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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:294
\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@@ -192,15 +192,15 @@\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 This site provides a good overview of what the current release and its lifecycle is.
    \n \u00b2 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

This changelog contains a top-level entry for each release with sections on new features, API changes and notable bug-fixes (not all bug-fixes will be listed).

\n

Get to know SeqAn3 with our tutorials.

\n

Please see the release announcement: https://www.seqan.de/announcing-seqan3/

\n

See the porting guide for some help on porting: https://docs.seqan.de/seqan3/main_user/howto_porting.html

\n

See the documentation on API stability to learn about when API changes are allowed.

\n-

\n+

\n 3.4.0

\n-

\n+

\n New features

\n

I/O

\n \n-

\n+

\n Notable Bug-fixes

\n

Alphabet

\n \n

Alignment

\n
    \n
  • Fixed an issue that caused incorrect begin and end positions for banded alignments (#3269).
    • \n
\n

I/O

\n \n-

\n+

\n API changes

\n

Compiler

\n
    \n
  • Supported compiler:
      \n
    • GCC 12, 13, 14
      • \n
    • Clang 17, 18, 19
      • \n
    • IntelOneAPI/IntelLLVM 2024.0
      • \n@@ -201,17 +201,17 @@\n

      Dependencies

      \n
        \n
      • We now use Doxygen version 1.9.8 to build our documentation (#3197).
        • \n
      • We bumped the minimal CMake version to 3.20 (#3314).
        • \n
      • Dependencies are now managed via CPM instead of submodules (#3328).
        • \n
      • The build_system directory was renamed to cmake (#3292).
        • \n
      \n-

      \n+

      \n 3.3.0

      \n-

      \n+

      \n New features

      \n

      Alignment

      \n \n

      Alphabet

      \n@@ -224,15 +224,15 @@\n \n

      Search

      \n \n-

      \n+

      \n Notable Bug-fixes

      \n

      Alignment

      \n
        \n
      • Resolved an issue resulting in a wrong alignment score (#3098).
        • \n
      \n

      I/O

      \n \n

      Utility

      \n
        \n
      • Fixed spin delay having no effect on the PowerPC platform (#3129).
        • \n
      \n-

      \n+

      \n API changes

      \n

      Alignment

      \n \n

      Compiler

      \n
        \n@@ -258,17 +258,17 @@\n

        Dependencies

        \n
          \n
        • We require at least CMake 3.16 for our test suite. Note that the minimum requirement for using SeqAn3 is unchanged (#3050).
          • \n
        • We now use Doxygen version 1.9.6 to build our documentation (#3116).
          • \n
        • Updated sdsl-lite to 3.0.3 (#3170, #3174).
          • \n
        • Compatibility with SeqAn2: SeqAn2's namespace was changed from seqan to seqan2. For interoperability, an up-to-date checkout of SeqAn2's main branch is required (#3156).
          • \n
        \n-

        \n+

        \n 3.2.0

        \n-

        \n+

        \n New features

        \n

        Alphabet

        \n \n

        I/O

        \n@@ -279,15 +279,15 @@\n
          \n
        • Improved performance of seqan3::counting_vector::operator+= (#2930).
          • \n
        \n

        Utility

        \n \n-

        \n+

        \n Notable Bug-fixes

        \n

        Core

        \n
          \n
        • Added missing implementations for AVX512 (#2920 and #2926).
          • \n
        \n

        IO

        \n
          \n@@ -301,15 +301,15 @@\n
        \n

        Utility

        \n
          \n
        • seqan3::views::single_pass_input cannot propagate the std::ranges::output_range property because it cannot satisfy the following requirement (#2775): cpp *it++ = value; // must be the same as *it = value; ++it; // but it actually would be the same as ++it; *it = value;
          • \n
        • Fixed signature of seqan3::detail::store_sse4. This might have affected some public API (#2893).
          • \n
        • Relaxed seqan3::views::to_simd requirements to be C++20-compatible (#2849).
          • \n
        \n-

        \n+

        \n API changes

        \n

        GCC 7, 8, and 9 have been removed. All headers in seqan3/std/ except charconv and new have been deprecated, please use the equivalent std includes. The namespace std::cpp20 has been deprecated, please use std::.

        \n

        seqan3::views::to has been changed to seqan3::ranges::to. Since it is not a view anymore, it cannot be properly deprecated. Please keep this in mind if you encounter errors with seqan3::views::to.

        \n

        Compiler

        \n
          \n
        • Dropped support for GCC 7 and 8 (#2891).
          • \n
        • Dropped support for GCC 9 (#2952).
          • \n@@ -331,43 +331,43 @@\n

          Dependencies

          \n
            \n
          • We now use Doxygen version 1.9.4 to build our documentation (#2979).
            • \n
          • Removed range-v3 (#2998).
            • \n
          • Updated cereal to 1.3.2 (#3012).
            • \n
          • Updated sdsl-lite to 3.0.1 (#3012).
            • \n
          \n-

          \n+

          \n 3.1.0

          \n-

          \n+

          \n New features

          \n

          Build system

          \n
            \n
          • We now use Doxygen version 1.9.2 to build our documentation (#2765).
            • \n
          \n-

          \n+

          \n Notable Bug-fixes

          \n

          Argument Parser

          \n
            \n
          • Fixed an issue that led to the wrong option type being printed on errors (#2836).
            • \n
          \n

          Search

          \n
            \n
          • Resolved an issue that prevented the FM-Index from being constructed correctly for inputs larger than 4 GiB (#2756).
            • \n
          \n-

          \n+

          \n API changes

          \n

          The files deprecated in 3.0.3 (denoted by [deleted without replacement]) have been removed.

          \n-

          \n+

          \n 3.0.3

          \n

          Note that 3.1.0 will be the first API stable release and interfaces in this release might still change.

          \n
            \n
          • Check out our updated SeqAn3 Cookbook. It contains a listing of code examples on how to perform particular tasks using the library.
            • \n
          • SeqAn 3.0.3 is known to compile with GCC 7.5, 8.4, 9.3, 10.3, and 11.1. Future versions (e.g. GCC 11.2 and 12) might work, but were not yet available at the time of this release.
            • \n
          \n-

          \n+

          \n New features

          \n

          Alphabet

          \n
            \n
          • Added seqan3::phred94, a quality type that represents the full Phred Score range (Sanger format) and is used for PacBio Phred scores of HiFi reads (#2290).
            • \n
          \n

          Argument Parser

          \n

Search

\n \n-

\n+

\n 3.0.2

\n

Note that 3.1.0 will be the first API stable release and interfaces in this release might still change.

\n \n-

\n+

\n New features

\n

Alignment

\n \n@@ -761,15 +761,15 @@\n \n

Search

\n \n-

\n+

\n API changes

\n \n

Alignment

\n

\n Notable Bug-fixes

\n

Alignment

\n \n

Argument Parser

\n@@ -880,18 +880,18 @@\n
  • seqan3::fm_index and seqan3::bi_fm_index construct the index correctly if a collection with a single text is passed as input (#1892).
    • \n \n

    Range

    \n \n-

    \n+

    \n 3.0.1

    \n

    Note that 3.1.0 will be the first API stable release and interfaces in this release might still change.

