--- /srv/rebuilderd/tmp/rebuilderdzLv6IT/inputs/seqan3-doc_3.4.0~rc.3+ds-4_all.deb +++ /srv/rebuilderd/tmp/rebuilderdzLv6IT/out/seqan3-doc_3.4.0~rc.3+ds-4_all.deb ├── file list │ @@ -1,3 +1,3 @@ │ -rw-r--r-- 0 0 0 4 2025-04-23 13:22:40.000000 debian-binary │ --rw-r--r-- 0 0 0 81156 2025-04-23 13:22:40.000000 control.tar.xz │ --rw-r--r-- 0 0 0 2744012 2025-04-23 13:22:40.000000 data.tar.xz │ +-rw-r--r-- 0 0 0 81164 2025-04-23 13:22:40.000000 control.tar.xz │ +-rw-r--r-- 0 0 0 2713516 2025-04-23 13:22:40.000000 data.tar.xz ├── control.tar.xz │ ├── control.tar │ │ ├── file list │ │ │ @@ -1,3 +1,3 @@ │ │ │ drwxr-xr-x 0 root (0) root (0) 0 2025-04-23 13:22:40.000000 ./ │ │ │ -rw-r--r-- 0 root (0) root (0) 866 2025-04-23 13:22:40.000000 ./control │ │ │ --rw-r--r-- 0 root (0) root (0) 375371 2025-04-23 13:22:40.000000 ./md5sums │ │ │ +-rw-r--r-- 0 root (0) root (0) 375281 2025-04-23 13:22:40.000000 ./md5sums │ │ ├── ./control │ │ │ @@ -1,13 +1,13 @@ │ │ │ Package: seqan3-doc │ │ │ Source: seqan3 │ │ │ Version: 3.4.0~rc.3+ds-4 │ │ │ Architecture: all │ │ │ Maintainer: Debian Med Packaging Team │ │ │ -Installed-Size: 55060 │ │ │ +Installed-Size: 53062 │ │ │ Depends: doxygen-awesome-css │ │ │ Suggests: libseqan3-dev │ │ │ Section: doc │ │ │ Priority: optional │ │ │ Multi-Arch: foreign │ │ │ Homepage: https://www.seqan.de/ │ │ │ Description: C++ library for the analysis of biological sequences v3 (documentation) │ │ ├── ./md5sums │ │ │ ├── ./md5sums │ │ │ │┄ Files differ │ │ │ ├── line order │ │ │ │ @@ -1116,15 +1116,14 @@ │ │ │ │ usr/share/doc/libseqan3-dev/html/dir_000053_000035.html │ │ │ │ usr/share/doc/libseqan3-dev/html/dir_000053_000090.html │ │ │ │ usr/share/doc/libseqan3-dev/html/dir_000053_000100.html │ │ │ │ usr/share/doc/libseqan3-dev/html/dir_000054_000016.html │ │ │ │ usr/share/doc/libseqan3-dev/html/dir_000054_000029.html │ │ │ │ usr/share/doc/libseqan3-dev/html/dir_000054_000035.html │ │ │ │ usr/share/doc/libseqan3-dev/html/dir_000054_000064.html │ │ │ │ -usr/share/doc/libseqan3-dev/html/dir_000054_000100.html │ │ │ │ usr/share/doc/libseqan3-dev/html/dir_000055_000035.html │ │ │ │ usr/share/doc/libseqan3-dev/html/dir_000056_000035.html │ │ │ │ usr/share/doc/libseqan3-dev/html/dir_000057_000097.html │ │ │ │ usr/share/doc/libseqan3-dev/html/dir_000058_000035.html │ │ │ │ usr/share/doc/libseqan3-dev/html/dir_000060_000035.html │ │ │ │ usr/share/doc/libseqan3-dev/html/dir_000062_000035.html │ │ │ │ usr/share/doc/libseqan3-dev/html/dir_000064_000016.html ├── data.tar.xz │ ├── data.tar │ │ ├── file list │ │ │ @@ -1,21 +1,21 @@ │ │ │ drwxr-xr-x 0 root (0) root (0) 0 2025-04-23 13:22:40.000000 ./ │ │ │ drwxr-xr-x 0 root (0) root (0) 0 2025-04-23 13:22:40.000000 ./usr/ │ │ │ drwxr-xr-x 0 root (0) root (0) 0 2025-04-23 13:22:40.000000 ./usr/share/ │ │ │ drwxr-xr-x 0 root (0) root (0) 0 2025-04-23 13:22:40.000000 ./usr/share/doc/ │ │ │ drwxr-xr-x 0 root (0) root (0) 0 2025-04-23 13:22:40.000000 ./usr/share/doc/libseqan3-dev/ │ │ │ drwxr-xr-x 0 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(0) root (0) 9501 2025-04-23 13:22:40.000000 ./usr/share/doc/libseqan3-dev/html/about_code_of_conduct.html │ │ │ -rw-r--r-- 0 root (0) root (0) 13260 2025-04-23 13:22:40.000000 ./usr/share/doc/libseqan3-dev/html/about_contributing.html │ │ │ -rw-r--r-- 0 root (0) root (0) 11360 2025-04-23 13:22:40.000000 ./usr/share/doc/libseqan3-dev/html/about_copyright.html │ │ │ -rw-r--r-- 0 root (0) root (0) 10713 2025-04-23 13:22:40.000000 ./usr/share/doc/libseqan3-dev/html/about_customisation.html │ │ │ @@ -24,60 +24,60 @@ │ │ │ -rw-r--r-- 0 root (0) root (0) 6603 2025-04-23 13:22:40.000000 ./usr/share/doc/libseqan3-dev/html/adaptor__for__view__without__args_8hpp.html │ │ │ -rw-r--r-- 0 root (0) root (0) 13544 2025-04-23 13:22:40.000000 ./usr/share/doc/libseqan3-dev/html/adaptor__for__view__without__args_8hpp_source.html │ │ │ -rw-r--r-- 0 root (0) root (0) 6554 2025-04-23 13:22:40.000000 ./usr/share/doc/libseqan3-dev/html/adaptor__from__functor_8hpp.html │ │ │ -rw-r--r-- 0 root (0) root (0) 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./usr/share/doc/libseqan3-dev/html/uint_8hpp.html │ │ │ --rw-r--r-- 0 root (0) root (0) 23848 2025-04-23 13:22:40.000000 ./usr/share/doc/libseqan3-dev/html/uint_8hpp_source.html │ │ │ +-rw-r--r-- 0 root (0) root (0) 21679 2025-04-23 13:22:40.000000 ./usr/share/doc/libseqan3-dev/html/uint_8hpp_source.html │ │ │ -rw-r--r-- 0 root (0) root (0) 6514 2025-04-23 13:22:40.000000 ./usr/share/doc/libseqan3-dev/html/unidirectional__search__algorithm_8hpp.html │ │ │ -rw-r--r-- 0 root (0) root (0) 49337 2025-04-23 13:22:40.000000 ./usr/share/doc/libseqan3-dev/html/unidirectional__search__algorithm_8hpp_source.html │ │ │ -rw-r--r-- 0 root (0) root (0) 6067 2025-04-23 13:22:40.000000 ./usr/share/doc/libseqan3-dev/html/usergroup0.html │ │ │ -rw-r--r-- 0 root (0) root (0) 7097 2025-04-23 13:22:40.000000 ./usr/share/doc/libseqan3-dev/html/usergroup1.html │ │ │ -rw-r--r-- 0 root (0) root (0) 6555 2025-04-23 13:22:40.000000 ./usr/share/doc/libseqan3-dev/html/usergroup2.html │ │ │ -rw-r--r-- 0 root (0) 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17
│ │ │
18namespace seqan3
│ │ │
19{
│ │ │
│ │ │
79class aa10li : public aminoacid_base<aa10li, 10>
│ │ │
80{
│ │ │
81private:
│ │ │ -
83 using base_t = aminoacid_base<aa10li, 10>;
│ │ │ +
83 using base_t = aminoacid_base<aa10li, 10>;
│ │ │
84
│ │ │
86 friend base_t;
│ │ │
89 friend base_t::base_t;
│ │ │
91
│ │ │
92public:
│ │ │ -
96 constexpr aa10li() noexcept = default;
│ │ │ -
97 constexpr aa10li(aa10li const &) noexcept = default;
│ │ │ -
98 constexpr aa10li(aa10li &&) noexcept = default;
│ │ │ -
99 constexpr aa10li & operator=(aa10li const &) noexcept = default;
│ │ │ -
100 constexpr aa10li & operator=(aa10li &&) noexcept = default;
│ │ │ -
101 ~aa10li() noexcept = default;
│ │ │ +
96 constexpr aa10li() noexcept = default;
│ │ │ +
97 constexpr aa10li(aa10li const &) noexcept = default;
│ │ │ +
98 constexpr aa10li(aa10li &&) noexcept = default;
│ │ │ +
99 constexpr aa10li & operator=(aa10li const &) noexcept = default;
│ │ │ +
100 constexpr aa10li & operator=(aa10li &&) noexcept = default;
│ │ │ +
101 ~aa10li() noexcept = default;
│ │ │
102
│ │ │ -
104 using base_t::base_t;
│ │ │ +
104 using base_t::base_t;
│ │ │
106
│ │ │ -
107private:
│ │ │ -
109 static constexpr char_type rank_to_char_table[alphabet_size]{'A', 'B', 'C', 'F', 'G', 'H', 'I', 'J', 'K', 'P'};
│ │ │ +
107private:
│ │ │ +
109 static constexpr char_type rank_to_char_table[alphabet_size]{'A', 'B', 'C', 'F', 'G', 'H', 'I', 'J', 'K', 'P'};
│ │ │
110
│ │ │ -
112 static constexpr rank_type char_to_rank(char_type const chr)
│ │ │ +
112 static constexpr rank_type char_to_rank(char_type const chr)
│ │ │
113 {
│ │ │
114 using index_t = std::make_unsigned_t<char_type>;
│ │ │ -
115 return char_to_rank_table[static_cast<index_t>(chr)];
│ │ │ +
115 return char_to_rank_table[static_cast<index_t>(chr)];
│ │ │
116 }
│ │ │
117
│ │ │
119 static constexpr char_type rank_to_char(rank_type const rank)
│ │ │
120 {
│ │ │
121 return rank_to_char_table[rank];
│ │ │
122 }
│ │ │
123
│ │ │ @@ -236,28 +236,28 @@ │ │ │
189
│ │ │
190// ------------------------------------------------------------------
│ │ │
191// literals
│ │ │
192// ------------------------------------------------------------------
│ │ │
193inline namespace literals
│ │ │
194{
│ │ │
195
│ │ │ -
209constexpr aa10li operator""_aa10li(char const c) noexcept
│ │ │ +
209constexpr aa10li operator""_aa10li(char const c) noexcept
│ │ │
210{
│ │ │ -
211 return aa10li{}.assign_char(c);
│ │ │ +
211 return aa10li{}.assign_char(c);
│ │ │
212}
│ │ │
213
│ │ │ -
225SEQAN3_WORKAROUND_LITERAL aa10li_vector operator""_aa10li(char const * const s, size_t const n)
│ │ │ +
225SEQAN3_WORKAROUND_LITERAL aa10li_vector operator""_aa10li(char const * const s, size_t const n)
│ │ │
226{
│ │ │ -
227 aa10li_vector r;
│ │ │ -
228 r.resize(n);
│ │ │ +
227 aa10li_vector r;
│ │ │ +
228 r.resize(n);
│ │ │
229
│ │ │ -
230 for (size_t i = 0; i < n; ++i)
│ │ │ -
231 r[i].assign_char(s[i]);
│ │ │ +
230 for (size_t i = 0; i < n; ++i)
│ │ │ +
231 r[i].assign_char(s[i]);
│ │ │
232
│ │ │ -
233 return r;
│ │ │ +
233 return r;
│ │ │
234}
│ │ │
236
│ │ │
237} // namespace literals
│ │ │
238
│ │ │
239} // namespace seqan3
│ │ │
concept.hpp
Provides seqan3::aminoacid_alphabet.
│ │ │
aminoacid_base.hpp
Provides seqan3::aminoacid_base.
│ │ │ @@ -266,21 +266,21 @@ │ │ │
seqan3::aa10li::aa10li
constexpr aa10li() noexcept=default
Defaulted.
│ │ │
seqan3::alphabet_base< aa10li, size, char >
│ │ │
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
│ │ │
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
│ │ │
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
│ │ │
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
│ │ │
seqan3::aminoacid_base
A CRTP-base that refines seqan3::alphabet_base and is used by the amino acids.
Definition aminoacid_base.hpp:30
│ │ │ -
seqan3::debug_stream_type
A "pretty printer" for most SeqAn data structures and related types.
Definition debug_stream_type.hpp:79
│ │ │ │ │ │
std::array::fill
T fill(T... args)
│ │ │ │ │ │
seqan3
The main SeqAn3 namespace.
Definition aligned_sequence_concept.hpp:26
│ │ │
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
│ │ │
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:294
│ │ │ +
std::vector::resize
T resize(T... args)
│ │ │
transform.hpp
Provides utilities for modifying characters.
│ │ │ │ │ │
│ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │
│ │ │

