n", but on Windows an additional carriage return is recommend...
Definition: sequence_file/output_options.hpp:42
bool fasta_blank_before_id
Insert a single space after ">" (or ";") before the actual ID.
Definition: sequence_file/output_options.hpp:30
Provides seqan3::detail::take_line and seqan3::detail::take_line_or_throw.
Provides seqan3::views::take_until and seqan3::views::take_until_or_throw.
Provides seqan3::views::to_char.
Provides traits to inspect some information of a type, for example its name.