    \n-

    \n+

    \n New features

    \n

    Alphabet

    \n \n

    Alignment

    \n@@ -939,15 +939,15 @@\n \n

    Std

    \n \n-

    \n+

    \n API changes

    \n \n

    Alphabet

    \n@@ -994,30 +994,30 @@\n

    Search

    \n \n-

    \n+

    \n Notable Bug-fixes

    \n \n-

    \n+

    \n 3.0.0 (\"Escala\")

    \n

    This is the initial release of SeqAn3. It is an entirely new library so there is no changelog that covers the differences to SeqAn2.

    \n

    Note that 3.1.0 will be the first API stable release and interfaces in this release might still change.

    \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/about_code_of_conduct.html", "source2": "./usr/share/doc/libseqan3-dev/html/about_code_of_conduct.html", "unified_diff": "@@ -126,25 +126,25 @@\n

    ‍A primary goal of all the conferences and user groups that refer to this Code of Conduct is to be inclusive to the largest number of contributors, with the most varied and diverse backgrounds possible. As such, we are committed to providing a friendly, safe and welcoming environment for all, regardless of gender, sexual orientation, ability, ethnicity, socioeconomic status and religion (or lack thereof).

    \n \n
    \n

    ‍A supplemental goal of this Code of Conduct is to increase open [source/culture/tech] citizenship by encouraging participants to recognize and strengthen the relationships between our actions and their effects on our community.

    \n
    \n

    Please have a look at the full text here: https://berlincodeofconduct.org/

    \n

    Many SeqAn core team members and contributors are employees and/or (PhD) students of Freie Universit\u00e4t Berlin and are thus also bound by the Academic Honour Code.

    \n-

    \n+

    \n Scope

    \n

    This Code of Conduct applies both within project spaces and in public spaces when an individual is representing the project or its community. In particular, it applies to:

    \n
      \n
    • Communication on GitHub, including issues, pull-requests and commit messages;
      • \n
    • the seqan-dev and seqan-team mailing lists;
      • \n
    • the Gitter chat rooms;
      • \n
    • social media accounts of SeqAn;
      • \n
    • SeqAn-related meetings in real life.
      • \n
    \n-

    \n+

    \n Enforcement

    \n

    If you observe a violation of this Code of Conduct, you can do one of the following, depending on the severity of the violation and your own capacity to deal with the offending person:

    \n
      \n
    • Try to resolve the matter immediately with the person by referring to this Code of Conduct.
      • \n
    • Raise the issue at a weekly meeting of the core team or by contacting a member of the core team. The core team is obligated to maintain confidentiality with regard to the reporter of an incident.
      • \n
    • If the problem is with a person on the core team, you can contact '; return false;\">Lutz Prechelt. He is a professor at Freie Universit\u00e4t Berlin and not directly involved with the SeqAn project. He has agreed to help find solutions or redirect to other helpful entities if cases are brought to him.
      • \n
    • Employees and students of Freie Universit\u00e4t Berlin can also contact one of the bodies representing specific interests.
      • \n"}, {"source1": "./usr/share/doc/libseqan3-dev/html/about_contributing.html", "source2": "./usr/share/doc/libseqan3-dev/html/about_contributing.html", "unified_diff": "@@ -119,31 +119,31 @@\n \n
      \n
      Contributing
      \n
      \n
      \n

      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.

      \n

      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.

      \n-

      \n+

      \n Pull request workflow

      \n

      The overall workflow of contributing changes to this repository is:

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

      \n+

      \n Creating an issue

      \n

      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.

      \n

      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.

      \n-

      \n+

      \n Creating commits

      \n

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

      \n

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

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

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

      \n

      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.

      \n-

      \n+

      \n Opening a pull-request (\"PR\")

      \n

      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.

      \n

      Here is a guide for setting up unit tests locally.

      \n

      If there are test failures that you don't understand, clearly indicate that you have seen the errors, but cannot resolve them \u2013 then the first reviewer will have a look at them. Otherwise the PR will be treated as still being work-in-progress.

      \n-

      \n+

      \n The review process

      \n

      Request first review

      \n

      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.

      \n

      Resolve comments

      \n

      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.

      \n

      Re-request review

      \n

      Now re-request a review from the previous reviewer either by clicking \"re-request review\" or by writing \"please review\n"}, {"source1": "./usr/share/doc/libseqan3-dev/html/about_copyright.html", "source2": "./usr/share/doc/libseqan3-dev/html/about_copyright.html", "unified_diff": "@@ -139,15 +139,15 @@\n

      \n
    \n \n \n
    Publication
    Title From theory to practice: Plug and play with succinct data structures.
    Dependencies

    \"\"

    \n

    \n
    \n-

    \n+

    \n Source code license

    \n

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

    \n
    Copyright (c) 2006-2023, Knut Reinert & Freie Universit\u00e4t Berlin
    \n
    Copyright (c) 2016-2023, Knut Reinert & MPI f\u00fcr molekulare Genetik
    \n
    All rights reserved.
    \n
    \n
    Redistribution and use in source and binary forms, with or without
    \n@@ -169,26 +169,26 @@\n
    FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL
    \n
    DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR
    \n
    SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER
    \n
    CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT
    \n
    LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY
    \n
    OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH
    \n
    DAMAGE.
    \n-

    \n+

    \n Documentation

    \n

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

    \n

    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:

    \n-

    \n+

    \n Submodules

    \n

    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\u2026), but please verify the respective license files yourself.

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

    Table of Contents

    \n-
    \n

    SeqAn clearly documents which of its interfaces are designed to be used with user-provided types and how this can be realised.

    \n-

    \n+

    \n Generic interfaces

    \n

    Templates are a core part of generic programming in C++, because they allow instantiating the code with different types or constants. SeqAn's API consists mostly of templates for exactly this reason, although we try to make this less visible by having the template parameters deduced in many scenarios.

    \n

    We strive to document the exact requirements for every template parameter in the API documentation; often these are also enforced via C++ concepts. Wherever other types meet the given requirements, you can use these types as arguments \u2013 independent of whether they are standard library types, your own types or types from another library. See C++ Concepts for more details on this.

    \n

    Some requirements are more elaborate and depend on a specialisation or \"overload\" of another entity from the SeqAn library. We call these \"customisation points\" (also known as \"extension points\").

    \n-

    \n+

    \n Customisation points

    \n

    One such customisation point is seqan3::to_rank. Instead of the seqan3::semialphabet concept looking directly for member functions or free functions in your namespace, it always checks for a valid definition of seqan3::to_rank which in turn resolves to different possible implementations.