First of all, thanks for wanting to contribute to SeqAn! Community is important to us and we strive to maintain a great culture and atmosphere. Please have a look at our Code of Conduct.

│ │ │

The following is a guide that helps stream-line the process of adding changes. If you haven't contributed to SeqAn before, don't worry about getting something wrong, that's absolutely OK. However, following this guide closely will reduce work for all of us and increases the chance of your changes being merged quickly.

│ │ │ -

│ │ │ +

│ │ │ Pull request workflow

│ │ │

The overall workflow of contributing changes to this repository is:

│ │ │
    │ │ │
  1. Create an issue with bug report or feature request.
    2. │ │ │
  2. Wait for comments from the team and then collectively decide on the best way to solve the issue.
    3. │ │ │
  3. Fork the repository and create a branch on your fork.
    4. │ │ │
  4. Commit the solution to your local branch.
    5. │ │ │
  5. Create a pull-request to our main branch from your branch.
    6. │ │ │
  6. Wait for reviews and resolve reviewer comments.
    7. │ │ │
  7. Wait for the PR to be merged.
    8. │ │ │
│ │ │ -

│ │ │ +

│ │ │ Creating an issue

│ │ │

Go to https://github.com/seqan/seqan3/issues and check if someone else has already reported the same issue. If not, create a new issue and follow the template.

│ │ │

We usually reply quickly to issues; if there is no reply within a week (and it's not prime vacation season in Europe) feel free to reply to the issue and explicitly mention @seqan/core.

│ │ │ -

│ │ │ +

│ │ │ Creating commits

│ │ │

If you have never used the Fork & Pull Model, have a look at this guide.

│ │ │

When creating commits to your branch and before requesting a pull, please ensure the following:

│ │ │
    │ │ │
  • Proper naming of commits (see below).
    • │ │ │
  • Content other than the first line is irrelevant in the commit message.
    • │ │ │
  • The number of commits should be minimal and commits shouldn't revert/change previous ones.
      │ │ │ @@ -157,20 +157,20 @@ │ │ │
      [FIX] Whenever you fix some wrong code in the source
      │ │ │
      [DOC] Whenever you do something only(!) related to the documentation
      │ │ │
      [INFRA] Whenever you change something of the build system or CI related
      │ │ │
      [TEST] Whenever you do something related to the tests (unit or benchmark)
      │ │ │
      [MISC] Whenever it does not fit to any of the above
      │ │ │

E.g. [FEATURE] add support for FOO or [FIX] divide by zero in alignment.

│ │ │

Alternatively, if your changes are so small that they would fit into one commit, don't worry about any of the above, just state "Please squash commits" in the PR and we will take care of the rest.

│ │ │ -

│ │ │ +

│ │ │ Opening a pull-request ("PR")

│ │ │

When you are done with committing changes to your branch and you have tested your changes, open a pull request. We have continuous integration in place that should inform you of test failures. Please try to resolve any breakage that your pull request introduces.

│ │ │

Here is a guide for setting up unit tests locally.

│ │ │

If there are test failures that you don't understand, clearly indicate that you have seen the errors, but cannot resolve them – then the first reviewer will have a look at them. Otherwise the PR will be treated as still being work-in-progress.

│ │ │ -

│ │ │ +

│ │ │ The review process

│ │ │

Request first review

│ │ │

After opening a PR it goes through the review process. This is a two-step process, first a regular member of the team needs to approve your changes, then one of the project owners (@h-2 or @rrahn) needs to approve and merge it. If you are a collaborator of the project and know the SeqAn team member best suitable for the review you can request a review yourself. Otherwise wait for a reviewer to be assigned to the PR. Do not request reviews from a project owner at this point. Always only request review from one person at a time.

│ │ │

Resolve comments

│ │ │

If you have not contributed to SeqAn before, you will likely receive a lot of comments on the style of your code. This is not a sign that we don't appreciate your contribution, but we have high code quality standards and everything must conform to our style guide. In the future we hope to automate this step. After you have received the first review, go through all comments and clarify any suggestions and requests. When you are confident that you know how to address all comments, implement the changes and update your PR.

│ │ │

Re-request review

│ │ │

Now re-request a review from the previous reviewer either by clicking "re-request review" or by writing "please review │ │ ├── ./usr/share/doc/libseqan3-dev/html/about_copyright.html │ │ │ @@ -139,15 +139,15 @@ │ │ │

│ │ │ │ │ │ │ │ │ Dependencies

│ │ │

│ │ │ │ │ │ │ │ │ -

│ │ │ +

│ │ │ Source code license

│ │ │

The contents of this repository/directory, in particular the library source code of SeqAn3, are licensed under the following terms:

│ │ │
Copyright (c) 2006-2023, Knut Reinert & Freie Universität Berlin
│ │ │
Copyright (c) 2016-2023, Knut Reinert & MPI für molekulare Genetik
│ │ │
All rights reserved.
│ │ │
│ │ │
Redistribution and use in source and binary forms, with or without
│ │ │ @@ -169,26 +169,26 @@ │ │ │
FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL
│ │ │
DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR
│ │ │
SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER
│ │ │
CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT
│ │ │
LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY
│ │ │
OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH
│ │ │
DAMAGE.
│ │ │ -

│ │ │ +

│ │ │ Documentation

│ │ │

The API documentation and manual are additionally provided under the terms of the Creative Commons Attribution 4.0 International License. This includes

│ │ │

The source code examples and snippets within the documentation are additionally provided under the terms of the Creative Commons Public Domain Dedication 1.0. This includes:

│ │ │ -

│ │ │ +

│ │ │ Submodules

│ │ │

This repository/directory may contain other projects' content in the submodules-subfolder. We try to ensure that all dependencies are permissively licensed (BSD/MIT/X11/ISC/Boost…), but please verify the respective license files yourself.

│ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ │ ├── html2text {} │ │ │ │ @@ -20,22 +20,22 @@ │ │ │ │ 17namespace _s_e_q_a_n_3_:_:_a_l_i_g_n___c_f_g │ │ │ │ 18{ │ │ │ │ _3_5class _m_i_n___s_c_o_r_e : private _p_i_p_e_a_b_l_e___c_o_n_f_i_g___e_l_e_m_e_n_t │ │ │ │ 36{ │ │ │ │ 37public: │ │ │ │ _3_9 int32_t _s_c_o_r_e{_s_t_d_:_:_n_u_m_e_r_i_c___l_i_m_i_t_s_<_i_n_t_3_2___t_>_:_:_l_o_w_e_s_t()}; │ │ │ │ 40 │ │ │ │ -_4_4 constexpr _m_i_n___s_c_o_r_e() _n_o_e_x_c_e_p_t = _d_e_f_a_u_l_t; │ │ │ │ -_4_5 _c_o_n_s_t_e_x_p_r _m_i_n___s_c_o_r_e(_m_i_n___s_c_o_r_e _c_o_n_s_t &) _n_o_e_x_c_e_p_t = _d_e_f_a_u_l_t; │ │ │ │ -_4_6 _c_o_n_s_t_e_x_p_r _m_i_n___s_c_o_r_e(_m_i_n___s_c_o_r_e &&) _n_o_e_x_c_e_p_t = _d_e_f_a_u_l_t; │ │ │ │ -_4_7 _c_o_n_s_t_e_x_p_r _m_i_n___s_c_o_r_e & _o_p_e_r_a_t_o_r=(_m_i_n___s_c_o_r_e _c_o_n_s_t &) _n_o_e_x_c_e_p_t = _d_e_f_a_u_l_t; │ │ │ │ -_4_8 _c_o_n_s_t_e_x_p_r _m_i_n___s_c_o_r_e & _o_p_e_r_a_t_o_r=(_m_i_n___s_c_o_r_e &&) _n_o_e_x_c_e_p_t = _d_e_f_a_u_l_t; │ │ │ │ -_4_9 ~_m_i_n___s_c_o_r_e() _n_o_e_x_c_e_p_t = _d_e_f_a_u_l_t; │ │ │ │ +_4_4 constexpr _m_i_n___s_c_o_r_e() noexcept = default; │ │ │ │ +_4_5 constexpr _m_i_n___s_c_o_r_e(_m_i_n___s_c_o_r_e const &) noexcept = default; │ │ │ │ +_4_6 constexpr _m_i_n___s_c_o_r_e(_m_i_n___s_c_o_r_e &&) noexcept = default; │ │ │ │ +_4_7 constexpr _m_i_n___s_c_o_r_e & operator=(_m_i_n___s_c_o_r_e const &) noexcept = default; │ │ │ │ +_4_8 constexpr _m_i_n___s_c_o_r_e & operator=(_m_i_n___s_c_o_r_e &&) noexcept = default; │ │ │ │ +_4_9 ~_m_i_n___s_c_o_r_e() noexcept = default; │ │ │ │ 50 │ │ │ │ -_5_5 _c_o_n_s_t_e_x_p_r _m_i_n___s_c_o_r_e(int32_t _c_o_n_s_t _s_c_o_r_e) : _s_c_o_r_e{_s_c_o_r_e} │ │ │ │ +_5_5 constexpr _m_i_n___s_c_o_r_e(int32_t const _s_c_o_r_e) : _s_c_o_r_e{_s_c_o_r_e} │ │ │ │ 56 {} │ │ │ │ 58 │ │ │ │ _6_0 static constexpr seqan3::detail::align_config_id id{seqan3::detail:: │ │ │ │ align_config_id::min_score}; │ │ │ │ 61}; │ │ │ │ 62 │ │ │ │ 63} // namespace seqan3::align_cfg │ │ │ │ @@ -48,17 +48,14 @@ │ │ │ │ _s_e_q_a_n_3_:_:_a_l_i_g_n___c_f_g_:_:_m_i_n___s_c_o_r_e_:_:_s_c_o_r_e │ │ │ │ int32_t score │ │ │ │ Minimal score for the distance computation [default: -infinity]. │ │ │ │ DDeeffiinniittiioonn align_config_min_score.hpp:39 │ │ │ │ _s_e_q_a_n_3_:_:_a_l_i_g_n___c_f_g_:_:_m_i_n___s_c_o_r_e_:_:_m_i_n___s_c_o_r_e │ │ │ │ constexpr min_score() noexcept=default │ │ │ │ Defaulted. │ │ │ │ -_s_e_q_a_n_3_:_:_d_e_b_u_g___s_t_r_e_a_m___t_y_p_e │ │ │ │ -A "pretty printer" for most SeqAn data structures and related types. │ │ │ │ -DDeeffiinniittiioonn debug_stream_type.hpp:79 │ │ │ │ _l_i_m_i_t_s │ │ │ │ _s_t_d_:_:_n_u_m_e_r_i_c___l_i_m_i_t_s_:_:_l_o_w_e_s_t │ │ │ │ T lowest(T... args) │ │ │ │ _s_e_q_a_n_3_:_:_a_l_i_g_n___c_f_g │ │ │ │ A special sub namespace for the alignment configurations. │ │ │ │ DDeeffiinniittiioonn align_config_band.hpp:22 │ │ │ │ _p_i_p_e_a_b_l_e___c_o_n_f_i_g___e_l_e_m_e_n_t_._h_p_p │ │ ├── ./usr/share/doc/libseqan3-dev/html/align__config__on__result_8hpp_source.html │ │ │ @@ -142,46 +142,45 @@ │ │ │
19{
│ │ │
20
│ │ │
49template <std::copy_constructible callback_t>
│ │ │
│ │ │
50class on_result : private seqan3::pipeable_config_element
│ │ │
51{
│ │ │
52public:
│ │ │ -
54 seqan3::detail::copyable_wrapper_t<callback_t> callback; // Allows lambdas with capture blocks.
│ │ │ +
54 seqan3::detail::copyable_wrapper_t<callback_t> callback; // Allows lambdas with capture blocks.
│ │ │
55
│ │ │
59 constexpr on_result() = default;
│ │ │
60 constexpr on_result(on_result const &) = default;
│ │ │
61 constexpr on_result(on_result &&) = default;
│ │ │
62 constexpr on_result & operator=(on_result const &) = default;
│ │ │
63 constexpr on_result & operator=(on_result &&) = default;
│ │ │
64 ~on_result() = default;
│ │ │
65
│ │ │
│ │ │ -
69 constexpr explicit on_result(callback_t && callback) : callback{std::forward<callback_t>(callback)}
│ │ │ +
69 constexpr explicit on_result(callback_t && callback) : callback{std::forward<callback_t>(callback)}
│ │ │
70 {}
│ │ │
│ │ │
72
│ │ │
75 static constexpr seqan3::detail::align_config_id id{seqan3::detail::align_config_id::on_result};
│ │ │
76};
│ │ │
│ │ │
77
│ │ │
82template <std::copy_constructible callback_t>
│ │ │ -
83on_result(callback_t &&) -> on_result<std::decay_t<callback_t>>;
│ │ │ +
83on_result(callback_t &&) -> on_result<std::decay_t<callback_t>>;
│ │ │
85} // namespace seqan3::align_cfg
│ │ │
detail.hpp
Provides some utility functions for the alignment configurations.
│ │ │
seqan3::align_cfg::on_result
Configuration element to provide a user defined callback function for the alignment.
Definition align_config_on_result.hpp:51
│ │ │
seqan3::align_cfg::on_result::~on_result
~on_result()=default
Defaulted.
│ │ │
seqan3::align_cfg::on_result::on_result
constexpr on_result()=default
Defaulted.
│ │ │
seqan3::align_cfg::on_result::on_result
constexpr on_result(on_result &&)=default
Defaulted.
│ │ │
seqan3::align_cfg::on_result::operator=
constexpr on_result & operator=(on_result &&)=default
Defaulted.
│ │ │
seqan3::align_cfg::on_result::operator=
constexpr on_result & operator=(on_result const &)=default
Defaulted.
│ │ │
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
│ │ │
seqan3::align_cfg::on_result::on_result
constexpr on_result(on_result const &)=default
Defaulted.
│ │ │
seqan3::align_cfg::on_result::callback
seqan3::detail::copyable_wrapper_t< callback_t > callback
The stored callable which will be invoked with the alignment result.
Definition align_config_on_result.hpp:54
│ │ │ -
seqan3::debug_stream_type
A "pretty printer" for most SeqAn data structures and related types.
Definition debug_stream_type.hpp:79
│ │ │
copyable_wrapper.hpp
Provides seqan3::detail::copyable_wrapper.
│ │ │
seqan3::align_cfg
A special sub namespace for the alignment configurations.
Definition align_config_band.hpp:22
│ │ │
std
SeqAn specific customisations in the standard namespace.
│ │ │
pipeable_config_element.hpp
Provides seqan3::pipeable_config_element.
│ │ │
seqan3::pipeable_config_element
Adds pipe interface to configuration elements.
Definition pipeable_config_element.hpp:29
│ │ │
type_traits
