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\n
Stability and long-term promises
\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

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 Dependencies

\"\"

\n

\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/align__config__min__score_8hpp_source.html", "source2": "./usr/share/doc/libseqan3-dev/html/align__config__min__score_8hpp_source.html", "unified_diff": "@@ -141,35 +141,36 @@\n
    18{
    \n
    \n
    35class min_score : private pipeable_config_element
    \n
    36{
    \n
    37public:
    \n
    39 int32_t score{std::numeric_limits<int32_t>::lowest()};
    \n
    40
    \n-
    44 constexpr min_score() noexcept = default;
    \n-
    45 constexpr min_score(min_score const &) noexcept = default;
    \n-
    46 constexpr min_score(min_score &&) noexcept = default;
    \n-
    47 constexpr min_score & operator=(min_score const &) noexcept = default;
    \n-
    48 constexpr min_score & operator=(min_score &&) noexcept = default;
    \n-
    49 ~min_score() noexcept = default;
    \n+
    44 constexpr min_score() noexcept = default;
    \n+
    45 constexpr min_score(min_score const &) noexcept = default;
    \n+
    46 constexpr min_score(min_score &&) noexcept = default;
    \n+
    47 constexpr min_score & operator=(min_score const &) noexcept = default;
    \n+
    48 constexpr min_score & operator=(min_score &&) noexcept = default;
    \n+
    49 ~min_score() noexcept = default;
    \n
    50
    \n
    \n-
    55 constexpr min_score(int32_t const score) : score{score}
    \n+
    55 constexpr min_score(int32_t const score) : score{score}
    \n
    56 {}
    \n
    \n
    58
    \n
    60 static constexpr seqan3::detail::align_config_id id{seqan3::detail::align_config_id::min_score};
    \n
    61};
    \n
    \n
    62
    \n
    63} // namespace seqan3::align_cfg
    \n
    detail.hpp
    Provides some utility functions for the alignment configurations.
    \n
    seqan3::align_cfg::min_score
    Sets the minimal score (maximal errors) allowed during an distance computation e.g....
    Definition align_config_min_score.hpp:36
    \n
    seqan3::align_cfg::min_score::score
    int32_t score
    Minimal score for the distance computation [default: -infinity].
    Definition align_config_min_score.hpp:39
    \n
    seqan3::align_cfg::min_score::min_score
    constexpr min_score() noexcept=default
    Defaulted.
    \n+
    seqan3::debug_stream_type
    A "pretty printer" for most SeqAn data structures and related types.
    Definition debug_stream_type.hpp:79
    \n \n
    std::numeric_limits::lowest
    T lowest(T... args)
    \n
    seqan3::align_cfg
    A special sub namespace for the alignment configurations.
    Definition align_config_band.hpp:22
    \n
    pipeable_config_element.hpp
    Provides seqan3::pipeable_config_element.
    \n