    \n

    To customise one of our customisation points, follow the instructions in its API documentation. Typically, you have the choice between the following options:

    \n
      \n
    1. Provide functionality as members.
      2. \n
    2. Provide friends or free functions inside the namespace of your type (will be picked up via argument dependent lookup).
      3. \n
    3. Specialise the respective template in seqan3::custom:: for that type and provide the needed functionality as static members of that specialisation (this is an \"upload space\" for specialisations).
      4. \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": "@@ -321,24 +321,23 @@\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": "@@ -224,25 +224,22 @@\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)(_\bs_\bt_\br_\be_\ba_\bm_\b__\bt & stream, detail::\n-advanceable_alignment_coordinate const _\ba_\br_\bg) const\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 314 {\n-315 stream << _\bs_\bt_\bd_\b:_\b:_\bt_\bi_\be(_\ba_\br_\bg.first, _\ba_\br_\bg.second);\n+315 stream << _\bs_\bt_\bd_\b:_\b:_\bt_\bi_\be(arg.first, arg.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": "@@ -160,149 +160,149 @@\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
      \n-
      81 explicit algorithm_result_generator_range(algorithm_executor_type && algorithm_executor) :
      \n-
      82 algorithm_executor_ptr{std::make_unique<algorithm_executor_type>(std::move(algorithm_executor))}
      \n+
      81 explicit algorithm_result_generator_range(algorithm_executor_type && algorithm_executor) :
      \n+
      82 algorithm_executor_ptr{std::make_unique<algorithm_executor_type>(std::move(algorithm_executor))}
      \n
      83 {}
      \n
      \n
      85
      \n
      \n
      97 constexpr algorithm_range_iterator begin()
      \n
      98 {
      \n
      99 return algorithm_range_iterator{*this};
      \n
      100 }
      \n
      \n
      101
      \n
      103 algorithm_range_iterator begin() const = delete;
      \n
      104
      \n
      \n-
      113 constexpr std::default_sentinel_t end() noexcept
      \n+
      113 constexpr std::default_sentinel_t end() noexcept
      \n
      114 {
      \n
      115 return std::default_sentinel;
      \n
      116 }
      \n
      \n
      117
      \n
      119 constexpr std::default_sentinel_t end() const = delete;
      \n
      121
      \n
      122protected:
      \n
      \n
      131 bool next()
      \n
      132 {
      \n
      133 if (!algorithm_executor_ptr)
      \n
      134 throw std::runtime_error{"No algorithm execution buffer available."};
      \n
      135
      \n-
      136 if (auto opt = algorithm_executor_ptr->next_result(); opt.has_value())
      \n+
      136 if (auto opt = algorithm_executor_ptr->next_result(); opt.has_value())
      \n
      137 {
      \n-
      138 cache = std::move(*opt);
      \n+
      138 cache = std::move(*opt);
      \n
      139 return true;
      \n
      140 }
      \n
      141
      \n
      142 return false;
      \n
      143 }
      \n
      \n
      144
      \n
      145private:
      \n
      147 std::unique_ptr<algorithm_executor_type> algorithm_executor_ptr{};
      \n
      149 algorithm_result_type cache{};
      \n
      150};
      \n
    \n
    151
    \n
    158template <typename algorithm_executor_type>
    \n-
    159algorithm_result_generator_range(algorithm_executor_type &&)
    \n-
    160 -> algorithm_result_generator_range<std::remove_reference_t<algorithm_executor_type>>;
    \n+
    159algorithm_result_generator_range(algorithm_executor_type &&)
    \n+
    160 -> algorithm_result_generator_range<std::remove_reference_t<algorithm_executor_type>>;
    \n
    162
    \n
    166template <typename algorithm_executor_type>
    \n
    \n-
    167class algorithm_result_generator_range<algorithm_executor_type>::algorithm_range_iterator
    \n+
    167class algorithm_result_generator_range<algorithm_executor_type>::algorithm_range_iterator
    \n
    168{
    \n
    169public:
    \n
    174 using difference_type = std::ptrdiff_t;
    \n
    176 using value_type = algorithm_result_type;
    \n
    178 using reference = std::add_lvalue_reference_t<value_type>;
    \n
    180 using pointer = std::add_pointer_t<value_type>;
    \n
    182 using iterator_category = std::input_iterator_tag;
    \n
    184
    \n-
    188 constexpr algorithm_range_iterator() noexcept = default;
    \n-
    189 constexpr algorithm_range_iterator(algorithm_range_iterator const &) noexcept = default;
    \n-
    190 constexpr algorithm_range_iterator(algorithm_range_iterator &&) noexcept = default;
    \n-
    191 constexpr algorithm_range_iterator & operator=(algorithm_range_iterator const &) noexcept = default;
    \n-
    192 constexpr algorithm_range_iterator & operator=(algorithm_range_iterator &&) noexcept = default;
    \n-
    193 ~algorithm_range_iterator() = default;
    \n+
    188 constexpr algorithm_range_iterator() noexcept = default;
    \n+
    189 constexpr algorithm_range_iterator(algorithm_range_iterator const &) noexcept = default;
    \n+
    190 constexpr algorithm_range_iterator(algorithm_range_iterator &&) noexcept = default;
    \n+
    191 constexpr algorithm_range_iterator & operator=(algorithm_range_iterator const &) noexcept = default;
    \n+
    192 constexpr algorithm_range_iterator & operator=(algorithm_range_iterator &&) noexcept = default;
    \n+
    193 ~algorithm_range_iterator() = default;
    \n
    194
    \n
    \n-
    196 explicit constexpr algorithm_range_iterator(algorithm_result_generator_range & range) :
    \n-
    197 range_ptr(std::addressof(range))
    \n+
    196 explicit constexpr algorithm_range_iterator(algorithm_result_generator_range & range) :
    \n+
    197 range_ptr(std::addressof(range))
    \n
    198 {
    \n
    199 ++(*this); // Fetch the next element.
    \n
    200 }
    \n
    \n
    202
    \n
    \n-
    211 reference operator*() const noexcept
    \n+
    211 reference operator*() const noexcept
    \n
    212 {
    \n
    213 return range_ptr->cache;
    \n
    214 }
    \n
    \n
    215
    \n
    \n-
    217 pointer operator->() const noexcept
    \n+
    217 pointer operator->() const noexcept
    \n
    218 {
    \n
    219 return &range_ptr->cache;
    \n
    220 }
    \n
    \n
    222
    \n
    \n
    227 algorithm_range_iterator & operator++(/*pre*/)
    \n
    228 {
    \n-
    229 assert(range_ptr != nullptr);
    \n+
    229 assert(range_ptr != nullptr);
    \n
    230
    \n
    231 at_end = !range_ptr->next();
    \n
    232 return *this;
    \n
    233 }
    \n
    \n
    234
    \n
    \n
    236 void operator++(int /*post*/)
    \n
    237 {
    \n
    238 ++(*this);
    \n
    239 }
    \n
    \n
    241
    \n
    \n-
    246 friend constexpr bool operator==(algorithm_range_iterator const & lhs, std::default_sentinel_t const &) noexcept
    \n+
