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2025-09-09 09:29:41.000000 ./usr/share/doc/libseqan3-dev/html/utility_2type__list_2all_8hpp.html\n -rw-r--r-- 0 root (0) root (0) 8483 2025-09-09 09:29:41.000000 ./usr/share/doc/libseqan3-dev/html/utility_2type__list_2all_8hpp_source.html\n -rw-r--r-- 0 root (0) root (0) 6410 2025-09-09 09:29:41.000000 ./usr/share/doc/libseqan3-dev/html/utility_2type__pack_2all_8hpp.html\n -rw-r--r-- 0 root (0) root (0) 8083 2025-09-09 09:29:41.000000 ./usr/share/doc/libseqan3-dev/html/utility_2type__pack_2all_8hpp_source.html\n -rw-r--r-- 0 root (0) root (0) 6416 2025-09-09 09:29:41.000000 ./usr/share/doc/libseqan3-dev/html/utility_2type__traits_2all_8hpp.html\n -rw-r--r-- 0 root (0) root (0) 9492 2025-09-09 09:29:41.000000 ./usr/share/doc/libseqan3-dev/html/utility_2type__traits_2all_8hpp_source.html\n -rw-r--r-- 0 root (0) root (0) 6436 2025-09-09 09:29:41.000000 ./usr/share/doc/libseqan3-dev/html/utility_2type__traits_2concept_8hpp.html\n -rw-r--r-- 0 root (0) root (0) 11091 2025-09-09 09:29:41.000000 ./usr/share/doc/libseqan3-dev/html/utility_2type__traits_2concept_8hpp_source.html\n -rw-r--r-- 0 root (0) root (0) 6396 2025-09-09 09:29:41.000000 ./usr/share/doc/libseqan3-dev/html/utility_2views_2all_8hpp.html\n -rw-r--r-- 0 root (0) root (0) 13755 2025-09-09 09:29:41.000000 ./usr/share/doc/libseqan3-dev/html/utility_2views_2all_8hpp_source.html\n -rw-r--r-- 0 root (0) root (0) 6416 2025-09-09 09:29:41.000000 ./usr/share/doc/libseqan3-dev/html/utility_2views_2convert_8hpp.html\n--rw-r--r-- 0 root (0) root (0) 12642 2025-09-09 09:29:41.000000 ./usr/share/doc/libseqan3-dev/html/utility_2views_2convert_8hpp_source.html\n+-rw-r--r-- 0 root (0) root (0) 13367 2025-09-09 09:29:41.000000 ./usr/share/doc/libseqan3-dev/html/utility_2views_2convert_8hpp_source.html\n -rw-r--r-- 0 root (0) root (0) 6439 2025-09-09 09:29:41.000000 ./usr/share/doc/libseqan3-dev/html/validate__char__for_8hpp.html\n--rw-r--r-- 0 root (0) root (0) 13841 2025-09-09 09:29:41.000000 ./usr/share/doc/libseqan3-dev/html/validate__char__for_8hpp_source.html\n+-rw-r--r-- 0 root (0) root (0) 14490 2025-09-09 09:29:41.000000 ./usr/share/doc/libseqan3-dev/html/validate__char__for_8hpp_source.html\n -rw-r--r-- 0 root (0) root (0) 6310 2025-09-09 09:29:41.000000 ./usr/share/doc/libseqan3-dev/html/validators_8hpp.html\n--rw-r--r-- 0 root (0) root (0) 201888 2025-09-09 09:29:41.000000 ./usr/share/doc/libseqan3-dev/html/validators_8hpp_source.html\n+-rw-r--r-- 0 root (0) root (0) 211837 2025-09-09 09:29:41.000000 ./usr/share/doc/libseqan3-dev/html/validators_8hpp_source.html\n -rw-r--r-- 0 root (0) root (0) 6388 2025-09-09 09:29:41.000000 ./usr/share/doc/libseqan3-dev/html/variant_8hpp.html\n--rw-r--r-- 0 root (0) root (0) 14945 2025-09-09 09:29:41.000000 ./usr/share/doc/libseqan3-dev/html/variant_8hpp_source.html\n+-rw-r--r-- 0 root (0) root (0) 15822 2025-09-09 09:29:41.000000 ./usr/share/doc/libseqan3-dev/html/variant_8hpp_source.html\n -rw-r--r-- 0 root (0) root (0) 2765 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./usr/share/doc-base/seqan3-doc.seqan-doc\n"}, {"source1": "./usr/share/doc/libseqan3-dev/html/aa10li_8hpp_source.html", "source2": "./usr/share/doc/libseqan3-dev/html/aa10li_8hpp_source.html", "unified_diff": "@@ -140,36 +140,36 @@\n
17
\n
18namespace seqan3
\n
19{
\n
\n
79class aa10li : public aminoacid_base<aa10li, 10>
\n
80{
\n
81private:
\n-
83 using base_t = aminoacid_base<aa10li, 10>;
\n+
83 using base_t = aminoacid_base<aa10li, 10>;
\n
84
\n
86 friend base_t;
\n
89 friend base_t::base_t;
\n
91
\n
92public:
\n-
96 constexpr aa10li() noexcept = default;
\n-
97 constexpr aa10li(aa10li const &) noexcept = default;
\n-
98 constexpr aa10li(aa10li &&) noexcept = default;
\n-
99 constexpr aa10li & operator=(aa10li const &) noexcept = default;
\n-
100 constexpr aa10li & operator=(aa10li &&) noexcept = default;
\n-
101 ~aa10li() noexcept = default;
\n+
96 constexpr aa10li() noexcept = default;
\n+
97 constexpr aa10li(aa10li const &) noexcept = default;
\n+
98 constexpr aa10li(aa10li &&) noexcept = default;
\n+
99 constexpr aa10li & operator=(aa10li const &) noexcept = default;
\n+
100 constexpr aa10li & operator=(aa10li &&) noexcept = default;
\n+
101 ~aa10li() noexcept = default;
\n
102
\n-
104 using base_t::base_t;
\n+
104 using base_t::base_t;
\n
106
\n-
107private:
\n-
109 static constexpr char_type rank_to_char_table[alphabet_size]{'A', 'B', 'C', 'F', 'G', 'H', 'I', 'J', 'K', 'P'};
\n+
107private:
\n+
109 static constexpr char_type rank_to_char_table[alphabet_size]{'A', 'B', 'C', 'F', 'G', 'H', 'I', 'J', 'K', 'P'};
\n
110
\n-
112 static constexpr rank_type char_to_rank(char_type const chr)
\n+
112 static constexpr rank_type char_to_rank(char_type const chr)
\n
113 {
\n
114 using index_t = std::make_unsigned_t<char_type>;
\n-
115 return char_to_rank_table[static_cast<index_t>(chr)];
\n+
115 return char_to_rank_table[static_cast<index_t>(chr)];
\n
116 }
\n
117
\n
119 static constexpr char_type rank_to_char(rank_type const rank)
\n
120 {
\n
121 return rank_to_char_table[rank];
\n
122 }
\n
123
\n@@ -236,28 +236,28 @@\n
189
\n
190// ------------------------------------------------------------------
\n
191// literals
\n
192// ------------------------------------------------------------------
\n
193inline namespace literals
\n
194{
\n
195
\n-
209constexpr aa10li operator""_aa10li(char const c) noexcept
\n+
209constexpr aa10li operator""_aa10li(char const c) noexcept
\n
210{
\n-
211 return aa10li{}.assign_char(c);
\n+
211 return aa10li{}.assign_char(c);
\n
212}
\n
213
\n-
225SEQAN3_WORKAROUND_LITERAL aa10li_vector operator""_aa10li(char const * const s, size_t const n)
\n+
225SEQAN3_WORKAROUND_LITERAL aa10li_vector operator""_aa10li(char const * const s, size_t const n)
\n
226{
\n-
227 aa10li_vector r;
\n-
228 r.resize(n);
\n+
227 aa10li_vector r;
\n+
228 r.resize(n);
\n
229
\n-
230 for (size_t i = 0; i < n; ++i)
\n-
231 r[i].assign_char(s[i]);
\n+
230 for (size_t i = 0; i < n; ++i)
\n+
231 r[i].assign_char(s[i]);
\n
232
\n-
233 return r;
\n+
233 return r;
\n
234}
\n
236
\n
237} // namespace literals
\n
238
\n
239} // namespace seqan3
\n
concept.hpp
Provides seqan3::aminoacid_alphabet.
\n
aminoacid_base.hpp
Provides seqan3::aminoacid_base.
\n@@ -266,21 +266,21 @@\n
seqan3::aa10li::aa10li
constexpr aa10li() noexcept=default
Defaulted.
\n
seqan3::alphabet_base< aa10li, size, char >
\n
seqan3::alphabet_base::assign_char
constexpr derived_type & assign_char(char_type const chr) noexcept
Assign from a character, implicitly converts invalid characters.
Definition alphabet_base.hpp:160
\n
seqan3::alphabet_base::rank_type
detail::min_viable_uint_t< size - 1 > rank_type
The type of the alphabet when represented as a number (e.g. via to_rank()).
Definition alphabet_base.hpp:77
\n
seqan3::alphabet_base::alphabet_size
static constexpr detail::min_viable_uint_t< size > alphabet_size
The size of the alphabet, i.e. the number of different values it can take.
Definition alphabet_base.hpp:196
\n
seqan3::alphabet_base::char_type
std::conditional_t< std::same_as< char_t, void >, char, char_t > char_type
The char representation; conditional needed to make semi alphabet definitions legal.
Definition alphabet_base.hpp:69
\n
seqan3::aminoacid_base
A CRTP-base that refines seqan3::alphabet_base and is used by the amino acids.
Definition aminoacid_base.hpp:30
\n+
seqan3::debug_stream_type
A "pretty printer" for most SeqAn data structures and related types.
Definition debug_stream_type.hpp:79
\n \n
std::array::fill
T fill(T... args)
\n \n
seqan3
The main SeqAn3 namespace.
Definition aligned_sequence_concept.hpp:26
\n
seqan3::to_lower
constexpr char_type to_lower(char_type const c) noexcept
Converts 'A'-'Z' to 'a'-'z' respectively; other characters are returned as is.
Definition transform.hpp:74
\n
SEQAN3_WORKAROUND_LITERAL
#define SEQAN3_WORKAROUND_LITERAL
Our char literals returning std::vector should be constexpr if constexpr std::vector is supported.
Definition platform.hpp:310
\n-
std::vector::resize
T resize(T... args)
\n
transform.hpp
Provides utilities for modifying characters.
\n \n
\n \n \n \n \n \n \n \n \n
\n

Table of Contents

\n \n
\n

SeqAn3 adheres to semantic versioning and provides a stable API within one major release (all of seqan-3.*.*) unless otherwise noted.

\n

There is no ABI stability.

\n

Many of the rules on this page are derived from the abseil library.

\n

\n API stability

\n@@ -153,15 +153,15 @@\n

In the very rare case that we feel a breaking change to the API is unavoidable, we promise to provide the following update path:

    \n
  • A new minor version is introduced that supports the new API.
    • \n
  • The old API is still supported, but might be marked [[deprecated]].
    • \n
  • We provide very extensive documentation on the change or an automated tool that converts your code from using the old API to using the new API.
    • \n
  • The next (or another future) minor version removes the old API.
    • \n
\n
Warning
As a special case of point 2, the entire 3.0.* release is not stable. We will do our best not to break things, but similar to the releases of GCC, we start labelling entities as stable starting from seqan-3.1.0. Please refer to the documentation of the individual entities for their stability status.
\n-

\n+

\n ABI stability

\n

No guarantees of any kind are provided in regard to the in-memory representation of our data structures. We intend for SeqAn to be built from source. The internal layout of our types may change at any point, without notice. In particular, building SeqAn in the presence of different C++ standard library types may change SeqAn types, especially for pre-adopted types in the std module \u2014 these will resolve to standard library types as of C++20.

\n

We do promise, however, that SeqAn3 data structures\u00b9 serialised to disk are de-serialisable by later versions of SeqAn3. The reverse is not true, however, and re-serialising a data structure serialised by a previous release might result in a different (updated) on-disk format.

\n

\u00b9 Iff they are API stable.

\n

\n Platform stability

\n

The main requirement for SeqAn3 is that your operating system provides one of the compilers supported by us. In general, we only support the latest three major compiler versions. We currently support the following compilers on 64-bit operating systems with little-endian CPU architectures:

    \n@@ -191,15 +191,15 @@\n \n FreeBSD the latest stable release \n \n

    \"Support\" in this context does not imply that we package SeqAn for these operating systems (although we do in some cases), it merely states that you should be able to build applications that depend on SeqAn on the given platforms. This implies the availability of a supported compiler in the default package repositories or via easy-to-use third party services.

    \n

    More platforms and compilers will be added during the SeqAn3 lifecycle, but some will be marked as experimentally supported which means support may be dropped again later on.

    \n

    We promise to provide good forward-compatibility with the C++ standard. And we will strive to fix any warnings that are added by newer versions of a supported compiler.

    \n

    \u00b9 We consider CentOS 7 / RedHat Enterprise Linux (RHEL) 7 as being community-supported. That means issues and patches are welcome, but we do not actively test for those operating systems. See this related issue.

    \n-

    \n+

    \n Dependencies

    \n

    We may add additional dependencies in future minor releases of SeqAn or raise the required versions of current dependencies. However, we promise not to add required dependencies that result in new licensing obligations or link-time dependencies.

    \n
\n \n \n \n
\n

Table of Contents

\n-
\n

SeqAn is a research project and depends strongly on being correctly attributed. Please always cite the correct research papers when you develop software based on SeqAn. This will help us continue to acquire funding and improve the library.

\n-

\n+

\n Publications

\n

SeqAn3 has not yet been published academically, for now cite SeqAn2:

\n \n \n \n \n \n@@ -143,15 +143,15 @@\n \n \n \n \n \n
Publication
Title The SeqAn C++ template library for efficient sequence analysis: A resource for programmers.
Authors Reinert, K., Dadi, T. H., Ehrhardt, M., Hauswedell, H., Mehringer, S., Rahn, R., ... & Urgese, G.
Journal Journal of biotechnology, 261, 157-168
Links original
\n

Certain compontents of SeqAn are published separately. If you make strong use of one of those compononts and/or specifically compare to that component, please cite the respective publication additionally.

\n-

\n+

\n Alignment module

\n \n \n \n \n \n \n@@ -160,15 +160,15 @@\n \n \n \n \n \n
Publication
Title Generic accelerated sequence alignment in SeqAn using vectorization and multi-threading.
Authors Rahn, R., Budach, S., Costanza, P., Ehrhardt, M., Hancox, J., & Reinert, K
Journal Bioinformatics, 34(20), 3437-3445
Links original
\n

Cite the above publication when you make strong use of the alignment module, in particular if you rely on the high-performance computing capabilities.