    seqan3::pipeable_config_element
    Adds pipe interface to configuration elements.
    Definition pipeable_config_element.hpp:29
    \n
\n \n", "details": [{"source1": "html2text {}", "source2": "html2text {}", "unified_diff": "@@ -20,22 +20,22 @@\n 17namespace _\bs_\be_\bq_\ba_\bn_\b3_\b:_\b:_\ba_\bl_\bi_\bg_\bn_\b__\bc_\bf_\bg\n 18{\n _\b3_\b5class _\bm_\bi_\bn_\b__\bs_\bc_\bo_\br_\be : private _\bp_\bi_\bp_\be_\ba_\bb_\bl_\be_\b__\bc_\bo_\bn_\bf_\bi_\bg_\b__\be_\bl_\be_\bm_\be_\bn_\bt\n 36{\n 37public:\n _\b3_\b9 int32_t _\bs_\bc_\bo_\br_\be{_\bs_\bt_\bd_\b:_\b:_\bn_\bu_\bm_\be_\br_\bi_\bc_\b__\bl_\bi_\bm_\bi_\bt_\bs_\b<_\bi_\bn_\bt_\b3_\b2_\b__\bt_\b>_\b:_\b:_\bl_\bo_\bw_\be_\bs_\bt()};\n 40\n-_\b4_\b4 constexpr _\bm_\bi_\bn_\b__\bs_\bc_\bo_\br_\be() noexcept = default;\n-_\b4_\b5 constexpr _\bm_\bi_\bn_\b__\bs_\bc_\bo_\br_\be(_\bm_\bi_\bn_\b__\bs_\bc_\bo_\br_\be const &) noexcept = default;\n-_\b4_\b6 constexpr _\bm_\bi_\bn_\b__\bs_\bc_\bo_\br_\be(_\bm_\bi_\bn_\b__\bs_\bc_\bo_\br_\be &&) noexcept = default;\n-_\b4_\b7 constexpr _\bm_\bi_\bn_\b__\bs_\bc_\bo_\br_\be & operator=(_\bm_\bi_\bn_\b__\bs_\bc_\bo_\br_\be const &) noexcept = default;\n-_\b4_\b8 constexpr _\bm_\bi_\bn_\b__\bs_\bc_\bo_\br_\be & operator=(_\bm_\bi_\bn_\b__\bs_\bc_\bo_\br_\be &&) noexcept = default;\n-_\b4_\b9 ~_\bm_\bi_\bn_\b__\bs_\bc_\bo_\br_\be() noexcept = default;\n+_\b4_\b4 constexpr _\bm_\bi_\bn_\b__\bs_\bc_\bo_\br_\be() _\bn_\bo_\be_\bx_\bc_\be_\bp_\bt = _\bd_\be_\bf_\ba_\bu_\bl_\bt;\n+_\b4_\b5 _\bc_\bo_\bn_\bs_\bt_\be_\bx_\bp_\br _\bm_\bi_\bn_\b__\bs_\bc_\bo_\br_\be(_\bm_\bi_\bn_\b__\bs_\bc_\bo_\br_\be _\bc_\bo_\bn_\bs_\bt &) _\bn_\bo_\be_\bx_\bc_\be_\bp_\bt = _\bd_\be_\bf_\ba_\bu_\bl_\bt;\n+_\b4_\b6 _\bc_\bo_\bn_\bs_\bt_\be_\bx_\bp_\br _\bm_\bi_\bn_\b__\bs_\bc_\bo_\br_\be(_\bm_\bi_\bn_\b__\bs_\bc_\bo_\br_\be &&) _\bn_\bo_\be_\bx_\bc_\be_\bp_\bt = _\bd_\be_\bf_\ba_\bu_\bl_\bt;\n+_\b4_\b7 _\bc_\bo_\bn_\bs_\bt_\be_\bx_\bp_\br _\bm_\bi_\bn_\b__\bs_\bc_\bo_\br_\be & _\bo_\bp_\be_\br_\ba_\bt_\bo_\br=(_\bm_\bi_\bn_\b__\bs_\bc_\bo_\br_\be _\bc_\bo_\bn_\bs_\bt &) _\bn_\bo_\be_\bx_\bc_\be_\bp_\bt = _\bd_\be_\bf_\ba_\bu_\bl_\bt;\n+_\b4_\b8 _\bc_\bo_\bn_\bs_\bt_\be_\bx_\bp_\br _\bm_\bi_\bn_\b__\bs_\bc_\bo_\br_\be & _\bo_\bp_\be_\br_\ba_\bt_\bo_\br=(_\bm_\bi_\bn_\b__\bs_\bc_\bo_\br_\be &&) _\bn_\bo_\be_\bx_\bc_\be_\bp_\bt = _\bd_\be_\bf_\ba_\bu_\bl_\bt;\n+_\b4_\b9 ~_\bm_\bi_\bn_\b__\bs_\bc_\bo_\br_\be() _\bn_\bo_\be_\bx_\bc_\be_\bp_\bt = _\bd_\be_\bf_\ba_\bu_\bl_\bt;\n 50\n-_\b5_\b5 constexpr _\bm_\bi_\bn_\b__\bs_\bc_\bo_\br_\be(int32_t const _\bs_\bc_\bo_\br_\be) : _\bs_\bc_\bo_\br_\be{_\bs_\bc_\bo_\br_\be}\n+_\b5_\b5 _\bc_\bo_\bn_\bs_\bt_\be_\bx_\bp_\br _\bm_\bi_\bn_\b__\bs_\bc_\bo_\br_\be(int32_t _\bc_\bo_\bn_\bs_\bt _\bs_\bc_\bo_\br_\be) : _\bs_\bc_\bo_\br_\be{_\bs_\bc_\bo_\br_\be}\n 56 {}\n 58\n _\b6_\b0 static constexpr seqan3::detail::align_config_id id{seqan3::detail::\n align_config_id::min_score};\n 61};\n 62\n 63} // namespace seqan3::align_cfg\n@@ -48,14 +48,17 @@\n _\bs_\be_\bq_\ba_\bn_\b3_\b:_\b:_\ba_\bl_\bi_\bg_\bn_\b__\bc_\bf_\bg_\b:_\b:_\bm_\bi_\bn_\b__\bs_\bc_\bo_\br_\be_\b:_\b:_\bs_\bc_\bo_\br_\be\n int32_t score\n Minimal score for the distance computation [default: -infinity].