    246 friend constexpr bool operator==(algorithm_range_iterator const & lhs, std::default_sentinel_t const &) noexcept
    \n
    247 {
    \n-
    248 return lhs.at_end;
    \n+
    248 return lhs.at_end;
    \n
    249 }
    \n
    \n
    250
    \n
    \n-
    252 friend constexpr bool operator==(std::default_sentinel_t const & lhs, algorithm_range_iterator const & rhs) noexcept
    \n+
    252 friend constexpr bool operator==(std::default_sentinel_t const & lhs, algorithm_range_iterator const & rhs) noexcept
    \n
    253 {
    \n-
    254 return rhs == lhs;
    \n+
    254 return rhs == lhs;
    \n
    255 }
    \n
    \n
    256
    \n
    \n-
    258 friend constexpr bool operator!=(algorithm_range_iterator const & lhs, std::default_sentinel_t const & rhs) noexcept
    \n+
    258 friend constexpr bool operator!=(algorithm_range_iterator const & lhs, std::default_sentinel_t const & rhs) noexcept
    \n
    259 {
    \n-
    260 return !(lhs == rhs);
    \n+
    260 return !(lhs == rhs);
    \n
    261 }
    \n
    \n
    262
    \n
    \n-
    264 friend constexpr bool operator!=(std::default_sentinel_t const & lhs, algorithm_range_iterator const & rhs) noexcept
    \n+
    264 friend constexpr bool operator!=(std::default_sentinel_t const & lhs, algorithm_range_iterator const & rhs) noexcept
    \n
    265 {
    \n-
    266 return rhs != lhs;
    \n+
    266 return rhs != lhs;
    \n
    267 }
    \n
    \n
    269
    \n
    270private:
    \n
    272 algorithm_result_generator_range * range_ptr{};
    \n
    274 bool at_end{true};
    \n
    275};
    \n@@ -334,15 +334,14 @@\n
    seqan3::algorithm_result_generator_range::next
    bool next()
    Receives the next algorithm result from the executor buffer.
    Definition algorithm_result_generator_range.hpp:131
    \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:97
    \n
    seqan3::algorithm_result_generator_range::algorithm_result_generator_range
    algorithm_result_generator_range(algorithm_executor_type &&algorithm_executor)
    Constructs a new algorithm range by taking ownership over the passed algorithm buffer.
    Definition algorithm_result_generator_range.hpp:81
    \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 \n \n", "details": [{"source1": "html2text {}", "source2": "html2text {}", "unified_diff": "@@ -44,136 +44,136 @@\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(_\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+_\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 72\n-_\b8_\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 &&\n-_\ba_\bl_\bg_\bo_\br_\bi_\bt_\bh_\bm_\b__\be_\bx_\be_\bc_\bu_\bt_\bo_\br) :\n-82 algorithm_executor_ptr{_\bs_\bt_\bd::make_unique<_\ba_\bl_\bg_\bo_\br_\bi_\bt_\bh_\bm_\b__\be_\bx_\be_\bc_\bu_\bt_\bo_\br_\b__\bt_\by_\bp_\be>(_\bs_\bt_\bd::move\n-(_\ba_\bl_\bg_\bo_\br_\bi_\bt_\bh_\bm_\b__\be_\bx_\be_\bc_\bu_\bt_\bo_\br))}\n+_\b8_\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 &&\n+algorithm_executor) :\n+82 algorithm_executor_ptr{_\bs_\bt_\bd::make_unique(_\bs_\bt_\bd::move\n+(algorithm_executor))}\n 83 {}\n 85\n _\b9_\b7 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 98 {\n 99 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 100 }\n 101\n _\b1_\b0_\b3 _\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 104\n-_\b1_\b1_\b3 constexpr std::default_sentinel_t _\be_\bn_\bd() _\bn_\bo_\be_\bx_\bc_\be_\bp_\bt\n+_\b1_\b1_\b3 constexpr std::default_sentinel_t _\be_\bn_\bd() noexcept\n 114 {\n 115 return std::default_sentinel;\n 116 }\n 117\n _\b1_\b1_\b9 constexpr std::default_sentinel_t _\be_\bn_\bd() const = delete;\n 121\n 122protected:\n _\b1_\b3_\b1 bool _\bn_\be_\bx_\bt()\n 132 {\n 133 if (!algorithm_executor_ptr)\n 134 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 135\n-136 if (auto _\bo_\bp_\bt = algorithm_executor_ptr->next_result(); _\bo_\bp_\bt.has_value())\n+136 if (auto opt = algorithm_executor_ptr->next_result(); opt.has_value())\n 137 {\n-138 cache = std::move(*_\bo_\bp_\bt);\n+138 cache = std::move(*opt);\n 139 return true;\n 140 }\n 141\n 142 return false;\n 143 }\n 144\n 145private:\n 147 _\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 149 algorithm_result_type cache{};\n 150};\n 151\n 158template \n-_\b1_\b5_\b9_\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+_\b1_\b5_\b9_\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 160 -> _\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 162\n 166template \n-_\b1_\b6_\b7class _\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+_\b1_\b6_\b7class _\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 _\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 168{\n 169public:\n _\b1_\b7_\b4 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_\b6 using _\bv_\ba_\bl_\bu_\be_\b__\bt_\by_\bp_\be = algorithm_result_type;\n _\b1_\b7_\b8 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_\b0 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_\b2 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 184\n-_\b1_\b8_\b8 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_\b8_\b9 _\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_\b0 _\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_\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 & _\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_\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 & _\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_\b3 ~_\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+_\b1_\b8_\b8 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_\b8_\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(_\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_\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(_\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_\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 & 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_\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 & 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_\b3 ~_\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 194\n-_\b1_\b9_\b6 _\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-197 range_ptr(_\bs_\bt_\bd::addressof(_\br_\ba_\bn_\bg_\be))\n+_\b1_\b9_\b6 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+197 range_ptr(_\bs_\bt_\bd::addressof(range))\n 198 {\n 199 ++(*this); // Fetch the next element.