\n-

\n+

\n Search module

\n \n \n \n \n \n \n"}, {"source1": "./usr/share/doc/libseqan3-dev/html/advanceable__alignment__coordinate_8hpp_source.html", "source2": "./usr/share/doc/libseqan3-dev/html/advanceable__alignment__coordinate_8hpp_source.html", "unified_diff": "@@ -321,23 +321,24 @@\n
296
\n
304template <auto state_t>
\n
\n
305struct advanceable_alignment_coordinate_printer<detail::advanceable_alignment_coordinate<state_t>>
\n
306{
\n
312 template <typename stream_t>
\n
\n-
313 constexpr void operator()(stream_t & stream, detail::advanceable_alignment_coordinate<state_t> const arg) const
\n+
313 constexpr void operator()(stream_t & stream, detail::advanceable_alignment_coordinate<state_t> const arg) const
\n
314 {
\n-
315 stream << std::tie(arg.first, arg.second);
\n+
315 stream << std::tie(arg.first, arg.second);
\n
316 }
\n
\n
317};
\n
\n
318
\n
319} // namespace seqan3
\n+
seqan3::debug_stream_type
A "pretty printer" for most SeqAn data structures and related types.
Definition debug_stream_type.hpp:79
\n
debug_stream_type.hpp
Provides seqan3::debug_stream and related types.
\n
seqan3::field::offset
@ offset
Sequence (seqan3::field::seq) relative start position (0-based), unsigned value.
\n \n \n
matrix_coordinate.hpp
Provides seqan3::detail::matrix_index, seqan3::detail::matrix_coordinate and associated strong types.
\n
seqan3
The main SeqAn3 namespace.
Definition aligned_sequence_concept.hpp:26
\n
std::rel_ops::operator!=
T operator!=(T... args)
\n", "details": [{"source1": "html2text {}", "source2": "html2text {}", "unified_diff": "@@ -224,22 +224,25 @@\n 295{\n 296\n 304template \n _\b3_\b0_\b5struct _\ba_\bd_\bv_\ba_\bn_\bc_\be_\ba_\bb_\bl_\be_\b__\ba_\bl_\bi_\bg_\bn_\bm_\be_\bn_\bt_\b__\bc_\bo_\bo_\br_\bd_\bi_\bn_\ba_\bt_\be_\b__\bp_\br_\bi_\bn_\bt_\be_\br>\n 306{\n 312 template \n-_\b3_\b1_\b3 constexpr void _\bo_\bp_\be_\br_\ba_\bt_\bo_\br_\b(_\b)(stream_t & stream, detail::\n-advanceable_alignment_coordinate const arg) const\n+_\b3_\b1_\b3 constexpr void _\bo_\bp_\be_\br_\ba_\bt_\bo_\br_\b(_\b)(_\bs_\bt_\br_\be_\ba_\bm_\b__\bt & stream, detail::\n+advanceable_alignment_coordinate const _\ba_\br_\bg) const\n 314 {\n-315 stream << _\bs_\bt_\bd_\b:_\b:_\bt_\bi_\be(arg.first, arg.second);\n+315 stream << _\bs_\bt_\bd_\b:_\b:_\bt_\bi_\be(_\ba_\br_\bg.first, _\ba_\br_\bg.second);\n 316 }\n 317};\n 318\n 319} // namespace seqan3\n+_\bs_\be_\bq_\ba_\bn_\b3_\b:_\b:_\bd_\be_\bb_\bu_\bg_\b__\bs_\bt_\br_\be_\ba_\bm_\b__\bt_\by_\bp_\be\n+A \"pretty printer\" for most SeqAn data structures and related types.\n+D\bDe\bef\bfi\bin\bni\bit\bti\bio\bon\bn debug_stream_type.hpp:79\n _\bd_\be_\bb_\bu_\bg_\b__\bs_\bt_\br_\be_\ba_\bm_\b__\bt_\by_\bp_\be_\b._\bh_\bp_\bp\n Provides seqan3::debug_stream and related types.\n _\bs_\be_\bq_\ba_\bn_\b3_\b:_\b:_\bf_\bi_\be_\bl_\bd_\b:_\b:_\bo_\bf_\bf_\bs_\be_\bt\n @ offset\n Sequence (seqan3::field::seq) relative start position (0-based), unsigned\n value.\n _\bi_\bt_\be_\br_\ba_\bt_\bo_\br\n"}]}, {"source1": "./usr/share/doc/libseqan3-dev/html/algorithm__result__generator__range_8hpp_source.html", "source2": "./usr/share/doc/libseqan3-dev/html/algorithm__result__generator__range_8hpp_source.html", "unified_diff": "@@ -160,151 +160,151 @@\n
63 algorithm_result_generator_range(algorithm_result_generator_range const &) = delete;
\n
64 algorithm_result_generator_range(algorithm_result_generator_range &&) = default;
\n
65 algorithm_result_generator_range &
\n
66 operator=(algorithm_result_generator_range const &) = delete;
\n
67 algorithm_result_generator_range & operator=(algorithm_result_generator_range &&) = default;
\n
68 ~algorithm_result_generator_range() = default;
\n
69
\n-
71 explicit algorithm_result_generator_range(algorithm_executor_type const & algorithm_executor) = delete;
\n+
71 explicit algorithm_result_generator_range(algorithm_executor_type const & algorithm_executor) = delete;
\n
72
\n-
81 SEQAN3_WORKAROUND_GCC_BOGUS_MEMCPY_START(-Warray-bounds)
\n+
81 SEQAN3_WORKAROUND_GCC_BOGUS_MEMCPY_START(-Warray-bounds)
\n
\n-
82 explicit algorithm_result_generator_range(algorithm_executor_type && algorithm_executor) :
\n-
83 algorithm_executor_ptr{std::make_unique<algorithm_executor_type>(std::move(algorithm_executor))}
\n+
82 explicit algorithm_result_generator_range(algorithm_executor_type && algorithm_executor) :
\n+
83 algorithm_executor_ptr{std::make_unique<algorithm_executor_type>(std::move(algorithm_executor))}
\n
84 {}
\n
\n
85 SEQAN3_WORKAROUND_GCC_BOGUS_MEMCPY_STOP
\n
87
\n
\n
99 constexpr algorithm_range_iterator begin()
\n
100 {
\n
101 return algorithm_range_iterator{*this};
\n
102 }
\n
\n
103
\n
105 algorithm_range_iterator begin() const = delete;
\n
106
\n
\n-
115 constexpr std::default_sentinel_t end() noexcept
\n+
115 constexpr std::default_sentinel_t end() noexcept
\n
116 {
\n
117 return std::default_sentinel;
\n
118 }
\n
\n
119
\n
121 constexpr std::default_sentinel_t end() const = delete;
\n
123
\n
124protected:
\n
\n
133 bool next()
\n
134 {
\n
135 if (!algorithm_executor_ptr)
\n
136 throw std::runtime_error{"No algorithm execution buffer available."};
\n
137
\n-
138 if (auto opt = algorithm_executor_ptr->next_result(); opt.has_value())
\n+
138 if (auto opt = algorithm_executor_ptr->next_result(); opt.has_value())
\n
139 {
\n-
140 cache = std::move(*opt);
\n+
140 cache = std::move(*opt);
\n
141 return true;
\n
142 }
\n
143
\n
144 return false;
\n
145 }
\n
\n
146
\n
147private:
\n
149 std::unique_ptr<algorithm_executor_type> algorithm_executor_ptr{};
\n
151 algorithm_result_type cache{};
\n
152};
\n \n
153
\n
160template <typename algorithm_executor_type>
\n-
161algorithm_result_generator_range(algorithm_executor_type &&)
\n-
162 -> algorithm_result_generator_range<std::remove_reference_t<algorithm_executor_type>>;
\n+
161algorithm_result_generator_range(algorithm_executor_type &&)
\n+
162 -> algorithm_result_generator_range<std::remove_reference_t<algorithm_executor_type>>;
\n
164
\n
168template <typename algorithm_executor_type>
\n
\n-
169class algorithm_result_generator_range<algorithm_executor_type>::algorithm_range_iterator
\n+
169class algorithm_result_generator_range<algorithm_executor_type>::algorithm_range_iterator
\n
170{
\n
171public:
\n
176 using difference_type = std::ptrdiff_t;
\n
178 using value_type = algorithm_result_type;
\n
180 using reference = std::add_lvalue_reference_t<value_type>;
\n
182 using pointer = std::add_pointer_t<value_type>;
\n
184 using iterator_category = std::input_iterator_tag;
\n
186
\n-
190 constexpr algorithm_range_iterator() noexcept = default;
\n-
191 constexpr algorithm_range_iterator(algorithm_range_iterator const &) noexcept = default;
\n-
192 constexpr algorithm_range_iterator(algorithm_range_iterator &&) noexcept = default;
\n-
193 constexpr algorithm_range_iterator & operator=(algorithm_range_iterator const &) noexcept = default;
\n-
194 constexpr algorithm_range_iterator & operator=(algorithm_range_iterator &&) noexcept = default;
\n-
195 ~algorithm_range_iterator() = default;
\n+
190 constexpr algorithm_range_iterator() noexcept = default;
\n+
191 constexpr algorithm_range_iterator(algorithm_range_iterator const &) noexcept = default;
\n+
192 constexpr algorithm_range_iterator(algorithm_range_iterator &&) noexcept = default;
\n+
193 constexpr algorithm_range_iterator & operator=(algorithm_range_iterator const &) noexcept = default;
\n+
194 constexpr algorithm_range_iterator & operator=(algorithm_range_iterator &&) noexcept = default;
\n+
195 ~algorithm_range_iterator() = default;
\n
196
\n
\n-
198 explicit constexpr algorithm_range_iterator(algorithm_result_generator_range & range) :
\n-
199 range_ptr(std::addressof(range))
\n+
198 explicit constexpr algorithm_range_iterator(algorithm_result_generator_range & range) :
\n+
199 range_ptr(std::addressof(range))
\n
200 {
\n
201 ++(*this); // Fetch the next element.
\n
202 }
\n
\n
204
\n
\n-
213 reference operator*() const noexcept
\n+
213 reference operator*() const noexcept
\n
214 {
\n
215 return range_ptr->cache;
\n
216 }
\n
\n
217
\n
\n-
219 pointer operator->() const noexcept
\n+
219 pointer operator->() const noexcept
\n
220 {
\n
221 return &range_ptr->cache;
\n
222 }
\n
\n
224
\n
\n
229 algorithm_range_iterator & operator++(/*pre*/)
\n
230 {
\n-
231 assert(range_ptr != nullptr);
\n+
231 assert(range_ptr != nullptr);
\n
232
\n
233 at_end = !range_ptr->next();
\n
234 return *this;
\n
235 }
\n
\n
236
\n
\n
238 void operator++(int /*post*/)
\n
239 {
\n
240 ++(*this);
\n
241 }
\n
\n
243
\n
\n-
248 friend constexpr bool operator==(algorithm_range_iterator const & lhs, std::default_sentinel_t const &) noexcept
\n+
248 friend constexpr bool operator==(algorithm_range_iterator const & lhs, std::default_sentinel_t const &) noexcept
\n
249 {
\n-
250 return lhs.at_end;
\n+
250 return lhs.at_end;
\n
251 }
\n
\n
252
\n
\n-
254 friend constexpr bool operator==(std::default_sentinel_t const & lhs, algorithm_range_iterator const & rhs) noexcept
\n+
254 friend constexpr bool operator==(std::default_sentinel_t const & lhs, algorithm_range_iterator const & rhs) noexcept
\n
255 {
\n-
256 return rhs == lhs;
\n+
256 return rhs == lhs;
\n
257 }
\n
\n
258
\n
\n-
260 friend constexpr bool operator!=(algorithm_range_iterator const & lhs, std::default_sentinel_t const & rhs) noexcept
\n+
260 friend constexpr bool operator!=(algorithm_range_iterator const & lhs, std::default_sentinel_t const & rhs) noexcept
\n
261 {
\n-
262 return !(lhs == rhs);
\n+
262 return !(lhs == rhs);
\n
263 }
\n
\n
264
\n
\n-
266 friend constexpr bool operator!=(std::default_sentinel_t const & lhs, algorithm_range_iterator const & rhs) noexcept
\n+
266 friend constexpr bool operator!=(std::default_sentinel_t const & lhs, algorithm_range_iterator const & rhs) noexcept
\n
267 {
\n-
268 return rhs != lhs;
\n+
268 return rhs != lhs;
\n
269 }
\n
\n
271
\n
272private:
\n
274 algorithm_result_generator_range * range_ptr{};
\n
276 bool at_end{true};
\n
277};
\n@@ -335,14 +335,15 @@\n
seqan3::algorithm_result_generator_range::operator=
algorithm_result_generator_range & operator=(algorithm_result_generator_range const &)=delete
This is a move-only type.
\n
seqan3::algorithm_result_generator_range::next
bool next()
Receives the next algorithm result from the executor buffer.
Definition algorithm_result_generator_range.hpp:133
\n
seqan3::algorithm_result_generator_range::begin
algorithm_range_iterator begin() const =delete
This range is not const-iterable.
\n
seqan3::algorithm_result_generator_range::algorithm_result_generator_range
algorithm_result_generator_range()=default
Defaulted.
\n
seqan3::algorithm_result_generator_range::begin
constexpr algorithm_range_iterator begin()
Returns an iterator to the first element of the algorithm range.
Definition algorithm_result_generator_range.hpp:99
\n
seqan3::algorithm_result_generator_range::algorithm_result_generator_range
algorithm_result_generator_range(algorithm_executor_type &&) -> algorithm_result_generator_range< std::remove_reference_t< algorithm_executor_type > >
Deduces from the passed algorithm_executor_type.
\n
seqan3::algorithm_result_generator_range::~algorithm_result_generator_range
~algorithm_result_generator_range()=default
Defaulted.
\n+
seqan3::debug_stream_type
A "pretty printer" for most SeqAn data structures and related types.
Definition debug_stream_type.hpp:79
\n \n \n
seqan3
The main SeqAn3 namespace.
Definition aligned_sequence_concept.hpp:26
\n
std
SeqAn specific customisations in the standard namespace.
\n
platform.hpp
Provides platform and dependency checks.
\n
SEQAN3_WORKAROUND_GCC_BOGUS_MEMCPY_START
#define SEQAN3_WORKAROUND_GCC_BOGUS_MEMCPY_START(...)
Denotes the start of a block where diagnostics are ignored.
Definition platform.hpp:268
\n
SEQAN3_WORKAROUND_GCC_BOGUS_MEMCPY_STOP
#define SEQAN3_WORKAROUND_GCC_BOGUS_MEMCPY_STOP
Denotes the end of a block where diagnostics are ignored.
Definition platform.hpp:277