\n D\bDe\bef\bfi\bin\bni\bit\bti\bio\bon\bn align_config_min_score.hpp:39\n _\bs_\be_\bq_\ba_\bn_\b3_\b:_\b:_\ba_\bl_\bi_\bg_\bn_\b__\bc_\bf_\bg_\b:_\b:_\bm_\bi_\bn_\b__\bs_\bc_\bo_\br_\be_\b:_\b:_\bm_\bi_\bn_\b__\bs_\bc_\bo_\br_\be\n constexpr min_score() noexcept=default\n Defaulted.\n+_\bs_\be_\bq_\ba_\bn_\b3_\b:_\b:_\bd_\be_\bb_\bu_\bg_\b__\bs_\bt_\br_\be_\ba_\bm_\b__\bt_\by_\bp_\be\n+A \"pretty printer\" for most SeqAn data structures and related types.\n+D\bDe\bef\bfi\bin\bni\bit\bti\bio\bon\bn debug_stream_type.hpp:79\n _\bl_\bi_\bm_\bi_\bt_\bs\n _\bs_\bt_\bd_\b:_\b:_\bn_\bu_\bm_\be_\br_\bi_\bc_\b__\bl_\bi_\bm_\bi_\bt_\bs_\b:_\b:_\bl_\bo_\bw_\be_\bs_\bt\n T lowest(T... args)\n _\bs_\be_\bq_\ba_\bn_\b3_\b:_\b:_\ba_\bl_\bi_\bg_\bn_\b__\bc_\bf_\bg\n A special sub namespace for the alignment configurations.\n D\bDe\bef\bfi\bin\bni\bit\bti\bio\bon\bn align_config_band.hpp:22\n _\bp_\bi_\bp_\be_\ba_\bb_\bl_\be_\b__\bc_\bo_\bn_\bf_\bi_\bg_\b__\be_\bl_\be_\bm_\be_\bn_\bt_\b._\bh_\bp_\bp\n"}]}, {"source1": "./usr/share/doc/libseqan3-dev/html/align__config__on__result_8hpp_source.html", "source2": "./usr/share/doc/libseqan3-dev/html/align__config__on__result_8hpp_source.html", "unified_diff": "@@ -142,45 +142,46 @@\n
19{
\n
20
\n
49template <std::copy_constructible callback_t>
\n
\n
50class on_result : private seqan3::pipeable_config_element
\n
51{
\n
52public:
\n-
54 seqan3::detail::copyable_wrapper_t<callback_t> callback; // Allows lambdas with capture blocks.
\n+
54 seqan3::detail::copyable_wrapper_t<callback_t> callback; // Allows lambdas with capture blocks.
\n
55
\n
59 constexpr on_result() = default;
\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": "@@ -21,34 +21,34 @@\n 18namespace _\bs_\be_\bq_\ba_\bn_\b3_\b:_\b:_\ba_\bl_\bi_\bg_\bn_\b__\bc_\bf_\bg\n 19{\n 20\n 49template \n _\b5_\b0class _\bo_\bn_\b__\br_\be_\bs_\bu_\bl_\bt : private _\bs_\be_\bq_\ba_\bn_\b3_\b:_\b:_\bp_\bi_\bp_\be_\ba_\bb_\bl_\be_\b__\bc_\bo_\bn_\bf_\bi_\bg_\b__\be_\bl_\be_\bm_\be_\bn_\bt\n 51{\n 52public:\n-_\b5_\b4 seqan3::detail::copyable_wrapper_t _\bc_\ba_\bl_\bl_\bb_\ba_\bc_\bk; // Allows lambdas\n+_\b5_\b4 _\bs_\be_\bq_\ba_\bn_\b3_\b:_\b:_\bd_\be_\bt_\ba_\bi_\bl_\b:_\b:_\bc_\bo_\bp_\by_\ba_\bb_\bl_\be_\b__\bw_\br_\ba_\bp_\bp_\be_\br_\b__\bt_\b<_\bc_\ba_\bl_\bl_\bb_\ba_\bc_\bk_\b__\bt_\b> _\bc_\ba_\bl_\bl_\bb_\ba_\bc_\bk; // Allows lambdas\n with capture blocks.