\n 200 }\n 202\n-_\b2_\b1_\b1 _\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+_\b2_\b1_\b1 _\br_\be_\bf_\be_\br_\be_\bn_\bc_\be _\bo_\bp_\be_\br_\ba_\bt_\bo_\br_\b*() const noexcept\n 212 {\n 213 return range_ptr->cache;\n 214 }\n 215\n-_\b2_\b1_\b7 _\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+_\b2_\b1_\b7 _\bp_\bo_\bi_\bn_\bt_\be_\br _\bo_\bp_\be_\br_\ba_\bt_\bo_\br_\b-_\b>() const noexcept\n 218 {\n 219 return &range_ptr->cache;\n 220 }\n 222\n _\b2_\b2_\b7 _\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 228 {\n-229 _\ba_\bs_\bs_\be_\br_\bt(range_ptr != nullptr);\n+229 assert(range_ptr != nullptr);\n 230\n 231 at_end = !range_ptr->next();\n 232 return *this;\n 233 }\n 234\n _\b2_\b3_\b6 void _\bo_\bp_\be_\br_\ba_\bt_\bo_\br_\b+_\b+(int /*post*/)\n 237 {\n 238 ++(*this);\n 239 }\n 241\n-_\b2_\b4_\b6 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+_\b2_\b4_\b6 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 &) noexcept\n 247 {\n-248 return _\bl_\bh_\bs.at_end;\n+248 return lhs.at_end;\n 249 }\n 250\n-_\b2_\b5_\b2 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+_\b2_\b5_\b2 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 253 {\n-254 return _\br_\bh_\bs == _\bl_\bh_\bs;\n+254 return rhs == lhs;\n 255 }\n 256\n-_\b2_\b5_\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 & _\br_\bh_\bs) noexcept\n+_\b2_\b5_\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+std::default_sentinel_t const & rhs) noexcept\n 259 {\n-260 return !(_\bl_\bh_\bs == _\br_\bh_\bs);\n+260 return !(lhs == rhs);\n 261 }\n 262\n-_\b2_\b6_\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+_\b2_\b6_\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 265 {\n-266 return _\br_\bh_\bs != _\bl_\bh_\bs;\n+266 return rhs != lhs;\n 267 }\n 269\n 270private:\n 272 _\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 274 bool at_end{true};\n 275};\n 276\n@@ -281,17 +281,14 @@\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": "@@ -142,33 +142,39 @@\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::debug_stream_type
    A "pretty printer" for most SeqAn data structures and related types.
    Definition debug_stream_type.hpp:79
    \n+
    seqan3::qualified
    Joins an arbitrary alphabet with a quality alphabet.
    Definition qualified.hpp:59
    \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::dna4q
    qualified< dna4, phred42 > dna4q
    An alphabet that stores a seqan3::dna4 letter and an seqan3::phred42 letter at each position.
    Definition aliases.hpp:31
    \n+
    seqan3::rna15q
    qualified< rna15, phred42 > rna15q
    An alphabet that stores a seqan3::rna15 letter and an seqan3::qualified letter at each position.
    Definition aliases.hpp:66
    \n+
    seqan3::dna5q
    qualified< dna5, phred42 > dna5q
    An alphabet that stores a seqan3::dna5 letter and an seqan3::phred42 letter at each position.
    Definition aliases.hpp:38
    \n+
    seqan3::dna15q
    qualified< dna15, phred42 > dna15q
    An alphabet that stores a seqan3::dna15 letter and an seqan3::qualified letter at each position.
    Definition aliases.hpp:59
    \n+
    seqan3::rna4q
    qualified< rna4, phred42 > rna4q
    An alphabet that stores a seqan3::rna4 letter and an seqan3::phred42 letter at each position.
    Definition aliases.hpp:45
    \n+
    seqan3::rna5q
    qualified< rna5, phred42 > rna5q
    An alphabet that stores a seqan3::rna5 letter and an seqan3::phred42 letter at each position.
    Definition aliases.hpp:52
    \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
    rna4.hpp
    Provides seqan3::rna4, container aliases and string literals.
    \n
    rna5.hpp
    Provides seqan3::rna5, container aliases and string literals.
    \n
    \n", "details": [{"source1": "html2text {}", "source2": "html2text {}", "unified_diff": "@@ -39,23 +39,53 @@\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:_\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:_\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 _\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_\b:_\b:_\bd_\bn_\ba_\b4_\bq\n+qualified< dna4, phred42 > dna4q\n+An alphabet that stores a seqan3::dna4 letter and an seqan3::phred42 letter at\n+each position.\n+D\bDe\bef\bfi\bin\bni\bit\bti\bio\bon\bn aliases.hpp:31\n+_\bs_\be_\bq_\ba_\bn_\b3_\b:_\b:_\br_\bn_\ba_\b1_\b5_\bq\n+qualified< rna15, phred42 > rna15q\n+An alphabet that stores a seqan3::rna15 letter and an seqan3::qualified letter\n+at each position.\n+D\bDe\bef\bfi\bin\bni\bit\bti\bio\bon\bn aliases.hpp:66\n+_\bs_\be_\bq_\ba_\bn_\b3_\b:_\b:_\bd_\bn_\ba_\b5_\bq\n+qualified< dna5, phred42 > dna5q\n+An alphabet that stores a seqan3::dna5 letter and an seqan3::phred42 letter at\n+each position.\n+D\bDe\bef\bfi\bin\bni\bit\bti\bio\bon\bn aliases.hpp:38\n+_\bs_\be_\bq_\ba_\bn_\b3_\b:_\b:_\bd_\bn_\ba_\b1_\b5_\bq\n+qualified< dna15, phred42 > dna15q\n+An alphabet that stores a seqan3::dna15 letter and an seqan3::qualified letter\n+at each position.\n+D\bDe\bef\bfi\bin\bni\bit\bti\bio\bon\bn aliases.hpp:59\n+_\bs_\be_\bq_\ba_\bn_\b3_\b:_\b:_\br_\bn_\ba_\b4_\bq\n+qualified< rna4, phred42 > rna4q\n+An alphabet that stores a seqan3::rna4 letter and an seqan3::phred42 letter at\n+each position.\n+D\bDe\bef\bfi\bin\bni\bit\bti\bio\bon\bn aliases.hpp:45\n+_\bs_\be_\bq_\ba_\bn_\b3_\b:_\b:_\br_\bn_\ba_\b5_\bq\n+qualified< rna5, phred42 > rna5q\n+An alphabet that stores a seqan3::rna5 letter and an seqan3::phred42 letter at\n+each position.\n+D\bDe\bef\bfi\bin\bni\bit\bti\bio\bon\bn aliases.hpp:52\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 _\bp_\bh_\br_\be_\bd_\b4_\b2_\b._\bh_\bp_\bp\n Provides seqan3::phred42 quality scores.\n _\bq_\bu_\ba_\bl_\bi_\bf_\bi_\be_\bd_\b._\bh_\bp_\bp\n Provides quality alphabet composites.\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-
    141 constexpr method_global(seqan3::align_cfg::free_end_gaps_sequence1_leading free_sequence1_leading,
    \n-
    142 seqan3::align_cfg::free_end_gaps_sequence2_leading free_sequence2_leading,
    \n-
    143 seqan3::align_cfg::free_end_gaps_sequence1_trailing free_sequence1_trailing,
    \n-
    144 seqan3::align_cfg::free_end_gaps_sequence2_trailing free_sequence2_trailing) noexcept :
    \n-
    145 free_end_gaps_sequence1_leading{free_sequence1_leading.get()},
    \n-
    146 free_end_gaps_sequence2_leading{free_sequence2_leading.get()},
    \n-
    147 free_end_gaps_sequence1_trailing{free_sequence1_trailing.get()},
    \n+
    141 constexpr method_global(seqan3::align_cfg::free_end_gaps_sequence1_leading free_sequence1_leading,
    \n+
    142 seqan3::align_cfg::free_end_gaps_sequence2_leading free_sequence2_leading,
    \n+
    143 seqan3::align_cfg::free_end_gaps_sequence1_trailing free_sequence1_trailing,
    \n+
    144 seqan3::align_cfg::free_end_gaps_sequence2_trailing free_sequence2_trailing) noexcept :
    \n+
    145 free_end_gaps_sequence1_leading{free_sequence1_leading.get()},
    \n+
    146 free_end_gaps_sequence2_leading{free_sequence2_leading.get()},
    \n+
    147 free_end_gaps_sequence1_trailing{free_sequence1_trailing.get()},
    \n
    148 free_end_gaps_sequence2_trailing{free_sequence2_trailing.get()}
    \n
    149 {}
    \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@@ -235,15 +235,14 @@\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-_\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+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 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-_\bf_\br_\be_\be_\b__\bs_\be_\bq_\bu_\be_\bn_\bc_\be_\b1_\b__\bt_\br_\ba_\bi_\bl_\bi_\bn_\bg,\n+free_sequence1_trailing,\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-_\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+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 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@@ -158,17 +158,14 @@\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": "@@ -142,35 +142,34 @@\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+