│ │ │ │ │ │ ├── html2text {} │ │ │ │ @@ -21,34 +21,34 @@ │ │ │ │ 18namespace _s_e_q_a_n_3_:_:_a_l_i_g_n___c_f_g │ │ │ │ 19{ │ │ │ │ 20 │ │ │ │ 49template │ │ │ │ _5_0class _o_n___r_e_s_u_l_t : private _s_e_q_a_n_3_:_:_p_i_p_e_a_b_l_e___c_o_n_f_i_g___e_l_e_m_e_n_t │ │ │ │ 51{ │ │ │ │ 52public: │ │ │ │ -_5_4 _s_e_q_a_n_3_:_:_d_e_t_a_i_l_:_:_c_o_p_y_a_b_l_e___w_r_a_p_p_e_r___t_<_c_a_l_l_b_a_c_k___t_> _c_a_l_l_b_a_c_k; // Allows lambdas │ │ │ │ +_5_4 seqan3::detail::copyable_wrapper_t _c_a_l_l_b_a_c_k; // Allows lambdas │ │ │ │ with capture blocks. │ │ │ │ 55 │ │ │ │ _5_9 constexpr _o_n___r_e_s_u_l_t() = default; │ │ │ │ _6_0 constexpr _o_n___r_e_s_u_l_t(_o_n___r_e_s_u_l_t const &) = default; │ │ │ │ _6_1 constexpr _o_n___r_e_s_u_l_t(_o_n___r_e_s_u_l_t &&) = default; │ │ │ │ _6_2 constexpr _o_n___r_e_s_u_l_t & _o_p_e_r_a_t_o_r_=(_o_n___r_e_s_u_l_t const &) = default; │ │ │ │ _6_3 constexpr _o_n___r_e_s_u_l_t & _o_p_e_r_a_t_o_r_=(_o_n___r_e_s_u_l_t &&) = default; │ │ │ │ _6_4 _~_o_n___r_e_s_u_l_t() = default; │ │ │ │ 65 │ │ │ │ -_6_9 constexpr explicit _o_n___r_e_s_u_l_t(_c_a_l_l_b_a_c_k___t && _c_a_l_l_b_a_c_k) : _c_a_l_l_b_a_c_k{_s_t_d:: │ │ │ │ -forward<_c_a_l_l_b_a_c_k___t>(_c_a_l_l_b_a_c_k)} │ │ │ │ +_6_9 constexpr explicit _o_n___r_e_s_u_l_t(callback_t && _c_a_l_l_b_a_c_k) : _c_a_l_l_b_a_c_k{_s_t_d:: │ │ │ │ +forward(_c_a_l_l_b_a_c_k)} │ │ │ │ 70 {} │ │ │ │ 72 │ │ │ │ 75 static constexpr seqan3::detail::align_config_id id{seqan3::detail:: │ │ │ │ align_config_id::on_result}; │ │ │ │ 76}; │ │ │ │ 77 │ │ │ │ 82template │ │ │ │ -_8_3_o_n___r_e_s_u_l_t(_c_a_l_l_b_a_c_k___t &&) -> _o_n___r_e_s_u_l_t_<_s_t_d_:_:_d_e_c_a_y___t_<_c_a_l_l_b_a_c_k___t_>>; │ │ │ │ +_8_3_o_n___r_e_s_u_l_t(callback_t &&) -> _o_n___r_e_s_u_l_t_<_s_t_d_:_:_d_e_c_a_y___t_<_c_a_l_l_b_a_c_k___t_>>; │ │ │ │ 85} // namespace seqan3::align_cfg │ │ │ │ _d_e_t_a_i_l_._h_p_p │ │ │ │ Provides some utility functions for the alignment configurations. │ │ │ │ _s_e_q_a_n_3_:_:_a_l_i_g_n___c_f_g_:_:_o_n___r_e_s_u_l_t │ │ │ │ Configuration element to provide a user defined callback function for the │ │ │ │ alignment. │ │ │ │ DDeeffiinniittiioonn align_config_on_result.hpp:51 │ │ │ │ @@ -74,17 +74,14 @@ │ │ │ │ _s_e_q_a_n_3_:_:_a_l_i_g_n___c_f_g_:_:_o_n___r_e_s_u_l_t_:_:_o_n___r_e_s_u_l_t │ │ │ │ constexpr on_result(on_result const &)=default │ │ │ │ Defaulted. │ │ │ │ _s_e_q_a_n_3_:_:_a_l_i_g_n___c_f_g_:_:_o_n___r_e_s_u_l_t_:_:_c_a_l_l_b_a_c_k │ │ │ │ seqan3::detail::copyable_wrapper_t< callback_t > callback │ │ │ │ The stored callable which will be invoked with the alignment result. │ │ │ │ DDeeffiinniittiioonn align_config_on_result.hpp:54 │ │ │ │ -_s_e_q_a_n_3_:_:_d_e_b_u_g___s_t_r_e_a_m___t_y_p_e │ │ │ │ -A "pretty printer" for most SeqAn data structures and related types. │ │ │ │ -DDeeffiinniittiioonn debug_stream_type.hpp:79 │ │ │ │ _c_o_p_y_a_b_l_e___w_r_a_p_p_e_r_._h_p_p │ │ │ │ Provides seqan3::detail::copyable_wrapper. │ │ │ │ _s_e_q_a_n_3_:_:_a_l_i_g_n___c_f_g │ │ │ │ A special sub namespace for the alignment configurations. │ │ │ │ DDeeffiinniittiioonn align_config_band.hpp:22 │ │ │ │ _s_t_d │ │ │ │ SeqAn specific customisations in the standard namespace. │ │ ├── ./usr/share/doc/libseqan3-dev/html/align__config__scoring__scheme_8hpp_source.html │ │ │ @@ -162,30 +162,29 @@ │ │ │ │ │ │
67
│ │ │
70 static constexpr seqan3::detail::align_config_id id{seqan3::detail::align_config_id::scoring};
│ │ │
71};
│ │ │ │ │ │
72
│ │ │
79template <typename scheme_t>
│ │ │ -
80scoring_scheme(scheme_t) -> scoring_scheme<std::remove_cvref_t<scheme_t>>;
│ │ │ +
80scoring_scheme(scheme_t) -> scoring_scheme<std::remove_cvref_t<scheme_t>>;
│ │ │
82
│ │ │
83} // namespace seqan3::align_cfg
│ │ │
detail.hpp
Provides some utility functions for the alignment configurations.
│ │ │
basic.hpp
Provides various type traits on generic types.
│ │ │
seqan3::align_cfg::scoring_scheme
Sets the scoring scheme for the alignment algorithm.
Definition align_config_scoring_scheme.hpp:42
│ │ │
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
│ │ │
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.
│ │ │
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
│ │ │
seqan3::align_cfg::scoring_scheme::operator=
constexpr scoring_scheme & operator=(scoring_scheme &&)=default
Defaulted.
│ │ │
seqan3::align_cfg::scoring_scheme::scoring_scheme
constexpr scoring_scheme()=default
Defaulted.
│ │ │
seqan3::align_cfg::scoring_scheme::operator=
constexpr scoring_scheme & operator=(scoring_scheme const &)=default
Defaulted.
│ │ │
seqan3::align_cfg::scoring_scheme::scoring_scheme
constexpr scoring_scheme(scoring_scheme const &)=default
Defaulted.
│ │ │
seqan3::align_cfg::scoring_scheme::scoring_scheme
constexpr scoring_scheme(scoring_scheme &&)=default
Defaulted.
│ │ │
seqan3::align_cfg::scoring_scheme::~scoring_scheme
~scoring_scheme()=default
Defaulted.
│ │ │ -
seqan3::debug_stream_type
A "pretty printer" for most SeqAn data structures and related types.
Definition debug_stream_type.hpp:79
│ │ │
seqan3::align_cfg
A special sub namespace for the alignment configurations.
Definition align_config_band.hpp:22
│ │ │
std
SeqAn specific customisations in the standard namespace.
│ │ │
pipeable_config_element.hpp
Provides seqan3::pipeable_config_element.
│ │ │
scoring_scheme_concept.hpp
Provides seqan3::scoring_scheme_for.
│ │ │
seqan3::pipeable_config_element
Adds pipe interface to configuration elements.
Definition pipeable_config_element.hpp:29
│ │ │ │ │ │ │ │ │ ├── html2text {} │ │ │ │ @@ -40,15 +40,15 @@ │ │ │ │ 65 {} │ │ │ │ 67 │ │ │ │ 70 static constexpr seqan3::detail::align_config_id id{seqan3::detail:: │ │ │ │ align_config_id::scoring}; │ │ │ │ 71}; │ │ │ │ 72 │ │ │ │ 79template │ │ │ │ -_8_0_s_c_o_r_i_n_g___s_c_h_e_m_e(_s_c_h_e_m_e___t) -> _s_c_o_r_i_n_g___s_c_h_e_m_e_<_s_t_d_:_:_r_e_m_o_v_e___c_v_r_e_f___t_<_s_c_h_e_m_e___t_>>; │ │ │ │ +_8_0_s_c_o_r_i_n_g___s_c_h_e_m_e(scheme_t) -> _s_c_o_r_i_n_g___s_c_h_e_m_e_<_s_t_d_:_:_r_e_m_o_v_e___c_v_r_e_f___t_<_s_c_h_e_m_e___t_>>; │ │ │ │ 82 │ │ │ │ 83} // namespace seqan3::align_cfg │ │ │ │ _d_e_t_a_i_l_._h_p_p │ │ │ │ Provides some utility functions for the alignment configurations. │ │ │ │ _b_a_s_i_c_._h_p_p │ │ │ │ Provides various type traits on generic types. │ │ │ │ _s_e_q_a_n_3_:_:_a_l_i_g_n___c_f_g_:_:_s_c_o_r_i_n_g___s_c_h_e_m_e │ │ │ │ @@ -79,17 +79,14 @@ │ │ │ │ Defaulted. │ │ │ │ _s_e_q_a_n_3_:_:_a_l_i_g_n___c_f_g_:_:_s_c_o_r_i_n_g___s_c_h_e_m_e_:_:_s_c_o_r_i_n_g___s_c_h_e_m_e │ │ │ │ constexpr scoring_scheme(scoring_scheme &&)=default │ │ │ │ Defaulted. │ │ │ │ _s_e_q_a_n_3_:_:_a_l_i_g_n___c_f_g_:_:_s_c_o_r_i_n_g___s_c_h_e_m_e_:_:_~_s_c_o_r_i_n_g___s_c_h_e_m_e │ │ │ │ ~scoring_scheme()=default │ │ │ │ Defaulted. │ │ │ │ -_s_e_q_a_n_3_:_:_d_e_b_u_g___s_t_r_e_a_m___t_y_p_e │ │ │ │ -A "pretty printer" for most SeqAn data structures and related types. │ │ │ │ -DDeeffiinniittiioonn debug_stream_type.hpp:79 │ │ │ │ _s_e_q_a_n_3_:_:_a_l_i_g_n___c_f_g │ │ │ │ A special sub namespace for the alignment configurations. │ │ │ │ DDeeffiinniittiioonn align_config_band.hpp:22 │ │ │ │ _s_t_d │ │ │ │ SeqAn specific customisations in the standard namespace. │ │ │ │ _p_i_p_e_a_b_l_e___c_o_n_f_i_g___e_l_e_m_e_n_t_._h_p_p │ │ │ │ Provides seqan3::pipeable_config_element. │ │ ├── ./usr/share/doc/libseqan3-dev/html/align__pairwise_8hpp_source.html │ │ │ @@ -154,21 +154,21 @@ │ │ │
31{
│ │ │
32
│ │ │
127template <typename sequence_t, typename alignment_config_t>
│ │ │
128 requires detail::align_pairwise_single_input<sequence_t>
│ │ │
129 && std::copy_constructible<std::remove_reference_t<sequence_t>>
│ │ │
130 && detail::is_type_specialisation_of_v<alignment_config_t, configuration>
│ │ │
│ │ │ -
131constexpr auto align_pairwise(sequence_t && seq, alignment_config_t const & config)
│ │ │ +
131constexpr auto align_pairwise(sequence_t && seq, alignment_config_t const & config)
│ │ │
132{
│ │ │
133 using std::get;
│ │ │
134
│ │ │