\n", "details": [{"source1": "html2text {}", "source2": "html2text {}", "unified_diff": "@@ -44,138 +44,138 @@\n default;\n 65 _\ba_\bl_\bg_\bo_\br_\bi_\bt_\bh_\bm_\b__\br_\be_\bs_\bu_\bl_\bt_\b__\bg_\be_\bn_\be_\br_\ba_\bt_\bo_\br_\b__\br_\ba_\bn_\bg_\be &\n _\b6_\b6 _\bo_\bp_\be_\br_\ba_\bt_\bo_\br_\b=(_\ba_\bl_\bg_\bo_\br_\bi_\bt_\bh_\bm_\b__\br_\be_\bs_\bu_\bl_\bt_\b__\bg_\be_\bn_\be_\br_\ba_\bt_\bo_\br_\b__\br_\ba_\bn_\bg_\be const &) = delete;\n _\b6_\b7 _\ba_\bl_\bg_\bo_\br_\bi_\bt_\bh_\bm_\b__\br_\be_\bs_\bu_\bl_\bt_\b__\bg_\be_\bn_\be_\br_\ba_\bt_\bo_\br_\b__\br_\ba_\bn_\bg_\be & _\bo_\bp_\be_\br_\ba_\bt_\bo_\br_\b=\n (_\ba_\bl_\bg_\bo_\br_\bi_\bt_\bh_\bm_\b__\br_\be_\bs_\bu_\bl_\bt_\b__\bg_\be_\bn_\be_\br_\ba_\bt_\bo_\br_\b__\br_\ba_\bn_\bg_\be &&) = default;\n _\b6_\b8 _\b~_\ba_\bl_\bg_\bo_\br_\bi_\bt_\bh_\bm_\b__\br_\be_\bs_\bu_\bl_\bt_\b__\bg_\be_\bn_\be_\br_\ba_\bt_\bo_\br_\b__\br_\ba_\bn_\bg_\be() = default;\n 69\n-_\b7_\b1 explicit _\ba_\bl_\bg_\bo_\br_\bi_\bt_\bh_\bm_\b__\br_\be_\bs_\bu_\bl_\bt_\b__\bg_\be_\bn_\be_\br_\ba_\bt_\bo_\br_\b__\br_\ba_\bn_\bg_\be(algorithm_executor_type const &\n-algorithm_executor) = delete;\n+_\b7_\b1 explicit _\ba_\bl_\bg_\bo_\br_\bi_\bt_\bh_\bm_\b__\br_\be_\bs_\bu_\bl_\bt_\b__\bg_\be_\bn_\be_\br_\ba_\bt_\bo_\br_\b__\br_\ba_\bn_\bg_\be(_\ba_\bl_\bg_\bo_\br_\bi_\bt_\bh_\bm_\b__\be_\bx_\be_\bc_\bu_\bt_\bo_\br_\b__\bt_\by_\bp_\be const &\n+_\ba_\bl_\bg_\bo_\br_\bi_\bt_\bh_\bm_\b__\be_\bx_\be_\bc_\bu_\bt_\bo_\br) = delete;\n 72\n-81 _\bS_\bE_\bQ_\bA_\bN_\b3_\b__\bW_\bO_\bR_\bK_\bA_\bR_\bO_\bU_\bN_\bD_\b__\bG_\bC_\bC_\b__\bB_\bO_\bG_\bU_\bS_\b__\bM_\bE_\bM_\bC_\bP_\bY_\b__\bS_\bT_\bA_\bR_\bT(-Warray-bounds)\n-_\b8_\b2 explicit _\ba_\bl_\bg_\bo_\br_\bi_\bt_\bh_\bm_\b__\br_\be_\bs_\bu_\bl_\bt_\b__\bg_\be_\bn_\be_\br_\ba_\bt_\bo_\br_\b__\br_\ba_\bn_\bg_\be(algorithm_executor_type &&\n-algorithm_executor) :\n+81 _\bS_\bE_\bQ_\bA_\bN_\b3_\b__\bW_\bO_\bR_\bK_\bA_\bR_\bO_\bU_\bN_\bD_\b__\bG_\bC_\bC_\b__\bB_\bO_\bG_\bU_\bS_\b__\bM_\bE_\bM_\bC_\bP_\bY_\b__\bS_\bT_\bA_\bR_\bT(-_\bW_\ba_\br_\br_\ba_\by-_\bb_\bo_\bu_\bn_\bd_\bs)\n+_\b8_\b2 _\be_\bx_\bp_\bl_\bi_\bc_\bi_\bt _\ba_\bl_\bg_\bo_\br_\bi_\bt_\bh_\bm_\b__\br_\be_\bs_\bu_\bl_\bt_\b__\bg_\be_\bn_\be_\br_\ba_\bt_\bo_\br_\b__\br_\ba_\bn_\bg_\be(_\ba_\bl_\bg_\bo_\br_\bi_\bt_\bh_\bm_\b__\be_\bx_\be_\bc_\bu_\bt_\bo_\br_\b__\bt_\by_\bp_\be &&\n+_\ba_\bl_\bg_\bo_\br_\bi_\bt_\bh_\bm_\b__\be_\bx_\be_\bc_\bu_\bt_\bo_\br) :\n 83 algorithm_executor_ptr{std::make_unique(std::move\n-(algorithm_executor))}\n+(_\ba_\bl_\bg_\bo_\br_\bi_\bt_\bh_\bm_\b__\be_\bx_\be_\bc_\bu_\bt_\bo_\br))}\n 84 {}\n 85 _\bS_\bE_\bQ_\bA_\bN_\b3_\b__\bW_\bO_\bR_\bK_\bA_\bR_\bO_\bU_\bN_\bD_\b__\bG_\bC_\bC_\b__\bB_\bO_\bG_\bU_\bS_\b__\bM_\bE_\bM_\bC_\bP_\bY_\b__\bS_\bT_\bO_\bP\n 87\n _\b9_\b9 constexpr _\ba_\bl_\bg_\bo_\br_\bi_\bt_\bh_\bm_\b__\br_\ba_\bn_\bg_\be_\b__\bi_\bt_\be_\br_\ba_\bt_\bo_\br _\bb_\be_\bg_\bi_\bn()\n 100 {\n 101 return _\ba_\bl_\bg_\bo_\br_\bi_\bt_\bh_\bm_\b__\br_\ba_\bn_\bg_\be_\b__\bi_\bt_\be_\br_\ba_\bt_\bo_\br{*this};\n 102 }\n 103\n _\b1_\b0_\b5 _\ba_\bl_\bg_\bo_\br_\bi_\bt_\bh_\bm_\b__\br_\ba_\bn_\bg_\be_\b__\bi_\bt_\be_\br_\ba_\bt_\bo_\br _\bb_\be_\bg_\bi_\bn() const = delete;\n 106\n-_\b1_\b1_\b5 constexpr std::default_sentinel_t _\be_\bn_\bd() noexcept\n+_\b1_\b1_\b5 constexpr std::default_sentinel_t _\be_\bn_\bd() _\bn_\bo_\be_\bx_\bc_\be_\bp_\bt\n 116 {\n 117 return std::default_sentinel;\n 118 }\n 119\n _\b1_\b2_\b1 constexpr std::default_sentinel_t _\be_\bn_\bd() const = delete;\n 123\n 124protected:\n _\b1_\b3_\b3 bool _\bn_\be_\bx_\bt()\n 134 {\n 135 if (!algorithm_executor_ptr)\n 136 throw _\bs_\bt_\bd_\b:_\b:_\br_\bu_\bn_\bt_\bi_\bm_\be_\b__\be_\br_\br_\bo_\br{\"No algorithm execution buffer available.\"};\n 137\n-138 if (auto opt = algorithm_executor_ptr->next_result(); opt.has_value())\n+138 if (auto _\bo_\bp_\bt = algorithm_executor_ptr->next_result(); _\bo_\bp_\bt.has_value())\n 139 {\n-140 cache = std::move(*opt);\n+140 cache = std::move(*_\bo_\bp_\bt);\n 141 return true;\n 142 }\n 143\n 144 return false;\n 145 }\n 146\n 147private:\n 149 _\bs_\bt_\bd_\b:_\b:_\bu_\bn_\bi_\bq_\bu_\be_\b__\bp_\bt_\br_\b<_\ba_\bl_\bg_\bo_\br_\bi_\bt_\bh_\bm_\b__\be_\bx_\be_\bc_\bu_\bt_\bo_\br_\b__\bt_\by_\bp_\be_\b> algorithm_executor_ptr{};\n 151 algorithm_result_type cache{};\n 152};\n 153\n 160template \n-_\b1_\b6_\b1_\ba_\bl_\bg_\bo_\br_\bi_\bt_\bh_\bm_\b__\br_\be_\bs_\bu_\bl_\bt_\b__\bg_\be_\bn_\be_\br_\ba_\bt_\bo_\br_\b__\br_\ba_\bn_\bg_\be(algorithm_executor_type &&)\n+_\b1_\b6_\b1_\ba_\bl_\bg_\bo_\br_\bi_\bt_\bh_\bm_\b__\br_\be_\bs_\bu_\bl_\bt_\b__\bg_\be_\bn_\be_\br_\ba_\bt_\bo_\br_\b__\br_\ba_\bn_\bg_\be(_\ba_\bl_\bg_\bo_\br_\bi_\bt_\bh_\bm_\b__\be_\bx_\be_\bc_\bu_\bt_\bo_\br_\b__\bt_\by_\bp_\be &&)\n 162 -> _\ba_\bl_\bg_\bo_\br_\bi_\bt_\bh_\bm_\b__\br_\be_\bs_\bu_\bl_\bt_\b__\bg_\be_\bn_\be_\br_\ba_\bt_\bo_\br_\b__\br_\ba_\bn_\bg_\be_\b<_\bs_\bt_\bd_\b:_\b:\n _\br_\be_\bm_\bo_\bv_\be_\b__\br_\be_\bf_\be_\br_\be_\bn_\bc_\be_\b__\bt_\b<_\ba_\bl_\bg_\bo_\br_\bi_\bt_\bh_\bm_\b__\be_\bx_\be_\bc_\bu_\bt_\bo_\br_\b__\bt_\by_\bp_\be_\b>>;\n 164\n 168template \n-_\b1_\b6_\b9class _\ba_\bl_\bg_\bo_\br_\bi_\bt_\bh_\bm_\b__\br_\be_\bs_\bu_\bl_\bt_\b__\bg_\be_\bn_\be_\br_\ba_\bt_\bo_\br_\b__\br_\ba_\bn_\bg_\be::\n+_\b1_\b6_\b9class _\ba_\bl_\bg_\bo_\br_\bi_\bt_\bh_\bm_\b__\br_\be_\bs_\bu_\bl_\bt_\b__\bg_\be_\bn_\be_\br_\ba_\bt_\bo_\br_\b__\br_\ba_\bn_\bg_\be<_\ba_\bl_\bg_\bo_\br_\bi_\bt_\bh_\bm_\b__\be_\bx_\be_\bc_\bu_\bt_\bo_\br_\b__\bt_\by_\bp_\be>::\n _\ba_\bl_\bg_\bo_\br_\bi_\bt_\bh_\bm_\b__\br_\ba_\bn_\bg_\be_\b__\bi_\bt_\be_\br_\ba_\bt_\bo_\br\n 170{\n 171public:\n _\b1_\b7_\b6 using _\bd_\bi_\bf_\bf_\be_\br_\be_\bn_\bc_\be_\b__\bt_\by_\bp_\be = _\bs_\bt_\bd_\b:_\b:_\bp_\bt_\br_\bd_\bi_\bf_\bf_\b__\bt;\n _\b1_\b7_\b8 using _\bv_\ba_\bl_\bu_\be_\b__\bt_\by_\bp_\be = algorithm_result_type;\n _\b1_\b8_\b0 using _\br_\be_\bf_\be_\br_\be_\bn_\bc_\be = _\bs_\bt_\bd_\b:_\b:_\ba_\bd_\bd_\b__\bl_\bv_\ba_\bl_\bu_\be_\b__\br_\be_\bf_\be_\br_\be_\bn_\bc_\be_\b__\bt_\b<_\bv_\ba_\bl_\bu_\be_\b__\bt_\by_\bp_\be_\b>;\n _\b1_\b8_\b2 using _\bp_\bo_\bi_\bn_\bt_\be_\br = _\bs_\bt_\bd_\b:_\b:_\ba_\bd_\bd_\b__\bp_\bo_\bi_\bn_\bt_\be_\br_\b__\bt_\b<_\bv_\ba_\bl_\bu_\be_\b__\bt_\by_\bp_\be_\b>;\n _\b1_\b8_\b4 using _\bi_\bt_\be_\br_\ba_\bt_\bo_\br_\b__\bc_\ba_\bt_\be_\bg_\bo_\br_\by = _\bs_\bt_\bd_\b:_\b:_\bi_\bn_\bp_\bu_\bt_\b__\bi_\bt_\be_\br_\ba_\bt_\bo_\br_\b__\bt_\ba_\bg;\n 186\n-_\b1_\b9_\b0 constexpr _\ba_\bl_\bg_\bo_\br_\bi_\bt_\bh_\bm_\b__\br_\ba_\bn_\bg_\be_\b__\bi_\bt_\be_\br_\ba_\bt_\bo_\br() noexcept = default;\n-_\b1_\b9_\b1 constexpr _\ba_\bl_\bg_\bo_\br_\bi_\bt_\bh_\bm_\b__\br_\ba_\bn_\bg_\be_\b__\bi_\bt_\be_\br_\ba_\bt_\bo_\br(_\ba_\bl_\bg_\bo_\br_\bi_\bt_\bh_\bm_\b__\br_\ba_\bn_\bg_\be_\b__\bi_\bt_\be_\br_\ba_\bt_\bo_\br const &)\n-noexcept = default;\n-_\b1_\b9_\b2 constexpr _\ba_\bl_\bg_\bo_\br_\bi_\bt_\bh_\bm_\b__\br_\ba_\bn_\bg_\be_\b__\bi_\bt_\be_\br_\ba_\bt_\bo_\br(_\ba_\bl_\bg_\bo_\br_\bi_\bt_\bh_\bm_\b__\br_\ba_\bn_\bg_\be_\b__\bi_\bt_\be_\br_\ba_\bt_\bo_\br &&) noexcept =\n-default;\n-_\b1_\b9_\b3 constexpr _\ba_\bl_\bg_\bo_\br_\bi_\bt_\bh_\bm_\b__\br_\ba_\bn_\bg_\be_\b__\bi_\bt_\be_\br_\ba_\bt_\bo_\br & operator=(_\ba_\bl_\bg_\bo_\br_\bi_\bt_\bh_\bm_\b__\br_\ba_\bn_\bg_\be_\b__\bi_\bt_\be_\br_\ba_\bt_\bo_\br\n-const &) noexcept = default;\n-_\b1_\b9_\b4 constexpr _\ba_\bl_\bg_\bo_\br_\bi_\bt_\bh_\bm_\b__\br_\ba_\bn_\bg_\be_\b__\bi_\bt_\be_\br_\ba_\bt_\bo_\br & operator=(_\ba_\bl_\bg_\bo_\br_\bi_\bt_\bh_\bm_\b__\br_\ba_\bn_\bg_\be_\b__\bi_\bt_\be_\br_\ba_\bt_\bo_\br &&)\n-noexcept = default;\n-_\b1_\b9_\b5 ~_\ba_\bl_\bg_\bo_\br_\bi_\bt_\bh_\bm_\b__\br_\ba_\bn_\bg_\be_\b__\bi_\bt_\be_\br_\ba_\bt_\bo_\br() = default;\n+_\b1_\b9_\b0 constexpr _\ba_\bl_\bg_\bo_\br_\bi_\bt_\bh_\bm_\b__\br_\ba_\bn_\bg_\be_\b__\bi_\bt_\be_\br_\ba_\bt_\bo_\br() _\bn_\bo_\be_\bx_\bc_\be_\bp_\bt = _\bd_\be_\bf_\ba_\bu_\bl_\bt;\n+_\b1_\b9_\b1 _\bc_\bo_\bn_\bs_\bt_\be_\bx_\bp_\br _\ba_\bl_\bg_\bo_\br_\bi_\bt_\bh_\bm_\b__\br_\ba_\bn_\bg_\be_\b__\bi_\bt_\be_\br_\ba_\bt_\bo_\br(_\ba_\bl_\bg_\bo_\br_\bi_\bt_\bh_\bm_\b__\br_\ba_\bn_\bg_\be_\b__\bi_\bt_\be_\br_\ba_\bt_\bo_\br _\bc_\bo_\bn_\bs_\bt &)\n+_\bn_\bo_\be_\bx_\bc_\be_\bp_\bt = _\bd_\be_\bf_\ba_\bu_\bl_\bt;\n+_\b1_\b9_\b2 _\bc_\bo_\bn_\bs_\bt_\be_\bx_\bp_\br _\ba_\bl_\bg_\bo_\br_\bi_\bt_\bh_\bm_\b__\br_\ba_\bn_\bg_\be_\b__\bi_\bt_\be_\br_\ba_\bt_\bo_\br(_\ba_\bl_\bg_\bo_\br_\bi_\bt_\bh_\bm_\b__\br_\ba_\bn_\bg_\be_\b__\bi_\bt_\be_\br_\ba_\bt_\bo_\br &&) _\bn_\bo_\be_\bx_\bc_\be_\bp_\bt =\n+_\bd_\be_\bf_\ba_\bu_\bl_\bt;\n+_\b1_\b9_\b3 _\bc_\bo_\bn_\bs_\bt_\be_\bx_\bp_\br _\ba_\bl_\bg_\bo_\br_\bi_\bt_\bh_\bm_\b__\br_\ba_\bn_\bg_\be_\b__\bi_\bt_\be_\br_\ba_\bt_\bo_\br & _\bo_\bp_\be_\br_\ba_\bt_\bo_\br=(_\ba_\bl_\bg_\bo_\br_\bi_\bt_\bh_\bm_\b__\br_\ba_\bn_\bg_\be_\b__\bi_\bt_\be_\br_\ba_\bt_\bo_\br\n+_\bc_\bo_\bn_\bs_\bt &) _\bn_\bo_\be_\bx_\bc_\be_\bp_\bt = _\bd_\be_\bf_\ba_\bu_\bl_\bt;\n+_\b1_\b9_\b4 _\bc_\bo_\bn_\bs_\bt_\be_\bx_\bp_\br _\ba_\bl_\bg_\bo_\br_\bi_\bt_\bh_\bm_\b__\br_\ba_\bn_\bg_\be_\b__\bi_\bt_\be_\br_\ba_\bt_\bo_\br & _\bo_\bp_\be_\br_\ba_\bt_\bo_\br=(_\ba_\bl_\bg_\bo_\br_\bi_\bt_\bh_\bm_\b__\br_\ba_\bn_\bg_\be_\b__\bi_\bt_\be_\br_\ba_\bt_\bo_\br &&)\n+_\bn_\bo_\be_\bx_\bc_\be_\bp_\bt = _\bd_\be_\bf_\ba_\bu_\bl_\bt;\n+_\b1_\b9_\b5 ~_\ba_\bl_\bg_\bo_\br_\bi_\bt_\bh_\bm_\b__\br_\ba_\bn_\bg_\be_\b__\bi_\bt_\be_\br_\ba_\bt_\bo_\br() = _\bd_\be_\bf_\ba_\bu_\bl_\bt;\n 196\n-_\b1_\b9_\b8 explicit constexpr _\ba_\bl_\bg_\bo_\br_\bi_\bt_\bh_\bm_\b__\br_\ba_\bn_\bg_\be_\b__\bi_\bt_\be_\br_\ba_\bt_\bo_\br\n-(_\ba_\bl_\bg_\bo_\br_\bi_\bt_\bh_\bm_\b__\br_\be_\bs_\bu_\bl_\bt_\b__\bg_\be_\bn_\be_\br_\ba_\bt_\bo_\br_\b__\br_\ba_\bn_\bg_\be & range) :\n-199 range_ptr(_\bs_\bt_\bd::addressof(range))\n+_\b1_\b9_\b8 _\be_\bx_\bp_\bl_\bi_\bc_\bi_\bt _\bc_\bo_\bn_\bs_\bt_\be_\bx_\bp_\br _\ba_\bl_\bg_\bo_\br_\bi_\bt_\bh_\bm_\b__\br_\ba_\bn_\bg_\be_\b__\bi_\bt_\be_\br_\ba_\bt_\bo_\br\n+(_\ba_\bl_\bg_\bo_\br_\bi_\bt_\bh_\bm_\b__\br_\be_\bs_\bu_\bl_\bt_\b__\bg_\be_\bn_\be_\br_\ba_\bt_\bo_\br_\b__\br_\ba_\bn_\bg_\be & _\br_\ba_\bn_\bg_\be) :\n+199 range_ptr(_\bs_\bt_\bd::addressof(_\br_\ba_\bn_\bg_\be))\n 200 {\n 201 ++(*this); // Fetch the next element.\n 202 }\n 204\n-_\b2_\b1_\b3 _\br_\be_\bf_\be_\br_\be_\bn_\bc_\be _\bo_\bp_\be_\br_\ba_\bt_\bo_\br_\b*() const noexcept\n+_\b2_\b1_\b3 _\br_\be_\bf_\be_\br_\be_\bn_\bc_\be _\bo_\bp_\be_\br_\ba_\bt_\bo_\br_\b*() _\bc_\bo_\bn_\bs_\bt _\bn_\bo_\be_\bx_\bc_\be_\bp_\bt\n 214 {\n 215 return range_ptr->cache;\n 216 }\n 217\n-_\b2_\b1_\b9 _\bp_\bo_\bi_\bn_\bt_\be_\br _\bo_\bp_\be_\br_\ba_\bt_\bo_\br_\b-_\b>() const noexcept\n+_\b2_\b1_\b9 _\bp_\bo_\bi_\bn_\bt_\be_\br _\bo_\bp_\be_\br_\ba_\bt_\bo_\br_\b-_\b>() _\bc_\bo_\bn_\bs_\bt _\bn_\bo_\be_\bx_\bc_\be_\bp_\bt\n 220 {\n 221 return &range_ptr->cache;\n 222 }\n 224\n _\b2_\b2_\b9 _\ba_\bl_\bg_\bo_\br_\bi_\bt_\bh_\bm_\b__\br_\ba_\bn_\bg_\be_\b__\bi_\bt_\be_\br_\ba_\bt_\bo_\br & _\bo_\bp_\be_\br_\ba_\bt_\bo_\br_\b+_\b+(/*pre*/)\n 230 {\n-231 assert(range_ptr != nullptr);\n+231 _\ba_\bs_\bs_\be_\br_\bt(range_ptr != nullptr);\n 232\n 233 at_end = !range_ptr->next();\n 234 return *this;\n 235 }\n 236\n _\b2_\b3_\b8 void _\bo_\bp_\be_\br_\ba_\bt_\bo_\br_\b+_\b+(int /*post*/)\n 239 {\n 240 ++(*this);\n 241 }\n 243\n-_\b2_\b4_\b8 friend constexpr bool _\bo_\bp_\be_\br_\ba_\bt_\bo_\br_\b=_\b=(_\ba_\bl_\bg_\bo_\br_\bi_\bt_\bh_\bm_\b__\br_\ba_\bn_\bg_\be_\b__\bi_\bt_\be_\br_\ba_\bt_\bo_\br const & lhs,\n+_\b2_\b4_\b8 friend constexpr bool _\bo_\bp_\be_\br_\ba_\bt_\bo_\br_\b=_\b=(_\ba_\bl_\bg_\bo_\br_\bi_\bt_\bh_\bm_\b__\br_\ba_\bn_\bg_\be_\b__\bi_\bt_\be_\br_\ba_\bt_\bo_\br const & _\bl_\bh_\bs,\n std::default_sentinel_t const &) noexcept\n 249 {\n-250 return lhs.at_end;\n+250 return _\bl_\bh_\bs.at_end;\n 251 }\n 252\n-_\b2_\b5_\b4 friend constexpr bool _\bo_\bp_\be_\br_\ba_\bt_\bo_\br_\b=_\b=(std::default_sentinel_t const & lhs,\n-_\ba_\bl_\bg_\bo_\br_\bi_\bt_\bh_\bm_\b__\br_\ba_\bn_\bg_\be_\b__\bi_\bt_\be_\br_\ba_\bt_\bo_\br const & rhs) noexcept\n+_\b2_\b5_\b4 friend constexpr bool _\bo_\bp_\be_\br_\ba_\bt_\bo_\br_\b=_\b=(std::default_sentinel_t const & _\bl_\bh_\bs,\n+_\ba_\bl_\bg_\bo_\br_\bi_\bt_\bh_\bm_\b__\br_\ba_\bn_\bg_\be_\b__\bi_\bt_\be_\br_\ba_\bt_\bo_\br const & _\br_\bh_\bs) noexcept\n 255 {\n-256 return rhs == lhs;\n+256 return _\br_\bh_\bs == _\bl_\bh_\bs;\n 257 }\n 258\n-_\b2_\b6_\b0 friend constexpr bool _\bo_\bp_\be_\br_\ba_\bt_\bo_\br_\b!_\b=(_\ba_\bl_\bg_\bo_\br_\bi_\bt_\bh_\bm_\b__\br_\ba_\bn_\bg_\be_\b__\bi_\bt_\be_\br_\ba_\bt_\bo_\br const & lhs,\n-std::default_sentinel_t const & rhs) noexcept\n+_\b2_\b6_\b0 friend constexpr bool _\bo_\bp_\be_\br_\ba_\bt_\bo_\br_\b!_\b=(_\ba_\bl_\bg_\bo_\br_\bi_\bt_\bh_\bm_\b__\br_\ba_\bn_\bg_\be_\b__\bi_\bt_\be_\br_\ba_\bt_\bo_\br const & _\bl_\bh_\bs,\n+std::default_sentinel_t const & _\br_\bh_\bs) noexcept\n 261 {\n-262 return !(lhs == rhs);\n+262 return !(_\bl_\bh_\bs == _\br_\bh_\bs);\n 263 }\n 264\n-_\b2_\b6_\b6 friend constexpr bool _\bo_\bp_\be_\br_\ba_\bt_\bo_\br_\b!_\b=(std::default_sentinel_t const & lhs,\n-_\ba_\bl_\bg_\bo_\br_\bi_\bt_\bh_\bm_\b__\br_\ba_\bn_\bg_\be_\b__\bi_\bt_\be_\br_\ba_\bt_\bo_\br const & rhs) noexcept\n+_\b2_\b6_\b6 friend constexpr bool _\bo_\bp_\be_\br_\ba_\bt_\bo_\br_\b!_\b=(std::default_sentinel_t const & _\bl_\bh_\bs,\n+_\ba_\bl_\bg_\bo_\br_\bi_\bt_\bh_\bm_\b__\br_\ba_\bn_\bg_\be_\b__\bi_\bt_\be_\br_\ba_\bt_\bo_\br const & _\br_\bh_\bs) noexcept\n 267 {\n-268 return rhs != lhs;\n+268 return _\br_\bh_\bs != _\bl_\bh_\bs;\n 269 }\n 271\n 272private:\n 274 _\ba_\bl_\bg_\bo_\br_\bi_\bt_\bh_\bm_\b__\br_\be_\bs_\bu_\bl_\bt_\b__\bg_\be_\bn_\be_\br_\ba_\bt_\bo_\br_\b__\br_\ba_\bn_\bg_\be * range_ptr{};\n 276 bool at_end{true};\n 277};\n 278\n@@ -278,14 +278,17 @@\n algorithm_result_generator_range(algorithm_executor_type &&) -\n > algorithm_result_generator_range< std::remove_reference_t<\n algorithm_executor_type > >\n Deduces from the passed algorithm_executor_type.\n _\bs_\be_\bq_\ba_\bn_\b3_\b:_\b:_\ba_\bl_\bg_\bo_\br_\bi_\bt_\bh_\bm_\b__\br_\be_\bs_\bu_\bl_\bt_\b__\bg_\be_\bn_\be_\br_\ba_\bt_\bo_\br_\b__\br_\ba_\bn_\bg_\be_\b:_\b:_\b~_\ba_\bl_\bg_\bo_\br_\bi_\bt_\bh_\bm_\b__\br_\be_\bs_\bu_\bl_\bt_\b__\bg_\be_\bn_\be_\br_\ba_\bt_\bo_\br_\b__\br_\ba_\bn_\bg_\be\n ~algorithm_result_generator_range()=default\n Defaulted.\n+_\bs_\be_\bq_\ba_\bn_\b3_\b:_\b:_\bd_\be_\bb_\bu_\bg_\b__\bs_\bt_\br_\be_\ba_\bm_\b__\bt_\by_\bp_\be\n+A \"pretty printer\" for most SeqAn data structures and related types.\n+D\bDe\bef\bfi\bin\bni\bit\bti\bio\bon\bn debug_stream_type.hpp:79\n _\bs_\bt_\bd_\b:_\b:_\bi_\bn_\bp_\bu_\bt_\b__\bi_\bt_\be_\br_\ba_\bt_\bo_\br_\b__\bt_\ba_\bg\n _\bm_\be_\bm_\bo_\br_\by\n _\bs_\be_\bq_\ba_\bn_\b3\n The main SeqAn3 namespace.\n D\bDe\bef\bfi\bin\bni\bit\bti\bio\bon\bn aligned_sequence_concept.hpp:26\n _\bs_\bt_\bd\n SeqAn specific customisations in the standard namespace.\n"}]}, {"source1": "./usr/share/doc/libseqan3-dev/html/aliases_8hpp_source.html", "source2": "./usr/share/doc/libseqan3-dev/html/aliases_8hpp_source.html", "unified_diff": "@@ -142,30 +142,30 @@\n