    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
    limits
    \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": "@@ -21,21 +21,21 @@\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 &) _\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+_\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 50\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+_\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 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@@ -48,17 +48,14 @@\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": "@@ -152,36 +152,35 @@\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::copy_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::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::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
    \n-
    seqan3::debug_stream_type
    A "pretty printer" for most SeqAn data structures and related types.
    Definition debug_stream_type.hpp:79
    \n
    copyable_wrapper.hpp
    Provides seqan3::detail::copyable_wrapper.
    \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
    type_traits
    \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(_\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+_\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 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(_\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+_\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 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@@ -74,17 +74,14 @@\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:_\ba_\bl_\bi_\bg_\bn_\b__\bc_\bf_\bg_\b:_\b:_\bo_\bn_\b__\br_\be_\bs_\bu_\bl_\bt_\b:_\b:_\bc_\ba_\bl_\bl_\bb_\ba_\bc_\bk\n seqan3::detail::copyable_wrapper_t< callback_t > callback\n The stored callable which will be invoked with the alignment result.\n D\bDe\bef\bfi\bin\bni\bit\bti\bio\bon\bn align_config_on_result.hpp:54\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 _\bc_\bo_\bp_\by_\ba_\bb_\bl_\be_\b__\bw_\br_\ba_\bp_\bp_\be_\br_\b._\bh_\bp_\bp\n Provides seqan3::detail::copyable_wrapper.\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"}]}, {"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": "@@ -162,30 +162,29 @@\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(_\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+_\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 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@@ -79,17 +79,14 @@\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": "@@ -154,21 +154,21 @@\n
    31{
    \n
    32
    \n
    127template <typename sequence_t, typename alignment_config_t>
    \n
    128 requires detail::align_pairwise_single_input<sequence_t>
    \n
    129 && std::copy_constructible<std::remove_reference_t<sequence_t>>
    \n
    130 && detail::is_type_specialisation_of_v<alignment_config_t, configuration>
    \n
    \n-
    131constexpr auto align_pairwise(sequence_t && seq, alignment_config_t const & config)
    \n+
    131constexpr auto align_pairwise(sequence_t && seq, alignment_config_t const & config)
    \n
    132{
    \n
    133 using std::get;
    \n
    134
    \n
    135 if constexpr (std::is_lvalue_reference_v<sequence_t>) // Forward tuple elements as references.
    \n
    136 {
    \n-
    137 return align_pairwise(std::tie(get<0>(seq), get<1>(seq)), config);
    \n+
    137 return align_pairwise(std::tie(get<0>(seq), get<1>(seq)), config);
    \n
    138 }
    \n
    139 else
    \n
    140 {
    \n
    141 static_assert(std::tuple_size_v<std::remove_reference_t<sequence_t>> == 2,
    \n
    142 "Alignment configuration error: Expects exactly two sequences for pairwise alignments.");
    \n
    143
    \n
    144 static_assert(std::ranges::viewable_range<std::tuple_element_t<0, std::remove_reference_t<sequence_t>>>
    \n@@ -245,15 +245,14 @@\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
    all_view.hpp
    Provides seqan3::detail::all.
    \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:131
    \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": "@@ -33,23 +33,23 @@\n 30namespace _\bs_\be_\bq_\ba_\bn_\b3\n 31{\n 32\n 127template \n 128 requires detail::align_pairwise_single_input\n 129 && std::copy_constructible>\n 130 && detail::is_type_specialisation_of_v\n-_\b1_\b3_\b1constexpr 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+_\b1_\b3_\b1constexpr 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 config)\n 132{\n 133 using std::get;\n 134\n 135 if constexpr (std::is_lvalue_reference_v) // Forward tuple\n elements as references.\n 136 {\n-137 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 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 138 }\n 139 else\n 140 {\n 141 static_assert(std::tuple_size_v> == 2,\n 142 \"Alignment configuration error: Expects exactly two sequences for pairwise\n alignments.\");\n 143\n@@ -155,17 +155,14 @@\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 _\ba_\bl_\bl_\b__\bv_\bi_\be_\bw_\b._\bh_\bp_\bp\n Provides seqan3::detail::all.\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": "@@ -147,133 +147,134 @@\n
    24{
    \n
    25
    \n
    72template <typename value_t, size_t alignment_v = __STDCPP_DEFAULT_NEW_ALIGNMENT__>
    \n
    \n
    73class aligned_allocator
    \n
    74{
    \n
    75public:
    \n-
    77 static constexpr size_t alignment = alignment_v;
    \n+
    77 static constexpr size_t alignment = alignment_v;
    \n
    78
    \n-
    80 using value_type = value_t;
    \n-
    82 using pointer = value_type *;
    \n+
    80 using value_type = value_t;
    \n+
    82 using pointer = value_type *;
    \n
    84 using difference_type = typename std::pointer_traits<pointer>::difference_type;
    \n
    86 using size_type = std::make_unsigned_t<difference_type>;
    \n
    87
    \n
    89 using is_always_equal = std::true_type;
    \n
    90
    \n
    94 aligned_allocator() = default;
    \n
    95 aligned_allocator(aligned_allocator const &) = default;
    \n
    96 aligned_allocator(aligned_allocator &&) = default;
    \n
    97 aligned_allocator & operator=(aligned_allocator const &) = default;
    \n
    98 aligned_allocator & operator=(aligned_allocator &&) = default;
    \n
    99 ~aligned_allocator() = default;
    \n
    100
    \n
    102 template <class other_value_type, size_t other_alignment>
    \n \n
    106
    \n
    \n-
    138 [[nodiscard]] pointer allocate(size_type const n) const
    \n+
    138 [[nodiscard]] pointer allocate(size_type const n) const
    \n
    139 {
    \n
    140 constexpr size_type max_size = std::numeric_limits<size_type>::max() / sizeof(value_type);
    \n