\n 55\n _\b5_\b9 constexpr _\bo_\bn_\b__\br_\be_\bs_\bu_\bl_\bt() = default;\n _\b6_\b0 constexpr _\bo_\bn_\b__\br_\be_\bs_\bu_\bl_\bt(_\bo_\bn_\b__\br_\be_\bs_\bu_\bl_\bt const &) = default;\n _\b6_\b1 constexpr _\bo_\bn_\b__\br_\be_\bs_\bu_\bl_\bt(_\bo_\bn_\b__\br_\be_\bs_\bu_\bl_\bt &&) = default;\n _\b6_\b2 constexpr _\bo_\bn_\b__\br_\be_\bs_\bu_\bl_\bt & _\bo_\bp_\be_\br_\ba_\bt_\bo_\br_\b=(_\bo_\bn_\b__\br_\be_\bs_\bu_\bl_\bt const &) = default;\n _\b6_\b3 constexpr _\bo_\bn_\b__\br_\be_\bs_\bu_\bl_\bt & _\bo_\bp_\be_\br_\ba_\bt_\bo_\br_\b=(_\bo_\bn_\b__\br_\be_\bs_\bu_\bl_\bt &&) = default;\n _\b6_\b4 _\b~_\bo_\bn_\b__\br_\be_\bs_\bu_\bl_\bt() = default;\n 65\n-_\b6_\b9 constexpr explicit _\bo_\bn_\b__\br_\be_\bs_\bu_\bl_\bt(callback_t && _\bc_\ba_\bl_\bl_\bb_\ba_\bc_\bk) : _\bc_\ba_\bl_\bl_\bb_\ba_\bc_\bk{_\bs_\bt_\bd::\n-forward(_\bc_\ba_\bl_\bl_\bb_\ba_\bc_\bk)}\n+_\b6_\b9 constexpr explicit _\bo_\bn_\b__\br_\be_\bs_\bu_\bl_\bt(_\bc_\ba_\bl_\bl_\bb_\ba_\bc_\bk_\b__\bt && _\bc_\ba_\bl_\bl_\bb_\ba_\bc_\bk) : _\bc_\ba_\bl_\bl_\bb_\ba_\bc_\bk{_\bs_\bt_\bd::\n+forward<_\bc_\ba_\bl_\bl_\bb_\ba_\bc_\bk_\b__\bt>(_\bc_\ba_\bl_\bl_\bb_\ba_\bc_\bk)}\n 70 {}\n 72\n 75 static constexpr seqan3::detail::align_config_id id{seqan3::detail::\n align_config_id::on_result};\n 76};\n 77\n 82template \n-_\b8_\b3_\bo_\bn_\b__\br_\be_\bs_\bu_\bl_\bt(callback_t &&) -> _\bo_\bn_\b__\br_\be_\bs_\bu_\bl_\bt_\b<_\bs_\bt_\bd_\b:_\b:_\bd_\be_\bc_\ba_\by_\b__\bt_\b<_\bc_\ba_\bl_\bl_\bb_\ba_\bc_\bk_\b__\bt_\b>>;\n+_\b8_\b3_\bo_\bn_\b__\br_\be_\bs_\bu_\bl_\bt(_\bc_\ba_\bl_\bl_\bb_\ba_\bc_\bk_\b__\bt &&) -> _\bo_\bn_\b__\br_\be_\bs_\bu_\bl_\bt_\b<_\bs_\bt_\bd_\b:_\b:_\bd_\be_\bc_\ba_\by_\b__\bt_\b<_\bc_\ba_\bl_\bl_\bb_\ba_\bc_\bk_\b__\bt_\b>>;\n 85} // namespace seqan3::align_cfg\n _\bd_\be_\bt_\ba_\bi_\bl_\b._\bh_\bp_\bp\n Provides some utility functions for the alignment configurations.\n _\bs_\be_\bq_\ba_\bn_\b3_\b:_\b:_\ba_\bl_\bi_\bg_\bn_\b__\bc_\bf_\bg_\b:_\b:_\bo_\bn_\b__\br_\be_\bs_\bu_\bl_\bt\n Configuration element to provide a user defined callback function for the\n alignment.\n D\bDe\bef\bfi\bin\bni\bit\bti\bio\bon\bn align_config_on_result.hpp:51\n@@ -74,14 +74,17 @@\n _\bs_\be_\bq_\ba_\bn_\b3_\b:_\b:_\ba_\bl_\bi_\bg_\bn_\b__\bc_\bf_\bg_\b:_\b:_\bo_\bn_\b__\br_\be_\bs_\bu_\bl_\bt_\b:_\b:_\bo_\bn_\b__\br_\be_\bs_\bu_\bl_\bt\n constexpr on_result(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/aligned__sequence__concept_8hpp_source.html", "source2": "./usr/share/doc/libseqan3-dev/html/aligned__sequence__concept_8hpp_source.html", "unified_diff": "@@ -144,18 +144,18 @@\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
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@@ -336,14 +336,15 @@\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": "@@ -25,19 +25,19 @@\n 22// unaligned_seq transformation trait\n 23// --------------------------------------------------------------------------\n -------------------------------------------\n 24\n _\b2_\b5namespace seqan3::detail\n 26{\n 27\n-29template