19#include <seqan3/alphabet/quality/concept.hpp>
\n
20#include <seqan3/alphabet/quality/phred42.hpp>
\n
21#include <seqan3/alphabet/quality/qualified.hpp>
\n
22
\n
23namespace seqan3
\n
24{
\n
25
\n-
31using dna4q = qualified<dna4, phred42>;
\n+
31using dna4q = qualified<dna4, phred42>;
\n
32
\n-
38using dna5q = qualified<dna5, phred42>;
\n+
38using dna5q = qualified<dna5, phred42>;
\n
39
\n-
45using rna4q = qualified<rna4, phred42>;
\n+
45using rna4q = qualified<rna4, phred42>;
\n
46
\n-
52using rna5q = qualified<rna5, phred42>;
\n+
52using rna5q = qualified<rna5, phred42>;
\n
53
\n-
59using dna15q = qualified<dna15, phred42>;
\n+
59using dna15q = qualified<dna15, phred42>;
\n
60
\n-
66using rna15q = qualified<rna15, phred42>;
\n+
66using rna15q = qualified<rna15, phred42>;
\n
67
\n
68} // namespace seqan3
\n
concept.hpp
Core alphabet concept and free function/type trait wrappers.
\n
concept.hpp
Quality alphabet concept.
\n-
seqan3::qualified
Joins an arbitrary alphabet with a quality alphabet.
Definition qualified.hpp:59
\n+
seqan3::debug_stream_type
A "pretty printer" for most SeqAn data structures and related types.
Definition debug_stream_type.hpp:79
\n
dna15.hpp
Provides seqan3::dna15, container aliases and string literals.
\n
dna4.hpp
Provides seqan3::dna4, container aliases and string literals.
\n
dna5.hpp
Provides seqan3::dna5, container aliases and string literals.
\n
seqan3
The main SeqAn3 namespace.
Definition aligned_sequence_concept.hpp:26
\n
phred42.hpp
Provides seqan3::phred42 quality scores.
\n
qualified.hpp
Provides quality alphabet composites.
\n
rna15.hpp
Provides seqan3::rna15, container aliases and string literals.
\n", "details": [{"source1": "html2text {}", "source2": "html2text {}", "unified_diff": "@@ -39,17 +39,17 @@\n _\b6_\b6using _\br_\bn_\ba_\b1_\b5_\bq = _\bq_\bu_\ba_\bl_\bi_\bf_\bi_\be_\bd_\b<_\br_\bn_\ba_\b1_\b5_\b,_\b _\bp_\bh_\br_\be_\bd_\b4_\b2_\b>;\n 67\n 68} // namespace seqan3\n _\bc_\bo_\bn_\bc_\be_\bp_\bt_\b._\bh_\bp_\bp\n Core alphabet concept and free function/type trait wrappers.\n _\bc_\bo_\bn_\bc_\be_\bp_\bt_\b._\bh_\bp_\bp\n Quality alphabet concept.\n-_\bs_\be_\bq_\ba_\bn_\b3_\b:_\b:_\bq_\bu_\ba_\bl_\bi_\bf_\bi_\be_\bd\n-Joins an arbitrary alphabet with a quality alphabet.\n-D\bDe\bef\bfi\bin\bni\bit\bti\bio\bon\bn qualified.hpp:59\n+_\bs_\be_\bq_\ba_\bn_\b3_\b:_\b:_\bd_\be_\bb_\bu_\bg_\b__\bs_\bt_\br_\be_\ba_\bm_\b__\bt_\by_\bp_\be\n+A \"pretty printer\" for most SeqAn data structures and related types.\n+D\bDe\bef\bfi\bin\bni\bit\bti\bio\bon\bn debug_stream_type.hpp:79\n _\bd_\bn_\ba_\b1_\b5_\b._\bh_\bp_\bp\n Provides seqan3::dna15, container aliases and string literals.\n _\bd_\bn_\ba_\b4_\b._\bh_\bp_\bp\n Provides seqan3::dna4, container aliases and string literals.\n _\bd_\bn_\ba_\b5_\b._\bh_\bp_\bp\n Provides seqan3::dna5, container aliases and string literals.\n _\bs_\be_\bq_\ba_\bn_\b3\n"}]}, {"source1": "./usr/share/doc/libseqan3-dev/html/align__config__method_8hpp_source.html", "source2": "./usr/share/doc/libseqan3-dev/html/align__config__method_8hpp_source.html", "unified_diff": "@@ -196,21 +196,21 @@\n
125 method_global(method_global const &) = default;
\n
126 method_global(method_global &&) = default;
\n
127 method_global & operator=(method_global const &) = default;
\n
128 method_global & operator=(method_global &&) = default;
\n
129 ~method_global() = default;
\n
130
\n \n
151
\n
153 bool free_end_gaps_sequence1_leading{false};
\n
155 bool free_end_gaps_sequence2_leading{false};
\n
157 bool free_end_gaps_sequence1_trailing{false};
\n@@ -235,14 +235,15 @@\n
seqan3::align_cfg::method_local
Sets the local alignment method.
Definition align_config_method.hpp:42
\n
seqan3::align_cfg::method_local::method_local
method_local(method_local const &)=default
Defaulted.
\n
seqan3::align_cfg::method_local::~method_local
~method_local()=default
Defaulted.
\n
seqan3::align_cfg::method_local::method_local
method_local()=default
Defaulted.
\n
seqan3::align_cfg::method_local::method_local
method_local(method_local &&)=default
Defaulted.
\n
seqan3::align_cfg::method_local::operator=
method_local & operator=(method_local const &)=default
Defaulted.
\n
seqan3::align_cfg::method_local::operator=
method_local & operator=(method_local &&)=default
Defaulted.
\n+
seqan3::debug_stream_type
A "pretty printer" for most SeqAn data structures and related types.
Definition debug_stream_type.hpp:79
\n
empty_type.hpp
Provides seqan3::detail::empty_type.
\n
seqan3::align_cfg
A special sub namespace for the alignment configurations.
Definition align_config_band.hpp:22
\n
pipeable_config_element.hpp
Provides seqan3::pipeable_config_element.
\n
strong_type.hpp
Provides basic data structure for strong types.
\n
seqan3::align_cfg::free_end_gaps_sequence1_leading
A strong type representing free_end_gaps_sequence1_leading of the seqan3::align_cfg::method_global.
Definition align_config_method.hpp:65
\n
seqan3::align_cfg::free_end_gaps_sequence1_leading::base_t
seqan3::detail::strong_type< bool, free_end_gaps_sequence1_leading > base_t
The type of the strong type base class.
Definition align_config_method.hpp:67
\n
seqan3::align_cfg::free_end_gaps_sequence1_trailing
A strong type representing free_end_gaps_sequence1_trailing of the seqan3::align_cfg::method_global.
Definition align_config_method.hpp:85
\n", "details": [{"source1": "html2text {}", "source2": "html2text {}", "unified_diff": "@@ -74,23 +74,23 @@\n _\b1_\b2_\b5 _\bm_\be_\bt_\bh_\bo_\bd_\b__\bg_\bl_\bo_\bb_\ba_\bl(_\bm_\be_\bt_\bh_\bo_\bd_\b__\bg_\bl_\bo_\bb_\ba_\bl const &) = default;\n _\b1_\b2_\b6 _\bm_\be_\bt_\bh_\bo_\bd_\b__\bg_\bl_\bo_\bb_\ba_\bl(_\bm_\be_\bt_\bh_\bo_\bd_\b__\bg_\bl_\bo_\bb_\ba_\bl &&) = default;\n _\b1_\b2_\b7 _\bm_\be_\bt_\bh_\bo_\bd_\b__\bg_\bl_\bo_\bb_\ba_\bl & _\bo_\bp_\be_\br_\ba_\bt_\bo_\br_\b=(_\bm_\be_\bt_\bh_\bo_\bd_\b__\bg_\bl_\bo_\bb_\ba_\bl const &) = default;\n _\b1_\b2_\b8 _\bm_\be_\bt_\bh_\bo_\bd_\b__\bg_\bl_\bo_\bb_\ba_\bl & _\bo_\bp_\be_\br_\ba_\bt_\bo_\br_\b=(_\bm_\be_\bt_\bh_\bo_\bd_\b__\bg_\bl_\bo_\bb_\ba_\bl &&) = default;\n _\b1_\b2_\b9 _\b~_\bm_\be_\bt_\bh_\bo_\bd_\b__\bg_\bl_\bo_\bb_\ba_\bl() = default;\n 130\n _\b1_\b4_\b1 constexpr _\bm_\be_\bt_\bh_\bo_\bd_\b__\bg_\bl_\bo_\bb_\ba_\bl(_\bs_\be_\bq_\ba_\bn_\b3_\b:_\b:_\ba_\bl_\bi_\bg_\bn_\b__\bc_\bf_\bg_\b:_\b:_\bf_\br_\be_\be_\b__\be_\bn_\bd_\b__\bg_\ba_\bp_\bs_\b__\bs_\be_\bq_\bu_\be_\bn_\bc_\be_\b1_\b__\bl_\be_\ba_\bd_\bi_\bn_\bg\n-free_sequence1_leading,\n-142 _\bs_\be_\bq_\ba_\bn_\b3_\b:_\b:_\ba_\bl_\bi_\bg_\bn_\b__\bc_\bf_\bg_\b:_\b:_\bf_\br_\be_\be_\b__\be_\bn_\bd_\b__\bg_\ba_\bp_\bs_\b__\bs_\be_\bq_\bu_\be_\bn_\bc_\be_\b2_\b__\bl_\be_\ba_\bd_\bi_\bn_\bg free_sequence2_leading,\n+_\bf_\br_\be_\be_\b__\bs_\be_\bq_\bu_\be_\bn_\bc_\be_\b1_\b__\bl_\be_\ba_\bd_\bi_\bn_\bg,\n+142 _\bs_\be_\bq_\ba_\bn_\b3_\b:_\b:_\ba_\bl_\bi_\bg_\bn_\b__\bc_\bf_\bg_\b:_\b:_\bf_\br_\be_\be_\b__\be_\bn_\bd_\b__\bg_\ba_\bp_\bs_\b__\bs_\be_\bq_\bu_\be_\bn_\bc_\be_\b2_\b__\bl_\be_\ba_\bd_\bi_\bn_\bg _\bf_\br_\be_\be_\b__\bs_\be_\bq_\bu_\be_\bn_\bc_\be_\b2_\b__\bl_\be_\ba_\bd_\bi_\bn_\bg,\n 143 _\bs_\be_\bq_\ba_\bn_\b3_\b:_\b:_\ba_\bl_\bi_\bg_\bn_\b__\bc_\bf_\bg_\b:_\b:_\bf_\br_\be_\be_\b__\be_\bn_\bd_\b__\bg_\ba_\bp_\bs_\b__\bs_\be_\bq_\bu_\be_\bn_\bc_\be_\b1_\b__\bt_\br_\ba_\bi_\bl_\bi_\bn_\bg\n-free_sequence1_trailing,\n+_\bf_\br_\be_\be_\b__\bs_\be_\bq_\bu_\be_\bn_\bc_\be_\b1_\b__\bt_\br_\ba_\bi_\bl_\bi_\bn_\bg,\n 144 _\bs_\be_\bq_\ba_\bn_\b3_\b:_\b:_\ba_\bl_\bi_\bg_\bn_\b__\bc_\bf_\bg_\b:_\b:_\bf_\br_\be_\be_\b__\be_\bn_\bd_\b__\bg_\ba_\bp_\bs_\b__\bs_\be_\bq_\bu_\be_\bn_\bc_\be_\b2_\b__\bt_\br_\ba_\bi_\bl_\bi_\bn_\bg\n-free_sequence2_trailing) noexcept :\n-145 _\bf_\br_\be_\be_\b__\be_\bn_\bd_\b__\bg_\ba_\bp_\bs_\b__\bs_\be_\bq_\bu_\be_\bn_\bc_\be_\b1_\b__\bl_\be_\ba_\bd_\bi_\bn_\bg{free_sequence1_leading.get()},\n-146 _\bf_\br_\be_\be_\b__\be_\bn_\bd_\b__\bg_\ba_\bp_\bs_\b__\bs_\be_\bq_\bu_\be_\bn_\bc_\be_\b2_\b__\bl_\be_\ba_\bd_\bi_\bn_\bg{free_sequence2_leading.get()},\n-147 _\bf_\br_\be_\be_\b__\be_\bn_\bd_\b__\bg_\ba_\bp_\bs_\b__\bs_\be_\bq_\bu_\be_\bn_\bc_\be_\b1_\b__\bt_\br_\ba_\bi_\bl_\bi_\bn_\bg{free_sequence1_trailing.get()},\n+_\bf_\br_\be_\be_\b__\bs_\be_\bq_\bu_\be_\bn_\bc_\be_\b2_\b__\bt_\br_\ba_\bi_\bl_\bi_\bn_\bg) _\bn_\bo_\be_\bx_\bc_\be_\bp_\bt :\n+145 _\bf_\br_\be_\be_\b__\be_\bn_\bd_\b__\bg_\ba_\bp_\bs_\b__\bs_\be_\bq_\bu_\be_\bn_\bc_\be_\b1_\b__\bl_\be_\ba_\bd_\bi_\bn_\bg{_\bf_\br_\be_\be_\b__\bs_\be_\bq_\bu_\be_\bn_\bc_\be_\b1_\b__\bl_\be_\ba_\bd_\bi_\bn_\bg.get()},\n+146 _\bf_\br_\be_\be_\b__\be_\bn_\bd_\b__\bg_\ba_\bp_\bs_\b__\bs_\be_\bq_\bu_\be_\bn_\bc_\be_\b2_\b__\bl_\be_\ba_\bd_\bi_\bn_\bg{_\bf_\br_\be_\be_\b__\bs_\be_\bq_\bu_\be_\bn_\bc_\be_\b2_\b__\bl_\be_\ba_\bd_\bi_\bn_\bg.get()},\n+147 _\bf_\br_\be_\be_\b__\be_\bn_\bd_\b__\bg_\ba_\bp_\bs_\b__\bs_\be_\bq_\bu_\be_\bn_\bc_\be_\b1_\b__\bt_\br_\ba_\bi_\bl_\bi_\bn_\bg{_\bf_\br_\be_\be_\b__\bs_\be_\bq_\bu_\be_\bn_\bc_\be_\b1_\b__\bt_\br_\ba_\bi_\bl_\bi_\bn_\bg.get()},\n 148 _\bf_\br_\be_\be_\b__\be_\bn_\bd_\b__\bg_\ba_\bp_\bs_\b__\bs_\be_\bq_\bu_\be_\bn_\bc_\be_\b2_\b__\bt_\br_\ba_\bi_\bl_\bi_\bn_\bg{free_sequence2_trailing.get()}\n 149 {}\n 151\n _\b1_\b5_\b3 bool _\bf_\br_\be_\be_\b__\be_\bn_\bd_\b__\bg_\ba_\bp_\bs_\b__\bs_\be_\bq_\bu_\be_\bn_\bc_\be_\b1_\b__\bl_\be_\ba_\bd_\bi_\bn_\bg{false};\n _\b1_\b5_\b5 bool _\bf_\br_\be_\be_\b__\be_\bn_\bd_\b__\bg_\ba_\bp_\bs_\b__\bs_\be_\bq_\bu_\be_\bn_\bc_\be_\b2_\b__\bl_\be_\ba_\bd_\bi_\bn_\bg{false};\n _\b1_\b5_\b7 bool _\bf_\br_\be_\be_\b__\be_\bn_\bd_\b__\bg_\ba_\bp_\bs_\b__\bs_\be_\bq_\bu_\be_\bn_\bc_\be_\b1_\b__\bt_\br_\ba_\bi_\bl_\bi_\bn_\bg{false};\n _\b1_\b5_\b9 bool _\bf_\br_\be_\be_\b__\be_\bn_\bd_\b__\bg_\ba_\bp_\bs_\b__\bs_\be_\bq_\bu_\be_\bn_\bc_\be_\b2_\b__\bt_\br_\ba_\bi_\bl_\bi_\bn_\bg{false};\n@@ -158,14 +158,17 @@\n Defaulted.\n _\bs_\be_\bq_\ba_\bn_\b3_\b:_\b:_\ba_\bl_\bi_\bg_\bn_\b__\bc_\bf_\bg_\b:_\b:_\bm_\be_\bt_\bh_\bo_\bd_\b__\bl_\bo_\bc_\ba_\bl_\b:_\b:_\bo_\bp_\be_\br_\ba_\bt_\bo_\br_\b=\n method_local & operator=(method_local const &)=default\n Defaulted.\n _\bs_\be_\bq_\ba_\bn_\b3_\b:_\b:_\ba_\bl_\bi_\bg_\bn_\b__\bc_\bf_\bg_\b:_\b:_\bm_\be_\bt_\bh_\bo_\bd_\b__\bl_\bo_\bc_\ba_\bl_\b:_\b:_\bo_\bp_\be_\br_\ba_\bt_\bo_\br_\b=\n method_local & operator=(method_local &&)=default\n Defaulted.\n+_\bs_\be_\bq_\ba_\bn_\b3_\b:_\b:_\bd_\be_\bb_\bu_\bg_\b__\bs_\bt_\br_\be_\ba_\bm_\b__\bt_\by_\bp_\be\n+A \"pretty printer\" for most SeqAn data structures and related types.\n+D\bDe\bef\bfi\bin\bni\bit\bti\bio\bon\bn debug_stream_type.hpp:79\n _\be_\bm_\bp_\bt_\by_\b__\bt_\by_\bp_\be_\b._\bh_\bp_\bp\n Provides seqan3::detail::empty_type.\n _\bs_\be_\bq_\ba_\bn_\b3_\b:_\b:_\ba_\bl_\bi_\bg_\bn_\b__\bc_\bf_\bg\n A special sub namespace for the alignment configurations.\n D\bDe\bef\bfi\bin\bni\bit\bti\bio\bon\bn align_config_band.hpp:22\n _\bp_\bi_\bp_\be_\ba_\bb_\bl_\be_\b__\bc_\bo_\bn_\bf_\bi_\bg_\b__\be_\bl_\be_\bm_\be_\bn_\bt_\b._\bh_\bp_\bp\n Provides seqan3::pipeable_config_element.\n"}]}, {"source1": "./usr/share/doc/libseqan3-dev/html/align__config__min__score_8hpp_source.html", "source2": "./usr/share/doc/libseqan3-dev/html/align__config__min__score_8hpp_source.html", "unified_diff": "@@ -141,35 +141,36 @@\n
18{
\n
\n
35class min_score : private pipeable_config_element
\n
36{
\n
37public:
\n
39 int32_t score{std::numeric_limits<int32_t>::lowest()};
\n
40
\n-
44 constexpr min_score() noexcept = default;
\n-
45 constexpr min_score(min_score const &) noexcept = default;
\n-
46 constexpr min_score(min_score &&) noexcept = default;
\n-
47 constexpr min_score & operator=(min_score const &) noexcept = default;
\n-
48 constexpr min_score & operator=(min_score &&) noexcept = default;