135 if constexpr (std::is_lvalue_reference_v<sequence_t>) // Forward tuple elements as references.
│ │ │
136 {
│ │ │ -
137 return align_pairwise(std::tie(get<0>(seq), get<1>(seq)), config);
│ │ │ +
137 return align_pairwise(std::tie(get<0>(seq), get<1>(seq)), config);
│ │ │
138 }
│ │ │
139 else
│ │ │
140 {
│ │ │
141 static_assert(std::tuple_size_v<std::remove_reference_t<sequence_t>> == 2,
│ │ │
142 "Alignment configuration error: Expects exactly two sequences for pairwise alignments.");
│ │ │
143
│ │ │
144 static_assert(std::ranges::viewable_range<std::tuple_element_t<0, std::remove_reference_t<sequence_t>>>
│ │ │ @@ -245,15 +245,14 @@ │ │ │
algorithm_result_generator_range.hpp
Provides seqan3::detail::algorithm_result_generator_range.
│ │ │
concept.hpp
Provides concepts needed internally for the alignment algorithms.
│ │ │
type_traits.hpp
Provides helper type traits for the configuration and execution of the alignment algorithm.
│ │ │
alignment_configurator.hpp
Provides seqan3::detail::alignment_selector.
│ │ │
alignment_result.hpp
Provides seqan3::alignment_result.
│ │ │
all_view.hpp
Provides seqan3::detail::all.
│ │ │
basic.hpp
Provides various type traits on generic types.
│ │ │ -
seqan3::debug_stream_type
A "pretty printer" for most SeqAn data structures and related types.
Definition debug_stream_type.hpp:79
│ │ │ │ │ │ │ │ │
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
│ │ │
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:131
│ │ │
seqan3::field::seq
@ seq
The "sequence", usually a range of nucleotides or amino acids.
│ │ │
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
│ │ │
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
│ │ │ ├── html2text {} │ │ │ │ @@ -33,23 +33,23 @@ │ │ │ │ 30namespace _s_e_q_a_n_3 │ │ │ │ 31{ │ │ │ │ 32 │ │ │ │ 127template │ │ │ │ 128 requires detail::align_pairwise_single_input │ │ │ │ 129 && std::copy_constructible> │ │ │ │ 130 && detail::is_type_specialisation_of_v │ │ │ │ -_1_3_1constexpr auto _a_l_i_g_n___p_a_i_r_w_i_s_e(_s_e_q_u_e_n_c_e___t && _s_e_q, _a_l_i_g_n_m_e_n_t___c_o_n_f_i_g___t const & │ │ │ │ +_1_3_1constexpr auto _a_l_i_g_n___p_a_i_r_w_i_s_e(sequence_t && _s_e_q, alignment_config_t const & │ │ │ │ config) │ │ │ │ 132{ │ │ │ │ 133 using std::get; │ │ │ │ 134 │ │ │ │ 135 if constexpr (std::is_lvalue_reference_v) // Forward tuple │ │ │ │ elements as references. │ │ │ │ 136 { │ │ │ │ -137 return _a_l_i_g_n___p_a_i_r_w_i_s_e(_s_t_d_:_:_t_i_e(_g_e_t_<_0_>(_s_e_q), _g_e_t_<_1_>(_s_e_q)), config); │ │ │ │ +137 return _a_l_i_g_n___p_a_i_r_w_i_s_e(_s_t_d_:_:_t_i_e(get<0>(_s_e_q), get<1>(_s_e_q)), config); │ │ │ │ 138 } │ │ │ │ 139 else │ │ │ │ 140 { │ │ │ │ 141 static_assert(std::tuple_size_v> == 2, │ │ │ │ 142 "Alignment configuration error: Expects exactly two sequences for pairwise │ │ │ │ alignments."); │ │ │ │ 143 │ │ │ │ @@ -155,17 +155,14 @@ │ │ │ │ Provides seqan3::detail::alignment_selector. │ │ │ │ _a_l_i_g_n_m_e_n_t___r_e_s_u_l_t_._h_p_p │ │ │ │ Provides seqan3::alignment_result. │ │ │ │ _a_l_l___v_i_e_w_._h_p_p │ │ │ │ Provides seqan3::detail::all. │ │ │ │ _b_a_s_i_c_._h_p_p │ │ │ │ Provides various type traits on generic types. │ │ │ │ -_s_e_q_a_n_3_:_:_d_e_b_u_g___s_t_r_e_a_m___t_y_p_e │ │ │ │ -A "pretty printer" for most SeqAn data structures and related types. │ │ │ │ -DDeeffiinniittiioonn debug_stream_type.hpp:79 │ │ │ │ _s_t_d_:_:_c_o_n_d_i_t_i_o_n_a_l___t │ │ │ │ _f_u_n_c_t_i_o_n_a_l │ │ │ │ _s_e_q_a_n_3_:_:_a_l_i_g_n___c_f_g_:_:_p_a_r_a_l_l_e_l │ │ │ │ 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. │ │ ├── ./usr/share/doc/libseqan3-dev/html/aligned__allocator_8hpp_source.html │ │ │ @@ -147,123 +147,123 @@ │ │ │
24{
│ │ │
25
│ │ │
72template <typename value_t, size_t alignment_v = __STDCPP_DEFAULT_NEW_ALIGNMENT__>
│ │ │
│ │ │
73class aligned_allocator
│ │ │
74{
│ │ │
75public:
│ │ │ -
77 static constexpr size_t alignment = alignment_v;
│ │ │ +
77 static constexpr size_t alignment = alignment_v;
│ │ │
78
│ │ │ -
80 using value_type = value_t;
│ │ │ -
82 using pointer = value_type *;
│ │ │ +
80 using value_type = value_t;
│ │ │ +
82 using pointer = value_type *;
│ │ │
84 using difference_type = typename std::pointer_traits<pointer>::difference_type;
│ │ │
86 using size_type = std::make_unsigned_t<difference_type>;
│ │ │
87
│ │ │
89 using is_always_equal = std::true_type;
│ │ │
90
│ │ │
94 aligned_allocator() = default;
│ │ │
95 aligned_allocator(aligned_allocator const &) = default;
│ │ │
96 aligned_allocator(aligned_allocator &&) = default;
│ │ │
97 aligned_allocator & operator=(aligned_allocator const &) = default;
│ │ │
98 aligned_allocator & operator=(aligned_allocator &&) = default;
│ │ │
99 ~aligned_allocator() = default;
│ │ │
100
│ │ │
102 template <class other_value_type, size_t other_alignment>
│ │ │
│ │ │ -
103 constexpr aligned_allocator(aligned_allocator<other_value_type, other_alignment> const &) noexcept
│ │ │ +
103 constexpr aligned_allocator(aligned_allocator<other_value_type, other_alignment> const &) noexcept
│ │ │
104 {}
│ │ │
│ │ │
106
│ │ │
│ │ │ -
138 [[nodiscard]] pointer allocate(size_type const n) const
│ │ │ +
138 [[nodiscard]] pointer allocate(size_type const n) const
│ │ │
139 {
│ │ │
140 constexpr size_type max_size = std::numeric_limits<size_type>::max() / sizeof(value_type);
│ │ │
141 if (n > max_size)
│ │ │
142 throw std::bad_alloc{};
│ │ │
143
│ │ │ -
144 size_t bytes_to_allocate = n * sizeof(value_type);
│ │ │ -
145 if constexpr (alignment <= __STDCPP_DEFAULT_NEW_ALIGNMENT__)
│ │ │ -
146 return static_cast<pointer>(::operator new(bytes_to_allocate));
│ │ │ +
144 size_t bytes_to_allocate = n * sizeof(value_type);
│ │ │ +
145 if constexpr (alignment <= __STDCPP_DEFAULT_NEW_ALIGNMENT__)
│ │ │ +
146 return static_cast<pointer>(::operator new(bytes_to_allocate));
│ │ │
147 else // Use alignment aware allocator function.
│ │ │ -
148 return static_cast<pointer>(::operator new(bytes_to_allocate, static_cast<std::align_val_t>(alignment)));
│ │ │ +
148 return static_cast<pointer>(::operator new(bytes_to_allocate, static_cast<std::align_val_t>(alignment)));
│ │ │
149 }
│ │ │
│ │ │
150
│ │ │
│ │ │ -
177 void deallocate(pointer const p, size_type const n) const noexcept
│ │ │ +
177 void deallocate(pointer const p, size_type const n) const noexcept
│ │ │
178 {
│ │ │ -
179 size_t bytes_to_deallocate = n * sizeof(value_type);
│ │ │ +
179 size_t bytes_to_deallocate = n * sizeof(value_type);
│ │ │
180
│ │ │
181 // Clang doesn't have __cpp_sized_deallocation defined by default even though this is a C++14! feature
│ │ │
182 // > In Clang 3.7 and later, sized deallocation is only enabled if the user passes the `-fsized-deallocation`
│ │ │
183 // > flag.
│ │ │
184 // see also https://clang.llvm.org/cxx_status.html#n3778
│ │ │
185#if __cpp_sized_deallocation >= 201309
│ │ │
186 // gcc
│ │ │ -
187 if constexpr (alignment <= __STDCPP_DEFAULT_NEW_ALIGNMENT__)
│ │ │ -
188 ::operator delete(p, bytes_to_deallocate);
│ │ │ +
187 if constexpr (alignment <= __STDCPP_DEFAULT_NEW_ALIGNMENT__)
│ │ │ +
188 ::operator delete(p, bytes_to_deallocate);