    141 if (n > max_size)
    \n
    142 throw std::bad_alloc{};
    \n
    143
    \n-
    144 size_t bytes_to_allocate = n * sizeof(value_type);
    \n-
    145 if constexpr (alignment <= __STDCPP_DEFAULT_NEW_ALIGNMENT__)
    \n-
    146 return static_cast<pointer>(::operator new(bytes_to_allocate));
    \n+
    144 size_t bytes_to_allocate = n * sizeof(value_type);
    \n+
    145 if constexpr (alignment <= __STDCPP_DEFAULT_NEW_ALIGNMENT__)
    \n+
    146 return static_cast<pointer>(::operator new(bytes_to_allocate));
    \n
    147 else // Use alignment aware allocator function.
    \n-
    148 return static_cast<pointer>(::operator new(bytes_to_allocate, static_cast<std::align_val_t>(alignment)));
    \n+
    148 return static_cast<pointer>(::operator new(bytes_to_allocate, static_cast<std::align_val_t>(alignment)));
    \n
    149 }
    \n
    \n
    150
    \n
    \n-
    177 void deallocate(pointer const p, size_type const n) const noexcept
    \n+
    177 void deallocate(pointer const p, size_type const n) const noexcept
    \n
    178 {
    \n-
    179 size_t bytes_to_deallocate = n * sizeof(value_type);
    \n+
    179 size_t bytes_to_deallocate = n * sizeof(value_type);
    \n
    180
    \n
    181 // Clang doesn't have __cpp_sized_deallocation defined by default even though this is a C++14! feature
    \n
    182 // > In Clang 3.7 and later, sized deallocation is only enabled if the user passes the `-fsized-deallocation`
    \n
    183 // > flag.
    \n
    184 // see also https://clang.llvm.org/cxx_status.html#n3778
    \n
    185#if __cpp_sized_deallocation >= 201309
    \n
    186 // gcc
    \n-
    187 if constexpr (alignment <= __STDCPP_DEFAULT_NEW_ALIGNMENT__)
    \n-
    188 ::operator delete(p, bytes_to_deallocate);
    \n+
    187 if constexpr (alignment <= __STDCPP_DEFAULT_NEW_ALIGNMENT__)
    \n+
    188 ::operator delete(p, bytes_to_deallocate);
    \n
    189 else // Use alignment aware deallocator function.
    \n-
    190 ::operator delete(p, bytes_to_deallocate, static_cast<std::align_val_t>(alignment));
    \n+
    190 ::operator delete(p, bytes_to_deallocate, static_cast<std::align_val_t>(alignment));
    \n
    191#else /*__cpp_sized_deallocation >= 201309*/
    \n
    192 // e.g. clang++
    \n-
    193 (void)bytes_to_deallocate;
    \n-
    194 if constexpr (alignment <= __STDCPP_DEFAULT_NEW_ALIGNMENT__)
    \n+
    193 (void)bytes_to_deallocate;
    \n+
    194 if constexpr (alignment <= __STDCPP_DEFAULT_NEW_ALIGNMENT__)
    \n
    195 ::operator delete(p);
    \n
    196 else // Use alignment aware deallocator function.
    \n
    197 ::operator delete(p, static_cast<std::align_val_t>(alignment));
    \n
    198#endif // __cpp_sized_deallocation >= 201309
    \n
    199 }
    \n
    \n
    200
    \n
    211 template <typename new_value_type>
    \n
    \n
    212 struct rebind
    \n
    213 {
    \n-
    215 static constexpr size_t other_alignment = std::max(alignof(new_value_type), alignment);
    \n-
    217 using other = aligned_allocator<new_value_type, other_alignment>;
    \n+
    215 static constexpr size_t other_alignment = std::max(alignof(new_value_type), alignment);
    \n+
    217 using other = aligned_allocator<new_value_type, other_alignment>;
    \n
    218 };
    \n
    \n
    219
    \n
    224 template <class value_type2, size_t alignment2>
    \n
    \n-
    225 constexpr bool operator==(aligned_allocator<value_type2, alignment2> const &) noexcept
    \n+
    225 constexpr bool operator==(aligned_allocator<value_type2, alignment2> const &) noexcept
    \n
    226 {
    \n-
    227 return alignment == alignment2;
    \n+
    227 return alignment == alignment2;
    \n
    228 }
    \n
    \n
    229
    \n
    231 template <class value_type2, size_t alignment2>
    \n
    \n-
    232 constexpr bool operator!=(aligned_allocator<value_type2, alignment2> const &) noexcept
    \n+
    232 constexpr bool operator!=(aligned_allocator<value_type2, alignment2> const &) noexcept
    \n
    233 {
    \n-
    234 return alignment != alignment2;
    \n+
    234 return alignment != alignment2;
    \n
    235 }
    \n
    \n
    237};
    \n
    \n
    238
    \n
    239} // namespace seqan3
    \n \n \n
    seqan3::aligned_allocator
    Allocates uninitialized storage whose memory-alignment is specified by alignment.
    Definition aligned_allocator.hpp:74
    \n
    seqan3::aligned_allocator::value_type
    value_t value_type
    The value type of the allocation.
    Definition aligned_allocator.hpp:80
    \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:177
    \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:225
    \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:138
    \n+
    seqan3::aligned_allocator::pointer
    value_type * pointer
    The pointer type of the allocation.
    Definition aligned_allocator.hpp:82
    \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:103
    \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:232
    \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:77
    \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:84
    \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 \n
    seqan3::aligned_allocator::rebind
    The aligned_allocator member template class aligned_allocator::rebind provides a way to obtain an all...
    Definition aligned_allocator.hpp:213
    \n
    seqan3::aligned_allocator::rebind::other_alignment
    static constexpr size_t other_alignment
    The alignment for the rebound allocator.
    Definition aligned_allocator.hpp:215
    \n+
    seqan3::aligned_allocator::rebind::other
    aligned_allocator< new_value_type, other_alignment > other
    The type of the allocator for a different value type.
    Definition aligned_allocator.hpp:217
    \n \n
    \n \n \n", "details": [{"source1": "html2text {}", "source2": "html2text {}", "unified_diff": "@@ -29,17 +29,17 @@\n 24{\n 25\n 72template \n _\b7_\b3class _\ba_\bl_\bi_\bg_\bn_\be_\bd_\b__\ba_\bl_\bl_\bo_\bc_\ba_\bt_\bo_\br\n 74{\n 75public:\n-_\b7_\b7 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+_\b7_\b7 static constexpr size_t _\ba_\bl_\bi_\bg_\bn_\bm_\be_\bn_\bt = alignment_v;\n 78\n-_\b8_\b0 using _\bv_\ba_\bl_\bu_\be_\b__\bt_\by_\bp_\be = _\bv_\ba_\bl_\bu_\be_\b__\bt;\n+_\b8_\b0 using _\bv_\ba_\bl_\bu_\be_\b__\bt_\by_\bp_\be = value_t;\n _\b8_\b2 using _\bp_\bo_\bi_\bn_\bt_\be_\br = _\bv_\ba_\bl_\bu_\be_\b__\bt_\by_\bp_\be *;\n _\b8_\b4 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_\b6 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 87\n _\b8_\b9 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 90\n@@ -51,76 +51,76 @@\n _\b9_\b9 _\b~_\ba_\bl_\bi_\bg_\bn_\be_\bd_\b__\ba_\bl_\bl_\bo_\bc_\ba_\bt_\bo_\br() = default;\n 100\n 102 template \n _\b1_\b0_\b3 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 104 {}\n 106\n-_\b1_\b3_\b8 [[_\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+_\b1_\b3_\b8 [[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 139 {\n 140 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 141 if (n > max_size)\n 142 throw _\bs_\bt_\bd_\b:_\b:_\bb_\ba_\bd_\b__\ba_\bl_\bl_\bo_\bc{};\n 143\n-144 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-145 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-146 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+144 size_t bytes_to_allocate = n * sizeof(_\bv_\ba_\bl_\bu_\be_\b__\bt_\by_\bp_\be);\n+145 if constexpr (_\ba_\bl_\bi_\bg_\bn_\bm_\be_\bn_\bt <= __STDCPP_DEFAULT_NEW_ALIGNMENT__)\n+146 return static_cast<_\bp_\bo_\bi_\bn_\bt_\be_\br>(::operator new(bytes_to_allocate));\n 147 else // Use alignment aware allocator function.