\n-
49 ~min_score() noexcept = default;
\n+
44 constexpr min_score() noexcept = default;
\n+
45 constexpr min_score(min_score const &) noexcept = default;
\n+
46 constexpr min_score(min_score &&) noexcept = default;
\n+
47 constexpr min_score & operator=(min_score const &) noexcept = default;
\n+
48 constexpr min_score & operator=(min_score &&) noexcept = default;
\n+
49 ~min_score() noexcept = default;
\n
50
\n
\n-
55 constexpr min_score(int32_t const score) : score{score}
\n+
55 constexpr min_score(int32_t const score) : score{score}
\n
56 {}
\n
\n
58
\n
60 static constexpr seqan3::detail::align_config_id id{seqan3::detail::align_config_id::min_score};
\n
61};
\n
\n
62
\n
63} // namespace seqan3::align_cfg
\n
detail.hpp
Provides some utility functions for the alignment configurations.
\n
seqan3::align_cfg::min_score
Sets the minimal score (maximal errors) allowed during an distance computation e.g....
Definition align_config_min_score.hpp:36
\n
seqan3::align_cfg::min_score::score
int32_t score
Minimal score for the distance computation [default: -infinity].
Definition align_config_min_score.hpp:39
\n
seqan3::align_cfg::min_score::min_score
constexpr min_score() noexcept=default
Defaulted.
\n+
seqan3::debug_stream_type
A "pretty printer" for most SeqAn data structures and related types.
Definition debug_stream_type.hpp:79
\n \n
std::numeric_limits::lowest
T lowest(T... args)
\n
seqan3::align_cfg
A special sub namespace for the alignment configurations.
Definition align_config_band.hpp:22
\n
pipeable_config_element.hpp
Provides seqan3::pipeable_config_element.
\n
seqan3::pipeable_config_element
Adds pipe interface to configuration elements.
Definition pipeable_config_element.hpp:29
\n
\n \n", "details": [{"source1": "html2text {}", "source2": "html2text {}", "unified_diff": "@@ -20,22 +20,22 @@\n 17namespace _\bs_\be_\bq_\ba_\bn_\b3_\b:_\b:_\ba_\bl_\bi_\bg_\bn_\b__\bc_\bf_\bg\n 18{\n _\b3_\b5class _\bm_\bi_\bn_\b__\bs_\bc_\bo_\br_\be : private _\bp_\bi_\bp_\be_\ba_\bb_\bl_\be_\b__\bc_\bo_\bn_\bf_\bi_\bg_\b__\be_\bl_\be_\bm_\be_\bn_\bt\n 36{\n 37public:\n _\b3_\b9 int32_t _\bs_\bc_\bo_\br_\be{_\bs_\bt_\bd_\b:_\b:_\bn_\bu_\bm_\be_\br_\bi_\bc_\b__\bl_\bi_\bm_\bi_\bt_\bs_\b<_\bi_\bn_\bt_\b3_\b2_\b__\bt_\b>_\b:_\b:_\bl_\bo_\bw_\be_\bs_\bt()};\n 40\n-_\b4_\b4 constexpr _\bm_\bi_\bn_\b__\bs_\bc_\bo_\br_\be() noexcept = default;\n-_\b4_\b5 constexpr _\bm_\bi_\bn_\b__\bs_\bc_\bo_\br_\be(_\bm_\bi_\bn_\b__\bs_\bc_\bo_\br_\be const &) noexcept = default;\n-_\b4_\b6 constexpr _\bm_\bi_\bn_\b__\bs_\bc_\bo_\br_\be(_\bm_\bi_\bn_\b__\bs_\bc_\bo_\br_\be &&) noexcept = default;\n-_\b4_\b7 constexpr _\bm_\bi_\bn_\b__\bs_\bc_\bo_\br_\be & operator=(_\bm_\bi_\bn_\b__\bs_\bc_\bo_\br_\be const &) noexcept = default;\n-_\b4_\b8 constexpr _\bm_\bi_\bn_\b__\bs_\bc_\bo_\br_\be & operator=(_\bm_\bi_\bn_\b__\bs_\bc_\bo_\br_\be &&) noexcept = default;\n-_\b4_\b9 ~_\bm_\bi_\bn_\b__\bs_\bc_\bo_\br_\be() noexcept = default;\n+_\b4_\b4 constexpr _\bm_\bi_\bn_\b__\bs_\bc_\bo_\br_\be() _\bn_\bo_\be_\bx_\bc_\be_\bp_\bt = _\bd_\be_\bf_\ba_\bu_\bl_\bt;\n+_\b4_\b5 _\bc_\bo_\bn_\bs_\bt_\be_\bx_\bp_\br _\bm_\bi_\bn_\b__\bs_\bc_\bo_\br_\be(_\bm_\bi_\bn_\b__\bs_\bc_\bo_\br_\be _\bc_\bo_\bn_\bs_\bt &) _\bn_\bo_\be_\bx_\bc_\be_\bp_\bt = _\bd_\be_\bf_\ba_\bu_\bl_\bt;\n+_\b4_\b6 _\bc_\bo_\bn_\bs_\bt_\be_\bx_\bp_\br _\bm_\bi_\bn_\b__\bs_\bc_\bo_\br_\be(_\bm_\bi_\bn_\b__\bs_\bc_\bo_\br_\be &&) _\bn_\bo_\be_\bx_\bc_\be_\bp_\bt = _\bd_\be_\bf_\ba_\bu_\bl_\bt;\n+_\b4_\b7 _\bc_\bo_\bn_\bs_\bt_\be_\bx_\bp_\br _\bm_\bi_\bn_\b__\bs_\bc_\bo_\br_\be & _\bo_\bp_\be_\br_\ba_\bt_\bo_\br=(_\bm_\bi_\bn_\b__\bs_\bc_\bo_\br_\be _\bc_\bo_\bn_\bs_\bt &) _\bn_\bo_\be_\bx_\bc_\be_\bp_\bt = _\bd_\be_\bf_\ba_\bu_\bl_\bt;\n+_\b4_\b8 _\bc_\bo_\bn_\bs_\bt_\be_\bx_\bp_\br _\bm_\bi_\bn_\b__\bs_\bc_\bo_\br_\be & _\bo_\bp_\be_\br_\ba_\bt_\bo_\br=(_\bm_\bi_\bn_\b__\bs_\bc_\bo_\br_\be &&) _\bn_\bo_\be_\bx_\bc_\be_\bp_\bt = _\bd_\be_\bf_\ba_\bu_\bl_\bt;\n+_\b4_\b9 ~_\bm_\bi_\bn_\b__\bs_\bc_\bo_\br_\be() _\bn_\bo_\be_\bx_\bc_\be_\bp_\bt = _\bd_\be_\bf_\ba_\bu_\bl_\bt;\n 50\n-_\b5_\b5 constexpr _\bm_\bi_\bn_\b__\bs_\bc_\bo_\br_\be(int32_t const _\bs_\bc_\bo_\br_\be) : _\bs_\bc_\bo_\br_\be{_\bs_\bc_\bo_\br_\be}\n+_\b5_\b5 _\bc_\bo_\bn_\bs_\bt_\be_\bx_\bp_\br _\bm_\bi_\bn_\b__\bs_\bc_\bo_\br_\be(int32_t _\bc_\bo_\bn_\bs_\bt _\bs_\bc_\bo_\br_\be) : _\bs_\bc_\bo_\br_\be{_\bs_\bc_\bo_\br_\be}\n 56 {}\n 58\n _\b6_\b0 static constexpr seqan3::detail::align_config_id id{seqan3::detail::\n align_config_id::min_score};\n 61};\n 62\n 63} // namespace seqan3::align_cfg\n@@ -48,14 +48,17 @@\n _\bs_\be_\bq_\ba_\bn_\b3_\b:_\b:_\ba_\bl_\bi_\bg_\bn_\b__\bc_\bf_\bg_\b:_\b:_\bm_\bi_\bn_\b__\bs_\bc_\bo_\br_\be_\b:_\b:_\bs_\bc_\bo_\br_\be\n int32_t score\n Minimal score for the distance computation [default: -infinity].\n D\bDe\bef\bfi\bin\bni\bit\bti\bio\bon\bn align_config_min_score.hpp:39\n _\bs_\be_\bq_\ba_\bn_\b3_\b:_\b:_\ba_\bl_\bi_\bg_\bn_\b__\bc_\bf_\bg_\b:_\b:_\bm_\bi_\bn_\b__\bs_\bc_\bo_\br_\be_\b:_\b:_\bm_\bi_\bn_\b__\bs_\bc_\bo_\br_\be\n constexpr min_score() noexcept=default\n Defaulted.\n+_\bs_\be_\bq_\ba_\bn_\b3_\b:_\b:_\bd_\be_\bb_\bu_\bg_\b__\bs_\bt_\br_\be_\ba_\bm_\b__\bt_\by_\bp_\be\n+A \"pretty printer\" for most SeqAn data structures and related types.\n+D\bDe\bef\bfi\bin\bni\bit\bti\bio\bon\bn debug_stream_type.hpp:79\n _\bl_\bi_\bm_\bi_\bt_\bs\n _\bs_\bt_\bd_\b:_\b:_\bn_\bu_\bm_\be_\br_\bi_\bc_\b__\bl_\bi_\bm_\bi_\bt_\bs_\b:_\b:_\bl_\bo_\bw_\be_\bs_\bt\n T lowest(T... args)\n _\bs_\be_\bq_\ba_\bn_\b3_\b:_\b:_\ba_\bl_\bi_\bg_\bn_\b__\bc_\bf_\bg\n A special sub namespace for the alignment configurations.\n D\bDe\bef\bfi\bin\bni\bit\bti\bio\bon\bn align_config_band.hpp:22\n _\bp_\bi_\bp_\be_\ba_\bb_\bl_\be_\b__\bc_\bo_\bn_\bf_\bi_\bg_\b__\be_\bl_\be_\bm_\be_\bn_\bt_\b._\bh_\bp_\bp\n"}]}, {"source1": "./usr/share/doc/libseqan3-dev/html/align__config__on__result_8hpp_source.html", "source2": "./usr/share/doc/libseqan3-dev/html/align__config__on__result_8hpp_source.html", "unified_diff": "@@ -152,35 +152,36 @@\n
60 constexpr on_result(on_result const &) = default;
\n
61 constexpr on_result(on_result &&) = default;
\n
62 constexpr on_result & operator=(on_result const &) = default;
\n
63 constexpr on_result & operator=(on_result &&) = default;
\n
64 ~on_result() = default;
\n
65
\n
\n-
69 constexpr explicit on_result(callback_t && callback) : callback{std::forward<callback_t>(callback)}
\n+
69 constexpr explicit on_result(callback_t && callback) : callback{std::forward<callback_t>(callback)}
\n
70 {}
\n
\n
72
\n
75 static constexpr seqan3::detail::align_config_id id{seqan3::detail::align_config_id::on_result};
\n
76};
\n \n
77
\n
82template <std::move_constructible callback_t>
\n-
83on_result(callback_t &&) -> on_result<std::decay_t<callback_t>>;
\n+
83on_result(callback_t &&) -> on_result<std::decay_t<callback_t>>;
\n
85} // namespace seqan3::align_cfg
\n
detail.hpp
Provides some utility functions for the alignment configurations.
\n
seqan3::align_cfg::on_result
Configuration element to provide a user defined callback function for the alignment.
Definition align_config_on_result.hpp:51
\n
seqan3::align_cfg::on_result::~on_result
~on_result()=default
Defaulted.
\n
seqan3::align_cfg::on_result::callback
seqan::stl::detail::movable_box_t< callback_t > callback
The stored callable which will be invoked with the alignment result.
Definition align_config_on_result.hpp:54
\n
seqan3::align_cfg::on_result::on_result
constexpr on_result()=default
Defaulted.
\n
seqan3::align_cfg::on_result::on_result
constexpr on_result(on_result &&)=default
Defaulted.
\n
seqan3::align_cfg::on_result::operator=
constexpr on_result & operator=(on_result &&)=default
Defaulted.
\n
seqan3::align_cfg::on_result::operator=
constexpr on_result & operator=(on_result const &)=default
Defaulted.
\n
seqan3::align_cfg::on_result::on_result
constexpr on_result(callback_t &&callback)
Constructs the configuration element with the given user callback.
Definition align_config_on_result.hpp:69
\n
seqan3::align_cfg::on_result::on_result
constexpr on_result(on_result const &)=default
Defaulted.
\n+
seqan3::debug_stream_type
A "pretty printer" for most SeqAn data structures and related types.
Definition debug_stream_type.hpp:79
\n
seqan3::align_cfg
A special sub namespace for the alignment configurations.
Definition align_config_band.hpp:22
\n
std
SeqAn specific customisations in the standard namespace.
\n
pipeable_config_element.hpp
Provides seqan3::pipeable_config_element.
\n
seqan3::pipeable_config_element
Adds pipe interface to configuration elements.
Definition pipeable_config_element.hpp:29
\n \n \n \n", "details": [{"source1": "html2text {}", "source2": "html2text {}", "unified_diff": "@@ -31,24 +31,24 @@\n _\b5_\b9 constexpr _\bo_\bn_\b__\br_\be_\bs_\bu_\bl_\bt() = default;\n _\b6_\b0 constexpr _\bo_\bn_\b__\br_\be_\bs_\bu_\bl_\bt(_\bo_\bn_\b__\br_\be_\bs_\bu_\bl_\bt const &) = default;\n _\b6_\b1 constexpr _\bo_\bn_\b__\br_\be_\bs_\bu_\bl_\bt(_\bo_\bn_\b__\br_\be_\bs_\bu_\bl_\bt &&) = default;\n _\b6_\b2 constexpr _\bo_\bn_\b__\br_\be_\bs_\bu_\bl_\bt & _\bo_\bp_\be_\br_\ba_\bt_\bo_\br_\b=(_\bo_\bn_\b__\br_\be_\bs_\bu_\bl_\bt const &) = default;\n _\b6_\b3 constexpr _\bo_\bn_\b__\br_\be_\bs_\bu_\bl_\bt & _\bo_\bp_\be_\br_\ba_\bt_\bo_\br_\b=(_\bo_\bn_\b__\br_\be_\bs_\bu_\bl_\bt &&) = default;\n _\b6_\b4 _\b~_\bo_\bn_\b__\br_\be_\bs_\bu_\bl_\bt() = default;\n 65\n-_\b6_\b9 constexpr explicit _\bo_\bn_\b__\br_\be_\bs_\bu_\bl_\bt(callback_t && _\bc_\ba_\bl_\bl_\bb_\ba_\bc_\bk) : _\bc_\ba_\bl_\bl_\bb_\ba_\bc_\bk{_\bs_\bt_\bd::\n-forward(_\bc_\ba_\bl_\bl_\bb_\ba_\bc_\bk)}\n+_\b6_\b9 constexpr explicit _\bo_\bn_\b__\br_\be_\bs_\bu_\bl_\bt(_\bc_\ba_\bl_\bl_\bb_\ba_\bc_\bk_\b__\bt && _\bc_\ba_\bl_\bl_\bb_\ba_\bc_\bk) : _\bc_\ba_\bl_\bl_\bb_\ba_\bc_\bk{_\bs_\bt_\bd::\n+forward<_\bc_\ba_\bl_\bl_\bb_\ba_\bc_\bk_\b__\bt>(_\bc_\ba_\bl_\bl_\bb_\ba_\bc_\bk)}\n 70 {}\n 72\n 75 static constexpr seqan3::detail::align_config_id id{seqan3::detail::\n align_config_id::on_result};\n 76};\n 77\n 82template \n-_\b8_\b3_\bo_\bn_\b__\br_\be_\bs_\bu_\bl_\bt(callback_t &&) -> _\bo_\bn_\b__\br_\be_\bs_\bu_\bl_\bt_\b<_\bs_\bt_\bd_\b:_\b:_\bd_\be_\bc_\ba_\by_\b__\bt_\b<_\bc_\ba_\bl_\bl_\bb_\ba_\bc_\bk_\b__\bt_\b>>;\n+_\b8_\b3_\bo_\bn_\b__\br_\be_\bs_\bu_\bl_\bt(_\bc_\ba_\bl_\bl_\bb_\ba_\bc_\bk_\b__\bt &&) -> _\bo_\bn_\b__\br_\be_\bs_\bu_\bl_\bt_\b<_\bs_\bt_\bd_\b:_\b:_\bd_\be_\bc_\ba_\by_\b__\bt_\b<_\bc_\ba_\bl_\bl_\bb_\ba_\bc_\bk_\b__\bt_\b>>;\n 85} // namespace seqan3::align_cfg\n _\bd_\be_\bt_\ba_\bi_\bl_\b._\bh_\bp_\bp\n Provides some utility functions for the alignment configurations.\n _\bs_\be_\bq_\ba_\bn_\b3_\b:_\b:_\ba_\bl_\bi_\bg_\bn_\b__\bc_\bf_\bg_\b:_\b:_\bo_\bn_\b__\br_\be_\bs_\bu_\bl_\bt\n Configuration element to provide a user defined callback function for the\n alignment.\n D\bDe\bef\bfi\bin\bni\bit\bti\bio\bon\bn align_config_on_result.hpp:51\n@@ -74,14 +74,17 @@\n _\bs_\be_\bq_\ba_\bn_\b3_\b:_\b:_\ba_\bl_\bi_\bg_\bn_\b__\bc_\bf_\bg_\b:_\b:_\bo_\bn_\b__\br_\be_\bs_\bu_\bl_\bt_\b:_\b:_\bo_\bn_\b__\br_\be_\bs_\bu_\bl_\bt\n constexpr on_result(callback_t &&callback)\n Constructs the configuration element with the given user callback.\n D\bDe\bef\bfi\bin\bni\bit\bti\bio\bon\bn align_config_on_result.hpp:69\n _\bs_\be_\bq_\ba_\bn_\b3_\b:_\b:_\ba_\bl_\bi_\bg_\bn_\b__\bc_\bf_\bg_\b:_\b:_\bo_\bn_\b__\br_\be_\bs_\bu_\bl_\bt_\b:_\b:_\bo_\bn_\b__\br_\be_\bs_\bu_\bl_\bt\n constexpr on_result(on_result const &)=default\n Defaulted.\n+_\bs_\be_\bq_\ba_\bn_\b3_\b:_\b:_\bd_\be_\bb_\bu_\bg_\b__\bs_\bt_\br_\be_\ba_\bm_\b__\bt_\by_\bp_\be\n+A \"pretty printer\" for most SeqAn data structures and related types.\n+D\bDe\bef\bfi\bin\bni\bit\bti\bio\bon\bn debug_stream_type.hpp:79\n _\bs_\be_\bq_\ba_\bn_\b3_\b:_\b:_\ba_\bl_\bi_\bg_\bn_\b__\bc_\bf_\bg\n A special sub namespace for the alignment configurations.\n D\bDe\bef\bfi\bin\bni\bit\bti\bio\bon\bn align_config_band.hpp:22\n _\bs_\bt_\bd\n SeqAn specific customisations in the standard namespace.\n _\bp_\bi_\bp_\be_\ba_\bb_\bl_\be_\b__\bc_\bo_\bn_\bf_\bi_\bg_\b__\be_\bl_\be_\bm_\be_\bn_\bt_\b._\bh_\bp_\bp\n Provides seqan3::pipeable_config_element.\n"}]}, {"source1": "./usr/share/doc/libseqan3-dev/html/align__config__scoring__scheme_8hpp_source.html", "source2": "./usr/share/doc/libseqan3-dev/html/align__config__scoring__scheme_8hpp_source.html", "unified_diff": "@@ -162,29 +162,30 @@\n \n
67
\n
70 static constexpr seqan3::detail::align_config_id id{seqan3::detail::align_config_id::scoring};
\n
71};
\n \n
72
\n
79template <typename scheme_t>
\n-
80scoring_scheme(scheme_t) -> scoring_scheme<std::remove_cvref_t<scheme_t>>;
\n+
80scoring_scheme(scheme_t) -> scoring_scheme<std::remove_cvref_t<scheme_t>>;
\n
82
\n
83} // namespace seqan3::align_cfg
\n
detail.hpp
Provides some utility functions for the alignment configurations.
\n
basic.hpp
Provides various type traits on generic types.