│ │ │
189 else // Use alignment aware deallocator function.
│ │ │ -
190 ::operator delete(p, bytes_to_deallocate, static_cast<std::align_val_t>(alignment));
│ │ │ +
190 ::operator delete(p, bytes_to_deallocate, static_cast<std::align_val_t>(alignment));
│ │ │
191#else /*__cpp_sized_deallocation >= 201309*/
│ │ │
192 // e.g. clang++
│ │ │ -
193 (void)bytes_to_deallocate;
│ │ │ -
194 if constexpr (alignment <= __STDCPP_DEFAULT_NEW_ALIGNMENT__)
│ │ │ +
193 (void)bytes_to_deallocate;
│ │ │ +
194 if constexpr (alignment <= __STDCPP_DEFAULT_NEW_ALIGNMENT__)
│ │ │
195 ::operator delete(p);
│ │ │
196 else // Use alignment aware deallocator function.
│ │ │
197 ::operator delete(p, static_cast<std::align_val_t>(alignment));
│ │ │
198#endif // __cpp_sized_deallocation >= 201309
│ │ │
199 }
│ │ │
│ │ │
200
│ │ │
211 template <typename new_value_type>
│ │ │
│ │ │
212 struct rebind
│ │ │
213 {
│ │ │ -
215 static constexpr size_t other_alignment = std::max(alignof(new_value_type), alignment);
│ │ │ -
217 using other = aligned_allocator<new_value_type, other_alignment>;
│ │ │ +
215 static constexpr size_t other_alignment = std::max(alignof(new_value_type), alignment);
│ │ │ +
217 using other = aligned_allocator<new_value_type, other_alignment>;
│ │ │
218 };
│ │ │
│ │ │
219
│ │ │
224 template <class value_type2, size_t alignment2>
│ │ │
│ │ │ -
225 constexpr bool operator==(aligned_allocator<value_type2, alignment2> const &) noexcept
│ │ │ +
225 constexpr bool operator==(aligned_allocator<value_type2, alignment2> const &) noexcept
│ │ │
226 {
│ │ │ -
227 return alignment == alignment2;
│ │ │ +
227 return alignment == alignment2;
│ │ │
228 }
│ │ │
│ │ │
229
│ │ │
231 template <class value_type2, size_t alignment2>
│ │ │
│ │ │ -
232 constexpr bool operator!=(aligned_allocator<value_type2, alignment2> const &) noexcept
│ │ │ +
232 constexpr bool operator!=(aligned_allocator<value_type2, alignment2> const &) noexcept
│ │ │
233 {
│ │ │ -
234 return alignment != alignment2;
│ │ │ +
234 return alignment != alignment2;
│ │ │
235 }
│ │ │
│ │ │
237};
│ │ │
│ │ │
238
│ │ │
239} // namespace seqan3
│ │ │ │ │ │ │ │ │
seqan3::aligned_allocator
Allocates uninitialized storage whose memory-alignment is specified by alignment.
Definition aligned_allocator.hpp:74
│ │ │
seqan3::aligned_allocator::value_type
value_t value_type
The value type of the allocation.
Definition aligned_allocator.hpp:80
│ │ │
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:177
│ │ │
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:225
│ │ │
seqan3::aligned_allocator::operator=
aligned_allocator & operator=(aligned_allocator &&)=default
Defaulted.
│ │ │
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:138
│ │ │ +
seqan3::aligned_allocator::pointer
value_type * pointer
The pointer type of the allocation.
Definition aligned_allocator.hpp:82
│ │ │
seqan3::aligned_allocator::operator=
aligned_allocator & operator=(aligned_allocator const &)=default
Defaulted.
│ │ │
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:103
│ │ │
seqan3::aligned_allocator::~aligned_allocator
~aligned_allocator()=default
Defaulted.
│ │ │
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:232
│ │ │
seqan3::aligned_allocator::aligned_allocator
aligned_allocator(aligned_allocator const &)=default
Defaulted.
│ │ │
seqan3::aligned_allocator::alignment
static constexpr size_t alignment
The memory-alignment of the allocation.
Definition aligned_allocator.hpp:77
│ │ │
seqan3::aligned_allocator::aligned_allocator
aligned_allocator(aligned_allocator &&)=default
Defaulted.
│ │ │
seqan3::aligned_allocator::aligned_allocator
aligned_allocator()=default
Defaulted.
│ │ │
seqan3::aligned_allocator::difference_type
typename std::pointer_traits< pointer >::difference_type difference_type
The difference type of the allocation.
Definition aligned_allocator.hpp:84
│ │ │ -
seqan3::debug_stream_type
A "pretty printer" for most SeqAn data structures and related types.
Definition debug_stream_type.hpp:79
│ │ │ │ │ │ │ │ │ │ │ │
std::numeric_limits::max
T max(T... args)
│ │ │ │ │ │
seqan3
The main SeqAn3 namespace.
Definition aligned_sequence_concept.hpp:26
│ │ │
platform.hpp
Provides platform and dependency checks.
│ │ │ ├── html2text {} │ │ │ │ @@ -29,17 +29,17 @@ │ │ │ │ 24{ │ │ │ │ 25 │ │ │ │ 72template │ │ │ │ _7_3class _a_l_i_g_n_e_d___a_l_l_o_c_a_t_o_r │ │ │ │ 74{ │ │ │ │ 75public: │ │ │ │ -_7_7 static constexpr size_t _a_l_i_g_n_m_e_n_t = _a_l_i_g_n_m_e_n_t___v; │ │ │ │ +_7_7 static constexpr size_t _a_l_i_g_n_m_e_n_t = alignment_v; │ │ │ │ 78 │ │ │ │ -_8_0 using _v_a_l_u_e___t_y_p_e = _v_a_l_u_e___t; │ │ │ │ +_8_0 using _v_a_l_u_e___t_y_p_e = value_t; │ │ │ │ _8_2 using _p_o_i_n_t_e_r = _v_a_l_u_e___t_y_p_e *; │ │ │ │ _8_4 using _d_i_f_f_e_r_e_n_c_e___t_y_p_e = typename _s_t_d_:_:_p_o_i_n_t_e_r___t_r_a_i_t_s_<_p_o_i_n_t_e_r_>_:_: │ │ │ │ _d_i_f_f_e_r_e_n_c_e___t_y_p_e; │ │ │ │ _8_6 using _s_i_z_e___t_y_p_e = _s_t_d_:_:_m_a_k_e___u_n_s_i_g_n_e_d___t_<_d_i_f_f_e_r_e_n_c_e___t_y_p_e_>; │ │ │ │ 87 │ │ │ │ _8_9 using _i_s___a_l_w_a_y_s___e_q_u_a_l = _s_t_d_:_:_t_r_u_e___t_y_p_e; │ │ │ │ 90 │ │ │ │ @@ -51,76 +51,76 @@ │ │ │ │ _9_9 _~_a_l_i_g_n_e_d___a_l_l_o_c_a_t_o_r() = default; │ │ │ │ 100 │ │ │ │ 102 template │ │ │ │ _1_0_3 constexpr _a_l_i_g_n_e_d___a_l_l_o_c_a_t_o_r(_a_l_i_g_n_e_d___a_l_l_o_c_a_t_o_r_<_o_t_h_e_r___v_a_l_u_e___t_y_p_e_, │ │ │ │ _o_t_h_e_r___a_l_i_g_n_m_e_n_t_> const &) noexcept │ │ │ │ 104 {} │ │ │ │ 106 │ │ │ │ -_1_3_8 [[_n_o_d_i_s_c_a_r_d]] _p_o_i_n_t_e_r _a_l_l_o_c_a_t_e(_s_i_z_e___t_y_p_e const n) const │ │ │ │ +_1_3_8 [[nodiscard]] _p_o_i_n_t_e_r _a_l_l_o_c_a_t_e(_s_i_z_e___t_y_p_e const n) const │ │ │ │ 139 { │ │ │ │ 140 constexpr _s_i_z_e___t_y_p_e max_size = _s_t_d_:_:_n_u_m_e_r_i_c___l_i_m_i_t_s_<_s_i_z_e___t_y_p_e_>_:_:_m_a_x() / │ │ │ │ sizeof(_v_a_l_u_e___t_y_p_e); │ │ │ │ 141 if (n > max_size) │ │ │ │ 142 throw _s_t_d_:_:_b_a_d___a_l_l_o_c{}; │ │ │ │ 143 │ │ │ │ -144 size_t _b_y_t_e_s___t_o___a_l_l_o_c_a_t_e = n * sizeof(_v_a_l_u_e___t_y_p_e); │ │ │ │ -145 if constexpr (_a_l_i_g_n_m_e_n_t <= _____S_T_D_C_P_P___D_E_F_A_U_L_T___N_E_W___A_L_I_G_N_M_E_N_T____) │ │ │ │ -146 return static_cast<_p_o_i_n_t_e_r>(::operator new(_b_y_t_e_s___t_o___a_l_l_o_c_a_t_e)); │ │ │ │ +144 size_t bytes_to_allocate = n * sizeof(_v_a_l_u_e___t_y_p_e); │ │ │ │ +145 if constexpr (_a_l_i_g_n_m_e_n_t <= __STDCPP_DEFAULT_NEW_ALIGNMENT__) │ │ │ │ +146 return static_cast<_p_o_i_n_t_e_r>(::operator new(bytes_to_allocate)); │ │ │ │ 147 else // Use alignment aware allocator function. │ │ │ │ -148 return static_cast<_p_o_i_n_t_e_r>(::operator new(_b_y_t_e_s___t_o___a_l_l_o_c_a_t_e, │ │ │ │ +148 return static_cast<_p_o_i_n_t_e_r>(::operator new(bytes_to_allocate, │ │ │ │ static_cast<_s_t_d_:_:_a_l_i_g_n___v_a_l___t>(_a_l_i_g_n_m_e_n_t))); │ │ │ │ 149 } │ │ │ │ 150 │ │ │ │ _1_7_7 void _d_e_a_l_l_o_c_a_t_e(_p_o_i_n_t_e_r const p, _s_i_z_e___t_y_p_e const n) const noexcept │ │ │ │ 178 { │ │ │ │ -179 size_t _b_y_t_e_s___t_o___d_e_a_l_l_o_c_a_t_e = n * sizeof(_v_a_l_u_e___t_y_p_e); │ │ │ │ +179 size_t