\n-148 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+148 return static_cast<_\bp_\bo_\bi_\bn_\bt_\be_\br>(::operator new(bytes_to_allocate,\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 149 }\n 150\n _\b1_\b7_\b7 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 178 {\n-179 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+179 size_t bytes_to_deallocate = n * sizeof(_\bv_\ba_\bl_\bu_\be_\b__\bt_\by_\bp_\be);\n 180\n 181 // Clang doesn't have __cpp_sized_deallocation defined by default even\n though this is a C++14! feature\n 182 // > In Clang 3.7 and later, sized deallocation is only enabled if the user\n passes the `-fsized-deallocation`\n 183 // > flag.\n 184 // see also https://clang.llvm.org/cxx_status.html#n3778\n 185#if __cpp_sized_deallocation >= 201309\n 186 // gcc\n-187 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-188 ::operator delete(p, _\bb_\by_\bt_\be_\bs_\b__\bt_\bo_\b__\bd_\be_\ba_\bl_\bl_\bo_\bc_\ba_\bt_\be);\n+187 if constexpr (_\ba_\bl_\bi_\bg_\bn_\bm_\be_\bn_\bt <= __STDCPP_DEFAULT_NEW_ALIGNMENT__)\n+188 ::operator delete(p, bytes_to_deallocate);\n 189 else // Use alignment aware deallocator function.\n-190 ::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+190 ::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 (_\ba_\bl_\bi_\bg_\bn_\bm_\be_\bn_\bt));\n 191#else /*__cpp_sized_deallocation >= 201309*/\n 192 // e.g. clang++\n-193 (_\bv_\bo_\bi_\bd)_\bb_\by_\bt_\be_\bs_\b__\bt_\bo_\b__\bd_\be_\ba_\bl_\bl_\bo_\bc_\ba_\bt_\be;\n-194 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+193 (void)bytes_to_deallocate;\n+194 if constexpr (_\ba_\bl_\bi_\bg_\bn_\bm_\be_\bn_\bt <= __STDCPP_DEFAULT_NEW_ALIGNMENT__)\n 195 ::operator delete(p);\n 196 else // Use alignment aware deallocator function.\n 197 ::operator delete(p, 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 198#endif // __cpp_sized_deallocation >= 201309\n 199 }\n 200\n 211 template \n _\b2_\b1_\b2 struct _\br_\be_\bb_\bi_\bn_\bd\n 213 {\n-_\b2_\b1_\b5 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+_\b2_\b1_\b5 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 _\ba_\bl_\bi_\bg_\bn_\bm_\be_\bn_\bt);\n _\b2_\b1_\b7 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 218 };\n 219\n 224 template \n _\b2_\b2_\b5 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 226 {\n-227 return _\ba_\bl_\bi_\bg_\bn_\bm_\be_\bn_\bt == _\ba_\bl_\bi_\bg_\bn_\bm_\be_\bn_\bt_\b2;\n+227 return _\ba_\bl_\bi_\bg_\bn_\bm_\be_\bn_\bt == alignment2;\n 228 }\n 229\n 231 template \n _\b2_\b3_\b2 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 233 {\n-234 return _\ba_\bl_\bi_\bg_\bn_\bm_\be_\bn_\bt != _\ba_\bl_\bi_\bg_\bn_\bm_\be_\bn_\bt_\b2;\n+234 return _\ba_\bl_\bi_\bg_\bn_\bm_\be_\bn_\bt != alignment2;\n 235 }\n 237};\n 238\n 239} // namespace seqan3\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 _\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\n@@ -144,14 +144,18 @@\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:138\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:82\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@@ -177,17 +181,14 @@\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:_\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:84\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@@ -200,14 +201,18 @@\n The aligned_allocator member template class aligned_allocator::rebind provides\n a way to obtain an all...\n D\bDe\bef\bfi\bin\bni\bit\bti\bio\bon\bn aligned_allocator.hpp:213\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:_\br_\be_\bb_\bi_\bn_\bd_\b:_\b:_\bo_\bt_\bh_\be_\br_\b__\ba_\bl_\bi_\bg_\bn_\bm_\be_\bn_\bt\n static constexpr size_t other_alignment\n The alignment for the rebound allocator.\n D\bDe\bef\bfi\bin\bni\bit\bti\bio\bon\bn aligned_allocator.hpp:215\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:_\br_\be_\bb_\bi_\bn_\bd_\b:_\b:_\bo_\bt_\bh_\be_\br\n+aligned_allocator< new_value_type, other_alignment > other\n+The type of the allocator for a different value type.\n+D\bDe\bef\bfi\bin\bni\bit\bti\bio\bon\bn aligned_allocator.hpp:217\n _\bt_\by_\bp_\be_\b__\bt_\br_\ba_\bi_\bt_\bs\n _\bH_\bi_\bd_\be_\b _\bm_\be\n * Version:\n _\bs_\be_\bq_\ba_\bn_\b3\n _\bu_\bt_\bi_\bl_\bi_\bt_\by\n _\bc_\bo_\bn_\bt_\ba_\bi_\bn_\be_\br\n _\ba_\bl_\bi_\bg_\bn_\be_\bd_\b__\ba_\bl_\bl_\bo_\bc_\ba_\bt_\bo_\br_\b._\bh_\bp_\bp\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:175
    \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": "@@ -193,31 +193,30 @@\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:175\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@@ -325,25 +325,26 @@\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::debug_stream_type
    A "pretty printer" for most SeqAn data structures and related types.
    Definition debug_stream_type.hpp:79
    \n+
    seqan3::alphabet_variant
    A combined alphabet that can hold values of either of its alternatives..
    Definition alphabet_variant.hpp:127
    \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
    \n
    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
    \n
    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
    \n
    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
    \n
    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
    \n
    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
    \n
    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
    \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)
    An implementation of seqan3::writable_aligned_sequence::insert_gap for sequence containers.
    Definition aligned_sequence_concept.hpp:252
    \n
    aligned_sequence
    The generic concept for an aligned sequence.
    \n+
    container
    The (most general) container concept as defined by the standard library.
    \n
    sequence
    The generic concept for a (biological) sequence.
    \n
    weakly_assignable_from
    Resolves to std::is_assignable_v<t>.
    \n
    writable_aligned_sequence
    The generic concept for an aligned sequence that is writable.
    \n
    seqan3
    The main SeqAn3 namespace.
    Definition aligned_sequence_concept.hpp:26
    \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:252
    \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:261
    \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