\n
seqan3::align_cfg::scoring_scheme
Sets the scoring scheme for the alignment algorithm.
Definition align_config_scoring_scheme.hpp:42
\n
seqan3::align_cfg::scoring_scheme::scoring_scheme
constexpr scoring_scheme(scoring_scheme_t scheme)
Initialises the scoring scheme config with the given scheme.
Definition align_config_scoring_scheme.hpp:64
\n
seqan3::align_cfg::scoring_scheme::scoring_scheme
scoring_scheme(scheme_t) -> scoring_scheme< std::remove_cvref_t< scheme_t > >
Deduces the scoring scheme type from the constructor argument.
\n
seqan3::align_cfg::scoring_scheme::scheme
scoring_scheme_t scheme
The scoring scheme to be used in the alignment algorithm.
Definition align_config_scoring_scheme.hpp:45
\n
seqan3::align_cfg::scoring_scheme::operator=
constexpr scoring_scheme & operator=(scoring_scheme &&)=default
Defaulted.
\n
seqan3::align_cfg::scoring_scheme::scoring_scheme
constexpr scoring_scheme()=default
Defaulted.
\n
seqan3::align_cfg::scoring_scheme::operator=
constexpr scoring_scheme & operator=(scoring_scheme const &)=default
Defaulted.
\n
seqan3::align_cfg::scoring_scheme::scoring_scheme
constexpr scoring_scheme(scoring_scheme const &)=default
Defaulted.
\n
seqan3::align_cfg::scoring_scheme::scoring_scheme
constexpr scoring_scheme(scoring_scheme &&)=default
Defaulted.
\n
seqan3::align_cfg::scoring_scheme::~scoring_scheme
~scoring_scheme()=default
Defaulted.
\n+
seqan3::debug_stream_type
A "pretty printer" for most SeqAn data structures and related types.
Definition debug_stream_type.hpp:79
\n
seqan3::align_cfg
A special sub namespace for the alignment configurations.
Definition align_config_band.hpp:22
\n
std
SeqAn specific customisations in the standard namespace.
\n
pipeable_config_element.hpp
Provides seqan3::pipeable_config_element.
\n
scoring_scheme_concept.hpp
Provides seqan3::scoring_scheme_for.
\n
seqan3::pipeable_config_element
Adds pipe interface to configuration elements.
Definition pipeable_config_element.hpp:29
\n \n \n", "details": [{"source1": "html2text {}", "source2": "html2text {}", "unified_diff": "@@ -40,15 +40,15 @@\n 65 {}\n 67\n 70 static constexpr seqan3::detail::align_config_id id{seqan3::detail::\n align_config_id::scoring};\n 71};\n 72\n 79template \n-_\b8_\b0_\bs_\bc_\bo_\br_\bi_\bn_\bg_\b__\bs_\bc_\bh_\be_\bm_\be(scheme_t) -> _\bs_\bc_\bo_\br_\bi_\bn_\bg_\b__\bs_\bc_\bh_\be_\bm_\be_\b<_\bs_\bt_\bd_\b:_\b:_\br_\be_\bm_\bo_\bv_\be_\b__\bc_\bv_\br_\be_\bf_\b__\bt_\b<_\bs_\bc_\bh_\be_\bm_\be_\b__\bt_\b>>;\n+_\b8_\b0_\bs_\bc_\bo_\br_\bi_\bn_\bg_\b__\bs_\bc_\bh_\be_\bm_\be(_\bs_\bc_\bh_\be_\bm_\be_\b__\bt) -> _\bs_\bc_\bo_\br_\bi_\bn_\bg_\b__\bs_\bc_\bh_\be_\bm_\be_\b<_\bs_\bt_\bd_\b:_\b:_\br_\be_\bm_\bo_\bv_\be_\b__\bc_\bv_\br_\be_\bf_\b__\bt_\b<_\bs_\bc_\bh_\be_\bm_\be_\b__\bt_\b>>;\n 82\n 83} // namespace seqan3::align_cfg\n _\bd_\be_\bt_\ba_\bi_\bl_\b._\bh_\bp_\bp\n Provides some utility functions for the alignment configurations.\n _\bb_\ba_\bs_\bi_\bc_\b._\bh_\bp_\bp\n Provides various type traits on generic types.\n _\bs_\be_\bq_\ba_\bn_\b3_\b:_\b:_\ba_\bl_\bi_\bg_\bn_\b__\bc_\bf_\bg_\b:_\b:_\bs_\bc_\bo_\br_\bi_\bn_\bg_\b__\bs_\bc_\bh_\be_\bm_\be\n@@ -79,14 +79,17 @@\n Defaulted.\n _\bs_\be_\bq_\ba_\bn_\b3_\b:_\b:_\ba_\bl_\bi_\bg_\bn_\b__\bc_\bf_\bg_\b:_\b:_\bs_\bc_\bo_\br_\bi_\bn_\bg_\b__\bs_\bc_\bh_\be_\bm_\be_\b:_\b:_\bs_\bc_\bo_\br_\bi_\bn_\bg_\b__\bs_\bc_\bh_\be_\bm_\be\n constexpr scoring_scheme(scoring_scheme &&)=default\n Defaulted.\n _\bs_\be_\bq_\ba_\bn_\b3_\b:_\b:_\ba_\bl_\bi_\bg_\bn_\b__\bc_\bf_\bg_\b:_\b:_\bs_\bc_\bo_\br_\bi_\bn_\bg_\b__\bs_\bc_\bh_\be_\bm_\be_\b:_\b:_\b~_\bs_\bc_\bo_\br_\bi_\bn_\bg_\b__\bs_\bc_\bh_\be_\bm_\be\n ~scoring_scheme()=default\n Defaulted.\n+_\bs_\be_\bq_\ba_\bn_\b3_\b:_\b:_\bd_\be_\bb_\bu_\bg_\b__\bs_\bt_\br_\be_\ba_\bm_\b__\bt_\by_\bp_\be\n+A \"pretty printer\" for most SeqAn data structures and related types.\n+D\bDe\bef\bfi\bin\bni\bit\bti\bio\bon\bn debug_stream_type.hpp:79\n _\bs_\be_\bq_\ba_\bn_\b3_\b:_\b:_\ba_\bl_\bi_\bg_\bn_\b__\bc_\bf_\bg\n A special sub namespace for the alignment configurations.\n D\bDe\bef\bfi\bin\bni\bit\bti\bio\bon\bn align_config_band.hpp:22\n _\bs_\bt_\bd\n SeqAn specific customisations in the standard namespace.\n _\bp_\bi_\bp_\be_\ba_\bb_\bl_\be_\b__\bc_\bo_\bn_\bf_\bi_\bg_\b__\be_\bl_\be_\bm_\be_\bn_\bt_\b._\bh_\bp_\bp\n Provides seqan3::pipeable_config_element.\n"}]}, {"source1": "./usr/share/doc/libseqan3-dev/html/align__pairwise_8hpp_source.html", "source2": "./usr/share/doc/libseqan3-dev/html/align__pairwise_8hpp_source.html", "unified_diff": "@@ -153,21 +153,21 @@\n
30{
\n
31
\n
126template <typename sequence_t, typename alignment_config_t>
\n
127 requires detail::align_pairwise_single_input<sequence_t>
\n
128 && std::copy_constructible<std::remove_reference_t<sequence_t>>
\n
129 && detail::is_type_specialisation_of_v<alignment_config_t, configuration>
\n
\n-
130constexpr auto align_pairwise(sequence_t && seq, alignment_config_t const & config)
\n+
130constexpr auto align_pairwise(sequence_t && seq, alignment_config_t const & config)
\n
131{
\n
132 using std::get;
\n
133
\n
134 if constexpr (std::is_lvalue_reference_v<sequence_t>) // Forward tuple elements as references.
\n
135 {
\n-
136 return align_pairwise(std::tie(get<0>(seq), get<1>(seq)), config);
\n+
136 return align_pairwise(std::tie(get<0>(seq), get<1>(seq)), config);
\n
137 }
\n
138 else
\n
139 {
\n
140 static_assert(std::tuple_size_v<std::remove_reference_t<sequence_t>> == 2,
\n
141 "Alignment configuration error: Expects exactly two sequences for pairwise alignments.");
\n
142
\n
143 static_assert(std::ranges::viewable_range<std::tuple_element_t<0, std::remove_reference_t<sequence_t>>>
\n@@ -243,14 +243,15 @@\n
algorithm_executor_blocking.hpp
Provides seqan3::detail::algorithm_executor_blocking.
\n
algorithm_result_generator_range.hpp
Provides seqan3::detail::algorithm_result_generator_range.
\n
concept.hpp
Provides concepts needed internally for the alignment algorithms.
\n
type_traits.hpp
Provides helper type traits for the configuration and execution of the alignment algorithm.
\n
alignment_configurator.hpp
Provides seqan3::detail::alignment_selector.
\n
alignment_result.hpp
Provides seqan3::alignment_result.
\n
basic.hpp
Provides various type traits on generic types.
\n+
seqan3::debug_stream_type
A "pretty printer" for most SeqAn data structures and related types.
Definition debug_stream_type.hpp:79
\n \n \n
seqan3::align_cfg::parallel
seqan3::detail::parallel_mode< std::integral_constant< seqan3::detail::align_config_id, seqan3::detail::align_config_id::parallel > > parallel
Enables the parallel execution of the alignment algorithm if possible for the given configuration.
Definition align_config_parallel.hpp:35
\n
seqan3::align_pairwise
constexpr auto align_pairwise(sequence_t &&seq, alignment_config_t const &config)
Computes the pairwise alignment for a pair of sequences or a range over sequence pairs.
Definition align_pairwise.hpp:130
\n
seqan3::field::seq
@ seq
The "sequence", usually a range of nucleotides or amino acids.
\n
seqan3::views::zip
seqan::stl::views::zip zip
A view adaptor that takes several views and returns tuple-like values from every i-th element of each...
Definition zip.hpp:24
\n
seqan3::views::chunk
seqan::stl::views::chunk chunk
A view adaptor that divides a range into chunks. <dl class="no-api">This entity is not part of the Se...
Definition chunk.hpp:23
\n", "details": [{"source1": "html2text {}", "source2": "html2text {}", "unified_diff": "@@ -32,23 +32,23 @@\n 29namespace _\bs_\be_\bq_\ba_\bn_\b3\n 30{\n 31\n 126template \n 127 requires detail::align_pairwise_single_input\n 128 && std::copy_constructible>\n 129 && detail::is_type_specialisation_of_v\n-_\b1_\b3_\b0constexpr auto _\ba_\bl_\bi_\bg_\bn_\b__\bp_\ba_\bi_\br_\bw_\bi_\bs_\be(sequence_t && _\bs_\be_\bq, alignment_config_t const &\n+_\b1_\b3_\b0constexpr auto _\ba_\bl_\bi_\bg_\bn_\b__\bp_\ba_\bi_\br_\bw_\bi_\bs_\be(_\bs_\be_\bq_\bu_\be_\bn_\bc_\be_\b__\bt && _\bs_\be_\bq, _\ba_\bl_\bi_\bg_\bn_\bm_\be_\bn_\bt_\b__\bc_\bo_\bn_\bf_\bi_\bg_\b__\bt const &\n config)\n 131{\n 132 using std::get;\n 133\n 134 if constexpr (std::is_lvalue_reference_v) // Forward tuple\n elements as references.\n 135 {\n-136 return _\ba_\bl_\bi_\bg_\bn_\b__\bp_\ba_\bi_\br_\bw_\bi_\bs_\be(_\bs_\bt_\bd_\b:_\b:_\bt_\bi_\be(get<0>(_\bs_\be_\bq), get<1>(_\bs_\be_\bq)), config);\n+136 return _\ba_\bl_\bi_\bg_\bn_\b__\bp_\ba_\bi_\br_\bw_\bi_\bs_\be(_\bs_\bt_\bd_\b:_\b:_\bt_\bi_\be(_\bg_\be_\bt_\b<_\b0_\b>(_\bs_\be_\bq), _\bg_\be_\bt_\b<_\b1_\b>(_\bs_\be_\bq)), config);\n 137 }\n 138 else\n 139 {\n 140 static_assert(std::tuple_size_v> == 2,\n 141 \"Alignment configuration error: Expects exactly two sequences for pairwise\n alignments.\");\n 142\n@@ -152,14 +152,17 @@\n alignment algorithm.\n _\ba_\bl_\bi_\bg_\bn_\bm_\be_\bn_\bt_\b__\bc_\bo_\bn_\bf_\bi_\bg_\bu_\br_\ba_\bt_\bo_\br_\b._\bh_\bp_\bp\n Provides seqan3::detail::alignment_selector.\n _\ba_\bl_\bi_\bg_\bn_\bm_\be_\bn_\bt_\b__\br_\be_\bs_\bu_\bl_\bt_\b._\bh_\bp_\bp\n Provides seqan3::alignment_result.\n _\bb_\ba_\bs_\bi_\bc_\b._\bh_\bp_\bp\n Provides various type traits on generic types.\n+_\bs_\be_\bq_\ba_\bn_\b3_\b:_\b:_\bd_\be_\bb_\bu_\bg_\b__\bs_\bt_\br_\be_\ba_\bm_\b__\bt_\by_\bp_\be\n+A \"pretty printer\" for most SeqAn data structures and related types.\n+D\bDe\bef\bfi\bin\bni\bit\bti\bio\bon\bn debug_stream_type.hpp:79\n _\bs_\bt_\bd_\b:_\b:_\bc_\bo_\bn_\bd_\bi_\bt_\bi_\bo_\bn_\ba_\bl_\b__\bt\n _\bf_\bu_\bn_\bc_\bt_\bi_\bo_\bn_\ba_\bl\n _\bs_\be_\bq_\ba_\bn_\b3_\b:_\b:_\ba_\bl_\bi_\bg_\bn_\b__\bc_\bf_\bg_\b:_\b:_\bp_\ba_\br_\ba_\bl_\bl_\be_\bl\n seqan3::detail::parallel_mode< std::integral_constant< seqan3::detail::\n align_config_id, seqan3::detail::align_config_id::parallel > > parallel\n Enables the parallel execution of the alignment algorithm if possible for the\n given configuration.\n"}]}, {"source1": "./usr/share/doc/libseqan3-dev/html/aligned__allocator_8hpp_source.html", "source2": "./usr/share/doc/libseqan3-dev/html/aligned__allocator_8hpp_source.html", "unified_diff": "@@ -143,85 +143,85 @@\n
20{
\n
21
\n
68template <typename value_t, size_t alignment_v = __STDCPP_DEFAULT_NEW_ALIGNMENT__>
\n
\n
69class aligned_allocator
\n
70{
\n
71public:
\n-
73 static constexpr size_t alignment = alignment_v;
\n+
73 static constexpr size_t alignment = alignment_v;
\n
74
\n-
76 using value_type = value_t;
\n-
78 using pointer = value_type *;
\n+
76 using value_type = value_t;
\n+
78 using pointer = value_type *;
\n
80 using difference_type = typename std::pointer_traits<pointer>::difference_type;
\n
82 using size_type = std::make_unsigned_t<difference_type>;
\n
83
\n
85 using is_always_equal = std::true_type;
\n
86
\n
90 aligned_allocator() = default;
\n
91 aligned_allocator(aligned_allocator const &) = default;
\n
92 aligned_allocator(aligned_allocator &&) = default;
\n
93 aligned_allocator & operator=(aligned_allocator const &) = default;
\n
94 aligned_allocator & operator=(aligned_allocator &&) = default;
\n
95 ~aligned_allocator() = default;
\n
96
\n
98 template <class other_value_type, size_t other_alignment>
\n \n
102
\n
\n-
134 [[nodiscard]] pointer allocate(size_type const n) const
\n+
134 [[nodiscard]] pointer allocate(size_type const n) const
\n
135 {
\n
136 constexpr size_type max_size = std::numeric_limits<size_type>::max() / sizeof(value_type);
\n
137 if (n > max_size)
\n
138 throw std::bad_alloc{};
\n
139
\n-
140 size_t bytes_to_allocate = n * sizeof(value_type);
\n-
141 if constexpr (alignment <= __STDCPP_DEFAULT_NEW_ALIGNMENT__)
\n-
142 return static_cast<pointer>(::operator new(bytes_to_allocate));
\n+
140 size_t bytes_to_allocate = n * sizeof(value_type);
\n+
141 if constexpr (alignment <= __STDCPP_DEFAULT_NEW_ALIGNMENT__)
\n+
142 return static_cast<pointer>(::operator new(bytes_to_allocate));
\n
143 else // Use alignment aware allocator function.
\n-
144 return static_cast<pointer>(::operator new(bytes_to_allocate, static_cast<std::align_val_t>(alignment)));
\n+
144 return static_cast<pointer>(::operator new(bytes_to_allocate, static_cast<std::align_val_t>(alignment)));
\n
145 }
\n
\n
146
\n
\n-
173 void deallocate(pointer const p, size_type const n) const noexcept
\n+
173 void deallocate(pointer const p, size_type const n) const noexcept
\n
174 {
\n-
175 size_t bytes_to_deallocate = n * sizeof(value_type);
\n+
175 size_t bytes_to_deallocate = n * sizeof(value_type);
\n
176
\n-
177 if constexpr (alignment <= __STDCPP_DEFAULT_NEW_ALIGNMENT__)
\n-
178 ::operator delete(p, bytes_to_deallocate);
\n+
177 if constexpr (alignment <= __STDCPP_DEFAULT_NEW_ALIGNMENT__)
\n+
178 ::operator delete(p, bytes_to_deallocate);
\n
179 else // Use alignment aware deallocator function.
\n-
180 ::operator delete(p, bytes_to_deallocate, static_cast<std::align_val_t>(alignment));
\n+
180 ::operator delete(p, bytes_to_deallocate, static_cast<std::align_val_t>(alignment));