bytes_to_deallocate = n * sizeof(_v_a_l_u_e___t_y_p_e); │ │ │ │ 180 │ │ │ │ 181 // Clang doesn't have __cpp_sized_deallocation defined by default even │ │ │ │ though this is a C++14! feature │ │ │ │ 182 // > In Clang 3.7 and later, sized deallocation is only enabled if the user │ │ │ │ passes the `-fsized-deallocation` │ │ │ │ 183 // > flag. │ │ │ │ 184 // see also https://clang.llvm.org/cxx_status.html#n3778 │ │ │ │ 185#if __cpp_sized_deallocation >= 201309 │ │ │ │ 186 // gcc │ │ │ │ -187 if constexpr (_a_l_i_g_n_m_e_n_t <= _____S_T_D_C_P_P___D_E_F_A_U_L_T___N_E_W___A_L_I_G_N_M_E_N_T____) │ │ │ │ -188 ::operator delete(p, _b_y_t_e_s___t_o___d_e_a_l_l_o_c_a_t_e); │ │ │ │ +187 if constexpr (_a_l_i_g_n_m_e_n_t <= __STDCPP_DEFAULT_NEW_ALIGNMENT__) │ │ │ │ +188 ::operator delete(p, bytes_to_deallocate); │ │ │ │ 189 else // Use alignment aware deallocator function. │ │ │ │ -190 ::operator delete(p, _b_y_t_e_s___t_o___d_e_a_l_l_o_c_a_t_e, static_cast<_s_t_d_:_:_a_l_i_g_n___v_a_l___t> │ │ │ │ +190 ::operator delete(p, bytes_to_deallocate, static_cast<_s_t_d_:_:_a_l_i_g_n___v_a_l___t> │ │ │ │ (_a_l_i_g_n_m_e_n_t)); │ │ │ │ 191#else /*__cpp_sized_deallocation >= 201309*/ │ │ │ │ 192 // e.g. clang++ │ │ │ │ -193 (_v_o_i_d)_b_y_t_e_s___t_o___d_e_a_l_l_o_c_a_t_e; │ │ │ │ -194 if constexpr (_a_l_i_g_n_m_e_n_t <= _____S_T_D_C_P_P___D_E_F_A_U_L_T___N_E_W___A_L_I_G_N_M_E_N_T____) │ │ │ │ +193 (void)bytes_to_deallocate; │ │ │ │ +194 if constexpr (_a_l_i_g_n_m_e_n_t <= __STDCPP_DEFAULT_NEW_ALIGNMENT__) │ │ │ │ 195 ::operator delete(p); │ │ │ │ 196 else // Use alignment aware deallocator function. │ │ │ │ 197 ::operator delete(p, static_cast<_s_t_d_:_:_a_l_i_g_n___v_a_l___t>(_a_l_i_g_n_m_e_n_t)); │ │ │ │ 198#endif // __cpp_sized_deallocation >= 201309 │ │ │ │ 199 } │ │ │ │ 200 │ │ │ │ 211 template │ │ │ │ _2_1_2 struct _r_e_b_i_n_d │ │ │ │ 213 { │ │ │ │ -_2_1_5 static constexpr size_t _o_t_h_e_r___a_l_i_g_n_m_e_n_t = _s_t_d_:_:_m_a_x(alignof(_n_e_w___v_a_l_u_e___t_y_p_e), │ │ │ │ +_2_1_5 static constexpr size_t _o_t_h_e_r___a_l_i_g_n_m_e_n_t = _s_t_d_:_:_m_a_x(alignof(new_value_type), │ │ │ │ _a_l_i_g_n_m_e_n_t); │ │ │ │ _2_1_7 using _o_t_h_e_r = _a_l_i_g_n_e_d___a_l_l_o_c_a_t_o_r_<_n_e_w___v_a_l_u_e___t_y_p_e_,_ _o_t_h_e_r___a_l_i_g_n_m_e_n_t_>; │ │ │ │ 218 }; │ │ │ │ 219 │ │ │ │ 224 template │ │ │ │ _2_2_5 constexpr bool _o_p_e_r_a_t_o_r_=_=(_a_l_i_g_n_e_d___a_l_l_o_c_a_t_o_r_<_v_a_l_u_e___t_y_p_e_2_,_ _a_l_i_g_n_m_e_n_t_2_> const │ │ │ │ &) noexcept │ │ │ │ 226 { │ │ │ │ -227 return _a_l_i_g_n_m_e_n_t == _a_l_i_g_n_m_e_n_t_2; │ │ │ │ +227 return _a_l_i_g_n_m_e_n_t == alignment2; │ │ │ │ 228 } │ │ │ │ 229 │ │ │ │ 231 template │ │ │ │ _2_3_2 constexpr bool _o_p_e_r_a_t_o_r_!_=(_a_l_i_g_n_e_d___a_l_l_o_c_a_t_o_r_<_v_a_l_u_e___t_y_p_e_2_,_ _a_l_i_g_n_m_e_n_t_2_> const │ │ │ │ &) noexcept │ │ │ │ 233 { │ │ │ │ -234 return _a_l_i_g_n_m_e_n_t != _a_l_i_g_n_m_e_n_t_2; │ │ │ │ +234 return _a_l_i_g_n_m_e_n_t != alignment2; │ │ │ │ 235 } │ │ │ │ 237}; │ │ │ │ 238 │ │ │ │ 239} // namespace seqan3 │ │ │ │ _s_t_d_:_:_a_l_i_g_n___v_a_l___t │ │ │ │ _s_t_d_:_:_b_a_d___a_l_l_o_c │ │ │ │ _s_e_q_a_n_3_:_:_a_l_i_g_n_e_d___a_l_l_o_c_a_t_o_r │ │ │ │ @@ -144,14 +144,18 @@ │ │ │ │ _s_e_q_a_n_3_:_:_a_l_i_g_n_e_d___a_l_l_o_c_a_t_o_r_:_:_o_p_e_r_a_t_o_r_= │ │ │ │ aligned_allocator & operator=(aligned_allocator &&)=default │ │ │ │ Defaulted. │ │ │ │ _s_e_q_a_n_3_:_:_a_l_i_g_n_e_d___a_l_l_o_c_a_t_o_r_:_:_a_l_l_o_c_a_t_e │ │ │ │ pointer allocate(size_type const n) const │ │ │ │ Allocates sufficiently large memory to hold n many elements of value_type. │ │ │ │ DDeeffiinniittiioonn aligned_allocator.hpp:138 │ │ │ │ +_s_e_q_a_n_3_:_:_a_l_i_g_n_e_d___a_l_l_o_c_a_t_o_r_:_:_p_o_i_n_t_e_r │ │ │ │ +value_type * pointer │ │ │ │ +The pointer type of the allocation. │ │ │ │ +DDeeffiinniittiioonn aligned_allocator.hpp:82 │ │ │ │ _s_e_q_a_n_3_:_:_a_l_i_g_n_e_d___a_l_l_o_c_a_t_o_r_:_:_o_p_e_r_a_t_o_r_= │ │ │ │ aligned_allocator & operator=(aligned_allocator const &)=default │ │ │ │ Defaulted. │ │ │ │ _s_e_q_a_n_3_:_:_a_l_i_g_n_e_d___a_l_l_o_c_a_t_o_r_:_:_a_l_i_g_n_e_d___a_l_l_o_c_a_t_o_r │ │ │ │ constexpr aligned_allocator(aligned_allocator< other_value_type, │ │ │ │ other_alignment > const &) noexcept │ │ │ │ Copy constructor with different value type and alignment. │ │ │ │ @@ -177,17 +181,14 @@ │ │ │ │ _s_e_q_a_n_3_:_:_a_l_i_g_n_e_d___a_l_l_o_c_a_t_o_r_:_:_a_l_i_g_n_e_d___a_l_l_o_c_a_t_o_r │ │ │ │ aligned_allocator()=default │ │ │ │ Defaulted. │ │ │ │ _s_e_q_a_n_3_:_:_a_l_i_g_n_e_d___a_l_l_o_c_a_t_o_r_:_:_d_i_f_f_e_r_e_n_c_e___t_y_p_e │ │ │ │ typename std::pointer_traits< pointer >::difference_type difference_type │ │ │ │ The difference type of the allocation. │ │ │ │ DDeeffiinniittiioonn aligned_allocator.hpp:84 │ │ │ │ -_s_e_q_a_n_3_:_:_d_e_b_u_g___s_t_r_e_a_m___t_y_p_e │ │ │ │ -A "pretty printer" for most SeqAn data structures and related types. │ │ │ │ -DDeeffiinniittiioonn debug_stream_type.hpp:79 │ │ │ │ _s_t_d_:_:_t_r_u_e___t_y_p_e │ │ │ │ _l_i_m_i_t_s │ │ │ │ _s_t_d_:_:_m_a_k_e___u_n_s_i_g_n_e_d___t │ │ │ │ _s_t_d_:_:_n_u_m_e_r_i_c___l_i_m_i_t_s_:_:_m_a_x │ │ │ │ T max(T... args) │ │ │ │ _m_e_m_o_r_y │ │ │ │ _s_e_q_a_n_3 │ │ ├── ./usr/share/doc/libseqan3-dev/html/aligned__sequence__builder_8hpp_source.html │ │ │ @@ -170,17 +170,17 @@ │ │ │
66
│ │ │
74template <std::ranges::viewable_range first_sequence_t, std::ranges::viewable_range second_sequence_t>
│ │ │
75struct make_pairwise_alignment_type
│ │ │
76{
│ │ │
78 using first_aligned_t = typename make_aligned_sequence_type<first_sequence_t>::type;
│ │ │
80 using second_aligned_t = typename make_aligned_sequence_type<second_sequence_t>::type;
│ │ │
81
│ │ │ -
82 static_assert(seqan3::writable_aligned_sequence<first_aligned_t>,
│ │ │ +
82 static_assert(seqan3::writable_aligned_sequence<first_aligned_t>,
│ │ │
83 "first_aligned_t is required to model seqan3::writable_aligned_sequence!");
│ │ │ -
84 static_assert(seqan3::writable_aligned_sequence<second_aligned_t>,
│ │ │ +
84 static_assert(seqan3::writable_aligned_sequence<second_aligned_t>,
│ │ │
85 "second_aligned_t is required to model seqan3::writable_aligned_sequence!");
│ │ │
86
│ │ │
88 using type = std::tuple<first_aligned_t, second_aligned_t>;
│ │ │
89};
│ │ │
90
│ │ │
112template <std::ranges::viewable_range fst_sequence_t, std::ranges::viewable_range sec_sequence_t>
│ │ │
113class aligned_sequence_builder
│ │ │ @@ -285,20 +285,20 @@ │ │ │
246};
│ │ │
247
│ │ │
253template <std::ranges::viewable_range fst_sequence_t, std::ranges::viewable_range sec_sequence_t>
│ │ │
254aligned_sequence_builder(fst_sequence_t &&,
│ │ │
255 sec_sequence_t &&) -> aligned_sequence_builder<fst_sequence_t, sec_sequence_t>;
│ │ │
257} // namespace seqan3::detail
│ │ │
aligned_sequence_concept.hpp
Includes the aligned_sequence and the related insert_gap and erase_gap functions to enable stl contai...
│ │ │ -
seqan3::debug_stream_type
A "pretty printer" for most SeqAn data structures and related types.
Definition debug_stream_type.hpp:79
│ │ │
std::vector::emplace_back
T emplace_back(T... args)