\n
181 }
\n
\n
182
\n
193 template <typename new_value_type>
\n
\n
194 struct rebind
\n
195 {
\n-
197 static constexpr size_t other_alignment = std::max(alignof(new_value_type), alignment);
\n-
199 using other = aligned_allocator<new_value_type, other_alignment>;
\n+
197 static constexpr size_t other_alignment = std::max(alignof(new_value_type), alignment);
\n+
199 using other = aligned_allocator<new_value_type, other_alignment>;
\n
200 };
\n
\n
201
\n
206 template <class value_type2, size_t alignment2>
\n
\n-
207 constexpr bool operator==(aligned_allocator<value_type2, alignment2> const &) noexcept
\n+
207 constexpr bool operator==(aligned_allocator<value_type2, alignment2> const &) noexcept
\n
208 {
\n-
209 return alignment == alignment2;
\n+
209 return alignment == alignment2;
\n
210 }
\n
\n
211
\n
213 template <class value_type2, size_t alignment2>
\n
\n-
214 constexpr bool operator!=(aligned_allocator<value_type2, alignment2> const &) noexcept
\n+
214 constexpr bool operator!=(aligned_allocator<value_type2, alignment2> const &) noexcept
\n
215 {
\n-
216 return alignment != alignment2;
\n+
216 return alignment != alignment2;
\n
217 }
\n
\n
219};
\n
\n
220
\n
221} // namespace seqan3
\n \n@@ -229,24 +229,24 @@\n \n
seqan3::aligned_allocator
Allocates uninitialized storage whose memory-alignment is specified by alignment.
Definition aligned_allocator.hpp:70
\n
seqan3::aligned_allocator::value_type
value_t value_type
The value type of the allocation.
Definition aligned_allocator.hpp:76
\n
seqan3::aligned_allocator::deallocate
void deallocate(pointer const p, size_type const n) const noexcept
Deallocates the storage referenced by the pointer p, which must be a pointer obtained by an earlier c...
Definition aligned_allocator.hpp:173
\n
seqan3::aligned_allocator::operator==
constexpr bool operator==(aligned_allocator< value_type2, alignment2 > const &) noexcept
Returns true if the memory-alignment matches.
Definition aligned_allocator.hpp:207
\n
seqan3::aligned_allocator::operator=
aligned_allocator & operator=(aligned_allocator &&)=default
Defaulted.
\n
seqan3::aligned_allocator::allocate
pointer allocate(size_type const n) const
Allocates sufficiently large memory to hold n many elements of value_type.
Definition aligned_allocator.hpp:134
\n-
seqan3::aligned_allocator::pointer
value_type * pointer
The pointer type of the allocation.
Definition aligned_allocator.hpp:78
\n
seqan3::aligned_allocator::operator=
aligned_allocator & operator=(aligned_allocator const &)=default
Defaulted.
\n
seqan3::aligned_allocator::aligned_allocator
constexpr aligned_allocator(aligned_allocator< other_value_type, other_alignment > const &) noexcept
Copy constructor with different value type and alignment.
Definition aligned_allocator.hpp:99
\n
seqan3::aligned_allocator::~aligned_allocator
~aligned_allocator()=default
Defaulted.
\n
seqan3::aligned_allocator::operator!=
constexpr bool operator!=(aligned_allocator< value_type2, alignment2 > const &) noexcept
Returns false if the memory-alignment mismatches.
Definition aligned_allocator.hpp:214
\n
seqan3::aligned_allocator::aligned_allocator
aligned_allocator(aligned_allocator const &)=default
Defaulted.
\n
seqan3::aligned_allocator::alignment
static constexpr size_t alignment
The memory-alignment of the allocation.
Definition aligned_allocator.hpp:73
\n
seqan3::aligned_allocator::aligned_allocator
aligned_allocator(aligned_allocator &&)=default
Defaulted.
\n
seqan3::aligned_allocator::aligned_allocator
aligned_allocator()=default
Defaulted.
\n
seqan3::aligned_allocator::difference_type
typename std::pointer_traits< pointer >::difference_type difference_type
The difference type of the allocation.
Definition aligned_allocator.hpp:80
\n+
seqan3::debug_stream_type
A "pretty printer" for most SeqAn data structures and related types.
Definition debug_stream_type.hpp:79
\n \n \n \n
std::numeric_limits::max
T max(T... args)
\n \n
seqan3
The main SeqAn3 namespace.
Definition aligned_sequence_concept.hpp:26
\n
platform.hpp
Provides platform and dependency checks.
\n", "details": [{"source1": "html2text {}", "source2": "html2text {}", "unified_diff": "@@ -23,17 +23,17 @@\n 20{\n 21\n 68template \n _\b6_\b9class _\ba_\bl_\bi_\bg_\bn_\be_\bd_\b__\ba_\bl_\bl_\bo_\bc_\ba_\bt_\bo_\br\n 70{\n 71public:\n-_\b7_\b3 static constexpr size_t _\ba_\bl_\bi_\bg_\bn_\bm_\be_\bn_\bt = alignment_v;\n+_\b7_\b3 static constexpr size_t _\ba_\bl_\bi_\bg_\bn_\bm_\be_\bn_\bt = _\ba_\bl_\bi_\bg_\bn_\bm_\be_\bn_\bt_\b__\bv;\n 74\n-_\b7_\b6 using _\bv_\ba_\bl_\bu_\be_\b__\bt_\by_\bp_\be = value_t;\n+_\b7_\b6 using _\bv_\ba_\bl_\bu_\be_\b__\bt_\by_\bp_\be = _\bv_\ba_\bl_\bu_\be_\b__\bt;\n _\b7_\b8 using _\bp_\bo_\bi_\bn_\bt_\be_\br = _\bv_\ba_\bl_\bu_\be_\b__\bt_\by_\bp_\be *;\n _\b8_\b0 using _\bd_\bi_\bf_\bf_\be_\br_\be_\bn_\bc_\be_\b__\bt_\by_\bp_\be = typename _\bs_\bt_\bd_\b:_\b:_\bp_\bo_\bi_\bn_\bt_\be_\br_\b__\bt_\br_\ba_\bi_\bt_\bs_\b<_\bp_\bo_\bi_\bn_\bt_\be_\br_\b>_\b:_\b:\n _\bd_\bi_\bf_\bf_\be_\br_\be_\bn_\bc_\be_\b__\bt_\by_\bp_\be;\n _\b8_\b2 using _\bs_\bi_\bz_\be_\b__\bt_\by_\bp_\be = _\bs_\bt_\bd_\b:_\b:_\bm_\ba_\bk_\be_\b__\bu_\bn_\bs_\bi_\bg_\bn_\be_\bd_\b__\bt_\b<_\bd_\bi_\bf_\bf_\be_\br_\be_\bn_\bc_\be_\b__\bt_\by_\bp_\be_\b>;\n 83\n _\b8_\b5 using _\bi_\bs_\b__\ba_\bl_\bw_\ba_\by_\bs_\b__\be_\bq_\bu_\ba_\bl = _\bs_\bt_\bd_\b:_\b:_\bt_\br_\bu_\be_\b__\bt_\by_\bp_\be;\n 86\n@@ -45,60 +45,60 @@\n _\b9_\b5 _\b~_\ba_\bl_\bi_\bg_\bn_\be_\bd_\b__\ba_\bl_\bl_\bo_\bc_\ba_\bt_\bo_\br() = default;\n 96\n 98 template \n _\b9_\b9 constexpr _\ba_\bl_\bi_\bg_\bn_\be_\bd_\b__\ba_\bl_\bl_\bo_\bc_\ba_\bt_\bo_\br(_\ba_\bl_\bi_\bg_\bn_\be_\bd_\b__\ba_\bl_\bl_\bo_\bc_\ba_\bt_\bo_\br_\b<_\bo_\bt_\bh_\be_\br_\b__\bv_\ba_\bl_\bu_\be_\b__\bt_\by_\bp_\be_\b,\n _\bo_\bt_\bh_\be_\br_\b__\ba_\bl_\bi_\bg_\bn_\bm_\be_\bn_\bt_\b> const &) noexcept\n 100 {}\n 102\n-_\b1_\b3_\b4 [[nodiscard]] _\bp_\bo_\bi_\bn_\bt_\be_\br _\ba_\bl_\bl_\bo_\bc_\ba_\bt_\be(_\bs_\bi_\bz_\be_\b__\bt_\by_\bp_\be const n) const\n+_\b1_\b3_\b4 [[_\bn_\bo_\bd_\bi_\bs_\bc_\ba_\br_\bd]] _\bp_\bo_\bi_\bn_\bt_\be_\br _\ba_\bl_\bl_\bo_\bc_\ba_\bt_\be(_\bs_\bi_\bz_\be_\b__\bt_\by_\bp_\be const n) const\n 135 {\n 136 constexpr _\bs_\bi_\bz_\be_\b__\bt_\by_\bp_\be max_size = _\bs_\bt_\bd_\b:_\b:_\bn_\bu_\bm_\be_\br_\bi_\bc_\b__\bl_\bi_\bm_\bi_\bt_\bs_\b<_\bs_\bi_\bz_\be_\b__\bt_\by_\bp_\be_\b>_\b:_\b:_\bm_\ba_\bx() /\n sizeof(_\bv_\ba_\bl_\bu_\be_\b__\bt_\by_\bp_\be);\n 137 if (n > max_size)\n 138 throw _\bs_\bt_\bd_\b:_\b:_\bb_\ba_\bd_\b__\ba_\bl_\bl_\bo_\bc{};\n 139\n-140 size_t bytes_to_allocate = n * sizeof(_\bv_\ba_\bl_\bu_\be_\b__\bt_\by_\bp_\be);\n-141 if constexpr (_\ba_\bl_\bi_\bg_\bn_\bm_\be_\bn_\bt <= __STDCPP_DEFAULT_NEW_ALIGNMENT__)\n-142 return static_cast<_\bp_\bo_\bi_\bn_\bt_\be_\br>(::operator new(bytes_to_allocate));\n+140 size_t _\bb_\by_\bt_\be_\bs_\b__\bt_\bo_\b__\ba_\bl_\bl_\bo_\bc_\ba_\bt_\be = n * sizeof(_\bv_\ba_\bl_\bu_\be_\b__\bt_\by_\bp_\be);\n+141 if constexpr (_\ba_\bl_\bi_\bg_\bn_\bm_\be_\bn_\bt <= _\b__\b__\bS_\bT_\bD_\bC_\bP_\bP_\b__\bD_\bE_\bF_\bA_\bU_\bL_\bT_\b__\bN_\bE_\bW_\b__\bA_\bL_\bI_\bG_\bN_\bM_\bE_\bN_\bT_\b__\b_)\n+142 return static_cast<_\bp_\bo_\bi_\bn_\bt_\be_\br>(::operator new(_\bb_\by_\bt_\be_\bs_\b__\bt_\bo_\b__\ba_\bl_\bl_\bo_\bc_\ba_\bt_\be));\n 143 else // Use alignment aware allocator function.\n-144 return static_cast<_\bp_\bo_\bi_\bn_\bt_\be_\br>(::operator new(bytes_to_allocate,\n+144 return static_cast<_\bp_\bo_\bi_\bn_\bt_\be_\br>(::operator new(_\bb_\by_\bt_\be_\bs_\b__\bt_\bo_\b__\ba_\bl_\bl_\bo_\bc_\ba_\bt_\be,\n static_cast<_\bs_\bt_\bd_\b:_\b:_\ba_\bl_\bi_\bg_\bn_\b__\bv_\ba_\bl_\b__\bt>(_\ba_\bl_\bi_\bg_\bn_\bm_\be_\bn_\bt)));\n 145 }\n 146\n _\b1_\b7_\b3 void _\bd_\be_\ba_\bl_\bl_\bo_\bc_\ba_\bt_\be(_\bp_\bo_\bi_\bn_\bt_\be_\br const p, _\bs_\bi_\bz_\be_\b__\bt_\by_\bp_\be const n) const noexcept\n 174 {\n-175 size_t bytes_to_deallocate = n * sizeof(_\bv_\ba_\bl_\bu_\be_\b__\bt_\by_\bp_\be);\n+175 size_t _\bb_\by_\bt_\be_\bs_\b__\bt_\bo_\b__\bd_\be_\ba_\bl_\bl_\bo_\bc_\ba_\bt_\be = n * sizeof(_\bv_\ba_\bl_\bu_\be_\b__\bt_\by_\bp_\be);\n 176\n-177 if constexpr (_\ba_\bl_\bi_\bg_\bn_\bm_\be_\bn_\bt <= __STDCPP_DEFAULT_NEW_ALIGNMENT__)\n-178 ::operator delete(p, bytes_to_deallocate);\n+177 if constexpr (_\ba_\bl_\bi_\bg_\bn_\bm_\be_\bn_\bt <= _\b__\b__\bS_\bT_\bD_\bC_\bP_\bP_\b__\bD_\bE_\bF_\bA_\bU_\bL_\bT_\b__\bN_\bE_\bW_\b__\bA_\bL_\bI_\bG_\bN_\bM_\bE_\bN_\bT_\b__\b_)\n+178 ::operator delete(p, _\bb_\by_\bt_\be_\bs_\b__\bt_\bo_\b__\bd_\be_\ba_\bl_\bl_\bo_\bc_\ba_\bt_\be);\n 179 else // Use alignment aware deallocator function.\n-180 ::operator delete(p, bytes_to_deallocate, static_cast<_\bs_\bt_\bd_\b:_\b:_\ba_\bl_\bi_\bg_\bn_\b__\bv_\ba_\bl_\b__\bt>\n+180 ::operator delete(p, _\bb_\by_\bt_\be_\bs_\b__\bt_\bo_\b__\bd_\be_\ba_\bl_\bl_\bo_\bc_\ba_\bt_\be, static_cast<_\bs_\bt_\bd_\b:_\b:_\ba_\bl_\bi_\bg_\bn_\b__\bv_\ba_\bl_\b__\bt>\n (_\ba_\bl_\bi_\bg_\bn_\bm_\be_\bn_\bt));\n 181 }\n 182\n 193 template \n _\b1_\b9_\b4 struct _\br_\be_\bb_\bi_\bn_\bd\n 195 {\n-_\b1_\b9_\b7 static constexpr size_t _\bo_\bt_\bh_\be_\br_\b__\ba_\bl_\bi_\bg_\bn_\bm_\be_\bn_\bt = _\bs_\bt_\bd_\b:_\b:_\bm_\ba_\bx(alignof(new_value_type),\n+_\b1_\b9_\b7 static constexpr size_t _\bo_\bt_\bh_\be_\br_\b__\ba_\bl_\bi_\bg_\bn_\bm_\be_\bn_\bt = _\bs_\bt_\bd_\b:_\b:_\bm_\ba_\bx(alignof(_\bn_\be_\bw_\b__\bv_\ba_\bl_\bu_\be_\b__\bt_\by_\bp_\be),\n _\ba_\bl_\bi_\bg_\bn_\bm_\be_\bn_\bt);\n _\b1_\b9_\b9 using _\bo_\bt_\bh_\be_\br = _\ba_\bl_\bi_\bg_\bn_\be_\bd_\b__\ba_\bl_\bl_\bo_\bc_\ba_\bt_\bo_\br_\b<_\bn_\be_\bw_\b__\bv_\ba_\bl_\bu_\be_\b__\bt_\by_\bp_\be_\b,_\b _\bo_\bt_\bh_\be_\br_\b__\ba_\bl_\bi_\bg_\bn_\bm_\be_\bn_\bt_\b>;\n 200 };\n 201\n 206 template \n _\b2_\b0_\b7 constexpr bool _\bo_\bp_\be_\br_\ba_\bt_\bo_\br_\b=_\b=(_\ba_\bl_\bi_\bg_\bn_\be_\bd_\b__\ba_\bl_\bl_\bo_\bc_\ba_\bt_\bo_\br_\b<_\bv_\ba_\bl_\bu_\be_\b__\bt_\by_\bp_\be_\b2_\b,_\b _\ba_\bl_\bi_\bg_\bn_\bm_\be_\bn_\bt_\b2_\b> const\n &) noexcept\n 208 {\n-209 return _\ba_\bl_\bi_\bg_\bn_\bm_\be_\bn_\bt == alignment2;\n+209 return _\ba_\bl_\bi_\bg_\bn_\bm_\be_\bn_\bt == _\ba_\bl_\bi_\bg_\bn_\bm_\be_\bn_\bt_\b2;\n 210 }\n 211\n 213 template \n _\b2_\b1_\b4 constexpr bool _\bo_\bp_\be_\br_\ba_\bt_\bo_\br_\b!_\b=(_\ba_\bl_\bi_\bg_\bn_\be_\bd_\b__\ba_\bl_\bl_\bo_\bc_\ba_\bt_\bo_\br_\b<_\bv_\ba_\bl_\bu_\be_\b__\bt_\by_\bp_\be_\b2_\b,_\b _\ba_\bl_\bi_\bg_\bn_\bm_\be_\bn_\bt_\b2_\b> const\n &) noexcept\n 215 {\n-216 return _\ba_\bl_\bi_\bg_\bn_\bm_\be_\bn_\bt != alignment2;\n+216 return _\ba_\bl_\bi_\bg_\bn_\bm_\be_\bn_\bt != _\ba_\bl_\bi_\bg_\bn_\bm_\be_\bn_\bt_\b2;\n 217 }\n 219};\n 220\n 221} // namespace seqan3\n _\ba_\bl_\bg_\bo_\br_\bi_\bt_\bh_\bm\n _\bs_\bt_\bd_\b:_\b:_\ba_\bl_\bi_\bg_\bn_\b__\bv_\ba_\bl_\b__\bt\n _\bs_\bt_\bd_\b:_\b:_\bb_\ba_\bd_\b__\ba_\bl_\bl_\bo_\bc\n@@ -123,18 +123,14 @@\n _\bs_\be_\bq_\ba_\bn_\b3_\b:_\b:_\ba_\bl_\bi_\bg_\bn_\be_\bd_\b__\ba_\bl_\bl_\bo_\bc_\ba_\bt_\bo_\br_\b:_\b:_\bo_\bp_\be_\br_\ba_\bt_\bo_\br_\b=\n aligned_allocator & operator=(aligned_allocator &&)=default\n Defaulted.\n _\bs_\be_\bq_\ba_\bn_\b3_\b:_\b:_\ba_\bl_\bi_\bg_\bn_\be_\bd_\b__\ba_\bl_\bl_\bo_\bc_\ba_\bt_\bo_\br_\b:_\b:_\ba_\bl_\bl_\bo_\bc_\ba_\bt_\be\n pointer allocate(size_type const n) const\n Allocates sufficiently large memory to hold n many elements of value_type.\n D\bDe\bef\bfi\bin\bni\bit\bti\bio\bon\bn aligned_allocator.hpp:134\n-_\bs_\be_\bq_\ba_\bn_\b3_\b:_\b:_\ba_\bl_\bi_\bg_\bn_\be_\bd_\b__\ba_\bl_\bl_\bo_\bc_\ba_\bt_\bo_\br_\b:_\b:_\bp_\bo_\bi_\bn_\bt_\be_\br\n-value_type * pointer\n-The pointer type of the allocation.\n-D\bDe\bef\bfi\bin\bni\bit\bti\bio\bon\bn aligned_allocator.hpp:78\n _\bs_\be_\bq_\ba_\bn_\b3_\b:_\b:_\ba_\bl_\bi_\bg_\bn_\be_\bd_\b__\ba_\bl_\bl_\bo_\bc_\ba_\bt_\bo_\br_\b:_\b:_\bo_\bp_\be_\br_\ba_\bt_\bo_\br_\b=\n aligned_allocator & operator=(aligned_allocator const &)=default\n Defaulted.\n _\bs_\be_\bq_\ba_\bn_\b3_\b:_\b:_\ba_\bl_\bi_\bg_\bn_\be_\bd_\b__\ba_\bl_\bl_\bo_\bc_\ba_\bt_\bo_\br_\b:_\b:_\ba_\bl_\bi_\bg_\bn_\be_\bd_\b__\ba_\bl_\bl_\bo_\bc_\ba_\bt_\bo_\br\n constexpr aligned_allocator(aligned_allocator< other_value_type,\n other_alignment > const &) noexcept\n Copy constructor with different value type and alignment.\n@@ -160,14 +156,17 @@\n _\bs_\be_\bq_\ba_\bn_\b3_\b:_\b:_\ba_\bl_\bi_\bg_\bn_\be_\bd_\b__\ba_\bl_\bl_\bo_\bc_\ba_\bt_\bo_\br_\b:_\b:_\ba_\bl_\bi_\bg_\bn_\be_\bd_\b__\ba_\bl_\bl_\bo_\bc_\ba_\bt_\bo_\br\n aligned_allocator()=default\n Defaulted.\n _\bs_\be_\bq_\ba_\bn_\b3_\b:_\b:_\ba_\bl_\bi_\bg_\bn_\be_\bd_\b__\ba_\bl_\bl_\bo_\bc_\ba_\bt_\bo_\br_\b:_\b:_\bd_\bi_\bf_\bf_\be_\br_\be_\bn_\bc_\be_\b__\bt_\by_\bp_\be\n typename std::pointer_traits< pointer >::difference_type difference_type\n The difference type of the allocation.\n D\bDe\bef\bfi\bin\bni\bit\bti\bio\bon\bn aligned_allocator.hpp:80\n+_\bs_\be_\bq_\ba_\bn_\b3_\b:_\b:_\bd_\be_\bb_\bu_\bg_\b__\bs_\bt_\br_\be_\ba_\bm_\b__\bt_\by_\bp_\be\n+A \"pretty printer\" for most SeqAn data structures and related types.\n+D\bDe\bef\bfi\bin\bni\bit\bti\bio\bon\bn debug_stream_type.hpp:79\n _\bs_\bt_\bd_\b:_\b:_\bt_\br_\bu_\be_\b__\bt_\by_\bp_\be\n _\bl_\bi_\bm_\bi_\bt_\bs\n _\bs_\bt_\bd_\b:_\b:_\bm_\ba_\bk_\be_\b__\bu_\bn_\bs_\bi_\bg_\bn_\be_\bd_\b__\bt\n _\bs_\bt_\bd_\b:_\b:_\bn_\bu_\bm_\be_\br_\bi_\bc_\b__\bl_\bi_\bm_\bi_\bt_\bs_\b:_\b:_\bm_\ba_\bx\n T max(T... args)\n _\bm_\be_\bm_\bo_\br_\by\n _\bs_\be_\bq_\ba_\bn_\b3\n"}]}, {"source1": "./usr/share/doc/libseqan3-dev/html/aligned__sequence__builder_8hpp_source.html", "source2": "./usr/share/doc/libseqan3-dev/html/aligned__sequence__builder_8hpp_source.html", "unified_diff": "@@ -170,17 +170,17 @@\n
66
\n
74template <std::ranges::viewable_range first_sequence_t, std::ranges::viewable_range second_sequence_t>
\n
75struct make_pairwise_alignment_type
\n
76{
\n
78 using first_aligned_t = typename make_aligned_sequence_type<first_sequence_t>::type;
\n
80 using second_aligned_t = typename make_aligned_sequence_type<second_sequence_t>::type;
\n
81
\n-
82 static_assert(seqan3::writable_aligned_sequence<first_aligned_t>,
\n+
82 static_assert(seqan3::writable_aligned_sequence<first_aligned_t>,
\n
83 "first_aligned_t is required to model seqan3::writable_aligned_sequence!");
\n-
84 static_assert(seqan3::writable_aligned_sequence<second_aligned_t>,
\n+
84 static_assert(seqan3::writable_aligned_sequence<second_aligned_t>,
\n
85 "second_aligned_t is required to model seqan3::writable_aligned_sequence!");
\n
86
\n
88 using type = std::tuple<first_aligned_t, second_aligned_t>;
\n
89};
\n
90
\n
112template <std::ranges::viewable_range fst_sequence_t, std::ranges::viewable_range sec_sequence_t>
\n
113class aligned_sequence_builder
\n@@ -285,20 +285,20 @@\n
246};
\n
247
\n
253template <std::ranges::viewable_range fst_sequence_t, std::ranges::viewable_range sec_sequence_t>
\n
254aligned_sequence_builder(fst_sequence_t &&,
\n
255 sec_sequence_t &&) -> aligned_sequence_builder<fst_sequence_t, sec_sequence_t>;
\n
257} // namespace seqan3::detail
\n
aligned_sequence_concept.hpp
Includes the aligned_sequence and the related insert_gap and erase_gap functions to enable stl contai...
\n+
seqan3::debug_stream_type
A "pretty printer" for most SeqAn data structures and related types.
Definition debug_stream_type.hpp:79
\n
std::vector::emplace_back
T emplace_back(T... args)
\n
gap_decorator.hpp
Provides seqan3::gap_decorator.
\n
gapped.hpp
Provides seqan3::gapped.
\n
seqan3::field::alignment
@ alignment
The (pairwise) alignment stored in an object that models seqan3::detail::pairwise_alignment.
\n
seqan3::views::slice
constexpr auto slice
A view adaptor that returns a half-open interval on the underlying range.
Definition slice.hpp:137
\n-
writable_aligned_sequence
The generic concept for an aligned sequence that is writable.
\n
is_class_template_declarable.hpp
Provides a type trait for verifying valid template declarations.
\n
lazy_conditional.hpp
Provides lazy template instantiation traits.
\n
matrix_coordinate.hpp
Provides seqan3::detail::matrix_index, seqan3::detail::matrix_coordinate and associated strong types.
\n
std
SeqAn specific customisations in the standard namespace.
\n \n
slice.hpp
Provides seqan3::views::slice.
\n
std::tie
T tie(T... args)
\n", "details": [{"source1": "html2text {}", "source2": "html2text {}", "unified_diff": "@@ -193,30 +193,31 @@\n 254aligned_sequence_builder(fst_sequence_t &&,\n 255 sec_sequence_t &&) -> aligned_sequence_builder;\n 257} // namespace seqan3::detail\n _\ba_\bl_\bi_\bg_\bn_\be_\bd_\b__\bs_\be_\bq_\bu_\be_\bn_\bc_\be_\b__\bc_\bo_\bn_\bc_\be_\bp_\bt_\b._\bh_\bp_\bp\n Includes the aligned_sequence and the related insert_gap and erase_gap\n functions to enable stl contai...\n+_\bs_\be_\bq_\ba_\bn_\b3_\b:_\b:_\bd_\be_\bb_\bu_\bg_\b__\bs_\bt_\br_\be_\ba_\bm_\b__\bt_\by_\bp_\be\n+A \"pretty printer\" for most SeqAn data structures and related types.\n+D\bDe\bef\bfi\bin\bni\bit\bti\bio\bon\bn debug_stream_type.hpp:79\n _\bs_\bt_\bd_\b:_\b:_\bv_\be_\bc_\bt_\bo_\br_\b:_\b:_\be_\bm_\bp_\bl_\ba_\bc_\be_\b__\bb_\ba_\bc_\bk\n T emplace_back(T... args)\n _\bg_\ba_\bp_\b__\bd_\be_\bc_\bo_\br_\ba_\bt_\bo_\br_\b._\bh_\bp_\bp\n Provides seqan3::gap_decorator.\n _\bg_\ba_\bp_\bp_\be_\bd_\b._\bh_\bp_\bp\n Provides seqan3::gapped.\n _\bs_\be_\bq_\ba_\bn_\b3_\b:_\b:_\bf_\bi_\be_\bl_\bd_\b:_\b:_\ba_\bl_\bi_\bg_\bn_\bm_\be_\bn_\bt\n @ alignment\n The (pairwise) alignment stored in an object that models seqan3::detail::\n pairwise_alignment.\n _\bs_\be_\bq_\ba_\bn_\b3_\b:_\b:_\bv_\bi_\be_\bw_\bs_\b:_\b:_\bs_\bl_\bi_\bc_\be\n constexpr auto slice\n A view adaptor that returns a half-open interval on the underlying range.\n D\bDe\bef\bfi\bin\bni\bit\bti\bio\bon\bn slice.hpp:137\n-_\bw_\br_\bi_\bt_\ba_\bb_\bl_\be_\b__\ba_\bl_\bi_\bg_\bn_\be_\bd_\b__\bs_\be_\bq_\bu_\be_\bn_\bc_\be\n-The generic concept for an aligned sequence that is writable.\n _\bi_\bs_\b__\bc_\bl_\ba_\bs_\bs_\b__\bt_\be_\bm_\bp_\bl_\ba_\bt_\be_\b__\bd_\be_\bc_\bl_\ba_\br_\ba_\bb_\bl_\be_\b._\bh_\bp_\bp\n Provides a type trait for verifying valid template declarations.\n _\bl_\ba_\bz_\by_\b__\bc_\bo_\bn_\bd_\bi_\bt_\bi_\bo_\bn_\ba_\bl_\b._\bh_\bp_\bp\n Provides lazy template instantiation traits.\n _\bm_\ba_\bt_\br_\bi_\bx_\b__\bc_\bo_\bo_\br_\bd_\bi_\bn_\ba_\bt_\be_\b._\bh_\bp_\bp\n Provides seqan3::detail::matrix_index, seqan3::detail::matrix_coordinate and\n associated strong types.\n"}]}, {"source1": "./usr/share/doc/libseqan3-dev/html/aligned__sequence__concept_8hpp_source.html", "source2": "./usr/share/doc/libseqan3-dev/html/aligned__sequence__concept_8hpp_source.html", "unified_diff": "@@ -144,28 +144,28 @@\n
22// unaligned_seq transformation trait
\n
23// ---------------------------------------------------------------------------------------------------------------------
\n
24
\n
\n
25namespace seqan3::detail
\n
26{
\n
27
\n-
29template <template <typename...> typename container_type, typename seq_alph_t, typename... rest_t>
\n-
30 requires container<container_type<gapped<seq_alph_t>, rest_t...>>
\n+
29template <template <typename...> typename container_type, typename seq_alph_t, typename... rest_t>
\n+
30 requires container<container_type<gapped<seq_alph_t>, rest_t...>>
\n
31constexpr auto
\n-
32 remove_gap_from_value_type(container_type<gapped<seq_alph_t>, rest_t...>) -> container_type<seq_alph_t, rest_t...>;
\n+
32 remove_gap_from_value_type(container_type<gapped<seq_alph_t>, rest_t...>) -> container_type<seq_alph_t, rest_t...>;
\n
33
\n-
35template <template <typename...> typename container_type,
\n+
35template <template <typename...> typename container_type,
\n
36 template <typename...>
\n
37 typename allocator_type,
\n-
38 typename seq_alph_t,
\n-
39 typename... rest_t>
\n-
40 requires container<container_type<gapped<seq_alph_t>, allocator_type<gapped<seq_alph_t>>, rest_t...>>
\n+
38 typename seq_alph_t,
\n+
39 typename... rest_t>
\n+
40 requires container<container_type<gapped<seq_alph_t>, allocator_type<gapped<seq_alph_t>>, rest_t...>>
\n
41constexpr auto
\n-
42 remove_gap_from_value_type(container_type<gapped<seq_alph_t>, allocator_type<gapped<seq_alph_t>>, rest_t...>)
\n-
43 -> container_type<seq_alph_t, allocator_type<seq_alph_t>, rest_t...>;
\n+
42 remove_gap_from_value_type(container_type<gapped<seq_alph_t>, allocator_type<gapped<seq_alph_t>>, rest_t...>)
\n+
43 -> container_type<seq_alph_t, allocator_type<seq_alph_t>, rest_t...>;
\n
44
\n
46template <typename t>
\n
47struct unaligned_seq
\n
48{};
\n
49
\n
51template <typename t>
\n
52 requires (!requires { typename std::remove_reference_t<t>::unaligned_sequence_type; })
\n@@ -325,26 +325,25 @@\n
477inline constexpr bool all_model_aligned_seq = (aligned_sequence<elems> && ...);
\n
478
\n
482template <typename... elems>
\n
483inline constexpr bool all_model_aligned_seq<type_list<elems...>> = all_model_aligned_seq<elems...>;
\n
484} // namespace seqan3::detail
\n \n
exception.hpp
Includes customized exception types for the alignment module .
\n-
seqan3::alphabet_variant
A combined alphabet that can hold values of either of its alternatives..
Definition alphabet_variant.hpp:127
\n+
seqan3::debug_stream_type
A "pretty printer" for most SeqAn data structures and related types.
Definition debug_stream_type.hpp:79
\n
gapped.hpp
Provides seqan3::gapped.
\n
writable_aligned_sequence::insert_gap
aligned_seq_t::iterator insert_gap(aligned_seq_t &aligned_seq, typename aligned_seq_t::const_iterator pos_it, typename aligned_seq_t::size_type size)
An implementation of seqan3::writable_aligned_sequence::insert_gap for sequence containers.
Definition aligned_sequence_concept.hpp:276
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writable_aligned_sequence::assign_unaligned
void assign_unaligned(aligned_seq_t &aligned_seq, unaligned_sequence_type &&unaligned_seq)
An implementation of seqan3::writable_aligned_sequence::assign_unaligned_sequence for sequence contai...
Definition aligned_sequence_concept.hpp:372
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writable_aligned_sequence::erase_gap
std::ranges::iterator_t< range_type > erase_gap(range_type &rng, std::ranges::iterator_t< range_type > const first, std::ranges::iterator_t< range_type > const last)
An implementation of seqan3::writable_aligned_sequence::erase_gap for ranges with the corresponding m...
Definition aligned_sequence_concept.hpp:461
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writable_aligned_sequence::erase_gap
aligned_seq_t::iterator erase_gap(aligned_seq_t &aligned_seq, typename aligned_seq_t::const_iterator pos_it)
An implementation of seqan3::writable_aligned_sequence::erase_gap for sequence containers.
Definition aligned_sequence_concept.hpp:304
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writable_aligned_sequence::erase_gap
std::ranges::iterator_t< range_type > erase_gap(range_type &rng, std::ranges::iterator_t< range_type > const pos_it)
An implementation of seqan3::writable_aligned_sequence::erase_gap for ranges with the corresponding m...
Definition aligned_sequence_concept.hpp:434
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writable_aligned_sequence::erase_gap
aligned_seq_t::iterator erase_gap(aligned_seq_t &aligned_seq, typename aligned_seq_t::const_iterator first, typename aligned_seq_t::const_iterator last)
An implementation of seqan3::writable_aligned_sequence::erase_gap for sequence containers.
Definition aligned_sequence_concept.hpp:335
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writable_aligned_sequence::insert_gap
std::ranges::iterator_t< range_type > insert_gap(range_type &rng, std::ranges::iterator_t< range_type > const pos_it, typename range_type::size_type const size=1)
An implementation of seqan3::writable_aligned_sequence::insert_gap for ranges with the corresponding ...
Definition aligned_sequence_concept.hpp:409
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writable_aligned_sequence::insert_gap
aligned_seq_t::iterator insert_gap(aligned_seq_t &aligned_seq, typename aligned_seq_t::const_iterator pos_it)
An implementation of seqan3::writable_aligned_sequence::insert_gap for sequence containers.
Definition aligned_sequence_concept.hpp:252
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aligned_sequence
The generic concept for an aligned sequence.
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container
The (most general) container concept as defined by the standard library.
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sequence
The generic concept for a (biological) sequence.
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weakly_assignable_from
Resolves to std::is_assignable_v<t>.
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writable_aligned_sequence
The generic concept for an aligned sequence that is writable.
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seqan3
The main SeqAn3 namespace.
Definition aligned_sequence_concept.hpp:26
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SEQAN3_WORKAROUND_GCC_BOGUS_MEMCPY_START
#define SEQAN3_WORKAROUND_GCC_BOGUS_MEMCPY_START(...)
Denotes the start of a block where diagnostics are ignored.
Definition platform.hpp:268
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SEQAN3_WORKAROUND_GCC_BOGUS_MEMCPY_STOP
#define SEQAN3_WORKAROUND_GCC_BOGUS_MEMCPY_STOP
Denotes the end of a block where diagnostics are ignored.
Definition platform.hpp:277
\n \n", "details": [{"source1": "html2text {}", "source2": "html2text {}", "unified_diff": "@@ -25,32 +25,32 @@\n 22// unaligned_seq transformation trait\n 23// --------------------------------------------------------------------------\n -------------------------------------------\n 24\n _\b2_\b5namespace seqan3::detail\n 26{\n 27\n-29template
Publication
Title From theory to practice: Plug and play with succinct data structures.