│ │ │
gap_decorator.hpp
Provides seqan3::gap_decorator.
│ │ │
gapped.hpp
Provides seqan3::gapped.
│ │ │
seqan3::field::alignment
@ alignment
The (pairwise) alignment stored in an object that models seqan3::detail::pairwise_alignment.
│ │ │
seqan3::views::slice
constexpr auto slice
A view adaptor that returns a half-open interval on the underlying range.
Definition slice.hpp:175
│ │ │ +
writable_aligned_sequence
The generic concept for an aligned sequence that is writable.
│ │ │
is_class_template_declarable.hpp
Provides a type trait for verifying valid template declarations.
│ │ │
lazy_conditional.hpp
Provides lazy template instantiation traits.
│ │ │
matrix_coordinate.hpp
Provides seqan3::detail::matrix_index, seqan3::detail::matrix_coordinate and associated strong types.
│ │ │
std
SeqAn specific customisations in the standard namespace.
│ │ │ │ │ │
slice.hpp
Provides seqan3::views::slice.
│ │ │
std::tie
T tie(T... args)
│ │ │ ├── html2text {} │ │ │ │ @@ -193,31 +193,30 @@ │ │ │ │ 254aligned_sequence_builder(fst_sequence_t &&, │ │ │ │ 255 sec_sequence_t &&) -> aligned_sequence_builder; │ │ │ │ 257} // namespace seqan3::detail │ │ │ │ _a_l_i_g_n_e_d___s_e_q_u_e_n_c_e___c_o_n_c_e_p_t_._h_p_p │ │ │ │ Includes the aligned_sequence and the related insert_gap and erase_gap │ │ │ │ functions to enable stl contai... │ │ │ │ -_s_e_q_a_n_3_:_:_d_e_b_u_g___s_t_r_e_a_m___t_y_p_e │ │ │ │ -A "pretty printer" for most SeqAn data structures and related types. │ │ │ │ -DDeeffiinniittiioonn debug_stream_type.hpp:79 │ │ │ │ _s_t_d_:_:_v_e_c_t_o_r_:_:_e_m_p_l_a_c_e___b_a_c_k │ │ │ │ T emplace_back(T... args) │ │ │ │ _g_a_p___d_e_c_o_r_a_t_o_r_._h_p_p │ │ │ │ Provides seqan3::gap_decorator. │ │ │ │ _g_a_p_p_e_d_._h_p_p │ │ │ │ Provides seqan3::gapped. │ │ │ │ _s_e_q_a_n_3_:_:_f_i_e_l_d_:_:_a_l_i_g_n_m_e_n_t │ │ │ │ @ alignment │ │ │ │ The (pairwise) alignment stored in an object that models seqan3::detail:: │ │ │ │ pairwise_alignment. │ │ │ │ _s_e_q_a_n_3_:_:_v_i_e_w_s_:_:_s_l_i_c_e │ │ │ │ constexpr auto slice │ │ │ │ A view adaptor that returns a half-open interval on the underlying range. │ │ │ │ DDeeffiinniittiioonn slice.hpp:175 │ │ │ │ +_w_r_i_t_a_b_l_e___a_l_i_g_n_e_d___s_e_q_u_e_n_c_e │ │ │ │ +The generic concept for an aligned sequence that is writable. │ │ │ │ _i_s___c_l_a_s_s___t_e_m_p_l_a_t_e___d_e_c_l_a_r_a_b_l_e_._h_p_p │ │ │ │ Provides a type trait for verifying valid template declarations. │ │ │ │ _l_a_z_y___c_o_n_d_i_t_i_o_n_a_l_._h_p_p │ │ │ │ Provides lazy template instantiation traits. │ │ │ │ _m_a_t_r_i_x___c_o_o_r_d_i_n_a_t_e_._h_p_p │ │ │ │ Provides seqan3::detail::matrix_index, seqan3::detail::matrix_coordinate and │ │ │ │ associated strong types. │ │ ├── ./usr/share/doc/libseqan3-dev/html/aligned__sequence__concept_8hpp_source.html │ │ │ @@ -144,28 +144,28 @@ │ │ │
22// unaligned_seq transformation trait
│ │ │
23// ---------------------------------------------------------------------------------------------------------------------
│ │ │
24
│ │ │
│ │ │
25namespace seqan3::detail
│ │ │
26{
│ │ │
27
│ │ │ -
29template <template <typename...> typename container_type, typename seq_alph_t, typename... rest_t>
│ │ │ -
30 requires container<container_type<gapped<seq_alph_t>, rest_t...>>
│ │ │ +
29template <template <typename...> typename container_type, typename seq_alph_t, typename... rest_t>
│ │ │ +
30 requires container<container_type<gapped<seq_alph_t>, rest_t...>>
│ │ │
31constexpr auto
│ │ │ -
32 remove_gap_from_value_type(container_type<gapped<seq_alph_t>, rest_t...>) -> container_type<seq_alph_t, rest_t...>;
│ │ │ +
32 remove_gap_from_value_type(container_type<gapped<seq_alph_t>, rest_t...>) -> container_type<seq_alph_t, rest_t...>;
│ │ │
33
│ │ │ -
35template <template <typename...> typename container_type,
│ │ │ +
35template <template <typename...> typename container_type,
│ │ │
36 template <typename...>
│ │ │
37 typename allocator_type,
│ │ │ -
38 typename seq_alph_t,
│ │ │ -
39 typename... rest_t>
│ │ │ -
40 requires container<container_type<gapped<seq_alph_t>, allocator_type<gapped<seq_alph_t>>, rest_t...>>
│ │ │ +
38 typename seq_alph_t,
│ │ │ +
39 typename... rest_t>
│ │ │ +
40 requires container<container_type<gapped<seq_alph_t>, allocator_type<gapped<seq_alph_t>>, rest_t...>>
│ │ │
41constexpr auto
│ │ │ -
42 remove_gap_from_value_type(container_type<gapped<seq_alph_t>, allocator_type<gapped<seq_alph_t>>, rest_t...>)
│ │ │ -
43 -> container_type<seq_alph_t, allocator_type<seq_alph_t>, rest_t...>;
│ │ │ +
42 remove_gap_from_value_type(container_type<gapped<seq_alph_t>, allocator_type<gapped<seq_alph_t>>, rest_t...>)
│ │ │ +
43 -> container_type<seq_alph_t, allocator_type<seq_alph_t>, rest_t...>;
│ │ │
44
│ │ │
46template <typename t>
│ │ │
47struct unaligned_seq
│ │ │
48{};
│ │ │
49
│ │ │
51template <typename t>
│ │ │
52 requires (!requires { typename std::remove_reference_t<t>::unaligned_sequence_type; })
│ │ │ @@ -325,25 +325,26 @@ │ │ │
477inline constexpr bool all_model_aligned_seq = (aligned_sequence<elems> && ...);
│ │ │
478
│ │ │
482template <typename... elems>
│ │ │
483inline constexpr bool all_model_aligned_seq<type_list<elems...>> = all_model_aligned_seq<elems...>;
│ │ │
484} // namespace seqan3::detail
│ │ │ │ │ │
exception.hpp
Includes customized exception types for the alignment module .
│ │ │ -
seqan3::debug_stream_type
A "pretty printer" for most SeqAn data structures and related types.
Definition debug_stream_type.hpp:79
│ │ │ +
seqan3::alphabet_variant
A combined alphabet that can hold values of either of its alternatives..
Definition alphabet_variant.hpp:127
│ │ │
gapped.hpp
Provides seqan3::gapped.
│ │ │
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
│ │ │
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
│ │ │
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
│ │ │
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
│ │ │
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
│ │ │
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
│ │ │
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
│ │ │
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
│ │ │
aligned_sequence
The generic concept for an aligned sequence.
│ │ │ +
container
The (most general) container concept as defined by the standard library.
│ │ │
sequence
The generic concept for a (biological) sequence.
│ │ │
weakly_assignable_from
Resolves to std::is_assignable_v<t>.
│ │ │
writable_aligned_sequence
The generic concept for an aligned sequence that is writable.
│ │ │
seqan3
The main SeqAn3 namespace.
Definition aligned_sequence_concept.hpp:26
│ │ │
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:252
│ │ │
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:261
│ │ │ │ │ │ ├── html2text {} │ │ │ │ @@ -25,32 +25,32 @@ │ │ │ │ 22// unaligned_seq transformation trait │ │ │ │ 23// -------------------------------------------------------------------------- │ │ │ │ ------------------------------------------- │ │ │ │ 24 │ │ │ │ _2_5namespace seqan3::detail │ │ │ │ 26{ │ │ │ │ 27 │ │ │ │ -29template